Multiple sequence alignment - TraesCS2A01G040300

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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 TraesCS2A01G040300 chr2A 100.000 3165 0 0 803 3967 16561763 16558599 0.000000e+00 5845.0
1 TraesCS2A01G040300 chr2A 100.000 538 0 0 1 538 16562565 16562028 0.000000e+00 994.0
2 TraesCS2A01G040300 chr2D 93.754 1745 65 14 803 2517 14270210 14268480 0.000000e+00 2579.0
3 TraesCS2A01G040300 chr2D 94.860 642 26 4 2559 3196 14268473 14267835 0.000000e+00 996.0
4 TraesCS2A01G040300 chr2D 87.101 783 52 21 3201 3967 14267793 14267044 0.000000e+00 841.0
5 TraesCS2A01G040300 chr2D 83.900 559 40 33 1 538 14270733 14270204 4.610000e-134 488.0
6 TraesCS2A01G040300 chr2B 91.064 1175 69 20 2050 3196 26109490 26108324 0.000000e+00 1555.0
7 TraesCS2A01G040300 chr2B 93.155 672 34 5 1348 2007 26110167 26109496 0.000000e+00 976.0
8 TraesCS2A01G040300 chr2B 87.596 782 58 17 3201 3967 26108282 26107525 0.000000e+00 870.0
9 TraesCS2A01G040300 chr2B 81.413 651 78 20 2056 2696 20559959 20560576 3.560000e-135 492.0
10 TraesCS2A01G040300 chr2B 81.399 586 38 29 1 538 26111281 26110719 2.850000e-111 412.0
11 TraesCS2A01G040300 chr3D 83.390 590 39 16 2802 3375 593343763 593344309 3.560000e-135 492.0
12 TraesCS2A01G040300 chr3D 82.886 596 52 28 3386 3967 593344352 593344911 1.280000e-134 490.0
13 TraesCS2A01G040300 chr5A 92.038 314 16 5 1464 1776 630721581 630721886 2.190000e-117 433.0
14 TraesCS2A01G040300 chr5A 88.696 345 28 7 1463 1802 639277079 639276741 1.030000e-110 411.0
15 TraesCS2A01G040300 chr5D 91.693 313 20 1 1463 1775 448349338 448349644 2.830000e-116 429.0
16 TraesCS2A01G040300 chr5D 90.741 324 22 3 1463 1784 235714838 235714521 3.660000e-115 425.0
17 TraesCS2A01G040300 chr6D 90.741 324 22 5 1463 1784 53540921 53540604 3.660000e-115 425.0
18 TraesCS2A01G040300 chr4A 91.429 315 19 3 1463 1776 366765650 366765957 3.660000e-115 425.0
19 TraesCS2A01G040300 chr4A 90.432 324 22 3 1463 1784 411835380 411835064 6.130000e-113 418.0
20 TraesCS2A01G040300 chr4A 90.764 314 23 1 1463 1776 33006537 33006844 7.930000e-112 414.0
21 TraesCS2A01G040300 chr3B 88.122 362 28 6 3506 3867 796538121 796538467 2.210000e-112 416.0
22 TraesCS2A01G040300 chr7A 89.198 324 27 3 1463 1784 24784413 24784096 7.990000e-107 398.0
23 TraesCS2A01G040300 chr7B 97.872 47 0 1 2168 2214 744688124 744688169 3.290000e-11 80.5
24 TraesCS2A01G040300 chr5B 97.778 45 0 1 2168 2212 88900619 88900576 4.250000e-10 76.8


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 TraesCS2A01G040300 chr2A 16558599 16562565 3966 True 3419.50 5845 100.00000 1 3967 2 chr2A.!!$R1 3966
1 TraesCS2A01G040300 chr2D 14267044 14270733 3689 True 1226.00 2579 89.90375 1 3967 4 chr2D.!!$R1 3966
2 TraesCS2A01G040300 chr2B 26107525 26111281 3756 True 953.25 1555 88.30350 1 3967 4 chr2B.!!$R1 3966
3 TraesCS2A01G040300 chr2B 20559959 20560576 617 False 492.00 492 81.41300 2056 2696 1 chr2B.!!$F1 640
4 TraesCS2A01G040300 chr3D 593343763 593344911 1148 False 491.00 492 83.13800 2802 3967 2 chr3D.!!$F1 1165

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
331 368 0.320050 GCTCTCCTCATTCCGATCCC 59.680 60.000 0.0 0.0 0.0 3.85 F
333 370 0.563173 TCTCCTCATTCCGATCCCCT 59.437 55.000 0.0 0.0 0.0 4.79 F
1183 1262 0.321996 GCACCCGTTCCTCTTCTTCT 59.678 55.000 0.0 0.0 0.0 2.85 F
2043 2140 1.134907 CCAGGTTGCCATTGATGCTTC 60.135 52.381 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 1249 0.108089 GGCGGGAGAAGAAGAGGAAC 60.108 60.000 0.00 0.00 0.00 3.62 R
1412 1500 0.734253 GACGATGAGCAGCTTGTCGT 60.734 55.000 26.57 26.57 46.78 4.34 R
2519 2628 1.447314 GCACACCGTACTAGCCACC 60.447 63.158 0.00 0.00 0.00 4.61 R
3275 3488 0.752743 AGAAAGGCAGCTGCACACAA 60.753 50.000 37.63 0.00 44.36 3.33 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
84 88 4.426313 GGGGTGCCGGGGAAGAAG 62.426 72.222 2.18 0.00 0.00 2.85
115 120 2.159379 CGAGGGCTAAAATGGAAAGTGC 60.159 50.000 0.00 0.00 0.00 4.40
217 242 1.377202 TCCCAGCATTTCAGCGTCC 60.377 57.895 0.00 0.00 40.15 4.79
220 245 2.044946 AGCATTTCAGCGTCCCCC 60.045 61.111 0.00 0.00 40.15 5.40
224 249 0.965439 CATTTCAGCGTCCCCCAAAA 59.035 50.000 0.00 0.00 0.00 2.44
234 259 1.068125 GTCCCCCAAAATTCCGTTTCG 60.068 52.381 0.00 0.00 0.00 3.46
270 297 9.869757 GGGTAATTATTTAACACTTGCTTGATT 57.130 29.630 0.00 0.00 0.00 2.57
325 362 1.227497 CCGCAGCTCTCCTCATTCC 60.227 63.158 0.00 0.00 0.00 3.01
326 363 1.591059 CGCAGCTCTCCTCATTCCG 60.591 63.158 0.00 0.00 0.00 4.30
327 364 1.819229 GCAGCTCTCCTCATTCCGA 59.181 57.895 0.00 0.00 0.00 4.55
328 365 0.392336 GCAGCTCTCCTCATTCCGAT 59.608 55.000 0.00 0.00 0.00 4.18
329 366 1.605202 GCAGCTCTCCTCATTCCGATC 60.605 57.143 0.00 0.00 0.00 3.69
330 367 1.000731 CAGCTCTCCTCATTCCGATCC 59.999 57.143 0.00 0.00 0.00 3.36
331 368 0.320050 GCTCTCCTCATTCCGATCCC 59.680 60.000 0.00 0.00 0.00 3.85
332 369 0.972883 CTCTCCTCATTCCGATCCCC 59.027 60.000 0.00 0.00 0.00 4.81
333 370 0.563173 TCTCCTCATTCCGATCCCCT 59.437 55.000 0.00 0.00 0.00 4.79
344 381 0.755686 CGATCCCCTCTCCTTCCAAG 59.244 60.000 0.00 0.00 0.00 3.61
345 382 1.886422 GATCCCCTCTCCTTCCAAGT 58.114 55.000 0.00 0.00 0.00 3.16
346 383 2.200955 GATCCCCTCTCCTTCCAAGTT 58.799 52.381 0.00 0.00 0.00 2.66
347 384 1.657804 TCCCCTCTCCTTCCAAGTTC 58.342 55.000 0.00 0.00 0.00 3.01
348 385 0.621082 CCCCTCTCCTTCCAAGTTCC 59.379 60.000 0.00 0.00 0.00 3.62
349 386 1.362224 CCCTCTCCTTCCAAGTTCCA 58.638 55.000 0.00 0.00 0.00 3.53
350 387 1.705186 CCCTCTCCTTCCAAGTTCCAA 59.295 52.381 0.00 0.00 0.00 3.53
351 388 2.310052 CCCTCTCCTTCCAAGTTCCAAT 59.690 50.000 0.00 0.00 0.00 3.16
352 389 3.615155 CCTCTCCTTCCAAGTTCCAATC 58.385 50.000 0.00 0.00 0.00 2.67
353 390 3.615155 CTCTCCTTCCAAGTTCCAATCC 58.385 50.000 0.00 0.00 0.00 3.01
354 391 2.986019 TCTCCTTCCAAGTTCCAATCCA 59.014 45.455 0.00 0.00 0.00 3.41
355 392 3.593328 TCTCCTTCCAAGTTCCAATCCAT 59.407 43.478 0.00 0.00 0.00 3.41
356 393 3.950395 CTCCTTCCAAGTTCCAATCCATC 59.050 47.826 0.00 0.00 0.00 3.51
396 433 4.798682 TCGCCTTCCTCCTCCCCC 62.799 72.222 0.00 0.00 0.00 5.40
397 434 4.806339 CGCCTTCCTCCTCCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
398 435 3.093172 GCCTTCCTCCTCCCCCTG 61.093 72.222 0.00 0.00 0.00 4.45
399 436 3.093172 CCTTCCTCCTCCCCCTGC 61.093 72.222 0.00 0.00 0.00 4.85
400 437 2.041928 CTTCCTCCTCCCCCTGCT 59.958 66.667 0.00 0.00 0.00 4.24
401 438 2.041265 TTCCTCCTCCCCCTGCTC 59.959 66.667 0.00 0.00 0.00 4.26
402 439 2.829639 CTTCCTCCTCCCCCTGCTCA 62.830 65.000 0.00 0.00 0.00 4.26
531 590 1.113788 CGCCACCATCCATTCCATTT 58.886 50.000 0.00 0.00 0.00 2.32
532 591 1.067516 CGCCACCATCCATTCCATTTC 59.932 52.381 0.00 0.00 0.00 2.17
533 592 1.413812 GCCACCATCCATTCCATTTCC 59.586 52.381 0.00 0.00 0.00 3.13
534 593 2.749600 CCACCATCCATTCCATTTCCA 58.250 47.619 0.00 0.00 0.00 3.53
535 594 3.311091 CCACCATCCATTCCATTTCCAT 58.689 45.455 0.00 0.00 0.00 3.41
536 595 3.712733 CCACCATCCATTCCATTTCCATT 59.287 43.478 0.00 0.00 0.00 3.16
537 596 4.202284 CCACCATCCATTCCATTTCCATTC 60.202 45.833 0.00 0.00 0.00 2.67
847 916 2.124151 CTCCATCCGCCCCCTTTG 60.124 66.667 0.00 0.00 0.00 2.77
905 978 1.227853 CTTTCTTATCCCCCGCCCG 60.228 63.158 0.00 0.00 0.00 6.13
930 1003 4.075793 CTCCCCGGACCCCTCAGA 62.076 72.222 0.73 0.00 0.00 3.27
975 1048 2.028876 CCGGTTTTTCTTGGTCTTGGT 58.971 47.619 0.00 0.00 0.00 3.67
976 1049 2.034179 CCGGTTTTTCTTGGTCTTGGTC 59.966 50.000 0.00 0.00 0.00 4.02
977 1050 2.949644 CGGTTTTTCTTGGTCTTGGTCT 59.050 45.455 0.00 0.00 0.00 3.85
978 1051 3.380320 CGGTTTTTCTTGGTCTTGGTCTT 59.620 43.478 0.00 0.00 0.00 3.01
1183 1262 0.321996 GCACCCGTTCCTCTTCTTCT 59.678 55.000 0.00 0.00 0.00 2.85
1266 1345 2.443016 CTCCTCTCCCACCTCCCG 60.443 72.222 0.00 0.00 0.00 5.14
1285 1364 3.869934 TCCACCACACCCTCCCCT 61.870 66.667 0.00 0.00 0.00 4.79
1288 1367 4.677151 ACCACACCCTCCCCTCCC 62.677 72.222 0.00 0.00 0.00 4.30
1323 1402 3.966543 CACCCCACCCACCTCCAC 61.967 72.222 0.00 0.00 0.00 4.02
1326 1405 3.966543 CCCACCCACCTCCACCAC 61.967 72.222 0.00 0.00 0.00 4.16
1329 1408 3.175710 ACCCACCTCCACCACCAC 61.176 66.667 0.00 0.00 0.00 4.16
1331 1410 3.966543 CCACCTCCACCACCACCC 61.967 72.222 0.00 0.00 0.00 4.61
1383 1462 3.566853 TACCTAGCCGACGACGCG 61.567 66.667 3.53 3.53 38.29 6.01
1855 1950 8.417106 TGCAGTCTTTGACCAATTTTTATTACA 58.583 29.630 0.00 0.00 32.18 2.41
1917 2012 4.382362 GCTTTCTAGGATGGCAAAGCAAAT 60.382 41.667 15.65 0.00 46.61 2.32
1984 2080 8.306761 AGTTGCTATCCGAATTGAAAATTTCTT 58.693 29.630 7.29 0.00 0.00 2.52
1985 2081 8.925700 GTTGCTATCCGAATTGAAAATTTCTTT 58.074 29.630 7.29 1.24 0.00 2.52
1986 2082 8.687824 TGCTATCCGAATTGAAAATTTCTTTC 57.312 30.769 7.29 8.97 0.00 2.62
2013 2110 6.752351 TCTTAGAAGATTCGTTAGTGCACATC 59.248 38.462 21.04 11.85 0.00 3.06
2018 2115 5.872635 AGATTCGTTAGTGCACATCATTTG 58.127 37.500 21.04 1.86 0.00 2.32
2043 2140 1.134907 CCAGGTTGCCATTGATGCTTC 60.135 52.381 0.00 0.00 0.00 3.86
2128 2225 7.934855 ATGAATCTGAAACTTTATGCTCTGT 57.065 32.000 0.00 0.00 0.00 3.41
2163 2260 8.196771 GGATAAAATTGGATGATGTGTAAAGCA 58.803 33.333 0.00 0.00 0.00 3.91
2488 2597 4.002316 GCTTCTCTTTGCATCTCTTGAGT 58.998 43.478 0.00 0.00 0.00 3.41
2489 2598 4.093261 GCTTCTCTTTGCATCTCTTGAGTC 59.907 45.833 0.00 0.00 0.00 3.36
2519 2628 5.300752 ACCATGTTCAAGTCAAGTACTCTG 58.699 41.667 0.00 0.00 37.50 3.35
2523 2632 4.058817 GTTCAAGTCAAGTACTCTGGTGG 58.941 47.826 0.00 0.00 37.50 4.61
2524 2633 2.037251 TCAAGTCAAGTACTCTGGTGGC 59.963 50.000 0.00 0.00 37.50 5.01
2525 2634 2.016905 AGTCAAGTACTCTGGTGGCT 57.983 50.000 0.00 0.00 30.33 4.75
2526 2635 3.170991 AGTCAAGTACTCTGGTGGCTA 57.829 47.619 0.00 0.00 30.33 3.93
2527 2636 3.093057 AGTCAAGTACTCTGGTGGCTAG 58.907 50.000 0.00 0.00 30.33 3.42
2528 2637 2.826725 GTCAAGTACTCTGGTGGCTAGT 59.173 50.000 0.00 0.00 0.00 2.57
2529 2638 4.015084 GTCAAGTACTCTGGTGGCTAGTA 58.985 47.826 0.00 0.00 0.00 1.82
2530 2639 4.015084 TCAAGTACTCTGGTGGCTAGTAC 58.985 47.826 0.00 0.00 43.79 2.73
2531 2640 2.641305 AGTACTCTGGTGGCTAGTACG 58.359 52.381 0.00 0.00 46.53 3.67
2532 2641 1.674962 GTACTCTGGTGGCTAGTACGG 59.325 57.143 0.00 0.00 37.08 4.02
2533 2642 0.039326 ACTCTGGTGGCTAGTACGGT 59.961 55.000 0.00 0.00 0.00 4.83
2534 2643 0.456221 CTCTGGTGGCTAGTACGGTG 59.544 60.000 0.00 0.00 0.00 4.94
2535 2644 0.251474 TCTGGTGGCTAGTACGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
2536 2645 0.108804 CTGGTGGCTAGTACGGTGTG 60.109 60.000 0.00 0.00 0.00 3.82
2537 2646 1.447314 GGTGGCTAGTACGGTGTGC 60.447 63.158 0.00 0.00 0.00 4.57
2538 2647 1.804326 GTGGCTAGTACGGTGTGCG 60.804 63.158 0.00 0.00 0.00 5.34
2539 2648 2.270257 TGGCTAGTACGGTGTGCGT 61.270 57.895 0.00 0.00 0.00 5.24
2540 2649 1.804326 GGCTAGTACGGTGTGCGTG 60.804 63.158 0.00 0.00 0.00 5.34
2541 2650 1.080974 GCTAGTACGGTGTGCGTGT 60.081 57.895 0.00 0.00 0.00 4.49
2542 2651 0.665369 GCTAGTACGGTGTGCGTGTT 60.665 55.000 0.00 0.00 0.00 3.32
2543 2652 1.334054 CTAGTACGGTGTGCGTGTTC 58.666 55.000 0.00 0.00 0.00 3.18
2544 2653 0.667453 TAGTACGGTGTGCGTGTTCA 59.333 50.000 0.00 0.00 0.00 3.18
2545 2654 0.032952 AGTACGGTGTGCGTGTTCAT 59.967 50.000 0.00 0.00 0.00 2.57
2546 2655 0.863144 GTACGGTGTGCGTGTTCATT 59.137 50.000 0.00 0.00 0.00 2.57
2547 2656 1.262151 GTACGGTGTGCGTGTTCATTT 59.738 47.619 0.00 0.00 0.00 2.32
2548 2657 0.736053 ACGGTGTGCGTGTTCATTTT 59.264 45.000 0.00 0.00 0.00 1.82
2549 2658 1.941294 ACGGTGTGCGTGTTCATTTTA 59.059 42.857 0.00 0.00 0.00 1.52
2550 2659 2.355132 ACGGTGTGCGTGTTCATTTTAA 59.645 40.909 0.00 0.00 0.00 1.52
2551 2660 3.003897 ACGGTGTGCGTGTTCATTTTAAT 59.996 39.130 0.00 0.00 0.00 1.40
2552 2661 3.978217 CGGTGTGCGTGTTCATTTTAATT 59.022 39.130 0.00 0.00 0.00 1.40
2553 2662 4.143639 CGGTGTGCGTGTTCATTTTAATTG 60.144 41.667 0.00 0.00 0.00 2.32
2554 2663 4.979197 GGTGTGCGTGTTCATTTTAATTGA 59.021 37.500 0.00 0.00 0.00 2.57
2555 2664 5.633182 GGTGTGCGTGTTCATTTTAATTGAT 59.367 36.000 0.00 0.00 0.00 2.57
2556 2665 6.183359 GGTGTGCGTGTTCATTTTAATTGATC 60.183 38.462 0.00 0.00 0.00 2.92
2557 2666 6.582295 GTGTGCGTGTTCATTTTAATTGATCT 59.418 34.615 0.00 0.00 0.00 2.75
2624 2773 6.866248 TGGAAATTCGAAAGATAACAAAAGGC 59.134 34.615 0.00 0.00 41.60 4.35
2625 2774 6.033513 GGAAATTCGAAAGATAACAAAAGGCG 59.966 38.462 0.00 0.00 41.60 5.52
2734 2894 3.815856 TTGCAAGCTTTGTTTGGATCA 57.184 38.095 0.00 0.00 0.00 2.92
3043 3205 0.739813 ACTTTTCGATCCCCTTCGCG 60.740 55.000 0.00 0.00 38.97 5.87
3055 3221 1.671850 CCCTTCGCGAACTCTGCTTTA 60.672 52.381 19.38 0.00 0.00 1.85
3134 3305 1.387084 CTTCAACTTGACGCTAGCGAC 59.613 52.381 41.33 34.59 42.83 5.19
3152 3324 3.777478 CGACTATACACGGGTGTCATTT 58.223 45.455 7.88 0.00 43.74 2.32
3275 3488 0.183971 TTGGTTGACGGGGACAATGT 59.816 50.000 0.00 0.00 0.00 2.71
3288 3504 0.249155 ACAATGTTGTGTGCAGCTGC 60.249 50.000 31.89 31.89 40.49 5.25
3310 3530 4.261572 GCCTTTCTGTCACTGTGCAATTAA 60.262 41.667 2.12 0.00 0.00 1.40
3313 3533 7.592938 CCTTTCTGTCACTGTGCAATTAATTA 58.407 34.615 2.12 0.00 0.00 1.40
3314 3534 8.246180 CCTTTCTGTCACTGTGCAATTAATTAT 58.754 33.333 2.12 0.00 0.00 1.28
3315 3535 9.630098 CTTTCTGTCACTGTGCAATTAATTATT 57.370 29.630 2.12 0.00 0.00 1.40
3316 3536 9.979578 TTTCTGTCACTGTGCAATTAATTATTT 57.020 25.926 2.12 0.00 0.00 1.40
3317 3537 9.979578 TTCTGTCACTGTGCAATTAATTATTTT 57.020 25.926 2.12 0.00 0.00 1.82
3342 3562 9.656040 TTTCATGGAAAATTTTCTACATCATGG 57.344 29.630 28.02 18.22 34.98 3.66
3375 3595 9.238368 AGATTGGTTCCGTTTAATAATTTCTGA 57.762 29.630 0.00 0.00 0.00 3.27
3376 3596 9.285770 GATTGGTTCCGTTTAATAATTTCTGAC 57.714 33.333 0.00 0.00 0.00 3.51
3377 3597 7.747155 TGGTTCCGTTTAATAATTTCTGACA 57.253 32.000 0.00 0.00 0.00 3.58
3378 3598 8.167605 TGGTTCCGTTTAATAATTTCTGACAA 57.832 30.769 0.00 0.00 0.00 3.18
3379 3599 8.798402 TGGTTCCGTTTAATAATTTCTGACAAT 58.202 29.630 0.00 0.00 0.00 2.71
3380 3600 9.634163 GGTTCCGTTTAATAATTTCTGACAATT 57.366 29.630 0.00 4.21 0.00 2.32
3400 3652 9.912634 GACAATTTGAACTGAATAATGAAGGAA 57.087 29.630 2.79 0.00 0.00 3.36
3420 3672 1.347221 CGGTTCAAATCGCTACCGC 59.653 57.895 0.00 0.00 45.75 5.68
3429 3681 2.251409 ATCGCTACCGCACTCTAGTA 57.749 50.000 0.00 0.00 35.30 1.82
3500 3757 5.189736 ACATCCTAAGAACCAGACTATGCAA 59.810 40.000 0.00 0.00 0.00 4.08
3501 3758 5.957771 TCCTAAGAACCAGACTATGCAAT 57.042 39.130 0.00 0.00 0.00 3.56
3502 3759 6.313519 TCCTAAGAACCAGACTATGCAATT 57.686 37.500 0.00 0.00 0.00 2.32
3503 3760 6.721318 TCCTAAGAACCAGACTATGCAATTT 58.279 36.000 0.00 0.00 0.00 1.82
3504 3761 7.175104 TCCTAAGAACCAGACTATGCAATTTT 58.825 34.615 0.00 0.00 0.00 1.82
3505 3762 7.669722 TCCTAAGAACCAGACTATGCAATTTTT 59.330 33.333 0.00 0.00 0.00 1.94
3537 3794 2.455674 TGCATACATCACCGCTATCC 57.544 50.000 0.00 0.00 0.00 2.59
3548 3805 0.463833 CCGCTATCCCTTTCGCCTTT 60.464 55.000 0.00 0.00 0.00 3.11
3554 3811 4.214332 GCTATCCCTTTCGCCTTTGAATAG 59.786 45.833 0.00 0.00 0.00 1.73
3592 3852 3.214328 ACGGATTTGCTTCTGAACAAGT 58.786 40.909 0.00 4.08 0.00 3.16
3595 3855 4.676924 CGGATTTGCTTCTGAACAAGTTTC 59.323 41.667 5.85 0.00 0.00 2.78
3752 4012 2.303022 CCAGGCTGACTTACCTTTGAGA 59.697 50.000 17.94 0.00 32.56 3.27
3753 4013 3.244561 CCAGGCTGACTTACCTTTGAGAA 60.245 47.826 17.94 0.00 32.56 2.87
3754 4014 3.999663 CAGGCTGACTTACCTTTGAGAAG 59.000 47.826 9.42 0.00 32.56 2.85
3802 4068 4.561606 CGTTGCTACATAGTAGTTTTCGCT 59.438 41.667 6.11 0.00 0.00 4.93
3873 4139 2.870411 ACTCAACTCTTTGCCGTGTAAC 59.130 45.455 0.00 0.00 32.17 2.50
3926 4193 3.883830 TGAGTTGCAAAAGCCAAAAGA 57.116 38.095 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.692406 GGTCGGGTTGCCTCGAGT 61.692 66.667 12.31 0.00 36.00 4.18
43 44 2.494918 CTCCACGCCTAGGTTCGG 59.505 66.667 11.31 8.34 0.00 4.30
49 50 3.470888 CACCCCCTCCACGCCTAG 61.471 72.222 0.00 0.00 0.00 3.02
70 74 0.596577 GTTTTCTTCTTCCCCGGCAC 59.403 55.000 0.00 0.00 0.00 5.01
74 78 4.060205 TCGTTAAGTTTTCTTCTTCCCCG 58.940 43.478 0.00 0.00 40.91 5.73
77 81 4.083431 GCCCTCGTTAAGTTTTCTTCTTCC 60.083 45.833 0.00 0.00 40.91 3.46
84 88 6.072342 TCCATTTTAGCCCTCGTTAAGTTTTC 60.072 38.462 0.00 0.00 0.00 2.29
217 242 2.156098 TCTCGAAACGGAATTTTGGGG 58.844 47.619 0.00 0.00 33.36 4.96
220 245 7.298122 CCCATATATCTCGAAACGGAATTTTG 58.702 38.462 0.00 0.00 33.42 2.44
224 249 4.530946 ACCCCATATATCTCGAAACGGAAT 59.469 41.667 0.00 0.00 0.00 3.01
270 297 3.159472 TCTACGGACAGAGGCTGTAAAA 58.841 45.455 0.00 0.00 45.44 1.52
325 362 0.755686 CTTGGAAGGAGAGGGGATCG 59.244 60.000 0.00 0.00 0.00 3.69
326 363 1.886422 ACTTGGAAGGAGAGGGGATC 58.114 55.000 0.00 0.00 0.00 3.36
327 364 2.200955 GAACTTGGAAGGAGAGGGGAT 58.799 52.381 0.00 0.00 0.00 3.85
328 365 1.657804 GAACTTGGAAGGAGAGGGGA 58.342 55.000 0.00 0.00 0.00 4.81
329 366 0.621082 GGAACTTGGAAGGAGAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
330 367 1.362224 TGGAACTTGGAAGGAGAGGG 58.638 55.000 0.00 0.00 0.00 4.30
331 368 3.615155 GATTGGAACTTGGAAGGAGAGG 58.385 50.000 0.00 0.00 0.00 3.69
332 369 3.009473 TGGATTGGAACTTGGAAGGAGAG 59.991 47.826 0.00 0.00 0.00 3.20
333 370 2.986019 TGGATTGGAACTTGGAAGGAGA 59.014 45.455 0.00 0.00 0.00 3.71
398 435 4.858680 GTTAGGCGGGGGCTGAGC 62.859 72.222 0.00 0.00 39.30 4.26
399 436 4.176752 GGTTAGGCGGGGGCTGAG 62.177 72.222 1.54 0.00 39.30 3.35
400 437 4.733725 AGGTTAGGCGGGGGCTGA 62.734 66.667 1.54 0.00 39.30 4.26
401 438 4.176752 GAGGTTAGGCGGGGGCTG 62.177 72.222 1.54 0.00 39.30 4.85
469 528 3.539791 GGCGGCCAATGGAATGGG 61.540 66.667 15.62 0.00 41.90 4.00
847 916 2.434359 CCGGCGGGAGTCAAAGAC 60.434 66.667 20.56 0.00 34.06 3.01
877 946 2.562635 GGATAAGAAAGCGGGGAGTTC 58.437 52.381 0.00 0.00 0.00 3.01
909 982 4.077180 AGGGGTCCGGGGAGAGAC 62.077 72.222 0.00 0.00 0.00 3.36
910 983 3.752167 GAGGGGTCCGGGGAGAGA 61.752 72.222 0.00 0.00 0.00 3.10
911 984 4.075793 TGAGGGGTCCGGGGAGAG 62.076 72.222 0.00 0.00 0.00 3.20
959 1032 4.605183 TCCAAGACCAAGACCAAGAAAAA 58.395 39.130 0.00 0.00 0.00 1.94
960 1033 4.243793 TCCAAGACCAAGACCAAGAAAA 57.756 40.909 0.00 0.00 0.00 2.29
975 1048 1.065418 GCCTCCGAATTCCTTCCAAGA 60.065 52.381 0.00 0.00 0.00 3.02
976 1049 1.383523 GCCTCCGAATTCCTTCCAAG 58.616 55.000 0.00 0.00 0.00 3.61
977 1050 0.392461 CGCCTCCGAATTCCTTCCAA 60.392 55.000 0.00 0.00 36.29 3.53
978 1051 1.220749 CGCCTCCGAATTCCTTCCA 59.779 57.895 0.00 0.00 36.29 3.53
1159 1238 3.384532 GAGGAACGGGTGCGGGTA 61.385 66.667 0.00 0.00 0.00 3.69
1170 1249 0.108089 GGCGGGAGAAGAAGAGGAAC 60.108 60.000 0.00 0.00 0.00 3.62
1266 1345 4.035102 GGGAGGGTGTGGTGGAGC 62.035 72.222 0.00 0.00 0.00 4.70
1285 1364 2.637640 GGGAGGAGGAGGAGTGGGA 61.638 68.421 0.00 0.00 0.00 4.37
1288 1367 2.041405 GGGGGAGGAGGAGGAGTG 60.041 72.222 0.00 0.00 0.00 3.51
1310 1389 3.966543 GGTGGTGGAGGTGGGTGG 61.967 72.222 0.00 0.00 0.00 4.61
1331 1410 4.100084 TCATGGGCTGGTCCTGCG 62.100 66.667 13.98 1.34 34.39 5.18
1341 1420 4.746309 TGCTGCTGGGTCATGGGC 62.746 66.667 0.00 0.00 0.00 5.36
1412 1500 0.734253 GACGATGAGCAGCTTGTCGT 60.734 55.000 26.57 26.57 46.78 4.34
1455 1543 1.736586 CAGGTAGTAGGCCTGCGAG 59.263 63.158 17.99 0.87 45.72 5.03
1855 1950 6.719301 ACTTGGATCTTGATTCTTCAGATGT 58.281 36.000 0.00 0.00 32.27 3.06
1861 1956 6.824305 TTGGAACTTGGATCTTGATTCTTC 57.176 37.500 0.00 0.00 0.00 2.87
1917 2012 7.056006 TGATATTTCAGCTCTAGATGCCAAAA 58.944 34.615 9.65 10.33 0.00 2.44
1984 2080 7.328737 GTGCACTAACGAATCTTCTAAGAAGAA 59.671 37.037 10.32 4.60 39.47 2.52
1985 2081 6.807230 GTGCACTAACGAATCTTCTAAGAAGA 59.193 38.462 10.32 3.89 38.77 2.87
1986 2082 6.586463 TGTGCACTAACGAATCTTCTAAGAAG 59.414 38.462 19.41 0.00 38.77 2.85
1993 2090 5.725110 ATGATGTGCACTAACGAATCTTC 57.275 39.130 19.41 0.00 0.00 2.87
2047 2144 2.095059 CAGGCAAGGAATGTGTGCTAAC 60.095 50.000 0.00 0.00 38.36 2.34
2048 2145 2.161855 CAGGCAAGGAATGTGTGCTAA 58.838 47.619 0.00 0.00 38.36 3.09
2488 2597 4.967036 TGACTTGAACATGGTATGTGTGA 58.033 39.130 0.00 0.00 44.07 3.58
2489 2598 5.239306 ACTTGACTTGAACATGGTATGTGTG 59.761 40.000 0.00 0.00 44.07 3.82
2519 2628 1.447314 GCACACCGTACTAGCCACC 60.447 63.158 0.00 0.00 0.00 4.61
2530 2639 2.672188 TAAAATGAACACGCACACCG 57.328 45.000 0.00 0.00 44.21 4.94
2531 2640 4.979197 TCAATTAAAATGAACACGCACACC 59.021 37.500 0.00 0.00 0.00 4.16
2532 2641 6.582295 AGATCAATTAAAATGAACACGCACAC 59.418 34.615 0.00 0.00 0.00 3.82
2533 2642 6.581919 CAGATCAATTAAAATGAACACGCACA 59.418 34.615 0.00 0.00 0.00 4.57
2534 2643 6.452872 GCAGATCAATTAAAATGAACACGCAC 60.453 38.462 0.00 0.00 0.00 5.34
2535 2644 5.572511 GCAGATCAATTAAAATGAACACGCA 59.427 36.000 0.00 0.00 0.00 5.24
2536 2645 5.572511 TGCAGATCAATTAAAATGAACACGC 59.427 36.000 0.00 4.69 0.00 5.34
2537 2646 7.745022 ATGCAGATCAATTAAAATGAACACG 57.255 32.000 0.00 0.00 0.00 4.49
2538 2647 9.749490 CAAATGCAGATCAATTAAAATGAACAC 57.251 29.630 0.00 0.00 0.00 3.32
2539 2648 9.491675 ACAAATGCAGATCAATTAAAATGAACA 57.508 25.926 0.00 0.00 0.00 3.18
2540 2649 9.962759 GACAAATGCAGATCAATTAAAATGAAC 57.037 29.630 0.00 0.00 0.00 3.18
2541 2650 9.153721 GGACAAATGCAGATCAATTAAAATGAA 57.846 29.630 0.00 0.00 0.00 2.57
2542 2651 8.533657 AGGACAAATGCAGATCAATTAAAATGA 58.466 29.630 0.00 0.00 0.00 2.57
2543 2652 8.600625 CAGGACAAATGCAGATCAATTAAAATG 58.399 33.333 0.00 0.00 0.00 2.32
2544 2653 8.316214 ACAGGACAAATGCAGATCAATTAAAAT 58.684 29.630 0.00 0.00 0.00 1.82
2545 2654 7.669427 ACAGGACAAATGCAGATCAATTAAAA 58.331 30.769 0.00 0.00 0.00 1.52
2546 2655 7.230849 ACAGGACAAATGCAGATCAATTAAA 57.769 32.000 0.00 0.00 0.00 1.52
2547 2656 6.127647 GGACAGGACAAATGCAGATCAATTAA 60.128 38.462 0.00 0.00 0.00 1.40
2548 2657 5.357878 GGACAGGACAAATGCAGATCAATTA 59.642 40.000 0.00 0.00 0.00 1.40
2549 2658 4.159135 GGACAGGACAAATGCAGATCAATT 59.841 41.667 0.00 0.00 0.00 2.32
2550 2659 3.698040 GGACAGGACAAATGCAGATCAAT 59.302 43.478 0.00 0.00 0.00 2.57
2551 2660 3.084039 GGACAGGACAAATGCAGATCAA 58.916 45.455 0.00 0.00 0.00 2.57
2552 2661 2.306805 AGGACAGGACAAATGCAGATCA 59.693 45.455 0.00 0.00 0.00 2.92
2553 2662 2.996631 AGGACAGGACAAATGCAGATC 58.003 47.619 0.00 0.00 0.00 2.75
2554 2663 4.265073 GTTAGGACAGGACAAATGCAGAT 58.735 43.478 0.00 0.00 0.00 2.90
2555 2664 3.559171 GGTTAGGACAGGACAAATGCAGA 60.559 47.826 0.00 0.00 0.00 4.26
2556 2665 2.749621 GGTTAGGACAGGACAAATGCAG 59.250 50.000 0.00 0.00 0.00 4.41
2557 2666 2.790433 GGTTAGGACAGGACAAATGCA 58.210 47.619 0.00 0.00 0.00 3.96
2624 2773 5.295431 TCTTATTTTGCTCCATTGACACG 57.705 39.130 0.00 0.00 0.00 4.49
2625 2774 6.446318 TGTTCTTATTTTGCTCCATTGACAC 58.554 36.000 0.00 0.00 0.00 3.67
2734 2894 4.822685 TGCAGAAAAACATGGCCAATAT 57.177 36.364 10.96 0.00 0.00 1.28
3043 3205 2.929398 GCAGAGAGCTAAAGCAGAGTTC 59.071 50.000 4.54 0.00 45.16 3.01
3134 3305 3.869065 ACCAAATGACACCCGTGTATAG 58.131 45.455 0.00 0.00 45.05 1.31
3152 3324 4.974645 AGAGACAGGACAAACATAACCA 57.025 40.909 0.00 0.00 0.00 3.67
3275 3488 0.752743 AGAAAGGCAGCTGCACACAA 60.753 50.000 37.63 0.00 44.36 3.33
3288 3504 3.996150 AATTGCACAGTGACAGAAAGG 57.004 42.857 4.15 0.00 0.00 3.11
3316 3536 9.656040 CCATGATGTAGAAAATTTTCCATGAAA 57.344 29.630 29.33 15.77 35.62 2.69
3317 3537 9.033711 TCCATGATGTAGAAAATTTTCCATGAA 57.966 29.630 29.33 18.22 35.62 2.57
3327 3547 6.582636 TCTAGCGTTCCATGATGTAGAAAAT 58.417 36.000 0.00 0.00 0.00 1.82
3328 3548 5.972935 TCTAGCGTTCCATGATGTAGAAAA 58.027 37.500 0.00 0.00 0.00 2.29
3342 3562 2.005971 ACGGAACCAATCTAGCGTTC 57.994 50.000 0.00 0.00 36.08 3.95
3375 3595 9.918630 CTTCCTTCATTATTCAGTTCAAATTGT 57.081 29.630 0.00 0.00 0.00 2.71
3376 3596 8.866956 GCTTCCTTCATTATTCAGTTCAAATTG 58.133 33.333 0.00 0.00 0.00 2.32
3377 3597 7.756722 CGCTTCCTTCATTATTCAGTTCAAATT 59.243 33.333 0.00 0.00 0.00 1.82
3378 3598 7.253422 CGCTTCCTTCATTATTCAGTTCAAAT 58.747 34.615 0.00 0.00 0.00 2.32
3379 3599 6.349280 CCGCTTCCTTCATTATTCAGTTCAAA 60.349 38.462 0.00 0.00 0.00 2.69
3380 3600 5.123820 CCGCTTCCTTCATTATTCAGTTCAA 59.876 40.000 0.00 0.00 0.00 2.69
3382 3602 4.636206 ACCGCTTCCTTCATTATTCAGTTC 59.364 41.667 0.00 0.00 0.00 3.01
3383 3603 4.589908 ACCGCTTCCTTCATTATTCAGTT 58.410 39.130 0.00 0.00 0.00 3.16
3478 3735 5.957771 TTGCATAGTCTGGTTCTTAGGAT 57.042 39.130 0.00 0.00 0.00 3.24
3508 3765 4.305769 GGTGATGTATGCAAACAAAAGCA 58.694 39.130 0.00 0.00 45.92 3.91
3509 3766 3.364621 CGGTGATGTATGCAAACAAAAGC 59.635 43.478 0.00 0.00 32.02 3.51
3510 3767 3.364621 GCGGTGATGTATGCAAACAAAAG 59.635 43.478 0.00 0.00 32.02 2.27
3511 3768 3.005261 AGCGGTGATGTATGCAAACAAAA 59.995 39.130 0.00 0.00 32.02 2.44
3521 3778 3.306088 CGAAAGGGATAGCGGTGATGTAT 60.306 47.826 0.00 0.00 0.00 2.29
3537 3794 4.010349 AGAACCTATTCAAAGGCGAAAGG 58.990 43.478 0.00 0.00 40.62 3.11
3569 3829 4.452455 ACTTGTTCAGAAGCAAATCCGTAG 59.548 41.667 0.00 0.00 0.00 3.51
3570 3830 4.385825 ACTTGTTCAGAAGCAAATCCGTA 58.614 39.130 0.00 0.00 0.00 4.02
3571 3831 3.214328 ACTTGTTCAGAAGCAAATCCGT 58.786 40.909 0.00 0.00 0.00 4.69
3572 3832 3.904136 ACTTGTTCAGAAGCAAATCCG 57.096 42.857 0.00 0.00 0.00 4.18
3573 3833 4.676924 CGAAACTTGTTCAGAAGCAAATCC 59.323 41.667 0.00 0.00 0.00 3.01
3574 3834 5.273944 ACGAAACTTGTTCAGAAGCAAATC 58.726 37.500 0.00 0.00 0.00 2.17
3575 3835 5.248870 ACGAAACTTGTTCAGAAGCAAAT 57.751 34.783 0.00 0.00 0.00 2.32
3576 3836 4.695217 ACGAAACTTGTTCAGAAGCAAA 57.305 36.364 0.00 0.00 0.00 3.68
3577 3837 4.034742 GGTACGAAACTTGTTCAGAAGCAA 59.965 41.667 0.00 0.00 0.00 3.91
3578 3838 3.558418 GGTACGAAACTTGTTCAGAAGCA 59.442 43.478 0.00 0.00 0.00 3.91
3581 3841 6.576185 ACTAAGGTACGAAACTTGTTCAGAA 58.424 36.000 0.00 0.00 0.00 3.02
3592 3852 5.753744 CATTGCAACAACTAAGGTACGAAA 58.246 37.500 0.00 0.00 0.00 3.46
3595 3855 3.058570 TGCATTGCAACAACTAAGGTACG 60.059 43.478 9.33 0.00 34.76 3.67
3627 3887 7.118535 GGGTTCAGATAAAGTTTGAAGAGACTC 59.881 40.741 0.00 0.00 32.00 3.36
3873 4139 4.463209 ACAAATCGCGACAACATTTACAG 58.537 39.130 12.93 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.