Multiple sequence alignment - TraesCS6D01G247300

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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 TraesCS6D01G247300 chr6D 100.000 3206 0 0 1 3206 350912209 350915414 0.000000e+00 5921
1 TraesCS6D01G247300 chr6D 83.368 956 93 27 1 897 318082724 318081776 0.000000e+00 824
2 TraesCS6D01G247300 chr6D 86.570 551 52 5 1 529 38707994 38707444 3.560000e-164 588
3 TraesCS6D01G247300 chr6B 93.379 2764 131 26 382 3106 528918413 528915663 0.000000e+00 4043
4 TraesCS6D01G247300 chr6B 82.391 778 80 20 235 958 506275479 506276253 2.720000e-175 625
5 TraesCS6D01G247300 chr6A 91.673 2702 130 31 442 3106 492808758 492806115 0.000000e+00 3655
6 TraesCS6D01G247300 chr6A 89.655 464 30 2 1 446 492820001 492819538 2.770000e-160 575
7 TraesCS6D01G247300 chr1B 85.060 1004 103 19 1 958 642758962 642757960 0.000000e+00 979
8 TraesCS6D01G247300 chr1B 85.060 1004 103 19 1 958 642764032 642763030 0.000000e+00 979
9 TraesCS6D01G247300 chr4D 85.000 1000 95 25 1 958 91236858 91235872 0.000000e+00 965
10 TraesCS6D01G247300 chr4D 94.488 127 4 3 3080 3206 407376756 407376633 3.260000e-45 193
11 TraesCS6D01G247300 chr2B 85.079 945 93 20 1 899 787138113 787137171 0.000000e+00 920
12 TraesCS6D01G247300 chr2B 82.942 938 116 24 1 899 685263997 685264929 0.000000e+00 806
13 TraesCS6D01G247300 chr2B 95.200 125 4 2 3082 3206 442219469 442219591 2.520000e-46 196
14 TraesCS6D01G247300 chr3A 83.945 953 93 22 1 899 725228640 725227694 0.000000e+00 857
15 TraesCS6D01G247300 chr3A 79.124 388 37 15 611 955 568030853 568030467 8.950000e-56 228
16 TraesCS6D01G247300 chr5D 83.857 954 88 20 2 898 564890680 564889736 0.000000e+00 848
17 TraesCS6D01G247300 chr5D 82.255 958 107 27 1 899 60257678 60258631 0.000000e+00 769
18 TraesCS6D01G247300 chr5D 85.554 713 79 12 1 690 331399467 331400178 0.000000e+00 725
19 TraesCS6D01G247300 chr5D 96.667 120 3 1 3087 3206 561038167 561038285 7.020000e-47 198
20 TraesCS6D01G247300 chr5D 94.531 128 5 2 3080 3206 461988076 461988202 2.520000e-46 196
21 TraesCS6D01G247300 chr5B 83.266 992 92 26 1 946 640559528 640560491 0.000000e+00 845
22 TraesCS6D01G247300 chr5B 85.641 195 25 3 715 906 599298315 599298509 5.420000e-48 202
23 TraesCS6D01G247300 chr7D 83.369 938 99 17 1 899 631681809 631682728 0.000000e+00 815
24 TraesCS6D01G247300 chr7D 85.162 647 73 5 1 624 515488343 515488989 2.700000e-180 641
25 TraesCS6D01G247300 chr7D 96.667 120 3 1 3087 3206 112471068 112471186 7.020000e-47 198
26 TraesCS6D01G247300 chr7D 96.667 120 2 2 3087 3206 233599168 233599285 7.020000e-47 198
27 TraesCS6D01G247300 chr4A 83.068 880 112 16 1 846 102860189 102859313 0.000000e+00 765
28 TraesCS6D01G247300 chr3D 87.644 607 51 6 1 584 153073314 153073919 0.000000e+00 684
29 TraesCS6D01G247300 chr3D 81.153 902 114 28 1 849 384439634 384438736 0.000000e+00 673
30 TraesCS6D01G247300 chr3D 91.200 125 11 0 1 125 14178301 14178425 1.530000e-38 171
31 TraesCS6D01G247300 chr3B 84.520 562 54 9 420 948 224271945 224272506 2.830000e-145 525
32 TraesCS6D01G247300 chr3B 83.750 560 56 9 422 948 223657487 223658044 6.180000e-137 497
33 TraesCS6D01G247300 chr1D 97.500 120 2 1 3088 3206 148785236 148785117 1.510000e-48 204
34 TraesCS6D01G247300 chr1D 97.458 118 2 1 3089 3206 200861159 200861275 1.950000e-47 200
35 TraesCS6D01G247300 chr1D 92.481 133 8 2 3075 3206 206147525 206147656 4.220000e-44 189


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 TraesCS6D01G247300 chr6D 350912209 350915414 3205 False 5921 5921 100.000 1 3206 1 chr6D.!!$F1 3205
1 TraesCS6D01G247300 chr6D 318081776 318082724 948 True 824 824 83.368 1 897 1 chr6D.!!$R2 896
2 TraesCS6D01G247300 chr6D 38707444 38707994 550 True 588 588 86.570 1 529 1 chr6D.!!$R1 528
3 TraesCS6D01G247300 chr6B 528915663 528918413 2750 True 4043 4043 93.379 382 3106 1 chr6B.!!$R1 2724
4 TraesCS6D01G247300 chr6B 506275479 506276253 774 False 625 625 82.391 235 958 1 chr6B.!!$F1 723
5 TraesCS6D01G247300 chr6A 492806115 492808758 2643 True 3655 3655 91.673 442 3106 1 chr6A.!!$R1 2664
6 TraesCS6D01G247300 chr1B 642757960 642758962 1002 True 979 979 85.060 1 958 1 chr1B.!!$R1 957
7 TraesCS6D01G247300 chr1B 642763030 642764032 1002 True 979 979 85.060 1 958 1 chr1B.!!$R2 957
8 TraesCS6D01G247300 chr4D 91235872 91236858 986 True 965 965 85.000 1 958 1 chr4D.!!$R1 957
9 TraesCS6D01G247300 chr2B 787137171 787138113 942 True 920 920 85.079 1 899 1 chr2B.!!$R1 898
10 TraesCS6D01G247300 chr2B 685263997 685264929 932 False 806 806 82.942 1 899 1 chr2B.!!$F2 898
11 TraesCS6D01G247300 chr3A 725227694 725228640 946 True 857 857 83.945 1 899 1 chr3A.!!$R2 898
12 TraesCS6D01G247300 chr5D 564889736 564890680 944 True 848 848 83.857 2 898 1 chr5D.!!$R1 896
13 TraesCS6D01G247300 chr5D 60257678 60258631 953 False 769 769 82.255 1 899 1 chr5D.!!$F1 898
14 TraesCS6D01G247300 chr5D 331399467 331400178 711 False 725 725 85.554 1 690 1 chr5D.!!$F2 689
15 TraesCS6D01G247300 chr5B 640559528 640560491 963 False 845 845 83.266 1 946 1 chr5B.!!$F2 945
16 TraesCS6D01G247300 chr7D 631681809 631682728 919 False 815 815 83.369 1 899 1 chr7D.!!$F4 898
17 TraesCS6D01G247300 chr7D 515488343 515488989 646 False 641 641 85.162 1 624 1 chr7D.!!$F3 623
18 TraesCS6D01G247300 chr4A 102859313 102860189 876 True 765 765 83.068 1 846 1 chr4A.!!$R1 845
19 TraesCS6D01G247300 chr3D 153073314 153073919 605 False 684 684 87.644 1 584 1 chr3D.!!$F2 583
20 TraesCS6D01G247300 chr3D 384438736 384439634 898 True 673 673 81.153 1 849 1 chr3D.!!$R1 848
21 TraesCS6D01G247300 chr3B 224271945 224272506 561 False 525 525 84.520 420 948 1 chr3B.!!$F2 528
22 TraesCS6D01G247300 chr3B 223657487 223658044 557 False 497 497 83.750 422 948 1 chr3B.!!$F1 526

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
322 339 0.429363 CAAAACAATTCCGCGTTCGC 59.571 50.0 4.92 7.14 0.0 4.70 F
1922 2149 0.515564 GGTGTGTACGCGCTTGATTT 59.484 50.0 18.68 0.00 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2246 1.079543 CTCCTCCACTCCGCAGTTG 60.080 63.158 0.0 0.0 0.0 3.16 R
3151 3394 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.0 0.0 0.0 2.40 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
147 164 3.507162 TCATTCTTTGGTCTGCCTGAA 57.493 42.857 0.00 0.00 35.27 3.02
153 170 3.265221 TCTTTGGTCTGCCTGAATCTCAT 59.735 43.478 0.00 0.00 35.27 2.90
179 196 4.184629 GACTTGAATGTGCTACCGAGATT 58.815 43.478 0.00 0.00 0.00 2.40
191 208 5.419788 TGCTACCGAGATTACCTCTGTTTTA 59.580 40.000 0.00 0.00 39.56 1.52
217 234 3.809905 CTTATACAAGGTGAAGCTCCCC 58.190 50.000 0.00 0.00 0.00 4.81
322 339 0.429363 CAAAACAATTCCGCGTTCGC 59.571 50.000 4.92 7.14 0.00 4.70
348 375 5.186797 AGAAAAACACTCACCCAATGTCAAA 59.813 36.000 0.00 0.00 0.00 2.69
376 403 3.192212 GCAAGGAAAGATGTGGAAAGAGG 59.808 47.826 0.00 0.00 0.00 3.69
511 542 4.693538 TTGAAGACGAGAGAGAGATGTG 57.306 45.455 0.00 0.00 0.00 3.21
735 871 6.360844 TCGGTTTGTAAACTTTGAATTCGA 57.639 33.333 7.36 0.00 38.89 3.71
738 894 7.377397 TCGGTTTGTAAACTTTGAATTCGATTG 59.623 33.333 7.36 0.00 38.89 2.67
804 968 9.045223 TGCTTAGTTTCTATATGTGTGCTAATG 57.955 33.333 0.00 0.00 0.00 1.90
853 1048 8.257830 TCGCAAGGTTTAGAAAAACAATTTTT 57.742 26.923 0.00 0.00 45.68 1.94
905 1121 4.467082 TCGGGCCAAAACTTAGTATACTCA 59.533 41.667 9.12 0.00 0.00 3.41
909 1127 6.093633 GGGCCAAAACTTAGTATACTCAACTG 59.906 42.308 9.12 1.18 0.00 3.16
918 1136 8.035984 ACTTAGTATACTCAACTGAGCCTTTTC 58.964 37.037 9.12 0.00 45.79 2.29
919 1137 6.613153 AGTATACTCAACTGAGCCTTTTCT 57.387 37.500 6.63 0.00 45.79 2.52
921 1139 7.454225 AGTATACTCAACTGAGCCTTTTCTTT 58.546 34.615 6.63 0.00 45.79 2.52
950 1170 9.769093 CTAAATTTTAGTGGATCGGTTAAAGTG 57.231 33.333 7.84 0.00 0.00 3.16
954 1174 0.988832 TGGATCGGTTAAAGTGGCCT 59.011 50.000 3.32 0.00 0.00 5.19
955 1175 2.093341 GTGGATCGGTTAAAGTGGCCTA 60.093 50.000 3.32 0.00 0.00 3.93
957 1177 3.203716 GGATCGGTTAAAGTGGCCTAAG 58.796 50.000 3.32 0.00 0.00 2.18
961 1181 2.027469 CGGTTAAAGTGGCCTAAGGTCT 60.027 50.000 3.32 0.00 0.00 3.85
964 1184 1.446016 AAAGTGGCCTAAGGTCTGGT 58.554 50.000 3.32 0.00 0.00 4.00
1008 1235 1.754234 CCTACCAACCATGCTGCCC 60.754 63.158 0.00 0.00 0.00 5.36
1040 1267 2.609299 TCGAACCTGCCCATCCCA 60.609 61.111 0.00 0.00 0.00 4.37
1284 1511 4.821589 CTCTGCCCCGACTTCCGC 62.822 72.222 0.00 0.00 36.84 5.54
1428 1655 3.448686 CTTCAATAGCCTACACCTCGTG 58.551 50.000 0.00 0.00 39.75 4.35
1827 2054 4.467084 GTTGCTGCCGGGGATCGA 62.467 66.667 2.18 0.00 42.43 3.59
1922 2149 0.515564 GGTGTGTACGCGCTTGATTT 59.484 50.000 18.68 0.00 0.00 2.17
2117 2344 2.438434 GGAGGCATCACCCAACGG 60.438 66.667 0.00 0.00 40.58 4.44
2262 2489 5.011635 TGGAACAGCTGTCTACATTCAGTTA 59.988 40.000 21.95 0.00 34.57 2.24
2302 2529 7.849804 ATACTGAGCCTATTGTTACTTTGTG 57.150 36.000 0.00 0.00 0.00 3.33
2307 2534 4.772100 AGCCTATTGTTACTTTGTGGCATT 59.228 37.500 0.00 0.00 41.33 3.56
2372 2602 4.548494 TGTGAATATTTGTGCTTGTGCTG 58.452 39.130 0.00 0.00 40.48 4.41
2380 2610 2.637947 TGTGCTTGTGCTGTTCTGTTA 58.362 42.857 0.00 0.00 40.48 2.41
2418 2648 2.868583 TGCATCTCTCTTAAGATTGCGC 59.131 45.455 5.44 0.00 40.67 6.09
2435 2665 2.048222 CGGCCTGCAACTTCTCGA 60.048 61.111 0.00 0.00 0.00 4.04
2501 2731 3.853307 GCCAATTGTTGCACTGTACTGTC 60.853 47.826 4.43 0.00 0.00 3.51
2542 2772 6.593770 TGCATCGAAAACTGCTCTTTAATCTA 59.406 34.615 9.89 0.00 39.16 1.98
2543 2773 6.902417 GCATCGAAAACTGCTCTTTAATCTAC 59.098 38.462 1.49 0.00 35.49 2.59
2544 2774 7.201565 GCATCGAAAACTGCTCTTTAATCTACT 60.202 37.037 1.49 0.00 35.49 2.57
2554 2784 9.887406 CTGCTCTTTAATCTACTAGTTACTAGC 57.113 37.037 18.29 3.90 37.57 3.42
2610 2842 6.155475 TCCCTTCATTGTTTTTGGTTAGTG 57.845 37.500 0.00 0.00 0.00 2.74
2611 2843 5.069781 TCCCTTCATTGTTTTTGGTTAGTGG 59.930 40.000 0.00 0.00 0.00 4.00
2612 2844 5.069781 CCCTTCATTGTTTTTGGTTAGTGGA 59.930 40.000 0.00 0.00 0.00 4.02
2613 2845 6.215845 CCTTCATTGTTTTTGGTTAGTGGAG 58.784 40.000 0.00 0.00 0.00 3.86
2790 3023 1.428448 TTCTCAGTTTCACATCCGCG 58.572 50.000 0.00 0.00 0.00 6.46
2806 3039 2.033194 GCGGTTCCACACAGTAGGC 61.033 63.158 0.00 0.00 0.00 3.93
2881 3114 8.121305 TGACATGATTGTTATGCCTTAAGTTT 57.879 30.769 0.00 0.00 35.79 2.66
2931 3164 9.607988 TGATACGTTTGTTAGTGGATGATTAAT 57.392 29.630 0.00 0.00 0.00 1.40
3025 3258 9.941664 GAATAGTCCACATGTTCTCATAATTTG 57.058 33.333 0.00 0.00 32.47 2.32
3097 3340 4.758688 TGAATGTTAGTCGTGATCAGCAT 58.241 39.130 0.00 0.00 0.00 3.79
3098 3341 4.567959 TGAATGTTAGTCGTGATCAGCATG 59.432 41.667 0.00 0.00 37.54 4.06
3099 3342 3.592898 TGTTAGTCGTGATCAGCATGT 57.407 42.857 0.00 0.00 37.40 3.21
3100 3343 3.253230 TGTTAGTCGTGATCAGCATGTG 58.747 45.455 0.00 0.00 37.40 3.21
3101 3344 3.056891 TGTTAGTCGTGATCAGCATGTGA 60.057 43.478 0.00 0.00 40.38 3.58
3102 3345 2.001812 AGTCGTGATCAGCATGTGAC 57.998 50.000 0.00 0.00 38.28 3.67
3106 3349 1.450134 TGATCAGCATGTGACGCCC 60.450 57.895 0.00 0.00 38.28 6.13
3107 3350 2.124570 ATCAGCATGTGACGCCCC 60.125 61.111 0.00 0.00 38.28 5.80
3108 3351 3.704231 ATCAGCATGTGACGCCCCC 62.704 63.158 0.00 0.00 38.28 5.40
3111 3354 4.856801 GCATGTGACGCCCCCGAT 62.857 66.667 0.00 0.00 38.29 4.18
3112 3355 2.124736 CATGTGACGCCCCCGATT 60.125 61.111 0.00 0.00 38.29 3.34
3113 3356 1.748879 CATGTGACGCCCCCGATTT 60.749 57.895 0.00 0.00 38.29 2.17
3114 3357 1.748879 ATGTGACGCCCCCGATTTG 60.749 57.895 0.00 0.00 38.29 2.32
3115 3358 2.046700 GTGACGCCCCCGATTTGA 60.047 61.111 0.00 0.00 38.29 2.69
3116 3359 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
3117 3360 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
3118 3361 4.770874 ACGCCCCCGATTTGACCG 62.771 66.667 0.00 0.00 38.29 4.79
3119 3362 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
3120 3363 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
3121 3364 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
3122 3365 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
3123 3366 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
3124 3367 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
3125 3368 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
3126 3369 2.094078 CCCCGATTTGACCGTACACTAA 60.094 50.000 0.00 0.00 0.00 2.24
3127 3370 3.431207 CCCCGATTTGACCGTACACTAAT 60.431 47.826 0.00 0.00 0.00 1.73
3128 3371 3.800506 CCCGATTTGACCGTACACTAATC 59.199 47.826 0.00 2.04 0.00 1.75
3129 3372 4.426416 CCGATTTGACCGTACACTAATCA 58.574 43.478 13.93 0.90 32.03 2.57
3130 3373 5.047847 CCGATTTGACCGTACACTAATCAT 58.952 41.667 13.93 0.00 32.03 2.45
3131 3374 5.051039 CCGATTTGACCGTACACTAATCATG 60.051 44.000 13.93 0.00 32.03 3.07
3132 3375 5.556382 CGATTTGACCGTACACTAATCATGC 60.556 44.000 13.93 0.00 32.03 4.06
3133 3376 3.878160 TGACCGTACACTAATCATGCA 57.122 42.857 0.00 0.00 0.00 3.96
3134 3377 3.517602 TGACCGTACACTAATCATGCAC 58.482 45.455 0.00 0.00 0.00 4.57
3135 3378 2.534349 GACCGTACACTAATCATGCACG 59.466 50.000 0.00 0.00 36.74 5.34
3136 3379 1.257936 CCGTACACTAATCATGCACGC 59.742 52.381 0.00 0.00 35.86 5.34
3137 3380 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
3138 3381 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
3139 3382 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
3140 3383 3.201726 ACACTAATCATGCACGCAAAC 57.798 42.857 0.00 0.00 0.00 2.93
3153 3396 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
3154 3397 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
3155 3398 2.344441 CGCAAACGTGTACGATCAAGAT 59.656 45.455 11.79 0.00 43.02 2.40
3156 3399 3.539592 CGCAAACGTGTACGATCAAGATC 60.540 47.826 11.79 0.00 43.02 2.75
3157 3400 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
3158 3401 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
3159 3402 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
3160 3403 2.099263 ACGTGTACGATCAAGATCAGGG 59.901 50.000 11.79 0.00 43.02 4.45
3161 3404 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
3162 3405 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
3163 3406 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
3164 3407 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
3165 3408 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
3166 3409 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
3167 3410 2.542618 CGATCAAGATCAGGGACTCACG 60.543 54.545 10.39 0.00 34.60 4.35
3168 3411 1.186200 TCAAGATCAGGGACTCACGG 58.814 55.000 0.00 0.00 34.60 4.94
3169 3412 0.176680 CAAGATCAGGGACTCACGGG 59.823 60.000 0.00 0.00 34.60 5.28
3170 3413 0.041238 AAGATCAGGGACTCACGGGA 59.959 55.000 0.00 0.00 34.60 5.14
3171 3414 0.041238 AGATCAGGGACTCACGGGAA 59.959 55.000 0.00 0.00 34.60 3.97
3172 3415 0.461961 GATCAGGGACTCACGGGAAG 59.538 60.000 0.00 0.00 34.60 3.46
3173 3416 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
3174 3417 0.041238 TCAGGGACTCACGGGAAGAT 59.959 55.000 0.00 0.00 34.60 2.40
3175 3418 1.286849 TCAGGGACTCACGGGAAGATA 59.713 52.381 0.00 0.00 34.60 1.98
3176 3419 2.091278 TCAGGGACTCACGGGAAGATAT 60.091 50.000 0.00 0.00 34.60 1.63
3177 3420 2.297597 CAGGGACTCACGGGAAGATATC 59.702 54.545 0.00 0.00 34.60 1.63
3178 3421 2.091278 AGGGACTCACGGGAAGATATCA 60.091 50.000 5.32 0.00 0.00 2.15
3179 3422 2.036089 GGGACTCACGGGAAGATATCAC 59.964 54.545 5.32 0.00 0.00 3.06
3180 3423 2.693591 GGACTCACGGGAAGATATCACA 59.306 50.000 5.32 0.00 0.00 3.58
3181 3424 3.132289 GGACTCACGGGAAGATATCACAA 59.868 47.826 5.32 0.00 0.00 3.33
3182 3425 4.113354 GACTCACGGGAAGATATCACAAC 58.887 47.826 5.32 0.00 0.00 3.32
3183 3426 3.513912 ACTCACGGGAAGATATCACAACA 59.486 43.478 5.32 0.00 0.00 3.33
3184 3427 3.857052 TCACGGGAAGATATCACAACAC 58.143 45.455 5.32 0.00 0.00 3.32
3185 3428 3.259625 TCACGGGAAGATATCACAACACA 59.740 43.478 5.32 0.00 0.00 3.72
3186 3429 4.000325 CACGGGAAGATATCACAACACAA 59.000 43.478 5.32 0.00 0.00 3.33
3187 3430 4.000988 ACGGGAAGATATCACAACACAAC 58.999 43.478 5.32 0.00 0.00 3.32
3188 3431 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
3189 3432 4.330074 CGGGAAGATATCACAACACAACTC 59.670 45.833 5.32 0.00 0.00 3.01
3190 3433 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
3191 3434 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
3192 3435 6.535508 GGGAAGATATCACAACACAACTCTAC 59.464 42.308 5.32 0.00 0.00 2.59
3193 3436 7.097192 GGAAGATATCACAACACAACTCTACA 58.903 38.462 5.32 0.00 0.00 2.74
3194 3437 7.602644 GGAAGATATCACAACACAACTCTACAA 59.397 37.037 5.32 0.00 0.00 2.41
3195 3438 7.891183 AGATATCACAACACAACTCTACAAC 57.109 36.000 5.32 0.00 0.00 3.32
3196 3439 7.441836 AGATATCACAACACAACTCTACAACA 58.558 34.615 5.32 0.00 0.00 3.33
3197 3440 8.097038 AGATATCACAACACAACTCTACAACAT 58.903 33.333 5.32 0.00 0.00 2.71
3198 3441 9.366216 GATATCACAACACAACTCTACAACATA 57.634 33.333 0.00 0.00 0.00 2.29
3199 3442 9.719355 ATATCACAACACAACTCTACAACATAA 57.281 29.630 0.00 0.00 0.00 1.90
3200 3443 7.851387 TCACAACACAACTCTACAACATAAA 57.149 32.000 0.00 0.00 0.00 1.40
3201 3444 8.445275 TCACAACACAACTCTACAACATAAAT 57.555 30.769 0.00 0.00 0.00 1.40
3202 3445 9.549078 TCACAACACAACTCTACAACATAAATA 57.451 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 164 7.443575 GGTAGCACATTCAAGTCATTATGAGAT 59.556 37.037 0.00 0.00 0.00 2.75
153 170 5.079689 TCGGTAGCACATTCAAGTCATTA 57.920 39.130 0.00 0.00 0.00 1.90
191 208 3.264450 AGCTTCACCTTGTATAAGCCTGT 59.736 43.478 0.00 0.00 44.24 4.00
217 234 0.242825 TTGACCGAGTAGTCGCAAGG 59.757 55.000 14.65 3.54 45.41 3.61
243 260 5.588958 GGTAGTAACCCATCGAGTAGTTT 57.411 43.478 2.57 0.00 40.21 2.66
322 339 5.009854 ACATTGGGTGAGTGTTTTTCTTG 57.990 39.130 0.00 0.00 0.00 3.02
348 375 2.298163 CCACATCTTTCCTTGCAGCTTT 59.702 45.455 0.00 0.00 0.00 3.51
376 403 2.813779 CTTATGAAGCACACCGAAGC 57.186 50.000 0.00 0.00 0.00 3.86
511 542 5.168569 TGGTGATGTATCGAAAGTTCTCAC 58.831 41.667 0.00 0.00 0.00 3.51
606 639 3.071892 TGGGTATGAACTTGACGGTTCTT 59.928 43.478 8.47 5.32 44.02 2.52
905 1121 7.588497 ATTTAGTGAAAGAAAAGGCTCAGTT 57.412 32.000 0.00 0.00 0.00 3.16
909 1127 9.967346 ACTAAAATTTAGTGAAAGAAAAGGCTC 57.033 29.630 16.69 0.00 0.00 4.70
918 1136 8.040716 ACCGATCCACTAAAATTTAGTGAAAG 57.959 34.615 34.66 23.03 45.69 2.62
919 1137 7.989416 ACCGATCCACTAAAATTTAGTGAAA 57.011 32.000 34.66 25.47 45.69 2.69
921 1139 9.504708 TTTAACCGATCCACTAAAATTTAGTGA 57.495 29.630 34.66 24.37 45.69 3.41
950 1170 2.456073 TCTCTACCAGACCTTAGGCC 57.544 55.000 0.00 0.00 0.00 5.19
954 1174 3.954904 GTGAGCATCTCTACCAGACCTTA 59.045 47.826 0.00 0.00 32.26 2.69
955 1175 2.763448 GTGAGCATCTCTACCAGACCTT 59.237 50.000 0.00 0.00 32.26 3.50
957 1177 1.410882 GGTGAGCATCTCTACCAGACC 59.589 57.143 9.17 0.00 34.34 3.85
961 1181 1.676678 GCCGGTGAGCATCTCTACCA 61.677 60.000 1.90 0.00 34.06 3.25
964 1184 1.816537 GTGCCGGTGAGCATCTCTA 59.183 57.895 1.90 0.00 46.24 2.43
1046 1273 3.712881 GAAGTGTGGTGCGGTCGC 61.713 66.667 8.54 8.54 42.35 5.19
1318 1545 1.152008 GGATGGGGTAGGAGAGGGG 60.152 68.421 0.00 0.00 0.00 4.79
1827 2054 1.302351 GAAGAGCACCAGCAGCAGT 60.302 57.895 0.00 0.00 45.49 4.40
2004 2231 2.203139 TTGCCCACGTCCACACAG 60.203 61.111 0.00 0.00 0.00 3.66
2019 2246 1.079543 CTCCTCCACTCCGCAGTTG 60.080 63.158 0.00 0.00 0.00 3.16
2117 2344 2.489722 GAGTTCAATCCAAGCCCTTCAC 59.510 50.000 0.00 0.00 0.00 3.18
2262 2489 8.267894 AGGCTCAGTATTGACATTACAATAAGT 58.732 33.333 9.53 0.00 42.03 2.24
2307 2534 5.334028 CGTAATGCGAGCATTTCCATATGAA 60.334 40.000 25.48 4.58 43.32 2.57
2380 2610 8.148437 AGAGATGCACATAGATATCTCCAAAT 57.852 34.615 8.95 0.00 44.06 2.32
2418 2648 1.667830 TTCGAGAAGTTGCAGGCCG 60.668 57.895 0.00 0.00 0.00 6.13
2435 2665 6.643388 TCATATGATGCTCAGTGTGTAAGTT 58.357 36.000 0.00 0.00 0.00 2.66
2474 2704 0.249996 AGTGCAACAATTGGCAAGCC 60.250 50.000 10.83 3.61 42.45 4.35
2554 2784 3.698040 AGAAAATGGCCAGCTTCATGTAG 59.302 43.478 24.30 0.00 0.00 2.74
2596 2826 6.316890 GTCAAGTACTCCACTAACCAAAAACA 59.683 38.462 0.00 0.00 36.04 2.83
2603 2833 5.464030 TTCAGTCAAGTACTCCACTAACC 57.536 43.478 0.00 0.00 36.04 2.85
2738 2971 9.995003 GAAGTAGAGGATCATTCACTATCAATT 57.005 33.333 0.00 0.00 37.82 2.32
2787 3020 1.736645 CCTACTGTGTGGAACCGCG 60.737 63.158 0.00 0.00 34.36 6.46
2790 3023 2.271944 AAAGCCTACTGTGTGGAACC 57.728 50.000 5.96 0.00 34.36 3.62
2881 3114 3.936453 GCGTGATAACAGGAATGGTTACA 59.064 43.478 0.00 0.00 33.89 2.41
2931 3164 3.504520 TGACGCTGATAACACAGTAGTCA 59.495 43.478 17.33 17.33 45.11 3.41
3025 3258 9.750125 AAAAGGATTTGTAGAAAGAATTGTGAC 57.250 29.630 0.00 0.00 39.02 3.67
3097 3340 2.359354 CAAATCGGGGGCGTCACA 60.359 61.111 0.00 0.00 0.00 3.58
3098 3341 2.046700 TCAAATCGGGGGCGTCAC 60.047 61.111 0.00 0.00 0.00 3.67
3099 3342 2.046700 GTCAAATCGGGGGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
3100 3343 2.822701 GGTCAAATCGGGGGCGTC 60.823 66.667 0.00 0.00 0.00 5.19
3101 3344 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
3102 3345 3.374012 TACGGTCAAATCGGGGGCG 62.374 63.158 0.00 0.00 0.00 6.13
3106 3349 2.945447 TAGTGTACGGTCAAATCGGG 57.055 50.000 0.00 0.00 0.00 5.14
3107 3350 4.426416 TGATTAGTGTACGGTCAAATCGG 58.574 43.478 0.00 0.00 0.00 4.18
3108 3351 5.556382 GCATGATTAGTGTACGGTCAAATCG 60.556 44.000 0.00 0.00 0.00 3.34
3109 3352 5.293324 TGCATGATTAGTGTACGGTCAAATC 59.707 40.000 0.00 0.00 0.00 2.17
3110 3353 5.064707 GTGCATGATTAGTGTACGGTCAAAT 59.935 40.000 0.00 0.00 0.00 2.32
3111 3354 4.390603 GTGCATGATTAGTGTACGGTCAAA 59.609 41.667 0.00 0.00 0.00 2.69
3112 3355 3.930229 GTGCATGATTAGTGTACGGTCAA 59.070 43.478 0.00 0.00 0.00 3.18
3113 3356 3.517602 GTGCATGATTAGTGTACGGTCA 58.482 45.455 0.00 0.00 0.00 4.02
3114 3357 2.534349 CGTGCATGATTAGTGTACGGTC 59.466 50.000 0.00 0.00 46.91 4.79
3115 3358 2.536365 CGTGCATGATTAGTGTACGGT 58.464 47.619 0.00 0.00 46.91 4.83
3118 3361 4.088648 GTTTGCGTGCATGATTAGTGTAC 58.911 43.478 10.93 0.00 0.00 2.90
3119 3362 3.181525 CGTTTGCGTGCATGATTAGTGTA 60.182 43.478 10.93 0.00 0.00 2.90
3120 3363 2.412716 CGTTTGCGTGCATGATTAGTGT 60.413 45.455 10.93 0.00 0.00 3.55
3121 3364 2.168384 CGTTTGCGTGCATGATTAGTG 58.832 47.619 10.93 0.00 0.00 2.74
3122 3365 2.525750 CGTTTGCGTGCATGATTAGT 57.474 45.000 10.93 0.00 0.00 2.24
3134 3377 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
3135 3378 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
3136 3379 4.031765 CCTGATCTTGATCGTACACGTTTG 59.968 45.833 1.19 0.00 40.80 2.93
3137 3380 4.174009 CCTGATCTTGATCGTACACGTTT 58.826 43.478 1.19 0.00 40.80 3.60
3138 3381 3.428999 CCCTGATCTTGATCGTACACGTT 60.429 47.826 1.19 0.00 40.80 3.99
3139 3382 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
3140 3383 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
3141 3384 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
3142 3385 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
3143 3386 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
3144 3387 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
3145 3388 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
3146 3389 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
3147 3390 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
3148 3391 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
3149 3392 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
3150 3393 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
3151 3394 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.00 0.00 2.40
3152 3395 0.041238 TTCCCGTGAGTCCCTGATCT 59.959 55.000 0.00 0.00 0.00 2.75
3153 3396 0.461961 CTTCCCGTGAGTCCCTGATC 59.538 60.000 0.00 0.00 0.00 2.92
3154 3397 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
3155 3398 0.041238 ATCTTCCCGTGAGTCCCTGA 59.959 55.000 0.00 0.00 0.00 3.86
3156 3399 1.776662 TATCTTCCCGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
3157 3400 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
3158 3401 2.036089 GTGATATCTTCCCGTGAGTCCC 59.964 54.545 3.98 0.00 0.00 4.46
3159 3402 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
3160 3403 4.113354 GTTGTGATATCTTCCCGTGAGTC 58.887 47.826 3.98 0.00 0.00 3.36
3161 3404 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
3162 3405 3.865745 GTGTTGTGATATCTTCCCGTGAG 59.134 47.826 3.98 0.00 0.00 3.51
3163 3406 3.259625 TGTGTTGTGATATCTTCCCGTGA 59.740 43.478 3.98 0.00 0.00 4.35
3164 3407 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
3165 3408 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
3166 3409 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
3167 3410 5.491982 AGAGTTGTGTTGTGATATCTTCCC 58.508 41.667 3.98 0.00 0.00 3.97
3168 3411 7.097192 TGTAGAGTTGTGTTGTGATATCTTCC 58.903 38.462 3.98 0.00 0.00 3.46
3169 3412 8.436200 GTTGTAGAGTTGTGTTGTGATATCTTC 58.564 37.037 3.98 0.00 0.00 2.87
3170 3413 7.931407 TGTTGTAGAGTTGTGTTGTGATATCTT 59.069 33.333 3.98 0.00 0.00 2.40
3171 3414 7.441836 TGTTGTAGAGTTGTGTTGTGATATCT 58.558 34.615 3.98 0.00 0.00 1.98
3172 3415 7.652300 TGTTGTAGAGTTGTGTTGTGATATC 57.348 36.000 0.00 0.00 0.00 1.63
3173 3416 9.719355 TTATGTTGTAGAGTTGTGTTGTGATAT 57.281 29.630 0.00 0.00 0.00 1.63
3174 3417 9.549078 TTTATGTTGTAGAGTTGTGTTGTGATA 57.451 29.630 0.00 0.00 0.00 2.15
3175 3418 8.445275 TTTATGTTGTAGAGTTGTGTTGTGAT 57.555 30.769 0.00 0.00 0.00 3.06
3176 3419 7.851387 TTTATGTTGTAGAGTTGTGTTGTGA 57.149 32.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.