Multiple sequence alignment - TraesCS4B01G073800

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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 TraesCS4B01G073800 chr4B 100.000 3813 0 0 1 3813 69162023 69165835 0.000000e+00 7042.0
1 TraesCS4B01G073800 chr4D 96.197 3208 64 19 1 3205 47437814 47440966 0.000000e+00 5195.0
2 TraesCS4B01G073800 chr4D 90.566 371 29 5 3447 3813 47441158 47441526 1.590000e-133 486.0
3 TraesCS4B01G073800 chr4D 95.726 117 4 1 3209 3325 35630667 35630782 1.810000e-43 187.0
4 TraesCS4B01G073800 chr4D 97.248 109 3 0 3212 3320 324169133 324169025 6.500000e-43 185.0
5 TraesCS4B01G073800 chr4A 96.684 1900 45 5 3 1900 550958572 550956689 0.000000e+00 3144.0
6 TraesCS4B01G073800 chr4A 91.530 366 28 3 3450 3813 550956229 550955865 5.690000e-138 501.0
7 TraesCS4B01G073800 chr4A 94.949 297 8 2 2910 3206 550956689 550956400 3.470000e-125 459.0
8 TraesCS4B01G073800 chr7D 97.321 112 3 0 3209 3320 520967986 520967875 1.400000e-44 191.0
9 TraesCS4B01G073800 chr3D 95.726 117 4 1 3207 3322 411046929 411047045 1.810000e-43 187.0
10 TraesCS4B01G073800 chr6D 96.429 112 4 0 3209 3320 13575002 13574891 6.500000e-43 185.0
11 TraesCS4B01G073800 chr6D 96.429 112 4 0 3209 3320 450814051 450813940 6.500000e-43 185.0
12 TraesCS4B01G073800 chr6D 89.412 85 9 0 2136 2220 3320694 3320610 1.450000e-19 108.0
13 TraesCS4B01G073800 chr6D 88.235 85 10 0 2136 2220 3326568 3326484 6.740000e-18 102.0
14 TraesCS4B01G073800 chr6D 87.059 85 11 0 2136 2220 3332445 3332361 3.140000e-16 97.1
15 TraesCS4B01G073800 chr6D 87.059 85 11 0 2136 2220 3338325 3338241 3.140000e-16 97.1
16 TraesCS4B01G073800 chr3B 95.690 116 4 1 3209 3324 606560116 606560230 6.500000e-43 185.0
17 TraesCS4B01G073800 chr3B 79.630 108 21 1 3617 3723 731484347 731484240 4.080000e-10 76.8
18 TraesCS4B01G073800 chrUn 95.652 115 4 1 3209 3323 273853262 273853375 2.340000e-42 183.0
19 TraesCS4B01G073800 chr6B 92.126 127 7 3 3209 3335 380300058 380299935 3.910000e-40 176.0
20 TraesCS4B01G073800 chr6B 86.517 89 12 0 2133 2221 715708359 715708447 8.720000e-17 99.0
21 TraesCS4B01G073800 chr6B 85.227 88 13 0 2133 2220 6678786 6678873 1.460000e-14 91.6
22 TraesCS4B01G073800 chr5B 92.537 67 5 0 2155 2221 123753478 123753544 3.140000e-16 97.1
23 TraesCS4B01G073800 chr5B 84.270 89 14 0 2133 2221 658549425 658549513 1.890000e-13 87.9


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 TraesCS4B01G073800 chr4B 69162023 69165835 3812 False 7042.0 7042 100.000000 1 3813 1 chr4B.!!$F1 3812
1 TraesCS4B01G073800 chr4D 47437814 47441526 3712 False 2840.5 5195 93.381500 1 3813 2 chr4D.!!$F2 3812
2 TraesCS4B01G073800 chr4A 550955865 550958572 2707 True 1368.0 3144 94.387667 3 3813 3 chr4A.!!$R1 3810

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
846 849 0.036010 ACTCCTGTGGAAATCTGGCG 60.036 55.0 0.0 0.0 0.00 5.69 F
1758 1761 1.201429 AGGTGATGGTGGACCCTGAC 61.201 60.0 0.0 0.0 32.03 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 2689 0.538287 AAGTTTGCTCTCCACCCTGC 60.538 55.0 0.0 0.0 0.0 4.85 R
3255 3260 0.325765 ACCCCTACCCAGCTTCTCTC 60.326 60.0 0.0 0.0 0.0 3.20 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
87 88 8.537049 TTCATTTCATTGAACAAATCCATGTC 57.463 30.769 0.00 0.00 33.84 3.06
216 217 3.090037 TGGACTAGTGAGACTTGGTAGC 58.910 50.000 0.00 0.00 0.00 3.58
242 243 1.846007 TAAAATGCATGGGCGAACCT 58.154 45.000 0.00 0.00 45.35 3.50
277 278 7.082602 GCTGGAGATGCATAATTTCAACATAG 58.917 38.462 0.00 0.00 0.00 2.23
419 420 5.503927 AGAGACTGCCATATTGTGAATTGT 58.496 37.500 0.00 0.00 0.00 2.71
568 570 2.286294 GGTCATCATTTCAGCTAGCACG 59.714 50.000 18.83 7.72 0.00 5.34
684 687 0.036952 AGAGAATGTGTGACAGGGCG 60.037 55.000 0.00 0.00 0.00 6.13
685 688 1.003355 AGAATGTGTGACAGGGCGG 60.003 57.895 0.00 0.00 0.00 6.13
846 849 0.036010 ACTCCTGTGGAAATCTGGCG 60.036 55.000 0.00 0.00 0.00 5.69
928 931 6.061441 TCAACTTCTAATCAAGCCAGAACAA 58.939 36.000 0.00 0.00 0.00 2.83
941 944 3.795877 CCAGAACAACAAGCCACATTTT 58.204 40.909 0.00 0.00 0.00 1.82
1012 1015 5.787380 TCTTCCCAATCATGTCGATGATAG 58.213 41.667 2.04 0.00 46.79 2.08
1229 1232 5.708948 TGTAAGTTTGCATGCTTGATAACC 58.291 37.500 20.33 0.00 0.00 2.85
1758 1761 1.201429 AGGTGATGGTGGACCCTGAC 61.201 60.000 0.00 0.00 32.03 3.51
1817 1820 5.071115 ACCTTCATTGGTAAGCTCCTCTATC 59.929 44.000 0.00 0.00 38.79 2.08
1896 1899 2.417933 CGCTTTATATGCATGCCCTCTC 59.582 50.000 16.68 0.00 0.00 3.20
1975 1978 9.141400 GTACTAATCACTCAATTTCGACTTTCT 57.859 33.333 0.00 0.00 0.00 2.52
2043 2046 6.815089 TGCAAGTTTTGGTAAGTGATTTGAT 58.185 32.000 0.00 0.00 0.00 2.57
2126 2131 3.547249 CTTGCACTGCCACGGCTTG 62.547 63.158 9.92 7.67 42.51 4.01
2164 2169 9.674068 TGTCCAGATACAGATATATCTAGACAC 57.326 37.037 14.92 6.49 46.39 3.67
2165 2170 9.674068 GTCCAGATACAGATATATCTAGACACA 57.326 37.037 14.92 0.00 43.82 3.72
2206 2211 8.153550 ACATCCATATCCAGACAAATCTAAGAC 58.846 37.037 0.00 0.00 32.25 3.01
2292 2297 9.825972 TCTAATTTGACGAAAGCTTCAATAAAG 57.174 29.630 0.00 0.00 33.07 1.85
2309 2314 8.338072 TCAATAAAGCGTGGGTTTTATTAGAA 57.662 30.769 7.88 0.00 43.37 2.10
2310 2315 8.962679 TCAATAAAGCGTGGGTTTTATTAGAAT 58.037 29.630 7.88 0.00 43.37 2.40
2446 2451 6.604795 AGCCAGTTGTTATCATAGAAATGCTT 59.395 34.615 0.00 0.00 32.76 3.91
2623 2628 4.988598 AGCCCACGTCCAACTGCG 62.989 66.667 0.00 0.00 0.00 5.18
2684 2689 1.065926 TCAGGCAGACCACTTATGCAG 60.066 52.381 0.00 0.00 41.78 4.41
2779 2784 4.776349 TGTACTTCAACTGCCAAAGAGAA 58.224 39.130 0.00 0.00 0.00 2.87
2835 2840 1.746470 ATAGTTGGGCGCAACCTTAC 58.254 50.000 34.89 17.16 39.10 2.34
2836 2841 0.321830 TAGTTGGGCGCAACCTTACC 60.322 55.000 34.89 15.61 39.10 2.85
2837 2842 1.602605 GTTGGGCGCAACCTTACCT 60.603 57.895 30.53 0.00 39.10 3.08
2838 2843 1.302993 TTGGGCGCAACCTTACCTC 60.303 57.895 12.81 0.00 39.10 3.85
2839 2844 2.437895 GGGCGCAACCTTACCTCC 60.438 66.667 10.83 0.00 39.10 4.30
2840 2845 2.669240 GGCGCAACCTTACCTCCT 59.331 61.111 10.83 0.00 34.51 3.69
2841 2846 1.619807 GGGCGCAACCTTACCTCCTA 61.620 60.000 10.83 0.00 39.10 2.94
2842 2847 0.468648 GGCGCAACCTTACCTCCTAT 59.531 55.000 10.83 0.00 34.51 2.57
2843 2848 1.690352 GGCGCAACCTTACCTCCTATA 59.310 52.381 10.83 0.00 34.51 1.31
2844 2849 2.302157 GGCGCAACCTTACCTCCTATAT 59.698 50.000 10.83 0.00 34.51 0.86
2845 2850 3.512724 GGCGCAACCTTACCTCCTATATA 59.487 47.826 10.83 0.00 34.51 0.86
2846 2851 4.161754 GGCGCAACCTTACCTCCTATATAT 59.838 45.833 10.83 0.00 34.51 0.86
2847 2852 5.361857 GGCGCAACCTTACCTCCTATATATA 59.638 44.000 10.83 0.00 34.51 0.86
2848 2853 6.041751 GGCGCAACCTTACCTCCTATATATAT 59.958 42.308 10.83 0.00 34.51 0.86
2849 2854 7.232127 GGCGCAACCTTACCTCCTATATATATA 59.768 40.741 10.83 2.49 34.51 0.86
2850 2855 8.804204 GCGCAACCTTACCTCCTATATATATAT 58.196 37.037 0.30 10.10 0.00 0.86
3170 3175 9.122779 TGAAATACAGATGATTCAATGTATGCA 57.877 29.630 20.14 18.26 38.51 3.96
3174 3179 6.665465 ACAGATGATTCAATGTATGCATTCG 58.335 36.000 3.54 3.29 42.91 3.34
3208 3213 2.554806 TATACGACCAGTTGCTCGTG 57.445 50.000 11.57 0.00 42.90 4.35
3209 3214 0.885879 ATACGACCAGTTGCTCGTGA 59.114 50.000 11.57 0.00 42.90 4.35
3210 3215 0.039798 TACGACCAGTTGCTCGTGAC 60.040 55.000 11.57 0.00 42.90 3.67
3212 3217 1.668151 GACCAGTTGCTCGTGACCC 60.668 63.158 0.00 0.00 0.00 4.46
3215 3220 0.320374 CCAGTTGCTCGTGACCCTAA 59.680 55.000 0.00 0.00 0.00 2.69
3216 3221 1.429463 CAGTTGCTCGTGACCCTAAC 58.571 55.000 0.00 0.00 0.00 2.34
3217 3222 1.000955 CAGTTGCTCGTGACCCTAACT 59.999 52.381 0.00 0.00 0.00 2.24
3218 3223 2.230508 CAGTTGCTCGTGACCCTAACTA 59.769 50.000 0.00 0.00 0.00 2.24
3219 3224 2.492484 AGTTGCTCGTGACCCTAACTAG 59.508 50.000 0.00 0.00 0.00 2.57
3221 3226 3.014304 TGCTCGTGACCCTAACTAGAT 57.986 47.619 0.00 0.00 0.00 1.98
3223 3228 4.135306 TGCTCGTGACCCTAACTAGATAG 58.865 47.826 0.00 0.00 0.00 2.08
3226 3231 5.562635 CTCGTGACCCTAACTAGATAGGAT 58.437 45.833 23.97 10.14 44.46 3.24
3227 3232 5.950023 TCGTGACCCTAACTAGATAGGATT 58.050 41.667 23.97 12.39 44.46 3.01
3228 3233 5.768662 TCGTGACCCTAACTAGATAGGATTG 59.231 44.000 23.97 12.05 44.46 2.67
3229 3234 5.535406 CGTGACCCTAACTAGATAGGATTGT 59.465 44.000 23.97 14.76 44.46 2.71
3230 3235 6.713903 CGTGACCCTAACTAGATAGGATTGTA 59.286 42.308 23.97 6.14 44.46 2.41
3231 3236 7.230108 CGTGACCCTAACTAGATAGGATTGTAA 59.770 40.741 23.97 7.15 44.46 2.41
3232 3237 8.921205 GTGACCCTAACTAGATAGGATTGTAAA 58.079 37.037 23.97 6.29 44.46 2.01
3233 3238 9.496710 TGACCCTAACTAGATAGGATTGTAAAA 57.503 33.333 23.97 4.33 44.46 1.52
3234 3239 9.761504 GACCCTAACTAGATAGGATTGTAAAAC 57.238 37.037 23.97 2.40 44.46 2.43
3235 3240 9.275572 ACCCTAACTAGATAGGATTGTAAAACA 57.724 33.333 23.97 0.00 44.46 2.83
3244 3249 7.836183 AGATAGGATTGTAAAACAAATGGAGCT 59.164 33.333 0.00 0.00 41.96 4.09
3245 3250 6.272822 AGGATTGTAAAACAAATGGAGCTC 57.727 37.500 4.71 4.71 41.96 4.09
3246 3251 5.774690 AGGATTGTAAAACAAATGGAGCTCA 59.225 36.000 17.19 1.87 41.96 4.26
3247 3252 6.267471 AGGATTGTAAAACAAATGGAGCTCAA 59.733 34.615 17.19 4.05 41.96 3.02
3248 3253 6.928492 GGATTGTAAAACAAATGGAGCTCAAA 59.072 34.615 17.19 3.06 41.96 2.69
3251 3256 7.288810 TGTAAAACAAATGGAGCTCAAAGAT 57.711 32.000 17.19 0.00 0.00 2.40
3253 3258 7.867403 TGTAAAACAAATGGAGCTCAAAGATTC 59.133 33.333 17.19 0.00 0.00 2.52
3255 3260 5.640189 ACAAATGGAGCTCAAAGATTCTG 57.360 39.130 17.19 10.33 0.00 3.02
3256 3261 5.319453 ACAAATGGAGCTCAAAGATTCTGA 58.681 37.500 17.19 0.00 0.00 3.27
3258 3263 5.432680 AATGGAGCTCAAAGATTCTGAGA 57.567 39.130 17.19 0.00 42.51 3.27
3260 3265 4.092279 TGGAGCTCAAAGATTCTGAGAGA 58.908 43.478 17.19 0.47 42.51 3.10
3263 3268 4.506758 AGCTCAAAGATTCTGAGAGAAGC 58.493 43.478 15.90 7.40 42.51 3.86
3270 3275 4.320608 GATTCTGAGAGAAGCTGGGTAG 57.679 50.000 0.00 0.00 37.62 3.18
3271 3276 2.151502 TCTGAGAGAAGCTGGGTAGG 57.848 55.000 0.00 0.00 0.00 3.18
3273 3278 0.325671 TGAGAGAAGCTGGGTAGGGG 60.326 60.000 0.00 0.00 0.00 4.79
3274 3279 0.325765 GAGAGAAGCTGGGTAGGGGT 60.326 60.000 0.00 0.00 0.00 4.95
3275 3280 0.325765 AGAGAAGCTGGGTAGGGGTC 60.326 60.000 0.00 0.00 0.00 4.46
3278 3283 3.248248 AAGCTGGGTAGGGGTCGGA 62.248 63.158 0.00 0.00 0.00 4.55
3281 3286 2.041206 GCTGGGTAGGGGTCGGATTC 62.041 65.000 0.00 0.00 0.00 2.52
3283 3288 0.935942 TGGGTAGGGGTCGGATTCTA 59.064 55.000 0.00 0.00 0.00 2.10
3284 3289 1.133262 TGGGTAGGGGTCGGATTCTAG 60.133 57.143 0.00 0.00 0.00 2.43
3285 3290 1.630223 GGTAGGGGTCGGATTCTAGG 58.370 60.000 0.00 0.00 0.00 3.02
3287 3292 2.516906 GTAGGGGTCGGATTCTAGGAG 58.483 57.143 0.00 0.00 0.00 3.69
3290 3295 2.180308 AGGGGTCGGATTCTAGGAGAAT 59.820 50.000 1.34 1.34 46.84 2.40
3314 3319 4.170292 CCAGATTCTGGCAAAAGAACTG 57.830 45.455 19.49 12.95 45.13 3.16
3315 3320 3.057033 CCAGATTCTGGCAAAAGAACTGG 60.057 47.826 19.49 18.64 45.13 4.00
3316 3321 3.057033 CAGATTCTGGCAAAAGAACTGGG 60.057 47.826 5.73 0.00 38.95 4.45
3317 3322 1.039856 TTCTGGCAAAAGAACTGGGC 58.960 50.000 0.00 0.00 31.19 5.36
3318 3323 0.827507 TCTGGCAAAAGAACTGGGCC 60.828 55.000 0.00 0.00 44.82 5.80
3339 3344 3.603532 CTGAAATGCTCTAGACAAGGCA 58.396 45.455 6.83 6.83 36.32 4.75
3343 3348 3.920231 ATGCTCTAGACAAGGCAATCA 57.080 42.857 8.30 0.00 35.76 2.57
3363 3369 8.011106 GCAATCAAACCTATGTTGAACATTTTG 58.989 33.333 16.75 18.79 39.88 2.44
3364 3370 9.044150 CAATCAAACCTATGTTGAACATTTTGT 57.956 29.630 22.84 13.90 39.88 2.83
3399 3407 9.683069 CATAGTTTAAGAGCAGTTTGAAAACAT 57.317 29.630 8.53 0.00 41.30 2.71
3438 3446 7.406799 AAAAAGGTGAATCGTATTTTGCAAG 57.593 32.000 0.00 0.00 0.00 4.01
3439 3447 4.096732 AGGTGAATCGTATTTTGCAAGC 57.903 40.909 0.00 0.00 0.00 4.01
3440 3448 3.758554 AGGTGAATCGTATTTTGCAAGCT 59.241 39.130 0.00 0.00 0.00 3.74
3441 3449 4.098416 GGTGAATCGTATTTTGCAAGCTC 58.902 43.478 0.00 0.00 0.00 4.09
3442 3450 4.379394 GGTGAATCGTATTTTGCAAGCTCA 60.379 41.667 0.00 0.00 0.00 4.26
3443 3451 5.335127 GTGAATCGTATTTTGCAAGCTCAT 58.665 37.500 0.00 0.00 0.00 2.90
3444 3452 5.801947 GTGAATCGTATTTTGCAAGCTCATT 59.198 36.000 0.00 0.00 0.00 2.57
3445 3453 6.308766 GTGAATCGTATTTTGCAAGCTCATTT 59.691 34.615 0.00 0.00 0.00 2.32
3448 3456 5.767269 TCGTATTTTGCAAGCTCATTTTCA 58.233 33.333 0.00 0.00 0.00 2.69
3454 3462 4.087510 TGCAAGCTCATTTTCAGAATCG 57.912 40.909 0.00 0.00 0.00 3.34
3466 3474 7.754924 TCATTTTCAGAATCGTATTTTCAAGCC 59.245 33.333 0.00 0.00 0.00 4.35
3484 3492 3.985008 AGCCCATTTTCAAACCGTTTAC 58.015 40.909 0.00 0.00 0.00 2.01
3503 3511 6.183360 CGTTTACCAGAATGATGCTAATGGTT 60.183 38.462 0.00 0.00 41.20 3.67
3510 3518 7.013559 CCAGAATGATGCTAATGGTTTGACATA 59.986 37.037 0.00 0.00 39.69 2.29
3530 3538 3.806625 AGAAAGTTGCTGCAAATGTGT 57.193 38.095 17.80 6.75 0.00 3.72
3545 3553 9.409312 CTGCAAATGTGTTCATCTTTTATGTAA 57.591 29.630 0.00 0.00 32.56 2.41
3546 3554 9.926158 TGCAAATGTGTTCATCTTTTATGTAAT 57.074 25.926 0.00 0.00 32.56 1.89
3569 3579 3.680777 TTCCCCAAATTCCCTATGGTC 57.319 47.619 0.00 0.00 32.13 4.02
3582 3592 6.749036 TCCCTATGGTCTAAGAGGAATTTC 57.251 41.667 0.00 0.00 0.00 2.17
3669 3680 6.293698 ACAGAGTGATGCAAATGATATAGCA 58.706 36.000 0.00 0.00 41.73 3.49
3688 3699 5.473066 AGCACTGGAAAGTTTATGCAAAT 57.527 34.783 13.16 0.00 35.51 2.32
3710 3721 9.961265 CAAATGCACTCATATTTCATGTAGATT 57.039 29.630 0.00 0.00 31.46 2.40
3767 3778 6.445357 TGAAAACAGGTAGAAGTTTGAACC 57.555 37.500 0.00 0.00 37.94 3.62
3804 3816 8.347004 TGCTTTCATTTATCAATGGTTAGTCA 57.653 30.769 0.00 0.00 40.41 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 9.509956 ACATGGATTTGTTCAATGAAATGAAAT 57.490 25.926 0.00 3.23 37.92 2.17
216 217 4.880759 TCGCCCATGCATTTTATAATTGG 58.119 39.130 0.00 0.00 37.32 3.16
242 243 1.202734 GCATCTCCAGCCTCAGCATTA 60.203 52.381 0.00 0.00 43.56 1.90
277 278 7.595130 GTCAAGGAAATCAACAAAGGATACAAC 59.405 37.037 0.00 0.00 41.41 3.32
419 420 3.408634 TGTGACATCAGAGACGTGACTA 58.591 45.455 0.00 0.00 0.00 2.59
568 570 0.454600 CATGAAGCATGACACTGCCC 59.545 55.000 0.00 1.68 43.81 5.36
684 687 5.923684 TCGTTTGTGAATAAATCTTTTGGCC 59.076 36.000 0.00 0.00 0.00 5.36
685 688 7.401484 TTCGTTTGTGAATAAATCTTTTGGC 57.599 32.000 0.00 0.00 0.00 4.52
815 818 2.614057 CCACAGGAGTTTCGGAATATGC 59.386 50.000 0.00 0.00 0.00 3.14
846 849 0.824759 AACCTGATCAGTAGCCGGAC 59.175 55.000 21.11 0.00 0.00 4.79
928 931 3.084786 GGAGAGCTAAAATGTGGCTTGT 58.915 45.455 0.00 0.00 36.37 3.16
941 944 3.009695 GCTAGGATAGGACAGGAGAGCTA 59.990 52.174 0.00 0.00 39.70 3.32
1012 1015 2.224867 CCAATGGGTCCCTGGACATATC 60.225 54.545 17.64 5.25 46.20 1.63
1270 1273 7.323049 TGATTTCAAGTAAGTCGGAAAAACA 57.677 32.000 0.00 0.00 33.47 2.83
1676 1679 9.974980 GTCCTGTTCACCAATTTTAGAAATTAA 57.025 29.630 0.00 0.00 0.00 1.40
1677 1680 9.137459 TGTCCTGTTCACCAATTTTAGAAATTA 57.863 29.630 0.00 0.00 0.00 1.40
1758 1761 2.115910 TTGCTGGGGCTTGGTGAG 59.884 61.111 0.00 0.00 39.59 3.51
1896 1899 5.128205 TCAACCAGAAAGAGGATGCATATG 58.872 41.667 0.00 0.00 0.00 1.78
1975 1978 8.094548 GTCTGTTACCAACCTATATATGCATGA 58.905 37.037 10.16 0.00 0.00 3.07
2043 2046 9.098355 GTAACATTGCAGTTACTGATAGATCAA 57.902 33.333 17.40 9.64 46.41 2.57
2126 2131 7.497595 TCTGTATCTGGACAAATGTACCATAC 58.502 38.462 7.54 7.54 33.08 2.39
2168 2173 9.429109 TCTGGATATGGATGTAGTTAACACTAA 57.571 33.333 8.61 0.00 42.09 2.24
2169 2174 8.857098 GTCTGGATATGGATGTAGTTAACACTA 58.143 37.037 8.61 0.00 42.09 2.74
2170 2175 7.344612 TGTCTGGATATGGATGTAGTTAACACT 59.655 37.037 8.61 0.00 42.09 3.55
2171 2176 7.497595 TGTCTGGATATGGATGTAGTTAACAC 58.502 38.462 8.61 4.94 42.09 3.32
2172 2177 7.669089 TGTCTGGATATGGATGTAGTTAACA 57.331 36.000 8.61 0.00 43.86 2.41
2173 2178 8.958119 TTTGTCTGGATATGGATGTAGTTAAC 57.042 34.615 0.00 0.00 0.00 2.01
2174 2179 9.778741 GATTTGTCTGGATATGGATGTAGTTAA 57.221 33.333 0.00 0.00 0.00 2.01
2175 2180 9.159254 AGATTTGTCTGGATATGGATGTAGTTA 57.841 33.333 0.00 0.00 0.00 2.24
2176 2181 8.038862 AGATTTGTCTGGATATGGATGTAGTT 57.961 34.615 0.00 0.00 0.00 2.24
2177 2182 7.623999 AGATTTGTCTGGATATGGATGTAGT 57.376 36.000 0.00 0.00 0.00 2.73
2178 2183 9.650539 CTTAGATTTGTCTGGATATGGATGTAG 57.349 37.037 0.00 0.00 0.00 2.74
2179 2184 9.379770 TCTTAGATTTGTCTGGATATGGATGTA 57.620 33.333 0.00 0.00 0.00 2.29
2180 2185 8.153550 GTCTTAGATTTGTCTGGATATGGATGT 58.846 37.037 0.00 0.00 0.00 3.06
2181 2186 8.152898 TGTCTTAGATTTGTCTGGATATGGATG 58.847 37.037 0.00 0.00 0.00 3.51
2182 2187 8.267620 TGTCTTAGATTTGTCTGGATATGGAT 57.732 34.615 0.00 0.00 0.00 3.41
2183 2188 7.675161 TGTCTTAGATTTGTCTGGATATGGA 57.325 36.000 0.00 0.00 0.00 3.41
2184 2189 7.989741 ACTTGTCTTAGATTTGTCTGGATATGG 59.010 37.037 0.00 0.00 0.00 2.74
2185 2190 8.954950 ACTTGTCTTAGATTTGTCTGGATATG 57.045 34.615 0.00 0.00 0.00 1.78
2206 2211 7.759886 TCATACTCTTCGGTCTCAAATTACTTG 59.240 37.037 0.00 0.00 36.25 3.16
2217 2222 6.461788 GCCTCTAATTTCATACTCTTCGGTCT 60.462 42.308 0.00 0.00 0.00 3.85
2221 2226 6.292596 GCAAGCCTCTAATTTCATACTCTTCG 60.293 42.308 0.00 0.00 0.00 3.79
2315 2320 2.210116 GGCGATAATCGAAGCCTGAAA 58.790 47.619 10.56 0.00 43.74 2.69
2457 2462 9.679661 TGATAAAAAGTGGCTTCTATGTTGATA 57.320 29.630 0.00 0.00 0.00 2.15
2623 2628 3.189702 TGAAAACGAAACGATGGATTCCC 59.810 43.478 0.00 0.00 0.00 3.97
2684 2689 0.538287 AAGTTTGCTCTCCACCCTGC 60.538 55.000 0.00 0.00 0.00 4.85
2779 2784 2.555227 CCTTCTACCACCACAGCCATTT 60.555 50.000 0.00 0.00 0.00 2.32
2856 2861 9.764363 CTCACACCAGAAACAGCTTTATATATA 57.236 33.333 0.00 0.00 0.00 0.86
2857 2862 8.267894 ACTCACACCAGAAACAGCTTTATATAT 58.732 33.333 0.00 0.00 0.00 0.86
2864 2869 2.717639 ACTCACACCAGAAACAGCTT 57.282 45.000 0.00 0.00 0.00 3.74
2867 2872 2.223572 GGCAAACTCACACCAGAAACAG 60.224 50.000 0.00 0.00 0.00 3.16
3141 3146 7.035840 ACATTGAATCATCTGTATTTCAGCC 57.964 36.000 0.00 0.00 43.32 4.85
3155 3160 4.227512 GCCGAATGCATACATTGAATCA 57.772 40.909 0.00 0.00 46.59 2.57
3208 3213 9.761504 GTTTTACAATCCTATCTAGTTAGGGTC 57.238 37.037 21.70 3.01 39.45 4.46
3209 3214 9.275572 TGTTTTACAATCCTATCTAGTTAGGGT 57.724 33.333 21.70 15.04 39.45 4.34
3217 3222 9.120538 GCTCCATTTGTTTTACAATCCTATCTA 57.879 33.333 0.00 0.00 38.00 1.98
3218 3223 7.836183 AGCTCCATTTGTTTTACAATCCTATCT 59.164 33.333 0.00 0.00 38.00 1.98
3219 3224 8.000780 AGCTCCATTTGTTTTACAATCCTATC 57.999 34.615 0.00 0.00 38.00 2.08
3221 3226 6.945435 TGAGCTCCATTTGTTTTACAATCCTA 59.055 34.615 12.15 0.00 38.00 2.94
3223 3228 6.024552 TGAGCTCCATTTGTTTTACAATCC 57.975 37.500 12.15 0.00 38.00 3.01
3226 3231 7.106439 TCTTTGAGCTCCATTTGTTTTACAA 57.894 32.000 12.15 0.00 36.11 2.41
3227 3232 6.707440 TCTTTGAGCTCCATTTGTTTTACA 57.293 33.333 12.15 0.00 0.00 2.41
3228 3233 8.084684 AGAATCTTTGAGCTCCATTTGTTTTAC 58.915 33.333 12.15 0.00 0.00 2.01
3229 3234 8.084073 CAGAATCTTTGAGCTCCATTTGTTTTA 58.916 33.333 12.15 0.00 0.00 1.52
3230 3235 6.927381 CAGAATCTTTGAGCTCCATTTGTTTT 59.073 34.615 12.15 0.00 0.00 2.43
3231 3236 6.266103 TCAGAATCTTTGAGCTCCATTTGTTT 59.734 34.615 12.15 0.00 0.00 2.83
3232 3237 5.771666 TCAGAATCTTTGAGCTCCATTTGTT 59.228 36.000 12.15 0.00 0.00 2.83
3233 3238 5.319453 TCAGAATCTTTGAGCTCCATTTGT 58.681 37.500 12.15 0.00 0.00 2.83
3234 3239 5.646793 TCTCAGAATCTTTGAGCTCCATTTG 59.353 40.000 12.15 6.12 41.41 2.32
3235 3240 5.813383 TCTCAGAATCTTTGAGCTCCATTT 58.187 37.500 12.15 0.00 41.41 2.32
3236 3241 5.189342 TCTCTCAGAATCTTTGAGCTCCATT 59.811 40.000 12.15 4.19 41.41 3.16
3237 3242 4.715792 TCTCTCAGAATCTTTGAGCTCCAT 59.284 41.667 12.15 0.00 41.41 3.41
3238 3243 4.092279 TCTCTCAGAATCTTTGAGCTCCA 58.908 43.478 12.15 0.00 41.41 3.86
3239 3244 4.734398 TCTCTCAGAATCTTTGAGCTCC 57.266 45.455 12.15 0.00 41.41 4.70
3241 3246 4.223477 AGCTTCTCTCAGAATCTTTGAGCT 59.777 41.667 0.00 0.00 41.41 4.09
3242 3247 4.330620 CAGCTTCTCTCAGAATCTTTGAGC 59.669 45.833 4.90 0.00 41.41 4.26
3244 3249 4.323333 CCCAGCTTCTCTCAGAATCTTTGA 60.323 45.833 0.00 0.00 33.13 2.69
3245 3250 3.940221 CCCAGCTTCTCTCAGAATCTTTG 59.060 47.826 0.00 0.00 33.13 2.77
3246 3251 3.586618 ACCCAGCTTCTCTCAGAATCTTT 59.413 43.478 0.00 0.00 33.13 2.52
3247 3252 3.180507 ACCCAGCTTCTCTCAGAATCTT 58.819 45.455 0.00 0.00 33.13 2.40
3248 3253 2.831565 ACCCAGCTTCTCTCAGAATCT 58.168 47.619 0.00 0.00 33.13 2.40
3251 3256 2.461695 CCTACCCAGCTTCTCTCAGAA 58.538 52.381 0.00 0.00 32.50 3.02
3253 3258 1.118838 CCCTACCCAGCTTCTCTCAG 58.881 60.000 0.00 0.00 0.00 3.35
3255 3260 0.325765 ACCCCTACCCAGCTTCTCTC 60.326 60.000 0.00 0.00 0.00 3.20
3256 3261 0.325765 GACCCCTACCCAGCTTCTCT 60.326 60.000 0.00 0.00 0.00 3.10
3258 3263 1.686110 CGACCCCTACCCAGCTTCT 60.686 63.158 0.00 0.00 0.00 2.85
3260 3265 2.547123 ATCCGACCCCTACCCAGCTT 62.547 60.000 0.00 0.00 0.00 3.74
3263 3268 0.398664 AGAATCCGACCCCTACCCAG 60.399 60.000 0.00 0.00 0.00 4.45
3265 3270 1.630223 CTAGAATCCGACCCCTACCC 58.370 60.000 0.00 0.00 0.00 3.69
3267 3272 2.107901 TCTCCTAGAATCCGACCCCTAC 59.892 54.545 0.00 0.00 0.00 3.18
3268 3273 2.425818 TCTCCTAGAATCCGACCCCTA 58.574 52.381 0.00 0.00 0.00 3.53
3269 3274 1.232909 TCTCCTAGAATCCGACCCCT 58.767 55.000 0.00 0.00 0.00 4.79
3270 3275 2.083628 TTCTCCTAGAATCCGACCCC 57.916 55.000 0.00 0.00 0.00 4.95
3294 3299 3.057033 CCCAGTTCTTTTGCCAGAATCTG 60.057 47.826 2.68 2.68 35.23 2.90
3295 3300 3.160269 CCCAGTTCTTTTGCCAGAATCT 58.840 45.455 0.00 0.00 35.23 2.40
3296 3301 2.353109 GCCCAGTTCTTTTGCCAGAATC 60.353 50.000 0.00 0.00 35.23 2.52
3297 3302 1.620323 GCCCAGTTCTTTTGCCAGAAT 59.380 47.619 0.00 0.00 35.23 2.40
3298 3303 1.039856 GCCCAGTTCTTTTGCCAGAA 58.960 50.000 0.00 0.00 0.00 3.02
3299 3304 0.827507 GGCCCAGTTCTTTTGCCAGA 60.828 55.000 0.00 0.00 41.76 3.86
3300 3305 0.829182 AGGCCCAGTTCTTTTGCCAG 60.829 55.000 0.00 0.00 44.60 4.85
3301 3306 1.114722 CAGGCCCAGTTCTTTTGCCA 61.115 55.000 0.00 0.00 44.60 4.92
3302 3307 0.827507 TCAGGCCCAGTTCTTTTGCC 60.828 55.000 0.00 0.00 42.48 4.52
3303 3308 1.039856 TTCAGGCCCAGTTCTTTTGC 58.960 50.000 0.00 0.00 0.00 3.68
3304 3309 3.656559 CATTTCAGGCCCAGTTCTTTTG 58.343 45.455 0.00 0.00 0.00 2.44
3305 3310 2.037641 GCATTTCAGGCCCAGTTCTTTT 59.962 45.455 0.00 0.00 0.00 2.27
3306 3311 1.620323 GCATTTCAGGCCCAGTTCTTT 59.380 47.619 0.00 0.00 0.00 2.52
3307 3312 1.203100 AGCATTTCAGGCCCAGTTCTT 60.203 47.619 0.00 0.00 0.00 2.52
3308 3313 0.407139 AGCATTTCAGGCCCAGTTCT 59.593 50.000 0.00 0.00 0.00 3.01
3309 3314 0.813821 GAGCATTTCAGGCCCAGTTC 59.186 55.000 0.00 0.00 0.00 3.01
3310 3315 0.407139 AGAGCATTTCAGGCCCAGTT 59.593 50.000 0.00 0.00 0.00 3.16
3311 3316 1.211457 CTAGAGCATTTCAGGCCCAGT 59.789 52.381 0.00 0.00 0.00 4.00
3312 3317 1.487976 TCTAGAGCATTTCAGGCCCAG 59.512 52.381 0.00 0.00 0.00 4.45
3313 3318 1.210478 GTCTAGAGCATTTCAGGCCCA 59.790 52.381 0.00 0.00 0.00 5.36
3314 3319 1.210478 TGTCTAGAGCATTTCAGGCCC 59.790 52.381 0.00 0.00 0.00 5.80
3315 3320 2.698855 TGTCTAGAGCATTTCAGGCC 57.301 50.000 0.00 0.00 0.00 5.19
3316 3321 2.941720 CCTTGTCTAGAGCATTTCAGGC 59.058 50.000 0.00 0.00 0.00 4.85
3317 3322 2.941720 GCCTTGTCTAGAGCATTTCAGG 59.058 50.000 0.00 0.22 0.00 3.86
3318 3323 3.603532 TGCCTTGTCTAGAGCATTTCAG 58.396 45.455 0.00 0.00 0.00 3.02
3339 3344 9.044150 CACAAAATGTTCAACATAGGTTTGATT 57.956 29.630 23.81 7.79 37.97 2.57
3343 3348 9.612066 ATTTCACAAAATGTTCAACATAGGTTT 57.388 25.926 2.67 0.00 37.97 3.27
3420 3428 4.722194 TGAGCTTGCAAAATACGATTCAC 58.278 39.130 0.00 0.00 0.00 3.18
3421 3429 5.565592 ATGAGCTTGCAAAATACGATTCA 57.434 34.783 0.00 0.00 0.00 2.57
3422 3430 6.875926 AAATGAGCTTGCAAAATACGATTC 57.124 33.333 0.00 0.00 0.00 2.52
3423 3431 6.867816 TGAAAATGAGCTTGCAAAATACGATT 59.132 30.769 0.00 0.00 0.00 3.34
3424 3432 6.389091 TGAAAATGAGCTTGCAAAATACGAT 58.611 32.000 0.00 0.00 0.00 3.73
3425 3433 5.767269 TGAAAATGAGCTTGCAAAATACGA 58.233 33.333 0.00 0.00 0.00 3.43
3426 3434 5.858049 TCTGAAAATGAGCTTGCAAAATACG 59.142 36.000 0.00 0.00 0.00 3.06
3427 3435 7.642071 TTCTGAAAATGAGCTTGCAAAATAC 57.358 32.000 0.00 0.00 0.00 1.89
3428 3436 7.274033 CGATTCTGAAAATGAGCTTGCAAAATA 59.726 33.333 0.00 0.00 0.00 1.40
3429 3437 6.090358 CGATTCTGAAAATGAGCTTGCAAAAT 59.910 34.615 0.00 0.00 0.00 1.82
3430 3438 5.403166 CGATTCTGAAAATGAGCTTGCAAAA 59.597 36.000 0.00 0.00 0.00 2.44
3431 3439 4.919168 CGATTCTGAAAATGAGCTTGCAAA 59.081 37.500 0.00 0.00 0.00 3.68
3432 3440 4.022935 ACGATTCTGAAAATGAGCTTGCAA 60.023 37.500 0.00 0.00 0.00 4.08
3433 3441 3.503363 ACGATTCTGAAAATGAGCTTGCA 59.497 39.130 0.00 0.00 0.00 4.08
3434 3442 4.088823 ACGATTCTGAAAATGAGCTTGC 57.911 40.909 0.00 0.00 0.00 4.01
3435 3443 8.679288 AAAATACGATTCTGAAAATGAGCTTG 57.321 30.769 0.00 0.00 0.00 4.01
3436 3444 8.514594 TGAAAATACGATTCTGAAAATGAGCTT 58.485 29.630 0.00 0.00 0.00 3.74
3437 3445 8.044060 TGAAAATACGATTCTGAAAATGAGCT 57.956 30.769 0.00 0.00 0.00 4.09
3438 3446 8.673626 TTGAAAATACGATTCTGAAAATGAGC 57.326 30.769 0.00 0.00 0.00 4.26
3439 3447 8.792538 GCTTGAAAATACGATTCTGAAAATGAG 58.207 33.333 0.00 0.00 0.00 2.90
3440 3448 7.754924 GGCTTGAAAATACGATTCTGAAAATGA 59.245 33.333 0.00 0.00 0.00 2.57
3441 3449 7.009540 GGGCTTGAAAATACGATTCTGAAAATG 59.990 37.037 0.00 0.00 0.00 2.32
3442 3450 7.035612 GGGCTTGAAAATACGATTCTGAAAAT 58.964 34.615 0.00 0.00 0.00 1.82
3443 3451 6.015856 TGGGCTTGAAAATACGATTCTGAAAA 60.016 34.615 0.00 0.00 0.00 2.29
3444 3452 5.475220 TGGGCTTGAAAATACGATTCTGAAA 59.525 36.000 0.00 0.00 0.00 2.69
3445 3453 5.007034 TGGGCTTGAAAATACGATTCTGAA 58.993 37.500 0.00 0.00 0.00 3.02
3448 3456 6.530019 AAATGGGCTTGAAAATACGATTCT 57.470 33.333 0.00 0.00 0.00 2.40
3454 3462 6.347321 CGGTTTGAAAATGGGCTTGAAAATAC 60.347 38.462 0.00 0.00 0.00 1.89
3466 3474 5.189659 TCTGGTAAACGGTTTGAAAATGG 57.810 39.130 16.05 1.08 0.00 3.16
3484 3492 5.125900 TGTCAAACCATTAGCATCATTCTGG 59.874 40.000 0.00 0.00 0.00 3.86
3503 3511 5.512753 TTTGCAGCAACTTTCTATGTCAA 57.487 34.783 7.54 0.00 0.00 3.18
3510 3518 3.806625 ACACATTTGCAGCAACTTTCT 57.193 38.095 7.54 0.00 0.00 2.52
3545 3553 5.358306 ACCATAGGGAATTTGGGGAAAAAT 58.642 37.500 0.00 0.00 38.05 1.82
3546 3554 4.769050 ACCATAGGGAATTTGGGGAAAAA 58.231 39.130 0.00 0.00 38.05 1.94
3547 3555 4.046618 AGACCATAGGGAATTTGGGGAAAA 59.953 41.667 0.00 0.00 38.05 2.29
3551 3560 4.415512 TCTTAGACCATAGGGAATTTGGGG 59.584 45.833 0.00 0.00 38.05 4.96
3569 3579 8.606040 TTTGCCATTTTTGAAATTCCTCTTAG 57.394 30.769 0.00 0.00 0.00 2.18
3751 3762 8.109634 ACATCAATATGGTTCAAACTTCTACCT 58.890 33.333 0.00 0.00 37.43 3.08


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

AutoCloner maintained by Alex Coulton.