Multiple sequence alignment - TraesCS4A01G467900

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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 TraesCS4A01G467900 chr4A 100.000 3182 0 0 1 3182 729818252 729821433 0.000000e+00 5877.0
1 TraesCS4A01G467900 chr4A 84.853 2588 294 55 163 2692 729156460 729159007 0.000000e+00 2518.0
2 TraesCS4A01G467900 chr4A 90.987 1631 132 6 1063 2692 728443472 728441856 0.000000e+00 2183.0
3 TraesCS4A01G467900 chr4A 89.087 1008 101 3 1687 2692 729678543 729679543 0.000000e+00 1243.0
4 TraesCS4A01G467900 chr4A 86.915 1154 64 18 576 1689 729677355 729678461 0.000000e+00 1214.0
5 TraesCS4A01G467900 chr4A 79.077 1539 234 43 1063 2562 727080699 727079210 0.000000e+00 977.0
6 TraesCS4A01G467900 chr4A 78.913 1527 229 50 806 2281 730004642 730003158 0.000000e+00 950.0
7 TraesCS4A01G467900 chr4A 79.577 1229 205 28 1063 2271 729426043 729424841 0.000000e+00 837.0
8 TraesCS4A01G467900 chr4A 79.518 1245 195 38 1063 2272 730322853 730324072 0.000000e+00 832.0
9 TraesCS4A01G467900 chr4A 75.745 1208 219 39 1394 2569 727711493 727712658 1.000000e-149 540.0
10 TraesCS4A01G467900 chr4A 79.167 816 136 24 1891 2692 728553360 728552565 4.670000e-148 534.0
11 TraesCS4A01G467900 chr4A 90.339 383 33 3 2804 3182 729159390 729159772 1.700000e-137 499.0
12 TraesCS4A01G467900 chr4A 79.848 660 111 14 24 674 729924582 729925228 2.240000e-126 462.0
13 TraesCS4A01G467900 chr4A 80.556 468 47 25 800 1232 728662470 728662012 1.420000e-83 320.0
14 TraesCS4A01G467900 chr4A 89.516 248 23 1 800 1047 730061497 730061253 8.570000e-81 311.0
15 TraesCS4A01G467900 chr4A 79.108 426 80 9 24 445 729659544 729659964 5.190000e-73 285.0
16 TraesCS4A01G467900 chr4A 80.978 184 7 6 603 761 728698568 728698388 1.550000e-23 121.0
17 TraesCS4A01G467900 chr4A 87.255 102 12 1 546 646 730005022 730004921 7.210000e-22 115.0
18 TraesCS4A01G467900 chr7D 88.543 2182 160 32 575 2692 8818414 8820569 0.000000e+00 2562.0
19 TraesCS4A01G467900 chr7D 77.734 2021 293 77 479 2425 10466144 10464207 0.000000e+00 1094.0
20 TraesCS4A01G467900 chr7D 79.412 1530 245 36 1063 2564 10974161 10972674 0.000000e+00 1016.0
21 TraesCS4A01G467900 chr7D 78.865 1533 238 43 1063 2563 11066920 11068398 0.000000e+00 957.0
22 TraesCS4A01G467900 chr7D 77.047 806 139 20 1891 2692 9361062 9361825 3.790000e-114 422.0
23 TraesCS4A01G467900 chr7D 79.673 551 70 25 858 1385 8870015 8870546 3.020000e-95 359.0
24 TraesCS4A01G467900 chr7D 86.348 293 34 5 2804 3093 8871766 8872055 6.630000e-82 315.0
25 TraesCS4A01G467900 chr7D 87.671 73 6 2 603 675 9223140 9223209 7.320000e-12 82.4
26 TraesCS4A01G467900 chr7A 90.069 1601 107 26 712 2290 9381743 9383313 0.000000e+00 2028.0
27 TraesCS4A01G467900 chr7A 78.479 1538 256 42 1063 2570 10169881 10168389 0.000000e+00 937.0
28 TraesCS4A01G467900 chr7A 78.735 1533 224 50 1063 2564 10269764 10271225 0.000000e+00 931.0
29 TraesCS4A01G467900 chr7A 77.033 1611 286 57 1049 2609 10091956 10090380 0.000000e+00 848.0
30 TraesCS4A01G467900 chr7A 81.108 704 116 14 1869 2563 10168140 10167445 6.000000e-152 547.0
31 TraesCS4A01G467900 chr7A 90.566 53 5 0 997 1049 114414450 114414398 1.580000e-08 71.3
32 TraesCS4A01G467900 chr4B 78.597 1967 281 74 803 2692 654201732 654203635 0.000000e+00 1171.0
33 TraesCS4A01G467900 chr4D 79.736 1668 247 50 1054 2692 507352153 507350548 0.000000e+00 1123.0
34 TraesCS4A01G467900 chr5A 79.615 1609 222 60 801 2342 691820801 691822370 0.000000e+00 1057.0
35 TraesCS4A01G467900 chr5A 100.000 114 0 0 2692 2805 104599189 104599302 8.940000e-51 211.0
36 TraesCS4A01G467900 chr5A 96.154 130 4 1 2675 2804 341156226 341156098 8.940000e-51 211.0
37 TraesCS4A01G467900 chr5A 99.145 117 1 0 2688 2804 475376658 475376774 8.940000e-51 211.0
38 TraesCS4A01G467900 chr3B 100.000 116 0 0 2689 2804 276475692 276475577 6.910000e-52 215.0
39 TraesCS4A01G467900 chr1A 100.000 115 0 0 2690 2804 47208061 47208175 2.490000e-51 213.0
40 TraesCS4A01G467900 chr1A 80.380 158 31 0 284 441 41834887 41834730 1.550000e-23 121.0
41 TraesCS4A01G467900 chr7B 99.145 117 1 0 2692 2808 255064694 255064578 8.940000e-51 211.0
42 TraesCS4A01G467900 chr6A 100.000 114 0 0 2691 2804 545146938 545147051 8.940000e-51 211.0
43 TraesCS4A01G467900 chr2A 100.000 114 0 0 2691 2804 50920202 50920089 8.940000e-51 211.0
44 TraesCS4A01G467900 chr2A 100.000 114 0 0 2691 2804 462692794 462692907 8.940000e-51 211.0
45 TraesCS4A01G467900 chr1D 78.537 205 42 2 238 441 41771834 41771631 1.990000e-27 134.0
46 TraesCS4A01G467900 chr1B 95.312 64 0 1 726 786 65683969 65684032 7.260000e-17 99.0


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 TraesCS4A01G467900 chr4A 729818252 729821433 3181 False 5877.0 5877 100.0000 1 3182 1 chr4A.!!$F3 3181
1 TraesCS4A01G467900 chr4A 728441856 728443472 1616 True 2183.0 2183 90.9870 1063 2692 1 chr4A.!!$R2 1629
2 TraesCS4A01G467900 chr4A 729156460 729159772 3312 False 1508.5 2518 87.5960 163 3182 2 chr4A.!!$F6 3019
3 TraesCS4A01G467900 chr4A 729677355 729679543 2188 False 1228.5 1243 88.0010 576 2692 2 chr4A.!!$F7 2116
4 TraesCS4A01G467900 chr4A 727079210 727080699 1489 True 977.0 977 79.0770 1063 2562 1 chr4A.!!$R1 1499
5 TraesCS4A01G467900 chr4A 729424841 729426043 1202 True 837.0 837 79.5770 1063 2271 1 chr4A.!!$R6 1208
6 TraesCS4A01G467900 chr4A 730322853 730324072 1219 False 832.0 832 79.5180 1063 2272 1 chr4A.!!$F5 1209
7 TraesCS4A01G467900 chr4A 727711493 727712658 1165 False 540.0 540 75.7450 1394 2569 1 chr4A.!!$F1 1175
8 TraesCS4A01G467900 chr4A 728552565 728553360 795 True 534.0 534 79.1670 1891 2692 1 chr4A.!!$R3 801
9 TraesCS4A01G467900 chr4A 730003158 730005022 1864 True 532.5 950 83.0840 546 2281 2 chr4A.!!$R8 1735
10 TraesCS4A01G467900 chr4A 729924582 729925228 646 False 462.0 462 79.8480 24 674 1 chr4A.!!$F4 650
11 TraesCS4A01G467900 chr7D 8818414 8820569 2155 False 2562.0 2562 88.5430 575 2692 1 chr7D.!!$F1 2117
12 TraesCS4A01G467900 chr7D 10464207 10466144 1937 True 1094.0 1094 77.7340 479 2425 1 chr7D.!!$R1 1946
13 TraesCS4A01G467900 chr7D 10972674 10974161 1487 True 1016.0 1016 79.4120 1063 2564 1 chr7D.!!$R2 1501
14 TraesCS4A01G467900 chr7D 11066920 11068398 1478 False 957.0 957 78.8650 1063 2563 1 chr7D.!!$F4 1500
15 TraesCS4A01G467900 chr7D 9361062 9361825 763 False 422.0 422 77.0470 1891 2692 1 chr7D.!!$F3 801
16 TraesCS4A01G467900 chr7D 8870015 8872055 2040 False 337.0 359 83.0105 858 3093 2 chr7D.!!$F5 2235
17 TraesCS4A01G467900 chr7A 9381743 9383313 1570 False 2028.0 2028 90.0690 712 2290 1 chr7A.!!$F1 1578
18 TraesCS4A01G467900 chr7A 10269764 10271225 1461 False 931.0 931 78.7350 1063 2564 1 chr7A.!!$F2 1501
19 TraesCS4A01G467900 chr7A 10090380 10091956 1576 True 848.0 848 77.0330 1049 2609 1 chr7A.!!$R1 1560
20 TraesCS4A01G467900 chr7A 10167445 10169881 2436 True 742.0 937 79.7935 1063 2570 2 chr7A.!!$R3 1507
21 TraesCS4A01G467900 chr4B 654201732 654203635 1903 False 1171.0 1171 78.5970 803 2692 1 chr4B.!!$F1 1889
22 TraesCS4A01G467900 chr4D 507350548 507352153 1605 True 1123.0 1123 79.7360 1054 2692 1 chr4D.!!$R1 1638
23 TraesCS4A01G467900 chr5A 691820801 691822370 1569 False 1057.0 1057 79.6150 801 2342 1 chr5A.!!$F3 1541

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
293 294 0.040246 GCCCTCGTCGAGCTATACAC 60.04 60.0 17.02 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2824 0.749649 ACCAGCAAATTCAACGGCAA 59.25 45.0 0.0 0.0 0.0 4.52 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
23 24 6.885735 AGAAAATCGAAAAACCAGTTTGTG 57.114 33.333 0.00 0.00 32.36 3.33
39 40 4.082463 AGTTTGTGGAAAGTTCAAAAGCGA 60.082 37.500 0.00 0.00 33.80 4.93
42 43 3.380004 TGTGGAAAGTTCAAAAGCGATGT 59.620 39.130 0.00 0.00 0.00 3.06
69 70 3.990959 AACCTTTAGAGAAGGCTCAGG 57.009 47.619 4.77 0.00 43.81 3.86
70 71 2.909217 ACCTTTAGAGAAGGCTCAGGT 58.091 47.619 4.77 0.00 43.81 4.00
72 73 3.262151 ACCTTTAGAGAAGGCTCAGGTTC 59.738 47.826 4.77 0.00 40.34 3.62
75 76 0.251832 AGAGAAGGCTCAGGTTCGGA 60.252 55.000 0.00 0.00 43.81 4.55
79 80 2.683933 GGCTCAGGTTCGGAGGGA 60.684 66.667 0.00 0.00 32.96 4.20
82 83 1.045911 GCTCAGGTTCGGAGGGAGAT 61.046 60.000 0.00 0.00 32.96 2.75
84 85 0.041238 TCAGGTTCGGAGGGAGATGT 59.959 55.000 0.00 0.00 0.00 3.06
85 86 0.461961 CAGGTTCGGAGGGAGATGTC 59.538 60.000 0.00 0.00 0.00 3.06
87 88 0.747852 GGTTCGGAGGGAGATGTCTC 59.252 60.000 1.33 1.33 42.14 3.36
88 89 1.475403 GTTCGGAGGGAGATGTCTCA 58.525 55.000 11.78 0.00 44.60 3.27
92 93 1.703411 GGAGGGAGATGTCTCAGAGG 58.297 60.000 11.78 0.00 44.60 3.69
109 110 2.430367 GAGGTGGTCTTGGCGGTT 59.570 61.111 0.00 0.00 0.00 4.44
112 113 2.258726 GGTGGTCTTGGCGGTTGAC 61.259 63.158 0.00 0.00 0.00 3.18
116 117 1.527380 GTCTTGGCGGTTGACCCAA 60.527 57.895 0.00 0.00 38.71 4.12
125 126 2.283532 TTGACCCAATTGGCCCCG 60.284 61.111 19.75 7.93 37.83 5.73
131 132 3.389662 CAATTGGCCCCGGGTTGG 61.390 66.667 21.85 5.09 37.55 3.77
138 139 3.015145 CCCCGGGTTGGAGATGGT 61.015 66.667 21.85 0.00 42.00 3.55
144 145 1.745489 GGTTGGAGATGGTGGACGC 60.745 63.158 0.00 0.00 0.00 5.19
145 146 1.745489 GTTGGAGATGGTGGACGCC 60.745 63.158 0.00 0.00 0.00 5.68
146 147 2.966732 TTGGAGATGGTGGACGCCC 61.967 63.158 0.00 0.00 0.00 6.13
147 148 3.083997 GGAGATGGTGGACGCCCT 61.084 66.667 0.00 0.00 0.00 5.19
153 154 3.998672 GGTGGACGCCCTTGTCGA 61.999 66.667 0.00 0.00 39.83 4.20
154 155 2.737376 GTGGACGCCCTTGTCGAC 60.737 66.667 9.11 9.11 39.76 4.20
161 162 3.691342 CCCTTGTCGACGGGCTGA 61.691 66.667 14.64 0.00 32.83 4.26
176 177 1.271840 GCTGACATCACCCCCACCTA 61.272 60.000 0.00 0.00 0.00 3.08
186 187 0.111253 CCCCCACCTATTGATGGAGC 59.889 60.000 0.00 0.00 38.34 4.70
192 193 1.566563 CTATTGATGGAGCACGCGC 59.433 57.895 5.73 0.00 38.99 6.86
212 213 2.202676 GAGCACTTCCGCCTCTCG 60.203 66.667 0.00 0.00 38.08 4.04
229 230 1.191489 TCGATGGTGGAAGGAGCACA 61.191 55.000 0.00 0.00 0.00 4.57
233 234 1.191489 TGGTGGAAGGAGCACATCGA 61.191 55.000 0.00 0.00 0.00 3.59
246 247 2.765807 ATCGAGGGGGAGGTGCAG 60.766 66.667 0.00 0.00 0.00 4.41
249 250 3.334054 GAGGGGGAGGTGCAGCTT 61.334 66.667 21.18 2.79 0.00 3.74
264 265 2.031012 CTTGAGGCGGTGCTGTCA 59.969 61.111 0.00 0.00 0.00 3.58
265 266 2.031012 TTGAGGCGGTGCTGTCAG 59.969 61.111 0.00 0.00 0.00 3.51
271 272 2.566529 CGGTGCTGTCAGACGCTA 59.433 61.111 3.32 3.47 0.00 4.26
272 273 1.139734 CGGTGCTGTCAGACGCTAT 59.860 57.895 3.32 0.00 0.00 2.97
273 274 0.380733 CGGTGCTGTCAGACGCTATA 59.619 55.000 3.32 0.00 0.00 1.31
288 289 1.944892 GCTATAGCCCTCGTCGAGCTA 60.945 57.143 17.02 16.39 42.88 3.32
292 293 0.179026 AGCCCTCGTCGAGCTATACA 60.179 55.000 17.02 0.00 34.38 2.29
293 294 0.040246 GCCCTCGTCGAGCTATACAC 60.040 60.000 17.02 0.00 0.00 2.90
294 295 1.595466 CCCTCGTCGAGCTATACACT 58.405 55.000 17.02 0.00 0.00 3.55
295 296 2.763933 CCCTCGTCGAGCTATACACTA 58.236 52.381 17.02 0.00 0.00 2.74
298 299 3.362791 CCTCGTCGAGCTATACACTAACG 60.363 52.174 17.02 0.00 0.00 3.18
311 312 0.108329 ACTAACGCGTCCCTCATTGG 60.108 55.000 14.44 0.00 0.00 3.16
316 317 2.464459 GCGTCCCTCATTGGCGAAG 61.464 63.158 0.00 0.00 0.00 3.79
372 373 4.364409 GTGTTGACGAACCGCCGC 62.364 66.667 0.00 0.00 0.00 6.53
398 399 2.497273 TCTTCATTCATGACCGAGAGCA 59.503 45.455 0.00 0.00 36.36 4.26
407 408 0.454196 GACCGAGAGCAGGAGAAGAC 59.546 60.000 0.00 0.00 0.00 3.01
423 430 4.670765 AGAAGACCTTTGCAAATGAGGAT 58.329 39.130 20.16 7.32 34.61 3.24
426 433 2.167075 GACCTTTGCAAATGAGGATGGG 59.833 50.000 20.16 13.92 34.61 4.00
445 452 2.203167 AGATGCCTCATGCTGCCG 60.203 61.111 0.00 0.00 42.00 5.69
446 453 2.515523 GATGCCTCATGCTGCCGT 60.516 61.111 0.00 0.00 42.00 5.68
476 483 1.418373 GATGGTTGTTTCGGCAAAGC 58.582 50.000 0.00 0.00 0.00 3.51
486 494 2.361104 GGCAAAGCGGTGATCCCA 60.361 61.111 0.00 0.00 0.00 4.37
507 515 0.473694 TCCCCTCAGACAAGGAGCAA 60.474 55.000 0.00 0.00 38.87 3.91
560 568 5.543507 ATTCCTGGATGTAGTTCTAGCTG 57.456 43.478 0.00 0.00 0.00 4.24
612 624 3.162068 CGAGTTGTAGTTGTAGCTCGTC 58.838 50.000 0.00 0.00 40.31 4.20
700 749 2.982488 AGACATATAGGGGGCAAGAAGG 59.018 50.000 0.00 0.00 0.00 3.46
701 750 2.040412 GACATATAGGGGGCAAGAAGGG 59.960 54.545 0.00 0.00 0.00 3.95
796 895 0.457851 GTCCTCCTGTGATCCTGTCG 59.542 60.000 0.00 0.00 0.00 4.35
798 897 1.142748 CTCCTGTGATCCTGTCGCC 59.857 63.158 0.00 0.00 36.49 5.54
982 1276 2.367512 CCCTGCCTAGGCCCTTCT 60.368 66.667 30.81 0.00 43.16 2.85
983 1277 2.750657 CCCTGCCTAGGCCCTTCTG 61.751 68.421 30.81 13.02 43.16 3.02
984 1278 2.191641 CTGCCTAGGCCCTTCTGC 59.808 66.667 30.81 3.73 41.09 4.26
985 1279 2.285668 TGCCTAGGCCCTTCTGCT 60.286 61.111 30.81 0.00 41.09 4.24
986 1280 1.919600 CTGCCTAGGCCCTTCTGCTT 61.920 60.000 30.81 0.00 41.09 3.91
987 1281 1.153066 GCCTAGGCCCTTCTGCTTC 60.153 63.158 24.19 0.00 34.56 3.86
988 1282 1.529309 CCTAGGCCCTTCTGCTTCC 59.471 63.158 0.00 0.00 0.00 3.46
989 1283 1.274703 CCTAGGCCCTTCTGCTTCCA 61.275 60.000 0.00 0.00 0.00 3.53
990 1284 0.107459 CTAGGCCCTTCTGCTTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
991 1285 0.547712 TAGGCCCTTCTGCTTCCACT 60.548 55.000 0.00 0.00 0.00 4.00
992 1286 1.377856 GGCCCTTCTGCTTCCACTC 60.378 63.158 0.00 0.00 0.00 3.51
993 1287 1.377856 GCCCTTCTGCTTCCACTCC 60.378 63.158 0.00 0.00 0.00 3.85
994 1288 1.301293 CCCTTCTGCTTCCACTCCC 59.699 63.158 0.00 0.00 0.00 4.30
995 1289 1.078848 CCTTCTGCTTCCACTCCCG 60.079 63.158 0.00 0.00 0.00 5.14
996 1290 1.743252 CTTCTGCTTCCACTCCCGC 60.743 63.158 0.00 0.00 0.00 6.13
997 1291 2.177594 CTTCTGCTTCCACTCCCGCT 62.178 60.000 0.00 0.00 0.00 5.52
998 1292 2.125350 CTGCTTCCACTCCCGCTC 60.125 66.667 0.00 0.00 0.00 5.03
1473 1874 3.124921 CCGCCTGTGCCCGTAAAG 61.125 66.667 0.00 0.00 0.00 1.85
2086 2621 3.635331 CAACATCAGAAAGTTGGCTGTG 58.365 45.455 10.02 6.51 40.97 3.66
2221 2766 0.843309 TGTGCTTCCTCCCAAGAACA 59.157 50.000 0.00 0.00 39.31 3.18
2238 2783 3.070302 AGAACAGTCTCTTCTTTCGGCTT 59.930 43.478 0.00 0.00 0.00 4.35
2272 2820 2.599082 GTGTACTTCGGAATCTGCTTCG 59.401 50.000 0.00 0.00 34.45 3.79
2273 2821 2.194271 GTACTTCGGAATCTGCTTCGG 58.806 52.381 0.00 0.00 34.45 4.30
2276 2824 0.895530 TTCGGAATCTGCTTCGGTCT 59.104 50.000 0.00 0.00 36.05 3.85
2375 2933 8.141909 CAGATGAAGCATAATGTCATTTCCAAT 58.858 33.333 2.79 0.00 32.18 3.16
2405 2979 2.435372 ACTCTTGGTCTGTTTTGCCA 57.565 45.000 0.00 0.00 0.00 4.92
2428 3003 2.544486 GCACTGGCCTTTTTCTTGACAG 60.544 50.000 3.32 0.00 0.00 3.51
2439 3014 7.468631 GCCTTTTTCTTGACAGATGTTAGTTCA 60.469 37.037 0.00 0.00 0.00 3.18
2454 3032 9.503427 GATGTTAGTTCAATGTGGCTAAATTAC 57.497 33.333 0.00 0.00 0.00 1.89
2526 4062 6.769822 CCTAAATCCTACTGCAGATTGTGAAT 59.230 38.462 23.35 0.00 33.08 2.57
2564 4106 3.926616 AGGTTCAATCAGACTGGTTACG 58.073 45.455 0.00 0.00 0.00 3.18
2571 4121 0.250124 CAGACTGGTTACGGGTGCAA 60.250 55.000 0.00 0.00 0.00 4.08
2572 4122 0.250166 AGACTGGTTACGGGTGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
2589 4139 2.808244 CAACCGTGCAATGTCTTGTTT 58.192 42.857 0.00 0.00 34.69 2.83
2606 4156 8.783093 TGTCTTGTTTACCTTATTCATTCAGTG 58.217 33.333 0.00 0.00 0.00 3.66
2628 4178 5.133707 GTTTTGGTAAAACGTTGCCTTTC 57.866 39.130 0.00 0.00 41.04 2.62
2633 4183 2.888834 AAAACGTTGCCTTTCAGCAT 57.111 40.000 0.00 0.00 43.64 3.79
2638 4188 1.689959 GTTGCCTTTCAGCATGTTCG 58.310 50.000 0.00 0.00 43.64 3.95
2658 4208 4.987832 TCGTTTTATGTGTGTTTGCTGTT 58.012 34.783 0.00 0.00 0.00 3.16
2659 4209 5.403246 TCGTTTTATGTGTGTTTGCTGTTT 58.597 33.333 0.00 0.00 0.00 2.83
2672 4222 6.414987 GTGTTTGCTGTTTCTAGTGAATTCAC 59.585 38.462 27.69 27.69 46.77 3.18
2692 4242 8.715191 ATTCACTAGAGCTTTTGATCTGTTAG 57.285 34.615 0.00 0.00 45.75 2.34
2693 4243 6.634805 TCACTAGAGCTTTTGATCTGTTAGG 58.365 40.000 0.00 0.00 45.75 2.69
2694 4244 5.814705 CACTAGAGCTTTTGATCTGTTAGGG 59.185 44.000 0.00 0.00 45.75 3.53
2695 4245 3.615155 AGAGCTTTTGATCTGTTAGGGC 58.385 45.455 0.00 0.00 44.39 5.19
2696 4246 3.009473 AGAGCTTTTGATCTGTTAGGGCA 59.991 43.478 0.00 0.00 44.39 5.36
2698 4248 3.507622 AGCTTTTGATCTGTTAGGGCAAC 59.492 43.478 0.00 0.00 37.67 4.17
2710 4260 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2711 4261 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2712 4262 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2714 4264 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2720 4270 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2721 4271 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2722 4272 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2726 4276 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2739 4289 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2740 4290 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2742 4292 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2743 4293 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2744 4294 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2745 4295 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2746 4296 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2747 4297 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2750 4300 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2751 4301 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2752 4302 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2753 4303 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2754 4304 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2755 4305 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2756 4306 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2766 4316 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2767 4317 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2768 4318 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2769 4319 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2770 4320 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2771 4321 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2773 4323 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2774 4324 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2775 4325 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2776 4326 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2777 4327 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2780 4330 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2781 4331 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2782 4332 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2783 4333 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2784 4334 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2785 4335 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2787 4337 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2789 4339 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2791 4341 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2806 4356 3.840666 TCTGTAAGAGGCTGTTTCCATCT 59.159 43.478 0.90 0.00 38.67 2.90
2807 4357 3.937706 CTGTAAGAGGCTGTTTCCATCTG 59.062 47.826 0.90 0.00 34.07 2.90
2808 4358 3.327757 TGTAAGAGGCTGTTTCCATCTGT 59.672 43.478 0.90 0.00 0.00 3.41
2809 4359 3.515602 AAGAGGCTGTTTCCATCTGTT 57.484 42.857 0.00 0.00 0.00 3.16
2811 4361 4.213564 AGAGGCTGTTTCCATCTGTTAG 57.786 45.455 0.00 0.00 0.00 2.34
2833 4654 5.950883 AGTCACAGAGAAATTGCATCAATG 58.049 37.500 0.00 0.00 34.04 2.82
2881 4702 6.220726 TGTACTCTTGTATGAATAGCAGCA 57.779 37.500 0.00 0.00 0.00 4.41
3043 4866 2.340337 GCTGTGTTGATTGATTTGGCC 58.660 47.619 0.00 0.00 0.00 5.36
3045 4868 1.336702 TGTGTTGATTGATTTGGCCGC 60.337 47.619 0.00 0.00 0.00 6.53
3066 4890 1.266989 GTTGCTACCCTGTTTGAGTGC 59.733 52.381 0.00 0.00 0.00 4.40
3100 4924 6.539324 CGTTGTTTCCGTATATTTGTGATGT 58.461 36.000 0.00 0.00 0.00 3.06
3103 4927 7.067532 TGTTTCCGTATATTTGTGATGTGAC 57.932 36.000 0.00 0.00 0.00 3.67
3117 4941 4.505922 GTGATGTGACGATTCCTGATTCTC 59.494 45.833 0.00 0.00 0.00 2.87
3123 4947 3.722147 ACGATTCCTGATTCTCGAATGG 58.278 45.455 0.00 5.58 35.24 3.16
3124 4948 3.133003 ACGATTCCTGATTCTCGAATGGT 59.867 43.478 0.00 7.57 35.24 3.55
3128 4952 6.292381 CGATTCCTGATTCTCGAATGGTTTAC 60.292 42.308 0.00 0.00 33.07 2.01
3139 4965 9.985730 TTCTCGAATGGTTTACTTTTAAGACTA 57.014 29.630 0.00 0.00 0.00 2.59
3175 5001 8.970691 ATGGAAAATATGAACTGAAAAAGTCG 57.029 30.769 0.00 0.00 38.56 4.18
3177 5003 8.289618 TGGAAAATATGAACTGAAAAAGTCGAG 58.710 33.333 0.00 0.00 38.56 4.04
3178 5004 8.290325 GGAAAATATGAACTGAAAAAGTCGAGT 58.710 33.333 0.00 0.00 38.56 4.18
3180 5006 9.450807 AAAATATGAACTGAAAAAGTCGAGTTG 57.549 29.630 6.19 0.00 38.56 3.16
3181 5007 7.962964 ATATGAACTGAAAAAGTCGAGTTGA 57.037 32.000 6.19 0.00 38.56 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.725362 TCCACAAACTGGTTTTTCGATTTT 58.275 33.333 0.00 0.00 41.52 1.82
5 6 4.993029 TTCCACAAACTGGTTTTTCGAT 57.007 36.364 0.00 0.00 41.52 3.59
6 7 4.218852 ACTTTCCACAAACTGGTTTTTCGA 59.781 37.500 0.00 0.00 41.52 3.71
7 8 4.490743 ACTTTCCACAAACTGGTTTTTCG 58.509 39.130 0.00 0.00 41.52 3.46
8 9 5.929415 TGAACTTTCCACAAACTGGTTTTTC 59.071 36.000 0.00 0.00 41.52 2.29
9 10 5.859495 TGAACTTTCCACAAACTGGTTTTT 58.141 33.333 0.00 0.00 41.52 1.94
10 11 5.476091 TGAACTTTCCACAAACTGGTTTT 57.524 34.783 0.00 0.00 41.52 2.43
11 12 5.476091 TTGAACTTTCCACAAACTGGTTT 57.524 34.783 0.00 0.00 41.52 3.27
12 13 5.476091 TTTGAACTTTCCACAAACTGGTT 57.524 34.783 0.00 0.00 41.52 3.67
13 14 5.476091 TTTTGAACTTTCCACAAACTGGT 57.524 34.783 0.00 0.00 41.52 4.00
14 15 4.329801 GCTTTTGAACTTTCCACAAACTGG 59.670 41.667 0.00 0.00 42.29 4.00
15 16 4.031652 CGCTTTTGAACTTTCCACAAACTG 59.968 41.667 0.00 0.00 34.09 3.16
16 17 4.082463 TCGCTTTTGAACTTTCCACAAACT 60.082 37.500 0.00 0.00 34.09 2.66
17 18 4.170256 TCGCTTTTGAACTTTCCACAAAC 58.830 39.130 0.00 0.00 34.09 2.93
18 19 4.442375 TCGCTTTTGAACTTTCCACAAA 57.558 36.364 0.00 0.00 0.00 2.83
19 20 4.142271 ACATCGCTTTTGAACTTTCCACAA 60.142 37.500 0.00 0.00 0.00 3.33
20 21 3.380004 ACATCGCTTTTGAACTTTCCACA 59.620 39.130 0.00 0.00 0.00 4.17
21 22 3.730715 CACATCGCTTTTGAACTTTCCAC 59.269 43.478 0.00 0.00 0.00 4.02
22 23 3.243367 CCACATCGCTTTTGAACTTTCCA 60.243 43.478 0.00 0.00 0.00 3.53
23 24 3.004315 TCCACATCGCTTTTGAACTTTCC 59.996 43.478 0.00 0.00 0.00 3.13
24 25 4.223320 TCCACATCGCTTTTGAACTTTC 57.777 40.909 0.00 0.00 0.00 2.62
25 26 4.647424 TTCCACATCGCTTTTGAACTTT 57.353 36.364 0.00 0.00 0.00 2.66
26 27 4.647424 TTTCCACATCGCTTTTGAACTT 57.353 36.364 0.00 0.00 0.00 2.66
27 28 4.647424 TTTTCCACATCGCTTTTGAACT 57.353 36.364 0.00 0.00 0.00 3.01
50 51 2.909217 ACCTGAGCCTTCTCTAAAGGT 58.091 47.619 5.76 0.00 38.02 3.50
54 55 1.825474 CCGAACCTGAGCCTTCTCTAA 59.175 52.381 0.00 0.00 40.03 2.10
69 70 1.407258 CTGAGACATCTCCCTCCGAAC 59.593 57.143 6.44 0.00 42.20 3.95
70 71 1.285078 TCTGAGACATCTCCCTCCGAA 59.715 52.381 6.44 0.00 42.20 4.30
72 73 1.317613 CTCTGAGACATCTCCCTCCG 58.682 60.000 6.44 0.00 42.20 4.63
75 76 1.217689 CCTCCTCTGAGACATCTCCCT 59.782 57.143 6.17 0.00 41.42 4.20
79 80 1.360852 ACCACCTCCTCTGAGACATCT 59.639 52.381 6.17 0.00 41.42 2.90
82 83 0.780637 AGACCACCTCCTCTGAGACA 59.219 55.000 6.17 0.00 41.42 3.41
84 85 1.551099 CCAAGACCACCTCCTCTGAGA 60.551 57.143 6.17 0.00 41.42 3.27
85 86 0.901124 CCAAGACCACCTCCTCTGAG 59.099 60.000 0.00 0.00 38.42 3.35
87 88 1.298014 GCCAAGACCACCTCCTCTG 59.702 63.158 0.00 0.00 0.00 3.35
88 89 2.286523 CGCCAAGACCACCTCCTCT 61.287 63.158 0.00 0.00 0.00 3.69
92 93 1.966451 CAACCGCCAAGACCACCTC 60.966 63.158 0.00 0.00 0.00 3.85
109 110 4.374584 CCGGGGCCAATTGGGTCA 62.375 66.667 25.73 0.00 45.89 4.02
116 117 4.060667 CTCCAACCCGGGGCCAAT 62.061 66.667 27.92 0.00 34.36 3.16
125 126 1.078426 CGTCCACCATCTCCAACCC 60.078 63.158 0.00 0.00 0.00 4.11
131 132 1.450312 CAAGGGCGTCCACCATCTC 60.450 63.158 9.71 0.00 34.83 2.75
138 139 4.351938 CGTCGACAAGGGCGTCCA 62.352 66.667 17.16 0.00 34.83 4.02
145 146 2.432628 GTCAGCCCGTCGACAAGG 60.433 66.667 17.16 16.30 32.24 3.61
146 147 1.078759 GATGTCAGCCCGTCGACAAG 61.079 60.000 17.16 6.92 44.78 3.16
147 148 1.080093 GATGTCAGCCCGTCGACAA 60.080 57.895 17.16 0.00 44.78 3.18
158 159 1.511613 ATAGGTGGGGGTGATGTCAG 58.488 55.000 0.00 0.00 0.00 3.51
161 162 1.979809 TCAATAGGTGGGGGTGATGT 58.020 50.000 0.00 0.00 0.00 3.06
176 177 3.566853 CGCGCGTGCTCCATCAAT 61.567 61.111 24.19 0.00 39.65 2.57
212 213 1.673168 GATGTGCTCCTTCCACCATC 58.327 55.000 0.00 0.00 32.30 3.51
220 221 2.370445 CCCCCTCGATGTGCTCCTT 61.370 63.158 0.00 0.00 0.00 3.36
229 230 2.765807 CTGCACCTCCCCCTCGAT 60.766 66.667 0.00 0.00 0.00 3.59
233 234 3.655211 CAAGCTGCACCTCCCCCT 61.655 66.667 1.02 0.00 0.00 4.79
246 247 3.426568 GACAGCACCGCCTCAAGC 61.427 66.667 0.00 0.00 38.52 4.01
249 250 2.917227 TCTGACAGCACCGCCTCA 60.917 61.111 0.00 0.00 0.00 3.86
257 258 0.385751 GGCTATAGCGTCTGACAGCA 59.614 55.000 18.30 10.99 43.26 4.41
260 261 1.319541 GAGGGCTATAGCGTCTGACA 58.680 55.000 18.30 0.00 43.26 3.58
261 262 0.238817 CGAGGGCTATAGCGTCTGAC 59.761 60.000 18.30 3.37 43.26 3.51
262 263 0.179026 ACGAGGGCTATAGCGTCTGA 60.179 55.000 18.30 0.00 43.26 3.27
264 265 2.631427 GACGAGGGCTATAGCGTCT 58.369 57.895 18.30 17.05 46.74 4.18
265 266 1.207085 CGACGAGGGCTATAGCGTC 59.793 63.158 18.30 17.11 46.78 5.19
288 289 1.466856 TGAGGGACGCGTTAGTGTAT 58.533 50.000 15.53 0.00 41.83 2.29
292 293 0.108329 CCAATGAGGGACGCGTTAGT 60.108 55.000 15.53 0.00 34.53 2.24
293 294 1.429148 GCCAATGAGGGACGCGTTAG 61.429 60.000 15.53 0.00 34.53 2.34
294 295 1.448893 GCCAATGAGGGACGCGTTA 60.449 57.895 15.53 0.00 34.53 3.18
295 296 2.746277 GCCAATGAGGGACGCGTT 60.746 61.111 15.53 0.00 38.01 4.84
298 299 2.435938 TTCGCCAATGAGGGACGC 60.436 61.111 0.00 0.00 38.09 5.19
311 312 0.107654 AAGGATGGTGTAGGCTTCGC 60.108 55.000 0.00 0.00 0.00 4.70
316 317 1.134371 GGACTCAAGGATGGTGTAGGC 60.134 57.143 0.00 0.00 0.00 3.93
317 318 2.187958 TGGACTCAAGGATGGTGTAGG 58.812 52.381 0.00 0.00 0.00 3.18
319 320 2.430694 CGATGGACTCAAGGATGGTGTA 59.569 50.000 0.00 0.00 0.00 2.90
320 321 1.208052 CGATGGACTCAAGGATGGTGT 59.792 52.381 0.00 0.00 0.00 4.16
322 323 1.759445 CTCGATGGACTCAAGGATGGT 59.241 52.381 0.00 0.00 0.00 3.55
372 373 4.056740 CTCGGTCATGAATGAAGATCCTG 58.943 47.826 0.00 0.00 38.75 3.86
386 387 1.110442 CTTCTCCTGCTCTCGGTCAT 58.890 55.000 0.00 0.00 0.00 3.06
398 399 4.077822 CTCATTTGCAAAGGTCTTCTCCT 58.922 43.478 21.93 0.00 39.84 3.69
407 408 1.134610 GCCCATCCTCATTTGCAAAGG 60.135 52.381 17.43 17.43 0.00 3.11
463 470 1.169661 ATCACCGCTTTGCCGAAACA 61.170 50.000 0.00 0.00 0.00 2.83
486 494 0.915364 GCTCCTTGTCTGAGGGGATT 59.085 55.000 0.00 0.00 39.88 3.01
541 549 3.034635 ACCAGCTAGAACTACATCCAGG 58.965 50.000 0.00 0.00 0.00 4.45
578 586 7.328737 ACAACTACAACTCGTTCATAGATTCAC 59.671 37.037 5.18 0.00 0.00 3.18
982 1276 3.706373 GGAGCGGGAGTGGAAGCA 61.706 66.667 0.00 0.00 0.00 3.91
983 1277 3.036429 ATGGAGCGGGAGTGGAAGC 62.036 63.158 0.00 0.00 0.00 3.86
984 1278 1.153289 CATGGAGCGGGAGTGGAAG 60.153 63.158 0.00 0.00 0.00 3.46
985 1279 2.669133 CCATGGAGCGGGAGTGGAA 61.669 63.158 5.56 0.00 31.59 3.53
986 1280 3.083349 CCATGGAGCGGGAGTGGA 61.083 66.667 5.56 0.00 31.59 4.02
987 1281 3.083349 TCCATGGAGCGGGAGTGG 61.083 66.667 11.44 0.00 0.00 4.00
988 1282 2.503061 CTCCATGGAGCGGGAGTG 59.497 66.667 28.45 3.76 44.59 3.51
997 1291 2.444706 CTCCGCCTCCTCCATGGA 60.445 66.667 15.27 15.27 43.86 3.41
998 1292 1.626356 TTTCTCCGCCTCCTCCATGG 61.626 60.000 4.97 4.97 37.10 3.66
1202 1540 4.019411 TGATGGTCATGTAGAAGAAGCCAA 60.019 41.667 0.00 0.00 0.00 4.52
1469 1864 7.067421 ACCTGTGGTACAGCTATATCTCTTTA 58.933 38.462 3.49 0.00 44.63 1.85
1473 1874 5.074115 AGACCTGTGGTACAGCTATATCTC 58.926 45.833 3.49 0.00 44.63 2.75
2054 2589 8.400186 CAACTTTCTGATGTTGCATATCATACA 58.600 33.333 12.81 2.21 37.36 2.29
2086 2621 6.765915 AATGCCTTTCTCAAGATTAAGGAC 57.234 37.500 12.64 6.42 39.60 3.85
2221 2766 4.602340 TGTTAAGCCGAAAGAAGAGACT 57.398 40.909 0.00 0.00 0.00 3.24
2238 2783 4.214545 CCGAAGTACACAGGCAAATTGTTA 59.785 41.667 0.00 0.00 0.00 2.41
2272 2820 1.000274 AGCAAATTCAACGGCAAGACC 60.000 47.619 0.00 0.00 0.00 3.85
2273 2821 2.053627 CAGCAAATTCAACGGCAAGAC 58.946 47.619 0.00 0.00 0.00 3.01
2276 2824 0.749649 ACCAGCAAATTCAACGGCAA 59.250 45.000 0.00 0.00 0.00 4.52
2282 2830 3.658757 GGTAAGCACCAGCAAATTCAA 57.341 42.857 0.00 0.00 45.04 2.69
2375 2933 5.680619 ACAGACCAAGAGTAACAATGTTCA 58.319 37.500 0.22 0.00 0.00 3.18
2405 2979 2.101415 GTCAAGAAAAAGGCCAGTGCTT 59.899 45.455 5.01 0.00 37.74 3.91
2415 2989 9.956720 ATTGAACTAACATCTGTCAAGAAAAAG 57.043 29.630 0.00 0.00 35.59 2.27
2418 2993 8.344831 CACATTGAACTAACATCTGTCAAGAAA 58.655 33.333 0.00 0.00 35.59 2.52
2428 3003 9.503427 GTAATTTAGCCACATTGAACTAACATC 57.497 33.333 0.00 0.00 0.00 3.06
2439 3014 7.201696 CCGATTACAGTGTAATTTAGCCACATT 60.202 37.037 25.50 3.84 0.00 2.71
2454 3032 4.822026 AGAAAGGAAGACCGATTACAGTG 58.178 43.478 0.00 0.00 41.83 3.66
2526 4062 6.659745 TGAACCTTTTAGTACACTAGCAGA 57.340 37.500 0.00 0.00 0.00 4.26
2571 4121 2.292292 GGTAAACAAGACATTGCACGGT 59.708 45.455 0.00 0.00 40.27 4.83
2572 4122 2.552315 AGGTAAACAAGACATTGCACGG 59.448 45.455 0.00 0.00 40.27 4.94
2573 4123 3.896648 AGGTAAACAAGACATTGCACG 57.103 42.857 0.00 0.00 40.27 5.34
2574 4124 7.367285 TGAATAAGGTAAACAAGACATTGCAC 58.633 34.615 0.00 0.00 40.27 4.57
2575 4125 7.517614 TGAATAAGGTAAACAAGACATTGCA 57.482 32.000 0.00 0.00 40.27 4.08
2576 4126 8.986477 AATGAATAAGGTAAACAAGACATTGC 57.014 30.769 0.00 0.00 40.27 3.56
2585 4135 9.743057 CAAAACACTGAATGAATAAGGTAAACA 57.257 29.630 0.00 0.00 0.00 2.83
2589 4139 9.575868 TTACCAAAACACTGAATGAATAAGGTA 57.424 29.630 0.00 0.00 0.00 3.08
2606 4156 4.626172 TGAAAGGCAACGTTTTACCAAAAC 59.374 37.500 12.83 4.76 45.56 2.43
2619 4169 1.001378 ACGAACATGCTGAAAGGCAAC 60.001 47.619 0.00 0.00 45.68 4.17
2620 4170 1.317613 ACGAACATGCTGAAAGGCAA 58.682 45.000 0.00 0.00 45.68 4.52
2628 4178 4.536065 ACACACATAAAACGAACATGCTG 58.464 39.130 0.00 0.00 0.00 4.41
2633 4183 4.795795 CAGCAAACACACATAAAACGAACA 59.204 37.500 0.00 0.00 0.00 3.18
2638 4188 6.885735 AGAAACAGCAAACACACATAAAAC 57.114 33.333 0.00 0.00 0.00 2.43
2672 4222 4.813697 GCCCTAACAGATCAAAAGCTCTAG 59.186 45.833 0.00 0.00 0.00 2.43
2682 4232 1.281867 CCAGGTTGCCCTAACAGATCA 59.718 52.381 0.00 0.00 39.89 2.92
2692 4242 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2693 4243 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2694 4244 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2695 4245 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2696 4246 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2721 4271 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2722 4272 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2724 4274 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2726 4276 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2727 4277 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2728 4278 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2730 4280 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2731 4281 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2732 4282 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2733 4283 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2735 4285 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2736 4286 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2739 4289 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2740 4290 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2745 4295 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2746 4296 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2747 4297 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2750 4300 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2751 4301 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2752 4302 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2753 4303 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2754 4304 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2755 4305 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2756 4306 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2757 4307 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2758 4308 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2760 4310 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2764 4314 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2765 4315 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2766 4316 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2767 4317 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2768 4318 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2769 4319 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2770 4320 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2771 4321 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2773 4323 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2774 4324 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2775 4325 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2776 4326 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2777 4327 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2780 4330 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2781 4331 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2782 4332 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2806 4356 5.997129 TGATGCAATTTCTCTGTGACTAACA 59.003 36.000 0.00 0.00 37.22 2.41
2807 4357 6.486253 TGATGCAATTTCTCTGTGACTAAC 57.514 37.500 0.00 0.00 0.00 2.34
2808 4358 7.362315 CCATTGATGCAATTTCTCTGTGACTAA 60.362 37.037 0.00 0.00 31.05 2.24
2809 4359 6.094464 CCATTGATGCAATTTCTCTGTGACTA 59.906 38.462 0.00 0.00 31.05 2.59
2811 4361 5.100259 CCATTGATGCAATTTCTCTGTGAC 58.900 41.667 0.00 0.00 31.05 3.67
2858 4679 6.220726 TGCTGCTATTCATACAAGAGTACA 57.779 37.500 0.00 0.00 31.96 2.90
2870 4691 1.441732 CGCCTGCATGCTGCTATTCA 61.442 55.000 23.82 1.14 45.31 2.57
2871 4692 1.162181 TCGCCTGCATGCTGCTATTC 61.162 55.000 23.82 9.05 45.31 1.75
2881 4702 2.440409 ACTGATTTCTTTCGCCTGCAT 58.560 42.857 0.00 0.00 0.00 3.96
2888 4709 4.926238 ACTCTGCTGTACTGATTTCTTTCG 59.074 41.667 3.61 0.00 0.00 3.46
2956 4779 3.005684 ACACACAAATACCCTGCATGTTG 59.994 43.478 0.00 0.00 0.00 3.33
2957 4780 3.230134 ACACACAAATACCCTGCATGTT 58.770 40.909 0.00 0.00 0.00 2.71
3043 4866 1.206578 CAAACAGGGTAGCAACGCG 59.793 57.895 3.53 3.53 43.08 6.01
3045 4868 1.531149 CACTCAAACAGGGTAGCAACG 59.469 52.381 0.00 0.00 0.00 4.10
3100 4924 4.363138 CATTCGAGAATCAGGAATCGTCA 58.637 43.478 0.00 0.00 36.58 4.35
3103 4927 3.722147 ACCATTCGAGAATCAGGAATCG 58.278 45.455 8.59 0.00 36.54 3.34
3141 4967 9.690913 TCAGTTCATATTTTCCATTCTCATTCT 57.309 29.630 0.00 0.00 0.00 2.40
3155 4981 8.836413 TCAACTCGACTTTTTCAGTTCATATTT 58.164 29.630 0.00 0.00 35.01 1.40
3157 4983 7.962964 TCAACTCGACTTTTTCAGTTCATAT 57.037 32.000 0.00 0.00 35.01 1.78


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

AutoCloner maintained by Alex Coulton.