Multiple sequence alignment - TraesCS2B01G300900

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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 TraesCS2B01G300900 chr2B 100.000 4625 0 0 1 4625 423670575 423665951 0.000000e+00 8541.0
1 TraesCS2B01G300900 chr2B 77.647 595 106 16 13 591 490315667 490315084 2.060000e-88 337.0
2 TraesCS2B01G300900 chr2D 93.681 2184 75 22 1624 3784 355687398 355685255 0.000000e+00 3210.0
3 TraesCS2B01G300900 chr2D 95.902 610 11 5 954 1563 355687992 355687397 0.000000e+00 976.0
4 TraesCS2B01G300900 chr2D 95.780 545 13 3 4084 4623 355684835 355684296 0.000000e+00 870.0
5 TraesCS2B01G300900 chr2D 91.826 575 33 7 1 574 355702050 355701489 0.000000e+00 789.0
6 TraesCS2B01G300900 chr2D 92.486 346 23 2 3739 4083 355685255 355684912 4.160000e-135 492.0
7 TraesCS2B01G300900 chr2D 95.789 285 8 4 652 933 355689877 355689594 1.520000e-124 457.0
8 TraesCS2B01G300900 chr2D 75.461 542 96 22 5 515 75499774 75499239 3.600000e-56 230.0
9 TraesCS2B01G300900 chr2D 100.000 50 0 0 563 612 355689913 355689864 4.930000e-15 93.5
10 TraesCS2B01G300900 chr2A 92.857 2184 91 34 1624 3784 475880561 475878420 0.000000e+00 3109.0
11 TraesCS2B01G300900 chr2A 93.976 913 26 9 652 1563 475881444 475880560 0.000000e+00 1354.0
12 TraesCS2B01G300900 chr2A 93.603 891 43 5 3739 4623 475878420 475877538 0.000000e+00 1317.0
13 TraesCS2B01G300900 chr2A 90.081 615 58 3 1 612 475882045 475881431 0.000000e+00 795.0
14 TraesCS2B01G300900 chr2A 93.478 46 2 1 2826 2871 278919345 278919389 2.990000e-07 67.6
15 TraesCS2B01G300900 chr6D 78.674 558 91 21 13 555 455014244 455014788 3.430000e-91 346.0
16 TraesCS2B01G300900 chr7B 76.696 678 120 19 1 663 114197286 114197940 4.430000e-90 342.0
17 TraesCS2B01G300900 chr6A 76.779 534 91 21 7 527 180588859 180589372 7.630000e-68 268.0
18 TraesCS2B01G300900 chr6A 75.357 560 106 23 5 548 479348828 479349371 1.660000e-59 241.0
19 TraesCS2B01G300900 chr3A 72.630 559 104 31 16 560 673295955 673295432 6.240000e-29 139.0
20 TraesCS2B01G300900 chr7A 78.947 190 37 3 13 200 573972762 573972574 4.860000e-25 126.0
21 TraesCS2B01G300900 chr7A 100.000 28 0 0 2874 2901 713877061 713877034 8.000000e-03 52.8
22 TraesCS2B01G300900 chr4B 97.619 42 1 0 2830 2871 99064598 99064557 6.420000e-09 73.1
23 TraesCS2B01G300900 chr4A 93.182 44 2 1 2828 2871 488252251 488252293 3.860000e-06 63.9
24 TraesCS2B01G300900 chrUn 96.774 31 1 0 2871 2901 378256997 378257027 8.000000e-03 52.8
25 TraesCS2B01G300900 chr3B 96.875 32 0 1 2871 2901 13772393 13772362 8.000000e-03 52.8


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 TraesCS2B01G300900 chr2B 423665951 423670575 4624 True 8541.000000 8541 100.000000 1 4625 1 chr2B.!!$R1 4624
1 TraesCS2B01G300900 chr2B 490315084 490315667 583 True 337.000000 337 77.647000 13 591 1 chr2B.!!$R2 578
2 TraesCS2B01G300900 chr2D 355684296 355689913 5617 True 1016.416667 3210 95.606333 563 4623 6 chr2D.!!$R3 4060
3 TraesCS2B01G300900 chr2D 355701489 355702050 561 True 789.000000 789 91.826000 1 574 1 chr2D.!!$R2 573
4 TraesCS2B01G300900 chr2D 75499239 75499774 535 True 230.000000 230 75.461000 5 515 1 chr2D.!!$R1 510
5 TraesCS2B01G300900 chr2A 475877538 475882045 4507 True 1643.750000 3109 92.629250 1 4623 4 chr2A.!!$R1 4622
6 TraesCS2B01G300900 chr6D 455014244 455014788 544 False 346.000000 346 78.674000 13 555 1 chr6D.!!$F1 542
7 TraesCS2B01G300900 chr7B 114197286 114197940 654 False 342.000000 342 76.696000 1 663 1 chr7B.!!$F1 662
8 TraesCS2B01G300900 chr6A 180588859 180589372 513 False 268.000000 268 76.779000 7 527 1 chr6A.!!$F1 520
9 TraesCS2B01G300900 chr6A 479348828 479349371 543 False 241.000000 241 75.357000 5 548 1 chr6A.!!$F2 543

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
225 262 1.135603 CGGGTTCAATCATGCAGTGTG 60.136 52.381 0.00 0.0 0.00 3.82 F
1206 2845 0.818445 GGCACCTCGAGGAGACGATA 60.818 60.000 37.69 0.0 41.39 2.92 F
1589 3228 0.033504 CGGGATCCATGTACCTTCGG 59.966 60.000 15.23 0.0 0.00 4.30 F
1594 3233 0.252330 TCCATGTACCTTCGGTGGGA 60.252 55.000 0.00 0.0 36.19 4.37 F
3343 4999 0.521242 CGAGTGGCGTTAAATGCAGC 60.521 55.000 0.00 0.0 34.64 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 3207 0.250338 GAAGGTACATGGATCCCGCC 60.250 60.0 9.90 4.25 0.00 6.13 R
2335 3986 0.036952 ACTTGGAGGTGCATCTGACG 60.037 55.0 2.86 0.00 0.00 4.35 R
3358 5014 0.584876 GGTGCACCTTACACGTGTTC 59.415 55.0 28.55 9.73 38.98 3.18 R
3571 5236 2.357009 CCAATTGCACAGCTATGGACTC 59.643 50.0 0.00 0.00 31.55 3.36 R
4227 6027 0.462759 GCCCACTGTGACCTGATAGC 60.463 60.0 9.86 0.00 0.00 2.97 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
66 68 9.770097 ATACGATGAATTGTCACTTTATGATCT 57.230 29.630 0.00 0.00 40.28 2.75
205 213 4.339530 TCAGAGTGAGTGGTGTATGATAGC 59.660 45.833 0.00 0.00 0.00 2.97
225 262 1.135603 CGGGTTCAATCATGCAGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
232 269 6.427853 GGTTCAATCATGCAGTGTGCTATATA 59.572 38.462 0.00 0.00 45.31 0.86
234 271 5.634859 TCAATCATGCAGTGTGCTATATACG 59.365 40.000 0.00 0.00 45.31 3.06
540 593 4.759516 ATTTAATCGCCGTTGAACTGTT 57.240 36.364 0.00 0.00 0.00 3.16
666 719 7.247728 TGTTTTCTCGATGTACCATTTTATGC 58.752 34.615 0.00 0.00 0.00 3.14
897 952 5.447818 GCACTGGCATTCAAATAGTAGACAC 60.448 44.000 0.00 0.00 40.72 3.67
1105 2744 3.151958 TAAGCTCAGATCGGCGGCC 62.152 63.158 9.54 9.54 0.00 6.13
1206 2845 0.818445 GGCACCTCGAGGAGACGATA 60.818 60.000 37.69 0.00 41.39 2.92
1347 2986 2.597217 CAAAACGCAGCTCCCCCA 60.597 61.111 0.00 0.00 0.00 4.96
1533 3172 1.160137 GGCCATGCGATCCTAACATC 58.840 55.000 0.00 0.00 0.00 3.06
1544 3183 5.274718 CGATCCTAACATCTATCATACCGC 58.725 45.833 0.00 0.00 0.00 5.68
1563 3202 1.338200 GCGTGTGAACCTGAGGAGAAT 60.338 52.381 4.99 0.00 0.00 2.40
1564 3203 2.341257 CGTGTGAACCTGAGGAGAATG 58.659 52.381 4.99 0.00 0.00 2.67
1565 3204 2.289072 CGTGTGAACCTGAGGAGAATGT 60.289 50.000 4.99 0.00 0.00 2.71
1566 3205 3.070018 GTGTGAACCTGAGGAGAATGTG 58.930 50.000 4.99 0.00 0.00 3.21
1567 3206 2.079925 GTGAACCTGAGGAGAATGTGC 58.920 52.381 4.99 0.00 0.00 4.57
1568 3207 1.338105 TGAACCTGAGGAGAATGTGCG 60.338 52.381 4.99 0.00 0.00 5.34
1569 3208 0.036010 AACCTGAGGAGAATGTGCGG 60.036 55.000 4.99 0.00 0.00 5.69
1570 3209 1.817099 CCTGAGGAGAATGTGCGGC 60.817 63.158 0.00 0.00 0.00 6.53
1571 3210 2.125552 TGAGGAGAATGTGCGGCG 60.126 61.111 0.51 0.51 0.00 6.46
1572 3211 2.892425 GAGGAGAATGTGCGGCGG 60.892 66.667 9.78 0.00 0.00 6.13
1573 3212 4.473520 AGGAGAATGTGCGGCGGG 62.474 66.667 9.78 0.00 0.00 6.13
1574 3213 4.467084 GGAGAATGTGCGGCGGGA 62.467 66.667 9.78 0.00 0.00 5.14
1575 3214 2.203070 GAGAATGTGCGGCGGGAT 60.203 61.111 9.78 0.00 0.00 3.85
1576 3215 2.203070 AGAATGTGCGGCGGGATC 60.203 61.111 9.78 0.00 0.00 3.36
1577 3216 3.279875 GAATGTGCGGCGGGATCC 61.280 66.667 9.78 1.92 0.00 3.36
1578 3217 4.108299 AATGTGCGGCGGGATCCA 62.108 61.111 15.23 0.00 0.00 3.41
1579 3218 3.420206 AATGTGCGGCGGGATCCAT 62.420 57.895 15.23 0.00 0.00 3.41
1580 3219 4.854924 TGTGCGGCGGGATCCATG 62.855 66.667 15.23 6.47 0.00 3.66
1581 3220 4.856801 GTGCGGCGGGATCCATGT 62.857 66.667 15.23 0.00 0.00 3.21
1582 3221 3.157949 TGCGGCGGGATCCATGTA 61.158 61.111 15.23 0.00 0.00 2.29
1583 3222 2.665185 GCGGCGGGATCCATGTAC 60.665 66.667 15.23 2.44 0.00 2.90
1584 3223 2.030562 CGGCGGGATCCATGTACC 59.969 66.667 15.23 5.91 0.00 3.34
1585 3224 2.507854 CGGCGGGATCCATGTACCT 61.508 63.158 15.23 0.00 0.00 3.08
1586 3225 1.837090 GGCGGGATCCATGTACCTT 59.163 57.895 15.23 0.00 0.00 3.50
1587 3226 0.250338 GGCGGGATCCATGTACCTTC 60.250 60.000 15.23 0.00 0.00 3.46
1588 3227 0.600255 GCGGGATCCATGTACCTTCG 60.600 60.000 15.23 5.47 0.00 3.79
1589 3228 0.033504 CGGGATCCATGTACCTTCGG 59.966 60.000 15.23 0.00 0.00 4.30
1590 3229 1.129058 GGGATCCATGTACCTTCGGT 58.871 55.000 15.23 0.00 40.16 4.69
1591 3230 1.202651 GGGATCCATGTACCTTCGGTG 60.203 57.143 15.23 0.00 36.19 4.94
1592 3231 1.202651 GGATCCATGTACCTTCGGTGG 60.203 57.143 6.95 0.00 36.19 4.61
1593 3232 0.837272 ATCCATGTACCTTCGGTGGG 59.163 55.000 0.00 0.00 36.19 4.61
1594 3233 0.252330 TCCATGTACCTTCGGTGGGA 60.252 55.000 0.00 0.00 36.19 4.37
1595 3234 0.616371 CCATGTACCTTCGGTGGGAA 59.384 55.000 0.00 0.00 36.19 3.97
1596 3235 1.003812 CCATGTACCTTCGGTGGGAAA 59.996 52.381 0.00 0.00 36.19 3.13
1597 3236 2.356135 CATGTACCTTCGGTGGGAAAG 58.644 52.381 0.00 0.00 36.19 2.62
1598 3237 1.719529 TGTACCTTCGGTGGGAAAGA 58.280 50.000 0.00 0.00 36.19 2.52
1599 3238 2.262637 TGTACCTTCGGTGGGAAAGAT 58.737 47.619 0.00 0.00 36.19 2.40
1600 3239 2.640826 TGTACCTTCGGTGGGAAAGATT 59.359 45.455 0.00 0.00 36.19 2.40
1601 3240 2.200373 ACCTTCGGTGGGAAAGATTG 57.800 50.000 0.00 0.00 32.98 2.67
1602 3241 1.423921 ACCTTCGGTGGGAAAGATTGT 59.576 47.619 0.00 0.00 32.98 2.71
1603 3242 2.640826 ACCTTCGGTGGGAAAGATTGTA 59.359 45.455 0.00 0.00 32.98 2.41
1604 3243 3.270877 CCTTCGGTGGGAAAGATTGTAG 58.729 50.000 0.00 0.00 33.34 2.74
1605 3244 3.055385 CCTTCGGTGGGAAAGATTGTAGA 60.055 47.826 0.00 0.00 33.34 2.59
1606 3245 4.564821 CCTTCGGTGGGAAAGATTGTAGAA 60.565 45.833 0.00 0.00 33.34 2.10
1607 3246 3.934068 TCGGTGGGAAAGATTGTAGAAC 58.066 45.455 0.00 0.00 0.00 3.01
1608 3247 3.325425 TCGGTGGGAAAGATTGTAGAACA 59.675 43.478 0.00 0.00 0.00 3.18
1609 3248 4.069304 CGGTGGGAAAGATTGTAGAACAA 58.931 43.478 0.00 0.00 42.95 2.83
1610 3249 4.083484 CGGTGGGAAAGATTGTAGAACAAC 60.083 45.833 0.00 0.00 41.40 3.32
1611 3250 5.070685 GGTGGGAAAGATTGTAGAACAACT 58.929 41.667 0.00 0.00 41.40 3.16
1612 3251 6.235664 GGTGGGAAAGATTGTAGAACAACTA 58.764 40.000 0.00 0.00 41.40 2.24
1613 3252 6.884836 GGTGGGAAAGATTGTAGAACAACTAT 59.115 38.462 0.00 0.00 41.40 2.12
1614 3253 7.065923 GGTGGGAAAGATTGTAGAACAACTATC 59.934 40.741 0.00 0.00 41.40 2.08
1615 3254 7.065923 GTGGGAAAGATTGTAGAACAACTATCC 59.934 40.741 0.00 1.92 41.40 2.59
1616 3255 6.258068 GGGAAAGATTGTAGAACAACTATCCG 59.742 42.308 0.00 0.00 41.40 4.18
1617 3256 6.258068 GGAAAGATTGTAGAACAACTATCCGG 59.742 42.308 0.00 0.00 41.40 5.14
1618 3257 6.540438 AAGATTGTAGAACAACTATCCGGA 57.460 37.500 6.61 6.61 41.40 5.14
1619 3258 6.732896 AGATTGTAGAACAACTATCCGGAT 57.267 37.500 22.95 22.95 41.40 4.18
1620 3259 6.516718 AGATTGTAGAACAACTATCCGGATG 58.483 40.000 27.55 18.17 41.40 3.51
1621 3260 5.670792 TTGTAGAACAACTATCCGGATGT 57.329 39.130 27.55 18.81 32.34 3.06
1622 3261 5.670792 TGTAGAACAACTATCCGGATGTT 57.329 39.130 27.55 22.71 38.62 2.71
1635 3274 5.031066 TCCGGATGTTAAATTAGGGACAG 57.969 43.478 0.00 0.00 0.00 3.51
1685 3328 6.129179 ACATTTCGATTTTGGAGATATGGGT 58.871 36.000 0.00 0.00 30.97 4.51
1705 3348 6.698380 TGGGTCTATTTGAAACTAGTGAGTC 58.302 40.000 0.00 0.00 33.58 3.36
1717 3360 4.781934 ACTAGTGAGTCAAGTGCCTTTTT 58.218 39.130 0.00 0.00 0.00 1.94
1730 3373 2.872245 TGCCTTTTTCTTGTCTGACTCG 59.128 45.455 9.51 0.22 0.00 4.18
1732 3375 3.748568 GCCTTTTTCTTGTCTGACTCGAT 59.251 43.478 9.51 0.00 0.00 3.59
1735 3378 6.092807 GCCTTTTTCTTGTCTGACTCGATAAT 59.907 38.462 9.51 0.00 0.00 1.28
1736 3379 7.277981 GCCTTTTTCTTGTCTGACTCGATAATA 59.722 37.037 9.51 0.00 0.00 0.98
1737 3380 9.151471 CCTTTTTCTTGTCTGACTCGATAATAA 57.849 33.333 9.51 0.00 0.00 1.40
1741 3384 9.869757 TTTCTTGTCTGACTCGATAATAAATCA 57.130 29.630 9.51 0.00 0.00 2.57
1742 3385 9.869757 TTCTTGTCTGACTCGATAATAAATCAA 57.130 29.630 9.51 0.00 0.00 2.57
1771 3414 7.881643 ATGCATAACATTTTTAGCAAACGAA 57.118 28.000 0.00 0.00 34.40 3.85
1796 3439 2.429971 TGCCACATTTGAGCAGTTGAAA 59.570 40.909 0.00 0.00 31.65 2.69
1825 3468 7.442666 GCTAACCATTATTTCCCTAGAACAGAG 59.557 40.741 0.00 0.00 0.00 3.35
1878 3522 3.135994 GCGAACAAGAACTTTGGGTAGA 58.864 45.455 0.00 0.00 0.00 2.59
2040 3691 6.355397 AGCTATGATTGAATCAACAGAACG 57.645 37.500 12.36 0.00 43.50 3.95
2112 3763 4.017808 AGTGCTCGTGATTACTAGGTTCT 58.982 43.478 0.00 0.00 0.00 3.01
2125 3776 5.857822 ACTAGGTTCTCATTTTGTTACGC 57.142 39.130 0.00 0.00 0.00 4.42
2307 3958 6.143206 TCAGGATATTATCAGGAACCAGTCA 58.857 40.000 6.04 0.00 0.00 3.41
2322 3973 3.162666 CCAGTCAGTACTTGGTACCAGA 58.837 50.000 15.65 4.86 39.58 3.86
2335 3986 3.251571 GGTACCAGATCAGTCGTTGAAC 58.748 50.000 7.15 0.00 39.77 3.18
2348 3999 1.512926 GTTGAACGTCAGATGCACCT 58.487 50.000 0.00 0.00 0.00 4.00
2478 4129 1.616159 GGTCTTTGGCTGCAAACCTA 58.384 50.000 0.50 0.00 0.00 3.08
2502 4153 3.465403 CCCAGACAGAGCCCCTCG 61.465 72.222 0.00 0.00 35.36 4.63
2506 4157 1.077625 AGACAGAGCCCCTCGTTCT 59.922 57.895 0.00 0.00 35.36 3.01
2673 4326 4.467082 TCTGCATGCCTTGAATTTACCAAT 59.533 37.500 16.68 0.00 0.00 3.16
2696 4349 7.783090 ATGTTGATGTATGTCTTTAGAGCAG 57.217 36.000 0.00 0.00 0.00 4.24
2823 4477 2.461695 TCCCTAGTGGAAGCTTCTCTG 58.538 52.381 25.05 16.00 41.40 3.35
2838 4492 6.066032 AGCTTCTCTGTATAGTACTTCCTCC 58.934 44.000 0.00 0.00 0.00 4.30
2855 4509 6.101296 ACTTCCTCCGTCCCAAATTATAAGAT 59.899 38.462 0.00 0.00 0.00 2.40
2967 4622 8.671384 TTACAATATCCGTCTTTTAATCCAGG 57.329 34.615 0.00 0.00 0.00 4.45
2975 4630 5.878116 CCGTCTTTTAATCCAGGAACATGTA 59.122 40.000 0.00 0.00 0.00 2.29
3158 4813 6.881065 TGCTGCTAATCAATTCTTACAAGTCT 59.119 34.615 0.00 0.00 0.00 3.24
3176 4831 3.906846 AGTCTCAAGGGATCTGACAGTTT 59.093 43.478 1.59 0.00 0.00 2.66
3200 4855 3.604667 TGCCAAGGCCAAACTGCG 61.605 61.111 5.01 0.00 41.09 5.18
3206 4861 4.097863 GGCCAAACTGCGTACGGC 62.098 66.667 18.39 9.59 42.21 5.68
3223 4878 1.594862 CGGCGCTCTCTTTAATTGGAG 59.405 52.381 7.64 0.00 0.00 3.86
3262 4917 4.345257 ACCAAAGTAGATGCGATATGACCT 59.655 41.667 0.00 0.00 0.00 3.85
3288 4944 9.814899 TGATCACTGTTACAAAATTGTGAAATT 57.185 25.926 1.62 0.00 42.31 1.82
3343 4999 0.521242 CGAGTGGCGTTAAATGCAGC 60.521 55.000 0.00 0.00 34.64 5.25
3358 5014 0.727398 GCAGCTTTGCTAGTAACCGG 59.273 55.000 0.00 0.00 36.40 5.28
3380 5044 1.234821 CACGTGTAAGGTGCACCAAT 58.765 50.000 36.39 26.15 46.32 3.16
3403 5067 1.528129 GCTATGGCCATAACAGGAGC 58.472 55.000 25.38 21.35 0.00 4.70
3407 5071 3.710209 ATGGCCATAACAGGAGCTATC 57.290 47.619 19.18 0.00 0.00 2.08
3481 5146 7.416964 TCCCTTTCTTTTCTTTTGTGATCAA 57.583 32.000 0.00 0.00 0.00 2.57
3506 5171 5.295787 TGTTTATGTGGACTTGTGTTCTGTC 59.704 40.000 0.00 0.00 0.00 3.51
3527 5192 7.120285 TCTGTCTGGAGCATATTCTTTTCTTTG 59.880 37.037 0.00 0.00 0.00 2.77
3571 5236 9.546909 GATCGTGATATGCCTGTAAAATATTTG 57.453 33.333 0.39 0.00 0.00 2.32
3577 5242 8.995027 ATATGCCTGTAAAATATTTGAGTCCA 57.005 30.769 0.39 0.00 0.00 4.02
3619 5287 6.988522 TCCCATTCGATCGTATTTATTCAGA 58.011 36.000 15.94 0.00 0.00 3.27
3620 5288 7.090808 TCCCATTCGATCGTATTTATTCAGAG 58.909 38.462 15.94 0.00 0.00 3.35
3633 5301 7.979786 ATTTATTCAGAGGGAGTTCTGTAGA 57.020 36.000 3.26 0.00 43.96 2.59
3669 5337 7.259290 TCTAAGTTTTTCGCATGAGAGTTTT 57.741 32.000 0.00 0.00 0.00 2.43
3683 5351 5.880901 TGAGAGTTTTAGAGCCTTTGGAAT 58.119 37.500 0.00 0.00 0.00 3.01
3684 5352 5.707298 TGAGAGTTTTAGAGCCTTTGGAATG 59.293 40.000 0.00 0.00 0.00 2.67
3685 5353 5.880901 AGAGTTTTAGAGCCTTTGGAATGA 58.119 37.500 0.00 0.00 0.00 2.57
3686 5354 6.488715 AGAGTTTTAGAGCCTTTGGAATGAT 58.511 36.000 0.00 0.00 0.00 2.45
3687 5355 6.376581 AGAGTTTTAGAGCCTTTGGAATGATG 59.623 38.462 0.00 0.00 0.00 3.07
3695 5363 2.223876 CCTTTGGAATGATGGAATGGCG 60.224 50.000 0.00 0.00 0.00 5.69
3723 5395 7.065216 AGAATATGTTCTGTTCACATTCACG 57.935 36.000 3.62 0.00 42.97 4.35
3763 5479 4.394795 CATTCGCTCTTAACCAAGAAACG 58.605 43.478 0.00 0.00 40.28 3.60
3764 5480 1.796459 TCGCTCTTAACCAAGAAACGC 59.204 47.619 5.19 0.00 40.28 4.84
3784 5500 4.142026 ACGCCTTCATGCAATACTGTAGTA 60.142 41.667 0.00 0.00 34.67 1.82
3797 5513 8.601476 GCAATACTGTAGTAAAACACCTACATC 58.399 37.037 0.00 0.00 33.76 3.06
3875 5591 9.589111 TTGTTTAGTTTTCCTTGTTTCATAACC 57.411 29.630 0.00 0.00 33.15 2.85
3877 5593 9.589111 GTTTAGTTTTCCTTGTTTCATAACCAA 57.411 29.630 0.00 0.00 33.15 3.67
3884 5600 9.921637 TTTCCTTGTTTCATAACCAAATACATC 57.078 29.630 0.00 0.00 33.15 3.06
3886 5602 8.739039 TCCTTGTTTCATAACCAAATACATCTG 58.261 33.333 0.00 0.00 33.15 2.90
3888 5604 7.459795 TGTTTCATAACCAAATACATCTGCA 57.540 32.000 0.00 0.00 33.15 4.41
3951 5667 5.665459 ACTAGTAGCTCATGTGAACAATCC 58.335 41.667 0.00 0.00 0.00 3.01
3968 5684 0.320073 TCCGGTTCTCGAAATTGCGT 60.320 50.000 5.57 0.00 42.43 5.24
3993 5709 3.777478 CCATGCATCATTCAGTGGAAAC 58.223 45.455 0.00 0.00 36.43 2.78
4003 5719 7.364522 TCATTCAGTGGAAACGAAAGAATAG 57.635 36.000 0.00 0.00 36.43 1.73
4079 5879 4.892934 TCATAACCTGCCATTCCCAATTAC 59.107 41.667 0.00 0.00 0.00 1.89
4080 5880 3.473113 AACCTGCCATTCCCAATTACT 57.527 42.857 0.00 0.00 0.00 2.24
4081 5881 3.018423 ACCTGCCATTCCCAATTACTC 57.982 47.619 0.00 0.00 0.00 2.59
4082 5882 2.310538 CCTGCCATTCCCAATTACTCC 58.689 52.381 0.00 0.00 0.00 3.85
4083 5883 1.949525 CTGCCATTCCCAATTACTCCG 59.050 52.381 0.00 0.00 0.00 4.63
4084 5884 1.283613 TGCCATTCCCAATTACTCCGT 59.716 47.619 0.00 0.00 0.00 4.69
4085 5885 2.506231 TGCCATTCCCAATTACTCCGTA 59.494 45.455 0.00 0.00 0.00 4.02
4119 5919 4.806330 ACAGACAACACTACATAGAACCG 58.194 43.478 0.00 0.00 0.00 4.44
4161 5961 2.995547 GGGTGTTACTCCCGGCAT 59.004 61.111 6.75 0.00 35.27 4.40
4172 5972 1.006102 CCCGGCATCTACATCGTCC 60.006 63.158 0.00 0.00 0.00 4.79
4227 6027 2.284150 CACTGTACAAACTGGACACACG 59.716 50.000 0.00 0.00 36.02 4.49
4360 6165 5.970317 TGTCGATTTCTACCAGTAAGTCA 57.030 39.130 0.00 0.00 0.00 3.41
4363 6168 8.058667 TGTCGATTTCTACCAGTAAGTCATTA 57.941 34.615 0.00 0.00 0.00 1.90
4449 6254 1.531423 AGTGCACTGCTGAGATTTGG 58.469 50.000 20.97 0.00 0.00 3.28
4488 6293 4.990426 ACAAAACCAAATGCACTCTAATGC 59.010 37.500 0.00 0.00 46.32 3.56
4513 6318 6.546395 GTTCTACATAGCTGTCAACATTTGG 58.454 40.000 0.00 0.00 36.79 3.28
4624 6429 8.561738 TTACACATCAAAGAGTAAGATTTCCC 57.438 34.615 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 144 5.125578 GGCCAAAGAAGAAAAATAGATCGGT 59.874 40.000 0.00 0.00 0.00 4.69
205 213 1.135603 CACACTGCATGATTGAACCCG 60.136 52.381 0.00 0.00 0.00 5.28
225 262 5.238868 TCACCTCTTGTCACTCGTATATAGC 59.761 44.000 0.00 0.00 0.00 2.97
232 269 1.399714 TGTCACCTCTTGTCACTCGT 58.600 50.000 0.00 0.00 0.00 4.18
234 271 3.181475 TGTCTTGTCACCTCTTGTCACTC 60.181 47.826 0.00 0.00 0.00 3.51
551 604 7.761409 TCTCCAAGCAAAATATATGTGTTGTC 58.239 34.615 4.50 0.00 0.00 3.18
561 614 4.801164 AGCCATCTCTCCAAGCAAAATAT 58.199 39.130 0.00 0.00 0.00 1.28
666 719 4.142359 GGTACATAGTCTCACCACTCACAG 60.142 50.000 0.00 0.00 0.00 3.66
758 812 7.759465 ACAACATCAGCTGAATAGAGAAAATG 58.241 34.615 22.50 12.55 0.00 2.32
865 920 0.523072 GAATGCCAGTGCGTTGTCAT 59.477 50.000 0.00 0.00 46.55 3.06
1067 2706 0.752376 GCTCGGTCCTGGTAGCTACT 60.752 60.000 22.74 0.00 32.18 2.57
1068 2707 0.752376 AGCTCGGTCCTGGTAGCTAC 60.752 60.000 15.88 15.88 43.29 3.58
1074 2713 1.305381 AGCTTAGCTCGGTCCTGGT 60.305 57.895 0.00 0.00 30.62 4.00
1105 2744 1.439644 GCCTGAACCCTAGCTCTCG 59.560 63.158 0.00 0.00 0.00 4.04
1533 3172 2.124903 GGTTCACACGCGGTATGATAG 58.875 52.381 12.47 0.00 0.00 2.08
1544 3183 2.289072 ACATTCTCCTCAGGTTCACACG 60.289 50.000 0.00 0.00 0.00 4.49
1563 3202 4.854924 CATGGATCCCGCCGCACA 62.855 66.667 9.90 0.00 0.00 4.57
1564 3203 3.454587 TACATGGATCCCGCCGCAC 62.455 63.158 9.90 0.00 0.00 5.34
1565 3204 3.157949 TACATGGATCCCGCCGCA 61.158 61.111 9.90 0.00 0.00 5.69
1566 3205 2.665185 GTACATGGATCCCGCCGC 60.665 66.667 9.90 0.00 0.00 6.53
1567 3206 2.030562 GGTACATGGATCCCGCCG 59.969 66.667 9.90 0.00 0.00 6.46
1568 3207 0.250338 GAAGGTACATGGATCCCGCC 60.250 60.000 9.90 4.25 0.00 6.13
1569 3208 0.600255 CGAAGGTACATGGATCCCGC 60.600 60.000 9.90 0.00 0.00 6.13
1570 3209 3.588277 CGAAGGTACATGGATCCCG 57.412 57.895 9.90 2.64 0.00 5.14
1584 3223 4.202245 TCTACAATCTTTCCCACCGAAG 57.798 45.455 0.00 0.00 0.00 3.79
1585 3224 4.202377 TGTTCTACAATCTTTCCCACCGAA 60.202 41.667 0.00 0.00 0.00 4.30
1586 3225 3.325425 TGTTCTACAATCTTTCCCACCGA 59.675 43.478 0.00 0.00 0.00 4.69
1587 3226 3.670625 TGTTCTACAATCTTTCCCACCG 58.329 45.455 0.00 0.00 0.00 4.94
1588 3227 5.070685 AGTTGTTCTACAATCTTTCCCACC 58.929 41.667 0.00 0.00 40.59 4.61
1589 3228 7.065923 GGATAGTTGTTCTACAATCTTTCCCAC 59.934 40.741 13.73 0.00 40.59 4.61
1590 3229 7.110155 GGATAGTTGTTCTACAATCTTTCCCA 58.890 38.462 13.73 0.00 40.59 4.37
1591 3230 6.258068 CGGATAGTTGTTCTACAATCTTTCCC 59.742 42.308 16.17 0.00 40.59 3.97
1592 3231 6.258068 CCGGATAGTTGTTCTACAATCTTTCC 59.742 42.308 0.00 14.20 40.59 3.13
1593 3232 7.039882 TCCGGATAGTTGTTCTACAATCTTTC 58.960 38.462 0.00 0.00 40.59 2.62
1594 3233 6.942976 TCCGGATAGTTGTTCTACAATCTTT 58.057 36.000 0.00 0.00 40.59 2.52
1595 3234 6.540438 TCCGGATAGTTGTTCTACAATCTT 57.460 37.500 0.00 0.00 40.59 2.40
1596 3235 6.098409 ACATCCGGATAGTTGTTCTACAATCT 59.902 38.462 18.63 0.00 40.59 2.40
1597 3236 6.281405 ACATCCGGATAGTTGTTCTACAATC 58.719 40.000 18.63 0.00 40.59 2.67
1598 3237 6.235231 ACATCCGGATAGTTGTTCTACAAT 57.765 37.500 18.63 0.00 40.59 2.71
1599 3238 5.670792 ACATCCGGATAGTTGTTCTACAA 57.329 39.130 18.63 0.00 35.42 2.41
1600 3239 5.670792 AACATCCGGATAGTTGTTCTACA 57.329 39.130 18.63 0.00 0.00 2.74
1601 3240 8.658499 ATTTAACATCCGGATAGTTGTTCTAC 57.342 34.615 27.99 0.00 34.39 2.59
1603 3242 9.326413 CTAATTTAACATCCGGATAGTTGTTCT 57.674 33.333 27.99 17.97 34.39 3.01
1604 3243 8.557029 CCTAATTTAACATCCGGATAGTTGTTC 58.443 37.037 27.99 0.00 34.39 3.18
1605 3244 7.501225 CCCTAATTTAACATCCGGATAGTTGTT 59.499 37.037 27.99 25.07 36.37 2.83
1606 3245 6.996282 CCCTAATTTAACATCCGGATAGTTGT 59.004 38.462 27.99 18.63 0.00 3.32
1607 3246 7.172703 GTCCCTAATTTAACATCCGGATAGTTG 59.827 40.741 27.99 18.08 0.00 3.16
1608 3247 7.147444 TGTCCCTAATTTAACATCCGGATAGTT 60.147 37.037 25.34 25.34 0.00 2.24
1609 3248 6.328148 TGTCCCTAATTTAACATCCGGATAGT 59.672 38.462 18.63 14.69 0.00 2.12
1610 3249 6.765403 TGTCCCTAATTTAACATCCGGATAG 58.235 40.000 18.63 14.01 0.00 2.08
1611 3250 6.328148 ACTGTCCCTAATTTAACATCCGGATA 59.672 38.462 18.63 0.42 0.00 2.59
1612 3251 5.132144 ACTGTCCCTAATTTAACATCCGGAT 59.868 40.000 12.38 12.38 0.00 4.18
1613 3252 4.472108 ACTGTCCCTAATTTAACATCCGGA 59.528 41.667 6.61 6.61 0.00 5.14
1614 3253 4.777463 ACTGTCCCTAATTTAACATCCGG 58.223 43.478 0.00 0.00 0.00 5.14
1615 3254 5.878116 TGAACTGTCCCTAATTTAACATCCG 59.122 40.000 0.00 0.00 0.00 4.18
1616 3255 7.696992 TTGAACTGTCCCTAATTTAACATCC 57.303 36.000 0.00 0.00 0.00 3.51
1617 3256 8.190784 CCATTGAACTGTCCCTAATTTAACATC 58.809 37.037 0.00 0.00 0.00 3.06
1618 3257 7.673926 ACCATTGAACTGTCCCTAATTTAACAT 59.326 33.333 0.00 0.00 0.00 2.71
1619 3258 7.007723 ACCATTGAACTGTCCCTAATTTAACA 58.992 34.615 0.00 0.00 0.00 2.41
1620 3259 7.462571 ACCATTGAACTGTCCCTAATTTAAC 57.537 36.000 0.00 0.00 0.00 2.01
1621 3260 8.164733 TGTACCATTGAACTGTCCCTAATTTAA 58.835 33.333 0.00 0.00 0.00 1.52
1622 3261 7.691213 TGTACCATTGAACTGTCCCTAATTTA 58.309 34.615 0.00 0.00 0.00 1.40
1635 3274 7.437862 TCATTTTTCAAAGCTGTACCATTGAAC 59.562 33.333 8.20 0.00 40.40 3.18
1685 3328 7.385205 GCACTTGACTCACTAGTTTCAAATAGA 59.615 37.037 10.90 0.00 35.56 1.98
1767 3410 3.059166 GCTCAAATGTGGCAAAATTCGT 58.941 40.909 0.00 0.00 0.00 3.85
1771 3414 3.756933 ACTGCTCAAATGTGGCAAAAT 57.243 38.095 0.00 0.00 32.70 1.82
1796 3439 8.058847 TGTTCTAGGGAAATAATGGTTAGCATT 58.941 33.333 14.17 14.17 32.81 3.56
1928 3579 1.772453 GATAATCAACCCCCTTCCCGA 59.228 52.381 0.00 0.00 0.00 5.14
1931 3582 3.399305 AGGATGATAATCAACCCCCTTCC 59.601 47.826 0.00 0.00 39.85 3.46
2040 3691 5.463724 GGAATTAGATCGACACTGGATGTTC 59.536 44.000 0.00 0.00 43.56 3.18
2275 3926 5.188555 TCCTGATAATATCCTGAGTCATGCC 59.811 44.000 0.00 0.00 0.00 4.40
2307 3958 3.695060 CGACTGATCTGGTACCAAGTACT 59.305 47.826 17.11 0.00 38.85 2.73
2322 3973 3.577649 ATCTGACGTTCAACGACTGAT 57.422 42.857 22.29 22.29 46.05 2.90
2335 3986 0.036952 ACTTGGAGGTGCATCTGACG 60.037 55.000 2.86 0.00 0.00 4.35
2348 3999 9.177608 CATCTCATTCAAAATAGGTTACTTGGA 57.822 33.333 0.00 0.00 0.00 3.53
2478 4129 1.202940 GGGCTCTGTCTGGGAAACTTT 60.203 52.381 0.00 0.00 0.00 2.66
2502 4153 6.036470 CCAGAACCAAGACAAAGAAAAGAAC 58.964 40.000 0.00 0.00 0.00 3.01
2506 4157 5.993748 AACCAGAACCAAGACAAAGAAAA 57.006 34.783 0.00 0.00 0.00 2.29
2641 4292 1.107538 AGGCATGCAGATGATGGCAC 61.108 55.000 21.36 0.00 46.23 5.01
2673 4326 6.591448 CACTGCTCTAAAGACATACATCAACA 59.409 38.462 0.00 0.00 0.00 3.33
2696 4349 2.223805 CCTCTGGAAAACCTTGTTGCAC 60.224 50.000 0.00 0.00 0.00 4.57
2764 4418 6.022107 TCTAGTGATTGCTAGGGGTACTTA 57.978 41.667 0.00 0.00 39.05 2.24
2823 4477 3.825328 TGGGACGGAGGAAGTACTATAC 58.175 50.000 0.00 0.00 0.00 1.47
2838 4492 8.032451 ACCAAAAACATCTTATAATTTGGGACG 58.968 33.333 21.54 5.68 46.89 4.79
2855 4509 9.796180 TTATAAGACTTTAGCCTACCAAAAACA 57.204 29.630 0.00 0.00 0.00 2.83
2975 4630 8.508875 CCTTACCAGAAAAATGTACGTTATGTT 58.491 33.333 0.00 0.00 0.00 2.71
3158 4813 4.566278 CCATCAAACTGTCAGATCCCTTGA 60.566 45.833 6.91 7.51 0.00 3.02
3176 4831 2.669744 TTTGGCCTTGGCACCCATCA 62.670 55.000 14.04 0.00 37.98 3.07
3200 4855 2.284417 CCAATTAAAGAGAGCGCCGTAC 59.716 50.000 2.29 0.00 0.00 3.67
3223 4878 5.440610 ACTTTGGTCATATCCCATTCACTC 58.559 41.667 0.00 0.00 0.00 3.51
3262 4917 9.814899 AATTTCACAATTTTGTAACAGTGATCA 57.185 25.926 0.00 0.00 39.91 2.92
3288 4944 2.307392 TCCTTAAGGGCAATACAGCACA 59.693 45.455 21.53 0.00 41.46 4.57
3343 4999 2.410730 CGTGTTCCGGTTACTAGCAAAG 59.589 50.000 0.00 0.00 0.00 2.77
3358 5014 0.584876 GGTGCACCTTACACGTGTTC 59.415 55.000 28.55 9.73 38.98 3.18
3401 5065 7.072562 TCCTCAGAGAAAATAGAAGGATAGCT 58.927 38.462 0.00 0.00 0.00 3.32
3403 5067 9.927668 GAATCCTCAGAGAAAATAGAAGGATAG 57.072 37.037 0.00 0.00 33.77 2.08
3407 5071 6.699642 GTCGAATCCTCAGAGAAAATAGAAGG 59.300 42.308 0.00 0.00 0.00 3.46
3481 5146 5.827797 ACAGAACACAAGTCCACATAAACAT 59.172 36.000 0.00 0.00 0.00 2.71
3506 5171 7.754027 CACTTCAAAGAAAAGAATATGCTCCAG 59.246 37.037 0.00 0.00 0.00 3.86
3527 5192 4.212214 ACGATCTTTCAGCACTTTCACTTC 59.788 41.667 0.00 0.00 0.00 3.01
3571 5236 2.357009 CCAATTGCACAGCTATGGACTC 59.643 50.000 0.00 0.00 31.55 3.36
3577 5242 2.648059 GGAGACCAATTGCACAGCTAT 58.352 47.619 0.00 0.00 0.00 2.97
3633 5301 7.606456 TGCGAAAAACTTAGAAGGATATCAGTT 59.394 33.333 4.83 1.73 0.00 3.16
3669 5337 4.860802 TTCCATCATTCCAAAGGCTCTA 57.139 40.909 0.00 0.00 0.00 2.43
3683 5351 1.543607 TTCTTTGCGCCATTCCATCA 58.456 45.000 4.18 0.00 0.00 3.07
3684 5352 2.877043 ATTCTTTGCGCCATTCCATC 57.123 45.000 4.18 0.00 0.00 3.51
3685 5353 3.638160 ACATATTCTTTGCGCCATTCCAT 59.362 39.130 4.18 0.00 0.00 3.41
3686 5354 3.023119 ACATATTCTTTGCGCCATTCCA 58.977 40.909 4.18 0.00 0.00 3.53
3687 5355 3.715628 ACATATTCTTTGCGCCATTCC 57.284 42.857 4.18 0.00 0.00 3.01
3695 5363 7.809331 TGAATGTGAACAGAACATATTCTTTGC 59.191 33.333 14.61 0.00 42.91 3.68
3723 5395 4.322567 GAATGGCAGGAATCCTCTATCAC 58.677 47.826 0.00 0.00 0.00 3.06
3763 5479 6.677781 TTTACTACAGTATTGCATGAAGGC 57.322 37.500 0.00 0.00 0.00 4.35
3764 5480 7.962918 GTGTTTTACTACAGTATTGCATGAAGG 59.037 37.037 0.00 0.00 0.00 3.46
3784 5500 8.100791 TGCAAGAAGTATAGATGTAGGTGTTTT 58.899 33.333 0.00 0.00 0.00 2.43
3797 5513 5.992217 GGTCCCTAATGTGCAAGAAGTATAG 59.008 44.000 0.00 0.00 0.00 1.31
3799 5515 4.385310 GGGTCCCTAATGTGCAAGAAGTAT 60.385 45.833 0.00 0.00 0.00 2.12
3874 5590 5.840243 TCTTTGGATGCAGATGTATTTGG 57.160 39.130 0.00 0.00 0.00 3.28
3875 5591 7.034685 TGATCTTTGGATGCAGATGTATTTG 57.965 36.000 0.00 0.00 29.41 2.32
3877 5593 7.486647 GTTTGATCTTTGGATGCAGATGTATT 58.513 34.615 0.00 0.00 29.41 1.89
3884 5600 2.749076 TCCGTTTGATCTTTGGATGCAG 59.251 45.455 0.00 0.00 31.46 4.41
3886 5602 3.957468 GATCCGTTTGATCTTTGGATGC 58.043 45.455 12.14 3.76 45.46 3.91
3917 5633 9.803315 CACATGAGCTACTAGTAACTAAATTGA 57.197 33.333 5.80 0.00 0.00 2.57
3951 5667 1.323534 CCTACGCAATTTCGAGAACCG 59.676 52.381 4.06 0.00 40.25 4.44
3968 5684 2.578786 CACTGAATGATGCATGGCCTA 58.421 47.619 2.46 0.00 0.00 3.93
3993 5709 5.355350 AGAATTTGGTCAGCCTATTCTTTCG 59.645 40.000 0.00 0.00 40.52 3.46
4003 5719 2.280628 CTCGGTAGAATTTGGTCAGCC 58.719 52.381 0.00 0.00 0.00 4.85
4079 5879 9.017669 GTTGTCTGTAAGTTATGTATTACGGAG 57.982 37.037 6.82 0.00 44.09 4.63
4080 5880 8.522003 TGTTGTCTGTAAGTTATGTATTACGGA 58.478 33.333 3.17 3.17 42.28 4.69
4081 5881 8.589629 GTGTTGTCTGTAAGTTATGTATTACGG 58.410 37.037 0.00 0.00 38.88 4.02
4082 5882 9.350357 AGTGTTGTCTGTAAGTTATGTATTACG 57.650 33.333 0.00 0.00 35.16 3.18
4119 5919 9.103861 CCTTCTGTTATCTAAAAAGAGGATGAC 57.896 37.037 0.00 0.00 0.00 3.06
4161 5961 3.281158 TGGTTGTATCGGACGATGTAGA 58.719 45.455 16.70 0.00 36.17 2.59
4172 5972 5.407502 TGTTGTAGAGTGATGGTTGTATCG 58.592 41.667 0.00 0.00 0.00 2.92
4227 6027 0.462759 GCCCACTGTGACCTGATAGC 60.463 60.000 9.86 0.00 0.00 2.97
4360 6165 7.164122 AGGCAACATCATCGATACTTGATAAT 58.836 34.615 0.00 0.00 41.41 1.28
4363 6168 4.965814 AGGCAACATCATCGATACTTGAT 58.034 39.130 0.00 0.00 41.41 2.57
4488 6293 6.243551 CAAATGTTGACAGCTATGTAGAACG 58.756 40.000 0.00 0.00 40.68 3.95


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

AutoCloner maintained by Alex Coulton.