Multiple sequence alignment - TraesCS7D01G188200

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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 TraesCS7D01G188200 chr7D 100.000 6651 0 0 1 6651 140774344 140767694 0.000000e+00 12283
1 TraesCS7D01G188200 chr7A 95.296 2955 90 16 3684 6593 142650151 142647201 0.000000e+00 4641
2 TraesCS7D01G188200 chr7A 94.064 2173 82 17 1530 3683 142652325 142650181 0.000000e+00 3254
3 TraesCS7D01G188200 chr7A 93.351 1113 28 14 512 1623 142653338 142652271 0.000000e+00 1604
4 TraesCS7D01G188200 chr7A 93.969 514 29 2 1 513 142656150 142655638 0.000000e+00 776
5 TraesCS7D01G188200 chr7A 83.175 315 35 10 2183 2492 142651379 142651078 8.500000e-69 272
6 TraesCS7D01G188200 chr7B 94.403 2537 94 18 3684 6200 105837674 105835166 0.000000e+00 3855
7 TraesCS7D01G188200 chr7B 95.149 2185 77 19 1519 3683 105839879 105837704 0.000000e+00 3421
8 TraesCS7D01G188200 chr7B 90.522 1667 100 33 1 1651 105841445 105839821 0.000000e+00 2150
9 TraesCS7D01G188200 chr7B 96.377 138 5 0 6514 6651 105834842 105834705 1.870000e-55 228
10 TraesCS7D01G188200 chr7B 85.795 176 7 9 6235 6410 105835066 105834909 3.190000e-38 171
11 TraesCS7D01G188200 chr4D 82.143 168 20 9 5898 6060 402529387 402529549 1.160000e-27 135


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 TraesCS7D01G188200 chr7D 140767694 140774344 6650 True 12283.0 12283 100.0000 1 6651 1 chr7D.!!$R1 6650
1 TraesCS7D01G188200 chr7A 142647201 142656150 8949 True 2109.4 4641 91.9710 1 6593 5 chr7A.!!$R1 6592
2 TraesCS7D01G188200 chr7B 105834705 105841445 6740 True 1965.0 3855 92.4492 1 6651 5 chr7B.!!$R1 6650

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
47 48 0.454196 CCCCTAATTTTTGTCGCCGG 59.546 55.000 0.0 0.0 0.00 6.13 F
752 3064 0.534203 TTTCAGTTCCACACTCGCCC 60.534 55.000 0.0 0.0 30.92 6.13 F
839 3151 1.077276 TTTCCTCCGAATTTCCCCCA 58.923 50.000 0.0 0.0 0.00 4.96 F
1604 3941 1.133761 GCAGGGGAATAAGAAGGGGAC 60.134 57.143 0.0 0.0 0.00 4.46 F
1935 4350 1.257743 TGGTAGTGGAGTGAGCTGTC 58.742 55.000 0.0 0.0 0.00 3.51 F
2215 4630 1.824852 CCCTTGTTTGCCATCCCTAAC 59.175 52.381 0.0 0.0 0.00 2.34 F
3946 6434 1.040339 TGTTGGGTGGTTGGAGTTGC 61.040 55.000 0.0 0.0 0.00 4.17 F
4015 6503 2.341846 TGGAGTTTGGACTGGTTGTC 57.658 50.000 0.0 0.0 44.63 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 4036 0.900182 CCACCCCCTTCTTTCTTGGC 60.900 60.000 0.00 0.00 0.00 4.52 R
1710 4125 1.672320 CATGGGCATGCCAAACACA 59.328 52.632 36.56 24.92 37.98 3.72 R
2754 5170 0.297820 CTCGGCAAGAACGCGAATAC 59.702 55.000 15.93 0.24 0.00 1.89 R
2756 5172 0.669318 TTCTCGGCAAGAACGCGAAT 60.669 50.000 15.93 0.00 39.12 3.34 R
2758 5174 2.337170 TTCTCGGCAAGAACGCGA 59.663 55.556 15.93 0.00 39.12 5.87 R
4020 6508 0.595095 GAGCTTGAACCCAGCTGTTG 59.405 55.000 13.81 5.93 39.21 3.33 R
5185 7682 0.531200 GAACAGTGGTCCGGTAGAGG 59.469 60.000 0.00 0.00 0.00 3.69 R
5822 8325 0.885879 ACAGCAACATGGACAGCATG 59.114 50.000 0.00 0.00 46.00 4.06 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
28 29 8.635983 GTGAACTCTTTAATTATTTCCGCAAAC 58.364 33.333 0.00 0.00 0.00 2.93
47 48 0.454196 CCCCTAATTTTTGTCGCCGG 59.546 55.000 0.00 0.00 0.00 6.13
65 66 1.324383 GGCGGGTTTCTCCAAAGAAA 58.676 50.000 0.00 0.00 46.72 2.52
182 183 7.190501 AGGGAACAATTAGTCTACCTAAGTCT 58.809 38.462 0.00 0.00 38.99 3.24
195 196 1.354368 CTAAGTCTGGGGGCAAAGGAA 59.646 52.381 0.00 0.00 0.00 3.36
198 199 1.465188 TCTGGGGGCAAAGGAAGGA 60.465 57.895 0.00 0.00 0.00 3.36
222 223 7.231925 GGAAGTGTGAACCCTTTATTTCCTTAA 59.768 37.037 0.00 0.00 31.25 1.85
239 240 3.256558 CTTAAAACCCTAACCTCCGTCG 58.743 50.000 0.00 0.00 0.00 5.12
312 314 8.607441 TTGATAGTCTTATTGTACATGATGGC 57.393 34.615 0.00 0.00 0.00 4.40
393 396 5.365605 AGGGATACATTGACATCGGAAGTTA 59.634 40.000 0.00 0.00 39.74 2.24
446 449 1.401905 GCATTCTAAAGTCCAAGCCGG 59.598 52.381 0.00 0.00 0.00 6.13
452 462 0.838987 AAAGTCCAAGCCGGGGAGTA 60.839 55.000 2.18 0.00 37.09 2.59
752 3064 0.534203 TTTCAGTTCCACACTCGCCC 60.534 55.000 0.00 0.00 30.92 6.13
839 3151 1.077276 TTTCCTCCGAATTTCCCCCA 58.923 50.000 0.00 0.00 0.00 4.96
915 3228 2.205022 TGTTCTGCCCTTCCAGATTG 57.795 50.000 0.00 0.00 41.18 2.67
968 3281 4.935885 TTTGTGGTGATTTTGTTGTTGC 57.064 36.364 0.00 0.00 0.00 4.17
1266 3603 1.831389 CTGTGCAGAAACCGTCCACG 61.831 60.000 0.00 0.00 39.44 4.94
1483 3820 2.028020 AGTAGTGGTGGTAGCAAGAAGC 60.028 50.000 0.00 0.00 46.19 3.86
1604 3941 1.133761 GCAGGGGAATAAGAAGGGGAC 60.134 57.143 0.00 0.00 0.00 4.46
1710 4125 1.371558 GGAGTGCTTCCAGAACCGT 59.628 57.895 3.32 0.00 46.01 4.83
1856 4271 4.700213 CGGGATAAACCTTGTCAGAAATGT 59.300 41.667 0.00 0.00 38.98 2.71
1902 4317 8.854117 GCTCAGGTAATCTTGATTTTCCATTAT 58.146 33.333 14.54 0.00 0.00 1.28
1935 4350 1.257743 TGGTAGTGGAGTGAGCTGTC 58.742 55.000 0.00 0.00 0.00 3.51
2080 4495 9.255304 CACACTATTTCTAGAAAGATAAGCTCC 57.745 37.037 21.75 0.00 33.32 4.70
2176 4591 3.310227 TGTTCGTAAGCGTTCACAAACAT 59.690 39.130 0.00 0.00 39.49 2.71
2177 4592 4.507021 TGTTCGTAAGCGTTCACAAACATA 59.493 37.500 0.00 0.00 39.49 2.29
2215 4630 1.824852 CCCTTGTTTGCCATCCCTAAC 59.175 52.381 0.00 0.00 0.00 2.34
2390 4805 8.826710 TGGTCATCATCAAATAATAGTTTCGTC 58.173 33.333 0.00 0.00 0.00 4.20
2609 5024 8.388656 TCCTTAGTTTTGTATCTTCTACCCAT 57.611 34.615 0.00 0.00 0.00 4.00
2684 5099 4.201628 CGAATCATCGTTCTGTTCTCCAAC 60.202 45.833 0.00 0.00 44.06 3.77
2738 5153 3.615224 AAATGGCCAACTTAATGCCTG 57.385 42.857 10.96 0.00 45.56 4.85
2749 5165 6.377146 CCAACTTAATGCCTGTACCAGTTATT 59.623 38.462 0.00 0.00 0.00 1.40
2750 5166 7.415206 CCAACTTAATGCCTGTACCAGTTATTC 60.415 40.741 0.00 0.00 0.00 1.75
2751 5167 6.958767 ACTTAATGCCTGTACCAGTTATTCT 58.041 36.000 0.00 0.00 0.00 2.40
2752 5168 8.086143 ACTTAATGCCTGTACCAGTTATTCTA 57.914 34.615 0.00 0.00 0.00 2.10
2753 5169 8.714906 ACTTAATGCCTGTACCAGTTATTCTAT 58.285 33.333 0.00 0.00 0.00 1.98
2754 5170 8.902540 TTAATGCCTGTACCAGTTATTCTATG 57.097 34.615 0.00 0.00 0.00 2.23
2756 5172 7.612065 ATGCCTGTACCAGTTATTCTATGTA 57.388 36.000 0.00 0.00 0.00 2.29
2758 5174 8.029782 TGCCTGTACCAGTTATTCTATGTATT 57.970 34.615 0.00 0.00 0.00 1.89
2759 5175 8.148351 TGCCTGTACCAGTTATTCTATGTATTC 58.852 37.037 0.00 0.00 0.00 1.75
2760 5176 7.328737 GCCTGTACCAGTTATTCTATGTATTCG 59.671 40.741 0.00 0.00 0.00 3.34
2842 5258 3.831911 CCTTCCCTTTTGGTGCTTGATTA 59.168 43.478 0.00 0.00 38.10 1.75
2893 5309 5.403246 TGCAACACACAAGAAACGTTAAAT 58.597 33.333 0.00 0.00 0.00 1.40
2954 5371 5.195001 TGGTTTCTTCATGGTAAAGCAAC 57.805 39.130 13.88 8.07 37.58 4.17
3182 5633 5.424757 TGGGTGGTAGAACTTGAAATATCG 58.575 41.667 0.00 0.00 0.00 2.92
3183 5634 5.188163 TGGGTGGTAGAACTTGAAATATCGA 59.812 40.000 0.00 0.00 0.00 3.59
3184 5635 6.126883 TGGGTGGTAGAACTTGAAATATCGAT 60.127 38.462 2.16 2.16 0.00 3.59
3185 5636 6.202954 GGGTGGTAGAACTTGAAATATCGATG 59.797 42.308 8.54 0.00 0.00 3.84
3186 5637 6.202954 GGTGGTAGAACTTGAAATATCGATGG 59.797 42.308 8.54 0.00 0.00 3.51
3187 5638 6.202954 GTGGTAGAACTTGAAATATCGATGGG 59.797 42.308 8.54 0.00 0.00 4.00
3188 5639 6.126883 TGGTAGAACTTGAAATATCGATGGGT 60.127 38.462 8.54 0.00 0.00 4.51
3189 5640 6.766467 GGTAGAACTTGAAATATCGATGGGTT 59.234 38.462 8.54 0.00 0.00 4.11
3190 5641 7.929785 GGTAGAACTTGAAATATCGATGGGTTA 59.070 37.037 8.54 0.00 0.00 2.85
3191 5642 8.979574 GTAGAACTTGAAATATCGATGGGTTAG 58.020 37.037 8.54 1.27 0.00 2.34
3192 5643 7.792032 AGAACTTGAAATATCGATGGGTTAGA 58.208 34.615 8.54 0.00 0.00 2.10
3193 5644 8.432805 AGAACTTGAAATATCGATGGGTTAGAT 58.567 33.333 8.54 0.00 0.00 1.98
3194 5645 7.969536 ACTTGAAATATCGATGGGTTAGATG 57.030 36.000 8.54 0.00 0.00 2.90
3195 5646 7.509546 ACTTGAAATATCGATGGGTTAGATGT 58.490 34.615 8.54 0.00 0.00 3.06
3196 5647 8.647796 ACTTGAAATATCGATGGGTTAGATGTA 58.352 33.333 8.54 0.00 0.00 2.29
3197 5648 9.144747 CTTGAAATATCGATGGGTTAGATGTAG 57.855 37.037 8.54 0.00 0.00 2.74
3252 5703 6.997239 AAATAACCCCTCGTATGAAGAAAC 57.003 37.500 0.00 0.00 0.00 2.78
3308 5759 6.040391 CCAATCTAACCACTCCAAACTCAAAA 59.960 38.462 0.00 0.00 0.00 2.44
3343 5794 9.458374 CAATTGTCCGTCTAAAAAGTTTACAAT 57.542 29.630 0.00 4.15 36.79 2.71
3351 5802 9.103048 CGTCTAAAAAGTTTACAATGTTAGCAG 57.897 33.333 0.00 0.00 0.00 4.24
3555 6007 5.529060 GCAAAAGCATAACTACCTAGCATCT 59.471 40.000 0.00 0.00 0.00 2.90
3605 6057 9.934190 CCTTGTTTTGTTTAAGATTTTCATTGG 57.066 29.630 0.00 0.00 0.00 3.16
3632 6084 3.311048 GCATGCTTCTCTTGGTAGTTAGC 59.689 47.826 11.37 0.00 0.00 3.09
3640 6092 6.721571 TCTCTTGGTAGTTAGCGAATTTTG 57.278 37.500 0.00 0.00 0.00 2.44
3690 6171 2.633488 GAGGATGGTGGCACTTCTTAC 58.367 52.381 18.45 0.76 0.00 2.34
3788 6269 2.819019 TGAATGCGAAAATGAAGAGGCA 59.181 40.909 0.00 0.00 34.60 4.75
3807 6288 3.393800 GCATGCGATATGTTAGTGGTCT 58.606 45.455 0.00 0.00 0.00 3.85
3869 6357 7.535139 ACCATAGTTGTATTTTGTATGCACAC 58.465 34.615 0.00 0.00 33.30 3.82
3946 6434 1.040339 TGTTGGGTGGTTGGAGTTGC 61.040 55.000 0.00 0.00 0.00 4.17
3984 6472 6.060788 GGAGATCATAGGCTGAAGTTTTGAT 58.939 40.000 0.00 0.00 37.44 2.57
4015 6503 2.341846 TGGAGTTTGGACTGGTTGTC 57.658 50.000 0.00 0.00 44.63 3.18
4020 6508 3.813724 GAGTTTGGACTGGTTGTCTTACC 59.186 47.826 0.00 0.00 44.74 2.85
4057 6545 2.939103 GCTCAATGTGTTAGCCCTGTAG 59.061 50.000 0.00 0.00 0.00 2.74
4095 6583 3.181485 GGTATAGAGGACAGCAGACACAC 60.181 52.174 0.00 0.00 0.00 3.82
4147 6635 6.017109 CACTATTTTATGGGTGAAGGATTCCG 60.017 42.308 0.00 0.00 46.93 4.30
4174 6662 6.382859 ACAACCTTTTGATTAAAACTGGACCT 59.617 34.615 7.68 0.00 36.48 3.85
4228 6716 9.014297 AGGGTATTCTTATTGTTCTCAAAACTG 57.986 33.333 0.00 0.00 37.11 3.16
4433 6921 4.652822 ACAGAACTATTGTGGGAGTTTCC 58.347 43.478 0.00 0.00 36.04 3.13
4975 7469 8.728088 AAGTTCAAATTCGTATGTTTTGCTAG 57.272 30.769 7.71 0.00 31.88 3.42
5023 7517 8.740123 TTGTGGTTATTACAATACTACCATGG 57.260 34.615 11.19 11.19 35.41 3.66
5027 7521 8.056400 TGGTTATTACAATACTACCATGGCTTT 58.944 33.333 13.04 0.00 30.58 3.51
5043 7537 9.726438 ACCATGGCTTTACTGAAGTTATATATC 57.274 33.333 13.04 0.00 37.69 1.63
5286 7783 1.078710 AGGAACTCTACCGCCCAGT 59.921 57.895 0.00 0.00 0.00 4.00
5592 8089 2.671619 TACAGCAAGGGCCAACGC 60.672 61.111 6.18 4.80 42.56 4.84
5702 8203 1.068417 TTGTACTGCCAGTCGCGTT 59.932 52.632 5.77 0.00 42.08 4.84
5822 8325 2.134789 ATGGCATTCAGGTTCAGACC 57.865 50.000 0.00 0.00 46.92 3.85
5955 8458 1.003118 AGGTCGTCAAATTGGCTAGCA 59.997 47.619 18.24 0.00 0.00 3.49
5981 8484 6.417191 ACGTGTGTTATATGCCACTAAAAG 57.583 37.500 0.00 0.00 32.76 2.27
6018 8522 7.490962 TTCTTCGCTGAATGAAGTTCTAAAA 57.509 32.000 4.17 0.00 42.68 1.52
6100 8604 7.427606 GCTAGTCAAATTGAAGATCGAAACATG 59.572 37.037 0.00 0.00 0.00 3.21
6125 8629 3.630312 TGTGCTCTCCTTACAAACCAAAC 59.370 43.478 0.00 0.00 0.00 2.93
6186 8690 1.202268 GCAACATCTGAGCATGCTTCC 60.202 52.381 23.61 10.79 34.29 3.46
6192 8696 1.209019 TCTGAGCATGCTTCCTCTTCC 59.791 52.381 23.61 6.74 0.00 3.46
6346 8916 1.754234 AAGATGGTTGGGATGCGGC 60.754 57.895 0.00 0.00 0.00 6.53
6462 9032 4.899239 GATCTGGTCTGCGGCGGG 62.899 72.222 9.78 0.00 0.00 6.13
6478 9057 2.592861 GGGGATGACGCTGGATGC 60.593 66.667 0.00 0.00 38.57 3.91
6553 9153 0.895530 CTCGTGGTGGTATGGTGTCT 59.104 55.000 0.00 0.00 0.00 3.41
6617 9217 1.534336 TTGCATTGCAGCGTGGGATT 61.534 50.000 11.76 0.00 40.61 3.01
6627 9227 0.526211 GCGTGGGATTGAAGAAACCC 59.474 55.000 0.00 0.00 42.37 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.454196 CCGGCGACAAAAATTAGGGG 59.546 55.000 9.30 0.00 0.00 4.79
65 66 6.481976 TGTGACATTGTTAACGTCATCTCTTT 59.518 34.615 15.06 0.00 41.39 2.52
182 183 1.368268 ACTTCCTTCCTTTGCCCCCA 61.368 55.000 0.00 0.00 0.00 4.96
195 196 5.077564 GGAAATAAAGGGTTCACACTTCCT 58.922 41.667 0.00 0.00 38.96 3.36
198 199 8.541899 TTTAAGGAAATAAAGGGTTCACACTT 57.458 30.769 0.00 0.00 42.33 3.16
222 223 1.001293 GAACGACGGAGGTTAGGGTTT 59.999 52.381 0.00 0.00 0.00 3.27
239 240 4.664188 TCACTTTGTAAAAACCTGCGAAC 58.336 39.130 0.00 0.00 0.00 3.95
312 314 7.158697 TCTCGGGTTCATTGTATATAATGTGG 58.841 38.462 18.37 7.72 38.77 4.17
373 376 7.279615 TCCAATAACTTCCGATGTCAATGTAT 58.720 34.615 0.00 0.00 0.00 2.29
375 378 5.496556 TCCAATAACTTCCGATGTCAATGT 58.503 37.500 0.00 0.00 0.00 2.71
393 396 3.499338 ACCATGTGTGTTGTCATCCAAT 58.501 40.909 0.00 0.00 35.02 3.16
752 3064 4.771356 TTCGCGAAGACGGCGAGG 62.771 66.667 19.38 0.00 43.68 4.63
874 3187 1.772063 GAACGGGGGATTCAATCGCG 61.772 60.000 8.27 0.00 42.56 5.87
915 3228 1.327764 GCCCATCAAAATCGACGAGAC 59.672 52.381 3.01 0.00 0.00 3.36
1101 3414 4.821589 GCCGAACCAGAGCCGGAG 62.822 72.222 5.05 0.00 45.58 4.63
1220 3533 4.760047 CAGGTTCGTCCCTGCCGG 62.760 72.222 0.00 0.00 45.19 6.13
1225 3538 4.658786 AGGGGCAGGTTCGTCCCT 62.659 66.667 0.00 0.00 44.43 4.20
1226 3539 4.410400 CAGGGGCAGGTTCGTCCC 62.410 72.222 0.00 0.00 39.67 4.46
1483 3820 2.774234 TCTCCTTATGCCCCTTCTTCTG 59.226 50.000 0.00 0.00 0.00 3.02
1621 4036 0.900182 CCACCCCCTTCTTTCTTGGC 60.900 60.000 0.00 0.00 0.00 4.52
1710 4125 1.672320 CATGGGCATGCCAAACACA 59.328 52.632 36.56 24.92 37.98 3.72
2018 4433 9.539825 GATTTCTACTCATGTGTCATGTCTAAT 57.460 33.333 3.19 0.00 0.00 1.73
2080 4495 2.233676 GGCCCTGTTTGGACCTAAAATG 59.766 50.000 0.00 0.00 38.35 2.32
2176 4591 6.101150 ACAAGGGCATACATCCTCATTACTTA 59.899 38.462 0.00 0.00 32.02 2.24
2177 4592 5.103940 ACAAGGGCATACATCCTCATTACTT 60.104 40.000 0.00 0.00 32.02 2.24
2215 4630 8.251026 TCACCAGTCTATTCTACTAACACATTG 58.749 37.037 0.00 0.00 0.00 2.82
2434 4849 2.301870 ACTGGTCGAGGCATTTAAGTCA 59.698 45.455 0.00 0.00 0.00 3.41
2560 4975 4.183865 CCCTATGCACATATATGGACACG 58.816 47.826 16.96 8.78 0.00 4.49
2609 5024 7.386851 GCCTAGCTACATCTTCCATAATAACA 58.613 38.462 0.00 0.00 0.00 2.41
2674 5089 7.337938 TGCATCTCAATTATAGTTGGAGAACA 58.662 34.615 7.99 9.01 34.17 3.18
2738 5153 6.860023 ACGCGAATACATAGAATAACTGGTAC 59.140 38.462 15.93 0.00 0.00 3.34
2749 5165 3.120792 GGCAAGAACGCGAATACATAGA 58.879 45.455 15.93 0.00 0.00 1.98
2750 5166 2.097396 CGGCAAGAACGCGAATACATAG 60.097 50.000 15.93 0.00 0.00 2.23
2751 5167 1.855978 CGGCAAGAACGCGAATACATA 59.144 47.619 15.93 0.00 0.00 2.29
2752 5168 0.650512 CGGCAAGAACGCGAATACAT 59.349 50.000 15.93 0.00 0.00 2.29
2753 5169 0.388778 TCGGCAAGAACGCGAATACA 60.389 50.000 15.93 0.00 0.00 2.29
2754 5170 0.297820 CTCGGCAAGAACGCGAATAC 59.702 55.000 15.93 0.24 0.00 1.89
2756 5172 0.669318 TTCTCGGCAAGAACGCGAAT 60.669 50.000 15.93 0.00 39.12 3.34
2758 5174 2.337170 TTCTCGGCAAGAACGCGA 59.663 55.556 15.93 0.00 39.12 5.87
2954 5371 9.853555 TGGTACATAATTTGATAACTGCAAAAG 57.146 29.630 0.00 0.00 38.57 2.27
3007 5425 6.158598 CCATTTAACATGAGAAAACCAGTGG 58.841 40.000 7.91 7.91 0.00 4.00
3182 5633 6.472686 AAGTGTCTCTACATCTAACCCATC 57.527 41.667 0.00 0.00 38.08 3.51
3183 5634 7.973048 TTAAGTGTCTCTACATCTAACCCAT 57.027 36.000 0.00 0.00 38.08 4.00
3184 5635 7.672660 TCTTTAAGTGTCTCTACATCTAACCCA 59.327 37.037 0.00 0.00 38.08 4.51
3185 5636 8.064336 TCTTTAAGTGTCTCTACATCTAACCC 57.936 38.462 0.00 0.00 38.08 4.11
3186 5637 9.522804 CATCTTTAAGTGTCTCTACATCTAACC 57.477 37.037 0.00 0.00 38.08 2.85
3187 5638 9.026074 GCATCTTTAAGTGTCTCTACATCTAAC 57.974 37.037 0.00 0.00 38.08 2.34
3188 5639 8.749354 TGCATCTTTAAGTGTCTCTACATCTAA 58.251 33.333 0.00 0.00 38.08 2.10
3189 5640 8.293699 TGCATCTTTAAGTGTCTCTACATCTA 57.706 34.615 0.00 0.00 38.08 1.98
3190 5641 7.175347 TGCATCTTTAAGTGTCTCTACATCT 57.825 36.000 0.00 0.00 38.08 2.90
3191 5642 7.547370 AGTTGCATCTTTAAGTGTCTCTACATC 59.453 37.037 0.00 0.00 38.08 3.06
3192 5643 7.332926 CAGTTGCATCTTTAAGTGTCTCTACAT 59.667 37.037 0.00 0.00 38.08 2.29
3193 5644 6.646653 CAGTTGCATCTTTAAGTGTCTCTACA 59.353 38.462 0.00 0.00 0.00 2.74
3194 5645 6.868864 TCAGTTGCATCTTTAAGTGTCTCTAC 59.131 38.462 0.00 0.00 0.00 2.59
3195 5646 6.993079 TCAGTTGCATCTTTAAGTGTCTCTA 58.007 36.000 0.00 0.00 0.00 2.43
3196 5647 5.858381 TCAGTTGCATCTTTAAGTGTCTCT 58.142 37.500 0.00 0.00 0.00 3.10
3197 5648 6.148480 ACATCAGTTGCATCTTTAAGTGTCTC 59.852 38.462 0.00 0.00 0.00 3.36
3308 5759 7.624360 TTTAGACGGACAATTGAATAAGCAT 57.376 32.000 13.59 0.00 0.00 3.79
3343 5794 6.532988 AAAACCCTTTTACAACTGCTAACA 57.467 33.333 0.00 0.00 0.00 2.41
3525 5977 6.168270 AGGTAGTTATGCTTTTGCCAAAAA 57.832 33.333 3.91 0.00 46.87 1.94
3526 5978 5.799827 AGGTAGTTATGCTTTTGCCAAAA 57.200 34.783 2.15 2.15 46.87 2.44
3703 6184 6.947644 TGCAATGCACAATATAGATCACTT 57.052 33.333 2.72 0.00 31.71 3.16
3704 6185 6.947644 TTGCAATGCACAATATAGATCACT 57.052 33.333 7.72 0.00 38.71 3.41
3788 6269 4.262207 CCAGAGACCACTAACATATCGCAT 60.262 45.833 0.00 0.00 0.00 4.73
3869 6357 9.821662 GTAAATACAACTACAAGCAAAACTAGG 57.178 33.333 0.00 0.00 0.00 3.02
3984 6472 3.392947 TCCAAACTCCAATGTACAGGACA 59.607 43.478 0.33 0.00 43.97 4.02
4015 6503 2.270352 TGAACCCAGCTGTTGGTAAG 57.730 50.000 14.21 0.00 46.25 2.34
4020 6508 0.595095 GAGCTTGAACCCAGCTGTTG 59.405 55.000 13.81 5.93 39.21 3.33
4057 6545 7.339721 TCCTCTATACCACTTACAGCTATATGC 59.660 40.741 0.00 0.00 43.29 3.14
4095 6583 4.864247 GGCCACTGTAAGCACATAAAATTG 59.136 41.667 0.00 0.00 37.60 2.32
4147 6635 6.019075 GTCCAGTTTTAATCAAAAGGTTGTGC 60.019 38.462 0.00 0.00 34.34 4.57
4174 6662 7.476540 TCAGTACTAACTTCTCTGGCATAAA 57.523 36.000 0.00 0.00 31.97 1.40
4228 6716 6.446318 TCACCTACATCAAAAACATCAAAGC 58.554 36.000 0.00 0.00 0.00 3.51
4238 6726 8.286800 CAGTCGTAAATTTCACCTACATCAAAA 58.713 33.333 0.00 0.00 0.00 2.44
4433 6921 8.568732 ACAAGGTAAAAACGTCATTTATGTTG 57.431 30.769 17.91 17.91 37.39 3.33
4975 7469 5.041951 TGTGTTCAACTGTCAGTTTGAAC 57.958 39.130 30.01 30.01 41.32 3.18
5018 7512 8.873830 CGATATATAACTTCAGTAAAGCCATGG 58.126 37.037 7.63 7.63 38.67 3.66
5027 7521 9.128404 ACCAGAACACGATATATAACTTCAGTA 57.872 33.333 0.00 0.00 0.00 2.74
5043 7537 4.369182 ACTTCAGTAAAGACCAGAACACG 58.631 43.478 0.00 0.00 38.44 4.49
5051 7545 8.699283 ACACGATAATAACTTCAGTAAAGACC 57.301 34.615 0.00 0.00 38.44 3.85
5185 7682 0.531200 GAACAGTGGTCCGGTAGAGG 59.469 60.000 0.00 0.00 0.00 3.69
5673 8170 1.300311 CAGTACAACCGACGGCACA 60.300 57.895 15.39 0.00 0.00 4.57
5702 8203 5.838531 AACCAAAAAGTAAACATCCGACA 57.161 34.783 0.00 0.00 0.00 4.35
5768 8271 5.124457 AGCAGTTTAACAGGCATACAAGATG 59.876 40.000 12.74 0.00 0.00 2.90
5822 8325 0.885879 ACAGCAACATGGACAGCATG 59.114 50.000 0.00 0.00 46.00 4.06
5955 8458 6.804770 TTAGTGGCATATAACACACGTTTT 57.195 33.333 10.49 0.00 39.99 2.43
5981 8484 3.846896 CAGCGAAGAATCCGACGATATAC 59.153 47.826 0.00 0.00 0.00 1.47
5990 8493 2.932614 ACTTCATTCAGCGAAGAATCCG 59.067 45.455 6.89 0.00 42.05 4.18
6018 8522 5.707411 GTGTACGCCACGAAAAGTATATT 57.293 39.130 0.00 0.00 33.61 1.28
6075 8579 8.446273 ACATGTTTCGATCTTCAATTTGACTAG 58.554 33.333 0.00 0.00 0.00 2.57
6100 8604 2.548480 GGTTTGTAAGGAGAGCACACAC 59.452 50.000 0.00 0.00 0.00 3.82
6125 8629 0.540454 GAAAACCCCTACTCCCTCCG 59.460 60.000 0.00 0.00 0.00 4.63
6192 8696 4.729918 GGCCACCACCTCAGCCAG 62.730 72.222 0.00 0.00 45.07 4.85
6346 8916 1.021390 GGATGTCACAGCCGGAACAG 61.021 60.000 5.05 0.00 27.64 3.16
6358 8928 2.265739 GTGGAGCTGCGGATGTCA 59.734 61.111 0.00 0.00 0.00 3.58
6359 8929 2.887568 CGTGGAGCTGCGGATGTC 60.888 66.667 0.00 0.00 0.00 3.06
6399 8969 2.971452 GTCGGGTCACTGTCCTCC 59.029 66.667 0.00 0.00 0.00 4.30
6430 9000 1.220749 GATCTACAAGCCACGCCCA 59.779 57.895 0.00 0.00 0.00 5.36
6517 9117 1.377366 GAGGCTCATCGACGACCTCA 61.377 60.000 21.23 0.00 45.16 3.86
6617 9217 0.035439 GCCGGAGATGGGTTTCTTCA 60.035 55.000 5.05 0.00 0.00 3.02
6627 9227 2.584418 CGAGCACAGCCGGAGATG 60.584 66.667 5.05 2.26 0.00 2.90


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

AutoCloner maintained by Alex Coulton.