Multiple sequence alignment - TraesCS7B01G447800

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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 TraesCS7B01G447800 chr7B 100.000 2285 0 0 1 2285 710959532 710957248 0.000000e+00 4220
1 TraesCS7B01G447800 chr7B 95.253 969 36 6 649 1608 211695019 211695986 0.000000e+00 1526
2 TraesCS7B01G447800 chr7B 94.500 200 7 3 1416 1611 592642691 592642492 2.850000e-79 305
3 TraesCS7B01G447800 chr7A 95.846 963 33 5 652 1608 6752330 6751369 0.000000e+00 1550
4 TraesCS7B01G447800 chr7A 97.393 652 17 0 1 652 6754185 6753534 0.000000e+00 1110
5 TraesCS7B01G447800 chr7A 78.435 524 92 11 1695 2206 562004461 562004975 2.830000e-84 322
6 TraesCS7B01G447800 chr7A 73.473 524 99 21 1695 2206 679058483 679057988 6.530000e-36 161
7 TraesCS7B01G447800 chr2B 95.657 967 31 8 652 1608 798711419 798710454 0.000000e+00 1543
8 TraesCS7B01G447800 chr2B 94.792 960 43 4 649 1603 607300851 607301808 0.000000e+00 1489
9 TraesCS7B01G447800 chr2B 97.853 652 14 0 1 652 798713272 798712621 0.000000e+00 1127
10 TraesCS7B01G447800 chr2B 97.546 652 16 0 1 652 607250966 607251617 0.000000e+00 1116
11 TraesCS7B01G447800 chr2B 81.739 230 36 3 1842 2071 198274621 198274844 1.080000e-43 187
12 TraesCS7B01G447800 chr1B 95.322 962 39 4 652 1608 388170228 388169268 0.000000e+00 1522
13 TraesCS7B01G447800 chr1B 95.135 966 40 5 649 1608 394374970 394375934 0.000000e+00 1517
14 TraesCS7B01G447800 chr1B 97.853 652 14 0 1 652 388172080 388171429 0.000000e+00 1127
15 TraesCS7B01G447800 chr1B 97.090 653 18 1 1 652 656529243 656529895 0.000000e+00 1099
16 TraesCS7B01G447800 chr1B 96.779 652 21 0 1 652 394373120 394373771 0.000000e+00 1088
17 TraesCS7B01G447800 chr1B 83.598 189 25 4 2015 2202 493648173 493648356 3.020000e-39 172
18 TraesCS7B01G447800 chr1B 90.090 111 5 5 1504 1609 338604650 338604759 3.060000e-29 139
19 TraesCS7B01G447800 chr5B 95.150 969 38 6 649 1609 123020816 123021783 0.000000e+00 1520
20 TraesCS7B01G447800 chr5B 97.393 652 17 0 1 652 123018966 123019617 0.000000e+00 1110
21 TraesCS7B01G447800 chr5B 82.553 235 35 6 1842 2071 489339157 489338924 3.850000e-48 202
22 TraesCS7B01G447800 chr5B 74.463 419 76 13 1778 2184 2549039 2549438 3.930000e-33 152
23 TraesCS7B01G447800 chr6B 94.928 966 43 4 649 1609 717064740 717065704 0.000000e+00 1507
24 TraesCS7B01G447800 chr6B 96.933 652 20 0 1 652 717062892 717063543 0.000000e+00 1094
25 TraesCS7B01G447800 chr1A 94.819 965 42 5 649 1608 579648178 579649139 0.000000e+00 1498
26 TraesCS7B01G447800 chr1A 79.756 410 68 8 1689 2089 163377216 163377619 1.340000e-72 283
27 TraesCS7B01G447800 chr4B 96.933 652 20 0 1 652 630346093 630345442 0.000000e+00 1094
28 TraesCS7B01G447800 chr4A 90.339 383 24 6 1228 1608 570903318 570903689 2.030000e-140 508
29 TraesCS7B01G447800 chr4A 82.716 162 20 5 1445 1600 647120047 647120206 1.100000e-28 137
30 TraesCS7B01G447800 chr4A 82.716 162 20 6 1445 1604 734886567 734886412 1.100000e-28 137
31 TraesCS7B01G447800 chr3B 79.497 517 86 13 1698 2203 700232334 700231827 1.300000e-92 350
32 TraesCS7B01G447800 chr3B 75.442 452 85 15 1631 2071 27991946 27992382 1.790000e-46 196
33 TraesCS7B01G447800 chr2D 78.320 512 81 13 1696 2196 102304412 102304904 1.030000e-78 303
34 TraesCS7B01G447800 chr2A 78.082 511 79 10 1695 2196 475869214 475868728 2.220000e-75 292
35 TraesCS7B01G447800 chr3A 77.087 515 75 23 1646 2144 653919300 653918813 8.100000e-65 257
36 TraesCS7B01G447800 chr5D 78.147 421 68 10 1794 2203 472371823 472371416 1.750000e-61 246
37 TraesCS7B01G447800 chr1D 83.043 230 35 4 1842 2067 8462070 8461841 2.980000e-49 206
38 TraesCS7B01G447800 chr1D 76.289 388 70 12 1753 2135 341181080 341180710 1.080000e-43 187
39 TraesCS7B01G447800 chr4D 84.343 198 27 3 2003 2199 7470292 7470098 8.330000e-45 191
40 TraesCS7B01G447800 chr7D 85.294 170 12 9 1445 1608 469633047 469632885 1.820000e-36 163
41 TraesCS7B01G447800 chr5A 79.679 187 8 16 1445 1608 604749596 604749775 8.630000e-20 108
42 TraesCS7B01G447800 chr5A 78.857 175 18 11 1448 1604 9724300 9724127 1.440000e-17 100


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 TraesCS7B01G447800 chr7B 710957248 710959532 2284 True 4220.0 4220 100.0000 1 2285 1 chr7B.!!$R2 2284
1 TraesCS7B01G447800 chr7B 211695019 211695986 967 False 1526.0 1526 95.2530 649 1608 1 chr7B.!!$F1 959
2 TraesCS7B01G447800 chr7A 6751369 6754185 2816 True 1330.0 1550 96.6195 1 1608 2 chr7A.!!$R2 1607
3 TraesCS7B01G447800 chr7A 562004461 562004975 514 False 322.0 322 78.4350 1695 2206 1 chr7A.!!$F1 511
4 TraesCS7B01G447800 chr2B 607300851 607301808 957 False 1489.0 1489 94.7920 649 1603 1 chr2B.!!$F3 954
5 TraesCS7B01G447800 chr2B 798710454 798713272 2818 True 1335.0 1543 96.7550 1 1608 2 chr2B.!!$R1 1607
6 TraesCS7B01G447800 chr2B 607250966 607251617 651 False 1116.0 1116 97.5460 1 652 1 chr2B.!!$F2 651
7 TraesCS7B01G447800 chr1B 388169268 388172080 2812 True 1324.5 1522 96.5875 1 1608 2 chr1B.!!$R1 1607
8 TraesCS7B01G447800 chr1B 394373120 394375934 2814 False 1302.5 1517 95.9570 1 1608 2 chr1B.!!$F4 1607
9 TraesCS7B01G447800 chr1B 656529243 656529895 652 False 1099.0 1099 97.0900 1 652 1 chr1B.!!$F3 651
10 TraesCS7B01G447800 chr5B 123018966 123021783 2817 False 1315.0 1520 96.2715 1 1609 2 chr5B.!!$F2 1608
11 TraesCS7B01G447800 chr6B 717062892 717065704 2812 False 1300.5 1507 95.9305 1 1609 2 chr6B.!!$F1 1608
12 TraesCS7B01G447800 chr1A 579648178 579649139 961 False 1498.0 1498 94.8190 649 1608 1 chr1A.!!$F2 959
13 TraesCS7B01G447800 chr4B 630345442 630346093 651 True 1094.0 1094 96.9330 1 652 1 chr4B.!!$R1 651
14 TraesCS7B01G447800 chr3B 700231827 700232334 507 True 350.0 350 79.4970 1698 2203 1 chr3B.!!$R1 505

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
673 3079 1.301423 TCCTTCAAAACGTCAACGGG 58.699 50.0 7.53 0.0 44.95 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 4676 0.103026 TGCTATACTGCTGCAGACCG 59.897 55.0 34.28 19.27 35.18 4.79 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
142 144 7.882271 AGAAACTACTTCTGAGCATGAAAATCT 59.118 33.333 0.00 0.00 43.09 2.40
170 172 4.299586 TGAGGTGAATAAAGATGGTGCA 57.700 40.909 0.00 0.00 0.00 4.57
445 447 6.959639 AAGTAATGGTGAGTTTGTTGACAT 57.040 33.333 0.00 0.00 0.00 3.06
527 529 5.186996 TCAAATCAAAACTGAGCAAGTCC 57.813 39.130 0.00 0.00 38.56 3.85
573 575 1.498865 CTGGAAGCGTTTGAGTGCGT 61.499 55.000 0.00 0.00 35.87 5.24
673 3079 1.301423 TCCTTCAAAACGTCAACGGG 58.699 50.000 7.53 0.00 44.95 5.28
698 3104 5.831702 AGAAAGAGGCATCATGATGAAAC 57.168 39.130 34.65 23.43 41.20 2.78
792 3201 5.300034 TGACAATGCAGTTCTTTCATTGACT 59.700 36.000 20.75 8.32 45.87 3.41
797 3206 5.610398 TGCAGTTCTTTCATTGACTAGTCA 58.390 37.500 21.74 21.74 37.91 3.41
805 3214 8.908786 TCTTTCATTGACTAGTCACTTTGATT 57.091 30.769 25.13 2.07 39.66 2.57
881 3291 2.846206 AGTCCCTGGATGATAGCAAACA 59.154 45.455 0.00 0.00 0.00 2.83
905 3315 3.058293 CAGGAATGTTGCGCTACTTTTGA 60.058 43.478 22.01 2.48 0.00 2.69
966 3376 7.430992 TCTTCATGATTTTGTCTCAGAGTTG 57.569 36.000 0.00 0.00 0.00 3.16
1125 3535 6.147000 CCTCAGCTGAAAGAAGTTTCTCTAAC 59.853 42.308 18.85 0.00 42.39 2.34
1191 3601 3.607490 AGATTGAATGGCCTGGCTATT 57.393 42.857 27.55 27.55 42.17 1.73
1314 3725 9.477484 ACTGAAGTATTATTGTTATCGATGGAC 57.523 33.333 8.54 7.46 0.00 4.02
1600 4020 2.742372 CCTCCGAAACACAGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
1623 4043 3.152865 TGGAGCGCCAGTACCAAA 58.847 55.556 4.49 0.00 39.92 3.28
1624 4044 1.682849 TGGAGCGCCAGTACCAAAT 59.317 52.632 4.49 0.00 39.92 2.32
1625 4045 0.037590 TGGAGCGCCAGTACCAAATT 59.962 50.000 4.49 0.00 39.92 1.82
1626 4046 0.451783 GGAGCGCCAGTACCAAATTG 59.548 55.000 2.29 0.00 0.00 2.32
1627 4047 1.448985 GAGCGCCAGTACCAAATTGA 58.551 50.000 2.29 0.00 0.00 2.57
1628 4048 1.398390 GAGCGCCAGTACCAAATTGAG 59.602 52.381 2.29 0.00 0.00 3.02
1629 4049 0.179163 GCGCCAGTACCAAATTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
1630 4050 1.164411 CGCCAGTACCAAATTGAGCA 58.836 50.000 0.00 0.00 0.00 4.26
1631 4051 1.131126 CGCCAGTACCAAATTGAGCAG 59.869 52.381 0.00 0.00 0.00 4.24
1632 4052 1.474077 GCCAGTACCAAATTGAGCAGG 59.526 52.381 0.00 0.00 0.00 4.85
1633 4053 2.879756 GCCAGTACCAAATTGAGCAGGA 60.880 50.000 0.00 0.00 0.00 3.86
1634 4054 3.012518 CCAGTACCAAATTGAGCAGGAG 58.987 50.000 0.00 0.00 0.00 3.69
1635 4055 3.307691 CCAGTACCAAATTGAGCAGGAGA 60.308 47.826 0.00 0.00 0.00 3.71
1636 4056 4.521146 CAGTACCAAATTGAGCAGGAGAT 58.479 43.478 0.00 0.00 0.00 2.75
1637 4057 4.574013 CAGTACCAAATTGAGCAGGAGATC 59.426 45.833 0.00 0.00 0.00 2.75
1638 4058 3.010200 ACCAAATTGAGCAGGAGATCC 57.990 47.619 0.00 0.00 0.00 3.36
1639 4059 1.945394 CCAAATTGAGCAGGAGATCCG 59.055 52.381 0.00 0.00 42.08 4.18
1640 4060 1.945394 CAAATTGAGCAGGAGATCCGG 59.055 52.381 0.00 0.00 42.08 5.14
1641 4061 0.471617 AATTGAGCAGGAGATCCGGG 59.528 55.000 0.00 0.00 42.08 5.73
1642 4062 2.049627 ATTGAGCAGGAGATCCGGGC 62.050 60.000 0.00 9.67 42.08 6.13
1643 4063 4.292178 GAGCAGGAGATCCGGGCG 62.292 72.222 0.00 0.00 43.05 6.13
1644 4064 4.841617 AGCAGGAGATCCGGGCGA 62.842 66.667 0.00 0.00 43.05 5.54
1645 4065 4.292178 GCAGGAGATCCGGGCGAG 62.292 72.222 0.00 0.00 42.08 5.03
1646 4066 3.610669 CAGGAGATCCGGGCGAGG 61.611 72.222 0.00 0.00 42.08 4.63
1647 4067 4.144727 AGGAGATCCGGGCGAGGT 62.145 66.667 0.00 0.00 42.08 3.85
1648 4068 3.917760 GGAGATCCGGGCGAGGTG 61.918 72.222 0.00 0.00 0.00 4.00
1649 4069 3.148279 GAGATCCGGGCGAGGTGT 61.148 66.667 0.00 0.00 0.00 4.16
1650 4070 3.432051 GAGATCCGGGCGAGGTGTG 62.432 68.421 0.00 0.00 0.00 3.82
1671 4091 2.887568 CCTGCATCGCTGTCGGTC 60.888 66.667 0.00 0.00 36.13 4.79
1672 4092 2.182791 CTGCATCGCTGTCGGTCT 59.817 61.111 0.00 0.00 36.13 3.85
1673 4093 2.125952 TGCATCGCTGTCGGTCTG 60.126 61.111 0.00 0.00 36.13 3.51
1674 4094 3.558411 GCATCGCTGTCGGTCTGC 61.558 66.667 0.00 0.00 37.59 4.26
1679 4099 4.400109 GCTGTCGGTCTGCGTCGA 62.400 66.667 0.00 0.00 0.00 4.20
1680 4100 2.202362 CTGTCGGTCTGCGTCGAG 60.202 66.667 0.00 0.00 36.00 4.04
1681 4101 2.667199 TGTCGGTCTGCGTCGAGA 60.667 61.111 0.00 0.00 36.00 4.04
1682 4102 2.202324 GTCGGTCTGCGTCGAGAC 60.202 66.667 13.26 13.26 41.55 3.36
1683 4103 2.358369 TCGGTCTGCGTCGAGACT 60.358 61.111 18.10 0.00 41.90 3.24
1684 4104 1.964891 TCGGTCTGCGTCGAGACTT 60.965 57.895 18.10 0.00 41.90 3.01
1685 4105 1.797933 CGGTCTGCGTCGAGACTTG 60.798 63.158 18.10 11.12 41.90 3.16
1686 4106 1.286260 GGTCTGCGTCGAGACTTGT 59.714 57.895 18.10 0.00 41.90 3.16
1687 4107 0.729816 GGTCTGCGTCGAGACTTGTC 60.730 60.000 18.10 0.00 41.90 3.18
1688 4108 1.060726 GTCTGCGTCGAGACTTGTCG 61.061 60.000 13.97 5.13 39.52 4.35
1689 4109 1.797933 CTGCGTCGAGACTTGTCGG 60.798 63.158 10.69 0.00 40.49 4.79
1690 4110 2.183858 CTGCGTCGAGACTTGTCGGA 62.184 60.000 10.69 7.31 40.49 4.55
1691 4111 1.512310 GCGTCGAGACTTGTCGGAG 60.512 63.158 10.69 0.00 40.49 4.63
1692 4112 1.512310 CGTCGAGACTTGTCGGAGC 60.512 63.158 1.81 0.00 40.49 4.70
1693 4113 1.153997 GTCGAGACTTGTCGGAGCC 60.154 63.158 0.00 0.00 40.49 4.70
1711 4131 1.671901 CCGAGGAGGAAGAGGAGCAC 61.672 65.000 0.00 0.00 45.00 4.40
1714 4134 0.178891 AGGAGGAAGAGGAGCACCAA 60.179 55.000 2.07 0.00 38.94 3.67
1738 4158 3.871623 TCCGAGGGAGATGGCTAAT 57.128 52.632 0.00 0.00 0.00 1.73
1751 4171 2.832838 TGGCTAATCCAGAGAAGGACA 58.167 47.619 0.00 0.00 41.30 4.02
1755 4175 2.797177 AATCCAGAGAAGGACAAGGC 57.203 50.000 0.00 0.00 41.30 4.35
1776 4196 4.847444 GCAGCCGGAAGAGGAGCC 62.847 72.222 5.05 0.00 0.00 4.70
1814 4234 0.038166 GGGCTTCAACATGGAGGACA 59.962 55.000 0.00 0.00 0.00 4.02
1825 4245 4.131088 GAGGACACGGAGGCGGTC 62.131 72.222 0.00 0.00 0.00 4.79
1873 4302 0.625683 AGGCCATCCTGGAGTCCATT 60.626 55.000 13.56 0.00 40.96 3.16
1875 4304 0.533755 GCCATCCTGGAGTCCATTCG 60.534 60.000 13.56 0.47 40.96 3.34
1892 4321 0.398522 TCGGGATGAGGCCTATGTGT 60.399 55.000 4.42 0.00 0.00 3.72
1957 4386 3.285306 GGTTTTCGCCGAATTCGAC 57.715 52.632 28.76 17.08 43.02 4.20
1958 4387 0.513820 GGTTTTCGCCGAATTCGACA 59.486 50.000 28.76 9.19 43.02 4.35
1999 4429 2.284995 GGGGAGCAGTGGAGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
2058 4488 2.690497 CACGGTGATAGTGGACATCTCT 59.310 50.000 0.74 0.00 36.06 3.10
2079 4510 5.698104 TCTGACGAGGATTAGGGTGTATAA 58.302 41.667 0.00 0.00 0.00 0.98
2084 4515 7.230108 TGACGAGGATTAGGGTGTATAAGTTAG 59.770 40.741 0.00 0.00 0.00 2.34
2094 4525 8.834004 AGGGTGTATAAGTTAGTTGATCTACA 57.166 34.615 9.96 0.00 0.00 2.74
2113 4545 7.634671 TCTACATAGTACGTGGATTTTCTCA 57.365 36.000 0.00 0.00 0.00 3.27
2146 4578 7.029563 GCTTTTGTATGGATCTAAGGTTTGTG 58.970 38.462 0.00 0.00 0.00 3.33
2164 4596 6.042781 GGTTTGTGGTATGAGGTATCCAGATA 59.957 42.308 0.00 0.00 0.00 1.98
2184 4616 5.825151 AGATACAGAGGAGCAAATTTAAGGC 59.175 40.000 0.00 0.00 0.00 4.35
2185 4617 3.766545 ACAGAGGAGCAAATTTAAGGCA 58.233 40.909 2.29 0.00 0.00 4.75
2206 4638 3.499737 CCGGTCATTGTCCGCAGC 61.500 66.667 15.60 0.00 45.71 5.25
2207 4639 3.499737 CGGTCATTGTCCGCAGCC 61.500 66.667 9.33 0.00 41.48 4.85
2208 4640 2.359850 GGTCATTGTCCGCAGCCA 60.360 61.111 0.00 0.00 0.00 4.75
2209 4641 1.971167 GGTCATTGTCCGCAGCCAA 60.971 57.895 0.00 0.00 0.00 4.52
2210 4642 1.523154 GGTCATTGTCCGCAGCCAAA 61.523 55.000 0.00 0.00 0.00 3.28
2211 4643 0.387239 GTCATTGTCCGCAGCCAAAC 60.387 55.000 0.00 0.00 0.00 2.93
2212 4644 1.442520 CATTGTCCGCAGCCAAACG 60.443 57.895 0.00 0.00 0.00 3.60
2219 4651 2.746277 GCAGCCAAACGGACGGAT 60.746 61.111 0.00 0.00 0.00 4.18
2220 4652 3.039202 GCAGCCAAACGGACGGATG 62.039 63.158 0.00 0.69 41.70 3.51
2221 4653 2.746277 AGCCAAACGGACGGATGC 60.746 61.111 0.00 0.00 0.00 3.91
2222 4654 2.746277 GCCAAACGGACGGATGCT 60.746 61.111 0.00 0.00 0.00 3.79
2223 4655 1.448893 GCCAAACGGACGGATGCTA 60.449 57.895 0.00 0.00 0.00 3.49
2224 4656 1.702491 GCCAAACGGACGGATGCTAC 61.702 60.000 0.00 0.00 0.00 3.58
2225 4657 1.418342 CCAAACGGACGGATGCTACG 61.418 60.000 0.00 0.00 37.36 3.51
2226 4658 1.153706 AAACGGACGGATGCTACGG 60.154 57.895 0.00 0.00 35.23 4.02
2227 4659 1.880819 AAACGGACGGATGCTACGGT 61.881 55.000 0.00 0.00 35.23 4.83
2228 4660 1.031571 AACGGACGGATGCTACGGTA 61.032 55.000 0.00 0.00 35.23 4.02
2229 4661 1.009222 CGGACGGATGCTACGGTAC 60.009 63.158 0.00 0.00 35.23 3.34
2243 4675 4.487412 GTACGGTGGCGACGGGAG 62.487 72.222 10.98 0.00 35.23 4.30
2261 4693 2.892305 GCGGTCTGCAGCAGTATAG 58.108 57.895 22.10 12.73 45.45 1.31
2262 4694 1.218230 GCGGTCTGCAGCAGTATAGC 61.218 60.000 22.10 17.97 45.45 2.97
2263 4695 0.103026 CGGTCTGCAGCAGTATAGCA 59.897 55.000 22.10 0.00 36.85 3.49
2264 4696 1.576356 GGTCTGCAGCAGTATAGCAC 58.424 55.000 22.10 11.35 36.85 4.40
2265 4697 1.137872 GGTCTGCAGCAGTATAGCACT 59.862 52.381 22.10 0.00 38.32 4.40
2266 4698 2.468831 GTCTGCAGCAGTATAGCACTC 58.531 52.381 22.10 0.18 34.26 3.51
2267 4699 1.410517 TCTGCAGCAGTATAGCACTCC 59.589 52.381 22.10 0.00 34.26 3.85
2268 4700 1.411977 CTGCAGCAGTATAGCACTCCT 59.588 52.381 14.90 0.00 34.26 3.69
2269 4701 1.833630 TGCAGCAGTATAGCACTCCTT 59.166 47.619 0.00 0.00 34.26 3.36
2270 4702 2.208431 GCAGCAGTATAGCACTCCTTG 58.792 52.381 0.00 0.00 34.26 3.61
2271 4703 2.159043 GCAGCAGTATAGCACTCCTTGA 60.159 50.000 0.00 0.00 34.26 3.02
2272 4704 3.679917 GCAGCAGTATAGCACTCCTTGAA 60.680 47.826 0.00 0.00 34.26 2.69
2273 4705 4.507710 CAGCAGTATAGCACTCCTTGAAA 58.492 43.478 0.00 0.00 34.26 2.69
2274 4706 4.937620 CAGCAGTATAGCACTCCTTGAAAA 59.062 41.667 0.00 0.00 34.26 2.29
2275 4707 5.064452 CAGCAGTATAGCACTCCTTGAAAAG 59.936 44.000 0.00 0.00 38.62 2.27
2276 4708 5.046304 AGCAGTATAGCACTCCTTGAAAAGA 60.046 40.000 0.00 0.00 40.58 2.52
2277 4709 5.643777 GCAGTATAGCACTCCTTGAAAAGAA 59.356 40.000 0.00 0.00 40.58 2.52
2278 4710 6.183360 GCAGTATAGCACTCCTTGAAAAGAAG 60.183 42.308 0.00 0.00 40.58 2.85
2279 4711 6.876257 CAGTATAGCACTCCTTGAAAAGAAGT 59.124 38.462 0.00 0.00 40.58 3.01
2280 4712 7.064016 CAGTATAGCACTCCTTGAAAAGAAGTC 59.936 40.741 0.00 0.00 40.58 3.01
2281 4713 7.038658 AGTATAGCACTCCTTGAAAAGAAGTCT 60.039 37.037 0.00 0.00 45.77 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 144 7.770433 CACCATCTTTATTCACCTCAACATCTA 59.230 37.037 0.00 0.00 0.00 1.98
159 161 0.963962 CCTGTGCTTGCACCATCTTT 59.036 50.000 21.01 0.00 0.00 2.52
170 172 2.603075 TTATTTGCTCCCCTGTGCTT 57.397 45.000 0.00 0.00 32.27 3.91
527 529 1.911057 ATCCATCAGATGCCAGCATG 58.089 50.000 10.41 0.00 36.70 4.06
573 575 5.930569 CACTGTTCTCATGATCTTTGAGACA 59.069 40.000 21.31 19.66 46.92 3.41
673 3079 6.446781 TTCATCATGATGCCTCTTTCTTTC 57.553 37.500 27.68 0.00 38.65 2.62
698 3104 9.865321 ACAATTGTATTTCTTCTTGATCATTGG 57.135 29.630 9.97 0.00 0.00 3.16
805 3214 9.936759 AAACACCTTTTCAAATTTCTTCAACTA 57.063 25.926 0.00 0.00 0.00 2.24
857 3267 1.688735 TGCTATCATCCAGGGACTTCG 59.311 52.381 0.00 0.00 34.60 3.79
865 3275 4.264253 TCCTGTTGTTTGCTATCATCCAG 58.736 43.478 0.00 0.00 0.00 3.86
881 3291 2.185004 AGTAGCGCAACATTCCTGTT 57.815 45.000 11.47 0.00 46.54 3.16
966 3376 3.796717 GCAAAGTTACCTGCAACACTTTC 59.203 43.478 8.51 3.23 37.36 2.62
1191 3601 5.045012 AGATATCCTTCTCAATGCAGCAA 57.955 39.130 0.00 0.00 0.00 3.91
1305 3716 5.067936 ACGAAATTAGACTGAGTCCATCGAT 59.932 40.000 21.26 0.00 32.18 3.59
1398 3809 9.840427 CAATAATAACCAAATTCGAACTGACTT 57.160 29.630 0.00 0.00 0.00 3.01
1609 4029 1.453155 CTCAATTTGGTACTGGCGCT 58.547 50.000 7.64 0.00 0.00 5.92
1610 4030 0.179163 GCTCAATTTGGTACTGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
1611 4031 1.131126 CTGCTCAATTTGGTACTGGCG 59.869 52.381 0.00 0.00 0.00 5.69
1612 4032 1.474077 CCTGCTCAATTTGGTACTGGC 59.526 52.381 0.00 0.00 0.00 4.85
1613 4033 3.012518 CTCCTGCTCAATTTGGTACTGG 58.987 50.000 0.00 1.19 0.00 4.00
1614 4034 3.942829 TCTCCTGCTCAATTTGGTACTG 58.057 45.455 0.00 0.00 0.00 2.74
1615 4035 4.384647 GGATCTCCTGCTCAATTTGGTACT 60.385 45.833 0.00 0.00 0.00 2.73
1616 4036 3.879892 GGATCTCCTGCTCAATTTGGTAC 59.120 47.826 0.00 0.00 0.00 3.34
1617 4037 3.432186 CGGATCTCCTGCTCAATTTGGTA 60.432 47.826 0.00 0.00 0.00 3.25
1618 4038 2.681976 CGGATCTCCTGCTCAATTTGGT 60.682 50.000 0.00 0.00 0.00 3.67
1619 4039 1.945394 CGGATCTCCTGCTCAATTTGG 59.055 52.381 0.00 0.00 0.00 3.28
1620 4040 1.945394 CCGGATCTCCTGCTCAATTTG 59.055 52.381 0.00 0.00 0.00 2.32
1621 4041 1.133976 CCCGGATCTCCTGCTCAATTT 60.134 52.381 0.73 0.00 0.00 1.82
1622 4042 0.471617 CCCGGATCTCCTGCTCAATT 59.528 55.000 0.73 0.00 0.00 2.32
1623 4043 2.049627 GCCCGGATCTCCTGCTCAAT 62.050 60.000 0.73 0.00 0.00 2.57
1624 4044 2.735772 GCCCGGATCTCCTGCTCAA 61.736 63.158 0.73 0.00 0.00 3.02
1625 4045 3.157252 GCCCGGATCTCCTGCTCA 61.157 66.667 0.73 0.00 0.00 4.26
1626 4046 4.292178 CGCCCGGATCTCCTGCTC 62.292 72.222 0.73 0.00 31.70 4.26
1627 4047 4.841617 TCGCCCGGATCTCCTGCT 62.842 66.667 0.73 0.00 31.70 4.24
1628 4048 4.292178 CTCGCCCGGATCTCCTGC 62.292 72.222 0.73 0.00 0.00 4.85
1629 4049 3.610669 CCTCGCCCGGATCTCCTG 61.611 72.222 0.73 0.00 0.00 3.86
1630 4050 4.144727 ACCTCGCCCGGATCTCCT 62.145 66.667 0.73 0.00 0.00 3.69
1631 4051 3.917760 CACCTCGCCCGGATCTCC 61.918 72.222 0.73 0.00 0.00 3.71
1632 4052 3.148279 ACACCTCGCCCGGATCTC 61.148 66.667 0.73 0.00 0.00 2.75
1633 4053 3.461773 CACACCTCGCCCGGATCT 61.462 66.667 0.73 0.00 0.00 2.75
1654 4074 2.887568 GACCGACAGCGATGCAGG 60.888 66.667 12.61 12.61 40.82 4.85
1655 4075 2.163390 CAGACCGACAGCGATGCAG 61.163 63.158 0.00 0.00 40.82 4.41
1656 4076 2.125952 CAGACCGACAGCGATGCA 60.126 61.111 0.00 0.00 40.82 3.96
1657 4077 3.558411 GCAGACCGACAGCGATGC 61.558 66.667 0.00 0.00 40.82 3.91
1662 4082 4.400109 TCGACGCAGACCGACAGC 62.400 66.667 0.00 0.00 41.02 4.40
1663 4083 2.202362 CTCGACGCAGACCGACAG 60.202 66.667 0.00 0.00 41.02 3.51
1664 4084 2.667199 TCTCGACGCAGACCGACA 60.667 61.111 0.00 0.00 41.02 4.35
1665 4085 2.185103 AAGTCTCGACGCAGACCGAC 62.185 60.000 17.92 6.52 43.53 4.79
1666 4086 1.964891 AAGTCTCGACGCAGACCGA 60.965 57.895 17.92 0.00 43.53 4.69
1667 4087 1.797933 CAAGTCTCGACGCAGACCG 60.798 63.158 17.92 10.06 43.53 4.79
1668 4088 0.729816 GACAAGTCTCGACGCAGACC 60.730 60.000 17.92 5.37 43.53 3.85
1669 4089 1.060726 CGACAAGTCTCGACGCAGAC 61.061 60.000 15.33 15.33 42.91 3.51
1670 4090 1.206831 CGACAAGTCTCGACGCAGA 59.793 57.895 0.00 0.00 35.58 4.26
1671 4091 1.797933 CCGACAAGTCTCGACGCAG 60.798 63.158 0.00 0.00 35.58 5.18
1672 4092 2.183858 CTCCGACAAGTCTCGACGCA 62.184 60.000 0.00 0.00 35.58 5.24
1673 4093 1.512310 CTCCGACAAGTCTCGACGC 60.512 63.158 0.00 0.00 35.58 5.19
1674 4094 1.512310 GCTCCGACAAGTCTCGACG 60.512 63.158 0.00 0.00 35.58 5.12
1675 4095 1.153997 GGCTCCGACAAGTCTCGAC 60.154 63.158 0.00 0.00 35.58 4.20
1676 4096 2.687805 CGGCTCCGACAAGTCTCGA 61.688 63.158 1.35 0.00 42.83 4.04
1677 4097 2.202492 CGGCTCCGACAAGTCTCG 60.202 66.667 1.35 0.00 42.83 4.04
1678 4098 1.137825 CTCGGCTCCGACAAGTCTC 59.862 63.158 6.95 0.00 44.01 3.36
1679 4099 2.344203 CCTCGGCTCCGACAAGTCT 61.344 63.158 6.95 0.00 44.01 3.24
1680 4100 2.182030 CCTCGGCTCCGACAAGTC 59.818 66.667 6.95 0.00 44.01 3.01
1681 4101 2.282958 TCCTCGGCTCCGACAAGT 60.283 61.111 6.95 0.00 44.01 3.16
1682 4102 2.492090 CTCCTCGGCTCCGACAAG 59.508 66.667 6.95 4.10 44.01 3.16
1683 4103 3.068691 CCTCCTCGGCTCCGACAA 61.069 66.667 6.95 0.00 44.01 3.18
1684 4104 3.578968 TTCCTCCTCGGCTCCGACA 62.579 63.158 6.95 0.00 44.01 4.35
1685 4105 2.754658 TTCCTCCTCGGCTCCGAC 60.755 66.667 6.95 0.00 44.01 4.79
1686 4106 2.440430 CTTCCTCCTCGGCTCCGA 60.440 66.667 10.84 10.84 46.87 4.55
1687 4107 2.440430 TCTTCCTCCTCGGCTCCG 60.440 66.667 1.14 1.14 41.35 4.63
1688 4108 2.131067 CCTCTTCCTCCTCGGCTCC 61.131 68.421 0.00 0.00 0.00 4.70
1689 4109 1.076632 TCCTCTTCCTCCTCGGCTC 60.077 63.158 0.00 0.00 0.00 4.70
1690 4110 1.076339 CTCCTCTTCCTCCTCGGCT 60.076 63.158 0.00 0.00 0.00 5.52
1691 4111 2.791868 GCTCCTCTTCCTCCTCGGC 61.792 68.421 0.00 0.00 0.00 5.54
1692 4112 1.380515 TGCTCCTCTTCCTCCTCGG 60.381 63.158 0.00 0.00 0.00 4.63
1693 4113 1.671901 GGTGCTCCTCTTCCTCCTCG 61.672 65.000 0.00 0.00 0.00 4.63
1735 4155 2.168521 CGCCTTGTCCTTCTCTGGATTA 59.831 50.000 0.00 0.00 38.52 1.75
1738 4158 1.544825 CCGCCTTGTCCTTCTCTGGA 61.545 60.000 0.00 0.00 0.00 3.86
1741 4161 1.893919 GCTCCGCCTTGTCCTTCTCT 61.894 60.000 0.00 0.00 0.00 3.10
1745 4165 2.348998 CTGCTCCGCCTTGTCCTT 59.651 61.111 0.00 0.00 0.00 3.36
1792 4212 1.002134 CTCCATGTTGAAGCCCGGT 60.002 57.895 0.00 0.00 0.00 5.28
1826 4246 2.180017 CATGTTGGCCGCTTGAGC 59.820 61.111 0.00 0.00 37.78 4.26
1827 4247 2.879907 CCATGTTGGCCGCTTGAG 59.120 61.111 12.56 2.53 0.00 3.02
1873 4302 0.398522 ACACATAGGCCTCATCCCGA 60.399 55.000 9.68 0.00 0.00 5.14
1875 4304 1.625818 CCTACACATAGGCCTCATCCC 59.374 57.143 9.68 0.00 41.80 3.85
1892 4321 1.138266 GATGAACTGCCGGTTAGCCTA 59.862 52.381 1.90 0.00 38.41 3.93
1917 4346 4.452733 CGGTCTCCGCCTGTTCCC 62.453 72.222 0.00 0.00 41.17 3.97
1947 4376 1.200483 CATCTCCGTGTCGAATTCGG 58.800 55.000 26.47 11.89 44.76 4.30
1951 4380 0.747255 CCTCCATCTCCGTGTCGAAT 59.253 55.000 0.00 0.00 0.00 3.34
1952 4381 1.945354 GCCTCCATCTCCGTGTCGAA 61.945 60.000 0.00 0.00 0.00 3.71
1957 4386 3.144120 CTCCGCCTCCATCTCCGTG 62.144 68.421 0.00 0.00 0.00 4.94
1958 4387 2.835431 CTCCGCCTCCATCTCCGT 60.835 66.667 0.00 0.00 0.00 4.69
1983 4412 1.610673 TGACTCCTCCACTGCTCCC 60.611 63.158 0.00 0.00 0.00 4.30
1988 4417 0.531657 CAGCTCTGACTCCTCCACTG 59.468 60.000 0.00 0.00 0.00 3.66
1991 4420 2.346541 CGCAGCTCTGACTCCTCCA 61.347 63.158 0.29 0.00 0.00 3.86
1992 4421 2.493973 CGCAGCTCTGACTCCTCC 59.506 66.667 0.29 0.00 0.00 4.30
2013 4443 2.445085 TCCGGATACATGGGCGGT 60.445 61.111 0.00 0.00 0.00 5.68
2042 4472 3.886123 TCGTCAGAGATGTCCACTATCA 58.114 45.455 0.00 0.00 0.00 2.15
2058 4488 5.452255 ACTTATACACCCTAATCCTCGTCA 58.548 41.667 0.00 0.00 0.00 4.35
2079 4510 7.772292 TCCACGTACTATGTAGATCAACTAACT 59.228 37.037 0.00 0.00 32.49 2.24
2084 4515 8.644318 AAAATCCACGTACTATGTAGATCAAC 57.356 34.615 0.00 0.00 0.00 3.18
2094 4525 9.832445 ATGTAAATGAGAAAATCCACGTACTAT 57.168 29.630 0.00 0.00 0.00 2.12
2097 4528 6.687105 GCATGTAAATGAGAAAATCCACGTAC 59.313 38.462 0.00 0.00 0.00 3.67
2117 4549 6.426587 ACCTTAGATCCATACAAAAGCATGT 58.573 36.000 0.00 0.00 37.32 3.21
2146 4578 5.654650 CCTCTGTATCTGGATACCTCATACC 59.345 48.000 15.45 0.00 42.19 2.73
2164 4596 3.766545 TGCCTTAAATTTGCTCCTCTGT 58.233 40.909 0.00 0.00 0.00 3.41
2206 4638 1.418342 CGTAGCATCCGTCCGTTTGG 61.418 60.000 0.00 0.00 0.00 3.28
2207 4639 1.418342 CCGTAGCATCCGTCCGTTTG 61.418 60.000 0.00 0.00 0.00 2.93
2208 4640 1.153706 CCGTAGCATCCGTCCGTTT 60.154 57.895 0.00 0.00 0.00 3.60
2209 4641 1.031571 TACCGTAGCATCCGTCCGTT 61.032 55.000 0.00 0.00 0.00 4.44
2210 4642 1.451927 TACCGTAGCATCCGTCCGT 60.452 57.895 0.00 0.00 0.00 4.69
2211 4643 1.009222 GTACCGTAGCATCCGTCCG 60.009 63.158 0.00 0.00 0.00 4.79
2212 4644 1.009222 CGTACCGTAGCATCCGTCC 60.009 63.158 0.00 0.00 0.00 4.79
2213 4645 1.009222 CCGTACCGTAGCATCCGTC 60.009 63.158 0.00 0.00 0.00 4.79
2214 4646 1.750399 ACCGTACCGTAGCATCCGT 60.750 57.895 0.00 0.00 0.00 4.69
2215 4647 1.298863 CACCGTACCGTAGCATCCG 60.299 63.158 0.00 0.00 0.00 4.18
2216 4648 1.066918 CCACCGTACCGTAGCATCC 59.933 63.158 0.00 0.00 0.00 3.51
2217 4649 1.590792 GCCACCGTACCGTAGCATC 60.591 63.158 0.41 0.00 0.00 3.91
2218 4650 2.497770 GCCACCGTACCGTAGCAT 59.502 61.111 0.41 0.00 0.00 3.79
2219 4651 4.118995 CGCCACCGTACCGTAGCA 62.119 66.667 5.74 0.00 0.00 3.49
2220 4652 3.814268 TCGCCACCGTACCGTAGC 61.814 66.667 0.00 0.00 35.54 3.58
2221 4653 2.100991 GTCGCCACCGTACCGTAG 59.899 66.667 0.00 0.00 35.54 3.51
2222 4654 3.798650 CGTCGCCACCGTACCGTA 61.799 66.667 0.00 0.00 35.54 4.02
2226 4658 4.487412 CTCCCGTCGCCACCGTAC 62.487 72.222 0.00 0.00 35.54 3.67
2236 4668 4.803426 CTGCAGACCGCTCCCGTC 62.803 72.222 8.42 0.00 43.06 4.79
2240 4672 2.303549 ATACTGCTGCAGACCGCTCC 62.304 60.000 34.28 0.00 43.06 4.70
2241 4673 0.385751 TATACTGCTGCAGACCGCTC 59.614 55.000 34.28 0.00 43.06 5.03
2242 4674 0.387202 CTATACTGCTGCAGACCGCT 59.613 55.000 34.28 15.19 43.06 5.52
2243 4675 1.218230 GCTATACTGCTGCAGACCGC 61.218 60.000 34.28 23.99 42.89 5.68
2244 4676 0.103026 TGCTATACTGCTGCAGACCG 59.897 55.000 34.28 19.27 35.18 4.79
2245 4677 1.137872 AGTGCTATACTGCTGCAGACC 59.862 52.381 34.28 16.92 38.49 3.85
2246 4678 2.468831 GAGTGCTATACTGCTGCAGAC 58.531 52.381 34.28 20.52 40.53 3.51
2247 4679 1.410517 GGAGTGCTATACTGCTGCAGA 59.589 52.381 34.28 18.63 43.69 4.26
2248 4680 1.863267 GGAGTGCTATACTGCTGCAG 58.137 55.000 27.02 27.02 43.69 4.41
2253 4685 8.486333 ACTTCTTTTCAAGGAGTGCTATACTGC 61.486 40.741 0.00 0.00 45.68 4.40
2254 4686 6.876257 ACTTCTTTTCAAGGAGTGCTATACTG 59.124 38.462 0.00 0.00 45.68 2.74
2255 4687 7.010339 ACTTCTTTTCAAGGAGTGCTATACT 57.990 36.000 0.00 0.00 45.68 2.12


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

AutoCloner maintained by Alex Coulton.