Multiple sequence alignment - TraesCS2A01G280300

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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 TraesCS2A01G280300 chr2A 100.000 3326 0 0 1 3326 468332749 468329424 0.000000e+00 6143.0
1 TraesCS2A01G280300 chr2A 89.815 108 8 2 2954 3059 777958553 777958659 5.790000e-28 135.0
2 TraesCS2A01G280300 chr2A 94.595 37 1 1 179 214 568995239 568995203 4.640000e-04 56.5
3 TraesCS2A01G280300 chr4B 93.973 1261 59 7 357 1603 624152671 624151414 0.000000e+00 1892.0
4 TraesCS2A01G280300 chr4B 77.970 463 63 18 1618 2049 95086405 95086859 1.530000e-63 254.0
5 TraesCS2A01G280300 chr4B 83.770 191 26 4 1617 1804 123920422 123920234 3.410000e-40 176.0
6 TraesCS2A01G280300 chr4B 89.524 105 10 1 2954 3057 461741049 461741153 7.490000e-27 132.0
7 TraesCS2A01G280300 chr4B 91.667 96 7 1 2955 3049 660478276 660478181 7.490000e-27 132.0
8 TraesCS2A01G280300 chr2B 92.999 1257 73 5 357 1600 584727569 584726315 0.000000e+00 1820.0
9 TraesCS2A01G280300 chr2B 89.326 356 35 3 1 356 416846497 416846145 8.470000e-121 444.0
10 TraesCS2A01G280300 chr2B 95.050 202 9 1 3126 3326 416845739 416845538 1.930000e-82 316.0
11 TraesCS2A01G280300 chr2B 98.485 66 1 0 3059 3124 416845969 416845904 2.100000e-22 117.0
12 TraesCS2A01G280300 chr2B 92.857 56 3 1 3003 3057 707260664 707260609 2.750000e-11 80.5
13 TraesCS2A01G280300 chr3B 91.017 1258 94 7 353 1597 684500653 684501904 0.000000e+00 1679.0
14 TraesCS2A01G280300 chr3B 82.883 666 75 19 1618 2250 785507287 785506628 2.240000e-156 562.0
15 TraesCS2A01G280300 chr3B 80.162 247 35 12 2269 2506 785503647 785503406 4.410000e-39 172.0
16 TraesCS2A01G280300 chr7A 90.215 1257 106 8 357 1599 733209497 733208244 0.000000e+00 1624.0
17 TraesCS2A01G280300 chr7A 90.441 952 76 10 663 1600 456184093 456183143 0.000000e+00 1240.0
18 TraesCS2A01G280300 chr1D 89.107 1276 88 19 357 1600 465548806 465550062 0.000000e+00 1539.0
19 TraesCS2A01G280300 chr1D 87.719 399 42 3 2035 2427 203592751 203593148 3.020000e-125 459.0
20 TraesCS2A01G280300 chr1D 80.726 441 57 19 1618 2036 487049193 487049627 5.350000e-83 318.0
21 TraesCS2A01G280300 chr1D 88.835 206 23 0 1617 1822 203593544 203593339 1.530000e-63 254.0
22 TraesCS2A01G280300 chr1D 90.588 85 8 0 1852 1936 203592598 203592682 2.710000e-21 113.0
23 TraesCS2A01G280300 chr3A 91.043 949 72 9 663 1600 26417940 26418886 0.000000e+00 1269.0
24 TraesCS2A01G280300 chr3A 84.492 187 24 4 1618 1801 19965074 19965258 2.640000e-41 180.0
25 TraesCS2A01G280300 chr3A 85.185 81 9 3 171 251 146193015 146192938 2.750000e-11 80.5
26 TraesCS2A01G280300 chr7D 90.501 958 75 10 658 1600 509578770 509577814 0.000000e+00 1251.0
27 TraesCS2A01G280300 chr7D 90.566 106 7 2 2954 3057 21085154 21085050 1.610000e-28 137.0
28 TraesCS2A01G280300 chr7D 85.714 70 7 2 185 252 412655748 412655816 1.660000e-08 71.3
29 TraesCS2A01G280300 chr7B 91.116 923 73 8 686 1600 615763938 615763017 0.000000e+00 1242.0
30 TraesCS2A01G280300 chr1A 88.901 892 70 8 1890 2777 559779773 559780639 0.000000e+00 1072.0
31 TraesCS2A01G280300 chr1A 89.046 283 22 5 1621 1902 559725789 559726063 3.180000e-90 342.0
32 TraesCS2A01G280300 chr2D 93.175 337 22 1 357 692 15366262 15366598 8.290000e-136 494.0
33 TraesCS2A01G280300 chr2D 96.269 268 10 0 3059 3326 350766016 350765749 1.100000e-119 440.0
34 TraesCS2A01G280300 chr2D 92.115 279 20 2 78 356 350766475 350766199 3.110000e-105 392.0
35 TraesCS2A01G280300 chr2D 77.974 622 79 33 2196 2778 26512081 26512683 1.480000e-88 337.0
36 TraesCS2A01G280300 chr2D 93.258 178 9 3 2778 2953 350766185 350766009 3.290000e-65 259.0
37 TraesCS2A01G280300 chr2D 96.842 95 3 0 1 95 350766581 350766487 3.430000e-35 159.0
38 TraesCS2A01G280300 chr5B 83.838 198 27 4 1610 1804 214107478 214107283 2.040000e-42 183.0
39 TraesCS2A01G280300 chr5B 83.957 187 25 4 1618 1801 366004163 366004347 1.230000e-39 174.0
40 TraesCS2A01G280300 chr4A 84.043 188 25 4 1617 1801 729826230 729826415 3.410000e-40 176.0
41 TraesCS2A01G280300 chr4A 85.455 110 14 2 2949 3057 455928490 455928382 2.710000e-21 113.0
42 TraesCS2A01G280300 chr4A 89.286 56 6 0 288 343 600303368 600303423 1.660000e-08 71.3
43 TraesCS2A01G280300 chr5D 91.429 105 8 1 2954 3057 483632790 483632686 3.460000e-30 143.0
44 TraesCS2A01G280300 chr4D 89.333 75 6 2 261 333 230490073 230490147 3.530000e-15 93.5
45 TraesCS2A01G280300 chr6A 84.270 89 10 2 171 256 115273346 115273259 2.130000e-12 84.2
46 TraesCS2A01G280300 chr3D 86.441 59 5 3 2839 2894 267284218 267284160 9.960000e-06 62.1


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 TraesCS2A01G280300 chr2A 468329424 468332749 3325 True 6143.000000 6143 100.0000 1 3326 1 chr2A.!!$R1 3325
1 TraesCS2A01G280300 chr4B 624151414 624152671 1257 True 1892.000000 1892 93.9730 357 1603 1 chr4B.!!$R2 1246
2 TraesCS2A01G280300 chr2B 584726315 584727569 1254 True 1820.000000 1820 92.9990 357 1600 1 chr2B.!!$R1 1243
3 TraesCS2A01G280300 chr2B 416845538 416846497 959 True 292.333333 444 94.2870 1 3326 3 chr2B.!!$R3 3325
4 TraesCS2A01G280300 chr3B 684500653 684501904 1251 False 1679.000000 1679 91.0170 353 1597 1 chr3B.!!$F1 1244
5 TraesCS2A01G280300 chr3B 785503406 785507287 3881 True 367.000000 562 81.5225 1618 2506 2 chr3B.!!$R1 888
6 TraesCS2A01G280300 chr7A 733208244 733209497 1253 True 1624.000000 1624 90.2150 357 1599 1 chr7A.!!$R2 1242
7 TraesCS2A01G280300 chr7A 456183143 456184093 950 True 1240.000000 1240 90.4410 663 1600 1 chr7A.!!$R1 937
8 TraesCS2A01G280300 chr1D 465548806 465550062 1256 False 1539.000000 1539 89.1070 357 1600 1 chr1D.!!$F1 1243
9 TraesCS2A01G280300 chr1D 203592598 203593148 550 False 286.000000 459 89.1535 1852 2427 2 chr1D.!!$F3 575
10 TraesCS2A01G280300 chr3A 26417940 26418886 946 False 1269.000000 1269 91.0430 663 1600 1 chr3A.!!$F2 937
11 TraesCS2A01G280300 chr7D 509577814 509578770 956 True 1251.000000 1251 90.5010 658 1600 1 chr7D.!!$R2 942
12 TraesCS2A01G280300 chr7B 615763017 615763938 921 True 1242.000000 1242 91.1160 686 1600 1 chr7B.!!$R1 914
13 TraesCS2A01G280300 chr1A 559779773 559780639 866 False 1072.000000 1072 88.9010 1890 2777 1 chr1A.!!$F2 887
14 TraesCS2A01G280300 chr2D 26512081 26512683 602 False 337.000000 337 77.9740 2196 2778 1 chr2D.!!$F2 582
15 TraesCS2A01G280300 chr2D 350765749 350766581 832 True 312.500000 440 94.6210 1 3326 4 chr2D.!!$R1 3325

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
864 918 0.804989 CCTTCTTGTTGGCATCGTCC 59.195 55.0 0.0 0.0 0.0 4.79 F
1062 1116 0.250684 TGATGGGCGTGTGTGATGTT 60.251 50.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1936 0.175989 CCTAGCTCCGTCTGGTTTCC 59.824 60.0 0.00 0.0 36.3 3.13 R
3041 6189 0.036010 AAATGGACACGGCTCCTCTG 60.036 55.0 2.64 0.0 0.0 3.35 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
84 85 1.397390 GGAGGGCCGGTCGAATAGAA 61.397 60.000 1.90 0.00 0.00 2.10
123 153 0.896923 TAGTGGCGTCCGGTAACATT 59.103 50.000 0.00 0.00 0.00 2.71
137 167 5.220970 CCGGTAACATTTTGGGATCACATAC 60.221 44.000 0.00 0.00 0.00 2.39
154 184 7.258022 TCACATACAATCAATAAATGGACCG 57.742 36.000 0.00 0.00 0.00 4.79
474 508 1.992834 TGGATGCGCAAGGGACCTA 60.993 57.895 17.11 2.17 38.28 3.08
710 764 1.630878 GGGTGAAGGTGGTCAGATTCT 59.369 52.381 0.00 0.00 0.00 2.40
769 823 3.142838 GCATGATGTGCGGGGCTT 61.143 61.111 0.00 0.00 45.23 4.35
864 918 0.804989 CCTTCTTGTTGGCATCGTCC 59.195 55.000 0.00 0.00 0.00 4.79
905 959 1.903404 CGCAGCTTTGGGGGAAACT 60.903 57.895 0.00 0.00 0.00 2.66
955 1009 3.669251 GCTCTAGCATCGTATTCCCTT 57.331 47.619 0.00 0.00 41.59 3.95
970 1024 1.977009 CCTTTTGGGGGCTTCGTCC 60.977 63.158 0.00 0.00 35.46 4.79
990 1044 2.550423 CCTTGGAGCTAGGCATCATCAG 60.550 54.545 0.00 0.00 0.00 2.90
1024 1078 2.115911 GTTGGTGGTGTTGGCGTCA 61.116 57.895 0.00 0.00 0.00 4.35
1062 1116 0.250684 TGATGGGCGTGTGTGATGTT 60.251 50.000 0.00 0.00 0.00 2.71
1082 1136 2.281484 AGACGCGGCAATGGTTGT 60.281 55.556 17.71 0.00 0.00 3.32
1189 1247 2.125912 GCGACGATGACAGGCAGT 60.126 61.111 0.00 0.00 0.00 4.40
1345 1406 1.354368 CTCTATGGTGTGGGTTGGGTT 59.646 52.381 0.00 0.00 0.00 4.11
1402 1463 0.610687 GAGATTAGGGAGGGCGATGG 59.389 60.000 0.00 0.00 0.00 3.51
1455 1516 1.148310 GGTGTGTGATGTTGACGAGG 58.852 55.000 0.00 0.00 0.00 4.63
1493 1562 2.014128 GTGGTATTATGTGTGCCGCTT 58.986 47.619 0.00 0.00 0.00 4.68
1508 1577 2.524300 GCTTAGCGGTTTGTGACGA 58.476 52.632 0.00 0.00 0.00 4.20
1639 1714 6.406849 GGGGAGCAATTTGATAAAATAGCACA 60.407 38.462 0.00 0.00 0.00 4.57
1640 1715 7.212274 GGGAGCAATTTGATAAAATAGCACAT 58.788 34.615 0.00 0.00 0.00 3.21
1643 1718 9.910511 GAGCAATTTGATAAAATAGCACATTTG 57.089 29.630 0.00 0.00 0.00 2.32
1656 1731 2.415512 GCACATTTGTCCTCGTACCTTC 59.584 50.000 0.00 0.00 0.00 3.46
1668 1743 6.929606 GTCCTCGTACCTTCATAAAATAGCAT 59.070 38.462 0.00 0.00 0.00 3.79
1670 1745 8.086522 TCCTCGTACCTTCATAAAATAGCATAC 58.913 37.037 0.00 0.00 0.00 2.39
1690 1765 9.696917 AGCATACCTTTCTTTTTGTTTGATTAG 57.303 29.630 0.00 0.00 0.00 1.73
1697 1772 9.211485 CTTTCTTTTTGTTTGATTAGATGGCAT 57.789 29.630 0.00 0.00 0.00 4.40
1699 1774 9.638239 TTCTTTTTGTTTGATTAGATGGCATAC 57.362 29.630 0.00 0.00 0.00 2.39
1762 1837 4.623932 TTCTCAATTCTCCGATATGGGG 57.376 45.455 3.67 0.00 40.98 4.96
1771 1846 1.899814 TCCGATATGGGGCTACATGTC 59.100 52.381 0.00 8.56 38.76 3.06
1779 1854 7.600375 CGATATGGGGCTACATGTCATAATATC 59.400 40.741 0.00 8.49 38.45 1.63
1840 1936 3.679980 ACTGAACGATCGATCAAAACAGG 59.320 43.478 25.34 16.25 0.00 4.00
1842 1938 3.259064 GAACGATCGATCAAAACAGGGA 58.741 45.455 24.34 0.00 0.00 4.20
1843 1939 3.328382 ACGATCGATCAAAACAGGGAA 57.672 42.857 24.34 0.00 0.00 3.97
1845 1941 3.435671 ACGATCGATCAAAACAGGGAAAC 59.564 43.478 24.34 0.00 0.00 2.78
1865 1963 1.464734 CAGACGGAGCTAGGAAGACA 58.535 55.000 0.00 0.00 0.00 3.41
1869 1967 1.040339 CGGAGCTAGGAAGACAGGCT 61.040 60.000 0.00 0.00 35.86 4.58
1961 2074 1.043116 CGTACTGCCCTGATCTCCCA 61.043 60.000 0.00 0.00 0.00 4.37
2048 2171 1.341531 CGTGAGTCACAGGTTTCCTCT 59.658 52.381 22.66 0.00 33.40 3.69
2097 2221 0.108186 TCATCTGGCGTAACAGCAGG 60.108 55.000 0.00 0.00 38.36 4.85
2119 2243 4.399303 GGTAAAGCTAAGCCATCAACACAT 59.601 41.667 0.00 0.00 0.00 3.21
2122 2246 6.780457 AAAGCTAAGCCATCAACACATAAT 57.220 33.333 0.00 0.00 0.00 1.28
2124 2248 8.469309 AAAGCTAAGCCATCAACACATAATAT 57.531 30.769 0.00 0.00 0.00 1.28
2167 2291 2.536066 TCAAGCAGCACTACTTCCCTA 58.464 47.619 0.00 0.00 0.00 3.53
2193 2318 2.362397 AGCTAGCAACTATAGCAGCGAA 59.638 45.455 18.83 4.06 46.57 4.70
2247 2373 1.135257 CAGCTAACTACAGCAGCGAGT 60.135 52.381 0.00 0.00 44.35 4.18
2303 5395 2.201022 ACGGAGCGAACTGGACTGT 61.201 57.895 0.00 0.00 0.00 3.55
2352 5444 2.592308 GCCCTTCTTCTCCGGCAT 59.408 61.111 0.00 0.00 41.25 4.40
2369 5461 2.351244 ATGGCGAGGAAGCAGTCGA 61.351 57.895 0.00 0.00 38.50 4.20
2533 5675 5.710984 TCGTTCCTCTGTTTCTATGTTCTC 58.289 41.667 0.00 0.00 0.00 2.87
2536 5678 5.568685 TCCTCTGTTTCTATGTTCTCTCG 57.431 43.478 0.00 0.00 0.00 4.04
2539 5681 5.124776 CCTCTGTTTCTATGTTCTCTCGTCT 59.875 44.000 0.00 0.00 0.00 4.18
2584 5726 1.254026 TCGATCGAACCAGTTGACCT 58.746 50.000 16.99 0.00 0.00 3.85
2634 5776 6.334989 TGTCCAAAGTATTATGACGTGTAGG 58.665 40.000 0.00 0.00 0.00 3.18
2636 5778 4.510340 CCAAAGTATTATGACGTGTAGGCC 59.490 45.833 0.00 0.00 0.00 5.19
2642 5784 1.789523 ATGACGTGTAGGCCCATACT 58.210 50.000 0.00 0.00 0.00 2.12
2644 5786 2.737544 TGACGTGTAGGCCCATACTTA 58.262 47.619 0.00 0.00 0.00 2.24
2682 5824 9.758651 AAAAAGTCAGTTTGTACCATTTTATCC 57.241 29.630 0.00 0.00 0.00 2.59
2686 5832 6.751888 GTCAGTTTGTACCATTTTATCCATGC 59.248 38.462 0.00 0.00 0.00 4.06
2747 5893 9.640963 AGATATGCTATTTTATCAAGGTACGAC 57.359 33.333 0.00 0.00 0.00 4.34
2870 6018 0.544223 TTATATGCGGGTGTGGCACT 59.456 50.000 19.83 0.00 44.23 4.40
2895 6043 1.707427 AGCCACAAATCCTCTTCCAGT 59.293 47.619 0.00 0.00 0.00 4.00
2944 6092 5.048083 GGACAACTGGTTTCTTATTCATGCA 60.048 40.000 0.00 0.00 0.00 3.96
2945 6093 6.350445 GGACAACTGGTTTCTTATTCATGCAT 60.350 38.462 0.00 0.00 0.00 3.96
2946 6094 6.996509 ACAACTGGTTTCTTATTCATGCATT 58.003 32.000 0.00 0.00 0.00 3.56
2947 6095 7.444299 ACAACTGGTTTCTTATTCATGCATTT 58.556 30.769 0.00 0.00 0.00 2.32
2948 6096 7.933033 ACAACTGGTTTCTTATTCATGCATTTT 59.067 29.630 0.00 0.00 0.00 1.82
2949 6097 8.776470 CAACTGGTTTCTTATTCATGCATTTTT 58.224 29.630 0.00 0.00 0.00 1.94
2950 6098 8.538409 ACTGGTTTCTTATTCATGCATTTTTC 57.462 30.769 0.00 0.00 0.00 2.29
2951 6099 8.149647 ACTGGTTTCTTATTCATGCATTTTTCA 58.850 29.630 0.00 0.00 0.00 2.69
2952 6100 9.158233 CTGGTTTCTTATTCATGCATTTTTCAT 57.842 29.630 0.00 0.00 0.00 2.57
2953 6101 8.937884 TGGTTTCTTATTCATGCATTTTTCATG 58.062 29.630 0.00 0.00 41.87 3.07
2954 6102 8.392612 GGTTTCTTATTCATGCATTTTTCATGG 58.607 33.333 0.00 0.00 41.11 3.66
2955 6103 9.153721 GTTTCTTATTCATGCATTTTTCATGGA 57.846 29.630 0.00 0.00 41.11 3.41
2956 6104 8.936070 TTCTTATTCATGCATTTTTCATGGAG 57.064 30.769 0.00 0.00 41.11 3.86
2957 6105 6.982141 TCTTATTCATGCATTTTTCATGGAGC 59.018 34.615 0.00 0.00 41.11 4.70
2958 6106 3.530265 TCATGCATTTTTCATGGAGCC 57.470 42.857 0.00 0.00 41.11 4.70
2959 6107 2.159212 TCATGCATTTTTCATGGAGCCG 60.159 45.455 0.00 0.00 41.11 5.52
2960 6108 0.531657 TGCATTTTTCATGGAGCCGG 59.468 50.000 0.00 0.00 0.00 6.13
2961 6109 0.817013 GCATTTTTCATGGAGCCGGA 59.183 50.000 5.05 0.00 0.00 5.14
2962 6110 1.410153 GCATTTTTCATGGAGCCGGAT 59.590 47.619 5.05 0.00 0.00 4.18
2963 6111 2.544486 GCATTTTTCATGGAGCCGGATC 60.544 50.000 12.38 12.38 0.00 3.36
2964 6112 1.762708 TTTTTCATGGAGCCGGATCC 58.237 50.000 32.10 32.10 40.03 3.36
2965 6113 0.918983 TTTTCATGGAGCCGGATCCT 59.081 50.000 36.82 21.00 40.29 3.24
2966 6114 0.469917 TTTCATGGAGCCGGATCCTC 59.530 55.000 36.82 18.78 40.29 3.71
2967 6115 0.399091 TTCATGGAGCCGGATCCTCT 60.399 55.000 36.82 22.63 40.29 3.69
2968 6116 1.117749 TCATGGAGCCGGATCCTCTG 61.118 60.000 36.82 30.94 40.29 3.35
2969 6117 1.117749 CATGGAGCCGGATCCTCTGA 61.118 60.000 36.82 19.46 40.29 3.27
2970 6118 1.118356 ATGGAGCCGGATCCTCTGAC 61.118 60.000 36.82 12.29 40.29 3.51
2971 6119 2.725008 GAGCCGGATCCTCTGACG 59.275 66.667 9.02 0.00 0.00 4.35
2972 6120 2.043852 AGCCGGATCCTCTGACGT 60.044 61.111 5.05 0.00 0.00 4.34
2973 6121 0.818445 GAGCCGGATCCTCTGACGTA 60.818 60.000 9.02 0.00 0.00 3.57
2974 6122 1.102222 AGCCGGATCCTCTGACGTAC 61.102 60.000 5.05 0.00 0.00 3.67
2975 6123 1.647629 CCGGATCCTCTGACGTACG 59.352 63.158 15.01 15.01 0.00 3.67
2976 6124 1.647629 CGGATCCTCTGACGTACGG 59.352 63.158 21.06 1.50 0.00 4.02
2977 6125 1.359475 GGATCCTCTGACGTACGGC 59.641 63.158 21.06 18.72 0.00 5.68
2978 6126 1.359475 GATCCTCTGACGTACGGCC 59.641 63.158 20.48 10.81 0.00 6.13
2979 6127 2.073037 GATCCTCTGACGTACGGCCC 62.073 65.000 20.48 8.13 0.00 5.80
2980 6128 4.189188 CCTCTGACGTACGGCCCG 62.189 72.222 20.48 10.07 0.00 6.13
2981 6129 4.849329 CTCTGACGTACGGCCCGC 62.849 72.222 20.48 3.09 0.00 6.13
3024 6172 4.802051 CCCGGGGCCACATGTCAG 62.802 72.222 14.71 0.00 0.00 3.51
3025 6173 4.033776 CCGGGGCCACATGTCAGT 62.034 66.667 5.46 0.00 0.00 3.41
3026 6174 2.747460 CGGGGCCACATGTCAGTG 60.747 66.667 5.46 0.00 39.21 3.66
3032 6180 3.434319 CACATGTCAGTGGGCGGC 61.434 66.667 0.00 0.00 35.88 6.53
3033 6181 3.952508 ACATGTCAGTGGGCGGCA 61.953 61.111 12.47 0.00 0.00 5.69
3034 6182 3.434319 CATGTCAGTGGGCGGCAC 61.434 66.667 12.47 7.39 0.00 5.01
3049 6197 3.791539 CACGACATGCAGAGGAGC 58.208 61.111 0.00 0.00 0.00 4.70
3050 6198 1.812922 CACGACATGCAGAGGAGCC 60.813 63.158 0.00 0.00 0.00 4.70
3051 6199 2.584418 CGACATGCAGAGGAGCCG 60.584 66.667 0.00 0.00 0.00 5.52
3052 6200 2.581354 GACATGCAGAGGAGCCGT 59.419 61.111 0.00 0.00 0.00 5.68
3053 6201 1.812922 GACATGCAGAGGAGCCGTG 60.813 63.158 0.00 0.00 0.00 4.94
3054 6202 2.267006 CATGCAGAGGAGCCGTGT 59.733 61.111 0.00 0.00 0.00 4.49
3055 6203 1.812922 CATGCAGAGGAGCCGTGTC 60.813 63.158 0.00 0.00 0.00 3.67
3056 6204 3.023949 ATGCAGAGGAGCCGTGTCC 62.024 63.158 0.00 0.00 36.79 4.02
3057 6205 3.695606 GCAGAGGAGCCGTGTCCA 61.696 66.667 3.31 0.00 39.34 4.02
3106 6254 3.382865 TGCAGAGCAACCATGTTAAACAA 59.617 39.130 0.00 0.00 34.76 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 128 2.261671 CGGACGCCACTAGTTGCT 59.738 61.111 16.16 4.31 0.00 3.91
100 130 0.244450 TTACCGGACGCCACTAGTTG 59.756 55.000 9.46 0.00 0.00 3.16
137 167 8.340618 AGATATTCCGGTCCATTTATTGATTG 57.659 34.615 0.00 0.00 0.00 2.67
147 177 4.558095 CGTTCGTTAGATATTCCGGTCCAT 60.558 45.833 0.00 0.00 0.00 3.41
154 184 8.967552 ATAATCTGACGTTCGTTAGATATTCC 57.032 34.615 24.77 1.67 39.49 3.01
164 194 6.691818 GTCATGTCTAATAATCTGACGTTCGT 59.308 38.462 0.00 0.00 33.81 3.85
205 235 6.357579 TCCTTGACAAACATAAATTGCCAT 57.642 33.333 0.00 0.00 0.00 4.40
240 270 3.932545 TCAATTACCGTGCTTGCAAAT 57.067 38.095 0.00 0.00 0.00 2.32
285 315 7.429636 TTTGACCTTTTTACTGAGAATACCG 57.570 36.000 0.00 0.00 0.00 4.02
338 368 3.187227 CGCCCTTTCATTAAGATCCATCG 59.813 47.826 0.00 0.00 35.80 3.84
397 427 1.292223 GAAGCACCACCTCACGCTA 59.708 57.895 0.00 0.00 33.45 4.26
526 560 4.344865 GAAGCCCTTGTCCGCCCA 62.345 66.667 0.00 0.00 0.00 5.36
710 764 2.359354 CCGTGGTCAAATCCGGCA 60.359 61.111 0.00 0.00 33.20 5.69
769 823 2.973899 GCCCGAGTCAGCTTCTCA 59.026 61.111 13.79 0.00 32.79 3.27
781 835 1.374252 GAGACAAGCTTTCGCCCGA 60.374 57.895 0.00 0.00 36.60 5.14
864 918 0.252479 ATTGGAGCTGAGAGTGCCTG 59.748 55.000 0.00 0.00 0.00 4.85
955 1009 1.228429 CAAGGACGAAGCCCCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
970 1024 2.550423 CCTGATGATGCCTAGCTCCAAG 60.550 54.545 0.00 0.00 0.00 3.61
990 1044 3.325201 AACTTCCATCGGTCCCGCC 62.325 63.158 0.00 0.00 39.59 6.13
1024 1078 1.039856 ATCGTTGCCACAAAAGCCTT 58.960 45.000 0.00 0.00 0.00 4.35
1062 1116 3.545124 AACCATTGCCGCGTCTCCA 62.545 57.895 4.92 0.00 0.00 3.86
1082 1136 2.883572 GGAGAAGAGCCGACTACCA 58.116 57.895 0.00 0.00 0.00 3.25
1189 1247 1.822990 GACCATCGAACAGACCACCTA 59.177 52.381 0.00 0.00 0.00 3.08
1345 1406 5.043903 CGACTTCTCTGAAGACAAAAGTCA 58.956 41.667 13.42 0.00 36.25 3.41
1359 1420 1.200484 GAAAGCGACTCCGACTTCTCT 59.800 52.381 0.00 0.00 38.22 3.10
1402 1463 2.356667 CTTCTCCCCAACAGGCCC 59.643 66.667 0.00 0.00 0.00 5.80
1493 1562 2.156117 CGAAAATCGTCACAAACCGCTA 59.844 45.455 0.00 0.00 34.72 4.26
1508 1577 1.174078 ACGGAAAACCGGGCGAAAAT 61.174 50.000 6.32 0.00 37.53 1.82
1574 1647 3.878160 TTTTGAAACGGAGGCAAAAGT 57.122 38.095 0.00 0.00 36.80 2.66
1600 1675 2.108776 TGCTCCCCATTCTATTCCCATG 59.891 50.000 0.00 0.00 0.00 3.66
1603 1678 3.532641 ATTGCTCCCCATTCTATTCCC 57.467 47.619 0.00 0.00 0.00 3.97
1604 1679 4.895297 TCAAATTGCTCCCCATTCTATTCC 59.105 41.667 0.00 0.00 0.00 3.01
1605 1680 6.661304 ATCAAATTGCTCCCCATTCTATTC 57.339 37.500 0.00 0.00 0.00 1.75
1606 1681 8.551682 TTTATCAAATTGCTCCCCATTCTATT 57.448 30.769 0.00 0.00 0.00 1.73
1607 1682 8.551682 TTTTATCAAATTGCTCCCCATTCTAT 57.448 30.769 0.00 0.00 0.00 1.98
1608 1683 7.969690 TTTTATCAAATTGCTCCCCATTCTA 57.030 32.000 0.00 0.00 0.00 2.10
1609 1684 6.872585 TTTTATCAAATTGCTCCCCATTCT 57.127 33.333 0.00 0.00 0.00 2.40
1610 1685 7.386025 GCTATTTTATCAAATTGCTCCCCATTC 59.614 37.037 10.35 0.00 43.66 2.67
1611 1686 7.147514 TGCTATTTTATCAAATTGCTCCCCATT 60.148 33.333 16.18 0.00 45.80 3.16
1612 1687 6.327104 TGCTATTTTATCAAATTGCTCCCCAT 59.673 34.615 16.18 0.00 45.80 4.00
1613 1688 5.660417 TGCTATTTTATCAAATTGCTCCCCA 59.340 36.000 16.18 0.00 45.80 4.96
1614 1689 5.985530 GTGCTATTTTATCAAATTGCTCCCC 59.014 40.000 16.18 3.15 45.80 4.81
1615 1690 6.572519 TGTGCTATTTTATCAAATTGCTCCC 58.427 36.000 16.18 7.86 45.80 4.30
1616 1691 8.652810 AATGTGCTATTTTATCAAATTGCTCC 57.347 30.769 16.18 9.62 45.80 4.70
1639 1714 9.326413 CTATTTTATGAAGGTACGAGGACAAAT 57.674 33.333 0.00 0.00 0.00 2.32
1640 1715 7.279313 GCTATTTTATGAAGGTACGAGGACAAA 59.721 37.037 0.00 0.00 0.00 2.83
1643 1718 6.278363 TGCTATTTTATGAAGGTACGAGGAC 58.722 40.000 0.00 0.00 0.00 3.85
1670 1745 7.656948 TGCCATCTAATCAAACAAAAAGAAAGG 59.343 33.333 0.00 0.00 0.00 3.11
1690 1765 3.571401 CCATGGAGGAAAAGTATGCCATC 59.429 47.826 5.56 0.00 41.22 3.51
1697 1772 7.446106 TTTATCTAGCCATGGAGGAAAAGTA 57.554 36.000 18.40 0.00 41.22 2.24
1699 1774 7.255730 CCATTTTATCTAGCCATGGAGGAAAAG 60.256 40.741 18.40 2.56 41.22 2.27
1743 1818 2.304180 AGCCCCATATCGGAGAATTGAG 59.696 50.000 0.00 0.00 43.58 3.02
1750 1825 1.902508 ACATGTAGCCCCATATCGGAG 59.097 52.381 0.00 0.00 36.56 4.63
1753 1828 3.616956 ATGACATGTAGCCCCATATCG 57.383 47.619 0.00 0.00 0.00 2.92
1754 1829 8.654997 AGATATTATGACATGTAGCCCCATATC 58.345 37.037 0.00 6.28 0.00 1.63
1755 1830 8.572884 AGATATTATGACATGTAGCCCCATAT 57.427 34.615 0.00 0.00 0.00 1.78
1760 1835 6.595716 GTCCAAGATATTATGACATGTAGCCC 59.404 42.308 0.00 0.00 0.00 5.19
1762 1837 7.090808 TCGTCCAAGATATTATGACATGTAGC 58.909 38.462 0.00 0.00 0.00 3.58
1771 1846 6.207417 AGGGCAAAATCGTCCAAGATATTATG 59.793 38.462 0.00 0.00 30.91 1.90
1779 1854 2.610232 CCAAAGGGCAAAATCGTCCAAG 60.610 50.000 0.00 0.00 30.91 3.61
1812 1887 4.713824 TGATCGATCGTTCAGTTAACCT 57.286 40.909 21.77 0.00 34.33 3.50
1813 1888 5.773239 TTTGATCGATCGTTCAGTTAACC 57.227 39.130 23.64 0.67 34.33 2.85
1814 1889 6.586751 TGTTTTGATCGATCGTTCAGTTAAC 58.413 36.000 23.64 24.46 34.52 2.01
1815 1890 6.128661 CCTGTTTTGATCGATCGTTCAGTTAA 60.129 38.462 23.64 15.36 0.00 2.01
1816 1891 5.347635 CCTGTTTTGATCGATCGTTCAGTTA 59.652 40.000 23.64 10.92 0.00 2.24
1817 1892 4.152402 CCTGTTTTGATCGATCGTTCAGTT 59.848 41.667 23.64 1.93 0.00 3.16
1818 1893 3.679980 CCTGTTTTGATCGATCGTTCAGT 59.320 43.478 23.64 4.59 0.00 3.41
1819 1894 3.062639 CCCTGTTTTGATCGATCGTTCAG 59.937 47.826 23.64 20.99 0.00 3.02
1820 1895 3.000041 CCCTGTTTTGATCGATCGTTCA 59.000 45.455 21.77 21.77 0.00 3.18
1821 1896 3.259064 TCCCTGTTTTGATCGATCGTTC 58.741 45.455 20.03 16.74 0.00 3.95
1822 1897 3.328382 TCCCTGTTTTGATCGATCGTT 57.672 42.857 20.03 6.71 0.00 3.85
1823 1898 3.328382 TTCCCTGTTTTGATCGATCGT 57.672 42.857 20.03 2.13 0.00 3.73
1824 1899 3.181510 GGTTTCCCTGTTTTGATCGATCG 60.182 47.826 20.03 9.36 0.00 3.69
1825 1900 3.756434 TGGTTTCCCTGTTTTGATCGATC 59.244 43.478 18.72 18.72 0.00 3.69
1826 1901 3.758554 CTGGTTTCCCTGTTTTGATCGAT 59.241 43.478 0.00 0.00 0.00 3.59
1840 1936 0.175989 CCTAGCTCCGTCTGGTTTCC 59.824 60.000 0.00 0.00 36.30 3.13
1842 1938 1.550976 CTTCCTAGCTCCGTCTGGTTT 59.449 52.381 0.00 0.00 36.30 3.27
1843 1939 1.187087 CTTCCTAGCTCCGTCTGGTT 58.813 55.000 0.00 0.00 36.30 3.67
1845 1941 0.741915 GTCTTCCTAGCTCCGTCTGG 59.258 60.000 0.00 0.00 0.00 3.86
1846 1942 1.403679 CTGTCTTCCTAGCTCCGTCTG 59.596 57.143 0.00 0.00 0.00 3.51
1847 1943 1.683629 CCTGTCTTCCTAGCTCCGTCT 60.684 57.143 0.00 0.00 0.00 4.18
1856 1954 3.019003 GCGGCAGCCTGTCTTCCTA 62.019 63.158 10.54 0.00 37.42 2.94
1936 2041 1.664321 ATCAGGGCAGTACGTCGGTC 61.664 60.000 0.00 0.00 0.00 4.79
2097 2221 5.567138 ATGTGTTGATGGCTTAGCTTTAC 57.433 39.130 3.59 0.00 0.00 2.01
2119 2243 9.622004 GAAGATAGCGCACTAACAACTATATTA 57.378 33.333 11.47 0.00 28.01 0.98
2122 2246 7.273320 AGAAGATAGCGCACTAACAACTATA 57.727 36.000 11.47 0.00 30.45 1.31
2124 2248 5.578005 AGAAGATAGCGCACTAACAACTA 57.422 39.130 11.47 0.00 30.45 2.24
2167 2291 5.293560 GCTGCTATAGTTGCTAGCTTTAGT 58.706 41.667 17.23 6.93 41.73 2.24
2193 2318 1.004918 GTACTTGGTCGTGGCTGCT 60.005 57.895 0.00 0.00 0.00 4.24
2203 2328 2.557317 CTGGTCGTTGTTGTACTTGGT 58.443 47.619 0.00 0.00 0.00 3.67
2348 5440 3.207669 CTGCTTCCTCGCCATGCC 61.208 66.667 0.00 0.00 0.00 4.40
2352 5444 2.492449 CTTCGACTGCTTCCTCGCCA 62.492 60.000 0.00 0.00 0.00 5.69
2369 5461 4.430765 CCGCCGTACTCCGTGCTT 62.431 66.667 0.00 0.00 32.67 3.91
2431 5544 2.581409 ATCGCCCGTTTCTACGCG 60.581 61.111 3.53 3.53 46.27 6.01
2456 5569 2.187946 CCCGTGGCATCACCTCTC 59.812 66.667 0.00 0.00 40.65 3.20
2457 5570 2.815684 TACCCCGTGGCATCACCTCT 62.816 60.000 0.00 0.00 40.65 3.69
2533 5675 2.162608 ACGAGACAATCCAGAAGACGAG 59.837 50.000 0.00 0.00 0.00 4.18
2536 5678 3.428316 GGAGACGAGACAATCCAGAAGAC 60.428 52.174 0.00 0.00 0.00 3.01
2539 5681 2.755655 GAGGAGACGAGACAATCCAGAA 59.244 50.000 0.00 0.00 34.08 3.02
2584 5726 1.063266 ACCCTTTGGTCTTTTCTGCCA 60.063 47.619 0.00 0.00 43.06 4.92
2671 5813 5.484998 ACTTTTCCTGCATGGATAAAATGGT 59.515 36.000 5.83 2.74 45.68 3.55
2682 5824 0.675083 TGGCACACTTTTCCTGCATG 59.325 50.000 0.00 0.00 32.20 4.06
2725 5871 6.509656 TCGTCGTACCTTGATAAAATAGCAT 58.490 36.000 0.00 0.00 0.00 3.79
2747 5893 6.726035 TTTGATAAAAGAGCACGTTTTTCG 57.274 33.333 0.08 0.00 46.00 3.46
2760 5906 7.650903 GCCCATTCTAGAGCAATTTGATAAAAG 59.349 37.037 0.00 0.00 0.00 2.27
2842 5990 7.829706 TGCCACACCCGCATATAATATTAAATA 59.170 33.333 0.00 0.00 0.00 1.40
2858 6006 3.633094 CTCTCGAGTGCCACACCCG 62.633 68.421 13.13 0.00 36.95 5.28
2870 6018 1.561643 AGAGGATTTGTGGCTCTCGA 58.438 50.000 0.00 0.00 0.00 4.04
2944 6092 2.091665 AGGATCCGGCTCCATGAAAAAT 60.092 45.455 25.68 0.00 37.81 1.82
2945 6093 1.284785 AGGATCCGGCTCCATGAAAAA 59.715 47.619 25.68 0.00 37.81 1.94
2946 6094 0.918983 AGGATCCGGCTCCATGAAAA 59.081 50.000 25.68 0.00 37.81 2.29
2947 6095 0.469917 GAGGATCCGGCTCCATGAAA 59.530 55.000 25.68 0.00 37.81 2.69
2948 6096 0.399091 AGAGGATCCGGCTCCATGAA 60.399 55.000 25.68 0.00 37.81 2.57
2949 6097 1.117749 CAGAGGATCCGGCTCCATGA 61.118 60.000 25.68 0.00 37.81 3.07
2950 6098 1.117749 TCAGAGGATCCGGCTCCATG 61.118 60.000 25.68 21.72 37.81 3.66
2951 6099 1.118356 GTCAGAGGATCCGGCTCCAT 61.118 60.000 25.68 11.42 37.81 3.41
2952 6100 1.758514 GTCAGAGGATCCGGCTCCA 60.759 63.158 25.68 2.34 37.81 3.86
2953 6101 2.851071 CGTCAGAGGATCCGGCTCC 61.851 68.421 16.90 16.90 33.66 4.70
2954 6102 0.818445 TACGTCAGAGGATCCGGCTC 60.818 60.000 5.98 0.00 33.66 4.70
2955 6103 1.102222 GTACGTCAGAGGATCCGGCT 61.102 60.000 5.98 5.15 33.66 5.52
2956 6104 1.359475 GTACGTCAGAGGATCCGGC 59.641 63.158 5.98 2.53 33.66 6.13
2957 6105 1.647629 CGTACGTCAGAGGATCCGG 59.352 63.158 7.22 0.00 33.66 5.14
2958 6106 1.647629 CCGTACGTCAGAGGATCCG 59.352 63.158 15.21 0.00 33.66 4.18
2959 6107 1.359475 GCCGTACGTCAGAGGATCC 59.641 63.158 15.21 2.48 33.66 3.36
2960 6108 1.359475 GGCCGTACGTCAGAGGATC 59.641 63.158 15.21 0.00 0.00 3.36
2961 6109 2.125961 GGGCCGTACGTCAGAGGAT 61.126 63.158 15.21 0.00 0.00 3.24
2962 6110 2.753043 GGGCCGTACGTCAGAGGA 60.753 66.667 15.21 0.00 0.00 3.71
2963 6111 4.189188 CGGGCCGTACGTCAGAGG 62.189 72.222 19.97 0.00 0.00 3.69
2964 6112 4.849329 GCGGGCCGTACGTCAGAG 62.849 72.222 28.82 0.00 0.00 3.35
3007 6155 4.802051 CTGACATGTGGCCCCGGG 62.802 72.222 15.80 15.80 0.00 5.73
3008 6156 4.033776 ACTGACATGTGGCCCCGG 62.034 66.667 1.15 0.00 0.00 5.73
3009 6157 2.747460 CACTGACATGTGGCCCCG 60.747 66.667 1.15 0.00 34.56 5.73
3015 6163 3.434319 GCCGCCCACTGACATGTG 61.434 66.667 1.15 0.00 37.66 3.21
3016 6164 3.952508 TGCCGCCCACTGACATGT 61.953 61.111 0.00 0.00 0.00 3.21
3017 6165 3.434319 GTGCCGCCCACTGACATG 61.434 66.667 0.00 0.00 41.35 3.21
3032 6180 1.812922 GGCTCCTCTGCATGTCGTG 60.813 63.158 0.00 0.00 34.04 4.35
3033 6181 2.581354 GGCTCCTCTGCATGTCGT 59.419 61.111 0.00 0.00 34.04 4.34
3034 6182 2.584418 CGGCTCCTCTGCATGTCG 60.584 66.667 0.00 0.00 34.04 4.35
3035 6183 1.812922 CACGGCTCCTCTGCATGTC 60.813 63.158 0.00 0.00 34.04 3.06
3036 6184 2.267006 CACGGCTCCTCTGCATGT 59.733 61.111 0.00 0.00 34.04 3.21
3037 6185 1.812922 GACACGGCTCCTCTGCATG 60.813 63.158 0.00 0.00 34.04 4.06
3038 6186 2.581354 GACACGGCTCCTCTGCAT 59.419 61.111 0.00 0.00 34.04 3.96
3039 6187 3.695606 GGACACGGCTCCTCTGCA 61.696 66.667 0.00 0.00 34.04 4.41
3040 6188 2.527951 AATGGACACGGCTCCTCTGC 62.528 60.000 2.64 0.00 0.00 4.26
3041 6189 0.036010 AAATGGACACGGCTCCTCTG 60.036 55.000 2.64 0.00 0.00 3.35
3042 6190 0.693049 AAAATGGACACGGCTCCTCT 59.307 50.000 2.64 0.00 0.00 3.69
3043 6191 1.468914 GAAAAATGGACACGGCTCCTC 59.531 52.381 2.64 0.00 0.00 3.71
3044 6192 1.202879 TGAAAAATGGACACGGCTCCT 60.203 47.619 2.64 0.00 0.00 3.69
3045 6193 1.243902 TGAAAAATGGACACGGCTCC 58.756 50.000 0.00 0.00 0.00 4.70
3046 6194 4.695217 TTATGAAAAATGGACACGGCTC 57.305 40.909 0.00 0.00 0.00 4.70
3047 6195 6.377146 ACTTATTATGAAAAATGGACACGGCT 59.623 34.615 0.00 0.00 0.00 5.52
3048 6196 6.560711 ACTTATTATGAAAAATGGACACGGC 58.439 36.000 0.00 0.00 0.00 5.68
3106 6254 6.653989 ACATCTGCTTAGTAGTGCCTTTATT 58.346 36.000 0.00 0.00 0.00 1.40
3248 6560 7.341805 AGCTAAATCTGGCTGATTCTTTTAGA 58.658 34.615 18.28 0.00 43.99 2.10


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

AutoCloner maintained by Alex Coulton.