Multiple sequence alignment - TraesCS4D01G349400

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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 TraesCS4D01G349400 chr4D 100.000 3172 0 0 2071 5242 502480772 502483943 0.000000e+00 5858.0
1 TraesCS4D01G349400 chr4D 100.000 1850 0 0 1 1850 502478702 502480551 0.000000e+00 3417.0
2 TraesCS4D01G349400 chr4D 76.667 330 64 10 999 1325 509239604 509239285 2.510000e-38 171.0
3 TraesCS4D01G349400 chr5A 92.993 2098 97 23 3159 5241 685738894 685740956 0.000000e+00 3014.0
4 TraesCS4D01G349400 chr5A 93.705 1398 75 10 39 1430 685735847 685737237 0.000000e+00 2082.0
5 TraesCS4D01G349400 chr5A 89.104 1083 81 15 2071 3137 685737737 685738798 0.000000e+00 1312.0
6 TraesCS4D01G349400 chr5A 94.886 176 8 1 1676 1850 685737521 685737696 1.860000e-69 274.0
7 TraesCS4D01G349400 chr5A 77.508 329 53 15 999 1325 698012692 698012383 1.500000e-40 178.0
8 TraesCS4D01G349400 chr5A 75.405 370 69 17 2071 2430 660428881 660428524 5.430000e-35 159.0
9 TraesCS4D01G349400 chr4B 93.973 1908 73 13 3159 5057 646856509 646858383 0.000000e+00 2848.0
10 TraesCS4D01G349400 chr4B 90.467 1626 116 13 43 1664 646842564 646844154 0.000000e+00 2108.0
11 TraesCS4D01G349400 chr4B 88.682 645 59 10 2072 2711 646855263 646855898 0.000000e+00 774.0
12 TraesCS4D01G349400 chr4B 93.824 421 26 0 2709 3129 646855991 646856411 7.410000e-178 634.0
13 TraesCS4D01G349400 chr4B 95.455 198 6 3 5042 5239 646858735 646858929 3.940000e-81 313.0
14 TraesCS4D01G349400 chr4B 92.899 169 11 1 1674 1841 646844899 646845067 1.460000e-60 244.0
15 TraesCS4D01G349400 chr4B 76.737 331 65 10 999 1325 657808123 657808445 1.940000e-39 174.0
16 TraesCS4D01G349400 chr5D 76.744 602 96 20 83 660 501084752 501084171 3.970000e-76 296.0
17 TraesCS4D01G349400 chr5D 75.417 480 93 19 2101 2568 269297529 269297063 5.320000e-50 209.0
18 TraesCS4D01G349400 chr6B 76.382 597 94 27 78 651 508829140 508829712 1.440000e-70 278.0
19 TraesCS4D01G349400 chr6D 76.373 601 85 28 84 660 315978186 315977619 2.410000e-68 270.0
20 TraesCS4D01G349400 chr6D 74.247 730 138 30 78 786 291417086 291417786 1.450000e-65 261.0
21 TraesCS4D01G349400 chr4A 76.983 517 76 28 175 659 590605199 590604694 6.740000e-64 255.0
22 TraesCS4D01G349400 chr3A 76.923 325 63 11 1004 1326 549257447 549257133 1.940000e-39 174.0
23 TraesCS4D01G349400 chr3A 100.000 36 0 0 43 78 88212354 88212319 3.390000e-07 67.6
24 TraesCS4D01G349400 chr7D 76.453 327 61 13 1004 1326 262860246 262859932 4.200000e-36 163.0
25 TraesCS4D01G349400 chr7D 93.478 46 2 1 1 45 253149276 253149321 3.390000e-07 67.6
26 TraesCS4D01G349400 chr7D 97.059 34 1 0 45 78 245470734 245470767 2.040000e-04 58.4
27 TraesCS4D01G349400 chr7D 94.118 34 2 0 45 78 72281790 72281823 9.000000e-03 52.8
28 TraesCS4D01G349400 chr5B 85.401 137 20 0 85 221 554524955 554524819 5.470000e-30 143.0
29 TraesCS4D01G349400 chr5B 93.478 46 3 0 1 46 437302853 437302898 9.420000e-08 69.4
30 TraesCS4D01G349400 chr2D 75.077 325 65 11 1006 1326 165691238 165690926 2.550000e-28 137.0
31 TraesCS4D01G349400 chr2D 93.750 48 2 1 1 47 300893471 300893424 2.620000e-08 71.3
32 TraesCS4D01G349400 chr2D 93.333 45 3 0 1 45 172008491 172008535 3.390000e-07 67.6
33 TraesCS4D01G349400 chr2D 93.333 45 2 1 1 45 33097731 33097774 1.220000e-06 65.8
34 TraesCS4D01G349400 chr2D 97.222 36 1 0 43 78 638381113 638381078 1.580000e-05 62.1
35 TraesCS4D01G349400 chr1A 88.542 96 9 2 2473 2567 589854836 589854742 1.190000e-21 115.0
36 TraesCS4D01G349400 chr3D 75.875 257 40 14 1039 1295 453209274 453209508 1.540000e-20 111.0
37 TraesCS4D01G349400 chr3D 97.059 34 1 0 45 78 307839937 307839970 2.040000e-04 58.4
38 TraesCS4D01G349400 chr1D 95.652 46 2 0 1 46 376769191 376769146 2.020000e-09 75.0
39 TraesCS4D01G349400 chr1D 93.617 47 2 1 3 48 279897133 279897179 9.420000e-08 69.4
40 TraesCS4D01G349400 chr1D 93.617 47 2 1 1 46 290358888 290358842 9.420000e-08 69.4
41 TraesCS4D01G349400 chr6A 95.652 46 1 1 1 45 467018099 467018144 7.280000e-09 73.1
42 TraesCS4D01G349400 chr2B 94.595 37 1 1 45 81 50496600 50496635 7.330000e-04 56.5


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 TraesCS4D01G349400 chr4D 502478702 502483943 5241 False 4637.50 5858 100.0000 1 5242 2 chr4D.!!$F1 5241
1 TraesCS4D01G349400 chr5A 685735847 685740956 5109 False 1670.50 3014 92.6720 39 5241 4 chr5A.!!$F1 5202
2 TraesCS4D01G349400 chr4B 646842564 646845067 2503 False 1176.00 2108 91.6830 43 1841 2 chr4B.!!$F2 1798
3 TraesCS4D01G349400 chr4B 646855263 646858929 3666 False 1142.25 2848 92.9835 2072 5239 4 chr4B.!!$F3 3167
4 TraesCS4D01G349400 chr5D 501084171 501084752 581 True 296.00 296 76.7440 83 660 1 chr5D.!!$R2 577
5 TraesCS4D01G349400 chr6B 508829140 508829712 572 False 278.00 278 76.3820 78 651 1 chr6B.!!$F1 573
6 TraesCS4D01G349400 chr6D 315977619 315978186 567 True 270.00 270 76.3730 84 660 1 chr6D.!!$R1 576
7 TraesCS4D01G349400 chr6D 291417086 291417786 700 False 261.00 261 74.2470 78 786 1 chr6D.!!$F1 708
8 TraesCS4D01G349400 chr4A 590604694 590605199 505 True 255.00 255 76.9830 175 659 1 chr4A.!!$R1 484

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
37 38 0.037605 CGAGGTCTGCCGGTTTTAGT 60.038 55.0 1.90 0.0 40.50 2.24 F
296 313 0.244450 TAAACACCGAGTACCCTGCG 59.756 55.0 0.00 0.0 0.00 5.18 F
465 513 0.472925 TAGTCCAAGGTGGGCAGTCA 60.473 55.0 1.08 0.0 46.77 3.41 F
2379 3182 0.039618 AATCAATCGTGGGGGCACTT 59.960 50.0 0.00 0.0 0.00 3.16 F
3144 4060 0.043485 TATCCACACCCTGGGCTACA 59.957 55.0 14.08 0.0 41.06 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1493 0.598065 GAAAGGGACAATGCAGCGTT 59.402 50.0 0.00 0.0 0.0 4.84 R
2153 2954 0.249868 CCAGCAAACTCGAGACCACA 60.250 55.0 21.68 0.0 0.0 4.17 R
2425 3231 0.539518 AACTGGCAAAAACCCCACAC 59.460 50.0 0.00 0.0 0.0 3.82 R
4223 5217 0.179089 ATCAGAGGCAGCACGATGAC 60.179 55.0 0.00 0.0 0.0 3.06 R
4801 5813 0.320771 GCGGCTCTTCAGAACCTTCA 60.321 55.0 0.00 0.0 0.0 3.02 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
29 30 3.528370 CCTACCCGAGGTCTGCCG 61.528 72.222 0.00 0.00 40.98 5.69
30 31 3.528370 CTACCCGAGGTCTGCCGG 61.528 72.222 0.00 0.00 44.94 6.13
31 32 4.371417 TACCCGAGGTCTGCCGGT 62.371 66.667 1.90 0.00 43.93 5.28
32 33 3.892104 TACCCGAGGTCTGCCGGTT 62.892 63.158 1.90 0.00 43.93 4.44
33 34 4.016706 CCCGAGGTCTGCCGGTTT 62.017 66.667 1.90 0.00 43.93 3.27
34 35 2.032071 CCGAGGTCTGCCGGTTTT 59.968 61.111 1.90 0.00 40.78 2.43
35 36 1.294138 CCGAGGTCTGCCGGTTTTA 59.706 57.895 1.90 0.00 40.78 1.52
36 37 0.739813 CCGAGGTCTGCCGGTTTTAG 60.740 60.000 1.90 0.00 40.78 1.85
37 38 0.037605 CGAGGTCTGCCGGTTTTAGT 60.038 55.000 1.90 0.00 40.50 2.24
101 102 3.639716 TCGCAAAAGTTCATGATGCAA 57.360 38.095 16.26 0.00 36.84 4.08
268 285 1.133253 CCTCGCATCGCACAACAAG 59.867 57.895 0.00 0.00 0.00 3.16
296 313 0.244450 TAAACACCGAGTACCCTGCG 59.756 55.000 0.00 0.00 0.00 5.18
465 513 0.472925 TAGTCCAAGGTGGGCAGTCA 60.473 55.000 1.08 0.00 46.77 3.41
521 570 3.537874 GCGGCCGGAGAGGTACAT 61.538 66.667 29.38 0.00 43.70 2.29
533 582 2.507547 GTACATCGGCGGCGTCAA 60.508 61.111 31.06 12.96 0.00 3.18
542 591 2.032634 GCGGCGTCAAACCATGAGA 61.033 57.895 9.37 0.00 39.19 3.27
621 674 1.705002 TTGAGTGAGGTGGGGGTGTG 61.705 60.000 0.00 0.00 0.00 3.82
673 729 1.882623 GCACAGCTTCCTAAGTTTGCT 59.117 47.619 0.00 0.00 0.00 3.91
711 767 1.535204 AACCATTCGTACCGGTCCGT 61.535 55.000 19.59 0.00 30.91 4.69
723 779 1.411246 CCGGTCCGTAGATGGATGAAA 59.589 52.381 11.06 0.00 40.91 2.69
747 806 2.620585 TCGCATTGGATGACAAAACACA 59.379 40.909 0.00 0.00 43.46 3.72
749 808 3.609373 CGCATTGGATGACAAAACACATC 59.391 43.478 0.00 0.00 43.46 3.06
793 852 1.217882 CCGATGGTTTGATAGTCGCC 58.782 55.000 0.00 0.00 0.00 5.54
819 878 2.464459 GCAGAATGAACTCCCCGCG 61.464 63.158 0.00 0.00 39.69 6.46
1176 1235 5.752036 TTCTCAATCCACTGATCTCTTGT 57.248 39.130 0.00 0.00 0.00 3.16
1614 1673 6.057627 TCTAAATTTTGACCGTTTAACGCA 57.942 33.333 12.41 2.78 40.91 5.24
1619 1678 5.623174 TTTTGACCGTTTAACGCAATTTC 57.377 34.783 12.41 3.63 40.91 2.17
1651 1710 3.904136 ACAGGAGAAACGCTCATTTTG 57.096 42.857 0.00 0.00 45.81 2.44
1664 1723 4.375698 CGCTCATTTTGAAGTTGTGTAACG 59.624 41.667 0.00 0.00 42.39 3.18
1666 1725 5.236655 TCATTTTGAAGTTGTGTAACGCA 57.763 34.783 0.00 0.00 42.39 5.24
1667 1726 5.641709 TCATTTTGAAGTTGTGTAACGCAA 58.358 33.333 0.00 0.00 42.39 4.85
1669 1728 6.754209 TCATTTTGAAGTTGTGTAACGCAATT 59.246 30.769 0.00 0.00 42.39 2.32
1670 1729 6.952935 TTTTGAAGTTGTGTAACGCAATTT 57.047 29.167 0.00 0.00 42.39 1.82
1671 1730 6.561945 TTTGAAGTTGTGTAACGCAATTTC 57.438 33.333 16.07 16.07 44.74 2.17
1779 2580 7.704578 TGAGTACTATCTATCCTATGCCAAC 57.295 40.000 0.00 0.00 0.00 3.77
1813 2614 5.766150 TGACCAATAAGTGTTTGTCCAAG 57.234 39.130 0.00 0.00 0.00 3.61
1816 2617 6.549364 TGACCAATAAGTGTTTGTCCAAGATT 59.451 34.615 0.00 0.00 0.00 2.40
2131 2932 2.218603 GTGTTGATTGGTCTCGTTGGT 58.781 47.619 0.00 0.00 0.00 3.67
2153 2954 2.618559 GGAGGTAGTGGAAGTCGAGACT 60.619 54.545 0.00 0.00 44.94 3.24
2235 3036 3.087253 CCATGAGGTGGGGCCGTA 61.087 66.667 0.00 0.00 44.79 4.02
2247 3048 4.493747 GCCGTAGCTTCGCTCCGT 62.494 66.667 7.29 0.00 36.30 4.69
2251 3052 0.179181 CGTAGCTTCGCTCCGTGTTA 60.179 55.000 0.00 0.00 40.44 2.41
2273 3074 2.472059 GCATTCCGGCGCTTCATGA 61.472 57.895 7.64 0.00 0.00 3.07
2300 3103 0.400213 GGTCTGTCATGGTTGTGGGA 59.600 55.000 0.00 0.00 0.00 4.37
2302 3105 1.347707 GTCTGTCATGGTTGTGGGAGA 59.652 52.381 0.00 0.00 0.00 3.71
2311 3114 1.686052 GGTTGTGGGAGATTTTGCACA 59.314 47.619 0.00 0.00 0.00 4.57
2334 3137 2.161410 TGTGCCTTAATCAATCGTGTGC 59.839 45.455 0.00 0.00 0.00 4.57
2336 3139 3.621268 GTGCCTTAATCAATCGTGTGCTA 59.379 43.478 0.00 0.00 0.00 3.49
2339 3142 4.693283 CCTTAATCAATCGTGTGCTAGGA 58.307 43.478 0.00 0.00 0.00 2.94
2376 3179 1.409521 CCTTAATCAATCGTGGGGGCA 60.410 52.381 0.00 0.00 0.00 5.36
2378 3181 0.916086 TAATCAATCGTGGGGGCACT 59.084 50.000 0.00 0.00 0.00 4.40
2379 3182 0.039618 AATCAATCGTGGGGGCACTT 59.960 50.000 0.00 0.00 0.00 3.16
2425 3231 0.739462 AGTCGTGTGGTGTGTGTGTG 60.739 55.000 0.00 0.00 0.00 3.82
2426 3232 1.017177 GTCGTGTGGTGTGTGTGTGT 61.017 55.000 0.00 0.00 0.00 3.72
2427 3233 1.016653 TCGTGTGGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
2428 3234 1.295357 CGTGTGGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
2429 3235 0.167908 GTGTGGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2430 3236 0.957888 TGTGGTGTGTGTGTGTGTGG 60.958 55.000 0.00 0.00 0.00 4.17
2441 3247 0.904865 TGTGTGTGGGGTTTTTGCCA 60.905 50.000 0.00 0.00 0.00 4.92
2471 3277 4.839121 TCAATTAACCGTGCCTCTGTATT 58.161 39.130 0.00 0.00 0.00 1.89
2483 3290 3.165071 CCTCTGTATTGGGTTTTTGCCT 58.835 45.455 0.00 0.00 0.00 4.75
2555 3362 2.938428 ATTCTCTGTCCCTCTCAGGT 57.062 50.000 0.00 0.00 31.93 4.00
2556 3363 1.930251 TTCTCTGTCCCTCTCAGGTG 58.070 55.000 0.00 0.00 31.93 4.00
2557 3364 0.780637 TCTCTGTCCCTCTCAGGTGT 59.219 55.000 0.00 0.00 31.93 4.16
2559 3366 1.548269 CTCTGTCCCTCTCAGGTGTTC 59.452 57.143 0.00 0.00 31.93 3.18
2560 3367 1.148027 TCTGTCCCTCTCAGGTGTTCT 59.852 52.381 0.00 0.00 31.93 3.01
2582 3391 2.910688 AAAAACAGAGGTGAGAGCGA 57.089 45.000 0.00 0.00 0.00 4.93
2649 3458 5.940192 TGAGCAACATTTTCATAAGACGT 57.060 34.783 0.00 0.00 0.00 4.34
2665 3474 9.104965 TCATAAGACGTCACTTATTTTATTGGG 57.895 33.333 19.50 0.61 39.92 4.12
2692 3503 0.338120 TGAATCCCCAATTCCCCACC 59.662 55.000 0.00 0.00 42.74 4.61
2783 3689 3.607741 TCAGAGAGTACGGGAACACTAG 58.392 50.000 0.00 0.00 0.00 2.57
2814 3720 8.099537 CCATCTGTGCAGATAATAGGAATAAGT 58.900 37.037 13.60 0.00 45.78 2.24
2906 3814 7.173390 AGCAACCTTGAGTAGTAAATTGTTCTC 59.827 37.037 0.00 0.00 0.00 2.87
3081 3997 7.923878 TGTTTACTTATGTTTTCTTTTGCCTCC 59.076 33.333 0.00 0.00 0.00 4.30
3137 4053 3.817084 CAGTTATGCATATCCACACCCTG 59.183 47.826 7.36 1.08 0.00 4.45
3138 4054 3.149196 GTTATGCATATCCACACCCTGG 58.851 50.000 7.36 0.00 42.29 4.45
3139 4055 0.479815 ATGCATATCCACACCCTGGG 59.520 55.000 12.28 12.28 41.06 4.45
3140 4056 1.529244 GCATATCCACACCCTGGGC 60.529 63.158 14.08 0.00 41.06 5.36
3141 4057 1.999634 GCATATCCACACCCTGGGCT 62.000 60.000 14.08 0.00 41.06 5.19
3143 4059 1.072331 CATATCCACACCCTGGGCTAC 59.928 57.143 14.08 0.00 41.06 3.58
3144 4060 0.043485 TATCCACACCCTGGGCTACA 59.957 55.000 14.08 0.00 41.06 2.74
3146 4062 1.063070 TCCACACCCTGGGCTACAAA 61.063 55.000 14.08 0.00 41.06 2.83
3147 4063 0.609131 CCACACCCTGGGCTACAAAG 60.609 60.000 14.08 0.00 36.18 2.77
3148 4064 0.609131 CACACCCTGGGCTACAAAGG 60.609 60.000 14.08 0.00 0.00 3.11
3149 4065 0.770557 ACACCCTGGGCTACAAAGGA 60.771 55.000 14.08 0.00 32.43 3.36
3150 4066 0.404040 CACCCTGGGCTACAAAGGAA 59.596 55.000 14.08 0.00 32.43 3.36
3151 4067 0.404426 ACCCTGGGCTACAAAGGAAC 59.596 55.000 14.08 0.00 32.43 3.62
3407 4401 1.105457 TGCTGACATTTGCCATAGCC 58.895 50.000 0.00 0.00 38.69 3.93
3424 4418 3.470645 AGCCGTAGTGTCTTTGACTTT 57.529 42.857 0.00 0.00 33.15 2.66
3534 4528 2.724977 TCGTCGAAAGCTGACTCATT 57.275 45.000 0.00 0.00 34.17 2.57
3550 4544 2.791560 CTCATTGAGCCGTCGAACATAG 59.208 50.000 0.00 0.00 0.00 2.23
3647 4641 2.408271 TTCCACAGAATGCTAGCTGG 57.592 50.000 17.23 13.88 42.53 4.85
3655 4649 4.455877 ACAGAATGCTAGCTGGTTGTAAAC 59.544 41.667 17.23 0.00 44.37 2.01
3673 4667 4.942761 AAACCTGTGCATTTCTTCATGT 57.057 36.364 0.00 0.00 0.00 3.21
3674 4668 3.928727 ACCTGTGCATTTCTTCATGTG 57.071 42.857 0.00 0.00 0.00 3.21
3675 4669 2.029649 ACCTGTGCATTTCTTCATGTGC 60.030 45.455 0.00 0.00 38.05 4.57
3676 4670 2.029739 CCTGTGCATTTCTTCATGTGCA 60.030 45.455 2.55 2.55 44.50 4.57
3765 4759 0.918799 ATACCCCATGGACAGCACCA 60.919 55.000 15.22 0.00 44.41 4.17
4223 5217 0.183014 AGATGGGCATGCCAAGAGAG 59.817 55.000 36.56 0.00 37.98 3.20
4243 5237 0.538584 TCATCGTGCTGCCTCTGATT 59.461 50.000 0.00 0.00 0.00 2.57
4267 5263 2.264794 GCCCGGCCGGATACATAG 59.735 66.667 45.44 26.84 37.50 2.23
4340 5343 9.894783 GATTTATTAAGATAGCACGAGTGAGTA 57.105 33.333 7.50 0.00 0.00 2.59
4474 5481 5.328565 TGCTGATGACCTGCTATATACTCT 58.671 41.667 0.00 0.00 40.01 3.24
4475 5482 5.417266 TGCTGATGACCTGCTATATACTCTC 59.583 44.000 0.00 0.00 40.01 3.20
4579 5590 8.947055 ATTGTGAACTGTTCTTTTAGCAAATT 57.053 26.923 20.18 2.20 0.00 1.82
4581 5592 9.862371 TTGTGAACTGTTCTTTTAGCAAATTAA 57.138 25.926 20.18 0.00 0.00 1.40
4647 5658 8.781067 TCGAACAAACTGAAATACAAATGAAG 57.219 30.769 0.00 0.00 0.00 3.02
4648 5659 8.616942 TCGAACAAACTGAAATACAAATGAAGA 58.383 29.630 0.00 0.00 0.00 2.87
4697 5709 2.557056 ACACTCGGATTCTTCGAAGTCA 59.443 45.455 23.85 12.93 36.15 3.41
4801 5813 8.627403 CATTGAGCCACAGACTGAAATAATATT 58.373 33.333 10.08 0.00 0.00 1.28
4848 5860 7.083062 AGTCCATGCCAGAATCTATAATCAA 57.917 36.000 0.00 0.00 0.00 2.57
4849 5861 7.520798 AGTCCATGCCAGAATCTATAATCAAA 58.479 34.615 0.00 0.00 0.00 2.69
4850 5862 7.664731 AGTCCATGCCAGAATCTATAATCAAAG 59.335 37.037 0.00 0.00 0.00 2.77
4851 5863 6.432162 TCCATGCCAGAATCTATAATCAAAGC 59.568 38.462 0.00 0.00 0.00 3.51
4852 5864 6.349944 CCATGCCAGAATCTATAATCAAAGCC 60.350 42.308 0.00 0.00 0.00 4.35
4853 5865 5.072741 TGCCAGAATCTATAATCAAAGCCC 58.927 41.667 0.00 0.00 0.00 5.19
4854 5866 5.072741 GCCAGAATCTATAATCAAAGCCCA 58.927 41.667 0.00 0.00 0.00 5.36
4855 5867 5.048434 GCCAGAATCTATAATCAAAGCCCAC 60.048 44.000 0.00 0.00 0.00 4.61
4856 5868 6.064060 CCAGAATCTATAATCAAAGCCCACA 58.936 40.000 0.00 0.00 0.00 4.17
4857 5869 6.547141 CCAGAATCTATAATCAAAGCCCACAA 59.453 38.462 0.00 0.00 0.00 3.33
4858 5870 7.255381 CCAGAATCTATAATCAAAGCCCACAAG 60.255 40.741 0.00 0.00 0.00 3.16
4859 5871 6.774656 AGAATCTATAATCAAAGCCCACAAGG 59.225 38.462 0.00 0.00 39.47 3.61
4912 5924 5.938004 CCTCACAAGGCAAGTTGTCAAACT 61.938 45.833 10.65 0.00 41.35 2.66
4919 5931 4.044426 GGCAAGTTGTCAAACTGTTGATC 58.956 43.478 1.68 0.00 46.15 2.92
4920 5932 4.202050 GGCAAGTTGTCAAACTGTTGATCT 60.202 41.667 1.68 0.00 46.15 2.75
4921 5933 5.008613 GGCAAGTTGTCAAACTGTTGATCTA 59.991 40.000 1.68 0.00 46.15 1.98
4922 5934 6.294176 GGCAAGTTGTCAAACTGTTGATCTAT 60.294 38.462 1.68 0.00 46.15 1.98
4923 5935 6.580041 GCAAGTTGTCAAACTGTTGATCTATG 59.420 38.462 4.48 0.00 46.15 2.23
4924 5936 6.808008 AGTTGTCAAACTGTTGATCTATGG 57.192 37.500 0.00 0.00 45.12 2.74
4925 5937 6.533730 AGTTGTCAAACTGTTGATCTATGGA 58.466 36.000 0.00 0.00 45.12 3.41
4997 6009 3.631250 GGGAATCTAATCAAAGCCCACA 58.369 45.455 0.00 0.00 34.25 4.17
5033 6046 2.198426 CACCAACCCCAAGGCAGT 59.802 61.111 0.00 0.00 36.11 4.40
5074 6454 3.204827 CAAGATCGGGGCTTGCCG 61.205 66.667 5.49 0.00 36.66 5.69
5196 6576 0.176910 GGGCTTCTCTTTCCCTCTCG 59.823 60.000 0.00 0.00 37.08 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.528370 CCGGCAGACCTCGGGTAG 61.528 72.222 0.00 0.00 42.32 3.18
14 15 3.892104 AACCGGCAGACCTCGGGTA 62.892 63.158 0.00 0.00 45.54 3.69
18 19 0.037605 ACTAAAACCGGCAGACCTCG 60.038 55.000 0.00 0.00 0.00 4.63
19 20 2.614779 GTACTAAAACCGGCAGACCTC 58.385 52.381 0.00 0.00 0.00 3.85
20 21 1.277273 GGTACTAAAACCGGCAGACCT 59.723 52.381 0.00 0.00 0.00 3.85
21 22 1.730501 GGTACTAAAACCGGCAGACC 58.269 55.000 0.00 0.00 0.00 3.85
29 30 7.263496 AGATCATAAGTGTCGGTACTAAAACC 58.737 38.462 0.00 0.00 36.08 3.27
30 31 7.434602 GGAGATCATAAGTGTCGGTACTAAAAC 59.565 40.741 0.00 0.00 0.00 2.43
31 32 7.123098 TGGAGATCATAAGTGTCGGTACTAAAA 59.877 37.037 0.00 0.00 0.00 1.52
32 33 6.604396 TGGAGATCATAAGTGTCGGTACTAAA 59.396 38.462 0.00 0.00 0.00 1.85
33 34 6.124340 TGGAGATCATAAGTGTCGGTACTAA 58.876 40.000 0.00 0.00 0.00 2.24
34 35 5.687780 TGGAGATCATAAGTGTCGGTACTA 58.312 41.667 0.00 0.00 0.00 1.82
35 36 4.533815 TGGAGATCATAAGTGTCGGTACT 58.466 43.478 0.00 0.00 0.00 2.73
36 37 4.913335 TGGAGATCATAAGTGTCGGTAC 57.087 45.455 0.00 0.00 0.00 3.34
37 38 4.280929 CCATGGAGATCATAAGTGTCGGTA 59.719 45.833 5.56 0.00 34.12 4.02
101 102 0.748005 GGCGGTACACCATCTGCAAT 60.748 55.000 0.00 0.00 37.65 3.56
169 170 3.650369 GAAAGAACTTCGCGCCCA 58.350 55.556 0.00 0.00 0.00 5.36
335 364 7.257722 CAGGTGTTTAGTCAAATGTTTGAGTT 58.742 34.615 17.98 8.70 45.84 3.01
336 365 6.680378 GCAGGTGTTTAGTCAAATGTTTGAGT 60.680 38.462 17.19 17.19 46.80 3.41
338 367 5.451242 GGCAGGTGTTTAGTCAAATGTTTGA 60.451 40.000 4.16 4.16 44.31 2.69
339 368 4.744631 GGCAGGTGTTTAGTCAAATGTTTG 59.255 41.667 0.00 0.00 39.48 2.93
340 369 4.404073 TGGCAGGTGTTTAGTCAAATGTTT 59.596 37.500 0.00 0.00 0.00 2.83
389 418 4.101448 CCTTCTCACCCCTGCCGG 62.101 72.222 0.00 0.00 0.00 6.13
414 460 2.897350 CAAGAATCCCTCCGCGGC 60.897 66.667 23.51 4.02 0.00 6.53
416 462 2.203070 CCCAAGAATCCCTCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
521 570 4.690719 ATGGTTTGACGCCGCCGA 62.691 61.111 0.00 0.00 38.29 5.54
533 582 0.904649 TCATCCGCACTCTCATGGTT 59.095 50.000 0.00 0.00 0.00 3.67
542 591 2.162681 CCCTTTCTTTTCATCCGCACT 58.837 47.619 0.00 0.00 0.00 4.40
621 674 4.262249 GGACATTAGCCACATAGGACTCTC 60.262 50.000 0.00 0.00 41.22 3.20
660 715 4.681744 CAAACTGCAAGCAAACTTAGGAA 58.318 39.130 0.00 0.00 37.60 3.36
699 755 2.149722 ATCCATCTACGGACCGGTACG 61.150 57.143 37.10 37.10 45.16 3.67
700 756 1.268899 CATCCATCTACGGACCGGTAC 59.731 57.143 20.00 7.05 38.07 3.34
701 757 1.143481 TCATCCATCTACGGACCGGTA 59.857 52.381 20.00 7.38 38.07 4.02
711 767 6.710278 TCCAATGCGATATTTCATCCATCTA 58.290 36.000 0.00 0.00 0.00 1.98
723 779 5.125257 TGTGTTTTGTCATCCAATGCGATAT 59.875 36.000 0.00 0.00 31.81 1.63
793 852 3.127030 GGGAGTTCATTCTGCCGTTTAAG 59.873 47.826 0.00 0.00 36.31 1.85
1176 1235 6.646653 GTGCATCGACCAGATCAAATTATAGA 59.353 38.462 0.00 0.00 37.52 1.98
1434 1493 0.598065 GAAAGGGACAATGCAGCGTT 59.402 50.000 0.00 0.00 0.00 4.84
1619 1678 5.215160 CGTTTCTCCTGTTCAAATTCCTTG 58.785 41.667 0.00 0.00 36.25 3.61
1638 1697 4.743493 ACACAACTTCAAAATGAGCGTTT 58.257 34.783 0.00 0.00 0.00 3.60
1651 1710 5.741982 AGTTGAAATTGCGTTACACAACTTC 59.258 36.000 0.00 1.09 41.95 3.01
1664 1723 6.768029 TTTTCTGCACATAGTTGAAATTGC 57.232 33.333 0.00 0.00 0.00 3.56
1666 1725 7.599998 GGACATTTTCTGCACATAGTTGAAATT 59.400 33.333 0.00 0.00 0.00 1.82
1667 1726 7.092716 GGACATTTTCTGCACATAGTTGAAAT 58.907 34.615 0.00 0.00 0.00 2.17
1669 1728 5.048083 GGGACATTTTCTGCACATAGTTGAA 60.048 40.000 0.00 0.00 0.00 2.69
1670 1729 4.458989 GGGACATTTTCTGCACATAGTTGA 59.541 41.667 0.00 0.00 0.00 3.18
1671 1730 4.460382 AGGGACATTTTCTGCACATAGTTG 59.540 41.667 0.00 0.00 0.00 3.16
1672 1731 4.666512 AGGGACATTTTCTGCACATAGTT 58.333 39.130 0.00 0.00 0.00 2.24
2081 2882 0.524862 CAACCAACAGATGCAGGCTC 59.475 55.000 0.00 0.00 0.00 4.70
2131 2932 1.353358 TCTCGACTTCCACTACCTCCA 59.647 52.381 0.00 0.00 0.00 3.86
2153 2954 0.249868 CCAGCAAACTCGAGACCACA 60.250 55.000 21.68 0.00 0.00 4.17
2219 3020 2.505982 CTACGGCCCCACCTCATG 59.494 66.667 0.00 0.00 35.61 3.07
2247 3048 1.743623 CGCCGGAATGCCACTAACA 60.744 57.895 5.05 0.00 0.00 2.41
2251 3052 4.722700 AAGCGCCGGAATGCCACT 62.723 61.111 5.05 0.00 0.00 4.00
2273 3074 2.607750 ATGACAGACCCCACCGCT 60.608 61.111 0.00 0.00 0.00 5.52
2311 3114 4.675146 GCACACGATTGATTAAGGCACAAT 60.675 41.667 0.00 0.00 37.03 2.71
2400 3206 3.244078 ACACACACCACACGACTGATAAT 60.244 43.478 0.00 0.00 0.00 1.28
2425 3231 0.539518 AACTGGCAAAAACCCCACAC 59.460 50.000 0.00 0.00 0.00 3.82
2426 3232 1.280457 AAACTGGCAAAAACCCCACA 58.720 45.000 0.00 0.00 0.00 4.17
2427 3233 2.411628 AAAACTGGCAAAAACCCCAC 57.588 45.000 0.00 0.00 0.00 4.61
2428 3234 2.573915 AGAAAAACTGGCAAAAACCCCA 59.426 40.909 0.00 0.00 0.00 4.96
2429 3235 3.202906 GAGAAAAACTGGCAAAAACCCC 58.797 45.455 0.00 0.00 0.00 4.95
2430 3236 3.867857 TGAGAAAAACTGGCAAAAACCC 58.132 40.909 0.00 0.00 0.00 4.11
2441 3247 4.583073 AGGCACGGTTAATTGAGAAAAACT 59.417 37.500 0.00 0.00 0.00 2.66
2471 3277 2.252714 GGATAACCAGGCAAAAACCCA 58.747 47.619 0.00 0.00 35.97 4.51
2483 3290 3.849563 CCGGTTAATCAGGGATAACCA 57.150 47.619 13.39 0.00 43.89 3.67
2574 3383 6.372937 CCTACAGAATAGATATGTCGCTCTCA 59.627 42.308 0.00 0.00 0.00 3.27
2577 3386 6.503589 ACCTACAGAATAGATATGTCGCTC 57.496 41.667 0.00 0.00 0.00 5.03
2649 3458 7.726291 TCAACCTTGACCCAATAAAATAAGTGA 59.274 33.333 0.00 0.00 31.01 3.41
2660 3469 2.559705 GGGGATTCAACCTTGACCCAAT 60.560 50.000 13.23 0.00 42.41 3.16
2665 3474 3.195610 GGAATTGGGGATTCAACCTTGAC 59.804 47.826 1.72 0.00 44.91 3.18
2761 3667 3.088789 AGTGTTCCCGTACTCTCTGAT 57.911 47.619 0.00 0.00 0.00 2.90
2783 3689 2.627515 TATCTGCACAGATGGGAAGC 57.372 50.000 20.79 0.00 46.80 3.86
2852 3759 9.003658 AGGAACAATTTCAGACATTGTAAGTAG 57.996 33.333 14.10 0.00 42.80 2.57
2906 3814 7.042925 GGTGAGGCGTTTACTATAACATAAGTG 60.043 40.741 0.00 0.00 0.00 3.16
2919 3827 4.142227 TGAAGAGATAGGTGAGGCGTTTAC 60.142 45.833 0.00 0.00 0.00 2.01
2923 3831 1.751924 GTGAAGAGATAGGTGAGGCGT 59.248 52.381 0.00 0.00 0.00 5.68
3144 4060 5.169836 CTTTGACTACGCAAAGTTCCTTT 57.830 39.130 0.00 0.00 45.97 3.11
3152 4068 3.527533 ACTGACACTTTGACTACGCAAA 58.472 40.909 0.00 0.00 36.43 3.68
3153 4069 3.120792 GACTGACACTTTGACTACGCAA 58.879 45.455 0.00 0.00 0.00 4.85
3155 4071 3.014604 AGACTGACACTTTGACTACGC 57.985 47.619 0.00 0.00 0.00 4.42
3156 4072 8.182227 TCATATAAGACTGACACTTTGACTACG 58.818 37.037 0.00 0.00 0.00 3.51
3157 4073 9.291664 GTCATATAAGACTGACACTTTGACTAC 57.708 37.037 0.83 0.00 41.13 2.73
3387 4381 1.202336 GGCTATGGCAAATGTCAGCAC 60.202 52.381 2.58 0.00 40.87 4.40
3407 4401 9.488124 GAGTATAGTAAAGTCAAAGACACTACG 57.512 37.037 0.00 0.00 34.60 3.51
3454 4448 9.719355 ATGAACTAACAATGTATACAGACACAA 57.281 29.630 11.91 0.00 30.52 3.33
3488 4482 1.876849 AGCAGGATGACCATGAGACT 58.123 50.000 0.00 0.00 39.69 3.24
3534 4528 1.170442 TGTCTATGTTCGACGGCTCA 58.830 50.000 0.00 0.00 34.17 4.26
3550 4544 7.073342 AGACAAAAATTAGAAGCCGTATGTC 57.927 36.000 0.00 0.00 35.03 3.06
3647 4641 5.587289 TGAAGAAATGCACAGGTTTACAAC 58.413 37.500 0.00 0.00 0.00 3.32
3655 4649 2.029739 TGCACATGAAGAAATGCACAGG 60.030 45.455 0.00 0.00 42.92 4.00
3673 4667 0.676466 CCAGTTCGGCCTAACATGCA 60.676 55.000 21.13 0.00 0.00 3.96
3674 4668 0.392461 TCCAGTTCGGCCTAACATGC 60.392 55.000 21.13 0.00 33.14 4.06
3675 4669 1.942657 CATCCAGTTCGGCCTAACATG 59.057 52.381 21.13 15.13 33.14 3.21
3676 4670 1.747206 GCATCCAGTTCGGCCTAACAT 60.747 52.381 21.13 4.46 33.14 2.71
3765 4759 0.895100 AGACGGCATGGCAAACACAT 60.895 50.000 20.37 0.00 0.00 3.21
4223 5217 0.179089 ATCAGAGGCAGCACGATGAC 60.179 55.000 0.00 0.00 0.00 3.06
4257 5253 1.067974 TGTTGGGCGTCTATGTATCCG 59.932 52.381 0.00 0.00 0.00 4.18
4267 5263 1.098712 TGTCTTGGTTGTTGGGCGTC 61.099 55.000 0.00 0.00 0.00 5.19
4340 5343 3.307339 GGAGTTCAATCTCAGCCTCACTT 60.307 47.826 0.00 0.00 36.30 3.16
4474 5481 7.942341 ACAAACCTGTGAAATTAATACCTCTGA 59.058 33.333 0.00 0.00 33.30 3.27
4475 5482 8.110860 ACAAACCTGTGAAATTAATACCTCTG 57.889 34.615 0.00 0.00 33.30 3.35
4697 5709 5.486526 CAAAAGGTGAAGCTAGAGATGACT 58.513 41.667 0.00 0.00 0.00 3.41
4801 5813 0.320771 GCGGCTCTTCAGAACCTTCA 60.321 55.000 0.00 0.00 0.00 3.02
4851 5863 1.331214 ACATGTTCTTGCCTTGTGGG 58.669 50.000 0.00 0.00 38.36 4.61
4852 5864 2.101249 ACAACATGTTCTTGCCTTGTGG 59.899 45.455 8.48 0.00 0.00 4.17
4853 5865 3.117794 CACAACATGTTCTTGCCTTGTG 58.882 45.455 8.48 8.33 34.35 3.33
4854 5866 2.101249 CCACAACATGTTCTTGCCTTGT 59.899 45.455 8.48 0.00 0.00 3.16
4855 5867 2.101249 ACCACAACATGTTCTTGCCTTG 59.899 45.455 8.48 0.00 0.00 3.61
4856 5868 2.387757 ACCACAACATGTTCTTGCCTT 58.612 42.857 8.48 0.00 0.00 4.35
4857 5869 2.071778 ACCACAACATGTTCTTGCCT 57.928 45.000 8.48 0.00 0.00 4.75
4858 5870 2.472816 CAACCACAACATGTTCTTGCC 58.527 47.619 8.48 0.00 0.00 4.52
4859 5871 2.472816 CCAACCACAACATGTTCTTGC 58.527 47.619 8.48 0.00 0.00 4.01
4860 5872 2.224018 CCCCAACCACAACATGTTCTTG 60.224 50.000 8.48 8.83 0.00 3.02
4861 5873 2.038659 CCCCAACCACAACATGTTCTT 58.961 47.619 8.48 0.00 0.00 2.52
4862 5874 1.216678 TCCCCAACCACAACATGTTCT 59.783 47.619 8.48 0.00 0.00 3.01
4912 5924 4.219725 TCGGCGATAATCCATAGATCAACA 59.780 41.667 4.99 0.00 0.00 3.33
4919 5931 3.914312 ACAGTTCGGCGATAATCCATAG 58.086 45.455 11.76 0.00 0.00 2.23
4920 5932 3.319689 TGACAGTTCGGCGATAATCCATA 59.680 43.478 11.76 0.00 0.00 2.74
4921 5933 2.102420 TGACAGTTCGGCGATAATCCAT 59.898 45.455 11.76 0.00 0.00 3.41
4922 5934 1.478916 TGACAGTTCGGCGATAATCCA 59.521 47.619 11.76 3.98 0.00 3.41
4923 5935 2.128035 CTGACAGTTCGGCGATAATCC 58.872 52.381 11.76 1.05 0.00 3.01
4924 5936 2.789893 GACTGACAGTTCGGCGATAATC 59.210 50.000 11.76 7.21 0.00 1.75
4925 5937 2.165641 TGACTGACAGTTCGGCGATAAT 59.834 45.455 11.76 0.00 0.00 1.28
4997 6009 0.674895 GGGCAGCGAAGAAGTGTCAT 60.675 55.000 0.00 0.00 0.00 3.06
5033 6046 2.542020 TCGGTGTCTCATGCTTTGAA 57.458 45.000 0.00 0.00 32.78 2.69
5074 6454 0.326264 ATATTGGAGCCCCGCAGATC 59.674 55.000 0.00 0.00 34.29 2.75
5179 6559 1.822371 ACTCGAGAGGGAAAGAGAAGC 59.178 52.381 21.68 0.00 34.98 3.86
5196 6576 1.308783 GCCCTAGCTGCCACAAACTC 61.309 60.000 0.00 0.00 35.50 3.01


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

AutoCloner maintained by Alex Coulton.