Multiple sequence alignment - TraesCS4B01G230100

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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 TraesCS4B01G230100 chr4B 100.000 4967 0 0 1 4967 481232878 481237844 0.000000e+00 9173
1 TraesCS4B01G230100 chr4D 93.769 2616 102 28 353 2935 391451690 391454277 0.000000e+00 3871
2 TraesCS4B01G230100 chr4D 93.568 1306 52 16 3098 4384 391454278 391455570 0.000000e+00 1917
3 TraesCS4B01G230100 chr4D 94.472 597 27 2 4376 4967 391462774 391463369 0.000000e+00 915
4 TraesCS4B01G230100 chr4D 81.928 332 26 14 26 357 391430090 391430387 2.970000e-62 250
5 TraesCS4B01G230100 chr4A 89.489 2445 123 48 33 2421 73135963 73138329 0.000000e+00 2968
6 TraesCS4B01G230100 chr4A 90.058 1559 86 35 3459 4967 73139550 73141089 0.000000e+00 1956
7 TraesCS4B01G230100 chr4A 93.103 377 20 3 3098 3471 73139161 73139534 9.400000e-152 547
8 TraesCS4B01G230100 chr4A 89.535 344 25 7 2595 2935 73138825 73139160 4.600000e-115 425
9 TraesCS4B01G230100 chr4A 92.169 166 11 2 2935 3099 642589576 642589412 2.990000e-57 233
10 TraesCS4B01G230100 chr4A 92.169 166 11 2 2935 3099 665604122 665604286 2.990000e-57 233
11 TraesCS4B01G230100 chr4A 91.124 169 13 2 2932 3099 642332526 642332359 1.390000e-55 228
12 TraesCS4B01G230100 chr4A 87.097 124 8 2 2410 2533 73138524 73138639 3.120000e-27 134
13 TraesCS4B01G230100 chr6B 92.398 171 11 2 2931 3100 147089436 147089605 4.970000e-60 243
14 TraesCS4B01G230100 chr3B 92.169 166 11 2 2935 3099 755167560 755167396 2.990000e-57 233
15 TraesCS4B01G230100 chr2B 91.566 166 12 2 2935 3099 472909784 472909620 1.390000e-55 228
16 TraesCS4B01G230100 chr5B 90.533 169 15 1 2932 3099 424161205 424161373 6.470000e-54 222
17 TraesCS4B01G230100 chrUn 90.476 168 14 2 2935 3101 321005421 321005255 2.330000e-53 220
18 TraesCS4B01G230100 chr1B 88.889 180 16 4 2928 3104 21471840 21471662 8.370000e-53 219


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 TraesCS4B01G230100 chr4B 481232878 481237844 4966 False 9173 9173 100.0000 1 4967 1 chr4B.!!$F1 4966
1 TraesCS4B01G230100 chr4D 391451690 391455570 3880 False 2894 3871 93.6685 353 4384 2 chr4D.!!$F3 4031
2 TraesCS4B01G230100 chr4D 391462774 391463369 595 False 915 915 94.4720 4376 4967 1 chr4D.!!$F2 591
3 TraesCS4B01G230100 chr4A 73135963 73141089 5126 False 1206 2968 89.8564 33 4967 5 chr4A.!!$F2 4934

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
67 68 0.179137 TGTAGTTGAGCTCGCGGATG 60.179 55.0 6.13 0.0 0.00 3.51 F
579 582 0.464373 CAGTCCACCACAACTGCTGT 60.464 55.0 0.00 0.0 36.76 4.40 F
1390 1426 0.254178 ACCACCATGCTTAGGCTCTG 59.746 55.0 0.00 0.0 39.59 3.35 F
2812 3208 0.392998 AGCATCGGGTTACTTGCCAG 60.393 55.0 0.00 0.0 35.71 4.85 F
2941 3339 0.178987 ATGCGTCGGATCTACTCCCT 60.179 55.0 0.00 0.0 41.49 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1388 0.976641 TTGGCGGTCTCTGATTGAGT 59.023 50.0 0.00 0.00 43.13 3.41 R
2144 2203 1.098712 GCCAAAACCTCACGGACACA 61.099 55.0 0.00 0.00 0.00 3.72 R
2814 3210 0.250901 AGTGGTAAACTGGCTGGCTG 60.251 55.0 6.56 6.56 37.88 4.85 R
3671 4110 0.321122 CTTCAGCTTGTCGCCCTTCT 60.321 55.0 0.00 0.00 40.39 2.85 R
4519 4983 0.531532 CGTTCCTGGCCTATCTGCAG 60.532 60.0 7.63 7.63 0.00 4.41 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
26 27 9.377383 CGCAATTATTTTACCGAAAACCTATAG 57.623 33.333 0.00 0.00 37.37 1.31
34 35 8.947055 TTTACCGAAAACCTATAGAACATACC 57.053 34.615 0.00 0.00 0.00 2.73
63 64 5.212934 TCTATTATTGTAGTTGAGCTCGCG 58.787 41.667 9.64 0.00 0.00 5.87
67 68 0.179137 TGTAGTTGAGCTCGCGGATG 60.179 55.000 6.13 0.00 0.00 3.51
74 75 2.125512 GCTCGCGGATGACAACCT 60.126 61.111 6.13 0.00 0.00 3.50
76 77 1.874019 CTCGCGGATGACAACCTCG 60.874 63.158 6.13 7.74 37.04 4.63
81 82 1.471676 GCGGATGACAACCTCGAGATT 60.472 52.381 15.71 0.00 0.00 2.40
95 96 3.074412 TCGAGATTTTGCTTCTTGGACC 58.926 45.455 0.00 0.00 0.00 4.46
100 101 4.834496 AGATTTTGCTTCTTGGACCATTGA 59.166 37.500 0.00 0.00 0.00 2.57
108 109 3.134127 GGACCATTGACAGCGGCC 61.134 66.667 0.00 0.00 0.00 6.13
112 113 3.818787 CATTGACAGCGGCCCTGC 61.819 66.667 18.07 7.77 45.78 4.85
137 138 2.096496 GCTTGTCATAGCAATGAAGCGT 59.904 45.455 0.00 0.00 43.69 5.07
162 163 3.821841 AGCGCTTACAGTTTTTATGCAC 58.178 40.909 2.64 0.00 0.00 4.57
163 164 3.252215 AGCGCTTACAGTTTTTATGCACA 59.748 39.130 2.64 0.00 0.00 4.57
164 165 4.082787 AGCGCTTACAGTTTTTATGCACAT 60.083 37.500 2.64 0.00 0.00 3.21
165 166 4.262976 GCGCTTACAGTTTTTATGCACATC 59.737 41.667 0.00 0.00 0.00 3.06
173 174 8.792830 ACAGTTTTTATGCACATCTATACACT 57.207 30.769 0.00 0.00 0.00 3.55
184 185 9.838975 TGCACATCTATACACTTTTTGTTATTG 57.161 29.630 0.00 0.00 39.91 1.90
250 251 5.159209 GTGCAACAATGAGATCTCAAAAGG 58.841 41.667 28.40 18.92 39.13 3.11
255 256 7.699812 GCAACAATGAGATCTCAAAAGGTATTC 59.300 37.037 28.40 12.21 43.58 1.75
266 267 7.806690 TCTCAAAAGGTATTCAAAACATCGAG 58.193 34.615 0.00 0.00 0.00 4.04
269 270 8.792633 TCAAAAGGTATTCAAAACATCGAGAAT 58.207 29.630 0.00 0.00 35.17 2.40
270 271 8.853345 CAAAAGGTATTCAAAACATCGAGAATG 58.147 33.333 5.78 0.00 41.48 2.67
332 333 8.463607 ACACTTGTAAAAATAATATTGGTCCGG 58.536 33.333 0.00 0.00 0.00 5.14
345 348 1.348366 TGGTCCGGCAAAGCTTAACTA 59.652 47.619 0.00 0.00 0.00 2.24
366 369 6.435164 ACTAGCCAATAAATTCCCAGAACAT 58.565 36.000 0.00 0.00 0.00 2.71
372 375 7.418942 GCCAATAAATTCCCAGAACATTACCAT 60.419 37.037 0.00 0.00 0.00 3.55
398 401 3.576982 GGAACCTTTTTCCTAACCCCAAG 59.423 47.826 0.00 0.00 35.73 3.61
458 461 2.623889 ACGAAGCTGACAGTCACTAGTT 59.376 45.455 0.00 0.00 0.00 2.24
479 482 0.527817 GTAGGCGTTGGATGGACTCG 60.528 60.000 0.00 0.00 0.00 4.18
492 495 1.298859 GGACTCGCTTTCGTGGCAAT 61.299 55.000 0.00 0.00 38.85 3.56
501 504 1.295357 TTCGTGGCAATAGCACACCG 61.295 55.000 0.00 0.00 44.61 4.94
505 508 1.674322 GGCAATAGCACACCGGTGT 60.674 57.895 34.41 34.41 46.95 4.16
533 536 4.624125 GCTGGACATAGGAGTTTTGCTAGT 60.624 45.833 0.00 0.00 30.25 2.57
553 556 4.341783 GCACCAGAGCCAGCCAGT 62.342 66.667 0.00 0.00 0.00 4.00
576 579 2.555547 GCCAGTCCACCACAACTGC 61.556 63.158 0.00 0.00 41.24 4.40
577 580 1.149174 CCAGTCCACCACAACTGCT 59.851 57.895 0.00 0.00 41.24 4.24
579 582 0.464373 CAGTCCACCACAACTGCTGT 60.464 55.000 0.00 0.00 36.76 4.40
668 688 4.026744 CCTCTTTGACCACCTAGAGATCA 58.973 47.826 0.00 0.00 37.00 2.92
672 692 3.474798 TGACCACCTAGAGATCAAGGT 57.525 47.619 8.24 8.24 34.56 3.50
691 711 3.323691 AGGTTCAAAAGGCGGCTTTTATT 59.676 39.130 38.89 22.36 35.09 1.40
730 750 0.550393 GTCCTCCCCCTTTCTTCCCT 60.550 60.000 0.00 0.00 0.00 4.20
731 751 0.550147 TCCTCCCCCTTTCTTCCCTG 60.550 60.000 0.00 0.00 0.00 4.45
732 752 1.304617 CTCCCCCTTTCTTCCCTGC 59.695 63.158 0.00 0.00 0.00 4.85
749 769 2.125952 CCTCGCGTCACTGCATCA 60.126 61.111 5.77 0.00 34.15 3.07
799 819 3.369381 GACATCCGGTCACATCCAG 57.631 57.895 0.00 0.00 46.19 3.86
803 823 4.489771 CCGGTCACATCCAGCCCC 62.490 72.222 0.00 0.00 0.00 5.80
865 889 1.227734 TCCCGCGGCCTATTTAAGC 60.228 57.895 22.85 0.00 0.00 3.09
901 925 1.759236 GTCCAACGTTTCCCTCCCT 59.241 57.895 0.00 0.00 0.00 4.20
1059 1092 0.745468 ACCCTCTCGATCCGCTTTAC 59.255 55.000 0.00 0.00 0.00 2.01
1362 1398 4.039124 TGTCTGTGTGCTAACTCAATCAGA 59.961 41.667 0.00 0.00 29.86 3.27
1390 1426 0.254178 ACCACCATGCTTAGGCTCTG 59.746 55.000 0.00 0.00 39.59 3.35
1408 1448 5.104859 GGCTCTGGTAGATCATCATCATCAT 60.105 44.000 0.00 0.00 0.00 2.45
1420 1460 1.027357 ATCATCATCCCAACTTGCGC 58.973 50.000 0.00 0.00 0.00 6.09
1453 1497 6.547880 TGGAGTGCTGGTTTTTCTTATTGTTA 59.452 34.615 0.00 0.00 0.00 2.41
1454 1498 7.068839 TGGAGTGCTGGTTTTTCTTATTGTTAA 59.931 33.333 0.00 0.00 0.00 2.01
1455 1499 8.088365 GGAGTGCTGGTTTTTCTTATTGTTAAT 58.912 33.333 0.00 0.00 0.00 1.40
1469 1513 1.813753 TTAATCGGCCACTGAGCGC 60.814 57.895 2.24 0.00 0.00 5.92
2107 2166 3.817084 ACGAATACGAGGATACATCGGAA 59.183 43.478 10.24 0.00 44.36 4.30
2115 2174 2.158900 AGGATACATCGGAAGGCAACTG 60.159 50.000 0.00 0.00 46.25 3.16
2134 2193 4.319177 ACTGACATAAGGTTCAACTCTGC 58.681 43.478 0.00 0.00 0.00 4.26
2144 2203 3.946201 AACTCTGCGCAGGGTGCT 61.946 61.111 41.57 25.85 42.33 4.40
2357 2416 1.404391 CACGAGTAAGTACATCGCCCT 59.596 52.381 8.96 0.00 40.02 5.19
2397 2464 2.023741 GCATGCCGCAAGTCGATG 59.976 61.111 6.36 0.00 41.67 3.84
2453 2726 0.478507 GCTGCCTATGGGTAATGGGT 59.521 55.000 0.00 0.00 39.14 4.51
2533 2831 1.787012 CCAACACTTGCCAGCATTTC 58.213 50.000 0.00 0.00 0.00 2.17
2539 2837 2.226437 CACTTGCCAGCATTTCGTAAGT 59.774 45.455 0.00 0.00 39.48 2.24
2540 2838 2.884639 ACTTGCCAGCATTTCGTAAGTT 59.115 40.909 0.00 0.00 39.48 2.66
2546 2848 4.201822 GCCAGCATTTCGTAAGTTTAGAGG 60.202 45.833 0.00 0.00 39.48 3.69
2613 3009 5.003872 CGTACTATAGAATGCATCACATCGC 59.996 44.000 6.78 0.00 38.34 4.58
2656 3052 0.788391 CCGGCCGAATATTAAGCGAC 59.212 55.000 30.73 0.00 0.00 5.19
2776 3172 0.988832 ACCGGTAAATCAAGGGCAGA 59.011 50.000 4.49 0.00 0.00 4.26
2777 3173 1.564348 ACCGGTAAATCAAGGGCAGAT 59.436 47.619 4.49 0.00 0.00 2.90
2778 3174 2.775384 ACCGGTAAATCAAGGGCAGATA 59.225 45.455 4.49 0.00 0.00 1.98
2779 3175 3.139077 CCGGTAAATCAAGGGCAGATAC 58.861 50.000 0.00 0.00 0.00 2.24
2812 3208 0.392998 AGCATCGGGTTACTTGCCAG 60.393 55.000 0.00 0.00 35.71 4.85
2813 3209 1.993369 GCATCGGGTTACTTGCCAGC 61.993 60.000 0.00 0.00 0.00 4.85
2814 3210 1.077716 ATCGGGTTACTTGCCAGCC 60.078 57.895 0.00 0.00 0.00 4.85
2815 3211 1.847798 ATCGGGTTACTTGCCAGCCA 61.848 55.000 0.00 0.00 0.00 4.75
2887 3285 1.323534 GTAGGCACGCACGACAAATAG 59.676 52.381 0.00 0.00 0.00 1.73
2890 3288 1.060122 GGCACGCACGACAAATAGTAC 59.940 52.381 0.00 0.00 0.00 2.73
2893 3291 3.795101 GCACGCACGACAAATAGTACTAT 59.205 43.478 9.71 9.71 0.00 2.12
2894 3292 4.266976 GCACGCACGACAAATAGTACTATT 59.733 41.667 20.27 20.27 37.36 1.73
2895 3293 5.456497 GCACGCACGACAAATAGTACTATTA 59.544 40.000 24.86 0.00 34.90 0.98
2896 3294 6.020440 GCACGCACGACAAATAGTACTATTAA 60.020 38.462 24.86 0.00 34.90 1.40
2897 3295 7.544596 CACGCACGACAAATAGTACTATTAAG 58.455 38.462 24.86 21.53 34.90 1.85
2898 3296 6.197842 ACGCACGACAAATAGTACTATTAAGC 59.802 38.462 24.86 19.49 34.90 3.09
2903 3301 7.642978 ACGACAAATAGTACTATTAAGCACTCG 59.357 37.037 24.86 22.94 34.90 4.18
2930 3328 2.456119 GCCAGAGTGAATGCGTCGG 61.456 63.158 0.00 0.00 0.00 4.79
2935 3333 2.033424 CAGAGTGAATGCGTCGGATCTA 59.967 50.000 0.00 0.00 0.00 1.98
2936 3334 2.033550 AGAGTGAATGCGTCGGATCTAC 59.966 50.000 0.00 2.62 0.00 2.59
2937 3335 2.025155 AGTGAATGCGTCGGATCTACT 58.975 47.619 0.00 4.96 0.00 2.57
2938 3336 2.033550 AGTGAATGCGTCGGATCTACTC 59.966 50.000 0.00 0.00 0.00 2.59
2939 3337 1.337071 TGAATGCGTCGGATCTACTCC 59.663 52.381 0.00 0.00 41.07 3.85
2940 3338 0.674534 AATGCGTCGGATCTACTCCC 59.325 55.000 0.00 0.00 41.49 4.30
2941 3339 0.178987 ATGCGTCGGATCTACTCCCT 60.179 55.000 0.00 0.00 41.49 4.20
2942 3340 0.818445 TGCGTCGGATCTACTCCCTC 60.818 60.000 0.00 0.00 41.49 4.30
2943 3341 1.517210 GCGTCGGATCTACTCCCTCC 61.517 65.000 0.00 0.00 41.49 4.30
2945 3343 4.903026 CGGATCTACTCCCTCCGT 57.097 61.111 2.18 0.00 45.30 4.69
2946 3344 3.112965 CGGATCTACTCCCTCCGTT 57.887 57.895 2.18 0.00 45.30 4.44
2947 3345 0.953003 CGGATCTACTCCCTCCGTTC 59.047 60.000 2.18 0.00 45.30 3.95
2948 3346 1.477195 CGGATCTACTCCCTCCGTTCT 60.477 57.143 2.18 0.00 45.30 3.01
2949 3347 2.224475 CGGATCTACTCCCTCCGTTCTA 60.224 54.545 2.18 0.00 45.30 2.10
2950 3348 3.746751 CGGATCTACTCCCTCCGTTCTAA 60.747 52.174 2.18 0.00 45.30 2.10
2951 3349 4.213513 GGATCTACTCCCTCCGTTCTAAA 58.786 47.826 0.00 0.00 38.19 1.85
2952 3350 4.833938 GGATCTACTCCCTCCGTTCTAAAT 59.166 45.833 0.00 0.00 38.19 1.40
2953 3351 6.008960 GGATCTACTCCCTCCGTTCTAAATA 58.991 44.000 0.00 0.00 38.19 1.40
2954 3352 6.664384 GGATCTACTCCCTCCGTTCTAAATAT 59.336 42.308 0.00 0.00 38.19 1.28
2955 3353 7.833183 GGATCTACTCCCTCCGTTCTAAATATA 59.167 40.741 0.00 0.00 38.19 0.86
2956 3354 9.240734 GATCTACTCCCTCCGTTCTAAATATAA 57.759 37.037 0.00 0.00 0.00 0.98
2957 3355 8.632906 TCTACTCCCTCCGTTCTAAATATAAG 57.367 38.462 0.00 0.00 0.00 1.73
2958 3356 8.223330 TCTACTCCCTCCGTTCTAAATATAAGT 58.777 37.037 0.00 0.00 0.00 2.24
2959 3357 7.287512 ACTCCCTCCGTTCTAAATATAAGTC 57.712 40.000 0.00 0.00 0.00 3.01
2960 3358 7.068061 ACTCCCTCCGTTCTAAATATAAGTCT 58.932 38.462 0.00 0.00 0.00 3.24
2961 3359 7.564292 ACTCCCTCCGTTCTAAATATAAGTCTT 59.436 37.037 0.00 0.00 0.00 3.01
2962 3360 8.315220 TCCCTCCGTTCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2963 3361 8.765517 TCCCTCCGTTCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
2964 3362 9.392259 CCCTCCGTTCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2990 3388 8.057536 AGTGGTTTCAAATAAACTACAACACA 57.942 30.769 16.15 0.00 41.96 3.72
2991 3389 8.691797 AGTGGTTTCAAATAAACTACAACACAT 58.308 29.630 16.15 0.00 41.96 3.21
2992 3390 8.751335 GTGGTTTCAAATAAACTACAACACATG 58.249 33.333 10.92 0.00 40.11 3.21
2993 3391 7.923344 TGGTTTCAAATAAACTACAACACATGG 59.077 33.333 0.00 0.00 0.00 3.66
2994 3392 8.138712 GGTTTCAAATAAACTACAACACATGGA 58.861 33.333 0.00 0.00 0.00 3.41
2995 3393 9.691362 GTTTCAAATAAACTACAACACATGGAT 57.309 29.630 0.00 0.00 0.00 3.41
2996 3394 9.689976 TTTCAAATAAACTACAACACATGGATG 57.310 29.630 0.00 0.00 0.00 3.51
2997 3395 8.402798 TCAAATAAACTACAACACATGGATGT 57.597 30.769 0.00 1.49 42.84 3.06
2998 3396 9.508642 TCAAATAAACTACAACACATGGATGTA 57.491 29.630 0.00 2.67 39.39 2.29
3005 3403 9.982651 AACTACAACACATGGATGTATATAGAC 57.017 33.333 0.00 0.00 39.39 2.59
3006 3404 9.143155 ACTACAACACATGGATGTATATAGACA 57.857 33.333 2.07 2.07 39.39 3.41
3037 3435 9.555727 TTAGAGTGTAAACTTACTCATTTTGCT 57.444 29.630 7.09 0.00 44.41 3.91
3038 3436 8.451908 AGAGTGTAAACTTACTCATTTTGCTT 57.548 30.769 7.09 0.00 44.41 3.91
3039 3437 8.903820 AGAGTGTAAACTTACTCATTTTGCTTT 58.096 29.630 7.09 0.00 44.41 3.51
3040 3438 8.856490 AGTGTAAACTTACTCATTTTGCTTTG 57.144 30.769 1.58 0.00 34.77 2.77
3041 3439 8.466798 AGTGTAAACTTACTCATTTTGCTTTGT 58.533 29.630 1.58 0.00 34.77 2.83
3042 3440 9.724839 GTGTAAACTTACTCATTTTGCTTTGTA 57.275 29.630 1.58 0.00 34.77 2.41
3048 3446 9.284968 ACTTACTCATTTTGCTTTGTATGTAGT 57.715 29.630 0.00 0.00 0.00 2.73
3049 3447 9.760660 CTTACTCATTTTGCTTTGTATGTAGTC 57.239 33.333 0.00 0.00 0.00 2.59
3050 3448 7.145932 ACTCATTTTGCTTTGTATGTAGTCC 57.854 36.000 0.00 0.00 0.00 3.85
3051 3449 6.151144 ACTCATTTTGCTTTGTATGTAGTCCC 59.849 38.462 0.00 0.00 0.00 4.46
3052 3450 6.245408 TCATTTTGCTTTGTATGTAGTCCCT 58.755 36.000 0.00 0.00 0.00 4.20
3053 3451 6.719370 TCATTTTGCTTTGTATGTAGTCCCTT 59.281 34.615 0.00 0.00 0.00 3.95
3054 3452 5.957842 TTTGCTTTGTATGTAGTCCCTTG 57.042 39.130 0.00 0.00 0.00 3.61
3055 3453 4.634012 TGCTTTGTATGTAGTCCCTTGT 57.366 40.909 0.00 0.00 0.00 3.16
3056 3454 4.980573 TGCTTTGTATGTAGTCCCTTGTT 58.019 39.130 0.00 0.00 0.00 2.83
3057 3455 6.116711 TGCTTTGTATGTAGTCCCTTGTTA 57.883 37.500 0.00 0.00 0.00 2.41
3058 3456 6.535540 TGCTTTGTATGTAGTCCCTTGTTAA 58.464 36.000 0.00 0.00 0.00 2.01
3059 3457 6.999272 TGCTTTGTATGTAGTCCCTTGTTAAA 59.001 34.615 0.00 0.00 0.00 1.52
3060 3458 7.502895 TGCTTTGTATGTAGTCCCTTGTTAAAA 59.497 33.333 0.00 0.00 0.00 1.52
3061 3459 8.520351 GCTTTGTATGTAGTCCCTTGTTAAAAT 58.480 33.333 0.00 0.00 0.00 1.82
3063 3461 9.802039 TTTGTATGTAGTCCCTTGTTAAAATCT 57.198 29.630 0.00 0.00 0.00 2.40
3064 3462 9.444600 TTGTATGTAGTCCCTTGTTAAAATCTC 57.555 33.333 0.00 0.00 0.00 2.75
3065 3463 8.822805 TGTATGTAGTCCCTTGTTAAAATCTCT 58.177 33.333 0.00 0.00 0.00 3.10
3095 3493 9.703677 AAAAATTTATATTTAGGAACGGAGGGA 57.296 29.630 0.00 0.00 32.85 4.20
3096 3494 8.919777 AAATTTATATTTAGGAACGGAGGGAG 57.080 34.615 0.00 0.00 32.25 4.30
3121 3519 0.752658 TCTATGCCAGACCGGTGATG 59.247 55.000 14.63 11.08 36.97 3.07
3122 3520 0.465705 CTATGCCAGACCGGTGATGT 59.534 55.000 14.63 0.00 36.97 3.06
3131 3529 2.024655 AGACCGGTGATGTAGGGAAGTA 60.025 50.000 14.63 0.00 0.00 2.24
3133 3531 2.292061 ACCGGTGATGTAGGGAAGTAGT 60.292 50.000 6.12 0.00 0.00 2.73
3136 3534 3.568853 CGGTGATGTAGGGAAGTAGTAGG 59.431 52.174 0.00 0.00 0.00 3.18
3151 3549 9.310449 GGAAGTAGTAGGAGTATGAAATATCCA 57.690 37.037 0.00 0.00 32.39 3.41
3170 3568 1.662122 CACTTAATGGCGACGGTAACC 59.338 52.381 0.00 0.00 0.00 2.85
3204 3602 7.177216 TCCACAATCAGAATGCTTAATTTCACT 59.823 33.333 0.00 0.00 34.76 3.41
3285 3683 1.988406 GGTAGACCTTGACCGGCCT 60.988 63.158 0.00 0.00 0.00 5.19
3346 3744 2.124570 CGGGTGATCCTGCTTGGG 60.125 66.667 0.00 0.00 36.20 4.12
3401 3799 3.691342 CCCGGTTGCTGGTCGAGA 61.691 66.667 0.00 0.00 0.00 4.04
3441 3839 1.661480 TGGACAACGACCAGGTACG 59.339 57.895 0.00 0.49 33.22 3.67
3455 3853 2.416547 CAGGTACGAATTCAACCAGCAG 59.583 50.000 22.53 10.23 35.64 4.24
3460 3858 3.149196 ACGAATTCAACCAGCAGACAAT 58.851 40.909 6.22 0.00 0.00 2.71
3472 3870 6.109359 ACCAGCAGACAATGATCTAACTTAC 58.891 40.000 0.00 0.00 0.00 2.34
3498 3932 9.840427 CTATACAAAACACGAGGAAATTCAAAT 57.160 29.630 0.00 0.00 0.00 2.32
3522 3961 4.692228 TCAAACTTTGAAAACTCATGGGC 58.308 39.130 1.47 0.00 36.59 5.36
3536 3975 2.097304 TCATGGGCGATTTGATTGTTCG 59.903 45.455 0.00 0.00 36.02 3.95
3660 4099 2.417936 GCCTACTACGGCTGCTCC 59.582 66.667 0.00 0.00 46.63 4.70
4059 4509 4.515944 ACGTAGTAAAGATCCATCCTCTCG 59.484 45.833 0.00 0.00 41.94 4.04
4071 4521 3.243367 CCATCCTCTCGATCTGTTCTGTC 60.243 52.174 0.00 0.00 0.00 3.51
4073 4523 4.489306 TCCTCTCGATCTGTTCTGTCTA 57.511 45.455 0.00 0.00 0.00 2.59
4205 4660 3.136763 CACTCTTGTTGATGCAGTGAGT 58.863 45.455 0.00 0.00 35.79 3.41
4218 4674 1.052124 AGTGAGTTTGTCCCGACCCA 61.052 55.000 0.00 0.00 0.00 4.51
4240 4696 0.763035 ACTTGTTTGGCCGGACTAGT 59.237 50.000 9.82 15.95 0.00 2.57
4308 4765 3.006940 TCGCCATGAACAACCTTCATAC 58.993 45.455 0.00 0.00 37.06 2.39
4315 4772 6.151648 CCATGAACAACCTTCATACATCAGTT 59.848 38.462 0.00 0.00 37.06 3.16
4316 4773 6.558771 TGAACAACCTTCATACATCAGTTG 57.441 37.500 0.00 0.00 40.24 3.16
4317 4774 5.473162 TGAACAACCTTCATACATCAGTTGG 59.527 40.000 0.00 0.00 39.06 3.77
4318 4775 5.241403 ACAACCTTCATACATCAGTTGGA 57.759 39.130 0.00 0.00 39.06 3.53
4319 4776 5.248640 ACAACCTTCATACATCAGTTGGAG 58.751 41.667 0.00 0.00 39.06 3.86
4401 4862 1.280998 CCACCCCGTTCCTGACTTTAT 59.719 52.381 0.00 0.00 0.00 1.40
4408 4869 3.369052 CCGTTCCTGACTTTATGCACCTA 60.369 47.826 0.00 0.00 0.00 3.08
4519 4983 0.524414 GACCGGTGGCCATAAACAAC 59.476 55.000 14.63 0.00 0.00 3.32
4581 5045 7.938140 TGTGGGAGTAGATTAAAATCCAAAG 57.062 36.000 0.00 0.00 36.04 2.77
4627 5096 7.565029 TCAACCTCTAATCACAATATCTCAGGA 59.435 37.037 0.00 0.00 0.00 3.86
4648 5117 1.361204 TGGTTTCATCCCTCTCAGCA 58.639 50.000 0.00 0.00 0.00 4.41
4658 5127 1.433471 CTCTCAGCATGCGTCCGTA 59.567 57.895 13.01 0.00 34.76 4.02
4676 5152 4.158949 TCCGTAGTGTACATGCACAGTATT 59.841 41.667 15.17 0.00 41.52 1.89
4702 5178 0.249953 TAGAAAAAGTGCCGCGGTGA 60.250 50.000 28.70 11.39 0.00 4.02
4772 5253 1.941377 TTCCAGCAGCCCAAATTCAT 58.059 45.000 0.00 0.00 0.00 2.57
4903 5392 1.175654 CCAATTTGCCCAATTTGCCC 58.824 50.000 9.12 0.00 32.24 5.36
4960 5449 1.949133 GCCGATGATCTTGCGCGTA 60.949 57.895 8.43 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.377383 CTATAGGTTTTCGGTAAAATAATTGCG 57.623 33.333 0.00 0.00 36.96 4.85
8 9 9.382275 GGTATGTTCTATAGGTTTTCGGTAAAA 57.618 33.333 0.00 0.00 32.15 1.52
9 10 8.538701 TGGTATGTTCTATAGGTTTTCGGTAAA 58.461 33.333 0.00 0.00 0.00 2.01
10 11 8.076910 TGGTATGTTCTATAGGTTTTCGGTAA 57.923 34.615 0.00 0.00 0.00 2.85
11 12 7.658525 TGGTATGTTCTATAGGTTTTCGGTA 57.341 36.000 0.00 0.00 0.00 4.02
12 13 6.549433 TGGTATGTTCTATAGGTTTTCGGT 57.451 37.500 0.00 0.00 0.00 4.69
13 14 8.446599 AAATGGTATGTTCTATAGGTTTTCGG 57.553 34.615 0.00 0.00 0.00 4.30
51 52 1.153745 GTCATCCGCGAGCTCAACT 60.154 57.895 15.40 0.00 0.00 3.16
63 64 3.181506 GCAAAATCTCGAGGTTGTCATCC 60.182 47.826 12.63 0.00 0.00 3.51
67 68 3.748568 AGAAGCAAAATCTCGAGGTTGTC 59.251 43.478 12.63 8.76 0.00 3.18
74 75 3.074412 GGTCCAAGAAGCAAAATCTCGA 58.926 45.455 0.00 0.00 0.00 4.04
76 77 5.047802 TCAATGGTCCAAGAAGCAAAATCTC 60.048 40.000 0.00 0.00 0.00 2.75
81 82 3.295093 TGTCAATGGTCCAAGAAGCAAA 58.705 40.909 0.00 0.00 0.00 3.68
95 96 3.818787 GCAGGGCCGCTGTCAATG 61.819 66.667 18.80 0.00 0.00 2.82
108 109 1.099879 GCTATGACAAGCAGGGCAGG 61.100 60.000 5.18 0.00 42.30 4.85
116 117 2.096496 ACGCTTCATTGCTATGACAAGC 59.904 45.455 18.95 18.95 40.42 4.01
137 138 5.410132 TGCATAAAAACTGTAAGCGCTTCTA 59.590 36.000 28.82 15.76 37.60 2.10
148 149 8.792830 AGTGTATAGATGTGCATAAAAACTGT 57.207 30.769 0.00 0.00 0.00 3.55
183 184 9.699410 CCTTGATATAATATGCCCCTTTTATCA 57.301 33.333 0.00 0.00 0.00 2.15
184 185 9.920946 TCCTTGATATAATATGCCCCTTTTATC 57.079 33.333 0.00 0.00 0.00 1.75
230 231 8.733458 TGAATACCTTTTGAGATCTCATTGTTG 58.267 33.333 25.64 15.17 39.64 3.33
250 251 9.425893 CATGTACATTCTCGATGTTTTGAATAC 57.574 33.333 5.37 0.00 46.80 1.89
255 256 6.901887 GCTACATGTACATTCTCGATGTTTTG 59.098 38.462 5.37 0.00 46.80 2.44
322 323 2.750712 GTTAAGCTTTGCCGGACCAATA 59.249 45.455 5.05 0.00 0.00 1.90
325 326 0.109723 AGTTAAGCTTTGCCGGACCA 59.890 50.000 5.05 0.00 0.00 4.02
345 348 6.098266 GGTAATGTTCTGGGAATTTATTGGCT 59.902 38.462 0.00 0.00 0.00 4.75
347 350 7.416964 TGGTAATGTTCTGGGAATTTATTGG 57.583 36.000 0.00 0.00 0.00 3.16
372 375 4.202599 GGGGTTAGGAAAAAGGTTCCAGTA 60.203 45.833 7.80 0.00 41.00 2.74
398 401 0.570272 CGTTTTCGGTGTGCTTTTGC 59.430 50.000 0.00 0.00 42.17 3.68
458 461 2.029623 GAGTCCATCCAACGCCTACTA 58.970 52.381 0.00 0.00 0.00 1.82
479 482 0.521291 TGTGCTATTGCCACGAAAGC 59.479 50.000 0.00 0.00 38.71 3.51
492 495 0.245539 GCTAAGACACCGGTGTGCTA 59.754 55.000 43.34 29.37 46.86 3.49
501 504 3.031736 TCCTATGTCCAGCTAAGACACC 58.968 50.000 18.23 0.00 46.43 4.16
505 508 5.734720 CAAAACTCCTATGTCCAGCTAAGA 58.265 41.667 0.00 0.00 0.00 2.10
533 536 2.261430 CTGGCTGGCTCTGGTGCATA 62.261 60.000 2.00 0.00 34.04 3.14
553 556 1.687297 TTGTGGTGGACTGGCGTACA 61.687 55.000 0.00 0.00 0.00 2.90
577 580 1.581934 CGGTGAGAAGCTGTTCAACA 58.418 50.000 14.13 0.00 34.82 3.33
579 582 0.884704 GCCGGTGAGAAGCTGTTCAA 60.885 55.000 1.90 0.00 34.82 2.69
583 597 4.021925 GGGCCGGTGAGAAGCTGT 62.022 66.667 1.90 0.00 0.00 4.40
668 688 1.119684 AAAGCCGCCTTTTGAACCTT 58.880 45.000 0.00 0.00 38.06 3.50
691 711 3.936203 GTGGCCGTGACAGTGGGA 61.936 66.667 0.00 0.00 0.00 4.37
711 731 0.550393 AGGGAAGAAAGGGGGAGGAC 60.550 60.000 0.00 0.00 0.00 3.85
731 751 3.558411 GATGCAGTGACGCGAGGC 61.558 66.667 15.93 9.23 42.12 4.70
732 752 2.125952 TGATGCAGTGACGCGAGG 60.126 61.111 15.93 0.00 33.35 4.63
803 823 1.058748 CAAATCGTGCCACTACGCG 59.941 57.895 3.53 3.53 43.40 6.01
865 889 4.815108 GGGGTAGGCAAAGCGGGG 62.815 72.222 0.00 0.00 0.00 5.73
901 925 5.626142 TGTGCTAAGTAAAGTGGAATGGAA 58.374 37.500 0.00 0.00 0.00 3.53
962 993 3.319198 CACCGTGGCCAGTAGGGT 61.319 66.667 21.67 16.61 39.65 4.34
963 994 4.778143 GCACCGTGGCCAGTAGGG 62.778 72.222 21.67 16.05 40.85 3.53
1059 1092 4.944069 AGCTAGCTAGGGCCGGGG 62.944 72.222 17.69 0.00 39.73 5.73
1346 1382 3.182967 CGGTCTCTGATTGAGTTAGCAC 58.817 50.000 0.00 0.00 43.13 4.40
1352 1388 0.976641 TTGGCGGTCTCTGATTGAGT 59.023 50.000 0.00 0.00 43.13 3.41
1362 1398 2.034066 CATGGTGGTTGGCGGTCT 59.966 61.111 0.00 0.00 0.00 3.85
1367 1403 1.948721 GCCTAAGCATGGTGGTTGGC 61.949 60.000 0.00 6.57 41.18 4.52
1390 1426 5.688814 TGGGATGATGATGATGATCTACC 57.311 43.478 0.00 0.00 0.00 3.18
1453 1497 4.087892 AGCGCTCAGTGGCCGATT 62.088 61.111 2.64 0.00 0.00 3.34
1454 1498 4.521062 GAGCGCTCAGTGGCCGAT 62.521 66.667 31.91 0.00 0.00 4.18
2107 2166 3.788227 TGAACCTTATGTCAGTTGCCT 57.212 42.857 0.00 0.00 0.00 4.75
2115 2174 2.094417 GCGCAGAGTTGAACCTTATGTC 59.906 50.000 0.30 0.00 0.00 3.06
2123 2182 1.598130 ACCCTGCGCAGAGTTGAAC 60.598 57.895 38.06 0.00 0.00 3.18
2144 2203 1.098712 GCCAAAACCTCACGGACACA 61.099 55.000 0.00 0.00 0.00 3.72
2357 2416 1.202132 GGAGCGCACGAAAATAATGCA 60.202 47.619 11.47 0.00 39.39 3.96
2397 2464 1.864029 GCAGCAAACCAAACGGACTTC 60.864 52.381 0.00 0.00 0.00 3.01
2453 2726 2.615391 TGTGAGAGGAATGGGTGTACA 58.385 47.619 0.00 0.00 0.00 2.90
2519 2792 2.504367 ACTTACGAAATGCTGGCAAGT 58.496 42.857 0.00 1.17 0.00 3.16
2527 2825 3.626217 CCCCCTCTAAACTTACGAAATGC 59.374 47.826 0.00 0.00 0.00 3.56
2533 2831 2.169769 TGATGCCCCCTCTAAACTTACG 59.830 50.000 0.00 0.00 0.00 3.18
2568 2870 3.914966 CGTTCAACTAGTGTACAGCTGAG 59.085 47.826 23.35 8.63 0.00 3.35
2574 2880 9.435688 TTCTATAGTACGTTCAACTAGTGTACA 57.564 33.333 17.77 0.00 38.24 2.90
2585 2891 6.801575 TGTGATGCATTCTATAGTACGTTCA 58.198 36.000 0.00 0.00 0.00 3.18
2613 3009 2.051345 GCGACAAAACCGGCAGTG 60.051 61.111 0.00 0.00 0.00 3.66
2645 3041 6.090358 CCGTTGATATTTCCGTCGCTTAATAT 59.910 38.462 0.00 0.00 0.00 1.28
2656 3052 1.278637 GCGGCCGTTGATATTTCCG 59.721 57.895 28.70 0.00 39.81 4.30
2776 3172 2.623535 TGCTGAACGGCAAATACGTAT 58.376 42.857 1.14 1.14 44.83 3.06
2777 3173 2.081725 TGCTGAACGGCAAATACGTA 57.918 45.000 5.81 0.00 44.83 3.57
2779 3175 1.592110 CGATGCTGAACGGCAAATACG 60.592 52.381 12.30 11.38 45.68 3.06
2812 3208 2.343426 GGTAAACTGGCTGGCTGGC 61.343 63.158 11.09 11.09 42.18 4.85
2813 3209 1.074775 TGGTAAACTGGCTGGCTGG 59.925 57.895 12.46 3.50 0.00 4.85
2814 3210 0.250901 AGTGGTAAACTGGCTGGCTG 60.251 55.000 6.56 6.56 37.88 4.85
2815 3211 2.155065 AGTGGTAAACTGGCTGGCT 58.845 52.632 2.00 0.00 37.88 4.75
2838 3236 2.033747 CCGTGACATGATCAATACGTGC 60.034 50.000 17.23 3.54 39.72 5.34
2882 3280 7.713750 TGCTCGAGTGCTTAATAGTACTATTT 58.286 34.615 28.42 12.99 45.79 1.40
2887 3285 5.341617 ACTTGCTCGAGTGCTTAATAGTAC 58.658 41.667 15.13 0.00 37.27 2.73
2890 3288 4.442733 GCTACTTGCTCGAGTGCTTAATAG 59.557 45.833 15.13 8.23 38.95 1.73
2893 3291 2.607187 GCTACTTGCTCGAGTGCTTAA 58.393 47.619 15.13 1.67 38.95 1.85
2894 3292 1.135083 GGCTACTTGCTCGAGTGCTTA 60.135 52.381 15.13 0.36 42.39 3.09
2895 3293 0.390472 GGCTACTTGCTCGAGTGCTT 60.390 55.000 15.13 0.00 42.39 3.91
2896 3294 1.216710 GGCTACTTGCTCGAGTGCT 59.783 57.895 15.13 0.00 42.39 4.40
2897 3295 1.079819 TGGCTACTTGCTCGAGTGC 60.080 57.895 15.13 1.33 42.39 4.40
2898 3296 0.528017 TCTGGCTACTTGCTCGAGTG 59.472 55.000 15.13 7.44 42.39 3.51
2903 3301 2.751166 TTCACTCTGGCTACTTGCTC 57.249 50.000 0.00 0.00 42.39 4.26
2930 3328 7.706100 ATATTTAGAACGGAGGGAGTAGATC 57.294 40.000 0.00 0.00 0.00 2.75
2935 3333 7.068061 AGACTTATATTTAGAACGGAGGGAGT 58.932 38.462 0.00 0.00 0.00 3.85
2936 3334 7.527568 AGACTTATATTTAGAACGGAGGGAG 57.472 40.000 0.00 0.00 0.00 4.30
2937 3335 7.909485 AAGACTTATATTTAGAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2938 3336 8.959705 AAAAGACTTATATTTAGAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
2964 3362 9.175312 TGTGTTGTAGTTTATTTGAAACCACTA 57.825 29.630 1.57 0.00 0.00 2.74
2965 3363 8.057536 TGTGTTGTAGTTTATTTGAAACCACT 57.942 30.769 1.57 0.00 0.00 4.00
2966 3364 8.751335 CATGTGTTGTAGTTTATTTGAAACCAC 58.249 33.333 0.00 0.00 0.00 4.16
2967 3365 7.923344 CCATGTGTTGTAGTTTATTTGAAACCA 59.077 33.333 0.00 0.00 0.00 3.67
2968 3366 8.138712 TCCATGTGTTGTAGTTTATTTGAAACC 58.861 33.333 0.00 0.00 0.00 3.27
2969 3367 9.691362 ATCCATGTGTTGTAGTTTATTTGAAAC 57.309 29.630 0.00 0.00 0.00 2.78
2970 3368 9.689976 CATCCATGTGTTGTAGTTTATTTGAAA 57.310 29.630 0.00 0.00 0.00 2.69
2971 3369 8.855110 ACATCCATGTGTTGTAGTTTATTTGAA 58.145 29.630 0.00 0.00 40.03 2.69
2972 3370 8.402798 ACATCCATGTGTTGTAGTTTATTTGA 57.597 30.769 0.00 0.00 40.03 2.69
2979 3377 9.982651 GTCTATATACATCCATGTGTTGTAGTT 57.017 33.333 2.26 0.00 41.89 2.24
2980 3378 9.143155 TGTCTATATACATCCATGTGTTGTAGT 57.857 33.333 2.26 0.00 41.89 2.73
3011 3409 9.555727 AGCAAAATGAGTAAGTTTACACTCTAA 57.444 29.630 5.99 0.00 41.46 2.10
3012 3410 9.555727 AAGCAAAATGAGTAAGTTTACACTCTA 57.444 29.630 5.99 0.00 41.46 2.43
3013 3411 8.451908 AAGCAAAATGAGTAAGTTTACACTCT 57.548 30.769 5.99 0.00 41.46 3.24
3014 3412 8.958043 CAAAGCAAAATGAGTAAGTTTACACTC 58.042 33.333 4.97 0.00 41.31 3.51
3015 3413 8.466798 ACAAAGCAAAATGAGTAAGTTTACACT 58.533 29.630 4.97 0.00 36.12 3.55
3016 3414 8.628882 ACAAAGCAAAATGAGTAAGTTTACAC 57.371 30.769 4.97 0.00 36.12 2.90
3022 3420 9.284968 ACTACATACAAAGCAAAATGAGTAAGT 57.715 29.630 0.00 0.00 0.00 2.24
3023 3421 9.760660 GACTACATACAAAGCAAAATGAGTAAG 57.239 33.333 0.00 0.00 0.00 2.34
3024 3422 8.726988 GGACTACATACAAAGCAAAATGAGTAA 58.273 33.333 0.00 0.00 0.00 2.24
3025 3423 7.335924 GGGACTACATACAAAGCAAAATGAGTA 59.664 37.037 0.00 0.00 0.00 2.59
3026 3424 6.151144 GGGACTACATACAAAGCAAAATGAGT 59.849 38.462 0.00 0.00 0.00 3.41
3027 3425 6.375455 AGGGACTACATACAAAGCAAAATGAG 59.625 38.462 0.00 0.00 36.02 2.90
3028 3426 6.245408 AGGGACTACATACAAAGCAAAATGA 58.755 36.000 0.00 0.00 36.02 2.57
3029 3427 6.515272 AGGGACTACATACAAAGCAAAATG 57.485 37.500 0.00 0.00 36.02 2.32
3030 3428 6.493458 ACAAGGGACTACATACAAAGCAAAAT 59.507 34.615 0.00 0.00 38.49 1.82
3031 3429 5.830991 ACAAGGGACTACATACAAAGCAAAA 59.169 36.000 0.00 0.00 38.49 2.44
3032 3430 5.381757 ACAAGGGACTACATACAAAGCAAA 58.618 37.500 0.00 0.00 38.49 3.68
3033 3431 4.980573 ACAAGGGACTACATACAAAGCAA 58.019 39.130 0.00 0.00 38.49 3.91
3034 3432 4.634012 ACAAGGGACTACATACAAAGCA 57.366 40.909 0.00 0.00 38.49 3.91
3035 3433 7.443259 TTTAACAAGGGACTACATACAAAGC 57.557 36.000 0.00 0.00 38.49 3.51
3037 3435 9.802039 AGATTTTAACAAGGGACTACATACAAA 57.198 29.630 0.00 0.00 38.49 2.83
3038 3436 9.444600 GAGATTTTAACAAGGGACTACATACAA 57.555 33.333 0.00 0.00 38.49 2.41
3039 3437 8.822805 AGAGATTTTAACAAGGGACTACATACA 58.177 33.333 0.00 0.00 38.49 2.29
3069 3467 9.703677 TCCCTCCGTTCCTAAATATAAATTTTT 57.296 29.630 0.00 0.00 36.67 1.94
3070 3468 9.350951 CTCCCTCCGTTCCTAAATATAAATTTT 57.649 33.333 0.00 0.00 36.67 1.82
3071 3469 8.500238 ACTCCCTCCGTTCCTAAATATAAATTT 58.500 33.333 0.00 0.00 38.80 1.82
3072 3470 8.042286 ACTCCCTCCGTTCCTAAATATAAATT 57.958 34.615 0.00 0.00 0.00 1.82
3073 3471 7.628501 ACTCCCTCCGTTCCTAAATATAAAT 57.371 36.000 0.00 0.00 0.00 1.40
3074 3472 8.731591 ATACTCCCTCCGTTCCTAAATATAAA 57.268 34.615 0.00 0.00 0.00 1.40
3075 3473 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
3076 3474 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
3077 3475 7.628501 AAATACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
3078 3476 7.346436 AGAAAATACTCCCTCCGTTCCTAAATA 59.654 37.037 0.00 0.00 0.00 1.40
3079 3477 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
3080 3478 5.486419 AGAAAATACTCCCTCCGTTCCTAAA 59.514 40.000 0.00 0.00 0.00 1.85
3081 3479 5.028131 AGAAAATACTCCCTCCGTTCCTAA 58.972 41.667 0.00 0.00 0.00 2.69
3082 3480 4.617593 AGAAAATACTCCCTCCGTTCCTA 58.382 43.478 0.00 0.00 0.00 2.94
3083 3481 3.451890 AGAAAATACTCCCTCCGTTCCT 58.548 45.455 0.00 0.00 0.00 3.36
3084 3482 3.908643 AGAAAATACTCCCTCCGTTCC 57.091 47.619 0.00 0.00 0.00 3.62
3085 3483 4.750598 GCATAGAAAATACTCCCTCCGTTC 59.249 45.833 0.00 0.00 0.00 3.95
3086 3484 4.444449 GGCATAGAAAATACTCCCTCCGTT 60.444 45.833 0.00 0.00 0.00 4.44
3087 3485 3.071167 GGCATAGAAAATACTCCCTCCGT 59.929 47.826 0.00 0.00 0.00 4.69
3088 3486 3.071023 TGGCATAGAAAATACTCCCTCCG 59.929 47.826 0.00 0.00 0.00 4.63
3089 3487 4.348168 TCTGGCATAGAAAATACTCCCTCC 59.652 45.833 0.00 0.00 30.84 4.30
3090 3488 5.301555 GTCTGGCATAGAAAATACTCCCTC 58.698 45.833 0.00 0.00 37.12 4.30
3091 3489 4.103311 GGTCTGGCATAGAAAATACTCCCT 59.897 45.833 0.00 0.00 37.12 4.20
3092 3490 4.390264 GGTCTGGCATAGAAAATACTCCC 58.610 47.826 0.00 0.00 37.12 4.30
3093 3491 4.058817 CGGTCTGGCATAGAAAATACTCC 58.941 47.826 0.00 0.00 37.12 3.85
3094 3492 4.058817 CCGGTCTGGCATAGAAAATACTC 58.941 47.826 0.00 0.00 37.12 2.59
3095 3493 3.454812 ACCGGTCTGGCATAGAAAATACT 59.545 43.478 0.00 0.00 43.94 2.12
3096 3494 3.560068 CACCGGTCTGGCATAGAAAATAC 59.440 47.826 2.59 0.00 43.94 1.89
3121 3519 8.709272 ATTTCATACTCCTACTACTTCCCTAC 57.291 38.462 0.00 0.00 0.00 3.18
3151 3549 1.736696 CGGTTACCGTCGCCATTAAGT 60.737 52.381 16.53 0.00 42.73 2.24
3170 3568 3.624326 TTCTGATTGTGGAAACTTGCG 57.376 42.857 0.00 0.00 0.00 4.85
3285 3683 4.634012 AAGAAACTATACTGGCACACCA 57.366 40.909 0.00 0.00 46.51 4.17
3346 3744 2.559231 GGAGATCCGATAGTTGAGGTCC 59.441 54.545 0.00 0.00 0.00 4.46
3397 3795 1.153939 CTTCCAGTCGTGCCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3401 3799 2.584391 GGGTCTTCCAGTCGTGCCT 61.584 63.158 0.00 0.00 35.00 4.75
3441 3839 4.771590 TCATTGTCTGCTGGTTGAATTC 57.228 40.909 0.00 0.00 0.00 2.17
3472 3870 9.840427 ATTTGAATTTCCTCGTGTTTTGTATAG 57.160 29.630 0.00 0.00 0.00 1.31
3501 3935 3.490526 CGCCCATGAGTTTTCAAAGTTTG 59.509 43.478 9.44 9.44 36.78 2.93
3502 3936 3.383185 TCGCCCATGAGTTTTCAAAGTTT 59.617 39.130 0.00 0.00 36.78 2.66
3505 3939 3.855689 ATCGCCCATGAGTTTTCAAAG 57.144 42.857 0.00 0.00 36.78 2.77
3506 3940 4.038522 TCAAATCGCCCATGAGTTTTCAAA 59.961 37.500 0.00 0.00 36.78 2.69
3509 3943 3.848272 TCAAATCGCCCATGAGTTTTC 57.152 42.857 0.00 0.00 0.00 2.29
3516 3955 2.159393 ACGAACAATCAAATCGCCCATG 60.159 45.455 0.00 0.00 40.09 3.66
3522 3961 3.181550 GCTGCAAACGAACAATCAAATCG 60.182 43.478 0.00 0.00 42.05 3.34
3660 4099 2.679716 CCCTTCTTCCCCAGCTGG 59.320 66.667 26.87 26.87 0.00 4.85
3671 4110 0.321122 CTTCAGCTTGTCGCCCTTCT 60.321 55.000 0.00 0.00 40.39 2.85
3991 4436 8.428186 TTTTATGTACTCTCTTTCGTTTGTGT 57.572 30.769 0.00 0.00 0.00 3.72
4035 4482 5.699915 CGAGAGGATGGATCTTTACTACGTA 59.300 44.000 0.00 0.00 0.00 3.57
4036 4483 4.515944 CGAGAGGATGGATCTTTACTACGT 59.484 45.833 0.00 0.00 0.00 3.57
4037 4484 4.755629 TCGAGAGGATGGATCTTTACTACG 59.244 45.833 0.00 0.00 0.00 3.51
4057 4507 5.883115 ACTCAGAATAGACAGAACAGATCGA 59.117 40.000 0.00 0.00 0.00 3.59
4058 4508 5.970612 CACTCAGAATAGACAGAACAGATCG 59.029 44.000 0.00 0.00 0.00 3.69
4059 4509 6.862209 ACACTCAGAATAGACAGAACAGATC 58.138 40.000 0.00 0.00 0.00 2.75
4071 4521 7.048629 AGACATGTATGGACACTCAGAATAG 57.951 40.000 0.00 0.00 38.76 1.73
4073 4523 5.946942 AGACATGTATGGACACTCAGAAT 57.053 39.130 0.00 0.00 38.76 2.40
4170 4625 3.128938 ACAAGAGTGCGATCTACTGTACC 59.871 47.826 4.45 0.00 0.00 3.34
4205 4660 1.751924 CAAGTTTTGGGTCGGGACAAA 59.248 47.619 0.75 0.00 0.00 2.83
4218 4674 1.480789 AGTCCGGCCAAACAAGTTTT 58.519 45.000 2.24 0.00 0.00 2.43
4240 4696 2.495409 TTTACAGCGACAACTCGTCA 57.505 45.000 0.00 0.00 45.70 4.35
4259 4716 4.506802 GCCCCATATTTCCTCGTAGGATTT 60.507 45.833 4.72 0.00 45.34 2.17
4260 4717 3.009143 GCCCCATATTTCCTCGTAGGATT 59.991 47.826 4.72 0.25 45.34 3.01
4315 4772 3.119137 CCACTCATTCGTACATCACTCCA 60.119 47.826 0.00 0.00 0.00 3.86
4316 4773 3.119101 ACCACTCATTCGTACATCACTCC 60.119 47.826 0.00 0.00 0.00 3.85
4317 4774 4.111375 ACCACTCATTCGTACATCACTC 57.889 45.455 0.00 0.00 0.00 3.51
4318 4775 4.142227 GGTACCACTCATTCGTACATCACT 60.142 45.833 7.15 0.00 35.18 3.41
4319 4776 4.110482 GGTACCACTCATTCGTACATCAC 58.890 47.826 7.15 0.00 35.18 3.06
4401 4862 5.865085 AGAAGAGTACAAAATGTAGGTGCA 58.135 37.500 0.00 0.00 32.84 4.57
4408 4869 8.517878 CATTGGATCAAGAAGAGTACAAAATGT 58.482 33.333 0.00 0.00 0.00 2.71
4519 4983 0.531532 CGTTCCTGGCCTATCTGCAG 60.532 60.000 7.63 7.63 0.00 4.41
4627 5096 2.309755 TGCTGAGAGGGATGAAACCAAT 59.690 45.455 0.00 0.00 0.00 3.16
4648 5117 1.801395 GCATGTACACTACGGACGCAT 60.801 52.381 0.00 0.00 0.00 4.73
4658 5127 4.222810 TGGAGAATACTGTGCATGTACACT 59.777 41.667 13.02 8.06 41.30 3.55
4676 5152 2.747446 GCGGCACTTTTTCTAATGGAGA 59.253 45.455 0.00 0.00 0.00 3.71
4702 5178 1.000521 CCATGGCCCATGACAGTGT 60.001 57.895 25.42 0.00 43.81 3.55
4745 5226 2.747460 GCTGCTGGAATGCGACCA 60.747 61.111 0.00 0.00 35.36 4.02
4772 5253 3.869912 GCAGACAATCTTAACAGAGCCCA 60.870 47.826 0.00 0.00 30.36 5.36
4803 5292 1.265365 GGAACAAGCAGCAGAGAACAC 59.735 52.381 0.00 0.00 0.00 3.32
4842 5331 1.742880 GCACTTCATCCGCTCTGCA 60.743 57.895 0.00 0.00 0.00 4.41
4903 5392 2.782163 CAAGATCATCGCAACTTGCAG 58.218 47.619 14.10 6.87 45.36 4.41
4948 5437 2.288969 GACAGGTACGCGCAAGATC 58.711 57.895 5.73 0.00 43.02 2.75


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

AutoCloner maintained by Alex Coulton.