Multiple sequence alignment - TraesCS4D01G112900

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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 TraesCS4D01G112900 chr4D 100.000 7100 0 0 1 7100 93603531 93610630 0.000000e+00 13112.0
1 TraesCS4D01G112900 chr4A 96.051 6280 166 31 465 6697 488257730 488251486 0.000000e+00 10148.0
2 TraesCS4D01G112900 chr4A 91.990 387 20 7 6717 7100 488251416 488251038 3.770000e-147 532.0
3 TraesCS4D01G112900 chr4A 89.796 98 6 2 6776 6873 487918525 487918432 9.670000e-24 122.0
4 TraesCS4D01G112900 chr4B 96.173 5487 132 36 1649 7100 132049042 132054485 0.000000e+00 8898.0
5 TraesCS4D01G112900 chr4B 92.759 1091 37 19 588 1661 132047817 132048882 0.000000e+00 1539.0
6 TraesCS4D01G112900 chr4B 90.625 96 8 1 4632 4726 453246241 453246336 7.480000e-25 126.0
7 TraesCS4D01G112900 chr4B 96.875 32 1 0 563 594 132047775 132047806 4.000000e-03 54.7
8 TraesCS4D01G112900 chr3B 91.624 394 19 4 1 394 825258112 825257733 3.770000e-147 532.0
9 TraesCS4D01G112900 chr3D 92.417 211 12 2 1 211 85584989 85584783 1.500000e-76 298.0
10 TraesCS4D01G112900 chr3D 83.598 189 8 3 208 396 85583061 85582896 9.540000e-34 156.0
11 TraesCS4D01G112900 chr3D 92.708 96 4 3 4647 4739 509255188 509255093 1.240000e-27 135.0
12 TraesCS4D01G112900 chr6D 85.401 274 21 10 76 343 373052518 373052258 4.220000e-67 267.0
13 TraesCS4D01G112900 chr6D 96.364 55 2 0 5027 5081 267532888 267532942 2.730000e-14 91.6
14 TraesCS4D01G112900 chr6D 96.364 55 2 0 5027 5081 368753531 368753585 2.730000e-14 91.6
15 TraesCS4D01G112900 chr5D 74.545 495 89 22 2565 3046 212561534 212562004 1.570000e-41 182.0
16 TraesCS4D01G112900 chr5D 76.602 359 60 19 1000 1349 212559478 212559821 7.320000e-40 176.0
17 TraesCS4D01G112900 chr5D 91.667 96 7 1 4630 4724 56448452 56448547 1.610000e-26 132.0
18 TraesCS4D01G112900 chr5D 77.215 158 33 3 2320 2475 212561016 212561172 9.810000e-14 89.8
19 TraesCS4D01G112900 chr5A 76.724 348 60 15 1011 1349 275953113 275953448 2.630000e-39 174.0
20 TraesCS4D01G112900 chr5A 78.947 209 35 4 2847 3046 275955580 275955788 4.470000e-27 134.0
21 TraesCS4D01G112900 chr5A 92.553 94 6 1 4631 4723 481105296 481105389 4.470000e-27 134.0
22 TraesCS4D01G112900 chr5A 92.941 85 6 0 5847 5931 370102518 370102434 2.690000e-24 124.0
23 TraesCS4D01G112900 chr5A 78.616 159 29 5 2320 2475 275954676 275954832 4.530000e-17 100.0
24 TraesCS4D01G112900 chr5B 73.737 495 93 22 2565 3046 226628827 226629297 7.370000e-35 159.0
25 TraesCS4D01G112900 chr5B 77.987 159 30 5 2320 2475 226628320 226628476 2.110000e-15 95.3
26 TraesCS4D01G112900 chr3A 89.189 111 10 2 4632 4741 533623244 533623353 3.450000e-28 137.0
27 TraesCS4D01G112900 chr3A 90.909 88 8 0 5847 5934 465824274 465824187 1.250000e-22 119.0
28 TraesCS4D01G112900 chr2D 91.753 97 6 2 4632 4726 462859876 462859780 4.470000e-27 134.0
29 TraesCS4D01G112900 chr1B 91.667 96 7 1 4629 4723 117222084 117222179 1.610000e-26 132.0
30 TraesCS4D01G112900 chr6B 93.103 87 6 0 5847 5933 680933309 680933223 2.080000e-25 128.0
31 TraesCS4D01G112900 chr6B 98.182 55 1 0 5027 5081 554790053 554790107 5.860000e-16 97.1
32 TraesCS4D01G112900 chr1D 89.899 99 10 0 5846 5944 449276393 449276295 2.080000e-25 128.0
33 TraesCS4D01G112900 chr2B 92.222 90 5 2 5844 5931 258639667 258639578 7.480000e-25 126.0
34 TraesCS4D01G112900 chr2B 91.111 90 8 0 5843 5932 491348060 491347971 9.670000e-24 122.0
35 TraesCS4D01G112900 chr1A 92.045 88 7 0 5847 5934 80687938 80687851 2.690000e-24 124.0
36 TraesCS4D01G112900 chr6A 79.114 158 24 7 1 153 515277914 515277761 4.530000e-17 100.0
37 TraesCS4D01G112900 chr7D 87.500 88 8 3 4997 5081 246031078 246031165 1.630000e-16 99.0
38 TraesCS4D01G112900 chr7B 86.364 88 9 3 4997 5081 222306771 222306858 7.580000e-15 93.5
39 TraesCS4D01G112900 chrUn 96.364 55 2 0 5027 5081 730564 730510 2.730000e-14 91.6
40 TraesCS4D01G112900 chrUn 96.364 55 2 0 5027 5081 229396403 229396457 2.730000e-14 91.6


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 TraesCS4D01G112900 chr4D 93603531 93610630 7099 False 13112.000000 13112 100.0000 1 7100 1 chr4D.!!$F1 7099
1 TraesCS4D01G112900 chr4A 488251038 488257730 6692 True 5340.000000 10148 94.0205 465 7100 2 chr4A.!!$R2 6635
2 TraesCS4D01G112900 chr4B 132047775 132054485 6710 False 3497.233333 8898 95.2690 563 7100 3 chr4B.!!$F2 6537
3 TraesCS4D01G112900 chr3D 85582896 85584989 2093 True 227.000000 298 88.0075 1 396 2 chr3D.!!$R2 395

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
671 2412 0.462937 CGTGGTCCAGGTCAAACACA 60.463 55.000 3.24 0.00 0.00 3.72 F
1215 2964 0.035915 TCATCCCCGTTTGATTCGCA 60.036 50.000 0.00 0.00 0.00 5.10 F
2635 4571 0.248296 CACTAGAGTCGAGCCTTCGC 60.248 60.000 0.00 0.00 46.28 4.70 F
3259 5195 2.223876 GCTTGCTCTGAGATGAGAGAGG 60.224 54.545 9.28 0.00 41.95 3.69 F
3650 5586 2.408050 CAATATCGTAGCAGGCAGTCC 58.592 52.381 0.00 0.00 0.00 3.85 F
5086 7040 0.258484 CCCCTGTCCATGGCATTACA 59.742 55.000 6.96 5.26 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 4538 0.389948 CTAGTGCTGAACCACGGGAC 60.390 60.0 0.00 0.0 44.76 4.46 R
3185 5121 1.658994 AGTTCAAACAAAGACGGCGA 58.341 45.0 16.62 0.0 0.00 5.54 R
4513 6459 0.691078 TCCTAGCCGCATTCCTCCTT 60.691 55.0 0.00 0.0 0.00 3.36 R
5057 7011 1.282653 TGGACAGGGGTGTGTGGAAA 61.283 55.0 0.00 0.0 0.00 3.13 R
5503 7461 3.129871 CTCAGCTATAGCAAGCCTCAAC 58.870 50.0 26.07 0.0 43.86 3.18 R
6114 8073 0.250989 CTTTGCGGGGTTGGGTCTTA 60.251 55.0 0.00 0.0 0.00 2.10 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
18 19 3.324170 GTCCTGTACATGTCCGTCG 57.676 57.895 0.00 0.00 0.00 5.12
19 20 0.524862 GTCCTGTACATGTCCGTCGT 59.475 55.000 0.00 0.00 0.00 4.34
20 21 0.806868 TCCTGTACATGTCCGTCGTC 59.193 55.000 0.00 0.00 0.00 4.20
28 29 2.993264 GTCCGTCGTCCCCTTCCA 60.993 66.667 0.00 0.00 0.00 3.53
32 33 0.754217 CCGTCGTCCCCTTCCATCTA 60.754 60.000 0.00 0.00 0.00 1.98
35 36 1.619332 GTCGTCCCCTTCCATCTATCC 59.381 57.143 0.00 0.00 0.00 2.59
38 39 2.756576 CGTCCCCTTCCATCTATCCTCA 60.757 54.545 0.00 0.00 0.00 3.86
67 68 0.809636 CTGCGACACACAAGACCACA 60.810 55.000 0.00 0.00 0.00 4.17
80 81 0.745468 GACCACACCGATCTCCCTAC 59.255 60.000 0.00 0.00 0.00 3.18
96 97 3.201266 TCCCTACGCAATAAAGGTTCCAT 59.799 43.478 0.00 0.00 0.00 3.41
98 99 4.196193 CCTACGCAATAAAGGTTCCATCA 58.804 43.478 0.00 0.00 0.00 3.07
106 107 1.056660 AAGGTTCCATCAGTCGTGGT 58.943 50.000 0.00 0.00 37.96 4.16
143 144 0.623723 TCCGGCCAAGGCTTCTAATT 59.376 50.000 11.40 0.00 41.60 1.40
211 212 1.401552 CAATCGATCGGTGTTGCCAAT 59.598 47.619 16.41 0.00 36.97 3.16
216 1942 3.064682 TCGATCGGTGTTGCCAATTTATG 59.935 43.478 16.41 0.00 36.97 1.90
319 2045 0.960861 CTTTCGGGGGAAACAGAGGC 60.961 60.000 0.00 0.00 0.00 4.70
320 2046 2.420466 TTTCGGGGGAAACAGAGGCC 62.420 60.000 0.00 0.00 0.00 5.19
321 2047 4.778143 CGGGGGAAACAGAGGCCG 62.778 72.222 0.00 0.00 0.00 6.13
344 2070 1.565156 GCTGTGCGTCGTTGGATTCA 61.565 55.000 0.00 0.00 0.00 2.57
352 2078 1.327764 GTCGTTGGATTCAATCGGAGC 59.672 52.381 8.29 0.00 35.10 4.70
390 2116 4.785453 GGGAGCAGGCAAGTCCCG 62.785 72.222 1.79 0.00 40.76 5.14
396 2122 2.203788 AGGCAAGTCCCGTCCAGA 60.204 61.111 0.00 0.00 34.51 3.86
397 2123 2.266055 GGCAAGTCCCGTCCAGAG 59.734 66.667 0.00 0.00 0.00 3.35
398 2124 2.584391 GGCAAGTCCCGTCCAGAGT 61.584 63.158 0.00 0.00 0.00 3.24
399 2125 1.374758 GCAAGTCCCGTCCAGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
400 2126 1.293498 CAAGTCCCGTCCAGAGTGG 59.707 63.158 0.00 0.00 39.43 4.00
401 2127 1.155390 AAGTCCCGTCCAGAGTGGA 59.845 57.895 0.00 0.00 45.98 4.02
408 2134 2.121385 TCCAGAGTGGAGCAGCCT 59.879 61.111 0.00 0.00 42.67 4.58
409 2135 2.268280 CCAGAGTGGAGCAGCCTG 59.732 66.667 0.00 0.00 40.96 4.85
410 2136 2.436292 CAGAGTGGAGCAGCCTGC 60.436 66.667 9.13 9.13 45.46 4.85
423 2149 2.805845 CAGCCTGCTGCAAAATGATAC 58.194 47.619 6.16 0.00 44.83 2.24
424 2150 2.426024 CAGCCTGCTGCAAAATGATACT 59.574 45.455 6.16 0.00 44.83 2.12
425 2151 2.686915 AGCCTGCTGCAAAATGATACTC 59.313 45.455 3.02 0.00 44.83 2.59
426 2152 2.223665 GCCTGCTGCAAAATGATACTCC 60.224 50.000 3.02 0.00 40.77 3.85
427 2153 3.285484 CCTGCTGCAAAATGATACTCCT 58.715 45.455 3.02 0.00 0.00 3.69
428 2154 3.698040 CCTGCTGCAAAATGATACTCCTT 59.302 43.478 3.02 0.00 0.00 3.36
429 2155 4.201990 CCTGCTGCAAAATGATACTCCTTC 60.202 45.833 3.02 0.00 0.00 3.46
430 2156 4.592942 TGCTGCAAAATGATACTCCTTCT 58.407 39.130 0.00 0.00 0.00 2.85
431 2157 4.397103 TGCTGCAAAATGATACTCCTTCTG 59.603 41.667 0.00 0.00 0.00 3.02
432 2158 4.397417 GCTGCAAAATGATACTCCTTCTGT 59.603 41.667 0.00 0.00 0.00 3.41
433 2159 5.105997 GCTGCAAAATGATACTCCTTCTGTT 60.106 40.000 0.00 0.00 0.00 3.16
434 2160 6.500684 TGCAAAATGATACTCCTTCTGTTC 57.499 37.500 0.00 0.00 0.00 3.18
435 2161 5.415701 TGCAAAATGATACTCCTTCTGTTCC 59.584 40.000 0.00 0.00 0.00 3.62
436 2162 5.415701 GCAAAATGATACTCCTTCTGTTCCA 59.584 40.000 0.00 0.00 0.00 3.53
437 2163 6.071952 GCAAAATGATACTCCTTCTGTTCCAA 60.072 38.462 0.00 0.00 0.00 3.53
438 2164 7.523709 GCAAAATGATACTCCTTCTGTTCCAAA 60.524 37.037 0.00 0.00 0.00 3.28
439 2165 8.359642 CAAAATGATACTCCTTCTGTTCCAAAA 58.640 33.333 0.00 0.00 0.00 2.44
440 2166 8.655935 AAATGATACTCCTTCTGTTCCAAAAT 57.344 30.769 0.00 0.00 0.00 1.82
441 2167 9.753674 AAATGATACTCCTTCTGTTCCAAAATA 57.246 29.630 0.00 0.00 0.00 1.40
442 2168 9.927081 AATGATACTCCTTCTGTTCCAAAATAT 57.073 29.630 0.00 0.00 0.00 1.28
448 2174 8.606830 ACTCCTTCTGTTCCAAAATATAAGAGT 58.393 33.333 0.00 0.00 0.00 3.24
453 2179 9.627123 TTCTGTTCCAAAATATAAGAGTATGGG 57.373 33.333 0.00 0.00 0.00 4.00
454 2180 8.998814 TCTGTTCCAAAATATAAGAGTATGGGA 58.001 33.333 0.00 0.00 0.00 4.37
455 2181 9.799106 CTGTTCCAAAATATAAGAGTATGGGAT 57.201 33.333 0.00 0.00 0.00 3.85
456 2182 9.573166 TGTTCCAAAATATAAGAGTATGGGATG 57.427 33.333 0.00 0.00 0.00 3.51
457 2183 9.014297 GTTCCAAAATATAAGAGTATGGGATGG 57.986 37.037 0.00 0.00 0.00 3.51
458 2184 8.518720 TCCAAAATATAAGAGTATGGGATGGA 57.481 34.615 0.00 0.00 0.00 3.41
459 2185 8.605947 TCCAAAATATAAGAGTATGGGATGGAG 58.394 37.037 0.00 0.00 0.00 3.86
460 2186 7.831193 CCAAAATATAAGAGTATGGGATGGAGG 59.169 40.741 0.00 0.00 0.00 4.30
461 2187 7.516450 AAATATAAGAGTATGGGATGGAGGG 57.484 40.000 0.00 0.00 0.00 4.30
462 2188 4.785173 ATAAGAGTATGGGATGGAGGGA 57.215 45.455 0.00 0.00 0.00 4.20
463 2189 2.711895 AGAGTATGGGATGGAGGGAG 57.288 55.000 0.00 0.00 0.00 4.30
481 2207 7.162082 GGAGGGAGTAATATTCAAATCACGAT 58.838 38.462 0.00 0.00 0.00 3.73
629 2370 4.742201 CTGGACCCACTCCGTGCG 62.742 72.222 0.00 0.00 43.03 5.34
667 2408 2.280524 CGCGTGGTCCAGGTCAAA 60.281 61.111 12.99 0.00 0.00 2.69
668 2409 2.604174 CGCGTGGTCCAGGTCAAAC 61.604 63.158 12.99 0.00 0.00 2.93
669 2410 1.525077 GCGTGGTCCAGGTCAAACA 60.525 57.895 12.99 0.00 0.00 2.83
670 2411 1.782028 GCGTGGTCCAGGTCAAACAC 61.782 60.000 12.99 0.00 0.00 3.32
671 2412 0.462937 CGTGGTCCAGGTCAAACACA 60.463 55.000 3.24 0.00 0.00 3.72
714 2455 1.393883 GAGGCGTTCGAACCATTCTTC 59.606 52.381 22.07 10.79 0.00 2.87
715 2456 1.002087 AGGCGTTCGAACCATTCTTCT 59.998 47.619 22.07 6.74 0.00 2.85
716 2457 1.393883 GGCGTTCGAACCATTCTTCTC 59.606 52.381 22.07 0.00 0.00 2.87
753 2494 4.042060 CACAACCACGTCGTCGCG 62.042 66.667 0.00 0.00 41.18 5.87
754 2495 4.557605 ACAACCACGTCGTCGCGT 62.558 61.111 5.77 8.54 46.88 6.01
755 2496 3.749373 CAACCACGTCGTCGCGTC 61.749 66.667 5.77 0.00 43.83 5.19
901 2642 1.955529 TTCTCGAAGCGCACGCATTC 61.956 55.000 18.24 15.37 44.88 2.67
934 2675 4.804420 AGATCTCCCAGGCCGGCA 62.804 66.667 30.85 5.63 0.00 5.69
1178 2919 4.410400 CACCCAGGTCCCGCTTCC 62.410 72.222 0.00 0.00 0.00 3.46
1195 2944 0.991920 TCCCCTCCTTCACATTCCAC 59.008 55.000 0.00 0.00 0.00 4.02
1214 2963 0.657840 CTCATCCCCGTTTGATTCGC 59.342 55.000 0.00 0.00 0.00 4.70
1215 2964 0.035915 TCATCCCCGTTTGATTCGCA 60.036 50.000 0.00 0.00 0.00 5.10
1219 2974 1.029408 CCCCGTTTGATTCGCATCCA 61.029 55.000 0.00 0.00 0.00 3.41
1247 3002 1.865340 GACGTGGTTCGCTTTTCTCTT 59.135 47.619 0.00 0.00 44.19 2.85
1251 3006 0.881796 GGTTCGCTTTTCTCTTGGGG 59.118 55.000 0.00 0.00 0.00 4.96
1252 3007 0.881796 GTTCGCTTTTCTCTTGGGGG 59.118 55.000 0.00 0.00 0.00 5.40
1381 3136 1.567504 GGTACATGAACATCGACCCG 58.432 55.000 0.00 0.00 0.00 5.28
1414 3170 8.606040 ATTTTCAAACATTTTACCTGGATGTG 57.394 30.769 0.00 0.00 34.47 3.21
1415 3171 6.723298 TTCAAACATTTTACCTGGATGTGT 57.277 33.333 0.00 0.00 34.47 3.72
1431 3187 1.135915 TGTGTGTGGTGGTCAATTTGC 59.864 47.619 0.00 0.00 0.00 3.68
1476 3235 3.802685 CGTCTTATGGATCTTTCGGGAAC 59.197 47.826 0.00 0.00 0.00 3.62
1545 3304 5.881447 TGTTGCGGTATTTAATATGCGTTT 58.119 33.333 7.35 0.00 0.00 3.60
1557 3316 8.466617 TTTAATATGCGTTTTGTGGGGTATAT 57.533 30.769 0.00 0.00 0.00 0.86
1558 3317 9.570468 TTTAATATGCGTTTTGTGGGGTATATA 57.430 29.630 0.00 0.00 0.00 0.86
1559 3318 9.570468 TTAATATGCGTTTTGTGGGGTATATAA 57.430 29.630 0.00 0.00 0.00 0.98
1560 3319 8.466617 AATATGCGTTTTGTGGGGTATATAAA 57.533 30.769 0.00 0.00 0.00 1.40
1694 3628 6.613271 AGATCCAGTGAGTGATATAGTTTGGT 59.387 38.462 0.00 0.00 0.00 3.67
1706 3640 9.880157 GTGATATAGTTTGGTACTTTTAGGTCA 57.120 33.333 0.00 0.00 38.33 4.02
1911 3846 8.132995 ACTTACTAACTTTGTGTAAACATTGCC 58.867 33.333 0.00 0.00 0.00 4.52
2070 4005 1.986378 CTGAATCACGTCAACGGTCTC 59.014 52.381 7.53 0.00 44.95 3.36
2124 4059 6.409704 AGAATTTAAGCAGCTGATGACTACA 58.590 36.000 20.43 0.00 0.00 2.74
2193 4129 9.642312 CTACATTCATGTTCATTTCTTATGTCG 57.358 33.333 0.00 0.00 41.97 4.35
2200 4136 9.277565 CATGTTCATTTCTTATGTCGGTAAAAG 57.722 33.333 0.00 0.00 0.00 2.27
2366 4302 5.355350 GCTTGGAAACTGCTGTATACAAGAT 59.645 40.000 24.72 0.00 34.71 2.40
2367 4303 6.538742 GCTTGGAAACTGCTGTATACAAGATA 59.461 38.462 24.72 0.00 34.71 1.98
2415 4351 2.551459 GCCACTCATGAATGACATAGCC 59.449 50.000 5.56 0.00 37.46 3.93
2561 4497 3.962063 TGACACCTGAGTTACTAACACCA 59.038 43.478 1.79 0.00 0.00 4.17
2585 4521 8.487176 CCATGTGCAAAGTCAAGTTAAATTTAC 58.513 33.333 0.00 0.00 0.00 2.01
2602 4538 9.726438 TTAAATTTACCCTCTTTCTTCAGAGAG 57.274 33.333 0.00 0.00 42.81 3.20
2635 4571 0.248296 CACTAGAGTCGAGCCTTCGC 60.248 60.000 0.00 0.00 46.28 4.70
3138 5074 4.416620 GTTCCGTGTCATTGTTGTTTTCA 58.583 39.130 0.00 0.00 0.00 2.69
3185 5121 4.406456 TGGTGAGCACTACCAAATTTCAT 58.594 39.130 4.49 0.00 44.79 2.57
3259 5195 2.223876 GCTTGCTCTGAGATGAGAGAGG 60.224 54.545 9.28 0.00 41.95 3.69
3650 5586 2.408050 CAATATCGTAGCAGGCAGTCC 58.592 52.381 0.00 0.00 0.00 3.85
3737 5673 3.559242 TGGCTTGCATTTAGTTGTTTTGC 59.441 39.130 0.00 0.00 0.00 3.68
3890 5834 6.308371 GTTTCAGGAATTCGAAACTGGTAA 57.692 37.500 21.89 14.74 44.83 2.85
4114 6060 5.452496 GGCAATCTGCTCACTTAGTGATCTA 60.452 44.000 15.91 5.09 44.28 1.98
4513 6459 3.389656 TGGCATCCAAGATAATACCGTCA 59.610 43.478 0.00 0.00 0.00 4.35
4523 6469 6.102897 AGATAATACCGTCAAGGAGGAATG 57.897 41.667 0.00 0.00 45.00 2.67
4580 6526 4.786425 ACAATTGAGGGAGAATTAGGAGC 58.214 43.478 13.59 0.00 0.00 4.70
4790 6744 6.103353 TCCTCTCTATTCTCTCAATCCTACCA 59.897 42.308 0.00 0.00 0.00 3.25
4896 6850 3.125316 CCTGCATTTTGGTGTCAAGTTG 58.875 45.455 0.00 0.00 33.98 3.16
4956 6910 6.036083 CCAAACCATAGTAAGAGTCAATGTCG 59.964 42.308 0.00 0.00 0.00 4.35
5002 6956 3.252400 ACACACGTCGTCTTACAACAAA 58.748 40.909 0.00 0.00 0.00 2.83
5006 6960 3.710653 CACGTCGTCTTACAACAAAAACG 59.289 43.478 0.00 0.00 0.00 3.60
5057 7011 2.682594 TCTGGCACATGGATAGCTAGT 58.317 47.619 0.00 0.00 38.20 2.57
5081 7035 2.858476 ACACCCCTGTCCATGGCA 60.858 61.111 6.96 7.80 0.00 4.92
5086 7040 0.258484 CCCCTGTCCATGGCATTACA 59.742 55.000 6.96 5.26 0.00 2.41
5152 7106 6.183360 CCATGTCCTGTGCTTCAGTAATTAAG 60.183 42.308 8.23 0.00 42.19 1.85
5160 7114 7.475015 TGTGCTTCAGTAATTAAGATCATTGC 58.525 34.615 0.00 0.00 0.00 3.56
5701 7659 8.810652 TTGCAGTTCCAGAATTACAAAATTAC 57.189 30.769 0.00 0.00 35.41 1.89
5730 7688 2.609747 TGTCTGTCCTCTAAAGCACCT 58.390 47.619 0.00 0.00 0.00 4.00
5757 7716 2.668550 GTTGACTGACGGGGTGGC 60.669 66.667 0.00 0.00 0.00 5.01
5796 7755 6.184789 ACTTTGGAGAACAACACTTCCTTAA 58.815 36.000 0.00 0.00 39.19 1.85
5813 7772 3.068873 CCTTAATCTTCTCCAGGACTCCG 59.931 52.174 0.00 0.00 0.00 4.63
5822 7781 1.070134 TCCAGGACTCCGTTCAACTTG 59.930 52.381 0.00 0.00 0.00 3.16
5842 7801 4.564782 TGGAATGATCTCAGCTGTTCTT 57.435 40.909 14.67 5.29 0.00 2.52
5921 7880 7.989416 AAAAGACGTCTTATAATTTGGGACA 57.011 32.000 29.91 0.00 34.61 4.02
6040 7999 2.222027 CTGAACTGGTGGACAAACTCC 58.778 52.381 0.00 0.00 39.97 3.85
6114 8073 0.613260 TGTAAGGTCTCTGCGGCATT 59.387 50.000 1.75 0.00 0.00 3.56
6238 8197 3.457234 CACCACAGAAAAGAAAAAGGGC 58.543 45.455 0.00 0.00 0.00 5.19
6360 8319 5.613329 TGTTGTTCTATCGTGTTAACCCTT 58.387 37.500 2.48 0.00 0.00 3.95
6449 8408 6.527023 CAGCAAGATTTGTTCTAATGAGCTTG 59.473 38.462 0.00 0.00 33.05 4.01
6566 8526 0.178992 TGTTGGCTTGGTCCTTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
6572 8532 2.290960 GGCTTGGTCCTTCAGGTGTTAT 60.291 50.000 0.00 0.00 36.34 1.89
6617 8577 1.132199 CGTTTCCGATCCACGACTCG 61.132 60.000 0.00 0.00 45.77 4.18
6677 8637 3.949132 TGCAAATGATACCTAGTGCACA 58.051 40.909 21.04 4.13 37.09 4.57
6678 8638 4.525996 TGCAAATGATACCTAGTGCACAT 58.474 39.130 21.04 2.45 37.09 3.21
6679 8639 5.679601 TGCAAATGATACCTAGTGCACATA 58.320 37.500 21.04 7.67 37.09 2.29
6680 8640 6.118852 TGCAAATGATACCTAGTGCACATAA 58.881 36.000 21.04 2.80 37.09 1.90
6681 8641 6.038161 TGCAAATGATACCTAGTGCACATAAC 59.962 38.462 21.04 5.33 37.09 1.89
6682 8642 6.038161 GCAAATGATACCTAGTGCACATAACA 59.962 38.462 21.04 10.63 32.29 2.41
6683 8643 7.255242 GCAAATGATACCTAGTGCACATAACAT 60.255 37.037 21.04 12.30 32.29 2.71
6690 8650 9.929180 ATACCTAGTGCACATAACATATAACAG 57.071 33.333 21.04 0.00 0.00 3.16
6715 8675 8.531982 AGATAACAGCAGAGACAAATACTACAA 58.468 33.333 0.00 0.00 0.00 2.41
6834 8854 6.128145 GCTCACGAATATATCTCTGTCTGCTA 60.128 42.308 0.00 0.00 0.00 3.49
6835 8855 7.371126 TCACGAATATATCTCTGTCTGCTAG 57.629 40.000 0.00 0.00 0.00 3.42
6836 8856 6.937465 TCACGAATATATCTCTGTCTGCTAGT 59.063 38.462 0.00 0.00 0.00 2.57
6871 8891 4.940046 ACACAATCAGCAGAAATAGTGAGG 59.060 41.667 0.00 0.00 0.00 3.86
6917 8937 8.150296 GGCCAAAGCAAAATAAATAGACCATAT 58.850 33.333 0.00 0.00 42.56 1.78
6962 8982 6.432162 ACACTTGTCTTATGCATCAACATCTT 59.568 34.615 0.19 0.00 0.00 2.40
6995 9016 4.283467 AGGCAAATAAAAACCAGGAACTCC 59.717 41.667 0.00 0.00 34.60 3.85
7059 9080 1.927174 CGTAGACTGCAACATAGCACC 59.073 52.381 0.00 0.00 40.11 5.01
7085 9106 1.697432 TCTGTTTCCCTGGAATCACGT 59.303 47.619 5.73 0.00 33.79 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.977808 TGAGGATAGATGGAAGGGGAC 58.022 52.381 0.00 0.00 0.00 4.46
19 20 3.591789 CTTGAGGATAGATGGAAGGGGA 58.408 50.000 0.00 0.00 0.00 4.81
20 21 2.039613 GCTTGAGGATAGATGGAAGGGG 59.960 54.545 0.00 0.00 0.00 4.79
28 29 0.319383 CGCTGCGCTTGAGGATAGAT 60.319 55.000 9.88 0.00 0.00 1.98
51 52 1.487452 CGGTGTGGTCTTGTGTGTCG 61.487 60.000 0.00 0.00 0.00 4.35
54 55 1.148310 GATCGGTGTGGTCTTGTGTG 58.852 55.000 0.00 0.00 0.00 3.82
67 68 1.991121 TATTGCGTAGGGAGATCGGT 58.009 50.000 0.00 0.00 0.00 4.69
80 81 3.242413 CGACTGATGGAACCTTTATTGCG 60.242 47.826 0.00 0.00 0.00 4.85
96 97 0.032130 GAGAGTTGCACCACGACTGA 59.968 55.000 0.00 0.00 43.54 3.41
98 99 1.367840 GGAGAGTTGCACCACGACT 59.632 57.895 0.00 0.00 46.38 4.18
106 107 0.250467 GAGTTGGCTGGAGAGTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
187 188 1.290203 CAACACCGATCGATTGGGAG 58.710 55.000 30.99 24.78 35.53 4.30
211 212 3.655615 AAATACCAGGCGACCCATAAA 57.344 42.857 0.00 0.00 0.00 1.40
216 1942 1.743394 CAAGAAAATACCAGGCGACCC 59.257 52.381 0.00 0.00 0.00 4.46
250 1976 2.084546 CCACCTCTCCATCCGTTTTTC 58.915 52.381 0.00 0.00 0.00 2.29
280 2006 3.145422 AAAAACCAGCCCCGTTGCG 62.145 57.895 0.00 0.00 36.02 4.85
281 2007 2.818841 AAAAACCAGCCCCGTTGC 59.181 55.556 0.00 0.00 0.00 4.17
323 2049 4.980805 TCCAACGACGCACAGCCC 62.981 66.667 0.00 0.00 0.00 5.19
324 2050 2.240612 GAATCCAACGACGCACAGCC 62.241 60.000 0.00 0.00 0.00 4.85
325 2051 1.132640 GAATCCAACGACGCACAGC 59.867 57.895 0.00 0.00 0.00 4.40
326 2052 0.865111 TTGAATCCAACGACGCACAG 59.135 50.000 0.00 0.00 0.00 3.66
327 2053 1.463056 GATTGAATCCAACGACGCACA 59.537 47.619 0.00 0.00 34.72 4.57
328 2054 1.526986 CGATTGAATCCAACGACGCAC 60.527 52.381 0.00 0.00 34.72 5.34
329 2055 0.718904 CGATTGAATCCAACGACGCA 59.281 50.000 0.00 0.00 34.72 5.24
330 2056 0.026285 CCGATTGAATCCAACGACGC 59.974 55.000 0.00 0.00 34.72 5.19
331 2057 1.588404 CTCCGATTGAATCCAACGACG 59.412 52.381 0.00 0.00 34.72 5.12
332 2058 1.327764 GCTCCGATTGAATCCAACGAC 59.672 52.381 0.00 0.00 34.72 4.34
344 2070 1.277557 GCTCCCATCTATGCTCCGATT 59.722 52.381 0.00 0.00 0.00 3.34
352 2078 0.319040 CGGTCGTGCTCCCATCTATG 60.319 60.000 0.00 0.00 0.00 2.23
386 2112 2.680352 GCTCCACTCTGGACGGGA 60.680 66.667 0.00 0.00 42.67 5.14
390 2116 2.267324 GGCTGCTCCACTCTGGAC 59.733 66.667 0.00 0.00 42.67 4.02
403 2129 2.426024 AGTATCATTTTGCAGCAGGCTG 59.574 45.455 16.68 16.68 45.15 4.85
404 2130 2.686915 GAGTATCATTTTGCAGCAGGCT 59.313 45.455 0.00 0.00 38.25 4.58
405 2131 2.223665 GGAGTATCATTTTGCAGCAGGC 60.224 50.000 0.00 0.00 39.51 4.85
406 2132 3.285484 AGGAGTATCATTTTGCAGCAGG 58.715 45.455 0.00 0.00 36.25 4.85
407 2133 4.639310 AGAAGGAGTATCATTTTGCAGCAG 59.361 41.667 0.00 0.00 40.37 4.24
408 2134 4.397103 CAGAAGGAGTATCATTTTGCAGCA 59.603 41.667 0.00 0.00 40.37 4.41
409 2135 4.397417 ACAGAAGGAGTATCATTTTGCAGC 59.603 41.667 0.00 0.00 43.65 5.25
410 2136 6.404074 GGAACAGAAGGAGTATCATTTTGCAG 60.404 42.308 0.00 0.00 43.65 4.41
411 2137 5.415701 GGAACAGAAGGAGTATCATTTTGCA 59.584 40.000 0.00 0.00 43.65 4.08
412 2138 5.415701 TGGAACAGAAGGAGTATCATTTTGC 59.584 40.000 0.00 0.00 43.65 3.68
413 2139 7.452880 TTGGAACAGAAGGAGTATCATTTTG 57.547 36.000 0.00 0.00 45.08 2.44
414 2140 8.477419 TTTTGGAACAGAAGGAGTATCATTTT 57.523 30.769 0.00 0.00 40.37 1.82
415 2141 8.655935 ATTTTGGAACAGAAGGAGTATCATTT 57.344 30.769 0.00 0.00 40.37 2.32
416 2142 9.927081 ATATTTTGGAACAGAAGGAGTATCATT 57.073 29.630 0.00 0.00 44.59 2.57
422 2148 8.606830 ACTCTTATATTTTGGAACAGAAGGAGT 58.393 33.333 0.00 0.00 42.39 3.85
427 2153 9.627123 CCCATACTCTTATATTTTGGAACAGAA 57.373 33.333 0.00 0.00 42.39 3.02
428 2154 8.998814 TCCCATACTCTTATATTTTGGAACAGA 58.001 33.333 0.00 0.00 42.39 3.41
429 2155 9.799106 ATCCCATACTCTTATATTTTGGAACAG 57.201 33.333 0.00 0.00 42.39 3.16
430 2156 9.573166 CATCCCATACTCTTATATTTTGGAACA 57.427 33.333 0.00 0.00 0.00 3.18
431 2157 9.014297 CCATCCCATACTCTTATATTTTGGAAC 57.986 37.037 0.00 0.00 0.00 3.62
432 2158 8.954729 TCCATCCCATACTCTTATATTTTGGAA 58.045 33.333 0.00 0.00 0.00 3.53
433 2159 8.518720 TCCATCCCATACTCTTATATTTTGGA 57.481 34.615 0.00 0.00 0.00 3.53
434 2160 7.831193 CCTCCATCCCATACTCTTATATTTTGG 59.169 40.741 0.00 0.00 0.00 3.28
435 2161 7.831193 CCCTCCATCCCATACTCTTATATTTTG 59.169 40.741 0.00 0.00 0.00 2.44
436 2162 7.744068 TCCCTCCATCCCATACTCTTATATTTT 59.256 37.037 0.00 0.00 0.00 1.82
437 2163 7.263901 TCCCTCCATCCCATACTCTTATATTT 58.736 38.462 0.00 0.00 0.00 1.40
438 2164 6.826727 TCCCTCCATCCCATACTCTTATATT 58.173 40.000 0.00 0.00 0.00 1.28
439 2165 6.009388 ACTCCCTCCATCCCATACTCTTATAT 60.009 42.308 0.00 0.00 0.00 0.86
440 2166 5.318889 ACTCCCTCCATCCCATACTCTTATA 59.681 44.000 0.00 0.00 0.00 0.98
441 2167 4.110426 ACTCCCTCCATCCCATACTCTTAT 59.890 45.833 0.00 0.00 0.00 1.73
442 2168 3.471306 ACTCCCTCCATCCCATACTCTTA 59.529 47.826 0.00 0.00 0.00 2.10
443 2169 2.251338 ACTCCCTCCATCCCATACTCTT 59.749 50.000 0.00 0.00 0.00 2.85
444 2170 1.869648 ACTCCCTCCATCCCATACTCT 59.130 52.381 0.00 0.00 0.00 3.24
445 2171 2.407340 ACTCCCTCCATCCCATACTC 57.593 55.000 0.00 0.00 0.00 2.59
446 2172 4.510303 ATTACTCCCTCCATCCCATACT 57.490 45.455 0.00 0.00 0.00 2.12
447 2173 6.443849 TGAATATTACTCCCTCCATCCCATAC 59.556 42.308 0.00 0.00 0.00 2.39
448 2174 6.580167 TGAATATTACTCCCTCCATCCCATA 58.420 40.000 0.00 0.00 0.00 2.74
449 2175 5.424068 TGAATATTACTCCCTCCATCCCAT 58.576 41.667 0.00 0.00 0.00 4.00
450 2176 4.838403 TGAATATTACTCCCTCCATCCCA 58.162 43.478 0.00 0.00 0.00 4.37
451 2177 5.843019 TTGAATATTACTCCCTCCATCCC 57.157 43.478 0.00 0.00 0.00 3.85
452 2178 7.391833 GTGATTTGAATATTACTCCCTCCATCC 59.608 40.741 0.00 0.00 0.00 3.51
453 2179 7.118390 CGTGATTTGAATATTACTCCCTCCATC 59.882 40.741 0.00 0.00 0.00 3.51
454 2180 6.936900 CGTGATTTGAATATTACTCCCTCCAT 59.063 38.462 0.00 0.00 0.00 3.41
455 2181 6.099125 TCGTGATTTGAATATTACTCCCTCCA 59.901 38.462 0.00 0.00 0.00 3.86
456 2182 6.522054 TCGTGATTTGAATATTACTCCCTCC 58.478 40.000 0.00 0.00 0.00 4.30
457 2183 7.657761 ACATCGTGATTTGAATATTACTCCCTC 59.342 37.037 0.00 0.00 0.00 4.30
458 2184 7.509546 ACATCGTGATTTGAATATTACTCCCT 58.490 34.615 0.00 0.00 0.00 4.20
459 2185 7.730364 ACATCGTGATTTGAATATTACTCCC 57.270 36.000 0.00 0.00 0.00 4.30
460 2186 8.283291 GGAACATCGTGATTTGAATATTACTCC 58.717 37.037 0.00 0.00 0.00 3.85
461 2187 8.826710 TGGAACATCGTGATTTGAATATTACTC 58.173 33.333 0.00 0.00 0.00 2.59
462 2188 8.731275 TGGAACATCGTGATTTGAATATTACT 57.269 30.769 0.00 0.00 0.00 2.24
594 2320 2.288025 GGGAGTGGTGGTTAGCGGA 61.288 63.158 0.00 0.00 0.00 5.54
667 2408 2.126071 CGAGATTCGGGCGTGTGT 60.126 61.111 0.00 0.00 36.00 3.72
1173 2914 1.683319 GGAATGTGAAGGAGGGGAAGC 60.683 57.143 0.00 0.00 0.00 3.86
1176 2917 0.991920 GTGGAATGTGAAGGAGGGGA 59.008 55.000 0.00 0.00 0.00 4.81
1178 2919 1.630369 TGAGTGGAATGTGAAGGAGGG 59.370 52.381 0.00 0.00 0.00 4.30
1195 2944 0.657840 GCGAATCAAACGGGGATGAG 59.342 55.000 0.00 0.00 0.00 2.90
1214 2963 3.021541 CACGTCAGTCGAGTGGATG 57.978 57.895 19.86 13.58 42.86 3.51
1219 2974 1.281960 CGAACCACGTCAGTCGAGT 59.718 57.895 5.57 0.00 42.86 4.18
1251 3006 2.167075 CCTCACCTGCATTTCATTTCCC 59.833 50.000 0.00 0.00 0.00 3.97
1252 3007 3.091545 TCCTCACCTGCATTTCATTTCC 58.908 45.455 0.00 0.00 0.00 3.13
1381 3136 6.141527 GGTAAAATGTTTGAAAATTTTGCGGC 59.858 34.615 8.47 0.00 38.49 6.53
1414 3170 2.621055 TGTAGCAAATTGACCACCACAC 59.379 45.455 0.00 0.00 0.00 3.82
1415 3171 2.937519 TGTAGCAAATTGACCACCACA 58.062 42.857 0.00 0.00 0.00 4.17
1476 3235 1.468565 CGCTCATTGGGCACATTTCAG 60.469 52.381 9.60 0.00 0.00 3.02
1505 3264 6.016718 CCGCAACAAATTTTAATCATTGCAG 58.983 36.000 6.83 0.43 40.71 4.41
1545 3304 7.454553 ACATGGTAGTTTATATACCCCACAA 57.545 36.000 0.00 0.00 41.78 3.33
1560 3319 8.686334 GGTGATGATTGAATTTAACATGGTAGT 58.314 33.333 0.00 0.00 0.00 2.73
1694 3628 8.943594 ACCCAAATTAATGTGACCTAAAAGTA 57.056 30.769 7.23 0.00 0.00 2.24
1705 3639 7.336679 TCATCTACAGTGACCCAAATTAATGTG 59.663 37.037 0.00 0.00 0.00 3.21
1706 3640 7.402054 TCATCTACAGTGACCCAAATTAATGT 58.598 34.615 0.00 0.00 0.00 2.71
1766 3700 7.123098 TGCCATTTTCACATAACAAGATGATCT 59.877 33.333 0.00 0.00 0.00 2.75
1783 3717 2.444351 CGAGAAATCGCTGCCATTTTC 58.556 47.619 6.67 7.40 0.00 2.29
1851 3785 5.007823 TCAAAGCCTTTTGCAAACAATCATG 59.992 36.000 12.39 7.95 42.71 3.07
1911 3846 1.468914 GCCTCGGCCTAAAGTTTGAAG 59.531 52.381 0.00 0.00 34.56 3.02
2070 4005 5.303747 TCTTCAGAGAAGACTTCGCTAAG 57.696 43.478 19.40 19.66 37.74 2.18
2193 4129 6.370718 ACCATCGTAGACAACATTCTTTTACC 59.629 38.462 0.00 0.00 42.51 2.85
2200 4136 7.277981 ACAGATAAACCATCGTAGACAACATTC 59.722 37.037 0.00 0.00 42.51 2.67
2366 4302 2.885135 TGGAGGAACTAGTGTCGGTA 57.115 50.000 0.00 0.00 41.55 4.02
2367 4303 1.893801 CTTGGAGGAACTAGTGTCGGT 59.106 52.381 0.00 0.00 41.55 4.69
2543 4479 4.802918 GCACATGGTGTTAGTAACTCAGGT 60.803 45.833 14.00 15.13 35.75 4.00
2561 4497 7.655732 GGGTAAATTTAACTTGACTTTGCACAT 59.344 33.333 12.85 0.00 0.00 3.21
2602 4538 0.389948 CTAGTGCTGAACCACGGGAC 60.390 60.000 0.00 0.00 44.76 4.46
2635 4571 5.998363 AGTAAGTTTTTCTACTCCCAGCTTG 59.002 40.000 0.00 0.00 0.00 4.01
2844 4780 4.389374 TCGCAGATTTTTCTTTCTCCAGT 58.611 39.130 0.00 0.00 0.00 4.00
2966 4902 5.675684 TTTCAGGAGACCTTTTGCTTTTT 57.324 34.783 0.00 0.00 0.00 1.94
3138 5074 9.309516 CAAAAGCATCATAGCATAAGTTGAAAT 57.690 29.630 0.00 0.00 36.85 2.17
3185 5121 1.658994 AGTTCAAACAAAGACGGCGA 58.341 45.000 16.62 0.00 0.00 5.54
3259 5195 1.133790 CTTAGTCAAGCCCAATGCAGC 59.866 52.381 0.00 0.00 44.83 5.25
3581 5517 4.096190 AGCAGACAGGCTTTATGCATAT 57.904 40.909 20.90 0.00 42.71 1.78
3650 5586 6.712549 TCACAACTCTGTATAGTTATCGACG 58.287 40.000 0.00 0.00 37.61 5.12
4513 6459 0.691078 TCCTAGCCGCATTCCTCCTT 60.691 55.000 0.00 0.00 0.00 3.36
4523 6469 1.646189 CAGACTCTTTTCCTAGCCGC 58.354 55.000 0.00 0.00 0.00 6.53
4580 6526 4.943705 ACAACACTTCCTAATGTGCCATAG 59.056 41.667 0.00 0.00 37.68 2.23
4783 6737 4.224370 GGTGAGAAAGTTATGGTGGTAGGA 59.776 45.833 0.00 0.00 0.00 2.94
4790 6744 4.505039 GGTGACTGGTGAGAAAGTTATGGT 60.505 45.833 0.00 0.00 0.00 3.55
4896 6850 5.036117 TCCTATTGGGATGTAAGCAACTC 57.964 43.478 0.00 0.00 39.58 3.01
4956 6910 6.473758 ACTAGAGTTACAAAAGGAATCCACC 58.526 40.000 0.61 0.00 0.00 4.61
5002 6956 4.396790 TGACTAAAGGCTTTGTTGTCGTTT 59.603 37.500 22.32 0.00 0.00 3.60
5006 6960 4.893424 TGTGACTAAAGGCTTTGTTGTC 57.107 40.909 22.32 22.92 0.00 3.18
5057 7011 1.282653 TGGACAGGGGTGTGTGGAAA 61.283 55.000 0.00 0.00 0.00 3.13
5086 7040 9.686683 AAACAAAGATAGATACTAGCAACCATT 57.313 29.630 0.00 0.00 0.00 3.16
5152 7106 3.698029 AAATACAGCACGGCAATGATC 57.302 42.857 0.00 0.00 0.00 2.92
5160 7114 4.574421 TCCAATCATGTAAATACAGCACGG 59.426 41.667 0.00 0.00 39.92 4.94
5205 7159 5.772521 TGAAAGAAATAAAACAGAGGCAGC 58.227 37.500 0.00 0.00 0.00 5.25
5503 7461 3.129871 CTCAGCTATAGCAAGCCTCAAC 58.870 50.000 26.07 0.00 43.86 3.18
5701 7659 6.536941 GCTTTAGAGGACAGACAAAATAGAGG 59.463 42.308 0.00 0.00 0.00 3.69
5730 7688 5.104693 ACCCCGTCAGTCAACATAAATGATA 60.105 40.000 0.00 0.00 0.00 2.15
5757 7716 6.280855 CTCCAAAGTATAAAGTTTTGGGGG 57.719 41.667 13.46 5.48 44.85 5.40
5796 7755 2.104170 GAACGGAGTCCTGGAGAAGAT 58.896 52.381 7.77 0.00 45.00 2.40
5813 7772 4.699257 AGCTGAGATCATTCCAAGTTGAAC 59.301 41.667 3.87 0.00 0.00 3.18
5822 7781 9.364989 GTATATAAGAACAGCTGAGATCATTCC 57.635 37.037 23.35 0.00 0.00 3.01
5901 7860 5.753921 CCTCTGTCCCAAATTATAAGACGTC 59.246 44.000 7.70 7.70 0.00 4.34
5974 7933 1.452145 TTCTTGCCGCTCCCAACAAC 61.452 55.000 0.00 0.00 0.00 3.32
6012 7971 0.620556 CCACCAGTTCAGGGCTGTAT 59.379 55.000 0.00 0.00 32.41 2.29
6040 7999 2.224314 GCCCTTCAAAGAACTCGTTCAG 59.776 50.000 11.90 0.86 41.84 3.02
6114 8073 0.250989 CTTTGCGGGGTTGGGTCTTA 60.251 55.000 0.00 0.00 0.00 2.10
6238 8197 3.426859 CACTGAGACTACGAAACAGCAAG 59.573 47.826 0.00 0.00 32.67 4.01
6449 8408 8.652810 TGAGTACTAGGTAACAAGTGAAAAAC 57.347 34.615 0.00 0.00 41.41 2.43
6572 8532 9.494271 GAGTTGTATTAGAATTGCCATCTATGA 57.506 33.333 0.00 0.00 29.93 2.15
6678 8638 9.967346 GTCTCTGCTGTTATCTGTTATATGTTA 57.033 33.333 0.00 0.00 0.00 2.41
6679 8639 8.478066 TGTCTCTGCTGTTATCTGTTATATGTT 58.522 33.333 0.00 0.00 0.00 2.71
6680 8640 8.011844 TGTCTCTGCTGTTATCTGTTATATGT 57.988 34.615 0.00 0.00 0.00 2.29
6681 8641 8.877808 TTGTCTCTGCTGTTATCTGTTATATG 57.122 34.615 0.00 0.00 0.00 1.78
6690 8650 8.703604 TTGTAGTATTTGTCTCTGCTGTTATC 57.296 34.615 0.00 0.00 0.00 1.75
6715 8675 2.290641 TGTGCCCGTCTGGAATGTTAAT 60.291 45.455 0.00 0.00 37.49 1.40
6778 8798 8.458843 TCATGCTTTACTAATTTCCTTTAGCAC 58.541 33.333 0.00 0.00 38.72 4.40
6834 8854 2.455674 TTGTGTCGCTGAATGCTACT 57.544 45.000 0.00 0.00 38.09 2.57
6835 8855 2.672874 TGATTGTGTCGCTGAATGCTAC 59.327 45.455 0.00 0.00 40.11 3.58
6836 8856 2.931969 CTGATTGTGTCGCTGAATGCTA 59.068 45.455 0.00 0.00 40.11 3.49
6917 8937 5.067674 AGTGTTGCTCAAATTGCAGTCTTTA 59.932 36.000 0.00 0.00 41.71 1.85
6927 8947 5.922544 GCATAAGACAAGTGTTGCTCAAATT 59.077 36.000 0.00 0.00 0.00 1.82
6962 8982 2.791347 TTATTTGCCTGGCGACCTTA 57.209 45.000 14.98 0.00 0.00 2.69
7005 9026 1.110442 TTGGGTCTTTGGCTTGTGTG 58.890 50.000 0.00 0.00 0.00 3.82
7020 9041 1.821936 TGCAAGGCACTGTTTTGGG 59.178 52.632 0.00 0.00 40.86 4.12
7059 9080 2.584835 TCCAGGGAAACAGATGGTTG 57.415 50.000 0.00 0.00 40.35 3.77


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

AutoCloner maintained by Alex Coulton.