Multiple sequence alignment - TraesCS7B01G050500

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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 TraesCS7B01G050500 chr7B 100.000 4044 0 0 1 4044 52351104 52347061 0.000000e+00 7468
1 TraesCS7B01G050500 chr7D 92.196 3588 137 59 17 3525 97618176 97614653 0.000000e+00 4942
2 TraesCS7B01G050500 chr7D 86.327 490 36 13 3571 4044 97614654 97614180 4.660000e-139 505
3 TraesCS7B01G050500 chr7A 93.422 2721 88 35 853 3525 100182322 100179645 0.000000e+00 3949
4 TraesCS7B01G050500 chr7A 87.642 704 51 18 1 683 100183336 100182648 0.000000e+00 785
5 TraesCS7B01G050500 chr7A 90.447 492 27 9 3571 4044 100179646 100179157 7.380000e-177 630


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 TraesCS7B01G050500 chr7B 52347061 52351104 4043 True 7468.0 7468 100.000000 1 4044 1 chr7B.!!$R1 4043
1 TraesCS7B01G050500 chr7D 97614180 97618176 3996 True 2723.5 4942 89.261500 17 4044 2 chr7D.!!$R1 4027
2 TraesCS7B01G050500 chr7A 100179157 100183336 4179 True 1788.0 3949 90.503667 1 4044 3 chr7A.!!$R1 4043

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
139 145 0.109272 TTACCTGTTGCGCTCTCGAG 60.109 55.0 9.73 5.93 38.10 4.04 F
781 822 0.174617 GCTACCTTCTTGCTCTCGCT 59.825 55.0 0.00 0.00 36.97 4.93 F
1340 1540 0.178964 CACCCCAGCAAAGAAAGGGA 60.179 55.0 0.00 0.00 44.30 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 1359 0.396435 TGGATCCAACTCGTGCAAGT 59.604 50.0 13.46 0.0 0.00 3.16 R
2574 2834 0.321919 GATCACAAGCCTCTGCACCA 60.322 55.0 0.00 0.0 41.13 4.17 R
3258 3530 0.679640 CGCTCTCACTCCTGGTCTCT 60.680 60.0 0.00 0.0 0.00 3.10 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
139 145 0.109272 TTACCTGTTGCGCTCTCGAG 60.109 55.000 9.73 5.93 38.10 4.04
215 234 4.436998 CGCGTTCTCTCCCGCCTT 62.437 66.667 0.00 0.00 46.83 4.35
244 263 3.893763 CGGTCGATGCGAGGCTCT 61.894 66.667 13.50 0.00 36.23 4.09
287 309 2.748647 CGGCCGTTACAAAGGGGG 60.749 66.667 19.50 0.00 36.93 5.40
302 324 2.660802 GGGAGGAAAAGGCGACGA 59.339 61.111 0.00 0.00 0.00 4.20
324 346 0.445436 ACGACGACAAGTAGCGTAGG 59.555 55.000 0.00 0.00 41.34 3.18
327 349 1.585521 CGACAAGTAGCGTAGGCGG 60.586 63.158 1.05 0.00 46.35 6.13
329 351 2.585247 CAAGTAGCGTAGGCGGCC 60.585 66.667 12.11 12.11 46.35 6.13
331 353 2.432300 AAGTAGCGTAGGCGGCCAT 61.432 57.895 23.09 8.98 46.35 4.40
433 455 3.379372 TCTTCCCCTCGAATGTTACTACG 59.621 47.826 0.00 0.00 0.00 3.51
434 456 2.726821 TCCCCTCGAATGTTACTACGT 58.273 47.619 0.00 0.00 0.00 3.57
435 457 3.884895 TCCCCTCGAATGTTACTACGTA 58.115 45.455 0.00 0.00 0.00 3.57
437 459 3.243201 CCCCTCGAATGTTACTACGTACC 60.243 52.174 0.00 0.00 0.00 3.34
438 460 3.378112 CCCTCGAATGTTACTACGTACCA 59.622 47.826 0.00 0.00 0.00 3.25
439 461 4.142403 CCCTCGAATGTTACTACGTACCAA 60.142 45.833 0.00 0.00 0.00 3.67
537 568 2.357760 GCTTGTCACGGGGCGTTA 60.358 61.111 0.00 0.00 38.32 3.18
593 624 2.055100 GTGCGAGAAACTGAGAGTGTC 58.945 52.381 0.00 0.00 32.53 3.67
594 625 1.957177 TGCGAGAAACTGAGAGTGTCT 59.043 47.619 0.00 0.00 45.20 3.41
759 800 2.162754 GCAACCGTCCGTGTATCCG 61.163 63.158 0.00 0.00 0.00 4.18
772 813 0.388294 GTATCCGCCGCTACCTTCTT 59.612 55.000 0.00 0.00 0.00 2.52
781 822 0.174617 GCTACCTTCTTGCTCTCGCT 59.825 55.000 0.00 0.00 36.97 4.93
783 824 0.452184 TACCTTCTTGCTCTCGCTCG 59.548 55.000 0.00 0.00 36.97 5.03
787 828 1.590610 TTCTTGCTCTCGCTCGCTCT 61.591 55.000 0.00 0.00 36.97 4.09
788 829 1.586042 CTTGCTCTCGCTCGCTCTC 60.586 63.158 0.00 0.00 36.97 3.20
789 830 1.992233 CTTGCTCTCGCTCGCTCTCT 61.992 60.000 0.00 0.00 36.97 3.10
790 831 1.987704 TTGCTCTCGCTCGCTCTCTC 61.988 60.000 0.00 0.00 36.97 3.20
791 832 2.180204 GCTCTCGCTCGCTCTCTCT 61.180 63.158 0.00 0.00 0.00 3.10
792 833 1.934463 CTCTCGCTCGCTCTCTCTC 59.066 63.158 0.00 0.00 0.00 3.20
793 834 1.821241 CTCTCGCTCGCTCTCTCTCG 61.821 65.000 0.00 0.00 0.00 4.04
794 835 2.125472 TCGCTCGCTCTCTCTCGT 60.125 61.111 0.00 0.00 0.00 4.18
829 1021 0.677842 CCCGCCCGCCCTATATATAC 59.322 60.000 0.00 0.00 0.00 1.47
830 1022 0.677842 CCGCCCGCCCTATATATACC 59.322 60.000 0.00 0.00 0.00 2.73
834 1026 1.335145 CCGCCCTATATATACCGGGG 58.665 60.000 15.56 12.91 37.17 5.73
835 1027 1.412074 CCGCCCTATATATACCGGGGT 60.412 57.143 15.56 0.00 39.28 4.95
836 1028 1.959282 CGCCCTATATATACCGGGGTC 59.041 57.143 15.56 8.55 39.28 4.46
837 1029 2.423947 CGCCCTATATATACCGGGGTCT 60.424 54.545 15.56 0.00 39.28 3.85
838 1030 2.963782 GCCCTATATATACCGGGGTCTG 59.036 54.545 15.56 0.00 39.28 3.51
839 1031 2.963782 CCCTATATATACCGGGGTCTGC 59.036 54.545 6.32 0.00 32.91 4.26
840 1032 2.963782 CCTATATATACCGGGGTCTGCC 59.036 54.545 6.32 0.00 0.00 4.85
842 1034 1.252904 TATATACCGGGGTCTGCCGC 61.253 60.000 6.32 0.00 43.52 6.53
843 1035 3.899622 TATATACCGGGGTCTGCCGCA 62.900 57.143 6.32 0.00 46.90 5.69
850 1042 4.767255 GGTCTGCCGCACTCCAGG 62.767 72.222 0.00 0.00 0.00 4.45
851 1043 3.695606 GTCTGCCGCACTCCAGGA 61.696 66.667 0.00 0.00 0.00 3.86
957 1153 4.651962 AGAGGAGAAGGGTAGCAAATCTAC 59.348 45.833 0.00 0.00 45.44 2.59
960 1156 6.386284 AGGAGAAGGGTAGCAAATCTACTAT 58.614 40.000 4.35 0.00 45.46 2.12
965 1161 7.345914 AGAAGGGTAGCAAATCTACTATCAGTT 59.654 37.037 0.00 0.00 45.46 3.16
1062 1258 5.829924 CACCTTCGGTATCCTAGGTACTTAA 59.170 44.000 9.08 8.22 35.16 1.85
1063 1259 6.492772 CACCTTCGGTATCCTAGGTACTTAAT 59.507 42.308 9.08 0.00 35.16 1.40
1064 1260 7.015001 CACCTTCGGTATCCTAGGTACTTAATT 59.985 40.741 9.08 0.00 35.16 1.40
1065 1261 8.227507 ACCTTCGGTATCCTAGGTACTTAATTA 58.772 37.037 9.08 0.00 35.46 1.40
1068 1264 8.396272 TCGGTATCCTAGGTACTTAATTACAC 57.604 38.462 9.08 0.00 41.75 2.90
1135 1331 3.068732 GCTTCTGTTTCTTCTGCCCTTTT 59.931 43.478 0.00 0.00 0.00 2.27
1155 1351 6.040166 CCTTTTGGAAAGGATCATCGATGATT 59.960 38.462 34.92 23.29 44.28 2.57
1163 1359 3.368427 GGATCATCGATGATTCCGGCTTA 60.368 47.826 34.92 10.11 46.84 3.09
1211 1411 0.954452 CCTTGCTCAACACACCCTTC 59.046 55.000 0.00 0.00 0.00 3.46
1212 1412 1.477558 CCTTGCTCAACACACCCTTCT 60.478 52.381 0.00 0.00 0.00 2.85
1230 1430 2.138656 CTGCCTGCTTGTGTGCCTTC 62.139 60.000 0.00 0.00 0.00 3.46
1256 1456 5.587844 TCAATCTCTTTCATTGAGCTAAGCC 59.412 40.000 0.00 0.00 35.71 4.35
1258 1458 4.511527 TCTCTTTCATTGAGCTAAGCCAG 58.488 43.478 0.00 0.00 0.00 4.85
1340 1540 0.178964 CACCCCAGCAAAGAAAGGGA 60.179 55.000 0.00 0.00 44.30 4.20
1341 1541 0.560688 ACCCCAGCAAAGAAAGGGAA 59.439 50.000 0.00 0.00 44.30 3.97
1563 1767 2.711009 ACTGATGGTCTTCCTTTCACCA 59.289 45.455 0.00 0.00 44.36 4.17
1573 1777 3.569194 TCCTTTCACCACTGTAAGCAA 57.431 42.857 0.00 0.00 37.60 3.91
1616 1820 7.735917 TCTCCTGTTCAGTCTTCAGAAAAATA 58.264 34.615 0.00 0.00 0.00 1.40
1617 1821 8.378565 TCTCCTGTTCAGTCTTCAGAAAAATAT 58.621 33.333 0.00 0.00 0.00 1.28
1618 1822 9.658799 CTCCTGTTCAGTCTTCAGAAAAATATA 57.341 33.333 0.00 0.00 0.00 0.86
1619 1823 9.436957 TCCTGTTCAGTCTTCAGAAAAATATAC 57.563 33.333 0.00 0.00 0.00 1.47
1620 1824 9.442047 CCTGTTCAGTCTTCAGAAAAATATACT 57.558 33.333 0.00 0.00 0.00 2.12
1622 1826 9.778741 TGTTCAGTCTTCAGAAAAATATACTGT 57.221 29.630 0.00 0.00 35.68 3.55
1627 1831 9.668497 AGTCTTCAGAAAAATATACTGTAACCC 57.332 33.333 0.00 0.00 33.93 4.11
1628 1832 9.668497 GTCTTCAGAAAAATATACTGTAACCCT 57.332 33.333 0.00 0.00 33.93 4.34
1629 1833 9.667107 TCTTCAGAAAAATATACTGTAACCCTG 57.333 33.333 0.00 0.00 33.93 4.45
1630 1834 7.859325 TCAGAAAAATATACTGTAACCCTGC 57.141 36.000 0.00 0.00 33.93 4.85
1631 1835 7.398829 TCAGAAAAATATACTGTAACCCTGCA 58.601 34.615 0.00 0.00 33.93 4.41
1632 1836 8.052748 TCAGAAAAATATACTGTAACCCTGCAT 58.947 33.333 0.00 0.00 33.93 3.96
1633 1837 9.337396 CAGAAAAATATACTGTAACCCTGCATA 57.663 33.333 0.00 0.00 0.00 3.14
1634 1838 9.561069 AGAAAAATATACTGTAACCCTGCATAG 57.439 33.333 0.00 0.00 0.00 2.23
1635 1839 9.555727 GAAAAATATACTGTAACCCTGCATAGA 57.444 33.333 0.00 0.00 0.00 1.98
1636 1840 9.914834 AAAAATATACTGTAACCCTGCATAGAA 57.085 29.630 0.00 0.00 0.00 2.10
1637 1841 9.914834 AAAATATACTGTAACCCTGCATAGAAA 57.085 29.630 0.00 0.00 0.00 2.52
1638 1842 9.914834 AAATATACTGTAACCCTGCATAGAAAA 57.085 29.630 0.00 0.00 0.00 2.29
1639 1843 9.914834 AATATACTGTAACCCTGCATAGAAAAA 57.085 29.630 0.00 0.00 0.00 1.94
1681 1887 5.742063 ACATCTATGTAGATCCATGCATGG 58.258 41.667 35.76 35.76 43.57 3.66
1880 2097 6.593770 TGAGACAACATAACGCTGAATATTGT 59.406 34.615 0.00 0.00 0.00 2.71
1948 2166 2.321719 TGTCACTGTTAGGTAGGTGCA 58.678 47.619 0.00 0.00 0.00 4.57
2108 2366 3.023119 ACTCTGACGAATCTCTGATGCT 58.977 45.455 0.00 0.00 0.00 3.79
2109 2367 3.066621 ACTCTGACGAATCTCTGATGCTC 59.933 47.826 0.00 0.00 0.00 4.26
2513 2772 7.185318 TCGTAAGGACCCATTTAATCTTACA 57.815 36.000 11.41 1.20 37.48 2.41
2547 2807 3.611025 AAGGTTTGTGGATTGAAGGGA 57.389 42.857 0.00 0.00 0.00 4.20
2554 2814 7.898636 AGGTTTGTGGATTGAAGGGATTAATTA 59.101 33.333 0.00 0.00 0.00 1.40
2644 2904 0.035458 CGCTGTCCTTCTTCCTGGTT 59.965 55.000 0.00 0.00 0.00 3.67
2668 2928 2.434185 GCCGTCATCTGGTTCGCA 60.434 61.111 0.00 0.00 0.00 5.10
2815 3075 1.260538 ACGAGGAGATGAAGCTGCCA 61.261 55.000 0.00 0.00 0.00 4.92
2917 3180 2.671070 CCCATTGACGTGCTCCCT 59.329 61.111 0.00 0.00 0.00 4.20
2992 3261 1.001764 CCAGAACATGCTCAGGCCA 60.002 57.895 5.01 0.00 37.74 5.36
3103 3373 1.440476 GGCGATAAGTGGGTACGCT 59.560 57.895 11.59 0.00 46.71 5.07
3178 3448 2.263021 GCACTGTGTGGCTGCATCA 61.263 57.895 9.86 0.00 33.64 3.07
3258 3530 3.208594 GACTGCATGCCATGTATGAAGA 58.791 45.455 16.68 0.00 33.92 2.87
3448 3729 9.806448 AATAAATTTGGGGCCCATTTATTATTC 57.194 29.630 34.76 13.01 37.13 1.75
3449 3730 6.838401 AATTTGGGGCCCATTTATTATTCA 57.162 33.333 29.34 3.63 31.53 2.57
3452 3733 5.149584 TGGGGCCCATTTATTATTCAGAA 57.850 39.130 24.76 0.00 0.00 3.02
3460 3741 7.432252 GCCCATTTATTATTCAGAACAGAAACG 59.568 37.037 0.00 0.00 0.00 3.60
3466 3752 6.946229 TTATTCAGAACAGAAACGCTACTC 57.054 37.500 0.00 0.00 0.00 2.59
3472 3758 4.985409 AGAACAGAAACGCTACTCTGAAAG 59.015 41.667 11.42 0.00 41.38 2.62
3503 3791 5.065474 TGAGTTTCGTGTAAAAACCTTGGAG 59.935 40.000 0.00 0.00 37.33 3.86
3525 3813 7.398618 TGGAGAGAAAGAGAGATGTCATAGTTT 59.601 37.037 0.00 0.00 0.00 2.66
3526 3814 8.257306 GGAGAGAAAGAGAGATGTCATAGTTTT 58.743 37.037 0.00 0.00 0.00 2.43
3527 3815 9.651913 GAGAGAAAGAGAGATGTCATAGTTTTT 57.348 33.333 0.00 0.00 0.00 1.94
3528 3816 9.651913 AGAGAAAGAGAGATGTCATAGTTTTTC 57.348 33.333 0.00 0.00 0.00 2.29
3529 3817 9.651913 GAGAAAGAGAGATGTCATAGTTTTTCT 57.348 33.333 9.66 9.66 34.82 2.52
3553 3841 9.840427 TCTTTTCTTTTTGTGTGTTAAAGAGAG 57.160 29.630 0.00 0.00 38.64 3.20
3554 3842 9.840427 CTTTTCTTTTTGTGTGTTAAAGAGAGA 57.160 29.630 0.00 0.00 38.64 3.10
3556 3844 9.787532 TTTCTTTTTGTGTGTTAAAGAGAGATG 57.212 29.630 0.00 0.00 38.64 2.90
3557 3845 8.506168 TCTTTTTGTGTGTTAAAGAGAGATGT 57.494 30.769 0.00 0.00 34.07 3.06
3558 3846 8.612619 TCTTTTTGTGTGTTAAAGAGAGATGTC 58.387 33.333 0.00 0.00 34.07 3.06
3559 3847 7.857734 TTTTGTGTGTTAAAGAGAGATGTCA 57.142 32.000 0.00 0.00 0.00 3.58
3560 3848 8.450578 TTTTGTGTGTTAAAGAGAGATGTCAT 57.549 30.769 0.00 0.00 0.00 3.06
3561 3849 7.425577 TTGTGTGTTAAAGAGAGATGTCATG 57.574 36.000 0.00 0.00 0.00 3.07
3562 3850 5.934043 TGTGTGTTAAAGAGAGATGTCATGG 59.066 40.000 0.00 0.00 0.00 3.66
3563 3851 5.934625 GTGTGTTAAAGAGAGATGTCATGGT 59.065 40.000 0.00 0.00 0.00 3.55
3564 3852 6.428159 GTGTGTTAAAGAGAGATGTCATGGTT 59.572 38.462 0.00 0.00 0.00 3.67
3565 3853 7.602644 GTGTGTTAAAGAGAGATGTCATGGTTA 59.397 37.037 0.00 0.00 0.00 2.85
3566 3854 7.819415 TGTGTTAAAGAGAGATGTCATGGTTAG 59.181 37.037 0.00 0.00 0.00 2.34
3567 3855 7.278868 GTGTTAAAGAGAGATGTCATGGTTAGG 59.721 40.741 0.00 0.00 0.00 2.69
3568 3856 7.180229 TGTTAAAGAGAGATGTCATGGTTAGGA 59.820 37.037 0.00 0.00 0.00 2.94
3569 3857 5.606348 AAGAGAGATGTCATGGTTAGGAC 57.394 43.478 0.00 0.00 38.08 3.85
3570 3858 4.877773 AGAGAGATGTCATGGTTAGGACT 58.122 43.478 0.00 0.00 38.39 3.85
3571 3859 5.276440 AGAGAGATGTCATGGTTAGGACTT 58.724 41.667 0.00 0.00 38.39 3.01
3585 3873 8.065385 TGGTTAGGACTTAGGAGGAAGATATA 57.935 38.462 0.00 0.00 0.00 0.86
3601 3889 9.331282 AGGAAGATATAGTAGTGAAAAATGTGC 57.669 33.333 0.00 0.00 0.00 4.57
3623 3911 0.872021 GTCATGGCCTCGATCGTCAC 60.872 60.000 15.94 5.27 0.00 3.67
3713 4015 5.605534 CGTGAGGATTCAACTATCTTCCAT 58.394 41.667 0.00 0.00 34.49 3.41
3808 4110 2.357009 ACCTATGCGGAGTTACAGTACG 59.643 50.000 0.00 0.00 36.31 3.67
3815 4117 2.975851 CGGAGTTACAGTACGTGACAAC 59.024 50.000 0.00 9.30 36.59 3.32
3846 4149 8.579850 TTCATCACATAATTCACCTTTTAGCT 57.420 30.769 0.00 0.00 0.00 3.32
3863 4166 8.890718 CCTTTTAGCTTTATAGGTTTAGTCACC 58.109 37.037 0.00 0.00 37.04 4.02
3864 4167 9.444600 CTTTTAGCTTTATAGGTTTAGTCACCA 57.555 33.333 0.00 0.00 39.62 4.17
3891 4194 4.616181 CCTAAAAGGTGTTTCTATGCCG 57.384 45.455 0.00 0.00 0.00 5.69
4017 4360 4.783055 TCTAGGTAGGTCATCAGTGTCTC 58.217 47.826 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 145 2.943653 CAAAGAACGTGTCCGGGC 59.056 61.111 0.00 0.00 38.78 6.13
207 213 1.971357 GATCAATCTCCTAAGGCGGGA 59.029 52.381 0.00 0.00 0.00 5.14
214 233 3.305403 GCATCGACCGATCAATCTCCTAA 60.305 47.826 1.46 0.00 31.62 2.69
215 234 2.229062 GCATCGACCGATCAATCTCCTA 59.771 50.000 1.46 0.00 31.62 2.94
287 309 1.080974 TCGTCGTCGCCTTTTCCTC 60.081 57.895 0.00 0.00 36.96 3.71
302 324 1.154525 CGCTACTTGTCGTCGTCGT 60.155 57.895 1.33 0.00 38.33 4.34
324 346 2.954868 CTCACGTACGATGGCCGC 60.955 66.667 24.41 0.00 43.32 6.53
327 349 3.617538 GCGCTCACGTACGATGGC 61.618 66.667 24.41 19.30 42.83 4.40
329 351 3.312504 CCGCGCTCACGTACGATG 61.313 66.667 24.41 16.05 42.83 3.84
433 455 1.375523 CCTGGCCGTCTGTTGGTAC 60.376 63.158 0.00 0.00 0.00 3.34
434 456 1.122632 TTCCTGGCCGTCTGTTGGTA 61.123 55.000 0.00 0.00 0.00 3.25
435 457 1.990160 TTTCCTGGCCGTCTGTTGGT 61.990 55.000 0.00 0.00 0.00 3.67
437 459 1.841663 CGTTTCCTGGCCGTCTGTTG 61.842 60.000 0.00 0.00 0.00 3.33
438 460 1.597027 CGTTTCCTGGCCGTCTGTT 60.597 57.895 0.00 0.00 0.00 3.16
439 461 2.030562 CGTTTCCTGGCCGTCTGT 59.969 61.111 0.00 0.00 0.00 3.41
488 519 1.532078 TGGGACGCACTACTGACCA 60.532 57.895 0.00 0.00 0.00 4.02
537 568 3.624777 CTGGCCTCAGTCAATTAATGGT 58.375 45.455 3.32 0.00 36.30 3.55
593 624 1.065928 GTCGAGCCGGTCCATACAG 59.934 63.158 1.90 0.00 0.00 2.74
594 625 2.420568 GGTCGAGCCGGTCCATACA 61.421 63.158 1.90 0.00 0.00 2.29
683 718 0.537188 CACTAATGAGCCTGTCCCGT 59.463 55.000 0.00 0.00 0.00 5.28
688 723 2.566833 TTGCACACTAATGAGCCTGT 57.433 45.000 0.00 0.00 41.32 4.00
759 800 0.808060 GAGAGCAAGAAGGTAGCGGC 60.808 60.000 0.00 0.00 0.00 6.53
781 822 1.153329 GGGAGACGAGAGAGAGCGA 60.153 63.158 0.00 0.00 0.00 4.93
783 824 1.826487 GGGGGAGACGAGAGAGAGC 60.826 68.421 0.00 0.00 0.00 4.09
812 1004 0.313043 CGGTATATATAGGGCGGGCG 59.687 60.000 0.00 0.00 0.00 6.13
813 1005 0.677842 CCGGTATATATAGGGCGGGC 59.322 60.000 0.00 0.00 0.00 6.13
814 1006 1.335145 CCCGGTATATATAGGGCGGG 58.665 60.000 11.18 0.00 37.07 6.13
817 1009 2.963782 CAGACCCCGGTATATATAGGGC 59.036 54.545 16.11 4.86 41.86 5.19
818 1010 2.963782 GCAGACCCCGGTATATATAGGG 59.036 54.545 15.08 15.08 43.88 3.53
833 1025 4.767255 CCTGGAGTGCGGCAGACC 62.767 72.222 1.18 10.66 0.00 3.85
834 1026 2.914777 GATCCTGGAGTGCGGCAGAC 62.915 65.000 1.18 0.00 0.00 3.51
835 1027 2.685017 ATCCTGGAGTGCGGCAGA 60.685 61.111 1.18 0.00 0.00 4.26
836 1028 2.202987 GATCCTGGAGTGCGGCAG 60.203 66.667 1.18 0.00 0.00 4.85
837 1029 2.685017 AGATCCTGGAGTGCGGCA 60.685 61.111 0.00 0.00 0.00 5.69
838 1030 2.107953 GAGATCCTGGAGTGCGGC 59.892 66.667 1.52 0.00 0.00 6.53
839 1031 1.617018 TTGGAGATCCTGGAGTGCGG 61.617 60.000 1.52 0.00 36.82 5.69
840 1032 0.179089 CTTGGAGATCCTGGAGTGCG 60.179 60.000 1.52 0.00 36.82 5.34
842 1034 1.138661 GCTCTTGGAGATCCTGGAGTG 59.861 57.143 16.81 8.34 37.51 3.51
843 1035 1.494960 GCTCTTGGAGATCCTGGAGT 58.505 55.000 16.81 0.00 37.51 3.85
845 1037 0.692419 GGGCTCTTGGAGATCCTGGA 60.692 60.000 0.00 0.00 31.39 3.86
846 1038 0.984961 TGGGCTCTTGGAGATCCTGG 60.985 60.000 0.00 0.00 31.39 4.45
847 1039 0.914644 TTGGGCTCTTGGAGATCCTG 59.085 55.000 0.00 0.00 31.39 3.86
848 1040 0.915364 GTTGGGCTCTTGGAGATCCT 59.085 55.000 0.00 0.00 31.39 3.24
850 1042 1.092345 GCGTTGGGCTCTTGGAGATC 61.092 60.000 0.00 0.00 39.11 2.75
851 1043 1.078143 GCGTTGGGCTCTTGGAGAT 60.078 57.895 0.00 0.00 39.11 2.75
957 1153 4.509970 TCGAACACACAAACCAACTGATAG 59.490 41.667 0.00 0.00 0.00 2.08
960 1156 2.675844 CTCGAACACACAAACCAACTGA 59.324 45.455 0.00 0.00 0.00 3.41
965 1161 2.093394 TCTTCCTCGAACACACAAACCA 60.093 45.455 0.00 0.00 0.00 3.67
1062 1258 3.900971 TGGATGGATGCATGTGTGTAAT 58.099 40.909 2.46 0.00 0.00 1.89
1063 1259 3.362870 TGGATGGATGCATGTGTGTAA 57.637 42.857 2.46 0.00 0.00 2.41
1064 1260 3.581265 ATGGATGGATGCATGTGTGTA 57.419 42.857 2.46 0.00 37.46 2.90
1065 1261 2.447408 ATGGATGGATGCATGTGTGT 57.553 45.000 2.46 0.00 37.46 3.72
1135 1331 4.645535 GGAATCATCGATGATCCTTTCCA 58.354 43.478 33.68 14.30 46.22 3.53
1155 1351 1.080093 CTCGTGCAAGTAAGCCGGA 60.080 57.895 5.05 0.00 0.00 5.14
1163 1359 0.396435 TGGATCCAACTCGTGCAAGT 59.604 50.000 13.46 0.00 0.00 3.16
1211 1411 2.138656 GAAGGCACACAAGCAGGCAG 62.139 60.000 0.00 0.00 35.83 4.85
1212 1412 2.123769 AAGGCACACAAGCAGGCA 60.124 55.556 0.00 0.00 35.83 4.75
1230 1430 7.188157 GCTTAGCTCAATGAAAGAGATTGAAG 58.812 38.462 0.00 0.00 38.92 3.02
1258 1458 4.095610 CCATTTATTCGGAACAGAAACGC 58.904 43.478 0.00 0.00 33.43 4.84
1476 1680 3.805422 GTCAGTTATGTGTCAACCAACGA 59.195 43.478 0.00 0.00 0.00 3.85
1563 1767 5.527582 CAGTTAAGTTGAGGTTGCTTACAGT 59.472 40.000 0.00 0.00 0.00 3.55
1573 1777 3.244249 GGAGAGTGCAGTTAAGTTGAGGT 60.244 47.826 0.00 0.00 0.00 3.85
1618 1822 9.338622 GTATATTTTTCTATGCAGGGTTACAGT 57.661 33.333 0.00 0.00 0.00 3.55
1619 1823 9.561069 AGTATATTTTTCTATGCAGGGTTACAG 57.439 33.333 0.00 0.00 0.00 2.74
1620 1824 9.337396 CAGTATATTTTTCTATGCAGGGTTACA 57.663 33.333 0.00 0.00 0.00 2.41
1621 1825 9.338622 ACAGTATATTTTTCTATGCAGGGTTAC 57.661 33.333 0.00 0.00 0.00 2.50
1623 1827 9.914834 TTACAGTATATTTTTCTATGCAGGGTT 57.085 29.630 0.00 0.00 0.00 4.11
1624 1828 9.338622 GTTACAGTATATTTTTCTATGCAGGGT 57.661 33.333 0.00 0.00 0.00 4.34
1625 1829 8.784043 GGTTACAGTATATTTTTCTATGCAGGG 58.216 37.037 0.00 0.00 0.00 4.45
1626 1830 8.784043 GGGTTACAGTATATTTTTCTATGCAGG 58.216 37.037 0.00 0.00 0.00 4.85
1627 1831 9.561069 AGGGTTACAGTATATTTTTCTATGCAG 57.439 33.333 0.00 0.00 0.00 4.41
1628 1832 9.337396 CAGGGTTACAGTATATTTTTCTATGCA 57.663 33.333 0.00 0.00 0.00 3.96
1629 1833 8.290325 GCAGGGTTACAGTATATTTTTCTATGC 58.710 37.037 0.00 0.00 0.00 3.14
1630 1834 9.337396 TGCAGGGTTACAGTATATTTTTCTATG 57.663 33.333 0.00 0.00 0.00 2.23
1633 1837 9.338622 GTATGCAGGGTTACAGTATATTTTTCT 57.661 33.333 0.00 0.00 0.00 2.52
1634 1838 9.116067 TGTATGCAGGGTTACAGTATATTTTTC 57.884 33.333 0.00 0.00 0.00 2.29
1635 1839 9.640952 ATGTATGCAGGGTTACAGTATATTTTT 57.359 29.630 4.38 0.00 32.24 1.94
1636 1840 9.284968 GATGTATGCAGGGTTACAGTATATTTT 57.715 33.333 4.38 0.00 32.24 1.82
1637 1841 8.660435 AGATGTATGCAGGGTTACAGTATATTT 58.340 33.333 4.38 0.00 32.24 1.40
1638 1842 8.207350 AGATGTATGCAGGGTTACAGTATATT 57.793 34.615 4.38 0.00 32.24 1.28
1639 1843 7.798710 AGATGTATGCAGGGTTACAGTATAT 57.201 36.000 4.38 0.00 32.24 0.86
1640 1844 8.749354 CATAGATGTATGCAGGGTTACAGTATA 58.251 37.037 4.38 0.00 32.24 1.47
1681 1887 2.991250 AGACATACACATGACAAGGGC 58.009 47.619 0.00 0.00 35.96 5.19
1948 2166 1.686587 TGTAGTACACTGCACTGCACT 59.313 47.619 0.00 4.85 34.29 4.40
1974 2192 4.572909 AGCTAAACTAACTAACAACCCGG 58.427 43.478 0.00 0.00 0.00 5.73
1975 2193 4.628766 GGAGCTAAACTAACTAACAACCCG 59.371 45.833 0.00 0.00 0.00 5.28
1976 2194 5.802465 AGGAGCTAAACTAACTAACAACCC 58.198 41.667 0.00 0.00 0.00 4.11
2513 2772 6.213600 TCCACAAACCTTAAAGAGATCTAGCT 59.786 38.462 0.00 0.00 0.00 3.32
2554 2814 5.048224 CACCAGCAAGAAGACAATCAAGATT 60.048 40.000 0.00 0.00 0.00 2.40
2574 2834 0.321919 GATCACAAGCCTCTGCACCA 60.322 55.000 0.00 0.00 41.13 4.17
2575 2835 1.028868 GGATCACAAGCCTCTGCACC 61.029 60.000 0.00 0.00 41.13 5.01
2644 2904 2.491621 CAGATGACGGCGCTGAGA 59.508 61.111 25.98 8.98 0.00 3.27
2668 2928 1.878522 CTTCTTGAGCGCGCCGTAT 60.879 57.895 30.33 9.44 0.00 3.06
2815 3075 1.668294 CACCTCCTTGACGTGCTCT 59.332 57.895 0.00 0.00 0.00 4.09
3155 3425 1.526686 CAGCCACACAGTGCTCCAA 60.527 57.895 0.00 0.00 31.34 3.53
3258 3530 0.679640 CGCTCTCACTCCTGGTCTCT 60.680 60.000 0.00 0.00 0.00 3.10
3448 3729 3.902150 TCAGAGTAGCGTTTCTGTTCTG 58.098 45.455 12.12 0.00 41.21 3.02
3449 3730 4.585955 TTCAGAGTAGCGTTTCTGTTCT 57.414 40.909 12.12 0.00 41.21 3.01
3452 3733 4.551388 CTCTTTCAGAGTAGCGTTTCTGT 58.449 43.478 12.12 0.00 41.21 3.41
3460 3741 4.142182 ACTCATGAGCTCTTTCAGAGTAGC 60.142 45.833 22.83 0.00 44.12 3.58
3466 3752 3.993081 ACGAAACTCATGAGCTCTTTCAG 59.007 43.478 25.18 21.02 0.00 3.02
3472 3758 5.591643 TTTTACACGAAACTCATGAGCTC 57.408 39.130 22.83 17.28 0.00 4.09
3475 3761 6.300354 AGGTTTTTACACGAAACTCATGAG 57.700 37.500 21.37 21.37 37.22 2.90
3484 3770 5.026038 TCTCTCCAAGGTTTTTACACGAA 57.974 39.130 0.00 0.00 0.00 3.85
3486 3772 5.526111 TCTTTCTCTCCAAGGTTTTTACACG 59.474 40.000 0.00 0.00 0.00 4.49
3503 3791 9.651913 AGAAAAACTATGACATCTCTCTTTCTC 57.348 33.333 0.00 0.00 0.00 2.87
3527 3815 9.840427 CTCTCTTTAACACACAAAAAGAAAAGA 57.160 29.630 0.00 0.00 38.42 2.52
3528 3816 9.840427 TCTCTCTTTAACACACAAAAAGAAAAG 57.160 29.630 0.00 0.00 38.42 2.27
3530 3818 9.787532 CATCTCTCTTTAACACACAAAAAGAAA 57.212 29.630 0.00 0.00 38.42 2.52
3531 3819 8.956426 ACATCTCTCTTTAACACACAAAAAGAA 58.044 29.630 0.00 0.00 38.42 2.52
3532 3820 8.506168 ACATCTCTCTTTAACACACAAAAAGA 57.494 30.769 0.00 0.00 37.00 2.52
3533 3821 8.397906 TGACATCTCTCTTTAACACACAAAAAG 58.602 33.333 0.00 0.00 0.00 2.27
3534 3822 8.275015 TGACATCTCTCTTTAACACACAAAAA 57.725 30.769 0.00 0.00 0.00 1.94
3535 3823 7.857734 TGACATCTCTCTTTAACACACAAAA 57.142 32.000 0.00 0.00 0.00 2.44
3536 3824 7.041167 CCATGACATCTCTCTTTAACACACAAA 60.041 37.037 0.00 0.00 0.00 2.83
3537 3825 6.427853 CCATGACATCTCTCTTTAACACACAA 59.572 38.462 0.00 0.00 0.00 3.33
3538 3826 5.934043 CCATGACATCTCTCTTTAACACACA 59.066 40.000 0.00 0.00 0.00 3.72
3539 3827 5.934625 ACCATGACATCTCTCTTTAACACAC 59.065 40.000 0.00 0.00 0.00 3.82
3540 3828 6.114187 ACCATGACATCTCTCTTTAACACA 57.886 37.500 0.00 0.00 0.00 3.72
3541 3829 7.278868 CCTAACCATGACATCTCTCTTTAACAC 59.721 40.741 0.00 0.00 0.00 3.32
3542 3830 7.180229 TCCTAACCATGACATCTCTCTTTAACA 59.820 37.037 0.00 0.00 0.00 2.41
3543 3831 7.492994 GTCCTAACCATGACATCTCTCTTTAAC 59.507 40.741 0.00 0.00 0.00 2.01
3544 3832 7.400339 AGTCCTAACCATGACATCTCTCTTTAA 59.600 37.037 0.00 0.00 33.89 1.52
3545 3833 6.897966 AGTCCTAACCATGACATCTCTCTTTA 59.102 38.462 0.00 0.00 33.89 1.85
3546 3834 5.723887 AGTCCTAACCATGACATCTCTCTTT 59.276 40.000 0.00 0.00 33.89 2.52
3547 3835 5.276440 AGTCCTAACCATGACATCTCTCTT 58.724 41.667 0.00 0.00 33.89 2.85
3548 3836 4.877773 AGTCCTAACCATGACATCTCTCT 58.122 43.478 0.00 0.00 33.89 3.10
3549 3837 5.606348 AAGTCCTAACCATGACATCTCTC 57.394 43.478 0.00 0.00 33.89 3.20
3550 3838 5.600484 CCTAAGTCCTAACCATGACATCTCT 59.400 44.000 0.00 0.00 33.89 3.10
3551 3839 5.598830 TCCTAAGTCCTAACCATGACATCTC 59.401 44.000 0.00 0.00 33.89 2.75
3552 3840 5.529289 TCCTAAGTCCTAACCATGACATCT 58.471 41.667 0.00 0.00 33.89 2.90
3553 3841 5.221541 CCTCCTAAGTCCTAACCATGACATC 60.222 48.000 0.00 0.00 33.89 3.06
3554 3842 4.656112 CCTCCTAAGTCCTAACCATGACAT 59.344 45.833 0.00 0.00 33.89 3.06
3555 3843 4.030913 CCTCCTAAGTCCTAACCATGACA 58.969 47.826 0.00 0.00 33.89 3.58
3556 3844 4.287552 TCCTCCTAAGTCCTAACCATGAC 58.712 47.826 0.00 0.00 0.00 3.06
3557 3845 4.620086 TCCTCCTAAGTCCTAACCATGA 57.380 45.455 0.00 0.00 0.00 3.07
3558 3846 4.962995 TCTTCCTCCTAAGTCCTAACCATG 59.037 45.833 0.00 0.00 0.00 3.66
3559 3847 5.222278 TCTTCCTCCTAAGTCCTAACCAT 57.778 43.478 0.00 0.00 0.00 3.55
3560 3848 4.687262 TCTTCCTCCTAAGTCCTAACCA 57.313 45.455 0.00 0.00 0.00 3.67
3561 3849 8.172070 ACTATATCTTCCTCCTAAGTCCTAACC 58.828 40.741 0.00 0.00 0.00 2.85
3564 3852 9.632463 ACTACTATATCTTCCTCCTAAGTCCTA 57.368 37.037 0.00 0.00 0.00 2.94
3565 3853 8.387813 CACTACTATATCTTCCTCCTAAGTCCT 58.612 40.741 0.00 0.00 0.00 3.85
3566 3854 8.384718 TCACTACTATATCTTCCTCCTAAGTCC 58.615 40.741 0.00 0.00 0.00 3.85
3567 3855 9.796180 TTCACTACTATATCTTCCTCCTAAGTC 57.204 37.037 0.00 0.00 0.00 3.01
3585 3873 4.377021 TGACTCGCACATTTTTCACTACT 58.623 39.130 0.00 0.00 0.00 2.57
3588 3876 3.058016 CCATGACTCGCACATTTTTCACT 60.058 43.478 0.00 0.00 0.00 3.41
3623 3911 1.090052 GCTAGCTGTGCGGTTAAGGG 61.090 60.000 7.70 0.00 0.00 3.95
3713 4015 8.469200 CAAAGAGCCAAAGATATCATTAAACCA 58.531 33.333 5.32 0.00 0.00 3.67
3888 4191 1.300697 CGGCTGAGGTTATACCGGC 60.301 63.158 0.00 0.00 44.90 6.13
3891 4194 1.202498 GGTGTCGGCTGAGGTTATACC 60.202 57.143 0.00 0.00 38.99 2.73
3929 4232 6.808829 ACACCACGATTACCGAGAATAATAA 58.191 36.000 0.00 0.00 41.76 1.40
4002 4345 1.815613 CTCGTGAGACACTGATGACCT 59.184 52.381 0.00 0.00 35.39 3.85


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

AutoCloner maintained by Alex Coulton.