Multiple sequence alignment - TraesCS4A01G379100

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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 TraesCS4A01G379100 chr4A 100.000 2672 0 0 1 2672 656706892 656709563 0.000000e+00 4935.0
1 TraesCS4A01G379100 chr4A 95.436 1972 77 6 106 2075 656499868 656497908 0.000000e+00 3131.0
2 TraesCS4A01G379100 chr4A 76.878 1371 240 45 445 1771 656249679 656251016 0.000000e+00 704.0
3 TraesCS4A01G379100 chr4A 76.006 1242 212 51 506 1704 650831042 650832240 4.990000e-157 564.0
4 TraesCS4A01G379100 chr4A 83.966 580 50 16 2100 2672 656497955 656497412 1.420000e-142 516.0
5 TraesCS4A01G379100 chr4A 75.247 1216 233 43 543 1727 656550844 656552022 1.420000e-142 516.0
6 TraesCS4A01G379100 chr4A 78.026 851 137 28 1036 1871 655442941 655443756 8.600000e-135 490.0
7 TraesCS4A01G379100 chr4A 80.824 631 103 14 1353 1972 655663943 655664566 1.860000e-131 479.0
8 TraesCS4A01G379100 chr4A 78.571 756 128 22 1040 1771 656472942 656473687 4.030000e-128 468.0
9 TraesCS4A01G379100 chr4A 93.269 104 6 1 10 113 656500211 656500109 4.610000e-33 152.0
10 TraesCS4A01G379100 chr4A 100.000 75 0 0 2100 2174 656708919 656708993 3.590000e-29 139.0
11 TraesCS4A01G379100 chr4A 100.000 75 0 0 2028 2102 656708991 656709065 3.590000e-29 139.0
12 TraesCS4A01G379100 chr4A 85.526 76 2 5 2393 2468 656266364 656266430 1.330000e-08 71.3
13 TraesCS4A01G379100 chr4A 84.416 77 1 7 2393 2468 656483498 656483564 6.170000e-07 65.8
14 TraesCS4A01G379100 chr7D 78.045 1371 218 54 445 1771 44538210 44539541 0.000000e+00 787.0
15 TraesCS4A01G379100 chr7D 78.844 969 159 33 1035 1970 44531074 44532029 1.760000e-171 612.0
16 TraesCS4A01G379100 chr7D 76.414 1238 214 44 506 1704 43169430 43168232 4.920000e-167 597.0
17 TraesCS4A01G379100 chr7D 74.812 532 99 21 1447 1963 44580169 44579658 9.690000e-50 207.0
18 TraesCS4A01G379100 chr7A 78.926 968 159 30 1035 1971 47001066 47002019 1.360000e-172 616.0
19 TraesCS4A01G379100 chr7A 78.911 863 132 34 1036 1871 47283650 47284489 8.420000e-150 540.0
20 TraesCS4A01G379100 chr7A 75.000 600 95 32 546 1120 47033970 47033401 2.680000e-55 226.0
21 TraesCS4A01G379100 chr7A 88.679 53 4 2 1803 1853 46812863 46812915 2.220000e-06 63.9
22 TraesCS4A01G379100 chr3A 73.908 824 162 34 828 1634 11865564 11866351 5.630000e-72 281.0
23 TraesCS4A01G379100 chr3D 80.176 227 31 7 1639 1853 510331620 510331844 9.900000e-35 158.0


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 TraesCS4A01G379100 chr4A 656706892 656709563 2671 False 1737.666667 4935 100.000000 1 2672 3 chr4A.!!$F9 2671
1 TraesCS4A01G379100 chr4A 656497412 656500211 2799 True 1266.333333 3131 90.890333 10 2672 3 chr4A.!!$R1 2662
2 TraesCS4A01G379100 chr4A 656249679 656251016 1337 False 704.000000 704 76.878000 445 1771 1 chr4A.!!$F4 1326
3 TraesCS4A01G379100 chr4A 650831042 650832240 1198 False 564.000000 564 76.006000 506 1704 1 chr4A.!!$F1 1198
4 TraesCS4A01G379100 chr4A 656550844 656552022 1178 False 516.000000 516 75.247000 543 1727 1 chr4A.!!$F8 1184
5 TraesCS4A01G379100 chr4A 655442941 655443756 815 False 490.000000 490 78.026000 1036 1871 1 chr4A.!!$F2 835
6 TraesCS4A01G379100 chr4A 655663943 655664566 623 False 479.000000 479 80.824000 1353 1972 1 chr4A.!!$F3 619
7 TraesCS4A01G379100 chr4A 656472942 656473687 745 False 468.000000 468 78.571000 1040 1771 1 chr4A.!!$F6 731
8 TraesCS4A01G379100 chr7D 44538210 44539541 1331 False 787.000000 787 78.045000 445 1771 1 chr7D.!!$F2 1326
9 TraesCS4A01G379100 chr7D 44531074 44532029 955 False 612.000000 612 78.844000 1035 1970 1 chr7D.!!$F1 935
10 TraesCS4A01G379100 chr7D 43168232 43169430 1198 True 597.000000 597 76.414000 506 1704 1 chr7D.!!$R1 1198
11 TraesCS4A01G379100 chr7D 44579658 44580169 511 True 207.000000 207 74.812000 1447 1963 1 chr7D.!!$R2 516
12 TraesCS4A01G379100 chr7A 47001066 47002019 953 False 616.000000 616 78.926000 1035 1971 1 chr7A.!!$F2 936
13 TraesCS4A01G379100 chr7A 47283650 47284489 839 False 540.000000 540 78.911000 1036 1871 1 chr7A.!!$F3 835
14 TraesCS4A01G379100 chr7A 47033401 47033970 569 True 226.000000 226 75.000000 546 1120 1 chr7A.!!$R1 574
15 TraesCS4A01G379100 chr3A 11865564 11866351 787 False 281.000000 281 73.908000 828 1634 1 chr3A.!!$F1 806

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
861 1123 0.179065 CTCATCATCCTGGCGCAGAA 60.179 55.0 10.83 0.0 32.44 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2661 0.251341 ACCCCAGCATCACTTCCAAC 60.251 55.0 0.0 0.0 0.0 3.77 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
28 29 9.914131 ACAAAACTGCTCCTTTTTAGATTTATC 57.086 29.630 0.00 0.00 0.00 1.75
29 30 9.912634 CAAAACTGCTCCTTTTTAGATTTATCA 57.087 29.630 0.00 0.00 0.00 2.15
31 32 7.326968 ACTGCTCCTTTTTAGATTTATCAGC 57.673 36.000 0.00 0.00 0.00 4.26
46 47 8.986847 AGATTTATCAGCGATTTTAGATCTGTG 58.013 33.333 5.18 0.00 0.00 3.66
53 54 8.946085 TCAGCGATTTTAGATCTGTGTAAATTT 58.054 29.630 5.18 0.00 0.00 1.82
77 78 9.661563 TTTTACATTTTAGATCCGTGTAGATGT 57.338 29.630 0.00 0.00 0.00 3.06
200 449 8.445275 AATACACTTTGCATTTCGGATATGTA 57.555 30.769 9.63 3.18 0.00 2.29
267 516 1.229428 CGCCGATTATGACCATTGCT 58.771 50.000 0.00 0.00 0.00 3.91
268 517 1.603802 CGCCGATTATGACCATTGCTT 59.396 47.619 0.00 0.00 0.00 3.91
330 579 4.223700 AGATGAGTAGCTCCATGACAACAA 59.776 41.667 0.00 0.00 0.00 2.83
435 684 6.290294 ACGTACAAACTAGGTACCATGAAT 57.710 37.500 15.94 0.00 38.26 2.57
437 686 7.260603 ACGTACAAACTAGGTACCATGAATAC 58.739 38.462 15.94 6.68 38.26 1.89
438 687 7.093814 ACGTACAAACTAGGTACCATGAATACA 60.094 37.037 15.94 0.00 38.26 2.29
490 743 5.728351 TTATGTGCCGTACTAATGCTTTC 57.272 39.130 0.00 0.00 0.00 2.62
554 813 1.061411 CGCGATACCGTCTTCGACA 59.939 57.895 0.00 0.00 37.55 4.35
666 925 1.302511 GCACCACTTCCACCGACAT 60.303 57.895 0.00 0.00 0.00 3.06
773 1035 4.646040 CCAATGATCAAAAGATACTGCCCA 59.354 41.667 0.00 0.00 0.00 5.36
800 1062 0.731417 GTATGCAGGCAGAAGCACTG 59.269 55.000 0.00 6.57 44.49 3.66
859 1121 1.597302 CCTCATCATCCTGGCGCAG 60.597 63.158 10.83 4.65 0.00 5.18
860 1122 1.444672 CTCATCATCCTGGCGCAGA 59.555 57.895 10.83 2.49 32.44 4.26
861 1123 0.179065 CTCATCATCCTGGCGCAGAA 60.179 55.000 10.83 0.00 32.44 3.02
862 1124 0.462581 TCATCATCCTGGCGCAGAAC 60.463 55.000 10.83 0.00 32.44 3.01
864 1126 2.930385 ATCATCCTGGCGCAGAACGG 62.930 60.000 10.83 1.10 43.93 4.44
1073 1363 0.107945 GTCCTCACAGTGGGATCAGC 60.108 60.000 0.33 0.00 33.89 4.26
1164 1461 2.588877 CCGGTCCATCATCGTGGC 60.589 66.667 0.00 0.00 39.19 5.01
1194 1500 3.595819 GCAGTGGGCCTCAACATC 58.404 61.111 4.53 0.00 36.11 3.06
1244 1550 4.783621 GCACATGAGCCGCCCAGA 62.784 66.667 3.43 0.00 0.00 3.86
1280 1601 4.365514 TGGTGTCATTGTTGGATACTGT 57.634 40.909 0.00 0.00 37.61 3.55
1388 1712 5.304686 TGGGGCTTTCAGTACCATATTAG 57.695 43.478 0.00 0.00 0.00 1.73
1490 1817 6.268825 TGAGCTGGTTATCGATTATCCTAC 57.731 41.667 1.71 1.37 0.00 3.18
1517 1844 4.460034 TCTGCTGCATTGTAACATTGATGT 59.540 37.500 1.31 0.00 44.20 3.06
1597 1927 0.820226 TCGTCTCCAAGAGAGCATGG 59.180 55.000 0.00 0.00 42.90 3.66
1620 1950 5.748630 GGTTTCACTTCCATTGTTTGAGAAC 59.251 40.000 0.00 0.00 36.29 3.01
1634 1964 5.532406 TGTTTGAGAACCAAGAAGAAGATGG 59.468 40.000 0.00 0.00 40.16 3.51
1653 1983 0.951040 GTGTGAACAAGGAGCCTCCG 60.951 60.000 4.80 0.00 42.75 4.63
1708 2050 7.461182 CCATCTTAATGGTTTGGACTTGTTA 57.539 36.000 0.00 0.00 46.43 2.41
1748 2091 1.818419 TCCATCCCATGTGAGCCATA 58.182 50.000 0.00 0.00 30.71 2.74
1906 2277 6.314917 TGGAGTATCTATGCTATGGAACTGA 58.685 40.000 0.00 0.00 33.73 3.41
1926 2297 4.906618 TGATGTACTGTTCTCCCCTTTTC 58.093 43.478 0.00 0.00 0.00 2.29
1943 2314 5.585844 CCCTTTTCACTTTCAGTTTGCATTT 59.414 36.000 0.00 0.00 0.00 2.32
1993 2364 1.892474 TGCTGGGGTCATTTTAGTTGC 59.108 47.619 0.00 0.00 0.00 4.17
2016 2387 5.008415 GCTGAGATGGCTAGTTTACGTACTA 59.992 44.000 0.00 0.00 0.00 1.82
2053 2424 9.903682 CTTAACATTTCATGATTCTTGTTCAGT 57.096 29.630 13.18 0.00 0.00 3.41
2075 2446 3.691118 TGCACACTTTGATCCTATTGCTC 59.309 43.478 0.00 0.00 0.00 4.26
2076 2447 3.944015 GCACACTTTGATCCTATTGCTCT 59.056 43.478 0.00 0.00 0.00 4.09
2079 2450 4.946157 ACACTTTGATCCTATTGCTCTTGG 59.054 41.667 0.00 0.00 0.00 3.61
2080 2451 3.950395 ACTTTGATCCTATTGCTCTTGGC 59.050 43.478 0.00 0.00 42.22 4.52
2100 2471 4.379243 CCGGTCGCTCCAGCAACT 62.379 66.667 0.00 0.00 42.21 3.16
2101 2472 2.357517 CGGTCGCTCCAGCAACTT 60.358 61.111 0.00 0.00 42.21 2.66
2102 2473 1.080093 CGGTCGCTCCAGCAACTTA 60.080 57.895 0.00 0.00 42.21 2.24
2103 2474 0.669318 CGGTCGCTCCAGCAACTTAA 60.669 55.000 0.00 0.00 42.21 1.85
2104 2475 0.796927 GGTCGCTCCAGCAACTTAAC 59.203 55.000 0.00 0.00 42.21 2.01
2105 2476 1.508632 GTCGCTCCAGCAACTTAACA 58.491 50.000 0.00 0.00 42.21 2.41
2106 2477 2.076863 GTCGCTCCAGCAACTTAACAT 58.923 47.619 0.00 0.00 42.21 2.71
2107 2478 2.484264 GTCGCTCCAGCAACTTAACATT 59.516 45.455 0.00 0.00 42.21 2.71
2108 2479 3.058224 GTCGCTCCAGCAACTTAACATTT 60.058 43.478 0.00 0.00 42.21 2.32
2109 2480 3.188460 TCGCTCCAGCAACTTAACATTTC 59.812 43.478 0.00 0.00 42.21 2.17
2110 2481 3.058293 CGCTCCAGCAACTTAACATTTCA 60.058 43.478 0.00 0.00 42.21 2.69
2111 2482 4.379813 CGCTCCAGCAACTTAACATTTCAT 60.380 41.667 0.00 0.00 42.21 2.57
2112 2483 4.860907 GCTCCAGCAACTTAACATTTCATG 59.139 41.667 0.00 0.00 41.59 3.07
2113 2484 5.335897 GCTCCAGCAACTTAACATTTCATGA 60.336 40.000 0.00 0.00 41.59 3.07
2114 2485 6.626623 GCTCCAGCAACTTAACATTTCATGAT 60.627 38.462 0.00 0.00 41.59 2.45
2115 2486 7.230849 TCCAGCAACTTAACATTTCATGATT 57.769 32.000 0.00 0.00 0.00 2.57
2116 2487 7.315142 TCCAGCAACTTAACATTTCATGATTC 58.685 34.615 0.00 0.00 0.00 2.52
2117 2488 7.177216 TCCAGCAACTTAACATTTCATGATTCT 59.823 33.333 0.00 0.00 0.00 2.40
2118 2489 7.816031 CCAGCAACTTAACATTTCATGATTCTT 59.184 33.333 0.00 0.00 0.00 2.52
2119 2490 8.644619 CAGCAACTTAACATTTCATGATTCTTG 58.355 33.333 0.00 0.00 0.00 3.02
2120 2491 8.362639 AGCAACTTAACATTTCATGATTCTTGT 58.637 29.630 0.00 0.00 0.00 3.16
2121 2492 8.981647 GCAACTTAACATTTCATGATTCTTGTT 58.018 29.630 13.88 13.88 0.00 2.83
2124 2495 9.903682 ACTTAACATTTCATGATTCTTGTTCAG 57.096 29.630 13.18 13.68 0.00 3.02
2125 2496 9.903682 CTTAACATTTCATGATTCTTGTTCAGT 57.096 29.630 13.18 0.00 0.00 3.41
2126 2497 9.681692 TTAACATTTCATGATTCTTGTTCAGTG 57.318 29.630 13.18 0.00 0.00 3.66
2127 2498 6.154445 ACATTTCATGATTCTTGTTCAGTGC 58.846 36.000 0.00 0.00 0.00 4.40
2128 2499 5.771153 TTTCATGATTCTTGTTCAGTGCA 57.229 34.783 0.00 0.00 0.00 4.57
2129 2500 4.754372 TCATGATTCTTGTTCAGTGCAC 57.246 40.909 9.40 9.40 0.00 4.57
2130 2501 4.136051 TCATGATTCTTGTTCAGTGCACA 58.864 39.130 21.04 0.00 0.00 4.57
2131 2502 3.969117 TGATTCTTGTTCAGTGCACAC 57.031 42.857 21.04 9.34 0.00 3.82
2132 2503 3.544684 TGATTCTTGTTCAGTGCACACT 58.455 40.909 21.04 0.00 43.61 3.55
2133 2504 3.947196 TGATTCTTGTTCAGTGCACACTT 59.053 39.130 21.04 0.00 40.20 3.16
2134 2505 4.398988 TGATTCTTGTTCAGTGCACACTTT 59.601 37.500 21.04 0.00 40.20 2.66
2135 2506 3.763097 TCTTGTTCAGTGCACACTTTG 57.237 42.857 21.04 8.64 40.20 2.77
2136 2507 3.342719 TCTTGTTCAGTGCACACTTTGA 58.657 40.909 21.04 11.14 40.20 2.69
2137 2508 3.947196 TCTTGTTCAGTGCACACTTTGAT 59.053 39.130 21.04 0.00 40.20 2.57
2138 2509 3.969117 TGTTCAGTGCACACTTTGATC 57.031 42.857 21.04 12.87 40.20 2.92
2139 2510 2.618241 TGTTCAGTGCACACTTTGATCC 59.382 45.455 21.04 8.08 40.20 3.36
2140 2511 2.880890 GTTCAGTGCACACTTTGATCCT 59.119 45.455 21.04 0.00 40.20 3.24
2141 2512 4.065088 GTTCAGTGCACACTTTGATCCTA 58.935 43.478 21.04 0.00 40.20 2.94
2142 2513 4.558226 TCAGTGCACACTTTGATCCTAT 57.442 40.909 21.04 0.00 40.20 2.57
2143 2514 4.910195 TCAGTGCACACTTTGATCCTATT 58.090 39.130 21.04 0.00 40.20 1.73
2144 2515 4.696877 TCAGTGCACACTTTGATCCTATTG 59.303 41.667 21.04 3.01 40.20 1.90
2145 2516 3.441572 AGTGCACACTTTGATCCTATTGC 59.558 43.478 21.04 0.00 38.83 3.56
2146 2517 3.441572 GTGCACACTTTGATCCTATTGCT 59.558 43.478 13.17 0.00 0.00 3.91
2147 2518 3.691118 TGCACACTTTGATCCTATTGCTC 59.309 43.478 0.00 0.00 0.00 4.26
2148 2519 3.944015 GCACACTTTGATCCTATTGCTCT 59.056 43.478 0.00 0.00 0.00 4.09
2149 2520 4.397417 GCACACTTTGATCCTATTGCTCTT 59.603 41.667 0.00 0.00 0.00 2.85
2150 2521 5.675575 GCACACTTTGATCCTATTGCTCTTG 60.676 44.000 0.00 0.00 0.00 3.02
2151 2522 4.946157 ACACTTTGATCCTATTGCTCTTGG 59.054 41.667 0.00 0.00 0.00 3.61
2152 2523 3.950395 ACTTTGATCCTATTGCTCTTGGC 59.050 43.478 0.00 0.00 42.22 4.52
2224 2596 2.436417 GAAGCTGGCTGTGATTTGGTA 58.564 47.619 0.00 0.00 0.00 3.25
2228 2600 2.099756 GCTGGCTGTGATTTGGTATTCC 59.900 50.000 0.00 0.00 0.00 3.01
2254 2626 3.795877 AGTTTTGGCCATTGTTGAAGTG 58.204 40.909 6.09 0.00 0.00 3.16
2264 2636 3.951775 TTGTTGAAGTGTTTGGCAAGT 57.048 38.095 0.00 0.00 0.00 3.16
2265 2637 3.229276 TGTTGAAGTGTTTGGCAAGTG 57.771 42.857 0.00 0.00 0.00 3.16
2266 2638 2.822561 TGTTGAAGTGTTTGGCAAGTGA 59.177 40.909 0.00 0.00 0.00 3.41
2267 2639 3.446873 TGTTGAAGTGTTTGGCAAGTGAT 59.553 39.130 0.00 0.00 0.00 3.06
2268 2640 4.081752 TGTTGAAGTGTTTGGCAAGTGATT 60.082 37.500 0.00 0.00 0.00 2.57
2269 2641 4.305989 TGAAGTGTTTGGCAAGTGATTC 57.694 40.909 0.00 5.35 0.00 2.52
2270 2642 3.953612 TGAAGTGTTTGGCAAGTGATTCT 59.046 39.130 0.00 0.00 0.00 2.40
2271 2643 4.402155 TGAAGTGTTTGGCAAGTGATTCTT 59.598 37.500 0.00 1.51 36.75 2.52
2282 2654 3.228188 AGTGATTCTTGGGCTGTTTGA 57.772 42.857 0.00 0.00 0.00 2.69
2289 2661 5.840243 TTCTTGGGCTGTTTGATGATATG 57.160 39.130 0.00 0.00 0.00 1.78
2344 2716 2.612972 GCTTCTGTGTCCAAGATTCGGA 60.613 50.000 0.00 0.00 0.00 4.55
2345 2717 3.664107 CTTCTGTGTCCAAGATTCGGAA 58.336 45.455 0.00 0.00 33.29 4.30
2347 2719 5.414789 TTCTGTGTCCAAGATTCGGAATA 57.585 39.130 2.65 0.00 33.29 1.75
2383 2755 0.685785 TGGAAAGCTGGTGTTTGCCA 60.686 50.000 0.00 0.00 39.41 4.92
2489 2862 0.176680 CTCGGCACTGTTATCAGGCT 59.823 55.000 5.80 0.00 45.14 4.58
2505 2878 0.886563 GGCTGTGCTCAAAGCTGAAT 59.113 50.000 11.43 0.00 42.97 2.57
2507 2880 1.811359 GCTGTGCTCAAAGCTGAATCT 59.189 47.619 4.84 0.00 42.97 2.40
2513 2886 4.214119 GTGCTCAAAGCTGAATCTGTTGTA 59.786 41.667 0.11 0.00 42.97 2.41
2514 2887 5.005740 TGCTCAAAGCTGAATCTGTTGTAT 58.994 37.500 0.11 0.00 42.97 2.29
2515 2888 5.474532 TGCTCAAAGCTGAATCTGTTGTATT 59.525 36.000 0.11 0.00 42.97 1.89
2516 2889 5.798934 GCTCAAAGCTGAATCTGTTGTATTG 59.201 40.000 0.00 0.00 38.45 1.90
2520 2893 6.639632 AAGCTGAATCTGTTGTATTGTGTT 57.360 33.333 0.00 0.00 0.00 3.32
2521 2894 6.639632 AGCTGAATCTGTTGTATTGTGTTT 57.360 33.333 0.00 0.00 0.00 2.83
2522 2895 7.042797 AGCTGAATCTGTTGTATTGTGTTTT 57.957 32.000 0.00 0.00 0.00 2.43
2523 2896 8.165239 AGCTGAATCTGTTGTATTGTGTTTTA 57.835 30.769 0.00 0.00 0.00 1.52
2524 2897 8.292448 AGCTGAATCTGTTGTATTGTGTTTTAG 58.708 33.333 0.00 0.00 0.00 1.85
2525 2898 8.076178 GCTGAATCTGTTGTATTGTGTTTTAGT 58.924 33.333 0.00 0.00 0.00 2.24
2526 2899 9.950680 CTGAATCTGTTGTATTGTGTTTTAGTT 57.049 29.630 0.00 0.00 0.00 2.24
2529 2902 7.979115 TCTGTTGTATTGTGTTTTAGTTTGC 57.021 32.000 0.00 0.00 0.00 3.68
2530 2903 6.689241 TCTGTTGTATTGTGTTTTAGTTTGCG 59.311 34.615 0.00 0.00 0.00 4.85
2531 2904 6.323266 TGTTGTATTGTGTTTTAGTTTGCGT 58.677 32.000 0.00 0.00 0.00 5.24
2532 2905 6.807230 TGTTGTATTGTGTTTTAGTTTGCGTT 59.193 30.769 0.00 0.00 0.00 4.84
2533 2906 7.328737 TGTTGTATTGTGTTTTAGTTTGCGTTT 59.671 29.630 0.00 0.00 0.00 3.60
2534 2907 7.813852 TGTATTGTGTTTTAGTTTGCGTTTT 57.186 28.000 0.00 0.00 0.00 2.43
2535 2908 7.886696 TGTATTGTGTTTTAGTTTGCGTTTTC 58.113 30.769 0.00 0.00 0.00 2.29
2536 2909 6.952935 ATTGTGTTTTAGTTTGCGTTTTCA 57.047 29.167 0.00 0.00 0.00 2.69
2537 2910 5.748872 TGTGTTTTAGTTTGCGTTTTCAC 57.251 34.783 0.00 0.00 0.00 3.18
2538 2911 5.462405 TGTGTTTTAGTTTGCGTTTTCACT 58.538 33.333 0.00 0.00 0.00 3.41
2539 2912 5.343593 TGTGTTTTAGTTTGCGTTTTCACTG 59.656 36.000 0.00 0.00 0.00 3.66
2540 2913 5.569823 GTGTTTTAGTTTGCGTTTTCACTGA 59.430 36.000 0.00 0.00 0.00 3.41
2541 2914 6.252655 GTGTTTTAGTTTGCGTTTTCACTGAT 59.747 34.615 0.00 0.00 0.00 2.90
2542 2915 6.252441 TGTTTTAGTTTGCGTTTTCACTGATG 59.748 34.615 0.00 0.00 0.00 3.07
2543 2916 5.493133 TTAGTTTGCGTTTTCACTGATGT 57.507 34.783 0.00 0.00 0.00 3.06
2544 2917 6.606234 TTAGTTTGCGTTTTCACTGATGTA 57.394 33.333 0.00 0.00 0.00 2.29
2545 2918 5.689383 AGTTTGCGTTTTCACTGATGTAT 57.311 34.783 0.00 0.00 0.00 2.29
2546 2919 5.689819 AGTTTGCGTTTTCACTGATGTATC 58.310 37.500 0.00 0.00 0.00 2.24
2547 2920 5.238432 AGTTTGCGTTTTCACTGATGTATCA 59.762 36.000 0.00 0.00 35.16 2.15
2548 2921 5.878332 TTGCGTTTTCACTGATGTATCAT 57.122 34.783 0.00 0.00 36.02 2.45
2549 2922 5.220557 TGCGTTTTCACTGATGTATCATG 57.779 39.130 0.00 0.00 36.02 3.07
2550 2923 4.694982 TGCGTTTTCACTGATGTATCATGT 59.305 37.500 0.00 0.00 36.02 3.21
2551 2924 5.163864 TGCGTTTTCACTGATGTATCATGTC 60.164 40.000 0.00 0.00 36.02 3.06
2552 2925 5.727791 GCGTTTTCACTGATGTATCATGTCC 60.728 44.000 0.00 0.00 36.02 4.02
2553 2926 5.220662 CGTTTTCACTGATGTATCATGTCCC 60.221 44.000 0.00 0.00 36.02 4.46
2563 2936 8.506168 TGATGTATCATGTCCCTTTTACTTTC 57.494 34.615 0.00 0.00 0.00 2.62
2589 2996 6.809630 AAAAGGAGCTAATTCTCAGTTCAC 57.190 37.500 0.00 0.00 34.84 3.18
2603 3010 1.425066 AGTTCACCTTTGCCTGGATGA 59.575 47.619 0.00 0.00 0.00 2.92
2650 3057 4.410099 ACTGTTTGACCATGATGTTCCAT 58.590 39.130 0.00 0.00 0.00 3.41
2658 3065 8.681486 TTGACCATGATGTTCCATTATCTAAG 57.319 34.615 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.767816 TCTAAAAAGGAGCAGTTTTGTCC 57.232 39.130 0.00 0.00 0.00 4.02
1 2 9.914131 ATAAATCTAAAAAGGAGCAGTTTTGTC 57.086 29.630 0.00 0.00 0.00 3.18
2 3 9.914131 GATAAATCTAAAAAGGAGCAGTTTTGT 57.086 29.630 0.00 0.00 0.00 2.83
3 4 9.912634 TGATAAATCTAAAAAGGAGCAGTTTTG 57.087 29.630 0.00 0.00 0.00 2.44
5 6 8.246871 GCTGATAAATCTAAAAAGGAGCAGTTT 58.753 33.333 0.00 0.00 0.00 2.66
6 7 7.414540 CGCTGATAAATCTAAAAAGGAGCAGTT 60.415 37.037 0.00 0.00 0.00 3.16
7 8 6.037610 CGCTGATAAATCTAAAAAGGAGCAGT 59.962 38.462 0.00 0.00 0.00 4.40
8 9 6.258727 TCGCTGATAAATCTAAAAAGGAGCAG 59.741 38.462 0.00 0.00 0.00 4.24
28 29 9.559958 AAAATTTACACAGATCTAAAATCGCTG 57.440 29.630 0.00 0.00 0.00 5.18
56 57 8.642908 TGTAACATCTACACGGATCTAAAATG 57.357 34.615 0.00 0.00 0.00 2.32
267 516 0.756294 TGCGTCCCAGAGAGACAAAA 59.244 50.000 0.00 0.00 33.70 2.44
268 517 0.033504 GTGCGTCCCAGAGAGACAAA 59.966 55.000 0.00 0.00 33.70 2.83
330 579 7.739498 ATTAGGCGTACAATTTATTCGGATT 57.261 32.000 0.00 0.00 0.00 3.01
666 925 2.575735 TGGTGGTGCTGAAGGATGAATA 59.424 45.455 0.00 0.00 0.00 1.75
800 1062 2.740904 GCATAAGGTCGACCCCTGTAAC 60.741 54.545 30.82 11.11 34.19 2.50
864 1126 4.749099 CAGATGTAGTAATCAGGCTTCTGC 59.251 45.833 0.00 0.00 38.36 4.26
865 1127 5.911752 ACAGATGTAGTAATCAGGCTTCTG 58.088 41.667 4.45 4.45 39.78 3.02
866 1128 7.418025 GGTTACAGATGTAGTAATCAGGCTTCT 60.418 40.741 0.00 0.00 33.75 2.85
1073 1363 2.825836 GGATGCGTCTTGGCTGGG 60.826 66.667 5.77 0.00 0.00 4.45
1123 1416 2.966732 AATCACGGGCCGACATGGT 61.967 57.895 35.78 14.83 41.21 3.55
1244 1550 1.635487 ACACCATATCACCCAACTGCT 59.365 47.619 0.00 0.00 0.00 4.24
1296 1617 1.136446 GTACAATCCGTGCGACACAAC 60.136 52.381 9.95 0.00 33.40 3.32
1308 1629 3.930848 CCAAAGTGACGTAGGTACAATCC 59.069 47.826 0.00 0.00 0.00 3.01
1388 1712 3.044059 GCCACCATCGCTGACAAGC 62.044 63.158 0.00 0.00 46.66 4.01
1490 1817 2.153645 TGTTACAATGCAGCAGACTGG 58.846 47.619 0.00 0.00 44.63 4.00
1517 1844 8.879759 CGCTTTCTAGATTTCCTATAAACACAA 58.120 33.333 0.00 0.00 0.00 3.33
1525 1852 6.183360 TGCTCTTCGCTTTCTAGATTTCCTAT 60.183 38.462 0.00 0.00 40.11 2.57
1597 1927 5.748630 GGTTCTCAAACAATGGAAGTGAAAC 59.251 40.000 0.00 0.00 37.10 2.78
1620 1950 4.136796 TGTTCACACCATCTTCTTCTTGG 58.863 43.478 0.00 0.00 36.56 3.61
1634 1964 0.951040 CGGAGGCTCCTTGTTCACAC 60.951 60.000 29.81 1.02 33.30 3.82
1653 1983 5.402867 GCGTCTTTATAGCACTATGAGGAAC 59.597 44.000 0.30 0.00 0.00 3.62
1695 2037 5.006261 GGCACAACAAATAACAAGTCCAAAC 59.994 40.000 0.00 0.00 0.00 2.93
1708 2050 2.086610 ACTCCAAGGGCACAACAAAT 57.913 45.000 0.00 0.00 0.00 2.32
1906 2277 4.351111 AGTGAAAAGGGGAGAACAGTACAT 59.649 41.667 0.00 0.00 0.00 2.29
1943 2314 7.943952 CAATAATGCCGTTCGTGATTTTAAAA 58.056 30.769 2.51 2.51 0.00 1.52
1993 2364 5.502153 AGTACGTAAACTAGCCATCTCAG 57.498 43.478 0.00 0.00 0.00 3.35
2016 2387 7.168219 TCATGAAATGTTAAGCTACAGAAGGT 58.832 34.615 0.00 0.00 46.80 3.50
2053 2424 3.689347 AGCAATAGGATCAAAGTGTGCA 58.311 40.909 0.00 0.00 33.21 4.57
2087 2458 2.472695 ATGTTAAGTTGCTGGAGCGA 57.527 45.000 0.00 0.00 45.83 4.93
2088 2459 3.058293 TGAAATGTTAAGTTGCTGGAGCG 60.058 43.478 0.00 0.00 45.83 5.03
2089 2460 4.503741 TGAAATGTTAAGTTGCTGGAGC 57.496 40.909 0.00 0.00 42.50 4.70
2090 2461 6.258230 TCATGAAATGTTAAGTTGCTGGAG 57.742 37.500 0.00 0.00 46.80 3.86
2091 2462 6.839124 ATCATGAAATGTTAAGTTGCTGGA 57.161 33.333 0.00 0.00 46.80 3.86
2092 2463 7.318141 AGAATCATGAAATGTTAAGTTGCTGG 58.682 34.615 0.00 0.00 46.80 4.85
2093 2464 8.644619 CAAGAATCATGAAATGTTAAGTTGCTG 58.355 33.333 0.00 0.00 46.80 4.41
2094 2465 8.362639 ACAAGAATCATGAAATGTTAAGTTGCT 58.637 29.630 0.00 0.00 46.80 3.91
2095 2466 8.524870 ACAAGAATCATGAAATGTTAAGTTGC 57.475 30.769 0.00 0.00 46.80 4.17
2098 2469 9.903682 CTGAACAAGAATCATGAAATGTTAAGT 57.096 29.630 14.71 1.07 46.80 2.24
2099 2470 9.903682 ACTGAACAAGAATCATGAAATGTTAAG 57.096 29.630 19.20 19.20 46.80 1.85
2100 2471 9.681692 CACTGAACAAGAATCATGAAATGTTAA 57.318 29.630 14.71 9.50 46.80 2.01
2101 2472 7.809331 GCACTGAACAAGAATCATGAAATGTTA 59.191 33.333 14.71 6.85 46.80 2.41
2102 2473 6.643770 GCACTGAACAAGAATCATGAAATGTT 59.356 34.615 14.66 14.66 46.80 2.71
2103 2474 6.154445 GCACTGAACAAGAATCATGAAATGT 58.846 36.000 0.00 0.00 46.80 2.71
2105 2476 6.154445 GTGCACTGAACAAGAATCATGAAAT 58.846 36.000 10.32 0.00 0.00 2.17
2106 2477 5.067544 TGTGCACTGAACAAGAATCATGAAA 59.932 36.000 19.41 0.00 0.00 2.69
2107 2478 4.579753 TGTGCACTGAACAAGAATCATGAA 59.420 37.500 19.41 0.00 0.00 2.57
2108 2479 4.023792 GTGTGCACTGAACAAGAATCATGA 60.024 41.667 19.41 0.00 0.00 3.07
2109 2480 4.023450 AGTGTGCACTGAACAAGAATCATG 60.023 41.667 19.41 0.00 40.75 3.07
2110 2481 4.139786 AGTGTGCACTGAACAAGAATCAT 58.860 39.130 19.41 0.00 40.75 2.45
2111 2482 3.544684 AGTGTGCACTGAACAAGAATCA 58.455 40.909 19.41 0.00 40.75 2.57
2112 2483 4.558538 AAGTGTGCACTGAACAAGAATC 57.441 40.909 19.41 0.00 41.58 2.52
2113 2484 4.398988 TCAAAGTGTGCACTGAACAAGAAT 59.601 37.500 19.41 0.00 41.58 2.40
2114 2485 3.755905 TCAAAGTGTGCACTGAACAAGAA 59.244 39.130 19.41 0.00 41.58 2.52
2115 2486 3.342719 TCAAAGTGTGCACTGAACAAGA 58.657 40.909 19.41 4.76 41.58 3.02
2116 2487 3.763097 TCAAAGTGTGCACTGAACAAG 57.237 42.857 19.41 2.36 41.58 3.16
2117 2488 3.066621 GGATCAAAGTGTGCACTGAACAA 59.933 43.478 19.41 0.03 41.58 2.83
2118 2489 2.618241 GGATCAAAGTGTGCACTGAACA 59.382 45.455 19.41 0.00 41.58 3.18
2119 2490 2.880890 AGGATCAAAGTGTGCACTGAAC 59.119 45.455 19.41 11.50 41.58 3.18
2120 2491 3.213206 AGGATCAAAGTGTGCACTGAA 57.787 42.857 19.41 0.00 41.58 3.02
2121 2492 2.936919 AGGATCAAAGTGTGCACTGA 57.063 45.000 19.41 13.58 41.58 3.41
2122 2493 4.673580 GCAATAGGATCAAAGTGTGCACTG 60.674 45.833 19.41 7.99 41.58 3.66
2123 2494 3.441572 GCAATAGGATCAAAGTGTGCACT 59.558 43.478 19.41 0.00 44.94 4.40
2124 2495 3.441572 AGCAATAGGATCAAAGTGTGCAC 59.558 43.478 10.75 10.75 33.21 4.57
2125 2496 3.689347 AGCAATAGGATCAAAGTGTGCA 58.311 40.909 0.00 0.00 33.21 4.57
2126 2497 3.944015 AGAGCAATAGGATCAAAGTGTGC 59.056 43.478 0.00 0.00 33.23 4.57
2127 2498 5.163683 CCAAGAGCAATAGGATCAAAGTGTG 60.164 44.000 0.00 0.00 33.23 3.82
2128 2499 4.946157 CCAAGAGCAATAGGATCAAAGTGT 59.054 41.667 0.00 0.00 33.23 3.55
2129 2500 4.201990 GCCAAGAGCAATAGGATCAAAGTG 60.202 45.833 0.00 0.00 42.97 3.16
2130 2501 3.950395 GCCAAGAGCAATAGGATCAAAGT 59.050 43.478 0.00 0.00 42.97 2.66
2131 2502 4.564940 GCCAAGAGCAATAGGATCAAAG 57.435 45.455 0.00 0.00 42.97 2.77
2159 2530 1.146041 ACACAAGTTGCTGGAGCGA 59.854 52.632 1.81 0.00 45.83 4.93
2160 2531 1.280746 CACACAAGTTGCTGGAGCG 59.719 57.895 1.81 0.00 45.83 5.03
2161 2532 0.819259 TCCACACAAGTTGCTGGAGC 60.819 55.000 15.79 0.00 42.50 4.70
2162 2533 1.202687 TCTCCACACAAGTTGCTGGAG 60.203 52.381 29.04 29.04 45.59 3.86
2163 2534 0.836606 TCTCCACACAAGTTGCTGGA 59.163 50.000 17.82 17.82 35.41 3.86
2164 2535 1.901591 ATCTCCACACAAGTTGCTGG 58.098 50.000 12.24 12.24 0.00 4.85
2165 2536 3.996150 AAATCTCCACACAAGTTGCTG 57.004 42.857 1.81 3.49 0.00 4.41
2224 2596 1.846007 TGGCCAAAACTATGCGGAAT 58.154 45.000 0.61 0.00 0.00 3.01
2228 2600 2.652941 ACAATGGCCAAAACTATGCG 57.347 45.000 10.96 0.00 0.00 4.73
2264 2636 3.765381 TCATCAAACAGCCCAAGAATCA 58.235 40.909 0.00 0.00 0.00 2.57
2265 2637 4.996788 ATCATCAAACAGCCCAAGAATC 57.003 40.909 0.00 0.00 0.00 2.52
2266 2638 5.895534 ACATATCATCAAACAGCCCAAGAAT 59.104 36.000 0.00 0.00 0.00 2.40
2267 2639 5.263599 ACATATCATCAAACAGCCCAAGAA 58.736 37.500 0.00 0.00 0.00 2.52
2268 2640 4.858850 ACATATCATCAAACAGCCCAAGA 58.141 39.130 0.00 0.00 0.00 3.02
2269 2641 5.345702 CAACATATCATCAAACAGCCCAAG 58.654 41.667 0.00 0.00 0.00 3.61
2270 2642 4.160065 CCAACATATCATCAAACAGCCCAA 59.840 41.667 0.00 0.00 0.00 4.12
2271 2643 3.700539 CCAACATATCATCAAACAGCCCA 59.299 43.478 0.00 0.00 0.00 5.36
2272 2644 3.953612 TCCAACATATCATCAAACAGCCC 59.046 43.478 0.00 0.00 0.00 5.19
2273 2645 5.126061 ACTTCCAACATATCATCAAACAGCC 59.874 40.000 0.00 0.00 0.00 4.85
2282 2654 4.825634 CCAGCATCACTTCCAACATATCAT 59.174 41.667 0.00 0.00 0.00 2.45
2289 2661 0.251341 ACCCCAGCATCACTTCCAAC 60.251 55.000 0.00 0.00 0.00 3.77
2347 2719 8.195436 CAGCTTTCCAACATATTGATCAAGATT 58.805 33.333 12.82 0.00 38.15 2.40
2359 2731 3.243704 GCAAACACCAGCTTTCCAACATA 60.244 43.478 0.00 0.00 0.00 2.29
2391 2763 4.460263 TCAGCAGCCTTACAGAAAGAAAA 58.540 39.130 0.00 0.00 37.38 2.29
2392 2764 4.085357 TCAGCAGCCTTACAGAAAGAAA 57.915 40.909 0.00 0.00 37.38 2.52
2393 2765 3.769739 TCAGCAGCCTTACAGAAAGAA 57.230 42.857 0.00 0.00 37.38 2.52
2394 2766 3.008375 ACATCAGCAGCCTTACAGAAAGA 59.992 43.478 0.00 0.00 37.38 2.52
2395 2767 3.126514 CACATCAGCAGCCTTACAGAAAG 59.873 47.826 0.00 0.00 34.73 2.62
2410 2782 2.614779 ACGCAAGAGACATCACATCAG 58.385 47.619 0.00 0.00 43.62 2.90
2435 2807 7.006653 GCAAATCGGTTAAACACAAACAAAAAC 59.993 33.333 0.00 0.00 0.00 2.43
2484 2857 0.887836 TCAGCTTTGAGCACAGCCTG 60.888 55.000 5.10 0.00 45.56 4.85
2489 2862 2.854963 ACAGATTCAGCTTTGAGCACA 58.145 42.857 2.47 0.00 45.56 4.57
2505 2878 6.689241 CGCAAACTAAAACACAATACAACAGA 59.311 34.615 0.00 0.00 0.00 3.41
2507 2880 6.323266 ACGCAAACTAAAACACAATACAACA 58.677 32.000 0.00 0.00 0.00 3.33
2513 2886 6.588373 AGTGAAAACGCAAACTAAAACACAAT 59.412 30.769 0.00 0.00 0.00 2.71
2514 2887 5.921408 AGTGAAAACGCAAACTAAAACACAA 59.079 32.000 0.00 0.00 0.00 3.33
2515 2888 5.343593 CAGTGAAAACGCAAACTAAAACACA 59.656 36.000 0.00 0.00 0.00 3.72
2516 2889 5.569823 TCAGTGAAAACGCAAACTAAAACAC 59.430 36.000 0.00 0.00 0.00 3.32
2520 2893 5.885881 ACATCAGTGAAAACGCAAACTAAA 58.114 33.333 0.00 0.00 0.00 1.85
2521 2894 5.493133 ACATCAGTGAAAACGCAAACTAA 57.507 34.783 0.00 0.00 0.00 2.24
2522 2895 6.425417 TGATACATCAGTGAAAACGCAAACTA 59.575 34.615 0.00 0.00 32.11 2.24
2523 2896 5.238432 TGATACATCAGTGAAAACGCAAACT 59.762 36.000 0.00 0.00 32.11 2.66
2524 2897 5.448438 TGATACATCAGTGAAAACGCAAAC 58.552 37.500 0.00 0.00 32.11 2.93
2525 2898 5.681337 TGATACATCAGTGAAAACGCAAA 57.319 34.783 0.00 0.00 32.11 3.68
2526 2899 5.181056 ACATGATACATCAGTGAAAACGCAA 59.819 36.000 0.00 0.00 40.64 4.85
2527 2900 4.694982 ACATGATACATCAGTGAAAACGCA 59.305 37.500 0.00 0.00 40.64 5.24
2528 2901 5.221891 ACATGATACATCAGTGAAAACGC 57.778 39.130 0.00 0.00 40.64 4.84
2529 2902 5.220662 GGGACATGATACATCAGTGAAAACG 60.221 44.000 0.00 0.00 40.64 3.60
2530 2903 5.882557 AGGGACATGATACATCAGTGAAAAC 59.117 40.000 0.00 0.00 40.64 2.43
2531 2904 6.065976 AGGGACATGATACATCAGTGAAAA 57.934 37.500 0.00 0.00 40.64 2.29
2532 2905 5.698741 AGGGACATGATACATCAGTGAAA 57.301 39.130 0.00 0.00 40.64 2.69
2533 2906 5.698741 AAGGGACATGATACATCAGTGAA 57.301 39.130 0.00 0.00 40.64 3.18
2534 2907 5.698741 AAAGGGACATGATACATCAGTGA 57.301 39.130 0.00 0.00 40.64 3.41
2535 2908 7.050377 AGTAAAAGGGACATGATACATCAGTG 58.950 38.462 0.00 0.45 40.64 3.66
2536 2909 7.200434 AGTAAAAGGGACATGATACATCAGT 57.800 36.000 0.00 0.00 40.64 3.41
2537 2910 8.511604 AAAGTAAAAGGGACATGATACATCAG 57.488 34.615 0.00 0.00 40.64 2.90
2538 2911 8.106462 TGAAAGTAAAAGGGACATGATACATCA 58.894 33.333 0.00 0.00 41.70 3.07
2539 2912 8.506168 TGAAAGTAAAAGGGACATGATACATC 57.494 34.615 0.00 0.00 0.00 3.06
2540 2913 8.877864 TTGAAAGTAAAAGGGACATGATACAT 57.122 30.769 0.00 0.00 0.00 2.29
2541 2914 8.698973 TTTGAAAGTAAAAGGGACATGATACA 57.301 30.769 0.00 0.00 0.00 2.29
2542 2915 9.974980 TTTTTGAAAGTAAAAGGGACATGATAC 57.025 29.630 0.00 0.00 31.80 2.24
2569 2942 4.100373 AGGTGAACTGAGAATTAGCTCCT 58.900 43.478 0.00 0.00 33.95 3.69
2586 2993 1.704628 TCTTCATCCAGGCAAAGGTGA 59.295 47.619 0.00 0.00 0.00 4.02
2589 2996 5.738208 GCATAAATCTTCATCCAGGCAAAGG 60.738 44.000 0.00 0.00 0.00 3.11
2603 3010 7.227512 GTCACCATGTAAGCTAGCATAAATCTT 59.772 37.037 18.83 2.75 0.00 2.40


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

AutoCloner maintained by Alex Coulton.