Multiple sequence alignment - TraesCS4A01G238500

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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 TraesCS4A01G238500 chr4A 100.000 3614 0 0 1 3614 547927686 547931299 0.000000e+00 6674
1 TraesCS4A01G238500 chr4B 90.501 3116 147 64 590 3614 73101549 73104606 0.000000e+00 3976
2 TraesCS4A01G238500 chr4B 88.029 543 36 17 1 539 73100795 73101312 1.840000e-172 616
3 TraesCS4A01G238500 chr4D 90.782 3005 140 58 644 3614 49501199 49498298 0.000000e+00 3888
4 TraesCS4A01G238500 chr4D 87.722 562 30 19 1 538 49501979 49501433 1.430000e-173 619


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 TraesCS4A01G238500 chr4A 547927686 547931299 3613 False 6674.0 6674 100.000 1 3614 1 chr4A.!!$F1 3613
1 TraesCS4A01G238500 chr4B 73100795 73104606 3811 False 2296.0 3976 89.265 1 3614 2 chr4B.!!$F1 3613
2 TraesCS4A01G238500 chr4D 49498298 49501979 3681 True 2253.5 3888 89.252 1 3614 2 chr4D.!!$R1 3613

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
946 1215 0.179032 AACACCACCAATCTCGCACA 60.179 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2820 3139 1.671845 GGCCGTCAAAGTACACAAACA 59.328 47.619 0.0 0.0 0.0 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
38 39 2.620585 GCTGGTGGAGATCATTAAAGCC 59.379 50.000 0.00 0.00 0.00 4.35
74 77 9.916360 TGTGAGATATAGATATATACCCAACGT 57.084 33.333 0.00 0.00 0.00 3.99
113 125 4.559643 ACTCCTTTTTGTGTTTTTAACGCG 59.440 37.500 3.53 3.53 44.64 6.01
149 161 0.811281 ACAAGCGTACGTACCCTACC 59.189 55.000 19.67 3.89 0.00 3.18
150 162 1.098050 CAAGCGTACGTACCCTACCT 58.902 55.000 19.67 6.00 0.00 3.08
151 163 2.288666 CAAGCGTACGTACCCTACCTA 58.711 52.381 19.67 0.00 0.00 3.08
152 164 1.954927 AGCGTACGTACCCTACCTAC 58.045 55.000 19.67 0.00 0.00 3.18
153 165 0.582005 GCGTACGTACCCTACCTACG 59.418 60.000 19.67 8.66 42.49 3.51
154 166 1.217882 CGTACGTACCCTACCTACGG 58.782 60.000 19.67 0.00 41.08 4.02
169 181 2.747446 CCTACGGGTTCATTCAAACAGG 59.253 50.000 0.00 0.00 0.00 4.00
170 182 0.958822 ACGGGTTCATTCAAACAGGC 59.041 50.000 0.00 0.00 0.00 4.85
181 193 1.900498 AAACAGGCTGCTGGAGTGC 60.900 57.895 15.89 0.00 0.00 4.40
203 215 6.483640 GTGCCTTCACCTACTCTATAATTTGG 59.516 42.308 0.00 0.00 37.24 3.28
204 216 6.385759 TGCCTTCACCTACTCTATAATTTGGA 59.614 38.462 0.00 0.00 0.00 3.53
304 327 6.151144 AGCCAGACACTTTGATTAACATAACC 59.849 38.462 0.00 0.00 0.00 2.85
389 415 0.454789 TGGTGTACACGCATCGTACG 60.455 55.000 19.41 9.53 41.76 3.67
410 437 4.627467 ACGACTTCACTTTGCAGCTTATAG 59.373 41.667 0.00 0.00 0.00 1.31
444 471 6.881602 TGCACCAAAACTGATGTATACATGTA 59.118 34.615 22.93 8.27 36.57 2.29
454 481 9.409918 ACTGATGTATACATGTACACTAACTCT 57.590 33.333 22.93 0.00 37.40 3.24
471 498 7.974501 CACTAACTCTTATCTACCACAACGAAT 59.025 37.037 0.00 0.00 0.00 3.34
481 508 8.677148 ATCTACCACAACGAATTTATATGCTT 57.323 30.769 0.00 0.00 0.00 3.91
568 820 7.441836 AGTTGTTCCAGAACTTTTTCTTTTGT 58.558 30.769 11.56 0.00 40.34 2.83
620 872 9.003658 AGGAAATAGTTGTTCTAGACATTTGTG 57.996 33.333 0.00 0.00 38.26 3.33
626 878 7.916552 AGTTGTTCTAGACATTTGTGTACAAC 58.083 34.615 17.54 17.54 38.26 3.32
724 976 1.341209 CAAACCCCAGTTCCTGAAAGC 59.659 52.381 0.00 0.00 34.19 3.51
852 1111 1.677966 GTTCCCGGGAAAAGAGGCC 60.678 63.158 37.18 19.18 35.75 5.19
946 1215 0.179032 AACACCACCAATCTCGCACA 60.179 50.000 0.00 0.00 0.00 4.57
947 1216 0.179032 ACACCACCAATCTCGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
964 1233 4.024556 CGCACAATCCTAATCCTAAGCAAG 60.025 45.833 0.00 0.00 0.00 4.01
965 1234 5.126067 GCACAATCCTAATCCTAAGCAAGA 58.874 41.667 0.00 0.00 0.00 3.02
966 1235 5.238214 GCACAATCCTAATCCTAAGCAAGAG 59.762 44.000 0.00 0.00 0.00 2.85
967 1236 6.352516 CACAATCCTAATCCTAAGCAAGAGT 58.647 40.000 0.00 0.00 0.00 3.24
968 1237 6.481644 CACAATCCTAATCCTAAGCAAGAGTC 59.518 42.308 0.00 0.00 0.00 3.36
1086 1356 2.442272 AGCAGCGTCGGGAGGTAT 60.442 61.111 0.00 0.00 0.00 2.73
1200 1470 2.105128 GCCATCCTCACCGACTCG 59.895 66.667 0.00 0.00 0.00 4.18
1229 1499 3.108289 CACCGTGCTCGACTGCAG 61.108 66.667 13.48 13.48 44.20 4.41
1297 1567 2.046988 CGTCCAACCCGGGTTACC 60.047 66.667 37.78 25.11 36.46 2.85
1306 1576 2.347490 CGGGTTACCAGCAGTGCT 59.653 61.111 13.14 13.14 40.77 4.40
1332 1602 0.674895 GCACCAAGAGCGACCTGATT 60.675 55.000 0.00 0.00 0.00 2.57
1335 1605 1.072331 ACCAAGAGCGACCTGATTGTT 59.928 47.619 0.00 0.00 0.00 2.83
1359 1629 1.379044 GGCTGTGGCTGCTATGGTT 60.379 57.895 0.00 0.00 38.73 3.67
1362 1632 0.322816 CTGTGGCTGCTATGGTTGGT 60.323 55.000 0.00 0.00 0.00 3.67
1485 1755 2.766651 TCCATCCCCTACCGCACC 60.767 66.667 0.00 0.00 0.00 5.01
1530 1800 2.224499 GGGCATCATCTTCTTCCTCCTC 60.224 54.545 0.00 0.00 0.00 3.71
1617 1887 0.685131 TCGGGATCGGCTTGTTCCTA 60.685 55.000 6.57 0.00 36.78 2.94
1662 1932 4.702274 GGCCTTGGCATGGTGGGT 62.702 66.667 19.40 0.00 0.00 4.51
1983 2253 4.400961 GGGCAGCTCAGCTTCGGT 62.401 66.667 0.00 0.00 36.40 4.69
2091 2361 2.505557 GAGTACGGCGGGTTCACG 60.506 66.667 13.24 0.00 0.00 4.35
2697 2996 2.482664 GGACACAGAGCATCATCGTGAT 60.483 50.000 0.00 0.00 37.65 3.06
2698 2997 2.793790 GACACAGAGCATCATCGTGATC 59.206 50.000 0.00 0.00 34.28 2.92
2699 2998 2.133553 CACAGAGCATCATCGTGATCC 58.866 52.381 0.00 0.00 34.28 3.36
2723 3022 4.406003 GTGACATGGGATTAGGACTACTGT 59.594 45.833 0.00 0.00 0.00 3.55
2724 3023 5.597182 GTGACATGGGATTAGGACTACTGTA 59.403 44.000 0.00 0.00 0.00 2.74
2725 3024 6.267928 GTGACATGGGATTAGGACTACTGTAT 59.732 42.308 0.00 0.00 0.00 2.29
2726 3025 6.267699 TGACATGGGATTAGGACTACTGTATG 59.732 42.308 0.00 0.00 0.00 2.39
2727 3026 6.143915 ACATGGGATTAGGACTACTGTATGT 58.856 40.000 0.00 0.00 0.00 2.29
2728 3027 7.302948 ACATGGGATTAGGACTACTGTATGTA 58.697 38.462 0.00 0.00 0.00 2.29
2729 3028 7.232941 ACATGGGATTAGGACTACTGTATGTAC 59.767 40.741 0.00 0.00 0.00 2.90
2730 3029 6.919158 TGGGATTAGGACTACTGTATGTACT 58.081 40.000 0.00 7.15 0.00 2.73
2731 3030 6.776116 TGGGATTAGGACTACTGTATGTACTG 59.224 42.308 10.53 0.00 0.00 2.74
2739 3038 6.204495 GGACTACTGTATGTACTGGTAGTAGC 59.796 46.154 19.09 14.25 41.44 3.58
2765 3084 0.385390 AGTTGTGCTTGGAAAAGGCG 59.615 50.000 0.00 0.00 0.00 5.52
2766 3085 0.597377 GTTGTGCTTGGAAAAGGCGG 60.597 55.000 0.00 0.00 0.00 6.13
2767 3086 2.049156 GTGCTTGGAAAAGGCGGC 60.049 61.111 0.00 0.00 0.00 6.53
2781 3100 4.003788 CGGCAGTGGGAACGGTCT 62.004 66.667 0.00 0.00 0.00 3.85
2782 3101 2.047179 GGCAGTGGGAACGGTCTC 60.047 66.667 0.00 0.00 0.00 3.36
2818 3137 1.548081 TTGATGTGCAAGGACCCATG 58.452 50.000 0.00 0.00 31.55 3.66
2819 3138 0.697658 TGATGTGCAAGGACCCATGA 59.302 50.000 0.00 0.00 0.00 3.07
2820 3139 1.285667 TGATGTGCAAGGACCCATGAT 59.714 47.619 0.00 0.00 0.00 2.45
2873 3198 2.286654 GCTCACATTGATTTCGCTAGCC 60.287 50.000 9.66 0.00 0.00 3.93
2889 3214 0.248458 AGCCAGCACGTTTGTTTTCG 60.248 50.000 0.00 0.00 0.00 3.46
2890 3215 0.524604 GCCAGCACGTTTGTTTTCGT 60.525 50.000 0.00 0.00 40.99 3.85
2895 3237 4.843984 CCAGCACGTTTGTTTTCGTATAAG 59.156 41.667 0.00 0.00 38.52 1.73
2931 3273 4.503741 TTTGCTTGCATAGAGGTCAAAC 57.496 40.909 0.00 0.00 0.00 2.93
2952 3294 2.320367 CTATCATTACTCGCAGGACGC 58.680 52.381 0.00 0.00 43.23 5.19
2953 3295 0.249489 ATCATTACTCGCAGGACGCC 60.249 55.000 0.00 0.00 43.23 5.68
2955 3297 0.872021 CATTACTCGCAGGACGCCTC 60.872 60.000 0.00 0.00 43.23 4.70
2956 3298 2.017559 ATTACTCGCAGGACGCCTCC 62.018 60.000 0.00 0.00 43.23 4.30
2957 3299 3.931190 TACTCGCAGGACGCCTCCA 62.931 63.158 4.47 0.00 43.23 3.86
2958 3300 4.069232 CTCGCAGGACGCCTCCAA 62.069 66.667 4.47 0.00 43.23 3.53
2959 3301 3.589654 CTCGCAGGACGCCTCCAAA 62.590 63.158 4.47 0.00 43.23 3.28
2960 3302 2.668212 CGCAGGACGCCTCCAAAA 60.668 61.111 4.47 0.00 39.39 2.44
2961 3303 2.680913 CGCAGGACGCCTCCAAAAG 61.681 63.158 4.47 0.00 39.39 2.27
2984 3329 7.979786 AGGAGAGAACTTTGAGATTGGTATA 57.020 36.000 0.00 0.00 0.00 1.47
2985 3330 8.560124 AGGAGAGAACTTTGAGATTGGTATAT 57.440 34.615 0.00 0.00 0.00 0.86
2997 3342 5.482908 AGATTGGTATATGCGATGAACTCC 58.517 41.667 0.00 0.00 0.00 3.85
2999 3344 4.681074 TGGTATATGCGATGAACTCCAA 57.319 40.909 0.00 0.00 0.00 3.53
3000 3345 4.631131 TGGTATATGCGATGAACTCCAAG 58.369 43.478 0.00 0.00 0.00 3.61
3002 3347 3.845781 ATATGCGATGAACTCCAAGGT 57.154 42.857 0.00 0.00 0.00 3.50
3003 3348 2.496899 ATGCGATGAACTCCAAGGTT 57.503 45.000 0.00 0.00 0.00 3.50
3005 3350 2.695359 TGCGATGAACTCCAAGGTTAC 58.305 47.619 0.00 0.00 0.00 2.50
3007 3352 3.512329 TGCGATGAACTCCAAGGTTACTA 59.488 43.478 0.00 0.00 0.00 1.82
3008 3353 3.864003 GCGATGAACTCCAAGGTTACTAC 59.136 47.826 0.00 0.00 0.00 2.73
3009 3354 4.381718 GCGATGAACTCCAAGGTTACTACT 60.382 45.833 0.00 0.00 0.00 2.57
3010 3355 5.103000 CGATGAACTCCAAGGTTACTACTG 58.897 45.833 0.00 0.00 0.00 2.74
3011 3356 5.336531 CGATGAACTCCAAGGTTACTACTGT 60.337 44.000 0.00 0.00 0.00 3.55
3012 3357 5.881923 TGAACTCCAAGGTTACTACTGTT 57.118 39.130 0.00 0.00 0.00 3.16
3013 3358 5.850614 TGAACTCCAAGGTTACTACTGTTC 58.149 41.667 0.00 0.00 33.94 3.18
3014 3359 4.516365 ACTCCAAGGTTACTACTGTTCG 57.484 45.455 0.00 0.00 0.00 3.95
3015 3360 4.147321 ACTCCAAGGTTACTACTGTTCGA 58.853 43.478 0.00 0.00 0.00 3.71
3016 3361 4.022503 ACTCCAAGGTTACTACTGTTCGAC 60.023 45.833 0.00 0.00 0.00 4.20
3017 3362 3.890756 TCCAAGGTTACTACTGTTCGACA 59.109 43.478 0.00 0.00 0.00 4.35
3070 3415 0.822811 AGCAGCACGTCATGATCTCT 59.177 50.000 0.00 0.00 0.00 3.10
3071 3416 1.206610 AGCAGCACGTCATGATCTCTT 59.793 47.619 0.00 0.00 0.00 2.85
3072 3417 1.326852 GCAGCACGTCATGATCTCTTG 59.673 52.381 0.00 0.00 0.00 3.02
3113 3458 2.866156 TCTCAAGTCAAGCGTGAAAGTG 59.134 45.455 3.20 3.18 35.30 3.16
3114 3459 2.866156 CTCAAGTCAAGCGTGAAAGTGA 59.134 45.455 3.20 7.36 35.30 3.41
3115 3460 3.266636 TCAAGTCAAGCGTGAAAGTGAA 58.733 40.909 3.20 0.00 34.87 3.18
3116 3461 3.687212 TCAAGTCAAGCGTGAAAGTGAAA 59.313 39.130 3.20 0.00 34.87 2.69
3117 3462 3.951979 AGTCAAGCGTGAAAGTGAAAG 57.048 42.857 3.20 0.00 34.87 2.62
3118 3463 3.270877 AGTCAAGCGTGAAAGTGAAAGT 58.729 40.909 3.20 0.00 34.87 2.66
3119 3464 3.063997 AGTCAAGCGTGAAAGTGAAAGTG 59.936 43.478 3.20 0.00 34.87 3.16
3120 3465 3.006940 TCAAGCGTGAAAGTGAAAGTGT 58.993 40.909 0.00 0.00 0.00 3.55
3121 3466 4.033587 GTCAAGCGTGAAAGTGAAAGTGTA 59.966 41.667 3.20 0.00 34.87 2.90
3135 3484 9.511144 AAGTGAAAGTGTAATAAAAGGTTTTCG 57.489 29.630 0.00 0.00 0.00 3.46
3141 3490 5.854866 GTGTAATAAAAGGTTTTCGGTGCTC 59.145 40.000 0.00 0.00 0.00 4.26
3269 3623 0.466963 AAACGAACGGAGTGGGAACT 59.533 50.000 0.00 0.00 45.00 3.01
3273 3627 0.966920 GAACGGAGTGGGAACTGAGA 59.033 55.000 0.00 0.00 45.00 3.27
3355 3725 1.340017 CGTGTGGATTGGGGATGTCTT 60.340 52.381 0.00 0.00 0.00 3.01
3418 3788 3.078837 TCCCTGCCACGTAATCTTTTTC 58.921 45.455 0.00 0.00 0.00 2.29
3424 3794 3.681593 CCACGTAATCTTTTTCCCTCCA 58.318 45.455 0.00 0.00 0.00 3.86
3468 3838 1.657751 GGTTCGAAAGCTGGATGGGC 61.658 60.000 0.00 0.00 0.00 5.36
3499 3869 2.487265 GGAAATGTGTGGTCTGGTGTCT 60.487 50.000 0.00 0.00 0.00 3.41
3546 3918 1.970447 CTTCGACTTGTCCTCTCGTG 58.030 55.000 0.00 0.00 0.00 4.35
3555 3927 2.014857 TGTCCTCTCGTGTTATCGGAG 58.985 52.381 0.00 0.00 0.00 4.63
3569 3945 1.675641 CGGAGCCCCAAGGTTCAAG 60.676 63.158 0.00 0.00 44.90 3.02
3570 3946 1.460699 GGAGCCCCAAGGTTCAAGT 59.539 57.895 0.00 0.00 44.90 3.16
3574 3950 2.557056 GAGCCCCAAGGTTCAAGTAAAC 59.443 50.000 0.00 0.00 42.72 2.01
3599 3975 1.028330 ACTGTTCATGCGCCTGGATG 61.028 55.000 12.90 5.97 44.58 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 5.118642 AGGAGTTGAAGACGTACTACAAC 57.881 43.478 14.87 14.87 40.37 3.32
74 77 5.779529 AAGGAGTTGAAGACGTACTACAA 57.220 39.130 0.68 0.00 0.00 2.41
75 78 5.779529 AAAGGAGTTGAAGACGTACTACA 57.220 39.130 0.68 0.00 0.00 2.74
78 81 5.293569 CACAAAAAGGAGTTGAAGACGTACT 59.706 40.000 0.00 0.00 0.00 2.73
84 87 9.198837 GTTAAAAACACAAAAAGGAGTTGAAGA 57.801 29.630 0.00 0.00 0.00 2.87
124 136 3.056607 AGGGTACGTACGCTTGTTTACAT 60.057 43.478 32.55 13.17 45.71 2.29
149 161 2.161609 GCCTGTTTGAATGAACCCGTAG 59.838 50.000 0.00 0.00 0.00 3.51
150 162 2.156098 GCCTGTTTGAATGAACCCGTA 58.844 47.619 0.00 0.00 0.00 4.02
151 163 0.958822 GCCTGTTTGAATGAACCCGT 59.041 50.000 0.00 0.00 0.00 5.28
152 164 1.068333 CAGCCTGTTTGAATGAACCCG 60.068 52.381 0.00 0.00 0.00 5.28
153 165 1.337167 GCAGCCTGTTTGAATGAACCC 60.337 52.381 0.00 0.00 0.00 4.11
154 166 1.615392 AGCAGCCTGTTTGAATGAACC 59.385 47.619 0.00 0.00 0.00 3.62
169 181 2.033141 TGAAGGCACTCCAGCAGC 59.967 61.111 0.00 0.00 38.49 5.25
170 182 1.673665 GGTGAAGGCACTCCAGCAG 60.674 63.158 0.00 0.00 42.03 4.24
181 193 9.853177 AATTCCAAATTATAGAGTAGGTGAAGG 57.147 33.333 0.00 0.00 0.00 3.46
204 216 9.609346 ACTTTACGCTAGTATATTCCAACAATT 57.391 29.630 0.00 0.00 32.12 2.32
222 245 1.202382 AGGCCACGAGATACTTTACGC 60.202 52.381 5.01 0.00 0.00 4.42
304 327 8.183104 TGAACTGGATACTAATGATCCACTAG 57.817 38.462 0.13 0.00 46.40 2.57
372 396 0.903187 GTCGTACGATGCGTGTACAC 59.097 55.000 22.57 16.32 41.76 2.90
389 415 6.538444 GTTCTATAAGCTGCAAAGTGAAGTC 58.462 40.000 1.02 0.00 0.00 3.01
410 437 2.794350 CAGTTTTGGTGCATTTCCGTTC 59.206 45.455 0.00 0.00 0.00 3.95
444 471 6.432162 TCGTTGTGGTAGATAAGAGTTAGTGT 59.568 38.462 0.00 0.00 0.00 3.55
454 481 9.772973 AGCATATAAATTCGTTGTGGTAGATAA 57.227 29.630 0.00 0.00 0.00 1.75
538 565 8.753497 AGAAAAAGTTCTGGAACAACTATCTT 57.247 30.769 14.67 0.00 42.73 2.40
539 566 8.753497 AAGAAAAAGTTCTGGAACAACTATCT 57.247 30.769 14.67 8.77 43.59 1.98
544 796 7.360017 CCACAAAAGAAAAAGTTCTGGAACAAC 60.360 37.037 14.67 3.00 43.59 3.32
583 835 9.847224 AGAACAACTATTTCCTCAAAACTCTTA 57.153 29.630 0.00 0.00 0.00 2.10
584 836 8.753497 AGAACAACTATTTCCTCAAAACTCTT 57.247 30.769 0.00 0.00 0.00 2.85
585 837 9.495572 CTAGAACAACTATTTCCTCAAAACTCT 57.504 33.333 0.00 0.00 0.00 3.24
586 838 9.490379 TCTAGAACAACTATTTCCTCAAAACTC 57.510 33.333 0.00 0.00 0.00 3.01
587 839 9.274206 GTCTAGAACAACTATTTCCTCAAAACT 57.726 33.333 0.00 0.00 0.00 2.66
588 840 9.052759 TGTCTAGAACAACTATTTCCTCAAAAC 57.947 33.333 0.00 0.00 34.03 2.43
589 841 9.793259 ATGTCTAGAACAACTATTTCCTCAAAA 57.207 29.630 0.00 0.00 42.37 2.44
590 842 9.793259 AATGTCTAGAACAACTATTTCCTCAAA 57.207 29.630 0.00 0.00 42.37 2.69
591 843 9.793259 AAATGTCTAGAACAACTATTTCCTCAA 57.207 29.630 0.00 0.00 42.37 3.02
592 844 9.219603 CAAATGTCTAGAACAACTATTTCCTCA 57.780 33.333 0.00 0.00 42.37 3.86
593 845 9.220767 ACAAATGTCTAGAACAACTATTTCCTC 57.779 33.333 0.00 0.00 42.37 3.71
594 846 9.003658 CACAAATGTCTAGAACAACTATTTCCT 57.996 33.333 0.00 0.00 42.37 3.36
595 847 8.784043 ACACAAATGTCTAGAACAACTATTTCC 58.216 33.333 0.00 0.00 42.37 3.13
598 850 9.772973 TGTACACAAATGTCTAGAACAACTATT 57.227 29.630 0.00 0.00 42.37 1.73
599 851 9.772973 TTGTACACAAATGTCTAGAACAACTAT 57.227 29.630 0.00 0.00 42.37 2.12
600 852 9.037737 GTTGTACACAAATGTCTAGAACAACTA 57.962 33.333 17.80 0.00 43.60 2.24
601 853 7.551262 TGTTGTACACAAATGTCTAGAACAACT 59.449 33.333 22.27 4.62 45.37 3.16
602 854 7.690228 TGTTGTACACAAATGTCTAGAACAAC 58.310 34.615 18.06 18.06 45.36 3.32
603 855 7.011950 CCTGTTGTACACAAATGTCTAGAACAA 59.988 37.037 10.92 0.00 40.48 2.83
604 856 6.481976 CCTGTTGTACACAAATGTCTAGAACA 59.518 38.462 9.85 9.85 40.48 3.18
620 872 4.822026 AGAGATTGTAGTGCCTGTTGTAC 58.178 43.478 0.00 0.00 0.00 2.90
623 875 4.199432 AGAGAGATTGTAGTGCCTGTTG 57.801 45.455 0.00 0.00 0.00 3.33
724 976 2.866510 CGCAAATGTCGCTGCACG 60.867 61.111 0.00 2.79 45.62 5.34
752 1004 3.863142 AACTCATCGTACTGGTGTACC 57.137 47.619 0.00 0.00 44.48 3.34
755 1007 2.897969 AGGAAACTCATCGTACTGGTGT 59.102 45.455 0.00 0.00 32.90 4.16
756 1008 3.594603 AGGAAACTCATCGTACTGGTG 57.405 47.619 0.00 0.00 32.90 4.17
804 1063 1.076995 AGAATTTAGTGGGCCCGCC 60.077 57.895 32.01 17.72 0.00 6.13
806 1065 1.094785 CACAGAATTTAGTGGGCCCG 58.905 55.000 19.37 0.00 32.24 6.13
852 1111 4.394712 GAGGTGGGCCCACTCACG 62.395 72.222 45.38 0.00 45.52 4.35
876 1135 1.336609 ACGAAAACACGAGTAGGGAGC 60.337 52.381 0.00 0.00 37.03 4.70
887 1146 4.329256 GTCCCTGCTCTTATACGAAAACAC 59.671 45.833 0.00 0.00 0.00 3.32
946 1215 5.598830 TCGACTCTTGCTTAGGATTAGGATT 59.401 40.000 0.00 0.00 0.00 3.01
947 1216 5.141182 TCGACTCTTGCTTAGGATTAGGAT 58.859 41.667 0.00 0.00 0.00 3.24
964 1233 3.119673 TCTGCTCTGATGTTTCTCGACTC 60.120 47.826 0.00 0.00 0.00 3.36
965 1234 2.822561 TCTGCTCTGATGTTTCTCGACT 59.177 45.455 0.00 0.00 0.00 4.18
966 1235 3.178267 CTCTGCTCTGATGTTTCTCGAC 58.822 50.000 0.00 0.00 0.00 4.20
967 1236 2.416566 GCTCTGCTCTGATGTTTCTCGA 60.417 50.000 0.00 0.00 0.00 4.04
968 1237 1.925847 GCTCTGCTCTGATGTTTCTCG 59.074 52.381 0.00 0.00 0.00 4.04
1068 1338 2.017559 AATACCTCCCGACGCTGCTC 62.018 60.000 0.00 0.00 0.00 4.26
1082 1352 1.202188 GCGCCTCAAGCTTGAAATACC 60.202 52.381 28.16 13.99 40.39 2.73
1086 1356 2.945984 CGCGCCTCAAGCTTGAAA 59.054 55.556 28.16 9.08 40.39 2.69
1293 1563 1.965930 CGCCAAGCACTGCTGGTAA 60.966 57.895 3.73 0.00 39.62 2.85
1353 1623 0.693622 TGGCGAAGGAACCAACCATA 59.306 50.000 0.00 0.00 31.46 2.74
1359 1629 2.354729 CCCATGGCGAAGGAACCA 59.645 61.111 6.09 0.00 41.06 3.67
1464 1734 3.616721 CGGTAGGGGATGGAGCCG 61.617 72.222 0.00 0.00 0.00 5.52
1617 1887 2.203788 TGGAGACCGGTGAAGGCT 60.204 61.111 14.63 0.62 33.69 4.58
2253 2523 2.436824 GCCAGGAAGAAGGCCGAC 60.437 66.667 0.00 0.00 45.18 4.79
2606 2882 7.527961 GAAACAAGTTTATCCGGTCACACGG 62.528 48.000 0.00 0.00 43.16 4.94
2617 2893 4.995487 ACACGAGGAGGAAACAAGTTTATC 59.005 41.667 0.00 0.77 32.11 1.75
2618 2894 4.969484 ACACGAGGAGGAAACAAGTTTAT 58.031 39.130 0.00 0.00 32.11 1.40
2620 2896 3.118371 AGACACGAGGAGGAAACAAGTTT 60.118 43.478 0.00 0.00 35.14 2.66
2621 2897 2.434702 AGACACGAGGAGGAAACAAGTT 59.565 45.455 0.00 0.00 0.00 2.66
2622 2898 2.036089 GAGACACGAGGAGGAAACAAGT 59.964 50.000 0.00 0.00 0.00 3.16
2623 2899 2.297597 AGAGACACGAGGAGGAAACAAG 59.702 50.000 0.00 0.00 0.00 3.16
2697 2996 1.760613 GTCCTAATCCCATGTCACGGA 59.239 52.381 0.00 0.00 0.00 4.69
2698 2997 1.762957 AGTCCTAATCCCATGTCACGG 59.237 52.381 0.00 0.00 0.00 4.94
2699 2998 3.637229 AGTAGTCCTAATCCCATGTCACG 59.363 47.826 0.00 0.00 0.00 4.35
2723 3022 7.114754 ACTACAGTTGCTACTACCAGTACATA 58.885 38.462 0.00 0.00 31.96 2.29
2724 3023 5.950549 ACTACAGTTGCTACTACCAGTACAT 59.049 40.000 0.00 0.00 31.96 2.29
2725 3024 5.319453 ACTACAGTTGCTACTACCAGTACA 58.681 41.667 0.00 0.00 31.96 2.90
2726 3025 5.893897 ACTACAGTTGCTACTACCAGTAC 57.106 43.478 0.00 0.00 31.96 2.73
2765 3084 2.047179 GAGACCGTTCCCACTGCC 60.047 66.667 0.00 0.00 0.00 4.85
2766 3085 2.432628 CGAGACCGTTCCCACTGC 60.433 66.667 0.00 0.00 0.00 4.40
2778 3097 4.086199 AGAATCTCAAACGAGACGAGAC 57.914 45.455 0.00 0.00 42.28 3.36
2779 3098 4.215613 TCAAGAATCTCAAACGAGACGAGA 59.784 41.667 0.00 0.00 42.28 4.04
2780 3099 4.476862 TCAAGAATCTCAAACGAGACGAG 58.523 43.478 0.00 0.00 42.28 4.18
2781 3100 4.499037 TCAAGAATCTCAAACGAGACGA 57.501 40.909 0.00 0.00 42.28 4.20
2782 3101 4.623167 ACATCAAGAATCTCAAACGAGACG 59.377 41.667 0.00 0.00 42.28 4.18
2813 3132 5.460646 GTCAAAGTACACAAACATCATGGG 58.539 41.667 0.00 0.00 0.00 4.00
2814 3133 5.146460 CGTCAAAGTACACAAACATCATGG 58.854 41.667 0.00 0.00 0.00 3.66
2815 3134 5.146460 CCGTCAAAGTACACAAACATCATG 58.854 41.667 0.00 0.00 0.00 3.07
2816 3135 4.320202 GCCGTCAAAGTACACAAACATCAT 60.320 41.667 0.00 0.00 0.00 2.45
2818 3137 3.551551 GCCGTCAAAGTACACAAACATC 58.448 45.455 0.00 0.00 0.00 3.06
2819 3138 2.292292 GGCCGTCAAAGTACACAAACAT 59.708 45.455 0.00 0.00 0.00 2.71
2820 3139 1.671845 GGCCGTCAAAGTACACAAACA 59.328 47.619 0.00 0.00 0.00 2.83
2873 3198 5.437263 ACTTATACGAAAACAAACGTGCTG 58.563 37.500 0.00 0.00 42.61 4.41
2883 3208 6.401796 CCTGCCAGTACAACTTATACGAAAAC 60.402 42.308 0.00 0.00 0.00 2.43
2889 3214 6.608610 CAAAACCTGCCAGTACAACTTATAC 58.391 40.000 0.00 0.00 0.00 1.47
2890 3215 5.182380 GCAAAACCTGCCAGTACAACTTATA 59.818 40.000 0.00 0.00 46.13 0.98
2895 3237 2.134201 GCAAAACCTGCCAGTACAAC 57.866 50.000 0.00 0.00 46.13 3.32
2931 3273 2.922758 GCGTCCTGCGAGTAATGATAGG 60.923 54.545 0.00 0.00 44.77 2.57
2943 3285 2.668212 TTTTGGAGGCGTCCTGCG 60.668 61.111 24.96 0.00 45.25 5.18
2955 3297 6.294397 CCAATCTCAAAGTTCTCTCCTTTTGG 60.294 42.308 0.00 0.00 42.21 3.28
2956 3298 6.264067 ACCAATCTCAAAGTTCTCTCCTTTTG 59.736 38.462 0.00 0.00 29.89 2.44
2957 3299 6.368805 ACCAATCTCAAAGTTCTCTCCTTTT 58.631 36.000 0.00 0.00 29.89 2.27
2958 3300 5.946486 ACCAATCTCAAAGTTCTCTCCTTT 58.054 37.500 0.00 0.00 32.48 3.11
2959 3301 5.574970 ACCAATCTCAAAGTTCTCTCCTT 57.425 39.130 0.00 0.00 0.00 3.36
2960 3302 6.882768 ATACCAATCTCAAAGTTCTCTCCT 57.117 37.500 0.00 0.00 0.00 3.69
2961 3303 7.172361 GCATATACCAATCTCAAAGTTCTCTCC 59.828 40.741 0.00 0.00 0.00 3.71
2962 3304 7.095857 CGCATATACCAATCTCAAAGTTCTCTC 60.096 40.741 0.00 0.00 0.00 3.20
2963 3305 6.703607 CGCATATACCAATCTCAAAGTTCTCT 59.296 38.462 0.00 0.00 0.00 3.10
2964 3306 6.701841 TCGCATATACCAATCTCAAAGTTCTC 59.298 38.462 0.00 0.00 0.00 2.87
2984 3329 2.496899 AACCTTGGAGTTCATCGCAT 57.503 45.000 0.00 0.00 0.00 4.73
2985 3330 2.301870 AGTAACCTTGGAGTTCATCGCA 59.698 45.455 0.00 0.00 0.00 5.10
3022 3367 5.938125 AGTTGCATCCGATACTAGTGTTTTT 59.062 36.000 5.39 0.00 0.00 1.94
3023 3368 5.488341 AGTTGCATCCGATACTAGTGTTTT 58.512 37.500 5.39 0.00 0.00 2.43
3024 3369 5.086104 AGTTGCATCCGATACTAGTGTTT 57.914 39.130 5.39 0.00 0.00 2.83
3029 3374 4.682787 TCACAAGTTGCATCCGATACTAG 58.317 43.478 1.81 0.00 0.00 2.57
3070 3415 7.773224 TGAGAAGAAAATAACCTCACAAGACAA 59.227 33.333 0.00 0.00 0.00 3.18
3071 3416 7.279615 TGAGAAGAAAATAACCTCACAAGACA 58.720 34.615 0.00 0.00 0.00 3.41
3072 3417 7.730364 TGAGAAGAAAATAACCTCACAAGAC 57.270 36.000 0.00 0.00 0.00 3.01
3113 3458 7.096353 GCACCGAAAACCTTTTATTACACTTTC 60.096 37.037 0.00 0.00 0.00 2.62
3114 3459 6.698329 GCACCGAAAACCTTTTATTACACTTT 59.302 34.615 0.00 0.00 0.00 2.66
3115 3460 6.040054 AGCACCGAAAACCTTTTATTACACTT 59.960 34.615 0.00 0.00 0.00 3.16
3116 3461 5.533528 AGCACCGAAAACCTTTTATTACACT 59.466 36.000 0.00 0.00 0.00 3.55
3117 3462 5.765176 AGCACCGAAAACCTTTTATTACAC 58.235 37.500 0.00 0.00 0.00 2.90
3118 3463 5.334260 CGAGCACCGAAAACCTTTTATTACA 60.334 40.000 0.00 0.00 41.76 2.41
3119 3464 5.084055 CGAGCACCGAAAACCTTTTATTAC 58.916 41.667 0.00 0.00 41.76 1.89
3120 3465 4.378666 GCGAGCACCGAAAACCTTTTATTA 60.379 41.667 2.63 0.00 41.76 0.98
3121 3466 3.610821 GCGAGCACCGAAAACCTTTTATT 60.611 43.478 2.63 0.00 41.76 1.40
3269 3623 1.184431 CTCCTGAGCTGAGCTTCTCA 58.816 55.000 9.00 0.91 39.88 3.27
3273 3627 2.102925 GCTTATCTCCTGAGCTGAGCTT 59.897 50.000 9.00 0.00 39.88 3.74
3355 3725 2.571757 CAGCCGTCGTCAGCCTTA 59.428 61.111 0.00 0.00 0.00 2.69
3418 3788 2.290896 TGCAGATGGTTTTACTGGAGGG 60.291 50.000 0.00 0.00 33.00 4.30
3424 3794 4.265073 GTCCAGATGCAGATGGTTTTACT 58.735 43.478 17.12 0.00 37.84 2.24
3468 3838 1.405105 CACACATTTCCGGCAATAGGG 59.595 52.381 0.00 0.00 0.00 3.53
3499 3869 2.094234 TCTCGGAATCATTGACTTGCGA 60.094 45.455 17.36 17.36 41.82 5.10
3546 3918 0.255033 AACCTTGGGGCTCCGATAAC 59.745 55.000 0.00 0.00 35.63 1.89
3555 3927 1.616865 GGTTTACTTGAACCTTGGGGC 59.383 52.381 0.00 0.00 44.55 5.80
3569 3945 4.615541 GCGCATGAACAGTTTTAGGTTTAC 59.384 41.667 0.30 0.00 0.00 2.01
3570 3946 4.320641 GGCGCATGAACAGTTTTAGGTTTA 60.321 41.667 10.83 0.00 0.00 2.01
3574 3950 1.812571 AGGCGCATGAACAGTTTTAGG 59.187 47.619 10.83 0.00 0.00 2.69
3577 3953 0.314935 CCAGGCGCATGAACAGTTTT 59.685 50.000 25.72 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.