Multiple sequence alignment - TraesCS2A01G531100

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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 TraesCS2A01G531100 chr2A 100.000 3710 0 0 1 3710 748503994 748500285 0.000000e+00 6852.0
1 TraesCS2A01G531100 chr2A 89.893 2434 227 11 365 2781 748437497 748439928 0.000000e+00 3114.0
2 TraesCS2A01G531100 chr2A 89.085 2492 250 16 271 2759 746620269 746622741 0.000000e+00 3075.0
3 TraesCS2A01G531100 chr2A 87.664 2586 279 21 198 2781 748284970 748287517 0.000000e+00 2972.0
4 TraesCS2A01G531100 chr2D 89.406 2662 248 16 153 2781 617910066 617907406 0.000000e+00 3323.0
5 TraesCS2A01G531100 chr2D 88.836 2714 273 15 70 2782 617546143 617548827 0.000000e+00 3306.0
6 TraesCS2A01G531100 chr2D 88.805 2644 253 20 139 2759 617538568 617541191 0.000000e+00 3203.0
7 TraesCS2A01G531100 chr2D 89.658 2427 238 5 368 2781 617887255 617889681 0.000000e+00 3079.0
8 TraesCS2A01G531100 chr2D 88.059 2571 271 22 216 2759 617633628 617636189 0.000000e+00 3014.0
9 TraesCS2A01G531100 chr2B 88.537 2687 251 25 75 2759 753931583 753928952 0.000000e+00 3203.0
10 TraesCS2A01G531100 chr2B 89.710 2449 239 11 317 2759 753792720 753795161 0.000000e+00 3114.0
11 TraesCS2A01G531100 chr2B 84.185 411 32 15 4 405 753939058 753938672 5.850000e-98 368.0
12 TraesCS2A01G531100 chr2B 85.616 146 13 1 3573 3710 646628037 646628182 2.990000e-31 147.0
13 TraesCS2A01G531100 chr7B 86.646 2269 227 32 69 2323 726150014 726152220 0.000000e+00 2442.0
14 TraesCS2A01G531100 chr4B 92.077 934 44 9 2796 3710 193994180 193993258 0.000000e+00 1288.0
15 TraesCS2A01G531100 chr4B 91.111 45 2 2 2846 2889 404626309 404626266 4.000000e-05 60.2
16 TraesCS2A01G531100 chr7D 83.942 411 50 8 3096 3502 49888226 49887828 2.700000e-101 379.0
17 TraesCS2A01G531100 chr4A 84.304 395 49 5 3109 3502 664488675 664488293 1.260000e-99 374.0
18 TraesCS2A01G531100 chr7A 83.051 413 54 7 3094 3502 52971762 52971362 9.800000e-96 361.0


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 TraesCS2A01G531100 chr2A 748500285 748503994 3709 True 6852 6852 100.000 1 3710 1 chr2A.!!$R1 3709
1 TraesCS2A01G531100 chr2A 748437497 748439928 2431 False 3114 3114 89.893 365 2781 1 chr2A.!!$F3 2416
2 TraesCS2A01G531100 chr2A 746620269 746622741 2472 False 3075 3075 89.085 271 2759 1 chr2A.!!$F1 2488
3 TraesCS2A01G531100 chr2A 748284970 748287517 2547 False 2972 2972 87.664 198 2781 1 chr2A.!!$F2 2583
4 TraesCS2A01G531100 chr2D 617907406 617910066 2660 True 3323 3323 89.406 153 2781 1 chr2D.!!$R1 2628
5 TraesCS2A01G531100 chr2D 617546143 617548827 2684 False 3306 3306 88.836 70 2782 1 chr2D.!!$F2 2712
6 TraesCS2A01G531100 chr2D 617538568 617541191 2623 False 3203 3203 88.805 139 2759 1 chr2D.!!$F1 2620
7 TraesCS2A01G531100 chr2D 617887255 617889681 2426 False 3079 3079 89.658 368 2781 1 chr2D.!!$F4 2413
8 TraesCS2A01G531100 chr2D 617633628 617636189 2561 False 3014 3014 88.059 216 2759 1 chr2D.!!$F3 2543
9 TraesCS2A01G531100 chr2B 753928952 753931583 2631 True 3203 3203 88.537 75 2759 1 chr2B.!!$R1 2684
10 TraesCS2A01G531100 chr2B 753792720 753795161 2441 False 3114 3114 89.710 317 2759 1 chr2B.!!$F2 2442
11 TraesCS2A01G531100 chr7B 726150014 726152220 2206 False 2442 2442 86.646 69 2323 1 chr7B.!!$F1 2254
12 TraesCS2A01G531100 chr4B 193993258 193994180 922 True 1288 1288 92.077 2796 3710 1 chr4B.!!$R1 914

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
44 45 0.046242 ATTCATCTCCCCACTCCCCA 59.954 55.0 0.00 0.00 0.0 4.96 F
62 63 0.106217 CAGTCCTCCCTCCTCCTCTC 60.106 65.0 0.00 0.00 0.0 3.20 F
67 68 0.106217 CTCCCTCCTCCTCTCCAGTC 60.106 65.0 0.00 0.00 0.0 3.51 F
852 940 0.177604 CTACTCAAGGGGCTCTGCAG 59.822 60.0 7.63 7.63 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2014 1.346068 ACTCAGTGCTTTCTCCACCTC 59.654 52.381 0.00 0.00 33.75 3.85 R
2063 2165 6.675413 ATATAATAGTCGTGGGCTTAACCA 57.325 37.500 0.00 0.00 42.05 3.67 R
2132 2234 9.153721 TCATCATATCAAAATTTTCCTTTGCAC 57.846 29.630 0.00 0.00 34.43 4.57 R
2786 2889 2.307098 CAGAGAACTGGGGAATTCACCT 59.693 50.000 26.87 7.54 41.04 4.00 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
25 26 3.126001 GGAATGATCCAACGGCATAGA 57.874 47.619 0.00 0.00 45.79 1.98
26 27 3.679389 GGAATGATCCAACGGCATAGAT 58.321 45.455 0.00 0.00 45.79 1.98
27 28 4.074970 GGAATGATCCAACGGCATAGATT 58.925 43.478 0.00 0.00 45.79 2.40
28 29 4.154918 GGAATGATCCAACGGCATAGATTC 59.845 45.833 0.00 0.00 45.79 2.52
29 30 3.836365 TGATCCAACGGCATAGATTCA 57.164 42.857 0.00 0.00 0.00 2.57
30 31 4.356405 TGATCCAACGGCATAGATTCAT 57.644 40.909 0.00 0.00 0.00 2.57
31 32 4.318332 TGATCCAACGGCATAGATTCATC 58.682 43.478 0.00 0.00 0.00 2.92
32 33 4.040829 TGATCCAACGGCATAGATTCATCT 59.959 41.667 0.00 0.00 40.86 2.90
33 34 3.995199 TCCAACGGCATAGATTCATCTC 58.005 45.455 0.00 0.00 38.32 2.75
34 35 3.070018 CCAACGGCATAGATTCATCTCC 58.930 50.000 0.00 0.00 38.32 3.71
35 36 3.070018 CAACGGCATAGATTCATCTCCC 58.930 50.000 0.00 0.00 38.32 4.30
36 37 1.625818 ACGGCATAGATTCATCTCCCC 59.374 52.381 0.00 0.00 38.32 4.81
37 38 1.625315 CGGCATAGATTCATCTCCCCA 59.375 52.381 0.00 0.00 38.32 4.96
38 39 2.613977 CGGCATAGATTCATCTCCCCAC 60.614 54.545 0.00 0.00 38.32 4.61
39 40 2.641815 GGCATAGATTCATCTCCCCACT 59.358 50.000 0.00 0.00 38.32 4.00
40 41 3.307339 GGCATAGATTCATCTCCCCACTC 60.307 52.174 0.00 0.00 38.32 3.51
41 42 3.307339 GCATAGATTCATCTCCCCACTCC 60.307 52.174 0.00 0.00 38.32 3.85
42 43 1.813102 AGATTCATCTCCCCACTCCC 58.187 55.000 0.00 0.00 29.30 4.30
43 44 0.767998 GATTCATCTCCCCACTCCCC 59.232 60.000 0.00 0.00 0.00 4.81
44 45 0.046242 ATTCATCTCCCCACTCCCCA 59.954 55.000 0.00 0.00 0.00 4.96
45 46 0.621571 TTCATCTCCCCACTCCCCAG 60.622 60.000 0.00 0.00 0.00 4.45
46 47 1.307343 CATCTCCCCACTCCCCAGT 60.307 63.158 0.00 0.00 0.00 4.00
47 48 1.003573 ATCTCCCCACTCCCCAGTC 59.996 63.158 0.00 0.00 0.00 3.51
48 49 2.553438 ATCTCCCCACTCCCCAGTCC 62.553 65.000 0.00 0.00 0.00 3.85
49 50 3.208592 TCCCCACTCCCCAGTCCT 61.209 66.667 0.00 0.00 0.00 3.85
50 51 2.689034 CCCCACTCCCCAGTCCTC 60.689 72.222 0.00 0.00 0.00 3.71
51 52 2.689034 CCCACTCCCCAGTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
52 53 2.689034 CCACTCCCCAGTCCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
53 54 2.452114 CACTCCCCAGTCCTCCCT 59.548 66.667 0.00 0.00 0.00 4.20
54 55 1.687493 CACTCCCCAGTCCTCCCTC 60.687 68.421 0.00 0.00 0.00 4.30
55 56 2.041405 CTCCCCAGTCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
56 57 2.540910 TCCCCAGTCCTCCCTCCT 60.541 66.667 0.00 0.00 0.00 3.69
57 58 2.041405 CCCCAGTCCTCCCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
58 59 2.041405 CCCAGTCCTCCCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
59 60 2.641746 CCCAGTCCTCCCTCCTCCT 61.642 68.421 0.00 0.00 0.00 3.69
60 61 1.075600 CCAGTCCTCCCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
61 62 1.589399 CCAGTCCTCCCTCCTCCTCT 61.589 65.000 0.00 0.00 0.00 3.69
62 63 0.106217 CAGTCCTCCCTCCTCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
63 64 1.231928 GTCCTCCCTCCTCCTCTCC 59.768 68.421 0.00 0.00 0.00 3.71
64 65 1.230650 TCCTCCCTCCTCCTCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
65 66 1.232792 CCTCCCTCCTCCTCTCCAG 59.767 68.421 0.00 0.00 0.00 3.86
66 67 1.589399 CCTCCCTCCTCCTCTCCAGT 61.589 65.000 0.00 0.00 0.00 4.00
67 68 0.106217 CTCCCTCCTCCTCTCCAGTC 60.106 65.000 0.00 0.00 0.00 3.51
127 128 2.177778 GTTCCCGTCCTCGTCGAC 59.822 66.667 5.18 5.18 35.01 4.20
133 134 3.507009 GTCCTCGTCGACGGAGGG 61.507 72.222 34.88 31.12 40.29 4.30
134 135 4.790962 TCCTCGTCGACGGAGGGG 62.791 72.222 34.88 29.40 40.29 4.79
160 161 2.280592 GTGCGTTGTTCCTCCCGT 60.281 61.111 0.00 0.00 0.00 5.28
167 168 0.882927 TTGTTCCTCCCGTGCTTTCG 60.883 55.000 0.00 0.00 0.00 3.46
196 197 2.683933 GGGGCCTCCTCTTCGTCA 60.684 66.667 0.84 0.00 0.00 4.35
235 236 2.160221 CATTGATTGCAACCCGCGC 61.160 57.895 0.00 0.00 46.97 6.86
362 379 1.383803 GGTCTCTCAGCCTCCCCAT 60.384 63.158 0.00 0.00 0.00 4.00
446 534 2.304180 TCCTCCTTCAAGGCTTCTTCAG 59.696 50.000 0.00 0.00 36.29 3.02
449 537 2.711009 TCCTTCAAGGCTTCTTCAGGAA 59.289 45.455 0.00 0.00 35.54 3.36
451 539 3.891366 CCTTCAAGGCTTCTTCAGGAAAA 59.109 43.478 0.00 0.00 33.01 2.29
453 541 3.222603 TCAAGGCTTCTTCAGGAAAACC 58.777 45.455 0.00 0.00 33.07 3.27
454 542 2.958355 CAAGGCTTCTTCAGGAAAACCA 59.042 45.455 0.00 0.00 34.47 3.67
513 601 1.595655 TGCGCGCTGGAACACTAAA 60.596 52.632 33.29 3.51 0.00 1.85
538 626 3.276846 GACGCGCACCACCTGTTT 61.277 61.111 5.73 0.00 0.00 2.83
575 663 4.530857 CCGCCGCCTTCCCAGTAG 62.531 72.222 0.00 0.00 0.00 2.57
586 674 2.746375 CCCAGTAGGCGGGCTGAAT 61.746 63.158 15.11 0.00 36.72 2.57
782 870 1.133668 ACTTGGTGCTTGCCTTCTTCT 60.134 47.619 0.00 0.00 0.00 2.85
806 894 1.920325 CTCCTCAGGTTGGGGCTGA 60.920 63.158 0.00 0.00 38.12 4.26
819 907 0.807496 GGGCTGAGCTTGAATGTCAC 59.193 55.000 3.72 0.00 0.00 3.67
835 923 3.042682 TGTCACCTCCTTCAACAACCTA 58.957 45.455 0.00 0.00 0.00 3.08
852 940 0.177604 CTACTCAAGGGGCTCTGCAG 59.822 60.000 7.63 7.63 0.00 4.41
853 941 0.545309 TACTCAAGGGGCTCTGCAGT 60.545 55.000 14.67 4.06 0.00 4.40
855 944 1.834856 CTCAAGGGGCTCTGCAGTCA 61.835 60.000 14.67 0.00 0.00 3.41
880 969 3.471495 GTACAAATGAGGCTTTGGACG 57.529 47.619 0.00 0.00 39.47 4.79
891 980 1.572085 CTTTGGACGTGCTGCTCCAG 61.572 60.000 8.99 0.00 37.85 3.86
925 1014 2.433145 ACTGTGCGCCTGATGTCG 60.433 61.111 4.18 0.00 0.00 4.35
972 1061 3.859386 GCTGTTTGAAACAAGGTGAAGTG 59.141 43.478 12.26 0.00 41.61 3.16
975 1064 4.157656 TGTTTGAAACAAGGTGAAGTGGAG 59.842 41.667 8.51 0.00 38.72 3.86
992 1081 2.233676 TGGAGAAAGCGTGCAATCTCTA 59.766 45.455 19.52 14.25 38.64 2.43
995 1084 1.324736 GAAAGCGTGCAATCTCTACCG 59.675 52.381 0.00 0.00 0.00 4.02
1008 1097 4.902443 TCTCTACCGTGAGATGATCAAC 57.098 45.455 0.00 0.00 40.43 3.18
1028 1117 1.457346 CTGGGAGTTCAACCTGATGC 58.543 55.000 0.00 0.00 0.00 3.91
1040 1129 0.179100 CCTGATGCGGTGACCTACAG 60.179 60.000 0.00 3.89 0.00 2.74
1045 1134 1.517832 GCGGTGACCTACAGCTCAT 59.482 57.895 0.00 0.00 45.46 2.90
1124 1213 4.571919 CAAATGGTTGATCAAGGCATTGT 58.428 39.130 8.80 0.00 36.83 2.71
1137 1226 6.135454 TCAAGGCATTGTACCCAATATCATT 58.865 36.000 11.36 0.00 39.28 2.57
1140 1229 5.705441 AGGCATTGTACCCAATATCATTACG 59.295 40.000 0.00 0.00 39.28 3.18
1160 1249 8.947115 CATTACGTATACTAGTCTGATCCATGA 58.053 37.037 0.00 0.00 0.00 3.07
1185 1274 3.698250 CACTTCGGGTCAGTGGAAA 57.302 52.632 0.00 0.00 38.43 3.13
1198 1287 1.699634 AGTGGAAAGCAGCAGTTAGGA 59.300 47.619 0.00 0.00 0.00 2.94
1221 1310 9.178758 AGGATATTCAAAGAAATGACAAGTACC 57.821 33.333 0.00 0.00 0.00 3.34
1237 1326 2.145536 GTACCGGTGTTCGACCAAATT 58.854 47.619 19.93 0.00 46.55 1.82
1260 1349 7.490962 TTCTGTCACGTTGAACTCATTTATT 57.509 32.000 0.00 0.00 0.00 1.40
1283 1372 4.771577 TGATTCCCTTTGCAAGCATAGAAA 59.228 37.500 13.03 7.97 0.00 2.52
1320 1409 5.136105 AGAGATATTTTTGACTCCATGGCC 58.864 41.667 6.96 0.00 0.00 5.36
1326 1415 1.523154 TTGACTCCATGGCCGCAAAC 61.523 55.000 6.96 0.00 0.00 2.93
1360 1449 9.495382 AACCTGATATTTTCTCCTACTCTACTT 57.505 33.333 0.00 0.00 0.00 2.24
1501 1590 3.449377 TGCTAAACGTGGACTGATGGATA 59.551 43.478 0.00 0.00 0.00 2.59
1596 1685 2.743664 GGATTCACTTTGCAAAATGGGC 59.256 45.455 19.53 9.59 0.00 5.36
1754 1843 8.306313 TCTGAAGCAATTAATAGAGGTCTGTA 57.694 34.615 0.00 0.00 0.00 2.74
1778 1867 9.011407 GTATTCTAACAGTGTGTTCTTCTATCG 57.989 37.037 0.00 0.00 40.22 2.92
1815 1916 6.828502 CTTTGCAAAGAAGGAAAGGTAAAC 57.171 37.500 31.24 0.00 41.49 2.01
1860 1961 2.447408 TCCTAGGTATTGGTCAGCGA 57.553 50.000 9.08 0.00 0.00 4.93
2063 2165 0.687354 AGGGAAATGTCACTCAGCGT 59.313 50.000 0.00 0.00 28.08 5.07
2132 2234 2.260844 TGCTCTGGGAGAACAGTTTG 57.739 50.000 0.00 0.00 39.48 2.93
2145 2247 5.733676 AGAACAGTTTGTGCAAAGGAAAAT 58.266 33.333 0.00 0.00 0.00 1.82
2148 2250 6.816134 ACAGTTTGTGCAAAGGAAAATTTT 57.184 29.167 2.28 2.28 0.00 1.82
2149 2251 6.610456 ACAGTTTGTGCAAAGGAAAATTTTG 58.390 32.000 8.47 0.00 38.30 2.44
2153 2255 9.341078 AGTTTGTGCAAAGGAAAATTTTGATAT 57.659 25.926 8.47 0.00 37.65 1.63
2196 2298 1.810151 GTGGGCGTTGACACATACAAT 59.190 47.619 0.00 0.00 37.54 2.71
2317 2419 5.889853 ACACTCAATACCATGATTTCTGCAT 59.110 36.000 0.00 0.00 0.00 3.96
2465 2567 5.009310 TGGCAGATGCTGATGATATGTTTTC 59.991 40.000 4.59 0.00 41.70 2.29
2568 2670 6.534634 AGTTGTAAAGGCTGTGACTTATCTT 58.465 36.000 0.00 0.00 26.79 2.40
2656 2758 6.463053 TCTCAAGGAAAGGGAAATTAAGGA 57.537 37.500 0.00 0.00 0.00 3.36
2732 2835 9.383519 CTGACAATTGATACAGTATTACTTGGT 57.616 33.333 13.59 5.76 0.00 3.67
2853 2956 4.077300 TCTTCTGAACACAGTGCAGATT 57.923 40.909 8.57 0.00 46.28 2.40
2889 2992 5.189539 AGAAGAGGAAGAATCTTGAGGAAGG 59.810 44.000 0.00 0.00 37.14 3.46
2918 3021 6.655003 TGGTGAATAACAAGGTGAATTCTCTC 59.345 38.462 7.05 0.00 30.43 3.20
2925 3028 5.715070 ACAAGGTGAATTCTCTCTCTAACG 58.285 41.667 7.05 0.00 0.00 3.18
2932 3035 6.525280 GTGAATTCTCTCTCTAACGAAGTCAC 59.475 42.308 13.24 13.24 46.72 3.67
2989 3092 9.643693 ATTTTATTTTGCTTATGTTCCTGTGAG 57.356 29.630 0.00 0.00 0.00 3.51
3026 3129 8.572855 ACTGAATCCATCTTTTCTAAGAAAGG 57.427 34.615 0.00 0.00 43.32 3.11
3039 3142 3.852858 AAGAAAGGATGAATTGGGGGT 57.147 42.857 0.00 0.00 0.00 4.95
3040 3143 4.965283 AAGAAAGGATGAATTGGGGGTA 57.035 40.909 0.00 0.00 0.00 3.69
3041 3144 4.526438 AGAAAGGATGAATTGGGGGTAG 57.474 45.455 0.00 0.00 0.00 3.18
3043 3146 2.605825 AGGATGAATTGGGGGTAGGA 57.394 50.000 0.00 0.00 0.00 2.94
3045 3148 2.785857 AGGATGAATTGGGGGTAGGAAG 59.214 50.000 0.00 0.00 0.00 3.46
3082 3189 5.410439 TGTTCGGCCTGTTTATAACTTCTTC 59.590 40.000 0.00 0.00 0.00 2.87
3089 3197 7.121315 GGCCTGTTTATAACTTCTTCATTCACT 59.879 37.037 0.00 0.00 0.00 3.41
3090 3198 9.162764 GCCTGTTTATAACTTCTTCATTCACTA 57.837 33.333 0.00 0.00 0.00 2.74
3158 3266 3.266772 TCCTCTTGGATGGCTATTGTTGT 59.733 43.478 0.00 0.00 37.46 3.32
3159 3267 4.473196 TCCTCTTGGATGGCTATTGTTGTA 59.527 41.667 0.00 0.00 37.46 2.41
3160 3268 4.818546 CCTCTTGGATGGCTATTGTTGTAG 59.181 45.833 0.00 0.00 34.57 2.74
3161 3269 5.431765 CTCTTGGATGGCTATTGTTGTAGT 58.568 41.667 0.00 0.00 0.00 2.73
3190 3298 0.248539 GCGGCGGTTTTTGTAACACA 60.249 50.000 9.78 0.00 0.00 3.72
3203 3311 2.432874 TGTAACACACAGCAGTAGTGGT 59.567 45.455 13.40 10.51 41.21 4.16
3209 3317 1.466167 CACAGCAGTAGTGGTTGCATC 59.534 52.381 0.00 0.00 42.67 3.91
3244 3352 7.439157 TCTGTTTTTACATGGATGTTCTCAG 57.561 36.000 0.00 1.97 41.97 3.35
3271 3379 4.879104 TGCCAAAGAATGCAAAAACAAG 57.121 36.364 0.00 0.00 33.87 3.16
3276 3384 6.708676 CCAAAGAATGCAAAAACAAGAAGAC 58.291 36.000 0.00 0.00 0.00 3.01
3287 3397 3.971032 ACAAGAAGACAAAAAGGCTCG 57.029 42.857 0.00 0.00 30.53 5.03
3300 3410 3.482783 GCTCGCTCCACTTCGTGC 61.483 66.667 0.00 0.00 37.88 5.34
3313 3423 3.368236 CACTTCGTGCTAAAGCTACTTCC 59.632 47.826 3.26 0.00 42.66 3.46
3381 3491 5.013495 AGTTTCAGGAAGACTGGAATGATCA 59.987 40.000 0.00 0.00 46.16 2.92
3435 3545 4.770010 TGACTTGAAAGTTGAAACCAAGGT 59.230 37.500 12.34 0.00 39.88 3.50
3503 3613 7.766278 TCTCTCCTTTGTCATCTTTGTATTAGC 59.234 37.037 0.00 0.00 0.00 3.09
3526 3636 3.763097 TGCAGCATTTCTTATCCAACG 57.237 42.857 0.00 0.00 0.00 4.10
3541 3654 7.834681 TCTTATCCAACGCTATCTATCACCTAT 59.165 37.037 0.00 0.00 0.00 2.57
3573 3686 6.481976 GTGGAATGATTACGTGGACAATGATA 59.518 38.462 0.00 0.00 0.00 2.15
3574 3687 6.481976 TGGAATGATTACGTGGACAATGATAC 59.518 38.462 0.00 0.00 0.00 2.24
3603 3716 2.791560 CAGCATGATACCGAAAGACTCG 59.208 50.000 0.00 0.00 43.41 4.18
3633 3746 8.537223 GTCAATTTGATATTTCACATGTCATGC 58.463 33.333 12.91 0.00 0.00 4.06
3641 3754 2.772287 TCACATGTCATGCCGTTACAA 58.228 42.857 12.91 0.00 0.00 2.41
3642 3755 2.482336 TCACATGTCATGCCGTTACAAC 59.518 45.455 12.91 0.00 0.00 3.32
3652 3765 4.955925 TGCCGTTACAACCATCATTAAG 57.044 40.909 0.00 0.00 0.00 1.85
3676 3789 2.559231 GGGTGAGATCGATTACTCCTCC 59.441 54.545 17.05 14.86 32.84 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.407437 GCCGTTGGATCATTCCTCAGT 60.407 52.381 0.00 0.00 43.07 3.41
1 2 1.303309 GCCGTTGGATCATTCCTCAG 58.697 55.000 0.00 0.00 43.07 3.35
2 3 0.617935 TGCCGTTGGATCATTCCTCA 59.382 50.000 0.00 0.00 43.07 3.86
3 4 1.972872 ATGCCGTTGGATCATTCCTC 58.027 50.000 0.00 0.00 43.07 3.71
4 5 2.705658 TCTATGCCGTTGGATCATTCCT 59.294 45.455 0.00 0.00 43.07 3.36
6 7 4.756642 TGAATCTATGCCGTTGGATCATTC 59.243 41.667 0.00 0.00 0.00 2.67
7 8 4.717877 TGAATCTATGCCGTTGGATCATT 58.282 39.130 0.00 0.00 0.00 2.57
8 9 4.356405 TGAATCTATGCCGTTGGATCAT 57.644 40.909 0.00 0.00 0.00 2.45
9 10 3.836365 TGAATCTATGCCGTTGGATCA 57.164 42.857 0.00 0.00 0.00 2.92
10 11 4.573900 AGATGAATCTATGCCGTTGGATC 58.426 43.478 0.00 0.00 34.85 3.36
11 12 4.564406 GGAGATGAATCTATGCCGTTGGAT 60.564 45.833 0.00 0.00 37.25 3.41
12 13 3.244215 GGAGATGAATCTATGCCGTTGGA 60.244 47.826 0.00 0.00 37.25 3.53
13 14 3.070018 GGAGATGAATCTATGCCGTTGG 58.930 50.000 0.00 0.00 37.25 3.77
14 15 3.070018 GGGAGATGAATCTATGCCGTTG 58.930 50.000 0.00 0.00 37.25 4.10
15 16 2.039084 GGGGAGATGAATCTATGCCGTT 59.961 50.000 0.00 0.00 37.25 4.44
16 17 1.625818 GGGGAGATGAATCTATGCCGT 59.374 52.381 0.00 0.00 37.25 5.68
17 18 1.625315 TGGGGAGATGAATCTATGCCG 59.375 52.381 0.00 0.00 37.25 5.69
18 19 2.641815 AGTGGGGAGATGAATCTATGCC 59.358 50.000 0.00 0.00 37.25 4.40
19 20 3.307339 GGAGTGGGGAGATGAATCTATGC 60.307 52.174 0.00 0.00 37.25 3.14
20 21 3.262915 GGGAGTGGGGAGATGAATCTATG 59.737 52.174 0.00 0.00 37.25 2.23
21 22 3.525862 GGGAGTGGGGAGATGAATCTAT 58.474 50.000 0.00 0.00 37.25 1.98
22 23 2.427889 GGGGAGTGGGGAGATGAATCTA 60.428 54.545 0.00 0.00 37.25 1.98
23 24 1.697291 GGGGAGTGGGGAGATGAATCT 60.697 57.143 0.00 0.00 40.50 2.40
24 25 0.767998 GGGGAGTGGGGAGATGAATC 59.232 60.000 0.00 0.00 0.00 2.52
25 26 0.046242 TGGGGAGTGGGGAGATGAAT 59.954 55.000 0.00 0.00 0.00 2.57
26 27 0.621571 CTGGGGAGTGGGGAGATGAA 60.622 60.000 0.00 0.00 0.00 2.57
27 28 1.003442 CTGGGGAGTGGGGAGATGA 59.997 63.158 0.00 0.00 0.00 2.92
28 29 1.307343 ACTGGGGAGTGGGGAGATG 60.307 63.158 0.00 0.00 0.00 2.90
29 30 1.003573 GACTGGGGAGTGGGGAGAT 59.996 63.158 0.00 0.00 0.00 2.75
30 31 2.450243 GACTGGGGAGTGGGGAGA 59.550 66.667 0.00 0.00 0.00 3.71
31 32 2.689034 GGACTGGGGAGTGGGGAG 60.689 72.222 0.00 0.00 0.00 4.30
32 33 3.208592 AGGACTGGGGAGTGGGGA 61.209 66.667 0.00 0.00 0.00 4.81
33 34 2.689034 GAGGACTGGGGAGTGGGG 60.689 72.222 0.00 0.00 0.00 4.96
34 35 2.689034 GGAGGACTGGGGAGTGGG 60.689 72.222 0.00 0.00 0.00 4.61
35 36 2.689034 GGGAGGACTGGGGAGTGG 60.689 72.222 0.00 0.00 0.00 4.00
36 37 1.687493 GAGGGAGGACTGGGGAGTG 60.687 68.421 0.00 0.00 0.00 3.51
37 38 2.781406 GAGGGAGGACTGGGGAGT 59.219 66.667 0.00 0.00 0.00 3.85
38 39 2.041405 GGAGGGAGGACTGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
39 40 2.540910 AGGAGGGAGGACTGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
40 41 2.041405 GAGGAGGGAGGACTGGGG 60.041 72.222 0.00 0.00 0.00 4.96
41 42 2.041405 GGAGGAGGGAGGACTGGG 60.041 72.222 0.00 0.00 0.00 4.45
42 43 1.075600 GAGGAGGAGGGAGGACTGG 60.076 68.421 0.00 0.00 0.00 4.00
43 44 0.106217 GAGAGGAGGAGGGAGGACTG 60.106 65.000 0.00 0.00 0.00 3.51
44 45 1.293683 GGAGAGGAGGAGGGAGGACT 61.294 65.000 0.00 0.00 0.00 3.85
45 46 1.231928 GGAGAGGAGGAGGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
46 47 1.230650 TGGAGAGGAGGAGGGAGGA 60.231 63.158 0.00 0.00 0.00 3.71
47 48 1.232792 CTGGAGAGGAGGAGGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
48 49 0.106217 GACTGGAGAGGAGGAGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
49 50 0.851332 TGACTGGAGAGGAGGAGGGA 60.851 60.000 0.00 0.00 0.00 4.20
50 51 0.396974 CTGACTGGAGAGGAGGAGGG 60.397 65.000 0.00 0.00 0.00 4.30
51 52 1.042559 GCTGACTGGAGAGGAGGAGG 61.043 65.000 0.00 0.00 0.00 4.30
52 53 1.042559 GGCTGACTGGAGAGGAGGAG 61.043 65.000 0.00 0.00 0.00 3.69
53 54 1.000993 GGCTGACTGGAGAGGAGGA 59.999 63.158 0.00 0.00 0.00 3.71
54 55 2.422231 CGGCTGACTGGAGAGGAGG 61.422 68.421 0.00 0.00 0.00 4.30
55 56 3.074999 GCGGCTGACTGGAGAGGAG 62.075 68.421 0.00 0.00 0.00 3.69
56 57 3.071206 GCGGCTGACTGGAGAGGA 61.071 66.667 0.00 0.00 0.00 3.71
57 58 3.073735 AGCGGCTGACTGGAGAGG 61.074 66.667 0.00 0.00 0.00 3.69
58 59 2.493973 GAGCGGCTGACTGGAGAG 59.506 66.667 7.50 0.00 0.00 3.20
59 60 3.443925 CGAGCGGCTGACTGGAGA 61.444 66.667 7.50 0.00 0.00 3.71
116 117 3.507009 CCCTCCGTCGACGAGGAC 61.507 72.222 36.48 8.48 43.02 3.85
135 136 2.954753 GAACAACGCACCTCCGCTG 61.955 63.158 0.00 0.00 0.00 5.18
136 137 2.665185 GAACAACGCACCTCCGCT 60.665 61.111 0.00 0.00 0.00 5.52
137 138 3.723348 GGAACAACGCACCTCCGC 61.723 66.667 0.00 0.00 0.00 5.54
148 149 0.882927 CGAAAGCACGGGAGGAACAA 60.883 55.000 0.00 0.00 0.00 2.83
411 466 2.841988 AGGAGGCGGAGATGGAGC 60.842 66.667 0.00 0.00 0.00 4.70
446 534 0.250338 ACAGGAGCTCGTGGTTTTCC 60.250 55.000 33.05 7.98 41.14 3.13
449 537 1.006102 CGACAGGAGCTCGTGGTTT 60.006 57.895 33.05 17.50 36.17 3.27
451 539 4.057428 GCGACAGGAGCTCGTGGT 62.057 66.667 33.05 21.47 36.17 4.16
508 596 1.590147 CGCGTCCTCCTGGTTTAGT 59.410 57.895 0.00 0.00 34.23 2.24
538 626 1.468520 GCTTGGCTTAGCAATTCGTCA 59.531 47.619 6.53 0.00 40.89 4.35
575 663 1.751437 AGAAAGTTATTCAGCCCGCC 58.249 50.000 0.00 0.00 0.00 6.13
586 674 1.871039 GCGAGTGTGGCAAGAAAGTTA 59.129 47.619 0.00 0.00 0.00 2.24
652 740 2.342279 CGGTTGAAGAGGGCGACA 59.658 61.111 0.00 0.00 0.00 4.35
770 858 2.694760 GGCGGCAGAAGAAGGCAAG 61.695 63.158 3.07 0.00 0.00 4.01
782 870 4.020617 CAACCTGAGGAGGCGGCA 62.021 66.667 13.08 0.00 44.33 5.69
806 894 2.373169 TGAAGGAGGTGACATTCAAGCT 59.627 45.455 0.00 0.00 29.99 3.74
819 907 4.319177 CTTGAGTAGGTTGTTGAAGGAGG 58.681 47.826 0.00 0.00 0.00 4.30
835 923 1.835927 GACTGCAGAGCCCCTTGAGT 61.836 60.000 23.35 0.00 0.00 3.41
852 940 2.484264 AGCCTCATTTGTACGCTTTGAC 59.516 45.455 0.00 0.00 0.00 3.18
853 941 2.778299 AGCCTCATTTGTACGCTTTGA 58.222 42.857 0.00 0.00 0.00 2.69
891 980 1.584742 GTCTAGTTCGGGCGTACGC 60.585 63.158 31.54 31.54 41.06 4.42
894 983 0.806868 CACAGTCTAGTTCGGGCGTA 59.193 55.000 0.00 0.00 0.00 4.42
925 1014 6.195983 CCGTTGATTACTATGTTGTACGAGAC 59.804 42.308 0.00 0.00 0.00 3.36
972 1061 1.731720 AGAGATTGCACGCTTTCTCC 58.268 50.000 14.26 2.73 36.16 3.71
975 1064 1.324736 CGGTAGAGATTGCACGCTTTC 59.675 52.381 0.00 0.00 0.00 2.62
992 1081 1.208052 CCAGGTTGATCATCTCACGGT 59.792 52.381 0.00 0.00 32.17 4.83
995 1084 2.503356 ACTCCCAGGTTGATCATCTCAC 59.497 50.000 0.00 0.00 32.17 3.51
1006 1095 1.518367 TCAGGTTGAACTCCCAGGTT 58.482 50.000 0.00 0.00 0.00 3.50
1008 1097 1.952367 GCATCAGGTTGAACTCCCAGG 60.952 57.143 0.00 0.00 0.00 4.45
1040 1129 4.201812 TGCTTAGTGCGTTGATAAATGAGC 60.202 41.667 0.00 0.00 46.63 4.26
1045 1134 4.153475 GGACTTGCTTAGTGCGTTGATAAA 59.847 41.667 0.00 0.00 46.63 1.40
1160 1249 3.873910 CACTGACCCGAAGTGGAATATT 58.126 45.455 0.00 0.00 41.13 1.28
1185 1274 5.994250 TCTTTGAATATCCTAACTGCTGCT 58.006 37.500 0.00 0.00 0.00 4.24
1198 1287 7.610305 ACCGGTACTTGTCATTTCTTTGAATAT 59.390 33.333 4.49 0.00 0.00 1.28
1237 1326 6.704050 TCAATAAATGAGTTCAACGTGACAGA 59.296 34.615 0.00 0.00 33.04 3.41
1260 1349 3.966979 TCTATGCTTGCAAAGGGAATCA 58.033 40.909 0.00 0.00 46.35 2.57
1283 1372 9.171877 CAAAAATATCTCTAGCTTCCTTTGTCT 57.828 33.333 0.00 0.00 0.00 3.41
1320 1409 2.656973 GGTTTGTGGCCGTTTGCG 60.657 61.111 0.00 0.00 42.61 4.85
1326 1415 3.443681 AGAAAATATCAGGTTTGTGGCCG 59.556 43.478 0.00 0.00 0.00 6.13
1360 1449 4.643463 TCTTTCACATACCCGTTAAGCAA 58.357 39.130 0.00 0.00 0.00 3.91
1501 1590 2.401583 TCGAACATGTGCATAGCCTT 57.598 45.000 4.29 0.00 0.00 4.35
1596 1685 1.597302 CAGAGCGGCATCCATCCTG 60.597 63.158 1.45 0.00 0.00 3.86
1608 1697 5.801350 TCTGATTAAATTTGTCCAGAGCG 57.199 39.130 0.00 0.00 0.00 5.03
1754 1843 7.542477 CACGATAGAAGAACACACTGTTAGAAT 59.458 37.037 0.00 0.00 39.55 2.40
1778 1867 6.432107 TCTTTGCAAAGGTCGTTTATTACAC 58.568 36.000 33.01 0.00 36.67 2.90
1815 1916 2.609459 GTCAAACATATCCTGTGCCTCG 59.391 50.000 0.00 0.00 38.39 4.63
1860 1961 6.818644 GTGAAGTGTACATAATCACATCAGGT 59.181 38.462 22.97 0.00 40.92 4.00
1912 2014 1.346068 ACTCAGTGCTTTCTCCACCTC 59.654 52.381 0.00 0.00 33.75 3.85
2063 2165 6.675413 ATATAATAGTCGTGGGCTTAACCA 57.325 37.500 0.00 0.00 42.05 3.67
2132 2234 9.153721 TCATCATATCAAAATTTTCCTTTGCAC 57.846 29.630 0.00 0.00 34.43 4.57
2145 2247 7.838884 TGCCACTTTCAATCATCATATCAAAA 58.161 30.769 0.00 0.00 0.00 2.44
2148 2250 7.175467 GGTATGCCACTTTCAATCATCATATCA 59.825 37.037 0.00 0.00 34.09 2.15
2149 2251 7.175467 TGGTATGCCACTTTCAATCATCATATC 59.825 37.037 0.00 0.00 40.46 1.63
2153 2255 4.598022 TGGTATGCCACTTTCAATCATCA 58.402 39.130 0.00 0.00 40.46 3.07
2568 2670 4.050553 GCTGTTTTGCATCAAGTTTAGCA 58.949 39.130 0.00 0.00 34.79 3.49
2782 2885 3.117131 AGAACTGGGGAATTCACCTTGTT 60.117 43.478 27.01 27.01 41.04 2.83
2783 2886 2.447047 AGAACTGGGGAATTCACCTTGT 59.553 45.455 26.87 21.15 41.04 3.16
2784 2887 3.084786 GAGAACTGGGGAATTCACCTTG 58.915 50.000 26.87 20.54 41.04 3.61
2785 2888 2.989571 AGAGAACTGGGGAATTCACCTT 59.010 45.455 26.87 14.34 41.04 3.50
2786 2889 2.307098 CAGAGAACTGGGGAATTCACCT 59.693 50.000 26.87 7.54 41.04 4.00
2787 2890 2.716217 CAGAGAACTGGGGAATTCACC 58.284 52.381 20.58 20.58 40.14 4.02
2833 2936 4.274214 TCAAATCTGCACTGTGTTCAGAAG 59.726 41.667 17.89 12.55 39.00 2.85
2845 2948 7.420800 TCTTCTCTTCTTTTTCAAATCTGCAC 58.579 34.615 0.00 0.00 0.00 4.57
2853 2956 8.986929 ATTCTTCCTCTTCTCTTCTTTTTCAA 57.013 30.769 0.00 0.00 0.00 2.69
2889 2992 7.926018 AGAATTCACCTTGTTATTCACCAAAAC 59.074 33.333 8.44 0.00 31.12 2.43
2937 3040 4.282195 ACAATAACATCAAAAGGCGGGAAA 59.718 37.500 0.00 0.00 0.00 3.13
2984 3087 7.287696 TGGATTCAGTATAGAACATAGCTCACA 59.712 37.037 0.00 0.00 0.00 3.58
2989 3092 9.717942 AAAGATGGATTCAGTATAGAACATAGC 57.282 33.333 0.00 0.00 0.00 2.97
3026 3129 3.953542 ACTTCCTACCCCCAATTCATC 57.046 47.619 0.00 0.00 0.00 2.92
3028 3131 4.791334 TGAATACTTCCTACCCCCAATTCA 59.209 41.667 0.00 0.00 31.59 2.57
3039 3142 6.816640 CCGAACATTCAACTGAATACTTCCTA 59.183 38.462 4.66 0.00 42.41 2.94
3040 3143 5.643777 CCGAACATTCAACTGAATACTTCCT 59.356 40.000 4.66 0.00 42.41 3.36
3041 3144 5.673818 GCCGAACATTCAACTGAATACTTCC 60.674 44.000 4.66 0.00 42.41 3.46
3043 3146 4.156008 GGCCGAACATTCAACTGAATACTT 59.844 41.667 4.66 0.50 42.41 2.24
3045 3148 3.689649 AGGCCGAACATTCAACTGAATAC 59.310 43.478 4.66 0.54 42.41 1.89
3082 3189 7.017645 CGGTTTCAGTCTTCAAATAGTGAATG 58.982 38.462 0.00 0.00 45.27 2.67
3089 3197 7.662258 TGTAATTCCGGTTTCAGTCTTCAAATA 59.338 33.333 0.00 0.00 0.00 1.40
3090 3198 6.488683 TGTAATTCCGGTTTCAGTCTTCAAAT 59.511 34.615 0.00 0.00 0.00 2.32
3158 3266 1.001181 ACCGCCGCTCAGTTTTTACTA 59.999 47.619 0.00 0.00 0.00 1.82
3159 3267 0.250166 ACCGCCGCTCAGTTTTTACT 60.250 50.000 0.00 0.00 0.00 2.24
3160 3268 0.589708 AACCGCCGCTCAGTTTTTAC 59.410 50.000 0.00 0.00 0.00 2.01
3161 3269 1.310904 AAACCGCCGCTCAGTTTTTA 58.689 45.000 0.00 0.00 29.64 1.52
3190 3298 1.813513 GATGCAACCACTACTGCTGT 58.186 50.000 0.66 0.66 39.38 4.40
3203 3311 3.930336 ACAGATCTCTTGTTCGATGCAA 58.070 40.909 0.00 0.00 0.00 4.08
3209 3317 7.017645 CCATGTAAAAACAGATCTCTTGTTCG 58.982 38.462 0.00 0.00 0.00 3.95
3244 3352 5.421212 TTTTGCATTCTTTGGCATTTGAC 57.579 34.783 0.00 0.00 40.17 3.18
3271 3379 1.197949 GGAGCGAGCCTTTTTGTCTTC 59.802 52.381 0.00 0.00 0.00 2.87
3276 3384 0.954452 AAGTGGAGCGAGCCTTTTTG 59.046 50.000 0.00 0.00 0.00 2.44
3408 3518 8.792633 CCTTGGTTTCAACTTTCAAGTCATATA 58.207 33.333 0.00 0.00 38.57 0.86
3416 3526 5.474825 GTTGACCTTGGTTTCAACTTTCAA 58.525 37.500 13.69 0.72 45.45 2.69
3417 3527 5.066968 GTTGACCTTGGTTTCAACTTTCA 57.933 39.130 13.69 0.00 45.45 2.69
3435 3545 7.042725 CGTTTTCTTGAGTGAGAATGTAGTTGA 60.043 37.037 0.00 0.00 35.70 3.18
3503 3613 5.446709 CGTTGGATAAGAAATGCTGCATAG 58.553 41.667 16.58 0.00 0.00 2.23
3526 3636 7.507277 TCCACATATCCATAGGTGATAGATAGC 59.493 40.741 11.97 0.00 45.08 2.97
3541 3654 5.071115 TCCACGTAATCATTCCACATATCCA 59.929 40.000 0.00 0.00 0.00 3.41
3573 3686 4.188462 TCGGTATCATGCTGAATTTTCGT 58.812 39.130 0.00 0.00 0.00 3.85
3574 3687 4.794248 TCGGTATCATGCTGAATTTTCG 57.206 40.909 0.00 0.00 0.00 3.46
3595 3708 3.476552 TCAAATTGACAGCCGAGTCTTT 58.523 40.909 0.00 0.00 39.27 2.52
3603 3716 7.037438 ACATGTGAAATATCAAATTGACAGCC 58.963 34.615 0.00 0.00 37.30 4.85
3608 3721 7.707464 GGCATGACATGTGAAATATCAAATTGA 59.293 33.333 16.62 0.00 37.30 2.57
3609 3722 7.306341 CGGCATGACATGTGAAATATCAAATTG 60.306 37.037 16.62 0.00 37.30 2.32
3633 3746 4.201910 CCAGCTTAATGATGGTTGTAACGG 60.202 45.833 0.00 0.00 46.49 4.44
3652 3765 2.288518 GGAGTAATCGATCTCACCCAGC 60.289 54.545 14.16 0.00 32.93 4.85
3676 3789 8.988064 ACTACAACAACATATCTTCTGTACAG 57.012 34.615 17.17 17.17 0.00 2.74


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

AutoCloner maintained by Alex Coulton.