Multiple sequence alignment - TraesCS2A01G154400

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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 TraesCS2A01G154400 chr2A 100.000 5168 0 0 1 5168 101904185 101909352 0.000000e+00 9544.0
1 TraesCS2A01G154400 chr2A 100.000 3497 0 0 5476 8972 101909660 101913156 0.000000e+00 6458.0
2 TraesCS2A01G154400 chr2A 87.786 131 13 2 6791 6920 485222074 485222202 5.610000e-32 150.0
3 TraesCS2A01G154400 chr2A 79.464 224 35 8 6704 6920 485201419 485201638 2.020000e-31 148.0
4 TraesCS2A01G154400 chr2A 89.474 57 3 1 325 378 140498466 140498522 1.620000e-07 69.4
5 TraesCS2A01G154400 chr2D 95.749 4399 127 12 162 4534 102866897 102871261 0.000000e+00 7033.0
6 TraesCS2A01G154400 chr2D 93.421 2736 117 16 5572 8285 102872127 102874821 0.000000e+00 3997.0
7 TraesCS2A01G154400 chr2D 97.802 637 6 2 4534 5168 102871334 102871964 0.000000e+00 1092.0
8 TraesCS2A01G154400 chr2D 88.668 503 41 6 8485 8972 102875118 102875619 4.640000e-167 599.0
9 TraesCS2A01G154400 chr2D 100.000 98 0 0 5476 5573 102871991 102872088 1.990000e-41 182.0
10 TraesCS2A01G154400 chr2D 87.931 58 3 3 325 378 133034280 133034337 2.090000e-06 65.8
11 TraesCS2A01G154400 chr2B 95.014 3309 106 27 157 3439 154244085 154247360 0.000000e+00 5142.0
12 TraesCS2A01G154400 chr2B 94.757 2918 95 24 5572 8468 154250713 154253593 0.000000e+00 4488.0
13 TraesCS2A01G154400 chr2B 95.625 1120 27 3 3435 4534 154248725 154249842 0.000000e+00 1777.0
14 TraesCS2A01G154400 chr2B 97.953 635 13 0 4534 5168 154249916 154250550 0.000000e+00 1101.0
15 TraesCS2A01G154400 chr2B 89.575 518 21 6 8469 8972 154253806 154254304 2.130000e-175 627.0
16 TraesCS2A01G154400 chr2B 96.939 98 3 0 5476 5573 154250577 154250674 2.000000e-36 165.0
17 TraesCS2A01G154400 chr2B 87.755 49 6 0 351 399 188713999 188714047 3.500000e-04 58.4
18 TraesCS2A01G154400 chr4B 88.056 2227 230 28 975 3187 96942019 96939815 0.000000e+00 2606.0
19 TraesCS2A01G154400 chr4B 85.036 1263 146 29 5682 6920 96937275 96936032 0.000000e+00 1245.0
20 TraesCS2A01G154400 chr4B 81.271 1212 174 39 3243 4434 96939670 96938492 0.000000e+00 931.0
21 TraesCS2A01G154400 chr4B 84.105 648 80 15 4530 5166 96938337 96937702 9.960000e-169 604.0
22 TraesCS2A01G154400 chr4D 87.831 2227 240 24 975 3186 66322070 66319860 0.000000e+00 2582.0
23 TraesCS2A01G154400 chr4D 84.817 1258 152 28 5682 6920 66317482 66316245 0.000000e+00 1229.0
24 TraesCS2A01G154400 chr4D 81.188 1212 171 39 3280 4470 66319736 66318561 0.000000e+00 922.0
25 TraesCS2A01G154400 chr4D 83.667 649 81 16 4530 5168 66318464 66317831 1.000000e-163 588.0
26 TraesCS2A01G154400 chr4A 87.718 2182 235 28 975 3142 515007118 515004956 0.000000e+00 2514.0
27 TraesCS2A01G154400 chr4A 81.559 1963 252 74 3243 5168 515004796 515002907 0.000000e+00 1519.0
28 TraesCS2A01G154400 chr4A 85.310 1273 135 36 5682 6920 515002658 515001404 0.000000e+00 1267.0
29 TraesCS2A01G154400 chr4A 81.250 208 29 7 6720 6920 597816016 597816220 9.320000e-35 159.0
30 TraesCS2A01G154400 chrUn 93.369 377 21 4 2298 2673 479413074 479413447 1.020000e-153 555.0
31 TraesCS2A01G154400 chr7B 93.694 111 7 0 6509 6619 697907636 697907746 5.570000e-37 167.0
32 TraesCS2A01G154400 chr6B 80.269 223 35 6 6704 6920 95971513 95971732 9.320000e-35 159.0
33 TraesCS2A01G154400 chr6B 96.875 64 1 1 3915 3978 686923767 686923829 1.230000e-18 106.0
34 TraesCS2A01G154400 chr3B 93.333 105 7 0 6816 6920 757905822 757905926 1.210000e-33 156.0
35 TraesCS2A01G154400 chr7D 89.655 116 9 3 4325 4440 218414526 218414414 2.610000e-30 145.0
36 TraesCS2A01G154400 chr1D 98.113 53 1 0 61 113 475927184 475927236 9.590000e-15 93.5
37 TraesCS2A01G154400 chr3A 95.745 47 1 1 68 113 630938721 630938675 3.470000e-09 75.0


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 TraesCS2A01G154400 chr2A 101904185 101913156 8971 False 8001.000000 9544 100.000000 1 8972 2 chr2A.!!$F4 8971
1 TraesCS2A01G154400 chr2D 102866897 102875619 8722 False 2580.600000 7033 95.128000 162 8972 5 chr2D.!!$F2 8810
2 TraesCS2A01G154400 chr2B 154244085 154254304 10219 False 2216.666667 5142 94.977167 157 8972 6 chr2B.!!$F2 8815
3 TraesCS2A01G154400 chr4B 96936032 96942019 5987 True 1346.500000 2606 84.617000 975 6920 4 chr4B.!!$R1 5945
4 TraesCS2A01G154400 chr4D 66316245 66322070 5825 True 1330.250000 2582 84.375750 975 6920 4 chr4D.!!$R1 5945
5 TraesCS2A01G154400 chr4A 515001404 515007118 5714 True 1766.666667 2514 84.862333 975 6920 3 chr4A.!!$R1 5945

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
142 143 0.110486 TCCAAGGACAACTTCAGGCC 59.890 55.000 0.00 0.00 37.29 5.19 F
216 217 0.328258 TCAAAGCAGGCCCTTAGACC 59.672 55.000 0.00 0.00 0.00 3.85 F
1245 1275 0.462047 CCAAGGATGAGGCCGTACAC 60.462 60.000 0.00 0.00 0.00 2.90 F
1380 1410 2.601666 TCGGCTCACACCTCTGCT 60.602 61.111 0.00 0.00 0.00 4.24 F
2337 2377 2.293399 GGATCGCAAGTTTCAACCAGTT 59.707 45.455 0.00 0.00 39.48 3.16 F
3592 5162 4.338964 TGAGTGTCATTTTGTGCTGTTGAT 59.661 37.500 0.00 0.00 0.00 2.57 F
4164 5760 0.327591 CTTCCCTTGCTCTTCAGGCT 59.672 55.000 0.00 0.00 0.00 4.58 F
5573 7305 3.064545 GGCAGAGAACACAGATGCAATAC 59.935 47.826 0.00 0.00 38.63 1.89 F
6619 8542 1.341976 ACTGCTGGTCAAAGGTTGGTT 60.342 47.619 0.00 0.00 0.00 3.67 F
6947 8881 0.038526 ATATGCTACGCCGTACCAGC 60.039 55.000 3.61 3.61 34.56 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1815 0.602638 CCACGTGACAAGGCTGCTTA 60.603 55.000 19.30 0.00 0.00 3.09 R
1944 1974 1.765314 CTCCCATCTGGTTGACTAGGG 59.235 57.143 0.00 0.00 36.50 3.53 R
2319 2359 6.811253 ATTATAACTGGTTGAAACTTGCGA 57.189 33.333 0.00 0.00 0.00 5.10 R
3272 3407 4.518211 CCAAAGAGACAACTGCAGAATCTT 59.482 41.667 23.35 17.09 0.00 2.40 R
4035 5629 0.460109 TCCGGATCACATGTTCAGCG 60.460 55.000 0.00 0.00 0.00 5.18 R
4917 6620 0.729116 CACCTGCATAAACCTCAGCG 59.271 55.000 0.00 0.00 0.00 5.18 R
6036 7940 4.632688 CCCTAAATTTTTGCAGCTGAATGG 59.367 41.667 20.43 5.89 0.00 3.16 R
6881 8815 0.637195 TCCAGCCTCCTAACTAGCCT 59.363 55.000 0.00 0.00 0.00 4.58 R
7738 9688 0.391597 ACACGGTCAGTTGGTTCGAT 59.608 50.000 0.00 0.00 0.00 3.59 R
8554 10784 0.529378 GGCAGTTCAGCTTGGAATGG 59.471 55.000 0.00 0.00 34.17 3.16 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
38 39 3.443588 AAAAACAGGCAGCGTCCC 58.556 55.556 0.00 0.00 0.00 4.46
39 40 1.454847 AAAAACAGGCAGCGTCCCA 60.455 52.632 0.00 0.00 0.00 4.37
40 41 1.455383 AAAAACAGGCAGCGTCCCAG 61.455 55.000 0.00 0.00 0.00 4.45
46 47 3.730761 GCAGCGTCCCAGCACAAG 61.731 66.667 0.00 0.00 40.15 3.16
47 48 3.730761 CAGCGTCCCAGCACAAGC 61.731 66.667 0.00 0.00 40.15 4.01
103 104 3.269347 CGTTCCCGGCGCCTTATG 61.269 66.667 26.68 8.69 0.00 1.90
104 105 3.583086 GTTCCCGGCGCCTTATGC 61.583 66.667 26.68 8.18 0.00 3.14
116 117 3.113260 GCCTTATGCGCCCTATATAGG 57.887 52.381 20.43 20.43 43.25 2.57
117 118 2.698797 GCCTTATGCGCCCTATATAGGA 59.301 50.000 27.58 10.07 46.63 2.94
118 119 3.243907 GCCTTATGCGCCCTATATAGGAG 60.244 52.174 27.58 20.88 46.63 3.69
119 120 3.322254 CCTTATGCGCCCTATATAGGAGG 59.678 52.174 27.58 19.72 46.63 4.30
120 121 2.848678 ATGCGCCCTATATAGGAGGA 57.151 50.000 27.58 21.29 46.63 3.71
121 122 2.145397 TGCGCCCTATATAGGAGGAG 57.855 55.000 27.58 15.39 46.63 3.69
122 123 1.639108 TGCGCCCTATATAGGAGGAGA 59.361 52.381 27.58 6.83 46.63 3.71
123 124 2.245028 TGCGCCCTATATAGGAGGAGAT 59.755 50.000 27.58 0.00 46.63 2.75
124 125 2.888414 GCGCCCTATATAGGAGGAGATC 59.112 54.545 27.58 7.61 46.63 2.75
136 137 3.990959 GAGGAGATCCAAGGACAACTT 57.009 47.619 0.92 0.00 41.00 2.66
137 138 3.867857 GAGGAGATCCAAGGACAACTTC 58.132 50.000 0.92 0.00 37.29 3.01
138 139 3.251484 AGGAGATCCAAGGACAACTTCA 58.749 45.455 0.92 0.00 37.29 3.02
139 140 3.262915 AGGAGATCCAAGGACAACTTCAG 59.737 47.826 0.92 0.00 37.29 3.02
140 141 3.604582 GAGATCCAAGGACAACTTCAGG 58.395 50.000 0.00 0.00 37.29 3.86
141 142 2.087646 GATCCAAGGACAACTTCAGGC 58.912 52.381 0.00 0.00 37.29 4.85
142 143 0.110486 TCCAAGGACAACTTCAGGCC 59.890 55.000 0.00 0.00 37.29 5.19
143 144 0.178992 CCAAGGACAACTTCAGGCCA 60.179 55.000 5.01 0.00 37.29 5.36
144 145 1.242076 CAAGGACAACTTCAGGCCAG 58.758 55.000 5.01 0.00 37.29 4.85
145 146 0.111253 AAGGACAACTTCAGGCCAGG 59.889 55.000 5.01 0.00 32.85 4.45
146 147 0.768221 AGGACAACTTCAGGCCAGGA 60.768 55.000 5.01 0.00 0.00 3.86
147 148 0.110486 GGACAACTTCAGGCCAGGAA 59.890 55.000 5.01 7.69 0.00 3.36
148 149 1.478654 GGACAACTTCAGGCCAGGAAA 60.479 52.381 5.01 0.00 0.00 3.13
149 150 2.306847 GACAACTTCAGGCCAGGAAAA 58.693 47.619 5.01 0.00 0.00 2.29
150 151 2.893489 GACAACTTCAGGCCAGGAAAAT 59.107 45.455 5.01 0.00 0.00 1.82
151 152 3.308401 ACAACTTCAGGCCAGGAAAATT 58.692 40.909 5.01 3.19 0.00 1.82
152 153 3.321968 ACAACTTCAGGCCAGGAAAATTC 59.678 43.478 5.01 0.00 0.00 2.17
153 154 3.532641 ACTTCAGGCCAGGAAAATTCT 57.467 42.857 5.01 0.00 0.00 2.40
154 155 3.160269 ACTTCAGGCCAGGAAAATTCTG 58.840 45.455 5.01 0.00 0.00 3.02
155 156 3.181429 ACTTCAGGCCAGGAAAATTCTGA 60.181 43.478 5.01 0.00 34.36 3.27
156 157 2.795329 TCAGGCCAGGAAAATTCTGAC 58.205 47.619 5.01 0.00 34.36 3.51
157 158 1.821136 CAGGCCAGGAAAATTCTGACC 59.179 52.381 5.01 0.00 35.40 4.02
158 159 1.186200 GGCCAGGAAAATTCTGACCC 58.814 55.000 0.00 0.00 34.36 4.46
159 160 1.549950 GGCCAGGAAAATTCTGACCCA 60.550 52.381 0.00 0.00 34.36 4.51
160 161 2.460669 GCCAGGAAAATTCTGACCCAT 58.539 47.619 0.00 0.00 34.36 4.00
166 167 5.009010 CAGGAAAATTCTGACCCATATTCCG 59.991 44.000 0.00 0.00 39.95 4.30
174 175 2.281484 CCATATTCCGGGGCCGTG 60.281 66.667 0.00 0.00 37.81 4.94
185 186 1.227342 GGGGCCGTGTTTTTGCATTG 61.227 55.000 0.00 0.00 0.00 2.82
216 217 0.328258 TCAAAGCAGGCCCTTAGACC 59.672 55.000 0.00 0.00 0.00 3.85
227 228 1.571457 CCCTTAGACCTCCTCTCCTGA 59.429 57.143 0.00 0.00 0.00 3.86
307 308 1.135112 CCAATGCGGCTCTAAAAACCC 60.135 52.381 0.00 0.00 0.00 4.11
308 309 1.135112 CAATGCGGCTCTAAAAACCCC 60.135 52.381 0.00 0.00 0.00 4.95
464 466 4.504916 CTCGTCGCCTCCCTGCTG 62.505 72.222 0.00 0.00 0.00 4.41
625 629 2.481969 CCTGCTTAGCGTATCTTGCTGA 60.482 50.000 0.00 0.00 43.85 4.26
638 642 7.096722 GCGTATCTTGCTGAAATTGATTCATTC 60.097 37.037 0.00 0.00 46.62 2.67
680 684 4.358851 CGTTTGTTCTGGCAATTTTCTGA 58.641 39.130 0.00 0.00 0.00 3.27
781 789 2.661537 CACTCCACGCAGTTCGCA 60.662 61.111 0.00 0.00 41.61 5.10
789 797 1.463056 CACGCAGTTCGCATAGGAAAA 59.537 47.619 0.00 0.00 41.61 2.29
900 928 0.899720 CAAGCTGGCCAAATCCACAT 59.100 50.000 7.01 0.00 31.74 3.21
910 938 4.100498 GGCCAAATCCACATCATTCTTGAT 59.900 41.667 0.00 0.00 43.51 2.57
946 974 1.243902 ATAGTCTAGCGCTGCTCCTC 58.756 55.000 22.90 4.50 40.44 3.71
973 1001 4.149598 TGTTTTCTTTCCTCTTAAGGGGC 58.850 43.478 17.35 0.34 43.56 5.80
993 1023 2.848302 GCGCAAGTAATGTTTCTGATGC 59.152 45.455 0.30 0.00 41.68 3.91
997 1027 5.905733 CGCAAGTAATGTTTCTGATGCTATG 59.094 40.000 0.00 0.00 0.00 2.23
1014 1044 4.759564 GCTGCTGCAATTGACTCG 57.240 55.556 10.34 0.00 39.41 4.18
1031 1061 4.402474 TGACTCGTGTTCCTGATGTGATAT 59.598 41.667 0.00 0.00 0.00 1.63
1083 1113 2.352960 GGAGAATTCCAGCAAGCGTAAG 59.647 50.000 0.65 0.00 43.45 2.34
1170 1200 4.373116 TCGACTGCCAAGCGTCCC 62.373 66.667 6.16 0.00 32.00 4.46
1203 1233 1.450134 GTGCATCCATGAGGTCGCA 60.450 57.895 0.00 0.00 39.61 5.10
1245 1275 0.462047 CCAAGGATGAGGCCGTACAC 60.462 60.000 0.00 0.00 0.00 2.90
1380 1410 2.601666 TCGGCTCACACCTCTGCT 60.602 61.111 0.00 0.00 0.00 4.24
1944 1974 3.847037 CAAGACACATTTGCAAAGCAC 57.153 42.857 18.19 7.18 38.71 4.40
2113 2144 9.132521 CTGGACTTATTGTGCTTTCTAAATTTG 57.867 33.333 0.00 0.00 37.91 2.32
2287 2327 8.178313 TCTACTCATATCCTCGCTTAATTTCA 57.822 34.615 0.00 0.00 0.00 2.69
2337 2377 2.293399 GGATCGCAAGTTTCAACCAGTT 59.707 45.455 0.00 0.00 39.48 3.16
3019 3063 7.214467 TGAATTTTGTACAAGCCCTTCTTAG 57.786 36.000 8.56 0.00 32.74 2.18
3272 3407 6.778559 TGATTTGATCAAATGCATCCCTATCA 59.221 34.615 32.89 20.05 40.77 2.15
3290 3487 5.523188 CCTATCAAGATTCTGCAGTTGTCTC 59.477 44.000 14.67 4.81 0.00 3.36
3308 3505 4.518970 TGTCTCTTTGGGTTGATTAAGCAC 59.481 41.667 0.00 0.00 36.03 4.40
3373 3570 8.801299 TGATGCAAATGGTTTCTATTTCACTTA 58.199 29.630 0.00 0.00 0.00 2.24
3401 3598 5.533528 TCATGGTTCTCATTGCAATAGATGG 59.466 40.000 12.53 0.00 32.92 3.51
3539 5108 4.768968 ACATTTGAAGGATATATGGCCTGC 59.231 41.667 3.32 0.00 34.00 4.85
3592 5162 4.338964 TGAGTGTCATTTTGTGCTGTTGAT 59.661 37.500 0.00 0.00 0.00 2.57
3893 5487 5.499139 TTTAGTCTGACTTTTGCTTGGTG 57.501 39.130 16.53 0.00 0.00 4.17
4035 5629 1.379309 TGCGGAGGGCCAATTTACC 60.379 57.895 6.18 0.00 42.61 2.85
4094 5688 6.861065 TCAGTATGAAAAGGTTTGTCTCAC 57.139 37.500 0.00 0.00 45.97 3.51
4164 5760 0.327591 CTTCCCTTGCTCTTCAGGCT 59.672 55.000 0.00 0.00 0.00 4.58
4254 5850 8.722394 GGAGAGGTATGCTATTTTAATTGTAGC 58.278 37.037 7.11 7.11 40.85 3.58
4553 6248 6.648725 GCTGTAAATTTGCACAAATTCCCTTA 59.351 34.615 18.79 7.56 46.76 2.69
5143 6848 8.434661 CGCTTTTTAATCTTGTTAATGTTGCAT 58.565 29.630 0.00 0.00 0.00 3.96
5573 7305 3.064545 GGCAGAGAACACAGATGCAATAC 59.935 47.826 0.00 0.00 38.63 1.89
5758 7651 5.011090 TCATAAACTTGATGGTCTCGAGG 57.989 43.478 13.56 0.00 39.43 4.63
5998 7897 8.609176 TGGTTAATTCTTTGTATACTTGATCGC 58.391 33.333 4.17 0.00 0.00 4.58
6035 7939 6.937436 AATGTGTTCTTACGTTTTTCTCCT 57.063 33.333 0.00 0.00 0.00 3.69
6036 7940 5.978934 TGTGTTCTTACGTTTTTCTCCTC 57.021 39.130 0.00 0.00 0.00 3.71
6037 7941 4.812626 TGTGTTCTTACGTTTTTCTCCTCC 59.187 41.667 0.00 0.00 0.00 4.30
6414 8318 2.977178 CAACTCTCGGAGGCTGCT 59.023 61.111 4.02 0.00 33.35 4.24
6453 8369 4.006989 TGCATACTTGTTGTATCACCACC 58.993 43.478 0.00 0.00 39.66 4.61
6507 8430 6.324601 AGTGGGATCTCTGATTTCTCATTT 57.675 37.500 0.00 0.00 0.00 2.32
6549 8472 7.151999 AGAATGCAAATTGGACGTAAATGTA 57.848 32.000 0.00 0.00 0.00 2.29
6619 8542 1.341976 ACTGCTGGTCAAAGGTTGGTT 60.342 47.619 0.00 0.00 0.00 3.67
6661 8590 6.502136 TTGTGATGCCATACATTTTTCGTA 57.498 33.333 0.00 0.00 39.84 3.43
6721 8650 8.905660 TTTCCAATTGTGACATTTGATCATTT 57.094 26.923 18.62 0.00 29.53 2.32
6772 8702 9.503427 GCAATGTTACTCTACATGTTTAATTCC 57.497 33.333 2.30 0.00 38.69 3.01
6881 8815 7.894708 TGACATTTTTGAAGGAAGCATCATAA 58.105 30.769 0.00 0.00 0.00 1.90
6928 8862 4.260139 TCTAAATCAGGTACGTGTTGCA 57.740 40.909 14.78 0.00 0.00 4.08
6940 8874 0.042188 GTGTTGCATATGCTACGCCG 60.042 55.000 32.28 0.00 46.92 6.46
6947 8881 0.038526 ATATGCTACGCCGTACCAGC 60.039 55.000 3.61 3.61 34.56 4.85
6997 8931 4.341806 TGTCATTTGGGACATTCATATGGC 59.658 41.667 2.13 0.00 42.56 4.40
7005 8939 2.549754 GACATTCATATGGCCTCCAACG 59.450 50.000 3.32 0.00 36.95 4.10
7176 9116 5.242393 AGTTTGACTGCATGCTTTGTAAGAT 59.758 36.000 20.33 0.00 0.00 2.40
7178 9118 3.441222 TGACTGCATGCTTTGTAAGATGG 59.559 43.478 20.33 0.00 0.00 3.51
7202 9142 6.459923 GCACATACTCTATTTAGGGAAGGAG 58.540 44.000 0.00 0.00 0.00 3.69
7217 9157 4.080526 GGGAAGGAGGCAGTAAATCACTTA 60.081 45.833 0.00 0.00 34.26 2.24
7218 9158 5.398012 GGGAAGGAGGCAGTAAATCACTTAT 60.398 44.000 0.00 0.00 34.26 1.73
7243 9185 3.129813 TCAGAATGTCTGGCATTGAATGC 59.870 43.478 21.24 21.24 46.90 3.56
7330 9273 1.078759 GCATCCGTGTCGAGGAAGTG 61.079 60.000 0.00 0.00 41.69 3.16
7338 9282 4.174009 CGTGTCGAGGAAGTGTATTTCAT 58.826 43.478 0.00 0.00 0.00 2.57
7409 9353 2.749076 TGCATGGCTCAATTACTCACAC 59.251 45.455 0.00 0.00 0.00 3.82
7411 9355 3.426695 GCATGGCTCAATTACTCACACAC 60.427 47.826 0.00 0.00 0.00 3.82
7568 9518 3.126001 TGTTGCTTCTGTAGAGGTTGG 57.874 47.619 0.00 0.00 0.00 3.77
7597 9547 2.802787 CTCCGTAGAGGTTGGCTATG 57.197 55.000 0.00 0.00 41.99 2.23
7598 9548 2.032620 CTCCGTAGAGGTTGGCTATGT 58.967 52.381 0.00 0.00 41.99 2.29
7599 9549 2.431057 CTCCGTAGAGGTTGGCTATGTT 59.569 50.000 0.00 0.00 41.99 2.71
7600 9550 2.167693 TCCGTAGAGGTTGGCTATGTTG 59.832 50.000 0.00 0.00 41.99 3.33
7601 9551 1.933853 CGTAGAGGTTGGCTATGTTGC 59.066 52.381 0.00 0.00 0.00 4.17
7612 9562 3.014604 GCTATGTTGCCTACGTAGAGG 57.985 52.381 24.15 12.27 45.43 3.69
7613 9563 2.361438 GCTATGTTGCCTACGTAGAGGT 59.639 50.000 24.15 6.20 45.43 3.85
7614 9564 3.181478 GCTATGTTGCCTACGTAGAGGTT 60.181 47.826 24.15 6.13 45.43 3.50
7615 9565 2.736144 TGTTGCCTACGTAGAGGTTG 57.264 50.000 24.15 7.75 39.02 3.77
7672 9622 1.185315 GCCCTTTTCTGCATGCCTAA 58.815 50.000 16.68 6.46 0.00 2.69
7673 9623 1.758862 GCCCTTTTCTGCATGCCTAAT 59.241 47.619 16.68 0.00 0.00 1.73
7701 9651 2.638480 TTCCTGTTCCCAAGTCTGTG 57.362 50.000 0.00 0.00 0.00 3.66
7721 9671 4.202253 TGTGCACAGTCAACAGAAGTAGAT 60.202 41.667 17.42 0.00 0.00 1.98
7738 9688 9.502091 AGAAGTAGATGTGCATTGTTTTACTTA 57.498 29.630 0.00 0.00 32.14 2.24
7760 9711 1.658994 GAACCAACTGACCGTGTGAA 58.341 50.000 0.00 0.00 0.00 3.18
7761 9712 2.218603 GAACCAACTGACCGTGTGAAT 58.781 47.619 0.00 0.00 0.00 2.57
7762 9713 1.878953 ACCAACTGACCGTGTGAATC 58.121 50.000 0.00 0.00 0.00 2.52
7763 9714 1.416401 ACCAACTGACCGTGTGAATCT 59.584 47.619 0.00 0.00 0.00 2.40
7764 9715 1.800586 CCAACTGACCGTGTGAATCTG 59.199 52.381 0.00 0.00 0.00 2.90
7893 9844 3.618594 CCAACTCATTGTACCTGTGATCG 59.381 47.826 0.00 0.00 33.60 3.69
7919 9870 2.774234 AGCTCCAGCAGTTGTACCATAT 59.226 45.455 0.48 0.00 45.16 1.78
7958 9909 5.583854 CAGAGCAAATGTAGCTGTCTTGTAT 59.416 40.000 0.00 0.00 43.58 2.29
7959 9910 6.093219 CAGAGCAAATGTAGCTGTCTTGTATT 59.907 38.462 0.00 0.00 43.58 1.89
8013 9972 0.313987 TATGTCGCAGCGTAGGATGG 59.686 55.000 15.93 0.00 0.00 3.51
8014 9973 1.391933 ATGTCGCAGCGTAGGATGGA 61.392 55.000 15.93 0.00 0.00 3.41
8015 9974 1.299468 GTCGCAGCGTAGGATGGAG 60.299 63.158 15.93 0.00 0.00 3.86
8016 9975 1.453197 TCGCAGCGTAGGATGGAGA 60.453 57.895 15.93 0.00 0.00 3.71
8017 9976 0.823769 TCGCAGCGTAGGATGGAGAT 60.824 55.000 15.93 0.00 0.00 2.75
8018 9977 0.665670 CGCAGCGTAGGATGGAGATG 60.666 60.000 6.65 0.00 0.00 2.90
8059 10018 0.958822 CCTTAGGCCGCAACTGTTTT 59.041 50.000 0.00 0.00 0.00 2.43
8125 10085 4.819105 AAGTGGTCCGATGTCTGAAATA 57.181 40.909 0.00 0.00 0.00 1.40
8130 10090 3.521560 GTCCGATGTCTGAAATAGCACA 58.478 45.455 0.00 0.00 0.00 4.57
8241 10201 1.816074 TTACATTTCCACGGCCTGTC 58.184 50.000 0.00 0.00 0.00 3.51
8275 10235 7.819900 GTCTAGTTGGTTACTGAAAGATCATGT 59.180 37.037 0.00 0.00 37.73 3.21
8325 10328 6.140786 GCTGAACGAACGTGATATATCAGTA 58.859 40.000 15.83 0.00 37.51 2.74
8384 10387 7.713734 ATTGAGATGGTGATCATTGAAGTTT 57.286 32.000 0.00 0.00 35.97 2.66
8417 10420 0.181587 TTTTCCGTGAGAACTGGGCA 59.818 50.000 0.00 0.00 32.95 5.36
8431 10434 0.965439 TGGGCATCAAAGTTTTCGGG 59.035 50.000 0.00 0.00 0.00 5.14
8518 10748 2.351924 TTTGGCCGCCAAACTCTCCT 62.352 55.000 29.88 0.00 46.92 3.69
8519 10749 2.747855 GGCCGCCAAACTCTCCTG 60.748 66.667 3.91 0.00 0.00 3.86
8544 10774 6.878317 AGCCCTTTAATTTAAGAATGCCTTC 58.122 36.000 5.78 0.00 36.34 3.46
8554 10784 7.945033 TTTAAGAATGCCTTCATGTTTCAAC 57.055 32.000 4.48 0.00 36.34 3.18
8572 10802 1.251251 ACCATTCCAAGCTGAACTGC 58.749 50.000 0.00 0.00 0.00 4.40
8603 10837 3.304726 GGTGAAGGCACTAAAGCAGTTTC 60.305 47.826 0.00 0.00 44.52 2.78
8667 10901 4.813027 ACATAGCCAAACAGCTCAAATTG 58.187 39.130 0.00 0.00 43.67 2.32
8670 10904 2.694628 AGCCAAACAGCTCAAATTGTCA 59.305 40.909 0.00 0.00 39.48 3.58
8760 11008 4.898829 TTACATATTGCCATGACACAGC 57.101 40.909 0.00 0.00 0.00 4.40
8817 11065 6.816640 TCCACTGGATTTAAGAAACATCTACG 59.183 38.462 0.00 0.00 0.00 3.51
8818 11066 6.816640 CCACTGGATTTAAGAAACATCTACGA 59.183 38.462 0.00 0.00 0.00 3.43
8819 11067 7.333423 CCACTGGATTTAAGAAACATCTACGAA 59.667 37.037 0.00 0.00 0.00 3.85
8820 11068 8.383619 CACTGGATTTAAGAAACATCTACGAAG 58.616 37.037 0.00 0.00 0.00 3.79
8821 11069 7.549488 ACTGGATTTAAGAAACATCTACGAAGG 59.451 37.037 0.00 0.00 0.00 3.46
8822 11070 6.315393 TGGATTTAAGAAACATCTACGAAGGC 59.685 38.462 0.00 0.00 0.00 4.35
8823 11071 6.238402 GGATTTAAGAAACATCTACGAAGGCC 60.238 42.308 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.454847 TGGGACGCTGCCTGTTTTT 60.455 52.632 0.00 0.00 0.00 1.94
22 23 1.898574 CTGGGACGCTGCCTGTTTT 60.899 57.895 0.00 0.00 0.00 2.43
23 24 2.281761 CTGGGACGCTGCCTGTTT 60.282 61.111 0.00 0.00 0.00 2.83
29 30 3.730761 CTTGTGCTGGGACGCTGC 61.731 66.667 13.50 13.50 0.00 5.25
30 31 3.730761 GCTTGTGCTGGGACGCTG 61.731 66.667 0.00 0.00 36.03 5.18
87 88 3.583086 GCATAAGGCGCCGGGAAC 61.583 66.667 23.20 8.55 0.00 3.62
96 97 2.698797 TCCTATATAGGGCGCATAAGGC 59.301 50.000 25.54 0.00 43.79 4.35
97 98 3.322254 CCTCCTATATAGGGCGCATAAGG 59.678 52.174 25.54 18.93 43.79 2.69
98 99 4.215908 TCCTCCTATATAGGGCGCATAAG 58.784 47.826 25.54 14.63 43.79 1.73
99 100 4.079385 TCTCCTCCTATATAGGGCGCATAA 60.079 45.833 25.54 6.45 43.79 1.90
100 101 3.462205 TCTCCTCCTATATAGGGCGCATA 59.538 47.826 25.54 7.12 43.79 3.14
101 102 2.245028 TCTCCTCCTATATAGGGCGCAT 59.755 50.000 25.54 0.00 43.79 4.73
102 103 1.639108 TCTCCTCCTATATAGGGCGCA 59.361 52.381 25.54 8.14 43.79 6.09
103 104 2.438800 TCTCCTCCTATATAGGGCGC 57.561 55.000 25.54 0.00 43.79 6.53
104 105 3.117474 TGGATCTCCTCCTATATAGGGCG 60.117 52.174 25.54 17.26 45.21 6.13
105 106 4.544564 TGGATCTCCTCCTATATAGGGC 57.455 50.000 25.54 8.87 45.21 5.19
106 107 5.196779 TCCTTGGATCTCCTCCTATATAGGG 59.803 48.000 25.54 16.76 45.21 3.53
107 108 6.133356 GTCCTTGGATCTCCTCCTATATAGG 58.867 48.000 21.21 21.21 45.21 2.57
108 109 6.736581 TGTCCTTGGATCTCCTCCTATATAG 58.263 44.000 2.46 2.46 45.21 1.31
109 110 6.736561 TGTCCTTGGATCTCCTCCTATATA 57.263 41.667 0.00 0.00 45.21 0.86
110 111 5.623551 TGTCCTTGGATCTCCTCCTATAT 57.376 43.478 0.00 0.00 45.21 0.86
111 112 5.103043 AGTTGTCCTTGGATCTCCTCCTATA 60.103 44.000 0.00 0.00 45.21 1.31
112 113 3.970640 GTTGTCCTTGGATCTCCTCCTAT 59.029 47.826 0.00 0.00 45.21 2.57
113 114 3.012959 AGTTGTCCTTGGATCTCCTCCTA 59.987 47.826 0.00 0.00 45.21 2.94
114 115 2.192263 GTTGTCCTTGGATCTCCTCCT 58.808 52.381 0.00 0.00 45.21 3.69
115 116 2.192263 AGTTGTCCTTGGATCTCCTCC 58.808 52.381 0.00 0.00 45.19 4.30
116 117 3.261897 TGAAGTTGTCCTTGGATCTCCTC 59.738 47.826 0.00 0.00 36.82 3.71
117 118 3.251484 TGAAGTTGTCCTTGGATCTCCT 58.749 45.455 0.00 0.00 36.82 3.69
118 119 3.604582 CTGAAGTTGTCCTTGGATCTCC 58.395 50.000 0.00 0.00 32.03 3.71
119 120 3.604582 CCTGAAGTTGTCCTTGGATCTC 58.395 50.000 0.00 0.00 32.03 2.75
120 121 2.290577 GCCTGAAGTTGTCCTTGGATCT 60.291 50.000 0.00 0.00 32.03 2.75
121 122 2.087646 GCCTGAAGTTGTCCTTGGATC 58.912 52.381 0.00 0.00 32.03 3.36
122 123 1.272147 GGCCTGAAGTTGTCCTTGGAT 60.272 52.381 0.00 0.00 32.03 3.41
123 124 0.110486 GGCCTGAAGTTGTCCTTGGA 59.890 55.000 0.00 0.00 32.03 3.53
124 125 0.178992 TGGCCTGAAGTTGTCCTTGG 60.179 55.000 3.32 0.00 32.03 3.61
125 126 1.242076 CTGGCCTGAAGTTGTCCTTG 58.758 55.000 3.32 0.00 32.03 3.61
126 127 0.111253 CCTGGCCTGAAGTTGTCCTT 59.889 55.000 11.88 0.00 35.59 3.36
127 128 0.768221 TCCTGGCCTGAAGTTGTCCT 60.768 55.000 11.88 0.00 0.00 3.85
128 129 0.110486 TTCCTGGCCTGAAGTTGTCC 59.890 55.000 11.88 0.00 0.00 4.02
129 130 1.981256 TTTCCTGGCCTGAAGTTGTC 58.019 50.000 11.88 0.00 0.00 3.18
130 131 2.452600 TTTTCCTGGCCTGAAGTTGT 57.547 45.000 11.88 0.00 0.00 3.32
131 132 3.575687 AGAATTTTCCTGGCCTGAAGTTG 59.424 43.478 11.88 0.00 0.00 3.16
132 133 3.575687 CAGAATTTTCCTGGCCTGAAGTT 59.424 43.478 11.88 9.07 0.00 2.66
133 134 3.160269 CAGAATTTTCCTGGCCTGAAGT 58.840 45.455 11.88 0.00 0.00 3.01
134 135 3.192212 GTCAGAATTTTCCTGGCCTGAAG 59.808 47.826 11.88 0.00 33.20 3.02
135 136 3.157087 GTCAGAATTTTCCTGGCCTGAA 58.843 45.455 11.88 7.71 33.20 3.02
136 137 2.795329 GTCAGAATTTTCCTGGCCTGA 58.205 47.619 11.88 0.66 30.48 3.86
140 141 1.923356 TGGGTCAGAATTTTCCTGGC 58.077 50.000 0.00 0.00 35.64 4.85
141 142 5.302823 GGAATATGGGTCAGAATTTTCCTGG 59.697 44.000 0.00 0.00 33.54 4.45
142 143 5.009010 CGGAATATGGGTCAGAATTTTCCTG 59.991 44.000 0.00 0.00 33.92 3.86
143 144 5.133221 CGGAATATGGGTCAGAATTTTCCT 58.867 41.667 0.00 0.00 33.92 3.36
144 145 4.278419 CCGGAATATGGGTCAGAATTTTCC 59.722 45.833 0.00 0.00 33.20 3.13
145 146 4.278419 CCCGGAATATGGGTCAGAATTTTC 59.722 45.833 0.73 0.00 42.07 2.29
146 147 4.215109 CCCGGAATATGGGTCAGAATTTT 58.785 43.478 0.73 0.00 42.07 1.82
147 148 3.436470 CCCCGGAATATGGGTCAGAATTT 60.436 47.826 0.73 0.00 45.86 1.82
148 149 2.108250 CCCCGGAATATGGGTCAGAATT 59.892 50.000 0.73 0.00 45.86 2.17
149 150 1.705186 CCCCGGAATATGGGTCAGAAT 59.295 52.381 0.73 0.00 45.86 2.40
150 151 1.136828 CCCCGGAATATGGGTCAGAA 58.863 55.000 0.73 0.00 45.86 3.02
151 152 1.415672 GCCCCGGAATATGGGTCAGA 61.416 60.000 0.73 0.00 45.86 3.27
152 153 1.073199 GCCCCGGAATATGGGTCAG 59.927 63.158 0.73 0.00 45.86 3.51
153 154 2.457323 GGCCCCGGAATATGGGTCA 61.457 63.158 0.73 0.00 46.14 4.02
154 155 2.434774 GGCCCCGGAATATGGGTC 59.565 66.667 0.73 0.00 45.86 4.46
155 156 3.566210 CGGCCCCGGAATATGGGT 61.566 66.667 0.73 0.00 45.86 4.51
156 157 3.566210 ACGGCCCCGGAATATGGG 61.566 66.667 0.73 0.00 46.93 4.00
157 158 2.281484 CACGGCCCCGGAATATGG 60.281 66.667 0.73 0.00 44.69 2.74
158 159 0.750182 AAACACGGCCCCGGAATATG 60.750 55.000 0.73 2.36 44.69 1.78
159 160 0.033894 AAAACACGGCCCCGGAATAT 60.034 50.000 0.73 0.00 44.69 1.28
160 161 0.251253 AAAAACACGGCCCCGGAATA 60.251 50.000 0.73 0.00 44.69 1.75
166 167 1.070615 AATGCAAAAACACGGCCCC 59.929 52.632 0.00 0.00 0.00 5.80
174 175 2.223688 GGCCCAAAACCAATGCAAAAAC 60.224 45.455 0.00 0.00 0.00 2.43
185 186 0.396060 TGCTTTGATGGCCCAAAACC 59.604 50.000 0.00 0.00 35.83 3.27
216 217 2.157640 ACATGAGGTCAGGAGAGGAG 57.842 55.000 0.00 0.00 0.00 3.69
227 228 0.251341 GTGGGCTTGGAACATGAGGT 60.251 55.000 0.00 0.00 39.30 3.85
286 287 1.816224 GGTTTTTAGAGCCGCATTGGA 59.184 47.619 0.00 0.00 42.00 3.53
307 308 1.693103 GGGTACAGGGGAAGAGGGG 60.693 68.421 0.00 0.00 0.00 4.79
308 309 0.640495 TAGGGTACAGGGGAAGAGGG 59.360 60.000 0.00 0.00 0.00 4.30
625 629 8.776376 AACATAAAAGCGGAATGAATCAATTT 57.224 26.923 0.00 0.00 0.00 1.82
638 642 0.730840 GACCGGGAACATAAAAGCGG 59.269 55.000 6.32 0.00 0.00 5.52
690 694 9.693739 ACCACTTCACCACATCAAATATTTATA 57.306 29.630 0.00 0.00 0.00 0.98
781 789 4.062991 GTGAACAGTGGACGTTTTCCTAT 58.937 43.478 0.00 0.00 46.10 2.57
789 797 1.651987 CAACAGTGAACAGTGGACGT 58.348 50.000 13.14 0.00 36.10 4.34
900 928 8.902540 ATTACCGCTTAACATATCAAGAATGA 57.097 30.769 0.00 0.00 40.57 2.57
927 955 1.243902 GAGGAGCAGCGCTAGACTAT 58.756 55.000 10.99 0.18 39.88 2.12
929 957 2.477176 CGAGGAGCAGCGCTAGACT 61.477 63.158 10.99 8.25 39.88 3.24
932 960 0.312416 ATTACGAGGAGCAGCGCTAG 59.688 55.000 10.99 5.98 39.88 3.42
946 974 7.361799 CCCCTTAAGAGGAAAGAAAACATTACG 60.362 40.741 3.36 0.00 46.74 3.18
973 1001 4.346734 AGCATCAGAAACATTACTTGCG 57.653 40.909 0.00 0.00 34.20 4.85
997 1027 0.453950 CACGAGTCAATTGCAGCAGC 60.454 55.000 0.00 0.00 42.57 5.25
1014 1044 5.163301 ACCTACCATATCACATCAGGAACAC 60.163 44.000 0.00 0.00 0.00 3.32
1031 1061 5.188163 TCCATTTCTTCGATACAACCTACCA 59.812 40.000 0.00 0.00 0.00 3.25
1083 1113 4.828925 GAGCTCAGCTCGGGTGCC 62.829 72.222 11.89 0.00 45.85 5.01
1203 1233 1.262640 AATCGTAGCCGTTGGGGACT 61.263 55.000 0.00 0.00 38.47 3.85
1245 1275 0.893727 CAGGGTTTGAAAGGGTCCCG 60.894 60.000 0.99 0.00 42.57 5.14
1380 1410 4.467084 GCGATGGCCGTCTTCCCA 62.467 66.667 22.53 0.00 41.15 4.37
1728 1758 4.676196 GCATTTGACATGGTAGCAGAAAGG 60.676 45.833 0.00 0.56 0.00 3.11
1785 1815 0.602638 CCACGTGACAAGGCTGCTTA 60.603 55.000 19.30 0.00 0.00 3.09
1944 1974 1.765314 CTCCCATCTGGTTGACTAGGG 59.235 57.143 0.00 0.00 36.50 3.53
2113 2144 8.324163 AGAAAGTGTAACCATCTATTGTTGAC 57.676 34.615 0.00 0.00 37.80 3.18
2264 2302 9.778741 AATTGAAATTAAGCGAGGATATGAGTA 57.221 29.630 0.00 0.00 0.00 2.59
2319 2359 6.811253 ATTATAACTGGTTGAAACTTGCGA 57.189 33.333 0.00 0.00 0.00 5.10
2965 3007 8.405971 ACCTAATAAATCTATCCATATGCCCA 57.594 34.615 0.00 0.00 0.00 5.36
3272 3407 4.518211 CCAAAGAGACAACTGCAGAATCTT 59.482 41.667 23.35 17.09 0.00 2.40
3290 3487 5.782047 TCATTGTGCTTAATCAACCCAAAG 58.218 37.500 0.00 0.00 0.00 2.77
3308 3505 7.061441 GCAGTTATCAGTTGTCACATTTCATTG 59.939 37.037 0.00 0.00 0.00 2.82
3373 3570 7.512130 TCTATTGCAATGAGAACCATGACTAT 58.488 34.615 22.27 0.00 35.24 2.12
3525 5094 2.619074 GGTTGGAGCAGGCCATATATCC 60.619 54.545 5.01 5.49 37.86 2.59
3534 5103 1.376553 GTGAGAGGTTGGAGCAGGC 60.377 63.158 0.00 0.00 0.00 4.85
3539 5108 1.930251 TCAGAGGTGAGAGGTTGGAG 58.070 55.000 0.00 0.00 0.00 3.86
3592 5162 1.073763 CCATCTCTTGGGTGGACAACA 59.926 52.381 0.00 0.00 42.33 3.33
3638 5208 9.632807 AAGCTAAGTGAATATCGATATGAGAAC 57.367 33.333 18.42 13.36 0.00 3.01
4035 5629 0.460109 TCCGGATCACATGTTCAGCG 60.460 55.000 0.00 0.00 0.00 5.18
4094 5688 3.442273 GGAGAGGCATCTATAAGAGGTCG 59.558 52.174 0.00 0.00 35.53 4.79
4254 5850 7.113965 GTCAAACAGAAGAACAGTTATGCATTG 59.886 37.037 3.54 0.00 0.00 2.82
4780 6480 2.685224 GCATTTCTCCCTTCTCCCCTTC 60.685 54.545 0.00 0.00 0.00 3.46
4917 6620 0.729116 CACCTGCATAAACCTCAGCG 59.271 55.000 0.00 0.00 0.00 5.18
5143 6848 5.610398 TCTAGACAGAAATGTCACTTGCAA 58.390 37.500 10.72 0.00 41.02 4.08
5573 7305 6.799512 ACAGAAAGAAAATGACAACAGAAGG 58.200 36.000 0.00 0.00 0.00 3.46
5856 7755 9.996554 TTGATCAGACTAAGACACAAAAATAGA 57.003 29.630 0.00 0.00 0.00 1.98
5998 7897 5.403246 AGAACACATTTAGCTCTGTACGAG 58.597 41.667 9.48 9.48 42.88 4.18
6035 7939 5.481105 CCTAAATTTTTGCAGCTGAATGGA 58.519 37.500 20.43 0.00 0.00 3.41
6036 7940 4.632688 CCCTAAATTTTTGCAGCTGAATGG 59.367 41.667 20.43 5.89 0.00 3.16
6037 7941 5.481105 TCCCTAAATTTTTGCAGCTGAATG 58.519 37.500 20.43 0.00 0.00 2.67
6414 8318 6.889198 AGTATGCACCTCAGCTATTTTTCTA 58.111 36.000 0.00 0.00 34.99 2.10
6507 8430 6.038382 TGCATTCTCGTTGTACCTAAAACAAA 59.962 34.615 0.00 0.00 38.50 2.83
6721 8650 2.513317 TGATGGGGTGATTAGGCATGAA 59.487 45.455 0.00 0.00 0.00 2.57
6772 8702 7.737744 CGATATAGAGCTAAAGAAATTGCAACG 59.262 37.037 0.00 0.00 0.00 4.10
6881 8815 0.637195 TCCAGCCTCCTAACTAGCCT 59.363 55.000 0.00 0.00 0.00 4.58
6947 8881 0.809241 GCGAATGGAGAGAGCAGGTG 60.809 60.000 0.00 0.00 0.00 4.00
6990 8924 2.613026 TGTACGTTGGAGGCCATATG 57.387 50.000 5.01 0.00 31.53 1.78
6997 8931 3.679980 CAGTCAAAGATGTACGTTGGAGG 59.320 47.826 0.00 0.00 38.24 4.30
7176 9116 5.071788 CCTTCCCTAAATAGAGTATGTGCCA 59.928 44.000 0.00 0.00 0.00 4.92
7178 9118 6.420913 TCCTTCCCTAAATAGAGTATGTGC 57.579 41.667 0.00 0.00 0.00 4.57
7196 9136 8.910351 ATTATAAGTGATTTACTGCCTCCTTC 57.090 34.615 0.00 0.00 40.26 3.46
7217 9157 7.658261 CATTCAATGCCAGACATTCTGATTAT 58.342 34.615 4.70 0.00 46.28 1.28
7218 9158 6.460537 GCATTCAATGCCAGACATTCTGATTA 60.461 38.462 11.67 0.00 46.28 1.75
7243 9185 4.460382 ACTTGCACATTGATCTAAACAGGG 59.540 41.667 0.00 0.00 0.00 4.45
7251 9193 5.970317 TTGATTCACTTGCACATTGATCT 57.030 34.783 0.00 0.00 0.00 2.75
7330 9273 2.475519 CGGCCGTGTCACAATGAAATAC 60.476 50.000 19.50 0.00 0.00 1.89
7338 9282 1.066787 TCATATTCGGCCGTGTCACAA 60.067 47.619 27.15 11.51 0.00 3.33
7568 9518 2.141535 CTCTACGGAGGCAACATAGC 57.858 55.000 0.00 0.00 41.41 2.97
7592 9542 2.361438 ACCTCTACGTAGGCAACATAGC 59.639 50.000 22.01 0.00 40.62 2.97
7593 9543 4.097437 TCAACCTCTACGTAGGCAACATAG 59.903 45.833 22.01 10.06 40.62 2.23
7595 9545 2.829720 TCAACCTCTACGTAGGCAACAT 59.170 45.455 22.01 2.18 40.62 2.71
7596 9546 2.029649 GTCAACCTCTACGTAGGCAACA 60.030 50.000 22.01 1.74 40.62 3.33
7597 9547 2.230750 AGTCAACCTCTACGTAGGCAAC 59.769 50.000 22.01 11.67 40.62 4.17
7598 9548 2.522185 AGTCAACCTCTACGTAGGCAA 58.478 47.619 22.01 2.50 40.62 4.52
7599 9549 2.211250 AGTCAACCTCTACGTAGGCA 57.789 50.000 22.01 3.26 40.62 4.75
7600 9550 5.062528 ACTATAGTCAACCTCTACGTAGGC 58.937 45.833 22.01 0.00 40.62 3.93
7601 9551 8.845413 ATTACTATAGTCAACCTCTACGTAGG 57.155 38.462 22.01 12.76 42.82 3.18
7603 9553 9.618890 ACAATTACTATAGTCAACCTCTACGTA 57.381 33.333 9.12 0.00 0.00 3.57
7604 9554 8.404000 CACAATTACTATAGTCAACCTCTACGT 58.596 37.037 9.12 0.00 0.00 3.57
7605 9555 8.618677 TCACAATTACTATAGTCAACCTCTACG 58.381 37.037 9.12 0.00 0.00 3.51
7606 9556 9.733219 GTCACAATTACTATAGTCAACCTCTAC 57.267 37.037 9.12 0.00 0.00 2.59
7607 9557 9.696572 AGTCACAATTACTATAGTCAACCTCTA 57.303 33.333 9.12 0.00 0.00 2.43
7608 9558 8.470805 CAGTCACAATTACTATAGTCAACCTCT 58.529 37.037 9.12 0.00 0.00 3.69
7609 9559 8.467598 TCAGTCACAATTACTATAGTCAACCTC 58.532 37.037 9.12 0.00 0.00 3.85
7610 9560 8.251721 GTCAGTCACAATTACTATAGTCAACCT 58.748 37.037 9.12 0.00 0.00 3.50
7611 9561 8.033038 TGTCAGTCACAATTACTATAGTCAACC 58.967 37.037 9.12 0.00 29.30 3.77
7612 9562 8.981724 TGTCAGTCACAATTACTATAGTCAAC 57.018 34.615 9.12 0.00 29.30 3.18
7613 9563 9.803315 GATGTCAGTCACAATTACTATAGTCAA 57.197 33.333 9.12 3.20 38.97 3.18
7614 9564 8.414003 GGATGTCAGTCACAATTACTATAGTCA 58.586 37.037 9.12 0.00 38.97 3.41
7615 9565 8.414003 TGGATGTCAGTCACAATTACTATAGTC 58.586 37.037 9.12 0.00 38.97 2.59
7672 9622 6.314917 ACTTGGGAACAGGAAAATGAAGTAT 58.685 36.000 0.00 0.00 44.54 2.12
7673 9623 5.701224 ACTTGGGAACAGGAAAATGAAGTA 58.299 37.500 0.00 0.00 44.54 2.24
7701 9651 4.151335 CACATCTACTTCTGTTGACTGTGC 59.849 45.833 0.00 0.00 34.61 4.57
7721 9671 6.017026 TGGTTCGATAAGTAAAACAATGCACA 60.017 34.615 0.00 0.00 0.00 4.57
7738 9688 0.391597 ACACGGTCAGTTGGTTCGAT 59.608 50.000 0.00 0.00 0.00 3.59
7760 9711 9.553064 CTTTTAGCTGGTATAAACAGATCAGAT 57.447 33.333 9.29 0.00 38.20 2.90
7761 9712 7.495934 GCTTTTAGCTGGTATAAACAGATCAGA 59.504 37.037 9.29 0.00 38.45 3.27
7762 9713 7.634522 GCTTTTAGCTGGTATAAACAGATCAG 58.365 38.462 9.29 0.00 38.45 2.90
7763 9714 7.553881 GCTTTTAGCTGGTATAAACAGATCA 57.446 36.000 9.29 0.00 38.45 2.92
7893 9844 1.673665 CAACTGCTGGAGCTCCACC 60.674 63.158 32.00 25.37 42.01 4.61
7919 9870 3.313791 TGCTCTGCTAACATATACCCCA 58.686 45.455 0.00 0.00 0.00 4.96
7958 9909 3.244146 CCCATGCCATGTCAAAGACAAAA 60.244 43.478 3.63 0.00 45.96 2.44
7959 9910 2.299582 CCCATGCCATGTCAAAGACAAA 59.700 45.455 3.63 0.00 45.96 2.83
8015 9974 9.376075 GGGTTTACTAAAGTAGAAGGTTACATC 57.624 37.037 0.00 0.00 0.00 3.06
8016 9975 9.109246 AGGGTTTACTAAAGTAGAAGGTTACAT 57.891 33.333 0.00 0.00 0.00 2.29
8017 9976 8.496534 AGGGTTTACTAAAGTAGAAGGTTACA 57.503 34.615 0.00 0.00 0.00 2.41
8059 10018 7.959689 GCAGATTGCTTCTAATCTTCTGATA 57.040 36.000 0.00 0.00 43.08 2.15
8125 10085 9.765795 GAGACAGGTATAATACTATTTTGTGCT 57.234 33.333 0.00 0.00 0.00 4.40
8177 10137 4.618227 GCATCCAAAACCTGATAACCACAC 60.618 45.833 0.00 0.00 0.00 3.82
8241 10201 7.406031 TCAGTAACCAACTAGACTCCATAAG 57.594 40.000 0.00 0.00 35.76 1.73
8275 10235 1.640149 TCCCCAAAGCATCTTCATGGA 59.360 47.619 0.00 0.00 32.82 3.41
8325 10328 4.394920 CCTGTTAGAAACATAACGCCATGT 59.605 41.667 0.00 0.00 41.26 3.21
8384 10387 3.559655 CACGGAAAAATATGGCGATCTCA 59.440 43.478 0.00 0.00 0.00 3.27
8417 10420 5.336451 GCCATAACTTCCCGAAAACTTTGAT 60.336 40.000 0.00 0.00 0.00 2.57
8431 10434 9.807649 ATAATTCAACAATTCTGCCATAACTTC 57.192 29.630 0.00 0.00 33.95 3.01
8518 10748 5.957774 AGGCATTCTTAAATTAAAGGGCTCA 59.042 36.000 0.00 0.00 0.00 4.26
8519 10749 6.471233 AGGCATTCTTAAATTAAAGGGCTC 57.529 37.500 0.00 0.00 0.00 4.70
8544 10774 3.991773 CAGCTTGGAATGGTTGAAACATG 59.008 43.478 0.00 0.00 0.00 3.21
8554 10784 0.529378 GGCAGTTCAGCTTGGAATGG 59.471 55.000 0.00 0.00 34.17 3.16
8603 10837 6.643770 AGAACATTTGCTTGCTATTGTTTCTG 59.356 34.615 14.52 0.00 0.00 3.02
8667 10901 4.938226 CCTGTTCTTAATTCTGGAGGTGAC 59.062 45.833 0.00 0.00 0.00 3.67
8670 10904 3.589288 AGCCTGTTCTTAATTCTGGAGGT 59.411 43.478 0.00 0.00 0.00 3.85
8760 11008 3.185246 AGTGTCTCTGGTTGAACTGTG 57.815 47.619 0.00 0.00 0.00 3.66
8821 11069 4.735132 TGCACGGCGTACTCTGGC 62.735 66.667 14.22 11.91 0.00 4.85
8822 11070 2.507102 CTGCACGGCGTACTCTGG 60.507 66.667 14.22 0.00 0.00 3.86
8823 11071 3.181967 GCTGCACGGCGTACTCTG 61.182 66.667 14.22 10.15 0.00 3.35


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

AutoCloner maintained by Alex Coulton.