Multiple sequence alignment - TraesCS2B01G552800

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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 TraesCS2B01G552800 chr2B 100.000 3902 0 0 1 3902 748699958 748703859 0.000000e+00 7206.0
1 TraesCS2B01G552800 chr2B 84.087 553 68 11 3365 3902 748588962 748588415 2.080000e-142 516.0
2 TraesCS2B01G552800 chr2B 84.086 465 46 17 2601 3053 748589601 748589153 1.300000e-114 424.0
3 TraesCS2B01G552800 chr2B 78.235 510 89 15 3324 3829 748573449 748572958 1.360000e-79 307.0
4 TraesCS2B01G552800 chr2B 85.526 76 11 0 2915 2990 748581147 748581072 3.230000e-11 80.5
5 TraesCS2B01G552800 chr2A 92.610 2950 166 25 1 2926 744978850 744981771 0.000000e+00 4193.0
6 TraesCS2B01G552800 chr2A 83.814 797 92 16 3105 3890 744994343 744995113 0.000000e+00 723.0
7 TraesCS2B01G552800 chr2A 85.597 486 64 2 3423 3902 744905479 744904994 4.500000e-139 505.0
8 TraesCS2B01G552800 chr2A 95.122 82 2 2 3094 3174 744981814 744981894 1.140000e-25 128.0
9 TraesCS2B01G552800 chr2A 100.000 30 0 0 3091 3120 744994316 744994345 5.450000e-04 56.5
10 TraesCS2B01G552800 chr2D 92.333 1852 121 7 1087 2926 613322459 613324301 0.000000e+00 2614.0
11 TraesCS2B01G552800 chr2D 87.589 1120 91 22 2 1085 613321287 613322394 0.000000e+00 1254.0
12 TraesCS2B01G552800 chr2D 91.755 752 42 7 3170 3902 613324467 613325217 0.000000e+00 1027.0
13 TraesCS2B01G552800 chr2D 83.363 553 72 13 3364 3902 613235184 613234638 9.740000e-136 494.0
14 TraesCS2B01G552800 chr2D 85.470 468 44 16 2601 3057 613235871 613235417 2.120000e-127 466.0
15 TraesCS2B01G552800 chr2D 82.600 500 66 12 3178 3659 613238116 613237620 4.660000e-114 422.0
16 TraesCS2B01G552800 chr2D 86.007 293 20 14 2619 2903 613238702 613238423 1.060000e-75 294.0
17 TraesCS2B01G552800 chr2D 75.832 571 102 23 3279 3829 613225008 613224454 1.390000e-64 257.0
18 TraesCS2B01G552800 chr2D 100.000 32 0 0 3089 3120 613324376 613324407 4.210000e-05 60.2
19 TraesCS2B01G552800 chr5A 90.345 145 12 2 3441 3584 521768588 521768731 5.150000e-44 189.0
20 TraesCS2B01G552800 chr5A 83.832 167 24 3 3457 3622 521797872 521798036 5.220000e-34 156.0
21 TraesCS2B01G552800 chr5D 88.276 145 15 2 3441 3584 410346740 410346883 5.180000e-39 172.0


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 TraesCS2B01G552800 chr2B 748699958 748703859 3901 False 7206.00 7206 100.00000 1 3902 1 chr2B.!!$F1 3901
1 TraesCS2B01G552800 chr2B 748588415 748589601 1186 True 470.00 516 84.08650 2601 3902 2 chr2B.!!$R3 1301
2 TraesCS2B01G552800 chr2A 744978850 744981894 3044 False 2160.50 4193 93.86600 1 3174 2 chr2A.!!$F1 3173
3 TraesCS2B01G552800 chr2A 744994316 744995113 797 False 389.75 723 91.90700 3091 3890 2 chr2A.!!$F2 799
4 TraesCS2B01G552800 chr2D 613321287 613325217 3930 False 1238.80 2614 92.91925 2 3902 4 chr2D.!!$F1 3900
5 TraesCS2B01G552800 chr2D 613234638 613238702 4064 True 419.00 494 84.36000 2601 3902 4 chr2D.!!$R2 1301
6 TraesCS2B01G552800 chr2D 613224454 613225008 554 True 257.00 257 75.83200 3279 3829 1 chr2D.!!$R1 550

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
934 990 0.676736 GGGGTTTTGATTGTTCGGCA 59.323 50.0 0.0 0.0 0.00 5.69 F
2555 2674 0.394899 AAGCAGGGCCTAAGCATGAC 60.395 55.0 17.2 0.0 42.56 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 2895 0.036952 ACTCTGCATGTGTTCTCCCG 60.037 55.000 0.0 0.0 0.00 5.14 R
3455 3810 1.300963 GCAGCAGGATCTCCACCAA 59.699 57.895 0.0 0.0 38.89 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
158 175 3.317993 ACAATTTTCTTCCACTTGTCCCG 59.682 43.478 0.00 0.00 0.00 5.14
219 236 9.880157 TCCAACTCAAATTTACAGTATAGGTAC 57.120 33.333 3.07 0.00 0.00 3.34
244 261 8.679288 CTGAAATCAGCTGTATTGGTTTTAAG 57.321 34.615 14.67 3.18 37.15 1.85
260 291 1.091537 TAAGCAAACACCATAGCGCC 58.908 50.000 2.29 0.00 0.00 6.53
274 305 2.572191 AGCGCCAATTCATGTTCATG 57.428 45.000 2.29 6.46 0.00 3.07
293 324 1.535028 TGTCAAGCAAACACCATAGCG 59.465 47.619 0.00 0.00 0.00 4.26
340 382 8.685427 CCATTTCCTCATGTACATTAATGAACA 58.315 33.333 22.16 3.97 32.60 3.18
409 451 4.226761 GTTAGCATTTTTGTCCAAGGTCG 58.773 43.478 0.00 0.00 0.00 4.79
452 494 9.565090 TTAATCTCATATGTCTGGATTTCCTTG 57.435 33.333 1.90 0.00 36.82 3.61
457 499 3.507162 TGTCTGGATTTCCTTGCAAGA 57.493 42.857 28.05 8.51 36.82 3.02
463 505 4.897140 TGGATTTCCTTGCAAGATTTTGG 58.103 39.130 28.05 10.96 36.82 3.28
487 529 9.967451 TGGATCACTTTATTATTTTCACCTGTA 57.033 29.630 0.00 0.00 0.00 2.74
539 581 2.359900 GTTGTGGATGAGTAGGCTTGG 58.640 52.381 0.00 0.00 0.00 3.61
610 653 7.250569 TCTGTCAGTTGTTTTCTTTTGATCAC 58.749 34.615 0.00 0.00 0.00 3.06
681 724 6.541641 GCAGATCTCAGAGGACATTTAATTGT 59.458 38.462 2.71 2.71 0.00 2.71
686 729 6.650807 TCTCAGAGGACATTTAATTGTGTGAC 59.349 38.462 7.69 0.00 0.00 3.67
764 807 1.372582 CCGTAGTGCTGCAACATCAT 58.627 50.000 2.77 0.00 0.00 2.45
776 819 3.120683 TGCAACATCATCGTTTCTCGTTC 60.121 43.478 0.00 0.00 40.80 3.95
840 883 1.271379 GGCTTTCTTGGTAGTGGCTCA 60.271 52.381 0.00 0.00 0.00 4.26
863 906 2.753989 TGCAAGAACATTGACGTGTG 57.246 45.000 0.00 0.00 31.49 3.82
934 990 0.676736 GGGGTTTTGATTGTTCGGCA 59.323 50.000 0.00 0.00 0.00 5.69
936 992 1.611491 GGGTTTTGATTGTTCGGCAGA 59.389 47.619 0.00 0.00 0.00 4.26
937 993 2.035321 GGGTTTTGATTGTTCGGCAGAA 59.965 45.455 0.00 0.00 0.00 3.02
938 994 3.308530 GGTTTTGATTGTTCGGCAGAAG 58.691 45.455 0.00 0.00 36.99 2.85
940 996 1.896220 TTGATTGTTCGGCAGAAGCT 58.104 45.000 0.00 0.00 41.70 3.74
941 997 2.760634 TGATTGTTCGGCAGAAGCTA 57.239 45.000 0.00 0.00 41.70 3.32
942 998 3.266510 TGATTGTTCGGCAGAAGCTAT 57.733 42.857 0.00 0.00 41.70 2.97
943 999 3.609853 TGATTGTTCGGCAGAAGCTATT 58.390 40.909 0.00 0.00 41.70 1.73
944 1000 3.374988 TGATTGTTCGGCAGAAGCTATTG 59.625 43.478 0.00 0.00 41.70 1.90
945 1001 1.737838 TGTTCGGCAGAAGCTATTGG 58.262 50.000 0.00 0.00 41.70 3.16
951 1007 1.467920 GCAGAAGCTATTGGCCACTT 58.532 50.000 3.88 5.24 43.05 3.16
995 1051 8.679725 TCTCTGTCCTAATCCTACCTTATACAT 58.320 37.037 0.00 0.00 0.00 2.29
1295 1414 1.702401 TGCAAGTGATCCTGGGTTACA 59.298 47.619 4.56 0.00 0.00 2.41
1432 1551 2.362077 TCAACTTCAGCCAAAAGGAAGC 59.638 45.455 0.00 0.00 41.26 3.86
1478 1597 3.349927 TGTTTGCTCCAAGATCAGATGG 58.650 45.455 0.00 0.32 38.09 3.51
1566 1685 5.350914 GGCCGATCATGATTTATCTCTTGAG 59.649 44.000 10.14 0.00 34.13 3.02
1574 1693 3.592898 TTTATCTCTTGAGCAGCACGA 57.407 42.857 0.00 0.00 0.00 4.35
1639 1758 1.725641 TGCCGCAACTTCAGATACAG 58.274 50.000 0.00 0.00 0.00 2.74
1737 1856 3.732849 GGAAGGGGTGCCTCAGGG 61.733 72.222 0.00 0.00 0.00 4.45
1848 1967 2.747855 GGAGGAAAGCGGTGCCAG 60.748 66.667 9.14 0.00 0.00 4.85
1963 2082 3.142393 CGCGGGGAAGATCAGGAT 58.858 61.111 0.00 0.00 0.00 3.24
1974 2093 6.462067 GGGGAAGATCAGGATTTTGCATAAAG 60.462 42.308 6.43 0.00 0.00 1.85
2265 2384 1.592400 CTAAGAGTGTCCACGGCGGA 61.592 60.000 13.24 0.00 43.61 5.54
2555 2674 0.394899 AAGCAGGGCCTAAGCATGAC 60.395 55.000 17.20 0.00 42.56 3.06
2587 2706 3.391160 TTCAGCGGGATCGTCGTCG 62.391 63.158 8.50 0.00 38.89 5.12
2613 2845 3.211963 GGCGGCATGGACCATGTC 61.212 66.667 30.55 28.54 43.10 3.06
2658 2890 4.426112 TCAGACTGCTGCGGCGAG 62.426 66.667 12.98 13.61 42.01 5.03
2660 2892 4.427661 AGACTGCTGCGGCGAGTC 62.428 66.667 28.28 28.28 41.89 3.36
2752 2990 3.243975 ACCATCGTCTTCGTTTAACCTGT 60.244 43.478 0.00 0.00 38.33 4.00
2777 3018 1.135575 CAATGGCCACGAAGAAGAAGC 60.136 52.381 8.16 0.00 0.00 3.86
2783 3024 1.541233 CCACGAAGAAGAAGCTGGTGT 60.541 52.381 0.00 0.00 0.00 4.16
2820 3061 4.668118 GGGTTCGTCGTGCCGGAA 62.668 66.667 5.05 0.00 0.00 4.30
2919 3160 4.452114 TCCTGATGAAAACGACACATCTTG 59.548 41.667 0.00 0.00 40.39 3.02
2948 3191 7.557358 TGTGGTTTGAGCATATTATGATTCTGT 59.443 33.333 7.87 0.00 0.00 3.41
2964 3207 1.553248 TCTGTGCCTAGCAACCGTATT 59.447 47.619 0.00 0.00 41.47 1.89
2975 3218 2.601763 GCAACCGTATTACTCTTGACCG 59.398 50.000 5.11 0.00 0.00 4.79
2976 3219 3.841643 CAACCGTATTACTCTTGACCGT 58.158 45.455 0.00 0.00 0.00 4.83
2990 3233 0.804989 GACCGTCATTGGGCTTTGAG 59.195 55.000 0.00 0.00 32.64 3.02
2991 3234 0.110486 ACCGTCATTGGGCTTTGAGT 59.890 50.000 0.00 0.00 0.00 3.41
2992 3235 1.349688 ACCGTCATTGGGCTTTGAGTA 59.650 47.619 0.00 0.00 0.00 2.59
2993 3236 2.224670 ACCGTCATTGGGCTTTGAGTAA 60.225 45.455 0.00 0.00 0.00 2.24
2994 3237 3.016736 CCGTCATTGGGCTTTGAGTAAT 58.983 45.455 0.00 0.00 0.00 1.89
2995 3238 3.065371 CCGTCATTGGGCTTTGAGTAATC 59.935 47.826 0.00 0.00 0.00 1.75
2997 3240 4.273318 GTCATTGGGCTTTGAGTAATCCT 58.727 43.478 0.00 0.00 0.00 3.24
2999 3242 5.185828 GTCATTGGGCTTTGAGTAATCCTTT 59.814 40.000 0.00 0.00 0.00 3.11
3000 3243 5.185635 TCATTGGGCTTTGAGTAATCCTTTG 59.814 40.000 0.00 0.00 0.00 2.77
3001 3244 4.380843 TGGGCTTTGAGTAATCCTTTGA 57.619 40.909 0.00 0.00 0.00 2.69
3002 3245 4.335416 TGGGCTTTGAGTAATCCTTTGAG 58.665 43.478 0.00 0.00 0.00 3.02
3003 3246 3.129462 GGGCTTTGAGTAATCCTTTGAGC 59.871 47.826 0.00 0.00 0.00 4.26
3004 3247 3.758554 GGCTTTGAGTAATCCTTTGAGCA 59.241 43.478 0.00 0.00 0.00 4.26
3007 3250 6.264067 GGCTTTGAGTAATCCTTTGAGCATAT 59.736 38.462 0.00 0.00 0.00 1.78
3008 3251 7.445402 GGCTTTGAGTAATCCTTTGAGCATATA 59.555 37.037 0.00 0.00 0.00 0.86
3009 3252 8.840321 GCTTTGAGTAATCCTTTGAGCATATAA 58.160 33.333 0.00 0.00 0.00 0.98
3012 3255 9.547753 TTGAGTAATCCTTTGAGCATATAAGAC 57.452 33.333 0.00 0.00 0.00 3.01
3013 3256 8.928448 TGAGTAATCCTTTGAGCATATAAGACT 58.072 33.333 0.00 0.00 0.00 3.24
3014 3257 9.202273 GAGTAATCCTTTGAGCATATAAGACTG 57.798 37.037 0.00 0.00 0.00 3.51
3015 3258 8.709308 AGTAATCCTTTGAGCATATAAGACTGT 58.291 33.333 0.00 0.00 0.00 3.55
3016 3259 8.983724 GTAATCCTTTGAGCATATAAGACTGTC 58.016 37.037 0.00 0.00 0.00 3.51
3017 3260 6.544928 TCCTTTGAGCATATAAGACTGTCA 57.455 37.500 10.88 0.00 0.00 3.58
3018 3261 6.577103 TCCTTTGAGCATATAAGACTGTCAG 58.423 40.000 10.88 0.00 0.00 3.51
3019 3262 5.236047 CCTTTGAGCATATAAGACTGTCAGC 59.764 44.000 10.88 4.25 0.00 4.26
3020 3263 3.969899 TGAGCATATAAGACTGTCAGCG 58.030 45.455 10.88 0.00 0.00 5.18
3021 3264 3.381590 TGAGCATATAAGACTGTCAGCGT 59.618 43.478 10.88 0.00 0.00 5.07
3022 3265 3.711086 AGCATATAAGACTGTCAGCGTG 58.289 45.455 10.88 3.61 0.00 5.34
3023 3266 3.131223 AGCATATAAGACTGTCAGCGTGT 59.869 43.478 10.88 0.00 0.00 4.49
3024 3267 4.338400 AGCATATAAGACTGTCAGCGTGTA 59.662 41.667 10.88 0.00 0.00 2.90
3025 3268 5.041287 GCATATAAGACTGTCAGCGTGTAA 58.959 41.667 10.88 0.00 0.00 2.41
3026 3269 5.692204 GCATATAAGACTGTCAGCGTGTAAT 59.308 40.000 10.88 0.00 0.00 1.89
3027 3270 6.861572 GCATATAAGACTGTCAGCGTGTAATA 59.138 38.462 10.88 0.00 0.00 0.98
3028 3271 7.148950 GCATATAAGACTGTCAGCGTGTAATAC 60.149 40.741 10.88 0.00 0.00 1.89
3029 3272 4.785511 AAGACTGTCAGCGTGTAATACT 57.214 40.909 10.88 0.00 0.00 2.12
3030 3273 4.785511 AGACTGTCAGCGTGTAATACTT 57.214 40.909 10.88 0.00 0.00 2.24
3031 3274 4.486090 AGACTGTCAGCGTGTAATACTTG 58.514 43.478 10.88 0.00 0.00 3.16
3032 3275 4.022242 AGACTGTCAGCGTGTAATACTTGT 60.022 41.667 10.88 0.00 0.00 3.16
3033 3276 3.987868 ACTGTCAGCGTGTAATACTTGTG 59.012 43.478 0.00 0.00 0.00 3.33
3034 3277 3.985008 TGTCAGCGTGTAATACTTGTGT 58.015 40.909 0.00 0.00 0.00 3.72
3035 3278 5.123805 TGTCAGCGTGTAATACTTGTGTA 57.876 39.130 0.00 0.00 0.00 2.90
3036 3279 4.919168 TGTCAGCGTGTAATACTTGTGTAC 59.081 41.667 0.00 0.00 0.00 2.90
3037 3280 4.919168 GTCAGCGTGTAATACTTGTGTACA 59.081 41.667 0.00 0.00 0.00 2.90
3038 3281 4.919168 TCAGCGTGTAATACTTGTGTACAC 59.081 41.667 19.36 19.36 42.65 2.90
3039 3282 4.682401 CAGCGTGTAATACTTGTGTACACA 59.318 41.667 24.62 24.62 45.09 3.72
3040 3283 4.921515 AGCGTGTAATACTTGTGTACACAG 59.078 41.667 26.52 21.74 45.09 3.66
3041 3284 4.433805 GCGTGTAATACTTGTGTACACAGC 60.434 45.833 26.52 18.60 45.09 4.40
3042 3285 4.921515 CGTGTAATACTTGTGTACACAGCT 59.078 41.667 26.52 18.10 45.09 4.24
3043 3286 5.404366 CGTGTAATACTTGTGTACACAGCTT 59.596 40.000 26.52 19.44 45.09 3.74
3044 3287 6.399669 CGTGTAATACTTGTGTACACAGCTTC 60.400 42.308 26.52 15.17 45.09 3.86
3045 3288 5.631929 TGTAATACTTGTGTACACAGCTTCG 59.368 40.000 26.52 16.22 42.94 3.79
3046 3289 1.865865 ACTTGTGTACACAGCTTCGG 58.134 50.000 26.52 15.87 42.94 4.30
3047 3290 1.138266 ACTTGTGTACACAGCTTCGGT 59.862 47.619 26.52 16.40 42.94 4.69
3048 3291 1.526887 CTTGTGTACACAGCTTCGGTG 59.473 52.381 26.52 8.74 42.94 4.94
3050 3293 1.682323 TGTGTACACAGCTTCGGTGTA 59.318 47.619 24.62 10.58 46.94 2.90
3055 3298 2.236766 ACACAGCTTCGGTGTACTAGT 58.763 47.619 6.53 0.00 46.94 2.57
3056 3299 2.626743 ACACAGCTTCGGTGTACTAGTT 59.373 45.455 6.53 0.00 46.94 2.24
3057 3300 3.069158 ACACAGCTTCGGTGTACTAGTTT 59.931 43.478 6.53 0.00 46.94 2.66
3058 3301 3.673809 CACAGCTTCGGTGTACTAGTTTC 59.326 47.826 0.00 0.00 42.60 2.78
3059 3302 3.251571 CAGCTTCGGTGTACTAGTTTCC 58.748 50.000 0.00 0.58 0.00 3.13
3060 3303 3.056749 CAGCTTCGGTGTACTAGTTTCCT 60.057 47.826 0.00 0.00 0.00 3.36
3061 3304 3.577415 AGCTTCGGTGTACTAGTTTCCTT 59.423 43.478 0.00 0.00 0.00 3.36
3062 3305 3.678548 GCTTCGGTGTACTAGTTTCCTTG 59.321 47.826 0.00 0.00 0.00 3.61
3063 3306 4.798593 GCTTCGGTGTACTAGTTTCCTTGT 60.799 45.833 0.00 0.00 0.00 3.16
3064 3307 4.247267 TCGGTGTACTAGTTTCCTTGTG 57.753 45.455 0.00 0.00 0.00 3.33
3065 3308 3.638160 TCGGTGTACTAGTTTCCTTGTGT 59.362 43.478 0.00 0.00 0.00 3.72
3066 3309 4.826733 TCGGTGTACTAGTTTCCTTGTGTA 59.173 41.667 0.00 0.00 0.00 2.90
3067 3310 4.919754 CGGTGTACTAGTTTCCTTGTGTAC 59.080 45.833 0.00 0.00 0.00 2.90
3068 3311 5.507817 CGGTGTACTAGTTTCCTTGTGTACA 60.508 44.000 0.00 0.00 38.18 2.90
3069 3312 6.760161 GTGTACTAGTTTCCTTGTGTACAC 57.240 41.667 19.36 19.36 46.83 2.90
3076 3319 2.148916 TCCTTGTGTACACAGCTTCG 57.851 50.000 26.52 14.14 42.94 3.79
3086 3329 1.138266 ACACAGCTTCGGTGTACTTGT 59.862 47.619 6.53 0.00 46.94 3.16
3144 3459 7.567571 CGTCTATGAACGAAATTGCATTATCT 58.432 34.615 0.00 0.00 45.37 1.98
3167 3482 5.752892 TGAACTTGTATTGGTACGCAAAA 57.247 34.783 1.64 0.00 33.36 2.44
3171 3486 5.875930 ACTTGTATTGGTACGCAAAATAGC 58.124 37.500 1.64 0.00 33.36 2.97
3198 3513 5.146460 TGAAATTTCGAAATCTTCTGTGCG 58.854 37.500 27.09 0.00 0.00 5.34
3205 3520 3.291585 GAAATCTTCTGTGCGTGTTGTG 58.708 45.455 0.00 0.00 0.00 3.33
3211 3533 1.129624 TCTGTGCGTGTTGTGTCAAAC 59.870 47.619 0.00 0.00 0.00 2.93
3245 3578 4.641396 TCATCACGTTCTCACCAAAGAAT 58.359 39.130 0.00 0.00 37.59 2.40
3265 3598 8.814038 AAGAATCTTTCCAAATAGCAGTACAT 57.186 30.769 0.00 0.00 0.00 2.29
3304 3644 3.154827 ACCAAGTCGGAATCAAACCAT 57.845 42.857 0.00 0.00 38.63 3.55
3346 3688 0.317519 GAAAACGACCGTGCAAAGGG 60.318 55.000 13.32 6.32 41.07 3.95
3407 3762 5.481473 AGCAAGAAGGGAAAATAGATTGCAA 59.519 36.000 0.00 0.00 43.13 4.08
3409 3764 6.690530 CAAGAAGGGAAAATAGATTGCAACA 58.309 36.000 0.00 0.00 0.00 3.33
3455 3810 3.222354 GAGTTGCCCACGGACGTCT 62.222 63.158 16.46 0.00 0.00 4.18
3629 3994 4.373116 TCGGCGACCTGTCCAAGC 62.373 66.667 4.99 0.00 0.00 4.01
3693 4058 2.824880 TACCATACATGCGGCCCCC 61.825 63.158 0.00 0.00 0.00 5.40
3848 4221 1.679680 CACTCTCGTATTTCCCGCCTA 59.320 52.381 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 160 1.344065 TTAGCGGGACAAGTGGAAGA 58.656 50.000 0.00 0.00 0.00 2.87
219 236 7.274250 GCTTAAAACCAATACAGCTGATTTCAG 59.726 37.037 23.35 6.79 46.40 3.02
244 261 0.173255 ATTGGCGCTATGGTGTTTGC 59.827 50.000 7.64 0.00 0.00 3.68
260 291 6.201234 TGTTTGCTTGACATGAACATGAATTG 59.799 34.615 19.56 9.09 41.20 2.32
274 305 1.729149 GCGCTATGGTGTTTGCTTGAC 60.729 52.381 0.00 0.00 0.00 3.18
293 324 8.882415 AATGGTGAATCATGATTAGAATTTGC 57.118 30.769 20.75 6.72 0.00 3.68
340 382 1.745087 CAGCCGGTGCATGTATTTTCT 59.255 47.619 1.90 0.00 41.13 2.52
409 451 8.997621 TGAGATTAACAAGTACCAGTTCATAC 57.002 34.615 4.03 0.38 0.00 2.39
539 581 8.142551 TGAAGGAGAACTCAAAAGACTAAGTAC 58.857 37.037 4.23 0.00 0.00 2.73
686 729 5.240183 ACAGAATCCACAAACAGACTTCATG 59.760 40.000 0.00 0.00 0.00 3.07
764 807 1.286880 GGTCCCGAACGAGAAACGA 59.713 57.895 0.00 0.00 45.77 3.85
776 819 1.810412 GCAATAGGCTTACTGGTCCCG 60.810 57.143 0.00 0.00 40.25 5.14
828 871 0.399833 TGCAATGTGAGCCACTACCA 59.600 50.000 6.83 0.00 35.11 3.25
840 883 3.066621 ACACGTCAATGTTCTTGCAATGT 59.933 39.130 0.00 0.00 0.00 2.71
934 990 2.040278 TGTCAAGTGGCCAATAGCTTCT 59.960 45.455 7.24 0.00 43.05 2.85
936 992 2.440409 CTGTCAAGTGGCCAATAGCTT 58.560 47.619 7.24 3.14 43.05 3.74
937 993 1.952367 GCTGTCAAGTGGCCAATAGCT 60.952 52.381 16.46 3.13 43.05 3.32
938 994 0.453390 GCTGTCAAGTGGCCAATAGC 59.547 55.000 7.24 8.79 42.60 2.97
940 996 1.305219 GCGCTGTCAAGTGGCCAATA 61.305 55.000 7.24 0.00 34.30 1.90
941 997 2.629656 GCGCTGTCAAGTGGCCAAT 61.630 57.895 7.24 1.65 34.30 3.16
942 998 3.286751 GCGCTGTCAAGTGGCCAA 61.287 61.111 7.24 0.00 34.30 4.52
943 999 4.254709 AGCGCTGTCAAGTGGCCA 62.255 61.111 10.39 0.00 34.30 5.36
944 1000 2.507110 TAGAGCGCTGTCAAGTGGCC 62.507 60.000 18.48 0.00 34.30 5.36
945 1001 1.079819 TAGAGCGCTGTCAAGTGGC 60.080 57.895 18.48 0.00 34.30 5.01
951 1007 2.162608 GAGAAAGACTAGAGCGCTGTCA 59.837 50.000 18.48 0.00 33.56 3.58
995 1051 6.811574 AGGTCCATCCCAGTACACATATATA 58.188 40.000 0.00 0.00 36.75 0.86
1002 1058 4.772886 ATTAAGGTCCATCCCAGTACAC 57.227 45.455 0.00 0.00 36.75 2.90
1004 1060 6.042781 TGTCATATTAAGGTCCATCCCAGTAC 59.957 42.308 0.00 0.00 36.75 2.73
1295 1414 0.398318 GCCTCTTGAAGTGTCCACCT 59.602 55.000 0.00 0.00 0.00 4.00
1301 1420 0.761187 TGAGCTGCCTCTTGAAGTGT 59.239 50.000 0.00 0.00 38.93 3.55
1302 1421 1.805345 CTTGAGCTGCCTCTTGAAGTG 59.195 52.381 0.00 0.00 38.93 3.16
1432 1551 3.201290 GTGACAGCTCATAATCACCTGG 58.799 50.000 0.00 0.00 36.31 4.45
1478 1597 7.302524 TGCCGTTGTTCTATCAATAAAAAGAC 58.697 34.615 0.00 0.00 0.00 3.01
1566 1685 0.670546 TAAGCTCAACCTCGTGCTGC 60.671 55.000 0.00 0.00 35.97 5.25
1574 1693 1.612442 TCGGGGCTAAGCTCAACCT 60.612 57.895 0.00 0.00 0.00 3.50
1623 1742 6.730175 ACTATCTACTGTATCTGAAGTTGCG 58.270 40.000 0.00 0.00 0.00 4.85
1639 1758 6.663953 TGCTCCCCATTATCAGTACTATCTAC 59.336 42.308 0.00 0.00 0.00 2.59
1731 1850 1.839994 TGGGAAATACAGAGCCCTGAG 59.160 52.381 0.65 0.00 43.02 3.35
1737 1856 0.947244 CGCCATGGGAAATACAGAGC 59.053 55.000 15.13 0.00 0.00 4.09
1743 1862 2.203280 CCGCCGCCATGGGAAATA 60.203 61.111 15.13 0.00 38.63 1.40
1848 1967 0.609131 TTTTGGTGCAGCCTAGCTCC 60.609 55.000 14.36 7.35 45.82 4.70
1921 2040 3.813150 GGAGCACTCCTGAACCCT 58.187 61.111 9.54 0.00 46.16 4.34
1947 2066 1.678101 CAAAATCCTGATCTTCCCCGC 59.322 52.381 0.00 0.00 0.00 6.13
1974 2093 2.266055 CTCTTCCCTCCACCGTGC 59.734 66.667 0.00 0.00 0.00 5.34
2028 2147 1.761174 GATGCACACCCCGGGATAT 59.239 57.895 26.32 3.49 0.00 1.63
2241 2360 1.825474 CCGTGGACACTCTTAGGACAT 59.175 52.381 0.56 0.00 0.00 3.06
2265 2384 1.893808 CACCACGCAGAAGCTGGTT 60.894 57.895 8.26 0.00 44.45 3.67
2596 2727 3.211963 GACATGGTCCATGCCGCC 61.212 66.667 28.57 13.49 44.80 6.13
2613 2845 1.686052 CCGGGGAGAGAAGAAGAGATG 59.314 57.143 0.00 0.00 0.00 2.90
2640 2872 4.426112 TCGCCGCAGCAGTCTGAG 62.426 66.667 3.32 0.00 42.95 3.35
2658 2890 1.352156 GCATGTGTTCTCCCGACGAC 61.352 60.000 0.00 0.00 0.00 4.34
2660 2892 1.354337 CTGCATGTGTTCTCCCGACG 61.354 60.000 0.00 0.00 0.00 5.12
2662 2894 0.247460 CTCTGCATGTGTTCTCCCGA 59.753 55.000 0.00 0.00 0.00 5.14
2663 2895 0.036952 ACTCTGCATGTGTTCTCCCG 60.037 55.000 0.00 0.00 0.00 5.14
2664 2896 1.446907 CACTCTGCATGTGTTCTCCC 58.553 55.000 10.67 0.00 0.00 4.30
2666 2898 0.801251 GCCACTCTGCATGTGTTCTC 59.199 55.000 15.69 2.81 33.92 2.87
2667 2899 0.109153 TGCCACTCTGCATGTGTTCT 59.891 50.000 15.69 0.00 36.04 3.01
2765 3003 2.622064 AACACCAGCTTCTTCTTCGT 57.378 45.000 0.00 0.00 0.00 3.85
2766 3004 2.413453 GCTAACACCAGCTTCTTCTTCG 59.587 50.000 0.00 0.00 38.57 3.79
2767 3005 2.744741 GGCTAACACCAGCTTCTTCTTC 59.255 50.000 0.00 0.00 41.50 2.87
2777 3018 2.267961 GGTCCCGGCTAACACCAG 59.732 66.667 0.00 0.00 0.00 4.00
2783 3024 1.612442 AAGCTCTGGTCCCGGCTAA 60.612 57.895 0.00 0.00 34.40 3.09
2820 3061 3.953775 CCACCGTGCACCCTTCCT 61.954 66.667 12.15 0.00 0.00 3.36
2919 3160 6.435430 TCATAATATGCTCAAACCACACAC 57.565 37.500 0.00 0.00 0.00 3.82
2926 3167 6.860023 GGCACAGAATCATAATATGCTCAAAC 59.140 38.462 0.00 0.00 0.00 2.93
2927 3168 6.774170 AGGCACAGAATCATAATATGCTCAAA 59.226 34.615 0.00 0.00 0.00 2.69
2948 3191 3.028850 AGAGTAATACGGTTGCTAGGCA 58.971 45.455 0.00 0.00 36.47 4.75
2964 3207 1.066430 GCCCAATGACGGTCAAGAGTA 60.066 52.381 15.72 0.00 0.00 2.59
2975 3218 4.273318 AGGATTACTCAAAGCCCAATGAC 58.727 43.478 0.00 0.00 45.32 3.06
2976 3219 4.591321 AGGATTACTCAAAGCCCAATGA 57.409 40.909 0.00 0.00 45.32 2.57
2990 3233 8.894768 ACAGTCTTATATGCTCAAAGGATTAC 57.105 34.615 0.00 0.00 0.00 1.89
2991 3234 8.704668 TGACAGTCTTATATGCTCAAAGGATTA 58.295 33.333 1.31 0.00 0.00 1.75
2992 3235 7.568349 TGACAGTCTTATATGCTCAAAGGATT 58.432 34.615 1.31 0.00 0.00 3.01
2993 3236 7.129457 TGACAGTCTTATATGCTCAAAGGAT 57.871 36.000 1.31 0.00 0.00 3.24
2994 3237 6.544928 TGACAGTCTTATATGCTCAAAGGA 57.455 37.500 1.31 0.00 0.00 3.36
2995 3238 5.236047 GCTGACAGTCTTATATGCTCAAAGG 59.764 44.000 3.99 0.00 0.00 3.11
2997 3240 4.805719 CGCTGACAGTCTTATATGCTCAAA 59.194 41.667 3.99 0.00 0.00 2.69
2999 3242 3.381590 ACGCTGACAGTCTTATATGCTCA 59.618 43.478 3.99 0.00 0.00 4.26
3000 3243 3.733224 CACGCTGACAGTCTTATATGCTC 59.267 47.826 3.99 0.00 0.00 4.26
3001 3244 3.131223 ACACGCTGACAGTCTTATATGCT 59.869 43.478 3.99 0.00 0.00 3.79
3002 3245 3.448686 ACACGCTGACAGTCTTATATGC 58.551 45.455 3.99 0.00 0.00 3.14
3003 3246 8.076781 AGTATTACACGCTGACAGTCTTATATG 58.923 37.037 3.99 0.00 0.00 1.78
3004 3247 8.167605 AGTATTACACGCTGACAGTCTTATAT 57.832 34.615 3.99 0.00 0.00 0.86
3007 3250 5.892160 AGTATTACACGCTGACAGTCTTA 57.108 39.130 3.99 0.00 0.00 2.10
3008 3251 4.785511 AGTATTACACGCTGACAGTCTT 57.214 40.909 3.99 0.00 0.00 3.01
3009 3252 4.022242 ACAAGTATTACACGCTGACAGTCT 60.022 41.667 3.99 0.00 0.00 3.24
3010 3253 4.090066 CACAAGTATTACACGCTGACAGTC 59.910 45.833 3.99 0.00 0.00 3.51
3011 3254 3.987868 CACAAGTATTACACGCTGACAGT 59.012 43.478 3.99 0.00 0.00 3.55
3012 3255 3.987868 ACACAAGTATTACACGCTGACAG 59.012 43.478 0.00 0.00 0.00 3.51
3013 3256 3.985008 ACACAAGTATTACACGCTGACA 58.015 40.909 0.00 0.00 0.00 3.58
3014 3257 4.919168 TGTACACAAGTATTACACGCTGAC 59.081 41.667 0.00 0.00 31.84 3.51
3015 3258 4.919168 GTGTACACAAGTATTACACGCTGA 59.081 41.667 21.14 0.00 37.08 4.26
3016 3259 4.682401 TGTGTACACAAGTATTACACGCTG 59.318 41.667 26.07 0.00 45.72 5.18
3017 3260 4.873817 TGTGTACACAAGTATTACACGCT 58.126 39.130 26.07 0.00 45.72 5.07
3018 3261 4.433805 GCTGTGTACACAAGTATTACACGC 60.434 45.833 27.66 19.13 45.72 5.34
3019 3262 4.921515 AGCTGTGTACACAAGTATTACACG 59.078 41.667 27.66 13.87 45.72 4.49
3020 3263 6.399669 CGAAGCTGTGTACACAAGTATTACAC 60.400 42.308 27.66 11.93 43.91 2.90
3021 3264 5.631929 CGAAGCTGTGTACACAAGTATTACA 59.368 40.000 27.66 3.63 41.33 2.41
3022 3265 5.061808 CCGAAGCTGTGTACACAAGTATTAC 59.938 44.000 27.66 14.49 41.33 1.89
3023 3266 5.165676 CCGAAGCTGTGTACACAAGTATTA 58.834 41.667 27.66 5.02 41.33 0.98
3024 3267 3.994392 CCGAAGCTGTGTACACAAGTATT 59.006 43.478 27.66 18.88 41.33 1.89
3025 3268 3.006537 ACCGAAGCTGTGTACACAAGTAT 59.993 43.478 27.66 15.00 41.33 2.12
3026 3269 2.363038 ACCGAAGCTGTGTACACAAGTA 59.637 45.455 27.66 6.86 41.33 2.24
3027 3270 1.138266 ACCGAAGCTGTGTACACAAGT 59.862 47.619 27.66 15.79 41.33 3.16
3028 3271 1.526887 CACCGAAGCTGTGTACACAAG 59.473 52.381 27.66 21.31 41.33 3.16
3029 3272 1.134640 ACACCGAAGCTGTGTACACAA 60.135 47.619 27.66 12.99 44.73 3.33
3030 3273 0.462375 ACACCGAAGCTGTGTACACA 59.538 50.000 26.37 26.37 44.73 3.72
3031 3274 2.427232 TACACCGAAGCTGTGTACAC 57.573 50.000 19.36 19.36 44.73 2.90
3034 3277 3.415212 ACTAGTACACCGAAGCTGTGTA 58.585 45.455 10.58 10.58 44.73 2.90
3036 3279 3.299340 AACTAGTACACCGAAGCTGTG 57.701 47.619 0.00 1.32 39.63 3.66
3037 3280 3.305881 GGAAACTAGTACACCGAAGCTGT 60.306 47.826 0.00 0.00 0.00 4.40
3038 3281 3.056749 AGGAAACTAGTACACCGAAGCTG 60.057 47.826 0.00 0.00 40.61 4.24
3039 3282 3.163467 AGGAAACTAGTACACCGAAGCT 58.837 45.455 0.00 0.00 40.61 3.74
3040 3283 3.589495 AGGAAACTAGTACACCGAAGC 57.411 47.619 0.00 0.00 40.61 3.86
3041 3284 4.684703 CACAAGGAAACTAGTACACCGAAG 59.315 45.833 0.00 0.00 42.68 3.79
3042 3285 4.099881 ACACAAGGAAACTAGTACACCGAA 59.900 41.667 0.00 0.00 42.68 4.30
3043 3286 3.638160 ACACAAGGAAACTAGTACACCGA 59.362 43.478 0.00 0.00 42.68 4.69
3044 3287 3.986277 ACACAAGGAAACTAGTACACCG 58.014 45.455 0.00 0.00 42.68 4.94
3045 3288 5.846203 TGTACACAAGGAAACTAGTACACC 58.154 41.667 0.00 0.04 42.89 4.16
3047 3290 6.468333 TGTGTACACAAGGAAACTAGTACA 57.532 37.500 26.07 0.00 44.21 2.90
3048 3291 5.404667 GCTGTGTACACAAGGAAACTAGTAC 59.595 44.000 27.66 0.00 42.68 2.73
3049 3292 5.303589 AGCTGTGTACACAAGGAAACTAGTA 59.696 40.000 27.66 2.12 42.68 1.82
3050 3293 4.101119 AGCTGTGTACACAAGGAAACTAGT 59.899 41.667 27.66 0.00 42.68 2.57
3051 3294 4.632153 AGCTGTGTACACAAGGAAACTAG 58.368 43.478 27.66 14.54 42.68 2.57
3052 3295 4.682778 AGCTGTGTACACAAGGAAACTA 57.317 40.909 27.66 3.56 42.68 2.24
3054 3297 3.303132 CGAAGCTGTGTACACAAGGAAAC 60.303 47.826 27.66 15.81 41.33 2.78
3055 3298 2.869801 CGAAGCTGTGTACACAAGGAAA 59.130 45.455 27.66 5.75 41.33 3.13
3056 3299 2.479837 CGAAGCTGTGTACACAAGGAA 58.520 47.619 27.66 6.48 41.33 3.36
3057 3300 1.270094 CCGAAGCTGTGTACACAAGGA 60.270 52.381 27.66 6.86 41.33 3.36
3058 3301 1.148310 CCGAAGCTGTGTACACAAGG 58.852 55.000 27.66 18.60 41.33 3.61
3059 3302 1.526887 CACCGAAGCTGTGTACACAAG 59.473 52.381 27.66 21.31 41.33 3.16
3060 3303 1.134640 ACACCGAAGCTGTGTACACAA 60.135 47.619 27.66 12.99 44.73 3.33
3061 3304 0.462375 ACACCGAAGCTGTGTACACA 59.538 50.000 26.37 26.37 44.73 3.72
3062 3305 2.427232 TACACCGAAGCTGTGTACAC 57.573 50.000 19.36 19.36 44.73 2.90
3065 3308 2.363038 ACAAGTACACCGAAGCTGTGTA 59.637 45.455 10.58 10.58 44.73 2.90
3067 3310 1.865865 ACAAGTACACCGAAGCTGTG 58.134 50.000 1.32 1.32 39.63 3.66
3068 3311 2.614829 AACAAGTACACCGAAGCTGT 57.385 45.000 0.00 0.00 0.00 4.40
3069 3312 2.223377 GGAAACAAGTACACCGAAGCTG 59.777 50.000 0.00 0.00 0.00 4.24
3076 3319 4.877251 TGTACACAAGGAAACAAGTACACC 59.123 41.667 0.00 0.00 37.49 4.16
3086 3329 4.141711 ACTGAAGCTCTGTACACAAGGAAA 60.142 41.667 0.00 0.00 0.00 3.13
3144 3459 5.752892 TTTGCGTACCAATACAAGTTCAA 57.247 34.783 0.00 0.00 32.49 2.69
3167 3482 6.436843 AGATTTCGAAATTTCAACGGCTAT 57.563 33.333 23.49 0.00 0.00 2.97
3171 3486 6.086765 CACAGAAGATTTCGAAATTTCAACGG 59.913 38.462 27.91 21.13 34.02 4.44
3198 3513 2.477189 CGGAACAGGTTTGACACAACAC 60.477 50.000 0.00 0.00 0.00 3.32
3205 3520 4.723248 GATGAAATCGGAACAGGTTTGAC 58.277 43.478 0.00 0.00 31.13 3.18
3265 3598 6.999871 ACTTGGTAACCGATTTCCTCTTTAAA 59.000 34.615 0.00 0.00 0.00 1.52
3273 3613 2.004733 CCGACTTGGTAACCGATTTCC 58.995 52.381 0.00 0.00 0.00 3.13
3304 3644 5.868258 TCGTTTGTATTTAACATCACGGCTA 59.132 36.000 9.27 0.00 41.84 3.93
3346 3688 1.440353 GTTCACCACGATGCGTTGC 60.440 57.895 0.00 0.00 38.32 4.17
3407 3762 1.745115 CGTCGTCCATGGCCATTGT 60.745 57.895 17.92 0.00 0.00 2.71
3409 3764 2.824041 GCGTCGTCCATGGCCATT 60.824 61.111 17.92 0.00 0.00 3.16
3455 3810 1.300963 GCAGCAGGATCTCCACCAA 59.699 57.895 0.00 0.00 38.89 3.67
3542 3897 2.046988 CTGCATCTCCGTGGTGCA 60.047 61.111 12.04 12.04 45.69 4.57
3848 4221 3.152400 GGAGGTGTATCGCCCCGT 61.152 66.667 0.00 0.00 33.99 5.28
3854 4227 1.409427 GTTCTCCCAGGAGGTGTATCG 59.591 57.143 13.73 0.00 42.20 2.92


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

AutoCloner maintained by Alex Coulton.