Multiple sequence alignment - TraesCS2D01G446400

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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 TraesCS2D01G446400 chr2D 100.000 3103 0 0 1 3103 556618141 556621243 0.000000e+00 5731.0
1 TraesCS2D01G446400 chr2D 90.016 2564 158 52 581 3103 556365081 556367587 0.000000e+00 3227.0
2 TraesCS2D01G446400 chr2D 90.078 1673 105 30 614 2268 556407664 556409293 0.000000e+00 2113.0
3 TraesCS2D01G446400 chr2D 93.744 1135 56 6 1979 3103 556333878 556335007 0.000000e+00 1688.0
4 TraesCS2D01G446400 chr2D 83.643 1559 164 28 763 2256 556267000 556268532 0.000000e+00 1382.0
5 TraesCS2D01G446400 chr2D 82.728 1488 174 33 830 2256 556350383 556351848 0.000000e+00 1247.0
6 TraesCS2D01G446400 chr2D 91.946 745 43 8 2265 2997 556411563 556412302 0.000000e+00 1027.0
7 TraesCS2D01G446400 chr2D 86.463 820 66 23 999 1799 556642397 556643190 0.000000e+00 857.0
8 TraesCS2D01G446400 chr2D 82.470 907 68 31 611 1506 556318081 556318907 0.000000e+00 710.0
9 TraesCS2D01G446400 chr2D 91.368 475 34 4 1501 1968 556333284 556333758 0.000000e+00 643.0
10 TraesCS2D01G446400 chr2D 80.126 951 108 36 1384 2256 556339285 556340232 4.370000e-178 634.0
11 TraesCS2D01G446400 chr2D 81.271 299 29 17 183 479 556349797 556350070 1.870000e-52 217.0
12 TraesCS2D01G446400 chr2D 94.495 109 6 0 2995 3103 556421605 556421713 5.320000e-38 169.0
13 TraesCS2D01G446400 chr2D 84.146 82 8 3 10 86 556349687 556349768 1.190000e-09 75.0
14 TraesCS2D01G446400 chr2A 92.531 2169 93 34 964 3103 696219181 696221309 0.000000e+00 3044.0
15 TraesCS2D01G446400 chr2A 89.539 1281 101 12 1591 2846 696307690 696308962 0.000000e+00 1592.0
16 TraesCS2D01G446400 chr2A 83.313 1654 158 58 658 2256 696040132 696041722 0.000000e+00 1417.0
17 TraesCS2D01G446400 chr2A 82.185 1712 201 47 625 2256 695998750 696000437 0.000000e+00 1376.0
18 TraesCS2D01G446400 chr2A 92.453 742 44 8 861 1592 696306895 696307634 0.000000e+00 1050.0
19 TraesCS2D01G446400 chr2A 100.000 31 0 0 523 553 696218691 696218721 1.200000e-04 58.4
20 TraesCS2D01G446400 chr2B 88.197 1686 124 35 715 2374 663885751 663887387 0.000000e+00 1941.0
21 TraesCS2D01G446400 chr2B 83.549 1702 173 44 625 2249 663828606 663830277 0.000000e+00 1493.0
22 TraesCS2D01G446400 chr2B 83.213 1525 150 54 621 2105 663837643 663839101 0.000000e+00 1301.0
23 TraesCS2D01G446400 chr2B 78.413 315 53 11 1809 2110 663899586 663899898 1.140000e-44 191.0
24 TraesCS2D01G446400 chr2B 82.018 228 25 10 179 404 663885271 663885484 2.460000e-41 180.0
25 TraesCS2D01G446400 chr3B 100.000 28 0 0 474 501 30132730 30132757 6.000000e-03 52.8


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 TraesCS2D01G446400 chr2D 556618141 556621243 3102 False 5731.0 5731 100.0000 1 3103 1 chr2D.!!$F6 3102
1 TraesCS2D01G446400 chr2D 556365081 556367587 2506 False 3227.0 3227 90.0160 581 3103 1 chr2D.!!$F4 2522
2 TraesCS2D01G446400 chr2D 556407664 556412302 4638 False 1570.0 2113 91.0120 614 2997 2 chr2D.!!$F10 2383
3 TraesCS2D01G446400 chr2D 556267000 556268532 1532 False 1382.0 1382 83.6430 763 2256 1 chr2D.!!$F1 1493
4 TraesCS2D01G446400 chr2D 556333284 556335007 1723 False 1165.5 1688 92.5560 1501 3103 2 chr2D.!!$F8 1602
5 TraesCS2D01G446400 chr2D 556642397 556643190 793 False 857.0 857 86.4630 999 1799 1 chr2D.!!$F7 800
6 TraesCS2D01G446400 chr2D 556318081 556318907 826 False 710.0 710 82.4700 611 1506 1 chr2D.!!$F2 895
7 TraesCS2D01G446400 chr2D 556339285 556340232 947 False 634.0 634 80.1260 1384 2256 1 chr2D.!!$F3 872
8 TraesCS2D01G446400 chr2D 556349687 556351848 2161 False 513.0 1247 82.7150 10 2256 3 chr2D.!!$F9 2246
9 TraesCS2D01G446400 chr2A 696218691 696221309 2618 False 1551.2 3044 96.2655 523 3103 2 chr2A.!!$F3 2580
10 TraesCS2D01G446400 chr2A 696040132 696041722 1590 False 1417.0 1417 83.3130 658 2256 1 chr2A.!!$F2 1598
11 TraesCS2D01G446400 chr2A 695998750 696000437 1687 False 1376.0 1376 82.1850 625 2256 1 chr2A.!!$F1 1631
12 TraesCS2D01G446400 chr2A 696306895 696308962 2067 False 1321.0 1592 90.9960 861 2846 2 chr2A.!!$F4 1985
13 TraesCS2D01G446400 chr2B 663828606 663830277 1671 False 1493.0 1493 83.5490 625 2249 1 chr2B.!!$F1 1624
14 TraesCS2D01G446400 chr2B 663837643 663839101 1458 False 1301.0 1301 83.2130 621 2105 1 chr2B.!!$F2 1484
15 TraesCS2D01G446400 chr2B 663885271 663887387 2116 False 1060.5 1941 85.1075 179 2374 2 chr2B.!!$F4 2195

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
147 153 0.039256 CCGTACGTTCTCGGGAAACA 60.039 55.0 15.21 0.0 42.61 2.83 F
511 519 0.322546 GGGCAGGTTTCCTCATTCGT 60.323 55.0 0.00 0.0 0.00 3.85 F
1592 1910 0.391597 AGACCAACCACGACGTCAAT 59.608 50.0 17.16 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 1585 0.674895 CAAAAGGTCGAGCTGGAGGG 60.675 60.000 19.39 2.88 0.00 4.30 R
1919 2263 1.078918 CTGATCAGCCCGTTCAGCA 60.079 57.895 10.38 0.00 35.27 4.41 R
2910 5757 1.405933 CCTCTGCGACATGTCCAATCA 60.406 52.381 20.03 11.42 0.00 2.57 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
37 38 0.894835 GCCATGTCCCGTGGAAAATT 59.105 50.000 6.66 0.00 42.73 1.82
41 42 3.195396 CCATGTCCCGTGGAAAATTTGAT 59.805 43.478 0.00 0.00 42.73 2.57
60 61 3.759544 ACGAGAGAACGTCTGGCA 58.240 55.556 0.00 0.00 43.02 4.92
61 62 2.268022 ACGAGAGAACGTCTGGCAT 58.732 52.632 0.00 0.00 43.02 4.40
62 63 0.171455 ACGAGAGAACGTCTGGCATC 59.829 55.000 0.00 0.00 43.02 3.91
63 64 0.171231 CGAGAGAACGTCTGGCATCA 59.829 55.000 0.00 0.00 34.71 3.07
64 65 1.202348 CGAGAGAACGTCTGGCATCAT 60.202 52.381 0.00 0.00 34.71 2.45
65 66 2.200067 GAGAGAACGTCTGGCATCATG 58.800 52.381 0.00 0.00 34.71 3.07
66 67 1.134580 AGAGAACGTCTGGCATCATGG 60.135 52.381 0.00 0.00 32.57 3.66
67 68 0.615331 AGAACGTCTGGCATCATGGT 59.385 50.000 0.00 0.00 0.00 3.55
68 69 1.009829 GAACGTCTGGCATCATGGTC 58.990 55.000 0.00 0.00 0.00 4.02
86 92 3.196463 GGTCATGAGCACTCAGATTCAG 58.804 50.000 19.79 0.00 43.61 3.02
87 93 3.118847 GGTCATGAGCACTCAGATTCAGA 60.119 47.826 19.79 0.00 43.61 3.27
88 94 4.502016 GTCATGAGCACTCAGATTCAGAA 58.498 43.478 6.50 0.00 43.61 3.02
89 95 4.567558 GTCATGAGCACTCAGATTCAGAAG 59.432 45.833 6.50 0.00 43.61 2.85
90 96 2.969990 TGAGCACTCAGATTCAGAAGC 58.030 47.619 0.00 0.00 34.14 3.86
91 97 2.301009 TGAGCACTCAGATTCAGAAGCA 59.699 45.455 0.31 0.00 34.14 3.91
92 98 2.931325 GAGCACTCAGATTCAGAAGCAG 59.069 50.000 0.31 0.00 0.00 4.24
93 99 1.397692 GCACTCAGATTCAGAAGCAGC 59.602 52.381 0.31 0.00 0.00 5.25
94 100 2.696506 CACTCAGATTCAGAAGCAGCA 58.303 47.619 0.31 0.00 0.00 4.41
95 101 2.415857 CACTCAGATTCAGAAGCAGCAC 59.584 50.000 0.31 0.00 0.00 4.40
96 102 2.038164 ACTCAGATTCAGAAGCAGCACA 59.962 45.455 0.31 0.00 0.00 4.57
97 103 2.673862 CTCAGATTCAGAAGCAGCACAG 59.326 50.000 0.31 0.00 0.00 3.66
98 104 1.738350 CAGATTCAGAAGCAGCACAGG 59.262 52.381 0.31 0.00 0.00 4.00
99 105 1.627329 AGATTCAGAAGCAGCACAGGA 59.373 47.619 0.31 0.00 0.00 3.86
100 106 2.239150 AGATTCAGAAGCAGCACAGGAT 59.761 45.455 0.31 0.00 0.00 3.24
101 107 2.105006 TTCAGAAGCAGCACAGGATC 57.895 50.000 0.00 0.00 0.00 3.36
102 108 0.108472 TCAGAAGCAGCACAGGATCG 60.108 55.000 0.00 0.00 0.00 3.69
103 109 0.108472 CAGAAGCAGCACAGGATCGA 60.108 55.000 0.00 0.00 0.00 3.59
104 110 0.175302 AGAAGCAGCACAGGATCGAG 59.825 55.000 0.00 0.00 0.00 4.04
105 111 1.427592 GAAGCAGCACAGGATCGAGC 61.428 60.000 0.00 0.00 0.00 5.03
106 112 1.897225 AAGCAGCACAGGATCGAGCT 61.897 55.000 0.00 0.00 37.95 4.09
107 113 1.039785 AGCAGCACAGGATCGAGCTA 61.040 55.000 0.00 0.00 35.19 3.32
108 114 0.873743 GCAGCACAGGATCGAGCTAC 60.874 60.000 0.00 0.00 35.19 3.58
109 115 0.457443 CAGCACAGGATCGAGCTACA 59.543 55.000 0.00 0.00 35.19 2.74
110 116 1.134995 CAGCACAGGATCGAGCTACAA 60.135 52.381 0.00 0.00 35.19 2.41
111 117 1.135915 AGCACAGGATCGAGCTACAAG 59.864 52.381 0.00 0.00 35.19 3.16
112 118 1.135139 GCACAGGATCGAGCTACAAGA 59.865 52.381 0.00 0.00 0.00 3.02
113 119 2.417379 GCACAGGATCGAGCTACAAGAA 60.417 50.000 0.00 0.00 0.00 2.52
114 120 3.182967 CACAGGATCGAGCTACAAGAAC 58.817 50.000 0.00 0.00 0.00 3.01
115 121 2.826128 ACAGGATCGAGCTACAAGAACA 59.174 45.455 0.00 0.00 0.00 3.18
116 122 3.258372 ACAGGATCGAGCTACAAGAACAA 59.742 43.478 0.00 0.00 0.00 2.83
117 123 3.862267 CAGGATCGAGCTACAAGAACAAG 59.138 47.826 0.00 0.00 0.00 3.16
118 124 3.764434 AGGATCGAGCTACAAGAACAAGA 59.236 43.478 0.00 0.00 0.00 3.02
119 125 4.109050 GGATCGAGCTACAAGAACAAGAG 58.891 47.826 0.00 0.00 0.00 2.85
120 126 2.947852 TCGAGCTACAAGAACAAGAGC 58.052 47.619 0.00 0.00 0.00 4.09
121 127 1.996191 CGAGCTACAAGAACAAGAGCC 59.004 52.381 0.00 0.00 33.50 4.70
122 128 2.610479 CGAGCTACAAGAACAAGAGCCA 60.610 50.000 0.00 0.00 33.50 4.75
123 129 2.739379 GAGCTACAAGAACAAGAGCCAC 59.261 50.000 0.00 0.00 33.50 5.01
124 130 1.461127 GCTACAAGAACAAGAGCCACG 59.539 52.381 0.00 0.00 0.00 4.94
125 131 2.069273 CTACAAGAACAAGAGCCACGG 58.931 52.381 0.00 0.00 0.00 4.94
126 132 0.180406 ACAAGAACAAGAGCCACGGT 59.820 50.000 0.00 0.00 0.00 4.83
127 133 0.588252 CAAGAACAAGAGCCACGGTG 59.412 55.000 0.00 0.00 0.00 4.94
128 134 1.166531 AAGAACAAGAGCCACGGTGC 61.167 55.000 1.68 0.00 0.00 5.01
129 135 2.594592 AACAAGAGCCACGGTGCC 60.595 61.111 1.68 0.00 0.00 5.01
130 136 4.988598 ACAAGAGCCACGGTGCCG 62.989 66.667 9.29 9.29 46.03 5.69
140 146 2.872925 CGGTGCCGTACGTTCTCG 60.873 66.667 15.21 8.99 37.61 4.04
142 148 2.505557 GTGCCGTACGTTCTCGGG 60.506 66.667 21.40 4.84 45.85 5.14
143 149 2.672651 TGCCGTACGTTCTCGGGA 60.673 61.111 21.40 17.99 45.85 5.14
144 150 2.267351 TGCCGTACGTTCTCGGGAA 61.267 57.895 21.40 0.00 43.78 3.97
145 151 1.080569 GCCGTACGTTCTCGGGAAA 60.081 57.895 21.40 0.00 45.85 3.13
146 152 1.347097 GCCGTACGTTCTCGGGAAAC 61.347 60.000 21.40 0.00 45.85 2.78
147 153 0.039256 CCGTACGTTCTCGGGAAACA 60.039 55.000 15.21 0.00 42.61 2.83
160 166 3.057876 TCGGGAAACATCGGTCATTTTTG 60.058 43.478 0.00 0.00 0.00 2.44
162 168 4.485163 GGGAAACATCGGTCATTTTTGAG 58.515 43.478 0.00 0.00 0.00 3.02
164 170 4.545610 GAAACATCGGTCATTTTTGAGCA 58.454 39.130 6.06 0.00 36.21 4.26
165 171 4.789012 AACATCGGTCATTTTTGAGCAT 57.211 36.364 6.06 0.00 36.21 3.79
166 172 4.789012 ACATCGGTCATTTTTGAGCATT 57.211 36.364 6.06 0.00 36.21 3.56
167 173 5.138125 ACATCGGTCATTTTTGAGCATTT 57.862 34.783 6.06 0.00 36.21 2.32
169 175 3.911868 TCGGTCATTTTTGAGCATTTGG 58.088 40.909 6.06 0.00 36.21 3.28
170 176 3.320541 TCGGTCATTTTTGAGCATTTGGT 59.679 39.130 6.06 0.00 36.21 3.67
171 177 4.057432 CGGTCATTTTTGAGCATTTGGTT 58.943 39.130 6.06 0.00 36.21 3.67
174 180 4.272991 GTCATTTTTGAGCATTTGGTTGCA 59.727 37.500 0.00 0.00 45.23 4.08
175 181 4.880120 TCATTTTTGAGCATTTGGTTGCAA 59.120 33.333 0.00 0.00 45.23 4.08
176 182 4.879104 TTTTTGAGCATTTGGTTGCAAG 57.121 36.364 0.00 0.00 45.23 4.01
177 183 3.815856 TTTGAGCATTTGGTTGCAAGA 57.184 38.095 0.00 0.00 45.23 3.02
199 205 2.519013 CAGGCTTAACTTTTGGGAGCT 58.481 47.619 0.00 0.00 33.96 4.09
201 208 1.067565 GGCTTAACTTTTGGGAGCTGC 60.068 52.381 0.00 0.00 33.96 5.25
224 231 6.033966 GCTTTCCACGAGTATTTTAATTGGG 58.966 40.000 0.00 0.00 0.00 4.12
225 232 5.570234 TTCCACGAGTATTTTAATTGGGC 57.430 39.130 0.00 0.00 0.00 5.36
244 251 2.271800 GCTCTTCACCGAATTCACGAT 58.728 47.619 6.22 0.00 35.09 3.73
258 265 6.897136 CGAATTCACGATCCAAATCATTTGGT 60.897 38.462 25.58 14.77 46.37 3.67
299 306 7.862675 AGCACCAGTAGGATTAGTTAAGAAAT 58.137 34.615 0.00 0.00 38.69 2.17
300 307 8.989131 AGCACCAGTAGGATTAGTTAAGAAATA 58.011 33.333 0.00 0.00 38.69 1.40
301 308 9.780186 GCACCAGTAGGATTAGTTAAGAAATAT 57.220 33.333 0.00 0.00 38.69 1.28
348 355 7.331791 AGGATAAGAATCGTGGGCTATTATTC 58.668 38.462 0.00 0.00 32.44 1.75
350 357 7.278868 GGATAAGAATCGTGGGCTATTATTCTG 59.721 40.741 10.09 0.00 37.08 3.02
353 360 5.992217 AGAATCGTGGGCTATTATTCTGTTC 59.008 40.000 8.99 0.00 35.98 3.18
357 364 4.452455 CGTGGGCTATTATTCTGTTCCATC 59.548 45.833 0.00 0.00 0.00 3.51
395 402 6.177610 ACATGGACGTAATTTGGAACATACT 58.822 36.000 0.00 0.00 39.30 2.12
449 456 1.067985 CACTGTGTCGATCAGCACTCT 60.068 52.381 16.69 0.00 36.50 3.24
466 474 3.835395 CACTCTAAGGAAGGAACAGAGGT 59.165 47.826 0.00 0.00 37.62 3.85
473 481 2.904434 GGAAGGAACAGAGGTAGGTTCA 59.096 50.000 6.82 0.00 43.96 3.18
479 487 4.508662 GAACAGAGGTAGGTTCATCCTTG 58.491 47.826 0.00 0.00 45.67 3.61
481 489 3.107601 CAGAGGTAGGTTCATCCTTGGA 58.892 50.000 0.00 0.00 45.67 3.53
483 491 2.436173 GAGGTAGGTTCATCCTTGGAGG 59.564 54.545 0.00 0.00 45.67 4.30
491 499 4.750289 TCCTTGGAGGATAGCCCC 57.250 61.111 0.00 0.00 40.06 5.80
492 500 1.459539 TCCTTGGAGGATAGCCCCG 60.460 63.158 0.00 0.00 40.06 5.73
493 501 2.520536 CCTTGGAGGATAGCCCCGG 61.521 68.421 0.00 0.00 37.67 5.73
494 502 2.447765 TTGGAGGATAGCCCCGGG 60.448 66.667 15.80 15.80 34.66 5.73
505 513 4.426313 CCCCGGGCAGGTTTCCTC 62.426 72.222 17.73 0.00 38.74 3.71
506 514 3.646715 CCCGGGCAGGTTTCCTCA 61.647 66.667 8.08 0.00 38.74 3.86
507 515 2.677228 CCGGGCAGGTTTCCTCAT 59.323 61.111 0.00 0.00 34.51 2.90
508 516 1.000896 CCGGGCAGGTTTCCTCATT 60.001 57.895 0.00 0.00 34.51 2.57
509 517 1.032114 CCGGGCAGGTTTCCTCATTC 61.032 60.000 0.00 0.00 34.51 2.67
510 518 1.369091 CGGGCAGGTTTCCTCATTCG 61.369 60.000 0.00 0.00 0.00 3.34
511 519 0.322546 GGGCAGGTTTCCTCATTCGT 60.323 55.000 0.00 0.00 0.00 3.85
512 520 1.534729 GGCAGGTTTCCTCATTCGTT 58.465 50.000 0.00 0.00 0.00 3.85
570 586 0.924090 CTCGCGTGCTTAACCAGATC 59.076 55.000 5.77 0.00 0.00 2.75
571 587 0.459585 TCGCGTGCTTAACCAGATCC 60.460 55.000 5.77 0.00 0.00 3.36
572 588 1.429148 CGCGTGCTTAACCAGATCCC 61.429 60.000 0.00 0.00 0.00 3.85
573 589 1.429148 GCGTGCTTAACCAGATCCCG 61.429 60.000 0.00 0.00 0.00 5.14
575 591 1.404986 CGTGCTTAACCAGATCCCGAA 60.405 52.381 0.00 0.00 0.00 4.30
576 592 2.741878 CGTGCTTAACCAGATCCCGAAT 60.742 50.000 0.00 0.00 0.00 3.34
577 593 3.279434 GTGCTTAACCAGATCCCGAATT 58.721 45.455 0.00 0.00 0.00 2.17
598 709 2.918345 GCCTTGCGACATGCCACAA 61.918 57.895 0.00 0.00 45.60 3.33
608 719 2.754552 GACATGCCACAAAGGAAGCATA 59.245 45.455 0.00 0.00 43.85 3.14
609 720 3.368248 ACATGCCACAAAGGAAGCATAT 58.632 40.909 0.00 0.00 43.85 1.78
610 721 3.131577 ACATGCCACAAAGGAAGCATATG 59.868 43.478 0.00 0.00 43.85 1.78
611 722 2.806434 TGCCACAAAGGAAGCATATGT 58.194 42.857 4.29 0.00 41.22 2.29
612 723 3.961849 TGCCACAAAGGAAGCATATGTA 58.038 40.909 4.29 0.00 41.22 2.29
660 774 0.535335 GGTCTTACGTGGCCAGATCA 59.465 55.000 5.11 0.00 0.00 2.92
672 786 1.296392 CAGATCACCGGAGCAACCA 59.704 57.895 9.46 0.00 38.90 3.67
676 790 4.263572 CACCGGAGCAACCACCCA 62.264 66.667 9.46 0.00 38.90 4.51
718 835 4.748102 ACACGCCTATTGTTTATGGTATCG 59.252 41.667 0.00 0.00 0.00 2.92
733 850 4.751060 TGGTATCGGACATACACAAACTC 58.249 43.478 0.00 0.00 0.00 3.01
737 854 2.232941 TCGGACATACACAAACTCTCCC 59.767 50.000 0.00 0.00 0.00 4.30
741 858 4.396166 GGACATACACAAACTCTCCCAATG 59.604 45.833 0.00 0.00 0.00 2.82
760 877 0.457443 GCTAATGGCCAAGGCAGAAC 59.543 55.000 10.96 0.00 42.43 3.01
770 892 2.490903 CCAAGGCAGAACAAGAATGGAG 59.509 50.000 0.00 0.00 0.00 3.86
874 1005 9.139734 CGTCTCCTCTACTCCTCTATATATACT 57.860 40.741 0.00 0.00 0.00 2.12
877 1008 9.670442 CTCCTCTACTCCTCTATATATACTCCT 57.330 40.741 0.00 0.00 0.00 3.69
890 1024 1.573108 TACTCCTGCCAAGGGAAGAG 58.427 55.000 4.86 4.86 44.62 2.85
930 1107 1.895798 TCTGACTTCTGGCCACTACAG 59.104 52.381 0.00 7.79 37.30 2.74
1307 1515 3.432252 GTCAAATCCAACTACTCCACACG 59.568 47.826 0.00 0.00 0.00 4.49
1312 1544 1.608025 CCAACTACTCCACACGCACAT 60.608 52.381 0.00 0.00 0.00 3.21
1359 1595 1.280421 ACTGTCAATTCCCTCCAGCTC 59.720 52.381 0.00 0.00 0.00 4.09
1372 1611 0.962356 CCAGCTCGACCTTTTGCCAT 60.962 55.000 0.00 0.00 0.00 4.40
1373 1612 1.678728 CCAGCTCGACCTTTTGCCATA 60.679 52.381 0.00 0.00 0.00 2.74
1374 1613 1.667724 CAGCTCGACCTTTTGCCATAG 59.332 52.381 0.00 0.00 0.00 2.23
1375 1614 1.279271 AGCTCGACCTTTTGCCATAGT 59.721 47.619 0.00 0.00 0.00 2.12
1376 1615 2.084546 GCTCGACCTTTTGCCATAGTT 58.915 47.619 0.00 0.00 0.00 2.24
1377 1616 2.159517 GCTCGACCTTTTGCCATAGTTG 60.160 50.000 0.00 0.00 0.00 3.16
1378 1617 1.810151 TCGACCTTTTGCCATAGTTGC 59.190 47.619 0.00 0.00 0.00 4.17
1379 1618 1.812571 CGACCTTTTGCCATAGTTGCT 59.187 47.619 0.00 0.00 0.00 3.91
1380 1619 3.006940 CGACCTTTTGCCATAGTTGCTA 58.993 45.455 0.00 0.00 0.00 3.49
1381 1620 3.181510 CGACCTTTTGCCATAGTTGCTAC 60.182 47.826 0.00 0.00 0.00 3.58
1382 1621 2.747446 ACCTTTTGCCATAGTTGCTACG 59.253 45.455 0.00 0.00 0.00 3.51
1385 1624 4.201783 CCTTTTGCCATAGTTGCTACGTAC 60.202 45.833 0.00 0.00 0.00 3.67
1388 1627 3.777478 TGCCATAGTTGCTACGTACTTC 58.223 45.455 0.00 0.00 0.00 3.01
1521 1782 1.301716 ACGCACATCCGCAAGAAGT 60.302 52.632 0.00 0.00 43.02 3.01
1592 1910 0.391597 AGACCAACCACGACGTCAAT 59.608 50.000 17.16 0.00 0.00 2.57
1770 2088 1.299620 CTGGCTGCAGCAAACACAC 60.300 57.895 37.63 20.06 44.36 3.82
1927 2271 1.081641 CCTTTGCAGCTGCTGAACG 60.082 57.895 36.61 21.44 42.66 3.95
1962 2315 1.939934 GCAACACTGCCGCTTCATATA 59.060 47.619 0.00 0.00 43.26 0.86
2154 2672 5.234329 GTGTTAGATCCATCATAACGGTGTG 59.766 44.000 0.00 0.00 33.13 3.82
2271 5082 6.098017 ACTCGTGCTACACTTTCCTTATAAC 58.902 40.000 0.00 0.00 31.34 1.89
2374 5195 5.154222 GTGGCGCTTAAGATATAATTTGGC 58.846 41.667 7.64 0.00 0.00 4.52
2376 5197 5.534654 TGGCGCTTAAGATATAATTTGGCTT 59.465 36.000 7.64 0.00 0.00 4.35
2392 5213 0.464554 GCTTCAATCCGGCCTTAGCT 60.465 55.000 0.00 0.00 39.73 3.32
2427 5262 3.780294 TGGCTTACTCACAACCCATCTAT 59.220 43.478 0.00 0.00 0.00 1.98
2485 5320 8.807667 AAAAGCTGAGTACATTTCATTTTCAG 57.192 30.769 0.00 0.00 35.03 3.02
2489 5324 9.066892 AGCTGAGTACATTTCATTTTCAGTAAA 57.933 29.630 0.00 0.00 34.55 2.01
2573 5410 8.867112 AAATTTGATGTATAGAGCTGCAAATG 57.133 30.769 1.02 0.00 35.43 2.32
2574 5411 6.381481 TTTGATGTATAGAGCTGCAAATGG 57.619 37.500 1.02 0.00 0.00 3.16
2706 5546 4.407296 ACCTTGAAAATAGCAAAACCACCA 59.593 37.500 0.00 0.00 0.00 4.17
2720 5561 2.167662 ACCACCATTTGTTTCCGGATC 58.832 47.619 4.15 2.09 0.00 3.36
2811 5658 2.819608 TCTAGCAAATTCAGTGGCAACC 59.180 45.455 0.00 0.00 0.00 3.77
2866 5713 6.834168 ATAGAACCACACTTAACAATTGGG 57.166 37.500 10.83 0.94 0.00 4.12
2869 5716 3.034635 ACCACACTTAACAATTGGGCAA 58.965 40.909 10.83 0.00 0.00 4.52
2897 5744 5.048573 TCACATGATGGTCACATTCAAAGTG 60.049 40.000 0.00 7.98 37.47 3.16
2909 5756 3.811722 TTCAAAGTGACATGACGCATC 57.188 42.857 11.18 0.00 0.00 3.91
2910 5757 3.044235 TCAAAGTGACATGACGCATCT 57.956 42.857 11.18 0.00 0.00 2.90
2936 5783 2.104859 CATGTCGCAGAGGGCACAG 61.105 63.158 0.00 0.00 45.17 3.66
3023 5870 1.153686 GTCTAACCCTCGCCGTTCC 60.154 63.158 0.00 0.00 0.00 3.62
3045 5892 6.518493 TCCGGTTGGTTCATTGTATCTATAC 58.482 40.000 0.00 0.00 36.30 1.47
3069 5916 4.238761 TCACTCTTAGACGTTGTTCCAG 57.761 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.476291 GCTCATGACCATGATGCCAGA 60.476 52.381 12.51 0.00 45.74 3.86
55 56 0.952280 GCTCATGACCATGATGCCAG 59.048 55.000 12.51 3.15 45.74 4.85
56 57 0.256464 TGCTCATGACCATGATGCCA 59.744 50.000 20.71 13.48 45.74 4.92
57 58 0.666913 GTGCTCATGACCATGATGCC 59.333 55.000 20.71 11.85 45.74 4.40
58 59 1.602851 GAGTGCTCATGACCATGATGC 59.397 52.381 12.51 16.24 45.74 3.91
59 60 2.872858 CTGAGTGCTCATGACCATGATG 59.127 50.000 12.51 8.51 45.74 3.07
60 61 2.770232 TCTGAGTGCTCATGACCATGAT 59.230 45.455 12.51 0.00 45.74 2.45
61 62 2.181975 TCTGAGTGCTCATGACCATGA 58.818 47.619 11.68 11.68 44.83 3.07
62 63 2.685850 TCTGAGTGCTCATGACCATG 57.314 50.000 2.06 3.70 39.13 3.66
63 64 3.199289 TGAATCTGAGTGCTCATGACCAT 59.801 43.478 2.06 0.00 39.13 3.55
64 65 2.568509 TGAATCTGAGTGCTCATGACCA 59.431 45.455 2.06 0.00 39.13 4.02
65 66 3.118847 TCTGAATCTGAGTGCTCATGACC 60.119 47.826 2.06 0.00 39.13 4.02
66 67 4.120792 TCTGAATCTGAGTGCTCATGAC 57.879 45.455 2.06 0.00 39.13 3.06
67 68 4.756502 CTTCTGAATCTGAGTGCTCATGA 58.243 43.478 2.06 0.00 39.13 3.07
68 69 3.310227 GCTTCTGAATCTGAGTGCTCATG 59.690 47.826 2.06 0.00 39.13 3.07
86 92 1.427592 GCTCGATCCTGTGCTGCTTC 61.428 60.000 0.00 0.00 0.00 3.86
87 93 1.449246 GCTCGATCCTGTGCTGCTT 60.449 57.895 0.00 0.00 0.00 3.91
88 94 1.039785 TAGCTCGATCCTGTGCTGCT 61.040 55.000 0.00 0.44 38.94 4.24
89 95 0.873743 GTAGCTCGATCCTGTGCTGC 60.874 60.000 4.97 0.04 38.94 5.25
90 96 0.457443 TGTAGCTCGATCCTGTGCTG 59.543 55.000 4.97 0.00 38.94 4.41
91 97 1.135915 CTTGTAGCTCGATCCTGTGCT 59.864 52.381 0.00 0.08 41.23 4.40
92 98 1.135139 TCTTGTAGCTCGATCCTGTGC 59.865 52.381 0.00 0.00 0.00 4.57
93 99 3.182967 GTTCTTGTAGCTCGATCCTGTG 58.817 50.000 0.00 0.00 0.00 3.66
94 100 2.826128 TGTTCTTGTAGCTCGATCCTGT 59.174 45.455 0.00 0.00 0.00 4.00
95 101 3.510388 TGTTCTTGTAGCTCGATCCTG 57.490 47.619 0.00 0.00 0.00 3.86
96 102 3.764434 TCTTGTTCTTGTAGCTCGATCCT 59.236 43.478 0.00 0.00 0.00 3.24
97 103 4.109050 CTCTTGTTCTTGTAGCTCGATCC 58.891 47.826 0.00 0.00 0.00 3.36
98 104 3.549873 GCTCTTGTTCTTGTAGCTCGATC 59.450 47.826 0.00 0.00 0.00 3.69
99 105 3.516615 GCTCTTGTTCTTGTAGCTCGAT 58.483 45.455 0.00 0.00 0.00 3.59
100 106 2.352814 GGCTCTTGTTCTTGTAGCTCGA 60.353 50.000 0.00 0.00 33.67 4.04
101 107 1.996191 GGCTCTTGTTCTTGTAGCTCG 59.004 52.381 0.00 0.00 33.67 5.03
102 108 2.739379 GTGGCTCTTGTTCTTGTAGCTC 59.261 50.000 0.00 0.00 33.67 4.09
103 109 2.772287 GTGGCTCTTGTTCTTGTAGCT 58.228 47.619 0.00 0.00 33.67 3.32
104 110 1.461127 CGTGGCTCTTGTTCTTGTAGC 59.539 52.381 0.00 0.00 0.00 3.58
105 111 2.069273 CCGTGGCTCTTGTTCTTGTAG 58.931 52.381 0.00 0.00 0.00 2.74
106 112 1.414919 ACCGTGGCTCTTGTTCTTGTA 59.585 47.619 0.00 0.00 0.00 2.41
107 113 0.180406 ACCGTGGCTCTTGTTCTTGT 59.820 50.000 0.00 0.00 0.00 3.16
108 114 0.588252 CACCGTGGCTCTTGTTCTTG 59.412 55.000 0.00 0.00 0.00 3.02
109 115 1.166531 GCACCGTGGCTCTTGTTCTT 61.167 55.000 0.00 0.00 0.00 2.52
110 116 1.598130 GCACCGTGGCTCTTGTTCT 60.598 57.895 0.00 0.00 0.00 3.01
111 117 2.617274 GGCACCGTGGCTCTTGTTC 61.617 63.158 17.45 0.00 40.14 3.18
112 118 2.594592 GGCACCGTGGCTCTTGTT 60.595 61.111 17.45 0.00 40.14 2.83
113 119 4.988598 CGGCACCGTGGCTCTTGT 62.989 66.667 21.49 0.00 41.25 3.16
123 129 2.872925 CGAGAACGTACGGCACCG 60.873 66.667 21.06 13.33 38.91 4.94
124 130 2.505557 CCGAGAACGTACGGCACC 60.506 66.667 21.06 5.34 42.55 5.01
125 131 2.476534 TTCCCGAGAACGTACGGCAC 62.477 60.000 21.06 10.12 46.59 5.01
126 132 1.804396 TTTCCCGAGAACGTACGGCA 61.804 55.000 21.06 5.89 46.59 5.69
127 133 1.080569 TTTCCCGAGAACGTACGGC 60.081 57.895 21.06 11.21 46.59 5.68
129 135 1.916000 GATGTTTCCCGAGAACGTACG 59.084 52.381 15.01 15.01 37.88 3.67
130 136 1.916000 CGATGTTTCCCGAGAACGTAC 59.084 52.381 0.00 0.00 37.88 3.67
131 137 1.135315 CCGATGTTTCCCGAGAACGTA 60.135 52.381 0.00 0.00 37.88 3.57
132 138 0.389426 CCGATGTTTCCCGAGAACGT 60.389 55.000 0.00 0.00 37.88 3.99
133 139 0.389426 ACCGATGTTTCCCGAGAACG 60.389 55.000 0.00 0.00 39.43 3.95
134 140 1.337447 TGACCGATGTTTCCCGAGAAC 60.337 52.381 0.00 0.00 0.00 3.01
135 141 0.970640 TGACCGATGTTTCCCGAGAA 59.029 50.000 0.00 0.00 0.00 2.87
136 142 1.191535 ATGACCGATGTTTCCCGAGA 58.808 50.000 0.00 0.00 0.00 4.04
137 143 2.024176 AATGACCGATGTTTCCCGAG 57.976 50.000 0.00 0.00 0.00 4.63
138 144 2.483014 AAATGACCGATGTTTCCCGA 57.517 45.000 0.00 0.00 0.00 5.14
139 145 3.057876 TCAAAAATGACCGATGTTTCCCG 60.058 43.478 0.00 0.00 0.00 5.14
140 146 4.485163 CTCAAAAATGACCGATGTTTCCC 58.515 43.478 0.00 0.00 0.00 3.97
141 147 3.920412 GCTCAAAAATGACCGATGTTTCC 59.080 43.478 0.00 0.00 0.00 3.13
142 148 4.545610 TGCTCAAAAATGACCGATGTTTC 58.454 39.130 0.00 0.00 0.00 2.78
143 149 4.582701 TGCTCAAAAATGACCGATGTTT 57.417 36.364 0.00 0.00 0.00 2.83
144 150 4.789012 ATGCTCAAAAATGACCGATGTT 57.211 36.364 0.00 0.00 0.00 2.71
145 151 4.789012 AATGCTCAAAAATGACCGATGT 57.211 36.364 0.00 0.00 0.00 3.06
146 152 4.327898 CCAAATGCTCAAAAATGACCGATG 59.672 41.667 0.00 0.00 0.00 3.84
147 153 4.021192 ACCAAATGCTCAAAAATGACCGAT 60.021 37.500 0.00 0.00 0.00 4.18
160 166 1.706443 GCTCTTGCAACCAAATGCTC 58.294 50.000 0.00 0.00 46.54 4.26
174 180 2.893489 CCCAAAAGTTAAGCCTGCTCTT 59.107 45.455 0.00 0.00 0.00 2.85
175 181 2.108250 TCCCAAAAGTTAAGCCTGCTCT 59.892 45.455 0.00 0.00 0.00 4.09
176 182 2.489722 CTCCCAAAAGTTAAGCCTGCTC 59.510 50.000 0.00 0.00 0.00 4.26
177 183 2.519013 CTCCCAAAAGTTAAGCCTGCT 58.481 47.619 0.00 0.00 0.00 4.24
184 190 3.320826 GGAAAGCAGCTCCCAAAAGTTAA 59.679 43.478 0.00 0.00 0.00 2.01
199 205 6.349777 CCCAATTAAAATACTCGTGGAAAGCA 60.350 38.462 0.00 0.00 0.00 3.91
201 208 6.033966 GCCCAATTAAAATACTCGTGGAAAG 58.966 40.000 0.00 0.00 0.00 2.62
224 231 1.710013 TCGTGAATTCGGTGAAGAGC 58.290 50.000 0.04 0.00 0.00 4.09
225 232 2.860735 GGATCGTGAATTCGGTGAAGAG 59.139 50.000 0.04 0.00 0.00 2.85
258 265 3.149196 GGTGCTCTTGATTGAGGTTTCA 58.851 45.455 0.00 0.00 34.82 2.69
274 281 6.869206 TTCTTAACTAATCCTACTGGTGCT 57.131 37.500 0.00 0.00 34.23 4.40
275 282 9.780186 ATATTTCTTAACTAATCCTACTGGTGC 57.220 33.333 0.00 0.00 34.23 5.01
312 319 9.669887 CCACGATTCTTATCCTACTACTACTAT 57.330 37.037 0.00 0.00 0.00 2.12
313 320 8.099537 CCCACGATTCTTATCCTACTACTACTA 58.900 40.741 0.00 0.00 0.00 1.82
314 321 6.941436 CCCACGATTCTTATCCTACTACTACT 59.059 42.308 0.00 0.00 0.00 2.57
315 322 6.349197 GCCCACGATTCTTATCCTACTACTAC 60.349 46.154 0.00 0.00 0.00 2.73
350 357 3.594603 TTTGGTCTCTCGAGATGGAAC 57.405 47.619 17.03 13.95 39.97 3.62
353 360 3.319137 TGTTTTGGTCTCTCGAGATGG 57.681 47.619 17.03 5.37 39.97 3.51
357 364 2.996621 GTCCATGTTTTGGTCTCTCGAG 59.003 50.000 5.93 5.93 46.52 4.04
449 456 4.415224 ACCTACCTCTGTTCCTTCCTTA 57.585 45.455 0.00 0.00 0.00 2.69
488 496 4.426313 GAGGAAACCTGCCCGGGG 62.426 72.222 25.28 9.31 36.97 5.73
489 497 2.499303 AATGAGGAAACCTGCCCGGG 62.499 60.000 19.09 19.09 36.97 5.73
490 498 1.000896 AATGAGGAAACCTGCCCGG 60.001 57.895 0.00 0.00 31.76 5.73
491 499 1.369091 CGAATGAGGAAACCTGCCCG 61.369 60.000 0.00 0.00 31.76 6.13
492 500 0.322546 ACGAATGAGGAAACCTGCCC 60.323 55.000 0.00 0.00 31.76 5.36
493 501 1.468914 GAACGAATGAGGAAACCTGCC 59.531 52.381 0.00 0.00 31.76 4.85
494 502 1.128692 CGAACGAATGAGGAAACCTGC 59.871 52.381 0.00 0.00 31.76 4.85
495 503 2.157668 CACGAACGAATGAGGAAACCTG 59.842 50.000 0.14 0.00 31.76 4.00
496 504 2.413837 CACGAACGAATGAGGAAACCT 58.586 47.619 0.14 0.00 36.03 3.50
497 505 1.463444 CCACGAACGAATGAGGAAACC 59.537 52.381 0.14 0.00 0.00 3.27
498 506 1.136057 GCCACGAACGAATGAGGAAAC 60.136 52.381 0.14 0.00 0.00 2.78
499 507 1.153353 GCCACGAACGAATGAGGAAA 58.847 50.000 0.14 0.00 0.00 3.13
500 508 0.034198 TGCCACGAACGAATGAGGAA 59.966 50.000 0.14 0.00 0.00 3.36
501 509 0.669318 GTGCCACGAACGAATGAGGA 60.669 55.000 0.14 0.00 0.00 3.71
502 510 0.948623 TGTGCCACGAACGAATGAGG 60.949 55.000 0.14 0.00 0.00 3.86
503 511 0.865111 TTGTGCCACGAACGAATGAG 59.135 50.000 0.14 0.00 0.00 2.90
504 512 0.865111 CTTGTGCCACGAACGAATGA 59.135 50.000 0.14 0.00 0.00 2.57
505 513 0.725784 GCTTGTGCCACGAACGAATG 60.726 55.000 0.14 0.00 0.00 2.67
506 514 0.884704 AGCTTGTGCCACGAACGAAT 60.885 50.000 0.14 0.00 40.80 3.34
507 515 0.249531 TAGCTTGTGCCACGAACGAA 60.250 50.000 0.00 0.00 40.80 3.85
508 516 0.942410 GTAGCTTGTGCCACGAACGA 60.942 55.000 0.00 0.00 40.80 3.85
509 517 1.491563 GTAGCTTGTGCCACGAACG 59.508 57.895 0.00 0.00 40.80 3.95
572 588 1.705337 ATGTCGCAAGGCCGAATTCG 61.705 55.000 20.92 20.92 45.49 3.34
573 589 0.248215 CATGTCGCAAGGCCGAATTC 60.248 55.000 0.00 0.00 45.49 2.17
575 591 2.764314 GCATGTCGCAAGGCCGAAT 61.764 57.895 0.00 0.00 45.49 3.34
576 592 3.430862 GCATGTCGCAAGGCCGAA 61.431 61.111 0.00 0.00 45.49 4.30
598 709 5.297776 GCAGTTCACATACATATGCTTCCTT 59.702 40.000 1.58 0.00 37.19 3.36
608 719 2.098607 GCATGCTGCAGTTCACATACAT 59.901 45.455 16.64 4.47 44.26 2.29
609 720 1.469703 GCATGCTGCAGTTCACATACA 59.530 47.619 16.64 1.93 44.26 2.29
610 721 2.184385 GCATGCTGCAGTTCACATAC 57.816 50.000 16.64 1.05 44.26 2.39
660 774 4.265056 GTGGGTGGTTGCTCCGGT 62.265 66.667 0.00 0.00 39.52 5.28
672 786 3.764237 ACGATGTAAGTCAAAGTGGGT 57.236 42.857 0.00 0.00 0.00 4.51
703 817 7.276658 TGTGTATGTCCGATACCATAAACAAT 58.723 34.615 0.00 0.00 38.31 2.71
711 825 4.464951 AGAGTTTGTGTATGTCCGATACCA 59.535 41.667 0.00 0.00 0.00 3.25
718 835 3.695830 TGGGAGAGTTTGTGTATGTCC 57.304 47.619 0.00 0.00 0.00 4.02
733 850 1.684983 CTTGGCCATTAGCATTGGGAG 59.315 52.381 6.09 0.00 46.50 4.30
737 854 0.825410 TGCCTTGGCCATTAGCATTG 59.175 50.000 18.05 0.00 46.50 2.82
741 858 0.457443 GTTCTGCCTTGGCCATTAGC 59.543 55.000 6.09 11.04 42.60 3.09
760 877 3.193267 TGCGAATTTTCCCTCCATTCTTG 59.807 43.478 0.00 0.00 0.00 3.02
770 892 2.268730 CAGAAGCTGCGAATTTTCCC 57.731 50.000 0.00 0.00 0.00 3.97
817 947 0.543410 TGGTCGTACCCCATGACAGT 60.543 55.000 0.00 0.00 43.88 3.55
844 975 2.716864 GAGTAGAGGAGACGGCGC 59.283 66.667 6.90 0.00 0.00 6.53
845 976 1.153127 AGGAGTAGAGGAGACGGCG 60.153 63.158 4.80 4.80 0.00 6.46
851 982 9.670442 AGGAGTATATATAGAGGAGTAGAGGAG 57.330 40.741 0.00 0.00 0.00 3.69
874 1005 1.544825 CGTCTCTTCCCTTGGCAGGA 61.545 60.000 0.00 0.00 44.19 3.86
875 1006 1.078848 CGTCTCTTCCCTTGGCAGG 60.079 63.158 0.00 0.00 40.45 4.85
877 1008 0.034896 GTTCGTCTCTTCCCTTGGCA 59.965 55.000 0.00 0.00 0.00 4.92
890 1024 4.560819 CAGAACTCAGAAGCTATGTTCGTC 59.439 45.833 0.00 0.00 41.05 4.20
930 1107 0.807667 CTACTGGTGGCTGTGATCGC 60.808 60.000 0.00 0.00 0.00 4.58
1181 1380 1.303888 TCGGAGCGGAGGTAGTTGT 60.304 57.895 0.00 0.00 39.88 3.32
1307 1515 0.886490 ATGGCGGCTAAGCTATGTGC 60.886 55.000 11.43 0.00 36.95 4.57
1312 1544 2.111043 GGCATGGCGGCTAAGCTA 59.889 61.111 13.07 0.00 37.17 3.32
1349 1585 0.674895 CAAAAGGTCGAGCTGGAGGG 60.675 60.000 19.39 2.88 0.00 4.30
1359 1595 1.812571 AGCAACTATGGCAAAAGGTCG 59.187 47.619 0.00 0.00 0.00 4.79
1372 1611 7.678947 AAGACTAAGAAGTACGTAGCAACTA 57.321 36.000 0.00 0.00 35.56 2.24
1373 1612 6.572167 AAGACTAAGAAGTACGTAGCAACT 57.428 37.500 0.00 0.00 35.56 3.16
1374 1613 6.860023 TCAAAGACTAAGAAGTACGTAGCAAC 59.140 38.462 0.00 0.00 35.56 4.17
1375 1614 6.973843 TCAAAGACTAAGAAGTACGTAGCAA 58.026 36.000 0.00 0.00 35.56 3.91
1376 1615 6.206243 ACTCAAAGACTAAGAAGTACGTAGCA 59.794 38.462 0.00 0.00 35.56 3.49
1377 1616 6.610456 ACTCAAAGACTAAGAAGTACGTAGC 58.390 40.000 0.00 0.00 35.56 3.58
1378 1617 8.903723 CAAACTCAAAGACTAAGAAGTACGTAG 58.096 37.037 0.00 0.00 35.56 3.51
1379 1618 8.623903 TCAAACTCAAAGACTAAGAAGTACGTA 58.376 33.333 0.00 0.00 35.56 3.57
1380 1619 7.434602 GTCAAACTCAAAGACTAAGAAGTACGT 59.565 37.037 0.00 0.00 35.56 3.57
1381 1620 7.434307 TGTCAAACTCAAAGACTAAGAAGTACG 59.566 37.037 0.00 0.00 35.56 3.67
1382 1621 8.541312 GTGTCAAACTCAAAGACTAAGAAGTAC 58.459 37.037 0.00 0.00 35.56 2.73
1385 1624 7.492669 TCAGTGTCAAACTCAAAGACTAAGAAG 59.507 37.037 0.00 0.00 36.83 2.85
1388 1627 6.535150 TGTCAGTGTCAAACTCAAAGACTAAG 59.465 38.462 0.00 0.00 36.83 2.18
1908 2252 1.789078 CGTTCAGCAGCTGCAAAGGT 61.789 55.000 38.24 16.73 45.16 3.50
1919 2263 1.078918 CTGATCAGCCCGTTCAGCA 60.079 57.895 10.38 0.00 35.27 4.41
2154 2672 8.005466 CACAAACAAATCAATGAATGTTGTAGC 58.995 33.333 15.33 0.00 36.23 3.58
2231 2768 2.998670 ACGAGTCACATCAAATCAGCAG 59.001 45.455 0.00 0.00 0.00 4.24
2374 5195 2.910688 TAGCTAAGGCCGGATTGAAG 57.089 50.000 5.05 0.00 39.73 3.02
2376 5197 3.258372 CACTATAGCTAAGGCCGGATTGA 59.742 47.826 5.05 0.00 39.73 2.57
2392 5213 8.756486 TGTGAGTAAGCCAGTATAACACTATA 57.244 34.615 0.00 0.00 34.98 1.31
2427 5262 7.325660 ACATCTTAGGTTCGTTCGTATTAGA 57.674 36.000 0.00 0.00 0.00 2.10
2554 5390 5.059161 TCACCATTTGCAGCTCTATACATC 58.941 41.667 0.00 0.00 0.00 3.06
2607 5444 9.959749 GGTTTTCTTGTGAATATGTTTGTAAGA 57.040 29.630 0.00 0.00 31.56 2.10
2706 5546 5.863965 ACCAATTTTGATCCGGAAACAAAT 58.136 33.333 28.06 20.07 34.33 2.32
2720 5561 5.177327 CGAAAACCATCCTGAACCAATTTTG 59.823 40.000 0.00 0.00 0.00 2.44
2768 5615 5.593095 AGAAAAGTTAAGGTTCCAAGTGGAC 59.407 40.000 0.00 0.00 45.39 4.02
2784 5631 5.068987 TGCCACTGAATTTGCTAGAAAAGTT 59.931 36.000 1.58 0.00 0.00 2.66
2785 5632 4.584325 TGCCACTGAATTTGCTAGAAAAGT 59.416 37.500 1.58 0.00 0.00 2.66
2786 5633 5.125100 TGCCACTGAATTTGCTAGAAAAG 57.875 39.130 1.58 0.00 0.00 2.27
2811 5658 4.771590 TTGCACTAAATCTGGCTTCAAG 57.228 40.909 0.00 0.00 0.00 3.02
2866 5713 4.558178 TGTGACCATCATGTGAAAATTGC 58.442 39.130 0.00 0.00 0.00 3.56
2869 5716 6.593268 TGAATGTGACCATCATGTGAAAAT 57.407 33.333 0.00 0.00 0.00 1.82
2897 5744 2.286294 GTCCAATCAGATGCGTCATGTC 59.714 50.000 8.99 0.00 0.00 3.06
2909 5756 1.931841 CTCTGCGACATGTCCAATCAG 59.068 52.381 20.03 19.01 0.00 2.90
2910 5757 1.405933 CCTCTGCGACATGTCCAATCA 60.406 52.381 20.03 11.42 0.00 2.57
2936 5783 7.646548 ACAAAAATAGGCTTCTATTTCTCCC 57.353 36.000 10.58 0.00 46.92 4.30
2939 5786 9.397280 GTCCTACAAAAATAGGCTTCTATTTCT 57.603 33.333 10.58 0.00 46.92 2.52
3023 5870 9.355215 GATAGTATAGATACAATGAACCAACCG 57.645 37.037 2.66 0.00 35.74 4.44
3045 5892 5.950883 TGGAACAACGTCTAAGAGTGATAG 58.049 41.667 0.00 0.00 31.92 2.08
3059 5906 2.672996 CCCCAGGCTGGAACAACG 60.673 66.667 34.84 16.26 40.96 4.10


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

AutoCloner maintained by Alex Coulton.