Multiple sequence alignment - TraesCS2D01G470600

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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 TraesCS2D01G470600 chr2D 100.000 7792 0 0 1 7792 574909510 574901719 0.000000e+00 14390.0
1 TraesCS2D01G470600 chr2D 87.625 2610 274 27 31 2615 549741388 549738803 0.000000e+00 2985.0
2 TraesCS2D01G470600 chr2D 87.471 2610 271 30 31 2615 550254139 550251561 0.000000e+00 2957.0
3 TraesCS2D01G470600 chr2D 87.347 2608 281 30 31 2615 549931936 549929355 0.000000e+00 2942.0
4 TraesCS2D01G470600 chr2D 88.718 2402 245 17 193 2578 551152167 551149776 0.000000e+00 2911.0
5 TraesCS2D01G470600 chr2D 87.073 2607 290 28 31 2615 550660619 550663200 0.000000e+00 2904.0
6 TraesCS2D01G470600 chr2D 91.316 1520 124 3 5414 6932 549735657 549734145 0.000000e+00 2069.0
7 TraesCS2D01G470600 chr2D 91.059 1521 127 6 5415 6932 550667177 550668691 0.000000e+00 2047.0
8 TraesCS2D01G470600 chr2D 88.257 1635 127 28 3498 5073 551437974 551439602 0.000000e+00 1895.0
9 TraesCS2D01G470600 chr2D 83.018 1796 203 69 2688 4418 550663398 550665156 0.000000e+00 1533.0
10 TraesCS2D01G470600 chr2D 98.201 834 15 0 6959 7792 315110261 315111094 0.000000e+00 1458.0
11 TraesCS2D01G470600 chr2D 86.213 1146 131 20 3874 5002 549737279 549736144 0.000000e+00 1216.0
12 TraesCS2D01G470600 chr2D 93.020 831 46 9 6965 7792 54603462 54602641 0.000000e+00 1203.0
13 TraesCS2D01G470600 chr2D 86.782 1097 122 16 3874 4955 550250038 550248950 0.000000e+00 1201.0
14 TraesCS2D01G470600 chr2D 85.313 1103 112 29 2691 3751 549929154 549928060 0.000000e+00 1094.0
15 TraesCS2D01G470600 chr2D 83.408 1109 124 33 2688 3751 551149514 551148421 0.000000e+00 974.0
16 TraesCS2D01G470600 chr2D 91.082 684 47 8 2831 3507 551437109 551437785 0.000000e+00 913.0
17 TraesCS2D01G470600 chr2D 86.124 836 74 25 2744 3544 550251330 550250502 0.000000e+00 863.0
18 TraesCS2D01G470600 chr2D 82.081 692 84 26 3758 4418 549928027 549927345 8.830000e-154 555.0
19 TraesCS2D01G470600 chr2D 88.550 131 13 2 2688 2817 551430843 551430972 2.910000e-34 158.0
20 TraesCS2D01G470600 chr2D 88.525 122 12 2 5296 5416 551439832 551439952 6.300000e-31 147.0
21 TraesCS2D01G470600 chr2D 75.309 243 35 17 20 248 25619170 25619401 8.330000e-15 93.5
22 TraesCS2D01G470600 chr2B 96.005 5282 185 13 2 5273 691012029 691006764 0.000000e+00 8562.0
23 TraesCS2D01G470600 chr2B 90.478 2615 208 24 16 2615 656611589 656609001 0.000000e+00 3411.0
24 TraesCS2D01G470600 chr2B 89.678 2674 227 23 17 2672 656942300 656944942 0.000000e+00 3363.0
25 TraesCS2D01G470600 chr2B 87.837 2557 264 26 31 2562 656000270 655997736 0.000000e+00 2955.0
26 TraesCS2D01G470600 chr2B 87.198 2609 288 30 31 2615 656241149 656238563 0.000000e+00 2926.0
27 TraesCS2D01G470600 chr2B 88.318 2431 251 23 193 2610 656362138 656359728 0.000000e+00 2885.0
28 TraesCS2D01G470600 chr2B 88.575 2442 191 45 2691 5073 656608807 656606395 0.000000e+00 2883.0
29 TraesCS2D01G470600 chr2B 96.041 1667 53 6 5269 6932 691006665 691005009 0.000000e+00 2700.0
30 TraesCS2D01G470600 chr2B 93.618 1520 87 6 5415 6932 656606066 656604555 0.000000e+00 2261.0
31 TraesCS2D01G470600 chr2B 93.673 1470 81 6 5464 6932 656948256 656949714 0.000000e+00 2189.0
32 TraesCS2D01G470600 chr2B 91.047 1519 128 3 5415 6932 655994373 655992862 0.000000e+00 2045.0
33 TraesCS2D01G470600 chr2B 88.279 1493 128 20 3627 5073 656946055 656947546 0.000000e+00 1744.0
34 TraesCS2D01G470600 chr2B 90.311 836 53 12 2688 3507 656945084 656945907 0.000000e+00 1070.0
35 TraesCS2D01G470600 chr2B 84.546 1113 99 30 2691 3751 656238362 656237271 0.000000e+00 1035.0
36 TraesCS2D01G470600 chr2B 81.250 688 92 24 3759 4418 656237237 656236559 8.960000e-144 521.0
37 TraesCS2D01G470600 chr2B 86.667 390 52 0 2149 2538 652282497 652282886 4.320000e-117 433.0
38 TraesCS2D01G470600 chr2B 86.066 122 15 2 5296 5416 656947699 656947819 6.350000e-26 130.0
39 TraesCS2D01G470600 chr2B 75.309 243 35 17 20 248 41201559 41201328 8.330000e-15 93.5
40 TraesCS2D01G470600 chr5D 87.634 2604 287 27 24 2614 395722640 395725221 0.000000e+00 2992.0
41 TraesCS2D01G470600 chr5D 87.774 2462 269 18 123 2578 395920981 395923416 0.000000e+00 2850.0
42 TraesCS2D01G470600 chr5D 91.244 1519 132 1 5415 6932 395926252 395927770 0.000000e+00 2067.0
43 TraesCS2D01G470600 chr5D 90.849 1519 138 1 5415 6932 395728313 395729831 0.000000e+00 2034.0
44 TraesCS2D01G470600 chr5D 87.500 1208 132 13 3872 5065 395924831 395926033 0.000000e+00 1376.0
45 TraesCS2D01G470600 chr5D 88.728 967 79 15 2812 3751 395725498 395726461 0.000000e+00 1155.0
46 TraesCS2D01G470600 chr5D 85.209 1102 115 27 2691 3749 395923631 395924727 0.000000e+00 1088.0
47 TraesCS2D01G470600 chr5D 78.617 1258 235 19 213 1458 247753092 247754327 0.000000e+00 802.0
48 TraesCS2D01G470600 chr5D 86.266 466 52 8 3291 3751 391987870 391988328 5.430000e-136 496.0
49 TraesCS2D01G470600 chr5D 86.260 262 33 3 2935 3195 247757602 247757861 1.660000e-71 281.0
50 TraesCS2D01G470600 chr5B 87.510 2506 260 29 123 2615 475987391 475989856 0.000000e+00 2844.0
51 TraesCS2D01G470600 chr5B 91.310 1519 130 2 5415 6932 475992584 475994101 0.000000e+00 2073.0
52 TraesCS2D01G470600 chr5B 86.786 1173 137 11 3872 5029 475991182 475992351 0.000000e+00 1291.0
53 TraesCS2D01G470600 chr5B 92.382 827 50 10 6970 7792 704318596 704319413 0.000000e+00 1166.0
54 TraesCS2D01G470600 chr5B 84.950 1103 117 26 2691 3751 475990026 475991121 0.000000e+00 1072.0
55 TraesCS2D01G470600 chr5B 86.052 466 54 8 3291 3751 472749748 472750207 2.530000e-134 490.0
56 TraesCS2D01G470600 chr7B 79.160 2356 436 35 202 2538 56360439 56362758 0.000000e+00 1580.0
57 TraesCS2D01G470600 chr7B 78.798 2363 432 48 202 2538 56995084 56992765 0.000000e+00 1524.0
58 TraesCS2D01G470600 chr7B 81.818 583 83 15 2921 3495 56992524 56991957 1.180000e-127 468.0
59 TraesCS2D01G470600 chr7B 81.197 585 89 17 2915 3492 56362991 56363561 1.190000e-122 451.0
60 TraesCS2D01G470600 chr5A 86.672 1208 144 12 3872 5066 501828145 501829348 0.000000e+00 1323.0
61 TraesCS2D01G470600 chr5A 86.696 1135 135 10 3872 4993 501819789 501820920 0.000000e+00 1245.0
62 TraesCS2D01G470600 chr5A 84.727 1100 121 26 2691 3749 501826948 501828041 0.000000e+00 1057.0
63 TraesCS2D01G470600 chr5A 84.545 1100 123 26 2691 3749 501818592 501819685 0.000000e+00 1046.0
64 TraesCS2D01G470600 chr6D 95.864 822 22 2 6974 7792 316413803 316414615 0.000000e+00 1319.0
65 TraesCS2D01G470600 chr6D 83.750 400 59 3 1424 1818 291721555 291721953 2.650000e-99 374.0
66 TraesCS2D01G470600 chr6D 83.377 385 58 3 1424 1803 443292696 443293079 1.240000e-92 351.0
67 TraesCS2D01G470600 chr7D 80.276 1739 301 34 813 2538 100649818 100651527 0.000000e+00 1273.0
68 TraesCS2D01G470600 chr7D 92.512 828 51 8 6968 7792 220313288 220314107 0.000000e+00 1175.0
69 TraesCS2D01G470600 chr7D 92.373 826 51 10 6970 7792 2215397 2216213 0.000000e+00 1166.0
70 TraesCS2D01G470600 chr7D 80.513 585 91 19 2915 3492 100651760 100652328 2.010000e-115 427.0
71 TraesCS2D01G470600 chr7A 92.892 830 47 8 6968 7792 10089376 10088554 0.000000e+00 1195.0
72 TraesCS2D01G470600 chr3B 93.432 807 43 8 6989 7792 224828419 224829218 0.000000e+00 1188.0
73 TraesCS2D01G470600 chr2A 92.225 836 53 9 6960 7792 86268327 86269153 0.000000e+00 1173.0
74 TraesCS2D01G470600 chr2A 75.000 244 35 18 20 248 28022800 28022568 1.080000e-13 89.8
75 TraesCS2D01G470600 chr3D 83.250 400 61 3 1424 1818 117815620 117815222 5.750000e-96 363.0
76 TraesCS2D01G470600 chr3D 97.959 49 1 0 5120 5168 23086982 23087030 1.390000e-12 86.1


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 TraesCS2D01G470600 chr2D 574901719 574909510 7791 True 14390.000000 14390 100.000000 1 7792 1 chr2D.!!$R2 7791
1 TraesCS2D01G470600 chr2D 550660619 550668691 8072 False 2161.333333 2904 87.050000 31 6932 3 chr2D.!!$F4 6901
2 TraesCS2D01G470600 chr2D 549734145 549741388 7243 True 2090.000000 2985 88.384667 31 6932 3 chr2D.!!$R3 6901
3 TraesCS2D01G470600 chr2D 551148421 551152167 3746 True 1942.500000 2911 86.063000 193 3751 2 chr2D.!!$R6 3558
4 TraesCS2D01G470600 chr2D 550248950 550254139 5189 True 1673.666667 2957 86.792333 31 4955 3 chr2D.!!$R5 4924
5 TraesCS2D01G470600 chr2D 549927345 549931936 4591 True 1530.333333 2942 84.913667 31 4418 3 chr2D.!!$R4 4387
6 TraesCS2D01G470600 chr2D 315110261 315111094 833 False 1458.000000 1458 98.201000 6959 7792 1 chr2D.!!$F2 833
7 TraesCS2D01G470600 chr2D 54602641 54603462 821 True 1203.000000 1203 93.020000 6965 7792 1 chr2D.!!$R1 827
8 TraesCS2D01G470600 chr2D 551437109 551439952 2843 False 985.000000 1895 89.288000 2831 5416 3 chr2D.!!$F5 2585
9 TraesCS2D01G470600 chr2B 691005009 691012029 7020 True 5631.000000 8562 96.023000 2 6932 2 chr2B.!!$R6 6930
10 TraesCS2D01G470600 chr2B 656359728 656362138 2410 True 2885.000000 2885 88.318000 193 2610 1 chr2B.!!$R2 2417
11 TraesCS2D01G470600 chr2B 656604555 656611589 7034 True 2851.666667 3411 90.890333 16 6932 3 chr2B.!!$R5 6916
12 TraesCS2D01G470600 chr2B 655992862 656000270 7408 True 2500.000000 2955 89.442000 31 6932 2 chr2B.!!$R3 6901
13 TraesCS2D01G470600 chr2B 656942300 656949714 7414 False 1699.200000 3363 89.601400 17 6932 5 chr2B.!!$F2 6915
14 TraesCS2D01G470600 chr2B 656236559 656241149 4590 True 1494.000000 2926 84.331333 31 4418 3 chr2B.!!$R4 4387
15 TraesCS2D01G470600 chr5D 395722640 395729831 7191 False 2060.333333 2992 89.070333 24 6932 3 chr5D.!!$F3 6908
16 TraesCS2D01G470600 chr5D 395920981 395927770 6789 False 1845.250000 2850 87.931750 123 6932 4 chr5D.!!$F4 6809
17 TraesCS2D01G470600 chr5D 247753092 247757861 4769 False 541.500000 802 82.438500 213 3195 2 chr5D.!!$F2 2982
18 TraesCS2D01G470600 chr5B 475987391 475994101 6710 False 1820.000000 2844 87.639000 123 6932 4 chr5B.!!$F3 6809
19 TraesCS2D01G470600 chr5B 704318596 704319413 817 False 1166.000000 1166 92.382000 6970 7792 1 chr5B.!!$F2 822
20 TraesCS2D01G470600 chr7B 56360439 56363561 3122 False 1015.500000 1580 80.178500 202 3492 2 chr7B.!!$F1 3290
21 TraesCS2D01G470600 chr7B 56991957 56995084 3127 True 996.000000 1524 80.308000 202 3495 2 chr7B.!!$R1 3293
22 TraesCS2D01G470600 chr5A 501826948 501829348 2400 False 1190.000000 1323 85.699500 2691 5066 2 chr5A.!!$F2 2375
23 TraesCS2D01G470600 chr5A 501818592 501820920 2328 False 1145.500000 1245 85.620500 2691 4993 2 chr5A.!!$F1 2302
24 TraesCS2D01G470600 chr6D 316413803 316414615 812 False 1319.000000 1319 95.864000 6974 7792 1 chr6D.!!$F2 818
25 TraesCS2D01G470600 chr7D 220313288 220314107 819 False 1175.000000 1175 92.512000 6968 7792 1 chr7D.!!$F2 824
26 TraesCS2D01G470600 chr7D 2215397 2216213 816 False 1166.000000 1166 92.373000 6970 7792 1 chr7D.!!$F1 822
27 TraesCS2D01G470600 chr7D 100649818 100652328 2510 False 850.000000 1273 80.394500 813 3492 2 chr7D.!!$F3 2679
28 TraesCS2D01G470600 chr7A 10088554 10089376 822 True 1195.000000 1195 92.892000 6968 7792 1 chr7A.!!$R1 824
29 TraesCS2D01G470600 chr3B 224828419 224829218 799 False 1188.000000 1188 93.432000 6989 7792 1 chr3B.!!$F1 803
30 TraesCS2D01G470600 chr2A 86268327 86269153 826 False 1173.000000 1173 92.225000 6960 7792 1 chr2A.!!$F1 832

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
29 31 0.606604 GACTGCGGTAACCTCCTTGA 59.393 55.000 0.00 0.00 0.00 3.02 F
503 539 1.427368 AGGACTTAAACCACCATGGCA 59.573 47.619 13.04 0.00 42.67 4.92 F
871 932 1.880027 GTGAGGATGTTTGTGGTGTCC 59.120 52.381 0.00 0.00 0.00 4.02 F
1854 3076 2.880268 ACATCACATGGATATTGCACCG 59.120 45.455 0.00 0.00 33.95 4.94 F
3044 5061 1.226773 GATGGCTTTCATGTGCGGC 60.227 57.895 0.00 0.00 35.97 6.53 F
4721 8200 0.694444 ATACTTGGGAGGTCGGGCAT 60.694 55.000 0.00 0.00 0.00 4.40 F
5687 10202 0.720027 CAAGATCTCGTGCAGTGCAG 59.280 55.000 20.42 12.88 40.08 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 3173 1.193323 CTCAGCTGACAGTCATCCCT 58.807 55.000 13.74 0.00 0.00 4.20 R
2425 3665 2.496899 TTGTCTTCCCTTCCATCAGC 57.503 50.000 0.00 0.00 0.00 4.26 R
2643 3909 5.241506 ACCATGTATGCTTCAAAATATCCCG 59.758 40.000 0.00 0.00 0.00 5.14 R
3751 6085 1.399440 CACATGTCCCTGAAAGCATCG 59.601 52.381 0.00 0.00 0.00 3.84 R
4775 8254 0.673985 TAGACCTTGGGATGCGATCG 59.326 55.000 11.69 11.69 0.00 3.69 R
6507 11022 0.758310 TGAGCACCAAACCCATGCAA 60.758 50.000 0.00 0.00 41.97 4.08 R
6945 11462 0.035056 AGGGTGAATCTCCTTTGCGG 60.035 55.000 1.11 0.00 0.00 5.69 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
29 31 0.606604 GACTGCGGTAACCTCCTTGA 59.393 55.000 0.00 0.00 0.00 3.02
44 46 4.309099 CTCCTTGAGATATGAGCAGCTTC 58.691 47.826 0.00 0.00 0.00 3.86
66 68 1.802960 GCCCTGTATTGATCATCGCTG 59.197 52.381 0.00 0.00 0.00 5.18
74 76 2.678471 TGATCATCGCTGCTTCTTCA 57.322 45.000 0.00 0.00 0.00 3.02
75 77 3.189618 TGATCATCGCTGCTTCTTCAT 57.810 42.857 0.00 0.00 0.00 2.57
76 78 3.538591 TGATCATCGCTGCTTCTTCATT 58.461 40.909 0.00 0.00 0.00 2.57
77 79 4.696455 TGATCATCGCTGCTTCTTCATTA 58.304 39.130 0.00 0.00 0.00 1.90
112 127 6.536731 AATCGACTCTGCTAGCATTAATTG 57.463 37.500 19.72 5.38 0.00 2.32
171 197 9.618890 TTTGCTAGCTATAATCATGTCTTTCTT 57.381 29.630 17.23 0.00 0.00 2.52
305 336 2.432146 TCAGATCTATGCTCACGCCTTT 59.568 45.455 0.00 0.00 34.43 3.11
333 364 1.444553 GTGAAGCACCCTCGTCGAG 60.445 63.158 15.53 15.53 0.00 4.04
405 441 5.825532 TGTGGACTTTTGGGATAATGATGA 58.174 37.500 0.00 0.00 0.00 2.92
409 445 5.244626 GGACTTTTGGGATAATGATGATGGG 59.755 44.000 0.00 0.00 0.00 4.00
480 516 6.711277 TGTCTAGCATAAAACCTGAATCTGT 58.289 36.000 0.00 0.00 0.00 3.41
503 539 1.427368 AGGACTTAAACCACCATGGCA 59.573 47.619 13.04 0.00 42.67 4.92
537 573 3.571590 TGGCAATGGTTACTGAGGTTTT 58.428 40.909 0.00 0.00 0.00 2.43
587 632 5.824429 TCAGAGTCAAAGTTGCAAAGAATG 58.176 37.500 0.00 0.00 0.00 2.67
616 664 7.201435 GGTTTGCAAGAAGACTTAAACAAACTG 60.201 37.037 22.00 3.47 43.43 3.16
683 731 7.068716 GGATATGGAAAGCACTTACCTTTGATT 59.931 37.037 0.00 0.00 32.98 2.57
685 733 4.237724 GGAAAGCACTTACCTTTGATTGC 58.762 43.478 0.00 0.00 32.98 3.56
871 932 1.880027 GTGAGGATGTTTGTGGTGTCC 59.120 52.381 0.00 0.00 0.00 4.02
886 947 4.939439 GTGGTGTCCGTATTAAACAGGATT 59.061 41.667 0.51 0.00 34.68 3.01
933 998 5.578727 AGAGCAACTACTTTCGATTAAGCTG 59.421 40.000 0.00 0.00 0.00 4.24
937 1002 6.684555 GCAACTACTTTCGATTAAGCTGAATG 59.315 38.462 0.00 0.00 0.00 2.67
957 1022 4.077300 TGAATCACAGGTGGATGCTATC 57.923 45.455 0.00 0.00 0.00 2.08
958 1023 3.455543 TGAATCACAGGTGGATGCTATCA 59.544 43.478 0.00 0.00 0.00 2.15
964 1029 5.366477 TCACAGGTGGATGCTATCAAATCTA 59.634 40.000 0.00 0.00 0.00 1.98
973 1038 8.599792 TGGATGCTATCAAATCTATCATCTCAA 58.400 33.333 0.00 0.00 32.03 3.02
1297 1362 3.644805 GTGTCGACGAACTTGTTGAAA 57.355 42.857 11.62 0.00 34.13 2.69
1707 2929 3.949132 TGAAGCAAGGTACACATGCATA 58.051 40.909 16.04 2.93 42.45 3.14
1854 3076 2.880268 ACATCACATGGATATTGCACCG 59.120 45.455 0.00 0.00 33.95 4.94
1951 3173 7.055667 TGGCTAAAATATGTTGTTTTGGTCA 57.944 32.000 0.00 0.00 38.65 4.02
2144 3381 6.308371 TCTTCCTTTTATGTTCCGTTTGTC 57.692 37.500 0.00 0.00 0.00 3.18
2167 3404 7.121168 TGTCATTGATCTGTTTTTGATAGTCCC 59.879 37.037 0.00 0.00 0.00 4.46
2215 3453 6.321690 TCTCTAGGTATGTAAAGAAGCTGGAC 59.678 42.308 0.00 0.00 0.00 4.02
2425 3665 5.188194 GCAGCTACACGTTAATAAATGTCG 58.812 41.667 0.00 0.00 32.35 4.35
2496 3736 7.047271 ACATGGTTGAAGTTGCTATTGTTTTT 58.953 30.769 0.00 0.00 0.00 1.94
2909 4922 6.701400 CCTTGTCCAAAATTTGACCACTTAAG 59.299 38.462 7.37 0.00 0.00 1.85
2910 4923 7.411486 TTGTCCAAAATTTGACCACTTAAGA 57.589 32.000 10.09 0.00 0.00 2.10
2913 4927 9.137459 TGTCCAAAATTTGACCACTTAAGATTA 57.863 29.630 10.09 0.00 0.00 1.75
2942 4959 2.037641 GCTTGGAAAAAGACAGGCCAAT 59.962 45.455 5.01 0.00 37.91 3.16
3013 5030 8.275632 GCAATTAAAACTAGACTTGGCAAAAAG 58.724 33.333 0.00 0.00 0.00 2.27
3044 5061 1.226773 GATGGCTTTCATGTGCGGC 60.227 57.895 0.00 0.00 35.97 6.53
3299 5331 1.462616 TGGATTGTTGGGAATGCTCG 58.537 50.000 0.00 0.00 0.00 5.03
3470 5502 1.606668 TGCTGATTCGGTGGTTTTCAC 59.393 47.619 0.00 0.00 45.34 3.18
3621 5914 4.811024 TGTGAGACTCATTCTTGTTGTCAC 59.189 41.667 8.73 0.00 33.22 3.67
3631 5924 2.696707 TCTTGTTGTCACGGAGTTAGGT 59.303 45.455 0.00 0.00 41.61 3.08
3751 6085 2.233922 TGCTAGGCTGTTTCCTCTGTAC 59.766 50.000 0.00 0.00 37.66 2.90
3782 6143 5.565509 TCAGGGACATGTGCTATTTTGTAA 58.434 37.500 17.44 0.00 0.00 2.41
3791 6152 7.756722 ACATGTGCTATTTTGTAAGATGCTTTC 59.243 33.333 0.00 0.00 0.00 2.62
3858 6337 7.445707 GTGAACCTCCTAGTTTTCTTGAAGAAT 59.554 37.037 8.64 0.00 33.67 2.40
3889 6392 2.704725 TCATTTTTCTCAGGTTGCGC 57.295 45.000 0.00 0.00 0.00 6.09
3904 6407 4.979815 AGGTTGCGCTTTTTGTATTTGTAC 59.020 37.500 9.73 0.00 0.00 2.90
4121 6624 5.222027 TGGAGTATTGACATGGAGAAAACCA 60.222 40.000 0.00 0.00 44.41 3.67
4123 6626 6.127897 GGAGTATTGACATGGAGAAAACCAAG 60.128 42.308 0.00 0.00 43.47 3.61
4300 6815 4.351874 TGTTAATGGGCTATACTCTGGC 57.648 45.455 0.00 0.00 0.00 4.85
4313 6833 6.319911 GCTATACTCTGGCCTCTTCAATTTTT 59.680 38.462 3.32 0.00 0.00 1.94
4379 6905 5.300034 TGCCTAGAAATGAAATGCATGTAGG 59.700 40.000 0.00 0.00 38.06 3.18
4491 7446 4.971830 CGCTATAACATGGATTGCAAAGTG 59.028 41.667 1.71 2.70 0.00 3.16
4506 7461 3.192001 GCAAAGTGGATGCTCATGAAGAA 59.808 43.478 0.00 0.00 40.64 2.52
4519 7482 3.685139 ATGAAGAACATGGTCTCGTGT 57.315 42.857 15.08 0.00 44.34 4.49
4721 8200 0.694444 ATACTTGGGAGGTCGGGCAT 60.694 55.000 0.00 0.00 0.00 4.40
4775 8254 9.688592 AATGATTCAAAAAGAGAAACTGTCATC 57.311 29.630 0.00 0.00 0.00 2.92
4809 8288 3.903467 AGGTCTAAATTTGGATGGAGCC 58.097 45.455 7.56 4.02 0.00 4.70
4959 8442 3.611766 AGGTAAGTCTGTTGAATCGGG 57.388 47.619 0.00 0.00 0.00 5.14
5159 8969 4.395583 GCAAGAGCGTGGCTGTGC 62.396 66.667 0.00 0.96 39.88 4.57
5189 8999 3.815401 CAGACCAAAGTTCGATTCCTGTT 59.185 43.478 0.00 0.00 0.00 3.16
5206 9016 4.082463 TCCTGTTGGCGGAATTTATTTCAC 60.082 41.667 0.00 0.00 35.94 3.18
5215 9025 6.752815 GGCGGAATTTATTTCACGGATTAAAA 59.247 34.615 0.00 0.00 35.94 1.52
5217 9027 7.253850 GCGGAATTTATTTCACGGATTAAAACC 60.254 37.037 0.00 0.00 35.94 3.27
5224 9034 5.873179 TTCACGGATTAAAACCTGATGTC 57.127 39.130 0.00 0.00 0.00 3.06
5231 9041 1.995376 AAAACCTGATGTCCCACACC 58.005 50.000 0.00 0.00 0.00 4.16
5232 9042 1.149101 AAACCTGATGTCCCACACCT 58.851 50.000 0.00 0.00 0.00 4.00
5233 9043 1.149101 AACCTGATGTCCCACACCTT 58.851 50.000 0.00 0.00 0.00 3.50
5243 9053 3.181448 TGTCCCACACCTTCTTCTTAACC 60.181 47.826 0.00 0.00 0.00 2.85
5280 9203 3.801997 CTCCCCCATTCGCAGGCT 61.802 66.667 0.00 0.00 0.00 4.58
5459 9611 1.002430 GGCACTGGTGATGTCTCTGAA 59.998 52.381 4.79 0.00 0.00 3.02
5621 10136 3.235157 ACATGCCGGACATCATTTTTG 57.765 42.857 5.05 0.00 36.64 2.44
5665 10180 1.107114 TCTAGCTTTGAGAGAGGCCG 58.893 55.000 0.00 0.00 0.00 6.13
5687 10202 0.720027 CAAGATCTCGTGCAGTGCAG 59.280 55.000 20.42 12.88 40.08 4.41
5834 10349 2.062971 AGGGCACATATCAAGCAAGG 57.937 50.000 0.00 0.00 0.00 3.61
5897 10412 7.850003 GTGATGCTCTCAGATAAAAGAATTTCG 59.150 37.037 0.00 0.00 33.01 3.46
5905 10420 9.752274 CTCAGATAAAAGAATTTCGTCTTTGAG 57.248 33.333 1.19 1.29 45.09 3.02
6158 10673 1.406539 CTTTTTGCTGGTGACACTGCT 59.593 47.619 19.19 0.00 36.43 4.24
6310 10825 9.859427 TGATATGTTCCAATTGTCTCAAAATTC 57.141 29.630 4.43 0.00 0.00 2.17
6358 10873 1.678101 GGCACAAAGTATCATGAGGCC 59.322 52.381 0.09 0.00 34.98 5.19
6406 10921 5.470098 GTGTTGACAAGCTTAATCCAGAGAA 59.530 40.000 0.00 0.00 0.00 2.87
6507 11022 9.313118 GAGAAAACAAAAGTCAACATGGTAATT 57.687 29.630 0.00 0.00 0.00 1.40
6525 11040 0.392336 TTTGCATGGGTTTGGTGCTC 59.608 50.000 0.00 0.00 39.52 4.26
6826 11343 8.978874 TCTGTATGGCTACATGAAACATAAAT 57.021 30.769 0.00 0.00 37.24 1.40
6932 11449 2.416202 TCTATGTTGCAATCACACGCAG 59.584 45.455 0.59 0.00 39.75 5.18
6933 11450 0.387622 ATGTTGCAATCACACGCAGC 60.388 50.000 0.59 0.00 39.75 5.25
6934 11451 1.730547 GTTGCAATCACACGCAGCC 60.731 57.895 0.59 0.00 39.75 4.85
6935 11452 2.192187 TTGCAATCACACGCAGCCA 61.192 52.632 0.00 0.00 39.75 4.75
6936 11453 1.525718 TTGCAATCACACGCAGCCAT 61.526 50.000 0.00 0.00 39.75 4.40
6937 11454 1.226491 GCAATCACACGCAGCCATC 60.226 57.895 0.00 0.00 0.00 3.51
6938 11455 1.430632 CAATCACACGCAGCCATCC 59.569 57.895 0.00 0.00 0.00 3.51
6939 11456 2.108514 AATCACACGCAGCCATCCG 61.109 57.895 0.00 0.00 0.00 4.18
7399 11923 2.989824 CCTGGTGGTCTCGTCGGT 60.990 66.667 0.00 0.00 0.00 4.69
7492 12016 2.583441 CCTGAGGCTGGGTGTTCGA 61.583 63.158 0.00 0.00 0.00 3.71
7531 12055 4.056125 CACCAGCTGCGAGTCGGA 62.056 66.667 15.52 11.18 0.00 4.55
7687 12211 0.541863 GTTCCAGACCGGATGATGGT 59.458 55.000 9.46 0.00 45.80 3.55
7740 12265 1.159713 CGTTTGTGGAGCAGTGCTGA 61.160 55.000 25.35 5.76 39.88 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.802685 GGTTACCGCAGTCAATCATAGAC 59.197 47.826 0.00 0.00 36.26 2.59
1 2 3.704566 AGGTTACCGCAGTCAATCATAGA 59.295 43.478 0.00 0.00 0.00 1.98
3 4 3.181469 GGAGGTTACCGCAGTCAATCATA 60.181 47.826 7.54 0.00 0.00 2.15
4 5 2.420129 GGAGGTTACCGCAGTCAATCAT 60.420 50.000 7.54 0.00 0.00 2.45
5 6 1.066430 GGAGGTTACCGCAGTCAATCA 60.066 52.381 7.54 0.00 0.00 2.57
7 8 1.276622 AGGAGGTTACCGCAGTCAAT 58.723 50.000 7.54 0.00 34.73 2.57
29 31 1.072015 GGGCTGAAGCTGCTCATATCT 59.928 52.381 1.00 0.00 41.70 1.98
44 46 1.802960 GCGATGATCAATACAGGGCTG 59.197 52.381 0.00 0.00 0.00 4.85
75 77 9.330063 AGCAGAGTCGATTTCAATTTCATATAA 57.670 29.630 0.00 0.00 0.00 0.98
76 78 8.893219 AGCAGAGTCGATTTCAATTTCATATA 57.107 30.769 0.00 0.00 0.00 0.86
77 79 7.798596 AGCAGAGTCGATTTCAATTTCATAT 57.201 32.000 0.00 0.00 0.00 1.78
112 127 4.826556 ACAGTTCCTTGAGTAGAGAATGC 58.173 43.478 0.00 0.00 0.00 3.56
118 133 4.480115 TCTCCAACAGTTCCTTGAGTAGA 58.520 43.478 0.00 0.00 0.00 2.59
119 134 4.873746 TCTCCAACAGTTCCTTGAGTAG 57.126 45.455 0.00 0.00 0.00 2.57
121 143 4.349342 AGATTCTCCAACAGTTCCTTGAGT 59.651 41.667 0.00 0.00 0.00 3.41
187 217 4.335315 GTCACAACCTGAACACAAATGAGA 59.665 41.667 0.00 0.00 0.00 3.27
305 336 2.906389 AGGGTGCTTCACTGATGAGTTA 59.094 45.455 0.00 0.00 35.83 2.24
333 364 3.181469 TGCTACCTCCATGGAACGTATTC 60.181 47.826 17.00 12.89 39.71 1.75
405 441 8.114301 AGTATAATTCCCAGTAGAAAACCCAT 57.886 34.615 0.00 0.00 0.00 4.00
480 516 3.054655 GCCATGGTGGTTTAAGTCCTCTA 60.055 47.826 14.67 0.00 40.46 2.43
503 539 2.691526 CCATTGCCAAGCAGTATGTCAT 59.308 45.455 0.00 0.00 40.61 3.06
537 573 6.748045 GCCCTTCTGGTATTCATCATCCATAA 60.748 42.308 0.00 0.00 36.04 1.90
587 632 6.096695 TGTTTAAGTCTTCTTGCAAACCAAC 58.903 36.000 0.00 0.77 34.13 3.77
596 644 7.250569 TGCTTCAGTTTGTTTAAGTCTTCTTG 58.749 34.615 0.00 0.00 35.36 3.02
616 664 7.766219 ATTGTTGAGAAATATTGCATGCTTC 57.234 32.000 20.33 13.51 0.00 3.86
683 731 4.525874 TGTGAAATTGTTATCCATGTGGCA 59.474 37.500 0.00 0.00 34.44 4.92
685 733 6.271488 ACTGTGAAATTGTTATCCATGTGG 57.729 37.500 0.00 0.00 0.00 4.17
871 932 5.365619 ACAGCCCTAATCCTGTTTAATACG 58.634 41.667 0.00 0.00 39.11 3.06
886 947 2.158534 TGAAAGAAGCCAAACAGCCCTA 60.159 45.455 0.00 0.00 0.00 3.53
933 998 3.285484 AGCATCCACCTGTGATTCATTC 58.715 45.455 0.00 0.00 0.00 2.67
937 1002 4.077300 TGATAGCATCCACCTGTGATTC 57.923 45.455 0.00 0.00 0.00 2.52
958 1023 9.896645 ACATTGTACAGTTGAGATGATAGATTT 57.103 29.630 13.13 0.00 0.00 2.17
964 1029 5.188434 CCCACATTGTACAGTTGAGATGAT 58.812 41.667 13.13 0.00 0.00 2.45
973 1038 2.161855 CACATGCCCACATTGTACAGT 58.838 47.619 0.00 0.00 32.87 3.55
1043 1108 2.088423 CCCACAATAAAGCGCTAACCA 58.912 47.619 12.05 0.00 0.00 3.67
1297 1362 1.272490 TCCTGACGACGATGAAAAGCT 59.728 47.619 0.00 0.00 0.00 3.74
1707 2929 6.712547 AGTGTAGCAGATCTTTAAGCAACTTT 59.287 34.615 5.65 0.00 0.00 2.66
1854 3076 7.746475 GCCTCATTAACAATTAATACATCGAGC 59.254 37.037 0.00 0.00 34.22 5.03
1951 3173 1.193323 CTCAGCTGACAGTCATCCCT 58.807 55.000 13.74 0.00 0.00 4.20
2144 3381 7.395190 TGGGACTATCAAAAACAGATCAATG 57.605 36.000 0.00 0.00 0.00 2.82
2277 3517 2.874701 ACAAGGATTCATGCGATACTGC 59.125 45.455 0.00 0.00 0.00 4.40
2337 3577 5.653769 CAGGACATTGGAACCATCTAACATT 59.346 40.000 0.00 0.00 0.00 2.71
2425 3665 2.496899 TTGTCTTCCCTTCCATCAGC 57.503 50.000 0.00 0.00 0.00 4.26
2496 3736 9.573166 CATTTAAAGATGGTATGGATTAGGTGA 57.427 33.333 0.00 0.00 0.00 4.02
2643 3909 5.241506 ACCATGTATGCTTCAAAATATCCCG 59.758 40.000 0.00 0.00 0.00 5.14
2909 4922 6.529477 GTCTTTTTCCAAGCTGCAGAATAATC 59.471 38.462 20.43 0.00 0.00 1.75
2910 4923 6.015180 TGTCTTTTTCCAAGCTGCAGAATAAT 60.015 34.615 20.43 0.00 0.00 1.28
2913 4927 3.638160 TGTCTTTTTCCAAGCTGCAGAAT 59.362 39.130 20.43 1.05 0.00 2.40
2942 4959 2.324330 CCACGCCGATGCTGAAACA 61.324 57.895 0.00 0.00 34.43 2.83
3013 5030 6.358118 TGAAAGCCATCACATTTATCGTAC 57.642 37.500 0.00 0.00 0.00 3.67
3044 5061 3.084786 GGAAACCCTCAATGGACTTCAG 58.915 50.000 0.00 0.00 38.35 3.02
3246 5271 6.429078 GCCTGCATGAAATAGAACATCAGATA 59.571 38.462 0.00 0.00 30.82 1.98
3299 5331 4.866486 CGGTCCCACTTTTATACAGTGTAC 59.134 45.833 4.80 7.50 40.19 2.90
3470 5502 5.373812 ACTTACCTTCCATCTGGTATTGG 57.626 43.478 0.00 0.00 38.45 3.16
3558 5851 2.161609 GTGGTTCGCATTCTGGGTAAAG 59.838 50.000 0.00 0.00 0.00 1.85
3621 5914 9.028185 GTGTATATTCAGTAAAACCTAACTCCG 57.972 37.037 0.00 0.00 0.00 4.63
3654 5955 6.493978 TGAACACACACAAAATCACACTATG 58.506 36.000 0.00 0.00 0.00 2.23
3751 6085 1.399440 CACATGTCCCTGAAAGCATCG 59.601 52.381 0.00 0.00 0.00 3.84
3782 6143 7.800092 AGAACCATATAACTGAGAAAGCATCT 58.200 34.615 0.00 0.00 42.61 2.90
3858 6337 8.383175 ACCTGAGAAAAATGAAGGAACAGTATA 58.617 33.333 0.00 0.00 0.00 1.47
3868 6347 2.982470 GCGCAACCTGAGAAAAATGAAG 59.018 45.455 0.30 0.00 0.00 3.02
3889 6392 9.528018 ACCTGTTGAATGTACAAATACAAAAAG 57.472 29.630 0.00 5.88 44.47 2.27
3904 6407 4.631377 TCGCTAAGAATGACCTGTTGAATG 59.369 41.667 0.00 0.00 0.00 2.67
4196 6699 7.206687 GTGTACATGGAAAACAAATTCTGGAA 58.793 34.615 0.00 0.00 0.00 3.53
4199 6702 5.629020 CCGTGTACATGGAAAACAAATTCTG 59.371 40.000 27.31 0.00 39.90 3.02
4307 6822 9.947433 TCAAGCATCAAAGGATAATGAAAAATT 57.053 25.926 0.00 0.00 30.87 1.82
4313 6833 7.885009 TTGATCAAGCATCAAAGGATAATGA 57.115 32.000 3.38 0.00 46.68 2.57
4345 6870 9.599322 CATTTCATTTCTAGGCACGATATTTAC 57.401 33.333 0.00 0.00 0.00 2.01
4379 6905 5.105187 AGGAGGGCAAAAATTAGAAGAATGC 60.105 40.000 0.00 0.00 0.00 3.56
4506 7461 5.791336 ATGATGTATACACGAGACCATGT 57.209 39.130 7.96 0.00 0.00 3.21
4519 7482 9.531158 TGAATTTTCCATGGCATATGATGTATA 57.469 29.630 6.96 0.00 0.00 1.47
4721 8200 4.452825 TGTCAATACAGTGGTTTTTCCGA 58.547 39.130 0.00 0.00 39.52 4.55
4775 8254 0.673985 TAGACCTTGGGATGCGATCG 59.326 55.000 11.69 11.69 0.00 3.69
4809 8288 2.125952 TCATCTGCCGCAGACACG 60.126 61.111 25.18 16.05 43.63 4.49
4956 8438 1.814394 GTACTTTTAAACAGGGGCCCG 59.186 52.381 18.95 14.94 0.00 6.13
4959 8442 7.555195 ACATATGTAGTACTTTTAAACAGGGGC 59.445 37.037 6.56 0.00 0.00 5.80
5189 8999 2.712709 TCCGTGAAATAAATTCCGCCA 58.287 42.857 0.00 0.00 37.22 5.69
5206 9016 3.377172 GTGGGACATCAGGTTTTAATCCG 59.623 47.826 0.00 0.00 44.52 4.18
5215 9025 0.693049 GAAGGTGTGGGACATCAGGT 59.307 55.000 0.00 0.00 44.52 4.00
5217 9027 2.304180 AGAAGAAGGTGTGGGACATCAG 59.696 50.000 0.00 0.00 44.52 2.90
5224 9034 3.502123 TGGTTAAGAAGAAGGTGTGGG 57.498 47.619 0.00 0.00 0.00 4.61
5258 9068 4.570874 GCGAATGGGGGAGGAGCC 62.571 72.222 0.00 0.00 0.00 4.70
5259 9069 3.764160 CTGCGAATGGGGGAGGAGC 62.764 68.421 0.00 0.00 0.00 4.70
5280 9203 4.488136 CACGCCCAGCCCAGCATA 62.488 66.667 0.00 0.00 0.00 3.14
5318 9261 2.681064 GCCCCAAGCATGGCTCAA 60.681 61.111 1.35 0.00 46.09 3.02
5621 10136 9.736023 GACTTCATTTCACCATAAAATACATCC 57.264 33.333 0.00 0.00 0.00 3.51
5665 10180 1.127582 GCACTGCACGAGATCTTGAAC 59.872 52.381 17.27 8.30 0.00 3.18
6158 10673 5.866207 TCGATACCTCTTGCTATAGTCTGA 58.134 41.667 0.84 0.00 0.00 3.27
6358 10873 3.822735 TGATGGGAAAAAGAAGCACAGAG 59.177 43.478 0.00 0.00 0.00 3.35
6406 10921 2.628657 GCTTCTCCGTATACCAGTCCAT 59.371 50.000 0.00 0.00 0.00 3.41
6507 11022 0.758310 TGAGCACCAAACCCATGCAA 60.758 50.000 0.00 0.00 41.97 4.08
6525 11040 6.476706 TCATCACGAACTAATATGACTTGCTG 59.523 38.462 0.00 0.00 0.00 4.41
6826 11343 4.981812 TCCTCGGAGTGTGCTATAATAGA 58.018 43.478 4.02 0.00 0.00 1.98
6941 11458 3.440356 GAATCTCCTTTGCGGCGCG 62.440 63.158 28.09 13.05 0.00 6.86
6942 11459 2.398554 TGAATCTCCTTTGCGGCGC 61.399 57.895 27.44 27.44 0.00 6.53
6943 11460 1.425428 GTGAATCTCCTTTGCGGCG 59.575 57.895 0.51 0.51 0.00 6.46
6944 11461 1.657751 GGGTGAATCTCCTTTGCGGC 61.658 60.000 1.11 0.00 0.00 6.53
6945 11462 0.035056 AGGGTGAATCTCCTTTGCGG 60.035 55.000 1.11 0.00 0.00 5.69
6946 11463 2.555199 CTAGGGTGAATCTCCTTTGCG 58.445 52.381 1.11 0.00 34.75 4.85
6947 11464 2.293170 GCTAGGGTGAATCTCCTTTGC 58.707 52.381 4.51 4.51 34.75 3.68
6948 11465 2.422093 GGGCTAGGGTGAATCTCCTTTG 60.422 54.545 1.11 0.00 34.75 2.77
6949 11466 1.847088 GGGCTAGGGTGAATCTCCTTT 59.153 52.381 1.11 0.00 34.75 3.11
6950 11467 1.512735 GGGCTAGGGTGAATCTCCTT 58.487 55.000 1.11 0.00 34.75 3.36
6951 11468 0.400670 GGGGCTAGGGTGAATCTCCT 60.401 60.000 1.11 1.57 37.18 3.69
6952 11469 1.419720 GGGGGCTAGGGTGAATCTCC 61.420 65.000 0.00 0.00 0.00 3.71
6953 11470 1.759459 CGGGGGCTAGGGTGAATCTC 61.759 65.000 0.00 0.00 0.00 2.75
6954 11471 1.766461 CGGGGGCTAGGGTGAATCT 60.766 63.158 0.00 0.00 0.00 2.40
6955 11472 2.829592 CGGGGGCTAGGGTGAATC 59.170 66.667 0.00 0.00 0.00 2.52
6956 11473 3.489513 GCGGGGGCTAGGGTGAAT 61.490 66.667 0.00 0.00 0.00 2.57
7399 11923 0.976641 AGATCTGAACGAAGGTGCCA 59.023 50.000 0.00 0.00 0.00 4.92
7492 12016 3.007398 GCTAGATGACGGATCCCAAGATT 59.993 47.826 6.06 0.00 30.90 2.40
7531 12055 1.901591 TCACCGGAAACTACGTCTCT 58.098 50.000 9.46 0.00 0.00 3.10
7740 12265 0.689623 CACCTCCTGCCTCTGACTTT 59.310 55.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.