Multiple sequence alignment - TraesCS2D01G579300

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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 TraesCS2D01G579300 chr2D 100.000 5274 0 0 1 5274 641952401 641947128 0.000000e+00 9740.0
1 TraesCS2D01G579300 chr2D 96.877 1633 45 4 1 1628 597898519 597896888 0.000000e+00 2728.0
2 TraesCS2D01G579300 chr2D 96.978 1059 22 7 1625 2678 597896858 597895805 0.000000e+00 1770.0
3 TraesCS2D01G579300 chr2D 96.900 871 16 2 3537 4396 597894888 597894018 0.000000e+00 1448.0
4 TraesCS2D01G579300 chr2D 97.150 421 6 1 3183 3603 597895271 597894857 0.000000e+00 706.0
5 TraesCS2D01G579300 chr2D 97.458 354 5 1 4395 4748 597893913 597893564 7.560000e-168 601.0
6 TraesCS2D01G579300 chr2D 86.497 511 41 15 4782 5274 597893564 597893064 2.160000e-148 536.0
7 TraesCS2D01G579300 chr2D 90.418 407 32 4 804 1204 641609372 641609777 3.620000e-146 529.0
8 TraesCS2D01G579300 chr2D 98.653 297 2 1 2772 3066 597895768 597895472 4.680000e-145 525.0
9 TraesCS2D01G579300 chr2D 78.922 816 128 17 3537 4321 641880842 641880040 1.010000e-141 514.0
10 TraesCS2D01G579300 chr2D 88.824 340 33 3 804 1142 598020000 598020335 3.800000e-111 412.0
11 TraesCS2D01G579300 chr2D 88.358 335 34 3 804 1137 598048191 598048521 1.060000e-106 398.0
12 TraesCS2D01G579300 chr2D 95.021 241 6 4 1210 1444 641609816 641610056 1.790000e-99 374.0
13 TraesCS2D01G579300 chr2D 82.234 394 50 13 2258 2644 641881642 641881262 6.590000e-84 322.0
14 TraesCS2D01G579300 chr2D 83.838 297 32 8 4388 4678 641880001 641879715 8.710000e-68 268.0
15 TraesCS2D01G579300 chr2D 93.220 118 7 1 4668 4785 641879694 641879578 7.020000e-39 172.0
16 TraesCS2D01G579300 chr2D 89.744 117 7 2 1476 1587 641610295 641610411 1.530000e-30 145.0
17 TraesCS2D01G579300 chr2D 93.651 63 2 1 2710 2772 597895808 597895748 5.620000e-15 93.5
18 TraesCS2D01G579300 chr2B 90.167 1139 102 8 1 1136 799958264 799959395 0.000000e+00 1474.0
19 TraesCS2D01G579300 chr2B 95.511 891 25 3 3537 4412 799971119 799972009 0.000000e+00 1410.0
20 TraesCS2D01G579300 chr2B 89.479 979 57 18 1681 2649 799968981 799969923 0.000000e+00 1195.0
21 TraesCS2D01G579300 chr2B 98.228 395 6 1 3210 3603 799970756 799971150 0.000000e+00 689.0
22 TraesCS2D01G579300 chr2B 98.371 307 3 1 2795 3099 799969926 799970232 6.010000e-149 538.0
23 TraesCS2D01G579300 chr2B 84.518 394 51 6 2258 2644 799289217 799289607 1.070000e-101 381.0
24 TraesCS2D01G579300 chr2B 93.750 224 9 3 1227 1450 799968306 799968524 1.090000e-86 331.0
25 TraesCS2D01G579300 chr2B 88.806 268 22 5 4411 4678 799972059 799972318 6.590000e-84 322.0
26 TraesCS2D01G579300 chr2B 78.220 528 65 26 4791 5272 190056557 190057080 5.170000e-75 292.0
27 TraesCS2D01G579300 chr2B 93.220 118 7 1 4668 4785 799972339 799972455 7.020000e-39 172.0
28 TraesCS2D01G579300 chr2B 88.785 107 7 2 1483 1587 799968768 799968871 5.540000e-25 126.0
29 TraesCS2D01G579300 chr6D 90.319 816 73 6 1 811 161339114 161338300 0.000000e+00 1064.0
30 TraesCS2D01G579300 chr6D 89.621 819 74 11 1 811 111980681 111981496 0.000000e+00 1031.0
31 TraesCS2D01G579300 chr6D 83.080 526 45 18 4791 5272 94321564 94321039 6.270000e-119 438.0
32 TraesCS2D01G579300 chr4D 90.049 814 73 7 1 810 473729026 473728217 0.000000e+00 1048.0
33 TraesCS2D01G579300 chr3D 90.172 814 67 12 6 811 365616771 365617579 0.000000e+00 1048.0
34 TraesCS2D01G579300 chr3D 82.766 499 45 20 4793 5272 56545195 56545671 1.770000e-109 407.0
35 TraesCS2D01G579300 chr3D 79.967 604 36 30 2659 3237 336538817 336538274 3.000000e-97 366.0
36 TraesCS2D01G579300 chr3D 80.851 517 54 25 4792 5272 548820056 548820563 1.080000e-96 364.0
37 TraesCS2D01G579300 chr3D 82.759 319 40 13 4963 5272 63347550 63347238 2.420000e-68 270.0
38 TraesCS2D01G579300 chr5D 90.136 811 71 9 6 811 34224463 34225269 0.000000e+00 1046.0
39 TraesCS2D01G579300 chr5D 78.150 508 83 20 4789 5272 404490775 404491278 1.110000e-76 298.0
40 TraesCS2D01G579300 chr5D 81.481 324 42 8 4963 5270 372065944 372065623 3.150000e-62 250.0
41 TraesCS2D01G579300 chr7D 89.816 815 76 6 1 811 476983430 476982619 0.000000e+00 1038.0
42 TraesCS2D01G579300 chr7D 89.706 816 77 6 1 811 253219968 253220781 0.000000e+00 1035.0
43 TraesCS2D01G579300 chr2A 79.778 811 132 12 3542 4321 766847785 766846976 1.280000e-155 560.0
44 TraesCS2D01G579300 chr2A 87.805 410 43 4 804 1207 766712280 766712688 1.720000e-129 473.0
45 TraesCS2D01G579300 chr2A 78.601 486 71 20 2185 2644 766848688 766848210 1.860000e-74 291.0
46 TraesCS2D01G579300 chr2A 84.848 297 29 8 4388 4678 766846937 766846651 8.640000e-73 285.0
47 TraesCS2D01G579300 chr2A 81.988 322 36 10 4791 5094 778762577 778762894 2.440000e-63 254.0
48 TraesCS2D01G579300 chr2A 90.761 184 17 0 5089 5272 751551632 751551449 4.080000e-61 246.0
49 TraesCS2D01G579300 chr2A 94.118 119 7 0 4667 4785 766846631 766846513 1.170000e-41 182.0
50 TraesCS2D01G579300 chr2A 92.105 114 7 1 1476 1587 766712925 766713038 5.470000e-35 159.0
51 TraesCS2D01G579300 chr2A 92.793 111 4 2 1210 1320 766712724 766712830 1.970000e-34 158.0
52 TraesCS2D01G579300 chr3B 82.043 607 43 19 2659 3237 434404706 434404138 1.730000e-124 457.0
53 TraesCS2D01G579300 chr3B 78.352 522 63 26 4791 5268 33335480 33334965 5.170000e-75 292.0
54 TraesCS2D01G579300 chr3B 78.979 333 32 15 4968 5274 79784457 79784137 5.390000e-45 193.0
55 TraesCS2D01G579300 chr3A 80.629 604 33 30 2659 3237 453820271 453819727 1.780000e-104 390.0
56 TraesCS2D01G579300 chr3A 79.887 532 52 27 4791 5268 628309264 628308734 6.540000e-89 339.0
57 TraesCS2D01G579300 chr1D 81.431 517 59 16 4789 5272 204802105 204801593 6.400000e-104 388.0
58 TraesCS2D01G579300 chr1D 81.595 326 43 12 4965 5274 363858101 363858425 2.440000e-63 254.0
59 TraesCS2D01G579300 chr1D 84.170 259 23 14 5022 5274 463986456 463986210 8.830000e-58 235.0
60 TraesCS2D01G579300 chr5B 80.784 536 46 30 4789 5272 450455886 450456416 3.000000e-97 366.0
61 TraesCS2D01G579300 chr4B 82.209 326 41 8 4965 5274 158282343 158282667 1.130000e-66 265.0
62 TraesCS2D01G579300 chrUn 76.758 512 81 18 4791 5272 7155291 7155794 8.770000e-63 252.0
63 TraesCS2D01G579300 chrUn 85.034 147 18 4 5130 5274 146937088 146936944 4.260000e-31 147.0
64 TraesCS2D01G579300 chr7B 89.947 189 19 0 5086 5274 687818785 687818973 1.470000e-60 244.0
65 TraesCS2D01G579300 chr7B 89.947 189 19 0 5086 5274 687854477 687854665 1.470000e-60 244.0
66 TraesCS2D01G579300 chr6B 81.090 312 48 9 4968 5274 699886118 699885813 6.830000e-59 239.0
67 TraesCS2D01G579300 chr6B 87.209 172 18 3 4791 4961 142210471 142210639 5.390000e-45 193.0


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 TraesCS2D01G579300 chr2D 641947128 641952401 5273 True 9740.000000 9740 100.000000 1 5274 1 chr2D.!!$R1 5273
1 TraesCS2D01G579300 chr2D 597893064 597898519 5455 True 1050.937500 2728 95.520500 1 5274 8 chr2D.!!$R2 5273
2 TraesCS2D01G579300 chr2D 641609372 641610411 1039 False 349.333333 529 91.727667 804 1587 3 chr2D.!!$F3 783
3 TraesCS2D01G579300 chr2D 641879578 641881642 2064 True 319.000000 514 84.553500 2258 4785 4 chr2D.!!$R3 2527
4 TraesCS2D01G579300 chr2B 799958264 799959395 1131 False 1474.000000 1474 90.167000 1 1136 1 chr2B.!!$F3 1135
5 TraesCS2D01G579300 chr2B 799968306 799972455 4149 False 597.875000 1410 93.268750 1227 4785 8 chr2B.!!$F4 3558
6 TraesCS2D01G579300 chr2B 190056557 190057080 523 False 292.000000 292 78.220000 4791 5272 1 chr2B.!!$F1 481
7 TraesCS2D01G579300 chr6D 161338300 161339114 814 True 1064.000000 1064 90.319000 1 811 1 chr6D.!!$R2 810
8 TraesCS2D01G579300 chr6D 111980681 111981496 815 False 1031.000000 1031 89.621000 1 811 1 chr6D.!!$F1 810
9 TraesCS2D01G579300 chr6D 94321039 94321564 525 True 438.000000 438 83.080000 4791 5272 1 chr6D.!!$R1 481
10 TraesCS2D01G579300 chr4D 473728217 473729026 809 True 1048.000000 1048 90.049000 1 810 1 chr4D.!!$R1 809
11 TraesCS2D01G579300 chr3D 365616771 365617579 808 False 1048.000000 1048 90.172000 6 811 1 chr3D.!!$F2 805
12 TraesCS2D01G579300 chr3D 336538274 336538817 543 True 366.000000 366 79.967000 2659 3237 1 chr3D.!!$R2 578
13 TraesCS2D01G579300 chr3D 548820056 548820563 507 False 364.000000 364 80.851000 4792 5272 1 chr3D.!!$F3 480
14 TraesCS2D01G579300 chr5D 34224463 34225269 806 False 1046.000000 1046 90.136000 6 811 1 chr5D.!!$F1 805
15 TraesCS2D01G579300 chr5D 404490775 404491278 503 False 298.000000 298 78.150000 4789 5272 1 chr5D.!!$F2 483
16 TraesCS2D01G579300 chr7D 476982619 476983430 811 True 1038.000000 1038 89.816000 1 811 1 chr7D.!!$R1 810
17 TraesCS2D01G579300 chr7D 253219968 253220781 813 False 1035.000000 1035 89.706000 1 811 1 chr7D.!!$F1 810
18 TraesCS2D01G579300 chr2A 766846513 766848688 2175 True 329.500000 560 84.336250 2185 4785 4 chr2A.!!$R2 2600
19 TraesCS2D01G579300 chr2A 766712280 766713038 758 False 263.333333 473 90.901000 804 1587 3 chr2A.!!$F2 783
20 TraesCS2D01G579300 chr3B 434404138 434404706 568 True 457.000000 457 82.043000 2659 3237 1 chr3B.!!$R3 578
21 TraesCS2D01G579300 chr3B 33334965 33335480 515 True 292.000000 292 78.352000 4791 5268 1 chr3B.!!$R1 477
22 TraesCS2D01G579300 chr3A 453819727 453820271 544 True 390.000000 390 80.629000 2659 3237 1 chr3A.!!$R1 578
23 TraesCS2D01G579300 chr3A 628308734 628309264 530 True 339.000000 339 79.887000 4791 5268 1 chr3A.!!$R2 477
24 TraesCS2D01G579300 chr1D 204801593 204802105 512 True 388.000000 388 81.431000 4789 5272 1 chr1D.!!$R1 483
25 TraesCS2D01G579300 chr5B 450455886 450456416 530 False 366.000000 366 80.784000 4789 5272 1 chr5B.!!$F1 483
26 TraesCS2D01G579300 chrUn 7155291 7155794 503 False 252.000000 252 76.758000 4791 5272 1 chrUn.!!$F1 481

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
200 204 0.611618 AATGGAGTCCAAATGCGGCA 60.612 50.000 17.71 4.58 36.95 5.69 F
879 896 2.202557 CGGTGCATGCTCGTCGTA 60.203 61.111 20.33 0.00 0.00 3.43 F
2113 2442 0.465097 CAATGAAGGAGGCAGCGGAT 60.465 55.000 0.00 0.00 0.00 4.18 F
2385 2721 2.043852 GTGAGGGAGGCCGAGAGA 60.044 66.667 0.00 0.00 0.00 3.10 F
3176 3565 2.931512 ACACGGTTCAACAAAACAGG 57.068 45.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1169 1190 0.872021 CGCGTCAGTGATAAGCCTCC 60.872 60.0 0.00 0.0 0.0 4.30 R
2385 2721 0.105555 CCCTCTGCCTCTCCATCTCT 60.106 60.0 0.00 0.0 0.0 3.10 R
3301 4082 0.178068 GGATACCGGATGTGCAGTGT 59.822 55.0 9.46 0.0 0.0 3.55 R
4121 4977 0.741221 GGGAAGTGGACACGATCAGC 60.741 60.0 11.47 0.0 36.2 4.26 R
5118 6280 0.172803 GATCTCGGCGTTGTACCAGT 59.827 55.0 6.85 0.0 0.0 4.00 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
200 204 0.611618 AATGGAGTCCAAATGCGGCA 60.612 50.000 17.71 4.58 36.95 5.69
657 669 5.750524 TGGGATCCGATGAATTTTGAGTTA 58.249 37.500 5.45 0.00 0.00 2.24
815 831 5.712152 AGAGGTGTTTTGTGATGGAAATC 57.288 39.130 0.00 0.00 0.00 2.17
858 875 2.927477 GTTGTCGTTGGAATCATCGCTA 59.073 45.455 0.00 0.00 36.39 4.26
863 880 2.216488 CGTTGGAATCATCGCTAGTTCG 59.784 50.000 0.00 0.00 30.78 3.95
879 896 2.202557 CGGTGCATGCTCGTCGTA 60.203 61.111 20.33 0.00 0.00 3.43
1071 1092 7.805071 GCACTGATGGTATATTTTGACATTAGC 59.195 37.037 0.00 0.00 30.89 3.09
1122 1143 6.357367 GGTTGAGGAGGACAATAACACATAT 58.643 40.000 0.00 0.00 0.00 1.78
1169 1190 0.600255 ACCGTCTTGAAAGTCCTGCG 60.600 55.000 0.00 0.00 0.00 5.18
1450 1510 5.106475 ACGAGTGTAGAAGAGAAGACATGTC 60.106 44.000 18.47 18.47 0.00 3.06
1675 2004 1.644372 CGGAGACAGAGATCGACGG 59.356 63.158 0.00 0.00 0.00 4.79
1772 2101 1.883732 CGGAGAGAGCGGAAAGACA 59.116 57.895 0.00 0.00 0.00 3.41
1918 2247 2.196749 CAGCAGCAGGTATACTTGACG 58.803 52.381 18.42 9.03 0.00 4.35
2113 2442 0.465097 CAATGAAGGAGGCAGCGGAT 60.465 55.000 0.00 0.00 0.00 4.18
2194 2523 5.293319 AGTTGGATGAAGAGATGGAGATG 57.707 43.478 0.00 0.00 0.00 2.90
2212 2541 4.629122 AGATGGGAAGGAAGATGAAGAGA 58.371 43.478 0.00 0.00 0.00 3.10
2213 2546 5.226015 AGATGGGAAGGAAGATGAAGAGAT 58.774 41.667 0.00 0.00 0.00 2.75
2217 2550 3.713764 GGAAGGAAGATGAAGAGATGGGA 59.286 47.826 0.00 0.00 0.00 4.37
2219 2552 5.367302 GAAGGAAGATGAAGAGATGGGAAG 58.633 45.833 0.00 0.00 0.00 3.46
2275 2611 3.762407 TTCTGTCCCACGAATTCTTGA 57.238 42.857 13.20 0.00 0.00 3.02
2339 2675 2.591923 TGAGTTGGCCATGCTGTTTAA 58.408 42.857 6.09 0.00 0.00 1.52
2372 2708 2.176798 AGGAGGAGTATGAGAGGGTGAG 59.823 54.545 0.00 0.00 0.00 3.51
2379 2715 2.766229 GAGAGGGTGAGGGAGGCC 60.766 72.222 0.00 0.00 0.00 5.19
2385 2721 2.043852 GTGAGGGAGGCCGAGAGA 60.044 66.667 0.00 0.00 0.00 3.10
2452 2806 3.119919 GGAGAAGAACAAGCAGCAGATTG 60.120 47.826 5.47 5.47 46.22 2.67
2531 2885 3.548770 TCAAAGAGTGGATGGATGATGC 58.451 45.455 0.00 0.00 0.00 3.91
2772 3126 6.726490 TGTCCTATTATTCACCAGTACCTC 57.274 41.667 0.00 0.00 0.00 3.85
2773 3127 5.601313 TGTCCTATTATTCACCAGTACCTCC 59.399 44.000 0.00 0.00 0.00 4.30
2774 3128 5.839606 GTCCTATTATTCACCAGTACCTCCT 59.160 44.000 0.00 0.00 0.00 3.69
2775 3129 7.008941 GTCCTATTATTCACCAGTACCTCCTA 58.991 42.308 0.00 0.00 0.00 2.94
2776 3130 7.674772 GTCCTATTATTCACCAGTACCTCCTAT 59.325 40.741 0.00 0.00 0.00 2.57
2777 3131 8.239478 TCCTATTATTCACCAGTACCTCCTATT 58.761 37.037 0.00 0.00 0.00 1.73
2778 3132 9.543231 CCTATTATTCACCAGTACCTCCTATTA 57.457 37.037 0.00 0.00 0.00 0.98
2782 3136 7.931015 ATTCACCAGTACCTCCTATTATTCA 57.069 36.000 0.00 0.00 0.00 2.57
2783 3137 6.726490 TCACCAGTACCTCCTATTATTCAC 57.274 41.667 0.00 0.00 0.00 3.18
2784 3138 5.601313 TCACCAGTACCTCCTATTATTCACC 59.399 44.000 0.00 0.00 0.00 4.02
2785 3139 5.365605 CACCAGTACCTCCTATTATTCACCA 59.634 44.000 0.00 0.00 0.00 4.17
2786 3140 5.602978 ACCAGTACCTCCTATTATTCACCAG 59.397 44.000 0.00 0.00 0.00 4.00
2787 3141 5.602978 CCAGTACCTCCTATTATTCACCAGT 59.397 44.000 0.00 0.00 0.00 4.00
2788 3142 6.781014 CCAGTACCTCCTATTATTCACCAGTA 59.219 42.308 0.00 0.00 0.00 2.74
2789 3143 7.255871 CCAGTACCTCCTATTATTCACCAGTAC 60.256 44.444 0.00 0.00 0.00 2.73
2790 3144 6.781507 AGTACCTCCTATTATTCACCAGTACC 59.218 42.308 0.00 0.00 0.00 3.34
2791 3145 5.789535 ACCTCCTATTATTCACCAGTACCT 58.210 41.667 0.00 0.00 0.00 3.08
3131 3520 7.540474 TGTGGTATAAGGACTGAGGAATATC 57.460 40.000 0.00 0.00 0.00 1.63
3143 3532 5.132648 ACTGAGGAATATCTGGGTAAATGCA 59.867 40.000 0.00 0.00 0.00 3.96
3144 3533 6.012337 TGAGGAATATCTGGGTAAATGCAA 57.988 37.500 0.00 0.00 0.00 4.08
3176 3565 2.931512 ACACGGTTCAACAAAACAGG 57.068 45.000 0.00 0.00 0.00 4.00
3185 3574 3.287222 TCAACAAAACAGGGGAGAAGTG 58.713 45.455 0.00 0.00 0.00 3.16
3301 4082 6.816640 CGACATTAAGTCCTCTCCAATTTACA 59.183 38.462 0.00 0.00 44.66 2.41
3311 4092 4.397420 TCTCCAATTTACACACTGCACAT 58.603 39.130 0.00 0.00 0.00 3.21
3568 4352 9.635520 TGTCCTCTTCTTCTTTTAAGTAATACG 57.364 33.333 0.00 0.00 0.00 3.06
3589 4373 6.152932 ACGTACTTCTTTGTCCTCTGTTTA 57.847 37.500 0.00 0.00 0.00 2.01
3659 4494 3.291584 TGATCGCAGGACTCTTATCTGT 58.708 45.455 0.00 0.00 0.00 3.41
3835 4688 5.601313 ACCTTTACTCTTCGATAGCCCATTA 59.399 40.000 0.00 0.00 0.00 1.90
4121 4977 5.406780 GCCTATGTTGATTCTGGTTCTATCG 59.593 44.000 0.00 0.00 0.00 2.92
4204 5060 3.515901 GTGGTTCTGAGGTGGAGATTACT 59.484 47.826 0.00 0.00 0.00 2.24
4621 5674 1.352352 CTTGTGAAGGGTGTCCTCCAT 59.648 52.381 0.00 0.00 44.07 3.41
4766 5849 6.981762 CAGATAGATTCTGCAACTGAAGTT 57.018 37.500 0.00 0.00 45.16 2.66
4767 5850 6.773080 CAGATAGATTCTGCAACTGAAGTTG 58.227 40.000 17.07 17.07 45.16 3.16
4768 5851 6.370994 CAGATAGATTCTGCAACTGAAGTTGT 59.629 38.462 21.03 4.37 45.16 3.32
4769 5852 7.547019 CAGATAGATTCTGCAACTGAAGTTGTA 59.453 37.037 21.03 16.85 45.16 2.41
4878 5965 2.590291 TTTTCACGCGCTCCAGCA 60.590 55.556 5.73 0.00 42.21 4.41
4938 6030 1.375326 GGGGAGAAAGCTGTCGGTT 59.625 57.895 0.00 0.00 0.00 4.44
4940 6032 0.250338 GGGAGAAAGCTGTCGGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
5053 6189 0.949105 GCTTTCTCGCCGTTTCCTCA 60.949 55.000 0.00 0.00 0.00 3.86
5126 6290 2.745037 GCCCCAACGACTGGTACA 59.255 61.111 7.39 0.00 44.76 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 177 5.066375 CGCATTTGGACTCCATTTGATAAGA 59.934 40.000 0.00 0.00 31.53 2.10
313 323 2.917897 GCCCCACAACCCATCAGGA 61.918 63.158 0.00 0.00 39.89 3.86
683 696 8.961294 ATAAGAGATCAAAGAAGACTCCAATG 57.039 34.615 0.00 0.00 0.00 2.82
742 757 7.826690 GTTGGCCTAACTAAATCAAAGATTCA 58.173 34.615 3.32 0.00 36.34 2.57
815 831 0.824109 TAGGTCGGCTCTCAATGTGG 59.176 55.000 0.00 0.00 0.00 4.17
845 862 1.754803 ACCGAACTAGCGATGATTCCA 59.245 47.619 0.00 0.00 0.00 3.53
858 875 1.738099 GACGAGCATGCACCGAACT 60.738 57.895 30.11 14.32 0.00 3.01
863 880 0.094730 GTTTACGACGAGCATGCACC 59.905 55.000 21.98 10.27 0.00 5.01
1071 1092 2.932614 GAGGTCGATTGTTCATCACAGG 59.067 50.000 0.00 0.00 36.48 4.00
1122 1143 6.112927 ACAGACCGGTTAAAATTAGGTACA 57.887 37.500 9.42 0.00 35.00 2.90
1169 1190 0.872021 CGCGTCAGTGATAAGCCTCC 60.872 60.000 0.00 0.00 0.00 4.30
1690 2019 4.521062 GACCCGCTGCTCATCGCT 62.521 66.667 0.00 0.00 40.11 4.93
1918 2247 1.201647 TCCAGAACATCGAAGTCGTCC 59.798 52.381 0.00 0.00 40.80 4.79
2099 2428 2.739996 CCTCATCCGCTGCCTCCTT 61.740 63.158 0.00 0.00 0.00 3.36
2113 2442 3.245911 CCATCATCCTATCCCTCTCCTCA 60.246 52.174 0.00 0.00 0.00 3.86
2194 2523 3.181446 CCCATCTCTTCATCTTCCTTCCC 60.181 52.174 0.00 0.00 0.00 3.97
2212 2541 4.050037 TCATTCCTCATCTTCCTTCCCAT 58.950 43.478 0.00 0.00 0.00 4.00
2213 2546 3.463825 TCATTCCTCATCTTCCTTCCCA 58.536 45.455 0.00 0.00 0.00 4.37
2217 2550 6.511017 TCATCATCATTCCTCATCTTCCTT 57.489 37.500 0.00 0.00 0.00 3.36
2219 2552 4.696402 GCTCATCATCATTCCTCATCTTCC 59.304 45.833 0.00 0.00 0.00 3.46
2275 2611 2.307098 CCAGGACATTGGAGGAGAGTTT 59.693 50.000 0.00 0.00 40.87 2.66
2339 2675 0.338120 CTCCTCCTCTTCCTCCACCT 59.662 60.000 0.00 0.00 0.00 4.00
2372 2708 1.152830 ATCTCTCTCTCGGCCTCCC 59.847 63.158 0.00 0.00 0.00 4.30
2379 2715 1.238439 GCCTCTCCATCTCTCTCTCG 58.762 60.000 0.00 0.00 0.00 4.04
2385 2721 0.105555 CCCTCTGCCTCTCCATCTCT 60.106 60.000 0.00 0.00 0.00 3.10
2452 2806 2.435059 GCGCTCCTCCTTCACCAC 60.435 66.667 0.00 0.00 0.00 4.16
2531 2885 1.072666 GCCTGCGAAAAATTCCAGCG 61.073 55.000 0.00 0.00 31.05 5.18
2736 3090 0.898326 TAGGACAGCGAGTGCCAGAA 60.898 55.000 0.59 0.00 44.31 3.02
2737 3091 0.684479 ATAGGACAGCGAGTGCCAGA 60.684 55.000 0.59 0.00 44.31 3.86
2785 3139 3.901844 ACCTTATGACACACACAGGTACT 59.098 43.478 0.00 0.00 41.22 2.73
2786 3140 3.994392 CACCTTATGACACACACAGGTAC 59.006 47.826 0.00 0.00 41.14 3.34
2787 3141 3.556213 GCACCTTATGACACACACAGGTA 60.556 47.826 0.00 0.00 41.14 3.08
2788 3142 2.810400 GCACCTTATGACACACACAGGT 60.810 50.000 0.00 0.00 42.77 4.00
2789 3143 1.806542 GCACCTTATGACACACACAGG 59.193 52.381 0.00 0.00 37.94 4.00
2790 3144 1.460743 CGCACCTTATGACACACACAG 59.539 52.381 0.00 0.00 0.00 3.66
2791 3145 1.507562 CGCACCTTATGACACACACA 58.492 50.000 0.00 0.00 0.00 3.72
2874 3236 4.160814 TGCCGCTTACTGGAATTTAGTAGA 59.839 41.667 0.00 0.00 32.67 2.59
3131 3520 5.415701 AGTGTGAATACTTGCATTTACCCAG 59.584 40.000 0.00 0.00 0.00 4.45
3143 3532 5.603596 TGAACCGTGTAAGTGTGAATACTT 58.396 37.500 0.00 0.00 43.03 2.24
3144 3533 5.204409 TGAACCGTGTAAGTGTGAATACT 57.796 39.130 0.00 0.00 0.00 2.12
3176 3565 2.501723 TCAAGCAGATACCACTTCTCCC 59.498 50.000 0.00 0.00 0.00 4.30
3185 3574 5.669477 ACAAAGAGATCTCAAGCAGATACC 58.331 41.667 24.39 0.00 42.48 2.73
3301 4082 0.178068 GGATACCGGATGTGCAGTGT 59.822 55.000 9.46 0.00 0.00 3.55
3311 4092 1.764854 GGGGCAGAAGGATACCGGA 60.765 63.158 9.46 0.00 37.17 5.14
3642 4477 1.135915 AGCACAGATAAGAGTCCTGCG 59.864 52.381 0.00 0.00 31.09 5.18
3659 4494 3.240134 GAGACGGGCCAGTCAAGCA 62.240 63.158 33.24 0.00 43.24 3.91
3835 4688 1.267121 ACCTCAACTCCGCAGTACAT 58.733 50.000 0.00 0.00 30.14 2.29
4121 4977 0.741221 GGGAAGTGGACACGATCAGC 60.741 60.000 11.47 0.00 36.20 4.26
4204 5060 3.140073 AACCCGGGACCATGCAACA 62.140 57.895 32.02 0.00 0.00 3.33
4621 5674 1.485124 AGCACACGATCTACCATCCA 58.515 50.000 0.00 0.00 0.00 3.41
4757 5840 8.753497 AAAGGAAATTCTCTACAACTTCAGTT 57.247 30.769 0.00 0.00 39.12 3.16
4758 5841 8.753497 AAAAGGAAATTCTCTACAACTTCAGT 57.247 30.769 0.00 0.00 0.00 3.41
4759 5842 8.840321 TGAAAAGGAAATTCTCTACAACTTCAG 58.160 33.333 0.00 0.00 0.00 3.02
4760 5843 8.621286 GTGAAAAGGAAATTCTCTACAACTTCA 58.379 33.333 0.00 0.00 0.00 3.02
4761 5844 8.621286 TGTGAAAAGGAAATTCTCTACAACTTC 58.379 33.333 0.00 0.00 0.00 3.01
4762 5845 8.519799 TGTGAAAAGGAAATTCTCTACAACTT 57.480 30.769 0.00 0.00 0.00 2.66
4763 5846 8.697507 ATGTGAAAAGGAAATTCTCTACAACT 57.302 30.769 0.00 0.00 0.00 3.16
4768 5851 9.167311 GCTCTTATGTGAAAAGGAAATTCTCTA 57.833 33.333 0.00 0.00 0.00 2.43
4769 5852 7.667219 TGCTCTTATGTGAAAAGGAAATTCTCT 59.333 33.333 0.00 0.00 0.00 3.10
4770 5853 7.820648 TGCTCTTATGTGAAAAGGAAATTCTC 58.179 34.615 0.00 0.00 0.00 2.87
4771 5854 7.765695 TGCTCTTATGTGAAAAGGAAATTCT 57.234 32.000 0.00 0.00 0.00 2.40
4772 5855 8.465201 AGATGCTCTTATGTGAAAAGGAAATTC 58.535 33.333 0.00 0.00 0.00 2.17
4773 5856 8.358582 AGATGCTCTTATGTGAAAAGGAAATT 57.641 30.769 0.00 0.00 0.00 1.82
4774 5857 7.067981 GGAGATGCTCTTATGTGAAAAGGAAAT 59.932 37.037 0.00 0.00 0.00 2.17
4775 5858 6.375455 GGAGATGCTCTTATGTGAAAAGGAAA 59.625 38.462 0.00 0.00 0.00 3.13
4776 5859 5.882557 GGAGATGCTCTTATGTGAAAAGGAA 59.117 40.000 0.00 0.00 0.00 3.36
4777 5860 5.045651 TGGAGATGCTCTTATGTGAAAAGGA 60.046 40.000 0.00 0.00 0.00 3.36
4778 5861 5.188434 TGGAGATGCTCTTATGTGAAAAGG 58.812 41.667 0.00 0.00 0.00 3.11
4779 5862 6.149973 TGTTGGAGATGCTCTTATGTGAAAAG 59.850 38.462 0.00 0.00 0.00 2.27
4780 5863 6.003326 TGTTGGAGATGCTCTTATGTGAAAA 58.997 36.000 0.00 0.00 0.00 2.29
4938 6030 1.006086 CGCGCCAAATCTATCACACA 58.994 50.000 0.00 0.00 0.00 3.72
4940 6032 1.436195 GGCGCGCCAAATCTATCACA 61.436 55.000 43.55 0.00 35.81 3.58
5104 6266 4.680237 CAGTCGTTGGGGCGCTCA 62.680 66.667 10.74 4.50 0.00 4.26
5118 6280 0.172803 GATCTCGGCGTTGTACCAGT 59.827 55.000 6.85 0.00 0.00 4.00
5237 6404 1.011968 TCACGAAAGTTCATCCGCGG 61.012 55.000 22.12 22.12 46.40 6.46


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

AutoCloner maintained by Alex Coulton.