Multiple sequence alignment - TraesCS5D01G350000

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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 TraesCS5D01G350000 chr5D 100.000 2576 0 0 1 2576 434555208 434552633 0.000000e+00 4758.0
1 TraesCS5D01G350000 chr5D 87.250 800 78 8 978 1757 434672440 434673235 0.000000e+00 891.0
2 TraesCS5D01G350000 chr5D 82.848 618 68 8 1988 2576 434569619 434569011 1.060000e-143 520.0
3 TraesCS5D01G350000 chr5D 83.446 592 62 21 1998 2576 434604021 434603453 3.800000e-143 518.0
4 TraesCS5D01G350000 chr5D 81.731 624 69 18 1988 2576 434662572 434663185 1.790000e-131 479.0
5 TraesCS5D01G350000 chr5D 82.293 593 66 16 1988 2551 434576264 434575682 6.450000e-131 477.0
6 TraesCS5D01G350000 chr5D 81.159 621 63 14 1988 2576 434655189 434655787 1.410000e-122 449.0
7 TraesCS5D01G350000 chr5D 74.901 1012 168 46 823 1757 434711357 434712359 1.450000e-102 383.0
8 TraesCS5D01G350000 chr5D 78.896 616 90 25 1167 1757 434653661 434654261 5.200000e-102 381.0
9 TraesCS5D01G350000 chr5D 94.958 238 8 1 2343 2576 434673981 434674218 1.130000e-98 370.0
10 TraesCS5D01G350000 chr5D 88.312 231 22 5 580 806 434711009 434711238 3.270000e-69 272.0
11 TraesCS5D01G350000 chr5D 74.963 675 120 24 803 1438 434578264 434577600 5.470000e-67 265.0
12 TraesCS5D01G350000 chr5D 75.828 604 93 26 1173 1757 434571125 434570556 9.150000e-65 257.0
13 TraesCS5D01G350000 chr5D 90.306 196 18 1 1799 1993 434673242 434673437 3.290000e-64 255.0
14 TraesCS5D01G350000 chr5D 74.927 686 107 32 803 1437 434607683 434607012 1.180000e-63 254.0
15 TraesCS5D01G350000 chr5D 89.796 196 19 1 1799 1993 434577294 434577099 1.530000e-62 250.0
16 TraesCS5D01G350000 chr5D 82.584 178 22 6 410 580 434710872 434711047 5.740000e-32 148.0
17 TraesCS5D01G350000 chr5D 100.000 31 0 0 550 580 434554621 434554591 9.960000e-05 58.4
18 TraesCS5D01G350000 chr5D 100.000 31 0 0 588 618 434554659 434554629 9.960000e-05 58.4
19 TraesCS5D01G350000 chr5B 85.599 993 85 13 814 1751 527497504 527496515 0.000000e+00 989.0
20 TraesCS5D01G350000 chr5B 84.669 998 89 21 826 1765 527775422 527774431 0.000000e+00 937.0
21 TraesCS5D01G350000 chr5B 89.850 601 39 8 1988 2576 527773231 527772641 0.000000e+00 752.0
22 TraesCS5D01G350000 chr5B 84.477 612 63 11 1988 2576 527787052 527786450 2.220000e-160 575.0
23 TraesCS5D01G350000 chr5B 82.820 617 68 12 1988 2576 527608166 527607560 3.800000e-143 518.0
24 TraesCS5D01G350000 chr5B 91.954 348 12 6 248 580 527498080 527497734 8.340000e-130 473.0
25 TraesCS5D01G350000 chr5B 77.833 609 97 23 1173 1757 527788622 527788028 2.450000e-90 342.0
26 TraesCS5D01G350000 chr5B 96.569 204 7 0 2343 2546 527495766 527495563 3.180000e-89 339.0
27 TraesCS5D01G350000 chr5B 92.140 229 16 2 580 806 527497772 527497544 3.200000e-84 322.0
28 TraesCS5D01G350000 chr5B 87.546 273 17 5 1 256 527502700 527502428 1.500000e-77 300.0
29 TraesCS5D01G350000 chr5B 76.656 604 104 22 1173 1757 527609687 527609102 1.500000e-77 300.0
30 TraesCS5D01G350000 chr5B 78.304 507 71 15 1993 2464 528537925 528537423 9.020000e-75 291.0
31 TraesCS5D01G350000 chr5B 77.515 507 73 19 1993 2463 527058576 527059077 1.520000e-67 267.0
32 TraesCS5D01G350000 chr5B 88.265 196 20 2 1799 1993 527496504 527496311 5.540000e-57 231.0
33 TraesCS5D01G350000 chr5B 93.478 138 9 0 1856 1993 527774389 527774252 3.360000e-49 206.0
34 TraesCS5D01G350000 chr5B 83.412 211 26 5 39 240 701594673 701594883 1.220000e-43 187.0
35 TraesCS5D01G350000 chr5B 81.343 134 15 6 110 234 115868201 115868069 1.630000e-17 100.0
36 TraesCS5D01G350000 chr5B 100.000 29 0 0 2548 2576 527495395 527495367 1.000000e-03 54.7
37 TraesCS5D01G350000 chr5A 77.741 611 80 18 1993 2562 549154193 549153598 8.890000e-85 324.0
38 TraesCS5D01G350000 chr5A 79.355 155 28 4 1994 2145 549199460 549199307 3.510000e-19 106.0
39 TraesCS5D01G350000 chr5A 93.750 48 1 2 1756 1801 633856912 633856959 1.280000e-08 71.3
40 TraesCS5D01G350000 chr7A 89.706 204 21 0 26 229 4200879 4201082 7.070000e-66 261.0
41 TraesCS5D01G350000 chr7A 77.513 378 68 12 404 779 693303361 693302999 7.220000e-51 211.0
42 TraesCS5D01G350000 chr7A 91.837 49 2 2 1755 1801 473023825 473023873 1.650000e-07 67.6
43 TraesCS5D01G350000 chr2A 88.235 204 15 5 34 229 10163036 10163238 4.290000e-58 235.0
44 TraesCS5D01G350000 chr2A 88.800 125 14 0 21 145 10162901 10163025 1.230000e-33 154.0
45 TraesCS5D01G350000 chr2B 83.265 245 25 7 1 229 719167636 719167880 7.220000e-51 211.0
46 TraesCS5D01G350000 chr2B 91.667 48 2 1 1756 1801 47692709 47692662 5.950000e-07 65.8
47 TraesCS5D01G350000 chr2B 91.667 48 2 1 1756 1801 47698128 47698081 5.950000e-07 65.8
48 TraesCS5D01G350000 chr2B 91.667 48 2 1 1756 1801 47719096 47719049 5.950000e-07 65.8
49 TraesCS5D01G350000 chr6D 86.471 170 18 3 1 170 58708711 58708547 5.660000e-42 182.0
50 TraesCS5D01G350000 chr4B 85.443 158 19 3 21 176 18701389 18701544 7.380000e-36 161.0
51 TraesCS5D01G350000 chr7D 91.837 49 2 2 1755 1801 412016459 412016507 1.650000e-07 67.6
52 TraesCS5D01G350000 chr7B 91.837 49 2 2 1755 1801 426367739 426367787 1.650000e-07 67.6
53 TraesCS5D01G350000 chr4D 92.000 50 1 3 1755 1801 259497373 259497324 1.650000e-07 67.6
54 TraesCS5D01G350000 chr2D 91.667 48 2 2 1756 1801 192181474 192181521 5.950000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G350000 chr5D 434552633 434555208 2575 True 1624.933333 4758 100.000000 1 2576 3 chr5D.!!$R1 2575
1 TraesCS5D01G350000 chr5D 434672440 434674218 1778 False 505.333333 891 90.838000 978 2576 3 chr5D.!!$F3 1598
2 TraesCS5D01G350000 chr5D 434662572 434663185 613 False 479.000000 479 81.731000 1988 2576 1 chr5D.!!$F1 588
3 TraesCS5D01G350000 chr5D 434653661 434655787 2126 False 415.000000 449 80.027500 1167 2576 2 chr5D.!!$F2 1409
4 TraesCS5D01G350000 chr5D 434569011 434571125 2114 True 388.500000 520 79.338000 1173 2576 2 chr5D.!!$R2 1403
5 TraesCS5D01G350000 chr5D 434603453 434607683 4230 True 386.000000 518 79.186500 803 2576 2 chr5D.!!$R4 1773
6 TraesCS5D01G350000 chr5D 434575682 434578264 2582 True 330.666667 477 82.350667 803 2551 3 chr5D.!!$R3 1748
7 TraesCS5D01G350000 chr5D 434710872 434712359 1487 False 267.666667 383 81.932333 410 1757 3 chr5D.!!$F4 1347
8 TraesCS5D01G350000 chr5B 527772641 527775422 2781 True 631.666667 937 89.332333 826 2576 3 chr5B.!!$R6 1750
9 TraesCS5D01G350000 chr5B 527786450 527788622 2172 True 458.500000 575 81.155000 1173 2576 2 chr5B.!!$R7 1403
10 TraesCS5D01G350000 chr5B 527607560 527609687 2127 True 409.000000 518 79.738000 1173 2576 2 chr5B.!!$R5 1403
11 TraesCS5D01G350000 chr5B 527495367 527498080 2713 True 401.450000 989 92.421167 248 2576 6 chr5B.!!$R4 2328
12 TraesCS5D01G350000 chr5B 528537423 528537925 502 True 291.000000 291 78.304000 1993 2464 1 chr5B.!!$R3 471
13 TraesCS5D01G350000 chr5B 527058576 527059077 501 False 267.000000 267 77.515000 1993 2463 1 chr5B.!!$F1 470
14 TraesCS5D01G350000 chr5A 549153598 549154193 595 True 324.000000 324 77.741000 1993 2562 1 chr5A.!!$R1 569

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
76 77 0.108756 GGCCCGCGATTAGTCCTATC 60.109 60.0 8.23 0.0 0.0 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 5411 0.459585 CATTGCCTTGTGATGCCAGC 60.46 55.0 0.0 0.0 0.0 4.85 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
72 73 4.963428 CCGGCCCGCGATTAGTCC 62.963 72.222 8.23 0.00 0.00 3.85
73 74 3.912907 CGGCCCGCGATTAGTCCT 61.913 66.667 8.23 0.00 0.00 3.85
74 75 2.558286 CGGCCCGCGATTAGTCCTA 61.558 63.158 8.23 0.00 0.00 2.94
75 76 1.874345 CGGCCCGCGATTAGTCCTAT 61.874 60.000 8.23 0.00 0.00 2.57
76 77 0.108756 GGCCCGCGATTAGTCCTATC 60.109 60.000 8.23 0.00 0.00 2.08
77 78 0.456312 GCCCGCGATTAGTCCTATCG 60.456 60.000 8.23 0.00 40.42 2.92
78 79 0.879765 CCCGCGATTAGTCCTATCGT 59.120 55.000 8.23 0.00 39.71 3.73
79 80 1.401148 CCCGCGATTAGTCCTATCGTG 60.401 57.143 8.23 10.77 44.79 4.35
80 81 1.328439 CGCGATTAGTCCTATCGTGC 58.672 55.000 0.00 0.00 40.57 5.34
81 82 1.699343 GCGATTAGTCCTATCGTGCC 58.301 55.000 0.00 0.00 39.71 5.01
82 83 1.965083 CGATTAGTCCTATCGTGCCG 58.035 55.000 0.00 0.00 33.60 5.69
83 84 1.401148 CGATTAGTCCTATCGTGCCGG 60.401 57.143 0.00 0.00 33.60 6.13
84 85 0.966920 ATTAGTCCTATCGTGCCGGG 59.033 55.000 2.18 0.00 0.00 5.73
85 86 1.741327 TTAGTCCTATCGTGCCGGGC 61.741 60.000 13.32 13.32 0.00 6.13
86 87 2.635787 TAGTCCTATCGTGCCGGGCT 62.636 60.000 21.46 1.61 36.57 5.19
87 88 3.536917 TCCTATCGTGCCGGGCTG 61.537 66.667 21.46 12.88 0.00 4.85
88 89 4.609018 CCTATCGTGCCGGGCTGG 62.609 72.222 21.46 8.39 42.50 4.85
126 127 2.042639 GCCCAGACATGGCCCAAT 60.043 61.111 0.00 0.00 46.19 3.16
127 128 2.428925 GCCCAGACATGGCCCAATG 61.429 63.158 0.00 0.00 46.19 2.82
128 129 2.428925 CCCAGACATGGCCCAATGC 61.429 63.158 0.00 0.00 46.19 3.56
129 130 2.777972 CCAGACATGGCCCAATGCG 61.778 63.158 0.00 0.00 40.52 4.73
130 131 2.048023 CAGACATGGCCCAATGCGT 61.048 57.895 0.00 0.00 42.61 5.24
131 132 2.048023 AGACATGGCCCAATGCGTG 61.048 57.895 0.00 0.00 42.61 5.34
132 133 2.035469 ACATGGCCCAATGCGTGA 59.965 55.556 0.00 0.00 42.61 4.35
133 134 1.380246 ACATGGCCCAATGCGTGAT 60.380 52.632 0.00 0.00 42.61 3.06
134 135 1.066752 CATGGCCCAATGCGTGATG 59.933 57.895 0.00 0.00 42.61 3.07
135 136 2.788640 ATGGCCCAATGCGTGATGC 61.789 57.895 0.00 0.00 46.70 3.91
155 156 4.778143 GCCTGGCACGACCCGATT 62.778 66.667 15.17 0.00 37.83 3.34
156 157 2.897207 CCTGGCACGACCCGATTA 59.103 61.111 0.00 0.00 37.83 1.75
157 158 1.227263 CCTGGCACGACCCGATTAG 60.227 63.158 0.00 0.00 37.83 1.73
158 159 1.883084 CTGGCACGACCCGATTAGC 60.883 63.158 0.00 0.00 37.83 3.09
159 160 2.588034 GGCACGACCCGATTAGCC 60.588 66.667 0.00 0.00 34.71 3.93
160 161 2.588034 GCACGACCCGATTAGCCC 60.588 66.667 0.00 0.00 0.00 5.19
161 162 2.279252 CACGACCCGATTAGCCCG 60.279 66.667 0.00 0.00 0.00 6.13
162 163 2.757099 ACGACCCGATTAGCCCGT 60.757 61.111 0.00 0.00 0.00 5.28
163 164 2.279252 CGACCCGATTAGCCCGTG 60.279 66.667 0.00 0.00 0.00 4.94
164 165 2.588034 GACCCGATTAGCCCGTGC 60.588 66.667 0.00 0.00 37.95 5.34
165 166 4.171103 ACCCGATTAGCCCGTGCC 62.171 66.667 0.00 0.00 38.69 5.01
224 225 2.816012 AAAAACCGGCCCGTTTGG 59.184 55.556 20.73 7.51 36.12 3.28
233 234 2.033448 CCCGTTTGGCCAGCTGTA 59.967 61.111 13.81 0.00 0.00 2.74
234 235 2.332654 CCCGTTTGGCCAGCTGTAC 61.333 63.158 13.81 5.41 0.00 2.90
235 236 1.302511 CCGTTTGGCCAGCTGTACT 60.303 57.895 13.81 0.00 0.00 2.73
236 237 1.298859 CCGTTTGGCCAGCTGTACTC 61.299 60.000 13.81 0.00 0.00 2.59
237 238 0.320771 CGTTTGGCCAGCTGTACTCT 60.321 55.000 13.81 0.00 0.00 3.24
238 239 1.160137 GTTTGGCCAGCTGTACTCTG 58.840 55.000 13.81 8.22 0.00 3.35
245 246 2.593346 CAGCTGTACTCTGGATGACC 57.407 55.000 5.25 0.00 0.00 4.02
246 247 2.106566 CAGCTGTACTCTGGATGACCT 58.893 52.381 5.25 0.00 37.04 3.85
266 267 0.191064 CCCATACTCCCAGGGCTCTA 59.809 60.000 0.00 0.00 35.44 2.43
334 335 1.329256 ACAGTAGTTGGCTCTCGTGT 58.671 50.000 0.00 0.00 0.00 4.49
336 337 1.269723 CAGTAGTTGGCTCTCGTGTGA 59.730 52.381 0.00 0.00 0.00 3.58
527 537 0.601046 TCACCGCTTCTTCTGCAGTG 60.601 55.000 14.67 8.33 39.42 3.66
549 559 4.394712 CCCCTCACCGCCACTCAC 62.395 72.222 0.00 0.00 0.00 3.51
550 560 4.394712 CCCTCACCGCCACTCACC 62.395 72.222 0.00 0.00 0.00 4.02
551 561 4.742201 CCTCACCGCCACTCACCG 62.742 72.222 0.00 0.00 0.00 4.94
558 568 4.314440 GCCACTCACCGCCACTCA 62.314 66.667 0.00 0.00 0.00 3.41
559 569 2.357517 CCACTCACCGCCACTCAC 60.358 66.667 0.00 0.00 0.00 3.51
560 570 2.357517 CACTCACCGCCACTCACC 60.358 66.667 0.00 0.00 0.00 4.02
561 571 3.991051 ACTCACCGCCACTCACCG 61.991 66.667 0.00 0.00 0.00 4.94
569 579 4.742201 CCACTCACCGCCGGACAG 62.742 72.222 11.71 7.41 0.00 3.51
718 729 8.958119 TTATTATTCCTAGTTTGCAATCGACT 57.042 30.769 0.00 3.44 0.00 4.18
720 731 3.953712 TCCTAGTTTGCAATCGACTCA 57.046 42.857 5.55 0.00 0.00 3.41
721 732 3.849911 TCCTAGTTTGCAATCGACTCAG 58.150 45.455 5.55 0.17 0.00 3.35
722 733 3.258372 TCCTAGTTTGCAATCGACTCAGT 59.742 43.478 5.55 0.00 0.00 3.41
723 734 3.614616 CCTAGTTTGCAATCGACTCAGTC 59.385 47.826 5.55 0.00 0.00 3.51
737 750 2.026262 ACTCAGTCCACACCAGTTTTGT 60.026 45.455 0.00 0.00 0.00 2.83
747 760 8.138712 GTCCACACCAGTTTTGTGATATTTTTA 58.861 33.333 4.05 0.00 46.18 1.52
773 786 6.069963 AGGGTTCAGTTAATGCTAGTTCATCT 60.070 38.462 0.00 0.00 0.00 2.90
779 792 9.371136 TCAGTTAATGCTAGTTCATCTTGTAAG 57.629 33.333 0.00 0.00 0.00 2.34
807 821 2.755103 GGTCTTTGGCCCAGTTCATAAG 59.245 50.000 0.00 0.00 0.00 1.73
919 1040 7.637519 GTGAATCATCATTTCTACGTTGATGTG 59.362 37.037 20.80 13.61 44.47 3.21
920 1041 7.548780 TGAATCATCATTTCTACGTTGATGTGA 59.451 33.333 20.80 17.29 44.47 3.58
921 1042 8.442632 AATCATCATTTCTACGTTGATGTGAT 57.557 30.769 20.80 18.38 44.47 3.06
923 1044 7.687445 TCATCATTTCTACGTTGATGTGATTG 58.313 34.615 20.80 15.81 44.47 2.67
924 1045 7.334171 TCATCATTTCTACGTTGATGTGATTGT 59.666 33.333 20.80 4.75 44.47 2.71
987 1135 2.503356 AGGGAGATCGCTCAAGTCAATT 59.497 45.455 0.00 0.00 43.14 2.32
1082 1230 0.545171 CCACATCCTGATGCTCTGGT 59.455 55.000 7.04 0.00 42.39 4.00
1130 1278 1.959899 GCGACACGTTGCATCTCCAG 61.960 60.000 4.48 0.00 39.74 3.86
1135 1283 2.440980 GTTGCATCTCCAGCCCCC 60.441 66.667 0.00 0.00 0.00 5.40
1155 1303 2.169769 CCCCATCTACGCCTTTTGTCTA 59.830 50.000 0.00 0.00 0.00 2.59
1169 1317 5.691754 CCTTTTGTCTAAAACAGATGTTGGC 59.308 40.000 0.00 0.00 39.58 4.52
1180 1328 1.880027 AGATGTTGGCCAACTTCGTTC 59.120 47.619 38.42 28.76 44.97 3.95
1199 1356 1.472082 TCGCAATTTCGGCAATGACAT 59.528 42.857 0.00 0.00 0.00 3.06
1204 1361 1.462616 TTTCGGCAATGACATCAGGG 58.537 50.000 0.00 0.00 0.00 4.45
1207 1364 1.442526 CGGCAATGACATCAGGGAGC 61.443 60.000 0.00 0.00 0.00 4.70
1212 1369 1.817087 ATGACATCAGGGAGCTGGAT 58.183 50.000 0.00 0.00 0.00 3.41
1392 1571 4.121669 GCTCTCGCCGCACAGAGA 62.122 66.667 17.09 8.05 38.85 3.10
1398 1577 1.029947 TCGCCGCACAGAGACTCATA 61.030 55.000 5.02 0.00 0.00 2.15
1461 1664 0.460311 CTAGGGCGGTCGATGAGTTT 59.540 55.000 0.00 0.00 0.00 2.66
1466 1669 1.925185 GGCGGTCGATGAGTTTAACTC 59.075 52.381 17.34 17.34 45.26 3.01
1561 3389 0.304705 CACTTCACGTGCAACCACTC 59.695 55.000 11.67 0.00 39.86 3.51
1564 3392 4.354212 CACGTGCAACCACTCGCG 62.354 66.667 0.82 0.00 39.86 5.87
1664 3500 3.392616 TGGATCCTTATCTGGCTTCCTTC 59.607 47.826 14.23 0.00 33.24 3.46
1680 3516 3.754965 TCCTTCTGTAGTTTGCTGCATT 58.245 40.909 1.84 0.00 36.76 3.56
1689 3526 4.764679 AGTTTGCTGCATTTCGTTATCA 57.235 36.364 1.84 0.00 0.00 2.15
1750 3599 1.263776 CTTGTCAGCGATCGAGTGTC 58.736 55.000 21.57 13.04 0.00 3.67
1757 3613 3.439129 TCAGCGATCGAGTGTCTCTTAAA 59.561 43.478 21.57 0.00 0.00 1.52
1765 3621 8.005466 CGATCGAGTGTCTCTTAAATAGTACTC 58.995 40.741 10.26 0.00 0.00 2.59
1766 3622 8.734218 ATCGAGTGTCTCTTAAATAGTACTCA 57.266 34.615 0.00 0.00 33.19 3.41
1767 3623 7.972527 TCGAGTGTCTCTTAAATAGTACTCAC 58.027 38.462 0.00 0.00 33.19 3.51
1768 3624 7.823310 TCGAGTGTCTCTTAAATAGTACTCACT 59.177 37.037 0.00 2.18 38.91 3.41
1769 3625 8.117988 CGAGTGTCTCTTAAATAGTACTCACTC 58.882 40.741 17.55 17.55 42.20 3.51
1770 3626 8.283699 AGTGTCTCTTAAATAGTACTCACTCC 57.716 38.462 0.00 0.00 36.14 3.85
1771 3627 7.889073 AGTGTCTCTTAAATAGTACTCACTCCA 59.111 37.037 0.00 0.00 36.14 3.86
1772 3628 7.969508 GTGTCTCTTAAATAGTACTCACTCCAC 59.030 40.741 0.00 0.00 36.14 4.02
1773 3629 7.122353 TGTCTCTTAAATAGTACTCACTCCACC 59.878 40.741 0.00 0.00 36.14 4.61
1774 3630 7.122353 GTCTCTTAAATAGTACTCACTCCACCA 59.878 40.741 0.00 0.00 36.14 4.17
1775 3631 7.839705 TCTCTTAAATAGTACTCACTCCACCAT 59.160 37.037 0.00 0.00 36.14 3.55
1776 3632 9.132923 CTCTTAAATAGTACTCACTCCACCATA 57.867 37.037 0.00 0.00 36.14 2.74
1777 3633 9.656323 TCTTAAATAGTACTCACTCCACCATAT 57.344 33.333 0.00 0.00 36.14 1.78
1781 3637 9.435570 AAATAGTACTCACTCCACCATATTACT 57.564 33.333 0.00 0.00 36.14 2.24
1782 3638 9.435570 AATAGTACTCACTCCACCATATTACTT 57.564 33.333 0.00 0.00 36.14 2.24
1783 3639 7.113658 AGTACTCACTCCACCATATTACTTG 57.886 40.000 0.00 0.00 0.00 3.16
1784 3640 6.668283 AGTACTCACTCCACCATATTACTTGT 59.332 38.462 0.00 0.00 0.00 3.16
1785 3641 5.978814 ACTCACTCCACCATATTACTTGTC 58.021 41.667 0.00 0.00 0.00 3.18
1786 3642 5.006153 TCACTCCACCATATTACTTGTCG 57.994 43.478 0.00 0.00 0.00 4.35
1787 3643 3.555956 CACTCCACCATATTACTTGTCGC 59.444 47.826 0.00 0.00 0.00 5.19
1788 3644 3.451178 ACTCCACCATATTACTTGTCGCT 59.549 43.478 0.00 0.00 0.00 4.93
1789 3645 4.051922 CTCCACCATATTACTTGTCGCTC 58.948 47.826 0.00 0.00 0.00 5.03
1790 3646 3.449377 TCCACCATATTACTTGTCGCTCA 59.551 43.478 0.00 0.00 0.00 4.26
1791 3647 4.081365 TCCACCATATTACTTGTCGCTCAA 60.081 41.667 0.00 0.00 34.61 3.02
1792 3648 4.634004 CCACCATATTACTTGTCGCTCAAA 59.366 41.667 0.00 0.00 35.48 2.69
1793 3649 5.296780 CCACCATATTACTTGTCGCTCAAAT 59.703 40.000 0.00 0.00 35.48 2.32
1794 3650 6.194463 CACCATATTACTTGTCGCTCAAATG 58.806 40.000 0.00 0.00 35.48 2.32
1795 3651 5.296780 ACCATATTACTTGTCGCTCAAATGG 59.703 40.000 13.82 13.82 41.48 3.16
1796 3652 5.527214 CCATATTACTTGTCGCTCAAATGGA 59.473 40.000 11.69 0.00 39.71 3.41
1797 3653 6.205464 CCATATTACTTGTCGCTCAAATGGAT 59.795 38.462 11.69 0.01 39.71 3.41
1798 3654 4.944962 TTACTTGTCGCTCAAATGGATG 57.055 40.909 0.00 0.00 35.48 3.51
1799 3655 2.783135 ACTTGTCGCTCAAATGGATGT 58.217 42.857 0.00 0.00 35.48 3.06
1822 3679 9.632638 ATGTAATAGTTCTATCAAATTGTGCCT 57.367 29.630 0.00 0.00 0.00 4.75
1851 3708 5.858581 CGCTTGGCCTGCTATAATTAATTTC 59.141 40.000 16.82 0.00 0.00 2.17
1871 3728 6.517914 TTTCGTACAATGGAATTTGTTTGC 57.482 33.333 0.00 0.00 40.25 3.68
1881 3738 4.162320 TGGAATTTGTTTGCCACCAAGTTA 59.838 37.500 0.00 0.00 31.52 2.24
2010 5332 1.560505 TGTCACCATAGAGCTCAGCA 58.439 50.000 17.77 0.23 0.00 4.41
2057 5380 2.574006 TTCTCCTGAGCAAGCACATT 57.426 45.000 0.00 0.00 0.00 2.71
2072 5411 4.371786 AGCACATTACATACTCCATCACG 58.628 43.478 0.00 0.00 0.00 4.35
2170 5529 1.975680 ACACCAATGGTACCTCGAAGT 59.024 47.619 14.36 1.41 32.11 3.01
2261 5632 4.048696 GGCTGAGCCTCTTCCTCT 57.951 61.111 17.96 0.00 46.69 3.69
2262 5633 2.295904 GGCTGAGCCTCTTCCTCTT 58.704 57.895 17.96 0.00 46.69 2.85
2263 5634 1.490574 GGCTGAGCCTCTTCCTCTTA 58.509 55.000 17.96 0.00 46.69 2.10
2264 5635 1.834263 GGCTGAGCCTCTTCCTCTTAA 59.166 52.381 17.96 0.00 46.69 1.85
2302 5677 2.298163 CCACTTCTTTGCCAATTGAGCT 59.702 45.455 7.12 0.00 0.00 4.09
2377 5759 0.526524 CGGAGAAGTGAGCGATGGAC 60.527 60.000 0.00 0.00 0.00 4.02
2423 5808 1.901833 TGAGCTGATGAAGTGGTGCTA 59.098 47.619 0.00 0.00 0.00 3.49
2532 5932 1.288633 ACAAGGCCATGGGATCATCAA 59.711 47.619 15.13 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.862744 TAGGCCCGCCTCGATCGAT 62.863 63.158 19.78 0.00 44.43 3.59
3 4 3.862744 ATAGGCCCGCCTCGATCGA 62.863 63.158 18.32 18.32 44.43 3.59
5 6 2.574399 GATAGGCCCGCCTCGATC 59.426 66.667 12.53 7.12 44.43 3.69
6 7 3.374402 CGATAGGCCCGCCTCGAT 61.374 66.667 12.53 0.40 44.43 3.59
55 56 4.963428 GGACTAATCGCGGGCCGG 62.963 72.222 29.48 17.85 37.59 6.13
56 57 1.874345 ATAGGACTAATCGCGGGCCG 61.874 60.000 24.35 24.35 38.61 6.13
57 58 0.108756 GATAGGACTAATCGCGGGCC 60.109 60.000 6.13 0.17 0.00 5.80
58 59 0.456312 CGATAGGACTAATCGCGGGC 60.456 60.000 6.13 0.00 0.00 6.13
59 60 0.879765 ACGATAGGACTAATCGCGGG 59.120 55.000 6.13 0.00 41.05 6.13
60 61 1.965083 CACGATAGGACTAATCGCGG 58.035 55.000 6.13 0.00 41.05 6.46
61 62 1.328439 GCACGATAGGACTAATCGCG 58.672 55.000 0.00 0.00 41.05 5.87
62 63 1.699343 GGCACGATAGGACTAATCGC 58.301 55.000 5.46 0.00 41.05 4.58
110 111 2.428925 GCATTGGGCCATGTCTGGG 61.429 63.158 7.26 0.00 43.36 4.45
111 112 2.777972 CGCATTGGGCCATGTCTGG 61.778 63.158 7.26 0.00 46.17 3.86
112 113 2.048023 ACGCATTGGGCCATGTCTG 61.048 57.895 7.26 4.22 40.31 3.51
113 114 2.048023 CACGCATTGGGCCATGTCT 61.048 57.895 7.26 0.00 40.31 3.41
114 115 1.386525 ATCACGCATTGGGCCATGTC 61.387 55.000 7.26 0.00 40.31 3.06
115 116 1.380246 ATCACGCATTGGGCCATGT 60.380 52.632 7.26 0.56 40.31 3.21
116 117 1.066752 CATCACGCATTGGGCCATG 59.933 57.895 7.26 9.36 40.31 3.66
117 118 2.788640 GCATCACGCATTGGGCCAT 61.789 57.895 7.26 0.00 41.79 4.40
118 119 3.451004 GCATCACGCATTGGGCCA 61.451 61.111 0.00 0.00 41.79 5.36
119 120 4.557605 CGCATCACGCATTGGGCC 62.558 66.667 0.00 0.00 42.60 5.80
138 139 3.379865 TAATCGGGTCGTGCCAGGC 62.380 63.158 3.66 3.66 39.65 4.85
139 140 1.227263 CTAATCGGGTCGTGCCAGG 60.227 63.158 1.70 0.00 39.65 4.45
140 141 1.883084 GCTAATCGGGTCGTGCCAG 60.883 63.158 1.70 0.00 39.65 4.85
141 142 2.185867 GCTAATCGGGTCGTGCCA 59.814 61.111 1.70 0.00 39.65 4.92
142 143 2.588034 GGCTAATCGGGTCGTGCC 60.588 66.667 0.00 0.00 0.00 5.01
143 144 2.588034 GGGCTAATCGGGTCGTGC 60.588 66.667 0.00 0.00 0.00 5.34
144 145 2.279252 CGGGCTAATCGGGTCGTG 60.279 66.667 0.00 0.00 0.00 4.35
145 146 2.757099 ACGGGCTAATCGGGTCGT 60.757 61.111 0.00 0.00 0.00 4.34
146 147 2.279252 CACGGGCTAATCGGGTCG 60.279 66.667 0.00 0.00 0.00 4.79
147 148 2.588034 GCACGGGCTAATCGGGTC 60.588 66.667 0.00 0.00 36.96 4.46
148 149 4.171103 GGCACGGGCTAATCGGGT 62.171 66.667 10.74 0.00 40.87 5.28
207 208 2.816012 CCAAACGGGCCGGTTTTT 59.184 55.556 32.12 17.08 38.01 1.94
216 217 2.033448 TACAGCTGGCCAAACGGG 59.967 61.111 19.93 2.80 40.85 5.28
217 218 1.298859 GAGTACAGCTGGCCAAACGG 61.299 60.000 19.93 5.37 0.00 4.44
218 219 0.320771 AGAGTACAGCTGGCCAAACG 60.321 55.000 19.93 0.00 0.00 3.60
219 220 1.160137 CAGAGTACAGCTGGCCAAAC 58.840 55.000 19.93 1.16 0.00 2.93
220 221 0.036732 CCAGAGTACAGCTGGCCAAA 59.963 55.000 19.93 0.00 45.66 3.28
221 222 1.679311 CCAGAGTACAGCTGGCCAA 59.321 57.895 19.93 0.00 45.66 4.52
222 223 3.392228 CCAGAGTACAGCTGGCCA 58.608 61.111 19.93 4.71 45.66 5.36
226 227 2.100584 GAGGTCATCCAGAGTACAGCTG 59.899 54.545 13.48 13.48 35.89 4.24
227 228 2.383855 GAGGTCATCCAGAGTACAGCT 58.616 52.381 0.00 0.00 35.89 4.24
228 229 2.880963 GAGGTCATCCAGAGTACAGC 57.119 55.000 0.00 0.00 35.89 4.40
239 240 1.974236 CTGGGAGTATGGGAGGTCATC 59.026 57.143 0.00 0.00 0.00 2.92
240 241 1.415126 CCTGGGAGTATGGGAGGTCAT 60.415 57.143 0.00 0.00 0.00 3.06
241 242 0.031111 CCTGGGAGTATGGGAGGTCA 60.031 60.000 0.00 0.00 0.00 4.02
242 243 0.764752 CCCTGGGAGTATGGGAGGTC 60.765 65.000 7.01 0.00 43.47 3.85
243 244 1.318380 CCCTGGGAGTATGGGAGGT 59.682 63.158 7.01 0.00 43.47 3.85
244 245 2.150051 GCCCTGGGAGTATGGGAGG 61.150 68.421 19.27 0.00 43.47 4.30
245 246 1.074167 AGCCCTGGGAGTATGGGAG 60.074 63.158 19.27 0.00 43.47 4.30
246 247 1.074471 GAGCCCTGGGAGTATGGGA 60.074 63.158 19.27 0.00 43.47 4.37
266 267 9.936329 ACCCCATAAACAAAGAAATATACAGAT 57.064 29.630 0.00 0.00 0.00 2.90
303 304 5.127031 AGCCAACTACTGTTTCAACACAAAT 59.873 36.000 0.00 0.00 34.70 2.32
334 335 1.184970 TCACCCAGTCACGCAGATCA 61.185 55.000 0.00 0.00 0.00 2.92
336 337 0.615331 ATTCACCCAGTCACGCAGAT 59.385 50.000 0.00 0.00 0.00 2.90
541 551 4.314440 TGAGTGGCGGTGAGTGGC 62.314 66.667 0.00 0.00 0.00 5.01
542 552 2.357517 GTGAGTGGCGGTGAGTGG 60.358 66.667 0.00 0.00 0.00 4.00
543 553 2.357517 GGTGAGTGGCGGTGAGTG 60.358 66.667 0.00 0.00 0.00 3.51
544 554 3.991051 CGGTGAGTGGCGGTGAGT 61.991 66.667 0.00 0.00 0.00 3.41
552 562 4.742201 CTGTCCGGCGGTGAGTGG 62.742 72.222 27.32 7.68 0.00 4.00
707 718 1.069978 TGTGGACTGAGTCGATTGCAA 59.930 47.619 0.00 0.00 32.65 4.08
714 725 0.389391 AACTGGTGTGGACTGAGTCG 59.611 55.000 6.50 0.00 32.65 4.18
715 726 2.614057 CAAAACTGGTGTGGACTGAGTC 59.386 50.000 3.47 3.47 0.00 3.36
717 728 2.355756 CACAAAACTGGTGTGGACTGAG 59.644 50.000 0.00 0.00 42.20 3.35
718 729 2.026729 TCACAAAACTGGTGTGGACTGA 60.027 45.455 4.83 0.00 45.27 3.41
720 731 2.799126 TCACAAAACTGGTGTGGACT 57.201 45.000 4.83 0.00 45.27 3.85
721 732 5.705609 AATATCACAAAACTGGTGTGGAC 57.294 39.130 4.83 0.00 45.27 4.02
722 733 6.723298 AAAATATCACAAAACTGGTGTGGA 57.277 33.333 4.83 0.00 45.27 4.02
723 734 8.879342 TTAAAAATATCACAAAACTGGTGTGG 57.121 30.769 4.83 0.00 45.27 4.17
747 760 5.876357 TGAACTAGCATTAACTGAACCCTT 58.124 37.500 0.00 0.00 0.00 3.95
773 786 3.420893 CCAAAGACCATGAGCCTTACAA 58.579 45.455 0.00 0.00 0.00 2.41
779 792 2.054453 GGGCCAAAGACCATGAGCC 61.054 63.158 4.39 0.00 39.73 4.70
933 1076 3.817647 GCTGCCAAGGTGATAGAAATAGG 59.182 47.826 0.00 0.00 0.00 2.57
943 1086 1.228245 GGTCTTGCTGCCAAGGTGA 60.228 57.895 0.00 0.00 46.69 4.02
1034 1182 1.352352 CCCCGGCCATCTCAATAAGAT 59.648 52.381 2.24 0.00 46.04 2.40
1039 1187 4.209866 GCCCCCGGCCATCTCAAT 62.210 66.667 2.24 0.00 44.06 2.57
1114 1262 1.672356 GGCTGGAGATGCAACGTGT 60.672 57.895 0.00 0.00 0.00 4.49
1135 1283 2.403252 AGACAAAAGGCGTAGATGGG 57.597 50.000 0.00 0.00 0.00 4.00
1138 1286 6.228258 TCTGTTTTAGACAAAAGGCGTAGAT 58.772 36.000 0.00 0.00 37.93 1.98
1141 1289 5.761234 ACATCTGTTTTAGACAAAAGGCGTA 59.239 36.000 0.00 0.00 38.49 4.42
1142 1290 4.578928 ACATCTGTTTTAGACAAAAGGCGT 59.421 37.500 0.00 0.00 38.49 5.68
1143 1291 5.108385 ACATCTGTTTTAGACAAAAGGCG 57.892 39.130 0.00 0.00 38.49 5.52
1147 1295 5.127845 TGGCCAACATCTGTTTTAGACAAAA 59.872 36.000 0.61 0.00 38.49 2.44
1148 1296 4.646945 TGGCCAACATCTGTTTTAGACAAA 59.353 37.500 0.61 0.00 38.49 2.83
1155 1303 3.490761 CGAAGTTGGCCAACATCTGTTTT 60.491 43.478 41.88 28.46 43.47 2.43
1180 1328 1.847999 GATGTCATTGCCGAAATTGCG 59.152 47.619 0.00 0.00 0.00 4.85
1199 1356 1.794714 GAGGTTATCCAGCTCCCTGA 58.205 55.000 0.00 0.00 43.33 3.86
1207 1364 1.804372 GCGAGCAGTGAGGTTATCCAG 60.804 57.143 0.00 0.00 35.89 3.86
1212 1369 1.605058 GGAGGCGAGCAGTGAGGTTA 61.605 60.000 0.00 0.00 0.00 2.85
1263 1432 2.300967 GGCAGTGGGGGAGACATCA 61.301 63.158 0.00 0.00 0.00 3.07
1265 1434 3.017581 GGGCAGTGGGGGAGACAT 61.018 66.667 0.00 0.00 0.00 3.06
1296 1465 4.516698 GCACGGAATAGATCATTTCCATGT 59.483 41.667 20.42 11.83 41.25 3.21
1342 1511 4.457496 CTCCACAGGCGCGGTCAT 62.457 66.667 8.83 0.00 0.00 3.06
1355 1534 3.396767 CCTCAAGGCAGAGCTCCA 58.603 61.111 10.93 0.00 34.26 3.86
1392 1571 1.555075 AGGTGGTCATGCGTTATGAGT 59.445 47.619 4.99 0.00 46.09 3.41
1398 1577 1.374252 GTCGAGGTGGTCATGCGTT 60.374 57.895 0.00 0.00 0.00 4.84
1441 1644 2.017559 AACTCATCGACCGCCCTAGC 62.018 60.000 0.00 0.00 0.00 3.42
1445 1648 1.004595 GTTAAACTCATCGACCGCCC 58.995 55.000 0.00 0.00 0.00 6.13
1561 3389 2.316119 AGCTTTTACTTTGCTTCGCG 57.684 45.000 0.00 0.00 32.61 5.87
1564 3392 5.107337 GGCAATCAAGCTTTTACTTTGCTTC 60.107 40.000 19.46 7.95 44.04 3.86
1618 3446 4.285790 ACCCTCCTGGCCCCTTCA 62.286 66.667 0.00 0.00 37.83 3.02
1664 3500 3.542712 ACGAAATGCAGCAAACTACAG 57.457 42.857 0.00 0.00 0.00 2.74
1680 3516 5.759506 TTTGTTCTTGGCTTGATAACGAA 57.240 34.783 0.00 0.00 0.00 3.85
1689 3526 6.280855 AGTAGTTGTTTTTGTTCTTGGCTT 57.719 33.333 0.00 0.00 0.00 4.35
1750 3599 7.406031 TGGTGGAGTGAGTACTATTTAAGAG 57.594 40.000 0.00 0.00 37.25 2.85
1757 3613 8.861086 CAAGTAATATGGTGGAGTGAGTACTAT 58.139 37.037 0.00 0.00 37.25 2.12
1765 3621 3.555956 GCGACAAGTAATATGGTGGAGTG 59.444 47.826 0.00 0.00 0.00 3.51
1766 3622 3.451178 AGCGACAAGTAATATGGTGGAGT 59.549 43.478 0.00 0.00 0.00 3.85
1767 3623 4.051922 GAGCGACAAGTAATATGGTGGAG 58.948 47.826 0.00 0.00 0.00 3.86
1768 3624 3.449377 TGAGCGACAAGTAATATGGTGGA 59.551 43.478 0.00 0.00 0.00 4.02
1769 3625 3.792401 TGAGCGACAAGTAATATGGTGG 58.208 45.455 0.00 0.00 0.00 4.61
1770 3626 5.794687 TTTGAGCGACAAGTAATATGGTG 57.205 39.130 0.00 0.00 39.77 4.17
1771 3627 5.296780 CCATTTGAGCGACAAGTAATATGGT 59.703 40.000 13.83 0.00 37.22 3.55
1772 3628 5.527214 TCCATTTGAGCGACAAGTAATATGG 59.473 40.000 14.97 14.97 40.44 2.74
1773 3629 6.603237 TCCATTTGAGCGACAAGTAATATG 57.397 37.500 0.00 0.00 39.77 1.78
1774 3630 6.767902 ACATCCATTTGAGCGACAAGTAATAT 59.232 34.615 0.00 0.00 39.77 1.28
1775 3631 6.112734 ACATCCATTTGAGCGACAAGTAATA 58.887 36.000 0.00 0.00 39.77 0.98
1776 3632 4.943705 ACATCCATTTGAGCGACAAGTAAT 59.056 37.500 0.00 0.00 39.77 1.89
1777 3633 4.323417 ACATCCATTTGAGCGACAAGTAA 58.677 39.130 0.00 0.00 39.77 2.24
1778 3634 3.937814 ACATCCATTTGAGCGACAAGTA 58.062 40.909 0.00 0.00 39.77 2.24
1779 3635 2.783135 ACATCCATTTGAGCGACAAGT 58.217 42.857 0.00 0.00 39.77 3.16
1780 3636 4.944962 TTACATCCATTTGAGCGACAAG 57.055 40.909 0.00 0.00 39.77 3.16
1781 3637 6.112734 ACTATTACATCCATTTGAGCGACAA 58.887 36.000 0.00 0.00 36.65 3.18
1782 3638 5.670485 ACTATTACATCCATTTGAGCGACA 58.330 37.500 0.00 0.00 0.00 4.35
1783 3639 6.480320 AGAACTATTACATCCATTTGAGCGAC 59.520 38.462 0.00 0.00 0.00 5.19
1784 3640 6.582636 AGAACTATTACATCCATTTGAGCGA 58.417 36.000 0.00 0.00 0.00 4.93
1785 3641 6.851222 AGAACTATTACATCCATTTGAGCG 57.149 37.500 0.00 0.00 0.00 5.03
1786 3642 9.494271 TGATAGAACTATTACATCCATTTGAGC 57.506 33.333 0.00 0.00 0.00 4.26
1794 3650 9.884465 GCACAATTTGATAGAACTATTACATCC 57.116 33.333 2.79 0.00 0.00 3.51
1795 3651 9.884465 GGCACAATTTGATAGAACTATTACATC 57.116 33.333 2.79 0.00 0.00 3.06
1796 3652 9.632638 AGGCACAATTTGATAGAACTATTACAT 57.367 29.630 2.79 0.00 0.00 2.29
1797 3653 9.461312 AAGGCACAATTTGATAGAACTATTACA 57.539 29.630 2.79 0.00 0.00 2.41
1798 3654 9.722056 CAAGGCACAATTTGATAGAACTATTAC 57.278 33.333 2.79 0.00 0.00 1.89
1799 3655 9.461312 ACAAGGCACAATTTGATAGAACTATTA 57.539 29.630 2.79 0.00 0.00 0.98
1815 3672 2.412525 CAAGCGCACAAGGCACAA 59.587 55.556 11.47 0.00 45.17 3.33
1822 3679 3.722355 TATAGCAGGCCAAGCGCACAA 62.722 52.381 11.47 0.00 40.31 3.33
1851 3708 4.149747 GTGGCAAACAAATTCCATTGTACG 59.850 41.667 0.00 0.00 42.49 3.67
2010 5332 0.878961 GCCGAGGTTGAGAACGTGTT 60.879 55.000 0.00 0.00 0.00 3.32
2057 5380 1.068588 GCCAGCGTGATGGAGTATGTA 59.931 52.381 8.61 0.00 43.57 2.29
2072 5411 0.459585 CATTGCCTTGTGATGCCAGC 60.460 55.000 0.00 0.00 0.00 4.85
2123 5464 0.689080 GCTCCTGAGGATGTCCCAGA 60.689 60.000 0.00 0.43 36.83 3.86
2377 5759 3.938963 ACCACCAACAGAGCATTATAACG 59.061 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.