Multiple sequence alignment - TraesCS6B01G204600

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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 TraesCS6B01G204600 chr6B 100.000 5288 0 0 1 5288 255263523 255268810 0.000000e+00 9766
1 TraesCS6B01G204600 chr6D 92.878 2696 137 23 251 2931 143396350 143399005 0.000000e+00 3864
2 TraesCS6B01G204600 chr6D 94.070 1602 73 11 3090 4675 143399003 143400598 0.000000e+00 2412
3 TraesCS6B01G204600 chr6D 85.401 137 6 6 5095 5223 143400971 143401101 4.300000e-26 130
4 TraesCS6B01G204600 chr6A 95.258 1645 49 10 3090 4716 205106827 205105194 0.000000e+00 2579
5 TraesCS6B01G204600 chr6A 94.166 1217 54 9 1158 2369 205109061 205107857 0.000000e+00 1838
6 TraesCS6B01G204600 chr6A 90.839 644 43 11 1 634 205110364 205109727 0.000000e+00 848
7 TraesCS6B01G204600 chr6A 97.662 385 9 0 2365 2749 205107600 205107216 0.000000e+00 662
8 TraesCS6B01G204600 chr6A 93.143 350 18 5 4752 5101 205105197 205104854 4.720000e-140 508
9 TraesCS6B01G204600 chr6A 95.135 185 5 2 2748 2931 205107006 205106825 6.700000e-74 289
10 TraesCS6B01G204600 chr6A 93.064 173 6 4 5116 5288 205104744 205104578 1.140000e-61 248
11 TraesCS6B01G204600 chr6A 86.555 238 11 10 902 1120 205109292 205109057 5.290000e-60 243
12 TraesCS6B01G204600 chr7B 96.951 164 5 0 2929 3092 339685603 339685440 5.220000e-70 276
13 TraesCS6B01G204600 chr5B 97.516 161 4 0 2929 3089 693967649 693967489 5.220000e-70 276
14 TraesCS6B01G204600 chr4A 93.976 166 9 1 2929 3094 517406632 517406468 3.160000e-62 250
15 TraesCS6B01G204600 chr4D 93.413 167 9 2 2929 3095 334164552 334164388 4.090000e-61 246
16 TraesCS6B01G204600 chr3D 93.413 167 10 1 2928 3094 87926162 87925997 4.090000e-61 246
17 TraesCS6B01G204600 chr7A 91.573 178 13 2 2929 3106 32959956 32959781 1.470000e-60 244
18 TraesCS6B01G204600 chr7A 91.573 178 13 2 2929 3106 115779298 115779123 1.470000e-60 244
19 TraesCS6B01G204600 chr5A 91.573 178 13 2 2929 3106 697731945 697731770 1.470000e-60 244
20 TraesCS6B01G204600 chr2D 91.477 176 13 2 2929 3103 87407525 87407351 1.900000e-59 241
21 TraesCS6B01G204600 chr2B 78.363 171 26 10 4781 4947 497415716 497415879 3.370000e-17 100


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 TraesCS6B01G204600 chr6B 255263523 255268810 5287 False 9766.000000 9766 100.00000 1 5288 1 chr6B.!!$F1 5287
1 TraesCS6B01G204600 chr6D 143396350 143401101 4751 False 2135.333333 3864 90.78300 251 5223 3 chr6D.!!$F1 4972
2 TraesCS6B01G204600 chr6A 205104578 205110364 5786 True 901.875000 2579 93.22775 1 5288 8 chr6A.!!$R1 5287

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
799 810 0.171455 CCCGAGAACGAGAACTCCTG 59.829 60.000 0.00 0.00 42.66 3.86 F
1121 1319 0.677288 GTACAAGGGTGGGGTTTTGC 59.323 55.000 0.00 0.00 0.00 3.68 F
1146 1344 1.129917 TGGGGGAACTCGTACAACAA 58.870 50.000 0.00 0.00 0.00 2.83 F
1648 1856 1.137872 ACATGGCGGATCTTCTCACTC 59.862 52.381 0.00 0.00 0.00 3.51 F
2578 3051 0.591170 CCCCAAATGTCGTGACACAC 59.409 55.000 4.57 4.03 45.05 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1856 0.603707 TCGCCAACTGAAGCTCCTTG 60.604 55.000 0.00 0.00 0.00 3.61 R
2535 3008 1.148273 GGCCACCTGTCAGTGACAA 59.852 57.895 25.41 10.69 42.26 3.18 R
2578 3051 1.491670 CCCGTTCAGTGATCATAGCG 58.508 55.000 0.00 1.90 0.00 4.26 R
3152 3837 1.888512 GTCACCACATGGCACTTCAAT 59.111 47.619 0.00 0.00 39.32 2.57 R
4372 5068 0.111639 GTGAAGGGCCCAAGTAACCA 59.888 55.000 27.56 7.58 0.00 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
26 27 5.450818 TTAGTCATGGGAATTAAGGCAGT 57.549 39.130 0.00 0.00 0.00 4.40
37 38 6.260271 GGGAATTAAGGCAGTACTAATCACAC 59.740 42.308 0.00 0.00 0.00 3.82
48 49 6.479001 CAGTACTAATCACACGAATTAAGGGG 59.521 42.308 0.00 0.00 0.00 4.79
49 50 4.777463 ACTAATCACACGAATTAAGGGGG 58.223 43.478 0.00 0.00 0.00 5.40
69 70 5.870706 GGGGGTTTTGTTGGATTTTGATTA 58.129 37.500 0.00 0.00 0.00 1.75
92 93 3.924073 GCTATTTTTCACGGGCGAAATTT 59.076 39.130 3.89 0.00 34.94 1.82
183 192 0.824109 CCCTATGCACTTGGACGAGA 59.176 55.000 0.00 0.00 0.00 4.04
186 195 2.093973 CCTATGCACTTGGACGAGAAGT 60.094 50.000 0.00 0.00 33.82 3.01
192 201 4.927425 TGCACTTGGACGAGAAGTATAAAC 59.073 41.667 0.00 0.00 32.27 2.01
199 208 6.392354 TGGACGAGAAGTATAAACGAACATT 58.608 36.000 0.00 0.00 0.00 2.71
234 244 9.574458 TGTCAAAAGAAAATGAACAACGATTAA 57.426 25.926 0.00 0.00 0.00 1.40
244 254 8.506140 AATGAACAACGATTAACACTGATTTG 57.494 30.769 0.00 0.00 0.00 2.32
444 454 6.515531 GCAATCTTCTCATCTTTGGTCAAACA 60.516 38.462 0.00 0.00 0.00 2.83
460 470 1.767759 AACATAGCCATCCAACAGCC 58.232 50.000 0.00 0.00 0.00 4.85
551 562 3.065306 CCCTACCGTCAGCCACAA 58.935 61.111 0.00 0.00 0.00 3.33
658 669 1.299544 GGTTCAAAACCCGCCAACG 60.300 57.895 0.00 0.00 46.12 4.10
791 802 2.809601 CAACGCCCCGAGAACGAG 60.810 66.667 0.00 0.00 42.66 4.18
797 808 1.511768 CCCCGAGAACGAGAACTCC 59.488 63.158 0.00 0.00 42.66 3.85
798 809 0.966370 CCCCGAGAACGAGAACTCCT 60.966 60.000 0.00 0.00 42.66 3.69
799 810 0.171455 CCCGAGAACGAGAACTCCTG 59.829 60.000 0.00 0.00 42.66 3.86
800 811 0.882474 CCGAGAACGAGAACTCCTGT 59.118 55.000 0.00 0.00 42.66 4.00
801 812 1.401670 CCGAGAACGAGAACTCCTGTG 60.402 57.143 0.00 0.00 42.66 3.66
821 832 1.958902 CTGTGCTGCCCCTCTCTCTC 61.959 65.000 0.00 0.00 0.00 3.20
826 837 2.123033 GCCCCTCTCTCTCTCCCC 60.123 72.222 0.00 0.00 0.00 4.81
971 1151 1.921869 TTTGAGGGAGATTCGGGGCC 61.922 60.000 0.00 0.00 0.00 5.80
972 1152 3.930012 GAGGGAGATTCGGGGCCG 61.930 72.222 0.00 0.00 41.35 6.13
1051 1231 4.265056 GGTGAGTGGCAACGGGGT 62.265 66.667 0.00 0.00 42.51 4.95
1053 1233 3.164977 TGAGTGGCAACGGGGTGA 61.165 61.111 0.00 0.00 42.51 4.02
1065 1245 3.261981 ACGGGGTGATTTAGCTTACTG 57.738 47.619 0.00 0.00 0.00 2.74
1066 1246 2.093128 ACGGGGTGATTTAGCTTACTGG 60.093 50.000 0.00 0.00 0.00 4.00
1121 1319 0.677288 GTACAAGGGTGGGGTTTTGC 59.323 55.000 0.00 0.00 0.00 3.68
1143 1341 2.487625 CCTTTTGGGGGAACTCGTACAA 60.488 50.000 0.00 0.00 35.46 2.41
1146 1344 1.129917 TGGGGGAACTCGTACAACAA 58.870 50.000 0.00 0.00 0.00 2.83
1186 1384 2.096248 GTTGTTGGTTTGTGTGGGAGA 58.904 47.619 0.00 0.00 0.00 3.71
1255 1453 3.713858 TGTGTTGTTGATTGGCTTGAG 57.286 42.857 0.00 0.00 0.00 3.02
1341 1539 9.740239 TCATTTCTGATTTGCTCATAAATTAGC 57.260 29.630 0.00 0.00 38.12 3.09
1386 1585 7.581213 ATCGGGAATATTGCTGTTAATTTGA 57.419 32.000 14.65 0.00 0.00 2.69
1490 1689 3.904136 AGGAAATTGTTCAGACTTGCG 57.096 42.857 0.00 0.00 35.25 4.85
1531 1731 1.339631 TGCTAACATTGCGGCCTTACT 60.340 47.619 0.00 0.00 0.00 2.24
1542 1742 1.202336 CGGCCTTACTTAGTGTACCCG 60.202 57.143 0.00 0.00 33.99 5.28
1550 1750 6.404074 CCTTACTTAGTGTACCCGACAAGTAG 60.404 46.154 0.00 0.00 40.66 2.57
1557 1757 4.992951 GTGTACCCGACAAGTAGTTGAATT 59.007 41.667 17.23 0.00 40.66 2.17
1559 1759 6.017687 GTGTACCCGACAAGTAGTTGAATTTT 60.018 38.462 17.23 0.00 40.66 1.82
1587 1792 8.721478 TGAAGAAGTTCTAATAATCTGTTGTGC 58.279 33.333 5.65 0.00 33.38 4.57
1588 1793 8.854614 AAGAAGTTCTAATAATCTGTTGTGCT 57.145 30.769 5.65 0.00 0.00 4.40
1589 1794 8.485976 AGAAGTTCTAATAATCTGTTGTGCTC 57.514 34.615 2.75 0.00 0.00 4.26
1590 1795 7.550906 AGAAGTTCTAATAATCTGTTGTGCTCC 59.449 37.037 2.75 0.00 0.00 4.70
1636 1844 2.047274 AAGGACACGACATGGCGG 60.047 61.111 27.41 16.68 37.09 6.13
1648 1856 1.137872 ACATGGCGGATCTTCTCACTC 59.862 52.381 0.00 0.00 0.00 3.51
1684 1892 3.003897 TGGCGACCAACAATTTCAACTAC 59.996 43.478 0.00 0.00 0.00 2.73
1767 1975 1.203187 ACAGGTGCAGTCCCTCTCTTA 60.203 52.381 0.00 0.00 0.00 2.10
1917 2125 4.558496 CGGTTGTTGGTGCTTGTGATTTAT 60.558 41.667 0.00 0.00 0.00 1.40
1918 2126 5.335269 CGGTTGTTGGTGCTTGTGATTTATA 60.335 40.000 0.00 0.00 0.00 0.98
1965 2173 5.873179 TTTATTTCTGGTTTCTAGTGCCG 57.127 39.130 0.00 0.00 0.00 5.69
2002 2210 1.804748 GTTGTAGTTTTCAGAGCCCGG 59.195 52.381 0.00 0.00 0.00 5.73
2188 2397 5.601313 TCACTTTACCGAGGATATAGCCTTT 59.399 40.000 11.65 1.59 38.73 3.11
2208 2417 3.857157 TGCTTTGTGGTAGAGAAGGTT 57.143 42.857 0.00 0.00 0.00 3.50
2237 2449 6.956435 TGATCACAAGCTAGATAGGACCATAT 59.044 38.462 0.00 0.00 0.00 1.78
2535 3008 3.822735 CTGATAAACGATGCCCCATCATT 59.177 43.478 6.09 3.20 40.54 2.57
2578 3051 0.591170 CCCCAAATGTCGTGACACAC 59.409 55.000 4.57 4.03 45.05 3.82
2635 3108 3.914426 ATCTACCTGCTAGTTTGTGGG 57.086 47.619 0.00 0.00 0.00 4.61
2738 3211 7.337942 AGCATATTAAAGGGAGTTGAAACAGAG 59.662 37.037 0.00 0.00 0.00 3.35
2934 3619 7.486647 TCGACTTTATTATGACTGTTACTCCC 58.513 38.462 0.00 0.00 0.00 4.30
2935 3620 7.341256 TCGACTTTATTATGACTGTTACTCCCT 59.659 37.037 0.00 0.00 0.00 4.20
2936 3621 7.648510 CGACTTTATTATGACTGTTACTCCCTC 59.351 40.741 0.00 0.00 0.00 4.30
2937 3622 7.793036 ACTTTATTATGACTGTTACTCCCTCC 58.207 38.462 0.00 0.00 0.00 4.30
2938 3623 7.402071 ACTTTATTATGACTGTTACTCCCTCCA 59.598 37.037 0.00 0.00 0.00 3.86
2939 3624 7.931015 TTATTATGACTGTTACTCCCTCCAT 57.069 36.000 0.00 0.00 0.00 3.41
2940 3625 6.831664 ATTATGACTGTTACTCCCTCCATT 57.168 37.500 0.00 0.00 0.00 3.16
2941 3626 4.762289 ATGACTGTTACTCCCTCCATTC 57.238 45.455 0.00 0.00 0.00 2.67
2942 3627 2.838202 TGACTGTTACTCCCTCCATTCC 59.162 50.000 0.00 0.00 0.00 3.01
2943 3628 3.108376 GACTGTTACTCCCTCCATTCCT 58.892 50.000 0.00 0.00 0.00 3.36
2944 3629 4.264668 TGACTGTTACTCCCTCCATTCCTA 60.265 45.833 0.00 0.00 0.00 2.94
2945 3630 4.695606 ACTGTTACTCCCTCCATTCCTAA 58.304 43.478 0.00 0.00 0.00 2.69
2946 3631 5.098663 ACTGTTACTCCCTCCATTCCTAAA 58.901 41.667 0.00 0.00 0.00 1.85
2947 3632 5.731678 ACTGTTACTCCCTCCATTCCTAAAT 59.268 40.000 0.00 0.00 0.00 1.40
2948 3633 6.906901 ACTGTTACTCCCTCCATTCCTAAATA 59.093 38.462 0.00 0.00 0.00 1.40
2949 3634 7.572861 ACTGTTACTCCCTCCATTCCTAAATAT 59.427 37.037 0.00 0.00 0.00 1.28
2950 3635 9.101325 CTGTTACTCCCTCCATTCCTAAATATA 57.899 37.037 0.00 0.00 0.00 0.86
2951 3636 9.455144 TGTTACTCCCTCCATTCCTAAATATAA 57.545 33.333 0.00 0.00 0.00 0.98
2952 3637 9.945904 GTTACTCCCTCCATTCCTAAATATAAG 57.054 37.037 0.00 0.00 0.00 1.73
2953 3638 9.684702 TTACTCCCTCCATTCCTAAATATAAGT 57.315 33.333 0.00 0.00 0.00 2.24
2954 3639 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
2955 3640 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
2956 3641 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
2957 3642 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
2958 3643 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
2986 3671 9.698309 AGAGATTTCCAATATGAACTACATACG 57.302 33.333 0.00 0.00 43.12 3.06
2987 3672 8.833231 AGATTTCCAATATGAACTACATACGG 57.167 34.615 0.00 0.00 43.12 4.02
2988 3673 8.647796 AGATTTCCAATATGAACTACATACGGA 58.352 33.333 0.00 0.00 43.12 4.69
2989 3674 9.436957 GATTTCCAATATGAACTACATACGGAT 57.563 33.333 0.00 0.00 43.12 4.18
2990 3675 8.601845 TTTCCAATATGAACTACATACGGATG 57.398 34.615 5.94 5.94 43.12 3.51
2992 3677 8.411991 TCCAATATGAACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
2993 3678 9.031537 TCCAATATGAACTACATACGGATGTAT 57.968 33.333 20.64 7.28 45.42 2.29
3000 3685 9.729281 TGAACTACATACGGATGTATATAGACA 57.271 33.333 20.64 12.87 45.42 3.41
3021 3706 8.425577 AGACATATTTTAGAGTGTACATGCAC 57.574 34.615 0.00 0.00 39.51 4.57
3032 3717 6.727824 AGTGTACATGCACTCATTTTACTC 57.272 37.500 0.00 0.00 45.63 2.59
3033 3718 5.643777 AGTGTACATGCACTCATTTTACTCC 59.356 40.000 0.00 0.00 45.63 3.85
3034 3719 4.629634 TGTACATGCACTCATTTTACTCCG 59.370 41.667 0.00 0.00 0.00 4.63
3035 3720 3.674997 ACATGCACTCATTTTACTCCGT 58.325 40.909 0.00 0.00 0.00 4.69
3036 3721 4.827692 ACATGCACTCATTTTACTCCGTA 58.172 39.130 0.00 0.00 0.00 4.02
3037 3722 5.428253 ACATGCACTCATTTTACTCCGTAT 58.572 37.500 0.00 0.00 0.00 3.06
3038 3723 5.294306 ACATGCACTCATTTTACTCCGTATG 59.706 40.000 0.00 0.00 0.00 2.39
3039 3724 4.827692 TGCACTCATTTTACTCCGTATGT 58.172 39.130 0.00 0.00 0.00 2.29
3040 3725 5.968254 TGCACTCATTTTACTCCGTATGTA 58.032 37.500 0.00 0.00 0.00 2.29
3041 3726 6.040247 TGCACTCATTTTACTCCGTATGTAG 58.960 40.000 0.00 0.00 0.00 2.74
3042 3727 6.040878 GCACTCATTTTACTCCGTATGTAGT 58.959 40.000 0.00 0.00 0.00 2.73
3043 3728 6.198591 GCACTCATTTTACTCCGTATGTAGTC 59.801 42.308 0.00 0.00 0.00 2.59
3044 3729 6.696148 CACTCATTTTACTCCGTATGTAGTCC 59.304 42.308 0.00 0.00 0.00 3.85
3045 3730 6.379133 ACTCATTTTACTCCGTATGTAGTCCA 59.621 38.462 0.00 0.00 0.00 4.02
3046 3731 7.069578 ACTCATTTTACTCCGTATGTAGTCCAT 59.930 37.037 0.00 0.00 37.58 3.41
3047 3732 8.467963 TCATTTTACTCCGTATGTAGTCCATA 57.532 34.615 0.00 0.00 34.86 2.74
3048 3733 8.573885 TCATTTTACTCCGTATGTAGTCCATAG 58.426 37.037 0.00 0.00 36.71 2.23
3049 3734 7.886629 TTTTACTCCGTATGTAGTCCATAGT 57.113 36.000 0.00 0.00 36.71 2.12
3050 3735 6.872628 TTACTCCGTATGTAGTCCATAGTG 57.127 41.667 0.00 0.00 36.71 2.74
3051 3736 4.142790 ACTCCGTATGTAGTCCATAGTGG 58.857 47.826 0.00 0.00 36.71 4.00
3052 3737 4.141321 ACTCCGTATGTAGTCCATAGTGGA 60.141 45.833 0.00 0.00 45.98 4.02
3067 3752 8.380742 TCCATAGTGGAATCTCTTAAAAGACT 57.619 34.615 0.00 0.00 45.00 3.24
3068 3753 8.826765 TCCATAGTGGAATCTCTTAAAAGACTT 58.173 33.333 0.00 0.00 45.00 3.01
3086 3771 9.907229 AAAAGACTTATATTTAGGAACAGAGGG 57.093 33.333 0.00 0.00 0.00 4.30
3087 3772 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
3088 3773 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
3152 3837 9.332301 CAGAAGTTTTAAGTTGTTACGTTTCAA 57.668 29.630 0.00 0.00 0.00 2.69
3239 3924 6.385766 AATTGCATTTTAATTCCTCCCCAA 57.614 33.333 0.00 0.00 0.00 4.12
3251 3936 1.209747 CCTCCCCAACCTAGTTAGCAC 59.790 57.143 0.00 0.00 0.00 4.40
3862 4547 0.814457 CTACAGCTTCGGAGTGCTCT 59.186 55.000 4.90 0.00 36.49 4.09
3891 4576 2.672996 GCCAGCGGAAAGAAGCCA 60.673 61.111 0.00 0.00 0.00 4.75
3984 4669 1.153289 CAAGGAGATGGCTGACCCG 60.153 63.158 0.00 0.00 35.87 5.28
4158 4846 4.515361 AGAATGATCTGTTCAAGCCTCAG 58.485 43.478 12.04 0.00 38.03 3.35
4332 5026 0.322816 CCTTCCTGGGATGTGTGTGG 60.323 60.000 0.00 0.00 0.00 4.17
4371 5067 5.449314 CGTATGGTTGTTTCTTGTTGTTGGA 60.449 40.000 0.00 0.00 0.00 3.53
4372 5068 5.612725 ATGGTTGTTTCTTGTTGTTGGAT 57.387 34.783 0.00 0.00 0.00 3.41
4418 5117 3.261897 CCAGAGATGTACTTGTGGTTCCT 59.738 47.826 0.00 0.00 31.98 3.36
4469 5169 3.684305 TGTGATGTGGCTTGTAAGATTCG 59.316 43.478 0.00 0.00 0.00 3.34
4480 5180 5.810587 GCTTGTAAGATTCGTATTGGACTGA 59.189 40.000 0.00 0.00 0.00 3.41
4498 5198 5.063564 GGACTGATTCCGACAATAACAAGTC 59.936 44.000 0.00 0.00 33.46 3.01
4521 5222 3.678056 TCATGTGTTCCTGTACTCACC 57.322 47.619 0.00 0.00 0.00 4.02
4554 5255 6.127814 ACTCATCAATTATCTGGTGTGCAAAG 60.128 38.462 0.00 0.00 0.00 2.77
4589 5290 4.091509 CGACTTATACTTGCGCAAAAGACT 59.908 41.667 29.45 14.56 0.00 3.24
4717 5468 8.831738 AGGCTACAGATAGTATCTCTGAATAGA 58.168 37.037 9.84 0.00 42.22 1.98
4730 5481 7.891183 TCTCTGAATAGACAAGTTTAACTGC 57.109 36.000 0.00 0.00 0.00 4.40
4732 5483 7.600375 TCTCTGAATAGACAAGTTTAACTGCAG 59.400 37.037 13.48 13.48 0.00 4.41
4733 5484 7.441836 TCTGAATAGACAAGTTTAACTGCAGA 58.558 34.615 23.35 0.00 0.00 4.26
4735 5486 8.445275 TGAATAGACAAGTTTAACTGCAGAAA 57.555 30.769 23.35 11.47 0.00 2.52
4736 5487 9.066892 TGAATAGACAAGTTTAACTGCAGAAAT 57.933 29.630 23.35 8.69 0.00 2.17
4740 5491 8.451908 AGACAAGTTTAACTGCAGAAATAACT 57.548 30.769 23.35 18.95 0.00 2.24
4745 5496 8.671384 AGTTTAACTGCAGAAATAACTACACA 57.329 30.769 23.35 0.00 0.00 3.72
4797 5548 0.106569 TATACTCCCTCCGTTCCGCA 60.107 55.000 0.00 0.00 0.00 5.69
4841 5592 7.432350 TTTCAAAAGTCAAATTTGTGCTTGT 57.568 28.000 21.83 17.09 38.57 3.16
4912 5663 8.267620 ACTTGTATCATCAGATCCATCCTTAA 57.732 34.615 0.00 0.00 35.67 1.85
5155 6009 0.842030 TGCTGGACCATGGAGAGGTT 60.842 55.000 21.47 0.00 40.09 3.50
5180 6034 4.875536 TGAACAATACTATGCGCATTCAGT 59.124 37.500 30.42 27.07 0.00 3.41
5192 6053 2.159612 CGCATTCAGTTCACAGGTGATG 60.160 50.000 2.52 0.00 39.64 3.07
5201 6062 3.929955 TCACAGGTGATGCATTATCCA 57.070 42.857 0.00 0.00 34.77 3.41
5225 6086 8.367911 CCATACATAACTATAGCTCAAAGGTCA 58.632 37.037 0.00 0.00 0.00 4.02
5226 6087 9.764363 CATACATAACTATAGCTCAAAGGTCAA 57.236 33.333 0.00 0.00 0.00 3.18
5267 6128 6.611642 ACCTACAGAGCATAGGATTTCTAACA 59.388 38.462 5.08 0.00 41.70 2.41
5274 6135 7.071698 AGAGCATAGGATTTCTAACAAGGATGA 59.928 37.037 0.00 0.00 0.00 2.92
5276 6137 7.500559 AGCATAGGATTTCTAACAAGGATGAAC 59.499 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.998074 TGATTAGTACTGCCTTAATTCCCATG 59.002 38.462 5.39 0.00 0.00 3.66
26 27 5.920903 CCCCCTTAATTCGTGTGATTAGTA 58.079 41.667 0.00 0.00 0.00 1.82
48 49 6.230472 AGCTAATCAAAATCCAACAAAACCC 58.770 36.000 0.00 0.00 0.00 4.11
49 50 9.435688 AATAGCTAATCAAAATCCAACAAAACC 57.564 29.630 0.00 0.00 0.00 3.27
69 70 1.816074 TTCGCCCGTGAAAAATAGCT 58.184 45.000 0.00 0.00 0.00 3.32
92 93 1.791103 CTCGTTCGCCCCAAGCAAAA 61.791 55.000 0.00 0.00 44.04 2.44
95 96 2.954684 ATCTCGTTCGCCCCAAGCA 61.955 57.895 0.00 0.00 44.04 3.91
96 97 2.125106 ATCTCGTTCGCCCCAAGC 60.125 61.111 0.00 0.00 38.52 4.01
216 225 8.728088 ATCAGTGTTAATCGTTGTTCATTTTC 57.272 30.769 0.00 0.00 0.00 2.29
227 237 5.120830 GCTCAGACAAATCAGTGTTAATCGT 59.879 40.000 0.00 0.00 0.00 3.73
234 244 2.936919 TGGCTCAGACAAATCAGTGT 57.063 45.000 0.00 0.00 0.00 3.55
244 254 3.676646 GCAAAACATTCATTGGCTCAGAC 59.323 43.478 0.00 0.00 0.00 3.51
276 286 0.732571 ATTGCGTTGCATCTTACGGG 59.267 50.000 10.40 0.00 38.76 5.28
277 287 2.542766 AATTGCGTTGCATCTTACGG 57.457 45.000 10.40 0.00 38.76 4.02
278 288 3.869014 CAAATTGCGTTGCATCTTACG 57.131 42.857 4.31 4.31 38.76 3.18
351 361 8.697507 ATGTTATTTTAGATGGATTGGGAGAC 57.302 34.615 0.00 0.00 0.00 3.36
444 454 0.466922 GCTGGCTGTTGGATGGCTAT 60.467 55.000 0.00 0.00 0.00 2.97
497 508 1.140452 GGGCCCGGGTTTTTGTTTTTA 59.860 47.619 24.63 0.00 0.00 1.52
791 802 1.849976 GCAGCACAGCACAGGAGTTC 61.850 60.000 0.00 0.00 0.00 3.01
797 808 4.655647 AGGGGCAGCACAGCACAG 62.656 66.667 0.00 0.00 40.53 3.66
798 809 4.648626 GAGGGGCAGCACAGCACA 62.649 66.667 0.00 0.00 40.53 4.57
799 810 4.341783 AGAGGGGCAGCACAGCAC 62.342 66.667 0.00 0.00 37.14 4.40
800 811 4.025858 GAGAGGGGCAGCACAGCA 62.026 66.667 0.00 0.00 35.83 4.41
801 812 3.678951 GAGAGAGGGGCAGCACAGC 62.679 68.421 0.00 0.00 0.00 4.40
826 837 1.190833 AGCACAGGAGACTCAGTGGG 61.191 60.000 21.61 13.39 40.21 4.61
1051 1231 5.865085 ACACACTTCCAGTAAGCTAAATCA 58.135 37.500 0.00 0.00 38.93 2.57
1053 1233 7.425606 CAAAACACACTTCCAGTAAGCTAAAT 58.574 34.615 0.00 0.00 38.93 1.40
1065 1245 2.384828 ACTTCCCCAAAACACACTTCC 58.615 47.619 0.00 0.00 0.00 3.46
1066 1246 4.180817 CAAACTTCCCCAAAACACACTTC 58.819 43.478 0.00 0.00 0.00 3.01
1071 1251 1.834896 ACCCAAACTTCCCCAAAACAC 59.165 47.619 0.00 0.00 0.00 3.32
1072 1252 2.112190 GACCCAAACTTCCCCAAAACA 58.888 47.619 0.00 0.00 0.00 2.83
1143 1341 9.097257 CAACAAATAAAACTGGAACAATCTTGT 57.903 29.630 0.00 0.00 44.72 3.16
1146 1344 9.097257 CAACAACAAATAAAACTGGAACAATCT 57.903 29.630 0.00 0.00 38.70 2.40
1164 1362 2.232452 CTCCCACACAAACCAACAACAA 59.768 45.455 0.00 0.00 0.00 2.83
1167 1365 2.516227 TCTCCCACACAAACCAACAA 57.484 45.000 0.00 0.00 0.00 2.83
1228 1426 7.812191 TCAAGCCAATCAACAACACATAATAAC 59.188 33.333 0.00 0.00 0.00 1.89
1255 1453 6.044682 CCCCAGAATCAAAATCAATTGCTAC 58.955 40.000 0.00 0.00 0.00 3.58
1407 1606 6.446781 AAAATCTGCACTCCATTGTATCTG 57.553 37.500 0.00 0.00 0.00 2.90
1413 1612 5.412640 TGCATAAAAATCTGCACTCCATTG 58.587 37.500 0.00 0.00 43.11 2.82
1458 1657 8.859090 TCTGAACAATTTCCTTCACAACATATT 58.141 29.630 0.00 0.00 0.00 1.28
1461 1660 6.322201 AGTCTGAACAATTTCCTTCACAACAT 59.678 34.615 0.00 0.00 0.00 2.71
1464 1663 6.563422 CAAGTCTGAACAATTTCCTTCACAA 58.437 36.000 0.00 0.00 0.00 3.33
1531 1731 4.826733 TCAACTACTTGTCGGGTACACTAA 59.173 41.667 0.00 0.00 38.00 2.24
1542 1742 9.657121 CTTCTTCAGAAAATTCAACTACTTGTC 57.343 33.333 0.00 0.00 33.07 3.18
1584 1789 2.272471 GTTGGGCCCTAGGAGCAC 59.728 66.667 25.70 13.92 0.00 4.40
1636 1844 4.081752 TGAAGCTCCTTGAGTGAGAAGATC 60.082 45.833 0.00 0.00 31.26 2.75
1648 1856 0.603707 TCGCCAACTGAAGCTCCTTG 60.604 55.000 0.00 0.00 0.00 3.61
1684 1892 3.074412 ACCTTCACCAAGCTTGTTATCG 58.926 45.455 24.35 11.48 0.00 2.92
1871 2079 2.838202 GGGACTCCACTTCATTGTCCTA 59.162 50.000 9.81 0.00 44.60 2.94
2002 2210 9.912634 TTGTTGTTCATTCTCAAAGAATATTCC 57.087 29.630 11.92 0.00 42.67 3.01
2188 2397 3.857157 AACCTTCTCTACCACAAAGCA 57.143 42.857 0.00 0.00 0.00 3.91
2208 2417 6.239430 GGTCCTATCTAGCTTGTGATCATGAA 60.239 42.308 0.00 0.00 0.00 2.57
2247 2459 1.794714 ACCTCCTCGGCTGTATTCAT 58.205 50.000 0.00 0.00 35.61 2.57
2535 3008 1.148273 GGCCACCTGTCAGTGACAA 59.852 57.895 25.41 10.69 42.26 3.18
2578 3051 1.491670 CCCGTTCAGTGATCATAGCG 58.508 55.000 0.00 1.90 0.00 4.26
2928 3613 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
2929 3614 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
2930 3615 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
2931 3616 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
2932 3617 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
2960 3645 9.698309 CGTATGTAGTTCATATTGGAAATCTCT 57.302 33.333 0.00 0.00 40.54 3.10
2961 3646 8.926710 CCGTATGTAGTTCATATTGGAAATCTC 58.073 37.037 5.56 0.00 40.54 2.75
2962 3647 8.647796 TCCGTATGTAGTTCATATTGGAAATCT 58.352 33.333 9.72 0.00 40.31 2.40
2963 3648 8.827177 TCCGTATGTAGTTCATATTGGAAATC 57.173 34.615 9.72 0.00 40.31 2.17
2964 3649 9.219603 CATCCGTATGTAGTTCATATTGGAAAT 57.780 33.333 13.81 0.00 43.20 2.17
2965 3650 8.208224 ACATCCGTATGTAGTTCATATTGGAAA 58.792 33.333 13.81 0.00 44.66 3.13
2966 3651 7.732025 ACATCCGTATGTAGTTCATATTGGAA 58.268 34.615 13.81 3.55 44.66 3.53
2967 3652 7.297936 ACATCCGTATGTAGTTCATATTGGA 57.702 36.000 12.80 12.80 44.66 3.53
2995 3680 9.529325 GTGCATGTACACTCTAAAATATGTCTA 57.471 33.333 9.26 0.00 37.58 2.59
2996 3681 8.425577 GTGCATGTACACTCTAAAATATGTCT 57.574 34.615 9.26 0.00 37.58 3.41
3010 3695 5.445939 CGGAGTAAAATGAGTGCATGTACAC 60.446 44.000 16.62 10.50 41.02 2.90
3011 3696 4.629634 CGGAGTAAAATGAGTGCATGTACA 59.370 41.667 16.62 0.00 34.26 2.90
3012 3697 4.630069 ACGGAGTAAAATGAGTGCATGTAC 59.370 41.667 5.71 5.71 41.94 2.90
3013 3698 4.827692 ACGGAGTAAAATGAGTGCATGTA 58.172 39.130 0.00 0.00 41.94 2.29
3014 3699 3.674997 ACGGAGTAAAATGAGTGCATGT 58.325 40.909 0.00 0.00 41.94 3.21
3025 3710 7.201848 CCACTATGGACTACATACGGAGTAAAA 60.202 40.741 0.00 0.00 43.87 1.52
3026 3711 6.263842 CCACTATGGACTACATACGGAGTAAA 59.736 42.308 0.00 0.00 43.87 2.01
3027 3712 5.766670 CCACTATGGACTACATACGGAGTAA 59.233 44.000 0.00 0.00 43.87 2.24
3028 3713 5.072193 TCCACTATGGACTACATACGGAGTA 59.928 44.000 0.00 0.00 45.10 2.59
3029 3714 4.141321 TCCACTATGGACTACATACGGAGT 60.141 45.833 0.00 0.00 42.67 3.85
3030 3715 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
3031 3716 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
3040 3725 8.261522 GTCTTTTAAGAGATTCCACTATGGACT 58.738 37.037 0.00 0.00 40.22 3.85
3041 3726 8.261522 AGTCTTTTAAGAGATTCCACTATGGAC 58.738 37.037 0.00 0.00 40.22 4.02
3042 3727 8.380742 AGTCTTTTAAGAGATTCCACTATGGA 57.619 34.615 0.00 0.00 39.33 3.41
3060 3745 9.907229 CCCTCTGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
3061 3746 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
3062 3747 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
3063 3748 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
3064 3749 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
3065 3750 9.145442 GTACTCCCTCTGTTCCTAAATATAAGT 57.855 37.037 0.00 0.00 0.00 2.24
3066 3751 9.144298 TGTACTCCCTCTGTTCCTAAATATAAG 57.856 37.037 0.00 0.00 0.00 1.73
3067 3752 9.670442 ATGTACTCCCTCTGTTCCTAAATATAA 57.330 33.333 0.00 0.00 0.00 0.98
3068 3753 9.670442 AATGTACTCCCTCTGTTCCTAAATATA 57.330 33.333 0.00 0.00 0.00 0.86
3069 3754 8.568617 AATGTACTCCCTCTGTTCCTAAATAT 57.431 34.615 0.00 0.00 0.00 1.28
3070 3755 7.989947 AATGTACTCCCTCTGTTCCTAAATA 57.010 36.000 0.00 0.00 0.00 1.40
3071 3756 6.893020 AATGTACTCCCTCTGTTCCTAAAT 57.107 37.500 0.00 0.00 0.00 1.40
3072 3757 6.271391 TGAAATGTACTCCCTCTGTTCCTAAA 59.729 38.462 0.00 0.00 0.00 1.85
3073 3758 5.783360 TGAAATGTACTCCCTCTGTTCCTAA 59.217 40.000 0.00 0.00 0.00 2.69
3074 3759 5.338632 TGAAATGTACTCCCTCTGTTCCTA 58.661 41.667 0.00 0.00 0.00 2.94
3075 3760 4.168101 TGAAATGTACTCCCTCTGTTCCT 58.832 43.478 0.00 0.00 0.00 3.36
3076 3761 4.553330 TGAAATGTACTCCCTCTGTTCC 57.447 45.455 0.00 0.00 0.00 3.62
3077 3762 5.734720 TCATGAAATGTACTCCCTCTGTTC 58.265 41.667 0.00 0.00 46.80 3.18
3078 3763 5.485353 TCTCATGAAATGTACTCCCTCTGTT 59.515 40.000 0.00 0.00 46.80 3.16
3079 3764 5.026121 TCTCATGAAATGTACTCCCTCTGT 58.974 41.667 0.00 0.00 46.80 3.41
3080 3765 5.604758 TCTCATGAAATGTACTCCCTCTG 57.395 43.478 0.00 0.00 46.80 3.35
3081 3766 5.723887 ACTTCTCATGAAATGTACTCCCTCT 59.276 40.000 0.00 0.00 46.80 3.69
3082 3767 5.983540 ACTTCTCATGAAATGTACTCCCTC 58.016 41.667 0.00 0.00 46.80 4.30
3083 3768 6.380079 AACTTCTCATGAAATGTACTCCCT 57.620 37.500 0.00 0.00 46.80 4.20
3084 3769 6.431234 ACAAACTTCTCATGAAATGTACTCCC 59.569 38.462 0.00 0.00 46.80 4.30
3085 3770 7.440523 ACAAACTTCTCATGAAATGTACTCC 57.559 36.000 0.00 0.00 46.80 3.85
3086 3771 9.209175 ACTACAAACTTCTCATGAAATGTACTC 57.791 33.333 0.00 0.00 46.80 2.59
3087 3772 9.561069 AACTACAAACTTCTCATGAAATGTACT 57.439 29.630 0.00 0.00 46.80 2.73
3088 3773 9.599322 CAACTACAAACTTCTCATGAAATGTAC 57.401 33.333 0.00 0.00 46.80 2.90
3152 3837 1.888512 GTCACCACATGGCACTTCAAT 59.111 47.619 0.00 0.00 39.32 2.57
3239 3924 3.240302 ACAGTTGAGGTGCTAACTAGGT 58.760 45.455 0.00 0.00 35.50 3.08
3251 3936 7.390440 TCTGTTACATGGAATAAACAGTTGAGG 59.610 37.037 18.30 3.31 44.00 3.86
3615 4300 5.428253 TGGTGATGAAGATAACTACAAGGC 58.572 41.667 0.00 0.00 0.00 4.35
3862 4547 4.308526 GCTGGCAAGCTCTAGCAA 57.691 55.556 5.60 0.00 46.60 3.91
3891 4576 4.335037 GTCGTAGGGTTTATCTTCTCGACT 59.665 45.833 0.00 0.00 40.81 4.18
4158 4846 3.655810 CTGGACAGAGCTGGTCGGC 62.656 68.421 6.91 1.84 36.12 5.54
4324 5018 3.625313 CAGACATACACAAACCACACACA 59.375 43.478 0.00 0.00 0.00 3.72
4325 5019 3.548014 GCAGACATACACAAACCACACAC 60.548 47.826 0.00 0.00 0.00 3.82
4332 5026 3.682858 ACCATACGCAGACATACACAAAC 59.317 43.478 0.00 0.00 0.00 2.93
4371 5067 1.080638 TGAAGGGCCCAAGTAACCAT 58.919 50.000 27.56 0.00 0.00 3.55
4372 5068 0.111639 GTGAAGGGCCCAAGTAACCA 59.888 55.000 27.56 7.58 0.00 3.67
4418 5117 8.557864 CATTGCCAAAAGAAATCAACAATACAA 58.442 29.630 0.00 0.00 0.00 2.41
4498 5198 3.428870 GTGAGTACAGGAACACATGAACG 59.571 47.826 0.00 0.00 34.05 3.95
4521 5222 9.740239 CACCAGATAATTGATGAGTTAAATTGG 57.260 33.333 0.00 0.00 0.00 3.16
4589 5290 7.106439 TGGTAAAATCTGCTTGAGTGAAAAA 57.894 32.000 0.00 0.00 0.00 1.94
4648 5359 6.899393 AATATGTTCTCCATGTGTGTTTGT 57.101 33.333 0.00 0.00 34.86 2.83
4717 5468 9.116067 TGTAGTTATTTCTGCAGTTAAACTTGT 57.884 29.630 22.04 9.12 0.00 3.16
4720 5471 8.671384 TGTGTAGTTATTTCTGCAGTTAAACT 57.329 30.769 14.67 19.01 31.39 2.66
5063 5814 6.785488 TTGTCTGTAGCTTGTTTCATACTG 57.215 37.500 0.00 0.00 0.00 2.74
5067 5818 7.446625 AGAGATTTTGTCTGTAGCTTGTTTCAT 59.553 33.333 0.00 0.00 37.29 2.57
5081 5832 6.294397 GCCAGTTCAATTCAGAGATTTTGTCT 60.294 38.462 0.00 0.00 40.81 3.41
5155 6009 6.128035 ACTGAATGCGCATAGTATTGTTCAAA 60.128 34.615 25.61 0.00 35.27 2.69
5180 6034 4.233632 TGGATAATGCATCACCTGTGAA 57.766 40.909 0.00 0.00 43.58 3.18


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

AutoCloner maintained by Alex Coulton.