Multiple sequence alignment - TraesCS2A01G180000

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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 TraesCS2A01G180000 chr2A 100.000 3497 0 0 1 3497 138828502 138825006 0.000000e+00 6458.0
1 TraesCS2A01G180000 chr2A 83.922 510 44 11 2897 3369 138656184 138655676 1.480000e-123 453.0
2 TraesCS2A01G180000 chr2A 82.394 142 18 3 11 152 690330472 690330338 2.210000e-22 117.0
3 TraesCS2A01G180000 chr2D 90.250 2318 89 46 632 2843 131778293 131776007 0.000000e+00 2902.0
4 TraesCS2A01G180000 chr2D 89.256 363 26 10 2897 3248 547282953 547282593 3.200000e-120 442.0
5 TraesCS2A01G180000 chr2D 95.536 112 5 0 2785 2896 131764368 131764257 2.770000e-41 180.0
6 TraesCS2A01G180000 chr2D 92.623 122 9 0 3240 3361 547282565 547282444 3.590000e-40 176.0
7 TraesCS2A01G180000 chr2D 76.471 136 19 10 3360 3492 582128927 582129052 1.050000e-05 62.1
8 TraesCS2A01G180000 chr2B 89.675 2305 93 49 657 2892 186311390 186313618 0.000000e+00 2804.0
9 TraesCS2A01G180000 chr2B 88.717 1356 65 37 1587 2875 185776831 185775497 0.000000e+00 1576.0
10 TraesCS2A01G180000 chr2B 96.429 112 4 0 2785 2896 186376510 186376621 5.960000e-43 185.0
11 TraesCS2A01G180000 chr3A 96.006 626 25 0 1 626 509516856 509516231 0.000000e+00 1018.0
12 TraesCS2A01G180000 chr3A 76.056 284 46 13 2894 3162 69477324 69477048 1.020000e-25 128.0
13 TraesCS2A01G180000 chr3A 100.000 30 0 0 3443 3472 110457012 110456983 4.880000e-04 56.5
14 TraesCS2A01G180000 chr3A 100.000 30 0 0 3443 3472 110458061 110458032 4.880000e-04 56.5
15 TraesCS2A01G180000 chr5A 96.248 613 23 0 1 613 372246015 372245403 0.000000e+00 1005.0
16 TraesCS2A01G180000 chr5A 77.551 686 118 25 1219 1877 649441483 649442159 7.080000e-102 381.0
17 TraesCS2A01G180000 chr4D 84.765 617 55 15 2897 3488 6772520 6773122 1.810000e-162 582.0
18 TraesCS2A01G180000 chr4D 81.302 722 103 27 1171 1885 386831148 386831844 1.100000e-154 556.0
19 TraesCS2A01G180000 chr4D 84.426 366 36 13 2899 3248 458088632 458088272 1.200000e-89 340.0
20 TraesCS2A01G180000 chr4D 96.774 31 1 0 2379 2409 386832715 386832745 6.000000e-03 52.8
21 TraesCS2A01G180000 chr4A 81.717 722 100 25 1171 1885 68141434 68142130 1.090000e-159 573.0
22 TraesCS2A01G180000 chr4A 79.464 112 18 5 3361 3469 626829408 626829517 1.350000e-09 75.0
23 TraesCS2A01G180000 chr4A 96.875 32 1 0 2379 2410 68142965 68142996 2.000000e-03 54.7
24 TraesCS2A01G180000 chr4B 81.025 722 105 25 1171 1885 474378549 474379245 2.370000e-151 545.0
25 TraesCS2A01G180000 chr4B 85.399 363 38 7 2897 3246 439990333 439990693 2.570000e-96 363.0
26 TraesCS2A01G180000 chr4B 96.875 32 1 0 2379 2410 474380100 474380131 2.000000e-03 54.7
27 TraesCS2A01G180000 chr1D 88.705 363 27 6 2897 3248 80439597 80439956 6.930000e-117 431.0
28 TraesCS2A01G180000 chr1D 79.730 518 57 21 2897 3373 147782371 147782881 7.240000e-87 331.0
29 TraesCS2A01G180000 chr1D 80.714 280 28 14 3241 3495 80439985 80440263 9.900000e-46 195.0
30 TraesCS2A01G180000 chr1D 74.263 373 67 22 2897 3249 283801733 283801370 2.830000e-26 130.0
31 TraesCS2A01G180000 chr1D 77.075 253 36 12 2897 3136 341416481 341416724 3.660000e-25 126.0
32 TraesCS2A01G180000 chr7B 80.265 603 81 20 2897 3468 334245275 334244680 1.500000e-113 420.0
33 TraesCS2A01G180000 chr7B 74.286 560 83 35 2897 3406 707460945 707461493 2.770000e-41 180.0
34 TraesCS2A01G180000 chr7B 77.432 257 39 11 2897 3140 454722549 454722299 6.090000e-28 135.0
35 TraesCS2A01G180000 chr5D 86.849 365 34 6 2895 3248 109821116 109821477 2.530000e-106 396.0
36 TraesCS2A01G180000 chr5D 85.399 363 38 6 2899 3248 109937004 109937364 2.570000e-96 363.0
37 TraesCS2A01G180000 chr5D 77.047 684 110 32 1219 1877 520910023 520910684 2.000000e-92 350.0
38 TraesCS2A01G180000 chr5D 83.270 263 28 4 3241 3488 109821506 109821767 9.760000e-56 228.0
39 TraesCS2A01G180000 chr5B 76.580 696 116 35 1219 1877 656925819 656926504 4.320000e-89 339.0
40 TraesCS2A01G180000 chr7D 81.882 425 50 18 2897 3304 372358608 372358194 2.010000e-87 333.0
41 TraesCS2A01G180000 chr7D 78.846 156 24 9 3345 3495 422288612 422288461 2.870000e-16 97.1
42 TraesCS2A01G180000 chr1A 79.018 448 51 21 2897 3305 460475341 460475784 2.070000e-67 267.0
43 TraesCS2A01G180000 chr1B 80.193 207 31 8 426 627 413970168 413970369 2.810000e-31 147.0
44 TraesCS2A01G180000 chr3D 75.719 313 43 25 2892 3181 308120310 308120612 3.660000e-25 126.0
45 TraesCS2A01G180000 chr6D 86.667 90 9 3 3215 3303 345249541 345249454 2.870000e-16 97.1
46 TraesCS2A01G180000 chr6D 93.548 62 4 0 3243 3304 264388894 264388955 3.720000e-15 93.5
47 TraesCS2A01G180000 chr6D 100.000 28 0 0 434 461 322531373 322531346 6.000000e-03 52.8
48 TraesCS2A01G180000 chr3B 100.000 29 0 0 3353 3381 184495927 184495899 2.000000e-03 54.7


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 TraesCS2A01G180000 chr2A 138825006 138828502 3496 True 6458.00 6458 100.0000 1 3497 1 chr2A.!!$R2 3496
1 TraesCS2A01G180000 chr2A 138655676 138656184 508 True 453.00 453 83.9220 2897 3369 1 chr2A.!!$R1 472
2 TraesCS2A01G180000 chr2D 131776007 131778293 2286 True 2902.00 2902 90.2500 632 2843 1 chr2D.!!$R2 2211
3 TraesCS2A01G180000 chr2D 547282444 547282953 509 True 309.00 442 90.9395 2897 3361 2 chr2D.!!$R3 464
4 TraesCS2A01G180000 chr2B 186311390 186313618 2228 False 2804.00 2804 89.6750 657 2892 1 chr2B.!!$F1 2235
5 TraesCS2A01G180000 chr2B 185775497 185776831 1334 True 1576.00 1576 88.7170 1587 2875 1 chr2B.!!$R1 1288
6 TraesCS2A01G180000 chr3A 509516231 509516856 625 True 1018.00 1018 96.0060 1 626 1 chr3A.!!$R2 625
7 TraesCS2A01G180000 chr5A 372245403 372246015 612 True 1005.00 1005 96.2480 1 613 1 chr5A.!!$R1 612
8 TraesCS2A01G180000 chr5A 649441483 649442159 676 False 381.00 381 77.5510 1219 1877 1 chr5A.!!$F1 658
9 TraesCS2A01G180000 chr4D 6772520 6773122 602 False 582.00 582 84.7650 2897 3488 1 chr4D.!!$F1 591
10 TraesCS2A01G180000 chr4D 386831148 386832745 1597 False 304.40 556 89.0380 1171 2409 2 chr4D.!!$F2 1238
11 TraesCS2A01G180000 chr4A 68141434 68142996 1562 False 313.85 573 89.2960 1171 2410 2 chr4A.!!$F2 1239
12 TraesCS2A01G180000 chr4B 474378549 474380131 1582 False 299.85 545 88.9500 1171 2410 2 chr4B.!!$F2 1239
13 TraesCS2A01G180000 chr1D 147782371 147782881 510 False 331.00 331 79.7300 2897 3373 1 chr1D.!!$F1 476
14 TraesCS2A01G180000 chr1D 80439597 80440263 666 False 313.00 431 84.7095 2897 3495 2 chr1D.!!$F3 598
15 TraesCS2A01G180000 chr7B 334244680 334245275 595 True 420.00 420 80.2650 2897 3468 1 chr7B.!!$R1 571
16 TraesCS2A01G180000 chr5D 520910023 520910684 661 False 350.00 350 77.0470 1219 1877 1 chr5D.!!$F2 658
17 TraesCS2A01G180000 chr5D 109821116 109821767 651 False 312.00 396 85.0595 2895 3488 2 chr5D.!!$F3 593
18 TraesCS2A01G180000 chr5B 656925819 656926504 685 False 339.00 339 76.5800 1219 1877 1 chr5B.!!$F1 658

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
63 64 0.105778 TGTTGTGGCATGTGAGTCGA 59.894 50.0 0.0 0.0 0.00 4.20 F
927 929 0.317479 GTGAGTACCGAGCAGTTGGT 59.683 55.0 0.0 0.0 43.69 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 1932 0.107945 GTCAGTGGAGGAGTGATGGC 60.108 60.0 0.00 0.0 36.38 4.40 R
2673 3368 0.451783 CCTTGGCCGAGTTACAATGC 59.548 55.0 19.14 0.0 0.00 3.56 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
63 64 0.105778 TGTTGTGGCATGTGAGTCGA 59.894 50.000 0.00 0.00 0.00 4.20
101 102 1.198713 GCCCTGATCCAACTCTGAGA 58.801 55.000 12.44 0.00 0.00 3.27
144 145 1.448540 CGTCGGCAAGCATCTCCTT 60.449 57.895 0.00 0.00 0.00 3.36
459 460 2.214920 AGAGTTTTCGTCCGCCCCT 61.215 57.895 0.00 0.00 0.00 4.79
522 523 9.547753 GTTATTTGGACAGCTAGATCTAAATGA 57.452 33.333 18.54 12.01 36.86 2.57
599 600 4.011698 GGGTGCGTTTAGGGAAGAAAATA 58.988 43.478 0.00 0.00 0.00 1.40
613 614 9.489084 AGGGAAGAAAATATTTGCTTGTTTAAC 57.511 29.630 23.59 9.64 36.18 2.01
614 615 8.432359 GGGAAGAAAATATTTGCTTGTTTAACG 58.568 33.333 23.59 0.00 36.18 3.18
626 627 7.395190 TGCTTGTTTAACGGTAGTAGAGATA 57.605 36.000 0.00 0.00 0.00 1.98
627 628 7.478322 TGCTTGTTTAACGGTAGTAGAGATAG 58.522 38.462 0.00 0.00 0.00 2.08
628 629 7.337689 TGCTTGTTTAACGGTAGTAGAGATAGA 59.662 37.037 0.00 0.00 0.00 1.98
629 630 7.856894 GCTTGTTTAACGGTAGTAGAGATAGAG 59.143 40.741 0.00 0.00 0.00 2.43
630 631 9.107177 CTTGTTTAACGGTAGTAGAGATAGAGA 57.893 37.037 0.00 0.00 0.00 3.10
717 719 4.112433 TGCCCATGCTCGATGCCA 62.112 61.111 4.73 0.00 42.00 4.92
718 720 3.589881 GCCCATGCTCGATGCCAC 61.590 66.667 4.73 0.00 42.00 5.01
719 721 2.903855 CCCATGCTCGATGCCACC 60.904 66.667 4.73 0.00 42.00 4.61
720 722 3.274586 CCATGCTCGATGCCACCG 61.275 66.667 4.73 0.00 42.00 4.94
721 723 3.274586 CATGCTCGATGCCACCGG 61.275 66.667 0.00 0.00 42.00 5.28
755 757 5.894964 ACCCAAACAAAGGCTAAAGTAAAGA 59.105 36.000 0.00 0.00 0.00 2.52
756 758 6.381707 ACCCAAACAAAGGCTAAAGTAAAGAA 59.618 34.615 0.00 0.00 0.00 2.52
757 759 6.923508 CCCAAACAAAGGCTAAAGTAAAGAAG 59.076 38.462 0.00 0.00 0.00 2.85
802 804 0.772517 CCCCCTCCCCTATCCTTTCC 60.773 65.000 0.00 0.00 0.00 3.13
817 819 0.698818 TTTCCCCCTCTCTTTCCTGC 59.301 55.000 0.00 0.00 0.00 4.85
827 829 3.401243 CTTTCCTGCGCGCCCATTC 62.401 63.158 30.77 0.00 0.00 2.67
861 863 2.918934 TCCATCTCCTCCAAATCAACCA 59.081 45.455 0.00 0.00 0.00 3.67
862 864 3.333381 TCCATCTCCTCCAAATCAACCAA 59.667 43.478 0.00 0.00 0.00 3.67
896 898 1.269448 CACACACCATTACCAGTTGCC 59.731 52.381 0.00 0.00 0.00 4.52
912 914 0.884514 TGCCGAAGAGTGAGAGTGAG 59.115 55.000 0.00 0.00 0.00 3.51
913 915 0.885196 GCCGAAGAGTGAGAGTGAGT 59.115 55.000 0.00 0.00 0.00 3.41
914 916 2.085320 GCCGAAGAGTGAGAGTGAGTA 58.915 52.381 0.00 0.00 0.00 2.59
915 917 2.159490 GCCGAAGAGTGAGAGTGAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
916 918 2.420722 CCGAAGAGTGAGAGTGAGTACC 59.579 54.545 0.00 0.00 0.00 3.34
917 919 2.094575 CGAAGAGTGAGAGTGAGTACCG 59.905 54.545 0.00 0.00 0.00 4.02
918 920 3.336468 GAAGAGTGAGAGTGAGTACCGA 58.664 50.000 0.00 0.00 0.00 4.69
924 926 1.813786 GAGAGTGAGTACCGAGCAGTT 59.186 52.381 0.00 0.00 0.00 3.16
927 929 0.317479 GTGAGTACCGAGCAGTTGGT 59.683 55.000 0.00 0.00 43.69 3.67
960 962 3.167945 GACATTGCACGCGCTTGC 61.168 61.111 29.82 29.82 43.31 4.01
962 964 4.703799 CATTGCACGCGCTTGCCA 62.704 61.111 32.45 24.25 42.25 4.92
983 985 0.526310 CGAGCTCTGCATTGCGTCTA 60.526 55.000 12.85 0.00 0.00 2.59
1068 1070 9.927081 ATTTCATGGAGAGGTAAATAGATTTGT 57.073 29.630 0.00 0.00 0.00 2.83
1107 1109 3.096092 TGGTTTCTTCTTTGCTTGGTGT 58.904 40.909 0.00 0.00 0.00 4.16
1115 1117 2.092968 TCTTTGCTTGGTGTGAGTGAGT 60.093 45.455 0.00 0.00 0.00 3.41
1124 1126 2.609737 GGTGTGAGTGAGTTTCGGTAGG 60.610 54.545 0.00 0.00 0.00 3.18
1892 1924 1.304547 ACCCCGAGGTCAGTCTCAG 60.305 63.158 0.00 0.00 46.45 3.35
1900 1932 2.487762 GAGGTCAGTCTCAGTCTCAGTG 59.512 54.545 0.00 0.00 34.13 3.66
1904 1936 1.549620 CAGTCTCAGTCTCAGTGCCAT 59.450 52.381 0.00 0.00 0.00 4.40
1915 2140 4.625800 GTGCCATCACTCCTCCAC 57.374 61.111 0.00 0.00 40.03 4.02
1933 2322 3.316573 CTGACGCCCTCCAAGTCCC 62.317 68.421 0.00 0.00 34.24 4.46
2565 3251 5.412904 GTGAAAAGAGAGATTGGTTGTAGGG 59.587 44.000 0.00 0.00 0.00 3.53
2573 3259 6.890293 AGAGATTGGTTGTAGGGTTAGATTC 58.110 40.000 0.00 0.00 0.00 2.52
2578 3264 3.703052 GGTTGTAGGGTTAGATTCGGAGA 59.297 47.826 0.00 0.00 0.00 3.71
2619 3305 4.915085 CGTGTTGATGGGATTTTGTTGTAC 59.085 41.667 0.00 0.00 0.00 2.90
2638 3333 6.783892 TGTACGTAGATTGTTGGTTAAACC 57.216 37.500 0.00 0.00 38.06 3.27
2670 3365 4.299978 GCTTAGTTCAGCTCCGGTATAAG 58.700 47.826 0.00 0.00 36.79 1.73
2671 3366 4.202131 GCTTAGTTCAGCTCCGGTATAAGT 60.202 45.833 0.00 0.00 36.79 2.24
2672 3367 5.009410 GCTTAGTTCAGCTCCGGTATAAGTA 59.991 44.000 0.00 0.00 36.79 2.24
2673 3368 6.630444 TTAGTTCAGCTCCGGTATAAGTAG 57.370 41.667 0.00 0.00 0.00 2.57
2686 3381 5.628193 CGGTATAAGTAGCATTGTAACTCGG 59.372 44.000 0.00 0.00 0.00 4.63
2689 3384 1.553248 AGTAGCATTGTAACTCGGCCA 59.447 47.619 2.24 0.00 0.00 5.36
2741 3436 2.584608 CAGGGACACTTAGGCGGG 59.415 66.667 0.00 0.00 0.00 6.13
2825 3525 6.543100 TCAGCTTTGAAAAATCAGCCAAAATT 59.457 30.769 0.00 0.00 32.25 1.82
2843 3543 6.147492 CCAAAATTTGATTCGAGCAATTTCCA 59.853 34.615 7.37 0.00 0.00 3.53
2846 3549 4.424061 TTGATTCGAGCAATTTCCAGTG 57.576 40.909 0.00 0.00 0.00 3.66
2852 3555 7.335673 TGATTCGAGCAATTTCCAGTGTATTTA 59.664 33.333 0.00 0.00 0.00 1.40
2854 3557 5.064707 TCGAGCAATTTCCAGTGTATTTAGC 59.935 40.000 0.00 0.00 0.00 3.09
2867 3571 7.066284 CCAGTGTATTTAGCTAAAGCACATTCT 59.934 37.037 33.77 24.64 45.16 2.40
2888 3596 7.759489 TTCTGATGTACTTTAGTGCCAAAAT 57.241 32.000 0.00 0.00 0.00 1.82
2892 3600 5.720371 TGTACTTTAGTGCCAAAATGCAT 57.280 34.783 0.00 0.00 44.30 3.96
2893 3601 6.825944 TGTACTTTAGTGCCAAAATGCATA 57.174 33.333 0.00 0.00 44.30 3.14
2915 3623 5.780958 AACTGTTAGGGCTTATTTCTCCT 57.219 39.130 0.00 0.00 0.00 3.69
2981 3698 7.709613 GCATTGAGCATTTCAGGATATTTCTTT 59.290 33.333 0.00 0.00 44.79 2.52
2995 3713 8.055181 AGGATATTTCTTTATTTGGCAGAGACA 58.945 33.333 0.00 0.00 0.00 3.41
3006 3725 4.156455 TGGCAGAGACAATTTCTATCCC 57.844 45.455 0.00 0.00 33.22 3.85
3081 3803 6.291377 ACTTGAGTCGTAGGATATACCGTAA 58.709 40.000 0.00 0.00 44.74 3.18
3093 3816 7.649715 AGGATATACCGTAATATCAAGAGGGA 58.350 38.462 13.31 0.00 44.74 4.20
3103 3826 3.944055 ATCAAGAGGGAATCCGTATCG 57.056 47.619 0.00 0.00 38.33 2.92
3153 3876 0.322546 CAACTCCCTTGCACCCCTAC 60.323 60.000 0.00 0.00 0.00 3.18
3309 4081 1.684248 GGTTCAGCGGTAGTCCCTCTA 60.684 57.143 0.00 0.00 0.00 2.43
3381 4166 2.029623 CAGTAGTACCGCACCTACCAT 58.970 52.381 0.00 0.00 0.00 3.55
3382 4167 3.216800 CAGTAGTACCGCACCTACCATA 58.783 50.000 0.00 0.00 0.00 2.74
3388 4173 1.595382 CGCACCTACCATAGCTGCC 60.595 63.158 0.00 0.00 34.64 4.85
3434 4220 0.343372 TATCCCTCCCCTGTGCTCTT 59.657 55.000 0.00 0.00 0.00 2.85
3469 4256 1.683365 GGTCCCAGCGGTAGTACCA 60.683 63.158 19.41 0.00 38.47 3.25
3473 4260 1.153628 CCAGCGGTAGTACCACTGC 60.154 63.158 25.83 16.41 44.83 4.40
3475 4262 2.202703 GCGGTAGTACCACTGCGG 60.203 66.667 19.41 2.89 40.76 5.69
3496 4283 4.977126 GCGGTAGTATCGCGCGCT 62.977 66.667 30.48 19.99 43.71 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 275 3.521529 GACGGTCACAGGCAGCAGT 62.522 63.158 2.62 0.00 0.00 4.40
278 279 3.939837 ATGCGACGGTCACAGGCAG 62.940 63.158 9.10 0.00 37.01 4.85
522 523 5.775813 AGAGCCTCATGATTATGCCTATT 57.224 39.130 0.00 0.00 34.21 1.73
569 570 0.671163 CTAAACGCACCCCGCTAACA 60.671 55.000 0.00 0.00 41.76 2.41
599 600 7.156673 TCTCTACTACCGTTAAACAAGCAAAT 58.843 34.615 0.00 0.00 0.00 2.32
613 614 9.834628 GATGATTTTTCTCTATCTCTACTACCG 57.165 37.037 0.00 0.00 0.00 4.02
626 627 4.142816 CGCCGTGAAAGATGATTTTTCTCT 60.143 41.667 9.44 0.00 35.94 3.10
627 628 4.091424 CGCCGTGAAAGATGATTTTTCTC 58.909 43.478 9.44 5.48 35.94 2.87
628 629 3.119849 CCGCCGTGAAAGATGATTTTTCT 60.120 43.478 9.44 0.00 35.94 2.52
629 630 3.171277 CCGCCGTGAAAGATGATTTTTC 58.829 45.455 1.83 1.83 35.59 2.29
630 631 2.094752 CCCGCCGTGAAAGATGATTTTT 60.095 45.455 0.00 0.00 0.00 1.94
755 757 0.321653 GTGTGGCTCCCGATGAACTT 60.322 55.000 0.00 0.00 0.00 2.66
756 758 1.194781 AGTGTGGCTCCCGATGAACT 61.195 55.000 0.00 0.00 0.00 3.01
757 759 0.535335 TAGTGTGGCTCCCGATGAAC 59.465 55.000 0.00 0.00 0.00 3.18
802 804 2.124942 GCGCAGGAAAGAGAGGGG 60.125 66.667 0.30 0.00 0.00 4.79
827 829 1.410882 GAGATGGAGAAAGACGAGGGG 59.589 57.143 0.00 0.00 0.00 4.79
861 863 1.134640 TGTGTGGTAGCGTGACAGTTT 60.135 47.619 0.00 0.00 0.00 2.66
862 864 0.462375 TGTGTGGTAGCGTGACAGTT 59.538 50.000 0.00 0.00 0.00 3.16
896 898 2.094575 CGGTACTCACTCTCACTCTTCG 59.905 54.545 0.00 0.00 0.00 3.79
912 914 2.380410 CGCACCAACTGCTCGGTAC 61.380 63.158 0.00 0.00 44.64 3.34
913 915 2.048597 CGCACCAACTGCTCGGTA 60.049 61.111 0.00 0.00 44.64 4.02
916 918 4.081030 CAGCGCACCAACTGCTCG 62.081 66.667 11.47 0.00 44.64 5.03
924 926 4.687215 GGACAGAGCAGCGCACCA 62.687 66.667 11.47 0.00 0.00 4.17
927 929 3.305516 TCAGGACAGAGCAGCGCA 61.306 61.111 11.47 0.00 0.00 6.09
960 962 2.758089 GCAATGCAGAGCTCGGTGG 61.758 63.158 15.48 4.70 0.00 4.61
962 964 2.816958 CGCAATGCAGAGCTCGGT 60.817 61.111 15.48 0.00 0.00 4.69
983 985 2.166829 CCATCGAGGATAGCTGCTAGT 58.833 52.381 15.41 2.22 41.22 2.57
1068 1070 2.238646 ACCAGGAAGCATCGATTTACCA 59.761 45.455 0.00 0.00 0.00 3.25
1107 1109 2.005370 ACCCTACCGAAACTCACTCA 57.995 50.000 0.00 0.00 0.00 3.41
1115 1117 0.178533 CCGCCATTACCCTACCGAAA 59.821 55.000 0.00 0.00 0.00 3.46
1124 1126 4.547367 AGCTCGCCCGCCATTACC 62.547 66.667 0.00 0.00 0.00 2.85
1900 1932 0.107945 GTCAGTGGAGGAGTGATGGC 60.108 60.000 0.00 0.00 36.38 4.40
1904 1936 2.276116 GGCGTCAGTGGAGGAGTGA 61.276 63.158 0.00 0.00 0.00 3.41
1915 2140 2.266055 GGACTTGGAGGGCGTCAG 59.734 66.667 9.66 1.35 0.00 3.51
1933 2322 0.804989 GGCAAGAACCAACCAGATCG 59.195 55.000 0.00 0.00 0.00 3.69
1986 2404 5.981088 GATCTGCAGATCTCTTCCTATCA 57.019 43.478 38.16 6.93 45.60 2.15
2565 3251 6.496338 ACAATGGTTTTCTCCGAATCTAAC 57.504 37.500 0.00 0.00 0.00 2.34
2573 3259 5.399013 GGAATGTTACAATGGTTTTCTCCG 58.601 41.667 0.00 0.00 0.00 4.63
2578 3264 5.523438 ACACGGAATGTTACAATGGTTTT 57.477 34.783 0.00 0.00 38.98 2.43
2619 3305 5.121142 ACATCGGTTTAACCAACAATCTACG 59.879 40.000 14.97 0.00 38.47 3.51
2670 3365 2.018542 TGGCCGAGTTACAATGCTAC 57.981 50.000 0.00 0.00 0.00 3.58
2671 3366 2.627945 CTTGGCCGAGTTACAATGCTA 58.372 47.619 12.40 0.00 0.00 3.49
2672 3367 1.453155 CTTGGCCGAGTTACAATGCT 58.547 50.000 12.40 0.00 0.00 3.79
2673 3368 0.451783 CCTTGGCCGAGTTACAATGC 59.548 55.000 19.14 0.00 0.00 3.56
2703 3398 1.470979 CGTTGTCTCGGTTAGGGATGG 60.471 57.143 0.00 0.00 0.00 3.51
2741 3436 4.082463 TGGTCCTGAAACTGAAACAAACAC 60.082 41.667 0.00 0.00 0.00 3.32
2825 3525 3.820467 ACACTGGAAATTGCTCGAATCAA 59.180 39.130 2.76 2.76 0.00 2.57
2843 3543 7.824289 TCAGAATGTGCTTTAGCTAAATACACT 59.176 33.333 31.68 23.91 37.00 3.55
2846 3549 8.616076 ACATCAGAATGTGCTTTAGCTAAATAC 58.384 33.333 18.93 19.13 44.51 1.89
2867 3571 5.242615 TGCATTTTGGCACTAAAGTACATCA 59.757 36.000 0.00 0.00 39.25 3.07
2888 3596 6.423182 AGAAATAAGCCCTAACAGTTATGCA 58.577 36.000 14.28 0.00 0.00 3.96
2892 3600 6.886178 AGGAGAAATAAGCCCTAACAGTTA 57.114 37.500 0.00 0.00 0.00 2.24
2893 3601 5.780958 AGGAGAAATAAGCCCTAACAGTT 57.219 39.130 0.00 0.00 0.00 3.16
2915 3623 6.723298 ACATCAATCACCAAAACCACTTAA 57.277 33.333 0.00 0.00 0.00 1.85
2977 3694 7.765695 AGAAATTGTCTCTGCCAAATAAAGA 57.234 32.000 0.00 0.00 0.00 2.52
2981 3698 6.772716 GGGATAGAAATTGTCTCTGCCAAATA 59.227 38.462 0.00 0.00 39.81 1.40
2995 3713 6.949463 TCTTTTAAACACCGGGGATAGAAATT 59.051 34.615 12.96 0.00 0.00 1.82
3006 3725 3.185797 CCGTCTTCTCTTTTAAACACCGG 59.814 47.826 0.00 0.00 0.00 5.28
3036 3758 3.682858 GTCCATCGAAAATGAAACGAGGA 59.317 43.478 0.00 0.00 39.55 3.71
3081 3803 5.584253 CGATACGGATTCCCTCTTGATAT 57.416 43.478 0.00 0.00 0.00 1.63
3103 3826 2.969262 TGATTCCACCCAAACCTTTTCC 59.031 45.455 0.00 0.00 0.00 3.13
3153 3876 1.298859 CCAAAGACGCGGGAAAGAGG 61.299 60.000 12.47 0.00 0.00 3.69
3309 4081 0.900421 GGGGTCAGCGGTAGTAAGTT 59.100 55.000 0.00 0.00 0.00 2.66
3381 4166 2.771639 CGAGCGGTACTGGCAGCTA 61.772 63.158 15.89 3.51 39.83 3.32
3382 4167 4.135153 CGAGCGGTACTGGCAGCT 62.135 66.667 15.89 6.08 42.25 4.24
3434 4220 0.462937 ACCGTGCACAACAGCTTACA 60.463 50.000 18.64 0.00 34.99 2.41
3469 4256 1.956629 ATACTACCGCTTGCCGCAGT 61.957 55.000 0.00 0.00 39.08 4.40
3473 4260 3.917870 CGATACTACCGCTTGCCG 58.082 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.