Multiple sequence alignment - TraesCS6D01G377300

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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 TraesCS6D01G377300 chr6D 100.000 9049 0 0 1 9049 459917521 459926569 0.000000e+00 16711.0
1 TraesCS6D01G377300 chr6D 89.072 1153 114 9 6994 8140 459840923 459842069 0.000000e+00 1421.0
2 TraesCS6D01G377300 chr6D 88.700 1000 89 13 2350 3346 459919558 459920536 0.000000e+00 1199.0
3 TraesCS6D01G377300 chr6D 88.700 1000 89 13 2038 3016 459919870 459920866 0.000000e+00 1199.0
4 TraesCS6D01G377300 chr6D 83.650 1107 126 30 3986 5045 459837904 459839002 0.000000e+00 990.0
5 TraesCS6D01G377300 chr6D 84.366 710 78 17 2644 3346 459919524 459920207 0.000000e+00 665.0
6 TraesCS6D01G377300 chr6D 86.521 549 52 12 6052 6585 459839898 459840439 1.310000e-162 584.0
7 TraesCS6D01G377300 chr6D 89.577 355 35 2 6648 7001 459840538 459840891 4.980000e-122 449.0
8 TraesCS6D01G377300 chr6D 88.961 308 28 3 5752 6056 459839517 459839821 8.580000e-100 375.0
9 TraesCS6D01G377300 chr6D 83.539 243 25 9 5520 5758 459839243 459839474 7.120000e-51 213.0
10 TraesCS6D01G377300 chr6D 80.569 211 34 5 8227 8431 468079668 468079459 1.220000e-33 156.0
11 TraesCS6D01G377300 chr6D 86.667 105 6 1 6935 7031 459910605 459910709 9.610000e-20 110.0
12 TraesCS6D01G377300 chr6B 89.869 3435 188 65 1 3346 699534330 699537693 0.000000e+00 4268.0
13 TraesCS6D01G377300 chr6B 91.699 3072 175 30 298 3352 699590263 699593271 0.000000e+00 4187.0
14 TraesCS6D01G377300 chr6B 92.274 2071 101 18 3345 5368 699538092 699540150 0.000000e+00 2883.0
15 TraesCS6D01G377300 chr6B 94.966 1311 64 2 5366 6676 699540187 699541495 0.000000e+00 2054.0
16 TraesCS6D01G377300 chr6B 93.522 988 62 2 5690 6676 699605311 699606297 0.000000e+00 1469.0
17 TraesCS6D01G377300 chr6B 91.431 1097 52 14 6664 7758 699541779 699542835 0.000000e+00 1467.0
18 TraesCS6D01G377300 chr6B 88.985 1153 106 11 2078 3220 699536756 699537897 0.000000e+00 1406.0
19 TraesCS6D01G377300 chr6B 88.031 1153 126 9 6994 8140 699204608 699205754 0.000000e+00 1354.0
20 TraesCS6D01G377300 chr6B 86.548 1234 134 23 2004 3220 699592251 699593469 0.000000e+00 1330.0
21 TraesCS6D01G377300 chr6B 88.980 1098 78 16 7962 9035 699542841 699543919 0.000000e+00 1317.0
22 TraesCS6D01G377300 chr6B 92.484 918 60 3 7013 7927 699606760 699607671 0.000000e+00 1304.0
23 TraesCS6D01G377300 chr6B 88.756 1005 85 11 2350 3346 699536386 699537370 0.000000e+00 1205.0
24 TraesCS6D01G377300 chr6B 87.802 951 89 8 2396 3344 699592009 699592934 0.000000e+00 1088.0
25 TraesCS6D01G377300 chr6B 83.679 1109 124 32 3986 5045 699201604 699202704 0.000000e+00 992.0
26 TraesCS6D01G377300 chr6B 84.178 986 108 30 6052 7001 699203603 699204576 0.000000e+00 913.0
27 TraesCS6D01G377300 chr6B 84.667 900 117 15 2004 2890 699537006 699537897 0.000000e+00 878.0
28 TraesCS6D01G377300 chr6B 92.734 523 27 4 3838 4353 699603418 699603936 0.000000e+00 745.0
29 TraesCS6D01G377300 chr6B 85.714 714 53 13 4345 5032 699604618 699605308 0.000000e+00 708.0
30 TraesCS6D01G377300 chr6B 91.321 507 34 5 3345 3842 699593665 699594170 0.000000e+00 684.0
31 TraesCS6D01G377300 chr6B 87.987 308 31 3 5752 6056 699203222 699203526 8.640000e-95 359.0
32 TraesCS6D01G377300 chr6B 96.000 200 5 3 6658 6855 699606563 699606761 1.130000e-83 322.0
33 TraesCS6D01G377300 chr6B 87.407 270 23 3 1 259 699573771 699574040 5.310000e-77 300.0
34 TraesCS6D01G377300 chr6B 87.156 218 20 2 7923 8140 699609932 699610141 3.260000e-59 241.0
35 TraesCS6D01G377300 chr6B 83.654 104 9 1 6936 7031 699463988 699464091 3.480000e-14 91.6
36 TraesCS6D01G377300 chr6A 93.651 2284 82 26 1073 3346 605847231 605849461 0.000000e+00 3356.0
37 TraesCS6D01G377300 chr6A 95.595 2043 64 5 3345 5368 605849863 605851898 0.000000e+00 3251.0
38 TraesCS6D01G377300 chr6A 90.861 2451 123 39 1 2419 605846182 605848563 0.000000e+00 3192.0
39 TraesCS6D01G377300 chr6A 96.142 1633 52 3 6682 8309 605858429 605860055 0.000000e+00 2656.0
40 TraesCS6D01G377300 chr6A 96.432 1121 39 1 5366 6486 605851944 605853063 0.000000e+00 1847.0
41 TraesCS6D01G377300 chr6A 89.919 1111 98 9 2119 3220 605848561 605849666 0.000000e+00 1419.0
42 TraesCS6D01G377300 chr6A 87.008 1193 116 18 6994 8176 605564008 605565171 0.000000e+00 1308.0
43 TraesCS6D01G377300 chr6A 97.443 743 17 1 8307 9049 605860315 605861055 0.000000e+00 1266.0
44 TraesCS6D01G377300 chr6A 86.512 949 83 20 2399 3346 605848229 605849133 0.000000e+00 1002.0
45 TraesCS6D01G377300 chr6A 82.852 1108 135 32 3986 5045 605560980 605562080 0.000000e+00 942.0
46 TraesCS6D01G377300 chr6A 86.703 549 52 10 6052 6585 605562978 605563520 2.810000e-164 590.0
47 TraesCS6D01G377300 chr6A 79.913 692 75 33 2658 3346 605848174 605848804 4.980000e-122 449.0
48 TraesCS6D01G377300 chr6A 88.547 358 36 4 6648 7001 605563620 605563976 6.490000e-116 429.0
49 TraesCS6D01G377300 chr6A 88.350 309 29 4 5752 6056 605562596 605562901 1.860000e-96 364.0
50 TraesCS6D01G377300 chr6A 83.128 243 26 9 5520 5758 605562322 605562553 3.310000e-49 207.0
51 TraesCS6D01G377300 chr6A 81.364 220 36 3 8238 8452 109489728 109489509 3.360000e-39 174.0
52 TraesCS6D01G377300 chr6A 77.093 227 42 4 1724 1940 605560324 605560550 1.230000e-23 122.0
53 TraesCS6D01G377300 chr5D 85.952 420 45 8 1991 2398 459748056 459748473 3.880000e-118 436.0
54 TraesCS6D01G377300 chr5D 89.655 116 12 0 5253 5368 294634322 294634437 2.040000e-31 148.0
55 TraesCS6D01G377300 chr5B 86.142 267 30 5 2071 2331 564524273 564524538 1.920000e-71 281.0
56 TraesCS6D01G377300 chr5B 79.293 198 37 4 8217 8412 591550676 591550481 1.580000e-27 135.0
57 TraesCS6D01G377300 chr5B 91.935 62 5 0 2005 2066 564515932 564515993 4.500000e-13 87.9
58 TraesCS6D01G377300 chr5B 76.087 184 30 10 454 634 421503724 421503552 5.820000e-12 84.2
59 TraesCS6D01G377300 chr3A 81.974 233 35 5 8227 8452 27037714 27037482 3.330000e-44 191.0
60 TraesCS6D01G377300 chr7D 80.695 259 36 10 8203 8448 31566994 31567251 1.200000e-43 189.0
61 TraesCS6D01G377300 chr7D 75.355 211 44 7 498 704 8218029 8218235 2.690000e-15 95.3
62 TraesCS6D01G377300 chr7D 77.372 137 22 8 5047 5177 27975555 27975688 1.260000e-08 73.1
63 TraesCS6D01G377300 chr5A 90.909 121 10 1 5248 5368 387923964 387924083 2.610000e-35 161.0
64 TraesCS6D01G377300 chr7A 94.118 102 6 0 5265 5366 193561494 193561393 1.220000e-33 156.0
65 TraesCS6D01G377300 chr7A 81.679 131 19 5 5050 5177 669409938 669409810 4.470000e-18 104.0
66 TraesCS6D01G377300 chr7B 78.788 231 41 6 8218 8441 221969955 221970184 2.040000e-31 148.0
67 TraesCS6D01G377300 chr7B 90.566 106 8 2 5267 5372 656546566 656546463 1.230000e-28 139.0
68 TraesCS6D01G377300 chr4B 90.265 113 11 0 5257 5369 42400109 42399997 2.040000e-31 148.0
69 TraesCS6D01G377300 chr3B 78.298 235 39 8 8203 8426 92583712 92583479 3.410000e-29 141.0
70 TraesCS6D01G377300 chr3B 77.561 205 34 8 8254 8452 818983926 818983728 7.430000e-21 113.0
71 TraesCS6D01G377300 chr3B 80.000 130 23 3 5050 5177 156921883 156921755 9.670000e-15 93.5
72 TraesCS6D01G377300 chr4A 76.444 225 46 6 498 718 731674114 731673893 2.060000e-21 115.0
73 TraesCS6D01G377300 chr2D 80.147 136 20 5 448 582 14350821 14350692 2.690000e-15 95.3
74 TraesCS6D01G377300 chr2D 80.153 131 21 5 5050 5177 205891127 205891255 9.670000e-15 93.5
75 TraesCS6D01G377300 chr2D 79.839 124 21 4 5056 5177 451293428 451293549 4.500000e-13 87.9
76 TraesCS6D01G377300 chr1B 80.672 119 21 2 450 567 389944542 389944425 3.480000e-14 91.6
77 TraesCS6D01G377300 chr1B 96.970 33 1 0 677 709 2270305 2270273 1.000000e-03 56.5
78 TraesCS6D01G377300 chr2B 79.808 104 20 1 617 720 627066373 627066475 3.500000e-09 75.0
79 TraesCS6D01G377300 chr4D 100.000 35 0 0 455 489 47405578 47405544 2.110000e-06 65.8


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 TraesCS6D01G377300 chr6D 459917521 459926569 9048 False 16711.000000 16711 100.000000 1 9049 1 chr6D.!!$F2 9048
1 TraesCS6D01G377300 chr6D 459919524 459920866 1342 False 1021.000000 1199 87.255333 2038 3346 3 chr6D.!!$F4 1308
2 TraesCS6D01G377300 chr6D 459837904 459842069 4165 False 672.000000 1421 86.886667 3986 8140 6 chr6D.!!$F3 4154
3 TraesCS6D01G377300 chr6B 699534330 699543919 9589 False 1934.750000 4268 89.991000 1 9035 8 chr6B.!!$F4 9034
4 TraesCS6D01G377300 chr6B 699590263 699594170 3907 False 1822.250000 4187 89.342500 298 3842 4 chr6B.!!$F5 3544
5 TraesCS6D01G377300 chr6B 699201604 699205754 4150 False 904.500000 1354 85.968750 3986 8140 4 chr6B.!!$F3 4154
6 TraesCS6D01G377300 chr6B 699603418 699610141 6723 False 798.166667 1469 91.268333 3838 8140 6 chr6B.!!$F6 4302
7 TraesCS6D01G377300 chr6A 605846182 605853063 6881 False 2073.714286 3356 90.411857 1 6486 7 chr6A.!!$F2 6485
8 TraesCS6D01G377300 chr6A 605858429 605861055 2626 False 1961.000000 2656 96.792500 6682 9049 2 chr6A.!!$F3 2367
9 TraesCS6D01G377300 chr6A 605560324 605565171 4847 False 566.000000 1308 84.811571 1724 8176 7 chr6A.!!$F1 6452

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
711 746 0.179018 ATGGCCGGCTTCTACATTCC 60.179 55.000 28.56 5.64 0.00 3.01 F
1443 1513 0.108138 GCTTCCGTGTGCCTGATAGT 60.108 55.000 0.00 0.00 0.00 2.12 F
1589 1682 0.465705 TCCTTCATGATGGGCGAGTC 59.534 55.000 23.54 0.00 0.00 3.36 F
2417 2594 1.276989 TCGTTACTCATTTTCCCGCCT 59.723 47.619 0.00 0.00 0.00 5.52 F
2428 2605 1.580059 TTCCCGCCTTCTAAGATGGT 58.420 50.000 0.00 0.00 30.69 3.55 F
3389 3976 1.676746 ATGTAGGCTCGCTCGAGTAA 58.323 50.000 15.13 1.31 43.70 2.24 F
4259 4988 3.065925 GCAAGAAAGCGCCATAGAAGAAT 59.934 43.478 2.29 0.00 0.00 2.40 F
5286 6801 1.067071 GCGCAGTGGTAAAGTACTCCT 60.067 52.381 0.30 0.00 0.00 3.69 F
5533 7229 3.118811 GGATGAGAACTGAGCTAGCACTT 60.119 47.826 18.83 1.56 0.00 3.16 F
7327 9617 2.490903 GTTCATGCACTGGAAGCTCAAT 59.509 45.455 0.00 0.00 37.60 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1626 0.029300 CCAAACTGCAGACAACCACG 59.971 55.000 23.35 0.00 0.00 4.94 R
3388 3975 1.371145 CGAACCGCGCCAAAACATT 60.371 52.632 0.00 0.00 0.00 2.71 R
3389 3976 2.254051 CGAACCGCGCCAAAACAT 59.746 55.556 0.00 0.00 0.00 2.71 R
4259 4988 1.203237 TGGGCACATAGCTTAGCTGA 58.797 50.000 17.97 1.39 44.79 4.26 R
4493 5910 4.198530 TGAGAATTTATTGCCGCATGAGA 58.801 39.130 0.00 0.00 0.00 3.27 R
4634 6105 3.253188 GCCAGTGTTGAGTATTCTTTGCA 59.747 43.478 0.00 0.00 0.00 4.08 R
5624 7323 1.601166 TGGCATCTGCACATCTATGC 58.399 50.000 4.33 0.00 46.32 3.14 R
7310 9600 2.089980 GACATTGAGCTTCCAGTGCAT 58.910 47.619 0.00 0.00 0.00 3.96 R
7510 9800 0.396278 CTTGCTCCCATTTCTCCCCC 60.396 60.000 0.00 0.00 0.00 5.40 R
8731 13598 0.539901 GGTCCGGCTATCCTAGAGCA 60.540 60.000 0.00 0.00 41.98 4.26 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
76 82 2.907917 CCTCTAGGAGTCGGCGGG 60.908 72.222 7.21 0.00 37.39 6.13
97 103 3.391965 GCAGAACTGGCTAGATCAGATG 58.608 50.000 16.97 13.23 36.22 2.90
265 287 2.935481 CCCACCAGCAGAGGGGAA 60.935 66.667 1.82 0.00 43.57 3.97
311 333 0.722676 AGGTGGGATGAGGGGTAGAA 59.277 55.000 0.00 0.00 0.00 2.10
410 435 5.300792 GGGTTGTTGTGGAAAAAGATCAGTA 59.699 40.000 0.00 0.00 0.00 2.74
542 573 2.512986 AAATGGGGAATGGGCGCTGA 62.513 55.000 7.64 0.00 0.00 4.26
704 739 1.454479 CATTGGATGGCCGGCTTCT 60.454 57.895 28.56 11.32 36.79 2.85
711 746 0.179018 ATGGCCGGCTTCTACATTCC 60.179 55.000 28.56 5.64 0.00 3.01
729 764 2.050144 TCCTGTCCATGAGCTATTCCC 58.950 52.381 0.00 0.00 0.00 3.97
730 765 1.270518 CCTGTCCATGAGCTATTCCCG 60.271 57.143 0.00 0.00 0.00 5.14
845 902 2.042843 CCTCCACCCTCGTAGCCT 60.043 66.667 0.00 0.00 0.00 4.58
1050 1112 2.343758 GAGAGGGAACGCAGCACA 59.656 61.111 0.00 0.00 0.00 4.57
1126 1188 2.842256 GCCGGATCGAGGTAAGCGA 61.842 63.158 5.05 0.00 42.48 4.93
1134 1196 1.033574 CGAGGTAAGCGATTCCTCCT 58.966 55.000 19.40 13.03 43.20 3.69
1415 1485 1.169661 TGGAGTTTGTGCGCGGAATT 61.170 50.000 8.83 0.00 0.00 2.17
1427 1497 4.434483 GGAATTGGGGTTCCGCTT 57.566 55.556 7.39 0.00 38.41 4.68
1428 1498 2.189833 GGAATTGGGGTTCCGCTTC 58.810 57.895 7.39 4.00 38.41 3.86
1429 1499 1.320344 GGAATTGGGGTTCCGCTTCC 61.320 60.000 9.78 9.78 38.41 3.46
1430 1500 1.654023 GAATTGGGGTTCCGCTTCCG 61.654 60.000 7.39 0.00 35.24 4.30
1443 1513 0.108138 GCTTCCGTGTGCCTGATAGT 60.108 55.000 0.00 0.00 0.00 2.12
1458 1528 2.222213 TGATAGTTTCCGTGTGTTTGCG 59.778 45.455 0.00 0.00 0.00 4.85
1519 1589 1.182673 CATTTCGGCTCGATTTTGCG 58.817 50.000 0.00 0.00 35.23 4.85
1533 1626 5.343058 TCGATTTTGCGTAGTATAATACGGC 59.657 40.000 27.89 21.14 46.66 5.68
1589 1682 0.465705 TCCTTCATGATGGGCGAGTC 59.534 55.000 23.54 0.00 0.00 3.36
1616 1709 5.535783 GGGTTAGCTTTGTACTTTTACCCAA 59.464 40.000 0.00 0.00 41.80 4.12
1782 1877 5.751028 GCTACAGGAGATCAATTACACTCAC 59.249 44.000 0.00 0.00 0.00 3.51
1951 2059 3.910490 GTTGCCGGCAGCCAACAA 61.910 61.111 30.92 11.69 42.71 2.83
1986 2121 2.188829 CCGATGCCGATGCCAATGT 61.189 57.895 0.00 0.00 38.22 2.71
2003 2138 1.927487 TGTCGGTGTAAGGAAGCCTA 58.073 50.000 0.00 0.00 31.13 3.93
2280 2427 4.863491 AGCTGCATGTTTTTAGAACACTG 58.137 39.130 1.02 0.00 32.37 3.66
2415 2592 2.070783 TGTCGTTACTCATTTTCCCGC 58.929 47.619 0.00 0.00 0.00 6.13
2416 2593 1.395954 GTCGTTACTCATTTTCCCGCC 59.604 52.381 0.00 0.00 0.00 6.13
2417 2594 1.276989 TCGTTACTCATTTTCCCGCCT 59.723 47.619 0.00 0.00 0.00 5.52
2418 2595 2.081462 CGTTACTCATTTTCCCGCCTT 58.919 47.619 0.00 0.00 0.00 4.35
2419 2596 2.095372 CGTTACTCATTTTCCCGCCTTC 59.905 50.000 0.00 0.00 0.00 3.46
2420 2597 3.344515 GTTACTCATTTTCCCGCCTTCT 58.655 45.455 0.00 0.00 0.00 2.85
2421 2598 4.510571 GTTACTCATTTTCCCGCCTTCTA 58.489 43.478 0.00 0.00 0.00 2.10
2422 2599 3.713826 ACTCATTTTCCCGCCTTCTAA 57.286 42.857 0.00 0.00 0.00 2.10
2423 2600 3.610911 ACTCATTTTCCCGCCTTCTAAG 58.389 45.455 0.00 0.00 0.00 2.18
2424 2601 3.263425 ACTCATTTTCCCGCCTTCTAAGA 59.737 43.478 0.00 0.00 0.00 2.10
2425 2602 4.080299 ACTCATTTTCCCGCCTTCTAAGAT 60.080 41.667 0.00 0.00 0.00 2.40
2426 2603 4.199310 TCATTTTCCCGCCTTCTAAGATG 58.801 43.478 0.00 0.00 0.00 2.90
2427 2604 2.710096 TTTCCCGCCTTCTAAGATGG 57.290 50.000 0.00 0.00 0.00 3.51
2428 2605 1.580059 TTCCCGCCTTCTAAGATGGT 58.420 50.000 0.00 0.00 30.69 3.55
2429 2606 2.464796 TCCCGCCTTCTAAGATGGTA 57.535 50.000 0.00 0.00 30.69 3.25
2430 2607 2.754465 TCCCGCCTTCTAAGATGGTAA 58.246 47.619 0.00 0.00 30.69 2.85
2431 2608 3.314693 TCCCGCCTTCTAAGATGGTAAT 58.685 45.455 0.00 0.00 30.69 1.89
2432 2609 4.485875 TCCCGCCTTCTAAGATGGTAATA 58.514 43.478 0.00 0.00 30.69 0.98
2433 2610 5.091552 TCCCGCCTTCTAAGATGGTAATAT 58.908 41.667 0.00 0.00 30.69 1.28
2434 2611 5.546499 TCCCGCCTTCTAAGATGGTAATATT 59.454 40.000 0.00 0.00 30.69 1.28
2435 2612 6.043938 TCCCGCCTTCTAAGATGGTAATATTT 59.956 38.462 0.00 0.00 30.69 1.40
2436 2613 6.371825 CCCGCCTTCTAAGATGGTAATATTTC 59.628 42.308 0.00 0.00 30.69 2.17
3363 3950 7.095910 TGATGTTACTTATGGCCATTGTTTTG 58.904 34.615 26.37 10.25 0.00 2.44
3388 3975 2.141517 GTATGTAGGCTCGCTCGAGTA 58.858 52.381 15.13 1.67 43.70 2.59
3389 3976 1.676746 ATGTAGGCTCGCTCGAGTAA 58.323 50.000 15.13 1.31 43.70 2.24
3553 4140 3.692406 AAGACGGGGCGGACACTC 61.692 66.667 0.00 0.00 0.00 3.51
3581 4168 6.348498 ACGACATGTTCAATGGATCTAATCA 58.652 36.000 0.00 0.00 0.00 2.57
3733 4327 5.784578 ATTTTCACGGCTTTTTAAGGAGT 57.215 34.783 0.00 0.00 0.00 3.85
3742 4336 5.056480 GGCTTTTTAAGGAGTGCACAAAAT 58.944 37.500 21.04 5.02 0.00 1.82
4044 4767 6.183360 ACAGCTGGATGTTCTCAGAGTATTAG 60.183 42.308 19.93 0.00 33.11 1.73
4120 4846 4.586001 CCATAGGTTCAATGCTTTATGGCT 59.414 41.667 0.00 0.00 33.42 4.75
4169 4898 3.270027 GCCTTCCTTGTTTTGCAACTTT 58.730 40.909 0.00 0.00 33.58 2.66
4259 4988 3.065925 GCAAGAAAGCGCCATAGAAGAAT 59.934 43.478 2.29 0.00 0.00 2.40
4493 5910 9.692325 ATCAAGCAAAGGATTCTAATAACTCTT 57.308 29.630 0.00 0.00 0.00 2.85
4534 5969 3.387962 TCATCAAGGGCCAGAAGATACT 58.612 45.455 6.18 0.00 0.00 2.12
4535 5970 4.556697 TCATCAAGGGCCAGAAGATACTA 58.443 43.478 6.18 0.00 0.00 1.82
4536 5971 4.345257 TCATCAAGGGCCAGAAGATACTAC 59.655 45.833 6.18 0.00 0.00 2.73
4754 6225 6.714810 TGCAGATAAGGTATGTTTTGTGACTT 59.285 34.615 0.00 0.00 0.00 3.01
5233 6748 7.988249 AAAGGGCTATACAATTTTTACCCAT 57.012 32.000 0.00 0.00 38.64 4.00
5286 6801 1.067071 GCGCAGTGGTAAAGTACTCCT 60.067 52.381 0.30 0.00 0.00 3.69
5533 7229 3.118811 GGATGAGAACTGAGCTAGCACTT 60.119 47.826 18.83 1.56 0.00 3.16
5534 7230 4.502962 GATGAGAACTGAGCTAGCACTTT 58.497 43.478 18.83 8.32 0.00 2.66
5548 7244 5.119434 GCTAGCACTTTGTTCTGACTAGTTC 59.881 44.000 10.63 0.00 0.00 3.01
5624 7323 5.025826 GGAAAATTTGCGTCGTAACTATGG 58.974 41.667 0.00 0.00 0.00 2.74
5741 7443 8.706322 TGCCCTATTTATCTCGCTATATATGA 57.294 34.615 0.00 0.00 0.00 2.15
5959 7765 9.325198 CATTGGAGTAATGTTATTGCTACACTA 57.675 33.333 4.36 0.00 41.02 2.74
5963 7769 8.818057 GGAGTAATGTTATTGCTACACTAACAG 58.182 37.037 13.57 0.00 40.74 3.16
5971 7777 9.893305 GTTATTGCTACACTAACAGTTTTGAAT 57.107 29.630 0.00 0.00 32.32 2.57
6230 8118 3.645212 GACAGATGATCCTCCAGAATCCA 59.355 47.826 0.00 0.00 0.00 3.41
6244 8132 5.068987 TCCAGAATCCAAAGGTTCAACAAAG 59.931 40.000 0.00 0.00 0.00 2.77
6508 8408 5.452078 TTCATTGGTAGTTCTTTGCTTGG 57.548 39.130 0.00 0.00 0.00 3.61
6652 8606 6.206634 TCAGTTTCCATCACCATCTTGTTTAC 59.793 38.462 0.00 0.00 0.00 2.01
6855 9106 9.002600 CAGCATTGCATACCTTATACTCAAATA 57.997 33.333 11.91 0.00 0.00 1.40
7117 9407 3.199442 TGGAGTGAGGAGGTATGGAAA 57.801 47.619 0.00 0.00 0.00 3.13
7327 9617 2.490903 GTTCATGCACTGGAAGCTCAAT 59.509 45.455 0.00 0.00 37.60 2.57
7457 9747 7.386059 GGTTTAACCTTCATGGAATCAACAAT 58.614 34.615 6.92 0.00 39.71 2.71
7475 9765 8.674263 TCAACAATAATGTGCCAAGAAATTTT 57.326 26.923 0.00 0.00 40.46 1.82
7510 9800 0.108424 CCTGGAGCTTCTTCCTCACG 60.108 60.000 0.00 0.00 38.12 4.35
7528 9818 1.697297 GGGGGAGAAATGGGAGCAA 59.303 57.895 0.00 0.00 0.00 3.91
7539 9829 1.192146 TGGGAGCAAGCGTAGGAAGT 61.192 55.000 0.00 0.00 0.00 3.01
7641 9931 3.194116 CCTTCCCATCAATCAACAACCAG 59.806 47.826 0.00 0.00 0.00 4.00
8539 13403 3.144068 TCCAGGTCCCAATTGATCCTA 57.856 47.619 7.12 0.00 0.00 2.94
8650 13515 9.457436 GGACTTGTAAGGAAAAATATTAGGTCA 57.543 33.333 0.00 0.00 0.00 4.02
8731 13598 7.725844 ACTTAAGAAGAAATCATGGACAACCTT 59.274 33.333 10.09 0.00 37.04 3.50
8799 13666 7.690256 AGCAAAAGAGATAAGAAAGGACCTTA 58.310 34.615 7.30 0.00 0.00 2.69
8855 13722 2.743126 AGTCGGACTTTGAGACTCTACG 59.257 50.000 4.45 0.00 40.85 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.001020 ACGCCCATGCTTGGAATCA 60.001 52.632 19.85 0.00 46.92 2.57
60 61 3.597728 GCCCGCCGACTCCTAGAG 61.598 72.222 0.00 0.00 35.52 2.43
76 82 3.391965 CATCTGATCTAGCCAGTTCTGC 58.608 50.000 10.44 0.00 33.57 4.26
87 93 2.477104 TGGTGGCTCCATCTGATCTA 57.523 50.000 3.73 0.00 41.93 1.98
184 194 2.044946 GAAGGGCAGCGTTGGGAT 60.045 61.111 0.16 0.00 0.00 3.85
244 266 2.688666 CCTCTGCTGGTGGGGCTA 60.689 66.667 0.00 0.00 0.00 3.93
311 333 2.797278 CCTAGCATCGCCTCCGGTT 61.797 63.158 0.00 0.00 34.56 4.44
317 339 3.866582 GCCACCCTAGCATCGCCT 61.867 66.667 0.00 0.00 0.00 5.52
384 409 2.821437 TCTTTTTCCACAACAACCCCA 58.179 42.857 0.00 0.00 0.00 4.96
388 413 6.206498 GGTACTGATCTTTTTCCACAACAAC 58.794 40.000 0.00 0.00 0.00 3.32
389 414 5.008217 CGGTACTGATCTTTTTCCACAACAA 59.992 40.000 0.00 0.00 0.00 2.83
410 435 0.685458 AGTTATACACGAGGGCCGGT 60.685 55.000 1.90 0.00 43.93 5.28
496 524 1.912220 CAATGAGCCCCGGGAAGTA 59.088 57.895 26.32 5.92 0.00 2.24
542 573 9.859152 ATACTCTAACCTAGTCTAAATTACCGT 57.141 33.333 0.00 0.00 0.00 4.83
602 634 9.663904 CGATGATTTTTATACAAATCGGACAAT 57.336 29.630 15.97 6.78 43.47 2.71
704 739 5.221722 GGAATAGCTCATGGACAGGAATGTA 60.222 44.000 0.00 0.00 0.00 2.29
711 746 1.414181 ACGGGAATAGCTCATGGACAG 59.586 52.381 0.00 0.00 0.00 3.51
874 931 1.355718 GGAATGCCCTCCAGATCCCA 61.356 60.000 0.00 0.00 35.36 4.37
1004 1066 1.033574 CTCGATCGCCCTTCTTACCT 58.966 55.000 11.09 0.00 0.00 3.08
1017 1079 4.300743 TCGCTCGCTCGCTCGATC 62.301 66.667 0.00 0.00 37.87 3.69
1018 1080 4.306471 CTCGCTCGCTCGCTCGAT 62.306 66.667 0.00 0.00 37.87 3.59
1050 1112 0.325272 GTTTCTCCCTCGCCCTTCTT 59.675 55.000 0.00 0.00 0.00 2.52
1126 1188 0.029577 GGAGGGAGGGAAGGAGGAAT 60.030 60.000 0.00 0.00 0.00 3.01
1134 1196 1.396594 GAGGGAAGGAGGGAGGGAA 59.603 63.158 0.00 0.00 0.00 3.97
1348 1418 1.505353 CGAACTCGAACCCGCTAGT 59.495 57.895 0.00 0.00 43.02 2.57
1415 1485 4.323477 CACGGAAGCGGAACCCCA 62.323 66.667 0.00 0.00 0.00 4.96
1425 1495 2.386661 AACTATCAGGCACACGGAAG 57.613 50.000 0.00 0.00 0.00 3.46
1426 1496 2.614481 GGAAACTATCAGGCACACGGAA 60.614 50.000 0.00 0.00 0.00 4.30
1427 1497 1.066430 GGAAACTATCAGGCACACGGA 60.066 52.381 0.00 0.00 0.00 4.69
1428 1498 1.369625 GGAAACTATCAGGCACACGG 58.630 55.000 0.00 0.00 0.00 4.94
1429 1499 0.999406 CGGAAACTATCAGGCACACG 59.001 55.000 0.00 0.00 0.00 4.49
1430 1500 1.732259 CACGGAAACTATCAGGCACAC 59.268 52.381 0.00 0.00 0.00 3.82
1443 1513 2.409651 GGCGCAAACACACGGAAA 59.590 55.556 10.83 0.00 0.00 3.13
1458 1528 1.592223 CGATCCTAATCTCCCCGGC 59.408 63.158 0.00 0.00 0.00 6.13
1519 1589 4.610945 ACAACCACGCCGTATTATACTAC 58.389 43.478 0.00 0.00 0.00 2.73
1533 1626 0.029300 CCAAACTGCAGACAACCACG 59.971 55.000 23.35 0.00 0.00 4.94
1575 1668 0.816825 CCCAAGACTCGCCCATCATG 60.817 60.000 0.00 0.00 0.00 3.07
1589 1682 6.294342 GGGTAAAAGTACAAAGCTAACCCAAG 60.294 42.308 10.90 0.00 42.94 3.61
1616 1709 9.163899 GGAAAAAGAAGACGATAACTAAATCCT 57.836 33.333 0.00 0.00 0.00 3.24
1782 1877 6.146837 CGAGCCTACATAAGAGAATGAAATGG 59.853 42.308 0.00 0.00 0.00 3.16
1949 2057 1.809567 GCCTGGTCTTTGGTGGCTTG 61.810 60.000 0.00 0.00 40.36 4.01
1950 2058 1.531602 GCCTGGTCTTTGGTGGCTT 60.532 57.895 0.00 0.00 40.36 4.35
1951 2059 2.116125 GCCTGGTCTTTGGTGGCT 59.884 61.111 0.00 0.00 40.36 4.75
1981 2116 1.737793 GGCTTCCTTACACCGACATTG 59.262 52.381 0.00 0.00 0.00 2.82
1982 2117 1.628846 AGGCTTCCTTACACCGACATT 59.371 47.619 0.00 0.00 0.00 2.71
1986 2121 2.494870 GAGTTAGGCTTCCTTACACCGA 59.505 50.000 0.00 0.00 35.84 4.69
1989 2124 6.239092 GGAGATAGAGTTAGGCTTCCTTACAC 60.239 46.154 0.00 0.00 35.84 2.90
2003 2138 5.589452 ACAACGACGATAAGGAGATAGAGTT 59.411 40.000 0.00 0.00 0.00 3.01
2280 2427 9.023967 GGCTCATATCAAACATCAAACAAATAC 57.976 33.333 0.00 0.00 0.00 1.89
2415 2592 6.401153 GCGCGAAATATTACCATCTTAGAAGG 60.401 42.308 12.10 1.53 0.00 3.46
2416 2593 6.401153 GGCGCGAAATATTACCATCTTAGAAG 60.401 42.308 12.10 0.00 0.00 2.85
2417 2594 5.407387 GGCGCGAAATATTACCATCTTAGAA 59.593 40.000 12.10 0.00 0.00 2.10
2418 2595 4.927425 GGCGCGAAATATTACCATCTTAGA 59.073 41.667 12.10 0.00 0.00 2.10
2419 2596 4.929808 AGGCGCGAAATATTACCATCTTAG 59.070 41.667 12.10 0.00 0.00 2.18
2420 2597 4.890088 AGGCGCGAAATATTACCATCTTA 58.110 39.130 12.10 0.00 0.00 2.10
2421 2598 3.740115 AGGCGCGAAATATTACCATCTT 58.260 40.909 12.10 0.00 0.00 2.40
2422 2599 3.402628 AGGCGCGAAATATTACCATCT 57.597 42.857 12.10 0.00 0.00 2.90
2423 2600 4.483476 AAAGGCGCGAAATATTACCATC 57.517 40.909 12.10 0.00 0.00 3.51
2424 2601 4.911514 AAAAGGCGCGAAATATTACCAT 57.088 36.364 12.10 0.00 0.00 3.55
2425 2602 4.705337 AAAAAGGCGCGAAATATTACCA 57.295 36.364 12.10 0.00 0.00 3.25
3363 3950 2.667137 GAGCGAGCCTACATACATGAC 58.333 52.381 0.00 0.00 0.00 3.06
3388 3975 1.371145 CGAACCGCGCCAAAACATT 60.371 52.632 0.00 0.00 0.00 2.71
3389 3976 2.254051 CGAACCGCGCCAAAACAT 59.746 55.556 0.00 0.00 0.00 2.71
3535 4122 3.934391 GAGTGTCCGCCCCGTCTTG 62.934 68.421 0.00 0.00 0.00 3.02
3553 4140 6.609237 AGATCCATTGAACATGTCGTTATG 57.391 37.500 0.00 1.23 38.19 1.90
3581 4168 5.310857 AGGGAGAACTCAAGGTTTCTTACAT 59.689 40.000 4.23 0.00 38.41 2.29
3733 4327 1.297664 GGTGCAGCAAATTTTGTGCA 58.702 45.000 23.36 23.36 44.74 4.57
4259 4988 1.203237 TGGGCACATAGCTTAGCTGA 58.797 50.000 17.97 1.39 44.79 4.26
4493 5910 4.198530 TGAGAATTTATTGCCGCATGAGA 58.801 39.130 0.00 0.00 0.00 3.27
4534 5969 8.217131 TCTTACATTGATTACGTCTGCTAGTA 57.783 34.615 0.00 0.00 0.00 1.82
4535 5970 7.096884 TCTTACATTGATTACGTCTGCTAGT 57.903 36.000 0.00 0.00 0.00 2.57
4536 5971 7.488150 TGTTCTTACATTGATTACGTCTGCTAG 59.512 37.037 0.00 0.00 0.00 3.42
4634 6105 3.253188 GCCAGTGTTGAGTATTCTTTGCA 59.747 43.478 0.00 0.00 0.00 4.08
4754 6225 6.447162 CACAGTAGAAGAGTGTTGTATGACA 58.553 40.000 0.00 0.00 39.89 3.58
4924 6403 6.377146 ACATTATAGTTGGGTACAAAGGCAAG 59.623 38.462 0.00 0.00 38.54 4.01
5233 6748 9.567776 TGTCCTTCATTATTCTTGTTTGTTAGA 57.432 29.630 0.00 0.00 0.00 2.10
5404 6967 8.912988 CACACCAGGTGGATTTTTGTATATAAT 58.087 33.333 24.13 0.00 44.04 1.28
5624 7323 1.601166 TGGCATCTGCACATCTATGC 58.399 50.000 4.33 0.00 46.32 3.14
5741 7443 5.121768 GTGCACCATTTACTGACGAGTTTAT 59.878 40.000 5.22 0.00 33.21 1.40
5959 7765 7.538678 GCATCGAATTAGTCATTCAAAACTGTT 59.461 33.333 0.00 0.00 41.51 3.16
5963 7769 7.965107 AGAAGCATCGAATTAGTCATTCAAAAC 59.035 33.333 0.00 0.00 41.51 2.43
5971 7777 5.181056 TGCAAAAGAAGCATCGAATTAGTCA 59.819 36.000 0.00 0.00 37.02 3.41
6230 8118 6.418057 TGGAATATGCTTTGTTGAACCTTT 57.582 33.333 0.00 0.00 0.00 3.11
6468 8368 6.071728 CCAATGAAGCACTTCCTAAAAGATGT 60.072 38.462 7.88 0.00 38.77 3.06
6508 8408 4.055654 GCTGATGGATTCTCGGCC 57.944 61.111 0.00 0.00 38.77 6.13
6652 8606 7.041780 GGTGGTATAATACATGTCTCAAGCTTG 60.042 40.741 20.81 20.81 0.00 4.01
7117 9407 3.693085 CAGCATTGCATTCCAGTTACTCT 59.307 43.478 11.91 0.00 0.00 3.24
7310 9600 2.089980 GACATTGAGCTTCCAGTGCAT 58.910 47.619 0.00 0.00 0.00 3.96
7451 9741 8.016801 GGAAAATTTCTTGGCACATTATTGTTG 58.983 33.333 5.65 0.00 39.30 3.33
7452 9742 7.938490 AGGAAAATTTCTTGGCACATTATTGTT 59.062 29.630 5.65 0.00 39.30 2.83
7453 9743 7.452562 AGGAAAATTTCTTGGCACATTATTGT 58.547 30.769 5.65 0.00 39.30 2.71
7457 9747 6.295236 CCAGAGGAAAATTTCTTGGCACATTA 60.295 38.462 5.65 0.00 39.30 1.90
7487 9777 1.843206 GAGGAAGAAGCTCCAGGGAAT 59.157 52.381 0.00 0.00 38.02 3.01
7510 9800 0.396278 CTTGCTCCCATTTCTCCCCC 60.396 60.000 0.00 0.00 0.00 5.40
7528 9818 1.608283 GCTTGGTTGACTTCCTACGCT 60.608 52.381 0.00 0.00 0.00 5.07
7539 9829 5.827797 AGTATGACTTTTCAAGCTTGGTTGA 59.172 36.000 25.73 10.67 34.61 3.18
7641 9931 1.876156 CCACTGAGAAAGGCTGTTCAC 59.124 52.381 10.57 6.22 0.00 3.18
7682 9972 1.616159 GGTTGAGCCAGCTTTTACCA 58.384 50.000 11.58 0.00 37.17 3.25
8731 13598 0.539901 GGTCCGGCTATCCTAGAGCA 60.540 60.000 0.00 0.00 41.98 4.26
8799 13666 5.784578 AAGCATTGTGTATCATGATGCAT 57.215 34.783 26.22 10.64 44.08 3.96
8855 13722 3.264866 AACACCGAGTCTCCGACGC 62.265 63.158 0.00 0.00 37.67 5.19


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

AutoCloner maintained by Alex Coulton.