Multiple sequence alignment - TraesCS3B01G107300

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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 TraesCS3B01G107300 chr3B 100.000 3452 0 0 1 3452 72714471 72717922 0.000000e+00 6375.0
1 TraesCS3B01G107300 chr3B 90.578 1539 122 10 1482 3007 72923090 72924618 0.000000e+00 2017.0
2 TraesCS3B01G107300 chr3B 86.400 1500 107 37 1 1474 72921491 72922919 0.000000e+00 1550.0
3 TraesCS3B01G107300 chr3B 95.679 162 7 0 3291 3452 597600258 597600097 9.500000e-66 261.0
4 TraesCS3B01G107300 chr3B 95.092 163 8 0 3290 3452 675992268 675992106 1.230000e-64 257.0
5 TraesCS3B01G107300 chr3D 92.498 3359 128 37 1 3291 46484821 46488123 0.000000e+00 4693.0
6 TraesCS3B01G107300 chr3D 88.929 3044 250 48 1 3007 46523992 46526985 0.000000e+00 3674.0
7 TraesCS3B01G107300 chr3D 94.643 56 3 0 3146 3201 46527183 46527238 1.710000e-13 87.9
8 TraesCS3B01G107300 chr3A 92.326 3336 147 32 1 3291 57903744 57907015 0.000000e+00 4641.0
9 TraesCS3B01G107300 chr3A 91.969 1046 82 2 1391 2435 57981158 57980114 0.000000e+00 1465.0
10 TraesCS3B01G107300 chr3A 84.666 613 63 18 294 901 57915627 57916213 1.790000e-162 582.0
11 TraesCS3B01G107300 chr3A 87.728 383 39 4 2627 3007 57968394 57968018 1.140000e-119 440.0
12 TraesCS3B01G107300 chr3A 88.398 181 13 3 1 180 57915332 57915505 9.710000e-51 211.0
13 TraesCS3B01G107300 chr3A 92.241 116 4 2 2443 2554 57975401 57975287 3.570000e-35 159.0
14 TraesCS3B01G107300 chr5B 77.007 1383 286 28 997 2368 141148934 141147573 0.000000e+00 763.0
15 TraesCS3B01G107300 chr5A 77.007 1383 287 26 997 2368 143659705 143658343 0.000000e+00 763.0
16 TraesCS3B01G107300 chr5D 76.895 1385 283 32 997 2368 128643417 128642057 0.000000e+00 750.0
17 TraesCS3B01G107300 chr6B 75.698 1432 310 26 994 2402 120132595 120131179 0.000000e+00 682.0
18 TraesCS3B01G107300 chr6B 100.000 162 0 0 3291 3452 414049523 414049362 2.010000e-77 300.0
19 TraesCS3B01G107300 chr6D 75.768 1432 302 29 994 2398 53175718 53174305 0.000000e+00 680.0
20 TraesCS3B01G107300 chr7A 75.802 1434 292 39 994 2398 631984736 631986143 0.000000e+00 675.0
21 TraesCS3B01G107300 chr7B 75.732 1434 293 38 994 2398 591461942 591463349 0.000000e+00 669.0
22 TraesCS3B01G107300 chr7D 75.662 1434 294 37 994 2398 548231394 548232801 0.000000e+00 664.0
23 TraesCS3B01G107300 chr1B 75.672 1377 282 41 995 2337 46830010 46828653 3.760000e-179 638.0
24 TraesCS3B01G107300 chrUn 100.000 162 0 0 3291 3452 479242648 479242487 2.010000e-77 300.0
25 TraesCS3B01G107300 chr1D 96.319 163 6 0 3290 3452 467989613 467989775 5.680000e-68 268.0
26 TraesCS3B01G107300 chr6A 95.679 162 7 0 3291 3452 559881354 559881193 9.500000e-66 261.0
27 TraesCS3B01G107300 chr4B 95.679 162 7 0 3291 3452 376032800 376032961 9.500000e-66 261.0
28 TraesCS3B01G107300 chr4A 95.679 162 7 0 3291 3452 689216724 689216563 9.500000e-66 261.0
29 TraesCS3B01G107300 chr1A 95.679 162 7 0 3291 3452 260954895 260954734 9.500000e-66 261.0


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 TraesCS3B01G107300 chr3B 72714471 72717922 3451 False 6375.00 6375 100.000 1 3452 1 chr3B.!!$F1 3451
1 TraesCS3B01G107300 chr3B 72921491 72924618 3127 False 1783.50 2017 88.489 1 3007 2 chr3B.!!$F2 3006
2 TraesCS3B01G107300 chr3D 46484821 46488123 3302 False 4693.00 4693 92.498 1 3291 1 chr3D.!!$F1 3290
3 TraesCS3B01G107300 chr3D 46523992 46527238 3246 False 1880.95 3674 91.786 1 3201 2 chr3D.!!$F2 3200
4 TraesCS3B01G107300 chr3A 57903744 57907015 3271 False 4641.00 4641 92.326 1 3291 1 chr3A.!!$F1 3290
5 TraesCS3B01G107300 chr3A 57980114 57981158 1044 True 1465.00 1465 91.969 1391 2435 1 chr3A.!!$R3 1044
6 TraesCS3B01G107300 chr3A 57915332 57916213 881 False 396.50 582 86.532 1 901 2 chr3A.!!$F2 900
7 TraesCS3B01G107300 chr5B 141147573 141148934 1361 True 763.00 763 77.007 997 2368 1 chr5B.!!$R1 1371
8 TraesCS3B01G107300 chr5A 143658343 143659705 1362 True 763.00 763 77.007 997 2368 1 chr5A.!!$R1 1371
9 TraesCS3B01G107300 chr5D 128642057 128643417 1360 True 750.00 750 76.895 997 2368 1 chr5D.!!$R1 1371
10 TraesCS3B01G107300 chr6B 120131179 120132595 1416 True 682.00 682 75.698 994 2402 1 chr6B.!!$R1 1408
11 TraesCS3B01G107300 chr6D 53174305 53175718 1413 True 680.00 680 75.768 994 2398 1 chr6D.!!$R1 1404
12 TraesCS3B01G107300 chr7A 631984736 631986143 1407 False 675.00 675 75.802 994 2398 1 chr7A.!!$F1 1404
13 TraesCS3B01G107300 chr7B 591461942 591463349 1407 False 669.00 669 75.732 994 2398 1 chr7B.!!$F1 1404
14 TraesCS3B01G107300 chr7D 548231394 548232801 1407 False 664.00 664 75.662 994 2398 1 chr7D.!!$F1 1404
15 TraesCS3B01G107300 chr1B 46828653 46830010 1357 True 638.00 638 75.672 995 2337 1 chr1B.!!$R1 1342

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
40 41 0.038526 TTCTTCTCTCCCGTTCGTGC 60.039 55.0 0.0 0.0 0.0 5.34 F
303 344 0.320771 GATGTCGGTTCAGCAGGTGT 60.321 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2150 1.280421 AGGATCCAGCCAAAGTGAGAC 59.720 52.381 15.82 0.00 0.0 3.36 R
2964 3271 3.858238 CAGGCTTTGTTACTACGTAGAGC 59.142 47.826 28.74 22.88 0.0 4.09 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
40 41 0.038526 TTCTTCTCTCCCGTTCGTGC 60.039 55.000 0.00 0.00 0.00 5.34
41 42 0.894184 TCTTCTCTCCCGTTCGTGCT 60.894 55.000 0.00 0.00 0.00 4.40
42 43 0.734253 CTTCTCTCCCGTTCGTGCTG 60.734 60.000 0.00 0.00 0.00 4.41
43 44 1.176619 TTCTCTCCCGTTCGTGCTGA 61.177 55.000 0.00 0.00 0.00 4.26
44 45 1.444553 CTCTCCCGTTCGTGCTGAC 60.445 63.158 0.00 0.00 0.00 3.51
46 47 4.351938 TCCCGTTCGTGCTGACGG 62.352 66.667 7.88 7.88 46.11 4.79
91 99 1.878953 TCCGTCTGAAGAAAACAGCC 58.121 50.000 0.00 0.00 35.61 4.85
94 102 0.875059 GTCTGAAGAAAACAGCCCCG 59.125 55.000 0.00 0.00 35.61 5.73
120 129 3.057734 CGGTTCGTTAGCTCTCAACTTT 58.942 45.455 0.00 0.00 0.00 2.66
132 141 9.751542 TTAGCTCTCAACTTTAGATGCTTATAC 57.248 33.333 0.00 0.00 32.98 1.47
182 191 4.945543 TGGATGGTTGATTGACAGATGAAG 59.054 41.667 0.00 0.00 0.00 3.02
183 192 4.201990 GGATGGTTGATTGACAGATGAAGC 60.202 45.833 0.00 0.00 0.00 3.86
303 344 0.320771 GATGTCGGTTCAGCAGGTGT 60.321 55.000 0.00 0.00 0.00 4.16
313 354 4.572389 GGTTCAGCAGGTGTATGTTATCTG 59.428 45.833 0.00 0.00 0.00 2.90
331 386 7.872483 TGTTATCTGCTAGATTTGCATCGATTA 59.128 33.333 0.00 0.00 39.86 1.75
332 387 8.712363 GTTATCTGCTAGATTTGCATCGATTAA 58.288 33.333 0.00 0.00 39.86 1.40
379 434 4.021192 TCATCCTTGCTTTCATTTTCCCAC 60.021 41.667 0.00 0.00 0.00 4.61
399 454 5.303971 CCACCAATTCCAGATATGTCTCTC 58.696 45.833 0.00 0.00 30.42 3.20
403 458 5.938710 CCAATTCCAGATATGTCTCTCCATG 59.061 44.000 0.00 0.00 30.42 3.66
416 471 4.391216 GTCTCTCCATGATTGTGTGACTTG 59.609 45.833 0.00 0.00 0.00 3.16
459 514 8.310382 TGCTCAGAGATTTAGAGATAAATAGGC 58.690 37.037 0.00 0.00 30.51 3.93
483 538 6.402875 GCCGGTACCTTAGTTAATGTTCTTTG 60.403 42.308 10.90 0.00 0.00 2.77
489 544 7.658261 ACCTTAGTTAATGTTCTTTGGAAAGC 58.342 34.615 0.00 0.00 35.99 3.51
495 550 3.691049 TGTTCTTTGGAAAGCTGAACG 57.309 42.857 6.41 0.00 36.15 3.95
626 687 8.047310 ACTTAATGTCCAAAGGAGTATGTTAGG 58.953 37.037 0.00 0.00 29.39 2.69
631 694 6.713450 TGTCCAAAGGAGTATGTTAGGAAAAC 59.287 38.462 0.00 0.00 29.39 2.43
1032 1109 2.575532 CCAGAGGAACTGTTTGCAGAA 58.424 47.619 1.30 0.00 45.28 3.02
1132 1209 3.078153 AGATCAGAGGGGTGCTATCCATA 59.922 47.826 0.00 0.00 0.00 2.74
1158 1235 1.002624 TGGCCTTTTCCCTGCTACG 60.003 57.895 3.32 0.00 0.00 3.51
1480 1722 4.947388 TCCACCTTATTGACTGCCATAAAC 59.053 41.667 0.00 0.00 0.00 2.01
1894 2150 3.568538 AGCTGCAACAATCTTAAAAGCG 58.431 40.909 1.02 0.00 34.65 4.68
2664 2964 6.012745 AGAATCTGCAGGGTATTTTTGACTT 58.987 36.000 15.13 0.00 0.00 3.01
2964 3271 3.694072 TGAGTTGTCAGAGTTTTGTTGGG 59.306 43.478 0.00 0.00 0.00 4.12
3090 3471 9.383519 GGTCATTTGATTTGAGTGATAGAAGTA 57.616 33.333 0.00 0.00 0.00 2.24
3274 3665 1.740296 GCGAGCGTTCTAAGGGCAA 60.740 57.895 0.00 0.00 0.00 4.52
3291 3682 2.704065 GGCAACTACAAGGCTATCCCTA 59.296 50.000 0.00 0.00 45.62 3.53
3292 3683 3.135895 GGCAACTACAAGGCTATCCCTAA 59.864 47.826 0.00 0.00 45.62 2.69
3293 3684 4.381411 GCAACTACAAGGCTATCCCTAAG 58.619 47.826 0.00 0.00 45.62 2.18
3294 3685 4.743955 GCAACTACAAGGCTATCCCTAAGG 60.744 50.000 0.00 0.00 45.62 2.69
3295 3686 4.554553 ACTACAAGGCTATCCCTAAGGA 57.445 45.455 0.00 0.00 45.62 3.36
3308 3699 4.542697 TCCCTAAGGATGGCAATTTTACC 58.457 43.478 0.00 0.00 37.19 2.85
3309 3700 3.641436 CCCTAAGGATGGCAATTTTACCC 59.359 47.826 0.00 0.00 33.47 3.69
3310 3701 4.285863 CCTAAGGATGGCAATTTTACCCA 58.714 43.478 0.00 0.00 0.00 4.51
3311 3702 4.901250 CCTAAGGATGGCAATTTTACCCAT 59.099 41.667 0.00 0.00 41.83 4.00
3312 3703 4.758773 AAGGATGGCAATTTTACCCATG 57.241 40.909 0.00 0.00 39.36 3.66
3313 3704 3.040477 AGGATGGCAATTTTACCCATGG 58.960 45.455 4.14 4.14 39.36 3.66
3314 3705 2.104622 GGATGGCAATTTTACCCATGGG 59.895 50.000 30.23 30.23 39.36 4.00
3356 3747 2.595463 CCGCATGGGCAGGGTATG 60.595 66.667 3.80 0.00 41.24 2.39
3357 3748 2.595463 CGCATGGGCAGGGTATGG 60.595 66.667 0.00 0.00 41.24 2.74
3358 3749 2.926250 GCATGGGCAGGGTATGGA 59.074 61.111 0.00 0.00 40.72 3.41
3359 3750 1.529244 GCATGGGCAGGGTATGGAC 60.529 63.158 0.00 0.00 40.72 4.02
3360 3751 1.922057 CATGGGCAGGGTATGGACA 59.078 57.895 0.00 0.00 0.00 4.02
3361 3752 0.466189 CATGGGCAGGGTATGGACAC 60.466 60.000 0.00 0.00 0.00 3.67
3362 3753 0.918799 ATGGGCAGGGTATGGACACA 60.919 55.000 0.00 0.00 0.00 3.72
3363 3754 1.077716 GGGCAGGGTATGGACACAC 60.078 63.158 0.00 0.00 0.00 3.82
3364 3755 1.562672 GGGCAGGGTATGGACACACT 61.563 60.000 0.00 0.00 30.16 3.55
3365 3756 0.328258 GGCAGGGTATGGACACACTT 59.672 55.000 0.00 0.00 26.36 3.16
3366 3757 1.271926 GGCAGGGTATGGACACACTTT 60.272 52.381 0.00 0.00 26.36 2.66
3367 3758 2.514803 GCAGGGTATGGACACACTTTT 58.485 47.619 0.00 0.00 26.36 2.27
3368 3759 3.560453 GGCAGGGTATGGACACACTTTTA 60.560 47.826 0.00 0.00 26.36 1.52
3369 3760 4.270008 GCAGGGTATGGACACACTTTTAT 58.730 43.478 0.00 0.00 26.36 1.40
3370 3761 5.433526 GCAGGGTATGGACACACTTTTATA 58.566 41.667 0.00 0.00 26.36 0.98
3371 3762 5.296035 GCAGGGTATGGACACACTTTTATAC 59.704 44.000 0.00 0.00 26.36 1.47
3372 3763 5.820947 CAGGGTATGGACACACTTTTATACC 59.179 44.000 0.00 0.00 39.36 2.73
3374 3765 5.747342 GGTATGGACACACTTTTATACCCA 58.253 41.667 0.00 0.00 35.93 4.51
3375 3766 5.587443 GGTATGGACACACTTTTATACCCAC 59.413 44.000 0.00 0.00 35.93 4.61
3376 3767 3.666274 TGGACACACTTTTATACCCACG 58.334 45.455 0.00 0.00 0.00 4.94
3377 3768 3.071312 TGGACACACTTTTATACCCACGT 59.929 43.478 0.00 0.00 0.00 4.49
3378 3769 3.434299 GGACACACTTTTATACCCACGTG 59.566 47.826 9.08 9.08 0.00 4.49
3379 3770 4.060205 GACACACTTTTATACCCACGTGT 58.940 43.478 15.65 0.00 38.94 4.49
3380 3771 5.212532 ACACACTTTTATACCCACGTGTA 57.787 39.130 15.65 1.06 34.77 2.90
3381 3772 5.232463 ACACACTTTTATACCCACGTGTAG 58.768 41.667 15.65 8.07 34.77 2.74
3382 3773 5.221501 ACACACTTTTATACCCACGTGTAGT 60.222 40.000 15.65 13.82 34.77 2.73
3383 3774 6.015519 ACACACTTTTATACCCACGTGTAGTA 60.016 38.462 15.65 15.57 34.77 1.82
3384 3775 6.308766 CACACTTTTATACCCACGTGTAGTAC 59.691 42.308 15.65 0.00 34.23 2.73
3385 3776 5.807011 CACTTTTATACCCACGTGTAGTACC 59.193 44.000 15.65 0.00 0.00 3.34
3386 3777 5.105351 ACTTTTATACCCACGTGTAGTACCC 60.105 44.000 15.65 0.00 0.00 3.69
3387 3778 2.530460 ATACCCACGTGTAGTACCCA 57.470 50.000 15.65 0.00 0.00 4.51
3388 3779 2.530460 TACCCACGTGTAGTACCCAT 57.470 50.000 15.65 0.00 0.00 4.00
3389 3780 2.530460 ACCCACGTGTAGTACCCATA 57.470 50.000 15.65 0.00 0.00 2.74
3390 3781 3.036452 ACCCACGTGTAGTACCCATAT 57.964 47.619 15.65 0.00 0.00 1.78
3391 3782 2.961062 ACCCACGTGTAGTACCCATATC 59.039 50.000 15.65 0.00 0.00 1.63
3392 3783 2.298163 CCCACGTGTAGTACCCATATCC 59.702 54.545 15.65 0.00 0.00 2.59
3393 3784 3.228453 CCACGTGTAGTACCCATATCCT 58.772 50.000 15.65 0.00 0.00 3.24
3394 3785 4.401022 CCACGTGTAGTACCCATATCCTA 58.599 47.826 15.65 0.00 0.00 2.94
3395 3786 4.217118 CCACGTGTAGTACCCATATCCTAC 59.783 50.000 15.65 0.00 0.00 3.18
3396 3787 4.217118 CACGTGTAGTACCCATATCCTACC 59.783 50.000 7.58 0.00 30.98 3.18
3397 3788 3.760684 CGTGTAGTACCCATATCCTACCC 59.239 52.174 0.00 0.00 30.98 3.69
3398 3789 4.744237 GTGTAGTACCCATATCCTACCCA 58.256 47.826 0.00 0.00 30.98 4.51
3399 3790 5.339477 GTGTAGTACCCATATCCTACCCAT 58.661 45.833 0.00 0.00 30.98 4.00
3400 3791 5.783875 GTGTAGTACCCATATCCTACCCATT 59.216 44.000 0.00 0.00 30.98 3.16
3401 3792 6.955851 GTGTAGTACCCATATCCTACCCATTA 59.044 42.308 0.00 0.00 30.98 1.90
3402 3793 7.455638 GTGTAGTACCCATATCCTACCCATTAA 59.544 40.741 0.00 0.00 30.98 1.40
3403 3794 7.676893 TGTAGTACCCATATCCTACCCATTAAG 59.323 40.741 0.00 0.00 30.98 1.85
3404 3795 6.640925 AGTACCCATATCCTACCCATTAAGT 58.359 40.000 0.00 0.00 0.00 2.24
3405 3796 6.729569 AGTACCCATATCCTACCCATTAAGTC 59.270 42.308 0.00 0.00 0.00 3.01
3406 3797 5.482580 ACCCATATCCTACCCATTAAGTCA 58.517 41.667 0.00 0.00 0.00 3.41
3407 3798 6.098446 ACCCATATCCTACCCATTAAGTCAT 58.902 40.000 0.00 0.00 0.00 3.06
3408 3799 6.012508 ACCCATATCCTACCCATTAAGTCATG 60.013 42.308 0.00 0.00 0.00 3.07
3409 3800 6.418101 CCATATCCTACCCATTAAGTCATGG 58.582 44.000 0.00 0.00 43.26 3.66
3410 3801 6.215431 CCATATCCTACCCATTAAGTCATGGA 59.785 42.308 1.02 0.00 46.18 3.41
3411 3802 7.092264 CCATATCCTACCCATTAAGTCATGGAT 60.092 40.741 1.02 0.00 46.18 3.41
3412 3803 8.992349 CATATCCTACCCATTAAGTCATGGATA 58.008 37.037 1.02 0.00 46.18 2.59
3413 3804 6.935240 TCCTACCCATTAAGTCATGGATAG 57.065 41.667 1.02 0.00 46.18 2.08
3415 3806 6.054860 CTACCCATTAAGTCATGGATAGGG 57.945 45.833 1.02 0.00 46.18 3.53
3416 3807 4.315993 ACCCATTAAGTCATGGATAGGGT 58.684 43.478 1.02 0.00 46.18 4.34
3417 3808 5.482580 ACCCATTAAGTCATGGATAGGGTA 58.517 41.667 0.00 0.00 46.18 3.69
3418 3809 5.309806 ACCCATTAAGTCATGGATAGGGTAC 59.690 44.000 0.00 0.00 46.18 3.34
3419 3810 5.479306 CCATTAAGTCATGGATAGGGTACG 58.521 45.833 0.00 0.00 46.18 3.67
3420 3811 5.479306 CATTAAGTCATGGATAGGGTACGG 58.521 45.833 0.00 0.00 0.00 4.02
3421 3812 2.011122 AGTCATGGATAGGGTACGGG 57.989 55.000 0.00 0.00 0.00 5.28
3422 3813 1.219724 AGTCATGGATAGGGTACGGGT 59.780 52.381 0.00 0.00 0.00 5.28
3423 3814 2.448194 AGTCATGGATAGGGTACGGGTA 59.552 50.000 0.00 0.00 0.00 3.69
3424 3815 3.077088 AGTCATGGATAGGGTACGGGTAT 59.923 47.826 0.00 0.00 0.00 2.73
3425 3816 4.293102 AGTCATGGATAGGGTACGGGTATA 59.707 45.833 0.00 0.00 0.00 1.47
3426 3817 4.643784 GTCATGGATAGGGTACGGGTATAG 59.356 50.000 0.00 0.00 0.00 1.31
3427 3818 4.293102 TCATGGATAGGGTACGGGTATAGT 59.707 45.833 0.00 0.00 0.00 2.12
3428 3819 4.307032 TGGATAGGGTACGGGTATAGTC 57.693 50.000 0.00 0.00 0.00 2.59
3429 3820 3.918912 TGGATAGGGTACGGGTATAGTCT 59.081 47.826 0.00 0.00 0.00 3.24
3430 3821 4.354987 TGGATAGGGTACGGGTATAGTCTT 59.645 45.833 0.00 0.00 0.00 3.01
3431 3822 4.704057 GGATAGGGTACGGGTATAGTCTTG 59.296 50.000 0.00 0.00 0.00 3.02
3432 3823 3.677156 AGGGTACGGGTATAGTCTTGT 57.323 47.619 0.00 0.00 0.00 3.16
3433 3824 4.796110 AGGGTACGGGTATAGTCTTGTA 57.204 45.455 0.00 0.00 0.00 2.41
3434 3825 4.464947 AGGGTACGGGTATAGTCTTGTAC 58.535 47.826 0.00 0.00 33.27 2.90
3435 3826 3.570125 GGGTACGGGTATAGTCTTGTACC 59.430 52.174 10.16 10.16 46.97 3.34
3440 3831 3.722728 GGTATAGTCTTGTACCCACGG 57.277 52.381 0.00 0.00 35.60 4.94
3441 3832 2.363359 GGTATAGTCTTGTACCCACGGG 59.637 54.545 0.00 0.00 35.60 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 102 0.810016 AGAGCTAACGAACCGAGGTC 59.190 55.000 0.00 0.00 37.86 3.85
120 129 7.363007 GGAAGACATGATCCGTATAAGCATCTA 60.363 40.741 0.00 0.00 0.00 1.98
132 141 4.033358 CGAAAGAAAGGAAGACATGATCCG 59.967 45.833 0.00 0.00 40.78 4.18
182 191 1.226746 ACAACGCTAAGAACCACAGC 58.773 50.000 0.00 0.00 0.00 4.40
183 192 2.612212 ACAACAACGCTAAGAACCACAG 59.388 45.455 0.00 0.00 0.00 3.66
187 208 2.381589 GCAACAACAACGCTAAGAACC 58.618 47.619 0.00 0.00 0.00 3.62
303 344 7.378181 TCGATGCAAATCTAGCAGATAACATA 58.622 34.615 0.00 0.00 46.36 2.29
313 354 8.077836 ACTACTTTAATCGATGCAAATCTAGC 57.922 34.615 0.00 0.00 0.00 3.42
358 413 3.261643 GGTGGGAAAATGAAAGCAAGGAT 59.738 43.478 0.00 0.00 0.00 3.24
379 434 5.557576 TGGAGAGACATATCTGGAATTGG 57.442 43.478 0.00 0.00 34.34 3.16
399 454 2.229543 CCCACAAGTCACACAATCATGG 59.770 50.000 0.00 0.00 0.00 3.66
403 458 3.214328 AGAACCCACAAGTCACACAATC 58.786 45.455 0.00 0.00 0.00 2.67
416 471 2.024414 AGCAGACAACAAAGAACCCAC 58.976 47.619 0.00 0.00 0.00 4.61
459 514 6.093082 CCAAAGAACATTAACTAAGGTACCGG 59.907 42.308 6.18 0.00 29.18 5.28
489 544 9.964253 GTATATATCAAAGATTCATGCGTTCAG 57.036 33.333 0.00 0.00 0.00 3.02
561 622 9.965824 AAAGTACAACAATCGAAATTCTGAAAT 57.034 25.926 0.00 0.00 0.00 2.17
626 687 9.931210 CAATAGAACCGAAACTATATGGTTTTC 57.069 33.333 17.13 11.15 44.40 2.29
631 694 7.387673 TGCATCAATAGAACCGAAACTATATGG 59.612 37.037 0.00 0.00 0.00 2.74
830 902 9.364989 GCAAATTCATGCCTTACAAATAAGTAA 57.635 29.630 0.00 0.00 40.49 2.24
831 903 8.526978 TGCAAATTCATGCCTTACAAATAAGTA 58.473 29.630 0.00 0.00 45.83 2.24
832 904 7.331687 GTGCAAATTCATGCCTTACAAATAAGT 59.668 33.333 0.00 0.00 45.83 2.24
844 916 3.806625 ATACTGGTGCAAATTCATGCC 57.193 42.857 0.00 0.00 45.83 4.40
845 917 7.651808 ACTATTATACTGGTGCAAATTCATGC 58.348 34.615 0.00 0.00 46.58 4.06
855 927 9.077674 CGATCAAGATAACTATTATACTGGTGC 57.922 37.037 0.00 0.00 0.00 5.01
1032 1109 5.012893 GTCCTGGTGATCCTTTTGAGAAAT 58.987 41.667 0.00 0.00 34.23 2.17
1158 1235 2.439156 AGCGATGCCAAGGCTTCC 60.439 61.111 18.03 12.17 40.71 3.46
1480 1722 4.843728 TCCAACCAATCTTTGCTACCTAG 58.156 43.478 0.00 0.00 0.00 3.02
1601 1844 9.868277 TGATTTCAAACACAAACTTCTGTAAAT 57.132 25.926 0.00 0.00 0.00 1.40
1602 1845 9.698309 TTGATTTCAAACACAAACTTCTGTAAA 57.302 25.926 0.00 0.00 32.11 2.01
1603 1846 9.352784 CTTGATTTCAAACACAAACTTCTGTAA 57.647 29.630 0.00 0.00 35.15 2.41
1858 2114 1.336125 GCAGCTCTGGGATAATGCAAC 59.664 52.381 0.00 0.00 33.92 4.17
1894 2150 1.280421 AGGATCCAGCCAAAGTGAGAC 59.720 52.381 15.82 0.00 0.00 3.36
2964 3271 3.858238 CAGGCTTTGTTACTACGTAGAGC 59.142 47.826 28.74 22.88 0.00 4.09
3017 3356 0.975887 TGACAGTATGCTGCAGGTGA 59.024 50.000 17.12 0.00 46.30 4.02
3274 3665 4.554553 TCCTTAGGGATAGCCTTGTAGT 57.445 45.455 0.00 0.00 36.57 2.73
3291 3682 3.455543 CCATGGGTAAAATTGCCATCCTT 59.544 43.478 2.85 0.00 34.27 3.36
3292 3683 3.040477 CCATGGGTAAAATTGCCATCCT 58.960 45.455 2.85 0.00 34.27 3.24
3293 3684 2.104622 CCCATGGGTAAAATTGCCATCC 59.895 50.000 23.93 0.00 34.27 3.51
3294 3685 3.473923 CCCATGGGTAAAATTGCCATC 57.526 47.619 23.93 0.00 34.27 3.51
3339 3730 2.595463 CATACCCTGCCCATGCGG 60.595 66.667 0.00 0.00 43.89 5.69
3340 3731 2.595463 CCATACCCTGCCCATGCG 60.595 66.667 0.00 0.00 41.78 4.73
3341 3732 1.529244 GTCCATACCCTGCCCATGC 60.529 63.158 0.00 0.00 38.26 4.06
3342 3733 0.466189 GTGTCCATACCCTGCCCATG 60.466 60.000 0.00 0.00 0.00 3.66
3343 3734 0.918799 TGTGTCCATACCCTGCCCAT 60.919 55.000 0.00 0.00 0.00 4.00
3344 3735 1.540118 TGTGTCCATACCCTGCCCA 60.540 57.895 0.00 0.00 0.00 5.36
3345 3736 1.077716 GTGTGTCCATACCCTGCCC 60.078 63.158 0.00 0.00 0.00 5.36
3346 3737 0.328258 AAGTGTGTCCATACCCTGCC 59.672 55.000 0.00 0.00 0.00 4.85
3347 3738 2.200373 AAAGTGTGTCCATACCCTGC 57.800 50.000 0.00 0.00 0.00 4.85
3348 3739 5.820947 GGTATAAAAGTGTGTCCATACCCTG 59.179 44.000 0.00 0.00 34.39 4.45
3349 3740 5.997843 GGTATAAAAGTGTGTCCATACCCT 58.002 41.667 0.00 0.00 34.39 4.34
3350 3741 5.128205 GGGTATAAAAGTGTGTCCATACCC 58.872 45.833 10.90 10.90 46.49 3.69
3351 3742 5.587443 GTGGGTATAAAAGTGTGTCCATACC 59.413 44.000 0.00 0.00 37.99 2.73
3352 3743 5.292589 CGTGGGTATAAAAGTGTGTCCATAC 59.707 44.000 0.00 0.00 0.00 2.39
3353 3744 5.046448 ACGTGGGTATAAAAGTGTGTCCATA 60.046 40.000 0.00 0.00 0.00 2.74
3354 3745 4.258543 CGTGGGTATAAAAGTGTGTCCAT 58.741 43.478 0.00 0.00 0.00 3.41
3355 3746 3.071312 ACGTGGGTATAAAAGTGTGTCCA 59.929 43.478 0.00 0.00 0.00 4.02
3356 3747 3.434299 CACGTGGGTATAAAAGTGTGTCC 59.566 47.826 7.95 0.00 0.00 4.02
3357 3748 4.060205 ACACGTGGGTATAAAAGTGTGTC 58.940 43.478 21.57 0.00 40.70 3.67
3358 3749 4.075963 ACACGTGGGTATAAAAGTGTGT 57.924 40.909 21.57 0.00 40.70 3.72
3359 3750 5.232463 ACTACACGTGGGTATAAAAGTGTG 58.768 41.667 21.57 4.52 41.99 3.82
3360 3751 5.473066 ACTACACGTGGGTATAAAAGTGT 57.527 39.130 21.57 4.48 43.89 3.55
3361 3752 5.807011 GGTACTACACGTGGGTATAAAAGTG 59.193 44.000 21.57 0.00 35.89 3.16
3362 3753 5.105351 GGGTACTACACGTGGGTATAAAAGT 60.105 44.000 21.57 11.33 0.00 2.66
3363 3754 5.105392 TGGGTACTACACGTGGGTATAAAAG 60.105 44.000 21.57 6.25 0.00 2.27
3364 3755 4.774726 TGGGTACTACACGTGGGTATAAAA 59.225 41.667 21.57 7.30 0.00 1.52
3365 3756 4.348486 TGGGTACTACACGTGGGTATAAA 58.652 43.478 21.57 8.81 0.00 1.40
3366 3757 3.974719 TGGGTACTACACGTGGGTATAA 58.025 45.455 21.57 9.11 0.00 0.98
3367 3758 3.660970 TGGGTACTACACGTGGGTATA 57.339 47.619 21.57 9.98 0.00 1.47
3368 3759 2.530460 TGGGTACTACACGTGGGTAT 57.470 50.000 21.57 4.80 0.00 2.73
3369 3760 2.530460 ATGGGTACTACACGTGGGTA 57.470 50.000 21.57 18.29 0.00 3.69
3370 3761 2.530460 TATGGGTACTACACGTGGGT 57.470 50.000 21.57 19.31 0.00 4.51
3371 3762 2.298163 GGATATGGGTACTACACGTGGG 59.702 54.545 21.57 14.41 0.00 4.61
3372 3763 3.228453 AGGATATGGGTACTACACGTGG 58.772 50.000 21.57 5.28 0.00 4.94
3373 3764 4.217118 GGTAGGATATGGGTACTACACGTG 59.783 50.000 15.48 15.48 37.99 4.49
3374 3765 4.401925 GGTAGGATATGGGTACTACACGT 58.598 47.826 0.00 0.00 37.99 4.49
3375 3766 3.760684 GGGTAGGATATGGGTACTACACG 59.239 52.174 0.00 0.00 37.99 4.49
3376 3767 4.744237 TGGGTAGGATATGGGTACTACAC 58.256 47.826 0.00 0.00 39.62 2.90
3377 3768 5.626850 ATGGGTAGGATATGGGTACTACA 57.373 43.478 0.00 0.00 37.99 2.74
3378 3769 7.677319 ACTTAATGGGTAGGATATGGGTACTAC 59.323 40.741 0.00 0.00 36.07 2.73
3379 3770 7.782866 ACTTAATGGGTAGGATATGGGTACTA 58.217 38.462 0.00 0.00 0.00 1.82
3380 3771 6.640925 ACTTAATGGGTAGGATATGGGTACT 58.359 40.000 0.00 0.00 0.00 2.73
3381 3772 6.499350 TGACTTAATGGGTAGGATATGGGTAC 59.501 42.308 0.00 0.00 0.00 3.34
3382 3773 6.636003 TGACTTAATGGGTAGGATATGGGTA 58.364 40.000 0.00 0.00 0.00 3.69
3383 3774 5.482580 TGACTTAATGGGTAGGATATGGGT 58.517 41.667 0.00 0.00 0.00 4.51
3384 3775 6.418101 CATGACTTAATGGGTAGGATATGGG 58.582 44.000 0.00 0.00 0.00 4.00
3385 3776 6.215431 TCCATGACTTAATGGGTAGGATATGG 59.785 42.308 0.00 0.00 46.17 2.74
3386 3777 7.257790 TCCATGACTTAATGGGTAGGATATG 57.742 40.000 0.00 0.00 46.17 1.78
3393 3784 5.482580 ACCCTATCCATGACTTAATGGGTA 58.517 41.667 0.00 0.07 46.17 3.69
3394 3785 4.315993 ACCCTATCCATGACTTAATGGGT 58.684 43.478 0.00 0.00 46.17 4.51
3395 3786 5.568825 CGTACCCTATCCATGACTTAATGGG 60.569 48.000 0.00 0.00 46.17 4.00
3397 3788 5.479306 CCGTACCCTATCCATGACTTAATG 58.521 45.833 0.00 0.00 0.00 1.90
3398 3789 4.530946 CCCGTACCCTATCCATGACTTAAT 59.469 45.833 0.00 0.00 0.00 1.40
3399 3790 3.899360 CCCGTACCCTATCCATGACTTAA 59.101 47.826 0.00 0.00 0.00 1.85
3400 3791 3.117016 ACCCGTACCCTATCCATGACTTA 60.117 47.826 0.00 0.00 0.00 2.24
3401 3792 2.326428 CCCGTACCCTATCCATGACTT 58.674 52.381 0.00 0.00 0.00 3.01
3402 3793 1.219724 ACCCGTACCCTATCCATGACT 59.780 52.381 0.00 0.00 0.00 3.41
3403 3794 1.713297 ACCCGTACCCTATCCATGAC 58.287 55.000 0.00 0.00 0.00 3.06
3404 3795 3.839323 ATACCCGTACCCTATCCATGA 57.161 47.619 0.00 0.00 0.00 3.07
3405 3796 4.607239 ACTATACCCGTACCCTATCCATG 58.393 47.826 0.00 0.00 0.00 3.66
3406 3797 4.543337 AGACTATACCCGTACCCTATCCAT 59.457 45.833 0.00 0.00 0.00 3.41
3407 3798 3.918912 AGACTATACCCGTACCCTATCCA 59.081 47.826 0.00 0.00 0.00 3.41
3408 3799 4.582973 AGACTATACCCGTACCCTATCC 57.417 50.000 0.00 0.00 0.00 2.59
3409 3800 5.320277 ACAAGACTATACCCGTACCCTATC 58.680 45.833 0.00 0.00 0.00 2.08
3410 3801 5.330648 ACAAGACTATACCCGTACCCTAT 57.669 43.478 0.00 0.00 0.00 2.57
3411 3802 4.796110 ACAAGACTATACCCGTACCCTA 57.204 45.455 0.00 0.00 0.00 3.53
3412 3803 3.677156 ACAAGACTATACCCGTACCCT 57.323 47.619 0.00 0.00 0.00 4.34
3413 3804 3.570125 GGTACAAGACTATACCCGTACCC 59.430 52.174 0.00 0.00 41.88 3.69
3414 3805 4.837896 GGTACAAGACTATACCCGTACC 57.162 50.000 0.00 0.00 41.35 3.34
3420 3811 2.363359 CCCGTGGGTACAAGACTATACC 59.637 54.545 7.14 7.14 40.25 2.73
3421 3812 3.722728 CCCGTGGGTACAAGACTATAC 57.277 52.381 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.