Multiple sequence alignment - TraesCS1B01G249000

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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 TraesCS1B01G249000 chr1B 100.000 5624 0 0 1 5624 441389825 441384202 0.000000e+00 10386.0
1 TraesCS1B01G249000 chr1A 92.526 4589 195 69 1119 5624 410153147 410157670 0.000000e+00 6438.0
2 TraesCS1B01G249000 chr1A 90.096 1151 79 18 1 1124 410152040 410153182 0.000000e+00 1461.0
3 TraesCS1B01G249000 chr1A 100.000 29 0 0 2484 2512 494028053 494028081 3.000000e-03 54.7
4 TraesCS1B01G249000 chr1D 95.874 1939 54 8 3179 5103 326909946 326908020 0.000000e+00 3114.0
5 TraesCS1B01G249000 chr1D 94.298 1175 36 15 2041 3193 326911281 326910116 0.000000e+00 1770.0
6 TraesCS1B01G249000 chr1D 91.808 1123 63 18 1 1106 326913294 326912184 0.000000e+00 1537.0
7 TraesCS1B01G249000 chr1D 93.226 930 44 11 1134 2059 326912204 326911290 0.000000e+00 1351.0
8 TraesCS1B01G249000 chr1D 89.341 516 28 7 5130 5624 326908024 326907515 1.720000e-174 623.0
9 TraesCS1B01G249000 chr7A 91.800 1000 71 6 3643 4632 730504581 730505579 0.000000e+00 1382.0
10 TraesCS1B01G249000 chr7A 76.773 818 117 34 292 1095 730501139 730501897 1.900000e-104 390.0
11 TraesCS1B01G249000 chr7A 76.986 491 50 36 1453 1935 730502352 730502787 7.330000e-54 222.0
12 TraesCS1B01G249000 chr7A 96.721 61 2 0 2019 2079 730502900 730502960 9.970000e-18 102.0
13 TraesCS1B01G249000 chr7A 100.000 36 0 0 2091 2126 730502992 730503027 3.640000e-07 67.6
14 TraesCS1B01G249000 chr7D 91.717 1002 72 6 3643 4634 635517896 635516896 0.000000e+00 1380.0
15 TraesCS1B01G249000 chr7D 84.814 349 22 17 999 1328 635520423 635520087 7.030000e-84 322.0
16 TraesCS1B01G249000 chr7D 79.524 420 34 20 1621 2034 635519946 635519573 9.350000e-63 252.0
17 TraesCS1B01G249000 chr7D 94.915 59 3 0 2021 2079 635519553 635519495 6.000000e-15 93.5
18 TraesCS1B01G249000 chr7D 89.394 66 6 1 1379 1444 635520056 635519992 1.300000e-11 82.4
19 TraesCS1B01G249000 chr7D 97.059 34 1 0 2093 2126 635519461 635519428 2.190000e-04 58.4
20 TraesCS1B01G249000 chr7B 89.133 1003 97 7 3643 4635 740261012 740262012 0.000000e+00 1238.0
21 TraesCS1B01G249000 chr7B 93.146 569 35 4 4068 4634 740301807 740302373 0.000000e+00 832.0
22 TraesCS1B01G249000 chr7B 89.943 527 51 2 4106 4631 740239657 740240182 0.000000e+00 678.0
23 TraesCS1B01G249000 chr7B 89.540 478 44 4 3643 4115 740238714 740239190 8.060000e-168 601.0
24 TraesCS1B01G249000 chr7B 89.384 471 36 7 3643 4104 740763910 740764375 1.050000e-161 580.0
25 TraesCS1B01G249000 chr7B 88.960 471 38 7 3643 4104 740723049 740723514 2.270000e-158 569.0
26 TraesCS1B01G249000 chr7B 78.077 967 108 60 999 1935 740720389 740721281 3.000000e-142 516.0
27 TraesCS1B01G249000 chr7B 77.898 742 68 49 972 1698 740286733 740287393 1.910000e-99 374.0
28 TraesCS1B01G249000 chr7B 78.481 553 67 21 292 830 740254586 740255100 1.180000e-81 315.0
29 TraesCS1B01G249000 chr7B 83.750 320 21 11 999 1304 740758176 740758478 2.000000e-69 274.0
30 TraesCS1B01G249000 chr7B 86.147 231 17 11 4913 5133 740302677 740302902 9.420000e-58 235.0
31 TraesCS1B01G249000 chr7B 96.104 77 3 0 999 1075 740676958 740677034 5.920000e-25 126.0
32 TraesCS1B01G249000 chr7B 96.104 77 3 0 999 1075 740705567 740705643 5.920000e-25 126.0
33 TraesCS1B01G249000 chr7B 82.639 144 10 8 3373 3510 740238155 740238289 4.610000e-21 113.0
34 TraesCS1B01G249000 chr7B 92.063 63 3 1 2448 2510 740300701 740300761 2.790000e-13 87.9
35 TraesCS1B01G249000 chr7B 92.063 63 3 1 2448 2510 740721954 740722014 2.790000e-13 87.9
36 TraesCS1B01G249000 chr7B 90.769 65 3 2 2446 2510 740237698 740237759 3.610000e-12 84.2
37 TraesCS1B01G249000 chr7B 83.333 90 7 3 1205 1290 740256487 740256572 6.040000e-10 76.8
38 TraesCS1B01G249000 chr7B 100.000 34 0 0 2093 2126 740240861 740240894 4.700000e-06 63.9
39 TraesCS1B01G249000 chr7B 100.000 34 0 0 2093 2126 740721402 740721435 4.700000e-06 63.9
40 TraesCS1B01G249000 chr3B 74.571 932 210 24 3707 4621 773542576 773543497 3.180000e-102 383.0
41 TraesCS1B01G249000 chr3A 72.000 875 199 30 3699 4553 711297361 711296513 3.410000e-52 217.0


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 TraesCS1B01G249000 chr1B 441384202 441389825 5623 True 10386.000000 10386 100.0000 1 5624 1 chr1B.!!$R1 5623
1 TraesCS1B01G249000 chr1A 410152040 410157670 5630 False 3949.500000 6438 91.3110 1 5624 2 chr1A.!!$F2 5623
2 TraesCS1B01G249000 chr1D 326907515 326913294 5779 True 1679.000000 3114 92.9094 1 5624 5 chr1D.!!$R1 5623
3 TraesCS1B01G249000 chr7A 730501139 730505579 4440 False 432.720000 1382 88.4560 292 4632 5 chr7A.!!$F1 4340
4 TraesCS1B01G249000 chr7D 635516896 635520423 3527 True 364.716667 1380 89.5705 999 4634 6 chr7D.!!$R1 3635
5 TraesCS1B01G249000 chr7B 740261012 740262012 1000 False 1238.000000 1238 89.1330 3643 4635 1 chr7B.!!$F1 992
6 TraesCS1B01G249000 chr7B 740300701 740302902 2201 False 384.966667 832 90.4520 2448 5133 3 chr7B.!!$F9 2685
7 TraesCS1B01G249000 chr7B 740286733 740287393 660 False 374.000000 374 77.8980 972 1698 1 chr7B.!!$F2 726
8 TraesCS1B01G249000 chr7B 740720389 740723514 3125 False 309.200000 569 89.7750 999 4104 4 chr7B.!!$F10 3105
9 TraesCS1B01G249000 chr7B 740237698 740240894 3196 False 308.020000 678 90.5782 2093 4631 5 chr7B.!!$F7 2538
10 TraesCS1B01G249000 chr3B 773542576 773543497 921 False 383.000000 383 74.5710 3707 4621 1 chr3B.!!$F1 914
11 TraesCS1B01G249000 chr3A 711296513 711297361 848 True 217.000000 217 72.0000 3699 4553 1 chr3A.!!$R1 854

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
760 787 0.614979 GCCCACCACCAGACTCTCTA 60.615 60.0 0.00 0.00 0.0 2.43 F
1290 1563 0.181350 AAGGTAGCTAGCCATGGTGC 59.819 55.0 19.06 15.14 0.0 5.01 F
2671 3459 0.179056 TAATTGGACCGCAGCTAGGC 60.179 55.0 7.27 0.00 0.0 3.93 F
3175 3993 0.242825 CGGACACGAGTAGCCAAAGA 59.757 55.0 0.00 0.00 44.6 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2323 1.915141 AACATGGCACTGGAGAAAGG 58.085 50.000 0.00 0.0 0.00 3.11 R
3288 4307 1.067212 AGTCACGAGTTGGTGTCAGAC 59.933 52.381 0.00 0.0 39.00 3.51 R
3492 4840 1.226101 CGGCGATGCATGAACACAC 60.226 57.895 2.46 0.0 0.00 3.82 R
5152 7576 1.153168 CCATCTAGGCCACCCGTTG 60.153 63.158 5.01 0.0 35.76 4.10 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
22 23 3.377485 TCAATACCTTCTCTTCCGAGACG 59.623 47.826 0.00 0.00 45.61 4.18
63 64 7.654022 AGTGGAATAGGTCTTGTTTGAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
203 204 8.093307 TGATTTCTTGCAATATAGCCACAAAAA 58.907 29.630 0.00 0.00 0.00 1.94
261 276 7.786464 TCCCACTATTAGGTAGTAAAAGGTAGG 59.214 40.741 0.00 0.00 41.73 3.18
267 282 4.755437 AGGTAGTAAAAGGTAGGGTGACA 58.245 43.478 0.00 0.00 0.00 3.58
284 299 4.154918 GGTGACAAAAGGCTTCTGATGTAG 59.845 45.833 7.72 0.00 0.00 2.74
569 587 5.907866 TGAGTAAGACGTGAACATATCCA 57.092 39.130 0.00 0.00 0.00 3.41
571 589 6.693466 TGAGTAAGACGTGAACATATCCAAA 58.307 36.000 0.00 0.00 0.00 3.28
685 706 7.558161 TTGGTGCTACTATGAATGAATGAAG 57.442 36.000 0.00 0.00 0.00 3.02
686 707 6.057533 TGGTGCTACTATGAATGAATGAAGG 58.942 40.000 0.00 0.00 0.00 3.46
688 709 6.767902 GGTGCTACTATGAATGAATGAAGGAA 59.232 38.462 0.00 0.00 0.00 3.36
689 710 7.041508 GGTGCTACTATGAATGAATGAAGGAAG 60.042 40.741 0.00 0.00 0.00 3.46
690 711 6.994496 TGCTACTATGAATGAATGAAGGAAGG 59.006 38.462 0.00 0.00 0.00 3.46
691 712 6.429385 GCTACTATGAATGAATGAAGGAAGGG 59.571 42.308 0.00 0.00 0.00 3.95
692 713 5.699143 ACTATGAATGAATGAAGGAAGGGG 58.301 41.667 0.00 0.00 0.00 4.79
693 714 4.886755 ATGAATGAATGAAGGAAGGGGA 57.113 40.909 0.00 0.00 0.00 4.81
694 715 4.673328 TGAATGAATGAAGGAAGGGGAA 57.327 40.909 0.00 0.00 0.00 3.97
695 716 5.211078 TGAATGAATGAAGGAAGGGGAAT 57.789 39.130 0.00 0.00 0.00 3.01
696 717 5.203528 TGAATGAATGAAGGAAGGGGAATC 58.796 41.667 0.00 0.00 0.00 2.52
697 718 5.043881 TGAATGAATGAAGGAAGGGGAATCT 60.044 40.000 0.00 0.00 0.00 2.40
755 780 2.122413 TCTGCCCACCACCAGACT 60.122 61.111 0.00 0.00 33.44 3.24
756 781 2.177594 CTCTGCCCACCACCAGACTC 62.178 65.000 0.00 0.00 34.60 3.36
757 782 2.122413 TGCCCACCACCAGACTCT 60.122 61.111 0.00 0.00 0.00 3.24
760 787 0.614979 GCCCACCACCAGACTCTCTA 60.615 60.000 0.00 0.00 0.00 2.43
942 978 5.517770 CCAGAAAAGAAACAACAAGAGCTTG 59.482 40.000 8.60 8.60 45.58 4.01
948 984 4.813697 AGAAACAACAAGAGCTTGAGAGAC 59.186 41.667 16.47 4.29 42.93 3.36
949 985 4.414337 AACAACAAGAGCTTGAGAGACT 57.586 40.909 16.47 0.00 42.93 3.24
950 986 3.988819 ACAACAAGAGCTTGAGAGACTC 58.011 45.455 16.47 0.00 42.93 3.36
951 987 3.640967 ACAACAAGAGCTTGAGAGACTCT 59.359 43.478 16.47 4.14 42.93 3.24
952 988 4.100808 ACAACAAGAGCTTGAGAGACTCTT 59.899 41.667 16.47 0.00 42.15 2.85
954 990 3.587923 CAAGAGCTTGAGAGACTCTTGG 58.412 50.000 19.40 1.57 46.43 3.61
955 991 1.550072 AGAGCTTGAGAGACTCTTGGC 59.450 52.381 6.40 11.05 34.72 4.52
956 992 1.274728 GAGCTTGAGAGACTCTTGGCA 59.725 52.381 19.79 7.78 0.00 4.92
957 993 1.907936 AGCTTGAGAGACTCTTGGCAT 59.092 47.619 19.79 8.51 0.00 4.40
963 1009 1.277557 AGAGACTCTTGGCATCACACC 59.722 52.381 0.00 0.00 0.00 4.16
969 1015 1.855213 CTTGGCATCACACCCACACG 61.855 60.000 0.00 0.00 0.00 4.49
1103 1193 4.455606 CCTTCCTTCTCTCTCTCTCTCTC 58.544 52.174 0.00 0.00 0.00 3.20
1104 1194 4.164988 CCTTCCTTCTCTCTCTCTCTCTCT 59.835 50.000 0.00 0.00 0.00 3.10
1105 1195 5.359194 TTCCTTCTCTCTCTCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
1106 1196 4.624913 TCCTTCTCTCTCTCTCTCTCTCT 58.375 47.826 0.00 0.00 0.00 3.10
1107 1197 4.651503 TCCTTCTCTCTCTCTCTCTCTCTC 59.348 50.000 0.00 0.00 0.00 3.20
1108 1198 4.653341 CCTTCTCTCTCTCTCTCTCTCTCT 59.347 50.000 0.00 0.00 0.00 3.10
1109 1199 5.221422 CCTTCTCTCTCTCTCTCTCTCTCTC 60.221 52.000 0.00 0.00 0.00 3.20
1110 1200 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1111 1201 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1112 1202 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1113 1203 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1114 1204 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1115 1205 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1116 1206 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1117 1207 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1118 1208 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1119 1209 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1120 1210 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1121 1211 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1122 1212 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1123 1213 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1124 1214 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1125 1215 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1126 1216 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1127 1217 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1128 1218 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1129 1219 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1130 1220 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1131 1221 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1132 1222 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1212 1331 4.761739 TGCAGGGAGTTTGTTTAGAAGATG 59.238 41.667 0.00 0.00 0.00 2.90
1290 1563 0.181350 AAGGTAGCTAGCCATGGTGC 59.819 55.000 19.06 15.14 0.00 5.01
1427 1710 2.816360 CGCCATCAGTCGCATGGTG 61.816 63.158 0.00 1.03 43.69 4.17
1468 1752 4.762765 GCCGGTCTCTCATTCTCTATCTTA 59.237 45.833 1.90 0.00 0.00 2.10
1470 1754 6.239064 GCCGGTCTCTCATTCTCTATCTTAAA 60.239 42.308 1.90 0.00 0.00 1.52
1602 1888 9.440773 CTTGGAATTTGCTGCAGAGTATATATA 57.559 33.333 20.43 0.00 0.00 0.86
1603 1889 9.964354 TTGGAATTTGCTGCAGAGTATATATAT 57.036 29.630 20.43 0.00 0.00 0.86
1660 1946 1.000052 TGCACGTGTAATCGACCTTCA 60.000 47.619 18.38 0.00 34.70 3.02
2014 2323 4.674281 ATAAGTAGCTAAGCCAGTGTCC 57.326 45.455 0.00 0.00 0.00 4.02
2134 2522 1.972795 ACACGAGCCCTACCACTTAAA 59.027 47.619 0.00 0.00 0.00 1.52
2206 2596 4.435651 CCGTCGCTAACCATCTTTTTCTTC 60.436 45.833 0.00 0.00 0.00 2.87
2290 2689 0.811915 CAGTCCAGTGGTCCTACTCG 59.188 60.000 9.54 0.00 0.00 4.18
2291 2690 0.697079 AGTCCAGTGGTCCTACTCGA 59.303 55.000 9.54 0.00 0.00 4.04
2292 2691 1.285373 AGTCCAGTGGTCCTACTCGAT 59.715 52.381 9.54 0.00 0.00 3.59
2293 2692 1.677052 GTCCAGTGGTCCTACTCGATC 59.323 57.143 9.54 0.00 0.00 3.69
2355 2759 4.915085 AGTTTAACGAAAATGATTGCACCG 59.085 37.500 0.00 0.00 0.00 4.94
2534 3318 7.010339 AGAATTATGGCATAGGAAGTAGGTC 57.990 40.000 7.35 0.00 0.00 3.85
2575 3359 5.655090 TGCTAGTAGTAGTTGGCACTTGATA 59.345 40.000 6.47 0.00 34.06 2.15
2594 3378 4.651503 TGATAGAGCAGGAAGTTAAGAGGG 59.348 45.833 0.00 0.00 0.00 4.30
2633 3417 9.517609 GTGTACTTATATGGAGTACTTTGTCAG 57.482 37.037 21.77 0.00 46.07 3.51
2663 3451 2.199236 CTAGACCGTTAATTGGACCGC 58.801 52.381 3.91 0.00 0.00 5.68
2671 3459 0.179056 TAATTGGACCGCAGCTAGGC 60.179 55.000 7.27 0.00 0.00 3.93
2818 3608 3.005684 GCATGAGGTCTCTACTCTCCATG 59.994 52.174 0.00 0.00 35.98 3.66
2827 3619 7.566879 AGGTCTCTACTCTCCATGTATTCATTT 59.433 37.037 0.00 0.00 31.15 2.32
2875 3671 2.676176 CGTGTGGTCGACCTCTACTCTA 60.676 54.545 33.39 11.69 36.82 2.43
2899 3695 3.327439 CCCCTACAATATTCCTGGTCCT 58.673 50.000 0.00 0.00 0.00 3.85
3073 3886 8.537858 ACTAAATTAGGGTAGAGTTAGTTGGTG 58.462 37.037 4.92 0.00 29.71 4.17
3109 3927 4.333926 CAGCTAGGGTAAAAGATTCACTGC 59.666 45.833 0.00 0.00 0.00 4.40
3110 3928 4.019321 AGCTAGGGTAAAAGATTCACTGCA 60.019 41.667 0.00 0.00 0.00 4.41
3111 3929 4.095036 GCTAGGGTAAAAGATTCACTGCAC 59.905 45.833 0.00 0.00 0.00 4.57
3112 3930 4.373156 AGGGTAAAAGATTCACTGCACT 57.627 40.909 0.00 0.00 0.00 4.40
3113 3931 4.074970 AGGGTAAAAGATTCACTGCACTG 58.925 43.478 0.00 0.00 0.00 3.66
3159 3977 1.626825 CTTTAAGGTTGTCCCTCCGGA 59.373 52.381 2.93 2.93 45.47 5.14
3175 3993 0.242825 CGGACACGAGTAGCCAAAGA 59.757 55.000 0.00 0.00 44.60 2.52
3481 4821 1.538849 GCCAACAGGTCAAAAGGCTTG 60.539 52.381 0.00 0.00 39.02 4.01
3491 4839 1.406539 CAAAAGGCTTGCTCTGTGTGT 59.593 47.619 0.00 0.00 0.00 3.72
3492 4840 1.027357 AAAGGCTTGCTCTGTGTGTG 58.973 50.000 0.00 0.00 0.00 3.82
3493 4841 0.107017 AAGGCTTGCTCTGTGTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
3494 4842 0.816825 AGGCTTGCTCTGTGTGTGTG 60.817 55.000 0.00 0.00 0.00 3.82
3495 4843 1.097547 GGCTTGCTCTGTGTGTGTGT 61.098 55.000 0.00 0.00 0.00 3.72
3496 4844 0.028505 GCTTGCTCTGTGTGTGTGTG 59.971 55.000 0.00 0.00 0.00 3.82
3582 5120 1.209504 TGTCATCACGGGGAGGAATTC 59.790 52.381 0.00 0.00 38.18 2.17
3625 5395 6.868339 GTGCTAGCTTGGTGTGAATAATTTTT 59.132 34.615 17.23 0.00 0.00 1.94
3780 5570 0.951558 GCATGTTCAAGTCCAACGGT 59.048 50.000 0.00 0.00 0.00 4.83
3798 5588 1.070134 GGTATCAACTCCATGCGGCTA 59.930 52.381 0.00 0.00 0.00 3.93
4023 5820 2.267642 CTCGTCCCGGCCATGAAA 59.732 61.111 2.24 0.00 0.00 2.69
4665 7035 1.268437 GCTAGTGTCCGTATGTCCGTC 60.268 57.143 0.00 0.00 0.00 4.79
4833 7218 3.508845 ATGATTTACGATGGAAGGGGG 57.491 47.619 0.00 0.00 0.00 5.40
4852 7237 1.134670 GGGCAGATGTAAACGCTCTCT 60.135 52.381 0.00 0.00 0.00 3.10
5044 7436 6.340962 TCCAAGATACATGTATTAGTCGGG 57.659 41.667 19.19 13.49 0.00 5.14
5171 7595 2.375345 AACGGGTGGCCTAGATGGG 61.375 63.158 3.32 0.00 36.00 4.00
5236 7660 3.125573 TCGAGAGAGGGACGCACG 61.126 66.667 0.00 0.00 34.48 5.34
5237 7661 4.838486 CGAGAGAGGGACGCACGC 62.838 72.222 0.00 0.00 0.00 5.34
5238 7662 4.500116 GAGAGAGGGACGCACGCC 62.500 72.222 0.00 0.00 0.00 5.68
5246 7670 3.537874 GACGCACGCCCTAGGGAT 61.538 66.667 33.21 15.94 37.50 3.85
5252 7687 0.250038 CACGCCCTAGGGATGATGTG 60.250 60.000 33.21 23.53 37.50 3.21
5285 7720 6.201591 TGCCCATACCATTTTCTTCCTTTAT 58.798 36.000 0.00 0.00 0.00 1.40
5306 7741 9.965902 CTTTATTGCTCCCAAATCTACCTATAT 57.034 33.333 0.00 0.00 34.05 0.86
5307 7742 9.739276 TTTATTGCTCCCAAATCTACCTATATG 57.261 33.333 0.00 0.00 34.05 1.78
5308 7743 5.762179 TGCTCCCAAATCTACCTATATGG 57.238 43.478 0.00 0.00 42.93 2.74
5309 7744 5.411493 TGCTCCCAAATCTACCTATATGGA 58.589 41.667 0.00 0.00 39.71 3.41
5310 7745 5.485353 TGCTCCCAAATCTACCTATATGGAG 59.515 44.000 0.00 0.00 39.83 3.86
5411 7846 3.125829 TGGATACGTATATCTCGCCGAAC 59.874 47.826 8.34 0.00 37.85 3.95
5414 7849 0.594602 CGTATATCTCGCCGAACCCA 59.405 55.000 0.00 0.00 0.00 4.51
5455 7890 0.896019 CTCTCTGGTCGTCCCTGTGT 60.896 60.000 0.00 0.00 33.97 3.72
5482 7917 6.069206 ACCCACAGTGGAGATAAGTAGTACTA 60.069 42.308 22.37 0.00 40.96 1.82
5483 7918 6.487331 CCCACAGTGGAGATAAGTAGTACTAG 59.513 46.154 22.37 0.00 40.96 2.57
5484 7919 6.016943 CCACAGTGGAGATAAGTAGTACTAGC 60.017 46.154 15.35 0.00 40.96 3.42
5530 7986 6.857956 ACGATATACTGCTCCAGATGATAAC 58.142 40.000 0.00 0.00 35.18 1.89
5538 7994 4.047822 GCTCCAGATGATAACGTTCAGAG 58.952 47.826 2.82 2.08 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.470821 ACTTTTGGACTTGTCGTCTCG 58.529 47.619 0.00 0.00 42.44 4.04
22 23 6.445357 TTCCACTAAACTTTTGGACTTGTC 57.555 37.500 0.00 0.00 39.20 3.18
63 64 7.501225 ACTTTAATTAAGCATGGCCGTATACTT 59.499 33.333 0.00 4.70 37.37 2.24
173 174 8.570488 TGTGGCTATATTGCAAGAAATCAATAG 58.430 33.333 11.27 0.00 38.21 1.73
244 250 5.902760 TGTCACCCTACCTTTTACTACCTA 58.097 41.667 0.00 0.00 0.00 3.08
261 276 2.887152 ACATCAGAAGCCTTTTGTCACC 59.113 45.455 0.00 0.00 0.00 4.02
267 282 5.248477 TGGAGTACTACATCAGAAGCCTTTT 59.752 40.000 2.78 0.00 0.00 2.27
284 299 8.175716 CGGTCAATTTAAAGAGATTTGGAGTAC 58.824 37.037 0.00 0.00 0.00 2.73
360 376 4.932799 TCGGCTTCGATGTTCTTTTTATCA 59.067 37.500 0.00 0.00 38.07 2.15
440 456 3.729462 CGGAGTCTTGTTTGCGACAAAAA 60.729 43.478 6.87 0.00 46.99 1.94
450 468 1.208535 TGACACCACGGAGTCTTGTTT 59.791 47.619 13.71 0.00 41.61 2.83
460 478 3.122948 CGTAAGAAGAATTGACACCACGG 59.877 47.826 0.00 0.00 43.02 4.94
685 706 0.922626 AGGCAAGAGATTCCCCTTCC 59.077 55.000 0.00 0.00 0.00 3.46
686 707 2.158740 GGTAGGCAAGAGATTCCCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
688 709 1.010170 AGGTAGGCAAGAGATTCCCCT 59.990 52.381 0.00 0.00 0.00 4.79
689 710 1.141858 CAGGTAGGCAAGAGATTCCCC 59.858 57.143 0.00 0.00 0.00 4.81
690 711 1.475930 GCAGGTAGGCAAGAGATTCCC 60.476 57.143 0.00 0.00 0.00 3.97
691 712 1.210478 TGCAGGTAGGCAAGAGATTCC 59.790 52.381 0.00 0.00 41.65 3.01
692 713 2.698855 TGCAGGTAGGCAAGAGATTC 57.301 50.000 0.00 0.00 41.65 2.52
755 780 2.687014 CGTCACCCCCTTCTCATAGAGA 60.687 54.545 0.00 0.00 36.86 3.10
756 781 1.683917 CGTCACCCCCTTCTCATAGAG 59.316 57.143 0.00 0.00 0.00 2.43
757 782 1.776662 CGTCACCCCCTTCTCATAGA 58.223 55.000 0.00 0.00 0.00 1.98
760 787 1.274703 ATGCGTCACCCCCTTCTCAT 61.275 55.000 0.00 0.00 0.00 2.90
849 885 0.037590 TTTGGTCCAATCCACTCGGG 59.962 55.000 4.80 0.00 37.20 5.14
850 886 1.165270 GTTTGGTCCAATCCACTCGG 58.835 55.000 4.80 0.00 37.20 4.63
913 949 5.943416 TCTTGTTGTTTCTTTTCTGGTGAGA 59.057 36.000 0.00 0.00 0.00 3.27
942 978 2.615869 GTGTGATGCCAAGAGTCTCTC 58.384 52.381 1.96 0.00 0.00 3.20
948 984 0.250858 TGTGGGTGTGATGCCAAGAG 60.251 55.000 0.00 0.00 0.00 2.85
949 985 0.537143 GTGTGGGTGTGATGCCAAGA 60.537 55.000 0.00 0.00 0.00 3.02
950 986 1.855213 CGTGTGGGTGTGATGCCAAG 61.855 60.000 0.00 0.00 0.00 3.61
951 987 1.896183 CGTGTGGGTGTGATGCCAA 60.896 57.895 0.00 0.00 0.00 4.52
952 988 2.281414 CGTGTGGGTGTGATGCCA 60.281 61.111 0.00 0.00 0.00 4.92
953 989 3.737172 GCGTGTGGGTGTGATGCC 61.737 66.667 0.00 0.00 0.00 4.40
954 990 3.737172 GGCGTGTGGGTGTGATGC 61.737 66.667 0.00 0.00 0.00 3.91
955 991 3.055719 GGGCGTGTGGGTGTGATG 61.056 66.667 0.00 0.00 0.00 3.07
956 992 4.344865 GGGGCGTGTGGGTGTGAT 62.345 66.667 0.00 0.00 0.00 3.06
1103 1193 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1104 1194 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1105 1195 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1106 1196 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1107 1197 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1108 1198 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1109 1199 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1110 1200 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1111 1201 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1112 1202 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1113 1203 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1114 1204 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1115 1205 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1116 1206 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1117 1207 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1118 1208 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1119 1209 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1120 1210 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1121 1211 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1122 1212 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1123 1213 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1124 1214 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1125 1215 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1126 1216 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1127 1217 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1128 1218 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1129 1219 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1130 1220 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1131 1221 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
1132 1222 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
1188 1301 4.134563 TCTTCTAAACAAACTCCCTGCAC 58.865 43.478 0.00 0.00 0.00 4.57
1212 1331 8.788409 AAGCTAAGATTAACGTACGTATTACC 57.212 34.615 23.12 10.14 0.00 2.85
1265 1534 3.511934 CCATGGCTAGCTACCTTACCTAG 59.488 52.174 15.72 0.00 33.41 3.02
1266 1535 3.116862 ACCATGGCTAGCTACCTTACCTA 60.117 47.826 13.04 0.00 0.00 3.08
1267 1536 2.330216 CCATGGCTAGCTACCTTACCT 58.670 52.381 15.72 0.00 0.00 3.08
1268 1537 2.047830 ACCATGGCTAGCTACCTTACC 58.952 52.381 13.04 0.00 0.00 2.85
1290 1563 3.873361 AGAGATTTATGTGACCATGCGTG 59.127 43.478 0.00 0.00 32.29 5.34
1453 1736 5.627367 CGGACGCTTTAAGATAGAGAATGAG 59.373 44.000 0.00 0.00 0.00 2.90
1454 1737 5.067413 ACGGACGCTTTAAGATAGAGAATGA 59.933 40.000 0.00 0.00 0.00 2.57
1468 1752 1.647545 CCATGCATGACGGACGCTTT 61.648 55.000 28.31 0.00 0.00 3.51
1470 1754 2.512286 CCATGCATGACGGACGCT 60.512 61.111 28.31 0.00 0.00 5.07
1602 1888 8.340443 GTGCATGCGAATCATATATTGATGTAT 58.660 33.333 14.09 0.00 44.51 2.29
1603 1889 7.201635 GGTGCATGCGAATCATATATTGATGTA 60.202 37.037 14.09 0.00 44.51 2.29
1604 1890 6.403964 GGTGCATGCGAATCATATATTGATGT 60.404 38.462 14.09 0.00 44.51 3.06
1605 1891 5.969435 GGTGCATGCGAATCATATATTGATG 59.031 40.000 14.09 0.00 44.51 3.07
1963 2259 6.203338 CGTTAGTTAAACCTTCTGGCTTTGTA 59.797 38.462 0.00 0.00 34.33 2.41
2014 2323 1.915141 AACATGGCACTGGAGAAAGG 58.085 50.000 0.00 0.00 0.00 3.11
2134 2522 2.765689 TCAGGGAACAAACCACCAAT 57.234 45.000 0.00 0.00 0.00 3.16
2206 2596 2.033194 GTCCGCGGACCAAAGGAAG 61.033 63.158 41.88 5.57 39.08 3.46
2277 2676 4.023980 TGAAATGATCGAGTAGGACCACT 58.976 43.478 0.00 0.00 0.00 4.00
2290 2689 4.061596 GGTACTGGCTAGCTGAAATGATC 58.938 47.826 15.72 0.00 0.00 2.92
2291 2690 3.493350 CGGTACTGGCTAGCTGAAATGAT 60.493 47.826 15.72 0.00 0.00 2.45
2292 2691 2.159099 CGGTACTGGCTAGCTGAAATGA 60.159 50.000 15.72 0.00 0.00 2.57
2293 2692 2.205074 CGGTACTGGCTAGCTGAAATG 58.795 52.381 15.72 1.57 0.00 2.32
2355 2759 6.039493 TGAGTCAGTTACTATAACTAGCAGCC 59.961 42.308 1.05 0.00 39.07 4.85
2534 3318 4.942483 ACTAGCAGTACCACTACTACACTG 59.058 45.833 0.00 0.00 39.65 3.66
2575 3359 2.192263 CCCCTCTTAACTTCCTGCTCT 58.808 52.381 0.00 0.00 0.00 4.09
2594 3378 2.685850 AGTACACGCCACTTAATCCC 57.314 50.000 0.00 0.00 0.00 3.85
2633 3417 2.202623 CGGTCTAGCTCACGTGCC 60.203 66.667 11.67 3.14 0.00 5.01
2818 3608 5.681337 GCAGGAAGCCTAGAAATGAATAC 57.319 43.478 0.00 0.00 37.23 1.89
3046 3859 8.537858 ACCAACTAACTCTACCCTAATTTAGTG 58.462 37.037 2.88 0.00 31.70 2.74
3073 3886 3.772060 CCTAGCTGATTTGCTTGGTTC 57.228 47.619 0.00 0.00 46.00 3.62
3109 3927 4.380531 TGAACTTTGACTAGCTTCCAGTG 58.619 43.478 0.00 0.00 0.00 3.66
3110 3928 4.689612 TGAACTTTGACTAGCTTCCAGT 57.310 40.909 0.00 0.00 0.00 4.00
3111 3929 5.123027 GGAATGAACTTTGACTAGCTTCCAG 59.877 44.000 0.00 0.00 31.95 3.86
3112 3930 5.003804 GGAATGAACTTTGACTAGCTTCCA 58.996 41.667 0.00 0.00 31.95 3.53
3113 3931 5.249420 AGGAATGAACTTTGACTAGCTTCC 58.751 41.667 0.00 0.00 0.00 3.46
3288 4307 1.067212 AGTCACGAGTTGGTGTCAGAC 59.933 52.381 0.00 0.00 39.00 3.51
3481 4821 1.368641 TGAACACACACACACAGAGC 58.631 50.000 0.00 0.00 0.00 4.09
3491 4839 1.875262 GGCGATGCATGAACACACA 59.125 52.632 2.46 0.00 0.00 3.72
3492 4840 1.226101 CGGCGATGCATGAACACAC 60.226 57.895 2.46 0.00 0.00 3.82
3493 4841 3.037992 GCGGCGATGCATGAACACA 62.038 57.895 12.98 0.00 34.15 3.72
3494 4842 2.277501 GCGGCGATGCATGAACAC 60.278 61.111 12.98 0.00 34.15 3.32
3495 4843 3.507924 GGCGGCGATGCATGAACA 61.508 61.111 12.98 0.00 36.28 3.18
3496 4844 2.340453 AATGGCGGCGATGCATGAAC 62.340 55.000 12.98 0.00 36.28 3.18
3582 5120 2.357009 GCACTGTTCCATTGCCATAGAG 59.643 50.000 0.00 0.00 34.64 2.43
3655 5433 9.054922 GGTACATGTAACTTTGGTTAGTTAACA 57.945 33.333 13.87 0.00 41.04 2.41
3780 5570 4.758688 CATATAGCCGCATGGAGTTGATA 58.241 43.478 0.00 0.00 37.49 2.15
3798 5588 3.570212 GCCTGGTCGGGGGCATAT 61.570 66.667 0.00 0.00 46.84 1.78
3837 5628 3.593551 GACGACGTTGACGCCCGTA 62.594 63.158 19.11 0.00 46.17 4.02
4833 7218 2.159170 AGAGAGAGCGTTTACATCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
4852 7237 3.163630 TGCATGATGAATCGACGAAGA 57.836 42.857 0.00 0.00 0.00 2.87
5044 7436 6.515272 AGTGGGATGTGATTAATTGTGTTC 57.485 37.500 0.00 0.00 0.00 3.18
5152 7576 1.153168 CCATCTAGGCCACCCGTTG 60.153 63.158 5.01 0.00 35.76 4.10
5164 7588 1.689575 GGAGCTCCTGACACCCATCTA 60.690 57.143 26.25 0.00 0.00 1.98
5171 7595 3.775654 CGGGGGAGCTCCTGACAC 61.776 72.222 31.36 15.83 35.18 3.67
5236 7660 0.398318 GTCCACATCATCCCTAGGGC 59.602 60.000 24.42 0.48 34.68 5.19
5237 7661 0.681733 CGTCCACATCATCCCTAGGG 59.318 60.000 23.22 23.22 0.00 3.53
5238 7662 1.704641 TCGTCCACATCATCCCTAGG 58.295 55.000 0.06 0.06 0.00 3.02
5239 7663 2.232452 GGATCGTCCACATCATCCCTAG 59.768 54.545 0.00 0.00 36.28 3.02
5240 7664 2.158310 AGGATCGTCCACATCATCCCTA 60.158 50.000 6.78 0.00 39.61 3.53
5241 7665 1.051812 GGATCGTCCACATCATCCCT 58.948 55.000 0.00 0.00 36.28 4.20
5242 7666 1.051812 AGGATCGTCCACATCATCCC 58.948 55.000 6.78 0.00 39.61 3.85
5243 7667 1.875576 GCAGGATCGTCCACATCATCC 60.876 57.143 6.78 0.00 39.61 3.51
5244 7668 1.506493 GCAGGATCGTCCACATCATC 58.494 55.000 6.78 0.00 39.61 2.92
5245 7669 0.107456 GGCAGGATCGTCCACATCAT 59.893 55.000 6.78 0.00 39.61 2.45
5246 7670 1.522092 GGCAGGATCGTCCACATCA 59.478 57.895 6.78 0.00 39.61 3.07
5252 7687 1.371558 GGTATGGGCAGGATCGTCC 59.628 63.158 0.00 0.00 36.58 4.79
5285 7720 5.849475 TCCATATAGGTAGATTTGGGAGCAA 59.151 40.000 0.00 0.00 39.02 3.91
5306 7741 7.942341 AGTTGACAAAATAATCCAAGTACTCCA 59.058 33.333 0.00 0.00 0.00 3.86
5307 7742 8.336801 AGTTGACAAAATAATCCAAGTACTCC 57.663 34.615 0.00 0.00 0.00 3.85
5324 7759 1.463056 CGCAGCCGAATTAGTTGACAA 59.537 47.619 0.00 0.00 36.29 3.18
5360 7795 0.959553 ACGGATGATACCTACTGCGG 59.040 55.000 0.00 0.00 0.00 5.69
5411 7846 2.819595 CGCAGGACATCCGTTGGG 60.820 66.667 0.00 0.00 42.08 4.12
5414 7849 3.989698 CTCGCGCAGGACATCCGTT 62.990 63.158 8.75 0.00 42.08 4.44
5437 7872 0.402887 TACACAGGGACGACCAGAGA 59.597 55.000 6.20 0.00 43.89 3.10
5443 7878 2.051941 TGGGTTACACAGGGACGAC 58.948 57.895 0.00 0.00 0.00 4.34
5455 7890 5.586877 ACTACTTATCTCCACTGTGGGTTA 58.413 41.667 25.67 12.30 38.32 2.85
5530 7986 7.764443 TCCTTGGAATAAATTAGACTCTGAACG 59.236 37.037 0.00 0.00 0.00 3.95
5584 8040 3.134127 CTGGCTAGCCCCGTTTGC 61.134 66.667 30.81 3.73 34.56 3.68


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

AutoCloner maintained by Alex Coulton.