Multiple sequence alignment - TraesCS3D01G118400

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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 TraesCS3D01G118400 chr3D 100.000 3629 0 0 1 3629 72647825 72651453 0.000000e+00 6702
1 TraesCS3D01G118400 chr3D 89.567 1016 66 17 865 1845 72251871 72252881 0.000000e+00 1253
2 TraesCS3D01G118400 chr3D 87.500 624 36 22 2369 2964 72253532 72254141 0.000000e+00 682
3 TraesCS3D01G118400 chr3D 89.948 388 30 5 1993 2380 72253127 72253505 3.260000e-135 492
4 TraesCS3D01G118400 chr3D 84.014 294 17 13 395 684 416217329 416217596 4.650000e-64 255
5 TraesCS3D01G118400 chr3D 84.058 276 13 14 394 665 553177356 553177604 1.680000e-58 237
6 TraesCS3D01G118400 chr3D 91.566 166 8 1 1836 1995 72252910 72253075 1.310000e-54 224
7 TraesCS3D01G118400 chr3D 85.714 126 16 2 741 865 72251681 72251805 8.180000e-27 132
8 TraesCS3D01G118400 chr3A 89.277 1632 94 25 1993 3613 85271696 85273257 0.000000e+00 1969
9 TraesCS3D01G118400 chr3A 96.203 1106 36 3 735 1839 85270422 85271522 0.000000e+00 1805
10 TraesCS3D01G118400 chr3A 95.052 1152 43 3 1999 3150 85372507 85373644 0.000000e+00 1799
11 TraesCS3D01G118400 chr3A 96.371 937 30 3 904 1839 85371391 85372324 0.000000e+00 1539
12 TraesCS3D01G118400 chr3A 94.485 961 36 7 2355 3311 85544390 85545337 0.000000e+00 1465
13 TraesCS3D01G118400 chr3A 94.099 966 35 9 2355 3311 85475520 85476472 0.000000e+00 1448
14 TraesCS3D01G118400 chr3A 92.700 1000 65 5 841 1839 85464148 85465140 0.000000e+00 1435
15 TraesCS3D01G118400 chr3A 92.500 1000 67 3 841 1839 85533411 85534403 0.000000e+00 1424
16 TraesCS3D01G118400 chr3A 89.871 1007 68 12 865 1845 84649165 84650163 0.000000e+00 1264
17 TraesCS3D01G118400 chr3A 86.290 620 46 22 2369 2964 84650814 84651418 3.950000e-179 638
18 TraesCS3D01G118400 chr3A 90.722 388 30 3 1993 2380 84650406 84650787 2.500000e-141 512
19 TraesCS3D01G118400 chr3A 86.588 425 43 8 3208 3629 85387864 85388277 1.190000e-124 457
20 TraesCS3D01G118400 chr3A 93.130 262 15 1 1993 2254 85475263 85475521 7.350000e-102 381
21 TraesCS3D01G118400 chr3A 91.603 262 19 1 1993 2254 85544133 85544391 3.450000e-95 359
22 TraesCS3D01G118400 chr3A 85.838 346 27 12 3299 3626 85547592 85547933 7.460000e-92 348
23 TraesCS3D01G118400 chr3A 89.796 245 17 6 3299 3540 85478736 85478975 1.270000e-79 307
24 TraesCS3D01G118400 chr3A 84.561 285 19 11 395 677 703210984 703210723 3.590000e-65 259
25 TraesCS3D01G118400 chr3A 83.972 287 23 9 392 677 45151467 45151731 1.670000e-63 254
26 TraesCS3D01G118400 chr3A 82.877 292 26 12 391 681 192847372 192847640 1.300000e-59 241
27 TraesCS3D01G118400 chr3A 93.750 160 7 1 1839 1995 84650195 84650354 1.680000e-58 237
28 TraesCS3D01G118400 chr3A 100.000 118 0 0 1878 1995 85372329 85372446 6.100000e-53 219
29 TraesCS3D01G118400 chr3A 96.639 119 4 0 1877 1995 85271526 85271644 7.950000e-47 198
30 TraesCS3D01G118400 chr3A 96.581 117 4 0 1879 1995 85475095 85475211 1.030000e-45 195
31 TraesCS3D01G118400 chr3A 95.726 117 5 0 1879 1995 85543965 85544081 4.780000e-44 189
32 TraesCS3D01G118400 chr3A 83.108 148 18 2 725 865 84648952 84649099 1.060000e-25 128
33 TraesCS3D01G118400 chr3B 94.551 1248 52 7 1993 3240 118252336 118253567 0.000000e+00 1914
34 TraesCS3D01G118400 chr3B 89.171 1025 63 13 865 1845 118136481 118137501 0.000000e+00 1234
35 TraesCS3D01G118400 chr3B 95.231 629 24 4 865 1491 118251165 118251789 0.000000e+00 990
36 TraesCS3D01G118400 chr3B 91.339 508 21 11 1510 1995 118251778 118252284 0.000000e+00 673
37 TraesCS3D01G118400 chr3B 95.098 408 16 3 3225 3629 118253589 118253995 1.100000e-179 640
38 TraesCS3D01G118400 chr3B 86.320 519 38 18 2369 2859 118138155 118138668 5.330000e-148 534
39 TraesCS3D01G118400 chr3B 90.206 388 32 2 1993 2380 118137747 118138128 5.410000e-138 501
40 TraesCS3D01G118400 chr3B 87.500 216 24 2 149 361 118250122 118250337 2.800000e-61 246
41 TraesCS3D01G118400 chr3B 91.566 166 8 1 1836 1995 118137530 118137695 1.310000e-54 224
42 TraesCS3D01G118400 chr3B 92.593 135 9 1 731 865 118250987 118251120 3.700000e-45 193
43 TraesCS3D01G118400 chr3B 78.210 257 52 3 3376 3629 118255489 118255744 1.040000e-35 161
44 TraesCS3D01G118400 chr2A 85.315 286 13 9 396 677 585819146 585818886 5.970000e-68 268
45 TraesCS3D01G118400 chr2A 84.615 273 14 11 399 668 515301670 515301917 2.800000e-61 246
46 TraesCS3D01G118400 chr4D 85.017 287 14 12 395 677 48708656 48708917 7.730000e-67 265
47 TraesCS3D01G118400 chr4D 84.615 286 15 12 396 677 47750707 47750967 1.290000e-64 257
48 TraesCS3D01G118400 chr7A 84.965 286 14 11 396 677 535468312 535468572 2.780000e-66 263
49 TraesCS3D01G118400 chr7D 84.643 280 15 14 392 668 196722853 196723107 1.670000e-63 254
50 TraesCS3D01G118400 chr7D 83.737 289 19 11 392 677 574765858 574766121 7.780000e-62 248
51 TraesCS3D01G118400 chr7D 79.585 289 29 11 391 678 636699440 636699699 2.880000e-41 180
52 TraesCS3D01G118400 chr2D 83.392 283 24 8 396 677 377120841 377120581 1.300000e-59 241
53 TraesCS3D01G118400 chr2D 81.338 284 29 6 396 678 571203321 571203581 3.670000e-50 209
54 TraesCS3D01G118400 chr2B 81.185 287 30 11 396 681 97963993 97963730 3.670000e-50 209
55 TraesCS3D01G118400 chr5D 81.690 284 19 10 395 677 565094083 565093832 4.750000e-49 206
56 TraesCS3D01G118400 chr5A 79.577 284 35 10 395 677 28234913 28235174 8.000000e-42 182


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 TraesCS3D01G118400 chr3D 72647825 72651453 3628 False 6702.000000 6702 100.000000 1 3629 1 chr3D.!!$F1 3628
1 TraesCS3D01G118400 chr3D 72251681 72254141 2460 False 556.600000 1253 88.859000 741 2964 5 chr3D.!!$F4 2223
2 TraesCS3D01G118400 chr3A 85464148 85465140 992 False 1435.000000 1435 92.700000 841 1839 1 chr3A.!!$F3 998
3 TraesCS3D01G118400 chr3A 85533411 85534403 992 False 1424.000000 1424 92.500000 841 1839 1 chr3A.!!$F4 998
4 TraesCS3D01G118400 chr3A 85270422 85273257 2835 False 1324.000000 1969 94.039667 735 3613 3 chr3A.!!$F7 2878
5 TraesCS3D01G118400 chr3A 85371391 85373644 2253 False 1185.666667 1799 97.141000 904 3150 3 chr3A.!!$F8 2246
6 TraesCS3D01G118400 chr3A 85543965 85547933 3968 False 590.250000 1465 91.913000 1879 3626 4 chr3A.!!$F10 1747
7 TraesCS3D01G118400 chr3A 85475095 85478975 3880 False 582.750000 1448 93.401500 1879 3540 4 chr3A.!!$F9 1661
8 TraesCS3D01G118400 chr3A 84648952 84651418 2466 False 555.800000 1264 88.748200 725 2964 5 chr3A.!!$F6 2239
9 TraesCS3D01G118400 chr3B 118250122 118255744 5622 False 688.142857 1914 90.646000 149 3629 7 chr3B.!!$F2 3480
10 TraesCS3D01G118400 chr3B 118136481 118138668 2187 False 623.250000 1234 89.315750 865 2859 4 chr3B.!!$F1 1994

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
217 218 0.101399 CACGCCCTAGCTACTGTCTG 59.899 60.000 0.00 0.0 36.60 3.51 F
351 355 0.536006 GCCATCGGGATGAAAGAGGG 60.536 60.000 10.16 0.0 41.20 4.30 F
706 1168 0.850100 TTCTCCCTTTGGTTGCTCCA 59.150 50.000 0.00 0.0 45.60 3.86 F
716 1178 1.133513 TGGTTGCTCCAGGTGAAATGT 60.134 47.619 0.00 0.0 41.93 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2687 2.050077 GCGCTTGTTCTTGTGCCC 60.050 61.111 0.00 0.00 34.05 5.36 R
2101 2850 2.202623 GCTTCAGCTGCTGCATGC 60.203 61.111 24.38 21.33 42.74 4.06 R
2459 3247 1.147153 CCTGCCTAGCTAGTTGGGC 59.853 63.158 24.39 24.39 44.31 5.36 R
2714 3518 2.061773 CACTCAACGCTGACAAGTAGG 58.938 52.381 0.00 0.00 0.00 3.18 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
21 22 2.879002 TAGCCAGAATTCTCTCTGCG 57.121 50.000 4.57 0.00 41.36 5.18
22 23 0.901124 AGCCAGAATTCTCTCTGCGT 59.099 50.000 4.57 0.00 41.36 5.24
23 24 1.005340 GCCAGAATTCTCTCTGCGTG 58.995 55.000 4.57 0.00 41.36 5.34
24 25 1.404717 GCCAGAATTCTCTCTGCGTGA 60.405 52.381 4.57 0.00 41.36 4.35
25 26 2.538437 CCAGAATTCTCTCTGCGTGAG 58.462 52.381 4.57 0.64 41.36 3.51
41 42 4.116747 CGTGAGCTATCTTTTCTCCTGT 57.883 45.455 0.00 0.00 0.00 4.00
42 43 3.862267 CGTGAGCTATCTTTTCTCCTGTG 59.138 47.826 0.00 0.00 0.00 3.66
43 44 3.620821 GTGAGCTATCTTTTCTCCTGTGC 59.379 47.826 0.00 0.00 0.00 4.57
44 45 3.261643 TGAGCTATCTTTTCTCCTGTGCA 59.738 43.478 0.00 0.00 0.00 4.57
45 46 4.256920 GAGCTATCTTTTCTCCTGTGCAA 58.743 43.478 0.00 0.00 0.00 4.08
46 47 4.006319 AGCTATCTTTTCTCCTGTGCAAC 58.994 43.478 0.00 0.00 37.35 4.17
58 59 2.404265 TGTGCAACATTCAAGCGAAG 57.596 45.000 0.00 0.00 45.67 3.79
78 79 3.827505 ACAACCTGTGATGCCAAGT 57.172 47.368 0.00 0.00 0.00 3.16
79 80 1.321474 ACAACCTGTGATGCCAAGTG 58.679 50.000 0.00 0.00 0.00 3.16
80 81 0.599558 CAACCTGTGATGCCAAGTGG 59.400 55.000 0.00 0.00 38.53 4.00
81 82 0.478072 AACCTGTGATGCCAAGTGGA 59.522 50.000 0.18 0.00 37.39 4.02
82 83 0.478072 ACCTGTGATGCCAAGTGGAA 59.522 50.000 0.18 0.00 37.39 3.53
83 84 0.883833 CCTGTGATGCCAAGTGGAAC 59.116 55.000 0.18 0.00 37.39 3.62
98 99 4.546829 GTGGAACTATACCTTGGTGTCA 57.453 45.455 2.03 0.00 0.00 3.58
99 100 4.901868 GTGGAACTATACCTTGGTGTCAA 58.098 43.478 2.03 0.00 0.00 3.18
100 101 5.497474 GTGGAACTATACCTTGGTGTCAAT 58.503 41.667 2.03 0.00 31.75 2.57
101 102 5.354234 GTGGAACTATACCTTGGTGTCAATG 59.646 44.000 2.03 0.00 31.75 2.82
102 103 5.249622 TGGAACTATACCTTGGTGTCAATGA 59.750 40.000 2.03 0.00 31.75 2.57
103 104 6.177610 GGAACTATACCTTGGTGTCAATGAA 58.822 40.000 2.03 0.00 31.75 2.57
104 105 6.828785 GGAACTATACCTTGGTGTCAATGAAT 59.171 38.462 2.03 0.00 31.75 2.57
105 106 7.990886 GGAACTATACCTTGGTGTCAATGAATA 59.009 37.037 2.03 0.00 31.75 1.75
106 107 9.391006 GAACTATACCTTGGTGTCAATGAATAA 57.609 33.333 2.03 0.00 31.75 1.40
107 108 8.964476 ACTATACCTTGGTGTCAATGAATAAG 57.036 34.615 2.03 0.00 31.75 1.73
108 109 7.993183 ACTATACCTTGGTGTCAATGAATAAGG 59.007 37.037 2.03 11.81 39.20 2.69
109 110 4.998051 ACCTTGGTGTCAATGAATAAGGT 58.002 39.130 12.74 12.74 40.99 3.50
110 111 5.393866 ACCTTGGTGTCAATGAATAAGGTT 58.606 37.500 12.74 2.79 42.60 3.50
111 112 5.838521 ACCTTGGTGTCAATGAATAAGGTTT 59.161 36.000 12.74 0.00 42.60 3.27
112 113 6.326323 ACCTTGGTGTCAATGAATAAGGTTTT 59.674 34.615 12.74 0.00 42.60 2.43
113 114 7.507616 ACCTTGGTGTCAATGAATAAGGTTTTA 59.492 33.333 12.74 0.00 42.60 1.52
114 115 7.812669 CCTTGGTGTCAATGAATAAGGTTTTAC 59.187 37.037 0.00 0.00 31.75 2.01
115 116 8.472007 TTGGTGTCAATGAATAAGGTTTTACT 57.528 30.769 0.00 0.00 0.00 2.24
116 117 8.106247 TGGTGTCAATGAATAAGGTTTTACTC 57.894 34.615 0.00 0.00 0.00 2.59
117 118 7.942341 TGGTGTCAATGAATAAGGTTTTACTCT 59.058 33.333 0.00 0.00 0.00 3.24
118 119 9.444600 GGTGTCAATGAATAAGGTTTTACTCTA 57.555 33.333 0.00 0.00 0.00 2.43
120 121 9.667107 TGTCAATGAATAAGGTTTTACTCTAGG 57.333 33.333 0.00 0.00 0.00 3.02
121 122 9.668497 GTCAATGAATAAGGTTTTACTCTAGGT 57.332 33.333 0.00 0.00 0.00 3.08
132 133 9.892130 AGGTTTTACTCTAGGTTTTCATATCAG 57.108 33.333 0.00 0.00 0.00 2.90
133 134 8.613482 GGTTTTACTCTAGGTTTTCATATCAGC 58.387 37.037 0.00 0.00 0.00 4.26
134 135 9.162764 GTTTTACTCTAGGTTTTCATATCAGCA 57.837 33.333 0.00 0.00 0.00 4.41
135 136 9.733556 TTTTACTCTAGGTTTTCATATCAGCAA 57.266 29.630 0.00 0.00 0.00 3.91
136 137 8.718102 TTACTCTAGGTTTTCATATCAGCAAC 57.282 34.615 0.00 0.00 0.00 4.17
137 138 6.116126 ACTCTAGGTTTTCATATCAGCAACC 58.884 40.000 0.00 0.00 37.72 3.77
138 139 5.116180 TCTAGGTTTTCATATCAGCAACCG 58.884 41.667 0.00 0.00 41.61 4.44
139 140 3.686016 AGGTTTTCATATCAGCAACCGT 58.314 40.909 0.00 0.00 41.61 4.83
140 141 4.079253 AGGTTTTCATATCAGCAACCGTT 58.921 39.130 0.00 0.00 41.61 4.44
141 142 4.156008 AGGTTTTCATATCAGCAACCGTTC 59.844 41.667 0.00 0.00 41.61 3.95
142 143 4.156008 GGTTTTCATATCAGCAACCGTTCT 59.844 41.667 0.00 0.00 0.00 3.01
143 144 5.335661 GGTTTTCATATCAGCAACCGTTCTT 60.336 40.000 0.00 0.00 0.00 2.52
144 145 5.957842 TTTCATATCAGCAACCGTTCTTT 57.042 34.783 0.00 0.00 0.00 2.52
145 146 5.957842 TTCATATCAGCAACCGTTCTTTT 57.042 34.783 0.00 0.00 0.00 2.27
146 147 5.545658 TCATATCAGCAACCGTTCTTTTC 57.454 39.130 0.00 0.00 0.00 2.29
147 148 5.000591 TCATATCAGCAACCGTTCTTTTCA 58.999 37.500 0.00 0.00 0.00 2.69
165 166 7.149973 TCTTTTCAGCTTGATTTTGATTCTGG 58.850 34.615 0.00 0.00 0.00 3.86
175 176 1.462616 TTGATTCTGGTGAATGGGCG 58.537 50.000 0.00 0.00 42.43 6.13
176 177 0.394216 TGATTCTGGTGAATGGGCGG 60.394 55.000 0.00 0.00 42.43 6.13
182 183 1.077787 GGTGAATGGGCGGTCATGA 60.078 57.895 0.00 0.00 0.00 3.07
195 196 2.614057 CGGTCATGATTTACTGGCCTTC 59.386 50.000 3.32 0.00 34.91 3.46
209 210 4.148825 CTTCGCCACGCCCTAGCT 62.149 66.667 0.00 0.00 36.60 3.32
211 212 2.955751 CTTCGCCACGCCCTAGCTAC 62.956 65.000 0.00 0.00 36.60 3.58
212 213 3.528370 CGCCACGCCCTAGCTACT 61.528 66.667 0.00 0.00 36.60 2.57
217 218 0.101399 CACGCCCTAGCTACTGTCTG 59.899 60.000 0.00 0.00 36.60 3.51
233 235 1.059584 TCTGCTGGAAGTGGGGAACA 61.060 55.000 0.00 0.00 35.30 3.18
288 290 2.032071 GTGGGGCGCAGTAGTGTT 59.968 61.111 10.83 0.00 0.00 3.32
289 291 1.599797 GTGGGGCGCAGTAGTGTTT 60.600 57.895 10.83 0.00 0.00 2.83
303 305 6.042777 CAGTAGTGTTTGTCAGAAGAAGTGA 58.957 40.000 0.00 0.00 0.00 3.41
311 313 2.161211 GTCAGAAGAAGTGAGCAATGGC 59.839 50.000 0.00 0.00 41.61 4.40
313 315 1.074405 AGAAGAAGTGAGCAATGGCCA 59.926 47.619 8.56 8.56 42.56 5.36
330 332 1.584380 CCAGAGCAAGCAGTTGAGGC 61.584 60.000 0.00 0.00 35.46 4.70
331 333 1.303155 AGAGCAAGCAGTTGAGGCC 60.303 57.895 0.00 0.00 35.46 5.19
337 341 3.512516 GCAGTTGAGGCCGCCATC 61.513 66.667 13.15 7.03 0.00 3.51
338 342 3.197790 CAGTTGAGGCCGCCATCG 61.198 66.667 13.15 0.00 0.00 3.84
351 355 0.536006 GCCATCGGGATGAAAGAGGG 60.536 60.000 10.16 0.00 41.20 4.30
355 359 3.435601 CCATCGGGATGAAAGAGGGAAAT 60.436 47.826 10.16 0.00 41.20 2.17
376 795 1.215173 TGAGCCCCCATTCTATGTTGG 59.785 52.381 0.00 0.00 0.00 3.77
418 880 6.536582 GGTACTCCCTCCGTTTTTATTTACTC 59.463 42.308 0.00 0.00 0.00 2.59
428 890 8.550376 TCCGTTTTTATTTACTCCGCATATTAC 58.450 33.333 0.00 0.00 0.00 1.89
429 891 8.553696 CCGTTTTTATTTACTCCGCATATTACT 58.446 33.333 0.00 0.00 0.00 2.24
430 892 9.925268 CGTTTTTATTTACTCCGCATATTACTT 57.075 29.630 0.00 0.00 0.00 2.24
435 897 7.875327 ATTTACTCCGCATATTACTTTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
436 898 6.913873 TTACTCCGCATATTACTTTTGGTC 57.086 37.500 0.00 0.00 0.00 4.02
437 899 4.839121 ACTCCGCATATTACTTTTGGTCA 58.161 39.130 0.00 0.00 0.00 4.02
440 902 6.128007 ACTCCGCATATTACTTTTGGTCAAAG 60.128 38.462 0.00 0.00 46.70 2.77
450 912 5.514274 CTTTTGGTCAAAGTCAGGCTTTA 57.486 39.130 0.00 0.00 44.95 1.85
455 917 6.569179 TGGTCAAAGTCAGGCTTTATAAAC 57.431 37.500 0.00 0.00 44.95 2.01
462 924 7.817418 AAGTCAGGCTTTATAAACTTTGACA 57.183 32.000 21.37 0.00 36.92 3.58
527 989 8.821686 TCAATACCATTAGATTTGTGGAATGT 57.178 30.769 0.00 0.00 36.82 2.71
528 990 9.913310 TCAATACCATTAGATTTGTGGAATGTA 57.087 29.630 0.00 0.00 36.82 2.29
529 991 9.950680 CAATACCATTAGATTTGTGGAATGTAC 57.049 33.333 0.00 0.00 36.82 2.90
530 992 9.920946 AATACCATTAGATTTGTGGAATGTACT 57.079 29.630 0.00 0.00 36.82 2.73
531 993 9.920946 ATACCATTAGATTTGTGGAATGTACTT 57.079 29.630 0.00 0.00 36.82 2.24
532 994 8.281212 ACCATTAGATTTGTGGAATGTACTTC 57.719 34.615 0.00 0.00 36.82 3.01
619 1081 8.950007 TCCTTTCTATAAATTTGGTCCAACTT 57.050 30.769 2.98 2.10 0.00 2.66
635 1097 9.974980 TGGTCCAACTTTATAAAATTTGACTTC 57.025 29.630 17.75 7.69 0.00 3.01
655 1117 7.876936 ACTTCAGTCAACTCTAATATACGGA 57.123 36.000 0.00 0.00 0.00 4.69
656 1118 7.932335 ACTTCAGTCAACTCTAATATACGGAG 58.068 38.462 0.00 0.00 0.00 4.63
674 1136 6.812879 ACGGAGTAAATAAAAACAAGGGAG 57.187 37.500 0.00 0.00 41.94 4.30
675 1137 6.301486 ACGGAGTAAATAAAAACAAGGGAGT 58.699 36.000 0.00 0.00 41.94 3.85
676 1138 7.452562 ACGGAGTAAATAAAAACAAGGGAGTA 58.547 34.615 0.00 0.00 41.94 2.59
677 1139 7.938490 ACGGAGTAAATAAAAACAAGGGAGTAA 59.062 33.333 0.00 0.00 41.94 2.24
678 1140 8.232513 CGGAGTAAATAAAAACAAGGGAGTAAC 58.767 37.037 0.00 0.00 0.00 2.50
679 1141 9.070179 GGAGTAAATAAAAACAAGGGAGTAACA 57.930 33.333 0.00 0.00 0.00 2.41
684 1146 9.594478 AAATAAAAACAAGGGAGTAACAAACTG 57.406 29.630 0.00 0.00 39.07 3.16
685 1147 5.592104 AAAACAAGGGAGTAACAAACTGG 57.408 39.130 0.00 0.00 39.07 4.00
686 1148 4.513406 AACAAGGGAGTAACAAACTGGA 57.487 40.909 0.00 0.00 39.07 3.86
687 1149 4.724279 ACAAGGGAGTAACAAACTGGAT 57.276 40.909 0.00 0.00 39.07 3.41
688 1150 5.061721 ACAAGGGAGTAACAAACTGGATT 57.938 39.130 0.00 0.00 39.07 3.01
689 1151 5.070685 ACAAGGGAGTAACAAACTGGATTC 58.929 41.667 0.00 0.00 39.07 2.52
690 1152 5.163088 ACAAGGGAGTAACAAACTGGATTCT 60.163 40.000 0.00 0.00 39.07 2.40
691 1153 5.167303 AGGGAGTAACAAACTGGATTCTC 57.833 43.478 0.00 0.00 39.07 2.87
692 1154 4.019231 AGGGAGTAACAAACTGGATTCTCC 60.019 45.833 0.00 0.00 39.07 3.71
693 1155 4.262617 GGAGTAACAAACTGGATTCTCCC 58.737 47.826 0.00 0.00 39.07 4.30
694 1156 4.019231 GGAGTAACAAACTGGATTCTCCCT 60.019 45.833 0.00 0.00 39.07 4.20
695 1157 5.515008 GGAGTAACAAACTGGATTCTCCCTT 60.515 44.000 0.00 0.00 39.07 3.95
696 1158 5.953571 AGTAACAAACTGGATTCTCCCTTT 58.046 37.500 0.00 0.00 36.93 3.11
697 1159 5.770162 AGTAACAAACTGGATTCTCCCTTTG 59.230 40.000 9.97 9.97 38.32 2.77
698 1160 3.500343 ACAAACTGGATTCTCCCTTTGG 58.500 45.455 13.69 0.00 37.44 3.28
699 1161 3.117131 ACAAACTGGATTCTCCCTTTGGT 60.117 43.478 13.69 0.62 37.44 3.67
700 1162 3.897505 CAAACTGGATTCTCCCTTTGGTT 59.102 43.478 5.89 0.00 35.03 3.67
701 1163 3.160679 ACTGGATTCTCCCTTTGGTTG 57.839 47.619 0.00 0.00 35.03 3.77
702 1164 1.821136 CTGGATTCTCCCTTTGGTTGC 59.179 52.381 0.00 0.00 35.03 4.17
703 1165 1.428912 TGGATTCTCCCTTTGGTTGCT 59.571 47.619 0.00 0.00 35.03 3.91
704 1166 2.095461 GGATTCTCCCTTTGGTTGCTC 58.905 52.381 0.00 0.00 0.00 4.26
705 1167 2.095461 GATTCTCCCTTTGGTTGCTCC 58.905 52.381 0.00 0.00 0.00 4.70
706 1168 0.850100 TTCTCCCTTTGGTTGCTCCA 59.150 50.000 0.00 0.00 45.60 3.86
715 1177 1.619654 TGGTTGCTCCAGGTGAAATG 58.380 50.000 0.00 0.00 41.93 2.32
716 1178 1.133513 TGGTTGCTCCAGGTGAAATGT 60.134 47.619 0.00 0.00 41.93 2.71
717 1179 1.270550 GGTTGCTCCAGGTGAAATGTG 59.729 52.381 0.00 0.00 35.97 3.21
718 1180 1.956477 GTTGCTCCAGGTGAAATGTGT 59.044 47.619 0.00 0.00 0.00 3.72
719 1181 1.608055 TGCTCCAGGTGAAATGTGTG 58.392 50.000 0.00 0.00 0.00 3.82
720 1182 1.133823 TGCTCCAGGTGAAATGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
721 1183 1.956477 GCTCCAGGTGAAATGTGTGTT 59.044 47.619 0.00 0.00 0.00 3.32
722 1184 2.030805 GCTCCAGGTGAAATGTGTGTTC 60.031 50.000 0.00 0.00 0.00 3.18
723 1185 3.480470 CTCCAGGTGAAATGTGTGTTCT 58.520 45.455 0.00 0.00 0.00 3.01
926 1463 1.682684 CTCCTCTACACGGGCCAGT 60.683 63.158 4.39 2.79 0.00 4.00
961 1500 1.842381 GACCACAAGAGTCCCCCAGG 61.842 65.000 0.00 0.00 0.00 4.45
962 1501 2.352805 CACAAGAGTCCCCCAGGC 59.647 66.667 0.00 0.00 0.00 4.85
963 1502 2.121963 ACAAGAGTCCCCCAGGCA 60.122 61.111 0.00 0.00 0.00 4.75
964 1503 1.774217 ACAAGAGTCCCCCAGGCAA 60.774 57.895 0.00 0.00 0.00 4.52
965 1504 1.360393 ACAAGAGTCCCCCAGGCAAA 61.360 55.000 0.00 0.00 0.00 3.68
1298 1852 1.754234 GGAGATGGGCAACGGCATT 60.754 57.895 0.00 0.00 43.71 3.56
1722 2333 2.358003 GCGAGCTCACAGCCAAGT 60.358 61.111 15.40 0.00 43.77 3.16
2017 2766 1.227556 ACAAGAACAAGCGCCGTCT 60.228 52.632 2.29 0.00 0.00 4.18
2291 3040 2.026262 GGCCAAGAAGGAGTGGAACATA 60.026 50.000 0.00 0.00 40.18 2.29
2297 3046 3.450457 AGAAGGAGTGGAACATAGAGCAG 59.550 47.826 0.00 0.00 44.52 4.24
2459 3247 4.039092 CCCTCCACCACAGGGCAG 62.039 72.222 0.00 0.00 44.59 4.85
2622 3421 4.872124 TGTAATCAGCAGTAGCAGTTGATG 59.128 41.667 0.00 0.00 45.49 3.07
2714 3518 2.553086 TGCCCGGAATAATCGTTGTAC 58.447 47.619 0.73 0.00 0.00 2.90
3142 3976 1.842052 AAACCCCACAAAGTCACGTT 58.158 45.000 0.00 0.00 0.00 3.99
3169 4003 0.383949 ACGCACACCCAAATTGTCAC 59.616 50.000 0.00 0.00 0.00 3.67
3179 4013 1.879380 CAAATTGTCACGCCCTCTTGA 59.121 47.619 0.00 0.00 0.00 3.02
3180 4014 1.813513 AATTGTCACGCCCTCTTGAG 58.186 50.000 0.00 0.00 0.00 3.02
3192 4031 1.347817 CTCTTGAGTCGCCTCGCAAC 61.348 60.000 0.00 0.00 40.85 4.17
3231 4070 1.529438 ACGTTTACGCTCCAACACATG 59.471 47.619 1.60 0.00 44.43 3.21
3244 4120 1.581934 ACACATGACACGGTTCAGTG 58.418 50.000 0.00 12.36 46.83 3.66
3265 4141 3.833070 TGAAACTTCCTAGGTGACCTCTC 59.167 47.826 7.77 0.00 34.61 3.20
3266 4142 2.535836 ACTTCCTAGGTGACCTCTCC 57.464 55.000 7.77 0.00 34.61 3.71
3501 6656 3.825014 GACCGTGGCTTGATATACCTAGA 59.175 47.826 0.00 0.00 0.00 2.43
3502 6657 3.827302 ACCGTGGCTTGATATACCTAGAG 59.173 47.826 0.00 0.00 0.00 2.43
3540 6695 3.368427 CCAACAGTTTCCTCGATAGCTCA 60.368 47.826 0.00 0.00 0.00 4.26
3550 6713 4.054671 CCTCGATAGCTCATTTTGTCTCC 58.945 47.826 0.00 0.00 0.00 3.71
3563 6728 1.182667 TGTCTCCGACCATGTACCAG 58.817 55.000 0.00 0.00 0.00 4.00
3578 6743 6.460781 CATGTACCAGTTCTAGTGTTGGTAA 58.539 40.000 17.45 11.53 45.05 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.122297 CGCAGAGAGAATTCTGGCTAAG 58.878 50.000 14.00 2.31 43.80 2.18
1 2 2.497675 ACGCAGAGAGAATTCTGGCTAA 59.502 45.455 14.00 0.00 43.80 3.09
2 3 2.103373 ACGCAGAGAGAATTCTGGCTA 58.897 47.619 14.00 0.00 43.80 3.93
3 4 0.901124 ACGCAGAGAGAATTCTGGCT 59.099 50.000 14.00 4.34 43.80 4.75
4 5 1.005340 CACGCAGAGAGAATTCTGGC 58.995 55.000 14.00 9.95 43.80 4.85
5 6 2.662006 TCACGCAGAGAGAATTCTGG 57.338 50.000 14.00 0.74 43.80 3.86
16 17 3.429547 GGAGAAAAGATAGCTCACGCAGA 60.430 47.826 0.00 0.00 39.10 4.26
17 18 2.863137 GGAGAAAAGATAGCTCACGCAG 59.137 50.000 0.00 0.00 39.10 5.18
18 19 2.497675 AGGAGAAAAGATAGCTCACGCA 59.502 45.455 0.00 0.00 39.10 5.24
19 20 2.863137 CAGGAGAAAAGATAGCTCACGC 59.137 50.000 0.00 0.00 0.00 5.34
20 21 3.862267 CACAGGAGAAAAGATAGCTCACG 59.138 47.826 0.00 0.00 0.00 4.35
21 22 3.620821 GCACAGGAGAAAAGATAGCTCAC 59.379 47.826 0.00 0.00 0.00 3.51
22 23 3.261643 TGCACAGGAGAAAAGATAGCTCA 59.738 43.478 0.00 0.00 0.00 4.26
23 24 3.866651 TGCACAGGAGAAAAGATAGCTC 58.133 45.455 0.00 0.00 0.00 4.09
24 25 3.988976 TGCACAGGAGAAAAGATAGCT 57.011 42.857 0.00 0.00 0.00 3.32
25 26 3.753272 TGTTGCACAGGAGAAAAGATAGC 59.247 43.478 0.00 0.00 0.00 2.97
26 27 6.149973 TGAATGTTGCACAGGAGAAAAGATAG 59.850 38.462 0.00 0.00 0.00 2.08
27 28 6.003326 TGAATGTTGCACAGGAGAAAAGATA 58.997 36.000 0.00 0.00 0.00 1.98
28 29 4.828939 TGAATGTTGCACAGGAGAAAAGAT 59.171 37.500 0.00 0.00 0.00 2.40
29 30 4.206375 TGAATGTTGCACAGGAGAAAAGA 58.794 39.130 0.00 0.00 0.00 2.52
30 31 4.572985 TGAATGTTGCACAGGAGAAAAG 57.427 40.909 0.00 0.00 0.00 2.27
31 32 4.737352 GCTTGAATGTTGCACAGGAGAAAA 60.737 41.667 0.00 0.00 0.00 2.29
32 33 3.243501 GCTTGAATGTTGCACAGGAGAAA 60.244 43.478 0.00 0.00 0.00 2.52
33 34 2.294233 GCTTGAATGTTGCACAGGAGAA 59.706 45.455 0.00 0.00 0.00 2.87
34 35 1.881973 GCTTGAATGTTGCACAGGAGA 59.118 47.619 0.00 0.00 0.00 3.71
35 36 1.400629 CGCTTGAATGTTGCACAGGAG 60.401 52.381 0.00 0.00 0.00 3.69
36 37 0.592637 CGCTTGAATGTTGCACAGGA 59.407 50.000 0.00 0.00 0.00 3.86
37 38 0.592637 TCGCTTGAATGTTGCACAGG 59.407 50.000 0.00 0.00 0.00 4.00
38 39 2.313234 CTTCGCTTGAATGTTGCACAG 58.687 47.619 0.00 0.00 0.00 3.66
39 40 1.600164 GCTTCGCTTGAATGTTGCACA 60.600 47.619 0.00 0.00 0.00 4.57
40 41 1.055338 GCTTCGCTTGAATGTTGCAC 58.945 50.000 0.00 0.00 0.00 4.57
41 42 0.667453 TGCTTCGCTTGAATGTTGCA 59.333 45.000 0.00 0.00 29.68 4.08
42 43 1.055338 GTGCTTCGCTTGAATGTTGC 58.945 50.000 0.00 0.00 0.00 4.17
43 44 2.404265 TGTGCTTCGCTTGAATGTTG 57.596 45.000 0.00 0.00 0.00 3.33
44 45 2.543653 GGTTGTGCTTCGCTTGAATGTT 60.544 45.455 0.00 0.00 0.00 2.71
45 46 1.001378 GGTTGTGCTTCGCTTGAATGT 60.001 47.619 0.00 0.00 0.00 2.71
46 47 1.267806 AGGTTGTGCTTCGCTTGAATG 59.732 47.619 0.00 0.00 0.00 2.67
47 48 1.267806 CAGGTTGTGCTTCGCTTGAAT 59.732 47.619 0.00 0.00 0.00 2.57
48 49 0.662619 CAGGTTGTGCTTCGCTTGAA 59.337 50.000 0.00 0.00 0.00 2.69
49 50 0.463654 ACAGGTTGTGCTTCGCTTGA 60.464 50.000 0.00 0.00 0.00 3.02
50 51 0.317269 CACAGGTTGTGCTTCGCTTG 60.317 55.000 0.00 0.00 41.89 4.01
51 52 2.024918 CACAGGTTGTGCTTCGCTT 58.975 52.632 0.00 0.00 41.89 4.68
52 53 3.736483 CACAGGTTGTGCTTCGCT 58.264 55.556 0.00 0.00 41.89 4.93
60 61 1.321474 CACTTGGCATCACAGGTTGT 58.679 50.000 0.00 0.00 0.00 3.32
61 62 0.599558 CCACTTGGCATCACAGGTTG 59.400 55.000 0.00 0.00 0.00 3.77
62 63 0.478072 TCCACTTGGCATCACAGGTT 59.522 50.000 0.00 0.00 34.44 3.50
63 64 0.478072 TTCCACTTGGCATCACAGGT 59.522 50.000 0.00 0.00 34.44 4.00
64 65 0.883833 GTTCCACTTGGCATCACAGG 59.116 55.000 0.00 0.00 34.44 4.00
65 66 1.901591 AGTTCCACTTGGCATCACAG 58.098 50.000 0.00 0.00 34.44 3.66
66 67 3.719268 ATAGTTCCACTTGGCATCACA 57.281 42.857 0.00 0.00 34.44 3.58
67 68 3.877508 GGTATAGTTCCACTTGGCATCAC 59.122 47.826 0.00 0.00 34.44 3.06
68 69 3.780294 AGGTATAGTTCCACTTGGCATCA 59.220 43.478 0.00 0.00 34.44 3.07
69 70 4.423625 AGGTATAGTTCCACTTGGCATC 57.576 45.455 0.00 0.00 34.44 3.91
70 71 4.526970 CAAGGTATAGTTCCACTTGGCAT 58.473 43.478 0.00 0.00 35.96 4.40
71 72 3.950397 CAAGGTATAGTTCCACTTGGCA 58.050 45.455 0.00 0.00 35.96 4.92
74 75 4.906618 ACACCAAGGTATAGTTCCACTTG 58.093 43.478 0.00 0.00 38.52 3.16
75 76 4.595781 TGACACCAAGGTATAGTTCCACTT 59.404 41.667 0.00 0.00 0.00 3.16
76 77 4.164981 TGACACCAAGGTATAGTTCCACT 58.835 43.478 0.00 0.00 0.00 4.00
77 78 4.546829 TGACACCAAGGTATAGTTCCAC 57.453 45.455 0.00 0.00 0.00 4.02
78 79 5.249622 TCATTGACACCAAGGTATAGTTCCA 59.750 40.000 0.00 0.00 35.72 3.53
79 80 5.741011 TCATTGACACCAAGGTATAGTTCC 58.259 41.667 0.00 0.00 35.72 3.62
80 81 7.865706 ATTCATTGACACCAAGGTATAGTTC 57.134 36.000 0.00 0.00 35.72 3.01
81 82 9.396022 CTTATTCATTGACACCAAGGTATAGTT 57.604 33.333 0.00 0.00 35.72 2.24
82 83 7.993183 CCTTATTCATTGACACCAAGGTATAGT 59.007 37.037 0.00 0.00 35.72 2.12
83 84 7.993183 ACCTTATTCATTGACACCAAGGTATAG 59.007 37.037 14.28 0.00 41.80 1.31
84 85 7.867921 ACCTTATTCATTGACACCAAGGTATA 58.132 34.615 14.28 0.00 41.80 1.47
85 86 6.731467 ACCTTATTCATTGACACCAAGGTAT 58.269 36.000 14.28 0.00 41.80 2.73
86 87 6.134535 ACCTTATTCATTGACACCAAGGTA 57.865 37.500 14.28 0.00 41.80 3.08
87 88 4.998051 ACCTTATTCATTGACACCAAGGT 58.002 39.130 11.73 11.73 39.48 3.50
88 89 5.982890 AACCTTATTCATTGACACCAAGG 57.017 39.130 10.83 10.83 37.63 3.61
89 90 8.576442 AGTAAAACCTTATTCATTGACACCAAG 58.424 33.333 0.00 0.00 35.48 3.61
90 91 8.472007 AGTAAAACCTTATTCATTGACACCAA 57.528 30.769 0.00 0.00 36.61 3.67
91 92 7.942341 AGAGTAAAACCTTATTCATTGACACCA 59.058 33.333 0.00 0.00 0.00 4.17
92 93 8.336801 AGAGTAAAACCTTATTCATTGACACC 57.663 34.615 0.00 0.00 0.00 4.16
94 95 9.667107 CCTAGAGTAAAACCTTATTCATTGACA 57.333 33.333 0.00 0.00 0.00 3.58
95 96 9.668497 ACCTAGAGTAAAACCTTATTCATTGAC 57.332 33.333 0.00 0.00 0.00 3.18
106 107 9.892130 CTGATATGAAAACCTAGAGTAAAACCT 57.108 33.333 0.00 0.00 0.00 3.50
107 108 8.613482 GCTGATATGAAAACCTAGAGTAAAACC 58.387 37.037 0.00 0.00 0.00 3.27
108 109 9.162764 TGCTGATATGAAAACCTAGAGTAAAAC 57.837 33.333 0.00 0.00 0.00 2.43
109 110 9.733556 TTGCTGATATGAAAACCTAGAGTAAAA 57.266 29.630 0.00 0.00 0.00 1.52
110 111 9.162764 GTTGCTGATATGAAAACCTAGAGTAAA 57.837 33.333 0.00 0.00 0.00 2.01
111 112 7.769044 GGTTGCTGATATGAAAACCTAGAGTAA 59.231 37.037 0.00 0.00 37.81 2.24
112 113 7.272978 GGTTGCTGATATGAAAACCTAGAGTA 58.727 38.462 0.00 0.00 37.81 2.59
113 114 6.116126 GGTTGCTGATATGAAAACCTAGAGT 58.884 40.000 0.00 0.00 37.81 3.24
114 115 5.235186 CGGTTGCTGATATGAAAACCTAGAG 59.765 44.000 0.00 0.00 38.50 2.43
115 116 5.116180 CGGTTGCTGATATGAAAACCTAGA 58.884 41.667 0.00 0.00 38.50 2.43
116 117 4.876107 ACGGTTGCTGATATGAAAACCTAG 59.124 41.667 0.00 0.00 38.50 3.02
117 118 4.839121 ACGGTTGCTGATATGAAAACCTA 58.161 39.130 0.00 0.00 38.50 3.08
118 119 3.686016 ACGGTTGCTGATATGAAAACCT 58.314 40.909 0.00 0.00 38.50 3.50
119 120 4.156008 AGAACGGTTGCTGATATGAAAACC 59.844 41.667 0.00 0.00 37.51 3.27
120 121 5.296813 AGAACGGTTGCTGATATGAAAAC 57.703 39.130 0.00 0.00 0.00 2.43
121 122 5.957842 AAGAACGGTTGCTGATATGAAAA 57.042 34.783 0.00 0.00 0.00 2.29
122 123 5.957842 AAAGAACGGTTGCTGATATGAAA 57.042 34.783 0.00 0.00 0.00 2.69
123 124 5.471797 TGAAAAGAACGGTTGCTGATATGAA 59.528 36.000 0.00 0.00 0.00 2.57
124 125 5.000591 TGAAAAGAACGGTTGCTGATATGA 58.999 37.500 0.00 0.00 0.00 2.15
125 126 5.295431 TGAAAAGAACGGTTGCTGATATG 57.705 39.130 0.00 0.00 0.00 1.78
126 127 4.142600 GCTGAAAAGAACGGTTGCTGATAT 60.143 41.667 0.00 0.00 0.00 1.63
127 128 3.188460 GCTGAAAAGAACGGTTGCTGATA 59.812 43.478 0.00 0.00 0.00 2.15
128 129 2.030805 GCTGAAAAGAACGGTTGCTGAT 60.031 45.455 0.00 0.00 0.00 2.90
129 130 1.333619 GCTGAAAAGAACGGTTGCTGA 59.666 47.619 0.00 0.00 0.00 4.26
130 131 1.334869 AGCTGAAAAGAACGGTTGCTG 59.665 47.619 0.00 0.00 0.00 4.41
131 132 1.680338 AGCTGAAAAGAACGGTTGCT 58.320 45.000 0.00 0.00 0.00 3.91
132 133 2.119457 CAAGCTGAAAAGAACGGTTGC 58.881 47.619 0.00 0.00 0.00 4.17
133 134 3.691049 TCAAGCTGAAAAGAACGGTTG 57.309 42.857 0.00 0.00 36.51 3.77
134 135 4.918810 AATCAAGCTGAAAAGAACGGTT 57.081 36.364 0.00 0.00 0.00 4.44
135 136 4.918810 AAATCAAGCTGAAAAGAACGGT 57.081 36.364 0.00 0.00 0.00 4.83
136 137 5.280945 TCAAAATCAAGCTGAAAAGAACGG 58.719 37.500 0.00 0.00 0.00 4.44
137 138 6.998258 ATCAAAATCAAGCTGAAAAGAACG 57.002 33.333 0.00 0.00 0.00 3.95
138 139 8.485591 CAGAATCAAAATCAAGCTGAAAAGAAC 58.514 33.333 0.00 0.00 0.00 3.01
139 140 7.654520 CCAGAATCAAAATCAAGCTGAAAAGAA 59.345 33.333 0.00 0.00 0.00 2.52
140 141 7.149973 CCAGAATCAAAATCAAGCTGAAAAGA 58.850 34.615 0.00 0.00 0.00 2.52
141 142 6.927381 ACCAGAATCAAAATCAAGCTGAAAAG 59.073 34.615 0.00 0.00 0.00 2.27
142 143 6.702723 CACCAGAATCAAAATCAAGCTGAAAA 59.297 34.615 0.00 0.00 0.00 2.29
143 144 6.040729 TCACCAGAATCAAAATCAAGCTGAAA 59.959 34.615 0.00 0.00 0.00 2.69
144 145 5.535783 TCACCAGAATCAAAATCAAGCTGAA 59.464 36.000 0.00 0.00 0.00 3.02
145 146 5.072055 TCACCAGAATCAAAATCAAGCTGA 58.928 37.500 0.00 0.00 0.00 4.26
146 147 5.381174 TCACCAGAATCAAAATCAAGCTG 57.619 39.130 0.00 0.00 0.00 4.24
147 148 6.395629 CATTCACCAGAATCAAAATCAAGCT 58.604 36.000 0.00 0.00 42.46 3.74
165 166 1.392589 AATCATGACCGCCCATTCAC 58.607 50.000 0.00 0.00 0.00 3.18
175 176 2.614057 CGAAGGCCAGTAAATCATGACC 59.386 50.000 5.01 0.00 0.00 4.02
176 177 2.032178 GCGAAGGCCAGTAAATCATGAC 59.968 50.000 5.01 0.00 0.00 3.06
195 196 3.528370 AGTAGCTAGGGCGTGGCG 61.528 66.667 9.88 0.00 44.37 5.69
201 202 0.103937 CAGCAGACAGTAGCTAGGGC 59.896 60.000 0.00 0.00 39.50 5.19
209 210 0.976641 CCCACTTCCAGCAGACAGTA 59.023 55.000 0.00 0.00 0.00 2.74
211 212 1.002868 CCCCACTTCCAGCAGACAG 60.003 63.158 0.00 0.00 0.00 3.51
212 213 1.059584 TTCCCCACTTCCAGCAGACA 61.060 55.000 0.00 0.00 0.00 3.41
217 218 0.890683 CAATGTTCCCCACTTCCAGC 59.109 55.000 0.00 0.00 0.00 4.85
233 235 3.684788 CGGTTCGAATCTTTCTGGACAAT 59.315 43.478 6.88 0.00 0.00 2.71
271 273 1.599797 AAACACTACTGCGCCCCAC 60.600 57.895 4.18 0.00 0.00 4.61
288 290 3.817084 CCATTGCTCACTTCTTCTGACAA 59.183 43.478 0.00 0.00 0.00 3.18
289 291 3.405831 CCATTGCTCACTTCTTCTGACA 58.594 45.455 0.00 0.00 0.00 3.58
303 305 2.348888 GCTTGCTCTGGCCATTGCT 61.349 57.895 24.34 0.00 37.74 3.91
311 313 1.584380 GCCTCAACTGCTTGCTCTGG 61.584 60.000 0.00 0.00 0.00 3.86
313 315 1.303155 GGCCTCAACTGCTTGCTCT 60.303 57.895 0.00 0.00 0.00 4.09
331 333 0.882042 CCTCTTTCATCCCGATGGCG 60.882 60.000 4.90 0.00 39.24 5.69
337 341 3.620488 TCAATTTCCCTCTTTCATCCCG 58.380 45.455 0.00 0.00 0.00 5.14
338 342 3.382865 GCTCAATTTCCCTCTTTCATCCC 59.617 47.826 0.00 0.00 0.00 3.85
351 355 4.218312 ACATAGAATGGGGGCTCAATTTC 58.782 43.478 0.00 0.00 33.60 2.17
355 359 2.358090 CCAACATAGAATGGGGGCTCAA 60.358 50.000 0.00 0.00 32.87 3.02
376 795 2.457366 ACCATCGACAAGGTGTTCTC 57.543 50.000 5.33 0.00 36.60 2.87
428 890 4.391405 AAAGCCTGACTTTGACCAAAAG 57.609 40.909 0.00 0.00 47.00 2.27
440 902 8.507470 CTTTGTCAAAGTTTATAAAGCCTGAC 57.493 34.615 15.93 18.18 33.80 3.51
501 963 9.425248 ACATTCCACAAATCTAATGGTATTGAT 57.575 29.630 0.00 0.00 34.38 2.57
502 964 8.821686 ACATTCCACAAATCTAATGGTATTGA 57.178 30.769 0.00 0.00 34.38 2.57
503 965 9.950680 GTACATTCCACAAATCTAATGGTATTG 57.049 33.333 0.00 0.00 34.38 1.90
504 966 9.920946 AGTACATTCCACAAATCTAATGGTATT 57.079 29.630 0.00 0.00 34.38 1.89
505 967 9.920946 AAGTACATTCCACAAATCTAATGGTAT 57.079 29.630 0.00 0.00 34.38 2.73
506 968 9.391006 GAAGTACATTCCACAAATCTAATGGTA 57.609 33.333 0.00 0.00 34.38 3.25
507 969 8.281212 GAAGTACATTCCACAAATCTAATGGT 57.719 34.615 0.00 0.00 34.38 3.55
594 1056 8.950007 AAGTTGGACCAAATTTATAGAAAGGA 57.050 30.769 14.02 0.00 26.81 3.36
610 1072 9.974980 TGAAGTCAAATTTTATAAAGTTGGACC 57.025 29.630 25.81 17.18 38.57 4.46
630 1092 7.928103 TCCGTATATTAGAGTTGACTGAAGTC 58.072 38.462 3.41 3.41 44.97 3.01
631 1093 7.556996 ACTCCGTATATTAGAGTTGACTGAAGT 59.443 37.037 0.00 0.00 37.60 3.01
633 1095 7.876936 ACTCCGTATATTAGAGTTGACTGAA 57.123 36.000 0.00 0.00 37.60 3.02
634 1096 8.969260 TTACTCCGTATATTAGAGTTGACTGA 57.031 34.615 7.36 0.00 41.09 3.41
648 1110 9.603921 CTCCCTTGTTTTTATTTACTCCGTATA 57.396 33.333 0.00 0.00 0.00 1.47
650 1112 7.452562 ACTCCCTTGTTTTTATTTACTCCGTA 58.547 34.615 0.00 0.00 0.00 4.02
651 1113 6.301486 ACTCCCTTGTTTTTATTTACTCCGT 58.699 36.000 0.00 0.00 0.00 4.69
652 1114 6.812879 ACTCCCTTGTTTTTATTTACTCCG 57.187 37.500 0.00 0.00 0.00 4.63
653 1115 9.070179 TGTTACTCCCTTGTTTTTATTTACTCC 57.930 33.333 0.00 0.00 0.00 3.85
658 1120 9.594478 CAGTTTGTTACTCCCTTGTTTTTATTT 57.406 29.630 0.00 0.00 33.85 1.40
659 1121 8.201464 CCAGTTTGTTACTCCCTTGTTTTTATT 58.799 33.333 0.00 0.00 33.85 1.40
660 1122 7.562088 TCCAGTTTGTTACTCCCTTGTTTTTAT 59.438 33.333 0.00 0.00 33.85 1.40
661 1123 6.890814 TCCAGTTTGTTACTCCCTTGTTTTTA 59.109 34.615 0.00 0.00 33.85 1.52
662 1124 5.717654 TCCAGTTTGTTACTCCCTTGTTTTT 59.282 36.000 0.00 0.00 33.85 1.94
663 1125 5.265989 TCCAGTTTGTTACTCCCTTGTTTT 58.734 37.500 0.00 0.00 33.85 2.43
664 1126 4.862371 TCCAGTTTGTTACTCCCTTGTTT 58.138 39.130 0.00 0.00 33.85 2.83
665 1127 4.513406 TCCAGTTTGTTACTCCCTTGTT 57.487 40.909 0.00 0.00 33.85 2.83
666 1128 4.724279 ATCCAGTTTGTTACTCCCTTGT 57.276 40.909 0.00 0.00 33.85 3.16
667 1129 5.316987 AGAATCCAGTTTGTTACTCCCTTG 58.683 41.667 0.00 0.00 33.85 3.61
668 1130 5.561679 GAGAATCCAGTTTGTTACTCCCTT 58.438 41.667 0.00 0.00 33.85 3.95
669 1131 5.167303 GAGAATCCAGTTTGTTACTCCCT 57.833 43.478 0.00 0.00 33.85 4.20
685 1147 2.095461 GGAGCAACCAAAGGGAGAATC 58.905 52.381 0.00 0.00 38.79 2.52
686 1148 1.428912 TGGAGCAACCAAAGGGAGAAT 59.571 47.619 0.11 0.00 46.75 2.40
687 1149 0.850100 TGGAGCAACCAAAGGGAGAA 59.150 50.000 0.11 0.00 46.75 2.87
688 1150 2.550787 TGGAGCAACCAAAGGGAGA 58.449 52.632 0.11 0.00 46.75 3.71
697 1159 1.270550 CACATTTCACCTGGAGCAACC 59.729 52.381 0.00 0.00 39.54 3.77
698 1160 1.956477 ACACATTTCACCTGGAGCAAC 59.044 47.619 0.00 0.00 0.00 4.17
699 1161 1.955778 CACACATTTCACCTGGAGCAA 59.044 47.619 0.00 0.00 0.00 3.91
700 1162 1.133823 ACACACATTTCACCTGGAGCA 60.134 47.619 0.00 0.00 0.00 4.26
701 1163 1.609208 ACACACATTTCACCTGGAGC 58.391 50.000 0.00 0.00 0.00 4.70
702 1164 3.480470 AGAACACACATTTCACCTGGAG 58.520 45.455 0.00 0.00 0.00 3.86
703 1165 3.576078 AGAACACACATTTCACCTGGA 57.424 42.857 0.00 0.00 0.00 3.86
704 1166 4.133820 TGTAGAACACACATTTCACCTGG 58.866 43.478 0.00 0.00 30.04 4.45
705 1167 4.319766 GCTGTAGAACACACATTTCACCTG 60.320 45.833 0.00 0.00 32.33 4.00
706 1168 3.815401 GCTGTAGAACACACATTTCACCT 59.185 43.478 0.00 0.00 32.33 4.00
707 1169 3.058224 GGCTGTAGAACACACATTTCACC 60.058 47.826 0.00 0.00 32.33 4.02
708 1170 3.563808 TGGCTGTAGAACACACATTTCAC 59.436 43.478 0.00 0.00 32.33 3.18
709 1171 3.814625 TGGCTGTAGAACACACATTTCA 58.185 40.909 0.00 0.00 32.33 2.69
710 1172 3.365364 GCTGGCTGTAGAACACACATTTC 60.365 47.826 0.00 0.00 32.33 2.17
711 1173 2.554032 GCTGGCTGTAGAACACACATTT 59.446 45.455 0.00 0.00 32.33 2.32
712 1174 2.154462 GCTGGCTGTAGAACACACATT 58.846 47.619 0.00 0.00 32.33 2.71
713 1175 1.611673 GGCTGGCTGTAGAACACACAT 60.612 52.381 0.00 0.00 32.33 3.21
714 1176 0.250295 GGCTGGCTGTAGAACACACA 60.250 55.000 0.00 0.00 32.33 3.72
715 1177 1.291877 CGGCTGGCTGTAGAACACAC 61.292 60.000 0.00 0.00 32.33 3.82
716 1178 1.005037 CGGCTGGCTGTAGAACACA 60.005 57.895 0.00 0.00 35.30 3.72
717 1179 0.737715 CTCGGCTGGCTGTAGAACAC 60.738 60.000 0.00 0.00 0.00 3.32
718 1180 1.591703 CTCGGCTGGCTGTAGAACA 59.408 57.895 0.00 0.00 0.00 3.18
719 1181 1.153549 CCTCGGCTGGCTGTAGAAC 60.154 63.158 0.00 0.00 0.00 3.01
720 1182 1.304962 TCCTCGGCTGGCTGTAGAA 60.305 57.895 0.00 0.00 0.00 2.10
721 1183 1.754621 CTCCTCGGCTGGCTGTAGA 60.755 63.158 0.00 0.00 0.00 2.59
722 1184 2.811101 CTCCTCGGCTGGCTGTAG 59.189 66.667 0.00 0.00 0.00 2.74
723 1185 3.461773 GCTCCTCGGCTGGCTGTA 61.462 66.667 0.00 0.00 0.00 2.74
883 1419 1.676529 GAATAAAAAGGAGGAGCGGGC 59.323 52.381 0.00 0.00 0.00 6.13
926 1463 3.211045 GTGGTCAACTCTAGGTTTTGCA 58.789 45.455 0.00 0.00 35.74 4.08
1006 1548 2.202932 CAACCCTCTCCATCGGCG 60.203 66.667 0.00 0.00 0.00 6.46
1688 2299 2.981302 CCCATGGTGTCGAGCAGA 59.019 61.111 11.73 0.00 31.77 4.26
1995 2687 2.050077 GCGCTTGTTCTTGTGCCC 60.050 61.111 0.00 0.00 34.05 5.36
1997 2689 2.427410 CGGCGCTTGTTCTTGTGC 60.427 61.111 7.64 0.00 38.78 4.57
2100 2849 2.701780 GCTTCAGCTGCTGCATGCT 61.702 57.895 24.38 17.06 43.37 3.79
2101 2850 2.202623 GCTTCAGCTGCTGCATGC 60.203 61.111 24.38 21.33 42.74 4.06
2204 2953 2.361357 ACCTCGTACGCCAGCTCT 60.361 61.111 11.24 0.00 0.00 4.09
2459 3247 1.147153 CCTGCCTAGCTAGTTGGGC 59.853 63.158 24.39 24.39 44.31 5.36
2622 3421 3.565902 GGCAGGCATCTTACAGGTTATTC 59.434 47.826 0.00 0.00 0.00 1.75
2714 3518 2.061773 CACTCAACGCTGACAAGTAGG 58.938 52.381 0.00 0.00 0.00 3.18
3142 3976 1.195442 TTGGGTGTGCGTAGGATCCA 61.195 55.000 15.82 0.00 0.00 3.41
3169 4003 3.764466 AGGCGACTCAAGAGGGCG 61.764 66.667 1.73 6.20 32.90 6.13
3192 4031 1.670811 GTTCACGATGGTTATGGGCAG 59.329 52.381 0.00 0.00 0.00 4.85
3231 4070 2.287103 GGAAGTTTCACTGAACCGTGTC 59.713 50.000 0.00 0.00 36.33 3.67
3244 4120 3.196039 GGAGAGGTCACCTAGGAAGTTTC 59.804 52.174 17.98 7.46 31.76 2.78
3265 4141 1.635487 TGAGTTTGAATGGGGAGAGGG 59.365 52.381 0.00 0.00 0.00 4.30
3266 4142 2.716217 GTGAGTTTGAATGGGGAGAGG 58.284 52.381 0.00 0.00 0.00 3.69
3501 6656 6.365520 ACTGTTGGGAAAACTTGATTCTACT 58.634 36.000 0.00 0.00 0.00 2.57
3502 6657 6.635030 ACTGTTGGGAAAACTTGATTCTAC 57.365 37.500 0.00 0.00 0.00 2.59
3550 6713 3.192844 ACACTAGAACTGGTACATGGTCG 59.807 47.826 0.00 0.00 38.20 4.79
3563 6728 5.941948 AGTGCATTTACCAACACTAGAAC 57.058 39.130 0.00 0.00 41.41 3.01
3578 6743 1.194121 GGAAAGGGGGCAAGTGCATT 61.194 55.000 5.52 0.00 44.36 3.56


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

AutoCloner maintained by Alex Coulton.