Multiple sequence alignment - TraesCS3A01G398100

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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 TraesCS3A01G398100 chr3A 100.000 4002 0 0 1 4002 645151205 645147204 0.000000e+00 7391.0
1 TraesCS3A01G398100 chr3A 92.185 2380 153 14 971 3335 645392860 645390499 0.000000e+00 3334.0
2 TraesCS3A01G398100 chr3A 92.668 491 24 7 388 874 645393469 645392987 0.000000e+00 697.0
3 TraesCS3A01G398100 chr3A 88.246 570 39 8 3439 4002 645390500 645389953 0.000000e+00 656.0
4 TraesCS3A01G398100 chr3A 94.000 50 3 0 687 736 679696602 679696651 4.290000e-10 76.8
5 TraesCS3A01G398100 chr3B 95.897 3339 103 11 1 3335 669446148 669442840 0.000000e+00 5376.0
6 TraesCS3A01G398100 chr3B 88.565 481 42 8 388 865 669461492 669461022 4.490000e-159 571.0
7 TraesCS3A01G398100 chr3B 88.835 412 33 6 3441 3852 669442836 669442438 9.990000e-136 494.0
8 TraesCS3A01G398100 chr3B 92.000 50 3 1 685 734 413416763 413416811 7.180000e-08 69.4
9 TraesCS3A01G398100 chr3D 96.029 2367 72 7 971 3335 507044507 507042161 0.000000e+00 3831.0
10 TraesCS3A01G398100 chr3D 93.397 1787 111 7 1552 3335 507111070 507109288 0.000000e+00 2639.0
11 TraesCS3A01G398100 chr3D 89.860 572 29 12 3439 4002 507042162 507041612 0.000000e+00 708.0
12 TraesCS3A01G398100 chr3D 88.811 572 33 10 3439 4002 507109289 507108741 0.000000e+00 673.0
13 TraesCS3A01G398100 chr3D 89.054 539 41 10 388 915 507062995 507062464 0.000000e+00 652.0
14 TraesCS3A01G398100 chr3D 91.566 415 33 2 388 801 507111833 507111420 4.490000e-159 571.0
15 TraesCS3A01G398100 chr3D 89.646 367 37 1 20 385 206354862 206354496 2.180000e-127 466.0
16 TraesCS3A01G398100 chr3D 87.692 390 41 6 1 385 330262272 330262659 7.890000e-122 448.0
17 TraesCS3A01G398100 chr3D 80.800 250 21 12 3440 3682 507108221 507107992 1.910000e-38 171.0
18 TraesCS3A01G398100 chr5A 94.648 710 29 2 1814 2514 510160274 510160983 0.000000e+00 1092.0
19 TraesCS3A01G398100 chr5A 96.728 489 15 1 2564 3051 510160982 510161470 0.000000e+00 813.0
20 TraesCS3A01G398100 chr5A 96.667 120 2 2 3330 3448 95823191 95823073 8.770000e-47 198.0
21 TraesCS3A01G398100 chr5A 97.368 114 3 0 3327 3440 402092749 402092636 1.130000e-45 195.0
22 TraesCS3A01G398100 chr1B 89.119 386 41 1 1 385 270593881 270593496 2.800000e-131 479.0
23 TraesCS3A01G398100 chr4D 88.372 387 42 3 1 385 288459967 288460352 2.820000e-126 462.0
24 TraesCS3A01G398100 chr4D 87.113 388 46 4 1 385 208250128 208249742 1.710000e-118 436.0
25 TraesCS3A01G398100 chr4D 95.349 43 2 0 687 729 93455337 93455295 7.180000e-08 69.4
26 TraesCS3A01G398100 chr6B 87.798 377 44 2 1 377 384137645 384137271 1.320000e-119 440.0
27 TraesCS3A01G398100 chr6B 90.476 315 18 6 975 1289 701886587 701886889 4.820000e-109 405.0
28 TraesCS3A01G398100 chr5B 87.306 386 48 1 1 385 474789802 474790187 1.320000e-119 440.0
29 TraesCS3A01G398100 chr5B 87.080 387 47 3 1 385 211317958 211318343 6.140000e-118 435.0
30 TraesCS3A01G398100 chr5B 97.391 115 3 0 3329 3443 70910799 70910685 3.160000e-46 196.0
31 TraesCS3A01G398100 chr5B 90.566 53 3 2 687 738 362119571 362119520 7.180000e-08 69.4
32 TraesCS3A01G398100 chr6D 87.536 345 21 6 975 1319 460718092 460718414 2.920000e-101 379.0
33 TraesCS3A01G398100 chr6D 95.833 48 2 0 687 734 304279454 304279407 1.190000e-10 78.7
34 TraesCS3A01G398100 chr6D 95.745 47 2 0 687 733 292073414 292073368 4.290000e-10 76.8
35 TraesCS3A01G398100 chr6D 96.875 32 0 1 681 712 438882387 438882357 7.000000e-03 52.8
36 TraesCS3A01G398100 chr6A 83.759 431 34 19 890 1319 606975009 606975404 3.780000e-100 375.0
37 TraesCS3A01G398100 chr6A 96.639 119 3 1 3323 3440 108945302 108945420 3.160000e-46 196.0
38 TraesCS3A01G398100 chr6A 97.391 115 3 0 3334 3448 158088023 158087909 3.160000e-46 196.0
39 TraesCS3A01G398100 chr5D 99.099 111 1 0 3333 3443 231640376 231640486 2.440000e-47 200.0
40 TraesCS3A01G398100 chr5D 97.619 42 1 0 688 729 548952363 548952404 5.550000e-09 73.1
41 TraesCS3A01G398100 chr5D 95.455 44 2 0 687 730 314384672 314384629 2.000000e-08 71.3
42 TraesCS3A01G398100 chr2A 99.091 110 1 0 3334 3443 722814008 722814117 8.770000e-47 198.0
43 TraesCS3A01G398100 chr2A 96.552 116 4 0 3329 3444 57865502 57865387 4.080000e-45 193.0
44 TraesCS3A01G398100 chr2A 97.826 46 1 0 689 734 49850955 49851000 3.320000e-11 80.5
45 TraesCS3A01G398100 chr4A 94.400 125 6 1 3334 3457 632136356 632136480 1.470000e-44 191.0
46 TraesCS3A01G398100 chr1A 96.078 51 1 1 685 734 245526605 245526655 9.220000e-12 82.4
47 TraesCS3A01G398100 chr1D 93.750 48 3 0 685 732 21448364 21448317 5.550000e-09 73.1
48 TraesCS3A01G398100 chr1D 94.595 37 2 0 702 738 226457689 226457725 1.550000e-04 58.4


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 TraesCS3A01G398100 chr3A 645147204 645151205 4001 True 7391.000000 7391 100.0000 1 4002 1 chr3A.!!$R1 4001
1 TraesCS3A01G398100 chr3A 645389953 645393469 3516 True 1562.333333 3334 91.0330 388 4002 3 chr3A.!!$R2 3614
2 TraesCS3A01G398100 chr3B 669442438 669446148 3710 True 2935.000000 5376 92.3660 1 3852 2 chr3B.!!$R2 3851
3 TraesCS3A01G398100 chr3D 507041612 507044507 2895 True 2269.500000 3831 92.9445 971 4002 2 chr3D.!!$R3 3031
4 TraesCS3A01G398100 chr3D 507107992 507111833 3841 True 1013.500000 2639 88.6435 388 4002 4 chr3D.!!$R4 3614
5 TraesCS3A01G398100 chr3D 507062464 507062995 531 True 652.000000 652 89.0540 388 915 1 chr3D.!!$R2 527
6 TraesCS3A01G398100 chr5A 510160274 510161470 1196 False 952.500000 1092 95.6880 1814 3051 2 chr5A.!!$F1 1237

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
339 340 0.179134 GCTAGATCCTTCGCACACGT 60.179 55.0 0.0 0.0 41.18 4.49 F
1093 1186 0.250901 CCCCACAAGAGAACCACCAG 60.251 60.0 0.0 0.0 0.00 4.00 F
2079 2184 0.850100 TGCAAGGGGAAGAAGGTGAA 59.150 50.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1847 1.325640 CGCGTCCATCTTGTCAATCTG 59.674 52.381 0.00 0.0 0.00 2.90 R
2856 2970 2.412089 GGATGTGTCACTTCAAGCGTAC 59.588 50.000 17.82 0.0 0.00 3.67 R
3773 3911 0.921347 GCTAGTGCGGTGATTACACG 59.079 55.000 0.00 0.0 46.77 4.49 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
33 34 1.241315 CGCCGTTGTGGAATCCCTTT 61.241 55.000 0.00 0.00 42.00 3.11
102 103 5.104193 AGGTTAGACTCCACCGTAGAGAATA 60.104 44.000 0.58 0.00 38.21 1.75
114 115 7.815068 CCACCGTAGAGAATAATAGATCCTTTG 59.185 40.741 0.00 0.00 0.00 2.77
135 136 1.227497 CATTGAGCTCTCCCGAGGC 60.227 63.158 16.19 0.00 37.75 4.70
145 146 4.767255 CCCGAGGCAGCTCACACC 62.767 72.222 0.00 0.00 0.00 4.16
176 177 3.427573 TCGTACTCATCCTCCTTGTGAA 58.572 45.455 0.00 0.00 0.00 3.18
241 242 1.372307 CCGAACCTGGGTAAACCGT 59.628 57.895 0.00 0.00 44.64 4.83
242 243 0.250424 CCGAACCTGGGTAAACCGTT 60.250 55.000 0.00 0.00 44.64 4.44
268 269 0.902516 ACCTCTTCTTCCTGCTCGCT 60.903 55.000 0.00 0.00 0.00 4.93
273 274 0.532573 TTCTTCCTGCTCGCTCGAAT 59.467 50.000 0.00 0.00 0.00 3.34
278 279 1.941734 CTGCTCGCTCGAATCCGAC 60.942 63.158 0.00 0.00 40.30 4.79
339 340 0.179134 GCTAGATCCTTCGCACACGT 60.179 55.000 0.00 0.00 41.18 4.49
366 367 1.335810 GTTCGAACCTTGTTTGGGTCC 59.664 52.381 17.68 0.00 40.60 4.46
385 386 2.445845 TGGAGCCCCGATTCCGAT 60.446 61.111 0.00 0.00 38.22 4.18
492 493 1.205460 TTGAGGGGGCACTAGAACCC 61.205 60.000 14.35 14.35 46.24 4.11
575 576 9.360514 GTATTGCAAATAAAATTCATCGCATTG 57.639 29.630 1.71 0.00 0.00 2.82
590 591 7.610865 TCATCGCATTGTGTAGAATATCCATA 58.389 34.615 0.00 0.00 0.00 2.74
1039 1132 3.119849 CCTAATGCGAAACCTTTCACTGG 60.120 47.826 0.00 0.00 37.01 4.00
1061 1154 0.900647 CTCTCCCTCAACTCCCGTGT 60.901 60.000 0.00 0.00 0.00 4.49
1093 1186 0.250901 CCCCACAAGAGAACCACCAG 60.251 60.000 0.00 0.00 0.00 4.00
1564 1669 3.083997 GACCAGATCCCCACCGCT 61.084 66.667 0.00 0.00 0.00 5.52
1648 1753 3.817647 AGAACTGCTCTGGTAAAAAGCTG 59.182 43.478 0.00 0.00 39.85 4.24
1818 1923 1.064240 TGTGCCAGGATCATTGAGCAT 60.064 47.619 4.07 0.00 32.11 3.79
1867 1972 3.006859 TGTTCTGGAAGCTCGAGAAATCA 59.993 43.478 18.75 7.65 41.66 2.57
1912 2017 1.312815 AGTTCAGTGAGTTTGGCTGC 58.687 50.000 0.00 0.00 0.00 5.25
2015 2120 3.663025 GAGAAGATGATTAGCTCTGGGC 58.337 50.000 0.00 0.00 42.19 5.36
2079 2184 0.850100 TGCAAGGGGAAGAAGGTGAA 59.150 50.000 0.00 0.00 0.00 3.18
2279 2392 4.272504 CCGTTATACATAGTTTGTGCAGGG 59.727 45.833 0.00 0.00 39.48 4.45
2368 2481 4.158394 AGTGCAGTGTTCAACTTTGTCATT 59.842 37.500 0.00 0.00 36.83 2.57
2856 2970 5.363939 CCAAGAAGCATAGTTTCTCTAGGG 58.636 45.833 0.00 0.00 33.92 3.53
2893 3007 3.689161 CACATCCGCTAATCAGTTTTGGA 59.311 43.478 0.00 0.00 0.00 3.53
3108 3225 7.374272 TCACGCAAATTTTGATCCAATCTTAA 58.626 30.769 13.26 0.00 0.00 1.85
3286 3420 1.518325 TTGGTGCGTGATGTACAAGG 58.482 50.000 0.00 0.00 34.44 3.61
3327 3461 7.117956 TGTTATCGTGTAAAACATCGGAATGAA 59.882 33.333 0.00 0.00 36.67 2.57
3335 3469 7.753132 TGTAAAACATCGGAATGAAAATGCTAC 59.247 33.333 0.00 0.00 36.67 3.58
3336 3470 6.515272 AAACATCGGAATGAAAATGCTACT 57.485 33.333 0.00 0.00 36.67 2.57
3337 3471 5.741388 ACATCGGAATGAAAATGCTACTC 57.259 39.130 0.00 0.00 36.67 2.59
3338 3472 4.576463 ACATCGGAATGAAAATGCTACTCC 59.424 41.667 0.00 0.00 36.67 3.85
3339 3473 3.541632 TCGGAATGAAAATGCTACTCCC 58.458 45.455 0.00 0.00 0.00 4.30
3340 3474 3.199946 TCGGAATGAAAATGCTACTCCCT 59.800 43.478 0.00 0.00 0.00 4.20
3341 3475 3.561725 CGGAATGAAAATGCTACTCCCTC 59.438 47.826 0.00 0.00 0.00 4.30
3342 3476 3.885901 GGAATGAAAATGCTACTCCCTCC 59.114 47.826 0.00 0.00 0.00 4.30
3343 3477 2.691409 TGAAAATGCTACTCCCTCCG 57.309 50.000 0.00 0.00 0.00 4.63
3344 3478 1.906574 TGAAAATGCTACTCCCTCCGT 59.093 47.619 0.00 0.00 0.00 4.69
3345 3479 2.304761 TGAAAATGCTACTCCCTCCGTT 59.695 45.455 0.00 0.00 0.00 4.44
3346 3480 2.693267 AAATGCTACTCCCTCCGTTC 57.307 50.000 0.00 0.00 0.00 3.95
3347 3481 0.460311 AATGCTACTCCCTCCGTTCG 59.540 55.000 0.00 0.00 0.00 3.95
3348 3482 1.392710 ATGCTACTCCCTCCGTTCGG 61.393 60.000 4.74 4.74 0.00 4.30
3349 3483 1.751927 GCTACTCCCTCCGTTCGGA 60.752 63.158 13.34 13.34 0.00 4.55
3350 3484 1.318158 GCTACTCCCTCCGTTCGGAA 61.318 60.000 14.79 0.04 33.41 4.30
3351 3485 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
3352 3486 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3353 3487 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3354 3488 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3355 3489 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3356 3490 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3357 3491 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3358 3492 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3359 3493 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3360 3494 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3361 3495 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3362 3496 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3363 3497 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3364 3498 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3365 3499 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3366 3500 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3367 3501 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3368 3502 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3369 3503 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
3370 3504 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
3371 3505 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
3372 3506 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
3373 3507 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
3374 3508 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
3375 3509 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
3376 3510 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
3377 3511 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
3378 3512 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
3379 3513 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
3380 3514 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
3381 3515 6.015095 TGTCGCAGAAATGGATGTATCTAGAT 60.015 38.462 10.73 10.73 39.69 1.98
3382 3516 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
3383 3517 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
3384 3518 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
3385 3519 7.978414 CGCAGAAATGGATGTATCTAGATGTAT 59.022 37.037 15.79 9.11 0.00 2.29
3386 3520 9.664332 GCAGAAATGGATGTATCTAGATGTATT 57.336 33.333 15.79 4.32 0.00 1.89
3415 3549 8.952278 AGTTCTAGATACATTCATATCCGAGAC 58.048 37.037 0.00 0.00 32.76 3.36
3416 3550 8.731605 GTTCTAGATACATTCATATCCGAGACA 58.268 37.037 0.00 0.00 32.76 3.41
3417 3551 8.863872 TCTAGATACATTCATATCCGAGACAA 57.136 34.615 0.00 0.00 32.76 3.18
3418 3552 8.951243 TCTAGATACATTCATATCCGAGACAAG 58.049 37.037 0.00 0.00 32.76 3.16
3419 3553 7.531857 AGATACATTCATATCCGAGACAAGT 57.468 36.000 0.00 0.00 32.76 3.16
3420 3554 8.637196 AGATACATTCATATCCGAGACAAGTA 57.363 34.615 0.00 0.00 32.76 2.24
3421 3555 9.078990 AGATACATTCATATCCGAGACAAGTAA 57.921 33.333 0.00 0.00 32.76 2.24
3422 3556 9.862371 GATACATTCATATCCGAGACAAGTAAT 57.138 33.333 0.00 0.00 0.00 1.89
3424 3558 8.594881 ACATTCATATCCGAGACAAGTAATTC 57.405 34.615 0.00 0.00 0.00 2.17
3425 3559 7.657761 ACATTCATATCCGAGACAAGTAATTCC 59.342 37.037 0.00 0.00 0.00 3.01
3426 3560 5.769367 TCATATCCGAGACAAGTAATTCCG 58.231 41.667 0.00 0.00 0.00 4.30
3427 3561 5.533528 TCATATCCGAGACAAGTAATTCCGA 59.466 40.000 0.00 0.00 0.00 4.55
3428 3562 4.730949 ATCCGAGACAAGTAATTCCGAA 57.269 40.909 0.00 0.00 0.00 4.30
3429 3563 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
3430 3564 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3431 3565 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3432 3566 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3433 3567 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3434 3568 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3435 3569 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3436 3570 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3437 3571 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3438 3572 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3439 3573 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3448 3582 5.924825 CCGAACGGAGGGAGTATATTTTTAG 59.075 44.000 7.53 0.00 37.50 1.85
3477 3611 5.587388 ATTCATAGATTTGTTGGCACTGG 57.413 39.130 0.00 0.00 0.00 4.00
3478 3612 4.299586 TCATAGATTTGTTGGCACTGGA 57.700 40.909 0.00 0.00 0.00 3.86
3479 3613 4.661222 TCATAGATTTGTTGGCACTGGAA 58.339 39.130 0.00 0.00 0.00 3.53
3480 3614 5.076182 TCATAGATTTGTTGGCACTGGAAA 58.924 37.500 0.00 0.00 0.00 3.13
3481 3615 5.183713 TCATAGATTTGTTGGCACTGGAAAG 59.816 40.000 0.00 0.00 0.00 2.62
3482 3616 3.299503 AGATTTGTTGGCACTGGAAAGT 58.700 40.909 0.00 0.00 0.00 2.66
3483 3617 2.957491 TTTGTTGGCACTGGAAAGTG 57.043 45.000 1.45 1.45 42.32 3.16
3495 3629 3.709653 ACTGGAAAGTGGTAACTGACTCA 59.290 43.478 0.00 0.00 36.51 3.41
3521 3655 7.928167 AGCGAAGACACTTTCATTGATATGATA 59.072 33.333 0.00 0.00 40.37 2.15
3590 3724 6.377146 GGAGTAATTTTCTGGGAATGCACTTA 59.623 38.462 0.00 0.00 0.00 2.24
3660 3794 0.823356 TCTGCTGGGTCTTTTGTGCC 60.823 55.000 0.00 0.00 0.00 5.01
3682 3816 4.155462 CCCTATTCGGAGCATGATTTGATG 59.845 45.833 0.00 0.00 33.16 3.07
3697 3835 5.939883 TGATTTGATGGAGTTTAGTGTCTGG 59.060 40.000 0.00 0.00 0.00 3.86
3728 3866 8.182881 TCAGCTTTTCATTTGGTTTTGATTTTG 58.817 29.630 0.00 0.00 0.00 2.44
3773 3911 1.109323 AACAGTGCCTGCCCAGTTTC 61.109 55.000 2.50 0.00 34.37 2.78
3798 3936 2.907897 ATCACCGCACTAGCTTCGGC 62.908 60.000 15.19 5.04 46.49 5.54
3811 3949 0.872021 CTTCGGCTACTGCGATCACC 60.872 60.000 0.00 0.00 40.82 4.02
3812 3950 1.600511 TTCGGCTACTGCGATCACCA 61.601 55.000 0.00 0.00 40.82 4.17
3889 4031 5.587443 TGGTACATGAAATCTCAGCTGAATG 59.413 40.000 18.85 18.39 34.23 2.67
3911 4056 8.599624 AATGGAATTTTGAATAGTCATCTGGT 57.400 30.769 0.00 0.00 26.74 4.00
3912 4057 7.395190 TGGAATTTTGAATAGTCATCTGGTG 57.605 36.000 0.00 0.00 32.48 4.17
3913 4058 6.377996 TGGAATTTTGAATAGTCATCTGGTGG 59.622 38.462 0.00 0.00 32.48 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.187606 TCCCTCATAGCTTAGGCGGA 59.812 55.000 0.00 0.00 44.37 5.54
102 103 3.893813 GCTCAATGGCCAAAGGATCTATT 59.106 43.478 10.96 0.00 0.00 1.73
114 115 2.203126 CGGGAGAGCTCAATGGCC 60.203 66.667 17.77 8.61 0.00 5.36
145 146 5.236911 GGAGGATGAGTACGAACTAGTACAG 59.763 48.000 0.00 0.00 46.85 2.74
176 177 1.381056 TGCTTTGTGGTGGGTTGCT 60.381 52.632 0.00 0.00 0.00 3.91
238 239 0.393077 AGAAGAGGTGGACACAACGG 59.607 55.000 4.69 0.00 40.01 4.44
241 242 2.104792 CAGGAAGAAGAGGTGGACACAA 59.895 50.000 4.69 0.00 0.00 3.33
242 243 1.694150 CAGGAAGAAGAGGTGGACACA 59.306 52.381 4.69 0.00 0.00 3.72
268 269 2.279502 CTTGGCCTCGTCGGATTCGA 62.280 60.000 3.32 0.00 43.86 3.71
290 291 2.740055 CCGTGCTCACTGCCTCAC 60.740 66.667 0.00 0.00 42.00 3.51
315 316 0.962489 TGCGAAGGATCTAGCCTAGC 59.038 55.000 7.46 7.46 40.25 3.42
339 340 1.420430 ACAAGGTTCGAACTCTGGGA 58.580 50.000 26.32 0.00 0.00 4.37
366 367 4.891727 CGGAATCGGGGCTCCACG 62.892 72.222 1.96 3.79 0.00 4.94
377 378 6.345920 ACGAAATTCAACACTATCGGAATC 57.654 37.500 0.00 0.00 34.81 2.52
385 386 4.020928 TCCTGCCTACGAAATTCAACACTA 60.021 41.667 0.00 0.00 0.00 2.74
492 493 5.111989 TCAGAATGAGTATGAGCTTTTCCG 58.888 41.667 0.00 0.00 42.56 4.30
516 517 9.297586 CCAGTTACAGGTTTAAGAAAAGAAAAC 57.702 33.333 0.00 0.00 33.37 2.43
575 576 8.887717 GCTCCATTCAATATGGATATTCTACAC 58.112 37.037 6.93 0.00 46.12 2.90
590 591 9.021807 CCTAATGAATTATCTGCTCCATTCAAT 57.978 33.333 0.00 0.00 38.73 2.57
658 660 7.664318 TCAGAGGGACCTTTTATTCTACAAAAC 59.336 37.037 0.00 0.00 0.00 2.43
919 924 7.229306 TGTGCTAGTTGAATTTCAAGATCTTGT 59.771 33.333 29.80 14.62 37.00 3.16
1039 1132 1.671901 CGGGAGTTGAGGGAGAGAGC 61.672 65.000 0.00 0.00 0.00 4.09
1648 1753 1.803555 GCAGACTTGAACAAGAGGAGC 59.196 52.381 19.35 13.26 40.79 4.70
1742 1847 1.325640 CGCGTCCATCTTGTCAATCTG 59.674 52.381 0.00 0.00 0.00 2.90
1818 1923 1.679139 CACTTTGTTCAGCAGTGGGA 58.321 50.000 0.00 0.00 0.00 4.37
1867 1972 3.391382 ACCTCTAGCGCCGCCTTT 61.391 61.111 4.98 0.00 0.00 3.11
1912 2017 4.778415 CTGTCGCCGTCCGGAGTG 62.778 72.222 3.06 0.00 37.50 3.51
2079 2184 3.658725 AGGTATACTGAATGTGCCTCCT 58.341 45.455 2.25 0.00 0.00 3.69
2279 2392 4.771590 TTGCATCCTTCACATTCTTCAC 57.228 40.909 0.00 0.00 0.00 3.18
2368 2481 5.838955 TCTCCCTCTTTAGACAATCCTGTA 58.161 41.667 0.00 0.00 35.30 2.74
2856 2970 2.412089 GGATGTGTCACTTCAAGCGTAC 59.588 50.000 17.82 0.00 0.00 3.67
2893 3007 3.899980 AGAGCAAAAAGAGGGCAAATTCT 59.100 39.130 0.00 0.00 0.00 2.40
3108 3225 2.912956 TGTATCCTCCTTTGGCAAGTCT 59.087 45.455 0.00 0.00 0.00 3.24
3205 3325 9.429109 TTTTCCTTTTACTACTTCCCTTTTGAT 57.571 29.630 0.00 0.00 0.00 2.57
3206 3326 8.826293 TTTTCCTTTTACTACTTCCCTTTTGA 57.174 30.769 0.00 0.00 0.00 2.69
3207 3327 9.309516 GTTTTTCCTTTTACTACTTCCCTTTTG 57.690 33.333 0.00 0.00 0.00 2.44
3208 3328 9.038072 TGTTTTTCCTTTTACTACTTCCCTTTT 57.962 29.630 0.00 0.00 0.00 2.27
3209 3329 8.598202 TGTTTTTCCTTTTACTACTTCCCTTT 57.402 30.769 0.00 0.00 0.00 3.11
3210 3330 8.638873 CATGTTTTTCCTTTTACTACTTCCCTT 58.361 33.333 0.00 0.00 0.00 3.95
3211 3331 7.783119 ACATGTTTTTCCTTTTACTACTTCCCT 59.217 33.333 0.00 0.00 0.00 4.20
3212 3332 7.948357 ACATGTTTTTCCTTTTACTACTTCCC 58.052 34.615 0.00 0.00 0.00 3.97
3213 3333 9.244799 CAACATGTTTTTCCTTTTACTACTTCC 57.755 33.333 8.77 0.00 0.00 3.46
3216 3336 9.965824 CATCAACATGTTTTTCCTTTTACTACT 57.034 29.630 8.77 0.00 0.00 2.57
3217 3337 8.699749 GCATCAACATGTTTTTCCTTTTACTAC 58.300 33.333 8.77 0.00 31.86 2.73
3218 3338 8.417106 TGCATCAACATGTTTTTCCTTTTACTA 58.583 29.630 8.77 0.00 31.86 1.82
3219 3339 7.271511 TGCATCAACATGTTTTTCCTTTTACT 58.728 30.769 8.77 0.00 31.86 2.24
3220 3340 7.475771 TGCATCAACATGTTTTTCCTTTTAC 57.524 32.000 8.77 0.00 31.86 2.01
3221 3341 6.202570 GCTGCATCAACATGTTTTTCCTTTTA 59.797 34.615 8.77 0.00 31.86 1.52
3286 3420 5.062683 CACGATAACAGCATATAGGCATGTC 59.937 44.000 12.54 4.63 35.83 3.06
3327 3461 1.134788 CGAACGGAGGGAGTAGCATTT 60.135 52.381 0.00 0.00 0.00 2.32
3335 3469 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3336 3470 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3337 3471 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3338 3472 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3339 3473 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3340 3474 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3341 3475 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3342 3476 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3343 3477 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3344 3478 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3345 3479 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3346 3480 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
3347 3481 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
3348 3482 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
3349 3483 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
3350 3484 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
3351 3485 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
3352 3486 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
3353 3487 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
3354 3488 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
3355 3489 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
3356 3490 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
3357 3491 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3358 3492 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
3359 3493 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
3360 3494 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
3389 3523 8.952278 GTCTCGGATATGAATGTATCTAGAACT 58.048 37.037 0.00 0.00 31.35 3.01
3390 3524 8.731605 TGTCTCGGATATGAATGTATCTAGAAC 58.268 37.037 0.00 0.00 31.35 3.01
3391 3525 8.863872 TGTCTCGGATATGAATGTATCTAGAA 57.136 34.615 0.00 0.00 31.35 2.10
3392 3526 8.863872 TTGTCTCGGATATGAATGTATCTAGA 57.136 34.615 0.00 0.00 32.78 2.43
3393 3527 8.735315 ACTTGTCTCGGATATGAATGTATCTAG 58.265 37.037 0.00 0.00 32.78 2.43
3394 3528 8.637196 ACTTGTCTCGGATATGAATGTATCTA 57.363 34.615 0.00 0.00 32.78 1.98
3395 3529 7.531857 ACTTGTCTCGGATATGAATGTATCT 57.468 36.000 0.00 0.00 32.78 1.98
3396 3530 9.862371 ATTACTTGTCTCGGATATGAATGTATC 57.138 33.333 0.00 0.00 0.00 2.24
3398 3532 9.692749 GAATTACTTGTCTCGGATATGAATGTA 57.307 33.333 0.00 0.00 0.00 2.29
3399 3533 7.657761 GGAATTACTTGTCTCGGATATGAATGT 59.342 37.037 0.00 0.00 0.00 2.71
3400 3534 7.148738 CGGAATTACTTGTCTCGGATATGAATG 60.149 40.741 0.00 0.00 0.00 2.67
3401 3535 6.868864 CGGAATTACTTGTCTCGGATATGAAT 59.131 38.462 0.00 0.00 0.00 2.57
3402 3536 6.040054 TCGGAATTACTTGTCTCGGATATGAA 59.960 38.462 0.00 0.00 0.00 2.57
3403 3537 5.533528 TCGGAATTACTTGTCTCGGATATGA 59.466 40.000 0.00 0.00 0.00 2.15
3404 3538 5.769367 TCGGAATTACTTGTCTCGGATATG 58.231 41.667 0.00 0.00 0.00 1.78
3405 3539 6.214399 GTTCGGAATTACTTGTCTCGGATAT 58.786 40.000 0.00 0.00 0.00 1.63
3406 3540 5.585390 GTTCGGAATTACTTGTCTCGGATA 58.415 41.667 0.00 0.00 0.00 2.59
3407 3541 4.430908 GTTCGGAATTACTTGTCTCGGAT 58.569 43.478 0.00 0.00 0.00 4.18
3408 3542 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3409 3543 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3410 3544 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3411 3545 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3412 3546 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3413 3547 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3414 3548 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3415 3549 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3416 3550 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3417 3551 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3418 3552 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3419 3553 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3420 3554 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
3421 3555 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
3422 3556 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
3423 3557 2.965671 ATATACTCCCTCCGTTCGGA 57.034 50.000 13.34 13.34 0.00 4.55
3424 3558 4.332428 AAAATATACTCCCTCCGTTCGG 57.668 45.455 4.74 4.74 0.00 4.30
3425 3559 6.510536 ACTAAAAATATACTCCCTCCGTTCG 58.489 40.000 0.00 0.00 0.00 3.95
3426 3560 9.420551 CATACTAAAAATATACTCCCTCCGTTC 57.579 37.037 0.00 0.00 0.00 3.95
3427 3561 7.876582 GCATACTAAAAATATACTCCCTCCGTT 59.123 37.037 0.00 0.00 0.00 4.44
3428 3562 7.015877 TGCATACTAAAAATATACTCCCTCCGT 59.984 37.037 0.00 0.00 0.00 4.69
3429 3563 7.383687 TGCATACTAAAAATATACTCCCTCCG 58.616 38.462 0.00 0.00 0.00 4.63
3430 3564 9.740710 ATTGCATACTAAAAATATACTCCCTCC 57.259 33.333 0.00 0.00 0.00 4.30
3448 3582 6.979817 TGCCAACAAATCTATGAATTGCATAC 59.020 34.615 0.00 0.00 38.44 2.39
3477 3611 2.731976 CGCTGAGTCAGTTACCACTTTC 59.268 50.000 21.06 0.00 33.43 2.62
3478 3612 2.364324 TCGCTGAGTCAGTTACCACTTT 59.636 45.455 21.06 0.00 33.43 2.66
3479 3613 1.961394 TCGCTGAGTCAGTTACCACTT 59.039 47.619 21.06 0.00 33.43 3.16
3480 3614 1.617322 TCGCTGAGTCAGTTACCACT 58.383 50.000 21.06 0.00 33.43 4.00
3481 3615 2.030185 TCTTCGCTGAGTCAGTTACCAC 60.030 50.000 21.06 2.76 33.43 4.16
3482 3616 2.030185 GTCTTCGCTGAGTCAGTTACCA 60.030 50.000 21.06 0.94 33.43 3.25
3483 3617 2.030185 TGTCTTCGCTGAGTCAGTTACC 60.030 50.000 21.06 3.84 33.43 2.85
3495 3629 6.108687 TCATATCAATGAAAGTGTCTTCGCT 58.891 36.000 0.00 0.00 39.20 4.93
3521 3655 9.200817 ACTAATTGGCAATACATGTCCTTAAAT 57.799 29.630 14.05 0.00 30.45 1.40
3660 3794 4.155462 CCATCAAATCATGCTCCGAATAGG 59.845 45.833 0.00 0.00 42.97 2.57
3682 3816 5.086104 TGAATAGCCAGACACTAAACTCC 57.914 43.478 0.00 0.00 0.00 3.85
3728 3866 1.717194 TTTCAACGGGTCGCAGATAC 58.283 50.000 0.00 0.00 40.67 2.24
3773 3911 0.921347 GCTAGTGCGGTGATTACACG 59.079 55.000 0.00 0.00 46.77 4.49
3798 3936 1.067565 AGTGTGTGGTGATCGCAGTAG 60.068 52.381 8.82 0.00 36.43 2.57
3889 4031 6.183360 CCCACCAGATGACTATTCAAAATTCC 60.183 42.308 0.00 0.00 34.61 3.01
3911 4056 2.070039 CCTGATTAGGCCCGACCCA 61.070 63.158 0.00 0.00 40.58 4.51
3912 4057 1.759459 CTCCTGATTAGGCCCGACCC 61.759 65.000 0.00 0.00 44.22 4.46
3913 4058 1.049289 ACTCCTGATTAGGCCCGACC 61.049 60.000 0.00 0.00 44.22 4.79


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

AutoCloner maintained by Alex Coulton.