Multiple sequence alignment - TraesCS1A01G261400

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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 TraesCS1A01G261400 chr1A 100.000 6043 0 0 1 6043 455823698 455817656 0.000000e+00 11160.0
1 TraesCS1A01G261400 chr1A 85.462 509 33 15 3103 3577 455663991 455663490 5.440000e-135 492.0
2 TraesCS1A01G261400 chr1B 89.352 4583 267 89 1 4453 478261610 478257119 0.000000e+00 5555.0
3 TraesCS1A01G261400 chr1B 92.205 898 52 7 4445 5339 478257075 478256193 0.000000e+00 1254.0
4 TraesCS1A01G261400 chr1B 83.784 1073 137 15 4188 5260 478081146 478080111 0.000000e+00 983.0
5 TraesCS1A01G261400 chr1B 87.472 447 49 6 3683 4126 478096227 478095785 5.400000e-140 508.0
6 TraesCS1A01G261400 chr1B 85.535 318 38 5 1 313 478432896 478432582 5.840000e-85 326.0
7 TraesCS1A01G261400 chr1B 80.577 381 35 23 3103 3450 478097034 478096660 2.160000e-64 257.0
8 TraesCS1A01G261400 chr1B 83.568 213 17 6 2912 3106 478255480 478255268 3.720000e-42 183.0
9 TraesCS1A01G261400 chr1B 91.209 91 5 2 404 494 478432446 478432359 2.960000e-23 121.0
10 TraesCS1A01G261400 chr1B 97.561 41 1 0 2912 2952 478255525 478255485 3.020000e-08 71.3
11 TraesCS1A01G261400 chr1D 90.891 3546 152 66 346 3787 355474698 355471220 0.000000e+00 4601.0
12 TraesCS1A01G261400 chr1D 90.592 1403 99 17 3882 5271 355471026 355469644 0.000000e+00 1829.0
13 TraesCS1A01G261400 chr1D 84.809 1073 127 16 4188 5260 355439421 355438385 0.000000e+00 1046.0
14 TraesCS1A01G261400 chr1D 85.740 554 66 9 5502 6043 136247758 136248310 1.890000e-159 573.0
15 TraesCS1A01G261400 chr1D 88.341 446 40 10 3685 4126 355440748 355440311 5.370000e-145 525.0
16 TraesCS1A01G261400 chr1D 91.854 356 22 3 1 353 355475223 355474872 1.960000e-134 490.0
17 TraesCS1A01G261400 chr1D 82.720 353 24 10 3103 3423 355441474 355441127 4.610000e-71 279.0
18 TraesCS1A01G261400 chr1D 84.186 215 14 5 2912 3106 355468896 355468682 2.220000e-44 191.0
19 TraesCS1A01G261400 chr1D 92.523 107 8 0 3471 3577 355441128 355441022 2.920000e-33 154.0
20 TraesCS1A01G261400 chr7D 88.956 661 58 8 5392 6043 362102973 362102319 0.000000e+00 802.0
21 TraesCS1A01G261400 chr7D 86.996 669 62 11 5395 6043 211659197 211659860 0.000000e+00 730.0
22 TraesCS1A01G261400 chr2D 88.839 672 49 12 5394 6043 322946899 322946232 0.000000e+00 802.0
23 TraesCS1A01G261400 chr2D 85.347 662 76 10 5398 6043 167885046 167885702 0.000000e+00 665.0
24 TraesCS1A01G261400 chr2D 90.129 233 19 3 5813 6043 322946907 322947137 3.540000e-77 300.0
25 TraesCS1A01G261400 chr7B 87.558 651 74 6 5395 6043 295787992 295787347 0.000000e+00 747.0
26 TraesCS1A01G261400 chr3B 87.348 656 67 10 5399 6043 449188827 449189477 0.000000e+00 737.0
27 TraesCS1A01G261400 chr3B 86.186 666 69 16 5398 6043 377353967 377354629 0.000000e+00 699.0
28 TraesCS1A01G261400 chr3B 80.909 220 42 0 4206 4425 675040629 675040848 2.240000e-39 174.0
29 TraesCS1A01G261400 chr3D 84.615 637 75 10 2630 3244 2095951 2096586 4.000000e-171 612.0
30 TraesCS1A01G261400 chr3D 81.431 517 54 20 3293 3786 2096666 2097163 9.500000e-103 385.0
31 TraesCS1A01G261400 chr3D 92.982 228 15 1 5817 6043 135395196 135395423 1.260000e-86 331.0
32 TraesCS1A01G261400 chr3D 81.931 404 54 11 4186 4583 2097885 2098275 2.100000e-84 324.0
33 TraesCS1A01G261400 chr3D 81.364 220 41 0 4206 4425 512676072 512675853 4.810000e-41 180.0
34 TraesCS1A01G261400 chr3D 96.226 53 2 0 4825 4877 2098567 2098619 3.000000e-13 87.9
35 TraesCS1A01G261400 chr3A 81.795 769 94 21 2455 3198 6898311 6897564 2.410000e-168 603.0
36 TraesCS1A01G261400 chr3A 83.250 400 53 7 4186 4582 6893192 6892804 7.450000e-94 355.0
37 TraesCS1A01G261400 chr3A 78.682 516 63 16 3293 3786 6894427 6893937 3.540000e-77 300.0
38 TraesCS1A01G261400 chr3A 84.925 199 30 0 4825 5023 6892502 6892304 1.030000e-47 202.0
39 TraesCS1A01G261400 chr7A 86.559 558 57 10 5493 6043 244399859 244400405 3.120000e-167 599.0
40 TraesCS1A01G261400 chr5A 92.958 213 13 2 5832 6043 610346618 610346407 5.880000e-80 309.0
41 TraesCS1A01G261400 chr5B 91.943 211 13 4 5835 6043 701827490 701827282 5.920000e-75 292.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G261400 chr1A 455817656 455823698 6042 True 11160.000 11160 100.00000 1 6043 1 chr1A.!!$R2 6042
1 TraesCS1A01G261400 chr1A 455663490 455663991 501 True 492.000 492 85.46200 3103 3577 1 chr1A.!!$R1 474
2 TraesCS1A01G261400 chr1B 478255268 478261610 6342 True 1765.825 5555 90.67150 1 5339 4 chr1B.!!$R3 5338
3 TraesCS1A01G261400 chr1B 478080111 478081146 1035 True 983.000 983 83.78400 4188 5260 1 chr1B.!!$R1 1072
4 TraesCS1A01G261400 chr1B 478095785 478097034 1249 True 382.500 508 84.02450 3103 4126 2 chr1B.!!$R2 1023
5 TraesCS1A01G261400 chr1B 478432359 478432896 537 True 223.500 326 88.37200 1 494 2 chr1B.!!$R4 493
6 TraesCS1A01G261400 chr1D 355468682 355475223 6541 True 1777.750 4601 89.38075 1 5271 4 chr1D.!!$R2 5270
7 TraesCS1A01G261400 chr1D 136247758 136248310 552 False 573.000 573 85.74000 5502 6043 1 chr1D.!!$F1 541
8 TraesCS1A01G261400 chr1D 355438385 355441474 3089 True 501.000 1046 87.09825 3103 5260 4 chr1D.!!$R1 2157
9 TraesCS1A01G261400 chr7D 362102319 362102973 654 True 802.000 802 88.95600 5392 6043 1 chr7D.!!$R1 651
10 TraesCS1A01G261400 chr7D 211659197 211659860 663 False 730.000 730 86.99600 5395 6043 1 chr7D.!!$F1 648
11 TraesCS1A01G261400 chr2D 322946232 322946899 667 True 802.000 802 88.83900 5394 6043 1 chr2D.!!$R1 649
12 TraesCS1A01G261400 chr2D 167885046 167885702 656 False 665.000 665 85.34700 5398 6043 1 chr2D.!!$F1 645
13 TraesCS1A01G261400 chr7B 295787347 295787992 645 True 747.000 747 87.55800 5395 6043 1 chr7B.!!$R1 648
14 TraesCS1A01G261400 chr3B 449188827 449189477 650 False 737.000 737 87.34800 5399 6043 1 chr3B.!!$F2 644
15 TraesCS1A01G261400 chr3B 377353967 377354629 662 False 699.000 699 86.18600 5398 6043 1 chr3B.!!$F1 645
16 TraesCS1A01G261400 chr3D 2095951 2098619 2668 False 352.225 612 86.05075 2630 4877 4 chr3D.!!$F2 2247
17 TraesCS1A01G261400 chr3A 6892304 6898311 6007 True 365.000 603 82.16300 2455 5023 4 chr3A.!!$R1 2568
18 TraesCS1A01G261400 chr7A 244399859 244400405 546 False 599.000 599 86.55900 5493 6043 1 chr7A.!!$F1 550

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
815 1107 0.172803 CAAACGACGGCTAGCTACCT 59.827 55.0 15.72 0.0 0.00 3.08 F
1243 1539 0.438830 GCTCGTGTTCGTCCATTGAC 59.561 55.0 0.00 0.0 38.18 3.18 F
1741 2061 0.609131 CGGTGTGCCAAGGGAAGATT 60.609 55.0 0.00 0.0 34.09 2.40 F
2679 3017 0.687757 AAGCTCCGCTGATGTCCCTA 60.688 55.0 0.00 0.0 39.62 3.53 F
2825 3168 0.988832 ACCCACGGAATACCATGTGT 59.011 50.0 0.00 0.0 35.59 3.72 F
4711 9824 0.614697 TCTGCAGCTACAGCACCCTA 60.615 55.0 9.47 0.0 45.16 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1987 0.111061 TCTGCATTGCACCAAGGAGT 59.889 50.000 7.38 0.0 33.79 3.85 R
2322 2653 0.112412 ACCGGCCATCCTTTTCTGTT 59.888 50.000 0.00 0.0 0.00 3.16 R
2799 3141 1.473788 GGTATTCCGTGGGTAATGCGT 60.474 52.381 0.00 0.0 0.00 5.24 R
4649 9760 0.884704 GTGCAAGGACACATGGACGT 60.885 55.000 0.00 0.0 40.40 4.34 R
4787 9943 4.447054 GGAGATCAGAACATGCGTCAATAG 59.553 45.833 0.00 0.0 0.00 1.73 R
5823 11225 0.390603 CATTCGTGGAAGCCGTGGTA 60.391 55.000 0.00 0.0 0.00 3.25 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
107 109 2.358737 GGCGGTGGACTTGGTCTG 60.359 66.667 0.00 0.00 32.47 3.51
111 113 1.754380 CGGTGGACTTGGTCTGGTCA 61.754 60.000 0.00 0.00 34.49 4.02
113 115 0.250338 GTGGACTTGGTCTGGTCACC 60.250 60.000 0.00 0.00 36.90 4.02
136 142 2.526120 GCAGTAACAGCGATCGGCC 61.526 63.158 18.30 0.22 45.17 6.13
380 605 4.129737 CCGGCGGTGATCACGACT 62.130 66.667 19.97 0.00 37.17 4.18
423 663 0.372679 CGTCGAGAGCTACGTTGCTA 59.627 55.000 24.13 6.28 44.17 3.49
424 664 1.812662 GTCGAGAGCTACGTTGCTAC 58.187 55.000 24.13 18.59 44.17 3.58
425 665 1.397692 GTCGAGAGCTACGTTGCTACT 59.602 52.381 24.13 20.57 44.17 2.57
510 750 0.671251 GCGGACTAGACTAGCAGCAT 59.329 55.000 9.52 0.00 0.00 3.79
527 767 2.489329 AGCATCACTCCAATTCAAACCG 59.511 45.455 0.00 0.00 0.00 4.44
535 775 1.871039 CCAATTCAAACCGACGTGTCT 59.129 47.619 0.00 0.00 0.00 3.41
536 776 2.349438 CCAATTCAAACCGACGTGTCTG 60.349 50.000 0.00 0.00 0.00 3.51
537 777 0.865769 ATTCAAACCGACGTGTCTGC 59.134 50.000 0.00 0.00 0.00 4.26
608 860 5.888161 CAGTTTAGGAAGGTAATGAAGGCAT 59.112 40.000 0.00 0.00 35.92 4.40
609 861 7.054124 CAGTTTAGGAAGGTAATGAAGGCATA 58.946 38.462 0.00 0.00 33.44 3.14
610 862 7.012421 CAGTTTAGGAAGGTAATGAAGGCATAC 59.988 40.741 0.00 0.00 33.44 2.39
695 962 1.796617 GCGAGCATGCAAATTCAGGAC 60.797 52.381 21.98 0.00 34.15 3.85
697 964 1.470098 GAGCATGCAAATTCAGGACGT 59.530 47.619 21.98 0.00 0.00 4.34
711 978 5.092554 TCAGGACGTAATTGAAGGCATAA 57.907 39.130 0.00 0.00 0.00 1.90
716 983 6.093633 AGGACGTAATTGAAGGCATAACTTTC 59.906 38.462 0.00 0.00 0.00 2.62
753 1033 6.448006 GGTAGTATATCATGCGAACTGAAGT 58.552 40.000 0.00 0.00 0.00 3.01
815 1107 0.172803 CAAACGACGGCTAGCTACCT 59.827 55.000 15.72 0.00 0.00 3.08
893 1185 2.066262 CCGTGCCACCGCTATAATAAG 58.934 52.381 0.00 0.00 35.36 1.73
1143 1435 1.594331 GCAAGGTAATCCGTCATCCC 58.406 55.000 0.00 0.00 39.05 3.85
1146 1438 1.718280 AGGTAATCCGTCATCCCTCC 58.282 55.000 0.00 0.00 39.05 4.30
1177 1469 1.017387 GCCTGCCTTTATCACCTTCG 58.983 55.000 0.00 0.00 0.00 3.79
1226 1518 2.913765 CGATCTCCTCGCATCGGCT 61.914 63.158 0.00 0.00 41.14 5.52
1231 1523 4.498520 CCTCGCATCGGCTCGTGT 62.499 66.667 0.00 0.00 38.10 4.49
1240 1536 1.736645 CGGCTCGTGTTCGTCCATT 60.737 57.895 0.00 0.00 38.33 3.16
1241 1537 1.787847 GGCTCGTGTTCGTCCATTG 59.212 57.895 0.00 0.00 38.33 2.82
1242 1538 0.669318 GGCTCGTGTTCGTCCATTGA 60.669 55.000 0.00 0.00 38.33 2.57
1243 1539 0.438830 GCTCGTGTTCGTCCATTGAC 59.561 55.000 0.00 0.00 38.18 3.18
1257 1553 0.671781 ATTGACTGACTGCTCCGTGC 60.672 55.000 0.00 0.00 43.25 5.34
1341 1637 4.969484 TCCTCAAGGTCAAAGAAGGTAAC 58.031 43.478 0.00 0.00 36.34 2.50
1404 1708 2.819019 TGCTTCATTCGATTGCCAAGAA 59.181 40.909 11.03 0.87 0.00 2.52
1407 1711 4.656041 CTTCATTCGATTGCCAAGAACTC 58.344 43.478 2.39 0.00 0.00 3.01
1541 1859 2.358737 GTGGGGTTGCTCTCGGTG 60.359 66.667 0.00 0.00 0.00 4.94
1548 1866 2.504274 TTGCTCTCGGTGGGAACGT 61.504 57.895 0.00 0.00 0.00 3.99
1549 1867 2.126031 GCTCTCGGTGGGAACGTC 60.126 66.667 0.00 0.00 0.00 4.34
1550 1868 2.637383 GCTCTCGGTGGGAACGTCT 61.637 63.158 0.00 0.00 0.00 4.18
1551 1869 1.507174 CTCTCGGTGGGAACGTCTC 59.493 63.158 0.00 0.00 0.00 3.36
1572 1890 2.102420 CCCAACTGTTCCCCTGAAAAAC 59.898 50.000 0.00 0.00 30.79 2.43
1667 1987 5.966853 TCCATGTTGGGTATGATCAACTA 57.033 39.130 0.00 0.00 42.48 2.24
1732 2052 2.591429 CTGCTGACGGTGTGCCAA 60.591 61.111 0.00 0.00 34.09 4.52
1741 2061 0.609131 CGGTGTGCCAAGGGAAGATT 60.609 55.000 0.00 0.00 34.09 2.40
1850 2170 4.393062 CGACAAAGGAGCATCTTGTTACAT 59.607 41.667 0.00 0.00 33.73 2.29
1938 2258 2.409870 CGAAGGTGATTGGGCCAGC 61.410 63.158 6.23 3.65 0.00 4.85
2026 2348 0.749454 GGGAGCTACTGTGCCATTGG 60.749 60.000 0.00 0.00 0.00 3.16
2065 2395 5.125417 CAGTTGGAATTAGGTACCATTGTGG 59.875 44.000 15.94 0.00 45.02 4.17
2101 2432 7.430441 TGCAAACACTTAATTTTCTTAGGACC 58.570 34.615 0.00 0.00 0.00 4.46
2176 2507 1.693606 CACCCTTTTTGCCATTCCTGT 59.306 47.619 0.00 0.00 0.00 4.00
2177 2508 1.693606 ACCCTTTTTGCCATTCCTGTG 59.306 47.619 0.00 0.00 0.00 3.66
2178 2509 1.969923 CCCTTTTTGCCATTCCTGTGA 59.030 47.619 0.00 0.00 0.00 3.58
2322 2653 5.163099 ACAGCTGGGTATCATAAAGCCATAA 60.163 40.000 19.93 0.00 43.22 1.90
2555 2891 3.716872 TCCATTTATCCTTCCCACTCCTC 59.283 47.826 0.00 0.00 0.00 3.71
2565 2901 2.537143 TCCCACTCCTCCAGTCTTAAC 58.463 52.381 0.00 0.00 30.26 2.01
2570 2906 5.897824 CCCACTCCTCCAGTCTTAACTAATA 59.102 44.000 0.00 0.00 33.25 0.98
2597 2935 7.874940 TGAGTTTCTCACCATGTAAATTGAAG 58.125 34.615 0.00 0.00 35.39 3.02
2679 3017 0.687757 AAGCTCCGCTGATGTCCCTA 60.688 55.000 0.00 0.00 39.62 3.53
2799 3141 3.737047 GCCACTTATCAGTTACAGCGCTA 60.737 47.826 10.99 0.00 0.00 4.26
2821 3164 2.808933 CGCATTACCCACGGAATACCAT 60.809 50.000 0.00 0.00 35.59 3.55
2825 3168 0.988832 ACCCACGGAATACCATGTGT 59.011 50.000 0.00 0.00 35.59 3.72
2844 3189 3.301642 GTGTTGATAAGCTGATTTTGCGC 59.698 43.478 0.00 0.00 35.28 6.09
3048 3411 4.093998 CAGCATTGTTTAGAGCCACTACAG 59.906 45.833 0.00 0.00 0.00 2.74
3049 3412 3.181506 GCATTGTTTAGAGCCACTACAGC 60.182 47.826 0.00 0.00 0.00 4.40
3064 3427 4.807834 CACTACAGCTGTAACAGGATGATG 59.192 45.833 25.95 13.25 39.69 3.07
3198 3561 4.574013 GGTAAGCAATCATGAGGTCTTCTG 59.426 45.833 0.09 0.00 0.00 3.02
3200 3563 5.426689 AAGCAATCATGAGGTCTTCTGTA 57.573 39.130 0.09 0.00 0.00 2.74
3252 6653 9.378551 CATGGACTAGTAAAGTTTAGTTATGCA 57.621 33.333 8.25 8.72 39.07 3.96
3300 6705 8.614994 ATTTTAATACTGAAAGCGTGTATTGC 57.385 30.769 0.00 0.00 37.43 3.56
3578 7003 2.849943 AGGTGGTTGGCATAAGGTGATA 59.150 45.455 0.00 0.00 0.00 2.15
3587 7018 4.714802 TGGCATAAGGTGATACTACACACT 59.285 41.667 0.00 0.00 41.88 3.55
3625 7410 7.896811 TCTATATATACTGTTCCAAGCTGGTG 58.103 38.462 0.00 0.00 39.03 4.17
3665 7456 5.748402 TCAACTCATGTCTATTCCAAGCAT 58.252 37.500 0.00 0.00 0.00 3.79
3672 7463 7.337938 TCATGTCTATTCCAAGCATAACTCAA 58.662 34.615 0.00 0.00 0.00 3.02
3714 7505 4.594062 TCTTTTAGCTGGTACTTGTGGGTA 59.406 41.667 0.00 0.00 0.00 3.69
3760 7551 5.708948 TGAATGTTAATGGTAAGTTGCAGC 58.291 37.500 0.00 0.00 0.00 5.25
3803 7596 7.535997 CACTTGTATACACTGCAGTAACTCTA 58.464 38.462 21.20 4.47 0.00 2.43
3825 7964 4.488126 TTCGAGCCACTTTCAGAATTTG 57.512 40.909 0.00 0.00 0.00 2.32
3965 8109 2.705658 ACCAGAACCTGTCATGAGAACA 59.294 45.455 0.00 0.00 0.00 3.18
3995 8141 4.901868 TCCGCAAGATGGTTTACTAAACT 58.098 39.130 10.77 0.00 39.88 2.66
4177 8332 8.178964 TGTGTTATTTTAAACATCCGCTATGAC 58.821 33.333 3.20 0.00 41.18 3.06
4389 9401 1.266178 TCATCCTCTTCCAGAACGCA 58.734 50.000 0.00 0.00 0.00 5.24
4427 9439 2.497675 TCTTCTGGATACTGGTGAGCAC 59.502 50.000 0.00 0.00 35.97 4.40
4470 9488 7.894376 TCAAATTACGTTCGGTTAAGATCTT 57.106 32.000 13.56 13.56 0.00 2.40
4481 9544 7.582667 TCGGTTAAGATCTTATGACTGATCA 57.417 36.000 18.74 0.00 40.92 2.92
4482 9545 7.652727 TCGGTTAAGATCTTATGACTGATCAG 58.347 38.462 21.37 21.37 40.92 2.90
4489 9552 8.481492 AGATCTTATGACTGATCAGAACATCT 57.519 34.615 29.27 20.14 37.13 2.90
4500 9563 3.091545 TCAGAACATCTTTTGCCCCATC 58.908 45.455 0.00 0.00 0.00 3.51
4506 9569 2.496899 TCTTTTGCCCCATCTCTGTC 57.503 50.000 0.00 0.00 0.00 3.51
4507 9570 1.988107 TCTTTTGCCCCATCTCTGTCT 59.012 47.619 0.00 0.00 0.00 3.41
4649 9760 5.652014 ACATGACCTTTTTCTTGAACTGACA 59.348 36.000 0.00 0.00 0.00 3.58
4711 9824 0.614697 TCTGCAGCTACAGCACCCTA 60.615 55.000 9.47 0.00 45.16 3.53
4741 9854 1.665735 GCAATTGTAACACAGGTGCGG 60.666 52.381 7.40 0.00 32.61 5.69
4770 9888 9.702726 ATATTTCGACATCGTAAAATGTTTCTG 57.297 29.630 9.83 0.00 39.93 3.02
4823 9984 1.337167 TGATCTCCTCTGTTGTGTGCG 60.337 52.381 0.00 0.00 0.00 5.34
4927 10088 4.788925 TGAAGAAGGGGTTCAAGAAGAA 57.211 40.909 0.00 0.00 30.89 2.52
4994 10155 5.590259 GCCTTCTGCTAAGGTTGAAATGATA 59.410 40.000 16.64 0.00 39.60 2.15
5060 10221 9.775539 ATAGAATGATGTAGTATGGGTAGTGAT 57.224 33.333 0.00 0.00 0.00 3.06
5161 10322 1.468054 GCAAATAGTTCTTGCAGCCGG 60.468 52.381 0.00 0.00 46.78 6.13
5220 10387 5.459107 CGGTCCAAATAGTTTATCTCTCACG 59.541 44.000 0.00 0.00 0.00 4.35
5226 10393 1.134560 AGTTTATCTCTCACGGCGTCC 59.865 52.381 10.85 0.00 0.00 4.79
5294 10462 8.780249 TCATATAAAGAGCGCTTTTATTAACCC 58.220 33.333 27.12 9.29 41.43 4.11
5295 10463 4.713824 AAAGAGCGCTTTTATTAACCCC 57.286 40.909 13.26 0.00 41.43 4.95
5296 10464 3.359695 AGAGCGCTTTTATTAACCCCA 57.640 42.857 13.26 0.00 0.00 4.96
5313 10481 6.493189 AACCCCAACTCAAAATGTAACATT 57.507 33.333 0.00 0.00 0.00 2.71
5317 10485 7.289084 ACCCCAACTCAAAATGTAACATTAAGT 59.711 33.333 0.00 0.00 0.00 2.24
5339 10507 7.383102 AGTGAATACAAACATGATGAGGAAC 57.617 36.000 0.00 0.00 0.00 3.62
5340 10508 6.942005 AGTGAATACAAACATGATGAGGAACA 59.058 34.615 0.00 0.00 0.00 3.18
5341 10509 7.023575 GTGAATACAAACATGATGAGGAACAC 58.976 38.462 0.00 5.10 0.00 3.32
5342 10510 6.714356 TGAATACAAACATGATGAGGAACACA 59.286 34.615 0.00 0.00 0.00 3.72
5343 10511 4.836125 ACAAACATGATGAGGAACACAC 57.164 40.909 0.00 0.00 0.00 3.82
5344 10512 3.250762 ACAAACATGATGAGGAACACACG 59.749 43.478 0.00 0.00 0.00 4.49
5345 10513 2.099141 ACATGATGAGGAACACACGG 57.901 50.000 0.00 0.00 0.00 4.94
5346 10514 0.729116 CATGATGAGGAACACACGGC 59.271 55.000 0.00 0.00 0.00 5.68
5347 10515 0.324614 ATGATGAGGAACACACGGCA 59.675 50.000 0.00 0.00 0.00 5.69
5348 10516 0.324614 TGATGAGGAACACACGGCAT 59.675 50.000 0.00 0.00 0.00 4.40
5349 10517 1.009829 GATGAGGAACACACGGCATC 58.990 55.000 0.00 0.00 0.00 3.91
5350 10518 0.615331 ATGAGGAACACACGGCATCT 59.385 50.000 0.00 0.00 0.00 2.90
5351 10519 0.320683 TGAGGAACACACGGCATCTG 60.321 55.000 0.00 0.00 0.00 2.90
5352 10520 1.639298 GAGGAACACACGGCATCTGC 61.639 60.000 0.00 0.00 41.14 4.26
5353 10521 1.965930 GGAACACACGGCATCTGCA 60.966 57.895 4.33 0.00 44.36 4.41
5354 10522 1.308069 GGAACACACGGCATCTGCAT 61.308 55.000 4.33 0.00 44.36 3.96
5355 10523 1.368641 GAACACACGGCATCTGCATA 58.631 50.000 4.33 0.00 44.36 3.14
5356 10524 1.328680 GAACACACGGCATCTGCATAG 59.671 52.381 4.33 0.00 44.36 2.23
5357 10525 0.462581 ACACACGGCATCTGCATAGG 60.463 55.000 4.33 0.00 44.36 2.57
5358 10526 0.462581 CACACGGCATCTGCATAGGT 60.463 55.000 4.33 0.00 44.36 3.08
5359 10527 1.119684 ACACGGCATCTGCATAGGTA 58.880 50.000 4.33 0.00 44.36 3.08
5360 10528 1.484653 ACACGGCATCTGCATAGGTAA 59.515 47.619 4.33 0.00 44.36 2.85
5361 10529 2.138320 CACGGCATCTGCATAGGTAAG 58.862 52.381 4.33 0.00 44.36 2.34
5362 10530 2.039418 ACGGCATCTGCATAGGTAAGA 58.961 47.619 4.33 0.00 44.36 2.10
5363 10531 2.634940 ACGGCATCTGCATAGGTAAGAT 59.365 45.455 4.33 0.00 44.36 2.40
5364 10532 2.998670 CGGCATCTGCATAGGTAAGATG 59.001 50.000 14.23 14.23 46.60 2.90
5383 10551 3.444703 TGCACATAACCAAACACCAAC 57.555 42.857 0.00 0.00 0.00 3.77
5446 10614 1.080354 TCCCCCTCGTCAGGATTGT 59.920 57.895 0.00 0.00 43.65 2.71
5536 10713 7.090953 ACCGTCACTTTGAAAACTTCATAAA 57.909 32.000 0.00 0.00 39.84 1.40
5659 10839 7.011499 TGGTAAGTGCCTATCTGAGTTTTAA 57.989 36.000 0.00 0.00 0.00 1.52
5849 11251 2.359900 GGCTTCCACGAATGTCATTCT 58.640 47.619 20.59 7.60 37.13 2.40
5888 11290 6.421801 GCAAGCACTTAAAACATCTGTCATTT 59.578 34.615 0.00 0.00 0.00 2.32
5941 11367 5.128827 ACGTTCATGGTGGTATGATAAGAGT 59.871 40.000 0.00 0.00 36.97 3.24
5943 11369 6.201044 CGTTCATGGTGGTATGATAAGAGTTC 59.799 42.308 0.00 0.00 36.97 3.01
5949 11393 7.458397 TGGTGGTATGATAAGAGTTCAAACTT 58.542 34.615 0.00 0.00 39.88 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 109 4.382320 TTACTGCCGCCGGTGACC 62.382 66.667 18.79 7.67 0.00 4.02
119 122 2.230940 CGGCCGATCGCTGTTACTG 61.231 63.158 24.07 0.00 39.22 2.74
338 379 0.666577 GAGTGGAGTCGTTCAACGGG 60.667 60.000 10.69 0.00 42.81 5.28
375 596 2.344203 CGGCCTCCTCAGAAGTCGT 61.344 63.158 0.00 0.00 0.00 4.34
376 597 2.492090 CGGCCTCCTCAGAAGTCG 59.508 66.667 0.00 0.00 0.00 4.18
377 598 2.172483 TTGCGGCCTCCTCAGAAGTC 62.172 60.000 0.00 0.00 0.00 3.01
380 605 2.217038 AGTTGCGGCCTCCTCAGAA 61.217 57.895 0.00 0.00 0.00 3.02
404 629 0.372679 TAGCAACGTAGCTCTCGACG 59.627 55.000 16.17 11.18 45.26 5.12
510 750 2.139917 CGTCGGTTTGAATTGGAGTGA 58.860 47.619 0.00 0.00 0.00 3.41
559 799 0.387239 GTGGAAAATCAGTGGCACGC 60.387 55.000 12.71 0.00 40.45 5.34
608 860 4.219070 TCAAGCTTAGCGTCAAAGGTAGTA 59.781 41.667 0.00 0.00 33.74 1.82
609 861 3.006537 TCAAGCTTAGCGTCAAAGGTAGT 59.993 43.478 0.00 0.00 33.74 2.73
610 862 3.585862 TCAAGCTTAGCGTCAAAGGTAG 58.414 45.455 0.00 0.00 33.74 3.18
675 942 0.452987 TCCTGAATTTGCATGCTCGC 59.547 50.000 20.33 4.56 0.00 5.03
695 962 7.220683 CCATTGAAAGTTATGCCTTCAATTACG 59.779 37.037 6.54 0.00 0.00 3.18
697 964 7.041107 GCCATTGAAAGTTATGCCTTCAATTA 58.959 34.615 6.54 0.00 0.00 1.40
711 978 1.176527 CCGTGGATGCCATTGAAAGT 58.823 50.000 0.00 0.00 35.28 2.66
716 983 2.613026 TACTACCGTGGATGCCATTG 57.387 50.000 0.00 0.00 35.28 2.82
928 1220 5.183522 AGACGTTAGAGAAAGTACTGGAAGG 59.816 44.000 0.00 0.00 39.30 3.46
1200 1492 3.143338 GAGGAGATCGAAGGGGGC 58.857 66.667 0.00 0.00 0.00 5.80
1219 1511 2.158959 GGACGAACACGAGCCGATG 61.159 63.158 1.50 0.03 0.00 3.84
1240 1536 2.340078 GCACGGAGCAGTCAGTCA 59.660 61.111 0.00 0.00 44.79 3.41
1257 1553 2.357517 AGCCGTCGCAACCAAGAG 60.358 61.111 0.00 0.00 37.52 2.85
1404 1708 1.996798 TGAGTGGGACTTTCTCGAGT 58.003 50.000 13.13 0.00 0.00 4.18
1453 1758 5.146460 CACCACAATTTTGTCGACATACTG 58.854 41.667 20.80 15.74 39.91 2.74
1548 1866 0.104672 TCAGGGGAACAGTTGGGAGA 60.105 55.000 0.00 0.00 0.00 3.71
1549 1867 0.771127 TTCAGGGGAACAGTTGGGAG 59.229 55.000 0.00 0.00 0.00 4.30
1550 1868 1.227249 TTTCAGGGGAACAGTTGGGA 58.773 50.000 0.00 0.00 31.35 4.37
1551 1869 2.080654 TTTTCAGGGGAACAGTTGGG 57.919 50.000 0.00 0.00 31.35 4.12
1667 1987 0.111061 TCTGCATTGCACCAAGGAGT 59.889 50.000 7.38 0.00 33.79 3.85
1732 2052 5.575155 AATGCAGATGTTCTGAATCTTCCCT 60.575 40.000 8.65 0.00 41.87 4.20
1850 2170 1.345741 GATTCTGCCGATGATCTGGGA 59.654 52.381 0.00 2.37 0.00 4.37
1938 2258 5.596836 AGTATGTAATTTGCAATGGTGGG 57.403 39.130 0.00 0.00 0.00 4.61
2026 2348 1.270550 CAACTGCTCATCCAACCAACC 59.729 52.381 0.00 0.00 0.00 3.77
2065 2395 4.863152 AAGTGTTTGCATGCTCAAAAAC 57.137 36.364 20.33 19.66 41.95 2.43
2101 2432 5.306532 TCTTGTACCAAACTAGCTACGAG 57.693 43.478 0.00 0.00 31.78 4.18
2132 2463 1.845809 CGTGGCTCTGTCTGTTTGGC 61.846 60.000 0.00 0.00 0.00 4.52
2176 2507 7.281549 CACATCCTAAGATTGACAACATCATCA 59.718 37.037 0.00 0.00 37.11 3.07
2177 2508 7.496920 TCACATCCTAAGATTGACAACATCATC 59.503 37.037 0.00 0.00 37.11 2.92
2178 2509 7.341030 TCACATCCTAAGATTGACAACATCAT 58.659 34.615 0.00 0.00 37.11 2.45
2322 2653 0.112412 ACCGGCCATCCTTTTCTGTT 59.888 50.000 0.00 0.00 0.00 3.16
2570 2906 8.408043 TCAATTTACATGGTGAGAAACTCAAT 57.592 30.769 2.98 0.00 42.46 2.57
2679 3017 8.915057 AAATATGCAACTGATGTATAGCTTCT 57.085 30.769 0.00 0.00 39.53 2.85
2736 3074 6.407475 AAAAGCATTGTCAAAACACTGAAC 57.593 33.333 0.70 0.00 38.07 3.18
2799 3141 1.473788 GGTATTCCGTGGGTAATGCGT 60.474 52.381 0.00 0.00 0.00 5.24
2821 3164 4.475028 CGCAAAATCAGCTTATCAACACA 58.525 39.130 0.00 0.00 0.00 3.72
2825 3168 3.846423 TGCGCAAAATCAGCTTATCAA 57.154 38.095 8.16 0.00 0.00 2.57
2844 3189 7.866898 CCACTGATGTATCTGAGTAAGAGAATG 59.133 40.741 5.86 0.00 38.67 2.67
3048 3411 4.274459 GTGGAATCATCATCCTGTTACAGC 59.726 45.833 6.88 0.00 37.85 4.40
3049 3412 5.430886 TGTGGAATCATCATCCTGTTACAG 58.569 41.667 5.22 5.22 37.85 2.74
3064 3427 3.429410 GCCCTGCAGTTTATTGTGGAATC 60.429 47.826 13.81 0.00 0.00 2.52
3200 3563 9.971744 GCAATTTCGCAACATAAATTAATTCTT 57.028 25.926 0.10 0.00 34.40 2.52
3204 3567 8.336806 CCATGCAATTTCGCAACATAAATTAAT 58.663 29.630 0.00 0.00 46.87 1.40
3291 6696 4.318546 GGCTAATTAGTTCGGCAATACACG 60.319 45.833 13.91 0.00 0.00 4.49
3300 6705 3.211865 GGAAAGGGGCTAATTAGTTCGG 58.788 50.000 13.91 0.00 0.00 4.30
3625 7410 2.113860 TGAGCCAACCTGCATAGAAC 57.886 50.000 0.00 0.00 0.00 3.01
3714 7505 3.189287 GCAACAGAAAGATCACCACGAAT 59.811 43.478 0.00 0.00 0.00 3.34
3760 7551 5.008415 ACAAGTGCTGTTCAGAAAAGATGAG 59.992 40.000 4.30 0.00 32.99 2.90
3803 7596 4.761739 TCAAATTCTGAAAGTGGCTCGAAT 59.238 37.500 0.00 0.00 33.76 3.34
3825 7964 4.215613 AGCGTTTAGGACCAGATTGTTTTC 59.784 41.667 0.00 0.00 0.00 2.29
3965 8109 2.306847 ACCATCTTGCGGAACAAAACT 58.693 42.857 0.00 0.00 37.96 2.66
4044 8194 3.444742 CCCTGCAGATTAGCAAAATGTGA 59.555 43.478 17.39 0.00 45.13 3.58
4087 8240 5.299279 ACTTACAATAAGGGGAATGAATGCG 59.701 40.000 0.97 0.00 0.00 4.73
4149 8304 9.515020 CATAGCGGATGTTTAAAATAACACATT 57.485 29.630 0.00 0.00 40.53 2.71
4150 8305 8.898761 TCATAGCGGATGTTTAAAATAACACAT 58.101 29.630 0.00 0.00 40.53 3.21
4168 8323 4.079970 TGAGTATAAGAGGGTCATAGCGG 58.920 47.826 0.00 0.00 0.00 5.52
4177 8332 6.661805 GGGAATAGAGAGTGAGTATAAGAGGG 59.338 46.154 0.00 0.00 0.00 4.30
4389 9401 5.296283 CCAGAAGAAGAATGCAATCTCGAAT 59.704 40.000 4.38 0.00 0.00 3.34
4427 9439 1.455383 AAACTGGTGCCGCTTCAAGG 61.455 55.000 0.00 0.00 0.00 3.61
4433 9445 1.039856 AATTTGAAACTGGTGCCGCT 58.960 45.000 0.00 0.00 0.00 5.52
4435 9447 2.031508 ACGTAATTTGAAACTGGTGCCG 60.032 45.455 0.00 0.00 0.00 5.69
4470 9488 6.317140 GGCAAAAGATGTTCTGATCAGTCATA 59.683 38.462 24.40 13.36 32.98 2.15
4481 9544 3.011032 AGAGATGGGGCAAAAGATGTTCT 59.989 43.478 0.00 0.00 0.00 3.01
4482 9545 3.129988 CAGAGATGGGGCAAAAGATGTTC 59.870 47.826 0.00 0.00 0.00 3.18
4489 9552 2.978156 AAGACAGAGATGGGGCAAAA 57.022 45.000 0.00 0.00 0.00 2.44
4649 9760 0.884704 GTGCAAGGACACATGGACGT 60.885 55.000 0.00 0.00 40.40 4.34
4711 9824 5.312895 TGTGTTACAATTGCATACAGAGGT 58.687 37.500 5.05 0.00 0.00 3.85
4741 9854 6.427150 ACATTTTACGATGTCGAAATATGGC 58.573 36.000 9.67 0.00 43.02 4.40
4787 9943 4.447054 GGAGATCAGAACATGCGTCAATAG 59.553 45.833 0.00 0.00 0.00 1.73
4823 9984 5.091261 TCTTGTAGAAGCTTCCCATCTTC 57.909 43.478 22.81 2.50 39.08 2.87
5060 10221 4.253685 GCCATTGCTCTAGACAACACTAA 58.746 43.478 9.11 0.00 33.53 2.24
5161 10322 2.482864 CCTTGCCACCACAATGTTTTC 58.517 47.619 0.00 0.00 0.00 2.29
5226 10393 1.956170 AGCGACAGTTTGAGGCACG 60.956 57.895 0.00 0.00 0.00 5.34
5233 10400 1.205064 CCGAAGCAGCGACAGTTTG 59.795 57.895 0.00 0.00 0.00 2.93
5270 10438 7.722285 TGGGGTTAATAAAAGCGCTCTTTATAT 59.278 33.333 24.64 19.37 41.40 0.86
5271 10439 7.055378 TGGGGTTAATAAAAGCGCTCTTTATA 58.945 34.615 24.64 14.92 41.40 0.98
5291 10459 7.289084 ACTTAATGTTACATTTTGAGTTGGGGT 59.711 33.333 16.08 0.00 0.00 4.95
5292 10460 7.598493 CACTTAATGTTACATTTTGAGTTGGGG 59.402 37.037 16.08 3.68 0.00 4.96
5293 10461 8.356657 TCACTTAATGTTACATTTTGAGTTGGG 58.643 33.333 16.08 7.01 0.00 4.12
5294 10462 9.743057 TTCACTTAATGTTACATTTTGAGTTGG 57.257 29.630 16.08 7.57 0.00 3.77
5313 10481 8.946085 GTTCCTCATCATGTTTGTATTCACTTA 58.054 33.333 0.00 0.00 0.00 2.24
5317 10485 6.714356 TGTGTTCCTCATCATGTTTGTATTCA 59.286 34.615 0.00 0.00 0.00 2.57
5339 10507 0.462581 ACCTATGCAGATGCCGTGTG 60.463 55.000 1.72 0.00 41.18 3.82
5340 10508 1.119684 TACCTATGCAGATGCCGTGT 58.880 50.000 1.72 0.00 41.18 4.49
5341 10509 2.138320 CTTACCTATGCAGATGCCGTG 58.862 52.381 1.72 0.00 41.18 4.94
5342 10510 2.039418 TCTTACCTATGCAGATGCCGT 58.961 47.619 1.72 0.00 41.18 5.68
5343 10511 2.820059 TCTTACCTATGCAGATGCCG 57.180 50.000 1.72 0.00 41.18 5.69
5352 10520 7.066887 TGTTTGGTTATGTGCATCTTACCTATG 59.933 37.037 10.91 0.00 0.00 2.23
5353 10521 7.067008 GTGTTTGGTTATGTGCATCTTACCTAT 59.933 37.037 10.91 0.00 0.00 2.57
5354 10522 6.373216 GTGTTTGGTTATGTGCATCTTACCTA 59.627 38.462 10.91 2.96 0.00 3.08
5355 10523 5.183140 GTGTTTGGTTATGTGCATCTTACCT 59.817 40.000 10.91 0.00 0.00 3.08
5356 10524 5.399013 GTGTTTGGTTATGTGCATCTTACC 58.601 41.667 0.00 0.00 0.00 2.85
5357 10525 5.048364 TGGTGTTTGGTTATGTGCATCTTAC 60.048 40.000 0.00 0.00 0.00 2.34
5358 10526 5.073428 TGGTGTTTGGTTATGTGCATCTTA 58.927 37.500 0.00 0.00 0.00 2.10
5359 10527 3.894427 TGGTGTTTGGTTATGTGCATCTT 59.106 39.130 0.00 0.00 0.00 2.40
5360 10528 3.495331 TGGTGTTTGGTTATGTGCATCT 58.505 40.909 0.00 0.00 0.00 2.90
5361 10529 3.932545 TGGTGTTTGGTTATGTGCATC 57.067 42.857 0.00 0.00 0.00 3.91
5362 10530 3.386078 TGTTGGTGTTTGGTTATGTGCAT 59.614 39.130 0.00 0.00 0.00 3.96
5363 10531 2.760650 TGTTGGTGTTTGGTTATGTGCA 59.239 40.909 0.00 0.00 0.00 4.57
5364 10532 3.120041 GTGTTGGTGTTTGGTTATGTGC 58.880 45.455 0.00 0.00 0.00 4.57
5365 10533 4.377839 TGTGTTGGTGTTTGGTTATGTG 57.622 40.909 0.00 0.00 0.00 3.21
5366 10534 5.407407 TTTGTGTTGGTGTTTGGTTATGT 57.593 34.783 0.00 0.00 0.00 2.29
5367 10535 6.102663 TCTTTTGTGTTGGTGTTTGGTTATG 58.897 36.000 0.00 0.00 0.00 1.90
5368 10536 6.287589 TCTTTTGTGTTGGTGTTTGGTTAT 57.712 33.333 0.00 0.00 0.00 1.89
5369 10537 5.723672 TCTTTTGTGTTGGTGTTTGGTTA 57.276 34.783 0.00 0.00 0.00 2.85
5370 10538 4.608948 TCTTTTGTGTTGGTGTTTGGTT 57.391 36.364 0.00 0.00 0.00 3.67
5371 10539 4.608948 TTCTTTTGTGTTGGTGTTTGGT 57.391 36.364 0.00 0.00 0.00 3.67
5419 10587 1.192428 GACGAGGGGGACACAACTAT 58.808 55.000 0.00 0.00 0.00 2.12
5446 10614 5.659079 ACCACATGTTTTCAAAAACTAGGGA 59.341 36.000 16.77 0.19 46.37 4.20
5659 10839 6.156949 ACTGTTCATGGTGGTATGATAAGAGT 59.843 38.462 0.00 0.00 36.97 3.24
5739 11134 3.306502 CCTTGATGAAACTTGGCAAGCAT 60.307 43.478 26.45 20.45 35.75 3.79
5823 11225 0.390603 CATTCGTGGAAGCCGTGGTA 60.391 55.000 0.00 0.00 0.00 3.25
5824 11226 1.671054 CATTCGTGGAAGCCGTGGT 60.671 57.895 0.00 0.00 0.00 4.16
5830 11232 3.063180 CAGAGAATGACATTCGTGGAAGC 59.937 47.826 19.87 7.19 43.92 3.86
5849 11251 2.294233 GTGCTTGCCAAGTTTCATCAGA 59.706 45.455 6.28 0.00 0.00 3.27
5941 11367 2.380064 AGTGCCCATCCAAGTTTGAA 57.620 45.000 0.00 0.00 0.00 2.69
5943 11369 2.231235 GGTAAGTGCCCATCCAAGTTTG 59.769 50.000 0.00 0.00 0.00 2.93
5949 11393 0.774276 TGTTGGTAAGTGCCCATCCA 59.226 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.