Multiple sequence alignment - TraesCS5A01G442700

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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 TraesCS5A01G442700 chr5A 100.000 4570 0 0 1 4570 623001485 622996916 0.000000e+00 8440.0
1 TraesCS5A01G442700 chr5A 89.655 1015 86 15 2823 3826 623014472 623013466 0.000000e+00 1275.0
2 TraesCS5A01G442700 chr5A 89.599 548 37 9 1533 2065 623015786 623015244 0.000000e+00 678.0
3 TraesCS5A01G442700 chr5A 89.362 517 37 8 1533 2036 622423197 622422686 6.450000e-178 634.0
4 TraesCS5A01G442700 chr5A 89.362 517 37 8 1533 2036 622429553 622429042 6.450000e-178 634.0
5 TraesCS5A01G442700 chr5A 84.578 415 40 9 788 1199 622430345 622429952 1.540000e-104 390.0
6 TraesCS5A01G442700 chr5A 89.844 128 13 0 2694 2821 623014726 623014599 1.020000e-36 165.0
7 TraesCS5A01G442700 chr5D 89.194 1712 129 33 2132 3821 498673752 498672075 0.000000e+00 2085.0
8 TraesCS5A01G442700 chr5D 87.927 1317 104 31 2532 3820 498715487 498714198 0.000000e+00 1500.0
9 TraesCS5A01G442700 chr5D 94.977 438 20 2 1533 1969 498674220 498673784 0.000000e+00 686.0
10 TraesCS5A01G442700 chr5D 93.135 437 27 2 661 1096 498675061 498674627 4.990000e-179 638.0
11 TraesCS5A01G442700 chr5D 88.454 511 52 3 2725 3232 498630000 498629494 1.090000e-170 610.0
12 TraesCS5A01G442700 chr5D 90.732 410 29 6 1533 1937 498718024 498717619 5.200000e-149 538.0
13 TraesCS5A01G442700 chr5D 94.362 337 16 2 1201 1534 498674591 498674255 8.770000e-142 514.0
14 TraesCS5A01G442700 chr5D 85.442 419 55 6 2817 3232 498655025 498654610 9.080000e-117 431.0
15 TraesCS5A01G442700 chr5D 86.589 343 40 4 1200 1539 498656822 498656483 1.550000e-99 374.0
16 TraesCS5A01G442700 chr5D 79.381 582 74 33 3264 3821 498654612 498654053 7.220000e-98 368.0
17 TraesCS5A01G442700 chr5D 80.174 459 67 18 3365 3811 498629451 498629005 5.700000e-84 322.0
18 TraesCS5A01G442700 chr5D 94.444 90 4 1 2063 2151 526559565 526559654 2.220000e-28 137.0
19 TraesCS5A01G442700 chr5B 86.015 1330 114 35 2532 3826 618273446 618272154 0.000000e+00 1360.0
20 TraesCS5A01G442700 chr5B 81.689 1125 135 35 2706 3771 618197319 618196207 0.000000e+00 870.0
21 TraesCS5A01G442700 chr5B 89.162 692 47 11 2566 3241 618254976 618254297 0.000000e+00 837.0
22 TraesCS5A01G442700 chr5B 94.934 533 27 0 1533 2065 618256191 618255659 0.000000e+00 835.0
23 TraesCS5A01G442700 chr5B 89.641 502 45 6 1533 2029 618198239 618197740 2.320000e-177 632.0
24 TraesCS5A01G442700 chr5B 88.258 511 55 3 2725 3232 618127920 618127412 1.410000e-169 606.0
25 TraesCS5A01G442700 chr5B 88.844 493 40 11 1586 2065 618134574 618134084 3.940000e-165 592.0
26 TraesCS5A01G442700 chr5B 83.359 637 69 16 805 1421 618262416 618261797 5.170000e-154 555.0
27 TraesCS5A01G442700 chr5B 85.947 491 54 8 1533 2014 618159947 618159463 1.130000e-140 510.0
28 TraesCS5A01G442700 chr5B 88.265 392 38 6 2145 2535 618255661 618255277 3.220000e-126 462.0
29 TraesCS5A01G442700 chr5B 81.395 516 59 21 3314 3821 618254257 618253771 1.990000e-103 387.0
30 TraesCS5A01G442700 chr5B 81.638 354 48 13 3300 3646 618158168 618157825 1.250000e-70 278.0
31 TraesCS5A01G442700 chr5B 80.655 336 41 13 1209 1539 618160284 618159968 5.910000e-59 239.0
32 TraesCS5A01G442700 chr5B 100.000 29 0 0 2532 2560 618255254 618255226 2.000000e-03 54.7
33 TraesCS5A01G442700 chr2A 97.312 744 16 3 3827 4570 118218418 118219157 0.000000e+00 1260.0
34 TraesCS5A01G442700 chr2A 94.792 96 3 2 2060 2154 632952996 632952902 1.020000e-31 148.0
35 TraesCS5A01G442700 chr2A 91.262 103 5 4 681 782 772996487 772996388 2.220000e-28 137.0
36 TraesCS5A01G442700 chr2A 87.931 116 10 4 2063 2176 202889824 202889711 2.870000e-27 134.0
37 TraesCS5A01G442700 chr3B 94.758 744 34 4 3828 4570 174198183 174198922 0.000000e+00 1153.0
38 TraesCS5A01G442700 chr3B 92.934 651 36 5 1 645 364021583 364020937 0.000000e+00 939.0
39 TraesCS5A01G442700 chr3B 93.548 93 6 0 2054 2146 55740967 55741059 6.170000e-29 139.0
40 TraesCS5A01G442700 chr3B 88.350 103 8 4 681 782 25481807 25481708 2.230000e-23 121.0
41 TraesCS5A01G442700 chr6B 92.463 743 34 11 3828 4570 144916915 144917635 0.000000e+00 1042.0
42 TraesCS5A01G442700 chr6B 96.591 88 2 1 2061 2147 13827524 13827611 1.330000e-30 145.0
43 TraesCS5A01G442700 chr6B 91.089 101 6 3 2062 2159 179236341 179236241 2.870000e-27 134.0
44 TraesCS5A01G442700 chr6B 88.350 103 8 4 681 782 62647770 62647671 2.230000e-23 121.0
45 TraesCS5A01G442700 chr6A 92.523 642 47 1 1 642 108067341 108067981 0.000000e+00 918.0
46 TraesCS5A01G442700 chr6A 92.982 171 12 0 443 613 108018129 108018299 2.730000e-62 250.0
47 TraesCS5A01G442700 chr6A 95.556 90 4 0 300 389 108018050 108018139 1.330000e-30 145.0
48 TraesCS5A01G442700 chr1B 92.438 648 42 4 1 642 649616865 649617511 0.000000e+00 918.0
49 TraesCS5A01G442700 chr1B 89.423 104 7 4 680 782 7509919 7509819 1.330000e-25 128.0
50 TraesCS5A01G442700 chr1B 88.462 104 8 4 680 782 6254713 6254613 6.210000e-24 122.0
51 TraesCS5A01G442700 chr4B 88.525 671 45 6 1 642 217925744 217926411 0.000000e+00 784.0
52 TraesCS5A01G442700 chr7B 93.768 353 18 3 3818 4169 417892906 417893255 1.130000e-145 527.0
53 TraesCS5A01G442700 chr7B 93.500 200 11 2 4371 4570 417893251 417893448 3.460000e-76 296.0
54 TraesCS5A01G442700 chr7B 92.708 96 6 1 2061 2155 348195895 348195800 2.220000e-28 137.0
55 TraesCS5A01G442700 chr3A 77.519 516 93 15 4065 4568 738080627 738081131 5.780000e-74 289.0
56 TraesCS5A01G442700 chr2B 77.755 481 89 15 4071 4543 373476004 373475534 3.480000e-71 279.0
57 TraesCS5A01G442700 chr2B 87.919 149 18 0 3828 3976 53441469 53441321 4.700000e-40 176.0
58 TraesCS5A01G442700 chr2B 89.423 104 7 4 681 782 32131515 32131616 1.330000e-25 128.0
59 TraesCS5A01G442700 chr2D 87.821 156 19 0 3818 3973 478112205 478112360 2.810000e-42 183.0
60 TraesCS5A01G442700 chr7A 89.041 146 16 0 3828 3973 80200301 80200156 1.010000e-41 182.0
61 TraesCS5A01G442700 chr1A 89.041 146 16 0 3828 3973 536654765 536654910 1.010000e-41 182.0
62 TraesCS5A01G442700 chr1A 95.402 87 3 1 2062 2147 527083930 527084016 2.220000e-28 137.0
63 TraesCS5A01G442700 chr6D 88.356 146 17 0 3828 3973 467820826 467820681 4.700000e-40 176.0
64 TraesCS5A01G442700 chr4D 91.000 100 7 2 2063 2161 379147278 379147180 2.870000e-27 134.0
65 TraesCS5A01G442700 chr3D 90.291 103 6 4 681 782 15102981 15103080 1.030000e-26 132.0
66 TraesCS5A01G442700 chr3D 89.423 104 6 5 681 782 373997772 373997872 4.800000e-25 126.0


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 TraesCS5A01G442700 chr5A 622996916 623001485 4569 True 8440.000000 8440 100.000000 1 4570 1 chr5A.!!$R2 4569
1 TraesCS5A01G442700 chr5A 623013466 623015786 2320 True 706.000000 1275 89.699333 1533 3826 3 chr5A.!!$R4 2293
2 TraesCS5A01G442700 chr5A 622422686 622423197 511 True 634.000000 634 89.362000 1533 2036 1 chr5A.!!$R1 503
3 TraesCS5A01G442700 chr5A 622429042 622430345 1303 True 512.000000 634 86.970000 788 2036 2 chr5A.!!$R3 1248
4 TraesCS5A01G442700 chr5D 498714198 498718024 3826 True 1019.000000 1500 89.329500 1533 3820 2 chr5D.!!$R4 2287
5 TraesCS5A01G442700 chr5D 498672075 498675061 2986 True 980.750000 2085 92.917000 661 3821 4 chr5D.!!$R3 3160
6 TraesCS5A01G442700 chr5D 498629005 498630000 995 True 466.000000 610 84.314000 2725 3811 2 chr5D.!!$R1 1086
7 TraesCS5A01G442700 chr5D 498654053 498656822 2769 True 391.000000 431 83.804000 1200 3821 3 chr5D.!!$R2 2621
8 TraesCS5A01G442700 chr5B 618272154 618273446 1292 True 1360.000000 1360 86.015000 2532 3826 1 chr5B.!!$R4 1294
9 TraesCS5A01G442700 chr5B 618196207 618198239 2032 True 751.000000 870 85.665000 1533 3771 2 chr5B.!!$R6 2238
10 TraesCS5A01G442700 chr5B 618127412 618127920 508 True 606.000000 606 88.258000 2725 3232 1 chr5B.!!$R1 507
11 TraesCS5A01G442700 chr5B 618261797 618262416 619 True 555.000000 555 83.359000 805 1421 1 chr5B.!!$R3 616
12 TraesCS5A01G442700 chr5B 618253771 618256191 2420 True 515.140000 837 90.751200 1533 3821 5 chr5B.!!$R7 2288
13 TraesCS5A01G442700 chr5B 618157825 618160284 2459 True 342.333333 510 82.746667 1209 3646 3 chr5B.!!$R5 2437
14 TraesCS5A01G442700 chr2A 118218418 118219157 739 False 1260.000000 1260 97.312000 3827 4570 1 chr2A.!!$F1 743
15 TraesCS5A01G442700 chr3B 174198183 174198922 739 False 1153.000000 1153 94.758000 3828 4570 1 chr3B.!!$F2 742
16 TraesCS5A01G442700 chr3B 364020937 364021583 646 True 939.000000 939 92.934000 1 645 1 chr3B.!!$R2 644
17 TraesCS5A01G442700 chr6B 144916915 144917635 720 False 1042.000000 1042 92.463000 3828 4570 1 chr6B.!!$F2 742
18 TraesCS5A01G442700 chr6A 108067341 108067981 640 False 918.000000 918 92.523000 1 642 1 chr6A.!!$F1 641
19 TraesCS5A01G442700 chr1B 649616865 649617511 646 False 918.000000 918 92.438000 1 642 1 chr1B.!!$F1 641
20 TraesCS5A01G442700 chr4B 217925744 217926411 667 False 784.000000 784 88.525000 1 642 1 chr4B.!!$F1 641
21 TraesCS5A01G442700 chr7B 417892906 417893448 542 False 411.500000 527 93.634000 3818 4570 2 chr7B.!!$F1 752
22 TraesCS5A01G442700 chr3A 738080627 738081131 504 False 289.000000 289 77.519000 4065 4568 1 chr3A.!!$F1 503

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
468 486 1.453155 ATTTCATGCGGGAGTGACAC 58.547 50.000 0.00 0.0 0.00 3.67 F
1144 1180 0.321671 GGCAGCAGTGGTGTAGAGAA 59.678 55.000 22.50 0.0 33.19 2.87 F
1772 1905 1.072806 TCCTTCTGTGCTCACTTGCAT 59.927 47.619 1.47 0.0 45.23 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1802 0.248296 GTTCGGCAGCGTTGAAACAA 60.248 50.000 2.38 0.0 0.0 2.83 R
2734 4983 1.464608 CCGTACACATGAAACCAGCAG 59.535 52.381 0.00 0.0 0.0 4.24 R
3676 6326 0.033642 TACAAACGATGGGTGCGACA 59.966 50.000 0.00 0.0 0.0 4.35 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
393 411 3.913548 TGCGCAGTACAAATTTGTCAT 57.086 38.095 26.46 13.90 42.35 3.06
459 477 2.514902 CGTGGTACAAATTTCATGCGG 58.485 47.619 0.00 0.00 44.16 5.69
468 486 1.453155 ATTTCATGCGGGAGTGACAC 58.547 50.000 0.00 0.00 0.00 3.67
510 528 3.313249 CACAGCGAATCCTTGCAATATGA 59.687 43.478 0.00 0.00 0.00 2.15
543 561 8.208224 AGATTAACATATCCAACGGTGTCAATA 58.792 33.333 0.00 0.00 0.00 1.90
589 621 5.102953 AGCCACTAAATATGAGCTGTTCA 57.897 39.130 0.00 0.00 40.85 3.18
642 674 7.524290 AGTGCTACTGGTACACTATATAGGAA 58.476 38.462 14.25 0.00 42.65 3.36
645 677 9.682465 TGCTACTGGTACACTATATAGGAATAG 57.318 37.037 14.25 6.98 35.86 1.73
646 678 9.122779 GCTACTGGTACACTATATAGGAATAGG 57.877 40.741 14.25 1.98 34.34 2.57
649 681 8.902881 ACTGGTACACTATATAGGAATAGGAGT 58.097 37.037 14.25 5.05 34.34 3.85
732 764 6.190954 TGATATATCGAGGTGATACAACCG 57.809 41.667 8.19 0.00 45.53 4.44
749 781 3.869272 GCACTGAGCGAATGCCCG 61.869 66.667 0.00 0.00 44.31 6.13
757 789 4.161295 CGAATGCCCGGCCTCTGA 62.161 66.667 7.03 0.00 0.00 3.27
765 797 3.190849 CGGCCTCTGATGTGCACG 61.191 66.667 13.13 0.00 0.00 5.34
799 831 5.353956 GCCAACACAACCAAAAAGAAGAAAT 59.646 36.000 0.00 0.00 0.00 2.17
800 832 6.456853 GCCAACACAACCAAAAAGAAGAAATC 60.457 38.462 0.00 0.00 0.00 2.17
801 833 6.037062 CCAACACAACCAAAAAGAAGAAATCC 59.963 38.462 0.00 0.00 0.00 3.01
802 834 5.348164 ACACAACCAAAAAGAAGAAATCCG 58.652 37.500 0.00 0.00 0.00 4.18
940 975 1.839747 ACCAACGTCCCAGTGCCTA 60.840 57.895 0.00 0.00 0.00 3.93
948 983 2.546795 CGTCCCAGTGCCTAGATGATTC 60.547 54.545 0.00 0.00 0.00 2.52
949 984 2.703007 GTCCCAGTGCCTAGATGATTCT 59.297 50.000 0.00 0.00 35.90 2.40
956 991 3.106827 TGCCTAGATGATTCTGTGTGGA 58.893 45.455 0.00 0.00 33.17 4.02
960 995 5.678583 CCTAGATGATTCTGTGTGGAACAT 58.321 41.667 0.00 0.00 40.63 2.71
964 999 7.047891 TAGATGATTCTGTGTGGAACATTACC 58.952 38.462 0.00 0.00 40.63 2.85
1041 1077 2.359975 GCCCCACCTGAACTTCGG 60.360 66.667 0.00 0.00 0.00 4.30
1124 1160 1.733912 CATAGCTGCGCTCTGACAAAA 59.266 47.619 9.73 0.00 40.44 2.44
1128 1164 1.509644 CTGCGCTCTGACAAAAGGCA 61.510 55.000 9.73 0.00 0.00 4.75
1144 1180 0.321671 GGCAGCAGTGGTGTAGAGAA 59.678 55.000 22.50 0.00 33.19 2.87
1152 1188 2.111972 AGTGGTGTAGAGAAGGAGGGAA 59.888 50.000 0.00 0.00 0.00 3.97
1182 1218 9.640963 GACAAAGAGATGTGTGTTTATAGTAGT 57.359 33.333 0.00 0.00 32.57 2.73
1265 1342 5.643379 AAAAATCGCCAGCTTCTTCATAA 57.357 34.783 0.00 0.00 0.00 1.90
1313 1392 6.920210 GCTACTTCTGCAAAGATTTCTTTTGT 59.080 34.615 13.35 0.42 43.07 2.83
1314 1393 7.096312 GCTACTTCTGCAAAGATTTCTTTTGTG 60.096 37.037 13.35 0.00 43.07 3.33
1355 1434 4.378774 GTGTCTGGATCATCTTCATCCTG 58.621 47.826 0.00 0.48 40.66 3.86
1405 1494 5.700832 ACAACATATGAACTGAAGCTTTCGA 59.299 36.000 10.38 0.00 0.00 3.71
1516 1605 4.973168 TGCATAGTGGTTCTCTTGAAGTT 58.027 39.130 0.00 0.00 32.15 2.66
1669 1802 9.807921 TGAAATGTTATTCCCTTTAACTTCTCT 57.192 29.630 0.00 0.00 32.09 3.10
1772 1905 1.072806 TCCTTCTGTGCTCACTTGCAT 59.927 47.619 1.47 0.00 45.23 3.96
1815 1950 3.071023 CACCCTGTAGTCTGTTCTTTGGA 59.929 47.826 0.00 0.00 0.00 3.53
1954 3518 4.489306 AACTCCTAGTCTTTGGGTATGC 57.511 45.455 0.00 0.00 0.00 3.14
2090 3673 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
2108 3691 7.393841 AAGAGCGTTTAGATCAGTACTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2109 3692 6.787225 AGAGCGTTTAGATCAGTACTTAGTG 58.213 40.000 0.00 0.00 37.82 2.74
2110 3693 6.598457 AGAGCGTTTAGATCAGTACTTAGTGA 59.402 38.462 0.00 0.00 37.82 3.41
2111 3694 7.283580 AGAGCGTTTAGATCAGTACTTAGTGAT 59.716 37.037 6.32 6.32 46.17 3.06
2122 3705 8.865420 TCAGTACTTAGTGATCTAAACACTCT 57.135 34.615 0.00 0.00 45.58 3.24
2123 3706 9.298250 TCAGTACTTAGTGATCTAAACACTCTT 57.702 33.333 0.00 0.00 45.58 2.85
2246 4117 9.570488 GACATTATTTAGGTGATATAGGACGAC 57.430 37.037 0.00 0.00 0.00 4.34
2273 4146 6.797995 CCTACAAATTTGTGCATTTTTCATGC 59.202 34.615 29.72 0.00 42.31 4.06
2297 4171 8.127327 TGCTTTACATTACTAGCTAGTTCTACG 58.873 37.037 30.40 16.74 37.73 3.51
2313 4187 7.647907 AGTTCTACGTATTTGTTGTAACCAG 57.352 36.000 0.00 0.00 0.00 4.00
2316 4193 7.642071 TCTACGTATTTGTTGTAACCAGTTC 57.358 36.000 0.00 0.00 0.00 3.01
2388 4265 2.645838 AACAGAAAGCTTCAGAGGCA 57.354 45.000 7.36 0.00 0.00 4.75
2445 4322 8.818622 AGATGTATACTGGTGTAAGTCACTAA 57.181 34.615 4.17 0.00 45.50 2.24
2453 4330 3.532542 GTGTAAGTCACTAAGGCCCATC 58.467 50.000 0.00 0.00 43.13 3.51
2473 4350 3.955471 TCTTTATTGCCTGAAGGAGTGG 58.045 45.455 0.00 0.00 37.39 4.00
2734 4983 7.502120 AATGTATCTGCTTGTCCAATACATC 57.498 36.000 6.74 0.00 40.72 3.06
2908 5298 2.477825 CCTAGTCCAGATGATTGTGCG 58.522 52.381 0.00 0.00 0.00 5.34
2909 5299 2.477825 CTAGTCCAGATGATTGTGCGG 58.522 52.381 0.00 0.00 0.00 5.69
3034 5424 0.249238 CTTGCTATCGAGAAGGCGCT 60.249 55.000 7.64 0.00 0.00 5.92
3121 5517 9.828039 GATCATATGACTAATCATCTTATGGCA 57.172 33.333 7.78 0.00 42.15 4.92
3248 5648 1.344065 TTCGTGGTGTGTAGGGTGAT 58.656 50.000 0.00 0.00 0.00 3.06
3311 5893 7.959689 ATGATATCTTGATAGACAACTGTGC 57.040 36.000 3.98 0.00 34.56 4.57
3325 5909 1.721664 CTGTGCGCATGGAAGATGGG 61.722 60.000 15.91 0.00 35.41 4.00
3342 5928 3.988976 TGGGTCTCCATCTCTTTTGAG 57.011 47.619 0.00 0.00 42.09 3.02
3374 5987 6.950842 ACATGGATTCAGTCATTCAAGTCTA 58.049 36.000 0.00 0.00 0.00 2.59
3433 6057 2.404215 TCGCAGAAAGAACACTAGTGC 58.596 47.619 22.90 7.58 0.00 4.40
3440 6064 5.931146 CAGAAAGAACACTAGTGCTGATCTT 59.069 40.000 22.90 20.95 32.48 2.40
3443 6067 3.999663 AGAACACTAGTGCTGATCTTTGC 59.000 43.478 22.90 0.00 30.26 3.68
3446 6071 4.330250 ACACTAGTGCTGATCTTTGCATT 58.670 39.130 22.90 9.46 41.45 3.56
3460 6089 8.135529 TGATCTTTGCATTTCATGATTCATCTC 58.864 33.333 0.00 0.00 0.00 2.75
3464 6093 5.198207 TGCATTTCATGATTCATCTCCAGT 58.802 37.500 0.00 0.00 0.00 4.00
3484 6117 4.512944 CAGTGCAAGTTGTACACAGATTCT 59.487 41.667 23.54 0.16 35.34 2.40
3571 6204 1.295792 GCCGTGAAAAGTGACTGACA 58.704 50.000 0.00 0.00 0.00 3.58
3676 6326 6.742559 TTACCTGTGGTTCTTAAGACTTCT 57.257 37.500 4.18 0.00 37.09 2.85
3758 6425 6.974622 CAGTTCAAGTGTCAACAAGCTTTATT 59.025 34.615 0.00 0.00 0.00 1.40
3762 6429 7.518161 TCAAGTGTCAACAAGCTTTATTATCG 58.482 34.615 0.00 0.00 0.00 2.92
3771 6438 5.191059 CAAGCTTTATTATCGCAGAACGTC 58.809 41.667 0.00 0.00 43.58 4.34
3785 6452 5.231357 CGCAGAACGTCAAGCTTGTTATATA 59.769 40.000 25.19 2.57 36.87 0.86
3786 6453 6.074302 CGCAGAACGTCAAGCTTGTTATATAT 60.074 38.462 25.19 7.33 36.87 0.86
3789 6458 9.988350 CAGAACGTCAAGCTTGTTATATATTTT 57.012 29.630 25.19 7.48 0.00 1.82
3975 6646 3.307975 GCAGACATATCCATGGCCTACAT 60.308 47.826 6.96 0.00 41.63 2.29
3976 6647 4.808665 GCAGACATATCCATGGCCTACATT 60.809 45.833 6.96 0.00 41.63 2.71
3979 6650 6.006449 AGACATATCCATGGCCTACATTTTC 58.994 40.000 6.96 0.00 41.63 2.29
4047 6718 2.435059 GGCCGCTCTCACAAGGTC 60.435 66.667 0.00 0.00 0.00 3.85
4176 6847 2.241176 ACAACCACCATACCGGATGATT 59.759 45.455 9.46 0.00 37.82 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.667360 TCTTTCCGTTACCCAGTTTAGC 58.333 45.455 0.00 0.00 0.00 3.09
62 63 4.989168 ACTTGCAACTTAGTACTCTTTCCG 59.011 41.667 0.00 0.00 0.00 4.30
162 163 5.067674 TGGACAACTCTGATCAACCAAAAAG 59.932 40.000 0.00 0.00 0.00 2.27
249 260 8.265165 ACGGTTGAATAGATTTTACTTTCTCC 57.735 34.615 0.00 0.00 0.00 3.71
393 411 4.453480 AGAAATTTCTGGTGAACTCCCA 57.547 40.909 19.86 0.00 35.89 4.37
459 477 2.740055 CCTGCTGCGTGTCACTCC 60.740 66.667 0.65 0.00 0.00 3.85
510 528 5.702670 CGTTGGATATGTTAATCTGATGGCT 59.297 40.000 0.00 0.00 0.00 4.75
589 621 9.046296 CGTATAAGCTGTTGGATCTTTCTAATT 57.954 33.333 0.00 0.00 0.00 1.40
707 739 7.258441 CGGTTGTATCACCTCGATATATCAAT 58.742 38.462 13.11 0.00 38.85 2.57
709 741 5.392703 GCGGTTGTATCACCTCGATATATCA 60.393 44.000 13.11 0.00 38.85 2.15
732 764 3.869272 CGGGCATTCGCTCAGTGC 61.869 66.667 0.00 0.00 39.27 4.40
749 781 1.153289 ATCGTGCACATCAGAGGCC 60.153 57.895 18.64 0.00 0.00 5.19
765 797 0.385029 TTGTGTTGGCTGTGTGCATC 59.615 50.000 0.00 0.00 45.15 3.91
940 975 5.882557 GGTAATGTTCCACACAGAATCATCT 59.117 40.000 0.00 0.00 39.40 2.90
948 983 5.643664 CATTGATGGTAATGTTCCACACAG 58.356 41.667 0.00 0.00 39.40 3.66
949 984 4.082300 GCATTGATGGTAATGTTCCACACA 60.082 41.667 0.00 0.00 39.62 3.72
956 991 5.220912 CGTCTGATGCATTGATGGTAATGTT 60.221 40.000 0.00 0.00 39.62 2.71
960 995 2.613595 GCGTCTGATGCATTGATGGTAA 59.386 45.455 16.63 0.00 0.00 2.85
964 999 3.805971 TCTAAGCGTCTGATGCATTGATG 59.194 43.478 22.70 9.35 31.07 3.07
1110 1146 1.509644 CTGCCTTTTGTCAGAGCGCA 61.510 55.000 11.47 0.00 32.26 6.09
1124 1160 0.542938 TCTCTACACCACTGCTGCCT 60.543 55.000 0.00 0.00 0.00 4.75
1128 1164 2.175202 CTCCTTCTCTACACCACTGCT 58.825 52.381 0.00 0.00 0.00 4.24
1144 1180 2.112691 TCTCTTTGTCTCCTTCCCTCCT 59.887 50.000 0.00 0.00 0.00 3.69
1152 1188 4.696479 AACACACATCTCTTTGTCTCCT 57.304 40.909 0.00 0.00 0.00 3.69
1182 1218 7.568199 TGACATACTTTCGACATCATCTCTA 57.432 36.000 0.00 0.00 0.00 2.43
1265 1342 6.041979 AGCATTTTATGTTTCTTTGACCAGGT 59.958 34.615 0.00 0.00 0.00 4.00
1313 1392 4.776837 ACACCAAAATATGAATGGAAGGCA 59.223 37.500 8.29 0.00 37.66 4.75
1314 1393 5.127682 AGACACCAAAATATGAATGGAAGGC 59.872 40.000 8.29 3.74 37.66 4.35
1428 1517 8.068892 ACAAAATTTGTAAGACAAGGGTTACA 57.931 30.769 9.92 0.00 43.27 2.41
1516 1605 4.898829 CATTAACGAAATGGCTGGATGA 57.101 40.909 0.00 0.00 41.19 2.92
1669 1802 0.248296 GTTCGGCAGCGTTGAAACAA 60.248 50.000 2.38 0.00 0.00 2.83
1671 1804 0.657368 CAGTTCGGCAGCGTTGAAAC 60.657 55.000 2.38 4.09 0.00 2.78
1815 1950 8.540507 TCTACTCTAAATGATAGGCAGAACTT 57.459 34.615 0.00 0.00 0.00 2.66
1954 3518 4.213270 CACATTAATAGTACACCATGCGGG 59.787 45.833 0.00 0.00 44.81 6.13
1996 3568 2.694628 GGCAGGCACAATATCATCCAAA 59.305 45.455 0.00 0.00 0.00 3.28
2063 3646 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
2064 3647 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
2065 3648 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
2115 3698 9.853177 CCCTCCATAAAGAAATATAAGAGTGTT 57.147 33.333 0.00 0.00 0.00 3.32
2116 3699 9.225682 TCCCTCCATAAAGAAATATAAGAGTGT 57.774 33.333 0.00 0.00 0.00 3.55
2117 3700 9.717942 CTCCCTCCATAAAGAAATATAAGAGTG 57.282 37.037 0.00 0.00 0.00 3.51
2118 3701 9.453830 ACTCCCTCCATAAAGAAATATAAGAGT 57.546 33.333 0.00 0.00 0.00 3.24
2130 3713 9.726438 CCTAATTAATGTACTCCCTCCATAAAG 57.274 37.037 0.00 0.00 0.00 1.85
2131 3714 9.455144 TCCTAATTAATGTACTCCCTCCATAAA 57.545 33.333 0.00 0.00 0.00 1.40
2135 3718 8.014263 TGTATCCTAATTAATGTACTCCCTCCA 58.986 37.037 0.00 0.00 0.00 3.86
2220 4091 9.570488 GTCGTCCTATATCACCTAAATAATGTC 57.430 37.037 0.00 0.00 0.00 3.06
2227 4098 5.779529 GGTGTCGTCCTATATCACCTAAA 57.220 43.478 0.00 0.00 43.34 1.85
2242 4113 2.946329 TGCACAAATTTGTAGGTGTCGT 59.054 40.909 22.87 0.00 39.91 4.34
2243 4114 3.617540 TGCACAAATTTGTAGGTGTCG 57.382 42.857 22.87 10.37 39.91 4.35
2246 4117 7.244166 TGAAAAATGCACAAATTTGTAGGTG 57.756 32.000 22.87 12.16 39.91 4.00
2249 4120 7.577979 AGCATGAAAAATGCACAAATTTGTAG 58.422 30.769 22.87 17.23 46.77 2.74
2297 4171 8.920509 AAAACAGAACTGGTTACAACAAATAC 57.079 30.769 5.52 0.00 40.05 1.89
2313 4187 4.918810 ATCCTGACCACAAAAACAGAAC 57.081 40.909 0.00 0.00 32.90 3.01
2316 4193 4.278170 TGCTTATCCTGACCACAAAAACAG 59.722 41.667 0.00 0.00 0.00 3.16
2388 4265 8.870116 GCCACATAATATTTCCCTTCCTTAAAT 58.130 33.333 0.00 0.00 0.00 1.40
2453 4330 3.441572 CACCACTCCTTCAGGCAATAAAG 59.558 47.826 0.00 0.00 34.44 1.85
2561 4490 4.562757 GCCTTGTACTGTGGAACTGACATA 60.563 45.833 0.00 0.00 39.30 2.29
2734 4983 1.464608 CCGTACACATGAAACCAGCAG 59.535 52.381 0.00 0.00 0.00 4.24
2830 5208 5.307204 TGCAGCTTTTAGCAATTCCAAAAT 58.693 33.333 1.09 0.00 45.56 1.82
3103 5499 8.715998 CAAGTACATGCCATAAGATGATTAGTC 58.284 37.037 0.00 0.00 0.00 2.59
3248 5648 1.675310 CGAAGCAGGGGATTGCACA 60.675 57.895 0.52 0.00 46.47 4.57
3306 5888 1.721664 CCCATCTTCCATGCGCACAG 61.722 60.000 14.90 8.78 0.00 3.66
3311 5893 0.533755 GGAGACCCATCTTCCATGCG 60.534 60.000 0.00 0.00 34.34 4.73
3325 5909 9.267084 GTAATATTCCTCAAAAGAGATGGAGAC 57.733 37.037 0.00 0.00 0.00 3.36
3337 5923 9.342308 GACTGAATCCATGTAATATTCCTCAAA 57.658 33.333 0.00 0.00 0.00 2.69
3338 5924 8.493607 TGACTGAATCCATGTAATATTCCTCAA 58.506 33.333 0.00 0.00 0.00 3.02
3339 5925 8.033178 TGACTGAATCCATGTAATATTCCTCA 57.967 34.615 0.00 0.00 0.00 3.86
3341 5927 9.512588 GAATGACTGAATCCATGTAATATTCCT 57.487 33.333 0.00 0.00 0.00 3.36
3342 5928 9.288576 TGAATGACTGAATCCATGTAATATTCC 57.711 33.333 0.00 0.00 0.00 3.01
3433 6057 8.138074 AGATGAATCATGAAATGCAAAGATCAG 58.862 33.333 0.00 0.00 46.21 2.90
3440 6064 5.655090 ACTGGAGATGAATCATGAAATGCAA 59.345 36.000 0.00 0.00 46.21 4.08
3446 6071 4.224991 TGCACTGGAGATGAATCATGAA 57.775 40.909 0.00 0.00 0.00 2.57
3460 6089 2.560504 TCTGTGTACAACTTGCACTGG 58.439 47.619 0.00 0.00 41.23 4.00
3464 6093 5.007626 GTCAAGAATCTGTGTACAACTTGCA 59.992 40.000 0.00 0.00 35.00 4.08
3571 6204 5.587844 GGATTCTGCATGTAAGACTTGACAT 59.412 40.000 0.00 1.78 36.73 3.06
3654 6292 5.601313 ACAGAAGTCTTAAGAACCACAGGTA 59.399 40.000 6.78 0.00 33.12 3.08
3655 6293 4.409247 ACAGAAGTCTTAAGAACCACAGGT 59.591 41.667 6.78 0.00 37.65 4.00
3676 6326 0.033642 TACAAACGATGGGTGCGACA 59.966 50.000 0.00 0.00 0.00 4.35
3758 6425 1.992667 CAAGCTTGACGTTCTGCGATA 59.007 47.619 22.31 0.00 44.77 2.92
3762 6429 3.813529 ATAACAAGCTTGACGTTCTGC 57.186 42.857 32.50 0.00 0.00 4.26
3786 6453 9.921637 GTACTGAATTCCATGATTTAACCAAAA 57.078 29.630 2.27 0.00 0.00 2.44
3789 6458 8.106462 TCAGTACTGAATTCCATGATTTAACCA 58.894 33.333 23.24 0.00 36.53 3.67
4010 6681 4.790962 CAGCGAGCCCTGGCATGT 62.791 66.667 11.38 0.00 44.88 3.21
4128 6799 4.351054 CCTGGTGGTGGCAGTCCC 62.351 72.222 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.