Multiple sequence alignment - TraesCS4D01G327100

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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 TraesCS4D01G327100 chr4D 100.000 4133 0 0 1 4133 486624872 486620740 0.000000e+00 7633.0
1 TraesCS4D01G327100 chr4D 77.709 1458 279 38 1663 3103 486432429 486433857 0.000000e+00 850.0
2 TraesCS4D01G327100 chr5A 92.124 2679 131 29 1517 4133 666874241 666871581 0.000000e+00 3705.0
3 TraesCS4D01G327100 chr5A 94.550 1578 71 7 1623 3194 667067540 667069108 0.000000e+00 2423.0
4 TraesCS4D01G327100 chr5A 84.161 1490 222 11 1659 3141 666825175 666823693 0.000000e+00 1432.0
5 TraesCS4D01G327100 chr5A 88.667 803 44 23 748 1529 667066734 667067510 0.000000e+00 935.0
6 TraesCS4D01G327100 chr5A 77.967 1466 277 37 1687 3138 666751907 666750474 0.000000e+00 876.0
7 TraesCS4D01G327100 chr5A 83.311 749 84 16 37 753 667065951 667066690 0.000000e+00 652.0
8 TraesCS4D01G327100 chr5A 87.633 283 23 8 1228 1507 666826088 666825815 6.670000e-83 318.0
9 TraesCS4D01G327100 chr5A 86.667 240 32 0 1269 1508 666844083 666843844 2.450000e-67 267.0
10 TraesCS4D01G327100 chr5A 97.656 128 3 0 1394 1521 666876504 666876377 1.930000e-53 220.0
11 TraesCS4D01G327100 chr5A 84.656 189 11 4 1216 1401 666886615 666886442 5.490000e-39 172.0
12 TraesCS4D01G327100 chr4B 92.411 2451 116 26 769 3190 621189144 621191553 0.000000e+00 3432.0
13 TraesCS4D01G327100 chr4B 91.684 1912 117 21 1288 3190 621279396 621281274 0.000000e+00 2612.0
14 TraesCS4D01G327100 chr4B 84.059 1493 226 6 1657 3143 620967275 620965789 0.000000e+00 1428.0
15 TraesCS4D01G327100 chr4B 77.078 1492 288 44 1663 3136 620946788 620945333 0.000000e+00 811.0
16 TraesCS4D01G327100 chr4B 89.277 401 33 6 3471 3861 621095575 621095175 1.030000e-135 494.0
17 TraesCS4D01G327100 chr4B 84.701 451 36 18 5 432 621188707 621189147 1.780000e-113 420.0
18 TraesCS4D01G327100 chr4B 93.863 277 14 1 3860 4133 621095146 621094870 8.270000e-112 414.0
19 TraesCS4D01G327100 chr4B 87.226 274 20 10 1237 1507 620967941 620967680 8.690000e-77 298.0
20 TraesCS4D01G327100 chr4B 86.076 237 33 0 1272 1508 620971611 620971375 5.300000e-64 255.0
21 TraesCS4D01G327100 chr4B 77.528 178 34 4 3251 3425 621095849 621095675 7.310000e-18 102.0
22 TraesCS4D01G327100 chr6A 79.539 1129 193 29 1996 3102 31369043 31367931 0.000000e+00 771.0
23 TraesCS4D01G327100 chr6A 87.500 104 13 0 1682 1785 31369381 31369278 2.020000e-23 121.0
24 TraesCS4D01G327100 chr6A 79.389 131 23 4 630 757 532157578 532157449 5.690000e-14 89.8
25 TraesCS4D01G327100 chr6B 78.654 1129 205 28 1995 3102 56050140 56049027 0.000000e+00 717.0
26 TraesCS4D01G327100 chrUn 78.083 1127 213 26 1996 3102 103934273 103933161 0.000000e+00 682.0
27 TraesCS4D01G327100 chrUn 81.646 158 27 2 1682 1838 103934605 103934449 3.350000e-26 130.0
28 TraesCS4D01G327100 chr3B 89.535 258 27 0 3876 4133 133819675 133819932 1.110000e-85 327.0
29 TraesCS4D01G327100 chr3D 89.189 259 27 1 3876 4133 84911437 84911695 5.150000e-84 322.0
30 TraesCS4D01G327100 chr3A 89.147 258 28 0 3876 4133 101894380 101894637 5.150000e-84 322.0
31 TraesCS4D01G327100 chr1D 82.514 183 23 7 577 757 194470064 194469889 7.160000e-33 152.0


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 TraesCS4D01G327100 chr4D 486620740 486624872 4132 True 7633.000000 7633 100.000000 1 4133 1 chr4D.!!$R1 4132
1 TraesCS4D01G327100 chr4D 486432429 486433857 1428 False 850.000000 850 77.709000 1663 3103 1 chr4D.!!$F1 1440
2 TraesCS4D01G327100 chr5A 666871581 666876504 4923 True 1962.500000 3705 94.890000 1394 4133 2 chr5A.!!$R5 2739
3 TraesCS4D01G327100 chr5A 667065951 667069108 3157 False 1336.666667 2423 88.842667 37 3194 3 chr5A.!!$F1 3157
4 TraesCS4D01G327100 chr5A 666750474 666751907 1433 True 876.000000 876 77.967000 1687 3138 1 chr5A.!!$R1 1451
5 TraesCS4D01G327100 chr5A 666823693 666826088 2395 True 875.000000 1432 85.897000 1228 3141 2 chr5A.!!$R4 1913
6 TraesCS4D01G327100 chr4B 621279396 621281274 1878 False 2612.000000 2612 91.684000 1288 3190 1 chr4B.!!$F1 1902
7 TraesCS4D01G327100 chr4B 621188707 621191553 2846 False 1926.000000 3432 88.556000 5 3190 2 chr4B.!!$F2 3185
8 TraesCS4D01G327100 chr4B 620945333 620946788 1455 True 811.000000 811 77.078000 1663 3136 1 chr4B.!!$R1 1473
9 TraesCS4D01G327100 chr4B 620965789 620971611 5822 True 660.333333 1428 85.787000 1237 3143 3 chr4B.!!$R2 1906
10 TraesCS4D01G327100 chr4B 621094870 621095849 979 True 336.666667 494 86.889333 3251 4133 3 chr4B.!!$R3 882
11 TraesCS4D01G327100 chr6A 31367931 31369381 1450 True 446.000000 771 83.519500 1682 3102 2 chr6A.!!$R2 1420
12 TraesCS4D01G327100 chr6B 56049027 56050140 1113 True 717.000000 717 78.654000 1995 3102 1 chr6B.!!$R1 1107
13 TraesCS4D01G327100 chrUn 103933161 103934605 1444 True 406.000000 682 79.864500 1682 3102 2 chrUn.!!$R1 1420

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
676 718 0.179009 ACTCTGTGCAGTGTGGCAAT 60.179 50.0 6.16 0.00 46.93 3.56 F
1188 1286 0.728129 GCGCGTTTACTTCTTTGCCC 60.728 55.0 8.43 0.00 0.00 5.36 F
1980 7168 0.174389 GTCTCATCAAGAGCGCTCCA 59.826 55.0 32.94 18.17 44.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 7133 1.102222 ATGAGACCCTCGTAGTCCGC 61.102 60.0 0.0 0.0 34.67 5.54 R
3028 8240 0.179097 GTCGAGGTCTTGGGCAGATC 60.179 60.0 0.0 0.0 32.60 2.75 R
3637 8939 0.179234 TCAGGTTCACTCAAACGCCA 59.821 50.0 0.0 0.0 0.00 5.69 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
28 29 5.822519 TGTATAACCAATGAAGCTTAGGCAG 59.177 40.000 0.00 0.00 41.70 4.85
40 48 1.898330 TTAGGCAGCGGATCAGCACA 61.898 55.000 20.15 0.00 40.15 4.57
53 61 1.421268 TCAGCACAACCTGGAGTTCAT 59.579 47.619 0.00 0.00 36.18 2.57
132 140 1.071471 CAGTGCGACACCCTCCTTT 59.929 57.895 6.39 0.00 34.49 3.11
163 171 2.046313 GATGCAAAAGCACGTCAACTG 58.954 47.619 0.00 0.00 0.00 3.16
165 173 1.208642 GCAAAAGCACGTCAACTGGC 61.209 55.000 0.00 0.00 0.00 4.85
255 266 1.498865 CGGTACATGATTCTGCCCGC 61.499 60.000 0.00 0.00 30.42 6.13
277 288 4.129380 CCAGAAATTGAGCGATATGACCA 58.871 43.478 0.00 0.00 0.00 4.02
296 307 3.157087 CCAAACTGGAGGCAACACTTAT 58.843 45.455 0.00 0.00 40.96 1.73
300 311 2.910319 ACTGGAGGCAACACTTATACCA 59.090 45.455 0.00 0.00 41.41 3.25
321 344 4.563993 CCAGATTGGTAACGGTGACCTTTA 60.564 45.833 15.71 0.00 37.88 1.85
330 353 5.997384 AACGGTGACCTTTAGAGAGTTAT 57.003 39.130 0.00 0.00 0.00 1.89
340 363 7.331791 ACCTTTAGAGAGTTATCGAAAGCAAT 58.668 34.615 0.00 0.00 39.31 3.56
350 373 0.451383 CGAAAGCAATGATCCCGCAA 59.549 50.000 0.00 0.00 0.00 4.85
357 381 1.863155 AATGATCCCGCAACCACCCT 61.863 55.000 0.00 0.00 0.00 4.34
470 494 4.035324 CGAGCTGCATTTTCTCATCTTCAT 59.965 41.667 1.02 0.00 0.00 2.57
471 495 5.250235 AGCTGCATTTTCTCATCTTCATG 57.750 39.130 1.02 0.00 0.00 3.07
474 498 5.394224 TGCATTTTCTCATCTTCATGCAA 57.606 34.783 2.22 0.00 42.99 4.08
477 501 6.312672 TGCATTTTCTCATCTTCATGCAATTG 59.687 34.615 0.00 0.00 42.99 2.32
482 506 6.426980 TCTCATCTTCATGCAATTGTGTAC 57.573 37.500 7.40 0.00 0.00 2.90
487 511 6.185852 TCTTCATGCAATTGTGTACTGATG 57.814 37.500 7.40 6.03 0.00 3.07
493 517 3.674138 GCAATTGTGTACTGATGGGCTTG 60.674 47.826 7.40 0.00 0.00 4.01
512 536 2.235016 TGCAGACATGTTACCCCAAAC 58.765 47.619 0.00 0.00 0.00 2.93
513 537 1.199097 GCAGACATGTTACCCCAAACG 59.801 52.381 0.00 0.00 31.76 3.60
532 556 6.072948 CCAAACGTACCAAATCACTATGTTCA 60.073 38.462 0.00 0.00 0.00 3.18
533 557 7.356540 CAAACGTACCAAATCACTATGTTCAA 58.643 34.615 0.00 0.00 0.00 2.69
534 558 7.499321 AACGTACCAAATCACTATGTTCAAA 57.501 32.000 0.00 0.00 0.00 2.69
537 561 7.117812 ACGTACCAAATCACTATGTTCAAAGAG 59.882 37.037 0.00 0.00 0.00 2.85
539 563 7.678947 ACCAAATCACTATGTTCAAAGAGAG 57.321 36.000 0.00 0.00 0.00 3.20
575 617 6.263617 ACGCCTAACTAATTTTTGGACTTTGA 59.736 34.615 0.00 0.00 0.00 2.69
591 633 6.043411 GGACTTTGATAACTAGCGAACATCT 58.957 40.000 0.00 0.00 0.00 2.90
608 650 6.473455 CGAACATCTGATTTTTAAGCAATCCC 59.527 38.462 6.89 0.00 30.64 3.85
610 652 7.243604 ACATCTGATTTTTAAGCAATCCCAA 57.756 32.000 6.89 0.00 30.64 4.12
611 653 7.099120 ACATCTGATTTTTAAGCAATCCCAAC 58.901 34.615 6.89 0.00 30.64 3.77
616 658 3.546002 TTTAAGCAATCCCAACGAACG 57.454 42.857 0.00 0.00 0.00 3.95
623 665 0.392060 ATCCCAACGAACGCCCTTAC 60.392 55.000 0.00 0.00 0.00 2.34
626 668 1.620413 CCAACGAACGCCCTTACGAC 61.620 60.000 0.00 0.00 36.70 4.34
642 684 0.595053 CGACCGTCAGATCCCAATCG 60.595 60.000 0.00 0.00 36.97 3.34
645 687 1.762957 ACCGTCAGATCCCAATCGAAT 59.237 47.619 0.00 0.00 36.97 3.34
648 690 2.564771 GTCAGATCCCAATCGAATGCA 58.435 47.619 0.00 0.00 36.97 3.96
651 693 2.228103 CAGATCCCAATCGAATGCATGG 59.772 50.000 0.00 0.00 36.97 3.66
657 699 3.243805 CCCAATCGAATGCATGGCAATTA 60.244 43.478 0.00 0.00 43.62 1.40
662 704 3.313249 TCGAATGCATGGCAATTACTCTG 59.687 43.478 0.00 0.00 43.62 3.35
663 705 3.065786 CGAATGCATGGCAATTACTCTGT 59.934 43.478 0.00 0.00 43.62 3.41
667 709 2.479049 GCATGGCAATTACTCTGTGCAG 60.479 50.000 0.00 0.00 40.12 4.41
671 713 2.095567 GGCAATTACTCTGTGCAGTGTG 60.096 50.000 14.76 2.45 40.12 3.82
672 714 2.095567 GCAATTACTCTGTGCAGTGTGG 60.096 50.000 14.76 5.49 38.19 4.17
673 715 1.813513 ATTACTCTGTGCAGTGTGGC 58.186 50.000 14.76 0.00 36.63 5.01
675 717 0.467804 TACTCTGTGCAGTGTGGCAA 59.532 50.000 14.76 0.00 46.93 4.52
676 718 0.179009 ACTCTGTGCAGTGTGGCAAT 60.179 50.000 6.16 0.00 46.93 3.56
677 719 0.956633 CTCTGTGCAGTGTGGCAATT 59.043 50.000 0.00 0.00 46.93 2.32
679 721 1.755959 TCTGTGCAGTGTGGCAATTTT 59.244 42.857 0.00 0.00 46.93 1.82
681 723 2.277969 TGTGCAGTGTGGCAATTTTTG 58.722 42.857 0.00 0.00 46.93 2.44
682 724 2.278854 GTGCAGTGTGGCAATTTTTGT 58.721 42.857 0.00 0.00 46.93 2.83
683 725 3.118992 TGTGCAGTGTGGCAATTTTTGTA 60.119 39.130 0.00 0.00 46.93 2.41
684 726 3.245048 GTGCAGTGTGGCAATTTTTGTAC 59.755 43.478 0.00 0.00 46.93 2.90
685 727 3.118992 TGCAGTGTGGCAATTTTTGTACA 60.119 39.130 0.00 0.00 41.65 2.90
686 728 3.868077 GCAGTGTGGCAATTTTTGTACAA 59.132 39.130 3.59 3.59 33.82 2.41
687 729 4.511082 GCAGTGTGGCAATTTTTGTACAAT 59.489 37.500 9.56 0.00 33.82 2.71
689 731 6.648502 CAGTGTGGCAATTTTTGTACAATTC 58.351 36.000 9.56 0.00 33.82 2.17
714 756 9.995003 TCTTTTTATAACACATGGCATTTTTCT 57.005 25.926 0.00 0.00 0.00 2.52
721 763 6.899393 ACACATGGCATTTTTCTCTTTAGA 57.101 33.333 0.00 0.00 0.00 2.10
727 769 5.711506 TGGCATTTTTCTCTTTAGAGCATGA 59.288 36.000 0.00 0.00 41.80 3.07
745 787 5.301551 AGCATGACAAATCCTTACAACAACA 59.698 36.000 0.00 0.00 0.00 3.33
753 845 9.260002 ACAAATCCTTACAACAACATGAAAATC 57.740 29.630 0.00 0.00 0.00 2.17
767 859 5.627780 ACATGAAAATCTTAAAAACCGACGC 59.372 36.000 0.00 0.00 0.00 5.19
768 860 5.427036 TGAAAATCTTAAAAACCGACGCT 57.573 34.783 0.00 0.00 0.00 5.07
800 895 9.137459 TGTAACATTTCCTCTAATTTTGTTGGA 57.863 29.630 0.00 0.00 0.00 3.53
804 899 5.964958 TTCCTCTAATTTTGTTGGAGCAG 57.035 39.130 0.00 0.00 0.00 4.24
844 941 4.217550 CACGAAGTAATCCAACAACCCATT 59.782 41.667 0.00 0.00 41.61 3.16
929 1027 4.720902 TGCATCCCACACAGCCCG 62.721 66.667 0.00 0.00 0.00 6.13
930 1028 4.722700 GCATCCCACACAGCCCGT 62.723 66.667 0.00 0.00 0.00 5.28
986 1084 3.686241 CACTCTCACTCTCACTCTCAGAG 59.314 52.174 0.00 0.00 42.84 3.35
987 1085 3.273434 CTCTCACTCTCACTCTCAGAGG 58.727 54.545 6.64 0.00 41.66 3.69
991 1089 1.340991 ACTCTCACTCTCAGAGGAGGC 60.341 57.143 16.07 0.00 41.66 4.70
1036 1134 1.009449 GCGCTGCTCCGTAGACTAG 60.009 63.158 0.00 0.00 0.00 2.57
1094 1192 2.111878 CATCGGATCACCCCAGCC 59.888 66.667 0.00 0.00 0.00 4.85
1130 1228 4.072131 CACCATTATTCTAATCCCCACCG 58.928 47.826 0.00 0.00 0.00 4.94
1185 1283 1.378360 CGCGCGCGTTTACTTCTTTG 61.378 55.000 42.49 12.54 34.35 2.77
1188 1286 0.728129 GCGCGTTTACTTCTTTGCCC 60.728 55.000 8.43 0.00 0.00 5.36
1591 6178 1.359475 GCCCGTCCGTGATCTACTC 59.641 63.158 0.00 0.00 0.00 2.59
1592 6179 1.102222 GCCCGTCCGTGATCTACTCT 61.102 60.000 0.00 0.00 0.00 3.24
1600 6187 4.693566 GTCCGTGATCTACTCTATCTCAGG 59.306 50.000 0.00 0.00 0.00 3.86
1614 6238 6.806751 TCTATCTCAGGGTGAAAAATAGTCG 58.193 40.000 0.00 0.00 0.00 4.18
1626 6253 7.648510 GGTGAAAAATAGTCGGAGTGATAGTAG 59.351 40.741 0.00 0.00 0.00 2.57
1980 7168 0.174389 GTCTCATCAAGAGCGCTCCA 59.826 55.000 32.94 18.17 44.35 3.86
2323 7514 0.729116 CACGGTGCTCAACATGATCC 59.271 55.000 0.00 0.00 0.00 3.36
2331 7522 2.625737 CTCAACATGATCCTCAACGCT 58.374 47.619 0.00 0.00 0.00 5.07
2335 7526 0.178767 CATGATCCTCAACGCTCCCA 59.821 55.000 0.00 0.00 0.00 4.37
2436 7639 3.832492 GAGGAGCTCGGCTTCGCT 61.832 66.667 7.83 0.00 39.54 4.93
2682 7888 2.416296 CGTCATGAGCGGGTACTACAAA 60.416 50.000 0.00 0.00 0.00 2.83
2690 7896 3.119101 AGCGGGTACTACAAAGACATCAG 60.119 47.826 0.00 0.00 0.00 2.90
3026 8238 1.111116 AAGACGGTGGTGTTCGAGGA 61.111 55.000 0.00 0.00 0.00 3.71
3027 8239 1.080705 GACGGTGGTGTTCGAGGAG 60.081 63.158 0.00 0.00 0.00 3.69
3028 8240 2.261671 CGGTGGTGTTCGAGGAGG 59.738 66.667 0.00 0.00 0.00 4.30
3160 8382 8.489990 TTTGTTTGAAAATGATGTGACATGTT 57.510 26.923 1.23 0.00 31.34 2.71
3161 8383 7.697352 TGTTTGAAAATGATGTGACATGTTC 57.303 32.000 1.23 2.17 41.93 3.18
3194 8416 6.431198 GAAGCCATTCGGTTGTTAATTAGA 57.569 37.500 0.00 0.00 30.54 2.10
3195 8417 6.436843 AAGCCATTCGGTTGTTAATTAGAG 57.563 37.500 0.00 0.00 33.28 2.43
3197 8419 4.095782 GCCATTCGGTTGTTAATTAGAGCA 59.904 41.667 0.00 0.00 33.28 4.26
3293 8529 2.288457 ACACGGCATCCATAGATTCTCG 60.288 50.000 0.00 0.00 0.00 4.04
3304 8540 8.944029 CATCCATAGATTCTCGAGCAATATTTT 58.056 33.333 7.81 0.00 0.00 1.82
3325 8561 3.188492 TCAAACTCGTACGCTCAAACAA 58.812 40.909 11.24 0.00 0.00 2.83
3328 8564 2.132762 ACTCGTACGCTCAAACAAAGG 58.867 47.619 11.24 0.00 0.00 3.11
3390 8632 1.269448 ACAGTTTTGCGGCAATACCTG 59.731 47.619 25.69 24.54 35.61 4.00
3512 8808 4.836825 ACAGTACCATATGCATATCAGCC 58.163 43.478 16.46 5.68 0.00 4.85
3529 8825 3.130869 TCAGCCAACAATAATGGTGCATC 59.869 43.478 0.00 0.00 43.22 3.91
3542 8838 4.540153 GCATCCGGCAAAGAGCTA 57.460 55.556 0.00 0.00 44.79 3.32
3582 8884 6.462500 CCTCATTTCTGATAGAATCATCGGT 58.538 40.000 0.00 0.00 38.85 4.69
3602 8904 0.535797 GAAATCCTCGGTCGGTCCTT 59.464 55.000 0.00 0.00 0.00 3.36
3632 8934 3.258372 TGTTCTATCTTCAGACGCTTGGT 59.742 43.478 0.00 0.00 0.00 3.67
3637 8939 3.126001 TCTTCAGACGCTTGGTTGAAT 57.874 42.857 0.00 0.00 30.66 2.57
3647 8949 2.664916 CTTGGTTGAATGGCGTTTGAG 58.335 47.619 0.00 0.00 0.00 3.02
3650 8952 1.606668 GGTTGAATGGCGTTTGAGTGA 59.393 47.619 0.00 0.00 0.00 3.41
3701 9003 1.073897 AACCCTGTGCTTCAGCTCC 59.926 57.895 0.00 0.00 42.38 4.70
3704 9006 2.752358 CTGTGCTTCAGCTCCCCA 59.248 61.111 0.00 0.00 42.66 4.96
3716 9018 1.597027 CTCCCCACGGTGTGTTGTC 60.597 63.158 7.45 0.00 0.00 3.18
3719 9021 1.153249 CCCACGGTGTGTTGTCAGT 60.153 57.895 7.45 0.00 0.00 3.41
3767 9069 1.406898 CTGTCGCAGCTTCCTGAGATA 59.593 52.381 0.75 0.00 46.98 1.98
3789 9095 1.817099 CCATCTTCCTCCTGCGTGC 60.817 63.158 0.00 0.00 0.00 5.34
3794 9100 2.859273 CTTCCTCCTGCGTGCGGAAT 62.859 60.000 1.35 0.00 35.21 3.01
3825 9135 6.931838 AGTTTCAGATTAACATAGGACGACA 58.068 36.000 0.00 0.00 0.00 4.35
3835 9145 0.601558 TAGGACGACAGACACCTTGC 59.398 55.000 0.00 0.00 34.42 4.01
3858 9168 3.057033 GGCACTGCAGAGAATGAAACAAT 60.057 43.478 23.35 0.00 0.00 2.71
3926 9269 2.628696 TTCTTCGTACTCCGCCGCA 61.629 57.895 0.00 0.00 36.19 5.69
4016 9359 1.746991 GAAAGGCAGCGGGAAGAGG 60.747 63.158 0.00 0.00 0.00 3.69
4109 9452 5.064558 ACATATATCGTTCTCGGAGACACT 58.935 41.667 7.33 0.00 37.69 3.55
4110 9453 6.228995 ACATATATCGTTCTCGGAGACACTA 58.771 40.000 7.33 2.65 37.69 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.308229 GCCTAAGCTTCATTGGTTATACAGATG 60.308 40.741 0.00 0.00 35.50 2.90
1 2 6.712547 GCCTAAGCTTCATTGGTTATACAGAT 59.287 38.462 0.00 0.00 35.50 2.90
2 3 6.055588 GCCTAAGCTTCATTGGTTATACAGA 58.944 40.000 0.00 0.00 35.50 3.41
3 4 5.822519 TGCCTAAGCTTCATTGGTTATACAG 59.177 40.000 0.00 0.00 40.80 2.74
23 24 3.258228 TTGTGCTGATCCGCTGCCT 62.258 57.895 10.62 0.00 40.39 4.75
28 29 2.401766 CCAGGTTGTGCTGATCCGC 61.402 63.158 1.59 1.59 0.00 5.54
33 34 0.836606 TGAACTCCAGGTTGTGCTGA 59.163 50.000 0.00 0.00 38.41 4.26
40 48 1.205893 GCTCTCGATGAACTCCAGGTT 59.794 52.381 0.00 0.00 41.40 3.50
77 85 4.321230 CCTTAGGCATGTTGGAACTGTTTC 60.321 45.833 0.00 0.00 0.00 2.78
132 140 1.177895 TTTTGCATCTTGCCCTCGCA 61.178 50.000 0.00 0.00 44.23 5.10
151 159 1.372997 CTACGCCAGTTGACGTGCT 60.373 57.895 3.71 0.00 43.44 4.40
163 171 2.461110 CCACCGACAATGCTACGCC 61.461 63.158 0.00 0.00 0.00 5.68
165 173 1.079405 ACCCACCGACAATGCTACG 60.079 57.895 0.00 0.00 0.00 3.51
255 266 4.129380 TGGTCATATCGCTCAATTTCTGG 58.871 43.478 0.00 0.00 0.00 3.86
261 272 3.879295 CCAGTTTGGTCATATCGCTCAAT 59.121 43.478 0.00 0.00 31.35 2.57
277 288 4.202524 TGGTATAAGTGTTGCCTCCAGTTT 60.203 41.667 0.00 0.00 0.00 2.66
300 311 3.782656 AAAGGTCACCGTTACCAATCT 57.217 42.857 4.70 0.00 39.64 2.40
321 344 5.988561 GGATCATTGCTTTCGATAACTCTCT 59.011 40.000 0.00 0.00 0.00 3.10
330 353 0.392327 TGCGGGATCATTGCTTTCGA 60.392 50.000 0.00 0.00 0.00 3.71
340 363 2.933287 AGGGTGGTTGCGGGATCA 60.933 61.111 0.00 0.00 0.00 2.92
350 373 1.054406 CCATATCGTCCCAGGGTGGT 61.054 60.000 5.01 0.00 35.17 4.16
357 381 2.462723 TCAAGTCACCATATCGTCCCA 58.537 47.619 0.00 0.00 0.00 4.37
463 487 6.183360 CCATCAGTACACAATTGCATGAAGAT 60.183 38.462 5.05 0.49 0.00 2.40
470 494 1.818060 GCCCATCAGTACACAATTGCA 59.182 47.619 5.05 0.00 0.00 4.08
471 495 2.094675 AGCCCATCAGTACACAATTGC 58.905 47.619 5.05 0.00 0.00 3.56
474 498 2.094675 GCAAGCCCATCAGTACACAAT 58.905 47.619 0.00 0.00 0.00 2.71
477 501 1.089920 CTGCAAGCCCATCAGTACAC 58.910 55.000 0.00 0.00 0.00 2.90
482 506 0.738975 CATGTCTGCAAGCCCATCAG 59.261 55.000 0.00 0.00 0.00 2.90
487 511 0.811281 GGTAACATGTCTGCAAGCCC 59.189 55.000 0.00 0.00 0.00 5.19
493 517 1.199097 CGTTTGGGGTAACATGTCTGC 59.801 52.381 0.00 0.00 39.74 4.26
512 536 7.330946 TCTCTTTGAACATAGTGATTTGGTACG 59.669 37.037 0.00 0.00 0.00 3.67
513 537 8.547967 TCTCTTTGAACATAGTGATTTGGTAC 57.452 34.615 0.00 0.00 0.00 3.34
532 556 0.603975 GTCGCCTGGTTGCTCTCTTT 60.604 55.000 0.00 0.00 0.00 2.52
533 557 1.004440 GTCGCCTGGTTGCTCTCTT 60.004 57.895 0.00 0.00 0.00 2.85
534 558 2.659610 GTCGCCTGGTTGCTCTCT 59.340 61.111 0.00 0.00 0.00 3.10
558 600 9.490663 CGCTAGTTATCAAAGTCCAAAAATTAG 57.509 33.333 0.00 0.00 0.00 1.73
562 604 7.012515 TGTTCGCTAGTTATCAAAGTCCAAAAA 59.987 33.333 0.00 0.00 0.00 1.94
580 622 6.735678 TGCTTAAAAATCAGATGTTCGCTA 57.264 33.333 0.00 0.00 0.00 4.26
582 624 6.020360 GGATTGCTTAAAAATCAGATGTTCGC 60.020 38.462 10.94 0.00 36.03 4.70
591 633 5.713792 TCGTTGGGATTGCTTAAAAATCA 57.286 34.783 10.94 0.00 36.03 2.57
608 650 1.620413 GGTCGTAAGGGCGTTCGTTG 61.620 60.000 0.00 0.00 38.47 4.10
610 652 2.259511 GGTCGTAAGGGCGTTCGT 59.740 61.111 0.00 0.00 38.47 3.85
611 653 2.877582 CGGTCGTAAGGGCGTTCG 60.878 66.667 0.00 0.76 38.47 3.95
616 658 0.248949 GATCTGACGGTCGTAAGGGC 60.249 60.000 7.90 0.00 38.47 5.19
623 665 0.595053 CGATTGGGATCTGACGGTCG 60.595 60.000 3.34 0.00 0.00 4.79
626 668 2.138320 CATTCGATTGGGATCTGACGG 58.862 52.381 0.00 0.00 0.00 4.79
642 684 4.357142 CACAGAGTAATTGCCATGCATTC 58.643 43.478 0.00 0.00 38.76 2.67
645 687 1.473677 GCACAGAGTAATTGCCATGCA 59.526 47.619 0.00 0.00 36.47 3.96
648 690 2.751259 CACTGCACAGAGTAATTGCCAT 59.249 45.455 4.31 0.00 35.26 4.40
651 693 2.095567 CCACACTGCACAGAGTAATTGC 60.096 50.000 4.31 0.00 36.76 3.56
657 699 0.179009 ATTGCCACACTGCACAGAGT 60.179 50.000 4.31 0.00 41.88 3.24
662 704 2.278854 ACAAAAATTGCCACACTGCAC 58.721 42.857 0.00 0.00 41.88 4.57
663 705 2.687700 ACAAAAATTGCCACACTGCA 57.312 40.000 0.00 0.00 40.07 4.41
667 709 6.843069 AGAATTGTACAAAAATTGCCACAC 57.157 33.333 13.23 0.00 31.21 3.82
681 723 9.632807 TGCCATGTGTTATAAAAAGAATTGTAC 57.367 29.630 0.00 0.00 0.00 2.90
683 725 9.723601 AATGCCATGTGTTATAAAAAGAATTGT 57.276 25.926 0.00 0.00 0.00 2.71
699 741 5.803967 GCTCTAAAGAGAAAAATGCCATGTG 59.196 40.000 11.20 0.00 44.74 3.21
703 745 5.711506 TCATGCTCTAAAGAGAAAAATGCCA 59.288 36.000 11.20 0.00 44.74 4.92
708 750 8.299570 GGATTTGTCATGCTCTAAAGAGAAAAA 58.700 33.333 11.20 0.00 44.74 1.94
711 753 6.715280 AGGATTTGTCATGCTCTAAAGAGAA 58.285 36.000 11.20 0.00 44.74 2.87
714 756 7.394016 TGTAAGGATTTGTCATGCTCTAAAGA 58.606 34.615 0.00 0.00 0.00 2.52
721 763 5.301551 TGTTGTTGTAAGGATTTGTCATGCT 59.698 36.000 0.00 0.00 0.00 3.79
727 769 9.260002 GATTTTCATGTTGTTGTAAGGATTTGT 57.740 29.630 0.00 0.00 0.00 2.83
745 787 6.009115 AGCGTCGGTTTTTAAGATTTTCAT 57.991 33.333 0.00 0.00 0.00 2.57
753 845 5.504392 ACAAAACTAGCGTCGGTTTTTAAG 58.496 37.500 0.65 0.00 41.70 1.85
760 852 3.096489 TGTTACAAAACTAGCGTCGGT 57.904 42.857 1.19 1.19 36.51 4.69
795 890 0.320697 ACGGAAGTACCTGCTCCAAC 59.679 55.000 0.00 0.00 46.88 3.77
800 895 1.204941 CTTGCTACGGAAGTACCTGCT 59.795 52.381 0.00 0.00 46.88 4.24
804 899 1.356938 GTGCTTGCTACGGAAGTACC 58.643 55.000 5.33 0.00 46.88 3.34
844 941 1.142936 CACTGATGGGATGGGATGGA 58.857 55.000 0.00 0.00 0.00 3.41
930 1028 4.783621 GATCACGCAGGCAGGCCA 62.784 66.667 13.63 0.00 38.92 5.36
933 1031 2.202987 GAGGATCACGCAGGCAGG 60.203 66.667 0.00 0.00 33.17 4.85
934 1032 2.202987 GGAGGATCACGCAGGCAG 60.203 66.667 0.00 0.00 36.25 4.85
935 1033 2.685017 AGGAGGATCACGCAGGCA 60.685 61.111 0.00 0.00 36.25 4.75
1036 1134 3.199891 GCGGTGGCGATGGGTTAC 61.200 66.667 0.00 0.00 0.00 2.50
1094 1192 4.864334 GGTGGCGGATCAGCTGGG 62.864 72.222 17.48 2.23 37.29 4.45
1130 1228 3.520691 GGGTGGGATTAGAATAACCCC 57.479 52.381 0.00 0.00 41.23 4.95
1233 1331 0.322008 CAACCAGGCTGGAGAAGGAC 60.322 60.000 38.99 0.00 40.96 3.85
1591 6178 5.986135 CCGACTATTTTTCACCCTGAGATAG 59.014 44.000 0.00 0.00 0.00 2.08
1592 6179 5.659525 TCCGACTATTTTTCACCCTGAGATA 59.340 40.000 0.00 0.00 0.00 1.98
1600 6187 6.338937 ACTATCACTCCGACTATTTTTCACC 58.661 40.000 0.00 0.00 0.00 4.02
1614 6238 5.889289 ACAGAGAAGTTCCTACTATCACTCC 59.111 44.000 0.00 0.00 33.17 3.85
1728 6883 3.858868 GAACGTGCAGAGGACGGCA 62.859 63.158 15.07 0.00 43.99 5.69
1946 7131 3.885521 GACCCTCGTAGTCCGCCG 61.886 72.222 0.00 0.00 36.19 6.46
1948 7133 1.102222 ATGAGACCCTCGTAGTCCGC 61.102 60.000 0.00 0.00 34.67 5.54
1980 7168 2.355108 CCACCGGATGTCAAACTCAGAT 60.355 50.000 9.46 0.00 0.00 2.90
2682 7888 1.446792 CTTGGTCGCGCTGATGTCT 60.447 57.895 5.56 0.00 0.00 3.41
2690 7896 3.665675 ATGGACTCCTTGGTCGCGC 62.666 63.158 0.00 0.00 37.12 6.86
2919 8128 1.673033 CCGTCCTTCAGCTTCACGAAT 60.673 52.381 0.00 0.00 32.08 3.34
2980 8189 2.510238 GTAGTGCGGCAGCCTCTG 60.510 66.667 10.54 0.00 44.33 3.35
3026 8238 1.333636 CGAGGTCTTGGGCAGATCCT 61.334 60.000 0.00 0.00 36.35 3.24
3027 8239 1.144936 CGAGGTCTTGGGCAGATCC 59.855 63.158 0.00 0.00 32.08 3.36
3028 8240 0.179097 GTCGAGGTCTTGGGCAGATC 60.179 60.000 0.00 0.00 32.60 2.75
3210 8432 7.375053 TGCTCTGTTTGAGTGTAAAAAGTTTT 58.625 30.769 0.00 0.00 44.41 2.43
3230 8452 1.202687 TGTGTGTGCTTAGCTTGCTCT 60.203 47.619 5.60 0.00 0.00 4.09
3293 8529 5.448162 GCGTACGAGTTTGAAAATATTGCTC 59.552 40.000 21.65 0.00 0.00 4.26
3304 8540 2.811855 TGTTTGAGCGTACGAGTTTGA 58.188 42.857 21.65 0.00 0.00 2.69
3390 8632 4.749976 AGGAGTTGAAAGATTAGCTCGTC 58.250 43.478 0.00 0.00 0.00 4.20
3512 8808 2.799207 GCCGGATGCACCATTATTGTTG 60.799 50.000 5.05 0.00 40.77 3.33
3529 8825 2.109126 GGCAGTAGCTCTTTGCCGG 61.109 63.158 17.12 0.00 46.82 6.13
3542 8838 3.111265 AGGGAAATCCTCAGGCAGT 57.889 52.632 0.00 0.00 44.06 4.40
3582 8884 0.613853 AGGACCGACCGAGGATTTCA 60.614 55.000 0.00 0.00 44.74 2.69
3602 8904 3.523157 TCTGAAGATAGAACAATGGCCCA 59.477 43.478 0.00 0.00 0.00 5.36
3632 8934 2.034053 GGTTCACTCAAACGCCATTCAA 59.966 45.455 0.00 0.00 0.00 2.69
3637 8939 0.179234 TCAGGTTCACTCAAACGCCA 59.821 50.000 0.00 0.00 0.00 5.69
3701 9003 0.746563 AACTGACAACACACCGTGGG 60.747 55.000 0.00 0.00 37.94 4.61
3704 9006 2.210116 GATGAACTGACAACACACCGT 58.790 47.619 0.00 0.00 0.00 4.83
3716 9018 5.490139 ACGCTGAAATATTGGATGAACTG 57.510 39.130 0.00 0.00 0.00 3.16
3719 9021 4.438148 TCGACGCTGAAATATTGGATGAA 58.562 39.130 0.00 0.00 0.00 2.57
3767 9069 1.684386 CGCAGGAGGAAGATGGCTCT 61.684 60.000 0.00 0.00 0.00 4.09
3835 9145 1.135859 GTTTCATTCTCTGCAGTGCCG 60.136 52.381 14.67 6.40 0.00 5.69
3926 9269 0.620556 ATGACTTGCGGGAACTGGAT 59.379 50.000 0.00 0.00 32.89 3.41
3992 9335 1.303643 CCCGCTGCCTTTCTTCCTT 60.304 57.895 0.00 0.00 0.00 3.36
4022 9365 2.731451 CACAACATGGATACCGATAGCG 59.269 50.000 0.00 0.00 37.24 4.26
4079 9422 6.906659 TCCGAGAACGATATATGTCTTTACC 58.093 40.000 0.00 0.00 42.66 2.85
4109 9452 3.205338 CCATGCATCATTCGTGGAGTTA 58.795 45.455 0.00 0.00 41.91 2.24
4110 9453 2.019249 CCATGCATCATTCGTGGAGTT 58.981 47.619 0.00 0.00 41.91 3.01


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

AutoCloner maintained by Alex Coulton.