Multiple sequence alignment - TraesCS2A01G043200

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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 TraesCS2A01G043200 chr2A 100.000 4612 0 0 1 4612 17248740 17253351 0.000000e+00 8517.0
1 TraesCS2A01G043200 chr2A 98.754 562 7 0 4051 4612 17276531 17277092 0.000000e+00 1000.0
2 TraesCS2A01G043200 chr2A 98.221 562 10 0 4051 4612 16925883 16926444 0.000000e+00 983.0
3 TraesCS2A01G043200 chr2A 97.865 562 12 0 4051 4612 17296196 17296757 0.000000e+00 972.0
4 TraesCS2A01G043200 chr2A 76.552 145 22 10 2472 2605 718261611 718261468 8.280000e-08 69.4
5 TraesCS2A01G043200 chr2A 97.059 34 1 0 4003 4036 430720341 430720308 1.790000e-04 58.4
6 TraesCS2A01G043200 chr2D 95.578 2058 77 7 96 2147 15192964 15195013 0.000000e+00 3284.0
7 TraesCS2A01G043200 chr2D 94.124 1736 84 14 2263 3993 15195468 15197190 0.000000e+00 2625.0
8 TraesCS2A01G043200 chr2D 92.715 151 3 2 2119 2261 15195025 15195175 1.300000e-50 211.0
9 TraesCS2A01G043200 chr2D 94.898 98 5 0 1 98 15192786 15192883 2.220000e-33 154.0
10 TraesCS2A01G043200 chr2D 85.950 121 16 1 138 258 293572485 293572366 1.350000e-25 128.0
11 TraesCS2A01G043200 chr2D 82.051 156 20 8 2480 2629 64593175 64593328 4.840000e-25 126.0
12 TraesCS2A01G043200 chr2D 80.519 154 22 7 102 247 644831041 644830888 1.360000e-20 111.0
13 TraesCS2A01G043200 chr2D 72.797 261 50 12 2481 2731 557711164 557711413 8.280000e-08 69.4
14 TraesCS2A01G043200 chr2B 96.032 2016 75 4 1 2016 27085162 27087172 0.000000e+00 3275.0
15 TraesCS2A01G043200 chr2B 94.246 1790 81 12 2119 3894 27087423 27089204 0.000000e+00 2715.0
16 TraesCS2A01G043200 chr2B 74.794 607 116 25 1119 1701 27407067 27407660 5.960000e-59 239.0
17 TraesCS2A01G043200 chr2B 74.587 606 119 24 1119 1701 27356021 27356614 2.770000e-57 233.0
18 TraesCS2A01G043200 chr2B 91.781 146 6 3 2002 2147 27087280 27087419 1.010000e-46 198.0
19 TraesCS2A01G043200 chr2B 97.222 108 3 0 3901 4008 27089184 27089291 2.830000e-42 183.0
20 TraesCS2A01G043200 chrUn 98.754 562 7 0 4051 4612 349817311 349816750 0.000000e+00 1000.0
21 TraesCS2A01G043200 chrUn 98.577 562 8 0 4051 4612 349834873 349835434 0.000000e+00 994.0
22 TraesCS2A01G043200 chrUn 82.645 121 20 1 138 258 31367970 31367851 6.310000e-19 106.0
23 TraesCS2A01G043200 chrUn 88.889 45 4 1 3990 4034 446814764 446814807 2.000000e-03 54.7
24 TraesCS2A01G043200 chrUn 100.000 28 0 0 4007 4034 432310892 432310919 8.000000e-03 52.8
25 TraesCS2A01G043200 chr6A 97.869 563 11 1 4051 4612 34349696 34350258 0.000000e+00 972.0
26 TraesCS2A01G043200 chr6A 85.577 520 62 9 4022 4532 169568544 169569059 2.440000e-147 532.0
27 TraesCS2A01G043200 chr7B 89.298 598 54 7 4022 4612 444249138 444249732 0.000000e+00 741.0
28 TraesCS2A01G043200 chr7B 81.117 376 47 16 992 1363 69912890 69913245 3.510000e-71 279.0
29 TraesCS2A01G043200 chr7B 80.902 377 46 19 992 1363 70069273 70069628 1.630000e-69 274.0
30 TraesCS2A01G043200 chr7B 79.947 374 55 16 992 1363 69992775 69993130 1.650000e-64 257.0
31 TraesCS2A01G043200 chr3B 87.270 597 64 8 4026 4612 17638822 17639416 0.000000e+00 671.0
32 TraesCS2A01G043200 chr3B 88.414 561 60 4 4054 4612 36928216 36927659 0.000000e+00 671.0
33 TraesCS2A01G043200 chr3B 95.775 71 1 1 3076 3144 520448037 520447967 3.770000e-21 113.0
34 TraesCS2A01G043200 chr3B 79.545 132 21 6 2578 2706 151587322 151587450 6.360000e-14 89.8
35 TraesCS2A01G043200 chr3B 81.818 110 13 6 2690 2793 823268062 823267954 8.220000e-13 86.1
36 TraesCS2A01G043200 chr3B 97.561 41 1 0 4003 4043 821939783 821939823 2.300000e-08 71.3
37 TraesCS2A01G043200 chr4A 84.255 597 82 12 4022 4612 179966407 179966997 5.180000e-159 571.0
38 TraesCS2A01G043200 chr4A 86.538 104 14 0 138 241 718720284 718720181 1.050000e-21 115.0
39 TraesCS2A01G043200 chr4A 95.652 69 3 0 3076 3144 24503986 24504054 1.360000e-20 111.0
40 TraesCS2A01G043200 chr6B 81.551 374 51 14 992 1363 548948676 548949033 4.510000e-75 292.0
41 TraesCS2A01G043200 chr6B 81.283 374 52 14 992 1363 549029188 549029545 2.100000e-73 287.0
42 TraesCS2A01G043200 chr6B 75.439 228 29 22 2576 2792 167027841 167028052 8.220000e-13 86.1
43 TraesCS2A01G043200 chr6B 88.889 45 4 1 3990 4034 22524701 22524744 2.000000e-03 54.7
44 TraesCS2A01G043200 chr6B 88.889 45 4 1 3990 4034 22531555 22531598 2.000000e-03 54.7
45 TraesCS2A01G043200 chr6B 88.889 45 4 1 3990 4034 22538409 22538452 2.000000e-03 54.7
46 TraesCS2A01G043200 chr3D 76.950 282 44 15 2185 2461 111759513 111759778 1.730000e-29 141.0
47 TraesCS2A01G043200 chr3D 79.845 129 19 4 2481 2609 135015809 135015688 2.290000e-13 87.9
48 TraesCS2A01G043200 chr3D 89.362 47 2 3 4007 4051 76997214 76997169 6.450000e-04 56.5
49 TraesCS2A01G043200 chr1D 95.890 73 3 0 3076 3148 464799794 464799722 8.110000e-23 119.0
50 TraesCS2A01G043200 chr1A 84.298 121 18 1 138 258 245537719 245537600 2.920000e-22 117.0
51 TraesCS2A01G043200 chr1A 88.889 90 6 4 3063 3148 307037098 307037009 1.750000e-19 108.0
52 TraesCS2A01G043200 chr1A 81.395 129 20 3 2795 2920 449805638 449805511 8.160000e-18 102.0
53 TraesCS2A01G043200 chr7D 94.444 72 3 1 3076 3146 46702663 46702734 4.880000e-20 110.0
54 TraesCS2A01G043200 chr7D 91.250 80 4 2 3074 3151 614653777 614653699 6.310000e-19 106.0
55 TraesCS2A01G043200 chr7D 97.727 44 1 0 4007 4050 548760599 548760556 4.950000e-10 76.8
56 TraesCS2A01G043200 chr7D 97.059 34 1 0 4003 4036 116155908 116155875 1.790000e-04 58.4
57 TraesCS2A01G043200 chr7A 87.234 94 12 0 983 1076 712254134 712254227 1.750000e-19 108.0
58 TraesCS2A01G043200 chr7A 92.105 76 4 1 3071 3144 68881097 68881172 6.310000e-19 106.0
59 TraesCS2A01G043200 chr7A 97.059 34 1 0 4003 4036 39091020 39091053 1.790000e-04 58.4
60 TraesCS2A01G043200 chr5D 83.051 118 19 1 138 255 225589633 225589749 6.310000e-19 106.0
61 TraesCS2A01G043200 chr3A 82.400 125 17 5 115 238 726720151 726720031 2.270000e-18 104.0
62 TraesCS2A01G043200 chr3A 80.508 118 16 4 2492 2609 149924029 149923919 2.960000e-12 84.2
63 TraesCS2A01G043200 chr5B 75.000 220 41 9 2645 2856 686436223 686436436 6.360000e-14 89.8
64 TraesCS2A01G043200 chr6D 95.745 47 2 0 4004 4050 332307802 332307848 4.950000e-10 76.8
65 TraesCS2A01G043200 chr4D 97.059 34 1 0 4003 4036 457271410 457271377 1.790000e-04 58.4
66 TraesCS2A01G043200 chr4D 94.444 36 2 0 4003 4038 290316869 290316904 6.450000e-04 56.5


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 TraesCS2A01G043200 chr2A 17248740 17253351 4611 False 8517.00 8517 100.00000 1 4612 1 chr2A.!!$F2 4611
1 TraesCS2A01G043200 chr2A 17276531 17277092 561 False 1000.00 1000 98.75400 4051 4612 1 chr2A.!!$F3 561
2 TraesCS2A01G043200 chr2A 16925883 16926444 561 False 983.00 983 98.22100 4051 4612 1 chr2A.!!$F1 561
3 TraesCS2A01G043200 chr2A 17296196 17296757 561 False 972.00 972 97.86500 4051 4612 1 chr2A.!!$F4 561
4 TraesCS2A01G043200 chr2D 15192786 15197190 4404 False 1568.50 3284 94.32875 1 3993 4 chr2D.!!$F3 3992
5 TraesCS2A01G043200 chr2B 27085162 27089291 4129 False 1592.75 3275 94.82025 1 4008 4 chr2B.!!$F3 4007
6 TraesCS2A01G043200 chr2B 27407067 27407660 593 False 239.00 239 74.79400 1119 1701 1 chr2B.!!$F2 582
7 TraesCS2A01G043200 chr2B 27356021 27356614 593 False 233.00 233 74.58700 1119 1701 1 chr2B.!!$F1 582
8 TraesCS2A01G043200 chrUn 349816750 349817311 561 True 1000.00 1000 98.75400 4051 4612 1 chrUn.!!$R2 561
9 TraesCS2A01G043200 chrUn 349834873 349835434 561 False 994.00 994 98.57700 4051 4612 1 chrUn.!!$F1 561
10 TraesCS2A01G043200 chr6A 34349696 34350258 562 False 972.00 972 97.86900 4051 4612 1 chr6A.!!$F1 561
11 TraesCS2A01G043200 chr6A 169568544 169569059 515 False 532.00 532 85.57700 4022 4532 1 chr6A.!!$F2 510
12 TraesCS2A01G043200 chr7B 444249138 444249732 594 False 741.00 741 89.29800 4022 4612 1 chr7B.!!$F4 590
13 TraesCS2A01G043200 chr3B 17638822 17639416 594 False 671.00 671 87.27000 4026 4612 1 chr3B.!!$F1 586
14 TraesCS2A01G043200 chr3B 36927659 36928216 557 True 671.00 671 88.41400 4054 4612 1 chr3B.!!$R1 558
15 TraesCS2A01G043200 chr4A 179966407 179966997 590 False 571.00 571 84.25500 4022 4612 1 chr4A.!!$F2 590

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
208 290 0.595095 CTCCAAACAACTGAGCTGGC 59.405 55.000 0.00 0.00 0.0 4.85 F
952 1034 2.333581 GACGCCCCCAAACAAACG 59.666 61.111 0.00 0.00 0.0 3.60 F
1491 1589 0.109723 TTTGGCCGCTAGTTTCTGGT 59.890 50.000 0.00 0.00 0.0 4.00 F
1753 1870 0.748005 TTGGATTCGCTAGCCTTGGC 60.748 55.000 9.66 2.97 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1183 0.179936 GATCACCAGGCAAGAGGAGG 59.820 60.000 0.0 0.0 0.00 4.30 R
1753 1870 2.993899 ACGCAACGGATAGAGTTTGAAG 59.006 45.455 0.0 0.0 0.00 3.02 R
3433 4020 0.803768 CGATGCAGAGGTGTTCTCGG 60.804 60.000 0.0 0.0 46.82 4.63 R
3628 4216 0.321387 GGTGAGGGAAGGGAAACGTC 60.321 60.000 0.0 0.0 0.00 4.34 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
39 40 7.388224 CCATCACAAGATTTCATGAGATAGAGG 59.612 40.741 0.00 0.00 30.20 3.69
127 209 3.612472 TTAAAAGCACAGTACAACCGC 57.388 42.857 0.00 0.00 0.00 5.68
147 229 3.183172 CGCATATGCTCACATACACTCAC 59.817 47.826 24.56 0.00 41.50 3.51
172 254 0.737804 TGAAAGCACACACGCACATT 59.262 45.000 0.00 0.00 0.00 2.71
184 266 2.102420 CACGCACATTCTACCCCTATGA 59.898 50.000 0.00 0.00 0.00 2.15
198 280 2.290896 CCCTATGAGCACCTCCAAACAA 60.291 50.000 0.00 0.00 0.00 2.83
199 281 2.749621 CCTATGAGCACCTCCAAACAAC 59.250 50.000 0.00 0.00 0.00 3.32
205 287 1.972872 CACCTCCAAACAACTGAGCT 58.027 50.000 0.00 0.00 0.00 4.09
208 290 0.595095 CTCCAAACAACTGAGCTGGC 59.405 55.000 0.00 0.00 0.00 4.85
216 298 4.220693 ACAACTGAGCTGGCATAACATA 57.779 40.909 0.00 0.00 0.00 2.29
219 301 5.066893 ACAACTGAGCTGGCATAACATATTG 59.933 40.000 0.00 0.10 0.00 1.90
244 326 7.335171 TGAGATTGACAAAATCACCATAGACAG 59.665 37.037 0.00 0.00 36.92 3.51
279 361 9.982651 TCTACCATGTAGCATTTCTATTAGTTC 57.017 33.333 0.00 0.00 0.00 3.01
284 366 9.424319 CATGTAGCATTTCTATTAGTTCCGTAT 57.576 33.333 0.00 0.00 0.00 3.06
340 422 9.813446 ATTACAGTCTAAGTTAAACCTTATCCG 57.187 33.333 0.00 0.00 0.00 4.18
341 423 6.637657 ACAGTCTAAGTTAAACCTTATCCGG 58.362 40.000 0.00 0.00 0.00 5.14
377 459 2.860136 CACGGTACAGATGCATACACTG 59.140 50.000 11.31 11.31 37.62 3.66
394 476 2.686405 CACTGATAACCTGCATGCACAT 59.314 45.455 18.46 8.33 0.00 3.21
453 535 4.226846 TCCTCATGCTTCCTTGAAGAAGAT 59.773 41.667 7.98 0.00 45.08 2.40
582 664 2.821969 GTCCCTCTGTACCTGTTCGTAA 59.178 50.000 0.00 0.00 0.00 3.18
691 773 4.970662 TGGAGCTATTTTTCTCATGTGC 57.029 40.909 0.00 0.00 0.00 4.57
697 779 2.818130 TTTTTCTCATGTGCTTGGCC 57.182 45.000 0.00 0.00 0.00 5.36
715 797 4.157607 CGCAGGGTTGTTTGAGGT 57.842 55.556 0.00 0.00 0.00 3.85
716 798 3.315765 CGCAGGGTTGTTTGAGGTA 57.684 52.632 0.00 0.00 0.00 3.08
750 832 4.286291 GGTGTATTATTAGGTGGGAGAGGG 59.714 50.000 0.00 0.00 0.00 4.30
952 1034 2.333581 GACGCCCCCAAACAAACG 59.666 61.111 0.00 0.00 0.00 3.60
1101 1183 0.470341 AATTAAGCCGCCCTCCTCTC 59.530 55.000 0.00 0.00 0.00 3.20
1102 1184 1.411651 ATTAAGCCGCCCTCCTCTCC 61.412 60.000 0.00 0.00 0.00 3.71
1103 1185 2.531483 TTAAGCCGCCCTCCTCTCCT 62.531 60.000 0.00 0.00 0.00 3.69
1302 1393 1.262640 GGTTCTTCTACGGCCTCCCA 61.263 60.000 0.00 0.00 0.00 4.37
1314 1405 2.186903 CTCCCAATCGTCCACCCG 59.813 66.667 0.00 0.00 0.00 5.28
1465 1563 4.142026 CCCGGAAGAACAATTAATTTCCCC 60.142 45.833 0.73 5.19 35.07 4.81
1491 1589 0.109723 TTTGGCCGCTAGTTTCTGGT 59.890 50.000 0.00 0.00 0.00 4.00
1753 1870 0.748005 TTGGATTCGCTAGCCTTGGC 60.748 55.000 9.66 2.97 0.00 4.52
1767 1884 2.685388 GCCTTGGCTTCAAACTCTATCC 59.315 50.000 4.11 0.00 0.00 2.59
1839 1956 8.103305 TGATATTGATGCCCTATTTAGGAAGAC 58.897 37.037 5.16 0.00 46.63 3.01
1844 1961 2.439880 GCCCTATTTAGGAAGACCAGCT 59.560 50.000 5.16 0.00 46.63 4.24
2104 2343 9.639601 GATTTCCGACCTTTGATTCTTTTATTT 57.360 29.630 0.00 0.00 0.00 1.40
2119 2358 8.836268 TTCTTTTATTTTGCAGAATTGATGCT 57.164 26.923 7.89 0.00 44.17 3.79
2120 2359 8.470040 TCTTTTATTTTGCAGAATTGATGCTC 57.530 30.769 7.89 0.00 44.17 4.26
2147 2386 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
2273 2853 6.867816 CCTTCTGCTTTACATGTTTTTGCATA 59.132 34.615 2.30 0.55 0.00 3.14
2706 3293 9.904647 GCAATTACATGTAAATTGTATGCAAAG 57.095 29.630 21.57 0.01 36.38 2.77
3203 3790 7.053498 ACAAAAACTTTTACCTGCAAATGGAT 58.947 30.769 0.00 0.00 0.00 3.41
3410 3997 1.153628 GTCAGTACGCCCGCATCTT 60.154 57.895 0.00 0.00 0.00 2.40
3433 4020 0.759060 AAGTCCCAAACCCTGCCAAC 60.759 55.000 0.00 0.00 0.00 3.77
3441 4028 1.990160 AACCCTGCCAACCGAGAACA 61.990 55.000 0.00 0.00 0.00 3.18
3476 4064 9.675464 TCGATTTAACTGTGATACCCTATTTTT 57.325 29.630 0.00 0.00 0.00 1.94
3484 4072 8.050930 ACTGTGATACCCTATTTTTAATTCCGT 58.949 33.333 0.00 0.00 0.00 4.69
3617 4205 2.159653 CGCCACAGAGAACTAACATTGC 60.160 50.000 0.00 0.00 0.00 3.56
3645 4233 1.669440 CGACGTTTCCCTTCCCTCA 59.331 57.895 0.00 0.00 0.00 3.86
3760 4350 4.084287 ACCATTGTCGTCTGTCCTAGTAA 58.916 43.478 0.00 0.00 0.00 2.24
3816 4425 3.436704 CAGATTATGACACCACGCTTGTT 59.563 43.478 0.00 0.00 0.00 2.83
3817 4426 3.684788 AGATTATGACACCACGCTTGTTC 59.315 43.478 0.00 0.00 0.00 3.18
3890 4499 4.536065 CAGCGTTTCTGCATTCTTGTTTA 58.464 39.130 0.00 0.00 35.78 2.01
3891 4500 4.614284 CAGCGTTTCTGCATTCTTGTTTAG 59.386 41.667 0.00 0.00 35.78 1.85
3892 4501 4.275936 AGCGTTTCTGCATTCTTGTTTAGT 59.724 37.500 0.00 0.00 37.31 2.24
3893 4502 4.976116 GCGTTTCTGCATTCTTGTTTAGTT 59.024 37.500 0.00 0.00 34.15 2.24
3894 4503 5.458779 GCGTTTCTGCATTCTTGTTTAGTTT 59.541 36.000 0.00 0.00 34.15 2.66
3895 4504 6.019881 GCGTTTCTGCATTCTTGTTTAGTTTT 60.020 34.615 0.00 0.00 34.15 2.43
3896 4505 7.166804 GCGTTTCTGCATTCTTGTTTAGTTTTA 59.833 33.333 0.00 0.00 34.15 1.52
3897 4506 9.180678 CGTTTCTGCATTCTTGTTTAGTTTTAT 57.819 29.630 0.00 0.00 0.00 1.40
3951 4560 1.663739 GTGTGGGCAGACACGACTA 59.336 57.895 3.60 0.00 44.21 2.59
4008 4617 0.036105 ACATCGAGAGGCATGTGCAA 60.036 50.000 7.36 0.00 44.36 4.08
4009 4618 1.306148 CATCGAGAGGCATGTGCAAT 58.694 50.000 7.36 0.00 44.36 3.56
4010 4619 1.263484 CATCGAGAGGCATGTGCAATC 59.737 52.381 7.36 4.52 44.36 2.67
4011 4620 0.538584 TCGAGAGGCATGTGCAATCT 59.461 50.000 7.36 9.19 44.36 2.40
4012 4621 0.935898 CGAGAGGCATGTGCAATCTC 59.064 55.000 20.64 20.64 44.79 2.75
4013 4622 0.935898 GAGAGGCATGTGCAATCTCG 59.064 55.000 17.83 0.00 41.88 4.04
4014 4623 0.251354 AGAGGCATGTGCAATCTCGT 59.749 50.000 7.36 0.00 44.36 4.18
4015 4624 1.089920 GAGGCATGTGCAATCTCGTT 58.910 50.000 7.36 0.00 44.36 3.85
4016 4625 2.093500 AGAGGCATGTGCAATCTCGTTA 60.093 45.455 7.36 0.00 44.36 3.18
4017 4626 2.009774 AGGCATGTGCAATCTCGTTAC 58.990 47.619 7.36 0.00 44.36 2.50
4018 4627 1.064060 GGCATGTGCAATCTCGTTACC 59.936 52.381 7.36 0.00 44.36 2.85
4019 4628 1.267532 GCATGTGCAATCTCGTTACCG 60.268 52.381 0.00 0.00 41.59 4.02
4020 4629 1.327460 CATGTGCAATCTCGTTACCGG 59.673 52.381 0.00 0.00 33.95 5.28
4021 4630 1.017177 TGTGCAATCTCGTTACCGGC 61.017 55.000 0.00 0.00 33.95 6.13
4022 4631 1.017177 GTGCAATCTCGTTACCGGCA 61.017 55.000 0.00 0.00 33.95 5.69
4023 4632 0.320858 TGCAATCTCGTTACCGGCAA 60.321 50.000 0.00 0.00 33.95 4.52
4024 4633 0.373716 GCAATCTCGTTACCGGCAAG 59.626 55.000 0.00 0.00 33.95 4.01
4029 4638 0.526662 CTCGTTACCGGCAAGTCTCT 59.473 55.000 0.00 0.00 33.95 3.10
4089 4704 1.399727 CGTTGTTCCCTTTGTCATCGC 60.400 52.381 0.00 0.00 0.00 4.58
4336 4953 3.056035 CCTTTGGAGACACCTGTAGTACC 60.056 52.174 0.00 0.00 42.67 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.818136 TGATACAGGATTAGTGCAAAAGC 57.182 39.130 0.00 0.00 0.00 3.51
109 191 1.384525 TGCGGTTGTACTGTGCTTTT 58.615 45.000 0.00 0.00 0.00 2.27
127 209 4.060900 GGGTGAGTGTATGTGAGCATATG 58.939 47.826 0.00 0.00 39.49 1.78
147 229 1.086696 CGTGTGTGCTTTCATAGGGG 58.913 55.000 0.00 0.00 0.00 4.79
172 254 1.133136 GGAGGTGCTCATAGGGGTAGA 60.133 57.143 0.00 0.00 31.08 2.59
184 266 1.972872 CTCAGTTGTTTGGAGGTGCT 58.027 50.000 0.00 0.00 0.00 4.40
198 280 5.039920 TCAATATGTTATGCCAGCTCAGT 57.960 39.130 0.00 0.00 0.00 3.41
199 281 5.303165 TCTCAATATGTTATGCCAGCTCAG 58.697 41.667 0.00 0.00 0.00 3.35
205 287 7.878547 TTGTCAATCTCAATATGTTATGCCA 57.121 32.000 0.00 0.00 0.00 4.92
216 298 8.680903 GTCTATGGTGATTTTGTCAATCTCAAT 58.319 33.333 0.53 0.00 38.90 2.57
219 301 7.615582 TGTCTATGGTGATTTTGTCAATCTC 57.384 36.000 0.00 0.00 38.90 2.75
244 326 3.066342 TGCTACATGGTAGACTACGAAGC 59.934 47.826 11.01 11.01 0.00 3.86
279 361 9.850628 TCCGAGAGATTATATTGTTTTATACGG 57.149 33.333 0.00 0.00 0.00 4.02
317 399 6.438425 TCCGGATAAGGTTTAACTTAGACTGT 59.562 38.462 0.00 0.00 36.47 3.55
340 422 4.830826 ACCGTGTTTCTCAAAGAAATCC 57.169 40.909 5.50 0.00 44.94 3.01
341 423 6.202188 TCTGTACCGTGTTTCTCAAAGAAATC 59.798 38.462 5.50 2.67 44.94 2.17
377 459 3.788333 ACAATGTGCATGCAGGTTATC 57.212 42.857 23.41 8.85 0.00 1.75
394 476 0.030101 CGCGCTTTCAAAGGGAACAA 59.970 50.000 18.01 0.00 43.53 2.83
453 535 4.472833 ACTAACCTCTCTTCTACCCTCGTA 59.527 45.833 0.00 0.00 0.00 3.43
582 664 9.522804 TGAAAAACAAACAAAATCTAACGCTAT 57.477 25.926 0.00 0.00 0.00 2.97
655 737 6.889301 ATAGCTCCAAACACATCCATAATG 57.111 37.500 0.00 0.00 41.48 1.90
659 741 6.438425 AGAAAAATAGCTCCAAACACATCCAT 59.562 34.615 0.00 0.00 0.00 3.41
697 779 0.250553 TACCTCAAACAACCCTGCGG 60.251 55.000 0.00 0.00 0.00 5.69
952 1034 1.528129 CCTGAGAAAGGTTGGCTGTC 58.472 55.000 0.00 0.00 41.74 3.51
1101 1183 0.179936 GATCACCAGGCAAGAGGAGG 59.820 60.000 0.00 0.00 0.00 4.30
1102 1184 1.134461 CAGATCACCAGGCAAGAGGAG 60.134 57.143 0.00 0.00 0.00 3.69
1103 1185 0.907486 CAGATCACCAGGCAAGAGGA 59.093 55.000 0.00 0.00 0.00 3.71
1302 1393 1.375523 GCTGTTCGGGTGGACGATT 60.376 57.895 0.00 0.00 43.11 3.34
1314 1405 0.532573 TGATGACGAGGAGGCTGTTC 59.467 55.000 0.00 0.00 0.00 3.18
1475 1573 1.449778 GGACCAGAAACTAGCGGCC 60.450 63.158 0.00 0.00 0.00 6.13
1491 1589 0.638292 ATGGGTTAGGGACGTAGGGA 59.362 55.000 0.00 0.00 0.00 4.20
1753 1870 2.993899 ACGCAACGGATAGAGTTTGAAG 59.006 45.455 0.00 0.00 0.00 3.02
1767 1884 4.035054 CGGCATTAACACGCAACG 57.965 55.556 0.00 0.00 0.00 4.10
1839 1956 5.220931 GGTTCATGCAGATTAACTAAGCTGG 60.221 44.000 14.67 1.35 46.58 4.85
1844 1961 7.620880 ACTGTAGGTTCATGCAGATTAACTAA 58.379 34.615 9.21 0.00 36.52 2.24
1962 2079 4.667858 AGGGGGTTGCATTACCTATTGATA 59.332 41.667 7.49 0.00 38.30 2.15
2104 2343 4.081031 AGAGAGAGAGCATCAATTCTGCAA 60.081 41.667 11.12 0.00 42.15 4.08
2119 2358 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2120 2359 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2147 2386 3.383761 CCAAGAAGCCATGAAACAACAC 58.616 45.455 0.00 0.00 0.00 3.32
2423 3005 6.751888 ACAAGTTTACACTGAAAATTGCACTC 59.248 34.615 8.49 0.00 44.28 3.51
2424 3006 6.531240 CACAAGTTTACACTGAAAATTGCACT 59.469 34.615 8.49 0.00 44.28 4.40
2425 3007 6.310224 ACACAAGTTTACACTGAAAATTGCAC 59.690 34.615 8.49 0.00 44.28 4.57
2426 3008 6.309980 CACACAAGTTTACACTGAAAATTGCA 59.690 34.615 8.49 0.00 44.28 4.08
2427 3009 6.695245 CACACAAGTTTACACTGAAAATTGC 58.305 36.000 8.49 0.00 44.28 3.56
2428 3010 6.309980 TGCACACAAGTTTACACTGAAAATTG 59.690 34.615 7.33 7.33 45.32 2.32
2429 3011 6.393990 TGCACACAAGTTTACACTGAAAATT 58.606 32.000 0.00 0.00 31.60 1.82
2431 3013 5.378292 TGCACACAAGTTTACACTGAAAA 57.622 34.783 0.00 0.00 31.60 2.29
2676 3263 7.589587 GCATACAATTTACATGTAATTGCGCTA 59.410 33.333 24.88 0.00 36.88 4.26
2893 3480 3.415237 TGCACACAACTTTGCACAC 57.585 47.368 0.00 0.00 43.79 3.82
3385 3972 2.646719 GGCGTACTGACCGTCACA 59.353 61.111 0.00 0.00 0.00 3.58
3410 3997 1.408969 GCAGGGTTTGGGACTTTTCA 58.591 50.000 0.00 0.00 0.00 2.69
3433 4020 0.803768 CGATGCAGAGGTGTTCTCGG 60.804 60.000 0.00 0.00 46.82 4.63
3441 4028 3.935203 CACAGTTAAATCGATGCAGAGGT 59.065 43.478 0.00 0.00 0.00 3.85
3476 4064 4.641396 CATTAGGGATCTGCACGGAATTA 58.359 43.478 0.00 0.00 0.00 1.40
3484 4072 1.271001 CGATGGCATTAGGGATCTGCA 60.271 52.381 0.00 0.00 37.64 4.41
3628 4216 0.321387 GGTGAGGGAAGGGAAACGTC 60.321 60.000 0.00 0.00 0.00 4.34
3645 4233 1.405821 CCAAGCTTATCTCTCGACGGT 59.594 52.381 0.00 0.00 0.00 4.83
3760 4350 8.651389 TCAGCTGCATATATTAGGTCTACTTTT 58.349 33.333 9.47 0.00 0.00 2.27
3816 4425 8.637099 CAAATAGTGGATTGAGAGAGTATGAGA 58.363 37.037 0.00 0.00 0.00 3.27
3817 4426 8.637099 TCAAATAGTGGATTGAGAGAGTATGAG 58.363 37.037 0.00 0.00 32.14 2.90
3898 4507 6.257630 GCCAACTAAACAAGAATGCAGAAAAA 59.742 34.615 0.00 0.00 0.00 1.94
3899 4508 5.752955 GCCAACTAAACAAGAATGCAGAAAA 59.247 36.000 0.00 0.00 0.00 2.29
3900 4509 5.163468 TGCCAACTAAACAAGAATGCAGAAA 60.163 36.000 0.00 0.00 0.00 2.52
3901 4510 4.340666 TGCCAACTAAACAAGAATGCAGAA 59.659 37.500 0.00 0.00 0.00 3.02
3902 4511 3.888323 TGCCAACTAAACAAGAATGCAGA 59.112 39.130 0.00 0.00 0.00 4.26
3903 4512 4.241590 TGCCAACTAAACAAGAATGCAG 57.758 40.909 0.00 0.00 0.00 4.41
3904 4513 4.039004 ACATGCCAACTAAACAAGAATGCA 59.961 37.500 0.00 0.00 32.70 3.96
3905 4514 4.559153 ACATGCCAACTAAACAAGAATGC 58.441 39.130 0.00 0.00 0.00 3.56
3906 4515 8.761575 AATTACATGCCAACTAAACAAGAATG 57.238 30.769 0.00 0.00 0.00 2.67
3907 4516 9.206870 CAAATTACATGCCAACTAAACAAGAAT 57.793 29.630 0.00 0.00 0.00 2.40
3908 4517 8.200792 ACAAATTACATGCCAACTAAACAAGAA 58.799 29.630 0.00 0.00 0.00 2.52
3909 4518 7.651304 CACAAATTACATGCCAACTAAACAAGA 59.349 33.333 0.00 0.00 0.00 3.02
3910 4519 7.437862 ACACAAATTACATGCCAACTAAACAAG 59.562 33.333 0.00 0.00 0.00 3.16
3911 4520 7.223582 CACACAAATTACATGCCAACTAAACAA 59.776 33.333 0.00 0.00 0.00 2.83
3912 4521 6.699204 CACACAAATTACATGCCAACTAAACA 59.301 34.615 0.00 0.00 0.00 2.83
3913 4522 6.145371 CCACACAAATTACATGCCAACTAAAC 59.855 38.462 0.00 0.00 0.00 2.01
3914 4523 6.219473 CCACACAAATTACATGCCAACTAAA 58.781 36.000 0.00 0.00 0.00 1.85
3915 4524 5.279206 CCCACACAAATTACATGCCAACTAA 60.279 40.000 0.00 0.00 0.00 2.24
3951 4560 2.498885 AGCGAACCGGTAATAAAGTCCT 59.501 45.455 8.00 0.00 35.27 3.85
4013 4622 2.998670 GGTAAAGAGACTTGCCGGTAAC 59.001 50.000 0.00 0.00 0.00 2.50
4014 4623 2.353011 CGGTAAAGAGACTTGCCGGTAA 60.353 50.000 4.46 4.46 46.88 2.85
4015 4624 1.203052 CGGTAAAGAGACTTGCCGGTA 59.797 52.381 1.90 0.00 46.88 4.02
4016 4625 0.037605 CGGTAAAGAGACTTGCCGGT 60.038 55.000 1.90 0.00 46.88 5.28
4017 4626 2.750815 CGGTAAAGAGACTTGCCGG 58.249 57.895 0.00 0.00 46.88 6.13
4019 4628 0.321298 TGCCGGTAAAGAGACTTGCC 60.321 55.000 1.90 0.00 0.00 4.52
4020 4629 1.464997 CTTGCCGGTAAAGAGACTTGC 59.535 52.381 6.40 0.00 0.00 4.01
4021 4630 2.737252 GACTTGCCGGTAAAGAGACTTG 59.263 50.000 21.42 4.50 0.00 3.16
4022 4631 2.633481 AGACTTGCCGGTAAAGAGACTT 59.367 45.455 21.42 3.17 0.00 3.01
4023 4632 2.231721 GAGACTTGCCGGTAAAGAGACT 59.768 50.000 21.42 16.55 0.00 3.24
4024 4633 2.231721 AGAGACTTGCCGGTAAAGAGAC 59.768 50.000 21.42 13.32 0.00 3.36
4029 4638 3.071312 TGGTAAAGAGACTTGCCGGTAAA 59.929 43.478 6.40 0.00 34.04 2.01
4089 4704 3.736252 CGAATCTCGGGCAAGTAACATAG 59.264 47.826 0.00 0.00 36.00 2.23
4336 4953 5.677567 ACGTAACTGGGTGATTATAAAGGG 58.322 41.667 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.