Multiple sequence alignment - TraesCS2B01G187000

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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 TraesCS2B01G187000 chr2B 100.000 4951 0 0 1 4951 161721416 161726366 0.000000e+00 9143.0
1 TraesCS2B01G187000 chr2B 80.360 1833 238 69 2037 3825 162447667 162445913 0.000000e+00 1279.0
2 TraesCS2B01G187000 chr2B 86.778 1021 75 30 727 1692 162007423 162008438 0.000000e+00 1083.0
3 TraesCS2B01G187000 chr2B 84.661 1004 103 23 1965 2930 162008757 162009747 0.000000e+00 953.0
4 TraesCS2B01G187000 chr2B 87.694 772 59 14 742 1481 162449043 162448276 0.000000e+00 867.0
5 TraesCS2B01G187000 chr2B 88.952 525 46 5 3832 4350 162445875 162445357 5.410000e-179 638.0
6 TraesCS2B01G187000 chr2B 89.044 502 36 10 3834 4328 162010632 162011121 5.480000e-169 604.0
7 TraesCS2B01G187000 chr2B 85.495 455 50 9 3270 3720 162009946 162010388 1.260000e-125 460.0
8 TraesCS2B01G187000 chr2B 84.825 257 24 9 567 808 162496550 162496294 1.380000e-60 244.0
9 TraesCS2B01G187000 chr2B 85.366 246 20 8 4703 4942 162012126 162012361 1.780000e-59 241.0
10 TraesCS2B01G187000 chr2B 82.781 151 7 7 4494 4644 162011295 162011426 3.130000e-22 117.0
11 TraesCS2B01G187000 chr2D 95.537 1703 64 5 2512 4205 111590240 111591939 0.000000e+00 2713.0
12 TraesCS2B01G187000 chr2D 89.470 1339 80 22 501 1781 111588159 111589494 0.000000e+00 1635.0
13 TraesCS2B01G187000 chr2D 81.818 1760 195 69 1866 3570 112180140 112178451 0.000000e+00 1362.0
14 TraesCS2B01G187000 chr2D 85.610 1237 107 32 607 1781 112098917 112100144 0.000000e+00 1232.0
15 TraesCS2B01G187000 chr2D 85.889 1063 121 20 1884 2930 112100259 112101308 0.000000e+00 1105.0
16 TraesCS2B01G187000 chr2D 85.238 989 83 28 721 1657 112181356 112180379 0.000000e+00 959.0
17 TraesCS2B01G187000 chr2D 84.052 765 74 28 3601 4328 112101766 112102519 0.000000e+00 693.0
18 TraesCS2B01G187000 chr2D 92.157 459 19 3 4494 4951 111592386 111592828 2.510000e-177 632.0
19 TraesCS2B01G187000 chr2D 88.190 525 50 6 3832 4350 112178119 112177601 2.530000e-172 616.0
20 TraesCS2B01G187000 chr2D 92.236 322 21 2 2208 2529 111589910 111590227 2.100000e-123 453.0
21 TraesCS2B01G187000 chr2D 86.667 315 38 4 17 329 111587647 111587959 3.670000e-91 346.0
22 TraesCS2B01G187000 chr2D 81.598 413 46 18 3202 3599 112101324 112101721 1.030000e-81 315.0
23 TraesCS2B01G187000 chr2D 85.000 320 35 6 1866 2177 111589602 111589916 3.720000e-81 313.0
24 TraesCS2B01G187000 chr2D 90.909 143 8 4 4362 4504 111592203 111592340 2.350000e-43 187.0
25 TraesCS2B01G187000 chr2D 88.158 152 7 4 4494 4644 112102696 112102837 2.370000e-38 171.0
26 TraesCS2B01G187000 chr2D 87.200 125 7 4 4703 4827 112103577 112103692 3.110000e-27 134.0
27 TraesCS2B01G187000 chr2D 93.939 66 4 0 424 489 112096944 112097009 3.150000e-17 100.0
28 TraesCS2B01G187000 chr2D 97.674 43 1 0 1811 1853 112180166 112180124 1.910000e-09 75.0
29 TraesCS2B01G187000 chr2D 97.561 41 1 0 1811 1851 111589576 111589616 2.470000e-08 71.3
30 TraesCS2B01G187000 chr2A 89.325 1349 69 30 501 1781 111921428 111922769 0.000000e+00 1624.0
31 TraesCS2B01G187000 chr2A 89.615 1040 88 16 2582 3612 111923577 111924605 0.000000e+00 1304.0
32 TraesCS2B01G187000 chr2A 90.881 965 43 24 3586 4523 111924627 111925573 0.000000e+00 1253.0
33 TraesCS2B01G187000 chr2A 85.312 1171 103 40 580 1692 112744386 112745545 0.000000e+00 1146.0
34 TraesCS2B01G187000 chr2A 84.258 1207 117 35 553 1692 113312436 113311236 0.000000e+00 1109.0
35 TraesCS2B01G187000 chr2A 86.803 879 84 20 1992 2861 113310843 113309988 0.000000e+00 952.0
36 TraesCS2B01G187000 chr2A 90.780 705 34 16 1866 2546 111922876 111923573 0.000000e+00 913.0
37 TraesCS2B01G187000 chr2A 85.189 898 83 28 1992 2861 112745938 112746813 0.000000e+00 876.0
38 TraesCS2B01G187000 chr2A 88.337 523 45 8 3834 4350 113309512 113309000 9.110000e-172 614.0
39 TraesCS2B01G187000 chr2A 95.224 335 16 0 4617 4951 111925608 111925942 9.440000e-147 531.0
40 TraesCS2B01G187000 chr2A 90.561 392 25 8 3832 4213 112747467 112747856 4.420000e-140 508.0
41 TraesCS2B01G187000 chr2A 84.411 526 53 17 3209 3720 112746880 112747390 1.600000e-134 490.0
42 TraesCS2B01G187000 chr2A 77.816 586 90 23 3250 3825 113197017 113196462 4.780000e-85 326.0
43 TraesCS2B01G187000 chr2A 82.086 374 44 12 3209 3570 113309921 113309559 1.040000e-76 298.0
44 TraesCS2B01G187000 chr2A 82.677 254 18 9 4703 4944 112749182 112749421 8.400000e-48 202.0
45 TraesCS2B01G187000 chr2A 83.333 114 11 4 4494 4602 112748357 112748467 1.130000e-16 99.0
46 TraesCS2B01G187000 chr2A 100.000 41 0 0 1811 1851 112745753 112745793 5.310000e-10 76.8
47 TraesCS2B01G187000 chr2A 100.000 41 0 0 1811 1851 113311028 113310988 5.310000e-10 76.8
48 TraesCS2B01G187000 chr2A 95.349 43 2 0 4569 4611 111925575 111925617 8.890000e-08 69.4
49 TraesCS2B01G187000 chr6A 84.000 100 13 3 1383 1481 535154197 535154100 5.280000e-15 93.5


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 TraesCS2B01G187000 chr2B 161721416 161726366 4950 False 9143.000000 9143 100.000000 1 4951 1 chr2B.!!$F1 4950
1 TraesCS2B01G187000 chr2B 162445357 162449043 3686 True 928.000000 1279 85.668667 742 4350 3 chr2B.!!$R2 3608
2 TraesCS2B01G187000 chr2B 162007423 162012361 4938 False 576.333333 1083 85.687500 727 4942 6 chr2B.!!$F2 4215
3 TraesCS2B01G187000 chr2D 111587647 111592828 5181 False 793.787500 2713 91.192125 17 4951 8 chr2D.!!$F1 4934
4 TraesCS2B01G187000 chr2D 112177601 112181356 3755 True 753.000000 1362 88.230000 721 4350 4 chr2D.!!$R1 3629
5 TraesCS2B01G187000 chr2D 112096944 112103692 6748 False 535.714286 1232 86.635143 424 4827 7 chr2D.!!$F2 4403
6 TraesCS2B01G187000 chr2A 111921428 111925942 4514 False 949.066667 1624 91.862333 501 4951 6 chr2A.!!$F1 4450
7 TraesCS2B01G187000 chr2A 113309000 113312436 3436 True 609.960000 1109 88.296800 553 4350 5 chr2A.!!$R2 3797
8 TraesCS2B01G187000 chr2A 112744386 112749421 5035 False 485.400000 1146 87.354714 580 4944 7 chr2A.!!$F2 4364
9 TraesCS2B01G187000 chr2A 113196462 113197017 555 True 326.000000 326 77.816000 3250 3825 1 chr2A.!!$R1 575

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
869 2778 1.076438 CCACCTCCCTTTCCTTCCTT 58.924 55.000 0.00 0.00 0.00 3.36 F
1283 3208 0.393402 CACCTATGGCTGCTGCTTGA 60.393 55.000 15.64 0.45 39.59 3.02 F
2607 4906 1.204941 GGTGTATGAGAAGCTGACGGT 59.795 52.381 0.00 0.00 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 4029 0.171903 GGCGGAAGTACTAGTGCGAA 59.828 55.000 12.04 0.0 0.00 4.70 R
2963 5293 2.080693 GGTTACGACAATCATGTGCCA 58.919 47.619 0.00 0.0 40.74 4.92 R
4438 7563 0.029035 GATCGCATGCCAGCTTTCTG 59.971 55.000 13.15 0.0 40.02 3.02 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 30 1.833787 GCGGGGGTTCAGTCTTACCA 61.834 60.000 0.00 0.00 36.10 3.25
53 54 2.552585 TTTCGTTCGCTCTAGCCCCG 62.553 60.000 0.00 0.00 37.91 5.73
61 62 1.833049 CTCTAGCCCCGTCCCGAAT 60.833 63.158 0.00 0.00 0.00 3.34
65 66 2.866523 TAGCCCCGTCCCGAATGTCT 62.867 60.000 0.00 0.00 0.00 3.41
73 74 4.157105 CCCGTCCCGAATGTCTTTTTATTT 59.843 41.667 0.00 0.00 0.00 1.40
79 80 8.517056 GTCCCGAATGTCTTTTTATTTTCCTTA 58.483 33.333 0.00 0.00 0.00 2.69
96 97 6.756299 TTCCTTATAATAACCGCCGTTTTT 57.244 33.333 0.00 0.00 33.17 1.94
100 101 9.553064 TCCTTATAATAACCGCCGTTTTTATAA 57.447 29.630 20.71 20.71 41.24 0.98
127 129 5.523438 TTTCTTTCAGTAACCGCCATTTT 57.477 34.783 0.00 0.00 0.00 1.82
134 136 8.745464 TTTCAGTAACCGCCATTTTTAATAAC 57.255 30.769 0.00 0.00 0.00 1.89
135 137 6.854778 TCAGTAACCGCCATTTTTAATAACC 58.145 36.000 0.00 0.00 0.00 2.85
136 138 6.433404 TCAGTAACCGCCATTTTTAATAACCA 59.567 34.615 0.00 0.00 0.00 3.67
139 141 5.923733 ACCGCCATTTTTAATAACCATCA 57.076 34.783 0.00 0.00 0.00 3.07
152 154 9.474313 TTTAATAACCATCACTTTTATCCTGCT 57.526 29.630 0.00 0.00 0.00 4.24
188 190 4.343526 TGTAAAAACTGTGGGCATCATGTT 59.656 37.500 0.00 0.00 0.00 2.71
214 216 2.243810 TGCATTAAAGAAACCGCCCTT 58.756 42.857 0.00 0.00 0.00 3.95
221 223 1.587066 AGAAACCGCCCTTACCCATA 58.413 50.000 0.00 0.00 0.00 2.74
227 229 2.171237 ACCGCCCTTACCCATAGTTTAC 59.829 50.000 0.00 0.00 0.00 2.01
228 230 2.436911 CCGCCCTTACCCATAGTTTACT 59.563 50.000 0.00 0.00 0.00 2.24
229 231 3.642848 CCGCCCTTACCCATAGTTTACTA 59.357 47.826 0.00 0.00 0.00 1.82
231 233 5.396660 CCGCCCTTACCCATAGTTTACTAAA 60.397 44.000 0.00 0.00 31.39 1.85
239 242 7.662604 ACCCATAGTTTACTAAAACAACTCG 57.337 36.000 4.04 0.00 46.18 4.18
240 243 7.444299 ACCCATAGTTTACTAAAACAACTCGA 58.556 34.615 4.04 0.00 46.18 4.04
242 245 8.225777 CCCATAGTTTACTAAAACAACTCGAAC 58.774 37.037 4.04 0.00 46.18 3.95
245 248 6.699063 AGTTTACTAAAACAACTCGAACACG 58.301 36.000 4.04 0.00 46.18 4.49
315 318 6.542370 TCTTTCCCTTCTTCTAATAAATGCCG 59.458 38.462 0.00 0.00 0.00 5.69
323 326 9.334693 CTTCTTCTAATAAATGCCGATTTATGC 57.665 33.333 3.50 0.00 41.84 3.14
365 368 8.924511 ATAATCATCGGTTGATAATCCAGTTT 57.075 30.769 2.18 0.00 44.51 2.66
391 394 5.356882 TTTCTAAAACAACGATGAGCCTG 57.643 39.130 0.00 0.00 0.00 4.85
392 395 4.002906 TCTAAAACAACGATGAGCCTGT 57.997 40.909 0.00 0.00 0.00 4.00
393 396 4.385825 TCTAAAACAACGATGAGCCTGTT 58.614 39.130 0.00 0.00 33.51 3.16
394 397 4.819630 TCTAAAACAACGATGAGCCTGTTT 59.180 37.500 0.00 0.00 42.30 2.83
406 409 6.610075 ATGAGCCTGTTTGGTTTTCATTAT 57.390 33.333 0.00 0.00 38.35 1.28
411 414 8.189119 AGCCTGTTTGGTTTTCATTATAGAAA 57.811 30.769 0.00 0.00 38.35 2.52
412 415 8.088365 AGCCTGTTTGGTTTTCATTATAGAAAC 58.912 33.333 0.00 0.00 35.35 2.78
413 416 8.088365 GCCTGTTTGGTTTTCATTATAGAAACT 58.912 33.333 0.00 0.00 35.35 2.66
414 417 9.410556 CCTGTTTGGTTTTCATTATAGAAACTG 57.589 33.333 0.00 0.00 37.24 3.16
415 418 9.965824 CTGTTTGGTTTTCATTATAGAAACTGT 57.034 29.630 0.00 0.00 37.24 3.55
416 419 9.743057 TGTTTGGTTTTCATTATAGAAACTGTG 57.257 29.630 0.00 0.00 37.24 3.66
494 554 8.391075 ACAACAACATTATAATAATCTCCCCG 57.609 34.615 0.00 0.00 0.00 5.73
495 555 7.040686 ACAACAACATTATAATAATCTCCCCGC 60.041 37.037 0.00 0.00 0.00 6.13
496 556 6.539173 ACAACATTATAATAATCTCCCCGCA 58.461 36.000 0.00 0.00 0.00 5.69
497 557 7.001674 ACAACATTATAATAATCTCCCCGCAA 58.998 34.615 0.00 0.00 0.00 4.85
498 558 7.504238 ACAACATTATAATAATCTCCCCGCAAA 59.496 33.333 0.00 0.00 0.00 3.68
499 559 8.356657 CAACATTATAATAATCTCCCCGCAAAA 58.643 33.333 0.00 0.00 0.00 2.44
500 560 8.472007 ACATTATAATAATCTCCCCGCAAAAA 57.528 30.769 0.00 0.00 0.00 1.94
541 2182 8.704849 TCAAATCCCTCTTTGAAAAGTTATGA 57.295 30.769 2.88 0.00 41.03 2.15
625 2515 7.103641 AGAAATGTATGGTCACACGATTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
630 2520 7.423199 TGTATGGTCACACGATTTAGTATCTC 58.577 38.462 0.00 0.00 0.00 2.75
703 2595 5.685511 GTGAAACACAATTAACATGAAGCGT 59.314 36.000 0.00 0.00 36.32 5.07
704 2596 5.685068 TGAAACACAATTAACATGAAGCGTG 59.315 36.000 0.00 1.56 0.00 5.34
792 2698 5.659440 TCCACATAAAAATTCCAAGAGGC 57.341 39.130 0.00 0.00 33.74 4.70
860 2769 1.158007 ACCATCAAACCACCTCCCTT 58.842 50.000 0.00 0.00 0.00 3.95
869 2778 1.076438 CCACCTCCCTTTCCTTCCTT 58.924 55.000 0.00 0.00 0.00 3.36
912 2830 1.203523 TCAGCTTCTCCTTCTCTTCGC 59.796 52.381 0.00 0.00 0.00 4.70
976 2897 1.316706 CCGCTTCTTCGGTCTCTCCT 61.317 60.000 0.00 0.00 44.18 3.69
1162 3083 3.402681 CCTCGGGGGTGCTGATGT 61.403 66.667 0.00 0.00 0.00 3.06
1191 3112 1.260538 TGCTGGACTCGATGAAGGCT 61.261 55.000 0.00 0.00 0.00 4.58
1283 3208 0.393402 CACCTATGGCTGCTGCTTGA 60.393 55.000 15.64 0.45 39.59 3.02
1318 3262 3.881688 CCGATGATTGAGGAATCTTTGCT 59.118 43.478 0.00 0.00 39.10 3.91
1334 3278 1.442769 TGCTTGAATCGCAGGAGAAC 58.557 50.000 0.00 0.00 32.80 3.01
1483 3450 1.356059 TGAGGAGGTCAGTCTACTGCT 59.644 52.381 5.21 0.00 43.46 4.24
1553 3523 1.261619 CCTCGCACTGTTGTGTTCTTC 59.738 52.381 0.00 0.00 45.44 2.87
1661 3636 2.906389 AGAGACAAGGTACATTCCAGCA 59.094 45.455 0.00 0.00 0.00 4.41
1761 3826 2.685380 CCCCTCTCCTCCAGCGTT 60.685 66.667 0.00 0.00 0.00 4.84
1785 3850 3.991605 CGTAAACGGAATCTTCACCTG 57.008 47.619 0.00 0.00 35.37 4.00
1786 3851 3.323243 CGTAAACGGAATCTTCACCTGT 58.677 45.455 0.00 0.00 35.37 4.00
1788 3853 4.212636 CGTAAACGGAATCTTCACCTGTTT 59.787 41.667 0.00 0.00 37.06 2.83
1789 3854 5.277634 CGTAAACGGAATCTTCACCTGTTTT 60.278 40.000 0.00 0.00 35.91 2.43
1790 3855 5.592104 AAACGGAATCTTCACCTGTTTTT 57.408 34.783 0.00 0.00 33.19 1.94
1851 3973 3.565482 CACAACAGTACATGCAAAGAGGT 59.435 43.478 0.00 0.00 0.00 3.85
1852 3974 3.815401 ACAACAGTACATGCAAAGAGGTC 59.185 43.478 0.00 0.00 0.00 3.85
1854 3976 2.639839 ACAGTACATGCAAAGAGGTCCT 59.360 45.455 0.00 0.00 0.00 3.85
1855 3977 3.838317 ACAGTACATGCAAAGAGGTCCTA 59.162 43.478 0.00 0.00 0.00 2.94
1856 3978 4.286032 ACAGTACATGCAAAGAGGTCCTAA 59.714 41.667 0.00 0.00 0.00 2.69
1857 3979 5.221843 ACAGTACATGCAAAGAGGTCCTAAA 60.222 40.000 0.00 0.00 0.00 1.85
1858 3980 5.705441 CAGTACATGCAAAGAGGTCCTAAAA 59.295 40.000 0.00 0.00 0.00 1.52
1859 3981 6.206634 CAGTACATGCAAAGAGGTCCTAAAAA 59.793 38.462 0.00 0.00 0.00 1.94
1907 4029 4.319901 GCGATCGTTTTTATGAGCGTTTTT 59.680 37.500 17.81 0.00 45.03 1.94
1945 4070 1.349026 CCCACAGAATGACAGACAGGT 59.651 52.381 0.00 0.00 39.69 4.00
1946 4071 2.420642 CCACAGAATGACAGACAGGTG 58.579 52.381 0.00 0.00 39.69 4.00
1948 4073 3.006859 CCACAGAATGACAGACAGGTGTA 59.993 47.826 0.00 0.00 39.69 2.90
1949 4074 4.323028 CCACAGAATGACAGACAGGTGTAT 60.323 45.833 0.00 0.00 39.69 2.29
2034 4241 5.890985 AGCACTGTATTTGTATTTATGGGCA 59.109 36.000 0.00 0.00 0.00 5.36
2035 4242 6.379703 AGCACTGTATTTGTATTTATGGGCAA 59.620 34.615 0.00 0.00 0.00 4.52
2040 4247 5.674052 ATTTGTATTTATGGGCAAGTGCA 57.326 34.783 5.52 0.00 44.36 4.57
2048 4255 5.674052 TTATGGGCAAGTGCAAATATGTT 57.326 34.783 5.52 0.00 44.36 2.71
2186 4393 2.419297 CGACATCTCCCTTTCTCCCAAG 60.419 54.545 0.00 0.00 0.00 3.61
2417 4651 1.694696 GACCTGACCCTGTCTTTCACT 59.305 52.381 0.00 0.00 33.15 3.41
2489 4728 6.252995 TCCCAATCAACTATTAGCAACCTTT 58.747 36.000 0.00 0.00 0.00 3.11
2492 4731 7.029563 CCAATCAACTATTAGCAACCTTTGTC 58.970 38.462 0.00 0.00 0.00 3.18
2607 4906 1.204941 GGTGTATGAGAAGCTGACGGT 59.795 52.381 0.00 0.00 0.00 4.83
2683 4982 2.507102 CACTTCCGCTGCGTCGAT 60.507 61.111 21.59 0.55 0.00 3.59
2934 5264 5.568296 CCGTTGTTTTGTTTAGAAAACGTCA 59.432 36.000 9.69 0.00 45.12 4.35
2935 5265 6.251801 CCGTTGTTTTGTTTAGAAAACGTCAT 59.748 34.615 9.69 0.00 45.12 3.06
2940 5270 9.916987 TGTTTTGTTTAGAAAACGTCATCGCGT 62.917 37.037 5.77 0.00 45.12 6.01
2963 5293 2.094545 CCGCTTAGCCTGCAAAGAAAAT 60.095 45.455 0.00 0.00 0.00 1.82
2985 5324 1.529010 GCACATGATTGTCGTAACCGC 60.529 52.381 0.00 0.00 32.34 5.68
3004 5344 2.602694 CGCGGCGGTTTCTTTCTTTTTA 60.603 45.455 15.84 0.00 0.00 1.52
3068 5412 9.424319 AGTGTAGATACAAACATACACAGAAAG 57.576 33.333 14.62 0.00 46.64 2.62
3120 5464 7.219322 AGCCATAGAAACTTTGCAAAAGAAAT 58.781 30.769 13.84 2.49 0.00 2.17
3196 5542 3.300009 CGCAGCCTGTTGTTTAGAAAAG 58.700 45.455 0.00 0.00 0.00 2.27
3230 5594 7.113965 GTGCATGCATAAATATTGTTGCTACTC 59.886 37.037 25.64 0.00 36.10 2.59
3237 5706 5.762825 AATATTGTTGCTACTCCATGCAG 57.237 39.130 0.00 0.00 40.46 4.41
3243 5712 1.630369 TGCTACTCCATGCAGGTCTTT 59.370 47.619 0.00 0.00 39.02 2.52
3391 5875 2.703798 GCGCGGTACACCTGTCCTA 61.704 63.158 8.83 0.00 0.00 2.94
3693 6269 1.492176 ACGGCTAGCTACCTACCTACA 59.508 52.381 15.72 0.00 0.00 2.74
3722 6310 7.279615 AGCAACTACTACCATATATTGTGCAA 58.720 34.615 0.00 0.00 0.00 4.08
3774 6370 6.903419 TGACATATACTACATGCTCTCGAAG 58.097 40.000 0.00 0.00 0.00 3.79
3793 6389 3.418684 AGTGCTTCCCGATAAAGTTGT 57.581 42.857 0.00 0.00 0.00 3.32
4010 6798 4.901849 TGGAGTTCAAGCAGGCTATATAGT 59.098 41.667 11.38 0.00 0.00 2.12
4043 6831 5.813080 AGTCTAGCTTGTTTCGTTTTTGT 57.187 34.783 0.00 0.00 0.00 2.83
4135 6932 0.247736 GATCGAGCAGTGACCCTTGT 59.752 55.000 0.00 0.00 0.00 3.16
4219 7156 6.513180 CCTTCCGTTATTAGCTATGACAGAA 58.487 40.000 0.00 0.00 0.00 3.02
4220 7157 6.984474 CCTTCCGTTATTAGCTATGACAGAAA 59.016 38.462 0.00 0.00 0.00 2.52
4221 7158 7.657761 CCTTCCGTTATTAGCTATGACAGAAAT 59.342 37.037 0.00 0.00 0.00 2.17
4245 7182 1.351350 GGGAGTGACAAAGTAGCCCTT 59.649 52.381 0.00 0.00 33.79 3.95
4270 7207 6.655003 TCTTTTTCTCACCCTGCACTATAAAG 59.345 38.462 0.00 0.00 0.00 1.85
4299 7250 9.787532 GTTTTATTACTTGCTTCATCATTAGCA 57.212 29.630 0.00 0.00 45.06 3.49
4354 7395 9.938280 TGTTAAGTTATTCTTGTGCTAGTATGT 57.062 29.630 0.00 0.00 37.56 2.29
4366 7491 9.452065 CTTGTGCTAGTATGTTAGTACTATGTG 57.548 37.037 2.79 0.00 36.77 3.21
4367 7492 8.515695 TGTGCTAGTATGTTAGTACTATGTGT 57.484 34.615 2.79 0.00 36.77 3.72
4438 7563 2.018542 TGGTACTACGCAATCAAGGC 57.981 50.000 0.00 0.00 0.00 4.35
4441 7566 2.418197 GGTACTACGCAATCAAGGCAGA 60.418 50.000 0.00 0.00 0.00 4.26
4712 8635 1.301637 CATGATGCATCGGCCGGTA 60.302 57.895 27.83 10.37 40.13 4.02
4749 8672 2.437180 CTCTGCGCCCATGCTTCA 60.437 61.111 4.18 0.00 35.36 3.02
4757 8680 0.236711 GCCCATGCTTCAATCGATCG 59.763 55.000 9.36 9.36 33.53 3.69
4821 8753 7.870027 ACCAAGAATACTCTACTACTACTCCA 58.130 38.462 0.00 0.00 0.00 3.86
4839 8780 1.099689 CATGGCTCACACATGCATGA 58.900 50.000 32.75 10.76 39.23 3.07
4844 8785 2.479049 GGCTCACACATGCATGAATGAC 60.479 50.000 32.75 23.04 0.00 3.06
4893 8837 1.237285 AAACAGACATGCACCCGCTC 61.237 55.000 0.00 0.00 39.64 5.03
4918 8862 9.761504 TCTGTTTAATTGATCTTGCAATCAAAA 57.238 25.926 17.03 7.44 45.91 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.097361 GACTGAACCCCCGCCTCC 62.097 72.222 0.00 0.00 0.00 4.30
7 8 1.262640 TAAGACTGAACCCCCGCCTC 61.263 60.000 0.00 0.00 0.00 4.70
8 9 1.229400 TAAGACTGAACCCCCGCCT 60.229 57.895 0.00 0.00 0.00 5.52
9 10 1.078637 GTAAGACTGAACCCCCGCC 60.079 63.158 0.00 0.00 0.00 6.13
10 11 1.078637 GGTAAGACTGAACCCCCGC 60.079 63.158 0.00 0.00 0.00 6.13
11 12 0.688487 TTGGTAAGACTGAACCCCCG 59.312 55.000 5.09 0.00 34.69 5.73
12 13 2.511659 GTTTGGTAAGACTGAACCCCC 58.488 52.381 5.09 0.00 34.69 5.40
13 14 2.107726 AGGTTTGGTAAGACTGAACCCC 59.892 50.000 5.09 0.57 40.42 4.95
14 15 3.503800 AGGTTTGGTAAGACTGAACCC 57.496 47.619 5.09 0.00 40.42 4.11
15 16 4.024302 CGAAAGGTTTGGTAAGACTGAACC 60.024 45.833 1.06 1.06 39.97 3.62
16 17 4.573607 ACGAAAGGTTTGGTAAGACTGAAC 59.426 41.667 0.00 0.00 0.00 3.18
17 18 4.773013 ACGAAAGGTTTGGTAAGACTGAA 58.227 39.130 0.00 0.00 0.00 3.02
18 19 4.411256 ACGAAAGGTTTGGTAAGACTGA 57.589 40.909 0.00 0.00 0.00 3.41
19 20 4.318546 CGAACGAAAGGTTTGGTAAGACTG 60.319 45.833 0.00 0.00 39.50 3.51
20 21 3.805971 CGAACGAAAGGTTTGGTAAGACT 59.194 43.478 0.00 0.00 39.50 3.24
21 22 3.605461 GCGAACGAAAGGTTTGGTAAGAC 60.605 47.826 0.00 0.00 39.50 3.01
29 30 2.067013 GCTAGAGCGAACGAAAGGTTT 58.933 47.619 0.00 0.00 39.50 3.27
53 54 6.920817 AGGAAAATAAAAAGACATTCGGGAC 58.079 36.000 0.00 0.00 0.00 4.46
65 66 9.733219 CGGCGGTTATTATAAGGAAAATAAAAA 57.267 29.630 0.00 0.00 31.30 1.94
73 74 6.756299 AAAAACGGCGGTTATTATAAGGAA 57.244 33.333 12.04 0.00 34.62 3.36
127 129 9.474313 AAGCAGGATAAAAGTGATGGTTATTAA 57.526 29.630 0.00 0.00 0.00 1.40
134 136 6.458210 ACAAAAAGCAGGATAAAAGTGATGG 58.542 36.000 0.00 0.00 0.00 3.51
135 137 7.951530 AACAAAAAGCAGGATAAAAGTGATG 57.048 32.000 0.00 0.00 0.00 3.07
169 171 3.134442 ACAAACATGATGCCCACAGTTTT 59.866 39.130 0.00 0.00 35.48 2.43
174 176 3.464907 CAAAACAAACATGATGCCCACA 58.535 40.909 0.00 0.00 0.00 4.17
188 190 4.271291 GGCGGTTTCTTTAATGCAAAACAA 59.729 37.500 10.63 0.00 34.15 2.83
214 216 8.584157 TCGAGTTGTTTTAGTAAACTATGGGTA 58.416 33.333 0.00 0.00 43.25 3.69
221 223 6.311200 ACGTGTTCGAGTTGTTTTAGTAAACT 59.689 34.615 0.00 0.00 41.00 2.66
227 229 6.068931 CCATTACGTGTTCGAGTTGTTTTAG 58.931 40.000 0.00 0.00 40.62 1.85
228 230 5.523188 ACCATTACGTGTTCGAGTTGTTTTA 59.477 36.000 0.00 0.00 40.62 1.52
229 231 4.333372 ACCATTACGTGTTCGAGTTGTTTT 59.667 37.500 0.00 0.00 40.62 2.43
231 233 3.460103 ACCATTACGTGTTCGAGTTGTT 58.540 40.909 0.00 0.00 40.62 2.83
264 267 0.179084 GCGGCAGTTAGGTGCTATGA 60.179 55.000 0.00 0.00 43.45 2.15
266 269 0.105039 GAGCGGCAGTTAGGTGCTAT 59.895 55.000 1.45 0.00 43.45 2.97
336 339 9.875691 CTGGATTATCAACCGATGATTATTAGA 57.124 33.333 8.63 0.00 46.85 2.10
337 340 9.658799 ACTGGATTATCAACCGATGATTATTAG 57.341 33.333 8.63 9.67 46.85 1.73
339 342 8.924511 AACTGGATTATCAACCGATGATTATT 57.075 30.769 8.63 0.00 46.85 1.40
340 343 8.924511 AAACTGGATTATCAACCGATGATTAT 57.075 30.769 8.63 5.86 46.85 1.28
341 344 8.746052 AAAACTGGATTATCAACCGATGATTA 57.254 30.769 8.63 1.56 46.85 1.75
342 345 7.645058 AAAACTGGATTATCAACCGATGATT 57.355 32.000 8.63 0.00 46.85 2.57
369 372 4.819630 ACAGGCTCATCGTTGTTTTAGAAA 59.180 37.500 0.00 0.00 0.00 2.52
370 373 4.385825 ACAGGCTCATCGTTGTTTTAGAA 58.614 39.130 0.00 0.00 0.00 2.10
381 384 2.293122 TGAAAACCAAACAGGCTCATCG 59.707 45.455 0.00 0.00 43.14 3.84
383 386 4.961438 AATGAAAACCAAACAGGCTCAT 57.039 36.364 0.00 0.00 43.14 2.90
384 387 6.945435 TCTATAATGAAAACCAAACAGGCTCA 59.055 34.615 0.00 0.00 43.14 4.26
385 388 7.391148 TCTATAATGAAAACCAAACAGGCTC 57.609 36.000 0.00 0.00 43.14 4.70
387 390 8.088365 AGTTTCTATAATGAAAACCAAACAGGC 58.912 33.333 0.00 0.00 37.63 4.85
391 394 9.744468 ACACAGTTTCTATAATGAAAACCAAAC 57.256 29.630 0.00 0.00 37.63 2.93
442 502 7.552687 TCCAAAAATAGTCATACACACTCATCC 59.447 37.037 0.00 0.00 0.00 3.51
625 2515 8.851145 GTGAGCCGATATATTTATCCTGAGATA 58.149 37.037 0.00 0.00 33.67 1.98
646 2537 8.325421 TGTATACTGCTAGAGTTATAGTGAGC 57.675 38.462 4.17 0.00 35.96 4.26
703 2595 2.885135 ATGGTCTGTCCTGCATTTCA 57.115 45.000 0.00 0.00 37.07 2.69
704 2596 3.760684 AGAAATGGTCTGTCCTGCATTTC 59.239 43.478 1.46 1.46 38.55 2.17
711 2603 5.574970 AAGAAGAAGAAATGGTCTGTCCT 57.425 39.130 0.00 0.00 36.40 3.85
860 2769 1.132527 TCTGGGGAGTGAAGGAAGGAA 60.133 52.381 0.00 0.00 0.00 3.36
869 2778 0.613260 CGATGGTTTCTGGGGAGTGA 59.387 55.000 0.00 0.00 0.00 3.41
912 2830 1.017701 GCTTCAACGGGAGTAACGGG 61.018 60.000 0.00 0.00 46.69 5.28
976 2897 2.601666 AGAGCGGACCAGCACAGA 60.602 61.111 10.28 0.00 40.15 3.41
1162 3083 2.680352 GTCCAGCAGAGACCCGGA 60.680 66.667 0.73 0.00 0.00 5.14
1283 3208 2.806945 TCATCGGCTGGGAAAGAAAT 57.193 45.000 0.00 0.00 0.00 2.17
1318 3262 1.610624 GGTGGTTCTCCTGCGATTCAA 60.611 52.381 0.00 0.00 34.23 2.69
1334 3278 1.746615 CTCCAATGCTGACGGGTGG 60.747 63.158 0.00 0.00 0.00 4.61
1381 3325 0.877649 CATGACGATCTGCTTCCCCG 60.878 60.000 0.00 0.00 0.00 5.73
1553 3523 2.412325 GCGTCAAAGACCCACGTTAATG 60.412 50.000 0.00 0.00 35.91 1.90
1661 3636 2.116238 AGCACTACGGGATATGTTGGT 58.884 47.619 0.00 0.00 0.00 3.67
1710 3705 4.094739 GCACCAAGAAAGCAACAACAAAAT 59.905 37.500 0.00 0.00 0.00 1.82
1781 3846 1.269726 CGGCATGCAAGAAAAACAGGT 60.270 47.619 21.36 0.00 0.00 4.00
1782 3847 1.421382 CGGCATGCAAGAAAAACAGG 58.579 50.000 21.36 0.00 0.00 4.00
1783 3848 0.785979 GCGGCATGCAAGAAAAACAG 59.214 50.000 21.36 0.00 45.45 3.16
1784 3849 2.897780 GCGGCATGCAAGAAAAACA 58.102 47.368 21.36 0.00 45.45 2.83
1857 3979 6.371271 GTGCCCTTTTGCATGTACATATTTTT 59.629 34.615 8.32 0.00 44.30 1.94
1858 3980 5.874261 GTGCCCTTTTGCATGTACATATTTT 59.126 36.000 8.32 0.00 44.30 1.82
1859 3981 5.046735 TGTGCCCTTTTGCATGTACATATTT 60.047 36.000 8.32 0.00 44.30 1.40
1860 3982 4.465660 TGTGCCCTTTTGCATGTACATATT 59.534 37.500 8.32 0.00 44.30 1.28
1861 3983 4.022603 TGTGCCCTTTTGCATGTACATAT 58.977 39.130 8.32 0.00 44.30 1.78
1862 3984 3.425659 TGTGCCCTTTTGCATGTACATA 58.574 40.909 8.32 0.00 44.30 2.29
1863 3985 2.231964 CTGTGCCCTTTTGCATGTACAT 59.768 45.455 1.41 1.41 44.30 2.29
1864 3986 1.612950 CTGTGCCCTTTTGCATGTACA 59.387 47.619 0.00 0.00 44.30 2.90
1865 3987 1.669795 GCTGTGCCCTTTTGCATGTAC 60.670 52.381 0.00 0.00 44.30 2.90
1866 3988 0.602562 GCTGTGCCCTTTTGCATGTA 59.397 50.000 0.00 0.00 44.30 2.29
1867 3989 1.368579 GCTGTGCCCTTTTGCATGT 59.631 52.632 0.00 0.00 44.30 3.21
1868 3990 1.735198 CGCTGTGCCCTTTTGCATG 60.735 57.895 0.00 0.00 44.30 4.06
1869 3991 1.252904 ATCGCTGTGCCCTTTTGCAT 61.253 50.000 0.00 0.00 44.30 3.96
1870 3992 1.865788 GATCGCTGTGCCCTTTTGCA 61.866 55.000 0.00 0.00 39.37 4.08
1871 3993 1.153958 GATCGCTGTGCCCTTTTGC 60.154 57.895 0.00 0.00 0.00 3.68
1872 3994 1.135315 CGATCGCTGTGCCCTTTTG 59.865 57.895 0.26 0.00 0.00 2.44
1873 3995 0.889186 AACGATCGCTGTGCCCTTTT 60.889 50.000 16.60 0.00 0.00 2.27
1874 3996 0.889186 AAACGATCGCTGTGCCCTTT 60.889 50.000 16.60 2.47 0.00 3.11
1875 3997 0.889186 AAAACGATCGCTGTGCCCTT 60.889 50.000 16.60 0.00 0.00 3.95
1876 3998 0.889186 AAAAACGATCGCTGTGCCCT 60.889 50.000 16.60 0.00 0.00 5.19
1877 3999 0.800012 TAAAAACGATCGCTGTGCCC 59.200 50.000 16.60 0.00 0.00 5.36
1878 4000 2.095213 TCATAAAAACGATCGCTGTGCC 59.905 45.455 16.60 0.00 0.00 5.01
1879 4001 3.345714 CTCATAAAAACGATCGCTGTGC 58.654 45.455 16.60 0.00 0.00 4.57
1907 4029 0.171903 GGCGGAAGTACTAGTGCGAA 59.828 55.000 12.04 0.00 0.00 4.70
1998 4171 8.546597 ACAAATACAGTGCTCTTTTTGTTTTT 57.453 26.923 12.17 3.45 34.60 1.94
2040 4247 4.518970 AGTTGAACACCTGCGAACATATTT 59.481 37.500 0.00 0.00 0.00 1.40
2048 4255 1.400142 CACAAAGTTGAACACCTGCGA 59.600 47.619 0.00 0.00 0.00 5.10
2186 4393 9.353999 GAGAGAGAGAATAAGTCAAGAAGAAAC 57.646 37.037 0.00 0.00 0.00 2.78
2460 4699 9.515226 GGTTGCTAATAGTTGATTGGGAATATA 57.485 33.333 0.00 0.00 38.34 0.86
2683 4982 2.192979 GCATCCCATTCCGCCTCA 59.807 61.111 0.00 0.00 0.00 3.86
2749 5048 3.500471 GGACCTTTCTTCCCTTGGTGATT 60.500 47.826 0.00 0.00 0.00 2.57
2940 5270 2.282110 TTTGCAGGCTAAGCGGCA 60.282 55.556 1.45 0.00 41.46 5.69
2963 5293 2.080693 GGTTACGACAATCATGTGCCA 58.919 47.619 0.00 0.00 40.74 4.92
2985 5324 4.851010 TCTTAAAAAGAAAGAAACCGCCG 58.149 39.130 0.00 0.00 33.83 6.46
3068 5412 5.639931 GGTCTTTTCTTGGTCTCTCATGTAC 59.360 44.000 0.00 0.00 0.00 2.90
3230 5594 6.381801 CAAGTAAGTAAAAAGACCTGCATGG 58.618 40.000 0.00 0.00 42.93 3.66
3237 5706 8.430828 CGTTAGTAGCAAGTAAGTAAAAAGACC 58.569 37.037 0.00 0.00 0.00 3.85
3243 5712 9.965824 ACTTTACGTTAGTAGCAAGTAAGTAAA 57.034 29.630 0.00 0.00 34.13 2.01
3722 6310 2.713863 ACGGCTAGCTCTACTACTGT 57.286 50.000 15.72 0.00 0.00 3.55
3774 6370 4.226761 CAAACAACTTTATCGGGAAGCAC 58.773 43.478 0.00 0.00 0.00 4.40
3826 6422 5.782047 TGTCAAACTCAAAGCCCATAATTG 58.218 37.500 0.00 0.00 0.00 2.32
3992 6776 8.473358 TGTACTAACTATATAGCCTGCTTGAA 57.527 34.615 9.78 0.00 0.00 2.69
3995 6779 8.651589 TGATGTACTAACTATATAGCCTGCTT 57.348 34.615 9.78 0.00 0.00 3.91
4043 6831 4.505808 TGAAACGAAAGACACACCAAGTA 58.494 39.130 0.00 0.00 0.00 2.24
4135 6932 0.620556 CCTTCAGAGCCAAGGCCTAA 59.379 55.000 5.16 0.00 43.17 2.69
4219 7156 5.193679 GGCTACTTTGTCACTCCCATTATT 58.806 41.667 0.00 0.00 0.00 1.40
4220 7157 4.385310 GGGCTACTTTGTCACTCCCATTAT 60.385 45.833 0.00 0.00 32.68 1.28
4221 7158 3.054655 GGGCTACTTTGTCACTCCCATTA 60.055 47.826 0.00 0.00 32.68 1.90
4245 7182 4.640771 ATAGTGCAGGGTGAGAAAAAGA 57.359 40.909 0.00 0.00 0.00 2.52
4293 7244 8.155510 ACAGAGATCACATCATAACATGCTAAT 58.844 33.333 0.00 0.00 0.00 1.73
4299 7250 7.789026 TCTCAACAGAGATCACATCATAACAT 58.211 34.615 0.00 0.00 33.60 2.71
4340 7381 9.452065 CACATAGTACTAACATACTAGCACAAG 57.548 37.037 6.70 0.00 40.21 3.16
4353 7394 7.201145 CAGGTACCATGACACATAGTACTAAC 58.799 42.308 15.94 0.00 34.94 2.34
4354 7395 6.322969 CCAGGTACCATGACACATAGTACTAA 59.677 42.308 15.94 0.00 34.94 2.24
4356 7397 4.649674 CCAGGTACCATGACACATAGTACT 59.350 45.833 15.94 0.00 34.94 2.73
4357 7398 4.404715 ACCAGGTACCATGACACATAGTAC 59.595 45.833 15.94 10.35 34.01 2.73
4360 7401 3.490933 CGACCAGGTACCATGACACATAG 60.491 52.174 15.94 0.00 0.00 2.23
4366 7491 0.108329 CCACGACCAGGTACCATGAC 60.108 60.000 15.94 3.93 0.00 3.06
4367 7492 0.543410 ACCACGACCAGGTACCATGA 60.543 55.000 15.94 0.00 37.67 3.07
4424 7549 2.476854 GCTTTCTGCCTTGATTGCGTAG 60.477 50.000 0.00 0.00 35.15 3.51
4425 7550 1.468520 GCTTTCTGCCTTGATTGCGTA 59.531 47.619 0.00 0.00 35.15 4.42
4426 7551 0.242017 GCTTTCTGCCTTGATTGCGT 59.758 50.000 0.00 0.00 35.15 5.24
4427 7552 0.524862 AGCTTTCTGCCTTGATTGCG 59.475 50.000 0.00 0.00 44.23 4.85
4438 7563 0.029035 GATCGCATGCCAGCTTTCTG 59.971 55.000 13.15 0.00 40.02 3.02
4441 7566 1.434622 CTCGATCGCATGCCAGCTTT 61.435 55.000 13.15 0.00 0.00 3.51
4476 7614 0.390603 TACCCATACACACGCACTGC 60.391 55.000 0.00 0.00 0.00 4.40
4483 7621 3.065233 CACACATGCATACCCATACACAC 59.935 47.826 0.00 0.00 0.00 3.82
4578 7776 2.361119 CCATGCATTGATCTGAAGGTGG 59.639 50.000 0.00 0.00 0.00 4.61
4613 7816 1.731700 GCCACCAGCATGCAGTATG 59.268 57.895 21.98 12.10 42.97 2.39
4614 7817 1.820906 CGCCACCAGCATGCAGTAT 60.821 57.895 21.98 0.00 44.04 2.12
4615 7818 2.436469 CGCCACCAGCATGCAGTA 60.436 61.111 21.98 0.00 44.04 2.74
4619 7822 3.680620 TACTCCGCCACCAGCATGC 62.681 63.158 10.51 10.51 44.04 4.06
4620 7823 0.676466 TTTACTCCGCCACCAGCATG 60.676 55.000 0.00 0.00 44.04 4.06
4621 7824 0.255890 ATTTACTCCGCCACCAGCAT 59.744 50.000 0.00 0.00 44.04 3.79
4622 7825 0.037590 AATTTACTCCGCCACCAGCA 59.962 50.000 0.00 0.00 44.04 4.41
4623 7826 0.733150 GAATTTACTCCGCCACCAGC 59.267 55.000 0.00 0.00 38.52 4.85
4624 7827 1.339631 TGGAATTTACTCCGCCACCAG 60.340 52.381 0.00 0.00 38.44 4.00
4625 7828 0.693622 TGGAATTTACTCCGCCACCA 59.306 50.000 0.00 0.00 38.44 4.17
4749 8672 2.025727 GACCGACCGCGATCGATT 59.974 61.111 27.57 11.12 45.13 3.34
4767 8696 1.275066 GATTCGATGCTGCGTCTGC 59.725 57.895 18.79 2.96 43.20 4.26
4821 8753 1.842052 TTCATGCATGTGTGAGCCAT 58.158 45.000 25.43 0.00 0.00 4.40
4839 8780 2.715046 AGGTGAATGTGATGCGTCATT 58.285 42.857 12.67 2.88 36.60 2.57
4844 8785 1.935873 CAGGTAGGTGAATGTGATGCG 59.064 52.381 0.00 0.00 0.00 4.73
4918 8862 6.369005 CCGATCGACGTCAAATTATACTACT 58.631 40.000 18.66 0.00 40.78 2.57


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

AutoCloner maintained by Alex Coulton.