Multiple sequence alignment - TraesCS7B01G004400

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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 TraesCS7B01G004400 chr7B 100.000 5144 0 0 1 5144 2097613 2102756 0.000000e+00 9500.0
1 TraesCS7B01G004400 chr7B 96.519 2815 50 21 2347 5144 2075141 2077924 0.000000e+00 4612.0
2 TraesCS7B01G004400 chr7B 88.540 733 38 20 1629 2348 2074407 2075106 0.000000e+00 846.0
3 TraesCS7B01G004400 chr7B 87.952 415 27 9 949 1361 2067111 2067504 7.800000e-128 468.0
4 TraesCS7B01G004400 chr7B 82.743 452 66 9 4186 4632 553879740 553880184 4.830000e-105 392.0
5 TraesCS7B01G004400 chr7B 91.304 184 13 3 677 859 2066796 2066977 1.110000e-61 248.0
6 TraesCS7B01G004400 chr7B 96.241 133 5 0 1357 1489 2074244 2074376 8.670000e-53 219.0
7 TraesCS7B01G004400 chr7A 87.934 2536 190 56 2523 5026 63907356 63904905 0.000000e+00 2881.0
8 TraesCS7B01G004400 chr7A 87.544 562 45 17 1988 2531 63908066 63907512 1.220000e-175 627.0
9 TraesCS7B01G004400 chrUn 96.120 1598 58 3 3205 4799 83951654 83950058 0.000000e+00 2604.0
10 TraesCS7B01G004400 chrUn 94.219 1453 59 13 912 2348 83954125 83952682 0.000000e+00 2194.0
11 TraesCS7B01G004400 chrUn 95.393 738 20 11 2347 3076 83952647 83951916 0.000000e+00 1162.0
12 TraesCS7B01G004400 chrUn 98.246 114 2 0 4795 4908 83944873 83944760 3.140000e-47 200.0
13 TraesCS7B01G004400 chrUn 91.667 84 4 1 750 833 83955695 83955615 4.210000e-21 113.0
14 TraesCS7B01G004400 chr7D 91.495 1846 110 25 2347 4185 60021940 60020135 0.000000e+00 2495.0
15 TraesCS7B01G004400 chr7D 95.556 720 31 1 1629 2348 60022693 60021975 0.000000e+00 1151.0
16 TraesCS7B01G004400 chr7D 83.725 553 45 21 949 1491 60023257 60022740 1.000000e-131 481.0
17 TraesCS7B01G004400 chr7D 85.673 349 36 5 334 674 60024023 60023681 6.340000e-94 355.0
18 TraesCS7B01G004400 chr7D 92.347 196 10 5 665 859 60023577 60023386 1.820000e-69 274.0
19 TraesCS7B01G004400 chr7D 86.395 147 19 1 1 147 60024454 60024309 5.330000e-35 159.0
20 TraesCS7B01G004400 chr7D 84.337 166 14 3 4643 4804 60018914 60018757 8.920000e-33 152.0
21 TraesCS7B01G004400 chr2A 85.619 452 55 8 4185 4632 643499811 643500256 2.800000e-127 466.0
22 TraesCS7B01G004400 chr1D 83.864 440 65 4 4195 4632 411513563 411513128 1.030000e-111 414.0
23 TraesCS7B01G004400 chr1D 82.927 451 67 8 4189 4635 314684324 314683880 1.040000e-106 398.0
24 TraesCS7B01G004400 chr5B 83.559 444 64 6 4195 4635 490542712 490542275 1.720000e-109 407.0
25 TraesCS7B01G004400 chr2D 83.296 449 65 6 4189 4632 300882972 300883415 6.200000e-109 405.0
26 TraesCS7B01G004400 chr2D 87.129 101 13 0 1833 1933 9622233 9622333 1.170000e-21 115.0
27 TraesCS7B01G004400 chr5A 84.404 109 17 0 4022 4130 689916673 689916565 1.960000e-19 108.0
28 TraesCS7B01G004400 chr5A 85.714 84 12 0 1848 1931 701964759 701964676 7.090000e-14 89.8
29 TraesCS7B01G004400 chr4B 85.000 100 15 0 1833 1932 661170206 661170107 9.110000e-18 102.0
30 TraesCS7B01G004400 chr4B 83.810 105 17 0 4026 4130 652288699 652288595 3.280000e-17 100.0
31 TraesCS7B01G004400 chr4B 86.905 84 11 0 1848 1931 661187140 661187057 1.520000e-15 95.3
32 TraesCS7B01G004400 chr4B 86.905 84 11 0 1848 1931 662079940 662080023 1.520000e-15 95.3
33 TraesCS7B01G004400 chr3D 84.706 85 11 2 329 413 596166357 596166439 3.300000e-12 84.2


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 TraesCS7B01G004400 chr7B 2097613 2102756 5143 False 9500.000000 9500 100.000000 1 5144 1 chr7B.!!$F1 5143
1 TraesCS7B01G004400 chr7B 2074244 2077924 3680 False 1892.333333 4612 93.766667 1357 5144 3 chr7B.!!$F4 3787
2 TraesCS7B01G004400 chr7B 2066796 2067504 708 False 358.000000 468 89.628000 677 1361 2 chr7B.!!$F3 684
3 TraesCS7B01G004400 chr7A 63904905 63908066 3161 True 1754.000000 2881 87.739000 1988 5026 2 chr7A.!!$R1 3038
4 TraesCS7B01G004400 chrUn 83950058 83955695 5637 True 1518.250000 2604 94.349750 750 4799 4 chrUn.!!$R2 4049
5 TraesCS7B01G004400 chr7D 60018757 60024454 5697 True 723.857143 2495 88.504000 1 4804 7 chr7D.!!$R1 4803

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
524 625 0.245266 TAGACGCTGAAACGATGGCA 59.755 50.000 0.00 0.00 36.70 4.92 F
1281 2977 0.109723 ACAACCCATGCGTGGTAAGT 59.890 50.000 23.39 14.69 44.48 2.24 F
1290 2986 0.598158 GCGTGGTAAGTGTGACGGAA 60.598 55.000 0.00 0.00 32.45 4.30 F
1420 3122 1.136695 CAACCACTGCTTGAAAAGGCA 59.863 47.619 0.00 0.00 46.35 4.75 F
2553 4476 0.892358 CAAGACCCTGCATGTGCTGT 60.892 55.000 6.55 1.26 42.66 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 3114 0.028902 ACGACGCTGTTTGCCTTTTC 59.971 50.0 0.00 0.0 38.78 2.29 R
2120 3836 0.827089 CCATTTGCACAGACCCACCA 60.827 55.0 0.00 0.0 0.00 4.17 R
2518 4277 5.103940 AGGGTCTTGCCATATTGAACACTAT 60.104 40.0 0.00 0.0 39.65 2.12 R
3297 5391 0.868406 CGAGTCAAGTTTGAGTGCCC 59.132 55.0 6.92 0.0 40.75 5.36 R
4455 7017 0.466543 ATGCGGGGTGTAAGCGATTA 59.533 50.0 0.00 0.0 33.03 1.75 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
19 20 1.373497 CGCGTCAGAGGCTCAACTT 60.373 57.895 18.26 0.00 0.00 2.66
22 23 1.151668 CGTCAGAGGCTCAACTTTGG 58.848 55.000 18.26 0.00 0.00 3.28
51 52 1.025647 GTCTCGGCAGACGGTAGAGT 61.026 60.000 0.00 0.00 39.91 3.24
60 61 2.101770 CGGTAGAGTTCGTCGGGC 59.898 66.667 0.00 0.00 0.00 6.13
62 63 2.345760 GGTAGAGTTCGTCGGGCCA 61.346 63.158 4.39 0.00 0.00 5.36
68 69 1.445582 GTTCGTCGGGCCACTAGTG 60.446 63.158 16.34 16.34 0.00 2.74
88 89 0.541863 ACCATTGAGTCCATCCCGAC 59.458 55.000 0.00 0.00 0.00 4.79
91 92 1.065491 CATTGAGTCCATCCCGACCAA 60.065 52.381 0.00 0.00 32.91 3.67
151 198 3.051803 ACCTGGAGGAGTTATGAGATGGA 60.052 47.826 0.00 0.00 38.94 3.41
158 205 6.723977 GGAGGAGTTATGAGATGGAGTTCTAT 59.276 42.308 0.00 0.00 0.00 1.98
178 225 7.831691 TCTATTAGAAGAGGGATCTCAACAG 57.168 40.000 0.00 0.00 42.34 3.16
181 228 3.525862 AGAAGAGGGATCTCAACAGGTT 58.474 45.455 0.00 0.00 42.34 3.50
194 241 0.663153 ACAGGTTGAAGCGCAAGAAC 59.337 50.000 11.47 8.57 37.12 3.01
210 257 0.322546 GAACGATGGCAAGGAAGGGT 60.323 55.000 0.00 0.00 0.00 4.34
217 264 0.955919 GGCAAGGAAGGGTCTTCACG 60.956 60.000 9.48 0.00 0.00 4.35
224 271 0.396811 AAGGGTCTTCACGGGTCAAG 59.603 55.000 0.00 0.00 0.00 3.02
226 273 1.671379 GGTCTTCACGGGTCAAGGC 60.671 63.158 0.00 0.00 0.00 4.35
227 274 2.027625 GTCTTCACGGGTCAAGGCG 61.028 63.158 0.00 0.00 0.00 5.52
231 278 3.691342 CACGGGTCAAGGCGGAGA 61.691 66.667 0.00 0.00 0.00 3.71
240 287 0.465097 CAAGGCGGAGAAGGATGCAT 60.465 55.000 0.00 0.00 0.00 3.96
245 292 1.535685 GGAGAAGGATGCATGCCCT 59.464 57.895 16.68 12.71 0.00 5.19
247 294 0.536915 GAGAAGGATGCATGCCCTCC 60.537 60.000 22.65 22.65 31.17 4.30
273 320 2.414138 GTGGTTAACCTTGATTCCGACG 59.586 50.000 24.78 0.00 36.82 5.12
299 346 1.068474 GTGAGGTGTCCGACGAAATG 58.932 55.000 0.00 0.00 0.00 2.32
312 396 3.146847 GACGAAATGGACTGGGAACTTT 58.853 45.455 0.00 0.00 0.00 2.66
319 403 3.221771 TGGACTGGGAACTTTGAATGTG 58.778 45.455 0.00 0.00 0.00 3.21
321 405 3.004734 GGACTGGGAACTTTGAATGTGTG 59.995 47.826 0.00 0.00 0.00 3.82
323 407 2.297033 CTGGGAACTTTGAATGTGTGGG 59.703 50.000 0.00 0.00 0.00 4.61
332 432 3.524095 TGAATGTGTGGGACTTTGGAT 57.476 42.857 0.00 0.00 0.00 3.41
354 454 6.360148 GGATCGAAGTAGTATGAATGTTCGTC 59.640 42.308 0.00 0.00 38.31 4.20
355 455 6.185852 TCGAAGTAGTATGAATGTTCGTCA 57.814 37.500 0.00 0.00 38.31 4.35
356 456 6.255950 TCGAAGTAGTATGAATGTTCGTCAG 58.744 40.000 0.00 0.00 38.31 3.51
397 498 3.835395 TGTTTTGGGTGCCCTATTTTAGG 59.165 43.478 8.91 0.00 45.81 2.69
423 524 4.771127 TGGAGACGCCACTTTGTC 57.229 55.556 0.00 0.00 43.33 3.18
486 587 1.077357 ACAGACGTTTTGGTGCCCA 60.077 52.632 0.00 0.00 0.00 5.36
505 606 5.949354 TGCCCAAAAATAGTGTAGCTATTGT 59.051 36.000 0.00 0.00 46.54 2.71
509 610 8.827677 CCCAAAAATAGTGTAGCTATTGTAGAC 58.172 37.037 0.00 0.00 46.54 2.59
513 614 4.294416 AGTGTAGCTATTGTAGACGCTG 57.706 45.455 0.00 0.00 34.14 5.18
514 615 3.945921 AGTGTAGCTATTGTAGACGCTGA 59.054 43.478 0.00 0.00 34.14 4.26
522 623 1.990799 TGTAGACGCTGAAACGATGG 58.009 50.000 0.00 0.00 36.70 3.51
523 624 0.645868 GTAGACGCTGAAACGATGGC 59.354 55.000 0.00 0.00 36.70 4.40
524 625 0.245266 TAGACGCTGAAACGATGGCA 59.755 50.000 0.00 0.00 36.70 4.92
527 628 1.016130 ACGCTGAAACGATGGCAGAG 61.016 55.000 0.00 0.00 35.88 3.35
533 634 1.474077 GAAACGATGGCAGAGGCAATT 59.526 47.619 0.00 0.00 42.43 2.32
549 650 3.788937 GCAATTTGCAGCACTGGAATAT 58.211 40.909 16.35 0.68 44.26 1.28
556 657 3.672808 GCAGCACTGGAATATCTGCTAT 58.327 45.455 5.40 0.00 44.71 2.97
557 658 4.825422 GCAGCACTGGAATATCTGCTATA 58.175 43.478 5.40 0.00 44.71 1.31
558 659 5.426504 GCAGCACTGGAATATCTGCTATAT 58.573 41.667 5.40 0.00 44.71 0.86
559 660 6.577103 GCAGCACTGGAATATCTGCTATATA 58.423 40.000 5.40 0.00 44.71 0.86
560 661 7.215789 GCAGCACTGGAATATCTGCTATATAT 58.784 38.462 5.40 0.00 44.71 0.86
571 672 9.984190 AATATCTGCTATATATAGAGTCGTCGA 57.016 33.333 21.65 7.79 32.05 4.20
592 699 0.678395 AATTTCATTGCGTGGCACCA 59.322 45.000 12.86 8.38 38.71 4.17
598 705 0.678395 ATTGCGTGGCACCATGAAAA 59.322 45.000 12.86 6.50 38.71 2.29
609 716 4.379652 GCACCATGAAAAGTGTTGGAATT 58.620 39.130 0.00 0.00 36.35 2.17
630 737 2.436646 CTGCCAAGGGGTGCGTAG 60.437 66.667 0.00 0.00 36.17 3.51
674 781 2.020720 GCAGAGAGCAGTACTAGCAGA 58.979 52.381 16.27 0.00 44.79 4.26
736 955 3.319689 TCAAAAATCCCACCCGAAAGTTC 59.680 43.478 0.00 0.00 0.00 3.01
777 996 1.008194 ACGCTTGAACACGACGCTA 60.008 52.632 0.00 0.00 0.00 4.26
779 998 1.779683 GCTTGAACACGACGCTACC 59.220 57.895 0.00 0.00 0.00 3.18
780 999 0.666577 GCTTGAACACGACGCTACCT 60.667 55.000 0.00 0.00 0.00 3.08
781 1000 1.401931 GCTTGAACACGACGCTACCTA 60.402 52.381 0.00 0.00 0.00 3.08
783 1002 0.523072 TGAACACGACGCTACCTACC 59.477 55.000 0.00 0.00 0.00 3.18
784 1003 0.807496 GAACACGACGCTACCTACCT 59.193 55.000 0.00 0.00 0.00 3.08
785 1004 2.009774 GAACACGACGCTACCTACCTA 58.990 52.381 0.00 0.00 0.00 3.08
824 1043 1.227764 CAGTGGAGGATGCCCATCG 60.228 63.158 2.47 0.00 38.69 3.84
836 1055 0.892358 GCCCATCGGATCATGCATGT 60.892 55.000 25.43 13.42 0.00 3.21
838 1057 0.879090 CCATCGGATCATGCATGTGG 59.121 55.000 25.43 19.77 0.00 4.17
859 1078 1.027357 CACTGTCTGCACAAAAGCCT 58.973 50.000 0.00 0.00 29.82 4.58
860 1079 1.002033 CACTGTCTGCACAAAAGCCTC 60.002 52.381 0.00 0.00 29.82 4.70
862 1081 0.463654 TGTCTGCACAAAAGCCTCGT 60.464 50.000 0.00 0.00 0.00 4.18
865 1084 1.221466 CTGCACAAAAGCCTCGTCGA 61.221 55.000 0.00 0.00 0.00 4.20
866 1085 1.204312 GCACAAAAGCCTCGTCGAC 59.796 57.895 5.18 5.18 0.00 4.20
867 1086 1.495584 GCACAAAAGCCTCGTCGACA 61.496 55.000 17.16 1.87 0.00 4.35
870 1100 0.508641 CAAAAGCCTCGTCGACAGTG 59.491 55.000 17.16 9.09 0.00 3.66
896 1153 3.002862 TGCGTGGAATTAATATTGACGCC 59.997 43.478 21.55 8.12 44.16 5.68
947 2615 1.209640 GTGTGGACTCGTCGACTCC 59.790 63.158 14.70 14.25 38.81 3.85
987 2659 4.192000 GCACGCACTGCATACTCT 57.808 55.556 1.11 0.00 46.29 3.24
988 2660 2.460330 GCACGCACTGCATACTCTT 58.540 52.632 1.11 0.00 46.29 2.85
989 2661 1.640428 GCACGCACTGCATACTCTTA 58.360 50.000 1.11 0.00 46.29 2.10
990 2662 1.590238 GCACGCACTGCATACTCTTAG 59.410 52.381 1.11 0.00 46.29 2.18
993 2665 4.421058 CACGCACTGCATACTCTTAGTAA 58.579 43.478 1.11 0.00 33.89 2.24
1155 2845 1.435577 GTATGCACGTCTTCCGGTTT 58.564 50.000 0.00 0.00 42.24 3.27
1163 2853 1.305201 GTCTTCCGGTTTGACAAGCA 58.695 50.000 0.00 0.00 0.00 3.91
1188 2880 0.955178 ATCTCGTCAAGATCGGCGAT 59.045 50.000 24.26 24.26 40.99 4.58
1191 2883 0.248498 TCGTCAAGATCGGCGATGAC 60.248 55.000 29.20 26.47 38.98 3.06
1281 2977 0.109723 ACAACCCATGCGTGGTAAGT 59.890 50.000 23.39 14.69 44.48 2.24
1288 2984 0.669318 ATGCGTGGTAAGTGTGACGG 60.669 55.000 0.00 0.00 32.45 4.79
1290 2986 0.598158 GCGTGGTAAGTGTGACGGAA 60.598 55.000 0.00 0.00 32.45 4.30
1305 3001 4.149571 GTGACGGAATCGATCTTCATCATG 59.850 45.833 0.00 0.00 40.11 3.07
1412 3114 2.783135 AGTCCATACAACCACTGCTTG 58.217 47.619 0.00 0.00 0.00 4.01
1420 3122 1.136695 CAACCACTGCTTGAAAAGGCA 59.863 47.619 0.00 0.00 46.35 4.75
1450 3152 2.543012 CGTGCCTCAGATGCTTATGAAG 59.457 50.000 0.00 0.00 0.00 3.02
1453 3155 3.453717 TGCCTCAGATGCTTATGAAGACT 59.546 43.478 0.00 0.00 0.00 3.24
1606 3316 9.058174 TGTAAAATTCTCAGATTTTTACCGTCA 57.942 29.630 27.11 15.09 41.95 4.35
1607 3317 9.326339 GTAAAATTCTCAGATTTTTACCGTCAC 57.674 33.333 23.18 9.21 39.63 3.67
1608 3318 7.745620 AAATTCTCAGATTTTTACCGTCACT 57.254 32.000 0.00 0.00 0.00 3.41
1652 3362 6.128254 CGTCAAGATATATCGCTCAGGTCTTA 60.128 42.308 7.08 0.00 0.00 2.10
1952 3668 2.444700 ATTCACACGACCGACCACCC 62.445 60.000 0.00 0.00 0.00 4.61
1970 3686 4.588106 CCACCCCATGAATTTATGCATGTA 59.412 41.667 10.16 0.00 40.11 2.29
2120 3836 3.369471 CGGTAGGTGTGATTGATCTTGGT 60.369 47.826 0.00 0.00 0.00 3.67
2518 4277 4.927267 AACATTCTCCCAAGGTATCACA 57.073 40.909 0.00 0.00 0.00 3.58
2553 4476 0.892358 CAAGACCCTGCATGTGCTGT 60.892 55.000 6.55 1.26 42.66 4.40
3180 5274 8.801715 ATTTGCCATTTCATTCGTTATATGTC 57.198 30.769 0.00 0.00 0.00 3.06
3181 5275 6.934048 TGCCATTTCATTCGTTATATGTCA 57.066 33.333 0.00 0.00 0.00 3.58
3182 5276 7.509141 TGCCATTTCATTCGTTATATGTCAT 57.491 32.000 0.00 0.00 0.00 3.06
3183 5277 8.614469 TGCCATTTCATTCGTTATATGTCATA 57.386 30.769 0.00 0.00 0.00 2.15
3184 5278 9.230122 TGCCATTTCATTCGTTATATGTCATAT 57.770 29.630 10.20 10.20 0.00 1.78
3211 5305 9.282905 TCATCCATATATGTCATATTCCAAGGA 57.717 33.333 10.59 10.79 0.00 3.36
3297 5391 2.095008 AGTGCAGACGTGATGTAGTGAG 60.095 50.000 0.00 0.00 0.00 3.51
4164 6268 4.350520 TGACAATAGATGCCCCATGATACA 59.649 41.667 0.00 0.00 0.00 2.29
4370 6477 4.194678 AGAATCCTATAGACCCCGACAA 57.805 45.455 0.00 0.00 0.00 3.18
4429 6989 3.265737 AGGTTATGCTGTCACCCATGTTA 59.734 43.478 0.00 0.00 0.00 2.41
4455 7017 1.207791 CCTCCATAGCCACCTGTTCT 58.792 55.000 0.00 0.00 0.00 3.01
4527 7090 2.411031 CGTTGACCACGTATGAAGCAAC 60.411 50.000 0.00 0.00 44.49 4.17
4747 7685 8.783660 TGTATTACTCCCTAGATTGATTCAGT 57.216 34.615 0.00 0.00 0.00 3.41
4748 7686 8.642432 TGTATTACTCCCTAGATTGATTCAGTG 58.358 37.037 0.00 0.00 0.00 3.66
4749 7687 7.921041 ATTACTCCCTAGATTGATTCAGTGA 57.079 36.000 0.00 0.00 0.00 3.41
4750 7688 7.921041 TTACTCCCTAGATTGATTCAGTGAT 57.079 36.000 0.00 0.00 0.00 3.06
4751 7689 6.821616 ACTCCCTAGATTGATTCAGTGATT 57.178 37.500 0.00 0.00 0.00 2.57
4752 7690 6.825610 ACTCCCTAGATTGATTCAGTGATTC 58.174 40.000 7.88 7.88 0.00 2.52
4850 7788 4.532521 ACCCGCTCCTAAATATATGAAGCT 59.467 41.667 0.00 0.00 0.00 3.74
4998 7936 1.748403 GCCTCTGGCCGACATATGA 59.252 57.895 10.38 0.00 44.06 2.15
5115 8054 7.855375 TCAATCTGTGATGGATCTAGAAGTTT 58.145 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.301296 TCTCTCCAAAGTTGAGCCTCTG 59.699 50.000 0.00 0.00 0.00 3.35
37 38 1.881602 ACGAACTCTACCGTCTGCC 59.118 57.895 0.00 0.00 33.23 4.85
45 46 1.153881 GTGGCCCGACGAACTCTAC 60.154 63.158 0.00 0.00 0.00 2.59
46 47 0.035152 TAGTGGCCCGACGAACTCTA 60.035 55.000 0.00 0.00 0.00 2.43
47 48 1.303888 TAGTGGCCCGACGAACTCT 60.304 57.895 0.00 0.00 0.00 3.24
51 52 1.604308 TCACTAGTGGCCCGACGAA 60.604 57.895 22.48 0.00 0.00 3.85
60 61 2.567169 TGGACTCAATGGTCACTAGTGG 59.433 50.000 22.48 5.66 37.91 4.00
62 63 3.452627 GGATGGACTCAATGGTCACTAGT 59.547 47.826 0.00 0.00 37.91 2.57
68 69 0.830648 TCGGGATGGACTCAATGGTC 59.169 55.000 0.00 0.00 35.66 4.02
96 97 1.206578 CGACAACAATGCGGGTCAC 59.793 57.895 0.00 0.00 0.00 3.67
97 98 0.948623 CTCGACAACAATGCGGGTCA 60.949 55.000 0.00 0.00 0.00 4.02
100 101 0.953471 TTCCTCGACAACAATGCGGG 60.953 55.000 0.00 0.00 0.00 6.13
131 132 4.222336 ACTCCATCTCATAACTCCTCCAG 58.778 47.826 0.00 0.00 0.00 3.86
135 136 9.308000 CTAATAGAACTCCATCTCATAACTCCT 57.692 37.037 0.00 0.00 0.00 3.69
136 137 9.303116 TCTAATAGAACTCCATCTCATAACTCC 57.697 37.037 0.00 0.00 0.00 3.85
141 142 9.527157 CCTCTTCTAATAGAACTCCATCTCATA 57.473 37.037 0.00 0.00 29.89 2.15
151 198 7.841729 TGTTGAGATCCCTCTTCTAATAGAACT 59.158 37.037 0.00 0.00 40.10 3.01
158 205 4.689062 ACCTGTTGAGATCCCTCTTCTAA 58.311 43.478 0.00 0.00 40.10 2.10
178 225 0.517316 ATCGTTCTTGCGCTTCAACC 59.483 50.000 9.73 0.00 0.00 3.77
181 228 1.911293 GCCATCGTTCTTGCGCTTCA 61.911 55.000 9.73 0.00 0.00 3.02
194 241 0.035056 AAGACCCTTCCTTGCCATCG 60.035 55.000 0.00 0.00 0.00 3.84
210 257 2.342279 CGCCTTGACCCGTGAAGA 59.658 61.111 0.00 0.00 0.00 2.87
217 264 1.627297 ATCCTTCTCCGCCTTGACCC 61.627 60.000 0.00 0.00 0.00 4.46
224 271 2.550101 GCATGCATCCTTCTCCGCC 61.550 63.158 14.21 0.00 0.00 6.13
226 273 1.895707 GGGCATGCATCCTTCTCCG 60.896 63.158 21.36 0.00 0.00 4.63
227 274 0.536915 GAGGGCATGCATCCTTCTCC 60.537 60.000 21.36 8.68 32.74 3.71
231 278 2.194056 CGGAGGGCATGCATCCTT 59.806 61.111 28.53 7.99 32.74 3.36
245 292 0.108963 CAAGGTTAACCACACCCGGA 59.891 55.000 26.26 0.00 38.89 5.14
247 294 2.194201 ATCAAGGTTAACCACACCCG 57.806 50.000 26.26 7.84 38.89 5.28
257 304 2.267188 CGTCGTCGGAATCAAGGTTA 57.733 50.000 0.00 0.00 0.00 2.85
273 320 2.971452 GGACACCTCACTCCCGTC 59.029 66.667 0.00 0.00 0.00 4.79
299 346 3.004734 CACACATTCAAAGTTCCCAGTCC 59.995 47.826 0.00 0.00 0.00 3.85
312 396 3.420893 GATCCAAAGTCCCACACATTCA 58.579 45.455 0.00 0.00 0.00 2.57
319 403 2.474410 ACTTCGATCCAAAGTCCCAC 57.526 50.000 2.97 0.00 31.36 4.61
321 405 3.889520 ACTACTTCGATCCAAAGTCCC 57.110 47.619 10.54 0.00 38.00 4.46
323 407 7.707035 ACATTCATACTACTTCGATCCAAAGTC 59.293 37.037 10.54 0.00 38.00 3.01
332 432 6.093082 TCTGACGAACATTCATACTACTTCGA 59.907 38.462 4.74 0.00 35.59 3.71
364 464 1.625818 ACCCAAAACAGCAAAACCACA 59.374 42.857 0.00 0.00 0.00 4.17
365 465 2.006169 CACCCAAAACAGCAAAACCAC 58.994 47.619 0.00 0.00 0.00 4.16
366 466 1.677217 GCACCCAAAACAGCAAAACCA 60.677 47.619 0.00 0.00 0.00 3.67
397 498 1.285950 GGCGTCTCCAAAAGTTGCC 59.714 57.895 0.00 0.00 38.52 4.52
447 548 9.474920 GTCTGTGAAATAAAATTTTGGTCATCA 57.525 29.630 13.76 7.85 0.00 3.07
448 549 8.638565 CGTCTGTGAAATAAAATTTTGGTCATC 58.361 33.333 13.76 5.61 0.00 2.92
451 552 7.924103 ACGTCTGTGAAATAAAATTTTGGTC 57.076 32.000 13.76 8.21 0.00 4.02
452 553 8.710835 AAACGTCTGTGAAATAAAATTTTGGT 57.289 26.923 13.76 0.00 0.00 3.67
455 556 9.157104 ACCAAAACGTCTGTGAAATAAAATTTT 57.843 25.926 8.75 8.75 0.00 1.82
458 559 6.200097 GCACCAAAACGTCTGTGAAATAAAAT 59.800 34.615 9.89 0.00 0.00 1.82
461 562 4.498345 GGCACCAAAACGTCTGTGAAATAA 60.498 41.667 9.89 0.00 0.00 1.40
466 567 2.399856 GGCACCAAAACGTCTGTGA 58.600 52.632 9.89 0.00 0.00 3.58
493 594 4.288670 TCAGCGTCTACAATAGCTACAC 57.711 45.455 0.00 0.00 37.94 2.90
496 597 4.095334 TCGTTTCAGCGTCTACAATAGCTA 59.905 41.667 0.00 0.00 37.94 3.32
505 606 0.245266 TGCCATCGTTTCAGCGTCTA 59.755 50.000 0.00 0.00 0.00 2.59
509 610 1.699656 CCTCTGCCATCGTTTCAGCG 61.700 60.000 0.00 0.00 0.00 5.18
513 614 1.098050 ATTGCCTCTGCCATCGTTTC 58.902 50.000 0.00 0.00 36.33 2.78
514 615 1.549203 AATTGCCTCTGCCATCGTTT 58.451 45.000 0.00 0.00 36.33 3.60
522 623 1.012486 GTGCTGCAAATTGCCTCTGC 61.012 55.000 15.98 13.98 44.23 4.26
523 624 0.601558 AGTGCTGCAAATTGCCTCTG 59.398 50.000 15.98 4.46 44.23 3.35
524 625 0.601558 CAGTGCTGCAAATTGCCTCT 59.398 50.000 15.98 4.40 44.23 3.69
527 628 0.033781 TTCCAGTGCTGCAAATTGCC 59.966 50.000 15.98 1.18 44.23 4.52
549 650 6.628185 TGTCGACGACTCTATATATAGCAGA 58.372 40.000 26.86 0.00 33.15 4.26
592 699 6.260714 GGCAGAAAAATTCCAACACTTTTCAT 59.739 34.615 8.38 0.00 39.27 2.57
598 705 4.443315 CCTTGGCAGAAAAATTCCAACACT 60.443 41.667 0.00 0.00 35.07 3.55
609 716 2.199652 CGCACCCCTTGGCAGAAAA 61.200 57.895 0.00 0.00 33.59 2.29
630 737 3.756727 GCTGGGCTGCAAAGCTCC 61.757 66.667 15.91 1.50 33.54 4.70
674 781 4.787280 CTGCGGTCTCCCTCCCCT 62.787 72.222 0.00 0.00 0.00 4.79
777 996 3.830755 CACACAAGGTACAGTAGGTAGGT 59.169 47.826 0.00 0.00 31.13 3.08
779 998 3.194968 CCCACACAAGGTACAGTAGGTAG 59.805 52.174 0.00 0.00 31.13 3.18
780 999 3.167485 CCCACACAAGGTACAGTAGGTA 58.833 50.000 0.00 0.00 0.00 3.08
781 1000 1.975680 CCCACACAAGGTACAGTAGGT 59.024 52.381 0.00 0.00 0.00 3.08
783 1002 4.253685 CATTCCCACACAAGGTACAGTAG 58.746 47.826 0.00 0.00 0.00 2.57
784 1003 3.558321 GCATTCCCACACAAGGTACAGTA 60.558 47.826 0.00 0.00 0.00 2.74
785 1004 2.814097 GCATTCCCACACAAGGTACAGT 60.814 50.000 0.00 0.00 0.00 3.55
824 1043 1.674441 CAGTGACCACATGCATGATCC 59.326 52.381 32.75 17.45 0.00 3.36
836 1055 2.016318 CTTTTGTGCAGACAGTGACCA 58.984 47.619 0.00 0.00 32.26 4.02
838 1057 1.268743 GGCTTTTGTGCAGACAGTGAC 60.269 52.381 0.00 0.00 32.26 3.67
859 1078 1.443702 CGCATTCCACTGTCGACGA 60.444 57.895 11.62 0.00 0.00 4.20
860 1079 1.733041 ACGCATTCCACTGTCGACG 60.733 57.895 11.62 8.41 0.00 5.12
862 1081 1.374125 CCACGCATTCCACTGTCGA 60.374 57.895 0.00 0.00 0.00 4.20
865 1084 1.909700 AATTCCACGCATTCCACTGT 58.090 45.000 0.00 0.00 0.00 3.55
866 1085 4.637483 ATTAATTCCACGCATTCCACTG 57.363 40.909 0.00 0.00 0.00 3.66
867 1086 6.545666 TCAATATTAATTCCACGCATTCCACT 59.454 34.615 0.00 0.00 0.00 4.00
870 1100 5.851177 CGTCAATATTAATTCCACGCATTCC 59.149 40.000 0.00 0.00 0.00 3.01
1155 2845 1.827344 ACGAGATCCATCTGCTTGTCA 59.173 47.619 0.00 0.00 37.25 3.58
1188 2880 0.684535 TGGCAAAGACCTCGATGTCA 59.315 50.000 20.79 4.17 37.73 3.58
1191 2883 1.089920 CCTTGGCAAAGACCTCGATG 58.910 55.000 1.11 0.00 35.19 3.84
1203 2895 1.599518 CAACCAGCGTACCTTGGCA 60.600 57.895 9.60 0.00 0.00 4.92
1233 2925 4.220163 TGATGGAGTATCTGCATAGAGCTG 59.780 45.833 0.00 0.00 42.36 4.24
1281 2977 3.130340 TGATGAAGATCGATTCCGTCACA 59.870 43.478 0.00 1.25 37.05 3.58
1288 2984 7.797587 GTGAAATGACATGATGAAGATCGATTC 59.202 37.037 0.00 0.00 0.00 2.52
1290 2986 6.764560 TGTGAAATGACATGATGAAGATCGAT 59.235 34.615 0.00 0.00 0.00 3.59
1305 3001 6.729187 ACAAAAAGACTAGCTGTGAAATGAC 58.271 36.000 0.00 0.00 0.00 3.06
1412 3114 0.028902 ACGACGCTGTTTGCCTTTTC 59.971 50.000 0.00 0.00 38.78 2.29
1420 3122 1.956170 CTGAGGCACGACGCTGTTT 60.956 57.895 0.00 0.00 41.91 2.83
1440 3142 3.362706 ACGGGAGTAGTCTTCATAAGCA 58.637 45.455 0.00 0.00 44.60 3.91
1450 3152 3.593096 CCCAAGTTTAACGGGAGTAGTC 58.407 50.000 9.76 0.00 46.69 2.59
1453 3155 2.337849 ACCCCAAGTTTAACGGGAGTA 58.662 47.619 12.40 0.00 46.69 2.59
1503 3213 7.168219 TGAATATTTACCAGCCACCATAGATC 58.832 38.462 0.00 0.00 0.00 2.75
1545 3255 4.893829 AGAGATGATGAGATCCACATGG 57.106 45.455 7.57 0.00 0.00 3.66
1605 3315 7.095649 TGACGTCAAGTAATCTTTCAATCAGTG 60.096 37.037 17.62 0.00 0.00 3.66
1606 3316 6.929049 TGACGTCAAGTAATCTTTCAATCAGT 59.071 34.615 17.62 0.00 0.00 3.41
1607 3317 7.351414 TGACGTCAAGTAATCTTTCAATCAG 57.649 36.000 17.62 0.00 0.00 2.90
1608 3318 7.722795 TTGACGTCAAGTAATCTTTCAATCA 57.277 32.000 26.53 0.00 28.21 2.57
1652 3362 2.415357 CCGTCGCCTGCACATTTAATTT 60.415 45.455 0.00 0.00 0.00 1.82
1771 3481 7.255520 GGTTACTATATATCCATGCGTCCTAGG 60.256 44.444 0.82 0.82 0.00 3.02
1970 3686 9.399797 TGTTTGTATCTGATAAGAATTCATGCT 57.600 29.630 8.44 0.00 0.00 3.79
2120 3836 0.827089 CCATTTGCACAGACCCACCA 60.827 55.000 0.00 0.00 0.00 4.17
2348 4067 6.587206 TGCATGTTCAGGTATCAATTTTCA 57.413 33.333 0.00 0.00 0.00 2.69
2354 4110 5.712004 CATGTTTGCATGTTCAGGTATCAA 58.288 37.500 0.00 0.00 45.48 2.57
2493 4252 5.710099 GTGATACCTTGGGAGAATGTTTTGA 59.290 40.000 0.00 0.00 0.00 2.69
2518 4277 5.103940 AGGGTCTTGCCATATTGAACACTAT 60.104 40.000 0.00 0.00 39.65 2.12
2624 4548 6.375736 CCAACACCCCTTTTATTTTGTTTTGT 59.624 34.615 0.00 0.00 0.00 2.83
3114 5208 6.882140 TCAGTTATTGGGTTACTGGTTATGTG 59.118 38.462 0.00 0.00 39.71 3.21
3184 5278 9.910267 CCTTGGAATATGACATATATGGATGAA 57.090 33.333 16.96 0.00 0.00 2.57
3185 5279 9.282905 TCCTTGGAATATGACATATATGGATGA 57.717 33.333 16.96 0.44 0.00 2.92
3186 5280 9.910267 TTCCTTGGAATATGACATATATGGATG 57.090 33.333 16.96 0.00 0.00 3.51
3194 5288 9.066892 GCTGTATTTTCCTTGGAATATGACATA 57.933 33.333 13.20 0.00 0.00 2.29
3195 5289 7.781693 AGCTGTATTTTCCTTGGAATATGACAT 59.218 33.333 13.20 0.00 0.00 3.06
3196 5290 7.118723 AGCTGTATTTTCCTTGGAATATGACA 58.881 34.615 13.20 11.82 0.00 3.58
3197 5291 7.573968 AGCTGTATTTTCCTTGGAATATGAC 57.426 36.000 13.20 9.07 0.00 3.06
3198 5292 8.271458 TGTAGCTGTATTTTCCTTGGAATATGA 58.729 33.333 13.20 2.61 0.00 2.15
3199 5293 8.450578 TGTAGCTGTATTTTCCTTGGAATATG 57.549 34.615 13.20 1.74 0.00 1.78
3200 5294 9.646522 ATTGTAGCTGTATTTTCCTTGGAATAT 57.353 29.630 2.65 6.73 0.00 1.28
3201 5295 8.902806 CATTGTAGCTGTATTTTCCTTGGAATA 58.097 33.333 2.65 0.00 0.00 1.75
3202 5296 7.147846 CCATTGTAGCTGTATTTTCCTTGGAAT 60.148 37.037 2.65 0.00 0.00 3.01
3203 5297 6.152661 CCATTGTAGCTGTATTTTCCTTGGAA 59.847 38.462 0.00 0.00 0.00 3.53
3211 5305 5.815581 TCCTCACCATTGTAGCTGTATTTT 58.184 37.500 0.00 0.00 0.00 1.82
3297 5391 0.868406 CGAGTCAAGTTTGAGTGCCC 59.132 55.000 6.92 0.00 40.75 5.36
4164 6268 8.706322 AACAATAATTGTAAGGAAAGTCAGGT 57.294 30.769 0.00 0.00 44.59 4.00
4370 6477 4.139786 CACCAGCTTTGACATAGGCATAT 58.860 43.478 0.00 0.00 0.00 1.78
4429 6989 2.649816 AGGTGGCTATGGAGGTTTTTCT 59.350 45.455 0.00 0.00 0.00 2.52
4455 7017 0.466543 ATGCGGGGTGTAAGCGATTA 59.533 50.000 0.00 0.00 33.03 1.75
4519 7082 1.577468 CGGTGTACACAGTTGCTTCA 58.423 50.000 26.51 0.00 0.00 3.02
4527 7090 4.066490 TGGTTATTTTCCGGTGTACACAG 58.934 43.478 26.51 22.23 0.00 3.66
4784 7722 5.485620 ACCGGGTCTCTTAACAGATTTTAC 58.514 41.667 6.32 0.00 0.00 2.01
4989 7927 0.031043 TACGCGGGGTTCATATGTCG 59.969 55.000 12.47 2.39 0.00 4.35
4998 7936 2.037144 AGTCATATCTTACGCGGGGTT 58.963 47.619 12.47 0.00 0.00 4.11
5045 7983 4.099573 AGTTACCAGAAATCCATCGTCGAT 59.900 41.667 0.75 0.75 0.00 3.59
5089 8028 7.615039 ACTTCTAGATCCATCACAGATTGAT 57.385 36.000 0.00 0.00 46.75 2.57
5091 8030 7.042858 CGAAACTTCTAGATCCATCACAGATTG 60.043 40.741 0.00 0.00 0.00 2.67
5103 8042 8.912787 TTGATCTGTAACGAAACTTCTAGATC 57.087 34.615 0.00 0.00 39.60 2.75
5115 8054 6.312918 GTGAGCCTATTTTTGATCTGTAACGA 59.687 38.462 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.