Multiple sequence alignment - TraesCS4D01G128400

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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 TraesCS4D01G128400 chr4D 100.000 2222 0 0 1 2222 112723294 112725515 0.000000e+00 4104.0
1 TraesCS4D01G128400 chr4A 93.760 1234 47 8 605 1808 464697363 464696130 0.000000e+00 1825.0
2 TraesCS4D01G128400 chr4A 89.882 425 27 8 1807 2222 464695848 464695431 1.170000e-147 532.0
3 TraesCS4D01G128400 chr4A 88.303 436 39 8 1 433 464698227 464697801 1.520000e-141 512.0
4 TraesCS4D01G128400 chr4A 97.938 97 2 0 1712 1808 464696059 464695963 3.790000e-38 169.0
5 TraesCS4D01G128400 chr4B 93.214 840 25 12 673 1501 173173984 173174802 0.000000e+00 1206.0
6 TraesCS4D01G128400 chr4B 91.627 418 30 2 1808 2222 173175115 173175530 6.880000e-160 573.0
7 TraesCS4D01G128400 chr4B 92.708 384 27 1 1 384 173111137 173111519 8.970000e-154 553.0
8 TraesCS4D01G128400 chr4B 88.506 261 14 3 1542 1786 173174791 173175051 3.590000e-78 302.0
9 TraesCS4D01G128400 chr4B 95.238 63 3 0 417 479 173167666 173167604 1.400000e-17 100.0
10 TraesCS4D01G128400 chr5B 96.018 226 9 0 997 1222 246181016 246181241 3.490000e-98 368.0
11 TraesCS4D01G128400 chr5A 96.018 226 9 0 997 1222 299504522 299504297 3.490000e-98 368.0
12 TraesCS4D01G128400 chr5D 95.575 226 10 0 997 1222 224944013 224943788 1.620000e-96 363.0
13 TraesCS4D01G128400 chr6A 100.000 28 0 0 1807 1834 591774523 591774496 4.000000e-03 52.8


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 TraesCS4D01G128400 chr4D 112723294 112725515 2221 False 4104.000000 4104 100.000000 1 2222 1 chr4D.!!$F1 2221
1 TraesCS4D01G128400 chr4A 464695431 464698227 2796 True 759.500000 1825 92.470750 1 2222 4 chr4A.!!$R1 2221
2 TraesCS4D01G128400 chr4B 173173984 173175530 1546 False 693.666667 1206 91.115667 673 2222 3 chr4B.!!$F2 1549

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
497 802 0.034059 ACTTCGAACACTGCCCTCAG 59.966 55.0 0.0 0.0 45.71 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2623 0.109272 CAGAGCAAAGCAGTGCCATG 60.109 55.0 12.58 12.36 46.14 3.66 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
72 73 2.373502 AGAGAGGGTGGACCAAAGAAAG 59.626 50.000 0.00 0.00 43.89 2.62
73 74 1.202940 AGAGGGTGGACCAAAGAAAGC 60.203 52.381 0.00 0.00 43.89 3.51
82 84 1.136891 ACCAAAGAAAGCTTGTGGCAC 59.863 47.619 11.55 11.55 44.79 5.01
120 122 2.679355 GCGACAGCAACACACATAAA 57.321 45.000 0.00 0.00 44.35 1.40
121 123 2.574322 GCGACAGCAACACACATAAAG 58.426 47.619 0.00 0.00 44.35 1.85
122 124 2.574322 CGACAGCAACACACATAAAGC 58.426 47.619 0.00 0.00 0.00 3.51
125 127 0.881118 AGCAACACACATAAAGCGGG 59.119 50.000 0.00 0.00 0.00 6.13
126 128 0.596082 GCAACACACATAAAGCGGGT 59.404 50.000 0.00 0.00 0.00 5.28
127 129 1.000717 GCAACACACATAAAGCGGGTT 60.001 47.619 0.00 0.00 0.00 4.11
128 130 2.226912 GCAACACACATAAAGCGGGTTA 59.773 45.455 0.00 0.00 0.00 2.85
129 131 3.669557 GCAACACACATAAAGCGGGTTAG 60.670 47.826 0.00 0.00 0.00 2.34
164 166 6.730960 TTTTAGATGTTGAACCGACCATAC 57.269 37.500 0.00 0.00 0.00 2.39
165 167 2.888594 AGATGTTGAACCGACCATACG 58.111 47.619 0.00 0.00 0.00 3.06
167 169 1.785768 TGTTGAACCGACCATACGTG 58.214 50.000 0.00 0.00 0.00 4.49
169 171 2.223994 TGTTGAACCGACCATACGTGAA 60.224 45.455 0.00 0.00 0.00 3.18
170 172 2.068837 TGAACCGACCATACGTGAAC 57.931 50.000 0.00 0.00 0.00 3.18
173 175 0.963962 ACCGACCATACGTGAACACT 59.036 50.000 0.00 0.00 0.00 3.55
202 204 8.223769 CGATACATGGCTTATTCATTACACTTC 58.776 37.037 0.00 0.00 0.00 3.01
214 216 5.168569 TCATTACACTTCTTCCACGATGTC 58.831 41.667 0.00 0.00 0.00 3.06
242 244 2.095692 CGAATTCCACGATGTTGCATGA 59.904 45.455 0.00 0.00 0.00 3.07
243 245 3.429085 GAATTCCACGATGTTGCATGAC 58.571 45.455 0.00 0.00 0.00 3.06
250 252 1.068402 CGATGTTGCATGACAAAGGCA 60.068 47.619 0.00 0.00 40.82 4.75
251 253 2.607526 CGATGTTGCATGACAAAGGCAA 60.608 45.455 0.00 8.05 44.50 4.52
288 290 1.370051 GTGCAAGGACCGAAAACGC 60.370 57.895 0.00 0.00 0.00 4.84
289 291 1.525077 TGCAAGGACCGAAAACGCT 60.525 52.632 0.00 0.00 0.00 5.07
290 292 0.249953 TGCAAGGACCGAAAACGCTA 60.250 50.000 0.00 0.00 0.00 4.26
298 300 0.872388 CCGAAAACGCTAGTTGGCTT 59.128 50.000 0.00 0.00 41.05 4.35
303 305 0.688487 AACGCTAGTTGGCTTGGGTA 59.312 50.000 0.00 0.00 41.12 3.69
332 334 0.620556 TGAGCCAAAGGTCATCCCTC 59.379 55.000 0.00 0.00 45.47 4.30
337 339 0.745845 CAAAGGTCATCCCTCAGCCG 60.746 60.000 0.00 0.00 45.47 5.52
339 341 4.554036 GGTCATCCCTCAGCCGGC 62.554 72.222 21.89 21.89 0.00 6.13
359 361 3.814268 CGGGCGCAACAATCTGGG 61.814 66.667 10.83 0.00 0.00 4.45
368 370 2.289010 GCAACAATCTGGGAAGGTTTGG 60.289 50.000 0.00 0.00 0.00 3.28
371 373 2.378547 ACAATCTGGGAAGGTTTGGCTA 59.621 45.455 0.00 0.00 0.00 3.93
381 383 4.338400 GGAAGGTTTGGCTATTGTCATACC 59.662 45.833 12.15 12.15 45.90 2.73
386 388 6.792326 GGTTTGGCTATTGTCATACCTAAAC 58.208 40.000 12.65 0.00 43.46 2.01
400 402 8.557029 GTCATACCTAAACCTTGCATTGTATAC 58.443 37.037 0.00 0.00 0.00 1.47
401 403 8.491134 TCATACCTAAACCTTGCATTGTATACT 58.509 33.333 4.17 0.00 0.00 2.12
403 405 9.774413 ATACCTAAACCTTGCATTGTATACTAC 57.226 33.333 4.17 0.00 0.00 2.73
404 406 7.858498 ACCTAAACCTTGCATTGTATACTACT 58.142 34.615 4.17 0.00 0.00 2.57
405 407 8.984855 ACCTAAACCTTGCATTGTATACTACTA 58.015 33.333 4.17 0.00 0.00 1.82
406 408 9.257651 CCTAAACCTTGCATTGTATACTACTAC 57.742 37.037 4.17 0.00 0.00 2.73
407 409 7.766219 AAACCTTGCATTGTATACTACTACG 57.234 36.000 4.17 0.00 0.00 3.51
412 414 7.377928 CCTTGCATTGTATACTACTACGTGTAC 59.622 40.741 0.00 0.00 33.64 2.90
440 745 8.868522 AATACTTGATTCAAGATTGAGTTGGA 57.131 30.769 28.60 0.00 43.42 3.53
450 755 4.965814 AGATTGAGTTGGATCGCATATGT 58.034 39.130 4.29 0.00 0.00 2.29
451 756 5.371526 AGATTGAGTTGGATCGCATATGTT 58.628 37.500 4.29 0.00 0.00 2.71
467 772 1.855513 TGTTGGTAACCTTCGTCACG 58.144 50.000 0.00 0.00 0.00 4.35
472 777 1.468736 GGTAACCTTCGTCACGCCTAG 60.469 57.143 0.00 0.00 0.00 3.02
488 793 4.624452 ACGCCTAGAAATTACTTCGAACAC 59.376 41.667 0.00 0.00 39.22 3.32
489 794 4.863131 CGCCTAGAAATTACTTCGAACACT 59.137 41.667 0.00 0.00 39.22 3.55
490 795 5.220228 CGCCTAGAAATTACTTCGAACACTG 60.220 44.000 0.00 0.00 39.22 3.66
491 796 5.446073 GCCTAGAAATTACTTCGAACACTGC 60.446 44.000 0.00 0.00 39.22 4.40
494 799 3.418684 AATTACTTCGAACACTGCCCT 57.581 42.857 0.00 0.00 0.00 5.19
496 801 1.334160 TACTTCGAACACTGCCCTCA 58.666 50.000 0.00 0.00 0.00 3.86
497 802 0.034059 ACTTCGAACACTGCCCTCAG 59.966 55.000 0.00 0.00 45.71 3.35
498 803 1.294659 CTTCGAACACTGCCCTCAGC 61.295 60.000 0.00 0.00 44.10 4.26
499 804 2.731691 TTCGAACACTGCCCTCAGCC 62.732 60.000 0.00 0.00 44.10 4.85
500 805 2.360475 GAACACTGCCCTCAGCCC 60.360 66.667 0.00 0.00 44.10 5.19
517 826 1.754234 CCGGCTCAAAGGGGATTGG 60.754 63.158 0.00 0.00 0.00 3.16
523 832 2.728007 CTCAAAGGGGATTGGAACTCC 58.272 52.381 0.00 0.00 0.00 3.85
533 842 1.243342 TTGGAACTCCATGCAAGCGG 61.243 55.000 0.00 0.00 46.97 5.52
548 857 2.238942 AGCGGCGTCATGAATAATGA 57.761 45.000 9.37 0.00 43.24 2.57
559 868 6.327279 TCATGAATAATGACGGTATCGAGT 57.673 37.500 0.34 0.00 40.50 4.18
560 869 7.443259 TCATGAATAATGACGGTATCGAGTA 57.557 36.000 0.34 0.00 40.50 2.59
561 870 7.878036 TCATGAATAATGACGGTATCGAGTAA 58.122 34.615 0.34 0.00 40.50 2.24
562 871 7.806487 TCATGAATAATGACGGTATCGAGTAAC 59.194 37.037 0.34 0.00 40.50 2.50
563 872 6.441274 TGAATAATGACGGTATCGAGTAACC 58.559 40.000 0.34 4.67 40.11 2.85
579 888 0.249741 AACCGGAAGTGTCGTCTTGG 60.250 55.000 9.46 0.00 0.00 3.61
581 890 0.388649 CCGGAAGTGTCGTCTTGGAG 60.389 60.000 0.00 0.00 0.00 3.86
585 894 2.296471 GGAAGTGTCGTCTTGGAGAAGA 59.704 50.000 0.00 0.00 35.75 2.87
593 902 2.231716 TCTTGGAGAAGACCATCGGA 57.768 50.000 0.00 0.00 39.82 4.55
594 903 2.103373 TCTTGGAGAAGACCATCGGAG 58.897 52.381 0.00 0.00 39.82 4.63
595 904 1.827969 CTTGGAGAAGACCATCGGAGT 59.172 52.381 0.00 0.00 39.82 3.85
596 905 1.475403 TGGAGAAGACCATCGGAGTC 58.525 55.000 0.00 0.00 34.77 3.36
597 906 1.006043 TGGAGAAGACCATCGGAGTCT 59.994 52.381 0.00 0.00 46.50 3.24
627 936 2.737359 GCGAATGACCATCGGAGTTACA 60.737 50.000 0.00 0.00 40.54 2.41
633 942 3.243401 TGACCATCGGAGTTACATCATCG 60.243 47.826 0.00 0.00 0.00 3.84
643 952 4.191544 AGTTACATCATCGACACCAATGG 58.808 43.478 0.00 0.00 0.00 3.16
661 970 8.739039 CACCAATGGTAGATTTTGAGTATGAAA 58.261 33.333 3.85 0.00 32.11 2.69
713 1022 5.576447 AGGAAACAAATTGTTCTCAACGT 57.424 34.783 12.11 0.00 40.14 3.99
1284 1607 9.937175 GCACATGATTCCTTTTTATTACTACTC 57.063 33.333 0.00 0.00 0.00 2.59
1309 1632 7.888021 TCATAAGGGTTTGTTGTCTATGTGAAT 59.112 33.333 0.00 0.00 0.00 2.57
1330 1653 2.930826 TGGTTCTCCTTCTGTTGTCC 57.069 50.000 0.00 0.00 34.23 4.02
1398 1724 1.217882 AGACGCCTGTTTTCTGTTCG 58.782 50.000 0.00 0.00 0.00 3.95
1501 1827 3.303329 GGTTTCCGTTTTACCGTGAGTTC 60.303 47.826 0.00 0.00 0.00 3.01
1504 1830 2.890311 TCCGTTTTACCGTGAGTTCCTA 59.110 45.455 0.00 0.00 0.00 2.94
1530 1856 2.907910 ACGCTGCTTTGCTAATTGAG 57.092 45.000 0.00 0.00 0.00 3.02
1592 1918 6.657541 TGGTGGTAGATTGGTTGATTTAGTTC 59.342 38.462 0.00 0.00 0.00 3.01
1678 2004 6.564328 AGAACTTTTCTTACTGGCTTTTGTG 58.436 36.000 0.00 0.00 36.36 3.33
1695 2021 2.623535 TGTGTGCTACTTGTTCGTTGT 58.376 42.857 0.00 0.00 0.00 3.32
1706 2032 5.910614 ACTTGTTCGTTGTTAGGTTCTAGT 58.089 37.500 0.00 0.00 0.00 2.57
1849 2473 7.272299 GGTAGTAGAAAGTAACTAAACAGACGC 59.728 40.741 0.00 0.00 30.32 5.19
1992 2623 0.961753 CCTCCCTTGGTTTTGCTGAC 59.038 55.000 0.00 0.00 0.00 3.51
2004 2635 0.824595 TTGCTGACATGGCACTGCTT 60.825 50.000 13.44 0.00 39.55 3.91
2027 2658 4.757594 TGCTCTGTGTTTGCAAAGAAAAT 58.242 34.783 13.26 0.00 38.42 1.82
2030 2661 6.255453 TGCTCTGTGTTTGCAAAGAAAATAAC 59.745 34.615 13.26 0.00 38.42 1.89
2031 2662 6.292328 GCTCTGTGTTTGCAAAGAAAATAACC 60.292 38.462 13.26 0.00 38.42 2.85
2092 2723 3.974871 TTTGCTTTCCGTGTTTAGTCC 57.025 42.857 0.00 0.00 0.00 3.85
2093 2724 2.623878 TGCTTTCCGTGTTTAGTCCA 57.376 45.000 0.00 0.00 0.00 4.02
2099 2730 3.176552 TCCGTGTTTAGTCCAACGAAA 57.823 42.857 0.00 0.00 38.27 3.46
2116 2747 3.242712 ACGAAAACAAAGCTGATTTTGCG 59.757 39.130 11.27 11.27 40.80 4.85
2128 2759 8.931385 AAGCTGATTTTGCGTATTGAATTTAT 57.069 26.923 0.00 0.00 35.28 1.40
2162 2796 1.411977 ACTGCAGCTAATCATCGCTCT 59.588 47.619 15.27 0.00 33.45 4.09
2163 2797 1.793532 CTGCAGCTAATCATCGCTCTG 59.206 52.381 0.00 0.00 33.45 3.35
2178 2812 0.309922 CTCTGTTGCAGTGCAGGTTG 59.690 55.000 18.81 10.10 40.61 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.596082 AATTGTACGGTGCCACAAGC 59.404 50.000 0.00 0.00 38.01 4.01
73 74 3.669557 GCTTAATTGTACGGTGCCACAAG 60.670 47.826 0.00 0.00 38.01 3.16
82 84 2.032894 CGCATGGAGCTTAATTGTACGG 60.033 50.000 0.00 0.00 42.61 4.02
104 106 1.266718 CCGCTTTATGTGTGTTGCTGT 59.733 47.619 0.00 0.00 0.00 4.40
151 153 1.340568 TGTTCACGTATGGTCGGTTCA 59.659 47.619 0.00 0.00 34.94 3.18
164 166 1.324435 CATGTATCGGCAGTGTTCACG 59.676 52.381 0.00 0.00 0.00 4.35
165 167 1.665679 CCATGTATCGGCAGTGTTCAC 59.334 52.381 0.00 0.00 0.00 3.18
188 190 7.327975 ACATCGTGGAAGAAGTGTAATGAATA 58.672 34.615 0.00 0.00 0.00 1.75
189 191 6.173339 ACATCGTGGAAGAAGTGTAATGAAT 58.827 36.000 0.00 0.00 0.00 2.57
198 200 0.317160 TGCGACATCGTGGAAGAAGT 59.683 50.000 2.85 0.00 42.22 3.01
202 204 0.647410 GTGATGCGACATCGTGGAAG 59.353 55.000 12.88 0.00 42.22 3.46
214 216 0.930310 ATCGTGGAATTCGTGATGCG 59.070 50.000 0.00 0.00 43.01 4.73
224 226 2.435422 TGTCATGCAACATCGTGGAAT 58.565 42.857 0.00 0.00 0.00 3.01
227 229 2.587956 CTTTGTCATGCAACATCGTGG 58.412 47.619 0.00 0.00 36.72 4.94
230 232 1.068402 TGCCTTTGTCATGCAACATCG 60.068 47.619 0.00 0.00 36.72 3.84
288 290 2.618045 CCACCTTACCCAAGCCAACTAG 60.618 54.545 0.00 0.00 0.00 2.57
289 291 1.353022 CCACCTTACCCAAGCCAACTA 59.647 52.381 0.00 0.00 0.00 2.24
290 292 0.112412 CCACCTTACCCAAGCCAACT 59.888 55.000 0.00 0.00 0.00 3.16
298 300 1.998530 CTCATGCCCACCTTACCCA 59.001 57.895 0.00 0.00 0.00 4.51
342 344 3.814268 CCCAGATTGTTGCGCCCG 61.814 66.667 4.18 0.00 0.00 6.13
359 361 5.193679 AGGTATGACAATAGCCAAACCTTC 58.806 41.667 0.00 0.00 37.46 3.46
368 370 5.588648 TGCAAGGTTTAGGTATGACAATAGC 59.411 40.000 0.00 0.00 37.09 2.97
371 373 6.437162 ACAATGCAAGGTTTAGGTATGACAAT 59.563 34.615 0.00 0.00 0.00 2.71
381 383 8.965172 CGTAGTAGTATACAATGCAAGGTTTAG 58.035 37.037 5.50 0.00 46.26 1.85
386 388 6.270815 ACACGTAGTAGTATACAATGCAAGG 58.729 40.000 5.50 0.00 46.26 3.61
405 407 9.817809 ATCTTGAATCAAGTATTATGTACACGT 57.182 29.630 20.91 0.00 41.66 4.49
423 425 4.264253 TGCGATCCAACTCAATCTTGAAT 58.736 39.130 0.00 0.00 36.64 2.57
424 426 3.673902 TGCGATCCAACTCAATCTTGAA 58.326 40.909 0.00 0.00 36.64 2.69
439 744 4.084537 CGAAGGTTACCAACATATGCGATC 60.085 45.833 3.51 0.00 0.00 3.69
440 745 3.807622 CGAAGGTTACCAACATATGCGAT 59.192 43.478 3.51 0.00 0.00 4.58
450 755 0.600782 GGCGTGACGAAGGTTACCAA 60.601 55.000 10.10 0.00 29.32 3.67
451 756 1.005867 GGCGTGACGAAGGTTACCA 60.006 57.895 10.10 0.00 29.32 3.25
467 772 5.446073 GCAGTGTTCGAAGTAATTTCTAGGC 60.446 44.000 0.00 0.00 33.44 3.93
472 777 3.751698 AGGGCAGTGTTCGAAGTAATTTC 59.248 43.478 0.00 0.00 0.00 2.17
491 796 3.984193 CTTTGAGCCGGGCTGAGGG 62.984 68.421 29.31 10.77 39.88 4.30
494 799 4.033776 CCCTTTGAGCCGGGCTGA 62.034 66.667 29.31 17.11 39.88 4.26
497 802 3.662117 AATCCCCTTTGAGCCGGGC 62.662 63.158 12.11 12.11 39.22 6.13
498 803 1.754234 CAATCCCCTTTGAGCCGGG 60.754 63.158 2.18 0.00 40.29 5.73
499 804 1.754234 CCAATCCCCTTTGAGCCGG 60.754 63.158 0.00 0.00 0.00 6.13
500 805 0.323360 TTCCAATCCCCTTTGAGCCG 60.323 55.000 0.00 0.00 0.00 5.52
517 826 2.486966 GCCGCTTGCATGGAGTTC 59.513 61.111 4.46 0.00 40.77 3.01
523 832 2.255994 TTCATGACGCCGCTTGCATG 62.256 55.000 0.00 9.43 41.33 4.06
553 862 1.131883 CGACACTTCCGGTTACTCGAT 59.868 52.381 0.00 0.00 0.00 3.59
554 863 0.518636 CGACACTTCCGGTTACTCGA 59.481 55.000 0.00 0.00 0.00 4.04
555 864 0.239347 ACGACACTTCCGGTTACTCG 59.761 55.000 0.00 5.58 0.00 4.18
556 865 1.538950 AGACGACACTTCCGGTTACTC 59.461 52.381 0.00 0.00 0.00 2.59
557 866 1.613836 AGACGACACTTCCGGTTACT 58.386 50.000 0.00 0.00 0.00 2.24
558 867 2.056577 CAAGACGACACTTCCGGTTAC 58.943 52.381 0.00 0.00 0.00 2.50
559 868 1.000060 CCAAGACGACACTTCCGGTTA 60.000 52.381 0.00 0.00 0.00 2.85
560 869 0.249741 CCAAGACGACACTTCCGGTT 60.250 55.000 0.00 0.00 0.00 4.44
561 870 1.111116 TCCAAGACGACACTTCCGGT 61.111 55.000 0.00 0.00 0.00 5.28
562 871 0.388649 CTCCAAGACGACACTTCCGG 60.389 60.000 0.00 0.00 0.00 5.14
563 872 0.596577 TCTCCAAGACGACACTTCCG 59.403 55.000 0.00 0.00 0.00 4.30
564 873 2.296471 TCTTCTCCAAGACGACACTTCC 59.704 50.000 0.00 0.00 33.38 3.46
565 874 3.644884 TCTTCTCCAAGACGACACTTC 57.355 47.619 0.00 0.00 33.38 3.01
601 910 2.155279 TCCGATGGTCATTCGCAAAAA 58.845 42.857 0.00 0.00 0.00 1.94
602 911 1.737236 CTCCGATGGTCATTCGCAAAA 59.263 47.619 0.00 0.00 0.00 2.44
603 912 1.338674 ACTCCGATGGTCATTCGCAAA 60.339 47.619 0.00 0.00 0.00 3.68
604 913 0.249120 ACTCCGATGGTCATTCGCAA 59.751 50.000 0.00 0.00 0.00 4.85
605 914 0.249120 AACTCCGATGGTCATTCGCA 59.751 50.000 0.00 0.00 0.00 5.10
606 915 1.859080 GTAACTCCGATGGTCATTCGC 59.141 52.381 0.00 0.00 0.00 4.70
607 916 3.159353 TGTAACTCCGATGGTCATTCG 57.841 47.619 0.00 0.00 0.00 3.34
608 917 4.693283 TGATGTAACTCCGATGGTCATTC 58.307 43.478 0.00 0.00 0.00 2.67
609 918 4.753516 TGATGTAACTCCGATGGTCATT 57.246 40.909 0.00 0.00 0.00 2.57
610 919 4.559502 CGATGATGTAACTCCGATGGTCAT 60.560 45.833 0.00 0.00 0.00 3.06
611 920 3.243401 CGATGATGTAACTCCGATGGTCA 60.243 47.826 0.00 0.00 0.00 4.02
612 921 3.004419 TCGATGATGTAACTCCGATGGTC 59.996 47.826 0.00 0.00 0.00 4.02
613 922 2.956333 TCGATGATGTAACTCCGATGGT 59.044 45.455 0.00 0.00 0.00 3.55
614 923 3.243401 TGTCGATGATGTAACTCCGATGG 60.243 47.826 0.00 0.00 0.00 3.51
615 924 3.731216 GTGTCGATGATGTAACTCCGATG 59.269 47.826 0.00 0.00 0.00 3.84
616 925 3.243434 GGTGTCGATGATGTAACTCCGAT 60.243 47.826 0.00 0.00 0.00 4.18
617 926 2.098607 GGTGTCGATGATGTAACTCCGA 59.901 50.000 0.00 0.00 0.00 4.55
618 927 2.159296 TGGTGTCGATGATGTAACTCCG 60.159 50.000 0.00 0.00 0.00 4.63
619 928 3.520290 TGGTGTCGATGATGTAACTCC 57.480 47.619 0.00 0.00 0.00 3.85
627 936 4.963318 ATCTACCATTGGTGTCGATGAT 57.037 40.909 18.83 8.91 37.01 2.45
633 942 7.552687 TCATACTCAAAATCTACCATTGGTGTC 59.447 37.037 18.83 0.00 36.19 3.67
643 952 8.138365 TGCCGTATTTCATACTCAAAATCTAC 57.862 34.615 0.00 0.00 33.59 2.59
1237 1559 2.124277 AAGGCGAGGGGAATAACAAC 57.876 50.000 0.00 0.00 0.00 3.32
1284 1607 7.447374 TTCACATAGACAACAAACCCTTATG 57.553 36.000 0.00 0.00 0.00 1.90
1309 1632 3.056107 CGGACAACAGAAGGAGAACCATA 60.056 47.826 0.00 0.00 38.94 2.74
1330 1653 6.609237 TGCTTAATTTGAGATTCTCATCCG 57.391 37.500 16.82 4.82 40.39 4.18
1398 1724 7.862372 TCTGACTTTGCATACAAACTGAAAATC 59.138 33.333 0.00 0.00 40.84 2.17
1454 1780 6.364165 CCACAATTTCTAGTTCATTGCACTTG 59.636 38.462 0.00 0.00 32.08 3.16
1501 1827 2.663119 GCAAAGCAGCGTTTCAATTAGG 59.337 45.455 0.00 0.00 0.00 2.69
1504 1830 2.514205 AGCAAAGCAGCGTTTCAATT 57.486 40.000 0.00 0.00 40.15 2.32
1530 1856 3.680642 ACACACGCAAGCATATCATTC 57.319 42.857 0.00 0.00 45.62 2.67
1592 1918 4.599041 TCAACAAGGGGATAAACCTCATG 58.401 43.478 0.00 0.00 42.78 3.07
1678 2004 3.805971 ACCTAACAACGAACAAGTAGCAC 59.194 43.478 0.00 0.00 0.00 4.40
1849 2473 4.935702 TCAGCTTTCATGACCAAACAAAG 58.064 39.130 0.00 0.00 0.00 2.77
1992 2623 0.109272 CAGAGCAAAGCAGTGCCATG 60.109 55.000 12.58 12.36 46.14 3.66
2004 2635 3.865011 TTCTTTGCAAACACAGAGCAA 57.135 38.095 8.05 0.00 45.53 3.91
2027 2658 6.491745 TGTACTTGCATGGAAGATTTTGGTTA 59.508 34.615 30.84 9.40 0.00 2.85
2030 2661 5.389859 TGTACTTGCATGGAAGATTTTGG 57.610 39.130 30.84 6.28 0.00 3.28
2031 2662 6.880822 CATGTACTTGCATGGAAGATTTTG 57.119 37.500 30.84 18.29 41.70 2.44
2092 2723 4.957372 GCAAAATCAGCTTTGTTTTCGTTG 59.043 37.500 0.00 0.00 38.35 4.10
2093 2724 4.259770 CGCAAAATCAGCTTTGTTTTCGTT 60.260 37.500 0.00 0.00 38.35 3.85
2099 2730 5.527951 TCAATACGCAAAATCAGCTTTGTT 58.472 33.333 0.00 0.00 38.35 2.83
2128 2759 5.233083 AGCTGCAGTGAATTATAGGCATA 57.767 39.130 16.64 0.00 0.00 3.14
2137 2768 3.003068 GCGATGATTAGCTGCAGTGAATT 59.997 43.478 16.64 1.45 0.00 2.17
2138 2769 2.547211 GCGATGATTAGCTGCAGTGAAT 59.453 45.455 16.64 14.59 0.00 2.57
2139 2770 1.935873 GCGATGATTAGCTGCAGTGAA 59.064 47.619 16.64 10.16 0.00 3.18
2140 2771 1.137675 AGCGATGATTAGCTGCAGTGA 59.862 47.619 16.64 0.00 42.82 3.41
2142 2773 1.411977 AGAGCGATGATTAGCTGCAGT 59.588 47.619 16.64 4.79 44.69 4.40
2143 2774 1.793532 CAGAGCGATGATTAGCTGCAG 59.206 52.381 10.11 10.11 44.69 4.41
2148 2782 1.935873 TGCAACAGAGCGATGATTAGC 59.064 47.619 0.00 0.00 37.31 3.09
2162 2796 1.379710 ACCAACCTGCACTGCAACA 60.380 52.632 4.99 0.00 38.41 3.33
2163 2797 1.360192 GACCAACCTGCACTGCAAC 59.640 57.895 4.99 0.00 38.41 4.17
2178 2812 0.811281 GCAGGCAACAATAGGTGACC 59.189 55.000 0.00 0.00 41.41 4.02
2188 2822 0.178767 AGCTATCATCGCAGGCAACA 59.821 50.000 0.00 0.00 41.41 3.33


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

AutoCloner maintained by Alex Coulton.