Multiple sequence alignment - TraesCS3B01G200200

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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 TraesCS3B01G200200 chr3B 100.000 3246 0 0 1 3246 228809236 228805991 0.000000e+00 5995.0
1 TraesCS3B01G200200 chr3B 77.551 490 96 12 1717 2196 781210815 781211300 1.910000e-72 283.0
2 TraesCS3B01G200200 chr3B 80.743 296 53 4 2511 2804 204392771 204392478 9.060000e-56 228.0
3 TraesCS3B01G200200 chr3D 90.637 2510 105 46 1 2452 157551409 157548972 0.000000e+00 3214.0
4 TraesCS3B01G200200 chr3D 81.842 749 110 19 2512 3242 312884677 312885417 9.960000e-170 606.0
5 TraesCS3B01G200200 chr3A 89.776 1741 108 31 832 2559 170648376 170650059 0.000000e+00 2165.0
6 TraesCS3B01G200200 chr3A 90.255 862 23 20 1 836 170645071 170645897 0.000000e+00 1070.0
7 TraesCS3B01G200200 chr3A 83.683 668 85 11 2599 3246 170650024 170650687 2.770000e-170 608.0
8 TraesCS3B01G200200 chr3A 80.267 750 120 14 2514 3246 95471516 95470778 1.020000e-149 540.0
9 TraesCS3B01G200200 chr3A 87.143 140 15 2 2313 2452 170650707 170650843 4.340000e-34 156.0
10 TraesCS3B01G200200 chr4B 81.023 743 108 16 2512 3246 17466021 17465304 7.860000e-156 560.0
11 TraesCS3B01G200200 chr7D 81.748 652 112 6 2509 3155 184095250 184095899 3.690000e-149 538.0
12 TraesCS3B01G200200 chr4A 80.891 696 111 12 2568 3246 509349742 509350432 2.220000e-146 529.0
13 TraesCS3B01G200200 chr1D 81.168 685 105 13 2578 3246 341181637 341180961 2.220000e-146 529.0
14 TraesCS3B01G200200 chr1D 81.818 528 86 7 1704 2226 63922957 63922435 4.970000e-118 435.0
15 TraesCS3B01G200200 chr1D 91.071 56 5 0 1073 1128 63923094 63923039 3.470000e-10 76.8
16 TraesCS3B01G200200 chrUn 81.333 600 103 6 2512 3105 10319017 10319613 2.270000e-131 479.0
17 TraesCS3B01G200200 chr7A 80.122 654 117 11 2509 3155 186645346 186644699 2.930000e-130 475.0
18 TraesCS3B01G200200 chr1A 82.500 520 83 5 1711 2226 63005337 63004822 1.780000e-122 449.0
19 TraesCS3B01G200200 chr5D 77.833 609 117 14 2639 3239 325463278 325463876 8.560000e-96 361.0
20 TraesCS3B01G200200 chr6D 77.186 526 106 11 1713 2231 454996294 454995776 8.810000e-76 294.0
21 TraesCS3B01G200200 chr6D 76.458 480 107 5 1713 2189 455422130 455422606 4.160000e-64 255.0
22 TraesCS3B01G200200 chr6A 77.547 481 102 4 1713 2190 602131716 602132193 5.300000e-73 285.0
23 TraesCS3B01G200200 chr6A 75.625 480 111 5 1713 2189 602075864 602076340 1.950000e-57 233.0
24 TraesCS3B01G200200 chr2B 78.607 201 41 2 2509 2708 105734476 105734277 7.310000e-27 132.0


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 TraesCS3B01G200200 chr3B 228805991 228809236 3245 True 5995.00 5995 100.00000 1 3246 1 chr3B.!!$R2 3245
1 TraesCS3B01G200200 chr3D 157548972 157551409 2437 True 3214.00 3214 90.63700 1 2452 1 chr3D.!!$R1 2451
2 TraesCS3B01G200200 chr3D 312884677 312885417 740 False 606.00 606 81.84200 2512 3242 1 chr3D.!!$F1 730
3 TraesCS3B01G200200 chr3A 170645071 170650843 5772 False 999.75 2165 87.71425 1 3246 4 chr3A.!!$F1 3245
4 TraesCS3B01G200200 chr3A 95470778 95471516 738 True 540.00 540 80.26700 2514 3246 1 chr3A.!!$R1 732
5 TraesCS3B01G200200 chr4B 17465304 17466021 717 True 560.00 560 81.02300 2512 3246 1 chr4B.!!$R1 734
6 TraesCS3B01G200200 chr7D 184095250 184095899 649 False 538.00 538 81.74800 2509 3155 1 chr7D.!!$F1 646
7 TraesCS3B01G200200 chr4A 509349742 509350432 690 False 529.00 529 80.89100 2568 3246 1 chr4A.!!$F1 678
8 TraesCS3B01G200200 chr1D 341180961 341181637 676 True 529.00 529 81.16800 2578 3246 1 chr1D.!!$R1 668
9 TraesCS3B01G200200 chr1D 63922435 63923094 659 True 255.90 435 86.44450 1073 2226 2 chr1D.!!$R2 1153
10 TraesCS3B01G200200 chrUn 10319017 10319613 596 False 479.00 479 81.33300 2512 3105 1 chrUn.!!$F1 593
11 TraesCS3B01G200200 chr7A 186644699 186645346 647 True 475.00 475 80.12200 2509 3155 1 chr7A.!!$R1 646
12 TraesCS3B01G200200 chr1A 63004822 63005337 515 True 449.00 449 82.50000 1711 2226 1 chr1A.!!$R1 515
13 TraesCS3B01G200200 chr5D 325463278 325463876 598 False 361.00 361 77.83300 2639 3239 1 chr5D.!!$F1 600
14 TraesCS3B01G200200 chr6D 454995776 454996294 518 True 294.00 294 77.18600 1713 2231 1 chr6D.!!$R1 518

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
84 85 0.168788 CACGATGTGTCCAACCATGC 59.831 55.0 0.0 0.0 0.00 4.06 F
1195 3723 0.096628 CTGCTCTGCATTCAAGACGC 59.903 55.0 0.0 0.0 38.13 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 4198 0.167251 GGTACATTTGCCGTTGGACG 59.833 55.0 0.00 0.0 42.11 4.79 R
2575 5134 0.178533 TCAGGTTTTCGTGACCGGTT 59.821 50.0 9.42 0.0 42.11 4.44 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
81 82 0.602638 GCTCACGATGTGTCCAACCA 60.603 55.000 0.00 0.00 34.79 3.67
82 83 1.945819 GCTCACGATGTGTCCAACCAT 60.946 52.381 0.00 0.00 34.79 3.55
83 84 1.733912 CTCACGATGTGTCCAACCATG 59.266 52.381 0.00 0.00 34.79 3.66
84 85 0.168788 CACGATGTGTCCAACCATGC 59.831 55.000 0.00 0.00 0.00 4.06
85 86 1.298157 ACGATGTGTCCAACCATGCG 61.298 55.000 0.00 0.00 0.00 4.73
181 182 2.724174 GCCGGTTCAAATCAAGAAAACG 59.276 45.455 1.90 0.00 0.00 3.60
183 184 4.602995 CCGGTTCAAATCAAGAAAACGAA 58.397 39.130 0.00 0.00 32.69 3.85
306 323 1.144936 CCGATTCCTGACAGAGCCC 59.855 63.158 3.32 0.00 0.00 5.19
348 371 2.262471 CTACTCCACGGTAAGCGCGT 62.262 60.000 8.43 0.00 0.00 6.01
454 478 0.603569 ACCTACTGCCAGACTTGACG 59.396 55.000 0.00 0.00 0.00 4.35
493 517 2.677228 CCGGAGGCCTTGGTTCAT 59.323 61.111 6.77 0.00 46.14 2.57
522 546 2.047844 TCGCAGCTCACTTCAGGC 60.048 61.111 0.00 0.00 0.00 4.85
635 669 5.227238 ACAAAGCTTTATGCATCGAGAAG 57.773 39.130 12.25 5.13 45.94 2.85
636 670 4.937620 ACAAAGCTTTATGCATCGAGAAGA 59.062 37.500 12.25 0.00 45.94 2.87
638 672 4.662468 AGCTTTATGCATCGAGAAGAGA 57.338 40.909 0.19 0.00 45.94 3.10
639 673 5.016051 AGCTTTATGCATCGAGAAGAGAA 57.984 39.130 0.19 0.00 45.94 2.87
640 674 5.423015 AGCTTTATGCATCGAGAAGAGAAA 58.577 37.500 0.19 0.00 45.94 2.52
641 675 6.054295 AGCTTTATGCATCGAGAAGAGAAAT 58.946 36.000 0.19 0.00 45.94 2.17
642 676 6.018098 AGCTTTATGCATCGAGAAGAGAAATG 60.018 38.462 0.19 0.00 45.94 2.32
643 677 6.609237 TTTATGCATCGAGAAGAGAAATGG 57.391 37.500 0.19 0.00 0.00 3.16
644 678 3.616956 TGCATCGAGAAGAGAAATGGT 57.383 42.857 0.00 0.00 0.00 3.55
645 679 4.736126 TGCATCGAGAAGAGAAATGGTA 57.264 40.909 0.00 0.00 0.00 3.25
646 680 4.433615 TGCATCGAGAAGAGAAATGGTAC 58.566 43.478 0.00 0.00 0.00 3.34
647 681 4.160439 TGCATCGAGAAGAGAAATGGTACT 59.840 41.667 0.00 0.00 0.00 2.73
812 848 3.497031 GCTCCTTAACCCGCACGC 61.497 66.667 0.00 0.00 0.00 5.34
879 3398 5.657302 CACTCCTTCCCCGCTATATAAGTAT 59.343 44.000 0.00 0.00 0.00 2.12
939 3458 4.827087 CAGCAGCCATCGGAGCGT 62.827 66.667 0.00 0.00 34.64 5.07
942 3461 2.028190 CAGCCATCGGAGCGTAGG 59.972 66.667 0.00 0.00 34.64 3.18
945 3464 2.194212 GCCATCGGAGCGTAGGAGA 61.194 63.158 0.00 0.00 0.00 3.71
946 3465 1.953017 CCATCGGAGCGTAGGAGAG 59.047 63.158 0.00 0.00 0.00 3.20
947 3466 0.535328 CCATCGGAGCGTAGGAGAGA 60.535 60.000 0.00 0.00 0.00 3.10
948 3467 0.871722 CATCGGAGCGTAGGAGAGAG 59.128 60.000 0.00 0.00 0.00 3.20
949 3468 0.250553 ATCGGAGCGTAGGAGAGAGG 60.251 60.000 0.00 0.00 0.00 3.69
950 3469 2.548295 CGGAGCGTAGGAGAGAGGC 61.548 68.421 0.00 0.00 0.00 4.70
951 3470 2.548295 GGAGCGTAGGAGAGAGGCG 61.548 68.421 0.00 0.00 33.00 5.52
952 3471 1.524165 GAGCGTAGGAGAGAGGCGA 60.524 63.158 0.00 0.00 33.00 5.54
953 3472 1.503818 GAGCGTAGGAGAGAGGCGAG 61.504 65.000 0.00 0.00 33.00 5.03
954 3473 1.524165 GCGTAGGAGAGAGGCGAGA 60.524 63.158 0.00 0.00 0.00 4.04
955 3474 1.096386 GCGTAGGAGAGAGGCGAGAA 61.096 60.000 0.00 0.00 0.00 2.87
956 3475 1.380524 CGTAGGAGAGAGGCGAGAAA 58.619 55.000 0.00 0.00 0.00 2.52
957 3476 1.332375 CGTAGGAGAGAGGCGAGAAAG 59.668 57.143 0.00 0.00 0.00 2.62
958 3477 1.679153 GTAGGAGAGAGGCGAGAAAGG 59.321 57.143 0.00 0.00 0.00 3.11
959 3478 1.142965 GGAGAGAGGCGAGAAAGGC 59.857 63.158 0.00 0.00 0.00 4.35
960 3479 1.226831 GAGAGAGGCGAGAAAGGCG 60.227 63.158 0.00 0.00 41.99 5.52
961 3480 2.202810 GAGAGGCGAGAAAGGCGG 60.203 66.667 0.00 0.00 41.99 6.13
986 3505 0.239347 AGTTGAACAATCGCAGCAGC 59.761 50.000 0.00 0.00 37.42 5.25
1038 3561 2.282180 TCCGCCCTGTTTCTTGCC 60.282 61.111 0.00 0.00 0.00 4.52
1162 3685 6.413892 AGATCTCCTGAATTCCTCTTCAAAC 58.586 40.000 2.27 0.00 34.86 2.93
1188 3716 1.929836 CGGTACTTCTGCTCTGCATTC 59.070 52.381 0.00 0.00 38.13 2.67
1195 3723 0.096628 CTGCTCTGCATTCAAGACGC 59.903 55.000 0.00 0.00 38.13 5.19
1268 3796 7.876936 ACAGTAGGATAGAATTCACGTTAGA 57.123 36.000 8.44 0.00 0.00 2.10
1354 3889 3.994392 GTGCAATCGATATTACCGATGGT 59.006 43.478 0.00 0.00 44.85 3.55
1368 3903 5.825593 ACCGATGGTATGAATGGAAGTAT 57.174 39.130 0.00 0.00 32.11 2.12
1381 3916 8.856153 TGAATGGAAGTATACAAGTTTAGCAA 57.144 30.769 5.50 0.00 0.00 3.91
1415 3956 5.661458 TGATCATAGTCTTCCTTTCGAACC 58.339 41.667 0.00 0.00 0.00 3.62
1418 3959 5.661458 TCATAGTCTTCCTTTCGAACCATC 58.339 41.667 0.00 0.00 0.00 3.51
1432 3973 3.689161 CGAACCATCCAATAGTTTGCTCA 59.311 43.478 0.00 0.00 0.00 4.26
1603 4151 5.065914 CCATCATTCCGAACAACCAGATAT 58.934 41.667 0.00 0.00 0.00 1.63
1604 4152 6.183361 ACCATCATTCCGAACAACCAGATATA 60.183 38.462 0.00 0.00 0.00 0.86
1605 4153 6.147821 CCATCATTCCGAACAACCAGATATAC 59.852 42.308 0.00 0.00 0.00 1.47
1631 4179 1.937223 ACAACGCAAAAGATCGTGACA 59.063 42.857 0.00 0.00 39.06 3.58
1667 4217 0.167251 CGTCCAACGGCAAATGTACC 59.833 55.000 0.00 0.00 38.08 3.34
1668 4218 1.530323 GTCCAACGGCAAATGTACCT 58.470 50.000 0.00 0.00 0.00 3.08
1669 4219 2.702261 GTCCAACGGCAAATGTACCTA 58.298 47.619 0.00 0.00 0.00 3.08
1670 4220 2.417586 GTCCAACGGCAAATGTACCTAC 59.582 50.000 0.00 0.00 0.00 3.18
2119 4671 4.715130 AGCCAGCTCCCCGGTACA 62.715 66.667 0.00 0.00 0.00 2.90
2233 4785 0.883833 AGATCAAGGCCAAGTTTGCG 59.116 50.000 5.01 0.00 0.00 4.85
2236 4788 2.837291 AAGGCCAAGTTTGCGCCA 60.837 55.556 19.52 0.00 42.95 5.69
2319 4876 6.477360 GTGGTTCGTTTATTGATTTGTTGGTT 59.523 34.615 0.00 0.00 0.00 3.67
2320 4877 7.648510 GTGGTTCGTTTATTGATTTGTTGGTTA 59.351 33.333 0.00 0.00 0.00 2.85
2375 4932 0.163788 GTCGTGTCGTGCATTCTTGG 59.836 55.000 0.00 0.00 0.00 3.61
2379 4936 1.132640 GTCGTGCATTCTTGGCGAC 59.867 57.895 7.82 7.82 43.53 5.19
2407 4964 0.670546 CGACCTGTGTAAGTGGCCTG 60.671 60.000 3.32 0.00 0.00 4.85
2428 4985 6.016610 GCCTGAAGAACCACAAATTTGTACTA 60.017 38.462 22.87 6.45 39.91 1.82
2432 4989 9.048446 TGAAGAACCACAAATTTGTACTACTAC 57.952 33.333 22.87 12.96 39.91 2.73
2433 4990 9.269453 GAAGAACCACAAATTTGTACTACTACT 57.731 33.333 22.87 12.71 39.91 2.57
2438 4995 9.485206 ACCACAAATTTGTACTACTACTAAGTG 57.515 33.333 22.87 6.15 39.91 3.16
2456 5013 1.124780 TGGGACTGTTGGAGTTTCGA 58.875 50.000 0.00 0.00 33.83 3.71
2484 5041 4.753516 AAACCTTTTGGAAAAGTGGAGG 57.246 40.909 10.26 0.00 42.92 4.30
2523 5080 6.092122 TGTCCATTTTGTTAGAGCAATCTACG 59.908 38.462 0.00 0.00 0.00 3.51
2590 5150 2.219445 GTCACTAACCGGTCACGAAAAC 59.781 50.000 8.04 0.00 44.60 2.43
2623 5183 4.162690 GCCTCGAACGGGCCTCAT 62.163 66.667 0.84 0.00 43.49 2.90
2632 5192 2.063979 CGGGCCTCATACACCCAGA 61.064 63.158 0.84 0.00 44.49 3.86
2644 5204 3.625897 CCCAGACTGACCGGCACA 61.626 66.667 0.00 0.63 0.00 4.57
2681 5246 2.270434 ATATGAGGCGGATATGGGGT 57.730 50.000 0.00 0.00 0.00 4.95
2746 5322 1.734748 GAAACGCCCGAAAACCCAA 59.265 52.632 0.00 0.00 0.00 4.12
2756 5332 0.814812 GAAAACCCAACGGTCCGACA 60.815 55.000 20.51 0.00 43.71 4.35
2867 5444 3.739613 CCCCCAACCCTAGCCCAC 61.740 72.222 0.00 0.00 0.00 4.61
2872 5449 2.121689 AACCCTAGCCCACCCACA 60.122 61.111 0.00 0.00 0.00 4.17
2946 5523 4.050934 ACGCTGTCCGACATCGCA 62.051 61.111 21.39 0.00 40.92 5.10
2955 5532 2.709475 GACATCGCAATGGTCCGC 59.291 61.111 0.00 0.00 37.19 5.54
2964 5541 2.439960 AATGGTCCGCCGGCTGATA 61.440 57.895 26.68 16.76 37.67 2.15
3034 5611 3.391665 ATCTAGGCAAGGCGCGCTT 62.392 57.895 32.29 23.01 43.84 4.68
3092 5684 4.173924 GGAGGAGGAGCAGCAGCC 62.174 72.222 0.00 0.00 43.56 4.85
3109 5704 4.548513 CGGAGGAGGAGGGGGAGG 62.549 77.778 0.00 0.00 0.00 4.30
3110 5705 4.890306 GGAGGAGGAGGGGGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
3111 5706 4.095400 GAGGAGGAGGGGGAGGCA 62.095 72.222 0.00 0.00 0.00 4.75
3112 5707 4.101077 AGGAGGAGGGGGAGGCAG 62.101 72.222 0.00 0.00 0.00 4.85
3113 5708 4.095400 GGAGGAGGGGGAGGCAGA 62.095 72.222 0.00 0.00 0.00 4.26
3114 5709 2.445654 GAGGAGGGGGAGGCAGAG 60.446 72.222 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.608856 TTCACTTGGGTGCATCGCAT 60.609 50.000 0.00 0.00 41.91 4.73
82 83 1.228094 TTCACTTGGGTGCATCGCA 60.228 52.632 0.00 0.00 42.72 5.10
83 84 1.237285 ACTTCACTTGGGTGCATCGC 61.237 55.000 0.00 0.00 42.72 4.58
84 85 1.197721 GAACTTCACTTGGGTGCATCG 59.802 52.381 0.00 0.00 42.72 3.84
85 86 2.227388 CTGAACTTCACTTGGGTGCATC 59.773 50.000 0.00 0.00 42.72 3.91
181 182 6.984474 TCTACGAGGATGTGAACCAATTATTC 59.016 38.462 0.00 0.00 0.00 1.75
183 184 6.479972 TCTACGAGGATGTGAACCAATTAT 57.520 37.500 0.00 0.00 0.00 1.28
293 310 1.489481 CTACATGGGCTCTGTCAGGA 58.511 55.000 0.00 0.00 0.00 3.86
296 313 1.257750 ACGCTACATGGGCTCTGTCA 61.258 55.000 10.38 0.00 0.00 3.58
306 323 4.143242 GCATGCTAAGTATGACGCTACATG 60.143 45.833 11.37 0.00 36.37 3.21
348 371 3.706183 AGATGAGGATAGATGGCGATCA 58.294 45.455 11.55 0.00 0.00 2.92
445 469 1.956170 CGGCAAGCACGTCAAGTCT 60.956 57.895 0.00 0.00 0.00 3.24
483 507 4.398319 AGTACTTTGACCATGAACCAAGG 58.602 43.478 0.00 0.00 0.00 3.61
493 517 0.679505 AGCTGCGAGTACTTTGACCA 59.320 50.000 0.00 0.00 0.00 4.02
522 546 0.391263 GGGCTAGTTTGGTGACGGAG 60.391 60.000 0.00 0.00 0.00 4.63
635 669 9.453325 CGAGATTTAAGTAGAGTACCATTTCTC 57.547 37.037 0.00 0.00 0.00 2.87
636 670 9.186837 TCGAGATTTAAGTAGAGTACCATTTCT 57.813 33.333 0.00 0.00 0.00 2.52
639 673 9.583765 GTTTCGAGATTTAAGTAGAGTACCATT 57.416 33.333 0.00 0.00 0.00 3.16
640 674 7.914346 CGTTTCGAGATTTAAGTAGAGTACCAT 59.086 37.037 0.00 0.00 0.00 3.55
641 675 7.246311 CGTTTCGAGATTTAAGTAGAGTACCA 58.754 38.462 0.00 0.00 0.00 3.25
642 676 6.196168 GCGTTTCGAGATTTAAGTAGAGTACC 59.804 42.308 0.00 0.00 0.00 3.34
643 677 6.744537 TGCGTTTCGAGATTTAAGTAGAGTAC 59.255 38.462 0.00 0.00 0.00 2.73
644 678 6.845302 TGCGTTTCGAGATTTAAGTAGAGTA 58.155 36.000 0.00 0.00 0.00 2.59
645 679 5.706916 TGCGTTTCGAGATTTAAGTAGAGT 58.293 37.500 0.00 0.00 0.00 3.24
646 680 6.459330 GTTGCGTTTCGAGATTTAAGTAGAG 58.541 40.000 0.00 0.00 0.00 2.43
647 681 5.060077 CGTTGCGTTTCGAGATTTAAGTAGA 59.940 40.000 0.00 0.00 0.00 2.59
812 848 0.670162 CAAAGCAGAGTTGGTGTGGG 59.330 55.000 0.00 0.00 36.58 4.61
902 3421 2.281484 GCTGCCGGTCTGGTTTGA 60.281 61.111 1.90 0.00 41.21 2.69
923 3442 3.144120 CTACGCTCCGATGGCTGCT 62.144 63.158 0.00 0.00 0.00 4.24
938 3457 1.679153 CCTTTCTCGCCTCTCTCCTAC 59.321 57.143 0.00 0.00 0.00 3.18
939 3458 2.024825 GCCTTTCTCGCCTCTCTCCTA 61.025 57.143 0.00 0.00 0.00 2.94
942 3461 1.226831 CGCCTTTCTCGCCTCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
945 3464 4.459089 GCCGCCTTTCTCGCCTCT 62.459 66.667 0.00 0.00 0.00 3.69
959 3478 2.563086 GATTGTTCAACTCGCCGCCG 62.563 60.000 0.00 0.00 0.00 6.46
960 3479 1.134694 GATTGTTCAACTCGCCGCC 59.865 57.895 0.00 0.00 0.00 6.13
961 3480 1.225745 CGATTGTTCAACTCGCCGC 60.226 57.895 0.00 0.00 0.00 6.53
965 3484 0.512518 TGCTGCGATTGTTCAACTCG 59.487 50.000 0.00 0.00 35.57 4.18
966 3485 1.727213 GCTGCTGCGATTGTTCAACTC 60.727 52.381 0.00 0.00 0.00 3.01
967 3486 0.239347 GCTGCTGCGATTGTTCAACT 59.761 50.000 0.00 0.00 0.00 3.16
968 3487 2.716988 GCTGCTGCGATTGTTCAAC 58.283 52.632 0.00 0.00 0.00 3.18
986 3505 3.411114 ATCATGGTGCCCTGCTCCG 62.411 63.158 0.00 0.00 44.11 4.63
991 3510 2.728397 CCATCATCATGGTGCCCTG 58.272 57.895 0.00 0.00 44.46 4.45
1128 3651 2.302260 TCAGGAGATCTTGAGCTACGG 58.698 52.381 0.00 0.00 0.00 4.02
1162 3685 2.028130 AGAGCAGAAGTACCGATCCAG 58.972 52.381 0.00 0.00 0.00 3.86
1188 3716 1.200483 CTGTATAGCCGTGCGTCTTG 58.800 55.000 0.00 0.00 0.00 3.02
1289 3824 5.588648 GGCACTGGATTTAGCATTAACTACA 59.411 40.000 0.00 0.00 0.00 2.74
1295 3830 4.235079 ACTGGCACTGGATTTAGCATTA 57.765 40.909 0.00 0.00 0.00 1.90
1409 3950 3.938963 GAGCAAACTATTGGATGGTTCGA 59.061 43.478 0.00 0.00 37.02 3.71
1603 4151 4.501071 GATCTTTTGCGTTGTCCCTAGTA 58.499 43.478 0.00 0.00 0.00 1.82
1604 4152 2.922740 TCTTTTGCGTTGTCCCTAGT 57.077 45.000 0.00 0.00 0.00 2.57
1605 4153 2.348666 CGATCTTTTGCGTTGTCCCTAG 59.651 50.000 0.00 0.00 0.00 3.02
1648 4198 0.167251 GGTACATTTGCCGTTGGACG 59.833 55.000 0.00 0.00 42.11 4.79
1667 4217 3.784701 ACAGTTACATGAGGCTCGTAG 57.215 47.619 9.29 6.75 0.00 3.51
1668 4218 4.439700 GCTTACAGTTACATGAGGCTCGTA 60.440 45.833 9.29 3.47 0.00 3.43
1669 4219 3.676324 GCTTACAGTTACATGAGGCTCGT 60.676 47.826 10.42 6.73 0.00 4.18
1670 4220 2.860735 GCTTACAGTTACATGAGGCTCG 59.139 50.000 10.42 0.00 0.00 5.03
1954 4506 3.324099 GAAGCCGACGTCGAGCTCA 62.324 63.158 36.46 0.00 42.14 4.26
2083 4635 0.684535 TGTTGAAGGCCGAGATGACA 59.315 50.000 0.00 0.00 0.00 3.58
2116 4668 3.758715 CATGGCGATGGACTGTGTA 57.241 52.632 0.00 0.00 0.00 2.90
2233 4785 0.875059 CGGTCCTTCACTTCTTTGGC 59.125 55.000 0.00 0.00 0.00 4.52
2236 4788 1.270893 GCTCCGGTCCTTCACTTCTTT 60.271 52.381 0.00 0.00 0.00 2.52
2341 4898 4.673441 GACACGACTGCATTAGTATGACT 58.327 43.478 0.00 0.00 40.53 3.41
2379 4936 4.742201 CACAGGTCGCCAGTCGGG 62.742 72.222 0.00 0.00 39.05 5.14
2389 4946 0.685097 TCAGGCCACTTACACAGGTC 59.315 55.000 5.01 0.00 0.00 3.85
2407 4964 9.269453 AGTAGTAGTACAAATTTGTGGTTCTTC 57.731 33.333 29.72 19.21 42.31 2.87
2416 4973 9.148104 GTCCCACTTAGTAGTAGTACAAATTTG 57.852 37.037 16.67 16.67 31.96 2.32
2428 4985 3.833070 CTCCAACAGTCCCACTTAGTAGT 59.167 47.826 0.00 0.00 34.00 2.73
2432 4989 3.771577 AACTCCAACAGTCCCACTTAG 57.228 47.619 0.00 0.00 32.30 2.18
2433 4990 3.493699 CGAAACTCCAACAGTCCCACTTA 60.494 47.826 0.00 0.00 32.30 2.24
2434 4991 2.745152 CGAAACTCCAACAGTCCCACTT 60.745 50.000 0.00 0.00 32.30 3.16
2435 4992 1.202651 CGAAACTCCAACAGTCCCACT 60.203 52.381 0.00 0.00 32.30 4.00
2436 4993 1.202604 TCGAAACTCCAACAGTCCCAC 60.203 52.381 0.00 0.00 32.30 4.61
2437 4994 1.124780 TCGAAACTCCAACAGTCCCA 58.875 50.000 0.00 0.00 32.30 4.37
2438 4995 2.249844 TTCGAAACTCCAACAGTCCC 57.750 50.000 0.00 0.00 32.30 4.46
2480 5037 6.200878 TGGACAAATTATATTCTCCCCTCC 57.799 41.667 0.00 0.00 0.00 4.30
2483 5040 8.704668 ACAAAATGGACAAATTATATTCTCCCC 58.295 33.333 0.00 0.00 0.00 4.81
2575 5134 0.178533 TCAGGTTTTCGTGACCGGTT 59.821 50.000 9.42 0.00 42.11 4.44
2590 5150 4.436998 GCGTCCGTCTGGGTCAGG 62.437 72.222 0.00 0.00 37.00 3.86
2623 5183 2.280552 GCCGGTCAGTCTGGGTGTA 61.281 63.158 1.90 0.00 42.62 2.90
2632 5192 1.563924 TATAAGGTGTGCCGGTCAGT 58.436 50.000 1.90 0.00 40.50 3.41
2644 5204 6.297243 CCTCATATTTGGGCTGGATATAAGGT 60.297 42.308 0.00 0.00 0.00 3.50
2746 5322 3.853597 GAGGCGTTTGTCGGACCGT 62.854 63.158 14.79 0.00 40.26 4.83
2756 5332 4.736896 GCGACGGAGGAGGCGTTT 62.737 66.667 0.00 0.00 0.00 3.60
2867 5444 1.694133 GCAGAGAGGGAGGATGTGGG 61.694 65.000 0.00 0.00 0.00 4.61
2872 5449 2.841988 GGCGCAGAGAGGGAGGAT 60.842 66.667 10.83 0.00 0.00 3.24
2912 5489 1.003573 GTGGGAGAGTGGGGGAGAT 59.996 63.158 0.00 0.00 0.00 2.75
2946 5523 1.978455 TTATCAGCCGGCGGACCATT 61.978 55.000 31.76 18.04 34.57 3.16
2955 5532 0.868602 CGTACGTGGTTATCAGCCGG 60.869 60.000 7.22 0.00 0.00 6.13
2964 5541 0.528924 TGAGCATAGCGTACGTGGTT 59.471 50.000 17.90 2.02 0.00 3.67
3085 5662 3.847602 CTCCTCCTCCGGCTGCTG 61.848 72.222 0.00 0.26 0.00 4.41
3092 5684 4.548513 CCTCCCCCTCCTCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
3131 5726 4.770362 TCCGGATCCGCCACCTCA 62.770 66.667 29.12 2.59 38.24 3.86
3178 5792 1.599576 GAACTCCACCTCTGCCTCC 59.400 63.158 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.