Multiple sequence alignment - TraesCS7B01G220700

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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 TraesCS7B01G220700 chr7B 100.000 4167 0 0 1763 5929 412075202 412079368 0.000000e+00 7696.0
1 TraesCS7B01G220700 chr7B 100.000 1489 0 0 1 1489 412073440 412074928 0.000000e+00 2750.0
2 TraesCS7B01G220700 chr7B 90.200 949 75 13 2493 3435 411874584 411875520 0.000000e+00 1221.0
3 TraesCS7B01G220700 chr7B 91.562 557 43 3 3525 4078 411875519 411876074 0.000000e+00 765.0
4 TraesCS7B01G220700 chr7B 91.228 399 33 2 4074 4472 411879285 411879681 5.230000e-150 542.0
5 TraesCS7B01G220700 chr7B 100.000 41 0 0 1 41 221800673 221800713 6.370000e-10 76.8
6 TraesCS7B01G220700 chr7B 100.000 41 0 0 1 41 741255376 741255336 6.370000e-10 76.8
7 TraesCS7B01G220700 chr7B 92.857 42 2 1 692 732 411789818 411789859 6.420000e-05 60.2
8 TraesCS7B01G220700 chr7D 95.285 3054 118 12 1763 4802 402511129 402514170 0.000000e+00 4819.0
9 TraesCS7B01G220700 chr7D 91.307 1599 107 17 2361 3939 402346034 402347620 0.000000e+00 2154.0
10 TraesCS7B01G220700 chr7D 92.063 1071 46 15 4865 5929 402514410 402515447 0.000000e+00 1471.0
11 TraesCS7B01G220700 chr7D 90.604 745 27 9 562 1303 402510059 402510763 0.000000e+00 948.0
12 TraesCS7B01G220700 chr7D 91.408 547 17 6 42 564 402509477 402510017 0.000000e+00 723.0
13 TraesCS7B01G220700 chr7D 96.040 202 7 1 1288 1489 402510858 402511058 1.590000e-85 327.0
14 TraesCS7B01G220700 chr7D 95.238 42 1 1 692 732 402345828 402345869 1.380000e-06 65.8
15 TraesCS7B01G220700 chr7A 87.405 2906 290 38 1958 4825 460726188 460729055 0.000000e+00 3269.0
16 TraesCS7B01G220700 chr7A 91.232 2395 159 19 2201 4567 460441069 460443440 0.000000e+00 3212.0
17 TraesCS7B01G220700 chr7A 88.076 847 78 15 5098 5929 460730209 460731047 0.000000e+00 983.0
18 TraesCS7B01G220700 chr7A 86.611 844 65 23 681 1489 460725065 460725895 0.000000e+00 889.0
19 TraesCS7B01G220700 chr7A 85.950 847 88 19 5103 5929 460444874 460445709 0.000000e+00 876.0
20 TraesCS7B01G220700 chr7A 91.349 393 24 7 1763 2155 460333012 460333394 4.070000e-146 529.0
21 TraesCS7B01G220700 chr7A 90.833 240 19 3 4865 5103 460443897 460444134 9.590000e-83 318.0
22 TraesCS7B01G220700 chr7A 91.371 197 17 0 994 1190 460319156 460319352 2.720000e-68 270.0
23 TraesCS7B01G220700 chr7A 85.356 239 16 10 4868 5103 460729284 460729506 4.620000e-56 230.0
24 TraesCS7B01G220700 chr7A 88.421 190 10 3 371 551 460724727 460724913 1.000000e-52 219.0
25 TraesCS7B01G220700 chr7A 94.309 123 6 1 38 159 460724032 460724154 2.820000e-43 187.0
26 TraesCS7B01G220700 chr7A 83.133 166 18 4 1323 1487 460332803 460332959 6.190000e-30 143.0
27 TraesCS7B01G220700 chr7A 91.304 92 8 0 5012 5103 460704353 460704444 6.240000e-25 126.0
28 TraesCS7B01G220700 chr7A 86.792 106 8 3 427 531 460317898 460317998 4.860000e-21 113.0
29 TraesCS7B01G220700 chr7A 100.000 42 0 0 1 42 93070625 93070666 1.770000e-10 78.7
30 TraesCS7B01G220700 chr7A 97.500 40 1 0 693 732 460318181 460318220 1.070000e-07 69.4
31 TraesCS7B01G220700 chr7A 100.000 29 0 0 1193 1221 460332646 460332674 3.000000e-03 54.7
32 TraesCS7B01G220700 chr3A 100.000 42 0 0 1 42 572335386 572335345 1.770000e-10 78.7
33 TraesCS7B01G220700 chr5A 100.000 41 0 0 1 41 546353152 546353112 6.370000e-10 76.8
34 TraesCS7B01G220700 chr4B 100.000 41 0 0 1 41 22820661 22820701 6.370000e-10 76.8
35 TraesCS7B01G220700 chr4A 100.000 41 0 0 1 41 90880026 90880066 6.370000e-10 76.8
36 TraesCS7B01G220700 chr4A 100.000 41 0 0 1 41 695864255 695864295 6.370000e-10 76.8
37 TraesCS7B01G220700 chr2B 100.000 41 0 0 1 41 38050917 38050957 6.370000e-10 76.8


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 TraesCS7B01G220700 chr7B 412073440 412079368 5928 False 5223.000000 7696 100.000000 1 5929 2 chr7B.!!$F4 5928
1 TraesCS7B01G220700 chr7B 411874584 411879681 5097 False 842.666667 1221 90.996667 2493 4472 3 chr7B.!!$F3 1979
2 TraesCS7B01G220700 chr7D 402509477 402515447 5970 False 1657.600000 4819 93.080000 42 5929 5 chr7D.!!$F2 5887
3 TraesCS7B01G220700 chr7D 402345828 402347620 1792 False 1109.900000 2154 93.272500 692 3939 2 chr7D.!!$F1 3247
4 TraesCS7B01G220700 chr7A 460441069 460445709 4640 False 1468.666667 3212 89.338333 2201 5929 3 chr7A.!!$F5 3728
5 TraesCS7B01G220700 chr7A 460724032 460731047 7015 False 962.833333 3269 88.363000 38 5929 6 chr7A.!!$F6 5891
6 TraesCS7B01G220700 chr7A 460332646 460333394 748 False 242.233333 529 91.494000 1193 2155 3 chr7A.!!$F4 962

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
21 22 0.178990 AGAGGGTTGTGCTGGTTTCC 60.179 55.0 0.00 0.00 0.00 3.13 F
1395 2023 0.321653 GGACAGGGCCACAACTACTG 60.322 60.0 6.18 2.81 35.40 2.74 F
2177 2846 0.178961 ACCAAGAAAGGCCCAACTCC 60.179 55.0 0.00 0.00 0.00 3.85 F
3080 3785 0.179018 CCCCCAATCCCGAGTTCATC 60.179 60.0 0.00 0.00 0.00 2.92 F
4295 8231 1.632589 GCACCTTCAAGGGACCAATT 58.367 50.0 8.75 0.00 40.58 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2442 1.001293 AGCAGAGACTTCGATGCACAA 59.999 47.619 8.95 0.0 41.14 3.33 R
3147 3852 3.818961 ACGCAAGAACATCAGAACATG 57.181 42.857 0.00 0.0 43.62 3.21 R
4016 4734 1.909700 TGGAACATTGAGCCCTTCAC 58.090 50.000 0.00 0.0 34.94 3.18 R
4763 8704 0.251474 ACGGGCCATACGGATAGCTA 60.251 55.000 4.39 0.0 35.23 3.32 R
5575 10492 7.201435 GCACTTAAGAAACAGAAACCACAAAAG 60.201 37.037 10.09 0.0 0.00 2.27 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
19 20 2.568623 CTAGAGGGTTGTGCTGGTTT 57.431 50.000 0.00 0.00 0.00 3.27
20 21 2.427506 CTAGAGGGTTGTGCTGGTTTC 58.572 52.381 0.00 0.00 0.00 2.78
21 22 0.178990 AGAGGGTTGTGCTGGTTTCC 60.179 55.000 0.00 0.00 0.00 3.13
22 23 1.152546 AGGGTTGTGCTGGTTTCCC 60.153 57.895 0.00 0.00 35.56 3.97
23 24 1.456705 GGGTTGTGCTGGTTTCCCA 60.457 57.895 0.00 0.00 38.87 4.37
24 25 1.045911 GGGTTGTGCTGGTTTCCCAA 61.046 55.000 0.00 0.00 41.27 4.12
25 26 0.827368 GGTTGTGCTGGTTTCCCAAA 59.173 50.000 0.00 0.00 41.27 3.28
26 27 1.208293 GGTTGTGCTGGTTTCCCAAAA 59.792 47.619 0.00 0.00 41.27 2.44
27 28 2.276201 GTTGTGCTGGTTTCCCAAAAC 58.724 47.619 0.00 0.00 41.27 2.43
28 29 1.859302 TGTGCTGGTTTCCCAAAACT 58.141 45.000 1.53 0.00 43.55 2.66
29 30 2.183679 TGTGCTGGTTTCCCAAAACTT 58.816 42.857 1.53 0.00 43.55 2.66
30 31 3.366396 TGTGCTGGTTTCCCAAAACTTA 58.634 40.909 1.53 0.00 43.55 2.24
31 32 3.964031 TGTGCTGGTTTCCCAAAACTTAT 59.036 39.130 1.53 0.00 43.55 1.73
32 33 4.407296 TGTGCTGGTTTCCCAAAACTTATT 59.593 37.500 1.53 0.00 43.55 1.40
33 34 4.749598 GTGCTGGTTTCCCAAAACTTATTG 59.250 41.667 1.53 0.00 43.55 1.90
34 35 4.407296 TGCTGGTTTCCCAAAACTTATTGT 59.593 37.500 1.53 0.00 43.55 2.71
35 36 4.988540 GCTGGTTTCCCAAAACTTATTGTC 59.011 41.667 1.53 0.00 43.55 3.18
36 37 5.221441 GCTGGTTTCCCAAAACTTATTGTCT 60.221 40.000 1.53 0.00 43.55 3.41
37 38 6.685368 GCTGGTTTCCCAAAACTTATTGTCTT 60.685 38.462 1.53 0.00 43.55 3.01
38 39 7.470841 GCTGGTTTCCCAAAACTTATTGTCTTA 60.471 37.037 1.53 0.00 43.55 2.10
39 40 7.718525 TGGTTTCCCAAAACTTATTGTCTTAC 58.281 34.615 1.53 0.00 43.55 2.34
40 41 7.342284 TGGTTTCCCAAAACTTATTGTCTTACA 59.658 33.333 1.53 0.00 43.55 2.41
67 68 0.603569 ATTCCACGAGAGCTCAACGT 59.396 50.000 25.35 25.35 40.87 3.99
78 79 1.344438 AGCTCAACGTGGAAGACATGA 59.656 47.619 0.00 0.00 39.46 3.07
90 91 4.223700 TGGAAGACATGACAGCTGATTAGT 59.776 41.667 23.35 13.27 0.00 2.24
165 201 4.968259 TGCAAGTGGAGTGTTTATGTACT 58.032 39.130 0.00 0.00 0.00 2.73
166 202 6.014925 TCTGCAAGTGGAGTGTTTATGTACTA 60.015 38.462 0.00 0.00 34.87 1.82
241 289 2.874701 CGCAAGATTCTCCTAACCATGG 59.125 50.000 11.19 11.19 43.02 3.66
255 303 3.463048 ACCATGGCAAGAGGAGAATTT 57.537 42.857 13.04 0.00 0.00 1.82
258 306 3.118884 CCATGGCAAGAGGAGAATTTTGG 60.119 47.826 0.00 0.00 0.00 3.28
323 371 0.668706 ACAGACGAGTGTGAGCATGC 60.669 55.000 10.51 10.51 0.00 4.06
356 408 4.077982 AGACCTCCATTAATACCCCAGAGA 60.078 45.833 0.00 0.00 0.00 3.10
357 409 4.235372 ACCTCCATTAATACCCCAGAGAG 58.765 47.826 0.00 0.00 0.00 3.20
358 410 4.077982 ACCTCCATTAATACCCCAGAGAGA 60.078 45.833 0.00 0.00 0.00 3.10
359 411 4.530161 CCTCCATTAATACCCCAGAGAGAG 59.470 50.000 0.00 0.00 0.00 3.20
379 743 6.384015 AGAGAGAGAGAGAGAGAGTTGACATA 59.616 42.308 0.00 0.00 0.00 2.29
413 786 4.262121 CCAAAACAAGGCAGAATGTGATCA 60.262 41.667 0.00 0.00 39.31 2.92
443 816 2.967362 TGTGTGTTCGAGTGTCAAACT 58.033 42.857 0.00 0.00 43.85 2.66
588 1005 4.215349 CTGGCCAGAGCAAGCTAC 57.785 61.111 29.88 0.00 42.56 3.58
590 1007 2.266055 GGCCAGAGCAAGCTACGT 59.734 61.111 0.00 0.00 42.56 3.57
591 1008 1.254975 TGGCCAGAGCAAGCTACGTA 61.255 55.000 0.00 0.00 42.56 3.57
592 1009 0.528684 GGCCAGAGCAAGCTACGTAG 60.529 60.000 18.47 18.47 42.56 3.51
593 1010 0.528684 GCCAGAGCAAGCTACGTAGG 60.529 60.000 23.47 8.69 39.53 3.18
595 1012 1.476891 CCAGAGCAAGCTACGTAGGAA 59.523 52.381 23.47 0.00 0.00 3.36
620 1037 2.032377 TCGCGACTTTTTAGCTTGGTTG 60.032 45.455 3.71 0.00 0.00 3.77
662 1088 9.817809 ATATTCGCTCTCTAAGTAAACAAATGA 57.182 29.630 0.00 0.00 0.00 2.57
663 1089 7.582435 TTCGCTCTCTAAGTAAACAAATGAG 57.418 36.000 0.00 0.00 0.00 2.90
664 1090 6.920817 TCGCTCTCTAAGTAAACAAATGAGA 58.079 36.000 0.00 0.00 0.00 3.27
665 1091 7.548097 TCGCTCTCTAAGTAAACAAATGAGAT 58.452 34.615 0.00 0.00 0.00 2.75
666 1092 7.489435 TCGCTCTCTAAGTAAACAAATGAGATG 59.511 37.037 0.00 0.00 0.00 2.90
667 1093 7.405769 GCTCTCTAAGTAAACAAATGAGATGC 58.594 38.462 0.00 0.00 0.00 3.91
668 1094 7.466590 GCTCTCTAAGTAAACAAATGAGATGCC 60.467 40.741 0.00 0.00 0.00 4.40
669 1095 6.823689 TCTCTAAGTAAACAAATGAGATGCCC 59.176 38.462 0.00 0.00 0.00 5.36
670 1096 5.885912 TCTAAGTAAACAAATGAGATGCCCC 59.114 40.000 0.00 0.00 0.00 5.80
671 1097 3.016736 AGTAAACAAATGAGATGCCCCG 58.983 45.455 0.00 0.00 0.00 5.73
672 1098 0.532115 AAACAAATGAGATGCCCCGC 59.468 50.000 0.00 0.00 0.00 6.13
673 1099 0.611618 AACAAATGAGATGCCCCGCA 60.612 50.000 0.00 0.00 44.86 5.69
674 1100 0.611618 ACAAATGAGATGCCCCGCAA 60.612 50.000 0.00 0.00 43.62 4.85
675 1101 0.531657 CAAATGAGATGCCCCGCAAA 59.468 50.000 0.00 0.00 43.62 3.68
676 1102 1.067000 CAAATGAGATGCCCCGCAAAA 60.067 47.619 0.00 0.00 43.62 2.44
677 1103 1.265236 AATGAGATGCCCCGCAAAAA 58.735 45.000 0.00 0.00 43.62 1.94
736 1163 1.081041 CACGTACGTGGTGCTGCTA 60.081 57.895 35.09 0.00 42.00 3.49
862 1300 7.498900 CCTTATCAAATTGTACTGTATGCCTGA 59.501 37.037 0.00 0.00 0.00 3.86
930 1372 9.159364 TCATCTTTCTCATTATCAAGTCACTTG 57.841 33.333 11.69 11.69 42.25 3.16
1014 1475 3.362040 CAGGATGCCCAAAGAACCA 57.638 52.632 0.00 0.00 33.88 3.67
1082 1543 1.151668 CCTGGTTCTTCTTCTGCGTG 58.848 55.000 0.00 0.00 0.00 5.34
1122 1583 2.978156 TGTTCCAAGATTTCCAGCCT 57.022 45.000 0.00 0.00 0.00 4.58
1179 1640 1.136529 GTCTGCACGTGCGCATATATG 60.137 52.381 33.22 15.79 45.83 1.78
1191 1654 1.005512 ATATATGCGGGCGTGCGAA 60.006 52.632 0.00 0.00 37.81 4.70
1246 1726 4.821805 TCCACATCCTTGTCAAGTTTCTTC 59.178 41.667 11.61 0.00 32.34 2.87
1395 2023 0.321653 GGACAGGGCCACAACTACTG 60.322 60.000 6.18 2.81 35.40 2.74
1419 2047 7.523219 TGTTTTATGTTCATGTATTGGTCGAC 58.477 34.615 7.13 7.13 0.00 4.20
1812 2442 2.814336 GTTGCGAGAATCCAAGGTTCTT 59.186 45.455 0.00 0.00 36.13 2.52
1893 2524 1.395608 ACAATTACATTTCGCGGACCG 59.604 47.619 10.29 10.29 38.61 4.79
1953 2584 4.481463 AGTTGACTTGTTTTTGTGAACCG 58.519 39.130 0.00 0.00 32.22 4.44
1957 2588 4.454847 TGACTTGTTTTTGTGAACCGTGTA 59.545 37.500 0.00 0.00 0.00 2.90
2177 2846 0.178961 ACCAAGAAAGGCCCAACTCC 60.179 55.000 0.00 0.00 0.00 3.85
2388 3066 7.870509 TCCAAAAACTCATGATCCTGATTAG 57.129 36.000 0.00 0.00 0.00 1.73
2459 3149 6.257849 ACACGCATGTATAGTGACTTAATTGG 59.742 38.462 15.72 0.00 37.26 3.16
2460 3150 6.257849 CACGCATGTATAGTGACTTAATTGGT 59.742 38.462 0.00 0.00 38.06 3.67
2472 3163 8.188139 AGTGACTTAATTGGTTTGTGTTTACAG 58.812 33.333 0.00 0.00 38.23 2.74
2964 3668 9.563898 TTACTATAGTTTACTTCGTCACATGTG 57.436 33.333 20.18 20.18 0.00 3.21
3080 3785 0.179018 CCCCCAATCCCGAGTTCATC 60.179 60.000 0.00 0.00 0.00 2.92
3100 3805 7.373617 TCATCCTACCATTATAGCTTCAACA 57.626 36.000 0.00 0.00 0.00 3.33
3147 3852 7.617041 AGTGGATGTAAGAAAGTTAGAATGC 57.383 36.000 0.00 0.00 0.00 3.56
3187 3893 8.575565 TTGCGTAGACTTATTTGCTATTCTAG 57.424 34.615 0.00 0.00 0.00 2.43
3494 4210 9.927081 ATATCTTCCAGGTAAAATGATCAAAGT 57.073 29.630 0.00 0.00 0.00 2.66
3632 4350 7.015195 ACAATGAAAACAATATAGGTATGGGGC 59.985 37.037 0.00 0.00 0.00 5.80
3812 4530 4.336280 GGGTGAATTATCTATCAAGGGGC 58.664 47.826 0.00 0.00 0.00 5.80
3898 4616 7.095695 ACAATACAAGCATGGGTATGTAAAC 57.904 36.000 0.00 0.00 36.65 2.01
4125 8058 3.127376 AGAACAACACAACAACCGGTAAC 59.873 43.478 8.00 0.00 0.00 2.50
4161 8095 3.657398 AGGGATCACATGAGATTTGCA 57.343 42.857 7.10 0.00 0.00 4.08
4282 8218 3.570125 GCTTCTAAAGTTCTTGGCACCTT 59.430 43.478 0.00 0.00 0.00 3.50
4295 8231 1.632589 GCACCTTCAAGGGACCAATT 58.367 50.000 8.75 0.00 40.58 2.32
4297 8233 2.875296 CACCTTCAAGGGACCAATTCA 58.125 47.619 8.75 0.00 40.58 2.57
4307 8243 5.110814 AGGGACCAATTCATCGAATAACA 57.889 39.130 0.00 0.00 31.46 2.41
4335 8271 8.450578 AGTAAATGAAGAAATGAAGACACACA 57.549 30.769 0.00 0.00 0.00 3.72
4366 8302 4.708421 AGTTATGTTTCTAGGACCTACGCA 59.292 41.667 0.00 0.00 0.00 5.24
4371 8307 3.301794 TTCTAGGACCTACGCACCATA 57.698 47.619 0.00 0.00 0.00 2.74
4478 8416 5.690857 GCTCTCCTGAATTAACATACGGTAC 59.309 44.000 0.00 0.00 0.00 3.34
4500 8438 7.012421 GGTACTTTATATGGAACCTCTTTGCAG 59.988 40.741 0.00 0.00 39.19 4.41
4744 8685 8.686334 ACCTAATTTTAATTGTAGATGCACCAG 58.314 33.333 0.00 0.00 0.00 4.00
4763 8704 2.033299 CAGTCGTTGGAACAGCAAACAT 59.967 45.455 0.00 0.00 40.47 2.71
4772 8713 3.248602 GGAACAGCAAACATAGCTATCCG 59.751 47.826 2.34 0.00 41.14 4.18
4790 8731 1.374560 CGTATGGCCCGTGAAAATCA 58.625 50.000 0.00 0.00 0.00 2.57
4811 8752 1.066430 TGTTGCCGAGATACAACCTCC 60.066 52.381 3.66 0.00 44.38 4.30
4825 8766 8.164070 AGATACAACCTCCAATTGTAAGTCTTT 58.836 33.333 4.43 0.00 43.74 2.52
4827 8768 7.506328 ACAACCTCCAATTGTAAGTCTTTAC 57.494 36.000 4.43 0.00 38.51 2.01
4828 8769 6.489022 ACAACCTCCAATTGTAAGTCTTTACC 59.511 38.462 4.43 0.00 38.51 2.85
4848 8789 4.838152 CCCGGGGCACGTCTCATG 62.838 72.222 14.71 0.00 42.24 3.07
4850 8791 4.758251 CGGGGCACGTCTCATGCA 62.758 66.667 0.00 0.00 45.27 3.96
4851 8792 2.124570 GGGGCACGTCTCATGCAT 60.125 61.111 0.00 0.00 45.27 3.96
4852 8793 1.146041 GGGGCACGTCTCATGCATA 59.854 57.895 0.00 0.00 45.27 3.14
4853 8794 0.463654 GGGGCACGTCTCATGCATAA 60.464 55.000 0.00 0.00 45.27 1.90
4854 8795 0.657840 GGGCACGTCTCATGCATAAC 59.342 55.000 0.00 0.00 45.27 1.89
4855 8796 0.657840 GGCACGTCTCATGCATAACC 59.342 55.000 0.00 0.00 45.27 2.85
4856 8797 1.368641 GCACGTCTCATGCATAACCA 58.631 50.000 0.00 0.00 42.88 3.67
4857 8798 1.942657 GCACGTCTCATGCATAACCAT 59.057 47.619 0.00 0.00 42.88 3.55
4858 8799 2.286595 GCACGTCTCATGCATAACCATG 60.287 50.000 0.00 0.44 42.88 3.66
4859 8800 2.938451 CACGTCTCATGCATAACCATGT 59.062 45.455 0.00 0.00 42.44 3.21
4860 8801 2.938451 ACGTCTCATGCATAACCATGTG 59.062 45.455 0.00 0.91 42.44 3.21
4861 8802 2.938451 CGTCTCATGCATAACCATGTGT 59.062 45.455 0.00 0.00 42.44 3.72
4862 8803 3.001634 CGTCTCATGCATAACCATGTGTC 59.998 47.826 0.00 0.00 42.44 3.67
4863 8804 3.313526 GTCTCATGCATAACCATGTGTCC 59.686 47.826 0.00 0.00 42.44 4.02
4909 9037 8.761575 TGAAATCAAATTTTCTAGGTCAATGC 57.238 30.769 0.00 0.00 36.71 3.56
4966 9094 3.795561 AGTTCAATGAAGAAAGACGCG 57.204 42.857 3.53 3.53 0.00 6.01
4999 9127 4.374689 TTTGTTGGCCCTACATGAAGTA 57.625 40.909 0.00 0.00 0.00 2.24
5041 9169 7.206687 TGTGTCACGCATGAATAATATACTCA 58.793 34.615 0.00 0.00 36.31 3.41
5159 10040 9.801873 AGTTGCAAAATATTCACCATGTATTAC 57.198 29.630 0.00 0.00 0.00 1.89
5160 10041 9.579768 GTTGCAAAATATTCACCATGTATTACA 57.420 29.630 0.00 0.00 0.00 2.41
5170 10051 9.679661 ATTCACCATGTATTACAAAGACATACA 57.320 29.630 0.00 0.00 37.70 2.29
5171 10052 9.679661 TTCACCATGTATTACAAAGACATACAT 57.320 29.630 0.00 0.00 42.38 2.29
5172 10053 9.325198 TCACCATGTATTACAAAGACATACATC 57.675 33.333 0.00 0.00 40.57 3.06
5173 10054 9.108284 CACCATGTATTACAAAGACATACATCA 57.892 33.333 0.00 0.00 40.57 3.07
5174 10055 9.851686 ACCATGTATTACAAAGACATACATCAT 57.148 29.630 0.00 0.00 40.57 2.45
5419 10327 5.341196 CGGGTTTTAAGCAGTTTTATTGACG 59.659 40.000 0.00 0.00 0.00 4.35
5420 10328 6.440436 GGGTTTTAAGCAGTTTTATTGACGA 58.560 36.000 0.00 0.00 0.00 4.20
5573 10490 8.773404 TCCTTTCACGTTTTCCAAAATTTTTA 57.227 26.923 0.00 0.00 0.00 1.52
5574 10491 9.384764 TCCTTTCACGTTTTCCAAAATTTTTAT 57.615 25.926 0.00 0.00 0.00 1.40
5575 10492 9.644993 CCTTTCACGTTTTCCAAAATTTTTATC 57.355 29.630 0.00 0.00 0.00 1.75
5607 10526 6.034577 GGTTTCTGTTTCTTAAGTGCAACAAC 59.965 38.462 14.38 11.18 41.43 3.32
5627 10546 9.823098 CAACAACACTTGAAAATTTGAAAATGA 57.177 25.926 0.00 0.00 0.00 2.57
5675 10597 9.058174 TCTTCTTAATACATGGAAACGTTTTGA 57.942 29.630 15.89 5.18 0.00 2.69
5720 10645 6.418057 AACATGATTTTGGTAAAAGCCAGA 57.582 33.333 0.00 0.00 40.01 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.427506 GAAACCAGCACAACCCTCTAG 58.572 52.381 0.00 0.00 0.00 2.43
1 2 1.073284 GGAAACCAGCACAACCCTCTA 59.927 52.381 0.00 0.00 0.00 2.43
3 4 2.341452 GGAAACCAGCACAACCCTC 58.659 57.895 0.00 0.00 0.00 4.30
16 17 7.650504 GGTGTAAGACAATAAGTTTTGGGAAAC 59.349 37.037 0.00 0.00 44.35 2.78
17 18 7.468906 CGGTGTAAGACAATAAGTTTTGGGAAA 60.469 37.037 0.00 0.00 0.00 3.13
18 19 6.016943 CGGTGTAAGACAATAAGTTTTGGGAA 60.017 38.462 0.00 0.00 0.00 3.97
19 20 5.470777 CGGTGTAAGACAATAAGTTTTGGGA 59.529 40.000 0.00 0.00 0.00 4.37
20 21 5.470777 TCGGTGTAAGACAATAAGTTTTGGG 59.529 40.000 0.00 0.00 0.00 4.12
21 22 6.204108 ACTCGGTGTAAGACAATAAGTTTTGG 59.796 38.462 0.00 0.00 0.00 3.28
22 23 7.186021 ACTCGGTGTAAGACAATAAGTTTTG 57.814 36.000 0.00 0.00 0.00 2.44
23 24 8.891671 TTACTCGGTGTAAGACAATAAGTTTT 57.108 30.769 0.00 0.00 36.33 2.43
24 25 9.498176 AATTACTCGGTGTAAGACAATAAGTTT 57.502 29.630 8.42 0.00 43.46 2.66
25 26 9.148104 GAATTACTCGGTGTAAGACAATAAGTT 57.852 33.333 8.42 0.00 43.46 2.66
26 27 7.763071 GGAATTACTCGGTGTAAGACAATAAGT 59.237 37.037 8.42 0.00 43.46 2.24
27 28 7.762615 TGGAATTACTCGGTGTAAGACAATAAG 59.237 37.037 8.42 0.00 43.46 1.73
28 29 7.546667 GTGGAATTACTCGGTGTAAGACAATAA 59.453 37.037 8.42 0.00 43.46 1.40
29 30 7.037438 GTGGAATTACTCGGTGTAAGACAATA 58.963 38.462 8.42 0.00 43.46 1.90
30 31 5.873164 GTGGAATTACTCGGTGTAAGACAAT 59.127 40.000 8.42 0.00 43.46 2.71
31 32 5.232463 GTGGAATTACTCGGTGTAAGACAA 58.768 41.667 8.42 0.00 43.46 3.18
32 33 4.616604 CGTGGAATTACTCGGTGTAAGACA 60.617 45.833 4.18 4.96 43.46 3.41
33 34 3.855950 CGTGGAATTACTCGGTGTAAGAC 59.144 47.826 4.18 5.23 43.46 3.01
34 35 3.758023 TCGTGGAATTACTCGGTGTAAGA 59.242 43.478 11.94 0.00 43.46 2.10
35 36 4.100707 TCGTGGAATTACTCGGTGTAAG 57.899 45.455 11.94 0.00 43.46 2.34
36 37 3.758023 TCTCGTGGAATTACTCGGTGTAA 59.242 43.478 11.94 5.25 44.22 2.41
37 38 3.346315 TCTCGTGGAATTACTCGGTGTA 58.654 45.455 11.94 0.00 0.00 2.90
38 39 2.163815 CTCTCGTGGAATTACTCGGTGT 59.836 50.000 11.94 0.00 0.00 4.16
39 40 2.798680 CTCTCGTGGAATTACTCGGTG 58.201 52.381 11.94 6.11 0.00 4.94
40 41 1.134560 GCTCTCGTGGAATTACTCGGT 59.865 52.381 11.94 0.00 0.00 4.69
67 68 3.708403 AATCAGCTGTCATGTCTTCCA 57.292 42.857 14.67 0.00 0.00 3.53
78 79 0.108138 GGGCGACACTAATCAGCTGT 60.108 55.000 14.67 0.00 0.00 4.40
241 289 4.019174 TGGATCCAAAATTCTCCTCTTGC 58.981 43.478 13.46 0.00 0.00 4.01
255 303 4.297768 TCACCTAGTCATGATGGATCCAA 58.702 43.478 20.67 2.92 0.00 3.53
258 306 7.816995 GTCTAAATCACCTAGTCATGATGGATC 59.183 40.741 16.03 0.00 35.71 3.36
356 408 4.908601 TGTCAACTCTCTCTCTCTCTCT 57.091 45.455 0.00 0.00 0.00 3.10
357 409 7.220030 AGATATGTCAACTCTCTCTCTCTCTC 58.780 42.308 0.00 0.00 0.00 3.20
358 410 7.141758 AGATATGTCAACTCTCTCTCTCTCT 57.858 40.000 0.00 0.00 0.00 3.10
359 411 8.150945 ACTAGATATGTCAACTCTCTCTCTCTC 58.849 40.741 0.00 0.00 0.00 3.20
379 743 4.518249 GCCTTGTTTTGGCTCTACTAGAT 58.482 43.478 0.00 0.00 46.38 1.98
413 786 1.003851 CGAACACACAAACCACGTCT 58.996 50.000 0.00 0.00 0.00 4.18
455 828 1.546029 GTCAACTTTTCCATCTGCCCC 59.454 52.381 0.00 0.00 0.00 5.80
459 832 5.192327 AGCTTTGTCAACTTTTCCATCTG 57.808 39.130 0.00 0.00 0.00 2.90
588 1005 2.752144 AAGTCGCGATAGTTCCTACG 57.248 50.000 14.06 0.00 39.35 3.51
590 1007 5.039333 GCTAAAAAGTCGCGATAGTTCCTA 58.961 41.667 14.06 2.22 39.35 2.94
591 1008 3.864003 GCTAAAAAGTCGCGATAGTTCCT 59.136 43.478 14.06 0.00 39.35 3.36
592 1009 3.864003 AGCTAAAAAGTCGCGATAGTTCC 59.136 43.478 14.06 0.00 39.35 3.62
593 1010 5.248834 CAAGCTAAAAAGTCGCGATAGTTC 58.751 41.667 14.06 0.00 39.35 3.01
595 1012 3.617263 CCAAGCTAAAAAGTCGCGATAGT 59.383 43.478 14.06 0.00 39.35 2.12
620 1037 4.999751 GAATATTCGATGGTTCCTCTGC 57.000 45.455 0.00 0.00 0.00 4.26
679 1105 5.220989 CGTCATGCATGGATCATCTCTTTTT 60.221 40.000 25.97 0.00 0.00 1.94
680 1106 4.275196 CGTCATGCATGGATCATCTCTTTT 59.725 41.667 25.97 0.00 0.00 2.27
681 1107 3.813724 CGTCATGCATGGATCATCTCTTT 59.186 43.478 25.97 0.00 0.00 2.52
682 1108 3.400255 CGTCATGCATGGATCATCTCTT 58.600 45.455 25.97 0.00 0.00 2.85
683 1109 2.870835 GCGTCATGCATGGATCATCTCT 60.871 50.000 25.97 0.00 45.45 3.10
736 1163 3.503748 GTGGCAGCAGTCAAAGTTAATCT 59.496 43.478 0.00 0.00 0.00 2.40
862 1300 2.701006 GATGCGCGCGTACACAAT 59.299 55.556 32.35 12.22 0.00 2.71
919 1361 2.106338 TGGATCTTGGCAAGTGACTTGA 59.894 45.455 27.97 7.80 43.42 3.02
930 1372 2.358267 CTGATTGCTCTTGGATCTTGGC 59.642 50.000 0.00 0.00 0.00 4.52
1005 1466 1.372128 GCTGCGCCTTGGTTCTTTG 60.372 57.895 4.18 0.00 0.00 2.77
1014 1475 1.582968 CTGATTGTTGCTGCGCCTT 59.417 52.632 4.18 0.00 0.00 4.35
1082 1543 3.984508 TCGGACGGATAACAAGAGATC 57.015 47.619 0.00 0.00 0.00 2.75
1122 1583 6.720309 TGATCACCTCAAGGAAAATGTGATA 58.280 36.000 2.30 0.00 41.92 2.15
1182 1645 1.259544 CGAAACAAAGTTCGCACGCC 61.260 55.000 0.00 0.00 43.38 5.68
1191 1654 5.048294 GTGTAATCCCCATTCGAAACAAAGT 60.048 40.000 0.00 0.00 0.00 2.66
1246 1726 8.195436 TCAAGGGTAGAGTTTAATAATCACTCG 58.805 37.037 0.73 0.00 41.64 4.18
1395 2023 7.748847 AGTCGACCAATACATGAACATAAAAC 58.251 34.615 13.01 0.00 0.00 2.43
1812 2442 1.001293 AGCAGAGACTTCGATGCACAA 59.999 47.619 8.95 0.00 41.14 3.33
1913 2544 3.746045 ACTACGTCAGATTTGGTGTGT 57.254 42.857 0.00 0.00 0.00 3.72
1935 2566 3.828786 ACACGGTTCACAAAAACAAGTC 58.171 40.909 0.00 0.00 0.00 3.01
1953 2584 2.868583 AGATCATTGCGCAGATGTACAC 59.131 45.455 22.88 15.62 0.00 2.90
1957 2588 2.635714 TGAAGATCATTGCGCAGATGT 58.364 42.857 22.88 15.05 0.00 3.06
2177 2846 3.567164 ACAACCTGCTGAATTGTTCTCAG 59.433 43.478 7.18 0.00 42.73 3.35
2240 2918 8.560374 GGACATAAGTTTCATATAAGAGCCAAC 58.440 37.037 0.00 0.00 0.00 3.77
2316 2994 9.691362 AAATATGAACCACAAATTGACAAGTAC 57.309 29.630 0.00 0.00 0.00 2.73
2388 3066 8.451748 ACTCGCTTAAAAAGAATTGGATCTAAC 58.548 33.333 0.00 0.00 0.00 2.34
2424 3102 6.899771 CACTATACATGCGTGTGTGAAAATAC 59.100 38.462 21.92 0.00 39.39 1.89
2459 3149 8.238631 TGAGGAAACTAAACTGTAAACACAAAC 58.761 33.333 0.00 0.00 44.43 2.93
2460 3150 8.338072 TGAGGAAACTAAACTGTAAACACAAA 57.662 30.769 0.00 0.00 44.43 2.83
2472 3163 5.938125 TGTAAGCCATCTGAGGAAACTAAAC 59.062 40.000 0.00 0.00 44.43 2.01
2617 3308 6.591935 TGTTTCCATGGGTTGAGACTATATC 58.408 40.000 13.02 0.00 0.00 1.63
2955 3659 7.871853 ACCAGATAAACTAAAACACATGTGAC 58.128 34.615 31.94 7.92 0.00 3.67
3080 3785 6.992123 TGATGTGTTGAAGCTATAATGGTAGG 59.008 38.462 0.00 0.00 0.00 3.18
3100 3805 7.706179 CACTTACCAGTTTTGTCATTTTGATGT 59.294 33.333 0.00 0.00 0.00 3.06
3147 3852 3.818961 ACGCAAGAACATCAGAACATG 57.181 42.857 0.00 0.00 43.62 3.21
3187 3893 9.556030 GACTAAATGTGCCTTTTACATAACTTC 57.444 33.333 0.00 0.00 37.77 3.01
3525 4241 6.498651 CCTTGATAGGTAGTTCATCCCTACAT 59.501 42.308 0.00 0.00 37.18 2.29
3812 4530 3.118408 TGTTGATAGGATTTCCCACTCCG 60.118 47.826 0.00 0.00 36.62 4.63
3924 4642 7.484975 AGAGAAAATGTGTCTATCCTAGAACG 58.515 38.462 0.00 0.00 36.40 3.95
3939 4657 6.935167 ACACAAGTTTTGGAAGAGAAAATGT 58.065 32.000 0.00 0.00 34.12 2.71
4016 4734 1.909700 TGGAACATTGAGCCCTTCAC 58.090 50.000 0.00 0.00 34.94 3.18
4125 8058 9.933723 ATGTGATCCCTTTCTTAAAGAAAAATG 57.066 29.630 4.74 0.00 42.95 2.32
4282 8218 3.712016 TTCGATGAATTGGTCCCTTGA 57.288 42.857 0.00 0.00 0.00 3.02
4307 8243 9.778741 TGTGTCTTCATTTCTTCATTTACTACT 57.221 29.630 0.00 0.00 0.00 2.57
4320 8256 6.431234 ACTTTCCCTATGTGTGTCTTCATTTC 59.569 38.462 0.00 0.00 0.00 2.17
4335 8271 7.628101 AGGTCCTAGAAACATAACTTTCCCTAT 59.372 37.037 0.00 0.00 31.44 2.57
4478 8416 7.814264 ATCTGCAAAGAGGTTCCATATAAAG 57.186 36.000 0.00 0.00 0.00 1.85
4744 8685 2.774439 ATGTTTGCTGTTCCAACGAC 57.226 45.000 0.00 0.00 0.00 4.34
4763 8704 0.251474 ACGGGCCATACGGATAGCTA 60.251 55.000 4.39 0.00 35.23 3.32
4772 8713 2.687935 ACATGATTTTCACGGGCCATAC 59.312 45.455 4.39 0.00 0.00 2.39
4790 8731 2.420129 GGAGGTTGTATCTCGGCAACAT 60.420 50.000 9.20 2.42 44.70 2.71
4834 8775 0.463654 TTATGCATGAGACGTGCCCC 60.464 55.000 10.16 0.00 41.83 5.80
4835 8776 0.657840 GTTATGCATGAGACGTGCCC 59.342 55.000 10.16 0.00 41.83 5.36
4836 8777 0.657840 GGTTATGCATGAGACGTGCC 59.342 55.000 10.16 0.00 41.83 5.01
4837 8778 1.368641 TGGTTATGCATGAGACGTGC 58.631 50.000 10.16 8.72 42.81 5.34
4838 8779 2.938451 ACATGGTTATGCATGAGACGTG 59.062 45.455 10.16 11.03 37.85 4.49
4839 8780 2.938451 CACATGGTTATGCATGAGACGT 59.062 45.455 10.16 0.00 37.85 4.34
4840 8781 2.938451 ACACATGGTTATGCATGAGACG 59.062 45.455 10.16 0.00 37.85 4.18
4841 8782 3.313526 GGACACATGGTTATGCATGAGAC 59.686 47.826 10.16 5.32 37.85 3.36
4842 8783 3.054508 TGGACACATGGTTATGCATGAGA 60.055 43.478 10.16 0.00 37.85 3.27
4843 8784 3.281158 TGGACACATGGTTATGCATGAG 58.719 45.455 10.16 0.00 37.85 2.90
4844 8785 3.362870 TGGACACATGGTTATGCATGA 57.637 42.857 10.16 0.00 37.85 3.07
4845 8786 4.279922 ATCATGGACACATGGTTATGCATG 59.720 41.667 10.16 12.77 46.05 4.06
4846 8787 4.279922 CATCATGGACACATGGTTATGCAT 59.720 41.667 3.79 3.79 46.05 3.96
4847 8788 3.633065 CATCATGGACACATGGTTATGCA 59.367 43.478 7.75 0.00 46.05 3.96
4848 8789 3.884693 TCATCATGGACACATGGTTATGC 59.115 43.478 7.75 0.00 46.05 3.14
4849 8790 5.128205 AGTCATCATGGACACATGGTTATG 58.872 41.667 7.75 5.10 46.05 1.90
4850 8791 5.378230 AGTCATCATGGACACATGGTTAT 57.622 39.130 7.75 0.00 46.05 1.89
4851 8792 4.842531 AGTCATCATGGACACATGGTTA 57.157 40.909 7.75 0.00 46.05 2.85
4852 8793 3.726557 AGTCATCATGGACACATGGTT 57.273 42.857 7.75 0.00 46.05 3.67
4856 8797 5.282055 ACGATTAGTCATCATGGACACAT 57.718 39.130 5.12 0.00 40.29 3.21
4857 8798 4.736126 ACGATTAGTCATCATGGACACA 57.264 40.909 5.12 0.00 40.29 3.72
4909 9037 1.269831 GCTACCCAGAGGACATTAGCG 60.270 57.143 0.00 0.00 36.73 4.26
4966 9094 0.530431 CCAACAAAAGGCACCTGCAC 60.530 55.000 0.00 0.00 44.36 4.57
4999 9127 7.123190 CGTGACACATATATGCGTTTATTTGT 58.877 34.615 12.79 7.60 0.00 2.83
5105 9986 7.322699 CACGTTGAACATTTATGAAGTAACCAC 59.677 37.037 0.00 0.00 0.00 4.16
5144 10025 9.679661 TGTATGTCTTTGTAATACATGGTGAAT 57.320 29.630 0.00 0.00 35.54 2.57
5573 10490 8.749354 ACTTAAGAAACAGAAACCACAAAAGAT 58.251 29.630 10.09 0.00 0.00 2.40
5574 10491 8.026607 CACTTAAGAAACAGAAACCACAAAAGA 58.973 33.333 10.09 0.00 0.00 2.52
5575 10492 7.201435 GCACTTAAGAAACAGAAACCACAAAAG 60.201 37.037 10.09 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.