Multiple sequence alignment - TraesCS1A01G203800

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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 TraesCS1A01G203800 chr1A 100.000 2933 0 0 1 2933 365535062 365537994 0.000000e+00 5417.0
1 TraesCS1A01G203800 chr1A 97.748 755 17 0 2179 2933 518800612 518799858 0.000000e+00 1301.0
2 TraesCS1A01G203800 chr1A 92.639 557 30 3 8 553 567362523 567363079 0.000000e+00 791.0
3 TraesCS1A01G203800 chr1A 92.266 556 32 3 8 552 586757355 586756800 0.000000e+00 778.0
4 TraesCS1A01G203800 chr1A 87.943 141 6 1 423 552 570881179 570881039 3.910000e-34 156.0
5 TraesCS1A01G203800 chr1B 91.494 1493 75 21 553 2019 394853032 394854498 0.000000e+00 2006.0
6 TraesCS1A01G203800 chr1B 92.683 41 3 0 2085 2125 598878349 598878309 3.160000e-05 60.2
7 TraesCS1A01G203800 chr1D 90.199 1510 85 23 553 2035 293593159 293594632 0.000000e+00 1910.0
8 TraesCS1A01G203800 chr1D 90.877 570 39 3 1 558 19875244 19874676 0.000000e+00 752.0
9 TraesCS1A01G203800 chr6A 97.351 755 17 2 2179 2933 290956068 290955317 0.000000e+00 1280.0
10 TraesCS1A01G203800 chr5D 95.926 761 27 2 2176 2933 338103992 338104751 0.000000e+00 1230.0
11 TraesCS1A01G203800 chr5A 95.395 760 22 6 2175 2933 620985173 620984426 0.000000e+00 1197.0
12 TraesCS1A01G203800 chr7A 94.444 756 17 2 2178 2933 512260748 512261478 0.000000e+00 1140.0
13 TraesCS1A01G203800 chr7A 92.086 556 33 4 8 552 561804633 561805188 0.000000e+00 773.0
14 TraesCS1A01G203800 chr7A 88.710 558 52 7 7 553 598223349 598222792 0.000000e+00 671.0
15 TraesCS1A01G203800 chr7A 97.143 35 1 0 2048 2082 70830107 70830141 3.160000e-05 60.2
16 TraesCS1A01G203800 chr2A 92.446 556 30 4 8 552 332039826 332040380 0.000000e+00 784.0
17 TraesCS1A01G203800 chr2A 91.516 554 36 4 11 553 758093202 758092649 0.000000e+00 752.0
18 TraesCS1A01G203800 chr2A 88.725 541 57 1 12 552 87688185 87687649 0.000000e+00 658.0
19 TraesCS1A01G203800 chr2A 89.130 46 5 0 2080 2125 726570878 726570923 1.140000e-04 58.4
20 TraesCS1A01G203800 chr4D 90.305 557 45 4 6 554 453054578 453054023 0.000000e+00 721.0
21 TraesCS1A01G203800 chr4D 85.612 417 27 13 148 552 463688741 463688346 9.790000e-110 407.0
22 TraesCS1A01G203800 chr4D 87.302 63 2 5 2055 2115 409174458 409174516 1.890000e-07 67.6
23 TraesCS1A01G203800 chr2D 90.054 553 32 4 11 552 89271071 89270531 0.000000e+00 695.0
24 TraesCS1A01G203800 chr2D 77.108 166 33 5 2169 2332 648346464 648346302 1.120000e-14 91.6
25 TraesCS1A01G203800 chr2D 100.000 29 0 0 2054 2082 394048609 394048581 1.000000e-03 54.7
26 TraesCS1A01G203800 chr3D 92.340 470 33 3 6 472 579551723 579551254 0.000000e+00 665.0
27 TraesCS1A01G203800 chr3D 86.792 159 10 1 405 552 403934744 403934586 1.810000e-37 167.0
28 TraesCS1A01G203800 chr3D 95.098 102 5 0 451 552 11368680 11368781 8.410000e-36 161.0
29 TraesCS1A01G203800 chr3D 83.436 163 22 5 2172 2334 23828058 23827901 2.360000e-31 147.0
30 TraesCS1A01G203800 chr3D 82.716 81 10 4 2047 2126 561463972 561463895 5.250000e-08 69.4
31 TraesCS1A01G203800 chr3D 96.970 33 1 0 2050 2082 329496865 329496897 4.080000e-04 56.5
32 TraesCS1A01G203800 chr6D 82.255 541 77 17 19 552 393407376 393407904 1.600000e-122 449.0
33 TraesCS1A01G203800 chr6D 78.912 147 29 2 2178 2323 291636329 291636184 6.690000e-17 99.0
34 TraesCS1A01G203800 chr6D 97.143 35 1 0 2048 2082 382702865 382702899 3.160000e-05 60.2
35 TraesCS1A01G203800 chr5B 85.034 441 56 9 2330 2766 696704964 696705398 9.650000e-120 440.0
36 TraesCS1A01G203800 chr5B 96.970 33 1 0 2050 2082 466218938 466218906 4.080000e-04 56.5
37 TraesCS1A01G203800 chr4A 86.740 181 17 6 2755 2929 614602614 614602793 8.290000e-46 195.0
38 TraesCS1A01G203800 chr3A 76.220 164 32 7 2172 2332 353164901 353165060 2.420000e-11 80.5
39 TraesCS1A01G203800 chr3A 91.667 48 4 0 2082 2129 131437507 131437554 1.890000e-07 67.6
40 TraesCS1A01G203800 chr3A 94.872 39 2 0 2087 2125 13512368 13512406 8.780000e-06 62.1
41 TraesCS1A01G203800 chr2B 84.416 77 9 3 2051 2125 51810342 51810417 4.050000e-09 73.1
42 TraesCS1A01G203800 chr6B 93.182 44 3 0 2085 2128 288782507 288782464 6.780000e-07 65.8
43 TraesCS1A01G203800 chr7B 88.462 52 3 3 2121 2170 328806425 328806475 3.160000e-05 60.2
44 TraesCS1A01G203800 chr7B 97.059 34 1 0 2048 2081 692361065 692361098 1.140000e-04 58.4
45 TraesCS1A01G203800 chr4B 89.130 46 4 1 2081 2126 104816373 104816329 4.080000e-04 56.5


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 TraesCS1A01G203800 chr1A 365535062 365537994 2932 False 5417 5417 100.000 1 2933 1 chr1A.!!$F1 2932
1 TraesCS1A01G203800 chr1A 518799858 518800612 754 True 1301 1301 97.748 2179 2933 1 chr1A.!!$R1 754
2 TraesCS1A01G203800 chr1A 567362523 567363079 556 False 791 791 92.639 8 553 1 chr1A.!!$F2 545
3 TraesCS1A01G203800 chr1A 586756800 586757355 555 True 778 778 92.266 8 552 1 chr1A.!!$R3 544
4 TraesCS1A01G203800 chr1B 394853032 394854498 1466 False 2006 2006 91.494 553 2019 1 chr1B.!!$F1 1466
5 TraesCS1A01G203800 chr1D 293593159 293594632 1473 False 1910 1910 90.199 553 2035 1 chr1D.!!$F1 1482
6 TraesCS1A01G203800 chr1D 19874676 19875244 568 True 752 752 90.877 1 558 1 chr1D.!!$R1 557
7 TraesCS1A01G203800 chr6A 290955317 290956068 751 True 1280 1280 97.351 2179 2933 1 chr6A.!!$R1 754
8 TraesCS1A01G203800 chr5D 338103992 338104751 759 False 1230 1230 95.926 2176 2933 1 chr5D.!!$F1 757
9 TraesCS1A01G203800 chr5A 620984426 620985173 747 True 1197 1197 95.395 2175 2933 1 chr5A.!!$R1 758
10 TraesCS1A01G203800 chr7A 512260748 512261478 730 False 1140 1140 94.444 2178 2933 1 chr7A.!!$F2 755
11 TraesCS1A01G203800 chr7A 561804633 561805188 555 False 773 773 92.086 8 552 1 chr7A.!!$F3 544
12 TraesCS1A01G203800 chr7A 598222792 598223349 557 True 671 671 88.710 7 553 1 chr7A.!!$R1 546
13 TraesCS1A01G203800 chr2A 332039826 332040380 554 False 784 784 92.446 8 552 1 chr2A.!!$F1 544
14 TraesCS1A01G203800 chr2A 758092649 758093202 553 True 752 752 91.516 11 553 1 chr2A.!!$R2 542
15 TraesCS1A01G203800 chr2A 87687649 87688185 536 True 658 658 88.725 12 552 1 chr2A.!!$R1 540
16 TraesCS1A01G203800 chr4D 453054023 453054578 555 True 721 721 90.305 6 554 1 chr4D.!!$R1 548
17 TraesCS1A01G203800 chr2D 89270531 89271071 540 True 695 695 90.054 11 552 1 chr2D.!!$R1 541
18 TraesCS1A01G203800 chr6D 393407376 393407904 528 False 449 449 82.255 19 552 1 chr6D.!!$F2 533

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
587 625 0.526524 CTCTCGTCGGATTGAGGTGC 60.527 60.0 9.45 0.0 34.12 5.01 F
1577 1669 0.098025 ATTTTTGCCGTATCACCGCG 59.902 50.0 0.00 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1979 0.103208 GGTCGACCCTGCTGATGTAG 59.897 60.000 24.75 0.0 0.00 2.74 R
2643 2735 3.523564 AGGGGCAGACATATAAGTGTTGT 59.476 43.478 0.00 0.0 31.16 3.32 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
27 29 7.721286 TTGCGGTAAAATTGACAAATTTGAT 57.279 28.000 24.64 8.92 43.63 2.57
126 141 3.418675 CGAAGGCGTCACACTACAT 57.581 52.632 0.55 0.00 0.00 2.29
134 149 2.662791 GCGTCACACTACATTGTGCAAG 60.663 50.000 0.00 0.00 45.58 4.01
230 246 2.506061 CCTGAGAGCTAGGCGCCAT 61.506 63.158 31.54 16.46 40.39 4.40
241 257 5.938279 AGCTAGGCGCCATACTATATAGTA 58.062 41.667 31.54 21.91 40.25 1.82
418 434 4.347096 CGTTGGCCAGACGTGTAA 57.653 55.556 23.72 0.00 35.88 2.41
420 436 0.876777 CGTTGGCCAGACGTGTAACA 60.877 55.000 23.72 0.00 35.74 2.41
525 563 7.999878 CAGTTCATTTTGTGATTTGATTTCGTG 59.000 33.333 0.00 0.00 36.54 4.35
559 597 5.511234 TTTGTCAAATTTGCCCCATTTTG 57.489 34.783 13.54 0.00 0.00 2.44
575 613 2.781595 TTTGCGGGCTTCCTCTCGTC 62.782 60.000 0.00 0.00 0.00 4.20
587 625 0.526524 CTCTCGTCGGATTGAGGTGC 60.527 60.000 9.45 0.00 34.12 5.01
619 660 7.095229 GCATGAACTATGTCTGTTGAGTTGTTA 60.095 37.037 0.00 0.00 39.08 2.41
637 678 9.950680 GAGTTGTTAACAATCTTCAGAAATCAA 57.049 29.630 23.11 0.00 38.24 2.57
647 688 5.827666 TCTTCAGAAATCAAAACCGTTTCC 58.172 37.500 0.00 0.00 33.46 3.13
687 728 5.568685 TCGAGAAGACAAAGGTAGATCAG 57.431 43.478 0.00 0.00 0.00 2.90
698 739 5.568620 AAGGTAGATCAGTTGACTTTGGT 57.431 39.130 0.00 0.00 0.00 3.67
701 742 4.870991 GGTAGATCAGTTGACTTTGGTAGC 59.129 45.833 0.00 0.00 0.00 3.58
702 743 4.899352 AGATCAGTTGACTTTGGTAGCT 57.101 40.909 0.00 0.00 0.00 3.32
703 744 6.127423 GGTAGATCAGTTGACTTTGGTAGCTA 60.127 42.308 0.00 0.00 0.00 3.32
704 745 5.971763 AGATCAGTTGACTTTGGTAGCTAG 58.028 41.667 0.00 0.00 0.00 3.42
705 746 3.926616 TCAGTTGACTTTGGTAGCTAGC 58.073 45.455 16.08 16.08 0.00 3.42
706 747 3.578716 TCAGTTGACTTTGGTAGCTAGCT 59.421 43.478 23.12 23.12 0.00 3.32
711 752 6.996282 AGTTGACTTTGGTAGCTAGCTAAAAA 59.004 34.615 25.74 23.98 0.00 1.94
746 787 8.554528 CAAAAACTCGCTATGTTGAGATGATAT 58.445 33.333 0.00 0.00 36.11 1.63
774 843 5.975939 GCAAAATCTTGGCATAGAGAACATC 59.024 40.000 0.00 0.00 32.76 3.06
876 945 1.359848 CATCGTGGTACAGCTCAACC 58.640 55.000 7.01 7.01 41.80 3.77
879 948 0.892755 CGTGGTACAGCTCAACCCTA 59.107 55.000 10.77 0.00 41.80 3.53
992 1070 6.816640 TCACAGTATCGGAAAATTACTGAAGG 59.183 38.462 18.50 10.27 40.19 3.46
993 1071 6.594159 CACAGTATCGGAAAATTACTGAAGGT 59.406 38.462 18.50 0.00 40.19 3.50
1299 1377 4.373116 GCGCCGGACCAAGACTCA 62.373 66.667 5.05 0.00 0.00 3.41
1330 1408 3.653344 TGTGAGACAGTCATGTAAGCAC 58.347 45.455 2.66 0.00 40.68 4.40
1332 1410 4.522789 TGTGAGACAGTCATGTAAGCACTA 59.477 41.667 2.66 0.00 40.68 2.74
1333 1411 5.010617 TGTGAGACAGTCATGTAAGCACTAA 59.989 40.000 2.66 0.00 40.68 2.24
1338 1417 4.262635 ACAGTCATGTAAGCACTAAGCACT 60.263 41.667 0.00 0.00 41.73 4.40
1345 1424 2.743195 GCACTAAGCACTCGTCTGG 58.257 57.895 0.00 0.00 44.79 3.86
1359 1438 2.944349 TCGTCTGGTGTGCGTACATATA 59.056 45.455 10.21 0.00 39.39 0.86
1360 1439 3.566742 TCGTCTGGTGTGCGTACATATAT 59.433 43.478 10.21 0.00 39.39 0.86
1369 1448 7.033791 GGTGTGCGTACATATATAGCTTGTAT 58.966 38.462 10.21 0.00 39.39 2.29
1418 1502 4.828925 GCAGGAGGAGGTGCTCGC 62.829 72.222 0.00 0.00 36.71 5.03
1435 1519 2.908015 CGGTACCACATCAGGGGG 59.092 66.667 13.54 0.00 0.00 5.40
1436 1520 1.687840 CGGTACCACATCAGGGGGA 60.688 63.158 13.54 0.00 0.00 4.81
1567 1659 3.060339 GCACAACTCAGAAATTTTTGCCG 60.060 43.478 3.87 1.05 0.00 5.69
1569 1661 5.277825 CACAACTCAGAAATTTTTGCCGTA 58.722 37.500 3.87 0.00 0.00 4.02
1570 1662 5.920273 CACAACTCAGAAATTTTTGCCGTAT 59.080 36.000 3.87 0.00 0.00 3.06
1577 1669 0.098025 ATTTTTGCCGTATCACCGCG 59.902 50.000 0.00 0.00 0.00 6.46
1591 1683 3.132160 TCACCGCGTATTTCTTGAAACA 58.868 40.909 4.92 0.00 0.00 2.83
1597 1689 4.558470 CGCGTATTTCTTGAAACATGCATT 59.442 37.500 15.76 0.00 0.00 3.56
1695 1787 1.958715 CGTGTTGATGTGGTCGCCA 60.959 57.895 0.00 0.00 0.00 5.69
1800 1892 1.000233 TCTAAACGGGGAGCCGGTA 60.000 57.895 1.90 0.00 36.03 4.02
1821 1913 1.220749 CATGTACACTGACCCGGGG 59.779 63.158 27.92 12.73 0.00 5.73
1924 2016 3.217626 GACCTCACCAAATCATCCATCC 58.782 50.000 0.00 0.00 0.00 3.51
1937 2029 1.722034 TCCATCCAAGCCTAGCTAGG 58.278 55.000 32.12 32.12 46.42 3.02
1938 2030 1.220493 TCCATCCAAGCCTAGCTAGGA 59.780 52.381 38.74 20.92 46.63 2.94
1939 2031 1.346068 CCATCCAAGCCTAGCTAGGAC 59.654 57.143 38.74 28.65 46.63 3.85
1942 2034 1.043673 CCAAGCCTAGCTAGGACGGT 61.044 60.000 38.74 20.79 46.63 4.83
1944 2036 0.756070 AAGCCTAGCTAGGACGGTCC 60.756 60.000 38.74 21.64 46.63 4.46
1946 2038 2.553727 CCTAGCTAGGACGGTCCGC 61.554 68.421 32.79 18.45 46.63 5.54
1947 2039 1.526455 CTAGCTAGGACGGTCCGCT 60.526 63.158 25.85 25.85 42.75 5.52
1948 2040 1.508808 CTAGCTAGGACGGTCCGCTC 61.509 65.000 26.20 16.77 42.75 5.03
1956 2048 2.105128 CGGTCCGCTCACTCATCC 59.895 66.667 0.00 0.00 0.00 3.51
1962 2054 0.385029 CCGCTCACTCATCCTCTCTG 59.615 60.000 0.00 0.00 0.00 3.35
1984 2076 6.590292 TCTGGATTGAGTAATTGTTCGTTCTC 59.410 38.462 0.00 0.00 0.00 2.87
1985 2077 6.227522 TGGATTGAGTAATTGTTCGTTCTCA 58.772 36.000 0.00 0.00 0.00 3.27
1986 2078 6.878923 TGGATTGAGTAATTGTTCGTTCTCAT 59.121 34.615 0.00 0.00 33.10 2.90
1987 2079 7.148423 TGGATTGAGTAATTGTTCGTTCTCATG 60.148 37.037 0.00 0.00 33.10 3.07
1988 2080 6.480524 TTGAGTAATTGTTCGTTCTCATGG 57.519 37.500 0.00 0.00 33.10 3.66
1989 2081 5.789521 TGAGTAATTGTTCGTTCTCATGGA 58.210 37.500 0.00 0.00 0.00 3.41
1990 2082 6.227522 TGAGTAATTGTTCGTTCTCATGGAA 58.772 36.000 0.00 0.00 0.00 3.53
1991 2083 6.878923 TGAGTAATTGTTCGTTCTCATGGAAT 59.121 34.615 0.00 0.00 36.24 3.01
1992 2084 7.064609 TGAGTAATTGTTCGTTCTCATGGAATC 59.935 37.037 0.00 0.00 36.24 2.52
2009 2101 3.310774 GGAATCATGATGAACTCGTGGTG 59.689 47.826 9.46 0.00 40.68 4.17
2037 2129 2.452600 TTTTGAAGGGGAGTTGTGCT 57.547 45.000 0.00 0.00 0.00 4.40
2038 2130 2.452600 TTTGAAGGGGAGTTGTGCTT 57.547 45.000 0.00 0.00 0.00 3.91
2039 2131 2.452600 TTGAAGGGGAGTTGTGCTTT 57.547 45.000 0.00 0.00 0.00 3.51
2040 2132 2.452600 TGAAGGGGAGTTGTGCTTTT 57.547 45.000 0.00 0.00 0.00 2.27
2041 2133 2.745968 TGAAGGGGAGTTGTGCTTTTT 58.254 42.857 0.00 0.00 0.00 1.94
2061 2153 5.750352 TTTTTCAGTACTATTCCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
2062 2154 4.996788 TTTCAGTACTATTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
2063 2155 2.941480 TCAGTACTATTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
2064 2156 1.962100 CAGTACTATTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
2065 2157 1.572415 AGTACTATTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
2066 2158 2.179424 AGTACTATTCCCTCCGTCCCAT 59.821 50.000 0.00 0.00 0.00 4.00
2067 2159 3.400322 AGTACTATTCCCTCCGTCCCATA 59.600 47.826 0.00 0.00 0.00 2.74
2068 2160 3.339713 ACTATTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2069 2161 3.870559 ACTATTCCCTCCGTCCCATAAT 58.129 45.455 0.00 0.00 0.00 1.28
2070 2162 5.019657 ACTATTCCCTCCGTCCCATAATA 57.980 43.478 0.00 0.00 0.00 0.98
2071 2163 5.600749 ACTATTCCCTCCGTCCCATAATAT 58.399 41.667 0.00 0.00 0.00 1.28
2072 2164 6.748969 ACTATTCCCTCCGTCCCATAATATA 58.251 40.000 0.00 0.00 0.00 0.86
2073 2165 7.194050 ACTATTCCCTCCGTCCCATAATATAA 58.806 38.462 0.00 0.00 0.00 0.98
2074 2166 6.963117 ATTCCCTCCGTCCCATAATATAAA 57.037 37.500 0.00 0.00 0.00 1.40
2075 2167 6.766997 TTCCCTCCGTCCCATAATATAAAA 57.233 37.500 0.00 0.00 0.00 1.52
2076 2168 6.368779 TCCCTCCGTCCCATAATATAAAAG 57.631 41.667 0.00 0.00 0.00 2.27
2077 2169 4.941873 CCCTCCGTCCCATAATATAAAAGC 59.058 45.833 0.00 0.00 0.00 3.51
2078 2170 5.514136 CCCTCCGTCCCATAATATAAAAGCA 60.514 44.000 0.00 0.00 0.00 3.91
2079 2171 6.180472 CCTCCGTCCCATAATATAAAAGCAT 58.820 40.000 0.00 0.00 0.00 3.79
2080 2172 6.659242 CCTCCGTCCCATAATATAAAAGCATT 59.341 38.462 0.00 0.00 0.00 3.56
2081 2173 7.176690 CCTCCGTCCCATAATATAAAAGCATTT 59.823 37.037 0.00 0.00 42.41 2.32
2082 2174 9.226606 CTCCGTCCCATAATATAAAAGCATTTA 57.773 33.333 0.00 0.00 37.28 1.40
2083 2175 9.575868 TCCGTCCCATAATATAAAAGCATTTAA 57.424 29.630 0.00 0.00 37.28 1.52
2115 2207 9.712305 AAAACATCCTTATATTATGAGACGGAG 57.288 33.333 0.00 0.00 0.00 4.63
2116 2208 7.411486 ACATCCTTATATTATGAGACGGAGG 57.589 40.000 0.00 0.00 0.00 4.30
2117 2209 6.381420 ACATCCTTATATTATGAGACGGAGGG 59.619 42.308 0.00 0.00 0.00 4.30
2118 2210 6.148735 TCCTTATATTATGAGACGGAGGGA 57.851 41.667 0.00 0.00 0.00 4.20
2119 2211 6.188407 TCCTTATATTATGAGACGGAGGGAG 58.812 44.000 0.00 0.00 0.00 4.30
2120 2212 5.952947 CCTTATATTATGAGACGGAGGGAGT 59.047 44.000 0.00 0.00 0.00 3.85
2121 2213 7.037080 TCCTTATATTATGAGACGGAGGGAGTA 60.037 40.741 0.00 0.00 0.00 2.59
2122 2214 7.283580 CCTTATATTATGAGACGGAGGGAGTAG 59.716 44.444 0.00 0.00 0.00 2.57
2123 2215 4.726035 ATTATGAGACGGAGGGAGTAGA 57.274 45.455 0.00 0.00 0.00 2.59
2124 2216 4.726035 TTATGAGACGGAGGGAGTAGAT 57.274 45.455 0.00 0.00 0.00 1.98
2125 2217 5.837770 TTATGAGACGGAGGGAGTAGATA 57.162 43.478 0.00 0.00 0.00 1.98
2126 2218 4.726035 ATGAGACGGAGGGAGTAGATAA 57.274 45.455 0.00 0.00 0.00 1.75
2127 2219 4.726035 TGAGACGGAGGGAGTAGATAAT 57.274 45.455 0.00 0.00 0.00 1.28
2128 2220 5.837770 TGAGACGGAGGGAGTAGATAATA 57.162 43.478 0.00 0.00 0.00 0.98
2129 2221 5.558818 TGAGACGGAGGGAGTAGATAATAC 58.441 45.833 0.00 0.00 0.00 1.89
2130 2222 4.920999 AGACGGAGGGAGTAGATAATACC 58.079 47.826 0.00 0.00 0.00 2.73
2131 2223 4.015764 GACGGAGGGAGTAGATAATACCC 58.984 52.174 0.00 0.00 40.71 3.69
2132 2224 3.245550 ACGGAGGGAGTAGATAATACCCC 60.246 52.174 0.00 0.00 41.26 4.95
2133 2225 3.245514 CGGAGGGAGTAGATAATACCCCA 60.246 52.174 0.00 0.00 41.26 4.96
2134 2226 4.095211 GGAGGGAGTAGATAATACCCCAC 58.905 52.174 0.00 0.00 41.26 4.61
2135 2227 4.450265 GGAGGGAGTAGATAATACCCCACA 60.450 50.000 0.00 0.00 41.26 4.17
2136 2228 5.342866 GAGGGAGTAGATAATACCCCACAT 58.657 45.833 0.00 0.00 41.26 3.21
2137 2229 5.342866 AGGGAGTAGATAATACCCCACATC 58.657 45.833 0.00 0.00 41.26 3.06
2138 2230 5.078006 AGGGAGTAGATAATACCCCACATCT 59.922 44.000 0.00 0.00 41.26 2.90
2139 2231 5.187967 GGGAGTAGATAATACCCCACATCTG 59.812 48.000 0.00 0.00 35.00 2.90
2140 2232 5.780793 GGAGTAGATAATACCCCACATCTGT 59.219 44.000 0.00 0.00 0.00 3.41
2141 2233 6.270231 GGAGTAGATAATACCCCACATCTGTT 59.730 42.308 0.00 0.00 0.00 3.16
2142 2234 7.067496 AGTAGATAATACCCCACATCTGTTG 57.933 40.000 0.00 0.00 0.00 3.33
2143 2235 4.718961 AGATAATACCCCACATCTGTTGC 58.281 43.478 0.00 0.00 0.00 4.17
2144 2236 2.897271 AATACCCCACATCTGTTGCA 57.103 45.000 0.00 0.00 0.00 4.08
2145 2237 2.425143 ATACCCCACATCTGTTGCAG 57.575 50.000 0.00 0.00 0.00 4.41
2146 2238 1.357137 TACCCCACATCTGTTGCAGA 58.643 50.000 1.06 1.06 44.99 4.26
2147 2239 0.478072 ACCCCACATCTGTTGCAGAA 59.522 50.000 2.80 0.00 44.04 3.02
2148 2240 1.133513 ACCCCACATCTGTTGCAGAAA 60.134 47.619 2.80 0.00 44.04 2.52
2149 2241 2.173519 CCCCACATCTGTTGCAGAAAT 58.826 47.619 2.80 0.00 44.04 2.17
2150 2242 3.245229 ACCCCACATCTGTTGCAGAAATA 60.245 43.478 2.80 0.00 44.04 1.40
2151 2243 3.956199 CCCCACATCTGTTGCAGAAATAT 59.044 43.478 2.80 0.00 44.04 1.28
2152 2244 4.403432 CCCCACATCTGTTGCAGAAATATT 59.597 41.667 2.80 0.00 44.04 1.28
2153 2245 5.105228 CCCCACATCTGTTGCAGAAATATTT 60.105 40.000 0.00 0.00 44.04 1.40
2154 2246 6.400568 CCCACATCTGTTGCAGAAATATTTT 58.599 36.000 1.43 0.00 44.04 1.82
2155 2247 6.311935 CCCACATCTGTTGCAGAAATATTTTG 59.688 38.462 1.43 4.42 44.04 2.44
2156 2248 6.183360 CCACATCTGTTGCAGAAATATTTTGC 60.183 38.462 19.68 19.68 44.04 3.68
2157 2249 6.366604 CACATCTGTTGCAGAAATATTTTGCA 59.633 34.615 22.79 22.79 44.04 4.08
2377 2469 7.040340 TGACGATTCTAATCCTAAAGAGCCTAG 60.040 40.741 0.00 0.00 31.68 3.02
2597 2689 4.504858 CTTACGTAATGCCTCTCACCTTT 58.495 43.478 8.76 0.00 0.00 3.11
2626 2718 7.173562 AGTTGCATTATTTTTGTTGCACATCAT 59.826 29.630 0.00 0.00 44.16 2.45
2855 2952 5.048991 GCCATTCGAAACCGGTATTTCATAT 60.049 40.000 8.00 2.35 38.30 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.151308 AGATCAAATTTGTCAATTTTACCGCA 58.849 30.769 17.47 0.00 40.09 5.69
126 141 3.181451 CCTATCTATGAGGCCTTGCACAA 60.181 47.826 6.77 0.00 0.00 3.33
420 436 0.108138 GCAACGCCTCACAGATAGGT 60.108 55.000 0.00 0.00 36.43 3.08
455 493 1.021968 GACCTTTTTGTGTGACGCCT 58.978 50.000 0.00 0.00 0.00 5.52
525 563 5.989551 AATTTGACAAATTTGACCTGTGC 57.010 34.783 24.64 5.45 37.84 4.57
559 597 4.856607 CGACGAGAGGAAGCCCGC 62.857 72.222 0.00 0.00 37.58 6.13
587 625 8.877808 TCAACAGACATAGTTCATGCTATAAG 57.122 34.615 0.00 0.00 38.29 1.73
606 647 7.919690 TCTGAAGATTGTTAACAACTCAACAG 58.080 34.615 22.78 24.42 38.86 3.16
619 660 6.805713 ACGGTTTTGATTTCTGAAGATTGTT 58.194 32.000 0.00 0.00 0.00 2.83
637 678 4.705991 TGAAACTTAAGTGGGAAACGGTTT 59.294 37.500 9.34 5.68 0.00 3.27
647 688 4.994852 TCTCGATTGGTGAAACTTAAGTGG 59.005 41.667 9.34 0.00 36.74 4.00
687 728 6.796705 TTTTAGCTAGCTACCAAAGTCAAC 57.203 37.500 24.09 0.00 0.00 3.18
711 752 1.963515 AGCGAGTTTTTGCCAAGGATT 59.036 42.857 0.00 0.00 33.93 3.01
746 787 4.699735 TCTCTATGCCAAGATTTTGCGAAA 59.300 37.500 0.53 0.53 32.79 3.46
774 843 7.805542 CCATTCTGTACTCTGTAGATGATAACG 59.194 40.741 0.00 0.00 0.00 3.18
876 945 3.745975 TGCTTCTCGTTTGTCATGTTAGG 59.254 43.478 0.00 0.00 0.00 2.69
879 948 3.814842 TGATGCTTCTCGTTTGTCATGTT 59.185 39.130 0.88 0.00 0.00 2.71
1317 1395 4.499183 GAGTGCTTAGTGCTTACATGACT 58.501 43.478 0.00 0.00 43.37 3.41
1330 1408 1.702886 CACACCAGACGAGTGCTTAG 58.297 55.000 0.00 0.00 38.87 2.18
1332 1410 4.758692 CACACCAGACGAGTGCTT 57.241 55.556 0.00 0.00 38.87 3.91
1338 1417 1.166989 TATGTACGCACACCAGACGA 58.833 50.000 0.00 0.00 37.54 4.20
1341 1420 4.765339 AGCTATATATGTACGCACACCAGA 59.235 41.667 0.00 0.00 37.54 3.86
1343 1422 5.221362 ACAAGCTATATATGTACGCACACCA 60.221 40.000 0.00 0.00 37.54 4.17
1345 1424 7.462856 GCATACAAGCTATATATGTACGCACAC 60.463 40.741 8.30 0.00 38.29 3.82
1359 1438 3.006217 TCAGATCGCAGCATACAAGCTAT 59.994 43.478 0.00 0.00 44.54 2.97
1360 1439 2.362077 TCAGATCGCAGCATACAAGCTA 59.638 45.455 0.00 0.00 44.54 3.32
1369 1448 4.819761 GCCGGTCAGATCGCAGCA 62.820 66.667 1.90 0.00 0.00 4.41
1418 1502 1.268992 TTCCCCCTGATGTGGTACCG 61.269 60.000 7.57 0.00 0.00 4.02
1435 1519 2.594592 ACCGTGCCTGCCTTGTTC 60.595 61.111 0.00 0.00 0.00 3.18
1436 1520 2.906897 CACCGTGCCTGCCTTGTT 60.907 61.111 0.00 0.00 0.00 2.83
1509 1593 4.715130 TCCAGTACCGGCCCTGCT 62.715 66.667 14.04 0.00 0.00 4.24
1510 1594 3.462199 GATCCAGTACCGGCCCTGC 62.462 68.421 14.04 0.00 0.00 4.85
1511 1595 2.822399 GATCCAGTACCGGCCCTG 59.178 66.667 12.82 12.82 0.00 4.45
1551 1635 5.095490 GGTGATACGGCAAAAATTTCTGAG 58.905 41.667 0.00 0.00 0.00 3.35
1553 1637 3.851403 CGGTGATACGGCAAAAATTTCTG 59.149 43.478 0.00 0.00 0.00 3.02
1554 1638 3.672241 GCGGTGATACGGCAAAAATTTCT 60.672 43.478 6.63 0.00 42.97 2.52
1560 1652 0.389556 TACGCGGTGATACGGCAAAA 60.390 50.000 12.47 0.00 43.54 2.44
1567 1659 5.163933 TGTTTCAAGAAATACGCGGTGATAC 60.164 40.000 12.47 7.79 32.36 2.24
1569 1661 3.749088 TGTTTCAAGAAATACGCGGTGAT 59.251 39.130 12.47 0.00 32.36 3.06
1570 1662 3.132160 TGTTTCAAGAAATACGCGGTGA 58.868 40.909 12.47 0.00 32.36 4.02
1591 1683 8.268052 CGCGATTTGATTAATTTTACAATGCAT 58.732 29.630 0.00 0.00 0.00 3.96
1597 1689 6.034044 GGCAACGCGATTTGATTAATTTTACA 59.966 34.615 15.93 0.00 0.00 2.41
1651 1743 4.767255 CAGCGTCCTCCCCTGCAC 62.767 72.222 0.00 0.00 0.00 4.57
1654 1746 4.463879 CTGCAGCGTCCTCCCCTG 62.464 72.222 0.00 0.00 0.00 4.45
1695 1787 2.034879 CACGAGCTTCCGCACCAAT 61.035 57.895 0.00 0.00 39.10 3.16
1800 1892 0.323629 CCGGGTCAGTGTACATGGTT 59.676 55.000 0.00 0.00 0.00 3.67
1887 1979 0.103208 GGTCGACCCTGCTGATGTAG 59.897 60.000 24.75 0.00 0.00 2.74
1924 2016 0.386113 GACCGTCCTAGCTAGGCTTG 59.614 60.000 31.76 22.99 43.31 4.01
1937 2029 1.226717 GATGAGTGAGCGGACCGTC 60.227 63.158 16.73 12.11 0.00 4.79
1938 2030 2.711922 GGATGAGTGAGCGGACCGT 61.712 63.158 16.73 1.83 0.00 4.83
1939 2031 2.105128 GGATGAGTGAGCGGACCG 59.895 66.667 10.29 10.29 0.00 4.79
1942 2034 0.257328 AGAGAGGATGAGTGAGCGGA 59.743 55.000 0.00 0.00 0.00 5.54
1944 2036 0.385029 CCAGAGAGGATGAGTGAGCG 59.615 60.000 0.00 0.00 41.22 5.03
1956 2048 6.102663 ACGAACAATTACTCAATCCAGAGAG 58.897 40.000 0.00 0.00 38.98 3.20
1962 2054 6.721571 TGAGAACGAACAATTACTCAATCC 57.278 37.500 0.00 0.00 32.66 3.01
1969 2061 7.072177 TGATTCCATGAGAACGAACAATTAC 57.928 36.000 0.00 0.00 37.29 1.89
1985 2077 4.132336 CCACGAGTTCATCATGATTCCAT 58.868 43.478 5.16 0.00 0.00 3.41
1986 2078 3.055167 ACCACGAGTTCATCATGATTCCA 60.055 43.478 5.16 0.00 0.00 3.53
1987 2079 3.310774 CACCACGAGTTCATCATGATTCC 59.689 47.826 5.16 0.00 0.00 3.01
1988 2080 3.242543 GCACCACGAGTTCATCATGATTC 60.243 47.826 5.16 0.00 0.00 2.52
1989 2081 2.679837 GCACCACGAGTTCATCATGATT 59.320 45.455 5.16 0.00 0.00 2.57
1990 2082 2.093288 AGCACCACGAGTTCATCATGAT 60.093 45.455 1.18 1.18 0.00 2.45
1991 2083 1.276138 AGCACCACGAGTTCATCATGA 59.724 47.619 0.00 0.00 0.00 3.07
1992 2084 1.730501 AGCACCACGAGTTCATCATG 58.269 50.000 0.00 0.00 0.00 3.07
2020 2112 2.452600 AAAGCACAACTCCCCTTCAA 57.547 45.000 0.00 0.00 0.00 2.69
2021 2113 2.452600 AAAAGCACAACTCCCCTTCA 57.547 45.000 0.00 0.00 0.00 3.02
2039 2131 5.337813 GGACGGAGGGAATAGTACTGAAAAA 60.338 44.000 5.39 0.00 0.00 1.94
2040 2132 4.161001 GGACGGAGGGAATAGTACTGAAAA 59.839 45.833 5.39 0.00 0.00 2.29
2041 2133 3.703052 GGACGGAGGGAATAGTACTGAAA 59.297 47.826 5.39 0.00 0.00 2.69
2042 2134 3.294214 GGACGGAGGGAATAGTACTGAA 58.706 50.000 5.39 0.00 0.00 3.02
2043 2135 2.423947 GGGACGGAGGGAATAGTACTGA 60.424 54.545 5.39 0.00 0.00 3.41
2044 2136 1.962100 GGGACGGAGGGAATAGTACTG 59.038 57.143 5.39 0.00 0.00 2.74
2045 2137 1.572415 TGGGACGGAGGGAATAGTACT 59.428 52.381 0.00 0.00 0.00 2.73
2046 2138 2.077687 TGGGACGGAGGGAATAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2047 2139 4.474303 TTATGGGACGGAGGGAATAGTA 57.526 45.455 0.00 0.00 0.00 1.82
2048 2140 3.339713 TTATGGGACGGAGGGAATAGT 57.660 47.619 0.00 0.00 0.00 2.12
2049 2141 7.670605 TTATATTATGGGACGGAGGGAATAG 57.329 40.000 0.00 0.00 0.00 1.73
2050 2142 8.452138 TTTTATATTATGGGACGGAGGGAATA 57.548 34.615 0.00 0.00 0.00 1.75
2051 2143 6.963117 TTTATATTATGGGACGGAGGGAAT 57.037 37.500 0.00 0.00 0.00 3.01
2052 2144 6.746043 GCTTTTATATTATGGGACGGAGGGAA 60.746 42.308 0.00 0.00 0.00 3.97
2053 2145 5.280317 GCTTTTATATTATGGGACGGAGGGA 60.280 44.000 0.00 0.00 0.00 4.20
2054 2146 4.941873 GCTTTTATATTATGGGACGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
2055 2147 5.556915 TGCTTTTATATTATGGGACGGAGG 58.443 41.667 0.00 0.00 0.00 4.30
2056 2148 7.687941 AATGCTTTTATATTATGGGACGGAG 57.312 36.000 0.00 0.00 0.00 4.63
2057 2149 9.575868 TTAAATGCTTTTATATTATGGGACGGA 57.424 29.630 5.70 0.00 0.00 4.69
2089 2181 9.712305 CTCCGTCTCATAATATAAGGATGTTTT 57.288 33.333 0.00 0.00 0.00 2.43
2090 2182 8.314751 CCTCCGTCTCATAATATAAGGATGTTT 58.685 37.037 0.00 0.00 0.00 2.83
2091 2183 7.093289 CCCTCCGTCTCATAATATAAGGATGTT 60.093 40.741 0.00 0.00 0.00 2.71
2092 2184 6.381420 CCCTCCGTCTCATAATATAAGGATGT 59.619 42.308 0.00 0.00 0.00 3.06
2093 2185 6.607600 TCCCTCCGTCTCATAATATAAGGATG 59.392 42.308 0.00 0.00 0.00 3.51
2094 2186 6.742756 TCCCTCCGTCTCATAATATAAGGAT 58.257 40.000 0.00 0.00 0.00 3.24
2095 2187 6.148735 TCCCTCCGTCTCATAATATAAGGA 57.851 41.667 0.00 0.00 0.00 3.36
2096 2188 5.952947 ACTCCCTCCGTCTCATAATATAAGG 59.047 44.000 0.00 0.00 0.00 2.69
2097 2189 8.047911 TCTACTCCCTCCGTCTCATAATATAAG 58.952 40.741 0.00 0.00 0.00 1.73
2098 2190 7.925622 TCTACTCCCTCCGTCTCATAATATAA 58.074 38.462 0.00 0.00 0.00 0.98
2099 2191 7.506361 TCTACTCCCTCCGTCTCATAATATA 57.494 40.000 0.00 0.00 0.00 0.86
2100 2192 6.390048 TCTACTCCCTCCGTCTCATAATAT 57.610 41.667 0.00 0.00 0.00 1.28
2101 2193 5.837770 TCTACTCCCTCCGTCTCATAATA 57.162 43.478 0.00 0.00 0.00 0.98
2102 2194 4.726035 TCTACTCCCTCCGTCTCATAAT 57.274 45.455 0.00 0.00 0.00 1.28
2103 2195 4.726035 ATCTACTCCCTCCGTCTCATAA 57.274 45.455 0.00 0.00 0.00 1.90
2104 2196 5.837770 TTATCTACTCCCTCCGTCTCATA 57.162 43.478 0.00 0.00 0.00 2.15
2105 2197 4.726035 TTATCTACTCCCTCCGTCTCAT 57.274 45.455 0.00 0.00 0.00 2.90
2106 2198 4.726035 ATTATCTACTCCCTCCGTCTCA 57.274 45.455 0.00 0.00 0.00 3.27
2107 2199 4.943093 GGTATTATCTACTCCCTCCGTCTC 59.057 50.000 0.00 0.00 0.00 3.36
2108 2200 4.263860 GGGTATTATCTACTCCCTCCGTCT 60.264 50.000 0.00 0.00 35.63 4.18
2109 2201 4.015764 GGGTATTATCTACTCCCTCCGTC 58.984 52.174 0.00 0.00 35.63 4.79
2110 2202 3.245550 GGGGTATTATCTACTCCCTCCGT 60.246 52.174 0.00 0.00 38.31 4.69
2111 2203 3.245514 TGGGGTATTATCTACTCCCTCCG 60.246 52.174 0.00 0.00 37.27 4.63
2112 2204 4.095211 GTGGGGTATTATCTACTCCCTCC 58.905 52.174 0.00 0.00 37.27 4.30
2113 2205 4.748701 TGTGGGGTATTATCTACTCCCTC 58.251 47.826 0.00 0.00 37.27 4.30
2114 2206 4.845530 TGTGGGGTATTATCTACTCCCT 57.154 45.455 0.00 0.00 37.27 4.20
2115 2207 5.187967 CAGATGTGGGGTATTATCTACTCCC 59.812 48.000 0.00 0.00 37.27 4.30
2116 2208 5.780793 ACAGATGTGGGGTATTATCTACTCC 59.219 44.000 0.00 0.00 38.55 3.85
2117 2209 6.919775 ACAGATGTGGGGTATTATCTACTC 57.080 41.667 0.00 0.00 0.00 2.59
2118 2210 6.464465 GCAACAGATGTGGGGTATTATCTACT 60.464 42.308 0.00 0.00 0.00 2.57
2119 2211 5.701290 GCAACAGATGTGGGGTATTATCTAC 59.299 44.000 0.00 0.00 0.00 2.59
2120 2212 5.368230 TGCAACAGATGTGGGGTATTATCTA 59.632 40.000 0.00 0.00 0.00 1.98
2121 2213 4.165950 TGCAACAGATGTGGGGTATTATCT 59.834 41.667 0.00 0.00 0.00 1.98
2122 2214 4.460263 TGCAACAGATGTGGGGTATTATC 58.540 43.478 0.00 0.00 0.00 1.75
2123 2215 4.165950 TCTGCAACAGATGTGGGGTATTAT 59.834 41.667 0.00 0.00 35.39 1.28
2124 2216 3.521531 TCTGCAACAGATGTGGGGTATTA 59.478 43.478 0.00 0.00 35.39 0.98
2125 2217 2.308570 TCTGCAACAGATGTGGGGTATT 59.691 45.455 0.00 0.00 35.39 1.89
2126 2218 1.915489 TCTGCAACAGATGTGGGGTAT 59.085 47.619 0.00 0.00 35.39 2.73
2127 2219 1.357137 TCTGCAACAGATGTGGGGTA 58.643 50.000 0.00 0.00 35.39 3.69
2128 2220 0.478072 TTCTGCAACAGATGTGGGGT 59.522 50.000 0.00 0.00 40.39 4.95
2129 2221 1.619654 TTTCTGCAACAGATGTGGGG 58.380 50.000 0.00 0.00 40.39 4.96
2130 2222 5.587388 AATATTTCTGCAACAGATGTGGG 57.413 39.130 0.00 0.00 40.39 4.61
2131 2223 6.183360 GCAAAATATTTCTGCAACAGATGTGG 60.183 38.462 20.73 0.00 40.39 4.17
2132 2224 6.366604 TGCAAAATATTTCTGCAACAGATGTG 59.633 34.615 23.66 8.59 42.84 3.21
2133 2225 6.457355 TGCAAAATATTTCTGCAACAGATGT 58.543 32.000 23.66 0.00 42.84 3.06
2134 2226 6.954616 TGCAAAATATTTCTGCAACAGATG 57.045 33.333 23.66 9.12 42.84 2.90
2377 2469 8.371770 TGCCTTGGTATAAAACATTTGAAAAC 57.628 30.769 0.00 0.00 0.00 2.43
2464 2556 7.642586 GGCCTAAAACGCATTTACAATAACTAG 59.357 37.037 0.00 0.00 32.27 2.57
2466 2558 6.071840 TGGCCTAAAACGCATTTACAATAACT 60.072 34.615 3.32 0.00 32.27 2.24
2583 2675 3.620966 GCAACTAGAAAGGTGAGAGGCAT 60.621 47.826 0.00 0.00 43.70 4.40
2643 2735 3.523564 AGGGGCAGACATATAAGTGTTGT 59.476 43.478 0.00 0.00 31.16 3.32
2855 2952 4.381079 GGGATGTTGTGGCGCTAAATTAAA 60.381 41.667 7.64 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.