Multiple sequence alignment - TraesCS7A01G036500

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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 TraesCS7A01G036500 chr7A 100.000 7572 0 0 1 7572 16422707 16430278 0.000000e+00 13983
1 TraesCS7A01G036500 chr7A 93.957 5477 288 21 1018 6475 16311624 16317076 0.000000e+00 8240
2 TraesCS7A01G036500 chr7A 92.396 5037 305 37 1 4999 16377537 16382533 0.000000e+00 7108
3 TraesCS7A01G036500 chr7A 90.374 3231 238 34 4403 7572 15822539 15819321 0.000000e+00 4176
4 TraesCS7A01G036500 chr7A 93.250 1526 40 6 6083 7572 16393096 16394594 0.000000e+00 2189
5 TraesCS7A01G036500 chr7A 90.329 1582 141 9 2833 4407 15834333 15832757 0.000000e+00 2063
6 TraesCS7A01G036500 chr7A 88.370 1178 101 18 4 1164 15775331 15774173 0.000000e+00 1384
7 TraesCS7A01G036500 chr7A 88.370 1178 101 18 4 1164 15803456 15802298 0.000000e+00 1384
8 TraesCS7A01G036500 chr7A 92.701 959 52 4 1 957 16310356 16311298 0.000000e+00 1367
9 TraesCS7A01G036500 chr7A 92.990 485 26 2 6876 7359 16317432 16317909 0.000000e+00 701
10 TraesCS7A01G036500 chr7A 86.196 623 56 14 556 1164 15836898 15836292 0.000000e+00 647
11 TraesCS7A01G036500 chr7A 97.727 220 5 0 7353 7572 16322918 16323137 5.550000e-101 379
12 TraesCS7A01G036500 chr7A 97.727 220 5 0 7353 7572 16435054 16435273 5.550000e-101 379
13 TraesCS7A01G036500 chr7A 78.447 515 79 26 7077 7570 15816965 15816462 2.650000e-79 307
14 TraesCS7A01G036500 chr7D 93.446 6530 335 47 1112 7572 16763863 16757358 0.000000e+00 9601
15 TraesCS7A01G036500 chr7D 93.977 6077 300 24 1027 7045 17118667 17124735 0.000000e+00 9134
16 TraesCS7A01G036500 chr7D 94.790 4280 187 17 488 4737 16991552 16995825 0.000000e+00 6636
17 TraesCS7A01G036500 chr7D 92.857 896 56 5 1 889 17117423 17118317 0.000000e+00 1293
18 TraesCS7A01G036500 chr7D 98.374 246 2 1 6640 6885 16995822 16996065 1.510000e-116 431
19 TraesCS7A01G036500 chr4A 93.609 5805 317 32 1112 6885 717263657 717257876 0.000000e+00 8615
20 TraesCS7A01G036500 chr4A 93.510 5532 313 20 1192 6697 717749943 717755454 0.000000e+00 8185
21 TraesCS7A01G036500 chr4A 93.029 4117 237 32 3475 7572 717803039 717807124 0.000000e+00 5967
22 TraesCS7A01G036500 chr4A 93.470 3032 166 15 3448 6466 717287668 717284656 0.000000e+00 4473
23 TraesCS7A01G036500 chr4A 94.633 2478 119 7 3999 6466 717225661 717223188 0.000000e+00 3827
24 TraesCS7A01G036500 chr4A 91.429 2380 175 20 1112 3476 717800570 717802935 0.000000e+00 3238
25 TraesCS7A01G036500 chr4A 92.857 1834 118 12 1192 3016 717236579 717234750 0.000000e+00 2649
26 TraesCS7A01G036500 chr4A 92.672 696 28 7 6879 7572 717257851 717257177 0.000000e+00 981
27 TraesCS7A01G036500 chr4A 91.304 621 50 3 1 619 717817882 717818500 0.000000e+00 845
28 TraesCS7A01G036500 chr4A 94.242 521 26 4 7055 7572 717222519 717222000 0.000000e+00 793
29 TraesCS7A01G036500 chr4A 93.267 505 28 4 7070 7572 717284186 717283686 0.000000e+00 739
30 TraesCS7A01G036500 chr4A 95.423 437 17 2 6452 6885 717223176 717222740 0.000000e+00 693
31 TraesCS7A01G036500 chr4A 95.423 437 17 1 6452 6885 717284644 717284208 0.000000e+00 693
32 TraesCS7A01G036500 chr4A 90.133 527 47 2 4 529 717288995 717288473 0.000000e+00 680
33 TraesCS7A01G036500 chr4A 95.385 195 8 1 6876 7070 717755547 717755740 7.380000e-80 309
34 TraesCS7A01G036500 chr4A 91.146 192 7 1 6879 7070 717222714 717222533 1.260000e-62 252
35 TraesCS7A01G036500 chr7B 92.403 4541 281 33 303 4808 655804609 655809120 0.000000e+00 6416
36 TraesCS7A01G036500 chr7B 94.792 2093 100 6 4800 6885 655811491 655813581 0.000000e+00 3253
37 TraesCS7A01G036500 chr7B 92.089 2288 152 21 1 2273 655749191 655751464 0.000000e+00 3195
38 TraesCS7A01G036500 chr7B 90.936 1710 117 14 577 2273 655662698 655664382 0.000000e+00 2265
39 TraesCS7A01G036500 chr7B 93.672 964 59 2 2 963 655706650 655707613 0.000000e+00 1441
40 TraesCS7A01G036500 chr7B 91.218 706 50 4 6876 7572 655813604 655814306 0.000000e+00 950


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 TraesCS7A01G036500 chr7A 16422707 16430278 7571 False 13983.000000 13983 100.000000 1 7572 1 chr7A.!!$F4 7571
1 TraesCS7A01G036500 chr7A 16377537 16382533 4996 False 7108.000000 7108 92.396000 1 4999 1 chr7A.!!$F2 4998
2 TraesCS7A01G036500 chr7A 16310356 16317909 7553 False 3436.000000 8240 93.216000 1 7359 3 chr7A.!!$F6 7358
3 TraesCS7A01G036500 chr7A 15816462 15822539 6077 True 2241.500000 4176 84.410500 4403 7572 2 chr7A.!!$R3 3169
4 TraesCS7A01G036500 chr7A 16393096 16394594 1498 False 2189.000000 2189 93.250000 6083 7572 1 chr7A.!!$F3 1489
5 TraesCS7A01G036500 chr7A 15774173 15775331 1158 True 1384.000000 1384 88.370000 4 1164 1 chr7A.!!$R1 1160
6 TraesCS7A01G036500 chr7A 15802298 15803456 1158 True 1384.000000 1384 88.370000 4 1164 1 chr7A.!!$R2 1160
7 TraesCS7A01G036500 chr7A 15832757 15836898 4141 True 1355.000000 2063 88.262500 556 4407 2 chr7A.!!$R4 3851
8 TraesCS7A01G036500 chr7D 16757358 16763863 6505 True 9601.000000 9601 93.446000 1112 7572 1 chr7D.!!$R1 6460
9 TraesCS7A01G036500 chr7D 17117423 17124735 7312 False 5213.500000 9134 93.417000 1 7045 2 chr7D.!!$F2 7044
10 TraesCS7A01G036500 chr7D 16991552 16996065 4513 False 3533.500000 6636 96.582000 488 6885 2 chr7D.!!$F1 6397
11 TraesCS7A01G036500 chr4A 717257177 717263657 6480 True 4798.000000 8615 93.140500 1112 7572 2 chr4A.!!$R3 6460
12 TraesCS7A01G036500 chr4A 717800570 717807124 6554 False 4602.500000 5967 92.229000 1112 7572 2 chr4A.!!$F3 6460
13 TraesCS7A01G036500 chr4A 717749943 717755740 5797 False 4247.000000 8185 94.447500 1192 7070 2 chr4A.!!$F2 5878
14 TraesCS7A01G036500 chr4A 717234750 717236579 1829 True 2649.000000 2649 92.857000 1192 3016 1 chr4A.!!$R1 1824
15 TraesCS7A01G036500 chr4A 717283686 717288995 5309 True 1646.250000 4473 93.073250 4 7572 4 chr4A.!!$R4 7568
16 TraesCS7A01G036500 chr4A 717222000 717225661 3661 True 1391.250000 3827 93.861000 3999 7572 4 chr4A.!!$R2 3573
17 TraesCS7A01G036500 chr4A 717817882 717818500 618 False 845.000000 845 91.304000 1 619 1 chr4A.!!$F1 618
18 TraesCS7A01G036500 chr7B 655804609 655814306 9697 False 3539.666667 6416 92.804333 303 7572 3 chr7B.!!$F4 7269
19 TraesCS7A01G036500 chr7B 655749191 655751464 2273 False 3195.000000 3195 92.089000 1 2273 1 chr7B.!!$F3 2272
20 TraesCS7A01G036500 chr7B 655662698 655664382 1684 False 2265.000000 2265 90.936000 577 2273 1 chr7B.!!$F1 1696
21 TraesCS7A01G036500 chr7B 655706650 655707613 963 False 1441.000000 1441 93.672000 2 963 1 chr7B.!!$F2 961

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
349 354 1.160137 GCACCTCACATTGACTCACC 58.840 55.000 0.00 0.0 0.00 4.02 F
1282 1653 0.389817 CACGACTGGCATCGGAGAAA 60.390 55.000 18.63 0.0 46.56 2.52 F
2188 2584 1.064463 CCCTTGCCTTGCCAAGAGATA 60.064 52.381 5.89 0.0 43.79 1.98 F
2808 3227 0.326927 CCCTTCCAAGACCGGCTTTA 59.673 55.000 0.00 0.0 33.60 1.85 F
3812 4635 0.109342 ATGGGCCGATAGCTTCCTTG 59.891 55.000 0.00 0.0 43.05 3.61 F
4269 5110 0.179094 GATTGCCGGTATCGTGGACA 60.179 55.000 1.90 0.0 33.95 4.02 F
4635 5486 0.849417 GGATCATCTTCCTTGGCCCT 59.151 55.000 0.00 0.0 32.68 5.19 F
4754 5609 1.032014 GTGTTGTTGGTGGATGTGCT 58.968 50.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2542 0.532573 GGAGACTGATCACAAGGCGA 59.467 55.000 0.00 0.0 0.00 5.54 R
2407 2823 0.259647 TGGCCCATGCAGCTAAAGAT 59.740 50.000 0.00 0.0 40.13 2.40 R
3812 4635 0.107848 ACATAGGTGTGTTAGGCGGC 60.108 55.000 0.00 0.0 37.14 6.53 R
4269 5110 0.842467 CAGGAGGTGGGGAAGGTCTT 60.842 60.000 0.00 0.0 0.00 3.01 R
5767 9015 0.607762 TGCGGGCTGCTGACAAATAA 60.608 50.000 20.66 0.0 46.63 1.40 R
5879 9127 1.072331 GCATCCTCATAATGACCCGGT 59.928 52.381 0.00 0.0 0.00 5.28 R
6209 9457 1.128692 CTCGAGCGTTTTCATCCAACC 59.871 52.381 0.00 0.0 0.00 3.77 R
6637 9983 0.253894 CCCAGGCACATCTGACATGA 59.746 55.000 0.00 0.0 36.93 3.07 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 3.515901 GAGGACACATAGGACAAAGAGGT 59.484 47.826 0.00 0.00 0.00 3.85
46 48 3.642755 GGGTGACGAGTGTTGCAG 58.357 61.111 0.00 0.00 0.00 4.41
128 131 4.006319 GGTTGACAAGGAGAATCAGGAAG 58.994 47.826 0.00 0.00 36.25 3.46
136 139 8.940397 ACAAGGAGAATCAGGAAGAAAAATAA 57.060 30.769 0.00 0.00 36.25 1.40
171 175 4.775236 ACAAGAATTCTAGGAGGACATGC 58.225 43.478 8.75 0.00 0.00 4.06
210 214 1.618345 CCTGTGTCTAGGAGTGGAGCT 60.618 57.143 0.00 0.00 40.42 4.09
349 354 1.160137 GCACCTCACATTGACTCACC 58.840 55.000 0.00 0.00 0.00 4.02
350 355 1.543208 GCACCTCACATTGACTCACCA 60.543 52.381 0.00 0.00 0.00 4.17
400 409 1.290203 CAACACGCACAACTCTCAGT 58.710 50.000 0.00 0.00 0.00 3.41
458 468 2.930019 CACCACTGGGAGAGGGCA 60.930 66.667 0.00 0.00 38.05 5.36
646 661 7.741554 AATATCCTATTAAGCCTCCACCTAG 57.258 40.000 0.00 0.00 0.00 3.02
669 684 6.546484 AGTCTCTTCTCCCATTGAATTTCAA 58.454 36.000 13.88 13.88 41.09 2.69
819 835 3.376546 GCACAATCTAGCCTCCTCTTTTG 59.623 47.826 0.00 0.00 0.00 2.44
970 987 1.501654 GCCACTTTCCCCCTCTCCTT 61.502 60.000 0.00 0.00 0.00 3.36
983 1000 2.503765 CCTCTCCTTTCTTTCTCTCCCC 59.496 54.545 0.00 0.00 0.00 4.81
984 1001 3.449918 CTCTCCTTTCTTTCTCTCCCCT 58.550 50.000 0.00 0.00 0.00 4.79
986 1003 2.167487 CTCCTTTCTTTCTCTCCCCTCG 59.833 54.545 0.00 0.00 0.00 4.63
988 1005 1.552792 CTTTCTTTCTCTCCCCTCGCT 59.447 52.381 0.00 0.00 0.00 4.93
1038 1322 1.153823 CTCGACATCCACACCGACC 60.154 63.158 0.00 0.00 0.00 4.79
1097 1384 2.234913 GAGACAACCGCGTGGGGTAT 62.235 60.000 21.14 14.26 40.11 2.73
1100 1387 0.542805 ACAACCGCGTGGGGTATTAT 59.457 50.000 21.14 0.00 40.11 1.28
1173 1499 0.613292 ATCTGGAGTCACCGCAGTCT 60.613 55.000 0.00 0.00 42.61 3.24
1231 1602 4.933134 TGATGATTGGTGATGGAGGAAAA 58.067 39.130 0.00 0.00 0.00 2.29
1282 1653 0.389817 CACGACTGGCATCGGAGAAA 60.390 55.000 18.63 0.00 46.56 2.52
1575 1953 4.150359 GGAGATTGGAATTCATGCTCCAT 58.850 43.478 21.31 3.64 41.36 3.41
1632 2010 7.067008 ACACTCAGCGCCTTTATAAATTTACAT 59.933 33.333 2.29 0.00 0.00 2.29
1724 2102 7.418254 GCTCTCCAAATCACATCCCAAATATTT 60.418 37.037 0.00 0.00 0.00 1.40
1806 2191 7.195374 TGGGTAGTTTATAAGCAAGTCATCT 57.805 36.000 1.97 0.00 0.00 2.90
2037 2429 3.005791 TCACTATACACCAGATGATGCCG 59.994 47.826 0.00 0.00 0.00 5.69
2064 2456 3.124560 GAGTATCTTAACTCCAAGCCGC 58.875 50.000 0.00 0.00 40.06 6.53
2074 2466 1.968017 CCAAGCCGCCGATGCATAT 60.968 57.895 0.00 0.00 37.32 1.78
2147 2542 9.793259 TTTCAAGACTCTGGAACATAAACTATT 57.207 29.630 0.00 0.00 38.20 1.73
2150 2545 6.043411 AGACTCTGGAACATAAACTATTCGC 58.957 40.000 0.00 0.00 38.20 4.70
2188 2584 1.064463 CCCTTGCCTTGCCAAGAGATA 60.064 52.381 5.89 0.00 43.79 1.98
2225 2621 4.021104 TGCATATCCCAGAATCCTAGAACG 60.021 45.833 0.00 0.00 0.00 3.95
2311 2708 1.921869 CGCCCCACCTAAAGTCCCAT 61.922 60.000 0.00 0.00 0.00 4.00
2316 2713 4.044191 GCCCCACCTAAAGTCCCATATAAT 59.956 45.833 0.00 0.00 0.00 1.28
2355 2771 4.080638 ACAAAAGCCCAAGGACATTTGAAA 60.081 37.500 9.53 0.00 33.30 2.69
2379 2795 7.881775 AAATCCAAAGAAGTAAGTGTGAAGT 57.118 32.000 0.00 0.00 0.00 3.01
2407 2823 5.924356 TGAACCACTTACTTGATCAAGACA 58.076 37.500 36.15 22.27 40.79 3.41
2632 3050 8.747538 AAATAATAAAGAGCATTTAGTCGGGT 57.252 30.769 0.00 0.00 0.00 5.28
2639 3057 5.801380 AGAGCATTTAGTCGGGTTAAGAAA 58.199 37.500 0.00 0.00 0.00 2.52
2677 3095 6.434028 CCTTTGAAATAGATTTGGAGTGTCCA 59.566 38.462 0.00 0.00 46.61 4.02
2748 3167 9.725019 TTGTCATCAACAAACATTAGTCTAGAT 57.275 29.630 0.00 0.00 44.83 1.98
2808 3227 0.326927 CCCTTCCAAGACCGGCTTTA 59.673 55.000 0.00 0.00 33.60 1.85
2819 3238 5.546621 AGACCGGCTTTATTAAGATGCTA 57.453 39.130 0.00 0.00 32.92 3.49
2826 3245 6.116126 GGCTTTATTAAGATGCTATCCCGAT 58.884 40.000 0.00 0.00 32.92 4.18
2981 3677 2.273449 CAGTCATGGCCAGGGACC 59.727 66.667 27.74 13.73 31.99 4.46
3021 3717 4.822026 CGATGGTACTCTTTCCCATATCC 58.178 47.826 0.00 0.00 39.06 2.59
3029 3725 7.181125 GGTACTCTTTCCCATATCCACTCATAT 59.819 40.741 0.00 0.00 0.00 1.78
3079 3776 2.899900 TGGTCTGTCTCTGTATTGCAGT 59.100 45.455 1.55 0.00 45.23 4.40
3096 3796 4.093743 TGCAGTCATAGAGGAAAGTGGTA 58.906 43.478 0.00 0.00 0.00 3.25
3114 3814 4.027437 TGGTAGGAGCATATGTGTGTACA 58.973 43.478 4.29 0.00 41.89 2.90
3118 3818 5.165961 AGGAGCATATGTGTGTACAACTT 57.834 39.130 4.29 0.00 40.84 2.66
3122 3822 6.149474 GGAGCATATGTGTGTACAACTTTTCT 59.851 38.462 4.29 0.00 40.84 2.52
3174 3874 3.491447 GCAACTGCACTTTCAACCTGATT 60.491 43.478 0.00 0.00 41.59 2.57
3184 3884 5.593909 ACTTTCAACCTGATTGTCACATTGA 59.406 36.000 0.00 0.00 39.54 2.57
3308 4008 4.470602 TCTCGGATATCCAAGCTACTGAA 58.529 43.478 21.70 0.00 35.14 3.02
3328 4030 1.521450 AAGTGCTCATGCTGCCACAC 61.521 55.000 8.34 4.64 40.48 3.82
3582 4396 5.045215 CACCATCATGCACAATACAATTCC 58.955 41.667 0.00 0.00 0.00 3.01
3597 4411 2.368875 CAATTCCGGTGGCCTAGTATCT 59.631 50.000 3.32 0.00 0.00 1.98
3609 4423 7.122501 GGTGGCCTAGTATCTACCTAAGATTAC 59.877 44.444 3.32 0.00 42.62 1.89
3684 4498 1.024046 TATGTGCGCACGAGGCAAAT 61.024 50.000 33.22 21.68 45.17 2.32
3708 4522 3.456277 AGCTCTTCAACTATCCGGGATTT 59.544 43.478 15.98 1.04 0.00 2.17
3752 4574 8.503573 TCTAGATTAGGTGACTCATTTCTCCTA 58.496 37.037 0.00 0.00 43.67 2.94
3812 4635 0.109342 ATGGGCCGATAGCTTCCTTG 59.891 55.000 0.00 0.00 43.05 3.61
3962 4797 0.485099 ATTTACCCAACACTGCCCCA 59.515 50.000 0.00 0.00 0.00 4.96
3963 4798 0.468400 TTTACCCAACACTGCCCCAC 60.468 55.000 0.00 0.00 0.00 4.61
3970 4805 0.185901 AACACTGCCCCACTGTTCAT 59.814 50.000 0.00 0.00 0.00 2.57
4269 5110 0.179094 GATTGCCGGTATCGTGGACA 60.179 55.000 1.90 0.00 33.95 4.02
4382 5223 7.340122 TGTTTTGTTTGGAACATGATGTAGA 57.660 32.000 0.00 0.00 41.79 2.59
4393 5235 1.655484 TGATGTAGATGGTGCTTGCG 58.345 50.000 0.00 0.00 0.00 4.85
4407 5249 1.218875 CTTGCGTGTCACGTGGCTTA 61.219 55.000 25.18 0.00 44.73 3.09
4461 5311 6.882656 ACATGTACTAGTAGGAGTTCGAGTA 58.117 40.000 1.87 0.00 0.00 2.59
4470 5320 4.602340 AGGAGTTCGAGTAAAGCTTGAA 57.398 40.909 0.00 0.00 43.44 2.69
4611 5462 2.281761 CTCCACCGTGCAAGGCTT 60.282 61.111 19.37 0.00 33.69 4.35
4635 5486 0.849417 GGATCATCTTCCTTGGCCCT 59.151 55.000 0.00 0.00 32.68 5.19
4691 5546 3.632189 GCTCATCGCACTTTTGTTCTTT 58.368 40.909 0.00 0.00 38.92 2.52
4699 5554 5.297278 TCGCACTTTTGTTCTTTTTAGCCTA 59.703 36.000 0.00 0.00 0.00 3.93
4754 5609 1.032014 GTGTTGTTGGTGGATGTGCT 58.968 50.000 0.00 0.00 0.00 4.40
4886 8124 5.871531 AATGTTGATGAAATTTATCGCGC 57.128 34.783 0.00 0.00 0.00 6.86
5065 8304 6.459670 TTTCGATGGCAATACTGTAGTCTA 57.540 37.500 0.00 0.00 0.00 2.59
5070 8314 7.119407 TCGATGGCAATACTGTAGTCTATACTC 59.881 40.741 0.00 0.00 37.15 2.59
5071 8315 7.119992 CGATGGCAATACTGTAGTCTATACTCT 59.880 40.741 0.00 0.00 37.15 3.24
5072 8316 9.451002 GATGGCAATACTGTAGTCTATACTCTA 57.549 37.037 0.00 0.00 37.15 2.43
5073 8317 8.618702 TGGCAATACTGTAGTCTATACTCTAC 57.381 38.462 0.00 0.00 37.15 2.59
5074 8318 7.664731 TGGCAATACTGTAGTCTATACTCTACC 59.335 40.741 0.00 0.00 37.15 3.18
5080 8324 7.432869 ACTGTAGTCTATACTCTACCGTGTAG 58.567 42.308 5.09 5.09 34.86 2.74
5245 8493 8.192774 TCATGATCCTTAATGCAGAATTTGAAC 58.807 33.333 0.00 0.00 0.00 3.18
5268 8516 7.356089 ACCTGATATCATGCAAAACATCAAT 57.644 32.000 5.72 0.00 36.64 2.57
5424 8672 2.140405 CTGCCCTAGCTGGTATGCT 58.860 57.895 0.00 0.00 46.11 3.79
5451 8699 7.434307 GCATTCATGTCAATCAAATCTACCTTG 59.566 37.037 0.00 0.00 0.00 3.61
5506 8754 1.301716 GCCGACCAGACAAGCTCAA 60.302 57.895 0.00 0.00 0.00 3.02
5538 8786 1.619654 TTGGAAACACATGGGAGCTG 58.380 50.000 0.00 0.00 42.67 4.24
5747 8995 5.529060 GCTACAAAACCTTCATATCTCCAGG 59.471 44.000 0.00 0.00 0.00 4.45
5767 9015 2.487265 GGGGCGTCACCAGATTCATATT 60.487 50.000 0.00 0.00 42.05 1.28
5865 9113 7.649533 AAATGCACATTTGATCAAGGAGATA 57.350 32.000 8.41 0.00 39.36 1.98
5871 9119 7.877097 GCACATTTGATCAAGGAGATAGTATCT 59.123 37.037 12.62 12.62 43.70 1.98
6014 9262 1.605202 CGGAAATTTGGTGGCTTGTGG 60.605 52.381 0.00 0.00 0.00 4.17
6074 9322 4.963318 TCTCCATTGACTTCTCAACTGT 57.037 40.909 0.00 0.00 39.28 3.55
6112 9360 1.301293 GTGGAAGAGGGAGGCTTGG 59.699 63.158 0.00 0.00 0.00 3.61
6209 9457 1.146263 GGGGTGGCCTTGTCTATCG 59.854 63.158 3.32 0.00 0.00 2.92
6312 9560 3.363378 CGACGATCAATGCTTATCTTGCC 60.363 47.826 0.00 0.00 0.00 4.52
6351 9599 1.506493 CAGCTTGGGTATGAGATCGC 58.494 55.000 0.00 0.00 0.00 4.58
6403 9653 1.378762 GGCTGCACTTGGGGACTTA 59.621 57.895 0.50 0.00 0.00 2.24
6708 10055 7.217200 TGGTCCATACATCTATTTGTAGCTTC 58.783 38.462 0.00 0.00 35.65 3.86
6819 10166 3.882888 TCTGTCTGCCTAGTTTTTGTTGG 59.117 43.478 0.00 0.00 0.00 3.77
6820 10167 3.626930 TGTCTGCCTAGTTTTTGTTGGT 58.373 40.909 0.00 0.00 0.00 3.67
6991 10377 6.769822 CCCAAGCTATGTTCTCAATATTCACT 59.230 38.462 0.00 0.00 0.00 3.41
7120 10560 1.285962 AGCCCATGTTATCAAGTGCCT 59.714 47.619 0.00 0.00 0.00 4.75
7136 10576 6.042322 TCAAGTGCCTAGGTACAAGAAAACTA 59.958 38.462 28.92 4.09 33.14 2.24
7176 10616 8.506083 AGATGAGAAATAAAACATATGGGTCCT 58.494 33.333 7.80 0.00 0.00 3.85
7262 10706 5.236655 TGTAATGCAAGTTTCGAAACACA 57.763 34.783 35.29 29.28 41.30 3.72
7427 10873 3.230134 CCCAGGTTGACTCCAATTTCAA 58.770 45.455 0.00 0.00 34.39 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.114625 ACTCGTCACCCGACCTCA 59.885 61.111 0.00 0.00 41.60 3.86
46 48 3.134574 TGGTTGTGACCTCCATAACAC 57.865 47.619 0.00 0.00 45.26 3.32
121 123 4.295141 TCGCCCTTATTTTTCTTCCTGA 57.705 40.909 0.00 0.00 0.00 3.86
128 131 4.634443 TGTAGCTCTTCGCCCTTATTTTTC 59.366 41.667 0.00 0.00 40.39 2.29
136 139 1.267121 TTCTTGTAGCTCTTCGCCCT 58.733 50.000 0.00 0.00 40.39 5.19
171 175 1.469940 GGATGTCAGCGTGAGGTACTG 60.470 57.143 0.00 0.00 41.55 2.74
226 230 1.077716 GCCAATGCCCTTACCTCGT 60.078 57.895 0.00 0.00 0.00 4.18
245 249 9.254133 CTGTATACAAATAGTGAACCATCAGAG 57.746 37.037 7.06 0.00 35.88 3.35
422 431 2.529744 GGCCCACTTCTCACCCTGT 61.530 63.158 0.00 0.00 0.00 4.00
458 468 3.927142 CGTCCTCTCGTTTAAATTGCTCT 59.073 43.478 0.00 0.00 0.00 4.09
556 571 5.369699 TGGAGGCTTAATAGGAAGTTAGCAT 59.630 40.000 0.00 0.00 0.00 3.79
625 640 5.088026 GACTAGGTGGAGGCTTAATAGGAT 58.912 45.833 0.00 0.00 0.00 3.24
646 661 6.127786 CCTTGAAATTCAATGGGAGAAGAGAC 60.128 42.308 9.02 0.00 35.59 3.36
819 835 8.703604 TGAGATGCACAAACTCTATTACTAAC 57.296 34.615 0.00 0.00 0.00 2.34
970 987 1.187087 GAGCGAGGGGAGAGAAAGAA 58.813 55.000 0.00 0.00 0.00 2.52
983 1000 0.650512 GTGACGAGAGAGAGAGCGAG 59.349 60.000 0.00 0.00 0.00 5.03
984 1001 0.037232 TGTGACGAGAGAGAGAGCGA 60.037 55.000 0.00 0.00 0.00 4.93
986 1003 1.135803 GTGTGTGACGAGAGAGAGAGC 60.136 57.143 0.00 0.00 0.00 4.09
1073 1360 2.105528 ACGCGGTTGTCTCAACGT 59.894 55.556 12.47 0.00 0.00 3.99
1097 1384 3.446161 AGATCTGGACGGAAACACGATAA 59.554 43.478 0.00 0.00 37.61 1.75
1100 1387 1.067846 CAGATCTGGACGGAAACACGA 60.068 52.381 15.38 0.00 37.61 4.35
1173 1499 3.395630 GGGGAAACAGACGCCCTA 58.604 61.111 0.00 0.00 41.72 3.53
1282 1653 2.548067 CGAAGTGGAGGCAACAACTACT 60.548 50.000 0.00 0.00 38.20 2.57
1410 1784 8.110860 ACAAGTATAGTGTTTTCCCTCAATTG 57.889 34.615 0.00 0.00 0.00 2.32
1451 1825 4.345837 CCCCCATGTCTAATGATTGCAATT 59.654 41.667 14.33 0.70 0.00 2.32
1632 2010 2.304470 TGGCTCACTGGCTACACAATTA 59.696 45.455 0.00 0.00 42.34 1.40
1724 2102 7.549134 AGTTCTTCAAGTGCGACATATAATTGA 59.451 33.333 0.00 0.00 0.00 2.57
1837 2222 7.928307 TTTTCTGATTTTGATGTAGAGGAGG 57.072 36.000 0.00 0.00 0.00 4.30
2037 2429 5.813157 GCTTGGAGTTAAGATACTCAAGGAC 59.187 44.000 6.17 0.00 45.07 3.85
2064 2456 3.438087 GGTCATTTCCTCATATGCATCGG 59.562 47.826 0.19 0.00 0.00 4.18
2074 2466 6.373005 TTTCTAGACATGGTCATTTCCTCA 57.627 37.500 0.00 0.00 34.60 3.86
2147 2542 0.532573 GGAGACTGATCACAAGGCGA 59.467 55.000 0.00 0.00 0.00 5.54
2150 2545 1.065854 GGGTGGAGACTGATCACAAGG 60.066 57.143 0.00 0.00 33.45 3.61
2188 2584 7.949565 TCTGGGATATGCATATGTTTAACCAAT 59.050 33.333 23.76 0.00 0.00 3.16
2225 2621 3.562557 TGGTAAAACAAAAGAGAGGACGC 59.437 43.478 0.00 0.00 0.00 5.19
2256 2652 2.237143 CACAAGTCCATTGGCTCTCCTA 59.763 50.000 0.00 0.00 43.68 2.94
2355 2771 7.254795 CGACTTCACACTTACTTCTTTGGATTT 60.255 37.037 0.00 0.00 0.00 2.17
2374 2790 2.325583 AAGTGGTTCAAGCGACTTCA 57.674 45.000 0.00 0.00 0.00 3.02
2379 2795 3.462483 TCAAGTAAGTGGTTCAAGCGA 57.538 42.857 0.00 0.00 0.00 4.93
2407 2823 0.259647 TGGCCCATGCAGCTAAAGAT 59.740 50.000 0.00 0.00 40.13 2.40
2627 3045 7.037438 GTGTACATGATAGTTTCTTAACCCGA 58.963 38.462 0.00 0.00 34.71 5.14
2677 3095 3.628769 GGAAGAGAGGTGAGGGTAGTGAT 60.629 52.174 0.00 0.00 0.00 3.06
2743 3162 1.249407 GGGAGCCTCGGTGTATCTAG 58.751 60.000 0.00 0.00 0.00 2.43
2748 3167 3.549433 TTGGGGGAGCCTCGGTGTA 62.549 63.158 0.00 0.00 0.00 2.90
2808 3227 6.580788 CAGATGATCGGGATAGCATCTTAAT 58.419 40.000 9.10 0.00 43.47 1.40
2819 3238 0.839277 TGGTTGCAGATGATCGGGAT 59.161 50.000 0.00 0.00 0.00 3.85
2981 3677 0.457851 CGCTGGAGGGAACTACTGAG 59.542 60.000 0.00 0.00 44.03 3.35
3021 3717 4.445718 CGTGAAATCCTTCCGATATGAGTG 59.554 45.833 0.00 0.00 31.05 3.51
3029 3725 1.153353 GCAACGTGAAATCCTTCCGA 58.847 50.000 0.00 0.00 32.72 4.55
3079 3776 3.961408 GCTCCTACCACTTTCCTCTATGA 59.039 47.826 0.00 0.00 0.00 2.15
3096 3796 4.826274 AGTTGTACACACATATGCTCCT 57.174 40.909 1.58 0.00 33.76 3.69
3114 3814 8.787852 GGTGTGATTTATTCAGAGAGAAAAGTT 58.212 33.333 0.00 0.00 40.22 2.66
3118 3818 7.174946 GGTTGGTGTGATTTATTCAGAGAGAAA 59.825 37.037 0.00 0.00 40.22 2.52
3122 3822 5.253330 GGGTTGGTGTGATTTATTCAGAGA 58.747 41.667 0.00 0.00 34.17 3.10
3174 3874 5.243507 ACAGTATGGCAAAATCAATGTGACA 59.756 36.000 0.00 0.00 43.62 3.58
3308 4008 0.824595 TGTGGCAGCATGAGCACTTT 60.825 50.000 11.88 0.00 45.49 2.66
3328 4030 7.657354 TGATGATAGGTGATTTTTATGAGACGG 59.343 37.037 0.00 0.00 0.00 4.79
3467 4170 9.330063 TGAGGTACATCAATGTCTTAATTCATC 57.670 33.333 7.95 0.00 41.97 2.92
3557 4371 6.461927 GGAATTGTATTGTGCATGATGGTGAT 60.462 38.462 0.00 0.00 0.00 3.06
3559 4373 5.045215 GGAATTGTATTGTGCATGATGGTG 58.955 41.667 0.00 0.00 0.00 4.17
3582 4396 2.289592 AGGTAGATACTAGGCCACCG 57.710 55.000 5.01 0.00 0.00 4.94
3684 4498 3.638860 TCCCGGATAGTTGAAGAGCTAA 58.361 45.455 0.73 0.00 0.00 3.09
3708 4522 1.774217 AACTGTTGGGGCCTCAGGA 60.774 57.895 4.89 0.00 34.02 3.86
3752 4574 1.282157 GTGATAGGGAAGGCACCTGTT 59.718 52.381 5.77 0.00 39.12 3.16
3812 4635 0.107848 ACATAGGTGTGTTAGGCGGC 60.108 55.000 0.00 0.00 37.14 6.53
3962 4797 4.849813 TGATCAATCCCTGATGAACAGT 57.150 40.909 0.00 0.00 45.23 3.55
3970 4805 5.488919 AGGAAGTAAGTTGATCAATCCCTGA 59.511 40.000 12.12 0.00 38.81 3.86
4146 4981 3.465403 CTGGAGGGCGGAGGTGAG 61.465 72.222 0.00 0.00 0.00 3.51
4214 5050 6.128200 TGCTTGTATGTACAAATCAGAGCAAG 60.128 38.462 15.15 13.06 44.67 4.01
4269 5110 0.842467 CAGGAGGTGGGGAAGGTCTT 60.842 60.000 0.00 0.00 0.00 3.01
4382 5223 2.606961 CGTGACACGCAAGCACCAT 61.607 57.895 16.06 0.00 45.62 3.55
4393 5235 2.480845 AGAACTTAAGCCACGTGACAC 58.519 47.619 19.30 6.08 0.00 3.67
4407 5249 4.529716 TTGGTTAGTCCCCAAAGAACTT 57.470 40.909 0.00 0.00 38.98 2.66
4691 5546 2.843730 TCCATGGCAGAGTTAGGCTAAA 59.156 45.455 8.86 0.00 0.00 1.85
4699 5554 3.028850 CCAAATCATCCATGGCAGAGTT 58.971 45.455 6.96 9.88 0.00 3.01
4844 8079 9.985318 CAACATTTGAAATTAAAAAGTGCAAGA 57.015 25.926 0.00 0.00 0.00 3.02
4886 8124 2.974698 GATTCCGGGCCGCAGATG 60.975 66.667 23.20 6.60 0.00 2.90
4971 8210 8.257306 ACATTTGAAAAGAAAAGGCAAGTTCTA 58.743 29.630 0.00 0.00 32.90 2.10
5245 8493 6.581166 CGATTGATGTTTTGCATGATATCAGG 59.419 38.462 12.98 12.98 38.06 3.86
5268 8516 3.319198 GGGGTGTTGGAGCTCCGA 61.319 66.667 27.43 23.72 39.43 4.55
5424 8672 6.604396 AGGTAGATTTGATTGACATGAATGCA 59.396 34.615 0.00 0.00 0.00 3.96
5451 8699 4.475135 GGTGGGAAGAGCTCGCCC 62.475 72.222 30.11 30.11 42.12 6.13
5506 8754 3.821033 GTGTTTCCAATGTTAGAGCCAGT 59.179 43.478 0.00 0.00 0.00 4.00
5538 8786 8.254508 GGAGTACTTGGATATACAGGATCAATC 58.745 40.741 3.66 0.00 0.00 2.67
5747 8995 2.550830 ATATGAATCTGGTGACGCCC 57.449 50.000 1.74 0.00 36.04 6.13
5767 9015 0.607762 TGCGGGCTGCTGACAAATAA 60.608 50.000 20.66 0.00 46.63 1.40
5865 9113 3.581332 TGACCCGGTCTTTGAAAGATACT 59.419 43.478 18.54 0.00 40.18 2.12
5871 9119 4.912586 TCATAATGACCCGGTCTTTGAAA 58.087 39.130 22.91 8.68 33.22 2.69
5879 9127 1.072331 GCATCCTCATAATGACCCGGT 59.928 52.381 0.00 0.00 0.00 5.28
5976 9224 1.291272 GGAAAGCACGTACGGGTCT 59.709 57.895 20.35 13.74 0.00 3.85
6014 9262 3.574826 ACCAAGTAGGAGAAGTGTGTCTC 59.425 47.826 0.00 0.00 42.90 3.36
6074 9322 2.028476 ACGCTCACATACTTTGCAGGTA 60.028 45.455 4.50 4.50 0.00 3.08
6112 9360 3.917072 AGAAGAACGCCCACTTCTC 57.083 52.632 0.00 0.00 46.28 2.87
6209 9457 1.128692 CTCGAGCGTTTTCATCCAACC 59.871 52.381 0.00 0.00 0.00 3.77
6312 9560 3.004024 GCAAAGGATGTATGATTGCGG 57.996 47.619 0.00 0.00 37.27 5.69
6403 9653 5.599999 ACTAGAAGGAACATAGCGACAAT 57.400 39.130 0.00 0.00 0.00 2.71
6637 9983 0.253894 CCCAGGCACATCTGACATGA 59.746 55.000 0.00 0.00 36.93 3.07
6991 10377 3.117701 TGACAGTCTCATTGGGTGGAAAA 60.118 43.478 1.31 0.00 0.00 2.29
7080 10520 3.561528 GCTAGGCCTGTAACTTCCCTTTT 60.562 47.826 17.99 0.00 0.00 2.27
7120 10560 8.426489 ACAGATTGTGTAGTTTTCTTGTACCTA 58.574 33.333 0.00 0.00 37.75 3.08
7176 10616 3.627732 TTTTTCTGCGGCGATTACAAA 57.372 38.095 12.98 0.00 0.00 2.83
7262 10706 5.380043 AGTGGTTCACTGAATGTTCTTGAT 58.620 37.500 0.00 0.00 43.63 2.57
7427 10873 2.313317 TCAACACTGGAAGACGGTACT 58.687 47.619 0.00 0.00 36.76 2.73


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

AutoCloner maintained by Alex Coulton.