Multiple sequence alignment - TraesCS3D01G531400

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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 TraesCS3D01G531400 chr3D 100.000 3477 0 0 1 3477 607517248 607513772 0.000000e+00 6421.0
1 TraesCS3D01G531400 chr3D 88.000 525 55 6 224 743 548232298 548232819 6.380000e-172 614.0
2 TraesCS3D01G531400 chr3D 85.878 524 63 10 224 740 548210135 548210654 6.560000e-152 547.0
3 TraesCS3D01G531400 chr3D 81.039 385 60 11 2523 2897 119060835 119060454 9.440000e-76 294.0
4 TraesCS3D01G531400 chr2D 98.006 3259 56 2 79 3328 2088250 2091508 0.000000e+00 5650.0
5 TraesCS3D01G531400 chr2D 75.989 379 75 10 2520 2897 453599301 453599664 7.670000e-42 182.0
6 TraesCS3D01G531400 chr2D 98.214 56 1 0 21 76 2088145 2088200 7.940000e-17 99.0
7 TraesCS3D01G531400 chr2D 84.314 102 11 3 79 175 617728959 617728858 1.030000e-15 95.3
8 TraesCS3D01G531400 chr2D 100.000 33 0 0 3159 3191 2087567 2087599 1.040000e-05 62.1
9 TraesCS3D01G531400 chr2D 100.000 33 0 0 31 63 6459090 6459058 1.040000e-05 62.1
10 TraesCS3D01G531400 chr4D 89.129 1297 131 8 1604 2897 28562392 28561103 0.000000e+00 1605.0
11 TraesCS3D01G531400 chr4D 88.194 1296 149 3 1604 2896 28579752 28581046 0.000000e+00 1543.0
12 TraesCS3D01G531400 chr4D 87.069 232 30 0 2666 2897 477372636 477372867 2.660000e-66 263.0
13 TraesCS3D01G531400 chr4B 87.084 1293 136 12 1603 2894 622953145 622954407 0.000000e+00 1434.0
14 TraesCS3D01G531400 chr4B 88.538 759 85 2 1778 2536 57440673 57441429 0.000000e+00 918.0
15 TraesCS3D01G531400 chr4B 88.599 307 32 3 1439 1744 57440369 57440673 1.520000e-98 370.0
16 TraesCS3D01G531400 chr4B 92.742 124 8 1 1468 1590 622952524 622952647 9.920000e-41 178.0
17 TraesCS3D01G531400 chr2B 83.475 1295 161 24 1604 2897 783113254 783114496 0.000000e+00 1157.0
18 TraesCS3D01G531400 chr2B 87.705 122 14 1 1468 1588 783112270 783112391 1.300000e-29 141.0
19 TraesCS3D01G531400 chr2B 95.652 69 3 0 495 563 727220387 727220319 1.020000e-20 111.0
20 TraesCS3D01G531400 chr3B 90.819 806 72 2 1778 2583 223698834 223699637 0.000000e+00 1077.0
21 TraesCS3D01G531400 chr3B 88.589 482 55 0 991 1472 223698024 223698505 1.390000e-163 586.0
22 TraesCS3D01G531400 chr3B 90.196 306 29 1 1439 1744 223698530 223698834 6.990000e-107 398.0
23 TraesCS3D01G531400 chr3B 79.949 389 57 12 2519 2897 658501843 658501466 2.060000e-67 267.0
24 TraesCS3D01G531400 chr3B 87.234 188 24 0 868 1055 223697835 223698022 7.560000e-52 215.0
25 TraesCS3D01G531400 chr3B 81.938 227 28 11 528 743 534249246 534249470 2.760000e-41 180.0
26 TraesCS3D01G531400 chr3B 95.556 45 2 0 3433 3477 817321149 817321105 4.810000e-09 73.1
27 TraesCS3D01G531400 chr2A 88.476 807 84 4 1778 2583 166088237 166087439 0.000000e+00 966.0
28 TraesCS3D01G531400 chr2A 87.213 305 38 1 1440 1744 166088540 166088237 2.570000e-91 346.0
29 TraesCS3D01G531400 chr2A 90.638 235 22 0 750 984 166092527 166092293 2.610000e-81 313.0
30 TraesCS3D01G531400 chr2A 88.976 127 14 0 1344 1470 166088694 166088568 1.290000e-34 158.0
31 TraesCS3D01G531400 chrUn 88.630 730 82 1 1782 2510 288169610 288170339 0.000000e+00 887.0
32 TraesCS3D01G531400 chrUn 80.660 212 37 3 2690 2897 56397865 56398076 9.990000e-36 161.0
33 TraesCS3D01G531400 chrUn 94.872 39 2 0 32 70 131248959 131248997 1.040000e-05 62.1
34 TraesCS3D01G531400 chr6B 79.640 555 59 24 197 743 213158188 213158696 1.990000e-92 350.0
35 TraesCS3D01G531400 chr1A 86.411 287 37 2 1458 1744 25938032 25937748 2.610000e-81 313.0
36 TraesCS3D01G531400 chr1A 86.017 236 30 2 2662 2896 518742172 518742405 2.070000e-62 250.0
37 TraesCS3D01G531400 chr1B 87.004 277 26 6 72 340 51943150 51943424 1.570000e-78 303.0
38 TraesCS3D01G531400 chr1B 83.688 141 12 4 3202 3331 286973566 286973706 4.710000e-24 122.0
39 TraesCS3D01G531400 chr7A 80.362 387 61 10 2523 2897 701483023 701482640 2.640000e-71 279.0
40 TraesCS3D01G531400 chr7B 90.556 180 16 1 2989 3168 209598592 209598414 1.610000e-58 237.0
41 TraesCS3D01G531400 chr6A 95.276 127 6 0 1468 1594 183191857 183191731 5.880000e-48 202.0
42 TraesCS3D01G531400 chr6D 94.488 127 7 0 1468 1594 139919952 139919826 2.740000e-46 196.0
43 TraesCS3D01G531400 chr5D 86.624 157 15 4 70 220 462747495 462747651 5.970000e-38 169.0
44 TraesCS3D01G531400 chr5D 88.679 53 6 0 24 76 462747404 462747456 8.060000e-07 65.8
45 TraesCS3D01G531400 chr7D 85.987 157 16 4 70 220 557413923 557413767 2.780000e-36 163.0
46 TraesCS3D01G531400 chr7D 100.000 40 0 0 24 63 47265991 47265952 1.340000e-09 75.0
47 TraesCS3D01G531400 chr3A 86.093 151 19 1 3327 3477 740024916 740024768 9.990000e-36 161.0
48 TraesCS3D01G531400 chr1D 100.000 32 0 0 31 62 476431066 476431035 3.750000e-05 60.2


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 TraesCS3D01G531400 chr3D 607513772 607517248 3476 True 6421.000000 6421 100.00000 1 3477 1 chr3D.!!$R2 3476
1 TraesCS3D01G531400 chr3D 548232298 548232819 521 False 614.000000 614 88.00000 224 743 1 chr3D.!!$F2 519
2 TraesCS3D01G531400 chr3D 548210135 548210654 519 False 547.000000 547 85.87800 224 740 1 chr3D.!!$F1 516
3 TraesCS3D01G531400 chr2D 2087567 2091508 3941 False 1937.033333 5650 98.74000 21 3328 3 chr2D.!!$F2 3307
4 TraesCS3D01G531400 chr4D 28561103 28562392 1289 True 1605.000000 1605 89.12900 1604 2897 1 chr4D.!!$R1 1293
5 TraesCS3D01G531400 chr4D 28579752 28581046 1294 False 1543.000000 1543 88.19400 1604 2896 1 chr4D.!!$F1 1292
6 TraesCS3D01G531400 chr4B 622952524 622954407 1883 False 806.000000 1434 89.91300 1468 2894 2 chr4B.!!$F2 1426
7 TraesCS3D01G531400 chr4B 57440369 57441429 1060 False 644.000000 918 88.56850 1439 2536 2 chr4B.!!$F1 1097
8 TraesCS3D01G531400 chr2B 783112270 783114496 2226 False 649.000000 1157 85.59000 1468 2897 2 chr2B.!!$F1 1429
9 TraesCS3D01G531400 chr3B 223697835 223699637 1802 False 569.000000 1077 89.20950 868 2583 4 chr3B.!!$F2 1715
10 TraesCS3D01G531400 chr2A 166087439 166092527 5088 True 445.750000 966 88.82575 750 2583 4 chr2A.!!$R1 1833
11 TraesCS3D01G531400 chrUn 288169610 288170339 729 False 887.000000 887 88.63000 1782 2510 1 chrUn.!!$F3 728
12 TraesCS3D01G531400 chr6B 213158188 213158696 508 False 350.000000 350 79.64000 197 743 1 chr6B.!!$F1 546

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
857 1502 0.169672 CAGCGCCATCTTGAACCAAG 59.830 55.000 2.29 0.51 42.25 3.61 F
918 1563 0.898320 CATCGACCAGGTCAGTCCTT 59.102 55.000 20.13 0.00 45.67 3.36 F
1142 4837 1.694169 ACCCATCGCATCCCCTCTT 60.694 57.895 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 7120 0.102481 CAGCATGAGGGCAAAGATGC 59.898 55.000 0.0 0.00 46.68 3.91 R
2184 7372 0.517316 CAGCTTCTTTACGTGGGTGC 59.483 55.000 0.0 0.00 0.00 5.01 R
2719 7913 3.144506 ACAGAACCAAGATCAGTGCTTG 58.855 45.455 0.0 4.09 41.77 4.01 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
76 635 3.055591 CCTCCTCAATGATCGTGATTCG 58.944 50.000 0.00 0.00 41.41 3.34
91 697 3.552294 GTGATTCGTTCGGGAGAGATTTC 59.448 47.826 0.00 0.00 41.75 2.17
107 713 0.958382 TTTCGCCCGTTGGATCAAGG 60.958 55.000 0.00 0.00 0.00 3.61
370 985 3.529341 TTCCGTGGCACTGCGTGAT 62.529 57.895 16.72 0.00 35.23 3.06
409 1025 1.054406 GGTGGATGGCCTGCCTACTA 61.054 60.000 9.97 0.00 36.94 1.82
728 1373 5.681437 GCTCAGGTAGTTATTTGATCCGTCA 60.681 44.000 0.00 0.00 0.00 4.35
857 1502 0.169672 CAGCGCCATCTTGAACCAAG 59.830 55.000 2.29 0.51 42.25 3.61
879 1524 1.588932 CGCAGCGCCTCTTCGATTA 60.589 57.895 2.29 0.00 33.21 1.75
918 1563 0.898320 CATCGACCAGGTCAGTCCTT 59.102 55.000 20.13 0.00 45.67 3.36
1142 4837 1.694169 ACCCATCGCATCCCCTCTT 60.694 57.895 0.00 0.00 0.00 2.85
1359 5277 7.391620 CCTTGTAGGTGTTTCCTCAGTTAATA 58.608 38.462 0.00 0.00 44.42 0.98
1932 7120 3.508845 AATACTGATTCCCCATTCCCG 57.491 47.619 0.00 0.00 0.00 5.14
2719 7913 6.128715 CCTGTGTTCTATCAATGATCGTATGC 60.129 42.308 0.00 0.00 0.00 3.14
2904 8099 0.936764 CGAATCCGATCTGACGCAGG 60.937 60.000 6.95 0.00 38.22 4.85
3262 8457 2.747507 AAAGGCGCCGAACAATGCAC 62.748 55.000 23.20 0.00 0.00 4.57
3328 8527 1.897641 GCGCGATGCCTATCTAGTAC 58.102 55.000 12.10 0.00 37.76 2.73
3329 8528 1.199327 GCGCGATGCCTATCTAGTACA 59.801 52.381 12.10 0.00 37.76 2.90
3330 8529 2.159366 GCGCGATGCCTATCTAGTACAT 60.159 50.000 12.10 0.00 37.76 2.29
3331 8530 3.064958 GCGCGATGCCTATCTAGTACATA 59.935 47.826 12.10 0.00 37.76 2.29
3332 8531 4.589252 CGCGATGCCTATCTAGTACATAC 58.411 47.826 0.00 0.00 0.00 2.39
3333 8532 4.094442 CGCGATGCCTATCTAGTACATACA 59.906 45.833 0.00 0.00 0.00 2.29
3334 8533 5.333513 GCGATGCCTATCTAGTACATACAC 58.666 45.833 0.00 0.00 0.00 2.90
3335 8534 5.106277 GCGATGCCTATCTAGTACATACACA 60.106 44.000 0.00 0.00 0.00 3.72
3336 8535 6.315551 CGATGCCTATCTAGTACATACACAC 58.684 44.000 0.00 0.00 0.00 3.82
3337 8536 5.684550 TGCCTATCTAGTACATACACACG 57.315 43.478 0.00 0.00 0.00 4.49
3338 8537 4.517832 TGCCTATCTAGTACATACACACGG 59.482 45.833 0.00 0.00 0.00 4.94
3339 8538 4.758674 GCCTATCTAGTACATACACACGGA 59.241 45.833 0.00 0.00 0.00 4.69
3340 8539 5.106634 GCCTATCTAGTACATACACACGGAG 60.107 48.000 0.00 0.00 0.00 4.63
3341 8540 5.411977 CCTATCTAGTACATACACACGGAGG 59.588 48.000 0.00 0.00 0.00 4.30
3342 8541 4.492494 TCTAGTACATACACACGGAGGA 57.508 45.455 0.00 0.00 0.00 3.71
3343 8542 4.449131 TCTAGTACATACACACGGAGGAG 58.551 47.826 0.00 0.00 0.00 3.69
3344 8543 3.361281 AGTACATACACACGGAGGAGA 57.639 47.619 0.00 0.00 0.00 3.71
3345 8544 3.693807 AGTACATACACACGGAGGAGAA 58.306 45.455 0.00 0.00 0.00 2.87
3346 8545 4.084287 AGTACATACACACGGAGGAGAAA 58.916 43.478 0.00 0.00 0.00 2.52
3347 8546 4.525487 AGTACATACACACGGAGGAGAAAA 59.475 41.667 0.00 0.00 0.00 2.29
3348 8547 4.345859 ACATACACACGGAGGAGAAAAA 57.654 40.909 0.00 0.00 0.00 1.94
3349 8548 4.315803 ACATACACACGGAGGAGAAAAAG 58.684 43.478 0.00 0.00 0.00 2.27
3350 8549 2.256117 ACACACGGAGGAGAAAAAGG 57.744 50.000 0.00 0.00 0.00 3.11
3351 8550 1.202770 ACACACGGAGGAGAAAAAGGG 60.203 52.381 0.00 0.00 0.00 3.95
3352 8551 0.250770 ACACGGAGGAGAAAAAGGGC 60.251 55.000 0.00 0.00 0.00 5.19
3353 8552 0.250727 CACGGAGGAGAAAAAGGGCA 60.251 55.000 0.00 0.00 0.00 5.36
3354 8553 0.476771 ACGGAGGAGAAAAAGGGCAA 59.523 50.000 0.00 0.00 0.00 4.52
3355 8554 1.133606 ACGGAGGAGAAAAAGGGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
3356 8555 1.960689 CGGAGGAGAAAAAGGGCAAAA 59.039 47.619 0.00 0.00 0.00 2.44
3357 8556 2.288213 CGGAGGAGAAAAAGGGCAAAAC 60.288 50.000 0.00 0.00 0.00 2.43
3358 8557 2.288213 GGAGGAGAAAAAGGGCAAAACG 60.288 50.000 0.00 0.00 0.00 3.60
3359 8558 1.686587 AGGAGAAAAAGGGCAAAACGG 59.313 47.619 0.00 0.00 0.00 4.44
3360 8559 1.270094 GGAGAAAAAGGGCAAAACGGG 60.270 52.381 0.00 0.00 0.00 5.28
3361 8560 1.684450 GAGAAAAAGGGCAAAACGGGA 59.316 47.619 0.00 0.00 0.00 5.14
3362 8561 1.686587 AGAAAAAGGGCAAAACGGGAG 59.313 47.619 0.00 0.00 0.00 4.30
3363 8562 1.684450 GAAAAAGGGCAAAACGGGAGA 59.316 47.619 0.00 0.00 0.00 3.71
3364 8563 2.009681 AAAAGGGCAAAACGGGAGAT 57.990 45.000 0.00 0.00 0.00 2.75
3365 8564 1.256812 AAAGGGCAAAACGGGAGATG 58.743 50.000 0.00 0.00 0.00 2.90
3366 8565 0.404040 AAGGGCAAAACGGGAGATGA 59.596 50.000 0.00 0.00 0.00 2.92
3367 8566 0.404040 AGGGCAAAACGGGAGATGAA 59.596 50.000 0.00 0.00 0.00 2.57
3368 8567 0.811281 GGGCAAAACGGGAGATGAAG 59.189 55.000 0.00 0.00 0.00 3.02
3369 8568 1.613255 GGGCAAAACGGGAGATGAAGA 60.613 52.381 0.00 0.00 0.00 2.87
3370 8569 2.159382 GGCAAAACGGGAGATGAAGAA 58.841 47.619 0.00 0.00 0.00 2.52
3371 8570 2.556622 GGCAAAACGGGAGATGAAGAAA 59.443 45.455 0.00 0.00 0.00 2.52
3372 8571 3.366374 GGCAAAACGGGAGATGAAGAAAG 60.366 47.826 0.00 0.00 0.00 2.62
3373 8572 3.366374 GCAAAACGGGAGATGAAGAAAGG 60.366 47.826 0.00 0.00 0.00 3.11
3374 8573 3.790089 AAACGGGAGATGAAGAAAGGT 57.210 42.857 0.00 0.00 0.00 3.50
3375 8574 4.903045 AAACGGGAGATGAAGAAAGGTA 57.097 40.909 0.00 0.00 0.00 3.08
3376 8575 4.473477 AACGGGAGATGAAGAAAGGTAG 57.527 45.455 0.00 0.00 0.00 3.18
3377 8576 2.766828 ACGGGAGATGAAGAAAGGTAGG 59.233 50.000 0.00 0.00 0.00 3.18
3378 8577 3.031736 CGGGAGATGAAGAAAGGTAGGA 58.968 50.000 0.00 0.00 0.00 2.94
3379 8578 3.068873 CGGGAGATGAAGAAAGGTAGGAG 59.931 52.174 0.00 0.00 0.00 3.69
3380 8579 4.034410 GGGAGATGAAGAAAGGTAGGAGT 58.966 47.826 0.00 0.00 0.00 3.85
3381 8580 4.141824 GGGAGATGAAGAAAGGTAGGAGTG 60.142 50.000 0.00 0.00 0.00 3.51
3382 8581 4.712337 GGAGATGAAGAAAGGTAGGAGTGA 59.288 45.833 0.00 0.00 0.00 3.41
3383 8582 5.365314 GGAGATGAAGAAAGGTAGGAGTGAT 59.635 44.000 0.00 0.00 0.00 3.06
3384 8583 6.551601 GGAGATGAAGAAAGGTAGGAGTGATA 59.448 42.308 0.00 0.00 0.00 2.15
3385 8584 7.255801 GGAGATGAAGAAAGGTAGGAGTGATAG 60.256 44.444 0.00 0.00 0.00 2.08
3386 8585 7.129425 AGATGAAGAAAGGTAGGAGTGATAGT 58.871 38.462 0.00 0.00 0.00 2.12
3387 8586 7.621683 AGATGAAGAAAGGTAGGAGTGATAGTT 59.378 37.037 0.00 0.00 0.00 2.24
3388 8587 7.554959 TGAAGAAAGGTAGGAGTGATAGTTT 57.445 36.000 0.00 0.00 0.00 2.66
3389 8588 7.386851 TGAAGAAAGGTAGGAGTGATAGTTTG 58.613 38.462 0.00 0.00 0.00 2.93
3390 8589 5.735766 AGAAAGGTAGGAGTGATAGTTTGC 58.264 41.667 0.00 0.00 0.00 3.68
3391 8590 5.485708 AGAAAGGTAGGAGTGATAGTTTGCT 59.514 40.000 0.00 0.00 0.00 3.91
3392 8591 5.763876 AAGGTAGGAGTGATAGTTTGCTT 57.236 39.130 0.00 0.00 0.00 3.91
3393 8592 5.763876 AGGTAGGAGTGATAGTTTGCTTT 57.236 39.130 0.00 0.00 0.00 3.51
3394 8593 6.128138 AGGTAGGAGTGATAGTTTGCTTTT 57.872 37.500 0.00 0.00 0.00 2.27
3395 8594 7.253905 AGGTAGGAGTGATAGTTTGCTTTTA 57.746 36.000 0.00 0.00 0.00 1.52
3396 8595 7.686434 AGGTAGGAGTGATAGTTTGCTTTTAA 58.314 34.615 0.00 0.00 0.00 1.52
3397 8596 8.329502 AGGTAGGAGTGATAGTTTGCTTTTAAT 58.670 33.333 0.00 0.00 0.00 1.40
3398 8597 9.609346 GGTAGGAGTGATAGTTTGCTTTTAATA 57.391 33.333 0.00 0.00 0.00 0.98
3404 8603 9.607285 AGTGATAGTTTGCTTTTAATAAACACG 57.393 29.630 0.00 0.00 36.91 4.49
3405 8604 8.363029 GTGATAGTTTGCTTTTAATAAACACGC 58.637 33.333 0.00 0.00 36.91 5.34
3406 8605 7.539366 TGATAGTTTGCTTTTAATAAACACGCC 59.461 33.333 0.00 0.00 36.91 5.68
3407 8606 5.593010 AGTTTGCTTTTAATAAACACGCCA 58.407 33.333 0.00 0.00 36.91 5.69
3408 8607 5.689961 AGTTTGCTTTTAATAAACACGCCAG 59.310 36.000 0.00 0.00 36.91 4.85
3409 8608 4.167554 TGCTTTTAATAAACACGCCAGG 57.832 40.909 0.00 0.00 0.00 4.45
3410 8609 3.821600 TGCTTTTAATAAACACGCCAGGA 59.178 39.130 0.00 0.00 0.00 3.86
3411 8610 4.461081 TGCTTTTAATAAACACGCCAGGAT 59.539 37.500 0.00 0.00 0.00 3.24
3412 8611 5.047660 TGCTTTTAATAAACACGCCAGGATT 60.048 36.000 0.00 0.00 0.00 3.01
3413 8612 5.867174 GCTTTTAATAAACACGCCAGGATTT 59.133 36.000 0.00 0.00 0.00 2.17
3414 8613 6.367695 GCTTTTAATAAACACGCCAGGATTTT 59.632 34.615 0.00 0.00 0.00 1.82
3415 8614 7.095397 GCTTTTAATAAACACGCCAGGATTTTT 60.095 33.333 0.00 0.00 0.00 1.94
3416 8615 7.644986 TTTAATAAACACGCCAGGATTTTTG 57.355 32.000 0.00 0.00 0.00 2.44
3417 8616 4.864704 ATAAACACGCCAGGATTTTTGT 57.135 36.364 0.00 0.00 0.00 2.83
3418 8617 2.507339 AACACGCCAGGATTTTTGTG 57.493 45.000 0.00 0.00 0.00 3.33
3419 8618 0.031994 ACACGCCAGGATTTTTGTGC 59.968 50.000 0.00 0.00 0.00 4.57
3420 8619 1.003262 CACGCCAGGATTTTTGTGCG 61.003 55.000 0.00 0.00 46.69 5.34
3421 8620 1.285641 CGCCAGGATTTTTGTGCGT 59.714 52.632 0.00 0.00 37.44 5.24
3422 8621 1.003262 CGCCAGGATTTTTGTGCGTG 61.003 55.000 0.00 0.00 37.44 5.34
3423 8622 1.284297 GCCAGGATTTTTGTGCGTGC 61.284 55.000 0.00 0.00 0.00 5.34
3424 8623 0.667184 CCAGGATTTTTGTGCGTGCC 60.667 55.000 0.00 0.00 0.00 5.01
3425 8624 0.314935 CAGGATTTTTGTGCGTGCCT 59.685 50.000 0.00 0.00 0.00 4.75
3426 8625 1.039856 AGGATTTTTGTGCGTGCCTT 58.960 45.000 0.00 0.00 0.00 4.35
3427 8626 1.139163 GGATTTTTGTGCGTGCCTTG 58.861 50.000 0.00 0.00 0.00 3.61
3428 8627 0.508213 GATTTTTGTGCGTGCCTTGC 59.492 50.000 0.00 0.00 0.00 4.01
3429 8628 0.879839 ATTTTTGTGCGTGCCTTGCC 60.880 50.000 0.00 0.00 0.00 4.52
3430 8629 2.914777 TTTTTGTGCGTGCCTTGCCC 62.915 55.000 0.00 0.00 0.00 5.36
3431 8630 4.892965 TTGTGCGTGCCTTGCCCT 62.893 61.111 0.00 0.00 0.00 5.19
3436 8635 2.912025 CGTGCCTTGCCCTGGTTT 60.912 61.111 0.00 0.00 0.00 3.27
3437 8636 2.498056 CGTGCCTTGCCCTGGTTTT 61.498 57.895 0.00 0.00 0.00 2.43
3438 8637 1.829456 GTGCCTTGCCCTGGTTTTT 59.171 52.632 0.00 0.00 0.00 1.94
3439 8638 0.249868 GTGCCTTGCCCTGGTTTTTC 60.250 55.000 0.00 0.00 0.00 2.29
3440 8639 1.371183 GCCTTGCCCTGGTTTTTCC 59.629 57.895 0.00 0.00 0.00 3.13
3441 8640 1.121407 GCCTTGCCCTGGTTTTTCCT 61.121 55.000 0.00 0.00 37.07 3.36
3442 8641 0.681175 CCTTGCCCTGGTTTTTCCTG 59.319 55.000 0.00 0.00 37.07 3.86
3451 8650 3.656559 CTGGTTTTTCCTGGATGCTTTG 58.343 45.455 0.00 0.00 37.07 2.77
3452 8651 2.224257 TGGTTTTTCCTGGATGCTTTGC 60.224 45.455 0.00 0.00 37.07 3.68
3453 8652 2.224257 GGTTTTTCCTGGATGCTTTGCA 60.224 45.455 0.00 0.00 44.86 4.08
3454 8653 6.026998 TGGTTTTTCCTGGATGCTTTGCAT 62.027 41.667 4.60 4.60 43.88 3.96
3455 8654 6.742132 TGGTTTTTCCTGGATGCTTTGCATA 61.742 40.000 4.95 0.00 42.43 3.14
3462 8661 3.273048 TGCTTTGCATACCCGTGC 58.727 55.556 0.00 0.00 45.25 5.34
3463 8662 2.339556 TGCTTTGCATACCCGTGCC 61.340 57.895 0.00 0.00 44.43 5.01
3464 8663 3.063743 GCTTTGCATACCCGTGCCC 62.064 63.158 0.00 0.00 44.43 5.36
3465 8664 2.748251 TTTGCATACCCGTGCCCG 60.748 61.111 0.00 0.00 44.43 6.13
3466 8665 3.554696 TTTGCATACCCGTGCCCGT 62.555 57.895 0.00 0.00 44.43 5.28
3467 8666 3.554696 TTGCATACCCGTGCCCGTT 62.555 57.895 0.00 0.00 44.43 4.44
3468 8667 2.748647 GCATACCCGTGCCCGTTT 60.749 61.111 0.00 0.00 39.18 3.60
3469 8668 2.757056 GCATACCCGTGCCCGTTTC 61.757 63.158 0.00 0.00 39.18 2.78
3470 8669 2.110352 CATACCCGTGCCCGTTTCC 61.110 63.158 0.00 0.00 0.00 3.13
3471 8670 3.333899 ATACCCGTGCCCGTTTCCC 62.334 63.158 0.00 0.00 0.00 3.97
3474 8673 4.636435 CCGTGCCCGTTTCCCAGT 62.636 66.667 0.00 0.00 0.00 4.00
3475 8674 2.593436 CGTGCCCGTTTCCCAGTT 60.593 61.111 0.00 0.00 0.00 3.16
3476 8675 2.903547 CGTGCCCGTTTCCCAGTTG 61.904 63.158 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.222114 GTGCTAACTGCTAAGTTGCTTTG 58.778 43.478 1.42 0.00 46.30 2.77
1 2 3.882888 TGTGCTAACTGCTAAGTTGCTTT 59.117 39.130 1.42 0.00 46.30 3.51
2 3 3.476552 TGTGCTAACTGCTAAGTTGCTT 58.523 40.909 1.42 0.00 46.30 3.91
3 4 3.126001 TGTGCTAACTGCTAAGTTGCT 57.874 42.857 1.42 0.00 46.30 3.91
4 5 3.181506 GGATGTGCTAACTGCTAAGTTGC 60.182 47.826 1.42 4.32 46.30 4.17
5 6 4.002982 TGGATGTGCTAACTGCTAAGTTG 58.997 43.478 1.42 0.00 46.30 3.16
7 8 3.866651 CTGGATGTGCTAACTGCTAAGT 58.133 45.455 0.00 0.00 43.37 2.24
8 9 2.611292 GCTGGATGTGCTAACTGCTAAG 59.389 50.000 0.00 0.00 43.37 2.18
10 11 1.554617 TGCTGGATGTGCTAACTGCTA 59.445 47.619 0.00 0.00 43.37 3.49
11 12 0.325933 TGCTGGATGTGCTAACTGCT 59.674 50.000 0.00 0.00 43.37 4.24
12 13 1.167851 TTGCTGGATGTGCTAACTGC 58.832 50.000 0.00 0.00 43.25 4.40
14 15 4.785301 ACATATTGCTGGATGTGCTAACT 58.215 39.130 0.00 0.00 34.98 2.24
15 16 5.505173 AACATATTGCTGGATGTGCTAAC 57.495 39.130 0.00 0.00 36.42 2.34
16 17 6.356556 ACTAACATATTGCTGGATGTGCTAA 58.643 36.000 0.00 0.00 36.42 3.09
17 18 5.928976 ACTAACATATTGCTGGATGTGCTA 58.071 37.500 0.00 0.00 36.42 3.49
18 19 4.785301 ACTAACATATTGCTGGATGTGCT 58.215 39.130 0.00 0.00 36.42 4.40
19 20 5.276270 CAACTAACATATTGCTGGATGTGC 58.724 41.667 0.00 0.00 36.42 4.57
20 21 5.221106 CCCAACTAACATATTGCTGGATGTG 60.221 44.000 0.00 0.00 36.42 3.21
21 22 4.889409 CCCAACTAACATATTGCTGGATGT 59.111 41.667 0.00 0.00 37.91 3.06
25 26 3.316308 GCTCCCAACTAACATATTGCTGG 59.684 47.826 0.00 0.00 0.00 4.85
27 28 3.053693 TGGCTCCCAACTAACATATTGCT 60.054 43.478 0.00 0.00 0.00 3.91
76 635 0.810426 GGGCGAAATCTCTCCCGAAC 60.810 60.000 0.00 0.00 36.86 3.95
91 697 3.508840 GCCTTGATCCAACGGGCG 61.509 66.667 0.00 0.00 33.30 6.13
297 910 1.065551 GAATTAACAGGCGATGGCACC 59.934 52.381 1.01 0.00 42.47 5.01
304 917 1.079875 GGCGACGAATTAACAGGCGA 61.080 55.000 0.00 0.00 0.00 5.54
409 1025 2.427245 CGAGGCGAATGGGAGGAGT 61.427 63.158 0.00 0.00 0.00 3.85
728 1373 1.401409 CGATGCAACGAACAGGCAAAT 60.401 47.619 11.36 0.00 41.43 2.32
879 1524 0.462759 GAATTGAGCTGCGTAGGGCT 60.463 55.000 1.76 0.00 44.05 5.19
1142 4837 6.443934 TTTCCAGTCGTTCAGAAAAATCAA 57.556 33.333 0.00 0.00 0.00 2.57
1208 4903 2.224161 GCCCCTAGATGAGACATGTGTC 60.224 54.545 15.80 15.80 45.08 3.67
1280 4975 8.977412 TGTGATAGGTTCTAAATCATCACACTA 58.023 33.333 10.30 0.00 44.28 2.74
1932 7120 0.102481 CAGCATGAGGGCAAAGATGC 59.898 55.000 0.00 0.00 46.68 3.91
2184 7372 0.517316 CAGCTTCTTTACGTGGGTGC 59.483 55.000 0.00 0.00 0.00 5.01
2719 7913 3.144506 ACAGAACCAAGATCAGTGCTTG 58.855 45.455 0.00 4.09 41.77 4.01
2963 8158 7.606349 TGTATCACAGGATTATGAGCAGATAC 58.394 38.462 0.00 0.00 37.11 2.24
3262 8457 4.675114 GCCGCGAAATCCAAAACAATATAG 59.325 41.667 8.23 0.00 0.00 1.31
3328 8527 3.684788 CCTTTTTCTCCTCCGTGTGTATG 59.315 47.826 0.00 0.00 0.00 2.39
3329 8528 3.307480 CCCTTTTTCTCCTCCGTGTGTAT 60.307 47.826 0.00 0.00 0.00 2.29
3330 8529 2.038033 CCCTTTTTCTCCTCCGTGTGTA 59.962 50.000 0.00 0.00 0.00 2.90
3331 8530 1.202770 CCCTTTTTCTCCTCCGTGTGT 60.203 52.381 0.00 0.00 0.00 3.72
3332 8531 1.523758 CCCTTTTTCTCCTCCGTGTG 58.476 55.000 0.00 0.00 0.00 3.82
3333 8532 0.250770 GCCCTTTTTCTCCTCCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
3334 8533 0.250727 TGCCCTTTTTCTCCTCCGTG 60.251 55.000 0.00 0.00 0.00 4.94
3335 8534 0.476771 TTGCCCTTTTTCTCCTCCGT 59.523 50.000 0.00 0.00 0.00 4.69
3336 8535 1.616159 TTTGCCCTTTTTCTCCTCCG 58.384 50.000 0.00 0.00 0.00 4.63
3337 8536 2.288213 CGTTTTGCCCTTTTTCTCCTCC 60.288 50.000 0.00 0.00 0.00 4.30
3338 8537 2.288213 CCGTTTTGCCCTTTTTCTCCTC 60.288 50.000 0.00 0.00 0.00 3.71
3339 8538 1.686587 CCGTTTTGCCCTTTTTCTCCT 59.313 47.619 0.00 0.00 0.00 3.69
3340 8539 1.270094 CCCGTTTTGCCCTTTTTCTCC 60.270 52.381 0.00 0.00 0.00 3.71
3341 8540 1.684450 TCCCGTTTTGCCCTTTTTCTC 59.316 47.619 0.00 0.00 0.00 2.87
3342 8541 1.686587 CTCCCGTTTTGCCCTTTTTCT 59.313 47.619 0.00 0.00 0.00 2.52
3343 8542 1.684450 TCTCCCGTTTTGCCCTTTTTC 59.316 47.619 0.00 0.00 0.00 2.29
3344 8543 1.783071 TCTCCCGTTTTGCCCTTTTT 58.217 45.000 0.00 0.00 0.00 1.94
3345 8544 1.618343 CATCTCCCGTTTTGCCCTTTT 59.382 47.619 0.00 0.00 0.00 2.27
3346 8545 1.203001 TCATCTCCCGTTTTGCCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
3347 8546 0.404040 TCATCTCCCGTTTTGCCCTT 59.596 50.000 0.00 0.00 0.00 3.95
3348 8547 0.404040 TTCATCTCCCGTTTTGCCCT 59.596 50.000 0.00 0.00 0.00 5.19
3349 8548 0.811281 CTTCATCTCCCGTTTTGCCC 59.189 55.000 0.00 0.00 0.00 5.36
3350 8549 1.821216 TCTTCATCTCCCGTTTTGCC 58.179 50.000 0.00 0.00 0.00 4.52
3351 8550 3.366374 CCTTTCTTCATCTCCCGTTTTGC 60.366 47.826 0.00 0.00 0.00 3.68
3352 8551 3.821033 ACCTTTCTTCATCTCCCGTTTTG 59.179 43.478 0.00 0.00 0.00 2.44
3353 8552 4.100279 ACCTTTCTTCATCTCCCGTTTT 57.900 40.909 0.00 0.00 0.00 2.43
3354 8553 3.790089 ACCTTTCTTCATCTCCCGTTT 57.210 42.857 0.00 0.00 0.00 3.60
3355 8554 3.197983 CCTACCTTTCTTCATCTCCCGTT 59.802 47.826 0.00 0.00 0.00 4.44
3356 8555 2.766828 CCTACCTTTCTTCATCTCCCGT 59.233 50.000 0.00 0.00 0.00 5.28
3357 8556 3.031736 TCCTACCTTTCTTCATCTCCCG 58.968 50.000 0.00 0.00 0.00 5.14
3358 8557 4.034410 ACTCCTACCTTTCTTCATCTCCC 58.966 47.826 0.00 0.00 0.00 4.30
3359 8558 4.712337 TCACTCCTACCTTTCTTCATCTCC 59.288 45.833 0.00 0.00 0.00 3.71
3360 8559 5.923733 TCACTCCTACCTTTCTTCATCTC 57.076 43.478 0.00 0.00 0.00 2.75
3361 8560 7.129425 ACTATCACTCCTACCTTTCTTCATCT 58.871 38.462 0.00 0.00 0.00 2.90
3362 8561 7.354751 ACTATCACTCCTACCTTTCTTCATC 57.645 40.000 0.00 0.00 0.00 2.92
3363 8562 7.741554 AACTATCACTCCTACCTTTCTTCAT 57.258 36.000 0.00 0.00 0.00 2.57
3364 8563 7.386851 CAAACTATCACTCCTACCTTTCTTCA 58.613 38.462 0.00 0.00 0.00 3.02
3365 8564 6.314152 GCAAACTATCACTCCTACCTTTCTTC 59.686 42.308 0.00 0.00 0.00 2.87
3366 8565 6.013293 AGCAAACTATCACTCCTACCTTTCTT 60.013 38.462 0.00 0.00 0.00 2.52
3367 8566 5.485708 AGCAAACTATCACTCCTACCTTTCT 59.514 40.000 0.00 0.00 0.00 2.52
3368 8567 5.735766 AGCAAACTATCACTCCTACCTTTC 58.264 41.667 0.00 0.00 0.00 2.62
3369 8568 5.763876 AGCAAACTATCACTCCTACCTTT 57.236 39.130 0.00 0.00 0.00 3.11
3370 8569 5.763876 AAGCAAACTATCACTCCTACCTT 57.236 39.130 0.00 0.00 0.00 3.50
3371 8570 5.763876 AAAGCAAACTATCACTCCTACCT 57.236 39.130 0.00 0.00 0.00 3.08
3372 8571 7.916914 TTAAAAGCAAACTATCACTCCTACC 57.083 36.000 0.00 0.00 0.00 3.18
3378 8577 9.607285 CGTGTTTATTAAAAGCAAACTATCACT 57.393 29.630 0.00 0.00 34.12 3.41
3379 8578 8.363029 GCGTGTTTATTAAAAGCAAACTATCAC 58.637 33.333 0.00 0.00 34.12 3.06
3380 8579 7.539366 GGCGTGTTTATTAAAAGCAAACTATCA 59.461 33.333 11.83 0.00 34.12 2.15
3381 8580 7.539366 TGGCGTGTTTATTAAAAGCAAACTATC 59.461 33.333 11.83 0.00 34.12 2.08
3382 8581 7.371936 TGGCGTGTTTATTAAAAGCAAACTAT 58.628 30.769 11.83 0.00 34.12 2.12
3383 8582 6.736123 TGGCGTGTTTATTAAAAGCAAACTA 58.264 32.000 11.83 0.00 34.12 2.24
3384 8583 5.593010 TGGCGTGTTTATTAAAAGCAAACT 58.407 33.333 11.83 0.00 34.12 2.66
3385 8584 5.107645 CCTGGCGTGTTTATTAAAAGCAAAC 60.108 40.000 11.83 0.00 33.70 2.93
3386 8585 4.985409 CCTGGCGTGTTTATTAAAAGCAAA 59.015 37.500 11.83 3.06 0.00 3.68
3387 8586 4.278669 TCCTGGCGTGTTTATTAAAAGCAA 59.721 37.500 11.83 3.57 0.00 3.91
3388 8587 3.821600 TCCTGGCGTGTTTATTAAAAGCA 59.178 39.130 11.83 0.00 0.00 3.91
3389 8588 4.428615 TCCTGGCGTGTTTATTAAAAGC 57.571 40.909 0.00 0.00 0.00 3.51
3390 8589 7.883229 AAAATCCTGGCGTGTTTATTAAAAG 57.117 32.000 0.00 0.00 0.00 2.27
3391 8590 7.711339 ACAAAAATCCTGGCGTGTTTATTAAAA 59.289 29.630 0.00 0.00 0.00 1.52
3392 8591 7.169982 CACAAAAATCCTGGCGTGTTTATTAAA 59.830 33.333 0.00 0.00 0.00 1.52
3393 8592 6.642950 CACAAAAATCCTGGCGTGTTTATTAA 59.357 34.615 0.00 0.00 0.00 1.40
3394 8593 6.153067 CACAAAAATCCTGGCGTGTTTATTA 58.847 36.000 0.00 0.00 0.00 0.98
3395 8594 4.987912 CACAAAAATCCTGGCGTGTTTATT 59.012 37.500 0.00 0.00 0.00 1.40
3396 8595 4.555262 CACAAAAATCCTGGCGTGTTTAT 58.445 39.130 0.00 0.00 0.00 1.40
3397 8596 3.797184 GCACAAAAATCCTGGCGTGTTTA 60.797 43.478 0.00 0.00 0.00 2.01
3398 8597 2.820330 CACAAAAATCCTGGCGTGTTT 58.180 42.857 0.00 0.00 0.00 2.83
3399 8598 1.537990 GCACAAAAATCCTGGCGTGTT 60.538 47.619 0.00 0.00 0.00 3.32
3400 8599 0.031994 GCACAAAAATCCTGGCGTGT 59.968 50.000 0.00 0.00 0.00 4.49
3401 8600 1.003262 CGCACAAAAATCCTGGCGTG 61.003 55.000 0.00 0.00 39.65 5.34
3402 8601 1.285641 CGCACAAAAATCCTGGCGT 59.714 52.632 0.00 0.00 39.65 5.68
3403 8602 4.151417 CGCACAAAAATCCTGGCG 57.849 55.556 0.00 0.00 38.45 5.69
3404 8603 1.284297 GCACGCACAAAAATCCTGGC 61.284 55.000 0.00 0.00 0.00 4.85
3405 8604 0.667184 GGCACGCACAAAAATCCTGG 60.667 55.000 0.00 0.00 0.00 4.45
3406 8605 0.314935 AGGCACGCACAAAAATCCTG 59.685 50.000 0.00 0.00 0.00 3.86
3407 8606 1.039856 AAGGCACGCACAAAAATCCT 58.960 45.000 0.00 0.00 0.00 3.24
3408 8607 1.139163 CAAGGCACGCACAAAAATCC 58.861 50.000 0.00 0.00 0.00 3.01
3409 8608 0.508213 GCAAGGCACGCACAAAAATC 59.492 50.000 0.00 0.00 0.00 2.17
3410 8609 0.879839 GGCAAGGCACGCACAAAAAT 60.880 50.000 0.51 0.00 0.00 1.82
3411 8610 1.520342 GGCAAGGCACGCACAAAAA 60.520 52.632 0.51 0.00 0.00 1.94
3412 8611 2.105930 GGCAAGGCACGCACAAAA 59.894 55.556 0.51 0.00 0.00 2.44
3413 8612 3.910490 GGGCAAGGCACGCACAAA 61.910 61.111 0.51 0.00 31.27 2.83
3414 8613 4.892965 AGGGCAAGGCACGCACAA 62.893 61.111 3.16 0.00 36.86 3.33
3419 8618 2.026945 AAAAACCAGGGCAAGGCACG 62.027 55.000 0.00 0.00 36.86 5.34
3420 8619 0.249868 GAAAAACCAGGGCAAGGCAC 60.250 55.000 0.00 0.00 0.00 5.01
3421 8620 1.406860 GGAAAAACCAGGGCAAGGCA 61.407 55.000 0.00 0.00 38.79 4.75
3422 8621 1.121407 AGGAAAAACCAGGGCAAGGC 61.121 55.000 0.00 0.00 42.04 4.35
3423 8622 0.681175 CAGGAAAAACCAGGGCAAGG 59.319 55.000 0.00 0.00 42.04 3.61
3424 8623 0.681175 CCAGGAAAAACCAGGGCAAG 59.319 55.000 0.00 0.00 41.01 4.01
3425 8624 0.263172 TCCAGGAAAAACCAGGGCAA 59.737 50.000 0.00 0.00 44.27 4.52
3426 8625 0.486879 ATCCAGGAAAAACCAGGGCA 59.513 50.000 0.00 0.00 44.27 5.36
3427 8626 0.897621 CATCCAGGAAAAACCAGGGC 59.102 55.000 0.00 0.00 44.27 5.19
3428 8627 0.897621 GCATCCAGGAAAAACCAGGG 59.102 55.000 0.00 0.00 44.27 4.45
3429 8628 1.928868 AGCATCCAGGAAAAACCAGG 58.071 50.000 0.00 0.00 45.32 4.45
3430 8629 3.656559 CAAAGCATCCAGGAAAAACCAG 58.343 45.455 0.00 0.00 42.04 4.00
3431 8630 2.224257 GCAAAGCATCCAGGAAAAACCA 60.224 45.455 0.00 0.00 42.04 3.67
3432 8631 2.224257 TGCAAAGCATCCAGGAAAAACC 60.224 45.455 0.00 0.00 31.71 3.27
3433 8632 3.110447 TGCAAAGCATCCAGGAAAAAC 57.890 42.857 0.00 0.00 31.71 2.43
3445 8644 3.273048 GCACGGGTATGCAAAGCA 58.727 55.556 0.00 0.00 45.39 3.91
3451 8650 2.748647 AAACGGGCACGGGTATGC 60.749 61.111 15.46 0.00 46.48 3.14
3452 8651 2.110352 GGAAACGGGCACGGGTATG 61.110 63.158 15.46 0.00 46.48 2.39
3453 8652 2.269883 GGAAACGGGCACGGGTAT 59.730 61.111 15.46 0.00 46.48 2.73
3454 8653 4.019312 GGGAAACGGGCACGGGTA 62.019 66.667 15.46 0.00 46.48 3.69
3457 8656 4.636435 ACTGGGAAACGGGCACGG 62.636 66.667 15.46 0.00 46.48 4.94
3459 8658 3.039134 CAACTGGGAAACGGGCAC 58.961 61.111 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.