Multiple sequence alignment - TraesCS2B01G126400

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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 TraesCS2B01G126400 chr2B 100.000 2611 0 0 1 2611 94660054 94662664 0.000000e+00 4822.0
1 TraesCS2B01G126400 chr2B 100.000 321 0 0 3007 3327 94663060 94663380 7.950000e-166 593.0
2 TraesCS2B01G126400 chr2D 88.094 2629 143 59 50 2611 60326606 60329131 0.000000e+00 2964.0
3 TraesCS2B01G126400 chr2D 93.605 172 6 3 3024 3195 60329596 60329762 5.510000e-63 252.0
4 TraesCS2B01G126400 chr2D 87.850 107 8 3 3188 3291 60329795 60329899 1.620000e-23 121.0
5 TraesCS2B01G126400 chr2D 83.824 68 10 1 1 68 60325267 60325333 2.770000e-06 63.9
6 TraesCS2B01G126400 chr2A 90.357 1514 71 33 1066 2544 60807000 60805527 0.000000e+00 1917.0
7 TraesCS2B01G126400 chr2A 88.574 1094 51 23 1 1056 60808017 60806960 0.000000e+00 1260.0
8 TraesCS2B01G126400 chr2A 91.765 170 10 2 3024 3193 60805013 60804848 2.000000e-57 233.0
9 TraesCS2B01G126400 chr2A 96.970 132 4 0 3196 3327 60804810 60804679 4.320000e-54 222.0
10 TraesCS2B01G126400 chr4A 81.560 141 21 4 104 243 247906566 247906430 9.760000e-21 111.0
11 TraesCS2B01G126400 chr4A 93.023 43 3 0 2545 2587 680403784 680403742 2.770000e-06 63.9


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 TraesCS2B01G126400 chr2B 94660054 94663380 3326 False 2707.500 4822 100.00000 1 3327 2 chr2B.!!$F1 3326
1 TraesCS2B01G126400 chr2D 60325267 60329899 4632 False 850.225 2964 88.34325 1 3291 4 chr2D.!!$F1 3290
2 TraesCS2B01G126400 chr2A 60804679 60808017 3338 True 908.000 1917 91.91650 1 3327 4 chr2A.!!$R1 3326

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
528 1859 0.036105 TCGATGAAGGCACATGCACT 60.036 50.0 6.15 0.0 44.36 4.40 F
2053 3416 0.460311 GACCGACTGATGGACCGATT 59.540 55.0 0.00 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 3585 0.179145 GCGGGTCGATCGAGAAGAAA 60.179 55.0 20.09 0.0 0.0 2.52 R
3131 4587 1.132588 GTGTCTCGCTCTGTTGTCAC 58.867 55.0 0.00 0.0 0.0 3.67 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
71 1364 8.110860 ACCCTAGATTTGACATTACTTTTGTG 57.889 34.615 0.00 0.00 0.00 3.33
73 1366 7.393234 CCCTAGATTTGACATTACTTTTGTGGA 59.607 37.037 0.00 0.00 0.00 4.02
85 1378 4.266714 ACTTTTGTGGAGAGGAAACGAAA 58.733 39.130 0.00 0.00 0.00 3.46
90 1383 3.004315 TGTGGAGAGGAAACGAAAAATGC 59.996 43.478 0.00 0.00 0.00 3.56
94 1387 2.622942 AGAGGAAACGAAAAATGCTGCA 59.377 40.909 4.13 4.13 0.00 4.41
100 1393 4.829064 AACGAAAAATGCTGCAGAAGTA 57.171 36.364 20.43 0.00 0.00 2.24
102 1395 4.974591 ACGAAAAATGCTGCAGAAGTATC 58.025 39.130 20.43 7.85 29.81 2.24
149 1442 3.006110 CACACTTGGGCTTGATGACATTT 59.994 43.478 0.00 0.00 0.00 2.32
197 1490 5.123186 ACGAGATAAGTCGAGATGATGGATC 59.877 44.000 0.00 0.00 42.85 3.36
211 1522 0.719015 TGGATCAGGAGGAGGAGGTT 59.281 55.000 0.00 0.00 0.00 3.50
245 1556 3.643320 TGAGAGTCAAGCAAAGAGGAAGA 59.357 43.478 0.00 0.00 0.00 2.87
255 1566 4.530161 AGCAAAGAGGAAGAGAGTACATGT 59.470 41.667 2.69 2.69 0.00 3.21
256 1567 4.629200 GCAAAGAGGAAGAGAGTACATGTG 59.371 45.833 9.11 0.00 0.00 3.21
261 1573 6.668645 AGAGGAAGAGAGTACATGTGACTAT 58.331 40.000 9.11 5.52 0.00 2.12
289 1601 7.605309 TGATCTCTATGTTTGTGATATGATGCC 59.395 37.037 0.00 0.00 0.00 4.40
333 1647 9.978044 TGTGTTGAAATATGATCAATTTGTTCA 57.022 25.926 15.85 11.50 38.89 3.18
362 1693 7.805700 AGTTCAAAGTTTGTGAAACCAAAATG 58.194 30.769 15.08 0.00 42.34 2.32
389 1720 0.189574 TAGGGGATCTGCTAGCTGCT 59.810 55.000 17.23 7.57 43.37 4.24
390 1721 0.693767 AGGGGATCTGCTAGCTGCTT 60.694 55.000 17.23 6.44 43.37 3.91
391 1722 0.182299 GGGGATCTGCTAGCTGCTTT 59.818 55.000 17.23 3.89 43.37 3.51
392 1723 1.307097 GGGATCTGCTAGCTGCTTTG 58.693 55.000 17.23 2.48 43.37 2.77
393 1724 1.307097 GGATCTGCTAGCTGCTTTGG 58.693 55.000 17.23 0.00 43.37 3.28
394 1725 1.407989 GGATCTGCTAGCTGCTTTGGT 60.408 52.381 17.23 0.00 43.37 3.67
395 1726 2.158900 GGATCTGCTAGCTGCTTTGGTA 60.159 50.000 17.23 0.00 43.37 3.25
396 1727 2.386661 TCTGCTAGCTGCTTTGGTAC 57.613 50.000 17.23 0.00 43.37 3.34
397 1728 1.902508 TCTGCTAGCTGCTTTGGTACT 59.097 47.619 17.23 0.00 43.37 2.73
398 1729 2.303022 TCTGCTAGCTGCTTTGGTACTT 59.697 45.455 17.23 0.00 43.37 2.24
400 1731 4.020573 TCTGCTAGCTGCTTTGGTACTTTA 60.021 41.667 17.23 0.00 43.37 1.85
401 1732 4.253685 TGCTAGCTGCTTTGGTACTTTAG 58.746 43.478 17.23 0.00 43.37 1.85
402 1733 4.254492 GCTAGCTGCTTTGGTACTTTAGT 58.746 43.478 7.79 0.00 38.95 2.24
403 1734 5.046878 TGCTAGCTGCTTTGGTACTTTAGTA 60.047 40.000 17.23 0.00 43.37 1.82
404 1735 6.049790 GCTAGCTGCTTTGGTACTTTAGTAT 58.950 40.000 7.79 0.00 38.95 2.12
405 1736 7.147794 TGCTAGCTGCTTTGGTACTTTAGTATA 60.148 37.037 17.23 0.00 43.37 1.47
406 1737 7.382759 GCTAGCTGCTTTGGTACTTTAGTATAG 59.617 40.741 7.79 0.00 38.95 1.31
408 1739 7.493367 AGCTGCTTTGGTACTTTAGTATAGAG 58.507 38.462 0.00 0.00 32.54 2.43
409 1740 6.702282 GCTGCTTTGGTACTTTAGTATAGAGG 59.298 42.308 0.00 0.00 32.54 3.69
411 1742 8.548880 TGCTTTGGTACTTTAGTATAGAGGAT 57.451 34.615 0.00 0.00 32.54 3.24
412 1743 8.639761 TGCTTTGGTACTTTAGTATAGAGGATC 58.360 37.037 0.00 0.00 32.54 3.36
413 1744 8.089597 GCTTTGGTACTTTAGTATAGAGGATCC 58.910 40.741 2.48 2.48 31.01 3.36
414 1745 9.369672 CTTTGGTACTTTAGTATAGAGGATCCT 57.630 37.037 16.13 16.13 31.01 3.24
415 1746 8.937207 TTGGTACTTTAGTATAGAGGATCCTC 57.063 38.462 31.27 31.27 36.81 3.71
416 1747 7.468496 TGGTACTTTAGTATAGAGGATCCTCC 58.532 42.308 33.81 20.47 37.02 4.30
417 1748 7.074623 TGGTACTTTAGTATAGAGGATCCTCCA 59.925 40.741 33.81 24.19 37.02 3.86
418 1749 8.117312 GGTACTTTAGTATAGAGGATCCTCCAT 58.883 40.741 33.81 28.59 37.02 3.41
433 1764 9.102453 AGGATCCTCCATACTAAATAAAGTACC 57.898 37.037 9.02 0.00 39.61 3.34
506 1837 2.875317 GCTAGAGATGCCCTTAAACAGC 59.125 50.000 0.00 0.00 0.00 4.40
527 1858 0.804364 TTCGATGAAGGCACATGCAC 59.196 50.000 6.15 0.00 44.36 4.57
528 1859 0.036105 TCGATGAAGGCACATGCACT 60.036 50.000 6.15 0.00 44.36 4.40
591 1922 1.375396 ATGCCTTGTTGCGCGACTA 60.375 52.632 27.33 19.55 0.00 2.59
1004 2344 2.705127 GGAGCTTCTTCATCCTCATCCT 59.295 50.000 0.00 0.00 0.00 3.24
1011 2351 6.378661 TTCTTCATCCTCATCCTCTTGAAA 57.621 37.500 0.00 0.00 0.00 2.69
1054 2396 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1055 2397 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1056 2398 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1057 2399 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1058 2400 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1059 2401 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1060 2402 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1061 2403 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1062 2404 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1063 2405 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
1064 2406 5.960811 TCTCTCTCTCTCTCTCTCTCTCTTT 59.039 44.000 0.00 0.00 0.00 2.52
1065 2407 6.097554 TCTCTCTCTCTCTCTCTCTCTCTTTC 59.902 46.154 0.00 0.00 0.00 2.62
1066 2408 5.960811 TCTCTCTCTCTCTCTCTCTCTTTCT 59.039 44.000 0.00 0.00 0.00 2.52
1067 2409 6.097554 TCTCTCTCTCTCTCTCTCTCTTTCTC 59.902 46.154 0.00 0.00 0.00 2.87
1068 2410 5.960811 TCTCTCTCTCTCTCTCTCTTTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
1069 2411 6.097554 TCTCTCTCTCTCTCTCTCTTTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
1070 2412 5.960811 TCTCTCTCTCTCTCTCTTTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
1071 2413 6.441924 TCTCTCTCTCTCTCTCTTTCTCTCTT 59.558 42.308 0.00 0.00 0.00 2.85
1101 2443 5.684704 TCTCTCTCTCTCTCTCTCCATTTC 58.315 45.833 0.00 0.00 0.00 2.17
1102 2444 5.191522 TCTCTCTCTCTCTCTCTCCATTTCA 59.808 44.000 0.00 0.00 0.00 2.69
1103 2445 5.825532 TCTCTCTCTCTCTCTCCATTTCAA 58.174 41.667 0.00 0.00 0.00 2.69
1104 2446 5.887598 TCTCTCTCTCTCTCTCCATTTCAAG 59.112 44.000 0.00 0.00 0.00 3.02
1105 2447 4.402155 TCTCTCTCTCTCTCCATTTCAAGC 59.598 45.833 0.00 0.00 0.00 4.01
1106 2448 3.130164 TCTCTCTCTCTCCATTTCAAGCG 59.870 47.826 0.00 0.00 0.00 4.68
1107 2449 3.092301 TCTCTCTCTCCATTTCAAGCGA 58.908 45.455 0.00 0.00 0.00 4.93
1108 2450 3.130164 TCTCTCTCTCCATTTCAAGCGAG 59.870 47.826 0.00 0.00 0.00 5.03
1109 2451 1.932511 CTCTCTCCATTTCAAGCGAGC 59.067 52.381 0.00 0.00 0.00 5.03
1110 2452 1.012841 CTCTCCATTTCAAGCGAGCC 58.987 55.000 0.00 0.00 0.00 4.70
1111 2453 0.615331 TCTCCATTTCAAGCGAGCCT 59.385 50.000 0.00 0.00 0.00 4.58
1112 2454 1.003580 TCTCCATTTCAAGCGAGCCTT 59.996 47.619 0.00 0.00 0.00 4.35
1113 2455 1.399791 CTCCATTTCAAGCGAGCCTTC 59.600 52.381 0.00 0.00 0.00 3.46
1114 2456 1.167851 CCATTTCAAGCGAGCCTTCA 58.832 50.000 0.00 0.00 0.00 3.02
1115 2457 1.747355 CCATTTCAAGCGAGCCTTCAT 59.253 47.619 0.00 0.00 0.00 2.57
1116 2458 2.945008 CCATTTCAAGCGAGCCTTCATA 59.055 45.455 0.00 0.00 0.00 2.15
1117 2459 3.567164 CCATTTCAAGCGAGCCTTCATAT 59.433 43.478 0.00 0.00 0.00 1.78
1118 2460 4.756642 CCATTTCAAGCGAGCCTTCATATA 59.243 41.667 0.00 0.00 0.00 0.86
1119 2461 5.413833 CCATTTCAAGCGAGCCTTCATATAT 59.586 40.000 0.00 0.00 0.00 0.86
1120 2462 6.595326 CCATTTCAAGCGAGCCTTCATATATA 59.405 38.462 0.00 0.00 0.00 0.86
1121 2463 7.201591 CCATTTCAAGCGAGCCTTCATATATAG 60.202 40.741 0.00 0.00 0.00 1.31
1122 2464 6.590234 TTCAAGCGAGCCTTCATATATAGA 57.410 37.500 0.00 0.00 0.00 1.98
1128 2470 8.299990 AGCGAGCCTTCATATATAGAATTAGT 57.700 34.615 0.00 0.00 0.00 2.24
1134 2476 9.517609 GCCTTCATATATAGAATTAGTACGTGG 57.482 37.037 0.00 0.00 0.00 4.94
1163 2505 3.429492 ACTGCAGAGACAATCAGAGAGA 58.571 45.455 23.35 0.00 0.00 3.10
1164 2506 3.444742 ACTGCAGAGACAATCAGAGAGAG 59.555 47.826 23.35 0.00 0.00 3.20
1165 2507 3.694926 TGCAGAGACAATCAGAGAGAGA 58.305 45.455 0.00 0.00 0.00 3.10
1166 2508 3.695556 TGCAGAGACAATCAGAGAGAGAG 59.304 47.826 0.00 0.00 0.00 3.20
1167 2509 3.947196 GCAGAGACAATCAGAGAGAGAGA 59.053 47.826 0.00 0.00 0.00 3.10
1168 2510 4.036027 GCAGAGACAATCAGAGAGAGAGAG 59.964 50.000 0.00 0.00 0.00 3.20
1169 2511 5.430886 CAGAGACAATCAGAGAGAGAGAGA 58.569 45.833 0.00 0.00 0.00 3.10
1170 2512 5.526479 CAGAGACAATCAGAGAGAGAGAGAG 59.474 48.000 0.00 0.00 0.00 3.20
1174 2516 4.474651 ACAATCAGAGAGAGAGAGAGAGGA 59.525 45.833 0.00 0.00 0.00 3.71
1264 2609 2.918802 ACTCCCACGCGGTAACCA 60.919 61.111 12.47 0.00 0.00 3.67
1289 2634 1.172180 TCTTTTCGCTGCCCTTGGTG 61.172 55.000 0.00 0.00 0.00 4.17
1310 2655 4.580167 GTGGTGATCTTATGCTGCCATTAA 59.420 41.667 0.00 0.00 32.85 1.40
1311 2656 5.242393 GTGGTGATCTTATGCTGCCATTAAT 59.758 40.000 0.00 0.00 32.85 1.40
1312 2657 5.834742 TGGTGATCTTATGCTGCCATTAATT 59.165 36.000 0.00 0.00 32.85 1.40
1313 2658 7.003482 TGGTGATCTTATGCTGCCATTAATTA 58.997 34.615 0.00 0.00 32.85 1.40
1528 2877 6.487668 ACCGCACTGTGTATGTATACTGTATA 59.512 38.462 9.86 3.44 34.41 1.47
1529 2878 6.800408 CCGCACTGTGTATGTATACTGTATAC 59.200 42.308 24.40 24.40 41.06 1.47
1546 2895 7.303182 CTGTATACAGGACCTGAATTATCCA 57.697 40.000 28.56 11.29 40.20 3.41
1716 3067 3.564455 GTTCCTCGTGAACGTGTCT 57.436 52.632 2.37 0.00 43.65 3.41
1824 3175 2.723746 GCCGATACGTTCCGCCTA 59.276 61.111 0.00 0.00 0.00 3.93
1855 3214 1.133544 GGGGAGGAGAGGTACGTACAT 60.134 57.143 26.02 20.48 0.00 2.29
1877 3236 1.117150 ATACCCCTACGCGACAATGT 58.883 50.000 15.93 6.86 0.00 2.71
1910 3271 1.191535 AACTGATCCCCGATCGAACA 58.808 50.000 18.66 7.93 41.51 3.18
2016 3377 3.559238 AATTTGAGTTGATGGTGTCGC 57.441 42.857 0.00 0.00 0.00 5.19
2048 3411 1.805945 GCACGACCGACTGATGGAC 60.806 63.158 0.00 0.00 0.00 4.02
2049 3412 1.153823 CACGACCGACTGATGGACC 60.154 63.158 0.00 0.00 0.00 4.46
2053 3416 0.460311 GACCGACTGATGGACCGATT 59.540 55.000 0.00 0.00 0.00 3.34
2056 3419 1.280982 CGACTGATGGACCGATTGTG 58.719 55.000 0.00 0.00 0.00 3.33
2058 3421 2.673893 CGACTGATGGACCGATTGTGAA 60.674 50.000 0.00 0.00 0.00 3.18
2090 3453 6.127758 TGCTGATGCTCGGTTATTTTTGTATT 60.128 34.615 0.00 0.00 40.48 1.89
2234 3598 1.258982 CCCGCATTTTCTTCTCGATCG 59.741 52.381 9.36 9.36 0.00 3.69
2235 3599 2.193447 CCGCATTTTCTTCTCGATCGA 58.807 47.619 18.32 18.32 0.00 3.59
2238 3602 2.285488 GCATTTTCTTCTCGATCGACCC 59.715 50.000 15.15 0.00 0.00 4.46
2287 3656 1.466950 CTCGATCTACCGGATGAGCTC 59.533 57.143 9.46 6.82 34.33 4.09
2326 3695 4.880120 CCAGCTCAATCTCTAGCAATTCAA 59.120 41.667 0.00 0.00 41.32 2.69
2356 3725 7.357429 ACTATCTGTTGATGAGTGATGATGA 57.643 36.000 0.00 0.00 34.32 2.92
2357 3726 7.964624 ACTATCTGTTGATGAGTGATGATGAT 58.035 34.615 0.00 0.00 34.32 2.45
2358 3727 7.873505 ACTATCTGTTGATGAGTGATGATGATG 59.126 37.037 0.00 0.00 34.32 3.07
2359 3728 6.229936 TCTGTTGATGAGTGATGATGATGA 57.770 37.500 0.00 0.00 0.00 2.92
2360 3729 6.827727 TCTGTTGATGAGTGATGATGATGAT 58.172 36.000 0.00 0.00 0.00 2.45
2361 3730 6.706270 TCTGTTGATGAGTGATGATGATGATG 59.294 38.462 0.00 0.00 0.00 3.07
2372 3741 9.668497 AGTGATGATGATGATGGTAATTCTATG 57.332 33.333 0.00 0.00 0.00 2.23
2380 3749 9.645128 TGATGATGGTAATTCTATGGAATTTGT 57.355 29.630 20.46 6.41 46.36 2.83
2392 3761 7.130099 TCTATGGAATTTGTAGGTAGTCTGGA 58.870 38.462 0.00 0.00 0.00 3.86
2393 3762 5.677319 TGGAATTTGTAGGTAGTCTGGAG 57.323 43.478 0.00 0.00 0.00 3.86
2394 3763 4.469945 TGGAATTTGTAGGTAGTCTGGAGG 59.530 45.833 0.00 0.00 0.00 4.30
2395 3764 4.470304 GGAATTTGTAGGTAGTCTGGAGGT 59.530 45.833 0.00 0.00 0.00 3.85
2396 3765 5.395435 GGAATTTGTAGGTAGTCTGGAGGTC 60.395 48.000 0.00 0.00 0.00 3.85
2397 3766 2.414994 TGTAGGTAGTCTGGAGGTCG 57.585 55.000 0.00 0.00 0.00 4.79
2398 3767 1.911357 TGTAGGTAGTCTGGAGGTCGA 59.089 52.381 0.00 0.00 0.00 4.20
2399 3768 2.306805 TGTAGGTAGTCTGGAGGTCGAA 59.693 50.000 0.00 0.00 0.00 3.71
2400 3769 2.599408 AGGTAGTCTGGAGGTCGAAA 57.401 50.000 0.00 0.00 0.00 3.46
2401 3770 2.448453 AGGTAGTCTGGAGGTCGAAAG 58.552 52.381 0.00 0.00 0.00 2.62
2404 3773 3.760684 GGTAGTCTGGAGGTCGAAAGTTA 59.239 47.826 0.00 0.00 0.00 2.24
2405 3774 4.401837 GGTAGTCTGGAGGTCGAAAGTTAT 59.598 45.833 0.00 0.00 0.00 1.89
2407 3776 4.822026 AGTCTGGAGGTCGAAAGTTATTG 58.178 43.478 0.00 0.00 0.00 1.90
2408 3777 4.283722 AGTCTGGAGGTCGAAAGTTATTGT 59.716 41.667 0.00 0.00 0.00 2.71
2409 3778 4.626172 GTCTGGAGGTCGAAAGTTATTGTC 59.374 45.833 0.00 0.00 0.00 3.18
2410 3779 4.527038 TCTGGAGGTCGAAAGTTATTGTCT 59.473 41.667 0.00 0.00 0.00 3.41
2448 3817 3.093814 AGAATTTGCATGTGAGATGGCA 58.906 40.909 0.00 0.00 0.00 4.92
2449 3818 3.130516 AGAATTTGCATGTGAGATGGCAG 59.869 43.478 0.00 0.00 37.59 4.85
2501 3882 6.364945 GTTTTAGACCAACATATCCTCTGC 57.635 41.667 0.00 0.00 0.00 4.26
2502 3883 5.692115 TTTAGACCAACATATCCTCTGCA 57.308 39.130 0.00 0.00 0.00 4.41
2518 3899 4.397103 CCTCTGCATTTTCAGCTGTTCATA 59.603 41.667 14.67 0.00 34.19 2.15
2521 3902 6.172630 TCTGCATTTTCAGCTGTTCATACTA 58.827 36.000 14.67 0.00 34.19 1.82
2522 3903 6.092670 TCTGCATTTTCAGCTGTTCATACTAC 59.907 38.462 14.67 0.00 34.19 2.73
2552 3954 3.627395 TGATGCTATCTCCGTTTTGGT 57.373 42.857 0.00 0.00 39.52 3.67
2574 3976 8.641499 TGGTAGTTTAAATTGAACTGCAAAAG 57.359 30.769 17.29 0.00 40.21 2.27
2575 3977 7.223777 TGGTAGTTTAAATTGAACTGCAAAAGC 59.776 33.333 17.29 6.78 40.21 3.51
2599 4001 3.451178 TCTTACAATAGTGGACAGAGGGC 59.549 47.826 0.00 0.00 0.00 5.19
3053 4509 9.793259 TGAGAAAACAAAGGAAATATCAGTAGT 57.207 29.630 0.00 0.00 0.00 2.73
3087 4543 1.942657 GTGGCATGTTGCTCATACGAT 59.057 47.619 0.00 0.00 44.28 3.73
3095 4551 6.587990 GCATGTTGCTCATACGATATAGTTCT 59.412 38.462 0.00 0.00 40.96 3.01
3131 4587 0.519519 TTTTGCCTTATCCACACGCG 59.480 50.000 3.53 3.53 0.00 6.01
3143 4599 2.237751 ACACGCGTGACAACAGAGC 61.238 57.895 42.94 0.00 0.00 4.09
3181 4637 5.061179 AGTTTGGTTAGAACGTTGCATACT 58.939 37.500 5.00 0.00 32.38 2.12
3210 4708 6.295123 GGAGAAGTCATGTTGTTAGTGGACTA 60.295 42.308 0.00 0.00 34.75 2.59
3322 4820 0.825425 TTCGCCACCAATTGCCTCAA 60.825 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.517402 TGAAACCGCACCCACCAC 60.517 61.111 0.00 0.00 0.00 4.16
71 1364 3.826466 CAGCATTTTTCGTTTCCTCTCC 58.174 45.455 0.00 0.00 0.00 3.71
73 1366 2.622942 TGCAGCATTTTTCGTTTCCTCT 59.377 40.909 0.00 0.00 0.00 3.69
85 1378 4.529897 TCATGGATACTTCTGCAGCATTT 58.470 39.130 9.47 0.00 37.61 2.32
90 1383 6.879276 ATTCATTCATGGATACTTCTGCAG 57.121 37.500 7.63 7.63 37.61 4.41
149 1442 7.387673 CGTTTGATTATAGGGCATAGTCATTCA 59.612 37.037 0.00 0.00 36.19 2.57
197 1490 0.041833 TCCTCAACCTCCTCCTCCTG 59.958 60.000 0.00 0.00 0.00 3.86
211 1522 3.567478 TGACTCTCATCGATCTCCTCA 57.433 47.619 0.00 0.00 0.00 3.86
282 1594 9.550406 CAAACATGGATAATTTAAAGGCATCAT 57.450 29.630 0.00 0.00 0.00 2.45
298 1610 8.751242 TGATCATATTTCAACACAAACATGGAT 58.249 29.630 0.00 0.00 0.00 3.41
333 1647 9.495572 TTTGGTTTCACAAACTTTGAACTATTT 57.504 25.926 8.55 0.00 41.14 1.40
362 1693 6.040391 CAGCTAGCAGATCCCCTATCTTATAC 59.960 46.154 18.83 0.00 42.62 1.47
367 1698 2.818921 CAGCTAGCAGATCCCCTATCT 58.181 52.381 18.83 0.00 46.36 1.98
389 1720 9.364653 GAGGATCCTCTATACTAAAGTACCAAA 57.635 37.037 31.11 0.00 39.80 3.28
390 1721 8.937207 GAGGATCCTCTATACTAAAGTACCAA 57.063 38.462 31.11 0.00 39.80 3.67
437 1768 9.010029 CCAAAACAGCTTTCTATCCTACTTTAA 57.990 33.333 0.00 0.00 0.00 1.52
506 1837 1.402613 TGCATGTGCCTTCATCGAATG 59.597 47.619 2.07 0.00 41.18 2.67
527 1858 9.832445 TCATTCCCTAGCTAAACTAATTTGTAG 57.168 33.333 0.00 0.00 0.00 2.74
591 1922 0.863799 CGTCGCTGCAGCAATATGAT 59.136 50.000 36.03 0.00 42.21 2.45
696 2033 4.023193 AGTTTTTGAGATGCACCGGTTTAG 60.023 41.667 2.97 0.00 0.00 1.85
1004 2344 6.484288 AGAGAGAGAGAGAGATGTTTCAAGA 58.516 40.000 0.00 0.00 0.00 3.02
1011 2351 5.215069 AGAGAGAGAGAGAGAGAGAGATGT 58.785 45.833 0.00 0.00 0.00 3.06
1054 2396 7.020827 AGAGAGAAAGAGAGAAAGAGAGAGA 57.979 40.000 0.00 0.00 0.00 3.10
1055 2397 7.108847 AGAGAGAGAAAGAGAGAAAGAGAGAG 58.891 42.308 0.00 0.00 0.00 3.20
1056 2398 7.020827 AGAGAGAGAAAGAGAGAAAGAGAGA 57.979 40.000 0.00 0.00 0.00 3.10
1057 2399 7.108847 AGAGAGAGAGAAAGAGAGAAAGAGAG 58.891 42.308 0.00 0.00 0.00 3.20
1058 2400 7.020827 AGAGAGAGAGAAAGAGAGAAAGAGA 57.979 40.000 0.00 0.00 0.00 3.10
1059 2401 7.108847 AGAGAGAGAGAGAAAGAGAGAAAGAG 58.891 42.308 0.00 0.00 0.00 2.85
1060 2402 7.020827 AGAGAGAGAGAGAAAGAGAGAAAGA 57.979 40.000 0.00 0.00 0.00 2.52
1061 2403 7.108847 AGAGAGAGAGAGAGAAAGAGAGAAAG 58.891 42.308 0.00 0.00 0.00 2.62
1062 2404 7.020827 AGAGAGAGAGAGAGAAAGAGAGAAA 57.979 40.000 0.00 0.00 0.00 2.52
1063 2405 6.441924 AGAGAGAGAGAGAGAGAAAGAGAGAA 59.558 42.308 0.00 0.00 0.00 2.87
1064 2406 5.960811 AGAGAGAGAGAGAGAGAAAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
1065 2407 6.098124 AGAGAGAGAGAGAGAGAGAAAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
1066 2408 5.960811 AGAGAGAGAGAGAGAGAGAAAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
1067 2409 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
1068 2410 5.960811 AGAGAGAGAGAGAGAGAGAGAAAGA 59.039 44.000 0.00 0.00 0.00 2.52
1069 2411 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
1070 2412 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
1071 2413 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
1101 2443 7.840342 AATTCTATATATGAAGGCTCGCTTG 57.160 36.000 0.00 0.00 0.00 4.01
1102 2444 8.754080 ACTAATTCTATATATGAAGGCTCGCTT 58.246 33.333 0.00 0.00 0.00 4.68
1103 2445 8.299990 ACTAATTCTATATATGAAGGCTCGCT 57.700 34.615 0.00 0.00 0.00 4.93
1104 2446 9.453325 GTACTAATTCTATATATGAAGGCTCGC 57.547 37.037 0.00 0.00 0.00 5.03
1105 2447 9.653067 CGTACTAATTCTATATATGAAGGCTCG 57.347 37.037 0.00 0.00 0.00 5.03
1108 2450 9.517609 CCACGTACTAATTCTATATATGAAGGC 57.482 37.037 0.00 0.00 0.00 4.35
1118 2460 9.364653 AGTTAATCCTCCACGTACTAATTCTAT 57.635 33.333 0.00 0.00 0.00 1.98
1119 2461 8.627403 CAGTTAATCCTCCACGTACTAATTCTA 58.373 37.037 0.00 0.00 0.00 2.10
1120 2462 7.490000 CAGTTAATCCTCCACGTACTAATTCT 58.510 38.462 0.00 0.00 0.00 2.40
1121 2463 6.200475 GCAGTTAATCCTCCACGTACTAATTC 59.800 42.308 0.00 0.00 0.00 2.17
1122 2464 6.047231 GCAGTTAATCCTCCACGTACTAATT 58.953 40.000 0.00 0.00 0.00 1.40
1128 2470 3.093814 TCTGCAGTTAATCCTCCACGTA 58.906 45.455 14.67 0.00 0.00 3.57
1134 2476 5.423015 TGATTGTCTCTGCAGTTAATCCTC 58.577 41.667 14.67 4.94 0.00 3.71
1163 2505 3.820467 CGACATTATGCTCCTCTCTCTCT 59.180 47.826 0.00 0.00 0.00 3.10
1164 2506 3.818210 TCGACATTATGCTCCTCTCTCTC 59.182 47.826 0.00 0.00 0.00 3.20
1165 2507 3.820467 CTCGACATTATGCTCCTCTCTCT 59.180 47.826 0.00 0.00 0.00 3.10
1166 2508 3.057596 CCTCGACATTATGCTCCTCTCTC 60.058 52.174 0.00 0.00 0.00 3.20
1167 2509 2.890311 CCTCGACATTATGCTCCTCTCT 59.110 50.000 0.00 0.00 0.00 3.10
1168 2510 2.029470 CCCTCGACATTATGCTCCTCTC 60.029 54.545 0.00 0.00 0.00 3.20
1169 2511 1.967066 CCCTCGACATTATGCTCCTCT 59.033 52.381 0.00 0.00 0.00 3.69
1170 2512 1.964223 TCCCTCGACATTATGCTCCTC 59.036 52.381 0.00 0.00 0.00 3.71
1174 2516 0.032678 CGCTCCCTCGACATTATGCT 59.967 55.000 0.00 0.00 0.00 3.79
1236 2581 0.108615 CGTGGGAGTGAGTGATGGAC 60.109 60.000 0.00 0.00 0.00 4.02
1264 2609 2.617274 GGCAGCGAAAAGAGGCGTT 61.617 57.895 0.00 0.00 0.00 4.84
1289 2634 5.972107 ATTAATGGCAGCATAAGATCACC 57.028 39.130 0.00 0.00 0.00 4.02
1528 2877 4.785376 AGAACTGGATAATTCAGGTCCTGT 59.215 41.667 18.65 2.16 46.92 4.00
1529 2878 5.104776 TCAGAACTGGATAATTCAGGTCCTG 60.105 44.000 13.21 13.21 46.92 3.86
1546 2895 7.483580 AGTACATAACCTAAGCTTCAGAACT 57.516 36.000 0.00 0.00 0.00 3.01
1716 3067 2.347490 GGGCAGCTCTTGTCGGAA 59.653 61.111 0.00 0.00 29.93 4.30
1755 3106 1.684386 CCAGCTCCTCGAATGCCTCT 61.684 60.000 0.00 0.00 0.00 3.69
1761 3112 2.366167 AGGCCCAGCTCCTCGAAT 60.366 61.111 0.00 0.00 0.00 3.34
1836 3187 2.361643 ATGTACGTACCTCTCCTCCC 57.638 55.000 22.43 0.00 0.00 4.30
1855 3214 1.761449 TTGTCGCGTAGGGGTATGTA 58.239 50.000 5.77 0.00 42.39 2.29
2000 3361 0.666274 GTCGCGACACCATCAACTCA 60.666 55.000 33.09 0.00 0.00 3.41
2001 3362 0.388649 AGTCGCGACACCATCAACTC 60.389 55.000 37.85 9.43 0.00 3.01
2002 3363 0.885879 TAGTCGCGACACCATCAACT 59.114 50.000 37.85 18.31 0.00 3.16
2003 3364 1.269166 CTAGTCGCGACACCATCAAC 58.731 55.000 37.85 11.37 0.00 3.18
2004 3365 0.457853 GCTAGTCGCGACACCATCAA 60.458 55.000 37.85 14.55 0.00 2.57
2005 3366 1.138883 GCTAGTCGCGACACCATCA 59.861 57.895 37.85 15.88 0.00 3.07
2016 3377 2.716828 CGTGCGGTGTTGCTAGTCG 61.717 63.158 0.00 0.00 35.36 4.18
2024 3385 3.908081 AGTCGGTCGTGCGGTGTT 61.908 61.111 0.00 0.00 0.00 3.32
2029 3390 2.880879 CCATCAGTCGGTCGTGCG 60.881 66.667 0.00 0.00 0.00 5.34
2031 3394 1.153823 GGTCCATCAGTCGGTCGTG 60.154 63.158 0.00 0.00 0.00 4.35
2032 3395 2.697761 CGGTCCATCAGTCGGTCGT 61.698 63.158 0.00 0.00 0.00 4.34
2048 3411 4.122046 TCAGCACAGATATTCACAATCGG 58.878 43.478 0.00 0.00 0.00 4.18
2049 3412 5.676953 CATCAGCACAGATATTCACAATCG 58.323 41.667 0.00 0.00 0.00 3.34
2053 3416 4.124970 GAGCATCAGCACAGATATTCACA 58.875 43.478 0.00 0.00 45.49 3.58
2056 3419 2.735663 CCGAGCATCAGCACAGATATTC 59.264 50.000 0.00 0.00 45.49 1.75
2058 3421 1.690893 ACCGAGCATCAGCACAGATAT 59.309 47.619 0.00 0.00 45.49 1.63
2090 3453 4.580167 GCCTGGTTCTGCAACATCATATTA 59.420 41.667 0.00 0.00 33.70 0.98
2217 3581 2.285488 GGGTCGATCGAGAAGAAAATGC 59.715 50.000 20.09 2.04 0.00 3.56
2221 3585 0.179145 GCGGGTCGATCGAGAAGAAA 60.179 55.000 20.09 0.00 0.00 2.52
2287 3656 6.396829 TGAGCTGGATGTATATATCATCGG 57.603 41.667 11.14 2.01 41.54 4.18
2326 3695 7.468141 TCACTCATCAACAGATAGTACAAGT 57.532 36.000 0.00 0.00 0.00 3.16
2372 3741 4.470304 ACCTCCAGACTACCTACAAATTCC 59.530 45.833 0.00 0.00 0.00 3.01
2376 3745 3.087031 CGACCTCCAGACTACCTACAAA 58.913 50.000 0.00 0.00 0.00 2.83
2380 3749 3.009916 ACTTTCGACCTCCAGACTACCTA 59.990 47.826 0.00 0.00 0.00 3.08
2389 3758 4.039973 ACAGACAATAACTTTCGACCTCCA 59.960 41.667 0.00 0.00 0.00 3.86
2392 3761 6.423001 GTGTAACAGACAATAACTTTCGACCT 59.577 38.462 0.00 0.00 40.66 3.85
2393 3762 6.347160 GGTGTAACAGACAATAACTTTCGACC 60.347 42.308 0.00 0.00 40.66 4.79
2394 3763 6.587651 GGTGTAACAGACAATAACTTTCGAC 58.412 40.000 0.00 0.00 40.66 4.20
2395 3764 5.403166 CGGTGTAACAGACAATAACTTTCGA 59.597 40.000 0.00 0.00 40.66 3.71
2396 3765 5.176223 ACGGTGTAACAGACAATAACTTTCG 59.824 40.000 0.00 0.00 40.66 3.46
2397 3766 6.535274 ACGGTGTAACAGACAATAACTTTC 57.465 37.500 0.00 0.00 40.66 2.62
2398 3767 6.930667 AACGGTGTAACAGACAATAACTTT 57.069 33.333 0.00 0.00 40.66 2.66
2399 3768 6.316890 ACAAACGGTGTAACAGACAATAACTT 59.683 34.615 0.00 0.00 40.66 2.66
2400 3769 5.818857 ACAAACGGTGTAACAGACAATAACT 59.181 36.000 0.00 0.00 40.66 2.24
2401 3770 5.905181 CACAAACGGTGTAACAGACAATAAC 59.095 40.000 0.00 0.00 42.75 1.89
2404 3773 4.545823 CACAAACGGTGTAACAGACAAT 57.454 40.909 0.00 0.00 42.75 2.71
2449 3818 2.914289 CAGCAGGGAGGATGGTCC 59.086 66.667 0.00 0.00 36.58 4.46
2493 3874 3.083122 ACAGCTGAAAATGCAGAGGAT 57.917 42.857 23.35 0.00 38.14 3.24
2499 3880 5.939883 AGTAGTATGAACAGCTGAAAATGCA 59.060 36.000 23.35 2.30 0.00 3.96
2500 3881 6.314896 AGAGTAGTATGAACAGCTGAAAATGC 59.685 38.462 23.35 13.13 0.00 3.56
2501 3882 7.332926 ACAGAGTAGTATGAACAGCTGAAAATG 59.667 37.037 23.35 0.00 0.00 2.32
2502 3883 7.390027 ACAGAGTAGTATGAACAGCTGAAAAT 58.610 34.615 23.35 12.39 0.00 1.82
2518 3899 9.184523 GGAGATAGCATCATATTACAGAGTAGT 57.815 37.037 0.00 0.00 0.00 2.73
2521 3902 6.661377 ACGGAGATAGCATCATATTACAGAGT 59.339 38.462 0.00 0.00 0.00 3.24
2522 3903 7.094508 ACGGAGATAGCATCATATTACAGAG 57.905 40.000 0.00 0.00 0.00 3.35
2574 3976 4.106029 TCTGTCCACTATTGTAAGACGC 57.894 45.455 5.58 0.00 33.73 5.19
2575 3977 4.440250 CCCTCTGTCCACTATTGTAAGACG 60.440 50.000 5.58 0.00 33.73 4.18
3007 4411 8.913487 TTCTCATATGAGCAACATGTCAATAT 57.087 30.769 25.27 0.00 41.80 1.28
3008 4412 8.735692 TTTCTCATATGAGCAACATGTCAATA 57.264 30.769 25.27 3.14 41.80 1.90
3009 4413 7.634671 TTTCTCATATGAGCAACATGTCAAT 57.365 32.000 25.27 0.00 41.80 2.57
3010 4414 7.040548 TGTTTTCTCATATGAGCAACATGTCAA 60.041 33.333 28.87 15.48 41.80 3.18
3011 4415 6.430616 TGTTTTCTCATATGAGCAACATGTCA 59.569 34.615 28.87 16.78 41.80 3.58
3012 4416 6.845302 TGTTTTCTCATATGAGCAACATGTC 58.155 36.000 28.87 15.23 41.80 3.06
3016 4420 6.489700 TCCTTTGTTTTCTCATATGAGCAACA 59.510 34.615 28.87 28.87 40.31 3.33
3017 4421 6.913170 TCCTTTGTTTTCTCATATGAGCAAC 58.087 36.000 25.27 25.71 41.80 4.17
3018 4422 7.523293 TTCCTTTGTTTTCTCATATGAGCAA 57.477 32.000 25.27 19.19 41.80 3.91
3019 4423 7.523293 TTTCCTTTGTTTTCTCATATGAGCA 57.477 32.000 25.27 14.19 41.80 4.26
3052 4508 9.728021 GCAACATGCCACATGAGTAACTCATAC 62.728 44.444 14.17 0.00 42.25 2.39
3053 4509 7.840910 GCAACATGCCACATGAGTAACTCATA 61.841 42.308 14.17 0.00 42.25 2.15
3054 4510 7.113207 GCAACATGCCACATGAGTAACTCAT 62.113 44.000 14.17 0.00 43.65 2.90
3131 4587 1.132588 GTGTCTCGCTCTGTTGTCAC 58.867 55.000 0.00 0.00 0.00 3.67
3181 4637 4.525487 ACTAACAACATGACTTCTCCGGTA 59.475 41.667 0.00 0.00 0.00 4.02
3210 4708 7.878495 TCCTTTTATAGGGTCCATGTTGTAAT 58.122 34.615 0.00 0.00 44.86 1.89
3244 4742 6.367149 TGTTGAGTTGAATTCTCTCATCGAAG 59.633 38.462 23.66 0.00 37.91 3.79


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

AutoCloner maintained by Alex Coulton.