Multiple sequence alignment - TraesCS4A01G448100

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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 TraesCS4A01G448100 chr4A 100.000 7880 0 0 1 7880 714895540 714903419 0.000000e+00 14552.0
1 TraesCS4A01G448100 chrUn 98.180 3406 52 4 111 3515 314281970 314278574 0.000000e+00 5938.0
2 TraesCS4A01G448100 chrUn 99.247 2524 19 0 4115 6638 337683777 337681254 0.000000e+00 4556.0
3 TraesCS4A01G448100 chrUn 99.643 1961 6 1 5920 7880 268459750 268461709 0.000000e+00 3581.0
4 TraesCS4A01G448100 chrUn 99.643 1961 6 1 5920 7880 288956548 288954589 0.000000e+00 3581.0
5 TraesCS4A01G448100 chrUn 84.699 1013 150 5 5843 6851 340539923 340540934 0.000000e+00 1007.0
6 TraesCS4A01G448100 chrUn 87.379 103 12 1 1135 1236 245870939 245871041 5.000000e-22 117.0
7 TraesCS4A01G448100 chrUn 88.000 100 11 1 1138 1236 346953056 346952957 5.000000e-22 117.0
8 TraesCS4A01G448100 chr4B 97.084 2469 72 0 2620 5088 630049158 630046690 0.000000e+00 4161.0
9 TraesCS4A01G448100 chr3B 96.640 2470 82 1 2620 5088 760583349 760585818 0.000000e+00 4100.0
10 TraesCS4A01G448100 chr3B 94.826 2474 126 2 2620 5091 782178479 782176006 0.000000e+00 3858.0
11 TraesCS4A01G448100 chr3B 94.786 2474 127 2 2620 5091 782220161 782217688 0.000000e+00 3853.0
12 TraesCS4A01G448100 chr3B 94.745 2474 128 2 2620 5091 782261568 782259095 0.000000e+00 3847.0
13 TraesCS4A01G448100 chr3B 94.707 2475 128 3 2620 5091 782303382 782300908 0.000000e+00 3842.0
14 TraesCS4A01G448100 chr3B 92.437 119 8 1 1 119 70468409 70468526 1.360000e-37 169.0
15 TraesCS4A01G448100 chr3B 91.346 104 9 0 1 104 461614331 461614434 8.240000e-30 143.0
16 TraesCS4A01G448100 chr3B 97.959 49 1 0 5598 5646 34584361 34584409 1.410000e-12 86.1
17 TraesCS4A01G448100 chr3B 97.959 49 1 0 5598 5646 34638525 34638573 1.410000e-12 86.1
18 TraesCS4A01G448100 chr7B 95.707 2469 102 3 2620 5088 651410592 651413056 0.000000e+00 3969.0
19 TraesCS4A01G448100 chr1B 95.350 2473 112 3 2620 5091 409838610 409841080 0.000000e+00 3927.0
20 TraesCS4A01G448100 chr1B 88.268 1091 123 4 5765 6851 22823128 22822039 0.000000e+00 1301.0
21 TraesCS4A01G448100 chr1B 85.700 1000 139 4 5862 6859 635984694 635985691 0.000000e+00 1051.0
22 TraesCS4A01G448100 chr1B 78.720 1344 222 43 994 2300 22825049 22823733 0.000000e+00 839.0
23 TraesCS4A01G448100 chr1B 74.101 556 125 14 1739 2281 29923766 29924315 2.230000e-50 211.0
24 TraesCS4A01G448100 chr1B 78.451 297 56 3 1756 2045 635977633 635977928 3.750000e-43 187.0
25 TraesCS4A01G448100 chr1B 92.308 117 9 0 1 117 615013084 615013200 4.890000e-37 167.0
26 TraesCS4A01G448100 chr1B 90.654 107 10 0 7 113 583151961 583151855 8.240000e-30 143.0
27 TraesCS4A01G448100 chr1B 100.000 31 0 0 5615 5645 668131862 668131892 3.070000e-04 58.4
28 TraesCS4A01G448100 chr7A 94.431 2478 135 3 2617 5091 169002211 168999734 0.000000e+00 3808.0
29 TraesCS4A01G448100 chr6A 85.241 996 146 1 5865 6859 1335629 1334634 0.000000e+00 1024.0
30 TraesCS4A01G448100 chr6A 84.900 1000 149 2 5857 6854 3327128 3326129 0.000000e+00 1009.0
31 TraesCS4A01G448100 chr6A 77.703 296 54 8 1759 2045 1338781 1338489 3.780000e-38 171.0
32 TraesCS4A01G448100 chr6A 97.959 49 1 0 5598 5646 328040377 328040425 1.410000e-12 86.1
33 TraesCS4A01G448100 chr1D 85.035 989 147 1 5865 6852 2460089 2459101 0.000000e+00 1005.0
34 TraesCS4A01G448100 chr6B 93.636 110 6 1 6 115 92530631 92530739 6.330000e-36 163.0
35 TraesCS4A01G448100 chr6B 88.430 121 13 1 1 121 526740527 526740646 2.290000e-30 145.0
36 TraesCS4A01G448100 chr6B 97.297 37 0 1 7844 7880 34042153 34042118 2.370000e-05 62.1
37 TraesCS4A01G448100 chr2B 91.667 108 9 0 1 108 666035328 666035435 4.930000e-32 150.0
38 TraesCS4A01G448100 chr2B 100.000 35 0 0 5598 5632 786140852 786140886 1.840000e-06 65.8
39 TraesCS4A01G448100 chr3D 90.909 110 10 0 2 111 549355218 549355327 1.770000e-31 148.0
40 TraesCS4A01G448100 chr3A 85.833 120 17 0 1 120 726321218 726321337 2.310000e-25 128.0
41 TraesCS4A01G448100 chr2A 83.929 112 15 3 288 399 119301951 119302059 3.890000e-18 104.0
42 TraesCS4A01G448100 chr2A 87.931 58 4 3 5098 5154 755336864 755336809 1.840000e-06 65.8
43 TraesCS4A01G448100 chr6D 97.778 45 1 0 5603 5647 455097116 455097160 2.360000e-10 78.7
44 TraesCS4A01G448100 chr5A 95.455 44 1 1 5596 5638 378520051 378520094 1.420000e-07 69.4
45 TraesCS4A01G448100 chr5D 90.196 51 3 2 5598 5646 525186077 525186127 1.840000e-06 65.8


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 TraesCS4A01G448100 chr4A 714895540 714903419 7879 False 14552.0 14552 100.000 1 7880 1 chr4A.!!$F1 7879
1 TraesCS4A01G448100 chrUn 314278574 314281970 3396 True 5938.0 5938 98.180 111 3515 1 chrUn.!!$R2 3404
2 TraesCS4A01G448100 chrUn 337681254 337683777 2523 True 4556.0 4556 99.247 4115 6638 1 chrUn.!!$R3 2523
3 TraesCS4A01G448100 chrUn 268459750 268461709 1959 False 3581.0 3581 99.643 5920 7880 1 chrUn.!!$F2 1960
4 TraesCS4A01G448100 chrUn 288954589 288956548 1959 True 3581.0 3581 99.643 5920 7880 1 chrUn.!!$R1 1960
5 TraesCS4A01G448100 chrUn 340539923 340540934 1011 False 1007.0 1007 84.699 5843 6851 1 chrUn.!!$F3 1008
6 TraesCS4A01G448100 chr4B 630046690 630049158 2468 True 4161.0 4161 97.084 2620 5088 1 chr4B.!!$R1 2468
7 TraesCS4A01G448100 chr3B 760583349 760585818 2469 False 4100.0 4100 96.640 2620 5088 1 chr3B.!!$F5 2468
8 TraesCS4A01G448100 chr3B 782176006 782178479 2473 True 3858.0 3858 94.826 2620 5091 1 chr3B.!!$R1 2471
9 TraesCS4A01G448100 chr3B 782217688 782220161 2473 True 3853.0 3853 94.786 2620 5091 1 chr3B.!!$R2 2471
10 TraesCS4A01G448100 chr3B 782259095 782261568 2473 True 3847.0 3847 94.745 2620 5091 1 chr3B.!!$R3 2471
11 TraesCS4A01G448100 chr3B 782300908 782303382 2474 True 3842.0 3842 94.707 2620 5091 1 chr3B.!!$R4 2471
12 TraesCS4A01G448100 chr7B 651410592 651413056 2464 False 3969.0 3969 95.707 2620 5088 1 chr7B.!!$F1 2468
13 TraesCS4A01G448100 chr1B 409838610 409841080 2470 False 3927.0 3927 95.350 2620 5091 1 chr1B.!!$F2 2471
14 TraesCS4A01G448100 chr1B 22822039 22825049 3010 True 1070.0 1301 83.494 994 6851 2 chr1B.!!$R2 5857
15 TraesCS4A01G448100 chr1B 635984694 635985691 997 False 1051.0 1051 85.700 5862 6859 1 chr1B.!!$F5 997
16 TraesCS4A01G448100 chr1B 29923766 29924315 549 False 211.0 211 74.101 1739 2281 1 chr1B.!!$F1 542
17 TraesCS4A01G448100 chr7A 168999734 169002211 2477 True 3808.0 3808 94.431 2617 5091 1 chr7A.!!$R1 2474
18 TraesCS4A01G448100 chr6A 3326129 3327128 999 True 1009.0 1009 84.900 5857 6854 1 chr6A.!!$R1 997
19 TraesCS4A01G448100 chr6A 1334634 1338781 4147 True 597.5 1024 81.472 1759 6859 2 chr6A.!!$R2 5100
20 TraesCS4A01G448100 chr1D 2459101 2460089 988 True 1005.0 1005 85.035 5865 6852 1 chr1D.!!$R1 987

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
93 94 1.013596 TCTTTTCTGCCACACGTGTG 58.986 50.000 36.13 36.13 45.23 3.82 F
99 100 1.089481 CTGCCACACGTGTGACAGTT 61.089 55.000 40.27 11.39 46.80 3.16 F
1351 1358 0.947180 TCTTAACAGGTCGTTGCCGC 60.947 55.000 0.00 0.00 38.63 6.53 F
1464 1471 0.310854 CCAGCGGGTTGTTCAAGTTC 59.689 55.000 0.00 0.00 0.00 3.01 F
1481 1488 2.685897 AGTTCTACACGATGCCTCTCTC 59.314 50.000 0.00 0.00 0.00 3.20 F
3577 3737 1.267261 CATAGGCTTCTCTACGTCGGG 59.733 57.143 0.00 0.00 0.00 5.14 F
4559 4916 0.892755 CGTAGCCCCTTGTGTGTCTA 59.107 55.000 0.00 0.00 0.00 2.59 F
4770 5129 1.737236 TGGATTTCATGGAGCGTTTCG 59.263 47.619 0.00 0.00 0.00 3.46 F
5229 6040 4.019411 TGTCTGCATTGGATAACTTCTCCA 60.019 41.667 0.00 0.00 41.03 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1211 0.608640 CAGTGTACCTCGAAGCCCTT 59.391 55.000 0.00 0.0 0.00 3.95 R
1411 1418 1.043816 CACAGGTATGAGATCCCGCT 58.956 55.000 0.00 0.0 0.00 5.52 R
2943 3103 6.061441 TCACTTTTTGCAGGTTATCTTCAGA 58.939 36.000 0.00 0.0 0.00 3.27 R
3299 3459 7.906327 AGTTAAGGTACCCTTACGTATCAAAA 58.094 34.615 8.74 0.0 44.64 2.44 R
3577 3737 8.243426 TCAATATCCTTCTTTGTACAACATTGC 58.757 33.333 8.07 0.0 0.00 3.56 R
4770 5129 1.067060 GAAGGGGTTGTTGTCTTGCAC 59.933 52.381 0.00 0.0 0.00 4.57 R
5652 6860 8.034215 AGTGTGAAAATGAAAGTGAAAACATGA 58.966 29.630 0.00 0.0 0.00 3.07 R
5761 6969 9.983024 TGGAAATACCACTTTGGATAATCTAAA 57.017 29.630 0.00 0.0 44.64 1.85 R
6923 8386 2.009042 GCACACTGGTACTCATCAGGC 61.009 57.143 0.00 0.0 35.47 4.85 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
21 22 4.907879 ATCCAAAAAGATTCTCGGATGC 57.092 40.909 6.24 0.00 32.08 3.91
22 23 3.684908 TCCAAAAAGATTCTCGGATGCA 58.315 40.909 0.00 0.00 0.00 3.96
23 24 4.272489 TCCAAAAAGATTCTCGGATGCAT 58.728 39.130 0.00 0.00 0.00 3.96
24 25 4.096833 TCCAAAAAGATTCTCGGATGCATG 59.903 41.667 2.46 0.00 0.00 4.06
25 26 3.705043 AAAAGATTCTCGGATGCATGC 57.295 42.857 11.82 11.82 0.00 4.06
26 27 2.336945 AAGATTCTCGGATGCATGCA 57.663 45.000 25.04 25.04 0.00 3.96
27 28 2.563261 AGATTCTCGGATGCATGCAT 57.437 45.000 32.66 32.66 39.69 3.96
28 29 2.152016 AGATTCTCGGATGCATGCATG 58.848 47.619 36.73 23.05 36.70 4.06
51 52 4.531659 GGTGACGTGGCAATCTATTTAC 57.468 45.455 0.00 0.00 0.00 2.01
52 53 3.936453 GGTGACGTGGCAATCTATTTACA 59.064 43.478 0.00 0.00 0.00 2.41
53 54 4.574828 GGTGACGTGGCAATCTATTTACAT 59.425 41.667 0.00 0.00 0.00 2.29
54 55 5.065988 GGTGACGTGGCAATCTATTTACATT 59.934 40.000 0.00 0.00 0.00 2.71
55 56 6.259167 GGTGACGTGGCAATCTATTTACATTA 59.741 38.462 0.00 0.00 0.00 1.90
56 57 7.345192 GTGACGTGGCAATCTATTTACATTAG 58.655 38.462 0.00 0.00 0.00 1.73
57 58 7.223971 GTGACGTGGCAATCTATTTACATTAGA 59.776 37.037 0.00 0.00 0.00 2.10
58 59 7.438160 TGACGTGGCAATCTATTTACATTAGAG 59.562 37.037 0.00 0.00 0.00 2.43
59 60 7.497595 ACGTGGCAATCTATTTACATTAGAGA 58.502 34.615 0.00 0.00 0.00 3.10
60 61 8.150945 ACGTGGCAATCTATTTACATTAGAGAT 58.849 33.333 0.00 0.00 0.00 2.75
61 62 8.438513 CGTGGCAATCTATTTACATTAGAGATG 58.561 37.037 0.00 0.00 0.00 2.90
62 63 9.277783 GTGGCAATCTATTTACATTAGAGATGT 57.722 33.333 0.00 0.00 36.13 3.06
63 64 9.276590 TGGCAATCTATTTACATTAGAGATGTG 57.723 33.333 2.11 0.00 33.76 3.21
64 65 9.277783 GGCAATCTATTTACATTAGAGATGTGT 57.722 33.333 2.11 0.00 33.76 3.72
68 69 9.770097 ATCTATTTACATTAGAGATGTGTGGTG 57.230 33.333 2.11 0.00 33.76 4.17
69 70 6.683974 ATTTACATTAGAGATGTGTGGTGC 57.316 37.500 2.11 0.00 33.76 5.01
70 71 3.701205 ACATTAGAGATGTGTGGTGCA 57.299 42.857 0.00 0.00 0.00 4.57
71 72 4.226427 ACATTAGAGATGTGTGGTGCAT 57.774 40.909 0.00 0.00 0.00 3.96
72 73 4.194640 ACATTAGAGATGTGTGGTGCATC 58.805 43.478 0.00 0.00 42.08 3.91
79 80 4.510038 GATGTGTGGTGCATCTTCTTTT 57.490 40.909 0.00 0.00 39.53 2.27
80 81 3.988379 TGTGTGGTGCATCTTCTTTTC 57.012 42.857 0.00 0.00 0.00 2.29
81 82 3.554934 TGTGTGGTGCATCTTCTTTTCT 58.445 40.909 0.00 0.00 0.00 2.52
82 83 3.316029 TGTGTGGTGCATCTTCTTTTCTG 59.684 43.478 0.00 0.00 0.00 3.02
83 84 2.294233 TGTGGTGCATCTTCTTTTCTGC 59.706 45.455 0.00 0.00 35.21 4.26
84 85 1.888512 TGGTGCATCTTCTTTTCTGCC 59.111 47.619 0.00 0.00 33.70 4.85
85 86 1.888512 GGTGCATCTTCTTTTCTGCCA 59.111 47.619 0.00 0.00 33.70 4.92
86 87 2.352127 GGTGCATCTTCTTTTCTGCCAC 60.352 50.000 0.00 0.00 33.70 5.01
87 88 2.294233 GTGCATCTTCTTTTCTGCCACA 59.706 45.455 0.00 0.00 33.70 4.17
88 89 2.294233 TGCATCTTCTTTTCTGCCACAC 59.706 45.455 0.00 0.00 33.70 3.82
89 90 2.666619 GCATCTTCTTTTCTGCCACACG 60.667 50.000 0.00 0.00 0.00 4.49
90 91 2.325583 TCTTCTTTTCTGCCACACGT 57.674 45.000 0.00 0.00 0.00 4.49
91 92 1.939934 TCTTCTTTTCTGCCACACGTG 59.060 47.619 15.48 15.48 0.00 4.49
92 93 1.670811 CTTCTTTTCTGCCACACGTGT 59.329 47.619 17.22 17.22 0.00 4.49
93 94 1.013596 TCTTTTCTGCCACACGTGTG 58.986 50.000 36.13 36.13 45.23 3.82
97 98 3.323000 CTGCCACACGTGTGACAG 58.677 61.111 38.46 38.46 46.83 3.51
98 99 1.521457 CTGCCACACGTGTGACAGT 60.521 57.895 40.27 12.10 46.80 3.55
99 100 1.089481 CTGCCACACGTGTGACAGTT 61.089 55.000 40.27 11.39 46.80 3.16
100 101 1.804746 CTGCCACACGTGTGACAGTTA 60.805 52.381 40.27 20.65 46.80 2.24
101 102 3.122687 CTGCCACACGTGTGACAGTTAT 61.123 50.000 40.27 9.96 46.80 1.89
102 103 4.942934 CTGCCACACGTGTGACAGTTATC 61.943 52.174 40.27 22.90 46.80 1.75
105 106 2.658285 ACACGTGTGACAGTTATCGAC 58.342 47.619 22.71 0.00 0.00 4.20
106 107 1.642360 CACGTGTGACAGTTATCGACG 59.358 52.381 7.58 0.00 34.74 5.12
107 108 1.265095 ACGTGTGACAGTTATCGACGT 59.735 47.619 0.00 0.00 36.19 4.34
108 109 1.903139 CGTGTGACAGTTATCGACGTC 59.097 52.381 5.18 5.18 34.54 4.34
109 110 2.248487 GTGTGACAGTTATCGACGTCC 58.752 52.381 10.58 0.00 33.67 4.79
362 363 3.329542 ATGGATGTGGCGGACGCTT 62.330 57.895 16.72 0.00 41.60 4.68
530 531 2.076100 CACCTACGTGTGTACCGAGTA 58.924 52.381 0.00 0.00 35.10 2.59
587 588 7.113965 GCCATGCATTTTGATAATTAGAGTTCG 59.886 37.037 0.00 0.00 0.00 3.95
679 680 8.220755 TCTGTTTAATTATGTATGAGGCCAAC 57.779 34.615 5.01 0.00 0.00 3.77
887 888 6.641169 TGAACTAGCTAGTATGATGGAGTG 57.359 41.667 26.29 0.00 34.99 3.51
905 906 6.769512 TGGAGTGTATCAAGAAGCTAAACTT 58.230 36.000 0.00 0.00 42.98 2.66
1073 1080 3.106827 TGCTCCAGATATCTGTTGTGGA 58.893 45.455 27.03 18.12 42.27 4.02
1173 1180 1.188863 GCAACATCAGCATCCCCTTT 58.811 50.000 0.00 0.00 0.00 3.11
1191 1198 2.516225 CCTTTCGGAATCGGGCCC 60.516 66.667 13.57 13.57 36.95 5.80
1254 1261 4.436998 CGTCCTCCTCGCGCCTTT 62.437 66.667 0.00 0.00 0.00 3.11
1278 1285 2.481104 CGCAAGTGCTTTCCTTGGAAAA 60.481 45.455 14.75 0.09 39.72 2.29
1279 1286 3.126073 GCAAGTGCTTTCCTTGGAAAAG 58.874 45.455 14.75 10.38 39.72 2.27
1351 1358 0.947180 TCTTAACAGGTCGTTGCCGC 60.947 55.000 0.00 0.00 38.63 6.53
1449 1456 1.510480 GCACCACAGACAAGACCAGC 61.510 60.000 0.00 0.00 0.00 4.85
1464 1471 0.310854 CCAGCGGGTTGTTCAAGTTC 59.689 55.000 0.00 0.00 0.00 3.01
1481 1488 2.685897 AGTTCTACACGATGCCTCTCTC 59.314 50.000 0.00 0.00 0.00 3.20
3577 3737 1.267261 CATAGGCTTCTCTACGTCGGG 59.733 57.143 0.00 0.00 0.00 5.14
3638 3798 0.912487 TCCCCAAGCCACGTATCCTT 60.912 55.000 0.00 0.00 0.00 3.36
3975 4332 6.315393 GCTCATCATTTTGCCAAAAGAATCAT 59.685 34.615 8.75 0.00 33.22 2.45
3992 4349 9.703892 AAAGAATCATGATCGGTAGAAATCTAG 57.296 33.333 9.06 0.00 0.00 2.43
4059 4416 7.563924 AGAAACATAGGCATACTAGTAAGGACA 59.436 37.037 6.70 0.00 34.56 4.02
4559 4916 0.892755 CGTAGCCCCTTGTGTGTCTA 59.107 55.000 0.00 0.00 0.00 2.59
4770 5129 1.737236 TGGATTTCATGGAGCGTTTCG 59.263 47.619 0.00 0.00 0.00 3.46
5229 6040 4.019411 TGTCTGCATTGGATAACTTCTCCA 60.019 41.667 0.00 0.00 41.03 3.86
5650 6858 7.404671 AAAGCACCCTTTATCGAAAATATGT 57.595 32.000 0.00 0.00 39.44 2.29
5652 6860 7.404671 AGCACCCTTTATCGAAAATATGTTT 57.595 32.000 0.00 0.00 0.00 2.83
5811 7120 7.852945 CCATTTCTATACTTTCTTTTGCTAGCG 59.147 37.037 10.77 0.00 0.00 4.26
5823 7132 4.600012 TTTGCTAGCGCTTATTCACTTC 57.400 40.909 18.68 0.00 36.97 3.01
7383 8846 0.546122 AGCACAACAACCTCCACAGA 59.454 50.000 0.00 0.00 0.00 3.41
7501 8964 4.039703 TCTGTAACGAACTTGTTCAGTCG 58.960 43.478 13.05 3.21 32.94 4.18
7719 9182 5.060506 CCTACGGCCATATATTTGTCAACA 58.939 41.667 2.24 0.00 0.00 3.33
7838 9301 0.518636 CATTGTCAACTGCAGACGGG 59.481 55.000 23.35 6.53 38.83 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.272489 TGCATCCGAGAATCTTTTTGGAT 58.728 39.130 0.00 0.00 36.69 3.41
2 3 4.357142 CATGCATCCGAGAATCTTTTTGG 58.643 43.478 0.00 0.00 0.00 3.28
3 4 3.795101 GCATGCATCCGAGAATCTTTTTG 59.205 43.478 14.21 0.00 0.00 2.44
4 5 3.444742 TGCATGCATCCGAGAATCTTTTT 59.555 39.130 18.46 0.00 0.00 1.94
5 6 3.018856 TGCATGCATCCGAGAATCTTTT 58.981 40.909 18.46 0.00 0.00 2.27
6 7 2.646930 TGCATGCATCCGAGAATCTTT 58.353 42.857 18.46 0.00 0.00 2.52
7 8 2.336945 TGCATGCATCCGAGAATCTT 57.663 45.000 18.46 0.00 0.00 2.40
8 9 2.152016 CATGCATGCATCCGAGAATCT 58.848 47.619 30.07 3.48 33.90 2.40
9 10 2.613730 CATGCATGCATCCGAGAATC 57.386 50.000 30.07 0.00 33.90 2.52
21 22 2.098871 CACGTCACCGCATGCATG 59.901 61.111 22.70 22.70 37.70 4.06
22 23 3.126879 CCACGTCACCGCATGCAT 61.127 61.111 19.57 1.32 37.70 3.96
25 26 2.582202 GATTGCCACGTCACCGCATG 62.582 60.000 0.00 0.00 37.70 4.06
26 27 2.359850 ATTGCCACGTCACCGCAT 60.360 55.556 0.00 0.00 37.70 4.73
27 28 2.161078 TAGATTGCCACGTCACCGCA 62.161 55.000 0.00 0.00 37.70 5.69
28 29 0.810031 ATAGATTGCCACGTCACCGC 60.810 55.000 0.00 0.00 37.70 5.68
29 30 1.651987 AATAGATTGCCACGTCACCG 58.348 50.000 0.00 0.00 40.83 4.94
30 31 3.936453 TGTAAATAGATTGCCACGTCACC 59.064 43.478 0.00 0.00 0.00 4.02
31 32 5.734855 ATGTAAATAGATTGCCACGTCAC 57.265 39.130 0.00 0.00 0.00 3.67
32 33 7.269316 TCTAATGTAAATAGATTGCCACGTCA 58.731 34.615 0.00 0.00 0.00 4.35
33 34 7.652105 TCTCTAATGTAAATAGATTGCCACGTC 59.348 37.037 0.00 0.00 0.00 4.34
34 35 7.497595 TCTCTAATGTAAATAGATTGCCACGT 58.502 34.615 0.00 0.00 0.00 4.49
35 36 7.946655 TCTCTAATGTAAATAGATTGCCACG 57.053 36.000 0.00 0.00 0.00 4.94
36 37 9.277783 ACATCTCTAATGTAAATAGATTGCCAC 57.722 33.333 0.00 0.00 0.00 5.01
37 38 9.276590 CACATCTCTAATGTAAATAGATTGCCA 57.723 33.333 0.00 0.00 0.00 4.92
38 39 9.277783 ACACATCTCTAATGTAAATAGATTGCC 57.722 33.333 0.00 0.00 0.00 4.52
42 43 9.770097 CACCACACATCTCTAATGTAAATAGAT 57.230 33.333 0.00 0.00 0.00 1.98
43 44 7.710907 GCACCACACATCTCTAATGTAAATAGA 59.289 37.037 0.00 0.00 0.00 1.98
44 45 7.495606 TGCACCACACATCTCTAATGTAAATAG 59.504 37.037 0.00 0.00 0.00 1.73
45 46 7.334858 TGCACCACACATCTCTAATGTAAATA 58.665 34.615 0.00 0.00 0.00 1.40
46 47 6.179756 TGCACCACACATCTCTAATGTAAAT 58.820 36.000 0.00 0.00 0.00 1.40
47 48 5.555966 TGCACCACACATCTCTAATGTAAA 58.444 37.500 0.00 0.00 0.00 2.01
48 49 5.159273 TGCACCACACATCTCTAATGTAA 57.841 39.130 0.00 0.00 0.00 2.41
49 50 4.817318 TGCACCACACATCTCTAATGTA 57.183 40.909 0.00 0.00 0.00 2.29
50 51 3.701205 TGCACCACACATCTCTAATGT 57.299 42.857 0.00 0.00 0.00 2.71
51 52 4.808077 GATGCACCACACATCTCTAATG 57.192 45.455 0.00 0.00 40.63 1.90
58 59 4.217118 AGAAAAGAAGATGCACCACACATC 59.783 41.667 0.00 0.00 43.49 3.06
59 60 4.022589 CAGAAAAGAAGATGCACCACACAT 60.023 41.667 0.00 0.00 0.00 3.21
60 61 3.316029 CAGAAAAGAAGATGCACCACACA 59.684 43.478 0.00 0.00 0.00 3.72
61 62 3.854784 GCAGAAAAGAAGATGCACCACAC 60.855 47.826 0.00 0.00 38.54 3.82
62 63 2.294233 GCAGAAAAGAAGATGCACCACA 59.706 45.455 0.00 0.00 38.54 4.17
63 64 2.352127 GGCAGAAAAGAAGATGCACCAC 60.352 50.000 0.00 0.00 40.46 4.16
64 65 1.888512 GGCAGAAAAGAAGATGCACCA 59.111 47.619 0.00 0.00 40.46 4.17
65 66 1.888512 TGGCAGAAAAGAAGATGCACC 59.111 47.619 0.00 0.00 40.46 5.01
66 67 2.294233 TGTGGCAGAAAAGAAGATGCAC 59.706 45.455 0.00 0.00 40.46 4.57
67 68 2.294233 GTGTGGCAGAAAAGAAGATGCA 59.706 45.455 0.00 0.00 40.46 3.96
68 69 2.666619 CGTGTGGCAGAAAAGAAGATGC 60.667 50.000 0.00 0.00 37.95 3.91
69 70 2.549754 ACGTGTGGCAGAAAAGAAGATG 59.450 45.455 0.00 0.00 0.00 2.90
70 71 2.549754 CACGTGTGGCAGAAAAGAAGAT 59.450 45.455 7.58 0.00 0.00 2.40
71 72 1.939934 CACGTGTGGCAGAAAAGAAGA 59.060 47.619 7.58 0.00 0.00 2.87
72 73 1.670811 ACACGTGTGGCAGAAAAGAAG 59.329 47.619 22.71 0.00 34.19 2.85
73 74 1.400142 CACACGTGTGGCAGAAAAGAA 59.600 47.619 35.65 0.00 42.10 2.52
74 75 1.013596 CACACGTGTGGCAGAAAAGA 58.986 50.000 35.65 0.00 42.10 2.52
75 76 1.013596 TCACACGTGTGGCAGAAAAG 58.986 50.000 39.88 17.96 45.65 2.27
76 77 3.160872 TCACACGTGTGGCAGAAAA 57.839 47.368 39.88 21.78 45.65 2.29
77 78 4.943822 TCACACGTGTGGCAGAAA 57.056 50.000 39.88 22.46 45.65 2.52
83 84 1.719246 CGATAACTGTCACACGTGTGG 59.281 52.381 39.88 28.84 45.65 4.17
84 85 2.404029 GTCGATAACTGTCACACGTGTG 59.596 50.000 37.04 37.04 46.91 3.82
85 86 2.658285 GTCGATAACTGTCACACGTGT 58.342 47.619 17.22 17.22 0.00 4.49
86 87 1.642360 CGTCGATAACTGTCACACGTG 59.358 52.381 15.48 15.48 0.00 4.49
87 88 1.265095 ACGTCGATAACTGTCACACGT 59.735 47.619 0.00 0.00 34.35 4.49
88 89 1.903139 GACGTCGATAACTGTCACACG 59.097 52.381 0.00 0.00 34.02 4.49
89 90 2.095364 AGGACGTCGATAACTGTCACAC 60.095 50.000 9.92 0.00 34.90 3.82
90 91 2.156917 AGGACGTCGATAACTGTCACA 58.843 47.619 9.92 0.00 34.90 3.58
91 92 2.915738 AGGACGTCGATAACTGTCAC 57.084 50.000 9.92 0.00 34.90 3.67
92 93 5.048504 AGTTTTAGGACGTCGATAACTGTCA 60.049 40.000 17.84 2.04 34.90 3.58
93 94 5.397326 AGTTTTAGGACGTCGATAACTGTC 58.603 41.667 17.84 0.67 33.48 3.51
94 95 5.382618 AGTTTTAGGACGTCGATAACTGT 57.617 39.130 17.84 2.95 0.00 3.55
95 96 7.514747 GCATTAGTTTTAGGACGTCGATAACTG 60.515 40.741 23.13 14.57 0.00 3.16
96 97 6.474751 GCATTAGTTTTAGGACGTCGATAACT 59.525 38.462 20.47 20.47 0.00 2.24
97 98 6.254157 TGCATTAGTTTTAGGACGTCGATAAC 59.746 38.462 9.92 11.09 0.00 1.89
98 99 6.331845 TGCATTAGTTTTAGGACGTCGATAA 58.668 36.000 9.92 8.52 0.00 1.75
99 100 5.893687 TGCATTAGTTTTAGGACGTCGATA 58.106 37.500 9.92 2.04 0.00 2.92
100 101 4.751060 TGCATTAGTTTTAGGACGTCGAT 58.249 39.130 9.92 3.12 0.00 3.59
101 102 4.177165 TGCATTAGTTTTAGGACGTCGA 57.823 40.909 9.92 0.00 0.00 4.20
102 103 6.764877 ATATGCATTAGTTTTAGGACGTCG 57.235 37.500 3.54 0.00 0.00 5.12
104 105 9.772973 TCATAATATGCATTAGTTTTAGGACGT 57.227 29.630 3.54 0.00 30.22 4.34
230 231 5.413833 CACATCTAAGCACATCTTTTCACCT 59.586 40.000 0.00 0.00 36.25 4.00
231 232 5.412594 TCACATCTAAGCACATCTTTTCACC 59.587 40.000 0.00 0.00 36.25 4.02
232 233 6.486253 TCACATCTAAGCACATCTTTTCAC 57.514 37.500 0.00 0.00 36.25 3.18
233 234 8.833493 CATATCACATCTAAGCACATCTTTTCA 58.167 33.333 0.00 0.00 36.25 2.69
234 235 7.802251 GCATATCACATCTAAGCACATCTTTTC 59.198 37.037 0.00 0.00 36.25 2.29
538 539 6.928492 GGCACTTTTTGTTAATCCATCTTTCA 59.072 34.615 0.00 0.00 0.00 2.69
593 594 5.299949 ACAAAAGGCTGGAAATCACATTTC 58.700 37.500 0.00 1.01 46.05 2.17
679 680 3.109619 GACTCGGCGACTTTCTATCTTG 58.890 50.000 4.99 0.00 0.00 3.02
818 819 6.429692 TCCAACAGCCAATAAATATATGTCCG 59.570 38.462 0.00 0.00 0.00 4.79
959 960 4.579127 GGTTGCACACAGACCCTT 57.421 55.556 0.00 0.00 0.00 3.95
1204 1211 0.608640 CAGTGTACCTCGAAGCCCTT 59.391 55.000 0.00 0.00 0.00 3.95
1242 1249 4.796231 GCGAGAAAGGCGCGAGGA 62.796 66.667 12.10 0.00 45.27 3.71
1278 1285 2.284995 GAGCCCTCCCACTGGTCT 60.285 66.667 0.00 0.00 0.00 3.85
1279 1286 3.403558 GGAGCCCTCCCACTGGTC 61.404 72.222 2.81 0.00 43.94 4.02
1411 1418 1.043816 CACAGGTATGAGATCCCGCT 58.956 55.000 0.00 0.00 0.00 5.52
1449 1456 2.220133 CGTGTAGAACTTGAACAACCCG 59.780 50.000 0.00 0.00 0.00 5.28
1464 1471 1.686355 AGGAGAGAGGCATCGTGTAG 58.314 55.000 0.00 0.00 0.00 2.74
1481 1488 2.184167 ACGCCAAACGGTGTGAAGG 61.184 57.895 0.00 0.00 45.67 3.46
2943 3103 6.061441 TCACTTTTTGCAGGTTATCTTCAGA 58.939 36.000 0.00 0.00 0.00 3.27
3299 3459 7.906327 AGTTAAGGTACCCTTACGTATCAAAA 58.094 34.615 8.74 0.00 44.64 2.44
3577 3737 8.243426 TCAATATCCTTCTTTGTACAACATTGC 58.757 33.333 8.07 0.00 0.00 3.56
3638 3798 0.759959 TGCCACTACGAGGTTTTGGA 59.240 50.000 0.00 0.00 0.00 3.53
3695 3855 7.039714 GGAAGGGTTTGATGAGAGTTAAACAAT 60.040 37.037 0.00 0.00 35.35 2.71
3975 4332 5.871396 AAAGGCTAGATTTCTACCGATCA 57.129 39.130 0.00 0.00 0.00 2.92
3992 4349 2.282180 TGGGCGTCAGGAAAAGGC 60.282 61.111 0.00 0.00 0.00 4.35
4059 4416 7.659390 GGAGGACGATTGATTCTGATTAATTCT 59.341 37.037 0.00 0.00 0.00 2.40
4770 5129 1.067060 GAAGGGGTTGTTGTCTTGCAC 59.933 52.381 0.00 0.00 0.00 4.57
5154 5965 4.211374 AGAAAAGTTCACAGATTTCGACGG 59.789 41.667 0.00 0.00 36.99 4.79
5244 6055 5.772393 ACTGGATCACCTATAACCAAACA 57.228 39.130 0.00 0.00 37.04 2.83
5650 6858 9.212641 TGTGAAAATGAAAGTGAAAACATGAAA 57.787 25.926 0.00 0.00 0.00 2.69
5652 6860 8.034215 AGTGTGAAAATGAAAGTGAAAACATGA 58.966 29.630 0.00 0.00 0.00 3.07
5761 6969 9.983024 TGGAAATACCACTTTGGATAATCTAAA 57.017 29.630 0.00 0.00 44.64 1.85
6923 8386 2.009042 GCACACTGGTACTCATCAGGC 61.009 57.143 0.00 0.00 35.47 4.85
7383 8846 2.034305 CGTATCCGAGAAAATCCGACCT 59.966 50.000 0.00 0.00 35.63 3.85
7501 8964 6.433766 CAACTTCTTTTTGTGAGGACTGATC 58.566 40.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.