Multiple sequence alignment - TraesCS7A01G004200

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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 TraesCS7A01G004200 chr7A 100.000 3933 0 0 981 4913 2093388 2097320 0.000000e+00 7263.0
1 TraesCS7A01G004200 chr7A 96.036 3431 129 3 981 4408 2827339 2830765 0.000000e+00 5576.0
2 TraesCS7A01G004200 chr7A 88.288 2442 269 16 1901 4333 3780565 3782998 0.000000e+00 2909.0
3 TraesCS7A01G004200 chr7A 100.000 754 0 0 1 754 2092408 2093161 0.000000e+00 1393.0
4 TraesCS7A01G004200 chr7A 95.122 451 19 3 298 746 2826671 2827120 0.000000e+00 708.0
5 TraesCS7A01G004200 chr7A 80.349 916 140 14 993 1884 3779574 3780473 0.000000e+00 658.0
6 TraesCS7A01G004200 chr7A 96.154 286 10 1 4629 4913 2830813 2831098 2.680000e-127 466.0
7 TraesCS7A01G004200 chr7A 91.586 309 17 3 1 303 2826258 2826563 7.610000e-113 418.0
8 TraesCS7A01G004200 chr7A 92.857 112 8 0 4541 4652 3783024 3783135 3.930000e-36 163.0
9 TraesCS7A01G004200 chr7A 81.773 203 17 12 4722 4905 3783252 3783453 8.520000e-33 152.0
10 TraesCS7A01G004200 chr4A 92.344 3422 237 16 981 4397 739630461 739627060 0.000000e+00 4844.0
11 TraesCS7A01G004200 chr4A 92.185 3442 238 16 981 4408 742036051 742032627 0.000000e+00 4837.0
12 TraesCS7A01G004200 chr4A 90.994 3431 245 19 981 4397 740541131 740537751 0.000000e+00 4566.0
13 TraesCS7A01G004200 chr4A 80.157 2540 428 48 1887 4403 740209447 740206961 0.000000e+00 1829.0
14 TraesCS7A01G004200 chr4A 94.436 647 31 2 981 1622 739844222 739843576 0.000000e+00 990.0
15 TraesCS7A01G004200 chr4A 92.742 372 21 2 4541 4912 742032632 742032267 2.600000e-147 532.0
16 TraesCS7A01G004200 chr4A 87.636 461 26 7 298 754 739844721 739844288 1.580000e-139 507.0
17 TraesCS7A01G004200 chr4A 87.202 461 28 6 298 754 739630975 739630542 3.420000e-136 496.0
18 TraesCS7A01G004200 chr4A 87.202 461 28 6 298 754 742037012 742036579 3.420000e-136 496.0
19 TraesCS7A01G004200 chr4A 86.985 461 29 6 298 754 740541645 740541212 1.590000e-134 490.0
20 TraesCS7A01G004200 chr4A 89.008 373 26 10 4541 4912 740537741 740537383 9.700000e-122 448.0
21 TraesCS7A01G004200 chr4A 76.856 808 150 21 981 1770 740219870 740219082 5.880000e-114 422.0
22 TraesCS7A01G004200 chr4A 84.722 432 46 6 3958 4387 740161376 740161789 9.840000e-112 414.0
23 TraesCS7A01G004200 chr4A 90.154 325 18 2 4541 4865 739627050 739626740 1.270000e-110 411.0
24 TraesCS7A01G004200 chr4A 90.066 302 26 2 1 298 739728785 739728484 5.960000e-104 388.0
25 TraesCS7A01G004200 chr4A 89.803 304 25 1 1 298 742124022 742123719 7.710000e-103 385.0
26 TraesCS7A01G004200 chr4A 100.000 42 0 0 3904 3945 740161343 740161384 1.470000e-10 78.7
27 TraesCS7A01G004200 chr7D 85.982 3417 419 21 1001 4397 3858717 3855341 0.000000e+00 3602.0
28 TraesCS7A01G004200 chr7D 85.827 3415 411 41 981 4361 2408357 2411732 0.000000e+00 3557.0
29 TraesCS7A01G004200 chr7D 86.227 2534 318 12 1896 4408 2651653 2654176 0.000000e+00 2717.0
30 TraesCS7A01G004200 chr7D 80.394 2591 419 57 1854 4408 3688296 3690833 0.000000e+00 1888.0
31 TraesCS7A01G004200 chr7D 78.715 794 137 18 987 1770 3685928 3686699 7.340000e-138 501.0
32 TraesCS7A01G004200 chr7D 90.263 380 28 2 4543 4913 3855326 3854947 5.720000e-134 488.0
33 TraesCS7A01G004200 chr7D 77.793 734 140 11 981 1710 2650054 2650768 9.770000e-117 431.0
34 TraesCS7A01G004200 chr7D 90.068 292 19 6 4543 4831 2654173 2654457 2.160000e-98 370.0
35 TraesCS7A01G004200 chr7D 86.364 154 12 4 105 251 3859174 3859023 5.090000e-35 159.0
36 TraesCS7A01G004200 chrUn 87.202 461 28 6 298 754 444984922 444985355 3.420000e-136 496.0
37 TraesCS7A01G004200 chr5D 72.941 850 161 45 2544 3372 422947565 422946764 1.060000e-56 231.0
38 TraesCS7A01G004200 chr5D 100.000 31 0 0 1737 1767 29569562 29569532 1.910000e-04 58.4
39 TraesCS7A01G004200 chr5B 73.219 758 141 39 2599 3337 510560711 510559997 8.280000e-53 219.0
40 TraesCS7A01G004200 chr5B 88.356 146 9 7 4405 4547 699107654 699107794 8.460000e-38 169.0
41 TraesCS7A01G004200 chr5B 71.471 680 136 32 2599 3261 510510184 510510822 1.440000e-25 128.0
42 TraesCS7A01G004200 chr5B 100.000 31 0 0 1737 1767 21696803 21696773 1.910000e-04 58.4
43 TraesCS7A01G004200 chr5A 92.414 145 7 3 4405 4545 606956110 606956254 2.320000e-48 204.0
44 TraesCS7A01G004200 chr6A 91.111 135 3 5 4403 4534 82953771 82953899 1.820000e-39 174.0
45 TraesCS7A01G004200 chr6A 85.926 135 9 10 4404 4530 200245821 200245953 8.580000e-28 135.0
46 TraesCS7A01G004200 chr4B 88.356 146 12 4 4403 4548 441610330 441610190 2.350000e-38 171.0
47 TraesCS7A01G004200 chr4B 87.324 142 13 5 4403 4544 297398572 297398708 1.830000e-34 158.0
48 TraesCS7A01G004200 chr4B 97.778 90 2 0 4403 4492 575576906 575576817 6.580000e-34 156.0
49 TraesCS7A01G004200 chr4B 77.070 157 22 6 4391 4547 538805039 538804897 1.470000e-10 78.7
50 TraesCS7A01G004200 chr1B 87.179 156 7 5 4405 4547 90646621 90646776 1.090000e-36 165.0
51 TraesCS7A01G004200 chr2A 87.500 144 7 6 4404 4544 98103419 98103284 6.580000e-34 156.0
52 TraesCS7A01G004200 chr7B 91.071 112 1 4 4403 4514 109211618 109211720 5.130000e-30 143.0


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 TraesCS7A01G004200 chr7A 2092408 2097320 4912 False 4328.000000 7263 100.000000 1 4913 2 chr7A.!!$F1 4912
1 TraesCS7A01G004200 chr7A 2826258 2831098 4840 False 1792.000000 5576 94.724500 1 4913 4 chr7A.!!$F2 4912
2 TraesCS7A01G004200 chr7A 3779574 3783453 3879 False 970.500000 2909 85.816750 993 4905 4 chr7A.!!$F3 3912
3 TraesCS7A01G004200 chr4A 742032267 742037012 4745 True 1955.000000 4837 90.709667 298 4912 3 chr4A.!!$R8 4614
4 TraesCS7A01G004200 chr4A 739626740 739630975 4235 True 1917.000000 4844 89.900000 298 4865 3 chr4A.!!$R5 4567
5 TraesCS7A01G004200 chr4A 740537383 740541645 4262 True 1834.666667 4566 88.995667 298 4912 3 chr4A.!!$R7 4614
6 TraesCS7A01G004200 chr4A 740206961 740209447 2486 True 1829.000000 1829 80.157000 1887 4403 1 chr4A.!!$R2 2516
7 TraesCS7A01G004200 chr4A 739843576 739844721 1145 True 748.500000 990 91.036000 298 1622 2 chr4A.!!$R6 1324
8 TraesCS7A01G004200 chr4A 740219082 740219870 788 True 422.000000 422 76.856000 981 1770 1 chr4A.!!$R3 789
9 TraesCS7A01G004200 chr7D 2408357 2411732 3375 False 3557.000000 3557 85.827000 981 4361 1 chr7D.!!$F1 3380
10 TraesCS7A01G004200 chr7D 3854947 3859174 4227 True 1416.333333 3602 87.536333 105 4913 3 chr7D.!!$R1 4808
11 TraesCS7A01G004200 chr7D 3685928 3690833 4905 False 1194.500000 1888 79.554500 987 4408 2 chr7D.!!$F3 3421
12 TraesCS7A01G004200 chr7D 2650054 2654457 4403 False 1172.666667 2717 84.696000 981 4831 3 chr7D.!!$F2 3850
13 TraesCS7A01G004200 chr5D 422946764 422947565 801 True 231.000000 231 72.941000 2544 3372 1 chr5D.!!$R2 828
14 TraesCS7A01G004200 chr5B 510559997 510560711 714 True 219.000000 219 73.219000 2599 3337 1 chr5B.!!$R2 738

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
264 271 0.748005 AACGTGTGAGGCAGCTTTGT 60.748 50.000 0.00 0.00 0.0 2.83 F
292 299 0.958876 TGAGGATGCTTGCAGTGCTG 60.959 55.000 17.60 10.33 0.0 4.41 F
1554 1991 0.750850 CCGTTCCTGTGGGTATCGAT 59.249 55.000 2.16 2.16 0.0 3.59 F
2494 4608 1.475930 GGAGATGGTTAGCAGAAGGGC 60.476 57.143 0.00 0.00 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1971 0.612732 TCGATACCCACAGGAACGGT 60.613 55.000 0.00 0.0 37.10 4.83 R
2300 4398 1.134175 CCAGGTCGGCGCATAATTTTT 59.866 47.619 10.83 0.0 0.00 1.94 R
2549 4663 0.511653 GCTCCGGTCGACAAGTTTTC 59.488 55.000 18.91 0.0 0.00 2.29 R
4027 6173 1.021390 GCAAGTCGCAGCCTGTACAT 61.021 55.000 0.00 0.0 41.79 2.29 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
21 22 2.304470 TGCATGGTAGACTGCCAAGTTA 59.696 45.455 16.79 3.40 39.72 2.24
30 31 3.954258 AGACTGCCAAGTTAAAGCAAACT 59.046 39.130 0.00 0.00 41.46 2.66
32 33 5.008712 AGACTGCCAAGTTAAAGCAAACTAC 59.991 40.000 0.28 0.00 38.76 2.73
40 41 8.028938 CCAAGTTAAAGCAAACTACTAATGCAT 58.971 33.333 0.00 0.00 42.45 3.96
111 112 1.394917 GGTGCAGAGTTGATTAGTGCG 59.605 52.381 0.00 0.00 36.92 5.34
130 131 5.009610 AGTGCGTCCAATGTAACATTTTCTT 59.990 36.000 0.00 0.00 0.00 2.52
248 255 9.983804 GGAGATAAGTTTAAAAACCTATGAACG 57.016 33.333 2.02 0.00 39.71 3.95
253 260 7.556733 AGTTTAAAAACCTATGAACGTGTGA 57.443 32.000 2.02 0.00 39.71 3.58
264 271 0.748005 AACGTGTGAGGCAGCTTTGT 60.748 50.000 0.00 0.00 0.00 2.83
292 299 0.958876 TGAGGATGCTTGCAGTGCTG 60.959 55.000 17.60 10.33 0.00 4.41
305 425 2.737039 GCAGTGCTGTAGTAGGAGAAGC 60.737 54.545 8.18 0.00 0.00 3.86
354 474 3.738830 TTCTGCGGTTTACTACTGTGT 57.261 42.857 0.00 0.00 35.43 3.72
369 489 3.030291 ACTGTGTTTTTGATGCCTTCCA 58.970 40.909 0.00 0.00 0.00 3.53
370 490 3.450457 ACTGTGTTTTTGATGCCTTCCAA 59.550 39.130 0.00 0.00 0.00 3.53
570 695 8.906238 TTAACTTAGTATTCTGGTAGTCCCTT 57.094 34.615 0.00 0.00 0.00 3.95
589 714 6.934645 GTCCCTTCGATCCATATTAATTGACA 59.065 38.462 0.00 0.00 0.00 3.58
733 858 1.759445 GAGCTCTACTTCATCCAGCCA 59.241 52.381 6.43 0.00 0.00 4.75
1008 1437 2.365293 GAGAGAGAGAGAAATGGAGGCC 59.635 54.545 0.00 0.00 0.00 5.19
1111 1542 2.668457 CGGAAGAACCTGAAGAATGACG 59.332 50.000 0.00 0.00 36.31 4.35
1204 1638 2.202440 GCAGCAGTGAAGCGCATG 60.202 61.111 11.47 0.77 40.15 4.06
1281 1718 1.233019 GCTTCATGCACAGTGTGACT 58.767 50.000 27.37 9.74 42.31 3.41
1405 1842 6.744175 ATAGATCAGAAGATGCTTCCAAGA 57.256 37.500 3.71 1.39 33.72 3.02
1434 1871 6.630071 AGAAAAATACAGCAACAACAACAGT 58.370 32.000 0.00 0.00 0.00 3.55
1534 1971 2.242965 ACCCATTCATCAGCTTCCATCA 59.757 45.455 0.00 0.00 0.00 3.07
1554 1991 0.750850 CCGTTCCTGTGGGTATCGAT 59.249 55.000 2.16 2.16 0.00 3.59
1710 2167 1.575419 ATGAAGTACGGGCTTGGGTA 58.425 50.000 0.00 0.00 0.00 3.69
2494 4608 1.475930 GGAGATGGTTAGCAGAAGGGC 60.476 57.143 0.00 0.00 0.00 5.19
2549 4663 2.109774 TGCCCCCATTAGCAATTTCAG 58.890 47.619 0.00 0.00 35.69 3.02
2581 4695 1.597302 CGGAGCATCATCCAGCCAG 60.597 63.158 0.00 0.00 39.53 4.85
2715 4829 3.082579 GCAGTCTACCCCTCGCCTG 62.083 68.421 0.00 0.00 0.00 4.85
2717 4831 2.760385 GTCTACCCCTCGCCTGCT 60.760 66.667 0.00 0.00 0.00 4.24
2764 4878 0.179032 TCACGCAAGGCCAAGAGAAA 60.179 50.000 5.01 0.00 46.39 2.52
2785 4911 6.716628 AGAAATGCAAGGTTTATCTCTTGTCA 59.283 34.615 0.00 0.00 41.56 3.58
2808 4934 1.278985 TCACTGACAATCTTGGGCGAT 59.721 47.619 0.00 0.00 0.00 4.58
2960 5086 2.373335 TGCCTTGGGAAAGCTGTTAA 57.627 45.000 0.00 0.00 0.00 2.01
2962 5088 2.239400 GCCTTGGGAAAGCTGTTAAGT 58.761 47.619 0.00 0.00 0.00 2.24
3151 5277 4.357918 AAGCTACAGACTTGGTTGTCAT 57.642 40.909 0.00 0.00 39.27 3.06
3154 5280 3.189287 GCTACAGACTTGGTTGTCATTGG 59.811 47.826 0.00 0.00 39.27 3.16
3166 5292 3.333029 TGTCATTGGAGAGCGAATTGA 57.667 42.857 0.00 0.00 0.00 2.57
3266 5392 3.572255 ACAAAGGTGAAAATATGGTGCGT 59.428 39.130 0.00 0.00 0.00 5.24
3724 5851 0.107654 CCAAGAGGGAGCTTTACCGG 60.108 60.000 0.00 0.00 40.01 5.28
3768 5895 2.253392 GCAAAGATCTTGTTGCCTCG 57.747 50.000 17.76 0.00 43.49 4.63
4013 6158 5.473162 TCACATCCTGGTAATGACACTTTTG 59.527 40.000 2.65 0.00 0.00 2.44
4027 6173 4.910195 ACACTTTTGTCTATCATGCAGGA 58.090 39.130 2.36 2.36 0.00 3.86
4028 6174 5.503927 ACACTTTTGTCTATCATGCAGGAT 58.496 37.500 18.98 18.98 0.00 3.24
4241 6413 5.468072 CGAAGTTAATGATCTGCTAAGCCAT 59.532 40.000 0.00 0.00 0.00 4.40
4243 6415 5.933617 AGTTAATGATCTGCTAAGCCATGA 58.066 37.500 0.00 0.00 0.00 3.07
4294 6466 7.885922 TGGTGACTTCCTGCTGTAATAAATAAA 59.114 33.333 0.00 0.00 0.00 1.40
4329 6501 7.167468 GTCTGTTGTTTGACATGTATTTTGGTC 59.833 37.037 0.00 0.00 33.75 4.02
4336 6509 6.809630 TGACATGTATTTTGGTCATTTCGA 57.190 33.333 0.00 0.00 35.51 3.71
4353 6526 7.494625 GTCATTTCGATCCCAGTCAACTTAATA 59.505 37.037 0.00 0.00 0.00 0.98
4397 6570 9.630098 ATTTCTCACAAATTTAGCACTACAATG 57.370 29.630 0.00 0.00 0.00 2.82
4406 6583 8.943909 AATTTAGCACTACAATGTCCTAGTAC 57.056 34.615 0.00 0.00 0.00 2.73
4407 6584 7.713734 TTTAGCACTACAATGTCCTAGTACT 57.286 36.000 0.00 0.00 0.00 2.73
4408 6585 5.838531 AGCACTACAATGTCCTAGTACTC 57.161 43.478 0.00 0.00 0.00 2.59
4409 6586 4.645588 AGCACTACAATGTCCTAGTACTCC 59.354 45.833 0.00 0.00 0.00 3.85
4410 6587 4.202131 GCACTACAATGTCCTAGTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
4411 6588 5.202004 CACTACAATGTCCTAGTACTCCCT 58.798 45.833 0.00 0.00 0.00 4.20
4412 6589 5.299782 CACTACAATGTCCTAGTACTCCCTC 59.700 48.000 0.00 0.00 0.00 4.30
4413 6590 3.644335 ACAATGTCCTAGTACTCCCTCC 58.356 50.000 0.00 0.00 0.00 4.30
4414 6591 2.623889 CAATGTCCTAGTACTCCCTCCG 59.376 54.545 0.00 0.00 0.00 4.63
4415 6592 1.293062 TGTCCTAGTACTCCCTCCGT 58.707 55.000 0.00 0.00 0.00 4.69
4416 6593 1.211457 TGTCCTAGTACTCCCTCCGTC 59.789 57.143 0.00 0.00 0.00 4.79
4417 6594 0.842635 TCCTAGTACTCCCTCCGTCC 59.157 60.000 0.00 0.00 0.00 4.79
4418 6595 0.178995 CCTAGTACTCCCTCCGTCCC 60.179 65.000 0.00 0.00 0.00 4.46
4419 6596 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
4420 6597 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4421 6598 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
4422 6599 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4423 6600 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4424 6601 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4425 6602 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4426 6603 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4427 6604 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4428 6605 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4429 6606 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4430 6607 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4431 6608 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4432 6609 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4433 6610 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4434 6611 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4435 6612 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4436 6613 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4437 6614 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4438 6615 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4439 6616 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4440 6617 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4441 6618 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4442 6619 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4450 6627 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
4451 6628 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4452 6629 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4453 6630 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4454 6631 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4455 6632 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4476 6653 7.761038 TGTATCAAGATACAGATACATCCGT 57.239 36.000 16.67 0.00 46.88 4.69
4477 6654 8.857694 TGTATCAAGATACAGATACATCCGTA 57.142 34.615 16.67 0.00 46.88 4.02
4478 6655 9.462606 TGTATCAAGATACAGATACATCCGTAT 57.537 33.333 16.67 0.00 46.88 3.06
4479 6656 9.938670 GTATCAAGATACAGATACATCCGTATC 57.061 37.037 13.81 14.01 42.99 2.24
4495 6672 9.516546 ACATCCGTATCTAGACAAATCTATACA 57.483 33.333 0.00 0.00 36.81 2.29
4498 6675 9.175312 TCCGTATCTAGACAAATCTATACATCC 57.825 37.037 0.00 0.00 36.81 3.51
4499 6676 8.123575 CCGTATCTAGACAAATCTATACATCCG 58.876 40.741 0.00 0.00 36.81 4.18
4500 6677 8.666573 CGTATCTAGACAAATCTATACATCCGT 58.333 37.037 0.00 0.00 36.81 4.69
4504 6681 9.961264 TCTAGACAAATCTATACATCCGTATCT 57.039 33.333 0.00 0.00 39.17 1.98
4507 6684 9.961264 AGACAAATCTATACATCCGTATCTAGA 57.039 33.333 0.00 0.00 39.17 2.43
4508 6685 9.991388 GACAAATCTATACATCCGTATCTAGAC 57.009 37.037 0.00 0.00 39.17 2.59
4509 6686 9.516546 ACAAATCTATACATCCGTATCTAGACA 57.483 33.333 0.00 0.00 39.17 3.41
4514 6691 9.961264 TCTATACATCCGTATCTAGACAAATCT 57.039 33.333 0.00 0.00 39.17 2.40
4518 6695 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
4519 6696 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
4520 6697 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
4521 6698 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
4522 6699 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
4523 6700 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
4531 6708 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4532 6709 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4533 6710 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4534 6711 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4535 6712 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4536 6713 2.514803 AGACAAGAATTTTGGGACGGG 58.485 47.619 0.00 0.00 0.00 5.28
4537 6714 1.544246 GACAAGAATTTTGGGACGGGG 59.456 52.381 0.00 0.00 0.00 5.73
4538 6715 0.894835 CAAGAATTTTGGGACGGGGG 59.105 55.000 0.00 0.00 0.00 5.40
4563 6740 7.396339 GGGAGTACTTGTTTGGGATAAATTCTT 59.604 37.037 0.00 0.00 0.00 2.52
4745 6972 4.367039 TTTGCCTGTAGTTAGCTTCCTT 57.633 40.909 0.00 0.00 0.00 3.36
4748 6975 3.326588 TGCCTGTAGTTAGCTTCCTTTGA 59.673 43.478 0.00 0.00 0.00 2.69
4786 7013 2.227388 GGACTCTGAACATTTGGCTGTG 59.773 50.000 0.00 0.00 0.00 3.66
4865 7134 3.806667 GGAGATGCTGCCTGCCCT 61.807 66.667 0.00 0.00 42.00 5.19
4905 7178 6.098552 GCTGGTACTTATCTACCCTCTCTTTT 59.901 42.308 0.00 0.00 36.09 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.010349 GCTTTAACTTGGCAGTCTACCAT 58.990 43.478 0.00 0.00 36.96 3.55
6 7 5.008712 AGTTTGCTTTAACTTGGCAGTCTAC 59.991 40.000 0.00 0.00 34.81 2.59
21 22 4.381932 GGCCATGCATTAGTAGTTTGCTTT 60.382 41.667 0.00 0.00 37.28 3.51
30 31 0.467804 TCGCTGGCCATGCATTAGTA 59.532 50.000 21.86 3.01 0.00 1.82
32 33 0.956633 AATCGCTGGCCATGCATTAG 59.043 50.000 21.86 4.95 0.00 1.73
40 41 2.203056 CGATCCAATCGCTGGCCA 60.203 61.111 4.71 4.71 46.55 5.36
66 67 3.863041 GACACCTTGTCTCTGGGTTATC 58.137 50.000 0.00 0.00 43.73 1.75
94 95 1.661112 GGACGCACTAATCAACTCTGC 59.339 52.381 0.00 0.00 0.00 4.26
130 131 4.142271 ACTGCGTTCCTGTCAATTTGAAAA 60.142 37.500 0.00 0.00 0.00 2.29
141 142 3.196207 ATGGGCACTGCGTTCCTGT 62.196 57.895 0.00 0.00 0.00 4.00
156 157 0.109597 GTTTGGCTTGCTGTCGATGG 60.110 55.000 0.00 0.00 0.00 3.51
248 255 1.394917 CGATACAAAGCTGCCTCACAC 59.605 52.381 0.00 0.00 0.00 3.82
253 260 3.118629 TCAATCTCGATACAAAGCTGCCT 60.119 43.478 0.00 0.00 0.00 4.75
264 271 3.070015 TGCAAGCATCCTCAATCTCGATA 59.930 43.478 0.00 0.00 0.00 2.92
305 425 7.591006 AGAAAATCACTGCATAATGCTTTTG 57.409 32.000 10.32 0.00 45.31 2.44
354 474 3.966665 ACCTCTTTGGAAGGCATCAAAAA 59.033 39.130 0.00 0.00 39.71 1.94
558 683 1.776662 TGGATCGAAGGGACTACCAG 58.223 55.000 0.00 0.00 43.89 4.00
564 689 6.934645 TGTCAATTAATATGGATCGAAGGGAC 59.065 38.462 0.00 0.00 0.00 4.46
570 695 8.731275 ACTTTGTGTCAATTAATATGGATCGA 57.269 30.769 0.00 0.00 0.00 3.59
589 714 4.602340 ACTCACTCCGATACAACTTTGT 57.398 40.909 0.00 0.00 44.86 2.83
627 752 7.950512 ACAAAATATCTTGTTCACATGGTTGA 58.049 30.769 0.00 0.00 36.05 3.18
1111 1542 6.484540 CAAACTCATGCTTGATGTAGATGAC 58.515 40.000 2.33 0.00 33.29 3.06
1204 1638 2.541588 GCACAATATTGATCCACACCGC 60.542 50.000 22.16 6.23 0.00 5.68
1281 1718 3.587061 TCCCTTTTTCTGAGTCAGCCATA 59.413 43.478 15.72 0.00 0.00 2.74
1405 1842 7.275888 TGTTGTTGCTGTATTTTTCTCTCAT 57.724 32.000 0.00 0.00 0.00 2.90
1534 1971 0.612732 TCGATACCCACAGGAACGGT 60.613 55.000 0.00 0.00 37.10 4.83
2300 4398 1.134175 CCAGGTCGGCGCATAATTTTT 59.866 47.619 10.83 0.00 0.00 1.94
2494 4608 3.981071 TGTATTGTCTCTTGGGGACAG 57.019 47.619 0.51 0.00 43.29 3.51
2503 4617 7.840931 TCAACATCACTACATGTATTGTCTCT 58.159 34.615 19.26 4.65 39.87 3.10
2549 4663 0.511653 GCTCCGGTCGACAAGTTTTC 59.488 55.000 18.91 0.00 0.00 2.29
2581 4695 0.958382 TTGTTACCGCTGGCATCCAC 60.958 55.000 0.00 0.00 0.00 4.02
2715 4829 1.146358 GCCGTCGGATGTTACTGAGC 61.146 60.000 17.49 0.00 0.00 4.26
2717 4831 0.892755 AAGCCGTCGGATGTTACTGA 59.107 50.000 17.49 0.00 0.00 3.41
2764 4878 4.946157 CCTGACAAGAGATAAACCTTGCAT 59.054 41.667 0.00 0.00 42.46 3.96
2785 4911 1.271597 GCCCAAGATTGTCAGTGACCT 60.272 52.381 20.43 7.71 0.00 3.85
2808 4934 3.321648 AGGACAGATGGGTGCGCA 61.322 61.111 5.66 5.66 33.93 6.09
2960 5086 2.367567 TCTTTTGGAAGCACCGTAGACT 59.632 45.455 0.00 0.00 42.61 3.24
2962 5088 2.631062 TCTCTTTTGGAAGCACCGTAGA 59.369 45.455 0.00 0.00 42.61 2.59
3151 5277 3.882888 AGTGTTTTCAATTCGCTCTCCAA 59.117 39.130 0.00 0.00 0.00 3.53
3154 5280 3.814945 CCAGTGTTTTCAATTCGCTCTC 58.185 45.455 0.00 0.00 0.00 3.20
3166 5292 3.197549 ACAACAAATCCTGCCAGTGTTTT 59.802 39.130 0.00 0.00 30.20 2.43
3208 5334 3.119280 TGATCCATGAGCTGTGCAAATTG 60.119 43.478 0.00 0.00 0.00 2.32
3266 5392 2.669229 TGACGTCGGCGGTAGACA 60.669 61.111 16.39 2.76 43.45 3.41
3724 5851 3.123620 CTGCAGCGACTTGAGGCC 61.124 66.667 0.00 0.00 0.00 5.19
3768 5895 1.635663 CCAGTGACGTGCCGGAAATC 61.636 60.000 5.05 0.00 0.00 2.17
4013 6158 4.564041 CCTGTACATCCTGCATGATAGAC 58.436 47.826 4.01 6.37 36.21 2.59
4020 6166 3.794737 CAGCCTGTACATCCTGCAT 57.205 52.632 0.00 0.00 0.00 3.96
4027 6173 1.021390 GCAAGTCGCAGCCTGTACAT 61.021 55.000 0.00 0.00 41.79 2.29
4028 6174 1.667830 GCAAGTCGCAGCCTGTACA 60.668 57.895 0.00 0.00 41.79 2.90
4294 6466 6.389830 TGTCAAACAACAGACATAGCAAAT 57.610 33.333 0.00 0.00 39.65 2.32
4313 6485 6.809630 TCGAAATGACCAAAATACATGTCA 57.190 33.333 0.00 0.00 41.52 3.58
4323 6495 3.244735 TGACTGGGATCGAAATGACCAAA 60.245 43.478 0.00 0.00 0.00 3.28
4329 6501 6.683974 ATTAAGTTGACTGGGATCGAAATG 57.316 37.500 0.00 0.00 0.00 2.32
4336 6509 5.430089 AGAAGCCTATTAAGTTGACTGGGAT 59.570 40.000 0.00 0.00 0.00 3.85
4353 6526 6.098409 TGAGAAATAATACTCCGAAGAAGCCT 59.902 38.462 0.00 0.00 32.84 4.58
4397 6570 1.476652 GGACGGAGGGAGTACTAGGAC 60.477 61.905 0.00 0.00 0.00 3.85
4406 6583 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4407 6584 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4408 6585 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4409 6586 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4410 6587 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4411 6588 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4412 6589 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4413 6590 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4414 6591 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4415 6592 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4416 6593 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4424 6601 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
4425 6602 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
4426 6603 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
4427 6604 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
4428 6605 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
4429 6606 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
4445 6622 9.462606 TGTATCTGTATCTTGATACATCCGTAT 57.537 33.333 19.74 12.44 45.53 3.06
4446 6623 8.857694 TGTATCTGTATCTTGATACATCCGTA 57.142 34.615 19.74 10.28 45.53 4.02
4447 6624 7.761038 TGTATCTGTATCTTGATACATCCGT 57.239 36.000 19.74 10.99 45.53 4.69
4469 6646 9.516546 TGTATAGATTTGTCTAGATACGGATGT 57.483 33.333 0.00 0.00 0.00 3.06
4472 6649 9.175312 GGATGTATAGATTTGTCTAGATACGGA 57.825 37.037 0.00 0.00 0.00 4.69
4473 6650 8.123575 CGGATGTATAGATTTGTCTAGATACGG 58.876 40.741 0.00 0.00 0.00 4.02
4474 6651 8.666573 ACGGATGTATAGATTTGTCTAGATACG 58.333 37.037 0.00 0.00 0.00 3.06
4478 6655 9.961264 AGATACGGATGTATAGATTTGTCTAGA 57.039 33.333 0.00 0.00 41.37 2.43
4481 6658 9.961264 TCTAGATACGGATGTATAGATTTGTCT 57.039 33.333 0.00 0.00 41.37 3.41
4482 6659 9.991388 GTCTAGATACGGATGTATAGATTTGTC 57.009 37.037 0.00 0.00 41.37 3.18
4483 6660 9.516546 TGTCTAGATACGGATGTATAGATTTGT 57.483 33.333 0.00 0.00 41.37 2.83
4488 6665 9.961264 AGATTTGTCTAGATACGGATGTATAGA 57.039 33.333 0.00 0.00 41.37 1.98
4492 6669 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4493 6670 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4494 6671 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4495 6672 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4496 6673 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4497 6674 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
4505 6682 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4506 6683 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4507 6684 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4508 6685 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4509 6686 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4510 6687 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4511 6688 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4512 6689 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4513 6690 4.156008 CCCGTCCCAAAATTCTTGTCTTAG 59.844 45.833 0.00 0.00 0.00 2.18
4514 6691 4.076394 CCCGTCCCAAAATTCTTGTCTTA 58.924 43.478 0.00 0.00 0.00 2.10
4515 6692 2.890945 CCCGTCCCAAAATTCTTGTCTT 59.109 45.455 0.00 0.00 0.00 3.01
4516 6693 2.514803 CCCGTCCCAAAATTCTTGTCT 58.485 47.619 0.00 0.00 0.00 3.41
4517 6694 1.544246 CCCCGTCCCAAAATTCTTGTC 59.456 52.381 0.00 0.00 0.00 3.18
4518 6695 1.627864 CCCCGTCCCAAAATTCTTGT 58.372 50.000 0.00 0.00 0.00 3.16
4519 6696 0.894835 CCCCCGTCCCAAAATTCTTG 59.105 55.000 0.00 0.00 0.00 3.02
4520 6697 3.374318 CCCCCGTCCCAAAATTCTT 57.626 52.632 0.00 0.00 0.00 2.52
4535 6712 1.069775 TCCCAAACAAGTACTCCCCC 58.930 55.000 0.00 0.00 0.00 5.40
4536 6713 4.579647 TTATCCCAAACAAGTACTCCCC 57.420 45.455 0.00 0.00 0.00 4.81
4537 6714 6.890268 AGAATTTATCCCAAACAAGTACTCCC 59.110 38.462 0.00 0.00 0.00 4.30
4538 6715 7.939784 AGAATTTATCCCAAACAAGTACTCC 57.060 36.000 0.00 0.00 0.00 3.85
4539 6716 9.010029 TCAAGAATTTATCCCAAACAAGTACTC 57.990 33.333 0.00 0.00 0.00 2.59
4540 6717 8.934023 TCAAGAATTTATCCCAAACAAGTACT 57.066 30.769 0.00 0.00 0.00 2.73
4563 6740 7.119116 ACTGCGTGTCATGTAAATAAAGATTCA 59.881 33.333 0.00 0.00 0.00 2.57
4578 6755 0.952497 CAGGAAGCACTGCGTGTCAT 60.952 55.000 9.76 0.00 35.75 3.06
4582 6759 2.941333 CACAGGAAGCACTGCGTG 59.059 61.111 0.00 4.61 42.21 5.34
4583 6760 2.974698 GCACAGGAAGCACTGCGT 60.975 61.111 0.00 0.00 42.21 5.24
4584 6761 2.667536 AGCACAGGAAGCACTGCG 60.668 61.111 0.00 0.00 42.21 5.18
4745 6972 5.360714 AGTCCAGAAAACAGAGCAAAATCAA 59.639 36.000 0.00 0.00 0.00 2.57
4748 6975 5.009410 CAGAGTCCAGAAAACAGAGCAAAAT 59.991 40.000 0.00 0.00 0.00 1.82
4786 7013 1.813178 GCCTCAAACCTCAAGCTAACC 59.187 52.381 0.00 0.00 0.00 2.85
4865 7134 2.106074 CAGCCGGCATTAGCGTGAA 61.106 57.895 31.54 0.00 43.41 3.18


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

AutoCloner maintained by Alex Coulton.