Multiple sequence alignment - TraesCS2B01G079300

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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 TraesCS2B01G079300 chr2B 100.000 3109 0 0 1 3109 44312682 44309574 0.000000e+00 5742.0
1 TraesCS2B01G079300 chr2B 93.300 806 37 10 2310 3109 55696186 55695392 0.000000e+00 1173.0
2 TraesCS2B01G079300 chr2B 89.689 708 47 11 1321 2027 44286476 44285794 0.000000e+00 880.0
3 TraesCS2B01G079300 chr2B 90.123 567 32 8 1463 2027 44274404 44273860 0.000000e+00 715.0
4 TraesCS2B01G079300 chr2B 93.263 475 29 1 1463 1937 44191724 44191253 0.000000e+00 697.0
5 TraesCS2B01G079300 chr2B 82.536 836 84 36 2043 2836 109776748 109777563 0.000000e+00 678.0
6 TraesCS2B01G079300 chr2B 89.851 404 21 8 843 1231 44192174 44191776 4.630000e-138 501.0
7 TraesCS2B01G079300 chr2B 89.851 404 21 8 843 1231 44274854 44274456 4.630000e-138 501.0
8 TraesCS2B01G079300 chr2B 79.821 783 74 38 2099 2836 109069928 109070671 7.750000e-136 494.0
9 TraesCS2B01G079300 chr2B 83.603 433 44 14 851 1267 44287127 44286706 6.290000e-102 381.0
10 TraesCS2B01G079300 chr2B 90.385 52 5 0 733 784 605993347 605993398 5.560000e-08 69.4
11 TraesCS2B01G079300 chr2D 95.587 1201 45 4 843 2042 27884370 27883177 0.000000e+00 1917.0
12 TraesCS2B01G079300 chr2D 90.113 708 48 10 1321 2027 27860486 27859800 0.000000e+00 900.0
13 TraesCS2B01G079300 chr2D 94.872 468 21 1 1463 1930 27853945 27853481 0.000000e+00 728.0
14 TraesCS2B01G079300 chr2D 89.500 400 22 11 843 1224 27854401 27854004 3.600000e-134 488.0
15 TraesCS2B01G079300 chr2D 82.511 446 49 17 843 1271 27861147 27860714 6.340000e-97 364.0
16 TraesCS2B01G079300 chr2D 78.360 439 81 10 2666 3093 142715941 142715506 3.950000e-69 272.0
17 TraesCS2B01G079300 chr2D 83.406 229 28 9 623 847 27884673 27884451 1.460000e-48 204.0
18 TraesCS2B01G079300 chr2D 97.059 34 1 0 2780 2813 59143370 59143337 1.200000e-04 58.4
19 TraesCS2B01G079300 chr2A 95.017 1204 53 7 843 2042 30072924 30071724 0.000000e+00 1884.0
20 TraesCS2B01G079300 chr2A 90.960 708 42 10 1321 2027 30048630 30047944 0.000000e+00 933.0
21 TraesCS2B01G079300 chr2A 90.813 566 30 7 1463 2027 30021219 30020675 0.000000e+00 737.0
22 TraesCS2B01G079300 chr2A 81.137 721 128 5 132 847 30022478 30021761 3.480000e-159 571.0
23 TraesCS2B01G079300 chr2A 89.801 402 23 6 843 1231 30021667 30021271 1.660000e-137 499.0
24 TraesCS2B01G079300 chr2A 83.710 442 45 14 843 1267 30049291 30048860 2.910000e-105 392.0
25 TraesCS2B01G079300 chr2A 82.533 229 29 9 623 847 30073225 30073004 1.140000e-44 191.0
26 TraesCS2B01G079300 chr3D 83.490 1066 85 41 2065 3109 609285402 609284407 0.000000e+00 909.0
27 TraesCS2B01G079300 chrUn 85.290 809 64 21 2066 2865 34348994 34349756 0.000000e+00 784.0
28 TraesCS2B01G079300 chr4B 83.625 800 96 20 2046 2836 613087456 613086683 0.000000e+00 719.0
29 TraesCS2B01G079300 chr5B 81.774 823 96 24 2046 2836 598437491 598436691 9.400000e-180 640.0
30 TraesCS2B01G079300 chr5B 79.348 92 19 0 2049 2140 477354164 477354073 7.200000e-07 65.8
31 TraesCS2B01G079300 chr7B 78.828 836 101 35 2043 2836 653881137 653880336 7.750000e-136 494.0
32 TraesCS2B01G079300 chr3A 80.612 490 68 16 2259 2746 740044962 740045426 1.370000e-93 353.0
33 TraesCS2B01G079300 chr3A 81.685 273 47 2 2086 2357 1586622 1586352 1.120000e-54 224.0
34 TraesCS2B01G079300 chr7D 75.379 528 111 13 9 519 118868989 118868464 1.440000e-58 237.0
35 TraesCS2B01G079300 chr7D 100.000 28 0 0 518 545 419383555 419383582 6.000000e-03 52.8
36 TraesCS2B01G079300 chr1D 73.438 512 112 14 27 519 447319216 447319722 1.480000e-38 171.0
37 TraesCS2B01G079300 chr1D 91.837 49 3 1 518 565 481614739 481614787 2.000000e-07 67.6
38 TraesCS2B01G079300 chr1D 88.462 52 6 0 733 784 450923826 450923877 2.590000e-06 63.9
39 TraesCS2B01G079300 chr6B 87.640 89 7 3 701 788 717707761 717707846 1.970000e-17 100.0
40 TraesCS2B01G079300 chr6B 90.385 52 5 0 733 784 600190950 600191001 5.560000e-08 69.4
41 TraesCS2B01G079300 chr6B 90.385 52 5 0 733 784 600204669 600204720 5.560000e-08 69.4
42 TraesCS2B01G079300 chr1B 100.000 33 0 0 518 550 670210817 670210849 9.310000e-06 62.1
43 TraesCS2B01G079300 chr5D 89.362 47 5 0 2092 2138 302878591 302878637 3.350000e-05 60.2
44 TraesCS2B01G079300 chr1A 90.698 43 4 0 518 560 539902319 539902277 1.200000e-04 58.4
45 TraesCS2B01G079300 chr6A 100.000 30 0 0 520 549 209903522 209903493 4.330000e-04 56.5


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 TraesCS2B01G079300 chr2B 44309574 44312682 3108 True 5742.000000 5742 100.000000 1 3109 1 chr2B.!!$R1 3108
1 TraesCS2B01G079300 chr2B 55695392 55696186 794 True 1173.000000 1173 93.300000 2310 3109 1 chr2B.!!$R2 799
2 TraesCS2B01G079300 chr2B 109776748 109777563 815 False 678.000000 678 82.536000 2043 2836 1 chr2B.!!$F2 793
3 TraesCS2B01G079300 chr2B 44285794 44287127 1333 True 630.500000 880 86.646000 851 2027 2 chr2B.!!$R5 1176
4 TraesCS2B01G079300 chr2B 44273860 44274854 994 True 608.000000 715 89.987000 843 2027 2 chr2B.!!$R4 1184
5 TraesCS2B01G079300 chr2B 44191253 44192174 921 True 599.000000 697 91.557000 843 1937 2 chr2B.!!$R3 1094
6 TraesCS2B01G079300 chr2B 109069928 109070671 743 False 494.000000 494 79.821000 2099 2836 1 chr2B.!!$F1 737
7 TraesCS2B01G079300 chr2D 27883177 27884673 1496 True 1060.500000 1917 89.496500 623 2042 2 chr2D.!!$R5 1419
8 TraesCS2B01G079300 chr2D 27859800 27861147 1347 True 632.000000 900 86.312000 843 2027 2 chr2D.!!$R4 1184
9 TraesCS2B01G079300 chr2D 27853481 27854401 920 True 608.000000 728 92.186000 843 1930 2 chr2D.!!$R3 1087
10 TraesCS2B01G079300 chr2A 30071724 30073225 1501 True 1037.500000 1884 88.775000 623 2042 2 chr2A.!!$R3 1419
11 TraesCS2B01G079300 chr2A 30047944 30049291 1347 True 662.500000 933 87.335000 843 2027 2 chr2A.!!$R2 1184
12 TraesCS2B01G079300 chr2A 30020675 30022478 1803 True 602.333333 737 87.250333 132 2027 3 chr2A.!!$R1 1895
13 TraesCS2B01G079300 chr3D 609284407 609285402 995 True 909.000000 909 83.490000 2065 3109 1 chr3D.!!$R1 1044
14 TraesCS2B01G079300 chrUn 34348994 34349756 762 False 784.000000 784 85.290000 2066 2865 1 chrUn.!!$F1 799
15 TraesCS2B01G079300 chr4B 613086683 613087456 773 True 719.000000 719 83.625000 2046 2836 1 chr4B.!!$R1 790
16 TraesCS2B01G079300 chr5B 598436691 598437491 800 True 640.000000 640 81.774000 2046 2836 1 chr5B.!!$R2 790
17 TraesCS2B01G079300 chr7B 653880336 653881137 801 True 494.000000 494 78.828000 2043 2836 1 chr7B.!!$R1 793
18 TraesCS2B01G079300 chr7D 118868464 118868989 525 True 237.000000 237 75.379000 9 519 1 chr7D.!!$R1 510

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
434 452 0.040067 CTTGAAGAAAAAGCGCCGCT 60.040 50.0 5.39 5.39 42.56 5.52 F
873 992 0.107703 ACACAATGCATCCGACGGAT 60.108 50.0 23.78 23.78 44.21 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1809 0.331278 CCCTCAATTGGCCACACCTA 59.669 55.0 3.88 0.0 40.22 3.08 R
2415 2852 0.389025 CCTGCCCAGTTGTGTTTTCC 59.611 55.0 0.00 0.0 0.00 3.13 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
61 62 8.779354 ATCTATTATAAAGATTCACCGGAAGC 57.221 34.615 9.46 0.00 39.70 3.86
63 64 6.867662 ATTATAAAGATTCACCGGAAGCAG 57.132 37.500 9.46 0.00 41.82 4.24
67 68 3.356529 AGATTCACCGGAAGCAGAAAT 57.643 42.857 9.46 0.00 41.82 2.17
77 78 3.365364 CGGAAGCAGAAATCACCTCAAAC 60.365 47.826 0.00 0.00 0.00 2.93
80 81 5.279156 GGAAGCAGAAATCACCTCAAACATT 60.279 40.000 0.00 0.00 0.00 2.71
151 154 2.048597 CGAGCCGCTAACACACCA 60.049 61.111 0.00 0.00 0.00 4.17
156 159 0.596082 GCCGCTAACACACCATTGTT 59.404 50.000 0.00 0.00 42.46 2.83
157 160 1.401018 GCCGCTAACACACCATTGTTC 60.401 52.381 0.00 0.00 40.29 3.18
180 183 1.229177 TCCCACACTGGAGCTAGCA 60.229 57.895 18.83 0.00 40.96 3.49
196 199 2.996249 AGCATGACCTTGTCGATGAT 57.004 45.000 0.00 2.88 34.95 2.45
199 202 2.478134 GCATGACCTTGTCGATGATAGC 59.522 50.000 0.00 0.00 34.95 2.97
203 206 2.101582 GACCTTGTCGATGATAGCCAGT 59.898 50.000 0.00 0.00 0.00 4.00
204 207 2.159043 ACCTTGTCGATGATAGCCAGTG 60.159 50.000 0.00 0.00 0.00 3.66
218 221 1.879372 GCCAGTGAGTCTTCATGCACA 60.879 52.381 0.00 0.00 35.39 4.57
223 226 1.003928 TGAGTCTTCATGCACATGCCT 59.996 47.619 5.73 0.00 41.18 4.75
231 234 2.440627 TCATGCACATGCCTCTAAGGAT 59.559 45.455 5.73 0.00 41.18 3.24
241 244 2.433970 GCCTCTAAGGATCAGTGCTCTT 59.566 50.000 0.00 0.00 37.67 2.85
243 246 3.456280 CTCTAAGGATCAGTGCTCTTGC 58.544 50.000 0.00 0.00 40.20 4.01
283 288 4.599047 ATCCCTGAATCGATCTGAAGAC 57.401 45.455 0.00 0.00 0.00 3.01
284 289 2.695666 TCCCTGAATCGATCTGAAGACC 59.304 50.000 0.00 0.00 0.00 3.85
292 297 1.546029 CGATCTGAAGACCCTGACACA 59.454 52.381 0.00 0.00 0.00 3.72
297 302 4.792068 TCTGAAGACCCTGACACAAAATT 58.208 39.130 0.00 0.00 0.00 1.82
301 306 5.598005 TGAAGACCCTGACACAAAATTTCAT 59.402 36.000 0.00 0.00 0.00 2.57
305 310 5.988287 ACCCTGACACAAAATTTCATTGTT 58.012 33.333 0.00 0.00 38.90 2.83
308 313 5.332506 CCTGACACAAAATTTCATTGTTCGC 60.333 40.000 0.00 0.00 38.90 4.70
325 330 4.212425 TGTTCGCACACATAACGAGAAATT 59.788 37.500 0.00 0.00 37.11 1.82
333 338 7.360946 GCACACATAACGAGAAATTCTAACCTT 60.361 37.037 0.00 0.00 0.00 3.50
337 342 4.015872 ACGAGAAATTCTAACCTTGCCA 57.984 40.909 0.00 0.00 0.00 4.92
349 355 3.672295 CTTGCCACCCGAGGAGCTC 62.672 68.421 4.71 4.71 0.00 4.09
375 382 2.036098 TACGTCGGAGCTCCCCAA 59.964 61.111 27.20 10.11 0.00 4.12
377 384 0.974010 TACGTCGGAGCTCCCCAAAT 60.974 55.000 27.20 11.40 0.00 2.32
388 406 3.201045 AGCTCCCCAAATAGAGGAACTTC 59.799 47.826 0.00 0.00 41.55 3.01
391 409 5.760131 CTCCCCAAATAGAGGAACTTCAAT 58.240 41.667 0.00 0.00 41.55 2.57
417 435 5.163395 GGATCGGATCCTGAAAGACTAACTT 60.163 44.000 26.29 0.00 46.19 2.66
424 442 7.661847 GGATCCTGAAAGACTAACTTGAAGAAA 59.338 37.037 3.84 0.00 38.98 2.52
434 452 0.040067 CTTGAAGAAAAAGCGCCGCT 60.040 50.000 5.39 5.39 42.56 5.52
446 464 2.499685 GCCGCTATCCGTCCAAGT 59.500 61.111 0.00 0.00 34.38 3.16
448 466 1.515954 CCGCTATCCGTCCAAGTGT 59.484 57.895 0.00 0.00 34.38 3.55
450 468 0.172578 CGCTATCCGTCCAAGTGTCA 59.827 55.000 0.00 0.00 0.00 3.58
456 474 1.004918 CGTCCAAGTGTCACCCCTC 60.005 63.158 0.00 0.00 0.00 4.30
464 482 0.832135 GTGTCACCCCTCTGAGGACA 60.832 60.000 25.18 17.29 37.67 4.02
493 511 1.249407 CCCATCTACTAGCCGGAGAC 58.751 60.000 5.05 0.00 0.00 3.36
537 555 0.394899 CAGAGGGGAGGCAAATCCAC 60.395 60.000 4.47 0.46 43.73 4.02
544 562 1.372087 GAGGCAAATCCACAGGCTCG 61.372 60.000 0.00 0.00 43.53 5.03
546 564 3.056313 GCAAATCCACAGGCTCGCC 62.056 63.158 0.00 0.00 0.00 5.54
560 578 4.778415 CGCCGGCGGATATCGAGG 62.778 72.222 40.50 8.79 42.43 4.63
563 581 2.675423 CGGCGGATATCGAGGGGA 60.675 66.667 0.00 0.00 42.43 4.81
567 585 0.898789 GCGGATATCGAGGGGAGGAA 60.899 60.000 0.00 0.00 42.43 3.36
585 603 2.365582 GAAAGCTTTCCCTAATCGCCA 58.634 47.619 25.80 0.00 0.00 5.69
611 629 4.924462 CGAGAGGGAAAGAACTTGTTCTAC 59.076 45.833 15.28 12.26 0.00 2.59
612 630 5.230323 AGAGGGAAAGAACTTGTTCTACC 57.770 43.478 15.28 18.51 0.00 3.18
632 650 2.093658 CCTGTGGACGGTTACTATGCTT 60.094 50.000 0.00 0.00 0.00 3.91
692 710 7.499438 TTTTGAGAAACATTGTACAAACGTG 57.501 32.000 13.23 9.20 0.00 4.49
695 713 5.529430 TGAGAAACATTGTACAAACGTGGAT 59.471 36.000 13.23 3.87 0.00 3.41
705 723 5.407084 TGTACAAACGTGGATGTTCACATAG 59.593 40.000 7.14 0.00 36.57 2.23
706 724 3.751175 ACAAACGTGGATGTTCACATAGG 59.249 43.478 0.00 0.00 36.57 2.57
708 726 1.277842 ACGTGGATGTTCACATAGGCA 59.722 47.619 0.00 0.00 36.57 4.75
717 735 4.842574 TGTTCACATAGGCACATGTACAT 58.157 39.130 1.41 1.41 37.02 2.29
720 738 5.294734 TCACATAGGCACATGTACATCAT 57.705 39.130 5.07 0.00 37.02 2.45
722 740 5.070847 TCACATAGGCACATGTACATCATCT 59.929 40.000 5.07 4.32 37.02 2.90
724 742 5.306419 ACATAGGCACATGTACATCATCTCT 59.694 40.000 5.07 3.31 37.37 3.10
787 807 1.067516 GAGAGAGTGAGCCAGCAGATC 59.932 57.143 0.00 0.00 0.00 2.75
792 812 4.478203 AGAGTGAGCCAGCAGATCTTATA 58.522 43.478 0.00 0.00 0.00 0.98
830 850 1.671379 GGCCGAACCACTCAAGTCC 60.671 63.158 0.00 0.00 38.86 3.85
839 859 1.065854 CCACTCAAGTCCCATCCTCAC 60.066 57.143 0.00 0.00 0.00 3.51
872 991 1.018752 CACACAATGCATCCGACGGA 61.019 55.000 20.85 20.85 35.55 4.69
873 992 0.107703 ACACAATGCATCCGACGGAT 60.108 50.000 23.78 23.78 44.21 4.18
952 1071 1.136305 CACCCCTACCACATCTGTACG 59.864 57.143 0.00 0.00 0.00 3.67
962 1081 3.423123 CCACATCTGTACGAAAGAAACGC 60.423 47.826 0.00 0.00 0.00 4.84
963 1082 3.428870 CACATCTGTACGAAAGAAACGCT 59.571 43.478 0.00 0.00 0.00 5.07
985 1117 4.713824 GCTATATATAGCGTGGTGACCA 57.286 45.455 25.05 0.00 45.30 4.02
1038 1172 5.317262 TCCTCCTCTCCTCCAGATAATACAT 59.683 44.000 0.00 0.00 0.00 2.29
1209 1358 4.877251 GGTATGTCGGGCACTAATTAAACA 59.123 41.667 0.00 0.00 0.00 2.83
1305 1454 6.183360 CCTCGAAATAGGACCCATATACTAGC 60.183 46.154 0.00 0.00 39.15 3.42
1473 1809 5.516996 CATCTGTGCGCATTCTATTCATTT 58.483 37.500 15.91 0.00 0.00 2.32
1532 1868 0.117541 TGTCTTACCTGCCACCCCTA 59.882 55.000 0.00 0.00 0.00 3.53
1577 1913 0.107361 TCGACTACCTGATCCGCTCA 60.107 55.000 0.00 0.00 0.00 4.26
1700 2036 1.078426 GCCTATGTTCGGGTGCACT 60.078 57.895 17.98 0.00 0.00 4.40
1820 2156 1.639298 GCGTCAGCTTCATCGCCTTT 61.639 55.000 9.44 0.00 42.33 3.11
1931 2281 3.763897 ACTTTTGTCCAAAACTCTGCTGT 59.236 39.130 1.18 0.00 35.57 4.40
1946 2296 1.613925 TGCTGTACGACTCTGCTTTCT 59.386 47.619 0.00 0.00 0.00 2.52
1976 2326 7.604164 CGGAGCATACCTTTTGTTCTATATGAT 59.396 37.037 0.00 0.00 0.00 2.45
2054 2404 5.715434 AGGTCTATATCTTCTTCTTCGGC 57.285 43.478 0.00 0.00 0.00 5.54
2097 2449 5.050126 TGGACGAGATCTGTCTATACCTT 57.950 43.478 18.57 0.00 36.58 3.50
2153 2505 0.452184 ACGTCGCGAAGATCTGTCAT 59.548 50.000 28.43 0.00 0.00 3.06
2166 2518 7.468494 CGAAGATCTGTCATGTTCTGAGTCTAT 60.468 40.741 0.00 0.00 33.51 1.98
2167 2519 7.658525 AGATCTGTCATGTTCTGAGTCTATT 57.341 36.000 0.00 0.00 33.51 1.73
2223 2624 4.306600 AGCACCGATCAAAAATCCAAAAC 58.693 39.130 0.00 0.00 0.00 2.43
2238 2639 5.895636 TCCAAAACATAGTGTGCCTATTG 57.104 39.130 0.00 0.00 33.96 1.90
2262 2663 1.374758 CGAACACAGGACCTCCAGC 60.375 63.158 0.00 0.00 38.89 4.85
2298 2699 5.278577 GCTAATAGCCACCAGAACCATCTG 61.279 50.000 0.00 0.00 43.13 2.90
2322 2723 7.669427 TGGATTTGCTGATATTTTTGAAGTGT 58.331 30.769 0.00 0.00 0.00 3.55
2327 2728 9.462174 TTTGCTGATATTTTTGAAGTGTAGTTG 57.538 29.630 0.00 0.00 0.00 3.16
2409 2846 2.028130 TCAAAATTGGTGCACGGACTT 58.972 42.857 11.45 0.00 0.00 3.01
2410 2847 2.034053 TCAAAATTGGTGCACGGACTTC 59.966 45.455 11.45 0.00 0.00 3.01
2411 2848 1.981256 AAATTGGTGCACGGACTTCT 58.019 45.000 11.45 0.00 0.00 2.85
2412 2849 1.981256 AATTGGTGCACGGACTTCTT 58.019 45.000 11.45 0.00 0.00 2.52
2413 2850 1.981256 ATTGGTGCACGGACTTCTTT 58.019 45.000 11.45 0.00 0.00 2.52
2414 2851 1.757682 TTGGTGCACGGACTTCTTTT 58.242 45.000 11.45 0.00 0.00 2.27
2415 2852 1.021202 TGGTGCACGGACTTCTTTTG 58.979 50.000 11.45 0.00 0.00 2.44
2432 2869 1.561643 TTGGAAAACACAACTGGGCA 58.438 45.000 0.00 0.00 0.00 5.36
2881 3366 6.874278 ATTTTCTAGGGCCTAAGCATTTTT 57.126 33.333 15.43 0.00 42.56 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.998051 AGATCTTGTCCTTTAGGCCAAAA 58.002 39.130 5.01 0.00 32.15 2.44
31 32 9.712305 CCGGTGAATCTTTATAATAGATCTTGT 57.288 33.333 0.00 0.00 31.28 3.16
35 36 8.874816 GCTTCCGGTGAATCTTTATAATAGATC 58.125 37.037 0.00 0.00 31.28 2.75
60 61 7.945033 TTTTAATGTTTGAGGTGATTTCTGC 57.055 32.000 0.00 0.00 0.00 4.26
115 118 1.746615 TCTTCGCAGAGGCAATGGC 60.747 57.895 0.00 0.00 41.24 4.40
122 125 2.202676 GGCTCGTCTTCGCAGAGG 60.203 66.667 0.00 0.00 38.43 3.69
129 132 0.388134 TGTGTTAGCGGCTCGTCTTC 60.388 55.000 5.39 0.00 0.00 2.87
151 154 2.233271 CAGTGTGGGAGCAAGAACAAT 58.767 47.619 0.00 0.00 0.00 2.71
156 159 4.311700 TCCAGTGTGGGAGCAAGA 57.688 55.556 0.00 0.00 38.32 3.02
178 181 2.478134 GCTATCATCGACAAGGTCATGC 59.522 50.000 0.00 0.00 32.09 4.06
180 183 2.700371 TGGCTATCATCGACAAGGTCAT 59.300 45.455 0.00 0.00 32.09 3.06
196 199 1.901833 TGCATGAAGACTCACTGGCTA 59.098 47.619 0.00 0.00 33.30 3.93
199 202 2.174363 TGTGCATGAAGACTCACTGG 57.826 50.000 0.00 0.00 33.30 4.00
203 206 1.003928 AGGCATGTGCATGAAGACTCA 59.996 47.619 15.53 0.00 44.36 3.41
204 207 1.669779 GAGGCATGTGCATGAAGACTC 59.330 52.381 15.53 11.72 44.36 3.36
218 221 2.368221 GAGCACTGATCCTTAGAGGCAT 59.632 50.000 0.00 0.00 34.61 4.40
223 226 2.159184 CGCAAGAGCACTGATCCTTAGA 60.159 50.000 0.00 0.00 42.27 2.10
231 234 2.357881 CTGCCGCAAGAGCACTGA 60.358 61.111 0.00 0.00 42.27 3.41
283 288 5.175491 CGAACAATGAAATTTTGTGTCAGGG 59.825 40.000 0.00 0.00 37.38 4.45
284 289 5.332506 GCGAACAATGAAATTTTGTGTCAGG 60.333 40.000 0.00 0.00 37.38 3.86
292 297 7.563270 GTTATGTGTGCGAACAATGAAATTTT 58.437 30.769 0.00 0.00 31.22 1.82
297 302 3.495001 TCGTTATGTGTGCGAACAATGAA 59.505 39.130 0.00 0.00 32.81 2.57
301 306 2.745102 TCTCGTTATGTGTGCGAACAA 58.255 42.857 0.00 0.00 34.13 2.83
305 310 4.242475 AGAATTTCTCGTTATGTGTGCGA 58.758 39.130 0.00 0.00 0.00 5.10
308 313 7.596749 AGGTTAGAATTTCTCGTTATGTGTG 57.403 36.000 1.27 0.00 0.00 3.82
325 330 1.550130 CCTCGGGTGGCAAGGTTAGA 61.550 60.000 0.00 0.00 0.00 2.10
349 355 1.480219 GCTCCGACGTAGATTTGGCG 61.480 60.000 0.00 0.00 0.00 5.69
352 358 1.536284 GGGAGCTCCGACGTAGATTTG 60.536 57.143 26.36 0.00 36.71 2.32
353 359 0.745468 GGGAGCTCCGACGTAGATTT 59.255 55.000 26.36 0.00 36.71 2.17
375 382 6.782988 TCCGATCCTATTGAAGTTCCTCTATT 59.217 38.462 0.00 0.00 0.00 1.73
377 384 5.702266 TCCGATCCTATTGAAGTTCCTCTA 58.298 41.667 0.00 0.00 0.00 2.43
391 409 8.076347 AAGTTAGTCTTTCAGGATCCGATCCTA 61.076 40.741 26.50 12.08 45.12 2.94
404 422 7.186804 CGCTTTTTCTTCAAGTTAGTCTTTCA 58.813 34.615 0.00 0.00 33.63 2.69
417 435 1.396996 GATAGCGGCGCTTTTTCTTCA 59.603 47.619 40.77 20.01 40.44 3.02
424 442 2.585247 GACGGATAGCGGCGCTTT 60.585 61.111 40.77 32.39 40.44 3.51
434 452 0.899720 GGGTGACACTTGGACGGATA 59.100 55.000 5.39 0.00 0.00 2.59
446 464 0.105194 TTGTCCTCAGAGGGGTGACA 60.105 55.000 17.10 10.45 35.59 3.58
448 466 1.814429 TTTTGTCCTCAGAGGGGTGA 58.186 50.000 17.10 0.00 35.59 4.02
450 468 1.145119 GGTTTTTGTCCTCAGAGGGGT 59.855 52.381 17.10 0.00 35.59 4.95
456 474 2.107552 TGGGTAGGGTTTTTGTCCTCAG 59.892 50.000 0.00 0.00 34.75 3.35
464 482 4.165565 GGCTAGTAGATGGGTAGGGTTTTT 59.834 45.833 0.00 0.00 0.00 1.94
493 511 2.074729 AGGGGATTCCTAGTGTCTCG 57.925 55.000 2.01 0.00 45.98 4.04
525 543 1.372087 CGAGCCTGTGGATTTGCCTC 61.372 60.000 0.00 0.00 37.63 4.70
530 548 2.436646 CGGCGAGCCTGTGGATTT 60.437 61.111 12.70 0.00 0.00 2.17
531 549 4.473520 CCGGCGAGCCTGTGGATT 62.474 66.667 9.30 0.00 0.00 3.01
544 562 4.436998 CCCTCGATATCCGCCGGC 62.437 72.222 19.07 19.07 38.37 6.13
546 564 2.675423 TCCCCTCGATATCCGCCG 60.675 66.667 0.00 0.00 38.37 6.46
550 568 1.276705 GCTTTCCTCCCCTCGATATCC 59.723 57.143 0.00 0.00 0.00 2.59
555 573 0.613777 GAAAGCTTTCCTCCCCTCGA 59.386 55.000 25.80 0.00 0.00 4.04
556 574 3.160872 GAAAGCTTTCCTCCCCTCG 57.839 57.895 25.80 0.00 0.00 4.63
567 585 2.301346 CATGGCGATTAGGGAAAGCTT 58.699 47.619 0.00 0.00 0.00 3.74
585 603 2.039084 ACAAGTTCTTTCCCTCTCGCAT 59.961 45.455 0.00 0.00 0.00 4.73
589 607 5.012251 AGGTAGAACAAGTTCTTTCCCTCTC 59.988 44.000 19.38 3.25 46.95 3.20
611 629 1.480954 AGCATAGTAACCGTCCACAGG 59.519 52.381 0.00 0.00 0.00 4.00
612 630 2.930040 CAAGCATAGTAACCGTCCACAG 59.070 50.000 0.00 0.00 0.00 3.66
689 707 1.665679 GTGCCTATGTGAACATCCACG 59.334 52.381 0.00 0.00 39.80 4.94
692 710 3.282021 ACATGTGCCTATGTGAACATCC 58.718 45.455 0.00 0.00 39.68 3.51
695 713 4.278975 TGTACATGTGCCTATGTGAACA 57.721 40.909 9.11 7.32 41.18 3.18
705 723 6.226052 TCATAAGAGATGATGTACATGTGCC 58.774 40.000 14.43 0.00 39.56 5.01
706 724 7.719778 TTCATAAGAGATGATGTACATGTGC 57.280 36.000 14.43 8.01 39.56 4.57
708 726 7.935210 TGCATTCATAAGAGATGATGTACATGT 59.065 33.333 14.43 2.69 39.56 3.21
717 735 4.567959 CGTGTGTGCATTCATAAGAGATGA 59.432 41.667 0.00 0.00 0.00 2.92
720 738 2.672874 GCGTGTGTGCATTCATAAGAGA 59.327 45.455 0.00 0.00 34.15 3.10
722 740 2.421619 TGCGTGTGTGCATTCATAAGA 58.578 42.857 0.00 0.00 40.62 2.10
743 761 4.672587 AAGTGCTCATAGGCGAAGAATA 57.327 40.909 0.00 0.00 34.52 1.75
745 763 3.262420 GAAAGTGCTCATAGGCGAAGAA 58.738 45.455 0.00 0.00 34.52 2.52
749 767 0.815095 TCGAAAGTGCTCATAGGCGA 59.185 50.000 0.00 0.00 34.52 5.54
818 838 1.280457 GAGGATGGGACTTGAGTGGT 58.720 55.000 0.00 0.00 0.00 4.16
830 850 2.165030 GCTGGAAATTGTGTGAGGATGG 59.835 50.000 0.00 0.00 0.00 3.51
839 859 2.867287 TGTGTGTGCTGGAAATTGTG 57.133 45.000 0.00 0.00 0.00 3.33
872 991 3.244353 CCGGATCAGTGGAAGAAGCATAT 60.244 47.826 0.00 0.00 0.00 1.78
873 992 2.103094 CCGGATCAGTGGAAGAAGCATA 59.897 50.000 0.00 0.00 0.00 3.14
985 1117 0.038744 CACTTGAGACCCCATTGCCT 59.961 55.000 0.00 0.00 0.00 4.75
1209 1358 6.233434 TGCACTGACAAAGAAACTCATATCT 58.767 36.000 0.00 0.00 0.00 1.98
1305 1454 8.564574 TCAATAAAGCTTTGGTTGTACTTAGTG 58.435 33.333 25.47 12.85 0.00 2.74
1473 1809 0.331278 CCCTCAATTGGCCACACCTA 59.669 55.000 3.88 0.00 40.22 3.08
1700 2036 3.860605 AGCACCTGTGTGGCGTCA 61.861 61.111 0.00 0.00 42.99 4.35
1718 2054 0.898789 TGACCTCCTCCACCTCGTTC 60.899 60.000 0.00 0.00 0.00 3.95
1920 2256 2.608261 GCAGAGTCGTACAGCAGAGTTT 60.608 50.000 0.00 0.00 0.00 2.66
1931 2281 1.199327 CGGTCAGAAAGCAGAGTCGTA 59.801 52.381 0.00 0.00 0.00 3.43
1946 2296 1.349688 ACAAAAGGTATGCTCCGGTCA 59.650 47.619 0.00 0.73 0.00 4.02
1976 2326 9.089601 CCTATGTTCGTACATACATACACAAAA 57.910 33.333 10.46 0.00 43.12 2.44
2054 2404 2.411628 TGATGTATTCGGGGGTTGTG 57.588 50.000 0.00 0.00 0.00 3.33
2067 2419 4.889995 AGACAGATCTCGTCCATTGATGTA 59.110 41.667 16.74 0.00 33.70 2.29
2110 2462 7.549488 CGTATTTTCTTGAAAGACCATCCTACT 59.451 37.037 0.00 0.00 36.37 2.57
2126 2478 4.265556 CAGATCTTCGCGACGTATTTTCTT 59.734 41.667 9.15 0.00 0.00 2.52
2153 2505 3.686016 GGCCCAAAATAGACTCAGAACA 58.314 45.455 0.00 0.00 0.00 3.18
2206 2587 7.410728 GCACACTATGTTTTGGATTTTTGATCG 60.411 37.037 0.00 0.00 0.00 3.69
2211 2612 6.173427 AGGCACACTATGTTTTGGATTTTT 57.827 33.333 0.00 0.00 0.00 1.94
2238 2639 1.745489 GGTCCTGTGTTCGATGCCC 60.745 63.158 0.00 0.00 0.00 5.36
2262 2663 2.354821 GCTATTAGCAGTTTCCCAACCG 59.645 50.000 10.83 0.00 41.89 4.44
2273 2674 2.092968 TGGTTCTGGTGGCTATTAGCAG 60.093 50.000 17.11 6.26 44.75 4.24
2298 2699 9.294030 CTACACTTCAAAAATATCAGCAAATCC 57.706 33.333 0.00 0.00 0.00 3.01
2322 2723 8.796475 ACGTCTGTTCTAGGTAATAAACAACTA 58.204 33.333 0.00 0.00 31.75 2.24
2327 2728 8.612233 CAGTACGTCTGTTCTAGGTAATAAAC 57.388 38.462 0.00 0.00 39.17 2.01
2409 2846 3.368948 GCCCAGTTGTGTTTTCCAAAAGA 60.369 43.478 0.00 0.00 0.00 2.52
2410 2847 2.935849 GCCCAGTTGTGTTTTCCAAAAG 59.064 45.455 0.00 0.00 0.00 2.27
2411 2848 2.303022 TGCCCAGTTGTGTTTTCCAAAA 59.697 40.909 0.00 0.00 0.00 2.44
2412 2849 1.902508 TGCCCAGTTGTGTTTTCCAAA 59.097 42.857 0.00 0.00 0.00 3.28
2413 2850 1.480137 CTGCCCAGTTGTGTTTTCCAA 59.520 47.619 0.00 0.00 0.00 3.53
2414 2851 1.110442 CTGCCCAGTTGTGTTTTCCA 58.890 50.000 0.00 0.00 0.00 3.53
2415 2852 0.389025 CCTGCCCAGTTGTGTTTTCC 59.611 55.000 0.00 0.00 0.00 3.13
2432 2869 7.709149 AAAAATGCTTTAGCTAGAATGTCCT 57.291 32.000 3.10 0.00 42.66 3.85
2754 3237 4.393062 TCGCCAATTTGAAAAAGTTTTGCA 59.607 33.333 4.80 4.80 0.00 4.08
2759 3243 3.791245 TGCTCGCCAATTTGAAAAAGTT 58.209 36.364 0.00 0.00 0.00 2.66
2845 3329 6.459710 GGCCCTAGAAAATAAGAATGTTTCCG 60.460 42.308 0.00 0.00 32.74 4.30
3065 3550 8.744008 TTGTGAACAACAAAATTCGAAAACTA 57.256 26.923 0.00 0.00 45.85 2.24


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

AutoCloner maintained by Alex Coulton.