Multiple sequence alignment - TraesCS4B01G052800

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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 TraesCS4B01G052800 chr4B 100.000 4631 0 0 1 4631 41704854 41700224 0.000000e+00 8552.0
1 TraesCS4B01G052800 chr4B 97.143 35 1 0 4149 4183 664320999 664320965 5.000000e-05 60.2
2 TraesCS4B01G052800 chr4A 89.458 2950 137 68 1 2823 574388380 574391282 0.000000e+00 3565.0
3 TraesCS4B01G052800 chr4A 95.786 1139 44 2 3006 4144 574391604 574392738 0.000000e+00 1834.0
4 TraesCS4B01G052800 chr4A 85.992 514 34 21 4149 4630 574392772 574393279 2.470000e-142 516.0
5 TraesCS4B01G052800 chr4A 97.222 36 1 0 4148 4183 424369480 424369515 1.390000e-05 62.1
6 TraesCS4B01G052800 chr4D 94.789 2111 68 13 2057 4144 29171394 29169303 0.000000e+00 3251.0
7 TraesCS4B01G052800 chr4D 91.995 1699 73 29 366 2020 29173070 29171391 0.000000e+00 2326.0
8 TraesCS4B01G052800 chr4D 83.790 438 40 19 4221 4630 29169204 29168770 2.020000e-103 387.0
9 TraesCS4B01G052800 chr4D 89.963 269 9 6 127 377 29173619 29173351 9.600000e-87 331.0
10 TraesCS4B01G052800 chr4D 80.405 296 48 5 3467 3759 373830362 373830074 2.810000e-52 217.0
11 TraesCS4B01G052800 chr4D 85.714 119 14 3 4515 4630 497544211 497544093 6.290000e-24 122.0
12 TraesCS4B01G052800 chr4D 97.143 35 1 0 4149 4183 506898075 506898109 5.000000e-05 60.2
13 TraesCS4B01G052800 chr4D 100.000 29 0 0 4145 4173 460479137 460479165 2.000000e-03 54.7
14 TraesCS4B01G052800 chr2A 93.182 44 2 1 4148 4191 739473100 739473142 3.870000e-06 63.9
15 TraesCS4B01G052800 chr5A 97.222 36 1 0 4148 4183 450169032 450168997 1.390000e-05 62.1
16 TraesCS4B01G052800 chr5A 97.143 35 1 0 4149 4183 703349465 703349499 5.000000e-05 60.2
17 TraesCS4B01G052800 chr5B 97.059 34 1 0 4150 4183 328245585 328245552 1.800000e-04 58.4


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 TraesCS4B01G052800 chr4B 41700224 41704854 4630 True 8552.000000 8552 100.00000 1 4631 1 chr4B.!!$R1 4630
1 TraesCS4B01G052800 chr4A 574388380 574393279 4899 False 1971.666667 3565 90.41200 1 4630 3 chr4A.!!$F2 4629
2 TraesCS4B01G052800 chr4D 29168770 29173619 4849 True 1573.750000 3251 90.13425 127 4630 4 chr4D.!!$R3 4503

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
743 1105 0.519077 CAACTTCTTCCTCGGCAAGC 59.481 55.0 0.00 0.0 0.00 4.01 F
1006 1411 0.033011 ACTCCCTCTAGCCATGTCGT 60.033 55.0 0.00 0.0 0.00 4.34 F
2544 2974 0.179048 CACCAGGTGAGAACTGTGCA 60.179 55.0 15.35 0.0 35.23 4.57 F
3245 3875 0.179067 TCGACGGGCTGAAAACACTT 60.179 50.0 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 2143 0.542702 ACCCAGAATTGTGCAAGGGG 60.543 55.000 10.46 10.37 40.64 4.79 R
2950 3414 0.178903 TACAGTGAGGACCAAGGGCT 60.179 55.000 0.00 0.00 0.00 5.19 R
3569 4217 1.067821 CTGGAACCGAGTGATAGAGGC 59.932 57.143 0.00 0.00 0.00 4.70 R
4607 5352 0.178068 GTCGGATGTATGTGGGCAGT 59.822 55.000 0.00 0.00 0.00 4.40 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
24 25 2.752903 ACGGGTTCAAGGACAATTATGC 59.247 45.455 0.00 0.00 0.00 3.14
26 27 3.192422 CGGGTTCAAGGACAATTATGCAA 59.808 43.478 0.00 0.00 0.00 4.08
43 44 7.637631 TTATGCAAGTGGCTTGATGTATAAA 57.362 32.000 12.45 0.00 43.42 1.40
54 55 6.208644 GCTTGATGTATAAAAATGGACGCAT 58.791 36.000 0.00 0.00 0.00 4.73
56 57 5.984627 TGATGTATAAAAATGGACGCATCG 58.015 37.500 0.00 0.00 35.57 3.84
59 60 5.984627 TGTATAAAAATGGACGCATCGATG 58.015 37.500 21.27 21.27 0.00 3.84
100 111 5.094429 TGTGTGATATAATTGATGCACGC 57.906 39.130 0.00 0.00 36.23 5.34
101 112 4.574013 TGTGTGATATAATTGATGCACGCA 59.426 37.500 12.44 12.44 39.90 5.24
102 113 5.239087 TGTGTGATATAATTGATGCACGCAT 59.761 36.000 3.71 3.71 38.57 4.73
104 115 7.119553 TGTGTGATATAATTGATGCACGCATAT 59.880 33.333 4.13 0.00 38.57 1.78
106 117 7.119553 TGTGATATAATTGATGCACGCATATGT 59.880 33.333 4.13 0.00 36.70 2.29
174 187 0.528470 GGGTCGACCTCAGTGAGAAG 59.472 60.000 32.52 11.72 35.85 2.85
185 220 2.064762 CAGTGAGAAGCTTCCAACTCG 58.935 52.381 22.81 15.28 32.81 4.18
219 255 0.960286 GTCTACGGATCAGGTAGCCC 59.040 60.000 14.95 7.29 37.79 5.19
297 349 3.647636 TCCAAATTCCCAAGTCCAAACA 58.352 40.909 0.00 0.00 0.00 2.83
358 410 4.248842 CTGTCGCCACACCACCCA 62.249 66.667 0.00 0.00 0.00 4.51
520 866 4.377760 TCGCCCTCCTCCGTCCTT 62.378 66.667 0.00 0.00 0.00 3.36
524 870 4.194720 CCTCCTCCGTCCTTCGCG 62.195 72.222 0.00 0.00 38.35 5.87
621 967 4.459089 GCCTGACCTGCCGGAGAC 62.459 72.222 5.05 0.00 0.00 3.36
622 968 3.775654 CCTGACCTGCCGGAGACC 61.776 72.222 5.05 0.00 0.00 3.85
638 991 1.990060 ACCGGAGTCATGGTCAGGG 60.990 63.158 9.46 10.22 33.88 4.45
669 1028 3.582164 GGGGAACAGGAGAGTATCATCT 58.418 50.000 0.00 0.00 37.82 2.90
679 1038 2.355837 TATCATCTTCGCCGGCGC 60.356 61.111 42.78 9.12 39.59 6.53
724 1086 3.673484 TCGTCGACGGGGTCAACC 61.673 66.667 35.05 0.00 40.29 3.77
725 1087 3.980989 CGTCGACGGGGTCAACCA 61.981 66.667 29.70 0.00 42.91 3.67
726 1088 2.422591 GTCGACGGGGTCAACCAA 59.577 61.111 0.00 0.00 42.91 3.67
727 1089 1.957695 GTCGACGGGGTCAACCAAC 60.958 63.158 0.00 0.00 42.91 3.77
728 1090 2.135581 TCGACGGGGTCAACCAACT 61.136 57.895 0.89 0.00 42.91 3.16
729 1091 1.227734 CGACGGGGTCAACCAACTT 60.228 57.895 0.89 0.00 42.91 2.66
743 1105 0.519077 CAACTTCTTCCTCGGCAAGC 59.481 55.000 0.00 0.00 0.00 4.01
843 1206 4.796495 GTTGGATTCGCCGCCCCT 62.796 66.667 0.00 0.00 40.66 4.79
878 1246 1.679680 GGGAGCTTATTTAAACGCCCC 59.320 52.381 4.56 9.17 35.97 5.80
989 1376 4.552365 CCCCGCGCATGATCCACT 62.552 66.667 8.75 0.00 0.00 4.00
990 1377 2.969238 CCCGCGCATGATCCACTC 60.969 66.667 8.75 0.00 0.00 3.51
1003 1408 0.339859 TCCACTCCCTCTAGCCATGT 59.660 55.000 0.00 0.00 0.00 3.21
1006 1411 0.033011 ACTCCCTCTAGCCATGTCGT 60.033 55.000 0.00 0.00 0.00 4.34
1485 1911 2.933834 ACCACCCCGGGGAAGAAG 60.934 66.667 46.68 28.16 40.22 2.85
1594 2020 3.700970 TCGAGGCCATCAACCGCA 61.701 61.111 5.01 0.00 0.00 5.69
1595 2021 3.197790 CGAGGCCATCAACCGCAG 61.198 66.667 5.01 0.00 0.00 5.18
1680 2106 3.385384 CAGCTGCGACCAGGAGGA 61.385 66.667 0.00 0.00 39.54 3.71
1714 2143 2.198304 ATCTTCACCCGCACCCTTCC 62.198 60.000 0.00 0.00 0.00 3.46
1762 2191 6.096001 CCTGAATAAATTGGAGTGCTTAAGCT 59.904 38.462 26.90 9.03 42.66 3.74
1790 2219 7.293073 AGGCTATGGATTATTTCTGACAATGT 58.707 34.615 0.00 0.00 0.00 2.71
1791 2220 7.446625 AGGCTATGGATTATTTCTGACAATGTC 59.553 37.037 6.41 6.41 0.00 3.06
1829 2258 6.183360 GCTAAGCTGTTTACACCACTTCTATG 60.183 42.308 0.00 0.00 0.00 2.23
1867 2296 7.599998 GGATTGTTTGCTCAAATAGAACAATGT 59.400 33.333 15.04 0.00 32.74 2.71
1924 2353 7.745717 AGCCCAGTAATTATTGCTGATTACTA 58.254 34.615 21.48 0.00 43.56 1.82
2029 2458 6.558014 AGTCTGATGATAATTGGATCCTCTGT 59.442 38.462 14.23 0.00 0.00 3.41
2043 2472 2.359214 TCCTCTGTTGATAGCTACTGCG 59.641 50.000 0.00 0.00 45.42 5.18
2061 2490 3.994392 CTGCGGTAGTAGTTGACATTGTT 59.006 43.478 0.00 0.00 0.00 2.83
2067 2496 8.112449 GCGGTAGTAGTTGACATTGTTAAATAC 58.888 37.037 18.60 18.60 34.46 1.89
2484 2914 4.394712 CTCACCGACCTGCCCCAC 62.395 72.222 0.00 0.00 0.00 4.61
2544 2974 0.179048 CACCAGGTGAGAACTGTGCA 60.179 55.000 15.35 0.00 35.23 4.57
2610 3040 7.951347 AGATGGAACTATGCATTTTCTCTTT 57.049 32.000 3.54 0.00 37.78 2.52
2629 3059 4.688879 TCTTTAGATACAAACGCCACACTG 59.311 41.667 0.00 0.00 0.00 3.66
2718 3155 8.442632 TCCAATTGTTCATCTGATATCTTGAC 57.557 34.615 4.43 1.94 0.00 3.18
2753 3190 6.582636 AGGTAGCATCTGATATTTCAAACGA 58.417 36.000 0.00 0.00 0.00 3.85
2778 3215 5.590145 TGATGCGAAAATACATGGGATTTG 58.410 37.500 8.20 0.51 0.00 2.32
2785 3222 7.491048 GCGAAAATACATGGGATTTGTAATGTT 59.509 33.333 8.20 0.00 35.07 2.71
2814 3251 7.651808 GCATAATATTGTGCACTAATTCCTGT 58.348 34.615 26.63 0.00 43.66 4.00
2815 3252 8.783093 GCATAATATTGTGCACTAATTCCTGTA 58.217 33.333 26.63 0.00 43.66 2.74
2821 3258 8.807948 ATTGTGCACTAATTCCTGTATTAACT 57.192 30.769 19.41 0.00 0.00 2.24
2822 3259 8.630054 TTGTGCACTAATTCCTGTATTAACTT 57.370 30.769 19.41 0.00 0.00 2.66
2823 3260 8.630054 TGTGCACTAATTCCTGTATTAACTTT 57.370 30.769 19.41 0.00 0.00 2.66
2824 3261 9.073475 TGTGCACTAATTCCTGTATTAACTTTT 57.927 29.630 19.41 0.00 0.00 2.27
2825 3262 9.908152 GTGCACTAATTCCTGTATTAACTTTTT 57.092 29.630 10.32 0.00 0.00 1.94
2856 3319 9.120538 GGAATTCCTGTATTAACTTGATGCTAA 57.879 33.333 17.73 0.00 0.00 3.09
2915 3379 4.463186 ACGCTACTTTAGAGGTTGATCACT 59.537 41.667 0.00 0.00 0.00 3.41
2965 3429 1.003233 GTCAGCCCTTGGTCCTCAC 60.003 63.158 0.00 0.00 0.00 3.51
2973 3437 2.028020 CCCTTGGTCCTCACTGTAGAAC 60.028 54.545 0.00 0.00 0.00 3.01
2974 3438 2.632996 CCTTGGTCCTCACTGTAGAACA 59.367 50.000 0.00 0.00 0.00 3.18
3029 3657 0.670162 CCCATGTTCAATCATCCCGC 59.330 55.000 0.00 0.00 0.00 6.13
3109 3737 1.527034 TTCAGTTTAGCTGCTGCCTG 58.473 50.000 13.43 14.35 44.66 4.85
3138 3766 4.986659 CCTGTAGTAGTTTAACGTGTGCTT 59.013 41.667 0.00 0.00 0.00 3.91
3238 3868 1.003839 AAGCAATCGACGGGCTGAA 60.004 52.632 0.00 0.00 38.04 3.02
3245 3875 0.179067 TCGACGGGCTGAAAACACTT 60.179 50.000 0.00 0.00 0.00 3.16
3394 4029 7.829211 ACTTAGACAATCTTAAATGCCAAGCTA 59.171 33.333 0.00 0.00 0.00 3.32
3443 4078 3.071874 TCTTCACACATGTCCCATTCC 57.928 47.619 0.00 0.00 0.00 3.01
3465 4113 1.225855 GAGCGACCATTGTGTTGTGA 58.774 50.000 0.00 0.00 0.00 3.58
3526 4174 3.365265 CTTTGCACCACCTCCCGC 61.365 66.667 0.00 0.00 0.00 6.13
3534 4182 2.666190 CACCTCCCGCGCATATGG 60.666 66.667 8.75 6.58 0.00 2.74
3540 4188 2.591429 CCGCGCATATGGCTTGGA 60.591 61.111 8.75 0.00 41.67 3.53
3569 4217 3.244215 TGCTTACTGTTTCTGACCTCTGG 60.244 47.826 0.00 0.00 0.00 3.86
3584 4232 0.259065 TCTGGCCTCTATCACTCGGT 59.741 55.000 3.32 0.00 0.00 4.69
3655 4303 0.824759 ACGGGTAGGATCAGACAAGC 59.175 55.000 0.00 0.00 0.00 4.01
3878 4526 2.877335 AGGAGACGACGCTATTTGTTC 58.123 47.619 0.00 0.00 0.00 3.18
3912 4560 8.856490 TGAAACTTCAGAGAAATTAAACAAGC 57.144 30.769 0.00 0.00 32.50 4.01
3916 4564 5.034554 TCAGAGAAATTAAACAAGCGCTG 57.965 39.130 12.58 8.13 0.00 5.18
3950 4598 5.067283 AGGAACAAAATACGTTGAAAGTGCT 59.933 36.000 0.00 0.00 32.59 4.40
3951 4599 5.173131 GGAACAAAATACGTTGAAAGTGCTG 59.827 40.000 0.00 0.00 32.59 4.41
3952 4600 4.041723 ACAAAATACGTTGAAAGTGCTGC 58.958 39.130 0.00 0.00 32.59 5.25
4036 4684 1.171308 TGCTTTCTTCAGCAGCATCC 58.829 50.000 0.00 0.00 45.14 3.51
4063 4711 6.438741 TCTCACTTCCAGATTGAGTATTCTGT 59.561 38.462 0.00 0.00 38.12 3.41
4071 4719 8.041323 TCCAGATTGAGTATTCTGTTACCTTTC 58.959 37.037 0.00 0.00 38.12 2.62
4097 4745 7.014422 CGAGAGTAGGAAATCCCATTTAGTAGT 59.986 40.741 0.00 0.00 37.41 2.73
4144 4792 1.827969 TCAGAAAGCTACTCCCTCTGC 59.172 52.381 0.00 0.00 34.73 4.26
4145 4793 1.134551 CAGAAAGCTACTCCCTCTGCC 60.135 57.143 0.00 0.00 0.00 4.85
4146 4794 0.179097 GAAAGCTACTCCCTCTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
4147 4795 0.905337 AAAGCTACTCCCTCTGCCGT 60.905 55.000 0.00 0.00 0.00 5.68
4164 4870 4.751060 TGCCGTTAGTGATCTAAACGATT 58.249 39.130 21.34 0.00 37.81 3.34
4207 4913 9.378551 AGTACAATATATGCGTACATAATTGGG 57.621 33.333 20.00 0.00 41.99 4.12
4208 4914 7.083875 ACAATATATGCGTACATAATTGGGC 57.916 36.000 16.35 0.00 41.99 5.36
4209 4915 6.094881 ACAATATATGCGTACATAATTGGGCC 59.905 38.462 0.00 0.00 41.99 5.80
4210 4916 2.656947 ATGCGTACATAATTGGGCCT 57.343 45.000 4.53 0.00 33.67 5.19
4261 4967 8.421249 AAGCATCTATAGCTCTAGAATGAGTT 57.579 34.615 12.36 6.77 42.53 3.01
4332 5038 4.283722 ACAGGGACTTAGACTTCACGAATT 59.716 41.667 0.00 0.00 34.60 2.17
4333 5039 5.479375 ACAGGGACTTAGACTTCACGAATTA 59.521 40.000 0.00 0.00 34.60 1.40
4374 5080 3.869832 CAGCACATACAGAAGACTCATGG 59.130 47.826 0.00 0.00 0.00 3.66
4381 5087 3.759581 ACAGAAGACTCATGGTTGCATT 58.240 40.909 0.00 0.00 0.00 3.56
4382 5088 3.504906 ACAGAAGACTCATGGTTGCATTG 59.495 43.478 0.00 0.00 0.00 2.82
4383 5089 3.754850 CAGAAGACTCATGGTTGCATTGA 59.245 43.478 0.00 0.00 0.00 2.57
4384 5090 4.216902 CAGAAGACTCATGGTTGCATTGAA 59.783 41.667 0.00 0.00 0.00 2.69
4385 5091 4.217118 AGAAGACTCATGGTTGCATTGAAC 59.783 41.667 0.00 0.00 0.00 3.18
4386 5092 3.489355 AGACTCATGGTTGCATTGAACA 58.511 40.909 0.00 0.00 0.00 3.18
4387 5093 3.504906 AGACTCATGGTTGCATTGAACAG 59.495 43.478 0.00 0.00 0.00 3.16
4389 5095 3.254166 ACTCATGGTTGCATTGAACAGAC 59.746 43.478 0.00 0.00 0.00 3.51
4390 5096 3.489355 TCATGGTTGCATTGAACAGACT 58.511 40.909 0.00 0.00 0.00 3.24
4392 5098 3.213206 TGGTTGCATTGAACAGACTCT 57.787 42.857 0.00 0.00 0.00 3.24
4420 5149 0.727398 GATACACTGCAGAAACGGCC 59.273 55.000 23.35 0.00 0.00 6.13
4431 5160 1.279271 AGAAACGGCCAGTCTAGCAAT 59.721 47.619 2.24 0.00 0.00 3.56
4432 5161 2.500098 AGAAACGGCCAGTCTAGCAATA 59.500 45.455 2.24 0.00 0.00 1.90
4542 5283 1.068434 CAACCTGACCCGCAAATTTGT 59.932 47.619 19.03 0.00 0.00 2.83
4565 5307 2.680352 ATCCGTCCGCAGACAGGT 60.680 61.111 0.20 0.00 43.73 4.00
4588 5331 2.037772 GACCACTCCACAGACACTGATT 59.962 50.000 5.76 0.00 35.18 2.57
4590 5333 2.301296 CCACTCCACAGACACTGATTCT 59.699 50.000 5.76 0.00 35.18 2.40
4596 5340 1.277557 ACAGACACTGATTCTGAGGCC 59.722 52.381 14.36 0.00 42.81 5.19
4600 5345 2.587194 CTGATTCTGAGGCCGCCG 60.587 66.667 3.22 0.00 0.00 6.46
4630 5375 1.054406 CCCACATACATCCGACCCCT 61.054 60.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.181500 GCATAATTGTCCTTGAACCCGTC 60.181 47.826 0.00 0.00 0.00 4.79
9 10 3.193267 GCCACTTGCATAATTGTCCTTGA 59.807 43.478 0.00 0.00 40.77 3.02
14 15 4.439305 TCAAGCCACTTGCATAATTGTC 57.561 40.909 2.41 0.00 44.83 3.18
24 25 7.489113 GTCCATTTTTATACATCAAGCCACTTG 59.511 37.037 0.81 0.81 42.25 3.16
26 27 6.183360 CGTCCATTTTTATACATCAAGCCACT 60.183 38.462 0.00 0.00 0.00 4.00
134 145 5.221864 ACCCTCGAACCTCTTGTAATTCTTT 60.222 40.000 0.00 0.00 0.00 2.52
141 152 1.171308 CGACCCTCGAACCTCTTGTA 58.829 55.000 0.00 0.00 43.74 2.41
174 187 3.190953 ACTGTACTCTACGAGTTGGAAGC 59.809 47.826 1.45 0.00 40.28 3.86
185 220 2.030213 CGTAGACCGCACTGTACTCTAC 59.970 54.545 6.26 6.26 33.06 2.59
195 230 1.065928 CCTGATCCGTAGACCGCAC 59.934 63.158 0.00 0.00 34.38 5.34
354 406 0.968393 AAAACGTTGCAGGTGTGGGT 60.968 50.000 0.00 0.00 0.00 4.51
357 409 0.098025 ACGAAAACGTTGCAGGTGTG 59.902 50.000 0.00 0.00 0.00 3.82
358 410 0.806241 AACGAAAACGTTGCAGGTGT 59.194 45.000 0.00 0.00 0.00 4.16
461 807 0.608308 GGGGTGGGTAGTTGTTGAGC 60.608 60.000 0.00 0.00 0.00 4.26
604 950 4.459089 GTCTCCGGCAGGTCAGGC 62.459 72.222 1.81 0.00 39.05 4.85
620 966 1.990060 CCCTGACCATGACTCCGGT 60.990 63.158 0.00 0.00 38.56 5.28
621 967 2.903357 CCCTGACCATGACTCCGG 59.097 66.667 0.00 0.00 0.00 5.14
622 968 2.187946 GCCCTGACCATGACTCCG 59.812 66.667 0.00 0.00 0.00 4.63
623 969 2.187946 CGCCCTGACCATGACTCC 59.812 66.667 0.00 0.00 0.00 3.85
624 970 2.187946 CCGCCCTGACCATGACTC 59.812 66.667 0.00 0.00 0.00 3.36
625 971 4.101448 GCCGCCCTGACCATGACT 62.101 66.667 0.00 0.00 0.00 3.41
724 1086 0.519077 GCTTGCCGAGGAAGAAGTTG 59.481 55.000 8.85 0.00 0.00 3.16
725 1087 0.606673 GGCTTGCCGAGGAAGAAGTT 60.607 55.000 8.85 0.00 0.00 2.66
726 1088 1.003233 GGCTTGCCGAGGAAGAAGT 60.003 57.895 8.85 0.00 0.00 3.01
727 1089 1.003355 TGGCTTGCCGAGGAAGAAG 60.003 57.895 7.18 0.00 0.00 2.85
728 1090 1.003355 CTGGCTTGCCGAGGAAGAA 60.003 57.895 7.18 0.00 0.00 2.52
729 1091 2.665000 CTGGCTTGCCGAGGAAGA 59.335 61.111 7.18 0.00 0.00 2.87
893 1261 1.404391 CGGTTATCGTCCACTGTAGCT 59.596 52.381 0.00 0.00 0.00 3.32
989 1376 1.101635 CGACGACATGGCTAGAGGGA 61.102 60.000 0.00 0.00 0.00 4.20
990 1377 1.360551 CGACGACATGGCTAGAGGG 59.639 63.158 0.00 0.00 0.00 4.30
1304 1730 1.517832 GTCTCCAGGACCATCACGG 59.482 63.158 0.00 0.00 38.93 4.94
1680 2106 5.221661 GGGTGAAGATCTTACAATATCGGGT 60.222 44.000 8.25 0.00 0.00 5.28
1714 2143 0.542702 ACCCAGAATTGTGCAAGGGG 60.543 55.000 10.46 10.37 40.64 4.79
1762 2191 9.866655 ATTGTCAGAAATAATCCATAGCCTAAA 57.133 29.630 0.00 0.00 0.00 1.85
1829 2258 3.364864 GCAAACAATCCCAAAATTTCGCC 60.365 43.478 0.00 0.00 0.00 5.54
1867 2296 2.824689 ATTGGCCACACATCCACATA 57.175 45.000 3.88 0.00 30.97 2.29
1924 2353 1.526917 GGTGCAAGACCTGTGCTGT 60.527 57.895 0.00 0.00 42.25 4.40
2043 2472 8.598075 CGGTATTTAACAATGTCAACTACTACC 58.402 37.037 0.00 0.00 0.00 3.18
2061 2490 9.649316 AGGGAAATGAAAATAATCCGGTATTTA 57.351 29.630 9.73 4.16 33.50 1.40
2067 2496 5.852282 ACAGGGAAATGAAAATAATCCGG 57.148 39.130 0.00 0.00 0.00 5.14
2288 2718 1.533129 CGTTATCATCTGCCACGACGA 60.533 52.381 0.00 0.00 32.51 4.20
2541 2971 5.730550 CAGAGTACTACTAAAATGGGTGCA 58.269 41.667 0.00 0.00 0.00 4.57
2542 2972 4.571176 GCAGAGTACTACTAAAATGGGTGC 59.429 45.833 0.00 0.00 0.00 5.01
2544 2974 5.623824 CGTGCAGAGTACTACTAAAATGGGT 60.624 44.000 0.00 0.00 0.00 4.51
2610 3040 2.300723 ACCAGTGTGGCGTTTGTATCTA 59.699 45.455 0.00 0.00 42.67 1.98
2718 3155 4.519350 TCAGATGCTACCTATACACCGAAG 59.481 45.833 0.00 0.00 0.00 3.79
2753 3190 6.409524 AATCCCATGTATTTTCGCATCAAT 57.590 33.333 0.00 0.00 0.00 2.57
2796 3233 8.807948 AGTTAATACAGGAATTAGTGCACAAT 57.192 30.769 21.04 13.47 0.00 2.71
2824 3261 9.148879 TCAAGTTAATACAGGAATTCCCAAAAA 57.851 29.630 21.22 5.76 37.41 1.94
2825 3262 8.713708 TCAAGTTAATACAGGAATTCCCAAAA 57.286 30.769 21.22 4.92 37.41 2.44
2826 3263 8.748412 CATCAAGTTAATACAGGAATTCCCAAA 58.252 33.333 21.22 6.79 37.41 3.28
2827 3264 7.147915 GCATCAAGTTAATACAGGAATTCCCAA 60.148 37.037 21.22 7.16 37.41 4.12
2828 3265 6.321181 GCATCAAGTTAATACAGGAATTCCCA 59.679 38.462 21.22 7.17 37.41 4.37
2829 3266 6.547510 AGCATCAAGTTAATACAGGAATTCCC 59.452 38.462 21.22 2.94 36.42 3.97
2830 3267 7.573968 AGCATCAAGTTAATACAGGAATTCC 57.426 36.000 17.31 17.31 0.00 3.01
2898 3361 3.849911 TGCGAGTGATCAACCTCTAAAG 58.150 45.455 10.61 0.00 0.00 1.85
2915 3379 7.278868 ACCAACTAAATTCAAAAACAAATGCGA 59.721 29.630 0.00 0.00 0.00 5.10
2950 3414 0.178903 TACAGTGAGGACCAAGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
2973 3437 2.159382 ACTTGGTTGCGGGTAGATTTG 58.841 47.619 0.00 0.00 0.00 2.32
2974 3438 2.579410 ACTTGGTTGCGGGTAGATTT 57.421 45.000 0.00 0.00 0.00 2.17
2985 3449 9.244799 GGAAAACTGAAATACTTAACTTGGTTG 57.755 33.333 0.00 0.00 0.00 3.77
3029 3657 7.615582 ACACAACACATATCAAAGTATCAGG 57.384 36.000 0.00 0.00 0.00 3.86
3109 3737 4.171754 CGTTAAACTACTACAGGTCCAGC 58.828 47.826 0.00 0.00 0.00 4.85
3116 3744 7.807687 ATAAGCACACGTTAAACTACTACAG 57.192 36.000 0.00 0.00 0.00 2.74
3138 3766 7.467650 TGGCTAGCTAGATACCTTTGACTATA 58.532 38.462 25.15 0.00 0.00 1.31
3245 3875 4.811969 ACTGGGTGTCATTTCATACGTA 57.188 40.909 0.00 0.00 0.00 3.57
3411 4046 9.378551 GGACATGTGTGAAGATAACATAAGTAA 57.621 33.333 1.15 0.00 33.31 2.24
3443 4078 1.536766 ACAACACAATGGTCGCTCATG 59.463 47.619 0.00 0.00 0.00 3.07
3499 4147 3.118038 AGGTGGTGCAAAGAAGAACACTA 60.118 43.478 0.00 0.00 33.53 2.74
3534 4182 6.442513 AACAGTAAGCAAGATAATCCAAGC 57.557 37.500 0.00 0.00 0.00 4.01
3540 4188 7.398024 AGGTCAGAAACAGTAAGCAAGATAAT 58.602 34.615 0.00 0.00 0.00 1.28
3569 4217 1.067821 CTGGAACCGAGTGATAGAGGC 59.932 57.143 0.00 0.00 0.00 4.70
3584 4232 1.918293 AGTCGGTCATGCCCTGGAA 60.918 57.895 0.00 0.00 0.00 3.53
3916 4564 3.942130 ATTTTGTTCCTACAAGCCAGC 57.058 42.857 0.00 0.00 44.56 4.85
3950 4598 5.826643 ACCAGGAAAAATCAACTATAGGCA 58.173 37.500 4.43 0.00 0.00 4.75
3951 4599 6.775594 AACCAGGAAAAATCAACTATAGGC 57.224 37.500 4.43 0.00 0.00 3.93
4036 4684 7.492020 CAGAATACTCAATCTGGAAGTGAGAAG 59.508 40.741 16.39 0.00 41.08 2.85
4063 4711 5.128335 GGGATTTCCTACTCTCGAAAGGTAA 59.872 44.000 0.00 0.00 35.95 2.85
4071 4719 6.163135 ACTAAATGGGATTTCCTACTCTCG 57.837 41.667 0.00 0.00 36.20 4.04
4097 4745 1.453015 ACAGCCTGCAACGTTTCCA 60.453 52.632 0.00 0.00 0.00 3.53
4195 4901 4.765339 GGGTCATAAGGCCCAATTATGTAC 59.235 45.833 18.00 14.87 44.23 2.90
4206 4912 2.507407 TCTTGTTGGGTCATAAGGCC 57.493 50.000 0.00 0.00 0.00 5.19
4207 4913 6.524101 TTTATTCTTGTTGGGTCATAAGGC 57.476 37.500 0.00 0.00 0.00 4.35
4261 4967 8.955388 TGCACTGCTAAAATAGAATTGTGATTA 58.045 29.630 1.98 0.00 0.00 1.75
4346 5052 6.042638 AGTCTTCTGTATGTGCTGTGTATT 57.957 37.500 0.00 0.00 0.00 1.89
4351 5057 4.502016 CATGAGTCTTCTGTATGTGCTGT 58.498 43.478 0.00 0.00 0.00 4.40
4374 5080 4.320057 CCTTCAGAGTCTGTTCAATGCAAC 60.320 45.833 19.53 0.00 32.61 4.17
4381 5087 3.566351 TCTGTCCTTCAGAGTCTGTTCA 58.434 45.455 19.53 11.20 46.77 3.18
4392 5098 3.165071 TCTGCAGTGTATCTGTCCTTCA 58.835 45.455 14.67 0.00 45.23 3.02
4420 5149 7.081526 AGATTGCAAAGTTATTGCTAGACTG 57.918 36.000 1.71 0.00 45.13 3.51
4498 5238 7.003482 TGGAGATGCCATAATGTAGCAATAAA 58.997 34.615 0.00 0.00 43.33 1.40
4526 5266 1.665735 CCGAACAAATTTGCGGGTCAG 60.666 52.381 22.37 10.62 40.08 3.51
4578 5321 0.534412 CGGCCTCAGAATCAGTGTCT 59.466 55.000 0.00 0.00 0.00 3.41
4600 5345 1.165270 GTATGTGGGCAGTGTTGGAC 58.835 55.000 0.00 0.00 0.00 4.02
4607 5352 0.178068 GTCGGATGTATGTGGGCAGT 59.822 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.