Multiple sequence alignment - TraesCS3B01G512200

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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 TraesCS3B01G512200 chr3B 100.000 4056 0 0 1 4056 755768701 755772756 0.000000e+00 7491.0
1 TraesCS3B01G512200 chr3B 87.935 920 72 30 3161 4053 755606544 755607451 0.000000e+00 1048.0
2 TraesCS3B01G512200 chr3B 93.986 582 22 10 3161 3732 754722700 754723278 0.000000e+00 869.0
3 TraesCS3B01G512200 chr3B 92.463 544 26 9 2617 3158 755575769 755576299 0.000000e+00 763.0
4 TraesCS3B01G512200 chr3B 89.127 561 42 1 2606 3166 754722096 754722637 0.000000e+00 680.0
5 TraesCS3B01G512200 chr3B 92.890 436 27 3 2730 3163 755606046 755606479 7.400000e-177 630.0
6 TraesCS3B01G512200 chr3B 93.140 379 22 2 1903 2281 754719820 754720194 1.650000e-153 553.0
7 TraesCS3B01G512200 chr3B 89.485 447 34 9 3185 3621 754772324 754772767 1.650000e-153 553.0
8 TraesCS3B01G512200 chr3B 95.189 291 13 1 2279 2568 754720232 754720522 3.690000e-125 459.0
9 TraesCS3B01G512200 chr3B 91.445 339 10 7 1943 2281 755604953 755605272 8.000000e-122 448.0
10 TraesCS3B01G512200 chr3B 92.763 304 14 3 2279 2574 755605313 755605616 2.240000e-117 433.0
11 TraesCS3B01G512200 chr3B 89.701 301 26 4 2279 2574 754771109 754771409 2.960000e-101 379.0
12 TraesCS3B01G512200 chr3B 89.404 302 24 6 2275 2574 755575300 755575595 1.380000e-99 374.0
13 TraesCS3B01G512200 chr3B 86.859 312 15 14 834 1136 755573633 755573927 3.910000e-85 326.0
14 TraesCS3B01G512200 chr3B 89.057 265 17 8 844 1108 755707983 755708235 6.540000e-83 318.0
15 TraesCS3B01G512200 chr3B 86.032 315 20 12 844 1150 755604071 755604369 2.350000e-82 316.0
16 TraesCS3B01G512200 chr3B 84.118 340 20 16 844 1172 754718145 754718461 8.520000e-77 298.0
17 TraesCS3B01G512200 chr3B 90.476 210 14 5 3185 3389 755660831 755661039 5.170000e-69 272.0
18 TraesCS3B01G512200 chr3B 83.770 191 15 7 844 1023 754767490 754767675 2.510000e-37 167.0
19 TraesCS3B01G512200 chr3B 84.091 88 9 4 700 785 755573443 755573527 3.360000e-11 80.5
20 TraesCS3B01G512200 chr3B 100.000 29 0 0 2587 2615 754720698 754720726 2.000000e-03 54.7
21 TraesCS3B01G512200 chr3A 98.077 780 14 1 2279 3057 701123493 701124272 0.000000e+00 1356.0
22 TraesCS3B01G512200 chr3A 89.629 916 64 19 3161 4053 700954463 700955370 0.000000e+00 1136.0
23 TraesCS3B01G512200 chr3A 94.345 672 35 2 31 699 144453233 144452562 0.000000e+00 1027.0
24 TraesCS3B01G512200 chr3A 88.209 882 55 20 834 1690 701122138 701122995 0.000000e+00 1007.0
25 TraesCS3B01G512200 chr3A 92.561 578 32 4 2582 3158 700893612 700894179 0.000000e+00 819.0
26 TraesCS3B01G512200 chr3A 89.966 588 33 7 2582 3166 700953836 700954400 0.000000e+00 736.0
27 TraesCS3B01G512200 chr3A 93.624 298 16 3 2279 2574 700953376 700953672 3.720000e-120 442.0
28 TraesCS3B01G512200 chr3A 90.000 340 15 3 1943 2281 700953014 700953335 4.850000e-114 422.0
29 TraesCS3B01G512200 chr3A 87.542 297 34 3 2280 2574 700944961 700945256 1.400000e-89 340.0
30 TraesCS3B01G512200 chr3A 87.129 303 17 8 844 1145 700959237 700959518 1.410000e-84 324.0
31 TraesCS3B01G512200 chr3A 85.616 292 31 7 835 1126 701138021 701138301 3.070000e-76 296.0
32 TraesCS3B01G512200 chr3A 94.972 179 9 0 2103 2281 701123274 701123452 8.580000e-72 281.0
33 TraesCS3B01G512200 chr3A 83.706 313 14 14 838 1136 700891097 700891386 1.120000e-65 261.0
34 TraesCS3B01G512200 chr3A 96.178 157 4 2 981 1136 700907774 700907929 5.200000e-64 255.0
35 TraesCS3B01G512200 chr3A 93.571 140 5 2 700 837 701121858 701121995 5.310000e-49 206.0
36 TraesCS3B01G512200 chr3A 87.861 173 18 2 1578 1750 700891563 700891732 2.470000e-47 200.0
37 TraesCS3B01G512200 chr3A 97.727 44 1 0 1467 1510 701139226 701139269 4.350000e-10 76.8
38 TraesCS3B01G512200 chr3D 94.543 843 34 8 3222 4056 566298894 566298056 0.000000e+00 1291.0
39 TraesCS3B01G512200 chr3D 95.502 578 23 3 2588 3164 566422600 566422025 0.000000e+00 920.0
40 TraesCS3B01G512200 chr3D 94.746 590 21 5 2582 3164 566300130 566299544 0.000000e+00 909.0
41 TraesCS3B01G512200 chr3D 90.909 649 31 11 699 1332 566302204 566301569 0.000000e+00 846.0
42 TraesCS3B01G512200 chr3D 88.193 703 57 13 3367 4053 566397976 566397284 0.000000e+00 815.0
43 TraesCS3B01G512200 chr3D 93.160 424 26 3 2730 3152 566129640 566129219 1.600000e-173 619.0
44 TraesCS3B01G512200 chr3D 93.883 376 19 2 1906 2281 566132187 566131816 7.610000e-157 564.0
45 TraesCS3B01G512200 chr3D 96.764 309 8 2 2279 2585 566300557 566300249 7.770000e-142 514.0
46 TraesCS3B01G512200 chr3D 92.898 352 20 4 7 357 559773444 559773791 1.300000e-139 507.0
47 TraesCS3B01G512200 chr3D 95.960 297 11 1 2279 2574 566131775 566131479 7.880000e-132 481.0
48 TraesCS3B01G512200 chr3D 85.682 447 39 15 3185 3621 566391910 566391479 8.000000e-122 448.0
49 TraesCS3B01G512200 chr3D 89.535 344 20 10 3206 3542 566112551 566112217 4.850000e-114 422.0
50 TraesCS3B01G512200 chr3D 88.690 336 17 11 850 1182 566394932 566394615 1.370000e-104 390.0
51 TraesCS3B01G512200 chr3D 96.396 222 8 0 478 699 559774093 559774314 2.300000e-97 366.0
52 TraesCS3B01G512200 chr3D 86.943 314 23 7 834 1144 566103763 566103465 1.810000e-88 337.0
53 TraesCS3B01G512200 chr3D 87.582 306 15 6 834 1136 566423843 566423558 2.340000e-87 333.0
54 TraesCS3B01G512200 chr3D 96.089 179 7 0 2103 2281 566300776 566300598 3.970000e-75 292.0
55 TraesCS3B01G512200 chr3D 82.857 350 19 21 844 1178 566138681 566138358 3.990000e-70 276.0
56 TraesCS3B01G512200 chr3D 93.333 165 11 0 1386 1550 566301572 566301408 1.130000e-60 244.0
57 TraesCS3B01G512200 chr3D 87.283 173 18 3 1578 1750 566423386 566423218 1.150000e-45 195.0
58 TraesCS3B01G512200 chr3D 96.226 106 4 0 3264 3369 566409868 566409763 1.500000e-39 174.0
59 TraesCS3B01G512200 chr3D 92.920 113 4 3 3161 3269 566421960 566421848 1.170000e-35 161.0
60 TraesCS3B01G512200 chr3D 84.524 84 11 2 697 780 566424027 566423946 9.340000e-12 82.4
61 TraesCS3B01G512200 chr3D 92.727 55 4 0 2653 2707 566129698 566129644 3.360000e-11 80.5
62 TraesCS3B01G512200 chr3D 94.595 37 2 0 2582 2618 566131314 566131278 1.570000e-04 58.4
63 TraesCS3B01G512200 chr7B 95.007 701 28 4 4 699 138870590 138869892 0.000000e+00 1094.0
64 TraesCS3B01G512200 chr7B 88.828 367 34 6 5 370 226182364 226182004 1.030000e-120 444.0
65 TraesCS3B01G512200 chr7B 92.793 222 16 0 478 699 226181878 226181657 5.060000e-84 322.0
66 TraesCS3B01G512200 chr2B 94.452 703 36 2 1 700 793500297 793500999 0.000000e+00 1079.0
67 TraesCS3B01G512200 chr2B 92.377 223 17 0 478 700 47177763 47177985 6.540000e-83 318.0
68 TraesCS3B01G512200 chr1A 93.732 702 38 4 1 698 14427279 14427978 0.000000e+00 1048.0
69 TraesCS3B01G512200 chr1B 93.581 701 42 2 1 698 654272621 654273321 0.000000e+00 1042.0
70 TraesCS3B01G512200 chr6B 87.815 476 49 7 7 481 439969476 439969943 2.130000e-152 549.0
71 TraesCS3B01G512200 chr2D 90.609 394 29 7 5 396 95533388 95533001 2.160000e-142 516.0
72 TraesCS3B01G512200 chr2D 93.304 224 15 0 478 701 95532737 95532514 8.400000e-87 331.0
73 TraesCS3B01G512200 chr5D 83.513 279 36 7 1570 1846 537757097 537756827 6.730000e-63 252.0
74 TraesCS3B01G512200 chr4A 85.235 149 17 3 3477 3621 658223033 658223180 9.080000e-32 148.0


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 TraesCS3B01G512200 chr3B 755768701 755772756 4055 False 7491.000000 7491 100.000000 1 4056 1 chr3B.!!$F3 4055
1 TraesCS3B01G512200 chr3B 755604071 755607451 3380 False 575.000000 1048 90.213000 844 4053 5 chr3B.!!$F7 3209
2 TraesCS3B01G512200 chr3B 754718145 754723278 5133 False 485.616667 869 92.593333 844 3732 6 chr3B.!!$F4 2888
3 TraesCS3B01G512200 chr3B 755573443 755576299 2856 False 385.875000 763 88.204250 700 3158 4 chr3B.!!$F6 2458
4 TraesCS3B01G512200 chr3B 754767490 754772767 5277 False 366.333333 553 87.652000 844 3621 3 chr3B.!!$F5 2777
5 TraesCS3B01G512200 chr3A 144452562 144453233 671 True 1027.000000 1027 94.345000 31 699 1 chr3A.!!$R1 668
6 TraesCS3B01G512200 chr3A 701121858 701124272 2414 False 712.500000 1356 93.707250 700 3057 4 chr3A.!!$F5 2357
7 TraesCS3B01G512200 chr3A 700953014 700959518 6504 False 612.000000 1136 90.069600 844 4053 5 chr3A.!!$F4 3209
8 TraesCS3B01G512200 chr3A 700891097 700894179 3082 False 426.666667 819 88.042667 838 3158 3 chr3A.!!$F3 2320
9 TraesCS3B01G512200 chr3D 566298056 566302204 4148 True 682.666667 1291 94.397333 699 4056 6 chr3D.!!$R6 3357
10 TraesCS3B01G512200 chr3D 566391479 566397976 6497 True 551.000000 815 87.521667 850 4053 3 chr3D.!!$R7 3203
11 TraesCS3B01G512200 chr3D 559773444 559774314 870 False 436.500000 507 94.647000 7 699 2 chr3D.!!$F1 692
12 TraesCS3B01G512200 chr3D 566129219 566132187 2968 True 360.580000 619 94.065000 1906 3152 5 chr3D.!!$R5 1246
13 TraesCS3B01G512200 chr3D 566421848 566424027 2179 True 338.280000 920 89.562200 697 3269 5 chr3D.!!$R8 2572
14 TraesCS3B01G512200 chr7B 138869892 138870590 698 True 1094.000000 1094 95.007000 4 699 1 chr7B.!!$R1 695
15 TraesCS3B01G512200 chr7B 226181657 226182364 707 True 383.000000 444 90.810500 5 699 2 chr7B.!!$R2 694
16 TraesCS3B01G512200 chr2B 793500297 793500999 702 False 1079.000000 1079 94.452000 1 700 1 chr2B.!!$F2 699
17 TraesCS3B01G512200 chr1A 14427279 14427978 699 False 1048.000000 1048 93.732000 1 698 1 chr1A.!!$F1 697
18 TraesCS3B01G512200 chr1B 654272621 654273321 700 False 1042.000000 1042 93.581000 1 698 1 chr1B.!!$F1 697
19 TraesCS3B01G512200 chr2D 95532514 95533388 874 True 423.500000 516 91.956500 5 701 2 chr2D.!!$R1 696

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
849 1273 0.261991 ATTACCTCTCCGGCTCCTGA 59.738 55.0 0.0 0.0 35.61 3.86 F
1197 5003 0.547075 TCCCCCTTCGTGTGTTTTCA 59.453 50.0 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 6595 0.537143 TCCAGCAACCACATCACACC 60.537 55.0 0.0 0.0 0.0 4.16 R
3123 12444 0.608035 TCCCGAGCACATTTCAACCC 60.608 55.0 0.0 0.0 0.0 4.11 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
124 125 2.768344 CCCCTCCACACCGGCTAT 60.768 66.667 0.00 0.00 33.14 2.97
165 166 1.200716 AGATGCAGCCAAACATCAACG 59.799 47.619 0.00 0.00 44.16 4.10
183 184 0.396417 CGTCTCCTCCACTCCTCCAT 60.396 60.000 0.00 0.00 0.00 3.41
301 309 5.953183 TGTGTCAATTTGTTAGATGGATGC 58.047 37.500 0.00 0.00 0.00 3.91
726 950 3.308878 GAACGGCGTGCGCAGAAAT 62.309 57.895 21.76 8.53 44.11 2.17
727 951 3.593551 AACGGCGTGCGCAGAAATG 62.594 57.895 21.76 2.15 44.11 2.32
814 1042 0.608640 CAGAGGTACCCAGACCACAC 59.391 60.000 8.74 0.00 42.47 3.82
849 1273 0.261991 ATTACCTCTCCGGCTCCTGA 59.738 55.000 0.00 0.00 35.61 3.86
919 3134 4.758251 TGCCACAGATCCACGCCG 62.758 66.667 0.00 0.00 0.00 6.46
927 3142 4.473520 ATCCACGCCGGCAAGGAG 62.474 66.667 32.39 17.96 45.00 3.69
935 3150 2.892425 CGGCAAGGAGTCCATCGC 60.892 66.667 12.86 10.35 0.00 4.58
981 3196 2.202770 CAGAGCAGAGCAGAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
984 3199 2.362247 AGCAGAGCAGAGCCGAGA 60.362 61.111 0.00 0.00 0.00 4.04
1154 4919 3.711782 CCTCCCCTTCCCTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
1186 4992 3.528078 ACTAATTTCTTCCCTCCCCCTTC 59.472 47.826 0.00 0.00 0.00 3.46
1193 4999 2.526046 CCCTCCCCCTTCGTGTGTT 61.526 63.158 0.00 0.00 0.00 3.32
1196 5002 1.235724 CTCCCCCTTCGTGTGTTTTC 58.764 55.000 0.00 0.00 0.00 2.29
1197 5003 0.547075 TCCCCCTTCGTGTGTTTTCA 59.453 50.000 0.00 0.00 0.00 2.69
1198 5004 1.144093 TCCCCCTTCGTGTGTTTTCAT 59.856 47.619 0.00 0.00 0.00 2.57
1199 5005 1.269448 CCCCCTTCGTGTGTTTTCATG 59.731 52.381 0.00 0.00 0.00 3.07
1200 5006 1.269448 CCCCTTCGTGTGTTTTCATGG 59.731 52.381 0.00 0.00 0.00 3.66
1201 5007 2.226330 CCCTTCGTGTGTTTTCATGGA 58.774 47.619 0.00 0.00 0.00 3.41
1202 5008 2.226437 CCCTTCGTGTGTTTTCATGGAG 59.774 50.000 0.00 0.00 31.64 3.86
1203 5009 2.350772 CCTTCGTGTGTTTTCATGGAGC 60.351 50.000 0.00 0.00 30.76 4.70
1204 5010 1.960417 TCGTGTGTTTTCATGGAGCA 58.040 45.000 0.00 0.00 0.00 4.26
1205 5011 2.503331 TCGTGTGTTTTCATGGAGCAT 58.497 42.857 0.00 0.00 0.00 3.79
1206 5012 2.483877 TCGTGTGTTTTCATGGAGCATC 59.516 45.455 0.00 0.00 0.00 3.91
1207 5013 2.226200 CGTGTGTTTTCATGGAGCATCA 59.774 45.455 0.00 0.00 36.25 3.07
1208 5014 3.568538 GTGTGTTTTCATGGAGCATCAC 58.431 45.455 0.00 0.00 36.25 3.06
1209 5015 3.254166 GTGTGTTTTCATGGAGCATCACT 59.746 43.478 0.00 0.00 36.25 3.41
1210 5016 3.503363 TGTGTTTTCATGGAGCATCACTC 59.497 43.478 0.00 0.00 45.45 3.51
1221 5027 2.871022 GAGCATCACTCAAGTAGCATGG 59.129 50.000 0.00 0.00 45.49 3.66
1222 5028 1.332997 GCATCACTCAAGTAGCATGGC 59.667 52.381 0.00 0.00 0.00 4.40
1334 5591 2.107204 AGTCTTTCCACTGTCTTGGCAT 59.893 45.455 0.00 0.00 36.48 4.40
1343 5600 1.212751 GTCTTGGCATTGGCGGTTC 59.787 57.895 5.68 0.00 42.47 3.62
1400 5941 2.062636 AGGCTTTGGTCTTAGGTTGGA 58.937 47.619 0.00 0.00 0.00 3.53
1455 5997 5.464069 TGGGGAATATAGCAGAGACAAGTA 58.536 41.667 0.00 0.00 0.00 2.24
1709 6432 9.896645 AAGATTCTGAATGTTCTGCTAAATCTA 57.103 29.630 7.78 0.00 31.89 1.98
1734 6459 4.210955 TCGGCATTGAAAAAGCAAATCAAC 59.789 37.500 0.00 0.00 43.40 3.18
1754 6482 7.540474 TCAACTAGGAAACTAACTCATCTGT 57.460 36.000 0.00 0.00 43.83 3.41
1783 6527 1.859703 TGCACAAAAATGCTTGAAGCG 59.140 42.857 13.05 0.00 46.26 4.68
1802 6549 4.202441 AGCGACTGATGGATTAAAGCATT 58.798 39.130 0.00 0.00 0.00 3.56
1803 6550 5.368145 AGCGACTGATGGATTAAAGCATTA 58.632 37.500 0.00 0.00 0.00 1.90
1804 6551 6.000219 AGCGACTGATGGATTAAAGCATTAT 59.000 36.000 0.00 0.00 0.00 1.28
1805 6552 7.161404 AGCGACTGATGGATTAAAGCATTATA 58.839 34.615 0.00 0.00 0.00 0.98
1846 6593 4.236527 GGGACACCCATCAATCTTAACT 57.763 45.455 1.54 0.00 44.65 2.24
1847 6594 4.600062 GGGACACCCATCAATCTTAACTT 58.400 43.478 1.54 0.00 44.65 2.66
1848 6595 4.399303 GGGACACCCATCAATCTTAACTTG 59.601 45.833 1.54 0.00 44.65 3.16
1849 6596 4.399303 GGACACCCATCAATCTTAACTTGG 59.601 45.833 0.00 0.00 0.00 3.61
1851 6598 4.766891 ACACCCATCAATCTTAACTTGGTG 59.233 41.667 0.00 0.00 44.78 4.17
1859 6662 5.473162 TCAATCTTAACTTGGTGTGATGTGG 59.527 40.000 0.00 0.00 0.00 4.17
1868 8185 1.317613 GTGTGATGTGGTTGCTGGAA 58.682 50.000 0.00 0.00 0.00 3.53
1876 8193 5.479724 TGATGTGGTTGCTGGAAATTTATCA 59.520 36.000 0.00 0.00 0.00 2.15
1877 8194 5.999205 TGTGGTTGCTGGAAATTTATCAT 57.001 34.783 0.00 0.00 0.00 2.45
1878 8195 5.964758 TGTGGTTGCTGGAAATTTATCATC 58.035 37.500 0.00 0.00 0.00 2.92
1879 8196 5.716228 TGTGGTTGCTGGAAATTTATCATCT 59.284 36.000 0.00 0.00 0.00 2.90
1880 8197 6.038356 GTGGTTGCTGGAAATTTATCATCTG 58.962 40.000 0.00 0.00 0.00 2.90
1881 8198 5.127519 TGGTTGCTGGAAATTTATCATCTGG 59.872 40.000 0.00 0.00 0.00 3.86
1882 8199 5.452356 GGTTGCTGGAAATTTATCATCTGGG 60.452 44.000 0.00 0.00 0.00 4.45
1884 8201 5.271598 TGCTGGAAATTTATCATCTGGGTT 58.728 37.500 0.00 0.00 0.00 4.11
1885 8202 5.721000 TGCTGGAAATTTATCATCTGGGTTT 59.279 36.000 0.00 0.00 0.00 3.27
1886 8203 6.894654 TGCTGGAAATTTATCATCTGGGTTTA 59.105 34.615 0.00 0.00 0.00 2.01
1888 8205 8.084684 GCTGGAAATTTATCATCTGGGTTTATC 58.915 37.037 0.00 0.00 0.00 1.75
1889 8206 9.135189 CTGGAAATTTATCATCTGGGTTTATCA 57.865 33.333 0.00 0.00 0.00 2.15
1902 8257 4.590647 TGGGTTTATCATCTGTTTTTGCCA 59.409 37.500 0.00 0.00 0.00 4.92
1915 8586 5.119694 TGTTTTTGCCACAAAGGGTTTATC 58.880 37.500 0.00 0.00 38.09 1.75
1921 8592 3.429410 GCCACAAAGGGTTTATCATCTGC 60.429 47.826 0.00 0.00 38.09 4.26
1935 8606 1.741706 CATCTGCTAAGGTGGTTGCTG 59.258 52.381 0.00 0.00 30.15 4.41
2022 8693 0.997363 TCAGGGAGAACTCGGACCTA 59.003 55.000 0.00 0.00 0.00 3.08
2032 8703 3.889520 ACTCGGACCTAGGATGTTTTC 57.110 47.619 17.98 0.27 0.00 2.29
2496 9919 5.368523 TCTTCACACCCCGGATAATCTATTT 59.631 40.000 0.73 0.00 0.00 1.40
2725 12016 5.511234 GCTGTCATTTCTCATAGCCAAAT 57.489 39.130 0.00 0.00 0.00 2.32
2926 12247 2.583024 TCTTCATGTGGGATGTGCAA 57.417 45.000 0.00 0.00 0.00 4.08
3080 12401 1.810853 CACGTGCTCATGATCGCCA 60.811 57.895 0.82 0.00 0.00 5.69
3123 12444 3.107601 TCAGGACTCAGGAGGGTAAATG 58.892 50.000 0.83 0.00 0.00 2.32
3612 13563 3.478857 TCGCCAGTCTAAAAAGGACAA 57.521 42.857 0.00 0.00 36.29 3.18
3627 13586 6.391227 AAAGGACAAGTTGGTGAATTACTG 57.609 37.500 7.96 0.00 0.00 2.74
3654 13613 4.806775 GGTCCAGCAAACGTTAACAAATTT 59.193 37.500 0.00 0.33 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 4.203076 GCCGTCGATAGCCGGTGT 62.203 66.667 13.01 0.00 45.91 4.16
147 148 0.961019 ACGTTGATGTTTGGCTGCAT 59.039 45.000 0.50 0.00 0.00 3.96
165 166 1.118838 CATGGAGGAGTGGAGGAGAC 58.881 60.000 0.00 0.00 0.00 3.36
274 282 5.353956 TCCATCTAACAAATTGACACATCGG 59.646 40.000 0.00 0.00 0.00 4.18
602 826 4.580580 AGAATCTGGCGTTGAGTTCTTTTT 59.419 37.500 0.00 0.00 0.00 1.94
663 887 0.625849 ACCCGGGATTCTGCAGAATT 59.374 50.000 35.91 22.79 44.14 2.17
726 950 2.887337 TCGTCCGAGTATACGTACACA 58.113 47.619 6.78 0.00 39.99 3.72
727 951 3.246226 ACATCGTCCGAGTATACGTACAC 59.754 47.826 0.00 0.00 39.99 2.90
814 1042 0.172578 TAATCACTGAGCGTCCACCG 59.827 55.000 0.00 0.00 40.40 4.94
849 1273 1.707427 GGGGAAGGTGATGGCTATGAT 59.293 52.381 0.00 0.00 0.00 2.45
919 3134 2.514824 GGCGATGGACTCCTTGCC 60.515 66.667 9.22 9.22 35.04 4.52
927 3142 2.586357 GCGGAGAAGGCGATGGAC 60.586 66.667 0.00 0.00 0.00 4.02
935 3150 1.671901 GAGAGGTGAGGCGGAGAAGG 61.672 65.000 0.00 0.00 0.00 3.46
957 3172 1.363145 CTGCTCTGCTCTGCTTGCTC 61.363 60.000 0.00 0.00 0.00 4.26
981 3196 2.583520 CCCTGCTCTGCCTGTCTC 59.416 66.667 0.00 0.00 0.00 3.36
984 3199 2.285969 ATCCCCTGCTCTGCCTGT 60.286 61.111 0.00 0.00 0.00 4.00
1154 4919 5.042065 AGGGAAGAAATTAGTAGTAGGGGGA 60.042 44.000 0.00 0.00 0.00 4.81
1186 4992 2.226200 TGATGCTCCATGAAAACACACG 59.774 45.455 0.00 0.00 0.00 4.49
1193 4999 4.025040 ACTTGAGTGATGCTCCATGAAA 57.975 40.909 0.00 0.00 43.48 2.69
1196 5002 2.871022 GCTACTTGAGTGATGCTCCATG 59.129 50.000 0.00 0.00 43.48 3.66
1197 5003 2.502947 TGCTACTTGAGTGATGCTCCAT 59.497 45.455 0.00 0.00 43.48 3.41
1198 5004 1.901833 TGCTACTTGAGTGATGCTCCA 59.098 47.619 0.00 0.00 43.48 3.86
1199 5005 2.680312 TGCTACTTGAGTGATGCTCC 57.320 50.000 0.00 0.00 43.48 4.70
1200 5006 2.871022 CCATGCTACTTGAGTGATGCTC 59.129 50.000 0.00 0.00 44.36 4.26
1201 5007 2.915349 CCATGCTACTTGAGTGATGCT 58.085 47.619 0.00 0.00 0.00 3.79
1202 5008 1.332997 GCCATGCTACTTGAGTGATGC 59.667 52.381 0.00 0.00 0.00 3.91
1203 5009 2.871022 GAGCCATGCTACTTGAGTGATG 59.129 50.000 0.00 0.00 39.88 3.07
1204 5010 2.482664 CGAGCCATGCTACTTGAGTGAT 60.483 50.000 0.00 0.00 39.88 3.06
1205 5011 1.134995 CGAGCCATGCTACTTGAGTGA 60.135 52.381 0.00 0.00 39.88 3.41
1206 5012 1.284657 CGAGCCATGCTACTTGAGTG 58.715 55.000 0.00 0.00 39.88 3.51
1207 5013 0.898320 ACGAGCCATGCTACTTGAGT 59.102 50.000 0.00 0.00 39.88 3.41
1208 5014 1.284657 CACGAGCCATGCTACTTGAG 58.715 55.000 0.00 0.00 39.88 3.02
1209 5015 0.608130 ACACGAGCCATGCTACTTGA 59.392 50.000 0.00 0.00 39.88 3.02
1210 5016 0.723414 CACACGAGCCATGCTACTTG 59.277 55.000 0.00 0.00 39.88 3.16
1211 5017 0.321671 ACACACGAGCCATGCTACTT 59.678 50.000 0.00 0.00 39.88 2.24
1212 5018 0.321671 AACACACGAGCCATGCTACT 59.678 50.000 0.00 0.00 39.88 2.57
1213 5019 1.156736 AAACACACGAGCCATGCTAC 58.843 50.000 0.00 0.00 39.88 3.58
1214 5020 1.804151 GAAAACACACGAGCCATGCTA 59.196 47.619 0.00 0.00 39.88 3.49
1215 5021 0.593128 GAAAACACACGAGCCATGCT 59.407 50.000 0.00 0.00 43.88 3.79
1216 5022 0.593128 AGAAAACACACGAGCCATGC 59.407 50.000 0.00 0.00 0.00 4.06
1217 5023 2.653890 CAAGAAAACACACGAGCCATG 58.346 47.619 0.00 0.00 0.00 3.66
1218 5024 1.001378 GCAAGAAAACACACGAGCCAT 60.001 47.619 0.00 0.00 0.00 4.40
1219 5025 0.380378 GCAAGAAAACACACGAGCCA 59.620 50.000 0.00 0.00 0.00 4.75
1220 5026 0.380378 TGCAAGAAAACACACGAGCC 59.620 50.000 0.00 0.00 0.00 4.70
1221 5027 2.187351 TTGCAAGAAAACACACGAGC 57.813 45.000 0.00 0.00 0.00 5.03
1222 5028 4.797868 TGAATTTGCAAGAAAACACACGAG 59.202 37.500 0.00 0.00 0.00 4.18
1323 5580 1.526575 AACCGCCAATGCCAAGACAG 61.527 55.000 0.00 0.00 0.00 3.51
1334 5591 2.179764 GCTAATGCTGAACCGCCAA 58.820 52.632 0.00 0.00 36.03 4.52
1430 5971 4.963318 TGTCTCTGCTATATTCCCCAAG 57.037 45.455 0.00 0.00 0.00 3.61
1441 5983 2.832129 CCCAACCTACTTGTCTCTGCTA 59.168 50.000 0.00 0.00 0.00 3.49
1444 5986 2.632996 TCACCCAACCTACTTGTCTCTG 59.367 50.000 0.00 0.00 0.00 3.35
1455 5997 3.157087 CTGTGCTAAATTCACCCAACCT 58.843 45.455 0.00 0.00 33.71 3.50
1656 6379 5.529060 GCAGATAAAAGAGTAATCACCAGGG 59.471 44.000 0.00 0.00 0.00 4.45
1709 6432 3.451141 TTTGCTTTTTCAATGCCGAGT 57.549 38.095 0.00 0.00 0.00 4.18
1734 6459 7.032580 CAGTCACAGATGAGTTAGTTTCCTAG 58.967 42.308 0.00 0.00 36.27 3.02
1754 6482 2.544686 GCATTTTTGTGCATTGCAGTCA 59.455 40.909 12.53 4.60 44.43 3.41
1802 6549 8.338493 TCCCCGTAGTTGAGGTATCAATATATA 58.662 37.037 0.00 0.00 46.75 0.86
1803 6550 7.123847 GTCCCCGTAGTTGAGGTATCAATATAT 59.876 40.741 0.00 0.00 46.75 0.86
1804 6551 6.435277 GTCCCCGTAGTTGAGGTATCAATATA 59.565 42.308 0.00 0.00 46.75 0.86
1805 6552 5.245526 GTCCCCGTAGTTGAGGTATCAATAT 59.754 44.000 0.00 0.00 46.75 1.28
1846 6593 1.031235 CAGCAACCACATCACACCAA 58.969 50.000 0.00 0.00 0.00 3.67
1847 6594 0.822944 CCAGCAACCACATCACACCA 60.823 55.000 0.00 0.00 0.00 4.17
1848 6595 0.537143 TCCAGCAACCACATCACACC 60.537 55.000 0.00 0.00 0.00 4.16
1849 6596 1.317613 TTCCAGCAACCACATCACAC 58.682 50.000 0.00 0.00 0.00 3.82
1851 6598 3.665745 AATTTCCAGCAACCACATCAC 57.334 42.857 0.00 0.00 0.00 3.06
1859 6662 5.127682 ACCCAGATGATAAATTTCCAGCAAC 59.872 40.000 10.16 0.00 0.00 4.17
1868 8185 9.872684 ACAGATGATAAACCCAGATGATAAATT 57.127 29.630 0.00 0.00 0.00 1.82
1876 8193 6.351286 GGCAAAAACAGATGATAAACCCAGAT 60.351 38.462 0.00 0.00 0.00 2.90
1877 8194 5.047377 GGCAAAAACAGATGATAAACCCAGA 60.047 40.000 0.00 0.00 0.00 3.86
1878 8195 5.170748 GGCAAAAACAGATGATAAACCCAG 58.829 41.667 0.00 0.00 0.00 4.45
1879 8196 4.590647 TGGCAAAAACAGATGATAAACCCA 59.409 37.500 0.00 0.00 0.00 4.51
1880 8197 4.929211 GTGGCAAAAACAGATGATAAACCC 59.071 41.667 0.00 0.00 0.00 4.11
1881 8198 5.537188 TGTGGCAAAAACAGATGATAAACC 58.463 37.500 0.00 0.00 0.00 3.27
1882 8199 7.307337 CCTTTGTGGCAAAAACAGATGATAAAC 60.307 37.037 0.00 0.00 0.00 2.01
1884 8201 6.222389 CCTTTGTGGCAAAAACAGATGATAA 58.778 36.000 0.00 0.00 0.00 1.75
1885 8202 5.279406 CCCTTTGTGGCAAAAACAGATGATA 60.279 40.000 0.00 0.00 0.00 2.15
1886 8203 4.503643 CCCTTTGTGGCAAAAACAGATGAT 60.504 41.667 0.00 0.00 0.00 2.45
1888 8205 3.132925 CCCTTTGTGGCAAAAACAGATG 58.867 45.455 0.00 0.00 0.00 2.90
1889 8206 2.771372 ACCCTTTGTGGCAAAAACAGAT 59.229 40.909 0.00 0.00 0.00 2.90
1891 8208 2.689553 ACCCTTTGTGGCAAAAACAG 57.310 45.000 0.00 0.00 0.00 3.16
1892 8209 3.425162 AAACCCTTTGTGGCAAAAACA 57.575 38.095 0.00 0.00 0.00 2.83
1893 8210 5.119694 TGATAAACCCTTTGTGGCAAAAAC 58.880 37.500 0.00 0.00 0.00 2.43
1902 8257 5.888161 CCTTAGCAGATGATAAACCCTTTGT 59.112 40.000 0.00 0.00 0.00 2.83
1915 8586 1.741706 CAGCAACCACCTTAGCAGATG 59.258 52.381 0.00 0.00 0.00 2.90
1921 8592 3.056607 CCAATTTCCAGCAACCACCTTAG 60.057 47.826 0.00 0.00 0.00 2.18
1935 8606 7.710907 GGAAAGATTAATTACCAGCCAATTTCC 59.289 37.037 0.00 0.00 35.50 3.13
2022 8693 2.045340 CCGGCCCGAAAACATCCT 60.045 61.111 3.71 0.00 0.00 3.24
2032 8703 2.110420 GGAACTAATCCCGGCCCG 59.890 66.667 0.00 0.00 43.00 6.13
2145 8817 8.160106 TGGGTTAAATGAAAAACATATGGCTTT 58.840 29.630 7.80 5.87 38.38 3.51
2496 9919 6.073447 ACCCAGTCAACCATAACAATGATA 57.927 37.500 0.00 0.00 0.00 2.15
2725 12016 4.881273 ACTGTGCTTGTGAGATGTAACAAA 59.119 37.500 0.00 0.00 35.95 2.83
2784 12099 5.187772 TGCTAGCTCAAGATTCCAAGAACTA 59.812 40.000 17.23 0.00 0.00 2.24
2968 12289 2.654877 GCCAGGACGACCGAAAGA 59.345 61.111 0.00 0.00 41.83 2.52
3073 12394 2.240500 GCCTGACGTGATGGCGATC 61.241 63.158 1.08 1.08 37.11 3.69
3080 12401 3.055819 ACTGACAATTAGCCTGACGTGAT 60.056 43.478 0.00 0.00 0.00 3.06
3123 12444 0.608035 TCCCGAGCACATTTCAACCC 60.608 55.000 0.00 0.00 0.00 4.11
3612 13563 3.821033 GACCAAGCAGTAATTCACCAACT 59.179 43.478 0.00 0.00 0.00 3.16
3627 13586 0.948678 TAACGTTTGCTGGACCAAGC 59.051 50.000 5.91 2.20 43.82 4.01
3831 13792 7.961351 TGAAATATTGTTTGGAACACCAGAAT 58.039 30.769 0.00 0.00 41.97 2.40
3883 13847 6.790232 ACTCCAATTTCTCCTTTTTGAACA 57.210 33.333 0.00 0.00 0.00 3.18
4006 13978 2.063015 ATCCGTGAACACTTGGGCCA 62.063 55.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.