Multiple sequence alignment - TraesCS2A01G277700

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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 TraesCS2A01G277700 chr2A 100.000 5633 0 0 1 5633 459925809 459931441 0.000000e+00 10403.0
1 TraesCS2A01G277700 chr2A 93.137 510 34 1 3 512 459918398 459918906 0.000000e+00 747.0
2 TraesCS2A01G277700 chr2A 92.969 512 35 1 1 512 329614403 329614913 0.000000e+00 745.0
3 TraesCS2A01G277700 chr2A 91.866 418 27 3 2458 2873 459927135 459927547 1.360000e-160 577.0
4 TraesCS2A01G277700 chr2A 91.866 418 27 3 1327 1739 459928266 459928681 1.360000e-160 577.0
5 TraesCS2A01G277700 chr2A 92.929 99 5 2 1222 1319 459926996 459927093 5.880000e-30 143.0
6 TraesCS2A01G277700 chr2A 92.929 99 5 2 1188 1285 459927030 459927127 5.880000e-30 143.0
7 TraesCS2A01G277700 chr2D 94.457 1822 79 19 2920 4730 346161151 346162961 0.000000e+00 2785.0
8 TraesCS2A01G277700 chr2D 92.076 896 56 8 4750 5633 594382128 594381236 0.000000e+00 1247.0
9 TraesCS2A01G277700 chr2D 95.886 559 18 3 530 1088 346160351 346160904 0.000000e+00 900.0
10 TraesCS2A01G277700 chr2D 82.739 869 138 12 3773 4633 346100822 346101686 0.000000e+00 763.0
11 TraesCS2A01G277700 chr2D 94.456 487 17 6 3231 3712 346157978 346158459 0.000000e+00 741.0
12 TraesCS2A01G277700 chr2D 91.386 267 22 1 2975 3240 346157521 346157787 1.150000e-96 364.0
13 TraesCS2A01G277700 chr2D 85.933 327 33 10 1397 1718 632475931 632475613 2.510000e-88 337.0
14 TraesCS2A01G277700 chr2D 86.435 317 31 10 2541 2852 632475922 632475613 2.510000e-88 337.0
15 TraesCS2A01G277700 chr2D 86.235 247 21 10 2617 2860 19382099 19382335 7.240000e-64 255.0
16 TraesCS2A01G277700 chr2D 86.235 247 21 10 2617 2860 573453883 573453647 7.240000e-64 255.0
17 TraesCS2A01G277700 chr2D 86.235 247 21 10 2617 2860 573455212 573454976 7.240000e-64 255.0
18 TraesCS2A01G277700 chr2D 91.791 134 7 2 1091 1223 346161032 346161162 3.470000e-42 183.0
19 TraesCS2A01G277700 chr2D 100.000 33 0 0 1224 1256 346161129 346161161 1.690000e-05 62.1
20 TraesCS2A01G277700 chr2D 96.774 31 1 0 1266 1296 14568559 14568529 1.000000e-02 52.8
21 TraesCS2A01G277700 chr2B 93.544 1642 73 14 3096 4730 412185034 412186649 0.000000e+00 2414.0
22 TraesCS2A01G277700 chr2B 93.119 654 34 5 540 1191 412184373 412185017 0.000000e+00 948.0
23 TraesCS2A01G277700 chr2B 82.739 869 138 12 3773 4633 412180081 412180945 0.000000e+00 763.0
24 TraesCS2A01G277700 chr1B 92.472 890 61 2 4750 5633 324343176 324344065 0.000000e+00 1267.0
25 TraesCS2A01G277700 chr1B 81.180 356 60 5 1750 2101 301773839 301774191 4.300000e-71 279.0
26 TraesCS2A01G277700 chr1B 82.000 200 30 3 1750 1946 24244321 24244125 1.260000e-36 165.0
27 TraesCS2A01G277700 chr1B 85.535 159 18 5 2000 2154 40912463 40912306 1.620000e-35 161.0
28 TraesCS2A01G277700 chr1B 100.000 34 0 0 2843 2876 19068043 19068076 4.710000e-06 63.9
29 TraesCS2A01G277700 chr1B 100.000 28 0 0 1265 1292 562451389 562451362 1.000000e-02 52.8
30 TraesCS2A01G277700 chr3D 92.282 894 62 5 4746 5633 462266428 462265536 0.000000e+00 1262.0
31 TraesCS2A01G277700 chr3D 91.592 892 67 4 4750 5633 537651449 537650558 0.000000e+00 1225.0
32 TraesCS2A01G277700 chr3D 83.871 248 17 17 2617 2860 566054901 566055129 1.230000e-51 215.0
33 TraesCS2A01G277700 chr3B 92.058 894 65 2 4746 5633 555130964 555131857 0.000000e+00 1253.0
34 TraesCS2A01G277700 chr3B 91.160 905 68 5 4741 5633 62780920 62781824 0.000000e+00 1218.0
35 TraesCS2A01G277700 chr3B 88.793 116 13 0 2965 3080 98248884 98248769 5.880000e-30 143.0
36 TraesCS2A01G277700 chr3B 81.500 200 14 13 2452 2632 806049331 806049526 5.880000e-30 143.0
37 TraesCS2A01G277700 chr3B 91.489 94 6 2 1404 1497 806049435 806049526 1.650000e-25 128.0
38 TraesCS2A01G277700 chr6B 91.798 890 67 1 4750 5633 149157257 149158146 0.000000e+00 1234.0
39 TraesCS2A01G277700 chr6B 84.000 75 12 0 2319 2393 125214598 125214524 7.830000e-09 73.1
40 TraesCS2A01G277700 chr6B 84.058 69 11 0 2308 2376 111255963 111255895 3.640000e-07 67.6
41 TraesCS2A01G277700 chr4A 91.611 894 69 2 4746 5633 735439906 735440799 0.000000e+00 1230.0
42 TraesCS2A01G277700 chr4A 86.207 116 16 0 2965 3080 298126373 298126488 5.920000e-25 126.0
43 TraesCS2A01G277700 chr6D 91.685 890 68 2 4750 5633 388268561 388267672 0.000000e+00 1229.0
44 TraesCS2A01G277700 chr7A 93.945 512 29 2 1 512 630945868 630946377 0.000000e+00 773.0
45 TraesCS2A01G277700 chr7A 92.969 512 35 1 1 512 339019227 339019737 0.000000e+00 745.0
46 TraesCS2A01G277700 chr7A 90.385 52 4 1 2870 2921 65077747 65077697 3.640000e-07 67.6
47 TraesCS2A01G277700 chr7A 100.000 28 0 0 1753 1780 702231294 702231267 1.000000e-02 52.8
48 TraesCS2A01G277700 chr3A 93.359 512 33 1 1 512 347459354 347458844 0.000000e+00 756.0
49 TraesCS2A01G277700 chr3A 86.207 116 16 0 2965 3080 378362659 378362774 5.920000e-25 126.0
50 TraesCS2A01G277700 chr3A 100.000 28 0 0 1265 1292 58931267 58931294 1.000000e-02 52.8
51 TraesCS2A01G277700 chr1A 93.359 512 33 1 1 512 278276815 278276305 0.000000e+00 756.0
52 TraesCS2A01G277700 chr1A 92.578 512 37 1 1 512 590623206 590623716 0.000000e+00 734.0
53 TraesCS2A01G277700 chr1A 92.383 512 37 2 1 512 420107770 420107261 0.000000e+00 728.0
54 TraesCS2A01G277700 chr1A 81.117 376 66 4 1765 2137 267443558 267443931 4.270000e-76 296.0
55 TraesCS2A01G277700 chr6A 92.969 512 35 1 1 512 69593128 69592618 0.000000e+00 745.0
56 TraesCS2A01G277700 chr6A 79.891 184 35 2 4136 4318 36858946 36858764 3.540000e-27 134.0
57 TraesCS2A01G277700 chr4B 80.749 374 51 9 1765 2135 323786422 323786067 7.190000e-69 272.0
58 TraesCS2A01G277700 chr4B 84.962 133 19 1 2948 3080 13286216 13286085 3.540000e-27 134.0
59 TraesCS2A01G277700 chr4D 87.045 247 19 9 2617 2860 452394982 452395218 3.350000e-67 267.0
60 TraesCS2A01G277700 chr4D 86.640 247 20 9 2617 2860 452396304 452396540 1.560000e-65 261.0
61 TraesCS2A01G277700 chr4D 85.897 78 11 0 1732 1809 400411594 400411517 3.620000e-12 84.2
62 TraesCS2A01G277700 chr5A 83.240 179 25 4 1753 1929 474021422 474021247 5.840000e-35 159.0
63 TraesCS2A01G277700 chr5A 80.500 200 34 4 1732 1929 474122548 474122744 1.260000e-31 148.0
64 TraesCS2A01G277700 chr5A 81.967 183 26 6 1749 1929 474285368 474285191 1.260000e-31 148.0
65 TraesCS2A01G277700 chr5A 86.207 116 16 0 2965 3080 656696728 656696613 5.920000e-25 126.0
66 TraesCS2A01G277700 chr5A 80.000 160 30 2 4160 4318 489934350 489934508 3.570000e-22 117.0
67 TraesCS2A01G277700 chr5A 78.286 175 33 4 4121 4291 489844017 489844190 2.150000e-19 108.0
68 TraesCS2A01G277700 chr5B 81.366 161 26 4 4160 4318 465825142 465825300 1.650000e-25 128.0
69 TraesCS2A01G277700 chr5B 100.000 33 0 0 2845 2877 611685071 611685103 1.690000e-05 62.1
70 TraesCS2A01G277700 chr7B 86.207 116 16 0 2965 3080 680009767 680009652 5.920000e-25 126.0
71 TraesCS2A01G277700 chr7D 85.345 116 17 0 2965 3080 391948387 391948502 2.760000e-23 121.0
72 TraesCS2A01G277700 chr5D 77.273 198 38 6 4099 4291 387098602 387098797 5.970000e-20 110.0


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 TraesCS2A01G277700 chr2A 459925809 459931441 5632 False 10403.000000 10403 100.000000 1 5633 1 chr2A.!!$F3 5632
1 TraesCS2A01G277700 chr2A 459918398 459918906 508 False 747.000000 747 93.137000 3 512 1 chr2A.!!$F2 509
2 TraesCS2A01G277700 chr2A 329614403 329614913 510 False 745.000000 745 92.969000 1 512 1 chr2A.!!$F1 511
3 TraesCS2A01G277700 chr2A 459926996 459928681 1685 False 360.000000 577 92.397500 1188 2873 4 chr2A.!!$F4 1685
4 TraesCS2A01G277700 chr2D 594381236 594382128 892 True 1247.000000 1247 92.076000 4750 5633 1 chr2D.!!$R2 883
5 TraesCS2A01G277700 chr2D 346157521 346162961 5440 False 839.183333 2785 94.662667 530 4730 6 chr2D.!!$F3 4200
6 TraesCS2A01G277700 chr2D 346100822 346101686 864 False 763.000000 763 82.739000 3773 4633 1 chr2D.!!$F2 860
7 TraesCS2A01G277700 chr2D 573453647 573455212 1565 True 255.000000 255 86.235000 2617 2860 2 chr2D.!!$R3 243
8 TraesCS2A01G277700 chr2B 412180081 412186649 6568 False 1375.000000 2414 89.800667 540 4730 3 chr2B.!!$F1 4190
9 TraesCS2A01G277700 chr1B 324343176 324344065 889 False 1267.000000 1267 92.472000 4750 5633 1 chr1B.!!$F3 883
10 TraesCS2A01G277700 chr3D 462265536 462266428 892 True 1262.000000 1262 92.282000 4746 5633 1 chr3D.!!$R1 887
11 TraesCS2A01G277700 chr3D 537650558 537651449 891 True 1225.000000 1225 91.592000 4750 5633 1 chr3D.!!$R2 883
12 TraesCS2A01G277700 chr3B 555130964 555131857 893 False 1253.000000 1253 92.058000 4746 5633 1 chr3B.!!$F2 887
13 TraesCS2A01G277700 chr3B 62780920 62781824 904 False 1218.000000 1218 91.160000 4741 5633 1 chr3B.!!$F1 892
14 TraesCS2A01G277700 chr6B 149157257 149158146 889 False 1234.000000 1234 91.798000 4750 5633 1 chr6B.!!$F1 883
15 TraesCS2A01G277700 chr4A 735439906 735440799 893 False 1230.000000 1230 91.611000 4746 5633 1 chr4A.!!$F2 887
16 TraesCS2A01G277700 chr6D 388267672 388268561 889 True 1229.000000 1229 91.685000 4750 5633 1 chr6D.!!$R1 883
17 TraesCS2A01G277700 chr7A 630945868 630946377 509 False 773.000000 773 93.945000 1 512 1 chr7A.!!$F2 511
18 TraesCS2A01G277700 chr7A 339019227 339019737 510 False 745.000000 745 92.969000 1 512 1 chr7A.!!$F1 511
19 TraesCS2A01G277700 chr3A 347458844 347459354 510 True 756.000000 756 93.359000 1 512 1 chr3A.!!$R1 511
20 TraesCS2A01G277700 chr1A 278276305 278276815 510 True 756.000000 756 93.359000 1 512 1 chr1A.!!$R1 511
21 TraesCS2A01G277700 chr1A 590623206 590623716 510 False 734.000000 734 92.578000 1 512 1 chr1A.!!$F2 511
22 TraesCS2A01G277700 chr1A 420107261 420107770 509 True 728.000000 728 92.383000 1 512 1 chr1A.!!$R2 511
23 TraesCS2A01G277700 chr6A 69592618 69593128 510 True 745.000000 745 92.969000 1 512 1 chr6A.!!$R2 511
24 TraesCS2A01G277700 chr4D 452394982 452396540 1558 False 264.000000 267 86.842500 2617 2860 2 chr4D.!!$F1 243

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
939 4693 0.329596 ACCCAGCTCCATCCAAGAAC 59.670 55.0 0.00 0.00 0.00 3.01 F
2916 6797 0.255890 ACCAGACGCCATGGCTTATT 59.744 50.0 33.07 15.37 41.87 1.40 F
3029 6910 0.260816 TGGCTACTCGGTGACCCTAT 59.739 55.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2931 6812 0.172803 AACTAACCGAGCAGCTACCG 59.827 55.0 0.0 0.0 0.0 4.02 R
4389 8286 0.896226 AGTTGGGAGCTACTTCGACC 59.104 55.0 0.0 0.0 0.0 4.79 R
4978 8881 1.201429 ACCTCGGCAACCTCATCCTT 61.201 55.0 0.0 0.0 0.0 3.36 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
169 170 1.746787 GGTTCCGGGCGTCATATTTTT 59.253 47.619 0.00 0.00 0.00 1.94
232 233 1.202582 CGACCTTGGAGTGAGACGATT 59.797 52.381 0.00 0.00 0.00 3.34
389 391 1.693627 GGCCTTAGAGATGAGACCGA 58.306 55.000 0.00 0.00 0.00 4.69
413 415 7.469870 CGAATGACTATGGCCCAAATATCAAAA 60.470 37.037 0.00 0.00 0.00 2.44
414 416 7.673641 ATGACTATGGCCCAAATATCAAAAA 57.326 32.000 0.00 0.00 0.00 1.94
420 422 9.617523 CTATGGCCCAAATATCAAAAATTTTCT 57.382 29.630 3.41 0.00 0.00 2.52
485 487 8.260114 CCATTTGAGGCCATCTTAATTAAGTTT 58.740 33.333 21.69 10.37 34.93 2.66
657 4411 5.473039 CAACTATTCTTTTTCTTGCAGGGG 58.527 41.667 0.00 0.00 0.00 4.79
860 4614 2.710096 GCCTTTGGTAGATGGCAGTA 57.290 50.000 0.00 0.00 44.34 2.74
862 4616 3.555966 GCCTTTGGTAGATGGCAGTATT 58.444 45.455 0.00 0.00 44.34 1.89
897 4651 1.604593 CCCTCAAGTTGGGGCACTG 60.605 63.158 17.10 0.00 36.42 3.66
939 4693 0.329596 ACCCAGCTCCATCCAAGAAC 59.670 55.000 0.00 0.00 0.00 3.01
1092 4971 2.455032 CTTCTATCTCGGAAGCGTGTG 58.545 52.381 0.00 0.00 34.66 3.82
1117 4996 6.127366 GCTTTGGAATGGATGATCTTGGTAAA 60.127 38.462 0.00 0.00 0.00 2.01
1158 5037 6.198591 GCATCTGCTTTTCTGCAAATCTATTC 59.801 38.462 0.00 0.00 42.83 1.75
1186 5066 5.359194 AACCGTTTATCATCTGGAGACAT 57.641 39.130 0.00 0.00 41.51 3.06
2894 6775 4.477975 CACGAGACGAGCCCGACC 62.478 72.222 0.00 0.00 39.50 4.79
2908 6789 4.760047 GACCGCACCAGACGCCAT 62.760 66.667 0.00 0.00 0.00 4.40
2913 6794 2.360350 CACCAGACGCCATGGCTT 60.360 61.111 33.07 25.86 41.87 4.35
2914 6795 1.078497 CACCAGACGCCATGGCTTA 60.078 57.895 33.07 0.00 41.87 3.09
2915 6796 0.464373 CACCAGACGCCATGGCTTAT 60.464 55.000 33.07 20.21 41.87 1.73
2916 6797 0.255890 ACCAGACGCCATGGCTTATT 59.744 50.000 33.07 15.37 41.87 1.40
2917 6798 0.947244 CCAGACGCCATGGCTTATTC 59.053 55.000 33.07 22.24 39.32 1.75
2918 6799 1.475751 CCAGACGCCATGGCTTATTCT 60.476 52.381 33.07 23.92 39.32 2.40
2919 6800 2.224281 CCAGACGCCATGGCTTATTCTA 60.224 50.000 33.07 0.00 39.32 2.10
2920 6801 3.466836 CAGACGCCATGGCTTATTCTAA 58.533 45.455 33.07 0.00 39.32 2.10
2921 6802 3.248602 CAGACGCCATGGCTTATTCTAAC 59.751 47.826 33.07 11.17 39.32 2.34
2922 6803 3.118408 AGACGCCATGGCTTATTCTAACA 60.118 43.478 33.07 0.00 39.32 2.41
2923 6804 3.815401 GACGCCATGGCTTATTCTAACAT 59.185 43.478 33.07 4.86 39.32 2.71
2924 6805 3.815401 ACGCCATGGCTTATTCTAACATC 59.185 43.478 33.07 0.51 39.32 3.06
2925 6806 3.120546 CGCCATGGCTTATTCTAACATCG 60.121 47.826 33.07 9.54 39.32 3.84
2926 6807 3.815401 GCCATGGCTTATTCTAACATCGT 59.185 43.478 29.98 0.00 38.26 3.73
2927 6808 4.275936 GCCATGGCTTATTCTAACATCGTT 59.724 41.667 29.98 0.00 38.26 3.85
2928 6809 5.468746 GCCATGGCTTATTCTAACATCGTTA 59.531 40.000 29.98 0.00 38.26 3.18
2929 6810 6.017440 GCCATGGCTTATTCTAACATCGTTAA 60.017 38.462 29.98 0.00 38.26 2.01
2930 6811 7.352739 CCATGGCTTATTCTAACATCGTTAAC 58.647 38.462 0.00 0.00 0.00 2.01
2931 6812 6.913873 TGGCTTATTCTAACATCGTTAACC 57.086 37.500 0.00 0.00 0.00 2.85
2947 6828 3.203442 CCGGTAGCTGCTCGGTTA 58.797 61.111 18.55 0.00 39.04 2.85
2951 6832 1.641577 GGTAGCTGCTCGGTTAGTTG 58.358 55.000 4.91 0.00 0.00 3.16
2965 6846 5.481473 TCGGTTAGTTGGTGAGTTAATAGGT 59.519 40.000 0.00 0.00 0.00 3.08
2971 6852 9.590451 TTAGTTGGTGAGTTAATAGGTTAATCG 57.410 33.333 0.00 0.00 32.76 3.34
2972 6853 7.844009 AGTTGGTGAGTTAATAGGTTAATCGA 58.156 34.615 0.00 0.00 32.76 3.59
3023 6904 5.664294 TTAGTTTATTGGCTACTCGGTGA 57.336 39.130 0.00 0.00 0.00 4.02
3029 6910 0.260816 TGGCTACTCGGTGACCCTAT 59.739 55.000 0.00 0.00 0.00 2.57
3033 6914 2.748798 GCTACTCGGTGACCCTATGAGA 60.749 54.545 10.59 0.00 0.00 3.27
3035 6916 2.379972 ACTCGGTGACCCTATGAGAAG 58.620 52.381 10.59 0.00 0.00 2.85
3036 6917 2.025226 ACTCGGTGACCCTATGAGAAGA 60.025 50.000 10.59 0.00 0.00 2.87
3037 6918 3.226777 CTCGGTGACCCTATGAGAAGAT 58.773 50.000 0.00 0.00 0.00 2.40
3044 6925 8.314751 CGGTGACCCTATGAGAAGATATTAATT 58.685 37.037 0.00 0.00 0.00 1.40
3116 6998 7.492020 GCATGTATATTTGTGCTGAAATTTCCA 59.508 33.333 15.48 4.49 34.85 3.53
3171 7054 6.864165 GCTTCCTAGAAATAAGTAGATCGTGG 59.136 42.308 0.00 0.00 0.00 4.94
3221 7104 6.015434 GGACCCAATTGAGTTGACTTTGTAAT 60.015 38.462 7.12 0.00 40.37 1.89
3353 7237 3.388024 ACTGTTCTGTTACTCTTGGAGCA 59.612 43.478 0.00 0.00 32.04 4.26
3398 7283 1.831580 CTTGAGAGCTCCCCTTTTGG 58.168 55.000 10.93 0.00 39.97 3.28
3407 7292 3.054065 AGCTCCCCTTTTGGTAATCTGAG 60.054 47.826 0.00 0.00 38.10 3.35
3574 7460 7.097192 GTCCTTTTGTCCCTAAATTTCCATTC 58.903 38.462 0.00 0.00 0.00 2.67
3613 7499 7.473027 TGCATTTACTAGTTTACTTATCGCC 57.527 36.000 0.00 0.00 0.00 5.54
3718 7607 4.018597 AGTCAGAAGGAATGAATGGCTTCT 60.019 41.667 0.00 0.00 32.29 2.85
3987 7884 2.954868 GAGTACGTGGCGGCATCG 60.955 66.667 24.37 24.37 39.81 3.84
4350 8247 4.595538 ACGAACGGCGGCAAGTGA 62.596 61.111 13.24 0.00 46.49 3.41
4372 8269 2.437343 GCGTTCAAGCCGAGTCTCG 61.437 63.158 15.53 15.53 40.07 4.04
4395 8292 2.338620 CACGGCAGAGTGGTCGAA 59.661 61.111 0.00 0.00 38.35 3.71
4469 8366 2.067013 GAAGAAGCTGTCCACGGTTAC 58.933 52.381 0.00 0.00 0.00 2.50
4596 8493 1.884235 CGTGGGAAAAGAGCTTGAGT 58.116 50.000 0.00 0.00 0.00 3.41
4673 8570 7.815398 CATGCAATGCTTCAGTGTTTATTTA 57.185 32.000 6.82 0.00 37.62 1.40
4841 8738 5.333187 GCAGAGATTGAACTAATCATGCGAG 60.333 44.000 11.43 0.00 46.20 5.03
4878 8775 3.170791 ACAGATCACATCTAAGGCACG 57.829 47.619 0.00 0.00 37.58 5.34
4978 8881 0.880441 CATTGTCGCCCATGTTGTCA 59.120 50.000 0.00 0.00 0.00 3.58
5069 8972 1.956802 CGCCCCTCAAAAACCTGAC 59.043 57.895 0.00 0.00 0.00 3.51
5080 8983 3.547787 AACCTGACCGCCCCTCTCT 62.548 63.158 0.00 0.00 0.00 3.10
5100 9003 1.065636 TCGTACAGGATCACGAGAGGT 60.066 52.381 2.18 0.00 41.89 3.85
5109 9012 2.203182 ACGAGAGGTGGGGTTCCA 59.797 61.111 0.00 0.00 41.58 3.53
5123 9026 1.842920 TTCCAGAGGCCTGCTGTCA 60.843 57.895 12.00 3.61 39.07 3.58
5171 9074 2.290577 GGATGGAGAAGACTTGCTTGGT 60.291 50.000 0.00 0.00 36.83 3.67
5192 9095 1.353103 CGCAATGATCTGGAACGGC 59.647 57.895 0.00 0.00 32.53 5.68
5198 9101 1.079405 GATCTGGAACGGCGGTGAA 60.079 57.895 13.24 0.00 32.53 3.18
5215 9118 2.224784 GTGAAAAACCATACGAAGCGGT 59.775 45.455 0.00 0.00 33.32 5.68
5218 9121 0.035739 AAACCATACGAAGCGGTGGT 59.964 50.000 11.57 11.57 46.18 4.16
5237 9140 0.330604 TGGCTAGGGTAGACGTCTGT 59.669 55.000 28.12 11.94 36.27 3.41
5260 9163 1.479323 GACTATATAATGCGGGCCGGA 59.521 52.381 29.48 27.68 0.00 5.14
5271 9174 2.836360 GGCCGGATAGGTCGTGGA 60.836 66.667 5.05 0.00 43.70 4.02
5283 9186 1.003928 GGTCGTGGAAGTAAACCCCAT 59.996 52.381 0.00 0.00 31.94 4.00
5286 9189 4.520179 GTCGTGGAAGTAAACCCCATATT 58.480 43.478 0.00 0.00 31.94 1.28
5330 9233 7.088589 AGAATCGGAAATGGTTCAGTAATTG 57.911 36.000 0.00 0.00 35.25 2.32
5341 9244 2.536365 TCAGTAATTGACGCGTCCATC 58.464 47.619 34.34 18.43 0.00 3.51
5379 9282 7.523293 TGACTCATTAATTTTTCCTGAGCAA 57.477 32.000 0.00 0.00 37.45 3.91
5403 9306 9.335891 CAACAAAAATATAGACAACGTGCATAA 57.664 29.630 0.00 0.00 0.00 1.90
5427 9330 0.876342 GTCCTCGGCTCGGCTTAATG 60.876 60.000 0.00 0.00 0.00 1.90
5509 9422 0.526662 CGCGTGTAGGTCTCCTCTTT 59.473 55.000 0.00 0.00 34.61 2.52
5517 9430 4.287067 TGTAGGTCTCCTCTTTTCATGCTT 59.713 41.667 0.00 0.00 34.61 3.91
5540 9453 3.951775 ACAAGTGGTAGAAGAGCTCAG 57.048 47.619 17.77 0.00 0.00 3.35
5599 9514 4.324331 GGTGGGACTAAACTTTAGCCTCAT 60.324 45.833 8.26 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 2.297315 ACAGCGTGACTCTTCAATGAGA 59.703 45.455 0.00 0.00 37.50 3.27
389 391 7.673641 TTTTGATATTTGGGCCATAGTCATT 57.326 32.000 7.26 0.00 0.00 2.57
413 415 7.645402 AGTTCCGTATCGTCAAAAAGAAAATT 58.355 30.769 0.00 0.00 0.00 1.82
414 416 7.198306 AGTTCCGTATCGTCAAAAAGAAAAT 57.802 32.000 0.00 0.00 0.00 1.82
420 422 5.754406 TGAGAAAGTTCCGTATCGTCAAAAA 59.246 36.000 0.00 0.00 0.00 1.94
485 487 0.039617 CAGATTTTGGCACGGCGAAA 60.040 50.000 16.62 8.31 34.71 3.46
631 4385 4.545610 TGCAAGAAAAAGAATAGTTGCCG 58.454 39.130 0.00 0.00 39.62 5.69
688 4442 3.124270 TTGTCGCAATCGCCGCAT 61.124 55.556 0.00 0.00 35.26 4.73
792 4546 3.502920 CGTGATTGAGTTAGCTCTTCGT 58.497 45.455 8.15 0.00 42.13 3.85
897 4651 4.599047 AGAAGATAGCACAGGAGCATAC 57.401 45.455 0.00 0.00 36.85 2.39
905 4659 3.133721 AGCTGGGTTAGAAGATAGCACAG 59.866 47.826 0.00 0.00 33.81 3.66
1092 4971 3.703052 ACCAAGATCATCCATTCCAAAGC 59.297 43.478 0.00 0.00 0.00 3.51
1117 4996 4.571919 CAGATGCAATTCCACCAAAATGT 58.428 39.130 0.00 0.00 0.00 2.71
1158 5037 4.072131 CCAGATGATAAACGGTTATGGGG 58.928 47.826 11.19 0.97 29.69 4.96
2877 6758 4.477975 GGTCGGGCTCGTCTCGTG 62.478 72.222 5.57 0.00 37.69 4.35
2891 6772 4.760047 ATGGCGTCTGGTGCGGTC 62.760 66.667 0.00 0.00 0.00 4.79
2904 6785 3.815401 ACGATGTTAGAATAAGCCATGGC 59.185 43.478 30.12 30.12 42.33 4.40
2905 6786 7.352739 GTTAACGATGTTAGAATAAGCCATGG 58.647 38.462 7.63 7.63 0.00 3.66
2906 6787 7.352739 GGTTAACGATGTTAGAATAAGCCATG 58.647 38.462 0.00 0.00 0.00 3.66
2907 6788 7.492352 GGTTAACGATGTTAGAATAAGCCAT 57.508 36.000 0.00 0.00 0.00 4.40
2908 6789 6.913873 GGTTAACGATGTTAGAATAAGCCA 57.086 37.500 0.00 0.00 0.00 4.75
2924 6805 1.138047 CGAGCAGCTACCGGTTAACG 61.138 60.000 15.04 6.02 43.80 3.18
2925 6806 0.804933 CCGAGCAGCTACCGGTTAAC 60.805 60.000 15.04 2.06 38.55 2.01
2926 6807 1.514087 CCGAGCAGCTACCGGTTAA 59.486 57.895 15.04 0.00 38.55 2.01
2927 6808 3.203442 CCGAGCAGCTACCGGTTA 58.797 61.111 15.04 0.00 38.55 2.85
2931 6812 0.172803 AACTAACCGAGCAGCTACCG 59.827 55.000 0.00 0.00 0.00 4.02
2947 6828 7.763071 GTCGATTAACCTATTAACTCACCAACT 59.237 37.037 0.00 0.00 33.09 3.16
2951 6832 7.763071 ACTTGTCGATTAACCTATTAACTCACC 59.237 37.037 0.00 0.00 33.09 4.02
2970 6851 9.406828 TCATCCGATTAATAGATTAACTTGTCG 57.593 33.333 0.00 8.01 35.31 4.35
3018 6899 5.730296 AATATCTTCTCATAGGGTCACCG 57.270 43.478 0.00 0.00 43.47 4.94
3023 6904 7.988937 TGCCAATTAATATCTTCTCATAGGGT 58.011 34.615 0.00 0.00 0.00 4.34
3065 6946 9.377312 GCTAGTATCTTCTTCAAGAATTTGTCT 57.623 33.333 0.00 0.00 42.14 3.41
3080 6961 9.429359 AGCACAAATATACATGCTAGTATCTTC 57.571 33.333 5.88 0.00 46.36 2.87
3116 6998 9.273016 CATATCTAACAAAATCCCGATAAGTGT 57.727 33.333 0.00 0.00 0.00 3.55
3171 7054 1.664306 CGTAGCCCGTATCCCCTTC 59.336 63.158 0.00 0.00 0.00 3.46
3189 7072 1.271597 ACTCAATTGGGTCCACAGAGC 60.272 52.381 4.73 0.00 39.90 4.09
3221 7104 2.985539 TTTTTACAGCGCCCCCAGCA 62.986 55.000 2.29 0.00 44.04 4.41
3337 7221 3.076621 TGCAATGCTCCAAGAGTAACAG 58.923 45.455 6.82 0.00 31.39 3.16
3353 7237 6.368516 CCAATTGAACTAATTCGGTTTGCAAT 59.631 34.615 7.12 0.00 36.87 3.56
3391 7275 7.147976 CCTTTTGTTCTCAGATTACCAAAAGG 58.852 38.462 21.70 21.70 45.69 3.11
3587 7473 8.557029 GGCGATAAGTAAACTAGTAAATGCATT 58.443 33.333 5.99 5.99 0.00 3.56
3605 7491 3.146618 ACTCACTGTTACGGCGATAAG 57.853 47.619 16.62 8.01 0.00 1.73
3738 7627 8.602328 CGCAAGCATTTTGATAATTTGGAAATA 58.398 29.630 0.00 0.00 0.00 1.40
3987 7884 4.554036 GGGGCGGTGATGCTCTCC 62.554 72.222 0.00 0.00 35.04 3.71
4389 8286 0.896226 AGTTGGGAGCTACTTCGACC 59.104 55.000 0.00 0.00 0.00 4.79
4416 8313 1.529438 GTCAGAATGGACGCGACAAAA 59.471 47.619 15.93 0.00 36.16 2.44
4596 8493 4.292145 TTCCCCGTTGCATGGCCA 62.292 61.111 8.56 8.56 0.00 5.36
4748 8645 9.337396 TCGTAGTAATTTGCTCATATTTCCAAT 57.663 29.630 0.00 0.00 0.00 3.16
4806 8703 4.884458 TCAATCTCTGCTACTGTAGTCG 57.116 45.455 15.71 7.71 0.00 4.18
4841 8738 6.806249 GTGATCTGTTCATCTACTATGCTAGC 59.194 42.308 8.10 8.10 36.54 3.42
4872 8769 4.530710 TTCATGTTTCTAGTACGTGCCT 57.469 40.909 0.00 0.00 33.54 4.75
4878 8775 7.972277 TCGTGGTAGAATTCATGTTTCTAGTAC 59.028 37.037 16.18 15.71 36.59 2.73
4978 8881 1.201429 ACCTCGGCAACCTCATCCTT 61.201 55.000 0.00 0.00 0.00 3.36
5002 8905 2.480224 TCACGAACGACGACTTCTTT 57.520 45.000 0.00 0.00 45.77 2.52
5054 8957 1.524008 GGCGGTCAGGTTTTTGAGGG 61.524 60.000 0.00 0.00 0.00 4.30
5057 8960 1.529713 GGGGCGGTCAGGTTTTTGA 60.530 57.895 0.00 0.00 0.00 2.69
5069 8972 2.439701 TGTACGAGAGAGGGGCGG 60.440 66.667 0.00 0.00 0.00 6.13
5080 8983 1.065636 ACCTCTCGTGATCCTGTACGA 60.066 52.381 5.95 5.95 45.87 3.43
5100 9003 2.935481 CAGGCCTCTGGAACCCCA 60.935 66.667 0.00 0.00 40.95 4.96
5109 9012 0.835543 AGAAGTGACAGCAGGCCTCT 60.836 55.000 0.00 0.00 0.00 3.69
5123 9026 4.681978 GCGTGCACCGGGAGAAGT 62.682 66.667 12.15 0.00 36.94 3.01
5171 9074 1.368345 CGTTCCAGATCATTGCGCCA 61.368 55.000 4.18 0.00 0.00 5.69
5198 9101 1.161843 CCACCGCTTCGTATGGTTTT 58.838 50.000 0.00 0.00 32.48 2.43
5215 9118 0.682209 GACGTCTACCCTAGCCACCA 60.682 60.000 8.70 0.00 0.00 4.17
5218 9121 0.330604 ACAGACGTCTACCCTAGCCA 59.669 55.000 19.57 0.00 0.00 4.75
5237 9140 2.165641 CGGCCCGCATTATATAGTCAGA 59.834 50.000 0.00 0.00 0.00 3.27
5260 9163 2.502947 GGGGTTTACTTCCACGACCTAT 59.497 50.000 0.00 0.00 0.00 2.57
5271 9174 4.161001 ACGACTCGAATATGGGGTTTACTT 59.839 41.667 5.20 0.00 0.00 2.24
5283 9186 2.282407 TGGATCGTGACGACTCGAATA 58.718 47.619 10.91 3.50 43.33 1.75
5286 9189 0.876399 TTTGGATCGTGACGACTCGA 59.124 50.000 10.91 13.70 44.00 4.04
5330 9233 5.652744 AATTAGTAATTGATGGACGCGTC 57.347 39.130 30.67 30.67 0.00 5.19
5379 9282 8.726988 AGTTATGCACGTTGTCTATATTTTTGT 58.273 29.630 0.00 0.00 0.00 2.83
5403 9306 2.752238 CCGAGCCGAGGACAGAGT 60.752 66.667 0.00 0.00 0.00 3.24
5509 9422 7.847096 TCTTCTACCACTTGTATAAGCATGAA 58.153 34.615 0.00 0.00 34.98 2.57
5517 9430 5.067936 GCTGAGCTCTTCTACCACTTGTATA 59.932 44.000 16.19 0.00 0.00 1.47
5540 9453 5.423886 AGAGAGTTGCACCTCTTTATAAGC 58.576 41.667 15.62 0.56 41.85 3.09


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

AutoCloner maintained by Alex Coulton.