Multiple sequence alignment - TraesCS7D01G488600

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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 TraesCS7D01G488600 chr7D 100.000 2510 0 0 1 2510 598498061 598495552 0.000000e+00 4636.0
1 TraesCS7D01G488600 chr7D 86.878 884 77 25 666 1518 598485994 598485119 0.000000e+00 953.0
2 TraesCS7D01G488600 chr7D 90.698 258 23 1 1254 1510 598437866 598437609 2.390000e-90 342.0
3 TraesCS7D01G488600 chr7D 98.131 107 1 1 2405 2510 510609975 510610081 4.260000e-43 185.0
4 TraesCS7D01G488600 chr7D 75.920 299 55 8 1 283 598524370 598524073 1.210000e-28 137.0
5 TraesCS7D01G488600 chr7A 88.462 1014 57 28 794 1767 690930472 690929479 0.000000e+00 1170.0
6 TraesCS7D01G488600 chr7A 90.618 842 65 7 1 828 690931329 690930488 0.000000e+00 1105.0
7 TraesCS7D01G488600 chr7A 86.260 917 87 24 621 1518 690918876 690917980 0.000000e+00 959.0
8 TraesCS7D01G488600 chr7A 84.314 663 59 6 1769 2410 690929346 690928708 7.680000e-170 606.0
9 TraesCS7D01G488600 chr7A 90.152 132 10 3 2382 2510 634898540 634898409 4.290000e-38 169.0
10 TraesCS7D01G488600 chr7B 88.317 933 58 21 810 1715 677668123 677667215 0.000000e+00 1072.0
11 TraesCS7D01G488600 chr7B 87.976 840 84 11 1 828 677691174 677690340 0.000000e+00 976.0
12 TraesCS7D01G488600 chr7B 83.639 654 73 15 1 638 677692985 677692350 3.600000e-163 584.0
13 TraesCS7D01G488600 chr7B 80.095 844 116 26 1 828 677668964 677668157 4.650000e-162 580.0
14 TraesCS7D01G488600 chr7B 85.009 587 65 14 629 1208 677539133 677538563 2.170000e-160 575.0
15 TraesCS7D01G488600 chr7B 91.257 366 26 3 2024 2384 677643453 677643089 6.240000e-136 494.0
16 TraesCS7D01G488600 chr7B 95.276 254 11 1 1266 1518 677538470 677538217 3.890000e-108 401.0
17 TraesCS7D01G488600 chr7B 92.481 266 19 1 1253 1517 677522668 677522403 1.820000e-101 379.0
18 TraesCS7D01G488600 chr7B 91.912 272 18 4 1253 1520 677508028 677507757 6.550000e-101 377.0
19 TraesCS7D01G488600 chr7B 84.426 366 41 14 796 1154 677690317 677689961 1.850000e-91 346.0
20 TraesCS7D01G488600 chr7B 84.637 358 23 14 2033 2384 677666513 677666182 6.690000e-86 327.0
21 TraesCS7D01G488600 chr7B 88.485 165 10 6 1768 1928 677667005 677666846 9.160000e-45 191.0
22 TraesCS7D01G488600 chr7B 79.771 262 45 4 1 254 677360723 677360462 1.530000e-42 183.0
23 TraesCS7D01G488600 chr7B 77.358 265 45 7 1 250 677786282 677786018 2.600000e-30 143.0
24 TraesCS7D01G488600 chr7B 92.857 56 4 0 195 250 677940121 677940066 5.750000e-12 82.4
25 TraesCS7D01G488600 chr5D 79.696 724 100 39 810 1511 125738151 125737453 1.750000e-131 479.0
26 TraesCS7D01G488600 chr5D 97.273 110 2 1 2402 2510 352931651 352931760 4.260000e-43 185.0
27 TraesCS7D01G488600 chr4A 91.026 156 13 1 1047 1201 574385236 574385081 2.530000e-50 209.0
28 TraesCS7D01G488600 chr4A 94.737 114 4 2 2399 2510 17248108 17247995 2.570000e-40 176.0
29 TraesCS7D01G488600 chr4B 90.385 156 14 1 1047 1201 41743706 41743861 1.180000e-48 204.0
30 TraesCS7D01G488600 chr5A 99.048 105 0 1 2407 2510 630124088 630123984 1.190000e-43 187.0
31 TraesCS7D01G488600 chr5A 95.536 112 4 1 2400 2510 79287151 79287262 7.130000e-41 178.0
32 TraesCS7D01G488600 chr1D 96.429 112 3 1 2400 2510 290446036 290446147 1.530000e-42 183.0
33 TraesCS7D01G488600 chr2A 95.575 113 3 2 2399 2510 597848129 597848018 1.980000e-41 180.0
34 TraesCS7D01G488600 chr3A 95.536 112 3 2 2401 2510 451653210 451653321 7.130000e-41 178.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G488600 chr7D 598495552 598498061 2509 True 4636.000000 4636 100.0000 1 2510 1 chr7D.!!$R3 2509
1 TraesCS7D01G488600 chr7D 598485119 598485994 875 True 953.000000 953 86.8780 666 1518 1 chr7D.!!$R2 852
2 TraesCS7D01G488600 chr7A 690928708 690931329 2621 True 960.333333 1170 87.7980 1 2410 3 chr7A.!!$R3 2409
3 TraesCS7D01G488600 chr7A 690917980 690918876 896 True 959.000000 959 86.2600 621 1518 1 chr7A.!!$R2 897
4 TraesCS7D01G488600 chr7B 677689961 677692985 3024 True 635.333333 976 85.3470 1 1154 3 chr7B.!!$R9 1153
5 TraesCS7D01G488600 chr7B 677666182 677668964 2782 True 542.500000 1072 85.3835 1 2384 4 chr7B.!!$R8 2383
6 TraesCS7D01G488600 chr7B 677538217 677539133 916 True 488.000000 575 90.1425 629 1518 2 chr7B.!!$R7 889
7 TraesCS7D01G488600 chr5D 125737453 125738151 698 True 479.000000 479 79.6960 810 1511 1 chr5D.!!$R1 701

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
748 2582 0.037046 TAACCGCTCCTCCGAAAACC 60.037 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 4851 0.11319 CTCCAAACCAAAGGAGGCCT 59.887 55.0 3.86 3.86 46.11 5.19 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
75 81 5.943349 TGTAAAGAAAGATATCCACCCGA 57.057 39.130 0.00 0.00 0.00 5.14
170 179 2.156098 TGCTAAAGCCACGTTTTAGGG 58.844 47.619 16.20 2.91 37.01 3.53
171 180 1.471287 GCTAAAGCCACGTTTTAGGGG 59.529 52.381 16.20 2.25 37.01 4.79
216 2039 6.247903 CGCACACTACCACAAATATGTTAAG 58.752 40.000 0.00 0.00 37.82 1.85
302 2125 8.491958 TCTACTCCACATCATTACTCTACACTA 58.508 37.037 0.00 0.00 0.00 2.74
303 2126 7.336161 ACTCCACATCATTACTCTACACTAC 57.664 40.000 0.00 0.00 0.00 2.73
374 2197 0.247736 ACAAGAGTCGCCTTGGCTAG 59.752 55.000 10.12 0.00 45.76 3.42
379 2202 4.143333 TCGCCTTGGCTAGACGGC 62.143 66.667 10.12 4.46 39.14 5.68
429 2252 4.962151 CGAGAAAACGAAGAAAAACTCCAC 59.038 41.667 0.00 0.00 35.09 4.02
457 2280 3.044305 AAGGTCTCACGCTTGCGC 61.044 61.111 15.21 0.00 0.00 6.09
494 2317 1.284657 CTCGCTCAATGCAACTCGAT 58.715 50.000 0.00 0.00 43.06 3.59
519 2342 5.239744 TGATCTAGAGCTTCGAGATAACCAC 59.760 44.000 9.79 0.00 38.64 4.16
653 2480 1.598962 CGCCGGATCTGGATGCATT 60.599 57.895 25.54 0.00 0.00 3.56
656 2483 0.892358 CCGGATCTGGATGCATTGGG 60.892 60.000 16.28 0.00 0.00 4.12
677 2505 1.137479 TCTGAAAGTGAAACGGACGGT 59.863 47.619 0.00 0.00 45.86 4.83
696 2524 0.107800 TAGGAGACCTGTCCGACGAG 60.108 60.000 0.00 0.00 42.05 4.18
734 2562 2.934553 GACGATTTCCCTCCTTTAACCG 59.065 50.000 0.00 0.00 0.00 4.44
748 2582 0.037046 TAACCGCTCCTCCGAAAACC 60.037 55.000 0.00 0.00 0.00 3.27
782 2616 4.593864 GCCAACCCGCGCCAAAAA 62.594 61.111 0.00 0.00 0.00 1.94
801 2646 3.603158 AACAACCAAAAGTTTTCGCCT 57.397 38.095 0.00 0.00 36.18 5.52
803 2648 2.159156 ACAACCAAAAGTTTTCGCCTCC 60.159 45.455 0.00 0.00 36.18 4.30
804 2649 0.666374 ACCAAAAGTTTTCGCCTCCG 59.334 50.000 0.00 0.00 0.00 4.63
805 2650 0.948678 CCAAAAGTTTTCGCCTCCGA 59.051 50.000 0.00 0.00 42.66 4.55
808 2707 0.179040 AAAGTTTTCGCCTCCGACCA 60.179 50.000 0.00 0.00 44.30 4.02
958 2866 4.593864 GGCCATCTCTCCGCCGAC 62.594 72.222 0.00 0.00 31.92 4.79
1119 3027 2.263540 GTCGCCCGCTACCTCAAA 59.736 61.111 0.00 0.00 0.00 2.69
1176 3084 4.078516 GTCTACCTGGCCGCCGTT 62.079 66.667 4.58 0.00 0.00 4.44
1228 3171 1.305381 CCCCCTGTCTCGTTCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
1231 3174 1.324005 CCCTGTCTCGTTCTCCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
1233 3176 0.323908 CTGTCTCGTTCTCCTCCCCT 60.324 60.000 0.00 0.00 0.00 4.79
1234 3177 0.114560 TGTCTCGTTCTCCTCCCCTT 59.885 55.000 0.00 0.00 0.00 3.95
1244 3187 4.410400 CTCCCCTTCCCGCGCTTT 62.410 66.667 5.56 0.00 0.00 3.51
1263 3208 4.380444 GCTTTCTCTGTTCTCGATCTCACT 60.380 45.833 0.00 0.00 0.00 3.41
1281 3242 7.348080 TCTCACTGTTTCTTGTTTCTCTCTA 57.652 36.000 0.00 0.00 0.00 2.43
1302 3263 3.073735 CAGACCCTGGAGCTCGCT 61.074 66.667 7.83 0.00 0.00 4.93
1454 3415 4.742201 CCACACCACGCTCCTCCG 62.742 72.222 0.00 0.00 0.00 4.63
1518 3479 7.012799 GCTTCCCAGGAGTTTTAGATTAGATTG 59.987 40.741 0.00 0.00 0.00 2.67
1519 3480 6.900194 TCCCAGGAGTTTTAGATTAGATTGG 58.100 40.000 0.00 0.00 0.00 3.16
1520 3481 6.676632 TCCCAGGAGTTTTAGATTAGATTGGA 59.323 38.462 0.00 0.00 0.00 3.53
1557 3545 3.951306 TCGCAATCTTGTTCTTGTTGTG 58.049 40.909 0.00 0.00 0.00 3.33
1618 3606 6.205853 TGAAACGGATATGTTGCTACTGTTTT 59.794 34.615 0.00 0.00 39.21 2.43
1619 3607 7.388224 TGAAACGGATATGTTGCTACTGTTTTA 59.612 33.333 0.00 0.00 39.21 1.52
1620 3608 6.903883 ACGGATATGTTGCTACTGTTTTAG 57.096 37.500 0.00 0.00 0.00 1.85
1621 3609 5.293569 ACGGATATGTTGCTACTGTTTTAGC 59.706 40.000 0.00 0.00 44.21 3.09
1622 3610 5.523916 CGGATATGTTGCTACTGTTTTAGCT 59.476 40.000 0.00 0.00 44.26 3.32
1623 3611 6.700081 CGGATATGTTGCTACTGTTTTAGCTA 59.300 38.462 0.00 0.00 44.26 3.32
1629 3617 5.073311 TGCTACTGTTTTAGCTAGTCTGG 57.927 43.478 3.94 0.00 44.26 3.86
1631 3619 5.105716 TGCTACTGTTTTAGCTAGTCTGGAG 60.106 44.000 3.94 0.91 44.26 3.86
1681 3669 0.463654 TTGCACTGAAACGCCTCTGT 60.464 50.000 0.00 0.00 0.00 3.41
1690 3678 0.956633 AACGCCTCTGTACTGACGAA 59.043 50.000 16.19 0.00 0.00 3.85
1697 3685 4.238514 CCTCTGTACTGACGAAAAGGAAG 58.761 47.826 0.00 0.00 0.00 3.46
1708 3696 3.194755 ACGAAAAGGAAGGTTGCACTTTT 59.805 39.130 9.47 9.47 43.51 2.27
1709 3697 3.551485 CGAAAAGGAAGGTTGCACTTTTG 59.449 43.478 13.35 4.86 41.62 2.44
1710 3698 4.676723 CGAAAAGGAAGGTTGCACTTTTGA 60.677 41.667 13.35 0.00 41.62 2.69
1797 3981 1.131126 CACGAGCAACATCCACAATCC 59.869 52.381 0.00 0.00 0.00 3.01
1838 4029 2.334838 ACGCAAACTATTCAGACCGAC 58.665 47.619 0.00 0.00 0.00 4.79
1913 4111 0.325016 TCCAGCAGCAGGAGATGAGA 60.325 55.000 1.49 0.00 31.30 3.27
1916 4114 1.413077 CAGCAGCAGGAGATGAGATCA 59.587 52.381 0.00 0.00 31.30 2.92
1928 4126 2.084610 TGAGATCAAAGGAGCACACG 57.915 50.000 0.00 0.00 0.00 4.49
1965 4163 2.015587 GTCGTCTCACAGGGTACTAGG 58.984 57.143 0.00 0.00 0.00 3.02
1990 4188 7.201504 GGGTTACTCTAGCAGATTCGTAAAAAC 60.202 40.741 0.00 0.00 0.00 2.43
2000 4198 4.932200 AGATTCGTAAAAACTGAGCCTCTG 59.068 41.667 0.00 0.00 0.00 3.35
2001 4199 4.330944 TTCGTAAAAACTGAGCCTCTGA 57.669 40.909 5.53 0.00 0.00 3.27
2002 4200 4.537135 TCGTAAAAACTGAGCCTCTGAT 57.463 40.909 5.53 0.00 0.00 2.90
2003 4201 5.654603 TCGTAAAAACTGAGCCTCTGATA 57.345 39.130 5.53 0.00 0.00 2.15
2004 4202 6.222038 TCGTAAAAACTGAGCCTCTGATAT 57.778 37.500 5.53 0.00 0.00 1.63
2005 4203 7.342769 TCGTAAAAACTGAGCCTCTGATATA 57.657 36.000 5.53 0.00 0.00 0.86
2006 4204 7.778083 TCGTAAAAACTGAGCCTCTGATATAA 58.222 34.615 5.53 0.00 0.00 0.98
2007 4205 7.921214 TCGTAAAAACTGAGCCTCTGATATAAG 59.079 37.037 5.53 0.00 0.00 1.73
2008 4206 6.934048 AAAAACTGAGCCTCTGATATAAGC 57.066 37.500 5.53 0.00 0.00 3.09
2009 4207 5.885449 AAACTGAGCCTCTGATATAAGCT 57.115 39.130 5.53 0.00 36.25 3.74
2010 4208 5.885449 AACTGAGCCTCTGATATAAGCTT 57.115 39.130 3.48 3.48 32.97 3.74
2011 4209 5.885449 ACTGAGCCTCTGATATAAGCTTT 57.115 39.130 3.20 0.00 32.97 3.51
2012 4210 6.985653 ACTGAGCCTCTGATATAAGCTTTA 57.014 37.500 3.20 0.00 32.97 1.85
2013 4211 6.991938 ACTGAGCCTCTGATATAAGCTTTAG 58.008 40.000 3.20 0.00 32.97 1.85
2014 4212 6.780031 ACTGAGCCTCTGATATAAGCTTTAGA 59.220 38.462 3.20 0.86 32.97 2.10
2015 4213 7.039784 ACTGAGCCTCTGATATAAGCTTTAGAG 60.040 40.741 3.20 10.23 32.97 2.43
2093 4519 7.462571 AACTTTATAATTTGTCCTCCCACAC 57.537 36.000 0.00 0.00 0.00 3.82
2097 4523 5.982890 ATAATTTGTCCTCCCACACTTTG 57.017 39.130 0.00 0.00 0.00 2.77
2110 4536 5.362430 TCCCACACTTTGTTTAAATGCTCTT 59.638 36.000 0.00 0.00 0.00 2.85
2111 4537 5.463061 CCCACACTTTGTTTAAATGCTCTTG 59.537 40.000 0.00 0.00 0.00 3.02
2125 4551 2.064014 GCTCTTGCATTTCTTTGGCAC 58.936 47.619 0.00 0.00 37.26 5.01
2127 4553 1.000385 TCTTGCATTTCTTTGGCACGG 60.000 47.619 0.00 0.00 37.26 4.94
2150 4593 3.420839 ACACTTCACTTCTTTTTGCGG 57.579 42.857 0.00 0.00 0.00 5.69
2158 4601 5.221880 TCACTTCTTTTTGCGGAAATGATG 58.778 37.500 1.94 9.46 33.14 3.07
2159 4602 4.984161 CACTTCTTTTTGCGGAAATGATGT 59.016 37.500 1.94 10.02 38.85 3.06
2162 4605 2.077413 TTTTGCGGAAATGATGTGGC 57.923 45.000 1.94 0.00 0.00 5.01
2164 4607 2.121291 TTGCGGAAATGATGTGGCTA 57.879 45.000 0.00 0.00 0.00 3.93
2267 4710 0.176680 CACTCCTGCCGCTAGAACAT 59.823 55.000 0.00 0.00 0.00 2.71
2367 4810 4.810191 ATGAGAACTAGTTGGTGAGGTC 57.190 45.455 14.14 0.00 0.00 3.85
2378 4821 0.889186 GGTGAGGTCGTGCAAACCAT 60.889 55.000 18.93 6.71 39.39 3.55
2387 4830 4.854839 GGTCGTGCAAACCATGTAAAATAC 59.145 41.667 13.37 0.00 36.75 1.89
2389 4832 5.915758 GTCGTGCAAACCATGTAAAATACAA 59.084 36.000 0.00 0.00 42.76 2.41
2416 4859 9.736819 ATATAGAGCTAAATATTTAGGCCTCCT 57.263 33.333 28.27 19.25 40.31 3.69
2417 4860 6.771934 AGAGCTAAATATTTAGGCCTCCTT 57.228 37.500 28.27 14.11 40.31 3.36
2418 4861 7.155442 AGAGCTAAATATTTAGGCCTCCTTT 57.845 36.000 28.27 13.93 40.31 3.11
2419 4862 7.001073 AGAGCTAAATATTTAGGCCTCCTTTG 58.999 38.462 28.27 7.96 40.31 2.77
2420 4863 6.071320 AGCTAAATATTTAGGCCTCCTTTGG 58.929 40.000 28.27 6.48 40.31 3.28
2421 4864 5.833667 GCTAAATATTTAGGCCTCCTTTGGT 59.166 40.000 28.27 0.00 40.31 3.67
2422 4865 6.323996 GCTAAATATTTAGGCCTCCTTTGGTT 59.676 38.462 28.27 0.00 40.31 3.67
2423 4866 7.147724 GCTAAATATTTAGGCCTCCTTTGGTTT 60.148 37.037 28.27 6.13 40.31 3.27
2424 4867 6.544928 AATATTTAGGCCTCCTTTGGTTTG 57.455 37.500 9.68 0.00 34.61 2.93
2425 4868 2.302587 TTAGGCCTCCTTTGGTTTGG 57.697 50.000 9.68 0.00 34.61 3.28
2426 4869 1.451449 TAGGCCTCCTTTGGTTTGGA 58.549 50.000 9.68 0.00 34.61 3.53
2427 4870 0.113190 AGGCCTCCTTTGGTTTGGAG 59.887 55.000 0.00 0.00 46.91 3.86
2433 4876 3.092301 CTCCTTTGGTTTGGAGGAATCC 58.908 50.000 0.00 0.00 44.44 3.01
2434 4877 2.448961 TCCTTTGGTTTGGAGGAATCCA 59.551 45.455 0.61 0.00 36.67 3.41
2435 4878 3.077391 TCCTTTGGTTTGGAGGAATCCAT 59.923 43.478 0.61 0.00 39.86 3.41
2436 4879 4.293634 TCCTTTGGTTTGGAGGAATCCATA 59.706 41.667 0.61 0.00 39.86 2.74
2437 4880 4.646492 CCTTTGGTTTGGAGGAATCCATAG 59.354 45.833 0.61 0.00 39.86 2.23
2438 4881 3.951563 TGGTTTGGAGGAATCCATAGG 57.048 47.619 0.61 0.00 39.86 2.57
2439 4882 3.469859 TGGTTTGGAGGAATCCATAGGA 58.530 45.455 0.61 0.00 39.86 2.94
2440 4883 3.855599 TGGTTTGGAGGAATCCATAGGAA 59.144 43.478 0.61 0.00 39.86 3.36
2441 4884 4.482025 TGGTTTGGAGGAATCCATAGGAAT 59.518 41.667 0.61 0.00 39.86 3.01
2442 4885 5.043432 TGGTTTGGAGGAATCCATAGGAATT 60.043 40.000 0.61 0.00 39.86 2.17
2443 4886 5.536538 GGTTTGGAGGAATCCATAGGAATTC 59.463 44.000 0.61 0.00 39.86 2.17
2444 4887 6.368805 GTTTGGAGGAATCCATAGGAATTCT 58.631 40.000 0.61 0.00 39.86 2.40
2445 4888 7.421382 GGTTTGGAGGAATCCATAGGAATTCTA 60.421 40.741 0.61 0.00 39.86 2.10
2446 4889 6.942163 TGGAGGAATCCATAGGAATTCTAG 57.058 41.667 0.61 0.00 34.34 2.43
2447 4890 6.634041 TGGAGGAATCCATAGGAATTCTAGA 58.366 40.000 0.61 0.00 34.34 2.43
2448 4891 6.728164 TGGAGGAATCCATAGGAATTCTAGAG 59.272 42.308 0.61 0.00 34.34 2.43
2449 4892 6.156083 GGAGGAATCCATAGGAATTCTAGAGG 59.844 46.154 0.61 3.58 34.34 3.69
2450 4893 6.879922 AGGAATCCATAGGAATTCTAGAGGA 58.120 40.000 0.61 8.75 39.13 3.71
2451 4894 7.495171 AGGAATCCATAGGAATTCTAGAGGAT 58.505 38.462 0.61 10.52 43.13 3.24
2452 4895 8.637371 AGGAATCCATAGGAATTCTAGAGGATA 58.363 37.037 17.27 0.00 41.76 2.59
2453 4896 8.923270 GGAATCCATAGGAATTCTAGAGGATAG 58.077 40.741 17.27 0.00 41.76 2.08
2454 4897 8.852671 AATCCATAGGAATTCTAGAGGATAGG 57.147 38.462 17.27 5.25 41.76 2.57
2455 4898 7.605381 TCCATAGGAATTCTAGAGGATAGGA 57.395 40.000 5.23 0.00 33.70 2.94
2456 4899 8.193450 TCCATAGGAATTCTAGAGGATAGGAT 57.807 38.462 5.23 0.00 33.70 3.24
2457 4900 8.637371 TCCATAGGAATTCTAGAGGATAGGATT 58.363 37.037 5.23 0.00 33.70 3.01
2458 4901 8.923270 CCATAGGAATTCTAGAGGATAGGATTC 58.077 40.741 5.23 7.20 38.32 2.52
2459 4902 9.713684 CATAGGAATTCTAGAGGATAGGATTCT 57.286 37.037 13.16 5.20 38.80 2.40
2490 4933 3.895704 TTTCCTTTAGAGCCCTTTGGT 57.104 42.857 0.00 0.00 0.00 3.67
2491 4934 3.895704 TTCCTTTAGAGCCCTTTGGTT 57.104 42.857 0.00 0.00 0.00 3.67
2492 4935 3.434940 TCCTTTAGAGCCCTTTGGTTC 57.565 47.619 0.00 0.00 41.91 3.62
2493 4936 2.714250 TCCTTTAGAGCCCTTTGGTTCA 59.286 45.455 0.00 0.00 43.89 3.18
2494 4937 3.333680 TCCTTTAGAGCCCTTTGGTTCAT 59.666 43.478 0.00 0.00 43.89 2.57
2495 4938 4.538490 TCCTTTAGAGCCCTTTGGTTCATA 59.462 41.667 0.00 0.00 43.89 2.15
2496 4939 4.884164 CCTTTAGAGCCCTTTGGTTCATAG 59.116 45.833 0.00 0.00 43.89 2.23
2497 4940 4.503714 TTAGAGCCCTTTGGTTCATAGG 57.496 45.455 0.00 0.00 43.89 2.57
2498 4941 2.562296 AGAGCCCTTTGGTTCATAGGA 58.438 47.619 6.07 0.00 43.89 2.94
2499 4942 2.919602 AGAGCCCTTTGGTTCATAGGAA 59.080 45.455 6.07 0.00 43.89 3.36
2500 4943 3.529319 AGAGCCCTTTGGTTCATAGGAAT 59.471 43.478 6.07 0.00 43.89 3.01
2501 4944 3.633986 GAGCCCTTTGGTTCATAGGAATG 59.366 47.826 6.07 0.00 41.28 2.67
2502 4945 2.695147 GCCCTTTGGTTCATAGGAATGG 59.305 50.000 6.07 0.00 35.14 3.16
2503 4946 3.627237 GCCCTTTGGTTCATAGGAATGGA 60.627 47.826 6.07 0.00 35.14 3.41
2504 4947 4.808042 CCCTTTGGTTCATAGGAATGGAT 58.192 43.478 6.07 0.00 35.14 3.41
2505 4948 5.211201 CCCTTTGGTTCATAGGAATGGATT 58.789 41.667 6.07 0.00 35.14 3.01
2506 4949 5.302823 CCCTTTGGTTCATAGGAATGGATTC 59.697 44.000 6.07 0.00 35.14 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.604565 TGGCTATGTGATCACTATGAACTG 58.395 41.667 25.55 8.96 0.00 3.16
24 25 5.600069 TCTGGCTATGTGATCACTATGAACT 59.400 40.000 25.55 5.47 0.00 3.01
53 59 5.943349 TCGGGTGGATATCTTTCTTTACA 57.057 39.130 2.05 0.00 0.00 2.41
75 81 7.776969 ACTCAGAGATAAAATATGTTGGCACAT 59.223 33.333 3.79 7.52 46.07 3.21
107 113 4.463186 GTCTTGAGTACTACCACCATGACT 59.537 45.833 14.99 0.00 32.57 3.41
216 2039 4.706842 TCCTAATGCCTCCCAAATCTAC 57.293 45.455 0.00 0.00 0.00 2.59
302 2125 1.748329 TTGGCAGAGTGCGTCAGAGT 61.748 55.000 0.00 0.00 46.21 3.24
303 2126 0.390866 ATTGGCAGAGTGCGTCAGAG 60.391 55.000 0.00 0.00 46.21 3.35
329 2152 5.931146 ACTTCTAAGTCTGCATTCTCTTGTG 59.069 40.000 0.00 0.00 32.86 3.33
393 2216 1.614241 TTTCTCGCACTAGGGCCTCC 61.614 60.000 10.74 0.00 0.00 4.30
429 2252 0.874175 TGAGACCTTGTTCGTGCGTG 60.874 55.000 0.00 0.00 0.00 5.34
457 2280 2.087646 GAGGGGCAGTTTTCTTGCTAG 58.912 52.381 0.00 0.00 0.00 3.42
494 2317 5.828328 TGGTTATCTCGAAGCTCTAGATCAA 59.172 40.000 8.28 1.90 32.18 2.57
519 2342 9.672086 TCCAAGTTGTTTATTTATTCTCAAACG 57.328 29.630 1.45 0.00 34.38 3.60
578 2401 4.401925 ACTTCACCTGATTTTTCCCTCAG 58.598 43.478 0.00 0.00 38.88 3.35
653 2480 1.487142 TCCGTTTCACTTTCAGACCCA 59.513 47.619 0.00 0.00 0.00 4.51
656 2483 1.525619 CCGTCCGTTTCACTTTCAGAC 59.474 52.381 0.00 0.00 0.00 3.51
677 2505 0.107800 CTCGTCGGACAGGTCTCCTA 60.108 60.000 9.10 0.00 29.64 2.94
696 2524 2.262915 CCATCCGATCCTAGCCGC 59.737 66.667 0.00 0.00 0.00 6.53
734 2562 1.448013 CGGAGGTTTTCGGAGGAGC 60.448 63.158 0.00 0.00 0.00 4.70
748 2582 1.160329 GGCGATTTGGGATGACGGAG 61.160 60.000 0.00 0.00 0.00 4.63
781 2615 3.517602 GAGGCGAAAACTTTTGGTTGTT 58.482 40.909 0.00 0.00 38.29 2.83
782 2616 2.159156 GGAGGCGAAAACTTTTGGTTGT 60.159 45.455 0.00 0.00 38.29 3.32
801 2646 3.608662 GGTGACGTGGTGGTCGGA 61.609 66.667 0.00 0.00 39.83 4.55
834 2733 2.268920 GCGTGATTGGCTGGGAGA 59.731 61.111 0.00 0.00 0.00 3.71
934 2836 2.588201 GGAGAGATGGCCGGGATCC 61.588 68.421 1.92 1.92 0.00 3.36
982 2890 1.056660 ATCTTCTGGTTCACGGTGGT 58.943 50.000 8.50 0.00 0.00 4.16
1110 3018 2.457366 ACTTGCCGACTTTGAGGTAG 57.543 50.000 0.00 0.00 0.00 3.18
1119 3027 4.351938 TGCGCGTACTTGCCGACT 62.352 61.111 8.43 0.00 0.00 4.18
1167 3075 3.818787 TACTCGAGAACGGCGGCC 61.819 66.667 21.68 9.54 40.21 6.13
1211 3154 1.324005 GGAGGAGAACGAGACAGGGG 61.324 65.000 0.00 0.00 0.00 4.79
1218 3161 1.331399 GGGAAGGGGAGGAGAACGAG 61.331 65.000 0.00 0.00 0.00 4.18
1228 3171 4.404098 GAAAGCGCGGGAAGGGGA 62.404 66.667 8.83 0.00 0.00 4.81
1231 3174 2.103042 CAGAGAAAGCGCGGGAAGG 61.103 63.158 8.83 0.00 0.00 3.46
1233 3176 0.949105 GAACAGAGAAAGCGCGGGAA 60.949 55.000 8.83 0.00 0.00 3.97
1234 3177 1.374252 GAACAGAGAAAGCGCGGGA 60.374 57.895 8.83 0.00 0.00 5.14
1244 3187 3.680490 ACAGTGAGATCGAGAACAGAGA 58.320 45.455 0.00 0.00 0.00 3.10
1263 3208 9.046296 GTCTGAATTAGAGAGAAACAAGAAACA 57.954 33.333 0.00 0.00 35.70 2.83
1281 3242 0.539051 CGAGCTCCAGGGTCTGAATT 59.461 55.000 8.47 0.00 40.01 2.17
1454 3415 3.752339 CCTTGCCGGCCTTCTTGC 61.752 66.667 26.77 0.00 0.00 4.01
1518 3479 2.478539 GCGAGATGCATTCCAAGTTTCC 60.479 50.000 0.00 0.00 45.45 3.13
1519 3480 2.790387 GCGAGATGCATTCCAAGTTTC 58.210 47.619 0.00 0.00 45.45 2.78
1520 3481 2.927553 GCGAGATGCATTCCAAGTTT 57.072 45.000 0.00 0.00 45.45 2.66
1557 3545 3.537206 AAGGGCGTCACAGGCAGTC 62.537 63.158 0.00 0.00 38.57 3.51
1618 3606 2.885266 CGTATTGGCTCCAGACTAGCTA 59.115 50.000 0.00 0.00 39.97 3.32
1619 3607 1.683917 CGTATTGGCTCCAGACTAGCT 59.316 52.381 0.00 0.00 39.97 3.32
1620 3608 1.681793 TCGTATTGGCTCCAGACTAGC 59.318 52.381 0.00 0.00 39.33 3.42
1621 3609 3.381908 ACTTCGTATTGGCTCCAGACTAG 59.618 47.826 0.00 0.00 0.00 2.57
1622 3610 3.362706 ACTTCGTATTGGCTCCAGACTA 58.637 45.455 0.00 0.00 0.00 2.59
1623 3611 2.180276 ACTTCGTATTGGCTCCAGACT 58.820 47.619 0.00 0.00 0.00 3.24
1629 3617 5.500931 CGAATTCTGAACTTCGTATTGGCTC 60.501 44.000 18.33 0.00 39.42 4.70
1631 3619 4.578601 CGAATTCTGAACTTCGTATTGGC 58.421 43.478 18.33 0.00 39.42 4.52
1681 3669 3.135994 GCAACCTTCCTTTTCGTCAGTA 58.864 45.455 0.00 0.00 0.00 2.74
1690 3678 3.513515 TGTCAAAAGTGCAACCTTCCTTT 59.486 39.130 0.00 0.00 37.80 3.11
1697 3685 3.304928 CCTCATCTGTCAAAAGTGCAACC 60.305 47.826 0.00 0.00 37.80 3.77
1708 3696 7.738847 TGCAAAGATATATTCCTCATCTGTCA 58.261 34.615 0.00 0.00 0.00 3.58
1709 3697 8.789825 ATGCAAAGATATATTCCTCATCTGTC 57.210 34.615 0.00 0.00 0.00 3.51
1710 3698 9.584008 AAATGCAAAGATATATTCCTCATCTGT 57.416 29.630 0.00 0.00 0.00 3.41
1730 3733 7.860373 GTGCTCAATTATACGGATAAAAATGCA 59.140 33.333 3.71 10.14 31.28 3.96
1742 3745 9.567848 AAAATAACTTTGGTGCTCAATTATACG 57.432 29.630 0.00 0.00 34.98 3.06
1838 4029 3.509575 AGTAGTGGAGAGAACTTCAGCTG 59.490 47.826 7.63 7.63 31.55 4.24
1913 4111 0.957395 CTGCCGTGTGCTCCTTTGAT 60.957 55.000 0.00 0.00 42.00 2.57
1916 4114 2.980233 GCTGCCGTGTGCTCCTTT 60.980 61.111 0.00 0.00 42.00 3.11
1928 4126 1.806623 CGACTACCCAGTAATGCTGCC 60.807 57.143 0.00 0.00 43.71 4.85
1935 4133 3.079578 CTGTGAGACGACTACCCAGTAA 58.920 50.000 0.00 0.00 34.21 2.24
1940 4138 0.611340 ACCCTGTGAGACGACTACCC 60.611 60.000 0.00 0.00 0.00 3.69
1965 4163 7.544915 AGTTTTTACGAATCTGCTAGAGTAACC 59.455 37.037 0.00 0.00 0.00 2.85
1990 4188 7.225784 TCTAAAGCTTATATCAGAGGCTCAG 57.774 40.000 18.26 9.22 32.46 3.35
2010 4208 9.726438 AGCTTCTTAATTTTCTTAGTGCTCTAA 57.274 29.630 7.92 7.92 35.25 2.10
2011 4209 9.372369 GAGCTTCTTAATTTTCTTAGTGCTCTA 57.628 33.333 0.00 0.00 38.94 2.43
2012 4210 8.100164 AGAGCTTCTTAATTTTCTTAGTGCTCT 58.900 33.333 0.00 0.00 44.71 4.09
2013 4211 8.262715 AGAGCTTCTTAATTTTCTTAGTGCTC 57.737 34.615 0.00 0.00 41.31 4.26
2014 4212 9.377312 CTAGAGCTTCTTAATTTTCTTAGTGCT 57.623 33.333 0.00 0.00 0.00 4.40
2015 4213 8.608317 CCTAGAGCTTCTTAATTTTCTTAGTGC 58.392 37.037 0.00 0.00 0.00 4.40
2016 4214 9.877178 TCCTAGAGCTTCTTAATTTTCTTAGTG 57.123 33.333 0.00 0.00 0.00 2.74
2021 4219 9.800572 ACTTTTCCTAGAGCTTCTTAATTTTCT 57.199 29.630 0.00 0.00 0.00 2.52
2110 4536 1.006337 GCCGTGCCAAAGAAATGCA 60.006 52.632 0.00 0.00 0.00 3.96
2111 4537 0.599728 TTGCCGTGCCAAAGAAATGC 60.600 50.000 0.00 0.00 0.00 3.56
2125 4551 3.420839 AAAAGAAGTGAAGTGTTGCCG 57.579 42.857 0.00 0.00 0.00 5.69
2127 4553 3.000773 CGCAAAAAGAAGTGAAGTGTTGC 60.001 43.478 0.00 0.00 37.38 4.17
2343 4786 4.593206 ACCTCACCAACTAGTTCTCATTCA 59.407 41.667 4.77 0.00 0.00 2.57
2367 4810 6.755461 TTTGTATTTTACATGGTTTGCACG 57.245 33.333 0.00 0.00 38.68 5.34
2395 4838 6.207614 CCAAAGGAGGCCTAAATATTTAGCTC 59.792 42.308 24.19 23.13 38.99 4.09
2397 4840 5.833667 ACCAAAGGAGGCCTAAATATTTAGC 59.166 40.000 24.19 19.42 38.99 3.09
2398 4841 7.898014 AACCAAAGGAGGCCTAAATATTTAG 57.102 36.000 23.09 23.09 39.80 1.85
2401 4844 5.425217 CCAAACCAAAGGAGGCCTAAATATT 59.575 40.000 4.42 0.00 31.13 1.28
2406 4849 1.783979 TCCAAACCAAAGGAGGCCTAA 59.216 47.619 4.42 0.00 31.13 2.69
2408 4851 0.113190 CTCCAAACCAAAGGAGGCCT 59.887 55.000 3.86 3.86 46.11 5.19
2409 4852 2.658548 CTCCAAACCAAAGGAGGCC 58.341 57.895 0.00 0.00 46.11 5.19
2413 4856 3.169512 GGATTCCTCCAAACCAAAGGA 57.830 47.619 0.00 0.00 41.64 3.36
2424 4867 6.156083 CCTCTAGAATTCCTATGGATTCCTCC 59.844 46.154 0.65 0.00 42.45 4.30
2425 4868 6.957020 TCCTCTAGAATTCCTATGGATTCCTC 59.043 42.308 0.65 0.00 30.26 3.71
2426 4869 6.879922 TCCTCTAGAATTCCTATGGATTCCT 58.120 40.000 0.65 0.00 30.26 3.36
2427 4870 7.747809 ATCCTCTAGAATTCCTATGGATTCC 57.252 40.000 0.65 0.00 37.33 3.01
2428 4871 8.923270 CCTATCCTCTAGAATTCCTATGGATTC 58.077 40.741 19.06 0.00 39.33 2.52
2429 4872 8.637371 TCCTATCCTCTAGAATTCCTATGGATT 58.363 37.037 19.06 9.05 39.33 3.01
2430 4873 8.193450 TCCTATCCTCTAGAATTCCTATGGAT 57.807 38.462 18.35 18.35 40.49 3.41
2431 4874 7.605381 TCCTATCCTCTAGAATTCCTATGGA 57.395 40.000 0.65 6.11 35.69 3.41
2432 4875 8.852671 AATCCTATCCTCTAGAATTCCTATGG 57.147 38.462 0.65 0.49 0.00 2.74
2433 4876 9.713684 AGAATCCTATCCTCTAGAATTCCTATG 57.286 37.037 0.65 0.00 0.00 2.23
2468 4911 4.552674 ACCAAAGGGCTCTAAAGGAAAAA 58.447 39.130 5.94 0.00 37.90 1.94
2469 4912 4.193240 ACCAAAGGGCTCTAAAGGAAAA 57.807 40.909 5.94 0.00 37.90 2.29
2470 4913 3.895704 ACCAAAGGGCTCTAAAGGAAA 57.104 42.857 5.94 0.00 37.90 3.13
2471 4914 3.139397 TGAACCAAAGGGCTCTAAAGGAA 59.861 43.478 5.94 0.00 37.90 3.36
2472 4915 2.714250 TGAACCAAAGGGCTCTAAAGGA 59.286 45.455 5.94 0.00 37.90 3.36
2473 4916 3.154827 TGAACCAAAGGGCTCTAAAGG 57.845 47.619 0.00 0.00 37.90 3.11
2474 4917 4.884164 CCTATGAACCAAAGGGCTCTAAAG 59.116 45.833 0.00 0.00 37.90 1.85
2475 4918 4.538490 TCCTATGAACCAAAGGGCTCTAAA 59.462 41.667 0.00 0.00 37.90 1.85
2476 4919 4.108570 TCCTATGAACCAAAGGGCTCTAA 58.891 43.478 0.00 0.00 37.90 2.10
2477 4920 3.731431 TCCTATGAACCAAAGGGCTCTA 58.269 45.455 0.00 0.00 37.90 2.43
2478 4921 2.562296 TCCTATGAACCAAAGGGCTCT 58.438 47.619 0.00 0.00 37.90 4.09
2479 4922 3.366052 TTCCTATGAACCAAAGGGCTC 57.634 47.619 0.00 0.00 37.90 4.70
2480 4923 3.628257 CCATTCCTATGAACCAAAGGGCT 60.628 47.826 0.00 0.00 33.50 5.19
2481 4924 2.695147 CCATTCCTATGAACCAAAGGGC 59.305 50.000 0.00 0.00 33.50 5.19
2482 4925 4.249638 TCCATTCCTATGAACCAAAGGG 57.750 45.455 0.00 0.00 35.37 3.95
2483 4926 6.396829 GAATCCATTCCTATGAACCAAAGG 57.603 41.667 0.00 0.00 33.37 3.11


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

AutoCloner maintained by Alex Coulton.