Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005344.1 Hibiscus syriacus cultivar Beakdansim tig00012104_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: 640787
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 1 of 3
Found at i:10122 original size:8 final size:8
Alignment explanation
Indices: 10111--10144 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
10101 ATATTTTATA
10111 TATTTAAT
1 TATTTAAT
*
10119 TATTCAAT
1 TATTTAAT
*
10127 TATTTAAC
1 TATTTAAT
10135 TATTTAAT
1 TATTTAAT
10143 TA
1 TA
10145 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:15452 original size:2 final size:2
Alignment explanation
Indices: 15445--15531 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
15435 GGGTAAACAA
15445 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15485 AT AT AT -T 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
15526 AT AT AT
1 AT AT AT
15532 GTTTGAGCTT
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 79 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16296 original size:122 final size:121
Alignment explanation
Indices: 15787--16531 Score: 911
Period size: 121 Copynumber: 6.1 Consensus size: 121
15777 AGTTTTGGTC
* * * * * * *
15787 TGTTTTAGTATCTAAACTTTCAATTTTTTTTCCAAATCATATCTAACTTTTAATTTTTATTCCAT
1 TGTTTTAGTACCTAAACTTTCAA--TTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCAT
*** * * * *
15852 TTTAGTACCTTGTCGTTAAAAAATAAAC-CATATAGTACCTAAACTATCAGTTGCGATT
64 TTTAGTACC-CCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* * * *
15910 TGATTTGGTACATTAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
1 TGTTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
15975 TAGTACCACCCCGTT-AAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
66 TAGTACC-CCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* * * * * *
16031 TGTTTTGGTACATTAACTTTCAATTTTTTTAAAATCATACCTAACGTTTATTTTTCAATTCATTT
1 TGTTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
** * * * * *
16096 TAGTACCCGTCGTT-AAAAATTCAATGCGTTTAGTACCTAAACTATTAGTTTTGGTC
66 TAGTACCCCCCGTTAAAAAATT-AACGCGTTTAGTACCTAAACTATCAGTTGTGATT
*
16152 TATTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
1 TGTTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
*
16217 TAGTACCACCCCGTTAAAAAATCAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
66 TAGTACC-CCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* * * *
16274 TGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAACCATACCTAACATTTACTTTTCATTTCATT
1 TGTTTTAGTACCTAAACTTTCAA-TTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATT
** * * * * *
16339 TTAGTACCCGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTA
65 TTAGTACCCCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* *
16396 TGTTTTAGTACCTAAACTTTCATTTTTTTTCAAAAAACATACCTAACGTTTAGTTTTCATTTCAT
1 TGTTTTAGTACCTAAACTTTCA-ATTTTTTC-AAAATCATACCTAACGTTTAGTTTTCATTTCAT
* * *
16461 TTTAGTACCCCCACCGTTAAAAAAAATTAATGTGTTTAGTACCTAAACTATCAGTTGTGGTT
64 TTTAGTA-CCCC-CCGTT--AAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
16523 TGTTTTAGT
1 TGTTTTAGT
16532 TATTTTTATT
Statistics
Matches: 542, Mismatches: 69, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
120 21 0.04
121 236 0.44
122 124 0.23
123 107 0.20
124 3 0.01
125 4 0.01
127 47 0.09
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (121 bp):
TGTTTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTT
TAGTACCCCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
Found at i:16404 original size:244 final size:244
Alignment explanation
Indices: 15787--16528 Score: 1049
Period size: 242 Copynumber: 3.0 Consensus size: 244
15777 AGTTTTGGTC
* * * * * * *
15787 TGTTTTAGTATCTAAACTTTCAATTTTTTTTCCAAATCATATCTAACTTTTAATTTTTATTCCAT
1 TGTTTTGGTACCTAAACTTTCAA-TTTTTTTCAAAATCATACCTAACATTTAATTTTCATTTCAT
* * ** * * ** * * *
15852 TTTAGTACCTTGTCGTTAAAAA-ATAAACCATATAGTACCTAAACTATCAGTTGCGATTTGATTT
65 TTTAGTACC-CGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTATGTTTT
* * *
15916 GGTACATTAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC
129 AGTACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC
15981 CACCCCGTT-AAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
194 CACCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* * * * *
16031 TGTTTTGGTACATTAACTTTCAATTTTTTT-AAAATCATACCTAACGTTTATTTTTCAATTCATT
1 TGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAATCATACCTAACATTTAATTTTCATTTCATT
* * * *
16095 TTAGTACCCGTCGTTAAAAATTCAATGCGTTTAGTACCTAAACTATTAGTTTTGGTCTATTTTAG
66 TTAGTACCCGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTATGTTTTAG
16160 TACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCA
131 TACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCA
*
16225 CCCCGTTAAAAAATCAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
196 CCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
* *
16274 TGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAACCATACCTAACATTTACTTTTCATTTCATT
1 TGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAATCATACCTAACATTTAATTTTCATTTCATT
16339 TTAGTACCCGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTATGTTTTAG
66 TTAGTACCCGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTATGTTTTAG
* *
16404 TACCTAAACTTTCATTTTTTTTCAAAAAACATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC
131 TACCTAAACTTTCA-ATTTTTTC-AAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC
* * * *
16469 CCCCACCGTTAAAAAAAATTAATGTGTTTAGTACCTAAACTATCAGTTGTGGTT
194 CACC-CCGTT--AAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
16523 TGTTTT
1 TGTTTT
16529 AGTTATTTTT
Statistics
Matches: 444, Mismatches: 46, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
241 11 0.02
242 135 0.30
243 75 0.17
244 124 0.28
245 7 0.02
246 43 0.10
247 5 0.01
249 44 0.10
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (244 bp):
TGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAATCATACCTAACATTTAATTTTCATTTCATT
TTAGTACCCGTCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTATGTTTTAG
TACCTAAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCA
CCCCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAGTTGTGATT
Found at i:25823 original size:2 final size:2
Alignment explanation
Indices: 25816--25842 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25806 GGGTAAACAA
25816 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25843 ATTTATGTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26300 original size:122 final size:120
Alignment explanation
Indices: 26147--27070 Score: 1017
Period size: 122 Copynumber: 7.6 Consensus size: 120
26137 CCTAAACTAC
* * * *
26147 AAACTTTTAATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTAG
1 AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TTGTCG
* * * * *
26212 TTAAAAAATTAACGCATTTAGTACCTAAATTATCATTTGTGATTTGTCTTGGTACCT
65 TTAAAAAATTAACGCATTTAGTACCTAAACTATCATTT-TGGTCTGTTTTAGTACCT
* * * *
26269 AAAATTTCAATTTTTTCAAAATCATACCTAACATTTAG-TTTCATTTCATTTTAGTAAC-TGTTG
1 AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGT-ACTTGTCG
* * * *
26332 TTAAAAACTTAATGCGTTTAGTACCTAAACTATCAATTTTGGTCTATTTTAGTACCT
65 TTAAAAAATTAACGCATTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * * * * *
26389 AAACTTTTAAGTGTTTCAAAATCATATCTAACGTTTAGTTTTCA-TTCTATTTTAGTACAATGTC
1 AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTC-ATTTTAGTAC-TTGTC
* * *
26453 GTTAAAACATTAACG-AGTTTAGTACATAAATTATCAGTTTTGGTCTGTTTTAGTACCT
64 GTTAAAAAATTAACGCA-TTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* * *
26511 AAACTTCCAATTTTTTCAAAATCATACCTAACGTTTAG---T--TTTCATTTTAGTACTCGTCGT
1 AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGT
* * ** * * *
26571 TAAAAATTTAATGTGTTTAGTACCTAAACTATCAGTTTTGGTCAGTTTTAGAATCT
66 TAAAAAATTAACGCATTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* *
26627 AAACTTTCAATTTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAA-TTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TTGTC
* * *
26692 GTT-AAAAATTAACGCATTTAGTACCTAAACTATCATTTGTGATTTGTTTT-GATATCT
64 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCATTT-TGGTCTGTTTTAG-TACCT
* **
26749 AAACTTTCATTTTTTTTCAAAACCATATCC-AACGTTTAGTTTTCATTTCATTTTAGTACCCGTC
1 AAACTTTCA-ATTTTTTCAAAACCATA-CCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTC
* * * * *
26813 TTTAAAAATTTAATGCCTTTAGTACCTAAACTATCAGTTTTGGTCTATTTTAGTACCT
64 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* * **
26871 AAACTTTCATTTTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGT
1 AAACTTTCA--ATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTA-CTTGT
* * * * *
26936 CGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCT
63 CGTTAAAAAATTAACGCATTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * **
26995 AAACATTCATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCCGTCGT
1 AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGT
*
27060 TAAAAACTTAA
66 TAAAAAATTAA
27071 TAGGAGAATG
Statistics
Matches: 689, Mismatches: 85, Indels: 57
0.83 0.10 0.07
Matches are distributed among these distances:
116 60 0.09
117 35 0.05
118 3 0.00
119 1 0.00
120 85 0.12
121 61 0.09
122 326 0.47
123 57 0.08
124 60 0.09
125 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (120 bp):
AAACTTTCAATTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGT
TAAAAAATTAACGCATTTAGTACCTAAACTATCATTTTGGTCTGTTTTAGTACCT
Found at i:26308 original size:214 final size:214
Alignment explanation
Indices: 25935--26363 Score: 548
Period size: 214 Copynumber: 2.0 Consensus size: 214
25925 TTAGTACTTA
* * *
25935 AAACTTTTAATTTTTTTAAAATCATACTTAACGTTTAATTTTCATTTCATTTAATATCCACTGTT
1 AAACTTTTAATTTTTTCAAAACCATACTTAACATTTAATTTTCATTTCATTTAATATCCACTGTT
* * *
26000 AAAAAATTAACACGTTTAGTACCTAAACTATTAGTTGTAGTTTGTTTCAGTACCTAAACTTTCAA
66 AAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAGTTTGTTTCAGTACCTAAAATTTCAA
* *
26065 TTTTTTCAAAATCATACCTAACGTTTAG-T-TTTCATTTTAGT-ACTCATCGTTAAAAATTTAAT
131 TTTTTTCAAAATCATACCTAACATTTAGTTATTTCATTTTAGTAACT-ATCGTTAAAAACTTAAT
*
26127 GTGTTTAGTACCTAAACTAC
195 GCGTTTAGTACCTAAACTAC
* * ***
26147 AAACTTTTAATTTTTTCAAAACCATA-TCTAACATTTAGTTTTCATTTCATTTTAGTA-CTTTGT
1 AAACTTTTAATTTTTTCAAAACCATACT-TAACATTTAATTTTCATTTCA-TTTAATATC-CACT
* * * *
26210 AGTTAAAAAATTAACGCATTTAGTACCTAAATTATCATTTGT-GATTTGTCTT-GGTACCTAAAA
63 -GTTAAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAG-TTTGT-TTCAGTACCTAAAA
* *
26273 TTTCAATTTTTTCAAAATCATACCTAACATTTAGTTTCATTTCATTTTAGTAACTGTTGTTAAAA
125 TTTCAATTTTTTCAAAATCATACCTAACATTTAG-TT-ATTTCATTTTAGTAACTATCGTTAAAA
26338 ACTTAATGCGTTTAGTACCTAAACTA
188 ACTTAATGCGTTTAGTACCTAAACTA
26364 TCAATTTTGG
Statistics
Matches: 186, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
211 1 0.01
212 44 0.24
213 8 0.04
214 83 0.45
215 2 0.01
216 1 0.01
218 44 0.24
219 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (214 bp):
AAACTTTTAATTTTTTCAAAACCATACTTAACATTTAATTTTCATTTCATTTAATATCCACTGTT
AAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAGTTTGTTTCAGTACCTAAAATTTCAA
TTTTTTCAAAATCATACCTAACATTTAGTTATTTCATTTTAGTAACTATCGTTAAAAACTTAATG
CGTTTAGTACCTAAACTAC
Found at i:29460 original size:2 final size:2
Alignment explanation
Indices: 29453--29508 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
29443 CTTTTTAGAA
29453 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
29495 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
29509 TTAATAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48041 original size:74 final size:73
Alignment explanation
Indices: 47916--48052 Score: 179
Period size: 74 Copynumber: 1.9 Consensus size: 73
47906 TACGTCCATC
*
47916 CTAAAATTCGAATTTTCTTTGATCAATTATTTATTTTACTCATGGAATTCATCTTGAAAATTTTC
1 CTAAAATTCGAATTTTCTTTGATCAATTATTTATTTTACTCATAGAATTCATCTTG-AAATTTTC
47981 ATGCACAGT
65 ATGCACAGT
* * * **
47990 CTAAAA-TCTGAATTTTCTTTGATTAGTTATTTATTTTAAGT-ATAGCGTTCATCTTGAAATTTT
1 CTAAAATTC-GAATTTTCTTTGATCAATTATTTATTTT-ACTCATAGAATTCATCTTGAAATTTT
48053 ATTTATACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
73 9 0.16
74 44 0.80
75 2 0.04
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (73 bp):
CTAAAATTCGAATTTTCTTTGATCAATTATTTATTTTACTCATAGAATTCATCTTGAAATTTTCA
TGCACAGT
Found at i:52994 original size:21 final size:21
Alignment explanation
Indices: 52961--53019 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
52951 GGGTAAGAGC
*
52961 TTTT-TTAAATTTGAATTTGA
1 TTTTATTATATTTGAATTTGA
52981 TTTTATTATATTTGAATTTGA
1 TTTTATTATATTTGAATTTGA
*
53002 TTTTATTATATTTAAATT
1 TTTTATTATATTTGAATT
53020 CAAATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTATTATATTTGAATTTGA
Found at i:65478 original size:22 final size:22
Alignment explanation
Indices: 65453--65497 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
65443 CTTCGACACC
65453 CCAACCTCCGCCCT-CGCCGCCG
1 CCAA-CTCCGCCCTCCGCCGCCG
*
65475 CCAACTCCGCCCTCCGCCTCCG
1 CCAACTCCGCCCTCCGCCGCCG
65497 C
1 C
65498 TTCTACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.09, C:0.64, G:0.16, T:0.11
Consensus pattern (22 bp):
CCAACTCCGCCCTCCGCCGCCG
Found at i:75663 original size:43 final size:42
Alignment explanation
Indices: 75594--75698 Score: 158
Period size: 43 Copynumber: 2.5 Consensus size: 42
75584 AAGCATTTTA
75594 CGGCGTTTGTG-GTAAAAACGCCGTTAAAGAACATAACTATTG
1 CGGCGTTTGTGTG-AAAAACGCCGTTAAAGAACATAACTATTG
* * *
75636 CGTCGTTTGTGTGAATAAATGCCGTTAAAGAACATACCTATTG
1 CGGCGTTTGTGTGAA-AAACGCCGTTAAAGAACATAACTATTG
75679 CGGCGTTTGTGTGAAAAACG
1 CGGCGTTTGTGTGAAAAACG
75699 TTGTTAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 16 0.29
43 40 0.71
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
CGGCGTTTGTGTGAAAAACGCCGTTAAAGAACATAACTATTG
Found at i:75750 original size:43 final size:43
Alignment explanation
Indices: 75703--75798 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
75693 AAAACGTTGT
* * ** * *
75703 TAAATATTAACACCTATTGTGGCGTTTTTATTGAAAACGCCAC
1 TAAATATCAACAACTATTACGGCATTTCTATTGAAAACGCCAC
* * *
75746 TAAATATCGACAACTATTACGGCATTTCTATTGAAAATGCCGC
1 TAAATATCAACAACTATTACGGCATTTCTATTGAAAACGCCAC
75789 TAAATATCAA
1 TAAATATCAA
75799 AATTTATTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (43 bp):
TAAATATCAACAACTATTACGGCATTTCTATTGAAAACGCCAC
Found at i:78627 original size:14 final size:13
Alignment explanation
Indices: 78595--78625 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
78585 AGTAGTTCTC
*
78595 TTTTTCTTGTTTT
1 TTTTTCTGGTTTT
78608 TTTTTCTGGTTTT
1 TTTTTCTGGTTTT
78621 TTTTT
1 TTTTT
78626 TCCCTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTCTGGTTTT
Found at i:79210 original size:3 final size:3
Alignment explanation
Indices: 79202--79235 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
79192 ATGTAAATTA
79202 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
79236 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:79687 original size:130 final size:133
Alignment explanation
Indices: 79433--79759 Score: 441
Period size: 130 Copynumber: 2.5 Consensus size: 133
79423 CGTCTAAGGG
* * * *
79433 TGACATGGTTCCTACGTGATGAGGAAATCT-AGTC-GAGGGATGACACTGCTCATACATGATGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGA-TCTG-GGGATGACACGGCTCATACATGATGAA
* * *
79496 GAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGGGGACGACTGGTTAT
64 GAGTTCTTGGCCATC-TTA-GAAGAGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
79561 CTATGGT
127 CTATGGT
*
79568 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
*
79633 AGTTC-TGGCCATC-TA-AA-AGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
65 AGTTCTTGGCCATCTTAGAAGAGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTA
79694 TGGT
130 TGGT
* * * * *
79698 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACATGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGA
79760 GGACGGCTGG
Statistics
Matches: 174, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
129 19 0.11
130 81 0.47
131 2 0.01
133 2 0.01
135 40 0.23
136 30 0.17
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (133 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
GTTCTTGGCCATCTTAGAAGAGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAT
GGT
Found at i:79715 original size:43 final size:43
Alignment explanation
Indices: 79534--79730 Score: 179
Period size: 43 Copynumber: 4.6 Consensus size: 43
79524 ATAACTCGGT
* *
79534 TCCTACGTGATGGGGACGA-CTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGATGACACGGC
**
79577 TCCTACGTGATGAGGAGATCT-G--ATCTGGGGAATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTATGG-ATGACACGGC
* * * ** * * *
79618 TCATACGTGATGAAGAGTTCTGGCCATCTAAAAGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATCT--ATG-GATGACACGGC
* *
79664 TCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGATGACACGGC
79707 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGATCTGGT
79731 CTGGTGATGA
Statistics
Matches: 123, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
40 6 0.05
41 27 0.22
42 5 0.04
43 46 0.37
44 6 0.05
46 31 0.25
47 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTATGGATGACACGGC
Found at i:80056 original size:34 final size:36
Alignment explanation
Indices: 80007--80094 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 36
79997 CAAAGATTAG
* *
80007 TGTTTCGAGAGAAACAAACTCAAAGA-TGTTT-TTT
1 TGTTTCAAGAAAAACAAACTCAAAGATTGTTTGTTT
* *
80041 TGTTTTAAGAAAAACATACTCAAAGACTTTGTTTGTTT
1 TGTTTCAAGAAAAACAAACTCAAAGA--TTGTTTGTTT
80079 TGTTTCAAGAAAAACA
1 TGTTTCAAGAAAAACA
80095 GATTCAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
34 22 0.49
37 5 0.11
38 18 0.40
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (36 bp):
TGTTTCAAGAAAAACAAACTCAAAGATTGTTTGTTT
Found at i:80408 original size:15 final size:15
Alignment explanation
Indices: 80384--80427 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
80374 AAGATGATCT
*
80384 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
80399 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
80414 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
80428 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:80480 original size:31 final size:30
Alignment explanation
Indices: 80416--80490 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
80406 AGAGAAAATG
*
80416 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
80447 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
80478 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
80491 TGCCTCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:80593 original size:40 final size:40
Alignment explanation
Indices: 80523--80602 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
80513 GTTTTAATAA
*
80523 AAACAATCTCAAAGGTGGGTAGTTTTAAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGCAGTTTTAAAAGAAATTGTCT
* * *
80563 AAACGATCTCAAATGTGGGCA-TTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGCAGTTTT-AAAAGAAATTGTCT
80603 CGAGAGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGCAGTTTTAAAAGAAATTGTCT
Found at i:80655 original size:62 final size:62
Alignment explanation
Indices: 80584--80707 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
80574 AATGTGGGCA
* * *
80584 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * *
80645 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
80708 GGATCTCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 4 0.07
62 13 0.24
63 38 0.69
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:81042 original size:27 final size:28
Alignment explanation
Indices: 80977--81045 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
80967 TTAAGAGAGA
*
80977 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
81005 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
81033 CAAAGATTTTTTT
1 CAAAGATTTTTTT
81046 TTTTCACAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:81163 original size:26 final size:25
Alignment explanation
Indices: 81134--81245 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 25
81124 CAAAACTTTG
* *
81134 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
81160 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
81187 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
* *
81216 TATTCTAAAGGAACAAACTCAAAGATT
1 T-TTCAAAAGAAAC-AACTCAAAGATT
81243 TTT
1 TTT
81246 TTTCAAGAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.11
26 14 0.19
27 8 0.11
28 11 0.15
29 33 0.45
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:81217 original size:29 final size:29
Alignment explanation
Indices: 81149--81251 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 29
81139 AAATAAATAG
*
81149 ACTCAAAGA--TTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
81174 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
81203 ACTCCAAGATTTTTATTCTAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
81232 ACTCAAAGATTTTTTTTCAA
1 ACTCAAAGATTTTTATTCAA
81252 GAGAAACTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
25 9 0.13
27 3 0.04
28 11 0.16
29 44 0.66
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:81616 original size:36 final size:35
Alignment explanation
Indices: 81534--81635 Score: 100
Period size: 36 Copynumber: 2.9 Consensus size: 35
81524 TTAAGATATA
* * * * *
81534 GTCTCAAATGAGACAAAGTTTGTTTTT--GATATA
1 GTCTCAAACGAGACAAAATCTGTTTTTGAGAAATT
*
81567 GTCTCAAATGAGACAAAATCTGTTTTTAGAGAAATT
1 GTCTCAAACGAGACAAAATCTGTTTTT-GAGAAATT
* * *
81603 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 GTCTCAAACGAGACAAAATCTGTTTTTGAGAAA
81636 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 25 0.43
35 6 0.10
36 27 0.47
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (35 bp):
GTCTCAAACGAGACAAAATCTGTTTTTGAGAAATT
Found at i:81643 original size:35 final size:33
Alignment explanation
Indices: 81533--81650 Score: 128
Period size: 33 Copynumber: 3.4 Consensus size: 33
81523 TTTAAGATAT
* * *
81533 AGTCTCAAATGAGACAAAGTTTGTTTTTGATAT
1 AGTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
* * *
81566 AGTCTCAAATGAGACAAAATCTGTTTTTAGAGAA
1 AGTCTCAAGTGAGACAAAGTTTGTTTTT-GAGAA
*
81600 ATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAA
1 A--GTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
81635 ACGATCTCAAGTGAGA
1 A-G-TCTCAAGTGAGA
81651 TCAACTTTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
33 26 0.37
34 5 0.07
35 17 0.24
36 23 0.32
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (33 bp):
AGTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
Found at i:81660 original size:35 final size:36
Alignment explanation
Indices: 81504--81662 Score: 93
Period size: 33 Copynumber: 4.6 Consensus size: 36
81494 AATGATGTCC
* * *
81504 CAAGCGAGACGAAA-TTTG-CTTTA-AGATATAGTCT
1 CAAGCGAGAC-AAACTTTGTTTTTAGAGAAATCGTCT
** * * *
81538 CAAATGAGACAAAGTTTGTTTTT---GATATAGTCT
1 CAAGCGAGACAAACTTTGTTTTTAGAGAAATCGTCT
** * * *
81571 CAAATGAGACAAAATCTGTTTTTAGAGAAATTGTCT
1 CAAGCGAGACAAACTTTGTTTTTAGAGAAATCGTCT
*
81607 CAAGCGAGACAAAGTTTGTTTTT-GAGAAA-CGATCT
1 CAAGCGAGACAAACTTTGTTTTTAGAGAAATCG-TCT
*
81642 CAAGTGAGATC-AACTTTGTTT
1 CAAGCGAGA-CAAACTTTGTTT
81663 AATGTGAAAC
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
33 34 0.33
34 13 0.12
35 29 0.28
36 28 0.27
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
CAAGCGAGACAAACTTTGTTTTTAGAGAAATCGTCT
Found at i:81716 original size:101 final size:99
Alignment explanation
Indices: 81603--81830 Score: 250
Period size: 101 Copynumber: 2.3 Consensus size: 99
81593 TAGAGAAATT
* *
81603 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AGAAAC--GATCTCAA-GTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACATCT-AAGGTGAGAT----TTTGTTTA
* *
81664 -ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
60 TA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
81704 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTTTGTTTTTAGT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAAC-ATCTAAGGTGAGATTTTGTTTATAGT
* * *
81769 GAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
64 GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
81805 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
81831 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
100 5 0.05
101 85 0.77
102 7 0.06
104 2 0.02
105 11 0.10
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACATCTAAGGTGAGATTTTGTTTATAGTGA
AACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:81993 original size:36 final size:36
Alignment explanation
Indices: 81953--82051 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
81943 AAAGGGAAAA
**
81953 TGTCTCAAATGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
81989 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
82025 TGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTT
82052 TAGAAAAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
Found at i:82415 original size:4 final size:4
Alignment explanation
Indices: 82406--82483 Score: 97
Period size: 4 Copynumber: 20.0 Consensus size: 4
82396 TTTATGTATC
* *
82406 ATGT ATGT A--T ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATAT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
82452 ATGT ATGT ATGT GTAT ACGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
82484 GTATACTCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
4 60 0.97
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:83678 original size:12 final size:11
Alignment explanation
Indices: 83656--83777 Score: 84
Period size: 12 Copynumber: 10.5 Consensus size: 11
83646 TTTGTCCTCT
83656 TTTTGTTCTTTG
1 TTTT-TTCTTTG
83668 CTTTTTTCTTTG
1 -TTTTTTCTTTG
* *
83680 ACTTTTGCTTTG
1 -TTTTTTCTTTG
*
83692 ATTTTTCTTTG
1 TTTTTTCTTTG
*
83703 TTTTTGCTTTG
1 TTTTTTCTTTG
* *
83714 ATTTTTT-TCTC
1 -TTTTTTCTTTG
* *
83725 TCTTCTCTTTG
1 TTTTTTCTTTG
83736 TTTTTTTCTTTG
1 -TTTTTTCTTTG
83748 CTCTTTTCTCTTTG
1 -T-TTTT-TCTTTG
*
83762 ATTTTTCTTTG
1 TTTTTTCTTTG
83773 TTTTT
1 TTTTT
83778 GATTGGATCT
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
10 4 0.05
11 32 0.38
12 35 0.41
13 8 0.09
14 6 0.07
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.72
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:83696 original size:11 final size:11
Alignment explanation
Indices: 83670--83718 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
83660 GTTCTTTGCT
*
83670 TTTTTCTTTGA
1 TTTTGCTTTGA
83681 CTTTTGCTTTGA
1 -TTTTGCTTTGA
* *
83693 TTTTTCTTTGT
1 TTTTGCTTTGA
83704 TTTTGCTTTGA
1 TTTTGCTTTGA
83715 TTTT
1 TTTT
83719 TTTCTCTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGCTTTGA
Found at i:83707 original size:22 final size:22
Alignment explanation
Indices: 83670--83778 Score: 96
Period size: 22 Copynumber: 4.7 Consensus size: 22
83660 GTTCTTTGCT
*
83670 TTTTTCTTTGACTTTTGCTTTGA
1 TTTTTCTTTG-TTTTTGCTTTGA
83693 TTTTTCTTTGTTTTTGCTTTGA
1 TTTTTCTTTGTTTTTGCTTTGA
* * *
83715 TTTTT-TTCTCTCTTCT-CTTTGTT
1 TTTTTCTT-TGT-TTTTGCTTTG-A
*
83738 TTTTTCTTTGCTCTTTTCTCTTTGA
1 TTTTTCTTTG-T-TTTT-GCTTTGA
83763 TTTTTCTTTGTTTTTG
1 TTTTTCTTTGTTTTTG
83779 ATTGGATCTT
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
21 2 0.03
22 23 0.32
23 23 0.32
24 8 0.11
25 10 0.14
26 5 0.07
ACGTcount: A:0.04, C:0.15, G:0.10, T:0.72
Consensus pattern (22 bp):
TTTTTCTTTGTTTTTGCTTTGA
Found at i:83751 original size:19 final size:22
Alignment explanation
Indices: 83709--83753 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
83699 TTTGTTTTTG
*
83709 CTTTGATTTTTTTCTCTCTTCT
1 CTTTGATTTTTTTCTCTCTGCT
83731 CTTTG-TTTTTTTCT-T-TGCT
1 CTTTGATTTTTTTCTCTCTGCT
83750 CTTT
1 CTTT
83754 TCTCTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 9 0.41
22 5 0.23
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (22 bp):
CTTTGATTTTTTTCTCTCTGCT
Found at i:89224 original size:14 final size:13
Alignment explanation
Indices: 89192--89222 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
89182 AGTAGTTCTC
*
89192 TTTTTCTTGTTTT
1 TTTTTCTGGTTTT
89205 TTTTTCTGGTTTT
1 TTTTTCTGGTTTT
89218 TTTTT
1 TTTTT
89223 TCCCTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTCTGGTTTT
Found at i:89807 original size:3 final size:3
Alignment explanation
Indices: 89799--89838 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
89789 ATGTAAATTA
* *
89799 AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
89839 TACAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:90494 original size:27 final size:27
Alignment explanation
Indices: 90442--90495 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
90432 ATATTTTAGT
* * **
90442 TTCTAAATAATTAGTTTTTTTTATTAA
1 TTCTAAATAATTACTTGTTTAAATTAA
90469 TTCTAAATAATTACTTGTTTAAATTAA
1 TTCTAAATAATTACTTGTTTAAATTAA
90496 ATGATCAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (27 bp):
TTCTAAATAATTACTTGTTTAAATTAA
Found at i:95924 original size:24 final size:23
Alignment explanation
Indices: 95897--95943 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
95887 CGTAAACTAC
95897 CAAAAGACAAAGAAAAACGTGTCA
1 CAAAAG-CAAAGAAAAACGTGTCA
* *
95921 CAAAAGTAAAGATAAACGTGTCA
1 CAAAAGCAAAGAAAAACGTGTCA
95944 TAAAGGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.13
Consensus pattern (23 bp):
CAAAAGCAAAGAAAAACGTGTCA
Found at i:104667 original size:68 final size:70
Alignment explanation
Indices: 104556--104698 Score: 263
Period size: 68 Copynumber: 2.1 Consensus size: 70
104546 AAATTATTTC
*
104556 CCTAAAATCCTAATCAATATGCAAGTTGTAAATAGAAACAAGATATTCTATTGAAAATGCATAAA
1 CCTAAAATCCTAATCAATATGCAAGTTGTAAATAGAAACAAGATACTCTATTGAAAATGCATAAA
104621 ATAAT
66 ATAAT
104626 CCTAAAATCCTAATC-A-ATGCAAGTTGTAAATAGAAACAAGATACTCTATTGAAAATGCATAAA
1 CCTAAAATCCTAATCAATATGCAAGTTGTAAATAGAAACAAGATACTCTATTGAAAATGCATAAA
104689 ATAAT
66 ATAAT
104694 CCTAA
1 CCTAA
104699 CATTGTCCCC
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 56 0.78
69 1 0.01
70 15 0.21
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (70 bp):
CCTAAAATCCTAATCAATATGCAAGTTGTAAATAGAAACAAGATACTCTATTGAAAATGCATAAA
ATAAT
Found at i:114837 original size:48 final size:48
Alignment explanation
Indices: 114784--114884 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 48
114774 CCATAGACAC
* ** *
114784 ACATATACATATAATATGTATAAACATATACATGCAACATACATACAT
1 ACATATACATATAACATACATAAACATATACATGCAACATAAATACAT
* * * * *
114832 GCATATACATGTAACATACATACACATATACATGTAGCATAAATACAT
1 ACATATACATATAACATACATAAACATATACATGCAACATAAATACAT
114880 ACATA
1 ACATA
114885 CACAAAGAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.28
Consensus pattern (48 bp):
ACATATACATATAACATACATAAACATATACATGCAACATAAATACAT
Found at i:114842 original size:25 final size:24
Alignment explanation
Indices: 114808--114884 Score: 102
Period size: 25 Copynumber: 3.2 Consensus size: 24
114798 TATGTATAAA
*
114808 CATATACATGCAACATACATACAT
1 CATATACATGTAACATACATACAT
114832 GCATATACATGTAACATACATACA-
1 -CATATACATGTAACATACATACAT
* *
114856 CATATACATGTAGCATAAATACAT
1 CATATACATGTAACATACATACAT
114880 ACATA
1 -CATA
114885 CACAAAGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
23 21 0.45
25 26 0.55
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (24 bp):
CATATACATGTAACATACATACAT
Found at i:114863 original size:23 final size:23
Alignment explanation
Indices: 114782--114878 Score: 104
Period size: 23 Copynumber: 4.1 Consensus size: 23
114772 TACCATAGAC
* * **
114782 ACACATATACATATAATATGTAT
1 ACACATATACATGTAACATACAT
* *
114805 AAACATATACATGCAACATACAT
1 ACACATATACATGTAACATACAT
114828 ACATGCATATACATGTAACATACAT
1 ACA--CATATACATGTAACATACAT
* *
114853 ACACATATACATGTAGCATAAAT
1 ACACATATACATGTAACATACAT
114876 ACA
1 ACA
114879 TACATACACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 40 0.65
25 22 0.35
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (23 bp):
ACACATATACATGTAACATACAT
Found at i:114885 original size:23 final size:23
Alignment explanation
Indices: 114811--114886 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
114801 GTATAAACAT
* * *
114811 ATACATGCAACATACATACATGCAT
1 ATACATGTAACATAAATACA--CAC
* *
114836 ATACATGTAACATACATACACAT
1 ATACATGTAACATAAATACACAC
* *
114859 ATACATGTAGCATAAATACATAC
1 ATACATGTAACATAAATACACAC
114882 ATACA
1 ATACA
114887 CAAAGAAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 27 0.59
25 19 0.41
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (23 bp):
ATACATGTAACATAAATACACAC
Found at i:115682 original size:19 final size:19
Alignment explanation
Indices: 115658--115697 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
115648 TACATGGGTG
115658 AACACCAAACTATGGTCAA
1 AACACCAAACTATGGTCAA
115677 AACACCAAACTATGGTCAA
1 AACACCAAACTATGGTCAA
115696 AA
1 AA
115698 TTCATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.25, G:0.10, T:0.15
Consensus pattern (19 bp):
AACACCAAACTATGGTCAA
Found at i:117652 original size:25 final size:25
Alignment explanation
Indices: 117623--117670 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
117613 AATTACACAT
117623 TTAGTACATAAACTATCAGTTTTGA
1 TTAGTACATAAACTATCAGTTTTGA
* * *
117648 TTAGTACCTAAACTTTCATTTTT
1 TTAGTACATAAACTATCAGTTTT
117671 TAAAATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (25 bp):
TTAGTACATAAACTATCAGTTTTGA
Found at i:127432 original size:20 final size:20
Alignment explanation
Indices: 127396--127433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
127386 ATCATATTCC
**
127396 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
127416 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
127434 GTGAACCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:143102 original size:14 final size:14
Alignment explanation
Indices: 143083--143109 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
143073 GGCGGCCGGT
143083 TCTTAACGTTAAAA
1 TCTTAACGTTAAAA
143097 TCTTAACGTTAAA
1 TCTTAACGTTAAA
143110 TTTTGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TCTTAACGTTAAAA
Found at i:145938 original size:2 final size:2
Alignment explanation
Indices: 145931--145971 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
145921 TTTAATACTT
145931 TA TA 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 TA TA T
145972 GGCATATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:146570 original size:16 final size:16
Alignment explanation
Indices: 146549--146582 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
146539 TATAGTAAAA
146549 ATTTATATTTATACTT
1 ATTTATATTTATACTT
*
146565 ATTTATATTTATATTT
1 ATTTATATTTATACTT
146581 AT
1 AT
146583 AATAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATTTATACTT
Found at i:146590 original size:22 final size:22
Alignment explanation
Indices: 146549--146590 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
146539 TATAGTAAAA
* *
146549 ATTTATATTTATACTTATTTAT
1 ATTTATATTTATAATAATTTAT
146571 ATTTATATTTATAATAATTT
1 ATTTATATTTATAATAATTT
146591 GAATTGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTATATTTATAATAATTTAT
Found at i:147517 original size:60 final size:61
Alignment explanation
Indices: 147453--147568 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
147443 TGCTCCCCCG
* *
147453 ACTAT-AGAATATTA-TTTTATTGAAT-CATCTAATTATTAAAAATTACAAAATGATCCTTGA
1 ACTATAAG-ATATTACTTTTATTGAATCCCTC-AACTATTAAAAATTACAAAATGATCCTTGA
* * * *
147513 ACTATAAGATGTTACTTTTTTTGAGTCCCTCAACTATTAAAAGTTACAAAATGATC
1 ACTATAAGATATTACTTTTATTGAATCCCTCAACTATTAAAAATTACAAAATGATC
147569 TTCTCACTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
60 10 0.21
61 34 0.72
62 3 0.06
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (61 bp):
ACTATAAGATATTACTTTTATTGAATCCCTCAACTATTAAAAATTACAAAATGATCCTTGA
Found at i:156419 original size:24 final size:25
Alignment explanation
Indices: 156391--156438 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
156381 AATAATTATT
*
156391 TATTATT-TGATATATTTAT-AAAAC
1 TATTATTAT-ATATATGTATGAAAAC
156415 TATTATTATATATATGTATGAAAA
1 TATTATTATATATATGTATGAAAA
156439 TTTTCCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
TATTATTATATATATGTATGAAAAC
Found at i:162872 original size:21 final size:20
Alignment explanation
Indices: 162825--162873 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
162815 ACAAAAAAAG
* **
162825 TGCATAGTTTATATACTAAA
1 TGCATAGTTTACATAAGAAA
*
162845 TGTATAGTTTACCATAAGAAA
1 TGCATAGTTTA-CATAAGAAA
162866 TGCATAGT
1 TGCATAGT
162874 CAATACGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (20 bp):
TGCATAGTTTACATAAGAAA
Found at i:163481 original size:16 final size:17
Alignment explanation
Indices: 163460--163495 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
163450 TTTGAAACAA
163460 GTACATATAT-GTGTGT
1 GTACATATATAGTGTGT
163476 GTACATATATACGTGTGT
1 GTACATATATA-GTGTGT
163494 GT
1 GT
163496 GTGTGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (17 bp):
GTACATATATAGTGTGT
Found at i:169395 original size:19 final size:19
Alignment explanation
Indices: 169371--169408 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
169361 ACACAACATC
169371 ATTAATTCTTCTATATAGG
1 ATTAATTCTTCTATATAGG
169390 ATTAATTCTTCTATATAGG
1 ATTAATTCTTCTATATAGG
169409 TCCATCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTAATTCTTCTATATAGG
Found at i:174767 original size:60 final size:61
Alignment explanation
Indices: 174645--174791 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 61
174635 AACGTAATAA
* * * * *
174645 ATAATTGA-ATGACCATTTTGTAACTTTTAATAATCAAGAGATTCAATAAAACAACACTCT
1 ATAATCGAGATGATCATTTTGTAACTTTTAATAATCAAGAAATTAAATAAAACAACACCCT
* * * **
174705 ATAGTC-AGATGATCATTTTGTAACTTTTAATAGTCGAA-AAATTAAATAAAATAGTACCCT
1 ATAATCGAGATGATCATTTTGTAACTTTTAATAATC-AAGAAATTAAATAAAACAACACCCT
174765 ATAATCGAGA-GATCATTTGTGT-ACTTT
1 ATAATCGAGATGATCATTT-TGTAACTTT
174792 ATCCAATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 1 0.01
60 63 0.88
61 8 0.11
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (61 bp):
ATAATCGAGATGATCATTTTGTAACTTTTAATAATCAAGAAATTAAATAAAACAACACCCT
Found at i:182644 original size:37 final size:37
Alignment explanation
Indices: 182558--182658 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
182548 TTCGTCCTAT
* * * **
182558 TAGGATTCAAACTCTTAAAAATATGATAGAATTTTGT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
*
182595 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
* * *
182632 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
182659 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:183212 original size:2 final size:2
Alignment explanation
Indices: 183192--183232 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
183182 TTTTTAATAC
* *
183192 TA TA TT TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183233 CTTTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:183547 original size:16 final size:17
Alignment explanation
Indices: 183479--183562 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 17
183469 TAATATTTCA
*
183479 TTTATTTATTTATTTATT
1 TTTATTTATTCATTT-TT
**
183497 TTTCCTT-TT-ATTTTAT
1 TTTATTTATTCATTTT-T
* *
183513 TTT-TTTATAC-TTATT
1 TTTATTTATTCATTTTT
*
183528 TTTA-TTCTTCATTTTT
1 TTTATTTATTCATTTTT
183544 TTTATTTATTCATTTTT
1 TTTATTTATTCATTTTT
183561 TT
1 TT
183563 CCTCTAACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
15 11 0.22
16 20 0.39
17 15 0.29
18 5 0.10
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTCATTTTT
Found at i:183552 original size:26 final size:25
Alignment explanation
Indices: 183502--183553 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
183492 TTATTTTTCC
183502 TTTTATTTTATTTTTTTATACTTAT
1 TTTTATTTTATTTTTTTATACTTAT
*
183527 TTTTATTCTTCATTTTTTT-TATTTAT
1 TTTTATT-TT-ATTTTTTTATACTTAT
183553 T
1 T
183554 CATTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTATTTTATTTTTTTATACTTAT
Found at i:184295 original size:19 final size:19
Alignment explanation
Indices: 184271--184307 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
184261 ACCTTACTAA
184271 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
184290 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
184308 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:187738 original size:16 final size:15
Alignment explanation
Indices: 187706--187755 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
187696 CAATCAGAAC
187706 AAAAAGAAAAAAACA
1 AAAAAGAAAAAAACA
*
187721 AAAAAGAAAAGAAGCAA
1 AAAAAGAAAA-AAAC-A
*
187738 AAAAAGAAGAAAACA
1 AAAAAGAAAAAAACA
187753 AAA
1 AAA
187756 GAAAAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 14 0.47
16 6 0.20
17 10 0.33
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAACA
Found at i:187775 original size:20 final size:18
Alignment explanation
Indices: 187708--187786 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 18
187698 ATCAGAACAA
*
187708 AAAGAAAAAAACAAAAAAG
1 AAAGAACAAAA-AAAAAAG
*
187727 AAAAGAAGCAAAAAAAGAAG
1 -AAAGAA-CAAAAAAAAAAG
187747 -AA-AACAAAAGAAAAAAG
1 AAAGAACAAAA-AAAAAAG
187764 AAAGAACAAAAATCAAAAAG
1 AAAGAACAAAAA--AAAAAG
187784 AAA
1 AAA
187787 AAGGGACAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
16 5 0.10
17 8 0.16
18 5 0.10
19 7 0.14
20 21 0.42
21 4 0.08
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (18 bp):
AAAGAACAAAAAAAAAAG
Found at i:187788 original size:7 final size:7
Alignment explanation
Indices: 187706--187788 Score: 53
Period size: 7 Copynumber: 11.6 Consensus size: 7
187696 CAATCAGAAC
187706 AAAAAGAA
1 AAAAAG-A
*
187714 AAAAACA
1 AAAAAGA
187721 AAAAAGA
1 AAAAAGA
187728 AAAGAAGCAA
1 AAA-AAG--A
187738 AAAAAGA
1 AAAAAGA
*
187745 AGAAA-A
1 AAAAAGA
*
187751 CAAAAGA
1 AAAAAGA
187758 AAAAAGA
1 AAAAAGA
* *
187765 AAGAA-C
1 AAAAAGA
**
187771 AAAAATC
1 AAAAAGA
187778 AAAAAGA
1 AAAAAGA
187785 AAAA
1 AAAA
187789 GGGACAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
6 8 0.14
7 36 0.61
8 8 0.14
9 3 0.05
10 4 0.07
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:190350 original size:106 final size:106
Alignment explanation
Indices: 189392--190349 Score: 1567
Period size: 106 Copynumber: 9.0 Consensus size: 106
189382 ATATCGTGCC
* * * * * **
189392 ACTCGAGACAACACAAGTTCAGCTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
189457 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
189498 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
189563 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
189604 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
189669 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
189710 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
189775 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
189816 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
189881 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
189922 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
189987 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
190028 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
190093 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
190134 ACTCGAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
190199 AATTTCGGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * ** * *
190240 ACTCGAGACAGCACAAGCTCAACTTCACAACGAAGGG-GCGACTGACTGTCAACAAGCAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * *
190304 CAGTTTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
190346 ACTC
1 ACTC
190350 GGAACAGTAC
Statistics
Matches: 807, Mismatches: 44, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
105 2 0.00
106 805 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:190673 original size:83 final size:82
Alignment explanation
Indices: 190527--190708 Score: 229
Period size: 83 Copynumber: 2.2 Consensus size: 82
190517 TGTCCAACTC
* * *
190527 AAAGAAGGAGTATCTGTCAATAAAGACGTTCGAGTTCGATTACACTCAGCTCCAAAGCGCATCAT
1 AAAGAAGG-GTATCTGTCAATAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAAGCACATCAT
**
190592 TTACAGTATAGCTCAAGG
65 TTACAACATAGCTCAAGG
** * * * *
190610 CTAGAAGGGCTATCTGTCAGTAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
1 AAAGAAGGG-TATCTGTCAATAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAAGCACATCAT
*
190675 TTGCAACATAGCTCAAGG
65 TTACAACATAGCTCAAGG
190693 AAAGAAGGGTTATCTG
1 AAAGAAGGG-TATCTG
190709 CCATCAAAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
82 1 0.01
83 82 0.99
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (82 bp):
AAAGAAGGGTATCTGTCAATAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAAGCACATCATT
TACAACATAGCTCAAGG
Found at i:191240 original size:37 final size:37
Alignment explanation
Indices: 191183--191287 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
191173 CATTTTCGTC
* *
191183 CTACTAAGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
191220 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
191257 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
191288 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:191808 original size:22 final size:21
Alignment explanation
Indices: 191774--191854 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
191764 TTATACATGC
*
191774 ATATATTTTTTATTTATTTAT
1 ATATATTTATTATTTATTTAT
191795 AT-TCATTTAATTATTT-TTTAAT
1 ATAT-ATTT-ATTATTTATTT-AT
*
191817 ACTATATTTATTATTTATATAT
1 A-TATATTTATTATTTATTTAT
* * *
191839 ATGTATATATTTTTTA
1 ATATATTTATTATTTA
191855 AAATATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 21 0.43
22 19 0.39
23 7 0.14
24 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (21 bp):
ATATATTTATTATTTATTTAT
Found at i:191989 original size:17 final size:17
Alignment explanation
Indices: 191969--192001 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
191959 GGTTTATATA
191969 TTTATTTATTTT-TATTT
1 TTTATTT-TTTTATATTT
191986 TTTATTTTTTTATATT
1 TTTATTTTTTTATATT
192002 ATATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTATTTTTTTATATTT
Found at i:192073 original size:2 final size:2
Alignment explanation
Indices: 192066--192096 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
192056 TACTCATTAT
192066 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 T
192097 TAATATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:195173 original size:92 final size:92
Alignment explanation
Indices: 195071--195253 Score: 213
Period size: 92 Copynumber: 2.0 Consensus size: 92
195061 CATTTTCCCC
* * * * * * *
195071 GAGGGATCGATCCTTTTGAAAAGGGATTGATCCTATGCACAACAGAAAGTTTGGGATCGATTCTT
1 GAGGGATCGATCCATTTGAAAAGAGATCGATCCTATGCACAACAGAAACTTTGGAATCGATCCCT
195136 TTGGTCGAGGGACCGATCCTTTTTCTT
66 TTGGTCGAGGGACCGATCCTTTTTCTT
* * * **** *
195163 GAGGGGTCGATCCATTTGAAAAGAGATCGATCTTTTGTTGGATAGAAACTTTGGAATCGATCCCT
1 GAGGGATCGATCCATTTGAAAAGAGATCGATCCTATGCACAACAGAAACTTTGGAATCGATCCCT
* *
195228 TTGGTCGAGGGATCTATCCTTTTTCT
66 TTGGTCGAGGGACCGATCCTTTTTCT
195254 GGGAATGACT
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (92 bp):
GAGGGATCGATCCATTTGAAAAGAGATCGATCCTATGCACAACAGAAACTTTGGAATCGATCCCT
TTGGTCGAGGGACCGATCCTTTTTCTT
Found at i:198356 original size:100 final size:100
Alignment explanation
Indices: 198241--198438 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 100
198231 TATGATTTTG
*
198241 AAAAAATAAAAATTTAAGTA-CTGAAACAGAACAAAATCCTAGAGATGTAATTAAGGATGGGCAT
1 AAAAAATAAAAATTTAAGTATC-GAAACAGAACAAAATCCTAGAGATGCAATTAAGGATGGGCAT
*
198305 GAGA-CCTGAACCCGACGAGTTCCAACCCGACCCAGA
65 GAGAGCC-AAACCCGACGAGTTCCAACCCGACCCAGA
* *
198341 AAAAAATTAAAATTTAAGTATCGAAACAGACCAAAATCCTAGAGATGCAATTAAGGATGGGCATG
1 AAAAAATAAAAATTTAAGTATCGAAACAGAACAAAATCCTAGAGATGCAATTAAGGATGGGCATG
* *
198406 GGAGCCAAACCCGACGAGTTCCGACCCGACCCA
66 AGAGCCAAACCCGACGAGTTCCAACCCGACCCA
198439 ATCGGGTCGG
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
100 87 0.97
101 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (100 bp):
AAAAAATAAAAATTTAAGTATCGAAACAGAACAAAATCCTAGAGATGCAATTAAGGATGGGCATG
AGAGCCAAACCCGACGAGTTCCAACCCGACCCAGA
Found at i:201390 original size:14 final size:15
Alignment explanation
Indices: 201349--201390 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
201339 AAGATATTTG
201349 AACAAACTATTAATAC
1 AACAAA-TATTAATAC
*
201365 ACACATATATTAATA-
1 A-ACAAATATTAATAC
201380 AACAAATATTA
1 AACAAATATTA
201391 CTTCAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 9 0.39
17 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (15 bp):
AACAAATATTAATAC
Found at i:209925 original size:22 final size:22
Alignment explanation
Indices: 209891--209933 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
209881 CGTGTGTTGC
209891 GATTTAGGAATTTAGG-TTTTA
1 GATTTAGGAATTTAGGATTTTA
209912 GATTTAGGGAATTTAGGATTTT
1 GATTTA-GGAATTTAGGATTTT
209934 GAAGCTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (22 bp):
GATTTAGGAATTTAGGATTTTA
Found at i:210668 original size:51 final size:50
Alignment explanation
Indices: 210559--210674 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 50
210549 TATAATTTAA
* **
210559 TATTAATATTTTAGTATCAATTTAATATAAAAAATTAATATTTTAATATT
1 TATTAATATTTTAGTACCAATTTAATATAAAAAATTAATATTAAAATATT
* *
210609 AAGATAATATTTTAGTACCAATTTAATA-AAAAAA-TAATTATTAAAATATATT
1 TA-TTAATATTTTAGTACCAATTTAATATAAAAAATTAA-TATT-AAA-ATATT
210661 TATTAATAATTTTA
1 TATTAAT-ATTTTA
210675 ATAATATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
49 3 0.06
50 11 0.20
51 28 0.52
52 12 0.22
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (50 bp):
TATTAATATTTTAGTACCAATTTAATATAAAAAATTAATATTAAAATATT
Found at i:213669 original size:17 final size:18
Alignment explanation
Indices: 213643--213678 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
213633 TTAAAATATT
*
213643 TATAATAATTAT-TTATA
1 TATAAAAATTATATTATA
213660 TATAAAAATTATATTATA
1 TATAAAAATTATATTATA
213678 T
1 T
213679 GAATTCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAAATTATATTATA
Found at i:214213 original size:71 final size:74
Alignment explanation
Indices: 214101--214246 Score: 262
Period size: 71 Copynumber: 2.0 Consensus size: 74
214091 TACTTGCCAA
214101 GATTAATGTTAAAATACTTTTTTTAAAGAAATTCCTATTTATTGTTAGAACAAGAAGTCATCATT
1 GATTAATGTTAAAATAC-TTTTTTAAAGAAATTCCTATTTATTGTTAGAACAAGAAGTCATCATT
214166 CA-TGCCATC
65 CACTGCCATC
214175 GATTAATGTT-AAATAC-TTTTTAAAGAAATTCCTATTTATTGTTAGAACAAGAAGTCATCATTC
1 GATTAATGTTAAAATACTTTTTTAAAGAAATTCCTATTTATTGTTAGAACAAGAAGTCATCATTC
214238 ACTGCCATC
66 ACTGCCATC
214247 TCATTCATTA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
71 48 0.68
72 7 0.10
73 6 0.08
74 10 0.14
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (74 bp):
GATTAATGTTAAAATACTTTTTTAAAGAAATTCCTATTTATTGTTAGAACAAGAAGTCATCATTC
ACTGCCATC
Found at i:216554 original size:23 final size:23
Alignment explanation
Indices: 216528--216596 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
216518 TGTGTGATTA
216528 TGTTTCAATGTAATGATTCCCAG
1 TGTTTCAATGTAATGATTCCCAG
* * *
216551 TGTTATTATTGT-GTGATT---A-
1 TGTT-TCAATGTAATGATTCCCAG
216570 TGTTTCAATGTAATGATTCCCAG
1 TGTTTCAATGTAATGATTCCCAG
216593 TGTT
1 TGTT
216597 ATTATTGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 1 0.03
22 1 0.03
23 13 0.38
24 5 0.15
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (23 bp):
TGTTTCAATGTAATGATTCCCAG
Found at i:216576 original size:42 final size:42
Alignment explanation
Indices: 216517--216622 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
216507 ATTAATGGAT
216517 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
1 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
216559 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
1 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
*
216601 TTGTGTGATTATGTTTGAATGT
1 TTGTGTGATTATGTTTCAATGT
216623 CAATTTAAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (42 bp):
TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
Found at i:216586 original size:19 final size:19
Alignment explanation
Indices: 216522--216587 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
216512 TGGATTTGTG
216522 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
* * *
216541 TGATTCCCAGTGTTATTATTGT-G
1 TGATT---A-TGTT-TCAATGTAA
216564 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
216583 TGATT
1 TGATT
216588 CCCAGTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.14
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (19 bp):
TGATTATGTTTCAATGTAA
Found at i:216609 original size:23 final size:23
Alignment explanation
Indices: 216541--216610 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
216531 TTCAATGTAA
216541 TGATTCCCAGTGTTATTATTGTG
1 TGATTCCCAGTGTTATTATTGTG
* * *
216564 TGATT---A-TGTT-TCAATGTAA
1 TGATTCCCAGTGTTATTATTGT-G
216583 TGATTCCCAGTGTTATTATTGTG
1 TGATTCCCAGTGTTATTATTGTG
216606 TGATT
1 TGATT
216611 ATGTTTGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
19 9 0.26
20 1 0.03
22 1 0.03
23 14 0.40
24 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (23 bp):
TGATTCCCAGTGTTATTATTGTG
Found at i:217691 original size:3 final size:3
Alignment explanation
Indices: 217683--217717 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
217673 TAATACTTTA
217683 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
217718 AATCAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:229606 original size:21 final size:21
Alignment explanation
Indices: 229577--229617 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
229567 AGGGTTTTAA
*
229577 GTTACTGTTTAGAGTTTAAGG
1 GTTAATGTTTAGAGTTTAAGG
* *
229598 GTTAATGTTTTGGGTTTAAG
1 GTTAATGTTTAGAGTTTAAG
229618 TTATGGTGCA
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:0.22, C:0.02, G:0.29, T:0.46
Consensus pattern (21 bp):
GTTAATGTTTAGAGTTTAAGG
Found at i:230685 original size:21 final size:21
Alignment explanation
Indices: 230646--230695 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
230636 AACATGGCAA
* *
230646 ATGGAATGTCATGTTAGCACC
1 ATGGAATGTCACGTCAGCACC
* *
230667 ATGGACTGTCACGTCAGCATC
1 ATGGAATGTCACGTCAGCACC
*
230688 ATGAAATG
1 ATGGAATG
230696 ACATGCCAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (21 bp):
ATGGAATGTCACGTCAGCACC
Found at i:233765 original size:47 final size:47
Alignment explanation
Indices: 233696--233793 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
233686 ACTAACAAAC
233696 TCATATGATCATCTCAAAATCCTATATTCTCTGTTCTCATCATATGA
1 TCATATGATCATCTCAAAATCCTATATTCTCTGTTCTCATCATATGA
233743 TCATATGATCATCTCAAAATCCTATATTCTCTGTTCTCATCATATGA
1 TCATATGATCATCTCAAAATCCTATATTCTCTGTTCTCATCATATGA
233790 TCAT
1 TCAT
233794 CGTTGTTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (47 bp):
TCATATGATCATCTCAAAATCCTATATTCTCTGTTCTCATCATATGA
Found at i:235221 original size:2 final size:2
Alignment explanation
Indices: 235214--235240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
235204 GTACTGTTTC
235214 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
235241 GGAATTCAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239583 original size:32 final size:32
Alignment explanation
Indices: 239537--239603 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
239527 CTCAATTTTT
239537 TCAGATTCACAAGATACCTTTTCACCTAACAA
1 TCAGATTCACAAGATACCTTTTCACCTAACAA
*
239569 TCAGATTCATAAGATACCTTTTCACCTAACAA
1 TCAGATTCACAAGATACCTTTTCACCTAACAA
239601 TCA
1 TCA
239604 TGGTTCGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (32 bp):
TCAGATTCACAAGATACCTTTTCACCTAACAA
Found at i:239982 original size:30 final size:30
Alignment explanation
Indices: 239904--239984 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
239894 CCTAACATTC
* * *
239904 ACTTTTTGTTTCATTTTAATACCGTCGTTG
1 ACTTTTTGTTTCATTTTAGTACCCTCGTTA
*
239934 ACTTTTTGTTTTATTTTAGTACCC-CTGTTA
1 ACTTTTTGTTTCATTTTAGTACCCTC-GTTA
239964 ACTTTTTGTTTCATTTTAGTA
1 ACTTTTTGTTTCATTTTAGTA
239985 ACTAAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 44 0.98
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (30 bp):
ACTTTTTGTTTCATTTTAGTACCCTCGTTA
Found at i:241922 original size:40 final size:41
Alignment explanation
Indices: 241868--241960 Score: 154
Period size: 40 Copynumber: 2.3 Consensus size: 41
241858 CTAAATATAT
241868 ATATATATATAACAAGAACCTAATT-AAAAATAATATAAAA
1 ATATATATATAACAAGAACCTAATTAAAAAATAATATAAAA
*
241908 ATATATATATAACAAGAACTTAATTAAAAAATAATATAAAA
1 ATATATATATAACAAGAACCTAATTAAAAAATAATATAAAA
241949 ATAT-TATTATAA
1 ATATATA-TATAA
241961 TTATTTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
40 26 0.52
41 24 0.48
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.31
Consensus pattern (41 bp):
ATATATATATAACAAGAACCTAATTAAAAAATAATATAAAA
Found at i:259696 original size:126 final size:126
Alignment explanation
Indices: 259458--259713 Score: 320
Period size: 126 Copynumber: 2.0 Consensus size: 126
259448 TGGATTATTG
* * *
259458 AAAA-TAACGGCAAGAATCATAAACAACTGATTTAAGTTCCGGGATCGAAGACACGTGTTATGTA
1 AAAAGTAACGGCAAGAATCATAAACAACTGATCTAAGTTCCAGGATCGAAAACACGTGTTATGTA
* * * * * * *
259522 CATATTTAGTTTCCTATGTTTCAACGTCCCTACTCAAATGACCTATTATATGCCGGCTCTT
66 CATATTCAGTTACCTATGTTTCAACATCCCTACTCAAATAACCCATTATATGCCAGCTCCT
* * *
259583 AAAAGTAACGGTAAGAATCA-AAATCAACTGATCTAAGTTTCAGGATCGAAAACACGTGTTGTGT
1 AAAAGTAACGGCAAGAATCATAAA-CAACTGATCTAAGTTCCAGGATCGAAAACACGTGTTATGT
* ** *
259647 ACTTATTCA-TTCACCTATGTTTCAACATCCCTACTCCCATAACCCATTATATGTCAGCTCCT
65 ACATATTCAGTT-ACCTATGTTTCAACATCCCTACTCAAATAACCCATTATATGCCAGCTCCT
259709 AAAAG
1 AAAAG
259714 AAAAATTGAA
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
125 9 0.08
126 102 0.92
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (126 bp):
AAAAGTAACGGCAAGAATCATAAACAACTGATCTAAGTTCCAGGATCGAAAACACGTGTTATGTA
CATATTCAGTTACCTATGTTTCAACATCCCTACTCAAATAACCCATTATATGCCAGCTCCT
Found at i:260000 original size:126 final size:126
Alignment explanation
Indices: 259757--260050 Score: 403
Period size: 126 Copynumber: 2.3 Consensus size: 126
259747 CAAATAACAC
* * * * *
259757 AAAATCAAAACCAAACTTATCTAAGTTCAGGTATCGAAGCCACATGTTATGTACTTATTCAGTCT
1 AAAATCAAAATC-AACTTATCTAAGTTCCGGGATCGAAGACACATGTTATGTACTTATTCAATCT
*
259822 CCTATGTTCCAGCATCCCAACTCACATAACCCATTCAATGTCAGCTCTTAAAAGTAACGATA
65 CCTATGTTCCAACATCCCAACTCACATAACCCATTCAATGTCAGCTCTTAAAAGTAACGATA
* * *
259884 AGAATCAAAATCAACTGATCTAAGTTCCGGGATCGAAGACACAT-TGTATGTTCTTATTCAATCT
1 AAAATCAAAATCAACTTATCTAAGTTCCGGGATCGAAGACACATGT-TATGTACTTATTCAATCT
* * * * * *
259948 CCTATGTTTCAACATCCCTATTCACATAATCCATT-AGATGTCATCTCTTAAAAGTAACGGTA
65 CCTATGTTCCAACATCCCAACTCACATAACCCATTCA-ATGTCAGCTCTTAAAAGTAACGATA
*
260010 AAAATCAAAATCAACTTATCTAAGTCCCGGGATCGAAGACA
1 AAAATCAAAATCAACTTATCTAAGTTCCGGGATCGAAGACA
260051 TATGCTATAT
Statistics
Matches: 147, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
125 2 0.01
126 135 0.92
127 10 0.07
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (126 bp):
AAAATCAAAATCAACTTATCTAAGTTCCGGGATCGAAGACACATGTTATGTACTTATTCAATCTC
CTATGTTCCAACATCCCAACTCACATAACCCATTCAATGTCAGCTCTTAAAAGTAACGATA
Found at i:261428 original size:43 final size:43
Alignment explanation
Indices: 261337--261428 Score: 125
Period size: 43 Copynumber: 2.1 Consensus size: 43
261327 GTAAACGAGC
* * *
261337 AATATCTCAATTGGTAAGCGATGTTTTAAGAACAAGTTGGAGC
1 AATATCTCAATTGGTAAGCGATGTTTTAAGAACAAGTAGCAGA
261380 AATATCTCAATTGGTAAGCGATGTTTTAAGAACCAAG-AGCA-A
1 AATATCTCAATTGGTAAGCGATGTTTTAAGAA-CAAGTAGCAGA
261422 ATATATC
1 A-ATATC
261429 AGAATTATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 1 0.02
43 39 0.89
44 4 0.09
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (43 bp):
AATATCTCAATTGGTAAGCGATGTTTTAAGAACAAGTAGCAGA
Found at i:265186 original size:68 final size:68
Alignment explanation
Indices: 265077--265208 Score: 264
Period size: 68 Copynumber: 1.9 Consensus size: 68
265067 TTGCTTCTCC
265077 GGTGGCAATCTTGAGCGTCTCTACTTCCTTCTTCAGCTGTTCACTGAGAGCTGTGGTCAGAAGCT
1 GGTGGCAATCTTGAGCGTCTCTACTTCCTTCTTCAGCTGTTCACTGAGAGCTGTGGTCAGAAGCT
265142 TCT
66 TCT
265145 GGTGGCAATCTTGAGCGTCTCTACTTCCTTCTTCAGCTGTTCACTGAGAGCTGTGGTCAGAAGC
1 GGTGGCAATCTTGAGCGTCTCTACTTCCTTCTTCAGCTGTTCACTGAGAGCTGTGGTCAGAAGC
265209 GAACAATGAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.33
Consensus pattern (68 bp):
GGTGGCAATCTTGAGCGTCTCTACTTCCTTCTTCAGCTGTTCACTGAGAGCTGTGGTCAGAAGCT
TCT
Found at i:265764 original size:7 final size:8
Alignment explanation
Indices: 265747--265831 Score: 110
Period size: 7 Copynumber: 11.4 Consensus size: 8
265737 AACCACAAAC
265747 AGGCTGAT
1 AGGCTGAT
265755 AGGC-GAT
1 AGGCTGAT
265762 AGGCTGAT
1 AGGCTGAT
265770 AGGC-GAT
1 AGGCTGAT
265777 AGGC-GAT
1 AGGCTGAT
265784 AGGCTGAT
1 AGGCTGAT
*
265792 TGGCTGAT
1 AGGCTGAT
265800 AGGC-GAT
1 AGGCTGAT
265807 A-GCTGAT
1 AGGCTGAT
*
265814 -TGCTGAT
1 AGGCTGAT
265821 AGGCTGAT
1 AGGCTGAT
265829 AGG
1 AGG
265832 TGTGTGCATA
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
6 2 0.03
7 34 0.49
8 33 0.48
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.24
Consensus pattern (8 bp):
AGGCTGAT
Found at i:265767 original size:15 final size:15
Alignment explanation
Indices: 265747--265831 Score: 113
Period size: 15 Copynumber: 5.7 Consensus size: 15
265737 AACCACAAAC
265747 AGGCTGATAGGCGAT
1 AGGCTGATAGGCGAT
265762 AGGCTGATAGGCGAT
1 AGGCTGATAGGCGAT
265777 AGGC-GATAGGCTGAT
1 AGGCTGATAGGC-GAT
*
265792 TGGCTGATAGGCGAT
1 AGGCTGATAGGCGAT
*
265807 A-GCTGAT-TGCTGAT
1 AGGCTGATAGGC-GAT
265821 AGGCTGATAGG
1 AGGCTGATAGG
265832 TGTGTGCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
13 2 0.03
14 17 0.28
15 34 0.56
16 8 0.13
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.24
Consensus pattern (15 bp):
AGGCTGATAGGCGAT
Found at i:265777 original size:22 final size:23
Alignment explanation
Indices: 265747--265831 Score: 122
Period size: 22 Copynumber: 3.8 Consensus size: 23
265737 AACCACAAAC
265747 AGGCTGATAGGCGATAGGCTGAT
1 AGGCTGATAGGCGATAGGCTGAT
265770 AGGC-GATAGGCGATAGGCTGAT
1 AGGCTGATAGGCGATAGGCTGAT
*
265792 TGGCTGATAGGCGATA-GCTGAT
1 AGGCTGATAGGCGATAGGCTGAT
*
265814 -TGCTGATAGGCTGATAGG
1 AGGCTGATAGGC-GATAGG
265832 TGTGTGCATA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.18
22 31 0.54
23 16 0.28
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.24
Consensus pattern (23 bp):
AGGCTGATAGGCGATAGGCTGAT
Found at i:269012 original size:4 final size:4
Alignment explanation
Indices: 268975--269005 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
268965 GTATTTATGC
268975 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
269006 AATAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:270445 original size:58 final size:58
Alignment explanation
Indices: 270324--270601 Score: 339
Period size: 58 Copynumber: 4.8 Consensus size: 58
270314 TAAGAATATC
* * * * * * *
270324 ACTTTTGGTTCACTAACCTAAAATCAAGTC-A-GGCTAAGCTCGAAACCCAAACGGTGA
1 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTC-GAGCTCGAAAACCGAACAGTGA
* * * *
270381 ACTTTTGGCTGACTACGCTAAAATCAAGTCTATTTCGAGCTCGAAAACCGAACAGTTA
1 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCGAGCTCGAAAACCGAACAGTGA
* *
270439 ACTTTTGGTTGACTACCCTAAAATCGAGTCTATTTCGAGCTCGAAAA-CGAACAGTGA
1 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCGAGCTCGAAAACCGAACAGTGA
* * * *
270496 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCAAGCTCGAAACCCGAACGGTAA
1 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCGAGCTCGAAAACCGAACAGTGA
* * *
270554 ACTTCTCGTTGACTACCCTAAAATCGAGTCTATGTCGAGCTC-AAAACC
1 ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCGAGCTCGAAAACC
270602 CGAAAGATGC
Statistics
Matches: 192, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
57 83 0.43
58 108 0.56
59 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (58 bp):
ACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCGAGCTCGAAAACCGAACAGTGA
Found at i:270526 original size:115 final size:114
Alignment explanation
Indices: 270377--270600 Score: 349
Period size: 115 Copynumber: 2.0 Consensus size: 114
270367 AACCCAAACG
* * * *
270377 GTGAACTTTTGGCTGACTACGCTAAAATCAAGTCTATTTCGAGCTCGAAAACCGAACAGTTAACT
1 GTGAACTTTTGGCTGACTACCCTAAAATCAAGTCTATGTCAAGCTCGAAAACCGAACAGTAAACT
* * *
270442 TTTGGTTGACTACCCTAAAATCGAGTCTATTTCGAGCTCGAAAACGAACA
66 TCTCGTTGACTACCCTAAAATCGAGTCTATGTCGAGCTC-AAAACGAACA
* * *
270492 GTGAACTTTTGGTTGACTACCCTAAAATCAAGTCTATGTCAAGCTCGAAACCCGAACGGTAAACT
1 GTGAACTTTTGGCTGACTACCCTAAAATCAAGTCTATGTCAAGCTCGAAAACCGAACAGTAAACT
270557 TCTCGTTGACTACCCTAAAATCGAGTCTATGTCGAGCTCAAAAC
66 TCTCGTTGACTACCCTAAAATCGAGTCTATGTCGAGCTCAAAAC
270601 CCGAAAGATG
Statistics
Matches: 99, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 5 0.05
115 94 0.95
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (114 bp):
GTGAACTTTTGGCTGACTACCCTAAAATCAAGTCTATGTCAAGCTCGAAAACCGAACAGTAAACT
TCTCGTTGACTACCCTAAAATCGAGTCTATGTCGAGCTCAAAACGAACA
Found at i:276815 original size:5 final size:6
Alignment explanation
Indices: 276798--276822 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
276788 TAGTTAACCC
276798 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
276823 TGTAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:282872 original size:27 final size:27
Alignment explanation
Indices: 282822--282873 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
282812 TATGTAATGT
* * *
282822 ATATATTTCTACTATTTTTTCAAATAG
1 ATATATTTATACTATATTTGCAAATAG
*
282849 ATATATTTATACTCTATTTGCAAAT
1 ATATATTTATACTATATTTGCAAAT
282874 GATTATGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50
Consensus pattern (27 bp):
ATATATTTATACTATATTTGCAAATAG
Found at i:288517 original size:15 final size:16
Alignment explanation
Indices: 288499--288532 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
288489 ATATGTTTTG
288499 TTTATATATTTATT-A
1 TTTATATATTTATTCA
*
288514 TTTATTTATTTATTCA
1 TTTATATATTTATTCA
288530 TTT
1 TTT
288533 TAGTTGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATATTTATTCA
Found at i:288956 original size:16 final size:16
Alignment explanation
Indices: 288935--288965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
288925 AATTTTTGTC
288935 TTTAAAATGATTTTTT
1 TTTAAAATGATTTTTT
*
288951 TTTAAAATTATTTTT
1 TTTAAAATGATTTTT
288966 AAAAGACGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTAAAATGATTTTTT
Found at i:290286 original size:31 final size:32
Alignment explanation
Indices: 290214--290304 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
290204 TAAAAATTTA
*
290214 GGTACTAAAATGAAACAAAAAGTTAAC-AGCG
1 GGTACTAAAATGAAACAAAAAGTTAACGAGAG
290245 GGATACTAAAATGAAACAAAAAGTTAACGA-AG
1 GG-TACTAAAATGAAACAAAAAGTTAACGAGAG
* *
290277 GGTACTAAAATAAAACAAAAAGTAAACG
1 GGTACTAAAATGAAACAAAAAGTTAACG
290305 TTAGGTATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 26 0.47
32 28 0.51
33 1 0.02
ACGTcount: A:0.56, C:0.11, G:0.18, T:0.15
Consensus pattern (32 bp):
GGTACTAAAATGAAACAAAAAGTTAACGAGAG
Found at i:293490 original size:4 final size:4
Alignment explanation
Indices: 293481--293526 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
293471 GAGAGAGTTC
* * * *
293481 ATAT ATAT ATAT ATAT ATAT ACAT ATAT ATGT ATGT ATAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
293527 CTTACCAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:293492 original size:6 final size:6
Alignment explanation
Indices: 293481--293526 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
293471 GAGAGAGTTC
* * * *
293481 ATATAT ATATAT ATATAT ATACAT ATATAT GTATGT ATATGT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
293527 CTTACCAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:293496 original size:10 final size:10
Alignment explanation
Indices: 293481--293526 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
293471 GAGAGAGTTC
293481 ATATATATAT
1 ATATATATAT
293491 ATATATATAT
1 ATATATATAT
*
293501 ACATATATAT
1 ATATATATAT
* *
293511 GTATGTATAT
1 ATATATATAT
*
293521 GTATAT
1 ATATAT
293527 CTTACCAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:295933 original size:57 final size:56
Alignment explanation
Indices: 295808--295933 Score: 135
Period size: 57 Copynumber: 2.2 Consensus size: 56
295798 TTTATATATA
* * * * **
295808 TTAAATTTTAAAAAATATTTTTTATATTAGCTTATTAAATATATTTTTTTATTATT
1 TTAAATTTTAAAAAATATATTTTATATTAACTTACTAAATATATTATACTATTATT
* ** * *
295864 TGAAATGTTTAAAGTATATATTTTATCTTAATTTACTAAATATATTATACTATTATT
1 TTAAAT-TTTAAAAAATATATTTTATATTAACTTACTAAATATATTATACTATTATT
295921 TTAAATTATTAAA
1 TTAAATT-TTAAA
295934 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
56 6 0.11
57 50 0.89
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (56 bp):
TTAAATTTTAAAAAATATATTTTATATTAACTTACTAAATATATTATACTATTATT
Found at i:295934 original size:30 final size:28
Alignment explanation
Indices: 295839--295939 Score: 73
Period size: 30 Copynumber: 3.5 Consensus size: 28
295829 TTATATTAGC
* *
295839 TTATTAAATATATTTTTTTATTATTTGAAA
1 TTATTAAATATA--TTATTATTATTTTAAA
* *
295869 TGT-TTAAAGTATA-TATT-TTATCTTAAT
1 T-TATTAAA-TATATTATTATTATTTTAAA
*
295896 TTACTAAATATATTATACTATTATTTTAAA
1 TTATTAAATATATTAT--TATTATTTTAAA
*
295926 TTATTAAATTTATT
1 TTATTAAATATATT
295940 TTAATTTATT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
26 5 0.09
27 15 0.27
28 3 0.05
29 1 0.02
30 26 0.47
31 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
TTATTAAATATATTATTATTATTTTAAA
Found at i:295940 original size:19 final size:19
Alignment explanation
Indices: 295916--295952 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
295906 TATTATACTA
295916 TTATTTTAAATTATTAAAT
1 TTATTTTAAATTATTAAAT
*
295935 TTATTTTAATTTATTAAA
1 TTATTTTAAATTATTAAA
295953 AATATGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTAAATTATTAAAT
Found at i:299002 original size:15 final size:15
Alignment explanation
Indices: 298982--299018 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
298972 TTCTCTATTT
298982 CCTCCAACTGAGAGC
1 CCTCCAACTGAGAGC
298997 CCTCCAACTGAGAGC
1 CCTCCAACTGAGAGC
*
299012 GCTCCAA
1 CCTCCAA
299019 TTTAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.41, G:0.19, T:0.14
Consensus pattern (15 bp):
CCTCCAACTGAGAGC
Found at i:299442 original size:15 final size:15
Alignment explanation
Indices: 299419--299467 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
299409 TATTTAGCTA
* *
299419 GGCGGGCGGATGTGG
1 GGCGAGCGGATGCGG
299434 GGCGAGCGGATGCGG
1 GGCGAGCGGATGCGG
*
299449 GGC-AGGCGGATACGG
1 GGCGA-GCGGATGCGG
299464 GGCG
1 GGCG
299468 GGTAATGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.12, C:0.18, G:0.61, T:0.08
Consensus pattern (15 bp):
GGCGAGCGGATGCGG
Found at i:302208 original size:55 final size:55
Alignment explanation
Indices: 302140--302248 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
302130 ATGTCCAATA
* **
302140 ATAATACAGAAATTATTCACAAACAACCTATCACATTCATGCATTTACACACATG
1 ATAATACAAAAATTATTCACAAACAACCTATCACATTCATGCATACACACACATG
* * * *
302195 ATAATGCAAAAATTATTCATAAACAGCCTATCACGTTCATGCATACACACACAT
1 ATAATACAAAAATTATTCACAAACAACCTATCACATTCATGCATACACACACAT
302249 ATATATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (55 bp):
ATAATACAAAAATTATTCACAAACAACCTATCACATTCATGCATACACACACATG
Found at i:302546 original size:14 final size:14
Alignment explanation
Indices: 302523--302567 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
302513 TATAAACCCC
302523 AAACTCTAAACCTTA
1 AAACT-TAAACCTTA
*
302538 AAACTTAAAGCTTA
1 AAACTTAAACCTTA
* *
302552 AATCTTAAACCCTA
1 AAACTTAAACCTTA
302566 AA
1 AA
302568 TCCTAATCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (14 bp):
AAACTTAAACCTTA
Found at i:302546 original size:28 final size:27
Alignment explanation
Indices: 302473--302546 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 27
302463 CACCTCAATC
* *
302473 CCAAACCTAAACCTTAAACCCTAAACT
1 CCAAACCTAAAACTTAAACCCCAAACT
* *
302500 CCAAATC-ATAAATTATAAACCCCAAACT
1 CCAAACCTA-AAACT-TAAACCCCAAACT
*
302528 CTAAACCTTAAAACTTAAA
1 CCAAACC-TAAAACTTAAA
302547 GCTTAAATCT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.03
27 9 0.25
28 21 0.58
29 4 0.11
30 1 0.03
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.22
Consensus pattern (27 bp):
CCAAACCTAAAACTTAAACCCCAAACT
Found at i:302567 original size:21 final size:21
Alignment explanation
Indices: 302515--302567 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
302505 TCATAAATTA
*
302515 TAAACCCCAAACTCTAAACCT
1 TAAACCCTAAACTCTAAACCT
* * *
302536 TAAAACTTAAAGCT-TAAATCT
1 TAAACCCTAAA-CTCTAAACCT
302557 TAAACCCTAAA
1 TAAACCCTAAA
302568 TCCTAATCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACTCTAAACCT
Found at i:302568 original size:14 final size:15
Alignment explanation
Indices: 302478--302573 Score: 53
Period size: 14 Copynumber: 6.9 Consensus size: 15
302468 CAATCCCAAA
*
302478 CCTAAACCT-TAAAC
1 CCTAAATCTCTAAAC
* *
302492 CCTAAA-CTCCAAAT
1 CCTAAATCTCTAAAC
* *
302506 CATAAAT-TATAAAC
1 CCTAAATCTCTAAAC
*
302520 CCCAAA-CTCTAAAC
1 CCTAAATCTCTAAAC
* * *
302534 CTTAAAACT-TAAAG
1 CCTAAATCTCTAAAC
*
302548 CTTAAATCT-TAAAC
1 CCTAAATCTCTAAAC
302562 CCTAAATC-CTAA
1 CCTAAATCTCTAA
302574 TCCTAATCCT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
13 2 0.03
14 58 0.94
15 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (15 bp):
CCTAAATCTCTAAAC
Found at i:306291 original size:12 final size:12
Alignment explanation
Indices: 306274--306332 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
306264 AGAAGGAAAT
306274 AGAAAGGGGAAG
1 AGAAAGGGGAAG
306286 AGAAAGGGGAAG
1 AGAAAGGGGAAG
306298 AG--A-GGGAA-
1 AGAAAGGGGAAG
306306 AGAAAGGGGAAG
1 AGAAAGGGGAAG
*
306318 AGAAAGAGGAAG
1 AGAAAGGGGAAG
306330 AGA
1 AGA
306333 GGGAAAGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 2 0.05
11 5 0.12
12 28 0.67
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AGAAAGGGGAAG
Found at i:306311 original size:20 final size:21
Alignment explanation
Indices: 306280--306320 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
306270 AAATAGAAAG
306280 GGGAAGAGAAAGGGGAAGAGA
1 GGGAAGAGAAAGGGGAAGAGA
306301 GGGAA-AGAAAGGGGAAGAGA
1 GGGAAGAGAAAGGGGAAGAGA
306321 AAGAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (21 bp):
GGGAAGAGAAAGGGGAAGAGA
Done.