Multiple sequence alignment - TraesCS3B01G095000

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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 TraesCS3B01G095000 chr3B 100.000 8119 0 0 1 8119 63415637 63407519 0.000000e+00 14994.0
1 TraesCS3B01G095000 chr3B 89.349 169 13 4 7143 7308 63400134 63399968 2.970000e-49 207.0
2 TraesCS3B01G095000 chr3A 95.192 8090 261 57 101 8119 51477108 51469076 0.000000e+00 12667.0
3 TraesCS3B01G095000 chr3A 97.222 36 1 0 4546 4581 51472592 51472557 2.450000e-05 62.1
4 TraesCS3B01G095000 chr3D 94.110 4482 179 41 1 4434 40014851 40010407 0.000000e+00 6735.0
5 TraesCS3B01G095000 chr3D 96.502 3716 90 12 4434 8119 40010221 40006516 0.000000e+00 6106.0
6 TraesCS3B01G095000 chr3D 88.157 2187 238 16 5014 7197 25397174 25395006 0.000000e+00 2584.0
7 TraesCS3B01G095000 chr3D 82.731 747 88 23 3444 4153 25398684 25397942 1.920000e-175 627.0
8 TraesCS3B01G095000 chr3D 82.175 331 42 14 939 1264 40013069 40012751 1.340000e-67 268.0
9 TraesCS3B01G095000 chr3D 91.000 100 6 2 4426 4523 420315587 420315685 1.840000e-26 132.0
10 TraesCS3B01G095000 chr3D 77.561 205 33 8 4398 4595 25397762 25397564 2.400000e-20 111.0
11 TraesCS3B01G095000 chr3D 89.706 68 6 1 7569 7636 25392532 25392466 1.450000e-12 86.1
12 TraesCS3B01G095000 chr3D 97.143 35 1 0 4546 4580 40010060 40010026 8.800000e-05 60.2
13 TraesCS3B01G095000 chr7D 86.985 2305 262 23 5014 7315 37801896 37804165 0.000000e+00 2560.0
14 TraesCS3B01G095000 chr7D 82.620 771 90 24 3419 4150 37800360 37801125 6.870000e-180 641.0
15 TraesCS3B01G095000 chr7D 93.333 90 5 1 4434 4523 66526360 66526272 1.840000e-26 132.0
16 TraesCS3B01G095000 chr7D 76.923 234 37 12 4371 4595 37801281 37801506 5.150000e-22 117.0
17 TraesCS3B01G095000 chr7D 89.706 68 6 1 7569 7636 37806532 37806598 1.450000e-12 86.1
18 TraesCS3B01G095000 chr4A 87.785 2194 243 16 5014 7197 687180952 687178774 0.000000e+00 2543.0
19 TraesCS3B01G095000 chr4A 86.054 631 67 12 3420 4033 687182451 687181825 0.000000e+00 658.0
20 TraesCS3B01G095000 chr4A 85.714 98 8 5 4499 4595 687181443 687181351 1.860000e-16 99.0
21 TraesCS3B01G095000 chr7A 86.664 2302 264 23 5024 7315 37113835 37116103 0.000000e+00 2510.0
22 TraesCS3B01G095000 chr7A 85.327 627 71 12 3419 4030 37112277 37112897 5.350000e-176 628.0
23 TraesCS3B01G095000 chr7A 77.119 236 34 15 4363 4589 37113195 37113419 1.430000e-22 119.0
24 TraesCS3B01G095000 chr5B 93.333 90 5 1 4434 4523 639280710 639280798 1.840000e-26 132.0
25 TraesCS3B01G095000 chr5D 92.222 90 6 1 4434 4523 20302686 20302598 8.550000e-25 126.0
26 TraesCS3B01G095000 chr6B 83.810 105 15 2 2657 2761 141019428 141019530 1.860000e-16 99.0
27 TraesCS3B01G095000 chr6A 83.810 105 15 2 2657 2761 81849152 81849050 1.860000e-16 99.0
28 TraesCS3B01G095000 chr6D 82.857 105 16 2 2657 2761 65911281 65911383 8.680000e-15 93.5


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 TraesCS3B01G095000 chr3B 63407519 63415637 8118 True 14994.000000 14994 100.000000 1 8119 1 chr3B.!!$R2 8118
1 TraesCS3B01G095000 chr3A 51469076 51477108 8032 True 12667.000000 12667 95.192000 101 8119 1 chr3A.!!$R1 8018
2 TraesCS3B01G095000 chr3D 40006516 40014851 8335 True 3292.300000 6735 92.482500 1 8119 4 chr3D.!!$R2 8118
3 TraesCS3B01G095000 chr3D 25392466 25398684 6218 True 852.025000 2584 84.538750 3444 7636 4 chr3D.!!$R1 4192
4 TraesCS3B01G095000 chr7D 37800360 37806598 6238 False 851.025000 2560 84.058500 3419 7636 4 chr7D.!!$F1 4217
5 TraesCS3B01G095000 chr4A 687178774 687182451 3677 True 1100.000000 2543 86.517667 3420 7197 3 chr4A.!!$R1 3777
6 TraesCS3B01G095000 chr7A 37112277 37116103 3826 False 1085.666667 2510 83.036667 3419 7315 3 chr7A.!!$F1 3896

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
83 87 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.0 0.00 4.49 F
179 186 0.252467 CCTCCACCTCCACTCTTCCT 60.252 60.000 0.00 0.0 0.00 3.36 F
2067 2114 0.458669 TCTATTCCACGACCTTCCGC 59.541 55.000 0.00 0.0 0.00 5.54 F
2779 2832 1.153449 CGGCCATTGCTCGGTTCTA 60.153 57.895 2.24 0.0 37.74 2.10 F
4304 4415 2.009042 GCATGTCTACTGTGCCCTGAC 61.009 57.143 0.00 0.0 32.88 3.51 F
4897 5218 0.692476 TTAGTGCCCTGACTGCATGT 59.308 50.000 0.00 0.0 41.46 3.21 F
5010 5449 3.138304 TGTTTGTACTGTCATGACCTGC 58.862 45.455 22.85 11.8 0.00 4.85 F
6644 7100 0.329261 CCTGCAAGTCATGGGAAGGA 59.671 55.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1436 0.246635 CCGATGTCCGAACCTCTGTT 59.753 55.000 0.0 0.00 41.76 3.16 R
2144 2191 0.320771 CGAGTAACAGGCAAGCCAGT 60.321 55.000 14.4 8.74 37.43 4.00 R
3460 3531 0.458543 CGTAGCTGTTCCACGATGCT 60.459 55.000 0.0 0.00 37.89 3.79 R
4421 4548 0.036875 ACTGCCTACAAACTGCTCCC 59.963 55.000 0.0 0.00 0.00 4.30 R
5180 5626 3.194755 TGGTATCAACGAGAGCAAGCTTA 59.805 43.478 0.0 0.00 28.32 3.09 R
6062 6515 4.074259 CAACTGGAAAGACACCATCATCA 58.926 43.478 0.0 0.00 36.79 3.07 R
6968 7424 4.115199 GGAGGCGGGACCATTGCT 62.115 66.667 0.0 0.00 43.14 3.91 R
7591 10241 0.104409 AAAGACACAGGGAGGGGAGT 60.104 55.000 0.0 0.00 0.00 3.85 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
41 45 3.972276 GTTGCCCCTTTCGCGCAA 61.972 61.111 8.75 0.00 40.06 4.85
42 46 3.972276 TTGCCCCTTTCGCGCAAC 61.972 61.111 8.75 0.00 37.58 4.17
43 47 4.947147 TGCCCCTTTCGCGCAACT 62.947 61.111 8.75 0.00 0.00 3.16
83 87 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
84 88 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
85 89 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
86 90 3.860125 ACACACACACACACGCGC 61.860 61.111 5.73 0.00 0.00 6.86
87 91 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
131 135 2.512692 TATTGTGTTCCATGGCTGCT 57.487 45.000 6.96 0.00 0.00 4.24
145 149 1.133790 GGCTGCTTGGTGCTATTTCTG 59.866 52.381 0.00 0.00 43.37 3.02
179 186 0.252467 CCTCCACCTCCACTCTTCCT 60.252 60.000 0.00 0.00 0.00 3.36
221 228 2.231820 CGTCAAAACGGAGGTCACC 58.768 57.895 0.00 0.00 45.21 4.02
251 258 1.996191 GACGATGTCAAGGAGCTCAAC 59.004 52.381 17.19 8.32 32.09 3.18
341 348 2.257676 GCAAGCCAGAGTGCAAGC 59.742 61.111 0.00 0.00 40.58 4.01
353 360 2.349886 GAGTGCAAGCCTAGTGAAATCG 59.650 50.000 0.00 0.00 0.00 3.34
354 361 1.398390 GTGCAAGCCTAGTGAAATCGG 59.602 52.381 0.00 0.00 0.00 4.18
364 371 5.615289 CCTAGTGAAATCGGGAATTCTGAT 58.385 41.667 5.23 6.65 43.01 2.90
373 380 1.406539 GGGAATTCTGATGTTGCGCAT 59.593 47.619 12.75 0.00 41.24 4.73
374 381 2.618241 GGGAATTCTGATGTTGCGCATA 59.382 45.455 12.75 3.62 38.06 3.14
375 382 3.304257 GGGAATTCTGATGTTGCGCATAG 60.304 47.826 12.75 5.35 38.06 2.23
376 383 3.304257 GGAATTCTGATGTTGCGCATAGG 60.304 47.826 12.75 0.00 38.06 2.57
410 417 4.442073 ACGTATTGCGACCGTATATGTTTC 59.558 41.667 0.00 0.00 44.77 2.78
422 429 7.037438 ACCGTATATGTTTCTGTGTTTCGTAT 58.963 34.615 0.00 0.00 0.00 3.06
424 431 8.474577 CCGTATATGTTTCTGTGTTTCGTATAC 58.525 37.037 0.00 0.00 33.65 1.47
438 445 4.253352 TCGTATACGTTGCTTGCATTTC 57.747 40.909 23.67 0.00 40.80 2.17
451 458 4.612033 GCTTGCATTTCTTTTCCATGTTGC 60.612 41.667 0.00 0.00 0.00 4.17
462 469 4.614555 TTCCATGTTGCGACATTATCAC 57.385 40.909 17.30 0.00 43.92 3.06
681 689 4.838152 CATCCACGCCCTCCCACG 62.838 72.222 0.00 0.00 0.00 4.94
1060 1093 3.788797 GCTGTTGCTGTTGCGTATTATCC 60.789 47.826 0.00 0.00 43.34 2.59
1067 1100 4.959446 GCGTATTATCCTCGCGGT 57.041 55.556 6.13 0.00 40.51 5.68
1159 1194 1.217779 GCGCTCTTCTCTTCTGGCT 59.782 57.895 0.00 0.00 0.00 4.75
1230 1265 2.525629 TTCTCCTGCCCCACGACA 60.526 61.111 0.00 0.00 0.00 4.35
1270 1305 3.476552 TGTAAGAAAGGACTGGCTTGTG 58.523 45.455 0.00 0.00 0.00 3.33
1275 1310 1.392589 AAGGACTGGCTTGTGTGTTG 58.607 50.000 0.00 0.00 0.00 3.33
1317 1352 6.060028 TGTTTGCAGTTCATCTGTTTCTAC 57.940 37.500 0.00 0.00 45.23 2.59
1345 1380 3.686016 TGGACTAGTTCATCCTTTTGCC 58.314 45.455 0.00 0.00 35.86 4.52
1349 1384 1.215382 GTTCATCCTTTTGCCCGGC 59.785 57.895 1.04 1.04 0.00 6.13
1378 1413 0.462759 GAAATGAGGGCTGAGGTCGG 60.463 60.000 0.00 0.00 0.00 4.79
1399 1434 3.000925 GGATTTGTATCCGCACGTAGTTG 59.999 47.826 0.00 0.00 39.21 3.16
1401 1436 3.846423 TTGTATCCGCACGTAGTTGTA 57.154 42.857 0.00 0.00 41.61 2.41
1411 1446 3.427863 GCACGTAGTTGTAACAGAGGTTC 59.572 47.826 0.00 0.00 41.61 3.62
1451 1487 5.221661 GGATATCGGGTCTGTATTGGTCTTT 60.222 44.000 0.00 0.00 0.00 2.52
1572 1614 2.412325 CCAAATTGAACGTACGGTGCTC 60.412 50.000 21.06 10.64 0.00 4.26
1660 1705 7.387948 AGACTCACAAAATCTGTATGGTAACAC 59.612 37.037 0.00 0.00 44.37 3.32
1676 1721 4.096382 GGTAACACAACAGAGGGCATTATG 59.904 45.833 0.00 0.00 0.00 1.90
1680 1725 4.883585 ACACAACAGAGGGCATTATGTATG 59.116 41.667 0.00 0.00 37.31 2.39
1688 1733 6.093219 CAGAGGGCATTATGTATGTGCTTATC 59.907 42.308 0.00 0.00 38.83 1.75
1832 1877 1.376649 AGTTCCAGGGGATTCTTGCT 58.623 50.000 0.00 0.00 0.00 3.91
1842 1887 4.840115 AGGGGATTCTTGCTCAAAAATGAA 59.160 37.500 0.00 0.00 0.00 2.57
1874 1921 1.404315 CCAAGTTCCTACCTCGCTGTC 60.404 57.143 0.00 0.00 0.00 3.51
1897 1944 4.153296 CGCTGTTGTTGTGTGGTATTATCA 59.847 41.667 0.00 0.00 0.00 2.15
1899 1946 6.258160 GCTGTTGTTGTGTGGTATTATCATC 58.742 40.000 0.00 0.00 0.00 2.92
1901 1948 5.935206 TGTTGTTGTGTGGTATTATCATCGT 59.065 36.000 0.00 0.00 0.00 3.73
1925 1972 4.991687 GGTCCTGCTTCGATTAGGATTTAG 59.008 45.833 13.75 0.00 42.20 1.85
1928 1975 5.544176 TCCTGCTTCGATTAGGATTTAGGAT 59.456 40.000 8.30 0.00 35.76 3.24
1961 2008 1.595093 CGTGGAGGGGAAATTGGTGC 61.595 60.000 0.00 0.00 0.00 5.01
2067 2114 0.458669 TCTATTCCACGACCTTCCGC 59.541 55.000 0.00 0.00 0.00 5.54
2131 2178 5.476599 CCCATGTCTGTTTTGAAGGAATACA 59.523 40.000 0.00 0.00 0.00 2.29
2143 2190 6.990341 TGAAGGAATACATGATGTGTTGAG 57.010 37.500 12.34 0.00 42.29 3.02
2144 2191 6.710278 TGAAGGAATACATGATGTGTTGAGA 58.290 36.000 12.34 0.00 42.29 3.27
2226 2274 5.013079 TGGTTCTGTTCATGATGGACTAGTT 59.987 40.000 5.32 0.00 0.00 2.24
2267 2315 2.094494 TCCAGAAATGAGAGCTGACGTC 60.094 50.000 9.11 9.11 0.00 4.34
2652 2705 8.888579 TTTTTAAAATCCGTCATTAAAGGCAA 57.111 26.923 0.55 0.00 32.09 4.52
2779 2832 1.153449 CGGCCATTGCTCGGTTCTA 60.153 57.895 2.24 0.00 37.74 2.10
2963 3022 6.937436 ATATCAGTCGTGTCGGCATATATA 57.063 37.500 0.00 0.00 32.13 0.86
3318 3382 2.277084 GGTTCAGTCTGTCGTTTGTGT 58.723 47.619 0.00 0.00 0.00 3.72
3478 3549 2.194271 GTAGCATCGTGGAACAGCTAC 58.806 52.381 7.07 7.07 46.92 3.58
3822 3906 2.300723 ACAGGTATGCGTTGTTCTACCA 59.699 45.455 0.00 0.00 36.83 3.25
4052 4144 3.340814 ACTCTTCCATGTTACAGCCAG 57.659 47.619 0.00 0.00 0.00 4.85
4200 4311 5.887598 CCAATGATCTCAATCAACCTACCAA 59.112 40.000 0.00 0.00 44.85 3.67
4304 4415 2.009042 GCATGTCTACTGTGCCCTGAC 61.009 57.143 0.00 0.00 32.88 3.51
4421 4548 3.967332 AAATTCATGCCAACTTCAGGG 57.033 42.857 0.00 0.00 0.00 4.45
4605 4921 3.567164 AGGAAATAGATCTTGCCATTGCG 59.433 43.478 0.00 0.00 41.78 4.85
4660 4976 7.621428 AATATGCTTACATATAGGCAGCTTG 57.379 36.000 9.75 0.00 46.58 4.01
4880 5201 7.757941 TTCACATTGTGATCTGAATGGTTTA 57.242 32.000 19.63 0.00 42.40 2.01
4897 5218 0.692476 TTAGTGCCCTGACTGCATGT 59.308 50.000 0.00 0.00 41.46 3.21
4927 5252 9.773328 TTGTGATCGTTTTTCATTCTGAATATC 57.227 29.630 1.98 1.21 36.11 1.63
5010 5449 3.138304 TGTTTGTACTGTCATGACCTGC 58.862 45.455 22.85 11.80 0.00 4.85
5032 5478 8.028354 CCTGCAAATTGTAAATGTCACTCATTA 58.972 33.333 0.00 0.00 44.85 1.90
5218 5664 7.412563 CGTTGATACCACACAAAGGTAGTTATG 60.413 40.741 0.00 0.00 44.29 1.90
5372 5825 9.774071 TCTGATATCATAATAGATCCTCCACAA 57.226 33.333 5.72 0.00 0.00 3.33
6334 6787 3.195610 TGGTCGCAACAGATAAGAGATGT 59.804 43.478 0.00 0.00 0.00 3.06
6644 7100 0.329261 CCTGCAAGTCATGGGAAGGA 59.671 55.000 0.00 0.00 0.00 3.36
6968 7424 0.810648 CCCTTGATTTTAGCGCTGCA 59.189 50.000 22.90 3.00 0.00 4.41
7243 7699 7.443272 TGATCAATCACAAGCTAGGAATATGTG 59.557 37.037 6.17 6.17 42.01 3.21
7327 9926 7.152645 TCTCAAGGATGTTTTGACTACTGTAC 58.847 38.462 0.00 0.00 31.66 2.90
7338 9937 8.333186 GTTTTGACTACTGTACAGAAAACGAAT 58.667 33.333 29.30 6.73 0.00 3.34
7388 9987 8.784043 GCCTAATATTATTGATTTCCACGAACT 58.216 33.333 0.00 0.00 0.00 3.01
7436 10035 2.659428 GTTGCCTTCCATCTATGCCTT 58.341 47.619 0.00 0.00 0.00 4.35
7440 10039 3.142174 GCCTTCCATCTATGCCTTGTAC 58.858 50.000 0.00 0.00 0.00 2.90
7524 10124 4.237018 TGTCTAGGTTTAGTTTCCACCCT 58.763 43.478 0.00 0.00 0.00 4.34
7525 10125 4.041198 TGTCTAGGTTTAGTTTCCACCCTG 59.959 45.833 0.00 0.00 0.00 4.45
7591 10241 1.575788 TCCTAGATGGCTTCCTCTCCA 59.424 52.381 0.00 0.00 36.70 3.86
7599 10254 1.334384 GCTTCCTCTCCACTCCCCTC 61.334 65.000 0.00 0.00 0.00 4.30
7717 10372 2.351276 GGAATGGTGGTCGCTGGT 59.649 61.111 0.00 0.00 0.00 4.00
7802 10457 9.593134 CTTGCTACTAGATTAATTCTGTGACTT 57.407 33.333 0.00 0.00 35.79 3.01
7912 10567 4.093408 TGCTAGCTGCTTTTCTTTCATACG 59.907 41.667 17.23 0.00 43.37 3.06
7953 10609 2.539346 TCGAAGTACTTGCTAGCGAC 57.461 50.000 14.14 5.54 0.00 5.19
8030 10686 4.548916 CGATCGGTGAAATGAATTCTGACG 60.549 45.833 7.38 2.55 38.92 4.35
8038 10694 0.874390 TGAATTCTGACGGTTGCTGC 59.126 50.000 7.05 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 45 4.404073 GTGAGAGAGAGAGAGAGAGAGAGT 59.596 50.000 0.00 0.00 0.00 3.24
42 46 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
43 47 4.160439 GTGTGAGAGAGAGAGAGAGAGAGA 59.840 50.000 0.00 0.00 0.00 3.10
92 96 0.247655 ATATTCAAACTGCGCACGCG 60.248 50.000 5.66 3.53 45.51 6.01
93 97 1.895051 AATATTCAAACTGCGCACGC 58.105 45.000 5.66 8.33 42.35 5.34
94 98 5.027737 ACAATAATATTCAAACTGCGCACG 58.972 37.500 5.66 5.54 0.00 5.34
95 99 5.799936 ACACAATAATATTCAAACTGCGCAC 59.200 36.000 5.66 0.00 0.00 5.34
96 100 5.948588 ACACAATAATATTCAAACTGCGCA 58.051 33.333 10.98 10.98 0.00 6.09
97 101 6.020678 GGAACACAATAATATTCAAACTGCGC 60.021 38.462 0.00 0.00 0.00 6.09
98 102 7.026562 TGGAACACAATAATATTCAAACTGCG 58.973 34.615 0.00 0.00 0.00 5.18
145 149 2.930562 AGGAGTGGTGGGAGGTGC 60.931 66.667 0.00 0.00 0.00 5.01
179 186 5.121142 GCAAAGTGTAATTAGCTACGTGGAA 59.879 40.000 1.81 0.00 0.00 3.53
221 228 0.948623 TGACATCGTCCAAGGCAACG 60.949 55.000 0.00 0.00 46.39 4.10
251 258 1.252904 CCCATGTCACAGCTTTGGGG 61.253 60.000 6.31 0.00 42.79 4.96
319 326 2.331132 GCACTCTGGCTTGCTGACC 61.331 63.158 0.00 0.00 35.74 4.02
341 348 5.023533 TCAGAATTCCCGATTTCACTAGG 57.976 43.478 0.65 0.00 0.00 3.02
353 360 0.810648 TGCGCAACATCAGAATTCCC 59.189 50.000 8.16 0.00 0.00 3.97
354 361 2.857592 ATGCGCAACATCAGAATTCC 57.142 45.000 17.11 0.00 31.52 3.01
376 383 4.860261 AATACGTCGACGCGCCCC 62.860 66.667 35.92 0.00 44.43 5.80
385 392 2.299085 TATACGGTCGCAATACGTCG 57.701 50.000 0.00 0.00 44.19 5.12
391 398 4.270084 CACAGAAACATATACGGTCGCAAT 59.730 41.667 0.00 0.00 0.00 3.56
398 405 5.773239 ACGAAACACAGAAACATATACGG 57.227 39.130 0.00 0.00 0.00 4.02
410 417 4.382831 CAAGCAACGTATACGAAACACAG 58.617 43.478 30.77 11.19 43.02 3.66
422 429 4.202060 TGGAAAAGAAATGCAAGCAACGTA 60.202 37.500 0.00 0.00 0.00 3.57
424 431 3.122297 TGGAAAAGAAATGCAAGCAACG 58.878 40.909 0.00 0.00 0.00 4.10
438 445 5.512788 GTGATAATGTCGCAACATGGAAAAG 59.487 40.000 0.00 0.00 45.48 2.27
451 458 6.308041 TCTTGAGAAAACTCGTGATAATGTCG 59.692 38.462 0.00 0.00 0.00 4.35
462 469 0.435008 CCGCGTCTTGAGAAAACTCG 59.565 55.000 4.92 0.00 0.00 4.18
545 553 0.746063 TCCTTGCCAAAACTGCTGTG 59.254 50.000 0.00 0.00 0.00 3.66
620 628 3.185797 GGCTTTTCTACAATTGTCGTCGT 59.814 43.478 15.85 0.00 0.00 4.34
625 633 3.367395 GGCTGGGCTTTTCTACAATTGTC 60.367 47.826 15.85 0.00 0.00 3.18
684 692 2.440247 GGATTTGAGGCGTGGGGG 60.440 66.667 0.00 0.00 0.00 5.40
687 695 1.002134 AGGTGGATTTGAGGCGTGG 60.002 57.895 0.00 0.00 0.00 4.94
892 914 3.793144 CAGCGAAAGTGAGGCCGC 61.793 66.667 0.00 0.00 47.00 6.53
893 915 1.961277 AACAGCGAAAGTGAGGCCG 60.961 57.895 0.00 0.00 0.00 6.13
895 917 1.081840 GCAACAGCGAAAGTGAGGC 60.082 57.895 0.00 0.00 0.00 4.70
896 918 0.947244 AAGCAACAGCGAAAGTGAGG 59.053 50.000 0.00 0.00 0.00 3.86
897 919 2.763249 AAAGCAACAGCGAAAGTGAG 57.237 45.000 0.00 0.00 0.00 3.51
1010 1037 3.660865 GAAGGTAGGAACTCGAAAAGCA 58.339 45.455 0.00 0.00 41.75 3.91
1011 1038 2.666994 CGAAGGTAGGAACTCGAAAAGC 59.333 50.000 0.00 0.00 41.75 3.51
1012 1039 2.666994 GCGAAGGTAGGAACTCGAAAAG 59.333 50.000 0.00 0.00 41.75 2.27
1015 1042 1.201647 CAGCGAAGGTAGGAACTCGAA 59.798 52.381 0.00 0.00 41.75 3.71
1016 1043 0.809385 CAGCGAAGGTAGGAACTCGA 59.191 55.000 0.00 0.00 41.75 4.04
1017 1044 0.526662 ACAGCGAAGGTAGGAACTCG 59.473 55.000 0.00 0.00 41.75 4.18
1018 1045 1.467713 CGACAGCGAAGGTAGGAACTC 60.468 57.143 0.00 0.00 39.17 3.01
1019 1046 0.526662 CGACAGCGAAGGTAGGAACT 59.473 55.000 0.00 0.00 41.25 3.01
1020 1047 1.077089 GCGACAGCGAAGGTAGGAAC 61.077 60.000 0.00 0.00 40.82 3.62
1022 1049 2.882876 GCGACAGCGAAGGTAGGA 59.117 61.111 0.00 0.00 40.82 2.94
1067 1100 3.244215 CCTAAATCCTAATCGCAGCAGGA 60.244 47.826 1.76 1.76 42.52 3.86
1159 1194 2.806745 CGAAGAACAGAGCCTTGGTTGA 60.807 50.000 0.00 0.00 0.00 3.18
1230 1265 3.679389 ACAGAATTCAACTTCGCAGGAT 58.321 40.909 8.44 0.00 0.00 3.24
1270 1305 2.412089 AGAAAGATTACGCGAGCAACAC 59.588 45.455 15.93 2.33 0.00 3.32
1275 1310 5.391060 AACAATAGAAAGATTACGCGAGC 57.609 39.130 15.93 0.00 0.00 5.03
1317 1352 5.804944 AGGATGAACTAGTCCATCATGAG 57.195 43.478 21.89 0.00 40.55 2.90
1345 1380 1.674322 ATTTCTGGACCAACGCCGG 60.674 57.895 0.00 0.00 0.00 6.13
1349 1384 1.453155 CCCTCATTTCTGGACCAACG 58.547 55.000 0.00 0.00 0.00 4.10
1378 1413 3.615496 ACAACTACGTGCGGATACAAATC 59.385 43.478 0.00 0.00 0.00 2.17
1393 1428 4.233005 GTCCGAACCTCTGTTACAACTAC 58.767 47.826 0.00 0.00 33.97 2.73
1399 1434 2.527100 CGATGTCCGAACCTCTGTTAC 58.473 52.381 0.00 0.00 41.76 2.50
1401 1436 0.246635 CCGATGTCCGAACCTCTGTT 59.753 55.000 0.00 0.00 41.76 3.16
1572 1614 7.774157 AGAATCATATATTTGCCATGCCTCTAG 59.226 37.037 0.00 0.00 0.00 2.43
1660 1705 4.261322 GCACATACATAATGCCCTCTGTTG 60.261 45.833 0.00 0.00 39.39 3.33
1676 1721 8.233190 GCATAATTTCTGGAGATAAGCACATAC 58.767 37.037 0.00 0.00 0.00 2.39
1680 1725 6.624352 TGCATAATTTCTGGAGATAAGCAC 57.376 37.500 0.00 0.00 0.00 4.40
1874 1921 4.153296 TGATAATACCACACAACAACAGCG 59.847 41.667 0.00 0.00 0.00 5.18
1897 1944 0.537188 AATCGAAGCAGGACCACGAT 59.463 50.000 0.00 0.00 43.73 3.73
1899 1946 1.560923 CTAATCGAAGCAGGACCACG 58.439 55.000 0.00 0.00 0.00 4.94
1901 1948 1.860641 TCCTAATCGAAGCAGGACCA 58.139 50.000 8.50 0.00 33.48 4.02
1925 1972 1.521681 CGCCAAAGGTCCTCGATCC 60.522 63.158 0.00 0.00 0.00 3.36
1928 1975 2.342279 CACGCCAAAGGTCCTCGA 59.658 61.111 4.81 0.00 0.00 4.04
2095 2142 3.763897 ACAGACATGGGCTCCATTAAAAC 59.236 43.478 4.15 0.00 42.23 2.43
2131 2178 3.079578 CAAGCCAGTCTCAACACATCAT 58.920 45.455 0.00 0.00 0.00 2.45
2143 2190 1.443802 GAGTAACAGGCAAGCCAGTC 58.556 55.000 14.40 1.13 34.64 3.51
2144 2191 0.320771 CGAGTAACAGGCAAGCCAGT 60.321 55.000 14.40 8.74 37.43 4.00
2192 2240 2.035449 TGAACAGAACCAAGACGATCGT 59.965 45.455 22.97 22.97 0.00 3.73
2226 2274 4.288366 TGGATCAACACCAGACAAAGGATA 59.712 41.667 0.00 0.00 33.22 2.59
2631 2684 8.145122 ACTTTTTGCCTTTAATGACGGATTTTA 58.855 29.630 0.00 0.00 0.00 1.52
2807 2864 7.230466 AGACTAATACGTAAATGCCTTTTCG 57.770 36.000 10.92 10.92 39.94 3.46
2963 3022 9.807649 GTGATGCAATTAAAACCAAGATTCTAT 57.192 29.630 0.00 0.00 0.00 1.98
3180 3244 8.493607 TCAACCTTCCAATCAAGTATATCATCA 58.506 33.333 0.00 0.00 0.00 3.07
3185 3249 5.527582 GCGTCAACCTTCCAATCAAGTATAT 59.472 40.000 0.00 0.00 0.00 0.86
3318 3382 6.600427 TCGTATGACAGGTAGACAGAATTACA 59.400 38.462 0.00 0.00 0.00 2.41
3460 3531 0.458543 CGTAGCTGTTCCACGATGCT 60.459 55.000 0.00 0.00 37.89 3.79
3478 3549 2.515523 CCCTCTGCCATGCTTCCG 60.516 66.667 0.00 0.00 0.00 4.30
3822 3906 7.168219 TGGCTCTTCTACATGAACTACAAAAT 58.832 34.615 0.00 0.00 0.00 1.82
4052 4144 4.934602 CCTGGAGAAGACAAAAGAGATCAC 59.065 45.833 0.00 0.00 0.00 3.06
4200 4311 8.636213 CCAAAGCTCTTGGTTGATTTATATCAT 58.364 33.333 15.52 0.00 40.37 2.45
4228 4339 7.223971 GCATACTCGTTGTAATCATTCAAGGTA 59.776 37.037 0.00 0.00 34.45 3.08
4304 4415 9.258826 CAAGATACATCTCACAATAGGAAGAAG 57.741 37.037 0.00 0.00 35.76 2.85
4421 4548 0.036875 ACTGCCTACAAACTGCTCCC 59.963 55.000 0.00 0.00 0.00 4.30
4531 4845 7.166473 GCAATGGCAAGATTTAAATTCTAGACG 59.834 37.037 1.43 0.00 40.72 4.18
4605 4921 7.013655 AGTCCATGAATGATGCTATAAACCAAC 59.986 37.037 0.00 0.00 0.00 3.77
4656 4972 3.121445 GCAGTAACGAAGTGTAGTCAAGC 59.879 47.826 0.00 0.00 45.00 4.01
4660 4976 2.603953 GGGCAGTAACGAAGTGTAGTC 58.396 52.381 0.00 0.00 45.00 2.59
4742 5060 4.494091 AGTAGTGCAGATGCCTACAATT 57.506 40.909 23.42 9.94 42.22 2.32
4880 5201 1.002868 GACATGCAGTCAGGGCACT 60.003 57.895 10.30 0.00 46.77 4.40
4897 5218 7.702386 TCAGAATGAAAAACGATCACAAAAGA 58.298 30.769 0.00 0.00 45.97 2.52
4927 5252 9.344309 GAGAACTAAAGTAGCAGTAACTACAAG 57.656 37.037 4.67 2.11 44.14 3.16
4982 5409 6.636850 GGTCATGACAGTACAAACAATGAAAC 59.363 38.462 26.47 0.00 0.00 2.78
5032 5478 9.607988 TTTGGACAATATCGTATCACAAAGTAT 57.392 29.630 0.00 0.00 0.00 2.12
5180 5626 3.194755 TGGTATCAACGAGAGCAAGCTTA 59.805 43.478 0.00 0.00 28.32 3.09
5218 5664 9.543018 GTACAAAAGACATAATAAAGTGAGCAC 57.457 33.333 0.00 0.00 0.00 4.40
5372 5825 5.379706 AAGCAGGATTATTGGTAAGCTCT 57.620 39.130 0.00 0.00 0.00 4.09
6062 6515 4.074259 CAACTGGAAAGACACCATCATCA 58.926 43.478 0.00 0.00 36.79 3.07
6644 7100 5.520748 AATCAATGGAAGGTGTTAGAGGT 57.479 39.130 0.00 0.00 0.00 3.85
6968 7424 4.115199 GGAGGCGGGACCATTGCT 62.115 66.667 0.00 0.00 43.14 3.91
6996 7452 5.468409 GCTTCCTTCTAGGTTTATCTGATGC 59.532 44.000 0.00 0.00 36.53 3.91
7243 7699 4.425577 AGAATGGCGAGTTTGAACATTC 57.574 40.909 0.00 0.00 44.63 2.67
7327 9926 7.287950 TGAGTCGATGTAAAATTCGTTTTCTG 58.712 34.615 0.00 0.00 36.74 3.02
7338 9937 7.201609 GGCATAGATGTTTGAGTCGATGTAAAA 60.202 37.037 0.00 0.00 32.30 1.52
7400 9999 3.017442 GGCAACCAAAAGTAGATCTCCC 58.983 50.000 0.00 0.00 0.00 4.30
7436 10035 5.172687 TGTTCATGGAAGGCAATAGTACA 57.827 39.130 0.00 0.00 0.00 2.90
7440 10039 5.902613 TTCTTGTTCATGGAAGGCAATAG 57.097 39.130 0.00 0.00 0.00 1.73
7524 10124 4.890088 AGTTAAACGGCATTAGAGTCACA 58.110 39.130 0.00 0.00 0.00 3.58
7525 10125 5.618561 CAAGTTAAACGGCATTAGAGTCAC 58.381 41.667 0.00 0.00 0.00 3.67
7591 10241 0.104409 AAAGACACAGGGAGGGGAGT 60.104 55.000 0.00 0.00 0.00 3.85
7599 10254 1.545651 GGAGGGAACAAAGACACAGGG 60.546 57.143 0.00 0.00 0.00 4.45
7717 10372 0.826715 GCCAGTAGCCACAGATCTGA 59.173 55.000 29.27 3.06 34.35 3.27
7757 10412 3.589542 CCTCCACCTTTGGCCCCA 61.590 66.667 0.00 0.00 43.56 4.96
7762 10417 0.111253 AGCAAGACCTCCACCTTTGG 59.889 55.000 0.00 0.00 45.56 3.28
7802 10457 2.441750 AGAACTCAACCTAGCACCCAAA 59.558 45.455 0.00 0.00 0.00 3.28
7912 10567 5.342259 CGAATTCGAGGAAACCAAATCAAAC 59.658 40.000 23.29 0.00 43.02 2.93
8030 10686 0.457443 GGATTAGCCAAGCAGCAACC 59.543 55.000 0.00 0.00 36.34 3.77


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

AutoCloner maintained by Alex Coulton.