Multiple sequence alignment - TraesCS7A01G422500

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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 TraesCS7A01G422500 chr7A 100.000 4428 0 0 1 4428 612994956 612990529 0.000000e+00 8178.0
1 TraesCS7A01G422500 chr7A 94.737 38 2 0 1532 1569 612993301 612993264 4.780000e-05 60.2
2 TraesCS7A01G422500 chr7A 94.737 38 2 0 1656 1693 612993425 612993388 4.780000e-05 60.2
3 TraesCS7A01G422500 chr7D 89.171 4137 201 97 419 4413 532902864 532898833 0.000000e+00 4929.0
4 TraesCS7A01G422500 chr7D 91.325 2582 139 28 1604 4128 533434684 533432131 0.000000e+00 3448.0
5 TraesCS7A01G422500 chr7D 82.849 688 48 32 375 1037 533435328 533434686 1.800000e-153 553.0
6 TraesCS7A01G422500 chr7D 94.754 305 10 4 4120 4420 533430858 533430556 1.860000e-128 470.0
7 TraesCS7A01G422500 chr7D 87.500 248 17 10 1 247 533436037 533435803 1.570000e-69 274.0
8 TraesCS7A01G422500 chr7D 89.189 222 11 2 6 226 532903747 532903538 9.440000e-67 265.0
9 TraesCS7A01G422500 chr7D 87.778 90 8 2 3631 3718 532899462 532899374 7.840000e-18 102.0
10 TraesCS7A01G422500 chr7D 87.778 90 8 2 3631 3718 533432493 533432405 7.840000e-18 102.0
11 TraesCS7A01G422500 chr7D 97.500 40 1 0 1655 1694 532901745 532901706 7.950000e-08 69.4
12 TraesCS7A01G422500 chr7D 94.737 38 2 0 1532 1569 532901598 532901561 4.780000e-05 60.2
13 TraesCS7A01G422500 chr7B 86.656 4339 298 123 249 4409 573264928 573260693 0.000000e+00 4545.0
14 TraesCS7A01G422500 chr7B 86.806 144 18 1 249 391 573266513 573266370 4.580000e-35 159.0
15 TraesCS7A01G422500 chr7B 86.517 89 9 2 3631 3717 573261347 573261260 1.310000e-15 95.3
16 TraesCS7A01G422500 chr7B 82.143 112 7 5 136 247 573266770 573266672 2.840000e-12 84.2
17 TraesCS7A01G422500 chr7B 77.778 162 11 10 155 301 573265844 573265693 4.750000e-10 76.8
18 TraesCS7A01G422500 chr7B 97.500 40 1 0 1655 1694 573263651 573263612 7.950000e-08 69.4
19 TraesCS7A01G422500 chr7B 95.349 43 2 0 199 241 573266218 573266176 7.950000e-08 69.4
20 TraesCS7A01G422500 chr5B 87.875 800 83 10 2727 3517 479203663 479202869 0.000000e+00 928.0
21 TraesCS7A01G422500 chr5B 84.988 433 65 0 1786 2218 479204944 479204512 1.460000e-119 440.0
22 TraesCS7A01G422500 chr5B 95.556 45 2 0 606 650 479206733 479206689 6.140000e-09 73.1
23 TraesCS7A01G422500 chr5D 82.821 1042 99 40 2727 3719 398908843 398907833 0.000000e+00 859.0
24 TraesCS7A01G422500 chr5D 85.780 436 59 2 1786 2218 398910111 398909676 4.040000e-125 459.0
25 TraesCS7A01G422500 chr5D 95.833 48 2 0 603 650 398911857 398911810 1.320000e-10 78.7
26 TraesCS7A01G422500 chr5A 84.153 915 111 20 2732 3628 503952325 503953223 0.000000e+00 856.0
27 TraesCS7A01G422500 chr5A 84.687 431 66 0 1786 2216 503950727 503951157 8.800000e-117 431.0
28 TraesCS7A01G422500 chr6D 84.661 678 104 0 2732 3409 72229911 72229234 0.000000e+00 676.0
29 TraesCS7A01G422500 chr6B 84.412 680 106 0 2732 3411 146838513 146837834 0.000000e+00 669.0
30 TraesCS7A01G422500 chr6A 83.807 704 112 2 2727 3429 88855997 88855295 0.000000e+00 667.0


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 TraesCS7A01G422500 chr7A 612990529 612994956 4427 True 2766.133333 8178 96.491333 1 4428 3 chr7A.!!$R1 4427
1 TraesCS7A01G422500 chr7D 532898833 532903747 4914 True 1085.120000 4929 91.675000 6 4413 5 chr7D.!!$R1 4407
2 TraesCS7A01G422500 chr7D 533430556 533436037 5481 True 969.400000 3448 88.841200 1 4420 5 chr7D.!!$R2 4419
3 TraesCS7A01G422500 chr7B 573260693 573266770 6077 True 728.442857 4545 87.535571 136 4409 7 chr7B.!!$R1 4273
4 TraesCS7A01G422500 chr5B 479202869 479206733 3864 True 480.366667 928 89.473000 606 3517 3 chr5B.!!$R1 2911
5 TraesCS7A01G422500 chr5D 398907833 398911857 4024 True 465.566667 859 88.144667 603 3719 3 chr5D.!!$R1 3116
6 TraesCS7A01G422500 chr5A 503950727 503953223 2496 False 643.500000 856 84.420000 1786 3628 2 chr5A.!!$F1 1842
7 TraesCS7A01G422500 chr6D 72229234 72229911 677 True 676.000000 676 84.661000 2732 3409 1 chr6D.!!$R1 677
8 TraesCS7A01G422500 chr6B 146837834 146838513 679 True 669.000000 669 84.412000 2732 3411 1 chr6B.!!$R1 679
9 TraesCS7A01G422500 chr6A 88855295 88855997 702 True 667.000000 667 83.807000 2727 3429 1 chr6A.!!$R1 702

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
959 3070 0.253207 TTCCTTCCTTCCTCCCTCCC 60.253 60.0 0.00 0.00 0.00 4.30 F
1585 3769 0.035534 TGGATGAAGGCTTAAGCGCA 60.036 50.0 20.80 17.82 43.26 6.09 F
1652 3860 0.108472 GACTGTTACTACCACGGGGC 60.108 60.0 1.73 0.00 37.90 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 5199 1.003349 TCGCCATTTTCTACGGGGAAA 59.997 47.619 0.0 1.82 38.66 3.13 R
3052 7256 3.758023 TGGTGCCAAGAACATTGACTATG 59.242 43.478 0.0 0.00 40.26 2.23 R
3748 8010 9.675464 TCTTCATAACCCAATTCGTAATAAACT 57.325 29.630 0.0 0.00 0.00 2.66 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
34 35 6.263344 TGGTCTACGAAAATAGATCACTTCG 58.737 40.000 13.52 13.52 44.69 3.79
99 101 8.511465 CATATATGGAAAGTTTATGCAAGCAC 57.489 34.615 4.68 0.00 0.00 4.40
115 118 0.955905 GCACGAAACCCAAAGGCTAA 59.044 50.000 0.00 0.00 36.11 3.09
116 119 1.338655 GCACGAAACCCAAAGGCTAAA 59.661 47.619 0.00 0.00 36.11 1.85
117 120 2.223852 GCACGAAACCCAAAGGCTAAAA 60.224 45.455 0.00 0.00 36.11 1.52
118 121 3.738590 GCACGAAACCCAAAGGCTAAAAA 60.739 43.478 0.00 0.00 36.11 1.94
241 244 9.354673 GGATAACCCAAGATGATCAAAGAATAA 57.645 33.333 0.00 0.00 34.14 1.40
265 785 4.647853 AGTATATATAATCGGGCAGCCGAA 59.352 41.667 8.21 0.00 45.38 4.30
286 854 0.801067 GCGTAGGCGTAACCACTGAG 60.801 60.000 0.00 0.00 43.14 3.35
304 872 3.917988 TGAGTGATCATCATGGATACGC 58.082 45.455 0.00 0.00 42.51 4.42
359 1751 4.160635 CATCACGCGGCGAAACCC 62.161 66.667 30.94 0.00 33.26 4.11
369 1761 3.814268 CGAAACCCTGCCGCCATG 61.814 66.667 0.00 0.00 0.00 3.66
370 1762 3.451894 GAAACCCTGCCGCCATGG 61.452 66.667 7.63 7.63 42.50 3.66
372 1764 2.830186 GAAACCCTGCCGCCATGGTA 62.830 60.000 14.67 0.00 38.79 3.25
376 1768 4.181010 CTGCCGCCATGGTAGCCT 62.181 66.667 21.03 0.00 43.93 4.58
377 1769 4.175337 TGCCGCCATGGTAGCCTC 62.175 66.667 21.03 0.68 41.21 4.70
379 1771 4.609018 CCGCCATGGTAGCCTCGG 62.609 72.222 14.67 12.66 0.00 4.63
503 2562 1.975680 ACCCACATTTCACTCTACCGT 59.024 47.619 0.00 0.00 0.00 4.83
675 2752 2.045926 ATGGTGACGAAGCAGGGC 60.046 61.111 0.00 0.00 40.26 5.19
749 2846 1.145377 GGGGCGGCGGGTATATATG 59.855 63.158 9.78 0.00 0.00 1.78
761 2858 0.908910 TATATATGGGGCGGCCACAG 59.091 55.000 29.89 0.00 41.80 3.66
762 2859 1.852157 ATATATGGGGCGGCCACAGG 61.852 60.000 29.89 0.00 41.80 4.00
805 2911 3.499737 CCTGCCGCGTGTTCCATC 61.500 66.667 4.92 0.00 0.00 3.51
844 2952 2.510238 GCTGTACCTGAGCGCCAG 60.510 66.667 16.22 16.22 42.55 4.85
845 2953 2.510238 CTGTACCTGAGCGCCAGC 60.510 66.667 17.35 3.25 41.57 4.85
871 2982 1.426423 CATCGCCATCTTCCTCATCG 58.574 55.000 0.00 0.00 0.00 3.84
872 2983 0.320247 ATCGCCATCTTCCTCATCGC 60.320 55.000 0.00 0.00 0.00 4.58
873 2984 1.227350 CGCCATCTTCCTCATCGCA 60.227 57.895 0.00 0.00 0.00 5.10
874 2985 1.220169 CGCCATCTTCCTCATCGCAG 61.220 60.000 0.00 0.00 0.00 5.18
875 2986 1.505477 GCCATCTTCCTCATCGCAGC 61.505 60.000 0.00 0.00 0.00 5.25
876 2987 0.883814 CCATCTTCCTCATCGCAGCC 60.884 60.000 0.00 0.00 0.00 4.85
877 2988 0.883814 CATCTTCCTCATCGCAGCCC 60.884 60.000 0.00 0.00 0.00 5.19
878 2989 2.049627 ATCTTCCTCATCGCAGCCCC 62.050 60.000 0.00 0.00 0.00 5.80
879 2990 3.008517 TTCCTCATCGCAGCCCCA 61.009 61.111 0.00 0.00 0.00 4.96
880 2991 3.329542 TTCCTCATCGCAGCCCCAC 62.330 63.158 0.00 0.00 0.00 4.61
881 2992 4.864334 CCTCATCGCAGCCCCACC 62.864 72.222 0.00 0.00 0.00 4.61
900 3011 2.606519 CCACTCCCCCGAGTCCAA 60.607 66.667 0.00 0.00 46.90 3.53
901 3012 2.660064 CCACTCCCCCGAGTCCAAG 61.660 68.421 0.00 0.00 46.90 3.61
902 3013 1.913762 CACTCCCCCGAGTCCAAGT 60.914 63.158 0.00 0.00 46.90 3.16
903 3014 1.609794 ACTCCCCCGAGTCCAAGTC 60.610 63.158 0.00 0.00 46.90 3.01
904 3015 2.284405 TCCCCCGAGTCCAAGTCC 60.284 66.667 0.00 0.00 0.00 3.85
908 3019 2.261671 CCGAGTCCAAGTCCGTGG 59.738 66.667 0.00 0.00 40.33 4.94
913 3024 4.856789 TCCAAGTCCGTGGAGCTA 57.143 55.556 0.00 0.00 42.97 3.32
914 3025 2.273908 TCCAAGTCCGTGGAGCTAC 58.726 57.895 0.00 0.00 42.97 3.58
915 3026 1.153823 CCAAGTCCGTGGAGCTACG 60.154 63.158 1.93 1.93 41.65 3.51
917 3028 3.338126 AAGTCCGTGGAGCTACGCG 62.338 63.158 25.07 25.07 42.44 6.01
953 3064 1.543358 ACGTACGTTCCTTCCTTCCTC 59.457 52.381 16.72 0.00 0.00 3.71
957 3068 0.537653 CGTTCCTTCCTTCCTCCCTC 59.462 60.000 0.00 0.00 0.00 4.30
958 3069 0.913205 GTTCCTTCCTTCCTCCCTCC 59.087 60.000 0.00 0.00 0.00 4.30
959 3070 0.253207 TTCCTTCCTTCCTCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
960 3071 1.162951 TCCTTCCTTCCTCCCTCCCT 61.163 60.000 0.00 0.00 0.00 4.20
961 3072 0.692756 CCTTCCTTCCTCCCTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
962 3073 0.692756 CTTCCTTCCTCCCTCCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
963 3074 2.040359 CCTTCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
964 3075 2.652113 CCTTCCTCCCTCCCTCCCT 61.652 68.421 0.00 0.00 0.00 4.20
965 3076 1.074850 CTTCCTCCCTCCCTCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
966 3077 2.613576 CTTCCTCCCTCCCTCCCTCC 62.614 70.000 0.00 0.00 0.00 4.30
967 3078 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
968 3079 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1014 3128 2.279120 CTCATGCTCGGTCGCTCC 60.279 66.667 0.00 0.00 0.00 4.70
1062 3183 4.650377 GCGCTCCCCATCCCCATC 62.650 72.222 0.00 0.00 0.00 3.51
1063 3184 3.958860 CGCTCCCCATCCCCATCC 61.959 72.222 0.00 0.00 0.00 3.51
1064 3185 3.584403 GCTCCCCATCCCCATCCC 61.584 72.222 0.00 0.00 0.00 3.85
1065 3186 2.860971 CTCCCCATCCCCATCCCC 60.861 72.222 0.00 0.00 0.00 4.81
1066 3187 3.394792 TCCCCATCCCCATCCCCT 61.395 66.667 0.00 0.00 0.00 4.79
1067 3188 3.188161 CCCCATCCCCATCCCCTG 61.188 72.222 0.00 0.00 0.00 4.45
1148 3284 2.262915 GCGTCCTGAGGTGAGTGG 59.737 66.667 0.00 0.00 0.00 4.00
1149 3285 2.276116 GCGTCCTGAGGTGAGTGGA 61.276 63.158 0.00 0.00 0.00 4.02
1151 3287 1.179174 CGTCCTGAGGTGAGTGGACA 61.179 60.000 10.92 0.00 46.65 4.02
1194 3331 3.420482 CTTCTCCCCGCCCCCATT 61.420 66.667 0.00 0.00 0.00 3.16
1195 3332 2.944390 TTCTCCCCGCCCCCATTT 60.944 61.111 0.00 0.00 0.00 2.32
1197 3334 2.442087 CTCCCCGCCCCCATTTTC 60.442 66.667 0.00 0.00 0.00 2.29
1201 3338 1.613317 CCCCGCCCCCATTTTCTTTC 61.613 60.000 0.00 0.00 0.00 2.62
1207 3344 2.027192 GCCCCCATTTTCTTTCCTTTCC 60.027 50.000 0.00 0.00 0.00 3.13
1208 3345 3.520696 CCCCCATTTTCTTTCCTTTCCT 58.479 45.455 0.00 0.00 0.00 3.36
1209 3346 3.909995 CCCCCATTTTCTTTCCTTTCCTT 59.090 43.478 0.00 0.00 0.00 3.36
1210 3347 4.350816 CCCCCATTTTCTTTCCTTTCCTTT 59.649 41.667 0.00 0.00 0.00 3.11
1211 3348 5.513094 CCCCCATTTTCTTTCCTTTCCTTTC 60.513 44.000 0.00 0.00 0.00 2.62
1212 3349 5.513094 CCCCATTTTCTTTCCTTTCCTTTCC 60.513 44.000 0.00 0.00 0.00 3.13
1213 3350 5.307976 CCCATTTTCTTTCCTTTCCTTTCCT 59.692 40.000 0.00 0.00 0.00 3.36
1214 3351 6.183361 CCCATTTTCTTTCCTTTCCTTTCCTT 60.183 38.462 0.00 0.00 0.00 3.36
1215 3352 7.282585 CCATTTTCTTTCCTTTCCTTTCCTTT 58.717 34.615 0.00 0.00 0.00 3.11
1216 3353 7.442364 CCATTTTCTTTCCTTTCCTTTCCTTTC 59.558 37.037 0.00 0.00 0.00 2.62
1217 3354 6.479972 TTTCTTTCCTTTCCTTTCCTTTCC 57.520 37.500 0.00 0.00 0.00 3.13
1218 3355 5.403558 TCTTTCCTTTCCTTTCCTTTCCT 57.596 39.130 0.00 0.00 0.00 3.36
1219 3356 5.386060 TCTTTCCTTTCCTTTCCTTTCCTC 58.614 41.667 0.00 0.00 0.00 3.71
1220 3357 3.418684 TCCTTTCCTTTCCTTTCCTCG 57.581 47.619 0.00 0.00 0.00 4.63
1221 3358 2.709397 TCCTTTCCTTTCCTTTCCTCGT 59.291 45.455 0.00 0.00 0.00 4.18
1222 3359 3.905591 TCCTTTCCTTTCCTTTCCTCGTA 59.094 43.478 0.00 0.00 0.00 3.43
1223 3360 4.001652 CCTTTCCTTTCCTTTCCTCGTAC 58.998 47.826 0.00 0.00 0.00 3.67
1224 3361 4.262938 CCTTTCCTTTCCTTTCCTCGTACT 60.263 45.833 0.00 0.00 0.00 2.73
1225 3362 3.955650 TCCTTTCCTTTCCTCGTACTG 57.044 47.619 0.00 0.00 0.00 2.74
1239 3380 1.736645 TACTGCTTTCGTGAGGCGC 60.737 57.895 0.00 0.00 41.07 6.53
1268 3432 1.644786 GAATTGGGTCGCTTCCGGTG 61.645 60.000 0.00 0.00 34.56 4.94
1294 3458 1.299468 CCGCTAGGATGCTCGTGTC 60.299 63.158 0.00 0.00 41.02 3.67
1387 3551 1.096967 CCATGGATTGTGCTGCGCTA 61.097 55.000 5.56 7.32 0.00 4.26
1397 3561 2.821366 CTGCGCTAGCTGGGGTTG 60.821 66.667 13.93 5.24 45.42 3.77
1399 3563 3.127533 GCGCTAGCTGGGGTTGTG 61.128 66.667 13.93 0.00 41.01 3.33
1400 3564 2.436646 CGCTAGCTGGGGTTGTGG 60.437 66.667 13.93 0.00 0.00 4.17
1500 3670 7.176690 CACTGGTGTTAGGTTGAGGATAAAAAT 59.823 37.037 0.00 0.00 0.00 1.82
1501 3671 7.728532 ACTGGTGTTAGGTTGAGGATAAAAATT 59.271 33.333 0.00 0.00 0.00 1.82
1502 3672 7.891561 TGGTGTTAGGTTGAGGATAAAAATTG 58.108 34.615 0.00 0.00 0.00 2.32
1505 3675 7.328493 GTGTTAGGTTGAGGATAAAAATTGTGC 59.672 37.037 0.00 0.00 0.00 4.57
1513 3683 0.318762 TAAAAATTGTGCGGGGGTGC 59.681 50.000 0.00 0.00 0.00 5.01
1528 3698 1.470285 GGGTGCAAATACATGCTGCTG 60.470 52.381 0.00 0.00 46.54 4.41
1565 3749 8.367156 AGCTCATAAGACTTGGCAAAATTAAAA 58.633 29.630 0.00 0.00 0.00 1.52
1569 3753 9.434420 CATAAGACTTGGCAAAATTAAAATGGA 57.566 29.630 0.00 0.00 0.00 3.41
1571 3755 7.910441 AGACTTGGCAAAATTAAAATGGATG 57.090 32.000 0.00 0.00 0.00 3.51
1577 3761 5.882000 GGCAAAATTAAAATGGATGAAGGCT 59.118 36.000 0.00 0.00 0.00 4.58
1580 3764 8.945057 GCAAAATTAAAATGGATGAAGGCTTAA 58.055 29.630 0.00 0.00 0.00 1.85
1582 3766 8.722480 AAATTAAAATGGATGAAGGCTTAAGC 57.278 30.769 19.53 19.53 41.14 3.09
1585 3769 0.035534 TGGATGAAGGCTTAAGCGCA 60.036 50.000 20.80 17.82 43.26 6.09
1652 3860 0.108472 GACTGTTACTACCACGGGGC 60.108 60.000 1.73 0.00 37.90 5.80
1653 3861 0.543646 ACTGTTACTACCACGGGGCT 60.544 55.000 1.73 0.00 37.90 5.19
1713 3923 5.554070 TGGCACCCTAAACTAGTAAACTTC 58.446 41.667 0.00 0.00 0.00 3.01
1714 3924 4.628766 GGCACCCTAAACTAGTAAACTTCG 59.371 45.833 0.00 0.00 0.00 3.79
1725 3935 9.551734 AAACTAGTAAACTTCGTCCTTGTTATT 57.448 29.630 0.00 0.00 0.00 1.40
1754 5179 9.177608 CCTTCCATTGTTCTCAATTAATAGACA 57.822 33.333 0.00 0.00 41.66 3.41
1756 5181 8.213518 TCCATTGTTCTCAATTAATAGACAGC 57.786 34.615 0.00 0.00 41.66 4.40
1774 5199 7.010339 AGACAGCTAACTCTATGTTTCCTTT 57.990 36.000 0.00 0.00 39.89 3.11
1778 5203 7.175119 ACAGCTAACTCTATGTTTCCTTTTTCC 59.825 37.037 0.00 0.00 39.89 3.13
1871 5307 1.278985 TGGCAGACCATGTTCGAGATT 59.721 47.619 0.00 0.00 42.67 2.40
2192 5631 0.603707 CGCTGTCCAATGACCACTGT 60.604 55.000 0.00 0.00 41.01 3.55
2218 5657 3.569250 TTTCCTTTTTCAGGTATGCGC 57.431 42.857 0.00 0.00 44.37 6.09
2272 5734 6.126863 TCCATGTAGTCCTTCATTTGTTCT 57.873 37.500 0.00 0.00 0.00 3.01
2273 5735 6.173339 TCCATGTAGTCCTTCATTTGTTCTC 58.827 40.000 0.00 0.00 0.00 2.87
2307 5774 7.402054 ACCATAATAATCTGTTCACACCTCAA 58.598 34.615 0.00 0.00 0.00 3.02
2328 6054 7.320443 TCAAGTGTATGGCAAGATAATGTTC 57.680 36.000 0.00 0.00 0.00 3.18
2415 6145 7.168219 ACTAGTTGAGTTGCCAAAGAATGATA 58.832 34.615 0.00 0.00 33.13 2.15
2484 6641 1.347062 GCTTCTATAGCTGCTCCCCT 58.653 55.000 4.91 0.00 46.77 4.79
2551 6718 4.426416 CACATGGTATTTGCATGAACCTG 58.574 43.478 11.73 9.88 32.99 4.00
2626 6804 5.748402 TGAGCATCTTGTATTGGACTGATT 58.252 37.500 0.00 0.00 34.92 2.57
2644 6822 7.930865 GGACTGATTCTTAGATGCTTGTCTTAT 59.069 37.037 0.00 0.00 0.00 1.73
2661 6839 9.334693 CTTGTCTTATGAATTAGTCTTGTTTGC 57.665 33.333 0.00 0.00 0.00 3.68
2680 6858 6.073058 TGTTTGCTATCATGTCACTTTCTCAC 60.073 38.462 0.00 0.00 0.00 3.51
2716 6903 9.713684 ATCCTTTTTCTCCCATATTTGTCAATA 57.286 29.630 0.00 0.00 0.00 1.90
2718 6905 9.586435 CCTTTTTCTCCCATATTTGTCAATAAC 57.414 33.333 0.00 0.00 0.00 1.89
2721 6908 7.639113 TTCTCCCATATTTGTCAATAACACC 57.361 36.000 0.00 0.00 37.70 4.16
2724 6911 7.893302 TCTCCCATATTTGTCAATAACACCTTT 59.107 33.333 0.00 0.00 37.70 3.11
3148 7352 1.994399 AATCCCTTCCATACACCCCA 58.006 50.000 0.00 0.00 0.00 4.96
3199 7403 1.885871 GCACCCTCTTGCCATTGAC 59.114 57.895 0.00 0.00 36.42 3.18
3400 7605 0.983378 AGATGCTCCAGTACCACCCC 60.983 60.000 0.00 0.00 0.00 4.95
3748 8010 3.734463 TGTGTTGTAGAAGCGGAATTCA 58.266 40.909 7.93 0.00 0.00 2.57
3757 8019 8.193250 TGTAGAAGCGGAATTCAGTTTATTAC 57.807 34.615 7.93 12.91 0.00 1.89
3779 8041 4.636206 ACGAATTGGGTTATGAAGAAGCTC 59.364 41.667 0.00 0.00 0.00 4.09
3811 8073 4.410228 TGTAATCTTCTCTTCTCCCCATGG 59.590 45.833 4.14 4.14 0.00 3.66
3893 8156 6.071051 ACCTTGTTTTGCTTCTACCTTCAAAA 60.071 34.615 0.00 0.00 36.45 2.44
3938 8201 6.094881 GCTAGGAAATTGCAGTTTGTATGGTA 59.905 38.462 12.36 0.00 0.00 3.25
4008 8286 1.266718 CAATGCCGTACCACCATATGC 59.733 52.381 0.00 0.00 0.00 3.14
4009 8287 0.764890 ATGCCGTACCACCATATGCT 59.235 50.000 0.00 0.00 0.00 3.79
4010 8288 0.179059 TGCCGTACCACCATATGCTG 60.179 55.000 0.00 0.00 0.00 4.41
4013 8291 2.416747 CCGTACCACCATATGCTGATG 58.583 52.381 0.00 0.00 0.00 3.07
4014 8292 2.037121 CCGTACCACCATATGCTGATGA 59.963 50.000 0.00 0.00 0.00 2.92
4015 8293 3.059884 CGTACCACCATATGCTGATGAC 58.940 50.000 0.00 0.00 0.00 3.06
4070 8348 4.395231 GGTGGTCAAAGTTATTACTCCTGC 59.605 45.833 0.00 0.00 31.99 4.85
4106 8384 6.648192 AGAACTCATCCGAAGAATTCTGAAT 58.352 36.000 9.17 0.00 44.75 2.57
4136 9695 2.616510 CCTCAACTGGAGTGGTTGGATC 60.617 54.545 6.72 0.00 42.40 3.36
4256 9818 9.698309 AGATATGTGAGAAATATTAACTGACGG 57.302 33.333 0.00 0.00 0.00 4.79
4275 9837 2.292569 CGGAAATCCAAGATGCAGATGG 59.707 50.000 8.51 8.51 35.14 3.51
4298 9860 1.152694 CAGTGGGGCATGGTATGGG 60.153 63.158 0.00 0.00 0.00 4.00
4372 9934 2.613506 GGTTCCGTTGAAGCCCACG 61.614 63.158 0.00 0.00 41.96 4.94
4410 9972 2.384382 CAAAACGAGGCACATCACAAC 58.616 47.619 0.00 0.00 0.00 3.32
4413 9975 0.179059 ACGAGGCACATCACAACACA 60.179 50.000 0.00 0.00 0.00 3.72
4414 9976 0.235665 CGAGGCACATCACAACACAC 59.764 55.000 0.00 0.00 0.00 3.82
4420 9982 2.792196 GCACATCACAACACACACACAG 60.792 50.000 0.00 0.00 0.00 3.66
4421 9983 2.677337 CACATCACAACACACACACAGA 59.323 45.455 0.00 0.00 0.00 3.41
4422 9984 2.938451 ACATCACAACACACACACAGAG 59.062 45.455 0.00 0.00 0.00 3.35
4423 9985 3.197265 CATCACAACACACACACAGAGA 58.803 45.455 0.00 0.00 0.00 3.10
4424 9986 3.326836 TCACAACACACACACAGAGAA 57.673 42.857 0.00 0.00 0.00 2.87
4425 9987 3.669536 TCACAACACACACACAGAGAAA 58.330 40.909 0.00 0.00 0.00 2.52
4426 9988 4.068599 TCACAACACACACACAGAGAAAA 58.931 39.130 0.00 0.00 0.00 2.29
4427 9989 4.517075 TCACAACACACACACAGAGAAAAA 59.483 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.622770 ATCACGTCAATACAAAGAAACCC 57.377 39.130 0.00 0.00 0.00 4.11
93 95 0.597377 GCCTTTGGGTTTCGTGCTTG 60.597 55.000 0.00 0.00 34.45 4.01
116 119 9.673454 GAGTCCTAACATTTTGAATAACGTTTT 57.327 29.630 5.91 0.00 0.00 2.43
117 120 8.842280 TGAGTCCTAACATTTTGAATAACGTTT 58.158 29.630 5.91 0.00 0.00 3.60
118 121 8.385898 TGAGTCCTAACATTTTGAATAACGTT 57.614 30.769 5.88 5.88 0.00 3.99
119 122 7.972832 TGAGTCCTAACATTTTGAATAACGT 57.027 32.000 0.00 0.00 0.00 3.99
120 123 9.672086 TTTTGAGTCCTAACATTTTGAATAACG 57.328 29.630 0.00 0.00 0.00 3.18
125 128 9.311916 CAACATTTTGAGTCCTAACATTTTGAA 57.688 29.630 0.00 0.00 34.24 2.69
126 129 8.474025 ACAACATTTTGAGTCCTAACATTTTGA 58.526 29.630 0.00 0.00 36.48 2.69
127 130 8.647143 ACAACATTTTGAGTCCTAACATTTTG 57.353 30.769 0.00 0.00 36.48 2.44
132 135 7.397892 TTGAACAACATTTTGAGTCCTAACA 57.602 32.000 0.00 0.00 36.48 2.41
198 201 1.003718 CCTCCAACTTCGGGTCACC 60.004 63.158 0.00 0.00 0.00 4.02
206 209 4.569719 TCTTGGGTTATCCTCCAACTTC 57.430 45.455 0.00 0.00 38.04 3.01
265 785 0.459585 CAGTGGTTACGCCTACGCAT 60.460 55.000 0.00 0.00 45.53 4.73
286 854 2.350522 GGGCGTATCCATGATGATCAC 58.649 52.381 0.00 0.00 36.21 3.06
309 877 3.463944 AGTTTATCGCCCGAGGTATTTG 58.536 45.455 0.00 0.00 0.00 2.32
315 883 4.320971 CGAGTTTATCGCCCGAGG 57.679 61.111 0.00 0.00 45.98 4.63
359 1751 4.181010 AGGCTACCATGGCGGCAG 62.181 66.667 24.57 7.31 39.03 4.85
365 1757 3.792053 GACGCCGAGGCTACCATGG 62.792 68.421 11.19 11.19 39.32 3.66
369 1761 3.412879 GAGTGACGCCGAGGCTACC 62.413 68.421 12.70 1.84 39.32 3.18
370 1762 2.102553 GAGTGACGCCGAGGCTAC 59.897 66.667 12.70 8.46 39.32 3.58
373 1765 4.500116 GAGGAGTGACGCCGAGGC 62.500 72.222 3.59 3.59 37.85 4.70
374 1766 3.827898 GGAGGAGTGACGCCGAGG 61.828 72.222 0.00 0.00 0.00 4.63
375 1767 2.752238 AGGAGGAGTGACGCCGAG 60.752 66.667 0.00 0.00 0.00 4.63
376 1768 2.750637 GAGGAGGAGTGACGCCGA 60.751 66.667 0.00 0.00 0.00 5.54
377 1769 3.827898 GGAGGAGGAGTGACGCCG 61.828 72.222 0.00 0.00 0.00 6.46
378 1770 3.827898 CGGAGGAGGAGTGACGCC 61.828 72.222 0.00 0.00 0.00 5.68
379 1771 1.748122 TACGGAGGAGGAGTGACGC 60.748 63.158 0.00 0.00 0.00 5.19
380 1772 1.375098 GGTACGGAGGAGGAGTGACG 61.375 65.000 0.00 0.00 0.00 4.35
381 1773 2.491291 GGTACGGAGGAGGAGTGAC 58.509 63.158 0.00 0.00 0.00 3.67
476 2535 3.951680 AGAGTGAAATGTGGGTCGTTTTT 59.048 39.130 0.00 0.00 35.66 1.94
731 2828 1.145377 CATATATACCCGCCGCCCC 59.855 63.158 0.00 0.00 0.00 5.80
761 2858 3.090532 ACGATGAGGAAGGCCCCC 61.091 66.667 0.00 0.06 34.66 5.40
762 2859 1.627297 AAGACGATGAGGAAGGCCCC 61.627 60.000 0.00 0.00 34.66 5.80
763 2860 0.179070 GAAGACGATGAGGAAGGCCC 60.179 60.000 0.00 0.00 33.31 5.80
872 2983 4.351054 GGAGTGGTGGTGGGGCTG 62.351 72.222 0.00 0.00 0.00 4.85
878 2989 3.706373 CTCGGGGGAGTGGTGGTG 61.706 72.222 0.00 0.00 0.00 4.17
879 2990 4.250170 ACTCGGGGGAGTGGTGGT 62.250 66.667 0.00 0.00 33.58 4.16
880 2991 3.391382 GACTCGGGGGAGTGGTGG 61.391 72.222 0.81 0.00 35.23 4.61
881 2992 3.391382 GGACTCGGGGGAGTGGTG 61.391 72.222 0.81 0.00 35.23 4.17
932 3043 2.749621 GAGGAAGGAAGGAACGTACGTA 59.250 50.000 23.12 0.00 0.00 3.57
937 3048 0.178900 AGGGAGGAAGGAAGGAACGT 60.179 55.000 0.00 0.00 0.00 3.99
953 3064 2.040359 GAAGGGAGGGAGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
958 3069 3.635869 TTCGGGGAAGGGAGGGAGG 62.636 68.421 0.00 0.00 0.00 4.30
959 3070 0.988678 ATTTCGGGGAAGGGAGGGAG 60.989 60.000 0.00 0.00 0.00 4.30
960 3071 0.344080 TATTTCGGGGAAGGGAGGGA 59.656 55.000 0.00 0.00 0.00 4.20
961 3072 1.218844 TTATTTCGGGGAAGGGAGGG 58.781 55.000 0.00 0.00 0.00 4.30
962 3073 3.375647 TTTTATTTCGGGGAAGGGAGG 57.624 47.619 0.00 0.00 0.00 4.30
1000 3114 3.842923 CAGGGAGCGACCGAGCAT 61.843 66.667 0.00 0.00 40.11 3.79
1186 3323 2.027192 GGAAAGGAAAGAAAATGGGGGC 60.027 50.000 0.00 0.00 0.00 5.80
1189 3326 5.307976 AGGAAAGGAAAGGAAAGAAAATGGG 59.692 40.000 0.00 0.00 0.00 4.00
1192 3329 7.348274 AGGAAAGGAAAGGAAAGGAAAGAAAAT 59.652 33.333 0.00 0.00 0.00 1.82
1193 3330 6.672218 AGGAAAGGAAAGGAAAGGAAAGAAAA 59.328 34.615 0.00 0.00 0.00 2.29
1194 3331 6.202331 AGGAAAGGAAAGGAAAGGAAAGAAA 58.798 36.000 0.00 0.00 0.00 2.52
1195 3332 5.777449 AGGAAAGGAAAGGAAAGGAAAGAA 58.223 37.500 0.00 0.00 0.00 2.52
1197 3334 4.216472 CGAGGAAAGGAAAGGAAAGGAAAG 59.784 45.833 0.00 0.00 0.00 2.62
1201 3338 3.141767 ACGAGGAAAGGAAAGGAAAGG 57.858 47.619 0.00 0.00 0.00 3.11
1207 3344 3.320673 AGCAGTACGAGGAAAGGAAAG 57.679 47.619 0.00 0.00 0.00 2.62
1208 3345 3.764237 AAGCAGTACGAGGAAAGGAAA 57.236 42.857 0.00 0.00 0.00 3.13
1209 3346 3.660865 GAAAGCAGTACGAGGAAAGGAA 58.339 45.455 0.00 0.00 0.00 3.36
1210 3347 2.352421 CGAAAGCAGTACGAGGAAAGGA 60.352 50.000 0.00 0.00 0.00 3.36
1211 3348 1.993370 CGAAAGCAGTACGAGGAAAGG 59.007 52.381 0.00 0.00 0.00 3.11
1212 3349 2.408704 CACGAAAGCAGTACGAGGAAAG 59.591 50.000 0.00 0.00 0.00 2.62
1213 3350 2.034939 TCACGAAAGCAGTACGAGGAAA 59.965 45.455 0.00 0.00 0.00 3.13
1214 3351 1.610038 TCACGAAAGCAGTACGAGGAA 59.390 47.619 0.00 0.00 0.00 3.36
1215 3352 1.199327 CTCACGAAAGCAGTACGAGGA 59.801 52.381 0.00 0.00 0.00 3.71
1216 3353 1.618861 CTCACGAAAGCAGTACGAGG 58.381 55.000 0.00 0.00 0.00 4.63
1217 3354 1.618861 CCTCACGAAAGCAGTACGAG 58.381 55.000 0.00 0.00 0.00 4.18
1218 3355 0.388134 GCCTCACGAAAGCAGTACGA 60.388 55.000 0.00 0.00 0.00 3.43
1219 3356 2.070861 GCCTCACGAAAGCAGTACG 58.929 57.895 0.00 0.00 0.00 3.67
1239 3380 3.204827 CCCAATTCGGCTCCGCTG 61.205 66.667 2.96 1.20 39.59 5.18
1243 3384 3.202706 GCGACCCAATTCGGCTCC 61.203 66.667 0.00 0.00 39.50 4.70
1244 3385 1.706287 GAAGCGACCCAATTCGGCTC 61.706 60.000 0.00 0.00 39.50 4.70
1309 3473 1.575132 CGCATTTCGACGCAACTCG 60.575 57.895 0.00 0.00 41.67 4.18
1400 3564 4.423209 AGCCACCCTCTCTCCCCC 62.423 72.222 0.00 0.00 0.00 5.40
1473 3643 1.071699 TCCTCAACCTAACACCAGTGC 59.928 52.381 0.00 0.00 0.00 4.40
1500 3670 1.228583 TATTTGCACCCCCGCACAA 60.229 52.632 0.00 0.00 42.87 3.33
1501 3671 1.974343 GTATTTGCACCCCCGCACA 60.974 57.895 0.00 0.00 42.87 4.57
1502 3672 1.319614 ATGTATTTGCACCCCCGCAC 61.320 55.000 0.00 0.00 42.87 5.34
1505 3675 1.037030 AGCATGTATTTGCACCCCCG 61.037 55.000 0.00 0.00 45.23 5.73
1513 3683 4.158394 ACCTTTACCAGCAGCATGTATTTG 59.842 41.667 0.00 0.00 39.31 2.32
1517 3687 2.304470 TGACCTTTACCAGCAGCATGTA 59.696 45.455 0.00 0.00 39.31 2.29
1528 3698 5.735766 AGTCTTATGAGCTTGACCTTTACC 58.264 41.667 0.00 0.00 0.00 2.85
1565 3749 1.312815 GCGCTTAAGCCTTCATCCAT 58.687 50.000 21.53 0.00 37.91 3.41
1569 3753 0.940126 CGATGCGCTTAAGCCTTCAT 59.060 50.000 21.53 19.79 37.91 2.57
1570 3754 2.383170 CGATGCGCTTAAGCCTTCA 58.617 52.632 21.53 16.26 37.91 3.02
1592 3776 3.243501 ACAATTCATCATAACCATGGCGC 60.244 43.478 13.04 0.00 32.61 6.53
1594 3778 5.045215 CACACAATTCATCATAACCATGGC 58.955 41.667 13.04 0.00 32.61 4.40
1595 3779 6.037726 CACACACAATTCATCATAACCATGG 58.962 40.000 11.19 11.19 32.61 3.66
1597 3781 5.127519 CCCACACACAATTCATCATAACCAT 59.872 40.000 0.00 0.00 0.00 3.55
1599 3783 4.142182 CCCCACACACAATTCATCATAACC 60.142 45.833 0.00 0.00 0.00 2.85
1641 3849 2.289819 TGACTTTTTAGCCCCGTGGTAG 60.290 50.000 0.00 0.00 0.00 3.18
1647 3855 1.468914 GAGCTTGACTTTTTAGCCCCG 59.531 52.381 0.00 0.00 35.53 5.73
1652 3860 8.233190 CCAAGTCTTATGAGCTTGACTTTTTAG 58.767 37.037 17.33 6.50 44.32 1.85
1653 3861 7.308589 GCCAAGTCTTATGAGCTTGACTTTTTA 60.309 37.037 17.33 0.00 44.32 1.52
1713 3923 6.542370 ACAATGGAAGGATAATAACAAGGACG 59.458 38.462 0.00 0.00 0.00 4.79
1714 3924 7.881775 ACAATGGAAGGATAATAACAAGGAC 57.118 36.000 0.00 0.00 0.00 3.85
1727 3937 9.396022 GTCTATTAATTGAGAACAATGGAAGGA 57.604 33.333 0.00 0.00 44.67 3.36
1728 3938 9.177608 TGTCTATTAATTGAGAACAATGGAAGG 57.822 33.333 0.00 0.00 44.67 3.46
1754 5179 6.659668 GGGAAAAAGGAAACATAGAGTTAGCT 59.340 38.462 0.00 0.00 40.26 3.32
1756 5181 6.093633 CGGGGAAAAAGGAAACATAGAGTTAG 59.906 42.308 0.00 0.00 40.26 2.34
1774 5199 1.003349 TCGCCATTTTCTACGGGGAAA 59.997 47.619 0.00 1.82 38.66 3.13
1778 5203 1.948104 TCATCGCCATTTTCTACGGG 58.052 50.000 0.00 0.00 0.00 5.28
1808 5244 1.969589 GTTTCCCATGCCGTTCGGT 60.970 57.895 12.81 0.00 0.00 4.69
1871 5307 4.762825 GGCACGTACTTGGTGTCA 57.237 55.556 1.12 0.00 39.71 3.58
2218 5657 3.923017 AAGAATGAAAAACAGAGCCGG 57.077 42.857 0.00 0.00 0.00 6.13
2272 5734 9.778741 GAACAGATTATTATGGTAGAATGGTGA 57.221 33.333 0.00 0.00 0.00 4.02
2273 5735 9.559732 TGAACAGATTATTATGGTAGAATGGTG 57.440 33.333 0.00 0.00 0.00 4.17
2307 5774 7.944729 AAAGAACATTATCTTGCCATACACT 57.055 32.000 0.00 0.00 39.54 3.55
2334 6060 9.935682 CACTTAATGCAAATTAGTATGAACGAT 57.064 29.630 0.00 0.00 0.00 3.73
2415 6145 4.580167 TGCGCTTCTTCCATAAATTAGCAT 59.420 37.500 9.73 0.00 0.00 3.79
2484 6641 5.911752 TGCTTTTAAGAAATGCACTTCCAA 58.088 33.333 3.90 0.00 43.77 3.53
2551 6718 9.989869 GAAATAATTCACAGAGGCTTAAGTTAC 57.010 33.333 4.02 0.00 35.54 2.50
2644 6822 8.565896 ACATGATAGCAAACAAGACTAATTCA 57.434 30.769 0.00 0.00 0.00 2.57
2661 6839 8.489990 AAGAATGTGAGAAAGTGACATGATAG 57.510 34.615 0.00 0.00 30.69 2.08
2680 6858 5.948162 TGGGAGAAAAAGGATCAGAAGAATG 59.052 40.000 0.00 0.00 0.00 2.67
3052 7256 3.758023 TGGTGCCAAGAACATTGACTATG 59.242 43.478 0.00 0.00 40.26 2.23
3748 8010 9.675464 TCTTCATAACCCAATTCGTAATAAACT 57.325 29.630 0.00 0.00 0.00 2.66
3757 8019 4.260375 CGAGCTTCTTCATAACCCAATTCG 60.260 45.833 0.00 0.00 0.00 3.34
3779 8041 7.273815 GGAGAAGAGAAGATTACAACTTACACG 59.726 40.741 0.00 0.00 0.00 4.49
3811 8073 8.902735 GCAGCTTCTAAAATTACAACTTACAAC 58.097 33.333 0.00 0.00 0.00 3.32
3918 8181 9.423061 AGAAAATACCATACAAACTGCAATTTC 57.577 29.630 0.00 0.00 0.00 2.17
4008 8286 4.082026 TCAGTGTGTACATCAGGTCATCAG 60.082 45.833 0.00 0.00 0.00 2.90
4009 8287 3.831911 TCAGTGTGTACATCAGGTCATCA 59.168 43.478 0.00 0.00 0.00 3.07
4010 8288 4.456280 TCAGTGTGTACATCAGGTCATC 57.544 45.455 0.00 0.00 0.00 2.92
4013 8291 4.569943 ACATTCAGTGTGTACATCAGGTC 58.430 43.478 0.00 0.00 40.28 3.85
4014 8292 4.623932 ACATTCAGTGTGTACATCAGGT 57.376 40.909 0.00 0.00 40.28 4.00
4044 8322 6.094048 CAGGAGTAATAACTTTGACCACCATG 59.906 42.308 0.00 0.00 35.56 3.66
4070 8348 1.362224 TGAGTTCTTTCCCAGGGGAG 58.638 55.000 5.33 4.46 46.06 4.30
4106 8384 1.349026 CTCCAGTTGAGGGCTTGAGAA 59.651 52.381 0.00 0.00 37.45 2.87
4136 9695 6.964370 TCACATAGAAACACAAAGTGAAAACG 59.036 34.615 3.88 0.00 36.96 3.60
4256 9818 4.883585 TGTACCATCTGCATCTTGGATTTC 59.116 41.667 14.61 4.84 34.52 2.17
4275 9837 0.616371 TACCATGCCCCACTGTGTAC 59.384 55.000 7.08 0.00 0.00 2.90
4298 9860 1.669211 GGCGACAGTAGTGAACCAGTC 60.669 57.143 4.09 0.00 32.86 3.51
4372 9934 3.431725 GCGCTGCAGGGGTACAAC 61.432 66.667 29.52 10.16 0.00 3.32


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

AutoCloner maintained by Alex Coulton.