Multiple sequence alignment - TraesCS7B01G168500

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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 TraesCS7B01G168500 chr7B 100.000 4287 0 0 1 4287 236333798 236329512 0.000000e+00 7917
1 TraesCS7B01G168500 chr7B 92.407 619 42 3 1 614 13816647 13816029 0.000000e+00 878
2 TraesCS7B01G168500 chr7B 91.200 125 6 1 1174 1293 236332438 236332314 9.540000e-37 165
3 TraesCS7B01G168500 chr7B 91.200 125 6 1 1361 1485 236332625 236332506 9.540000e-37 165
4 TraesCS7B01G168500 chr7D 92.221 3921 153 58 1 3833 257112347 257108491 0.000000e+00 5411
5 TraesCS7B01G168500 chr7D 90.924 617 48 6 1 611 295606206 295606820 0.000000e+00 822
6 TraesCS7B01G168500 chr7D 92.291 467 14 4 3822 4287 257107938 257107493 1.000000e-180 643
7 TraesCS7B01G168500 chr7D 91.781 146 11 1 1174 1319 257110943 257110799 7.270000e-48 202
8 TraesCS7B01G168500 chr7D 92.800 125 4 1 1361 1485 257111129 257111010 4.410000e-40 176
9 TraesCS7B01G168500 chr7A 91.713 3753 158 52 619 4287 278452701 278456384 0.000000e+00 5066
10 TraesCS7B01G168500 chr7A 90.541 148 9 2 1174 1321 278453477 278453619 1.570000e-44 191
11 TraesCS7B01G168500 chr7A 92.000 125 5 1 1361 1485 278453285 278453404 2.050000e-38 171
12 TraesCS7B01G168500 chr5B 92.562 605 40 3 15 614 590246767 590246163 0.000000e+00 863
13 TraesCS7B01G168500 chr6D 91.761 619 45 5 1 614 58544827 58544210 0.000000e+00 856
14 TraesCS7B01G168500 chr5D 91.883 616 45 3 1 611 462418330 462418945 0.000000e+00 856
15 TraesCS7B01G168500 chr2A 91.558 616 46 4 1 611 487370836 487371450 0.000000e+00 845
16 TraesCS7B01G168500 chr4A 90.909 616 51 3 1 611 558841298 558841913 0.000000e+00 822
17 TraesCS7B01G168500 chr4B 90.584 616 53 3 1 611 631588207 631588822 0.000000e+00 811


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 TraesCS7B01G168500 chr7B 236329512 236333798 4286 True 2749.000000 7917 94.133333 1 4287 3 chr7B.!!$R2 4286
1 TraesCS7B01G168500 chr7B 13816029 13816647 618 True 878.000000 878 92.407000 1 614 1 chr7B.!!$R1 613
2 TraesCS7B01G168500 chr7D 257107493 257112347 4854 True 1608.000000 5411 92.273250 1 4287 4 chr7D.!!$R1 4286
3 TraesCS7B01G168500 chr7D 295606206 295606820 614 False 822.000000 822 90.924000 1 611 1 chr7D.!!$F1 610
4 TraesCS7B01G168500 chr7A 278452701 278456384 3683 False 1809.333333 5066 91.418000 619 4287 3 chr7A.!!$F1 3668
5 TraesCS7B01G168500 chr5B 590246163 590246767 604 True 863.000000 863 92.562000 15 614 1 chr5B.!!$R1 599
6 TraesCS7B01G168500 chr6D 58544210 58544827 617 True 856.000000 856 91.761000 1 614 1 chr6D.!!$R1 613
7 TraesCS7B01G168500 chr5D 462418330 462418945 615 False 856.000000 856 91.883000 1 611 1 chr5D.!!$F1 610
8 TraesCS7B01G168500 chr2A 487370836 487371450 614 False 845.000000 845 91.558000 1 611 1 chr2A.!!$F1 610
9 TraesCS7B01G168500 chr4A 558841298 558841913 615 False 822.000000 822 90.909000 1 611 1 chr4A.!!$F1 610
10 TraesCS7B01G168500 chr4B 631588207 631588822 615 False 811.000000 811 90.584000 1 611 1 chr4B.!!$F1 610

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
656 662 0.108567 GAGAAGAAGGAGCGGTCCAC 60.109 60.0 33.52 25.3 46.80 4.02 F
1249 1301 0.182299 CTCTGCTTCCATTCCCTCCC 59.818 60.0 0.00 0.0 0.00 4.30 F
1599 1666 0.323999 TGCTGCATCCTTGATTGGCT 60.324 50.0 0.00 0.0 0.00 4.75 F
2093 2174 0.534873 TAGCTGCTGCGTTACCATGA 59.465 50.0 13.43 0.0 45.42 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2063 1.843851 AGAGGGTCACTTTGGTCACAA 59.156 47.619 0.0 0.0 34.07 3.33 R
2869 2961 1.372499 GAACACGTCGTAGCTGCCA 60.372 57.895 0.0 0.0 0.00 4.92 R
2914 3006 1.522569 GAGCCCGGTCTTGCAGTAT 59.477 57.895 0.0 0.0 0.00 2.12 R
4070 4752 0.110486 ATCTCACGTGGGCAAAGGTT 59.890 50.000 17.0 0.0 0.00 3.50 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
53 54 2.863809 AGGTTCCAGCGAAAAACATCT 58.136 42.857 0.00 0.00 0.00 2.90
83 84 4.221924 TGTGTCAGGTTAATCGAATCCAGA 59.778 41.667 0.00 0.00 0.00 3.86
131 132 1.923395 TCGGGGGCCAATCAAGTCT 60.923 57.895 4.39 0.00 0.00 3.24
216 217 2.802816 CGAGCAATGGTGTATAAGGCTC 59.197 50.000 0.00 0.00 42.01 4.70
260 261 4.649692 CATTGCCTAGCCATATGTCTTCT 58.350 43.478 1.24 0.00 0.00 2.85
279 280 4.252971 TCTCAGAAACGAATTTCCGACT 57.747 40.909 0.00 0.00 44.66 4.18
280 281 3.987868 TCTCAGAAACGAATTTCCGACTG 59.012 43.478 0.00 0.00 44.66 3.51
281 282 2.478894 TCAGAAACGAATTTCCGACTGC 59.521 45.455 0.00 0.00 44.66 4.40
292 294 1.153449 CCGACTGCCCTTTATCGCA 60.153 57.895 0.00 0.00 33.25 5.10
336 338 1.083489 TTCTTTGCCGCCATTAGACG 58.917 50.000 0.00 0.00 0.00 4.18
340 342 2.107141 GCCGCCATTAGACGAGCT 59.893 61.111 0.00 0.00 0.00 4.09
476 478 6.046290 ACCATTTACTAAGTAGGGACACAC 57.954 41.667 0.00 0.00 0.00 3.82
509 511 3.386726 CAGGTCATGAATTCCAATGCCAT 59.613 43.478 2.27 0.00 0.00 4.40
520 522 4.314522 TCCAATGCCATCTTGGTCTTTA 57.685 40.909 2.30 0.00 43.07 1.85
544 547 4.021544 GGCCTACAAACCATGTTCATTTGA 60.022 41.667 13.00 0.00 43.63 2.69
586 592 5.711506 TCAGCATCTTCTTGCCAAAAGAATA 59.288 36.000 1.28 0.00 43.83 1.75
614 620 9.654663 ACATCTAAAATAGTCCAGTCTTTACAC 57.345 33.333 0.00 0.00 0.00 2.90
615 621 9.099454 CATCTAAAATAGTCCAGTCTTTACACC 57.901 37.037 0.00 0.00 0.00 4.16
617 623 3.521947 ATAGTCCAGTCTTTACACCGC 57.478 47.619 0.00 0.00 0.00 5.68
643 649 9.692749 CCGTTTATTTACATGCTATAGAGAAGA 57.307 33.333 3.21 0.00 0.00 2.87
654 660 1.765230 TAGAGAAGAAGGAGCGGTCC 58.235 55.000 26.17 26.17 44.33 4.46
656 662 0.108567 GAGAAGAAGGAGCGGTCCAC 60.109 60.000 33.52 25.30 46.80 4.02
777 788 2.042259 CACACACATGCCGATGCCT 61.042 57.895 0.00 0.00 36.33 4.75
929 941 2.046892 GCATCACTCGGTGCCACT 60.047 61.111 0.00 0.00 35.35 4.00
1249 1301 0.182299 CTCTGCTTCCATTCCCTCCC 59.818 60.000 0.00 0.00 0.00 4.30
1284 1336 4.707210 GAGCAGATTCTCGCAGTTAATC 57.293 45.455 9.67 0.00 32.72 1.75
1285 1337 3.119291 AGCAGATTCTCGCAGTTAATCG 58.881 45.455 9.67 0.00 35.83 3.34
1398 1456 0.383949 GGTTTTGCCTTGCTCGTTCA 59.616 50.000 0.00 0.00 0.00 3.18
1399 1457 1.600413 GGTTTTGCCTTGCTCGTTCAG 60.600 52.381 0.00 0.00 0.00 3.02
1599 1666 0.323999 TGCTGCATCCTTGATTGGCT 60.324 50.000 0.00 0.00 0.00 4.75
1709 1779 1.585002 TTGCAACTTCGCAACGTGC 60.585 52.632 0.00 0.00 46.61 5.34
1780 1850 5.049405 ACTGACAGAATTTGACGATCCAAAC 60.049 40.000 10.08 0.00 38.65 2.93
1849 1919 5.869579 TCACCTGCTCTACAATTCTCTTTT 58.130 37.500 0.00 0.00 0.00 2.27
1850 1920 5.934625 TCACCTGCTCTACAATTCTCTTTTC 59.065 40.000 0.00 0.00 0.00 2.29
1884 1956 9.398538 CTATAACTCAGAACTGTTACCTAGACT 57.601 37.037 0.00 0.00 32.43 3.24
2005 2077 7.057894 ACCTTTATTACTTGTGACCAAAGTGA 58.942 34.615 0.00 0.00 0.00 3.41
2046 2127 3.946558 GCCTTCATGCATCTTCTTCTTCT 59.053 43.478 0.00 0.00 0.00 2.85
2047 2128 4.398673 GCCTTCATGCATCTTCTTCTTCTT 59.601 41.667 0.00 0.00 0.00 2.52
2048 2129 5.448904 GCCTTCATGCATCTTCTTCTTCTTC 60.449 44.000 0.00 0.00 0.00 2.87
2049 2130 5.881443 CCTTCATGCATCTTCTTCTTCTTCT 59.119 40.000 0.00 0.00 0.00 2.85
2050 2131 6.374894 CCTTCATGCATCTTCTTCTTCTTCTT 59.625 38.462 0.00 0.00 0.00 2.52
2051 2132 6.981762 TCATGCATCTTCTTCTTCTTCTTC 57.018 37.500 0.00 0.00 0.00 2.87
2052 2133 6.709281 TCATGCATCTTCTTCTTCTTCTTCT 58.291 36.000 0.00 0.00 0.00 2.85
2053 2134 7.166851 TCATGCATCTTCTTCTTCTTCTTCTT 58.833 34.615 0.00 0.00 0.00 2.52
2054 2135 7.333921 TCATGCATCTTCTTCTTCTTCTTCTTC 59.666 37.037 0.00 0.00 0.00 2.87
2055 2136 6.767456 TGCATCTTCTTCTTCTTCTTCTTCT 58.233 36.000 0.00 0.00 0.00 2.85
2056 2137 7.222872 TGCATCTTCTTCTTCTTCTTCTTCTT 58.777 34.615 0.00 0.00 0.00 2.52
2057 2138 7.387397 TGCATCTTCTTCTTCTTCTTCTTCTTC 59.613 37.037 0.00 0.00 0.00 2.87
2093 2174 0.534873 TAGCTGCTGCGTTACCATGA 59.465 50.000 13.43 0.00 45.42 3.07
2286 2367 6.037500 TGCTCAAGTGACAATTATACAGATGC 59.962 38.462 0.00 0.00 0.00 3.91
2387 2479 3.448686 CTGGCATGTTTCCGAGTAGTAG 58.551 50.000 0.00 0.00 0.00 2.57
2388 2480 2.829720 TGGCATGTTTCCGAGTAGTAGT 59.170 45.455 0.00 0.00 0.00 2.73
2389 2481 4.018490 TGGCATGTTTCCGAGTAGTAGTA 58.982 43.478 0.00 0.00 0.00 1.82
2463 2555 8.824159 ATGAATAGAGAATGTATGTGTGTAGC 57.176 34.615 0.00 0.00 0.00 3.58
2464 2556 6.918022 TGAATAGAGAATGTATGTGTGTAGCG 59.082 38.462 0.00 0.00 0.00 4.26
2465 2557 4.720649 AGAGAATGTATGTGTGTAGCGT 57.279 40.909 0.00 0.00 0.00 5.07
2466 2558 4.424626 AGAGAATGTATGTGTGTAGCGTG 58.575 43.478 0.00 0.00 0.00 5.34
2483 2575 3.116300 GCGTGTACTATGGTCACTGATG 58.884 50.000 0.00 0.00 0.00 3.07
2508 2600 9.219603 TGAGTGAATTTGTTCTATCTCGAATTT 57.780 29.630 0.00 0.00 30.64 1.82
2644 2736 4.796495 ATTTCCGCCGGCTCACCC 62.796 66.667 26.68 0.00 0.00 4.61
2869 2961 1.073199 CCTGCTCCAGAACGGGTTT 59.927 57.895 0.00 0.00 32.44 3.27
3307 3402 1.531423 CAGGAGCTGCTGTTGTGATT 58.469 50.000 25.76 0.00 0.00 2.57
3312 3407 3.753272 GGAGCTGCTGTTGTGATTCTTTA 59.247 43.478 7.01 0.00 0.00 1.85
3327 3422 8.291740 TGTGATTCTTTATGTTTGATCTGTGTG 58.708 33.333 0.00 0.00 0.00 3.82
3328 3423 8.506437 GTGATTCTTTATGTTTGATCTGTGTGA 58.494 33.333 0.00 0.00 0.00 3.58
3329 3424 9.234827 TGATTCTTTATGTTTGATCTGTGTGAT 57.765 29.630 0.00 0.00 38.27 3.06
3351 3446 6.422701 TGATAGTTTGGAGTTTGTACTTCACG 59.577 38.462 0.00 0.00 39.66 4.35
3438 3533 6.989169 AGCAATTCACTCTGTATCATAGGAAC 59.011 38.462 0.00 0.00 0.00 3.62
3507 3602 3.586892 GACCAGGCTATAATCGGTTAGC 58.413 50.000 0.00 0.00 40.07 3.09
3585 3684 8.715191 ATTATCTGTTTCTGTTCTGTGATCTC 57.285 34.615 0.00 0.00 0.00 2.75
3586 3685 5.798125 TCTGTTTCTGTTCTGTGATCTCT 57.202 39.130 0.00 0.00 0.00 3.10
3587 3686 5.777802 TCTGTTTCTGTTCTGTGATCTCTC 58.222 41.667 0.00 0.00 0.00 3.20
3590 3709 7.231519 TCTGTTTCTGTTCTGTGATCTCTCTTA 59.768 37.037 0.00 0.00 0.00 2.10
3640 3759 0.033306 TGCCAATTAGCCTGCCATCA 60.033 50.000 0.00 0.00 0.00 3.07
3687 3806 0.179056 ACAGTGGTGGTCCGACAAAG 60.179 55.000 0.00 0.00 36.30 2.77
3736 3855 3.509575 TGGAGATTTTATTGTGTGTGCCC 59.490 43.478 0.00 0.00 0.00 5.36
3737 3856 3.763897 GGAGATTTTATTGTGTGTGCCCT 59.236 43.478 0.00 0.00 0.00 5.19
3738 3857 4.142381 GGAGATTTTATTGTGTGTGCCCTC 60.142 45.833 0.00 0.00 0.00 4.30
3739 3858 4.666512 AGATTTTATTGTGTGTGCCCTCT 58.333 39.130 0.00 0.00 0.00 3.69
3740 3859 5.815581 AGATTTTATTGTGTGTGCCCTCTA 58.184 37.500 0.00 0.00 0.00 2.43
3743 3862 5.957842 TTTATTGTGTGTGCCCTCTAAAG 57.042 39.130 0.00 0.00 0.00 1.85
3744 3863 3.788227 ATTGTGTGTGCCCTCTAAAGA 57.212 42.857 0.00 0.00 0.00 2.52
3746 3865 3.788227 TGTGTGTGCCCTCTAAAGAAT 57.212 42.857 0.00 0.00 0.00 2.40
3749 3868 4.892934 TGTGTGTGCCCTCTAAAGAATTTT 59.107 37.500 0.00 0.00 40.09 1.82
3750 3869 5.362430 TGTGTGTGCCCTCTAAAGAATTTTT 59.638 36.000 0.00 0.00 40.09 1.94
3751 3870 6.547880 TGTGTGTGCCCTCTAAAGAATTTTTA 59.452 34.615 0.00 0.00 40.09 1.52
3870 4552 4.183101 CACAACAAAATCCACAAAGTGCT 58.817 39.130 0.00 0.00 31.34 4.40
3905 4587 5.762179 AGTATTTCCAGGACTGATGACAA 57.238 39.130 0.00 0.00 0.00 3.18
4069 4751 4.675404 CGAAACTTCACCCTCGCT 57.325 55.556 0.00 0.00 0.00 4.93
4070 4752 3.806591 CGAAACTTCACCCTCGCTA 57.193 52.632 0.00 0.00 0.00 4.26
4091 4773 0.321564 CCTTTGCCCACGTGAGATGA 60.322 55.000 19.30 0.00 0.00 2.92
4186 4868 6.310467 TGTTTCTTCTGAATTTACTCGGATCG 59.690 38.462 0.00 0.00 30.77 3.69
4207 4890 2.357777 GGATGCCCTGCCCTTAACTTTA 60.358 50.000 0.00 0.00 0.00 1.85
4241 4924 4.072131 TGTGTGTTCCTCTGCCTTTAATC 58.928 43.478 0.00 0.00 0.00 1.75
4269 4952 4.136796 CCTCATAGACTCTCTCTCACCAG 58.863 52.174 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 0.759959 TTAACCTGACACAAGGCCGA 59.240 50.000 0.00 0.00 41.46 5.54
83 84 5.473504 GTCATGGCATAATCTTTTATCCCGT 59.526 40.000 0.00 0.00 29.30 5.28
151 152 1.286260 GTGCTCAGTTCGTCTCCGT 59.714 57.895 0.00 0.00 35.01 4.69
186 187 2.682856 ACACCATTGCTCGCGATAAAAT 59.317 40.909 10.36 7.26 0.00 1.82
216 217 2.479730 CCAGTCTCCGAGAACAATACCG 60.480 54.545 0.00 0.00 0.00 4.02
260 261 2.478894 GCAGTCGGAAATTCGTTTCTGA 59.521 45.455 8.02 8.02 42.29 3.27
279 280 1.816224 GGTCTTTTGCGATAAAGGGCA 59.184 47.619 9.05 0.00 36.12 5.36
280 281 1.134367 GGGTCTTTTGCGATAAAGGGC 59.866 52.381 9.05 1.51 36.12 5.19
281 282 2.442413 TGGGTCTTTTGCGATAAAGGG 58.558 47.619 9.05 0.00 36.12 3.95
292 294 3.551846 TCTCTTTCGCTTTGGGTCTTTT 58.448 40.909 0.00 0.00 0.00 2.27
336 338 0.436531 CGACTCGCACTTTTGAGCTC 59.563 55.000 6.82 6.82 35.61 4.09
429 431 7.013369 GGTTGTTCAAACTTCTTACTGAGGATT 59.987 37.037 0.00 0.00 0.00 3.01
509 511 4.506095 GGTTTGTAGGCCTAAAGACCAAGA 60.506 45.833 29.84 12.03 0.00 3.02
520 522 2.969821 TGAACATGGTTTGTAGGCCT 57.030 45.000 11.78 11.78 37.68 5.19
611 617 2.159490 GCATGTAAATAAACGGCGGTGT 60.159 45.455 13.24 0.00 0.00 4.16
614 620 4.742438 ATAGCATGTAAATAAACGGCGG 57.258 40.909 13.24 0.00 0.00 6.13
615 621 6.584942 TCTCTATAGCATGTAAATAAACGGCG 59.415 38.462 4.80 4.80 0.00 6.46
617 623 9.692749 TCTTCTCTATAGCATGTAAATAAACGG 57.307 33.333 0.00 0.00 0.00 4.44
643 649 3.322466 CCCAGTGGACCGCTCCTT 61.322 66.667 11.95 0.00 37.48 3.36
654 660 4.277423 ACCAAGTATTTCGTTTTCCCAGTG 59.723 41.667 0.00 0.00 0.00 3.66
656 662 5.009210 TCAACCAAGTATTTCGTTTTCCCAG 59.991 40.000 0.00 0.00 0.00 4.45
777 788 2.891580 GCTAGATATCTTGACACCCGGA 59.108 50.000 17.01 0.00 0.00 5.14
1249 1301 2.350537 GCTCGCGGACGTACGTAG 60.351 66.667 22.87 19.72 41.18 3.51
1284 1336 2.791256 CAAATACACCCCAGCGCG 59.209 61.111 0.00 0.00 0.00 6.86
1285 1337 2.270297 CTGCAAATACACCCCAGCGC 62.270 60.000 0.00 0.00 0.00 5.92
1290 1342 0.967380 AGCTGCTGCAAATACACCCC 60.967 55.000 18.42 0.00 42.74 4.95
1323 1375 1.160137 GAACGAGCAAGGCAGAACAT 58.840 50.000 0.00 0.00 0.00 2.71
1400 1458 2.048409 AGCACGAGCAGAGCAGTG 60.048 61.111 7.77 11.43 45.49 3.66
1401 1459 2.261052 GAGCACGAGCAGAGCAGT 59.739 61.111 7.77 0.00 45.49 4.40
1402 1460 1.806351 CAGAGCACGAGCAGAGCAG 60.806 63.158 7.77 0.00 45.49 4.24
1709 1779 6.455360 TGGCTATTATCTTTTCTGCCAAAG 57.545 37.500 0.00 0.00 44.67 2.77
1780 1850 2.016704 GCGTGGCATATCGAGTCCG 61.017 63.158 0.00 0.00 37.07 4.79
1849 1919 6.159293 CAGTTCTGAGTTATAGTTGCACAGA 58.841 40.000 0.00 0.00 0.00 3.41
1850 1920 5.928839 ACAGTTCTGAGTTATAGTTGCACAG 59.071 40.000 6.83 0.00 0.00 3.66
1884 1956 5.745312 AGATCATCAGTCACCAACAGTTA 57.255 39.130 0.00 0.00 0.00 2.24
1991 2063 1.843851 AGAGGGTCACTTTGGTCACAA 59.156 47.619 0.00 0.00 34.07 3.33
2005 2077 2.519013 GCATCAAAGTGGAAAGAGGGT 58.481 47.619 0.00 0.00 0.00 4.34
2046 2127 7.796054 TGGAAGAAGAAGAAGAAGAAGAAGAA 58.204 34.615 0.00 0.00 0.00 2.52
2047 2128 7.366847 TGGAAGAAGAAGAAGAAGAAGAAGA 57.633 36.000 0.00 0.00 0.00 2.87
2048 2129 6.147656 GCTGGAAGAAGAAGAAGAAGAAGAAG 59.852 42.308 0.00 0.00 34.07 2.85
2049 2130 5.994668 GCTGGAAGAAGAAGAAGAAGAAGAA 59.005 40.000 0.00 0.00 34.07 2.52
2050 2131 5.306678 AGCTGGAAGAAGAAGAAGAAGAAGA 59.693 40.000 0.00 0.00 34.07 2.87
2051 2132 5.550290 AGCTGGAAGAAGAAGAAGAAGAAG 58.450 41.667 0.00 0.00 34.07 2.85
2052 2133 5.559148 AGCTGGAAGAAGAAGAAGAAGAA 57.441 39.130 0.00 0.00 34.07 2.52
2053 2134 5.337169 GCTAGCTGGAAGAAGAAGAAGAAGA 60.337 44.000 7.70 0.00 34.07 2.87
2054 2135 4.869861 GCTAGCTGGAAGAAGAAGAAGAAG 59.130 45.833 7.70 0.00 34.07 2.85
2055 2136 4.530161 AGCTAGCTGGAAGAAGAAGAAGAA 59.470 41.667 18.57 0.00 34.07 2.52
2056 2137 4.081752 CAGCTAGCTGGAAGAAGAAGAAGA 60.082 45.833 33.06 0.00 40.17 2.87
2057 2138 4.183101 CAGCTAGCTGGAAGAAGAAGAAG 58.817 47.826 33.06 5.72 40.17 2.85
2093 2174 7.781056 TGGAAAAAGATGCAAAGTAAAAGAGT 58.219 30.769 0.00 0.00 0.00 3.24
2286 2367 2.037251 CGGTACATATGTCCAAGGAGGG 59.963 54.545 12.68 0.00 38.24 4.30
2387 2479 9.683069 CCTTATTGAATGGCTACAAATGAATAC 57.317 33.333 0.00 0.00 0.00 1.89
2388 2480 9.639563 TCCTTATTGAATGGCTACAAATGAATA 57.360 29.630 0.00 0.00 0.00 1.75
2389 2481 8.537728 TCCTTATTGAATGGCTACAAATGAAT 57.462 30.769 0.00 0.00 0.00 2.57
2447 2539 5.100259 AGTACACGCTACACACATACATTC 58.900 41.667 0.00 0.00 0.00 2.67
2463 2555 4.096532 ACTCATCAGTGACCATAGTACACG 59.903 45.833 0.00 0.00 39.19 4.49
2464 2556 5.584253 ACTCATCAGTGACCATAGTACAC 57.416 43.478 0.00 0.00 35.15 2.90
2483 2575 9.695884 GAAATTCGAGATAGAACAAATTCACTC 57.304 33.333 0.00 0.00 37.29 3.51
2489 2581 9.166173 TGACATGAAATTCGAGATAGAACAAAT 57.834 29.630 0.00 0.00 32.39 2.32
2508 2600 5.124936 CCTGAAGAAATTGAGCATGACATGA 59.875 40.000 19.76 0.00 0.00 3.07
2644 2736 4.452733 GGGAAGGTCGGGCACTCG 62.453 72.222 0.00 0.00 0.00 4.18
2869 2961 1.372499 GAACACGTCGTAGCTGCCA 60.372 57.895 0.00 0.00 0.00 4.92
2914 3006 1.522569 GAGCCCGGTCTTGCAGTAT 59.477 57.895 0.00 0.00 0.00 2.12
2944 3036 2.812619 CCTCCCGATGCCCTTCTCC 61.813 68.421 0.00 0.00 0.00 3.71
3307 3402 9.725019 AACTATCACACAGATCAAACATAAAGA 57.275 29.630 0.00 0.00 38.19 2.52
3312 3407 6.942005 TCCAAACTATCACACAGATCAAACAT 59.058 34.615 0.00 0.00 38.19 2.71
3327 3422 6.128634 CCGTGAAGTACAAACTCCAAACTATC 60.129 42.308 0.00 0.00 33.75 2.08
3328 3423 5.699458 CCGTGAAGTACAAACTCCAAACTAT 59.301 40.000 0.00 0.00 33.75 2.12
3329 3424 5.051816 CCGTGAAGTACAAACTCCAAACTA 58.948 41.667 0.00 0.00 33.75 2.24
3370 3465 8.679100 ACCTTCGATATCTATACTGCACTATTC 58.321 37.037 0.34 0.00 0.00 1.75
3438 3533 4.158764 ACGTCTAACAGGGAAGAAGATGAG 59.841 45.833 0.00 0.00 0.00 2.90
3521 3616 7.627939 GCAATTCACAGAGCAGAAACAGATAAT 60.628 37.037 0.00 0.00 0.00 1.28
3563 3662 6.211184 AGAGAGATCACAGAACAGAAACAGAT 59.789 38.462 0.00 0.00 0.00 2.90
3564 3663 5.538053 AGAGAGATCACAGAACAGAAACAGA 59.462 40.000 0.00 0.00 0.00 3.41
3565 3664 5.782047 AGAGAGATCACAGAACAGAAACAG 58.218 41.667 0.00 0.00 0.00 3.16
3567 3666 8.770438 AATAAGAGAGATCACAGAACAGAAAC 57.230 34.615 0.00 0.00 0.00 2.78
3568 3667 8.588472 TGAATAAGAGAGATCACAGAACAGAAA 58.412 33.333 0.00 0.00 0.00 2.52
3569 3668 8.127150 TGAATAAGAGAGATCACAGAACAGAA 57.873 34.615 0.00 0.00 0.00 3.02
3570 3669 7.709149 TGAATAAGAGAGATCACAGAACAGA 57.291 36.000 0.00 0.00 0.00 3.41
3571 3670 8.415553 AGATGAATAAGAGAGATCACAGAACAG 58.584 37.037 0.00 0.00 0.00 3.16
3572 3671 8.303780 AGATGAATAAGAGAGATCACAGAACA 57.696 34.615 0.00 0.00 0.00 3.18
3640 3759 0.727398 GTACTCGTAACGTAGCGGGT 59.273 55.000 18.67 18.67 44.57 5.28
3749 3868 8.141298 TGGACGCTCAAGGGAAATATATATAA 57.859 34.615 0.59 0.00 0.00 0.98
3750 3869 7.727578 TGGACGCTCAAGGGAAATATATATA 57.272 36.000 0.59 0.00 0.00 0.86
3751 3870 6.620877 TGGACGCTCAAGGGAAATATATAT 57.379 37.500 0.59 0.00 0.00 0.86
3787 3906 0.738975 GCAGGCCCCGACTAAAATTC 59.261 55.000 0.00 0.00 0.00 2.17
3870 4552 5.104360 CCTGGAAATACTTCAGGAATGGAGA 60.104 44.000 2.69 0.00 34.39 3.71
3905 4587 1.446099 CACCGACATGCTACGCTGT 60.446 57.895 0.00 0.00 0.00 4.40
4069 4751 0.759959 TCTCACGTGGGCAAAGGTTA 59.240 50.000 17.00 0.00 0.00 2.85
4070 4752 0.110486 ATCTCACGTGGGCAAAGGTT 59.890 50.000 17.00 0.00 0.00 3.50
4107 4789 2.579400 TCCATCCATCCATCCATCCATC 59.421 50.000 0.00 0.00 0.00 3.51
4108 4790 2.581246 CTCCATCCATCCATCCATCCAT 59.419 50.000 0.00 0.00 0.00 3.41
4109 4791 1.990327 CTCCATCCATCCATCCATCCA 59.010 52.381 0.00 0.00 0.00 3.41
4110 4792 1.284198 CCTCCATCCATCCATCCATCC 59.716 57.143 0.00 0.00 0.00 3.51
4111 4793 2.239150 CTCCTCCATCCATCCATCCATC 59.761 54.545 0.00 0.00 0.00 3.51
4112 4794 2.276391 CTCCTCCATCCATCCATCCAT 58.724 52.381 0.00 0.00 0.00 3.41
4113 4795 1.738474 CTCCTCCATCCATCCATCCA 58.262 55.000 0.00 0.00 0.00 3.41
4114 4796 0.990374 CCTCCTCCATCCATCCATCC 59.010 60.000 0.00 0.00 0.00 3.51
4186 4868 0.033109 AAGTTAAGGGCAGGGCATCC 60.033 55.000 0.00 0.00 0.00 3.51
4207 4890 4.536765 AGGAACACACACAGAGGAAAATT 58.463 39.130 0.00 0.00 0.00 1.82
4241 4924 3.896888 AGAGAGAGTCTATGAGGCCAATG 59.103 47.826 5.01 0.00 31.71 2.82


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

AutoCloner maintained by Alex Coulton.