Multiple sequence alignment - TraesCS7A01G285700

Loading Multiple Alignment...

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 TraesCS7A01G285700 chr7A 100.000 3043 0 0 1 3043 331174778 331177820 0.000000e+00 5620
1 TraesCS7A01G285700 chr7A 93.897 639 38 1 2405 3043 648951593 648952230 0.000000e+00 963
2 TraesCS7A01G285700 chr7A 87.524 529 60 4 456 983 199442280 199441757 9.330000e-170 606
3 TraesCS7A01G285700 chr7A 93.709 302 19 0 1711 2012 227065702 227066003 1.290000e-123 453
4 TraesCS7A01G285700 chr7A 83.333 270 35 10 1450 1715 55193622 55193359 1.090000e-59 241
5 TraesCS7A01G285700 chr3D 94.563 1030 54 2 2014 3043 322459314 322460341 0.000000e+00 1591
6 TraesCS7A01G285700 chr3D 94.886 528 27 0 2168 2695 421027892 421028419 0.000000e+00 826
7 TraesCS7A01G285700 chr3D 89.241 474 22 7 1 445 280074453 280073980 1.580000e-157 566
8 TraesCS7A01G285700 chr3D 89.053 475 22 8 1 445 277236417 277236891 2.050000e-156 562
9 TraesCS7A01G285700 chr3D 89.326 356 29 5 961 1312 588637872 588637522 3.600000e-119 438
10 TraesCS7A01G285700 chr3D 85.556 270 29 10 1450 1715 564479727 564479464 1.070000e-69 274
11 TraesCS7A01G285700 chr3D 91.346 104 7 1 2079 2182 601322361 601322260 1.140000e-29 141
12 TraesCS7A01G285700 chr2A 93.307 1031 66 3 2014 3043 256698783 256697755 0.000000e+00 1519
13 TraesCS7A01G285700 chr7D 89.326 1143 85 12 174 1285 45982646 45981510 0.000000e+00 1400
14 TraesCS7A01G285700 chr7D 93.694 111 7 0 1317 1427 45981431 45981321 1.880000e-37 167
15 TraesCS7A01G285700 chr6B 86.872 1135 102 24 174 1285 711531966 711530856 0.000000e+00 1227
16 TraesCS7A01G285700 chr6B 93.371 528 34 1 2168 2695 57390993 57391519 0.000000e+00 780
17 TraesCS7A01G285700 chr6B 84.108 667 43 19 1 636 108225491 108226125 1.220000e-163 586
18 TraesCS7A01G285700 chr6B 92.308 403 27 4 1317 1715 711530777 711530375 1.220000e-158 569
19 TraesCS7A01G285700 chr6B 93.709 302 18 1 1711 2012 686701856 686701556 4.630000e-123 451
20 TraesCS7A01G285700 chr6B 84.815 270 31 10 1450 1715 418731144 418730881 2.330000e-66 263
21 TraesCS7A01G285700 chr6B 94.815 135 7 0 2909 3043 190945723 190945857 8.550000e-51 211
22 TraesCS7A01G285700 chr6B 96.117 103 4 0 1317 1419 418731231 418731129 5.220000e-38 169
23 TraesCS7A01G285700 chr5D 88.358 962 61 18 174 1112 556581740 556580807 0.000000e+00 1109
24 TraesCS7A01G285700 chr5D 85.561 838 77 17 174 983 168394287 168393466 0.000000e+00 837
25 TraesCS7A01G285700 chr5D 88.352 704 33 24 1 671 504226289 504226976 0.000000e+00 800
26 TraesCS7A01G285700 chr5D 87.124 699 43 25 3 671 147615760 147616441 0.000000e+00 749
27 TraesCS7A01G285700 chr5D 85.960 698 45 14 1 671 511355443 511354772 0.000000e+00 697
28 TraesCS7A01G285700 chr5D 93.709 302 18 1 1711 2012 45713025 45713325 4.630000e-123 451
29 TraesCS7A01G285700 chr5D 89.888 356 28 4 961 1312 434898566 434898215 4.630000e-123 451
30 TraesCS7A01G285700 chr5D 91.339 127 11 0 1317 1443 168393135 168393009 1.120000e-39 174
31 TraesCS7A01G285700 chr2D 88.017 968 61 11 174 1112 586827945 586828886 0.000000e+00 1094
32 TraesCS7A01G285700 chr2D 93.662 568 29 7 1448 2012 100847696 100847133 0.000000e+00 843
33 TraesCS7A01G285700 chr2D 90.305 557 48 4 557 1112 10055784 10056335 0.000000e+00 725
34 TraesCS7A01G285700 chr2D 89.341 516 49 4 771 1285 648846460 648846970 0.000000e+00 643
35 TraesCS7A01G285700 chr2D 92.236 322 24 1 994 1314 100848149 100847828 3.580000e-124 455
36 TraesCS7A01G285700 chr2D 94.565 276 11 4 1442 1715 648847136 648847409 1.010000e-114 424
37 TraesCS7A01G285700 chr2D 94.382 178 10 0 447 624 100864610 100864433 1.070000e-69 274
38 TraesCS7A01G285700 chr2D 94.643 112 6 0 1317 1428 648847049 648847160 1.120000e-39 174
39 TraesCS7A01G285700 chr1B 91.476 657 53 2 2386 3042 586691644 586690991 0.000000e+00 900
40 TraesCS7A01G285700 chr1B 84.074 270 33 10 1450 1715 641931342 641931079 5.040000e-63 252
41 TraesCS7A01G285700 chr1B 96.117 103 4 0 1317 1419 26648394 26648496 5.220000e-38 169
42 TraesCS7A01G285700 chr1B 96.117 103 4 0 1317 1419 641931429 641931327 5.220000e-38 169
43 TraesCS7A01G285700 chr5A 94.017 585 34 1 2014 2598 516606593 516607176 0.000000e+00 885
44 TraesCS7A01G285700 chr1D 95.455 528 24 0 2168 2695 412906304 412905777 0.000000e+00 843
45 TraesCS7A01G285700 chr1D 95.265 528 25 0 2168 2695 412690468 412689941 0.000000e+00 837
46 TraesCS7A01G285700 chr1D 89.362 658 65 3 456 1112 16466399 16467052 0.000000e+00 822
47 TraesCS7A01G285700 chr1D 94.129 528 31 0 2168 2695 412822768 412822241 0.000000e+00 804
48 TraesCS7A01G285700 chr1D 88.789 223 20 5 1503 1722 491633136 491633356 5.000000e-68 268
49 TraesCS7A01G285700 chr1D 100.000 57 0 0 2014 2070 412822821 412822765 4.150000e-19 106
50 TraesCS7A01G285700 chr1D 100.000 57 0 0 2014 2070 412906357 412906301 4.150000e-19 106
51 TraesCS7A01G285700 chrUn 89.650 657 62 4 457 1112 70722100 70722751 0.000000e+00 832
52 TraesCS7A01G285700 chr3B 94.318 528 28 2 2168 2695 803653945 803653420 0.000000e+00 808
53 TraesCS7A01G285700 chr3B 94.040 302 17 1 1711 2012 56538155 56537855 9.940000e-125 457
54 TraesCS7A01G285700 chr3B 96.154 104 4 0 2079 2182 729581542 729581645 1.450000e-38 171
55 TraesCS7A01G285700 chr4D 88.445 701 35 18 1 671 67198904 67198220 0.000000e+00 804
56 TraesCS7A01G285700 chr5B 86.448 701 32 23 1 671 564296652 564297319 0.000000e+00 710
57 TraesCS7A01G285700 chr5B 86.325 702 32 22 1 671 564355037 564355705 0.000000e+00 706
58 TraesCS7A01G285700 chr5B 86.040 702 34 28 1 671 564417628 564418296 0.000000e+00 695
59 TraesCS7A01G285700 chr5B 91.176 510 28 10 1 505 17756083 17756580 0.000000e+00 676
60 TraesCS7A01G285700 chr5B 91.690 361 22 6 961 1319 298688969 298688615 7.580000e-136 494
61 TraesCS7A01G285700 chr5B 96.117 103 4 0 1317 1419 621789795 621789693 5.220000e-38 169
62 TraesCS7A01G285700 chr4A 91.136 361 24 6 961 1319 340789696 340790050 1.640000e-132 483
63 TraesCS7A01G285700 chr1A 90.000 360 31 3 961 1319 589440473 589440828 7.690000e-126 460
64 TraesCS7A01G285700 chr7B 93.377 302 19 1 1711 2012 112564730 112564430 2.150000e-121 446
65 TraesCS7A01G285700 chr7B 93.377 302 19 1 1711 2012 523548303 523548603 2.150000e-121 446
66 TraesCS7A01G285700 chr7B 95.785 261 10 1 2783 3043 703775565 703775306 1.300000e-113 420
67 TraesCS7A01G285700 chr7B 94.636 261 13 1 2783 3043 703749864 703749605 1.310000e-108 403
68 TraesCS7A01G285700 chr7B 95.556 135 6 0 2909 3043 596407472 596407606 1.840000e-52 217
69 TraesCS7A01G285700 chr7B 95.192 104 5 0 2079 2182 255414915 255414812 6.750000e-37 165
70 TraesCS7A01G285700 chr7B 92.793 111 7 1 2073 2182 255372008 255371898 3.140000e-35 159
71 TraesCS7A01G285700 chr7B 96.970 66 2 0 2014 2079 255372208 255372143 8.920000e-21 111
72 TraesCS7A01G285700 chr7B 96.970 66 2 0 2014 2079 255415115 255415050 8.920000e-21 111
73 TraesCS7A01G285700 chr4B 93.377 302 19 1 1711 2012 552353927 552353627 2.150000e-121 446
74 TraesCS7A01G285700 chr4B 94.074 135 8 0 2909 3043 279911487 279911353 3.980000e-49 206
75 TraesCS7A01G285700 chr4B 96.154 104 4 0 2079 2182 568681262 568681365 1.450000e-38 171
76 TraesCS7A01G285700 chr4B 96.117 103 4 0 1317 1419 244503936 244504038 5.220000e-38 169
77 TraesCS7A01G285700 chr2B 93.377 302 19 1 1711 2012 31965945 31966245 2.150000e-121 446
78 TraesCS7A01G285700 chr2B 84.815 270 31 10 1450 1715 750473420 750473683 2.330000e-66 263
79 TraesCS7A01G285700 chr6A 92.308 104 8 0 2079 2182 798356 798253 6.800000e-32 148
80 TraesCS7A01G285700 chr6A 95.714 70 2 1 2010 2079 798752 798684 8.920000e-21 111
81 TraesCS7A01G285700 chr6D 100.000 57 0 0 2014 2070 321602560 321602616 4.150000e-19 106


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 TraesCS7A01G285700 chr7A 331174778 331177820 3042 False 5620.000000 5620 100.000000 1 3043 1 chr7A.!!$F2 3042
1 TraesCS7A01G285700 chr7A 648951593 648952230 637 False 963.000000 963 93.897000 2405 3043 1 chr7A.!!$F3 638
2 TraesCS7A01G285700 chr7A 199441757 199442280 523 True 606.000000 606 87.524000 456 983 1 chr7A.!!$R2 527
3 TraesCS7A01G285700 chr3D 322459314 322460341 1027 False 1591.000000 1591 94.563000 2014 3043 1 chr3D.!!$F2 1029
4 TraesCS7A01G285700 chr3D 421027892 421028419 527 False 826.000000 826 94.886000 2168 2695 1 chr3D.!!$F3 527
5 TraesCS7A01G285700 chr2A 256697755 256698783 1028 True 1519.000000 1519 93.307000 2014 3043 1 chr2A.!!$R1 1029
6 TraesCS7A01G285700 chr7D 45981321 45982646 1325 True 783.500000 1400 91.510000 174 1427 2 chr7D.!!$R1 1253
7 TraesCS7A01G285700 chr6B 711530375 711531966 1591 True 898.000000 1227 89.590000 174 1715 2 chr6B.!!$R3 1541
8 TraesCS7A01G285700 chr6B 57390993 57391519 526 False 780.000000 780 93.371000 2168 2695 1 chr6B.!!$F1 527
9 TraesCS7A01G285700 chr6B 108225491 108226125 634 False 586.000000 586 84.108000 1 636 1 chr6B.!!$F2 635
10 TraesCS7A01G285700 chr5D 556580807 556581740 933 True 1109.000000 1109 88.358000 174 1112 1 chr5D.!!$R3 938
11 TraesCS7A01G285700 chr5D 504226289 504226976 687 False 800.000000 800 88.352000 1 671 1 chr5D.!!$F3 670
12 TraesCS7A01G285700 chr5D 147615760 147616441 681 False 749.000000 749 87.124000 3 671 1 chr5D.!!$F2 668
13 TraesCS7A01G285700 chr5D 511354772 511355443 671 True 697.000000 697 85.960000 1 671 1 chr5D.!!$R2 670
14 TraesCS7A01G285700 chr5D 168393009 168394287 1278 True 505.500000 837 88.450000 174 1443 2 chr5D.!!$R4 1269
15 TraesCS7A01G285700 chr2D 586827945 586828886 941 False 1094.000000 1094 88.017000 174 1112 1 chr2D.!!$F2 938
16 TraesCS7A01G285700 chr2D 10055784 10056335 551 False 725.000000 725 90.305000 557 1112 1 chr2D.!!$F1 555
17 TraesCS7A01G285700 chr2D 100847133 100848149 1016 True 649.000000 843 92.949000 994 2012 2 chr2D.!!$R2 1018
18 TraesCS7A01G285700 chr2D 648846460 648847409 949 False 413.666667 643 92.849667 771 1715 3 chr2D.!!$F3 944
19 TraesCS7A01G285700 chr1B 586690991 586691644 653 True 900.000000 900 91.476000 2386 3042 1 chr1B.!!$R1 656
20 TraesCS7A01G285700 chr5A 516606593 516607176 583 False 885.000000 885 94.017000 2014 2598 1 chr5A.!!$F1 584
21 TraesCS7A01G285700 chr1D 412689941 412690468 527 True 837.000000 837 95.265000 2168 2695 1 chr1D.!!$R1 527
22 TraesCS7A01G285700 chr1D 16466399 16467052 653 False 822.000000 822 89.362000 456 1112 1 chr1D.!!$F1 656
23 TraesCS7A01G285700 chr1D 412905777 412906357 580 True 474.500000 843 97.727500 2014 2695 2 chr1D.!!$R3 681
24 TraesCS7A01G285700 chr1D 412822241 412822821 580 True 455.000000 804 97.064500 2014 2695 2 chr1D.!!$R2 681
25 TraesCS7A01G285700 chrUn 70722100 70722751 651 False 832.000000 832 89.650000 457 1112 1 chrUn.!!$F1 655
26 TraesCS7A01G285700 chr3B 803653420 803653945 525 True 808.000000 808 94.318000 2168 2695 1 chr3B.!!$R2 527
27 TraesCS7A01G285700 chr4D 67198220 67198904 684 True 804.000000 804 88.445000 1 671 1 chr4D.!!$R1 670
28 TraesCS7A01G285700 chr5B 564296652 564297319 667 False 710.000000 710 86.448000 1 671 1 chr5B.!!$F2 670
29 TraesCS7A01G285700 chr5B 564355037 564355705 668 False 706.000000 706 86.325000 1 671 1 chr5B.!!$F3 670
30 TraesCS7A01G285700 chr5B 564417628 564418296 668 False 695.000000 695 86.040000 1 671 1 chr5B.!!$F4 670

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
358 368 0.309302 CCGCGTTTTGATTGGTCACA 59.691 50.0 4.92 0.0 33.11 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2356 0.107703 CAAAGATACCAGCTGGGCGA 60.108 55.0 35.42 20.92 42.05 5.54 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
37 39 7.276218 CCAACTATTTGGTCAATTGTGCATTAG 59.724 37.037 5.13 4.40 46.63 1.73
224 231 5.123027 GGTGGTTCAATTTTGCAACAAAGAA 59.877 36.000 0.00 0.00 0.00 2.52
267 274 9.518906 AACAAAATCAAAATGGAAAATGCTTTC 57.481 25.926 0.00 0.00 40.31 2.62
356 366 1.880271 TACCGCGTTTTGATTGGTCA 58.120 45.000 4.92 0.00 34.18 4.02
357 367 0.309612 ACCGCGTTTTGATTGGTCAC 59.690 50.000 4.92 0.00 33.11 3.67
358 368 0.309302 CCGCGTTTTGATTGGTCACA 59.691 50.000 4.92 0.00 33.11 3.58
423 458 2.039624 ACGGCCTCACCCTCTCAT 59.960 61.111 0.00 0.00 33.26 2.90
445 481 1.298340 CGTAGCCCAATCACCCACA 59.702 57.895 0.00 0.00 0.00 4.17
506 542 2.716203 CCTAGCCCTCTCCCTCCCA 61.716 68.421 0.00 0.00 0.00 4.37
523 559 2.909006 TCCCATAGATCTCAATCTGCCC 59.091 50.000 0.00 0.00 42.36 5.36
544 580 0.933700 CACCCCAACCCAATCCCTAT 59.066 55.000 0.00 0.00 0.00 2.57
559 595 1.329256 CCTATCCCCACGTAGTCCAG 58.671 60.000 0.00 0.00 41.61 3.86
597 633 2.915659 TTCTCCAGTCGCACCGGT 60.916 61.111 0.00 0.00 0.00 5.28
701 737 2.062448 AACTCCCTCCCTCCCACCTT 62.062 60.000 0.00 0.00 0.00 3.50
707 743 2.935481 CCCTCCCACCTTGCTCCA 60.935 66.667 0.00 0.00 0.00 3.86
728 764 1.062364 ATCCCGATCCAGATGCACAT 58.938 50.000 0.00 0.00 0.00 3.21
746 782 2.012673 CATACAGACAGAGCTTTGGGC 58.987 52.381 9.34 0.34 42.19 5.36
768 804 4.426112 CTGCTCGGCTGCTCACGA 62.426 66.667 0.00 0.00 37.56 4.35
789 825 4.052229 CGGTCCTTGGACGACGCT 62.052 66.667 12.97 0.00 0.00 5.07
805 841 2.125952 CTGATGTGCGCGAGGTGA 60.126 61.111 12.10 0.00 0.00 4.02
810 846 2.202743 GTGCGCGAGGTGATGCTA 60.203 61.111 12.10 0.00 0.00 3.49
817 853 1.244816 CGAGGTGATGCTATACCGGA 58.755 55.000 9.46 0.00 41.85 5.14
895 931 0.460311 CTAAGGAGAATGCGGTCGGT 59.540 55.000 0.00 0.00 0.00 4.69
929 965 2.707849 GGCGCCGACCTCTTCTACA 61.708 63.158 12.58 0.00 0.00 2.74
1113 1153 2.444706 CCTGATCCGGCCTCTGGA 60.445 66.667 18.87 5.49 40.46 3.86
1120 1160 2.434843 CCGGCCTCTGGATGCAGTA 61.435 63.158 14.43 0.38 0.00 2.74
1180 1220 1.887956 GCAAATCAAGGACCTGGAGCA 60.888 52.381 4.51 0.00 0.00 4.26
1181 1221 2.731572 CAAATCAAGGACCTGGAGCAT 58.268 47.619 4.51 0.00 0.00 3.79
1186 1226 4.101448 GGACCTGGAGCATGCCGT 62.101 66.667 15.66 2.69 0.00 5.68
1245 1285 0.248661 CATCGACAGCTACCTCACCG 60.249 60.000 0.00 0.00 0.00 4.94
1258 1298 3.760035 CACCGGGTCCGTCTCTGG 61.760 72.222 6.32 0.00 37.81 3.86
1285 1325 2.415090 GCCAGTGCTGCTTCTTACATTG 60.415 50.000 0.00 0.00 33.53 2.82
1329 1416 1.035923 TACGTTGTACCCCGTCAACA 58.964 50.000 9.80 0.00 42.48 3.33
1347 1434 2.685380 CCCCGCTCAAGGAGACCT 60.685 66.667 0.00 0.00 33.87 3.85
1361 1448 1.377202 GACCTTCGCCAGCATCCAA 60.377 57.895 0.00 0.00 0.00 3.53
1369 1456 1.831286 CCAGCATCCAATCCCAGGC 60.831 63.158 0.00 0.00 0.00 4.85
1424 1511 3.209410 CTCTGCTTCTCTCTCTCTCTCC 58.791 54.545 0.00 0.00 0.00 3.71
1428 1515 2.749800 GCTTCTCTCTCTCTCTCCCTCC 60.750 59.091 0.00 0.00 0.00 4.30
1432 1521 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
1436 1525 2.015726 TCTCTCCCTCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
1469 1558 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1548 1640 4.693566 TGGAAGATTGGTAGCAACTTAACG 59.306 41.667 9.99 0.00 0.00 3.18
1549 1641 4.694037 GGAAGATTGGTAGCAACTTAACGT 59.306 41.667 9.99 0.00 0.00 3.99
1566 1658 7.046033 ACTTAACGTTACATTTGCTAGGCTAT 58.954 34.615 7.70 0.00 0.00 2.97
1580 1672 4.399934 GCTAGGCTATCTGGGTACTGTATC 59.600 50.000 0.00 0.00 0.00 2.24
1629 1721 1.597797 TTACATTCGGTCCTCGGCGT 61.598 55.000 6.85 0.00 39.77 5.68
1731 1823 6.758416 CAGCTAGTTACTGTGAAGCATTATCA 59.242 38.462 7.48 0.00 35.63 2.15
1759 1851 0.252103 TCTTCCCTGCTCTTACCGGT 60.252 55.000 13.98 13.98 0.00 5.28
1760 1852 0.108138 CTTCCCTGCTCTTACCGGTG 60.108 60.000 19.93 0.15 0.00 4.94
1773 1865 5.247862 TCTTACCGGTGTCCTTTTAATTCC 58.752 41.667 19.93 0.00 0.00 3.01
1775 1867 1.131693 CCGGTGTCCTTTTAATTCCGC 59.868 52.381 0.00 0.00 35.95 5.54
1780 1872 4.396790 GGTGTCCTTTTAATTCCGCATGTA 59.603 41.667 0.00 0.00 0.00 2.29
1781 1873 5.067283 GGTGTCCTTTTAATTCCGCATGTAT 59.933 40.000 0.00 0.00 0.00 2.29
1841 1933 0.099968 TACGAGTTCAAGATCGGCGG 59.900 55.000 7.21 0.00 43.12 6.13
1893 1985 4.384208 CCCTTGGACCAAGTTATCGAGATT 60.384 45.833 28.45 0.00 39.58 2.40
1944 2036 5.976458 GATGAAATCTAGCTAGCTGGCTAT 58.024 41.667 29.26 16.46 42.84 2.97
1962 2054 5.983540 GGCTATAGTATGCCTTATGCTCTT 58.016 41.667 13.35 0.00 45.26 2.85
1976 2068 8.193438 GCCTTATGCTCTTGTTGATTTATTTCT 58.807 33.333 0.00 0.00 36.87 2.52
2012 2104 7.776933 TTGCAGTTCTATATTGATGAGTGAC 57.223 36.000 0.00 0.00 0.00 3.67
2089 2181 3.128764 GGCTCAGTGGCATACCTTTTTAC 59.871 47.826 0.00 0.00 41.37 2.01
2223 2315 4.481930 TCGCTTCATTCAAATTTGACGT 57.518 36.364 20.35 9.63 36.83 4.34
2264 2356 5.796424 ATGTTTCCTTCTGCTTGATTTGT 57.204 34.783 0.00 0.00 0.00 2.83
2511 2604 2.038689 CTGAGCTAGCATGACCATGGAT 59.961 50.000 21.47 1.98 39.16 3.41
2655 2748 3.757947 TCCCTGAGTCCATCTCTTACA 57.242 47.619 0.00 0.00 43.13 2.41
2670 2764 9.599866 CCATCTCTTACAAGTTGTATGATTACA 57.400 33.333 24.13 13.44 36.72 2.41
2683 2777 6.851609 TGTATGATTACACCATTTTGCTGTC 58.148 36.000 0.00 0.00 33.37 3.51
2761 2855 9.372369 GGATGGTTTGATATATCTGTTAGCTAC 57.628 37.037 13.79 0.00 0.00 3.58
2836 2930 9.467796 AGGCTTATTTTAGCTCTTTTAGTTCAT 57.532 29.630 0.00 0.00 40.99 2.57
2905 2999 8.597144 CATCGGTTATGTATGTACGTGTATAG 57.403 38.462 0.00 0.00 0.00 1.31
2917 3011 7.854557 TGTACGTGTATAGAGTGTTATCTGT 57.145 36.000 0.00 0.00 0.00 3.41
2946 3040 5.476599 AGTTGTATATGTGGTGCAATTGTGT 59.523 36.000 7.40 0.00 0.00 3.72
2970 3064 3.087031 AGCTACTAGTCGTGCTTGGTAA 58.913 45.455 0.00 0.00 30.96 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 163 6.268387 AGACCATTTTCCATTTTCATCACTGT 59.732 34.615 0.00 0.00 0.00 3.55
224 231 5.413309 TTTGTTGTGAAGAACCAACCAAT 57.587 34.783 0.00 0.00 0.00 3.16
322 332 2.593775 CGCGGTAAATGCTTTGACAATG 59.406 45.455 0.00 0.00 0.00 2.82
356 366 0.963962 AGTATCCGACGGTGTTGTGT 59.036 50.000 14.79 0.00 0.00 3.72
357 367 1.625616 GAGTATCCGACGGTGTTGTG 58.374 55.000 14.79 0.00 0.00 3.33
390 425 2.936032 GTGAGGGGGTGAGGGCTT 60.936 66.667 0.00 0.00 0.00 4.35
423 458 1.600107 GGTGATTGGGCTACGTGGA 59.400 57.895 1.81 0.00 0.00 4.02
445 481 2.122547 AGAAGGGGTCGTGGGTGT 60.123 61.111 0.00 0.00 0.00 4.16
506 542 2.641815 GTGGGGGCAGATTGAGATCTAT 59.358 50.000 0.00 0.00 40.67 1.98
523 559 2.038813 GGATTGGGTTGGGGTGGG 59.961 66.667 0.00 0.00 0.00 4.61
544 580 2.682494 GGCTGGACTACGTGGGGA 60.682 66.667 3.26 0.00 0.00 4.81
597 633 1.596934 GCGATGAGGTTGGAGGTCA 59.403 57.895 0.00 0.00 0.00 4.02
701 737 1.688884 TGGATCGGGATGTGGAGCA 60.689 57.895 0.00 0.00 0.00 4.26
707 743 0.107456 GTGCATCTGGATCGGGATGT 59.893 55.000 20.20 0.00 40.76 3.06
728 764 0.037326 CGCCCAAAGCTCTGTCTGTA 60.037 55.000 0.00 0.00 40.39 2.74
768 804 2.915659 TCGTCCAAGGACCGTGCT 60.916 61.111 13.35 0.00 41.76 4.40
769 805 2.737376 GTCGTCCAAGGACCGTGC 60.737 66.667 13.35 0.00 41.76 5.34
778 814 2.027073 GCACATCAGCGTCGTCCAA 61.027 57.895 0.00 0.00 0.00 3.53
789 825 1.810853 CATCACCTCGCGCACATCA 60.811 57.895 8.75 0.00 0.00 3.07
805 841 2.580601 GCCCGGTCCGGTATAGCAT 61.581 63.158 28.39 0.00 46.80 3.79
874 910 0.460311 CGACCGCATTCTCCTTAGGT 59.540 55.000 0.00 0.00 34.27 3.08
878 914 1.079127 CACCGACCGCATTCTCCTT 60.079 57.895 0.00 0.00 0.00 3.36
1113 1153 4.758688 TCGATGAAGATGTTGTACTGCAT 58.241 39.130 0.00 0.00 35.37 3.96
1120 1160 1.278985 TGCCCTCGATGAAGATGTTGT 59.721 47.619 0.00 0.00 0.00 3.32
1180 1220 3.537874 GCTCGACCCCTACGGCAT 61.538 66.667 0.00 0.00 33.26 4.40
1227 1267 1.384989 CCGGTGAGGTAGCTGTCGAT 61.385 60.000 0.00 0.00 34.51 3.59
1285 1325 1.593750 CGCTGGTAGGCAGATGAGC 60.594 63.158 0.00 0.00 0.00 4.26
1314 1359 1.451072 GGGTGTTGACGGGGTACAA 59.549 57.895 0.00 0.00 0.00 2.41
1329 1416 3.003763 GGTCTCCTTGAGCGGGGT 61.004 66.667 0.00 0.00 33.25 4.95
1347 1434 1.453745 GGGATTGGATGCTGGCGAA 60.454 57.895 0.00 0.00 0.00 4.70
1361 1448 3.099170 ATCTTGGCGGCCTGGGAT 61.099 61.111 21.46 16.49 0.00 3.85
1369 1456 0.598680 GTCATCCTCGATCTTGGCGG 60.599 60.000 0.00 0.00 0.00 6.13
1424 1511 2.018086 AGAGAGGGAGGGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
1428 1515 0.478507 GAGAGAGAGAGGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
1432 1521 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
1436 1525 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1469 1558 5.237344 CAGTGTGGAAAGAAACTGGAGTAAG 59.763 44.000 0.00 0.00 37.08 2.34
1548 1640 4.757149 CCCAGATAGCCTAGCAAATGTAAC 59.243 45.833 0.00 0.00 0.00 2.50
1549 1641 4.412199 ACCCAGATAGCCTAGCAAATGTAA 59.588 41.667 0.00 0.00 0.00 2.41
1566 1658 4.023980 CTGTCCAAGATACAGTACCCAGA 58.976 47.826 0.00 0.00 39.61 3.86
1629 1721 7.615365 AGCTACATCCAAAATCTACCAATTCAA 59.385 33.333 0.00 0.00 0.00 2.69
1731 1823 3.837355 AGAGCAGGGAAGAACAACATTT 58.163 40.909 0.00 0.00 0.00 2.32
1759 1851 6.767524 AATACATGCGGAATTAAAAGGACA 57.232 33.333 0.00 0.00 0.00 4.02
1760 1852 8.379902 CAAAAATACATGCGGAATTAAAAGGAC 58.620 33.333 0.00 0.00 0.00 3.85
1773 1865 7.754924 ACTCCTTCAATTACAAAAATACATGCG 59.245 33.333 0.00 0.00 0.00 4.73
1789 1881 5.534207 TGCACAAAATGAACTCCTTCAAT 57.466 34.783 0.00 0.00 39.90 2.57
1805 1897 2.512355 TACACCTCCGGCTGCACAA 61.512 57.895 0.50 0.00 0.00 3.33
1820 1912 1.466866 CGCCGATCTTGAACTCGTACA 60.467 52.381 0.00 0.00 33.11 2.90
1827 1919 2.435938 TGGCCGCCGATCTTGAAC 60.436 61.111 4.58 0.00 0.00 3.18
1864 1956 1.074951 CTTGGTCCAAGGGTGGGTC 59.925 63.158 22.23 0.00 46.01 4.46
1873 1965 5.677319 AGAATCTCGATAACTTGGTCCAA 57.323 39.130 3.76 3.76 0.00 3.53
1893 1985 5.717178 AGACTTATCCTTGTGCTTCTGTAGA 59.283 40.000 0.00 0.00 0.00 2.59
1962 2054 6.446318 AGAGCGCAAAAGAAATAAATCAACA 58.554 32.000 11.47 0.00 0.00 3.33
1976 2068 2.159254 AGAACTGCAAAAGAGCGCAAAA 60.159 40.909 11.47 0.00 37.76 2.44
2223 2315 5.212532 ACATTTCAAAAATACCAGCTGCA 57.787 34.783 8.66 0.00 0.00 4.41
2264 2356 0.107703 CAAAGATACCAGCTGGGCGA 60.108 55.000 35.42 20.92 42.05 5.54
2338 2431 3.651423 AGCTCCAAAGTTAAGGTACTGGT 59.349 43.478 0.00 0.00 40.86 4.00
2511 2604 3.763356 ATGCTGACGAGAGCCGCA 61.763 61.111 7.76 0.00 43.32 5.69
2565 2658 1.317613 TGTTGCCAAGCAGAACGATT 58.682 45.000 0.00 0.00 40.61 3.34
2584 2677 0.602905 GGGTGCAGACGCTTGTACTT 60.603 55.000 7.65 0.00 39.64 2.24
2670 2764 3.091545 CCCAGTATGACAGCAAAATGGT 58.908 45.455 0.00 0.00 39.69 3.55
2683 2777 3.257873 CAGAGGAGCATCTACCCAGTATG 59.742 52.174 0.00 0.00 33.73 2.39
2882 2976 7.657354 ACTCTATACACGTACATACATAACCGA 59.343 37.037 0.00 0.00 0.00 4.69
2901 2995 9.848710 ACAACTAGCTACAGATAACACTCTATA 57.151 33.333 0.00 0.00 0.00 1.31
2917 3011 5.862678 TGCACCACATATACAACTAGCTA 57.137 39.130 0.00 0.00 0.00 3.32
2946 3040 2.943690 CCAAGCACGACTAGTAGCTCTA 59.056 50.000 14.94 0.00 36.62 2.43
3013 3107 7.582435 ATTATTGCGTTCATCGATTAGTAGG 57.418 36.000 0.00 0.00 42.86 3.18


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

AutoCloner maintained by Alex Coulton.