Multiple sequence alignment - TraesCS6D01G190600

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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 TraesCS6D01G190600 chr6D 100.000 2312 0 0 1 2312 263142238 263139927 0.000000e+00 4270
1 TraesCS6D01G190600 chr6D 85.031 1129 129 24 497 1613 2788503 2787403 0.000000e+00 1112
2 TraesCS6D01G190600 chr6D 75.035 2119 341 114 69 2068 160417814 160419863 0.000000e+00 809
3 TraesCS6D01G190600 chr6D 88.986 572 34 9 68 610 263140701 263140130 0.000000e+00 680
4 TraesCS6D01G190600 chr6D 88.986 572 34 9 1538 2109 263142171 263141629 0.000000e+00 680
5 TraesCS6D01G190600 chr6D 79.167 288 28 11 68 324 160419320 160419606 1.100000e-38 171
6 TraesCS6D01G190600 chr6D 89.899 99 8 1 69 165 2866240 2866142 2.410000e-25 126
7 TraesCS6D01G190600 chr2A 85.993 1178 124 24 533 1705 495224748 495223607 0.000000e+00 1223
8 TraesCS6D01G190600 chr6A 86.271 1129 135 18 497 1613 1766084 1764964 0.000000e+00 1208
9 TraesCS6D01G190600 chr3D 87.795 1016 110 10 603 1612 559488009 559487002 0.000000e+00 1177
10 TraesCS6D01G190600 chr4D 85.841 1123 133 17 563 1681 454451155 454450055 0.000000e+00 1170
11 TraesCS6D01G190600 chr7D 85.870 1104 124 20 606 1699 603307662 603306581 0.000000e+00 1146
12 TraesCS6D01G190600 chr7D 77.670 2060 296 90 69 2072 105842825 105840874 0.000000e+00 1105
13 TraesCS6D01G190600 chr7D 81.475 583 43 34 1546 2111 105842818 105842284 3.550000e-113 418
14 TraesCS6D01G190600 chr7D 80.392 510 52 22 1613 2112 35324224 35323753 6.120000e-91 344
15 TraesCS6D01G190600 chr7D 79.053 549 65 31 68 595 105841372 105840853 4.760000e-87 331
16 TraesCS6D01G190600 chr7D 80.952 420 51 23 357 768 35325374 35324976 2.890000e-79 305
17 TraesCS6D01G190600 chr7D 83.283 329 29 9 1546 1872 40195905 40196209 1.750000e-71 279
18 TraesCS6D01G190600 chr7D 89.565 115 9 3 67 178 272282443 272282557 2.390000e-30 143
19 TraesCS6D01G190600 chr7D 86.777 121 13 2 66 183 16161585 16161465 5.180000e-27 132
20 TraesCS6D01G190600 chr7D 87.719 114 11 2 68 178 16157682 16157569 1.860000e-26 130
21 TraesCS6D01G190600 chr7D 85.965 114 13 3 68 178 16158980 16158867 4.040000e-23 119
22 TraesCS6D01G190600 chr4B 86.961 1020 107 11 606 1624 323785464 323786458 0.000000e+00 1123
23 TraesCS6D01G190600 chr4B 84.671 1109 150 12 588 1691 567198519 567197426 0.000000e+00 1088
24 TraesCS6D01G190600 chr5D 85.917 1058 127 10 606 1660 35656828 35657866 0.000000e+00 1109
25 TraesCS6D01G190600 chr2D 84.145 1129 131 29 588 1706 640588674 640589764 0.000000e+00 1050
26 TraesCS6D01G190600 chr2D 79.120 1159 165 42 932 2072 536931691 536930592 0.000000e+00 728
27 TraesCS6D01G190600 chr2D 82.131 582 54 21 1542 2111 536932517 536931974 9.740000e-124 453
28 TraesCS6D01G190600 chr4A 77.010 1953 301 92 173 2076 701043485 701045338 0.000000e+00 983
29 TraesCS6D01G190600 chr4A 80.500 600 63 33 1539 2112 701043345 701043916 5.950000e-111 411
30 TraesCS6D01G190600 chr5B 87.260 730 82 9 238 963 688707719 688708441 0.000000e+00 822
31 TraesCS6D01G190600 chr5B 85.806 775 81 17 1251 2020 688708434 688709184 0.000000e+00 795
32 TraesCS6D01G190600 chr5B 82.474 582 64 15 1539 2097 688707511 688708077 2.080000e-130 475
33 TraesCS6D01G190600 chr7A 82.738 504 51 23 1619 2111 86082176 86081698 1.280000e-112 416
34 TraesCS6D01G190600 chr3B 76.319 815 145 40 915 1706 813404456 813405245 2.150000e-105 392
35 TraesCS6D01G190600 chr3B 87.200 250 25 4 1861 2110 826181948 826181706 6.290000e-71 278
36 TraesCS6D01G190600 chr3B 88.136 236 22 4 364 599 826181948 826181719 2.260000e-70 276
37 TraesCS6D01G190600 chr3B 75.685 584 95 35 361 921 813403717 813404276 4.930000e-62 248
38 TraesCS6D01G190600 chr3B 91.525 118 10 0 238 355 826182128 826182011 1.840000e-36 163
39 TraesCS6D01G190600 chr3B 88.288 111 9 3 68 175 807203 807094 1.860000e-26 130
40 TraesCS6D01G190600 chr2B 76.366 677 122 29 1049 1707 6471848 6471192 1.710000e-86 329
41 TraesCS6D01G190600 chr1B 74.670 908 150 56 956 1810 21850618 21849738 1.710000e-86 329
42 TraesCS6D01G190600 chr1B 83.642 324 35 12 1537 1856 683150179 683150488 2.910000e-74 289
43 TraesCS6D01G190600 chr1B 86.747 249 24 3 362 610 683150544 683150783 3.790000e-68 268
44 TraesCS6D01G190600 chr1B 86.056 251 24 4 1859 2109 683150544 683150783 2.280000e-65 259
45 TraesCS6D01G190600 chr1B 81.783 258 22 9 123 355 683150226 683150483 2.340000e-45 193
46 TraesCS6D01G190600 chr5A 75.638 431 57 28 172 570 40623648 40624062 1.100000e-38 171
47 TraesCS6D01G190600 chr1A 77.778 279 32 8 68 324 586119304 586119574 6.660000e-31 145
48 TraesCS6D01G190600 chr1A 86.232 138 13 2 1721 1852 589669158 589669295 6.660000e-31 145
49 TraesCS6D01G190600 chr1D 86.325 117 13 3 65 178 442905013 442905129 8.670000e-25 124
50 TraesCS6D01G190600 chr3A 86.726 113 12 2 68 177 571838264 571838152 3.120000e-24 122
51 TraesCS6D01G190600 chr6B 88.889 99 8 2 69 165 223612216 223612313 4.040000e-23 119


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 TraesCS6D01G190600 chr6D 263139927 263142238 2311 True 1876.666667 4270 92.657333 1 2312 3 chr6D.!!$R3 2311
1 TraesCS6D01G190600 chr6D 2787403 2788503 1100 True 1112.000000 1112 85.031000 497 1613 1 chr6D.!!$R1 1116
2 TraesCS6D01G190600 chr6D 160417814 160419863 2049 False 490.000000 809 77.101000 68 2068 2 chr6D.!!$F1 2000
3 TraesCS6D01G190600 chr2A 495223607 495224748 1141 True 1223.000000 1223 85.993000 533 1705 1 chr2A.!!$R1 1172
4 TraesCS6D01G190600 chr6A 1764964 1766084 1120 True 1208.000000 1208 86.271000 497 1613 1 chr6A.!!$R1 1116
5 TraesCS6D01G190600 chr3D 559487002 559488009 1007 True 1177.000000 1177 87.795000 603 1612 1 chr3D.!!$R1 1009
6 TraesCS6D01G190600 chr4D 454450055 454451155 1100 True 1170.000000 1170 85.841000 563 1681 1 chr4D.!!$R1 1118
7 TraesCS6D01G190600 chr7D 603306581 603307662 1081 True 1146.000000 1146 85.870000 606 1699 1 chr7D.!!$R1 1093
8 TraesCS6D01G190600 chr7D 105840853 105842825 1972 True 618.000000 1105 79.399333 68 2111 3 chr7D.!!$R4 2043
9 TraesCS6D01G190600 chr7D 35323753 35325374 1621 True 324.500000 344 80.672000 357 2112 2 chr7D.!!$R3 1755
10 TraesCS6D01G190600 chr4B 323785464 323786458 994 False 1123.000000 1123 86.961000 606 1624 1 chr4B.!!$F1 1018
11 TraesCS6D01G190600 chr4B 567197426 567198519 1093 True 1088.000000 1088 84.671000 588 1691 1 chr4B.!!$R1 1103
12 TraesCS6D01G190600 chr5D 35656828 35657866 1038 False 1109.000000 1109 85.917000 606 1660 1 chr5D.!!$F1 1054
13 TraesCS6D01G190600 chr2D 640588674 640589764 1090 False 1050.000000 1050 84.145000 588 1706 1 chr2D.!!$F1 1118
14 TraesCS6D01G190600 chr2D 536930592 536932517 1925 True 590.500000 728 80.625500 932 2111 2 chr2D.!!$R1 1179
15 TraesCS6D01G190600 chr4A 701043345 701045338 1993 False 697.000000 983 78.755000 173 2112 2 chr4A.!!$F1 1939
16 TraesCS6D01G190600 chr5B 688707511 688709184 1673 False 697.333333 822 85.180000 238 2097 3 chr5B.!!$F1 1859
17 TraesCS6D01G190600 chr3B 813403717 813405245 1528 False 320.000000 392 76.002000 361 1706 2 chr3B.!!$F1 1345
18 TraesCS6D01G190600 chr2B 6471192 6471848 656 True 329.000000 329 76.366000 1049 1707 1 chr2B.!!$R1 658
19 TraesCS6D01G190600 chr1B 21849738 21850618 880 True 329.000000 329 74.670000 956 1810 1 chr1B.!!$R1 854
20 TraesCS6D01G190600 chr1B 683150179 683150783 604 False 252.250000 289 84.557000 123 2109 4 chr1B.!!$F1 1986

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
78 79 0.035036 TCACCGCGGTGTTGGAATAA 59.965 50.0 46.56 28.9 45.55 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2638 0.10852 AAATACATGGTCGCGTCCGT 60.109 50.0 17.4 14.57 35.54 4.69 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
61 62 4.025858 GCCTGCCACTGCTCCTCA 62.026 66.667 0.00 0.00 38.71 3.86
63 64 2.046507 CTGCCACTGCTCCTCACC 60.047 66.667 0.00 0.00 38.71 4.02
71 72 4.681978 GCTCCTCACCGCGGTGTT 62.682 66.667 46.56 19.83 45.55 3.32
75 76 2.280524 CTCACCGCGGTGTTGGAA 60.281 61.111 46.56 31.49 45.55 3.53
76 77 1.671054 CTCACCGCGGTGTTGGAAT 60.671 57.895 46.56 16.59 45.55 3.01
77 78 0.390603 CTCACCGCGGTGTTGGAATA 60.391 55.000 46.56 30.16 45.55 1.75
78 79 0.035036 TCACCGCGGTGTTGGAATAA 59.965 50.000 46.56 28.90 45.55 1.40
80 81 1.303091 ACCGCGGTGTTGGAATAAGC 61.303 55.000 33.75 0.00 0.00 3.09
82 83 1.302383 CGCGGTGTTGGAATAAGCCA 61.302 55.000 0.00 0.00 35.78 4.75
84 85 1.529226 CGGTGTTGGAATAAGCCACA 58.471 50.000 0.00 0.00 37.75 4.17
86 87 1.202348 GGTGTTGGAATAAGCCACAGC 59.798 52.381 0.00 0.00 37.75 4.40
87 88 1.135689 GTGTTGGAATAAGCCACAGCG 60.136 52.381 0.00 0.00 46.67 5.18
88 89 1.165270 GTTGGAATAAGCCACAGCGT 58.835 50.000 0.00 0.00 46.67 5.07
89 90 1.130561 GTTGGAATAAGCCACAGCGTC 59.869 52.381 0.00 0.00 46.67 5.19
90 91 0.613260 TGGAATAAGCCACAGCGTCT 59.387 50.000 0.00 0.00 46.67 4.18
93 94 0.324943 AATAAGCCACAGCGTCTGGT 59.675 50.000 10.80 0.00 46.67 4.00
105 106 2.283604 TCTGGTGCAGTCGGGCTA 60.284 61.111 0.00 0.00 32.61 3.93
107 108 2.603473 TGGTGCAGTCGGGCTAGT 60.603 61.111 0.00 0.00 34.04 2.57
108 109 2.184579 GGTGCAGTCGGGCTAGTC 59.815 66.667 0.00 0.00 34.04 2.59
109 110 2.202623 GTGCAGTCGGGCTAGTCG 60.203 66.667 0.00 0.00 34.04 4.18
112 113 4.208686 CAGTCGGGCTAGTCGGGC 62.209 72.222 0.00 0.00 0.00 6.13
158 159 4.320456 CACTGGTGCGGTCAGGCT 62.320 66.667 5.89 0.00 36.62 4.58
161 162 3.320879 CTGGTGCGGTCAGGCTCAT 62.321 63.158 0.00 0.00 0.00 2.90
162 163 2.512515 GGTGCGGTCAGGCTCATC 60.513 66.667 0.00 0.00 0.00 2.92
167 168 2.512515 GGTCAGGCTCATCGGTGC 60.513 66.667 0.00 0.00 0.00 5.01
168 169 2.265739 GTCAGGCTCATCGGTGCA 59.734 61.111 0.00 0.00 35.26 4.57
201 202 1.063006 GCAGCATGGCGTATGTGTG 59.937 57.895 0.00 3.88 39.08 3.82
202 203 1.647545 GCAGCATGGCGTATGTGTGT 61.648 55.000 0.00 0.00 39.08 3.72
204 205 1.226379 GCATGGCGTATGTGTGTGC 60.226 57.895 0.00 0.00 39.08 4.57
206 207 0.734309 CATGGCGTATGTGTGTGCAT 59.266 50.000 0.00 0.00 31.92 3.96
210 211 1.305219 GCGTATGTGTGTGCATGGGT 61.305 55.000 0.00 0.00 0.00 4.51
221 222 2.990967 CATGGGTGGTGTGTGGCC 60.991 66.667 0.00 0.00 0.00 5.36
222 223 3.506743 ATGGGTGGTGTGTGGCCA 61.507 61.111 0.00 0.00 0.00 5.36
226 227 3.276846 GTGGTGTGTGGCCACGTC 61.277 66.667 30.07 24.29 45.57 4.34
229 230 2.108157 GTGTGTGGCCACGTCAGA 59.892 61.111 30.07 10.28 44.92 3.27
231 232 0.884704 GTGTGTGGCCACGTCAGATT 60.885 55.000 30.07 0.00 44.92 2.40
232 233 0.602638 TGTGTGGCCACGTCAGATTC 60.603 55.000 30.07 12.81 44.92 2.52
233 234 1.374125 TGTGGCCACGTCAGATTCG 60.374 57.895 30.07 0.00 0.00 3.34
237 238 0.527817 GGCCACGTCAGATTCGTAGG 60.528 60.000 0.00 0.00 39.55 3.18
239 240 1.909376 CCACGTCAGATTCGTAGGTG 58.091 55.000 0.00 6.98 39.55 4.00
240 241 1.269166 CACGTCAGATTCGTAGGTGC 58.731 55.000 0.00 0.00 39.55 5.01
241 242 0.179171 ACGTCAGATTCGTAGGTGCG 60.179 55.000 0.00 0.00 39.78 5.34
330 380 1.153086 GCACCATGCAGTAGGGAGG 60.153 63.158 0.00 0.00 44.26 4.30
331 381 1.915078 GCACCATGCAGTAGGGAGGT 61.915 60.000 0.00 0.00 44.26 3.85
337 387 3.535561 CATGCAGTAGGGAGGTTGTTAG 58.464 50.000 0.00 0.00 0.00 2.34
373 433 3.919386 TGTTGTGTGCGCGTCGTG 61.919 61.111 8.43 0.25 0.00 4.35
437 506 3.094062 GCAGGAGACATGGGCGCTA 62.094 63.158 7.64 0.00 0.00 4.26
438 507 1.750930 CAGGAGACATGGGCGCTAT 59.249 57.895 7.64 0.00 0.00 2.97
492 567 5.869344 CGACCATGTATTTGTTGAGAAGAGA 59.131 40.000 0.00 0.00 0.00 3.10
493 568 6.035435 CGACCATGTATTTGTTGAGAAGAGAG 59.965 42.308 0.00 0.00 0.00 3.20
495 572 7.907389 ACCATGTATTTGTTGAGAAGAGAGTA 58.093 34.615 0.00 0.00 0.00 2.59
561 658 2.639839 ACTCCAGTGTATTGTGCTCCTT 59.360 45.455 0.00 0.00 0.00 3.36
601 722 3.055167 CCTGAGTGAGAGAGAGAGAGTGA 60.055 52.174 0.00 0.00 0.00 3.41
702 826 3.446570 GCGATGGCCTTGCAGCTT 61.447 61.111 3.32 0.00 34.05 3.74
706 830 3.574074 ATGGCCTTGCAGCTTCCGT 62.574 57.895 3.32 0.00 0.00 4.69
711 835 2.734673 CTTGCAGCTTCCGTCGCTC 61.735 63.158 0.00 0.00 35.07 5.03
833 957 1.153745 CCGGGAAGAGCAAGACGAG 60.154 63.158 0.00 0.00 0.00 4.18
839 963 1.122019 AAGAGCAAGACGAGGTGGGT 61.122 55.000 0.00 0.00 0.00 4.51
940 1250 1.590525 AAAGTGCGCTTCGTCGACA 60.591 52.632 13.92 0.00 33.01 4.35
1032 1342 2.277373 GAGCTGGACGACTACGCG 60.277 66.667 3.53 3.53 43.96 6.01
1285 1620 0.328926 TGGGCAGCTGATGATGACAA 59.671 50.000 20.43 0.00 39.86 3.18
1344 1683 3.635204 GGCTTCGGCGATCATGAG 58.365 61.111 11.76 5.69 42.91 2.90
1691 2211 2.474266 CGTGGCGTATGTGTGTGC 59.526 61.111 0.00 0.00 0.00 4.57
1697 2231 1.305219 GCGTATGTGTGTGCATGGGT 61.305 55.000 0.00 0.00 0.00 4.51
1814 2427 3.807538 GGAGCTGTGCATGCACCG 61.808 66.667 40.01 35.42 45.63 4.94
1958 2638 0.606401 GCTGCAGGACTACAAAGCCA 60.606 55.000 17.12 0.00 0.00 4.75
2006 2687 2.147150 GAGAGTTGGTGCTCTTGGAAC 58.853 52.381 0.00 0.00 45.03 3.62
2024 2705 1.070786 CAGTAACGGGGCTGTGTGT 59.929 57.895 0.00 0.00 0.00 3.72
2026 2707 2.281208 TAACGGGGCTGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
2078 2761 5.757988 TCCTTCTTCTTCTACCTCTAGTCC 58.242 45.833 0.00 0.00 0.00 3.85
2084 2767 5.362105 TCTTCTACCTCTAGTCCTGAGTC 57.638 47.826 0.00 0.00 0.00 3.36
2097 2780 3.197766 GTCCTGAGTCAGAGAGAGAGAGA 59.802 52.174 22.09 3.87 32.44 3.10
2099 2782 3.452264 CCTGAGTCAGAGAGAGAGAGAGA 59.548 52.174 22.09 0.00 32.44 3.10
2100 2783 4.442612 CCTGAGTCAGAGAGAGAGAGAGAG 60.443 54.167 22.09 0.00 32.44 3.20
2101 2784 3.118629 TGAGTCAGAGAGAGAGAGAGAGC 60.119 52.174 0.00 0.00 0.00 4.09
2102 2785 2.159043 AGTCAGAGAGAGAGAGAGAGCG 60.159 54.545 0.00 0.00 0.00 5.03
2103 2786 2.107366 TCAGAGAGAGAGAGAGAGCGA 58.893 52.381 0.00 0.00 0.00 4.93
2104 2787 2.159099 TCAGAGAGAGAGAGAGAGCGAC 60.159 54.545 0.00 0.00 0.00 5.19
2106 2789 2.236146 AGAGAGAGAGAGAGAGCGACAA 59.764 50.000 0.00 0.00 0.00 3.18
2107 2790 2.351726 GAGAGAGAGAGAGAGCGACAAC 59.648 54.545 0.00 0.00 0.00 3.32
2108 2791 2.080693 GAGAGAGAGAGAGCGACAACA 58.919 52.381 0.00 0.00 0.00 3.33
2109 2792 2.486203 GAGAGAGAGAGAGCGACAACAA 59.514 50.000 0.00 0.00 0.00 2.83
2110 2793 3.088532 AGAGAGAGAGAGCGACAACAAT 58.911 45.455 0.00 0.00 0.00 2.71
2111 2794 4.265893 AGAGAGAGAGAGCGACAACAATA 58.734 43.478 0.00 0.00 0.00 1.90
2112 2795 4.095782 AGAGAGAGAGAGCGACAACAATAC 59.904 45.833 0.00 0.00 0.00 1.89
2113 2796 3.102276 GAGAGAGAGCGACAACAATACG 58.898 50.000 0.00 0.00 0.00 3.06
2117 2800 2.276430 GCGACAACAATACGCGGC 60.276 61.111 12.47 0.00 42.65 6.53
2118 2801 2.398036 CGACAACAATACGCGGCC 59.602 61.111 12.47 0.00 0.00 6.13
2119 2802 2.789249 GACAACAATACGCGGCCC 59.211 61.111 12.47 0.00 0.00 5.80
2120 2803 2.748647 ACAACAATACGCGGCCCC 60.749 61.111 12.47 0.00 0.00 5.80
2121 2804 3.871574 CAACAATACGCGGCCCCG 61.872 66.667 12.47 8.60 43.09 5.73
2134 2817 4.790962 CCCCGCTGCTGTCATGCT 62.791 66.667 0.00 0.00 0.00 3.79
2135 2818 3.200593 CCCGCTGCTGTCATGCTC 61.201 66.667 0.00 0.00 0.00 4.26
2136 2819 3.200593 CCGCTGCTGTCATGCTCC 61.201 66.667 0.00 0.00 0.00 4.70
2137 2820 2.435410 CGCTGCTGTCATGCTCCA 60.435 61.111 0.00 0.00 0.00 3.86
2138 2821 2.747822 CGCTGCTGTCATGCTCCAC 61.748 63.158 0.00 0.00 0.00 4.02
2139 2822 2.404995 GCTGCTGTCATGCTCCACC 61.405 63.158 0.00 0.00 0.00 4.61
2140 2823 1.748122 CTGCTGTCATGCTCCACCC 60.748 63.158 0.00 0.00 0.00 4.61
2141 2824 2.352422 GCTGTCATGCTCCACCCA 59.648 61.111 0.00 0.00 0.00 4.51
2142 2825 2.042831 GCTGTCATGCTCCACCCAC 61.043 63.158 0.00 0.00 0.00 4.61
2143 2826 1.742880 CTGTCATGCTCCACCCACG 60.743 63.158 0.00 0.00 0.00 4.94
2144 2827 2.436646 GTCATGCTCCACCCACGG 60.437 66.667 0.00 0.00 0.00 4.94
2145 2828 4.408821 TCATGCTCCACCCACGGC 62.409 66.667 0.00 0.00 0.00 5.68
2146 2829 4.415150 CATGCTCCACCCACGGCT 62.415 66.667 0.00 0.00 0.00 5.52
2147 2830 3.650950 ATGCTCCACCCACGGCTT 61.651 61.111 0.00 0.00 0.00 4.35
2148 2831 3.925630 ATGCTCCACCCACGGCTTG 62.926 63.158 0.00 0.00 0.00 4.01
2149 2832 4.643387 GCTCCACCCACGGCTTGT 62.643 66.667 0.00 0.00 0.00 3.16
2150 2833 2.358737 CTCCACCCACGGCTTGTC 60.359 66.667 0.00 0.00 0.00 3.18
2151 2834 2.847234 TCCACCCACGGCTTGTCT 60.847 61.111 0.00 0.00 0.00 3.41
2152 2835 2.669569 CCACCCACGGCTTGTCTG 60.670 66.667 0.00 0.00 0.00 3.51
2153 2836 2.669569 CACCCACGGCTTGTCTGG 60.670 66.667 0.00 0.00 0.00 3.86
2154 2837 4.643387 ACCCACGGCTTGTCTGGC 62.643 66.667 0.00 0.00 0.00 4.85
2156 2839 4.335647 CCACGGCTTGTCTGGCCT 62.336 66.667 3.32 0.00 46.73 5.19
2157 2840 2.743928 CACGGCTTGTCTGGCCTC 60.744 66.667 3.32 0.00 46.73 4.70
2158 2841 4.021925 ACGGCTTGTCTGGCCTCC 62.022 66.667 3.32 0.00 46.73 4.30
2159 2842 3.710722 CGGCTTGTCTGGCCTCCT 61.711 66.667 3.32 0.00 46.73 3.69
2160 2843 2.359169 CGGCTTGTCTGGCCTCCTA 61.359 63.158 3.32 0.00 46.73 2.94
2161 2844 1.222113 GGCTTGTCTGGCCTCCTAC 59.778 63.158 3.32 0.00 45.57 3.18
2162 2845 1.153549 GCTTGTCTGGCCTCCTACG 60.154 63.158 3.32 0.00 0.00 3.51
2163 2846 1.153549 CTTGTCTGGCCTCCTACGC 60.154 63.158 3.32 0.00 0.00 4.42
2164 2847 2.890847 CTTGTCTGGCCTCCTACGCG 62.891 65.000 3.53 3.53 0.00 6.01
2165 2848 4.874977 GTCTGGCCTCCTACGCGC 62.875 72.222 5.73 0.00 0.00 6.86
2202 2885 4.070552 GCTGCTCGTTCGTCCCCT 62.071 66.667 0.00 0.00 0.00 4.79
2203 2886 2.182030 CTGCTCGTTCGTCCCCTC 59.818 66.667 0.00 0.00 0.00 4.30
2204 2887 3.685214 CTGCTCGTTCGTCCCCTCG 62.685 68.421 0.00 0.00 0.00 4.63
2205 2888 4.493747 GCTCGTTCGTCCCCTCGG 62.494 72.222 0.00 0.00 0.00 4.63
2206 2889 4.493747 CTCGTTCGTCCCCTCGGC 62.494 72.222 0.00 0.00 0.00 5.54
2235 2918 4.891727 CCGTCGCTGGCCGCTTAT 62.892 66.667 15.78 0.00 36.73 1.73
2236 2919 3.630148 CGTCGCTGGCCGCTTATG 61.630 66.667 15.78 7.13 36.73 1.90
2237 2920 3.941836 GTCGCTGGCCGCTTATGC 61.942 66.667 15.78 4.69 36.73 3.14
2244 2927 4.506255 GCCGCTTATGCCCCAGGT 62.506 66.667 0.00 0.00 35.36 4.00
2245 2928 2.203209 CCGCTTATGCCCCAGGTC 60.203 66.667 0.00 0.00 35.36 3.85
2246 2929 2.588877 CGCTTATGCCCCAGGTCG 60.589 66.667 0.00 0.00 35.36 4.79
2247 2930 2.902343 GCTTATGCCCCAGGTCGC 60.902 66.667 0.00 0.00 0.00 5.19
2248 2931 2.588877 CTTATGCCCCAGGTCGCG 60.589 66.667 0.00 0.00 0.00 5.87
2249 2932 4.169696 TTATGCCCCAGGTCGCGG 62.170 66.667 6.13 0.00 0.00 6.46
2286 2969 3.314331 CCCAGCCACAGTCCGACT 61.314 66.667 0.00 0.00 0.00 4.18
2294 2977 4.010575 CAGTCCGACTGGCTCTCT 57.989 61.111 19.29 0.00 42.35 3.10
2295 2978 1.510383 CAGTCCGACTGGCTCTCTG 59.490 63.158 19.29 0.00 42.35 3.35
2296 2979 1.075836 AGTCCGACTGGCTCTCTGT 59.924 57.895 0.00 0.00 34.14 3.41
2297 2980 1.214062 GTCCGACTGGCTCTCTGTG 59.786 63.158 0.00 0.00 34.14 3.66
2298 2981 1.979155 TCCGACTGGCTCTCTGTGG 60.979 63.158 0.00 0.00 34.14 4.17
2299 2982 2.125753 CGACTGGCTCTCTGTGGC 60.126 66.667 0.00 0.00 0.00 5.01
2304 2987 4.106925 GGCTCTCTGTGGCCTGGG 62.107 72.222 3.32 0.00 44.48 4.45
2305 2988 4.106925 GCTCTCTGTGGCCTGGGG 62.107 72.222 3.32 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.046507 GTGAGGAGCAGTGGCAGG 60.047 66.667 0.00 0.00 44.61 4.85
61 62 1.303091 GCTTATTCCAACACCGCGGT 61.303 55.000 28.70 28.70 0.00 5.68
63 64 1.302383 TGGCTTATTCCAACACCGCG 61.302 55.000 0.00 0.00 32.18 6.46
65 66 1.468520 CTGTGGCTTATTCCAACACCG 59.531 52.381 0.00 0.00 37.96 4.94
70 71 1.003118 AGACGCTGTGGCTTATTCCAA 59.997 47.619 0.00 0.00 37.96 3.53
71 72 0.613260 AGACGCTGTGGCTTATTCCA 59.387 50.000 0.00 0.00 36.09 3.53
75 76 0.391661 CACCAGACGCTGTGGCTTAT 60.392 55.000 0.00 0.00 38.83 1.73
76 77 1.005037 CACCAGACGCTGTGGCTTA 60.005 57.895 0.00 0.00 38.83 3.09
77 78 2.281070 CACCAGACGCTGTGGCTT 60.281 61.111 0.00 0.00 38.83 4.35
78 79 4.996434 GCACCAGACGCTGTGGCT 62.996 66.667 0.00 0.00 38.83 4.75
80 81 3.046087 CTGCACCAGACGCTGTGG 61.046 66.667 6.19 1.96 41.30 4.17
82 83 2.029666 GACTGCACCAGACGCTGT 59.970 61.111 0.00 0.00 43.24 4.40
84 85 4.363990 CCGACTGCACCAGACGCT 62.364 66.667 10.66 0.00 44.99 5.07
87 88 2.564553 CTAGCCCGACTGCACCAGAC 62.565 65.000 0.00 0.00 35.18 3.51
88 89 2.283604 TAGCCCGACTGCACCAGA 60.284 61.111 0.00 0.00 35.18 3.86
89 90 2.185350 CTAGCCCGACTGCACCAG 59.815 66.667 0.00 0.00 37.52 4.00
90 91 2.603473 ACTAGCCCGACTGCACCA 60.603 61.111 0.00 0.00 0.00 4.17
93 94 3.449227 CCGACTAGCCCGACTGCA 61.449 66.667 6.69 0.00 0.00 4.41
95 96 4.208686 GCCCGACTAGCCCGACTG 62.209 72.222 6.69 0.00 0.00 3.51
141 142 4.320456 AGCCTGACCGCACCAGTG 62.320 66.667 0.00 0.00 0.00 3.66
143 144 3.320879 ATGAGCCTGACCGCACCAG 62.321 63.158 0.00 0.00 0.00 4.00
144 145 3.315142 GATGAGCCTGACCGCACCA 62.315 63.158 0.00 0.00 0.00 4.17
153 154 3.190849 CGTGCACCGATGAGCCTG 61.191 66.667 12.15 0.00 39.56 4.85
179 180 4.552365 ATACGCCATGCTGCCGCT 62.552 61.111 0.70 0.00 36.97 5.52
180 181 4.318021 CATACGCCATGCTGCCGC 62.318 66.667 0.00 0.00 0.00 6.53
183 184 1.063006 CACACATACGCCATGCTGC 59.937 57.895 0.00 0.00 38.29 5.25
184 185 0.097499 CACACACATACGCCATGCTG 59.903 55.000 0.00 0.00 38.29 4.41
185 186 1.647545 GCACACACATACGCCATGCT 61.648 55.000 0.00 0.00 38.29 3.79
187 188 0.734309 ATGCACACACATACGCCATG 59.266 50.000 0.00 0.00 40.78 3.66
188 189 0.734309 CATGCACACACATACGCCAT 59.266 50.000 0.00 0.00 0.00 4.40
189 190 1.304509 CCATGCACACACATACGCCA 61.305 55.000 0.00 0.00 0.00 5.69
191 192 1.305219 ACCCATGCACACACATACGC 61.305 55.000 0.00 0.00 0.00 4.42
192 193 0.447406 CACCCATGCACACACATACG 59.553 55.000 0.00 0.00 0.00 3.06
193 194 0.810648 CCACCCATGCACACACATAC 59.189 55.000 0.00 0.00 0.00 2.39
194 195 0.403655 ACCACCCATGCACACACATA 59.596 50.000 0.00 0.00 0.00 2.29
195 196 1.153524 ACCACCCATGCACACACAT 59.846 52.632 0.00 0.00 0.00 3.21
196 197 1.827354 CACCACCCATGCACACACA 60.827 57.895 0.00 0.00 0.00 3.72
197 198 1.827789 ACACCACCCATGCACACAC 60.828 57.895 0.00 0.00 0.00 3.82
198 199 1.827354 CACACCACCCATGCACACA 60.827 57.895 0.00 0.00 0.00 3.72
201 202 2.563798 CCACACACCACCCATGCAC 61.564 63.158 0.00 0.00 0.00 4.57
202 203 2.203466 CCACACACCACCCATGCA 60.203 61.111 0.00 0.00 0.00 3.96
204 205 2.990967 GGCCACACACCACCCATG 60.991 66.667 0.00 0.00 0.00 3.66
221 222 1.269166 GCACCTACGAATCTGACGTG 58.731 55.000 0.00 0.00 43.73 4.49
222 223 0.179171 CGCACCTACGAATCTGACGT 60.179 55.000 0.00 0.00 45.75 4.34
223 224 0.179171 ACGCACCTACGAATCTGACG 60.179 55.000 0.00 0.00 36.70 4.35
224 225 1.135489 TCACGCACCTACGAATCTGAC 60.135 52.381 0.00 0.00 36.70 3.51
225 226 1.132453 CTCACGCACCTACGAATCTGA 59.868 52.381 0.00 0.00 36.70 3.27
226 227 1.135373 ACTCACGCACCTACGAATCTG 60.135 52.381 0.00 0.00 36.70 2.90
229 230 0.172803 GGACTCACGCACCTACGAAT 59.827 55.000 0.00 0.00 36.70 3.34
231 232 2.683859 CGGACTCACGCACCTACGA 61.684 63.158 0.00 0.00 36.70 3.43
232 233 2.202440 CGGACTCACGCACCTACG 60.202 66.667 0.00 0.00 39.50 3.51
233 234 1.443872 CACGGACTCACGCACCTAC 60.444 63.158 0.00 0.00 37.37 3.18
237 238 2.279252 ACACACGGACTCACGCAC 60.279 61.111 0.00 0.00 37.37 5.34
239 240 2.279252 ACACACACGGACTCACGC 60.279 61.111 0.00 0.00 37.37 5.34
240 241 2.585869 GCACACACACGGACTCACG 61.586 63.158 0.00 0.00 40.31 4.35
241 242 2.585869 CGCACACACACGGACTCAC 61.586 63.158 0.00 0.00 0.00 3.51
324 374 3.491766 TCTGATCCTAACAACCTCCCT 57.508 47.619 0.00 0.00 0.00 4.20
356 406 3.919386 CACGACGCGCACACAACA 61.919 61.111 5.73 0.00 0.00 3.33
437 506 4.141914 GGCTTTGTAGTCCTACAGCTACAT 60.142 45.833 14.55 0.00 45.57 2.29
438 507 3.194968 GGCTTTGTAGTCCTACAGCTACA 59.805 47.826 14.55 0.00 45.57 2.74
492 567 4.558898 CGTTACTGTTCCAAGAGCACTACT 60.559 45.833 0.00 0.00 0.00 2.57
493 568 3.673809 CGTTACTGTTCCAAGAGCACTAC 59.326 47.826 0.00 0.00 0.00 2.73
495 572 2.548067 CCGTTACTGTTCCAAGAGCACT 60.548 50.000 0.00 0.00 0.00 4.40
561 658 5.489637 ACTCAGGACTAGAGGTAGAAGAAGA 59.510 44.000 0.00 0.00 37.43 2.87
601 722 5.536161 AGCTCTGAATACCAAATGTTGTTGT 59.464 36.000 0.00 0.00 0.00 3.32
693 817 2.734673 GAGCGACGGAAGCTGCAAG 61.735 63.158 1.02 0.00 46.13 4.01
706 830 1.284297 TAGTTCGTCGTCGTGAGCGA 61.284 55.000 1.33 0.00 45.79 4.93
711 835 1.056464 CGGTGTAGTTCGTCGTCGTG 61.056 60.000 1.33 0.00 38.33 4.35
833 957 2.361610 CCAGCATCACCACCCACC 60.362 66.667 0.00 0.00 0.00 4.61
839 963 3.490031 AACACGCCCAGCATCACCA 62.490 57.895 0.00 0.00 0.00 4.17
1032 1342 4.115199 ATGCCGCTGACCTTCCCC 62.115 66.667 0.00 0.00 0.00 4.81
1104 1414 2.307363 CACGGTGTCGAGCAACTTT 58.693 52.632 0.00 0.00 40.11 2.66
1129 1439 2.510691 CACCGCGGCGTAAAGGAT 60.511 61.111 28.58 0.00 0.00 3.24
1130 1440 4.745751 CCACCGCGGCGTAAAGGA 62.746 66.667 28.58 0.00 0.00 3.36
1264 1598 0.952280 GTCATCATCAGCTGCCCATG 59.048 55.000 9.47 8.24 0.00 3.66
1499 1838 1.678123 CCTAGAGGAGTCCGTTGTCGA 60.678 57.143 2.76 0.00 36.90 4.20
1504 1843 1.753463 CGGCCTAGAGGAGTCCGTT 60.753 63.158 2.76 0.00 34.84 4.44
1544 1889 2.173669 CCAGACGCCGTGGCTTATG 61.174 63.158 9.55 7.17 39.32 1.90
1691 2211 2.990967 GGCCACACACCACCCATG 60.991 66.667 0.00 0.00 0.00 3.66
1840 2455 1.006086 CACAACGCGCTTGATCCATA 58.994 50.000 22.26 0.00 33.59 2.74
1958 2638 0.108520 AAATACATGGTCGCGTCCGT 60.109 50.000 17.40 14.57 35.54 4.69
2006 2687 1.070786 ACACACAGCCCCGTTACTG 59.929 57.895 0.00 0.00 39.86 2.74
2024 2705 1.476845 TAGAGTTTCACCCGGCTGCA 61.477 55.000 0.50 0.00 0.00 4.41
2026 2707 0.608640 ACTAGAGTTTCACCCGGCTG 59.391 55.000 0.00 0.00 0.00 4.85
2078 2761 4.691175 CTCTCTCTCTCTCTCTGACTCAG 58.309 52.174 0.00 0.00 0.00 3.35
2084 2767 2.205074 GTCGCTCTCTCTCTCTCTCTG 58.795 57.143 0.00 0.00 0.00 3.35
2097 2780 1.076533 CCGCGTATTGTTGTCGCTCT 61.077 55.000 4.92 0.00 46.31 4.09
2099 2782 2.736682 GCCGCGTATTGTTGTCGCT 61.737 57.895 4.92 0.00 46.31 4.93
2100 2783 2.276430 GCCGCGTATTGTTGTCGC 60.276 61.111 4.92 0.00 45.28 5.19
2101 2784 2.398036 GGCCGCGTATTGTTGTCG 59.602 61.111 4.92 0.00 0.00 4.35
2102 2785 2.757056 GGGGCCGCGTATTGTTGTC 61.757 63.158 3.09 0.00 0.00 3.18
2103 2786 2.748647 GGGGCCGCGTATTGTTGT 60.749 61.111 3.09 0.00 0.00 3.32
2104 2787 3.871574 CGGGGCCGCGTATTGTTG 61.872 66.667 32.15 3.21 0.00 3.33
2117 2800 4.790962 AGCATGACAGCAGCGGGG 62.791 66.667 0.00 0.00 36.85 5.73
2118 2801 3.200593 GAGCATGACAGCAGCGGG 61.201 66.667 0.00 0.00 36.85 6.13
2119 2802 3.200593 GGAGCATGACAGCAGCGG 61.201 66.667 0.00 0.00 36.85 5.52
2120 2803 2.435410 TGGAGCATGACAGCAGCG 60.435 61.111 0.00 0.00 36.85 5.18
2121 2804 2.404995 GGTGGAGCATGACAGCAGC 61.405 63.158 0.00 0.00 36.85 5.25
2122 2805 1.748122 GGGTGGAGCATGACAGCAG 60.748 63.158 13.90 0.00 36.86 4.24
2123 2806 2.352422 GGGTGGAGCATGACAGCA 59.648 61.111 13.90 0.00 36.86 4.41
2124 2807 2.042831 GTGGGTGGAGCATGACAGC 61.043 63.158 0.00 1.25 0.00 4.40
2125 2808 1.742880 CGTGGGTGGAGCATGACAG 60.743 63.158 0.00 0.00 0.00 3.51
2126 2809 2.347114 CGTGGGTGGAGCATGACA 59.653 61.111 0.00 0.00 0.00 3.58
2127 2810 2.436646 CCGTGGGTGGAGCATGAC 60.437 66.667 0.00 0.00 0.00 3.06
2128 2811 4.408821 GCCGTGGGTGGAGCATGA 62.409 66.667 0.00 0.00 0.00 3.07
2129 2812 3.925630 AAGCCGTGGGTGGAGCATG 62.926 63.158 0.00 0.00 0.00 4.06
2130 2813 3.650950 AAGCCGTGGGTGGAGCAT 61.651 61.111 0.00 0.00 0.00 3.79
2131 2814 4.641645 CAAGCCGTGGGTGGAGCA 62.642 66.667 0.00 0.00 0.00 4.26
2132 2815 4.643387 ACAAGCCGTGGGTGGAGC 62.643 66.667 0.00 0.00 0.00 4.70
2133 2816 2.358737 GACAAGCCGTGGGTGGAG 60.359 66.667 0.00 0.00 0.00 3.86
2134 2817 2.847234 AGACAAGCCGTGGGTGGA 60.847 61.111 0.00 0.00 0.00 4.02
2135 2818 2.669569 CAGACAAGCCGTGGGTGG 60.670 66.667 0.00 0.00 0.00 4.61
2136 2819 2.669569 CCAGACAAGCCGTGGGTG 60.670 66.667 0.00 0.00 0.00 4.61
2137 2820 4.643387 GCCAGACAAGCCGTGGGT 62.643 66.667 0.00 0.00 0.00 4.51
2144 2827 1.153549 CGTAGGAGGCCAGACAAGC 60.154 63.158 5.01 0.00 0.00 4.01
2145 2828 1.153549 GCGTAGGAGGCCAGACAAG 60.154 63.158 5.01 0.00 0.00 3.16
2146 2829 2.978824 GCGTAGGAGGCCAGACAA 59.021 61.111 5.01 0.00 0.00 3.18
2147 2830 3.449227 CGCGTAGGAGGCCAGACA 61.449 66.667 5.01 0.00 0.00 3.41
2148 2831 4.874977 GCGCGTAGGAGGCCAGAC 62.875 72.222 8.43 0.00 0.00 3.51
2185 2868 3.991536 GAGGGGACGAACGAGCAGC 62.992 68.421 0.14 0.00 0.00 5.25
2186 2869 2.182030 GAGGGGACGAACGAGCAG 59.818 66.667 0.14 0.00 0.00 4.24
2187 2870 3.744719 CGAGGGGACGAACGAGCA 61.745 66.667 0.14 0.00 35.09 4.26
2188 2871 4.493747 CCGAGGGGACGAACGAGC 62.494 72.222 0.14 0.00 34.06 5.03
2189 2872 4.493747 GCCGAGGGGACGAACGAG 62.494 72.222 0.14 0.00 34.06 4.18
2227 2910 4.506255 ACCTGGGGCATAAGCGGC 62.506 66.667 0.00 0.00 43.41 6.53
2228 2911 2.203209 GACCTGGGGCATAAGCGG 60.203 66.667 0.00 0.00 43.41 5.52
2229 2912 2.588877 CGACCTGGGGCATAAGCG 60.589 66.667 0.00 0.00 43.41 4.68
2230 2913 2.902343 GCGACCTGGGGCATAAGC 60.902 66.667 7.07 0.00 41.10 3.09
2231 2914 2.588877 CGCGACCTGGGGCATAAG 60.589 66.667 0.00 0.00 0.00 1.73
2232 2915 4.169696 CCGCGACCTGGGGCATAA 62.170 66.667 8.23 0.00 44.59 1.90
2269 2952 3.314331 AGTCGGACTGTGGCTGGG 61.314 66.667 10.41 0.00 0.00 4.45
2270 2953 2.047844 CAGTCGGACTGTGGCTGG 60.048 66.667 26.22 2.73 41.19 4.85
2271 2954 2.047844 CCAGTCGGACTGTGGCTG 60.048 66.667 30.32 15.15 44.50 4.85
2274 2957 2.219325 GAGAGCCAGTCGGACTGTGG 62.219 65.000 30.32 21.02 44.50 4.17
2275 2958 1.214062 GAGAGCCAGTCGGACTGTG 59.786 63.158 30.32 23.31 44.50 3.66
2276 2959 1.075836 AGAGAGCCAGTCGGACTGT 59.924 57.895 30.32 17.26 44.50 3.55
2277 2960 1.247419 ACAGAGAGCCAGTCGGACTG 61.247 60.000 27.29 27.29 45.53 3.51
2278 2961 1.075836 ACAGAGAGCCAGTCGGACT 59.924 57.895 4.45 4.45 0.00 3.85
2279 2962 1.214062 CACAGAGAGCCAGTCGGAC 59.786 63.158 0.00 0.00 0.00 4.79
2280 2963 1.979155 CCACAGAGAGCCAGTCGGA 60.979 63.158 0.00 0.00 0.00 4.55
2281 2964 2.575993 CCACAGAGAGCCAGTCGG 59.424 66.667 0.00 0.00 0.00 4.79
2282 2965 2.125753 GCCACAGAGAGCCAGTCG 60.126 66.667 0.00 0.00 0.00 4.18
2288 2971 4.106925 CCCCAGGCCACAGAGAGC 62.107 72.222 5.01 0.00 0.00 4.09
2289 2972 4.106925 GCCCCAGGCCACAGAGAG 62.107 72.222 5.01 0.00 44.06 3.20


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

AutoCloner maintained by Alex Coulton.