Multiple sequence alignment - TraesCS5B01G496200

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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 TraesCS5B01G496200 chr5B 100.000 5043 0 0 1 5043 663229847 663224805 0.000000e+00 9313.0
1 TraesCS5B01G496200 chr5D 94.116 3263 128 34 2 3242 527157792 527154572 0.000000e+00 4903.0
2 TraesCS5B01G496200 chr5D 94.488 762 34 5 3519 4280 527154321 527153568 0.000000e+00 1168.0
3 TraesCS5B01G496200 chr5D 90.684 526 25 9 4532 5043 527153162 527152647 0.000000e+00 678.0
4 TraesCS5B01G496200 chr5D 97.403 231 6 0 3233 3463 527154549 527154319 1.320000e-105 394.0
5 TraesCS5B01G496200 chr5D 92.920 226 15 1 4307 4532 527153443 527153219 1.350000e-85 327.0
6 TraesCS5B01G496200 chr5D 100.000 56 0 0 3459 3514 527570698 527570753 2.480000e-18 104.0
7 TraesCS5B01G496200 chr5D 100.000 56 0 0 3459 3514 527600261 527600316 2.480000e-18 104.0
8 TraesCS5B01G496200 chr5A 93.327 1978 92 11 1521 3463 654168611 654166639 0.000000e+00 2885.0
9 TraesCS5B01G496200 chr5A 91.172 1801 120 17 473 2256 654157934 654156156 0.000000e+00 2409.0
10 TraesCS5B01G496200 chr5A 93.523 1019 44 9 2241 3239 654156136 654155120 0.000000e+00 1496.0
11 TraesCS5B01G496200 chr5A 96.914 810 25 0 728 1537 654169471 654168662 0.000000e+00 1358.0
12 TraesCS5B01G496200 chr5A 86.819 1047 84 17 3519 4532 654154809 654153784 0.000000e+00 1120.0
13 TraesCS5B01G496200 chr5A 92.402 737 39 9 2 731 654170277 654169551 0.000000e+00 1035.0
14 TraesCS5B01G496200 chr5A 92.222 540 36 5 3519 4058 654166641 654166108 0.000000e+00 760.0
15 TraesCS5B01G496200 chr5A 88.911 514 24 11 4532 5043 654153729 654153247 2.010000e-168 603.0
16 TraesCS5B01G496200 chr5A 95.455 220 10 0 3245 3464 654155025 654154806 8.030000e-93 351.0
17 TraesCS5B01G496200 chr5A 83.654 312 37 9 5 313 654159266 654158966 1.070000e-71 281.0
18 TraesCS5B01G496200 chr2B 79.473 1632 253 55 648 2237 781540208 781538617 0.000000e+00 1083.0
19 TraesCS5B01G496200 chr2B 82.996 841 112 23 729 1554 781582070 781581246 0.000000e+00 732.0
20 TraesCS5B01G496200 chr2B 84.314 663 76 13 2827 3463 781579863 781579203 1.540000e-174 623.0
21 TraesCS5B01G496200 chr2B 84.686 542 68 12 967 1498 781541928 781541392 1.240000e-145 527.0
22 TraesCS5B01G496200 chr2B 84.778 427 53 8 2814 3237 781537326 781536909 7.810000e-113 418.0
23 TraesCS5B01G496200 chr2B 82.963 135 22 1 2620 2754 781537868 781537735 2.470000e-23 121.0
24 TraesCS5B01G496200 chr2A 78.139 1601 246 66 648 2215 775939957 775938428 0.000000e+00 922.0
25 TraesCS5B01G496200 chr2A 78.472 1440 194 60 729 2124 775978139 775976772 0.000000e+00 835.0
26 TraesCS5B01G496200 chr2A 84.163 663 77 12 2827 3463 775976057 775975397 7.170000e-173 617.0
27 TraesCS5B01G496200 chr2A 81.657 676 95 15 2818 3465 775942010 775941336 7.430000e-148 534.0
28 TraesCS5B01G496200 chr2A 81.348 445 71 9 3580 4023 775936874 775936441 8.030000e-93 351.0
29 TraesCS5B01G496200 chr2A 79.294 425 60 14 3600 4023 775941243 775940846 6.430000e-69 272.0
30 TraesCS5B01G496200 chr2D 79.262 1437 191 57 729 2124 651696650 651698020 0.000000e+00 904.0
31 TraesCS5B01G496200 chr2D 82.474 776 113 15 648 1414 651720945 651721706 0.000000e+00 658.0
32 TraesCS5B01G496200 chr2D 84.639 664 74 13 2827 3464 651698733 651699394 1.980000e-178 636.0
33 TraesCS5B01G496200 chr2D 83.964 661 81 17 2814 3463 651724017 651724663 1.200000e-170 610.0
34 TraesCS5B01G496200 chr2D 85.740 554 64 12 967 1511 651715663 651716210 5.660000e-159 571.0
35 TraesCS5B01G496200 chr2D 77.452 683 112 27 1531 2196 651722057 651722714 2.220000e-98 370.0
36 TraesCS5B01G496200 chr2D 86.383 235 31 1 3231 3465 651719274 651719507 6.480000e-64 255.0
37 TraesCS5B01G496200 chr2D 79.946 369 48 12 3656 4023 651719712 651720055 1.080000e-61 248.0
38 TraesCS5B01G496200 chr1A 96.970 66 0 2 3449 3514 430006376 430006439 5.340000e-20 110.0
39 TraesCS5B01G496200 chr3D 100.000 54 0 0 3461 3514 529777750 529777697 3.210000e-17 100.0
40 TraesCS5B01G496200 chr6D 98.246 57 0 1 3458 3514 74868173 74868118 1.160000e-16 99.0
41 TraesCS5B01G496200 chr6D 92.647 68 3 2 3458 3524 46709607 46709541 4.160000e-16 97.1
42 TraesCS5B01G496200 chr3B 98.246 57 0 1 3458 3514 219339016 219338961 1.160000e-16 99.0
43 TraesCS5B01G496200 chr3B 98.246 57 0 1 3458 3514 220626556 220626501 1.160000e-16 99.0
44 TraesCS5B01G496200 chr4B 89.041 73 5 3 3442 3514 285608347 285608416 2.500000e-13 87.9


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 TraesCS5B01G496200 chr5B 663224805 663229847 5042 True 9313.000000 9313 100.000000 1 5043 1 chr5B.!!$R1 5042
1 TraesCS5B01G496200 chr5D 527152647 527157792 5145 True 1494.000000 4903 93.922200 2 5043 5 chr5D.!!$R1 5041
2 TraesCS5B01G496200 chr5A 654166108 654170277 4169 True 1509.500000 2885 93.716250 2 4058 4 chr5A.!!$R2 4056
3 TraesCS5B01G496200 chr5A 654153247 654159266 6019 True 1043.333333 2409 89.922333 5 5043 6 chr5A.!!$R1 5038
4 TraesCS5B01G496200 chr2B 781579203 781582070 2867 True 677.500000 732 83.655000 729 3463 2 chr2B.!!$R2 2734
5 TraesCS5B01G496200 chr2B 781536909 781541928 5019 True 537.250000 1083 82.975000 648 3237 4 chr2B.!!$R1 2589
6 TraesCS5B01G496200 chr2A 775975397 775978139 2742 True 726.000000 835 81.317500 729 3463 2 chr2A.!!$R2 2734
7 TraesCS5B01G496200 chr2A 775936441 775942010 5569 True 519.750000 922 80.109500 648 4023 4 chr2A.!!$R1 3375
8 TraesCS5B01G496200 chr2D 651696650 651699394 2744 False 770.000000 904 81.950500 729 3464 2 chr2D.!!$F1 2735
9 TraesCS5B01G496200 chr2D 651715663 651724663 9000 False 452.000000 658 82.659833 648 4023 6 chr2D.!!$F2 3375

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
576 1455 0.039617 TCTTTTCATTTGTGCCGCGG 60.040 50.000 24.05 24.05 0.00 6.46 F
1672 7141 1.446618 CAATTGCAAGCCGGCCTTC 60.447 57.895 26.15 12.90 0.00 3.46 F
2536 8589 2.344872 GGCCCAAAAGCTTGCCTG 59.655 61.111 16.26 7.26 40.77 4.85 F
3477 10113 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 8589 0.599060 TTTCCGGCCGAAAAATGGTC 59.401 50.0 30.73 0.00 37.53 4.02 R
3066 9613 1.267121 TGAGCTGAGGTCCTTGGTAC 58.733 55.0 9.40 0.00 0.00 3.34 R
3946 10743 0.162933 CAAAGCTTGCTGCATTTGCG 59.837 50.0 12.57 0.08 45.94 4.85 R
4993 11995 0.526211 GCAAAGAGCCCCTTAAACCG 59.474 55.0 0.00 0.00 37.23 4.44 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
85 86 4.269603 CGAATTGACTCACTGAGCATTAGG 59.730 45.833 5.92 0.00 32.04 2.69
101 102 6.958767 AGCATTAGGTCACCAAGTACTATTT 58.041 36.000 0.00 0.00 0.00 1.40
102 103 7.402862 AGCATTAGGTCACCAAGTACTATTTT 58.597 34.615 0.00 0.00 0.00 1.82
225 229 2.451990 CGCATCGCACATTCCACGA 61.452 57.895 0.00 0.00 40.53 4.35
314 318 2.878991 GCATGTCGTCGCGCACTA 60.879 61.111 8.75 0.00 0.00 2.74
334 338 1.617947 GGAGCGACAGGGGATGTTCT 61.618 60.000 0.00 0.00 44.17 3.01
347 353 3.388350 GGGATGTTCTACCGAAGATTCCT 59.612 47.826 3.06 0.00 42.58 3.36
350 356 4.451629 TGTTCTACCGAAGATTCCTGTC 57.548 45.455 0.00 0.00 33.05 3.51
485 1361 0.396811 CCTTGACCGGGAAGTGAAGT 59.603 55.000 6.32 0.00 29.97 3.01
487 1363 2.236395 CCTTGACCGGGAAGTGAAGTAT 59.764 50.000 6.32 0.00 29.97 2.12
490 1366 4.360951 TGACCGGGAAGTGAAGTATTTT 57.639 40.909 6.32 0.00 0.00 1.82
576 1455 0.039617 TCTTTTCATTTGTGCCGCGG 60.040 50.000 24.05 24.05 0.00 6.46
639 1523 2.954318 GCTGTTGGGTAGATGCATCATT 59.046 45.455 27.81 11.41 0.00 2.57
713 5688 3.059634 GTGTCTTGCACAGCGTAAAAA 57.940 42.857 0.00 0.00 46.91 1.94
717 5692 5.005299 GTGTCTTGCACAGCGTAAAAATTTT 59.995 36.000 0.00 0.00 46.91 1.82
925 5992 2.115427 TGAGGTGTCCTGACAGTGAAA 58.885 47.619 0.00 0.00 42.74 2.69
941 6008 2.548057 GTGAAAGTTTGATGACGAGCCA 59.452 45.455 0.00 0.00 0.00 4.75
1216 6283 4.517285 TCTTTTCCTGGATCTGGATTTCG 58.483 43.478 0.00 0.00 31.78 3.46
1458 6536 3.912496 TGGGTGTATTCATGTGAGGAG 57.088 47.619 0.00 0.00 0.00 3.69
1571 6948 1.632920 TGCATCCATGTGTACCCTTGA 59.367 47.619 0.00 0.00 0.00 3.02
1672 7141 1.446618 CAATTGCAAGCCGGCCTTC 60.447 57.895 26.15 12.90 0.00 3.46
1756 7254 7.494952 GTGGGAAAGTAGCTATTTAGTTAGGTG 59.505 40.741 1.46 0.00 32.47 4.00
1927 7469 9.183368 TGTTATACATCTTATTGTGGCAAATCA 57.817 29.630 0.00 0.00 0.00 2.57
2301 8346 5.744345 GTGACGGACATAGTTGAGATTGTAG 59.256 44.000 0.00 0.00 0.00 2.74
2536 8589 2.344872 GGCCCAAAAGCTTGCCTG 59.655 61.111 16.26 7.26 40.77 4.85
2649 8770 7.439655 GGTGGAGATAACATCTTTGAGTGATAC 59.560 40.741 0.00 0.00 40.38 2.24
2667 8788 9.436957 GAGTGATACCTTTTTCTCTCATTAACA 57.563 33.333 0.00 0.00 34.31 2.41
2772 8898 6.743627 GTGAAATCAGTTGTTTAACGTGAACA 59.256 34.615 12.24 12.24 41.71 3.18
2847 9389 6.482524 ACCTACTTCTGTGTAGATGTGAGTA 58.517 40.000 10.46 0.00 41.63 2.59
2871 9413 9.216117 GTACTTTGATGAACTTGGTGTAGTAAT 57.784 33.333 0.00 0.00 0.00 1.89
2897 9440 8.160765 TGATAGTGGGAGTGAAAAATAAGTTCA 58.839 33.333 0.00 0.00 32.62 3.18
2950 9494 3.378112 TGATCAAAATTCCGTGGATCAGC 59.622 43.478 0.00 0.00 39.37 4.26
3066 9613 1.445410 TGTTGCCGTACTAGCGCTG 60.445 57.895 22.90 12.81 0.00 5.18
3122 9669 4.099266 CCACCCTCTTTTTCATCACACAAA 59.901 41.667 0.00 0.00 0.00 2.83
3148 9695 4.467769 AGTTGATATTCATGCCTCAAGGG 58.532 43.478 0.00 0.00 35.18 3.95
3464 10100 6.037940 TCGCAATCGTCTATTCTGTAAGTACT 59.962 38.462 0.00 0.00 36.96 2.73
3465 10101 6.357503 CGCAATCGTCTATTCTGTAAGTACTC 59.642 42.308 0.00 0.00 33.76 2.59
3466 10102 6.637658 GCAATCGTCTATTCTGTAAGTACTCC 59.362 42.308 0.00 0.00 33.76 3.85
3467 10103 6.880942 ATCGTCTATTCTGTAAGTACTCCC 57.119 41.667 0.00 0.00 33.76 4.30
3468 10104 5.999044 TCGTCTATTCTGTAAGTACTCCCT 58.001 41.667 0.00 0.00 33.76 4.20
3469 10105 6.054295 TCGTCTATTCTGTAAGTACTCCCTC 58.946 44.000 0.00 0.00 33.76 4.30
3470 10106 5.239087 CGTCTATTCTGTAAGTACTCCCTCC 59.761 48.000 0.00 0.00 33.76 4.30
3471 10107 5.239087 GTCTATTCTGTAAGTACTCCCTCCG 59.761 48.000 0.00 0.00 33.76 4.63
3472 10108 3.446442 TTCTGTAAGTACTCCCTCCGT 57.554 47.619 0.00 0.00 33.76 4.69
3473 10109 2.996631 TCTGTAAGTACTCCCTCCGTC 58.003 52.381 0.00 0.00 33.76 4.79
3474 10110 2.022934 CTGTAAGTACTCCCTCCGTCC 58.977 57.143 0.00 0.00 0.00 4.79
3475 10111 1.341383 TGTAAGTACTCCCTCCGTCCC 60.341 57.143 0.00 0.00 0.00 4.46
3476 10112 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3477 10113 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3478 10114 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3479 10115 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3480 10116 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3481 10117 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3482 10118 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3483 10119 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3484 10120 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3485 10121 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3486 10122 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3487 10123 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3488 10124 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3489 10125 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3490 10126 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3491 10127 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3492 10128 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3493 10129 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3494 10130 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3495 10131 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3496 10132 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3497 10133 8.074370 GTCCCAAAATAAGTGACTCAACTTTAC 58.926 37.037 0.00 0.00 40.77 2.01
3498 10134 7.776030 TCCCAAAATAAGTGACTCAACTTTACA 59.224 33.333 0.00 0.00 40.77 2.41
3499 10135 7.860872 CCCAAAATAAGTGACTCAACTTTACAC 59.139 37.037 0.00 0.00 40.77 2.90
3500 10136 8.621286 CCAAAATAAGTGACTCAACTTTACACT 58.379 33.333 0.00 0.00 40.77 3.55
3506 10142 8.788325 AAGTGACTCAACTTTACACTAACTTT 57.212 30.769 0.00 0.00 40.23 2.66
3507 10143 8.197988 AGTGACTCAACTTTACACTAACTTTG 57.802 34.615 0.00 0.00 39.52 2.77
3508 10144 7.822822 AGTGACTCAACTTTACACTAACTTTGT 59.177 33.333 0.00 0.00 39.52 2.83
3509 10145 9.090692 GTGACTCAACTTTACACTAACTTTGTA 57.909 33.333 0.00 0.00 0.00 2.41
3510 10146 9.090692 TGACTCAACTTTACACTAACTTTGTAC 57.909 33.333 0.00 0.00 0.00 2.90
3511 10147 9.310716 GACTCAACTTTACACTAACTTTGTACT 57.689 33.333 0.00 0.00 0.00 2.73
3517 10153 9.978044 ACTTTACACTAACTTTGTACTAAGAGG 57.022 33.333 21.48 13.06 0.00 3.69
3518 10154 9.420551 CTTTACACTAACTTTGTACTAAGAGGG 57.579 37.037 21.48 13.48 0.00 4.30
3519 10155 6.990908 ACACTAACTTTGTACTAAGAGGGT 57.009 37.500 21.48 14.04 0.00 4.34
3520 10156 9.586732 TTACACTAACTTTGTACTAAGAGGGTA 57.413 33.333 21.48 16.84 0.00 3.69
3521 10157 7.890515 ACACTAACTTTGTACTAAGAGGGTAC 58.109 38.462 21.48 0.00 39.70 3.34
3534 10170 2.661176 AGGGTACAAGAATCCCCTCA 57.339 50.000 0.00 0.00 44.33 3.86
3537 10173 3.660669 AGGGTACAAGAATCCCCTCAAAA 59.339 43.478 0.00 0.00 44.33 2.44
3542 10178 6.437477 GGTACAAGAATCCCCTCAAAAAGAAT 59.563 38.462 0.00 0.00 0.00 2.40
3543 10179 7.039011 GGTACAAGAATCCCCTCAAAAAGAATT 60.039 37.037 0.00 0.00 0.00 2.17
3818 10615 9.453572 ACAGAAGAGCTACATCAATTTTTATCA 57.546 29.630 0.00 0.00 0.00 2.15
3850 10647 2.499289 TCTCTCCCTTCTGATGAACAGC 59.501 50.000 0.00 0.00 45.38 4.40
3862 10659 4.827692 TGATGAACAGCGTAATAAGTGGT 58.172 39.130 0.00 0.00 0.00 4.16
3935 10732 2.091852 AGTAGCTCTCAGCAAGCAAC 57.908 50.000 0.00 0.00 45.56 4.17
3977 10774 3.257624 AGCAAGCTTTGATTTGGAGGAAG 59.742 43.478 0.00 0.00 0.00 3.46
4116 10938 1.694150 CTCAAGCGATCCCCATTAGGA 59.306 52.381 0.00 0.00 41.18 2.94
4157 10979 0.035056 GGAGATTGTGGGGAGTGGTG 60.035 60.000 0.00 0.00 0.00 4.17
4158 10980 0.035056 GAGATTGTGGGGAGTGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
4159 10981 0.772124 AGATTGTGGGGAGTGGTGGT 60.772 55.000 0.00 0.00 0.00 4.16
4185 11007 4.102367 AGCAATGGGTTCTCTTCCTATCTC 59.898 45.833 0.00 0.00 0.00 2.75
4240 11062 2.144482 TAAGCTAATACCCGCTTCGC 57.856 50.000 0.00 0.00 44.64 4.70
4258 11080 5.334105 GCTTCGCAGTCAAAACTCAGATAAA 60.334 40.000 0.00 0.00 31.71 1.40
4265 11087 9.334693 GCAGTCAAAACTCAGATAAATAAGTTG 57.665 33.333 0.00 0.00 32.53 3.16
4281 11103 4.795970 AAGTTGTAGCTCAAGTTTCACG 57.204 40.909 11.08 0.00 44.36 4.35
4282 11104 2.544267 AGTTGTAGCTCAAGTTTCACGC 59.456 45.455 0.00 0.00 36.41 5.34
4283 11105 2.232756 TGTAGCTCAAGTTTCACGCA 57.767 45.000 0.00 0.00 0.00 5.24
4284 11106 2.766313 TGTAGCTCAAGTTTCACGCAT 58.234 42.857 0.00 0.00 0.00 4.73
4285 11107 3.920446 TGTAGCTCAAGTTTCACGCATA 58.080 40.909 0.00 0.00 0.00 3.14
4302 11124 5.961263 CACGCATACGGGTTAGTTAAATTTC 59.039 40.000 0.00 0.00 46.04 2.17
4317 11243 6.258068 AGTTAAATTTCTACTAGCATGTCGCC 59.742 38.462 0.00 0.00 44.04 5.54
4356 11282 4.560128 GAATGTCGCTCTGCATCCTTATA 58.440 43.478 0.00 0.00 0.00 0.98
4361 11287 5.098893 GTCGCTCTGCATCCTTATATGTAG 58.901 45.833 0.00 0.00 39.95 2.74
4380 11306 2.783135 AGTCACGACAATCCATGCTTT 58.217 42.857 0.00 0.00 0.00 3.51
4383 11309 2.743664 TCACGACAATCCATGCTTTGAG 59.256 45.455 11.48 8.02 0.00 3.02
4557 11545 4.846779 TGGAACTGAAGTTGGCATTTAC 57.153 40.909 0.00 0.00 38.56 2.01
4638 11629 5.105797 GCATTGGACCTTTTCACATATGTCA 60.106 40.000 5.07 0.00 0.00 3.58
4661 11653 9.833182 GTCACTGATCCTTTCTTCTTTAATTTC 57.167 33.333 0.00 0.00 0.00 2.17
4662 11654 9.014297 TCACTGATCCTTTCTTCTTTAATTTCC 57.986 33.333 0.00 0.00 0.00 3.13
4784 11776 1.351017 CAACCTGCCTTCAGTTAGGGA 59.649 52.381 0.00 0.00 38.66 4.20
4854 11846 3.791245 TGCCTCAATGAAACACCAAAAC 58.209 40.909 0.00 0.00 0.00 2.43
4855 11847 3.196469 TGCCTCAATGAAACACCAAAACA 59.804 39.130 0.00 0.00 0.00 2.83
4856 11848 4.187694 GCCTCAATGAAACACCAAAACAA 58.812 39.130 0.00 0.00 0.00 2.83
4857 11849 4.270808 GCCTCAATGAAACACCAAAACAAG 59.729 41.667 0.00 0.00 0.00 3.16
4858 11850 5.418676 CCTCAATGAAACACCAAAACAAGT 58.581 37.500 0.00 0.00 0.00 3.16
4859 11851 6.568869 CCTCAATGAAACACCAAAACAAGTA 58.431 36.000 0.00 0.00 0.00 2.24
4860 11852 7.038659 CCTCAATGAAACACCAAAACAAGTAA 58.961 34.615 0.00 0.00 0.00 2.24
4861 11853 7.547370 CCTCAATGAAACACCAAAACAAGTAAA 59.453 33.333 0.00 0.00 0.00 2.01
4926 11923 2.102252 CCTTAGAGTCATCAGCCTGTCC 59.898 54.545 0.00 0.00 0.00 4.02
4930 11927 0.904865 AGTCATCAGCCTGTCCGGAA 60.905 55.000 5.23 0.00 33.16 4.30
4951 11948 6.572509 CGGAATTATCTACCAGACCCATAGTG 60.573 46.154 0.00 0.00 0.00 2.74
4993 11995 3.068307 ACACGGCAGATGGAGATACTTAC 59.932 47.826 0.00 0.00 0.00 2.34
4995 11997 2.351835 CGGCAGATGGAGATACTTACGG 60.352 54.545 0.00 0.00 0.00 4.02
5024 12027 1.348276 CTCTTTGCTGCAGTCTCGAG 58.652 55.000 16.64 5.93 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.161609 CCTTTTAGTGGCCGCAGTTAAG 59.838 50.000 20.59 14.85 0.00 1.85
189 193 6.564125 GCGATGCGTAGAAAACTAAAGCATAT 60.564 38.462 15.62 3.34 42.87 1.78
190 194 5.276678 GCGATGCGTAGAAAACTAAAGCATA 60.277 40.000 15.62 0.00 42.87 3.14
191 195 4.494199 GCGATGCGTAGAAAACTAAAGCAT 60.494 41.667 15.60 15.60 45.07 3.79
205 209 1.417577 CGTGGAATGTGCGATGCGTA 61.418 55.000 0.00 0.00 0.00 4.42
211 215 0.246360 AGATGTCGTGGAATGTGCGA 59.754 50.000 0.00 0.00 0.00 5.10
225 229 3.696051 GCATGGGTATGACAACAAGATGT 59.304 43.478 0.00 0.00 36.36 3.06
314 318 1.613630 AACATCCCCTGTCGCTCCT 60.614 57.895 0.00 0.00 36.98 3.69
334 338 3.830178 TGAAGTGACAGGAATCTTCGGTA 59.170 43.478 0.00 0.00 39.05 4.02
347 353 4.284829 TGCACCTCATATTGAAGTGACA 57.715 40.909 9.78 5.32 40.35 3.58
448 1063 6.348540 GGTCAAGGTGTCAAGAATTACATGAC 60.349 42.308 0.00 9.61 44.36 3.06
485 1361 7.668469 GGAAAAGGAGGTAGGAACTTCAAAATA 59.332 37.037 0.00 0.00 41.75 1.40
487 1363 5.831525 GGAAAAGGAGGTAGGAACTTCAAAA 59.168 40.000 0.00 0.00 41.75 2.44
490 1366 3.007614 CGGAAAAGGAGGTAGGAACTTCA 59.992 47.826 0.00 0.00 41.75 3.02
576 1455 4.990426 AGCATCCAACACTTAAAACATTGC 59.010 37.500 0.00 0.00 0.00 3.56
580 1459 5.843673 TGAAGCATCCAACACTTAAAACA 57.156 34.783 0.00 0.00 0.00 2.83
581 1460 7.653311 AGATTTGAAGCATCCAACACTTAAAAC 59.347 33.333 0.00 0.00 28.84 2.43
639 1523 4.299586 TCCAAGGTGCTTGTATGAATGA 57.700 40.909 0.00 0.00 39.58 2.57
706 5681 6.490877 ACTTCGCAACAGAAAATTTTTACG 57.509 33.333 4.63 3.86 0.00 3.18
713 5688 6.560253 ACATCTTACTTCGCAACAGAAAAT 57.440 33.333 0.00 0.00 0.00 1.82
717 5692 4.927425 GGTTACATCTTACTTCGCAACAGA 59.073 41.667 0.00 0.00 0.00 3.41
800 5866 4.130255 TGGAGGCCACACTAGTCC 57.870 61.111 5.01 0.81 0.00 3.85
925 5992 0.317160 TCGTGGCTCGTCATCAAACT 59.683 50.000 8.94 0.00 40.80 2.66
941 6008 7.919621 GCTTAAATACTACTACTTGTCCATCGT 59.080 37.037 0.00 0.00 0.00 3.73
1193 6260 4.574013 CGAAATCCAGATCCAGGAAAAGAG 59.426 45.833 8.43 0.00 38.93 2.85
1216 6283 4.727507 TCTCAGTTCATGCTTCCTAGAC 57.272 45.455 0.00 0.00 0.00 2.59
1458 6536 4.873827 TGTCTAACAACTCCAAGTCACAAC 59.126 41.667 0.00 0.00 0.00 3.32
1586 6965 7.035612 GGGATAAGCCTAATGAAAACAAAGTG 58.964 38.462 0.00 0.00 36.66 3.16
1592 6971 5.656859 ACCAAGGGATAAGCCTAATGAAAAC 59.343 40.000 0.00 0.00 36.66 2.43
1604 6983 2.290071 ACCAACACGACCAAGGGATAAG 60.290 50.000 0.00 0.00 0.00 1.73
1672 7141 7.210174 TGATATAACTGAAATTCTCTGTCGGG 58.790 38.462 0.00 0.00 35.33 5.14
1756 7254 8.283291 ACATTTCTGTCGAAAGTAAATCAGTTC 58.717 33.333 1.71 0.00 42.01 3.01
1943 7485 5.773176 ACACCCTGGAGAAACGAAATAAAAT 59.227 36.000 0.00 0.00 0.00 1.82
2039 7581 5.830000 AAGAAAGTTAACACTGGTTGGAC 57.170 39.130 8.61 0.00 37.88 4.02
2301 8346 4.773323 AGGCTGCAAAACATCTCTAAAC 57.227 40.909 0.50 0.00 0.00 2.01
2536 8589 0.599060 TTTCCGGCCGAAAAATGGTC 59.401 50.000 30.73 0.00 37.53 4.02
2649 8770 8.084073 TGAAGCAATGTTAATGAGAGAAAAAGG 58.916 33.333 0.00 0.00 0.00 3.11
2798 9288 3.436704 ACACAACTGATGGTTCATTAGCG 59.563 43.478 0.49 0.00 35.74 4.26
2847 9389 7.936847 TCATTACTACACCAAGTTCATCAAAGT 59.063 33.333 0.00 0.00 0.00 2.66
2871 9413 8.160765 TGAACTTATTTTTCACTCCCACTATCA 58.839 33.333 0.00 0.00 0.00 2.15
2897 9440 9.120538 AGTTCACATTGTATACAAAACAAGTCT 57.879 29.630 21.57 11.87 40.00 3.24
2950 9494 3.181507 CCATAAGTGGCACAAATCACTCG 60.182 47.826 21.41 0.59 44.16 4.18
3066 9613 1.267121 TGAGCTGAGGTCCTTGGTAC 58.733 55.000 9.40 0.00 0.00 3.34
3122 9669 5.219343 TGAGGCATGAATATCAACTCGAT 57.781 39.130 0.00 0.00 38.21 3.59
3148 9695 3.075134 AGGAGAATTCCCAATATCCAGCC 59.925 47.826 13.44 0.00 45.24 4.85
3464 10100 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3465 10101 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3466 10102 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3467 10103 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3468 10104 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3469 10105 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3470 10106 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3471 10107 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3472 10108 7.776030 TGTAAAGTTGAGTCACTTATTTTGGGA 59.224 33.333 0.00 0.00 35.87 4.37
3473 10109 7.860872 GTGTAAAGTTGAGTCACTTATTTTGGG 59.139 37.037 0.00 0.00 35.87 4.12
3474 10110 8.621286 AGTGTAAAGTTGAGTCACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3480 10116 9.880157 AAAGTTAGTGTAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 39.54 2.24
3481 10117 8.665685 CAAAGTTAGTGTAAAGTTGAGTCACTT 58.334 33.333 0.00 0.00 39.54 3.16
3482 10118 7.822822 ACAAAGTTAGTGTAAAGTTGAGTCACT 59.177 33.333 0.00 0.00 41.32 3.41
3483 10119 7.971455 ACAAAGTTAGTGTAAAGTTGAGTCAC 58.029 34.615 0.00 0.00 0.00 3.67
3484 10120 9.090692 GTACAAAGTTAGTGTAAAGTTGAGTCA 57.909 33.333 0.00 0.00 33.40 3.41
3485 10121 9.310716 AGTACAAAGTTAGTGTAAAGTTGAGTC 57.689 33.333 0.00 0.00 33.40 3.36
3491 10127 9.978044 CCTCTTAGTACAAAGTTAGTGTAAAGT 57.022 33.333 0.00 0.00 33.40 2.66
3492 10128 9.420551 CCCTCTTAGTACAAAGTTAGTGTAAAG 57.579 37.037 0.00 0.00 33.40 1.85
3493 10129 8.927411 ACCCTCTTAGTACAAAGTTAGTGTAAA 58.073 33.333 0.00 0.00 33.40 2.01
3494 10130 8.482852 ACCCTCTTAGTACAAAGTTAGTGTAA 57.517 34.615 0.00 0.00 33.40 2.41
3495 10131 9.014297 GTACCCTCTTAGTACAAAGTTAGTGTA 57.986 37.037 0.00 0.00 39.90 2.90
3496 10132 6.990908 ACCCTCTTAGTACAAAGTTAGTGT 57.009 37.500 0.00 0.00 0.00 3.55
3497 10133 7.889469 TGTACCCTCTTAGTACAAAGTTAGTG 58.111 38.462 1.45 0.00 45.28 2.74
3506 10142 5.659971 GGGATTCTTGTACCCTCTTAGTACA 59.340 44.000 0.00 0.00 46.27 2.90
3507 10143 5.070180 GGGGATTCTTGTACCCTCTTAGTAC 59.930 48.000 0.00 0.00 42.86 2.73
3508 10144 5.214293 GGGGATTCTTGTACCCTCTTAGTA 58.786 45.833 0.00 0.00 42.86 1.82
3509 10145 4.038633 GGGGATTCTTGTACCCTCTTAGT 58.961 47.826 0.00 0.00 42.86 2.24
3510 10146 4.691326 GGGGATTCTTGTACCCTCTTAG 57.309 50.000 0.00 0.00 42.86 2.18
3516 10152 3.732048 TTTGAGGGGATTCTTGTACCC 57.268 47.619 0.00 0.00 43.69 3.69
3517 10153 5.321927 TCTTTTTGAGGGGATTCTTGTACC 58.678 41.667 0.00 0.00 0.00 3.34
3518 10154 6.894339 TTCTTTTTGAGGGGATTCTTGTAC 57.106 37.500 0.00 0.00 0.00 2.90
3519 10155 9.594936 TTAATTCTTTTTGAGGGGATTCTTGTA 57.405 29.630 0.00 0.00 0.00 2.41
3520 10156 8.491045 TTAATTCTTTTTGAGGGGATTCTTGT 57.509 30.769 0.00 0.00 0.00 3.16
3521 10157 9.948964 ATTTAATTCTTTTTGAGGGGATTCTTG 57.051 29.630 0.00 0.00 0.00 3.02
3818 10615 5.545723 TCAGAAGGGAGAGAAGTTTCAAGAT 59.454 40.000 0.00 0.00 0.00 2.40
3827 10624 4.757594 CTGTTCATCAGAAGGGAGAGAAG 58.242 47.826 0.00 0.00 46.27 2.85
3830 10627 2.738000 CGCTGTTCATCAGAAGGGAGAG 60.738 54.545 0.00 0.00 46.27 3.20
3831 10628 1.205655 CGCTGTTCATCAGAAGGGAGA 59.794 52.381 0.00 0.00 46.27 3.71
3832 10629 1.066573 ACGCTGTTCATCAGAAGGGAG 60.067 52.381 0.00 0.00 46.27 4.30
3835 10632 5.812642 ACTTATTACGCTGTTCATCAGAAGG 59.187 40.000 0.00 0.00 46.27 3.46
3850 10647 1.635844 TCAGCGCACCACTTATTACG 58.364 50.000 11.47 0.00 0.00 3.18
3862 10659 2.672651 CCACCAACCATCAGCGCA 60.673 61.111 11.47 0.00 0.00 6.09
3935 10732 1.011904 CATTTGCGTCGATGCCTCG 60.012 57.895 26.06 7.61 46.41 4.63
3946 10743 0.162933 CAAAGCTTGCTGCATTTGCG 59.837 50.000 12.57 0.08 45.94 4.85
3977 10774 1.166531 ACTGGTGCACCGCTTTCTTC 61.167 55.000 30.07 4.16 39.43 2.87
4116 10938 3.673594 CGAGTCAAACGATCCTACAGCTT 60.674 47.826 0.00 0.00 0.00 3.74
4157 10979 3.536570 GAAGAGAACCCATTGCTCTACC 58.463 50.000 0.00 0.00 38.00 3.18
4158 10980 3.198853 AGGAAGAGAACCCATTGCTCTAC 59.801 47.826 0.00 0.00 38.00 2.59
4159 10981 3.454858 AGGAAGAGAACCCATTGCTCTA 58.545 45.455 0.00 0.00 38.00 2.43
4185 11007 2.935849 TGCCTATGTATGCACTTGAACG 59.064 45.455 0.00 0.00 31.31 3.95
4258 11080 5.107065 GCGTGAAACTTGAGCTACAACTTAT 60.107 40.000 0.00 0.00 34.56 1.73
4265 11087 3.241678 CGTATGCGTGAAACTTGAGCTAC 60.242 47.826 0.00 0.00 31.75 3.58
4271 11093 1.153353 ACCCGTATGCGTGAAACTTG 58.847 50.000 1.69 0.00 36.15 3.16
4280 11102 6.354039 AGAAATTTAACTAACCCGTATGCG 57.646 37.500 0.00 0.00 37.95 4.73
4281 11103 8.429493 AGTAGAAATTTAACTAACCCGTATGC 57.571 34.615 4.29 0.00 0.00 3.14
4283 11105 9.755804 GCTAGTAGAAATTTAACTAACCCGTAT 57.244 33.333 0.00 0.00 0.00 3.06
4284 11106 8.748412 TGCTAGTAGAAATTTAACTAACCCGTA 58.252 33.333 0.00 1.58 0.00 4.02
4285 11107 7.614494 TGCTAGTAGAAATTTAACTAACCCGT 58.386 34.615 0.00 0.00 0.00 5.28
4302 11124 2.667137 GCTAAGGCGACATGCTAGTAG 58.333 52.381 0.00 0.00 45.43 2.57
4317 11243 2.280186 CCGCTAAGGCCCGCTAAG 60.280 66.667 0.00 0.00 34.44 2.18
4356 11282 3.118629 AGCATGGATTGTCGTGACTACAT 60.119 43.478 1.23 0.00 0.00 2.29
4361 11287 2.483877 TCAAAGCATGGATTGTCGTGAC 59.516 45.455 0.00 0.00 0.00 3.67
4380 11306 3.324846 AGGATTACAGTTGCTCACACTCA 59.675 43.478 0.00 0.00 0.00 3.41
4383 11309 5.239525 AGAAAAGGATTACAGTTGCTCACAC 59.760 40.000 0.00 0.00 0.00 3.82
4424 11350 8.811017 AGAAAGTCAGAATCTAGAACATCTGAA 58.189 33.333 25.55 14.39 46.98 3.02
4589 11577 7.862873 GCCTTGTGAAATTATGGTAGCTATTTC 59.137 37.037 9.49 9.49 37.46 2.17
4638 11629 7.665974 ACGGAAATTAAAGAAGAAAGGATCAGT 59.334 33.333 0.00 0.00 0.00 3.41
4746 11738 8.682710 GGCAGGTTGTATGATAAGAATAAAACA 58.317 33.333 0.00 0.00 31.78 2.83
4754 11746 5.189736 ACTGAAGGCAGGTTGTATGATAAGA 59.810 40.000 0.00 0.00 46.60 2.10
4769 11761 1.965414 TGGATCCCTAACTGAAGGCA 58.035 50.000 9.90 0.00 35.09 4.75
4926 11923 4.891992 ATGGGTCTGGTAGATAATTCCG 57.108 45.455 0.00 0.00 0.00 4.30
4930 11927 5.727630 ACCACTATGGGTCTGGTAGATAAT 58.272 41.667 0.00 0.00 43.37 1.28
4993 11995 0.526211 GCAAAGAGCCCCTTAAACCG 59.474 55.000 0.00 0.00 37.23 4.44


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

AutoCloner maintained by Alex Coulton.