Multiple sequence alignment - TraesCS5B01G039900

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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 TraesCS5B01G039900 chr5B 100.000 3956 0 0 1 3956 44857705 44861660 0.000000e+00 7306
1 TraesCS5B01G039900 chr5D 93.926 3260 124 17 743 3956 45018252 45021483 0.000000e+00 4855
2 TraesCS5B01G039900 chr5D 83.285 694 49 22 20 674 45016279 45016944 9.530000e-161 577
3 TraesCS5B01G039900 chr5D 83.285 694 49 22 20 674 45017581 45018246 9.530000e-161 577
4 TraesCS5B01G039900 chr5D 92.547 161 9 3 743 901 45016950 45017109 1.110000e-55 228
5 TraesCS5B01G039900 chr5A 90.075 3355 172 56 106 3351 35654185 35657487 0.000000e+00 4202
6 TraesCS5B01G039900 chr5A 83.958 480 35 15 3406 3880 35657486 35657928 4.730000e-114 422
7 TraesCS5B01G039900 chr5A 95.000 80 4 0 3877 3956 35658114 35658193 4.150000e-25 126
8 TraesCS5B01G039900 chr7A 82.488 217 34 4 8 221 640628041 640628256 1.880000e-43 187
9 TraesCS5B01G039900 chr4A 82.353 221 31 6 8 221 675630489 675630708 6.750000e-43 185
10 TraesCS5B01G039900 chr3D 81.567 217 35 5 8 221 559727728 559727514 1.460000e-39 174
11 TraesCS5B01G039900 chr3D 81.567 217 35 5 8 221 559730197 559729983 1.460000e-39 174
12 TraesCS5B01G039900 chr3D 80.645 217 38 4 8 221 615241181 615241396 8.790000e-37 165
13 TraesCS5B01G039900 chr3D 79.237 236 43 6 8 240 559725503 559725271 4.090000e-35 159
14 TraesCS5B01G039900 chr1B 81.106 217 37 4 8 221 471021513 471021298 1.890000e-38 171


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 TraesCS5B01G039900 chr5B 44857705 44861660 3955 False 7306.000000 7306 100.000000 1 3956 1 chr5B.!!$F1 3955
1 TraesCS5B01G039900 chr5D 45016279 45021483 5204 False 1559.250000 4855 88.260750 20 3956 4 chr5D.!!$F1 3936
2 TraesCS5B01G039900 chr5A 35654185 35658193 4008 False 1583.333333 4202 89.677667 106 3956 3 chr5A.!!$F1 3850

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
482 497 0.243095 GGCTACGTCAAGACCGAAGT 59.757 55.0 0.0 0.0 0.00 3.01 F
1441 2820 0.037232 CGTCAACTTCTCCACCTCCC 60.037 60.0 0.0 0.0 0.00 4.30 F
1767 3146 0.103937 GCCTTCGAGATCACCTCCTG 59.896 60.0 0.0 0.0 38.71 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 3704 0.914417 TGGTGCCCTTCCCTCTAAGG 60.914 60.000 0.0 0.0 44.87 2.69 R
2902 4281 0.404040 AATCCCGCTTTCTGTCCCAA 59.596 50.000 0.0 0.0 0.00 4.12 R
3437 4844 1.547675 GGCACACAGAAATCCCCAGAA 60.548 52.381 0.0 0.0 0.00 3.02 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
36 37 7.637229 CATCATGCTTATACAAACCTCAGAAG 58.363 38.462 0.00 0.00 0.00 2.85
40 41 6.711277 TGCTTATACAAACCTCAGAAGACAT 58.289 36.000 0.00 0.00 0.00 3.06
57 58 6.944862 AGAAGACATTAAGACAAAATCAGCCT 59.055 34.615 0.00 0.00 0.00 4.58
66 67 2.170187 ACAAAATCAGCCTGCCAAACAA 59.830 40.909 0.00 0.00 0.00 2.83
74 75 1.151668 CCTGCCAAACAACTCTCGAG 58.848 55.000 5.93 5.93 0.00 4.04
92 93 8.702408 CTCTCGAGAGTACTATATTTTCAACG 57.298 38.462 30.44 2.96 37.40 4.10
97 98 8.734933 CGAGAGTACTATATTTTCAACGAAGTG 58.265 37.037 0.00 0.00 45.00 3.16
309 314 1.196911 TTTATGACCCCGTCGTCCAT 58.803 50.000 0.00 0.00 34.95 3.41
317 322 0.744874 CCCGTCGTCCATGTGTAGAT 59.255 55.000 0.00 0.00 0.00 1.98
318 323 1.136305 CCCGTCGTCCATGTGTAGATT 59.864 52.381 0.00 0.00 0.00 2.40
330 345 5.446473 CCATGTGTAGATTGCTTCGTTCTTC 60.446 44.000 0.00 0.00 0.00 2.87
384 399 2.235402 GTGACCGGAGATACCTTTTCCA 59.765 50.000 9.46 0.00 36.31 3.53
400 415 4.974792 CATCGCCTATGGACCGAG 57.025 61.111 0.00 0.00 34.21 4.63
443 458 2.811317 CGTCTTCGCTGGGCAGTC 60.811 66.667 0.00 0.00 0.00 3.51
444 459 2.343758 GTCTTCGCTGGGCAGTCA 59.656 61.111 0.00 0.00 0.00 3.41
459 474 1.846007 AGTCAGCCGAAGAGATGACT 58.154 50.000 6.62 6.62 45.69 3.41
467 482 2.099263 CCGAAGAGATGACTTTCGGCTA 59.901 50.000 11.33 0.00 35.60 3.93
472 487 1.816835 AGATGACTTTCGGCTACGTCA 59.183 47.619 0.00 0.00 41.85 4.35
482 497 0.243095 GGCTACGTCAAGACCGAAGT 59.757 55.000 0.00 0.00 0.00 3.01
502 520 1.299541 AGTCTTTGCTCAACACACGG 58.700 50.000 0.00 0.00 0.00 4.94
525 543 2.618709 CAAAGAATTCGGGATACAGGGC 59.381 50.000 0.00 0.00 39.74 5.19
543 561 3.744719 CGCGACCGTCCTCTTCCA 61.745 66.667 0.00 0.00 0.00 3.53
549 567 2.058595 CCGTCCTCTTCCACCCGAT 61.059 63.158 0.00 0.00 0.00 4.18
576 616 3.725010 GCTCATTTCTTCGCGATTTTCGT 60.725 43.478 10.88 0.00 42.81 3.85
577 617 3.986128 TCATTTCTTCGCGATTTTCGTC 58.014 40.909 10.88 0.00 42.81 4.20
578 618 3.678072 TCATTTCTTCGCGATTTTCGTCT 59.322 39.130 10.88 0.00 42.81 4.18
580 620 1.346365 TCTTCGCGATTTTCGTCTGG 58.654 50.000 10.88 0.00 42.81 3.86
623 664 1.812571 GATTCTCGTTGCCAACACCAT 59.187 47.619 8.51 0.00 0.00 3.55
625 666 0.950836 TCTCGTTGCCAACACCATTG 59.049 50.000 8.51 0.00 0.00 2.82
663 714 2.683211 AGTGTTGGAGGATGCCTTTT 57.317 45.000 0.00 0.00 31.76 2.27
668 719 1.075601 TGGAGGATGCCTTTTCAGGT 58.924 50.000 0.00 0.00 43.18 4.00
696 747 5.792741 TCCATTTTAGGTTGAATTTGCTGG 58.207 37.500 0.00 0.00 0.00 4.85
702 753 4.751767 AGGTTGAATTTGCTGGTTTGAA 57.248 36.364 0.00 0.00 0.00 2.69
703 754 4.441792 AGGTTGAATTTGCTGGTTTGAAC 58.558 39.130 0.00 0.00 0.00 3.18
704 755 4.162131 AGGTTGAATTTGCTGGTTTGAACT 59.838 37.500 0.00 0.00 0.00 3.01
705 756 4.875536 GGTTGAATTTGCTGGTTTGAACTT 59.124 37.500 0.00 0.00 0.00 2.66
706 757 5.220643 GGTTGAATTTGCTGGTTTGAACTTG 60.221 40.000 0.00 0.00 0.00 3.16
707 758 4.440880 TGAATTTGCTGGTTTGAACTTGG 58.559 39.130 0.00 0.00 0.00 3.61
708 759 4.161189 TGAATTTGCTGGTTTGAACTTGGA 59.839 37.500 0.00 0.00 0.00 3.53
709 760 4.751767 ATTTGCTGGTTTGAACTTGGAA 57.248 36.364 0.00 0.00 0.00 3.53
710 761 4.751767 TTTGCTGGTTTGAACTTGGAAT 57.248 36.364 0.00 0.00 0.00 3.01
711 762 3.731652 TGCTGGTTTGAACTTGGAATG 57.268 42.857 0.00 0.00 0.00 2.67
712 763 3.295093 TGCTGGTTTGAACTTGGAATGA 58.705 40.909 0.00 0.00 0.00 2.57
713 764 3.703556 TGCTGGTTTGAACTTGGAATGAA 59.296 39.130 0.00 0.00 0.00 2.57
714 765 4.202141 TGCTGGTTTGAACTTGGAATGAAG 60.202 41.667 0.00 0.00 0.00 3.02
715 766 4.202151 GCTGGTTTGAACTTGGAATGAAGT 60.202 41.667 0.00 0.00 37.81 3.01
716 767 5.682212 GCTGGTTTGAACTTGGAATGAAGTT 60.682 40.000 0.00 0.00 46.57 2.66
717 768 5.659463 TGGTTTGAACTTGGAATGAAGTTG 58.341 37.500 3.47 0.00 44.46 3.16
718 769 5.186797 TGGTTTGAACTTGGAATGAAGTTGT 59.813 36.000 3.47 0.00 44.46 3.32
719 770 6.378564 TGGTTTGAACTTGGAATGAAGTTGTA 59.621 34.615 3.47 0.00 44.46 2.41
720 771 7.069331 TGGTTTGAACTTGGAATGAAGTTGTAT 59.931 33.333 3.47 0.00 44.46 2.29
721 772 7.382218 GGTTTGAACTTGGAATGAAGTTGTATG 59.618 37.037 3.47 0.00 44.46 2.39
722 773 6.573664 TGAACTTGGAATGAAGTTGTATGG 57.426 37.500 3.47 0.00 44.46 2.74
723 774 5.048083 TGAACTTGGAATGAAGTTGTATGGC 60.048 40.000 3.47 0.00 44.46 4.40
814 868 6.577103 TGCTGTGGTTTCATTCAACAAAATA 58.423 32.000 0.00 0.00 0.00 1.40
825 879 8.421249 TCATTCAACAAAATAGGTGGATTTCT 57.579 30.769 0.00 0.00 0.00 2.52
826 880 8.522830 TCATTCAACAAAATAGGTGGATTTCTC 58.477 33.333 0.00 0.00 0.00 2.87
832 2190 7.886338 ACAAAATAGGTGGATTTCTCAGAAAC 58.114 34.615 0.68 0.00 0.00 2.78
920 2278 2.551071 GCCAAACTGCTGGTAGTTCTCT 60.551 50.000 4.70 0.00 39.86 3.10
928 2286 3.508012 TGCTGGTAGTTCTCTTCTCTGTC 59.492 47.826 0.00 0.00 0.00 3.51
969 2345 1.157276 CCCCTCCCAGATCCGATCT 59.843 63.158 4.96 4.96 41.15 2.75
970 2346 0.902516 CCCCTCCCAGATCCGATCTC 60.903 65.000 8.00 0.00 37.58 2.75
972 2348 1.247419 CCTCCCAGATCCGATCTCCG 61.247 65.000 8.00 1.85 37.58 4.63
1441 2820 0.037232 CGTCAACTTCTCCACCTCCC 60.037 60.000 0.00 0.00 0.00 4.30
1767 3146 0.103937 GCCTTCGAGATCACCTCCTG 59.896 60.000 0.00 0.00 38.71 3.86
1863 3242 2.003301 GACAGGAATTTCGAGCTGTCC 58.997 52.381 16.98 0.00 36.26 4.02
1896 3275 2.111251 GATTGGAGCTACCGCCCC 59.889 66.667 0.00 0.00 42.61 5.80
1944 3323 1.677576 CTGAACAAGCTGAAGTTGCCA 59.322 47.619 4.41 0.00 0.00 4.92
1977 3356 1.109920 ATCTGGATGACTCGGACCCG 61.110 60.000 1.31 1.31 41.35 5.28
2007 3386 1.796796 GAACAGCTGGTCGCCATTC 59.203 57.895 17.57 5.59 40.39 2.67
2224 3603 1.804151 ACACGAATATTGCAACTGCGT 59.196 42.857 10.35 10.35 45.83 5.24
2325 3704 1.367659 GGAACATGCTGCTGAGTCTC 58.632 55.000 0.00 0.00 0.00 3.36
2328 3707 0.982704 ACATGCTGCTGAGTCTCCTT 59.017 50.000 0.00 0.00 0.00 3.36
2508 3887 0.597118 TGAACACGCAATTTGCTGCC 60.597 50.000 18.57 11.31 42.25 4.85
2550 3929 1.972795 AGCAACATTGTTGATTGGGCT 59.027 42.857 29.04 16.61 0.00 5.19
2607 3986 2.497675 AGCAGGCGTGAAGAATCTCTTA 59.502 45.455 11.29 0.00 36.73 2.10
2610 3989 4.686972 CAGGCGTGAAGAATCTCTTATCA 58.313 43.478 0.00 0.00 36.73 2.15
2697 4076 3.816994 GGTGGACAACTACCTCTTGTTT 58.183 45.455 0.00 0.00 43.07 2.83
2757 4136 1.203237 AGAGGACCCTTCAGAGAAGCA 60.203 52.381 1.29 0.00 0.00 3.91
3037 4422 3.963428 ATAGTCTCTTGCCGACACTTT 57.037 42.857 0.00 0.00 33.89 2.66
3111 4499 2.635915 TCTCTGTTGTCGGGTTTATGGT 59.364 45.455 0.00 0.00 0.00 3.55
3347 4754 9.722056 GCGTTTCTTATGAATATCAGTCAAATT 57.278 29.630 0.00 0.00 31.56 1.82
3369 4776 3.243737 TGTTACGTATAGCCATGCTGGAG 60.244 47.826 0.00 0.00 40.96 3.86
3370 4777 1.414158 ACGTATAGCCATGCTGGAGT 58.586 50.000 6.40 0.00 40.96 3.85
3371 4778 2.594131 ACGTATAGCCATGCTGGAGTA 58.406 47.619 6.40 0.00 40.96 2.59
3372 4779 2.296471 ACGTATAGCCATGCTGGAGTAC 59.704 50.000 6.40 0.00 40.96 2.73
3373 4780 2.296190 CGTATAGCCATGCTGGAGTACA 59.704 50.000 6.40 0.00 40.96 2.90
3374 4781 3.056536 CGTATAGCCATGCTGGAGTACAT 60.057 47.826 6.40 0.00 40.96 2.29
3375 4782 4.157840 CGTATAGCCATGCTGGAGTACATA 59.842 45.833 6.40 0.00 40.96 2.29
3376 4783 5.163509 CGTATAGCCATGCTGGAGTACATAT 60.164 44.000 6.40 0.00 40.96 1.78
3401 4808 3.861840 TCTGGTCTTATGCAGCTTACAC 58.138 45.455 0.00 0.00 0.00 2.90
3413 4820 3.437049 GCAGCTTACACGAATTCCTTCTT 59.563 43.478 0.00 0.00 0.00 2.52
3416 4823 4.000988 GCTTACACGAATTCCTTCTTGGA 58.999 43.478 0.00 0.00 44.51 3.53
3480 4890 7.750229 CCTGTGGCAATAGTAACATATGAAT 57.250 36.000 10.38 0.17 0.00 2.57
3481 4891 8.846943 CCTGTGGCAATAGTAACATATGAATA 57.153 34.615 10.38 0.00 0.00 1.75
3482 4892 8.721478 CCTGTGGCAATAGTAACATATGAATAC 58.279 37.037 10.38 11.76 0.00 1.89
3483 4893 9.271828 CTGTGGCAATAGTAACATATGAATACA 57.728 33.333 10.38 4.44 0.00 2.29
3484 4894 9.620259 TGTGGCAATAGTAACATATGAATACAA 57.380 29.630 10.38 0.00 0.00 2.41
3486 4896 9.845740 TGGCAATAGTAACATATGAATACAAGT 57.154 29.630 10.38 0.41 0.00 3.16
3494 4904 9.632969 GTAACATATGAATACAAGTTGCTAACG 57.367 33.333 10.38 0.00 36.23 3.18
3495 4905 7.246674 ACATATGAATACAAGTTGCTAACGG 57.753 36.000 10.38 0.00 36.23 4.44
3526 4936 9.503427 GAAGCGCATATTACTTAAAAGAATGTT 57.497 29.630 11.47 0.00 0.00 2.71
3553 4963 5.450818 TGAATTAGTTGCCCCAGAATAGT 57.549 39.130 0.00 0.00 0.00 2.12
3566 4976 6.126409 CCCCAGAATAGTAAGGCATTAACAA 58.874 40.000 0.00 0.00 0.00 2.83
3567 4977 6.777580 CCCCAGAATAGTAAGGCATTAACAAT 59.222 38.462 0.00 0.00 0.00 2.71
3590 5000 4.133820 TGTATGTTTCAGGTGAGTTGTGG 58.866 43.478 0.00 0.00 0.00 4.17
3593 5003 2.026729 TGTTTCAGGTGAGTTGTGGTGA 60.027 45.455 0.00 0.00 0.00 4.02
3594 5004 3.214328 GTTTCAGGTGAGTTGTGGTGAT 58.786 45.455 0.00 0.00 0.00 3.06
3595 5005 2.549064 TCAGGTGAGTTGTGGTGATG 57.451 50.000 0.00 0.00 0.00 3.07
3596 5006 1.768275 TCAGGTGAGTTGTGGTGATGT 59.232 47.619 0.00 0.00 0.00 3.06
3597 5007 1.875514 CAGGTGAGTTGTGGTGATGTG 59.124 52.381 0.00 0.00 0.00 3.21
3598 5008 1.490490 AGGTGAGTTGTGGTGATGTGT 59.510 47.619 0.00 0.00 0.00 3.72
3601 5011 1.308047 GAGTTGTGGTGATGTGTGCA 58.692 50.000 0.00 0.00 0.00 4.57
3602 5012 1.265095 GAGTTGTGGTGATGTGTGCAG 59.735 52.381 0.00 0.00 0.00 4.41
3603 5013 1.024271 GTTGTGGTGATGTGTGCAGT 58.976 50.000 0.00 0.00 0.00 4.40
3604 5014 1.023502 TTGTGGTGATGTGTGCAGTG 58.976 50.000 0.00 0.00 0.00 3.66
3605 5015 1.283793 GTGGTGATGTGTGCAGTGC 59.716 57.895 8.58 8.58 0.00 4.40
3606 5016 1.153005 TGGTGATGTGTGCAGTGCA 60.153 52.632 15.37 15.37 35.60 4.57
3607 5017 0.750911 TGGTGATGTGTGCAGTGCAA 60.751 50.000 21.67 4.60 41.47 4.08
3608 5018 0.385029 GGTGATGTGTGCAGTGCAAA 59.615 50.000 21.67 12.81 41.47 3.68
3609 5019 1.000060 GGTGATGTGTGCAGTGCAAAT 60.000 47.619 21.67 13.93 41.47 2.32
3610 5020 2.055838 GTGATGTGTGCAGTGCAAATG 58.944 47.619 21.67 0.00 41.47 2.32
3611 5021 1.682323 TGATGTGTGCAGTGCAAATGT 59.318 42.857 21.67 7.27 41.47 2.71
3624 5034 8.344831 TGCAGTGCAAATGTACAATATATCTTC 58.655 33.333 17.26 0.00 34.76 2.87
3692 5102 2.052468 TGTCATCCCTCAGCATGCTAT 58.948 47.619 22.19 7.03 34.76 2.97
3714 5124 8.271487 GCTATTTTGCTGCATATTTTTAGCTTC 58.729 33.333 1.84 0.00 37.10 3.86
3715 5125 9.525409 CTATTTTGCTGCATATTTTTAGCTTCT 57.475 29.630 1.84 0.00 37.10 2.85
3716 5126 8.782339 ATTTTGCTGCATATTTTTAGCTTCTT 57.218 26.923 1.84 0.00 37.10 2.52
3722 5132 8.498358 GCTGCATATTTTTAGCTTCTTTGTTTT 58.502 29.630 0.00 0.00 33.53 2.43
3749 5163 6.761714 AGAACCCTATTACGCTGATTTTACAG 59.238 38.462 0.00 0.00 40.43 2.74
3765 5179 9.618890 TGATTTTACAGATATTCCAGGAGAAAG 57.381 33.333 0.00 0.00 38.21 2.62
3777 5191 4.780021 TCCAGGAGAAAGTGCTAGAAAGAT 59.220 41.667 0.00 0.00 0.00 2.40
3781 5195 6.479660 CAGGAGAAAGTGCTAGAAAGATCATC 59.520 42.308 0.00 0.00 0.00 2.92
3811 5225 1.541588 GCACAACCTCTGGAATCCAAC 59.458 52.381 2.61 0.00 30.80 3.77
3834 5248 5.304686 TCATGGTATGTAAATGAGGGACC 57.695 43.478 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.528690 TCTGAGGTTTGTATAAGCATGATGC 59.471 40.000 9.89 9.89 45.46 3.91
11 12 7.496920 TCTTCTGAGGTTTGTATAAGCATGATG 59.503 37.037 0.00 0.00 0.00 3.07
12 13 7.497249 GTCTTCTGAGGTTTGTATAAGCATGAT 59.503 37.037 0.00 0.00 0.00 2.45
13 14 6.818644 GTCTTCTGAGGTTTGTATAAGCATGA 59.181 38.462 0.00 0.00 0.00 3.07
14 15 6.595326 TGTCTTCTGAGGTTTGTATAAGCATG 59.405 38.462 0.00 0.00 0.00 4.06
15 16 6.711277 TGTCTTCTGAGGTTTGTATAAGCAT 58.289 36.000 0.00 0.00 0.00 3.79
16 17 6.109156 TGTCTTCTGAGGTTTGTATAAGCA 57.891 37.500 0.00 0.00 0.00 3.91
17 18 7.617041 AATGTCTTCTGAGGTTTGTATAAGC 57.383 36.000 0.00 0.00 0.00 3.09
30 31 7.094634 GGCTGATTTTGTCTTAATGTCTTCTGA 60.095 37.037 0.00 0.00 0.00 3.27
36 37 5.098211 GCAGGCTGATTTTGTCTTAATGTC 58.902 41.667 20.86 0.00 0.00 3.06
40 41 3.495331 TGGCAGGCTGATTTTGTCTTAA 58.505 40.909 20.86 0.00 0.00 1.85
57 58 2.154854 CTCTCGAGAGTTGTTTGGCA 57.845 50.000 30.44 0.00 37.40 4.92
74 75 7.763071 ACCCACTTCGTTGAAAATATAGTACTC 59.237 37.037 0.00 0.00 0.00 2.59
82 83 7.388500 CCTTACTAACCCACTTCGTTGAAAATA 59.612 37.037 0.00 0.00 0.00 1.40
92 93 6.210185 TGAGAGTAACCTTACTAACCCACTTC 59.790 42.308 0.00 0.00 43.64 3.01
97 98 6.380560 ACTGATGAGAGTAACCTTACTAACCC 59.619 42.308 0.00 0.00 43.64 4.11
138 139 7.972301 AGATCCCATGAAGTAGAATTAGGAAG 58.028 38.462 0.00 0.00 0.00 3.46
309 314 3.994392 GGAAGAACGAAGCAATCTACACA 59.006 43.478 0.00 0.00 0.00 3.72
317 322 1.938016 GCCTACGGAAGAACGAAGCAA 60.938 52.381 0.00 0.00 37.61 3.91
318 323 0.389426 GCCTACGGAAGAACGAAGCA 60.389 55.000 0.00 0.00 37.61 3.91
330 345 1.067821 GTGATCCTCTTCAGCCTACGG 59.932 57.143 0.00 0.00 0.00 4.02
366 381 2.102588 CGATGGAAAAGGTATCTCCGGT 59.897 50.000 0.00 0.00 41.99 5.28
384 399 0.962489 CTTCTCGGTCCATAGGCGAT 59.038 55.000 0.00 0.00 0.00 4.58
400 415 2.187163 GCCCAGACCGGCTACTTC 59.813 66.667 0.00 0.00 46.10 3.01
426 441 2.811317 GACTGCCCAGCGAAGACG 60.811 66.667 0.00 0.00 42.93 4.18
443 458 1.923204 CGAAAGTCATCTCTTCGGCTG 59.077 52.381 0.00 0.00 0.00 4.85
444 459 1.134965 CCGAAAGTCATCTCTTCGGCT 60.135 52.381 9.29 0.00 34.38 5.52
459 474 0.387622 CGGTCTTGACGTAGCCGAAA 60.388 55.000 12.83 0.00 44.57 3.46
467 482 2.502295 AGACTACTTCGGTCTTGACGT 58.498 47.619 0.00 0.00 40.65 4.34
482 497 2.101750 TCCGTGTGTTGAGCAAAGACTA 59.898 45.455 1.98 0.00 33.24 2.59
502 520 3.877508 CCCTGTATCCCGAATTCTTTGTC 59.122 47.826 3.52 0.00 0.00 3.18
525 543 4.493747 GGAAGAGGACGGTCGCGG 62.494 72.222 6.13 0.00 0.00 6.46
536 554 1.372087 GCAAGCATCGGGTGGAAGAG 61.372 60.000 0.00 0.00 0.00 2.85
543 561 1.098050 GAAATGAGCAAGCATCGGGT 58.902 50.000 0.00 0.00 0.00 5.28
549 567 0.166597 CGCGAAGAAATGAGCAAGCA 59.833 50.000 0.00 0.00 0.00 3.91
576 616 2.272146 GAAATGGAGGCGGCCAGA 59.728 61.111 23.09 4.28 42.15 3.86
577 617 3.204827 CGAAATGGAGGCGGCCAG 61.205 66.667 23.09 0.00 42.15 4.85
623 664 7.450074 ACACTACCTACAACATCATTCTTCAA 58.550 34.615 0.00 0.00 0.00 2.69
625 666 7.148407 CCAACACTACCTACAACATCATTCTTC 60.148 40.741 0.00 0.00 0.00 2.87
663 714 4.463050 ACCTAAAATGGAACCAACCTGA 57.537 40.909 0.00 0.00 0.00 3.86
668 719 6.484977 GCAAATTCAACCTAAAATGGAACCAA 59.515 34.615 0.00 0.00 0.00 3.67
696 747 7.382218 CCATACAACTTCATTCCAAGTTCAAAC 59.618 37.037 0.00 0.00 43.41 2.93
702 753 4.666512 AGCCATACAACTTCATTCCAAGT 58.333 39.130 0.00 0.00 38.30 3.16
703 754 6.757897 TTAGCCATACAACTTCATTCCAAG 57.242 37.500 0.00 0.00 0.00 3.61
704 755 6.071616 GGTTTAGCCATACAACTTCATTCCAA 60.072 38.462 0.00 0.00 37.17 3.53
705 756 5.417580 GGTTTAGCCATACAACTTCATTCCA 59.582 40.000 0.00 0.00 37.17 3.53
706 757 5.448632 CGGTTTAGCCATACAACTTCATTCC 60.449 44.000 0.00 0.00 36.97 3.01
707 758 5.123344 ACGGTTTAGCCATACAACTTCATTC 59.877 40.000 0.00 0.00 36.97 2.67
708 759 5.007682 ACGGTTTAGCCATACAACTTCATT 58.992 37.500 0.00 0.00 36.97 2.57
709 760 4.394920 CACGGTTTAGCCATACAACTTCAT 59.605 41.667 0.00 0.00 36.97 2.57
710 761 3.749088 CACGGTTTAGCCATACAACTTCA 59.251 43.478 0.00 0.00 36.97 3.02
711 762 3.749609 ACACGGTTTAGCCATACAACTTC 59.250 43.478 0.00 0.00 36.97 3.01
712 763 3.746940 ACACGGTTTAGCCATACAACTT 58.253 40.909 0.00 0.00 36.97 2.66
713 764 3.412237 ACACGGTTTAGCCATACAACT 57.588 42.857 0.00 0.00 36.97 3.16
714 765 4.223659 CAAACACGGTTTAGCCATACAAC 58.776 43.478 2.35 0.00 36.97 3.32
715 766 3.884091 ACAAACACGGTTTAGCCATACAA 59.116 39.130 2.35 0.00 36.97 2.41
716 767 3.478509 ACAAACACGGTTTAGCCATACA 58.521 40.909 2.35 0.00 36.97 2.29
717 768 5.806366 ATACAAACACGGTTTAGCCATAC 57.194 39.130 2.35 0.00 36.97 2.39
718 769 5.063691 CGAATACAAACACGGTTTAGCCATA 59.936 40.000 2.35 0.00 36.97 2.74
719 770 4.142773 CGAATACAAACACGGTTTAGCCAT 60.143 41.667 2.35 0.00 36.97 4.40
720 771 3.186817 CGAATACAAACACGGTTTAGCCA 59.813 43.478 2.35 0.00 36.97 4.75
721 772 3.187022 ACGAATACAAACACGGTTTAGCC 59.813 43.478 0.00 0.00 0.00 3.93
722 773 4.151157 AGACGAATACAAACACGGTTTAGC 59.849 41.667 0.00 0.00 0.00 3.09
723 774 5.389098 CCAGACGAATACAAACACGGTTTAG 60.389 44.000 0.00 1.51 0.00 1.85
814 868 6.607198 TCTTTTTGTTTCTGAGAAATCCACCT 59.393 34.615 11.20 0.00 0.00 4.00
825 879 4.750098 CCTCGTAGCTCTTTTTGTTTCTGA 59.250 41.667 0.00 0.00 0.00 3.27
826 880 4.611581 GCCTCGTAGCTCTTTTTGTTTCTG 60.612 45.833 0.00 0.00 0.00 3.02
832 2190 1.129437 GCAGCCTCGTAGCTCTTTTTG 59.871 52.381 0.00 0.00 42.61 2.44
920 2278 0.903454 GGGAAGTCGGGGACAGAGAA 60.903 60.000 0.00 0.00 34.60 2.87
928 2286 4.416601 AGGGGAGGGAAGTCGGGG 62.417 72.222 0.00 0.00 0.00 5.73
1085 2461 1.276421 AGAGTTGTCAATCAGGGGACG 59.724 52.381 0.00 0.00 36.83 4.79
1194 2573 1.292242 AGGATCTTGTAGGCCTCCTCA 59.708 52.381 9.68 4.58 34.61 3.86
1614 2993 1.064946 GAGCGAGGTGATGTCCGAG 59.935 63.158 0.00 0.00 0.00 4.63
1617 2996 1.226717 GACGAGCGAGGTGATGTCC 60.227 63.158 0.00 0.00 0.00 4.02
1896 3275 2.029073 AGCACGTCGTGGACCAAG 59.971 61.111 25.70 0.00 33.64 3.61
1944 3323 6.610830 AGTCATCCAGATCATACTTCTCTGTT 59.389 38.462 0.00 0.00 35.67 3.16
1977 3356 1.299850 GCTGTTCGCCACCCAAAAC 60.300 57.895 0.00 0.00 0.00 2.43
2007 3386 3.628646 CTCCTCGGCCACTTTGGGG 62.629 68.421 2.24 0.00 38.19 4.96
2229 3608 1.153289 CCTCTCCTTGATGTGCCCG 60.153 63.158 0.00 0.00 0.00 6.13
2325 3704 0.914417 TGGTGCCCTTCCCTCTAAGG 60.914 60.000 0.00 0.00 44.87 2.69
2328 3707 0.914417 CCTTGGTGCCCTTCCCTCTA 60.914 60.000 0.00 0.00 0.00 2.43
2373 3752 2.170607 TGCCTCAAAGGATAGCAGGTAC 59.829 50.000 0.00 0.00 37.67 3.34
2496 3875 3.174573 GACGCGGCAGCAAATTGC 61.175 61.111 7.34 10.41 45.49 3.56
2508 3887 2.127496 CTTGCTGTGCTTGACGCG 60.127 61.111 3.53 3.53 43.27 6.01
2511 3890 1.168407 TCCTGCTTGCTGTGCTTGAC 61.168 55.000 0.00 0.00 0.00 3.18
2520 3899 0.601558 CAATGTTGCTCCTGCTTGCT 59.398 50.000 0.00 0.00 40.48 3.91
2550 3929 2.029290 GGACTGTCCGTAAAGCTTCTCA 60.029 50.000 11.71 0.00 0.00 3.27
2607 3986 1.706995 CCAGCTGCCTCCCATCTGAT 61.707 60.000 8.66 0.00 39.47 2.90
2610 3989 3.806667 GCCAGCTGCCTCCCATCT 61.807 66.667 8.66 0.00 0.00 2.90
2691 4070 1.595093 GGGCCCGTGGATCAAACAAG 61.595 60.000 5.69 0.00 0.00 3.16
2697 4076 2.326529 ATCTAGGGGCCCGTGGATCA 62.327 60.000 31.34 13.12 28.40 2.92
2757 4136 5.071519 TCCACCACCAATCATGAAAACAATT 59.928 36.000 0.00 0.00 0.00 2.32
2902 4281 0.404040 AATCCCGCTTTCTGTCCCAA 59.596 50.000 0.00 0.00 0.00 4.12
3037 4422 2.634940 GCCTGGATCACTCCTTAGCATA 59.365 50.000 0.00 0.00 42.59 3.14
3111 4499 5.963176 TTGATAACTCATTCAAAGCAGCA 57.037 34.783 0.00 0.00 0.00 4.41
3369 4776 6.759272 TGCATAAGACCAGAAGGATATGTAC 58.241 40.000 0.00 0.00 38.69 2.90
3370 4777 6.519043 GCTGCATAAGACCAGAAGGATATGTA 60.519 42.308 0.00 0.00 38.69 2.29
3371 4778 5.744300 GCTGCATAAGACCAGAAGGATATGT 60.744 44.000 0.00 0.00 38.69 2.29
3372 4779 4.694509 GCTGCATAAGACCAGAAGGATATG 59.305 45.833 0.00 0.00 38.69 1.78
3373 4780 4.596643 AGCTGCATAAGACCAGAAGGATAT 59.403 41.667 1.02 0.00 38.69 1.63
3374 4781 3.969976 AGCTGCATAAGACCAGAAGGATA 59.030 43.478 1.02 0.00 38.69 2.59
3375 4782 2.776536 AGCTGCATAAGACCAGAAGGAT 59.223 45.455 1.02 0.00 38.69 3.24
3376 4783 2.191400 AGCTGCATAAGACCAGAAGGA 58.809 47.619 1.02 0.00 38.69 3.36
3413 4820 3.446873 GGTGAACCATGCATATTGTTCCA 59.553 43.478 22.78 13.75 37.87 3.53
3437 4844 1.547675 GGCACACAGAAATCCCCAGAA 60.548 52.381 0.00 0.00 0.00 3.02
3494 4904 2.760374 AGTAATATGCGCTTCTGCTCC 58.240 47.619 9.73 0.00 36.97 4.70
3495 4905 5.907197 TTAAGTAATATGCGCTTCTGCTC 57.093 39.130 9.73 0.00 36.97 4.26
3553 4963 9.853555 CTGAAACATACAATTGTTAATGCCTTA 57.146 29.630 17.78 2.74 38.85 2.69
3566 4976 5.241506 CCACAACTCACCTGAAACATACAAT 59.758 40.000 0.00 0.00 0.00 2.71
3567 4977 4.578516 CCACAACTCACCTGAAACATACAA 59.421 41.667 0.00 0.00 0.00 2.41
3590 5000 2.055838 CATTTGCACTGCACACATCAC 58.944 47.619 2.26 0.00 38.71 3.06
3593 5003 2.622470 TGTACATTTGCACTGCACACAT 59.378 40.909 2.26 0.00 38.71 3.21
3594 5004 2.019984 TGTACATTTGCACTGCACACA 58.980 42.857 2.26 0.83 38.71 3.72
3595 5005 2.772568 TGTACATTTGCACTGCACAC 57.227 45.000 2.26 0.00 38.71 3.82
3596 5006 5.641783 ATATTGTACATTTGCACTGCACA 57.358 34.783 2.26 0.00 38.71 4.57
3597 5007 7.642669 AGATATATTGTACATTTGCACTGCAC 58.357 34.615 2.26 0.00 38.71 4.57
3598 5008 7.806409 AGATATATTGTACATTTGCACTGCA 57.194 32.000 0.00 0.00 36.47 4.41
3609 5019 9.201989 ACTCCACAGAAGAAGATATATTGTACA 57.798 33.333 0.00 0.00 0.00 2.90
3624 5034 5.119694 GCTAATCCCTTAACTCCACAGAAG 58.880 45.833 0.00 0.00 0.00 2.85
3656 5066 4.460382 GGATGACATCCTCACAAAATGTGT 59.540 41.667 24.77 0.00 46.19 3.72
3678 5088 2.503920 GCAAAATAGCATGCTGAGGG 57.496 50.000 30.42 15.78 39.46 4.30
3692 5102 8.497554 CAAAGAAGCTAAAAATATGCAGCAAAA 58.502 29.630 0.00 0.00 36.47 2.44
3714 5124 6.072673 AGCGTAATAGGGTTCTGAAAACAAAG 60.073 38.462 0.00 0.00 0.00 2.77
3715 5125 5.766174 AGCGTAATAGGGTTCTGAAAACAAA 59.234 36.000 0.00 0.00 0.00 2.83
3716 5126 5.180492 CAGCGTAATAGGGTTCTGAAAACAA 59.820 40.000 0.00 0.00 0.00 2.83
3722 5132 5.353394 AAATCAGCGTAATAGGGTTCTGA 57.647 39.130 0.00 0.00 35.41 3.27
3749 5163 6.412362 TCTAGCACTTTCTCCTGGAATATC 57.588 41.667 0.00 0.00 33.53 1.63
3755 5169 4.543590 TCTTTCTAGCACTTTCTCCTGG 57.456 45.455 0.00 0.00 0.00 4.45
3765 5179 9.713740 CACAAAATAAGATGATCTTTCTAGCAC 57.286 33.333 13.54 0.00 37.89 4.40
3777 5191 5.769662 AGAGGTTGTGCACAAAATAAGATGA 59.230 36.000 32.61 5.04 37.63 2.92
3781 5195 4.278170 TCCAGAGGTTGTGCACAAAATAAG 59.722 41.667 32.61 21.16 37.63 1.73
3811 5225 5.163205 TGGTCCCTCATTTACATACCATGAG 60.163 44.000 0.00 2.01 42.47 2.90
3834 5248 2.479730 CCCGTAGTGAGGATTTCTCGTG 60.480 54.545 0.00 0.00 45.32 4.35
3888 5491 6.458206 GCAGTCACAATTACAACTGAAACAGA 60.458 38.462 14.23 0.00 41.26 3.41


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

AutoCloner maintained by Alex Coulton.