Multiple sequence alignment - TraesCS7D01G364400

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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 TraesCS7D01G364400 chr7D 100.000 7827 0 0 1 7827 469844627 469836801 0.000000e+00 14454.0
1 TraesCS7D01G364400 chr7D 90.795 239 22 0 5528 5766 407258582 407258820 3.520000e-83 320.0
2 TraesCS7D01G364400 chr7D 88.961 154 6 3 7189 7332 469833591 469833743 6.240000e-41 180.0
3 TraesCS7D01G364400 chr7B 97.229 4763 94 10 630 5380 493527433 493522697 0.000000e+00 8030.0
4 TraesCS7D01G364400 chr7B 96.431 1821 32 8 5381 7188 493522638 493520838 0.000000e+00 2972.0
5 TraesCS7D01G364400 chr7B 85.911 582 48 23 27 602 493527986 493527433 2.430000e-164 590.0
6 TraesCS7D01G364400 chr7B 88.703 239 27 0 5528 5766 418759417 418759655 7.680000e-75 292.0
7 TraesCS7D01G364400 chr7B 92.593 135 10 0 2095 2229 533773491 533773357 2.230000e-45 195.0
8 TraesCS7D01G364400 chr7A 92.517 1911 106 13 708 2593 529325564 529327462 0.000000e+00 2702.0
9 TraesCS7D01G364400 chr7A 93.210 1841 93 19 3552 5380 529328289 529330109 0.000000e+00 2678.0
10 TraesCS7D01G364400 chr7A 95.537 829 29 5 2716 3543 529327493 529328314 0.000000e+00 1319.0
11 TraesCS7D01G364400 chr7A 91.961 821 34 9 5762 6568 529330288 529331090 0.000000e+00 1122.0
12 TraesCS7D01G364400 chr7A 94.435 611 26 4 6578 7186 529331827 529332431 0.000000e+00 933.0
13 TraesCS7D01G364400 chr7A 91.852 135 11 0 2095 2229 573430966 573430832 1.040000e-43 189.0
14 TraesCS7D01G364400 chr7A 100.000 33 0 0 2635 2667 529327460 529327492 2.360000e-05 62.1
15 TraesCS7D01G364400 chr5D 91.217 649 23 8 7189 7827 558908046 558908670 0.000000e+00 852.0
16 TraesCS7D01G364400 chr5D 88.615 325 28 3 5977 6299 445650592 445650275 3.430000e-103 387.0
17 TraesCS7D01G364400 chr5D 87.278 338 31 4 5798 6133 445652731 445652404 7.410000e-100 375.0
18 TraesCS7D01G364400 chr5D 86.686 338 33 4 5798 6133 445650926 445650599 1.610000e-96 364.0
19 TraesCS7D01G364400 chr5D 83.616 354 50 8 3315 3666 544239395 544239742 7.570000e-85 326.0
20 TraesCS7D01G364400 chr5D 82.825 361 57 5 3314 3673 409571946 409571590 1.270000e-82 318.0
21 TraesCS7D01G364400 chr5D 81.566 396 12 8 7226 7621 561995474 561995140 3.600000e-68 270.0
22 TraesCS7D01G364400 chr5D 87.919 149 11 1 5977 6125 445652397 445652256 1.350000e-37 169.0
23 TraesCS7D01G364400 chr5D 89.147 129 9 4 5406 5533 445651067 445650943 1.050000e-33 156.0
24 TraesCS7D01G364400 chr5D 89.147 129 9 4 5406 5533 445652872 445652748 1.050000e-33 156.0
25 TraesCS7D01G364400 chrUn 91.420 641 22 4 7197 7827 1083950 1083333 0.000000e+00 848.0
26 TraesCS7D01G364400 chrUn 100.000 388 0 0 750 1137 480299476 480299089 0.000000e+00 717.0
27 TraesCS7D01G364400 chr2D 90.447 649 23 8 7189 7827 548612929 548613548 0.000000e+00 819.0
28 TraesCS7D01G364400 chr2D 92.806 139 9 1 2097 2235 489409416 489409553 4.790000e-47 200.0
29 TraesCS7D01G364400 chr2D 88.312 154 6 3 7189 7332 548628866 548628715 2.900000e-39 174.0
30 TraesCS7D01G364400 chr6A 87.328 655 46 8 7183 7827 383084032 383083405 0.000000e+00 715.0
31 TraesCS7D01G364400 chr6A 82.468 154 15 4 7189 7332 383080235 383080386 2.970000e-24 124.0
32 TraesCS7D01G364400 chr1D 89.646 367 38 0 2876 3242 302381908 302381542 1.190000e-127 468.0
33 TraesCS7D01G364400 chr1D 84.958 359 44 7 3313 3666 47331090 47330737 9.660000e-94 355.0
34 TraesCS7D01G364400 chr1D 90.952 210 18 1 995 1203 302382903 302382694 1.660000e-71 281.0
35 TraesCS7D01G364400 chr1D 85.870 92 10 2 5151 5241 225706223 225706134 2.330000e-15 95.3
36 TraesCS7D01G364400 chr1B 89.373 367 39 0 2876 3242 409250031 409249665 5.530000e-126 462.0
37 TraesCS7D01G364400 chr1B 85.515 359 43 6 3313 3666 67055292 67054938 4.460000e-97 366.0
38 TraesCS7D01G364400 chr1B 84.588 279 36 7 931 1203 409251041 409250764 3.600000e-68 270.0
39 TraesCS7D01G364400 chr1B 85.870 92 10 2 5151 5241 325813981 325813892 2.330000e-15 95.3
40 TraesCS7D01G364400 chr1A 88.828 367 41 0 2876 3242 377019243 377018877 1.200000e-122 451.0
41 TraesCS7D01G364400 chr1A 84.011 369 46 8 3313 3674 47213013 47212651 7.520000e-90 342.0
42 TraesCS7D01G364400 chr1A 90.476 210 19 1 995 1203 377020185 377019976 7.740000e-70 276.0
43 TraesCS7D01G364400 chr1A 78.212 179 20 10 5151 5314 292081884 292082058 6.460000e-16 97.1
44 TraesCS7D01G364400 chr6B 86.207 406 30 9 5762 6157 123492080 123491691 4.370000e-112 416.0
45 TraesCS7D01G364400 chr6B 90.000 130 9 3 5396 5524 123492203 123492077 1.750000e-36 165.0
46 TraesCS7D01G364400 chr6B 81.915 188 10 5 7470 7657 558602737 558602574 3.810000e-28 137.0
47 TraesCS7D01G364400 chr6D 86.146 397 39 10 5762 6157 75997910 75998291 1.570000e-111 414.0
48 TraesCS7D01G364400 chr6D 85.139 397 42 11 5762 6157 12621607 12621987 2.650000e-104 390.0
49 TraesCS7D01G364400 chr6D 88.703 239 23 3 5528 5766 386274287 386274521 9.940000e-74 289.0
50 TraesCS7D01G364400 chr6D 90.728 151 4 2 7189 7329 318968455 318968605 8.020000e-45 193.0
51 TraesCS7D01G364400 chr6D 88.462 156 5 4 7189 7332 318969118 318968964 8.070000e-40 176.0
52 TraesCS7D01G364400 chr6D 86.923 130 13 3 5396 5524 12621484 12621610 8.190000e-30 143.0
53 TraesCS7D01G364400 chr6D 86.923 130 13 3 5396 5524 75997787 75997913 8.190000e-30 143.0
54 TraesCS7D01G364400 chr5A 92.181 243 19 0 7520 7762 590288620 590288862 2.090000e-90 344.0
55 TraesCS7D01G364400 chr5A 92.216 167 7 3 7362 7528 590288323 590288163 1.700000e-56 231.0
56 TraesCS7D01G364400 chr3B 82.778 360 55 4 3317 3673 404620022 404620377 1.640000e-81 315.0
57 TraesCS7D01G364400 chr3D 82.303 356 57 5 3317 3666 315758788 315758433 3.550000e-78 303.0
58 TraesCS7D01G364400 chr3D 88.285 239 26 2 5530 5766 104811209 104811447 1.290000e-72 285.0
59 TraesCS7D01G364400 chr3D 94.118 136 7 1 2095 2229 524713580 524713715 1.030000e-48 206.0
60 TraesCS7D01G364400 chr3D 83.616 177 18 3 7191 7357 582823086 582823261 1.050000e-33 156.0
61 TraesCS7D01G364400 chr3D 81.699 153 17 5 7189 7332 582825209 582825059 4.960000e-22 117.0
62 TraesCS7D01G364400 chr5B 88.477 243 26 2 5525 5766 677578635 677578394 7.680000e-75 292.0
63 TraesCS7D01G364400 chr5B 75.330 227 37 16 5159 5377 476635425 476635210 3.010000e-14 91.6
64 TraesCS7D01G364400 chr4A 88.017 242 27 2 5527 5767 743396364 743396604 1.290000e-72 285.0
65 TraesCS7D01G364400 chr4A 94.574 129 7 0 2101 2229 60654286 60654158 4.790000e-47 200.0
66 TraesCS7D01G364400 chr3A 87.866 239 28 1 5527 5765 722805553 722805790 5.980000e-71 279.0
67 TraesCS7D01G364400 chr3A 94.074 135 8 0 2095 2229 659015374 659015508 1.030000e-48 206.0
68 TraesCS7D01G364400 chr2B 87.295 244 30 1 5528 5771 41130866 41131108 2.150000e-70 278.0
69 TraesCS7D01G364400 chr2B 77.021 235 33 14 5152 5370 662113896 662113667 1.780000e-21 115.0
70 TraesCS7D01G364400 chr2B 76.667 240 32 18 5149 5370 675861972 675861739 2.310000e-20 111.0
71 TraesCS7D01G364400 chr2B 76.250 240 33 18 5149 5370 447789855 447789622 1.070000e-18 106.0
72 TraesCS7D01G364400 chr2A 90.972 144 13 0 2092 2235 632952292 632952435 2.230000e-45 195.0
73 TraesCS7D01G364400 chr2A 87.821 156 8 3 7187 7332 16255878 16256032 1.040000e-38 172.0
74 TraesCS7D01G364400 chr4B 96.970 33 0 1 6576 6607 7475835 7475803 4.000000e-03 54.7


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 TraesCS7D01G364400 chr7D 469836801 469844627 7826 True 14454.000000 14454 100.000000 1 7827 1 chr7D.!!$R1 7826
1 TraesCS7D01G364400 chr7B 493520838 493527986 7148 True 3864.000000 8030 93.190333 27 7188 3 chr7B.!!$R2 7161
2 TraesCS7D01G364400 chr7A 529325564 529332431 6867 False 1469.350000 2702 94.610000 708 7186 6 chr7A.!!$F1 6478
3 TraesCS7D01G364400 chr5D 558908046 558908670 624 False 852.000000 852 91.217000 7189 7827 1 chr5D.!!$F2 638
4 TraesCS7D01G364400 chr5D 445650275 445652872 2597 True 267.833333 387 88.132000 5406 6299 6 chr5D.!!$R3 893
5 TraesCS7D01G364400 chrUn 1083333 1083950 617 True 848.000000 848 91.420000 7197 7827 1 chrUn.!!$R1 630
6 TraesCS7D01G364400 chr2D 548612929 548613548 619 False 819.000000 819 90.447000 7189 7827 1 chr2D.!!$F2 638
7 TraesCS7D01G364400 chr6A 383083405 383084032 627 True 715.000000 715 87.328000 7183 7827 1 chr6A.!!$R1 644
8 TraesCS7D01G364400 chr1D 302381542 302382903 1361 True 374.500000 468 90.299000 995 3242 2 chr1D.!!$R3 2247
9 TraesCS7D01G364400 chr1B 409249665 409251041 1376 True 366.000000 462 86.980500 931 3242 2 chr1B.!!$R3 2311
10 TraesCS7D01G364400 chr1A 377018877 377020185 1308 True 363.500000 451 89.652000 995 3242 2 chr1A.!!$R2 2247
11 TraesCS7D01G364400 chr6B 123491691 123492203 512 True 290.500000 416 88.103500 5396 6157 2 chr6B.!!$R2 761
12 TraesCS7D01G364400 chr6D 75997787 75998291 504 False 278.500000 414 86.534500 5396 6157 2 chr6D.!!$F4 761
13 TraesCS7D01G364400 chr6D 12621484 12621987 503 False 266.500000 390 86.031000 5396 6157 2 chr6D.!!$F3 761

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
649 653 0.835276 AGTACCCTAAATGGACCGGC 59.165 55.000 0.00 0.00 38.35 6.13 F
1287 1317 1.370051 GGAAGTTTTCGCGTGCCAC 60.370 57.895 5.77 0.00 0.00 5.01 F
2018 2076 2.040278 AGACATAGAGCCTTTGGTGCAA 59.960 45.455 0.00 0.00 0.00 4.08 F
2785 2849 1.363744 GCGGGCTGATGATATAGTGC 58.636 55.000 0.00 0.00 0.00 4.40 F
3578 3643 1.887854 CATGGTTGCATGTTGAGGTCA 59.112 47.619 0.00 0.00 0.00 4.02 F
4057 4123 0.689080 TGACTGCAGGAGGGAGGATC 60.689 60.000 19.93 3.35 39.67 3.36 F
4662 4731 1.215423 GAGGCATTATCCCACCAACCT 59.785 52.381 0.00 0.00 0.00 3.50 F
5190 5262 1.252904 CCCATGGTTGCCCTGTCAAG 61.253 60.000 11.73 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1526 0.391130 TTCCCATCCGAGCAGAAACG 60.391 55.000 0.00 0.0 0.00 3.60 R
2244 2306 0.961019 GCAGACAAATGTGAAGCCCA 59.039 50.000 0.00 0.0 0.00 5.36 R
3320 3385 1.071699 AGCAACACGTGAGGTACCATT 59.928 47.619 25.01 0.0 0.00 3.16 R
3927 3993 2.058705 TCAACACCACCAACCCATCTA 58.941 47.619 0.00 0.0 0.00 1.98 R
4995 5065 1.753073 CCCAGATCAACATTTGAGGGC 59.247 52.381 0.00 0.0 43.98 5.19 R
5819 5956 1.684983 GCCTGTGCAATGCCAGAATAT 59.315 47.619 20.13 0.0 37.47 1.28 R
6491 8615 0.807496 GACATGCCAAGAAGGTCAGC 59.193 55.000 0.00 0.0 40.61 4.26 R
6954 9807 4.263209 CACGTCACAAAACTAGATAGCTCG 59.737 45.833 0.00 0.0 0.00 5.03 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
17 18 4.204028 ACACAGTTTGGGCCGGCT 62.204 61.111 28.56 0.85 0.00 5.52
18 19 2.033448 CACAGTTTGGGCCGGCTA 59.967 61.111 28.56 13.55 0.00 3.93
19 20 1.602323 CACAGTTTGGGCCGGCTAA 60.602 57.895 28.56 19.06 0.00 3.09
20 21 1.303317 ACAGTTTGGGCCGGCTAAG 60.303 57.895 28.56 12.40 0.00 2.18
22 23 1.303317 AGTTTGGGCCGGCTAAGTG 60.303 57.895 28.56 0.00 0.00 3.16
56 57 5.942826 AGCTTTGGTTTTGGAAAATGTTCAA 59.057 32.000 0.00 0.00 35.25 2.69
85 86 5.221541 TGCGAAAAAGTTGGGGATTTGTAAT 60.222 36.000 0.00 0.00 0.00 1.89
86 87 5.699001 GCGAAAAAGTTGGGGATTTGTAATT 59.301 36.000 0.00 0.00 0.00 1.40
222 223 9.605955 GTTTTCAATTTTCAAAAATATTCCCGG 57.394 29.630 0.00 0.00 37.62 5.73
223 224 9.561069 TTTTCAATTTTCAAAAATATTCCCGGA 57.439 25.926 0.73 0.00 37.62 5.14
243 245 6.146898 CCGGATTATTTAAAAATGCTACGGG 58.853 40.000 0.00 0.00 35.59 5.28
255 257 8.664211 AAAAATGCTACGGGTTTTTAAAATCA 57.336 26.923 0.55 0.00 34.37 2.57
257 259 9.930693 AAAATGCTACGGGTTTTTAAAATCATA 57.069 25.926 0.55 0.00 0.00 2.15
258 260 8.920509 AATGCTACGGGTTTTTAAAATCATAC 57.079 30.769 0.55 0.00 0.00 2.39
259 261 6.544622 TGCTACGGGTTTTTAAAATCATACG 58.455 36.000 0.55 9.24 0.00 3.06
260 262 5.967088 GCTACGGGTTTTTAAAATCATACGG 59.033 40.000 0.55 0.00 0.00 4.02
261 263 6.183360 GCTACGGGTTTTTAAAATCATACGGA 60.183 38.462 0.55 3.72 0.00 4.69
262 264 6.185852 ACGGGTTTTTAAAATCATACGGAG 57.814 37.500 0.55 0.00 0.00 4.63
348 350 8.912988 TGGAAACAAATCCTGGATATCAAATAC 58.087 33.333 10.13 0.00 40.35 1.89
425 427 8.429641 GGTGTTCTAAACTCATAGAATATCCCA 58.570 37.037 0.62 0.00 42.26 4.37
588 592 9.036671 ACGACAGAAAAAGAAAACAAAGAAAAA 57.963 25.926 0.00 0.00 0.00 1.94
605 609 3.751479 AAAAATGGTGCAGGAAGGTTC 57.249 42.857 0.00 0.00 0.00 3.62
606 610 2.683211 AAATGGTGCAGGAAGGTTCT 57.317 45.000 0.00 0.00 0.00 3.01
607 611 3.806949 AAATGGTGCAGGAAGGTTCTA 57.193 42.857 0.00 0.00 0.00 2.10
608 612 3.356529 AATGGTGCAGGAAGGTTCTAG 57.643 47.619 0.00 0.00 0.00 2.43
609 613 0.984230 TGGTGCAGGAAGGTTCTAGG 59.016 55.000 0.00 0.00 0.00 3.02
610 614 1.276622 GGTGCAGGAAGGTTCTAGGA 58.723 55.000 0.00 0.00 0.00 2.94
611 615 1.066071 GGTGCAGGAAGGTTCTAGGAC 60.066 57.143 0.00 0.00 0.00 3.85
612 616 1.066071 GTGCAGGAAGGTTCTAGGACC 60.066 57.143 12.91 12.91 40.11 4.46
623 627 5.449107 GGTTCTAGGACCTTTTCAAAACC 57.551 43.478 13.55 0.00 36.73 3.27
624 628 4.891168 GGTTCTAGGACCTTTTCAAAACCA 59.109 41.667 13.55 0.00 36.73 3.67
625 629 5.009710 GGTTCTAGGACCTTTTCAAAACCAG 59.990 44.000 13.55 0.00 36.73 4.00
626 630 5.382664 TCTAGGACCTTTTCAAAACCAGT 57.617 39.130 0.00 0.00 0.00 4.00
627 631 5.130350 TCTAGGACCTTTTCAAAACCAGTG 58.870 41.667 0.00 0.00 0.00 3.66
628 632 3.031013 AGGACCTTTTCAAAACCAGTGG 58.969 45.455 7.91 7.91 0.00 4.00
634 638 4.037565 CCTTTTCAAAACCAGTGGGAGTAC 59.962 45.833 15.21 0.00 38.05 2.73
649 653 0.835276 AGTACCCTAAATGGACCGGC 59.165 55.000 0.00 0.00 38.35 6.13
691 695 4.465512 GCAGGGTGCGCGATTGTG 62.466 66.667 12.10 0.17 31.71 3.33
715 719 6.126825 TGCTTTAATTGAACATGGGCCAATAT 60.127 34.615 11.89 0.00 31.07 1.28
1243 1273 1.621814 TCCAGGTTTTAGGTCTGGTCG 59.378 52.381 8.24 0.00 45.97 4.79
1287 1317 1.370051 GGAAGTTTTCGCGTGCCAC 60.370 57.895 5.77 0.00 0.00 5.01
1471 1526 3.547413 GGCTAGTTTGTTGGTTTCGTCAC 60.547 47.826 0.00 0.00 0.00 3.67
1658 1713 6.507771 CGGTTGTGTTTTTAGCACTTCATTTG 60.508 38.462 0.00 0.00 37.70 2.32
2018 2076 2.040278 AGACATAGAGCCTTTGGTGCAA 59.960 45.455 0.00 0.00 0.00 4.08
2217 2279 8.047310 ACAAATCTAAGACAACTAATTCGGGAT 58.953 33.333 0.00 0.00 0.00 3.85
2244 2306 7.069950 GGAGGGAGTATTATTTTGGCTTGAATT 59.930 37.037 0.00 0.00 0.00 2.17
2403 2466 9.890629 TTAATTGCAGATGTTACTGTCTTATCT 57.109 29.630 0.00 0.00 39.73 1.98
2451 2514 5.890334 ACAATAATACCAATTCCGCAGTTG 58.110 37.500 0.00 0.00 0.00 3.16
2567 2630 5.343307 TTTAGTATAACCGTCCTTGACCC 57.657 43.478 0.00 0.00 0.00 4.46
2580 2643 3.396276 TCCTTGACCCCAAGTGAAATGTA 59.604 43.478 0.00 0.00 46.37 2.29
2785 2849 1.363744 GCGGGCTGATGATATAGTGC 58.636 55.000 0.00 0.00 0.00 4.40
2890 2955 2.736144 TCTACAGTGTTAGCCGTTGG 57.264 50.000 0.00 0.00 0.00 3.77
3320 3385 9.278978 TGATGTGTGCTCTTTTACAATAACTAA 57.721 29.630 0.00 0.00 0.00 2.24
3578 3643 1.887854 CATGGTTGCATGTTGAGGTCA 59.112 47.619 0.00 0.00 0.00 4.02
4057 4123 0.689080 TGACTGCAGGAGGGAGGATC 60.689 60.000 19.93 3.35 39.67 3.36
4483 4552 6.814954 AAATAGGCTGGATTAGTCAGAGAA 57.185 37.500 0.00 0.00 34.36 2.87
4498 4567 5.237344 AGTCAGAGAAAAGTCATTTGGAACG 59.763 40.000 0.00 0.00 0.00 3.95
4662 4731 1.215423 GAGGCATTATCCCACCAACCT 59.785 52.381 0.00 0.00 0.00 3.50
4948 5018 7.023575 GCTTATAAAATGACACCAGTGAACTG 58.976 38.462 4.48 3.35 43.40 3.16
4995 5065 5.277857 ACTATCCAAAGTCGTCCAATAGG 57.722 43.478 0.00 0.00 0.00 2.57
5190 5262 1.252904 CCCATGGTTGCCCTGTCAAG 61.253 60.000 11.73 0.00 0.00 3.02
5247 5321 5.448360 GCTTGCCAACAGATTAGCTAGAAAG 60.448 44.000 0.00 0.00 29.43 2.62
5380 5457 5.189736 TCACAATCTGAACATAACCTAGGCT 59.810 40.000 9.30 0.00 0.00 4.58
5381 5458 5.295292 CACAATCTGAACATAACCTAGGCTG 59.705 44.000 9.30 6.87 0.00 4.85
5382 5459 5.045578 ACAATCTGAACATAACCTAGGCTGT 60.046 40.000 9.30 7.56 0.00 4.40
5384 5461 6.808321 ATCTGAACATAACCTAGGCTGTTA 57.192 37.500 19.43 8.43 32.28 2.41
5559 5696 5.264395 CATCCTGGTTTATTGGTCCTCTTT 58.736 41.667 0.00 0.00 0.00 2.52
5622 5759 7.281774 ACAAAATGTTAATGCATGTCACCAAAA 59.718 29.630 0.00 0.00 0.00 2.44
5623 5760 7.982761 AAATGTTAATGCATGTCACCAAAAT 57.017 28.000 0.00 0.00 0.00 1.82
5624 5761 7.982761 AATGTTAATGCATGTCACCAAAATT 57.017 28.000 0.00 0.00 0.00 1.82
5625 5762 7.982761 ATGTTAATGCATGTCACCAAAATTT 57.017 28.000 0.00 0.00 0.00 1.82
5626 5763 9.499479 AATGTTAATGCATGTCACCAAAATTTA 57.501 25.926 0.00 0.00 0.00 1.40
5627 5764 9.669887 ATGTTAATGCATGTCACCAAAATTTAT 57.330 25.926 0.00 0.00 0.00 1.40
5632 5769 9.669887 AATGCATGTCACCAAAATTTATATTGT 57.330 25.926 0.00 0.00 0.00 2.71
5633 5770 9.669887 ATGCATGTCACCAAAATTTATATTGTT 57.330 25.926 0.00 0.00 0.00 2.83
5634 5771 9.499479 TGCATGTCACCAAAATTTATATTGTTT 57.501 25.926 0.00 0.00 0.00 2.83
5635 5772 9.757859 GCATGTCACCAAAATTTATATTGTTTG 57.242 29.630 0.00 0.00 0.00 2.93
5663 5800 8.554835 TCGTATTTGAACATAGTTTCCAATGA 57.445 30.769 0.00 0.00 0.00 2.57
5818 5955 6.989155 TTATACGGGTATCTTCTGATTGGT 57.011 37.500 0.00 0.00 34.32 3.67
5819 5956 8.481492 TTTATACGGGTATCTTCTGATTGGTA 57.519 34.615 0.00 0.00 34.32 3.25
5893 6040 7.725818 AAGTATTCATGATGCTCTATGTGTG 57.274 36.000 0.00 0.00 29.66 3.82
6018 6321 1.743394 CGAGCAGGTAATTGGGGTTTC 59.257 52.381 0.00 0.00 0.00 2.78
6327 8442 8.032451 ACTAATTAGCCGCATGTGTTTTTATTT 58.968 29.630 12.54 0.00 0.00 1.40
6329 8444 3.988819 AGCCGCATGTGTTTTTATTTGT 58.011 36.364 5.38 0.00 0.00 2.83
6472 8596 8.217131 AGTCACATTATGTAGTGTACGATGTA 57.783 34.615 0.00 0.00 37.07 2.29
6949 9802 3.358111 TGGAGTGGTCACTTGTTTTGA 57.642 42.857 5.02 0.00 42.66 2.69
6954 9807 5.248870 AGTGGTCACTTGTTTTGATTGAC 57.751 39.130 0.00 0.00 38.83 3.18
7054 9909 0.316689 GCCCTTCGTTGTGTTGTTCG 60.317 55.000 0.00 0.00 0.00 3.95
7159 10014 3.485463 TCTCAGGTAAAGTTGGTGTGG 57.515 47.619 0.00 0.00 0.00 4.17
7167 10022 0.916086 AAGTTGGTGTGGGTCAGACA 59.084 50.000 2.17 0.00 28.70 3.41
7224 10079 1.598130 GTGAAGAAGGCACGGCAGT 60.598 57.895 0.00 0.00 0.00 4.40
7284 10150 0.751643 ACGAACAGCAAAACAGCCCT 60.752 50.000 0.00 0.00 34.23 5.19
7285 10151 1.234821 CGAACAGCAAAACAGCCCTA 58.765 50.000 0.00 0.00 34.23 3.53
7372 10238 2.429069 GCCGGCAGCGTCAAAAAG 60.429 61.111 24.80 0.00 0.00 2.27
7373 10239 2.429069 CCGGCAGCGTCAAAAAGC 60.429 61.111 0.00 0.00 0.00 3.51
7374 10240 2.331098 CGGCAGCGTCAAAAAGCA 59.669 55.556 0.00 0.00 35.48 3.91
7375 10241 1.727022 CGGCAGCGTCAAAAAGCAG 60.727 57.895 0.00 0.00 35.48 4.24
7376 10242 2.018324 GGCAGCGTCAAAAAGCAGC 61.018 57.895 0.00 0.00 43.68 5.25
7377 10243 2.018324 GCAGCGTCAAAAAGCAGCC 61.018 57.895 0.00 0.00 39.49 4.85
7378 10244 1.727022 CAGCGTCAAAAAGCAGCCG 60.727 57.895 0.00 0.00 35.48 5.52
7379 10245 3.099574 GCGTCAAAAAGCAGCCGC 61.100 61.111 0.00 0.00 38.99 6.53
7380 10246 2.429069 CGTCAAAAAGCAGCCGCC 60.429 61.111 0.00 0.00 39.83 6.13
7381 10247 2.429069 GTCAAAAAGCAGCCGCCG 60.429 61.111 0.00 0.00 39.83 6.46
7404 10270 0.523335 CGTATTCTGGCGCCAAAAGC 60.523 55.000 32.09 18.95 38.52 3.51
7617 10483 9.927668 CCATATTCTTGAAGGTAAAACACAATT 57.072 29.630 0.00 0.00 0.00 2.32
7810 10676 5.183713 TCAATTGGGTAAGTGAGAAGCATTG 59.816 40.000 5.42 0.00 36.12 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.303317 CTTAGCCGGCCCAAACTGT 60.303 57.895 26.15 3.86 0.00 3.55
5 6 2.989881 GCACTTAGCCGGCCCAAAC 61.990 63.158 26.15 4.81 37.23 2.93
6 7 2.675075 GCACTTAGCCGGCCCAAA 60.675 61.111 26.15 14.63 37.23 3.28
22 23 1.734388 AACCAAAGCTTGTGTCCCGC 61.734 55.000 0.00 0.00 0.00 6.13
25 26 2.167487 TCCAAAACCAAAGCTTGTGTCC 59.833 45.455 0.00 0.00 0.00 4.02
32 33 5.495640 TGAACATTTTCCAAAACCAAAGCT 58.504 33.333 0.00 0.00 0.00 3.74
56 57 4.143986 TCCCCAACTTTTTCGCATTTTT 57.856 36.364 0.00 0.00 0.00 1.94
196 197 9.605955 CCGGGAATATTTTTGAAAATTGAAAAC 57.394 29.630 6.98 0.00 39.24 2.43
215 216 8.079809 CGTAGCATTTTTAAATAATCCGGGAAT 58.920 33.333 0.00 0.00 0.00 3.01
229 231 9.760077 TGATTTTAAAAACCCGTAGCATTTTTA 57.240 25.926 4.44 0.00 35.60 1.52
230 232 8.664211 TGATTTTAAAAACCCGTAGCATTTTT 57.336 26.923 4.44 0.00 37.05 1.94
240 242 6.185852 ACTCCGTATGATTTTAAAAACCCG 57.814 37.500 4.44 5.17 0.00 5.28
328 330 9.123902 TGAACAGTATTTGATATCCAGGATTTG 57.876 33.333 7.44 0.00 0.00 2.32
539 543 9.640963 TCGTTTTTCTCTTTGTTTTGGATTTTA 57.359 25.926 0.00 0.00 0.00 1.52
543 547 6.626302 TGTCGTTTTTCTCTTTGTTTTGGAT 58.374 32.000 0.00 0.00 0.00 3.41
544 548 6.015027 TGTCGTTTTTCTCTTTGTTTTGGA 57.985 33.333 0.00 0.00 0.00 3.53
546 550 7.561237 TTCTGTCGTTTTTCTCTTTGTTTTG 57.439 32.000 0.00 0.00 0.00 2.44
547 551 8.582433 TTTTCTGTCGTTTTTCTCTTTGTTTT 57.418 26.923 0.00 0.00 0.00 2.43
551 555 8.447787 TTCTTTTTCTGTCGTTTTTCTCTTTG 57.552 30.769 0.00 0.00 0.00 2.77
555 559 8.222984 TGTTTTCTTTTTCTGTCGTTTTTCTC 57.777 30.769 0.00 0.00 0.00 2.87
588 592 2.025887 CCTAGAACCTTCCTGCACCATT 60.026 50.000 0.00 0.00 0.00 3.16
590 594 0.984230 CCTAGAACCTTCCTGCACCA 59.016 55.000 0.00 0.00 0.00 4.17
591 595 1.066071 GTCCTAGAACCTTCCTGCACC 60.066 57.143 0.00 0.00 0.00 5.01
592 596 1.066071 GGTCCTAGAACCTTCCTGCAC 60.066 57.143 0.00 0.00 36.32 4.57
593 597 1.276622 GGTCCTAGAACCTTCCTGCA 58.723 55.000 0.00 0.00 36.32 4.41
601 605 4.891168 TGGTTTTGAAAAGGTCCTAGAACC 59.109 41.667 0.00 0.00 39.80 3.62
602 606 5.593095 ACTGGTTTTGAAAAGGTCCTAGAAC 59.407 40.000 0.00 0.00 0.00 3.01
603 607 5.592688 CACTGGTTTTGAAAAGGTCCTAGAA 59.407 40.000 0.00 0.00 0.00 2.10
604 608 5.130350 CACTGGTTTTGAAAAGGTCCTAGA 58.870 41.667 0.00 0.00 0.00 2.43
605 609 4.278419 CCACTGGTTTTGAAAAGGTCCTAG 59.722 45.833 0.00 0.00 0.00 3.02
606 610 4.211920 CCACTGGTTTTGAAAAGGTCCTA 58.788 43.478 0.00 0.00 0.00 2.94
607 611 3.031013 CCACTGGTTTTGAAAAGGTCCT 58.969 45.455 0.00 0.00 0.00 3.85
608 612 2.102420 CCCACTGGTTTTGAAAAGGTCC 59.898 50.000 0.00 0.00 0.00 4.46
609 613 3.028130 TCCCACTGGTTTTGAAAAGGTC 58.972 45.455 0.00 0.00 0.00 3.85
610 614 3.031013 CTCCCACTGGTTTTGAAAAGGT 58.969 45.455 0.00 0.00 0.00 3.50
611 615 3.031013 ACTCCCACTGGTTTTGAAAAGG 58.969 45.455 0.00 0.00 0.00 3.11
612 616 4.037565 GGTACTCCCACTGGTTTTGAAAAG 59.962 45.833 0.00 0.00 0.00 2.27
613 617 3.955551 GGTACTCCCACTGGTTTTGAAAA 59.044 43.478 0.00 0.00 0.00 2.29
614 618 3.558033 GGTACTCCCACTGGTTTTGAAA 58.442 45.455 0.00 0.00 0.00 2.69
615 619 3.217681 GGTACTCCCACTGGTTTTGAA 57.782 47.619 0.00 0.00 0.00 2.69
616 620 2.943036 GGTACTCCCACTGGTTTTGA 57.057 50.000 0.00 0.00 0.00 2.69
628 632 1.415289 CCGGTCCATTTAGGGTACTCC 59.585 57.143 0.00 0.00 38.24 3.85
634 638 2.194868 GGGCCGGTCCATTTAGGG 59.805 66.667 23.50 0.00 38.24 3.53
689 693 3.261580 GGCCCATGTTCAATTAAAGCAC 58.738 45.455 0.00 0.00 0.00 4.40
690 694 2.902486 TGGCCCATGTTCAATTAAAGCA 59.098 40.909 0.00 0.00 0.00 3.91
691 695 3.608316 TGGCCCATGTTCAATTAAAGC 57.392 42.857 0.00 0.00 0.00 3.51
692 696 8.614346 CAAATATTGGCCCATGTTCAATTAAAG 58.386 33.333 0.00 0.00 33.72 1.85
693 697 7.555554 CCAAATATTGGCCCATGTTCAATTAAA 59.444 33.333 0.00 0.00 45.17 1.52
694 698 7.052873 CCAAATATTGGCCCATGTTCAATTAA 58.947 34.615 0.00 0.00 45.17 1.40
695 699 6.590068 CCAAATATTGGCCCATGTTCAATTA 58.410 36.000 0.00 0.00 45.17 1.40
696 700 5.438833 CCAAATATTGGCCCATGTTCAATT 58.561 37.500 0.00 0.00 45.17 2.32
715 719 1.501604 AGGGTTTCTGGTAAGCCCAAA 59.498 47.619 11.59 0.00 44.65 3.28
1243 1273 0.459063 CGTACCAGGCTAACCGGAAC 60.459 60.000 9.46 0.00 42.76 3.62
1287 1317 2.278857 CCGACGCCGAAGATCCAG 60.279 66.667 0.00 0.00 38.22 3.86
1471 1526 0.391130 TTCCCATCCGAGCAGAAACG 60.391 55.000 0.00 0.00 0.00 3.60
1546 1601 1.065701 ACTAAGAGCACGCTCATACCG 59.934 52.381 20.51 5.58 44.99 4.02
1658 1713 8.837059 CAAATCAATTAAGTACGTAAGCACAAC 58.163 33.333 7.33 0.00 45.62 3.32
2217 2279 5.044476 TCAAGCCAAAATAATACTCCCTCCA 60.044 40.000 0.00 0.00 0.00 3.86
2244 2306 0.961019 GCAGACAAATGTGAAGCCCA 59.039 50.000 0.00 0.00 0.00 5.36
2403 2466 5.357878 ACAAAATGAGCTCAAGAGACAACAA 59.642 36.000 22.50 0.00 0.00 2.83
2451 2514 9.731819 TTCATGTAATGTCGATTCTAGAAGTAC 57.268 33.333 11.53 9.09 46.80 2.73
2502 2565 8.443937 CAACTTCTAAGGCTGTAACAAATAGTC 58.556 37.037 0.00 0.00 0.00 2.59
2543 2606 6.351711 GGGTCAAGGACGGTTATACTAAAAT 58.648 40.000 0.00 0.00 32.65 1.82
2594 2657 4.386652 CACGCTTTTCATTTCCTCAATTGG 59.613 41.667 5.42 0.00 0.00 3.16
2597 2660 3.826157 TCCACGCTTTTCATTTCCTCAAT 59.174 39.130 0.00 0.00 0.00 2.57
2785 2849 8.906867 AGAAATACTCCATCCATTACACATTTG 58.093 33.333 0.00 0.00 0.00 2.32
3320 3385 1.071699 AGCAACACGTGAGGTACCATT 59.928 47.619 25.01 0.00 0.00 3.16
3578 3643 7.364762 CCATACAATTATAGACGGGATAAGGCT 60.365 40.741 0.00 0.00 0.00 4.58
3927 3993 2.058705 TCAACACCACCAACCCATCTA 58.941 47.619 0.00 0.00 0.00 1.98
4057 4123 2.256117 ACTCTTGGAACCTTGGAACG 57.744 50.000 0.00 0.00 0.00 3.95
4402 4471 7.712639 TGTTTTACAAAGCAAATTAAGATGGCA 59.287 29.630 0.00 0.00 0.00 4.92
4483 4552 6.202516 TCTTTTGTCGTTCCAAATGACTTT 57.797 33.333 11.98 0.00 45.51 2.66
4498 4567 5.545658 TGTAAAGCATCCGATCTTTTGTC 57.454 39.130 9.60 4.83 34.67 3.18
4847 4916 4.393371 GGCATTTCTTCAGTTCTAGTGACC 59.607 45.833 0.00 0.00 0.00 4.02
4848 4917 4.997395 TGGCATTTCTTCAGTTCTAGTGAC 59.003 41.667 0.00 0.00 0.00 3.67
4948 5018 9.706846 GTTCATGGCATAAATTAGAAATTTTGC 57.293 29.630 0.00 15.82 0.00 3.68
4995 5065 1.753073 CCCAGATCAACATTTGAGGGC 59.247 52.381 0.00 0.00 43.98 5.19
5247 5321 7.516627 GCAAATGTTCATTTACCAACTGTTCAC 60.517 37.037 9.91 0.00 0.00 3.18
5559 5696 7.055667 TGGTCAAATTTAGGCACAAAATACA 57.944 32.000 0.00 0.00 0.00 2.29
5632 5769 9.834628 GGAAACTATGTTCAAATACGAATCAAA 57.165 29.630 0.00 0.00 0.00 2.69
5633 5770 9.004717 TGGAAACTATGTTCAAATACGAATCAA 57.995 29.630 0.00 0.00 0.00 2.57
5634 5771 8.554835 TGGAAACTATGTTCAAATACGAATCA 57.445 30.769 0.00 0.00 0.00 2.57
5636 5773 9.787532 CATTGGAAACTATGTTCAAATACGAAT 57.212 29.630 0.00 0.00 38.53 3.34
5637 5774 9.004717 TCATTGGAAACTATGTTCAAATACGAA 57.995 29.630 0.00 0.00 43.01 3.85
5753 5890 7.127405 TGACTGAAATGTATACTACCCCTGTA 58.873 38.462 4.17 0.00 0.00 2.74
5818 5955 2.886523 GCCTGTGCAATGCCAGAATATA 59.113 45.455 20.13 0.00 37.47 0.86
5819 5956 1.684983 GCCTGTGCAATGCCAGAATAT 59.315 47.619 20.13 0.00 37.47 1.28
5893 6040 3.949754 TGTTGATGATCAGATTCCTTGCC 59.050 43.478 0.09 0.00 0.00 4.52
6018 6321 5.333875 GCTTTCTTTTGTAGTACCAGTTCCG 60.334 44.000 0.00 0.00 0.00 4.30
6327 8442 9.996554 TTCTGAAATAAACTCTATCACAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
6491 8615 0.807496 GACATGCCAAGAAGGTCAGC 59.193 55.000 0.00 0.00 40.61 4.26
6949 9802 6.531948 GTCACAAAACTAGATAGCTCGTCAAT 59.468 38.462 0.00 0.00 0.00 2.57
6954 9807 4.263209 CACGTCACAAAACTAGATAGCTCG 59.737 45.833 0.00 0.00 0.00 5.03
7159 10014 5.276461 TGGTACACATCATATGTCTGACC 57.724 43.478 5.17 10.63 42.70 4.02
7167 10022 6.278363 GTCCGTAACTTGGTACACATCATAT 58.722 40.000 0.00 0.00 39.29 1.78
7224 10079 4.672587 AAGAACGGCTGAGATTATGCTA 57.327 40.909 0.00 0.00 0.00 3.49
7309 10175 3.331889 AGAAAGGAAGGAGAGATTTGGCA 59.668 43.478 0.00 0.00 0.00 4.92
7360 10226 1.727022 CGGCTGCTTTTTGACGCTG 60.727 57.895 0.00 0.00 0.00 5.18
7361 10227 2.639286 CGGCTGCTTTTTGACGCT 59.361 55.556 0.00 0.00 0.00 5.07
7362 10228 3.099574 GCGGCTGCTTTTTGACGC 61.100 61.111 11.21 0.00 40.19 5.19
7363 10229 2.429069 GGCGGCTGCTTTTTGACG 60.429 61.111 18.85 0.00 42.25 4.35
7364 10230 2.429069 CGGCGGCTGCTTTTTGAC 60.429 61.111 18.85 0.00 42.25 3.18
7365 10231 3.669344 CCGGCGGCTGCTTTTTGA 61.669 61.111 15.42 0.00 42.25 2.69
7376 10242 2.658593 CAGAATACGAGCCGGCGG 60.659 66.667 24.35 24.35 35.12 6.13
7377 10243 2.658593 CCAGAATACGAGCCGGCG 60.659 66.667 23.20 10.77 37.29 6.46
7378 10244 2.967615 GCCAGAATACGAGCCGGC 60.968 66.667 21.89 21.89 0.00 6.13
7379 10245 2.658593 CGCCAGAATACGAGCCGG 60.659 66.667 0.00 0.00 0.00 6.13
7380 10246 3.330853 GCGCCAGAATACGAGCCG 61.331 66.667 0.00 0.00 0.00 5.52
7381 10247 2.967615 GGCGCCAGAATACGAGCC 60.968 66.667 24.80 0.00 37.61 4.70
7404 10270 4.785453 GCCCAGCCGAGAACCTGG 62.785 72.222 0.00 0.00 46.49 4.45
7500 10366 1.722464 CGAGTTGATCGCCGTTTGTAA 59.278 47.619 0.00 0.00 45.98 2.41
7617 10483 1.144969 GACGGCAAACAAGATCGTGA 58.855 50.000 15.90 0.00 34.06 4.35


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

AutoCloner maintained by Alex Coulton.