Multiple sequence alignment - TraesCS4A01G399200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G399200 chr4A 100.000 6041 0 0 1 6041 673955630 673961670 0.000000e+00 11156.0
1 TraesCS4A01G399200 chr4A 79.702 537 67 25 3335 3849 674742901 674742385 3.460000e-92 350.0
2 TraesCS4A01G399200 chr4A 83.333 312 45 5 3230 3541 674621005 674621309 1.280000e-71 281.0
3 TraesCS4A01G399200 chr4A 83.432 169 23 4 2015 2178 674743962 674743794 1.050000e-32 152.0
4 TraesCS4A01G399200 chr4A 86.667 75 10 0 1193 1267 674744527 674744453 3.880000e-12 84.2
5 TraesCS4A01G399200 chr7D 92.729 5061 225 59 1071 6039 57093959 57088950 0.000000e+00 7175.0
6 TraesCS4A01G399200 chr7D 93.086 1215 70 5 2791 3997 57793943 57795151 0.000000e+00 1766.0
7 TraesCS4A01G399200 chr7D 92.349 745 47 9 126 868 57776846 57777582 0.000000e+00 1051.0
8 TraesCS4A01G399200 chr7D 85.520 884 83 23 865 1721 57777665 57778530 0.000000e+00 881.0
9 TraesCS4A01G399200 chr7D 81.176 255 36 8 773 1016 617736584 617736837 1.720000e-45 195.0
10 TraesCS4A01G399200 chr7D 87.129 101 13 0 4091 4191 57536853 57536953 1.380000e-21 115.0
11 TraesCS4A01G399200 chr7D 97.222 36 1 0 1741 1776 57791573 57791608 1.820000e-05 62.1
12 TraesCS4A01G399200 chr3D 93.042 4915 261 43 1060 5945 545262032 545257170 0.000000e+00 7107.0
13 TraesCS4A01G399200 chr3D 92.086 139 11 0 3 141 554048568 554048706 4.780000e-46 196.0
14 TraesCS4A01G399200 chr7A 94.865 3330 144 14 1863 5176 61819335 61816017 0.000000e+00 5177.0
15 TraesCS4A01G399200 chr7A 90.946 3700 219 48 315 3987 62082332 62085942 0.000000e+00 4870.0
16 TraesCS4A01G399200 chr7A 89.478 1302 115 8 3407 4695 61887265 61888557 0.000000e+00 1626.0
17 TraesCS4A01G399200 chr7A 89.618 838 65 12 1918 2739 61882612 61883443 0.000000e+00 1046.0
18 TraesCS4A01G399200 chr7A 89.495 733 44 17 5323 6039 61815697 61814982 0.000000e+00 896.0
19 TraesCS4A01G399200 chr7A 87.445 685 69 9 2736 3411 61883601 61884277 0.000000e+00 773.0
20 TraesCS4A01G399200 chr7A 94.659 337 12 6 1491 1824 61819666 61819333 8.980000e-143 518.0
21 TraesCS4A01G399200 chr7A 76.488 991 156 53 2313 3282 62743432 62742498 9.170000e-128 468.0
22 TraesCS4A01G399200 chr7A 88.547 358 32 6 1060 1408 61820369 61820012 5.600000e-115 425.0
23 TraesCS4A01G399200 chr7A 82.505 463 61 8 3543 4004 62738862 62738419 7.340000e-104 388.0
24 TraesCS4A01G399200 chr7A 85.263 285 25 8 1064 1345 61882291 61882561 1.660000e-70 278.0
25 TraesCS4A01G399200 chr7A 94.937 158 7 1 126 282 62081760 62081917 4.680000e-61 246.0
26 TraesCS4A01G399200 chr7A 80.480 333 42 13 1867 2178 62743972 62743642 3.640000e-57 233.0
27 TraesCS4A01G399200 chr7A 99.153 118 1 0 5175 5292 61815923 61815806 4.740000e-51 213.0
28 TraesCS4A01G399200 chr7A 83.598 189 25 6 3335 3522 62739033 62738850 8.050000e-39 172.0
29 TraesCS4A01G399200 chrUn 78.218 909 134 29 2386 3280 91222796 91223654 1.930000e-144 523.0
30 TraesCS4A01G399200 chrUn 80.667 450 61 15 3544 3985 91224372 91224803 5.840000e-85 326.0
31 TraesCS4A01G399200 chrUn 87.313 134 17 0 3284 3417 91224068 91224201 2.920000e-33 154.0
32 TraesCS4A01G399200 chr4B 96.000 125 5 0 3 127 33626030 33626154 2.850000e-48 204.0
33 TraesCS4A01G399200 chr6A 93.985 133 7 1 3 134 147152357 147152489 3.690000e-47 200.0
34 TraesCS4A01G399200 chr1B 90.196 153 11 4 3 153 419389144 419389294 4.780000e-46 196.0
35 TraesCS4A01G399200 chr1B 94.444 126 7 0 3 128 117271855 117271980 1.720000e-45 195.0
36 TraesCS4A01G399200 chr7B 94.444 126 7 0 3 128 64495286 64495161 1.720000e-45 195.0
37 TraesCS4A01G399200 chr5D 90.667 150 9 5 1 150 100453362 100453218 1.720000e-45 195.0
38 TraesCS4A01G399200 chr6D 93.651 126 8 0 3 128 377167581 377167456 7.990000e-44 189.0
39 TraesCS4A01G399200 chr2A 93.023 129 9 0 3 131 723117764 723117892 7.990000e-44 189.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G399200 chr4A 673955630 673961670 6040 False 11156.000000 11156 100.00000 1 6041 1 chr4A.!!$F1 6040
1 TraesCS4A01G399200 chr7D 57088950 57093959 5009 True 7175.000000 7175 92.72900 1071 6039 1 chr7D.!!$R1 4968
2 TraesCS4A01G399200 chr7D 57776846 57778530 1684 False 966.000000 1051 88.93450 126 1721 2 chr7D.!!$F3 1595
3 TraesCS4A01G399200 chr7D 57791573 57795151 3578 False 914.050000 1766 95.15400 1741 3997 2 chr7D.!!$F4 2256
4 TraesCS4A01G399200 chr3D 545257170 545262032 4862 True 7107.000000 7107 93.04200 1060 5945 1 chr3D.!!$R1 4885
5 TraesCS4A01G399200 chr7A 62081760 62085942 4182 False 2558.000000 4870 92.94150 126 3987 2 chr7A.!!$F2 3861
6 TraesCS4A01G399200 chr7A 61814982 61820369 5387 True 1445.800000 5177 93.34380 1060 6039 5 chr7A.!!$R1 4979
7 TraesCS4A01G399200 chr7A 61882291 61888557 6266 False 930.750000 1626 87.95100 1064 4695 4 chr7A.!!$F1 3631
8 TraesCS4A01G399200 chr7A 62738419 62743972 5553 True 315.250000 468 80.76775 1867 4004 4 chr7A.!!$R2 2137
9 TraesCS4A01G399200 chrUn 91222796 91224803 2007 False 334.333333 523 82.06600 2386 3985 3 chrUn.!!$F1 1599

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
107 108 0.400213 ACTGATTTTGGTGAGGCGGA 59.600 50.000 0.00 0.0 0.00 5.54 F
1451 1967 0.031010 AATCCCCCTCTAACCTCGCT 60.031 55.000 0.00 0.0 0.00 4.93 F
1687 2464 0.249398 CCCTCGTCGAGAAATTGGGT 59.751 55.000 23.74 0.0 0.00 4.51 F
2436 3349 2.655090 TCCTGTTGCCTGATTTGACA 57.345 45.000 0.00 0.0 0.00 3.58 F
3952 13384 1.135024 GCCCAAGTTATGCACACCATG 60.135 52.381 0.00 0.0 35.34 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 2246 0.106569 CCCTATCCACCTGCAATGCA 60.107 55.000 7.99 7.99 36.92 3.96 R
2908 5781 0.881118 AGTTTACTTGGCCATGCACG 59.119 50.000 18.17 2.06 0.00 5.34 R
3119 6003 1.745489 GCAGAACCGTGTGGATCCC 60.745 63.158 9.90 0.85 37.77 3.85 R
4327 13783 0.171007 CATGCACCACTTAAAGCCCG 59.829 55.000 0.00 0.00 0.00 6.13 R
5325 14985 1.068055 CAGTTTGATCACCCAAGCTGC 60.068 52.381 0.00 0.00 44.25 5.25 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.960417 GTTGGAGCTAGATGGAAGCC 58.040 55.000 0.00 0.00 41.02 4.35
20 21 1.210478 GTTGGAGCTAGATGGAAGCCA 59.790 52.381 0.00 0.00 41.02 4.75
21 22 1.583556 TGGAGCTAGATGGAAGCCAA 58.416 50.000 0.00 0.00 41.02 4.52
22 23 1.915489 TGGAGCTAGATGGAAGCCAAA 59.085 47.619 0.00 0.00 41.02 3.28
23 24 2.293170 GGAGCTAGATGGAAGCCAAAC 58.707 52.381 0.00 0.00 41.02 2.93
24 25 2.356125 GGAGCTAGATGGAAGCCAAACA 60.356 50.000 0.00 0.00 41.02 2.83
25 26 3.549794 GAGCTAGATGGAAGCCAAACAT 58.450 45.455 0.00 0.00 41.02 2.71
26 27 3.950395 GAGCTAGATGGAAGCCAAACATT 59.050 43.478 0.00 0.00 41.02 2.71
27 28 3.950395 AGCTAGATGGAAGCCAAACATTC 59.050 43.478 0.00 0.00 41.02 2.67
28 29 3.067320 GCTAGATGGAAGCCAAACATTCC 59.933 47.826 0.00 0.00 44.42 3.01
29 30 2.460669 AGATGGAAGCCAAACATTCCC 58.539 47.619 1.74 0.00 43.68 3.97
30 31 2.043526 AGATGGAAGCCAAACATTCCCT 59.956 45.455 1.74 0.00 43.68 4.20
31 32 2.397044 TGGAAGCCAAACATTCCCTT 57.603 45.000 1.74 0.00 43.68 3.95
32 33 2.688477 TGGAAGCCAAACATTCCCTTT 58.312 42.857 1.74 0.00 43.68 3.11
33 34 2.368221 TGGAAGCCAAACATTCCCTTTG 59.632 45.455 1.74 0.00 43.68 2.77
34 35 2.416747 GAAGCCAAACATTCCCTTTGC 58.583 47.619 0.00 0.00 0.00 3.68
35 36 1.720781 AGCCAAACATTCCCTTTGCT 58.279 45.000 0.00 0.00 0.00 3.91
36 37 2.888212 AGCCAAACATTCCCTTTGCTA 58.112 42.857 0.00 0.00 0.00 3.49
37 38 2.827921 AGCCAAACATTCCCTTTGCTAG 59.172 45.455 0.00 0.00 0.00 3.42
38 39 2.562738 GCCAAACATTCCCTTTGCTAGT 59.437 45.455 0.00 0.00 0.00 2.57
39 40 3.614870 GCCAAACATTCCCTTTGCTAGTG 60.615 47.826 0.00 0.00 0.00 2.74
40 41 3.578688 CAAACATTCCCTTTGCTAGTGC 58.421 45.455 0.00 0.00 40.20 4.40
41 42 2.887151 ACATTCCCTTTGCTAGTGCT 57.113 45.000 0.00 0.00 40.48 4.40
42 43 4.301072 AACATTCCCTTTGCTAGTGCTA 57.699 40.909 0.00 0.00 40.48 3.49
43 44 3.610911 ACATTCCCTTTGCTAGTGCTAC 58.389 45.455 0.00 0.00 40.48 3.58
44 45 3.009033 ACATTCCCTTTGCTAGTGCTACA 59.991 43.478 0.00 0.00 40.48 2.74
45 46 3.780804 TTCCCTTTGCTAGTGCTACAA 57.219 42.857 0.00 0.00 40.48 2.41
46 47 3.053831 TCCCTTTGCTAGTGCTACAAC 57.946 47.619 0.00 0.00 40.48 3.32
47 48 2.637872 TCCCTTTGCTAGTGCTACAACT 59.362 45.455 0.00 0.00 40.48 3.16
48 49 3.072476 TCCCTTTGCTAGTGCTACAACTT 59.928 43.478 0.00 0.00 40.48 2.66
49 50 3.437049 CCCTTTGCTAGTGCTACAACTTC 59.563 47.826 0.00 0.00 40.48 3.01
50 51 4.319177 CCTTTGCTAGTGCTACAACTTCT 58.681 43.478 0.00 0.00 40.48 2.85
51 52 4.153117 CCTTTGCTAGTGCTACAACTTCTG 59.847 45.833 0.00 0.00 40.48 3.02
52 53 4.600692 TTGCTAGTGCTACAACTTCTGA 57.399 40.909 0.00 0.00 40.48 3.27
53 54 4.600692 TGCTAGTGCTACAACTTCTGAA 57.399 40.909 0.00 0.00 40.48 3.02
54 55 5.152623 TGCTAGTGCTACAACTTCTGAAT 57.847 39.130 0.00 0.00 40.48 2.57
55 56 4.931601 TGCTAGTGCTACAACTTCTGAATG 59.068 41.667 0.00 0.00 40.48 2.67
56 57 5.171476 GCTAGTGCTACAACTTCTGAATGA 58.829 41.667 0.00 0.00 36.03 2.57
57 58 5.639506 GCTAGTGCTACAACTTCTGAATGAA 59.360 40.000 0.00 0.00 36.03 2.57
58 59 6.147821 GCTAGTGCTACAACTTCTGAATGAAA 59.852 38.462 0.00 0.00 33.42 2.69
59 60 6.305693 AGTGCTACAACTTCTGAATGAAAC 57.694 37.500 0.00 0.00 33.79 2.78
60 61 6.058183 AGTGCTACAACTTCTGAATGAAACT 58.942 36.000 0.00 0.00 33.79 2.66
61 62 6.017605 AGTGCTACAACTTCTGAATGAAACTG 60.018 38.462 0.00 0.00 33.79 3.16
62 63 5.149977 GCTACAACTTCTGAATGAAACTGC 58.850 41.667 0.00 0.00 33.79 4.40
63 64 5.049129 GCTACAACTTCTGAATGAAACTGCT 60.049 40.000 0.00 0.00 33.79 4.24
64 65 5.429957 ACAACTTCTGAATGAAACTGCTC 57.570 39.130 0.00 0.00 33.79 4.26
65 66 4.276926 ACAACTTCTGAATGAAACTGCTCC 59.723 41.667 0.00 0.00 33.79 4.70
66 67 4.090761 ACTTCTGAATGAAACTGCTCCA 57.909 40.909 0.00 0.00 33.79 3.86
67 68 4.464008 ACTTCTGAATGAAACTGCTCCAA 58.536 39.130 0.00 0.00 33.79 3.53
68 69 4.889409 ACTTCTGAATGAAACTGCTCCAAA 59.111 37.500 0.00 0.00 33.79 3.28
69 70 5.009410 ACTTCTGAATGAAACTGCTCCAAAG 59.991 40.000 0.00 0.00 33.79 2.77
70 71 4.464008 TCTGAATGAAACTGCTCCAAAGT 58.536 39.130 0.00 0.00 0.00 2.66
71 72 4.276678 TCTGAATGAAACTGCTCCAAAGTG 59.723 41.667 0.00 0.00 0.00 3.16
72 73 4.206375 TGAATGAAACTGCTCCAAAGTGA 58.794 39.130 0.00 0.00 0.00 3.41
73 74 4.644234 TGAATGAAACTGCTCCAAAGTGAA 59.356 37.500 0.00 0.00 0.00 3.18
74 75 5.302568 TGAATGAAACTGCTCCAAAGTGAAT 59.697 36.000 0.00 0.00 0.00 2.57
75 76 5.796424 ATGAAACTGCTCCAAAGTGAATT 57.204 34.783 0.00 0.00 0.00 2.17
76 77 5.596836 TGAAACTGCTCCAAAGTGAATTT 57.403 34.783 0.00 0.00 0.00 1.82
77 78 6.707440 TGAAACTGCTCCAAAGTGAATTTA 57.293 33.333 0.00 0.00 0.00 1.40
78 79 6.738114 TGAAACTGCTCCAAAGTGAATTTAG 58.262 36.000 0.00 0.00 0.00 1.85
79 80 6.321181 TGAAACTGCTCCAAAGTGAATTTAGT 59.679 34.615 0.00 0.00 0.00 2.24
80 81 5.695851 ACTGCTCCAAAGTGAATTTAGTG 57.304 39.130 0.00 0.00 0.00 2.74
81 82 4.520492 ACTGCTCCAAAGTGAATTTAGTGG 59.480 41.667 0.00 0.00 0.00 4.00
82 83 4.724399 TGCTCCAAAGTGAATTTAGTGGA 58.276 39.130 0.00 0.00 0.00 4.02
83 84 4.761739 TGCTCCAAAGTGAATTTAGTGGAG 59.238 41.667 15.25 15.25 39.74 3.86
84 85 4.762251 GCTCCAAAGTGAATTTAGTGGAGT 59.238 41.667 18.39 0.00 39.30 3.85
85 86 5.335191 GCTCCAAAGTGAATTTAGTGGAGTG 60.335 44.000 18.39 4.21 39.30 3.51
86 87 5.935945 TCCAAAGTGAATTTAGTGGAGTGA 58.064 37.500 0.00 0.00 0.00 3.41
87 88 6.361433 TCCAAAGTGAATTTAGTGGAGTGAA 58.639 36.000 0.00 0.00 0.00 3.18
88 89 6.831353 TCCAAAGTGAATTTAGTGGAGTGAAA 59.169 34.615 0.00 0.00 0.00 2.69
89 90 6.918022 CCAAAGTGAATTTAGTGGAGTGAAAC 59.082 38.462 0.00 0.00 0.00 2.78
104 105 3.642705 GTGAAACTGATTTTGGTGAGGC 58.357 45.455 0.00 0.00 0.00 4.70
105 106 2.293122 TGAAACTGATTTTGGTGAGGCG 59.707 45.455 0.00 0.00 0.00 5.52
106 107 1.247567 AACTGATTTTGGTGAGGCGG 58.752 50.000 0.00 0.00 0.00 6.13
107 108 0.400213 ACTGATTTTGGTGAGGCGGA 59.600 50.000 0.00 0.00 0.00 5.54
108 109 1.089920 CTGATTTTGGTGAGGCGGAG 58.910 55.000 0.00 0.00 0.00 4.63
121 122 3.972227 CGGAGCAGTCCCAAACAG 58.028 61.111 0.00 0.00 40.20 3.16
122 123 1.672356 CGGAGCAGTCCCAAACAGG 60.672 63.158 0.00 0.00 40.20 4.00
123 124 1.973812 GGAGCAGTCCCAAACAGGC 60.974 63.158 0.00 0.00 36.76 4.85
124 125 1.973812 GAGCAGTCCCAAACAGGCC 60.974 63.158 0.00 0.00 35.39 5.19
131 132 2.100197 GTCCCAAACAGGCCCTTTATC 58.900 52.381 0.00 0.00 35.39 1.75
132 133 1.713647 TCCCAAACAGGCCCTTTATCA 59.286 47.619 0.00 0.00 35.39 2.15
154 155 7.301868 TCATGCTTTATTTGAGTTTTTCCCT 57.698 32.000 0.00 0.00 0.00 4.20
156 157 7.872483 TCATGCTTTATTTGAGTTTTTCCCTTC 59.128 33.333 0.00 0.00 0.00 3.46
169 171 3.974871 TTCCCTTCGTTTAACACTTGC 57.025 42.857 0.00 0.00 0.00 4.01
176 178 3.135994 TCGTTTAACACTTGCTTCCCTC 58.864 45.455 0.00 0.00 0.00 4.30
200 202 5.394224 CGTGTTCATCCTCATACCACTAGTT 60.394 44.000 0.00 0.00 0.00 2.24
239 241 4.452455 GGAACCTTGCATTAGATGGTATCG 59.548 45.833 0.00 0.00 0.00 2.92
295 297 1.628846 CACCCCCTTGTGTTACTAGCT 59.371 52.381 0.00 0.00 0.00 3.32
297 299 2.188817 CCCCCTTGTGTTACTAGCTCT 58.811 52.381 0.00 0.00 0.00 4.09
300 302 2.832129 CCCTTGTGTTACTAGCTCTCCA 59.168 50.000 0.00 0.00 0.00 3.86
304 306 1.481363 GTGTTACTAGCTCTCCACCCC 59.519 57.143 0.00 0.00 0.00 4.95
305 307 1.078159 TGTTACTAGCTCTCCACCCCA 59.922 52.381 0.00 0.00 0.00 4.96
306 308 2.185387 GTTACTAGCTCTCCACCCCAA 58.815 52.381 0.00 0.00 0.00 4.12
307 309 2.570302 GTTACTAGCTCTCCACCCCAAA 59.430 50.000 0.00 0.00 0.00 3.28
365 749 3.754965 CCTCACTTGGTTCTTGGATCAA 58.245 45.455 0.00 0.00 0.00 2.57
368 752 3.138283 TCACTTGGTTCTTGGATCAACCT 59.862 43.478 12.47 0.00 42.40 3.50
369 753 3.254166 CACTTGGTTCTTGGATCAACCTG 59.746 47.826 12.47 8.59 42.40 4.00
374 758 4.082125 GGTTCTTGGATCAACCTGTCAAT 58.918 43.478 5.62 0.00 39.30 2.57
447 832 2.170012 TAGCCTACTGTACCCCAAGG 57.830 55.000 0.00 0.00 40.04 3.61
452 837 2.368875 CCTACTGTACCCCAAGGCTATG 59.631 54.545 0.00 0.00 36.11 2.23
475 860 7.831691 TGGATCCTCAAATGAACACTTTTTA 57.168 32.000 14.23 0.00 0.00 1.52
478 863 9.710900 GGATCCTCAAATGAACACTTTTTAAAT 57.289 29.630 3.84 0.00 0.00 1.40
687 1073 1.478105 GAAGGGATGACAAATGCACCC 59.522 52.381 0.00 0.00 37.79 4.61
698 1084 5.245751 TGACAAATGCACCCTATTTGAACAT 59.754 36.000 14.87 0.00 44.37 2.71
702 1088 3.088532 TGCACCCTATTTGAACATGACC 58.911 45.455 0.00 0.00 0.00 4.02
730 1116 6.178239 AGTTTAGCAACCAATTCGATGTAC 57.822 37.500 0.00 0.00 32.70 2.90
742 1128 1.459209 TCGATGTACTTTGCAAGTGCG 59.541 47.619 0.00 4.69 45.64 5.34
753 1139 1.576421 CAAGTGCGGCCTCAGAAAC 59.424 57.895 0.00 0.00 0.00 2.78
758 1144 0.881118 TGCGGCCTCAGAAACAAATC 59.119 50.000 0.00 0.00 0.00 2.17
839 1225 6.127647 GGTTTGTTCTCCTGCAAATATCATGA 60.128 38.462 0.00 0.00 37.02 3.07
1016 1503 8.340618 ACAAAATTCATGTCTTGCTACACTAT 57.659 30.769 0.00 0.00 30.75 2.12
1017 1504 8.796475 ACAAAATTCATGTCTTGCTACACTATT 58.204 29.630 0.00 0.00 30.75 1.73
1021 1508 6.538945 TCATGTCTTGCTACACTATTACCA 57.461 37.500 0.00 0.00 30.75 3.25
1049 1536 3.042887 GCAAAGGCACAAGTTTAAGACG 58.957 45.455 0.00 0.00 40.72 4.18
1114 1605 1.136891 GAAGCACAAAAGCCCACTTGT 59.863 47.619 0.00 0.00 35.85 3.16
1117 1608 0.389025 CACAAAAGCCCACTTGTCCC 59.611 55.000 0.00 0.00 35.85 4.46
1123 1614 1.002011 GCCCACTTGTCCCTTCTCC 60.002 63.158 0.00 0.00 0.00 3.71
1129 1620 1.132365 ACTTGTCCCTTCTCCCTTCCT 60.132 52.381 0.00 0.00 0.00 3.36
1130 1621 1.557371 CTTGTCCCTTCTCCCTTCCTC 59.443 57.143 0.00 0.00 0.00 3.71
1163 1655 1.550130 CCCTCTACCTTTGGACGCCA 61.550 60.000 0.00 0.00 0.00 5.69
1427 1941 2.584391 GCTTCGACCCACAGGAGGT 61.584 63.158 0.00 0.00 41.50 3.85
1428 1942 1.255667 GCTTCGACCCACAGGAGGTA 61.256 60.000 0.00 0.00 37.88 3.08
1429 1943 1.263356 CTTCGACCCACAGGAGGTAA 58.737 55.000 0.00 0.00 37.88 2.85
1430 1944 1.621814 CTTCGACCCACAGGAGGTAAA 59.378 52.381 0.00 0.00 37.88 2.01
1443 1959 3.014807 AGGAGGTAAACAATCCCCCTCTA 59.985 47.826 0.00 0.00 41.20 2.43
1444 1960 3.784202 GGAGGTAAACAATCCCCCTCTAA 59.216 47.826 0.00 0.00 41.20 2.10
1447 1963 3.526430 GGTAAACAATCCCCCTCTAACCT 59.474 47.826 0.00 0.00 0.00 3.50
1448 1964 4.384978 GGTAAACAATCCCCCTCTAACCTC 60.385 50.000 0.00 0.00 0.00 3.85
1449 1965 1.497161 ACAATCCCCCTCTAACCTCG 58.503 55.000 0.00 0.00 0.00 4.63
1451 1967 0.031010 AATCCCCCTCTAACCTCGCT 60.031 55.000 0.00 0.00 0.00 4.93
1452 1968 0.470268 ATCCCCCTCTAACCTCGCTC 60.470 60.000 0.00 0.00 0.00 5.03
1453 1969 2.134933 CCCCCTCTAACCTCGCTCC 61.135 68.421 0.00 0.00 0.00 4.70
1454 1970 2.491022 CCCCTCTAACCTCGCTCCG 61.491 68.421 0.00 0.00 0.00 4.63
1455 1971 1.753463 CCCTCTAACCTCGCTCCGT 60.753 63.158 0.00 0.00 0.00 4.69
1456 1972 1.321074 CCCTCTAACCTCGCTCCGTT 61.321 60.000 0.00 0.00 0.00 4.44
1457 1973 0.531200 CCTCTAACCTCGCTCCGTTT 59.469 55.000 0.00 0.00 0.00 3.60
1458 1974 1.067071 CCTCTAACCTCGCTCCGTTTT 60.067 52.381 0.00 0.00 0.00 2.43
1459 1975 2.260481 CTCTAACCTCGCTCCGTTTTC 58.740 52.381 0.00 0.00 0.00 2.29
1460 1976 0.989890 CTAACCTCGCTCCGTTTTCG 59.010 55.000 0.00 0.00 43.67 3.46
1471 1987 3.330275 GTTTTCGACCGCTGCAGT 58.670 55.556 16.64 0.00 0.00 4.40
1472 1988 1.204312 GTTTTCGACCGCTGCAGTC 59.796 57.895 16.64 5.94 0.00 3.51
1477 1993 3.695606 GACCGCTGCAGTCCCTGA 61.696 66.667 16.64 0.00 32.44 3.86
1495 2246 4.489771 CCCTCCCCGCGAGCATTT 62.490 66.667 8.23 0.00 37.27 2.32
1687 2464 0.249398 CCCTCGTCGAGAAATTGGGT 59.751 55.000 23.74 0.00 0.00 4.51
1939 2748 5.888691 TGTGACTTTCTTTTGTGCAGTTA 57.111 34.783 0.00 0.00 0.00 2.24
2085 2904 5.880901 ACCATTTCTCTGGATGTAACAACT 58.119 37.500 0.00 0.00 39.73 3.16
2183 3020 9.413048 GACCAACATAGTACTAGCATTAGATTC 57.587 37.037 8.85 0.00 0.00 2.52
2435 3348 5.643379 TTTATCCTGTTGCCTGATTTGAC 57.357 39.130 0.00 0.00 0.00 3.18
2436 3349 2.655090 TCCTGTTGCCTGATTTGACA 57.345 45.000 0.00 0.00 0.00 3.58
2816 5688 4.670221 GCATCTCGAACCATTTTCACACTC 60.670 45.833 0.00 0.00 0.00 3.51
3119 6003 5.801531 TGGTATACCCACAGCACTATTAG 57.198 43.478 19.42 0.00 38.72 1.73
3602 13023 5.593909 TGCTTGGTATGCTTATTAACATGCT 59.406 36.000 0.00 0.00 37.94 3.79
3808 13240 6.146673 TGCTGAATCAATAAGCGATATCAGTG 59.853 38.462 3.12 0.00 39.88 3.66
3843 13275 3.754323 CAGCATTTTACCTTTCGTGGGTA 59.246 43.478 0.00 0.00 38.19 3.69
3894 13326 6.729187 CCAGTTGCTAGCTAAAAATATGGTC 58.271 40.000 17.23 0.00 0.00 4.02
3952 13384 1.135024 GCCCAAGTTATGCACACCATG 60.135 52.381 0.00 0.00 35.34 3.66
4065 13521 2.738314 TGATGATCGCTGTGTGAAGTTG 59.262 45.455 0.00 0.00 0.00 3.16
4113 13569 4.708726 GCAAGGTGCAGAACAATTAGAT 57.291 40.909 0.00 0.00 44.26 1.98
4114 13570 5.818136 GCAAGGTGCAGAACAATTAGATA 57.182 39.130 0.00 0.00 44.26 1.98
4162 13618 3.622953 GCATTTACGGGTTCCTTTAGGGA 60.623 47.826 0.00 0.00 43.41 4.20
4327 13783 3.255149 TCGTGGAGGTTCTACTGAAAGAC 59.745 47.826 0.00 0.00 37.43 3.01
4459 13915 0.035439 AACCAAGACAGGCCCATACG 60.035 55.000 0.00 0.00 0.00 3.06
4528 13984 6.662414 AAGATTTTGTAATCGATCTTCGCA 57.338 33.333 0.00 0.00 43.99 5.10
4689 14149 1.290134 GATGGGTTCCTGGTCTCCTT 58.710 55.000 0.00 0.00 0.00 3.36
4690 14150 1.636003 GATGGGTTCCTGGTCTCCTTT 59.364 52.381 0.00 0.00 0.00 3.11
4691 14151 1.529744 TGGGTTCCTGGTCTCCTTTT 58.470 50.000 0.00 0.00 0.00 2.27
4695 14155 2.424379 GGTTCCTGGTCTCCTTTTGGTT 60.424 50.000 0.00 0.00 41.38 3.67
4727 14187 2.035449 TGGACGTGAACTGTGGAGTTAG 59.965 50.000 0.00 0.00 42.80 2.34
4771 14231 7.009179 TGGTCAGTCTTATCAGAATTCTGTT 57.991 36.000 29.80 24.77 44.12 3.16
4831 14291 5.690464 AGCAATTCTGATCAGTTCTACCT 57.310 39.130 21.92 9.95 0.00 3.08
4941 14401 2.094234 GCGAAACATAAATTGGGCCAGT 60.094 45.455 6.23 0.00 0.00 4.00
5025 14485 1.820519 TGCATTTCTTCTGTCATGGCC 59.179 47.619 0.00 0.00 0.00 5.36
5124 14584 8.141909 TCATCAGTTACTATCAATTTCCTACCG 58.858 37.037 0.00 0.00 0.00 4.02
5235 14808 1.606480 GCTGCACTGCTGTTACTGAGA 60.606 52.381 9.40 0.00 0.00 3.27
5327 14987 3.045142 GCTTTGAGCTGCTTGGCA 58.955 55.556 2.53 0.00 38.45 4.92
5429 15105 8.736244 GGTCTTATAAAGCAATTTGTAACCTCA 58.264 33.333 0.00 0.00 0.00 3.86
5488 15167 3.243535 GCAGACCACCAAGAAGGAAAAAG 60.244 47.826 0.00 0.00 41.22 2.27
5646 15325 9.237846 GTTTTCTTGAGTTAATGTTTCCTCTTG 57.762 33.333 0.00 0.00 0.00 3.02
5697 15379 7.230108 CAGCAATTGGATATGGTCAACTAAGAT 59.770 37.037 7.72 0.00 0.00 2.40
5743 15425 1.344763 AGTAGAGCTTGTGACCACACC 59.655 52.381 1.83 0.00 45.40 4.16
5750 15432 1.597663 CTTGTGACCACACCGAAGAAC 59.402 52.381 1.83 0.00 45.40 3.01
5781 15463 9.642327 TTTATGTATGCTTCTCTTGTTACGTAA 57.358 29.630 3.29 3.29 0.00 3.18
5826 15508 5.769484 TGACAATACTTACCTCTCGATCC 57.231 43.478 0.00 0.00 0.00 3.36
5859 15541 7.013823 AGGTATCTGGATATGATGGACAAAG 57.986 40.000 0.00 0.00 0.00 2.77
5900 15582 6.969993 TTTTGTAGGGCATAGTTTTTCTGT 57.030 33.333 0.00 0.00 0.00 3.41
5973 15655 5.755409 TTGCATCCTCCTCTACTTTACAA 57.245 39.130 0.00 0.00 0.00 2.41
6004 15686 6.713450 GGAAAGTACAGTCCATTAACTTTGGA 59.287 38.462 9.40 0.00 39.72 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.210478 TGGCTTCCATCTAGCTCCAAC 59.790 52.381 0.00 0.00 38.67 3.77
1 2 1.583556 TGGCTTCCATCTAGCTCCAA 58.416 50.000 0.00 0.00 38.67 3.53
2 3 1.583556 TTGGCTTCCATCTAGCTCCA 58.416 50.000 0.00 0.00 38.67 3.86
3 4 2.293170 GTTTGGCTTCCATCTAGCTCC 58.707 52.381 0.00 0.00 38.67 4.70
4 5 2.991250 TGTTTGGCTTCCATCTAGCTC 58.009 47.619 0.00 0.00 38.67 4.09
5 6 3.659183 ATGTTTGGCTTCCATCTAGCT 57.341 42.857 0.00 0.00 38.67 3.32
6 7 3.067320 GGAATGTTTGGCTTCCATCTAGC 59.933 47.826 0.00 0.00 40.57 3.42
7 8 3.633986 GGGAATGTTTGGCTTCCATCTAG 59.366 47.826 5.03 0.00 42.29 2.43
8 9 3.269381 AGGGAATGTTTGGCTTCCATCTA 59.731 43.478 5.03 0.00 42.29 1.98
9 10 2.043526 AGGGAATGTTTGGCTTCCATCT 59.956 45.455 5.03 0.00 42.29 2.90
10 11 2.460669 AGGGAATGTTTGGCTTCCATC 58.539 47.619 5.03 0.00 42.29 3.51
11 12 2.629017 AGGGAATGTTTGGCTTCCAT 57.371 45.000 5.03 0.00 42.29 3.41
12 13 2.368221 CAAAGGGAATGTTTGGCTTCCA 59.632 45.455 5.03 0.00 42.29 3.53
13 14 2.871637 GCAAAGGGAATGTTTGGCTTCC 60.872 50.000 0.00 0.00 40.22 3.46
14 15 2.037641 AGCAAAGGGAATGTTTGGCTTC 59.962 45.455 0.00 0.00 35.75 3.86
15 16 2.049372 AGCAAAGGGAATGTTTGGCTT 58.951 42.857 0.00 0.00 35.75 4.35
16 17 1.720781 AGCAAAGGGAATGTTTGGCT 58.279 45.000 0.00 0.00 35.75 4.75
17 18 2.562738 ACTAGCAAAGGGAATGTTTGGC 59.437 45.455 0.00 0.00 35.75 4.52
18 19 3.614870 GCACTAGCAAAGGGAATGTTTGG 60.615 47.826 0.00 0.00 41.58 3.28
19 20 3.256631 AGCACTAGCAAAGGGAATGTTTG 59.743 43.478 0.00 0.00 45.49 2.93
20 21 3.500343 AGCACTAGCAAAGGGAATGTTT 58.500 40.909 0.00 0.00 45.49 2.83
21 22 3.160679 AGCACTAGCAAAGGGAATGTT 57.839 42.857 0.00 0.00 45.49 2.71
22 23 2.887151 AGCACTAGCAAAGGGAATGT 57.113 45.000 0.00 0.00 45.49 2.71
23 24 3.609853 TGTAGCACTAGCAAAGGGAATG 58.390 45.455 0.00 0.00 45.49 2.67
24 25 4.010349 GTTGTAGCACTAGCAAAGGGAAT 58.990 43.478 0.00 0.00 45.49 3.01
25 26 3.072476 AGTTGTAGCACTAGCAAAGGGAA 59.928 43.478 0.00 0.00 45.49 3.97
26 27 2.637872 AGTTGTAGCACTAGCAAAGGGA 59.362 45.455 0.00 0.00 45.49 4.20
27 28 3.059352 AGTTGTAGCACTAGCAAAGGG 57.941 47.619 0.00 0.00 45.49 3.95
28 29 4.153117 CAGAAGTTGTAGCACTAGCAAAGG 59.847 45.833 0.00 0.00 45.49 3.11
29 30 4.991056 TCAGAAGTTGTAGCACTAGCAAAG 59.009 41.667 0.00 0.00 45.49 2.77
30 31 4.956085 TCAGAAGTTGTAGCACTAGCAAA 58.044 39.130 0.00 0.00 45.49 3.68
31 32 4.600692 TCAGAAGTTGTAGCACTAGCAA 57.399 40.909 0.00 0.00 45.49 3.91
32 33 4.600692 TTCAGAAGTTGTAGCACTAGCA 57.399 40.909 0.00 0.00 45.49 3.49
33 34 5.171476 TCATTCAGAAGTTGTAGCACTAGC 58.829 41.667 0.00 0.00 42.56 3.42
34 35 7.386299 AGTTTCATTCAGAAGTTGTAGCACTAG 59.614 37.037 0.00 0.00 37.57 2.57
35 36 7.171508 CAGTTTCATTCAGAAGTTGTAGCACTA 59.828 37.037 0.00 0.00 37.57 2.74
36 37 6.017605 CAGTTTCATTCAGAAGTTGTAGCACT 60.018 38.462 0.00 0.00 37.57 4.40
37 38 6.138761 CAGTTTCATTCAGAAGTTGTAGCAC 58.861 40.000 0.00 0.00 37.57 4.40
38 39 5.277974 GCAGTTTCATTCAGAAGTTGTAGCA 60.278 40.000 0.00 0.00 37.57 3.49
39 40 5.049129 AGCAGTTTCATTCAGAAGTTGTAGC 60.049 40.000 0.00 0.00 37.57 3.58
40 41 6.348050 GGAGCAGTTTCATTCAGAAGTTGTAG 60.348 42.308 0.00 0.00 37.57 2.74
41 42 5.470098 GGAGCAGTTTCATTCAGAAGTTGTA 59.530 40.000 0.00 0.00 37.57 2.41
42 43 4.276926 GGAGCAGTTTCATTCAGAAGTTGT 59.723 41.667 0.00 0.00 37.57 3.32
43 44 4.276678 TGGAGCAGTTTCATTCAGAAGTTG 59.723 41.667 0.00 0.00 37.57 3.16
44 45 4.464008 TGGAGCAGTTTCATTCAGAAGTT 58.536 39.130 0.00 0.00 37.57 2.66
45 46 4.090761 TGGAGCAGTTTCATTCAGAAGT 57.909 40.909 0.00 0.00 37.57 3.01
46 47 5.009410 ACTTTGGAGCAGTTTCATTCAGAAG 59.991 40.000 0.00 0.00 37.57 2.85
47 48 4.889409 ACTTTGGAGCAGTTTCATTCAGAA 59.111 37.500 0.00 0.00 0.00 3.02
48 49 4.276678 CACTTTGGAGCAGTTTCATTCAGA 59.723 41.667 0.00 0.00 0.00 3.27
49 50 4.276678 TCACTTTGGAGCAGTTTCATTCAG 59.723 41.667 0.00 0.00 0.00 3.02
50 51 4.206375 TCACTTTGGAGCAGTTTCATTCA 58.794 39.130 0.00 0.00 0.00 2.57
51 52 4.836125 TCACTTTGGAGCAGTTTCATTC 57.164 40.909 0.00 0.00 0.00 2.67
52 53 5.796424 ATTCACTTTGGAGCAGTTTCATT 57.204 34.783 0.00 0.00 0.00 2.57
53 54 5.796424 AATTCACTTTGGAGCAGTTTCAT 57.204 34.783 0.00 0.00 0.00 2.57
54 55 5.596836 AAATTCACTTTGGAGCAGTTTCA 57.403 34.783 0.00 0.00 0.00 2.69
55 56 6.638468 CACTAAATTCACTTTGGAGCAGTTTC 59.362 38.462 0.00 0.00 0.00 2.78
56 57 6.461509 CCACTAAATTCACTTTGGAGCAGTTT 60.462 38.462 0.00 0.00 0.00 2.66
57 58 5.010012 CCACTAAATTCACTTTGGAGCAGTT 59.990 40.000 0.00 0.00 0.00 3.16
58 59 4.520492 CCACTAAATTCACTTTGGAGCAGT 59.480 41.667 0.00 0.00 0.00 4.40
59 60 4.761739 TCCACTAAATTCACTTTGGAGCAG 59.238 41.667 0.00 0.00 0.00 4.24
60 61 4.724399 TCCACTAAATTCACTTTGGAGCA 58.276 39.130 0.00 0.00 0.00 4.26
61 62 4.762251 ACTCCACTAAATTCACTTTGGAGC 59.238 41.667 14.06 0.00 37.76 4.70
62 63 5.997746 TCACTCCACTAAATTCACTTTGGAG 59.002 40.000 12.82 12.82 39.10 3.86
63 64 5.935945 TCACTCCACTAAATTCACTTTGGA 58.064 37.500 0.00 0.00 0.00 3.53
64 65 6.633500 TTCACTCCACTAAATTCACTTTGG 57.367 37.500 0.00 0.00 0.00 3.28
65 66 7.645340 CAGTTTCACTCCACTAAATTCACTTTG 59.355 37.037 0.00 0.00 0.00 2.77
66 67 7.556275 TCAGTTTCACTCCACTAAATTCACTTT 59.444 33.333 0.00 0.00 0.00 2.66
67 68 7.054124 TCAGTTTCACTCCACTAAATTCACTT 58.946 34.615 0.00 0.00 0.00 3.16
68 69 6.591935 TCAGTTTCACTCCACTAAATTCACT 58.408 36.000 0.00 0.00 0.00 3.41
69 70 6.861065 TCAGTTTCACTCCACTAAATTCAC 57.139 37.500 0.00 0.00 0.00 3.18
70 71 8.463930 AAATCAGTTTCACTCCACTAAATTCA 57.536 30.769 0.00 0.00 0.00 2.57
71 72 9.185192 CAAAATCAGTTTCACTCCACTAAATTC 57.815 33.333 0.00 0.00 0.00 2.17
72 73 8.143835 CCAAAATCAGTTTCACTCCACTAAATT 58.856 33.333 0.00 0.00 0.00 1.82
73 74 7.287696 ACCAAAATCAGTTTCACTCCACTAAAT 59.712 33.333 0.00 0.00 0.00 1.40
74 75 6.605594 ACCAAAATCAGTTTCACTCCACTAAA 59.394 34.615 0.00 0.00 0.00 1.85
75 76 6.039270 CACCAAAATCAGTTTCACTCCACTAA 59.961 38.462 0.00 0.00 0.00 2.24
76 77 5.530915 CACCAAAATCAGTTTCACTCCACTA 59.469 40.000 0.00 0.00 0.00 2.74
77 78 4.339247 CACCAAAATCAGTTTCACTCCACT 59.661 41.667 0.00 0.00 0.00 4.00
78 79 4.338118 TCACCAAAATCAGTTTCACTCCAC 59.662 41.667 0.00 0.00 0.00 4.02
79 80 4.531854 TCACCAAAATCAGTTTCACTCCA 58.468 39.130 0.00 0.00 0.00 3.86
80 81 4.022849 CCTCACCAAAATCAGTTTCACTCC 60.023 45.833 0.00 0.00 0.00 3.85
81 82 4.557496 GCCTCACCAAAATCAGTTTCACTC 60.557 45.833 0.00 0.00 0.00 3.51
82 83 3.319122 GCCTCACCAAAATCAGTTTCACT 59.681 43.478 0.00 0.00 0.00 3.41
83 84 3.642705 GCCTCACCAAAATCAGTTTCAC 58.357 45.455 0.00 0.00 0.00 3.18
84 85 2.293122 CGCCTCACCAAAATCAGTTTCA 59.707 45.455 0.00 0.00 0.00 2.69
85 86 2.351738 CCGCCTCACCAAAATCAGTTTC 60.352 50.000 0.00 0.00 0.00 2.78
86 87 1.613437 CCGCCTCACCAAAATCAGTTT 59.387 47.619 0.00 0.00 0.00 2.66
87 88 1.202879 TCCGCCTCACCAAAATCAGTT 60.203 47.619 0.00 0.00 0.00 3.16
88 89 0.400213 TCCGCCTCACCAAAATCAGT 59.600 50.000 0.00 0.00 0.00 3.41
89 90 1.089920 CTCCGCCTCACCAAAATCAG 58.910 55.000 0.00 0.00 0.00 2.90
90 91 0.960364 GCTCCGCCTCACCAAAATCA 60.960 55.000 0.00 0.00 0.00 2.57
91 92 0.960364 TGCTCCGCCTCACCAAAATC 60.960 55.000 0.00 0.00 0.00 2.17
92 93 0.962356 CTGCTCCGCCTCACCAAAAT 60.962 55.000 0.00 0.00 0.00 1.82
93 94 1.600636 CTGCTCCGCCTCACCAAAA 60.601 57.895 0.00 0.00 0.00 2.44
94 95 2.032528 CTGCTCCGCCTCACCAAA 59.967 61.111 0.00 0.00 0.00 3.28
95 96 3.240134 GACTGCTCCGCCTCACCAA 62.240 63.158 0.00 0.00 0.00 3.67
96 97 3.695606 GACTGCTCCGCCTCACCA 61.696 66.667 0.00 0.00 0.00 4.17
97 98 4.459089 GGACTGCTCCGCCTCACC 62.459 72.222 0.00 0.00 0.00 4.02
98 99 4.459089 GGGACTGCTCCGCCTCAC 62.459 72.222 0.00 0.00 37.46 3.51
100 101 3.254024 TTTGGGACTGCTCCGCCTC 62.254 63.158 0.00 0.00 37.46 4.70
101 102 3.249189 TTTGGGACTGCTCCGCCT 61.249 61.111 0.00 0.00 37.46 5.52
102 103 3.056328 GTTTGGGACTGCTCCGCC 61.056 66.667 0.00 0.00 37.46 6.13
103 104 2.281484 TGTTTGGGACTGCTCCGC 60.281 61.111 0.00 0.00 37.46 5.54
104 105 1.672356 CCTGTTTGGGACTGCTCCG 60.672 63.158 0.00 0.00 37.46 4.63
105 106 1.973812 GCCTGTTTGGGACTGCTCC 60.974 63.158 0.00 0.00 36.00 4.70
106 107 1.973812 GGCCTGTTTGGGACTGCTC 60.974 63.158 0.00 0.00 36.00 4.26
107 108 2.116125 GGCCTGTTTGGGACTGCT 59.884 61.111 0.00 0.00 36.00 4.24
108 109 2.991540 GGGCCTGTTTGGGACTGC 60.992 66.667 0.84 0.00 34.11 4.40
109 110 0.469892 AAAGGGCCTGTTTGGGACTG 60.470 55.000 6.92 0.00 34.11 3.51
110 111 1.154430 TAAAGGGCCTGTTTGGGACT 58.846 50.000 6.92 0.00 34.11 3.85
111 112 2.100197 GATAAAGGGCCTGTTTGGGAC 58.900 52.381 6.92 0.00 36.00 4.46
112 113 1.713647 TGATAAAGGGCCTGTTTGGGA 59.286 47.619 6.92 0.00 36.00 4.37
113 114 2.230130 TGATAAAGGGCCTGTTTGGG 57.770 50.000 6.92 0.00 36.00 4.12
114 115 2.159057 GCATGATAAAGGGCCTGTTTGG 60.159 50.000 6.92 0.00 39.35 3.28
115 116 2.762327 AGCATGATAAAGGGCCTGTTTG 59.238 45.455 6.92 0.56 0.00 2.93
116 117 3.105959 AGCATGATAAAGGGCCTGTTT 57.894 42.857 6.92 0.00 0.00 2.83
117 118 2.834638 AGCATGATAAAGGGCCTGTT 57.165 45.000 6.92 6.50 0.00 3.16
118 119 2.834638 AAGCATGATAAAGGGCCTGT 57.165 45.000 6.92 3.10 0.00 4.00
119 120 5.796424 AATAAAGCATGATAAAGGGCCTG 57.204 39.130 6.92 0.00 0.00 4.85
120 121 5.898972 TCAAATAAAGCATGATAAAGGGCCT 59.101 36.000 0.00 0.00 0.00 5.19
121 122 6.160576 TCAAATAAAGCATGATAAAGGGCC 57.839 37.500 0.00 0.00 0.00 5.80
122 123 6.809869 ACTCAAATAAAGCATGATAAAGGGC 58.190 36.000 0.00 0.00 0.00 5.19
123 124 9.657419 AAAACTCAAATAAAGCATGATAAAGGG 57.343 29.630 0.00 0.00 0.00 3.95
131 132 7.148755 CGAAGGGAAAAACTCAAATAAAGCATG 60.149 37.037 0.00 0.00 0.00 4.06
132 133 6.868339 CGAAGGGAAAAACTCAAATAAAGCAT 59.132 34.615 0.00 0.00 0.00 3.79
154 155 3.547746 AGGGAAGCAAGTGTTAAACGAA 58.452 40.909 0.00 0.00 0.00 3.85
156 157 2.096417 CGAGGGAAGCAAGTGTTAAACG 60.096 50.000 0.00 0.00 0.00 3.60
169 171 1.550524 TGAGGATGAACACGAGGGAAG 59.449 52.381 0.00 0.00 0.00 3.46
176 178 3.526931 AGTGGTATGAGGATGAACACG 57.473 47.619 0.00 0.00 32.98 4.49
200 202 3.449737 AGGTTCCCGATCTTTACGATTCA 59.550 43.478 0.00 0.00 30.84 2.57
324 708 3.947834 AGGCTAATTTTGTGGGATCTTCG 59.052 43.478 0.00 0.00 0.00 3.79
365 749 8.888716 GTTTATTCAAAAACCAAATTGACAGGT 58.111 29.630 0.00 0.00 35.42 4.00
419 804 8.514533 TGGGGTACAGTAGGCTATTAATTATT 57.485 34.615 0.00 0.00 0.00 1.40
420 805 8.514533 TTGGGGTACAGTAGGCTATTAATTAT 57.485 34.615 0.00 0.00 0.00 1.28
421 806 7.016858 CCTTGGGGTACAGTAGGCTATTAATTA 59.983 40.741 0.00 0.00 0.00 1.40
447 832 5.128919 AGTGTTCATTTGAGGATCCATAGC 58.871 41.667 15.82 0.56 0.00 2.97
452 837 9.710900 ATTTAAAAAGTGTTCATTTGAGGATCC 57.289 29.630 2.48 2.48 0.00 3.36
670 1056 2.435372 TAGGGTGCATTTGTCATCCC 57.565 50.000 0.00 0.00 35.31 3.85
674 1060 4.586421 TGTTCAAATAGGGTGCATTTGTCA 59.414 37.500 9.01 7.53 41.83 3.58
687 1073 5.964958 ACTTGGTGGTCATGTTCAAATAG 57.035 39.130 0.00 0.00 30.70 1.73
698 1084 2.303175 GGTTGCTAAACTTGGTGGTCA 58.697 47.619 0.00 0.00 36.48 4.02
702 1088 3.980775 CGAATTGGTTGCTAAACTTGGTG 59.019 43.478 0.00 0.00 36.48 4.17
742 1128 6.813649 GGATTAAAAGATTTGTTTCTGAGGCC 59.186 38.462 0.00 0.00 0.00 5.19
753 1139 9.971922 AGTCTCTTTGTTGGATTAAAAGATTTG 57.028 29.630 0.00 0.00 38.77 2.32
758 1144 9.237846 GTTCAAGTCTCTTTGTTGGATTAAAAG 57.762 33.333 0.00 0.00 33.19 2.27
839 1225 3.571401 AGTAAGTTTGCTTGCATGCTTCT 59.429 39.130 23.31 15.55 39.36 2.85
1016 1503 2.103373 TGCCTTTGCAAGTTGTGGTAA 58.897 42.857 4.48 0.00 46.66 2.85
1017 1504 1.769026 TGCCTTTGCAAGTTGTGGTA 58.231 45.000 4.48 0.00 46.66 3.25
1018 1505 2.589494 TGCCTTTGCAAGTTGTGGT 58.411 47.368 4.48 0.00 46.66 4.16
1034 1521 3.128349 TGTCCTCGTCTTAAACTTGTGC 58.872 45.455 0.00 0.00 0.00 4.57
1049 1536 6.049149 TGGATTCGAAAATCTGTATGTCCTC 58.951 40.000 0.00 0.00 40.99 3.71
1114 1605 1.001760 CCGAGGAAGGGAGAAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
1117 1608 0.176910 GAAGCCGAGGAAGGGAGAAG 59.823 60.000 0.00 0.00 0.00 2.85
1123 1614 0.107654 AAATCCGAAGCCGAGGAAGG 60.108 55.000 0.00 0.00 40.32 3.46
1129 1620 0.107848 GAGGGAAAATCCGAAGCCGA 60.108 55.000 0.00 0.00 37.43 5.54
1130 1621 0.107654 AGAGGGAAAATCCGAAGCCG 60.108 55.000 0.00 0.00 37.43 5.52
1427 1941 3.453353 CGAGGTTAGAGGGGGATTGTTTA 59.547 47.826 0.00 0.00 0.00 2.01
1428 1942 2.238898 CGAGGTTAGAGGGGGATTGTTT 59.761 50.000 0.00 0.00 0.00 2.83
1429 1943 1.838077 CGAGGTTAGAGGGGGATTGTT 59.162 52.381 0.00 0.00 0.00 2.83
1430 1944 1.497161 CGAGGTTAGAGGGGGATTGT 58.503 55.000 0.00 0.00 0.00 2.71
1443 1959 0.942884 GTCGAAAACGGAGCGAGGTT 60.943 55.000 0.00 0.00 34.41 3.50
1444 1960 1.372623 GTCGAAAACGGAGCGAGGT 60.373 57.895 0.00 0.00 34.41 3.85
1449 1965 2.737376 AGCGGTCGAAAACGGAGC 60.737 61.111 7.40 0.00 0.00 4.70
1451 1967 3.039588 GCAGCGGTCGAAAACGGA 61.040 61.111 7.40 0.00 0.00 4.69
1452 1968 3.295228 CTGCAGCGGTCGAAAACGG 62.295 63.158 0.00 0.00 0.00 4.44
1453 1969 2.170985 CTGCAGCGGTCGAAAACG 59.829 61.111 0.00 0.00 0.00 3.60
1454 1970 1.204312 GACTGCAGCGGTCGAAAAC 59.796 57.895 18.74 0.00 29.77 2.43
1455 1971 1.959226 GGACTGCAGCGGTCGAAAA 60.959 57.895 25.13 0.00 40.37 2.29
1456 1972 2.357034 GGACTGCAGCGGTCGAAA 60.357 61.111 25.13 0.00 40.37 3.46
1457 1973 4.373116 GGGACTGCAGCGGTCGAA 62.373 66.667 25.13 0.00 40.37 3.71
1469 1985 4.400251 CGGGGAGGGTCAGGGACT 62.400 72.222 0.00 0.00 43.88 3.85
1492 2243 2.696707 CCTATCCACCTGCAATGCAAAT 59.303 45.455 9.92 0.00 38.41 2.32
1495 2246 0.106569 CCCTATCCACCTGCAATGCA 60.107 55.000 7.99 7.99 36.92 3.96
1687 2464 0.327924 AAATCTCACCATCACGGCCA 59.672 50.000 2.24 0.00 39.03 5.36
1884 2682 9.169468 GAACATCAACACAAACAAGTAACATAG 57.831 33.333 0.00 0.00 0.00 2.23
1939 2748 1.349026 CAGATCATAGGAATGCCCCGT 59.651 52.381 0.00 0.00 34.66 5.28
2085 2904 5.371526 GGAAGCACTTGATAAGATGGATGA 58.628 41.667 0.00 0.00 0.00 2.92
2183 3020 5.582269 AGACGAATATCACACAACATCCTTG 59.418 40.000 0.00 0.00 0.00 3.61
2396 3308 8.502738 ACAGGATAAATGACCACCTAATGTAAT 58.497 33.333 0.00 0.00 0.00 1.89
2755 4515 4.759693 ACAACAAACTCAGAGTCACAAACA 59.240 37.500 2.72 0.00 0.00 2.83
2908 5781 0.881118 AGTTTACTTGGCCATGCACG 59.119 50.000 18.17 2.06 0.00 5.34
3119 6003 1.745489 GCAGAACCGTGTGGATCCC 60.745 63.158 9.90 0.85 37.77 3.85
3610 13031 7.678947 ACAGCATGCTAAAATATCTGGATAC 57.321 36.000 22.19 0.00 42.53 2.24
3808 13240 2.033141 TGCTGCCCTCTGAGCAAC 59.967 61.111 0.00 0.00 42.22 4.17
3843 13275 8.582437 CATTCATCAACATTAGAAGGGCATAAT 58.418 33.333 0.00 0.00 0.00 1.28
3894 13326 2.614057 GGCCCAAGAATGTGATAACTCG 59.386 50.000 0.00 0.00 0.00 4.18
3952 13384 4.184629 CTCCTGTGATTTACTGTACTGGC 58.815 47.826 4.66 0.00 33.67 4.85
4113 13569 3.923273 TTAGGGCATGAGAGAGGGATA 57.077 47.619 0.00 0.00 0.00 2.59
4114 13570 2.803285 TTAGGGCATGAGAGAGGGAT 57.197 50.000 0.00 0.00 0.00 3.85
4162 13618 1.202855 AGCAGAGGACACAAGCAACAT 60.203 47.619 0.00 0.00 0.00 2.71
4327 13783 0.171007 CATGCACCACTTAAAGCCCG 59.829 55.000 0.00 0.00 0.00 6.13
4459 13915 6.863126 AGCAATAAATTTACACACTTCAGCAC 59.137 34.615 0.00 0.00 0.00 4.40
4689 14149 3.735591 GTCCAGCAGTACAGTAACCAAA 58.264 45.455 0.00 0.00 0.00 3.28
4690 14150 2.288579 CGTCCAGCAGTACAGTAACCAA 60.289 50.000 0.00 0.00 0.00 3.67
4691 14151 1.271379 CGTCCAGCAGTACAGTAACCA 59.729 52.381 0.00 0.00 0.00 3.67
4695 14155 1.900245 TCACGTCCAGCAGTACAGTA 58.100 50.000 0.00 0.00 0.00 2.74
4727 14187 5.128919 ACCAAGAGCTGAATGGATATGTTC 58.871 41.667 14.27 0.00 37.66 3.18
4771 14231 5.665459 GCTTGAATAGCTAGGACTTCTTGA 58.335 41.667 0.00 0.00 46.77 3.02
4801 14261 6.246420 ACTGATCAGAATTGCTTGTACAAC 57.754 37.500 29.27 2.86 31.03 3.32
4802 14262 6.712095 AGAACTGATCAGAATTGCTTGTACAA 59.288 34.615 29.27 8.28 0.00 2.41
4831 14291 9.884636 ATGCTACTTTACAACATTATCTACACA 57.115 29.630 0.00 0.00 0.00 3.72
4888 14348 7.062749 ACTTTACACTATCAAGACCTGACAA 57.937 36.000 0.00 0.00 36.69 3.18
4941 14401 8.882736 CACATGAATGCAGTATTACTACTTTGA 58.117 33.333 0.00 0.00 35.99 2.69
5004 14464 2.159282 GGCCATGACAGAAGAAATGCAG 60.159 50.000 0.00 0.00 0.00 4.41
5006 14466 1.820519 TGGCCATGACAGAAGAAATGC 59.179 47.619 0.00 0.00 0.00 3.56
5147 14607 5.317600 TCAGTGGCTGAGTCTAGATAGAT 57.682 43.478 0.00 0.00 35.39 1.98
5160 14620 8.285394 GTCATGTAAAATATACATCAGTGGCTG 58.715 37.037 0.00 0.00 36.13 4.85
5235 14808 6.936900 AGTTAGTGCACATCAAGAATAGTTGT 59.063 34.615 21.04 0.00 0.00 3.32
5325 14985 1.068055 CAGTTTGATCACCCAAGCTGC 60.068 52.381 0.00 0.00 44.25 5.25
5327 14987 1.202976 AGCAGTTTGATCACCCAAGCT 60.203 47.619 0.00 0.00 37.96 3.74
5328 14988 1.251251 AGCAGTTTGATCACCCAAGC 58.749 50.000 0.00 0.00 0.00 4.01
5329 14989 4.326504 AAAAGCAGTTTGATCACCCAAG 57.673 40.909 0.00 0.00 0.00 3.61
5429 15105 9.860898 GCAAAGAAAATGATGAAGTTTACCTAT 57.139 29.630 0.00 0.00 0.00 2.57
5441 15117 4.552355 TCTGCACAGCAAAGAAAATGATG 58.448 39.130 0.00 0.00 38.41 3.07
5672 15354 6.662755 TCTTAGTTGACCATATCCAATTGCT 58.337 36.000 0.00 0.00 0.00 3.91
5697 15379 7.822161 AATAGGCTGTGCAAACATATCAATA 57.178 32.000 0.00 0.00 0.00 1.90
5820 15502 9.937876 ATCCAGATACCTTAATAATAGGATCGA 57.062 33.333 0.00 0.00 36.58 3.59
5939 15621 5.544650 AGGAGGATGCAAACTTTTGAAATG 58.455 37.500 5.87 0.00 40.55 2.32
5973 15655 8.164070 AGTTAATGGACTGTACTTTCCAAGAAT 58.836 33.333 16.93 8.76 45.14 2.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.