Multiple sequence alignment - TraesCS7D01G306000

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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 TraesCS7D01G306000 chr7D 100.000 4088 0 0 1 4088 387226708 387222621 0.000000e+00 7550.0
1 TraesCS7D01G306000 chr7D 87.586 145 12 4 3751 3892 509615430 509615289 3.270000e-36 163.0
2 TraesCS7D01G306000 chr7B 96.241 3379 78 21 1 3364 382285396 382282052 0.000000e+00 5491.0
3 TraesCS7D01G306000 chr7B 85.784 204 21 6 3693 3889 382280331 382280129 4.140000e-50 209.0
4 TraesCS7D01G306000 chr7A 96.068 3052 71 23 291 3326 437074141 437071123 0.000000e+00 4926.0
5 TraesCS7D01G306000 chr7A 97.279 294 8 0 1 294 437076996 437076703 2.190000e-137 499.0
6 TraesCS7D01G306000 chr7A 81.250 400 49 23 3681 4074 437070494 437070115 2.390000e-77 300.0
7 TraesCS7D01G306000 chr7A 94.928 138 7 0 3505 3642 437070744 437070607 2.470000e-52 217.0
8 TraesCS7D01G306000 chr4B 84.672 137 10 7 3759 3893 92547220 92547347 4.290000e-25 126.0
9 TraesCS7D01G306000 chr4A 87.000 100 10 2 3759 3858 534164846 534164750 4.320000e-20 110.0
10 TraesCS7D01G306000 chr5A 79.688 128 9 11 3770 3892 29136073 29135958 4.380000e-10 76.8


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 TraesCS7D01G306000 chr7D 387222621 387226708 4087 True 7550.0 7550 100.00000 1 4088 1 chr7D.!!$R1 4087
1 TraesCS7D01G306000 chr7B 382280129 382285396 5267 True 2850.0 5491 91.01250 1 3889 2 chr7B.!!$R1 3888
2 TraesCS7D01G306000 chr7A 437070115 437076996 6881 True 1485.5 4926 92.38125 1 4074 4 chr7A.!!$R1 4073

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
354 2928 1.969200 GACTTACGGGGAGAAGGGGC 61.969 65.000 0.0 0.0 0.0 5.80 F
913 3488 4.472691 TTCGCTTCAACTTCATCACTTG 57.527 40.909 0.0 0.0 0.0 3.16 F
1803 4378 0.036952 ATGTCAGGAAGAGTGGTGCG 60.037 55.000 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 4022 1.418334 AACTCACAGAGGTGCTCAGT 58.582 50.0 0.00 0.0 44.87 3.41 R
2416 5004 0.249615 GCAGCAGCGATCATGTCCTA 60.250 55.0 0.00 0.0 0.00 2.94 R
3668 7865 0.541392 CTGTAGGCTGCCACCATACA 59.459 55.0 22.65 18.2 0.00 2.29 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
58 59 8.168790 TGATCATGTTGAGACAAGAAAATTGA 57.831 30.769 0.00 0.00 37.09 2.57
116 117 4.321899 GCAGTCCCTGTTTTAATGCAATGA 60.322 41.667 0.00 0.00 33.43 2.57
354 2928 1.969200 GACTTACGGGGAGAAGGGGC 61.969 65.000 0.00 0.00 0.00 5.80
913 3488 4.472691 TTCGCTTCAACTTCATCACTTG 57.527 40.909 0.00 0.00 0.00 3.16
973 3548 9.853555 ATAAATAGAACAACATTTGCAATTCGA 57.146 25.926 0.00 0.00 0.00 3.71
1023 3598 6.726490 ATGGATCCATTTCTTCTTTCCATG 57.274 37.500 22.15 0.00 40.16 3.66
1704 4279 1.852309 TGGCTTGATCCATATGGGTGT 59.148 47.619 21.78 8.31 38.11 4.16
1803 4378 0.036952 ATGTCAGGAAGAGTGGTGCG 60.037 55.000 0.00 0.00 0.00 5.34
1821 4396 1.475751 GCGTCCCTTGATGATGATGGT 60.476 52.381 0.00 0.00 0.00 3.55
1822 4397 2.216046 CGTCCCTTGATGATGATGGTG 58.784 52.381 0.00 0.00 0.00 4.17
1823 4398 2.158914 CGTCCCTTGATGATGATGGTGA 60.159 50.000 0.00 0.00 0.00 4.02
1954 4529 4.122337 TCCTTACTGTTACAGACCCTCA 57.878 45.455 20.07 0.00 35.18 3.86
1970 4545 7.559897 ACAGACCCTCAAGTTCATTTTCTTTAA 59.440 33.333 0.00 0.00 0.00 1.52
2018 4594 1.155889 TTGTGCTCTGTACCATTGCG 58.844 50.000 0.00 0.00 0.00 4.85
2026 4602 3.932710 CTCTGTACCATTGCGTGTGTTAT 59.067 43.478 0.00 0.00 0.00 1.89
2035 4611 5.689514 CCATTGCGTGTGTTATTCTTGAAAA 59.310 36.000 0.00 0.00 0.00 2.29
2039 4615 5.912396 TGCGTGTGTTATTCTTGAAAATGAC 59.088 36.000 0.00 0.00 0.00 3.06
2041 4617 7.041712 TGCGTGTGTTATTCTTGAAAATGACTA 60.042 33.333 0.00 0.00 0.00 2.59
2062 4638 2.816087 AGGCTTCATAGTTGTTGTGCAG 59.184 45.455 0.00 0.00 0.00 4.41
2200 4780 7.862372 TGATTTCACAGCAGAGTTTGTAATTTC 59.138 33.333 0.00 0.00 0.00 2.17
2265 4845 3.430931 GAGTAGCTGTTCTCGCTTGTAG 58.569 50.000 0.00 0.00 38.86 2.74
2416 5004 7.264947 TGATCATTCTGAATGTGTGTATACGT 58.735 34.615 25.08 0.00 39.87 3.57
2439 5027 0.531532 ACATGATCGCTGCTGCTACC 60.532 55.000 14.03 0.00 36.97 3.18
2527 5115 4.975490 TCCAGGAGGAGCTTGACA 57.025 55.556 0.00 0.00 39.61 3.58
2926 5514 0.035881 CAGGCTCTTCCACTGCTTCA 59.964 55.000 0.00 0.00 37.29 3.02
3135 5724 8.231692 TGTTTATCACAAGAATGGTGAAAGAA 57.768 30.769 0.00 0.00 29.87 2.52
3136 5725 8.859090 TGTTTATCACAAGAATGGTGAAAGAAT 58.141 29.630 0.00 0.00 29.87 2.40
3139 5728 9.513906 TTATCACAAGAATGGTGAAAGAATACA 57.486 29.630 0.00 0.00 0.00 2.29
3140 5729 8.585471 ATCACAAGAATGGTGAAAGAATACAT 57.415 30.769 0.00 0.00 0.00 2.29
3141 5730 8.044060 TCACAAGAATGGTGAAAGAATACATC 57.956 34.615 0.00 0.00 0.00 3.06
3142 5731 7.665145 TCACAAGAATGGTGAAAGAATACATCA 59.335 33.333 0.00 0.00 0.00 3.07
3143 5732 8.464404 CACAAGAATGGTGAAAGAATACATCAT 58.536 33.333 0.00 0.00 39.16 2.45
3144 5733 9.685276 ACAAGAATGGTGAAAGAATACATCATA 57.315 29.630 0.00 0.00 36.94 2.15
3145 5734 9.941664 CAAGAATGGTGAAAGAATACATCATAC 57.058 33.333 0.00 0.00 36.94 2.39
3146 5735 9.685276 AAGAATGGTGAAAGAATACATCATACA 57.315 29.630 0.00 0.00 36.94 2.29
3147 5736 9.857656 AGAATGGTGAAAGAATACATCATACAT 57.142 29.630 0.00 0.00 36.94 2.29
3236 5825 7.919091 CACGATGAATTGAATCATTTCCAGATT 59.081 33.333 13.32 0.00 40.08 2.40
3330 5922 9.062524 CAGAGATAGTAGCTTTGTAGTAGATGT 57.937 37.037 0.00 0.00 0.00 3.06
3351 5943 8.646004 AGATGTATGCACTTATCTTACTGATGT 58.354 33.333 0.00 0.00 36.65 3.06
3354 5946 8.141909 TGTATGCACTTATCTTACTGATGTACC 58.858 37.037 0.00 0.00 36.65 3.34
3372 6276 0.238289 CCGAACCATTGCCATATCGC 59.762 55.000 0.00 0.00 0.00 4.58
3395 6299 4.503910 TGTAACCATCTCGTCCATTCTTG 58.496 43.478 0.00 0.00 0.00 3.02
3396 6300 2.698855 ACCATCTCGTCCATTCTTGG 57.301 50.000 0.00 0.00 45.15 3.61
3397 6301 1.909302 ACCATCTCGTCCATTCTTGGT 59.091 47.619 0.00 0.00 44.06 3.67
3398 6302 2.283298 CCATCTCGTCCATTCTTGGTG 58.717 52.381 0.00 0.00 44.06 4.17
3399 6303 2.093500 CCATCTCGTCCATTCTTGGTGA 60.093 50.000 0.00 0.00 44.06 4.02
3400 6304 3.432749 CCATCTCGTCCATTCTTGGTGAT 60.433 47.826 0.00 0.00 44.06 3.06
3401 6305 4.202253 CCATCTCGTCCATTCTTGGTGATA 60.202 45.833 0.00 0.00 44.06 2.15
3402 6306 4.655762 TCTCGTCCATTCTTGGTGATAG 57.344 45.455 0.00 0.00 44.06 2.08
3403 6307 4.278310 TCTCGTCCATTCTTGGTGATAGA 58.722 43.478 0.00 0.00 44.06 1.98
3404 6308 4.895889 TCTCGTCCATTCTTGGTGATAGAT 59.104 41.667 0.00 0.00 44.06 1.98
3405 6309 4.948847 TCGTCCATTCTTGGTGATAGATG 58.051 43.478 0.00 0.00 44.06 2.90
3406 6310 4.649218 TCGTCCATTCTTGGTGATAGATGA 59.351 41.667 0.00 0.00 44.06 2.92
3407 6311 5.128663 TCGTCCATTCTTGGTGATAGATGAA 59.871 40.000 0.00 0.00 44.06 2.57
3408 6312 5.994054 CGTCCATTCTTGGTGATAGATGAAT 59.006 40.000 0.00 0.00 44.06 2.57
3409 6313 7.015195 TCGTCCATTCTTGGTGATAGATGAATA 59.985 37.037 0.00 0.00 44.06 1.75
3410 6314 7.657354 CGTCCATTCTTGGTGATAGATGAATAA 59.343 37.037 0.00 0.00 44.06 1.40
3411 6315 9.342308 GTCCATTCTTGGTGATAGATGAATAAA 57.658 33.333 0.00 0.00 44.06 1.40
3446 6350 6.405278 CAAACCAATTTGGACTAGGAAACT 57.595 37.500 22.19 0.00 40.96 2.66
3450 6354 5.301805 ACCAATTTGGACTAGGAAACTTGTG 59.698 40.000 22.19 0.00 46.54 3.33
3451 6355 5.534654 CCAATTTGGACTAGGAAACTTGTGA 59.465 40.000 10.03 0.00 46.54 3.58
3452 6356 6.209391 CCAATTTGGACTAGGAAACTTGTGAT 59.791 38.462 10.03 0.00 46.54 3.06
3453 6357 7.308435 CAATTTGGACTAGGAAACTTGTGATC 58.692 38.462 0.00 0.00 46.54 2.92
3454 6358 4.553330 TGGACTAGGAAACTTGTGATCC 57.447 45.455 0.00 0.00 46.54 3.36
3455 6359 3.907474 TGGACTAGGAAACTTGTGATCCA 59.093 43.478 0.00 0.00 46.54 3.41
3456 6360 4.349636 TGGACTAGGAAACTTGTGATCCAA 59.650 41.667 0.00 0.00 46.54 3.53
3457 6361 5.163141 TGGACTAGGAAACTTGTGATCCAAA 60.163 40.000 0.00 0.00 46.54 3.28
3458 6362 5.768164 GGACTAGGAAACTTGTGATCCAAAA 59.232 40.000 0.00 0.00 46.54 2.44
3459 6363 6.264518 GGACTAGGAAACTTGTGATCCAAAAA 59.735 38.462 0.00 0.00 46.54 1.94
3480 6384 5.941948 AAATAGTCTAACACTTGGCACAC 57.058 39.130 0.00 0.00 39.29 3.82
3492 6396 3.724508 TTGGCACACAAGTACAAATGG 57.275 42.857 0.00 0.00 39.29 3.16
3496 6400 3.554752 GGCACACAAGTACAAATGGCATT 60.555 43.478 6.96 6.96 33.20 3.56
3497 6401 4.057432 GCACACAAGTACAAATGGCATTT 58.943 39.130 19.39 19.39 0.00 2.32
3500 6404 6.346518 GCACACAAGTACAAATGGCATTTAAC 60.347 38.462 23.93 22.35 0.00 2.01
3501 6405 5.918011 ACACAAGTACAAATGGCATTTAACG 59.082 36.000 23.93 14.85 0.00 3.18
3502 6406 6.146216 CACAAGTACAAATGGCATTTAACGA 58.854 36.000 23.93 7.94 0.00 3.85
3503 6407 6.305399 CACAAGTACAAATGGCATTTAACGAG 59.695 38.462 23.93 20.76 0.00 4.18
3504 6408 4.981794 AGTACAAATGGCATTTAACGAGC 58.018 39.130 23.93 11.62 0.00 5.03
3505 6409 4.700213 AGTACAAATGGCATTTAACGAGCT 59.300 37.500 23.93 13.37 0.00 4.09
3517 6598 1.202973 AACGAGCTTCGCATCGATCG 61.203 55.000 9.36 9.36 45.12 3.69
3528 6609 2.412847 CGCATCGATCGCTATGTACTCA 60.413 50.000 11.09 0.00 0.00 3.41
3577 6666 0.033228 CTCCATGATCACGAGCTCCC 59.967 60.000 8.47 0.00 0.00 4.30
3578 6667 0.687427 TCCATGATCACGAGCTCCCA 60.687 55.000 8.47 0.00 0.00 4.37
3598 7685 3.383185 CCAGTCTAGCGAGAAGGAGAAAT 59.617 47.826 10.02 0.00 33.05 2.17
3631 7728 4.504858 CGGTGGCTATAGAAAGTTGAAGT 58.495 43.478 3.21 0.00 0.00 3.01
3671 7868 2.745281 GCGTGAGGCACCTATTTTTGTA 59.255 45.455 0.00 0.00 42.87 2.41
3672 7869 3.377172 GCGTGAGGCACCTATTTTTGTAT 59.623 43.478 0.00 0.00 42.87 2.29
3673 7870 4.730613 GCGTGAGGCACCTATTTTTGTATG 60.731 45.833 0.00 0.00 42.87 2.39
3674 7871 4.201910 CGTGAGGCACCTATTTTTGTATGG 60.202 45.833 0.00 0.00 0.00 2.74
3675 7872 4.705023 GTGAGGCACCTATTTTTGTATGGT 59.295 41.667 0.00 0.00 0.00 3.55
3677 7874 4.023291 AGGCACCTATTTTTGTATGGTGG 58.977 43.478 11.64 0.00 45.79 4.61
3678 7875 3.780902 GCACCTATTTTTGTATGGTGGC 58.219 45.455 11.64 1.98 45.79 5.01
3679 7876 3.194542 GCACCTATTTTTGTATGGTGGCA 59.805 43.478 11.64 0.00 45.79 4.92
3683 7880 2.008242 TTTTTGTATGGTGGCAGCCT 57.992 45.000 14.15 7.00 0.00 4.58
3721 7918 5.276868 CGTAGTAATTGCTGTATTCTGTGGC 60.277 44.000 6.28 0.00 0.00 5.01
3834 8054 1.298157 CGGGCTGAAATGAGCGAACA 61.298 55.000 0.00 0.00 40.13 3.18
3865 8087 9.472361 ACACTAAAACATGTATATACATCCGAC 57.528 33.333 22.81 0.00 44.57 4.79
3874 8096 9.208022 CATGTATATACATCCGACTCACAAAAT 57.792 33.333 22.81 0.00 44.57 1.82
3889 8111 8.237811 ACTCACAAAATGGTTAGAACATCTTT 57.762 30.769 0.00 0.00 0.00 2.52
3890 8112 9.349713 ACTCACAAAATGGTTAGAACATCTTTA 57.650 29.630 0.00 0.00 0.00 1.85
3897 8119 9.628500 AAATGGTTAGAACATCTTTATACTCCC 57.372 33.333 0.00 0.00 0.00 4.30
3898 8120 7.989947 TGGTTAGAACATCTTTATACTCCCT 57.010 36.000 0.00 0.00 0.00 4.20
3899 8121 8.388656 TGGTTAGAACATCTTTATACTCCCTT 57.611 34.615 0.00 0.00 0.00 3.95
3900 8122 8.483758 TGGTTAGAACATCTTTATACTCCCTTC 58.516 37.037 0.00 0.00 0.00 3.46
3901 8123 7.652507 GGTTAGAACATCTTTATACTCCCTTCG 59.347 40.741 0.00 0.00 0.00 3.79
3931 8153 0.661020 CAAGACGTTTTTGCGGAGGT 59.339 50.000 0.00 0.00 35.98 3.85
3932 8154 1.064952 CAAGACGTTTTTGCGGAGGTT 59.935 47.619 0.00 0.00 35.98 3.50
3941 8163 5.521544 GTTTTTGCGGAGGTTGTATTTGTA 58.478 37.500 0.00 0.00 0.00 2.41
3943 8165 5.769484 TTTGCGGAGGTTGTATTTGTAAA 57.231 34.783 0.00 0.00 0.00 2.01
3944 8166 4.752661 TGCGGAGGTTGTATTTGTAAAC 57.247 40.909 0.00 0.00 0.00 2.01
3945 8167 4.135306 TGCGGAGGTTGTATTTGTAAACA 58.865 39.130 0.00 0.00 0.00 2.83
3946 8168 4.214545 TGCGGAGGTTGTATTTGTAAACAG 59.785 41.667 0.00 0.00 0.00 3.16
3957 8179 9.974980 TTGTATTTGTAAACAGAGGGATTTTTC 57.025 29.630 0.00 0.00 0.00 2.29
3963 8185 9.594478 TTGTAAACAGAGGGATTTTTCTTTTTC 57.406 29.630 0.00 0.00 29.19 2.29
3965 8187 9.817809 GTAAACAGAGGGATTTTTCTTTTTCTT 57.182 29.630 0.00 0.00 29.19 2.52
3967 8189 9.739276 AAACAGAGGGATTTTTCTTTTTCTTTT 57.261 25.926 0.00 0.00 0.00 2.27
3968 8190 9.739276 AACAGAGGGATTTTTCTTTTTCTTTTT 57.261 25.926 0.00 0.00 0.00 1.94
3969 8191 9.166173 ACAGAGGGATTTTTCTTTTTCTTTTTG 57.834 29.630 0.00 0.00 0.00 2.44
3970 8192 9.382275 CAGAGGGATTTTTCTTTTTCTTTTTGA 57.618 29.630 0.00 0.00 0.00 2.69
3971 8193 9.605275 AGAGGGATTTTTCTTTTTCTTTTTGAG 57.395 29.630 0.00 0.00 0.00 3.02
3972 8194 9.599866 GAGGGATTTTTCTTTTTCTTTTTGAGA 57.400 29.630 0.00 0.00 0.00 3.27
3974 8196 9.988350 GGGATTTTTCTTTTTCTTTTTGAGAAC 57.012 29.630 0.00 0.00 43.90 3.01
3984 8206 9.667107 TTTTTCTTTTTGAGAACAGAGAGAGTA 57.333 29.630 0.00 0.00 43.90 2.59
3988 8210 9.482627 TCTTTTTGAGAACAGAGAGAGTATTTC 57.517 33.333 0.00 0.00 0.00 2.17
3997 8219 5.308237 ACAGAGAGAGTATTTCCCAACAACT 59.692 40.000 0.00 0.00 0.00 3.16
4020 8242 5.061179 TCTTTCTACACACCTAAAGCCAAC 58.939 41.667 0.00 0.00 0.00 3.77
4043 8265 4.636206 CGAGGCTAATTTTACCAAGAAGCT 59.364 41.667 0.00 0.00 0.00 3.74
4046 8268 7.012421 CGAGGCTAATTTTACCAAGAAGCTTAT 59.988 37.037 0.00 0.00 0.00 1.73
4049 8271 9.302345 GGCTAATTTTACCAAGAAGCTTATTTC 57.698 33.333 2.96 0.00 0.00 2.17
4087 8309 8.728088 AATAAATAAACAACAAGCAGACTTCG 57.272 30.769 0.00 0.00 32.29 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.695816 GCGAGCTCTTTCTGAAATCATCTAT 59.304 40.000 12.85 0.00 0.00 1.98
116 117 6.265196 TGTGTGCATAGAATCCTCAACTTTTT 59.735 34.615 0.00 0.00 0.00 1.94
354 2928 2.867287 TGTTCCATGTGTGCTTGTTG 57.133 45.000 0.00 0.00 0.00 3.33
482 3056 6.037610 GCAAATCTTACTCCAACATCTACCAG 59.962 42.308 0.00 0.00 0.00 4.00
535 3110 4.679373 AGGTGTTCTACATCTGCCTATG 57.321 45.455 0.00 0.00 38.32 2.23
623 3198 9.423061 GCACAAATTCTATTTCTACAAAACCAT 57.577 29.630 0.00 0.00 0.00 3.55
913 3488 6.580416 GTCAAGCTTGCTTATGAAAGAAACTC 59.420 38.462 21.99 0.00 34.37 3.01
973 3548 6.263168 GGTCACAAGCTAATGGCAATTATAGT 59.737 38.462 4.32 0.00 44.79 2.12
1287 3862 4.467084 GCCAATGTCCGAGGCCGA 62.467 66.667 0.00 0.00 42.58 5.54
1447 4022 1.418334 AACTCACAGAGGTGCTCAGT 58.582 50.000 0.00 0.00 44.87 3.41
1491 4066 3.430651 CCTCTCTGAGATTCACAGGCTTC 60.431 52.174 8.00 0.00 36.22 3.86
1704 4279 5.328565 TCAACCTCTCTCATCTTCTTCTCA 58.671 41.667 0.00 0.00 0.00 3.27
1803 4378 3.565764 TCACCATCATCATCAAGGGAC 57.434 47.619 0.00 0.00 0.00 4.46
1821 4396 6.485648 CCATGTCTTCTTTGCTATCATCATCA 59.514 38.462 0.00 0.00 0.00 3.07
1822 4397 6.709397 TCCATGTCTTCTTTGCTATCATCATC 59.291 38.462 0.00 0.00 0.00 2.92
1823 4398 6.485984 GTCCATGTCTTCTTTGCTATCATCAT 59.514 38.462 0.00 0.00 0.00 2.45
1954 4529 8.084684 CCAAGCTAGCTTAAAGAAAATGAACTT 58.915 33.333 28.87 0.00 34.50 2.66
1970 4545 4.367039 TGGTTAAAAGACCAAGCTAGCT 57.633 40.909 12.68 12.68 46.33 3.32
2018 4594 7.750903 GCCTAGTCATTTTCAAGAATAACACAC 59.249 37.037 0.00 0.00 0.00 3.82
2026 4602 8.103305 ACTATGAAGCCTAGTCATTTTCAAGAA 58.897 33.333 0.15 0.00 37.01 2.52
2035 4611 5.877012 CACAACAACTATGAAGCCTAGTCAT 59.123 40.000 0.57 0.57 39.12 3.06
2039 4615 4.002982 TGCACAACAACTATGAAGCCTAG 58.997 43.478 0.00 0.00 0.00 3.02
2041 4617 2.816087 CTGCACAACAACTATGAAGCCT 59.184 45.455 0.00 0.00 0.00 4.58
2200 4780 2.893489 CCAAACTTCTGGGGAAAAGAGG 59.107 50.000 0.00 0.00 32.32 3.69
2250 4830 8.906636 TTATTTAGTACTACAAGCGAGAACAG 57.093 34.615 0.91 0.00 0.00 3.16
2416 5004 0.249615 GCAGCAGCGATCATGTCCTA 60.250 55.000 0.00 0.00 0.00 2.94
2439 5027 3.547868 CGTTGGTCACTGATGAAGTATCG 59.452 47.826 0.00 0.00 36.83 2.92
2874 5462 3.402681 ACCAGGATCACGCCCAGG 61.403 66.667 0.00 0.00 0.00 4.45
3114 5703 9.685276 ATGTATTCTTTCACCATTCTTGTGATA 57.315 29.630 0.00 0.00 41.99 2.15
3236 5825 4.592997 TCCAGAGAGGAGACAGTGAATA 57.407 45.455 0.00 0.00 43.07 1.75
3330 5922 7.229907 TCGGTACATCAGTAAGATAAGTGCATA 59.770 37.037 0.00 0.00 34.43 3.14
3351 5943 2.761559 CGATATGGCAATGGTTCGGTA 58.238 47.619 0.00 0.00 0.00 4.02
3354 5946 1.069703 CAGCGATATGGCAATGGTTCG 60.070 52.381 12.54 0.00 34.64 3.95
3372 6276 4.392921 AGAATGGACGAGATGGTTACAG 57.607 45.455 0.00 0.00 0.00 2.74
3409 6313 9.990360 CCAAATTGGTTTGTAATACCTACTTTT 57.010 29.630 3.34 0.00 42.50 2.27
3410 6314 9.369672 TCCAAATTGGTTTGTAATACCTACTTT 57.630 29.630 12.28 0.00 42.50 2.66
3411 6315 8.799367 GTCCAAATTGGTTTGTAATACCTACTT 58.201 33.333 12.28 0.00 42.50 2.24
3413 6317 8.344446 AGTCCAAATTGGTTTGTAATACCTAC 57.656 34.615 12.28 0.00 42.50 3.18
3414 6318 9.675464 CTAGTCCAAATTGGTTTGTAATACCTA 57.325 33.333 12.28 0.00 42.50 3.08
3415 6319 7.614192 CCTAGTCCAAATTGGTTTGTAATACCT 59.386 37.037 12.28 0.00 42.50 3.08
3416 6320 7.612633 TCCTAGTCCAAATTGGTTTGTAATACC 59.387 37.037 12.28 0.00 42.50 2.73
3417 6321 8.570068 TCCTAGTCCAAATTGGTTTGTAATAC 57.430 34.615 12.28 0.01 42.50 1.89
3420 6324 7.562088 AGTTTCCTAGTCCAAATTGGTTTGTAA 59.438 33.333 12.28 0.00 42.50 2.41
3421 6325 7.064229 AGTTTCCTAGTCCAAATTGGTTTGTA 58.936 34.615 12.28 0.00 42.50 2.41
3423 6327 6.405278 AGTTTCCTAGTCCAAATTGGTTTG 57.595 37.500 12.28 3.30 43.43 2.93
3424 6328 6.382859 ACAAGTTTCCTAGTCCAAATTGGTTT 59.617 34.615 12.28 4.24 39.03 3.27
3425 6329 5.897250 ACAAGTTTCCTAGTCCAAATTGGTT 59.103 36.000 12.28 4.60 39.03 3.67
3427 6331 5.534654 TCACAAGTTTCCTAGTCCAAATTGG 59.465 40.000 5.48 5.48 39.43 3.16
3428 6332 6.633500 TCACAAGTTTCCTAGTCCAAATTG 57.367 37.500 5.08 5.08 0.00 2.32
3429 6333 6.434340 GGATCACAAGTTTCCTAGTCCAAATT 59.566 38.462 0.00 0.00 0.00 1.82
3430 6334 5.946377 GGATCACAAGTTTCCTAGTCCAAAT 59.054 40.000 0.00 0.00 0.00 2.32
3432 6336 4.349636 TGGATCACAAGTTTCCTAGTCCAA 59.650 41.667 0.00 0.00 30.86 3.53
3435 6339 6.877611 TTTTGGATCACAAGTTTCCTAGTC 57.122 37.500 0.00 0.00 40.82 2.59
3456 6360 6.320164 TGTGTGCCAAGTGTTAGACTATTTTT 59.680 34.615 0.00 0.00 33.09 1.94
3457 6361 5.825679 TGTGTGCCAAGTGTTAGACTATTTT 59.174 36.000 0.00 0.00 33.09 1.82
3458 6362 5.373222 TGTGTGCCAAGTGTTAGACTATTT 58.627 37.500 0.00 0.00 33.09 1.40
3459 6363 4.968259 TGTGTGCCAAGTGTTAGACTATT 58.032 39.130 0.00 0.00 33.09 1.73
3460 6364 4.617253 TGTGTGCCAAGTGTTAGACTAT 57.383 40.909 0.00 0.00 33.09 2.12
3461 6365 4.377021 CTTGTGTGCCAAGTGTTAGACTA 58.623 43.478 0.00 0.00 44.64 2.59
3462 6366 3.206150 CTTGTGTGCCAAGTGTTAGACT 58.794 45.455 0.00 0.00 44.64 3.24
3472 6376 2.223923 GCCATTTGTACTTGTGTGCCAA 60.224 45.455 0.00 0.00 0.00 4.52
3475 6379 2.791383 TGCCATTTGTACTTGTGTGC 57.209 45.000 0.00 0.00 0.00 4.57
3476 6380 6.129221 CGTTAAATGCCATTTGTACTTGTGTG 60.129 38.462 12.86 0.00 33.82 3.82
3477 6381 5.918011 CGTTAAATGCCATTTGTACTTGTGT 59.082 36.000 12.86 0.00 33.82 3.72
3478 6382 6.146216 TCGTTAAATGCCATTTGTACTTGTG 58.854 36.000 12.86 0.00 33.82 3.33
3480 6384 5.286082 GCTCGTTAAATGCCATTTGTACTTG 59.714 40.000 12.86 7.21 33.82 3.16
3483 6387 4.981794 AGCTCGTTAAATGCCATTTGTAC 58.018 39.130 12.86 9.43 33.82 2.90
3484 6388 5.636837 GAAGCTCGTTAAATGCCATTTGTA 58.363 37.500 12.86 0.00 33.82 2.41
3486 6390 3.543494 CGAAGCTCGTTAAATGCCATTTG 59.457 43.478 12.86 0.00 34.72 2.32
3488 6392 3.405170 CGAAGCTCGTTAAATGCCATT 57.595 42.857 0.00 0.00 34.72 3.16
3504 6408 1.691127 ACATAGCGATCGATGCGAAG 58.309 50.000 21.57 5.09 39.99 3.79
3505 6409 2.225727 AGTACATAGCGATCGATGCGAA 59.774 45.455 21.57 0.00 39.99 4.70
3517 6598 2.225068 ATGGCGTGTGAGTACATAGC 57.775 50.000 0.00 0.00 39.39 2.97
3528 6609 3.056304 GTTTGTGCATTTTATGGCGTGT 58.944 40.909 0.00 0.00 0.00 4.49
3577 6666 4.097135 TGATTTCTCCTTCTCGCTAGACTG 59.903 45.833 0.00 0.00 0.00 3.51
3578 6667 4.097286 GTGATTTCTCCTTCTCGCTAGACT 59.903 45.833 0.00 0.00 0.00 3.24
3625 7722 2.203195 ACAGCCGCTGCACTTCAA 60.203 55.556 20.56 0.00 41.13 2.69
3657 7854 3.194542 TGCCACCATACAAAAATAGGTGC 59.805 43.478 0.00 0.00 46.39 5.01
3663 7860 2.539302 AGGCTGCCACCATACAAAAAT 58.461 42.857 22.65 0.00 0.00 1.82
3664 7861 2.008242 AGGCTGCCACCATACAAAAA 57.992 45.000 22.65 0.00 0.00 1.94
3665 7862 2.224892 TGTAGGCTGCCACCATACAAAA 60.225 45.455 22.65 0.00 0.00 2.44
3666 7863 1.352687 TGTAGGCTGCCACCATACAAA 59.647 47.619 22.65 0.00 0.00 2.83
3667 7864 0.988063 TGTAGGCTGCCACCATACAA 59.012 50.000 22.65 3.16 0.00 2.41
3668 7865 0.541392 CTGTAGGCTGCCACCATACA 59.459 55.000 22.65 18.20 0.00 2.29
3671 7868 2.273449 GCTGTAGGCTGCCACCAT 59.727 61.111 22.65 1.88 38.06 3.55
3683 7880 3.391160 CTACGCGTCCGCAGCTGTA 62.391 63.158 18.63 4.94 42.06 2.74
3698 7895 5.584649 TGCCACAGAATACAGCAATTACTAC 59.415 40.000 0.00 0.00 0.00 2.73
3721 7918 5.654317 TGCACAAAAATATGTTTGCACTG 57.346 34.783 16.82 9.88 41.33 3.66
3803 8001 4.644103 TTTCAGCCCGTATGTAGTCTAC 57.356 45.455 2.81 2.81 0.00 2.59
3806 8004 4.051922 CTCATTTCAGCCCGTATGTAGTC 58.948 47.826 0.00 0.00 0.00 2.59
3862 8084 5.666969 TGTTCTAACCATTTTGTGAGTCG 57.333 39.130 0.00 0.00 0.00 4.18
3874 8096 7.989947 AGGGAGTATAAAGATGTTCTAACCA 57.010 36.000 0.00 0.00 0.00 3.67
3889 8111 6.554784 TGTATTATGGGACGAAGGGAGTATA 58.445 40.000 0.00 0.00 0.00 1.47
3890 8112 5.399991 TGTATTATGGGACGAAGGGAGTAT 58.600 41.667 0.00 0.00 0.00 2.12
3891 8113 4.806892 TGTATTATGGGACGAAGGGAGTA 58.193 43.478 0.00 0.00 0.00 2.59
3892 8114 3.649843 TGTATTATGGGACGAAGGGAGT 58.350 45.455 0.00 0.00 0.00 3.85
3893 8115 4.344102 TCTTGTATTATGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
3894 8116 4.100498 GTCTTGTATTATGGGACGAAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
3901 8123 5.798434 GCAAAAACGTCTTGTATTATGGGAC 59.202 40.000 10.89 0.00 0.00 4.46
3931 8153 9.974980 GAAAAATCCCTCTGTTTACAAATACAA 57.025 29.630 0.00 0.00 0.00 2.41
3932 8154 9.362151 AGAAAAATCCCTCTGTTTACAAATACA 57.638 29.630 0.00 0.00 0.00 2.29
3941 8163 9.739276 AAAAGAAAAAGAAAAATCCCTCTGTTT 57.261 25.926 0.00 0.00 32.82 2.83
3943 8165 9.166173 CAAAAAGAAAAAGAAAAATCCCTCTGT 57.834 29.630 0.00 0.00 0.00 3.41
3944 8166 9.382275 TCAAAAAGAAAAAGAAAAATCCCTCTG 57.618 29.630 0.00 0.00 0.00 3.35
3945 8167 9.605275 CTCAAAAAGAAAAAGAAAAATCCCTCT 57.395 29.630 0.00 0.00 0.00 3.69
3946 8168 9.599866 TCTCAAAAAGAAAAAGAAAAATCCCTC 57.400 29.630 0.00 0.00 0.00 4.30
3957 8179 8.672815 ACTCTCTCTGTTCTCAAAAAGAAAAAG 58.327 33.333 0.00 0.00 45.50 2.27
3963 8185 8.716909 GGAAATACTCTCTCTGTTCTCAAAAAG 58.283 37.037 0.00 0.00 0.00 2.27
3965 8187 7.162082 GGGAAATACTCTCTCTGTTCTCAAAA 58.838 38.462 0.00 0.00 0.00 2.44
3966 8188 6.270000 TGGGAAATACTCTCTCTGTTCTCAAA 59.730 38.462 0.00 0.00 0.00 2.69
3967 8189 5.780282 TGGGAAATACTCTCTCTGTTCTCAA 59.220 40.000 0.00 0.00 0.00 3.02
3968 8190 5.333581 TGGGAAATACTCTCTCTGTTCTCA 58.666 41.667 0.00 0.00 0.00 3.27
3969 8191 5.923733 TGGGAAATACTCTCTCTGTTCTC 57.076 43.478 0.00 0.00 0.00 2.87
3970 8192 5.544176 TGTTGGGAAATACTCTCTCTGTTCT 59.456 40.000 0.00 0.00 0.00 3.01
3971 8193 5.794894 TGTTGGGAAATACTCTCTCTGTTC 58.205 41.667 0.00 0.00 0.00 3.18
3972 8194 5.825593 TGTTGGGAAATACTCTCTCTGTT 57.174 39.130 0.00 0.00 0.00 3.16
3974 8196 5.799213 AGTTGTTGGGAAATACTCTCTCTG 58.201 41.667 0.00 0.00 0.00 3.35
3975 8197 5.782845 AGAGTTGTTGGGAAATACTCTCTCT 59.217 40.000 0.00 0.00 41.08 3.10
3977 8199 6.441088 AAGAGTTGTTGGGAAATACTCTCT 57.559 37.500 0.00 0.00 43.39 3.10
3978 8200 6.937465 AGAAAGAGTTGTTGGGAAATACTCTC 59.063 38.462 0.00 0.00 43.39 3.20
3979 8201 6.842676 AGAAAGAGTTGTTGGGAAATACTCT 58.157 36.000 0.00 0.00 45.42 3.24
3984 8206 6.039382 GTGTGTAGAAAGAGTTGTTGGGAAAT 59.961 38.462 0.00 0.00 0.00 2.17
3988 8210 3.564225 GGTGTGTAGAAAGAGTTGTTGGG 59.436 47.826 0.00 0.00 0.00 4.12
3997 8219 4.967084 TGGCTTTAGGTGTGTAGAAAGA 57.033 40.909 0.00 0.00 31.83 2.52
4020 8242 4.636206 AGCTTCTTGGTAAAATTAGCCTCG 59.364 41.667 0.00 0.00 0.00 4.63
4061 8283 9.180678 CGAAGTCTGCTTGTTGTTTATTTATTT 57.819 29.630 0.00 0.00 34.61 1.40


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

AutoCloner maintained by Alex Coulton.