Multiple sequence alignment - TraesCS7B01G043800

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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 TraesCS7B01G043800 chr7B 100.000 2645 0 0 1 2645 43671563 43674207 0.000000e+00 4885.0
1 TraesCS7B01G043800 chr7B 90.732 410 28 7 2244 2645 705890731 705890324 3.000000e-149 538.0
2 TraesCS7B01G043800 chr7B 84.971 346 50 2 34 379 374982241 374982584 1.510000e-92 350.0
3 TraesCS7B01G043800 chr5B 98.422 1014 15 1 1632 2645 639763896 639762884 0.000000e+00 1783.0
4 TraesCS7B01G043800 chr5B 86.040 351 47 1 35 385 17992459 17992807 2.490000e-100 375.0
5 TraesCS7B01G043800 chr7D 87.569 1263 102 31 3 1242 91105562 91106792 0.000000e+00 1411.0
6 TraesCS7B01G043800 chr7D 93.494 415 22 2 1219 1631 91106802 91107213 1.740000e-171 612.0
7 TraesCS7B01G043800 chr3B 90.990 1010 78 9 1631 2630 774821485 774822491 0.000000e+00 1349.0
8 TraesCS7B01G043800 chr3B 90.119 1012 84 12 1632 2630 486797459 486798467 0.000000e+00 1301.0
9 TraesCS7B01G043800 chr3B 89.778 1037 63 20 1632 2645 720235505 720234489 0.000000e+00 1288.0
10 TraesCS7B01G043800 chr6A 90.396 1010 83 10 1632 2630 592275681 592276687 0.000000e+00 1315.0
11 TraesCS7B01G043800 chr2B 90.958 741 54 9 1632 2363 16305889 16306625 0.000000e+00 985.0
12 TraesCS7B01G043800 chr2B 84.553 369 49 8 34 398 798271125 798270761 2.500000e-95 359.0
13 TraesCS7B01G043800 chr7A 90.865 624 47 7 1633 2250 669871236 669871855 0.000000e+00 828.0
14 TraesCS7B01G043800 chr7A 92.099 405 28 3 2244 2645 669871925 669872328 3.820000e-158 568.0
15 TraesCS7B01G043800 chr1B 90.385 624 46 12 1634 2250 576028806 576028190 0.000000e+00 808.0
16 TraesCS7B01G043800 chr1B 87.117 326 39 3 44 367 129139258 129138934 1.500000e-97 366.0
17 TraesCS7B01G043800 chr1B 87.243 243 22 4 1002 1240 632165602 632165839 4.340000e-68 268.0
18 TraesCS7B01G043800 chr2D 89.873 632 54 8 1625 2250 292291824 292292451 0.000000e+00 804.0
19 TraesCS7B01G043800 chr2D 85.054 368 48 7 34 398 635991250 635990887 4.160000e-98 368.0
20 TraesCS7B01G043800 chr2D 83.784 370 51 9 34 398 609193744 609193379 2.520000e-90 342.0
21 TraesCS7B01G043800 chr1D 82.669 727 86 21 924 1631 460158969 460159674 2.250000e-170 608.0
22 TraesCS7B01G043800 chr1D 95.833 48 2 0 421 468 460158752 460158799 7.850000e-11 78.7
23 TraesCS7B01G043800 chr1A 84.112 642 68 21 1002 1631 551641347 551641966 8.150000e-165 590.0
24 TraesCS7B01G043800 chrUn 92.462 398 26 3 2084 2478 478298924 478298528 1.370000e-157 566.0
25 TraesCS7B01G043800 chr3D 89.976 409 33 7 2244 2645 36169625 36170032 3.020000e-144 521.0
26 TraesCS7B01G043800 chr3D 83.673 392 48 13 34 414 5168712 5168326 3.240000e-94 355.0
27 TraesCS7B01G043800 chr4D 84.900 351 47 6 43 390 484939305 484939652 1.510000e-92 350.0
28 TraesCS7B01G043800 chr6D 84.857 350 48 5 33 379 23096102 23096449 5.420000e-92 348.0


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 TraesCS7B01G043800 chr7B 43671563 43674207 2644 False 4885.00 4885 100.0000 1 2645 1 chr7B.!!$F1 2644
1 TraesCS7B01G043800 chr5B 639762884 639763896 1012 True 1783.00 1783 98.4220 1632 2645 1 chr5B.!!$R1 1013
2 TraesCS7B01G043800 chr7D 91105562 91107213 1651 False 1011.50 1411 90.5315 3 1631 2 chr7D.!!$F1 1628
3 TraesCS7B01G043800 chr3B 774821485 774822491 1006 False 1349.00 1349 90.9900 1631 2630 1 chr3B.!!$F2 999
4 TraesCS7B01G043800 chr3B 486797459 486798467 1008 False 1301.00 1301 90.1190 1632 2630 1 chr3B.!!$F1 998
5 TraesCS7B01G043800 chr3B 720234489 720235505 1016 True 1288.00 1288 89.7780 1632 2645 1 chr3B.!!$R1 1013
6 TraesCS7B01G043800 chr6A 592275681 592276687 1006 False 1315.00 1315 90.3960 1632 2630 1 chr6A.!!$F1 998
7 TraesCS7B01G043800 chr2B 16305889 16306625 736 False 985.00 985 90.9580 1632 2363 1 chr2B.!!$F1 731
8 TraesCS7B01G043800 chr7A 669871236 669872328 1092 False 698.00 828 91.4820 1633 2645 2 chr7A.!!$F1 1012
9 TraesCS7B01G043800 chr1B 576028190 576028806 616 True 808.00 808 90.3850 1634 2250 1 chr1B.!!$R2 616
10 TraesCS7B01G043800 chr2D 292291824 292292451 627 False 804.00 804 89.8730 1625 2250 1 chr2D.!!$F1 625
11 TraesCS7B01G043800 chr1D 460158752 460159674 922 False 343.35 608 89.2510 421 1631 2 chr1D.!!$F1 1210
12 TraesCS7B01G043800 chr1A 551641347 551641966 619 False 590.00 590 84.1120 1002 1631 1 chr1A.!!$F1 629

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
922 952 0.102481 CGTGATCTCCGAATCCCGTT 59.898 55.0 0.0 0.0 36.31 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1864 3.706373 CTGCTGTACTGGGCCGGT 61.706 66.667 23.8 23.8 0.0 5.28 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
40 41 3.002038 ACTAACCTCTACCGAGAGTGG 57.998 52.381 1.54 2.50 46.93 4.00
42 43 1.313812 AACCTCTACCGAGAGTGGCG 61.314 60.000 1.54 0.00 46.93 5.69
57 58 3.587933 GCGTTTTGGCACACCGGA 61.588 61.111 9.46 0.00 39.29 5.14
60 61 3.283684 TTTTGGCACACCGGAGCG 61.284 61.111 9.46 0.00 39.29 5.03
93 94 8.507249 CCTGGTTTTCAAAATGTGTTTTAAACA 58.493 29.630 6.41 6.41 37.42 2.83
133 134 8.518151 AAAAAGCTTCAAACAAAAATTTGGTG 57.482 26.923 0.00 7.84 42.34 4.17
134 135 5.233957 AGCTTCAAACAAAAATTTGGTGC 57.766 34.783 10.38 3.81 42.34 5.01
159 160 7.112287 GCGTACATCTCGATATTATACATGCTC 59.888 40.741 0.00 0.00 0.00 4.26
161 162 9.958234 GTACATCTCGATATTATACATGCTCAT 57.042 33.333 0.00 0.00 0.00 2.90
183 184 7.708051 TCATAAAGTCATTTCACGAAAAACCA 58.292 30.769 0.00 0.00 33.56 3.67
197 198 6.020995 CACGAAAAACCAACAACTTATGTGTC 60.021 38.462 0.00 0.00 42.99 3.67
203 204 0.511221 ACAACTTATGTGTCGCGTGC 59.489 50.000 5.77 0.57 41.93 5.34
218 219 2.215363 CGCGTGCGAAAAAGACAAAATT 59.785 40.909 8.89 0.00 42.83 1.82
219 220 3.301515 CGCGTGCGAAAAAGACAAAATTT 60.302 39.130 8.89 0.00 42.83 1.82
221 222 4.259610 GCGTGCGAAAAAGACAAAATTTGA 60.260 37.500 13.19 0.00 0.00 2.69
224 225 5.616785 GTGCGAAAAAGACAAAATTTGATGC 59.383 36.000 13.19 1.72 0.00 3.91
225 226 5.523188 TGCGAAAAAGACAAAATTTGATGCT 59.477 32.000 13.19 3.98 0.00 3.79
226 227 6.699204 TGCGAAAAAGACAAAATTTGATGCTA 59.301 30.769 13.19 0.00 0.00 3.49
234 235 8.947055 AGACAAAATTTGATGCTAAAAAGTGT 57.053 26.923 13.19 0.00 0.00 3.55
255 256 6.457676 GTGTTTTTCACACGACATCTTTTTG 58.542 36.000 0.00 0.00 46.51 2.44
257 258 6.306837 TGTTTTTCACACGACATCTTTTTGTC 59.693 34.615 0.00 0.00 42.10 3.18
259 260 5.403897 TTCACACGACATCTTTTTGTCTC 57.596 39.130 0.00 0.00 43.10 3.36
274 275 8.234546 TCTTTTTGTCTCTTTTACACAAGTCAC 58.765 33.333 0.00 0.00 31.81 3.67
275 276 7.441890 TTTTGTCTCTTTTACACAAGTCACA 57.558 32.000 0.00 0.00 31.81 3.58
310 311 5.940192 TTTATCTGAAACTTGACGTGCAT 57.060 34.783 0.00 0.00 0.00 3.96
312 313 4.928661 ATCTGAAACTTGACGTGCATAC 57.071 40.909 0.00 0.00 0.00 2.39
321 322 7.786178 AACTTGACGTGCATACATATAATGT 57.214 32.000 0.00 0.00 46.92 2.71
325 326 6.386654 TGACGTGCATACATATAATGTCGAT 58.613 36.000 0.00 0.00 43.67 3.59
326 327 6.866248 TGACGTGCATACATATAATGTCGATT 59.134 34.615 0.00 0.00 43.67 3.34
336 337 2.704725 AATGTCGATTTGTGTGTGCC 57.295 45.000 0.00 0.00 0.00 5.01
344 345 5.460419 GTCGATTTGTGTGTGCCAAATTTTA 59.540 36.000 0.00 0.00 41.34 1.52
345 346 6.145371 GTCGATTTGTGTGTGCCAAATTTTAT 59.855 34.615 0.00 0.00 41.34 1.40
348 349 7.320797 CGATTTGTGTGTGCCAAATTTTATTTG 59.679 33.333 5.39 5.39 41.34 2.32
392 393 2.714259 TTTTTCCAGTGACAGGGCG 58.286 52.632 0.00 0.00 0.00 6.13
393 394 1.452145 TTTTTCCAGTGACAGGGCGC 61.452 55.000 0.00 0.00 0.00 6.53
394 395 4.680237 TTCCAGTGACAGGGCGCG 62.680 66.667 0.00 0.00 0.00 6.86
419 427 1.273048 TGCCAAAGCGAATTTCTGCAT 59.727 42.857 13.12 2.01 44.31 3.96
435 443 0.598065 GCATGGATCCCCGCAATAAC 59.402 55.000 9.90 0.00 34.29 1.89
487 495 8.310382 CAGATCCTAGGAAACAAATCTATCGAT 58.690 37.037 17.30 2.16 0.00 3.59
561 569 4.479786 AGAATAGGAAGCACAACCTCTC 57.520 45.455 0.00 0.00 37.68 3.20
565 573 1.546476 AGGAAGCACAACCTCTCTACG 59.454 52.381 0.00 0.00 0.00 3.51
566 574 1.272769 GGAAGCACAACCTCTCTACGT 59.727 52.381 0.00 0.00 0.00 3.57
567 575 2.490903 GGAAGCACAACCTCTCTACGTA 59.509 50.000 0.00 0.00 0.00 3.57
568 576 3.130693 GGAAGCACAACCTCTCTACGTAT 59.869 47.826 0.00 0.00 0.00 3.06
569 577 4.337555 GGAAGCACAACCTCTCTACGTATA 59.662 45.833 0.00 0.00 0.00 1.47
570 578 5.502153 AAGCACAACCTCTCTACGTATAG 57.498 43.478 0.00 0.00 0.00 1.31
571 579 4.778579 AGCACAACCTCTCTACGTATAGA 58.221 43.478 9.97 9.97 36.01 1.98
572 580 4.575645 AGCACAACCTCTCTACGTATAGAC 59.424 45.833 6.58 0.00 33.66 2.59
627 638 3.008594 TGGCCGATTCCTTTTCAAGTCTA 59.991 43.478 0.00 0.00 0.00 2.59
629 640 3.623510 GCCGATTCCTTTTCAAGTCTAGG 59.376 47.826 0.00 0.00 0.00 3.02
630 641 3.623510 CCGATTCCTTTTCAAGTCTAGGC 59.376 47.826 0.00 0.00 0.00 3.93
631 642 4.508662 CGATTCCTTTTCAAGTCTAGGCT 58.491 43.478 0.00 0.00 0.00 4.58
632 643 4.938226 CGATTCCTTTTCAAGTCTAGGCTT 59.062 41.667 3.04 3.04 0.00 4.35
633 644 5.412904 CGATTCCTTTTCAAGTCTAGGCTTT 59.587 40.000 6.92 0.00 0.00 3.51
734 752 3.451178 AGGGAACACTGATGCGTATACTT 59.549 43.478 0.56 0.00 0.00 2.24
735 753 3.555956 GGGAACACTGATGCGTATACTTG 59.444 47.826 0.56 0.00 0.00 3.16
736 754 3.001330 GGAACACTGATGCGTATACTTGC 59.999 47.826 0.56 0.00 0.00 4.01
737 755 3.526931 ACACTGATGCGTATACTTGCT 57.473 42.857 0.56 0.00 0.00 3.91
738 756 3.190079 ACACTGATGCGTATACTTGCTG 58.810 45.455 0.56 0.00 0.00 4.41
740 758 4.142249 ACACTGATGCGTATACTTGCTGTA 60.142 41.667 0.56 0.00 35.37 2.74
741 759 4.207224 CACTGATGCGTATACTTGCTGTAC 59.793 45.833 0.56 0.00 33.45 2.90
742 760 4.098044 ACTGATGCGTATACTTGCTGTACT 59.902 41.667 0.56 0.00 33.45 2.73
744 762 5.516996 TGATGCGTATACTTGCTGTACTAC 58.483 41.667 0.56 0.00 33.45 2.73
747 765 6.872628 TGCGTATACTTGCTGTACTACTAT 57.127 37.500 0.56 0.00 33.45 2.12
748 766 6.665465 TGCGTATACTTGCTGTACTACTATG 58.335 40.000 0.56 0.00 33.45 2.23
751 769 7.859377 GCGTATACTTGCTGTACTACTATGAAA 59.141 37.037 0.56 0.00 33.45 2.69
752 770 9.726232 CGTATACTTGCTGTACTACTATGAAAA 57.274 33.333 0.56 0.00 33.45 2.29
806 836 4.617959 TCCTAGCGCTGATGTGTATTTAC 58.382 43.478 22.90 0.00 0.00 2.01
816 846 6.037830 GCTGATGTGTATTTACGGTTACCAAT 59.962 38.462 1.13 0.00 0.00 3.16
820 850 5.642919 TGTGTATTTACGGTTACCAATCACC 59.357 40.000 1.13 0.00 0.00 4.02
847 877 4.142838 CGCGTACCTATGGTGATTATACGA 60.143 45.833 0.00 0.00 33.65 3.43
871 901 1.678627 CCTATCCAGGAGTGTCTCACG 59.321 57.143 0.00 0.00 45.91 4.35
903 933 4.188462 TGTGTGCACTATACCATAACTGC 58.812 43.478 19.41 0.00 0.00 4.40
912 942 2.604046 ACCATAACTGCGTGATCTCC 57.396 50.000 0.00 0.00 0.00 3.71
913 943 1.202417 ACCATAACTGCGTGATCTCCG 60.202 52.381 0.00 0.00 0.00 4.63
915 945 2.481276 CCATAACTGCGTGATCTCCGAA 60.481 50.000 9.14 0.00 0.00 4.30
916 946 3.384668 CATAACTGCGTGATCTCCGAAT 58.615 45.455 9.14 0.00 0.00 3.34
917 947 1.927895 AACTGCGTGATCTCCGAATC 58.072 50.000 9.14 0.00 0.00 2.52
919 949 0.598680 CTGCGTGATCTCCGAATCCC 60.599 60.000 9.14 0.00 0.00 3.85
920 950 1.661821 GCGTGATCTCCGAATCCCG 60.662 63.158 9.14 0.00 38.18 5.14
921 951 1.734137 CGTGATCTCCGAATCCCGT 59.266 57.895 0.00 0.00 36.31 5.28
922 952 0.102481 CGTGATCTCCGAATCCCGTT 59.898 55.000 0.00 0.00 36.31 4.44
946 976 5.006649 TGCAAATCTGTCATGCTTCGTATAC 59.993 40.000 0.00 0.00 40.66 1.47
986 1019 4.452114 TCGATGCACATGCCATAGTTAATC 59.548 41.667 0.49 0.00 41.18 1.75
1040 1076 2.360350 AGGTGTGCCATTGCCTCG 60.360 61.111 0.00 0.00 37.19 4.63
1056 1092 2.464865 CCTCGGATCGTGCTTCTAAAG 58.535 52.381 0.00 0.00 0.00 1.85
1149 1185 3.737559 TCATTGGGTGCCTTCTTATGT 57.262 42.857 0.00 0.00 0.00 2.29
1420 1493 2.140065 GCATATGCTGCGTCACTCTA 57.860 50.000 20.64 0.00 41.97 2.43
1479 1552 3.129287 CACAGGAATTGCCCAAGTATGAC 59.871 47.826 0.00 0.00 37.37 3.06
1480 1553 2.355756 CAGGAATTGCCCAAGTATGACG 59.644 50.000 0.00 0.00 37.37 4.35
1481 1554 2.238646 AGGAATTGCCCAAGTATGACGA 59.761 45.455 0.00 0.00 37.37 4.20
1499 1572 1.077501 ACGCAGCCCATACTTGCAT 60.078 52.632 0.00 0.00 37.69 3.96
1518 1591 2.810870 TACACGGGTGGGCATTAATT 57.189 45.000 0.00 0.00 34.19 1.40
1562 1640 4.746115 GTGTGTTGATTGATGCACATGTTT 59.254 37.500 0.00 0.00 42.66 2.83
1622 1704 0.101219 GTTGAAATCTGATGCGGCCC 59.899 55.000 0.00 0.00 0.00 5.80
1777 1864 5.066375 CGTAATCAGGATTTGCTGAATTGGA 59.934 40.000 5.86 0.00 32.98 3.53
2588 2773 7.700611 AGAAAGAAATAATTTTTACGTCGCG 57.299 32.000 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.966309 GCCAAAACGCCACTCTCGG 61.966 63.158 0.00 0.00 0.00 4.63
40 41 3.536498 CTCCGGTGTGCCAAAACGC 62.536 63.158 0.00 0.00 34.09 4.84
42 43 2.335011 GCTCCGGTGTGCCAAAAC 59.665 61.111 0.00 0.00 34.09 2.43
60 61 0.383949 TTTGAAAACCAGGAGCGTGC 59.616 50.000 0.00 0.00 0.00 5.34
62 63 2.693074 ACATTTTGAAAACCAGGAGCGT 59.307 40.909 0.00 0.00 0.00 5.07
63 64 3.052036 CACATTTTGAAAACCAGGAGCG 58.948 45.455 0.00 0.00 0.00 5.03
64 65 4.058721 ACACATTTTGAAAACCAGGAGC 57.941 40.909 0.00 0.00 0.00 4.70
65 66 6.983474 AAAACACATTTTGAAAACCAGGAG 57.017 33.333 0.00 0.00 36.64 3.69
66 67 8.722394 GTTTAAAACACATTTTGAAAACCAGGA 58.278 29.630 0.00 0.00 38.50 3.86
67 68 8.507249 TGTTTAAAACACATTTTGAAAACCAGG 58.493 29.630 0.00 0.00 36.38 4.45
113 114 4.027724 CGCACCAAATTTTTGTTTGAAGC 58.972 39.130 2.63 4.16 40.64 3.86
114 115 5.215239 ACGCACCAAATTTTTGTTTGAAG 57.785 34.783 2.63 1.38 40.64 3.02
115 116 5.637810 TGTACGCACCAAATTTTTGTTTGAA 59.362 32.000 2.63 0.00 40.64 2.69
123 124 3.749088 TCGAGATGTACGCACCAAATTTT 59.251 39.130 0.00 0.00 0.00 1.82
132 133 6.691388 GCATGTATAATATCGAGATGTACGCA 59.309 38.462 0.00 0.00 0.00 5.24
133 134 6.913132 AGCATGTATAATATCGAGATGTACGC 59.087 38.462 0.00 1.40 0.00 4.42
134 135 8.122952 TGAGCATGTATAATATCGAGATGTACG 58.877 37.037 0.00 0.00 0.00 3.67
159 160 7.922505 TGGTTTTTCGTGAAATGACTTTATG 57.077 32.000 0.00 0.00 0.00 1.90
161 162 7.313646 TGTTGGTTTTTCGTGAAATGACTTTA 58.686 30.769 0.00 0.00 0.00 1.85
183 184 1.070175 GCACGCGACACATAAGTTGTT 60.070 47.619 15.93 0.00 36.00 2.83
197 198 1.184349 TTTTGTCTTTTTCGCACGCG 58.816 45.000 3.53 3.53 41.35 6.01
203 204 9.913451 TTTTAGCATCAAATTTTGTCTTTTTCG 57.087 25.926 8.89 0.00 0.00 3.46
234 235 6.862944 GACAAAAAGATGTCGTGTGAAAAA 57.137 33.333 0.00 0.00 40.23 1.94
286 287 5.507077 TGCACGTCAAGTTTCAGATAAAAC 58.493 37.500 0.00 0.00 39.03 2.43
291 292 4.314961 TGTATGCACGTCAAGTTTCAGAT 58.685 39.130 0.00 0.00 0.00 2.90
310 311 7.254624 GGCACACACAAATCGACATTATATGTA 60.255 37.037 0.00 0.00 45.03 2.29
312 313 5.909054 GGCACACACAAATCGACATTATATG 59.091 40.000 0.00 0.00 0.00 1.78
321 322 3.724508 AATTTGGCACACACAAATCGA 57.275 38.095 4.14 0.00 45.07 3.59
325 326 6.599244 TCCAAATAAAATTTGGCACACACAAA 59.401 30.769 21.41 3.84 46.40 2.83
326 327 6.115446 TCCAAATAAAATTTGGCACACACAA 58.885 32.000 21.41 4.43 46.40 3.33
393 394 3.593551 ATTCGCTTTGGCACGCACG 62.594 57.895 8.45 1.04 38.60 5.34
394 395 0.939106 AAATTCGCTTTGGCACGCAC 60.939 50.000 8.45 0.00 38.60 5.34
395 396 0.662970 GAAATTCGCTTTGGCACGCA 60.663 50.000 8.45 0.00 38.60 5.24
396 397 0.387239 AGAAATTCGCTTTGGCACGC 60.387 50.000 0.00 0.00 38.60 5.34
419 427 1.525077 GCGTTATTGCGGGGATCCA 60.525 57.895 15.23 0.00 0.00 3.41
435 443 6.398621 CGAGATTAGAAACCACAATATACGCG 60.399 42.308 3.53 3.53 0.00 6.01
565 573 2.649614 GCCGGGAGCCGTCTATAC 59.350 66.667 2.18 0.00 46.80 1.47
566 574 2.981909 CGCCGGGAGCCGTCTATA 60.982 66.667 2.18 0.00 46.80 1.31
627 638 9.821765 CCTAAGAAGGAAAGGAAAGGAAAGCCT 62.822 44.444 0.00 0.00 46.69 4.58
629 640 6.260870 CTAAGAAGGAAAGGAAAGGAAAGC 57.739 41.667 0.00 0.00 0.00 3.51
751 769 9.793259 AGGGAAGTTTTTCTTTTCTTTTCTTTT 57.207 25.926 0.00 0.00 36.40 2.27
752 770 9.436957 GAGGGAAGTTTTTCTTTTCTTTTCTTT 57.563 29.630 0.00 0.00 36.40 2.52
753 771 7.759886 CGAGGGAAGTTTTTCTTTTCTTTTCTT 59.240 33.333 0.00 0.00 36.40 2.52
754 772 7.258441 CGAGGGAAGTTTTTCTTTTCTTTTCT 58.742 34.615 0.00 0.00 36.40 2.52
756 774 5.810587 GCGAGGGAAGTTTTTCTTTTCTTTT 59.189 36.000 0.00 0.00 36.40 2.27
757 775 5.105513 TGCGAGGGAAGTTTTTCTTTTCTTT 60.106 36.000 0.00 0.00 36.40 2.52
758 776 4.401202 TGCGAGGGAAGTTTTTCTTTTCTT 59.599 37.500 0.00 0.00 36.40 2.52
760 778 4.036380 TCTGCGAGGGAAGTTTTTCTTTTC 59.964 41.667 0.00 0.00 36.40 2.29
761 779 3.951680 TCTGCGAGGGAAGTTTTTCTTTT 59.048 39.130 0.00 0.00 36.40 2.27
762 780 3.551846 TCTGCGAGGGAAGTTTTTCTTT 58.448 40.909 0.00 0.00 36.40 2.52
763 781 3.208747 TCTGCGAGGGAAGTTTTTCTT 57.791 42.857 0.00 0.00 39.32 2.52
766 784 2.040412 AGGATCTGCGAGGGAAGTTTTT 59.960 45.455 0.00 0.00 0.00 1.94
767 785 1.630878 AGGATCTGCGAGGGAAGTTTT 59.369 47.619 0.00 0.00 0.00 2.43
768 786 1.280457 AGGATCTGCGAGGGAAGTTT 58.720 50.000 0.00 0.00 0.00 2.66
772 801 2.431023 GCTAGGATCTGCGAGGGAA 58.569 57.895 0.00 0.00 0.00 3.97
821 851 3.327754 CACCATAGGTACGCGCGC 61.328 66.667 32.58 23.91 32.11 6.86
822 852 0.596600 AATCACCATAGGTACGCGCG 60.597 55.000 30.96 30.96 32.11 6.86
823 853 2.427232 TAATCACCATAGGTACGCGC 57.573 50.000 5.73 0.00 32.11 6.86
831 861 8.361139 GGATAGGGATTCGTATAATCACCATAG 58.639 40.741 0.00 0.00 30.48 2.23
847 877 3.051803 TGAGACACTCCTGGATAGGGATT 60.052 47.826 0.00 0.00 44.70 3.01
903 933 0.102481 AACGGGATTCGGAGATCACG 59.898 55.000 17.31 17.31 43.07 4.35
912 942 1.468520 ACAGATTTGCAACGGGATTCG 59.531 47.619 0.00 0.00 45.88 3.34
913 943 2.487762 TGACAGATTTGCAACGGGATTC 59.512 45.455 0.00 0.00 0.00 2.52
915 945 2.198827 TGACAGATTTGCAACGGGAT 57.801 45.000 0.00 0.00 0.00 3.85
916 946 1.811965 CATGACAGATTTGCAACGGGA 59.188 47.619 0.00 0.00 0.00 5.14
917 947 1.733389 GCATGACAGATTTGCAACGGG 60.733 52.381 0.00 0.00 36.40 5.28
919 949 2.624316 AGCATGACAGATTTGCAACG 57.376 45.000 0.00 0.00 38.84 4.10
920 950 2.912967 CGAAGCATGACAGATTTGCAAC 59.087 45.455 0.00 0.00 38.84 4.17
921 951 2.553602 ACGAAGCATGACAGATTTGCAA 59.446 40.909 0.00 0.00 38.84 4.08
922 952 2.153645 ACGAAGCATGACAGATTTGCA 58.846 42.857 0.00 0.00 38.84 4.08
962 995 1.875009 ACTATGGCATGTGCATCGAG 58.125 50.000 10.98 0.00 44.36 4.04
986 1019 0.116541 ATATAGGGGGTCCGGGTCTG 59.883 60.000 0.00 0.00 38.33 3.51
1056 1092 3.053455 GTGTGCGAGATTATGAGGTAGC 58.947 50.000 0.00 0.00 0.00 3.58
1149 1185 8.151596 TGATGTGTACTTACATTGTACTCCAAA 58.848 33.333 0.00 0.00 41.15 3.28
1479 1552 2.813179 GCAAGTATGGGCTGCGTCG 61.813 63.158 0.00 0.00 0.00 5.12
1480 1553 1.097547 ATGCAAGTATGGGCTGCGTC 61.098 55.000 0.00 0.00 0.00 5.19
1481 1554 0.180171 TATGCAAGTATGGGCTGCGT 59.820 50.000 0.00 0.00 0.00 5.24
1499 1572 2.026169 TCAATTAATGCCCACCCGTGTA 60.026 45.455 0.00 0.00 0.00 2.90
1518 1591 7.868922 ACACACTATTTTACAGTCGTGTATTCA 59.131 33.333 0.00 0.00 38.98 2.57
1597 1679 3.484229 CCGCATCAGATTTCAACTCGTTC 60.484 47.826 0.00 0.00 0.00 3.95
1646 1728 6.636562 TTTCGCCTACAAATTGAAGGTTTA 57.363 33.333 0.00 0.00 32.67 2.01
1777 1864 3.706373 CTGCTGTACTGGGCCGGT 61.706 66.667 23.80 23.80 0.00 5.28
2114 2213 7.727186 AGAATATATGTGGCATGTCCTTGAAAT 59.273 33.333 0.00 0.00 35.26 2.17


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

AutoCloner maintained by Alex Coulton.