Multiple sequence alignment - TraesCS5A01G370400

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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 TraesCS5A01G370400 chr5A 100.000 2315 0 0 1 2315 569806519 569808833 0.000000e+00 4276
1 TraesCS5A01G370400 chr5A 97.706 654 15 0 1637 2290 458491116 458490463 0.000000e+00 1125
2 TraesCS5A01G370400 chr5A 97.706 654 14 1 1637 2290 490597492 490598144 0.000000e+00 1123
3 TraesCS5A01G370400 chr5A 97.401 654 17 0 1637 2290 15199086 15199739 0.000000e+00 1114
4 TraesCS5A01G370400 chr5A 97.008 635 19 0 1656 2290 705625501 705624867 0.000000e+00 1068
5 TraesCS5A01G370400 chr5A 96.011 351 13 1 1269 1619 405564385 405564734 9.280000e-159 569
6 TraesCS5A01G370400 chr4A 93.854 1025 28 6 1269 2290 562200652 562199660 0.000000e+00 1511
7 TraesCS5A01G370400 chr7A 92.766 1023 37 4 1268 2290 15405263 15404278 0.000000e+00 1445
8 TraesCS5A01G370400 chr7A 97.859 654 14 0 1637 2290 643585619 643584966 0.000000e+00 1131
9 TraesCS5A01G370400 chr7A 97.401 654 17 0 1637 2290 705708010 705708663 0.000000e+00 1114
10 TraesCS5A01G370400 chr7A 96.591 352 12 0 1268 1619 705707687 705708038 3.310000e-163 584
11 TraesCS5A01G370400 chr7A 95.531 358 14 1 1264 1619 312400782 312400425 2.580000e-159 571
12 TraesCS5A01G370400 chr4B 89.806 1030 52 25 1268 2290 662622379 662623362 0.000000e+00 1271
13 TraesCS5A01G370400 chr4B 95.181 83 3 1 1 82 85349920 85350002 1.870000e-26 130
14 TraesCS5A01G370400 chr3A 97.843 649 14 0 1642 2290 645950359 645951007 0.000000e+00 1122
15 TraesCS5A01G370400 chr3A 97.401 654 17 0 1637 2290 714840317 714839664 0.000000e+00 1114
16 TraesCS5A01G370400 chr2A 97.546 652 16 0 1639 2290 769173947 769174598 0.000000e+00 1116
17 TraesCS5A01G370400 chr2A 93.750 384 23 1 1268 1650 605659732 605660115 1.990000e-160 575
18 TraesCS5A01G370400 chr2A 96.286 350 12 1 1269 1618 740226414 740226762 7.170000e-160 573
19 TraesCS5A01G370400 chr5B 91.933 719 46 6 119 827 550562567 550563283 0.000000e+00 996
20 TraesCS5A01G370400 chr5B 92.093 430 30 2 842 1268 550563383 550563811 9.150000e-169 603
21 TraesCS5A01G370400 chr5B 89.931 437 36 4 1268 1697 6539374 6539809 7.230000e-155 556
22 TraesCS5A01G370400 chr5D 91.621 728 47 5 68 783 450637003 450637728 0.000000e+00 994
23 TraesCS5A01G370400 chr5D 91.743 436 25 6 843 1268 450637756 450638190 1.530000e-166 595
24 TraesCS5A01G370400 chr7B 91.795 390 28 3 1268 1657 68262320 68261935 7.280000e-150 540
25 TraesCS5A01G370400 chr7B 100.000 72 0 0 1 72 547472440 547472369 1.440000e-27 134
26 TraesCS5A01G370400 chr7D 98.667 75 1 0 1 75 126669736 126669810 1.440000e-27 134
27 TraesCS5A01G370400 chr7D 98.630 73 1 0 1 73 227507189 227507117 1.870000e-26 130
28 TraesCS5A01G370400 chr6B 100.000 72 0 0 1 72 4138091 4138020 1.440000e-27 134
29 TraesCS5A01G370400 chr6B 96.203 79 2 1 1 79 156651508 156651431 6.710000e-26 128
30 TraesCS5A01G370400 chr6B 96.154 78 3 0 1 78 714341419 714341342 6.710000e-26 128
31 TraesCS5A01G370400 chr6D 98.667 75 0 1 1 75 468540982 468540909 5.190000e-27 132
32 TraesCS5A01G370400 chr6D 100.000 70 0 0 1 70 32929183 32929252 1.870000e-26 130
33 TraesCS5A01G370400 chr6D 100.000 69 0 0 1 69 3196420 3196488 6.710000e-26 128
34 TraesCS5A01G370400 chr6D 100.000 69 0 0 1 69 25667074 25667006 6.710000e-26 128
35 TraesCS5A01G370400 chr6D 100.000 69 0 0 1 69 67156496 67156428 6.710000e-26 128
36 TraesCS5A01G370400 chr6D 96.104 77 3 0 1 77 457694059 457693983 2.410000e-25 126
37 TraesCS5A01G370400 chr2B 98.649 74 1 0 1 74 154145974 154145901 5.190000e-27 132
38 TraesCS5A01G370400 chr1B 100.000 71 0 0 1 71 669891505 669891575 5.190000e-27 132
39 TraesCS5A01G370400 chrUn 98.630 73 1 0 1 73 143995262 143995334 1.870000e-26 130
40 TraesCS5A01G370400 chrUn 100.000 70 0 0 1 70 355880563 355880494 1.870000e-26 130
41 TraesCS5A01G370400 chrUn 98.611 72 1 0 1 72 322990723 322990652 6.710000e-26 128
42 TraesCS5A01G370400 chrUn 97.297 74 2 0 1 74 150796019 150795946 2.410000e-25 126
43 TraesCS5A01G370400 chrUn 98.571 70 1 0 1 70 91488946 91489015 8.680000e-25 124
44 TraesCS5A01G370400 chrUn 98.571 70 1 0 1 70 110700207 110700138 8.680000e-25 124
45 TraesCS5A01G370400 chrUn 98.551 69 1 0 1 69 15981895 15981827 3.120000e-24 122
46 TraesCS5A01G370400 chrUn 98.551 69 1 0 1 69 40943202 40943134 3.120000e-24 122
47 TraesCS5A01G370400 chrUn 98.551 69 1 0 1 69 260324666 260324734 3.120000e-24 122
48 TraesCS5A01G370400 chrUn 97.222 72 2 0 1 72 267451472 267451401 3.120000e-24 122
49 TraesCS5A01G370400 chrUn 97.222 72 2 0 1 72 340254840 340254769 3.120000e-24 122
50 TraesCS5A01G370400 chr3D 100.000 70 0 0 1 70 419583041 419583110 1.870000e-26 130
51 TraesCS5A01G370400 chr3D 100.000 70 0 0 1 70 582122970 582123039 1.870000e-26 130
52 TraesCS5A01G370400 chr1D 98.630 73 1 0 1 73 202554449 202554521 1.870000e-26 130
53 TraesCS5A01G370400 chr1D 94.937 79 4 0 1 79 448026769 448026691 8.680000e-25 124
54 TraesCS5A01G370400 chr3B 96.203 79 2 1 1 79 205166431 205166354 6.710000e-26 128
55 TraesCS5A01G370400 chr2D 95.000 80 2 2 1 80 313224867 313224790 8.680000e-25 124
56 TraesCS5A01G370400 chr1A 94.937 79 4 0 1 79 374426098 374426020 8.680000e-25 124
57 TraesCS5A01G370400 chr1A 93.976 83 4 1 1 82 518077270 518077188 8.680000e-25 124


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 TraesCS5A01G370400 chr5A 569806519 569808833 2314 False 4276.0 4276 100.000 1 2315 1 chr5A.!!$F4 2314
1 TraesCS5A01G370400 chr5A 458490463 458491116 653 True 1125.0 1125 97.706 1637 2290 1 chr5A.!!$R1 653
2 TraesCS5A01G370400 chr5A 490597492 490598144 652 False 1123.0 1123 97.706 1637 2290 1 chr5A.!!$F3 653
3 TraesCS5A01G370400 chr5A 15199086 15199739 653 False 1114.0 1114 97.401 1637 2290 1 chr5A.!!$F1 653
4 TraesCS5A01G370400 chr5A 705624867 705625501 634 True 1068.0 1068 97.008 1656 2290 1 chr5A.!!$R2 634
5 TraesCS5A01G370400 chr4A 562199660 562200652 992 True 1511.0 1511 93.854 1269 2290 1 chr4A.!!$R1 1021
6 TraesCS5A01G370400 chr7A 15404278 15405263 985 True 1445.0 1445 92.766 1268 2290 1 chr7A.!!$R1 1022
7 TraesCS5A01G370400 chr7A 643584966 643585619 653 True 1131.0 1131 97.859 1637 2290 1 chr7A.!!$R3 653
8 TraesCS5A01G370400 chr7A 705707687 705708663 976 False 849.0 1114 96.996 1268 2290 2 chr7A.!!$F1 1022
9 TraesCS5A01G370400 chr4B 662622379 662623362 983 False 1271.0 1271 89.806 1268 2290 1 chr4B.!!$F2 1022
10 TraesCS5A01G370400 chr3A 645950359 645951007 648 False 1122.0 1122 97.843 1642 2290 1 chr3A.!!$F1 648
11 TraesCS5A01G370400 chr3A 714839664 714840317 653 True 1114.0 1114 97.401 1637 2290 1 chr3A.!!$R1 653
12 TraesCS5A01G370400 chr2A 769173947 769174598 651 False 1116.0 1116 97.546 1639 2290 1 chr2A.!!$F3 651
13 TraesCS5A01G370400 chr5B 550562567 550563811 1244 False 799.5 996 92.013 119 1268 2 chr5B.!!$F2 1149
14 TraesCS5A01G370400 chr5D 450637003 450638190 1187 False 794.5 994 91.682 68 1268 2 chr5D.!!$F1 1200

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
944 1060 0.03438 TCGATCGTCTCCCTGTCCTT 60.034 55.0 15.94 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2436 0.179215 GCGAATGGAAACGACAGCTG 60.179 55.0 13.48 13.48 0.0 4.24 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
40 41 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
41 42 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
42 43 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
43 44 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
44 45 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
45 46 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
46 47 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
47 48 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
48 49 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
49 50 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
50 51 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
51 52 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
52 53 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
53 54 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
54 55 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
55 56 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
56 57 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
57 58 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
58 59 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
59 60 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
60 61 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
61 62 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
62 63 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
63 64 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
64 65 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
65 66 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
66 67 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
82 83 5.570034 CGGAGGGAGTAGGTTTGTTCAATTA 60.570 44.000 0.00 0.00 0.00 1.40
98 99 7.479980 TGTTCAATTAGGATTTTTGGCTATCG 58.520 34.615 0.00 0.00 0.00 2.92
107 108 0.742990 TTTGGCTATCGTGGCTTCGG 60.743 55.000 3.35 0.00 0.00 4.30
112 113 0.596083 CTATCGTGGCTTCGGCTCTG 60.596 60.000 3.35 0.00 41.44 3.35
149 152 5.209240 GTTTCTCTAGATCATCCTTCGACG 58.791 45.833 0.00 0.00 0.00 5.12
165 168 2.528688 TCGACGCGAAATAGTTTGATCG 59.471 45.455 15.93 7.11 38.28 3.69
166 169 2.346376 CGACGCGAAATAGTTTGATCGG 60.346 50.000 15.93 0.00 35.91 4.18
203 206 0.109342 CCTCTGCTCTTGGTGTTGGT 59.891 55.000 0.00 0.00 0.00 3.67
209 212 2.224523 TGCTCTTGGTGTTGGTTCTAGG 60.225 50.000 0.00 0.00 0.00 3.02
281 284 1.003839 GTCATGGCGTCAAGGTCCA 60.004 57.895 0.00 0.00 0.00 4.02
320 323 3.190744 AGTCGTCTTCGTCATTCTTAGCA 59.809 43.478 0.00 0.00 38.33 3.49
336 339 0.980423 AGCACTTCTCCTTGTCCTCC 59.020 55.000 0.00 0.00 0.00 4.30
379 382 3.951563 TTTGGATAATGGCCACTAGCT 57.048 42.857 8.16 0.00 43.05 3.32
385 388 2.426842 AATGGCCACTAGCTTCTTCC 57.573 50.000 8.16 0.00 43.05 3.46
405 408 1.140816 GGCATATCTCGACGGCTTTC 58.859 55.000 0.00 0.00 0.00 2.62
438 441 1.129437 CAAAGTCTTGCTAGCTTCGGC 59.871 52.381 17.23 5.64 42.17 5.54
467 470 3.642705 CAGAGTTTCAGTCGTGACATCA 58.357 45.455 2.44 0.00 30.10 3.07
468 471 3.672397 CAGAGTTTCAGTCGTGACATCAG 59.328 47.826 2.44 0.00 30.10 2.90
502 506 3.887110 GGACATCAAGCATGAATCATGGA 59.113 43.478 22.95 13.05 41.64 3.41
599 611 0.466555 TTGTCCAAGGAACCGGTTGG 60.467 55.000 27.87 20.99 44.08 3.77
608 620 4.376225 AGGAACCGGTTGGAATTTCTAA 57.624 40.909 27.87 0.00 39.21 2.10
612 624 6.269077 AGGAACCGGTTGGAATTTCTAATTTT 59.731 34.615 27.87 0.00 39.21 1.82
684 699 9.724839 TTTGCATTAAGAACAACAACTACTTAC 57.275 29.630 0.00 0.00 0.00 2.34
741 756 3.067461 CCAACTCATTTTTCGGGTGACAA 59.933 43.478 0.00 0.00 0.00 3.18
753 768 8.576936 TTTTCGGGTGACAATTACAAAATAAC 57.423 30.769 0.00 0.00 0.00 1.89
757 772 6.804783 CGGGTGACAATTACAAAATAACTTCC 59.195 38.462 0.00 0.00 0.00 3.46
831 852 8.603242 AAATATACATGATTTACGTGGTCCTC 57.397 34.615 0.00 0.00 39.59 3.71
832 853 3.261981 ACATGATTTACGTGGTCCTCC 57.738 47.619 0.00 0.00 39.59 4.30
833 854 2.838202 ACATGATTTACGTGGTCCTCCT 59.162 45.455 0.00 0.00 39.59 3.69
834 855 4.028131 ACATGATTTACGTGGTCCTCCTA 58.972 43.478 0.00 0.00 39.59 2.94
836 857 3.705051 TGATTTACGTGGTCCTCCTACT 58.295 45.455 0.00 0.00 34.23 2.57
837 858 4.858850 TGATTTACGTGGTCCTCCTACTA 58.141 43.478 0.00 0.00 34.23 1.82
838 859 4.641989 TGATTTACGTGGTCCTCCTACTAC 59.358 45.833 0.00 0.00 34.23 2.73
840 861 3.165606 CGTGGTCCTCCTACTACGT 57.834 57.895 4.95 0.00 45.75 3.57
944 1060 0.034380 TCGATCGTCTCCCTGTCCTT 60.034 55.000 15.94 0.00 0.00 3.36
962 1078 4.213270 GTCCTTGCATATAAATACGCAGCA 59.787 41.667 0.00 0.00 35.47 4.41
966 1082 2.483877 GCATATAAATACGCAGCAGCCA 59.516 45.455 0.00 0.00 37.52 4.75
985 1101 1.153823 CCGATCGCAGAACCGAAGT 60.154 57.895 10.32 0.00 43.58 3.01
990 1106 0.671796 TCGCAGAACCGAAGTCAGAA 59.328 50.000 0.00 0.00 33.77 3.02
1252 1368 2.337532 CCAACTTCGACGACCCGT 59.662 61.111 0.00 0.00 45.10 5.28
1317 1433 2.027837 GGTTCGTAAGGCCCTTTAGTGA 60.028 50.000 0.00 0.00 38.47 3.41
1329 1445 4.777463 CCCTTTAGTGACGGTTCCATAAT 58.223 43.478 0.00 0.00 0.00 1.28
1332 1448 4.987408 TTAGTGACGGTTCCATAATCGA 57.013 40.909 0.00 0.00 41.92 3.59
1357 1473 4.821935 GTGTGGGCACTAAAGGCT 57.178 55.556 0.00 0.00 42.13 4.58
1593 1716 6.714492 ACACATTGTACACGTTATGCATATG 58.286 36.000 7.36 5.75 0.00 1.78
1635 1774 7.770801 ATATATATGTGTGTGTGTGTGTGTC 57.229 36.000 0.00 0.00 0.00 3.67
1851 1994 2.483877 GCACGATGACAATTGGAAGTGA 59.516 45.455 10.83 0.00 0.00 3.41
1990 2133 2.032681 GAGCTTGTCCCGCACCTT 59.967 61.111 0.00 0.00 0.00 3.50
2010 2153 6.094881 CACCTTTGTGAACTGTTAAGAAGGAA 59.905 38.462 19.57 0.00 45.76 3.36
2056 2199 9.067986 AGTTGTGTGACTAGATATCGATAATGA 57.932 33.333 9.61 0.00 0.00 2.57
2292 2438 6.476243 GCTAGCTAGCTAGTACTACTTCAG 57.524 45.833 39.05 21.46 45.67 3.02
2293 2439 5.106830 GCTAGCTAGCTAGTACTACTTCAGC 60.107 48.000 39.05 25.97 45.67 4.26
2294 2440 5.043737 AGCTAGCTAGTACTACTTCAGCT 57.956 43.478 17.69 18.53 44.43 4.24
2295 2441 4.819630 AGCTAGCTAGTACTACTTCAGCTG 59.180 45.833 21.99 7.63 42.34 4.24
2296 2442 4.577283 GCTAGCTAGTACTACTTCAGCTGT 59.423 45.833 21.99 4.90 42.34 4.40
2297 2443 5.277634 GCTAGCTAGTACTACTTCAGCTGTC 60.278 48.000 21.99 12.30 42.34 3.51
2298 2444 3.623960 AGCTAGTACTACTTCAGCTGTCG 59.376 47.826 14.83 8.49 40.92 4.35
2299 2445 3.374678 GCTAGTACTACTTCAGCTGTCGT 59.625 47.826 14.67 13.96 0.00 4.34
2300 2446 4.142643 GCTAGTACTACTTCAGCTGTCGTT 60.143 45.833 14.67 0.00 0.00 3.85
2301 2447 4.850347 AGTACTACTTCAGCTGTCGTTT 57.150 40.909 14.67 5.60 0.00 3.60
2302 2448 4.796369 AGTACTACTTCAGCTGTCGTTTC 58.204 43.478 14.67 0.00 0.00 2.78
2303 2449 3.027974 ACTACTTCAGCTGTCGTTTCC 57.972 47.619 14.67 0.00 0.00 3.13
2304 2450 2.364324 ACTACTTCAGCTGTCGTTTCCA 59.636 45.455 14.67 0.00 0.00 3.53
2305 2451 2.550830 ACTTCAGCTGTCGTTTCCAT 57.449 45.000 14.67 0.00 0.00 3.41
2306 2452 2.851195 ACTTCAGCTGTCGTTTCCATT 58.149 42.857 14.67 0.00 0.00 3.16
2307 2453 2.808543 ACTTCAGCTGTCGTTTCCATTC 59.191 45.455 14.67 0.00 0.00 2.67
2308 2454 1.428448 TCAGCTGTCGTTTCCATTCG 58.572 50.000 14.67 0.00 0.00 3.34
2309 2455 0.179215 CAGCTGTCGTTTCCATTCGC 60.179 55.000 5.25 0.00 0.00 4.70
2310 2456 1.134694 GCTGTCGTTTCCATTCGCC 59.865 57.895 0.00 0.00 0.00 5.54
2311 2457 1.298859 GCTGTCGTTTCCATTCGCCT 61.299 55.000 0.00 0.00 0.00 5.52
2312 2458 1.156736 CTGTCGTTTCCATTCGCCTT 58.843 50.000 0.00 0.00 0.00 4.35
2313 2459 1.128692 CTGTCGTTTCCATTCGCCTTC 59.871 52.381 0.00 0.00 0.00 3.46
2314 2460 0.446616 GTCGTTTCCATTCGCCTTCC 59.553 55.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
15 16 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
16 17 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
17 18 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
18 19 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
19 20 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
20 21 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
21 22 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
22 23 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
23 24 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
24 25 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
25 26 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
26 27 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
27 28 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
28 29 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
29 30 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
30 31 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
31 32 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
32 33 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
33 34 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
34 35 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
35 36 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
36 37 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
37 38 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
38 39 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
39 40 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
40 41 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
41 42 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
42 43 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
43 44 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
44 45 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
45 46 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
46 47 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
47 48 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
48 49 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
49 50 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
50 51 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
51 52 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
52 53 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
53 54 0.969409 AACCTACTCCCTCCGTTCGG 60.969 60.000 4.74 4.74 0.00 4.30
54 55 0.893447 AAACCTACTCCCTCCGTTCG 59.107 55.000 0.00 0.00 0.00 3.95
55 56 1.622312 ACAAACCTACTCCCTCCGTTC 59.378 52.381 0.00 0.00 0.00 3.95
56 57 1.725803 ACAAACCTACTCCCTCCGTT 58.274 50.000 0.00 0.00 0.00 4.44
57 58 1.622312 GAACAAACCTACTCCCTCCGT 59.378 52.381 0.00 0.00 0.00 4.69
58 59 1.621814 TGAACAAACCTACTCCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
59 60 3.782656 TTGAACAAACCTACTCCCTCC 57.217 47.619 0.00 0.00 0.00 4.30
60 61 5.880887 CCTAATTGAACAAACCTACTCCCTC 59.119 44.000 0.00 0.00 0.00 4.30
61 62 5.550403 TCCTAATTGAACAAACCTACTCCCT 59.450 40.000 0.00 0.00 0.00 4.20
62 63 5.812286 TCCTAATTGAACAAACCTACTCCC 58.188 41.667 0.00 0.00 0.00 4.30
63 64 7.939784 AATCCTAATTGAACAAACCTACTCC 57.060 36.000 0.00 0.00 0.00 3.85
65 66 9.981114 CAAAAATCCTAATTGAACAAACCTACT 57.019 29.630 0.00 0.00 0.00 2.57
66 67 9.203421 CCAAAAATCCTAATTGAACAAACCTAC 57.797 33.333 0.00 0.00 0.00 3.18
82 83 2.024414 GCCACGATAGCCAAAAATCCT 58.976 47.619 0.00 0.00 42.67 3.24
98 99 2.811317 CGTCAGAGCCGAAGCCAC 60.811 66.667 0.00 0.00 41.25 5.01
107 108 1.134560 ACCTTATTCGACCGTCAGAGC 59.865 52.381 0.00 0.00 0.00 4.09
112 113 4.107363 AGAGAAACCTTATTCGACCGTC 57.893 45.455 0.00 0.00 34.46 4.79
149 152 1.602377 CCCCCGATCAAACTATTTCGC 59.398 52.381 0.00 0.00 0.00 4.70
165 168 3.391382 CTGACCTGGTCGACCCCC 61.391 72.222 31.19 17.11 34.95 5.40
166 169 3.391382 CCTGACCTGGTCGACCCC 61.391 72.222 31.19 17.45 34.95 4.95
203 206 3.451402 TGCAGACACTACCTCCTAGAA 57.549 47.619 0.00 0.00 0.00 2.10
209 212 3.551046 CCATACGATGCAGACACTACCTC 60.551 52.174 0.00 0.00 0.00 3.85
281 284 2.352421 CGACTACCACCTTCGTCAACAT 60.352 50.000 0.00 0.00 0.00 2.71
320 323 2.381961 AGAGAGGAGGACAAGGAGAAGT 59.618 50.000 0.00 0.00 0.00 3.01
336 339 0.535328 TGGATCGTCGCCCTAGAGAG 60.535 60.000 0.00 0.00 0.00 3.20
379 382 1.001706 CGTCGAGATATGCCGGAAGAA 60.002 52.381 5.05 0.00 0.00 2.52
385 388 0.597637 AAAGCCGTCGAGATATGCCG 60.598 55.000 0.00 0.00 0.00 5.69
438 441 1.728971 GACTGAAACTCTGCATCACCG 59.271 52.381 0.00 0.00 0.00 4.94
467 470 0.107456 GATGTCCGTGATCCATGCCT 59.893 55.000 0.00 0.00 0.00 4.75
468 471 0.179048 TGATGTCCGTGATCCATGCC 60.179 55.000 0.00 0.00 0.00 4.40
512 516 2.126463 CTCGATGTCCGCACACGT 60.126 61.111 2.32 0.00 34.48 4.49
612 624 1.710816 CTTACAAGGCAACCCCCAAA 58.289 50.000 0.00 0.00 37.17 3.28
615 627 1.304962 CCCTTACAAGGCAACCCCC 60.305 63.158 2.22 0.00 45.10 5.40
677 689 4.583073 ACCCCAAAACAGCAAAGTAAGTAG 59.417 41.667 0.00 0.00 0.00 2.57
683 698 6.680148 ATTAATACCCCAAAACAGCAAAGT 57.320 33.333 0.00 0.00 0.00 2.66
684 699 7.659390 TCAAATTAATACCCCAAAACAGCAAAG 59.341 33.333 0.00 0.00 0.00 2.77
732 747 6.804783 GGAAGTTATTTTGTAATTGTCACCCG 59.195 38.462 0.00 0.00 0.00 5.28
810 831 4.654262 AGGAGGACCACGTAAATCATGTAT 59.346 41.667 0.00 0.00 38.94 2.29
815 836 3.705051 AGTAGGAGGACCACGTAAATCA 58.295 45.455 0.00 0.00 38.94 2.57
832 853 3.120060 AACTCAGGTTGCGTACGTAGTAG 60.120 47.826 17.90 8.66 37.78 2.57
833 854 2.426522 ACTCAGGTTGCGTACGTAGTA 58.573 47.619 17.90 0.00 45.11 1.82
834 855 1.610522 AACTCAGGTTGCGTACGTAGT 59.389 47.619 17.90 2.36 38.37 2.73
836 857 2.054687 CAACTCAGGTTGCGTACGTA 57.945 50.000 17.90 10.06 44.83 3.57
837 858 2.895039 CAACTCAGGTTGCGTACGT 58.105 52.632 17.90 0.00 44.83 3.57
838 859 1.602165 ACTCAACTCAGGTTGCGTACG 60.602 52.381 11.84 11.84 45.71 3.67
840 861 1.335597 CGACTCAACTCAGGTTGCGTA 60.336 52.381 4.81 0.00 46.93 4.42
878 984 2.435059 GCCGACTCCAACTCAGCC 60.435 66.667 0.00 0.00 0.00 4.85
879 985 2.811317 CGCCGACTCCAACTCAGC 60.811 66.667 0.00 0.00 0.00 4.26
909 1022 1.374252 CGAGGACTTTGGGTCGGTG 60.374 63.158 0.00 0.00 45.35 4.94
910 1023 0.903454 ATCGAGGACTTTGGGTCGGT 60.903 55.000 0.00 0.00 45.35 4.69
962 1078 2.125512 GTTCTGCGATCGGTGGCT 60.126 61.111 18.30 0.00 0.00 4.75
966 1082 1.153823 CTTCGGTTCTGCGATCGGT 60.154 57.895 18.30 0.00 0.00 4.69
985 1101 4.663166 GTCGTCATCTTCGATCTTTCTGA 58.337 43.478 0.00 0.00 39.45 3.27
990 1106 3.374367 TCTTCGTCGTCATCTTCGATCTT 59.626 43.478 0.00 0.00 39.45 2.40
1155 1271 2.037527 AGGACGTGGGAGAGGACC 59.962 66.667 0.00 0.00 0.00 4.46
1215 1331 1.221021 GATGTGGTCGAAGGGGTCC 59.779 63.158 0.00 0.00 0.00 4.46
1228 1344 0.037697 TCGTCGAAGTTGGGGATGTG 60.038 55.000 0.00 0.00 0.00 3.21
1285 1401 2.417651 CCTTACGAACCGGTGCTATTGA 60.418 50.000 8.52 0.00 0.00 2.57
1317 1433 4.724074 TTAGTGTCGATTATGGAACCGT 57.276 40.909 0.00 0.00 0.00 4.83
1357 1473 1.203288 TGAACCGGTACTAAAGGGGGA 60.203 52.381 8.00 0.00 0.00 4.81
1609 1748 9.476202 GACACACACACACACACATATATATAT 57.524 33.333 0.00 0.00 0.00 0.86
1610 1749 8.691797 AGACACACACACACACACATATATATA 58.308 33.333 0.00 0.00 0.00 0.86
1611 1750 7.555965 AGACACACACACACACACATATATAT 58.444 34.615 0.00 0.00 0.00 0.86
1612 1751 6.930731 AGACACACACACACACACATATATA 58.069 36.000 0.00 0.00 0.00 0.86
1613 1752 5.793817 AGACACACACACACACACATATAT 58.206 37.500 0.00 0.00 0.00 0.86
1614 1753 5.208463 AGACACACACACACACACATATA 57.792 39.130 0.00 0.00 0.00 0.86
1615 1754 4.071961 AGACACACACACACACACATAT 57.928 40.909 0.00 0.00 0.00 1.78
1616 1755 3.535280 AGACACACACACACACACATA 57.465 42.857 0.00 0.00 0.00 2.29
1617 1756 2.401583 AGACACACACACACACACAT 57.598 45.000 0.00 0.00 0.00 3.21
1618 1757 3.535280 ATAGACACACACACACACACA 57.465 42.857 0.00 0.00 0.00 3.72
1765 1908 6.376978 GCAACATGCATATGTAGGAGAAATC 58.623 40.000 12.50 0.00 46.54 2.17
1851 1994 1.141657 CCCATCGACCAGGTCATGAAT 59.858 52.381 23.44 9.63 32.09 2.57
1990 2133 7.873719 TGATTTCCTTCTTAACAGTTCACAA 57.126 32.000 0.00 0.00 0.00 3.33
2010 2153 9.955208 CACAACTAATACACATGCATATTGATT 57.045 29.630 13.16 7.61 0.00 2.57
2290 2436 0.179215 GCGAATGGAAACGACAGCTG 60.179 55.000 13.48 13.48 0.00 4.24
2291 2437 1.298859 GGCGAATGGAAACGACAGCT 61.299 55.000 0.00 0.00 37.49 4.24
2292 2438 1.134694 GGCGAATGGAAACGACAGC 59.865 57.895 0.00 0.00 37.49 4.40
2293 2439 1.128692 GAAGGCGAATGGAAACGACAG 59.871 52.381 0.00 0.00 40.24 3.51
2294 2440 1.153353 GAAGGCGAATGGAAACGACA 58.847 50.000 0.00 0.00 40.24 4.35
2295 2441 0.446616 GGAAGGCGAATGGAAACGAC 59.553 55.000 0.00 0.00 37.85 4.34
2296 2442 2.849081 GGAAGGCGAATGGAAACGA 58.151 52.632 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.