Multiple sequence alignment - TraesCS2B01G494000

Loading Multiple Alignment...

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 TraesCS2B01G494000 chr2B 100.000 3474 0 0 1 3474 691401045 691404518 0.000000e+00 6416.0
1 TraesCS2B01G494000 chr2B 90.843 1660 122 16 904 2553 691186837 691188476 0.000000e+00 2196.0
2 TraesCS2B01G494000 chr2B 84.918 1220 165 8 979 2187 691189286 691190497 0.000000e+00 1216.0
3 TraesCS2B01G494000 chr2B 83.786 1141 170 12 1060 2187 691413321 691414459 0.000000e+00 1068.0
4 TraesCS2B01G494000 chr2B 91.453 117 10 0 3138 3254 708353393 708353509 9.980000e-36 161.0
5 TraesCS2B01G494000 chr1B 95.662 876 34 3 1 875 142265133 142264261 0.000000e+00 1404.0
6 TraesCS2B01G494000 chr1B 83.846 130 18 3 34 161 100627097 100626969 1.690000e-23 121.0
7 TraesCS2B01G494000 chr1B 97.436 39 1 0 837 875 325985798 325985760 2.240000e-07 67.6
8 TraesCS2B01G494000 chr7B 93.002 886 41 9 1 875 426079830 426078955 0.000000e+00 1273.0
9 TraesCS2B01G494000 chr7B 88.064 377 30 8 255 623 410669363 410669732 1.920000e-117 433.0
10 TraesCS2B01G494000 chr7B 85.981 214 28 2 664 875 12235737 12235950 9.700000e-56 228.0
11 TraesCS2B01G494000 chr7B 87.895 190 19 3 1 188 410669073 410669260 1.620000e-53 220.0
12 TraesCS2B01G494000 chr1D 92.282 894 44 9 1 876 136524002 136523116 0.000000e+00 1245.0
13 TraesCS2B01G494000 chr1D 79.085 153 16 6 48 188 362330577 362330429 1.330000e-14 91.6
14 TraesCS2B01G494000 chr2D 85.438 1085 151 5 1024 2103 575216352 575217434 0.000000e+00 1122.0
15 TraesCS2B01G494000 chr2A 87.750 800 68 9 1751 2545 713453496 713454270 0.000000e+00 907.0
16 TraesCS2B01G494000 chr2A 85.990 778 104 3 1326 2099 713461404 713462180 0.000000e+00 828.0
17 TraesCS2B01G494000 chr2A 84.691 307 47 0 1024 1330 713455945 713456251 1.210000e-79 307.0
18 TraesCS2B01G494000 chr2A 85.778 225 20 2 3262 3474 713455225 713455449 9.700000e-56 228.0
19 TraesCS2B01G494000 chr2A 87.500 160 12 4 2937 3093 116167950 116167796 9.910000e-41 178.0
20 TraesCS2B01G494000 chr1A 92.496 613 30 6 160 764 20053957 20053353 0.000000e+00 863.0
21 TraesCS2B01G494000 chr5B 87.729 546 37 18 2559 3084 684091214 684091749 8.240000e-171 610.0
22 TraesCS2B01G494000 chr5B 88.781 517 29 11 2554 3059 118524001 118523503 1.070000e-169 606.0
23 TraesCS2B01G494000 chr5B 93.427 213 14 0 3042 3254 118523480 118523268 2.010000e-82 316.0
24 TraesCS2B01G494000 chr5B 89.671 213 21 1 3042 3254 684091741 684091952 1.590000e-68 270.0
25 TraesCS2B01G494000 chr5B 89.744 156 15 1 2557 2712 701523249 701523403 7.610000e-47 198.0
26 TraesCS2B01G494000 chr5B 87.500 56 6 1 820 875 68420857 68420911 2.890000e-06 63.9
27 TraesCS2B01G494000 chr6A 93.484 399 19 2 253 644 577734380 577733982 1.390000e-163 586.0
28 TraesCS2B01G494000 chr6A 85.823 395 49 5 255 642 166452470 166452076 2.500000e-111 412.0
29 TraesCS2B01G494000 chr6A 95.135 185 9 0 3 187 577734681 577734497 3.390000e-75 292.0
30 TraesCS2B01G494000 chr6A 86.441 59 7 1 822 880 206289548 206289605 2.890000e-06 63.9
31 TraesCS2B01G494000 chr3A 92.732 399 22 2 253 644 713636503 713636105 1.400000e-158 569.0
32 TraesCS2B01G494000 chr3A 95.135 185 9 0 3 187 713636804 713636620 3.390000e-75 292.0
33 TraesCS2B01G494000 chr3A 89.375 160 16 1 3098 3257 688491149 688490991 2.110000e-47 200.0
34 TraesCS2B01G494000 chr3A 84.746 59 9 0 820 878 24539345 24539287 3.740000e-05 60.2
35 TraesCS2B01G494000 chr4A 82.696 549 49 20 2555 3093 213023989 213024501 2.460000e-121 446.0
36 TraesCS2B01G494000 chr4A 89.151 212 23 0 3043 3254 213024517 213024728 7.390000e-67 265.0
37 TraesCS2B01G494000 chr5A 83.507 479 48 15 191 642 608429807 608430281 5.360000e-113 418.0
38 TraesCS2B01G494000 chr5A 85.561 187 21 4 2722 2906 3971386 3971568 1.270000e-44 191.0
39 TraesCS2B01G494000 chr5A 87.179 156 12 4 2937 3089 3971556 3971706 1.660000e-38 171.0
40 TraesCS2B01G494000 chr3B 86.111 396 46 7 255 642 809187337 809187731 5.360000e-113 418.0
41 TraesCS2B01G494000 chr3B 84.865 185 19 6 2722 2904 17906468 17906645 9.910000e-41 178.0
42 TraesCS2B01G494000 chr3B 84.324 185 20 6 2722 2904 17929703 17929880 4.610000e-39 172.0
43 TraesCS2B01G494000 chr3B 86.250 160 14 4 2937 3093 17906635 17906789 2.140000e-37 167.0
44 TraesCS2B01G494000 chr3B 91.129 124 7 4 2937 3059 806754272 806754392 7.710000e-37 165.0
45 TraesCS2B01G494000 chr3B 84.375 160 13 5 2937 3093 17929870 17930020 2.790000e-31 147.0
46 TraesCS2B01G494000 chr3D 84.459 444 46 16 2557 2998 582737005 582736583 1.930000e-112 416.0
47 TraesCS2B01G494000 chr7A 83.541 401 36 15 255 644 53284112 53284493 7.140000e-92 348.0
48 TraesCS2B01G494000 chr7A 89.062 256 23 2 2556 2811 111256140 111256390 2.600000e-81 313.0
49 TraesCS2B01G494000 chr7A 89.720 214 22 0 3042 3255 111289273 111289486 1.230000e-69 274.0
50 TraesCS2B01G494000 chr7A 85.915 213 24 6 2848 3059 111289043 111289250 4.510000e-54 222.0
51 TraesCS2B01G494000 chr7A 90.968 155 13 1 2558 2712 8650737 8650584 1.260000e-49 207.0
52 TraesCS2B01G494000 chr7A 86.559 186 19 4 2722 2906 695832901 695833081 2.110000e-47 200.0
53 TraesCS2B01G494000 chr7A 86.250 160 14 4 2937 3093 695833069 695833223 2.140000e-37 167.0
54 TraesCS2B01G494000 chr7A 95.122 41 2 0 837 877 69748217 69748177 8.050000e-07 65.8
55 TraesCS2B01G494000 chr7D 84.000 300 18 4 2556 2827 6495171 6494874 9.560000e-66 261.0
56 TraesCS2B01G494000 chr5D 91.875 160 13 0 3095 3254 339710561 339710402 1.250000e-54 224.0
57 TraesCS2B01G494000 chr5D 88.333 120 13 1 34 152 521249905 521250024 3.610000e-30 143.0
58 TraesCS2B01G494000 chr5D 80.519 154 13 5 48 188 487178732 487178881 6.130000e-18 102.0
59 TraesCS2B01G494000 chr6B 77.889 398 48 22 42 407 134815828 134815439 9.770000e-51 211.0
60 TraesCS2B01G494000 chr6B 88.462 156 16 2 2557 2712 620871506 620871659 1.650000e-43 187.0
61 TraesCS2B01G494000 chr6B 85.443 158 21 2 3101 3257 26075017 26074861 2.770000e-36 163.0
62 TraesCS2B01G494000 chrUn 87.568 185 15 6 2725 2906 30966363 30966184 1.260000e-49 207.0
63 TraesCS2B01G494000 chr6D 89.172 157 16 1 3099 3255 17275304 17275459 9.840000e-46 195.0
64 TraesCS2B01G494000 chr6D 82.192 219 24 8 661 875 347169777 347169984 1.280000e-39 174.0


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 TraesCS2B01G494000 chr2B 691401045 691404518 3473 False 6416.000000 6416 100.0000 1 3474 1 chr2B.!!$F1 3473
1 TraesCS2B01G494000 chr2B 691186837 691190497 3660 False 1706.000000 2196 87.8805 904 2553 2 chr2B.!!$F4 1649
2 TraesCS2B01G494000 chr2B 691413321 691414459 1138 False 1068.000000 1068 83.7860 1060 2187 1 chr2B.!!$F2 1127
3 TraesCS2B01G494000 chr1B 142264261 142265133 872 True 1404.000000 1404 95.6620 1 875 1 chr1B.!!$R2 874
4 TraesCS2B01G494000 chr7B 426078955 426079830 875 True 1273.000000 1273 93.0020 1 875 1 chr7B.!!$R1 874
5 TraesCS2B01G494000 chr7B 410669073 410669732 659 False 326.500000 433 87.9795 1 623 2 chr7B.!!$F2 622
6 TraesCS2B01G494000 chr1D 136523116 136524002 886 True 1245.000000 1245 92.2820 1 876 1 chr1D.!!$R1 875
7 TraesCS2B01G494000 chr2D 575216352 575217434 1082 False 1122.000000 1122 85.4380 1024 2103 1 chr2D.!!$F1 1079
8 TraesCS2B01G494000 chr2A 713461404 713462180 776 False 828.000000 828 85.9900 1326 2099 1 chr2A.!!$F1 773
9 TraesCS2B01G494000 chr2A 713453496 713456251 2755 False 480.666667 907 86.0730 1024 3474 3 chr2A.!!$F2 2450
10 TraesCS2B01G494000 chr1A 20053353 20053957 604 True 863.000000 863 92.4960 160 764 1 chr1A.!!$R1 604
11 TraesCS2B01G494000 chr5B 118523268 118524001 733 True 461.000000 606 91.1040 2554 3254 2 chr5B.!!$R1 700
12 TraesCS2B01G494000 chr5B 684091214 684091952 738 False 440.000000 610 88.7000 2559 3254 2 chr5B.!!$F3 695
13 TraesCS2B01G494000 chr6A 577733982 577734681 699 True 439.000000 586 94.3095 3 644 2 chr6A.!!$R2 641
14 TraesCS2B01G494000 chr3A 713636105 713636804 699 True 430.500000 569 93.9335 3 644 2 chr3A.!!$R3 641
15 TraesCS2B01G494000 chr4A 213023989 213024728 739 False 355.500000 446 85.9235 2555 3254 2 chr4A.!!$F1 699

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
889 982 1.028905 CCCTGTCTCAGAGTCGGATC 58.971 60.0 5.15 0.0 32.44 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 2613 1.094785 CCACATTTAACTGGAGCCGG 58.905 55.0 0.0 0.0 0.0 6.13 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
227 266 2.503356 GAGGAGGCAGATGAGGAGAAAA 59.497 50.000 0.00 0.00 0.00 2.29
304 381 1.927895 AGTTCTCGCGGATGATCAAC 58.072 50.000 6.13 0.00 0.00 3.18
411 488 7.707624 TCATGAGCCCATATTTAATTCATCC 57.292 36.000 0.00 0.00 0.00 3.51
442 519 5.627182 ATCTGCTAGTGTTGATGAGGAAT 57.373 39.130 0.00 0.00 0.00 3.01
484 562 2.826674 TGATCCAAGGAATTGGGGTC 57.173 50.000 7.15 6.74 42.32 4.46
485 563 2.287584 TGATCCAAGGAATTGGGGTCT 58.712 47.619 7.15 0.00 42.32 3.85
611 702 5.143376 ACTCAAGAAAAATGAGCAATGGG 57.857 39.130 3.57 0.00 46.56 4.00
878 971 3.775654 CAGGACCGGCCCTGTCTC 61.776 72.222 27.51 2.76 46.62 3.36
879 972 4.316823 AGGACCGGCCCTGTCTCA 62.317 66.667 9.27 0.00 37.37 3.27
880 973 3.775654 GGACCGGCCCTGTCTCAG 61.776 72.222 17.10 0.00 33.22 3.35
881 974 2.680352 GACCGGCCCTGTCTCAGA 60.680 66.667 0.00 0.00 32.44 3.27
882 975 2.681778 ACCGGCCCTGTCTCAGAG 60.682 66.667 0.00 0.00 32.44 3.35
883 976 2.681778 CCGGCCCTGTCTCAGAGT 60.682 66.667 0.00 0.00 32.44 3.24
884 977 2.716017 CCGGCCCTGTCTCAGAGTC 61.716 68.421 0.00 0.00 32.44 3.36
885 978 2.888863 GGCCCTGTCTCAGAGTCG 59.111 66.667 0.00 0.00 32.44 4.18
886 979 2.716017 GGCCCTGTCTCAGAGTCGG 61.716 68.421 0.00 0.00 32.44 4.79
887 980 1.679305 GCCCTGTCTCAGAGTCGGA 60.679 63.158 5.15 0.00 32.44 4.55
888 981 1.040339 GCCCTGTCTCAGAGTCGGAT 61.040 60.000 5.15 0.00 32.44 4.18
889 982 1.028905 CCCTGTCTCAGAGTCGGATC 58.971 60.000 5.15 0.00 32.44 3.36
890 983 1.028905 CCTGTCTCAGAGTCGGATCC 58.971 60.000 0.00 0.00 32.44 3.36
891 984 1.409521 CCTGTCTCAGAGTCGGATCCT 60.410 57.143 10.75 0.00 32.44 3.24
892 985 1.675483 CTGTCTCAGAGTCGGATCCTG 59.325 57.143 10.75 3.62 32.44 3.86
893 986 1.282157 TGTCTCAGAGTCGGATCCTGA 59.718 52.381 10.75 5.31 35.81 3.86
895 988 2.051334 CTCAGAGTCGGATCCTGAGT 57.949 55.000 21.45 14.22 45.26 3.41
896 989 2.374184 CTCAGAGTCGGATCCTGAGTT 58.626 52.381 21.45 5.42 45.26 3.01
897 990 2.757868 CTCAGAGTCGGATCCTGAGTTT 59.242 50.000 21.45 8.55 45.26 2.66
898 991 2.755655 TCAGAGTCGGATCCTGAGTTTC 59.244 50.000 10.75 7.22 33.50 2.78
899 992 2.757868 CAGAGTCGGATCCTGAGTTTCT 59.242 50.000 10.75 9.08 0.00 2.52
900 993 3.194542 CAGAGTCGGATCCTGAGTTTCTT 59.805 47.826 10.75 0.00 0.00 2.52
901 994 3.445805 AGAGTCGGATCCTGAGTTTCTTC 59.554 47.826 10.75 0.55 0.00 2.87
902 995 3.436243 AGTCGGATCCTGAGTTTCTTCT 58.564 45.455 10.75 0.00 0.00 2.85
907 1000 7.507616 AGTCGGATCCTGAGTTTCTTCTTATAT 59.492 37.037 10.75 0.00 0.00 0.86
935 1030 4.614555 TCGTATGCAGCAATTACCAAAG 57.385 40.909 0.00 0.00 0.00 2.77
954 1049 2.294074 AGATCGAGTTCTCCTTCTCCG 58.706 52.381 0.00 0.00 0.00 4.63
958 1053 3.415212 TCGAGTTCTCCTTCTCCGTAAA 58.585 45.455 0.00 0.00 0.00 2.01
959 1054 3.190118 TCGAGTTCTCCTTCTCCGTAAAC 59.810 47.826 0.00 0.00 0.00 2.01
961 1056 4.236147 GAGTTCTCCTTCTCCGTAAACAC 58.764 47.826 0.00 0.00 0.00 3.32
962 1057 3.640029 AGTTCTCCTTCTCCGTAAACACA 59.360 43.478 0.00 0.00 0.00 3.72
977 1076 1.459450 ACACAACAAGACCAACGCTT 58.541 45.000 0.00 0.00 0.00 4.68
978 1077 1.132262 ACACAACAAGACCAACGCTTG 59.868 47.619 0.00 0.00 46.20 4.01
988 1087 1.271001 ACCAACGCTTGTAACCTACCC 60.271 52.381 0.00 0.00 0.00 3.69
1001 1100 1.144057 CTACCCATCGTCCTGCACC 59.856 63.158 0.00 0.00 0.00 5.01
1002 1101 2.311688 CTACCCATCGTCCTGCACCC 62.312 65.000 0.00 0.00 0.00 4.61
1035 1134 3.286751 TGGGCAACAGCGCACTTC 61.287 61.111 11.47 0.00 44.87 3.01
1082 1181 4.034258 TCGTCGACGTGCTCCACC 62.034 66.667 34.40 0.00 40.80 4.61
1109 1208 0.607620 CCATGTCGGCCCACAATTTT 59.392 50.000 7.45 0.00 0.00 1.82
1143 1242 4.519437 CGCTGCTCGAGGGCATCA 62.519 66.667 15.58 1.81 41.63 3.07
1163 1262 2.644992 GCCGGCAAGTTTGTCAGG 59.355 61.111 24.80 1.00 31.86 3.86
1180 1279 1.132640 GGTCGAGCACATTCAACGC 59.867 57.895 10.30 0.00 0.00 4.84
1181 1280 1.291877 GGTCGAGCACATTCAACGCT 61.292 55.000 10.30 0.00 39.12 5.07
1192 1291 2.796483 TTCAACGCTGGCGGCTACAT 62.796 55.000 17.54 0.00 44.69 2.29
1253 1353 1.725557 GATCTAGTGACGCGGCCTCA 61.726 60.000 10.82 0.30 0.00 3.86
1258 1358 2.031919 TGACGCGGCCTCATGTTT 59.968 55.556 10.82 0.00 0.00 2.83
1268 1368 4.618227 GCGGCCTCATGTTTTCTTTATTGT 60.618 41.667 0.00 0.00 0.00 2.71
1273 1373 6.222389 CCTCATGTTTTCTTTATTGTGCCAA 58.778 36.000 0.00 0.00 0.00 4.52
1403 1503 0.828677 ACTACAGTTGGGGGTATCGC 59.171 55.000 0.00 0.00 0.00 4.58
1522 1626 0.456221 CGCAACAGGAGACCTATCGT 59.544 55.000 0.00 0.00 29.64 3.73
1530 1634 1.609555 GGAGACCTATCGTAGTGCCAG 59.390 57.143 0.00 0.00 0.00 4.85
1835 1944 1.174712 ACTTGCTTGTTGCTGCGGAT 61.175 50.000 0.00 0.00 43.37 4.18
1987 2096 7.761409 TGCATTCAGTTTATAAGTTCACCATC 58.239 34.615 0.00 0.00 0.00 3.51
2069 2178 6.211584 GTCCTTTGCTCATGGAGGATATACTA 59.788 42.308 0.00 0.00 40.21 1.82
2073 2182 7.855784 TTGCTCATGGAGGATATACTAAAGA 57.144 36.000 0.00 0.00 28.56 2.52
2086 2195 8.910944 GGATATACTAAAGAGTGTGTCCTACAA 58.089 37.037 9.42 0.00 45.77 2.41
2143 2253 7.651808 AGCAAAATATTATGCAGTCATGTACC 58.348 34.615 0.00 0.00 44.95 3.34
2169 2279 8.883731 CGACCATGTTAGATTTTAGTCATCTTT 58.116 33.333 0.00 0.00 32.94 2.52
2206 2321 3.998099 TTTTGCGATGATGTTTGACCA 57.002 38.095 0.00 0.00 0.00 4.02
2207 2322 4.517952 TTTTGCGATGATGTTTGACCAT 57.482 36.364 0.00 0.00 0.00 3.55
2208 2323 3.763097 TTGCGATGATGTTTGACCATC 57.237 42.857 0.00 0.00 41.32 3.51
2209 2324 2.989909 TGCGATGATGTTTGACCATCT 58.010 42.857 0.00 0.00 41.47 2.90
2210 2325 3.346315 TGCGATGATGTTTGACCATCTT 58.654 40.909 0.00 0.00 41.47 2.40
2211 2326 3.374988 TGCGATGATGTTTGACCATCTTC 59.625 43.478 0.00 0.00 41.47 2.87
2212 2327 3.624861 GCGATGATGTTTGACCATCTTCT 59.375 43.478 12.37 0.00 40.87 2.85
2213 2328 4.811024 GCGATGATGTTTGACCATCTTCTA 59.189 41.667 12.37 0.00 40.87 2.10
2214 2329 5.277058 GCGATGATGTTTGACCATCTTCTAC 60.277 44.000 12.37 4.50 40.87 2.59
2215 2330 5.235186 CGATGATGTTTGACCATCTTCTACC 59.765 44.000 12.37 0.00 40.87 3.18
2226 2341 6.432162 TGACCATCTTCTACCGTATATGGTAC 59.568 42.308 18.28 7.49 45.34 3.34
2230 2345 6.829229 TCTTCTACCGTATATGGTACCATG 57.171 41.667 33.41 20.21 43.56 3.66
2235 2350 9.483489 TTCTACCGTATATGGTACCATGATAAT 57.517 33.333 33.41 21.99 43.56 1.28
2237 2352 9.745880 CTACCGTATATGGTACCATGATAATTC 57.254 37.037 33.41 17.07 43.56 2.17
2279 2394 8.606602 GTTGCCATGATAATTCTTGGATTTTTC 58.393 33.333 10.99 0.00 45.66 2.29
2280 2395 7.849160 TGCCATGATAATTCTTGGATTTTTCA 58.151 30.769 10.99 0.00 45.66 2.69
2303 2418 8.865590 TCACTTAAAAACTACTCAATTTTGCC 57.134 30.769 0.00 0.00 0.00 4.52
2338 2453 7.270757 TGCATATACGATGGCTTACAAAAAT 57.729 32.000 0.00 0.00 0.00 1.82
2339 2454 7.359595 TGCATATACGATGGCTTACAAAAATC 58.640 34.615 0.00 0.00 0.00 2.17
2356 2475 7.910304 ACAAAAATCGAGAAAAGATAGGATCG 58.090 34.615 0.00 0.00 0.00 3.69
2380 2499 3.118884 AGTCCTGAATGATTTGCATTGCC 60.119 43.478 6.12 0.00 46.90 4.52
2396 2515 1.666872 GCCCGTCCGTGCCATATAC 60.667 63.158 0.00 0.00 0.00 1.47
2461 2580 6.667414 ACCATGGTGGCATCTAGAAATTAAAA 59.333 34.615 18.99 0.00 42.67 1.52
2494 2613 6.798482 TCATTGTTCCATTGATGAACTATGC 58.202 36.000 17.00 0.00 39.78 3.14
2501 2620 0.106708 TGATGAACTATGCCGGCTCC 59.893 55.000 29.70 10.38 0.00 4.70
2521 2640 3.099141 CCAGTTAAATGTGGGCCTTGAT 58.901 45.455 4.53 0.00 0.00 2.57
2523 2642 4.709397 CCAGTTAAATGTGGGCCTTGATTA 59.291 41.667 4.53 0.00 0.00 1.75
2535 2654 4.507335 GGGCCTTGATTATGCTTCCTATCA 60.507 45.833 0.84 0.00 0.00 2.15
2567 2686 7.939784 AAAGAGTTGGATGGAGTATTTAACC 57.060 36.000 0.00 0.00 0.00 2.85
2638 2855 7.279750 ACAAATTTGTACCGAAAACTACCAT 57.720 32.000 22.10 0.00 40.16 3.55
2750 3080 5.575157 TGCAATCAGGTCCCTACAATTTTA 58.425 37.500 0.00 0.00 0.00 1.52
2946 3417 0.249868 ACGACAAGTAGCAGCAGCAA 60.250 50.000 3.17 0.00 45.49 3.91
3037 3534 1.907222 CTCTGGCTGCATCCCTGTCA 61.907 60.000 3.68 0.00 0.00 3.58
3048 3675 3.369261 GCATCCCTGTCATGATAGCTAGG 60.369 52.174 13.67 9.89 0.00 3.02
3049 3676 2.894731 TCCCTGTCATGATAGCTAGGG 58.105 52.381 13.67 16.55 44.96 3.53
3117 3744 6.451393 TGCGCTAATCAGGTTTAATTTTTGT 58.549 32.000 9.73 0.00 0.00 2.83
3140 3767 9.587772 TTGTCTAATCAGTCTTTAAGTAGATGC 57.412 33.333 0.00 0.00 0.00 3.91
3178 3805 9.089601 GTTAAAGATTAGAGAAGAAGTGGTAGC 57.910 37.037 0.00 0.00 0.00 3.58
3264 3891 3.435327 TGTTAAATACTCAGTTGGCTGCG 59.565 43.478 0.00 0.00 42.29 5.18
3266 3893 2.185004 AATACTCAGTTGGCTGCGTT 57.815 45.000 0.00 0.00 40.65 4.84
3270 3897 0.320771 CTCAGTTGGCTGCGTTAGGT 60.321 55.000 0.00 0.00 42.29 3.08
3280 3907 0.968901 TGCGTTAGGTGGGATCGAGT 60.969 55.000 0.00 0.00 0.00 4.18
3286 3913 1.153628 GGTGGGATCGAGTTCACGG 60.154 63.158 0.00 0.00 0.00 4.94
3289 3916 1.810030 GGGATCGAGTTCACGGCAC 60.810 63.158 0.00 0.00 0.00 5.01
3314 3946 1.819632 CGGACCTTATGGCAGCCAC 60.820 63.158 19.10 1.92 35.80 5.01
3320 3952 1.064758 CCTTATGGCAGCCACCAACTA 60.065 52.381 19.10 1.05 44.65 2.24
3368 4008 7.284034 AGGTCCGATTTCTAACGAATAGTTCTA 59.716 37.037 0.00 0.00 43.06 2.10
3400 4040 8.809159 TTATTTTTGCAACGAATCAGATCAAA 57.191 26.923 0.00 0.00 0.00 2.69
3462 4102 0.107654 AATAGAGGGTGCGAGTTGCC 60.108 55.000 0.00 0.00 45.60 4.52
3468 4108 1.244019 GGGTGCGAGTTGCCAGAATT 61.244 55.000 0.00 0.00 45.60 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.194972 TCTCTGTAATCTAATCTGGCTATATGG 57.805 37.037 0.00 0.00 0.00 2.74
227 266 6.676990 AAAAAGAGATCCTTTCAATGCCTT 57.323 33.333 8.92 0.00 43.90 4.35
269 346 2.691011 AGAACTATCGCCAACTCCTCTC 59.309 50.000 0.00 0.00 0.00 3.20
304 381 2.638480 TCTTCCCGATTGGCATTAGG 57.362 50.000 0.00 1.99 0.00 2.69
484 562 4.093556 GTCCCTCGCTTTGTTATCAAGAAG 59.906 45.833 0.00 0.00 34.88 2.85
485 563 4.000988 GTCCCTCGCTTTGTTATCAAGAA 58.999 43.478 0.00 0.00 34.88 2.52
611 702 1.000283 CATCTCCTATCACGCACCTCC 60.000 57.143 0.00 0.00 0.00 4.30
660 751 7.660112 TCTAACATTCTGACATGCAAAATGTT 58.340 30.769 24.54 24.54 34.61 2.71
827 920 1.003812 CCGGGGTGAAACTACAATCCA 59.996 52.381 0.00 0.00 36.74 3.41
877 970 2.516227 AACTCAGGATCCGACTCTGA 57.484 50.000 5.98 3.15 36.30 3.27
878 971 2.757868 AGAAACTCAGGATCCGACTCTG 59.242 50.000 5.98 0.00 0.00 3.35
879 972 3.094484 AGAAACTCAGGATCCGACTCT 57.906 47.619 5.98 1.30 0.00 3.24
880 973 3.445805 AGAAGAAACTCAGGATCCGACTC 59.554 47.826 5.98 0.00 0.00 3.36
881 974 3.436243 AGAAGAAACTCAGGATCCGACT 58.564 45.455 5.98 0.00 0.00 4.18
882 975 3.878160 AGAAGAAACTCAGGATCCGAC 57.122 47.619 5.98 0.00 0.00 4.79
883 976 7.841282 ATATAAGAAGAAACTCAGGATCCGA 57.159 36.000 5.98 6.12 0.00 4.55
884 977 8.577296 TGTATATAAGAAGAAACTCAGGATCCG 58.423 37.037 5.98 1.36 0.00 4.18
896 989 9.974980 TGCATACGATGTTGTATATAAGAAGAA 57.025 29.630 0.00 0.00 33.37 2.52
897 990 9.626045 CTGCATACGATGTTGTATATAAGAAGA 57.374 33.333 0.00 0.00 33.37 2.87
898 991 8.376203 GCTGCATACGATGTTGTATATAAGAAG 58.624 37.037 0.00 0.00 33.37 2.85
899 992 7.870445 TGCTGCATACGATGTTGTATATAAGAA 59.130 33.333 0.00 0.00 33.37 2.52
900 993 7.375053 TGCTGCATACGATGTTGTATATAAGA 58.625 34.615 0.00 0.00 33.37 2.10
901 994 7.581011 TGCTGCATACGATGTTGTATATAAG 57.419 36.000 0.00 0.00 33.37 1.73
902 995 7.954788 TTGCTGCATACGATGTTGTATATAA 57.045 32.000 1.84 0.00 33.37 0.98
907 1000 5.007234 GGTAATTGCTGCATACGATGTTGTA 59.993 40.000 1.84 0.00 0.00 2.41
935 1030 2.018515 ACGGAGAAGGAGAACTCGATC 58.981 52.381 0.00 0.00 34.40 3.69
954 1049 3.103007 GCGTTGGTCTTGTTGTGTTTAC 58.897 45.455 0.00 0.00 0.00 2.01
958 1053 1.132262 CAAGCGTTGGTCTTGTTGTGT 59.868 47.619 0.00 0.00 36.93 3.72
959 1054 1.826327 CAAGCGTTGGTCTTGTTGTG 58.174 50.000 0.00 0.00 36.93 3.33
977 1076 2.104967 CAGGACGATGGGTAGGTTACA 58.895 52.381 0.00 0.00 0.00 2.41
978 1077 1.202498 GCAGGACGATGGGTAGGTTAC 60.202 57.143 0.00 0.00 0.00 2.50
1002 1101 0.687427 CCCATGGCAAAAGTAGGGGG 60.687 60.000 6.09 0.00 32.59 5.40
1015 1114 4.424566 GTGCGCTGTTGCCCATGG 62.425 66.667 9.73 4.14 35.36 3.66
1035 1134 3.805267 GCACTCGCCATGGAAGAG 58.195 61.111 26.45 26.45 37.96 2.85
1109 1208 1.374885 CGGGTAATCACGCACCACA 60.375 57.895 0.00 0.00 37.46 4.17
1143 1242 3.660111 GACAAACTTGCCGGCGCT 61.660 61.111 23.90 2.66 35.36 5.92
1163 1262 0.179240 CAGCGTTGAATGTGCTCGAC 60.179 55.000 0.00 0.00 36.69 4.20
1180 1279 1.227380 GTCCAGATGTAGCCGCCAG 60.227 63.158 0.00 0.00 0.00 4.85
1181 1280 2.900273 GTCCAGATGTAGCCGCCA 59.100 61.111 0.00 0.00 0.00 5.69
1192 1291 2.376109 GGTAGAACCTGATCGTCCAGA 58.624 52.381 8.07 0.00 36.29 3.86
1225 1325 2.423892 GCGTCACTAGATCTGTCCTTCA 59.576 50.000 5.18 0.00 0.00 3.02
1241 1341 1.573829 GAAAACATGAGGCCGCGTCA 61.574 55.000 17.50 17.50 32.83 4.35
1268 1368 3.565214 TCCTTCGCTGGGTTGGCA 61.565 61.111 0.00 0.00 0.00 4.92
1273 1373 2.915659 TCACGTCCTTCGCTGGGT 60.916 61.111 0.00 0.00 44.19 4.51
1300 1400 3.441496 TCTCCAACACGTTTAACGAGT 57.559 42.857 24.57 19.15 46.65 4.18
1436 1536 3.903783 CCATTGTTGGCGTCCGAT 58.096 55.556 0.00 0.00 35.85 4.18
1455 1556 1.737735 CGCATCTCACCGTGAAGCA 60.738 57.895 16.09 0.59 0.00 3.91
1567 1671 1.211212 CATCTGCACCTTCTCCATCCA 59.789 52.381 0.00 0.00 0.00 3.41
1829 1938 1.105167 CCACTCCGTACCTATCCGCA 61.105 60.000 0.00 0.00 0.00 5.69
1835 1944 3.202818 TCAACCTATCCACTCCGTACCTA 59.797 47.826 0.00 0.00 0.00 3.08
1987 2096 2.156917 TGACAGCCCGTAGTATATCCG 58.843 52.381 0.00 0.00 0.00 4.18
2015 2124 2.002586 ACGAGTTGCTTGAATCCATCG 58.997 47.619 0.00 0.00 35.21 3.84
2069 2178 6.726490 TTCTAGTTGTAGGACACACTCTTT 57.274 37.500 0.00 0.00 36.69 2.52
2073 2182 5.538813 TCACATTCTAGTTGTAGGACACACT 59.461 40.000 1.64 0.00 36.69 3.55
2083 2192 5.775701 AGTAGTCACCTCACATTCTAGTTGT 59.224 40.000 0.00 0.00 0.00 3.32
2086 2195 5.571285 TGAGTAGTCACCTCACATTCTAGT 58.429 41.667 0.00 0.00 34.12 2.57
2112 2221 7.420002 TGACTGCATAATATTTTGCTTGCTAG 58.580 34.615 24.97 17.80 39.60 3.42
2143 2253 8.425577 AAGATGACTAAAATCTAACATGGTCG 57.574 34.615 0.00 0.00 33.17 4.79
2195 2310 4.504858 ACGGTAGAAGATGGTCAAACATC 58.495 43.478 0.00 0.00 45.91 3.06
2196 2311 4.553330 ACGGTAGAAGATGGTCAAACAT 57.447 40.909 0.00 0.00 0.00 2.71
2197 2312 5.670792 ATACGGTAGAAGATGGTCAAACA 57.329 39.130 0.00 0.00 0.00 2.83
2198 2313 6.645415 CCATATACGGTAGAAGATGGTCAAAC 59.355 42.308 10.65 0.00 31.15 2.93
2199 2314 6.325545 ACCATATACGGTAGAAGATGGTCAAA 59.674 38.462 15.55 0.00 42.64 2.69
2200 2315 5.836898 ACCATATACGGTAGAAGATGGTCAA 59.163 40.000 15.55 0.00 42.64 3.18
2201 2316 5.391256 ACCATATACGGTAGAAGATGGTCA 58.609 41.667 15.55 0.00 42.64 4.02
2202 2317 5.979288 ACCATATACGGTAGAAGATGGTC 57.021 43.478 15.55 0.00 42.64 4.02
2203 2318 5.713861 GGTACCATATACGGTAGAAGATGGT 59.286 44.000 20.92 20.92 46.67 3.55
2204 2319 5.713389 TGGTACCATATACGGTAGAAGATGG 59.287 44.000 11.60 14.66 42.23 3.51
2205 2320 6.829229 TGGTACCATATACGGTAGAAGATG 57.171 41.667 11.60 0.00 42.23 2.90
2206 2321 7.179966 TCATGGTACCATATACGGTAGAAGAT 58.820 38.462 26.91 0.00 42.23 2.40
2207 2322 6.545567 TCATGGTACCATATACGGTAGAAGA 58.454 40.000 26.91 12.40 42.23 2.87
2208 2323 6.829229 TCATGGTACCATATACGGTAGAAG 57.171 41.667 26.91 10.25 42.23 2.85
2209 2324 8.882557 TTATCATGGTACCATATACGGTAGAA 57.117 34.615 26.91 8.41 42.23 2.10
2210 2325 9.483489 AATTATCATGGTACCATATACGGTAGA 57.517 33.333 26.91 16.97 42.23 2.59
2211 2326 9.745880 GAATTATCATGGTACCATATACGGTAG 57.254 37.037 26.91 12.19 42.23 3.18
2212 2327 9.483489 AGAATTATCATGGTACCATATACGGTA 57.517 33.333 26.91 12.44 40.67 4.02
2213 2328 8.375493 AGAATTATCATGGTACCATATACGGT 57.625 34.615 26.91 13.47 43.46 4.83
2214 2329 9.098355 CAAGAATTATCATGGTACCATATACGG 57.902 37.037 26.91 14.35 34.91 4.02
2215 2330 9.098355 CCAAGAATTATCATGGTACCATATACG 57.902 37.037 26.91 14.73 39.16 3.06
2279 2394 8.871686 AGGCAAAATTGAGTAGTTTTTAAGTG 57.128 30.769 0.00 0.00 0.00 3.16
2280 2395 9.884636 AAAGGCAAAATTGAGTAGTTTTTAAGT 57.115 25.926 0.00 0.00 0.00 2.24
2288 2403 7.833285 TTCCTAAAAGGCAAAATTGAGTAGT 57.167 32.000 0.00 0.00 34.61 2.73
2303 2418 7.023575 GCCATCGTATATGCAATTCCTAAAAG 58.976 38.462 0.00 0.00 0.00 2.27
2321 2436 4.250464 TCTCGATTTTTGTAAGCCATCGT 58.750 39.130 0.00 0.00 38.30 3.73
2338 2453 5.469421 GGACTACGATCCTATCTTTTCTCGA 59.531 44.000 0.00 0.00 35.68 4.04
2339 2454 5.691815 GGACTACGATCCTATCTTTTCTCG 58.308 45.833 0.00 0.00 35.68 4.04
2355 2474 5.268544 CAATGCAAATCATTCAGGACTACG 58.731 41.667 0.00 0.00 43.21 3.51
2356 2475 5.039333 GCAATGCAAATCATTCAGGACTAC 58.961 41.667 0.00 0.00 43.21 2.73
2380 2499 2.019951 GCGTATATGGCACGGACGG 61.020 63.158 15.77 2.12 39.75 4.79
2396 2515 2.027073 TGTTTGCTACTCGCTGGCG 61.027 57.895 8.80 8.80 40.11 5.69
2461 2580 5.147032 TCAATGGAACAATGAAGGGAAAGT 58.853 37.500 0.00 0.00 46.16 2.66
2494 2613 1.094785 CCACATTTAACTGGAGCCGG 58.905 55.000 0.00 0.00 0.00 6.13
2501 2620 4.806640 AATCAAGGCCCACATTTAACTG 57.193 40.909 0.00 0.00 0.00 3.16
2550 2669 9.016438 GTAGTTTTTGGTTAAATACTCCATCCA 57.984 33.333 0.00 0.00 38.47 3.41
2551 2670 8.464404 GGTAGTTTTTGGTTAAATACTCCATCC 58.536 37.037 0.00 0.00 38.47 3.51
2552 2671 9.016438 TGGTAGTTTTTGGTTAAATACTCCATC 57.984 33.333 0.00 0.00 38.47 3.51
2672 2889 4.390909 GGACGAAACGGTCAATTTACAGAT 59.609 41.667 0.00 0.00 38.70 2.90
2682 2899 4.552378 CGTTTAAAATGGACGAAACGGTCA 60.552 41.667 10.10 0.00 46.33 4.02
2750 3080 2.443416 GGGACCTGGTCGCTTTTAAAT 58.557 47.619 30.19 0.00 41.34 1.40
2823 3157 2.257371 CGCATGCTGCTTGTTGCT 59.743 55.556 17.13 0.00 42.25 3.91
2827 3161 3.744719 CTGCCGCATGCTGCTTGT 61.745 61.111 30.24 0.00 42.25 3.16
2888 3305 3.360340 GCTGCTGCTTGCTTCCGT 61.360 61.111 8.53 0.00 43.37 4.69
2930 3401 1.605710 CTTGTTGCTGCTGCTACTTGT 59.394 47.619 25.06 0.00 43.46 3.16
2967 3438 3.912907 GCGGCCGGAGCTAGCTAA 61.913 66.667 29.38 0.00 38.78 3.09
3028 3525 3.078153 TCCCTAGCTATCATGACAGGGAT 59.922 47.826 19.48 4.98 45.36 3.85
3117 3744 7.068348 ACCGCATCTACTTAAAGACTGATTAGA 59.932 37.037 0.00 0.00 0.00 2.10
3135 3762 8.788325 ATCTTTAACTAAAAACTACCGCATCT 57.212 30.769 0.00 0.00 0.00 2.90
3168 3795 5.385509 TTTATGCCAAAAGCTACCACTTC 57.614 39.130 0.00 0.00 44.23 3.01
3178 3805 8.376889 ACCACTTTACAAATTTATGCCAAAAG 57.623 30.769 0.00 0.00 0.00 2.27
3254 3881 1.302511 CCACCTAACGCAGCCAACT 60.303 57.895 0.00 0.00 0.00 3.16
3255 3882 2.332654 CCCACCTAACGCAGCCAAC 61.333 63.158 0.00 0.00 0.00 3.77
3256 3883 1.847798 ATCCCACCTAACGCAGCCAA 61.848 55.000 0.00 0.00 0.00 4.52
3264 3891 2.734492 CGTGAACTCGATCCCACCTAAC 60.734 54.545 0.00 0.00 0.00 2.34
3266 3893 1.100510 CGTGAACTCGATCCCACCTA 58.899 55.000 0.00 0.00 0.00 3.08
3270 3897 2.279810 TGCCGTGAACTCGATCCCA 61.280 57.895 0.00 0.00 0.00 4.37
3280 3907 1.176619 TCCGAAGAGAGTGCCGTGAA 61.177 55.000 0.00 0.00 0.00 3.18
3286 3913 2.482142 CCATAAGGTCCGAAGAGAGTGC 60.482 54.545 0.00 0.00 0.00 4.40
3289 3916 1.757118 TGCCATAAGGTCCGAAGAGAG 59.243 52.381 0.00 0.00 37.19 3.20
3320 3952 8.691661 ACCTTGTTTTCTATGTGATGTAGTTT 57.308 30.769 0.00 0.00 0.00 2.66
3368 4008 7.144661 TGATTCGTTGCAAAAATAAGTGATGT 58.855 30.769 0.00 0.00 0.00 3.06
3400 4040 9.950496 GATTCTCTCAACCCACACATATATAAT 57.050 33.333 0.00 0.00 0.00 1.28
3410 4050 4.943705 GCTTATTGATTCTCTCAACCCACA 59.056 41.667 0.00 0.00 46.37 4.17
3438 4078 1.202580 ACTCGCACCCTCTATTGATGC 60.203 52.381 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.