Multiple sequence alignment - TraesCS3B01G510100

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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 TraesCS3B01G510100 chr3B 100.000 3440 0 0 1 3440 754230359 754226920 0.000000e+00 6353.0
1 TraesCS3B01G510100 chr3B 100.000 736 0 0 2705 3440 754281422 754282157 0.000000e+00 1360.0
2 TraesCS3B01G510100 chr3B 84.362 243 35 2 612 852 538816096 538815855 5.740000e-58 235.0
3 TraesCS3B01G510100 chr3B 91.566 166 13 1 2497 2661 696323956 696324121 9.600000e-56 228.0
4 TraesCS3B01G510100 chr3B 83.621 116 19 0 1021 1136 805255604 805255719 3.630000e-20 110.0
5 TraesCS3B01G510100 chr3A 94.540 2381 102 14 138 2502 700216761 700214393 0.000000e+00 3651.0
6 TraesCS3B01G510100 chr3A 83.144 439 42 18 3034 3440 700214271 700213833 4.190000e-99 372.0
7 TraesCS3B01G510100 chr3A 84.615 117 18 0 1021 1137 728320820 728320936 2.170000e-22 117.0
8 TraesCS3B01G510100 chr3A 83.761 117 18 1 1023 1138 728007184 728007300 3.630000e-20 110.0
9 TraesCS3B01G510100 chr3A 80.833 120 21 2 2075 2193 509250699 509250581 3.660000e-15 93.5
10 TraesCS3B01G510100 chr3A 80.000 120 22 2 2075 2193 509376700 509376582 1.700000e-13 87.9
11 TraesCS3B01G510100 chr3D 95.967 1562 61 1 941 2502 565819678 565821237 0.000000e+00 2534.0
12 TraesCS3B01G510100 chr3D 92.359 301 17 4 384 684 565819204 565819498 1.140000e-114 424.0
13 TraesCS3B01G510100 chr3D 94.828 232 9 1 157 388 565818707 565818935 3.260000e-95 359.0
14 TraesCS3B01G510100 chr3D 87.451 255 28 2 3187 3437 565821458 565821712 1.210000e-74 291.0
15 TraesCS3B01G510100 chr3D 80.892 314 44 13 2499 2803 560940497 560940803 2.060000e-57 233.0
16 TraesCS3B01G510100 chr3D 83.133 249 40 2 605 852 21414391 21414638 3.450000e-55 226.0
17 TraesCS3B01G510100 chr3D 84.483 116 16 2 1023 1137 598037283 598037397 2.810000e-21 113.0
18 TraesCS3B01G510100 chr3D 80.000 120 22 2 2075 2193 388312580 388312462 1.700000e-13 87.9
19 TraesCS3B01G510100 chr3D 79.167 120 23 2 2075 2193 388324825 388324707 7.910000e-12 82.4
20 TraesCS3B01G510100 chr1B 83.333 312 42 7 2499 2804 658360837 658361144 2.610000e-71 279.0
21 TraesCS3B01G510100 chr1B 82.468 308 42 11 2498 2800 457463547 457463847 3.410000e-65 259.0
22 TraesCS3B01G510100 chr1B 83.200 250 40 2 605 852 562894163 562893914 9.600000e-56 228.0
23 TraesCS3B01G510100 chr1B 90.123 162 15 1 2860 3020 61612036 61612197 3.480000e-50 209.0
24 TraesCS3B01G510100 chr6B 82.637 311 45 8 2499 2804 147682316 147682622 2.040000e-67 267.0
25 TraesCS3B01G510100 chr6B 87.958 191 19 3 2492 2682 678073735 678073921 4.470000e-54 222.0
26 TraesCS3B01G510100 chr5B 81.789 313 45 10 2499 2804 528574587 528574280 5.700000e-63 252.0
27 TraesCS3B01G510100 chr5B 91.018 167 14 1 2501 2666 528508804 528508638 1.240000e-54 224.0
28 TraesCS3B01G510100 chr5B 89.820 167 16 1 2861 3026 346616343 346616177 2.690000e-51 213.0
29 TraesCS3B01G510100 chr5B 77.244 312 57 12 2499 2804 523569825 523569522 1.640000e-38 171.0
30 TraesCS3B01G510100 chr4D 85.062 241 34 2 612 851 428481825 428482064 9.540000e-61 244.0
31 TraesCS3B01G510100 chr4D 79.021 143 28 2 2074 2215 477913011 477913152 2.830000e-16 97.1
32 TraesCS3B01G510100 chr1D 81.529 314 42 13 2499 2804 267804306 267804001 9.540000e-61 244.0
33 TraesCS3B01G510100 chr1D 81.029 311 47 11 2498 2803 341513360 341513663 1.600000e-58 237.0
34 TraesCS3B01G510100 chr1D 90.123 162 16 0 2865 3026 299766213 299766052 9.670000e-51 211.0
35 TraesCS3B01G510100 chr1D 78.346 254 43 5 3187 3440 99816130 99815889 1.650000e-33 154.0
36 TraesCS3B01G510100 chr4A 83.984 256 38 3 599 852 467684117 467683863 3.430000e-60 243.0
37 TraesCS3B01G510100 chr4A 90.361 166 16 0 2861 3026 703715660 703715495 5.780000e-53 219.0
38 TraesCS3B01G510100 chr2D 84.615 247 35 3 608 852 74147108 74146863 3.430000e-60 243.0
39 TraesCS3B01G510100 chr2D 84.490 245 35 2 605 847 16177659 16177902 4.440000e-59 239.0
40 TraesCS3B01G510100 chr2D 90.566 53 4 1 480 532 99662094 99662043 6.160000e-08 69.4
41 TraesCS3B01G510100 chr2B 84.274 248 35 4 608 852 465133178 465132932 4.440000e-59 239.0
42 TraesCS3B01G510100 chr2B 91.617 167 13 1 2495 2661 62412198 62412033 2.670000e-56 230.0
43 TraesCS3B01G510100 chr2B 90.123 162 14 2 2861 3020 763446648 763446809 3.480000e-50 209.0
44 TraesCS3B01G510100 chr7B 91.250 160 14 0 2861 3020 632274157 632273998 5.780000e-53 219.0
45 TraesCS3B01G510100 chr7B 91.195 159 14 0 2862 3020 8886378 8886536 2.080000e-52 217.0
46 TraesCS3B01G510100 chr4B 79.808 312 51 11 2499 2803 28898566 28898872 2.080000e-52 217.0
47 TraesCS3B01G510100 chr4B 89.286 168 18 0 2859 3026 667396898 667396731 9.670000e-51 211.0
48 TraesCS3B01G510100 chr4B 72.330 412 93 17 1810 2215 604140122 604140518 3.630000e-20 110.0
49 TraesCS3B01G510100 chr5D 82.517 143 23 2 1023 1164 34051855 34051714 1.300000e-24 124.0
50 TraesCS3B01G510100 chr5D 81.944 144 22 4 1023 1164 34061347 34061206 6.030000e-23 119.0
51 TraesCS3B01G510100 chr5A 83.621 116 17 2 1023 1137 22723977 22724091 1.310000e-19 108.0
52 TraesCS3B01G510100 chr6A 81.553 103 17 2 2074 2175 8791666 8791565 2.200000e-12 84.2
53 TraesCS3B01G510100 chr6A 76.316 152 34 2 2074 2224 8867995 8867845 2.850000e-11 80.5


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 TraesCS3B01G510100 chr3B 754226920 754230359 3439 True 6353.0 6353 100.00000 1 3440 1 chr3B.!!$R2 3439
1 TraesCS3B01G510100 chr3B 754281422 754282157 735 False 1360.0 1360 100.00000 2705 3440 1 chr3B.!!$F2 735
2 TraesCS3B01G510100 chr3A 700213833 700216761 2928 True 2011.5 3651 88.84200 138 3440 2 chr3A.!!$R3 3302
3 TraesCS3B01G510100 chr3D 565818707 565821712 3005 False 902.0 2534 92.65125 157 3437 4 chr3D.!!$F4 3280

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
854 1129 0.179258 GCGCAGTAAAAACGACCTCG 60.179 55.0 0.3 0.0 46.33 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2686 3002 0.523072 TTGCTCCGTACGTAGTCCAC 59.477 55.0 15.21 0.0 43.93 4.02 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
17 18 4.902308 TACCGGTCACTTCGCATG 57.098 55.556 12.40 0.00 0.00 4.06
18 19 1.447140 TACCGGTCACTTCGCATGC 60.447 57.895 12.40 7.91 0.00 4.06
19 20 2.161078 TACCGGTCACTTCGCATGCA 62.161 55.000 12.40 1.73 0.00 3.96
20 21 2.108514 CCGGTCACTTCGCATGCAT 61.109 57.895 19.57 0.00 0.00 3.96
21 22 1.061411 CGGTCACTTCGCATGCATG 59.939 57.895 22.70 22.70 0.00 4.06
22 23 1.638388 CGGTCACTTCGCATGCATGT 61.638 55.000 26.79 9.87 0.00 3.21
23 24 1.368641 GGTCACTTCGCATGCATGTA 58.631 50.000 26.79 13.55 0.00 2.29
24 25 1.942657 GGTCACTTCGCATGCATGTAT 59.057 47.619 26.79 6.52 0.00 2.29
25 26 2.355756 GGTCACTTCGCATGCATGTATT 59.644 45.455 26.79 5.67 0.00 1.89
26 27 3.181497 GGTCACTTCGCATGCATGTATTT 60.181 43.478 26.79 6.37 0.00 1.40
27 28 4.414852 GTCACTTCGCATGCATGTATTTT 58.585 39.130 26.79 7.42 0.00 1.82
28 29 4.858692 GTCACTTCGCATGCATGTATTTTT 59.141 37.500 26.79 5.86 0.00 1.94
50 51 7.616103 TTTTATTGTGAGTATGCAAAACACG 57.384 32.000 0.00 0.00 34.72 4.49
51 52 4.829064 ATTGTGAGTATGCAAAACACGT 57.171 36.364 0.00 0.00 34.72 4.49
52 53 5.933187 ATTGTGAGTATGCAAAACACGTA 57.067 34.783 0.00 0.00 34.72 3.57
53 54 4.718858 TGTGAGTATGCAAAACACGTAC 57.281 40.909 0.00 0.00 34.72 3.67
54 55 4.373527 TGTGAGTATGCAAAACACGTACT 58.626 39.130 0.00 0.00 41.44 2.73
55 56 4.812091 TGTGAGTATGCAAAACACGTACTT 59.188 37.500 0.00 0.00 39.40 2.24
56 57 5.294799 TGTGAGTATGCAAAACACGTACTTT 59.705 36.000 0.00 0.00 39.40 2.66
57 58 6.183360 TGTGAGTATGCAAAACACGTACTTTT 60.183 34.615 0.00 0.00 39.40 2.27
58 59 6.689669 GTGAGTATGCAAAACACGTACTTTTT 59.310 34.615 0.00 0.00 39.40 1.94
92 93 9.899226 AAAAGAGAGCATAATTTACAACAAGTC 57.101 29.630 0.00 0.00 0.00 3.01
93 94 8.854614 AAGAGAGCATAATTTACAACAAGTCT 57.145 30.769 0.00 0.00 0.00 3.24
94 95 9.944376 AAGAGAGCATAATTTACAACAAGTCTA 57.056 29.630 0.00 0.00 0.00 2.59
95 96 9.593134 AGAGAGCATAATTTACAACAAGTCTAG 57.407 33.333 0.00 0.00 0.00 2.43
96 97 8.723942 AGAGCATAATTTACAACAAGTCTAGG 57.276 34.615 0.00 0.00 0.00 3.02
97 98 7.770897 AGAGCATAATTTACAACAAGTCTAGGG 59.229 37.037 0.00 0.00 0.00 3.53
98 99 7.630082 AGCATAATTTACAACAAGTCTAGGGA 58.370 34.615 0.00 0.00 0.00 4.20
99 100 7.770897 AGCATAATTTACAACAAGTCTAGGGAG 59.229 37.037 0.00 0.00 0.00 4.30
100 101 7.553044 GCATAATTTACAACAAGTCTAGGGAGT 59.447 37.037 0.00 0.00 0.00 3.85
101 102 9.449719 CATAATTTACAACAAGTCTAGGGAGTT 57.550 33.333 0.00 0.00 35.68 3.01
106 107 2.743636 CAAGTCTAGGGAGTTGCGAA 57.256 50.000 0.00 0.00 43.23 4.70
107 108 2.338500 CAAGTCTAGGGAGTTGCGAAC 58.662 52.381 0.00 0.00 43.23 3.95
108 109 1.629043 AGTCTAGGGAGTTGCGAACA 58.371 50.000 0.00 0.00 0.00 3.18
109 110 1.968493 AGTCTAGGGAGTTGCGAACAA 59.032 47.619 0.00 0.00 0.00 2.83
126 127 4.915704 GAACAACTCGAAAACAACATCCA 58.084 39.130 0.00 0.00 0.00 3.41
127 128 4.287238 ACAACTCGAAAACAACATCCAC 57.713 40.909 0.00 0.00 0.00 4.02
128 129 3.945285 ACAACTCGAAAACAACATCCACT 59.055 39.130 0.00 0.00 0.00 4.00
129 130 4.035208 ACAACTCGAAAACAACATCCACTC 59.965 41.667 0.00 0.00 0.00 3.51
130 131 3.139077 ACTCGAAAACAACATCCACTCC 58.861 45.455 0.00 0.00 0.00 3.85
131 132 3.138304 CTCGAAAACAACATCCACTCCA 58.862 45.455 0.00 0.00 0.00 3.86
132 133 3.750371 TCGAAAACAACATCCACTCCAT 58.250 40.909 0.00 0.00 0.00 3.41
133 134 4.141287 TCGAAAACAACATCCACTCCATT 58.859 39.130 0.00 0.00 0.00 3.16
134 135 4.215399 TCGAAAACAACATCCACTCCATTC 59.785 41.667 0.00 0.00 0.00 2.67
135 136 4.023279 CGAAAACAACATCCACTCCATTCA 60.023 41.667 0.00 0.00 0.00 2.57
136 137 5.507149 CGAAAACAACATCCACTCCATTCAA 60.507 40.000 0.00 0.00 0.00 2.69
173 174 2.229062 TCACAAAACGTTGCAAACCTCA 59.771 40.909 0.00 0.00 46.28 3.86
280 281 1.066787 GCTAGTGTGGGAGGAGTTCAC 60.067 57.143 0.00 0.00 0.00 3.18
281 282 1.202582 CTAGTGTGGGAGGAGTTCACG 59.797 57.143 0.00 0.00 34.43 4.35
282 283 0.759436 AGTGTGGGAGGAGTTCACGT 60.759 55.000 0.00 0.00 34.43 4.49
300 301 3.187637 CACGTACCATTTGACCGTTTCAT 59.812 43.478 0.00 0.00 32.84 2.57
334 335 0.738975 ACATCACCGTCGACGATCAT 59.261 50.000 37.65 21.89 43.02 2.45
360 361 1.405526 CCACCTTATCAGACCACGTGG 60.406 57.143 32.83 32.83 42.17 4.94
463 737 0.605319 CAAGTCAAGGCCCGCTACAA 60.605 55.000 0.00 0.00 0.00 2.41
536 810 1.072331 GTCAGTCAAGAGCCTTGGGAA 59.928 52.381 12.99 0.00 0.00 3.97
551 825 5.429130 CCTTGGGAACTACTCTACCATTTC 58.571 45.833 0.00 0.00 0.00 2.17
594 868 8.382030 TCGAAATATCTGCATGTTGATGTAAT 57.618 30.769 11.18 1.12 31.50 1.89
595 869 8.839343 TCGAAATATCTGCATGTTGATGTAATT 58.161 29.630 11.18 3.25 31.50 1.40
599 873 6.682423 ATCTGCATGTTGATGTAATTTCGA 57.318 33.333 0.00 0.00 31.50 3.71
615 889 5.959618 ATTTCGAAAATCTTCCTTCGGTT 57.040 34.783 15.66 0.00 43.55 4.44
668 942 9.543018 CCGAAAACAAAATATCTCTAGTTTGAC 57.457 33.333 11.20 0.00 42.62 3.18
818 1093 6.252441 TCGTCAAACATTGCAAAGTTTAACTG 59.748 34.615 26.87 19.55 36.28 3.16
821 1096 7.224557 GTCAAACATTGCAAAGTTTAACTGGAT 59.775 33.333 26.87 5.54 36.28 3.41
853 1128 0.863144 TGCGCAGTAAAAACGACCTC 59.137 50.000 5.66 0.00 0.00 3.85
854 1129 0.179258 GCGCAGTAAAAACGACCTCG 60.179 55.000 0.30 0.00 46.33 4.63
855 1130 1.411394 CGCAGTAAAAACGACCTCGA 58.589 50.000 0.78 0.00 43.02 4.04
856 1131 1.990563 CGCAGTAAAAACGACCTCGAT 59.009 47.619 0.78 0.00 43.02 3.59
857 1132 2.027688 CGCAGTAAAAACGACCTCGATC 59.972 50.000 0.78 0.00 43.02 3.69
1164 1468 1.294138 CCCGGAGTTTGGCTTCGTA 59.706 57.895 0.73 0.00 44.54 3.43
1167 1471 0.389948 CGGAGTTTGGCTTCGTAGCT 60.390 55.000 13.99 0.00 46.90 3.32
1232 1536 0.752658 ATCCTCGCCATGAACGATGA 59.247 50.000 14.73 14.73 39.12 2.92
1477 1781 8.046294 ACAGTCACTACTCACTACTAATTCTG 57.954 38.462 0.00 0.00 31.97 3.02
1806 2110 3.147595 CTCTCCACCATCGGCGGA 61.148 66.667 7.21 0.00 32.46 5.54
2162 2466 2.490148 CGACGCTGGAGGGCATCTA 61.490 63.158 0.00 0.00 0.00 1.98
2181 2485 4.115199 GAGGGGGTGCCGATGCTT 62.115 66.667 0.00 0.00 38.71 3.91
2273 2577 2.203480 GGTGGGCAAGCTGGAACA 60.203 61.111 0.00 0.00 0.00 3.18
2287 2591 0.312102 GGAACAGTGCAAGGTTGAGC 59.688 55.000 8.80 0.00 0.00 4.26
2316 2620 0.179000 CGAGGTTCATGGAAGGGGAG 59.821 60.000 0.00 0.00 0.00 4.30
2322 2626 0.698886 TCATGGAAGGGGAGGATGGG 60.699 60.000 0.00 0.00 0.00 4.00
2343 2647 2.068821 GGCCATGAGGGAGAGAGCA 61.069 63.158 0.00 0.00 40.01 4.26
2356 2660 1.278699 AGAGAGCAAAGGAGCTTCAGG 59.721 52.381 0.00 0.00 46.75 3.86
2427 2731 6.419116 CGGTAGACAAGTTGATAGATCACATG 59.581 42.308 10.54 0.00 36.36 3.21
2430 2734 7.117285 AGACAAGTTGATAGATCACATGCTA 57.883 36.000 10.54 0.00 36.36 3.49
2463 2777 4.935205 GTCAAAGTATACATGGTGCAGTCA 59.065 41.667 5.50 0.00 0.00 3.41
2502 2818 4.675114 GCTACGGCATGCAAACAATAATAC 59.325 41.667 21.36 0.00 38.54 1.89
2504 2820 4.920376 ACGGCATGCAAACAATAATACTC 58.080 39.130 21.36 0.00 0.00 2.59
2505 2821 4.202010 ACGGCATGCAAACAATAATACTCC 60.202 41.667 21.36 0.00 0.00 3.85
2506 2822 4.620982 GGCATGCAAACAATAATACTCCC 58.379 43.478 21.36 0.00 0.00 4.30
2507 2823 4.342092 GGCATGCAAACAATAATACTCCCT 59.658 41.667 21.36 0.00 0.00 4.20
2509 2825 5.507985 GCATGCAAACAATAATACTCCCTCC 60.508 44.000 14.21 0.00 0.00 4.30
2510 2826 4.196193 TGCAAACAATAATACTCCCTCCG 58.804 43.478 0.00 0.00 0.00 4.63
2511 2827 4.196971 GCAAACAATAATACTCCCTCCGT 58.803 43.478 0.00 0.00 0.00 4.69
2512 2828 4.638865 GCAAACAATAATACTCCCTCCGTT 59.361 41.667 0.00 0.00 0.00 4.44
2513 2829 5.220796 GCAAACAATAATACTCCCTCCGTTC 60.221 44.000 0.00 0.00 0.00 3.95
2514 2830 4.684484 ACAATAATACTCCCTCCGTTCC 57.316 45.455 0.00 0.00 0.00 3.62
2515 2831 4.296056 ACAATAATACTCCCTCCGTTCCT 58.704 43.478 0.00 0.00 0.00 3.36
2516 2832 5.461327 ACAATAATACTCCCTCCGTTCCTA 58.539 41.667 0.00 0.00 0.00 2.94
2517 2833 5.901276 ACAATAATACTCCCTCCGTTCCTAA 59.099 40.000 0.00 0.00 0.00 2.69
2518 2834 6.384886 ACAATAATACTCCCTCCGTTCCTAAA 59.615 38.462 0.00 0.00 0.00 1.85
2519 2835 7.072076 ACAATAATACTCCCTCCGTTCCTAAAT 59.928 37.037 0.00 0.00 0.00 1.40
2520 2836 8.591072 CAATAATACTCCCTCCGTTCCTAAATA 58.409 37.037 0.00 0.00 0.00 1.40
2521 2837 8.731591 ATAATACTCCCTCCGTTCCTAAATAA 57.268 34.615 0.00 0.00 0.00 1.40
2522 2838 7.441903 AATACTCCCTCCGTTCCTAAATAAA 57.558 36.000 0.00 0.00 0.00 1.40
2523 2839 5.767277 ACTCCCTCCGTTCCTAAATAAAA 57.233 39.130 0.00 0.00 0.00 1.52
2524 2840 5.742063 ACTCCCTCCGTTCCTAAATAAAAG 58.258 41.667 0.00 0.00 0.00 2.27
2525 2841 5.250082 ACTCCCTCCGTTCCTAAATAAAAGT 59.750 40.000 0.00 0.00 0.00 2.66
2526 2842 5.737860 TCCCTCCGTTCCTAAATAAAAGTC 58.262 41.667 0.00 0.00 0.00 3.01
2527 2843 5.486419 TCCCTCCGTTCCTAAATAAAAGTCT 59.514 40.000 0.00 0.00 0.00 3.24
2528 2844 6.013119 TCCCTCCGTTCCTAAATAAAAGTCTT 60.013 38.462 0.00 0.00 0.00 3.01
2529 2845 6.657966 CCCTCCGTTCCTAAATAAAAGTCTTT 59.342 38.462 0.00 0.00 0.00 2.52
2530 2846 7.825761 CCCTCCGTTCCTAAATAAAAGTCTTTA 59.174 37.037 0.00 0.00 0.00 1.85
2531 2847 8.880750 CCTCCGTTCCTAAATAAAAGTCTTTAG 58.119 37.037 0.00 0.00 35.60 1.85
2532 2848 9.649167 CTCCGTTCCTAAATAAAAGTCTTTAGA 57.351 33.333 0.00 0.00 37.19 2.10
2533 2849 9.649167 TCCGTTCCTAAATAAAAGTCTTTAGAG 57.351 33.333 0.00 0.00 37.19 2.43
2534 2850 9.649167 CCGTTCCTAAATAAAAGTCTTTAGAGA 57.351 33.333 0.00 0.00 37.19 3.10
2547 2863 8.940768 AAGTCTTTAGAGAGATTTCACTATGC 57.059 34.615 0.00 0.00 31.07 3.14
2548 2864 8.072321 AGTCTTTAGAGAGATTTCACTATGCA 57.928 34.615 0.00 0.00 31.07 3.96
2549 2865 8.703743 AGTCTTTAGAGAGATTTCACTATGCAT 58.296 33.333 3.79 3.79 31.07 3.96
2550 2866 8.977505 GTCTTTAGAGAGATTTCACTATGCATC 58.022 37.037 0.19 0.00 31.07 3.91
2551 2867 8.699130 TCTTTAGAGAGATTTCACTATGCATCA 58.301 33.333 0.19 0.00 0.00 3.07
2552 2868 8.654230 TTTAGAGAGATTTCACTATGCATCAC 57.346 34.615 0.19 0.00 0.00 3.06
2553 2869 6.231258 AGAGAGATTTCACTATGCATCACA 57.769 37.500 0.19 0.00 0.00 3.58
2554 2870 6.828788 AGAGAGATTTCACTATGCATCACAT 58.171 36.000 0.19 0.00 43.18 3.21
2555 2871 7.960262 AGAGAGATTTCACTATGCATCACATA 58.040 34.615 0.19 0.00 40.38 2.29
2556 2872 7.871973 AGAGAGATTTCACTATGCATCACATAC 59.128 37.037 0.19 0.00 40.38 2.39
2557 2873 6.644181 AGAGATTTCACTATGCATCACATACG 59.356 38.462 0.19 0.00 40.38 3.06
2558 2874 5.698089 AGATTTCACTATGCATCACATACGG 59.302 40.000 0.19 0.00 40.38 4.02
2559 2875 4.664150 TTCACTATGCATCACATACGGA 57.336 40.909 0.19 0.00 40.38 4.69
2560 2876 4.243007 TCACTATGCATCACATACGGAG 57.757 45.455 0.19 0.00 40.38 4.63
2579 2895 7.209471 ACGGAGTAAAATAAGTGAATTTGCA 57.791 32.000 0.00 0.00 41.94 4.08
2580 2896 7.826690 ACGGAGTAAAATAAGTGAATTTGCAT 58.173 30.769 0.00 0.00 41.94 3.96
2581 2897 8.952278 ACGGAGTAAAATAAGTGAATTTGCATA 58.048 29.630 0.00 0.00 41.94 3.14
2582 2898 9.221775 CGGAGTAAAATAAGTGAATTTGCATAC 57.778 33.333 0.00 0.00 0.00 2.39
2614 2930 9.627395 GCATCTATATATATTCGTATGTGGTCC 57.373 37.037 0.00 0.00 0.00 4.46
2621 2937 6.911250 ATATTCGTATGTGGTCCATAGTGA 57.089 37.500 0.00 0.00 36.71 3.41
2622 2938 5.607939 ATTCGTATGTGGTCCATAGTGAA 57.392 39.130 0.00 0.00 36.71 3.18
2623 2939 5.408880 TTCGTATGTGGTCCATAGTGAAA 57.591 39.130 0.00 0.00 36.71 2.69
2624 2940 5.607939 TCGTATGTGGTCCATAGTGAAAT 57.392 39.130 0.00 0.00 36.71 2.17
2625 2941 6.718522 TCGTATGTGGTCCATAGTGAAATA 57.281 37.500 0.00 0.00 36.71 1.40
2626 2942 6.509656 TCGTATGTGGTCCATAGTGAAATAC 58.490 40.000 0.00 0.00 36.71 1.89
2627 2943 5.694910 CGTATGTGGTCCATAGTGAAATACC 59.305 44.000 0.00 0.00 36.71 2.73
2628 2944 5.975988 ATGTGGTCCATAGTGAAATACCT 57.024 39.130 0.00 0.00 29.82 3.08
2629 2945 7.255695 CGTATGTGGTCCATAGTGAAATACCTA 60.256 40.741 0.00 0.00 36.71 3.08
2630 2946 6.229936 TGTGGTCCATAGTGAAATACCTAC 57.770 41.667 0.00 0.00 0.00 3.18
2631 2947 5.722441 TGTGGTCCATAGTGAAATACCTACA 59.278 40.000 0.00 0.00 0.00 2.74
2632 2948 6.213802 TGTGGTCCATAGTGAAATACCTACAA 59.786 38.462 0.00 0.00 0.00 2.41
2633 2949 7.107542 GTGGTCCATAGTGAAATACCTACAAA 58.892 38.462 0.00 0.00 0.00 2.83
2634 2950 7.280205 GTGGTCCATAGTGAAATACCTACAAAG 59.720 40.741 0.00 0.00 0.00 2.77
2635 2951 7.181305 TGGTCCATAGTGAAATACCTACAAAGA 59.819 37.037 0.00 0.00 0.00 2.52
2636 2952 7.494952 GGTCCATAGTGAAATACCTACAAAGAC 59.505 40.741 0.00 0.00 0.00 3.01
2637 2953 8.258708 GTCCATAGTGAAATACCTACAAAGACT 58.741 37.037 0.00 0.00 0.00 3.24
2638 2954 8.822805 TCCATAGTGAAATACCTACAAAGACTT 58.177 33.333 0.00 0.00 0.00 3.01
2655 2971 9.892130 ACAAAGACTTATATTTAGGAACAGAGG 57.108 33.333 0.00 0.00 0.00 3.69
2656 2972 9.331282 CAAAGACTTATATTTAGGAACAGAGGG 57.669 37.037 0.00 0.00 0.00 4.30
2657 2973 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
2658 2974 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
2659 2975 8.068733 AGACTTATATTTAGGAACAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
2660 2976 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
2661 2977 9.900112 ACTTATATTTAGGAACAGAGGGAGTAT 57.100 33.333 0.00 0.00 0.00 2.12
2665 2981 9.900112 ATATTTAGGAACAGAGGGAGTATAAGT 57.100 33.333 0.00 0.00 0.00 2.24
2666 2982 7.657023 TTTAGGAACAGAGGGAGTATAAGTC 57.343 40.000 0.00 0.00 0.00 3.01
2667 2983 5.475398 AGGAACAGAGGGAGTATAAGTCT 57.525 43.478 0.00 0.00 0.00 3.24
2668 2984 5.844601 AGGAACAGAGGGAGTATAAGTCTT 58.155 41.667 0.00 0.00 0.00 3.01
2669 2985 6.265304 AGGAACAGAGGGAGTATAAGTCTTT 58.735 40.000 0.00 0.00 0.00 2.52
2670 2986 6.155393 AGGAACAGAGGGAGTATAAGTCTTTG 59.845 42.308 0.00 0.00 0.00 2.77
2671 2987 6.070710 GGAACAGAGGGAGTATAAGTCTTTGT 60.071 42.308 0.00 0.00 0.00 2.83
2672 2988 7.123847 GGAACAGAGGGAGTATAAGTCTTTGTA 59.876 40.741 0.00 0.00 0.00 2.41
2673 2989 8.431910 AACAGAGGGAGTATAAGTCTTTGTAA 57.568 34.615 0.00 0.00 0.00 2.41
2674 2990 8.068892 ACAGAGGGAGTATAAGTCTTTGTAAG 57.931 38.462 0.00 0.00 0.00 2.34
2675 2991 7.124448 ACAGAGGGAGTATAAGTCTTTGTAAGG 59.876 40.741 0.00 0.00 0.00 2.69
2676 2992 7.342284 CAGAGGGAGTATAAGTCTTTGTAAGGA 59.658 40.741 0.00 0.00 0.00 3.36
2677 2993 8.068733 AGAGGGAGTATAAGTCTTTGTAAGGAT 58.931 37.037 0.00 0.00 0.00 3.24
2678 2994 8.625467 AGGGAGTATAAGTCTTTGTAAGGATT 57.375 34.615 0.00 0.00 0.00 3.01
2679 2995 8.706521 AGGGAGTATAAGTCTTTGTAAGGATTC 58.293 37.037 0.00 0.00 0.00 2.52
2680 2996 8.706521 GGGAGTATAAGTCTTTGTAAGGATTCT 58.293 37.037 0.00 0.00 0.00 2.40
2687 3003 8.667592 AAGTCTTTGTAAGGATTCTACTAGGT 57.332 34.615 0.00 0.00 0.00 3.08
2688 3004 8.068892 AGTCTTTGTAAGGATTCTACTAGGTG 57.931 38.462 0.00 0.00 0.00 4.00
2689 3005 7.124448 AGTCTTTGTAAGGATTCTACTAGGTGG 59.876 40.741 0.00 0.00 0.00 4.61
2690 3006 7.123847 GTCTTTGTAAGGATTCTACTAGGTGGA 59.876 40.741 0.00 0.00 0.00 4.02
2691 3007 6.786967 TTGTAAGGATTCTACTAGGTGGAC 57.213 41.667 0.00 0.00 0.00 4.02
2692 3008 6.088541 TGTAAGGATTCTACTAGGTGGACT 57.911 41.667 0.00 0.00 0.00 3.85
2693 3009 7.217028 TGTAAGGATTCTACTAGGTGGACTA 57.783 40.000 0.00 0.00 0.00 2.59
2694 3010 7.059156 TGTAAGGATTCTACTAGGTGGACTAC 58.941 42.308 0.00 0.00 0.00 2.73
2695 3011 4.716794 AGGATTCTACTAGGTGGACTACG 58.283 47.826 0.00 0.00 0.00 3.51
2696 3012 4.165758 AGGATTCTACTAGGTGGACTACGT 59.834 45.833 0.00 0.00 0.00 3.57
2697 3013 5.367937 AGGATTCTACTAGGTGGACTACGTA 59.632 44.000 0.00 0.00 0.00 3.57
2698 3014 5.468409 GGATTCTACTAGGTGGACTACGTAC 59.532 48.000 0.00 0.00 0.00 3.67
2699 3015 4.046938 TCTACTAGGTGGACTACGTACG 57.953 50.000 15.01 15.01 0.00 3.67
2700 3016 2.029838 ACTAGGTGGACTACGTACGG 57.970 55.000 21.06 5.00 0.00 4.02
2701 3017 1.555075 ACTAGGTGGACTACGTACGGA 59.445 52.381 21.06 10.81 0.00 4.69
2702 3018 2.208431 CTAGGTGGACTACGTACGGAG 58.792 57.143 25.90 25.90 0.00 4.63
2703 3019 1.028868 AGGTGGACTACGTACGGAGC 61.029 60.000 27.33 18.72 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.447140 GCATGCGAAGTGACCGGTA 60.447 57.895 7.34 0.00 0.00 4.02
1 2 2.742372 GCATGCGAAGTGACCGGT 60.742 61.111 6.92 6.92 0.00 5.28
2 3 2.108514 ATGCATGCGAAGTGACCGG 61.109 57.895 14.09 0.00 0.00 5.28
3 4 1.061411 CATGCATGCGAAGTGACCG 59.939 57.895 14.93 0.00 0.00 4.79
4 5 1.368641 TACATGCATGCGAAGTGACC 58.631 50.000 26.53 0.00 0.00 4.02
5 6 3.680642 AATACATGCATGCGAAGTGAC 57.319 42.857 26.53 0.00 0.00 3.67
6 7 4.700268 AAAATACATGCATGCGAAGTGA 57.300 36.364 26.53 3.84 0.00 3.41
25 26 7.702772 ACGTGTTTTGCATACTCACAATAAAAA 59.297 29.630 10.46 0.00 0.00 1.94
26 27 7.197017 ACGTGTTTTGCATACTCACAATAAAA 58.803 30.769 10.46 0.00 0.00 1.52
27 28 6.730175 ACGTGTTTTGCATACTCACAATAAA 58.270 32.000 10.46 0.00 0.00 1.40
28 29 6.307031 ACGTGTTTTGCATACTCACAATAA 57.693 33.333 10.46 0.00 0.00 1.40
29 30 5.933187 ACGTGTTTTGCATACTCACAATA 57.067 34.783 10.46 0.00 0.00 1.90
30 31 4.829064 ACGTGTTTTGCATACTCACAAT 57.171 36.364 10.46 0.00 0.00 2.71
31 32 4.812091 AGTACGTGTTTTGCATACTCACAA 59.188 37.500 0.00 0.00 0.00 3.33
32 33 4.373527 AGTACGTGTTTTGCATACTCACA 58.626 39.130 0.00 0.00 0.00 3.58
33 34 4.985044 AGTACGTGTTTTGCATACTCAC 57.015 40.909 0.00 0.00 0.00 3.51
34 35 5.994887 AAAGTACGTGTTTTGCATACTCA 57.005 34.783 0.00 0.00 0.00 3.41
66 67 9.899226 GACTTGTTGTAAATTATGCTCTCTTTT 57.101 29.630 0.00 0.00 0.00 2.27
67 68 9.289782 AGACTTGTTGTAAATTATGCTCTCTTT 57.710 29.630 0.00 0.00 0.00 2.52
68 69 8.854614 AGACTTGTTGTAAATTATGCTCTCTT 57.145 30.769 0.00 0.00 0.00 2.85
69 70 9.593134 CTAGACTTGTTGTAAATTATGCTCTCT 57.407 33.333 0.00 0.00 0.00 3.10
70 71 8.821894 CCTAGACTTGTTGTAAATTATGCTCTC 58.178 37.037 0.00 0.00 0.00 3.20
71 72 7.770897 CCCTAGACTTGTTGTAAATTATGCTCT 59.229 37.037 0.00 0.00 0.00 4.09
72 73 7.769044 TCCCTAGACTTGTTGTAAATTATGCTC 59.231 37.037 0.00 0.00 0.00 4.26
73 74 7.630082 TCCCTAGACTTGTTGTAAATTATGCT 58.370 34.615 0.00 0.00 0.00 3.79
74 75 7.553044 ACTCCCTAGACTTGTTGTAAATTATGC 59.447 37.037 0.00 0.00 0.00 3.14
75 76 9.449719 AACTCCCTAGACTTGTTGTAAATTATG 57.550 33.333 0.00 0.00 0.00 1.90
76 77 9.449719 CAACTCCCTAGACTTGTTGTAAATTAT 57.550 33.333 0.00 0.00 34.91 1.28
77 78 7.389607 GCAACTCCCTAGACTTGTTGTAAATTA 59.610 37.037 14.46 0.00 39.81 1.40
78 79 6.206829 GCAACTCCCTAGACTTGTTGTAAATT 59.793 38.462 14.46 0.00 39.81 1.82
79 80 5.705905 GCAACTCCCTAGACTTGTTGTAAAT 59.294 40.000 14.46 0.00 39.81 1.40
80 81 5.061179 GCAACTCCCTAGACTTGTTGTAAA 58.939 41.667 14.46 0.00 39.81 2.01
81 82 4.638304 GCAACTCCCTAGACTTGTTGTAA 58.362 43.478 14.46 0.00 39.81 2.41
82 83 3.305813 CGCAACTCCCTAGACTTGTTGTA 60.306 47.826 14.46 0.00 39.81 2.41
83 84 2.548067 CGCAACTCCCTAGACTTGTTGT 60.548 50.000 14.46 0.00 39.81 3.32
84 85 2.069273 CGCAACTCCCTAGACTTGTTG 58.931 52.381 0.00 2.70 40.38 3.33
85 86 1.968493 TCGCAACTCCCTAGACTTGTT 59.032 47.619 0.00 0.00 0.00 2.83
86 87 1.629043 TCGCAACTCCCTAGACTTGT 58.371 50.000 0.00 0.00 0.00 3.16
87 88 2.288825 TGTTCGCAACTCCCTAGACTTG 60.289 50.000 0.00 0.00 0.00 3.16
88 89 1.968493 TGTTCGCAACTCCCTAGACTT 59.032 47.619 0.00 0.00 0.00 3.01
89 90 1.629043 TGTTCGCAACTCCCTAGACT 58.371 50.000 0.00 0.00 0.00 3.24
90 91 2.450609 TTGTTCGCAACTCCCTAGAC 57.549 50.000 0.00 0.00 31.15 2.59
104 105 4.733405 GTGGATGTTGTTTTCGAGTTGTTC 59.267 41.667 0.00 0.00 0.00 3.18
105 106 4.398044 AGTGGATGTTGTTTTCGAGTTGTT 59.602 37.500 0.00 0.00 0.00 2.83
106 107 3.945285 AGTGGATGTTGTTTTCGAGTTGT 59.055 39.130 0.00 0.00 0.00 3.32
107 108 4.527564 GAGTGGATGTTGTTTTCGAGTTG 58.472 43.478 0.00 0.00 0.00 3.16
108 109 3.564225 GGAGTGGATGTTGTTTTCGAGTT 59.436 43.478 0.00 0.00 0.00 3.01
109 110 3.139077 GGAGTGGATGTTGTTTTCGAGT 58.861 45.455 0.00 0.00 0.00 4.18
110 111 3.138304 TGGAGTGGATGTTGTTTTCGAG 58.862 45.455 0.00 0.00 0.00 4.04
111 112 3.201353 TGGAGTGGATGTTGTTTTCGA 57.799 42.857 0.00 0.00 0.00 3.71
112 113 4.023279 TGAATGGAGTGGATGTTGTTTTCG 60.023 41.667 0.00 0.00 0.00 3.46
113 114 5.452078 TGAATGGAGTGGATGTTGTTTTC 57.548 39.130 0.00 0.00 0.00 2.29
114 115 5.867903 TTGAATGGAGTGGATGTTGTTTT 57.132 34.783 0.00 0.00 0.00 2.43
115 116 5.867903 TTTGAATGGAGTGGATGTTGTTT 57.132 34.783 0.00 0.00 0.00 2.83
116 117 5.363580 AGTTTTGAATGGAGTGGATGTTGTT 59.636 36.000 0.00 0.00 0.00 2.83
117 118 4.895297 AGTTTTGAATGGAGTGGATGTTGT 59.105 37.500 0.00 0.00 0.00 3.32
118 119 5.458041 AGTTTTGAATGGAGTGGATGTTG 57.542 39.130 0.00 0.00 0.00 3.33
119 120 5.711976 CCTAGTTTTGAATGGAGTGGATGTT 59.288 40.000 0.00 0.00 0.00 2.71
120 121 5.256474 CCTAGTTTTGAATGGAGTGGATGT 58.744 41.667 0.00 0.00 0.00 3.06
121 122 4.096984 GCCTAGTTTTGAATGGAGTGGATG 59.903 45.833 0.00 0.00 0.00 3.51
122 123 4.018050 AGCCTAGTTTTGAATGGAGTGGAT 60.018 41.667 0.00 0.00 0.00 3.41
123 124 3.330701 AGCCTAGTTTTGAATGGAGTGGA 59.669 43.478 0.00 0.00 0.00 4.02
124 125 3.690460 AGCCTAGTTTTGAATGGAGTGG 58.310 45.455 0.00 0.00 0.00 4.00
125 126 6.825721 AGAATAGCCTAGTTTTGAATGGAGTG 59.174 38.462 0.00 0.00 0.00 3.51
126 127 6.963322 AGAATAGCCTAGTTTTGAATGGAGT 58.037 36.000 0.00 0.00 0.00 3.85
127 128 7.278875 AGAGAATAGCCTAGTTTTGAATGGAG 58.721 38.462 0.00 0.00 0.00 3.86
128 129 7.092891 TGAGAGAATAGCCTAGTTTTGAATGGA 60.093 37.037 0.00 0.00 0.00 3.41
129 130 7.011857 GTGAGAGAATAGCCTAGTTTTGAATGG 59.988 40.741 0.00 0.00 0.00 3.16
130 131 7.550551 TGTGAGAGAATAGCCTAGTTTTGAATG 59.449 37.037 0.00 0.00 0.00 2.67
131 132 7.624549 TGTGAGAGAATAGCCTAGTTTTGAAT 58.375 34.615 0.00 0.00 0.00 2.57
132 133 7.004555 TGTGAGAGAATAGCCTAGTTTTGAA 57.995 36.000 0.00 0.00 0.00 2.69
133 134 6.605471 TGTGAGAGAATAGCCTAGTTTTGA 57.395 37.500 0.00 0.00 0.00 2.69
134 135 7.672983 TTTGTGAGAGAATAGCCTAGTTTTG 57.327 36.000 0.00 0.00 0.00 2.44
135 136 7.095187 CGTTTTGTGAGAGAATAGCCTAGTTTT 60.095 37.037 0.00 0.00 0.00 2.43
136 137 6.369065 CGTTTTGTGAGAGAATAGCCTAGTTT 59.631 38.462 0.00 0.00 0.00 2.66
280 281 3.682858 AGATGAAACGGTCAAATGGTACG 59.317 43.478 0.00 0.00 40.50 3.67
281 282 5.220340 CGTAGATGAAACGGTCAAATGGTAC 60.220 44.000 0.00 0.00 40.50 3.34
282 283 4.865925 CGTAGATGAAACGGTCAAATGGTA 59.134 41.667 0.00 0.00 40.50 3.25
300 301 2.279502 GATGTGCTGACGGGCGTAGA 62.280 60.000 0.00 0.00 34.52 2.59
334 335 2.225522 TGGTCTGATAAGGTGGACAGGA 60.226 50.000 0.00 0.00 0.00 3.86
512 786 3.152341 CCAAGGCTCTTGACTGACATTT 58.848 45.455 14.33 0.00 0.00 2.32
536 810 6.827727 ACACTTTGTGAAATGGTAGAGTAGT 58.172 36.000 4.61 0.00 36.96 2.73
576 850 6.682423 TCGAAATTACATCAACATGCAGAT 57.318 33.333 0.00 0.00 32.57 2.90
579 853 8.028354 AGATTTTCGAAATTACATCAACATGCA 58.972 29.630 12.12 0.00 32.57 3.96
679 953 8.865590 TCATTGTGAATGATGATGCTTTTATG 57.134 30.769 0.00 0.00 42.69 1.90
692 966 7.548427 ACAACATTGTTTTGTCATTGTGAATGA 59.452 29.630 0.00 0.00 41.05 2.57
794 1069 6.402017 CAGTTAAACTTTGCAATGTTTGACG 58.598 36.000 34.49 29.09 42.28 4.35
836 1111 1.411394 TCGAGGTCGTTTTTACTGCG 58.589 50.000 0.00 0.00 40.80 5.18
853 1128 3.677190 AGTTAGATACTCCCTCCGATCG 58.323 50.000 8.51 8.51 28.23 3.69
854 1129 5.318630 AGAAGTTAGATACTCCCTCCGATC 58.681 45.833 0.00 0.00 35.54 3.69
855 1130 5.327737 AGAAGTTAGATACTCCCTCCGAT 57.672 43.478 0.00 0.00 35.54 4.18
856 1131 4.792513 AGAAGTTAGATACTCCCTCCGA 57.207 45.455 0.00 0.00 35.54 4.55
857 1132 4.038162 CCAAGAAGTTAGATACTCCCTCCG 59.962 50.000 0.00 0.00 35.54 4.63
1105 1409 1.073923 GTTGAAGGTGGTGTGGAGGAT 59.926 52.381 0.00 0.00 0.00 3.24
1141 1445 1.789576 AAGCCAAACTCCGGGTGGAT 61.790 55.000 15.78 8.53 45.33 3.41
1142 1446 2.406002 GAAGCCAAACTCCGGGTGGA 62.406 60.000 15.78 0.00 43.88 4.02
1232 1536 2.607750 ACCCTGACGCCTCCATGT 60.608 61.111 0.00 0.00 0.00 3.21
1477 1781 5.137403 GTGATCACGATTAACAACACACAC 58.863 41.667 10.69 0.00 0.00 3.82
1590 1894 2.584391 GCTGGGGTCGAACAGGTCT 61.584 63.158 1.31 0.00 35.30 3.85
1938 2242 2.187946 CTGTTAGCGAGGCCCCAG 59.812 66.667 0.00 0.00 0.00 4.45
1950 2254 3.622060 GAAGGGCCTGCCGCTGTTA 62.622 63.158 6.92 0.00 36.75 2.41
1965 2269 2.261671 CGGACGACCCACAGGAAG 59.738 66.667 0.00 0.00 36.73 3.46
2273 2577 1.900498 GCCTGCTCAACCTTGCACT 60.900 57.895 0.00 0.00 35.20 4.40
2275 2579 2.753009 ATCGCCTGCTCAACCTTGCA 62.753 55.000 0.00 0.00 37.63 4.08
2287 2591 2.956964 GAACCTCGCGATCGCCTG 60.957 66.667 32.63 23.98 37.98 4.85
2322 2626 4.247380 CTCTCCCTCATGGCCGCC 62.247 72.222 1.04 1.04 0.00 6.13
2343 2647 2.234143 GCTTTGACCTGAAGCTCCTTT 58.766 47.619 1.85 0.00 44.63 3.11
2356 2660 1.471684 CAGAGCCTCCATTGCTTTGAC 59.528 52.381 0.00 0.00 41.95 3.18
2427 2731 8.123639 TGTATACTTTGACTCATAGGGATAGC 57.876 38.462 4.17 0.00 0.00 2.97
2430 2734 7.514127 ACCATGTATACTTTGACTCATAGGGAT 59.486 37.037 4.17 0.00 0.00 3.85
2463 2777 1.037493 TAGCCACACACGTTCTGACT 58.963 50.000 0.00 0.00 0.00 3.41
2502 2818 5.742063 ACTTTTATTTAGGAACGGAGGGAG 58.258 41.667 0.00 0.00 0.00 4.30
2504 2820 5.742063 AGACTTTTATTTAGGAACGGAGGG 58.258 41.667 0.00 0.00 0.00 4.30
2505 2821 7.683437 AAAGACTTTTATTTAGGAACGGAGG 57.317 36.000 0.00 0.00 0.00 4.30
2506 2822 9.649167 TCTAAAGACTTTTATTTAGGAACGGAG 57.351 33.333 5.61 0.00 38.79 4.63
2507 2823 9.649167 CTCTAAAGACTTTTATTTAGGAACGGA 57.351 33.333 5.61 0.00 38.79 4.69
2521 2837 9.377312 GCATAGTGAAATCTCTCTAAAGACTTT 57.623 33.333 5.62 5.62 32.78 2.66
2522 2838 8.535335 TGCATAGTGAAATCTCTCTAAAGACTT 58.465 33.333 0.00 0.00 32.78 3.01
2523 2839 8.072321 TGCATAGTGAAATCTCTCTAAAGACT 57.928 34.615 0.00 0.00 32.78 3.24
2524 2840 8.885494 ATGCATAGTGAAATCTCTCTAAAGAC 57.115 34.615 0.00 0.00 32.78 3.01
2525 2841 8.699130 TGATGCATAGTGAAATCTCTCTAAAGA 58.301 33.333 0.00 0.00 32.78 2.52
2526 2842 8.763356 GTGATGCATAGTGAAATCTCTCTAAAG 58.237 37.037 0.00 0.00 32.78 1.85
2527 2843 8.260114 TGTGATGCATAGTGAAATCTCTCTAAA 58.740 33.333 0.00 0.00 32.78 1.85
2528 2844 7.785033 TGTGATGCATAGTGAAATCTCTCTAA 58.215 34.615 0.00 0.00 32.78 2.10
2529 2845 7.352079 TGTGATGCATAGTGAAATCTCTCTA 57.648 36.000 0.00 0.00 33.38 2.43
2530 2846 6.231258 TGTGATGCATAGTGAAATCTCTCT 57.769 37.500 0.00 0.00 0.00 3.10
2531 2847 7.148836 CGTATGTGATGCATAGTGAAATCTCTC 60.149 40.741 0.00 0.00 40.42 3.20
2532 2848 6.644181 CGTATGTGATGCATAGTGAAATCTCT 59.356 38.462 0.00 0.00 40.42 3.10
2533 2849 6.128715 CCGTATGTGATGCATAGTGAAATCTC 60.129 42.308 0.00 0.00 40.42 2.75
2534 2850 5.698089 CCGTATGTGATGCATAGTGAAATCT 59.302 40.000 0.00 0.00 40.42 2.40
2535 2851 5.696270 TCCGTATGTGATGCATAGTGAAATC 59.304 40.000 0.00 0.00 40.42 2.17
2536 2852 5.610398 TCCGTATGTGATGCATAGTGAAAT 58.390 37.500 0.00 0.00 40.42 2.17
2537 2853 5.017294 TCCGTATGTGATGCATAGTGAAA 57.983 39.130 0.00 0.00 40.42 2.69
2538 2854 4.099419 ACTCCGTATGTGATGCATAGTGAA 59.901 41.667 0.00 0.00 40.42 3.18
2539 2855 3.636764 ACTCCGTATGTGATGCATAGTGA 59.363 43.478 0.00 0.00 40.42 3.41
2540 2856 3.982475 ACTCCGTATGTGATGCATAGTG 58.018 45.455 0.00 0.00 40.42 2.74
2541 2857 5.784578 TTACTCCGTATGTGATGCATAGT 57.215 39.130 0.00 0.00 40.42 2.12
2542 2858 7.658179 ATTTTACTCCGTATGTGATGCATAG 57.342 36.000 0.00 0.00 40.42 2.23
2543 2859 9.203421 CTTATTTTACTCCGTATGTGATGCATA 57.797 33.333 0.00 0.00 38.94 3.14
2544 2860 7.715249 ACTTATTTTACTCCGTATGTGATGCAT 59.285 33.333 0.00 0.00 41.42 3.96
2545 2861 7.011016 CACTTATTTTACTCCGTATGTGATGCA 59.989 37.037 0.00 0.00 0.00 3.96
2546 2862 7.223971 TCACTTATTTTACTCCGTATGTGATGC 59.776 37.037 0.00 0.00 30.84 3.91
2547 2863 8.642908 TCACTTATTTTACTCCGTATGTGATG 57.357 34.615 0.00 0.00 30.84 3.07
2548 2864 9.832445 ATTCACTTATTTTACTCCGTATGTGAT 57.168 29.630 0.00 0.00 33.82 3.06
2549 2865 9.661563 AATTCACTTATTTTACTCCGTATGTGA 57.338 29.630 0.00 0.00 32.69 3.58
2552 2868 9.221775 GCAAATTCACTTATTTTACTCCGTATG 57.778 33.333 0.00 0.00 0.00 2.39
2553 2869 8.952278 TGCAAATTCACTTATTTTACTCCGTAT 58.048 29.630 0.00 0.00 0.00 3.06
2554 2870 8.325421 TGCAAATTCACTTATTTTACTCCGTA 57.675 30.769 0.00 0.00 0.00 4.02
2555 2871 7.209471 TGCAAATTCACTTATTTTACTCCGT 57.791 32.000 0.00 0.00 0.00 4.69
2556 2872 9.221775 GTATGCAAATTCACTTATTTTACTCCG 57.778 33.333 0.00 0.00 0.00 4.63
2588 2904 9.627395 GGACCACATACGAATATATATAGATGC 57.373 37.037 0.00 0.00 0.00 3.91
2595 2911 9.689501 TCACTATGGACCACATACGAATATATA 57.310 33.333 0.00 0.00 41.03 0.86
2596 2912 8.589701 TCACTATGGACCACATACGAATATAT 57.410 34.615 0.00 0.00 41.03 0.86
2597 2913 8.411991 TTCACTATGGACCACATACGAATATA 57.588 34.615 0.00 0.00 41.03 0.86
2598 2914 6.911250 TCACTATGGACCACATACGAATAT 57.089 37.500 0.00 0.00 41.03 1.28
2599 2915 6.718522 TTCACTATGGACCACATACGAATA 57.281 37.500 0.00 0.00 41.03 1.75
2600 2916 5.607939 TTCACTATGGACCACATACGAAT 57.392 39.130 0.00 0.00 41.03 3.34
2601 2917 5.408880 TTTCACTATGGACCACATACGAA 57.591 39.130 0.00 0.00 41.03 3.85
2602 2918 5.607939 ATTTCACTATGGACCACATACGA 57.392 39.130 0.00 0.00 41.03 3.43
2603 2919 5.694910 GGTATTTCACTATGGACCACATACG 59.305 44.000 0.00 0.00 41.03 3.06
2604 2920 6.827727 AGGTATTTCACTATGGACCACATAC 58.172 40.000 0.00 0.00 41.03 2.39
2605 2921 7.565768 TGTAGGTATTTCACTATGGACCACATA 59.434 37.037 0.00 0.00 41.03 2.29
2606 2922 5.975988 AGGTATTTCACTATGGACCACAT 57.024 39.130 0.00 0.00 43.68 3.21
2607 2923 5.722441 TGTAGGTATTTCACTATGGACCACA 59.278 40.000 0.00 0.00 0.00 4.17
2608 2924 6.229936 TGTAGGTATTTCACTATGGACCAC 57.770 41.667 0.00 0.00 0.00 4.16
2609 2925 6.877668 TTGTAGGTATTTCACTATGGACCA 57.122 37.500 0.00 0.00 0.00 4.02
2610 2926 7.494952 GTCTTTGTAGGTATTTCACTATGGACC 59.505 40.741 0.00 0.00 0.00 4.46
2611 2927 8.258708 AGTCTTTGTAGGTATTTCACTATGGAC 58.741 37.037 0.00 0.00 0.00 4.02
2612 2928 8.375493 AGTCTTTGTAGGTATTTCACTATGGA 57.625 34.615 0.00 0.00 0.00 3.41
2629 2945 9.892130 CCTCTGTTCCTAAATATAAGTCTTTGT 57.108 33.333 0.00 0.00 0.00 2.83
2630 2946 9.331282 CCCTCTGTTCCTAAATATAAGTCTTTG 57.669 37.037 0.00 0.00 0.00 2.77
2631 2947 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
2632 2948 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
2633 2949 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
2634 2950 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
2635 2951 9.900112 ATACTCCCTCTGTTCCTAAATATAAGT 57.100 33.333 0.00 0.00 0.00 2.24
2639 2955 9.900112 ACTTATACTCCCTCTGTTCCTAAATAT 57.100 33.333 0.00 0.00 0.00 1.28
2640 2956 9.364653 GACTTATACTCCCTCTGTTCCTAAATA 57.635 37.037 0.00 0.00 0.00 1.40
2641 2957 8.068733 AGACTTATACTCCCTCTGTTCCTAAAT 58.931 37.037 0.00 0.00 0.00 1.40
2642 2958 7.420029 AGACTTATACTCCCTCTGTTCCTAAA 58.580 38.462 0.00 0.00 0.00 1.85
2643 2959 6.982899 AGACTTATACTCCCTCTGTTCCTAA 58.017 40.000 0.00 0.00 0.00 2.69
2644 2960 6.593759 AGACTTATACTCCCTCTGTTCCTA 57.406 41.667 0.00 0.00 0.00 2.94
2645 2961 5.475398 AGACTTATACTCCCTCTGTTCCT 57.525 43.478 0.00 0.00 0.00 3.36
2646 2962 6.070710 ACAAAGACTTATACTCCCTCTGTTCC 60.071 42.308 0.00 0.00 0.00 3.62
2647 2963 6.937392 ACAAAGACTTATACTCCCTCTGTTC 58.063 40.000 0.00 0.00 0.00 3.18
2648 2964 6.936968 ACAAAGACTTATACTCCCTCTGTT 57.063 37.500 0.00 0.00 0.00 3.16
2649 2965 7.124448 CCTTACAAAGACTTATACTCCCTCTGT 59.876 40.741 0.00 0.00 0.00 3.41
2650 2966 7.342284 TCCTTACAAAGACTTATACTCCCTCTG 59.658 40.741 0.00 0.00 0.00 3.35
2651 2967 7.420029 TCCTTACAAAGACTTATACTCCCTCT 58.580 38.462 0.00 0.00 0.00 3.69
2652 2968 7.657023 TCCTTACAAAGACTTATACTCCCTC 57.343 40.000 0.00 0.00 0.00 4.30
2653 2969 8.625467 AATCCTTACAAAGACTTATACTCCCT 57.375 34.615 0.00 0.00 0.00 4.20
2654 2970 8.706521 AGAATCCTTACAAAGACTTATACTCCC 58.293 37.037 0.00 0.00 0.00 4.30
2661 2977 9.765295 ACCTAGTAGAATCCTTACAAAGACTTA 57.235 33.333 0.00 0.00 0.00 2.24
2662 2978 8.532819 CACCTAGTAGAATCCTTACAAAGACTT 58.467 37.037 0.00 0.00 0.00 3.01
2663 2979 7.124448 CCACCTAGTAGAATCCTTACAAAGACT 59.876 40.741 0.00 0.00 0.00 3.24
2664 2980 7.123847 TCCACCTAGTAGAATCCTTACAAAGAC 59.876 40.741 0.00 0.00 0.00 3.01
2665 2981 7.123847 GTCCACCTAGTAGAATCCTTACAAAGA 59.876 40.741 0.00 0.00 0.00 2.52
2666 2982 7.124448 AGTCCACCTAGTAGAATCCTTACAAAG 59.876 40.741 0.00 0.00 0.00 2.77
2667 2983 6.958192 AGTCCACCTAGTAGAATCCTTACAAA 59.042 38.462 0.00 0.00 0.00 2.83
2668 2984 6.500336 AGTCCACCTAGTAGAATCCTTACAA 58.500 40.000 0.00 0.00 0.00 2.41
2669 2985 6.088541 AGTCCACCTAGTAGAATCCTTACA 57.911 41.667 0.00 0.00 0.00 2.41
2670 2986 6.204495 CGTAGTCCACCTAGTAGAATCCTTAC 59.796 46.154 0.00 0.00 0.00 2.34
2671 2987 6.126652 ACGTAGTCCACCTAGTAGAATCCTTA 60.127 42.308 0.00 0.00 29.74 2.69
2672 2988 5.131784 CGTAGTCCACCTAGTAGAATCCTT 58.868 45.833 0.00 0.00 0.00 3.36
2673 2989 4.165758 ACGTAGTCCACCTAGTAGAATCCT 59.834 45.833 0.00 0.00 29.74 3.24
2674 2990 4.459330 ACGTAGTCCACCTAGTAGAATCC 58.541 47.826 0.00 0.00 29.74 3.01
2675 2991 5.176590 CGTACGTAGTCCACCTAGTAGAATC 59.823 48.000 7.22 0.00 43.93 2.52
2676 2992 5.053145 CGTACGTAGTCCACCTAGTAGAAT 58.947 45.833 7.22 0.00 43.93 2.40
2677 2993 4.433615 CGTACGTAGTCCACCTAGTAGAA 58.566 47.826 7.22 0.00 43.93 2.10
2678 2994 3.181475 CCGTACGTAGTCCACCTAGTAGA 60.181 52.174 15.21 0.00 43.93 2.59
2679 2995 3.126831 CCGTACGTAGTCCACCTAGTAG 58.873 54.545 15.21 0.00 43.93 2.57
2680 2996 2.764010 TCCGTACGTAGTCCACCTAGTA 59.236 50.000 15.21 0.00 43.93 1.82
2681 2997 1.555075 TCCGTACGTAGTCCACCTAGT 59.445 52.381 15.21 0.00 43.93 2.57
2682 2998 2.208431 CTCCGTACGTAGTCCACCTAG 58.792 57.143 15.21 0.00 43.93 3.02
2683 2999 1.743772 GCTCCGTACGTAGTCCACCTA 60.744 57.143 15.21 0.00 43.93 3.08
2684 3000 1.028868 GCTCCGTACGTAGTCCACCT 61.029 60.000 15.21 0.00 43.93 4.00
2685 3001 1.308069 TGCTCCGTACGTAGTCCACC 61.308 60.000 15.21 0.00 43.93 4.61
2686 3002 0.523072 TTGCTCCGTACGTAGTCCAC 59.477 55.000 15.21 0.00 43.93 4.02
2687 3003 1.246649 TTTGCTCCGTACGTAGTCCA 58.753 50.000 15.21 0.00 43.93 4.02
2688 3004 2.352503 TTTTGCTCCGTACGTAGTCC 57.647 50.000 15.21 0.00 43.93 3.85
2689 3005 3.504863 TCATTTTGCTCCGTACGTAGTC 58.495 45.455 15.21 5.03 43.93 2.59
2691 3007 4.565166 TCATTCATTTTGCTCCGTACGTAG 59.435 41.667 15.21 9.26 0.00 3.51
2692 3008 4.496360 TCATTCATTTTGCTCCGTACGTA 58.504 39.130 15.21 0.00 0.00 3.57
2693 3009 3.331150 TCATTCATTTTGCTCCGTACGT 58.669 40.909 15.21 0.00 0.00 3.57
2694 3010 4.335082 TTCATTCATTTTGCTCCGTACG 57.665 40.909 8.69 8.69 0.00 3.67
2695 3011 6.124088 AGATTCATTCATTTTGCTCCGTAC 57.876 37.500 0.00 0.00 0.00 3.67
2696 3012 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
2697 3013 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
2698 3014 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
2699 3015 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.