Multiple sequence alignment - TraesCS2A01G248100

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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 TraesCS2A01G248100 chr2A 100.000 3166 0 0 1 3166 369217728 369214563 0.000000e+00 5847.0
1 TraesCS2A01G248100 chr2A 89.351 770 55 14 1473 2227 65175364 65174607 0.000000e+00 942.0
2 TraesCS2A01G248100 chr2A 81.839 892 131 15 570 1430 65176258 65175367 0.000000e+00 721.0
3 TraesCS2A01G248100 chr2A 85.851 417 37 9 2311 2721 65174578 65174178 1.050000e-114 424.0
4 TraesCS2A01G248100 chr2A 93.694 222 14 0 2871 3092 65174089 65173868 1.820000e-87 333.0
5 TraesCS2A01G248100 chr2A 100.000 30 0 0 1930 1959 65176548 65176519 4.410000e-04 56.5
6 TraesCS2A01G248100 chr2B 87.332 1634 157 25 1 1599 364927247 364928865 0.000000e+00 1825.0
7 TraesCS2A01G248100 chr2B 93.134 670 43 2 2055 2723 364948356 364949023 0.000000e+00 979.0
8 TraesCS2A01G248100 chr2B 92.944 411 27 2 1591 2000 364947955 364948364 5.850000e-167 597.0
9 TraesCS2A01G248100 chr2B 84.469 367 38 14 2739 3092 364949123 364949483 8.410000e-91 344.0
10 TraesCS2A01G248100 chr2B 84.615 104 16 0 2735 2838 36611217 36611114 1.550000e-18 104.0
11 TraesCS2A01G248100 chr2B 83.133 83 12 2 1378 1459 178796537 178796456 1.220000e-09 75.0
12 TraesCS2A01G248100 chr2D 93.822 696 41 2 1714 2408 296710806 296710112 0.000000e+00 1046.0
13 TraesCS2A01G248100 chr2D 87.528 890 65 28 1471 2338 63556082 63555217 0.000000e+00 987.0
14 TraesCS2A01G248100 chr2D 88.324 728 54 12 2392 3092 296709956 296709233 0.000000e+00 845.0
15 TraesCS2A01G248100 chr2D 84.766 768 104 10 677 1434 63556843 63556079 0.000000e+00 758.0
16 TraesCS2A01G248100 chr2D 87.037 324 27 4 2417 2731 63555220 63554903 5.020000e-93 351.0
17 TraesCS2A01G248100 chr2D 92.342 222 17 0 2871 3092 63554757 63554536 1.830000e-82 316.0
18 TraesCS2A01G248100 chr2D 72.770 426 83 24 1046 1463 22098305 22098705 2.580000e-21 113.0
19 TraesCS2A01G248100 chr2D 95.122 41 2 0 1 41 138452866 138452826 7.330000e-07 65.8
20 TraesCS2A01G248100 chr7D 78.337 457 75 17 17 457 622542296 622541848 1.120000e-69 274.0
21 TraesCS2A01G248100 chr7D 84.615 91 14 0 1369 1459 630793262 630793352 1.210000e-14 91.6
22 TraesCS2A01G248100 chr3A 80.339 295 49 8 13 302 661665609 661665899 6.880000e-52 215.0
23 TraesCS2A01G248100 chr3D 80.545 257 46 4 13 266 527132040 527132295 8.960000e-46 195.0
24 TraesCS2A01G248100 chr3D 96.000 50 2 0 1 50 233201632 233201681 7.280000e-12 82.4
25 TraesCS2A01G248100 chr7A 81.604 212 35 3 785 994 145394005 145393796 4.200000e-39 172.0
26 TraesCS2A01G248100 chr7A 77.720 193 34 9 795 981 256609593 256609782 3.340000e-20 110.0
27 TraesCS2A01G248100 chr7A 89.583 48 5 0 18 65 24982448 24982401 9.480000e-06 62.1
28 TraesCS2A01G248100 chr5B 81.731 208 34 4 790 994 615738833 615739039 1.510000e-38 171.0
29 TraesCS2A01G248100 chr5B 83.060 183 28 2 1137 1316 660752004 660752186 2.530000e-36 163.0
30 TraesCS2A01G248100 chr5B 82.645 121 21 0 2717 2837 318405886 318405766 1.200000e-19 108.0
31 TraesCS2A01G248100 chr5D 81.818 176 31 1 1097 1272 526000017 526000191 2.540000e-31 147.0
32 TraesCS2A01G248100 chr5D 82.645 121 21 0 2717 2837 280788467 280788347 1.200000e-19 108.0
33 TraesCS2A01G248100 chr5D 93.750 64 4 0 1 64 93099735 93099672 2.600000e-16 97.1
34 TraesCS2A01G248100 chr5D 98.000 50 1 0 1 50 219661755 219661706 1.560000e-13 87.9
35 TraesCS2A01G248100 chr5D 100.000 28 0 0 1434 1461 371288875 371288848 6.000000e-03 52.8
36 TraesCS2A01G248100 chr6A 78.571 238 33 14 559 778 112606474 112606711 1.180000e-29 141.0
37 TraesCS2A01G248100 chr6A 82.569 109 19 0 2730 2838 94378135 94378243 2.600000e-16 97.1
38 TraesCS2A01G248100 chr6A 81.356 118 20 2 2720 2836 27336419 27336535 9.350000e-16 95.3
39 TraesCS2A01G248100 chr6B 84.483 116 16 2 2717 2832 592980540 592980427 2.580000e-21 113.0
40 TraesCS2A01G248100 chr5A 83.471 121 20 0 2717 2837 371025614 371025734 2.580000e-21 113.0
41 TraesCS2A01G248100 chr5A 90.909 44 4 0 7 50 569298746 569298789 3.410000e-05 60.2
42 TraesCS2A01G248100 chr1D 86.869 99 13 0 2739 2837 12330957 12331055 9.280000e-21 111.0
43 TraesCS2A01G248100 chr1D 90.244 41 3 1 1419 1459 467382754 467382793 6.000000e-03 52.8
44 TraesCS2A01G248100 chr4A 92.857 42 2 1 1425 1466 35633472 35633432 3.410000e-05 60.2
45 TraesCS2A01G248100 chr7B 100.000 30 0 0 1430 1459 203199532 203199503 4.410000e-04 56.5
46 TraesCS2A01G248100 chrUn 100.000 28 0 0 1434 1461 345308925 345308952 6.000000e-03 52.8


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 TraesCS2A01G248100 chr2A 369214563 369217728 3165 True 5847.0 5847 100.000000 1 3166 1 chr2A.!!$R1 3165
1 TraesCS2A01G248100 chr2A 65173868 65176548 2680 True 495.3 942 90.147000 570 3092 5 chr2A.!!$R2 2522
2 TraesCS2A01G248100 chr2B 364927247 364928865 1618 False 1825.0 1825 87.332000 1 1599 1 chr2B.!!$F1 1598
3 TraesCS2A01G248100 chr2B 364947955 364949483 1528 False 640.0 979 90.182333 1591 3092 3 chr2B.!!$F2 1501
4 TraesCS2A01G248100 chr2D 296709233 296710806 1573 True 945.5 1046 91.073000 1714 3092 2 chr2D.!!$R3 1378
5 TraesCS2A01G248100 chr2D 63554536 63556843 2307 True 603.0 987 87.918250 677 3092 4 chr2D.!!$R2 2415

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
793 822 0.179234 TCCCGTGACAACTTGAGCAA 59.821 50.0 0.00 0.0 0.00 3.91 F
1185 1222 0.035458 GGACCGGGCTATCCATTCTG 59.965 60.0 7.57 0.0 34.87 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2161 0.664466 ATCACCATGATCTACGCGCG 60.664 55.0 30.96 30.96 29.59 6.86 R
3110 3521 0.036875 GCACTGGGGTGTTAGAAGCT 59.963 55.0 0.00 0.00 44.65 3.74 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
31 32 2.205074 CTGTCGTGGTATTCTCATGGC 58.795 52.381 0.00 0.00 0.00 4.40
73 75 0.813184 TCGTGTGGTTAGGGTCGATC 59.187 55.000 0.00 0.00 0.00 3.69
142 144 4.344978 ACACAGAGACATAGCTAGGTTCA 58.655 43.478 13.02 0.00 0.00 3.18
143 145 4.959210 ACACAGAGACATAGCTAGGTTCAT 59.041 41.667 13.02 2.07 0.00 2.57
176 178 3.337605 TGGAGGTAACAACCCTAGTCCTA 59.662 47.826 3.20 0.00 41.41 2.94
238 241 5.665459 CTCCAAGAGTTGTATTAGTGGAGG 58.335 45.833 8.61 0.00 44.53 4.30
282 285 2.523168 TGCCTCGAGTGTGTGGGA 60.523 61.111 12.31 0.00 0.00 4.37
328 336 1.131638 TATGGGACTGCTGGGATGTC 58.868 55.000 0.00 0.00 0.00 3.06
331 339 1.204146 GGGACTGCTGGGATGTCTTA 58.796 55.000 0.00 0.00 0.00 2.10
359 367 3.089284 GGTCTCCCAGGTTACAAAATGG 58.911 50.000 0.00 0.00 0.00 3.16
375 383 5.304357 ACAAAATGGTTAAGAAAGAGGGGTG 59.696 40.000 0.00 0.00 0.00 4.61
377 385 1.708551 TGGTTAAGAAAGAGGGGTGGG 59.291 52.381 0.00 0.00 0.00 4.61
416 424 2.774351 GCCTCTAGTGGGGCCCAT 60.774 66.667 31.48 19.71 42.30 4.00
419 427 1.414061 CCTCTAGTGGGGCCCATCAG 61.414 65.000 31.48 26.75 35.28 2.90
422 430 2.335092 CTAGTGGGGCCCATCAGCTG 62.335 65.000 31.48 7.63 35.28 4.24
423 431 4.052518 GTGGGGCCCATCAGCTGT 62.053 66.667 31.48 0.00 35.28 4.40
430 438 3.080641 CCATCAGCTGTGGGGTCA 58.919 61.111 21.10 0.00 32.98 4.02
437 445 1.228552 GCTGTGGGGTCATGTTGGT 60.229 57.895 0.00 0.00 0.00 3.67
439 447 0.955428 CTGTGGGGTCATGTTGGTCG 60.955 60.000 0.00 0.00 0.00 4.79
463 471 2.359107 CCGCCGGCTGCATGATAT 60.359 61.111 26.68 0.00 41.33 1.63
510 518 2.290323 GGAGTGGTTGACAGTATGCCTT 60.290 50.000 0.00 0.00 42.53 4.35
525 533 1.740296 CCTTTACAGTGTCGGGCCG 60.740 63.158 22.51 22.51 0.00 6.13
527 535 4.728102 TTACAGTGTCGGGCCGCG 62.728 66.667 23.83 9.28 0.00 6.46
540 548 2.735478 CCGCGTTGACGTAGGCAA 60.735 61.111 4.92 0.00 42.22 4.52
541 549 2.468532 CGCGTTGACGTAGGCAAC 59.531 61.111 8.59 8.59 41.57 4.17
542 550 2.858158 GCGTTGACGTAGGCAACC 59.142 61.111 12.53 2.95 41.88 3.77
543 551 2.674084 GCGTTGACGTAGGCAACCC 61.674 63.158 12.53 0.56 41.88 4.11
544 552 2.030958 CGTTGACGTAGGCAACCCC 61.031 63.158 12.53 0.00 41.88 4.95
545 553 2.030958 GTTGACGTAGGCAACCCCG 61.031 63.158 7.48 0.00 39.67 5.73
551 559 3.712907 TAGGCAACCCCGGTCAGC 61.713 66.667 0.00 0.00 39.21 4.26
574 582 1.192146 ACGGGTGACACTGTAGCCAT 61.192 55.000 5.39 0.00 34.18 4.40
575 583 0.740868 CGGGTGACACTGTAGCCATG 60.741 60.000 5.39 0.00 34.18 3.66
603 611 0.463116 GACGTGGTGGGTGTCTTGTT 60.463 55.000 0.00 0.00 0.00 2.83
604 612 0.831966 ACGTGGTGGGTGTCTTGTTA 59.168 50.000 0.00 0.00 0.00 2.41
608 616 2.997986 GTGGTGGGTGTCTTGTTATACG 59.002 50.000 0.00 0.00 0.00 3.06
619 627 5.703592 TGTCTTGTTATACGCTTGGATTTGT 59.296 36.000 0.00 0.00 0.00 2.83
620 628 6.021596 GTCTTGTTATACGCTTGGATTTGTG 58.978 40.000 0.00 0.00 0.00 3.33
621 629 5.703592 TCTTGTTATACGCTTGGATTTGTGT 59.296 36.000 0.00 0.00 0.00 3.72
629 638 0.592637 TTGGATTTGTGTGCGCTGAG 59.407 50.000 9.73 0.00 0.00 3.35
731 759 0.318762 GACCTGAGCCATCCCGATAC 59.681 60.000 0.00 0.00 0.00 2.24
748 776 8.036273 TCCCGATACTTTGAAATGTTAACTTC 57.964 34.615 7.22 4.02 0.00 3.01
793 822 0.179234 TCCCGTGACAACTTGAGCAA 59.821 50.000 0.00 0.00 0.00 3.91
845 874 7.939784 AAAAGGACATAGGGTTTTAAGCTAG 57.060 36.000 0.00 0.00 0.00 3.42
883 914 4.938832 CCTGTATAAAATCCGTTGTGTCCA 59.061 41.667 0.00 0.00 0.00 4.02
900 931 2.296190 GTCCATGTTTCCTTGTGTTCCC 59.704 50.000 0.00 0.00 0.00 3.97
903 934 3.005791 CCATGTTTCCTTGTGTTCCCTTC 59.994 47.826 0.00 0.00 0.00 3.46
952 983 1.249407 GGCCGAACCCACAAATACAA 58.751 50.000 0.00 0.00 0.00 2.41
1036 1067 1.518774 GCCACATTGGAGGCCATTG 59.481 57.895 5.01 6.76 44.09 2.82
1081 1118 1.173913 GTGGGTTTCTTTCATCCCCG 58.826 55.000 0.00 0.00 39.20 5.73
1184 1221 1.128188 GGGACCGGGCTATCCATTCT 61.128 60.000 7.57 0.00 36.65 2.40
1185 1222 0.035458 GGACCGGGCTATCCATTCTG 59.965 60.000 7.57 0.00 34.87 3.02
1214 1251 1.449423 CGGTCATCGATGGTGGCAA 60.449 57.895 24.61 1.60 42.43 4.52
1250 1287 3.695606 GCAGCGGGAGACAGGACA 61.696 66.667 0.00 0.00 0.00 4.02
1254 1291 4.803426 CGGGAGACAGGACAGCGC 62.803 72.222 0.00 0.00 0.00 5.92
1295 1338 1.165907 CCACTTTCACTCAGCCGCAA 61.166 55.000 0.00 0.00 0.00 4.85
1317 1360 2.368875 CGGGAGTGAGCATATTTAGGGT 59.631 50.000 0.00 0.00 0.00 4.34
1344 1387 2.496899 AGTGATTTTGGACTGCGGAT 57.503 45.000 0.00 0.00 0.00 4.18
1348 1391 2.684374 TGATTTTGGACTGCGGATGATG 59.316 45.455 0.00 0.00 0.00 3.07
1417 1461 8.726988 CGTAAGGGAAGAAAACTGAAATTATCA 58.273 33.333 0.00 0.00 36.38 2.15
1427 1471 6.619801 AACTGAAATTATCATCCCTTACGC 57.380 37.500 0.00 0.00 37.44 4.42
1430 1474 5.924356 TGAAATTATCATCCCTTACGCTCA 58.076 37.500 0.00 0.00 31.50 4.26
1459 1503 4.506802 GGGATCGGTTAGAAATGCCCTAAT 60.507 45.833 0.00 0.00 31.49 1.73
1460 1504 4.455877 GGATCGGTTAGAAATGCCCTAATG 59.544 45.833 0.00 0.00 0.00 1.90
1469 1513 6.625532 AGAAATGCCCTAATGGATTTTGTT 57.374 33.333 0.00 0.00 35.39 2.83
1481 1525 9.520204 CTAATGGATTTTGTTTGATGTATGGAC 57.480 33.333 0.00 0.00 0.00 4.02
1524 1568 7.722795 TGAAACATGAAGAACGAACATTCTA 57.277 32.000 0.00 0.00 37.99 2.10
1571 1615 4.813027 CAGTTTAGCAAAATGTCCAGCAT 58.187 39.130 0.00 0.00 40.03 3.79
1616 1663 8.421784 GGTAGTTTATGTATGGAGTGAGATGAA 58.578 37.037 0.00 0.00 0.00 2.57
1617 1664 9.988815 GTAGTTTATGTATGGAGTGAGATGAAT 57.011 33.333 0.00 0.00 0.00 2.57
1695 1757 5.610398 TGAGACTGCTTGTGAATAGACAAA 58.390 37.500 0.00 0.00 35.44 2.83
1756 1818 2.332063 GCACCAGAGCCTTAATGCTA 57.668 50.000 5.14 0.00 42.95 3.49
1783 1845 3.055747 GGAACTCCTCGAACTTGGATTCT 60.056 47.826 0.00 0.00 0.00 2.40
1792 1854 6.049955 TCGAACTTGGATTCTTACCATCTT 57.950 37.500 0.00 0.00 37.26 2.40
1793 1855 6.472887 TCGAACTTGGATTCTTACCATCTTT 58.527 36.000 0.00 0.00 37.26 2.52
1828 1891 3.449227 CGACGAGGTAGCCTGCCA 61.449 66.667 0.45 0.00 31.76 4.92
1833 1896 3.016971 AGGTAGCCTGCCATGCCA 61.017 61.111 0.45 0.00 29.57 4.92
1922 1985 2.584608 GTAGTGCGGGCAGGTGAT 59.415 61.111 0.00 0.00 0.00 3.06
1967 2030 3.387050 GGGATCTTGTACCCTGTATCGTT 59.613 47.826 0.00 0.00 42.56 3.85
1983 2046 1.203087 TCGTTGTCACCTCCCTTCCTA 60.203 52.381 0.00 0.00 0.00 2.94
1994 2057 2.432510 CTCCCTTCCTAAGTTGCGAGAT 59.567 50.000 0.00 0.00 0.00 2.75
2071 2134 2.664015 GGTAGAGGAGGTCCGTTGTAT 58.336 52.381 0.00 0.00 42.08 2.29
2164 2227 1.372499 GTGAGCGCCGTGTTGAGTA 60.372 57.895 2.29 0.00 0.00 2.59
2174 2237 3.067106 CCGTGTTGAGTAGCATGTTTCT 58.933 45.455 0.00 0.00 0.00 2.52
2183 2246 5.105473 TGAGTAGCATGTTTCTACTGTACCC 60.105 44.000 14.07 3.22 44.74 3.69
2387 2466 7.956328 AGTTTAGTCCTCAGGTTTTTCTTTT 57.044 32.000 0.00 0.00 0.00 2.27
2403 2482 9.811995 GTTTTTCTTTTAGGTTTCAACTACCAT 57.188 29.630 0.00 0.00 38.16 3.55
2405 2484 9.810545 TTTTCTTTTAGGTTTCAACTACCATTG 57.189 29.630 0.00 0.00 38.16 2.82
2406 2485 8.754991 TTCTTTTAGGTTTCAACTACCATTGA 57.245 30.769 0.00 0.00 38.16 2.57
2407 2486 8.754991 TCTTTTAGGTTTCAACTACCATTGAA 57.245 30.769 0.00 0.00 44.80 2.69
2408 2487 8.626526 TCTTTTAGGTTTCAACTACCATTGAAC 58.373 33.333 0.55 0.00 45.84 3.18
2409 2488 6.887626 TTAGGTTTCAACTACCATTGAACC 57.112 37.500 0.55 6.22 45.84 3.62
2410 2489 5.061721 AGGTTTCAACTACCATTGAACCT 57.938 39.130 12.57 12.57 45.84 3.50
2411 2490 5.454966 AGGTTTCAACTACCATTGAACCTT 58.545 37.500 12.57 0.00 45.84 3.50
2412 2491 5.301805 AGGTTTCAACTACCATTGAACCTTG 59.698 40.000 12.57 0.00 45.84 3.61
2570 2833 2.997303 TGTCACCACAATCGATTAACCG 59.003 45.455 10.97 0.68 0.00 4.44
2589 2852 5.059404 ACCGAAATGCACTAAAATTCCTG 57.941 39.130 0.00 0.00 0.00 3.86
2596 2859 9.428097 GAAATGCACTAAAATTCCTGATTTTCT 57.572 29.630 0.00 0.00 42.81 2.52
2647 2911 5.163550 CCACTTCTATAACATGTCTCGGTCA 60.164 44.000 0.00 0.00 0.00 4.02
2651 2915 1.191535 TAACATGTCTCGGTCAGGGG 58.808 55.000 0.00 0.00 0.00 4.79
2678 2943 8.816640 AAAACATGGTTGAAGTACATGATTTC 57.183 30.769 10.47 0.68 40.95 2.17
2689 2954 9.226606 TGAAGTACATGATTTCCGATACTTTTT 57.773 29.630 0.00 0.00 34.00 1.94
2727 2996 5.769162 ACCAGTTCTTCGTTAGTACTCTCTT 59.231 40.000 0.00 0.00 32.75 2.85
2737 3006 7.137426 TCGTTAGTACTCTCTTTGTTCAGAAC 58.863 38.462 6.32 6.32 0.00 3.01
2746 3099 8.616076 ACTCTCTTTGTTCAGAACTATTTGTTG 58.384 33.333 14.51 2.24 39.30 3.33
2811 3164 7.760340 ACATCTATTTTTGTCTAGTTCTCCGAC 59.240 37.037 0.00 0.00 0.00 4.79
3013 3424 2.591753 CCACCAGCATCCCGTCAT 59.408 61.111 0.00 0.00 0.00 3.06
3016 3427 2.300967 ACCAGCATCCCGTCATGGT 61.301 57.895 0.00 0.00 39.42 3.55
3051 3462 0.535102 CACCGGTGCCTCACTTCTTT 60.535 55.000 24.02 0.00 34.40 2.52
3068 3479 1.884579 CTTTTGCTGCTGTCCAGACAT 59.115 47.619 0.04 0.00 44.64 3.06
3073 3484 0.738762 CTGCTGTCCAGACATGACGG 60.739 60.000 0.00 0.00 44.64 4.79
3096 3507 3.662247 CAGAACTTGGAGTAGGTCGTT 57.338 47.619 0.00 0.00 36.95 3.85
3097 3508 4.778534 CAGAACTTGGAGTAGGTCGTTA 57.221 45.455 0.00 0.00 36.95 3.18
3098 3509 4.734917 CAGAACTTGGAGTAGGTCGTTAG 58.265 47.826 0.00 0.00 36.95 2.34
3099 3510 4.217983 CAGAACTTGGAGTAGGTCGTTAGT 59.782 45.833 0.00 0.00 36.95 2.24
3100 3511 4.458642 AGAACTTGGAGTAGGTCGTTAGTC 59.541 45.833 0.00 0.00 36.95 2.59
3101 3512 2.746362 ACTTGGAGTAGGTCGTTAGTCG 59.254 50.000 0.00 0.00 41.41 4.18
3102 3513 2.479566 TGGAGTAGGTCGTTAGTCGT 57.520 50.000 0.00 0.00 40.80 4.34
3103 3514 2.350522 TGGAGTAGGTCGTTAGTCGTC 58.649 52.381 0.00 0.00 40.80 4.20
3104 3515 1.668237 GGAGTAGGTCGTTAGTCGTCC 59.332 57.143 0.00 0.00 45.33 4.79
3105 3516 1.668237 GAGTAGGTCGTTAGTCGTCCC 59.332 57.143 0.00 0.00 45.93 4.46
3106 3517 0.375106 GTAGGTCGTTAGTCGTCCCG 59.625 60.000 0.00 0.00 45.93 5.14
3107 3518 1.369091 TAGGTCGTTAGTCGTCCCGC 61.369 60.000 0.00 0.00 45.93 6.13
3108 3519 2.202531 GTCGTTAGTCGTCCCGCC 60.203 66.667 0.00 0.00 40.80 6.13
3109 3520 2.360350 TCGTTAGTCGTCCCGCCT 60.360 61.111 0.00 0.00 40.80 5.52
3110 3521 1.078497 TCGTTAGTCGTCCCGCCTA 60.078 57.895 0.00 0.00 40.80 3.93
3111 3522 1.091771 TCGTTAGTCGTCCCGCCTAG 61.092 60.000 0.00 0.00 40.80 3.02
3112 3523 1.065436 GTTAGTCGTCCCGCCTAGC 59.935 63.158 0.00 0.00 0.00 3.42
3113 3524 1.077212 TTAGTCGTCCCGCCTAGCT 60.077 57.895 0.00 0.00 0.00 3.32
3114 3525 0.682209 TTAGTCGTCCCGCCTAGCTT 60.682 55.000 0.00 0.00 0.00 3.74
3115 3526 1.099879 TAGTCGTCCCGCCTAGCTTC 61.100 60.000 0.00 0.00 0.00 3.86
3116 3527 2.044252 TCGTCCCGCCTAGCTTCT 60.044 61.111 0.00 0.00 0.00 2.85
3117 3528 1.099879 GTCGTCCCGCCTAGCTTCTA 61.100 60.000 0.00 0.00 0.00 2.10
3118 3529 0.394762 TCGTCCCGCCTAGCTTCTAA 60.395 55.000 0.00 0.00 0.00 2.10
3119 3530 0.248949 CGTCCCGCCTAGCTTCTAAC 60.249 60.000 0.00 0.00 0.00 2.34
3120 3531 0.822164 GTCCCGCCTAGCTTCTAACA 59.178 55.000 0.00 0.00 0.00 2.41
3121 3532 0.822164 TCCCGCCTAGCTTCTAACAC 59.178 55.000 0.00 0.00 0.00 3.32
3122 3533 0.179081 CCCGCCTAGCTTCTAACACC 60.179 60.000 0.00 0.00 0.00 4.16
3123 3534 0.179081 CCGCCTAGCTTCTAACACCC 60.179 60.000 0.00 0.00 0.00 4.61
3124 3535 0.179081 CGCCTAGCTTCTAACACCCC 60.179 60.000 0.00 0.00 0.00 4.95
3125 3536 0.909623 GCCTAGCTTCTAACACCCCA 59.090 55.000 0.00 0.00 0.00 4.96
3126 3537 1.134371 GCCTAGCTTCTAACACCCCAG 60.134 57.143 0.00 0.00 0.00 4.45
3127 3538 2.188817 CCTAGCTTCTAACACCCCAGT 58.811 52.381 0.00 0.00 0.00 4.00
3140 3551 3.066190 CCAGTGCTGGCCACCATG 61.066 66.667 0.00 2.44 45.83 3.66
3141 3552 3.066190 CAGTGCTGGCCACCATGG 61.066 66.667 11.19 11.19 45.83 3.66
3142 3553 4.371417 AGTGCTGGCCACCATGGG 62.371 66.667 18.09 4.89 45.83 4.00
3151 3562 4.371417 CACCATGGGCAGGCACCT 62.371 66.667 18.09 0.00 0.00 4.00
3152 3563 4.371417 ACCATGGGCAGGCACCTG 62.371 66.667 18.09 12.54 46.15 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.159099 TCTGCCATGAGAATACCACGAC 60.159 50.000 0.00 0.00 0.00 4.34
15 16 2.602257 TCTGCCATGAGAATACCACG 57.398 50.000 0.00 0.00 0.00 4.94
97 99 0.735978 TCAGTGCACGTGCCTAATCG 60.736 55.000 35.72 19.27 41.18 3.34
219 222 7.455008 TCTTCTTCCTCCACTAATACAACTCTT 59.545 37.037 0.00 0.00 0.00 2.85
224 227 6.127310 GCTCTCTTCTTCCTCCACTAATACAA 60.127 42.308 0.00 0.00 0.00 2.41
282 285 1.813513 CGGCTCATTCTTTCCACACT 58.186 50.000 0.00 0.00 0.00 3.55
308 316 1.490490 GACATCCCAGCAGTCCCATAA 59.510 52.381 0.00 0.00 0.00 1.90
311 319 0.842030 AAGACATCCCAGCAGTCCCA 60.842 55.000 0.00 0.00 32.82 4.37
321 329 4.040584 GGAGACCCAAGTATAAGACATCCC 59.959 50.000 0.00 0.00 0.00 3.85
359 367 1.616187 GGCCCACCCCTCTTTCTTAAC 60.616 57.143 0.00 0.00 0.00 2.01
416 424 0.250858 CAACATGACCCCACAGCTGA 60.251 55.000 23.35 0.00 0.00 4.26
419 427 1.228552 ACCAACATGACCCCACAGC 60.229 57.895 0.00 0.00 0.00 4.40
422 430 0.322322 TACGACCAACATGACCCCAC 59.678 55.000 0.00 0.00 0.00 4.61
423 431 0.611200 CTACGACCAACATGACCCCA 59.389 55.000 0.00 0.00 0.00 4.96
430 438 2.995547 GGGCCCTACGACCAACAT 59.004 61.111 17.04 0.00 0.00 2.71
450 458 1.335810 AGCAACAATATCATGCAGCCG 59.664 47.619 9.23 0.00 42.45 5.52
458 466 4.430007 GTGACCTACGAGCAACAATATCA 58.570 43.478 0.00 0.00 0.00 2.15
496 504 4.968259 ACACTGTAAAGGCATACTGTCAA 58.032 39.130 9.10 0.00 36.27 3.18
499 507 3.585862 CGACACTGTAAAGGCATACTGT 58.414 45.455 7.03 7.03 38.14 3.55
502 510 2.277084 CCCGACACTGTAAAGGCATAC 58.723 52.381 0.00 0.00 0.00 2.39
510 518 4.728102 CGCGGCCCGACACTGTAA 62.728 66.667 7.68 0.00 40.02 2.41
525 533 2.674084 GGGTTGCCTACGTCAACGC 61.674 63.158 16.25 16.25 45.44 4.84
527 535 2.030958 CGGGGTTGCCTACGTCAAC 61.031 63.158 9.48 9.48 42.13 3.18
528 536 2.344500 CGGGGTTGCCTACGTCAA 59.656 61.111 0.00 0.00 0.00 3.18
533 541 2.267961 CTGACCGGGGTTGCCTAC 59.732 66.667 6.32 0.00 0.00 3.18
544 552 4.789075 CACCCGTACCGCTGACCG 62.789 72.222 0.00 0.00 0.00 4.79
545 553 3.376078 TCACCCGTACCGCTGACC 61.376 66.667 0.00 0.00 0.00 4.02
551 559 0.169672 CTACAGTGTCACCCGTACCG 59.830 60.000 0.00 0.00 0.00 4.02
560 568 1.205655 GAGAGCATGGCTACAGTGTCA 59.794 52.381 0.00 0.00 39.88 3.58
562 570 0.539051 GGAGAGCATGGCTACAGTGT 59.461 55.000 0.00 0.00 39.88 3.55
567 575 1.871408 CGTCATGGAGAGCATGGCTAC 60.871 57.143 0.00 0.00 39.88 3.58
603 611 2.350192 CGCACACAAATCCAAGCGTATA 59.650 45.455 0.00 0.00 40.25 1.47
604 612 1.130373 CGCACACAAATCCAAGCGTAT 59.870 47.619 0.00 0.00 40.25 3.06
608 616 1.005294 CAGCGCACACAAATCCAAGC 61.005 55.000 11.47 0.00 0.00 4.01
689 717 1.146774 TCAAATTGACTGGCCCTCCAA 59.853 47.619 0.00 1.24 42.91 3.53
731 759 9.801873 TCAAGGAAAGAAGTTAACATTTCAAAG 57.198 29.630 22.00 14.75 34.15 2.77
748 776 0.107654 CCGGGTAGGCTCAAGGAAAG 60.108 60.000 0.00 0.00 0.00 2.62
778 806 5.858581 GGAATACAATTGCTCAAGTTGTCAC 59.141 40.000 5.05 0.00 37.30 3.67
820 849 7.093902 GCTAGCTTAAAACCCTATGTCCTTTTT 60.094 37.037 7.70 0.00 0.00 1.94
829 858 5.057149 CGTCATGCTAGCTTAAAACCCTAT 58.943 41.667 17.23 0.00 0.00 2.57
845 874 2.045926 AGGTTCAGGCCGTCATGC 60.046 61.111 0.00 0.00 0.00 4.06
883 914 3.909732 TGAAGGGAACACAAGGAAACAT 58.090 40.909 0.00 0.00 0.00 2.71
900 931 3.243234 CGCCTAGTCAGTCCACTATGAAG 60.243 52.174 0.00 0.00 0.00 3.02
903 934 2.025155 ACGCCTAGTCAGTCCACTATG 58.975 52.381 0.00 0.00 0.00 2.23
952 983 0.267960 ACCGGGGATCAAGGATACCT 59.732 55.000 6.32 0.00 42.49 3.08
1039 1070 0.322008 GTCCAAGCTCCTCCAACTGG 60.322 60.000 0.00 0.00 0.00 4.00
1041 1072 1.492993 GGGTCCAAGCTCCTCCAACT 61.493 60.000 0.00 0.00 0.00 3.16
1070 1107 5.048153 GAAGAAAACTTCGGGGATGAAAG 57.952 43.478 0.00 0.00 34.02 2.62
1081 1118 0.163146 CCCGCGTCGAAGAAAACTTC 59.837 55.000 4.92 0.00 39.69 3.01
1152 1189 2.926242 GTCCCTTCCCACACCCGA 60.926 66.667 0.00 0.00 0.00 5.14
1153 1190 4.029809 GGTCCCTTCCCACACCCG 62.030 72.222 0.00 0.00 0.00 5.28
1184 1221 1.305297 ATGACCGTCTCTCTGGCCA 60.305 57.895 4.71 4.71 0.00 5.36
1185 1222 1.439644 GATGACCGTCTCTCTGGCC 59.560 63.158 0.00 0.00 0.00 5.36
1228 1265 3.535629 CTGTCTCCCGCTGCCACAA 62.536 63.158 0.00 0.00 0.00 3.33
1235 1272 3.386237 GCTGTCCTGTCTCCCGCT 61.386 66.667 0.00 0.00 0.00 5.52
1254 1291 1.296715 CCTCTTTCTCCCACCACCG 59.703 63.158 0.00 0.00 0.00 4.94
1295 1338 2.368875 CCCTAAATATGCTCACTCCCGT 59.631 50.000 0.00 0.00 0.00 5.28
1317 1360 4.022068 GCAGTCCAAAATCACTTCCAATCA 60.022 41.667 0.00 0.00 0.00 2.57
1400 1444 8.893727 CGTAAGGGATGATAATTTCAGTTTTCT 58.106 33.333 0.00 0.00 37.89 2.52
1407 1451 5.924356 TGAGCGTAAGGGATGATAATTTCA 58.076 37.500 0.00 0.00 36.81 2.69
1427 1471 4.035612 TCTAACCGATCCCCTATCTGAG 57.964 50.000 0.00 0.00 31.87 3.35
1430 1474 4.020128 GCATTTCTAACCGATCCCCTATCT 60.020 45.833 0.00 0.00 31.87 1.98
1459 1503 5.777223 TGGTCCATACATCAAACAAAATCCA 59.223 36.000 0.00 0.00 0.00 3.41
1460 1504 6.279513 TGGTCCATACATCAAACAAAATCC 57.720 37.500 0.00 0.00 0.00 3.01
1501 1545 7.572759 TGTAGAATGTTCGTTCTTCATGTTTC 58.427 34.615 11.69 0.00 39.15 2.78
1616 1663 3.638860 TGTGTCTGTCGACCCCTAATAT 58.361 45.455 14.12 0.00 39.47 1.28
1617 1664 3.090210 TGTGTCTGTCGACCCCTAATA 57.910 47.619 14.12 0.00 39.47 0.98
1641 1703 1.754803 ACATCGGCGACCATTCTAAGA 59.245 47.619 13.76 0.00 0.00 2.10
1750 1812 0.983378 AGGAGTTCCCGGCTAGCATT 60.983 55.000 18.24 0.00 40.87 3.56
1756 1818 2.283676 TTCGAGGAGTTCCCGGCT 60.284 61.111 0.00 0.00 40.87 5.52
1783 1845 0.693622 TCGCCACCCAAAGATGGTAA 59.306 50.000 0.00 0.00 46.01 2.85
1792 1854 2.668212 CGAAGCTTCGCCACCCAA 60.668 61.111 33.46 0.00 44.26 4.12
1922 1985 2.261671 GCGGGCTCTTCGAGTTCA 59.738 61.111 0.00 0.00 31.39 3.18
1967 2030 2.637872 CAACTTAGGAAGGGAGGTGACA 59.362 50.000 0.00 0.00 29.60 3.58
1983 2046 2.093973 CCACTACCTCATCTCGCAACTT 60.094 50.000 0.00 0.00 0.00 2.66
1994 2057 3.537795 ACTTCTACCACCACTACCTCA 57.462 47.619 0.00 0.00 0.00 3.86
2034 2097 2.581354 CCAGGCGTCCTCCTCTTG 59.419 66.667 0.00 0.00 33.25 3.02
2071 2134 2.273179 CCGTCGAACTCCCTGACCA 61.273 63.158 0.00 0.00 0.00 4.02
2097 2160 1.299089 CACCATGATCTACGCGCGA 60.299 57.895 39.36 19.16 0.00 5.87
2098 2161 0.664466 ATCACCATGATCTACGCGCG 60.664 55.000 30.96 30.96 29.59 6.86
2164 2227 2.565834 ACGGGTACAGTAGAAACATGCT 59.434 45.455 0.00 0.00 33.08 3.79
2174 2237 3.021695 CTCTTCATCCACGGGTACAGTA 58.978 50.000 0.00 0.00 33.08 2.74
2183 2246 3.594603 ACAAGGTACTCTTCATCCACG 57.405 47.619 0.00 0.00 38.49 4.94
2403 2482 5.475220 TCTCTGTGTTTTCAACAAGGTTCAA 59.525 36.000 0.00 0.00 44.16 2.69
2404 2483 5.007034 TCTCTGTGTTTTCAACAAGGTTCA 58.993 37.500 0.00 0.00 44.16 3.18
2405 2484 5.560966 TCTCTGTGTTTTCAACAAGGTTC 57.439 39.130 0.00 0.00 44.16 3.62
2406 2485 6.530019 AATCTCTGTGTTTTCAACAAGGTT 57.470 33.333 0.00 0.00 44.16 3.50
2407 2486 6.378280 AGAAATCTCTGTGTTTTCAACAAGGT 59.622 34.615 12.90 0.00 44.16 3.50
2408 2487 6.799512 AGAAATCTCTGTGTTTTCAACAAGG 58.200 36.000 12.90 0.00 44.16 3.61
2409 2488 7.905031 GAGAAATCTCTGTGTTTTCAACAAG 57.095 36.000 12.90 0.00 40.38 3.16
2445 2704 6.985117 TCATTTGACTGAAAAATGGGAAGAG 58.015 36.000 14.91 0.00 42.63 2.85
2561 2824 7.044314 GGAATTTTAGTGCATTTCGGTTAATCG 60.044 37.037 0.43 0.43 0.00 3.34
2566 2829 5.242838 TCAGGAATTTTAGTGCATTTCGGTT 59.757 36.000 0.00 0.00 0.00 4.44
2570 2833 9.428097 AGAAAATCAGGAATTTTAGTGCATTTC 57.572 29.630 0.00 0.00 45.47 2.17
2596 2859 6.897706 TCACATCTTGGATGAAATTGACAA 57.102 33.333 13.51 0.00 0.00 3.18
2647 2911 3.653164 ACTTCAACCATGTTTTTCCCCT 58.347 40.909 0.00 0.00 0.00 4.79
2651 2915 8.816640 AATCATGTACTTCAACCATGTTTTTC 57.183 30.769 0.00 0.00 37.73 2.29
2678 2943 2.159382 AGGTGCCACAAAAAGTATCGG 58.841 47.619 0.00 0.00 0.00 4.18
2689 2954 1.136828 ACTGGTCTTTAGGTGCCACA 58.863 50.000 0.00 0.00 0.00 4.17
2727 2996 7.873719 TTCTCCAACAAATAGTTCTGAACAA 57.126 32.000 21.50 0.80 38.74 2.83
2853 3215 8.519799 TCAAGGTAAAAGTCTTGTTCAAGATT 57.480 30.769 16.55 10.82 40.67 2.40
2857 3219 6.317893 GTCCTCAAGGTAAAAGTCTTGTTCAA 59.682 38.462 0.00 0.00 40.67 2.69
2858 3220 5.820947 GTCCTCAAGGTAAAAGTCTTGTTCA 59.179 40.000 0.00 0.00 40.67 3.18
2860 3222 5.589050 GTGTCCTCAAGGTAAAAGTCTTGTT 59.411 40.000 0.00 0.00 40.67 2.83
2861 3223 5.123936 GTGTCCTCAAGGTAAAAGTCTTGT 58.876 41.667 0.00 0.00 40.67 3.16
2868 3264 2.875933 CAAGCGTGTCCTCAAGGTAAAA 59.124 45.455 0.00 0.00 33.90 1.52
2876 3287 0.318441 CTTCCTCAAGCGTGTCCTCA 59.682 55.000 0.00 0.00 0.00 3.86
2990 3401 2.679342 GGGATGCTGGTGGCCTACA 61.679 63.158 3.32 1.39 40.92 2.74
3044 3455 1.952296 CTGGACAGCAGCAAAAGAAGT 59.048 47.619 0.00 0.00 0.00 3.01
3051 3462 0.397564 TCATGTCTGGACAGCAGCAA 59.602 50.000 9.33 0.00 45.48 3.91
3068 3479 2.111999 CTCCAAGTTCTGGCCCGTCA 62.112 60.000 0.00 0.00 45.98 4.35
3073 3484 0.984995 ACCTACTCCAAGTTCTGGCC 59.015 55.000 0.00 0.00 45.98 5.36
3101 3512 0.822164 TGTTAGAAGCTAGGCGGGAC 59.178 55.000 0.00 0.00 0.00 4.46
3102 3513 0.822164 GTGTTAGAAGCTAGGCGGGA 59.178 55.000 0.00 0.00 0.00 5.14
3103 3514 0.179081 GGTGTTAGAAGCTAGGCGGG 60.179 60.000 0.00 0.00 0.00 6.13
3104 3515 0.179081 GGGTGTTAGAAGCTAGGCGG 60.179 60.000 0.00 0.00 0.00 6.13
3105 3516 0.179081 GGGGTGTTAGAAGCTAGGCG 60.179 60.000 0.00 0.00 0.00 5.52
3106 3517 0.909623 TGGGGTGTTAGAAGCTAGGC 59.090 55.000 0.00 0.00 0.00 3.93
3107 3518 2.093447 CACTGGGGTGTTAGAAGCTAGG 60.093 54.545 0.00 0.00 38.54 3.02
3108 3519 2.678190 GCACTGGGGTGTTAGAAGCTAG 60.678 54.545 0.00 0.00 44.65 3.42
3109 3520 1.278127 GCACTGGGGTGTTAGAAGCTA 59.722 52.381 0.00 0.00 44.65 3.32
3110 3521 0.036875 GCACTGGGGTGTTAGAAGCT 59.963 55.000 0.00 0.00 44.65 3.74
3111 3522 0.036875 AGCACTGGGGTGTTAGAAGC 59.963 55.000 0.00 0.00 44.65 3.86
3112 3523 1.611673 CCAGCACTGGGGTGTTAGAAG 60.612 57.143 8.93 0.00 46.81 2.85
3113 3524 0.400213 CCAGCACTGGGGTGTTAGAA 59.600 55.000 8.93 0.00 46.81 2.10
3114 3525 2.066340 CCAGCACTGGGGTGTTAGA 58.934 57.895 8.93 0.00 46.81 2.10
3115 3526 4.722193 CCAGCACTGGGGTGTTAG 57.278 61.111 8.93 0.00 46.81 2.34
3124 3535 3.066190 CCATGGTGGCCAGCACTG 61.066 66.667 38.27 31.28 42.02 3.66
3125 3536 4.371417 CCCATGGTGGCCAGCACT 62.371 66.667 38.27 23.88 42.02 4.40
3134 3545 4.371417 AGGTGCCTGCCCATGGTG 62.371 66.667 11.73 3.26 0.00 4.17
3135 3546 4.371417 CAGGTGCCTGCCCATGGT 62.371 66.667 11.73 0.00 37.24 3.55


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

AutoCloner maintained by Alex Coulton.