Multiple sequence alignment - TraesCS4A01G102300

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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 TraesCS4A01G102300 chr4A 100.000 4717 0 0 1 4717 114789793 114794509 0.000000e+00 8711
1 TraesCS4A01G102300 chr4D 94.846 2930 73 30 5 2892 349913350 349910457 0.000000e+00 4503
2 TraesCS4A01G102300 chr4D 86.056 251 23 8 4201 4450 349910432 349910193 4.680000e-65 259
3 TraesCS4A01G102300 chr4B 94.186 2907 106 27 16 2892 433179928 433177055 0.000000e+00 4373
4 TraesCS4A01G102300 chr4B 94.870 1306 58 3 2902 4201 616649605 616648303 0.000000e+00 2032
5 TraesCS4A01G102300 chr4B 92.119 1307 87 11 2905 4201 637370315 637369015 0.000000e+00 1829
6 TraesCS4A01G102300 chr4B 84.393 519 61 9 4201 4717 433177060 433176560 4.240000e-135 492
7 TraesCS4A01G102300 chr6A 95.789 1306 51 3 2898 4201 510239603 510238300 0.000000e+00 2104
8 TraesCS4A01G102300 chr6A 94.870 1306 63 3 2898 4201 441299925 441298622 0.000000e+00 2037
9 TraesCS4A01G102300 chr6A 90.159 1321 110 15 2896 4200 121714388 121713072 0.000000e+00 1701
10 TraesCS4A01G102300 chr5B 94.793 1306 56 4 2902 4199 612313998 612315299 0.000000e+00 2025
11 TraesCS4A01G102300 chr5B 75.698 716 151 18 2902 3609 63284078 63283378 2.100000e-88 337
12 TraesCS4A01G102300 chr5A 95.429 1225 47 2 2984 4201 566037717 566038939 0.000000e+00 1943
13 TraesCS4A01G102300 chr1A 93.721 1306 66 4 2909 4201 561689446 561690748 0.000000e+00 1943
14 TraesCS4A01G102300 chr1B 91.527 1310 100 8 2902 4202 671462051 671460744 0.000000e+00 1794
15 TraesCS4A01G102300 chr7A 94.465 271 7 3 3939 4201 17379347 17379077 1.220000e-110 411
16 TraesCS4A01G102300 chr7A 87.931 116 12 2 2902 3015 25037727 25037612 8.230000e-28 135
17 TraesCS4A01G102300 chr7D 87.106 349 37 7 4373 4717 635663679 635663335 5.720000e-104 388
18 TraesCS4A01G102300 chr3B 78.034 651 116 22 2909 3550 11639399 11640031 7.400000e-103 385
19 TraesCS4A01G102300 chr3B 85.387 349 46 5 4371 4715 691284510 691284857 1.610000e-94 357
20 TraesCS4A01G102300 chr3D 85.920 348 45 2 4372 4716 379410426 379410080 7.460000e-98 368
21 TraesCS4A01G102300 chr3D 84.722 360 48 6 4360 4717 79441622 79441976 2.090000e-93 353
22 TraesCS4A01G102300 chr3D 85.057 348 48 3 4369 4714 578745028 578745373 7.510000e-93 351
23 TraesCS4A01G102300 chr1D 85.714 350 47 3 4370 4717 272535878 272536226 2.680000e-97 366
24 TraesCS4A01G102300 chr1D 84.986 353 50 3 4367 4717 482503441 482503090 5.810000e-94 355
25 TraesCS4A01G102300 chr2B 85.387 349 47 4 4372 4717 636877577 636877924 4.490000e-95 359
26 TraesCS4A01G102300 chr2B 89.899 99 7 3 4113 4208 293900824 293900922 1.780000e-24 124
27 TraesCS4A01G102300 chr2A 77.167 600 102 29 3620 4201 583091953 583092535 2.740000e-82 316


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 TraesCS4A01G102300 chr4A 114789793 114794509 4716 False 8711.0 8711 100.0000 1 4717 1 chr4A.!!$F1 4716
1 TraesCS4A01G102300 chr4D 349910193 349913350 3157 True 2381.0 4503 90.4510 5 4450 2 chr4D.!!$R1 4445
2 TraesCS4A01G102300 chr4B 433176560 433179928 3368 True 2432.5 4373 89.2895 16 4717 2 chr4B.!!$R3 4701
3 TraesCS4A01G102300 chr4B 616648303 616649605 1302 True 2032.0 2032 94.8700 2902 4201 1 chr4B.!!$R1 1299
4 TraesCS4A01G102300 chr4B 637369015 637370315 1300 True 1829.0 1829 92.1190 2905 4201 1 chr4B.!!$R2 1296
5 TraesCS4A01G102300 chr6A 510238300 510239603 1303 True 2104.0 2104 95.7890 2898 4201 1 chr6A.!!$R3 1303
6 TraesCS4A01G102300 chr6A 441298622 441299925 1303 True 2037.0 2037 94.8700 2898 4201 1 chr6A.!!$R2 1303
7 TraesCS4A01G102300 chr6A 121713072 121714388 1316 True 1701.0 1701 90.1590 2896 4200 1 chr6A.!!$R1 1304
8 TraesCS4A01G102300 chr5B 612313998 612315299 1301 False 2025.0 2025 94.7930 2902 4199 1 chr5B.!!$F1 1297
9 TraesCS4A01G102300 chr5B 63283378 63284078 700 True 337.0 337 75.6980 2902 3609 1 chr5B.!!$R1 707
10 TraesCS4A01G102300 chr5A 566037717 566038939 1222 False 1943.0 1943 95.4290 2984 4201 1 chr5A.!!$F1 1217
11 TraesCS4A01G102300 chr1A 561689446 561690748 1302 False 1943.0 1943 93.7210 2909 4201 1 chr1A.!!$F1 1292
12 TraesCS4A01G102300 chr1B 671460744 671462051 1307 True 1794.0 1794 91.5270 2902 4202 1 chr1B.!!$R1 1300
13 TraesCS4A01G102300 chr3B 11639399 11640031 632 False 385.0 385 78.0340 2909 3550 1 chr3B.!!$F1 641
14 TraesCS4A01G102300 chr2A 583091953 583092535 582 False 316.0 316 77.1670 3620 4201 1 chr2A.!!$F1 581

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
134 137 0.037790 GTATCATCCGCTCTGCCTCC 60.038 60.0 0.0 0.0 0.00 4.30 F
720 755 0.093026 CCATCGACTTTCGTTCACGC 59.907 55.0 0.0 0.0 41.35 5.34 F
1396 1453 0.595588 ACTCTCACTCTCACACGCAG 59.404 55.0 0.0 0.0 0.00 5.18 F
2831 2888 0.962489 CCCGAGGAGTAGCGATGATT 59.038 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1435 0.109365 CCTGCGTGTGAGAGTGAGAG 60.109 60.000 0.00 0.0 0.00 3.20 R
2471 2528 2.796425 GACGCTGATGAGCACGCAG 61.796 63.158 4.68 0.0 46.62 5.18 R
2976 3035 1.318158 GCGACGAGGTAGAGGGGAAA 61.318 60.000 0.00 0.0 0.00 3.13 R
4585 4694 0.036164 TGTTGCGCTGGTTCTATGGT 59.964 50.000 9.73 0.0 0.00 3.55 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
42 45 4.062677 AAATGATTCCATTTCCATGGCG 57.937 40.909 6.96 0.00 46.83 5.69
58 61 1.529010 GCGGCCCATCCATTGATCA 60.529 57.895 0.00 0.00 34.01 2.92
59 62 0.896940 GCGGCCCATCCATTGATCAT 60.897 55.000 0.00 0.00 34.01 2.45
60 63 1.171308 CGGCCCATCCATTGATCATC 58.829 55.000 0.00 0.00 34.01 2.92
63 66 2.168496 GCCCATCCATTGATCATCCAG 58.832 52.381 0.00 0.00 0.00 3.86
70 73 2.361119 CCATTGATCATCCAGTTGCAGG 59.639 50.000 0.00 0.00 0.00 4.85
134 137 0.037790 GTATCATCCGCTCTGCCTCC 60.038 60.000 0.00 0.00 0.00 4.30
270 278 1.196911 CATGTGTGCCCCAATCCAAT 58.803 50.000 0.00 0.00 0.00 3.16
271 279 1.137479 CATGTGTGCCCCAATCCAATC 59.863 52.381 0.00 0.00 0.00 2.67
272 280 0.614415 TGTGTGCCCCAATCCAATCC 60.614 55.000 0.00 0.00 0.00 3.01
273 281 0.614415 GTGTGCCCCAATCCAATCCA 60.614 55.000 0.00 0.00 0.00 3.41
274 282 0.115944 TGTGCCCCAATCCAATCCAA 59.884 50.000 0.00 0.00 0.00 3.53
315 327 2.651455 GTGCCAATTAGGGGTTCTACC 58.349 52.381 0.00 0.00 38.09 3.18
379 391 1.396653 CTGATGGATCCCCTTTGTGC 58.603 55.000 9.90 0.00 0.00 4.57
403 415 2.607668 TTCCTATGTGGCGTCGCTCG 62.608 60.000 18.11 0.00 43.12 5.03
446 459 3.443045 GCGGTGGCAATCAGTGGG 61.443 66.667 0.00 0.00 39.62 4.61
452 465 1.002624 GGCAATCAGTGGGGAACGA 60.003 57.895 0.00 0.00 0.00 3.85
460 486 1.137697 AGTGGGGAACGAAAGAGGTT 58.862 50.000 0.00 0.00 0.00 3.50
478 504 3.696051 AGGTTGCAATTGTATAGCCTGTG 59.304 43.478 0.59 0.00 0.00 3.66
479 505 3.443681 GGTTGCAATTGTATAGCCTGTGT 59.556 43.478 0.59 0.00 0.00 3.72
483 509 6.825944 TGCAATTGTATAGCCTGTGTTTTA 57.174 33.333 7.40 0.00 0.00 1.52
484 510 6.851609 TGCAATTGTATAGCCTGTGTTTTAG 58.148 36.000 7.40 0.00 0.00 1.85
585 620 1.526575 AATGGAGGCGCCTTTGTGTG 61.527 55.000 33.34 0.00 37.63 3.82
633 668 4.030452 GGGCACTCGCACAAGCAC 62.030 66.667 0.00 0.00 43.03 4.40
634 669 3.279116 GGCACTCGCACAAGCACA 61.279 61.111 0.00 0.00 42.27 4.57
718 753 2.942710 TCTCCATCGACTTTCGTTCAC 58.057 47.619 0.00 0.00 41.35 3.18
720 755 0.093026 CCATCGACTTTCGTTCACGC 59.907 55.000 0.00 0.00 41.35 5.34
735 770 2.893637 TCACGCCTATCTCTTTTGCTC 58.106 47.619 0.00 0.00 0.00 4.26
775 822 3.420839 AGATTTTATTTTGGCTCCGCG 57.579 42.857 0.00 0.00 0.00 6.46
794 847 1.788229 GGTTAATGGGGTGGGAATGG 58.212 55.000 0.00 0.00 0.00 3.16
797 850 3.562182 GTTAATGGGGTGGGAATGGTAG 58.438 50.000 0.00 0.00 0.00 3.18
817 870 5.528690 GGTAGGGGTACGTAATTTGGAATTC 59.471 44.000 0.00 0.00 0.00 2.17
893 950 1.027357 GCTGCTGATGGTGTTATGGG 58.973 55.000 0.00 0.00 0.00 4.00
894 951 1.683011 GCTGCTGATGGTGTTATGGGT 60.683 52.381 0.00 0.00 0.00 4.51
895 952 2.019249 CTGCTGATGGTGTTATGGGTG 58.981 52.381 0.00 0.00 0.00 4.61
928 985 2.665537 CTGTTGTGCTCGTCTCATTCTC 59.334 50.000 0.00 0.00 0.00 2.87
1006 1063 4.115199 AGGCCGAGGCAATGGACC 62.115 66.667 16.65 0.00 44.11 4.46
1326 1383 2.126228 CACATTGCCGCCAAGCAG 60.126 61.111 0.00 0.00 45.13 4.24
1369 1426 1.411977 TCTACGTCTAGTCCCCTCTCG 59.588 57.143 0.00 0.00 0.00 4.04
1378 1435 1.033202 GTCCCCTCTCGTCCTCTCAC 61.033 65.000 0.00 0.00 0.00 3.51
1396 1453 0.595588 ACTCTCACTCTCACACGCAG 59.404 55.000 0.00 0.00 0.00 5.18
1437 1494 7.943079 TCATGGTTTAGACAATGATTCATGT 57.057 32.000 0.00 1.05 40.51 3.21
1438 1495 8.352137 TCATGGTTTAGACAATGATTCATGTT 57.648 30.769 0.00 0.00 40.51 2.71
1439 1496 8.245491 TCATGGTTTAGACAATGATTCATGTTG 58.755 33.333 0.00 0.00 40.51 3.33
1440 1497 6.389091 TGGTTTAGACAATGATTCATGTTGC 58.611 36.000 0.00 0.00 0.00 4.17
1643 1700 4.299547 AAGACGGCGCTGCACTCA 62.300 61.111 18.15 0.00 0.00 3.41
1877 1934 3.643978 GCGCGGCACCAGATCATC 61.644 66.667 8.83 0.00 0.00 2.92
2471 2528 2.036256 AAGCTCATGTGGGTGGCC 59.964 61.111 0.00 0.00 0.00 5.36
2693 2750 2.603473 TCACACTCGGGGTCTGGG 60.603 66.667 0.00 0.00 0.00 4.45
2723 2780 2.876219 GAGTGGGTCGACGAGGAC 59.124 66.667 9.92 3.25 36.18 3.85
2784 2841 2.478370 CGCCCTAGTGCAACATTGATTG 60.478 50.000 0.00 0.00 41.43 2.67
2831 2888 0.962489 CCCGAGGAGTAGCGATGATT 59.038 55.000 0.00 0.00 0.00 2.57
2836 2893 3.251245 CGAGGAGTAGCGATGATTGTAGT 59.749 47.826 0.00 0.00 0.00 2.73
2868 2925 3.454371 TTTTATCCGGTAGCTCAGCTC 57.546 47.619 0.00 0.00 40.44 4.09
2877 2934 1.396301 GTAGCTCAGCTCATTGTGCAC 59.604 52.381 0.00 10.75 40.44 4.57
3340 3409 3.319198 CTGGGGGCGGTGTAGTGT 61.319 66.667 0.00 0.00 0.00 3.55
3459 3532 0.188342 TTTGCCTTTCTCCCCTGCTT 59.812 50.000 0.00 0.00 0.00 3.91
3471 3546 3.737172 CTGCTTGTTTCCGGGCGG 61.737 66.667 0.00 0.00 0.00 6.13
3557 3633 1.408969 GCCTTTGGTGAGTTTTGGGA 58.591 50.000 0.00 0.00 0.00 4.37
3563 3639 1.418264 TGGTGAGTTTTGGGACGATGA 59.582 47.619 0.00 0.00 0.00 2.92
3567 3643 3.314080 GTGAGTTTTGGGACGATGACAAA 59.686 43.478 0.00 0.00 32.77 2.83
3584 3661 2.301870 ACAAATCTGCTCCGTTGGTAGA 59.698 45.455 0.00 0.00 0.00 2.59
3612 3689 1.610554 GGCTACGTGGTTGGAGGCTA 61.611 60.000 0.00 0.00 0.00 3.93
3686 3771 2.386660 GCTTCTCCTCGTGTGCAGC 61.387 63.158 0.00 0.00 0.00 5.25
3815 3904 1.442769 GAGAGCGTTTGCATCTTCCA 58.557 50.000 0.00 0.00 46.23 3.53
3973 4065 0.319728 CCCTGGTGTCACTGAGTGAG 59.680 60.000 16.76 3.59 43.57 3.51
4014 4106 2.763933 CTTCACTCTCTTCAAGCTGCA 58.236 47.619 1.02 0.00 0.00 4.41
4242 4349 6.142139 CGTTTGCTGAATGTTGATTAGAACA 58.858 36.000 0.00 0.00 40.08 3.18
4243 4350 6.803320 CGTTTGCTGAATGTTGATTAGAACAT 59.197 34.615 0.00 0.00 46.35 2.71
4275 4382 4.532521 AGGAAGTACAGTAGCAAGGATGTT 59.467 41.667 0.00 0.00 0.00 2.71
4285 4392 1.335324 GCAAGGATGTTGTCAGTGCAC 60.335 52.381 9.40 9.40 37.81 4.57
4376 4484 9.866936 CACAAATCAATGTTCCATTACTTTTTG 57.133 29.630 0.00 0.00 0.00 2.44
4377 4485 9.612066 ACAAATCAATGTTCCATTACTTTTTGT 57.388 25.926 0.00 0.00 0.00 2.83
4383 4491 8.550376 CAATGTTCCATTACTTTTTGTTTCCAG 58.450 33.333 0.00 0.00 0.00 3.86
4416 4524 9.558648 TCAATCTATTCATTTTCAATTGTGACG 57.441 29.630 5.13 0.00 31.90 4.35
4422 4530 5.753744 TCATTTTCAATTGTGACGGTACAC 58.246 37.500 5.13 0.00 40.68 2.90
4432 4540 2.538449 GTGACGGTACACAGAACAACAG 59.462 50.000 0.00 0.00 40.11 3.16
4457 4565 9.975218 AGAGGTATAAAAATTACAACCATGTCT 57.025 29.630 0.00 0.00 41.05 3.41
4464 4572 4.640771 ATTACAACCATGTCTGTGGACT 57.359 40.909 7.08 0.00 42.02 3.85
4471 4579 2.753452 CCATGTCTGTGGACTACGTAGT 59.247 50.000 27.71 27.71 43.27 2.73
4490 4599 3.914312 AGTGACGACTACAACATTGGAG 58.086 45.455 2.10 2.10 44.88 3.86
4500 4609 1.000385 CAACATTGGAGCAAGCCGAAA 60.000 47.619 0.00 0.00 0.00 3.46
4524 4633 3.391665 CTGCCGTCATCACCCCTCC 62.392 68.421 0.00 0.00 0.00 4.30
4529 4638 1.050988 CGTCATCACCCCTCCCTCAT 61.051 60.000 0.00 0.00 0.00 2.90
4564 4673 7.553044 GGCAAACCTTATTGTAATAGACAGTCT 59.447 37.037 8.50 8.50 39.88 3.24
4569 4678 8.478877 ACCTTATTGTAATAGACAGTCTGGAAG 58.521 37.037 13.84 4.92 39.88 3.46
4571 4680 9.522804 CTTATTGTAATAGACAGTCTGGAAGTC 57.477 37.037 13.84 0.18 39.88 3.01
4602 4711 1.305219 GCACCATAGAACCAGCGCAA 61.305 55.000 11.47 0.00 0.00 4.85
4606 4715 0.729116 CATAGAACCAGCGCAACAGG 59.271 55.000 11.47 8.53 0.00 4.00
4607 4716 0.613260 ATAGAACCAGCGCAACAGGA 59.387 50.000 11.47 0.00 0.00 3.86
4620 4729 1.331756 CAACAGGATAGCAACCATCGC 59.668 52.381 0.00 0.00 0.00 4.58
4632 4741 1.656652 ACCATCGCCGATGAAGAAAG 58.343 50.000 27.59 12.35 42.09 2.62
4634 4743 1.594862 CCATCGCCGATGAAGAAAGTC 59.405 52.381 27.59 0.00 42.09 3.01
4641 4750 4.113354 GCCGATGAAGAAAGTCGTAGATT 58.887 43.478 0.00 0.00 40.67 2.40
4657 4766 8.212312 AGTCGTAGATTAGAAGGATCAAGTCTA 58.788 37.037 0.00 0.00 40.67 2.59
4674 4783 6.425721 TCAAGTCTATAAACACCCAAACGAAG 59.574 38.462 0.00 0.00 0.00 3.79
4675 4784 6.105397 AGTCTATAAACACCCAAACGAAGA 57.895 37.500 0.00 0.00 0.00 2.87
4676 4785 5.930569 AGTCTATAAACACCCAAACGAAGAC 59.069 40.000 0.00 0.00 0.00 3.01
4677 4786 4.925054 TCTATAAACACCCAAACGAAGACG 59.075 41.667 0.00 0.00 45.75 4.18
4678 4787 2.027003 AAACACCCAAACGAAGACGA 57.973 45.000 0.00 0.00 42.66 4.20
4679 4788 2.027003 AACACCCAAACGAAGACGAA 57.973 45.000 0.00 0.00 42.66 3.85
4680 4789 1.292992 ACACCCAAACGAAGACGAAC 58.707 50.000 0.00 0.00 42.66 3.95
4681 4790 1.292061 CACCCAAACGAAGACGAACA 58.708 50.000 0.00 0.00 42.66 3.18
4682 4791 1.666700 CACCCAAACGAAGACGAACAA 59.333 47.619 0.00 0.00 42.66 2.83
4683 4792 2.096174 CACCCAAACGAAGACGAACAAA 59.904 45.455 0.00 0.00 42.66 2.83
4684 4793 2.353579 ACCCAAACGAAGACGAACAAAG 59.646 45.455 0.00 0.00 42.66 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 45 1.203087 TGGATGATCAATGGATGGGCC 60.203 52.381 0.00 0.00 32.67 5.80
58 61 4.396166 CGATTAGAAAACCTGCAACTGGAT 59.604 41.667 0.00 0.00 0.00 3.41
59 62 3.751175 CGATTAGAAAACCTGCAACTGGA 59.249 43.478 0.00 0.00 0.00 3.86
60 63 3.751175 TCGATTAGAAAACCTGCAACTGG 59.249 43.478 0.00 0.00 0.00 4.00
63 66 4.494199 CGGATCGATTAGAAAACCTGCAAC 60.494 45.833 0.00 0.00 0.00 4.17
70 73 1.871676 GGGCCGGATCGATTAGAAAAC 59.128 52.381 5.05 0.00 0.00 2.43
134 137 4.183686 ACCGATCCGCACGTACCG 62.184 66.667 0.00 0.00 0.00 4.02
162 165 3.083349 TGAGCCATGGGACCCTCG 61.083 66.667 15.13 2.14 0.00 4.63
163 166 1.639635 ATGTGAGCCATGGGACCCTC 61.640 60.000 15.13 11.81 30.69 4.30
164 167 1.620589 ATGTGAGCCATGGGACCCT 60.621 57.895 15.13 0.79 30.69 4.34
199 202 0.169451 GGAAAAACATACCGGCGTGG 59.831 55.000 6.01 0.00 46.41 4.94
270 278 2.666207 CCACGAACGGGGATTGGA 59.334 61.111 10.14 0.00 42.48 3.53
290 302 3.887868 CCCTAATTGGCACCGCGC 61.888 66.667 0.00 0.00 41.28 6.86
315 327 4.909696 TCCAAACCCGCATTACAATATG 57.090 40.909 0.00 0.00 0.00 1.78
379 391 1.802880 CGACGCCACATAGGAAAGGAG 60.803 57.143 0.00 0.00 41.22 3.69
403 415 1.922570 TGCGATAAAGAAGAGGCGAC 58.077 50.000 0.00 0.00 0.00 5.19
446 459 3.243401 ACAATTGCAACCTCTTTCGTTCC 60.243 43.478 0.00 0.00 0.00 3.62
452 465 5.126061 CAGGCTATACAATTGCAACCTCTTT 59.874 40.000 0.00 0.00 32.56 2.52
460 486 5.720371 AAAACACAGGCTATACAATTGCA 57.280 34.783 5.05 0.00 32.56 4.08
478 504 6.127310 TGCCCATTCTCTCTCTCTACTAAAAC 60.127 42.308 0.00 0.00 0.00 2.43
479 505 5.958380 TGCCCATTCTCTCTCTCTACTAAAA 59.042 40.000 0.00 0.00 0.00 1.52
483 509 3.678965 TGCCCATTCTCTCTCTCTACT 57.321 47.619 0.00 0.00 0.00 2.57
484 510 4.953940 AATGCCCATTCTCTCTCTCTAC 57.046 45.455 0.00 0.00 0.00 2.59
585 620 4.621034 CCCGTCAATTTAATTTGCTCACAC 59.379 41.667 5.41 0.00 0.00 3.82
628 663 1.898094 TGCCATGCGAGTTGTGCTT 60.898 52.632 0.00 0.00 0.00 3.91
629 664 2.281692 TGCCATGCGAGTTGTGCT 60.282 55.556 0.00 0.00 0.00 4.40
632 667 2.620112 GCAGTGCCATGCGAGTTGT 61.620 57.895 2.85 0.00 36.28 3.32
633 668 2.177531 GCAGTGCCATGCGAGTTG 59.822 61.111 2.85 0.00 36.28 3.16
718 753 2.869192 GGAAGAGCAAAAGAGATAGGCG 59.131 50.000 0.00 0.00 0.00 5.52
720 755 6.825610 AGTATGGAAGAGCAAAAGAGATAGG 58.174 40.000 0.00 0.00 0.00 2.57
735 770 5.593679 TCTACGAAAAGGGAGTATGGAAG 57.406 43.478 0.00 0.00 0.00 3.46
775 822 1.007842 ACCATTCCCACCCCATTAACC 59.992 52.381 0.00 0.00 0.00 2.85
794 847 5.234972 CGAATTCCAAATTACGTACCCCTAC 59.765 44.000 0.00 0.00 0.00 3.18
797 850 3.313249 CCGAATTCCAAATTACGTACCCC 59.687 47.826 0.00 0.00 0.00 4.95
817 870 1.355796 TTGCGCGAATTCACCTACCG 61.356 55.000 12.10 0.00 0.00 4.02
893 950 1.271054 ACAACAGTCCATCAGAGGCAC 60.271 52.381 0.00 0.00 0.00 5.01
894 951 1.059098 ACAACAGTCCATCAGAGGCA 58.941 50.000 0.00 0.00 0.00 4.75
895 952 1.446907 CACAACAGTCCATCAGAGGC 58.553 55.000 0.00 0.00 0.00 4.70
1369 1426 2.747446 GTGAGAGTGAGAGTGAGAGGAC 59.253 54.545 0.00 0.00 0.00 3.85
1378 1435 0.109365 CCTGCGTGTGAGAGTGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
1418 1475 7.411157 GCAAGCAACATGAATCATTGTCTAAAC 60.411 37.037 0.00 0.00 0.00 2.01
1421 1478 5.416639 AGCAAGCAACATGAATCATTGTCTA 59.583 36.000 0.00 0.00 0.00 2.59
1422 1479 4.219944 AGCAAGCAACATGAATCATTGTCT 59.780 37.500 0.00 0.00 0.00 3.41
1423 1480 4.491676 AGCAAGCAACATGAATCATTGTC 58.508 39.130 0.00 0.00 0.00 3.18
1520 1577 3.334751 TTGAGCGCCGTCGTGTTG 61.335 61.111 2.29 0.00 38.14 3.33
2123 2180 4.195334 ATCCCCTGCATCCGCACC 62.195 66.667 0.00 0.00 45.36 5.01
2471 2528 2.796425 GACGCTGATGAGCACGCAG 61.796 63.158 4.68 0.00 46.62 5.18
2784 2841 1.877443 ACGTGGTAAATCAAGTGGTGC 59.123 47.619 0.00 0.00 0.00 5.01
2788 2845 4.860352 TCATCGTACGTGGTAAATCAAGTG 59.140 41.667 16.05 0.00 32.15 3.16
2831 2888 2.851263 AAAATGTCAGCCCGACTACA 57.149 45.000 5.56 0.00 45.60 2.74
2836 2893 2.285083 CGGATAAAAATGTCAGCCCGA 58.715 47.619 0.00 0.00 38.10 5.14
2877 2934 7.094549 GGGATCTCTAGTAATGCACACTAGTAG 60.095 44.444 25.54 21.69 43.90 2.57
2897 2954 4.888325 CGGGGGCAGAGGGGATCT 62.888 72.222 0.00 0.00 39.56 2.75
2976 3035 1.318158 GCGACGAGGTAGAGGGGAAA 61.318 60.000 0.00 0.00 0.00 3.13
3393 3464 1.481871 CTACATGTAGGGGACGGTGT 58.518 55.000 22.95 0.00 34.81 4.16
3395 3466 3.218974 CCTACATGTAGGGGACGGT 57.781 57.895 35.41 0.00 46.96 4.83
3557 3633 1.066858 ACGGAGCAGATTTGTCATCGT 60.067 47.619 0.00 0.00 0.00 3.73
3563 3639 2.301870 TCTACCAACGGAGCAGATTTGT 59.698 45.455 0.00 0.00 0.00 2.83
3567 3643 0.456221 CGTCTACCAACGGAGCAGAT 59.544 55.000 0.00 0.00 38.96 2.90
3612 3689 2.711542 CAATGGAGGAAGCCTAAACGT 58.288 47.619 0.00 0.00 31.76 3.99
3686 3771 0.689623 AACCTTGGCACTGAGAGGAG 59.310 55.000 9.11 0.00 33.47 3.69
3973 4065 0.671781 CCTCCATCGATCGCAATCCC 60.672 60.000 11.09 0.00 0.00 3.85
4014 4106 4.542697 TGAAGAAAAACTAAAGCCCAGGT 58.457 39.130 0.00 0.00 0.00 4.00
4242 4349 1.831736 CTGTACTTCCTCCCGTTCCAT 59.168 52.381 0.00 0.00 0.00 3.41
4243 4350 1.263356 CTGTACTTCCTCCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
4392 4500 8.522830 ACCGTCACAATTGAAAATGAATAGATT 58.477 29.630 13.59 0.00 31.90 2.40
4403 4511 4.443621 TCTGTGTACCGTCACAATTGAAA 58.556 39.130 13.59 0.00 45.70 2.69
4410 4518 2.094130 TGTTGTTCTGTGTACCGTCACA 60.094 45.455 0.00 5.49 44.54 3.58
4411 4519 2.538449 CTGTTGTTCTGTGTACCGTCAC 59.462 50.000 0.00 0.00 38.63 3.67
4416 4524 3.470645 ACCTCTGTTGTTCTGTGTACC 57.529 47.619 0.00 0.00 0.00 3.34
4471 4579 2.036604 TGCTCCAATGTTGTAGTCGTCA 59.963 45.455 0.00 0.00 0.00 4.35
4478 4586 1.164411 CGGCTTGCTCCAATGTTGTA 58.836 50.000 0.00 0.00 0.00 2.41
4480 4588 0.597568 TTCGGCTTGCTCCAATGTTG 59.402 50.000 0.00 0.00 0.00 3.33
4485 4594 2.616330 CGCTTTCGGCTTGCTCCAA 61.616 57.895 0.00 0.00 39.13 3.53
4507 4616 3.399181 GGAGGGGTGATGACGGCA 61.399 66.667 0.00 0.00 0.00 5.69
4510 4619 1.050988 ATGAGGGAGGGGTGATGACG 61.051 60.000 0.00 0.00 0.00 4.35
4524 4633 2.541547 TTTGCCTGGCTCCGATGAGG 62.542 60.000 21.03 0.00 39.14 3.86
4529 4638 1.485294 TAAGGTTTGCCTGGCTCCGA 61.485 55.000 21.03 10.12 46.33 4.55
4537 4646 7.402862 ACTGTCTATTACAATAAGGTTTGCCT 58.597 34.615 0.00 0.00 42.03 4.75
4550 4659 5.008331 ACGACTTCCAGACTGTCTATTACA 58.992 41.667 10.47 0.00 36.42 2.41
4554 4663 2.678836 CGACGACTTCCAGACTGTCTAT 59.321 50.000 10.47 0.00 0.00 1.98
4559 4668 1.004277 GCACGACGACTTCCAGACTG 61.004 60.000 0.00 0.00 0.00 3.51
4564 4673 0.242825 CCTTAGCACGACGACTTCCA 59.757 55.000 0.00 0.00 0.00 3.53
4585 4694 0.036164 TGTTGCGCTGGTTCTATGGT 59.964 50.000 9.73 0.00 0.00 3.55
4588 4697 0.613260 TCCTGTTGCGCTGGTTCTAT 59.387 50.000 9.73 0.00 37.45 1.98
4592 4701 1.026718 GCTATCCTGTTGCGCTGGTT 61.027 55.000 9.73 3.74 37.45 3.67
4602 4711 0.179045 GGCGATGGTTGCTATCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
4606 4715 0.792640 CATCGGCGATGGTTGCTATC 59.207 55.000 35.72 0.00 36.51 2.08
4607 4716 0.392706 TCATCGGCGATGGTTGCTAT 59.607 50.000 39.82 9.05 40.15 2.97
4620 4729 6.726230 TCTAATCTACGACTTTCTTCATCGG 58.274 40.000 0.00 0.00 40.16 4.18
4632 4741 7.266922 AGACTTGATCCTTCTAATCTACGAC 57.733 40.000 0.00 0.00 0.00 4.34
4641 4750 7.622081 TGGGTGTTTATAGACTTGATCCTTCTA 59.378 37.037 0.00 0.00 0.00 2.10
4657 4766 3.731089 TCGTCTTCGTTTGGGTGTTTAT 58.269 40.909 0.00 0.00 38.33 1.40
4674 4783 1.337447 TGGATCCGGTCTTTGTTCGTC 60.337 52.381 7.39 0.00 0.00 4.20
4675 4784 0.682852 TGGATCCGGTCTTTGTTCGT 59.317 50.000 7.39 0.00 0.00 3.85
4676 4785 1.803334 TTGGATCCGGTCTTTGTTCG 58.197 50.000 7.39 0.00 0.00 3.95
4677 4786 2.882137 TGTTTGGATCCGGTCTTTGTTC 59.118 45.455 7.39 0.00 0.00 3.18
4678 4787 2.884639 CTGTTTGGATCCGGTCTTTGTT 59.115 45.455 7.39 0.00 0.00 2.83
4679 4788 2.105821 TCTGTTTGGATCCGGTCTTTGT 59.894 45.455 7.39 0.00 0.00 2.83
4680 4789 2.778299 TCTGTTTGGATCCGGTCTTTG 58.222 47.619 7.39 0.00 0.00 2.77
4681 4790 3.610911 GATCTGTTTGGATCCGGTCTTT 58.389 45.455 7.39 0.00 36.91 2.52
4682 4791 3.268023 GATCTGTTTGGATCCGGTCTT 57.732 47.619 7.39 0.00 36.91 3.01
4683 4792 2.990066 GATCTGTTTGGATCCGGTCT 57.010 50.000 7.39 0.00 36.91 3.85


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

AutoCloner maintained by Alex Coulton.