Multiple sequence alignment - TraesCS2D01G001900

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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 TraesCS2D01G001900 chr2D 100.000 2900 0 0 1 2900 1620473 1623372 0.000000e+00 5356.0
1 TraesCS2D01G001900 chr2D 98.520 743 11 0 2 744 53801821 53802563 0.000000e+00 1312.0
2 TraesCS2D01G001900 chr2D 98.520 743 11 0 2 744 592168241 592168983 0.000000e+00 1312.0
3 TraesCS2D01G001900 chr2D 87.751 898 98 7 1032 1918 613819284 613818388 0.000000e+00 1038.0
4 TraesCS2D01G001900 chr2D 80.692 1041 163 19 740 1748 1818478 1817444 0.000000e+00 774.0
5 TraesCS2D01G001900 chr2D 79.905 1055 170 24 740 1758 648872601 648871553 0.000000e+00 736.0
6 TraesCS2D01G001900 chr2D 88.618 246 15 4 917 1150 6462464 6462708 1.320000e-73 287.0
7 TraesCS2D01G001900 chr2D 85.165 182 24 3 2710 2889 1669983 1670163 1.770000e-42 183.0
8 TraesCS2D01G001900 chr2D 93.750 96 5 1 2537 2631 528438235 528438330 3.010000e-30 143.0
9 TraesCS2D01G001900 chr2A 90.900 1022 70 5 746 1744 658417 659438 0.000000e+00 1351.0
10 TraesCS2D01G001900 chr2A 86.842 912 89 14 1032 1912 753535991 753536902 0.000000e+00 990.0
11 TraesCS2D01G001900 chr2A 86.512 734 93 4 1047 1776 702456 703187 0.000000e+00 802.0
12 TraesCS2D01G001900 chr2A 86.376 734 94 4 1047 1776 708027 708758 0.000000e+00 797.0
13 TraesCS2D01G001900 chr2A 95.812 191 8 0 2710 2900 703799 703989 2.810000e-80 309.0
14 TraesCS2D01G001900 chr2A 95.812 191 8 0 2710 2900 709370 709560 2.810000e-80 309.0
15 TraesCS2D01G001900 chr2A 87.302 252 24 5 1806 2049 660416 660667 6.120000e-72 281.0
16 TraesCS2D01G001900 chr2A 89.759 166 15 2 2715 2879 951227 951391 8.140000e-51 211.0
17 TraesCS2D01G001900 chr2A 85.922 206 14 8 2693 2888 682092 682292 3.790000e-49 206.0
18 TraesCS2D01G001900 chr2A 84.236 203 18 4 2306 2494 661357 661559 4.930000e-43 185.0
19 TraesCS2D01G001900 chr2A 85.315 143 19 2 1800 1940 1188139 1187997 2.330000e-31 147.0
20 TraesCS2D01G001900 chr2A 97.333 75 2 0 2091 2165 660663 660737 8.430000e-26 128.0
21 TraesCS2D01G001900 chr2A 87.500 96 6 4 2160 2251 661183 661276 3.950000e-19 106.0
22 TraesCS2D01G001900 chr3D 98.789 743 9 0 2 744 5208510 5209252 0.000000e+00 1323.0
23 TraesCS2D01G001900 chr3D 98.520 743 11 0 2 744 586021167 586020425 0.000000e+00 1312.0
24 TraesCS2D01G001900 chr7D 98.520 743 11 0 2 744 522399952 522400694 0.000000e+00 1312.0
25 TraesCS2D01G001900 chr7D 96.703 91 3 0 2547 2637 448931401 448931311 5.010000e-33 152.0
26 TraesCS2D01G001900 chr7D 90.991 111 6 3 2524 2634 76741508 76741614 2.330000e-31 147.0
27 TraesCS2D01G001900 chr7D 95.604 91 3 1 2545 2634 494673682 494673592 8.380000e-31 145.0
28 TraesCS2D01G001900 chr5D 98.520 743 11 0 2 744 448913911 448914653 0.000000e+00 1312.0
29 TraesCS2D01G001900 chr5D 96.512 86 3 0 2546 2631 545227873 545227788 3.010000e-30 143.0
30 TraesCS2D01G001900 chr5D 86.066 122 11 6 2547 2667 104972931 104973047 3.030000e-25 126.0
31 TraesCS2D01G001900 chr1D 98.520 743 11 0 2 744 445615167 445614425 0.000000e+00 1312.0
32 TraesCS2D01G001900 chrUn 98.385 743 12 0 2 744 223008645 223007903 0.000000e+00 1306.0
33 TraesCS2D01G001900 chr4D 98.385 743 12 0 2 744 468427240 468426498 0.000000e+00 1306.0
34 TraesCS2D01G001900 chr4D 87.179 117 14 1 2546 2661 7759968 7759852 6.520000e-27 132.0
35 TraesCS2D01G001900 chr3A 80.403 1041 166 22 740 1748 103018031 103019065 0.000000e+00 758.0
36 TraesCS2D01G001900 chr3A 78.371 1031 177 31 740 1748 61438510 61437504 6.820000e-176 627.0
37 TraesCS2D01G001900 chr3A 89.069 247 15 5 917 1152 359071275 359071030 2.190000e-76 296.0
38 TraesCS2D01G001900 chr2B 87.872 437 29 6 740 1152 319360113 319360549 2.600000e-135 492.0
39 TraesCS2D01G001900 chr2B 94.000 50 3 0 2840 2889 10215969 10215920 3.100000e-10 76.8
40 TraesCS2D01G001900 chr4A 87.348 411 28 4 766 1152 591017050 591017460 1.580000e-122 449.0
41 TraesCS2D01G001900 chr7B 95.652 92 4 0 2547 2638 829828 829737 6.470000e-32 148.0
42 TraesCS2D01G001900 chr4B 89.908 109 8 3 2529 2635 484771838 484771731 1.400000e-28 137.0


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 TraesCS2D01G001900 chr2D 1620473 1623372 2899 False 5356.0 5356 100.0000 1 2900 1 chr2D.!!$F1 2899
1 TraesCS2D01G001900 chr2D 53801821 53802563 742 False 1312.0 1312 98.5200 2 744 1 chr2D.!!$F4 742
2 TraesCS2D01G001900 chr2D 592168241 592168983 742 False 1312.0 1312 98.5200 2 744 1 chr2D.!!$F6 742
3 TraesCS2D01G001900 chr2D 613818388 613819284 896 True 1038.0 1038 87.7510 1032 1918 1 chr2D.!!$R2 886
4 TraesCS2D01G001900 chr2D 1817444 1818478 1034 True 774.0 774 80.6920 740 1748 1 chr2D.!!$R1 1008
5 TraesCS2D01G001900 chr2D 648871553 648872601 1048 True 736.0 736 79.9050 740 1758 1 chr2D.!!$R3 1018
6 TraesCS2D01G001900 chr2A 753535991 753536902 911 False 990.0 990 86.8420 1032 1912 1 chr2A.!!$F3 880
7 TraesCS2D01G001900 chr2A 702456 703989 1533 False 555.5 802 91.1620 1047 2900 2 chr2A.!!$F5 1853
8 TraesCS2D01G001900 chr2A 708027 709560 1533 False 553.0 797 91.0940 1047 2900 2 chr2A.!!$F6 1853
9 TraesCS2D01G001900 chr2A 658417 661559 3142 False 410.2 1351 89.4542 746 2494 5 chr2A.!!$F4 1748
10 TraesCS2D01G001900 chr3D 5208510 5209252 742 False 1323.0 1323 98.7890 2 744 1 chr3D.!!$F1 742
11 TraesCS2D01G001900 chr3D 586020425 586021167 742 True 1312.0 1312 98.5200 2 744 1 chr3D.!!$R1 742
12 TraesCS2D01G001900 chr7D 522399952 522400694 742 False 1312.0 1312 98.5200 2 744 1 chr7D.!!$F2 742
13 TraesCS2D01G001900 chr5D 448913911 448914653 742 False 1312.0 1312 98.5200 2 744 1 chr5D.!!$F2 742
14 TraesCS2D01G001900 chr1D 445614425 445615167 742 True 1312.0 1312 98.5200 2 744 1 chr1D.!!$R1 742
15 TraesCS2D01G001900 chrUn 223007903 223008645 742 True 1306.0 1306 98.3850 2 744 1 chrUn.!!$R1 742
16 TraesCS2D01G001900 chr4D 468426498 468427240 742 True 1306.0 1306 98.3850 2 744 1 chr4D.!!$R2 742
17 TraesCS2D01G001900 chr3A 103018031 103019065 1034 False 758.0 758 80.4030 740 1748 1 chr3A.!!$F1 1008
18 TraesCS2D01G001900 chr3A 61437504 61438510 1006 True 627.0 627 78.3710 740 1748 1 chr3A.!!$R1 1008

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
157 158 0.035317 TGTCTGTGCTCATCCCACAC 59.965 55.0 0.00 0.00 38.21 3.82 F
381 382 0.108585 AGGATTAATGCCATCCGCGT 59.891 50.0 4.92 0.00 44.57 6.01 F
1170 1200 0.251832 ATAGCGTCCTCCATCCGGAT 60.252 55.0 12.38 12.38 41.79 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1489 0.605589 CGAACCAGAGTCCAAGCTCT 59.394 55.0 0.0 0.0 45.87 4.09 R
1800 2870 0.825840 TCAACCCTTTCCCTTTGCCG 60.826 55.0 0.0 0.0 0.00 5.69 R
2711 4431 0.102300 TGTATCGATCCGGTGCTGTG 59.898 55.0 0.0 0.0 0.00 3.66 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
24 25 5.509163 CCCAGGTATATACTTTCGGTGTCAG 60.509 48.000 12.54 0.00 0.00 3.51
46 47 1.502990 AAACAGTGCGTGCATGCGTA 61.503 50.000 25.05 6.63 37.81 4.42
62 63 4.804868 TGCGTAGTATCCCTTGTTTGTA 57.195 40.909 0.00 0.00 0.00 2.41
141 142 3.440522 GTGCAGGTTAAATTCCTCCTGTC 59.559 47.826 17.79 12.92 46.23 3.51
157 158 0.035317 TGTCTGTGCTCATCCCACAC 59.965 55.000 0.00 0.00 38.21 3.82
381 382 0.108585 AGGATTAATGCCATCCGCGT 59.891 50.000 4.92 0.00 44.57 6.01
771 772 3.423179 TTTTTCACCGGACCGCAC 58.577 55.556 9.46 0.00 0.00 5.34
968 987 2.942804 TGTCTTCATTTCTTGCCCACA 58.057 42.857 0.00 0.00 0.00 4.17
1016 1046 0.436913 CGCATGTTACGCTTCGACAA 59.563 50.000 0.00 0.00 0.00 3.18
1170 1200 0.251832 ATAGCGTCCTCCATCCGGAT 60.252 55.000 12.38 12.38 41.79 4.18
1236 1266 1.302431 CACCACGTCCCTTGCATCA 60.302 57.895 0.00 0.00 0.00 3.07
1555 1592 2.587194 CGCCAGAGAAGATGCGGG 60.587 66.667 0.00 0.00 43.08 6.13
1701 1738 2.611971 GGACTGCAACGAGATGGTTACA 60.612 50.000 0.00 0.00 0.00 2.41
1765 2719 1.856802 CAGCAAAGGCAAAAGTGACC 58.143 50.000 0.00 0.00 44.61 4.02
1771 2725 4.557942 GCAAAAGTGACCATGCCG 57.442 55.556 0.00 0.00 32.73 5.69
1774 2728 1.930371 GCAAAAGTGACCATGCCGAAC 60.930 52.381 0.00 0.00 32.73 3.95
1782 2736 1.968017 CCATGCCGAACACAGCAGT 60.968 57.895 0.00 0.00 43.38 4.40
1784 2738 1.372582 CATGCCGAACACAGCAGTAT 58.627 50.000 0.00 0.00 43.38 2.12
1788 2742 2.009774 GCCGAACACAGCAGTATCAAT 58.990 47.619 0.00 0.00 0.00 2.57
1790 2744 2.352651 CCGAACACAGCAGTATCAATGG 59.647 50.000 0.00 0.00 0.00 3.16
1792 2746 3.062639 CGAACACAGCAGTATCAATGGTC 59.937 47.826 0.00 0.00 0.00 4.02
1795 2865 1.066215 ACAGCAGTATCAATGGTCGCA 60.066 47.619 0.00 0.00 0.00 5.10
1798 2868 0.578683 CAGTATCAATGGTCGCAGCG 59.421 55.000 9.06 9.06 0.00 5.18
1820 2890 0.679505 GGCAAAGGGAAAGGGTTGAC 59.320 55.000 0.00 0.00 0.00 3.18
1826 2896 2.251371 GAAAGGGTTGACGCGTGC 59.749 61.111 20.70 9.34 0.00 5.34
1851 2921 5.760253 CCTCCGTATGATTAAGCACAAATCT 59.240 40.000 0.00 0.00 34.95 2.40
1908 2978 2.941720 GGAGGTGCTCTGAATGATTCAC 59.058 50.000 3.29 0.00 35.46 3.18
1942 3012 4.672587 TTGACTTGCTGAACTCTAGTGT 57.327 40.909 0.00 0.00 0.00 3.55
1949 3019 4.371786 TGCTGAACTCTAGTGTTTGACTG 58.628 43.478 11.27 4.96 35.96 3.51
1953 3023 7.039993 TGCTGAACTCTAGTGTTTGACTGTATA 60.040 37.037 11.27 0.00 35.96 1.47
2004 3082 8.737168 ACTTTAGCATTCAGATTATGTGCTAA 57.263 30.769 12.50 12.50 44.98 3.09
2007 3085 4.512944 AGCATTCAGATTATGTGCTAACCG 59.487 41.667 0.00 0.00 38.95 4.44
2017 3095 8.774586 AGATTATGTGCTAACCGAATAATTGTC 58.225 33.333 0.00 0.00 0.00 3.18
2034 3112 3.988379 TGTCTGATGGCAAGTTTGAAC 57.012 42.857 0.00 0.00 0.00 3.18
2036 3114 3.565482 TGTCTGATGGCAAGTTTGAACTC 59.435 43.478 0.00 0.00 38.57 3.01
2039 3117 4.276678 TCTGATGGCAAGTTTGAACTCTTG 59.723 41.667 0.00 5.35 42.44 3.02
2040 3118 4.206375 TGATGGCAAGTTTGAACTCTTGA 58.794 39.130 11.64 0.00 42.22 3.02
2044 3122 3.815401 GGCAAGTTTGAACTCTTGAGCTA 59.185 43.478 11.64 0.00 42.22 3.32
2045 3123 4.457257 GGCAAGTTTGAACTCTTGAGCTAT 59.543 41.667 11.64 0.00 42.22 2.97
2046 3124 5.048434 GGCAAGTTTGAACTCTTGAGCTATT 60.048 40.000 11.64 0.00 42.22 1.73
2047 3125 5.855395 GCAAGTTTGAACTCTTGAGCTATTG 59.145 40.000 11.64 0.00 42.22 1.90
2048 3126 6.514048 GCAAGTTTGAACTCTTGAGCTATTGT 60.514 38.462 11.64 0.00 42.22 2.71
2049 3127 6.551385 AGTTTGAACTCTTGAGCTATTGTG 57.449 37.500 0.00 0.00 32.86 3.33
2050 3128 6.058183 AGTTTGAACTCTTGAGCTATTGTGT 58.942 36.000 0.00 0.00 32.86 3.72
2051 3129 6.543831 AGTTTGAACTCTTGAGCTATTGTGTT 59.456 34.615 0.00 0.00 32.86 3.32
2052 3130 7.715249 AGTTTGAACTCTTGAGCTATTGTGTTA 59.285 33.333 0.00 0.00 32.86 2.41
2053 3131 8.342634 GTTTGAACTCTTGAGCTATTGTGTTAA 58.657 33.333 0.00 0.00 0.00 2.01
2054 3132 7.658179 TGAACTCTTGAGCTATTGTGTTAAG 57.342 36.000 0.00 0.00 0.00 1.85
2055 3133 6.147821 TGAACTCTTGAGCTATTGTGTTAAGC 59.852 38.462 0.00 0.00 36.48 3.09
2057 3135 6.936279 ACTCTTGAGCTATTGTGTTAAGCTA 58.064 36.000 0.00 0.00 46.29 3.32
2058 3136 7.386851 ACTCTTGAGCTATTGTGTTAAGCTAA 58.613 34.615 0.00 0.00 46.29 3.09
2059 3137 8.043710 ACTCTTGAGCTATTGTGTTAAGCTAAT 58.956 33.333 0.00 0.00 46.29 1.73
2060 3138 8.792830 TCTTGAGCTATTGTGTTAAGCTAATT 57.207 30.769 0.00 0.00 46.29 1.40
2061 3139 8.668353 TCTTGAGCTATTGTGTTAAGCTAATTG 58.332 33.333 0.00 0.00 46.29 2.32
2062 3140 8.560355 TTGAGCTATTGTGTTAAGCTAATTGA 57.440 30.769 0.00 0.00 46.29 2.57
2063 3141 8.560355 TGAGCTATTGTGTTAAGCTAATTGAA 57.440 30.769 0.00 0.00 46.29 2.69
2064 3142 8.668353 TGAGCTATTGTGTTAAGCTAATTGAAG 58.332 33.333 0.00 0.00 46.29 3.02
2065 3143 8.792830 AGCTATTGTGTTAAGCTAATTGAAGA 57.207 30.769 0.00 0.00 44.55 2.87
2066 3144 9.231297 AGCTATTGTGTTAAGCTAATTGAAGAA 57.769 29.630 0.00 0.00 44.55 2.52
2067 3145 9.278734 GCTATTGTGTTAAGCTAATTGAAGAAC 57.721 33.333 0.00 0.00 33.40 3.01
2068 3146 9.774742 CTATTGTGTTAAGCTAATTGAAGAACC 57.225 33.333 0.00 0.00 0.00 3.62
2069 3147 6.569179 TGTGTTAAGCTAATTGAAGAACCC 57.431 37.500 0.00 0.00 0.00 4.11
2070 3148 6.065374 TGTGTTAAGCTAATTGAAGAACCCA 58.935 36.000 0.00 0.00 0.00 4.51
2071 3149 6.016610 TGTGTTAAGCTAATTGAAGAACCCAC 60.017 38.462 0.00 0.00 0.00 4.61
2072 3150 6.016610 GTGTTAAGCTAATTGAAGAACCCACA 60.017 38.462 0.00 0.00 0.00 4.17
2073 3151 6.719370 TGTTAAGCTAATTGAAGAACCCACAT 59.281 34.615 0.00 0.00 0.00 3.21
2074 3152 7.885922 TGTTAAGCTAATTGAAGAACCCACATA 59.114 33.333 0.00 0.00 0.00 2.29
2075 3153 8.903820 GTTAAGCTAATTGAAGAACCCACATAT 58.096 33.333 0.00 0.00 0.00 1.78
2077 3155 8.451908 AAGCTAATTGAAGAACCCACATATAC 57.548 34.615 0.00 0.00 0.00 1.47
2078 3156 7.573710 AGCTAATTGAAGAACCCACATATACA 58.426 34.615 0.00 0.00 0.00 2.29
2079 3157 8.052748 AGCTAATTGAAGAACCCACATATACAA 58.947 33.333 0.00 0.00 0.00 2.41
2080 3158 8.129211 GCTAATTGAAGAACCCACATATACAAC 58.871 37.037 0.00 0.00 0.00 3.32
2081 3159 7.404671 AATTGAAGAACCCACATATACAACC 57.595 36.000 0.00 0.00 0.00 3.77
2082 3160 5.506730 TGAAGAACCCACATATACAACCA 57.493 39.130 0.00 0.00 0.00 3.67
2083 3161 5.882040 TGAAGAACCCACATATACAACCAA 58.118 37.500 0.00 0.00 0.00 3.67
2084 3162 6.307776 TGAAGAACCCACATATACAACCAAA 58.692 36.000 0.00 0.00 0.00 3.28
2085 3163 6.778069 TGAAGAACCCACATATACAACCAAAA 59.222 34.615 0.00 0.00 0.00 2.44
2086 3164 7.287927 TGAAGAACCCACATATACAACCAAAAA 59.712 33.333 0.00 0.00 0.00 1.94
2116 3194 2.457366 ACTGCTAGTTTTCCCGAGTG 57.543 50.000 0.00 0.00 0.00 3.51
2180 3709 1.181786 TGGAATCCCAATTCGGCAAC 58.818 50.000 0.00 0.00 41.94 4.17
2181 3710 1.181786 GGAATCCCAATTCGGCAACA 58.818 50.000 0.00 0.00 41.94 3.33
2182 3711 1.756538 GGAATCCCAATTCGGCAACAT 59.243 47.619 0.00 0.00 41.94 2.71
2183 3712 2.481795 GGAATCCCAATTCGGCAACATG 60.482 50.000 0.00 0.00 41.94 3.21
2184 3713 1.851304 ATCCCAATTCGGCAACATGT 58.149 45.000 0.00 0.00 0.00 3.21
2185 3714 2.498644 TCCCAATTCGGCAACATGTA 57.501 45.000 0.00 0.00 0.00 2.29
2186 3715 3.011566 TCCCAATTCGGCAACATGTAT 57.988 42.857 0.00 0.00 0.00 2.29
2187 3716 2.687425 TCCCAATTCGGCAACATGTATG 59.313 45.455 0.00 1.04 0.00 2.39
2189 3718 2.462889 CAATTCGGCAACATGTATGGC 58.537 47.619 18.27 18.27 39.76 4.40
2190 3719 1.032014 ATTCGGCAACATGTATGGCC 58.968 50.000 20.46 20.46 42.98 5.36
2191 3720 1.034838 TTCGGCAACATGTATGGCCC 61.035 55.000 22.93 9.35 43.50 5.80
2257 3789 9.461312 TGCTAACATAAATATGAGTTTCCAACT 57.539 29.630 7.40 0.00 46.38 3.16
2357 3942 6.773976 AGTCAAAGTTGAACTCAAATTCCA 57.226 33.333 0.00 0.00 42.38 3.53
2359 3944 7.035612 AGTCAAAGTTGAACTCAAATTCCAAC 58.964 34.615 0.00 0.00 42.38 3.77
2378 3963 1.213926 ACAGATTTGGATGGAGGGAGC 59.786 52.381 0.00 0.00 0.00 4.70
2380 3965 1.493871 AGATTTGGATGGAGGGAGCAG 59.506 52.381 0.00 0.00 0.00 4.24
2443 4041 8.643752 CACAAATAACCGACCAAATTAAACATC 58.356 33.333 0.00 0.00 0.00 3.06
2465 4064 3.545873 CGTTGGTCATGTTTTCACACAAC 59.454 43.478 0.00 0.00 35.03 3.32
2494 4093 7.040823 ACTCTGCTTTCAACTCAGGAATTAAAG 60.041 37.037 0.00 0.00 0.00 1.85
2497 4096 5.860716 GCTTTCAACTCAGGAATTAAAGCAG 59.139 40.000 10.96 0.00 44.09 4.24
2498 4097 5.376854 TTCAACTCAGGAATTAAAGCAGC 57.623 39.130 0.00 0.00 0.00 5.25
2499 4098 4.397420 TCAACTCAGGAATTAAAGCAGCA 58.603 39.130 0.00 0.00 0.00 4.41
2500 4099 4.216257 TCAACTCAGGAATTAAAGCAGCAC 59.784 41.667 0.00 0.00 0.00 4.40
2502 4101 4.401925 ACTCAGGAATTAAAGCAGCACTT 58.598 39.130 0.00 0.00 41.70 3.16
2503 4102 5.560724 ACTCAGGAATTAAAGCAGCACTTA 58.439 37.500 0.00 0.00 37.75 2.24
2504 4103 6.003950 ACTCAGGAATTAAAGCAGCACTTAA 58.996 36.000 0.00 0.00 37.75 1.85
2505 4104 6.660949 ACTCAGGAATTAAAGCAGCACTTAAT 59.339 34.615 0.00 0.93 37.75 1.40
2506 4105 6.855836 TCAGGAATTAAAGCAGCACTTAATG 58.144 36.000 11.38 3.86 37.75 1.90
2507 4106 6.038356 CAGGAATTAAAGCAGCACTTAATGG 58.962 40.000 11.38 2.34 37.75 3.16
2508 4107 5.716703 AGGAATTAAAGCAGCACTTAATGGT 59.283 36.000 11.38 0.72 37.75 3.55
2519 4118 6.029346 AGCACTTAATGGTGATTTTTGAGG 57.971 37.500 0.00 0.00 37.74 3.86
2520 4119 5.047092 AGCACTTAATGGTGATTTTTGAGGG 60.047 40.000 0.00 0.00 37.74 4.30
2521 4120 5.170748 CACTTAATGGTGATTTTTGAGGGC 58.829 41.667 0.00 0.00 39.34 5.19
2522 4121 4.222810 ACTTAATGGTGATTTTTGAGGGCC 59.777 41.667 0.00 0.00 0.00 5.80
2523 4122 1.185315 ATGGTGATTTTTGAGGGCCG 58.815 50.000 0.00 0.00 0.00 6.13
2527 4126 2.091541 GTGATTTTTGAGGGCCGATCA 58.908 47.619 5.22 5.22 0.00 2.92
2539 4138 4.302067 AGGGCCGATCATATCCTATCAAT 58.698 43.478 0.00 0.00 0.00 2.57
2541 4140 4.101585 GGGCCGATCATATCCTATCAATCA 59.898 45.833 0.00 0.00 0.00 2.57
2542 4141 5.396772 GGGCCGATCATATCCTATCAATCAA 60.397 44.000 0.00 0.00 0.00 2.57
2543 4142 6.115446 GGCCGATCATATCCTATCAATCAAA 58.885 40.000 0.00 0.00 0.00 2.69
2544 4143 6.259608 GGCCGATCATATCCTATCAATCAAAG 59.740 42.308 0.00 0.00 0.00 2.77
2545 4144 6.259608 GCCGATCATATCCTATCAATCAAAGG 59.740 42.308 0.00 0.00 0.00 3.11
2547 4146 8.478066 CCGATCATATCCTATCAATCAAAGGTA 58.522 37.037 0.00 0.00 0.00 3.08
2548 4147 9.307121 CGATCATATCCTATCAATCAAAGGTAC 57.693 37.037 0.00 0.00 0.00 3.34
2554 4153 5.602978 TCCTATCAATCAAAGGTACTCCCTC 59.397 44.000 0.00 0.00 45.47 4.30
2555 4154 5.604650 CCTATCAATCAAAGGTACTCCCTCT 59.395 44.000 0.00 0.00 45.47 3.69
2556 4155 4.826274 TCAATCAAAGGTACTCCCTCTG 57.174 45.455 0.00 0.00 45.47 3.35
2557 4156 4.168101 TCAATCAAAGGTACTCCCTCTGT 58.832 43.478 0.00 0.00 45.47 3.41
2558 4157 4.223032 TCAATCAAAGGTACTCCCTCTGTC 59.777 45.833 0.00 0.00 45.47 3.51
2559 4158 2.537143 TCAAAGGTACTCCCTCTGTCC 58.463 52.381 0.00 0.00 45.47 4.02
2560 4159 1.555533 CAAAGGTACTCCCTCTGTCCC 59.444 57.143 0.00 0.00 45.47 4.46
2561 4160 0.790993 AAGGTACTCCCTCTGTCCCA 59.209 55.000 0.00 0.00 45.47 4.37
2562 4161 1.019650 AGGTACTCCCTCTGTCCCAT 58.980 55.000 0.00 0.00 40.71 4.00
2563 4162 2.224077 AGGTACTCCCTCTGTCCCATA 58.776 52.381 0.00 0.00 40.71 2.74
2564 4163 2.590611 AGGTACTCCCTCTGTCCCATAA 59.409 50.000 0.00 0.00 40.71 1.90
2565 4164 3.210074 AGGTACTCCCTCTGTCCCATAAT 59.790 47.826 0.00 0.00 40.71 1.28
2566 4165 4.422592 AGGTACTCCCTCTGTCCCATAATA 59.577 45.833 0.00 0.00 40.71 0.98
2567 4166 5.078006 AGGTACTCCCTCTGTCCCATAATAT 59.922 44.000 0.00 0.00 40.71 1.28
2568 4167 6.279682 AGGTACTCCCTCTGTCCCATAATATA 59.720 42.308 0.00 0.00 40.71 0.86
2569 4168 6.958192 GGTACTCCCTCTGTCCCATAATATAA 59.042 42.308 0.00 0.00 0.00 0.98
2571 4170 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2572 4171 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
2573 4172 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
2574 4173 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
2575 4174 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
2576 4175 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
2577 4176 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
2607 4206 7.781548 ACTAATGTAGTGTCAAAAACGTTCT 57.218 32.000 0.00 0.00 37.69 3.01
2608 4207 8.205131 ACTAATGTAGTGTCAAAAACGTTCTT 57.795 30.769 0.00 0.00 37.69 2.52
2609 4208 9.316730 ACTAATGTAGTGTCAAAAACGTTCTTA 57.683 29.630 0.00 0.00 37.69 2.10
2618 4217 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
2619 4218 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
2620 4219 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
2621 4220 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
2622 4221 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
2624 4223 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
2625 4224 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
2626 4225 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2627 4226 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2637 4266 2.173569 GGGACGGAGGGAGTACTAAGTA 59.826 54.545 0.00 0.00 0.00 2.24
2643 4272 5.426833 ACGGAGGGAGTACTAAGTAGACTTA 59.573 44.000 0.00 2.30 37.40 2.24
2644 4273 6.069963 ACGGAGGGAGTACTAAGTAGACTTAA 60.070 42.308 0.00 0.00 37.92 1.85
2670 4372 6.481313 CACTAAAGTCAGTACTGCATGCATAT 59.519 38.462 22.97 15.15 35.62 1.78
2671 4373 7.011763 CACTAAAGTCAGTACTGCATGCATATT 59.988 37.037 22.97 11.24 35.62 1.28
2672 4374 5.998454 AAGTCAGTACTGCATGCATATTC 57.002 39.130 22.97 10.52 35.62 1.75
2673 4375 5.287674 AGTCAGTACTGCATGCATATTCT 57.712 39.130 22.97 12.68 33.57 2.40
2674 4376 6.410942 AGTCAGTACTGCATGCATATTCTA 57.589 37.500 22.97 3.21 33.57 2.10
2684 4386 6.554419 TGCATGCATATTCTAAGTCAAACAC 58.446 36.000 18.46 0.00 0.00 3.32
2687 4389 7.703621 GCATGCATATTCTAAGTCAAACACAAT 59.296 33.333 14.21 0.00 0.00 2.71
2691 4393 9.210426 GCATATTCTAAGTCAAACACAATAACG 57.790 33.333 0.00 0.00 0.00 3.18
2720 4440 0.865111 TTGAATCGTTCACAGCACCG 59.135 50.000 0.76 0.00 39.87 4.94
2721 4441 0.948623 TGAATCGTTCACAGCACCGG 60.949 55.000 0.00 0.00 34.08 5.28
2730 4450 0.102300 CACAGCACCGGATCGATACA 59.898 55.000 9.46 0.00 0.00 2.29
2739 4459 1.588404 CGGATCGATACACTGTTGCAC 59.412 52.381 8.69 0.00 0.00 4.57
2753 4473 5.912396 CACTGTTGCACGTTAAACATGTAAT 59.088 36.000 11.99 0.00 35.82 1.89
2820 4540 2.028733 CTTTGCCGCCATTGTTGCC 61.029 57.895 0.00 0.00 0.00 4.52
2861 4581 6.150474 GCATTTGGTACCACTATTGTAGTTGT 59.850 38.462 16.04 0.49 38.16 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.342951 TGACACCGAAAGTATATACCTGGG 59.657 45.833 9.32 9.97 0.00 4.45
24 25 1.067199 GCATGCACGCACTGTTTAGC 61.067 55.000 14.21 0.00 0.00 3.09
46 47 5.487488 TCAGGACATACAAACAAGGGATACT 59.513 40.000 0.00 0.00 0.00 2.12
62 63 4.323104 GCTCTCAGTAACCTTTCAGGACAT 60.323 45.833 0.00 0.00 37.67 3.06
141 142 1.293963 CGTGTGTGGGATGAGCACAG 61.294 60.000 0.00 0.00 42.76 3.66
381 382 6.461231 CCAAGGAACGTATGGTTTGGTTTAAA 60.461 38.462 0.00 0.00 39.50 1.52
824 825 1.004044 CTTCTCCTCTTGGGTGCACAT 59.996 52.381 20.43 0.00 36.25 3.21
872 888 0.331278 TTGGCGGATTGATCTTGGGT 59.669 50.000 0.00 0.00 0.00 4.51
991 1021 0.668096 AAGCGTAACATGCGGTTCGA 60.668 50.000 3.31 0.00 45.05 3.71
1016 1046 2.710902 TAGCTGCAGCCGTCGATGT 61.711 57.895 34.39 16.24 43.38 3.06
1230 1260 0.890542 GCCAGAACCTGTGTGATGCA 60.891 55.000 0.00 0.00 0.00 3.96
1236 1266 1.526917 GCAGTGCCAGAACCTGTGT 60.527 57.895 2.85 0.00 0.00 3.72
1290 1321 1.760613 CCGTAGACCAAGGCATTCCTA 59.239 52.381 0.00 0.00 43.40 2.94
1333 1367 1.473080 GCCAGAGATGGAGAAGCAGAC 60.473 57.143 0.00 0.00 0.00 3.51
1428 1462 0.679640 AATCCGCCTTGCCATCGAAA 60.680 50.000 0.00 0.00 0.00 3.46
1455 1489 0.605589 CGAACCAGAGTCCAAGCTCT 59.394 55.000 0.00 0.00 45.87 4.09
1515 1552 1.079256 CTCCTCCCCTCTGACCACA 59.921 63.158 0.00 0.00 0.00 4.17
1555 1592 2.182842 GGTCATCATGCGCCCAGAC 61.183 63.158 4.18 5.98 0.00 3.51
1748 1785 2.137523 CATGGTCACTTTTGCCTTTGC 58.862 47.619 0.00 0.00 38.26 3.68
1771 2725 3.062639 CGACCATTGATACTGCTGTGTTC 59.937 47.826 6.48 4.27 0.00 3.18
1774 2728 1.328680 GCGACCATTGATACTGCTGTG 59.671 52.381 6.48 0.00 0.00 3.66
1795 2865 1.966451 CTTTCCCTTTGCCGTCGCT 60.966 57.895 0.00 0.00 35.36 4.93
1798 2868 0.826256 AACCCTTTCCCTTTGCCGTC 60.826 55.000 0.00 0.00 0.00 4.79
1800 2870 0.825840 TCAACCCTTTCCCTTTGCCG 60.826 55.000 0.00 0.00 0.00 5.69
1809 2879 2.251371 GCACGCGTCAACCCTTTC 59.749 61.111 9.86 0.00 0.00 2.62
1820 2890 2.971428 AATCATACGGAGGGCACGCG 62.971 60.000 3.53 3.53 34.00 6.01
1826 2896 3.469008 TGTGCTTAATCATACGGAGGG 57.531 47.619 0.00 0.00 0.00 4.30
1976 3050 9.177608 AGCACATAATCTGAATGCTAAAGTAAA 57.822 29.630 0.00 0.00 44.59 2.01
1996 3070 6.112734 TCAGACAATTATTCGGTTAGCACAT 58.887 36.000 0.00 0.00 0.00 3.21
1997 3071 5.483811 TCAGACAATTATTCGGTTAGCACA 58.516 37.500 0.00 0.00 0.00 4.57
2004 3082 3.884895 TGCCATCAGACAATTATTCGGT 58.115 40.909 0.00 0.00 0.00 4.69
2007 3085 7.315142 TCAAACTTGCCATCAGACAATTATTC 58.685 34.615 0.00 0.00 0.00 1.75
2017 3095 4.276678 TCAAGAGTTCAAACTTGCCATCAG 59.723 41.667 0.00 0.00 41.91 2.90
2034 3112 7.834068 TTAGCTTAACACAATAGCTCAAGAG 57.166 36.000 0.00 0.00 43.75 2.85
2036 3114 8.668353 TCAATTAGCTTAACACAATAGCTCAAG 58.332 33.333 0.00 0.00 43.75 3.02
2039 3117 8.883731 TCTTCAATTAGCTTAACACAATAGCTC 58.116 33.333 0.00 0.00 43.75 4.09
2040 3118 8.792830 TCTTCAATTAGCTTAACACAATAGCT 57.207 30.769 0.00 0.00 46.33 3.32
2044 3122 7.232534 TGGGTTCTTCAATTAGCTTAACACAAT 59.767 33.333 0.00 0.00 0.00 2.71
2045 3123 6.547880 TGGGTTCTTCAATTAGCTTAACACAA 59.452 34.615 0.00 0.00 0.00 3.33
2046 3124 6.016610 GTGGGTTCTTCAATTAGCTTAACACA 60.017 38.462 0.00 0.00 0.00 3.72
2047 3125 6.016610 TGTGGGTTCTTCAATTAGCTTAACAC 60.017 38.462 0.00 0.00 0.00 3.32
2048 3126 6.065374 TGTGGGTTCTTCAATTAGCTTAACA 58.935 36.000 0.00 0.00 0.00 2.41
2049 3127 6.569179 TGTGGGTTCTTCAATTAGCTTAAC 57.431 37.500 0.00 0.00 0.00 2.01
2051 3129 9.555727 GTATATGTGGGTTCTTCAATTAGCTTA 57.444 33.333 0.00 0.00 0.00 3.09
2052 3130 8.052748 TGTATATGTGGGTTCTTCAATTAGCTT 58.947 33.333 0.00 0.00 0.00 3.74
2053 3131 7.573710 TGTATATGTGGGTTCTTCAATTAGCT 58.426 34.615 0.00 0.00 0.00 3.32
2054 3132 7.801716 TGTATATGTGGGTTCTTCAATTAGC 57.198 36.000 0.00 0.00 0.00 3.09
2055 3133 8.621286 GGTTGTATATGTGGGTTCTTCAATTAG 58.379 37.037 0.00 0.00 0.00 1.73
2056 3134 8.110271 TGGTTGTATATGTGGGTTCTTCAATTA 58.890 33.333 0.00 0.00 0.00 1.40
2057 3135 6.951198 TGGTTGTATATGTGGGTTCTTCAATT 59.049 34.615 0.00 0.00 0.00 2.32
2058 3136 6.489603 TGGTTGTATATGTGGGTTCTTCAAT 58.510 36.000 0.00 0.00 0.00 2.57
2059 3137 5.882040 TGGTTGTATATGTGGGTTCTTCAA 58.118 37.500 0.00 0.00 0.00 2.69
2060 3138 5.506730 TGGTTGTATATGTGGGTTCTTCA 57.493 39.130 0.00 0.00 0.00 3.02
2061 3139 6.827586 TTTGGTTGTATATGTGGGTTCTTC 57.172 37.500 0.00 0.00 0.00 2.87
2062 3140 7.604657 TTTTTGGTTGTATATGTGGGTTCTT 57.395 32.000 0.00 0.00 0.00 2.52
2085 3163 8.957466 GGGAAAACTAGCAGTATACAATCTTTT 58.043 33.333 5.50 1.47 0.00 2.27
2086 3164 7.280205 CGGGAAAACTAGCAGTATACAATCTTT 59.720 37.037 5.50 0.00 0.00 2.52
2087 3165 6.761714 CGGGAAAACTAGCAGTATACAATCTT 59.238 38.462 5.50 0.00 0.00 2.40
2088 3166 6.097839 TCGGGAAAACTAGCAGTATACAATCT 59.902 38.462 5.50 1.58 0.00 2.40
2089 3167 6.278363 TCGGGAAAACTAGCAGTATACAATC 58.722 40.000 5.50 0.00 0.00 2.67
2116 3194 3.980238 CTCGATAGCACAACAGTTCAC 57.020 47.619 0.00 0.00 0.00 3.18
2173 3702 1.453015 GGGCCATACATGTTGCCGA 60.453 57.895 20.72 0.00 44.96 5.54
2180 3709 2.157640 TTTCAAGGGGGCCATACATG 57.842 50.000 4.39 0.00 0.00 3.21
2181 3710 3.419732 AATTTCAAGGGGGCCATACAT 57.580 42.857 4.39 0.00 0.00 2.29
2182 3711 2.836981 CAAATTTCAAGGGGGCCATACA 59.163 45.455 4.39 0.00 0.00 2.29
2183 3712 3.103742 TCAAATTTCAAGGGGGCCATAC 58.896 45.455 4.39 0.00 0.00 2.39
2184 3713 3.481559 TCAAATTTCAAGGGGGCCATA 57.518 42.857 4.39 0.00 0.00 2.74
2185 3714 2.305635 GTTCAAATTTCAAGGGGGCCAT 59.694 45.455 4.39 0.00 0.00 4.40
2186 3715 1.696884 GTTCAAATTTCAAGGGGGCCA 59.303 47.619 4.39 0.00 0.00 5.36
2187 3716 1.003118 GGTTCAAATTTCAAGGGGGCC 59.997 52.381 0.00 0.00 0.00 5.80
2189 3718 2.334023 TGGGTTCAAATTTCAAGGGGG 58.666 47.619 0.00 0.00 0.00 5.40
2190 3719 3.390967 AGTTGGGTTCAAATTTCAAGGGG 59.609 43.478 0.00 0.00 34.28 4.79
2191 3720 4.687901 AGTTGGGTTCAAATTTCAAGGG 57.312 40.909 0.00 0.00 34.28 3.95
2298 3883 8.962679 GCTACTACCTATATGAGATAGTTTGCT 58.037 37.037 0.00 0.00 0.00 3.91
2299 3884 8.740906 TGCTACTACCTATATGAGATAGTTTGC 58.259 37.037 0.00 0.00 0.00 3.68
2341 3926 7.042523 CCAAATCTGTTGGAATTTGAGTTCAAC 60.043 37.037 8.89 0.00 42.06 3.18
2344 3929 6.748132 TCCAAATCTGTTGGAATTTGAGTTC 58.252 36.000 5.33 0.00 44.90 3.01
2355 3940 2.025037 TCCCTCCATCCAAATCTGTTGG 60.025 50.000 0.00 0.00 40.87 3.77
2356 3941 3.285484 CTCCCTCCATCCAAATCTGTTG 58.715 50.000 0.00 0.00 0.00 3.33
2357 3942 2.357569 GCTCCCTCCATCCAAATCTGTT 60.358 50.000 0.00 0.00 0.00 3.16
2359 3944 1.213678 TGCTCCCTCCATCCAAATCTG 59.786 52.381 0.00 0.00 0.00 2.90
2378 3963 4.216472 TCAGACTTGAGCACTAGTGTACTG 59.784 45.833 23.44 18.73 32.85 2.74
2380 3965 4.768130 TCAGACTTGAGCACTAGTGTAC 57.232 45.455 23.44 17.13 32.85 2.90
2416 4014 7.713750 TGTTTAATTTGGTCGGTTATTTGTGA 58.286 30.769 0.00 0.00 0.00 3.58
2443 4041 3.412981 TGTGTGAAAACATGACCAACG 57.587 42.857 0.00 0.00 0.00 4.10
2451 4049 4.201950 GCAGAGTCTGTTGTGTGAAAACAT 60.202 41.667 21.06 0.00 36.95 2.71
2465 4064 3.065655 CCTGAGTTGAAAGCAGAGTCTG 58.934 50.000 16.21 16.21 34.12 3.51
2494 4093 5.229423 TCAAAAATCACCATTAAGTGCTGC 58.771 37.500 0.00 0.00 37.68 5.25
2497 4096 5.170748 CCCTCAAAAATCACCATTAAGTGC 58.829 41.667 0.00 0.00 37.68 4.40
2498 4097 5.170748 GCCCTCAAAAATCACCATTAAGTG 58.829 41.667 0.00 0.00 39.20 3.16
2499 4098 4.222810 GGCCCTCAAAAATCACCATTAAGT 59.777 41.667 0.00 0.00 0.00 2.24
2500 4099 4.677779 CGGCCCTCAAAAATCACCATTAAG 60.678 45.833 0.00 0.00 0.00 1.85
2502 4101 2.757868 CGGCCCTCAAAAATCACCATTA 59.242 45.455 0.00 0.00 0.00 1.90
2503 4102 1.550072 CGGCCCTCAAAAATCACCATT 59.450 47.619 0.00 0.00 0.00 3.16
2504 4103 1.185315 CGGCCCTCAAAAATCACCAT 58.815 50.000 0.00 0.00 0.00 3.55
2505 4104 0.111446 TCGGCCCTCAAAAATCACCA 59.889 50.000 0.00 0.00 0.00 4.17
2506 4105 1.405463 GATCGGCCCTCAAAAATCACC 59.595 52.381 0.00 0.00 0.00 4.02
2507 4106 2.091541 TGATCGGCCCTCAAAAATCAC 58.908 47.619 0.00 0.00 0.00 3.06
2508 4107 2.505650 TGATCGGCCCTCAAAAATCA 57.494 45.000 0.00 0.00 0.00 2.57
2509 4108 4.156739 GGATATGATCGGCCCTCAAAAATC 59.843 45.833 6.75 9.56 0.00 2.17
2510 4109 4.082125 GGATATGATCGGCCCTCAAAAAT 58.918 43.478 6.75 2.21 0.00 1.82
2511 4110 3.138283 AGGATATGATCGGCCCTCAAAAA 59.862 43.478 6.75 0.00 0.00 1.94
2512 4111 2.711009 AGGATATGATCGGCCCTCAAAA 59.289 45.455 6.75 0.00 0.00 2.44
2513 4112 2.338809 AGGATATGATCGGCCCTCAAA 58.661 47.619 6.75 0.00 0.00 2.69
2514 4113 2.030027 AGGATATGATCGGCCCTCAA 57.970 50.000 6.75 0.00 0.00 3.02
2515 4114 2.919772 TAGGATATGATCGGCCCTCA 57.080 50.000 5.20 5.20 0.00 3.86
2516 4115 3.300388 TGATAGGATATGATCGGCCCTC 58.700 50.000 0.00 0.00 0.00 4.30
2517 4116 3.404869 TGATAGGATATGATCGGCCCT 57.595 47.619 0.00 0.00 0.00 5.19
2518 4117 4.101585 TGATTGATAGGATATGATCGGCCC 59.898 45.833 0.00 0.00 0.00 5.80
2519 4118 5.282055 TGATTGATAGGATATGATCGGCC 57.718 43.478 0.00 0.00 0.00 6.13
2520 4119 6.259608 CCTTTGATTGATAGGATATGATCGGC 59.740 42.308 0.00 0.00 0.00 5.54
2521 4120 7.334090 ACCTTTGATTGATAGGATATGATCGG 58.666 38.462 0.00 0.00 33.21 4.18
2522 4121 9.307121 GTACCTTTGATTGATAGGATATGATCG 57.693 37.037 0.00 0.00 33.21 3.69
2527 4126 8.152023 GGGAGTACCTTTGATTGATAGGATAT 57.848 38.462 0.00 0.00 35.85 1.63
2582 4181 8.876275 AGAACGTTTTTGACACTACATTAGTA 57.124 30.769 0.46 0.00 37.23 1.82
2583 4182 7.781548 AGAACGTTTTTGACACTACATTAGT 57.218 32.000 0.46 0.00 40.28 2.24
2593 4192 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
2595 4194 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
2596 4195 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
2597 4196 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
2598 4197 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2599 4198 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
2600 4199 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
2601 4200 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2604 4203 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2605 4204 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2606 4205 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2607 4206 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2608 4207 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2609 4208 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2610 4209 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2611 4210 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2613 4212 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2614 4213 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2616 4215 1.064091 ACTTAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
2617 4216 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2618 4217 4.126437 GTCTACTTAGTACTCCCTCCGTC 58.874 52.174 0.00 0.00 0.00 4.79
2619 4218 3.779738 AGTCTACTTAGTACTCCCTCCGT 59.220 47.826 0.00 0.00 0.00 4.69
2620 4219 4.420522 AGTCTACTTAGTACTCCCTCCG 57.579 50.000 0.00 0.00 0.00 4.63
2621 4220 7.066887 GTGTTAAGTCTACTTAGTACTCCCTCC 59.933 44.444 0.00 0.00 39.36 4.30
2622 4221 7.828717 AGTGTTAAGTCTACTTAGTACTCCCTC 59.171 40.741 0.00 0.00 39.36 4.30
2624 4223 7.936496 AGTGTTAAGTCTACTTAGTACTCCC 57.064 40.000 0.00 1.55 39.36 4.30
2643 4272 4.452455 GCATGCAGTACTGACTTTAGTGTT 59.548 41.667 27.08 0.00 31.73 3.32
2644 4273 3.997021 GCATGCAGTACTGACTTTAGTGT 59.003 43.478 27.08 0.00 31.73 3.55
2651 4280 5.287674 AGAATATGCATGCAGTACTGACT 57.712 39.130 27.08 14.52 35.80 3.41
2655 4284 6.820335 TGACTTAGAATATGCATGCAGTACT 58.180 36.000 26.69 21.57 0.00 2.73
2658 4287 6.375174 TGTTTGACTTAGAATATGCATGCAGT 59.625 34.615 26.69 15.28 0.00 4.40
2691 4393 7.697710 TGCTGTGAACGATTCAATGATTAAATC 59.302 33.333 0.00 0.00 42.15 2.17
2692 4394 7.485913 GTGCTGTGAACGATTCAATGATTAAAT 59.514 33.333 0.00 0.00 42.15 1.40
2693 4395 6.801377 GTGCTGTGAACGATTCAATGATTAAA 59.199 34.615 0.00 0.00 42.15 1.52
2695 4397 5.163764 GGTGCTGTGAACGATTCAATGATTA 60.164 40.000 0.00 0.00 42.15 1.75
2697 4399 3.127548 GGTGCTGTGAACGATTCAATGAT 59.872 43.478 0.00 0.00 42.15 2.45
2698 4400 2.483877 GGTGCTGTGAACGATTCAATGA 59.516 45.455 0.00 0.00 42.15 2.57
2699 4401 2.725759 CGGTGCTGTGAACGATTCAATG 60.726 50.000 0.00 0.00 42.15 2.82
2701 4403 0.865111 CGGTGCTGTGAACGATTCAA 59.135 50.000 0.00 0.00 42.15 2.69
2703 4405 0.669318 TCCGGTGCTGTGAACGATTC 60.669 55.000 0.00 0.00 0.00 2.52
2706 4408 1.080093 GATCCGGTGCTGTGAACGA 60.080 57.895 0.00 0.00 0.00 3.85
2707 4409 2.444624 CGATCCGGTGCTGTGAACG 61.445 63.158 0.00 0.00 0.00 3.95
2708 4410 0.460284 ATCGATCCGGTGCTGTGAAC 60.460 55.000 0.00 0.00 0.00 3.18
2711 4431 0.102300 TGTATCGATCCGGTGCTGTG 59.898 55.000 0.00 0.00 0.00 3.66
2720 4440 1.588404 CGTGCAACAGTGTATCGATCC 59.412 52.381 0.00 0.00 35.74 3.36
2721 4441 2.259618 ACGTGCAACAGTGTATCGATC 58.740 47.619 0.00 0.00 35.74 3.69
2730 4450 5.487153 TTACATGTTTAACGTGCAACAGT 57.513 34.783 16.24 14.79 38.65 3.55
2753 4473 5.543507 ATGGTTAAGCACAAATCCAAACA 57.456 34.783 9.99 0.00 0.00 2.83
2861 4581 0.961019 GGTGCTGGCAAAGACAATGA 59.039 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.