Multiple sequence alignment - TraesCS2D01G421200

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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 TraesCS2D01G421200 chr2D 100.000 5331 0 0 1 5331 534946813 534952143 0.000000e+00 9845.0
1 TraesCS2D01G421200 chr2D 100.000 175 0 0 5797 5971 534952609 534952783 2.080000e-84 324.0
2 TraesCS2D01G421200 chr2D 79.256 511 65 21 3948 4427 612496778 612497278 9.660000e-83 318.0
3 TraesCS2D01G421200 chr2A 92.255 5010 206 57 456 5330 678183893 678188855 0.000000e+00 6935.0
4 TraesCS2D01G421200 chr2A 85.185 324 29 10 149 471 678183512 678183817 1.250000e-81 315.0
5 TraesCS2D01G421200 chr2A 92.537 134 5 2 5799 5929 678188864 678188995 2.840000e-43 187.0
6 TraesCS2D01G421200 chr2B 92.800 4847 200 63 537 5291 636196789 636201578 0.000000e+00 6879.0
7 TraesCS2D01G421200 chr2B 90.000 70 5 1 2312 2381 636198738 636198805 8.240000e-14 89.8
8 TraesCS2D01G421200 chr7D 79.961 509 63 18 3948 4427 321954017 321954515 7.410000e-89 339.0
9 TraesCS2D01G421200 chr7D 79.412 272 30 19 4412 4661 534458460 534458727 1.030000e-37 169.0
10 TraesCS2D01G421200 chr7D 93.805 113 2 2 4262 4374 534458352 534458459 1.330000e-36 165.0
11 TraesCS2D01G421200 chr7B 79.843 511 63 20 3948 4427 342715564 342716065 2.670000e-88 337.0
12 TraesCS2D01G421200 chr7B 79.026 267 35 9 4415 4661 107162942 107162677 4.790000e-36 163.0
13 TraesCS2D01G421200 chr3D 79.568 509 66 17 3948 4427 401021688 401021189 4.460000e-86 329.0
14 TraesCS2D01G421200 chr3D 79.412 272 30 19 4412 4661 29209590 29209857 1.030000e-37 169.0
15 TraesCS2D01G421200 chr3D 86.420 162 10 5 4220 4374 29209433 29209589 3.700000e-37 167.0
16 TraesCS2D01G421200 chr3D 78.731 268 32 19 4416 4661 595685550 595685814 8.010000e-34 156.0
17 TraesCS2D01G421200 chr5B 85.185 162 12 5 4220 4374 684135266 684135422 8.010000e-34 156.0
18 TraesCS2D01G421200 chr4D 78.229 271 36 18 4412 4661 448167538 448167806 1.040000e-32 152.0
19 TraesCS2D01G421200 chr5A 78.022 273 36 17 4412 4662 141066373 141066643 3.730000e-32 150.0
20 TraesCS2D01G421200 chr6B 77.656 273 35 19 4411 4661 653356213 653355945 6.240000e-30 143.0


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 TraesCS2D01G421200 chr2D 534946813 534952783 5970 False 5084.5 9845 100.000000 1 5971 2 chr2D.!!$F2 5970
1 TraesCS2D01G421200 chr2D 612496778 612497278 500 False 318.0 318 79.256000 3948 4427 1 chr2D.!!$F1 479
2 TraesCS2D01G421200 chr2A 678183512 678188995 5483 False 2479.0 6935 89.992333 149 5929 3 chr2A.!!$F1 5780
3 TraesCS2D01G421200 chr2B 636196789 636201578 4789 False 3484.4 6879 91.400000 537 5291 2 chr2B.!!$F1 4754
4 TraesCS2D01G421200 chr7B 342715564 342716065 501 False 337.0 337 79.843000 3948 4427 1 chr7B.!!$F1 479

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
105 106 0.041386 AGGAGTTCGGCTAGGAACCT 59.959 55.000 7.91 0.0 45.82 3.50 F
431 433 0.249741 CAAGTAATACGGGGCCGAGG 60.250 60.000 0.00 0.0 42.83 4.63 F
947 1096 0.315251 TGCTCATAATCTCCCTCGCG 59.685 55.000 0.00 0.0 0.00 5.87 F
1104 1278 0.539986 GGATGAAGGACTACGGCCAA 59.460 55.000 2.24 0.0 0.00 4.52 F
1541 1740 0.671251 TTTCGATTGTGGTGTTGCCC 59.329 50.000 0.00 0.0 36.04 5.36 F
2266 2468 1.051008 ATGGCGGCAGATCTCACATA 58.949 50.000 19.29 0.0 0.00 2.29 F
2598 2835 1.204704 GTTGGCCTTTCAGGTATTGGC 59.795 52.381 3.32 0.0 42.56 4.52 F
2679 2916 1.375268 GGCTGCTCAGTCCAGTGAC 60.375 63.158 0.00 0.0 42.09 3.67 F
4183 4458 0.693049 TGCCTCCTCTTCCAAACTCC 59.307 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1590 0.895100 GTGCAGAATTCCAGCCCACA 60.895 55.000 15.47 0.00 0.00 4.17 R
2249 2451 0.390860 AGTATGTGAGATCTGCCGCC 59.609 55.000 0.00 0.00 0.00 6.13 R
2474 2711 3.884895 ACGGATGAATAAAGATGCCACA 58.115 40.909 0.00 0.00 0.00 4.17 R
2557 2794 4.074970 ACATGAGGCGTCAAGAGAAAATT 58.925 39.130 17.59 0.00 35.88 1.82 R
3233 3471 2.159327 AGCTTTGCAGGCATCAAAAC 57.841 45.000 14.52 2.39 33.60 2.43 R
3626 3865 0.804989 GGAAGGTTGGATCTGCAACG 59.195 55.000 8.23 0.00 32.50 4.10 R
3861 4105 1.003718 GGAAAGAGGTCCACCACGG 60.004 63.158 0.00 0.00 37.65 4.94 R
4524 4820 1.006043 GGGGGAAAAGAAGAAGAGGGG 59.994 57.143 0.00 0.00 0.00 4.79 R
5796 6114 0.417437 TCTCTCTTCATCCCCACCCA 59.583 55.000 0.00 0.00 0.00 4.51 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
94 95 8.873215 TTAATGAGATAGCTTTTAGGAGTTCG 57.127 34.615 0.00 0.00 0.00 3.95
95 96 5.263968 TGAGATAGCTTTTAGGAGTTCGG 57.736 43.478 0.00 0.00 0.00 4.30
96 97 4.052608 GAGATAGCTTTTAGGAGTTCGGC 58.947 47.826 0.00 0.00 0.00 5.54
97 98 3.707102 AGATAGCTTTTAGGAGTTCGGCT 59.293 43.478 0.00 0.00 0.00 5.52
98 99 4.894114 AGATAGCTTTTAGGAGTTCGGCTA 59.106 41.667 0.00 0.00 35.71 3.93
99 100 3.528597 AGCTTTTAGGAGTTCGGCTAG 57.471 47.619 0.00 0.00 0.00 3.42
100 101 2.168728 AGCTTTTAGGAGTTCGGCTAGG 59.831 50.000 0.00 0.00 0.00 3.02
101 102 2.167900 GCTTTTAGGAGTTCGGCTAGGA 59.832 50.000 0.00 0.00 0.00 2.94
102 103 3.369157 GCTTTTAGGAGTTCGGCTAGGAA 60.369 47.826 0.00 0.00 0.00 3.36
103 104 3.881937 TTTAGGAGTTCGGCTAGGAAC 57.118 47.619 4.25 4.25 45.19 3.62
104 105 1.772836 TAGGAGTTCGGCTAGGAACC 58.227 55.000 7.91 0.00 45.82 3.62
105 106 0.041386 AGGAGTTCGGCTAGGAACCT 59.959 55.000 7.91 0.00 45.82 3.50
106 107 0.460722 GGAGTTCGGCTAGGAACCTC 59.539 60.000 7.91 5.88 45.82 3.85
107 108 1.476477 GAGTTCGGCTAGGAACCTCT 58.524 55.000 7.91 0.00 45.82 3.69
108 109 1.826096 GAGTTCGGCTAGGAACCTCTT 59.174 52.381 7.91 0.00 45.82 2.85
109 110 1.826096 AGTTCGGCTAGGAACCTCTTC 59.174 52.381 7.91 0.00 45.82 2.87
110 111 1.826096 GTTCGGCTAGGAACCTCTTCT 59.174 52.381 0.00 0.00 40.28 2.85
111 112 2.233305 TCGGCTAGGAACCTCTTCTT 57.767 50.000 0.00 0.00 0.00 2.52
112 113 2.537143 TCGGCTAGGAACCTCTTCTTT 58.463 47.619 0.00 0.00 0.00 2.52
113 114 2.904434 TCGGCTAGGAACCTCTTCTTTT 59.096 45.455 0.00 0.00 0.00 2.27
114 115 4.091549 TCGGCTAGGAACCTCTTCTTTTA 58.908 43.478 0.00 0.00 0.00 1.52
115 116 4.529377 TCGGCTAGGAACCTCTTCTTTTAA 59.471 41.667 0.00 0.00 0.00 1.52
116 117 4.630505 CGGCTAGGAACCTCTTCTTTTAAC 59.369 45.833 0.00 0.00 0.00 2.01
117 118 5.569026 CGGCTAGGAACCTCTTCTTTTAACT 60.569 44.000 0.00 0.00 0.00 2.24
118 119 5.875910 GGCTAGGAACCTCTTCTTTTAACTC 59.124 44.000 0.00 0.00 0.00 3.01
119 120 5.875910 GCTAGGAACCTCTTCTTTTAACTCC 59.124 44.000 0.00 0.00 0.00 3.85
120 121 6.295973 GCTAGGAACCTCTTCTTTTAACTCCT 60.296 42.308 0.00 0.00 35.09 3.69
121 122 6.116711 AGGAACCTCTTCTTTTAACTCCTC 57.883 41.667 0.00 0.00 0.00 3.71
122 123 5.607171 AGGAACCTCTTCTTTTAACTCCTCA 59.393 40.000 0.00 0.00 0.00 3.86
123 124 6.101296 AGGAACCTCTTCTTTTAACTCCTCAA 59.899 38.462 0.00 0.00 0.00 3.02
124 125 6.428465 GGAACCTCTTCTTTTAACTCCTCAAG 59.572 42.308 0.00 0.00 0.00 3.02
125 126 6.502074 ACCTCTTCTTTTAACTCCTCAAGT 57.498 37.500 0.00 0.00 41.10 3.16
127 128 7.347252 ACCTCTTCTTTTAACTCCTCAAGTTT 58.653 34.615 0.00 0.00 46.26 2.66
128 129 8.491958 ACCTCTTCTTTTAACTCCTCAAGTTTA 58.508 33.333 0.00 0.00 46.26 2.01
129 130 9.338622 CCTCTTCTTTTAACTCCTCAAGTTTAA 57.661 33.333 0.00 0.00 46.26 1.52
131 132 9.338622 TCTTCTTTTAACTCCTCAAGTTTAAGG 57.661 33.333 0.00 0.00 46.26 2.69
132 133 9.121658 CTTCTTTTAACTCCTCAAGTTTAAGGT 57.878 33.333 0.00 0.00 46.26 3.50
133 134 8.446599 TCTTTTAACTCCTCAAGTTTAAGGTG 57.553 34.615 0.00 2.38 46.26 4.00
134 135 7.501225 TCTTTTAACTCCTCAAGTTTAAGGTGG 59.499 37.037 0.00 0.00 46.26 4.61
135 136 3.141767 ACTCCTCAAGTTTAAGGTGGC 57.858 47.619 7.63 0.00 33.03 5.01
136 137 2.711547 ACTCCTCAAGTTTAAGGTGGCT 59.288 45.455 7.63 0.00 33.03 4.75
137 138 3.138468 ACTCCTCAAGTTTAAGGTGGCTT 59.862 43.478 7.63 0.00 33.03 4.35
138 139 4.145052 CTCCTCAAGTTTAAGGTGGCTTT 58.855 43.478 1.84 0.00 34.12 3.51
139 140 4.542697 TCCTCAAGTTTAAGGTGGCTTTT 58.457 39.130 1.84 0.00 34.12 2.27
140 141 4.340950 TCCTCAAGTTTAAGGTGGCTTTTG 59.659 41.667 1.84 0.00 34.12 2.44
141 142 4.340950 CCTCAAGTTTAAGGTGGCTTTTGA 59.659 41.667 0.00 0.00 0.00 2.69
142 143 5.163457 CCTCAAGTTTAAGGTGGCTTTTGAA 60.163 40.000 0.00 0.00 0.00 2.69
143 144 6.462909 CCTCAAGTTTAAGGTGGCTTTTGAAT 60.463 38.462 0.00 0.00 0.00 2.57
144 145 6.279882 TCAAGTTTAAGGTGGCTTTTGAATG 58.720 36.000 0.00 0.00 0.00 2.67
145 146 5.213891 AGTTTAAGGTGGCTTTTGAATGG 57.786 39.130 0.00 0.00 0.00 3.16
146 147 3.676291 TTAAGGTGGCTTTTGAATGGC 57.324 42.857 0.00 0.00 0.00 4.40
147 148 1.720781 AAGGTGGCTTTTGAATGGCT 58.279 45.000 5.11 0.00 0.00 4.75
154 155 5.473162 GGTGGCTTTTGAATGGCTAAATTTT 59.527 36.000 0.00 0.00 0.00 1.82
155 156 6.016360 GGTGGCTTTTGAATGGCTAAATTTTT 60.016 34.615 0.00 0.00 0.00 1.94
159 160 6.206438 GCTTTTGAATGGCTAAATTTTTGGGA 59.794 34.615 0.00 0.00 0.00 4.37
161 162 8.703378 TTTTGAATGGCTAAATTTTTGGGATT 57.297 26.923 0.00 0.00 0.00 3.01
163 164 7.013823 TGAATGGCTAAATTTTTGGGATTCA 57.986 32.000 0.00 2.67 0.00 2.57
167 168 9.972106 AATGGCTAAATTTTTGGGATTCAATTA 57.028 25.926 0.00 0.00 34.98 1.40
215 216 6.762187 ACACAGATGAGCTGAATAAAGATCAG 59.238 38.462 4.05 0.00 45.10 2.90
229 230 9.740239 GAATAAAGATCAGCAAGAAATATGCAA 57.260 29.630 0.00 0.00 46.22 4.08
243 244 8.133024 AGAAATATGCAAATTTGGGTTAGTGA 57.867 30.769 19.47 0.00 0.00 3.41
256 257 4.819630 TGGGTTAGTGATTAAATCCGCATC 59.180 41.667 0.00 0.00 0.00 3.91
260 261 4.156455 AGTGATTAAATCCGCATCTGGT 57.844 40.909 0.00 0.00 0.00 4.00
267 268 7.336679 TGATTAAATCCGCATCTGGTATTATGG 59.663 37.037 0.00 0.00 0.00 2.74
305 306 3.610911 CCTTCGGATGGGAATATAAGCC 58.389 50.000 2.05 0.00 0.00 4.35
306 307 3.262420 CTTCGGATGGGAATATAAGCCG 58.738 50.000 0.00 0.00 38.68 5.52
311 312 1.072266 TGGGAATATAAGCCGGGCAT 58.928 50.000 23.09 12.62 0.00 4.40
327 328 2.291605 GGGCATGGGTTTCTAGGTCTTT 60.292 50.000 0.00 0.00 0.00 2.52
328 329 3.053917 GGGCATGGGTTTCTAGGTCTTTA 60.054 47.826 0.00 0.00 0.00 1.85
339 340 8.343366 GGTTTCTAGGTCTTTAGTTTGACAAAG 58.657 37.037 0.00 0.00 35.11 2.77
351 353 8.918202 TTAGTTTGACAAAGGAATCAGTATGT 57.082 30.769 0.00 0.00 37.40 2.29
375 377 8.472413 TGTCATAAAACTACATGGTACTACCTC 58.528 37.037 6.79 0.00 39.58 3.85
380 382 4.396522 ACTACATGGTACTACCTCCGATC 58.603 47.826 6.79 0.00 39.58 3.69
389 391 5.948162 GGTACTACCTCCGATCCAATACATA 59.052 44.000 0.00 0.00 34.73 2.29
392 394 9.182214 GTACTACCTCCGATCCAATACATATAA 57.818 37.037 0.00 0.00 0.00 0.98
393 395 8.294954 ACTACCTCCGATCCAATACATATAAG 57.705 38.462 0.00 0.00 0.00 1.73
394 396 8.114102 ACTACCTCCGATCCAATACATATAAGA 58.886 37.037 0.00 0.00 0.00 2.10
395 397 7.979786 ACCTCCGATCCAATACATATAAGAT 57.020 36.000 0.00 0.00 0.00 2.40
396 398 7.786030 ACCTCCGATCCAATACATATAAGATG 58.214 38.462 0.00 0.00 0.00 2.90
397 399 7.400339 ACCTCCGATCCAATACATATAAGATGT 59.600 37.037 0.00 0.00 36.13 3.06
398 400 8.914011 CCTCCGATCCAATACATATAAGATGTA 58.086 37.037 0.00 0.00 38.66 2.29
401 403 9.698309 CCGATCCAATACATATAAGATGTATCC 57.302 37.037 9.44 0.00 42.48 2.59
402 404 9.399403 CGATCCAATACATATAAGATGTATCCG 57.601 37.037 9.44 5.33 42.48 4.18
410 412 7.671302 ACATATAAGATGTATCCGTTTCAGCT 58.329 34.615 0.00 0.00 0.00 4.24
413 415 5.339008 AAGATGTATCCGTTTCAGCTACA 57.661 39.130 0.00 0.00 0.00 2.74
426 428 2.101917 TCAGCTACAAGTAATACGGGGC 59.898 50.000 0.00 0.00 0.00 5.80
429 431 1.682854 CTACAAGTAATACGGGGCCGA 59.317 52.381 0.00 0.00 42.83 5.54
430 432 0.462789 ACAAGTAATACGGGGCCGAG 59.537 55.000 0.00 0.00 42.83 4.63
431 433 0.249741 CAAGTAATACGGGGCCGAGG 60.250 60.000 0.00 0.00 42.83 4.63
432 434 2.030113 GTAATACGGGGCCGAGGC 59.970 66.667 5.37 5.37 42.83 4.70
461 463 6.072119 GGGAGTAAGAAAATTCGTCCAACAAT 60.072 38.462 0.00 0.00 0.00 2.71
471 473 6.668541 ATTCGTCCAACAATGATTGTAGAG 57.331 37.500 11.70 4.96 44.59 2.43
472 474 5.400066 TCGTCCAACAATGATTGTAGAGA 57.600 39.130 11.70 6.05 44.59 3.10
473 475 5.410924 TCGTCCAACAATGATTGTAGAGAG 58.589 41.667 11.70 8.69 44.59 3.20
474 476 5.185056 TCGTCCAACAATGATTGTAGAGAGA 59.815 40.000 11.70 10.55 44.59 3.10
476 478 6.166279 GTCCAACAATGATTGTAGAGAGACA 58.834 40.000 11.70 0.00 44.59 3.41
492 588 3.701040 AGAGACATGTTTTTGTGGCAAGT 59.299 39.130 0.00 0.00 0.00 3.16
498 594 3.502920 TGTTTTTGTGGCAAGTAACGTG 58.497 40.909 0.00 0.00 0.00 4.49
503 599 1.666553 TGGCAAGTAACGTGCTCCG 60.667 57.895 7.45 0.00 41.88 4.63
534 630 6.049149 GCTAGTCAAATGCAGTAGATAACCA 58.951 40.000 0.00 0.00 0.00 3.67
588 684 7.816411 AGGGAGTAAAATTATCAGCCAAGTAT 58.184 34.615 0.00 0.00 0.00 2.12
589 685 8.945193 AGGGAGTAAAATTATCAGCCAAGTATA 58.055 33.333 0.00 0.00 0.00 1.47
590 686 9.220767 GGGAGTAAAATTATCAGCCAAGTATAG 57.779 37.037 0.00 0.00 0.00 1.31
591 687 9.780186 GGAGTAAAATTATCAGCCAAGTATAGT 57.220 33.333 0.00 0.00 0.00 2.12
642 741 2.751436 GTGGTCGCCATGGCATGT 60.751 61.111 34.93 0.00 42.06 3.21
651 750 0.659427 CCATGGCATGTGTAGCTTCG 59.341 55.000 24.80 3.63 0.00 3.79
947 1096 0.315251 TGCTCATAATCTCCCTCGCG 59.685 55.000 0.00 0.00 0.00 5.87
1104 1278 0.539986 GGATGAAGGACTACGGCCAA 59.460 55.000 2.24 0.00 0.00 4.52
1181 1355 1.313091 CGGGACATCGAGGTGAGACA 61.313 60.000 7.79 0.00 0.00 3.41
1182 1356 1.115467 GGGACATCGAGGTGAGACAT 58.885 55.000 7.79 0.00 0.00 3.06
1185 1359 2.688446 GGACATCGAGGTGAGACATACA 59.312 50.000 7.79 0.00 0.00 2.29
1206 1388 3.515286 CCCAATGCGCTGCTCCTG 61.515 66.667 9.73 0.00 0.00 3.86
1326 1525 5.154222 GGCATAACAAGTTACTTTCTGCAC 58.846 41.667 14.00 4.28 0.00 4.57
1340 1539 3.080300 TCTGCACCGGGATTGTTAATT 57.920 42.857 6.32 0.00 0.00 1.40
1391 1590 5.184864 TGGAATTATGCTTGTCGATTTGGTT 59.815 36.000 0.00 0.00 0.00 3.67
1412 1611 1.675641 GGGCTGGAATTCTGCACGT 60.676 57.895 19.73 0.00 41.38 4.49
1424 1623 0.957395 CTGCACGTGGAGCTGGATTT 60.957 55.000 24.45 0.00 0.00 2.17
1504 1703 3.562973 AGCAGCAATGTAAATCTCCATCG 59.437 43.478 0.00 0.00 0.00 3.84
1541 1740 0.671251 TTTCGATTGTGGTGTTGCCC 59.329 50.000 0.00 0.00 36.04 5.36
1584 1783 3.430895 GCATCTGTTTGCCATTTTGACAG 59.569 43.478 0.00 0.00 39.16 3.51
1702 1901 3.416156 AGGTCAGAGTTCCTTCATTTGC 58.584 45.455 0.00 0.00 0.00 3.68
1913 2115 2.123077 AGCCATCTCGGAGGGGAG 60.123 66.667 17.29 1.93 33.70 4.30
1997 2199 5.480422 TCCTGTTTTCTGATACTGCAGTCTA 59.520 40.000 25.56 7.32 37.20 2.59
2259 2461 1.896220 TTATTCCATGGCGGCAGATC 58.104 50.000 19.29 0.00 33.14 2.75
2266 2468 1.051008 ATGGCGGCAGATCTCACATA 58.949 50.000 19.29 0.00 0.00 2.29
2279 2481 7.404985 CAGATCTCACATACTGTAAATTGTGC 58.595 38.462 12.83 2.78 39.39 4.57
2298 2500 3.062099 GTGCACATCACTGTTATACACCG 59.938 47.826 13.17 0.00 42.38 4.94
2401 2637 2.225019 CCATAGCGGCAGATTTCACATC 59.775 50.000 1.45 0.00 0.00 3.06
2486 2723 6.747414 ACTATATCCAGTGTGGCATCTTTA 57.253 37.500 0.00 0.00 37.47 1.85
2494 2731 3.879295 AGTGTGGCATCTTTATTCATCCG 59.121 43.478 0.00 0.00 0.00 4.18
2528 2765 5.403466 GGAATTGCATTTCGCTGATAATTCC 59.597 40.000 13.59 0.00 40.32 3.01
2539 2776 6.223852 TCGCTGATAATTCCAATCTCCTTAC 58.776 40.000 0.00 0.00 0.00 2.34
2571 2808 9.778993 ATTGATCATTGTAATTTTCTCTTGACG 57.221 29.630 0.00 0.00 0.00 4.35
2598 2835 1.204704 GTTGGCCTTTCAGGTATTGGC 59.795 52.381 3.32 0.00 42.56 4.52
2679 2916 1.375268 GGCTGCTCAGTCCAGTGAC 60.375 63.158 0.00 0.00 42.09 3.67
2695 2932 9.654663 AGTCCAGTGACAGTAATATCTTTTAAC 57.345 33.333 0.00 0.00 44.33 2.01
2852 3090 3.798337 CACACGCAAATTCTTTGAAAGCT 59.202 39.130 0.00 0.00 43.26 3.74
2905 3143 9.057089 CAGGTAAGAACAAGTACAGAATTTTCT 57.943 33.333 0.00 0.00 38.25 2.52
2950 3188 6.400303 GCAATTCAACAAACATGTGCATACTC 60.400 38.462 0.00 0.00 0.00 2.59
3115 3353 3.006967 ACCGTGTTGCATCTTCTCTTACT 59.993 43.478 0.00 0.00 0.00 2.24
3170 3408 2.489971 TGGTCAGGAAGCAAAGTTACG 58.510 47.619 0.00 0.00 30.91 3.18
3181 3419 5.541098 AGCAAAGTTACGGTTTATAGCAC 57.459 39.130 0.00 0.00 0.00 4.40
3233 3471 7.020010 GTGTGATCTGAGAGTTTAAATGCAAG 58.980 38.462 0.00 0.00 0.00 4.01
3378 3616 4.649674 GCCGGTAATCTCCCATAGATATGA 59.350 45.833 1.90 0.00 44.56 2.15
3553 3791 5.416947 GGAGTTGATAACGTATTGGTGAGT 58.583 41.667 0.00 0.00 36.23 3.41
3580 3819 2.350804 CGCTTTGAGGTGTCATCTGATG 59.649 50.000 11.42 11.42 30.85 3.07
3641 3880 1.573829 TTCGCGTTGCAGATCCAACC 61.574 55.000 5.77 2.80 41.50 3.77
3861 4105 5.009610 TGTTGGAGTATTTGTTCAAAGAGGC 59.990 40.000 4.37 0.00 0.00 4.70
4018 4274 4.974645 TTCCCTCAATAACTGTGACACT 57.025 40.909 7.20 0.00 0.00 3.55
4020 4276 4.641396 TCCCTCAATAACTGTGACACTTG 58.359 43.478 7.20 2.81 0.00 3.16
4034 4290 9.120538 ACTGTGACACTTGAAACTAACATATTT 57.879 29.630 7.20 0.00 0.00 1.40
4137 4396 3.428870 CGTGTGAGTGTTTCTGTATCCAC 59.571 47.826 0.00 0.00 0.00 4.02
4183 4458 0.693049 TGCCTCCTCTTCCAAACTCC 59.307 55.000 0.00 0.00 0.00 3.85
4205 4483 4.922103 CCGAGTCTGGTTTTACAGTAGTTC 59.078 45.833 0.00 0.00 39.48 3.01
4334 4629 3.693085 ACTTGGCAATTGACATGCTCTAG 59.307 43.478 23.39 15.34 43.34 2.43
4524 4820 5.579718 TCGAGGTTCGATTTCTATTCTGTC 58.420 41.667 0.00 0.00 44.82 3.51
4575 4871 6.584185 TTGGGTTTAAAAGCTTGAGATACC 57.416 37.500 0.00 4.65 0.00 2.73
4790 5087 2.303175 GTTTGCCTGTACCCTGAAACA 58.697 47.619 0.00 0.00 0.00 2.83
4796 5093 2.553028 CCTGTACCCTGAAACATGCAGT 60.553 50.000 0.00 0.00 0.00 4.40
4803 5100 4.760204 ACCCTGAAACATGCAGTACTAAAC 59.240 41.667 0.00 0.00 0.00 2.01
4827 5124 1.531423 ACTCAGGCATTGCAAGACAG 58.469 50.000 11.39 0.00 0.00 3.51
4839 5136 2.291465 TGCAAGACAGAACAGATTGTGC 59.709 45.455 0.00 0.00 32.28 4.57
4858 5155 1.684248 GCTGGCCACCTTTCTCATGAT 60.684 52.381 0.00 0.00 0.00 2.45
4978 5275 1.001268 GATCTCGTTCTAGGCGCATCA 60.001 52.381 10.83 0.00 0.00 3.07
4983 5280 1.735700 CGTTCTAGGCGCATCAGTTCA 60.736 52.381 10.83 0.00 0.00 3.18
4984 5281 1.661112 GTTCTAGGCGCATCAGTTCAC 59.339 52.381 10.83 0.00 0.00 3.18
4990 5287 1.284982 GCGCATCAGTTCACGACAGT 61.285 55.000 0.30 0.00 0.00 3.55
5013 5310 2.715046 CAGCAAATGGAGGAAGCAGTA 58.285 47.619 0.00 0.00 0.00 2.74
5045 5351 0.602638 TGCAAGGTCGAACGAATGCT 60.603 50.000 22.97 0.00 34.06 3.79
5046 5352 0.095417 GCAAGGTCGAACGAATGCTC 59.905 55.000 17.84 0.30 31.85 4.26
5139 5451 6.423905 GCAGACTGTTGTATCTTTTGTGAGTA 59.576 38.462 3.99 0.00 0.00 2.59
5192 5504 6.649436 GCTTTTGCCATTTGTAACTCTTTTC 58.351 36.000 0.00 0.00 40.15 2.29
5265 5577 3.063997 CCCATTTATCTGCTGTCACGTTC 59.936 47.826 0.00 0.00 0.00 3.95
5301 5613 3.266772 TCTGAACCCCATTTATCTGTGCT 59.733 43.478 0.00 0.00 0.00 4.40
5310 5628 4.946157 CCATTTATCTGTGCTCTTGTCCTT 59.054 41.667 0.00 0.00 0.00 3.36
5318 5636 6.061441 TCTGTGCTCTTGTCCTTTCAAATTA 58.939 36.000 0.00 0.00 0.00 1.40
5330 5648 5.476599 TCCTTTCAAATTACCTGGACACATG 59.523 40.000 0.00 0.00 0.00 3.21
5874 6195 2.109181 GGCAGGCTATCCGGTCAC 59.891 66.667 0.00 0.00 37.47 3.67
5929 6250 1.747355 GACCATTCGACCGTCCTTAGA 59.253 52.381 0.00 0.00 0.00 2.10
5930 6251 1.749634 ACCATTCGACCGTCCTTAGAG 59.250 52.381 0.00 0.00 0.00 2.43
5931 6252 1.536284 CCATTCGACCGTCCTTAGAGC 60.536 57.143 0.00 0.00 0.00 4.09
5932 6253 1.134367 CATTCGACCGTCCTTAGAGCA 59.866 52.381 0.00 0.00 0.00 4.26
5933 6254 1.471119 TTCGACCGTCCTTAGAGCAT 58.529 50.000 0.00 0.00 0.00 3.79
5934 6255 1.022735 TCGACCGTCCTTAGAGCATC 58.977 55.000 0.00 0.00 0.00 3.91
5947 6268 1.005340 GAGCATCTTCAACAGGAGCG 58.995 55.000 0.00 0.00 0.00 5.03
5948 6269 1.023513 AGCATCTTCAACAGGAGCGC 61.024 55.000 0.00 0.00 0.00 5.92
5949 6270 1.023513 GCATCTTCAACAGGAGCGCT 61.024 55.000 11.27 11.27 0.00 5.92
5950 6271 1.740380 GCATCTTCAACAGGAGCGCTA 60.740 52.381 11.50 0.00 0.00 4.26
5951 6272 2.621338 CATCTTCAACAGGAGCGCTAA 58.379 47.619 11.50 0.00 0.00 3.09
5952 6273 2.831685 TCTTCAACAGGAGCGCTAAA 57.168 45.000 11.50 0.00 0.00 1.85
5953 6274 2.413837 TCTTCAACAGGAGCGCTAAAC 58.586 47.619 11.50 3.56 0.00 2.01
5954 6275 2.143122 CTTCAACAGGAGCGCTAAACA 58.857 47.619 11.50 0.00 0.00 2.83
5955 6276 2.248280 TCAACAGGAGCGCTAAACAA 57.752 45.000 11.50 0.00 0.00 2.83
5956 6277 2.143122 TCAACAGGAGCGCTAAACAAG 58.857 47.619 11.50 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 9.314321 CGAACTCCTAAAAGCTATCTCATTAAA 57.686 33.333 0.00 0.00 0.00 1.52
69 70 7.926555 CCGAACTCCTAAAAGCTATCTCATTAA 59.073 37.037 0.00 0.00 0.00 1.40
70 71 7.434492 CCGAACTCCTAAAAGCTATCTCATTA 58.566 38.462 0.00 0.00 0.00 1.90
71 72 6.284459 CCGAACTCCTAAAAGCTATCTCATT 58.716 40.000 0.00 0.00 0.00 2.57
72 73 5.740513 GCCGAACTCCTAAAAGCTATCTCAT 60.741 44.000 0.00 0.00 0.00 2.90
73 74 4.441634 GCCGAACTCCTAAAAGCTATCTCA 60.442 45.833 0.00 0.00 0.00 3.27
74 75 4.052608 GCCGAACTCCTAAAAGCTATCTC 58.947 47.826 0.00 0.00 0.00 2.75
75 76 3.707102 AGCCGAACTCCTAAAAGCTATCT 59.293 43.478 0.00 0.00 0.00 1.98
76 77 4.061357 AGCCGAACTCCTAAAAGCTATC 57.939 45.455 0.00 0.00 0.00 2.08
77 78 4.039366 CCTAGCCGAACTCCTAAAAGCTAT 59.961 45.833 0.00 0.00 31.50 2.97
78 79 3.383825 CCTAGCCGAACTCCTAAAAGCTA 59.616 47.826 0.00 0.00 0.00 3.32
79 80 2.168728 CCTAGCCGAACTCCTAAAAGCT 59.831 50.000 0.00 0.00 0.00 3.74
80 81 2.167900 TCCTAGCCGAACTCCTAAAAGC 59.832 50.000 0.00 0.00 0.00 3.51
81 82 4.182339 GTTCCTAGCCGAACTCCTAAAAG 58.818 47.826 5.02 0.00 39.27 2.27
82 83 3.055602 GGTTCCTAGCCGAACTCCTAAAA 60.056 47.826 10.50 0.00 41.58 1.52
83 84 2.498885 GGTTCCTAGCCGAACTCCTAAA 59.501 50.000 10.50 0.00 41.58 1.85
84 85 2.105766 GGTTCCTAGCCGAACTCCTAA 58.894 52.381 10.50 0.00 41.58 2.69
85 86 1.287146 AGGTTCCTAGCCGAACTCCTA 59.713 52.381 10.50 0.00 41.58 2.94
86 87 0.041386 AGGTTCCTAGCCGAACTCCT 59.959 55.000 10.50 0.32 41.58 3.69
87 88 0.460722 GAGGTTCCTAGCCGAACTCC 59.539 60.000 10.50 0.00 41.58 3.85
88 89 1.476477 AGAGGTTCCTAGCCGAACTC 58.524 55.000 10.50 4.17 41.58 3.01
89 90 1.826096 GAAGAGGTTCCTAGCCGAACT 59.174 52.381 10.50 0.00 41.58 3.01
90 91 1.826096 AGAAGAGGTTCCTAGCCGAAC 59.174 52.381 3.91 3.91 41.21 3.95
91 92 2.233305 AGAAGAGGTTCCTAGCCGAA 57.767 50.000 0.00 0.00 32.48 4.30
92 93 2.233305 AAGAAGAGGTTCCTAGCCGA 57.767 50.000 0.00 0.00 32.48 5.54
93 94 3.336138 AAAAGAAGAGGTTCCTAGCCG 57.664 47.619 0.00 0.00 32.48 5.52
94 95 5.806818 AGTTAAAAGAAGAGGTTCCTAGCC 58.193 41.667 0.00 0.00 32.48 3.93
95 96 5.875910 GGAGTTAAAAGAAGAGGTTCCTAGC 59.124 44.000 0.00 0.00 32.48 3.42
96 97 7.038941 TGAGGAGTTAAAAGAAGAGGTTCCTAG 60.039 40.741 0.00 0.00 32.95 3.02
97 98 6.785963 TGAGGAGTTAAAAGAAGAGGTTCCTA 59.214 38.462 0.00 0.00 32.95 2.94
98 99 5.607171 TGAGGAGTTAAAAGAAGAGGTTCCT 59.393 40.000 0.00 0.00 35.36 3.36
99 100 5.866207 TGAGGAGTTAAAAGAAGAGGTTCC 58.134 41.667 0.00 0.00 32.48 3.62
100 101 6.993308 ACTTGAGGAGTTAAAAGAAGAGGTTC 59.007 38.462 0.00 0.00 33.92 3.62
101 102 6.901300 ACTTGAGGAGTTAAAAGAAGAGGTT 58.099 36.000 0.00 0.00 33.92 3.50
102 103 6.502074 ACTTGAGGAGTTAAAAGAAGAGGT 57.498 37.500 0.00 0.00 33.92 3.85
115 116 2.711547 AGCCACCTTAAACTTGAGGAGT 59.288 45.455 7.24 0.00 41.47 3.85
116 117 3.425162 AGCCACCTTAAACTTGAGGAG 57.575 47.619 7.24 0.00 37.39 3.69
117 118 3.876309 AAGCCACCTTAAACTTGAGGA 57.124 42.857 7.24 0.00 37.39 3.71
118 119 4.340950 TCAAAAGCCACCTTAAACTTGAGG 59.659 41.667 0.00 0.00 39.65 3.86
119 120 5.514274 TCAAAAGCCACCTTAAACTTGAG 57.486 39.130 0.00 0.00 0.00 3.02
120 121 5.923733 TTCAAAAGCCACCTTAAACTTGA 57.076 34.783 0.00 0.00 0.00 3.02
121 122 5.466393 CCATTCAAAAGCCACCTTAAACTTG 59.534 40.000 0.00 0.00 0.00 3.16
122 123 5.610398 CCATTCAAAAGCCACCTTAAACTT 58.390 37.500 0.00 0.00 0.00 2.66
123 124 4.503123 GCCATTCAAAAGCCACCTTAAACT 60.503 41.667 0.00 0.00 0.00 2.66
124 125 3.745975 GCCATTCAAAAGCCACCTTAAAC 59.254 43.478 0.00 0.00 0.00 2.01
125 126 3.645687 AGCCATTCAAAAGCCACCTTAAA 59.354 39.130 0.00 0.00 0.00 1.52
126 127 3.238597 AGCCATTCAAAAGCCACCTTAA 58.761 40.909 0.00 0.00 0.00 1.85
127 128 2.888212 AGCCATTCAAAAGCCACCTTA 58.112 42.857 0.00 0.00 0.00 2.69
128 129 1.720781 AGCCATTCAAAAGCCACCTT 58.279 45.000 0.00 0.00 0.00 3.50
129 130 2.603075 TAGCCATTCAAAAGCCACCT 57.397 45.000 0.00 0.00 0.00 4.00
130 131 3.676291 TTTAGCCATTCAAAAGCCACC 57.324 42.857 0.00 0.00 0.00 4.61
131 132 6.558771 AAAATTTAGCCATTCAAAAGCCAC 57.441 33.333 0.00 0.00 0.00 5.01
132 133 6.016443 CCAAAAATTTAGCCATTCAAAAGCCA 60.016 34.615 0.00 0.00 0.00 4.75
133 134 6.380995 CCAAAAATTTAGCCATTCAAAAGCC 58.619 36.000 0.00 0.00 0.00 4.35
134 135 6.206438 TCCCAAAAATTTAGCCATTCAAAAGC 59.794 34.615 0.00 0.00 0.00 3.51
135 136 7.742556 TCCCAAAAATTTAGCCATTCAAAAG 57.257 32.000 0.00 0.00 0.00 2.27
136 137 8.703378 AATCCCAAAAATTTAGCCATTCAAAA 57.297 26.923 0.00 0.00 0.00 2.44
137 138 7.941238 TGAATCCCAAAAATTTAGCCATTCAAA 59.059 29.630 0.00 0.00 0.00 2.69
138 139 7.456725 TGAATCCCAAAAATTTAGCCATTCAA 58.543 30.769 0.00 0.00 0.00 2.69
139 140 7.013823 TGAATCCCAAAAATTTAGCCATTCA 57.986 32.000 0.00 0.43 0.00 2.57
140 141 7.920160 TTGAATCCCAAAAATTTAGCCATTC 57.080 32.000 0.00 0.00 0.00 2.67
141 142 8.882557 AATTGAATCCCAAAAATTTAGCCATT 57.117 26.923 0.00 0.00 38.43 3.16
142 143 9.972106 TTAATTGAATCCCAAAAATTTAGCCAT 57.028 25.926 0.00 0.00 38.43 4.40
143 144 9.799106 TTTAATTGAATCCCAAAAATTTAGCCA 57.201 25.926 0.00 0.00 38.43 4.75
154 155 5.279685 AGGGCATCTTTAATTGAATCCCAA 58.720 37.500 14.92 0.00 39.41 4.12
155 156 4.882559 AGGGCATCTTTAATTGAATCCCA 58.117 39.130 14.92 0.00 33.98 4.37
159 160 7.716799 TGTGTAAGGGCATCTTTAATTGAAT 57.283 32.000 0.00 0.00 36.93 2.57
161 162 6.663093 ACATGTGTAAGGGCATCTTTAATTGA 59.337 34.615 0.00 0.00 36.93 2.57
163 164 8.588290 TTACATGTGTAAGGGCATCTTTAATT 57.412 30.769 9.11 0.00 35.75 1.40
167 168 7.067008 GTGTATTACATGTGTAAGGGCATCTTT 59.933 37.037 9.11 0.00 42.94 2.52
215 216 6.499234 AACCCAAATTTGCATATTTCTTGC 57.501 33.333 12.92 0.00 40.55 4.01
229 230 6.153680 TGCGGATTTAATCACTAACCCAAATT 59.846 34.615 7.29 0.00 0.00 1.82
243 244 6.095440 GCCATAATACCAGATGCGGATTTAAT 59.905 38.462 0.00 0.00 0.00 1.40
305 306 0.463833 GACCTAGAAACCCATGCCCG 60.464 60.000 0.00 0.00 0.00 6.13
306 307 0.919710 AGACCTAGAAACCCATGCCC 59.080 55.000 0.00 0.00 0.00 5.36
311 312 6.126710 TGTCAAACTAAAGACCTAGAAACCCA 60.127 38.462 0.00 0.00 33.89 4.51
318 319 8.622948 ATTCCTTTGTCAAACTAAAGACCTAG 57.377 34.615 0.00 0.00 36.29 3.02
327 328 8.154203 TGACATACTGATTCCTTTGTCAAACTA 58.846 33.333 1.38 0.00 40.14 2.24
328 329 6.998074 TGACATACTGATTCCTTTGTCAAACT 59.002 34.615 1.38 0.00 40.14 2.66
351 353 7.201848 CGGAGGTAGTACCATGTAGTTTTATGA 60.202 40.741 21.49 0.00 41.95 2.15
366 368 5.979288 ATGTATTGGATCGGAGGTAGTAC 57.021 43.478 0.00 0.00 0.00 2.73
368 370 8.114102 TCTTATATGTATTGGATCGGAGGTAGT 58.886 37.037 0.00 0.00 0.00 2.73
371 373 7.400339 ACATCTTATATGTATTGGATCGGAGGT 59.600 37.037 0.00 0.00 0.00 3.85
375 377 9.698309 GGATACATCTTATATGTATTGGATCGG 57.302 37.037 10.96 0.00 43.10 4.18
389 391 7.050970 TGTAGCTGAAACGGATACATCTTAT 57.949 36.000 0.00 0.00 36.81 1.73
392 394 5.105310 ACTTGTAGCTGAAACGGATACATCT 60.105 40.000 9.01 0.00 40.53 2.90
393 395 5.109903 ACTTGTAGCTGAAACGGATACATC 58.890 41.667 9.01 0.00 40.53 3.06
394 396 5.086104 ACTTGTAGCTGAAACGGATACAT 57.914 39.130 9.01 0.00 40.53 2.29
395 397 4.530710 ACTTGTAGCTGAAACGGATACA 57.469 40.909 0.00 4.87 39.41 2.29
396 398 7.096722 CGTATTACTTGTAGCTGAAACGGATAC 60.097 40.741 0.00 0.00 32.90 2.24
397 399 6.914215 CGTATTACTTGTAGCTGAAACGGATA 59.086 38.462 0.00 0.00 0.00 2.59
398 400 5.747197 CGTATTACTTGTAGCTGAAACGGAT 59.253 40.000 0.00 0.00 0.00 4.18
399 401 5.097529 CGTATTACTTGTAGCTGAAACGGA 58.902 41.667 0.00 0.00 0.00 4.69
400 402 4.266976 CCGTATTACTTGTAGCTGAAACGG 59.733 45.833 0.00 1.47 39.98 4.44
401 403 4.266976 CCCGTATTACTTGTAGCTGAAACG 59.733 45.833 0.00 0.00 0.00 3.60
402 404 4.569564 CCCCGTATTACTTGTAGCTGAAAC 59.430 45.833 0.00 0.00 0.00 2.78
403 405 4.761975 CCCCGTATTACTTGTAGCTGAAA 58.238 43.478 0.00 0.00 0.00 2.69
410 412 1.682854 CTCGGCCCCGTATTACTTGTA 59.317 52.381 6.61 0.00 40.74 2.41
413 415 2.036428 GCCTCGGCCCCGTATTACTT 62.036 60.000 6.61 0.00 40.74 2.24
426 428 2.441532 TTACTCCCTCGGCCTCGG 60.442 66.667 0.00 0.00 36.95 4.63
429 431 1.652947 TTTTCTTACTCCCTCGGCCT 58.347 50.000 0.00 0.00 0.00 5.19
430 432 2.711978 ATTTTCTTACTCCCTCGGCC 57.288 50.000 0.00 0.00 0.00 6.13
431 433 2.608090 CGAATTTTCTTACTCCCTCGGC 59.392 50.000 0.00 0.00 0.00 5.54
432 434 3.858247 ACGAATTTTCTTACTCCCTCGG 58.142 45.455 0.00 0.00 0.00 4.63
433 435 3.864003 GGACGAATTTTCTTACTCCCTCG 59.136 47.826 0.00 0.00 0.00 4.63
461 463 7.041167 CCACAAAAACATGTCTCTCTACAATCA 60.041 37.037 0.00 0.00 32.02 2.57
471 473 4.045636 ACTTGCCACAAAAACATGTCTC 57.954 40.909 0.00 0.00 0.00 3.36
472 474 5.348164 GTTACTTGCCACAAAAACATGTCT 58.652 37.500 0.00 0.00 0.00 3.41
473 475 4.206200 CGTTACTTGCCACAAAAACATGTC 59.794 41.667 0.00 0.00 0.00 3.06
474 476 4.109050 CGTTACTTGCCACAAAAACATGT 58.891 39.130 0.00 0.00 0.00 3.21
476 478 4.109050 CACGTTACTTGCCACAAAAACAT 58.891 39.130 0.00 0.00 0.00 2.71
498 594 4.939509 TTTGACTAGCAAAATACGGAGC 57.060 40.909 9.09 0.00 43.18 4.70
588 684 8.136800 TGTTTACGGCGAATAATCAATCTACTA 58.863 33.333 16.62 0.00 0.00 1.82
589 685 6.982141 TGTTTACGGCGAATAATCAATCTACT 59.018 34.615 16.62 0.00 0.00 2.57
590 686 7.169035 TGTTTACGGCGAATAATCAATCTAC 57.831 36.000 16.62 0.00 0.00 2.59
591 687 7.117236 GGATGTTTACGGCGAATAATCAATCTA 59.883 37.037 16.62 0.00 0.00 1.98
592 688 6.073222 GGATGTTTACGGCGAATAATCAATCT 60.073 38.462 16.62 0.00 0.00 2.40
664 763 1.983605 CAGGTTGCGAACGTACTACAG 59.016 52.381 0.00 0.00 0.00 2.74
730 836 2.096442 GGTTATATACCGCGGCGCC 61.096 63.158 28.58 19.07 37.12 6.53
822 964 1.301677 CCAAAAGAGCCAGCTCGGAC 61.302 60.000 13.70 0.00 46.90 4.79
1181 1355 2.519302 GCGCATTGGGGCCTGTAT 60.519 61.111 0.30 0.00 46.43 2.29
1206 1388 4.452733 CGCCGGGAGAGGACCAAC 62.453 72.222 2.18 0.00 0.00 3.77
1326 1525 8.682710 TCTTTCTTTCATAATTAACAATCCCGG 58.317 33.333 0.00 0.00 0.00 5.73
1340 1539 8.410141 ACACAAAACCGAAATCTTTCTTTCATA 58.590 29.630 1.56 0.00 35.32 2.15
1391 1590 0.895100 GTGCAGAATTCCAGCCCACA 60.895 55.000 15.47 0.00 0.00 4.17
1412 1611 5.885352 TCGAAATCAAATAAATCCAGCTCCA 59.115 36.000 0.00 0.00 0.00 3.86
1424 1623 7.413000 GCAGCACTTTCTACTCGAAATCAAATA 60.413 37.037 0.00 0.00 40.62 1.40
1541 1740 3.419915 CTGCAAATTTCGATTGAGGTCG 58.580 45.455 1.45 0.00 42.74 4.79
1584 1783 1.828832 CTCCGTCAGTATTCAGTCGC 58.171 55.000 0.00 0.00 0.00 5.19
1702 1901 2.559668 ACTGGAATGATGGCAACTTGTG 59.440 45.455 0.00 0.00 37.61 3.33
1734 1936 5.358725 TGCTGATCAAAGATACACAATGCAT 59.641 36.000 0.00 0.00 0.00 3.96
1739 1941 7.692460 AAGAATGCTGATCAAAGATACACAA 57.308 32.000 0.00 0.00 0.00 3.33
1913 2115 2.200337 AAAAGGACAACGGCCAGCC 61.200 57.895 2.24 0.00 0.00 4.85
1972 2174 5.046014 AGACTGCAGTATCAGAAAACAGGAT 60.046 40.000 21.73 0.00 37.51 3.24
1997 2199 2.383442 ATGGGCGGTAGAGACTACAT 57.617 50.000 10.39 0.00 0.00 2.29
2199 2401 7.097192 ACTACAAACATCACTATGGTGTACTG 58.903 38.462 9.23 8.08 41.60 2.74
2249 2451 0.390860 AGTATGTGAGATCTGCCGCC 59.609 55.000 0.00 0.00 0.00 6.13
2279 2481 4.744570 AGACGGTGTATAACAGTGATGTG 58.255 43.478 0.00 0.00 37.32 3.21
2474 2711 3.884895 ACGGATGAATAAAGATGCCACA 58.115 40.909 0.00 0.00 0.00 4.17
2486 2723 6.874134 GCAATTCCATACTAGTACGGATGAAT 59.126 38.462 17.96 6.69 26.55 2.57
2494 2731 6.363473 GCGAAATGCAATTCCATACTAGTAC 58.637 40.000 4.31 0.00 45.45 2.73
2557 2794 4.074970 ACATGAGGCGTCAAGAGAAAATT 58.925 39.130 17.59 0.00 35.88 1.82
2679 2916 9.559958 CAAGCTTGTGGTTAAAAGATATTACTG 57.440 33.333 18.65 0.00 32.07 2.74
2695 2932 6.980397 ACAAAGAAAAATCTACAAGCTTGTGG 59.020 34.615 36.50 33.66 42.31 4.17
2852 3090 7.067008 GTCAGCCTCTAAGCCAAAATATTTACA 59.933 37.037 0.01 0.00 0.00 2.41
2905 3143 5.340439 TGCCATGAATATTCAATGCAACA 57.660 34.783 28.76 17.08 41.58 3.33
2950 3188 8.291032 AGATAACTCTTACTATTGGATTCGACG 58.709 37.037 0.00 0.00 0.00 5.12
3153 3391 2.922740 ACCGTAACTTTGCTTCCTGA 57.077 45.000 0.00 0.00 0.00 3.86
3159 3397 5.243207 AGTGCTATAAACCGTAACTTTGCT 58.757 37.500 0.00 0.00 0.00 3.91
3170 3408 9.961265 AACTTAGAAAACAAAGTGCTATAAACC 57.039 29.630 0.00 0.00 36.12 3.27
3233 3471 2.159327 AGCTTTGCAGGCATCAAAAC 57.841 45.000 14.52 2.39 33.60 2.43
3553 3791 1.270571 TGACACCTCAAAGCGCATGTA 60.271 47.619 11.47 0.00 0.00 2.29
3580 3819 1.696832 GCGAATGAGAAGGTGCGGAC 61.697 60.000 0.00 0.00 0.00 4.79
3626 3865 0.804989 GGAAGGTTGGATCTGCAACG 59.195 55.000 8.23 0.00 32.50 4.10
3641 3880 8.430431 CCCTTTTCTATAAAGTACCCTAGGAAG 58.570 40.741 11.48 0.08 0.00 3.46
3758 4002 4.564940 TGCCAAAAATGAAAATTGCCAC 57.435 36.364 0.00 0.00 0.00 5.01
3861 4105 1.003718 GGAAAGAGGTCCACCACGG 60.004 63.158 0.00 0.00 37.65 4.94
3996 4241 5.304686 AGTGTCACAGTTATTGAGGGAAA 57.695 39.130 5.62 0.00 0.00 3.13
4183 4458 5.770417 AGAACTACTGTAAAACCAGACTCG 58.230 41.667 0.00 0.00 36.30 4.18
4205 4483 6.109359 AGACATAAGCAGCAAGTAGGTAAAG 58.891 40.000 0.00 0.00 0.00 1.85
4334 4629 8.397906 TGCAACAGAACATAATTTATGCTAGAC 58.602 33.333 14.88 4.34 39.79 2.59
4502 4798 4.740695 GGACAGAATAGAAATCGAACCTCG 59.259 45.833 0.00 0.00 42.10 4.63
4516 4812 6.296489 GGAAAAGAAGAAGAGGGGACAGAATA 60.296 42.308 0.00 0.00 0.00 1.75
4524 4820 1.006043 GGGGGAAAAGAAGAAGAGGGG 59.994 57.143 0.00 0.00 0.00 4.79
4575 4871 4.037208 GGATTTTGAGATATGCACCAGTGG 59.963 45.833 7.91 7.91 0.00 4.00
4790 5087 4.968259 TGAGTTGTGGTTTAGTACTGCAT 58.032 39.130 5.39 0.00 0.00 3.96
4796 5093 4.634012 ATGCCTGAGTTGTGGTTTAGTA 57.366 40.909 0.00 0.00 0.00 1.82
4803 5100 0.675083 TTGCAATGCCTGAGTTGTGG 59.325 50.000 1.53 0.00 0.00 4.17
4827 5124 0.242017 GTGGCCAGCACAATCTGTTC 59.758 55.000 5.11 0.00 32.32 3.18
4839 5136 2.295885 GATCATGAGAAAGGTGGCCAG 58.704 52.381 5.11 0.00 0.00 4.85
4858 5155 1.136305 CGACGCCTATGAGAAAAGGGA 59.864 52.381 0.00 0.00 33.17 4.20
4978 5275 1.595382 GCTGCCACTGTCGTGAACT 60.595 57.895 0.00 0.00 43.97 3.01
4983 5280 1.518056 CCATTTGCTGCCACTGTCGT 61.518 55.000 0.00 0.00 0.00 4.34
4984 5281 1.210931 CCATTTGCTGCCACTGTCG 59.789 57.895 0.00 0.00 0.00 4.35
4990 5287 1.252904 GCTTCCTCCATTTGCTGCCA 61.253 55.000 0.00 0.00 0.00 4.92
5045 5351 1.674359 ACAACCAATGTCAACTGCGA 58.326 45.000 0.00 0.00 37.96 5.10
5046 5352 3.829886 ATACAACCAATGTCAACTGCG 57.170 42.857 0.00 0.00 42.70 5.18
5047 5353 5.119931 TCAATACAACCAATGTCAACTGC 57.880 39.130 0.00 0.00 42.70 4.40
5048 5354 5.048504 AGCTCAATACAACCAATGTCAACTG 60.049 40.000 0.00 0.00 42.70 3.16
5049 5355 5.048504 CAGCTCAATACAACCAATGTCAACT 60.049 40.000 0.00 0.00 42.70 3.16
5050 5356 5.048782 TCAGCTCAATACAACCAATGTCAAC 60.049 40.000 0.00 0.00 42.70 3.18
5051 5357 5.069318 TCAGCTCAATACAACCAATGTCAA 58.931 37.500 0.00 0.00 42.70 3.18
5114 5426 5.237344 ACTCACAAAAGATACAACAGTCTGC 59.763 40.000 0.00 0.00 0.00 4.26
5139 5451 3.118519 GCATTCAGAATCTGGGCCAATTT 60.119 43.478 8.04 3.67 31.51 1.82
5192 5504 1.926511 CTAAAGGGGCAGCAACAGCG 61.927 60.000 0.00 0.00 0.00 5.18
5265 5577 2.126307 CAGAGCGGACACTGTCGG 60.126 66.667 11.46 11.46 36.25 4.79
5301 5613 5.768164 GTCCAGGTAATTTGAAAGGACAAGA 59.232 40.000 0.00 0.00 42.65 3.02
5796 6114 0.417437 TCTCTCTTCATCCCCACCCA 59.583 55.000 0.00 0.00 0.00 4.51
5797 6115 1.419387 CATCTCTCTTCATCCCCACCC 59.581 57.143 0.00 0.00 0.00 4.61
5800 6118 5.519183 TTTTTCATCTCTCTTCATCCCCA 57.481 39.130 0.00 0.00 0.00 4.96
5824 6142 5.292101 CCCGATCTATCCGCAATAATTTCTC 59.708 44.000 0.00 0.00 0.00 2.87
5825 6143 5.178797 CCCGATCTATCCGCAATAATTTCT 58.821 41.667 0.00 0.00 0.00 2.52
5826 6144 4.935808 ACCCGATCTATCCGCAATAATTTC 59.064 41.667 0.00 0.00 0.00 2.17
5827 6145 4.906618 ACCCGATCTATCCGCAATAATTT 58.093 39.130 0.00 0.00 0.00 1.82
5829 6147 3.118738 GGACCCGATCTATCCGCAATAAT 60.119 47.826 0.00 0.00 0.00 1.28
5830 6148 2.232941 GGACCCGATCTATCCGCAATAA 59.767 50.000 0.00 0.00 0.00 1.40
5831 6149 1.822990 GGACCCGATCTATCCGCAATA 59.177 52.381 0.00 0.00 0.00 1.90
5874 6195 2.423373 CCTATGTGGGGAGGAAATGTGG 60.423 54.545 0.00 0.00 34.46 4.17
5916 6237 1.025812 AGATGCTCTAAGGACGGTCG 58.974 55.000 1.43 0.00 0.00 4.79
5917 6238 2.427453 TGAAGATGCTCTAAGGACGGTC 59.573 50.000 0.00 0.00 0.00 4.79
5929 6250 1.023513 GCGCTCCTGTTGAAGATGCT 61.024 55.000 0.00 0.00 0.00 3.79
5930 6251 1.023513 AGCGCTCCTGTTGAAGATGC 61.024 55.000 2.64 0.00 0.00 3.91
5931 6252 2.299993 TAGCGCTCCTGTTGAAGATG 57.700 50.000 16.34 0.00 0.00 2.90
5932 6253 3.003480 GTTTAGCGCTCCTGTTGAAGAT 58.997 45.455 16.34 0.00 0.00 2.40
5933 6254 2.224185 TGTTTAGCGCTCCTGTTGAAGA 60.224 45.455 16.34 0.00 0.00 2.87
5934 6255 2.143122 TGTTTAGCGCTCCTGTTGAAG 58.857 47.619 16.34 0.00 0.00 3.02
5935 6256 2.248280 TGTTTAGCGCTCCTGTTGAA 57.752 45.000 16.34 0.00 0.00 2.69
5936 6257 2.143122 CTTGTTTAGCGCTCCTGTTGA 58.857 47.619 16.34 0.00 0.00 3.18
5937 6258 1.400242 GCTTGTTTAGCGCTCCTGTTG 60.400 52.381 16.34 2.76 40.71 3.33
5938 6259 0.875059 GCTTGTTTAGCGCTCCTGTT 59.125 50.000 16.34 0.00 40.71 3.16
5939 6260 2.544726 GCTTGTTTAGCGCTCCTGT 58.455 52.632 16.34 0.00 40.71 4.00


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

AutoCloner maintained by Alex Coulton.