Multiple sequence alignment - TraesCS2B01G600400

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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 TraesCS2B01G600400 chr2B 100.000 4199 0 0 766 4964 783651216 783647018 0.000000e+00 7755.0
1 TraesCS2B01G600400 chr2B 90.606 990 69 17 1427 2399 783864624 783863642 0.000000e+00 1291.0
2 TraesCS2B01G600400 chr2B 100.000 518 0 0 1 518 783651981 783651464 0.000000e+00 957.0
3 TraesCS2B01G600400 chr2B 91.139 474 38 3 3 473 783867645 783867173 1.510000e-179 640.0
4 TraesCS2B01G600400 chr2B 90.717 474 40 3 3 473 784159395 784158923 3.260000e-176 628.0
5 TraesCS2B01G600400 chr2B 93.391 348 18 4 766 1111 783865279 783864935 1.230000e-140 510.0
6 TraesCS2B01G600400 chr2B 97.902 286 6 0 1145 1430 783864940 783864655 3.450000e-136 496.0
7 TraesCS2B01G600400 chr2B 87.500 56 4 3 1240 1293 450440848 450440902 1.490000e-05 62.1
8 TraesCS2B01G600400 chr2B 100.000 29 0 0 2418 2446 783649533 783649505 2.000000e-03 54.7
9 TraesCS2B01G600400 chr2B 100.000 29 0 0 2449 2477 783649564 783649536 2.000000e-03 54.7
10 TraesCS2B01G600400 chr4A 90.027 2547 241 8 2420 4964 152764842 152767377 0.000000e+00 3284.0
11 TraesCS2B01G600400 chr4A 75.362 552 124 9 3808 4354 16046207 16045663 6.380000e-64 255.0
12 TraesCS2B01G600400 chr6B 89.440 2519 253 8 2449 4964 485543663 485546171 0.000000e+00 3166.0
13 TraesCS2B01G600400 chr6B 85.530 2557 343 13 2415 4964 599435444 599432908 0.000000e+00 2647.0
14 TraesCS2B01G600400 chr6B 100.000 30 0 0 2417 2446 485543662 485543691 6.940000e-04 56.5
15 TraesCS2B01G600400 chr3B 91.115 1193 89 8 3784 4964 778990791 778991978 0.000000e+00 1600.0
16 TraesCS2B01G600400 chr3B 90.696 1193 94 8 3784 4964 778908579 778909766 0.000000e+00 1572.0
17 TraesCS2B01G600400 chr3B 89.796 49 4 1 54 102 4723212 4723259 1.490000e-05 62.1
18 TraesCS2B01G600400 chr3B 94.737 38 2 0 2699 2736 22641674 22641711 5.370000e-05 60.2
19 TraesCS2B01G600400 chr4D 88.575 884 91 6 4081 4964 47253181 47252308 0.000000e+00 1064.0
20 TraesCS2B01G600400 chrUn 93.158 380 25 1 4585 4964 479266061 479266439 1.560000e-154 556.0
21 TraesCS2B01G600400 chrUn 88.439 346 30 3 3784 4119 477919044 477919389 4.630000e-110 409.0
22 TraesCS2B01G600400 chr6D 80.519 154 27 3 5 156 456482747 456482899 1.130000e-21 115.0
23 TraesCS2B01G600400 chr3D 86.301 73 5 3 1304 1373 47613279 47613209 1.920000e-09 75.0
24 TraesCS2B01G600400 chr3A 97.561 41 1 0 3774 3814 700244379 700244419 2.480000e-08 71.3
25 TraesCS2B01G600400 chr7D 90.000 50 3 2 2435 2482 625375582 625375631 4.150000e-06 63.9


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 TraesCS2B01G600400 chr2B 783647018 783651981 4963 True 2205.35 7755 100.0000 1 4964 4 chr2B.!!$R2 4963
1 TraesCS2B01G600400 chr2B 783863642 783867645 4003 True 734.25 1291 93.2595 3 2399 4 chr2B.!!$R3 2396
2 TraesCS2B01G600400 chr4A 152764842 152767377 2535 False 3284.00 3284 90.0270 2420 4964 1 chr4A.!!$F1 2544
3 TraesCS2B01G600400 chr4A 16045663 16046207 544 True 255.00 255 75.3620 3808 4354 1 chr4A.!!$R1 546
4 TraesCS2B01G600400 chr6B 599432908 599435444 2536 True 2647.00 2647 85.5300 2415 4964 1 chr6B.!!$R1 2549
5 TraesCS2B01G600400 chr6B 485543662 485546171 2509 False 1611.25 3166 94.7200 2417 4964 2 chr6B.!!$F1 2547
6 TraesCS2B01G600400 chr3B 778990791 778991978 1187 False 1600.00 1600 91.1150 3784 4964 1 chr3B.!!$F4 1180
7 TraesCS2B01G600400 chr3B 778908579 778909766 1187 False 1572.00 1572 90.6960 3784 4964 1 chr3B.!!$F3 1180
8 TraesCS2B01G600400 chr4D 47252308 47253181 873 True 1064.00 1064 88.5750 4081 4964 1 chr4D.!!$R1 883

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
154 156 0.175989 GTCCAAGGACCATCGGAGAC 59.824 60.0 8.06 0.00 38.21 3.36 F
1516 3157 0.109735 GCACTTAAGGCGCCTGTTTC 60.110 55.0 33.60 13.58 0.00 2.78 F
2919 4580 0.179004 TGTGTTTGGGCGACTGGAAT 60.179 50.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 3174 0.673644 CGGATGGGGATTATGCGTCC 60.674 60.0 0.00 0.00 35.13 4.79 R
3283 4944 0.397941 CGTATGGCCCATGAGTCCAT 59.602 55.0 6.46 14.69 42.70 3.41 R
4023 5693 0.179092 GATAACAACCGGGCTACGCT 60.179 55.0 6.32 0.00 42.52 5.07 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
27 28 2.568623 ATTTCACCTTCAGAAGCCGT 57.431 45.000 4.41 0.00 0.00 5.68
36 37 4.643387 AGAAGCCGTTGCCGCCTT 62.643 61.111 0.00 0.00 33.97 4.35
51 52 2.545526 CCGCCTTGTCTTACTATGCATG 59.454 50.000 10.16 1.82 0.00 4.06
52 53 2.545526 CGCCTTGTCTTACTATGCATGG 59.454 50.000 10.16 9.41 0.00 3.66
75 76 7.662897 TGGCACAAACCCTAAAAATACTTTAG 58.337 34.615 0.00 0.00 31.92 1.85
95 97 6.628919 TTAGAAAACACCTAAAACAGAGCC 57.371 37.500 0.00 0.00 0.00 4.70
154 156 0.175989 GTCCAAGGACCATCGGAGAC 59.824 60.000 8.06 0.00 38.21 3.36
166 168 4.459089 GGAGACGGGGCAGACTGC 62.459 72.222 19.55 19.55 44.08 4.40
185 187 3.755628 GGCGGCACCGACTAGACA 61.756 66.667 14.43 0.00 45.30 3.41
218 220 3.512516 GCATTGGTCGCAGGAGGC 61.513 66.667 0.00 0.00 39.90 4.70
223 225 3.695606 GGTCGCAGGAGGCAGTGA 61.696 66.667 0.00 0.00 45.17 3.41
229 231 3.334054 AGGAGGCAGTGAAGGGGC 61.334 66.667 0.00 0.00 0.00 5.80
232 234 4.335647 AGGCAGTGAAGGGGCACG 62.336 66.667 0.00 0.00 43.42 5.34
238 240 4.974438 TGAAGGGGCACGGGGTCT 62.974 66.667 0.00 0.00 0.00 3.85
257 261 4.098196 GGTCTGCCTCTAGTTACGATCTTT 59.902 45.833 0.00 0.00 0.00 2.52
365 369 6.037098 CGTCAAATCACTTAGACTAGAAGGG 58.963 44.000 0.00 0.00 0.00 3.95
396 400 9.318041 CGCCGATCAAATATTAGTTAGATTTTG 57.682 33.333 0.00 0.00 0.00 2.44
460 464 7.724305 ATGATATGCATTTTCCTTTGATTGC 57.276 32.000 3.54 0.00 31.73 3.56
462 466 7.332557 TGATATGCATTTTCCTTTGATTGCTT 58.667 30.769 3.54 0.00 0.00 3.91
466 470 6.496571 TGCATTTTCCTTTGATTGCTTTTTG 58.503 32.000 0.00 0.00 0.00 2.44
467 471 5.916320 GCATTTTCCTTTGATTGCTTTTTGG 59.084 36.000 0.00 0.00 0.00 3.28
491 1074 6.128472 GGAAACAAATGTGATTGGAAATCAGC 60.128 38.462 2.96 0.70 34.56 4.26
505 1088 6.680810 TGGAAATCAGCAAAACTATGACAAG 58.319 36.000 0.00 0.00 0.00 3.16
516 1099 9.214953 GCAAAACTATGACAAGAATAAGAATCG 57.785 33.333 0.00 0.00 0.00 3.34
850 2455 3.319137 AGCAGTGCTTTCTCGTGATAA 57.681 42.857 13.14 0.00 33.89 1.75
1007 2612 6.804783 TGTCTTTTTCGAGAAAGGAAAAACAC 59.195 34.615 23.65 14.82 44.17 3.32
1014 2619 9.891064 TTTCGAGAAAGGAAAAACACAGCTGTG 62.891 40.741 38.76 38.76 39.72 3.66
1047 2652 3.715628 ATTGAAACAGGACAACAGTGC 57.284 42.857 0.00 0.00 0.00 4.40
1050 2657 2.024414 GAAACAGGACAACAGTGCCTT 58.976 47.619 0.00 0.00 31.35 4.35
1078 2685 2.952116 TCATTTTCCCCAGTTTTCGGT 58.048 42.857 0.00 0.00 0.00 4.69
1192 2799 8.659527 TCATATGGGTTCTAGCTTCAAATATCA 58.340 33.333 2.13 0.00 0.00 2.15
1222 2829 4.608073 AAAAACCAACATTGAAAACGGC 57.392 36.364 0.00 0.00 0.00 5.68
1311 2918 2.936498 ACTAACATATTGTCAGTGCGCC 59.064 45.455 4.18 0.00 25.11 6.53
1434 3075 1.087501 CCTTTTGCTCTCGGGTAAGC 58.912 55.000 0.00 0.00 39.02 3.09
1438 3079 1.544825 TTGCTCTCGGGTAAGCTGCT 61.545 55.000 0.00 0.00 39.31 4.24
1448 3089 2.290323 GGGTAAGCTGCTGGAAAGAGAA 60.290 50.000 1.35 0.00 0.00 2.87
1453 3094 1.069636 GCTGCTGGAAAGAGAACAACG 60.070 52.381 0.00 0.00 0.00 4.10
1467 3108 4.250305 AACGCGTGCCCACTTCCT 62.250 61.111 14.98 0.00 0.00 3.36
1499 3140 2.791347 TAGGCATTTCCTAAACGGCA 57.209 45.000 0.00 0.00 45.41 5.69
1516 3157 0.109735 GCACTTAAGGCGCCTGTTTC 60.110 55.000 33.60 13.58 0.00 2.78
1533 3174 4.358851 TGTTTCTTTGATTCCTGCAAACG 58.641 39.130 0.00 0.00 32.35 3.60
1561 3202 2.028125 ATCCCCATCCGCACTGTACG 62.028 60.000 0.00 0.00 0.00 3.67
1589 3230 3.754850 GGTAACCACCCAGTACAACATTC 59.245 47.826 0.00 0.00 39.11 2.67
1756 3397 9.778993 CTCGAGTTCATGAACATTTTTAATGAT 57.221 29.630 33.92 13.61 43.47 2.45
1917 3566 9.796062 CAATTCGATTAACCACTTTTCAAATTG 57.204 29.630 0.00 0.00 0.00 2.32
2080 3735 5.010820 TCCATGTGCATTTTTCAATCTGTGA 59.989 36.000 0.00 0.00 0.00 3.58
2081 3736 5.697178 CCATGTGCATTTTTCAATCTGTGAA 59.303 36.000 0.00 0.00 44.74 3.18
2082 3737 6.347079 CCATGTGCATTTTTCAATCTGTGAAC 60.347 38.462 0.00 0.00 46.09 3.18
2083 3738 5.658468 TGTGCATTTTTCAATCTGTGAACA 58.342 33.333 0.00 0.00 46.09 3.18
2214 3869 0.456824 GACAGTGAAGCGATCGAGCA 60.457 55.000 21.57 10.10 40.15 4.26
2222 3877 1.363744 AGCGATCGAGCAAAGGAAAG 58.636 50.000 21.57 0.00 40.15 2.62
2244 3899 0.179097 GCGAGCGAGAGAAAGGGAAT 60.179 55.000 0.00 0.00 0.00 3.01
2260 3915 1.537135 GGAATAGCGAGTGACCAGCTC 60.537 57.143 5.68 0.00 41.88 4.09
2291 3947 4.457496 CCCACGCGAGATGGCTGT 62.457 66.667 15.93 0.00 35.74 4.40
2307 3963 3.475566 GCTGTGTGAGCCCATTATCTA 57.524 47.619 0.00 0.00 42.54 1.98
2312 3968 4.067896 GTGTGAGCCCATTATCTACCATG 58.932 47.826 0.00 0.00 0.00 3.66
2327 3983 3.719173 ACCATGTGTTTTGTTAACCGG 57.281 42.857 0.00 0.00 0.00 5.28
2334 3990 5.619220 TGTGTTTTGTTAACCGGTACCTAT 58.381 37.500 8.00 0.00 0.00 2.57
2337 3993 7.096551 GTGTTTTGTTAACCGGTACCTATAGA 58.903 38.462 8.00 0.00 0.00 1.98
2338 3994 7.063426 GTGTTTTGTTAACCGGTACCTATAGAC 59.937 40.741 8.00 1.85 0.00 2.59
2340 3996 5.129368 TGTTAACCGGTACCTATAGACCT 57.871 43.478 8.00 0.00 33.21 3.85
2341 3997 5.518865 TGTTAACCGGTACCTATAGACCTT 58.481 41.667 8.00 0.00 33.21 3.50
2342 3998 5.360714 TGTTAACCGGTACCTATAGACCTTG 59.639 44.000 8.00 0.00 33.21 3.61
2344 4000 3.830121 ACCGGTACCTATAGACCTTGAG 58.170 50.000 4.49 0.00 33.21 3.02
2345 4001 3.461085 ACCGGTACCTATAGACCTTGAGA 59.539 47.826 4.49 0.00 33.21 3.27
2346 4002 4.106019 ACCGGTACCTATAGACCTTGAGAT 59.894 45.833 4.49 0.00 33.21 2.75
2348 4004 6.183361 ACCGGTACCTATAGACCTTGAGATTA 60.183 42.308 4.49 0.00 33.21 1.75
2363 4020 3.195661 GAGATTACGTCAAAGCGGGATT 58.804 45.455 0.00 0.00 35.98 3.01
2396 4053 3.761481 CGTGAAGCAAAGCCAAGAG 57.239 52.632 0.00 0.00 0.00 2.85
2397 4054 0.239347 CGTGAAGCAAAGCCAAGAGG 59.761 55.000 0.00 0.00 38.23 3.69
2407 4064 4.722193 CCAAGAGGCGGTCACAAT 57.278 55.556 0.00 0.00 0.00 2.71
2408 4065 3.853104 CCAAGAGGCGGTCACAATA 57.147 52.632 0.00 0.00 0.00 1.90
2409 4066 2.332063 CCAAGAGGCGGTCACAATAT 57.668 50.000 0.00 0.00 0.00 1.28
2410 4067 2.643551 CCAAGAGGCGGTCACAATATT 58.356 47.619 0.00 0.00 0.00 1.28
2411 4068 3.804036 CCAAGAGGCGGTCACAATATTA 58.196 45.455 0.00 0.00 0.00 0.98
2412 4069 4.389374 CCAAGAGGCGGTCACAATATTAT 58.611 43.478 0.00 0.00 0.00 1.28
2413 4070 4.452455 CCAAGAGGCGGTCACAATATTATC 59.548 45.833 0.00 0.00 0.00 1.75
2499 4158 5.127031 CCCCATCTACACCAAAAATACCAAG 59.873 44.000 0.00 0.00 0.00 3.61
2516 4175 3.138304 CCAAGTTTCTCACGTTGGATCA 58.862 45.455 0.00 0.00 41.82 2.92
2610 4270 4.314440 GTGACCACGCCCTCAGCA 62.314 66.667 0.00 0.00 44.04 4.41
2679 4339 2.229792 TGCAACTTGGAAGATCGCTTT 58.770 42.857 0.00 0.00 33.61 3.51
2688 4348 3.007506 TGGAAGATCGCTTTGTTGGACTA 59.992 43.478 0.00 0.00 33.61 2.59
2696 4357 4.003648 CGCTTTGTTGGACTAAATCTCCT 58.996 43.478 0.00 0.00 0.00 3.69
2883 4544 7.291566 TCTTCAAAACAATGAACCCTAACCTA 58.708 34.615 0.00 0.00 35.55 3.08
2919 4580 0.179004 TGTGTTTGGGCGACTGGAAT 60.179 50.000 0.00 0.00 0.00 3.01
2960 4621 4.403432 CCCATGGCTGTTTCAAGATAATGT 59.597 41.667 6.09 0.00 0.00 2.71
3017 4678 3.055819 GTCCAGGACTACAAGCTTGATCA 60.056 47.826 32.50 15.37 0.00 2.92
3051 4712 3.181434 GGGCAAGGATCATTGGTATACCA 60.181 47.826 21.05 21.05 45.94 3.25
3098 4759 5.593679 ATTGCTGAGAAAATAGCTGCAAT 57.406 34.783 8.75 8.75 45.55 3.56
3257 4918 6.696411 GGAAATATCCAGTGGAGTATGAGAG 58.304 44.000 18.69 0.00 45.79 3.20
3258 4919 6.495181 GGAAATATCCAGTGGAGTATGAGAGA 59.505 42.308 18.69 0.00 45.79 3.10
3283 4944 2.025605 TCCCGGAGTTCTGCTACTTCTA 60.026 50.000 0.73 0.00 0.00 2.10
3340 5001 0.394899 GGCATTCACAGGAAGGAGGG 60.395 60.000 0.00 0.00 36.97 4.30
3351 5012 0.329596 GAAGGAGGGCTGTGAATGGT 59.670 55.000 0.00 0.00 0.00 3.55
3522 5183 0.616891 GGTGGTAGACCCCAATTCGT 59.383 55.000 0.00 0.00 39.10 3.85
3636 5297 2.244695 CCCCTCCTTTGGGTTTTGTAC 58.755 52.381 0.00 0.00 45.70 2.90
3671 5332 0.978907 TGATTGAGAGCAGCACCTCA 59.021 50.000 12.04 12.04 37.61 3.86
3719 5380 2.951642 CACCCCGCAAAAGATACATGAT 59.048 45.455 0.00 0.00 0.00 2.45
3769 5430 2.657372 CTGAAGTGAACGAAGCTACGTC 59.343 50.000 0.00 0.00 45.83 4.34
3806 5467 3.157252 GAGGAGGATCGCTGGGCA 61.157 66.667 0.00 0.00 34.37 5.36
3869 5530 1.973812 GCGGCAGAAAGGGCTCTTT 60.974 57.895 12.48 12.48 45.09 2.52
3874 5535 1.270826 GCAGAAAGGGCTCTTTTGGAC 59.729 52.381 14.03 0.00 42.72 4.02
3936 5597 2.029020 AGACGCATCTGAACACAGCTAA 60.029 45.455 0.00 0.00 32.29 3.09
4023 5693 2.494870 GCGGTGGACTACTCCTTTTCTA 59.505 50.000 0.00 0.00 37.48 2.10
4048 5718 1.005450 AGCCCGGTTGTTATCCACATT 59.995 47.619 0.00 0.00 34.43 2.71
4051 5721 3.181494 GCCCGGTTGTTATCCACATTAAC 60.181 47.826 0.00 0.00 34.43 2.01
4161 5832 3.843619 TGGGAGGACAAACATCTGACATA 59.156 43.478 0.00 0.00 0.00 2.29
4169 5840 4.225042 ACAAACATCTGACATAGGGCTACA 59.775 41.667 0.00 0.00 0.00 2.74
4185 5857 2.743938 CTACATACGGGTCTGCATCAC 58.256 52.381 0.00 0.00 0.00 3.06
4186 5858 0.901827 ACATACGGGTCTGCATCACA 59.098 50.000 0.00 0.00 0.00 3.58
4308 5980 3.053842 ACTTCAGAGATGCATTGGTGGAT 60.054 43.478 0.00 0.00 39.30 3.41
4375 6047 2.686915 CGTAGACGTAGGTTGAGGGAAT 59.313 50.000 0.00 0.00 34.11 3.01
4457 6129 3.661911 TGCGCCGCATACAAAGTT 58.338 50.000 8.16 0.00 31.71 2.66
4501 6173 3.729965 CTAGAGGGTGCTGCTGGCG 62.730 68.421 0.00 0.00 45.43 5.69
4525 6197 5.007034 TGGACCAACAATCATACGTCAAAT 58.993 37.500 0.00 0.00 0.00 2.32
4527 6199 5.216566 ACCAACAATCATACGTCAAATCG 57.783 39.130 0.00 0.00 0.00 3.34
4544 6216 4.379174 GAAGCAGTTCGAAGCCCA 57.621 55.556 0.00 0.00 0.00 5.36
4621 6296 0.984230 TTGCATCTCGGACTCCCTTT 59.016 50.000 0.00 0.00 0.00 3.11
4667 6342 2.456340 AGGATCTCCATAGGTGGGATCA 59.544 50.000 18.78 0.00 44.97 2.92
4783 6458 1.647545 GCAGCGCAGGTTGCTCATTA 61.648 55.000 11.47 0.00 45.72 1.90
4791 6466 4.495349 CGCAGGTTGCTCATTAAGATTGAG 60.495 45.833 0.94 0.94 42.25 3.02
4860 6535 1.821216 ATTGGTTGAAGTTCGGCGAT 58.179 45.000 11.76 0.00 0.00 4.58
4873 6548 2.809446 TCGGCGATAGAAACACTCATG 58.191 47.619 4.99 0.00 39.76 3.07
4951 6626 9.040259 TGATGGATGAAAATGGTAATTGGTTAA 57.960 29.630 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.047731 GCTTCTGAAGGTGAAATAAGGCTTT 60.048 40.000 18.38 0.00 0.00 3.51
1 2 4.460731 GCTTCTGAAGGTGAAATAAGGCTT 59.539 41.667 18.38 4.58 0.00 4.35
27 28 2.627945 CATAGTAAGACAAGGCGGCAA 58.372 47.619 13.08 0.00 0.00 4.52
36 37 3.625649 TGTGCCATGCATAGTAAGACA 57.374 42.857 0.00 0.00 41.91 3.41
51 52 7.888424 TCTAAAGTATTTTTAGGGTTTGTGCC 58.112 34.615 6.78 0.00 40.09 5.01
52 53 9.752961 TTTCTAAAGTATTTTTAGGGTTTGTGC 57.247 29.630 6.78 0.00 40.09 4.57
75 76 3.889538 AGGGCTCTGTTTTAGGTGTTTTC 59.110 43.478 0.00 0.00 0.00 2.29
124 126 3.400205 GGTCCTTGGACCATGGAAACAC 61.400 54.545 28.49 16.27 44.39 3.32
148 150 4.135153 CAGTCTGCCCCGTCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
174 176 1.617357 GTTTCCCTGTGTCTAGTCGGT 59.383 52.381 0.00 0.00 0.00 4.69
203 205 2.270205 CTGCCTCCTGCGACCAAT 59.730 61.111 0.00 0.00 45.60 3.16
218 220 4.722700 CCCCGTGCCCCTTCACTG 62.723 72.222 0.00 0.00 34.92 3.66
229 231 1.258445 AACTAGAGGCAGACCCCGTG 61.258 60.000 0.00 0.00 36.11 4.94
232 234 0.745468 CGTAACTAGAGGCAGACCCC 59.255 60.000 0.00 0.00 36.11 4.95
238 240 4.288670 CGAAAGATCGTAACTAGAGGCA 57.711 45.455 0.00 0.00 44.06 4.75
334 338 6.978338 AGTCTAAGTGATTTGACGACTAACA 58.022 36.000 0.00 0.00 34.92 2.41
338 342 7.362229 CCTTCTAGTCTAAGTGATTTGACGACT 60.362 40.741 0.00 0.00 34.92 4.18
341 345 6.037098 CCCTTCTAGTCTAAGTGATTTGACG 58.963 44.000 0.00 0.00 34.92 4.35
365 369 6.467723 AACTAATATTTGATCGGCGATGTC 57.532 37.500 29.20 15.65 0.00 3.06
460 464 7.551035 TCCAATCACATTTGTTTCCAAAAAG 57.449 32.000 0.00 0.00 43.43 2.27
462 466 7.928307 TTTCCAATCACATTTGTTTCCAAAA 57.072 28.000 0.00 0.00 43.43 2.44
466 470 6.128472 GCTGATTTCCAATCACATTTGTTTCC 60.128 38.462 0.00 0.00 0.00 3.13
467 471 6.424509 TGCTGATTTCCAATCACATTTGTTTC 59.575 34.615 0.00 0.00 0.00 2.78
769 2374 3.181474 CGCCAAAACTAGGAAAACCCAAA 60.181 43.478 0.00 0.00 37.41 3.28
850 2455 0.179073 AACTGTGCTTCTCGTGTGCT 60.179 50.000 6.74 0.00 0.00 4.40
905 2510 2.875672 GCACAACTATGGCTCTTGTGGA 60.876 50.000 11.34 0.00 43.30 4.02
944 2549 4.397420 TGTTCAGGAAGCACACATTGTAT 58.603 39.130 0.00 0.00 0.00 2.29
951 2556 5.222631 CCTTTTTATGTTCAGGAAGCACAC 58.777 41.667 0.00 0.00 0.00 3.82
1057 2664 3.506398 ACCGAAAACTGGGGAAAATGAT 58.494 40.909 0.00 0.00 0.00 2.45
1148 2755 9.532494 CCCATATGAATAGGTTTGGATGATTAA 57.468 33.333 3.65 0.00 0.00 1.40
1212 2819 3.131223 TCCAAATGAACAGCCGTTTTCAA 59.869 39.130 0.00 0.00 35.42 2.69
1222 2829 5.199024 TGAACCATTGTCCAAATGAACAG 57.801 39.130 0.00 0.00 0.00 3.16
1311 2918 2.487934 CTTCTCTGGTGGTGACAAGTG 58.512 52.381 0.00 0.00 46.06 3.16
1373 2980 5.305644 ACTTAGAATCAGCCGGTCAATATCT 59.694 40.000 1.90 3.20 0.00 1.98
1434 3075 1.069636 GCGTTGTTCTCTTTCCAGCAG 60.070 52.381 0.00 0.00 0.00 4.24
1438 3079 0.934496 CACGCGTTGTTCTCTTTCCA 59.066 50.000 10.22 0.00 0.00 3.53
1448 3089 3.276846 GAAGTGGGCACGCGTTGT 61.277 61.111 10.22 0.00 36.20 3.32
1453 3094 3.365265 CCAAGGAAGTGGGCACGC 61.365 66.667 0.00 0.00 34.77 5.34
1499 3140 2.271944 AAGAAACAGGCGCCTTAAGT 57.728 45.000 30.60 20.16 0.00 2.24
1509 3150 4.589216 TTGCAGGAATCAAAGAAACAGG 57.411 40.909 0.00 0.00 0.00 4.00
1516 3157 2.665519 CGTCCGTTTGCAGGAATCAAAG 60.666 50.000 0.00 0.00 39.84 2.77
1533 3174 0.673644 CGGATGGGGATTATGCGTCC 60.674 60.000 0.00 0.00 35.13 4.79
1650 3291 7.497579 AGAAAACTGGCCGAAAACAAATAAATT 59.502 29.630 0.00 0.00 0.00 1.82
1659 3300 3.930229 ACAAAAGAAAACTGGCCGAAAAC 59.070 39.130 0.00 0.00 0.00 2.43
1660 3301 4.195225 ACAAAAGAAAACTGGCCGAAAA 57.805 36.364 0.00 0.00 0.00 2.29
1753 3394 9.835389 AAAAGTTCATGAATTCAAAAAGGATCA 57.165 25.926 13.09 0.00 0.00 2.92
1890 3539 9.757227 AATTTGAAAAGTGGTTAATCGAATTGA 57.243 25.926 0.00 0.00 34.44 2.57
1891 3540 9.796062 CAATTTGAAAAGTGGTTAATCGAATTG 57.204 29.630 10.63 10.63 41.64 2.32
1899 3548 9.883142 AAGTTCATCAATTTGAAAAGTGGTTAA 57.117 25.926 2.68 0.00 37.36 2.01
1955 3604 8.877808 AAGTTCAATGATTTGGAAAAAGAGTC 57.122 30.769 0.00 0.00 33.44 3.36
1956 3605 9.671279 AAAAGTTCAATGATTTGGAAAAAGAGT 57.329 25.926 0.00 0.00 33.44 3.24
2026 3681 9.408731 GAAAAAGTTCACGAATTTCATGAAAAC 57.591 29.630 23.91 18.47 34.28 2.43
2164 3819 4.345859 AACCAGTGACCGATTGACTTAA 57.654 40.909 0.00 0.00 0.00 1.85
2165 3820 4.062293 CAAACCAGTGACCGATTGACTTA 58.938 43.478 0.00 0.00 0.00 2.24
2173 3828 1.155424 GCGTTCAAACCAGTGACCGA 61.155 55.000 0.00 0.00 35.65 4.69
2214 3869 0.390472 CTCGCTCGCTCCTTTCCTTT 60.390 55.000 0.00 0.00 0.00 3.11
2222 3877 1.226831 CCTTTCTCTCGCTCGCTCC 60.227 63.158 0.00 0.00 0.00 4.70
2291 3947 3.716353 ACATGGTAGATAATGGGCTCACA 59.284 43.478 0.00 0.00 0.00 3.58
2307 3963 3.025262 ACCGGTTAACAAAACACATGGT 58.975 40.909 0.00 0.00 0.00 3.55
2312 3968 7.063426 GTCTATAGGTACCGGTTAACAAAACAC 59.937 40.741 15.04 0.00 0.00 3.32
2327 3983 7.443575 TGACGTAATCTCAAGGTCTATAGGTAC 59.556 40.741 0.00 0.00 33.87 3.34
2334 3990 5.408356 GCTTTGACGTAATCTCAAGGTCTA 58.592 41.667 0.00 0.00 33.87 2.59
2337 3993 2.993899 CGCTTTGACGTAATCTCAAGGT 59.006 45.455 0.00 0.00 29.65 3.50
2338 3994 2.348666 CCGCTTTGACGTAATCTCAAGG 59.651 50.000 0.00 0.00 0.00 3.61
2340 3996 2.028839 TCCCGCTTTGACGTAATCTCAA 60.029 45.455 0.00 0.00 0.00 3.02
2341 3997 1.546923 TCCCGCTTTGACGTAATCTCA 59.453 47.619 0.00 0.00 0.00 3.27
2342 3998 2.288961 TCCCGCTTTGACGTAATCTC 57.711 50.000 0.00 0.00 0.00 2.75
2344 4000 3.195661 AGAATCCCGCTTTGACGTAATC 58.804 45.455 0.00 0.00 0.00 1.75
2345 4001 3.261981 AGAATCCCGCTTTGACGTAAT 57.738 42.857 0.00 0.00 0.00 1.89
2346 4002 2.754946 AGAATCCCGCTTTGACGTAA 57.245 45.000 0.00 0.00 0.00 3.18
2348 4004 1.274167 TGTAGAATCCCGCTTTGACGT 59.726 47.619 0.00 0.00 0.00 4.34
2390 4047 2.332063 ATATTGTGACCGCCTCTTGG 57.668 50.000 0.00 0.00 0.00 3.61
2391 4048 5.300752 AGATAATATTGTGACCGCCTCTTG 58.699 41.667 0.00 0.00 0.00 3.02
2392 4049 5.552870 AGATAATATTGTGACCGCCTCTT 57.447 39.130 0.00 0.00 0.00 2.85
2393 4050 5.552870 AAGATAATATTGTGACCGCCTCT 57.447 39.130 0.00 0.00 0.00 3.69
2394 4051 6.619801 AAAAGATAATATTGTGACCGCCTC 57.380 37.500 0.00 0.00 0.00 4.70
2499 4158 2.737252 GGAGTGATCCAACGTGAGAAAC 59.263 50.000 0.00 0.00 0.00 2.78
2594 4254 4.007644 CTGCTGAGGGCGTGGTCA 62.008 66.667 0.00 0.00 45.43 4.02
2610 4270 1.910772 ACTTCCAGACGCTGCCTCT 60.911 57.895 0.00 0.00 0.00 3.69
2616 4276 4.379243 CCGCCACTTCCAGACGCT 62.379 66.667 0.00 0.00 0.00 5.07
2679 4339 4.349636 TCACCAAGGAGATTTAGTCCAACA 59.650 41.667 0.00 0.00 36.43 3.33
2696 4357 0.719015 ATCCTCCTCCTCCTCACCAA 59.281 55.000 0.00 0.00 0.00 3.67
2919 4580 0.679640 GGCCATTGTTCATGACCCGA 60.680 55.000 0.00 0.00 34.31 5.14
2951 4612 7.437713 TCCTCTATGACCACAACATTATCTT 57.562 36.000 0.00 0.00 0.00 2.40
3051 4712 6.157645 TCTCTTTCTTCTTCATAAGCCCATCT 59.842 38.462 0.00 0.00 0.00 2.90
3204 4865 3.896648 TTCAGATTCAGCGGAACAAAC 57.103 42.857 0.00 0.00 35.46 2.93
3283 4944 0.397941 CGTATGGCCCATGAGTCCAT 59.602 55.000 6.46 14.69 42.70 3.41
3340 5001 0.877071 CCAGTCACACCATTCACAGC 59.123 55.000 0.00 0.00 0.00 4.40
3351 5012 1.053835 TTCACCAGGAGCCAGTCACA 61.054 55.000 0.00 0.00 0.00 3.58
3425 5086 0.704076 CTCCCCCATTCCCACTTGAA 59.296 55.000 0.00 0.00 0.00 2.69
3522 5183 2.827322 CCATTGCACCCTCATTCTGAAA 59.173 45.455 0.00 0.00 0.00 2.69
3589 5250 1.457346 CAGGCCTCCAGATTTCACAC 58.543 55.000 0.00 0.00 0.00 3.82
3629 5290 6.826231 TCAGGTTCACTTTCTCATGTACAAAA 59.174 34.615 0.00 0.00 0.00 2.44
3636 5297 5.936372 TCTCAATCAGGTTCACTTTCTCATG 59.064 40.000 0.00 0.00 0.00 3.07
3671 5332 1.129058 AACTCTTGTCCACCGGTTCT 58.871 50.000 2.97 0.00 0.00 3.01
3719 5380 1.007600 TCAGATCTCTGCCTCTTGGGA 59.992 52.381 2.21 0.00 43.46 4.37
3769 5430 3.917760 GGGAGGTCGCCGATCCTG 61.918 72.222 11.99 0.00 33.83 3.86
3788 5449 2.841988 GCCCAGCGATCCTCCTCT 60.842 66.667 0.00 0.00 0.00 3.69
3801 5462 2.361757 CTGAGTGTTTTCATTGTGCCCA 59.638 45.455 0.00 0.00 0.00 5.36
3806 5467 3.554934 TCCAGCTGAGTGTTTTCATTGT 58.445 40.909 17.39 0.00 0.00 2.71
3833 5494 0.251916 GCAGTACTGGCCATACCACA 59.748 55.000 23.95 0.00 46.36 4.17
3869 5530 2.571653 CCCACTACTTCTGGATGTCCAA 59.428 50.000 2.97 0.00 46.97 3.53
3874 5535 0.181350 GCCCCCACTACTTCTGGATG 59.819 60.000 0.00 0.00 0.00 3.51
3936 5597 4.817318 TTCCTCAAAAGTTTGTTTGCCT 57.183 36.364 3.82 0.00 38.20 4.75
4023 5693 0.179092 GATAACAACCGGGCTACGCT 60.179 55.000 6.32 0.00 42.52 5.07
4071 5742 2.342650 CCTCCAACCACCGCATTGG 61.343 63.158 0.00 0.00 45.78 3.16
4073 5744 2.035626 CCCTCCAACCACCGCATT 59.964 61.111 0.00 0.00 0.00 3.56
4161 5832 1.400530 GCAGACCCGTATGTAGCCCT 61.401 60.000 0.00 0.00 0.00 5.19
4169 5840 1.134401 CCTTGTGATGCAGACCCGTAT 60.134 52.381 0.00 0.00 0.00 3.06
4308 5980 0.674581 CCATGTCCTCAAGCTCGCAA 60.675 55.000 0.00 0.00 0.00 4.85
4356 6028 2.429610 GCATTCCCTCAACCTACGTCTA 59.570 50.000 0.00 0.00 0.00 2.59
4375 6047 0.605083 CACACTGCTCTGTCTAGGCA 59.395 55.000 0.00 0.00 34.66 4.75
4457 6129 2.211410 ACCACCGGACGATGGTCAA 61.211 57.895 9.46 0.00 46.62 3.18
4501 6173 3.331150 TGACGTATGATTGTTGGTCCAC 58.669 45.455 0.00 0.00 0.00 4.02
4527 6199 1.135575 CAATGGGCTTCGAACTGCTTC 60.136 52.381 9.01 3.68 0.00 3.86
4544 6216 1.694048 CCTCCTCCTCCTGTAGCCAAT 60.694 57.143 0.00 0.00 0.00 3.16
4621 6296 1.957695 CTGCTGCAGTGCGTTGAGA 60.958 57.895 21.21 0.00 35.36 3.27
4667 6342 0.765510 AGGGGCTTTCAGAACTTCGT 59.234 50.000 0.00 0.00 0.00 3.85
4694 6369 6.502074 ACTCCTCCTTTAGTTCTTTCAAGT 57.498 37.500 0.00 0.00 0.00 3.16
4773 6448 7.150783 AGTTTCCTCAATCTTAATGAGCAAC 57.849 36.000 0.00 5.03 42.36 4.17
4783 6458 6.445139 TCCTTCTCCATAGTTTCCTCAATCTT 59.555 38.462 0.00 0.00 0.00 2.40
4791 6466 7.342581 AGATTTCTTCCTTCTCCATAGTTTCC 58.657 38.462 0.00 0.00 0.00 3.13
4873 6548 4.957372 CGCAGAAGCAAAATTGTTGAAAAC 59.043 37.500 0.00 0.00 44.64 2.43


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

AutoCloner maintained by Alex Coulton.