Multiple sequence alignment - TraesCS1B01G152200

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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 TraesCS1B01G152200 chr1B 100.000 9379 0 0 1 9379 242660153 242669531 0.000000e+00 17320.0
1 TraesCS1B01G152200 chr1B 88.605 509 38 9 8871 9379 29823022 29822534 1.350000e-167 601.0
2 TraesCS1B01G152200 chr1B 89.640 444 26 6 8876 9319 678570095 678570518 1.780000e-151 547.0
3 TraesCS1B01G152200 chr1B 89.213 343 23 9 8865 9200 242728532 242728197 5.240000e-112 416.0
4 TraesCS1B01G152200 chr1A 96.673 8898 213 34 1 8849 232066240 232075103 0.000000e+00 14715.0
5 TraesCS1B01G152200 chr1D 97.287 8663 171 25 1 8613 176345070 176353718 0.000000e+00 14637.0
6 TraesCS1B01G152200 chr1D 84.804 204 11 8 8629 8819 176353702 176353898 4.470000e-43 187.0
7 TraesCS1B01G152200 chrUn 93.372 513 28 6 8871 9379 101400288 101400798 0.000000e+00 754.0
8 TraesCS1B01G152200 chrUn 91.262 309 21 5 8875 9180 101578163 101577858 5.240000e-112 416.0
9 TraesCS1B01G152200 chr4B 88.583 508 32 5 8872 9379 655806549 655807030 2.260000e-165 593.0
10 TraesCS1B01G152200 chr4B 91.515 330 24 4 8871 9199 655818248 655817922 1.440000e-122 451.0
11 TraesCS1B01G152200 chr4B 82.166 314 44 8 1840 2147 558058022 558057715 9.340000e-65 259.0
12 TraesCS1B01G152200 chr4B 72.768 885 177 46 7527 8379 558051048 558050196 3.380000e-59 241.0
13 TraesCS1B01G152200 chr4B 80.147 136 16 6 985 1111 558059328 558059195 3.610000e-14 91.6
14 TraesCS1B01G152200 chr4B 83.721 86 13 1 5674 5758 558052320 558052235 7.810000e-11 80.5
15 TraesCS1B01G152200 chr5D 85.563 568 62 17 745 1300 417635445 417636004 2.270000e-160 577.0
16 TraesCS1B01G152200 chr5D 79.265 680 76 35 1299 1943 417636037 417636686 1.880000e-111 414.0
17 TraesCS1B01G152200 chr5D 88.306 248 25 3 1053 1296 45593016 45592769 2.560000e-75 294.0
18 TraesCS1B01G152200 chr2D 85.035 568 65 16 745 1300 80973981 80974540 2.290000e-155 560.0
19 TraesCS1B01G152200 chr2D 78.994 676 77 36 1299 1943 80974573 80975214 1.470000e-107 401.0
20 TraesCS1B01G152200 chr3A 89.171 434 29 5 8951 9379 455778775 455778355 8.340000e-145 525.0
21 TraesCS1B01G152200 chr3A 87.164 335 36 5 8871 9199 469500606 469500939 3.200000e-99 374.0
22 TraesCS1B01G152200 chr6B 90.691 333 26 4 8871 9200 62820632 62820962 1.120000e-118 438.0
23 TraesCS1B01G152200 chr5B 82.718 515 46 23 8871 9379 615384935 615384458 1.460000e-112 418.0
24 TraesCS1B01G152200 chr4D 82.446 507 54 21 8872 9376 506691710 506692183 2.440000e-110 411.0
25 TraesCS1B01G152200 chr4D 82.166 314 44 8 1840 2147 446151081 446150774 9.340000e-65 259.0
26 TraesCS1B01G152200 chr4D 71.910 890 188 44 7527 8385 446144175 446143317 1.600000e-47 202.0
27 TraesCS1B01G152200 chr4D 82.500 120 10 6 985 1095 446152401 446152284 2.790000e-15 95.3
28 TraesCS1B01G152200 chr4D 85.714 70 10 0 5674 5743 446145448 446145379 3.630000e-09 75.0
29 TraesCS1B01G152200 chr6D 82.249 507 56 18 8871 9376 381177494 381177967 3.150000e-109 407.0
30 TraesCS1B01G152200 chr6D 81.573 483 57 17 8898 9379 15599506 15599055 4.140000e-98 370.0
31 TraesCS1B01G152200 chr4A 86.982 338 33 9 8871 9204 741250628 741250958 4.140000e-98 370.0
32 TraesCS1B01G152200 chr4A 84.932 73 11 0 5671 5743 21212510 21212582 3.630000e-09 75.0
33 TraesCS1B01G152200 chr2A 93.750 192 12 0 9188 9379 155646230 155646039 1.190000e-73 289.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G152200 chr1B 242660153 242669531 9378 False 17320.0 17320 100.0000 1 9379 1 chr1B.!!$F1 9378
1 TraesCS1B01G152200 chr1A 232066240 232075103 8863 False 14715.0 14715 96.6730 1 8849 1 chr1A.!!$F1 8848
2 TraesCS1B01G152200 chr1D 176345070 176353898 8828 False 7412.0 14637 91.0455 1 8819 2 chr1D.!!$F1 8818
3 TraesCS1B01G152200 chrUn 101400288 101400798 510 False 754.0 754 93.3720 8871 9379 1 chrUn.!!$F1 508
4 TraesCS1B01G152200 chr5D 417635445 417636686 1241 False 495.5 577 82.4140 745 1943 2 chr5D.!!$F1 1198
5 TraesCS1B01G152200 chr2D 80973981 80975214 1233 False 480.5 560 82.0145 745 1943 2 chr2D.!!$F1 1198

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
245 247 1.130561 GTTGACGGGCAGTTGATTAGC 59.869 52.381 0.00 0.00 0.00 3.09 F
994 1011 1.627329 AGAGTGGCATCTTGCTTCTCA 59.373 47.619 18.40 1.43 44.28 3.27 F
1311 1369 1.160137 CAGGTGTTTCTAGCTGCCAC 58.840 55.000 0.00 0.00 39.06 5.01 F
1809 1918 2.097466 GTGATTGAATTACGCCCCTGTG 59.903 50.000 0.00 0.00 0.00 3.66 F
3103 3212 1.611673 GGCACCATGTCACAGCTAAGT 60.612 52.381 0.00 0.00 0.00 2.24 F
4072 4181 1.671328 GAGCTGACCGGGAAATTAAGC 59.329 52.381 6.32 0.00 0.00 3.09 F
5886 5996 2.038557 TCTTGTTTGGCAGAGTCCTACC 59.961 50.000 0.00 0.00 0.00 3.18 F
6265 6375 0.882927 TTTGACTTGAACGCGGGGAG 60.883 55.000 12.47 5.23 0.00 4.30 F
7419 7543 0.810426 TCGAGATGAGGAGTCGACCG 60.810 60.000 13.01 5.31 37.79 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1369 2.159128 AGAAGAGACATCATGTGCCTCG 60.159 50.000 0.00 0.00 29.59 4.63 R
2277 2386 1.129998 CAGCACGAGGAGCATTTTCAG 59.870 52.381 0.00 0.00 0.00 3.02 R
3103 3212 0.829333 GAGCTCCATCCTTCTCAGCA 59.171 55.000 0.87 0.00 32.17 4.41 R
3271 3380 2.029110 GCTTTCATTTTGTAGCTGGCCA 60.029 45.455 4.71 4.71 0.00 5.36 R
4361 4470 1.338973 CAACATCTGGTTTGCTGCTGT 59.661 47.619 0.00 0.00 37.72 4.40 R
6027 6137 3.181440 TGGCCTCTCAAGAACAAAGACAT 60.181 43.478 3.32 0.00 0.00 3.06 R
7386 7510 0.108804 TCTCGACGGCACTTGGAATC 60.109 55.000 0.00 0.00 0.00 2.52 R
7795 7925 0.547712 TCCCAGGTCTCTTCCCCTTG 60.548 60.000 0.00 0.00 0.00 3.61 R
9213 9388 0.618968 GGGAGAAGGGAGAAGCAGGA 60.619 60.000 0.00 0.00 0.00 3.86 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
112 114 2.443416 TCGATTCTTTCTCTCCCGTCA 58.557 47.619 0.00 0.00 0.00 4.35
234 236 2.131972 GAATTTTTGGTGTTGACGGGC 58.868 47.619 0.00 0.00 0.00 6.13
240 242 1.525077 GGTGTTGACGGGCAGTTGA 60.525 57.895 0.00 0.00 0.00 3.18
243 245 2.147958 GTGTTGACGGGCAGTTGATTA 58.852 47.619 0.00 0.00 0.00 1.75
245 247 1.130561 GTTGACGGGCAGTTGATTAGC 59.869 52.381 0.00 0.00 0.00 3.09
311 313 2.407846 ATCCTCGCCGCTGTGTATCG 62.408 60.000 0.00 0.00 0.00 2.92
429 431 4.502645 CACTTCTTTTTCCGTGCGATTTTT 59.497 37.500 0.00 0.00 0.00 1.94
994 1011 1.627329 AGAGTGGCATCTTGCTTCTCA 59.373 47.619 18.40 1.43 44.28 3.27
1204 1224 6.030849 CGATGTTACTAGGTTCTCTCAGTTG 58.969 44.000 0.00 0.00 0.00 3.16
1311 1369 1.160137 CAGGTGTTTCTAGCTGCCAC 58.840 55.000 0.00 0.00 39.06 5.01
1421 1481 7.770897 ACCTGTGTCATCTTCATATTTTCCTAC 59.229 37.037 0.00 0.00 0.00 3.18
1488 1550 5.183904 GCCCATAGGTTCTGCTTTAATATGG 59.816 44.000 0.00 0.00 38.48 2.74
1493 1555 6.396829 AGGTTCTGCTTTAATATGGAATGC 57.603 37.500 0.00 2.97 0.00 3.56
1684 1793 9.107367 GAGTTGAACTGAATTTTTCATAGTTCG 57.893 33.333 0.90 0.00 42.81 3.95
1701 1810 8.579006 TCATAGTTCGAAACCTAAAGTTCTGTA 58.421 33.333 0.00 0.00 37.88 2.74
1809 1918 2.097466 GTGATTGAATTACGCCCCTGTG 59.903 50.000 0.00 0.00 0.00 3.66
2277 2386 2.414559 CCAATGATTTGTCACTCGGTGC 60.415 50.000 0.00 0.00 32.98 5.01
2316 2425 3.870419 GCTGTTTTTGATGGAAAAGCACA 59.130 39.130 0.00 0.00 39.16 4.57
2500 2609 7.127032 ACTGAGATCCAAAATCAGAAGGATACT 59.873 37.037 14.05 0.00 46.33 2.12
2521 2630 2.810274 TGCTTCTCAGTTGCATTCTGAC 59.190 45.455 15.16 8.56 37.07 3.51
2525 2634 5.734220 GCTTCTCAGTTGCATTCTGACAAAA 60.734 40.000 15.16 10.34 37.07 2.44
2668 2777 4.759782 AGCTAAATAGTGCTGAATCACGT 58.240 39.130 0.00 0.00 41.61 4.49
2895 3004 5.961396 ATAGAGATCAAGATGGCAAATGC 57.039 39.130 0.00 0.00 41.14 3.56
3017 3126 4.201589 CCGAACTGCTTATACAACAACTCG 60.202 45.833 0.00 0.00 0.00 4.18
3019 3128 3.000727 ACTGCTTATACAACAACTCGGC 58.999 45.455 0.00 0.00 0.00 5.54
3081 3190 8.253113 ACTTCGAAATGAAATCCAAAGCATTAT 58.747 29.630 0.00 0.00 35.79 1.28
3103 3212 1.611673 GGCACCATGTCACAGCTAAGT 60.612 52.381 0.00 0.00 0.00 2.24
3271 3380 8.088463 AGAGAGAGGAAATTCACAGTATTCAT 57.912 34.615 0.00 0.00 0.00 2.57
3639 3748 3.993081 GGACAGATGAGTGAAAGTGTCAG 59.007 47.826 0.00 0.00 36.74 3.51
3641 3750 4.375272 ACAGATGAGTGAAAGTGTCAGTG 58.625 43.478 0.00 0.00 40.19 3.66
4072 4181 1.671328 GAGCTGACCGGGAAATTAAGC 59.329 52.381 6.32 0.00 0.00 3.09
4361 4470 5.494724 AGATGAATGCTCTAAAAGACAGCA 58.505 37.500 0.00 0.00 39.91 4.41
4680 4789 6.581166 GGTAAAAGTTTCGCTGTTATTTCAGG 59.419 38.462 0.00 0.00 36.12 3.86
4690 4799 5.355350 CGCTGTTATTTCAGGGAAGAATTCT 59.645 40.000 0.88 0.88 46.57 2.40
4739 4848 4.276678 TGAAAGCTGAGTTTGAAGACATGG 59.723 41.667 0.00 0.00 0.00 3.66
4864 4973 4.976224 AACCAACACTACAAACTCAACC 57.024 40.909 0.00 0.00 0.00 3.77
4986 5096 3.008330 TCGTAACTACAGAGAGTGCCTC 58.992 50.000 0.00 0.00 42.28 4.70
5026 5136 5.127031 AGAACATTACAGTGGTTGCAAAAGT 59.873 36.000 0.00 0.00 0.00 2.66
5325 5435 3.034721 TGGTTTATGCGAAAGACGAGT 57.965 42.857 0.00 0.00 45.77 4.18
5350 5460 6.463995 TGTGGCTCTTTTAAACAAATGTCT 57.536 33.333 0.00 0.00 0.00 3.41
5501 5611 4.766891 CACCACATGAAGGTCCTTAACATT 59.233 41.667 3.42 0.00 37.23 2.71
5507 5617 5.560722 TGAAGGTCCTTAACATTGACAGA 57.439 39.130 3.42 0.00 30.61 3.41
5547 5657 5.491982 AGATAGCTCAGGACGAAATTTTGT 58.508 37.500 10.97 10.97 0.00 2.83
5825 5935 7.781324 ACAAAATAACAGTGAAAGGGATCAT 57.219 32.000 0.00 0.00 0.00 2.45
5886 5996 2.038557 TCTTGTTTGGCAGAGTCCTACC 59.961 50.000 0.00 0.00 0.00 3.18
5957 6067 6.488769 TTGTCTAAGGAACACCAGTCTTTA 57.511 37.500 0.00 0.00 0.00 1.85
6023 6133 6.117488 TCTTAGAGAATGCATGATGCTTGAA 58.883 36.000 19.19 0.00 45.31 2.69
6027 6137 3.508402 AGAATGCATGATGCTTGAACACA 59.492 39.130 19.19 0.00 45.31 3.72
6265 6375 0.882927 TTTGACTTGAACGCGGGGAG 60.883 55.000 12.47 5.23 0.00 4.30
6310 6420 3.213206 TGAACTTGAGAGTTGCATGGT 57.787 42.857 0.00 0.00 45.88 3.55
6650 6760 5.302568 AGAATCTCTTCTGCTGATAGGTGAG 59.697 44.000 0.00 0.00 40.28 3.51
6699 6809 5.390991 GCAGTCTACAAAGAAATGGCACTAC 60.391 44.000 0.00 0.00 32.16 2.73
6814 6924 4.216257 TGAGGCTCTGCAGAAAAATGTAAC 59.784 41.667 18.85 3.53 0.00 2.50
6897 7019 5.994054 TCTAATCATATCAGTTTGCTGGAGC 59.006 40.000 0.00 0.00 42.78 4.70
6956 7078 8.844244 ACAGAATGCAAAGAGGTAATATTCATC 58.156 33.333 0.00 0.00 42.53 2.92
7040 7162 5.588240 CACTGCTATAACACTAATCGGTCA 58.412 41.667 0.00 0.00 0.00 4.02
7386 7510 2.846193 CACTTGGGGTGGTTATATCGG 58.154 52.381 0.00 0.00 41.90 4.18
7419 7543 0.810426 TCGAGATGAGGAGTCGACCG 60.810 60.000 13.01 5.31 37.79 4.79
7479 7603 4.404073 TCCAAGAGCTTAAAACAAAAGGCA 59.596 37.500 0.00 0.00 0.00 4.75
7568 7692 7.387397 GTCCAGATGATGAAGGATATTGAACTC 59.613 40.741 0.00 0.00 31.91 3.01
7783 7913 1.404315 GGTGAAGAGCGAGTACCCTTG 60.404 57.143 0.00 0.00 0.00 3.61
7795 7925 1.340568 GTACCCTTGGTCGGAGCTATC 59.659 57.143 8.82 0.00 37.09 2.08
7924 8054 1.078848 GACTGGCGAGCATCCAAGT 60.079 57.895 0.00 0.00 32.41 3.16
8099 8229 1.788258 CGCTGTCGGATAGCATGAAT 58.212 50.000 23.63 0.00 41.18 2.57
8387 8517 3.119352 GGACTGAGCCATGACCATTTTTC 60.119 47.826 0.00 0.00 0.00 2.29
8415 8547 3.610585 CGTGGCGGCAAGAAATAAGAAAA 60.611 43.478 19.90 0.00 0.00 2.29
8417 8549 3.250744 GGCGGCAAGAAATAAGAAAACC 58.749 45.455 3.07 0.00 0.00 3.27
8420 8552 4.988540 GCGGCAAGAAATAAGAAAACCTTT 59.011 37.500 0.00 0.00 36.34 3.11
8421 8553 5.118664 GCGGCAAGAAATAAGAAAACCTTTC 59.881 40.000 0.00 0.00 36.34 2.62
8423 8555 6.582672 CGGCAAGAAATAAGAAAACCTTTCTC 59.417 38.462 2.28 0.00 37.05 2.87
8424 8556 6.582672 GGCAAGAAATAAGAAAACCTTTCTCG 59.417 38.462 2.28 0.00 37.05 4.04
8521 8669 9.979578 ATTCAGAATAAGCTTGTGTATCTAGAG 57.020 33.333 9.86 0.00 0.00 2.43
8522 8670 8.526667 TCAGAATAAGCTTGTGTATCTAGAGT 57.473 34.615 9.86 0.00 0.00 3.24
8523 8671 9.628500 TCAGAATAAGCTTGTGTATCTAGAGTA 57.372 33.333 9.86 0.00 0.00 2.59
8580 8730 6.585702 TGTGTTAATTTTCTTCGGCATCAATG 59.414 34.615 0.00 0.00 0.00 2.82
8581 8731 6.806249 GTGTTAATTTTCTTCGGCATCAATGA 59.194 34.615 0.00 0.00 0.00 2.57
8583 8733 5.902613 AATTTTCTTCGGCATCAATGAGA 57.097 34.783 0.00 0.00 0.00 3.27
8584 8734 6.461110 AATTTTCTTCGGCATCAATGAGAT 57.539 33.333 0.00 0.00 37.48 2.75
8614 8764 7.732222 TGGATCAGGCATTTTATTTACCTTT 57.268 32.000 0.00 0.00 0.00 3.11
8615 8765 8.144862 TGGATCAGGCATTTTATTTACCTTTT 57.855 30.769 0.00 0.00 0.00 2.27
8616 8766 8.601546 TGGATCAGGCATTTTATTTACCTTTTT 58.398 29.630 0.00 0.00 0.00 1.94
8643 8793 9.705290 TTTTGAGAAGAAGGCATTTTATTTACC 57.295 29.630 0.00 0.00 0.00 2.85
8644 8794 8.650143 TTGAGAAGAAGGCATTTTATTTACCT 57.350 30.769 0.00 0.00 0.00 3.08
8645 8795 8.650143 TGAGAAGAAGGCATTTTATTTACCTT 57.350 30.769 0.00 0.00 43.33 3.50
8737 8894 1.302351 GAGGCTGTGTGCTGCTCTT 60.302 57.895 0.00 0.00 42.39 2.85
8745 8902 3.011517 TGCTGCTCTTCCCCTCCC 61.012 66.667 0.00 0.00 0.00 4.30
8751 8908 4.722535 TCTTCCCCTCCCAGCGCT 62.723 66.667 2.64 2.64 0.00 5.92
8849 9020 4.833478 ATGACATATGTCTATCAGGGCC 57.167 45.455 30.67 0.00 44.99 5.80
8850 9021 3.861846 TGACATATGTCTATCAGGGCCT 58.138 45.455 30.67 0.00 44.99 5.19
8851 9022 3.834813 TGACATATGTCTATCAGGGCCTC 59.165 47.826 30.67 6.43 44.99 4.70
8852 9023 4.093011 GACATATGTCTATCAGGGCCTCT 58.907 47.826 25.52 0.00 41.65 3.69
8853 9024 4.497516 ACATATGTCTATCAGGGCCTCTT 58.502 43.478 0.95 0.00 0.00 2.85
8854 9025 4.285517 ACATATGTCTATCAGGGCCTCTTG 59.714 45.833 0.95 0.00 0.00 3.02
8855 9026 0.833287 TGTCTATCAGGGCCTCTTGC 59.167 55.000 0.95 0.00 40.16 4.01
8856 9027 1.127343 GTCTATCAGGGCCTCTTGCT 58.873 55.000 0.95 0.00 40.92 3.91
8857 9028 1.488393 GTCTATCAGGGCCTCTTGCTT 59.512 52.381 0.95 0.00 40.92 3.91
8858 9029 1.765314 TCTATCAGGGCCTCTTGCTTC 59.235 52.381 0.95 0.00 40.92 3.86
8859 9030 1.487976 CTATCAGGGCCTCTTGCTTCA 59.512 52.381 0.95 0.00 40.92 3.02
8860 9031 0.034670 ATCAGGGCCTCTTGCTTCAC 60.035 55.000 0.95 0.00 40.92 3.18
8861 9032 1.130054 TCAGGGCCTCTTGCTTCACT 61.130 55.000 0.95 0.00 40.92 3.41
8862 9033 0.676151 CAGGGCCTCTTGCTTCACTC 60.676 60.000 0.95 0.00 40.92 3.51
8863 9034 0.839853 AGGGCCTCTTGCTTCACTCT 60.840 55.000 0.00 0.00 40.92 3.24
8864 9035 0.037447 GGGCCTCTTGCTTCACTCTT 59.963 55.000 0.84 0.00 40.92 2.85
8865 9036 1.279271 GGGCCTCTTGCTTCACTCTTA 59.721 52.381 0.84 0.00 40.92 2.10
8866 9037 2.092699 GGGCCTCTTGCTTCACTCTTAT 60.093 50.000 0.84 0.00 40.92 1.73
8867 9038 3.134804 GGGCCTCTTGCTTCACTCTTATA 59.865 47.826 0.84 0.00 40.92 0.98
8868 9039 4.202409 GGGCCTCTTGCTTCACTCTTATAT 60.202 45.833 0.84 0.00 40.92 0.86
8869 9040 4.754114 GGCCTCTTGCTTCACTCTTATATG 59.246 45.833 0.00 0.00 40.92 1.78
8873 9044 7.495901 CCTCTTGCTTCACTCTTATATGAGAA 58.504 38.462 19.55 6.44 37.50 2.87
8925 9096 4.379813 CGTTGACGTTAGCTTTAGTCCCTA 60.380 45.833 0.00 0.00 33.04 3.53
8941 9112 5.041015 AGTCCCTATGGTTACAAATACCCA 58.959 41.667 0.00 0.00 34.66 4.51
8944 9115 6.320418 GTCCCTATGGTTACAAATACCCAAAG 59.680 42.308 0.00 0.00 34.66 2.77
8954 9125 5.067954 ACAAATACCCAAAGTACAGTCACC 58.932 41.667 0.00 0.00 32.46 4.02
8955 9126 4.986054 AATACCCAAAGTACAGTCACCA 57.014 40.909 0.00 0.00 32.46 4.17
8962 9133 4.398044 CCAAAGTACAGTCACCAAACTTGT 59.602 41.667 0.00 0.00 31.09 3.16
8983 9154 1.144503 TCTAGGGGGTCATCTACGGTC 59.855 57.143 0.00 0.00 0.00 4.79
9003 9174 5.524646 CGGTCCATTATACGGTTTTGTGTAT 59.475 40.000 0.00 0.00 35.55 2.29
9011 9182 2.159626 ACGGTTTTGTGTATGTATGCGC 60.160 45.455 0.00 0.00 0.00 6.09
9038 9209 1.215382 CTCGAGTCAACCGATGCCA 59.785 57.895 3.62 0.00 35.35 4.92
9091 9263 1.151172 TCGATTACGCATGCACGCAT 61.151 50.000 19.57 3.31 39.58 4.73
9141 9316 1.214992 AAAGATCCCCCACCTGGTCC 61.215 60.000 0.00 0.00 0.00 4.46
9213 9388 4.070552 GCCGAACCGAGCCACTCT 62.071 66.667 0.00 0.00 0.00 3.24
9240 9415 0.547712 CTCCCTTCTCCCCTGGTTCA 60.548 60.000 0.00 0.00 0.00 3.18
9251 9426 2.434185 TGGTTCATCGTCGCTGCC 60.434 61.111 0.00 0.00 0.00 4.85
9276 9451 3.744719 TTCCTCGTCTCCGGCGTG 61.745 66.667 6.01 0.00 33.95 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 4.141711 ACAACTACAGGGTAATGATCGCAT 60.142 41.667 0.00 0.00 35.92 4.73
234 236 5.409826 AGAAAGAGAAACCGCTAATCAACTG 59.590 40.000 0.00 0.00 0.00 3.16
240 242 3.440522 GGCAAGAAAGAGAAACCGCTAAT 59.559 43.478 0.00 0.00 0.00 1.73
243 245 1.202818 AGGCAAGAAAGAGAAACCGCT 60.203 47.619 0.00 0.00 0.00 5.52
245 247 1.068954 GCAGGCAAGAAAGAGAAACCG 60.069 52.381 0.00 0.00 0.00 4.44
311 313 8.007716 CGGACGGAATACATAAATAAATCACAC 58.992 37.037 0.00 0.00 0.00 3.82
429 431 3.642848 AGCAAAATCAAGCCAGGAGAAAA 59.357 39.130 0.00 0.00 0.00 2.29
546 558 3.165058 TCACGCAATTAGACTAGCCAG 57.835 47.619 0.00 0.00 0.00 4.85
578 590 4.140924 GGTAATTGGATTGGGGGAGAGAAT 60.141 45.833 0.00 0.00 0.00 2.40
579 591 3.204382 GGTAATTGGATTGGGGGAGAGAA 59.796 47.826 0.00 0.00 0.00 2.87
994 1011 1.303561 ACACAGCCGCCATTGATGT 60.304 52.632 0.00 0.00 0.00 3.06
1204 1224 3.297979 CGAGCGTTGAAAATGTAATGTGC 59.702 43.478 0.00 0.00 34.61 4.57
1311 1369 2.159128 AGAAGAGACATCATGTGCCTCG 60.159 50.000 0.00 0.00 29.59 4.63
1421 1481 5.357878 TCAAAGCCTAGCATCCAATTACTTG 59.642 40.000 0.00 0.00 0.00 3.16
1684 1793 6.450545 ACTACCGTACAGAACTTTAGGTTTC 58.549 40.000 0.00 0.00 38.41 2.78
1701 1810 8.038944 ACAATGACTTTGTTATATGACTACCGT 58.961 33.333 1.02 0.00 46.51 4.83
1764 1873 5.641709 TGCAACAAAATGTTCTCGTACAAA 58.358 33.333 0.00 0.00 38.77 2.83
1782 1891 3.171277 GGCGTAATTCAATCACTGCAAC 58.829 45.455 0.00 0.00 0.00 4.17
2277 2386 1.129998 CAGCACGAGGAGCATTTTCAG 59.870 52.381 0.00 0.00 0.00 3.02
2316 2425 5.513094 GGGCTTTCAAAATTTAGGCCTTTCT 60.513 40.000 12.58 0.00 46.56 2.52
2500 2609 2.810274 GTCAGAATGCAACTGAGAAGCA 59.190 45.455 21.60 6.11 43.14 3.91
2525 2634 7.966812 TGGTCATACTGCAGAATAGATGTATT 58.033 34.615 23.35 0.00 0.00 1.89
2668 2777 9.574516 TCAAGCTCAGACTGTATCATACTATTA 57.425 33.333 1.59 0.00 0.00 0.98
2895 3004 6.373186 TCTGCATGAGCTCATCTAAATTTG 57.627 37.500 26.44 15.10 42.74 2.32
3017 3126 3.531538 TCAGTGAATTTATCTCACCGCC 58.468 45.455 0.00 0.00 43.53 6.13
3019 3128 5.359756 TCCATCAGTGAATTTATCTCACCG 58.640 41.667 0.00 0.00 43.53 4.94
3039 3148 3.323691 TCGAAGTTCACTCCTTGAATCCA 59.676 43.478 3.32 0.00 46.14 3.41
3081 3190 1.487850 TAGCTGTGACATGGTGCCCA 61.488 55.000 0.00 0.00 38.19 5.36
3103 3212 0.829333 GAGCTCCATCCTTCTCAGCA 59.171 55.000 0.87 0.00 32.17 4.41
3271 3380 2.029110 GCTTTCATTTTGTAGCTGGCCA 60.029 45.455 4.71 4.71 0.00 5.36
3300 3409 3.019564 AGAGCTGCTTCAGTTTGTGTTT 58.980 40.909 2.53 0.00 33.43 2.83
3556 3665 5.359194 TCTCCAGTTTCAACTTTGTCTCT 57.641 39.130 0.00 0.00 37.08 3.10
3639 3748 3.194005 TCAAAGTCAACTCCAGACCAC 57.806 47.619 0.00 0.00 36.68 4.16
3641 3750 4.273724 GTCTTTCAAAGTCAACTCCAGACC 59.726 45.833 0.00 0.00 36.68 3.85
4072 4181 4.122776 CCATCTTAATGTTCTCCACCTCG 58.877 47.826 0.00 0.00 0.00 4.63
4361 4470 1.338973 CAACATCTGGTTTGCTGCTGT 59.661 47.619 0.00 0.00 37.72 4.40
4680 4789 6.765036 TGACATCTCTAATGCAGAATTCTTCC 59.235 38.462 4.86 0.41 31.12 3.46
4690 4799 6.594744 ACCACATAATGACATCTCTAATGCA 58.405 36.000 0.00 0.00 0.00 3.96
4986 5096 8.506437 TGTAATGTTCTGTAGCTGAAATGAAAG 58.494 33.333 0.00 0.00 0.00 2.62
5026 5136 4.908601 TCAGAATGCTTACTTTCCAGGA 57.091 40.909 0.00 0.00 34.76 3.86
5325 5435 8.177119 AGACATTTGTTTAAAAGAGCCACATA 57.823 30.769 0.00 0.00 0.00 2.29
5350 5460 7.707464 CAGCATGATTTTCCAATGCATACTTTA 59.293 33.333 0.00 0.00 39.69 1.85
5360 5470 3.444742 TCTTCGCAGCATGATTTTCCAAT 59.555 39.130 0.00 0.00 39.69 3.16
5501 5611 3.196469 CAGCAGGTCCTAAATCTCTGTCA 59.804 47.826 0.00 0.00 0.00 3.58
5825 5935 5.494724 ACTAATGCTTCAATCTTCTGCAGA 58.505 37.500 13.74 13.74 37.07 4.26
5957 6067 5.324409 TCCAAGGCATTGTACTTCTCAATT 58.676 37.500 10.60 0.00 33.92 2.32
6023 6133 4.818546 CCTCTCAAGAACAAAGACATGTGT 59.181 41.667 1.15 0.00 32.81 3.72
6027 6137 3.181440 TGGCCTCTCAAGAACAAAGACAT 60.181 43.478 3.32 0.00 0.00 3.06
6094 6204 0.865769 AACTAAACTCAGCAACGCCG 59.134 50.000 0.00 0.00 0.00 6.46
6265 6375 3.137360 AGCCAATTCCTGGGAGATACTTC 59.863 47.826 0.00 0.00 46.54 3.01
6650 6760 5.542779 ACATTCACAGAAGAGGTTACTGTC 58.457 41.667 0.00 0.00 41.93 3.51
6699 6809 3.181483 GCCTTGGCTTCCATCATAAACTG 60.181 47.826 4.11 0.00 31.53 3.16
6814 6924 2.733227 GCATTTTCTTCCTGCATGTCGG 60.733 50.000 0.00 0.00 35.96 4.79
6956 7078 7.560368 CCTACTAGCCTAATAATCAAGGATGG 58.440 42.308 0.00 0.00 36.01 3.51
7184 7308 1.824852 TGACACGAGGATGTGCAGTAT 59.175 47.619 0.00 0.00 43.74 2.12
7386 7510 0.108804 TCTCGACGGCACTTGGAATC 60.109 55.000 0.00 0.00 0.00 2.52
7419 7543 3.490419 GCCATCATCTTTGCAGTGGAATC 60.490 47.826 0.00 0.00 0.00 2.52
7568 7692 6.675026 TGGATAGTAGGTTGATATTTCGTCG 58.325 40.000 0.00 0.00 0.00 5.12
7649 7773 0.749649 GCATCTCATCGTCCACCTCT 59.250 55.000 0.00 0.00 0.00 3.69
7783 7913 0.759436 TCCCCTTGATAGCTCCGACC 60.759 60.000 0.00 0.00 0.00 4.79
7795 7925 0.547712 TCCCAGGTCTCTTCCCCTTG 60.548 60.000 0.00 0.00 0.00 3.61
7924 8054 1.404717 GCTTCAGTTCCTCGATGCTCA 60.405 52.381 0.00 0.00 31.51 4.26
8415 8547 6.579865 TCTCTTTTTACAAGACGAGAAAGGT 58.420 36.000 0.00 0.00 0.00 3.50
8417 8549 9.211556 GTTTTCTCTTTTTACAAGACGAGAAAG 57.788 33.333 11.44 0.00 43.83 2.62
8420 8552 6.819649 TGGTTTTCTCTTTTTACAAGACGAGA 59.180 34.615 0.00 0.00 0.00 4.04
8421 8553 7.011828 TGGTTTTCTCTTTTTACAAGACGAG 57.988 36.000 0.00 0.00 0.00 4.18
8423 8555 8.557029 AGTATGGTTTTCTCTTTTTACAAGACG 58.443 33.333 0.00 0.00 0.00 4.18
8451 8599 2.496291 GGGGACACGCGCCTACTAT 61.496 63.158 5.73 0.00 45.70 2.12
8536 8686 1.076332 ATTTTACTCGCACCGACAGC 58.924 50.000 0.00 0.00 0.00 4.40
8546 8696 8.837059 CCGAAGAAAATTAACACATTTTACTCG 58.163 33.333 11.51 11.51 38.51 4.18
8618 8768 9.088987 AGGTAAATAAAATGCCTTCTTCTCAAA 57.911 29.630 0.00 0.00 0.00 2.69
8619 8769 8.650143 AGGTAAATAAAATGCCTTCTTCTCAA 57.350 30.769 0.00 0.00 0.00 3.02
8620 8770 8.522830 CAAGGTAAATAAAATGCCTTCTTCTCA 58.477 33.333 0.00 0.00 37.44 3.27
8621 8771 8.523658 ACAAGGTAAATAAAATGCCTTCTTCTC 58.476 33.333 0.00 0.00 37.44 2.87
8622 8772 8.422577 ACAAGGTAAATAAAATGCCTTCTTCT 57.577 30.769 0.00 0.00 37.44 2.85
8625 8775 8.197439 GCATACAAGGTAAATAAAATGCCTTCT 58.803 33.333 0.00 0.00 37.44 2.85
8626 8776 7.978975 TGCATACAAGGTAAATAAAATGCCTTC 59.021 33.333 0.00 0.00 37.44 3.46
8627 8777 7.846066 TGCATACAAGGTAAATAAAATGCCTT 58.154 30.769 0.00 0.00 39.86 4.35
8628 8778 7.416964 TGCATACAAGGTAAATAAAATGCCT 57.583 32.000 0.00 0.00 38.11 4.75
8629 8779 7.925483 TGATGCATACAAGGTAAATAAAATGCC 59.075 33.333 0.00 0.00 38.11 4.40
8630 8780 8.870160 TGATGCATACAAGGTAAATAAAATGC 57.130 30.769 0.00 0.00 39.08 3.56
8634 8784 8.849168 CCAGATGATGCATACAAGGTAAATAAA 58.151 33.333 0.00 0.00 0.00 1.40
8635 8785 7.448161 CCCAGATGATGCATACAAGGTAAATAA 59.552 37.037 0.00 0.00 0.00 1.40
8636 8786 6.942005 CCCAGATGATGCATACAAGGTAAATA 59.058 38.462 0.00 0.00 0.00 1.40
8637 8787 5.771666 CCCAGATGATGCATACAAGGTAAAT 59.228 40.000 0.00 0.00 0.00 1.40
8638 8788 5.132502 CCCAGATGATGCATACAAGGTAAA 58.867 41.667 0.00 0.00 0.00 2.01
8639 8789 4.165950 ACCCAGATGATGCATACAAGGTAA 59.834 41.667 0.00 0.00 0.00 2.85
8640 8790 3.716353 ACCCAGATGATGCATACAAGGTA 59.284 43.478 0.00 0.00 0.00 3.08
8641 8791 2.511218 ACCCAGATGATGCATACAAGGT 59.489 45.455 0.00 0.00 0.00 3.50
8642 8792 2.882761 CACCCAGATGATGCATACAAGG 59.117 50.000 0.00 0.00 0.00 3.61
8643 8793 3.562973 GTCACCCAGATGATGCATACAAG 59.437 47.826 0.00 0.00 0.00 3.16
8644 8794 3.054508 TGTCACCCAGATGATGCATACAA 60.055 43.478 0.00 0.00 0.00 2.41
8645 8795 2.504996 TGTCACCCAGATGATGCATACA 59.495 45.455 0.00 0.00 0.00 2.29
8770 8927 2.990479 GTCGGCAAGATCCCCAGT 59.010 61.111 0.00 0.00 0.00 4.00
8771 8928 2.202932 CGTCGGCAAGATCCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
8772 8929 4.467084 GCGTCGGCAAGATCCCCA 62.467 66.667 0.00 0.00 39.62 4.96
8849 9020 8.939201 TTTCTCATATAAGAGTGAAGCAAGAG 57.061 34.615 4.97 0.00 36.97 2.85
8850 9021 9.725019 TTTTTCTCATATAAGAGTGAAGCAAGA 57.275 29.630 4.97 0.00 36.97 3.02
8925 9096 7.235804 ACTGTACTTTGGGTATTTGTAACCAT 58.764 34.615 0.00 0.00 38.87 3.55
8941 9112 5.944007 AGAACAAGTTTGGTGACTGTACTTT 59.056 36.000 0.00 0.00 0.00 2.66
8944 9115 5.465724 CCTAGAACAAGTTTGGTGACTGTAC 59.534 44.000 0.00 0.00 0.00 2.90
8954 9125 3.502123 TGACCCCCTAGAACAAGTTTG 57.498 47.619 0.00 0.00 0.00 2.93
8955 9126 3.916989 AGATGACCCCCTAGAACAAGTTT 59.083 43.478 0.00 0.00 0.00 2.66
8962 9133 1.572415 ACCGTAGATGACCCCCTAGAA 59.428 52.381 0.00 0.00 0.00 2.10
8983 9154 7.801315 GCATACATACACAAAACCGTATAATGG 59.199 37.037 0.00 0.00 0.00 3.16
9003 9174 2.512286 GCCAGCTCAGCGCATACA 60.512 61.111 11.47 0.00 42.61 2.29
9011 9182 0.735632 GTTGACTCGAGCCAGCTCAG 60.736 60.000 19.08 16.09 42.86 3.35
9100 9272 7.766278 TCTTTTAATAACTGCCAGTTTTGCAAA 59.234 29.630 16.40 8.05 39.51 3.68
9120 9295 1.920351 GACCAGGTGGGGGATCTTTTA 59.080 52.381 0.00 0.00 42.91 1.52
9141 9316 2.105128 GACCAGGTGGCTCGATCG 59.895 66.667 9.36 9.36 39.32 3.69
9213 9388 0.618968 GGGAGAAGGGAGAAGCAGGA 60.619 60.000 0.00 0.00 0.00 3.86
9240 9415 4.498520 CACCTCGGCAGCGACGAT 62.499 66.667 6.94 0.00 44.17 3.73
9293 9468 2.125912 ACGACGAGCTCATGGTGC 60.126 61.111 15.40 0.00 0.00 5.01
9330 9505 3.508840 CTCCCAAATGGCGCGGAC 61.509 66.667 8.83 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.