Multiple sequence alignment - TraesCS6A01G314900

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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 TraesCS6A01G314900 chr6A 100.000 3821 0 0 1 3821 551637665 551641485 0.000000e+00 7057.0
1 TraesCS6A01G314900 chr6B 90.802 2544 145 45 6 2520 608995352 608997835 0.000000e+00 3319.0
2 TraesCS6A01G314900 chr6B 96.398 1305 31 4 2519 3821 608997859 608999149 0.000000e+00 2135.0
3 TraesCS6A01G314900 chr6D 97.262 1461 38 2 2362 3821 405082826 405084285 0.000000e+00 2475.0
4 TraesCS6A01G314900 chr6D 89.169 1745 91 39 1 1711 405081154 405082834 0.000000e+00 2085.0
5 TraesCS6A01G314900 chr2A 89.632 733 55 8 1615 2329 11922812 11922083 0.000000e+00 913.0
6 TraesCS6A01G314900 chr7A 89.112 597 41 12 1612 2189 42642252 42641661 0.000000e+00 721.0
7 TraesCS6A01G314900 chr7A 92.857 70 5 0 1567 1636 46717063 46717132 6.750000e-18 102.0
8 TraesCS6A01G314900 chr1A 79.116 996 134 37 1248 2222 523120764 523121706 1.510000e-173 619.0
9 TraesCS6A01G314900 chr1A 82.990 729 77 21 1507 2222 525007797 525007103 1.950000e-172 616.0
10 TraesCS6A01G314900 chr1A 82.579 729 79 22 1507 2222 525006781 525006088 1.960000e-167 599.0
11 TraesCS6A01G314900 chr1A 82.305 729 86 13 1505 2222 523126450 523127146 3.290000e-165 592.0
12 TraesCS6A01G314900 chr1A 81.641 719 105 14 1506 2222 525003773 525003080 4.280000e-159 571.0
13 TraesCS6A01G314900 chr1B 90.343 466 45 0 2586 3051 656526669 656526204 2.520000e-171 612.0
14 TraesCS6A01G314900 chr5B 89.957 468 45 2 2586 3051 264912595 264912128 1.520000e-168 603.0
15 TraesCS6A01G314900 chr5B 89.914 466 47 0 2586 3051 425667760 425668225 5.460000e-168 601.0
16 TraesCS6A01G314900 chr5B 85.579 423 51 5 1802 2222 439441989 439442403 5.860000e-118 435.0
17 TraesCS6A01G314900 chr5B 77.126 835 111 44 1162 1980 264913835 264913065 9.880000e-111 411.0
18 TraesCS6A01G314900 chr5B 85.933 327 43 3 2221 2545 439442321 439442646 2.830000e-91 346.0
19 TraesCS6A01G314900 chr5B 100.000 33 0 0 2587 2619 439442648 439442680 1.150000e-05 62.1
20 TraesCS6A01G314900 chr3B 88.841 466 52 0 2586 3051 174463768 174463303 1.190000e-159 573.0
21 TraesCS6A01G314900 chr3B 87.016 439 42 8 2618 3053 763474033 763473607 7.420000e-132 481.0
22 TraesCS6A01G314900 chr1D 93.417 319 19 2 2616 2933 11359482 11359799 4.470000e-129 472.0
23 TraesCS6A01G314900 chr1D 93.103 319 20 2 2616 2933 156285595 156285912 2.080000e-127 466.0
24 TraesCS6A01G314900 chr3D 93.559 295 17 2 2640 2933 459882811 459882518 4.530000e-119 438.0
25 TraesCS6A01G314900 chr3D 79.810 525 58 27 977 1479 353233794 353233296 4.730000e-89 339.0
26 TraesCS6A01G314900 chr3D 93.506 77 4 1 1565 1641 566655647 566655722 3.120000e-21 113.0
27 TraesCS6A01G314900 chr2B 87.048 332 37 4 2221 2549 4576306 4576634 1.680000e-98 370.0
28 TraesCS6A01G314900 chr2B 87.295 244 29 2 2221 2463 779041756 779041514 1.050000e-70 278.0
29 TraesCS6A01G314900 chr7D 86.747 332 38 4 2221 2549 77499301 77498973 7.800000e-97 364.0
30 TraesCS6A01G314900 chr7D 85.542 332 42 4 2221 2549 147585793 147586121 3.660000e-90 342.0
31 TraesCS6A01G314900 chr7B 86.364 330 36 6 2221 2545 98985339 98985664 6.070000e-93 351.0
32 TraesCS6A01G314900 chr7B 100.000 33 0 0 2587 2619 98985666 98985698 1.150000e-05 62.1
33 TraesCS6A01G314900 chr5D 86.145 332 39 5 2221 2549 120935342 120935669 6.070000e-93 351.0


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 TraesCS6A01G314900 chr6A 551637665 551641485 3820 False 7057.000000 7057 100.000000 1 3821 1 chr6A.!!$F1 3820
1 TraesCS6A01G314900 chr6B 608995352 608999149 3797 False 2727.000000 3319 93.600000 6 3821 2 chr6B.!!$F1 3815
2 TraesCS6A01G314900 chr6D 405081154 405084285 3131 False 2280.000000 2475 93.215500 1 3821 2 chr6D.!!$F1 3820
3 TraesCS6A01G314900 chr2A 11922083 11922812 729 True 913.000000 913 89.632000 1615 2329 1 chr2A.!!$R1 714
4 TraesCS6A01G314900 chr7A 42641661 42642252 591 True 721.000000 721 89.112000 1612 2189 1 chr7A.!!$R1 577
5 TraesCS6A01G314900 chr1A 523120764 523121706 942 False 619.000000 619 79.116000 1248 2222 1 chr1A.!!$F1 974
6 TraesCS6A01G314900 chr1A 525003080 525007797 4717 True 595.333333 616 82.403333 1506 2222 3 chr1A.!!$R1 716
7 TraesCS6A01G314900 chr1A 523126450 523127146 696 False 592.000000 592 82.305000 1505 2222 1 chr1A.!!$F2 717
8 TraesCS6A01G314900 chr5B 264912128 264913835 1707 True 507.000000 603 83.541500 1162 3051 2 chr5B.!!$R1 1889
9 TraesCS6A01G314900 chr5B 439441989 439442680 691 False 281.033333 435 90.504000 1802 2619 3 chr5B.!!$F2 817

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
280 282 0.036765 CCCCCGAGATCACAAAACGA 60.037 55.0 0.00 0.0 0.0 3.85 F
343 360 0.323302 ACACATCGCCACATACCACA 59.677 50.0 0.00 0.0 0.0 4.17 F
915 955 0.388649 GGTGCGGCGTGGATAGATAG 60.389 60.0 9.37 0.0 0.0 2.08 F
1737 1828 0.540597 AGGAAGGCAAAGCTTGGGTC 60.541 55.0 0.00 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1737 0.032540 CAGGGTTTGCTTCAGTTGGC 59.967 55.0 0.00 0.0 0.00 4.52 R
1862 1959 0.165944 GAACCCTTCAACGATGCGTG 59.834 55.0 0.00 0.0 39.99 5.34 R
1863 1960 0.953960 GGAACCCTTCAACGATGCGT 60.954 55.0 0.00 0.0 43.97 5.24 R
3576 7667 0.106167 ACGGGTCTAGCAGGCTGATA 60.106 55.0 20.86 16.4 0.00 2.15 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
22 23 0.502275 CGTGCGCAATGTTGGTTTTC 59.498 50.000 14.00 0.00 0.00 2.29
25 26 1.202302 TGCGCAATGTTGGTTTTCGAA 60.202 42.857 8.16 0.00 0.00 3.71
26 27 1.451651 GCGCAATGTTGGTTTTCGAAG 59.548 47.619 0.30 0.00 0.00 3.79
27 28 2.726633 CGCAATGTTGGTTTTCGAAGT 58.273 42.857 0.00 0.00 0.00 3.01
28 29 2.467305 CGCAATGTTGGTTTTCGAAGTG 59.533 45.455 0.00 0.00 0.00 3.16
30 31 2.793278 ATGTTGGTTTTCGAAGTGCC 57.207 45.000 0.00 2.95 0.00 5.01
31 32 1.464734 TGTTGGTTTTCGAAGTGCCA 58.535 45.000 11.66 11.66 0.00 4.92
44 45 1.629043 AGTGCCAGTTCCTTACGAGA 58.371 50.000 0.00 0.00 0.00 4.04
66 67 4.809673 AGGATTTGCCACGAAAGAAATTC 58.190 39.130 0.00 0.00 40.02 2.17
67 68 3.926527 GGATTTGCCACGAAAGAAATTCC 59.073 43.478 0.00 0.00 33.66 3.01
79 80 1.197910 GAAATTCCGTAGCGACCGAG 58.802 55.000 0.00 0.00 0.00 4.63
83 84 1.028330 TTCCGTAGCGACCGAGTCAT 61.028 55.000 5.15 0.00 32.09 3.06
161 162 4.155709 TGGCACCCAAATCTTGTGAAATA 58.844 39.130 0.00 0.00 31.66 1.40
166 168 6.567050 CACCCAAATCTTGTGAAATATCAGG 58.433 40.000 0.00 0.00 35.88 3.86
208 210 9.612620 ATTTATTACAACGAGCAAGAAAGAAAG 57.387 29.630 0.00 0.00 0.00 2.62
210 212 2.682856 ACAACGAGCAAGAAAGAAAGCA 59.317 40.909 0.00 0.00 0.00 3.91
229 231 8.584157 AGAAAGCATAAAAACACAATCACCATA 58.416 29.630 0.00 0.00 0.00 2.74
231 233 9.553064 AAAGCATAAAAACACAATCACCATAAA 57.447 25.926 0.00 0.00 0.00 1.40
233 235 9.553064 AGCATAAAAACACAATCACCATAAAAA 57.447 25.926 0.00 0.00 0.00 1.94
241 243 7.549839 ACACAATCACCATAAAAATCTCCATG 58.450 34.615 0.00 0.00 0.00 3.66
244 246 6.795144 ATCACCATAAAAATCTCCATGCAA 57.205 33.333 0.00 0.00 0.00 4.08
245 247 5.964758 TCACCATAAAAATCTCCATGCAAC 58.035 37.500 0.00 0.00 0.00 4.17
246 248 5.479724 TCACCATAAAAATCTCCATGCAACA 59.520 36.000 0.00 0.00 0.00 3.33
248 250 6.091169 CACCATAAAAATCTCCATGCAACAAC 59.909 38.462 0.00 0.00 0.00 3.32
249 251 6.014327 ACCATAAAAATCTCCATGCAACAACT 60.014 34.615 0.00 0.00 0.00 3.16
250 252 7.178274 ACCATAAAAATCTCCATGCAACAACTA 59.822 33.333 0.00 0.00 0.00 2.24
251 253 7.489113 CCATAAAAATCTCCATGCAACAACTAC 59.511 37.037 0.00 0.00 0.00 2.73
252 254 4.685169 AAATCTCCATGCAACAACTACG 57.315 40.909 0.00 0.00 0.00 3.51
253 255 2.831685 TCTCCATGCAACAACTACGT 57.168 45.000 0.00 0.00 0.00 3.57
255 257 1.464608 CTCCATGCAACAACTACGTGG 59.535 52.381 0.00 0.00 41.06 4.94
258 260 2.292016 CCATGCAACAACTACGTGGAAA 59.708 45.455 5.70 0.00 42.07 3.13
259 261 3.554524 CATGCAACAACTACGTGGAAAG 58.445 45.455 5.70 0.00 0.00 2.62
260 262 2.907634 TGCAACAACTACGTGGAAAGA 58.092 42.857 5.70 0.00 0.00 2.52
262 264 2.032290 GCAACAACTACGTGGAAAGACC 60.032 50.000 5.70 0.00 39.54 3.85
263 265 2.538512 ACAACTACGTGGAAAGACCC 57.461 50.000 5.70 0.00 38.00 4.46
271 273 0.178301 GTGGAAAGACCCCCGAGATC 59.822 60.000 0.00 0.00 38.00 2.75
280 282 0.036765 CCCCCGAGATCACAAAACGA 60.037 55.000 0.00 0.00 0.00 3.85
305 307 2.302260 TCTTCCCATGTTTGTTTCGCA 58.698 42.857 0.00 0.00 0.00 5.10
331 348 3.354089 AACAAGCCAAGAAACACATCG 57.646 42.857 0.00 0.00 0.00 3.84
340 357 2.356135 AGAAACACATCGCCACATACC 58.644 47.619 0.00 0.00 0.00 2.73
341 358 2.080693 GAAACACATCGCCACATACCA 58.919 47.619 0.00 0.00 0.00 3.25
342 359 1.448985 AACACATCGCCACATACCAC 58.551 50.000 0.00 0.00 0.00 4.16
343 360 0.323302 ACACATCGCCACATACCACA 59.677 50.000 0.00 0.00 0.00 4.17
344 361 1.065491 ACACATCGCCACATACCACAT 60.065 47.619 0.00 0.00 0.00 3.21
345 362 2.016318 CACATCGCCACATACCACATT 58.984 47.619 0.00 0.00 0.00 2.71
346 363 2.032054 CACATCGCCACATACCACATTC 59.968 50.000 0.00 0.00 0.00 2.67
347 364 2.287769 CATCGCCACATACCACATTCA 58.712 47.619 0.00 0.00 0.00 2.57
352 369 3.304190 CGCCACATACCACATTCATCATG 60.304 47.826 0.00 0.00 39.07 3.07
382 403 4.141344 ACCTAGAACAGAGGCTAGTCTAGG 60.141 50.000 25.75 25.75 46.35 3.02
411 433 9.323985 CAGAGGAGATAATAAGAAAGGAAACAG 57.676 37.037 0.00 0.00 0.00 3.16
417 439 5.613358 AATAAGAAAGGAAACAGACGCAG 57.387 39.130 0.00 0.00 0.00 5.18
683 707 3.791586 GCAGGCAGACCCTCCTCC 61.792 72.222 0.00 0.00 44.09 4.30
684 708 2.040278 CAGGCAGACCCTCCTCCT 59.960 66.667 0.00 0.00 44.09 3.69
686 710 2.766229 GGCAGACCCTCCTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
688 712 2.041405 CAGACCCTCCTCCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
804 835 9.778993 GTTTAGTTTATCCTTTTCGTTTATCCC 57.221 33.333 0.00 0.00 0.00 3.85
805 836 9.743581 TTTAGTTTATCCTTTTCGTTTATCCCT 57.256 29.630 0.00 0.00 0.00 4.20
807 838 8.645814 AGTTTATCCTTTTCGTTTATCCCTTT 57.354 30.769 0.00 0.00 0.00 3.11
808 839 8.520351 AGTTTATCCTTTTCGTTTATCCCTTTG 58.480 33.333 0.00 0.00 0.00 2.77
809 840 8.517056 GTTTATCCTTTTCGTTTATCCCTTTGA 58.483 33.333 0.00 0.00 0.00 2.69
859 890 3.039526 AGGGGGAGGAGGAGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
861 892 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
862 893 2.123033 GGGAGGAGGAGGAGGAGC 60.123 72.222 0.00 0.00 0.00 4.70
863 894 2.693017 GGAGGAGGAGGAGGAGCA 59.307 66.667 0.00 0.00 0.00 4.26
864 895 1.002274 GGAGGAGGAGGAGGAGCAA 59.998 63.158 0.00 0.00 0.00 3.91
865 896 1.334384 GGAGGAGGAGGAGGAGCAAC 61.334 65.000 0.00 0.00 0.00 4.17
866 897 1.306568 AGGAGGAGGAGGAGCAACC 60.307 63.158 0.00 0.00 39.35 3.77
867 898 2.726351 GGAGGAGGAGGAGCAACCG 61.726 68.421 0.00 0.00 44.74 4.44
885 925 0.814010 CGGGGAGTAAATTCGCAGGG 60.814 60.000 0.00 0.00 0.00 4.45
897 937 3.151022 GCAGGGAGAGACGAGGGG 61.151 72.222 0.00 0.00 0.00 4.79
899 939 2.055042 CAGGGAGAGACGAGGGGTG 61.055 68.421 0.00 0.00 0.00 4.61
913 953 2.421739 GGTGCGGCGTGGATAGAT 59.578 61.111 9.37 0.00 0.00 1.98
914 954 1.663739 GGTGCGGCGTGGATAGATA 59.336 57.895 9.37 0.00 0.00 1.98
915 955 0.388649 GGTGCGGCGTGGATAGATAG 60.389 60.000 9.37 0.00 0.00 2.08
916 956 0.596577 GTGCGGCGTGGATAGATAGA 59.403 55.000 9.37 0.00 0.00 1.98
917 957 1.202582 GTGCGGCGTGGATAGATAGAT 59.797 52.381 9.37 0.00 0.00 1.98
918 958 2.422479 GTGCGGCGTGGATAGATAGATA 59.578 50.000 9.37 0.00 0.00 1.98
919 959 2.683362 TGCGGCGTGGATAGATAGATAG 59.317 50.000 9.37 0.00 0.00 2.08
920 960 2.943690 GCGGCGTGGATAGATAGATAGA 59.056 50.000 9.37 0.00 0.00 1.98
995 1061 2.110006 GCCATTCTCGGGAGGAGC 59.890 66.667 0.00 0.00 42.82 4.70
997 1063 2.419198 CATTCTCGGGAGGAGCCG 59.581 66.667 0.00 0.00 42.82 5.52
1277 1343 2.679342 GGTACCCCCAGATGCTGCA 61.679 63.158 4.13 4.13 0.00 4.41
1347 1413 4.934797 AGATTGGATTTGGAAGGTGAGA 57.065 40.909 0.00 0.00 0.00 3.27
1480 1547 1.064060 GGCGATTTCTCGTTGGATTGG 59.936 52.381 0.00 0.00 46.71 3.16
1646 1726 5.515797 TCCTGTAAGTCTTATCACCATCG 57.484 43.478 0.00 0.00 0.00 3.84
1657 1737 2.947448 TCACCATCGTCATCTCAGTG 57.053 50.000 0.00 0.00 0.00 3.66
1658 1738 1.134995 TCACCATCGTCATCTCAGTGC 60.135 52.381 0.00 0.00 0.00 4.40
1688 1768 3.230743 CAAACCCTGCTAAAAATCCCG 57.769 47.619 0.00 0.00 0.00 5.14
1737 1828 0.540597 AGGAAGGCAAAGCTTGGGTC 60.541 55.000 0.00 0.00 0.00 4.46
1776 1867 3.589654 TTGCCTGTCCCTCGCTTCG 62.590 63.158 0.00 0.00 0.00 3.79
1806 1897 2.365635 ACCTATGTGCCGCTCCCT 60.366 61.111 0.00 0.00 0.00 4.20
1838 1929 2.570752 AGGTCAGTGAGTGATGCATCTT 59.429 45.455 26.32 15.16 37.56 2.40
1843 1934 6.047870 GTCAGTGAGTGATGCATCTTATCTT 58.952 40.000 26.32 11.45 37.56 2.40
1846 1937 8.087136 TCAGTGAGTGATGCATCTTATCTTATC 58.913 37.037 26.32 12.70 0.00 1.75
1862 1959 3.318275 TCTTATCACAGACCTCCGCATAC 59.682 47.826 0.00 0.00 0.00 2.39
1863 1960 1.485124 ATCACAGACCTCCGCATACA 58.515 50.000 0.00 0.00 0.00 2.29
1864 1961 0.530744 TCACAGACCTCCGCATACAC 59.469 55.000 0.00 0.00 0.00 2.90
1865 1962 0.802222 CACAGACCTCCGCATACACG 60.802 60.000 0.00 0.00 0.00 4.49
1882 1987 0.953960 ACGCATCGTTGAAGGGTTCC 60.954 55.000 0.00 0.00 36.35 3.62
1941 2047 0.465460 TGACAGGTGGTTGAGGCAAC 60.465 55.000 1.82 1.82 42.89 4.17
2122 2228 1.142748 CGACCTCATCCTGAGCACC 59.857 63.158 0.00 0.00 42.98 5.01
2290 6352 6.381994 ACCAGATCTCATTTTTGGTATGCATT 59.618 34.615 3.54 0.00 40.21 3.56
2492 6554 4.764172 AGGTAGTGATCAGCTCAATGTTC 58.236 43.478 0.00 0.00 35.07 3.18
2508 6570 7.571428 GCTCAATGTTCTCACTTACTAAACCAC 60.571 40.741 0.00 0.00 0.00 4.16
2516 6578 2.714793 ACTTACTAAACCACTTGCCCCT 59.285 45.455 0.00 0.00 0.00 4.79
3131 7220 4.013050 GAGAGCTCTATTGCCCTGTTTTT 58.987 43.478 18.25 0.00 0.00 1.94
3529 7620 9.252962 CTTTACCATTTGATTTGGAGCATAATC 57.747 33.333 0.00 0.00 37.69 1.75
3576 7667 1.974236 GAGTAGCACTGATGGCCCTAT 59.026 52.381 0.00 0.00 0.00 2.57
3637 7728 6.368791 TGTTGAATACTGTAGTGCAATCTGAC 59.631 38.462 0.00 0.00 0.00 3.51
3712 7804 2.289945 ACAGAAACTGAGATCCACCTGC 60.290 50.000 5.76 0.00 35.18 4.85
3743 7835 0.250234 TGCCATCTCTGTGCACCTAC 59.750 55.000 15.69 0.00 0.00 3.18
3750 7842 3.708451 TCTCTGTGCACCTACCTTCATA 58.292 45.455 15.69 0.00 0.00 2.15
3797 7889 4.194640 GCTAATGCCAAATCTGACTGAGA 58.805 43.478 0.00 0.00 34.25 3.27
3800 7892 6.183360 GCTAATGCCAAATCTGACTGAGAAAT 60.183 38.462 0.00 0.00 33.12 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.068474 CGTAAGGAACTGGCACTTCG 58.932 55.000 1.60 0.00 40.86 3.79
25 26 1.546476 CTCTCGTAAGGAACTGGCACT 59.454 52.381 0.00 0.00 40.86 4.40
26 27 1.404315 CCTCTCGTAAGGAACTGGCAC 60.404 57.143 0.19 0.00 40.86 5.01
27 28 0.895530 CCTCTCGTAAGGAACTGGCA 59.104 55.000 0.19 0.00 40.86 4.92
28 29 1.183549 TCCTCTCGTAAGGAACTGGC 58.816 55.000 6.14 0.00 42.56 4.85
44 45 4.321974 GGAATTTCTTTCGTGGCAAATCCT 60.322 41.667 0.00 0.00 34.98 3.24
66 67 1.298413 CATGACTCGGTCGCTACGG 60.298 63.158 0.00 0.00 34.95 4.02
67 68 0.098200 TTCATGACTCGGTCGCTACG 59.902 55.000 0.00 0.00 34.95 3.51
229 231 5.009610 ACGTAGTTGTTGCATGGAGATTTTT 59.990 36.000 0.00 0.00 37.78 1.94
231 233 4.072131 ACGTAGTTGTTGCATGGAGATTT 58.928 39.130 0.00 0.00 37.78 2.17
233 235 3.002791 CACGTAGTTGTTGCATGGAGAT 58.997 45.455 0.00 0.00 41.61 2.75
241 243 2.032290 GGTCTTTCCACGTAGTTGTTGC 60.032 50.000 0.00 0.00 41.61 4.17
244 246 1.071228 GGGGTCTTTCCACGTAGTTGT 59.929 52.381 0.00 0.00 41.61 3.32
245 247 1.609841 GGGGGTCTTTCCACGTAGTTG 60.610 57.143 0.00 0.00 41.61 3.16
246 248 0.689055 GGGGGTCTTTCCACGTAGTT 59.311 55.000 0.00 0.00 41.61 2.24
252 254 0.178301 GATCTCGGGGGTCTTTCCAC 59.822 60.000 0.00 0.00 39.32 4.02
253 255 0.252513 TGATCTCGGGGGTCTTTCCA 60.253 55.000 0.00 0.00 38.11 3.53
255 257 0.902531 TGTGATCTCGGGGGTCTTTC 59.097 55.000 0.00 0.00 0.00 2.62
258 260 1.003233 GTTTTGTGATCTCGGGGGTCT 59.997 52.381 0.00 0.00 0.00 3.85
259 261 1.450025 GTTTTGTGATCTCGGGGGTC 58.550 55.000 0.00 0.00 0.00 4.46
260 262 0.321298 CGTTTTGTGATCTCGGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
262 264 1.665679 CATCGTTTTGTGATCTCGGGG 59.334 52.381 0.00 0.00 0.00 5.73
263 265 2.346803 ACATCGTTTTGTGATCTCGGG 58.653 47.619 0.00 0.00 0.00 5.14
271 273 4.300189 TGGGAAGAAACATCGTTTTGTG 57.700 40.909 0.00 0.00 0.00 3.33
280 282 5.288804 CGAAACAAACATGGGAAGAAACAT 58.711 37.500 0.00 0.00 0.00 2.71
305 307 3.684305 GTGTTTCTTGGCTTGTTTGCTTT 59.316 39.130 0.00 0.00 0.00 3.51
313 315 1.666888 GGCGATGTGTTTCTTGGCTTG 60.667 52.381 0.00 0.00 0.00 4.01
331 348 4.233123 CATGATGAATGTGGTATGTGGC 57.767 45.455 0.00 0.00 0.00 5.01
342 359 9.599866 TGTTCTAGGTTAGTAACATGATGAATG 57.400 33.333 14.81 0.00 42.48 2.67
343 360 9.823647 CTGTTCTAGGTTAGTAACATGATGAAT 57.176 33.333 14.81 0.00 31.88 2.57
344 361 9.031537 TCTGTTCTAGGTTAGTAACATGATGAA 57.968 33.333 14.81 10.66 31.88 2.57
345 362 8.589701 TCTGTTCTAGGTTAGTAACATGATGA 57.410 34.615 14.81 5.75 31.88 2.92
346 363 7.923344 CCTCTGTTCTAGGTTAGTAACATGATG 59.077 40.741 14.81 0.00 31.88 3.07
347 364 7.418025 GCCTCTGTTCTAGGTTAGTAACATGAT 60.418 40.741 14.81 0.00 36.43 2.45
352 369 5.918426 AGCCTCTGTTCTAGGTTAGTAAC 57.082 43.478 4.32 4.32 36.43 2.50
382 403 7.296628 TCCTTTCTTATTATCTCCTCTGCTC 57.703 40.000 0.00 0.00 0.00 4.26
448 470 2.954753 CTTTGCGGCCACGACACTC 61.955 63.158 2.24 0.00 44.60 3.51
476 498 2.158696 TGTTTTTGGCATTTTCCTGGGG 60.159 45.455 0.00 0.00 0.00 4.96
667 691 2.040278 AGGAGGAGGGTCTGCCTG 59.960 66.667 0.00 0.00 33.84 4.85
778 809 9.778993 GGGATAAACGAAAAGGATAAACTAAAC 57.221 33.333 0.00 0.00 0.00 2.01
779 810 9.743581 AGGGATAAACGAAAAGGATAAACTAAA 57.256 29.630 0.00 0.00 0.00 1.85
780 811 9.743581 AAGGGATAAACGAAAAGGATAAACTAA 57.256 29.630 0.00 0.00 0.00 2.24
781 812 9.743581 AAAGGGATAAACGAAAAGGATAAACTA 57.256 29.630 0.00 0.00 0.00 2.24
782 813 8.520351 CAAAGGGATAAACGAAAAGGATAAACT 58.480 33.333 0.00 0.00 0.00 2.66
800 831 3.931907 TGATCCGTCAATCAAAGGGAT 57.068 42.857 0.00 0.00 42.53 3.85
801 832 3.263170 TCTTGATCCGTCAATCAAAGGGA 59.737 43.478 6.58 0.00 43.22 4.20
802 833 3.609853 TCTTGATCCGTCAATCAAAGGG 58.390 45.455 6.58 0.00 43.22 3.95
804 835 4.436050 CGGTTCTTGATCCGTCAATCAAAG 60.436 45.833 10.87 0.00 43.22 2.77
805 836 3.435327 CGGTTCTTGATCCGTCAATCAAA 59.565 43.478 10.87 0.00 43.22 2.69
807 838 2.616960 CGGTTCTTGATCCGTCAATCA 58.383 47.619 10.87 0.00 43.08 2.57
808 839 1.933853 CCGGTTCTTGATCCGTCAATC 59.066 52.381 15.98 0.00 43.08 2.67
809 840 1.406887 CCCGGTTCTTGATCCGTCAAT 60.407 52.381 15.98 0.00 43.08 2.57
826 857 2.143419 CCTCCAATCTCCCTCCCCG 61.143 68.421 0.00 0.00 0.00 5.73
859 890 2.014857 GAATTTACTCCCCGGTTGCTC 58.985 52.381 0.00 0.00 0.00 4.26
861 892 0.730840 CGAATTTACTCCCCGGTTGC 59.269 55.000 0.00 0.00 0.00 4.17
862 893 0.730840 GCGAATTTACTCCCCGGTTG 59.269 55.000 0.00 0.00 0.00 3.77
863 894 0.325602 TGCGAATTTACTCCCCGGTT 59.674 50.000 0.00 0.00 0.00 4.44
864 895 0.107848 CTGCGAATTTACTCCCCGGT 60.108 55.000 0.00 0.00 0.00 5.28
865 896 0.814010 CCTGCGAATTTACTCCCCGG 60.814 60.000 0.00 0.00 0.00 5.73
866 897 0.814010 CCCTGCGAATTTACTCCCCG 60.814 60.000 0.00 0.00 0.00 5.73
867 898 0.544697 TCCCTGCGAATTTACTCCCC 59.455 55.000 0.00 0.00 0.00 4.81
885 925 3.827898 CCGCACCCCTCGTCTCTC 61.828 72.222 0.00 0.00 0.00 3.20
897 937 0.596577 TCTATCTATCCACGCCGCAC 59.403 55.000 0.00 0.00 0.00 5.34
899 939 2.943690 TCTATCTATCTATCCACGCCGC 59.056 50.000 0.00 0.00 0.00 6.53
919 959 8.952979 CGATGCGAACTGATTTATCTATCTATC 58.047 37.037 0.00 0.00 0.00 2.08
920 960 7.918033 CCGATGCGAACTGATTTATCTATCTAT 59.082 37.037 0.00 0.00 0.00 1.98
1324 1390 5.586643 GTCTCACCTTCCAAATCCAATCTAC 59.413 44.000 0.00 0.00 0.00 2.59
1447 1513 0.108329 AATCGCCACTAGAACGGGTG 60.108 55.000 0.00 0.00 0.00 4.61
1607 1684 1.574339 AGGAAGGGGATAGACGGAGAA 59.426 52.381 0.00 0.00 0.00 2.87
1657 1737 0.032540 CAGGGTTTGCTTCAGTTGGC 59.967 55.000 0.00 0.00 0.00 4.52
1683 1763 4.507335 CCAATTCCTCCATGATTACGGGAT 60.507 45.833 0.00 0.00 0.00 3.85
1688 1768 6.603201 TGAGAAACCAATTCCTCCATGATTAC 59.397 38.462 0.00 0.00 38.94 1.89
1776 1867 3.244044 GCACATAGGTCTCCTCCATCTTC 60.244 52.174 0.00 0.00 34.61 2.87
1838 1929 3.562182 TGCGGAGGTCTGTGATAAGATA 58.438 45.455 0.00 0.00 0.00 1.98
1843 1934 2.361119 GTGTATGCGGAGGTCTGTGATA 59.639 50.000 0.00 0.00 0.00 2.15
1846 1937 0.802222 CGTGTATGCGGAGGTCTGTG 60.802 60.000 0.00 0.00 0.00 3.66
1862 1959 0.165944 GAACCCTTCAACGATGCGTG 59.834 55.000 0.00 0.00 39.99 5.34
1863 1960 0.953960 GGAACCCTTCAACGATGCGT 60.954 55.000 0.00 0.00 43.97 5.24
1864 1961 1.794222 GGAACCCTTCAACGATGCG 59.206 57.895 0.00 0.00 0.00 4.73
1865 1962 0.953960 ACGGAACCCTTCAACGATGC 60.954 55.000 0.00 0.00 0.00 3.91
1882 1987 9.483062 GATTAATTGAGATGAAACTGAAAGACG 57.517 33.333 0.00 0.00 37.43 4.18
1941 2047 1.160137 CCTTCCCTCAAACGCAGAAG 58.840 55.000 0.00 0.00 34.94 2.85
2122 2228 7.921214 TCTGATTTAACTCTCATACCTTTAGCG 59.079 37.037 0.00 0.00 0.00 4.26
2290 6352 5.507149 GCCGCCAAATTATACACATTGATCA 60.507 40.000 0.00 0.00 0.00 2.92
2492 6554 3.751698 GGGCAAGTGGTTTAGTAAGTGAG 59.248 47.826 0.00 0.00 0.00 3.51
2508 6570 2.514458 ACCATTTAGTGAGGGGCAAG 57.486 50.000 0.00 0.00 0.00 4.01
2516 6578 6.943146 TGCATTTACAGGTTACCATTTAGTGA 59.057 34.615 3.51 0.00 0.00 3.41
3131 7220 7.066525 GGAAACTGAATATGGAACCGAAATACA 59.933 37.037 0.00 0.00 0.00 2.29
3539 7630 5.418209 TGCTACTCTTAGTTCTCACTAACCC 59.582 44.000 0.00 0.00 40.06 4.11
3576 7667 0.106167 ACGGGTCTAGCAGGCTGATA 60.106 55.000 20.86 16.40 0.00 2.15
3712 7804 0.464373 AGATGGCAATGTAGGTGGCG 60.464 55.000 0.00 0.00 44.15 5.69
3743 7835 5.047802 ACAAAATGGTGCTTGACTATGAAGG 60.048 40.000 0.00 0.00 0.00 3.46
3750 7842 1.608590 CCGACAAAATGGTGCTTGACT 59.391 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.