Multiple sequence alignment - TraesCS5B01G242400

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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 TraesCS5B01G242400 chr5B 100.000 3633 0 0 1 3633 421838707 421835075 0.000000e+00 6709.0
1 TraesCS5B01G242400 chr5B 80.888 1261 192 39 509 1740 421861838 421860598 0.000000e+00 948.0
2 TraesCS5B01G242400 chr5B 82.737 643 93 11 2059 2694 421860133 421859502 1.140000e-154 556.0
3 TraesCS5B01G242400 chr5B 77.795 644 117 18 734 1366 421998516 421997888 1.230000e-99 374.0
4 TraesCS5B01G242400 chr5B 77.385 650 112 25 734 1366 422040731 422040100 1.600000e-93 353.0
5 TraesCS5B01G242400 chr5B 100.000 28 0 0 462 489 664499129 664499156 7.000000e-03 52.8
6 TraesCS5B01G242400 chr5A 93.431 2390 119 14 502 2884 458320568 458318210 0.000000e+00 3509.0
7 TraesCS5B01G242400 chr5A 80.500 1241 183 34 509 1711 458331497 458330278 0.000000e+00 896.0
8 TraesCS5B01G242400 chr5A 80.159 756 105 34 2105 2831 458329768 458329029 1.160000e-144 523.0
9 TraesCS5B01G242400 chr5A 83.616 531 81 4 533 1063 458493655 458493131 9.060000e-136 494.0
10 TraesCS5B01G242400 chr5A 78.034 651 111 22 730 1366 458525181 458524549 7.360000e-102 381.0
11 TraesCS5B01G242400 chr5A 77.966 649 112 18 734 1366 458562216 458561583 9.520000e-101 377.0
12 TraesCS5B01G242400 chr5A 85.657 251 20 10 3221 3462 458318147 458317904 2.170000e-62 250.0
13 TraesCS5B01G242400 chr5D 92.950 1688 85 20 502 2189 357065640 357063987 0.000000e+00 2427.0
14 TraesCS5B01G242400 chr5D 80.016 1271 195 42 509 1740 357080689 357079439 0.000000e+00 885.0
15 TraesCS5B01G242400 chr5D 88.330 497 40 12 2467 2946 357063670 357063175 6.760000e-162 580.0
16 TraesCS5B01G242400 chr5D 79.866 745 113 23 2105 2827 357078959 357078230 9.000000e-141 510.0
17 TraesCS5B01G242400 chr5D 78.428 649 107 23 734 1366 357396692 357396061 3.400000e-105 392.0
18 TraesCS5B01G242400 chr5D 89.641 251 17 7 3389 3633 357062934 357062687 9.800000e-81 311.0
19 TraesCS5B01G242400 chr5D 82.521 349 56 4 734 1078 357371823 357371476 5.900000e-78 302.0
20 TraesCS5B01G242400 chr5D 91.429 210 13 4 2174 2381 357063922 357063716 2.140000e-72 283.0
21 TraesCS5B01G242400 chr5D 88.839 224 12 7 3187 3402 357063178 357062960 2.780000e-66 263.0
22 TraesCS5B01G242400 chr5D 82.397 267 35 10 233 493 532818044 532818304 4.720000e-54 222.0
23 TraesCS5B01G242400 chr5D 81.818 253 34 8 246 493 423180339 423180094 6.150000e-48 202.0
24 TraesCS5B01G242400 chr5D 87.037 108 14 0 1259 1366 357371283 357371176 4.930000e-24 122.0
25 TraesCS5B01G242400 chr2A 97.688 519 7 3 2 516 375703188 375703705 0.000000e+00 887.0
26 TraesCS5B01G242400 chr1B 97.071 239 7 0 2947 3185 550703177 550703415 1.570000e-108 403.0
27 TraesCS5B01G242400 chr1B 97.537 203 5 0 2985 3187 550696490 550696692 7.470000e-92 348.0
28 TraesCS5B01G242400 chr1B 85.185 108 16 0 386 493 117190543 117190650 1.070000e-20 111.0
29 TraesCS5B01G242400 chr7D 92.887 239 16 1 2947 3185 178924453 178924690 2.690000e-91 346.0
30 TraesCS5B01G242400 chr7D 92.531 241 17 1 2947 3187 178879969 178880208 9.660000e-91 344.0
31 TraesCS5B01G242400 chr7D 91.701 241 18 2 2947 3187 178887650 178887888 2.090000e-87 333.0
32 TraesCS5B01G242400 chr7D 90.650 246 21 2 2943 3187 245492716 245492960 3.500000e-85 326.0
33 TraesCS5B01G242400 chr2B 91.286 241 21 0 2947 3187 794458541 794458781 2.700000e-86 329.0
34 TraesCS5B01G242400 chr2B 83.774 265 35 7 233 493 799551107 799551367 1.010000e-60 244.0
35 TraesCS5B01G242400 chr2B 82.642 265 36 8 233 493 458131881 458132139 3.650000e-55 226.0
36 TraesCS5B01G242400 chr2B 93.878 49 2 1 458 505 521320094 521320046 5.030000e-09 73.1
37 TraesCS5B01G242400 chr1A 90.947 243 20 2 2945 3187 489244410 489244650 3.500000e-85 326.0
38 TraesCS5B01G242400 chr6A 89.837 246 23 2 2943 3187 203762160 203761916 7.570000e-82 315.0
39 TraesCS5B01G242400 chr3D 80.934 257 29 12 233 484 484290849 484291090 6.190000e-43 185.0


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 TraesCS5B01G242400 chr5B 421835075 421838707 3632 True 6709.0 6709 100.0000 1 3633 1 chr5B.!!$R1 3632
1 TraesCS5B01G242400 chr5B 421859502 421861838 2336 True 752.0 948 81.8125 509 2694 2 chr5B.!!$R4 2185
2 TraesCS5B01G242400 chr5B 421997888 421998516 628 True 374.0 374 77.7950 734 1366 1 chr5B.!!$R2 632
3 TraesCS5B01G242400 chr5B 422040100 422040731 631 True 353.0 353 77.3850 734 1366 1 chr5B.!!$R3 632
4 TraesCS5B01G242400 chr5A 458317904 458320568 2664 True 1879.5 3509 89.5440 502 3462 2 chr5A.!!$R4 2960
5 TraesCS5B01G242400 chr5A 458329029 458331497 2468 True 709.5 896 80.3295 509 2831 2 chr5A.!!$R5 2322
6 TraesCS5B01G242400 chr5A 458493131 458493655 524 True 494.0 494 83.6160 533 1063 1 chr5A.!!$R1 530
7 TraesCS5B01G242400 chr5A 458524549 458525181 632 True 381.0 381 78.0340 730 1366 1 chr5A.!!$R2 636
8 TraesCS5B01G242400 chr5A 458561583 458562216 633 True 377.0 377 77.9660 734 1366 1 chr5A.!!$R3 632
9 TraesCS5B01G242400 chr5D 357062687 357065640 2953 True 772.8 2427 90.2378 502 3633 5 chr5D.!!$R3 3131
10 TraesCS5B01G242400 chr5D 357078230 357080689 2459 True 697.5 885 79.9410 509 2827 2 chr5D.!!$R4 2318
11 TraesCS5B01G242400 chr5D 357396061 357396692 631 True 392.0 392 78.4280 734 1366 1 chr5D.!!$R1 632
12 TraesCS5B01G242400 chr5D 357371176 357371823 647 True 212.0 302 84.7790 734 1366 2 chr5D.!!$R5 632
13 TraesCS5B01G242400 chr2A 375703188 375703705 517 False 887.0 887 97.6880 2 516 1 chr2A.!!$F1 514

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
609 615 0.322975 TCCTGTTGCTCCTTCTGCTC 59.677 55.0 0.0 0.0 0.00 4.26 F
956 966 0.465642 TCGAAGCCGCTCATCCTCTA 60.466 55.0 0.0 0.0 35.37 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1795 0.174845 TTACATAGCCTTCGCGTGCT 59.825 50.0 20.36 20.36 41.18 4.40 R
2950 3305 0.028770 CGTGGCATGTTGACGTGTTT 59.971 50.0 0.00 0.00 35.38 2.83 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
122 123 3.284449 GCTTGCCGACCGGTGTTT 61.284 61.111 14.63 0.00 37.65 2.83
214 215 1.472276 GCATTCGTGTAGCCGACGAG 61.472 60.000 0.00 0.00 45.89 4.18
237 238 3.181967 CGAGAGGCGACAAAGGCG 61.182 66.667 0.00 0.00 44.57 5.52
260 261 4.320928 TGTTTTGCTTCGCCGGCG 62.321 61.111 42.13 42.13 41.35 6.46
416 421 0.748367 GAAGAAAGGGGATGCGGGAC 60.748 60.000 0.00 0.00 0.00 4.46
531 536 4.796110 ATATACCCACCACAGCAGAATT 57.204 40.909 0.00 0.00 0.00 2.17
546 551 8.886719 CACAGCAGAATTATCTTTCACAAGATA 58.113 33.333 1.29 1.29 46.33 1.98
570 576 4.813161 ACGAAGTCAGAGGCAAATATGATG 59.187 41.667 0.00 0.00 29.74 3.07
574 580 4.411540 AGTCAGAGGCAAATATGATGAGGT 59.588 41.667 0.00 0.00 0.00 3.85
609 615 0.322975 TCCTGTTGCTCCTTCTGCTC 59.677 55.000 0.00 0.00 0.00 4.26
660 666 5.038744 GAGGATCAGCTCATGAGGTTCATG 61.039 50.000 24.44 13.47 44.84 3.07
693 700 1.346062 AGAAGAGGCAAGCTGACAGA 58.654 50.000 6.65 0.00 0.00 3.41
721 728 1.504359 TGCAAACGTAACCGAGGAAG 58.496 50.000 0.00 0.00 37.88 3.46
722 729 1.068895 TGCAAACGTAACCGAGGAAGA 59.931 47.619 0.00 0.00 37.88 2.87
723 730 2.137523 GCAAACGTAACCGAGGAAGAA 58.862 47.619 0.00 0.00 37.88 2.52
724 731 2.545106 GCAAACGTAACCGAGGAAGAAA 59.455 45.455 0.00 0.00 37.88 2.52
725 732 3.002553 GCAAACGTAACCGAGGAAGAAAA 59.997 43.478 0.00 0.00 37.88 2.29
728 735 2.223805 ACGTAACCGAGGAAGAAAACGT 60.224 45.455 0.00 0.00 37.49 3.99
880 890 1.067974 CCGGCTATGTCACGGTGAATA 59.932 52.381 13.23 11.44 42.53 1.75
927 937 1.833049 CTTCGTCGAGGCCCCCTAT 60.833 63.158 0.00 0.00 31.76 2.57
956 966 0.465642 TCGAAGCCGCTCATCCTCTA 60.466 55.000 0.00 0.00 35.37 2.43
1288 1339 1.073319 TGGTTGGAGAGGTTCCCCA 60.073 57.895 0.00 0.00 46.19 4.96
1353 1404 2.738521 CACTACGTGCCGCAGCTT 60.739 61.111 0.00 0.00 40.80 3.74
1446 1511 2.313234 CTTTCGCATGTGACTTTGCAG 58.687 47.619 8.86 0.00 38.80 4.41
1638 1706 1.007038 TTCACCCCGAAAGACGACG 60.007 57.895 0.00 0.00 45.77 5.12
1806 1887 6.376581 ACTCTCTTTCCCAATAAGAATTGCTG 59.623 38.462 0.00 0.00 41.06 4.41
1876 2059 1.058428 AGCTGGCTGGCTATGATCCA 61.058 55.000 2.00 0.00 41.16 3.41
1985 2168 5.770162 GCTTGCCCAAGAACAAGGTATATAT 59.230 40.000 11.96 0.00 42.82 0.86
1986 2169 6.940298 GCTTGCCCAAGAACAAGGTATATATA 59.060 38.462 11.96 0.00 42.82 0.86
2071 2307 0.236711 CGCAGCAGCTAATATGCACC 59.763 55.000 0.00 0.00 46.31 5.01
2072 2308 1.311859 GCAGCAGCTAATATGCACCA 58.688 50.000 0.00 0.00 46.31 4.17
2080 2316 2.797156 GCTAATATGCACCACACTCTCG 59.203 50.000 0.00 0.00 0.00 4.04
2087 2323 1.527311 GCACCACACTCTCGTTTCTTC 59.473 52.381 0.00 0.00 0.00 2.87
2371 2687 2.263540 CTTGGTACACCCCGGACG 59.736 66.667 0.73 0.00 39.29 4.79
2410 2726 1.394917 GTGCAGAAATAGACACCAGCG 59.605 52.381 0.00 0.00 0.00 5.18
2451 2768 7.634671 AATTCAGATATGATGTGTGCTTGAA 57.365 32.000 0.00 0.00 0.00 2.69
2456 2773 2.636647 TGATGTGTGCTTGAACCTGA 57.363 45.000 0.00 0.00 0.00 3.86
2475 2792 7.410120 ACCTGAGATGAAATTAATGGGTTTC 57.590 36.000 0.00 0.00 35.45 2.78
2476 2793 6.381133 ACCTGAGATGAAATTAATGGGTTTCC 59.619 38.462 0.00 0.00 34.29 3.13
2513 2830 2.483889 GGAGGCTATGTTCAGCAGTACC 60.484 54.545 0.00 0.00 43.67 3.34
2650 2967 2.875933 GTGACGTCCCAAACTGAATTGA 59.124 45.455 14.12 0.00 31.84 2.57
2658 2975 7.148239 ACGTCCCAAACTGAATTGAGATATTTC 60.148 37.037 0.00 0.00 31.84 2.17
2667 2984 5.525012 TGAATTGAGATATTTCGGCACTCAG 59.475 40.000 0.00 0.00 38.52 3.35
2699 3016 6.944557 TTACTGTGTGTTCTGATTCGTATG 57.055 37.500 0.00 0.00 0.00 2.39
2700 3017 3.679980 ACTGTGTGTTCTGATTCGTATGC 59.320 43.478 0.00 0.00 0.00 3.14
2705 3022 4.122776 GTGTTCTGATTCGTATGCTGGAT 58.877 43.478 0.00 0.00 0.00 3.41
2732 3062 9.489084 TCTATAAATAAATCGCTGCTTACACAT 57.511 29.630 0.00 0.00 0.00 3.21
2753 3086 3.702330 TGACTATGAAGTGCGGATAACG 58.298 45.455 0.00 0.00 40.29 3.18
2811 3150 2.890311 TGTGCTGAAAAGGGTTGTATGG 59.110 45.455 0.00 0.00 0.00 2.74
2861 3200 2.746277 ATCTGGTTTGCGCCGGAC 60.746 61.111 5.05 0.00 45.74 4.79
2874 3213 0.721718 GCCGGACGAACATCTTTGAG 59.278 55.000 5.05 0.00 0.00 3.02
2879 3218 4.211389 CGGACGAACATCTTTGAGTTTTG 58.789 43.478 0.00 0.00 0.00 2.44
2884 3223 7.206981 ACGAACATCTTTGAGTTTTGATCAT 57.793 32.000 0.00 0.00 0.00 2.45
2886 3225 8.230486 ACGAACATCTTTGAGTTTTGATCATAC 58.770 33.333 0.00 0.00 0.00 2.39
2887 3226 8.446273 CGAACATCTTTGAGTTTTGATCATACT 58.554 33.333 9.95 9.95 0.00 2.12
2890 3229 9.725019 ACATCTTTGAGTTTTGATCATACTGTA 57.275 29.630 13.88 0.00 0.00 2.74
2896 3235 7.463544 TGAGTTTTGATCATACTGTATTTGCG 58.536 34.615 13.88 0.00 0.00 4.85
2897 3236 6.258160 AGTTTTGATCATACTGTATTTGCGC 58.742 36.000 0.00 0.00 0.00 6.09
2898 3237 5.809719 TTTGATCATACTGTATTTGCGCA 57.190 34.783 5.66 5.66 0.00 6.09
2940 3295 2.490903 GCAATTCTCAGGACTGCATGTT 59.509 45.455 0.00 0.00 33.30 2.71
2946 3301 3.087031 CTCAGGACTGCATGTTGGAATT 58.913 45.455 0.00 0.00 0.00 2.17
2947 3302 2.821378 TCAGGACTGCATGTTGGAATTG 59.179 45.455 0.00 0.00 0.00 2.32
2948 3303 2.559668 CAGGACTGCATGTTGGAATTGT 59.440 45.455 0.00 0.00 0.00 2.71
2950 3305 4.218200 CAGGACTGCATGTTGGAATTGTTA 59.782 41.667 0.00 0.00 0.00 2.41
2951 3306 4.832266 AGGACTGCATGTTGGAATTGTTAA 59.168 37.500 0.00 0.00 0.00 2.01
2953 3308 5.405269 GGACTGCATGTTGGAATTGTTAAAC 59.595 40.000 0.00 0.00 0.00 2.01
2955 3310 5.752955 ACTGCATGTTGGAATTGTTAAACAC 59.247 36.000 0.00 0.00 35.51 3.32
2956 3311 4.742167 TGCATGTTGGAATTGTTAAACACG 59.258 37.500 0.00 0.00 35.51 4.49
2957 3312 4.742659 GCATGTTGGAATTGTTAAACACGT 59.257 37.500 0.00 0.00 35.51 4.49
2958 3313 5.108027 GCATGTTGGAATTGTTAAACACGTC 60.108 40.000 0.00 0.00 35.51 4.34
2959 3314 5.562506 TGTTGGAATTGTTAAACACGTCA 57.437 34.783 0.00 0.00 0.00 4.35
2960 3315 5.950883 TGTTGGAATTGTTAAACACGTCAA 58.049 33.333 0.00 0.00 0.00 3.18
2961 3316 5.800941 TGTTGGAATTGTTAAACACGTCAAC 59.199 36.000 0.00 0.00 31.68 3.18
2962 3317 5.562506 TGGAATTGTTAAACACGTCAACA 57.437 34.783 0.00 0.00 0.00 3.33
2963 3318 6.137794 TGGAATTGTTAAACACGTCAACAT 57.862 33.333 0.00 0.00 32.57 2.71
2964 3319 5.974158 TGGAATTGTTAAACACGTCAACATG 59.026 36.000 0.00 0.00 32.57 3.21
2965 3320 5.108027 GGAATTGTTAAACACGTCAACATGC 60.108 40.000 0.00 0.00 32.57 4.06
2966 3321 3.341857 TGTTAAACACGTCAACATGCC 57.658 42.857 0.00 0.00 0.00 4.40
2967 3322 2.683362 TGTTAAACACGTCAACATGCCA 59.317 40.909 0.00 0.00 0.00 4.92
2968 3323 3.040099 GTTAAACACGTCAACATGCCAC 58.960 45.455 0.00 0.00 0.00 5.01
2969 3324 0.028770 AAACACGTCAACATGCCACG 59.971 50.000 9.46 9.46 39.48 4.94
2970 3325 2.127270 CACGTCAACATGCCACGC 60.127 61.111 10.64 0.00 37.02 5.34
2971 3326 3.711842 ACGTCAACATGCCACGCG 61.712 61.111 3.53 3.53 37.02 6.01
2972 3327 3.410516 CGTCAACATGCCACGCGA 61.411 61.111 15.93 0.00 0.00 5.87
2973 3328 2.173382 GTCAACATGCCACGCGAC 59.827 61.111 15.93 1.62 0.00 5.19
2974 3329 2.280457 TCAACATGCCACGCGACA 60.280 55.556 15.93 8.61 0.00 4.35
2975 3330 1.670730 TCAACATGCCACGCGACAT 60.671 52.632 15.93 10.86 0.00 3.06
2977 3332 1.670730 AACATGCCACGCGACATGA 60.671 52.632 32.12 9.52 45.23 3.07
2978 3333 1.911293 AACATGCCACGCGACATGAC 61.911 55.000 32.12 10.68 45.23 3.06
2979 3334 2.047370 ATGCCACGCGACATGACA 60.047 55.556 15.93 0.00 0.00 3.58
2980 3335 2.102438 ATGCCACGCGACATGACAG 61.102 57.895 15.93 0.00 0.00 3.51
2981 3336 3.490759 GCCACGCGACATGACAGG 61.491 66.667 15.93 2.15 0.00 4.00
2982 3337 3.490759 CCACGCGACATGACAGGC 61.491 66.667 15.93 0.00 0.00 4.85
2987 3342 3.009140 CGACATGACAGGCGCATC 58.991 61.111 10.83 3.89 0.00 3.91
2988 3343 1.520120 CGACATGACAGGCGCATCT 60.520 57.895 10.83 0.00 0.00 2.90
2989 3344 1.485838 CGACATGACAGGCGCATCTC 61.486 60.000 10.83 0.00 0.00 2.75
2990 3345 0.460811 GACATGACAGGCGCATCTCA 60.461 55.000 10.83 5.98 0.00 3.27
2991 3346 0.179702 ACATGACAGGCGCATCTCAT 59.820 50.000 10.83 8.66 0.00 2.90
2992 3347 1.413812 ACATGACAGGCGCATCTCATA 59.586 47.619 12.39 0.00 0.00 2.15
2993 3348 2.067013 CATGACAGGCGCATCTCATAG 58.933 52.381 12.39 4.33 0.00 2.23
2994 3349 0.390492 TGACAGGCGCATCTCATAGG 59.610 55.000 10.83 0.00 0.00 2.57
2995 3350 0.676184 GACAGGCGCATCTCATAGGA 59.324 55.000 10.83 0.00 0.00 2.94
2996 3351 0.678395 ACAGGCGCATCTCATAGGAG 59.322 55.000 10.83 0.00 42.80 3.69
3014 3369 9.967451 TCATAGGAGATAGTTGAGATAGTTAGG 57.033 37.037 0.00 0.00 0.00 2.69
3015 3370 9.747898 CATAGGAGATAGTTGAGATAGTTAGGT 57.252 37.037 0.00 0.00 0.00 3.08
3017 3372 8.472007 AGGAGATAGTTGAGATAGTTAGGTTG 57.528 38.462 0.00 0.00 0.00 3.77
3018 3373 8.062536 AGGAGATAGTTGAGATAGTTAGGTTGT 58.937 37.037 0.00 0.00 0.00 3.32
3019 3374 8.697292 GGAGATAGTTGAGATAGTTAGGTTGTT 58.303 37.037 0.00 0.00 0.00 2.83
3061 3416 9.733556 TCTCATGTAACCTCTTATCTCTATCTC 57.266 37.037 0.00 0.00 0.00 2.75
3062 3417 8.871629 TCATGTAACCTCTTATCTCTATCTCC 57.128 38.462 0.00 0.00 0.00 3.71
3063 3418 8.674173 TCATGTAACCTCTTATCTCTATCTCCT 58.326 37.037 0.00 0.00 0.00 3.69
3064 3419 9.308000 CATGTAACCTCTTATCTCTATCTCCTT 57.692 37.037 0.00 0.00 0.00 3.36
3065 3420 9.890915 ATGTAACCTCTTATCTCTATCTCCTTT 57.109 33.333 0.00 0.00 0.00 3.11
3066 3421 9.357161 TGTAACCTCTTATCTCTATCTCCTTTC 57.643 37.037 0.00 0.00 0.00 2.62
3067 3422 9.582648 GTAACCTCTTATCTCTATCTCCTTTCT 57.417 37.037 0.00 0.00 0.00 2.52
3069 3424 8.477419 ACCTCTTATCTCTATCTCCTTTCTTG 57.523 38.462 0.00 0.00 0.00 3.02
3070 3425 8.285891 ACCTCTTATCTCTATCTCCTTTCTTGA 58.714 37.037 0.00 0.00 0.00 3.02
3071 3426 9.312904 CCTCTTATCTCTATCTCCTTTCTTGAT 57.687 37.037 0.00 0.00 0.00 2.57
3075 3430 7.781324 ATCTCTATCTCCTTTCTTGATCTCC 57.219 40.000 0.00 0.00 0.00 3.71
3076 3431 6.677552 TCTCTATCTCCTTTCTTGATCTCCA 58.322 40.000 0.00 0.00 0.00 3.86
3077 3432 7.128751 TCTCTATCTCCTTTCTTGATCTCCAA 58.871 38.462 0.00 0.00 0.00 3.53
3091 3446 8.498054 CTTGATCTCCAAGCTTGTAATCTAAA 57.502 34.615 24.35 12.99 44.90 1.85
3092 3447 9.118300 CTTGATCTCCAAGCTTGTAATCTAAAT 57.882 33.333 24.35 6.81 44.90 1.40
3093 3448 8.668510 TGATCTCCAAGCTTGTAATCTAAATC 57.331 34.615 24.35 14.41 0.00 2.17
3094 3449 8.267183 TGATCTCCAAGCTTGTAATCTAAATCA 58.733 33.333 24.35 16.36 0.00 2.57
3095 3450 7.849804 TCTCCAAGCTTGTAATCTAAATCAC 57.150 36.000 24.35 0.00 0.00 3.06
3096 3451 7.394016 TCTCCAAGCTTGTAATCTAAATCACA 58.606 34.615 24.35 0.00 0.00 3.58
3097 3452 8.049117 TCTCCAAGCTTGTAATCTAAATCACAT 58.951 33.333 24.35 0.00 0.00 3.21
3098 3453 7.988737 TCCAAGCTTGTAATCTAAATCACATG 58.011 34.615 24.35 3.63 0.00 3.21
3099 3454 7.611467 TCCAAGCTTGTAATCTAAATCACATGT 59.389 33.333 24.35 0.00 0.00 3.21
3100 3455 8.892723 CCAAGCTTGTAATCTAAATCACATGTA 58.107 33.333 24.35 0.00 0.00 2.29
3103 3458 8.562892 AGCTTGTAATCTAAATCACATGTATGC 58.437 33.333 0.00 0.00 0.00 3.14
3104 3459 7.531871 GCTTGTAATCTAAATCACATGTATGCG 59.468 37.037 0.00 0.00 0.00 4.73
3105 3460 6.887368 TGTAATCTAAATCACATGTATGCGC 58.113 36.000 0.00 0.00 0.00 6.09
3106 3461 6.705825 TGTAATCTAAATCACATGTATGCGCT 59.294 34.615 9.73 0.00 0.00 5.92
3107 3462 5.602458 ATCTAAATCACATGTATGCGCTG 57.398 39.130 9.73 0.00 0.00 5.18
3108 3463 4.441792 TCTAAATCACATGTATGCGCTGT 58.558 39.130 9.73 0.00 0.00 4.40
3109 3464 4.875536 TCTAAATCACATGTATGCGCTGTT 59.124 37.500 9.73 0.00 0.00 3.16
3110 3465 6.045955 TCTAAATCACATGTATGCGCTGTTA 58.954 36.000 9.73 0.00 0.00 2.41
3111 3466 5.756195 AAATCACATGTATGCGCTGTTAT 57.244 34.783 9.73 0.00 0.00 1.89
3112 3467 4.737353 ATCACATGTATGCGCTGTTATG 57.263 40.909 9.73 11.01 0.00 1.90
3113 3468 2.871633 TCACATGTATGCGCTGTTATGG 59.128 45.455 9.73 3.74 0.00 2.74
3114 3469 2.871633 CACATGTATGCGCTGTTATGGA 59.128 45.455 9.73 0.00 0.00 3.41
3115 3470 3.312146 CACATGTATGCGCTGTTATGGAA 59.688 43.478 9.73 0.00 0.00 3.53
3116 3471 3.561310 ACATGTATGCGCTGTTATGGAAG 59.439 43.478 9.73 0.00 0.00 3.46
3117 3472 2.560504 TGTATGCGCTGTTATGGAAGG 58.439 47.619 9.73 0.00 0.00 3.46
3118 3473 2.093181 TGTATGCGCTGTTATGGAAGGT 60.093 45.455 9.73 0.00 0.00 3.50
3119 3474 1.382522 ATGCGCTGTTATGGAAGGTG 58.617 50.000 9.73 0.00 0.00 4.00
3120 3475 1.305219 TGCGCTGTTATGGAAGGTGC 61.305 55.000 9.73 0.00 0.00 5.01
3121 3476 1.305219 GCGCTGTTATGGAAGGTGCA 61.305 55.000 0.00 0.00 34.17 4.57
3122 3477 0.447801 CGCTGTTATGGAAGGTGCAC 59.552 55.000 8.80 8.80 0.00 4.57
3123 3478 0.811281 GCTGTTATGGAAGGTGCACC 59.189 55.000 29.22 29.22 0.00 5.01
3124 3479 1.463674 CTGTTATGGAAGGTGCACCC 58.536 55.000 32.29 17.77 36.42 4.61
3125 3480 0.039035 TGTTATGGAAGGTGCACCCC 59.961 55.000 32.29 26.05 36.42 4.95
3126 3481 0.039035 GTTATGGAAGGTGCACCCCA 59.961 55.000 32.29 30.55 36.42 4.96
3127 3482 1.006813 TTATGGAAGGTGCACCCCAT 58.993 50.000 34.95 34.95 40.01 4.00
3128 3483 0.550914 TATGGAAGGTGCACCCCATC 59.449 55.000 36.05 28.43 38.48 3.51
3129 3484 1.217057 ATGGAAGGTGCACCCCATCT 61.217 55.000 30.58 17.60 34.29 2.90
3130 3485 0.548926 TGGAAGGTGCACCCCATCTA 60.549 55.000 32.29 21.73 32.40 1.98
3131 3486 0.846693 GGAAGGTGCACCCCATCTAT 59.153 55.000 32.29 9.20 32.40 1.98
3132 3487 1.215423 GGAAGGTGCACCCCATCTATT 59.785 52.381 32.29 17.86 32.40 1.73
3133 3488 2.358195 GGAAGGTGCACCCCATCTATTT 60.358 50.000 32.29 17.08 32.40 1.40
3134 3489 3.117663 GGAAGGTGCACCCCATCTATTTA 60.118 47.826 32.29 0.00 32.40 1.40
3135 3490 4.532834 GAAGGTGCACCCCATCTATTTAA 58.467 43.478 32.29 0.00 32.40 1.52
3136 3491 3.898482 AGGTGCACCCCATCTATTTAAC 58.102 45.455 32.29 1.80 31.60 2.01
3137 3492 3.268334 AGGTGCACCCCATCTATTTAACA 59.732 43.478 32.29 0.00 31.60 2.41
3138 3493 4.079212 AGGTGCACCCCATCTATTTAACAT 60.079 41.667 32.29 4.66 31.60 2.71
3139 3494 4.037923 GGTGCACCCCATCTATTTAACATG 59.962 45.833 26.31 0.00 0.00 3.21
3140 3495 4.887071 GTGCACCCCATCTATTTAACATGA 59.113 41.667 5.22 0.00 0.00 3.07
3141 3496 5.359576 GTGCACCCCATCTATTTAACATGAA 59.640 40.000 5.22 0.00 0.00 2.57
3142 3497 5.359576 TGCACCCCATCTATTTAACATGAAC 59.640 40.000 0.00 0.00 0.00 3.18
3143 3498 5.221244 GCACCCCATCTATTTAACATGAACC 60.221 44.000 0.00 0.00 0.00 3.62
3144 3499 5.301805 CACCCCATCTATTTAACATGAACCC 59.698 44.000 0.00 0.00 0.00 4.11
3145 3500 4.518970 CCCCATCTATTTAACATGAACCCG 59.481 45.833 0.00 0.00 0.00 5.28
3146 3501 5.130350 CCCATCTATTTAACATGAACCCGT 58.870 41.667 0.00 0.00 0.00 5.28
3147 3502 5.238650 CCCATCTATTTAACATGAACCCGTC 59.761 44.000 0.00 0.00 0.00 4.79
3148 3503 5.050363 CCATCTATTTAACATGAACCCGTCG 60.050 44.000 0.00 0.00 0.00 5.12
3149 3504 4.435425 TCTATTTAACATGAACCCGTCGG 58.565 43.478 3.60 3.60 0.00 4.79
3150 3505 1.158434 TTTAACATGAACCCGTCGGC 58.842 50.000 5.50 0.00 0.00 5.54
3151 3506 0.674269 TTAACATGAACCCGTCGGCC 60.674 55.000 5.50 0.00 0.00 6.13
3152 3507 1.546589 TAACATGAACCCGTCGGCCT 61.547 55.000 5.50 0.00 0.00 5.19
3153 3508 2.819595 CATGAACCCGTCGGCCTG 60.820 66.667 5.50 0.00 0.00 4.85
3154 3509 3.000819 ATGAACCCGTCGGCCTGA 61.001 61.111 5.50 0.00 0.00 3.86
3155 3510 3.019003 ATGAACCCGTCGGCCTGAG 62.019 63.158 5.50 0.00 0.00 3.35
3167 3522 2.507992 CCTGAGCGAGGCAAGACG 60.508 66.667 0.00 0.00 34.01 4.18
3168 3523 2.259818 CTGAGCGAGGCAAGACGT 59.740 61.111 0.00 0.00 0.00 4.34
3169 3524 1.373497 CTGAGCGAGGCAAGACGTT 60.373 57.895 0.00 0.00 0.00 3.99
3170 3525 1.347817 CTGAGCGAGGCAAGACGTTC 61.348 60.000 0.00 0.00 39.43 3.95
3171 3526 2.048127 AGCGAGGCAAGACGTTCC 60.048 61.111 0.00 0.00 0.00 3.62
3172 3527 3.479269 GCGAGGCAAGACGTTCCG 61.479 66.667 0.00 0.00 0.00 4.30
3173 3528 3.479269 CGAGGCAAGACGTTCCGC 61.479 66.667 0.00 0.00 0.00 5.54
3174 3529 2.048127 GAGGCAAGACGTTCCGCT 60.048 61.111 0.00 0.00 0.00 5.52
3175 3530 1.214589 GAGGCAAGACGTTCCGCTA 59.785 57.895 0.00 0.00 0.00 4.26
3176 3531 0.802607 GAGGCAAGACGTTCCGCTAG 60.803 60.000 0.00 0.00 0.00 3.42
3177 3532 1.080025 GGCAAGACGTTCCGCTAGT 60.080 57.895 0.00 0.00 0.00 2.57
3178 3533 0.669625 GGCAAGACGTTCCGCTAGTT 60.670 55.000 0.00 0.00 0.00 2.24
3179 3534 0.714439 GCAAGACGTTCCGCTAGTTC 59.286 55.000 0.00 0.00 0.00 3.01
3180 3535 0.982673 CAAGACGTTCCGCTAGTTCG 59.017 55.000 0.00 0.00 0.00 3.95
3181 3536 0.731855 AAGACGTTCCGCTAGTTCGC 60.732 55.000 0.00 0.00 0.00 4.70
3182 3537 1.443194 GACGTTCCGCTAGTTCGCA 60.443 57.895 0.00 0.00 0.00 5.10
3183 3538 1.671880 GACGTTCCGCTAGTTCGCAC 61.672 60.000 0.00 0.00 0.00 5.34
3184 3539 1.731613 CGTTCCGCTAGTTCGCACA 60.732 57.895 0.00 0.00 0.00 4.57
3185 3540 1.076533 CGTTCCGCTAGTTCGCACAT 61.077 55.000 0.00 0.00 0.00 3.21
3186 3541 0.370273 GTTCCGCTAGTTCGCACATG 59.630 55.000 0.00 0.00 0.00 3.21
3187 3542 0.245266 TTCCGCTAGTTCGCACATGA 59.755 50.000 0.00 0.00 0.00 3.07
3188 3543 0.245266 TCCGCTAGTTCGCACATGAA 59.755 50.000 0.00 0.00 0.00 2.57
3189 3544 1.134818 TCCGCTAGTTCGCACATGAAT 60.135 47.619 0.00 0.00 0.00 2.57
3190 3545 2.100087 TCCGCTAGTTCGCACATGAATA 59.900 45.455 0.00 0.00 0.00 1.75
3191 3546 3.059884 CCGCTAGTTCGCACATGAATAT 58.940 45.455 0.00 0.00 0.00 1.28
3192 3547 3.121944 CCGCTAGTTCGCACATGAATATC 59.878 47.826 0.00 0.00 0.00 1.63
3193 3548 3.121944 CGCTAGTTCGCACATGAATATCC 59.878 47.826 0.00 0.00 0.00 2.59
3194 3549 3.433615 GCTAGTTCGCACATGAATATCCC 59.566 47.826 0.00 0.00 0.00 3.85
3195 3550 2.851195 AGTTCGCACATGAATATCCCC 58.149 47.619 0.00 0.00 0.00 4.81
3196 3551 2.172505 AGTTCGCACATGAATATCCCCA 59.827 45.455 0.00 0.00 0.00 4.96
3197 3552 2.254546 TCGCACATGAATATCCCCAC 57.745 50.000 0.00 0.00 0.00 4.61
3198 3553 1.768275 TCGCACATGAATATCCCCACT 59.232 47.619 0.00 0.00 0.00 4.00
3399 3764 8.251026 TGTAACTAAGTGATCATCGTTCTCATT 58.749 33.333 0.00 0.00 0.00 2.57
3404 3808 5.970592 AGTGATCATCGTTCTCATTCTTCA 58.029 37.500 0.00 0.00 0.00 3.02
3444 3848 1.590932 CCTAGTAGCAATGGCAGCAG 58.409 55.000 0.00 0.00 44.61 4.24
3445 3849 0.942962 CTAGTAGCAATGGCAGCAGC 59.057 55.000 0.00 0.00 44.61 5.25
3483 3887 5.959618 ACCTTGGTAAAATACTGTTCTGC 57.040 39.130 0.00 0.00 0.00 4.26
3541 3951 4.762289 AGGGAAACTCTCATACATCACC 57.238 45.455 0.00 0.00 0.00 4.02
3542 3952 4.104086 AGGGAAACTCTCATACATCACCA 58.896 43.478 0.00 0.00 0.00 4.17
3578 3988 3.090037 GTGGTGCTCTCTCCTAACTGTA 58.910 50.000 0.00 0.00 0.00 2.74
3583 3993 4.081917 GTGCTCTCTCCTAACTGTAAGCTT 60.082 45.833 3.48 3.48 37.60 3.74
3611 4021 8.038944 TCTAAGCTTGGGTACAAACTATAACTG 58.961 37.037 9.86 0.00 32.11 3.16
3626 4036 1.808411 AACTGGACAACATACAGCCG 58.192 50.000 0.00 0.00 35.70 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.001330 GGTTCCAGCATAATCGAAAGACG 59.999 47.826 0.00 0.00 46.97 4.18
416 421 0.527817 GCCCGTAACCGTCAGATCTG 60.528 60.000 17.07 17.07 0.00 2.90
505 510 8.854237 ATTCTGCTGTGGTGGGTATATATATA 57.146 34.615 0.00 0.00 0.00 0.86
531 536 8.520351 TCTGACTTCGTTATCTTGTGAAAGATA 58.480 33.333 4.45 4.45 39.92 1.98
546 551 4.832248 TCATATTTGCCTCTGACTTCGTT 58.168 39.130 0.00 0.00 0.00 3.85
574 580 5.556915 CAACAGGAAGAAGGTAATGGTGTA 58.443 41.667 0.00 0.00 0.00 2.90
609 615 1.520120 ATCTGTGAGTGATGCGCCG 60.520 57.895 4.18 0.00 0.00 6.46
660 666 1.376037 CTTCTTGGCCGTGGACTCC 60.376 63.158 0.00 0.00 0.00 3.85
693 700 2.486592 GGTTACGTTTGCATTACTGGCT 59.513 45.455 0.00 0.00 0.00 4.75
721 728 3.284336 GGCCCATGGGACGTTTTC 58.716 61.111 36.00 14.45 37.50 2.29
880 890 3.823330 CTCGCGGCCGTACTCCTT 61.823 66.667 28.70 0.00 35.54 3.36
939 949 0.319469 GCTAGAGGATGAGCGGCTTC 60.319 60.000 2.97 0.00 0.00 3.86
956 966 4.335647 CAGGCCCACCGTTGAGCT 62.336 66.667 0.00 0.00 42.76 4.09
1288 1339 2.047560 GTCGCGGCCCTTGTACTT 60.048 61.111 6.13 0.00 0.00 2.24
1317 1368 3.094062 GCCACCATAGCTCTCGCCA 62.094 63.158 0.00 0.00 36.60 5.69
1353 1404 0.687920 TGAAGGTGATTACGGTGGCA 59.312 50.000 0.00 0.00 0.00 4.92
1463 1528 1.503542 GCATATGCATGGCTACCGC 59.496 57.895 22.84 0.00 41.59 5.68
1667 1735 0.767375 AGATGCCGCCTATGTGGAAT 59.233 50.000 1.26 0.00 43.59 3.01
1727 1795 0.174845 TTACATAGCCTTCGCGTGCT 59.825 50.000 20.36 20.36 41.18 4.40
1806 1887 4.125703 CTGTCTGACTGGCCATAGAAATC 58.874 47.826 5.51 0.23 0.00 2.17
1986 2169 8.034215 GCAGAACATTATGCAGATAGATAGAGT 58.966 37.037 6.36 0.00 44.32 3.24
2071 2307 1.795286 GCTGGAAGAAACGAGAGTGTG 59.205 52.381 0.00 0.00 39.80 3.82
2072 2308 1.603172 CGCTGGAAGAAACGAGAGTGT 60.603 52.381 0.00 0.00 39.80 3.55
2080 2316 0.250770 AAGGGGACGCTGGAAGAAAC 60.251 55.000 0.00 0.00 34.07 2.78
2087 2323 0.474184 ATAATGGAAGGGGACGCTGG 59.526 55.000 0.00 0.00 0.00 4.85
2371 2687 2.601763 CACAGCGGTTAATTACCTCGAC 59.398 50.000 0.00 0.00 45.40 4.20
2451 2768 6.381133 GGAAACCCATTAATTTCATCTCAGGT 59.619 38.462 2.61 0.00 36.69 4.00
2456 2773 5.127031 CACCGGAAACCCATTAATTTCATCT 59.873 40.000 9.46 0.00 36.69 2.90
2475 2792 0.834612 TCCAACCTATAAGCCACCGG 59.165 55.000 0.00 0.00 0.00 5.28
2476 2793 1.202651 CCTCCAACCTATAAGCCACCG 60.203 57.143 0.00 0.00 0.00 4.94
2513 2830 1.856265 GCAAACGTGAAGCCTCCCTG 61.856 60.000 0.00 0.00 0.00 4.45
2650 2967 4.679373 ACATCTGAGTGCCGAAATATCT 57.321 40.909 0.00 0.00 0.00 1.98
2658 2975 5.351465 ACAGTAAATTAACATCTGAGTGCCG 59.649 40.000 0.00 0.00 0.00 5.69
2699 3016 6.963805 GCAGCGATTTATTTATAGAATCCAGC 59.036 38.462 0.00 0.00 0.00 4.85
2700 3017 8.261492 AGCAGCGATTTATTTATAGAATCCAG 57.739 34.615 0.00 0.00 0.00 3.86
2705 3022 9.320352 TGTGTAAGCAGCGATTTATTTATAGAA 57.680 29.630 0.00 0.00 0.00 2.10
2732 3062 3.379057 TCGTTATCCGCACTTCATAGTCA 59.621 43.478 0.00 0.00 36.19 3.41
2811 3150 8.087982 TCACTCTATTCTTTTCATGTGAACAC 57.912 34.615 0.00 0.00 33.13 3.32
2861 3200 8.446273 AGTATGATCAAAACTCAAAGATGTTCG 58.554 33.333 0.00 0.00 0.00 3.95
2874 3213 6.027131 TGCGCAAATACAGTATGATCAAAAC 58.973 36.000 8.16 1.01 39.69 2.43
2879 3218 4.026062 TCGTTGCGCAAATACAGTATGATC 60.026 41.667 26.87 6.43 39.69 2.92
2884 3223 1.392168 GCTCGTTGCGCAAATACAGTA 59.608 47.619 26.87 0.00 0.00 2.74
2886 3225 0.165727 TGCTCGTTGCGCAAATACAG 59.834 50.000 26.87 17.93 46.63 2.74
2887 3226 0.165727 CTGCTCGTTGCGCAAATACA 59.834 50.000 26.87 18.71 46.63 2.29
2890 3229 0.523072 ATTCTGCTCGTTGCGCAAAT 59.477 45.000 26.87 9.27 46.63 2.32
2891 3230 0.385849 CATTCTGCTCGTTGCGCAAA 60.386 50.000 26.87 9.69 46.63 3.68
2894 3233 0.110238 TTTCATTCTGCTCGTTGCGC 60.110 50.000 0.00 0.00 46.63 6.09
2896 3235 2.998772 TGTTTTCATTCTGCTCGTTGC 58.001 42.857 0.00 0.00 43.25 4.17
2897 3236 3.976942 CCTTGTTTTCATTCTGCTCGTTG 59.023 43.478 0.00 0.00 0.00 4.10
2898 3237 3.550842 GCCTTGTTTTCATTCTGCTCGTT 60.551 43.478 0.00 0.00 0.00 3.85
2940 3295 5.562506 TGTTGACGTGTTTAACAATTCCA 57.437 34.783 0.00 0.00 31.95 3.53
2946 3301 2.683362 TGGCATGTTGACGTGTTTAACA 59.317 40.909 0.00 0.00 38.52 2.41
2947 3302 3.040099 GTGGCATGTTGACGTGTTTAAC 58.960 45.455 0.00 0.00 35.38 2.01
2948 3303 2.286477 CGTGGCATGTTGACGTGTTTAA 60.286 45.455 0.00 0.00 35.38 1.52
2950 3305 0.028770 CGTGGCATGTTGACGTGTTT 59.971 50.000 0.00 0.00 35.38 2.83
2951 3306 1.646540 CGTGGCATGTTGACGTGTT 59.353 52.632 0.00 0.00 35.38 3.32
2953 3308 2.127270 GCGTGGCATGTTGACGTG 60.127 61.111 8.75 0.00 35.52 4.49
2955 3310 3.410516 TCGCGTGGCATGTTGACG 61.411 61.111 5.77 3.38 36.18 4.35
2956 3311 1.911293 ATGTCGCGTGGCATGTTGAC 61.911 55.000 16.50 20.32 0.00 3.18
2957 3312 1.670730 ATGTCGCGTGGCATGTTGA 60.671 52.632 16.50 4.19 0.00 3.18
2958 3313 1.512522 CATGTCGCGTGGCATGTTG 60.513 57.895 30.36 11.56 38.06 3.33
2959 3314 1.670730 TCATGTCGCGTGGCATGTT 60.671 52.632 34.86 6.39 42.09 2.71
2960 3315 2.047370 TCATGTCGCGTGGCATGT 60.047 55.556 34.86 7.17 42.09 3.21
2961 3316 2.300597 CTGTCATGTCGCGTGGCATG 62.301 60.000 32.26 32.26 42.62 4.06
2962 3317 2.047370 TGTCATGTCGCGTGGCAT 60.047 55.556 10.91 10.91 29.50 4.40
2963 3318 2.738139 CTGTCATGTCGCGTGGCA 60.738 61.111 5.40 5.40 33.74 4.92
2964 3319 3.490759 CCTGTCATGTCGCGTGGC 61.491 66.667 5.77 0.00 0.00 5.01
2965 3320 3.490759 GCCTGTCATGTCGCGTGG 61.491 66.667 5.77 0.00 0.00 4.94
2966 3321 3.842126 CGCCTGTCATGTCGCGTG 61.842 66.667 5.77 0.00 39.78 5.34
2969 3324 3.160557 GATGCGCCTGTCATGTCGC 62.161 63.158 4.18 8.96 46.78 5.19
2970 3325 1.485838 GAGATGCGCCTGTCATGTCG 61.486 60.000 4.18 0.00 0.00 4.35
2971 3326 0.460811 TGAGATGCGCCTGTCATGTC 60.461 55.000 8.44 1.84 35.52 3.06
2972 3327 0.179702 ATGAGATGCGCCTGTCATGT 59.820 50.000 21.51 2.64 0.00 3.21
2973 3328 2.067013 CTATGAGATGCGCCTGTCATG 58.933 52.381 27.73 17.00 32.01 3.07
2974 3329 1.001746 CCTATGAGATGCGCCTGTCAT 59.998 52.381 24.47 24.47 34.11 3.06
2975 3330 0.390492 CCTATGAGATGCGCCTGTCA 59.610 55.000 14.53 14.53 0.00 3.58
2976 3331 0.676184 TCCTATGAGATGCGCCTGTC 59.324 55.000 4.18 3.36 0.00 3.51
2977 3332 0.678395 CTCCTATGAGATGCGCCTGT 59.322 55.000 4.18 0.00 41.42 4.00
2978 3333 0.964700 TCTCCTATGAGATGCGCCTG 59.035 55.000 4.18 0.00 42.73 4.85
2979 3334 3.446658 TCTCCTATGAGATGCGCCT 57.553 52.632 4.18 0.00 42.73 5.52
2988 3343 9.967451 CCTAACTATCTCAACTATCTCCTATGA 57.033 37.037 0.00 0.00 0.00 2.15
2989 3344 9.747898 ACCTAACTATCTCAACTATCTCCTATG 57.252 37.037 0.00 0.00 0.00 2.23
2991 3346 9.575868 CAACCTAACTATCTCAACTATCTCCTA 57.424 37.037 0.00 0.00 0.00 2.94
2992 3347 8.062536 ACAACCTAACTATCTCAACTATCTCCT 58.937 37.037 0.00 0.00 0.00 3.69
2993 3348 8.240267 ACAACCTAACTATCTCAACTATCTCC 57.760 38.462 0.00 0.00 0.00 3.71
3035 3390 9.733556 GAGATAGAGATAAGAGGTTACATGAGA 57.266 37.037 0.00 0.00 0.00 3.27
3036 3391 8.956426 GGAGATAGAGATAAGAGGTTACATGAG 58.044 40.741 0.00 0.00 0.00 2.90
3037 3392 8.674173 AGGAGATAGAGATAAGAGGTTACATGA 58.326 37.037 0.00 0.00 0.00 3.07
3038 3393 8.877864 AGGAGATAGAGATAAGAGGTTACATG 57.122 38.462 0.00 0.00 0.00 3.21
3039 3394 9.890915 AAAGGAGATAGAGATAAGAGGTTACAT 57.109 33.333 0.00 0.00 0.00 2.29
3040 3395 9.357161 GAAAGGAGATAGAGATAAGAGGTTACA 57.643 37.037 0.00 0.00 0.00 2.41
3041 3396 9.582648 AGAAAGGAGATAGAGATAAGAGGTTAC 57.417 37.037 0.00 0.00 0.00 2.50
3043 3398 8.923270 CAAGAAAGGAGATAGAGATAAGAGGTT 58.077 37.037 0.00 0.00 0.00 3.50
3044 3399 8.285891 TCAAGAAAGGAGATAGAGATAAGAGGT 58.714 37.037 0.00 0.00 0.00 3.85
3045 3400 8.704849 TCAAGAAAGGAGATAGAGATAAGAGG 57.295 38.462 0.00 0.00 0.00 3.69
3049 3404 9.308000 GGAGATCAAGAAAGGAGATAGAGATAA 57.692 37.037 0.00 0.00 0.00 1.75
3050 3405 8.452056 TGGAGATCAAGAAAGGAGATAGAGATA 58.548 37.037 0.00 0.00 0.00 1.98
3051 3406 7.304479 TGGAGATCAAGAAAGGAGATAGAGAT 58.696 38.462 0.00 0.00 0.00 2.75
3052 3407 6.677552 TGGAGATCAAGAAAGGAGATAGAGA 58.322 40.000 0.00 0.00 0.00 3.10
3053 3408 6.975196 TGGAGATCAAGAAAGGAGATAGAG 57.025 41.667 0.00 0.00 0.00 2.43
3067 3422 9.113838 GATTTAGATTACAAGCTTGGAGATCAA 57.886 33.333 29.18 17.94 0.00 2.57
3068 3423 8.267183 TGATTTAGATTACAAGCTTGGAGATCA 58.733 33.333 29.18 20.23 0.00 2.92
3069 3424 8.555361 GTGATTTAGATTACAAGCTTGGAGATC 58.445 37.037 29.18 24.66 0.00 2.75
3070 3425 8.049117 TGTGATTTAGATTACAAGCTTGGAGAT 58.951 33.333 29.18 18.87 29.80 2.75
3071 3426 7.394016 TGTGATTTAGATTACAAGCTTGGAGA 58.606 34.615 29.18 15.13 29.80 3.71
3072 3427 7.615582 TGTGATTTAGATTACAAGCTTGGAG 57.384 36.000 29.18 6.05 29.80 3.86
3073 3428 7.611467 ACATGTGATTTAGATTACAAGCTTGGA 59.389 33.333 29.18 20.21 35.67 3.53
3074 3429 7.765307 ACATGTGATTTAGATTACAAGCTTGG 58.235 34.615 29.18 12.28 35.67 3.61
3077 3432 8.562892 GCATACATGTGATTTAGATTACAAGCT 58.437 33.333 9.11 0.00 35.67 3.74
3078 3433 7.531871 CGCATACATGTGATTTAGATTACAAGC 59.468 37.037 9.11 0.00 40.61 4.01
3079 3434 7.531871 GCGCATACATGTGATTTAGATTACAAG 59.468 37.037 9.11 0.00 40.61 3.16
3080 3435 7.226523 AGCGCATACATGTGATTTAGATTACAA 59.773 33.333 11.47 0.00 40.61 2.41
3081 3436 6.705825 AGCGCATACATGTGATTTAGATTACA 59.294 34.615 11.47 0.00 40.61 2.41
3082 3437 7.011773 CAGCGCATACATGTGATTTAGATTAC 58.988 38.462 11.47 0.00 40.61 1.89
3083 3438 6.705825 ACAGCGCATACATGTGATTTAGATTA 59.294 34.615 11.47 0.00 40.61 1.75
3084 3439 5.528690 ACAGCGCATACATGTGATTTAGATT 59.471 36.000 11.47 0.00 40.61 2.40
3085 3440 5.059161 ACAGCGCATACATGTGATTTAGAT 58.941 37.500 11.47 0.00 40.61 1.98
3086 3441 4.441792 ACAGCGCATACATGTGATTTAGA 58.558 39.130 11.47 0.00 40.61 2.10
3087 3442 4.801147 ACAGCGCATACATGTGATTTAG 57.199 40.909 11.47 0.00 40.61 1.85
3088 3443 6.293353 CCATAACAGCGCATACATGTGATTTA 60.293 38.462 11.47 0.00 40.61 1.40
3089 3444 5.506151 CCATAACAGCGCATACATGTGATTT 60.506 40.000 11.47 0.00 40.61 2.17
3090 3445 4.023792 CCATAACAGCGCATACATGTGATT 60.024 41.667 11.47 0.00 40.61 2.57
3091 3446 3.499537 CCATAACAGCGCATACATGTGAT 59.500 43.478 11.47 0.00 40.61 3.06
3092 3447 2.871633 CCATAACAGCGCATACATGTGA 59.128 45.455 11.47 0.00 40.61 3.58
3093 3448 2.871633 TCCATAACAGCGCATACATGTG 59.128 45.455 11.47 0.00 41.07 3.21
3094 3449 3.192541 TCCATAACAGCGCATACATGT 57.807 42.857 11.47 2.69 0.00 3.21
3095 3450 3.058708 CCTTCCATAACAGCGCATACATG 60.059 47.826 11.47 7.63 0.00 3.21
3096 3451 3.141398 CCTTCCATAACAGCGCATACAT 58.859 45.455 11.47 0.00 0.00 2.29
3097 3452 2.093181 ACCTTCCATAACAGCGCATACA 60.093 45.455 11.47 0.00 0.00 2.29
3098 3453 2.287915 CACCTTCCATAACAGCGCATAC 59.712 50.000 11.47 0.00 0.00 2.39
3099 3454 2.560504 CACCTTCCATAACAGCGCATA 58.439 47.619 11.47 0.00 0.00 3.14
3100 3455 1.382522 CACCTTCCATAACAGCGCAT 58.617 50.000 11.47 0.00 0.00 4.73
3101 3456 1.305219 GCACCTTCCATAACAGCGCA 61.305 55.000 11.47 0.00 0.00 6.09
3102 3457 1.305219 TGCACCTTCCATAACAGCGC 61.305 55.000 0.00 0.00 0.00 5.92
3103 3458 0.447801 GTGCACCTTCCATAACAGCG 59.552 55.000 5.22 0.00 0.00 5.18
3104 3459 0.811281 GGTGCACCTTCCATAACAGC 59.189 55.000 29.12 0.00 0.00 4.40
3105 3460 1.463674 GGGTGCACCTTCCATAACAG 58.536 55.000 33.91 0.00 35.85 3.16
3106 3461 0.039035 GGGGTGCACCTTCCATAACA 59.961 55.000 33.91 0.00 40.03 2.41
3107 3462 0.039035 TGGGGTGCACCTTCCATAAC 59.961 55.000 33.91 15.35 40.03 1.89
3108 3463 1.006813 ATGGGGTGCACCTTCCATAA 58.993 50.000 33.27 15.82 36.63 1.90
3109 3464 0.550914 GATGGGGTGCACCTTCCATA 59.449 55.000 33.88 16.99 37.92 2.74
3110 3465 1.217057 AGATGGGGTGCACCTTCCAT 61.217 55.000 34.18 34.18 39.69 3.41
3111 3466 0.548926 TAGATGGGGTGCACCTTCCA 60.549 55.000 33.91 31.32 40.03 3.53
3112 3467 0.846693 ATAGATGGGGTGCACCTTCC 59.153 55.000 33.91 26.99 40.03 3.46
3113 3468 2.736670 AATAGATGGGGTGCACCTTC 57.263 50.000 33.91 25.76 40.03 3.46
3114 3469 4.264172 TGTTAAATAGATGGGGTGCACCTT 60.264 41.667 33.91 20.02 40.03 3.50
3115 3470 3.268334 TGTTAAATAGATGGGGTGCACCT 59.732 43.478 33.91 16.27 40.03 4.00
3116 3471 3.626930 TGTTAAATAGATGGGGTGCACC 58.373 45.455 28.57 28.57 39.11 5.01
3117 3472 4.887071 TCATGTTAAATAGATGGGGTGCAC 59.113 41.667 8.80 8.80 0.00 4.57
3118 3473 5.122707 TCATGTTAAATAGATGGGGTGCA 57.877 39.130 0.00 0.00 0.00 4.57
3119 3474 5.221244 GGTTCATGTTAAATAGATGGGGTGC 60.221 44.000 0.00 0.00 0.00 5.01
3120 3475 5.301805 GGGTTCATGTTAAATAGATGGGGTG 59.698 44.000 0.00 0.00 0.00 4.61
3121 3476 5.454966 GGGTTCATGTTAAATAGATGGGGT 58.545 41.667 0.00 0.00 0.00 4.95
3122 3477 4.518970 CGGGTTCATGTTAAATAGATGGGG 59.481 45.833 0.00 0.00 0.00 4.96
3123 3478 5.130350 ACGGGTTCATGTTAAATAGATGGG 58.870 41.667 0.00 0.00 0.00 4.00
3124 3479 5.050363 CGACGGGTTCATGTTAAATAGATGG 60.050 44.000 0.00 0.00 0.00 3.51
3125 3480 5.050363 CCGACGGGTTCATGTTAAATAGATG 60.050 44.000 5.81 0.00 0.00 2.90
3126 3481 5.054477 CCGACGGGTTCATGTTAAATAGAT 58.946 41.667 5.81 0.00 0.00 1.98
3127 3482 4.435425 CCGACGGGTTCATGTTAAATAGA 58.565 43.478 5.81 0.00 0.00 1.98
3128 3483 3.001939 GCCGACGGGTTCATGTTAAATAG 59.998 47.826 17.22 0.00 34.97 1.73
3129 3484 2.937799 GCCGACGGGTTCATGTTAAATA 59.062 45.455 17.22 0.00 34.97 1.40
3130 3485 1.741145 GCCGACGGGTTCATGTTAAAT 59.259 47.619 17.22 0.00 34.97 1.40
3131 3486 1.158434 GCCGACGGGTTCATGTTAAA 58.842 50.000 17.22 0.00 34.97 1.52
3132 3487 0.674269 GGCCGACGGGTTCATGTTAA 60.674 55.000 17.22 0.00 34.97 2.01
3133 3488 1.078988 GGCCGACGGGTTCATGTTA 60.079 57.895 17.22 0.00 34.97 2.41
3134 3489 2.359478 GGCCGACGGGTTCATGTT 60.359 61.111 17.22 0.00 34.97 2.71
3135 3490 3.319198 AGGCCGACGGGTTCATGT 61.319 61.111 17.22 0.00 34.97 3.21
3136 3491 2.819595 CAGGCCGACGGGTTCATG 60.820 66.667 17.22 2.94 34.97 3.07
3137 3492 3.000819 TCAGGCCGACGGGTTCAT 61.001 61.111 17.22 0.00 34.97 2.57
3138 3493 3.691342 CTCAGGCCGACGGGTTCA 61.691 66.667 17.22 0.00 34.97 3.18
3150 3505 2.507992 CGTCTTGCCTCGCTCAGG 60.508 66.667 0.00 0.00 46.82 3.86
3151 3506 1.347817 GAACGTCTTGCCTCGCTCAG 61.348 60.000 0.00 0.00 0.00 3.35
3152 3507 1.372997 GAACGTCTTGCCTCGCTCA 60.373 57.895 0.00 0.00 0.00 4.26
3153 3508 2.095252 GGAACGTCTTGCCTCGCTC 61.095 63.158 0.00 0.00 0.00 5.03
3154 3509 2.048127 GGAACGTCTTGCCTCGCT 60.048 61.111 0.00 0.00 0.00 4.93
3167 3522 0.370273 CATGTGCGAACTAGCGGAAC 59.630 55.000 0.00 0.00 40.67 3.62
3168 3523 0.245266 TCATGTGCGAACTAGCGGAA 59.755 50.000 0.00 0.00 40.67 4.30
3169 3524 0.245266 TTCATGTGCGAACTAGCGGA 59.755 50.000 0.00 0.00 40.67 5.54
3170 3525 1.290203 ATTCATGTGCGAACTAGCGG 58.710 50.000 0.00 0.00 40.67 5.52
3171 3526 3.121944 GGATATTCATGTGCGAACTAGCG 59.878 47.826 0.00 0.00 40.67 4.26
3172 3527 3.433615 GGGATATTCATGTGCGAACTAGC 59.566 47.826 0.00 0.00 37.71 3.42
3173 3528 3.997021 GGGGATATTCATGTGCGAACTAG 59.003 47.826 0.00 0.00 0.00 2.57
3174 3529 3.389656 TGGGGATATTCATGTGCGAACTA 59.610 43.478 0.00 0.00 0.00 2.24
3175 3530 2.172505 TGGGGATATTCATGTGCGAACT 59.827 45.455 0.00 0.00 0.00 3.01
3176 3531 2.290641 GTGGGGATATTCATGTGCGAAC 59.709 50.000 0.00 0.00 0.00 3.95
3177 3532 2.172505 AGTGGGGATATTCATGTGCGAA 59.827 45.455 0.00 0.00 0.00 4.70
3178 3533 1.768275 AGTGGGGATATTCATGTGCGA 59.232 47.619 0.00 0.00 0.00 5.10
3179 3534 2.260844 AGTGGGGATATTCATGTGCG 57.739 50.000 0.00 0.00 0.00 5.34
3180 3535 3.290710 ACAAGTGGGGATATTCATGTGC 58.709 45.455 0.00 0.00 0.00 4.57
3181 3536 4.949238 TGAACAAGTGGGGATATTCATGTG 59.051 41.667 0.00 0.00 0.00 3.21
3182 3537 5.191727 TGAACAAGTGGGGATATTCATGT 57.808 39.130 0.00 0.00 0.00 3.21
3183 3538 5.829391 TGATGAACAAGTGGGGATATTCATG 59.171 40.000 2.21 0.00 37.02 3.07
3184 3539 6.017211 TGATGAACAAGTGGGGATATTCAT 57.983 37.500 0.00 0.00 39.00 2.57
3185 3540 5.449297 TGATGAACAAGTGGGGATATTCA 57.551 39.130 0.00 0.00 0.00 2.57
3186 3541 7.362401 GCATATGATGAACAAGTGGGGATATTC 60.362 40.741 6.97 0.00 0.00 1.75
3187 3542 6.435277 GCATATGATGAACAAGTGGGGATATT 59.565 38.462 6.97 0.00 0.00 1.28
3188 3543 5.948162 GCATATGATGAACAAGTGGGGATAT 59.052 40.000 6.97 0.00 0.00 1.63
3189 3544 5.073554 AGCATATGATGAACAAGTGGGGATA 59.926 40.000 6.97 0.00 0.00 2.59
3190 3545 4.141088 AGCATATGATGAACAAGTGGGGAT 60.141 41.667 6.97 0.00 0.00 3.85
3191 3546 3.202818 AGCATATGATGAACAAGTGGGGA 59.797 43.478 6.97 0.00 0.00 4.81
3192 3547 3.559069 AGCATATGATGAACAAGTGGGG 58.441 45.455 6.97 0.00 0.00 4.96
3193 3548 5.371526 ACTAGCATATGATGAACAAGTGGG 58.628 41.667 6.97 0.00 0.00 4.61
3194 3549 6.932356 AACTAGCATATGATGAACAAGTGG 57.068 37.500 6.97 0.00 0.00 4.00
3242 3601 7.498443 ACCCGTCCTTGTATCTTTATAGAAAG 58.502 38.462 3.35 3.35 43.05 2.62
3381 3746 5.970592 TGAAGAATGAGAACGATGATCACT 58.029 37.500 0.00 0.00 0.00 3.41
3399 3764 9.449719 GGATTAGTCCTAACTTTTGATTGAAGA 57.550 33.333 0.00 0.00 41.60 2.87
3404 3808 9.059023 ACTAGGGATTAGTCCTAACTTTTGATT 57.941 33.333 4.04 0.00 44.44 2.57
3444 3848 0.732538 GGTTACACTTTGGCGCATGC 60.733 55.000 10.83 7.91 41.71 4.06
3445 3849 0.881118 AGGTTACACTTTGGCGCATG 59.119 50.000 10.83 1.14 0.00 4.06
3483 3887 3.063452 GTGTCATTATACGTTGCCAGTGG 59.937 47.826 4.20 4.20 0.00 4.00
3513 3917 4.408921 TGTATGAGAGTTTCCCTATGGGTG 59.591 45.833 2.25 0.00 44.74 4.61
3557 3967 1.896465 ACAGTTAGGAGAGAGCACCAC 59.104 52.381 0.00 0.00 0.00 4.16
3583 3993 9.223099 GTTATAGTTTGTACCCAAGCTTAGAAA 57.777 33.333 0.00 0.00 38.80 2.52
3595 4005 7.916914 ATGTTGTCCAGTTATAGTTTGTACC 57.083 36.000 0.00 0.00 0.00 3.34
3603 4013 4.745125 CGGCTGTATGTTGTCCAGTTATAG 59.255 45.833 0.00 0.00 0.00 1.31
3611 4021 0.748005 ATGCCGGCTGTATGTTGTCC 60.748 55.000 29.70 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.