Multiple sequence alignment - TraesCS1B01G077000

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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 TraesCS1B01G077000 chr1B 100.000 3336 0 0 1 3336 59604880 59601545 0.000000e+00 6161.0
1 TraesCS1B01G077000 chr1B 91.304 115 10 0 3043 3157 59601781 59601667 1.240000e-34 158.0
2 TraesCS1B01G077000 chr1B 91.304 115 10 0 3100 3214 59601838 59601724 1.240000e-34 158.0
3 TraesCS1B01G077000 chr1D 89.048 2438 120 72 240 2600 39951299 39948932 0.000000e+00 2887.0
4 TraesCS1B01G077000 chr1D 91.512 754 38 14 2598 3336 39948771 39948029 0.000000e+00 1014.0
5 TraesCS1B01G077000 chr1D 96.552 116 4 0 3100 3215 39948322 39948207 3.400000e-45 193.0
6 TraesCS1B01G077000 chr1D 93.333 60 4 0 166 225 39951399 39951340 4.580000e-14 89.8
7 TraesCS1B01G077000 chr1A 89.676 1821 71 35 546 2341 39410472 39408744 0.000000e+00 2213.0
8 TraesCS1B01G077000 chr1A 89.202 852 52 14 2395 3219 39408663 39407825 0.000000e+00 1027.0
9 TraesCS1B01G077000 chr1A 94.898 294 15 0 3043 3336 39407944 39407651 8.430000e-126 460.0
10 TraesCS1B01G077000 chr1A 90.000 300 17 7 240 527 39410813 39410515 3.140000e-100 375.0
11 TraesCS1B01G077000 chr1A 94.928 138 6 1 29 165 39413827 39413690 7.250000e-52 215.0
12 TraesCS1B01G077000 chr1A 93.333 120 8 0 3100 3219 39408001 39407882 9.510000e-41 178.0
13 TraesCS1B01G077000 chr1A 94.643 112 6 0 3046 3157 39407884 39407773 1.230000e-39 174.0


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 TraesCS1B01G077000 chr1B 59601545 59604880 3335 True 2159.000000 6161 94.202667 1 3336 3 chr1B.!!$R1 3335
1 TraesCS1B01G077000 chr1D 39948029 39951399 3370 True 1045.950000 2887 92.611250 166 3336 4 chr1D.!!$R1 3170
2 TraesCS1B01G077000 chr1A 39407651 39413827 6176 True 663.142857 2213 92.382857 29 3336 7 chr1A.!!$R1 3307

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
282 3098 0.309922 CCTCATCACGCATGATTGCC 59.690 55.0 0.0 0.0 43.40 4.52 F
973 3853 0.961753 AAACCAAACTAGCCAGCAGC 59.038 50.0 0.0 0.0 44.25 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 4719 0.027979 CAGCAAATGTACCATCGCGG 59.972 55.0 6.13 0.0 42.5 6.46 R
2379 5315 0.247537 GGCGAAAGGTTAATGCGACG 60.248 55.0 0.00 0.0 0.0 5.12 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
52 53 6.090628 CGAAGAAGAAGAAGAAGAAGACATGG 59.909 42.308 0.00 0.00 0.00 3.66
54 55 3.949132 AGAAGAAGAAGAAGACATGGGC 58.051 45.455 0.00 0.00 0.00 5.36
87 88 6.258354 TCCACCAGAAAGTAGGATACACTTA 58.742 40.000 0.00 0.00 46.26 2.24
98 99 7.643625 AGTAGGATACACTTATGTGCGTGGAT 61.644 42.308 8.58 0.00 46.26 3.41
128 129 2.285256 CGTGCGAACTGCTTATCATGAC 60.285 50.000 0.00 0.00 46.63 3.06
228 3014 1.773525 CGTCGTCGCTGTATGTACATG 59.226 52.381 18.81 2.92 35.36 3.21
231 3017 3.855379 GTCGTCGCTGTATGTACATGAAA 59.145 43.478 18.81 2.95 35.36 2.69
232 3018 3.855379 TCGTCGCTGTATGTACATGAAAC 59.145 43.478 18.81 9.31 35.36 2.78
233 3019 3.000078 CGTCGCTGTATGTACATGAAACC 60.000 47.826 18.81 2.47 35.36 3.27
234 3020 3.000078 GTCGCTGTATGTACATGAAACCG 60.000 47.826 18.81 13.38 35.36 4.44
238 3050 5.556382 CGCTGTATGTACATGAAACCGATTC 60.556 44.000 18.81 0.00 35.36 2.52
253 3065 1.308998 GATTCCTTGCACGGTATGGG 58.691 55.000 9.36 0.00 0.00 4.00
282 3098 0.309922 CCTCATCACGCATGATTGCC 59.690 55.000 0.00 0.00 43.40 4.52
287 3103 1.159713 TCACGCATGATTGCCCGATC 61.160 55.000 0.00 0.00 46.57 3.69
291 3107 1.227943 CATGATTGCCCGATCCGGT 60.228 57.895 0.00 0.00 46.80 5.28
325 3141 4.238514 GGCTTCGGCATATATATCGATCC 58.761 47.826 0.00 7.96 43.96 3.36
328 3144 5.509716 TTCGGCATATATATCGATCCGTT 57.490 39.130 16.18 0.00 36.99 4.44
350 3166 4.129737 CGCCCGTCGTGGTCTGAT 62.130 66.667 0.00 0.00 35.15 2.90
407 3223 4.100707 TGCAGCTTGATGAAGTTAATGC 57.899 40.909 0.00 0.93 32.15 3.56
425 3241 4.077184 GTGACCATCGTCCCGGCA 62.077 66.667 0.00 0.00 38.32 5.69
454 3274 6.485984 AGTCCATCATCATGAAACTAATCTGC 59.514 38.462 0.00 0.00 30.57 4.26
486 3306 1.473434 CCACCTTTATCGGCAGGAGAC 60.473 57.143 0.00 0.00 33.90 3.36
518 3341 1.295792 TGAAGCGTGTGTTCAACCTC 58.704 50.000 0.00 0.00 30.89 3.85
527 3350 1.668751 GTGTTCAACCTCGAGCAACAA 59.331 47.619 6.99 0.00 0.00 2.83
529 3352 2.750166 TGTTCAACCTCGAGCAACAAAA 59.250 40.909 6.99 0.00 0.00 2.44
530 3353 3.191581 TGTTCAACCTCGAGCAACAAAAA 59.808 39.130 6.99 0.00 0.00 1.94
556 3403 2.281276 CCCTTATTACGGCCGGGC 60.281 66.667 31.76 20.04 0.00 6.13
580 3427 7.169140 GGCTGTGTAAAAAGGTGTCTTATTTTG 59.831 37.037 0.00 0.00 32.01 2.44
627 3474 4.446413 GGCCCACATTGCTGCAGC 62.446 66.667 31.89 31.89 42.50 5.25
649 3496 2.099098 CACGTTTTGCAAACCCTTCTCT 59.901 45.455 12.39 0.00 0.00 3.10
650 3497 2.357952 ACGTTTTGCAAACCCTTCTCTC 59.642 45.455 12.39 0.00 0.00 3.20
654 3501 1.048601 TGCAAACCCTTCTCTCGAGT 58.951 50.000 13.13 0.00 0.00 4.18
670 3517 1.333791 CGAGTTGCGTCCAAAAGAACC 60.334 52.381 0.00 0.00 31.68 3.62
671 3518 1.673920 GAGTTGCGTCCAAAAGAACCA 59.326 47.619 0.00 0.00 31.68 3.67
732 3579 4.510340 GGGGTTAATCAATACGCACTACTG 59.490 45.833 0.00 0.00 0.00 2.74
739 3586 3.056821 TCAATACGCACTACTGCTCAGTT 60.057 43.478 7.92 0.00 41.77 3.16
765 3622 8.701895 TCAATAGGGTAGACGTTGAGAAATATT 58.298 33.333 0.00 0.00 0.00 1.28
837 3694 3.657350 CCACCCCACAACCCCGAT 61.657 66.667 0.00 0.00 0.00 4.18
963 3843 2.107366 CCAACCAGACCAAACCAAACT 58.893 47.619 0.00 0.00 0.00 2.66
970 3850 1.269723 GACCAAACCAAACTAGCCAGC 59.730 52.381 0.00 0.00 0.00 4.85
971 3851 1.327303 CCAAACCAAACTAGCCAGCA 58.673 50.000 0.00 0.00 0.00 4.41
972 3852 1.270550 CCAAACCAAACTAGCCAGCAG 59.729 52.381 0.00 0.00 0.00 4.24
973 3853 0.961753 AAACCAAACTAGCCAGCAGC 59.038 50.000 0.00 0.00 44.25 5.25
1152 4040 2.507547 TACGCGTCCAACATCGGC 60.508 61.111 18.63 0.00 0.00 5.54
1533 4421 3.463585 GTCATCGCCACCGGGGTA 61.464 66.667 6.32 0.00 39.65 3.69
1534 4422 2.684294 TCATCGCCACCGGGGTAA 60.684 61.111 6.32 0.00 39.65 2.85
1535 4423 2.512974 CATCGCCACCGGGGTAAC 60.513 66.667 6.32 0.00 39.65 2.50
1581 4469 2.796651 GCAGCAAGCTCCGAATGG 59.203 61.111 0.00 0.00 41.15 3.16
1603 4517 3.057969 TCCAAATCTTGATGTGCTCGT 57.942 42.857 0.00 0.00 0.00 4.18
1650 4569 2.185608 GAGCCGAGCTTCCACCTC 59.814 66.667 0.00 0.00 39.88 3.85
1729 4648 1.406860 GGGGATCCTGCTCTCCTCAC 61.407 65.000 12.58 0.00 32.57 3.51
1740 4659 5.221224 CCTGCTCTCCTCACAAGAGTAATAG 60.221 48.000 2.44 0.00 41.91 1.73
1742 4661 6.424032 TGCTCTCCTCACAAGAGTAATAGTA 58.576 40.000 2.44 0.00 41.91 1.82
1743 4662 6.319152 TGCTCTCCTCACAAGAGTAATAGTAC 59.681 42.308 0.00 0.00 41.91 2.73
1781 4700 6.146184 ACTTCATTCATCACGTTGACTTGTAG 59.854 38.462 0.00 0.00 0.00 2.74
1783 4702 6.683715 TCATTCATCACGTTGACTTGTAGTA 58.316 36.000 0.00 0.00 0.00 1.82
1784 4703 6.806739 TCATTCATCACGTTGACTTGTAGTAG 59.193 38.462 0.00 0.00 0.00 2.57
1785 4704 5.700722 TCATCACGTTGACTTGTAGTAGT 57.299 39.130 0.00 0.00 0.00 2.73
1786 4705 6.806388 TCATCACGTTGACTTGTAGTAGTA 57.194 37.500 0.00 0.00 0.00 1.82
1787 4706 6.605849 TCATCACGTTGACTTGTAGTAGTAC 58.394 40.000 0.37 0.37 0.00 2.73
1788 4707 6.429078 TCATCACGTTGACTTGTAGTAGTACT 59.571 38.462 8.14 8.14 0.00 2.73
1789 4708 5.993891 TCACGTTGACTTGTAGTAGTACTG 58.006 41.667 13.29 0.00 0.00 2.74
1790 4709 5.759763 TCACGTTGACTTGTAGTAGTACTGA 59.240 40.000 13.29 0.00 0.00 3.41
1791 4710 6.260714 TCACGTTGACTTGTAGTAGTACTGAA 59.739 38.462 13.29 4.95 0.00 3.02
1792 4711 6.914215 CACGTTGACTTGTAGTAGTACTGAAA 59.086 38.462 13.29 6.24 0.00 2.69
1793 4712 7.594015 CACGTTGACTTGTAGTAGTACTGAAAT 59.406 37.037 13.29 0.00 0.00 2.17
1794 4713 8.139989 ACGTTGACTTGTAGTAGTACTGAAATT 58.860 33.333 13.29 1.79 0.00 1.82
1795 4714 9.616634 CGTTGACTTGTAGTAGTACTGAAATTA 57.383 33.333 13.29 0.00 0.00 1.40
1803 4722 8.133627 TGTAGTAGTACTGAAATTATTCTCCGC 58.866 37.037 13.29 0.00 36.48 5.54
1804 4723 6.207213 AGTAGTACTGAAATTATTCTCCGCG 58.793 40.000 5.39 0.00 36.48 6.46
1808 4727 3.809832 ACTGAAATTATTCTCCGCGATGG 59.190 43.478 8.23 0.00 36.48 3.51
1832 4751 2.547299 TTTGCTGAAAATGGGGCTTG 57.453 45.000 0.00 0.00 0.00 4.01
1863 4782 0.392193 CGTGCAGGGAGAAGCTCAAT 60.392 55.000 0.00 0.00 31.08 2.57
1938 4857 1.445095 GACGCTGATGATGGAGCCT 59.555 57.895 0.00 0.00 30.98 4.58
2141 5077 5.414144 TGAACTTTTCAGATGAACACACACA 59.586 36.000 0.00 0.00 34.08 3.72
2142 5078 5.490139 ACTTTTCAGATGAACACACACAG 57.510 39.130 0.00 0.00 33.13 3.66
2143 5079 4.336433 ACTTTTCAGATGAACACACACAGG 59.664 41.667 0.00 0.00 33.13 4.00
2144 5080 3.558931 TTCAGATGAACACACACAGGT 57.441 42.857 0.00 0.00 0.00 4.00
2145 5081 3.558931 TCAGATGAACACACACAGGTT 57.441 42.857 0.00 0.00 0.00 3.50
2146 5082 4.681074 TCAGATGAACACACACAGGTTA 57.319 40.909 0.00 0.00 0.00 2.85
2147 5083 4.377021 TCAGATGAACACACACAGGTTAC 58.623 43.478 0.00 0.00 0.00 2.50
2148 5084 3.498397 CAGATGAACACACACAGGTTACC 59.502 47.826 0.00 0.00 0.00 2.85
2149 5085 3.391296 AGATGAACACACACAGGTTACCT 59.609 43.478 0.00 0.00 0.00 3.08
2180 5116 4.060038 ATGCGCCTTGTGCTTGGC 62.060 61.111 4.18 0.00 45.25 4.52
2379 5315 1.138661 CCTCCAGAAGATCTGCTGACC 59.861 57.143 29.60 0.40 42.98 4.02
2383 5319 0.453793 AGAAGATCTGCTGACCGTCG 59.546 55.000 1.03 0.00 0.00 5.12
2388 5324 0.459899 ATCTGCTGACCGTCGCATTA 59.540 50.000 15.23 9.39 35.32 1.90
2434 5399 0.537188 GATCCAAGTTCCGGCAGAGA 59.463 55.000 0.00 0.00 0.00 3.10
2442 5407 0.614697 TTCCGGCAGAGACCTGATGA 60.615 55.000 0.00 0.00 43.02 2.92
2477 5442 5.365619 AGACGACCAACCCATTTGTATATC 58.634 41.667 0.00 0.00 32.71 1.63
2536 5501 6.879458 AGTGTAGGACTTGGTGATGTTAAATC 59.121 38.462 0.00 0.00 0.00 2.17
2560 5525 3.701542 TCAGAAGCCGTTAGATCAGATGT 59.298 43.478 0.00 0.00 0.00 3.06
2579 5544 8.959548 TCAGATGTATTCATGCTTGTAAATTGT 58.040 29.630 0.00 0.00 34.06 2.71
2665 5808 9.950496 GATATATAAGACACCCTGATGAACATT 57.050 33.333 0.00 0.00 0.00 2.71
2719 5864 8.474710 AGGAGTACTACAAAAAGTAACTGAGA 57.525 34.615 8.10 0.00 33.85 3.27
2720 5865 8.921205 AGGAGTACTACAAAAAGTAACTGAGAA 58.079 33.333 8.10 0.00 33.85 2.87
2793 5938 3.256631 GGATCAAGTGCTTTGGACACAAT 59.743 43.478 0.00 0.00 40.59 2.71
2808 5953 8.492673 TTGGACACAATAGAATATCACAGTTC 57.507 34.615 0.00 0.00 0.00 3.01
2912 6058 5.049612 GGACAGCCTTTTGTACTAACTTCAC 60.050 44.000 0.00 0.00 0.00 3.18
2913 6059 5.681639 ACAGCCTTTTGTACTAACTTCACT 58.318 37.500 0.00 0.00 0.00 3.41
2914 6060 5.758784 ACAGCCTTTTGTACTAACTTCACTC 59.241 40.000 0.00 0.00 0.00 3.51
2915 6061 5.992217 CAGCCTTTTGTACTAACTTCACTCT 59.008 40.000 0.00 0.00 0.00 3.24
2917 6063 7.012421 CAGCCTTTTGTACTAACTTCACTCTTT 59.988 37.037 0.00 0.00 0.00 2.52
2918 6064 8.208903 AGCCTTTTGTACTAACTTCACTCTTTA 58.791 33.333 0.00 0.00 0.00 1.85
2988 6147 2.050144 AGTTCCTCTGGCAGAACAAGA 58.950 47.619 19.29 10.04 43.89 3.02
3025 6184 1.066143 TCGCCAAGAGAAATGGAGGAC 60.066 52.381 0.00 0.00 40.56 3.85
3058 6217 1.450312 CAGGGTCAATGGAGTCGCC 60.450 63.158 0.00 0.00 37.10 5.54
3113 6272 1.630369 CCTTCTGGGTCAATGGAGTCA 59.370 52.381 0.00 0.00 0.00 3.41
3147 6363 4.537688 AGATTGTCCTTGAGAAATGGAGGA 59.462 41.667 0.00 0.00 32.91 3.71
3157 6373 0.984230 AAATGGAGGACGCCTTCTGA 59.016 50.000 5.87 0.00 31.76 3.27
3226 6442 1.479709 GCTTCTGGCTCAGGAGAGTA 58.520 55.000 13.08 0.00 39.34 2.59
3262 6478 1.552226 CAATAGCCTGCGCATTTGTG 58.448 50.000 12.24 0.00 37.52 3.33
3274 6490 0.599558 CATTTGTGTGTGAGGCCAGG 59.400 55.000 5.01 0.00 0.00 4.45
3327 6543 2.880268 CAGGCTGGATATTTTGATGCGA 59.120 45.455 6.61 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.665264 CTTCTTCTTCGCTTTTTACACTTTAAT 57.335 29.630 0.00 0.00 0.00 1.40
12 13 8.885722 TCTTCTTCTTCGCTTTTTACACTTTAA 58.114 29.630 0.00 0.00 0.00 1.52
13 14 8.428186 TCTTCTTCTTCGCTTTTTACACTTTA 57.572 30.769 0.00 0.00 0.00 1.85
14 15 7.316544 TCTTCTTCTTCGCTTTTTACACTTT 57.683 32.000 0.00 0.00 0.00 2.66
15 16 6.920569 TCTTCTTCTTCGCTTTTTACACTT 57.079 33.333 0.00 0.00 0.00 3.16
16 17 6.761714 TCTTCTTCTTCTTCGCTTTTTACACT 59.238 34.615 0.00 0.00 0.00 3.55
17 18 6.945072 TCTTCTTCTTCTTCGCTTTTTACAC 58.055 36.000 0.00 0.00 0.00 2.90
18 19 7.494625 TCTTCTTCTTCTTCTTCGCTTTTTACA 59.505 33.333 0.00 0.00 0.00 2.41
19 20 7.852516 TCTTCTTCTTCTTCTTCGCTTTTTAC 58.147 34.615 0.00 0.00 0.00 2.01
20 21 8.433421 TTCTTCTTCTTCTTCTTCGCTTTTTA 57.567 30.769 0.00 0.00 0.00 1.52
21 22 6.927294 TCTTCTTCTTCTTCTTCGCTTTTT 57.073 33.333 0.00 0.00 0.00 1.94
22 23 6.763610 TCTTCTTCTTCTTCTTCTTCGCTTTT 59.236 34.615 0.00 0.00 0.00 2.27
23 24 6.201997 GTCTTCTTCTTCTTCTTCTTCGCTTT 59.798 38.462 0.00 0.00 0.00 3.51
24 25 5.694458 GTCTTCTTCTTCTTCTTCTTCGCTT 59.306 40.000 0.00 0.00 0.00 4.68
25 26 5.221342 TGTCTTCTTCTTCTTCTTCTTCGCT 60.221 40.000 0.00 0.00 0.00 4.93
26 27 4.985409 TGTCTTCTTCTTCTTCTTCTTCGC 59.015 41.667 0.00 0.00 0.00 4.70
27 28 6.090628 CCATGTCTTCTTCTTCTTCTTCTTCG 59.909 42.308 0.00 0.00 0.00 3.79
52 53 6.775594 ACTTTCTGGTGGATAAAATAAGCC 57.224 37.500 0.00 0.00 0.00 4.35
54 55 9.853177 ATCCTACTTTCTGGTGGATAAAATAAG 57.147 33.333 0.00 0.00 35.95 1.73
87 88 1.171549 TTGCACACATCCACGCACAT 61.172 50.000 0.00 0.00 33.29 3.21
98 99 2.103647 AGTTCGCACGTTGCACACA 61.104 52.632 9.95 0.00 45.36 3.72
117 118 3.853671 CGTTGCAAAAGGTCATGATAAGC 59.146 43.478 0.00 0.00 0.00 3.09
128 129 1.269206 ACATGACAGCGTTGCAAAAGG 60.269 47.619 0.00 0.00 0.00 3.11
228 3014 0.168128 CCGTGCAAGGAATCGGTTTC 59.832 55.000 14.14 0.00 38.45 2.78
232 3018 0.937304 CATACCGTGCAAGGAATCGG 59.063 55.000 26.25 17.38 46.98 4.18
233 3019 0.937304 CCATACCGTGCAAGGAATCG 59.063 55.000 26.25 5.32 34.73 3.34
234 3020 1.308998 CCCATACCGTGCAAGGAATC 58.691 55.000 26.25 0.00 34.73 2.52
238 3050 1.001393 AACCCCATACCGTGCAAGG 60.001 57.895 17.83 17.83 37.30 3.61
253 3065 1.021390 CGTGATGAGGGAGTGCAACC 61.021 60.000 0.00 0.00 37.80 3.77
291 3107 2.431260 GAAGCCGAACGTGCCGTA 60.431 61.111 9.29 0.00 39.99 4.02
350 3166 0.302589 CGTACGATCCATCACGTCGA 59.697 55.000 10.44 0.00 42.61 4.20
425 3241 9.553064 GATTAGTTTCATGATGATGGACTAGTT 57.447 33.333 0.00 0.00 33.75 2.24
486 3306 1.539827 ACGCTTCATTTTTCTTCCCGG 59.460 47.619 0.00 0.00 0.00 5.73
488 3308 3.243401 ACACACGCTTCATTTTTCTTCCC 60.243 43.478 0.00 0.00 0.00 3.97
529 3352 5.163591 CGGCCGTAATAAGGGAAGAAATTTT 60.164 40.000 19.50 0.00 31.98 1.82
530 3353 4.337274 CGGCCGTAATAAGGGAAGAAATTT 59.663 41.667 19.50 0.00 31.98 1.82
531 3354 3.881089 CGGCCGTAATAAGGGAAGAAATT 59.119 43.478 19.50 0.00 31.98 1.82
532 3355 3.473625 CGGCCGTAATAAGGGAAGAAAT 58.526 45.455 19.50 0.00 31.98 2.17
542 3365 1.153329 CACAGCCCGGCCGTAATAA 60.153 57.895 26.12 0.00 0.00 1.40
556 3403 9.450807 CTCAAAATAAGACACCTTTTTACACAG 57.549 33.333 0.00 0.00 33.94 3.66
560 3407 7.808381 GGAGCTCAAAATAAGACACCTTTTTAC 59.192 37.037 17.19 0.00 33.94 2.01
562 3409 6.323739 TGGAGCTCAAAATAAGACACCTTTTT 59.676 34.615 17.19 0.00 33.94 1.94
580 3427 2.234908 AGTACAATGGACAGTGGAGCTC 59.765 50.000 4.71 4.71 0.00 4.09
627 3474 1.136110 AGAAGGGTTTGCAAAACGTGG 59.864 47.619 22.05 0.00 0.00 4.94
649 3496 1.595794 GTTCTTTTGGACGCAACTCGA 59.404 47.619 0.00 0.00 41.67 4.04
650 3497 1.333791 GGTTCTTTTGGACGCAACTCG 60.334 52.381 0.00 0.00 45.38 4.18
654 3501 3.594603 TTTTGGTTCTTTTGGACGCAA 57.405 38.095 0.00 0.00 0.00 4.85
732 3579 3.130693 ACGTCTACCCTATTGAACTGAGC 59.869 47.826 0.00 0.00 0.00 4.26
739 3586 5.988310 TTTCTCAACGTCTACCCTATTGA 57.012 39.130 0.00 0.00 0.00 2.57
765 3622 1.834896 TCCCGCCAGCTTAAACATCTA 59.165 47.619 0.00 0.00 0.00 1.98
827 3684 4.778143 GCTGCCGATCGGGGTTGT 62.778 66.667 33.98 0.00 35.78 3.32
972 3852 4.722700 TTGCTTCCCGGAGCTGGC 62.723 66.667 15.49 7.20 43.11 4.85
973 3853 2.437359 CTTGCTTCCCGGAGCTGG 60.437 66.667 15.49 5.38 43.11 4.85
1152 4040 1.082300 CTTGTTGAGCAGCAGCACG 60.082 57.895 3.17 0.00 45.49 5.34
1580 4468 3.003068 CGAGCACATCAAGATTTGGATCC 59.997 47.826 4.20 4.20 32.44 3.36
1581 4469 3.624861 ACGAGCACATCAAGATTTGGATC 59.375 43.478 0.00 0.00 0.00 3.36
1603 4517 0.040157 GAAGCAACAATGTCAGCGCA 60.040 50.000 11.47 0.00 0.00 6.09
1647 4566 2.283298 CACATGATGAACCCGAAGAGG 58.717 52.381 0.00 0.00 40.63 3.69
1650 4569 0.374758 CGCACATGATGAACCCGAAG 59.625 55.000 0.00 0.00 0.00 3.79
1740 4659 9.973450 ATGAATGAAGTACTGTATGATGAGTAC 57.027 33.333 0.00 0.00 43.30 2.73
1742 4661 8.699130 TGATGAATGAAGTACTGTATGATGAGT 58.301 33.333 0.00 0.00 0.00 3.41
1743 4662 8.976471 GTGATGAATGAAGTACTGTATGATGAG 58.024 37.037 0.00 0.00 0.00 2.90
1747 4666 6.863275 ACGTGATGAATGAAGTACTGTATGA 58.137 36.000 0.00 0.00 0.00 2.15
1748 4667 7.275560 TCAACGTGATGAATGAAGTACTGTATG 59.724 37.037 0.00 0.00 0.00 2.39
1749 4668 7.275779 GTCAACGTGATGAATGAAGTACTGTAT 59.724 37.037 0.00 0.00 0.00 2.29
1750 4669 6.584942 GTCAACGTGATGAATGAAGTACTGTA 59.415 38.462 0.00 0.00 0.00 2.74
1751 4670 5.405571 GTCAACGTGATGAATGAAGTACTGT 59.594 40.000 0.00 0.00 0.00 3.55
1752 4671 5.635280 AGTCAACGTGATGAATGAAGTACTG 59.365 40.000 0.00 0.00 0.00 2.74
1753 4672 5.784177 AGTCAACGTGATGAATGAAGTACT 58.216 37.500 0.00 0.00 0.00 2.73
1754 4673 6.073765 ACAAGTCAACGTGATGAATGAAGTAC 60.074 38.462 9.88 0.00 0.00 2.73
1781 4700 6.204359 TCGCGGAGAATAATTTCAGTACTAC 58.796 40.000 6.13 0.00 34.08 2.73
1783 4702 5.258456 TCGCGGAGAATAATTTCAGTACT 57.742 39.130 6.13 0.00 34.08 2.73
1784 4703 5.107453 CCATCGCGGAGAATAATTTCAGTAC 60.107 44.000 6.13 0.00 36.56 2.73
1785 4704 4.988540 CCATCGCGGAGAATAATTTCAGTA 59.011 41.667 6.13 0.00 36.56 2.74
1786 4705 3.809832 CCATCGCGGAGAATAATTTCAGT 59.190 43.478 6.13 0.00 36.56 3.41
1787 4706 3.809832 ACCATCGCGGAGAATAATTTCAG 59.190 43.478 6.13 0.00 38.63 3.02
1788 4707 3.804036 ACCATCGCGGAGAATAATTTCA 58.196 40.909 6.13 0.00 38.63 2.69
1789 4708 4.748102 TGTACCATCGCGGAGAATAATTTC 59.252 41.667 6.13 0.00 38.63 2.17
1790 4709 4.699637 TGTACCATCGCGGAGAATAATTT 58.300 39.130 6.13 0.00 38.63 1.82
1791 4710 4.330944 TGTACCATCGCGGAGAATAATT 57.669 40.909 6.13 0.00 38.63 1.40
1792 4711 4.537135 ATGTACCATCGCGGAGAATAAT 57.463 40.909 6.13 0.00 38.63 1.28
1793 4712 4.330944 AATGTACCATCGCGGAGAATAA 57.669 40.909 6.13 0.00 38.63 1.40
1794 4713 4.055360 CAAATGTACCATCGCGGAGAATA 58.945 43.478 6.13 0.00 38.63 1.75
1795 4714 2.872245 CAAATGTACCATCGCGGAGAAT 59.128 45.455 6.13 0.00 38.63 2.40
1796 4715 2.276201 CAAATGTACCATCGCGGAGAA 58.724 47.619 6.13 0.00 38.63 2.87
1797 4716 1.934589 CAAATGTACCATCGCGGAGA 58.065 50.000 6.13 0.00 38.63 3.71
1798 4717 0.304705 GCAAATGTACCATCGCGGAG 59.695 55.000 6.13 0.00 38.63 4.63
1799 4718 0.107897 AGCAAATGTACCATCGCGGA 60.108 50.000 6.13 0.00 38.63 5.54
1800 4719 0.027979 CAGCAAATGTACCATCGCGG 59.972 55.000 6.13 0.00 42.50 6.46
1801 4720 1.006086 TCAGCAAATGTACCATCGCG 58.994 50.000 0.00 0.00 0.00 5.87
1802 4721 3.485947 TTTCAGCAAATGTACCATCGC 57.514 42.857 0.00 0.00 0.00 4.58
1803 4722 5.937165 CATTTTCAGCAAATGTACCATCG 57.063 39.130 0.00 0.00 44.83 3.84
1830 4749 0.897401 TGCACGCCATCAAATCCCAA 60.897 50.000 0.00 0.00 0.00 4.12
1832 4751 1.434696 CTGCACGCCATCAAATCCC 59.565 57.895 0.00 0.00 0.00 3.85
1993 4912 3.123620 GGAGTTGCCGAGCAGCAG 61.124 66.667 13.36 0.00 45.13 4.24
2102 5021 6.039605 TGAAAAGTTCAGTCAATGAGCATGAA 59.960 34.615 0.00 2.50 41.33 2.57
2180 5116 4.760047 CCCGAGGACCTGCAACGG 62.760 72.222 11.53 11.53 42.67 4.44
2345 5281 3.056328 GAGGCTTGTTCCCCACGC 61.056 66.667 0.00 0.00 37.59 5.34
2357 5293 0.831966 CAGCAGATCTTCTGGAGGCT 59.168 55.000 13.93 5.14 44.43 4.58
2379 5315 0.247537 GGCGAAAGGTTAATGCGACG 60.248 55.000 0.00 0.00 0.00 5.12
2383 5319 0.377203 CTCCGGCGAAAGGTTAATGC 59.623 55.000 9.30 0.00 0.00 3.56
2388 5324 2.047179 GAGCTCCGGCGAAAGGTT 60.047 61.111 9.30 0.00 44.37 3.50
2434 5399 0.832626 TCATCGTGCCATCATCAGGT 59.167 50.000 0.00 0.00 0.00 4.00
2442 5407 0.460284 GGTCGTCTTCATCGTGCCAT 60.460 55.000 0.00 0.00 0.00 4.40
2477 5442 2.408271 TGCACCTGGAGCAAGAATAG 57.592 50.000 16.60 0.00 39.39 1.73
2536 5501 4.313277 TCTGATCTAACGGCTTCTGATG 57.687 45.455 0.00 0.00 0.00 3.07
2541 5506 6.216569 TGAATACATCTGATCTAACGGCTTC 58.783 40.000 0.00 0.00 0.00 3.86
2560 5525 9.838975 CTACACAACAATTTACAAGCATGAATA 57.161 29.630 0.00 0.00 0.00 1.75
2579 5544 2.894765 TGTAGTAGTGCAGCCTACACAA 59.105 45.455 18.08 5.70 39.84 3.33
2687 5830 7.448469 TTACTTTTTGTAGTACTCCTACCGAGT 59.552 37.037 0.00 0.00 44.66 4.18
2691 5834 8.579863 TCAGTTACTTTTTGTAGTACTCCTACC 58.420 37.037 0.00 0.00 44.66 3.18
2698 5841 9.538508 TTCCTTCTCAGTTACTTTTTGTAGTAC 57.461 33.333 0.00 0.00 30.62 2.73
2763 5908 2.338577 AGCACTTGATCCTGGTATGC 57.661 50.000 0.00 0.00 0.00 3.14
2808 5953 4.701956 AAAAACGCAGGATATGGTTGAG 57.298 40.909 0.00 0.00 0.00 3.02
2817 5962 3.924686 CGAGTGTAGTAAAAACGCAGGAT 59.075 43.478 0.00 0.00 0.00 3.24
3025 6184 2.559840 CTGTTGGCGCAGAAGCTG 59.440 61.111 10.83 0.00 38.70 4.24
3058 6217 4.410228 TCTCAAGGACAATCTAATGGGGAG 59.590 45.833 0.00 0.00 0.00 4.30
3113 6272 2.478292 AGGACAATCTAATGGGGACGT 58.522 47.619 0.00 0.00 0.00 4.34
3147 6363 0.976641 TCCATTGACTCAGAAGGCGT 59.023 50.000 0.00 0.00 30.57 5.68
3244 6460 1.135315 CACACAAATGCGCAGGCTATT 60.135 47.619 18.32 0.76 40.82 1.73
3262 6478 1.001641 AAGCATCCTGGCCTCACAC 60.002 57.895 3.32 0.00 0.00 3.82
3274 6490 3.055094 TGACTCCTGTAAAGGGAAGCATC 60.055 47.826 0.00 0.00 31.92 3.91


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

AutoCloner maintained by Alex Coulton.