Multiple sequence alignment - TraesCS1B01G210800

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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 TraesCS1B01G210800 chr1B 100.000 5636 0 0 1 5636 383800807 383795172 0.000000e+00 10408
1 TraesCS1B01G210800 chr1D 95.885 2916 97 10 686 3591 282289447 282286545 0.000000e+00 4698
2 TraesCS1B01G210800 chr1D 97.799 1999 35 4 3642 5636 282286540 282284547 0.000000e+00 3439
3 TraesCS1B01G210800 chr1D 94.333 600 30 3 1 600 282290229 282289634 0.000000e+00 917
4 TraesCS1B01G210800 chr1A 95.747 2798 89 12 814 3591 354302831 354300044 0.000000e+00 4481
5 TraesCS1B01G210800 chr1A 97.899 1999 34 3 3642 5636 354300039 354298045 0.000000e+00 3452
6 TraesCS1B01G210800 chr1A 95.187 561 24 3 1 559 354304018 354303459 0.000000e+00 883
7 TraesCS1B01G210800 chr1A 95.192 104 4 1 688 790 354303251 354303148 4.520000e-36 163


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 TraesCS1B01G210800 chr1B 383795172 383800807 5635 True 10408.00 10408 100.000000 1 5636 1 chr1B.!!$R1 5635
1 TraesCS1B01G210800 chr1D 282284547 282290229 5682 True 3018.00 4698 96.005667 1 5636 3 chr1D.!!$R1 5635
2 TraesCS1B01G210800 chr1A 354298045 354304018 5973 True 2244.75 4481 96.006250 1 5636 4 chr1A.!!$R1 5635

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
648 651 0.325296 TCGTAAGGCCTGGACTGGAT 60.325 55.0 5.69 0.00 38.47 3.41 F
1615 2061 0.178964 CCAAGGTTTTCTCCCCAGCA 60.179 55.0 0.00 0.00 0.00 4.41 F
1666 2112 0.814010 CAGTAAGGCCGGTACCATGC 60.814 60.0 13.54 13.63 0.00 4.06 F
3208 3658 0.036952 ACACCGAGAATGAGGCAGTG 60.037 55.0 0.00 0.00 0.00 3.66 F
3623 4083 0.320771 TTCGAGAAACTGGCAGGAGC 60.321 55.0 20.34 7.04 41.10 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 2127 0.948623 ACAAGCGCATACGACAGCAA 60.949 50.0 11.47 0.0 43.93 3.91 R
2893 3339 0.250467 ACAGCATGCTTGTTCCGTCT 60.250 50.0 19.98 0.0 42.53 4.18 R
3604 4064 0.320771 GCTCCTGCCAGTTTCTCGAA 60.321 55.0 0.00 0.0 0.00 3.71 R
4069 4533 0.108329 ATCAACAGTTAGGCGGGTCG 60.108 55.0 0.00 0.0 0.00 4.79 R
4675 5139 0.250640 ACTGCTTCCTTCCAGCACTG 60.251 55.0 0.00 0.0 42.49 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
104 105 5.103290 TGATAACGAAAACTTGTTGCCTC 57.897 39.130 0.00 0.00 0.00 4.70
192 193 1.592223 GCAGAGGGCGTCACTAGTT 59.408 57.895 10.15 0.00 0.00 2.24
229 230 7.381408 CGAACTTTATAATCTGTAATCCAGCGA 59.619 37.037 0.00 0.00 41.25 4.93
240 241 5.879237 TGTAATCCAGCGATTTGACATTTC 58.121 37.500 0.00 0.00 39.49 2.17
261 262 6.992063 TTCTTCTTCTTCCATTGTGCTATC 57.008 37.500 0.00 0.00 0.00 2.08
371 373 1.523711 ATACAACGCATGGGCCTCG 60.524 57.895 10.10 8.50 36.38 4.63
385 387 3.764434 TGGGCCTCGTTTTTAATTGCATA 59.236 39.130 4.53 0.00 0.00 3.14
411 413 6.749923 AGAGCTTCATATTGTTGTTTCTCC 57.250 37.500 0.00 0.00 0.00 3.71
526 529 8.787852 TGCAGTATCATACTCTATCTACTTGTG 58.212 37.037 0.00 0.00 36.76 3.33
542 545 8.833231 TCTACTTGTGAAACCTCAAGATAAAG 57.167 34.615 11.07 4.40 42.22 1.85
544 547 5.827797 ACTTGTGAAACCTCAAGATAAAGCA 59.172 36.000 11.07 0.00 42.22 3.91
549 552 6.961554 GTGAAACCTCAAGATAAAGCAATACG 59.038 38.462 0.00 0.00 31.88 3.06
559 562 7.295952 AGATAAAGCAATACGACTTTGACAG 57.704 36.000 0.00 0.00 36.78 3.51
561 564 7.602644 AGATAAAGCAATACGACTTTGACAGAA 59.397 33.333 0.00 0.00 36.78 3.02
562 565 6.560253 AAAGCAATACGACTTTGACAGAAT 57.440 33.333 0.00 0.00 34.88 2.40
570 573 6.686130 ACGACTTTGACAGAATTAGTAACG 57.314 37.500 0.00 0.00 0.00 3.18
574 577 7.409449 CGACTTTGACAGAATTAGTAACGACAG 60.409 40.741 0.00 0.00 0.00 3.51
600 603 7.201513 GCAACAAAGCATTTAGTTTCAACTTGA 60.202 33.333 0.00 0.00 35.03 3.02
601 604 8.655092 CAACAAAGCATTTAGTTTCAACTTGAA 58.345 29.630 0.00 0.00 35.03 2.69
602 605 8.185003 ACAAAGCATTTAGTTTCAACTTGAAC 57.815 30.769 3.56 0.83 35.03 3.18
603 606 8.034804 ACAAAGCATTTAGTTTCAACTTGAACT 58.965 29.630 3.56 7.53 35.03 3.01
604 607 8.872845 CAAAGCATTTAGTTTCAACTTGAACTT 58.127 29.630 3.56 0.00 35.03 2.66
605 608 7.992180 AGCATTTAGTTTCAACTTGAACTTG 57.008 32.000 3.56 3.09 40.37 3.16
607 610 6.978080 GCATTTAGTTTCAACTTGAACTTGGA 59.022 34.615 3.56 0.00 40.37 3.53
611 614 9.621629 TTTAGTTTCAACTTGAACTTGGATAGA 57.378 29.630 3.56 0.00 40.37 1.98
636 639 6.830114 GTGAAACCATAAGATCTCGTAAGG 57.170 41.667 0.00 0.00 38.47 2.69
640 643 3.322254 ACCATAAGATCTCGTAAGGCCTG 59.678 47.826 5.69 0.00 38.47 4.85
641 644 3.306364 CCATAAGATCTCGTAAGGCCTGG 60.306 52.174 5.69 0.00 38.47 4.45
643 646 1.404843 AGATCTCGTAAGGCCTGGAC 58.595 55.000 5.69 7.06 38.47 4.02
644 647 1.063567 AGATCTCGTAAGGCCTGGACT 60.064 52.381 5.69 0.00 38.47 3.85
646 649 0.970937 TCTCGTAAGGCCTGGACTGG 60.971 60.000 5.69 3.57 38.47 4.00
647 650 0.970937 CTCGTAAGGCCTGGACTGGA 60.971 60.000 5.69 0.00 38.47 3.86
648 651 0.325296 TCGTAAGGCCTGGACTGGAT 60.325 55.000 5.69 0.00 38.47 3.41
649 652 0.541863 CGTAAGGCCTGGACTGGATT 59.458 55.000 5.69 0.00 0.00 3.01
650 653 1.760613 CGTAAGGCCTGGACTGGATTA 59.239 52.381 5.69 0.00 0.00 1.75
652 655 3.555168 CGTAAGGCCTGGACTGGATTATC 60.555 52.174 5.69 0.00 0.00 1.75
653 656 2.503869 AGGCCTGGACTGGATTATCT 57.496 50.000 3.11 0.00 0.00 1.98
656 659 2.439507 GGCCTGGACTGGATTATCTTCA 59.560 50.000 0.00 0.00 0.00 3.02
657 660 3.471680 GCCTGGACTGGATTATCTTCAC 58.528 50.000 0.00 0.00 0.00 3.18
660 784 4.444022 CCTGGACTGGATTATCTTCACTGG 60.444 50.000 0.00 0.00 0.00 4.00
665 789 2.439507 TGGATTATCTTCACTGGAGGCC 59.560 50.000 0.00 0.00 0.00 5.19
670 794 1.673665 CTTCACTGGAGGCCTGCAC 60.674 63.158 24.87 7.34 0.00 4.57
674 798 2.268280 CTGGAGGCCTGCACTGAG 59.732 66.667 24.87 10.07 0.00 3.35
678 802 1.342975 TGGAGGCCTGCACTGAGTATA 60.343 52.381 24.87 0.00 0.00 1.47
682 806 1.202580 GGCCTGCACTGAGTATACCTG 60.203 57.143 0.00 0.00 0.00 4.00
683 807 1.808133 GCCTGCACTGAGTATACCTGC 60.808 57.143 0.00 2.69 0.00 4.85
771 905 5.977635 TCAATGTTACTATGTCCAGACAGG 58.022 41.667 6.63 4.62 45.48 4.00
789 1223 7.255451 CCAGACAGGCAAAAGAAAATGTTACTA 60.255 37.037 0.00 0.00 0.00 1.82
806 1240 7.870509 TGTTACTATGTCCAGTACTCGTATT 57.129 36.000 0.00 0.00 30.76 1.89
807 1241 8.284945 TGTTACTATGTCCAGTACTCGTATTT 57.715 34.615 0.00 0.00 30.76 1.40
808 1242 8.186163 TGTTACTATGTCCAGTACTCGTATTTG 58.814 37.037 0.00 0.00 30.76 2.32
809 1243 6.145338 ACTATGTCCAGTACTCGTATTTGG 57.855 41.667 0.00 0.00 0.00 3.28
810 1244 3.880047 TGTCCAGTACTCGTATTTGGG 57.120 47.619 0.00 0.00 0.00 4.12
811 1245 3.433343 TGTCCAGTACTCGTATTTGGGA 58.567 45.455 0.00 0.00 0.00 4.37
812 1246 3.833650 TGTCCAGTACTCGTATTTGGGAA 59.166 43.478 0.00 0.00 0.00 3.97
1122 1556 3.893763 CCGCAGATCGTCGAGGCT 61.894 66.667 10.50 0.00 36.19 4.58
1615 2061 0.178964 CCAAGGTTTTCTCCCCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
1623 2069 2.046892 CTCCCCAGCACCACTTCG 60.047 66.667 0.00 0.00 0.00 3.79
1666 2112 0.814010 CAGTAAGGCCGGTACCATGC 60.814 60.000 13.54 13.63 0.00 4.06
1681 2127 2.362369 ATGCCCGAGCTACTGCAGT 61.362 57.895 25.12 25.12 42.74 4.40
2649 3095 1.243342 TGGAAGGCGCCAATGTTCAG 61.243 55.000 31.54 0.00 34.31 3.02
2660 3106 5.240891 CGCCAATGTTCAGATGGATAGTAT 58.759 41.667 10.31 0.00 36.27 2.12
2702 3148 3.058016 GTGCTCTTAGTGAAATTGCAGCA 60.058 43.478 0.00 0.00 0.00 4.41
2706 3152 5.706916 CTCTTAGTGAAATTGCAGCACATT 58.293 37.500 0.00 0.00 35.08 2.71
2757 3203 5.357742 TGCTCAATCTAGGCATGAAACTA 57.642 39.130 0.00 0.00 0.00 2.24
2759 3205 5.819379 TGCTCAATCTAGGCATGAAACTAAG 59.181 40.000 0.00 0.00 0.00 2.18
2820 3266 6.017852 GTCATAGATTCGTTTTGGAGGATTCC 60.018 42.308 0.00 0.00 44.31 3.01
2893 3339 7.170393 TGCTCAGCTTCATAGTCTACTTTTA 57.830 36.000 0.00 0.00 0.00 1.52
2915 3361 1.001378 ACGGAACAAGCATGCTGTTTC 60.001 47.619 23.48 23.88 0.00 2.78
3051 3501 4.691216 GCGCCCAACAAAAATTACCATAAA 59.309 37.500 0.00 0.00 0.00 1.40
3110 3560 8.873144 CCTTTTGAATATCATCCCACCATTATT 58.127 33.333 0.00 0.00 0.00 1.40
3208 3658 0.036952 ACACCGAGAATGAGGCAGTG 60.037 55.000 0.00 0.00 0.00 3.66
3211 3661 1.364626 CCGAGAATGAGGCAGTGTGC 61.365 60.000 0.00 0.00 44.08 4.57
3213 3663 1.367659 GAGAATGAGGCAGTGTGCTC 58.632 55.000 0.00 0.00 44.28 4.26
3217 3667 0.322277 ATGAGGCAGTGTGCTCTTGG 60.322 55.000 0.00 0.00 44.28 3.61
3242 3692 6.415867 GCAATATTGAATCTTTCCATGACACG 59.584 38.462 19.73 0.00 0.00 4.49
3256 3706 3.150848 TGACACGATGCTGATGTACTC 57.849 47.619 0.00 0.00 0.00 2.59
3298 3748 2.389962 AATGATTTTGCAATGCCGCT 57.610 40.000 1.53 0.00 0.00 5.52
3302 3752 2.426381 TGATTTTGCAATGCCGCTCATA 59.574 40.909 1.53 0.00 34.33 2.15
3303 3753 3.119209 TGATTTTGCAATGCCGCTCATAA 60.119 39.130 1.53 0.00 34.33 1.90
3421 3874 8.630278 ACAGTGTATCATCGTTACATAAGTTC 57.370 34.615 0.00 0.00 32.56 3.01
3422 3875 7.705325 ACAGTGTATCATCGTTACATAAGTTCC 59.295 37.037 0.00 0.00 32.56 3.62
3431 3884 5.813672 TCGTTACATAAGTTCCAACTATGCC 59.186 40.000 0.00 0.00 38.57 4.40
3563 4023 6.923508 TCCGTTTTAGCACTATCATGTCTATG 59.076 38.462 0.00 0.00 35.57 2.23
3565 4025 7.224753 CCGTTTTAGCACTATCATGTCTATGTT 59.775 37.037 0.00 0.00 35.73 2.71
3584 4044 8.984764 TCTATGTTTTATATGGAATACGCACAC 58.015 33.333 0.00 0.00 0.00 3.82
3591 4051 4.782019 ATGGAATACGCACACACATTTT 57.218 36.364 0.00 0.00 0.00 1.82
3621 4081 2.631160 TTTTCGAGAAACTGGCAGGA 57.369 45.000 20.34 1.80 0.00 3.86
3622 4082 2.169832 TTTCGAGAAACTGGCAGGAG 57.830 50.000 20.34 3.32 0.00 3.69
3623 4083 0.320771 TTCGAGAAACTGGCAGGAGC 60.321 55.000 20.34 7.04 41.10 4.70
3624 4084 2.097038 CGAGAAACTGGCAGGAGCG 61.097 63.158 20.34 10.84 43.41 5.03
3625 4085 2.359230 AGAAACTGGCAGGAGCGC 60.359 61.111 20.34 0.00 43.41 5.92
3626 4086 2.359230 GAAACTGGCAGGAGCGCT 60.359 61.111 20.34 11.27 43.41 5.92
3627 4087 2.359230 AAACTGGCAGGAGCGCTC 60.359 61.111 29.38 29.38 43.41 5.03
3639 4099 2.906354 GGAGCGCTCCTTTCAATTAGA 58.094 47.619 42.50 0.00 46.16 2.10
3640 4100 3.270877 GGAGCGCTCCTTTCAATTAGAA 58.729 45.455 42.50 0.00 46.16 2.10
3728 4192 4.406003 AGGTCAGGTACTTGTAAGCTATGG 59.594 45.833 4.75 0.00 34.60 2.74
3729 4193 4.161754 GGTCAGGTACTTGTAAGCTATGGT 59.838 45.833 4.75 0.00 34.60 3.55
3889 4353 6.713903 AGAGATATCCTATGCCAATTGTTGTG 59.286 38.462 4.43 0.00 0.00 3.33
3890 4354 6.604171 AGATATCCTATGCCAATTGTTGTGA 58.396 36.000 4.43 0.00 0.00 3.58
3891 4355 4.989279 ATCCTATGCCAATTGTTGTGAC 57.011 40.909 4.43 0.00 0.00 3.67
3892 4356 2.746904 TCCTATGCCAATTGTTGTGACG 59.253 45.455 4.43 0.00 0.00 4.35
3932 4396 4.136796 GCTGCAGATTAACCCATCATGTA 58.863 43.478 20.43 0.00 0.00 2.29
4069 4533 2.951229 TGGGTCAAGGGAAAGAGAAC 57.049 50.000 0.00 0.00 0.00 3.01
4102 4566 1.814394 TGTTGATTGGCAGCTGATGAC 59.186 47.619 20.43 4.47 37.50 3.06
4168 4632 0.465705 ATCCAGCCCAGACATACACG 59.534 55.000 0.00 0.00 0.00 4.49
4411 4875 7.443272 AGTTCTGCAAATTCATCATCGATATCA 59.557 33.333 0.00 0.00 0.00 2.15
4534 4998 6.532657 CACCAATAAGCCAGAATTGTTCATTC 59.467 38.462 0.00 0.00 41.73 2.67
4602 5066 0.674895 GCCAGGAGACAAAGCGTGAT 60.675 55.000 0.00 0.00 0.00 3.06
4747 5211 1.093972 TGCCAACATTGAGGTATGCG 58.906 50.000 0.00 0.00 0.00 4.73
4817 5281 6.380274 TGGTGAGTCTACTTTAGTAAGGGATG 59.620 42.308 0.00 0.00 35.61 3.51
4832 5296 8.164057 AGTAAGGGATGGAAATAGAAAGTCTT 57.836 34.615 0.00 0.00 0.00 3.01
4840 5304 4.324641 GGAAATAGAAAGTCTTGAGGGGCT 60.325 45.833 0.00 0.00 0.00 5.19
4842 5306 2.575805 AGAAAGTCTTGAGGGGCTTG 57.424 50.000 0.00 0.00 0.00 4.01
4921 5385 0.834687 AACCAGTAGCCCACCGAAGA 60.835 55.000 0.00 0.00 0.00 2.87
5095 5559 0.178921 TGCCCCACTCTGTCTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
5254 5718 2.171237 TGCTACTGGGATGGAGTCAATG 59.829 50.000 0.00 0.00 0.00 2.82
5269 5733 5.163673 GGAGTCAATGAGAAAGCTGGAATTC 60.164 44.000 0.00 0.00 0.00 2.17
5365 5829 1.490490 TCGGGATTAGCATTGGAAGCT 59.510 47.619 0.00 0.00 45.77 3.74
5614 6078 0.457851 GCACATAGCAGAGTCGGTCT 59.542 55.000 0.00 0.00 44.79 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.752879 TACACCGCCGCCTTGCTC 62.753 66.667 0.00 0.00 0.00 4.26
104 105 0.178068 CCAGACCAATAGGACACCCG 59.822 60.000 0.00 0.00 38.69 5.28
229 230 8.645110 ACAATGGAAGAAGAAGAAATGTCAAAT 58.355 29.630 0.00 0.00 0.00 2.32
240 241 5.006165 GTCGATAGCACAATGGAAGAAGAAG 59.994 44.000 0.00 0.00 0.00 2.85
261 262 0.948623 TTTCCTGCGTGTCCATGTCG 60.949 55.000 0.00 0.00 0.00 4.35
362 364 2.564947 TGCAATTAAAAACGAGGCCCAT 59.435 40.909 0.00 0.00 0.00 4.00
385 387 8.084684 GGAGAAACAACAATATGAAGCTCTTTT 58.915 33.333 0.00 0.00 0.00 2.27
397 399 5.473504 GCTTTCAGAGGGAGAAACAACAATA 59.526 40.000 0.00 0.00 32.09 1.90
411 413 0.251077 AAGGGTGCAGCTTTCAGAGG 60.251 55.000 16.65 0.00 0.00 3.69
526 529 7.064728 AGTCGTATTGCTTTATCTTGAGGTTTC 59.935 37.037 0.00 0.00 0.00 2.78
542 545 7.061752 ACTAATTCTGTCAAAGTCGTATTGC 57.938 36.000 0.00 0.00 0.00 3.56
544 547 8.857216 CGTTACTAATTCTGTCAAAGTCGTATT 58.143 33.333 0.00 0.00 0.00 1.89
549 552 7.619571 GCTGTCGTTACTAATTCTGTCAAAGTC 60.620 40.741 0.00 0.00 0.00 3.01
559 562 5.564127 GCTTTGTTGCTGTCGTTACTAATTC 59.436 40.000 0.00 0.00 0.00 2.17
561 564 4.513692 TGCTTTGTTGCTGTCGTTACTAAT 59.486 37.500 0.00 0.00 0.00 1.73
562 565 3.872182 TGCTTTGTTGCTGTCGTTACTAA 59.128 39.130 0.00 0.00 0.00 2.24
570 573 5.748152 TGAAACTAAATGCTTTGTTGCTGTC 59.252 36.000 0.00 0.00 0.00 3.51
574 577 6.588348 AGTTGAAACTAAATGCTTTGTTGC 57.412 33.333 0.00 0.00 37.52 4.17
600 603 4.993705 TGGTTTCACCTCTATCCAAGTT 57.006 40.909 0.00 0.00 39.58 2.66
601 604 6.443849 TCTTATGGTTTCACCTCTATCCAAGT 59.556 38.462 0.00 0.00 39.58 3.16
602 605 6.889198 TCTTATGGTTTCACCTCTATCCAAG 58.111 40.000 0.00 0.00 39.58 3.61
603 606 6.884472 TCTTATGGTTTCACCTCTATCCAA 57.116 37.500 0.00 0.00 39.58 3.53
604 607 6.846505 AGATCTTATGGTTTCACCTCTATCCA 59.153 38.462 0.00 0.00 39.58 3.41
605 608 7.309770 AGATCTTATGGTTTCACCTCTATCC 57.690 40.000 0.00 0.00 39.58 2.59
607 610 6.551601 ACGAGATCTTATGGTTTCACCTCTAT 59.448 38.462 0.00 0.00 39.58 1.98
611 614 6.407074 CCTTACGAGATCTTATGGTTTCACCT 60.407 42.308 0.00 0.00 39.58 4.00
630 633 0.541863 AATCCAGTCCAGGCCTTACG 59.458 55.000 0.00 1.32 0.00 3.18
632 635 3.941629 AGATAATCCAGTCCAGGCCTTA 58.058 45.455 0.00 0.00 0.00 2.69
633 636 2.781667 AGATAATCCAGTCCAGGCCTT 58.218 47.619 0.00 0.00 0.00 4.35
634 637 2.503869 AGATAATCCAGTCCAGGCCT 57.496 50.000 0.00 0.00 0.00 5.19
635 638 2.439507 TGAAGATAATCCAGTCCAGGCC 59.560 50.000 0.00 0.00 0.00 5.19
636 639 3.135530 AGTGAAGATAATCCAGTCCAGGC 59.864 47.826 0.00 0.00 0.00 4.85
640 643 4.202305 CCTCCAGTGAAGATAATCCAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
641 644 4.742138 GCCTCCAGTGAAGATAATCCAGTC 60.742 50.000 0.00 0.00 0.00 3.51
643 646 3.495806 GGCCTCCAGTGAAGATAATCCAG 60.496 52.174 0.00 0.00 0.00 3.86
644 647 2.439507 GGCCTCCAGTGAAGATAATCCA 59.560 50.000 0.00 0.00 0.00 3.41
646 649 3.737850 CAGGCCTCCAGTGAAGATAATC 58.262 50.000 0.00 0.00 0.00 1.75
647 650 2.158696 GCAGGCCTCCAGTGAAGATAAT 60.159 50.000 0.00 0.00 0.00 1.28
648 651 1.210478 GCAGGCCTCCAGTGAAGATAA 59.790 52.381 0.00 0.00 0.00 1.75
649 652 0.833287 GCAGGCCTCCAGTGAAGATA 59.167 55.000 0.00 0.00 0.00 1.98
650 653 1.203441 TGCAGGCCTCCAGTGAAGAT 61.203 55.000 0.00 0.00 0.00 2.40
652 655 1.673665 GTGCAGGCCTCCAGTGAAG 60.674 63.158 0.00 0.00 0.00 3.02
653 656 2.149383 AGTGCAGGCCTCCAGTGAA 61.149 57.895 2.20 0.00 0.00 3.18
656 659 2.527624 TCAGTGCAGGCCTCCAGT 60.528 61.111 0.00 0.00 0.00 4.00
657 660 1.260538 TACTCAGTGCAGGCCTCCAG 61.261 60.000 0.00 0.00 0.00 3.86
660 784 1.069358 GGTATACTCAGTGCAGGCCTC 59.931 57.143 0.00 0.00 0.00 4.70
665 789 1.405463 TCGCAGGTATACTCAGTGCAG 59.595 52.381 15.44 10.46 33.59 4.41
670 794 2.290916 ACATCGTCGCAGGTATACTCAG 59.709 50.000 2.25 0.00 0.00 3.35
674 798 2.124903 CCAACATCGTCGCAGGTATAC 58.875 52.381 0.00 0.00 0.00 1.47
678 802 0.821517 TATCCAACATCGTCGCAGGT 59.178 50.000 0.00 0.00 0.00 4.00
682 806 1.571919 AGCTTATCCAACATCGTCGC 58.428 50.000 0.00 0.00 0.00 5.19
683 807 3.448686 AGAAGCTTATCCAACATCGTCG 58.551 45.455 0.00 0.00 0.00 5.12
771 905 8.082242 ACTGGACATAGTAACATTTTCTTTTGC 58.918 33.333 0.00 0.00 0.00 3.68
789 1223 4.028131 TCCCAAATACGAGTACTGGACAT 58.972 43.478 12.28 1.77 0.00 3.06
806 1240 1.347062 GCAAACCTCCCAATTCCCAA 58.653 50.000 0.00 0.00 0.00 4.12
807 1241 0.544120 GGCAAACCTCCCAATTCCCA 60.544 55.000 0.00 0.00 0.00 4.37
808 1242 0.252239 AGGCAAACCTCCCAATTCCC 60.252 55.000 0.00 0.00 46.34 3.97
809 1243 0.897621 CAGGCAAACCTCCCAATTCC 59.102 55.000 0.00 0.00 46.34 3.01
810 1244 0.247460 GCAGGCAAACCTCCCAATTC 59.753 55.000 0.00 0.00 46.34 2.17
811 1245 1.194121 GGCAGGCAAACCTCCCAATT 61.194 55.000 0.00 0.00 46.34 2.32
812 1246 1.610379 GGCAGGCAAACCTCCCAAT 60.610 57.895 0.00 0.00 46.34 3.16
1096 1530 2.418910 CGATCTGCGGAGACAGGGT 61.419 63.158 9.49 0.00 38.26 4.34
1104 1538 3.889044 GCCTCGACGATCTGCGGA 61.889 66.667 0.00 0.00 46.49 5.54
1162 1596 2.125350 GGCGCACCAGAGGAAGAG 60.125 66.667 10.83 0.00 35.26 2.85
1404 1850 1.440938 CGAAGGCGTTGTGGTGGAAA 61.441 55.000 0.00 0.00 0.00 3.13
1615 2061 4.421479 CGAGGCGAGCGAAGTGGT 62.421 66.667 0.00 0.00 0.00 4.16
1623 2069 4.090057 GCAAACACCGAGGCGAGC 62.090 66.667 0.00 0.00 0.00 5.03
1666 2112 2.103042 GCAACTGCAGTAGCTCGGG 61.103 63.158 22.01 5.19 42.74 5.14
1681 2127 0.948623 ACAAGCGCATACGACAGCAA 60.949 50.000 11.47 0.00 43.93 3.91
2172 2618 2.112815 GGCTTCGGATGGAAACCCG 61.113 63.158 0.00 0.00 46.57 5.28
2649 3095 6.587990 CCACGTTGAATGAGATACTATCCATC 59.412 42.308 0.00 0.00 0.00 3.51
2660 3106 4.055360 CACAACTACCACGTTGAATGAGA 58.945 43.478 10.29 0.00 45.40 3.27
2702 3148 2.185004 AGCTGTTGCCGAACTAATGT 57.815 45.000 0.00 0.00 40.80 2.71
2706 3152 2.248280 TCAAAGCTGTTGCCGAACTA 57.752 45.000 0.00 0.00 40.80 2.24
2820 3266 2.422479 CCCATCACTTTCAGCACTGATG 59.578 50.000 0.31 0.00 39.64 3.07
2840 3286 1.929836 GATCGCATGTTGAGTCAGACC 59.070 52.381 0.00 0.00 0.00 3.85
2893 3339 0.250467 ACAGCATGCTTGTTCCGTCT 60.250 50.000 19.98 0.00 42.53 4.18
2896 3342 1.267806 AGAAACAGCATGCTTGTTCCG 59.732 47.619 25.93 15.16 42.53 4.30
2957 3404 9.620259 ATTTAGAATTTCTCCAGCCTTTAGTAG 57.380 33.333 1.27 0.00 0.00 2.57
2962 3409 7.781324 TTCATTTAGAATTTCTCCAGCCTTT 57.219 32.000 1.27 0.00 0.00 3.11
2995 3442 6.920210 GGAAAATGTTATAGCAAGGATCTTGC 59.080 38.462 20.97 20.97 45.22 4.01
3051 3501 8.361139 CCTACGAGGTAAACATCTCTTCAATAT 58.639 37.037 0.00 0.00 0.00 1.28
3134 3584 5.351740 GCATCTGAGTAGAACCCAAAGTTAC 59.648 44.000 0.00 0.00 39.40 2.50
3211 3661 7.104043 TGGAAAGATTCAATATTGCCAAGAG 57.896 36.000 1.48 0.00 36.26 2.85
3213 3663 7.437267 GTCATGGAAAGATTCAATATTGCCAAG 59.563 37.037 8.62 4.64 42.22 3.61
3217 3667 6.415867 CGTGTCATGGAAAGATTCAATATTGC 59.584 38.462 10.76 0.00 0.00 3.56
3226 3676 3.376234 CAGCATCGTGTCATGGAAAGATT 59.624 43.478 0.00 0.00 0.00 2.40
3242 3692 7.384660 CCTCTTGAAATAGAGTACATCAGCATC 59.615 40.741 0.00 0.00 40.04 3.91
3256 3706 8.616076 CATTTAGGTGTAAGCCTCTTGAAATAG 58.384 37.037 0.00 0.00 39.94 1.73
3302 3752 8.424133 ACCTGCAATTTCTTTCAAATCTAGTTT 58.576 29.630 0.00 0.00 0.00 2.66
3303 3753 7.955918 ACCTGCAATTTCTTTCAAATCTAGTT 58.044 30.769 0.00 0.00 0.00 2.24
3397 3850 7.704899 TGGAACTTATGTAACGATGATACACTG 59.295 37.037 0.00 0.00 36.19 3.66
3462 3921 4.402616 AATGGACTGGGAAATTCCTGAA 57.597 40.909 12.28 0.00 36.57 3.02
3464 3923 5.488262 AAAAATGGACTGGGAAATTCCTG 57.512 39.130 12.28 7.86 36.57 3.86
3497 3957 9.809096 TTTCTTTGTAAAAGTAATGCATCAACA 57.191 25.926 0.00 0.00 0.00 3.33
3510 3970 8.829612 ACAGAAATGCCATTTTCTTTGTAAAAG 58.170 29.630 3.82 0.00 41.95 2.27
3563 4023 6.777101 TGTGTGTGCGTATTCCATATAAAAC 58.223 36.000 0.00 0.00 0.00 2.43
3565 4025 7.561021 AATGTGTGTGCGTATTCCATATAAA 57.439 32.000 0.00 0.00 0.00 1.40
3601 4061 2.878406 CTCCTGCCAGTTTCTCGAAAAA 59.122 45.455 0.00 0.00 31.33 1.94
3602 4062 2.494059 CTCCTGCCAGTTTCTCGAAAA 58.506 47.619 0.00 0.00 31.33 2.29
3603 4063 1.878102 GCTCCTGCCAGTTTCTCGAAA 60.878 52.381 0.00 0.00 0.00 3.46
3604 4064 0.320771 GCTCCTGCCAGTTTCTCGAA 60.321 55.000 0.00 0.00 0.00 3.71
3605 4065 1.293498 GCTCCTGCCAGTTTCTCGA 59.707 57.895 0.00 0.00 0.00 4.04
3606 4066 2.097038 CGCTCCTGCCAGTTTCTCG 61.097 63.158 0.00 0.00 35.36 4.04
3607 4067 2.394563 GCGCTCCTGCCAGTTTCTC 61.395 63.158 0.00 0.00 35.36 2.87
3608 4068 2.359230 GCGCTCCTGCCAGTTTCT 60.359 61.111 0.00 0.00 35.36 2.52
3609 4069 2.359230 AGCGCTCCTGCCAGTTTC 60.359 61.111 2.64 0.00 35.36 2.78
3610 4070 2.359230 GAGCGCTCCTGCCAGTTT 60.359 61.111 27.22 0.00 35.36 2.66
3611 4071 4.400961 GGAGCGCTCCTGCCAGTT 62.401 66.667 42.50 3.20 46.16 3.16
3620 4080 4.184629 TCTTCTAATTGAAAGGAGCGCTC 58.815 43.478 29.38 29.38 33.79 5.03
3621 4081 4.207891 TCTTCTAATTGAAAGGAGCGCT 57.792 40.909 11.27 11.27 33.79 5.92
3622 4082 6.425114 TGATATCTTCTAATTGAAAGGAGCGC 59.575 38.462 0.00 0.00 33.79 5.92
3623 4083 7.655328 AGTGATATCTTCTAATTGAAAGGAGCG 59.345 37.037 3.98 0.00 33.79 5.03
3624 4084 8.900983 AGTGATATCTTCTAATTGAAAGGAGC 57.099 34.615 3.98 0.00 33.79 4.70
3631 4091 9.521841 AGACCGATAGTGATATCTTCTAATTGA 57.478 33.333 3.98 0.00 0.00 2.57
3632 4092 9.566530 CAGACCGATAGTGATATCTTCTAATTG 57.433 37.037 3.98 3.32 0.00 2.32
3633 4093 9.521841 TCAGACCGATAGTGATATCTTCTAATT 57.478 33.333 3.98 0.00 0.00 1.40
3634 4094 9.521841 TTCAGACCGATAGTGATATCTTCTAAT 57.478 33.333 3.98 0.00 0.00 1.73
3635 4095 8.919777 TTCAGACCGATAGTGATATCTTCTAA 57.080 34.615 3.98 0.00 0.00 2.10
3637 4097 9.173021 CTATTCAGACCGATAGTGATATCTTCT 57.827 37.037 3.98 5.40 0.00 2.85
3638 4098 8.402472 CCTATTCAGACCGATAGTGATATCTTC 58.598 40.741 3.98 0.00 0.00 2.87
3639 4099 8.110271 TCCTATTCAGACCGATAGTGATATCTT 58.890 37.037 3.98 0.00 0.00 2.40
3640 4100 7.634718 TCCTATTCAGACCGATAGTGATATCT 58.365 38.462 3.98 0.00 0.00 1.98
3652 4112 2.028130 AGCTCACTCCTATTCAGACCG 58.972 52.381 0.00 0.00 0.00 4.79
3752 4216 7.012421 GTCATTCTTTGGTCACAACTCTTACTT 59.988 37.037 0.00 0.00 36.06 2.24
3889 4353 3.308323 GCTGAATCCAGATCAAGTTCGTC 59.692 47.826 0.00 0.00 43.02 4.20
3890 4354 3.055530 AGCTGAATCCAGATCAAGTTCGT 60.056 43.478 0.00 0.00 43.02 3.85
3891 4355 3.309138 CAGCTGAATCCAGATCAAGTTCG 59.691 47.826 8.42 0.00 43.02 3.95
3892 4356 3.065095 GCAGCTGAATCCAGATCAAGTTC 59.935 47.826 20.43 0.00 43.02 3.01
3932 4396 5.356190 CACTCTATGAACCACATTCTGCATT 59.644 40.000 0.00 0.00 40.07 3.56
4069 4533 0.108329 ATCAACAGTTAGGCGGGTCG 60.108 55.000 0.00 0.00 0.00 4.79
4168 4632 2.044946 GGCAGGACACCCACCATC 60.045 66.667 0.00 0.00 32.75 3.51
4411 4875 1.076024 ACATCAAAGCAGGTGGGTGAT 59.924 47.619 0.00 0.00 0.00 3.06
4534 4998 2.046892 CTGGAAGAGTGGTGGCGG 60.047 66.667 0.00 0.00 34.07 6.13
4602 5066 6.267699 CCTGACATACCTACTTATCATCACCA 59.732 42.308 0.00 0.00 0.00 4.17
4675 5139 0.250640 ACTGCTTCCTTCCAGCACTG 60.251 55.000 0.00 0.00 42.49 3.66
4747 5211 4.870991 GCTTCACAGGTACTACAAAGGATC 59.129 45.833 0.00 0.00 36.02 3.36
4817 5281 3.948473 GCCCCTCAAGACTTTCTATTTCC 59.052 47.826 0.00 0.00 0.00 3.13
4832 5296 1.668826 ATGAAGGTACAAGCCCCTCA 58.331 50.000 0.00 0.00 0.00 3.86
4840 5304 3.826157 CCAGCTCCAAAATGAAGGTACAA 59.174 43.478 0.00 0.00 0.00 2.41
4842 5306 2.164422 GCCAGCTCCAAAATGAAGGTAC 59.836 50.000 0.00 0.00 0.00 3.34
4921 5385 1.971357 ACAGATCGTCTTCACCAGGTT 59.029 47.619 0.00 0.00 0.00 3.50
5095 5559 7.220740 TCAGTGTAGTTTCATGTTGGTATGAA 58.779 34.615 0.00 0.00 43.32 2.57
5380 5844 3.670377 GGTTGTTGCCTCCCACGC 61.670 66.667 0.00 0.00 0.00 5.34
5392 5856 1.685355 GCCCAGGCTTTTGTGGTTGT 61.685 55.000 0.08 0.00 38.26 3.32
5470 5934 2.666085 AGTGTATGTCGGCACTGGA 58.334 52.632 0.00 0.00 43.45 3.86
5614 6078 0.907230 TCATGATGGACCGTGGTGGA 60.907 55.000 0.00 0.00 42.00 4.02


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

AutoCloner maintained by Alex Coulton.