Multiple sequence alignment - TraesCS7D01G213500

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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 TraesCS7D01G213500 chr7D 100.000 4273 0 0 1 4273 172252418 172256690 0.000000e+00 7891
1 TraesCS7D01G213500 chr7D 92.424 198 10 5 2829 3024 312574099 312574293 1.170000e-70 278
2 TraesCS7D01G213500 chr7B 92.139 2506 103 35 1 2442 138249586 138252061 0.000000e+00 3450
3 TraesCS7D01G213500 chr7B 91.494 1011 67 10 3022 4018 138252684 138253689 0.000000e+00 1373
4 TraesCS7D01G213500 chr7B 96.742 399 13 0 2456 2854 138252275 138252673 0.000000e+00 665
5 TraesCS7D01G213500 chr7B 84.080 201 21 8 4081 4273 138253700 138253897 2.620000e-42 183
6 TraesCS7D01G213500 chr7A 94.283 1889 81 15 211 2088 174912606 174914478 0.000000e+00 2865
7 TraesCS7D01G213500 chr7A 91.383 1265 84 15 3022 4273 174915296 174916548 0.000000e+00 1709
8 TraesCS7D01G213500 chr7A 97.757 758 16 1 2103 2860 174914541 174915297 0.000000e+00 1304
9 TraesCS7D01G213500 chr7A 95.402 174 8 0 2858 3031 643187055 643186882 1.170000e-70 278
10 TraesCS7D01G213500 chr7A 94.350 177 9 1 2849 3025 61889790 61889965 1.960000e-68 270
11 TraesCS7D01G213500 chr2A 97.024 168 5 0 2856 3023 469790033 469790200 2.520000e-72 283
12 TraesCS7D01G213500 chr2B 95.858 169 7 0 2858 3026 519598860 519599028 1.510000e-69 274
13 TraesCS7D01G213500 chr5D 93.956 182 8 3 2843 3023 445106667 445106488 5.440000e-69 272
14 TraesCS7D01G213500 chr1D 94.857 175 8 1 2850 3023 285370998 285371172 5.440000e-69 272
15 TraesCS7D01G213500 chr1D 92.935 184 10 1 2851 3034 39948942 39948762 9.110000e-67 265
16 TraesCS7D01G213500 chr4D 93.889 180 8 3 2845 3024 486769367 486769191 7.040000e-68 268


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 TraesCS7D01G213500 chr7D 172252418 172256690 4272 False 7891.000000 7891 100.000000 1 4273 1 chr7D.!!$F1 4272
1 TraesCS7D01G213500 chr7B 138249586 138253897 4311 False 1417.750000 3450 91.113750 1 4273 4 chr7B.!!$F1 4272
2 TraesCS7D01G213500 chr7A 174912606 174916548 3942 False 1959.333333 2865 94.474333 211 4273 3 chr7A.!!$F2 4062

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
489 503 0.178924 CCCCAATCCCAATCCCCATC 60.179 60.000 0.00 0.0 0.00 3.51 F
490 504 0.178924 CCCAATCCCAATCCCCATCC 60.179 60.000 0.00 0.0 0.00 3.51 F
491 505 0.178924 CCAATCCCAATCCCCATCCC 60.179 60.000 0.00 0.0 0.00 3.85 F
492 506 0.178924 CAATCCCAATCCCCATCCCC 60.179 60.000 0.00 0.0 0.00 4.81 F
922 960 0.321653 GTGGCATCGAGGGTTTGAGT 60.322 55.000 0.00 0.0 0.00 3.41 F
1581 1620 1.134280 CAGGATGAAGGGCCTAGTGTG 60.134 57.143 6.41 0.0 39.69 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1334 0.392461 ACAATCCATGAACCCCGACG 60.392 55.000 0.00 0.00 0.00 5.12 R
1527 1566 0.536233 TGCACTCCGGCTTGCTTAAA 60.536 50.000 22.87 5.06 39.62 1.52 R
2398 2495 2.839486 TGTTGAAGTCTAGTGCTGGG 57.161 50.000 0.00 0.00 0.00 4.45 R
2728 3025 8.650143 AAAGGGCTTAAAATGAGAAACATAGA 57.350 30.769 0.00 0.00 38.38 1.98 R
3001 3304 2.065799 ACTCCCTCTGTTCCCAAATGT 58.934 47.619 0.00 0.00 0.00 2.71 R
3347 3655 0.673644 ATGTGAGCTGGTACAACCGC 60.674 55.000 0.00 5.23 42.58 5.68 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
29 30 2.983030 GGTGGCACATGGCGTTCA 60.983 61.111 20.82 0.00 44.52 3.18
38 39 1.026718 CATGGCGTTCAAGGAGGGAC 61.027 60.000 0.00 0.00 0.00 4.46
40 41 2.434359 GCGTTCAAGGAGGGACCG 60.434 66.667 0.00 0.00 44.74 4.79
42 43 2.669240 GTTCAAGGAGGGACCGGG 59.331 66.667 6.32 0.00 44.74 5.73
61 62 0.462581 GACAAGATCATGCGGCCAGA 60.463 55.000 2.24 0.00 0.00 3.86
65 66 1.146930 GATCATGCGGCCAGAAGGA 59.853 57.895 2.24 0.00 36.89 3.36
76 77 1.734477 CAGAAGGAGCGTGTGGTCG 60.734 63.158 0.00 0.00 43.60 4.79
78 79 1.006571 GAAGGAGCGTGTGGTCGAA 60.007 57.895 0.00 0.00 43.60 3.71
88 89 2.673833 GTGTGGTCGAAAACTCGAGAT 58.326 47.619 21.68 3.75 43.18 2.75
138 140 8.635765 CCAGCATTTGGGTATACTTATTACAT 57.364 34.615 2.25 0.00 43.75 2.29
139 141 9.077885 CCAGCATTTGGGTATACTTATTACATT 57.922 33.333 2.25 0.00 43.75 2.71
146 148 8.228035 TGGGTATACTTATTACATTTTGCACC 57.772 34.615 2.25 0.00 0.00 5.01
147 149 7.834681 TGGGTATACTTATTACATTTTGCACCA 59.165 33.333 2.25 0.00 0.00 4.17
166 168 6.765036 TGCACCAAAATAAACATCACAAACAT 59.235 30.769 0.00 0.00 0.00 2.71
170 172 9.255304 ACCAAAATAAACATCACAAACATGTAC 57.745 29.630 0.00 0.00 33.12 2.90
171 173 9.254133 CCAAAATAAACATCACAAACATGTACA 57.746 29.630 0.00 0.00 33.12 2.90
176 178 9.979578 ATAAACATCACAAACATGTACAAATGT 57.020 25.926 0.00 0.00 42.62 2.71
185 187 6.801539 AACATGTACAAATGTTCACGATCT 57.198 33.333 8.69 0.00 45.47 2.75
186 188 6.801539 ACATGTACAAATGTTCACGATCTT 57.198 33.333 0.00 0.00 37.50 2.40
187 189 6.831769 ACATGTACAAATGTTCACGATCTTC 58.168 36.000 0.00 0.00 37.50 2.87
188 190 5.856126 TGTACAAATGTTCACGATCTTCC 57.144 39.130 0.00 0.00 0.00 3.46
189 191 4.387559 TGTACAAATGTTCACGATCTTCCG 59.612 41.667 0.00 0.00 0.00 4.30
191 193 3.679980 ACAAATGTTCACGATCTTCCGAG 59.320 43.478 0.00 0.00 0.00 4.63
192 194 3.868757 AATGTTCACGATCTTCCGAGA 57.131 42.857 0.00 0.00 36.09 4.04
193 195 4.392921 AATGTTCACGATCTTCCGAGAT 57.607 40.909 0.00 0.00 45.27 2.75
194 196 5.515797 AATGTTCACGATCTTCCGAGATA 57.484 39.130 0.00 0.00 42.66 1.98
195 197 5.713792 ATGTTCACGATCTTCCGAGATAT 57.286 39.130 0.00 0.00 42.66 1.63
199 201 6.485648 TGTTCACGATCTTCCGAGATATAGAA 59.514 38.462 0.00 0.00 42.66 2.10
200 202 7.012989 TGTTCACGATCTTCCGAGATATAGAAA 59.987 37.037 0.00 0.00 42.66 2.52
201 203 7.506328 TCACGATCTTCCGAGATATAGAAAA 57.494 36.000 0.00 0.00 42.66 2.29
202 204 7.361127 TCACGATCTTCCGAGATATAGAAAAC 58.639 38.462 0.00 0.00 42.66 2.43
203 205 6.583050 CACGATCTTCCGAGATATAGAAAACC 59.417 42.308 0.00 0.00 42.66 3.27
204 206 5.795939 CGATCTTCCGAGATATAGAAAACCG 59.204 44.000 0.00 0.00 42.66 4.44
206 208 6.461110 TCTTCCGAGATATAGAAAACCGTT 57.539 37.500 0.00 0.00 0.00 4.44
208 210 7.325694 TCTTCCGAGATATAGAAAACCGTTTT 58.674 34.615 9.01 9.01 35.12 2.43
209 211 7.820872 TCTTCCGAGATATAGAAAACCGTTTTT 59.179 33.333 10.53 0.00 37.65 1.94
230 232 6.852858 TTTTTGTTTTGTTTATGCTAGCCC 57.147 33.333 13.29 0.00 0.00 5.19
297 300 2.098614 GTGAGATCTCTGCACTCTCCA 58.901 52.381 22.95 0.00 35.59 3.86
346 349 9.362539 ACATGCAAAAAGATCATGATTTCTTAC 57.637 29.630 10.14 0.00 39.80 2.34
424 438 0.903454 TCCTCTCTCCAAACGTCCCC 60.903 60.000 0.00 0.00 0.00 4.81
474 488 3.261677 GCACCTACCCCAACCCCA 61.262 66.667 0.00 0.00 0.00 4.96
476 490 2.092585 CACCTACCCCAACCCCAAT 58.907 57.895 0.00 0.00 0.00 3.16
488 502 0.935837 ACCCCAATCCCAATCCCCAT 60.936 55.000 0.00 0.00 0.00 4.00
489 503 0.178924 CCCCAATCCCAATCCCCATC 60.179 60.000 0.00 0.00 0.00 3.51
490 504 0.178924 CCCAATCCCAATCCCCATCC 60.179 60.000 0.00 0.00 0.00 3.51
491 505 0.178924 CCAATCCCAATCCCCATCCC 60.179 60.000 0.00 0.00 0.00 3.85
492 506 0.178924 CAATCCCAATCCCCATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
493 507 1.729267 AATCCCAATCCCCATCCCCG 61.729 60.000 0.00 0.00 0.00 5.73
581 595 4.087892 CCGTGCCCTACAGCTGCT 62.088 66.667 15.27 0.00 0.00 4.24
667 684 3.446570 CGCCGTCCCCGTTCTACT 61.447 66.667 0.00 0.00 0.00 2.57
678 695 2.157073 GTTCTACTTCGCGGCGTCC 61.157 63.158 22.90 0.00 0.00 4.79
733 768 2.163412 GCATTTTGCCGTCCAGTGATTA 59.837 45.455 0.00 0.00 37.42 1.75
746 781 3.244353 CCAGTGATTAGCTAGACCCCATG 60.244 52.174 0.00 0.00 0.00 3.66
757 792 1.062810 AGACCCCATGGACCTCTAGAC 60.063 57.143 15.22 0.00 34.81 2.59
824 859 5.051508 GCTTTCACTGTACTGCATTTGTTTG 60.052 40.000 0.00 0.00 0.00 2.93
870 908 1.467920 GGCTCACTGGATTCCCTTTG 58.532 55.000 0.00 0.00 0.00 2.77
873 911 3.157087 GCTCACTGGATTCCCTTTGAAA 58.843 45.455 0.00 0.00 36.33 2.69
908 946 2.277591 GGCTGCTGGATTTGTGGCA 61.278 57.895 0.00 0.00 0.00 4.92
922 960 0.321653 GTGGCATCGAGGGTTTGAGT 60.322 55.000 0.00 0.00 0.00 3.41
981 1020 1.256376 CATCGCAGATTTCGGTCTTCG 59.744 52.381 0.00 0.00 45.12 3.79
1023 1062 2.416162 GGAGACGAATGAGAAGAACGCT 60.416 50.000 0.00 0.00 0.00 5.07
1024 1063 3.181499 GGAGACGAATGAGAAGAACGCTA 60.181 47.826 0.00 0.00 0.00 4.26
1025 1064 4.413087 GAGACGAATGAGAAGAACGCTAA 58.587 43.478 0.00 0.00 0.00 3.09
1108 1147 3.338126 TTCTCGCTCTCGCCGGAAC 62.338 63.158 5.05 0.00 35.26 3.62
1404 1443 2.706190 CCCTCCTATGGGTAGTTTCCAG 59.294 54.545 0.00 0.00 42.25 3.86
1581 1620 1.134280 CAGGATGAAGGGCCTAGTGTG 60.134 57.143 6.41 0.00 39.69 3.82
1681 1722 6.019801 CGATTTCGATGGAACTTAGAATTCGT 60.020 38.462 0.00 0.00 43.02 3.85
2072 2121 2.152016 GACCTTGTTCCTGGTTGTAGC 58.848 52.381 0.00 0.00 36.59 3.58
2174 2271 5.479724 TCTCCACAATTCACATTATTGCCAA 59.520 36.000 0.00 0.00 36.65 4.52
2286 2383 3.679917 CGGCAAGTTGAGGTATGATGTCT 60.680 47.826 7.16 0.00 0.00 3.41
2340 2437 4.612712 GCGCTTTGCTGTAATGTGAACTTA 60.613 41.667 0.00 0.00 41.73 2.24
2398 2495 4.024893 TCGATGAAACTTTCAGCTGTCAAC 60.025 41.667 14.67 6.77 43.56 3.18
2507 2804 8.801299 TCATTTGTTTTCCTTGTGCTGATATAA 58.199 29.630 0.00 0.00 0.00 0.98
2508 2805 9.421806 CATTTGTTTTCCTTGTGCTGATATAAA 57.578 29.630 0.00 0.00 0.00 1.40
2728 3025 4.522789 GGTTTGTCCCATCACTTATTGTGT 59.477 41.667 0.00 0.00 46.27 3.72
2767 3064 9.785982 TTTTAAGCCCTTTAAAACAAATGCTAT 57.214 25.926 1.81 0.00 43.05 2.97
2830 3127 4.055710 TCCAATAGACCTACCACAGTGA 57.944 45.455 0.62 0.00 0.00 3.41
2858 3161 5.414789 TGTGTGGTAGTACATGCATTACT 57.585 39.130 18.92 18.92 34.15 2.24
2859 3162 6.532988 TGTGTGGTAGTACATGCATTACTA 57.467 37.500 17.52 17.52 31.99 1.82
2860 3163 6.334989 TGTGTGGTAGTACATGCATTACTAC 58.665 40.000 28.61 28.61 46.09 2.73
2861 3164 6.153851 TGTGTGGTAGTACATGCATTACTACT 59.846 38.462 31.29 23.17 46.07 2.57
2862 3165 6.696148 GTGTGGTAGTACATGCATTACTACTC 59.304 42.308 31.29 27.05 46.07 2.59
2863 3166 6.183360 TGTGGTAGTACATGCATTACTACTCC 60.183 42.308 31.29 26.16 46.07 3.85
2864 3167 5.303589 TGGTAGTACATGCATTACTACTCCC 59.696 44.000 31.29 24.18 46.07 4.30
2865 3168 5.539193 GGTAGTACATGCATTACTACTCCCT 59.461 44.000 31.29 13.73 46.07 4.20
2866 3169 5.793030 AGTACATGCATTACTACTCCCTC 57.207 43.478 15.52 0.00 0.00 4.30
2867 3170 4.589374 AGTACATGCATTACTACTCCCTCC 59.411 45.833 15.52 0.00 0.00 4.30
2868 3171 3.384168 ACATGCATTACTACTCCCTCCA 58.616 45.455 0.00 0.00 0.00 3.86
2869 3172 3.976654 ACATGCATTACTACTCCCTCCAT 59.023 43.478 0.00 0.00 0.00 3.41
2870 3173 4.413520 ACATGCATTACTACTCCCTCCATT 59.586 41.667 0.00 0.00 0.00 3.16
2871 3174 4.689612 TGCATTACTACTCCCTCCATTC 57.310 45.455 0.00 0.00 0.00 2.67
2872 3175 3.391296 TGCATTACTACTCCCTCCATTCC 59.609 47.826 0.00 0.00 0.00 3.01
2873 3176 3.648545 GCATTACTACTCCCTCCATTCCT 59.351 47.826 0.00 0.00 0.00 3.36
2874 3177 4.838986 GCATTACTACTCCCTCCATTCCTA 59.161 45.833 0.00 0.00 0.00 2.94
2875 3178 5.307196 GCATTACTACTCCCTCCATTCCTAA 59.693 44.000 0.00 0.00 0.00 2.69
2876 3179 6.183361 GCATTACTACTCCCTCCATTCCTAAA 60.183 42.308 0.00 0.00 0.00 1.85
2877 3180 7.474936 GCATTACTACTCCCTCCATTCCTAAAT 60.475 40.741 0.00 0.00 0.00 1.40
2878 3181 9.101325 CATTACTACTCCCTCCATTCCTAAATA 57.899 37.037 0.00 0.00 0.00 1.40
2879 3182 9.860393 ATTACTACTCCCTCCATTCCTAAATAT 57.140 33.333 0.00 0.00 0.00 1.28
2882 3185 9.327731 ACTACTCCCTCCATTCCTAAATATAAG 57.672 37.037 0.00 0.00 0.00 1.73
2883 3186 9.327731 CTACTCCCTCCATTCCTAAATATAAGT 57.672 37.037 0.00 0.00 0.00 2.24
2884 3187 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
2885 3188 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
2886 3189 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
2887 3190 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
2888 3191 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
2906 3209 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
2907 3210 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
2912 3215 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
2913 3216 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
2914 3217 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
2915 3218 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
2916 3219 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
2917 3220 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
2918 3221 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
2919 3222 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
2920 3223 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
2921 3224 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
2923 3226 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
2924 3227 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
2963 3266 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2964 3267 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2965 3268 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2966 3269 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2967 3270 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2968 3271 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2969 3272 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2970 3273 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2971 3274 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2972 3275 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2973 3276 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2974 3277 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2975 3278 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2976 3279 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2977 3280 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2978 3281 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2979 3282 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2980 3283 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2981 3284 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2982 3285 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2983 3286 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
2984 3287 3.827876 TCCGTATGTAGTCACTTGTTGGA 59.172 43.478 0.00 0.00 0.00 3.53
2985 3288 4.281435 TCCGTATGTAGTCACTTGTTGGAA 59.719 41.667 0.00 0.00 0.00 3.53
2986 3289 5.046878 TCCGTATGTAGTCACTTGTTGGAAT 60.047 40.000 0.00 0.00 0.00 3.01
2987 3290 5.291128 CCGTATGTAGTCACTTGTTGGAATC 59.709 44.000 0.00 0.00 0.00 2.52
2988 3291 6.100004 CGTATGTAGTCACTTGTTGGAATCT 58.900 40.000 0.00 0.00 0.00 2.40
2989 3292 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
2990 3293 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
2991 3294 6.174720 TGTAGTCACTTGTTGGAATCTCTT 57.825 37.500 0.00 0.00 0.00 2.85
2992 3295 7.297936 TGTAGTCACTTGTTGGAATCTCTTA 57.702 36.000 0.00 0.00 0.00 2.10
2993 3296 7.732025 TGTAGTCACTTGTTGGAATCTCTTAA 58.268 34.615 0.00 0.00 0.00 1.85
2994 3297 8.208224 TGTAGTCACTTGTTGGAATCTCTTAAA 58.792 33.333 0.00 0.00 0.00 1.52
2995 3298 9.052759 GTAGTCACTTGTTGGAATCTCTTAAAA 57.947 33.333 0.00 0.00 0.00 1.52
2996 3299 8.159344 AGTCACTTGTTGGAATCTCTTAAAAG 57.841 34.615 0.00 0.00 0.00 2.27
2997 3300 7.993183 AGTCACTTGTTGGAATCTCTTAAAAGA 59.007 33.333 0.00 0.00 0.00 2.52
2998 3301 8.070769 GTCACTTGTTGGAATCTCTTAAAAGAC 58.929 37.037 0.00 0.00 0.00 3.01
2999 3302 7.993183 TCACTTGTTGGAATCTCTTAAAAGACT 59.007 33.333 0.00 0.00 0.00 3.24
3000 3303 8.624776 CACTTGTTGGAATCTCTTAAAAGACTT 58.375 33.333 0.00 0.00 0.00 3.01
3001 3304 9.847224 ACTTGTTGGAATCTCTTAAAAGACTTA 57.153 29.630 0.00 0.00 0.00 2.24
3003 3306 9.621629 TTGTTGGAATCTCTTAAAAGACTTACA 57.378 29.630 0.00 0.00 0.00 2.41
3004 3307 9.793259 TGTTGGAATCTCTTAAAAGACTTACAT 57.207 29.630 0.00 0.00 0.00 2.29
3010 3313 9.807921 AATCTCTTAAAAGACTTACATTTGGGA 57.192 29.630 0.00 0.00 0.00 4.37
3011 3314 9.807921 ATCTCTTAAAAGACTTACATTTGGGAA 57.192 29.630 0.00 0.00 0.00 3.97
3012 3315 9.063615 TCTCTTAAAAGACTTACATTTGGGAAC 57.936 33.333 0.00 0.00 0.00 3.62
3013 3316 8.754991 TCTTAAAAGACTTACATTTGGGAACA 57.245 30.769 0.00 0.00 39.83 3.18
3014 3317 8.846211 TCTTAAAAGACTTACATTTGGGAACAG 58.154 33.333 0.00 0.00 44.54 3.16
3015 3318 8.754991 TTAAAAGACTTACATTTGGGAACAGA 57.245 30.769 0.00 0.00 44.54 3.41
3016 3319 6.884280 AAAGACTTACATTTGGGAACAGAG 57.116 37.500 0.00 0.00 44.54 3.35
3017 3320 4.911390 AGACTTACATTTGGGAACAGAGG 58.089 43.478 0.00 0.00 44.54 3.69
3018 3321 4.010349 GACTTACATTTGGGAACAGAGGG 58.990 47.826 0.00 0.00 44.54 4.30
3019 3322 3.655777 ACTTACATTTGGGAACAGAGGGA 59.344 43.478 0.00 0.00 44.54 4.20
3020 3323 2.887151 ACATTTGGGAACAGAGGGAG 57.113 50.000 0.00 0.00 44.54 4.30
3062 3365 9.191479 TCTATTGAAAAGAGAGTACCTTCTAGG 57.809 37.037 0.00 0.00 39.62 3.02
3274 3578 7.255942 CCAAGAATCAAATGGTAAACCTTGAGT 60.256 37.037 9.05 6.82 34.84 3.41
3286 3591 8.107095 TGGTAAACCTTGAGTAATAATTCTGCT 58.893 33.333 0.02 0.00 36.82 4.24
3323 3628 3.192001 CCATAATGGGCCATGAGATTTCG 59.808 47.826 22.01 3.06 32.67 3.46
3325 3630 2.734755 ATGGGCCATGAGATTTCGAA 57.265 45.000 20.49 0.00 0.00 3.71
3326 3631 2.042686 TGGGCCATGAGATTTCGAAG 57.957 50.000 0.00 0.00 0.00 3.79
3327 3632 0.665298 GGGCCATGAGATTTCGAAGC 59.335 55.000 4.39 0.00 0.00 3.86
3328 3633 0.665298 GGCCATGAGATTTCGAAGCC 59.335 55.000 0.00 5.21 0.00 4.35
3346 3654 1.542915 GCCACATGTGAGCTTGTTGAT 59.457 47.619 27.46 0.00 31.66 2.57
3347 3655 2.670229 GCCACATGTGAGCTTGTTGATG 60.670 50.000 27.46 6.68 31.66 3.07
3349 3657 1.198408 ACATGTGAGCTTGTTGATGCG 59.802 47.619 0.00 0.00 30.04 4.73
3353 3661 0.592637 TGAGCTTGTTGATGCGGTTG 59.407 50.000 0.00 0.00 0.00 3.77
3363 3671 0.391130 GATGCGGTTGTACCAGCTCA 60.391 55.000 11.74 0.00 38.47 4.26
3417 3725 7.910441 ATTGCTTAATTGTTGATTTCCCAAG 57.090 32.000 0.00 0.00 0.00 3.61
3435 3743 2.486472 AGACTGGAATCAGCACTTGG 57.514 50.000 0.00 0.00 44.59 3.61
3479 3789 3.135167 TCAGATGTGCCATCTGCTATTGA 59.865 43.478 27.24 14.73 43.79 2.57
3523 3833 1.009829 GCACGTCCACATGGAGATTC 58.990 55.000 0.00 0.00 46.49 2.52
3602 3915 1.600957 GCATCATGATGGTGAGTTCCG 59.399 52.381 31.62 7.75 39.16 4.30
3606 3919 3.334691 TCATGATGGTGAGTTCCGTTTC 58.665 45.455 0.00 0.00 0.00 2.78
3614 3927 1.270625 TGAGTTCCGTTTCGCCAGAAT 60.271 47.619 0.00 0.00 36.09 2.40
3648 3961 2.667470 GGTACCATCTAGCTCAGACCA 58.333 52.381 7.15 0.00 35.62 4.02
3691 4005 0.684535 TCCGCAAGATTCACACTCCA 59.315 50.000 0.00 0.00 43.02 3.86
3809 4127 7.606456 ACCATATAGAACTGTGTACTGGTTTTG 59.394 37.037 0.00 0.00 30.56 2.44
3829 4147 9.927668 GGTTTTGGATTTCTTGAGAATAAATGA 57.072 29.630 0.00 0.00 33.54 2.57
3941 4260 3.513680 GCATCTGTGCCATTTTCATCA 57.486 42.857 0.00 0.00 45.76 3.07
3957 4276 2.028385 TCATCATGATCGCCTCATCTGG 60.028 50.000 4.86 0.00 42.91 3.86
3963 4282 1.410517 GATCGCCTCATCTGGACTTGA 59.589 52.381 0.00 0.00 0.00 3.02
3981 4300 6.992063 ACTTGAATAGTCGATGAAAGCATT 57.008 33.333 0.00 0.00 29.77 3.56
3995 4314 4.022935 TGAAAGCATTCAAGAAACTGCGAT 60.023 37.500 1.05 0.00 42.47 4.58
4004 4323 4.272504 TCAAGAAACTGCGATTCTCGTTTT 59.727 37.500 0.00 0.00 42.81 2.43
4007 4326 4.452455 AGAAACTGCGATTCTCGTTTTGAT 59.548 37.500 0.00 0.00 42.81 2.57
4018 4337 5.947228 TCTCGTTTTGATGAATTTGCTCT 57.053 34.783 0.00 0.00 0.00 4.09
4035 4354 2.632028 GCTCTAGGGAAGATCATGAGCA 59.368 50.000 14.38 0.00 43.18 4.26
4058 4377 6.017770 GCATAGTCAGTCGAGTAGAACTACAT 60.018 42.308 13.34 0.54 38.48 2.29
4144 4479 5.532032 TCAATCTCAAATGAGTTCTGCAACA 59.468 36.000 10.06 0.00 42.60 3.33
4185 4520 7.010697 TGGATACATACAATTTTGCAGTACG 57.989 36.000 0.00 0.00 46.17 3.67
4197 4532 3.026630 TGCAGTACGTCTTTTCTGAGG 57.973 47.619 0.00 0.00 0.00 3.86
4218 4553 3.275143 GAAAAACCCAAACCAACCAAGG 58.725 45.455 0.00 0.00 0.00 3.61
4252 4587 8.725405 TGTTAACGAATATCATCAAAGCCTAA 57.275 30.769 0.26 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.475466 CGCCATGTGCCACCTGATC 61.475 63.158 1.33 0.00 36.24 2.92
12 13 2.476534 CTTGAACGCCATGTGCCACC 62.477 60.000 0.00 0.00 36.24 4.61
29 30 1.918800 CTTGTCCCGGTCCCTCCTT 60.919 63.158 0.00 0.00 0.00 3.36
38 39 1.889105 CCGCATGATCTTGTCCCGG 60.889 63.158 10.05 10.19 0.00 5.73
40 41 2.189499 GGCCGCATGATCTTGTCCC 61.189 63.158 10.05 4.95 0.00 4.46
42 43 0.462581 TCTGGCCGCATGATCTTGTC 60.463 55.000 10.05 2.58 0.00 3.18
61 62 0.179067 TTTTCGACCACACGCTCCTT 60.179 50.000 0.00 0.00 0.00 3.36
65 66 2.601562 GAGTTTTCGACCACACGCT 58.398 52.632 0.00 0.00 0.00 5.07
138 140 7.615582 TTGTGATGTTTATTTTGGTGCAAAA 57.384 28.000 0.00 0.00 45.41 2.44
139 141 7.119699 TGTTTGTGATGTTTATTTTGGTGCAAA 59.880 29.630 0.00 0.00 0.00 3.68
140 142 6.595326 TGTTTGTGATGTTTATTTTGGTGCAA 59.405 30.769 0.00 0.00 0.00 4.08
141 143 6.108687 TGTTTGTGATGTTTATTTTGGTGCA 58.891 32.000 0.00 0.00 0.00 4.57
142 144 6.595772 TGTTTGTGATGTTTATTTTGGTGC 57.404 33.333 0.00 0.00 0.00 5.01
143 145 8.140677 ACATGTTTGTGATGTTTATTTTGGTG 57.859 30.769 0.00 0.00 33.85 4.17
144 146 9.255304 GTACATGTTTGTGATGTTTATTTTGGT 57.745 29.630 2.30 0.00 36.53 3.67
145 147 9.254133 TGTACATGTTTGTGATGTTTATTTTGG 57.746 29.630 2.30 0.00 36.53 3.28
159 161 6.125327 TCGTGAACATTTGTACATGTTTGT 57.875 33.333 14.40 5.71 45.55 2.83
166 168 4.387559 CGGAAGATCGTGAACATTTGTACA 59.612 41.667 0.00 0.00 0.00 2.90
170 172 3.926527 TCTCGGAAGATCGTGAACATTTG 59.073 43.478 0.00 0.00 40.84 2.32
171 173 4.188247 TCTCGGAAGATCGTGAACATTT 57.812 40.909 0.00 0.00 40.84 2.32
173 175 5.713792 ATATCTCGGAAGATCGTGAACAT 57.286 39.130 0.00 0.00 41.46 2.71
175 177 6.483385 TCTATATCTCGGAAGATCGTGAAC 57.517 41.667 0.00 0.00 41.46 3.18
176 178 7.506328 TTTCTATATCTCGGAAGATCGTGAA 57.494 36.000 0.00 0.00 41.46 3.18
177 179 7.361127 GTTTTCTATATCTCGGAAGATCGTGA 58.639 38.462 0.00 0.00 41.46 4.35
178 180 6.583050 GGTTTTCTATATCTCGGAAGATCGTG 59.417 42.308 0.00 0.00 41.46 4.35
179 181 6.568081 CGGTTTTCTATATCTCGGAAGATCGT 60.568 42.308 0.00 0.00 41.46 3.73
182 184 6.651975 ACGGTTTTCTATATCTCGGAAGAT 57.348 37.500 0.00 0.00 44.57 2.40
183 185 6.461110 AACGGTTTTCTATATCTCGGAAGA 57.539 37.500 0.00 0.00 39.12 2.87
184 186 7.535489 AAAACGGTTTTCTATATCTCGGAAG 57.465 36.000 12.86 0.00 0.00 3.46
185 187 7.910441 AAAAACGGTTTTCTATATCTCGGAA 57.090 32.000 18.29 0.00 30.96 4.30
208 210 6.168270 AGGGCTAGCATAAACAAAACAAAA 57.832 33.333 18.24 0.00 0.00 2.44
209 211 5.799827 AGGGCTAGCATAAACAAAACAAA 57.200 34.783 18.24 0.00 0.00 2.83
210 212 5.799827 AAGGGCTAGCATAAACAAAACAA 57.200 34.783 18.24 0.00 0.00 2.83
211 213 5.799827 AAAGGGCTAGCATAAACAAAACA 57.200 34.783 18.24 0.00 0.00 2.83
212 214 8.032451 TGATAAAAGGGCTAGCATAAACAAAAC 58.968 33.333 18.24 0.00 0.00 2.43
213 215 8.032451 GTGATAAAAGGGCTAGCATAAACAAAA 58.968 33.333 18.24 0.00 0.00 2.44
214 216 7.543756 GTGATAAAAGGGCTAGCATAAACAAA 58.456 34.615 18.24 0.00 0.00 2.83
217 219 5.277828 CCGTGATAAAAGGGCTAGCATAAAC 60.278 44.000 18.24 0.00 0.00 2.01
218 220 4.819630 CCGTGATAAAAGGGCTAGCATAAA 59.180 41.667 18.24 0.00 0.00 1.40
219 221 4.385825 CCGTGATAAAAGGGCTAGCATAA 58.614 43.478 18.24 0.00 0.00 1.90
220 222 3.244422 CCCGTGATAAAAGGGCTAGCATA 60.244 47.826 18.24 1.63 41.06 3.14
224 226 2.807108 GCTCCCGTGATAAAAGGGCTAG 60.807 54.545 0.00 0.00 46.67 3.42
227 229 0.393808 TGCTCCCGTGATAAAAGGGC 60.394 55.000 0.00 0.00 46.67 5.19
230 232 3.074412 AGTGTTGCTCCCGTGATAAAAG 58.926 45.455 0.00 0.00 0.00 2.27
268 271 0.817634 AGAGATCTCACGCTCTCGGG 60.818 60.000 24.39 0.00 42.21 5.14
297 300 9.982651 ATGTAAATAAATACGAGTAGACAGCAT 57.017 29.630 0.00 0.00 0.00 3.79
365 368 6.594744 TGGATGGAGAACACGTATACTACTA 58.405 40.000 0.56 0.00 0.00 1.82
366 369 5.443283 TGGATGGAGAACACGTATACTACT 58.557 41.667 0.56 0.00 0.00 2.57
367 370 5.762825 TGGATGGAGAACACGTATACTAC 57.237 43.478 0.56 0.00 0.00 2.73
424 438 0.893447 AGGAAAGGAACGTACGGGAG 59.107 55.000 21.06 0.00 0.00 4.30
474 488 1.729267 CGGGGATGGGGATTGGGATT 61.729 60.000 0.00 0.00 0.00 3.01
476 490 2.776526 CGGGGATGGGGATTGGGA 60.777 66.667 0.00 0.00 0.00 4.37
493 507 2.772622 ATCGGGTGGGATGGGGAC 60.773 66.667 0.00 0.00 0.00 4.46
664 681 4.124351 CAGGGACGCCGCGAAGTA 62.124 66.667 21.79 0.00 0.00 2.24
733 768 0.399233 GAGGTCCATGGGGTCTAGCT 60.399 60.000 13.02 6.87 34.93 3.32
746 781 2.552031 GCCGAAAATGTCTAGAGGTCC 58.448 52.381 0.00 0.00 0.00 4.46
757 792 1.003545 CTAGATGGTGCGCCGAAAATG 60.004 52.381 12.58 0.00 37.67 2.32
870 908 0.099436 GCACAGGGATGCATCGTTTC 59.901 55.000 20.15 9.73 45.39 2.78
873 911 2.512286 CGCACAGGGATGCATCGT 60.512 61.111 20.15 10.05 46.47 3.73
908 946 3.866449 GCTTCAGAACTCAAACCCTCGAT 60.866 47.826 0.00 0.00 0.00 3.59
922 960 4.986645 TGCGGCGCTGCTTCAGAA 62.987 61.111 38.42 17.59 32.44 3.02
981 1020 2.214181 TTTCGCCTCTGTCGCTCCTC 62.214 60.000 0.00 0.00 0.00 3.71
1023 1062 6.387192 TGGTTCTTCTCCTCCAAATCATTA 57.613 37.500 0.00 0.00 0.00 1.90
1024 1063 5.259632 CTGGTTCTTCTCCTCCAAATCATT 58.740 41.667 0.00 0.00 0.00 2.57
1025 1064 4.853007 CTGGTTCTTCTCCTCCAAATCAT 58.147 43.478 0.00 0.00 0.00 2.45
1295 1334 0.392461 ACAATCCATGAACCCCGACG 60.392 55.000 0.00 0.00 0.00 5.12
1404 1443 4.514441 TCCCTAGACGTCTCAATATCGTTC 59.486 45.833 23.89 0.00 37.92 3.95
1527 1566 0.536233 TGCACTCCGGCTTGCTTAAA 60.536 50.000 22.87 5.06 39.62 1.52
1681 1722 4.009675 CCCACGATCCTTCATGAGAAAAA 58.990 43.478 0.00 0.00 32.35 1.94
2072 2121 8.874816 GGAGATAGTTAAGAAGTGCTTACTTTG 58.125 37.037 0.00 0.00 38.76 2.77
2136 2233 9.929180 TGAATTGTGGAGATAATATACAGCTAC 57.071 33.333 0.00 0.00 0.00 3.58
2174 2271 6.646240 ACAATTTTGCTTGTGAAAATAGCGAT 59.354 30.769 0.00 0.00 37.93 4.58
2286 2383 5.409520 TGCAAACAATGTTACAAGTTTTGCA 59.590 32.000 25.62 25.62 36.56 4.08
2319 2416 7.594758 TCAATTAAGTTCACATTACAGCAAAGC 59.405 33.333 0.00 0.00 0.00 3.51
2340 2437 5.302568 CCAATATGCACATACAGGGTCAATT 59.697 40.000 0.00 0.00 0.00 2.32
2398 2495 2.839486 TGTTGAAGTCTAGTGCTGGG 57.161 50.000 0.00 0.00 0.00 4.45
2728 3025 8.650143 AAAGGGCTTAAAATGAGAAACATAGA 57.350 30.769 0.00 0.00 38.38 1.98
2830 3127 5.739959 TGCATGTACTACCACACAATACAT 58.260 37.500 0.00 0.00 37.02 2.29
2858 3161 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
2859 3162 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
2860 3163 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
2861 3164 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
2862 3165 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
2880 3183 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
2881 3184 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
2886 3189 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52
2887 3190 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
2888 3191 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
2889 3192 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
2890 3193 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
2891 3194 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
2892 3195 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
2893 3196 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
2894 3197 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
2895 3198 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
2896 3199 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
2897 3200 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
2898 3201 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
2899 3202 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
2900 3203 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
2901 3204 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
2902 3205 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
2941 3244 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2942 3245 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2943 3246 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2944 3247 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2945 3248 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2946 3249 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2947 3250 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2948 3251 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2949 3252 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2950 3253 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2951 3254 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2952 3255 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2953 3256 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2954 3257 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2955 3258 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2956 3259 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2957 3260 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2958 3261 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2959 3262 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2960 3263 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2961 3264 4.082408 TCCAACAAGTGACTACATACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
2962 3265 3.827876 TCCAACAAGTGACTACATACGGA 59.172 43.478 0.00 0.00 0.00 4.69
2963 3266 4.182693 TCCAACAAGTGACTACATACGG 57.817 45.455 0.00 0.00 0.00 4.02
2964 3267 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
2965 3268 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
2966 3269 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
2967 3270 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
2968 3271 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
2969 3272 8.603242 TTTAAGAGATTCCAACAAGTGACTAC 57.397 34.615 0.00 0.00 0.00 2.73
2970 3273 9.273016 CTTTTAAGAGATTCCAACAAGTGACTA 57.727 33.333 0.00 0.00 0.00 2.59
2971 3274 7.993183 TCTTTTAAGAGATTCCAACAAGTGACT 59.007 33.333 0.00 0.00 0.00 3.41
2972 3275 8.070769 GTCTTTTAAGAGATTCCAACAAGTGAC 58.929 37.037 0.00 0.00 35.32 3.67
2973 3276 7.993183 AGTCTTTTAAGAGATTCCAACAAGTGA 59.007 33.333 0.00 0.00 35.32 3.41
2974 3277 8.159344 AGTCTTTTAAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 35.32 3.16
2975 3278 8.753497 AAGTCTTTTAAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 35.32 3.16
2977 3280 9.621629 TGTAAGTCTTTTAAGAGATTCCAACAA 57.378 29.630 0.00 0.00 35.32 2.83
2978 3281 9.793259 ATGTAAGTCTTTTAAGAGATTCCAACA 57.207 29.630 0.00 2.41 35.32 3.33
2984 3287 9.807921 TCCCAAATGTAAGTCTTTTAAGAGATT 57.192 29.630 0.00 0.00 35.32 2.40
2985 3288 9.807921 TTCCCAAATGTAAGTCTTTTAAGAGAT 57.192 29.630 0.00 0.00 35.32 2.75
2986 3289 9.063615 GTTCCCAAATGTAAGTCTTTTAAGAGA 57.936 33.333 0.00 0.00 35.32 3.10
2987 3290 8.846211 TGTTCCCAAATGTAAGTCTTTTAAGAG 58.154 33.333 0.00 0.00 35.32 2.85
2988 3291 8.754991 TGTTCCCAAATGTAAGTCTTTTAAGA 57.245 30.769 0.00 0.00 0.00 2.10
2989 3292 8.846211 TCTGTTCCCAAATGTAAGTCTTTTAAG 58.154 33.333 0.00 0.00 0.00 1.85
2990 3293 8.754991 TCTGTTCCCAAATGTAAGTCTTTTAA 57.245 30.769 0.00 0.00 0.00 1.52
2991 3294 7.447238 CCTCTGTTCCCAAATGTAAGTCTTTTA 59.553 37.037 0.00 0.00 0.00 1.52
2992 3295 6.265422 CCTCTGTTCCCAAATGTAAGTCTTTT 59.735 38.462 0.00 0.00 0.00 2.27
2993 3296 5.770162 CCTCTGTTCCCAAATGTAAGTCTTT 59.230 40.000 0.00 0.00 0.00 2.52
2994 3297 5.316987 CCTCTGTTCCCAAATGTAAGTCTT 58.683 41.667 0.00 0.00 0.00 3.01
2995 3298 4.263506 CCCTCTGTTCCCAAATGTAAGTCT 60.264 45.833 0.00 0.00 0.00 3.24
2996 3299 4.010349 CCCTCTGTTCCCAAATGTAAGTC 58.990 47.826 0.00 0.00 0.00 3.01
2997 3300 3.655777 TCCCTCTGTTCCCAAATGTAAGT 59.344 43.478 0.00 0.00 0.00 2.24
2998 3301 4.263506 ACTCCCTCTGTTCCCAAATGTAAG 60.264 45.833 0.00 0.00 0.00 2.34
2999 3302 3.655777 ACTCCCTCTGTTCCCAAATGTAA 59.344 43.478 0.00 0.00 0.00 2.41
3000 3303 3.256704 ACTCCCTCTGTTCCCAAATGTA 58.743 45.455 0.00 0.00 0.00 2.29
3001 3304 2.065799 ACTCCCTCTGTTCCCAAATGT 58.934 47.619 0.00 0.00 0.00 2.71
3002 3305 2.887151 ACTCCCTCTGTTCCCAAATG 57.113 50.000 0.00 0.00 0.00 2.32
3003 3306 3.532102 ACTACTCCCTCTGTTCCCAAAT 58.468 45.455 0.00 0.00 0.00 2.32
3004 3307 2.986050 ACTACTCCCTCTGTTCCCAAA 58.014 47.619 0.00 0.00 0.00 3.28
3005 3308 2.715763 ACTACTCCCTCTGTTCCCAA 57.284 50.000 0.00 0.00 0.00 4.12
3006 3309 2.158219 TGAACTACTCCCTCTGTTCCCA 60.158 50.000 0.00 0.00 38.29 4.37
3007 3310 2.537143 TGAACTACTCCCTCTGTTCCC 58.463 52.381 0.00 0.00 38.29 3.97
3008 3311 4.828072 AATGAACTACTCCCTCTGTTCC 57.172 45.455 0.00 0.00 38.29 3.62
3009 3312 6.282199 TGTAATGAACTACTCCCTCTGTTC 57.718 41.667 0.00 0.00 39.18 3.18
3010 3313 6.270231 AGTTGTAATGAACTACTCCCTCTGTT 59.730 38.462 0.00 0.00 39.57 3.16
3011 3314 5.780793 AGTTGTAATGAACTACTCCCTCTGT 59.219 40.000 0.00 0.00 39.57 3.41
3012 3315 6.287589 AGTTGTAATGAACTACTCCCTCTG 57.712 41.667 0.00 0.00 39.57 3.35
3013 3316 6.726764 AGAAGTTGTAATGAACTACTCCCTCT 59.273 38.462 0.00 0.00 42.35 3.69
3014 3317 6.937392 AGAAGTTGTAATGAACTACTCCCTC 58.063 40.000 0.00 0.00 42.35 4.30
3015 3318 6.936968 AGAAGTTGTAATGAACTACTCCCT 57.063 37.500 0.00 0.00 42.35 4.20
3016 3319 9.099454 CAATAGAAGTTGTAATGAACTACTCCC 57.901 37.037 0.00 0.00 42.35 4.30
3017 3320 9.871238 TCAATAGAAGTTGTAATGAACTACTCC 57.129 33.333 0.00 0.00 42.35 3.85
3062 3365 3.010420 CTGCACTAGGCCTAAAGGAAAC 58.990 50.000 14.85 0.11 43.89 2.78
3142 3446 7.852550 AGTCATAAGAGGATGAATCTGATCA 57.147 36.000 0.00 0.00 37.58 2.92
3152 3456 7.361031 GCAATATGCTCAAGTCATAAGAGGATG 60.361 40.741 0.00 0.00 40.10 3.51
3186 3490 7.645058 GGAACTCTCCATCAAAATTATTGGA 57.355 36.000 0.00 0.00 41.96 3.53
3283 3588 9.940798 CCATTATGGTCTCTTGCTTCAGTAGCA 62.941 44.444 2.48 0.00 44.86 3.49
3286 3591 5.396772 CCCATTATGGTCTCTTGCTTCAGTA 60.397 44.000 10.65 0.00 35.17 2.74
3289 3594 3.889815 CCCATTATGGTCTCTTGCTTCA 58.110 45.455 10.65 0.00 35.17 3.02
3301 3606 3.192001 CGAAATCTCATGGCCCATTATGG 59.808 47.826 3.85 3.85 37.25 2.74
3307 3612 2.018644 GCTTCGAAATCTCATGGCCCA 61.019 52.381 0.00 0.00 0.00 5.36
3323 3628 1.242076 ACAAGCTCACATGTGGCTTC 58.758 50.000 33.32 19.14 41.62 3.86
3325 3630 0.956633 CAACAAGCTCACATGTGGCT 59.043 50.000 26.48 26.48 38.25 4.75
3326 3631 0.953727 TCAACAAGCTCACATGTGGC 59.046 50.000 25.16 24.32 0.00 5.01
3327 3632 2.670229 GCATCAACAAGCTCACATGTGG 60.670 50.000 25.16 16.47 0.00 4.17
3328 3633 2.592194 GCATCAACAAGCTCACATGTG 58.408 47.619 20.18 20.18 0.00 3.21
3346 3654 1.301401 GTGAGCTGGTACAACCGCA 60.301 57.895 0.00 0.00 42.58 5.69
3347 3655 0.673644 ATGTGAGCTGGTACAACCGC 60.674 55.000 0.00 5.23 42.58 5.68
3349 3657 3.146066 TCAAATGTGAGCTGGTACAACC 58.854 45.455 0.00 0.00 38.70 3.77
3363 3671 4.878397 GGCTATACTTCAGTGCTCAAATGT 59.122 41.667 0.00 0.00 0.00 2.71
3417 3725 2.191128 ACCAAGTGCTGATTCCAGTC 57.809 50.000 0.00 0.00 42.35 3.51
3479 3789 0.827368 GTCGGATCTCCAGCTTCCTT 59.173 55.000 0.10 0.00 35.14 3.36
3505 3815 1.066215 TGGAATCTCCATGTGGACGTG 60.066 52.381 0.00 0.00 42.67 4.49
3523 3833 8.767478 AAATTTTCAGAGAATGTAATGCTTGG 57.233 30.769 0.00 0.00 26.21 3.61
3614 3927 1.332144 GGTACCCAGATACGGCCACA 61.332 60.000 2.24 0.00 0.00 4.17
3691 4005 6.579666 TCGAAGGCTGTTATATTATACCGT 57.420 37.500 0.00 0.00 0.00 4.83
3809 4127 6.548993 AGGCCTCATTTATTCTCAAGAAATCC 59.451 38.462 0.00 0.00 37.61 3.01
3931 4250 4.823790 TGAGGCGATCATGATGAAAATG 57.176 40.909 14.30 0.00 31.12 2.32
3957 4276 7.009568 AATGCTTTCATCGACTATTCAAGTC 57.990 36.000 0.00 0.00 40.69 3.01
3963 4282 7.615582 TTCTTGAATGCTTTCATCGACTATT 57.384 32.000 15.04 0.00 41.38 1.73
3995 4314 6.317789 AGAGCAAATTCATCAAAACGAGAA 57.682 33.333 0.00 0.00 0.00 2.87
4004 4323 5.698741 TCTTCCCTAGAGCAAATTCATCA 57.301 39.130 0.00 0.00 0.00 3.07
4007 4326 5.698741 TGATCTTCCCTAGAGCAAATTCA 57.301 39.130 0.00 0.00 45.77 2.57
4018 4337 5.397360 TGACTATGCTCATGATCTTCCCTA 58.603 41.667 0.00 0.00 0.00 3.53
4035 4354 9.781633 ATTATGTAGTTCTACTCGACTGACTAT 57.218 33.333 10.65 0.00 0.00 2.12
4079 4398 6.769512 TCACTTAAACTGGCTTCAGAACTAT 58.230 36.000 0.00 0.00 40.86 2.12
4120 4440 5.532032 TGTTGCAGAACTCATTTGAGATTGA 59.468 36.000 14.29 0.00 44.74 2.57
4121 4441 5.765176 TGTTGCAGAACTCATTTGAGATTG 58.235 37.500 14.29 9.58 44.74 2.67
4144 4479 7.701539 TGTATCCAGAGCAAAATTGTATGTT 57.298 32.000 0.00 0.00 0.00 2.71
4197 4532 3.275143 CCTTGGTTGGTTTGGGTTTTTC 58.725 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.