Multiple sequence alignment - TraesCS1A01G057700

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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 TraesCS1A01G057700 chr1A 100.000 3574 0 0 1 3574 38345764 38342191 0.000000e+00 6601.0
1 TraesCS1A01G057700 chr1A 92.920 565 30 5 62 616 576696418 576695854 0.000000e+00 813.0
2 TraesCS1A01G057700 chr1A 95.455 198 7 2 3377 3574 291226807 291227002 7.450000e-82 315.0
3 TraesCS1A01G057700 chr1A 95.455 198 8 1 3377 3574 488657665 488657469 7.450000e-82 315.0
4 TraesCS1A01G057700 chr3A 99.133 2421 17 4 1 2419 732953745 732951327 0.000000e+00 4351.0
5 TraesCS1A01G057700 chr3A 94.655 2133 91 12 2 2122 101775590 101777711 0.000000e+00 3286.0
6 TraesCS1A01G057700 chr3A 93.226 1919 103 14 220 2122 297824491 297822584 0.000000e+00 2798.0
7 TraesCS1A01G057700 chr4A 92.324 2879 167 22 527 3383 605879069 605881915 0.000000e+00 4043.0
8 TraesCS1A01G057700 chr4A 92.087 1289 89 8 2098 3383 294601268 294602546 0.000000e+00 1803.0
9 TraesCS1A01G057700 chr2A 98.806 2177 22 4 1 2174 671216846 671219021 0.000000e+00 3873.0
10 TraesCS1A01G057700 chr2A 93.817 2135 105 16 2 2120 547851547 547853670 0.000000e+00 3186.0
11 TraesCS1A01G057700 chr5D 94.984 2133 82 13 2 2122 4661296 4663415 0.000000e+00 3323.0
12 TraesCS1A01G057700 chr2D 94.084 2079 93 15 62 2123 16920688 16918623 0.000000e+00 3131.0
13 TraesCS1A01G057700 chr2D 93.958 1986 100 10 148 2122 221291612 221293588 0.000000e+00 2985.0
14 TraesCS1A01G057700 chr2D 96.364 55 2 0 2 56 16920778 16920724 1.370000e-14 91.6
15 TraesCS1A01G057700 chr5B 92.260 2080 140 14 1316 3383 669732891 669734961 0.000000e+00 2929.0
16 TraesCS1A01G057700 chr5B 90.635 1292 100 15 2100 3383 535569159 535570437 0.000000e+00 1696.0
17 TraesCS1A01G057700 chr1D 92.290 1297 85 10 2098 3387 369303150 369304438 0.000000e+00 1827.0
18 TraesCS1A01G057700 chr7B 91.524 1286 100 7 2101 3383 710130404 710129125 0.000000e+00 1762.0
19 TraesCS1A01G057700 chr7B 91.362 1285 103 5 2101 3382 710107698 710106419 0.000000e+00 1751.0
20 TraesCS1A01G057700 chr7B 90.916 1288 105 10 2101 3383 710047749 710046469 0.000000e+00 1720.0
21 TraesCS1A01G057700 chr7D 90.817 1285 105 9 2100 3379 15224984 15226260 0.000000e+00 1707.0
22 TraesCS1A01G057700 chr7D 93.021 917 43 13 62 973 52492279 52493179 0.000000e+00 1319.0
23 TraesCS1A01G057700 chr7D 95.455 198 7 2 3377 3574 145837116 145837311 7.450000e-82 315.0
24 TraesCS1A01G057700 chrUn 95.980 199 6 2 3376 3574 30593481 30593285 4.450000e-84 322.0
25 TraesCS1A01G057700 chrUn 95.477 199 7 2 3376 3574 30665272 30665076 2.070000e-82 316.0
26 TraesCS1A01G057700 chrUn 95.477 199 7 2 3376 3574 134501929 134501733 2.070000e-82 316.0
27 TraesCS1A01G057700 chr7A 96.429 196 5 2 3377 3572 694010877 694010684 4.450000e-84 322.0
28 TraesCS1A01G057700 chr3D 95.960 198 6 2 3377 3574 401007474 401007669 1.600000e-83 320.0
29 TraesCS1A01G057700 chr6A 95.455 198 7 2 3377 3574 552720909 552721104 7.450000e-82 315.0


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 TraesCS1A01G057700 chr1A 38342191 38345764 3573 True 6601.0 6601 100.000 1 3574 1 chr1A.!!$R1 3573
1 TraesCS1A01G057700 chr1A 576695854 576696418 564 True 813.0 813 92.920 62 616 1 chr1A.!!$R3 554
2 TraesCS1A01G057700 chr3A 732951327 732953745 2418 True 4351.0 4351 99.133 1 2419 1 chr3A.!!$R2 2418
3 TraesCS1A01G057700 chr3A 101775590 101777711 2121 False 3286.0 3286 94.655 2 2122 1 chr3A.!!$F1 2120
4 TraesCS1A01G057700 chr3A 297822584 297824491 1907 True 2798.0 2798 93.226 220 2122 1 chr3A.!!$R1 1902
5 TraesCS1A01G057700 chr4A 605879069 605881915 2846 False 4043.0 4043 92.324 527 3383 1 chr4A.!!$F2 2856
6 TraesCS1A01G057700 chr4A 294601268 294602546 1278 False 1803.0 1803 92.087 2098 3383 1 chr4A.!!$F1 1285
7 TraesCS1A01G057700 chr2A 671216846 671219021 2175 False 3873.0 3873 98.806 1 2174 1 chr2A.!!$F2 2173
8 TraesCS1A01G057700 chr2A 547851547 547853670 2123 False 3186.0 3186 93.817 2 2120 1 chr2A.!!$F1 2118
9 TraesCS1A01G057700 chr5D 4661296 4663415 2119 False 3323.0 3323 94.984 2 2122 1 chr5D.!!$F1 2120
10 TraesCS1A01G057700 chr2D 221291612 221293588 1976 False 2985.0 2985 93.958 148 2122 1 chr2D.!!$F1 1974
11 TraesCS1A01G057700 chr2D 16918623 16920778 2155 True 1611.3 3131 95.224 2 2123 2 chr2D.!!$R1 2121
12 TraesCS1A01G057700 chr5B 669732891 669734961 2070 False 2929.0 2929 92.260 1316 3383 1 chr5B.!!$F2 2067
13 TraesCS1A01G057700 chr5B 535569159 535570437 1278 False 1696.0 1696 90.635 2100 3383 1 chr5B.!!$F1 1283
14 TraesCS1A01G057700 chr1D 369303150 369304438 1288 False 1827.0 1827 92.290 2098 3387 1 chr1D.!!$F1 1289
15 TraesCS1A01G057700 chr7B 710129125 710130404 1279 True 1762.0 1762 91.524 2101 3383 1 chr7B.!!$R3 1282
16 TraesCS1A01G057700 chr7B 710106419 710107698 1279 True 1751.0 1751 91.362 2101 3382 1 chr7B.!!$R2 1281
17 TraesCS1A01G057700 chr7B 710046469 710047749 1280 True 1720.0 1720 90.916 2101 3383 1 chr7B.!!$R1 1282
18 TraesCS1A01G057700 chr7D 15224984 15226260 1276 False 1707.0 1707 90.817 2100 3379 1 chr7D.!!$F1 1279
19 TraesCS1A01G057700 chr7D 52492279 52493179 900 False 1319.0 1319 93.021 62 973 1 chr7D.!!$F2 911

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
1125 1194 6.549364 AGTTTTGTGATTTGTCCCATGTAAGA 59.451 34.615 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2935 3045 1.214367 CACGAACCGCTACACTTGTT 58.786 50.0 0.0 0.0 0.0 2.83 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
1125 1194 6.549364 AGTTTTGTGATTTGTCCCATGTAAGA 59.451 34.615 0.00 0.00 0.00 2.10
2176 2267 3.319122 ACAAAGAACCTGAAACTCATGGC 59.681 43.478 0.00 0.00 0.00 4.40
2471 2567 3.707793 CAGTTAGTCTGGCGATAGTTCC 58.292 50.000 0.00 0.00 40.23 3.62
2579 2682 3.383185 AGGATCCAAAGAACTAGCTCGAG 59.617 47.826 15.82 8.45 0.00 4.04
2591 2694 2.325583 AGCTCGAGTGGACTCTAGAG 57.674 55.000 18.49 18.49 37.83 2.43
2596 2699 1.740297 GAGTGGACTCTAGAGCACGA 58.260 55.000 19.97 8.69 39.81 4.35
2614 2717 4.791411 GCACGAACAATTTAGTCTTGGCAA 60.791 41.667 0.00 0.00 0.00 4.52
2617 2720 5.920273 ACGAACAATTTAGTCTTGGCAATTG 59.080 36.000 0.00 0.00 40.81 2.32
2787 2894 0.325203 ACCCACTTTTGGTTGCCACT 60.325 50.000 0.00 0.00 42.10 4.00
2795 2902 2.065899 TTGGTTGCCACTTGTTAGCT 57.934 45.000 0.00 0.00 30.78 3.32
2881 2988 6.317893 CCTATTTATCACCGCCAAAACTAGTT 59.682 38.462 1.12 1.12 0.00 2.24
2927 3037 6.321181 ACGACTGGAATATTTGTTGCCATAAT 59.679 34.615 0.00 0.00 0.00 1.28
3049 3159 0.719465 GTATGCACCACGAAACGAGG 59.281 55.000 6.13 6.13 42.89 4.63
3103 3213 1.954382 TCGCCATGAGCTATTAGTCGT 59.046 47.619 0.00 0.00 40.39 4.34
3144 3254 6.832520 TGCATTAAAGCTATCTCCACAAAA 57.167 33.333 4.10 0.00 34.99 2.44
3311 3421 3.932545 AATGCTGTTTCGTGGCAATAA 57.067 38.095 0.00 0.00 39.46 1.40
3383 3493 5.290386 CAATAGACCCGAATCCTTGTAGTC 58.710 45.833 0.00 0.00 0.00 2.59
3384 3494 3.103080 AGACCCGAATCCTTGTAGTCT 57.897 47.619 0.00 0.00 0.00 3.24
3385 3495 4.246712 AGACCCGAATCCTTGTAGTCTA 57.753 45.455 0.00 0.00 31.62 2.59
3386 3496 4.208746 AGACCCGAATCCTTGTAGTCTAG 58.791 47.826 0.00 0.00 31.62 2.43
3387 3497 4.079901 AGACCCGAATCCTTGTAGTCTAGA 60.080 45.833 0.00 0.00 31.62 2.43
3388 3498 3.952967 ACCCGAATCCTTGTAGTCTAGAC 59.047 47.826 15.41 15.41 0.00 2.59
3389 3499 3.952323 CCCGAATCCTTGTAGTCTAGACA 59.048 47.826 24.44 8.16 0.00 3.41
3390 3500 4.585162 CCCGAATCCTTGTAGTCTAGACAT 59.415 45.833 24.44 12.01 0.00 3.06
3391 3501 5.069251 CCCGAATCCTTGTAGTCTAGACATT 59.931 44.000 24.44 12.95 0.00 2.71
3392 3502 6.264744 CCCGAATCCTTGTAGTCTAGACATTA 59.735 42.308 24.44 6.70 0.00 1.90
3393 3503 7.364200 CCGAATCCTTGTAGTCTAGACATTAG 58.636 42.308 24.44 14.50 0.00 1.73
3394 3504 7.364200 CGAATCCTTGTAGTCTAGACATTAGG 58.636 42.308 24.44 21.40 0.00 2.69
3395 3505 7.228906 CGAATCCTTGTAGTCTAGACATTAGGA 59.771 40.741 25.30 25.30 34.16 2.94
3396 3506 7.826918 ATCCTTGTAGTCTAGACATTAGGAC 57.173 40.000 25.48 14.94 33.24 3.85
3397 3507 6.728411 TCCTTGTAGTCTAGACATTAGGACA 58.272 40.000 24.44 14.10 0.00 4.02
3398 3508 7.179966 TCCTTGTAGTCTAGACATTAGGACAA 58.820 38.462 24.44 19.14 0.00 3.18
3399 3509 7.672660 TCCTTGTAGTCTAGACATTAGGACAAA 59.327 37.037 24.44 6.92 0.00 2.83
3400 3510 8.478877 CCTTGTAGTCTAGACATTAGGACAAAT 58.521 37.037 24.44 2.07 0.00 2.32
3401 3511 9.877178 CTTGTAGTCTAGACATTAGGACAAATT 57.123 33.333 24.44 1.87 0.00 1.82
3402 3512 9.653287 TTGTAGTCTAGACATTAGGACAAATTG 57.347 33.333 24.44 0.00 0.00 2.32
3403 3513 7.764443 TGTAGTCTAGACATTAGGACAAATTGC 59.236 37.037 24.44 3.68 0.00 3.56
3404 3514 6.951971 AGTCTAGACATTAGGACAAATTGCT 58.048 36.000 24.44 0.00 0.00 3.91
3405 3515 8.079211 AGTCTAGACATTAGGACAAATTGCTA 57.921 34.615 24.44 0.00 0.00 3.49
3406 3516 8.540388 AGTCTAGACATTAGGACAAATTGCTAA 58.460 33.333 24.44 0.00 41.88 3.09
3407 3517 9.162764 GTCTAGACATTAGGACAAATTGCTAAA 57.837 33.333 18.20 0.00 41.10 1.85
3408 3518 9.162764 TCTAGACATTAGGACAAATTGCTAAAC 57.837 33.333 0.00 0.00 41.10 2.01
3409 3519 9.167311 CTAGACATTAGGACAAATTGCTAAACT 57.833 33.333 0.00 0.02 41.10 2.66
3410 3520 8.409358 AGACATTAGGACAAATTGCTAAACTT 57.591 30.769 0.00 0.00 41.10 2.66
3411 3521 8.515414 AGACATTAGGACAAATTGCTAAACTTC 58.485 33.333 0.00 0.00 41.10 3.01
3412 3522 8.177119 ACATTAGGACAAATTGCTAAACTTCA 57.823 30.769 0.00 0.00 41.10 3.02
3413 3523 8.637986 ACATTAGGACAAATTGCTAAACTTCAA 58.362 29.630 0.00 0.00 41.10 2.69
3414 3524 9.643693 CATTAGGACAAATTGCTAAACTTCAAT 57.356 29.630 0.00 0.00 41.10 2.57
3415 3525 9.860898 ATTAGGACAAATTGCTAAACTTCAATC 57.139 29.630 0.00 0.00 41.10 2.67
3416 3526 6.691508 AGGACAAATTGCTAAACTTCAATCC 58.308 36.000 0.00 0.00 32.27 3.01
3417 3527 6.267471 AGGACAAATTGCTAAACTTCAATCCA 59.733 34.615 0.00 0.00 32.27 3.41
3418 3528 6.928492 GGACAAATTGCTAAACTTCAATCCAA 59.072 34.615 0.00 0.00 32.27 3.53
3419 3529 7.116805 GGACAAATTGCTAAACTTCAATCCAAG 59.883 37.037 0.00 0.00 32.27 3.61
3420 3530 6.930722 ACAAATTGCTAAACTTCAATCCAAGG 59.069 34.615 0.00 0.00 32.27 3.61
3421 3531 5.665916 ATTGCTAAACTTCAATCCAAGGG 57.334 39.130 0.00 0.00 0.00 3.95
3422 3532 2.825532 TGCTAAACTTCAATCCAAGGGC 59.174 45.455 0.00 0.00 0.00 5.19
3423 3533 2.166459 GCTAAACTTCAATCCAAGGGCC 59.834 50.000 0.00 0.00 0.00 5.80
3424 3534 2.397044 AAACTTCAATCCAAGGGCCA 57.603 45.000 6.18 0.00 0.00 5.36
3425 3535 2.629017 AACTTCAATCCAAGGGCCAT 57.371 45.000 6.18 0.00 0.00 4.40
3426 3536 3.756082 AACTTCAATCCAAGGGCCATA 57.244 42.857 6.18 0.00 0.00 2.74
3427 3537 3.018423 ACTTCAATCCAAGGGCCATAC 57.982 47.619 6.18 0.00 0.00 2.39
3428 3538 2.311542 ACTTCAATCCAAGGGCCATACA 59.688 45.455 6.18 0.00 0.00 2.29
3429 3539 2.734755 TCAATCCAAGGGCCATACAG 57.265 50.000 6.18 0.00 0.00 2.74
3430 3540 2.204463 TCAATCCAAGGGCCATACAGA 58.796 47.619 6.18 0.00 0.00 3.41
3431 3541 2.580322 TCAATCCAAGGGCCATACAGAA 59.420 45.455 6.18 0.00 0.00 3.02
3432 3542 3.011144 TCAATCCAAGGGCCATACAGAAA 59.989 43.478 6.18 0.00 0.00 2.52
3433 3543 2.806945 TCCAAGGGCCATACAGAAAG 57.193 50.000 6.18 0.00 0.00 2.62
3434 3544 1.284785 TCCAAGGGCCATACAGAAAGG 59.715 52.381 6.18 0.00 0.00 3.11
3443 3553 3.012518 CCATACAGAAAGGCACTCAAGG 58.987 50.000 0.00 0.00 38.49 3.61
3444 3554 3.307691 CCATACAGAAAGGCACTCAAGGA 60.308 47.826 0.00 0.00 38.49 3.36
3445 3555 2.557920 ACAGAAAGGCACTCAAGGAG 57.442 50.000 0.00 0.00 38.49 3.69
3446 3556 2.050144 ACAGAAAGGCACTCAAGGAGA 58.950 47.619 0.00 0.00 38.49 3.71
3447 3557 2.439507 ACAGAAAGGCACTCAAGGAGAA 59.560 45.455 0.00 0.00 38.49 2.87
3448 3558 3.073650 ACAGAAAGGCACTCAAGGAGAAT 59.926 43.478 0.00 0.00 38.49 2.40
3449 3559 4.077822 CAGAAAGGCACTCAAGGAGAATT 58.922 43.478 0.00 0.00 38.49 2.17
3450 3560 4.155644 CAGAAAGGCACTCAAGGAGAATTC 59.844 45.833 0.00 0.00 38.49 2.17
3451 3561 4.042684 AGAAAGGCACTCAAGGAGAATTCT 59.957 41.667 7.95 7.95 38.49 2.40
3452 3562 3.347077 AGGCACTCAAGGAGAATTCTG 57.653 47.619 14.00 0.00 33.32 3.02
3453 3563 1.742268 GGCACTCAAGGAGAATTCTGC 59.258 52.381 18.49 18.49 33.32 4.26
3454 3564 2.430465 GCACTCAAGGAGAATTCTGCA 58.570 47.619 26.36 7.44 36.72 4.41
3455 3565 2.816087 GCACTCAAGGAGAATTCTGCAA 59.184 45.455 26.36 11.97 36.72 4.08
3456 3566 3.442977 GCACTCAAGGAGAATTCTGCAAT 59.557 43.478 26.36 13.51 36.72 3.56
3457 3567 4.674623 GCACTCAAGGAGAATTCTGCAATG 60.675 45.833 26.36 22.72 36.72 2.82
3458 3568 4.458295 CACTCAAGGAGAATTCTGCAATGT 59.542 41.667 26.36 16.36 36.72 2.71
3459 3569 5.048224 CACTCAAGGAGAATTCTGCAATGTT 60.048 40.000 26.36 10.93 36.72 2.71
3460 3570 6.149973 CACTCAAGGAGAATTCTGCAATGTTA 59.850 38.462 26.36 10.58 36.72 2.41
3461 3571 6.888632 ACTCAAGGAGAATTCTGCAATGTTAT 59.111 34.615 26.36 12.53 36.72 1.89
3462 3572 7.066766 ACTCAAGGAGAATTCTGCAATGTTATC 59.933 37.037 26.36 2.93 36.72 1.75
3463 3573 6.319658 TCAAGGAGAATTCTGCAATGTTATCC 59.680 38.462 26.36 11.50 36.72 2.59
3464 3574 5.759059 AGGAGAATTCTGCAATGTTATCCA 58.241 37.500 26.36 0.00 36.72 3.41
3465 3575 6.371278 AGGAGAATTCTGCAATGTTATCCAT 58.629 36.000 26.36 0.80 36.72 3.41
3466 3576 6.837568 AGGAGAATTCTGCAATGTTATCCATT 59.162 34.615 26.36 0.61 44.73 3.16
3467 3577 7.014038 AGGAGAATTCTGCAATGTTATCCATTC 59.986 37.037 26.36 0.85 41.93 2.67
3468 3578 7.201848 GGAGAATTCTGCAATGTTATCCATTCA 60.202 37.037 20.86 0.00 41.93 2.57
3469 3579 8.070034 AGAATTCTGCAATGTTATCCATTCAA 57.930 30.769 7.30 0.00 41.93 2.69
3470 3580 8.701895 AGAATTCTGCAATGTTATCCATTCAAT 58.298 29.630 7.30 0.00 41.93 2.57
3471 3581 9.321562 GAATTCTGCAATGTTATCCATTCAATT 57.678 29.630 0.00 0.00 41.93 2.32
3472 3582 9.675464 AATTCTGCAATGTTATCCATTCAATTT 57.325 25.926 0.00 0.00 41.93 1.82
3473 3583 8.481974 TTCTGCAATGTTATCCATTCAATTTG 57.518 30.769 0.00 0.00 41.93 2.32
3474 3584 6.535865 TCTGCAATGTTATCCATTCAATTTGC 59.464 34.615 0.00 0.00 41.93 3.68
3475 3585 6.408035 TGCAATGTTATCCATTCAATTTGCT 58.592 32.000 0.00 0.00 41.93 3.91
3476 3586 6.879993 TGCAATGTTATCCATTCAATTTGCTT 59.120 30.769 0.00 0.00 41.93 3.91
3477 3587 7.148390 TGCAATGTTATCCATTCAATTTGCTTG 60.148 33.333 0.00 0.00 41.93 4.01
3478 3588 7.064847 GCAATGTTATCCATTCAATTTGCTTGA 59.935 33.333 0.00 0.00 41.93 3.02
3501 3611 7.709947 TGAAATTGATGTCAAGATAATGAGCC 58.290 34.615 1.65 0.00 39.47 4.70
3502 3612 7.339976 TGAAATTGATGTCAAGATAATGAGCCA 59.660 33.333 1.65 0.00 39.47 4.75
3503 3613 7.649533 AATTGATGTCAAGATAATGAGCCAA 57.350 32.000 1.65 0.00 39.47 4.52
3504 3614 7.834881 ATTGATGTCAAGATAATGAGCCAAT 57.165 32.000 1.65 0.00 39.47 3.16
3505 3615 7.649533 TTGATGTCAAGATAATGAGCCAATT 57.350 32.000 0.00 0.00 0.00 2.32
3506 3616 7.034685 TGATGTCAAGATAATGAGCCAATTG 57.965 36.000 0.00 0.00 0.00 2.32
3507 3617 6.604396 TGATGTCAAGATAATGAGCCAATTGT 59.396 34.615 4.43 0.00 0.00 2.71
3508 3618 6.839124 TGTCAAGATAATGAGCCAATTGTT 57.161 33.333 4.43 0.00 0.00 2.83
3509 3619 7.230849 TGTCAAGATAATGAGCCAATTGTTT 57.769 32.000 4.43 0.00 0.00 2.83
3510 3620 7.315142 TGTCAAGATAATGAGCCAATTGTTTC 58.685 34.615 4.43 2.28 0.00 2.78
3511 3621 6.470235 GTCAAGATAATGAGCCAATTGTTTCG 59.530 38.462 4.43 0.00 0.00 3.46
3512 3622 6.150976 TCAAGATAATGAGCCAATTGTTTCGT 59.849 34.615 4.43 0.29 0.00 3.85
3513 3623 5.883661 AGATAATGAGCCAATTGTTTCGTG 58.116 37.500 4.43 0.00 0.00 4.35
3514 3624 5.415701 AGATAATGAGCCAATTGTTTCGTGT 59.584 36.000 4.43 0.00 0.00 4.49
3515 3625 2.772568 TGAGCCAATTGTTTCGTGTG 57.227 45.000 4.43 0.00 0.00 3.82
3516 3626 2.293170 TGAGCCAATTGTTTCGTGTGA 58.707 42.857 4.43 0.00 0.00 3.58
3517 3627 2.685388 TGAGCCAATTGTTTCGTGTGAA 59.315 40.909 4.43 0.00 0.00 3.18
3518 3628 3.317711 TGAGCCAATTGTTTCGTGTGAAT 59.682 39.130 4.43 0.00 33.20 2.57
3519 3629 4.517075 TGAGCCAATTGTTTCGTGTGAATA 59.483 37.500 4.43 0.00 33.20 1.75
3520 3630 5.009110 TGAGCCAATTGTTTCGTGTGAATAA 59.991 36.000 4.43 0.00 33.20 1.40
3521 3631 5.837437 AGCCAATTGTTTCGTGTGAATAAA 58.163 33.333 4.43 0.00 33.20 1.40
3522 3632 5.920273 AGCCAATTGTTTCGTGTGAATAAAG 59.080 36.000 4.43 0.00 33.20 1.85
3523 3633 5.388371 GCCAATTGTTTCGTGTGAATAAAGC 60.388 40.000 4.43 0.00 33.20 3.51
3524 3634 5.689514 CCAATTGTTTCGTGTGAATAAAGCA 59.310 36.000 4.43 0.00 33.20 3.91
3525 3635 6.345723 CCAATTGTTTCGTGTGAATAAAGCAC 60.346 38.462 4.43 0.00 33.20 4.40
3526 3636 4.884458 TGTTTCGTGTGAATAAAGCACA 57.116 36.364 0.00 0.00 43.41 4.57
3536 3646 7.979115 TGTGAATAAAGCACACACTTAAAAC 57.021 32.000 0.00 0.00 41.00 2.43
3537 3647 6.975772 TGTGAATAAAGCACACACTTAAAACC 59.024 34.615 0.00 0.00 41.00 3.27
3538 3648 6.975772 GTGAATAAAGCACACACTTAAAACCA 59.024 34.615 0.00 0.00 36.31 3.67
3539 3649 7.651704 GTGAATAAAGCACACACTTAAAACCAT 59.348 33.333 0.00 0.00 36.31 3.55
3540 3650 7.865385 TGAATAAAGCACACACTTAAAACCATC 59.135 33.333 0.00 0.00 0.00 3.51
3541 3651 5.590530 AAAGCACACACTTAAAACCATCA 57.409 34.783 0.00 0.00 0.00 3.07
3542 3652 5.789643 AAGCACACACTTAAAACCATCAT 57.210 34.783 0.00 0.00 0.00 2.45
3543 3653 5.125100 AGCACACACTTAAAACCATCATG 57.875 39.130 0.00 0.00 0.00 3.07
3544 3654 4.584325 AGCACACACTTAAAACCATCATGT 59.416 37.500 0.00 0.00 0.00 3.21
3545 3655 5.767665 AGCACACACTTAAAACCATCATGTA 59.232 36.000 0.00 0.00 0.00 2.29
3546 3656 6.072508 AGCACACACTTAAAACCATCATGTAG 60.073 38.462 0.00 0.00 0.00 2.74
3547 3657 6.072728 GCACACACTTAAAACCATCATGTAGA 60.073 38.462 0.00 0.00 0.00 2.59
3548 3658 7.362056 GCACACACTTAAAACCATCATGTAGAT 60.362 37.037 0.00 0.00 37.48 1.98
3549 3659 9.161629 CACACACTTAAAACCATCATGTAGATA 57.838 33.333 0.00 0.00 34.43 1.98
3550 3660 9.905713 ACACACTTAAAACCATCATGTAGATAT 57.094 29.630 0.00 0.00 34.43 1.63
3552 3662 9.905713 ACACTTAAAACCATCATGTAGATATGT 57.094 29.630 0.00 0.00 34.43 2.29
3567 3677 9.784531 ATGTAGATATGTCTTTTAGAACCATGG 57.215 33.333 11.19 11.19 35.87 3.66
3568 3678 8.988060 TGTAGATATGTCTTTTAGAACCATGGA 58.012 33.333 21.47 0.00 35.87 3.41
3569 3679 9.832445 GTAGATATGTCTTTTAGAACCATGGAA 57.168 33.333 21.47 0.00 35.87 3.53
3573 3683 7.881775 ATGTCTTTTAGAACCATGGAATACC 57.118 36.000 21.47 2.13 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 4.465446 CGGAGGAGGGGAGCCAGA 62.465 72.222 0.00 0.00 0.00 3.86
603 649 6.659242 CCAAAAACAGTGGTAATCCAGACTAT 59.341 38.462 0.00 0.00 45.24 2.12
1125 1194 2.102578 ACCACAAAGAGCAGTGCTTTT 58.897 42.857 20.80 17.56 39.88 2.27
2471 2567 4.824479 ATTCCAGCCCCATTGTTAAAAG 57.176 40.909 0.00 0.00 0.00 2.27
2543 2644 6.211986 TCTTTGGATCCTGCAATCAAGAAATT 59.788 34.615 14.23 0.00 0.00 1.82
2579 2682 1.540267 TGTTCGTGCTCTAGAGTCCAC 59.460 52.381 20.75 18.28 0.00 4.02
2591 2694 3.234386 GCCAAGACTAAATTGTTCGTGC 58.766 45.455 0.00 0.00 0.00 5.34
2596 2699 9.643693 CTAATCAATTGCCAAGACTAAATTGTT 57.356 29.630 0.00 4.47 39.75 2.83
2759 2866 1.650825 CAAAAGTGGGTTGTGGCAAC 58.349 50.000 3.62 3.62 0.00 4.17
2787 2894 8.973378 CAATTTAAATTTTCGTGGAGCTAACAA 58.027 29.630 10.77 0.00 0.00 2.83
2795 2902 5.520632 TGCGACAATTTAAATTTTCGTGGA 58.479 33.333 33.12 22.06 45.38 4.02
2881 2988 4.602995 GTCGTAACAGGAAATTGCAACAA 58.397 39.130 0.00 0.00 0.00 2.83
2927 3037 3.566322 ACCGCTACACTTGTTGCATTAAA 59.434 39.130 14.66 0.00 44.83 1.52
2935 3045 1.214367 CACGAACCGCTACACTTGTT 58.786 50.000 0.00 0.00 0.00 2.83
3049 3159 2.417243 GCAACAACCTATGCCAATGACC 60.417 50.000 0.00 0.00 36.56 4.02
3144 3254 5.889853 ACACTCATCTGATGCCACAATTTAT 59.110 36.000 12.78 0.00 0.00 1.40
3311 3421 5.086104 ACTGATTTGTGGCGATAAGTACT 57.914 39.130 0.00 0.00 0.00 2.73
3383 3493 9.167311 AGTTTAGCAATTTGTCCTAATGTCTAG 57.833 33.333 0.00 0.00 0.00 2.43
3384 3494 9.515226 AAGTTTAGCAATTTGTCCTAATGTCTA 57.485 29.630 0.00 0.00 0.00 2.59
3385 3495 8.409358 AAGTTTAGCAATTTGTCCTAATGTCT 57.591 30.769 0.00 0.00 0.00 3.41
3386 3496 8.296713 TGAAGTTTAGCAATTTGTCCTAATGTC 58.703 33.333 0.00 0.00 0.00 3.06
3387 3497 8.177119 TGAAGTTTAGCAATTTGTCCTAATGT 57.823 30.769 0.00 0.00 0.00 2.71
3388 3498 9.643693 ATTGAAGTTTAGCAATTTGTCCTAATG 57.356 29.630 0.00 0.00 31.02 1.90
3389 3499 9.860898 GATTGAAGTTTAGCAATTTGTCCTAAT 57.139 29.630 0.00 0.00 35.05 1.73
3390 3500 8.303876 GGATTGAAGTTTAGCAATTTGTCCTAA 58.696 33.333 0.00 0.00 35.05 2.69
3391 3501 7.450014 TGGATTGAAGTTTAGCAATTTGTCCTA 59.550 33.333 0.00 0.00 35.05 2.94
3392 3502 6.267471 TGGATTGAAGTTTAGCAATTTGTCCT 59.733 34.615 0.00 0.00 35.05 3.85
3393 3503 6.454795 TGGATTGAAGTTTAGCAATTTGTCC 58.545 36.000 0.00 0.00 35.05 4.02
3394 3504 7.116805 CCTTGGATTGAAGTTTAGCAATTTGTC 59.883 37.037 0.00 0.00 35.05 3.18
3395 3505 6.930722 CCTTGGATTGAAGTTTAGCAATTTGT 59.069 34.615 0.00 0.00 35.05 2.83
3396 3506 6.369615 CCCTTGGATTGAAGTTTAGCAATTTG 59.630 38.462 0.00 0.00 35.05 2.32
3397 3507 6.466812 CCCTTGGATTGAAGTTTAGCAATTT 58.533 36.000 0.00 0.00 35.05 1.82
3398 3508 5.569428 GCCCTTGGATTGAAGTTTAGCAATT 60.569 40.000 0.00 0.00 35.05 2.32
3399 3509 4.081476 GCCCTTGGATTGAAGTTTAGCAAT 60.081 41.667 0.00 0.00 37.43 3.56
3400 3510 3.258123 GCCCTTGGATTGAAGTTTAGCAA 59.742 43.478 0.00 0.00 0.00 3.91
3401 3511 2.825532 GCCCTTGGATTGAAGTTTAGCA 59.174 45.455 0.00 0.00 0.00 3.49
3402 3512 2.166459 GGCCCTTGGATTGAAGTTTAGC 59.834 50.000 0.00 0.00 0.00 3.09
3403 3513 3.430453 TGGCCCTTGGATTGAAGTTTAG 58.570 45.455 0.00 0.00 0.00 1.85
3404 3514 3.534357 TGGCCCTTGGATTGAAGTTTA 57.466 42.857 0.00 0.00 0.00 2.01
3405 3515 2.397044 TGGCCCTTGGATTGAAGTTT 57.603 45.000 0.00 0.00 0.00 2.66
3406 3516 2.629017 ATGGCCCTTGGATTGAAGTT 57.371 45.000 0.00 0.00 0.00 2.66
3407 3517 2.311542 TGTATGGCCCTTGGATTGAAGT 59.688 45.455 0.00 0.00 0.00 3.01
3408 3518 2.954318 CTGTATGGCCCTTGGATTGAAG 59.046 50.000 0.00 0.00 0.00 3.02
3409 3519 2.580322 TCTGTATGGCCCTTGGATTGAA 59.420 45.455 0.00 0.00 0.00 2.69
3410 3520 2.204463 TCTGTATGGCCCTTGGATTGA 58.796 47.619 0.00 0.00 0.00 2.57
3411 3521 2.734755 TCTGTATGGCCCTTGGATTG 57.265 50.000 0.00 0.00 0.00 2.67
3412 3522 3.628257 CCTTTCTGTATGGCCCTTGGATT 60.628 47.826 0.00 0.00 0.00 3.01
3413 3523 2.091665 CCTTTCTGTATGGCCCTTGGAT 60.092 50.000 0.00 0.00 0.00 3.41
3414 3524 1.284785 CCTTTCTGTATGGCCCTTGGA 59.715 52.381 0.00 0.00 0.00 3.53
3415 3525 1.767759 CCTTTCTGTATGGCCCTTGG 58.232 55.000 0.00 0.00 0.00 3.61
3416 3526 1.106285 GCCTTTCTGTATGGCCCTTG 58.894 55.000 0.00 0.00 40.36 3.61
3417 3527 0.704076 TGCCTTTCTGTATGGCCCTT 59.296 50.000 0.00 0.00 44.46 3.95
3418 3528 0.034089 GTGCCTTTCTGTATGGCCCT 60.034 55.000 0.00 0.00 44.46 5.19
3419 3529 0.034089 AGTGCCTTTCTGTATGGCCC 60.034 55.000 0.00 0.00 44.46 5.80
3420 3530 1.340017 TGAGTGCCTTTCTGTATGGCC 60.340 52.381 0.00 0.00 44.46 5.36
3421 3531 2.113860 TGAGTGCCTTTCTGTATGGC 57.886 50.000 4.53 4.53 45.12 4.40
3422 3532 3.012518 CCTTGAGTGCCTTTCTGTATGG 58.987 50.000 0.00 0.00 0.00 2.74
3423 3533 3.937706 CTCCTTGAGTGCCTTTCTGTATG 59.062 47.826 0.00 0.00 0.00 2.39
3424 3534 3.840666 TCTCCTTGAGTGCCTTTCTGTAT 59.159 43.478 0.00 0.00 0.00 2.29
3425 3535 3.239449 TCTCCTTGAGTGCCTTTCTGTA 58.761 45.455 0.00 0.00 0.00 2.74
3426 3536 2.050144 TCTCCTTGAGTGCCTTTCTGT 58.950 47.619 0.00 0.00 0.00 3.41
3427 3537 2.847327 TCTCCTTGAGTGCCTTTCTG 57.153 50.000 0.00 0.00 0.00 3.02
3428 3538 4.042684 AGAATTCTCCTTGAGTGCCTTTCT 59.957 41.667 0.88 0.00 0.00 2.52
3429 3539 4.155644 CAGAATTCTCCTTGAGTGCCTTTC 59.844 45.833 4.57 0.00 0.00 2.62
3430 3540 4.077822 CAGAATTCTCCTTGAGTGCCTTT 58.922 43.478 4.57 0.00 0.00 3.11
3431 3541 3.683802 CAGAATTCTCCTTGAGTGCCTT 58.316 45.455 4.57 0.00 0.00 4.35
3432 3542 2.617532 GCAGAATTCTCCTTGAGTGCCT 60.618 50.000 4.57 0.00 0.00 4.75
3433 3543 1.742268 GCAGAATTCTCCTTGAGTGCC 59.258 52.381 4.57 0.00 0.00 5.01
3434 3544 2.430465 TGCAGAATTCTCCTTGAGTGC 58.570 47.619 4.57 5.07 0.00 4.40
3435 3545 4.458295 ACATTGCAGAATTCTCCTTGAGTG 59.542 41.667 4.57 1.63 0.00 3.51
3436 3546 4.660168 ACATTGCAGAATTCTCCTTGAGT 58.340 39.130 4.57 0.00 0.00 3.41
3437 3547 5.640189 AACATTGCAGAATTCTCCTTGAG 57.360 39.130 4.57 0.00 0.00 3.02
3438 3548 6.319658 GGATAACATTGCAGAATTCTCCTTGA 59.680 38.462 4.57 0.00 0.00 3.02
3439 3549 6.095860 TGGATAACATTGCAGAATTCTCCTTG 59.904 38.462 4.57 1.82 0.00 3.61
3440 3550 6.189859 TGGATAACATTGCAGAATTCTCCTT 58.810 36.000 4.57 0.00 0.00 3.36
3441 3551 5.759059 TGGATAACATTGCAGAATTCTCCT 58.241 37.500 4.57 0.00 0.00 3.69
3442 3552 6.645790 ATGGATAACATTGCAGAATTCTCC 57.354 37.500 4.57 0.00 35.97 3.71
3468 3578 8.842358 ATCTTGACATCAATTTCAAGCAAATT 57.158 26.923 12.10 0.00 45.65 1.82
3469 3579 9.932207 TTATCTTGACATCAATTTCAAGCAAAT 57.068 25.926 12.10 5.78 45.65 2.32
3470 3580 9.932207 ATTATCTTGACATCAATTTCAAGCAAA 57.068 25.926 12.10 9.55 45.65 3.68
3471 3581 9.361315 CATTATCTTGACATCAATTTCAAGCAA 57.639 29.630 12.10 9.57 45.65 3.91
3472 3582 8.741841 TCATTATCTTGACATCAATTTCAAGCA 58.258 29.630 12.10 4.63 45.65 3.91
3473 3583 9.234384 CTCATTATCTTGACATCAATTTCAAGC 57.766 33.333 12.10 0.00 45.65 4.01
3474 3584 9.234384 GCTCATTATCTTGACATCAATTTCAAG 57.766 33.333 11.09 11.09 46.87 3.02
3475 3585 8.192774 GGCTCATTATCTTGACATCAATTTCAA 58.807 33.333 0.00 0.00 35.02 2.69
3476 3586 7.339976 TGGCTCATTATCTTGACATCAATTTCA 59.660 33.333 0.00 0.00 35.02 2.69
3477 3587 7.709947 TGGCTCATTATCTTGACATCAATTTC 58.290 34.615 0.00 0.00 35.02 2.17
3478 3588 7.649533 TGGCTCATTATCTTGACATCAATTT 57.350 32.000 0.00 0.00 35.02 1.82
3479 3589 7.649533 TTGGCTCATTATCTTGACATCAATT 57.350 32.000 0.00 0.00 35.02 2.32
3480 3590 7.834881 ATTGGCTCATTATCTTGACATCAAT 57.165 32.000 0.00 0.00 35.02 2.57
3481 3591 7.123098 ACAATTGGCTCATTATCTTGACATCAA 59.877 33.333 10.83 0.00 0.00 2.57
3482 3592 6.604396 ACAATTGGCTCATTATCTTGACATCA 59.396 34.615 10.83 0.00 0.00 3.07
3483 3593 7.035840 ACAATTGGCTCATTATCTTGACATC 57.964 36.000 10.83 0.00 0.00 3.06
3484 3594 7.414222 AACAATTGGCTCATTATCTTGACAT 57.586 32.000 10.83 0.00 0.00 3.06
3485 3595 6.839124 AACAATTGGCTCATTATCTTGACA 57.161 33.333 10.83 0.00 0.00 3.58
3486 3596 6.470235 CGAAACAATTGGCTCATTATCTTGAC 59.530 38.462 10.83 0.00 0.00 3.18
3487 3597 6.150976 ACGAAACAATTGGCTCATTATCTTGA 59.849 34.615 10.83 0.00 0.00 3.02
3488 3598 6.252015 CACGAAACAATTGGCTCATTATCTTG 59.748 38.462 10.83 0.00 0.00 3.02
3489 3599 6.071952 ACACGAAACAATTGGCTCATTATCTT 60.072 34.615 10.83 0.00 0.00 2.40
3490 3600 5.415701 ACACGAAACAATTGGCTCATTATCT 59.584 36.000 10.83 0.00 0.00 1.98
3491 3601 5.512788 CACACGAAACAATTGGCTCATTATC 59.487 40.000 10.83 0.00 0.00 1.75
3492 3602 5.182950 TCACACGAAACAATTGGCTCATTAT 59.817 36.000 10.83 0.00 0.00 1.28
3493 3603 4.517075 TCACACGAAACAATTGGCTCATTA 59.483 37.500 10.83 0.00 0.00 1.90
3494 3604 3.317711 TCACACGAAACAATTGGCTCATT 59.682 39.130 10.83 0.00 0.00 2.57
3495 3605 2.884012 TCACACGAAACAATTGGCTCAT 59.116 40.909 10.83 0.00 0.00 2.90
3496 3606 2.293170 TCACACGAAACAATTGGCTCA 58.707 42.857 10.83 0.00 0.00 4.26
3497 3607 3.347958 TTCACACGAAACAATTGGCTC 57.652 42.857 10.83 4.76 0.00 4.70
3498 3608 5.446143 TTATTCACACGAAACAATTGGCT 57.554 34.783 10.83 0.00 34.01 4.75
3499 3609 5.388371 GCTTTATTCACACGAAACAATTGGC 60.388 40.000 10.83 0.00 34.01 4.52
3500 3610 5.689514 TGCTTTATTCACACGAAACAATTGG 59.310 36.000 10.83 0.00 34.01 3.16
3501 3611 6.198029 TGTGCTTTATTCACACGAAACAATTG 59.802 34.615 3.24 3.24 39.29 2.32
3502 3612 6.269315 TGTGCTTTATTCACACGAAACAATT 58.731 32.000 0.00 0.00 39.29 2.32
3503 3613 5.826586 TGTGCTTTATTCACACGAAACAAT 58.173 33.333 0.00 0.00 39.29 2.71
3504 3614 5.236655 TGTGCTTTATTCACACGAAACAA 57.763 34.783 0.00 0.00 39.29 2.83
3505 3615 4.884458 TGTGCTTTATTCACACGAAACA 57.116 36.364 0.00 0.00 39.29 2.83
3512 3622 6.975772 GGTTTTAAGTGTGTGCTTTATTCACA 59.024 34.615 0.00 0.00 41.62 3.58
3513 3623 6.975772 TGGTTTTAAGTGTGTGCTTTATTCAC 59.024 34.615 0.00 0.00 35.14 3.18
3514 3624 7.101652 TGGTTTTAAGTGTGTGCTTTATTCA 57.898 32.000 0.00 0.00 0.00 2.57
3515 3625 7.865385 TGATGGTTTTAAGTGTGTGCTTTATTC 59.135 33.333 0.00 0.00 0.00 1.75
3516 3626 7.721402 TGATGGTTTTAAGTGTGTGCTTTATT 58.279 30.769 0.00 0.00 0.00 1.40
3517 3627 7.283625 TGATGGTTTTAAGTGTGTGCTTTAT 57.716 32.000 0.00 0.00 0.00 1.40
3518 3628 6.701145 TGATGGTTTTAAGTGTGTGCTTTA 57.299 33.333 0.00 0.00 0.00 1.85
3519 3629 5.590530 TGATGGTTTTAAGTGTGTGCTTT 57.409 34.783 0.00 0.00 0.00 3.51
3520 3630 5.068987 ACATGATGGTTTTAAGTGTGTGCTT 59.931 36.000 0.00 0.00 0.00 3.91
3521 3631 4.584325 ACATGATGGTTTTAAGTGTGTGCT 59.416 37.500 0.00 0.00 0.00 4.40
3522 3632 4.870363 ACATGATGGTTTTAAGTGTGTGC 58.130 39.130 0.00 0.00 0.00 4.57
3523 3633 7.433708 TCTACATGATGGTTTTAAGTGTGTG 57.566 36.000 0.00 0.00 0.00 3.82
3524 3634 9.905713 ATATCTACATGATGGTTTTAAGTGTGT 57.094 29.630 0.00 0.00 36.65 3.72
3526 3636 9.905713 ACATATCTACATGATGGTTTTAAGTGT 57.094 29.630 0.00 0.00 36.65 3.55
3541 3651 9.784531 CCATGGTTCTAAAAGACATATCTACAT 57.215 33.333 2.57 0.00 33.57 2.29
3542 3652 8.988060 TCCATGGTTCTAAAAGACATATCTACA 58.012 33.333 12.58 0.00 33.57 2.74
3543 3653 9.832445 TTCCATGGTTCTAAAAGACATATCTAC 57.168 33.333 12.58 0.00 33.57 2.59
3547 3657 9.574516 GGTATTCCATGGTTCTAAAAGACATAT 57.425 33.333 12.58 0.00 0.00 1.78
3548 3658 8.974060 GGTATTCCATGGTTCTAAAAGACATA 57.026 34.615 12.58 0.00 0.00 2.29
3549 3659 7.881775 GGTATTCCATGGTTCTAAAAGACAT 57.118 36.000 12.58 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.