Multiple sequence alignment - TraesCS7B01G412700

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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 TraesCS7B01G412700 chr7B 100.000 6466 0 0 1 6466 680275900 680282365 0.000000e+00 11941.0
1 TraesCS7B01G412700 chr7B 88.009 467 43 6 4370 4836 680277648 680278101 2.050000e-149 540.0
2 TraesCS7B01G412700 chr7B 88.009 467 43 6 1749 2202 680280269 680280735 2.050000e-149 540.0
3 TraesCS7B01G412700 chr7B 81.520 487 36 35 3220 3691 680276687 680277134 1.030000e-92 351.0
4 TraesCS7B01G412700 chr7B 81.520 487 36 35 788 1235 680279119 680279590 1.030000e-92 351.0
5 TraesCS7B01G412700 chr7B 95.652 138 4 2 4234 4371 138719402 138719537 3.030000e-53 220.0
6 TraesCS7B01G412700 chr7B 83.146 89 8 6 3121 3204 713790052 713789966 2.500000e-09 75.0
7 TraesCS7B01G412700 chr7B 84.416 77 8 3 3131 3204 713789969 713790044 8.990000e-09 73.1
8 TraesCS7B01G412700 chr7A 91.831 1469 92 17 4370 5834 692952599 692954043 0.000000e+00 2023.0
9 TraesCS7B01G412700 chr7A 86.509 1349 90 32 925 2210 692944897 692946216 0.000000e+00 1399.0
10 TraesCS7B01G412700 chr7A 90.389 926 81 6 1 922 692943212 692944133 0.000000e+00 1210.0
11 TraesCS7B01G412700 chr7A 90.749 908 52 12 3336 4233 692951696 692952581 0.000000e+00 1182.0
12 TraesCS7B01G412700 chr7A 84.043 1222 156 22 4370 5573 692945754 692946954 0.000000e+00 1140.0
13 TraesCS7B01G412700 chr7A 84.531 640 49 35 3378 4009 692944900 692945497 7.220000e-164 588.0
14 TraesCS7B01G412700 chr7A 83.655 673 42 31 893 1514 692951709 692952364 7.270000e-159 571.0
15 TraesCS7B01G412700 chr7A 88.753 489 24 15 2208 2695 692946860 692947318 2.620000e-158 569.0
16 TraesCS7B01G412700 chr7A 82.574 505 65 16 1704 2202 692952557 692953044 2.160000e-114 424.0
17 TraesCS7B01G412700 chr7A 86.423 383 34 5 6100 6466 692954671 692955051 2.810000e-108 403.0
18 TraesCS7B01G412700 chr7A 91.964 224 12 5 2703 2924 692947402 692947621 6.300000e-80 309.0
19 TraesCS7B01G412700 chr7A 86.139 101 11 2 2208 2305 692953684 692953784 8.870000e-19 106.0
20 TraesCS7B01G412700 chr7D 89.252 1498 133 20 4370 5851 601287671 601286186 0.000000e+00 1849.0
21 TraesCS7B01G412700 chr7D 89.343 1492 131 20 4370 5845 601310513 601311992 0.000000e+00 1849.0
22 TraesCS7B01G412700 chr7D 86.117 1030 71 25 3240 4234 601288682 601287690 0.000000e+00 1044.0
23 TraesCS7B01G412700 chr7D 86.117 1030 71 25 3240 4234 601309502 601310494 0.000000e+00 1044.0
24 TraesCS7B01G412700 chr7D 82.321 741 62 40 893 1590 601288573 601287859 4.350000e-161 579.0
25 TraesCS7B01G412700 chr7D 83.604 677 50 36 893 1526 601309611 601310269 4.350000e-161 579.0
26 TraesCS7B01G412700 chr7D 86.998 523 53 8 1693 2202 601287726 601287206 5.620000e-160 575.0
27 TraesCS7B01G412700 chr7D 86.998 523 53 8 1693 2202 601310458 601310978 5.620000e-160 575.0
28 TraesCS7B01G412700 chr7D 80.887 654 106 16 1 640 385424554 385425202 1.250000e-136 497.0
29 TraesCS7B01G412700 chr7D 85.994 357 43 5 1 354 582141455 582141807 6.120000e-100 375.0
30 TraesCS7B01G412700 chr7D 85.393 178 23 1 3803 3977 101077843 101078020 1.430000e-41 182.0
31 TraesCS7B01G412700 chr6B 80.684 673 100 12 1 646 216698994 216698325 4.500000e-136 496.0
32 TraesCS7B01G412700 chr6B 76.540 682 121 27 1 652 656545381 656544709 2.890000e-88 337.0
33 TraesCS7B01G412700 chr6B 95.620 137 5 1 4235 4371 592981347 592981482 1.090000e-52 219.0
34 TraesCS7B01G412700 chr6B 94.366 142 6 2 4231 4371 29276815 29276675 3.930000e-52 217.0
35 TraesCS7B01G412700 chr2D 80.357 672 103 13 3 646 187524253 187523583 3.510000e-132 483.0
36 TraesCS7B01G412700 chr4A 87.324 355 44 1 1 354 86929766 86930120 7.810000e-109 405.0
37 TraesCS7B01G412700 chr4A 86.761 355 46 1 1 354 689572910 689573264 1.690000e-105 394.0
38 TraesCS7B01G412700 chr6D 82.452 416 58 13 1 402 308909182 308908768 3.710000e-92 350.0
39 TraesCS7B01G412700 chr6D 80.456 307 55 3 344 646 3970520 3970215 5.040000e-56 230.0
40 TraesCS7B01G412700 chr2B 83.728 338 49 4 1 336 424494225 424494558 1.350000e-81 315.0
41 TraesCS7B01G412700 chr5B 97.122 139 2 2 4235 4371 477613767 477613905 3.900000e-57 233.0
42 TraesCS7B01G412700 chr5B 95.683 139 4 1 4231 4369 269950862 269950998 8.440000e-54 222.0
43 TraesCS7B01G412700 chr5B 81.395 86 8 5 3131 3208 621238725 621238810 5.410000e-06 63.9
44 TraesCS7B01G412700 chr1A 96.377 138 4 1 4234 4371 566336056 566335920 6.520000e-55 226.0
45 TraesCS7B01G412700 chr5A 95.683 139 4 2 4231 4369 540395980 540396116 8.440000e-54 222.0
46 TraesCS7B01G412700 chr2A 95.652 138 5 1 4234 4371 739853253 739853117 3.030000e-53 220.0
47 TraesCS7B01G412700 chr1B 92.806 139 10 0 4233 4371 118637275 118637413 1.100000e-47 202.0
48 TraesCS7B01G412700 chr3B 87.838 74 4 3 3131 3204 779032019 779032087 1.490000e-11 82.4
49 TraesCS7B01G412700 chr4B 84.615 78 9 2 3131 3208 401110998 401111072 2.500000e-09 75.0
50 TraesCS7B01G412700 chr6A 100.000 33 0 0 3175 3207 356209024 356208992 1.950000e-05 62.1
51 TraesCS7B01G412700 chr6A 97.059 34 1 0 3175 3208 567941136 567941103 2.520000e-04 58.4
52 TraesCS7B01G412700 chr4D 94.737 38 2 0 3170 3207 436892686 436892723 7.000000e-05 60.2
53 TraesCS7B01G412700 chr5D 92.500 40 2 1 3170 3208 30555089 30555050 1.000000e-03 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 TraesCS7B01G412700 chr7B 680275900 680282365 6465 False 11941.000000 11941 100.000000 1 6466 1 chr7B.!!$F2 6465
1 TraesCS7B01G412700 chr7B 680276687 680280735 4048 False 445.500000 540 84.764500 788 4836 4 chr7B.!!$F4 4048
2 TraesCS7B01G412700 chr7A 692943212 692947621 4409 False 869.166667 1399 87.698167 1 5573 6 chr7A.!!$F1 5572
3 TraesCS7B01G412700 chr7A 692951696 692955051 3355 False 784.833333 2023 86.895167 893 6466 6 chr7A.!!$F2 5573
4 TraesCS7B01G412700 chr7D 601286186 601288682 2496 True 1011.750000 1849 86.172000 893 5851 4 chr7D.!!$R1 4958
5 TraesCS7B01G412700 chr7D 601309502 601311992 2490 False 1011.750000 1849 86.515500 893 5845 4 chr7D.!!$F4 4952
6 TraesCS7B01G412700 chr7D 385424554 385425202 648 False 497.000000 497 80.887000 1 640 1 chr7D.!!$F2 639
7 TraesCS7B01G412700 chr6B 216698325 216698994 669 True 496.000000 496 80.684000 1 646 1 chr6B.!!$R2 645
8 TraesCS7B01G412700 chr6B 656544709 656545381 672 True 337.000000 337 76.540000 1 652 1 chr6B.!!$R3 651
9 TraesCS7B01G412700 chr2D 187523583 187524253 670 True 483.000000 483 80.357000 3 646 1 chr2D.!!$R1 643

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
192 194 0.465705 GAGGAGGACCGATCATGCAA 59.534 55.000 0.00 0.0 41.83 4.08 F
324 329 0.687354 ACGACTCCAAGCACCAGATT 59.313 50.000 0.00 0.0 0.00 2.40 F
424 456 1.226974 GTTGCTCGAGATGCCGCTA 60.227 57.895 18.75 0.0 0.00 4.26 F
657 690 1.271163 GGGTGATCTGTTTTCCGTCCA 60.271 52.381 0.00 0.0 0.00 4.02 F
5229 6930 0.108804 GGGTTCATCGTCGAGCTTCA 60.109 55.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4922 6582 1.825622 GGCAGCATGAAGTAGGGCC 60.826 63.158 0.0 0.00 39.69 5.80 R
5138 6798 0.250295 TGTTGCAGGGGAAGAACTCG 60.250 55.000 0.0 0.00 0.00 4.18 R
5210 6870 0.108804 TGAAGCTCGACGATGAACCC 60.109 55.000 0.0 0.00 0.00 4.11 R
5285 6986 1.542472 CTGTCATGCACCAATTCAGCA 59.458 47.619 0.0 0.00 43.14 4.41 R
6068 8059 0.037877 AGCTGCAAAGCACTGGAGAT 59.962 50.000 10.2 1.47 36.94 2.75 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
52 54 4.022416 TGTCAACAAACAACAGAGCTTTGT 60.022 37.500 3.61 3.61 39.30 2.83
75 77 4.891037 GCCCTCCTGGAGCCATGC 62.891 72.222 18.51 12.98 35.39 4.06
97 99 1.880796 TTGATATGGACGCGCACGG 60.881 57.895 5.73 0.00 46.04 4.94
158 160 1.944024 CGGCAGTAGTTTTGGAACACA 59.056 47.619 0.00 0.00 39.29 3.72
192 194 0.465705 GAGGAGGACCGATCATGCAA 59.534 55.000 0.00 0.00 41.83 4.08
301 306 4.767255 GGCCCTCGCTGTCCACAG 62.767 72.222 2.06 2.06 46.40 3.66
324 329 0.687354 ACGACTCCAAGCACCAGATT 59.313 50.000 0.00 0.00 0.00 2.40
424 456 1.226974 GTTGCTCGAGATGCCGCTA 60.227 57.895 18.75 0.00 0.00 4.26
575 608 4.426313 GGCGTGGAAAGGGGGAGG 62.426 72.222 0.00 0.00 0.00 4.30
577 610 3.330720 CGTGGAAAGGGGGAGGCT 61.331 66.667 0.00 0.00 0.00 4.58
578 611 1.993391 CGTGGAAAGGGGGAGGCTA 60.993 63.158 0.00 0.00 0.00 3.93
650 683 2.567615 AGCGACTAGGGTGATCTGTTTT 59.432 45.455 0.00 0.00 0.00 2.43
655 688 2.474410 AGGGTGATCTGTTTTCCGTC 57.526 50.000 0.00 0.00 0.00 4.79
657 690 1.271163 GGGTGATCTGTTTTCCGTCCA 60.271 52.381 0.00 0.00 0.00 4.02
684 717 2.809174 CACGGCGACTTCGATGCA 60.809 61.111 16.62 0.00 43.02 3.96
691 724 2.193447 GCGACTTCGATGCATTGTCTA 58.807 47.619 13.73 0.65 43.02 2.59
706 739 8.902540 TGCATTGTCTATTACGAATAGGAAAT 57.097 30.769 11.96 9.90 40.97 2.17
727 760 7.554118 GGAAATGATGGTCTTCTCACAATCTTA 59.446 37.037 0.00 0.00 0.00 2.10
759 792 5.007823 TGGTCGTGTACTTTGGTTTATTGTG 59.992 40.000 0.00 0.00 0.00 3.33
4922 6582 1.677633 CCCCGGTAACCAAGCAAGG 60.678 63.158 0.00 0.00 0.00 3.61
5013 6673 1.812922 CTGCTCCGCGCTCATCTTT 60.813 57.895 5.56 0.00 40.11 2.52
5135 6795 4.770010 CCTTGAAGTCCTCAGAGAGTAAGT 59.230 45.833 0.00 0.00 34.81 2.24
5138 6798 5.254901 TGAAGTCCTCAGAGAGTAAGTACC 58.745 45.833 0.00 0.00 0.00 3.34
5229 6930 0.108804 GGGTTCATCGTCGAGCTTCA 60.109 55.000 0.00 0.00 0.00 3.02
5242 6943 2.789092 CGAGCTTCACATGAAATTCGGC 60.789 50.000 0.00 6.97 36.83 5.54
5285 6986 1.302752 TGCTGCAATCGGCTGACTT 60.303 52.632 0.00 0.00 44.83 3.01
5315 7016 2.421107 GGTGCATGACAGGACTGATGAT 60.421 50.000 6.29 0.00 0.00 2.45
5482 7183 4.090761 AGTGATGAACTCAATGGTGTGT 57.909 40.909 0.00 0.00 31.64 3.72
5504 7205 5.602561 TGTAGGGCAAGTGATCATAGTATGT 59.397 40.000 9.94 0.00 0.00 2.29
5699 7400 4.940463 TCCATGTAACCTAATACACGAGC 58.060 43.478 0.00 0.00 38.53 5.03
5703 7404 6.641314 CCATGTAACCTAATACACGAGCTAAG 59.359 42.308 0.00 0.00 38.53 2.18
5718 7421 4.511454 CGAGCTAAGCATATAAAGGCACAA 59.489 41.667 0.00 0.00 33.96 3.33
5719 7422 5.333645 CGAGCTAAGCATATAAAGGCACAAG 60.334 44.000 0.00 0.00 33.96 3.16
5721 7424 6.591935 AGCTAAGCATATAAAGGCACAAGTA 58.408 36.000 0.00 0.00 33.96 2.24
5729 7432 9.612620 GCATATAAAGGCACAAGTATTTATCAC 57.387 33.333 0.00 0.00 31.93 3.06
5731 7434 7.859325 ATAAAGGCACAAGTATTTATCACGT 57.141 32.000 0.00 0.00 0.00 4.49
5738 7441 6.955963 GCACAAGTATTTATCACGTCAAAGAG 59.044 38.462 0.00 0.00 0.00 2.85
5768 7472 3.490249 CCAGCACATTTACCATGCTCATG 60.490 47.826 2.97 2.97 46.68 3.07
5793 7497 6.702716 TCAACTTGTTTCTACCCGAAAAAT 57.297 33.333 0.00 0.00 42.87 1.82
5818 7522 0.310854 GCCCTGGACACGAAAAACAG 59.689 55.000 0.00 0.00 0.00 3.16
5831 7535 3.312421 CGAAAAACAGCAGGAAACAGAGA 59.688 43.478 0.00 0.00 0.00 3.10
5845 7549 3.550437 ACAGAGACCCATGCAATACTC 57.450 47.619 0.00 0.00 0.00 2.59
5846 7550 2.171448 ACAGAGACCCATGCAATACTCC 59.829 50.000 0.00 0.00 0.00 3.85
5851 7555 1.640670 ACCCATGCAATACTCCCAACT 59.359 47.619 0.00 0.00 0.00 3.16
5852 7556 2.301346 CCCATGCAATACTCCCAACTC 58.699 52.381 0.00 0.00 0.00 3.01
5853 7557 2.301346 CCATGCAATACTCCCAACTCC 58.699 52.381 0.00 0.00 0.00 3.85
5856 7560 2.265367 TGCAATACTCCCAACTCCAGA 58.735 47.619 0.00 0.00 0.00 3.86
5869 7573 5.312079 CCAACTCCAGATTCTTTCTTCAGT 58.688 41.667 0.00 0.00 29.93 3.41
5874 7606 5.928976 TCCAGATTCTTTCTTCAGTCACAA 58.071 37.500 0.00 0.00 29.93 3.33
5888 7620 7.967854 TCTTCAGTCACAAAACTGTGTTAATTG 59.032 33.333 5.25 0.00 45.57 2.32
5889 7621 6.559810 TCAGTCACAAAACTGTGTTAATTGG 58.440 36.000 5.25 0.00 45.57 3.16
5933 7665 6.655930 ACTTTAGGAGTTATTATGGCCGAAA 58.344 36.000 0.00 0.00 33.92 3.46
5951 7683 1.242076 AATGCACACTGAGCAACTCC 58.758 50.000 5.19 0.00 46.27 3.85
5952 7684 0.109153 ATGCACACTGAGCAACTCCA 59.891 50.000 5.19 0.00 46.27 3.86
5954 7686 0.533755 GCACACTGAGCAACTCCAGT 60.534 55.000 0.00 0.00 0.00 4.00
5955 7687 1.959042 CACACTGAGCAACTCCAGTT 58.041 50.000 0.00 0.00 39.12 3.16
5994 7985 5.337169 GCGATATAGCTCCTGATCTTTTCCT 60.337 44.000 0.00 0.00 0.00 3.36
6053 8044 4.169452 TCCAGGGGACTTGGATGG 57.831 61.111 0.00 0.00 40.21 3.51
6055 8046 0.477597 TCCAGGGGACTTGGATGGTT 60.478 55.000 0.00 0.00 40.21 3.67
6056 8047 0.323725 CCAGGGGACTTGGATGGTTG 60.324 60.000 0.00 0.00 40.21 3.77
6057 8048 0.323725 CAGGGGACTTGGATGGTTGG 60.324 60.000 0.00 0.00 40.21 3.77
6059 8050 0.323451 GGGGACTTGGATGGTTGGTC 60.323 60.000 0.00 0.00 0.00 4.02
6063 8054 0.606401 ACTTGGATGGTTGGTCTGCG 60.606 55.000 0.00 0.00 0.00 5.18
6064 8055 1.303236 TTGGATGGTTGGTCTGCGG 60.303 57.895 0.00 0.00 0.00 5.69
6066 8057 2.040544 GGATGGTTGGTCTGCGGTG 61.041 63.158 0.00 0.00 0.00 4.94
6067 8058 2.672996 ATGGTTGGTCTGCGGTGC 60.673 61.111 0.00 0.00 0.00 5.01
6068 8059 3.490031 ATGGTTGGTCTGCGGTGCA 62.490 57.895 0.00 0.00 36.92 4.57
6069 8060 2.672996 GGTTGGTCTGCGGTGCAT 60.673 61.111 0.00 0.00 38.13 3.96
6074 8102 2.265739 GTCTGCGGTGCATCTCCA 59.734 61.111 0.00 0.00 38.13 3.86
6080 8108 1.376424 CGGTGCATCTCCAGTGCTT 60.376 57.895 0.00 0.00 42.92 3.91
6110 8138 2.229792 GTCAGTTCATTGGCTTGTGGA 58.770 47.619 0.00 0.00 0.00 4.02
6111 8139 2.030805 GTCAGTTCATTGGCTTGTGGAC 60.031 50.000 0.00 0.00 0.00 4.02
6112 8140 2.158623 TCAGTTCATTGGCTTGTGGACT 60.159 45.455 0.00 0.00 0.00 3.85
6113 8141 2.030540 CAGTTCATTGGCTTGTGGACTG 60.031 50.000 10.03 10.03 0.00 3.51
6114 8142 0.961019 TTCATTGGCTTGTGGACTGC 59.039 50.000 0.00 0.00 0.00 4.40
6115 8143 0.895100 TCATTGGCTTGTGGACTGCC 60.895 55.000 0.00 0.00 46.26 4.85
6127 8211 1.202989 TGGACTGCCAACCTGCAAATA 60.203 47.619 0.00 0.00 42.49 1.40
6156 8240 1.065126 GTTCTGCCTACCTCCAGCAAT 60.065 52.381 0.00 0.00 35.79 3.56
6173 8257 2.096069 GCAATACACAGGATGCTATGCG 60.096 50.000 0.00 0.00 42.53 4.73
6174 8258 2.462456 ATACACAGGATGCTATGCGG 57.538 50.000 0.00 0.00 42.53 5.69
6180 8264 0.319728 AGGATGCTATGCGGCTACAG 59.680 55.000 0.00 0.00 0.00 2.74
6224 8322 1.154225 GCCGTTTCTTCATGTGGCG 60.154 57.895 0.00 0.00 32.14 5.69
6227 8325 1.202065 CCGTTTCTTCATGTGGCGATG 60.202 52.381 0.00 0.00 0.00 3.84
6237 8337 2.045045 TGGCGATGGCTTTGGGAG 60.045 61.111 0.00 0.00 39.81 4.30
6242 8342 1.950484 GCGATGGCTTTGGGAGAGAAA 60.950 52.381 0.00 0.00 35.83 2.52
6247 8347 1.073923 GGCTTTGGGAGAGAAACCTCA 59.926 52.381 0.00 0.00 34.94 3.86
6251 8351 1.056660 TGGGAGAGAAACCTCACCAC 58.943 55.000 10.26 2.35 41.42 4.16
6261 8361 1.301716 CCTCACCACCGACAACCTG 60.302 63.158 0.00 0.00 0.00 4.00
6267 8367 0.030638 CCACCGACAACCTGCAAAAG 59.969 55.000 0.00 0.00 0.00 2.27
6270 8370 1.134220 ACCGACAACCTGCAAAAGAGA 60.134 47.619 0.00 0.00 0.00 3.10
6280 8380 0.600057 GCAAAAGAGAGGTTGGCCAG 59.400 55.000 5.11 0.00 37.19 4.85
6298 8398 2.618045 CCAGACAATGGGGAGTGTAACC 60.618 54.545 0.00 0.00 46.36 2.85
6323 8423 1.202428 CGATCGAGAGGAAGAAACCCC 60.202 57.143 10.26 0.00 0.00 4.95
6342 8442 1.986413 AGGTCACCTGATCCTGCAC 59.014 57.895 0.00 0.00 29.57 4.57
6384 8484 1.103803 GGCTACTGATCACGGACTGA 58.896 55.000 0.00 0.00 0.00 3.41
6394 8494 2.125753 CGGACTGACTGGCTCTGC 60.126 66.667 0.00 0.00 0.00 4.26
6434 8534 1.487976 GAATGACTCCAGATGCTCCCA 59.512 52.381 0.00 0.00 0.00 4.37
6448 8548 2.757099 CCCAGGCATCTTGGTGGC 60.757 66.667 0.00 0.00 44.31 5.01
6456 8556 1.479323 GCATCTTGGTGGCATGATGTT 59.521 47.619 17.36 0.00 38.34 2.71
6457 8557 2.737359 GCATCTTGGTGGCATGATGTTG 60.737 50.000 17.36 4.61 38.34 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 0.809636 TGCGCGTCCATATCAACCTG 60.810 55.000 8.43 0.00 0.00 4.00
107 109 3.383185 GCCCAAGGATATCTAGATCGGAG 59.617 52.174 8.95 0.00 0.00 4.63
192 194 1.324435 CATCGCATCACGTCAACGATT 59.676 47.619 9.88 0.00 41.18 3.34
301 306 3.050275 GTGCTTGGAGTCGTGGGC 61.050 66.667 0.00 0.00 0.00 5.36
324 329 3.818121 CTGGTGCCGGTTCCGTCAA 62.818 63.158 1.90 0.00 0.00 3.18
410 442 1.202973 CGTTGTAGCGGCATCTCGAG 61.203 60.000 5.93 5.93 0.00 4.04
546 579 2.639286 CACGCCACTGACAAAGGC 59.361 61.111 7.57 7.57 44.89 4.35
575 608 3.541713 CCCGCACCTCCTCCTAGC 61.542 72.222 0.00 0.00 0.00 3.42
596 629 2.818274 GCGAAACCCTAGCCACCG 60.818 66.667 0.00 0.00 0.00 4.94
627 660 0.671251 CAGATCACCCTAGTCGCTCC 59.329 60.000 0.00 0.00 0.00 4.70
691 724 8.432805 AGAAGACCATCATTTCCTATTCGTAAT 58.567 33.333 0.00 0.00 0.00 1.89
706 739 9.152327 AGATATAAGATTGTGAGAAGACCATCA 57.848 33.333 0.00 0.00 0.00 3.07
727 760 6.235664 ACCAAAGTACACGACCAAAAGATAT 58.764 36.000 0.00 0.00 0.00 1.63
729 762 4.457466 ACCAAAGTACACGACCAAAAGAT 58.543 39.130 0.00 0.00 0.00 2.40
735 768 5.007823 CACAATAAACCAAAGTACACGACCA 59.992 40.000 0.00 0.00 0.00 4.02
737 770 6.051646 ACACAATAAACCAAAGTACACGAC 57.948 37.500 0.00 0.00 0.00 4.34
782 815 6.484977 AGTTGATCTCTTTCAAACAGGTTCTC 59.515 38.462 0.00 0.00 37.36 2.87
4922 6582 1.825622 GGCAGCATGAAGTAGGGCC 60.826 63.158 0.00 0.00 39.69 5.80
5135 6795 0.543410 TGCAGGGGAAGAACTCGGTA 60.543 55.000 0.00 0.00 0.00 4.02
5138 6798 0.250295 TGTTGCAGGGGAAGAACTCG 60.250 55.000 0.00 0.00 0.00 4.18
5192 6852 7.615039 TGAACCCATGGAATGCATAATAATT 57.385 32.000 15.22 0.00 44.97 1.40
5210 6870 0.108804 TGAAGCTCGACGATGAACCC 60.109 55.000 0.00 0.00 0.00 4.11
5212 6872 1.698165 TGTGAAGCTCGACGATGAAC 58.302 50.000 0.00 0.00 0.00 3.18
5229 6930 1.670811 GGATGTCGCCGAATTTCATGT 59.329 47.619 0.00 0.00 0.00 3.21
5242 6943 3.547413 GCAACACATGATCATGGATGTCG 60.547 47.826 33.31 21.86 42.91 4.35
5285 6986 1.542472 CTGTCATGCACCAATTCAGCA 59.458 47.619 0.00 0.00 43.14 4.41
5315 7016 2.434331 GGTTGCACCCTGGCTACA 59.566 61.111 0.00 0.00 40.54 2.74
5477 7178 2.472695 TGATCACTTGCCCTACACAC 57.527 50.000 0.00 0.00 0.00 3.82
5482 7183 6.554982 AGAACATACTATGATCACTTGCCCTA 59.445 38.462 0.00 0.00 34.84 3.53
5686 7387 8.981724 TTTATATGCTTAGCTCGTGTATTAGG 57.018 34.615 5.60 0.00 0.00 2.69
5703 7404 9.612620 GTGATAAATACTTGTGCCTTTATATGC 57.387 33.333 0.00 0.00 0.00 3.14
5721 7424 8.827677 GGTTTATAGCTCTTTGACGTGATAAAT 58.172 33.333 0.00 0.00 0.00 1.40
5729 7432 3.932710 TGCTGGTTTATAGCTCTTTGACG 59.067 43.478 0.00 0.00 41.66 4.35
5731 7434 4.905429 TGTGCTGGTTTATAGCTCTTTGA 58.095 39.130 0.00 0.00 41.66 2.69
5738 7441 5.828299 TGGTAAATGTGCTGGTTTATAGC 57.172 39.130 0.00 0.00 41.49 2.97
5743 7446 2.899256 AGCATGGTAAATGTGCTGGTTT 59.101 40.909 0.00 0.00 46.60 3.27
5768 7472 5.488645 TTTCGGGTAGAAACAAGTTGAAC 57.511 39.130 10.54 0.45 43.35 3.18
5801 7505 1.002468 CTGCTGTTTTTCGTGTCCAGG 60.002 52.381 0.00 0.00 0.00 4.45
5818 7522 1.457346 CATGGGTCTCTGTTTCCTGC 58.543 55.000 0.00 0.00 0.00 4.85
5831 7535 1.640670 AGTTGGGAGTATTGCATGGGT 59.359 47.619 0.00 0.00 0.00 4.51
5845 7549 4.655963 TGAAGAAAGAATCTGGAGTTGGG 58.344 43.478 0.00 0.00 38.79 4.12
5846 7550 5.312079 ACTGAAGAAAGAATCTGGAGTTGG 58.688 41.667 0.00 0.00 38.79 3.77
5851 7555 5.551305 TGTGACTGAAGAAAGAATCTGGA 57.449 39.130 0.00 0.00 38.79 3.86
5852 7556 6.624352 TTTGTGACTGAAGAAAGAATCTGG 57.376 37.500 0.00 0.00 38.79 3.86
5853 7557 7.701445 AGTTTTGTGACTGAAGAAAGAATCTG 58.299 34.615 0.00 0.00 38.79 2.90
5874 7606 8.700439 ATACCTGTTACCAATTAACACAGTTT 57.300 30.769 0.00 0.00 44.32 2.66
5904 7636 9.148104 CGGCCATAATAACTCCTAAAGTAATAC 57.852 37.037 2.24 0.00 37.17 1.89
5906 7638 7.970102 TCGGCCATAATAACTCCTAAAGTAAT 58.030 34.615 2.24 0.00 37.17 1.89
5908 7640 6.982160 TCGGCCATAATAACTCCTAAAGTA 57.018 37.500 2.24 0.00 37.17 2.24
5909 7641 5.881923 TCGGCCATAATAACTCCTAAAGT 57.118 39.130 2.24 0.00 41.10 2.66
5910 7642 7.584987 CATTTCGGCCATAATAACTCCTAAAG 58.415 38.462 2.24 0.00 0.00 1.85
5911 7643 6.016610 GCATTTCGGCCATAATAACTCCTAAA 60.017 38.462 2.24 0.00 0.00 1.85
5912 7644 5.472137 GCATTTCGGCCATAATAACTCCTAA 59.528 40.000 2.24 0.00 0.00 2.69
5913 7645 5.001232 GCATTTCGGCCATAATAACTCCTA 58.999 41.667 2.24 0.00 0.00 2.94
5914 7646 3.821033 GCATTTCGGCCATAATAACTCCT 59.179 43.478 2.24 0.00 0.00 3.69
5915 7647 3.568007 TGCATTTCGGCCATAATAACTCC 59.432 43.478 2.24 0.00 0.00 3.85
5916 7648 4.036262 TGTGCATTTCGGCCATAATAACTC 59.964 41.667 2.24 0.00 0.00 3.01
5917 7649 3.951037 TGTGCATTTCGGCCATAATAACT 59.049 39.130 2.24 0.00 0.00 2.24
5918 7650 4.041723 GTGTGCATTTCGGCCATAATAAC 58.958 43.478 2.24 4.50 0.00 1.89
5919 7651 3.951037 AGTGTGCATTTCGGCCATAATAA 59.049 39.130 2.24 0.00 0.00 1.40
5920 7652 3.314913 CAGTGTGCATTTCGGCCATAATA 59.685 43.478 2.24 0.00 0.00 0.98
5921 7653 2.099592 CAGTGTGCATTTCGGCCATAAT 59.900 45.455 2.24 0.00 0.00 1.28
5933 7665 0.109153 TGGAGTTGCTCAGTGTGCAT 59.891 50.000 19.70 6.84 40.34 3.96
5951 7683 0.242825 CATTGCCAGTCAGCCAACTG 59.757 55.000 8.72 8.72 45.10 3.16
5952 7684 1.530013 GCATTGCCAGTCAGCCAACT 61.530 55.000 0.00 0.00 0.00 3.16
5954 7686 2.628696 CGCATTGCCAGTCAGCCAA 61.629 57.895 2.41 0.00 0.00 4.52
5955 7687 2.825075 ATCGCATTGCCAGTCAGCCA 62.825 55.000 2.41 0.00 0.00 4.75
5956 7688 0.815213 TATCGCATTGCCAGTCAGCC 60.815 55.000 2.41 0.00 0.00 4.85
5958 7690 2.414481 GCTATATCGCATTGCCAGTCAG 59.586 50.000 2.41 0.00 0.00 3.51
5959 7691 2.037641 AGCTATATCGCATTGCCAGTCA 59.962 45.455 2.41 0.00 0.00 3.41
5961 7693 2.613977 GGAGCTATATCGCATTGCCAGT 60.614 50.000 2.41 0.00 0.00 4.00
5965 7697 2.964740 TCAGGAGCTATATCGCATTGC 58.035 47.619 1.69 0.00 0.00 3.56
5966 7698 5.008619 AGATCAGGAGCTATATCGCATTG 57.991 43.478 1.69 0.00 0.00 2.82
5967 7699 5.674052 AAGATCAGGAGCTATATCGCATT 57.326 39.130 1.69 0.00 0.00 3.56
5968 7700 5.674052 AAAGATCAGGAGCTATATCGCAT 57.326 39.130 1.69 0.00 0.00 4.73
5969 7701 5.473931 GAAAAGATCAGGAGCTATATCGCA 58.526 41.667 1.69 0.00 0.00 5.10
5970 7702 4.867608 GGAAAAGATCAGGAGCTATATCGC 59.132 45.833 0.00 0.00 0.00 4.58
6021 8012 0.745486 CTGGACGATGGCAGATGCAA 60.745 55.000 7.19 0.00 44.36 4.08
6022 8013 1.153309 CTGGACGATGGCAGATGCA 60.153 57.895 7.19 0.00 44.36 3.96
6049 8040 2.690778 GCACCGCAGACCAACCATC 61.691 63.158 0.00 0.00 0.00 3.51
6050 8041 2.672996 GCACCGCAGACCAACCAT 60.673 61.111 0.00 0.00 0.00 3.55
6051 8042 3.490031 ATGCACCGCAGACCAACCA 62.490 57.895 0.00 0.00 43.65 3.67
6053 8044 1.639298 GAGATGCACCGCAGACCAAC 61.639 60.000 0.00 0.00 43.65 3.77
6055 8046 2.265739 GAGATGCACCGCAGACCA 59.734 61.111 0.00 0.00 43.65 4.02
6056 8047 2.512515 GGAGATGCACCGCAGACC 60.513 66.667 0.00 0.00 43.65 3.85
6057 8048 1.812922 CTGGAGATGCACCGCAGAC 60.813 63.158 0.00 0.00 43.65 3.51
6059 8050 2.104859 CACTGGAGATGCACCGCAG 61.105 63.158 0.00 0.00 43.65 5.18
6063 8054 0.524862 CAAAGCACTGGAGATGCACC 59.475 55.000 0.00 0.00 45.92 5.01
6064 8055 0.109412 GCAAAGCACTGGAGATGCAC 60.109 55.000 0.00 0.00 45.92 4.57
6066 8057 0.170561 CTGCAAAGCACTGGAGATGC 59.829 55.000 0.93 0.00 43.74 3.91
6067 8058 0.170561 GCTGCAAAGCACTGGAGATG 59.829 55.000 10.20 0.00 36.94 2.90
6068 8059 0.037877 AGCTGCAAAGCACTGGAGAT 59.962 50.000 10.20 1.47 36.94 2.75
6069 8060 0.179009 AAGCTGCAAAGCACTGGAGA 60.179 50.000 10.20 0.00 36.94 3.71
6074 8102 0.815213 TGACGAAGCTGCAAAGCACT 60.815 50.000 1.02 0.00 37.25 4.40
6080 8108 1.882912 ATGAACTGACGAAGCTGCAA 58.117 45.000 1.02 0.00 0.00 4.08
6090 8118 2.030805 GTCCACAAGCCAATGAACTGAC 60.031 50.000 0.00 0.00 0.00 3.51
6110 8138 1.888512 CTGTATTTGCAGGTTGGCAGT 59.111 47.619 0.00 0.00 45.88 4.40
6111 8139 1.403249 GCTGTATTTGCAGGTTGGCAG 60.403 52.381 0.00 0.00 45.88 4.85
6112 8140 0.602562 GCTGTATTTGCAGGTTGGCA 59.397 50.000 0.00 0.00 43.19 4.92
6113 8141 0.456653 CGCTGTATTTGCAGGTTGGC 60.457 55.000 0.00 0.00 37.00 4.52
6114 8142 0.456653 GCGCTGTATTTGCAGGTTGG 60.457 55.000 0.00 0.00 37.00 3.77
6115 8143 0.523072 AGCGCTGTATTTGCAGGTTG 59.477 50.000 10.39 0.00 37.00 3.77
6116 8144 2.009774 CTAGCGCTGTATTTGCAGGTT 58.990 47.619 22.90 0.00 37.00 3.50
6117 8145 1.066143 ACTAGCGCTGTATTTGCAGGT 60.066 47.619 22.90 0.28 37.00 4.00
6120 8148 2.672874 CAGAACTAGCGCTGTATTTGCA 59.327 45.455 22.90 0.00 0.00 4.08
6121 8149 2.537730 GCAGAACTAGCGCTGTATTTGC 60.538 50.000 22.90 19.68 34.66 3.68
6122 8150 2.030946 GGCAGAACTAGCGCTGTATTTG 59.969 50.000 22.90 13.91 34.66 2.32
6127 8211 0.173708 GTAGGCAGAACTAGCGCTGT 59.826 55.000 22.90 13.53 34.66 4.40
6156 8240 0.249868 GCCGCATAGCATCCTGTGTA 60.250 55.000 0.00 0.00 33.22 2.90
6196 8280 3.153919 TGAAGAAACGGCATTTAGGCTT 58.846 40.909 0.00 0.00 41.46 4.35
6224 8322 2.095461 GGTTTCTCTCCCAAAGCCATC 58.905 52.381 0.00 0.00 0.00 3.51
6227 8325 1.073923 TGAGGTTTCTCTCCCAAAGCC 59.926 52.381 0.00 0.00 40.58 4.35
6237 8337 0.391597 TGTCGGTGGTGAGGTTTCTC 59.608 55.000 0.00 0.00 40.36 2.87
6242 8342 1.764854 AGGTTGTCGGTGGTGAGGT 60.765 57.895 0.00 0.00 0.00 3.85
6247 8347 0.681564 TTTTGCAGGTTGTCGGTGGT 60.682 50.000 0.00 0.00 0.00 4.16
6251 8351 1.532868 CTCTCTTTTGCAGGTTGTCGG 59.467 52.381 0.00 0.00 0.00 4.79
6261 8361 0.600057 CTGGCCAACCTCTCTTTTGC 59.400 55.000 7.01 0.00 36.63 3.68
6267 8367 1.457346 CATTGTCTGGCCAACCTCTC 58.543 55.000 7.01 0.00 36.63 3.20
6270 8370 1.077265 CCCATTGTCTGGCCAACCT 59.923 57.895 7.01 0.00 44.46 3.50
6280 8380 3.434940 AAGGTTACACTCCCCATTGTC 57.565 47.619 0.00 0.00 0.00 3.18
6292 8392 2.416836 CCTCTCGATCGCAAAGGTTACA 60.417 50.000 11.09 0.00 0.00 2.41
6293 8393 2.159282 TCCTCTCGATCGCAAAGGTTAC 60.159 50.000 21.75 0.00 0.00 2.50
6298 8398 2.568696 TCTTCCTCTCGATCGCAAAG 57.431 50.000 11.09 2.75 0.00 2.77
6356 8456 3.256879 CGTGATCAGTAGCCATACCTGAT 59.743 47.826 0.00 1.27 34.89 2.90
6357 8457 2.623416 CGTGATCAGTAGCCATACCTGA 59.377 50.000 0.00 0.00 31.78 3.86
6369 8469 0.891373 CCAGTCAGTCCGTGATCAGT 59.109 55.000 0.00 0.00 37.56 3.41
6403 8503 1.198713 GAGTCATTCTGCAGGAGGGA 58.801 55.000 15.13 4.29 0.00 4.20
6434 8534 0.260816 ATCATGCCACCAAGATGCCT 59.739 50.000 0.00 0.00 28.95 4.75


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

AutoCloner maintained by Alex Coulton.