Multiple sequence alignment - TraesCS1B01G431500

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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 TraesCS1B01G431500 chr1B 100.000 4069 0 0 1 4069 655846675 655850743 0.000000e+00 7515
1 TraesCS1B01G431500 chr1B 83.602 1055 100 35 1 1007 24503253 24504282 0.000000e+00 922
2 TraesCS1B01G431500 chr1D 92.107 3611 195 48 1 3596 471838834 471842369 0.000000e+00 5007
3 TraesCS1B01G431500 chr1D 94.030 201 12 0 3719 3919 471842362 471842562 5.110000e-79 305
4 TraesCS1B01G431500 chr1A 90.508 3835 188 87 291 4069 566108932 566112646 0.000000e+00 4903
5 TraesCS1B01G431500 chr5B 85.340 382 56 0 1037 1418 487220488 487220869 2.950000e-106 396
6 TraesCS1B01G431500 chr5B 89.855 207 21 0 2541 2747 487222795 487223001 2.410000e-67 267
7 TraesCS1B01G431500 chr2D 80.134 448 48 14 1 435 245678681 245679100 3.080000e-76 296
8 TraesCS1B01G431500 chr5D 90.338 207 20 0 2541 2747 406333758 406333964 5.180000e-69 272
9 TraesCS1B01G431500 chr5A 90.338 207 20 0 2541 2747 511906069 511906275 5.180000e-69 272


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 TraesCS1B01G431500 chr1B 655846675 655850743 4068 False 7515.0 7515 100.0000 1 4069 1 chr1B.!!$F2 4068
1 TraesCS1B01G431500 chr1B 24503253 24504282 1029 False 922.0 922 83.6020 1 1007 1 chr1B.!!$F1 1006
2 TraesCS1B01G431500 chr1D 471838834 471842562 3728 False 2656.0 5007 93.0685 1 3919 2 chr1D.!!$F1 3918
3 TraesCS1B01G431500 chr1A 566108932 566112646 3714 False 4903.0 4903 90.5080 291 4069 1 chr1A.!!$F1 3778
4 TraesCS1B01G431500 chr5B 487220488 487223001 2513 False 331.5 396 87.5975 1037 2747 2 chr5B.!!$F1 1710

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
147 154 1.066152 TGATCCGACTCAAGCTGATCG 59.934 52.381 0.00 0.0 35.67 3.69 F
148 155 1.335182 GATCCGACTCAAGCTGATCGA 59.665 52.381 9.89 0.0 32.89 3.59 F
1457 1549 1.434622 CTGGCTGAAGTGCGCTATGG 61.435 60.000 9.73 0.0 0.00 2.74 F
2792 3822 1.094785 CGATTCCAACCCCACATGAC 58.905 55.000 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1361 0.038067 CATGGTCGACGTTGGTGGTA 60.038 55.0 9.92 0.0 0.00 3.25 R
1845 2254 0.689623 AGAAGAACCTGCAGGACCAG 59.310 55.0 39.19 12.8 38.94 4.00 R
2954 3984 0.033991 CCTCGGTCCTCTCCTTCTCA 60.034 60.0 0.00 0.0 0.00 3.27 R
4012 5061 0.036765 AACTGTATGCCGGAAAGCGA 60.037 50.0 5.05 0.0 34.65 4.93 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
62 63 7.630082 ACAGTCCTGGCATAAAAAGAGTTATA 58.370 34.615 0.00 0.00 34.19 0.98
63 64 7.553044 ACAGTCCTGGCATAAAAAGAGTTATAC 59.447 37.037 0.00 0.00 34.19 1.47
116 123 2.699846 TCAGTTTTGCCCTGCATTTCTT 59.300 40.909 0.00 0.00 38.76 2.52
121 128 3.891422 TTGCCCTGCATTTCTTAATGG 57.109 42.857 0.00 0.00 41.21 3.16
129 136 5.105635 CCTGCATTTCTTAATGGAAAGCTGA 60.106 40.000 0.00 0.00 40.88 4.26
145 152 1.202510 GCTGATCCGACTCAAGCTGAT 60.203 52.381 0.00 0.00 0.00 2.90
146 153 2.741612 CTGATCCGACTCAAGCTGATC 58.258 52.381 0.00 0.00 33.96 2.92
147 154 1.066152 TGATCCGACTCAAGCTGATCG 59.934 52.381 0.00 0.00 35.67 3.69
148 155 1.335182 GATCCGACTCAAGCTGATCGA 59.665 52.381 9.89 0.00 32.89 3.59
178 186 4.587262 ACAACTGTTTTCCCAAGGATAACC 59.413 41.667 12.51 0.00 40.97 2.85
228 238 4.339530 TGCACAACTTTTTGTATGGCAGTA 59.660 37.500 0.00 0.00 44.57 2.74
230 240 5.507315 GCACAACTTTTTGTATGGCAGTACT 60.507 40.000 0.00 0.00 44.57 2.73
275 286 3.708563 AAAAGAACACCAACACATCGG 57.291 42.857 0.00 0.00 0.00 4.18
499 547 4.084287 CCAATTATATGGCCACAGCTGAT 58.916 43.478 23.35 5.29 39.73 2.90
532 580 5.428253 GAGGCAATACACTAATCTGGACAA 58.572 41.667 0.00 0.00 0.00 3.18
660 712 2.566746 ACCTTCAGTTGATGATCCCCT 58.433 47.619 0.00 0.00 37.89 4.79
754 814 2.356278 GCTGGACCATGGCTCCAA 59.644 61.111 26.29 15.75 37.36 3.53
764 824 3.647590 ACCATGGCTCCAAAGAACATTTT 59.352 39.130 13.04 0.00 0.00 1.82
811 871 6.032094 CACATGACAAGGAATTAATGAGCAC 58.968 40.000 0.00 0.00 0.00 4.40
841 901 4.592942 AGCAATGGATGTGTACTGATGTT 58.407 39.130 0.00 0.00 0.00 2.71
842 902 4.397103 AGCAATGGATGTGTACTGATGTTG 59.603 41.667 0.00 0.00 0.00 3.33
1023 1115 3.343788 GAGCACCGACGAGACTGGG 62.344 68.421 0.00 0.00 0.00 4.45
1134 1226 4.524328 GGTGGTTTCATTGGATCCCATATC 59.476 45.833 9.90 0.00 31.53 1.63
1269 1361 3.157087 CATGGACAACTGCCTTAAGGTT 58.843 45.455 22.55 6.70 37.57 3.50
1428 1520 3.362693 GCGTGAAGAGGTTTGTAACTTCG 60.363 47.826 0.00 0.00 41.84 3.79
1450 1542 3.543680 TTACCTATCTGGCTGAAGTGC 57.456 47.619 0.00 0.00 40.22 4.40
1457 1549 1.434622 CTGGCTGAAGTGCGCTATGG 61.435 60.000 9.73 0.00 0.00 2.74
1504 1596 9.981114 AAATTTTTGTACCAAGTCTATTGGAAG 57.019 29.630 13.36 0.00 42.06 3.46
1505 1597 8.706322 ATTTTTGTACCAAGTCTATTGGAAGT 57.294 30.769 13.36 0.00 42.06 3.01
1767 2176 7.316640 TGTTTTCCTTTCGAATTGTTTCAAGA 58.683 30.769 0.00 0.00 0.00 3.02
1804 2213 4.737054 CAAGTACATTGCCTCAAATCCAC 58.263 43.478 0.00 0.00 30.65 4.02
1820 2229 7.788026 TCAAATCCACATAACTTACGTATCCT 58.212 34.615 0.00 0.00 0.00 3.24
1821 2230 7.709182 TCAAATCCACATAACTTACGTATCCTG 59.291 37.037 0.00 0.00 0.00 3.86
1822 2231 4.940463 TCCACATAACTTACGTATCCTGC 58.060 43.478 0.00 0.00 0.00 4.85
1845 2254 7.786114 TGCATTGATTCGATTTTGTTTTTCTC 58.214 30.769 0.00 0.00 0.00 2.87
2182 2707 5.510690 CCCTTTGGAACATGGAAAGGTAAAC 60.511 44.000 18.74 0.00 42.88 2.01
2227 2779 5.047377 TCACCCTGAGGCAAAATAATTCAAC 60.047 40.000 0.00 0.00 36.11 3.18
2229 2781 5.047092 ACCCTGAGGCAAAATAATTCAACTG 60.047 40.000 0.00 0.00 36.11 3.16
2388 2947 5.185442 GGGTGTTCTGAGGTATATAGCTACC 59.815 48.000 14.28 15.39 41.34 3.18
2407 3437 1.199789 CCCGTCACATTGTCCACATTG 59.800 52.381 0.98 0.98 34.44 2.82
2410 3440 3.125146 CCGTCACATTGTCCACATTGTAG 59.875 47.826 6.87 3.61 38.08 2.74
2511 3541 5.132897 TGGCAGAAATGATAAACCAACAC 57.867 39.130 0.00 0.00 0.00 3.32
2516 3546 6.867816 GCAGAAATGATAAACCAACACATTGA 59.132 34.615 0.00 0.00 38.15 2.57
2517 3547 7.148755 GCAGAAATGATAAACCAACACATTGAC 60.149 37.037 0.00 0.00 38.15 3.18
2521 3551 6.647334 TGATAAACCAACACATTGACACAT 57.353 33.333 0.00 0.00 38.15 3.21
2719 3749 2.641305 CTCATCAAGGAGAAGCTTGGG 58.359 52.381 2.10 0.00 37.05 4.12
2758 3788 5.368989 AGGCTCAAGGTAATGTAGCATAAC 58.631 41.667 0.00 0.00 34.85 1.89
2766 3796 8.677300 CAAGGTAATGTAGCATAACTGTCAAAT 58.323 33.333 0.00 0.00 0.00 2.32
2768 3798 9.326413 AGGTAATGTAGCATAACTGTCAAATAC 57.674 33.333 0.00 0.00 0.00 1.89
2792 3822 1.094785 CGATTCCAACCCCACATGAC 58.905 55.000 0.00 0.00 0.00 3.06
2865 3895 6.916360 TTTGATGGCTTCAGTAAAATCCTT 57.084 33.333 3.16 0.00 35.27 3.36
2867 3897 4.158394 TGATGGCTTCAGTAAAATCCTTGC 59.842 41.667 0.00 0.00 0.00 4.01
2885 3915 5.977725 TCCTTGCGAAGTCGAAGATAATTAG 59.022 40.000 4.59 0.00 43.02 1.73
2954 3984 3.522750 ACTTCTGGATCAAGGAGCAGATT 59.477 43.478 5.17 0.00 0.00 2.40
3068 4098 1.295423 GGCTGACGGCAAGGAGTAA 59.705 57.895 8.86 0.00 44.01 2.24
3069 4099 0.321298 GGCTGACGGCAAGGAGTAAA 60.321 55.000 8.86 0.00 44.01 2.01
3070 4100 0.796927 GCTGACGGCAAGGAGTAAAC 59.203 55.000 0.00 0.00 41.35 2.01
3073 4103 2.480419 CTGACGGCAAGGAGTAAACAAG 59.520 50.000 0.00 0.00 0.00 3.16
3101 4131 2.254546 TCAACGCCAGGCCTATTATG 57.745 50.000 3.98 1.20 0.00 1.90
3102 4132 0.593128 CAACGCCAGGCCTATTATGC 59.407 55.000 3.98 2.34 0.00 3.14
3123 4153 1.300465 CACTGCCCATCGATCGGAG 60.300 63.158 13.81 10.74 0.00 4.63
3134 4164 1.221840 GATCGGAGCCTTCCTTGCA 59.778 57.895 0.00 0.00 41.67 4.08
3137 4167 0.606401 TCGGAGCCTTCCTTGCAAAG 60.606 55.000 0.00 0.00 45.69 2.77
3164 4194 2.168106 CAGAGAGAATAGCACAGCCTGT 59.832 50.000 0.00 0.00 0.00 4.00
3199 4229 2.677836 TGCGCGATTTTTAGCAGATTCT 59.322 40.909 12.10 0.00 34.39 2.40
3215 4245 6.229733 GCAGATTCTAGTGCTCCTATTCATT 58.770 40.000 0.00 0.00 36.71 2.57
3225 4255 0.884704 CCTATTCATTGTCGCCCCCG 60.885 60.000 0.00 0.00 0.00 5.73
3227 4257 0.179067 TATTCATTGTCGCCCCCGTC 60.179 55.000 0.00 0.00 35.54 4.79
3259 4289 0.762418 TGTGTCACCGAATTCCTGGT 59.238 50.000 0.00 0.00 39.66 4.00
3301 4331 7.062957 TGGATGAAGAATAAGATCCCCTTTTC 58.937 38.462 0.00 0.00 34.54 2.29
3303 4333 8.440771 GGATGAAGAATAAGATCCCCTTTTCTA 58.559 37.037 0.00 0.00 34.36 2.10
3328 4360 2.847327 AGCTGAGCTGTATTGTGTGT 57.153 45.000 5.97 0.00 37.57 3.72
3389 4421 1.001974 ACTAGATGACTTGTTGCGCCA 59.998 47.619 4.18 0.00 0.00 5.69
3390 4422 2.283298 CTAGATGACTTGTTGCGCCAT 58.717 47.619 4.18 0.00 0.00 4.40
3391 4423 0.806868 AGATGACTTGTTGCGCCATG 59.193 50.000 4.18 1.07 0.00 3.66
3393 4425 0.608856 ATGACTTGTTGCGCCATGGA 60.609 50.000 18.40 0.00 0.00 3.41
3394 4426 0.608856 TGACTTGTTGCGCCATGGAT 60.609 50.000 18.40 0.00 0.00 3.41
3395 4427 0.099436 GACTTGTTGCGCCATGGATC 59.901 55.000 18.40 6.30 0.00 3.36
3396 4428 1.063006 CTTGTTGCGCCATGGATCG 59.937 57.895 18.40 12.02 0.00 3.69
3397 4429 1.368345 CTTGTTGCGCCATGGATCGA 61.368 55.000 18.40 2.37 0.00 3.59
3398 4430 1.643868 TTGTTGCGCCATGGATCGAC 61.644 55.000 18.40 15.60 0.00 4.20
3400 4432 1.376553 TTGCGCCATGGATCGACAA 60.377 52.632 18.40 15.02 0.00 3.18
3402 4434 0.105778 TGCGCCATGGATCGACAATA 59.894 50.000 18.40 0.00 0.00 1.90
3414 4446 7.689446 TGGATCGACAATAATAACCAAAACA 57.311 32.000 0.00 0.00 0.00 2.83
3434 4466 4.917385 ACATATGTGCTTAGTGAAACCCA 58.083 39.130 7.78 0.00 37.80 4.51
3435 4467 4.700213 ACATATGTGCTTAGTGAAACCCAC 59.300 41.667 7.78 0.00 46.03 4.61
3436 4468 1.975660 TGTGCTTAGTGAAACCCACC 58.024 50.000 0.00 0.00 46.87 4.61
3437 4469 0.872388 GTGCTTAGTGAAACCCACCG 59.128 55.000 0.00 0.00 46.87 4.94
3438 4470 0.759959 TGCTTAGTGAAACCCACCGA 59.240 50.000 0.00 0.00 46.87 4.69
3439 4471 1.141254 TGCTTAGTGAAACCCACCGAA 59.859 47.619 0.00 0.00 46.87 4.30
3440 4472 2.224670 TGCTTAGTGAAACCCACCGAAT 60.225 45.455 0.00 0.00 46.87 3.34
3441 4473 2.161609 GCTTAGTGAAACCCACCGAATG 59.838 50.000 0.00 0.00 46.87 2.67
3492 4525 3.095922 GCAGTAGGCCGGCTTAAAT 57.904 52.632 28.56 12.67 36.11 1.40
3493 4526 0.663153 GCAGTAGGCCGGCTTAAATG 59.337 55.000 28.56 24.07 36.11 2.32
3495 4528 2.365582 CAGTAGGCCGGCTTAAATGTT 58.634 47.619 28.56 4.24 0.00 2.71
3496 4529 2.354821 CAGTAGGCCGGCTTAAATGTTC 59.645 50.000 28.56 10.01 0.00 3.18
3498 4531 2.215942 AGGCCGGCTTAAATGTTCTT 57.784 45.000 28.56 0.00 0.00 2.52
3584 4617 3.894427 AGAAGCTCTGAAGAACTCACTCA 59.106 43.478 0.00 0.00 0.00 3.41
3605 4638 2.158755 ACAGAGCAAACAAGCTACTGGT 60.159 45.455 14.88 0.00 46.75 4.00
3606 4639 3.071023 ACAGAGCAAACAAGCTACTGGTA 59.929 43.478 14.88 0.00 46.75 3.25
3607 4640 3.433615 CAGAGCAAACAAGCTACTGGTAC 59.566 47.826 0.00 0.00 46.75 3.34
3608 4641 3.325135 AGAGCAAACAAGCTACTGGTACT 59.675 43.478 0.00 0.00 46.75 2.73
3609 4642 3.403038 AGCAAACAAGCTACTGGTACTG 58.597 45.455 0.00 0.00 44.50 2.74
3610 4643 2.484264 GCAAACAAGCTACTGGTACTGG 59.516 50.000 0.00 0.00 0.00 4.00
3669 4702 7.779798 AGCCTATTAACTTCCAATTAATCTGCA 59.220 33.333 10.91 0.00 34.39 4.41
3706 4739 0.609131 TAGGCTGCAAACCAAGGCTC 60.609 55.000 8.09 0.00 38.20 4.70
3726 4759 2.103094 TCGCAGTCCTTATAGCAAGCAT 59.897 45.455 0.00 0.00 0.00 3.79
3746 4779 1.821753 TGGCGTCATACAAAATTGGGG 59.178 47.619 0.00 0.00 0.00 4.96
3752 4785 4.142182 CGTCATACAAAATTGGGGCTGAAT 60.142 41.667 0.00 0.00 0.00 2.57
3768 4801 7.092979 TGGGGCTGAATCAAAAATAATTCATCA 60.093 33.333 0.00 0.00 40.19 3.07
3794 4827 7.066284 ACAATGCAGTTACAATCTATGAAGGAC 59.934 37.037 0.00 0.00 0.00 3.85
3845 4878 4.065088 TCATAACAATAGCGAGGATTGGC 58.935 43.478 8.59 0.00 38.39 4.52
3885 4918 4.390264 CTCAAGCAGTGGATCATCATCAT 58.610 43.478 0.00 0.00 0.00 2.45
3889 4922 3.646637 AGCAGTGGATCATCATCATCAGA 59.353 43.478 0.00 0.00 0.00 3.27
3890 4923 3.747010 GCAGTGGATCATCATCATCAGAC 59.253 47.826 0.00 0.00 0.00 3.51
3891 4924 4.316645 CAGTGGATCATCATCATCAGACC 58.683 47.826 0.00 0.00 0.00 3.85
3892 4925 4.040584 CAGTGGATCATCATCATCAGACCT 59.959 45.833 0.00 0.00 0.00 3.85
3893 4926 4.040584 AGTGGATCATCATCATCAGACCTG 59.959 45.833 0.00 0.00 0.00 4.00
3894 4927 4.040095 GTGGATCATCATCATCAGACCTGA 59.960 45.833 1.83 1.83 44.59 3.86
3895 4928 4.657039 TGGATCATCATCATCAGACCTGAA 59.343 41.667 3.62 0.00 43.58 3.02
3896 4929 4.996122 GGATCATCATCATCAGACCTGAAC 59.004 45.833 3.62 0.00 43.58 3.18
3897 4930 4.412796 TCATCATCATCAGACCTGAACC 57.587 45.455 3.62 0.00 43.58 3.62
3898 4931 3.135348 TCATCATCATCAGACCTGAACCC 59.865 47.826 3.62 0.00 43.58 4.11
3899 4932 1.839994 TCATCATCAGACCTGAACCCC 59.160 52.381 3.62 0.00 43.58 4.95
3900 4933 1.842562 CATCATCAGACCTGAACCCCT 59.157 52.381 3.62 0.00 43.58 4.79
3901 4934 2.044793 TCATCAGACCTGAACCCCTT 57.955 50.000 3.62 0.00 43.58 3.95
3902 4935 2.348472 TCATCAGACCTGAACCCCTTT 58.652 47.619 3.62 0.00 43.58 3.11
3903 4936 2.716424 TCATCAGACCTGAACCCCTTTT 59.284 45.455 3.62 0.00 43.58 2.27
3904 4937 2.951229 TCAGACCTGAACCCCTTTTC 57.049 50.000 0.00 0.00 36.53 2.29
3943 4992 2.566746 CCCAGATAATCCTATGCCCCT 58.433 52.381 0.00 0.00 0.00 4.79
3946 4995 3.308688 CCAGATAATCCTATGCCCCTTGG 60.309 52.174 0.00 0.00 0.00 3.61
4003 5052 0.322008 AAAGAGGAAGAGCCAAGCGG 60.322 55.000 0.00 0.00 40.02 5.52
4019 5068 0.233332 GCGGCTGATACATCGCTTTC 59.767 55.000 0.00 0.00 44.10 2.62
4021 5070 0.861837 GGCTGATACATCGCTTTCCG 59.138 55.000 6.18 0.00 38.61 4.30
4042 5091 1.194547 GCATACAGTTCACACACCACG 59.805 52.381 0.00 0.00 0.00 4.94
4050 5099 2.212869 TCACACACCACGACTACAAC 57.787 50.000 0.00 0.00 0.00 3.32
4058 5107 2.195096 CCACGACTACAACGACACAAA 58.805 47.619 0.00 0.00 34.70 2.83
4061 5110 3.061028 CACGACTACAACGACACAAACAA 59.939 43.478 0.00 0.00 34.70 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 123 3.450817 TGAGTCGGATCAGCTTTCCATTA 59.549 43.478 11.97 0.00 32.45 1.90
121 128 1.663135 GCTTGAGTCGGATCAGCTTTC 59.337 52.381 0.00 0.00 0.00 2.62
129 136 1.393603 TCGATCAGCTTGAGTCGGAT 58.606 50.000 0.00 0.00 32.41 4.18
166 173 3.769739 TCATCATCGGTTATCCTTGGG 57.230 47.619 0.00 0.00 0.00 4.12
178 186 5.796935 GTGTTGGTTCAGATTTTCATCATCG 59.203 40.000 0.00 0.00 0.00 3.84
256 267 2.616842 GACCGATGTGTTGGTGTTCTTT 59.383 45.455 0.00 0.00 42.46 2.52
259 270 1.588674 TGACCGATGTGTTGGTGTTC 58.411 50.000 0.00 0.00 42.46 3.18
261 272 1.071542 TCATGACCGATGTGTTGGTGT 59.928 47.619 0.00 0.00 42.46 4.16
264 275 2.002586 GTCTCATGACCGATGTGTTGG 58.997 52.381 0.00 0.00 37.24 3.77
266 277 3.244215 ACTTGTCTCATGACCGATGTGTT 60.244 43.478 0.00 0.00 42.28 3.32
267 278 2.300152 ACTTGTCTCATGACCGATGTGT 59.700 45.455 0.00 0.00 42.28 3.72
268 279 2.669924 CACTTGTCTCATGACCGATGTG 59.330 50.000 0.00 0.00 42.28 3.21
269 280 2.562738 TCACTTGTCTCATGACCGATGT 59.437 45.455 0.00 0.00 42.28 3.06
271 282 2.828520 AGTCACTTGTCTCATGACCGAT 59.171 45.455 0.00 0.00 43.10 4.18
272 283 2.239400 AGTCACTTGTCTCATGACCGA 58.761 47.619 0.00 0.00 43.10 4.69
273 284 2.732412 AGTCACTTGTCTCATGACCG 57.268 50.000 0.00 0.00 43.10 4.79
274 285 5.757850 AAAAAGTCACTTGTCTCATGACC 57.242 39.130 0.00 0.00 43.10 4.02
354 373 4.787598 CAAATCTTTCTATACCGCCATGC 58.212 43.478 0.00 0.00 0.00 4.06
499 547 8.951787 ATTAGTGTATTGCCTCGTTTTGTATA 57.048 30.769 0.00 0.00 0.00 1.47
660 712 1.813862 GCGGGCATAGTAAAGCATGGA 60.814 52.381 0.00 0.00 0.00 3.41
703 763 1.831106 AGCATACACATCTCCCGACAA 59.169 47.619 0.00 0.00 0.00 3.18
764 824 8.563732 TGTGTCTGAAATATTTCAATCAAACGA 58.436 29.630 26.57 17.37 45.61 3.85
783 843 7.381766 TCATTAATTCCTTGTCATGTGTCTG 57.618 36.000 0.00 0.00 0.00 3.51
811 871 2.092212 ACACATCCATTGCTTAGAGGGG 60.092 50.000 0.00 0.00 0.00 4.79
841 901 5.893824 TGCTAGGATTGAAGAGAGTACATCA 59.106 40.000 0.00 0.00 0.00 3.07
842 902 6.040391 ACTGCTAGGATTGAAGAGAGTACATC 59.960 42.308 0.00 0.00 0.00 3.06
910 997 4.984785 TGAATTTCTCTTCAGACAGACACG 59.015 41.667 0.00 0.00 31.65 4.49
914 1001 9.862371 GTATTAGTGAATTTCTCTTCAGACAGA 57.138 33.333 6.32 0.00 35.88 3.41
1269 1361 0.038067 CATGGTCGACGTTGGTGGTA 60.038 55.000 9.92 0.00 0.00 3.25
1428 1520 3.623510 GCACTTCAGCCAGATAGGTAAAC 59.376 47.826 0.00 0.00 40.61 2.01
1457 1549 9.699703 AAATTTAGATTTATCTCTAGACGAGCC 57.300 33.333 0.00 0.00 38.32 4.70
1486 1578 5.161943 ACCACTTCCAATAGACTTGGTAC 57.838 43.478 4.06 0.00 37.87 3.34
1487 1579 5.836024 AACCACTTCCAATAGACTTGGTA 57.164 39.130 4.06 0.00 38.44 3.25
1820 2229 7.652909 AGAGAAAAACAAAATCGAATCAATGCA 59.347 29.630 0.00 0.00 0.00 3.96
1821 2230 7.948363 CAGAGAAAAACAAAATCGAATCAATGC 59.052 33.333 0.00 0.00 0.00 3.56
1822 2231 8.430063 CCAGAGAAAAACAAAATCGAATCAATG 58.570 33.333 0.00 0.00 0.00 2.82
1845 2254 0.689623 AGAAGAACCTGCAGGACCAG 59.310 55.000 39.19 12.80 38.94 4.00
2182 2707 3.470709 ACATTATGATCGAGCTTGTGGG 58.529 45.455 0.90 0.00 0.00 4.61
2227 2779 1.269448 ACCGCCTAACAAATTGCACAG 59.731 47.619 0.00 0.00 0.00 3.66
2229 2781 1.727857 CGACCGCCTAACAAATTGCAC 60.728 52.381 0.00 0.00 0.00 4.57
2388 2947 1.879380 ACAATGTGGACAATGTGACGG 59.121 47.619 0.00 0.00 38.45 4.79
2517 3547 9.203421 TTGTCAATCTACAAAGTACAGTATGTG 57.797 33.333 0.00 0.00 42.61 3.21
2758 3788 4.503910 TGGAATCGTCAGGTATTTGACAG 58.496 43.478 6.91 0.77 46.11 3.51
2766 3796 0.906775 GGGGTTGGAATCGTCAGGTA 59.093 55.000 0.00 0.00 0.00 3.08
2768 3798 0.676782 GTGGGGTTGGAATCGTCAGG 60.677 60.000 0.00 0.00 0.00 3.86
2774 3804 2.214376 TGTCATGTGGGGTTGGAATC 57.786 50.000 0.00 0.00 0.00 2.52
2792 3822 6.801539 TGTAAAGAGCTTCAGGTGTTATTG 57.198 37.500 0.00 0.00 0.00 1.90
2843 3873 5.336690 GCAAGGATTTTACTGAAGCCATCAA 60.337 40.000 0.00 0.00 37.54 2.57
2865 3895 7.252708 TGTTACTAATTATCTTCGACTTCGCA 58.747 34.615 0.00 0.00 39.60 5.10
2885 3915 6.806739 GCACCAAAATTCAGAGGTATTGTTAC 59.193 38.462 0.00 0.00 32.01 2.50
2904 3934 0.034186 CTTAGGCCATCCTGCACCAA 60.034 55.000 5.01 0.00 44.08 3.67
2906 3936 1.152881 CCTTAGGCCATCCTGCACC 60.153 63.158 5.01 0.00 44.08 5.01
2954 3984 0.033991 CCTCGGTCCTCTCCTTCTCA 60.034 60.000 0.00 0.00 0.00 3.27
3059 4089 6.595326 TGATCTGCATACTTGTTTACTCCTTG 59.405 38.462 0.00 0.00 0.00 3.61
3068 4098 2.420022 GGCGTTGATCTGCATACTTGTT 59.580 45.455 7.32 0.00 0.00 2.83
3069 4099 2.009774 GGCGTTGATCTGCATACTTGT 58.990 47.619 7.32 0.00 0.00 3.16
3070 4100 2.009051 TGGCGTTGATCTGCATACTTG 58.991 47.619 7.32 0.00 0.00 3.16
3073 4103 0.940126 CCTGGCGTTGATCTGCATAC 59.060 55.000 7.32 0.00 0.00 2.39
3102 4132 2.969238 GATCGATGGGCAGTGGCG 60.969 66.667 10.99 0.00 42.47 5.69
3123 4153 2.297033 TGAATGTCTTTGCAAGGAAGGC 59.703 45.455 13.42 3.37 0.00 4.35
3134 4164 6.705302 TGTGCTATTCTCTCTGAATGTCTTT 58.295 36.000 0.00 0.00 44.40 2.52
3137 4167 4.507388 GCTGTGCTATTCTCTCTGAATGTC 59.493 45.833 0.00 0.00 44.40 3.06
3139 4169 3.808726 GGCTGTGCTATTCTCTCTGAATG 59.191 47.826 0.00 0.00 44.40 2.67
3140 4170 3.710677 AGGCTGTGCTATTCTCTCTGAAT 59.289 43.478 0.00 0.00 46.22 2.57
3141 4171 3.102972 AGGCTGTGCTATTCTCTCTGAA 58.897 45.455 0.00 0.00 39.24 3.02
3143 4173 2.168106 ACAGGCTGTGCTATTCTCTCTG 59.832 50.000 21.37 0.00 0.00 3.35
3144 4174 2.430332 GACAGGCTGTGCTATTCTCTCT 59.570 50.000 27.45 0.00 0.00 3.10
3145 4175 2.482839 GGACAGGCTGTGCTATTCTCTC 60.483 54.545 29.05 9.27 35.71 3.20
3164 4194 2.138179 GCGCATGGGGTAGGTAGGA 61.138 63.158 12.19 0.00 0.00 2.94
3199 4229 3.492656 GGCGACAATGAATAGGAGCACTA 60.493 47.826 0.00 0.00 35.80 2.74
3215 4245 0.253610 AATAATTGACGGGGGCGACA 59.746 50.000 0.00 0.00 0.00 4.35
3225 4255 7.970384 TCGGTGACACAAAGATAATAATTGAC 58.030 34.615 8.08 0.00 0.00 3.18
3227 4257 9.787532 AATTCGGTGACACAAAGATAATAATTG 57.212 29.630 8.08 0.00 0.00 2.32
3259 4289 8.044309 TCTTCATCCAATCAAAAGTTCGGTATA 58.956 33.333 0.00 0.00 0.00 1.47
3301 4331 6.093219 ACACAATACAGCTCAGCTTCAAATAG 59.907 38.462 0.00 0.00 36.40 1.73
3303 4333 4.763793 ACACAATACAGCTCAGCTTCAAAT 59.236 37.500 0.00 0.00 36.40 2.32
3389 4421 8.287439 TGTTTTGGTTATTATTGTCGATCCAT 57.713 30.769 0.00 0.00 0.00 3.41
3390 4422 7.689446 TGTTTTGGTTATTATTGTCGATCCA 57.311 32.000 0.00 0.00 0.00 3.41
3394 4426 9.995957 CACATATGTTTTGGTTATTATTGTCGA 57.004 29.630 5.37 0.00 0.00 4.20
3395 4427 8.742188 GCACATATGTTTTGGTTATTATTGTCG 58.258 33.333 5.37 0.00 0.00 4.35
3396 4428 9.801873 AGCACATATGTTTTGGTTATTATTGTC 57.198 29.630 5.37 0.00 0.00 3.18
3402 4434 9.019656 TCACTAAGCACATATGTTTTGGTTATT 57.980 29.630 5.37 3.61 33.88 1.40
3414 4446 4.270008 GGTGGGTTTCACTAAGCACATAT 58.730 43.478 0.00 0.00 45.38 1.78
3434 4466 1.877443 CTTTGGTTTCGGTCATTCGGT 59.123 47.619 0.00 0.00 0.00 4.69
3435 4467 1.877443 ACTTTGGTTTCGGTCATTCGG 59.123 47.619 0.00 0.00 0.00 4.30
3436 4468 4.708601 CTTACTTTGGTTTCGGTCATTCG 58.291 43.478 0.00 0.00 0.00 3.34
3437 4469 4.215613 AGCTTACTTTGGTTTCGGTCATTC 59.784 41.667 0.00 0.00 0.00 2.67
3438 4470 4.142038 AGCTTACTTTGGTTTCGGTCATT 58.858 39.130 0.00 0.00 0.00 2.57
3439 4471 3.751518 AGCTTACTTTGGTTTCGGTCAT 58.248 40.909 0.00 0.00 0.00 3.06
3440 4472 3.202829 AGCTTACTTTGGTTTCGGTCA 57.797 42.857 0.00 0.00 0.00 4.02
3441 4473 4.512571 TGTTAGCTTACTTTGGTTTCGGTC 59.487 41.667 4.27 0.00 0.00 4.79
3525 4558 7.898014 TCACCTCTTCAATTGAGCTACTATA 57.102 36.000 8.41 0.00 0.00 1.31
3536 4569 4.103153 TCAGTCCTGTTCACCTCTTCAATT 59.897 41.667 0.00 0.00 0.00 2.32
3543 4576 5.407407 TTCTATTCAGTCCTGTTCACCTC 57.593 43.478 0.00 0.00 0.00 3.85
3584 4617 2.158755 ACCAGTAGCTTGTTTGCTCTGT 60.159 45.455 0.00 0.00 42.97 3.41
3608 4641 6.947657 TAGCAATTACAGCTACTTGCGCCA 62.948 45.833 4.18 0.00 46.51 5.69
3609 4642 3.825959 AGCAATTACAGCTACTTGCGCC 61.826 50.000 4.18 0.00 46.51 6.53
3610 4643 1.398390 AGCAATTACAGCTACTTGCGC 59.602 47.619 0.00 0.00 46.51 6.09
3669 4702 6.429385 GCAGCCTAATCTATTAAGATGCACTT 59.571 38.462 13.82 0.00 42.51 3.16
3677 4710 6.942532 TGGTTTGCAGCCTAATCTATTAAG 57.057 37.500 10.19 0.00 0.00 1.85
3679 4712 5.827797 CCTTGGTTTGCAGCCTAATCTATTA 59.172 40.000 10.19 0.00 0.00 0.98
3680 4713 4.646492 CCTTGGTTTGCAGCCTAATCTATT 59.354 41.667 10.19 0.00 0.00 1.73
3682 4715 3.620488 CCTTGGTTTGCAGCCTAATCTA 58.380 45.455 10.19 0.00 0.00 1.98
3683 4716 2.450476 CCTTGGTTTGCAGCCTAATCT 58.550 47.619 10.19 0.00 0.00 2.40
3684 4717 1.134995 GCCTTGGTTTGCAGCCTAATC 60.135 52.381 10.19 0.00 0.00 1.75
3685 4718 0.897621 GCCTTGGTTTGCAGCCTAAT 59.102 50.000 10.19 0.00 0.00 1.73
3686 4719 0.178964 AGCCTTGGTTTGCAGCCTAA 60.179 50.000 10.19 0.00 0.00 2.69
3706 4739 1.939974 TGCTTGCTATAAGGACTGCG 58.060 50.000 0.00 0.00 0.00 5.18
3726 4759 1.821753 CCCCAATTTTGTATGACGCCA 59.178 47.619 0.00 0.00 0.00 5.69
3752 4785 9.491675 AACTGCATTGTGATGAATTATTTTTGA 57.508 25.926 0.00 0.00 35.16 2.69
3768 4801 7.066284 GTCCTTCATAGATTGTAACTGCATTGT 59.934 37.037 0.00 0.00 0.00 2.71
3835 4868 4.718940 ATTTTAGTTTGGCCAATCCTCG 57.281 40.909 21.26 0.00 35.26 4.63
3845 4878 5.743872 GCTTGAGGCGATAATTTTAGTTTGG 59.256 40.000 0.00 0.00 0.00 3.28
3885 4918 2.131854 TGAAAAGGGGTTCAGGTCTGA 58.868 47.619 0.00 0.00 37.91 3.27
3889 4922 1.970640 GCAATGAAAAGGGGTTCAGGT 59.029 47.619 0.00 0.00 40.72 4.00
3890 4923 1.969923 TGCAATGAAAAGGGGTTCAGG 59.030 47.619 0.00 0.00 40.72 3.86
3891 4924 2.892852 TCTGCAATGAAAAGGGGTTCAG 59.107 45.455 0.00 0.00 40.72 3.02
3892 4925 2.892852 CTCTGCAATGAAAAGGGGTTCA 59.107 45.455 0.00 0.00 41.59 3.18
3893 4926 2.893489 ACTCTGCAATGAAAAGGGGTTC 59.107 45.455 0.00 0.00 0.00 3.62
3894 4927 2.962859 ACTCTGCAATGAAAAGGGGTT 58.037 42.857 0.00 0.00 0.00 4.11
3895 4928 2.683211 ACTCTGCAATGAAAAGGGGT 57.317 45.000 0.00 0.00 0.00 4.95
3896 4929 4.524328 ACTTAACTCTGCAATGAAAAGGGG 59.476 41.667 0.00 0.00 0.00 4.79
3897 4930 5.474876 AGACTTAACTCTGCAATGAAAAGGG 59.525 40.000 0.00 0.00 0.00 3.95
3898 4931 6.376978 CAGACTTAACTCTGCAATGAAAAGG 58.623 40.000 0.00 0.00 31.57 3.11
3943 4992 4.160065 CCATTGTGTATCCATGAAAGCCAA 59.840 41.667 0.00 0.00 0.00 4.52
3946 4995 4.883585 TCTCCATTGTGTATCCATGAAAGC 59.116 41.667 0.00 0.00 0.00 3.51
3947 4996 5.530171 CCTCTCCATTGTGTATCCATGAAAG 59.470 44.000 0.00 0.00 0.00 2.62
3953 5002 3.181329 ACACCTCTCCATTGTGTATCCA 58.819 45.455 0.00 0.00 41.18 3.41
4003 5052 0.861837 CCGGAAAGCGATGTATCAGC 59.138 55.000 0.00 0.00 0.00 4.26
4012 5061 0.036765 AACTGTATGCCGGAAAGCGA 60.037 50.000 5.05 0.00 34.65 4.93
4019 5068 0.796312 GTGTGTGAACTGTATGCCGG 59.204 55.000 0.00 0.00 0.00 6.13
4021 5070 1.535462 GTGGTGTGTGAACTGTATGCC 59.465 52.381 0.00 0.00 0.00 4.40
4042 5091 4.547587 CGAGTTGTTTGTGTCGTTGTAGTC 60.548 45.833 0.00 0.00 0.00 2.59
4050 5099 2.307363 AGGCGAGTTGTTTGTGTCG 58.693 52.632 0.00 0.00 35.51 4.35


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

AutoCloner maintained by Alex Coulton.