Multiple sequence alignment - TraesCS4A01G483600

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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 TraesCS4A01G483600 chr4A 100.000 4475 0 0 1 4475 738513022 738517496 0.000000e+00 8264.0
1 TraesCS4A01G483600 chr3B 91.533 3732 139 50 1 3644 805336509 805340151 0.000000e+00 4977.0
2 TraesCS4A01G483600 chr3B 94.303 825 24 10 3639 4447 805340180 805340997 0.000000e+00 1242.0
3 TraesCS4A01G483600 chr3A 94.556 2792 64 17 881 3644 678314074 678316805 0.000000e+00 4233.0
4 TraesCS4A01G483600 chr3A 87.950 805 35 20 1 766 678313062 678313843 0.000000e+00 893.0
5 TraesCS4A01G483600 chr3A 96.364 385 10 2 3819 4203 678316983 678317363 8.170000e-177 630.0
6 TraesCS4A01G483600 chr3A 97.189 249 6 1 4200 4447 678317478 678317726 1.920000e-113 420.0
7 TraesCS4A01G483600 chr3A 94.702 151 8 0 3640 3790 678316835 678316985 7.480000e-58 235.0
8 TraesCS4A01G483600 chr3A 81.405 242 16 15 647 876 678313811 678314035 2.140000e-38 171.0
9 TraesCS4A01G483600 chr2D 78.162 2459 410 76 1069 3447 469984123 469986534 0.000000e+00 1448.0
10 TraesCS4A01G483600 chr2D 76.637 2444 453 74 1081 3447 599926518 599928920 0.000000e+00 1242.0
11 TraesCS4A01G483600 chr2D 75.083 903 200 22 2553 3447 380079646 380080531 9.020000e-107 398.0
12 TraesCS4A01G483600 chr2D 77.612 268 46 7 1070 1327 8348849 8348586 2.790000e-32 150.0
13 TraesCS4A01G483600 chr2A 76.619 2455 458 72 1069 3447 733628986 733631400 0.000000e+00 1247.0
14 TraesCS4A01G483600 chr2A 76.541 1428 239 62 1069 2442 611296243 611297628 0.000000e+00 693.0
15 TraesCS4A01G483600 chr2A 75.249 905 195 27 2553 3447 515303883 515304768 1.940000e-108 403.0
16 TraesCS4A01G483600 chr2B 78.343 2004 372 40 1490 3447 729767103 729769090 0.000000e+00 1240.0
17 TraesCS4A01G483600 chr2B 77.378 1808 308 66 1069 2816 548609596 548611362 0.000000e+00 979.0
18 TraesCS4A01G483600 chr2B 74.834 902 204 21 2553 3447 451455577 451456462 1.950000e-103 387.0
19 TraesCS4A01G483600 chr2B 78.731 268 43 7 1070 1327 4754215 4753952 2.770000e-37 167.0
20 TraesCS4A01G483600 chr5B 78.347 2009 362 43 1490 3445 13775627 13773639 0.000000e+00 1232.0
21 TraesCS4A01G483600 chr1D 76.447 2454 465 68 1073 3450 407672461 407670045 0.000000e+00 1225.0
22 TraesCS4A01G483600 chr1D 75.955 2462 472 74 1070 3447 6913247 6915672 0.000000e+00 1157.0
23 TraesCS4A01G483600 chr1D 75.901 2469 470 81 1070 3450 6714530 6712099 0.000000e+00 1147.0
24 TraesCS4A01G483600 chr1D 77.160 2014 370 58 1486 3445 6898974 6900951 0.000000e+00 1088.0
25 TraesCS4A01G483600 chr1D 76.973 2015 382 55 1490 3445 6721084 6719093 0.000000e+00 1075.0
26 TraesCS4A01G483600 chr1D 97.674 43 0 1 376 417 51833132 51833174 6.210000e-09 73.1
27 TraesCS4A01G483600 chr1D 97.674 43 0 1 376 417 254455465 254455423 6.210000e-09 73.1
28 TraesCS4A01G483600 chr1D 97.674 43 0 1 376 417 254455614 254455656 6.210000e-09 73.1
29 TraesCS4A01G483600 chr1D 97.674 43 0 1 376 417 254458246 254458204 6.210000e-09 73.1
30 TraesCS4A01G483600 chr1B 76.381 2443 471 65 1073 3450 548193602 548191201 0.000000e+00 1218.0
31 TraesCS4A01G483600 chr1B 75.659 2465 472 80 1070 3447 8819837 8817414 0.000000e+00 1110.0
32 TraesCS4A01G483600 chr1B 76.667 2010 391 53 1490 3445 8866720 8864735 0.000000e+00 1042.0
33 TraesCS4A01G483600 chr1B 75.213 2465 475 89 1070 3445 9161879 9164296 0.000000e+00 1042.0
34 TraesCS4A01G483600 chr1B 83.468 248 34 6 1 244 553141697 553141941 1.620000e-54 224.0
35 TraesCS4A01G483600 chr1B 82.353 238 35 6 1 234 579775018 579775252 2.730000e-47 200.0
36 TraesCS4A01G483600 chr1B 75.000 272 51 11 1069 1327 9175456 9175723 4.730000e-20 110.0
37 TraesCS4A01G483600 chr1A 76.194 2470 451 86 1070 3445 8332035 8334461 0.000000e+00 1177.0
38 TraesCS4A01G483600 chr1A 77.872 2011 356 56 1490 3445 8327657 8329633 0.000000e+00 1166.0
39 TraesCS4A01G483600 chr1A 77.667 2015 372 50 1490 3447 7835189 7837182 0.000000e+00 1157.0
40 TraesCS4A01G483600 chr4B 84.034 238 31 6 1 234 366942194 366942428 5.830000e-54 222.0
41 TraesCS4A01G483600 chr4B 82.917 240 34 6 1 236 22222824 22223060 4.540000e-50 209.0
42 TraesCS4A01G483600 chr7B 81.452 248 37 8 1 242 81306703 81306459 1.270000e-45 195.0
43 TraesCS4A01G483600 chr7D 75.170 294 61 9 1067 1357 491790865 491790581 1.310000e-25 128.0
44 TraesCS4A01G483600 chr7A 75.085 293 61 9 1068 1357 558082461 558082178 4.700000e-25 126.0
45 TraesCS4A01G483600 chrUn 97.674 43 0 1 376 417 423338500 423338542 6.210000e-09 73.1
46 TraesCS4A01G483600 chr6D 97.674 43 0 1 376 417 354353717 354353759 6.210000e-09 73.1
47 TraesCS4A01G483600 chr5D 97.674 43 0 1 376 417 6254455 6254497 6.210000e-09 73.1
48 TraesCS4A01G483600 chr5D 100.000 34 0 0 201 234 47803156 47803123 3.740000e-06 63.9


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 TraesCS4A01G483600 chr4A 738513022 738517496 4474 False 8264.0 8264 100.000000 1 4475 1 chr4A.!!$F1 4474
1 TraesCS4A01G483600 chr3B 805336509 805340997 4488 False 3109.5 4977 92.918000 1 4447 2 chr3B.!!$F1 4446
2 TraesCS4A01G483600 chr3A 678313062 678317726 4664 False 1097.0 4233 92.027667 1 4447 6 chr3A.!!$F1 4446
3 TraesCS4A01G483600 chr2D 469984123 469986534 2411 False 1448.0 1448 78.162000 1069 3447 1 chr2D.!!$F2 2378
4 TraesCS4A01G483600 chr2D 599926518 599928920 2402 False 1242.0 1242 76.637000 1081 3447 1 chr2D.!!$F3 2366
5 TraesCS4A01G483600 chr2D 380079646 380080531 885 False 398.0 398 75.083000 2553 3447 1 chr2D.!!$F1 894
6 TraesCS4A01G483600 chr2A 733628986 733631400 2414 False 1247.0 1247 76.619000 1069 3447 1 chr2A.!!$F3 2378
7 TraesCS4A01G483600 chr2A 611296243 611297628 1385 False 693.0 693 76.541000 1069 2442 1 chr2A.!!$F2 1373
8 TraesCS4A01G483600 chr2A 515303883 515304768 885 False 403.0 403 75.249000 2553 3447 1 chr2A.!!$F1 894
9 TraesCS4A01G483600 chr2B 729767103 729769090 1987 False 1240.0 1240 78.343000 1490 3447 1 chr2B.!!$F3 1957
10 TraesCS4A01G483600 chr2B 548609596 548611362 1766 False 979.0 979 77.378000 1069 2816 1 chr2B.!!$F2 1747
11 TraesCS4A01G483600 chr2B 451455577 451456462 885 False 387.0 387 74.834000 2553 3447 1 chr2B.!!$F1 894
12 TraesCS4A01G483600 chr5B 13773639 13775627 1988 True 1232.0 1232 78.347000 1490 3445 1 chr5B.!!$R1 1955
13 TraesCS4A01G483600 chr1D 407670045 407672461 2416 True 1225.0 1225 76.447000 1073 3450 1 chr1D.!!$R3 2377
14 TraesCS4A01G483600 chr1D 6913247 6915672 2425 False 1157.0 1157 75.955000 1070 3447 1 chr1D.!!$F2 2377
15 TraesCS4A01G483600 chr1D 6712099 6714530 2431 True 1147.0 1147 75.901000 1070 3450 1 chr1D.!!$R1 2380
16 TraesCS4A01G483600 chr1D 6898974 6900951 1977 False 1088.0 1088 77.160000 1486 3445 1 chr1D.!!$F1 1959
17 TraesCS4A01G483600 chr1D 6719093 6721084 1991 True 1075.0 1075 76.973000 1490 3445 1 chr1D.!!$R2 1955
18 TraesCS4A01G483600 chr1B 548191201 548193602 2401 True 1218.0 1218 76.381000 1073 3450 1 chr1B.!!$R3 2377
19 TraesCS4A01G483600 chr1B 8817414 8819837 2423 True 1110.0 1110 75.659000 1070 3447 1 chr1B.!!$R1 2377
20 TraesCS4A01G483600 chr1B 8864735 8866720 1985 True 1042.0 1042 76.667000 1490 3445 1 chr1B.!!$R2 1955
21 TraesCS4A01G483600 chr1B 9161879 9164296 2417 False 1042.0 1042 75.213000 1070 3445 1 chr1B.!!$F1 2375
22 TraesCS4A01G483600 chr1A 8327657 8334461 6804 False 1171.5 1177 77.033000 1070 3445 2 chr1A.!!$F2 2375
23 TraesCS4A01G483600 chr1A 7835189 7837182 1993 False 1157.0 1157 77.667000 1490 3447 1 chr1A.!!$F1 1957

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
873 1066 0.030638 GCTGCTCGGCAAACAAAGAA 59.969 50.000 0.00 0.0 38.41 2.52 F
925 1118 0.236711 GCATCGACTACATGCATGCC 59.763 55.000 26.53 12.0 45.19 4.40 F
2055 5503 0.035056 CACCACAGGATTGGGACCTC 60.035 60.000 0.00 0.0 41.49 3.85 F
2858 6362 1.899142 TGCTTTGGCCCTAAATTGGAC 59.101 47.619 0.00 0.0 37.74 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 5503 0.747255 ACCCTCCTGTTCGATCATCG 59.253 55.000 0.00 0.0 42.10 3.84 R
2478 5949 2.158900 ACCACACCACTTGAGTCTCTTG 60.159 50.000 0.65 0.0 0.00 3.02 R
3088 6592 0.672711 GGTGTAACAGGAACTCCGGC 60.673 60.000 0.00 0.0 39.98 6.13 R
4084 7673 1.204941 AGGTCTAGCAGGCACTTTACG 59.795 52.381 0.00 0.0 34.60 3.18 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
45 48 8.302515 AGGAATAATCTTTTGCTGACATCATT 57.697 30.769 0.00 0.00 0.00 2.57
114 117 1.199615 TACATGTCCTTCATCGGCCA 58.800 50.000 0.00 0.00 34.09 5.36
349 352 1.062002 GTTTATCGTCCACACATGCCG 59.938 52.381 0.00 0.00 0.00 5.69
450 472 3.478394 GAAGATCGCGTGCGTGCA 61.478 61.111 14.47 0.00 40.74 4.57
479 535 1.153509 CGGCGTGGTAACCTTAGGG 60.154 63.158 2.32 0.00 38.88 3.53
600 666 7.594758 TGCTAGTTTTCGGATTTTTCAGAAATG 59.405 33.333 0.00 0.00 34.74 2.32
606 672 6.832520 TCGGATTTTTCAGAAATGGATCAA 57.167 33.333 0.00 0.00 0.00 2.57
614 680 7.444629 TTTCAGAAATGGATCAAGAGAGTTG 57.555 36.000 0.00 0.00 0.00 3.16
735 801 3.390521 CAGACCCAGTGGCGGCTA 61.391 66.667 11.43 0.00 33.59 3.93
736 802 3.077556 AGACCCAGTGGCGGCTAG 61.078 66.667 11.43 0.00 33.59 3.42
766 832 3.008049 GTCAAGAACATGTACCTGGTCCT 59.992 47.826 12.03 0.00 33.09 3.85
767 833 3.007940 TCAAGAACATGTACCTGGTCCTG 59.992 47.826 12.03 9.98 33.09 3.86
769 835 2.567615 AGAACATGTACCTGGTCCTGTC 59.432 50.000 12.03 0.00 33.09 3.51
770 836 1.276622 ACATGTACCTGGTCCTGTCC 58.723 55.000 0.63 0.00 0.00 4.02
771 837 1.275666 CATGTACCTGGTCCTGTCCA 58.724 55.000 0.63 0.00 36.00 4.02
772 838 1.839994 CATGTACCTGGTCCTGTCCAT 59.160 52.381 0.63 0.00 36.84 3.41
792 939 4.329392 CATGCATGATTAGATGGTGCCTA 58.671 43.478 22.59 0.00 35.03 3.93
835 1028 3.469739 CTGCTTGGCAAACAAAGGAATT 58.530 40.909 4.71 0.00 38.41 2.17
837 1030 5.028549 TGCTTGGCAAACAAAGGAATTAA 57.971 34.783 0.00 0.00 38.91 1.40
838 1031 5.619220 TGCTTGGCAAACAAAGGAATTAAT 58.381 33.333 0.00 0.00 38.91 1.40
839 1032 5.700373 TGCTTGGCAAACAAAGGAATTAATC 59.300 36.000 0.00 0.00 38.91 1.75
841 1034 6.128472 GCTTGGCAAACAAAGGAATTAATCAG 60.128 38.462 0.00 0.00 38.91 2.90
842 1035 6.662865 TGGCAAACAAAGGAATTAATCAGA 57.337 33.333 0.00 0.00 0.00 3.27
843 1036 6.454795 TGGCAAACAAAGGAATTAATCAGAC 58.545 36.000 0.00 0.00 0.00 3.51
844 1037 5.869344 GGCAAACAAAGGAATTAATCAGACC 59.131 40.000 0.00 0.00 0.00 3.85
845 1038 5.869344 GCAAACAAAGGAATTAATCAGACCC 59.131 40.000 0.00 0.00 0.00 4.46
852 1045 3.372025 GGAATTAATCAGACCCAGTGGCT 60.372 47.826 2.61 0.00 33.59 4.75
869 1062 2.518112 TGGCTGCTCGGCAAACAA 60.518 55.556 0.00 0.00 46.25 2.83
871 1064 1.372128 GGCTGCTCGGCAAACAAAG 60.372 57.895 0.00 0.00 38.41 2.77
872 1065 1.654220 GCTGCTCGGCAAACAAAGA 59.346 52.632 0.00 0.00 38.41 2.52
873 1066 0.030638 GCTGCTCGGCAAACAAAGAA 59.969 50.000 0.00 0.00 38.41 2.52
875 1068 2.808244 CTGCTCGGCAAACAAAGAAAA 58.192 42.857 0.35 0.00 38.41 2.29
876 1069 3.186119 CTGCTCGGCAAACAAAGAAAAA 58.814 40.909 0.35 0.00 38.41 1.94
877 1070 3.186119 TGCTCGGCAAACAAAGAAAAAG 58.814 40.909 0.00 0.00 34.76 2.27
878 1071 2.539688 GCTCGGCAAACAAAGAAAAAGG 59.460 45.455 0.00 0.00 0.00 3.11
879 1072 3.736740 GCTCGGCAAACAAAGAAAAAGGA 60.737 43.478 0.00 0.00 0.00 3.36
920 1113 2.030946 GGAAGTTGCATCGACTACATGC 59.969 50.000 0.97 0.97 45.92 4.06
924 1117 3.742290 GCATCGACTACATGCATGC 57.258 52.632 26.53 11.82 45.19 4.06
925 1118 0.236711 GCATCGACTACATGCATGCC 59.763 55.000 26.53 12.00 45.19 4.40
926 1119 0.509929 CATCGACTACATGCATGCCG 59.490 55.000 26.53 21.94 0.00 5.69
943 1140 0.905357 CCGGCCCTTCCTCCATATAG 59.095 60.000 0.00 0.00 0.00 1.31
944 1141 0.250513 CGGCCCTTCCTCCATATAGC 59.749 60.000 0.00 0.00 0.00 2.97
945 1142 1.362224 GGCCCTTCCTCCATATAGCA 58.638 55.000 0.00 0.00 0.00 3.49
946 1143 1.003696 GGCCCTTCCTCCATATAGCAC 59.996 57.143 0.00 0.00 0.00 4.40
948 1145 2.307098 GCCCTTCCTCCATATAGCACAT 59.693 50.000 0.00 0.00 0.00 3.21
949 1146 3.519510 GCCCTTCCTCCATATAGCACATA 59.480 47.826 0.00 0.00 0.00 2.29
951 1148 4.383552 CCCTTCCTCCATATAGCACATAGC 60.384 50.000 0.00 0.00 46.19 2.97
1004 1201 4.695993 TCTTCGCCACGCCATGCA 62.696 61.111 0.00 0.00 0.00 3.96
1054 1251 4.883083 TCTTGTTCTCTACACACCATCAC 58.117 43.478 0.00 0.00 36.21 3.06
1159 4484 2.672996 GCTTCTTCCGGCCAAGCA 60.673 61.111 20.68 1.80 41.87 3.91
1160 4485 2.048603 GCTTCTTCCGGCCAAGCAT 61.049 57.895 20.68 0.00 41.87 3.79
1161 4486 1.805254 CTTCTTCCGGCCAAGCATG 59.195 57.895 2.24 0.00 0.00 4.06
1355 4740 2.017049 ACTAAGCAATGCCACCGAATC 58.983 47.619 0.00 0.00 0.00 2.52
1356 4741 1.334869 CTAAGCAATGCCACCGAATCC 59.665 52.381 0.00 0.00 0.00 3.01
1357 4742 0.611618 AAGCAATGCCACCGAATCCA 60.612 50.000 0.00 0.00 0.00 3.41
1394 4779 7.716998 GTCATCCACTCACCTTGTCAATAATAT 59.283 37.037 0.00 0.00 0.00 1.28
1395 4780 8.274322 TCATCCACTCACCTTGTCAATAATATT 58.726 33.333 0.00 0.00 0.00 1.28
1456 4871 1.804748 GGAACCTTAAGCTTGTGGTCG 59.195 52.381 20.54 2.03 31.64 4.79
1457 4872 2.490991 GAACCTTAAGCTTGTGGTCGT 58.509 47.619 20.54 10.01 31.64 4.34
1459 4874 3.036075 ACCTTAAGCTTGTGGTCGTAC 57.964 47.619 16.37 0.00 0.00 3.67
1460 4875 2.631545 ACCTTAAGCTTGTGGTCGTACT 59.368 45.455 16.37 0.00 0.00 2.73
1462 4877 2.624316 TAAGCTTGTGGTCGTACTCG 57.376 50.000 9.86 0.00 38.55 4.18
1463 4878 0.672342 AAGCTTGTGGTCGTACTCGT 59.328 50.000 0.00 0.00 38.33 4.18
1614 5035 3.551407 GATCCGGGTCTGGGCTCC 61.551 72.222 7.71 0.00 0.00 4.70
1714 5153 2.310538 GGCCATCCCCAAAATCAGTAG 58.689 52.381 0.00 0.00 0.00 2.57
1752 5191 4.445453 TGATCAACATGACACTAGGCATC 58.555 43.478 0.00 0.00 0.00 3.91
1953 5401 2.818132 CTCGATCCCTGCACTCCC 59.182 66.667 0.00 0.00 0.00 4.30
1978 5426 2.813226 TACCTGTGGGCCATTCACGC 62.813 60.000 10.70 0.00 37.91 5.34
1994 5442 4.530710 TCACGCTCTGTAGTGGTAATTT 57.469 40.909 0.00 0.00 38.77 1.82
2055 5503 0.035056 CACCACAGGATTGGGACCTC 60.035 60.000 0.00 0.00 41.49 3.85
2229 5689 2.734673 CGCAGAAGCTTGTCTCGGC 61.735 63.158 2.10 0.07 39.10 5.54
2297 5757 2.109774 CTGGCATGGGGAATTGCTTAA 58.890 47.619 0.00 0.00 38.88 1.85
2478 5949 9.241317 CTCATTATGTTGTTAATGATTTGGAGC 57.759 33.333 7.20 0.00 43.84 4.70
2858 6362 1.899142 TGCTTTGGCCCTAAATTGGAC 59.101 47.619 0.00 0.00 37.74 4.02
2926 6430 5.762045 ACTTGCATCATAGTTGTCACAAAC 58.238 37.500 0.00 0.00 0.00 2.93
2985 6489 3.797039 TCTAGATGCCTCATTTGTTCCG 58.203 45.455 0.00 0.00 0.00 4.30
3380 6905 8.239998 GGATAATAGGCTTACAATGATTGAAGC 58.760 37.037 22.56 22.56 40.17 3.86
3496 7045 5.473039 AGTTGGTGTCGGTGTTACTTATAC 58.527 41.667 0.00 0.00 0.00 1.47
3518 7067 2.778928 CGTCGTTCTAGCGATTTCTGAG 59.221 50.000 0.00 0.00 43.07 3.35
3538 7087 5.555966 TGAGTTGTATTATTGTCTGGTGCA 58.444 37.500 0.00 0.00 0.00 4.57
3559 7108 5.716228 TGCATGTGGTTCCAATTTCTCTTAT 59.284 36.000 0.00 0.00 0.00 1.73
3560 7109 6.127647 TGCATGTGGTTCCAATTTCTCTTATC 60.128 38.462 0.00 0.00 0.00 1.75
3561 7110 6.096001 GCATGTGGTTCCAATTTCTCTTATCT 59.904 38.462 0.00 0.00 0.00 1.98
3562 7111 7.363268 GCATGTGGTTCCAATTTCTCTTATCTT 60.363 37.037 0.00 0.00 0.00 2.40
3563 7112 9.177608 CATGTGGTTCCAATTTCTCTTATCTTA 57.822 33.333 0.00 0.00 0.00 2.10
3651 7234 9.490379 TCTCTATCTAAGAAAAACAACAAGGAC 57.510 33.333 0.00 0.00 32.46 3.85
3656 7239 2.949644 AGAAAAACAACAAGGACTCCCG 59.050 45.455 0.00 0.00 37.58 5.14
3673 7256 4.020485 ACTCCCGCTTTATGACAGTTAAGT 60.020 41.667 0.00 0.00 0.00 2.24
3712 7295 2.688446 TCTATGTAGGCGTCTTGACTGG 59.312 50.000 0.00 0.00 35.81 4.00
3838 7427 5.213891 ACCATTCCAATTGAAGGTTGAAC 57.786 39.130 7.12 0.00 36.14 3.18
3895 7484 5.575218 CGCAACGCTTTAGGGAATTAAAATT 59.425 36.000 0.41 0.00 0.00 1.82
4084 7673 4.802051 TCAAGGCGGCAGATGGGC 62.802 66.667 13.08 0.00 39.06 5.36
4135 7731 1.615392 GGGCTTCTTGCACATCTTGTT 59.385 47.619 0.00 0.00 46.29 2.83
4154 7750 4.312443 TGTTCTAATCAACACCTTCCGAC 58.688 43.478 0.00 0.00 31.08 4.79
4162 7758 1.129058 ACACCTTCCGACCTGTCTTT 58.871 50.000 0.00 0.00 0.00 2.52
4280 7995 9.949174 AAACCATTTCAAAATAAAATTGTCTGC 57.051 25.926 0.00 0.00 0.00 4.26
4447 8162 3.584848 AGCAGAGACTTAATCACAACCCT 59.415 43.478 0.00 0.00 0.00 4.34
4448 8163 4.042187 AGCAGAGACTTAATCACAACCCTT 59.958 41.667 0.00 0.00 0.00 3.95
4449 8164 4.393371 GCAGAGACTTAATCACAACCCTTC 59.607 45.833 0.00 0.00 0.00 3.46
4450 8165 4.938226 CAGAGACTTAATCACAACCCTTCC 59.062 45.833 0.00 0.00 0.00 3.46
4451 8166 4.846940 AGAGACTTAATCACAACCCTTCCT 59.153 41.667 0.00 0.00 0.00 3.36
4452 8167 5.310857 AGAGACTTAATCACAACCCTTCCTT 59.689 40.000 0.00 0.00 0.00 3.36
4453 8168 5.953571 AGACTTAATCACAACCCTTCCTTT 58.046 37.500 0.00 0.00 0.00 3.11
4454 8169 6.373759 AGACTTAATCACAACCCTTCCTTTT 58.626 36.000 0.00 0.00 0.00 2.27
4455 8170 6.839134 AGACTTAATCACAACCCTTCCTTTTT 59.161 34.615 0.00 0.00 0.00 1.94
4474 8189 5.673337 TTTTTCTTCCGTCTGATTCTGTG 57.327 39.130 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 48 5.290643 GCATGCAAACTACAAGACAAAACAA 59.709 36.000 14.21 0.00 0.00 2.83
121 124 6.659242 TCTCCTTTTTCCTTAATTGCGAATCT 59.341 34.615 0.00 0.00 0.00 2.40
339 342 1.016627 CATAAGACCCGGCATGTGTG 58.983 55.000 0.00 0.00 0.00 3.82
349 352 1.676006 CATCGCCAAACCATAAGACCC 59.324 52.381 0.00 0.00 0.00 4.46
413 435 3.822940 TCGACCCCGGCATATTTTTATT 58.177 40.909 0.00 0.00 36.24 1.40
600 666 4.249661 GGAAGTGACAACTCTCTTGATCC 58.750 47.826 0.00 0.00 34.77 3.36
640 706 2.029904 GATGAGCTTTCCGCACGAGC 62.030 60.000 0.00 0.00 42.61 5.03
665 731 3.716353 ACTAATCATGGACCAGGTGCATA 59.284 43.478 25.11 14.31 42.41 3.14
733 799 5.403246 ACATGTTCTTGACGAGTTAGCTAG 58.597 41.667 0.00 0.00 0.00 3.42
735 801 4.258702 ACATGTTCTTGACGAGTTAGCT 57.741 40.909 0.00 0.00 0.00 3.32
736 802 4.326548 GGTACATGTTCTTGACGAGTTAGC 59.673 45.833 2.30 0.00 0.00 3.09
766 832 4.139038 CACCATCTAATCATGCATGGACA 58.861 43.478 25.97 7.98 38.52 4.02
767 833 3.057736 GCACCATCTAATCATGCATGGAC 60.058 47.826 25.97 4.10 38.52 4.02
769 835 2.230508 GGCACCATCTAATCATGCATGG 59.769 50.000 25.97 11.90 41.52 3.66
770 836 3.154710 AGGCACCATCTAATCATGCATG 58.845 45.455 21.07 21.07 38.05 4.06
771 837 3.520691 AGGCACCATCTAATCATGCAT 57.479 42.857 0.00 0.00 38.05 3.96
772 838 3.808265 GCTAGGCACCATCTAATCATGCA 60.808 47.826 0.00 0.00 38.05 3.96
792 939 0.037605 GCCCACGTGTGTTAGTAGCT 60.038 55.000 15.65 0.00 0.00 3.32
819 1012 6.454795 GTCTGATTAATTCCTTTGTTTGCCA 58.545 36.000 0.00 0.00 0.00 4.92
852 1045 2.074230 CTTTGTTTGCCGAGCAGCCA 62.074 55.000 0.00 0.00 40.61 4.75
854 1047 0.030638 TTCTTTGTTTGCCGAGCAGC 59.969 50.000 0.00 0.00 40.61 5.25
855 1048 2.490328 TTTCTTTGTTTGCCGAGCAG 57.510 45.000 0.00 0.00 40.61 4.24
857 1050 2.539688 CCTTTTTCTTTGTTTGCCGAGC 59.460 45.455 0.00 0.00 0.00 5.03
858 1051 4.040445 TCCTTTTTCTTTGTTTGCCGAG 57.960 40.909 0.00 0.00 0.00 4.63
862 1055 5.331532 CGACGATTCCTTTTTCTTTGTTTGC 60.332 40.000 0.00 0.00 0.00 3.68
863 1056 5.173131 CCGACGATTCCTTTTTCTTTGTTTG 59.827 40.000 0.00 0.00 0.00 2.93
865 1058 4.337274 ACCGACGATTCCTTTTTCTTTGTT 59.663 37.500 0.00 0.00 0.00 2.83
867 1060 4.024387 TCACCGACGATTCCTTTTTCTTTG 60.024 41.667 0.00 0.00 0.00 2.77
869 1062 3.735591 TCACCGACGATTCCTTTTTCTT 58.264 40.909 0.00 0.00 0.00 2.52
871 1064 3.249080 TGTTCACCGACGATTCCTTTTTC 59.751 43.478 0.00 0.00 0.00 2.29
872 1065 3.207778 TGTTCACCGACGATTCCTTTTT 58.792 40.909 0.00 0.00 0.00 1.94
873 1066 2.841215 TGTTCACCGACGATTCCTTTT 58.159 42.857 0.00 0.00 0.00 2.27
875 1068 2.346803 CATGTTCACCGACGATTCCTT 58.653 47.619 0.00 0.00 0.00 3.36
876 1069 2.007049 GCATGTTCACCGACGATTCCT 61.007 52.381 0.00 0.00 0.00 3.36
877 1070 0.373716 GCATGTTCACCGACGATTCC 59.626 55.000 0.00 0.00 0.00 3.01
878 1071 1.075542 TGCATGTTCACCGACGATTC 58.924 50.000 0.00 0.00 0.00 2.52
879 1072 1.398041 CATGCATGTTCACCGACGATT 59.602 47.619 18.91 0.00 0.00 3.34
920 1113 4.883354 GGAGGAAGGGCCGGCATG 62.883 72.222 30.85 0.00 43.43 4.06
922 1115 3.875147 TATATGGAGGAAGGGCCGGCA 62.875 57.143 30.85 3.80 43.43 5.69
923 1116 1.198759 TATATGGAGGAAGGGCCGGC 61.199 60.000 21.18 21.18 43.43 6.13
924 1117 0.905357 CTATATGGAGGAAGGGCCGG 59.095 60.000 0.00 0.00 43.43 6.13
925 1118 0.250513 GCTATATGGAGGAAGGGCCG 59.749 60.000 0.00 0.00 43.43 6.13
926 1119 1.003696 GTGCTATATGGAGGAAGGGCC 59.996 57.143 0.00 0.00 0.00 5.80
943 1140 3.181477 ACTCTGTCTGATCTGCTATGTGC 60.181 47.826 0.00 0.00 43.25 4.57
944 1141 4.652421 ACTCTGTCTGATCTGCTATGTG 57.348 45.455 0.00 0.00 0.00 3.21
945 1142 4.278170 GCTACTCTGTCTGATCTGCTATGT 59.722 45.833 0.00 0.00 0.00 2.29
946 1143 4.520111 AGCTACTCTGTCTGATCTGCTATG 59.480 45.833 0.00 0.00 0.00 2.23
948 1145 4.163441 AGCTACTCTGTCTGATCTGCTA 57.837 45.455 0.00 0.00 0.00 3.49
949 1146 3.017048 AGCTACTCTGTCTGATCTGCT 57.983 47.619 0.00 0.00 0.00 4.24
951 1148 3.882288 TGCTAGCTACTCTGTCTGATCTG 59.118 47.826 17.23 0.00 0.00 2.90
952 1149 4.163441 TGCTAGCTACTCTGTCTGATCT 57.837 45.455 17.23 0.00 0.00 2.75
953 1150 5.241506 AGAATGCTAGCTACTCTGTCTGATC 59.758 44.000 17.23 0.00 0.00 2.92
954 1151 5.139727 AGAATGCTAGCTACTCTGTCTGAT 58.860 41.667 17.23 0.00 0.00 2.90
955 1152 4.531854 AGAATGCTAGCTACTCTGTCTGA 58.468 43.478 17.23 0.00 0.00 3.27
956 1153 4.337836 TGAGAATGCTAGCTACTCTGTCTG 59.662 45.833 24.57 0.00 0.00 3.51
957 1154 4.531854 TGAGAATGCTAGCTACTCTGTCT 58.468 43.478 24.57 14.27 0.00 3.41
958 1155 4.909696 TGAGAATGCTAGCTACTCTGTC 57.090 45.455 24.57 12.08 0.00 3.51
1004 1201 6.663093 CCAGAGCAGTAATATGTAGAGAGGAT 59.337 42.308 0.00 0.00 0.00 3.24
1408 4811 1.065854 CAAGAGAAGGGCACTAGTGGG 60.066 57.143 23.95 0.00 0.00 4.61
1444 4847 0.672342 ACGAGTACGACCACAAGCTT 59.328 50.000 0.00 0.00 42.66 3.74
1445 4848 1.467734 CTACGAGTACGACCACAAGCT 59.532 52.381 0.00 0.00 42.66 3.74
1452 4867 0.936600 GGCTCTCTACGAGTACGACC 59.063 60.000 0.00 0.00 41.98 4.79
1456 4871 1.881324 GGATGGGCTCTCTACGAGTAC 59.119 57.143 0.00 0.00 41.98 2.73
1457 4872 1.493446 TGGATGGGCTCTCTACGAGTA 59.507 52.381 0.00 0.00 41.98 2.59
1459 4874 1.403814 TTGGATGGGCTCTCTACGAG 58.596 55.000 0.00 0.00 42.88 4.18
1460 4875 1.688735 CATTGGATGGGCTCTCTACGA 59.311 52.381 0.00 0.00 0.00 3.43
1462 4877 1.141657 TGCATTGGATGGGCTCTCTAC 59.858 52.381 0.00 0.00 0.00 2.59
1463 4878 1.510492 TGCATTGGATGGGCTCTCTA 58.490 50.000 0.00 0.00 0.00 2.43
1714 5153 5.409520 TGTTGATCAGCTGTATGACTTTCAC 59.590 40.000 14.67 0.00 30.46 3.18
1752 5191 2.150014 AACCTTGGGTCCGGGGATTG 62.150 60.000 0.00 0.00 33.12 2.67
1953 5401 0.767375 ATGGCCCACAGGTAGCATAG 59.233 55.000 0.00 0.00 34.57 2.23
1978 5426 9.477484 GTATGGATGTAAATTACCACTACAGAG 57.523 37.037 0.18 0.00 35.19 3.35
2055 5503 0.747255 ACCCTCCTGTTCGATCATCG 59.253 55.000 0.00 0.00 42.10 3.84
2297 5757 5.182570 CCGATGCCATCATTCAGATTTACAT 59.817 40.000 5.40 0.00 33.72 2.29
2478 5949 2.158900 ACCACACCACTTGAGTCTCTTG 60.159 50.000 0.65 0.00 0.00 3.02
2682 6168 4.780021 ACCTCAGCTCTAAATTCCTTCTCA 59.220 41.667 0.00 0.00 0.00 3.27
2858 6362 5.707298 CCTATTGCTATTTGATACCTGGTGG 59.293 44.000 10.23 0.00 39.83 4.61
2926 6430 6.401474 GGCTTAATATCACAGTGTATGATGCG 60.401 42.308 0.00 0.00 37.38 4.73
2985 6489 3.253230 CATCCCAAAGTCCGCAATTTTC 58.747 45.455 0.00 0.00 0.00 2.29
3088 6592 0.672711 GGTGTAACAGGAACTCCGGC 60.673 60.000 0.00 0.00 39.98 6.13
3380 6905 1.484240 GACCCTCAAGGATCTGGACTG 59.516 57.143 0.00 0.00 39.89 3.51
3496 7045 1.846782 CAGAAATCGCTAGAACGACGG 59.153 52.381 0.00 0.00 46.28 4.79
3518 7067 6.029607 CACATGCACCAGACAATAATACAAC 58.970 40.000 0.00 0.00 0.00 3.32
3538 7087 9.927081 ATAAGATAAGAGAAATTGGAACCACAT 57.073 29.630 0.00 0.00 0.00 3.21
3560 7109 9.817365 GCATACATACAATCTTGCTTACATAAG 57.183 33.333 0.00 0.00 36.40 1.73
3561 7110 9.559732 AGCATACATACAATCTTGCTTACATAA 57.440 29.630 0.00 0.00 37.12 1.90
3562 7111 9.559732 AAGCATACATACAATCTTGCTTACATA 57.440 29.630 6.20 0.00 45.62 2.29
3563 7112 8.455903 AAGCATACATACAATCTTGCTTACAT 57.544 30.769 6.20 0.00 45.62 2.29
3607 7156 4.525024 AGAGAAATCAATCCTTGGAGCTG 58.475 43.478 0.00 0.00 0.00 4.24
3625 7174 9.490379 GTCCTTGTTGTTTTTCTTAGATAGAGA 57.510 33.333 0.00 0.00 33.51 3.10
3651 7234 4.330074 CACTTAACTGTCATAAAGCGGGAG 59.670 45.833 0.00 0.00 0.00 4.30
3656 7239 5.390567 CGGGTTCACTTAACTGTCATAAAGC 60.391 44.000 0.00 0.00 38.23 3.51
3673 7256 1.523154 GAATTGCTGTGGCGGGTTCA 61.523 55.000 0.00 0.00 42.25 3.18
3712 7295 3.440228 GAGACGAAACTCCAGCAGATAC 58.560 50.000 0.00 0.00 0.00 2.24
3838 7427 3.699067 GGCCAAAGAATGATCAATCACG 58.301 45.455 13.19 1.04 40.03 4.35
3895 7484 4.081642 GTCTAGTCCCTGTTGCTGTATTCA 60.082 45.833 0.00 0.00 0.00 2.57
4084 7673 1.204941 AGGTCTAGCAGGCACTTTACG 59.795 52.381 0.00 0.00 34.60 3.18
4135 7731 3.056107 CAGGTCGGAAGGTGTTGATTAGA 60.056 47.826 0.00 0.00 0.00 2.10
4154 7750 1.507141 GGGTGTCACGCAAAGACAGG 61.507 60.000 14.72 0.00 45.77 4.00
4162 7758 1.514678 GAAATGCAGGGTGTCACGCA 61.515 55.000 20.83 13.63 39.01 5.24
4452 8167 5.673337 CACAGAATCAGACGGAAGAAAAA 57.327 39.130 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.