Multiple sequence alignment - TraesCS5D01G190700

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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 TraesCS5D01G190700 chr5D 100.000 3631 0 0 1 3631 293094408 293098038 0.000000e+00 6706.0
1 TraesCS5D01G190700 chr5D 81.481 513 61 20 1936 2445 293164227 293164708 1.220000e-104 390.0
2 TraesCS5D01G190700 chr5D 78.464 534 83 21 1167 1693 293163367 293163875 1.630000e-83 320.0
3 TraesCS5D01G190700 chr5B 92.672 2006 84 27 782 2776 334593161 334595114 0.000000e+00 2832.0
4 TraesCS5D01G190700 chr5B 82.661 496 60 17 1945 2437 334683664 334684136 2.020000e-112 416.0
5 TraesCS5D01G190700 chr5B 77.954 567 90 21 1140 1693 334682760 334683304 4.520000e-84 322.0
6 TraesCS5D01G190700 chr5A 90.896 2164 105 45 789 2921 385955068 385957170 0.000000e+00 2820.0
7 TraesCS5D01G190700 chr5A 91.026 780 63 7 1 776 315277248 315276472 0.000000e+00 1046.0
8 TraesCS5D01G190700 chr5A 82.979 470 60 13 1980 2445 386163395 386163848 1.210000e-109 407.0
9 TraesCS5D01G190700 chr5A 92.143 140 11 0 2991 3130 385957185 385957324 7.950000e-47 198.0
10 TraesCS5D01G190700 chr6D 94.049 773 43 3 6 777 192100960 192100190 0.000000e+00 1170.0
11 TraesCS5D01G190700 chr6D 89.299 785 73 11 1 776 461537670 461538452 0.000000e+00 974.0
12 TraesCS5D01G190700 chr6D 88.931 786 74 9 1 784 160454939 160454165 0.000000e+00 957.0
13 TraesCS5D01G190700 chr6D 88.564 787 75 10 1 784 28279308 28280082 0.000000e+00 941.0
14 TraesCS5D01G190700 chr4D 91.985 786 60 3 1 786 177115135 177115917 0.000000e+00 1099.0
15 TraesCS5D01G190700 chr2D 91.199 784 66 3 2 785 181584270 181585050 0.000000e+00 1062.0
16 TraesCS5D01G190700 chr2D 81.499 627 94 1 3008 3612 53126503 53127129 2.520000e-136 496.0
17 TraesCS5D01G190700 chr2D 77.151 674 126 18 2973 3620 42864251 42864922 2.060000e-97 366.0
18 TraesCS5D01G190700 chr7A 89.017 783 78 4 1 776 651978540 651979321 0.000000e+00 963.0
19 TraesCS5D01G190700 chr7A 92.593 54 4 0 1633 1686 74159840 74159893 1.080000e-10 78.7
20 TraesCS5D01G190700 chr1D 89.189 777 75 5 1 772 479736220 479736992 0.000000e+00 961.0
21 TraesCS5D01G190700 chr7B 80.104 578 87 12 3079 3631 702225543 702226117 4.370000e-109 405.0
22 TraesCS5D01G190700 chr7B 89.474 57 6 0 1633 1689 8866772 8866716 5.030000e-09 73.1
23 TraesCS5D01G190700 chrUn 79.895 572 86 13 3085 3631 76048938 76048371 3.400000e-105 392.0
24 TraesCS5D01G190700 chr3B 79.545 572 89 12 3085 3631 651531807 651531239 2.050000e-102 383.0
25 TraesCS5D01G190700 chr1A 85.016 307 45 1 3030 3336 499201042 499201347 9.790000e-81 311.0
26 TraesCS5D01G190700 chr2B 81.081 370 64 4 2972 3336 657050844 657051212 1.280000e-74 291.0
27 TraesCS5D01G190700 chr2A 86.111 252 35 0 3085 3336 419186338 419186589 4.620000e-69 272.0
28 TraesCS5D01G190700 chr3A 83.803 284 45 1 3010 3292 60690161 60689878 5.980000e-68 268.0
29 TraesCS5D01G190700 chr7D 89.474 57 6 0 1633 1689 66697010 66696954 5.030000e-09 73.1


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 TraesCS5D01G190700 chr5D 293094408 293098038 3630 False 6706 6706 100.0000 1 3631 1 chr5D.!!$F1 3630
1 TraesCS5D01G190700 chr5D 293163367 293164708 1341 False 355 390 79.9725 1167 2445 2 chr5D.!!$F2 1278
2 TraesCS5D01G190700 chr5B 334593161 334595114 1953 False 2832 2832 92.6720 782 2776 1 chr5B.!!$F1 1994
3 TraesCS5D01G190700 chr5B 334682760 334684136 1376 False 369 416 80.3075 1140 2437 2 chr5B.!!$F2 1297
4 TraesCS5D01G190700 chr5A 385955068 385957324 2256 False 1509 2820 91.5195 789 3130 2 chr5A.!!$F2 2341
5 TraesCS5D01G190700 chr5A 315276472 315277248 776 True 1046 1046 91.0260 1 776 1 chr5A.!!$R1 775
6 TraesCS5D01G190700 chr6D 192100190 192100960 770 True 1170 1170 94.0490 6 777 1 chr6D.!!$R2 771
7 TraesCS5D01G190700 chr6D 461537670 461538452 782 False 974 974 89.2990 1 776 1 chr6D.!!$F2 775
8 TraesCS5D01G190700 chr6D 160454165 160454939 774 True 957 957 88.9310 1 784 1 chr6D.!!$R1 783
9 TraesCS5D01G190700 chr6D 28279308 28280082 774 False 941 941 88.5640 1 784 1 chr6D.!!$F1 783
10 TraesCS5D01G190700 chr4D 177115135 177115917 782 False 1099 1099 91.9850 1 786 1 chr4D.!!$F1 785
11 TraesCS5D01G190700 chr2D 181584270 181585050 780 False 1062 1062 91.1990 2 785 1 chr2D.!!$F3 783
12 TraesCS5D01G190700 chr2D 53126503 53127129 626 False 496 496 81.4990 3008 3612 1 chr2D.!!$F2 604
13 TraesCS5D01G190700 chr2D 42864251 42864922 671 False 366 366 77.1510 2973 3620 1 chr2D.!!$F1 647
14 TraesCS5D01G190700 chr7A 651978540 651979321 781 False 963 963 89.0170 1 776 1 chr7A.!!$F2 775
15 TraesCS5D01G190700 chr1D 479736220 479736992 772 False 961 961 89.1890 1 772 1 chr1D.!!$F1 771
16 TraesCS5D01G190700 chr7B 702225543 702226117 574 False 405 405 80.1040 3079 3631 1 chr7B.!!$F1 552
17 TraesCS5D01G190700 chrUn 76048371 76048938 567 True 392 392 79.8950 3085 3631 1 chrUn.!!$R1 546
18 TraesCS5D01G190700 chr3B 651531239 651531807 568 True 383 383 79.5450 3085 3631 1 chr3B.!!$R1 546

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
962 992 0.885596 TTAACCCAGACGCGGTTTGG 60.886 55.0 12.47 14.73 40.84 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2678 2925 0.539669 TCTTCCTCTGTCGCTGACCA 60.54 55.0 6.3 0.0 0.0 4.02 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
96 100 2.645838 AATCCGGATCTTCATGTGGG 57.354 50.000 19.43 0.00 0.00 4.61
173 177 4.697756 TCCGGTCTTTGCCCGCTG 62.698 66.667 0.00 0.00 44.13 5.18
218 222 2.266554 CACATCTTCTTCTCCTGCGTC 58.733 52.381 0.00 0.00 0.00 5.19
371 375 2.584391 GGCTCTCGTGTGGACCCTT 61.584 63.158 0.00 0.00 0.00 3.95
381 385 1.144093 TGTGGACCCTTTGGACGATTT 59.856 47.619 0.00 0.00 34.81 2.17
477 481 1.675641 CTTTGGCGGCCACTTAGCT 60.676 57.895 23.78 0.00 30.78 3.32
479 483 2.690653 TTTGGCGGCCACTTAGCTGT 62.691 55.000 23.78 0.00 41.44 4.40
484 488 1.608717 CGGCCACTTAGCTGTCCTCT 61.609 60.000 2.24 0.00 34.26 3.69
699 728 3.433031 CCTCTTGTTGTGTGACTTGGGTA 60.433 47.826 0.00 0.00 0.00 3.69
716 745 3.904965 TGGGTATGTGTGTTCTGGACTAA 59.095 43.478 0.00 0.00 0.00 2.24
754 783 5.230097 GCTCTTGGCGATTTGCTTTATTTAC 59.770 40.000 0.00 0.00 45.43 2.01
832 861 5.022021 GCATGTAAGATCGTTTGCTAACAC 58.978 41.667 11.52 1.53 33.75 3.32
858 887 1.234821 TCCGTTAGCTGCAAGTTTGG 58.765 50.000 1.02 0.00 35.30 3.28
892 921 3.472652 CATGGGATTGGCCAATCAAATG 58.527 45.455 43.88 38.80 46.77 2.32
962 992 0.885596 TTAACCCAGACGCGGTTTGG 60.886 55.000 12.47 14.73 40.84 3.28
992 1022 1.192428 ATAAGACCGCCTCCTTTCGT 58.808 50.000 0.00 0.00 0.00 3.85
1008 1038 2.743636 TCGTTTCACTCACCATCTCC 57.256 50.000 0.00 0.00 0.00 3.71
1009 1039 1.275291 TCGTTTCACTCACCATCTCCC 59.725 52.381 0.00 0.00 0.00 4.30
1037 1067 4.225984 CTCTCCGATCACATCTCGATTTC 58.774 47.826 0.00 0.00 38.38 2.17
1046 1076 4.098654 TCACATCTCGATTTCTCCTCTTCC 59.901 45.833 0.00 0.00 0.00 3.46
1052 1082 2.996621 CGATTTCTCCTCTTCCACACAC 59.003 50.000 0.00 0.00 0.00 3.82
1053 1083 3.554960 CGATTTCTCCTCTTCCACACACA 60.555 47.826 0.00 0.00 0.00 3.72
1054 1084 2.910688 TTCTCCTCTTCCACACACAC 57.089 50.000 0.00 0.00 0.00 3.82
1081 1111 3.705638 CACACACACTCGCTGCGG 61.706 66.667 23.03 15.00 0.00 5.69
1091 1121 0.165944 CTCGCTGCGGAATTCGTTTT 59.834 50.000 23.03 0.00 41.72 2.43
1286 1322 4.918201 CCGCCCAGATCTTCGCCC 62.918 72.222 0.00 0.00 0.00 6.13
1297 1333 2.035155 TTCGCCCTGACCGAGAGA 59.965 61.111 0.00 0.00 35.96 3.10
1326 1362 0.398522 ATGATCAGGTCCGGGCACTA 60.399 55.000 9.07 0.00 0.00 2.74
1471 1520 5.571741 TGAAACTATTCGATCTTGTCACGAC 59.428 40.000 0.00 0.00 38.46 4.34
1485 1534 8.996024 TCTTGTCACGACTAATTGATGAATAA 57.004 30.769 0.00 0.00 0.00 1.40
1807 1880 3.684305 CGGGGATTTTTGCTTTTGGATTC 59.316 43.478 0.00 0.00 0.00 2.52
1851 1924 6.126409 AGGTGTTCTTTTCAGTTGGTGAATA 58.874 36.000 0.00 0.00 44.89 1.75
1895 1968 2.093306 TTGTTCGGCATCCACTAGTG 57.907 50.000 16.34 16.34 0.00 2.74
1918 2005 1.665679 GTACACCTGTTGCATCCGATG 59.334 52.381 3.82 3.82 0.00 3.84
1919 2006 0.324614 ACACCTGTTGCATCCGATGA 59.675 50.000 12.79 0.00 0.00 2.92
2120 2347 1.514087 GTCCATAAGACGGTGGCGA 59.486 57.895 0.00 0.00 35.30 5.54
2476 2709 1.276138 TCTGAGTACGACGAGGTGGTA 59.724 52.381 0.00 0.00 0.00 3.25
2488 2721 2.654404 GTGGTATCCGCGCTCGTC 60.654 66.667 5.56 0.00 0.00 4.20
2573 2806 5.104374 ACGAGTTTGAGTTTGACGTTTCTA 58.896 37.500 0.00 0.00 0.00 2.10
2584 2817 1.732809 GACGTTTCTAGCTTCCTTGCC 59.267 52.381 0.00 0.00 0.00 4.52
2597 2830 1.487976 TCCTTGCCTGAGATGATGGTC 59.512 52.381 0.00 0.00 0.00 4.02
2610 2855 6.207417 TGAGATGATGGTCAAAAGAGAAAACC 59.793 38.462 0.00 0.00 0.00 3.27
2652 2898 7.754851 AAAAACGGGACTGTACAATTTAGAT 57.245 32.000 0.00 0.00 0.00 1.98
2678 2925 1.026718 CCCGCCGAGCTCTGATTTTT 61.027 55.000 12.85 0.00 0.00 1.94
2730 2977 2.191128 AGTTCTTCATGGGTCAGTGC 57.809 50.000 0.00 0.00 0.00 4.40
2759 3006 7.119846 GTGTTTGTGTAAGCTTTAGGAGATGAT 59.880 37.037 3.20 0.00 0.00 2.45
2760 3007 7.119699 TGTTTGTGTAAGCTTTAGGAGATGATG 59.880 37.037 3.20 0.00 0.00 3.07
2761 3008 6.544928 TGTGTAAGCTTTAGGAGATGATGA 57.455 37.500 3.20 0.00 0.00 2.92
2844 3094 9.060347 TCTATATACAACTAGTAGTTCCCAACG 57.940 37.037 12.75 3.68 36.03 4.10
2879 3129 7.491048 AGTGTAGTGGCAAAAACAAATTGTAAG 59.509 33.333 0.00 0.00 0.00 2.34
2896 3146 6.772360 TTGTAAGCAATGCATATTTCTCCA 57.228 33.333 8.35 0.00 0.00 3.86
2899 3149 3.634504 AGCAATGCATATTTCTCCACCA 58.365 40.909 8.35 0.00 0.00 4.17
2903 3153 4.785346 ATGCATATTTCTCCACCAGACT 57.215 40.909 0.00 0.00 0.00 3.24
2907 3157 6.480763 TGCATATTTCTCCACCAGACTTTTA 58.519 36.000 0.00 0.00 0.00 1.52
2910 3160 7.917505 GCATATTTCTCCACCAGACTTTTATTG 59.082 37.037 0.00 0.00 0.00 1.90
2911 3161 5.705609 TTTCTCCACCAGACTTTTATTGC 57.294 39.130 0.00 0.00 0.00 3.56
2913 3163 3.073798 TCTCCACCAGACTTTTATTGCCA 59.926 43.478 0.00 0.00 0.00 4.92
2914 3164 3.153919 TCCACCAGACTTTTATTGCCAC 58.846 45.455 0.00 0.00 0.00 5.01
2916 3166 3.573967 CCACCAGACTTTTATTGCCACTT 59.426 43.478 0.00 0.00 0.00 3.16
2936 3186 2.660670 TTTTCCCCTTAAACGAGGCA 57.339 45.000 0.00 0.00 35.37 4.75
2937 3187 2.660670 TTTCCCCTTAAACGAGGCAA 57.339 45.000 0.00 0.00 35.37 4.52
2938 3188 2.660670 TTCCCCTTAAACGAGGCAAA 57.339 45.000 0.00 0.00 35.37 3.68
2939 3189 2.660670 TCCCCTTAAACGAGGCAAAA 57.339 45.000 0.00 0.00 35.37 2.44
2940 3190 2.510613 TCCCCTTAAACGAGGCAAAAG 58.489 47.619 0.00 0.00 35.37 2.27
2941 3191 2.106857 TCCCCTTAAACGAGGCAAAAGA 59.893 45.455 0.00 0.00 35.37 2.52
2942 3192 3.089284 CCCCTTAAACGAGGCAAAAGAT 58.911 45.455 0.00 0.00 35.37 2.40
2943 3193 3.509967 CCCCTTAAACGAGGCAAAAGATT 59.490 43.478 0.00 0.00 35.37 2.40
2944 3194 4.021456 CCCCTTAAACGAGGCAAAAGATTT 60.021 41.667 0.00 0.00 35.37 2.17
2945 3195 5.184287 CCCCTTAAACGAGGCAAAAGATTTA 59.816 40.000 0.00 0.00 35.37 1.40
2946 3196 6.090783 CCCTTAAACGAGGCAAAAGATTTAC 58.909 40.000 0.00 0.00 35.37 2.01
2947 3197 5.793457 CCTTAAACGAGGCAAAAGATTTACG 59.207 40.000 0.00 0.00 0.00 3.18
2948 3198 4.823790 AAACGAGGCAAAAGATTTACGT 57.176 36.364 0.00 0.00 0.00 3.57
2949 3199 4.823790 AACGAGGCAAAAGATTTACGTT 57.176 36.364 0.00 0.00 37.77 3.99
2950 3200 4.823790 ACGAGGCAAAAGATTTACGTTT 57.176 36.364 0.00 0.00 0.00 3.60
2951 3201 5.177725 ACGAGGCAAAAGATTTACGTTTT 57.822 34.783 0.00 0.00 0.00 2.43
2952 3202 5.209977 ACGAGGCAAAAGATTTACGTTTTC 58.790 37.500 0.00 0.00 0.00 2.29
2953 3203 5.209240 CGAGGCAAAAGATTTACGTTTTCA 58.791 37.500 0.00 0.00 0.00 2.69
2954 3204 5.856455 CGAGGCAAAAGATTTACGTTTTCAT 59.144 36.000 0.00 0.00 0.00 2.57
2955 3205 6.362283 CGAGGCAAAAGATTTACGTTTTCATT 59.638 34.615 0.00 0.00 0.00 2.57
2956 3206 7.535940 CGAGGCAAAAGATTTACGTTTTCATTA 59.464 33.333 0.00 0.00 0.00 1.90
2957 3207 9.187455 GAGGCAAAAGATTTACGTTTTCATTAA 57.813 29.630 0.00 0.00 0.00 1.40
2958 3208 9.705290 AGGCAAAAGATTTACGTTTTCATTAAT 57.295 25.926 0.00 0.00 0.00 1.40
2969 3219 7.989416 ACGTTTTCATTAATTAGAACTGGGA 57.011 32.000 2.65 0.00 0.00 4.37
2970 3220 8.040716 ACGTTTTCATTAATTAGAACTGGGAG 57.959 34.615 2.65 0.00 0.00 4.30
2971 3221 7.881232 ACGTTTTCATTAATTAGAACTGGGAGA 59.119 33.333 2.65 0.00 0.00 3.71
2979 3229 9.907229 ATTAATTAGAACTGGGAGAAAACCTAG 57.093 33.333 0.00 0.00 42.88 3.02
2981 3231 7.569599 ATTAGAACTGGGAGAAAACCTAGAA 57.430 36.000 0.00 0.00 40.28 2.10
2984 3234 6.948589 AGAACTGGGAGAAAACCTAGAATAC 58.051 40.000 0.00 0.00 40.28 1.89
2987 3237 6.712276 ACTGGGAGAAAACCTAGAATACAAG 58.288 40.000 0.00 0.00 40.28 3.16
2995 3245 2.170607 ACCTAGAATACAAGCCGCACAT 59.829 45.455 0.00 0.00 0.00 3.21
3034 3287 6.456795 TGACCACAAACAATATCACAACAA 57.543 33.333 0.00 0.00 0.00 2.83
3104 3357 1.069703 CAAACAGTCGACCACAGCATG 60.070 52.381 13.01 4.45 46.00 4.06
3105 3358 1.230635 AACAGTCGACCACAGCATGC 61.231 55.000 13.01 10.51 42.53 4.06
3131 3384 1.171308 TGGCAGCTCTGATTTTGCTC 58.829 50.000 0.29 1.41 36.79 4.26
3133 3386 1.749634 GGCAGCTCTGATTTTGCTCAT 59.250 47.619 0.29 0.00 36.79 2.90
3137 3390 3.690139 CAGCTCTGATTTTGCTCATGAGT 59.310 43.478 23.38 3.38 34.51 3.41
3142 3395 6.638096 TCTGATTTTGCTCATGAGTTTCAA 57.362 33.333 23.38 15.82 0.00 2.69
3155 3408 6.603201 TCATGAGTTTCAAAGGAGAAAGTTGT 59.397 34.615 0.00 0.00 40.31 3.32
3168 3421 0.396811 AAGTTGTAAGCCTCGCACCT 59.603 50.000 0.00 0.00 0.00 4.00
3177 3430 0.752376 GCCTCGCACCTACCTAGTCT 60.752 60.000 0.00 0.00 0.00 3.24
3181 3434 1.211212 TCGCACCTACCTAGTCTAGCA 59.789 52.381 0.86 0.00 0.00 3.49
3183 3436 2.657143 GCACCTACCTAGTCTAGCACT 58.343 52.381 0.86 0.00 39.41 4.40
3213 3466 4.379243 CACCGCCCGCTGAAGACT 62.379 66.667 0.00 0.00 0.00 3.24
3217 3470 4.400961 GCCCGCTGAAGACTGCCT 62.401 66.667 0.00 0.00 37.62 4.75
3231 3484 1.911357 ACTGCCTTCATGGAGTCATCA 59.089 47.619 0.00 0.00 38.35 3.07
3243 3496 0.036105 AGTCATCATTGCCGCAGTGA 60.036 50.000 19.51 19.51 34.79 3.41
3288 3541 1.071385 CTCTGTCACAGCCAGAAACCT 59.929 52.381 0.00 0.00 38.42 3.50
3294 3547 1.470098 CACAGCCAGAAACCTGCATAC 59.530 52.381 0.00 0.00 32.37 2.39
3367 3643 2.838974 TTGCCACATGCGTCGCAAA 61.839 52.632 25.66 9.95 44.72 3.68
3369 3645 2.945984 CCACATGCGTCGCAAAGT 59.054 55.556 25.66 21.86 43.62 2.66
3370 3646 1.282570 CCACATGCGTCGCAAAGTT 59.717 52.632 25.66 4.30 43.62 2.66
3372 3648 1.464023 CCACATGCGTCGCAAAGTTAG 60.464 52.381 25.66 14.59 43.62 2.34
3384 3660 3.477530 GCAAAGTTAGACCAACCTCACT 58.522 45.455 0.00 0.00 37.93 3.41
3390 3666 1.410004 AGACCAACCTCACTGTCGAA 58.590 50.000 0.00 0.00 33.04 3.71
3426 3702 1.603456 ACAATGATGTGCACGTCCAA 58.397 45.000 31.08 17.43 38.69 3.53
3430 3706 0.682292 TGATGTGCACGTCCAACCTA 59.318 50.000 31.08 12.73 0.00 3.08
3433 3709 0.178301 TGTGCACGTCCAACCTACAA 59.822 50.000 13.13 0.00 0.00 2.41
3449 3725 4.019174 CCTACAAGAAGCACAAATGGGAT 58.981 43.478 0.00 0.00 0.00 3.85
3462 3738 5.419788 CACAAATGGGATCAAGATCTCCAAA 59.580 40.000 18.01 0.00 39.69 3.28
3467 3743 3.610911 GGATCAAGATCTCCAAAACGGT 58.389 45.455 9.69 0.00 37.92 4.83
3506 3782 3.876300 GTTGAAGACGATGCCGCT 58.124 55.556 0.00 0.00 39.95 5.52
3511 3787 2.629050 GAAGACGATGCCGCTGCCTA 62.629 60.000 0.00 0.00 39.95 3.93
3512 3788 2.635229 AAGACGATGCCGCTGCCTAG 62.635 60.000 0.00 0.00 39.95 3.02
3514 3790 2.202932 CGATGCCGCTGCCTAGTT 60.203 61.111 0.00 0.00 36.33 2.24
3536 3812 3.323691 TCAACCAGGATCTTGACTTTCGA 59.676 43.478 6.37 0.00 0.00 3.71
3539 3815 2.028112 CCAGGATCTTGACTTTCGACCA 60.028 50.000 6.37 0.00 0.00 4.02
3553 3829 2.184533 TCGACCAAAGATCTTGGCCTA 58.815 47.619 9.17 0.00 43.23 3.93
3554 3830 2.168521 TCGACCAAAGATCTTGGCCTAG 59.831 50.000 9.17 8.03 43.23 3.02
3558 3834 2.507471 CCAAAGATCTTGGCCTAGGAGT 59.493 50.000 14.75 1.05 32.18 3.85
3580 3856 2.715046 GAGGATGCACAAATCACCTCA 58.285 47.619 0.00 0.00 42.11 3.86
3582 3858 3.698040 GAGGATGCACAAATCACCTCAAT 59.302 43.478 0.00 0.00 42.11 2.57
3585 3861 4.098960 GGATGCACAAATCACCTCAATGAT 59.901 41.667 0.00 0.00 41.20 2.45
3586 3862 5.300034 GGATGCACAAATCACCTCAATGATA 59.700 40.000 0.00 0.00 38.40 2.15
3605 3881 1.741770 CCTCCAAGGAAGAACGCGG 60.742 63.158 12.47 0.00 37.67 6.46
3607 3883 2.668212 CCAAGGAAGAACGCGGCA 60.668 61.111 12.47 0.00 0.00 5.69
3612 3888 2.746277 GAAGAACGCGGCACCCAT 60.746 61.111 12.47 0.00 0.00 4.00
3625 3901 4.371417 CCCATGGGTGCCACTGCT 62.371 66.667 23.93 0.00 35.80 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 120 0.914417 GGACCTCCACCCCAGATGAA 60.914 60.000 0.00 0.00 35.64 2.57
117 121 1.306997 GGACCTCCACCCCAGATGA 60.307 63.158 0.00 0.00 35.64 2.92
119 123 2.365635 CGGACCTCCACCCCAGAT 60.366 66.667 0.00 0.00 35.14 2.90
298 302 0.903454 GGGGGAAGTCTGGAGTTCGA 60.903 60.000 10.77 0.00 40.70 3.71
371 375 4.022416 ACAAGCTTATTGCAAATCGTCCAA 60.022 37.500 1.71 0.00 45.94 3.53
381 385 3.426560 CGCTGAATCACAAGCTTATTGCA 60.427 43.478 0.00 0.00 45.94 4.08
699 728 5.221722 ACACAGATTAGTCCAGAACACACAT 60.222 40.000 0.00 0.00 0.00 3.21
716 745 3.603532 CCAAGAGCACACATACACAGAT 58.396 45.455 0.00 0.00 0.00 2.90
780 809 7.203255 ACCTTCAGCTTATGACACTTTTTAC 57.797 36.000 0.00 0.00 37.77 2.01
832 861 3.067461 ACTTGCAGCTAACGGATCTCTAG 59.933 47.826 0.00 0.00 0.00 2.43
892 921 2.427812 GGTGGGCTTAGTAGAGACTGTC 59.572 54.545 0.00 0.00 36.28 3.51
962 992 3.007635 GGCGGTCTTATATAATGGGCAC 58.992 50.000 0.00 0.00 0.00 5.01
992 1022 1.909302 GAGGGGAGATGGTGAGTGAAA 59.091 52.381 0.00 0.00 0.00 2.69
1008 1038 1.186200 TGTGATCGGAGAGTTGAGGG 58.814 55.000 0.00 0.00 43.63 4.30
1009 1039 2.692557 AGATGTGATCGGAGAGTTGAGG 59.307 50.000 0.00 0.00 43.63 3.86
1037 1067 1.138859 TGTGTGTGTGTGGAAGAGGAG 59.861 52.381 0.00 0.00 0.00 3.69
1046 1076 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1052 1082 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1053 1083 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1054 1084 1.128507 GAGTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1081 1111 2.888414 TCCCTGTCCCAAAAACGAATTC 59.112 45.455 0.00 0.00 0.00 2.17
1091 1121 2.596851 GCAGAGCTCCCTGTCCCAA 61.597 63.158 10.93 0.00 36.57 4.12
1243 1279 4.196778 TTGCAGTGGTCGGGGCAA 62.197 61.111 0.00 0.00 43.32 4.52
1297 1333 1.002888 GACCTGATCATGCCGATGGAT 59.997 52.381 0.00 0.00 33.17 3.41
1623 1672 4.007644 CTCCAGCTGTGGCCGTCA 62.008 66.667 13.81 0.00 44.60 4.35
1807 1880 1.291877 CGAAGAAGAACCAGTGCCCG 61.292 60.000 0.00 0.00 0.00 6.13
1851 1924 1.342174 CAACAGTGGAAAGGCTGCAAT 59.658 47.619 0.50 0.00 36.26 3.56
1895 1968 1.739067 GGATGCAACAGGTGTACTCC 58.261 55.000 5.81 5.81 0.00 3.85
1896 1969 1.067142 TCGGATGCAACAGGTGTACTC 60.067 52.381 0.00 0.00 0.00 2.59
1918 2005 2.100605 ACAATTCCTCTGGAGCGTTC 57.899 50.000 0.00 0.00 31.21 3.95
1919 2006 2.039084 AGAACAATTCCTCTGGAGCGTT 59.961 45.455 0.00 0.00 31.21 4.84
2226 2453 4.873129 CCTGATGACCCGCCGTCG 62.873 72.222 0.00 0.00 45.23 5.12
2227 2454 4.530857 CCCTGATGACCCGCCGTC 62.531 72.222 0.00 0.00 42.33 4.79
2407 2640 0.606096 TCATGGAGAAGCGGTTCGAA 59.394 50.000 20.64 11.25 37.79 3.71
2573 2806 1.283347 TCATCTCAGGCAAGGAAGCT 58.717 50.000 0.00 0.00 34.17 3.74
2584 2817 7.303998 GTTTTCTCTTTTGACCATCATCTCAG 58.696 38.462 0.00 0.00 0.00 3.35
2597 2830 7.805700 TGCTTTTCTTTTGGTTTTCTCTTTTG 58.194 30.769 0.00 0.00 0.00 2.44
2643 2889 3.186409 CGGCGGGTGATACATCTAAATTG 59.814 47.826 0.00 0.00 0.00 2.32
2645 2891 2.631062 TCGGCGGGTGATACATCTAAAT 59.369 45.455 7.21 0.00 0.00 1.40
2646 2892 2.033372 TCGGCGGGTGATACATCTAAA 58.967 47.619 7.21 0.00 0.00 1.85
2652 2898 2.758327 AGCTCGGCGGGTGATACA 60.758 61.111 9.26 0.00 0.00 2.29
2678 2925 0.539669 TCTTCCTCTGTCGCTGACCA 60.540 55.000 6.30 0.00 0.00 4.02
2730 2977 3.058501 CCTAAAGCTTACACAAACACCCG 60.059 47.826 0.00 0.00 0.00 5.28
2822 3069 6.319658 CCTCGTTGGGAACTACTAGTTGTATA 59.680 42.308 10.43 0.00 38.80 1.47
2825 3072 3.257624 CCTCGTTGGGAACTACTAGTTGT 59.742 47.826 6.17 1.41 38.80 3.32
2828 3075 3.166560 ACCTCGTTGGGAACTACTAGT 57.833 47.619 0.00 0.00 41.11 2.57
2839 3089 4.212636 CCACTACACTTTTTACCTCGTTGG 59.787 45.833 0.00 0.00 42.93 3.77
2843 3093 3.395639 TGCCACTACACTTTTTACCTCG 58.604 45.455 0.00 0.00 0.00 4.63
2844 3094 5.761165 TTTGCCACTACACTTTTTACCTC 57.239 39.130 0.00 0.00 0.00 3.85
2879 3129 3.633525 TCTGGTGGAGAAATATGCATTGC 59.366 43.478 3.54 0.46 0.00 3.56
2896 3146 5.869649 AAAAGTGGCAATAAAAGTCTGGT 57.130 34.783 0.00 0.00 0.00 4.00
2916 3166 2.946785 TGCCTCGTTTAAGGGGAAAAA 58.053 42.857 0.00 0.00 36.88 1.94
2921 3171 2.510613 TCTTTTGCCTCGTTTAAGGGG 58.489 47.619 0.00 0.00 36.88 4.79
2922 3172 4.783764 AATCTTTTGCCTCGTTTAAGGG 57.216 40.909 0.00 0.00 36.88 3.95
2923 3173 5.793457 CGTAAATCTTTTGCCTCGTTTAAGG 59.207 40.000 0.00 0.00 39.62 2.69
2924 3174 6.368213 ACGTAAATCTTTTGCCTCGTTTAAG 58.632 36.000 0.00 0.00 0.00 1.85
2927 3177 4.823790 ACGTAAATCTTTTGCCTCGTTT 57.176 36.364 0.00 0.00 0.00 3.60
2930 3180 5.209240 TGAAAACGTAAATCTTTTGCCTCG 58.791 37.500 0.00 0.00 0.00 4.63
2931 3181 7.637709 AATGAAAACGTAAATCTTTTGCCTC 57.362 32.000 0.00 0.00 0.00 4.70
2943 3193 9.504708 TCCCAGTTCTAATTAATGAAAACGTAA 57.495 29.630 0.00 0.00 0.00 3.18
2944 3194 9.158233 CTCCCAGTTCTAATTAATGAAAACGTA 57.842 33.333 0.00 0.00 0.00 3.57
2945 3195 7.881232 TCTCCCAGTTCTAATTAATGAAAACGT 59.119 33.333 0.00 0.00 0.00 3.99
2946 3196 8.263940 TCTCCCAGTTCTAATTAATGAAAACG 57.736 34.615 0.00 0.00 0.00 3.60
2950 3200 9.020731 GGTTTTCTCCCAGTTCTAATTAATGAA 57.979 33.333 0.00 0.00 0.00 2.57
2951 3201 8.390921 AGGTTTTCTCCCAGTTCTAATTAATGA 58.609 33.333 0.00 0.00 0.00 2.57
2952 3202 8.581253 AGGTTTTCTCCCAGTTCTAATTAATG 57.419 34.615 0.00 0.00 0.00 1.90
2953 3203 9.907229 CTAGGTTTTCTCCCAGTTCTAATTAAT 57.093 33.333 0.00 0.00 0.00 1.40
2954 3204 9.108111 TCTAGGTTTTCTCCCAGTTCTAATTAA 57.892 33.333 0.00 0.00 0.00 1.40
2955 3205 8.674925 TCTAGGTTTTCTCCCAGTTCTAATTA 57.325 34.615 0.00 0.00 0.00 1.40
2956 3206 7.569599 TCTAGGTTTTCTCCCAGTTCTAATT 57.430 36.000 0.00 0.00 0.00 1.40
2957 3207 7.569599 TTCTAGGTTTTCTCCCAGTTCTAAT 57.430 36.000 0.00 0.00 0.00 1.73
2958 3208 7.569599 ATTCTAGGTTTTCTCCCAGTTCTAA 57.430 36.000 0.00 0.00 0.00 2.10
2959 3209 7.676893 TGTATTCTAGGTTTTCTCCCAGTTCTA 59.323 37.037 0.00 0.00 0.00 2.10
2960 3210 6.500751 TGTATTCTAGGTTTTCTCCCAGTTCT 59.499 38.462 0.00 0.00 0.00 3.01
2961 3211 6.708285 TGTATTCTAGGTTTTCTCCCAGTTC 58.292 40.000 0.00 0.00 0.00 3.01
2962 3212 6.697641 TGTATTCTAGGTTTTCTCCCAGTT 57.302 37.500 0.00 0.00 0.00 3.16
2963 3213 6.697641 TTGTATTCTAGGTTTTCTCCCAGT 57.302 37.500 0.00 0.00 0.00 4.00
2964 3214 5.586643 GCTTGTATTCTAGGTTTTCTCCCAG 59.413 44.000 0.00 0.00 0.00 4.45
2965 3215 5.497474 GCTTGTATTCTAGGTTTTCTCCCA 58.503 41.667 0.00 0.00 0.00 4.37
2966 3216 4.882427 GGCTTGTATTCTAGGTTTTCTCCC 59.118 45.833 0.00 0.00 0.00 4.30
2967 3217 4.571176 CGGCTTGTATTCTAGGTTTTCTCC 59.429 45.833 0.00 0.00 0.00 3.71
2968 3218 4.034163 GCGGCTTGTATTCTAGGTTTTCTC 59.966 45.833 0.00 0.00 0.00 2.87
2969 3219 3.939592 GCGGCTTGTATTCTAGGTTTTCT 59.060 43.478 0.00 0.00 0.00 2.52
2970 3220 3.687698 TGCGGCTTGTATTCTAGGTTTTC 59.312 43.478 0.00 0.00 0.00 2.29
2971 3221 3.439129 GTGCGGCTTGTATTCTAGGTTTT 59.561 43.478 0.00 0.00 0.00 2.43
2979 3229 0.381801 CCCATGTGCGGCTTGTATTC 59.618 55.000 0.00 0.00 0.00 1.75
2981 3231 1.453745 CCCCATGTGCGGCTTGTAT 60.454 57.895 0.00 0.00 0.00 2.29
3001 3251 0.393820 TTTGTGGTCAGGTCGGGTAC 59.606 55.000 0.00 0.00 0.00 3.34
3002 3252 0.393820 GTTTGTGGTCAGGTCGGGTA 59.606 55.000 0.00 0.00 0.00 3.69
3005 3255 1.604604 ATTGTTTGTGGTCAGGTCGG 58.395 50.000 0.00 0.00 0.00 4.79
3104 3357 2.113433 CAGAGCTGCCATGTCCTGC 61.113 63.158 0.00 0.00 0.00 4.85
3105 3358 0.180642 ATCAGAGCTGCCATGTCCTG 59.819 55.000 0.00 0.00 0.00 3.86
3131 3384 6.799512 ACAACTTTCTCCTTTGAAACTCATG 58.200 36.000 0.00 0.00 33.11 3.07
3133 3386 7.415206 GCTTACAACTTTCTCCTTTGAAACTCA 60.415 37.037 0.00 0.00 33.11 3.41
3137 3390 5.891551 AGGCTTACAACTTTCTCCTTTGAAA 59.108 36.000 0.00 0.00 35.07 2.69
3142 3395 3.665190 CGAGGCTTACAACTTTCTCCTT 58.335 45.455 0.00 0.00 0.00 3.36
3155 3408 1.064166 ACTAGGTAGGTGCGAGGCTTA 60.064 52.381 0.00 0.00 0.00 3.09
3168 3421 4.504514 CCGGATGTAGTGCTAGACTAGGTA 60.505 50.000 11.48 0.00 37.87 3.08
3177 3430 1.319541 GCTCTCCGGATGTAGTGCTA 58.680 55.000 3.57 0.00 31.28 3.49
3181 3434 1.384989 CGGTGCTCTCCGGATGTAGT 61.385 60.000 3.57 0.00 45.88 2.73
3183 3436 3.521605 CGGTGCTCTCCGGATGTA 58.478 61.111 3.57 0.00 45.88 2.29
3213 3466 3.284617 CAATGATGACTCCATGAAGGCA 58.715 45.455 0.00 0.00 39.05 4.75
3217 3470 2.291365 CGGCAATGATGACTCCATGAA 58.709 47.619 0.00 0.00 32.09 2.57
3231 3484 2.629656 GCAAGGTCACTGCGGCAAT 61.630 57.895 3.44 0.00 0.00 3.56
3254 3507 1.000163 GACAGAGAAGTCGGAGTTGCA 60.000 52.381 2.13 0.00 0.00 4.08
3288 3541 2.420607 GCCAATGGGTATGCGTATGCA 61.421 52.381 12.96 12.96 46.64 3.96
3298 3551 2.045438 CTGGTGCGCCAATGGGTA 60.045 61.111 21.56 0.00 45.51 3.69
3367 3643 2.296471 CGACAGTGAGGTTGGTCTAACT 59.704 50.000 0.00 0.00 39.31 2.24
3369 3645 2.589720 TCGACAGTGAGGTTGGTCTAA 58.410 47.619 0.00 0.00 0.00 2.10
3370 3646 2.281539 TCGACAGTGAGGTTGGTCTA 57.718 50.000 0.00 0.00 0.00 2.59
3372 3648 1.499049 GTTCGACAGTGAGGTTGGTC 58.501 55.000 0.00 0.00 0.00 4.02
3384 3660 4.980805 GCAGGTGCCCGTTCGACA 62.981 66.667 0.00 0.00 34.31 4.35
3426 3702 3.157087 CCCATTTGTGCTTCTTGTAGGT 58.843 45.455 0.00 0.00 0.00 3.08
3430 3706 3.499338 TGATCCCATTTGTGCTTCTTGT 58.501 40.909 0.00 0.00 0.00 3.16
3433 3709 4.038271 TCTTGATCCCATTTGTGCTTCT 57.962 40.909 0.00 0.00 0.00 2.85
3449 3725 2.151202 GCACCGTTTTGGAGATCTTGA 58.849 47.619 0.00 0.00 42.00 3.02
3500 3776 1.671054 GTTGAACTAGGCAGCGGCA 60.671 57.895 11.88 0.00 43.71 5.69
3506 3782 2.551270 AGATCCTGGTTGAACTAGGCA 58.449 47.619 21.39 11.61 45.42 4.75
3511 3787 4.713792 AAGTCAAGATCCTGGTTGAACT 57.286 40.909 0.00 0.00 34.52 3.01
3512 3788 4.083802 CGAAAGTCAAGATCCTGGTTGAAC 60.084 45.833 0.33 0.00 34.52 3.18
3514 3790 3.323691 TCGAAAGTCAAGATCCTGGTTGA 59.676 43.478 0.00 0.00 0.00 3.18
3536 3812 2.507471 CTCCTAGGCCAAGATCTTTGGT 59.493 50.000 19.00 8.23 41.53 3.67
3539 3815 3.846588 TCAACTCCTAGGCCAAGATCTTT 59.153 43.478 5.01 0.00 0.00 2.52
3553 3829 2.957402 TTTGTGCATCCTCAACTCCT 57.043 45.000 0.00 0.00 0.00 3.69
3554 3830 3.084039 TGATTTGTGCATCCTCAACTCC 58.916 45.455 0.00 0.00 0.00 3.85
3558 3834 3.084039 GAGGTGATTTGTGCATCCTCAA 58.916 45.455 0.00 0.00 40.51 3.02
3580 3856 4.770795 CGTTCTTCCTTGGAGGTATCATT 58.229 43.478 0.00 0.00 36.53 2.57
3582 3858 2.093658 GCGTTCTTCCTTGGAGGTATCA 60.094 50.000 0.00 0.00 36.53 2.15
3585 3861 0.245539 CGCGTTCTTCCTTGGAGGTA 59.754 55.000 0.00 0.00 36.53 3.08
3586 3862 1.004918 CGCGTTCTTCCTTGGAGGT 60.005 57.895 0.00 0.00 36.53 3.85


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

AutoCloner maintained by Alex Coulton.