Multiple sequence alignment - TraesCS1B01G009500

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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 TraesCS1B01G009500 chr1B 100.000 5356 0 0 1 5356 4763351 4757996 0.000000e+00 9891.0
1 TraesCS1B01G009500 chr1B 89.822 2977 291 7 2057 5030 4590469 4587502 0.000000e+00 3808.0
2 TraesCS1B01G009500 chr1B 85.262 3535 465 36 854 4347 687785367 687788886 0.000000e+00 3591.0
3 TraesCS1B01G009500 chr1B 86.716 2311 272 23 2051 4342 3943534 3945828 0.000000e+00 2534.0
4 TraesCS1B01G009500 chr1B 85.149 1441 175 21 641 2058 4591964 4590540 0.000000e+00 1439.0
5 TraesCS1B01G009500 chr1B 84.105 1491 222 9 987 2471 4580502 4579021 0.000000e+00 1426.0
6 TraesCS1B01G009500 chr1B 84.048 1260 170 14 818 2059 4483828 4482582 0.000000e+00 1184.0
7 TraesCS1B01G009500 chr1B 86.304 1066 133 10 1002 2059 4856357 4855297 0.000000e+00 1147.0
8 TraesCS1B01G009500 chr1B 85.661 1067 136 15 1002 2058 4150801 4151860 0.000000e+00 1107.0
9 TraesCS1B01G009500 chr1B 85.106 1081 146 13 1002 2073 3942410 3943484 0.000000e+00 1090.0
10 TraesCS1B01G009500 chr1B 85.168 1072 143 13 997 2059 4510812 4509748 0.000000e+00 1085.0
11 TraesCS1B01G009500 chr1B 95.833 408 8 2 1 408 4592616 4592218 0.000000e+00 651.0
12 TraesCS1B01G009500 chr1B 86.822 387 42 8 3978 4357 4153941 4154325 1.780000e-114 424.0
13 TraesCS1B01G009500 chr1B 83.594 384 56 5 4769 5151 4099537 4099914 2.370000e-93 353.0
14 TraesCS1B01G009500 chr1B 82.768 383 57 4 4769 5151 3968459 3968832 3.090000e-87 333.0
15 TraesCS1B01G009500 chr1B 95.897 195 8 0 407 601 4592166 4591972 3.110000e-82 316.0
16 TraesCS1B01G009500 chr1B 86.331 278 34 3 4346 4621 687788995 687789270 3.140000e-77 300.0
17 TraesCS1B01G009500 chr1B 85.664 286 27 8 4680 4961 687789445 687789720 6.790000e-74 289.0
18 TraesCS1B01G009500 chr1B 88.372 215 21 3 4937 5151 4498741 4498531 6.880000e-64 255.0
19 TraesCS1B01G009500 chr1B 87.562 201 23 1 5154 5352 3968938 3969138 1.160000e-56 231.0
20 TraesCS1B01G009500 chr1B 82.061 262 45 2 4769 5030 4820650 4820391 6.980000e-54 222.0
21 TraesCS1B01G009500 chr1B 87.895 190 19 3 5160 5346 4528196 4528008 2.510000e-53 220.0
22 TraesCS1B01G009500 chr1B 81.818 264 43 5 4680 4940 4564117 4563856 3.250000e-52 217.0
23 TraesCS1B01G009500 chr1B 83.019 212 27 6 4345 4550 4558038 4557830 3.290000e-42 183.0
24 TraesCS1B01G009500 chr1B 81.731 208 30 7 4380 4586 3945963 3946163 3.320000e-37 167.0
25 TraesCS1B01G009500 chr1B 84.071 113 12 2 4985 5097 3946561 3946667 2.640000e-18 104.0
26 TraesCS1B01G009500 chr1B 86.047 86 11 1 152 237 4586159 4586075 2.050000e-14 91.6
27 TraesCS1B01G009500 chr1B 79.286 140 18 4 4985 5124 4015792 4015920 2.660000e-13 87.9
28 TraesCS1B01G009500 chr1A 90.568 3308 303 7 2047 5352 2983721 2987021 0.000000e+00 4372.0
29 TraesCS1B01G009500 chr1A 91.310 3015 235 17 2057 5065 3490650 3487657 0.000000e+00 4091.0
30 TraesCS1B01G009500 chr1A 86.384 3371 411 32 1002 4342 3681330 3677978 0.000000e+00 3639.0
31 TraesCS1B01G009500 chr1A 85.991 2477 317 14 1826 4283 3581509 3579044 0.000000e+00 2625.0
32 TraesCS1B01G009500 chr1A 86.553 1056 129 10 1012 2059 3657322 3656272 0.000000e+00 1151.0
33 TraesCS1B01G009500 chr1A 95.522 201 9 0 5154 5354 3487637 3487437 6.690000e-84 322.0
34 TraesCS1B01G009500 chr1A 81.481 297 37 12 4341 4624 3669101 3668810 1.500000e-55 228.0
35 TraesCS1B01G009500 chr1D 85.403 3535 459 39 854 4347 494546828 494550346 0.000000e+00 3616.0
36 TraesCS1B01G009500 chr1D 85.967 2544 325 18 1826 4347 448110 450643 0.000000e+00 2691.0
37 TraesCS1B01G009500 chr1D 87.624 2311 245 24 2057 4342 619982 617688 0.000000e+00 2645.0
38 TraesCS1B01G009500 chr1D 85.343 2579 331 33 1794 4342 460069 462630 0.000000e+00 2625.0
39 TraesCS1B01G009500 chr1D 80.949 1370 200 35 413 1750 723460 722120 0.000000e+00 1027.0
40 TraesCS1B01G009500 chr1D 82.642 386 58 6 4769 5151 463132 463511 3.090000e-87 333.0
41 TraesCS1B01G009500 chr1D 85.145 276 37 4 4346 4618 494550455 494550729 4.080000e-71 279.0
42 TraesCS1B01G009500 chr1D 80.827 266 41 7 4346 4606 694419 694159 3.270000e-47 200.0
43 TraesCS1B01G009500 chr3D 87.344 2323 258 20 2057 4357 560056954 560054646 0.000000e+00 2628.0


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 TraesCS1B01G009500 chr1B 4757996 4763351 5355 True 9891.000000 9891 100.000000 1 5356 1 chr1B.!!$R8 5355
1 TraesCS1B01G009500 chr1B 4579021 4580502 1481 True 1426.000000 1426 84.105000 987 2471 1 chr1B.!!$R7 1484
2 TraesCS1B01G009500 chr1B 687785367 687789720 4353 False 1393.333333 3591 85.752333 854 4961 3 chr1B.!!$F6 4107
3 TraesCS1B01G009500 chr1B 4586075 4592616 6541 True 1261.120000 3808 90.549600 1 5030 5 chr1B.!!$R11 5029
4 TraesCS1B01G009500 chr1B 4482582 4483828 1246 True 1184.000000 1184 84.048000 818 2059 1 chr1B.!!$R1 1241
5 TraesCS1B01G009500 chr1B 4855297 4856357 1060 True 1147.000000 1147 86.304000 1002 2059 1 chr1B.!!$R10 1057
6 TraesCS1B01G009500 chr1B 4509748 4510812 1064 True 1085.000000 1085 85.168000 997 2059 1 chr1B.!!$R3 1062
7 TraesCS1B01G009500 chr1B 3942410 3946667 4257 False 973.750000 2534 84.406000 1002 5097 4 chr1B.!!$F3 4095
8 TraesCS1B01G009500 chr1B 4150801 4154325 3524 False 765.500000 1107 86.241500 1002 4357 2 chr1B.!!$F5 3355
9 TraesCS1B01G009500 chr1B 3968459 3969138 679 False 282.000000 333 85.165000 4769 5352 2 chr1B.!!$F4 583
10 TraesCS1B01G009500 chr1A 2983721 2987021 3300 False 4372.000000 4372 90.568000 2047 5352 1 chr1A.!!$F1 3305
11 TraesCS1B01G009500 chr1A 3677978 3681330 3352 True 3639.000000 3639 86.384000 1002 4342 1 chr1A.!!$R4 3340
12 TraesCS1B01G009500 chr1A 3579044 3581509 2465 True 2625.000000 2625 85.991000 1826 4283 1 chr1A.!!$R1 2457
13 TraesCS1B01G009500 chr1A 3487437 3490650 3213 True 2206.500000 4091 93.416000 2057 5354 2 chr1A.!!$R5 3297
14 TraesCS1B01G009500 chr1A 3656272 3657322 1050 True 1151.000000 1151 86.553000 1012 2059 1 chr1A.!!$R2 1047
15 TraesCS1B01G009500 chr1D 448110 450643 2533 False 2691.000000 2691 85.967000 1826 4347 1 chr1D.!!$F1 2521
16 TraesCS1B01G009500 chr1D 617688 619982 2294 True 2645.000000 2645 87.624000 2057 4342 1 chr1D.!!$R1 2285
17 TraesCS1B01G009500 chr1D 494546828 494550729 3901 False 1947.500000 3616 85.274000 854 4618 2 chr1D.!!$F3 3764
18 TraesCS1B01G009500 chr1D 460069 463511 3442 False 1479.000000 2625 83.992500 1794 5151 2 chr1D.!!$F2 3357
19 TraesCS1B01G009500 chr1D 722120 723460 1340 True 1027.000000 1027 80.949000 413 1750 1 chr1D.!!$R3 1337
20 TraesCS1B01G009500 chr3D 560054646 560056954 2308 True 2628.000000 2628 87.344000 2057 4357 1 chr3D.!!$R1 2300

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
888 952 0.987294 ATGGGTTGACTGAGGACCTG 59.013 55.0 0.00 0.0 33.90 4.00 F
1041 1135 0.108585 TGGTGTTGTGCCTCCTCTTC 59.891 55.0 0.00 0.0 0.00 2.87 F
1157 1251 0.464013 CAGATGAGCTCTTGGCAGGG 60.464 60.0 16.19 0.0 44.79 4.45 F
3036 3279 0.963962 CCTTTGCAAGCATGGTGAGT 59.036 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2750 1.279271 AGCTGGTTACTTGCACCTAGG 59.721 52.381 7.41 7.41 35.07 3.02 R
2925 3168 1.153147 TTGCGGCAACACACCACTA 60.153 52.632 12.11 0.00 0.00 2.74 R
3079 3322 0.034896 AGTAGCCGTGTTGTTGGGAG 59.965 55.000 0.00 0.00 0.00 4.30 R
4591 5431 0.947180 ACAACGTGTCGTATGTGGGC 60.947 55.000 0.00 0.00 39.99 5.36 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
46 47 8.960591 CCAGACACCTAAAGATTTGTGATTAAT 58.039 33.333 0.00 0.00 33.08 1.40
65 66 8.573035 TGATTAATTAGTTGGTTTTGTGGAGTC 58.427 33.333 0.00 0.00 0.00 3.36
124 125 8.695456 ACCAAAGTGTCATTTTCAAAGTTATCT 58.305 29.630 0.00 0.00 0.00 1.98
170 171 5.564048 ACCGAAAGCACTAGTAGTAGAAG 57.436 43.478 11.68 4.79 0.00 2.85
171 172 5.008980 ACCGAAAGCACTAGTAGTAGAAGT 58.991 41.667 11.68 0.00 0.00 3.01
172 173 5.476254 ACCGAAAGCACTAGTAGTAGAAGTT 59.524 40.000 11.68 0.00 0.00 2.66
173 174 6.015603 ACCGAAAGCACTAGTAGTAGAAGTTT 60.016 38.462 11.68 6.97 0.00 2.66
174 175 7.175641 ACCGAAAGCACTAGTAGTAGAAGTTTA 59.824 37.037 11.68 0.00 0.00 2.01
314 315 2.624838 ACATGGCTTCCAACAAGACTTG 59.375 45.455 13.77 13.77 36.95 3.16
342 343 7.136289 TCCACGATTGTATTAACCAAAACTC 57.864 36.000 0.00 0.00 0.00 3.01
360 361 9.981114 CCAAAACTCAACATAGAAACCTTTATT 57.019 29.630 0.00 0.00 0.00 1.40
462 516 8.984891 TGGAATTGATACAACTTTAGCATTTG 57.015 30.769 0.00 0.00 0.00 2.32
621 676 4.533919 ATGATCAGTAGGAGTATGCTGC 57.466 45.455 0.09 0.00 37.36 5.25
648 703 2.982488 CCCTTATATCCCTGCCTTCACT 59.018 50.000 0.00 0.00 0.00 3.41
664 719 5.561725 GCCTTCACTCTTCACTTGCTTAAAG 60.562 44.000 0.00 0.00 42.07 1.85
681 737 8.846943 TGCTTAAAGAAATAAGTCATGACTCA 57.153 30.769 28.01 15.68 41.58 3.41
769 825 4.700692 ACAAAGAGATAGCGACAGACACTA 59.299 41.667 0.00 0.00 0.00 2.74
770 826 5.183331 ACAAAGAGATAGCGACAGACACTAA 59.817 40.000 0.00 0.00 0.00 2.24
824 888 1.159713 TGTTGTGCAGCTTCCACTCG 61.160 55.000 13.67 0.00 34.38 4.18
827 891 1.300931 GTGCAGCTTCCACTCGACA 60.301 57.895 6.96 0.00 0.00 4.35
836 900 3.403038 CTTCCACTCGACACCTTTTCAT 58.597 45.455 0.00 0.00 0.00 2.57
837 901 3.040147 TCCACTCGACACCTTTTCATC 57.960 47.619 0.00 0.00 0.00 2.92
839 903 2.738846 CCACTCGACACCTTTTCATCAG 59.261 50.000 0.00 0.00 0.00 2.90
862 926 7.962918 TCAGAAAAGAAAGAAAACTTTCACTCG 59.037 33.333 19.85 11.31 43.60 4.18
869 933 4.448210 AGAAAACTTTCACTCGGCTGTTA 58.552 39.130 5.07 0.00 39.61 2.41
872 936 2.699954 ACTTTCACTCGGCTGTTATGG 58.300 47.619 0.00 0.00 0.00 2.74
888 952 0.987294 ATGGGTTGACTGAGGACCTG 59.013 55.000 0.00 0.00 33.90 4.00
893 957 2.572104 GGTTGACTGAGGACCTGGTAAT 59.428 50.000 0.00 0.00 0.00 1.89
898 962 5.277250 TGACTGAGGACCTGGTAATAATGA 58.723 41.667 0.00 0.00 0.00 2.57
902 966 4.141801 TGAGGACCTGGTAATAATGAACGG 60.142 45.833 0.00 0.00 0.00 4.44
934 998 7.390440 TGGTTAAATACTCATCAACAGAGTTGG 59.610 37.037 9.72 0.00 43.47 3.77
937 1001 7.856145 AAATACTCATCAACAGAGTTGGATC 57.144 36.000 9.72 0.00 43.47 3.36
992 1071 2.491693 TCCCGAATTCCAGATGCAAAAC 59.508 45.455 0.00 0.00 0.00 2.43
1005 1096 2.414806 TGCAAAACGCGACCTATGTTA 58.585 42.857 15.93 0.00 46.97 2.41
1019 1110 5.712752 ACCTATGTTATACCTCTGCCTACA 58.287 41.667 0.00 0.00 0.00 2.74
1035 1126 0.250295 TACAGCTGGTGTTGTGCCTC 60.250 55.000 19.93 0.00 40.94 4.70
1041 1135 0.108585 TGGTGTTGTGCCTCCTCTTC 59.891 55.000 0.00 0.00 0.00 2.87
1048 1142 1.774254 TGTGCCTCCTCTTCCAAGAAA 59.226 47.619 0.00 0.00 34.03 2.52
1049 1143 2.224621 TGTGCCTCCTCTTCCAAGAAAG 60.225 50.000 0.00 0.00 34.03 2.62
1107 1201 1.856539 AACACATGGCCCTCCTCCAG 61.857 60.000 0.00 0.00 36.98 3.86
1119 1213 1.208293 CTCCTCCAGTGGAAAGCTACC 59.792 57.143 14.17 3.27 35.43 3.18
1157 1251 0.464013 CAGATGAGCTCTTGGCAGGG 60.464 60.000 16.19 0.00 44.79 4.45
1215 1309 2.672996 GCTGTTCACCATGGCCGT 60.673 61.111 13.04 0.00 0.00 5.68
1220 1314 1.082117 GTTCACCATGGCCGTCGTAG 61.082 60.000 13.04 0.00 0.00 3.51
1233 1327 2.364579 CGTAGGCCCTGGGTGGTA 60.365 66.667 15.56 0.55 0.00 3.25
1252 1346 1.488705 AACCAACATCTCCCTGCCGA 61.489 55.000 0.00 0.00 0.00 5.54
1338 1433 1.869767 GACCTCAGCAACAACAGTCTG 59.130 52.381 0.00 0.00 0.00 3.51
1391 1486 4.307432 CTGACATCACTTTCGGTACTTGT 58.693 43.478 0.00 0.00 0.00 3.16
1444 1539 2.579873 CTTATGAGATTGGTGGCCTGG 58.420 52.381 3.32 0.00 0.00 4.45
1507 1602 2.636893 GGACATATCCCTGCATCTCTGT 59.363 50.000 0.00 0.00 39.39 3.41
1562 1657 4.307032 ACCAAAACATGCTATCAGGTCT 57.693 40.909 0.00 0.00 36.02 3.85
1570 1665 5.150715 ACATGCTATCAGGTCTCATTCCTA 58.849 41.667 0.00 0.00 30.45 2.94
1751 1846 1.676006 AGTCCGTTTGCAAGTTCTTGG 59.324 47.619 13.35 0.00 0.00 3.61
1776 1871 7.414429 GGGCTTAATTCAAATGATTTTTCAGGC 60.414 37.037 0.00 0.00 0.00 4.85
1790 1885 2.925966 TCAGGCCCAATTCCAATCTT 57.074 45.000 0.00 0.00 0.00 2.40
1796 1891 4.078980 AGGCCCAATTCCAATCTTCATAGT 60.079 41.667 0.00 0.00 0.00 2.12
1848 1943 7.807977 TCTCTATGGAAATCAAATAACAGGC 57.192 36.000 0.00 0.00 0.00 4.85
1851 1946 4.963276 TGGAAATCAAATAACAGGCTCG 57.037 40.909 0.00 0.00 0.00 5.03
1869 1964 1.854939 TCGATACCCCCAGAACTAGGA 59.145 52.381 0.00 0.00 0.00 2.94
1894 1989 4.081309 ACCTCGCTATGCTAAACCAACTTA 60.081 41.667 0.00 0.00 0.00 2.24
1921 2016 7.485810 TCTCGACGAAAATCAAATATCTGGTA 58.514 34.615 0.00 0.00 0.00 3.25
1962 2057 4.051922 GGAACCTCACTATGCTCAATACG 58.948 47.826 0.00 0.00 0.00 3.06
1963 2058 4.441634 GGAACCTCACTATGCTCAATACGT 60.442 45.833 0.00 0.00 0.00 3.57
1966 2061 6.216801 ACCTCACTATGCTCAATACGTTTA 57.783 37.500 0.00 0.00 0.00 2.01
1973 2068 7.702772 CACTATGCTCAATACGTTTACTCTCTT 59.297 37.037 0.00 0.00 0.00 2.85
1974 2069 8.900781 ACTATGCTCAATACGTTTACTCTCTTA 58.099 33.333 0.00 0.00 0.00 2.10
2002 2097 3.525609 TCAAATCACAGGCCCAATACCTA 59.474 43.478 0.00 0.00 35.10 3.08
2034 2129 2.614520 CAGCTTGCTGAATCTCCAGATG 59.385 50.000 16.78 0.00 36.29 2.90
2065 2304 3.819902 GTCCAACAACCAAATAACCGGTA 59.180 43.478 8.00 0.00 33.17 4.02
2104 2343 4.693283 TGGCAATCTAATGAACCTCGTAG 58.307 43.478 0.00 0.00 0.00 3.51
2169 2408 3.541996 ACTTTTGGGAAGTTGCAAAGG 57.458 42.857 0.00 6.19 0.00 3.11
2170 2409 2.212652 CTTTTGGGAAGTTGCAAAGGC 58.787 47.619 0.00 0.00 41.68 4.35
2264 2503 2.031120 TGTTGAACTTGGGCTGGAAAG 58.969 47.619 0.00 0.00 0.00 2.62
2265 2504 2.306847 GTTGAACTTGGGCTGGAAAGA 58.693 47.619 0.00 0.00 0.00 2.52
2381 2620 8.960591 CATTCCAAGGAGTTTAAAGACATGTAT 58.039 33.333 0.00 0.00 0.00 2.29
2383 2622 9.667107 TTCCAAGGAGTTTAAAGACATGTATAG 57.333 33.333 0.00 0.00 0.00 1.31
2389 2628 8.182227 GGAGTTTAAAGACATGTATAGGTTTGC 58.818 37.037 0.00 0.00 0.00 3.68
2390 2629 7.748847 AGTTTAAAGACATGTATAGGTTTGCG 58.251 34.615 0.00 0.00 0.00 4.85
2409 2648 2.350484 GCGTAAACTTTCCCTTGACAGC 60.350 50.000 0.00 0.00 0.00 4.40
2427 2666 2.808543 CAGCAACCAACTAACAGGAGAC 59.191 50.000 0.00 0.00 0.00 3.36
2444 2683 5.028802 AGGAGACATCTCTCAGGATTTTGA 58.971 41.667 8.74 0.00 44.50 2.69
2493 2732 6.543831 TGATCTTGTCATCGAATAGACTCTCA 59.456 38.462 14.45 9.91 35.81 3.27
2506 2745 1.682854 GACTCTCAGGGCAGATCTCAG 59.317 57.143 0.00 0.00 0.00 3.35
2511 2750 3.055530 TCTCAGGGCAGATCTCAGAAAAC 60.056 47.826 0.00 0.00 0.00 2.43
2536 2775 2.225727 GGTGCAAGTAACCAGCTAACAC 59.774 50.000 0.00 0.00 37.65 3.32
2537 2776 2.875933 GTGCAAGTAACCAGCTAACACA 59.124 45.455 0.00 0.00 0.00 3.72
2622 2865 7.039644 TCCAACCTAGAAGAACTAAGACTTGAG 60.040 40.741 0.00 0.00 0.00 3.02
2624 2867 8.794553 CAACCTAGAAGAACTAAGACTTGAGTA 58.205 37.037 0.00 0.00 0.00 2.59
2643 2886 5.301805 TGAGTATAATCATCTCAGCGGTGAA 59.698 40.000 19.16 10.04 34.00 3.18
2667 2910 3.030291 TCCACCAGAAATGTGCACTTTT 58.970 40.909 25.65 25.65 32.30 2.27
2709 2952 6.477688 TGAACTTATCGTCGAACCAATTATCC 59.522 38.462 0.00 0.00 0.00 2.59
2712 2955 1.202440 TCGTCGAACCAATTATCCGGG 60.202 52.381 0.00 0.00 0.00 5.73
2715 2958 2.112998 TCGAACCAATTATCCGGGTCT 58.887 47.619 0.00 0.00 36.81 3.85
2807 3050 5.492565 TCAATACCTAAGGAACTAGGGGA 57.507 43.478 0.00 0.00 38.49 4.81
2816 3059 1.139853 GGAACTAGGGGACTGCATGAG 59.860 57.143 0.00 0.00 43.88 2.90
2847 3090 9.868277 TTGTTCTTAAAGATCAACAACAACAAT 57.132 25.926 0.00 0.00 34.56 2.71
2925 3168 6.942576 AGTTAGATGTGAGCAACAATAACCTT 59.057 34.615 17.80 6.94 43.61 3.50
2974 3217 6.069673 TGGGAAGTTGGAGATGCTAGAATTTA 60.070 38.462 0.00 0.00 0.00 1.40
3036 3279 0.963962 CCTTTGCAAGCATGGTGAGT 59.036 50.000 0.00 0.00 0.00 3.41
3151 3394 0.179043 TAAAGGTCTGTGCGGCAACA 60.179 50.000 3.23 4.64 0.00 3.33
3160 3403 2.747460 GCGGCAACATCTCTGGCA 60.747 61.111 0.00 0.00 39.23 4.92
3163 3406 0.745486 CGGCAACATCTCTGGCATGA 60.745 55.000 0.00 0.00 39.23 3.07
3315 3558 6.456795 AACAAGAGAAAACCTCAAGAAAGG 57.543 37.500 0.00 0.00 44.40 3.11
3328 3571 4.787551 TCAAGAAAGGGTTACTGCTGAAA 58.212 39.130 0.00 0.00 0.00 2.69
3344 3587 4.195416 GCTGAAAGAAGGGACCTATTCTG 58.805 47.826 11.70 11.08 35.95 3.02
3452 3695 3.491104 GGAGGATACGGCAAAGTCTACAG 60.491 52.174 0.00 0.00 46.39 2.74
3463 3706 0.603569 AGTCTACAGGGCACAACTCG 59.396 55.000 0.00 0.00 0.00 4.18
3608 3854 2.037641 TGTATGGATTCTGCTCCCATCG 59.962 50.000 0.00 0.00 40.77 3.84
3631 3877 9.764363 ATCGAGCATATAAATTTCTTGTCTACA 57.236 29.630 0.00 0.00 0.00 2.74
3682 3928 6.604795 CAGGACATTGGAAAATGAGGAACTAT 59.395 38.462 5.49 0.00 41.55 2.12
4253 4606 0.251077 CTTCTCCACAAGCAAGGCCT 60.251 55.000 0.00 0.00 0.00 5.19
4329 4682 3.343972 TGCCTTTCAGCGCACTTC 58.656 55.556 11.47 0.00 34.65 3.01
4348 5178 5.050567 CACTTCCGTTACAACAAGTAAGGAC 60.051 44.000 8.71 0.00 46.40 3.85
4377 5207 6.051074 TGATGACTCATTGTATGTCCATGTC 58.949 40.000 0.00 0.00 0.00 3.06
4404 5234 6.239396 TGTAGCCACTCTCCTGATATAGTAC 58.761 44.000 0.00 0.00 0.00 2.73
4417 5247 7.397476 TCCTGATATAGTACAAGATCACCATCC 59.603 40.741 0.00 0.00 0.00 3.51
4533 5366 9.571810 TTCTGACAATGCACAATATAATTTGTC 57.428 29.630 14.20 14.20 37.73 3.18
4624 5464 0.234884 CGTTGTTTCGGCTGTTCTCC 59.765 55.000 0.00 0.00 0.00 3.71
4719 5683 4.031426 CGGTCACGCTTTATTGTTCTCTAC 59.969 45.833 0.00 0.00 0.00 2.59
4720 5684 4.927425 GGTCACGCTTTATTGTTCTCTACA 59.073 41.667 0.00 0.00 34.12 2.74
5041 6029 9.023962 ACAAAGATGCAACCTAAGATGAAATTA 57.976 29.630 0.00 0.00 0.00 1.40
5181 6932 8.807118 TCAGAGACATACTAAGAACAAGATGTT 58.193 33.333 0.00 0.00 44.37 2.71
5221 6972 4.220602 AGCTCCATTTACCATTGTTCAACC 59.779 41.667 0.00 0.00 0.00 3.77
5248 6999 5.614308 TGCAGTGGTATATGAGGAAAGATG 58.386 41.667 0.00 0.00 0.00 2.90
5292 7045 1.000827 CAAAGCGCCAACCATGTACAA 60.001 47.619 2.29 0.00 0.00 2.41
5354 7107 4.329801 TCAGATACGAATTGATGTGTGTGC 59.670 41.667 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.991861 TGTAGACTCCACAAAACCAACTAA 58.008 37.500 0.00 0.00 0.00 2.24
88 89 9.959749 GAAAATGACACTTTGGTCTGTTAATTA 57.040 29.630 0.00 0.00 38.61 1.40
89 90 8.474025 TGAAAATGACACTTTGGTCTGTTAATT 58.526 29.630 0.00 0.00 38.61 1.40
90 91 8.006298 TGAAAATGACACTTTGGTCTGTTAAT 57.994 30.769 0.00 0.00 38.61 1.40
124 125 0.608856 ATCCAACACAATGGCTCGCA 60.609 50.000 0.00 0.00 40.46 5.10
170 171 3.816523 TCAAGTGGGTTGATTCGGTAAAC 59.183 43.478 0.00 0.00 40.45 2.01
171 172 4.069304 CTCAAGTGGGTTGATTCGGTAAA 58.931 43.478 0.00 0.00 44.44 2.01
172 173 3.670625 CTCAAGTGGGTTGATTCGGTAA 58.329 45.455 0.00 0.00 44.44 2.85
173 174 2.614481 GCTCAAGTGGGTTGATTCGGTA 60.614 50.000 0.00 0.00 44.44 4.02
174 175 1.882352 GCTCAAGTGGGTTGATTCGGT 60.882 52.381 0.00 0.00 44.44 4.69
314 315 6.687081 TTGGTTAATACAATCGTGGATTCC 57.313 37.500 0.00 0.00 37.68 3.01
387 388 4.627467 CAGTAACTGTCAGGGAAAATCTCG 59.373 45.833 4.53 0.00 0.00 4.04
390 391 7.117956 GTCTTACAGTAACTGTCAGGGAAAATC 59.882 40.741 4.53 0.00 41.21 2.17
462 516 4.168760 GTTTATCTGACCATGCAACTTGC 58.831 43.478 6.82 6.82 45.29 4.01
506 561 6.662865 TCTCATTTGATGGTATCTCCTCTC 57.337 41.667 0.00 0.00 37.07 3.20
610 665 1.069258 GGTACCCGCAGCATACTCC 59.931 63.158 0.00 0.00 0.00 3.85
611 666 4.752514 GGTACCCGCAGCATACTC 57.247 61.111 0.00 0.00 0.00 2.59
635 690 0.687354 GTGAAGAGTGAAGGCAGGGA 59.313 55.000 0.00 0.00 0.00 4.20
636 691 0.689623 AGTGAAGAGTGAAGGCAGGG 59.310 55.000 0.00 0.00 0.00 4.45
648 703 9.337396 TGACTTATTTCTTTAAGCAAGTGAAGA 57.663 29.630 6.06 0.00 33.34 2.87
664 719 9.376075 TCTTTCTCATGAGTCATGACTTATTTC 57.624 33.333 28.18 16.19 44.60 2.17
681 737 6.694445 TCTCTTCCTCCTTTTCTTTCTCAT 57.306 37.500 0.00 0.00 0.00 2.90
847 911 2.919228 ACAGCCGAGTGAAAGTTTTCT 58.081 42.857 6.21 0.00 38.02 2.52
848 912 3.692791 AACAGCCGAGTGAAAGTTTTC 57.307 42.857 0.00 0.00 37.69 2.29
849 913 4.023193 CCATAACAGCCGAGTGAAAGTTTT 60.023 41.667 0.00 0.00 0.00 2.43
850 914 3.502211 CCATAACAGCCGAGTGAAAGTTT 59.498 43.478 0.00 0.00 0.00 2.66
851 915 3.074412 CCATAACAGCCGAGTGAAAGTT 58.926 45.455 0.00 0.00 0.00 2.66
852 916 2.615493 CCCATAACAGCCGAGTGAAAGT 60.615 50.000 0.00 0.00 0.00 2.66
856 920 0.981183 AACCCATAACAGCCGAGTGA 59.019 50.000 0.00 0.00 0.00 3.41
862 926 2.359900 CTCAGTCAACCCATAACAGCC 58.640 52.381 0.00 0.00 0.00 4.85
869 933 0.987294 CAGGTCCTCAGTCAACCCAT 59.013 55.000 0.00 0.00 33.33 4.00
872 936 1.640917 TACCAGGTCCTCAGTCAACC 58.359 55.000 0.00 0.00 0.00 3.77
888 952 3.064820 CCAGTGTGCCGTTCATTATTACC 59.935 47.826 0.00 0.00 0.00 2.85
893 957 2.264005 AACCAGTGTGCCGTTCATTA 57.736 45.000 0.00 0.00 0.00 1.90
898 962 3.746940 AGTATTTAACCAGTGTGCCGTT 58.253 40.909 0.00 0.00 0.00 4.44
902 966 6.072728 TGTTGATGAGTATTTAACCAGTGTGC 60.073 38.462 0.00 0.00 0.00 4.57
934 998 3.560068 GGGGTGTGATTCAATACACGATC 59.440 47.826 0.00 0.00 46.13 3.69
937 1001 2.014128 GGGGGTGTGATTCAATACACG 58.986 52.381 0.00 0.00 46.13 4.49
963 1027 3.343617 TCTGGAATTCGGGAATGTGTTC 58.656 45.455 0.00 0.00 0.00 3.18
992 1071 3.822996 CAGAGGTATAACATAGGTCGCG 58.177 50.000 0.00 0.00 0.00 5.87
1005 1096 1.343478 ACCAGCTGTAGGCAGAGGTAT 60.343 52.381 13.81 0.00 44.91 2.73
1019 1110 2.113986 GGAGGCACAACACCAGCT 59.886 61.111 0.00 0.00 0.00 4.24
1035 1126 2.417933 CGCATGTCTTTCTTGGAAGAGG 59.582 50.000 0.00 0.00 36.39 3.69
1041 1135 1.135315 CGCCGCATGTCTTTCTTGG 59.865 57.895 0.00 0.00 0.00 3.61
1048 1142 4.783621 ATGGTGCGCCGCATGTCT 62.784 61.111 17.54 0.00 41.91 3.41
1049 1143 4.541482 CATGGTGCGCCGCATGTC 62.541 66.667 17.54 9.11 41.91 3.06
1073 1167 2.849942 TGTGTTGAGACCTCATTGTGG 58.150 47.619 3.21 3.21 39.64 4.17
1075 1169 3.415212 CCATGTGTTGAGACCTCATTGT 58.585 45.455 0.01 0.00 39.64 2.71
1078 1172 1.340405 GGCCATGTGTTGAGACCTCAT 60.340 52.381 0.00 0.00 39.64 2.90
1107 1201 0.321298 TCGCAAGGGTAGCTTTCCAC 60.321 55.000 0.00 0.00 38.47 4.02
1157 1251 0.249447 GTTGCAAGGGCTGGTGTTTC 60.249 55.000 0.00 0.00 41.91 2.78
1170 1264 1.971167 GATGCCCGTCCAGTTGCAA 60.971 57.895 0.00 0.00 37.27 4.08
1215 1309 2.458969 TTACCACCCAGGGCCTACGA 62.459 60.000 5.28 0.00 43.89 3.43
1220 1314 2.847650 TTGGTTACCACCCAGGGCC 61.848 63.158 4.91 0.00 43.49 5.80
1233 1327 1.002134 CGGCAGGGAGATGTTGGTT 60.002 57.895 0.00 0.00 0.00 3.67
1252 1346 3.142838 GCCACGGATGCCAGCATT 61.143 61.111 6.57 0.00 36.70 3.56
1355 1450 3.891977 TGATGTCAGGGAGCTGATACTAC 59.108 47.826 0.00 0.00 35.65 2.73
1391 1486 0.108585 GAGCTGGTTGTGGTGAAGGA 59.891 55.000 0.00 0.00 0.00 3.36
1444 1539 4.574892 AGCTCAAGAAGGCTTAGACTTTC 58.425 43.478 0.30 0.00 34.96 2.62
1507 1602 9.787435 AAGATCAGTTAACATTGTTAGGTTACA 57.213 29.630 8.61 0.00 30.90 2.41
1540 1635 4.666512 AGACCTGATAGCATGTTTTGGTT 58.333 39.130 0.00 0.00 37.26 3.67
1562 1657 4.141390 GCCTTCCAATCTCCTTAGGAATGA 60.141 45.833 1.41 0.00 39.26 2.57
1570 1665 2.376518 TGACAAGCCTTCCAATCTCCTT 59.623 45.455 0.00 0.00 0.00 3.36
1751 1846 7.414429 GGCCTGAAAAATCATTTGAATTAAGCC 60.414 37.037 0.00 0.00 0.00 4.35
1776 1871 7.504911 AGATTGACTATGAAGATTGGAATTGGG 59.495 37.037 0.00 0.00 0.00 4.12
1790 1885 8.417106 GGTTCATCTTAGTGAGATTGACTATGA 58.583 37.037 0.00 0.00 42.55 2.15
1796 1891 5.423015 GCTGGTTCATCTTAGTGAGATTGA 58.577 41.667 0.00 0.00 42.55 2.57
1848 1943 2.158505 TCCTAGTTCTGGGGGTATCGAG 60.159 54.545 2.55 0.00 0.00 4.04
1851 1946 3.136077 GGTTTCCTAGTTCTGGGGGTATC 59.864 52.174 2.55 0.00 0.00 2.24
1869 1964 3.343941 TGGTTTAGCATAGCGAGGTTT 57.656 42.857 0.00 0.00 0.00 3.27
1894 1989 7.495934 ACCAGATATTTGATTTTCGTCGAGAAT 59.504 33.333 10.51 10.51 38.86 2.40
1921 2016 3.798515 TCCCTAGTTCTGGTGGTATTGT 58.201 45.455 0.00 0.00 0.00 2.71
1966 2061 7.308830 GCCTGTGATTTGATTTGTTAAGAGAGT 60.309 37.037 0.00 0.00 0.00 3.24
1973 2068 4.155709 TGGGCCTGTGATTTGATTTGTTA 58.844 39.130 4.53 0.00 0.00 2.41
1974 2069 2.971330 TGGGCCTGTGATTTGATTTGTT 59.029 40.909 4.53 0.00 0.00 2.83
2002 2097 2.029623 CAGCAAGCTGCCCAATTCTAT 58.970 47.619 9.36 0.00 46.52 1.98
2015 2110 2.641305 ACATCTGGAGATTCAGCAAGC 58.359 47.619 0.00 0.00 34.91 4.01
2034 2129 5.570234 TTTGGTTGTTGGACAAGTCTAAC 57.430 39.130 18.80 18.80 46.88 2.34
2112 2351 4.218417 CCCGAAATTTGGTTCAGAGACAAT 59.782 41.667 0.00 0.00 0.00 2.71
2169 2408 1.889545 AGAGTTCCAGACTTTGCAGC 58.110 50.000 0.00 0.00 39.19 5.25
2170 2409 3.470709 TGAAGAGTTCCAGACTTTGCAG 58.529 45.455 0.00 0.00 39.19 4.41
2178 2417 9.436957 GATAACTTGTTATTGAAGAGTTCCAGA 57.563 33.333 7.35 0.00 33.13 3.86
2264 2503 5.238868 GGTAAAGGTCCTGAAAGTGAGTTTC 59.761 44.000 5.82 5.82 44.41 2.78
2265 2504 5.131067 GGTAAAGGTCCTGAAAGTGAGTTT 58.869 41.667 0.00 0.00 0.00 2.66
2381 2620 4.089408 AGGGAAAGTTTACGCAAACCTA 57.911 40.909 7.64 0.00 44.32 3.08
2383 2622 3.067040 TCAAGGGAAAGTTTACGCAAACC 59.933 43.478 7.64 0.00 44.32 3.27
2389 2628 2.875933 TGCTGTCAAGGGAAAGTTTACG 59.124 45.455 0.00 0.00 30.44 3.18
2390 2629 4.499188 GGTTGCTGTCAAGGGAAAGTTTAC 60.499 45.833 0.00 0.00 30.44 2.01
2409 2648 4.899502 AGATGTCTCCTGTTAGTTGGTTG 58.100 43.478 0.00 0.00 0.00 3.77
2427 2666 7.172875 GGATACACATCAAAATCCTGAGAGATG 59.827 40.741 0.00 0.00 38.92 2.90
2493 2732 2.273619 AGGTTTTCTGAGATCTGCCCT 58.726 47.619 0.00 0.00 0.00 5.19
2506 2745 4.139038 TGGTTACTTGCACCTAGGTTTTC 58.861 43.478 13.15 5.13 35.07 2.29
2511 2750 1.279271 AGCTGGTTACTTGCACCTAGG 59.721 52.381 7.41 7.41 35.07 3.02
2622 2865 7.360438 GGAATTTCACCGCTGAGATGATTATAC 60.360 40.741 0.00 0.00 0.00 1.47
2624 2867 5.471456 GGAATTTCACCGCTGAGATGATTAT 59.529 40.000 0.00 0.00 0.00 1.28
2643 2886 3.233507 AGTGCACATTTCTGGTGGAATT 58.766 40.909 21.04 0.00 38.35 2.17
2667 2910 8.681486 ATAAGTTCAGCACATATAGATTTGCA 57.319 30.769 10.82 0.00 40.58 4.08
2681 2924 2.029739 TGGTTCGACGATAAGTTCAGCA 60.030 45.455 0.00 0.00 0.00 4.41
2682 2925 2.602878 TGGTTCGACGATAAGTTCAGC 58.397 47.619 0.00 0.00 0.00 4.26
2712 2955 8.852135 AGCTTTTCTATCTGTGTAGGTATAGAC 58.148 37.037 0.00 0.00 32.19 2.59
2715 2958 8.762481 TCAGCTTTTCTATCTGTGTAGGTATA 57.238 34.615 0.00 0.00 0.00 1.47
2807 3050 8.097038 TCTTTAAGAACAATAGTCTCATGCAGT 58.903 33.333 0.00 0.00 0.00 4.40
2865 3108 5.678107 GCCTGCTAAATTTCCAATCTCACTG 60.678 44.000 0.00 0.00 0.00 3.66
2866 3109 4.400567 GCCTGCTAAATTTCCAATCTCACT 59.599 41.667 0.00 0.00 0.00 3.41
2870 3113 3.703052 CAGGCCTGCTAAATTTCCAATCT 59.297 43.478 22.33 0.00 0.00 2.40
2900 3143 6.476378 AGGTTATTGTTGCTCACATCTAACT 58.524 36.000 14.84 2.43 35.79 2.24
2925 3168 1.153147 TTGCGGCAACACACCACTA 60.153 52.632 12.11 0.00 0.00 2.74
3079 3322 0.034896 AGTAGCCGTGTTGTTGGGAG 59.965 55.000 0.00 0.00 0.00 4.30
3151 3394 1.632409 ACAAGGTGTCATGCCAGAGAT 59.368 47.619 0.00 0.00 0.00 2.75
3160 3403 5.630121 TGGAGTTGAATAACAAGGTGTCAT 58.370 37.500 0.00 0.00 39.30 3.06
3163 3406 5.048846 ACTGGAGTTGAATAACAAGGTGT 57.951 39.130 0.00 0.00 39.30 4.16
3315 3558 3.075148 GTCCCTTCTTTCAGCAGTAACC 58.925 50.000 0.00 0.00 0.00 2.85
3328 3571 4.263506 CCAAACACAGAATAGGTCCCTTCT 60.264 45.833 0.00 0.00 31.97 2.85
3344 3587 7.967890 AATCTTCCATCAAAATTCCAAACAC 57.032 32.000 0.00 0.00 0.00 3.32
3452 3695 1.026718 CCCATCTTCGAGTTGTGCCC 61.027 60.000 0.00 0.00 0.00 5.36
3463 3706 1.941999 GCAACCAGCTGCCCATCTTC 61.942 60.000 8.66 0.00 41.15 2.87
3631 3877 2.619074 GGCTTCCCTGCTGAATGTAGTT 60.619 50.000 0.00 0.00 0.00 2.24
3682 3928 2.238521 GTGCCAATCCAGTTCCTTTGA 58.761 47.619 0.00 0.00 0.00 2.69
4329 4682 3.641648 TCGTCCTTACTTGTTGTAACGG 58.358 45.455 0.00 0.00 36.33 4.44
4377 5207 3.902881 ATCAGGAGAGTGGCTACAAAG 57.097 47.619 2.02 0.00 0.00 2.77
4404 5234 1.386533 GGCACAGGATGGTGATCTTG 58.613 55.000 0.00 0.00 43.62 3.02
4533 5366 3.069443 ACATTTTACAAGCACCCCACAAG 59.931 43.478 0.00 0.00 0.00 3.16
4591 5431 0.947180 ACAACGTGTCGTATGTGGGC 60.947 55.000 0.00 0.00 39.99 5.36
4624 5464 7.442364 CCATATCAAGTACCCTTGTAGAATGTG 59.558 40.741 2.69 0.00 46.70 3.21
4740 5719 2.293122 TGTGATTTTTCCTGCTTGGTCG 59.707 45.455 0.00 0.00 37.07 4.79
4858 5839 4.619863 GCCGTACAATCCTCTGTAAGTCAA 60.620 45.833 0.00 0.00 33.66 3.18
5041 6029 6.884295 TGTTTAGCTTGTATTAGGCATGAAGT 59.116 34.615 0.00 0.00 33.01 3.01
5181 6932 7.946381 ATGGAGCTATTCTCTATACGATTGA 57.054 36.000 0.00 0.00 40.67 2.57
5248 6999 3.327626 TGTGCATGGACAAATTCATTGC 58.672 40.909 18.56 0.00 43.13 3.56
5292 7045 5.045578 AGCTATGGTGTAGGTTTGATCTTGT 60.046 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.