Multiple sequence alignment - TraesCS1D01G028700

Loading Multiple Alignment...

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 TraesCS1D01G028700 chr1D 100.000 4016 0 0 1 4016 11289034 11293049 0.000000e+00 7417.0
1 TraesCS1D01G028700 chr1D 88.782 2487 256 15 690 3172 11495877 11498344 0.000000e+00 3025.0
2 TraesCS1D01G028700 chr1D 86.319 2646 301 35 568 3184 11178354 11180967 0.000000e+00 2824.0
3 TraesCS1D01G028700 chr1D 85.430 2567 330 28 598 3144 11319548 11322090 0.000000e+00 2628.0
4 TraesCS1D01G028700 chr1D 87.683 479 42 2 12 490 11274161 11274622 3.530000e-150 542.0
5 TraesCS1D01G028700 chr1D 78.276 290 30 21 3581 3867 11323047 11323306 5.370000e-34 156.0
6 TraesCS1D01G028700 chr1D 82.993 147 14 7 3857 3992 11459215 11459361 5.450000e-24 122.0
7 TraesCS1D01G028700 chr1B 88.405 3424 324 21 12 3381 17017902 17014498 0.000000e+00 4056.0
8 TraesCS1D01G028700 chr1B 85.373 335 31 9 3581 3913 16861777 16862095 8.320000e-87 331.0
9 TraesCS1D01G028700 chr1B 85.535 159 17 6 3673 3828 16776971 16777126 1.160000e-35 161.0
10 TraesCS1D01G028700 chr1B 90.909 44 3 1 495 537 484695048 484695005 1.560000e-04 58.4
11 TraesCS1D01G028700 chr1A 90.401 2990 241 19 1 2986 13415015 13417962 0.000000e+00 3890.0
12 TraesCS1D01G028700 chr1A 88.233 2915 283 25 230 3137 13348565 13351426 0.000000e+00 3428.0
13 TraesCS1D01G028700 chr1A 89.425 2676 242 28 448 3112 13570986 13573631 0.000000e+00 3336.0
14 TraesCS1D01G028700 chr1A 88.832 2346 246 7 12 2346 12570196 12567856 0.000000e+00 2867.0
15 TraesCS1D01G028700 chr1A 88.119 2323 259 9 572 2881 12589225 12586907 0.000000e+00 2745.0
16 TraesCS1D01G028700 chr1A 84.962 2600 318 44 568 3155 13454591 13457129 0.000000e+00 2567.0
17 TraesCS1D01G028700 chr1A 81.970 660 69 26 3378 3992 12717963 12717309 7.700000e-142 514.0
18 TraesCS1D01G028700 chr1A 93.156 263 18 0 230 492 13570722 13570984 1.750000e-103 387.0
19 TraesCS1D01G028700 chr1A 88.393 224 18 7 3652 3870 12585415 12585195 3.080000e-66 263.0
20 TraesCS1D01G028700 chr1A 87.179 195 13 4 3199 3381 13351444 13351638 1.130000e-50 211.0
21 TraesCS1D01G028700 chr1A 90.476 147 13 1 3717 3862 13378670 13378816 4.100000e-45 193.0
22 TraesCS1D01G028700 chr1A 80.000 265 24 13 3600 3862 13418227 13418464 6.900000e-38 169.0
23 TraesCS1D01G028700 chr1A 77.891 294 39 16 2833 3122 13342719 13342990 4.150000e-35 159.0
24 TraesCS1D01G028700 chr1A 79.459 185 17 10 3600 3782 13668062 13668227 1.180000e-20 111.0
25 TraesCS1D01G028700 chrUn 81.667 660 71 26 3378 3992 311466853 311466199 1.670000e-138 503.0
26 TraesCS1D01G028700 chr4D 93.023 43 3 0 495 537 54449628 54449586 3.350000e-06 63.9
27 TraesCS1D01G028700 chr6B 100.000 30 0 0 508 537 15233329 15233300 5.610000e-04 56.5
28 TraesCS1D01G028700 chr6A 94.444 36 2 0 494 529 93798447 93798412 5.610000e-04 56.5


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 TraesCS1D01G028700 chr1D 11289034 11293049 4015 False 7417.0 7417 100.0000 1 4016 1 chr1D.!!$F3 4015
1 TraesCS1D01G028700 chr1D 11495877 11498344 2467 False 3025.0 3025 88.7820 690 3172 1 chr1D.!!$F5 2482
2 TraesCS1D01G028700 chr1D 11178354 11180967 2613 False 2824.0 2824 86.3190 568 3184 1 chr1D.!!$F1 2616
3 TraesCS1D01G028700 chr1D 11319548 11323306 3758 False 1392.0 2628 81.8530 598 3867 2 chr1D.!!$F6 3269
4 TraesCS1D01G028700 chr1B 17014498 17017902 3404 True 4056.0 4056 88.4050 12 3381 1 chr1B.!!$R1 3369
5 TraesCS1D01G028700 chr1A 12567856 12570196 2340 True 2867.0 2867 88.8320 12 2346 1 chr1A.!!$R1 2334
6 TraesCS1D01G028700 chr1A 13454591 13457129 2538 False 2567.0 2567 84.9620 568 3155 1 chr1A.!!$F3 2587
7 TraesCS1D01G028700 chr1A 13415015 13418464 3449 False 2029.5 3890 85.2005 1 3862 2 chr1A.!!$F6 3861
8 TraesCS1D01G028700 chr1A 13570722 13573631 2909 False 1861.5 3336 91.2905 230 3112 2 chr1A.!!$F7 2882
9 TraesCS1D01G028700 chr1A 13348565 13351638 3073 False 1819.5 3428 87.7060 230 3381 2 chr1A.!!$F5 3151
10 TraesCS1D01G028700 chr1A 12585195 12589225 4030 True 1504.0 2745 88.2560 572 3870 2 chr1A.!!$R3 3298
11 TraesCS1D01G028700 chr1A 12717309 12717963 654 True 514.0 514 81.9700 3378 3992 1 chr1A.!!$R2 614
12 TraesCS1D01G028700 chrUn 311466199 311466853 654 True 503.0 503 81.6670 3378 3992 1 chrUn.!!$R1 614

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
420 423 1.672881 GGTTCATCAGCTGCCATACAC 59.327 52.381 9.47 0.48 0.00 2.90 F
2151 2216 0.244994 AGCTTCACAGTCGCTTCGAT 59.755 50.000 0.00 0.00 38.42 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2355 0.608130 TTGCGCAGATGTACAGGAGT 59.392 50.0 11.31 0.0 0.00 3.85 R
3692 4597 0.036875 AACTTTCCAGGGAAGCTCGG 59.963 55.0 7.51 0.0 35.38 4.63 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
47 48 6.373359 GTAGTAAACTACTTCTCGTTGCAC 57.627 41.667 12.10 0.00 44.06 4.57
73 74 6.991938 AGTTGCTGTGGCTTAAATTTAATGA 58.008 32.000 10.97 0.00 39.59 2.57
242 245 4.320608 ACAAAGATCAAAACGGTGCATT 57.679 36.364 0.00 0.00 0.00 3.56
309 312 7.990886 AGTTAAATTAGCCCTTCGATATCACAA 59.009 33.333 3.12 0.00 0.00 3.33
420 423 1.672881 GGTTCATCAGCTGCCATACAC 59.327 52.381 9.47 0.48 0.00 2.90
443 446 2.307496 ATTGGTGGGCAAATCAGTGA 57.693 45.000 0.00 0.00 0.00 3.41
521 570 4.881273 CCATCCGATCCAAAATAAGTGTCA 59.119 41.667 0.00 0.00 0.00 3.58
525 574 4.498009 CCGATCCAAAATAAGTGTCATGGC 60.498 45.833 0.00 0.00 0.00 4.40
785 846 3.199946 CCACCCATATATTCGTATGGCCT 59.800 47.826 3.32 0.00 46.41 5.19
787 848 5.104693 CCACCCATATATTCGTATGGCCTTA 60.105 44.000 3.32 0.00 46.41 2.69
793 854 7.985184 CCATATATTCGTATGGCCTTAAGCTTA 59.015 37.037 3.32 0.86 43.26 3.09
1040 1102 1.561542 TGATTCCAGAAGGCTCTTCCC 59.438 52.381 10.27 0.00 34.51 3.97
1207 1269 3.106827 TGTGAGTGGGATATTCTGCTCA 58.893 45.455 4.61 4.61 0.00 4.26
1208 1270 3.713248 TGTGAGTGGGATATTCTGCTCAT 59.287 43.478 9.97 0.00 35.77 2.90
1266 1328 3.571590 AGAGGAGATGCGGAGAATACTT 58.428 45.455 0.00 0.00 0.00 2.24
1447 1509 9.601971 TTTTTCTCGGATTAAATTACTTCAACG 57.398 29.630 0.00 0.00 0.00 4.10
1449 1511 8.537049 TTCTCGGATTAAATTACTTCAACGAA 57.463 30.769 0.00 0.00 0.00 3.85
1486 1548 9.624373 GAAGTATGATCCAGCCAATATATGATT 57.376 33.333 0.00 0.00 0.00 2.57
1606 1671 4.264253 CACTGGGAATAGCATGTCTTCAA 58.736 43.478 0.00 0.00 0.00 2.69
1659 1724 7.384387 CAGAATAGAAATGAAGATCATCGAGCA 59.616 37.037 0.00 0.00 35.76 4.26
1666 1731 2.706339 AGATCATCGAGCAAAGCCTT 57.294 45.000 0.00 0.00 0.00 4.35
1736 1801 3.432749 CCACCTGCTGTTAGTATCATGCT 60.433 47.826 0.00 0.00 0.00 3.79
1776 1841 4.258702 AGTTCTGCGTGTACTTGATCTT 57.741 40.909 0.00 0.00 0.00 2.40
1778 1843 5.057149 AGTTCTGCGTGTACTTGATCTTTT 58.943 37.500 0.00 0.00 0.00 2.27
1856 1921 6.296030 GGACACTTAATTCACCTAAGGTACCA 60.296 42.308 15.94 0.00 32.11 3.25
1904 1969 2.938838 ACTCCCGACTGAGATAGGAAG 58.061 52.381 3.99 0.00 36.22 3.46
1930 1995 5.575157 TGCAGTTTTTGGAGGTATTGGATA 58.425 37.500 0.00 0.00 0.00 2.59
2050 2115 1.538512 CTGGTGTGTTGCAGAATCTGG 59.461 52.381 12.66 0.00 31.21 3.86
2052 2117 1.242076 GTGTGTTGCAGAATCTGGCT 58.758 50.000 12.66 0.00 31.21 4.75
2141 2206 4.613929 GCTGAGGGAGCTTCACAG 57.386 61.111 12.34 12.34 45.21 3.66
2149 2214 1.347817 GGAGCTTCACAGTCGCTTCG 61.348 60.000 0.00 0.00 33.47 3.79
2151 2216 0.244994 AGCTTCACAGTCGCTTCGAT 59.755 50.000 0.00 0.00 38.42 3.59
2169 2234 6.677781 TTCGATGATGGTAGTTTGGATTTC 57.322 37.500 0.00 0.00 0.00 2.17
2212 2280 3.007831 TCTGTGCAACCTACATCACATCA 59.992 43.478 0.00 0.00 38.56 3.07
2238 2306 8.579850 AAAGTCTAAGTATTGAATGCAATCCA 57.420 30.769 0.89 0.00 43.43 3.41
2283 2351 1.293498 TCTCTTGGGAGAACGCTGC 59.707 57.895 0.00 0.00 44.62 5.25
2287 2355 3.158537 TTGGGAGAACGCTGCGTGA 62.159 57.895 29.63 5.85 39.99 4.35
2301 2369 1.202348 TGCGTGACTCCTGTACATCTG 59.798 52.381 0.00 0.00 0.00 2.90
2316 2384 1.645265 CATCTGCGCAAATTTGTGTCG 59.355 47.619 27.52 19.25 40.65 4.35
2327 2395 1.177895 TTTGTGTCGTGCATGCCCAT 61.178 50.000 16.68 0.00 0.00 4.00
2338 2406 1.684248 GCATGCCCATCCAACTCTCTT 60.684 52.381 6.36 0.00 0.00 2.85
2368 2436 2.478292 GGTGGATAAAGAGAGACCCCA 58.522 52.381 0.00 0.00 0.00 4.96
2370 2438 2.838202 GTGGATAAAGAGAGACCCCACA 59.162 50.000 0.00 0.00 41.45 4.17
2412 2480 6.576551 GAGTTAATCCTCGATTCAGTGAAC 57.423 41.667 7.96 1.72 33.95 3.18
2470 2538 3.861840 CTGTTATCCCTTCGCTTTCTCA 58.138 45.455 0.00 0.00 0.00 3.27
2472 2540 3.513912 TGTTATCCCTTCGCTTTCTCAGA 59.486 43.478 0.00 0.00 0.00 3.27
2533 2601 2.109126 GCAGATGGGTTCCGCTGTC 61.109 63.158 0.00 0.00 33.20 3.51
2556 2624 5.938125 TCTGGTAGTCTTTAAGTTGGATTGC 59.062 40.000 0.00 0.00 0.00 3.56
2617 2685 0.678048 AAGGGCGGAATCAGTTGAGC 60.678 55.000 0.00 0.00 0.00 4.26
2620 2688 1.424493 GGCGGAATCAGTTGAGCTCG 61.424 60.000 9.64 0.00 0.00 5.03
2652 2720 2.115291 GGTGGCGAAAGAGGATGGC 61.115 63.158 0.00 0.00 0.00 4.40
2701 2769 2.456287 GAACCTGCTCTGCCTTCGGT 62.456 60.000 0.00 0.00 0.00 4.69
2740 2808 1.702401 TGTATTGTGGTGGAGCAAGGA 59.298 47.619 0.00 0.00 0.00 3.36
2760 2828 2.017668 TTGGGGAGGCAAAGGAAGCA 62.018 55.000 0.00 0.00 0.00 3.91
2765 2833 0.037447 GAGGCAAAGGAAGCAGAGGT 59.963 55.000 0.00 0.00 0.00 3.85
2798 2866 4.227134 CCTCGACGCCCATCCCAG 62.227 72.222 0.00 0.00 0.00 4.45
2807 2875 2.780040 CCATCCCAGCCATCCCCT 60.780 66.667 0.00 0.00 0.00 4.79
2814 2882 1.117150 CCAGCCATCCCCTGATTTTG 58.883 55.000 0.00 0.00 32.03 2.44
2836 2904 0.596577 TGAGATGAGGCCGCGTATAC 59.403 55.000 4.92 0.00 0.00 1.47
2837 2905 0.596577 GAGATGAGGCCGCGTATACA 59.403 55.000 4.92 0.08 0.00 2.29
2990 3100 1.336887 CGATTTGTGTGAGGACGAGGT 60.337 52.381 0.00 0.00 0.00 3.85
2991 3101 2.069273 GATTTGTGTGAGGACGAGGTG 58.931 52.381 0.00 0.00 0.00 4.00
2992 3102 0.105964 TTTGTGTGAGGACGAGGTGG 59.894 55.000 0.00 0.00 0.00 4.61
2993 3103 0.757561 TTGTGTGAGGACGAGGTGGA 60.758 55.000 0.00 0.00 0.00 4.02
2994 3104 1.289380 GTGTGAGGACGAGGTGGAC 59.711 63.158 0.00 0.00 0.00 4.02
2995 3105 1.153061 TGTGAGGACGAGGTGGACT 59.847 57.895 0.00 0.00 0.00 3.85
2996 3106 1.179174 TGTGAGGACGAGGTGGACTG 61.179 60.000 0.00 0.00 0.00 3.51
2997 3107 1.606601 TGAGGACGAGGTGGACTGG 60.607 63.158 0.00 0.00 0.00 4.00
2998 3108 1.606889 GAGGACGAGGTGGACTGGT 60.607 63.158 0.00 0.00 41.18 4.00
2999 3109 1.878656 GAGGACGAGGTGGACTGGTG 61.879 65.000 0.00 0.00 38.35 4.17
3000 3110 2.657237 GACGAGGTGGACTGGTGG 59.343 66.667 0.00 0.00 38.35 4.61
3160 3287 1.134401 TGCTTCACTAGTGGCTATGGC 60.134 52.381 22.48 16.15 37.82 4.40
3175 3302 7.927629 AGTGGCTATGGCAATTATAAACATTTG 59.072 33.333 2.58 0.00 40.46 2.32
3330 3518 6.044404 GGAAGATTTCTGGATAGGGGATGTTA 59.956 42.308 0.00 0.00 0.00 2.41
3416 4281 4.727507 TCTTGTTAGCATGGAGAGACTC 57.272 45.455 0.00 0.00 0.00 3.36
3427 4292 2.225369 TGGAGAGACTCTGTGATTGGGA 60.225 50.000 10.44 0.00 0.00 4.37
3428 4293 2.834549 GGAGAGACTCTGTGATTGGGAA 59.165 50.000 10.44 0.00 0.00 3.97
3436 4301 6.376581 AGACTCTGTGATTGGGAAATGAATTC 59.623 38.462 0.00 0.00 37.31 2.17
3450 4315 7.423844 GAAATGAATTCCAGGGGTAAAGATT 57.576 36.000 2.27 0.00 31.44 2.40
3475 4340 3.185880 TCTGGTTTCTGCTAGGGTAGT 57.814 47.619 0.00 0.00 0.00 2.73
3483 4348 1.279271 CTGCTAGGGTAGTGGCTGTTT 59.721 52.381 0.00 0.00 0.00 2.83
3547 4412 6.803587 AAATAGTTTCCCTATGGATCCCAT 57.196 37.500 9.90 5.63 46.99 4.00
3628 4532 2.892025 GCTGGTGGCATTGGAGATT 58.108 52.632 0.00 0.00 41.35 2.40
3640 4544 3.557577 TTGGAGATTGCATGTTTCACG 57.442 42.857 0.00 0.00 0.00 4.35
3692 4597 5.866092 GCAGAATTGAAGGATGGAAAAGTTC 59.134 40.000 0.00 0.00 0.00 3.01
3706 4619 0.836400 AAGTTCCGAGCTTCCCTGGA 60.836 55.000 0.00 0.00 0.00 3.86
3725 4638 5.530915 CCTGGAAAGTTGTGTGATGAGTTTA 59.469 40.000 0.00 0.00 0.00 2.01
3732 4645 9.965824 AAAGTTGTGTGATGAGTTTATTTTAGG 57.034 29.630 0.00 0.00 0.00 2.69
3773 4688 9.691362 GAAAGAGATATTGCTTGGTTTTGTAAA 57.309 29.630 0.00 0.00 0.00 2.01
3785 4701 9.406828 GCTTGGTTTTGTAAAGAATAAGTAAGG 57.593 33.333 0.00 0.00 0.00 2.69
3839 4756 3.499918 GCTTAGCTTTGCTTCAGTTGAGA 59.500 43.478 0.00 0.00 40.44 3.27
3843 4760 1.196354 CTTTGCTTCAGTTGAGAGCCG 59.804 52.381 11.21 0.00 0.00 5.52
3882 4800 4.388378 TTTGTTTTTAACCTGAACCGGG 57.612 40.909 6.32 0.00 35.68 5.73
3884 4802 1.682323 GTTTTTAACCTGAACCGGGCA 59.318 47.619 6.32 2.13 32.02 5.36
3892 4810 0.821711 CTGAACCGGGCAAACCTGAA 60.822 55.000 6.32 0.00 46.41 3.02
3894 4812 0.536460 GAACCGGGCAAACCTGAAGA 60.536 55.000 6.32 0.00 46.41 2.87
3896 4814 0.988832 ACCGGGCAAACCTGAAGATA 59.011 50.000 6.32 0.00 46.41 1.98
3943 4871 1.757699 ACCTGAGCTCCCTAATTCGAC 59.242 52.381 12.15 0.00 0.00 4.20
3949 4877 6.045072 TGAGCTCCCTAATTCGACTAAAAA 57.955 37.500 12.15 0.00 0.00 1.94
3950 4878 5.873164 TGAGCTCCCTAATTCGACTAAAAAC 59.127 40.000 12.15 0.00 0.00 2.43
3951 4879 6.051179 AGCTCCCTAATTCGACTAAAAACT 57.949 37.500 0.00 0.00 0.00 2.66
3952 4880 5.875359 AGCTCCCTAATTCGACTAAAAACTG 59.125 40.000 0.00 0.00 0.00 3.16
3953 4881 5.447413 GCTCCCTAATTCGACTAAAAACTGC 60.447 44.000 0.00 0.00 0.00 4.40
3973 4901 2.226330 CGGTTCACTGTTGGGATTTGA 58.774 47.619 0.00 0.00 0.00 2.69
3979 4907 6.657541 GGTTCACTGTTGGGATTTGATACTTA 59.342 38.462 0.00 0.00 0.00 2.24
3984 4912 9.191995 CACTGTTGGGATTTGATACTTAAAAAC 57.808 33.333 0.00 0.00 0.00 2.43
3985 4913 9.143155 ACTGTTGGGATTTGATACTTAAAAACT 57.857 29.630 0.00 0.00 0.00 2.66
4009 4937 9.344772 ACTATTTACCAACATGTTTCTGTTACA 57.655 29.630 8.77 0.00 37.25 2.41
4013 4941 8.678593 TTACCAACATGTTTCTGTTACATACA 57.321 30.769 8.77 0.00 37.25 2.29
4014 4942 7.575414 ACCAACATGTTTCTGTTACATACAA 57.425 32.000 8.77 0.00 37.25 2.41
4015 4943 8.001881 ACCAACATGTTTCTGTTACATACAAA 57.998 30.769 8.77 0.00 37.25 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.243426 TCATTAAATTTAAGCCACAGCAACTAG 58.757 33.333 15.45 0.00 43.56 2.57
55 56 7.675062 ACCAATGTCATTAAATTTAAGCCACA 58.325 30.769 15.45 15.79 0.00 4.17
73 74 5.473162 TGAGATGAATTTCGTTGACCAATGT 59.527 36.000 2.35 0.00 0.00 2.71
82 83 8.437360 TGTATAATGCTGAGATGAATTTCGTT 57.563 30.769 0.00 0.00 0.00 3.85
84 85 9.888878 AAATGTATAATGCTGAGATGAATTTCG 57.111 29.630 0.00 0.00 0.00 3.46
242 245 1.228429 GGGTAGCCTTTGGTGCACA 60.228 57.895 20.43 1.62 0.00 4.57
292 295 6.365970 AATAGATTGTGATATCGAAGGGCT 57.634 37.500 0.00 0.00 0.00 5.19
295 298 6.595716 GGGGAAATAGATTGTGATATCGAAGG 59.404 42.308 0.00 0.00 0.00 3.46
309 312 3.953542 AGGCGAAAAGGGGAAATAGAT 57.046 42.857 0.00 0.00 0.00 1.98
382 385 1.555533 ACCTCCCGGAGACTCAAATTC 59.444 52.381 16.69 0.00 0.00 2.17
411 414 3.497763 GCCCACCAATATAGTGTATGGCA 60.498 47.826 15.12 0.00 38.90 4.92
420 423 5.132502 TCACTGATTTGCCCACCAATATAG 58.867 41.667 0.00 0.00 32.49 1.31
521 570 9.260002 CAAAATAAGTGTTTGAACTAAAGCCAT 57.740 29.630 0.00 0.00 38.05 4.40
577 626 4.738839 GCTGCAGCAGTGACATAGATAGAA 60.739 45.833 33.36 0.00 41.59 2.10
661 711 4.107622 GTGCATTATGAACTGCCAATCAC 58.892 43.478 0.00 0.00 37.59 3.06
787 848 9.804758 GTAAAGTCTATACACATCACTAAGCTT 57.195 33.333 3.48 3.48 0.00 3.74
1040 1102 7.436673 CACTCTTGTCGGGAAATATTCTCTTAG 59.563 40.741 0.00 0.00 0.00 2.18
1207 1269 4.587520 TCCAGAGCCAAGGGACAT 57.412 55.556 0.00 0.00 0.00 3.06
1297 1359 9.959721 ACATAGGTACAATAGACAAGTTTTCAT 57.040 29.630 0.00 0.00 0.00 2.57
1425 1487 7.816031 AGTTCGTTGAAGTAATTTAATCCGAGA 59.184 33.333 0.00 0.00 0.00 4.04
1449 1511 8.317679 GGCTGGATCATACTTCTATTAATGAGT 58.682 37.037 0.00 2.62 32.25 3.41
1486 1548 3.260269 AGCACATACCTGGCCTAGATA 57.740 47.619 3.32 0.00 0.00 1.98
1606 1671 4.284485 GACAAACGGCGAACATTACTTTT 58.716 39.130 16.62 0.00 0.00 2.27
1655 1720 5.713025 TGATATTTGTGAAAGGCTTTGCTC 58.287 37.500 18.79 3.61 0.00 4.26
1659 1724 7.472334 ACTCATGATATTTGTGAAAGGCTTT 57.528 32.000 13.25 13.25 0.00 3.51
1666 1731 7.978975 TCGTGACATACTCATGATATTTGTGAA 59.021 33.333 0.00 0.00 39.61 3.18
1736 1801 4.689612 ACTTCAAACCTTGACAGAGCTA 57.310 40.909 0.00 0.00 39.87 3.32
1776 1841 2.136863 TCCCCAAGGTTACAGTCCAAA 58.863 47.619 0.00 0.00 0.00 3.28
1778 1843 1.822425 TTCCCCAAGGTTACAGTCCA 58.178 50.000 0.00 0.00 0.00 4.02
1829 1894 5.805728 ACCTTAGGTGAATTAAGTGTCCAG 58.194 41.667 1.74 0.00 32.98 3.86
1856 1921 3.393426 TTCCGGTACCTGATAGACCTT 57.607 47.619 10.90 0.00 0.00 3.50
1904 1969 1.616159 TACCTCCAAAAACTGCAGGC 58.384 50.000 19.93 0.00 0.00 4.85
1947 2012 2.158900 AGTGGACGGCAATTCATCTAGG 60.159 50.000 0.00 0.00 0.00 3.02
2000 2065 4.296621 ACCACCTTACAGGGATAAACAC 57.703 45.455 0.00 0.00 40.58 3.32
2026 2091 0.819259 TTCTGCAACACACCAGGAGC 60.819 55.000 0.00 0.00 0.00 4.70
2052 2117 2.576191 CCCCCTCAACACTTCTATGGAA 59.424 50.000 0.00 0.00 0.00 3.53
2080 2145 7.108194 TCTTGTGCAATAATGTTCAGAGAGAT 58.892 34.615 0.00 0.00 0.00 2.75
2139 2204 2.223595 ACTACCATCATCGAAGCGACTG 60.224 50.000 0.00 0.00 39.18 3.51
2141 2206 2.493713 ACTACCATCATCGAAGCGAC 57.506 50.000 0.00 0.00 39.18 5.19
2149 2214 8.908786 TCATAGAAATCCAAACTACCATCATC 57.091 34.615 0.00 0.00 0.00 2.92
2151 2216 7.775093 CCTTCATAGAAATCCAAACTACCATCA 59.225 37.037 0.00 0.00 0.00 3.07
2169 2234 5.574830 CAGAGACTTCACGAAACCTTCATAG 59.425 44.000 0.00 0.00 0.00 2.23
2212 2280 9.023962 TGGATTGCATTCAATACTTAGACTTTT 57.976 29.630 10.55 0.00 42.71 2.27
2229 2297 6.600882 AAAGATGTTTCTCTTGGATTGCAT 57.399 33.333 0.00 0.00 35.67 3.96
2238 2306 7.503566 TCCATCAGTTCAAAAGATGTTTCTCTT 59.496 33.333 0.00 0.00 37.93 2.85
2283 2351 1.795525 CGCAGATGTACAGGAGTCACG 60.796 57.143 0.33 0.00 0.00 4.35
2287 2355 0.608130 TTGCGCAGATGTACAGGAGT 59.392 50.000 11.31 0.00 0.00 3.85
2301 2369 1.205485 TGCACGACACAAATTTGCGC 61.205 50.000 18.12 0.00 35.90 6.09
2316 2384 0.682209 AGAGTTGGATGGGCATGCAC 60.682 55.000 21.36 18.25 38.89 4.57
2327 2395 1.270826 CTCGCAGTGAAGAGAGTTGGA 59.729 52.381 9.62 0.00 36.65 3.53
2338 2406 1.207089 CTTTATCCACCCTCGCAGTGA 59.793 52.381 0.00 0.00 37.42 3.41
2368 2436 2.096248 GGAGAGGTTCGAGAGATGTGT 58.904 52.381 0.00 0.00 41.60 3.72
2370 2438 1.065345 TCGGAGAGGTTCGAGAGATGT 60.065 52.381 0.00 0.00 41.60 3.06
2401 2469 2.412065 GCTGCACTTCGTTCACTGAATC 60.412 50.000 0.00 0.00 0.00 2.52
2412 2480 1.739562 GTCCTCCTGCTGCACTTCG 60.740 63.158 0.00 0.00 0.00 3.79
2454 2522 3.922171 ATTCTGAGAAAGCGAAGGGAT 57.078 42.857 0.00 0.00 0.00 3.85
2470 2538 1.668826 TGGTGGGTGCTCCTTATTCT 58.331 50.000 4.53 0.00 36.20 2.40
2472 2540 2.158385 TGTTTGGTGGGTGCTCCTTATT 60.158 45.455 4.53 0.00 36.20 1.40
2533 2601 5.163854 CGCAATCCAACTTAAAGACTACCAG 60.164 44.000 0.00 0.00 0.00 4.00
2556 2624 1.302383 TTATTTGCGTGGCTGACCCG 61.302 55.000 0.00 0.00 35.87 5.28
2652 2720 0.588252 CCAAGTCGAAGGCACAGTTG 59.412 55.000 0.00 0.00 0.00 3.16
2660 2728 2.747855 GCAGGCCCAAGTCGAAGG 60.748 66.667 0.00 0.00 0.00 3.46
2661 2729 2.032528 TGCAGGCCCAAGTCGAAG 59.967 61.111 0.00 0.00 0.00 3.79
2701 2769 1.071314 ATCCAAACCCTGACACCCCA 61.071 55.000 0.00 0.00 0.00 4.96
2740 2808 0.615827 GCTTCCTTTGCCTCCCCAAT 60.616 55.000 0.00 0.00 0.00 3.16
2760 2828 3.241530 TGCCTCACCGCAACCTCT 61.242 61.111 0.00 0.00 35.32 3.69
2798 2866 3.033184 TCAATCAAAATCAGGGGATGGC 58.967 45.455 0.00 0.00 32.92 4.40
2807 2875 3.628942 CGGCCTCATCTCAATCAAAATCA 59.371 43.478 0.00 0.00 0.00 2.57
2814 2882 0.032130 TACGCGGCCTCATCTCAATC 59.968 55.000 12.47 0.00 0.00 2.67
2836 2904 2.668457 GTGCGACATGAGTACCTTCTTG 59.332 50.000 0.00 0.00 0.00 3.02
2837 2905 2.353803 GGTGCGACATGAGTACCTTCTT 60.354 50.000 19.43 0.00 40.52 2.52
2935 3044 4.537688 ACCTTGGGAGATTCAGAGATCAAA 59.462 41.667 0.00 0.00 0.00 2.69
2990 3100 2.030027 ATCAGTTCTCCACCAGTCCA 57.970 50.000 0.00 0.00 0.00 4.02
2991 3101 3.008485 AGAAATCAGTTCTCCACCAGTCC 59.992 47.826 0.00 0.00 43.49 3.85
2992 3102 3.999663 CAGAAATCAGTTCTCCACCAGTC 59.000 47.826 0.00 0.00 45.25 3.51
2993 3103 3.648067 TCAGAAATCAGTTCTCCACCAGT 59.352 43.478 0.00 0.00 45.25 4.00
2994 3104 3.999663 GTCAGAAATCAGTTCTCCACCAG 59.000 47.826 0.00 0.00 45.25 4.00
2995 3105 3.554960 CGTCAGAAATCAGTTCTCCACCA 60.555 47.826 0.00 0.00 45.25 4.17
2996 3106 2.996621 CGTCAGAAATCAGTTCTCCACC 59.003 50.000 0.00 0.00 45.25 4.61
2997 3107 2.413453 GCGTCAGAAATCAGTTCTCCAC 59.587 50.000 0.00 0.00 45.25 4.02
2998 3108 2.037121 TGCGTCAGAAATCAGTTCTCCA 59.963 45.455 0.00 0.00 45.25 3.86
2999 3109 2.670414 CTGCGTCAGAAATCAGTTCTCC 59.330 50.000 1.18 0.00 45.25 3.71
3000 3110 3.579709 TCTGCGTCAGAAATCAGTTCTC 58.420 45.455 7.02 0.00 45.25 2.87
3032 3145 1.400846 GAGAGCACACCTGATGCAATG 59.599 52.381 0.00 0.00 45.92 2.82
3033 3146 1.003928 TGAGAGCACACCTGATGCAAT 59.996 47.619 0.00 0.00 45.92 3.56
3087 3205 5.491982 TCTAGACAATGGAGAAAGAAAGGC 58.508 41.667 0.00 0.00 0.00 4.35
3134 3255 2.158755 AGCCACTAGTGAAGCACAGTTT 60.159 45.455 24.68 0.32 36.74 2.66
3175 3302 6.998673 ACTTATGCATCCTAACCAATACCTTC 59.001 38.462 0.19 0.00 0.00 3.46
3330 3518 6.699575 ACTTGTCACTTGTCAGCTAAAATT 57.300 33.333 0.00 0.00 0.00 1.82
3377 3789 9.355215 CTAACAAGAACTGTATTAAGACGACAT 57.645 33.333 0.00 0.00 37.23 3.06
3379 3791 7.327761 TGCTAACAAGAACTGTATTAAGACGAC 59.672 37.037 0.00 0.00 37.23 4.34
3381 3793 7.576750 TGCTAACAAGAACTGTATTAAGACG 57.423 36.000 0.00 0.00 37.23 4.18
3382 3794 8.391106 CCATGCTAACAAGAACTGTATTAAGAC 58.609 37.037 0.00 0.00 37.23 3.01
3383 3795 8.318412 TCCATGCTAACAAGAACTGTATTAAGA 58.682 33.333 0.00 0.00 37.23 2.10
3384 3796 8.492673 TCCATGCTAACAAGAACTGTATTAAG 57.507 34.615 0.00 0.00 37.23 1.85
3397 4262 3.834813 ACAGAGTCTCTCCATGCTAACAA 59.165 43.478 0.00 0.00 0.00 2.83
3427 4292 6.156775 CCAATCTTTACCCCTGGAATTCATTT 59.843 38.462 7.93 0.00 0.00 2.32
3428 4293 5.662657 CCAATCTTTACCCCTGGAATTCATT 59.337 40.000 7.93 0.00 0.00 2.57
3436 4301 4.210331 CAGATTCCAATCTTTACCCCTGG 58.790 47.826 0.00 0.00 42.96 4.45
3450 4315 2.239654 CCCTAGCAGAAACCAGATTCCA 59.760 50.000 0.00 0.00 0.00 3.53
3547 4412 8.185506 TGTAAGTTAGAAACATCCTACACAGA 57.814 34.615 0.00 0.00 0.00 3.41
3596 4492 2.031919 CAGCAGTAACCCCACGCA 59.968 61.111 0.00 0.00 0.00 5.24
3621 4525 2.777094 TCGTGAAACATGCAATCTCCA 58.223 42.857 0.00 0.00 35.74 3.86
3640 4544 3.841222 CGCCCACGCAAAATGTTC 58.159 55.556 0.00 0.00 34.03 3.18
3665 4570 1.065199 TCCATCCTTCAATTCTGCGCT 60.065 47.619 9.73 0.00 0.00 5.92
3692 4597 0.036875 AACTTTCCAGGGAAGCTCGG 59.963 55.000 7.51 0.00 35.38 4.63
3701 4606 3.480470 ACTCATCACACAACTTTCCAGG 58.520 45.455 0.00 0.00 0.00 4.45
3706 4619 9.965824 CCTAAAATAAACTCATCACACAACTTT 57.034 29.630 0.00 0.00 0.00 2.66
3725 4638 1.539827 GCAACGACTGCCACCTAAAAT 59.460 47.619 0.00 0.00 46.13 1.82
3773 4688 5.546499 TCACTCCAACACCCTTACTTATTCT 59.454 40.000 0.00 0.00 0.00 2.40
3785 4701 3.690460 AGGATCAATTCACTCCAACACC 58.310 45.455 0.00 0.00 0.00 4.16
3821 4738 1.878734 GCTCTCAACTGAAGCAAAGCT 59.121 47.619 8.22 0.00 42.56 3.74
3839 4756 3.996124 AGAGCAGCAACGACGGCT 61.996 61.111 0.00 0.00 44.06 5.52
3843 4760 2.475200 AAAAACAGAGCAGCAACGAC 57.525 45.000 0.00 0.00 0.00 4.34
3864 4781 1.682323 TGCCCGGTTCAGGTTAAAAAC 59.318 47.619 0.00 0.00 0.00 2.43
3872 4790 2.115266 AGGTTTGCCCGGTTCAGG 59.885 61.111 0.00 0.00 38.74 3.86
3892 4810 8.759782 CCCCCTTCACGAAACTATAATATATCT 58.240 37.037 0.00 0.00 0.00 1.98
3920 4848 2.223923 CGAATTAGGGAGCTCAGGTGAG 60.224 54.545 17.19 2.37 44.75 3.51
3930 4858 5.220416 CGCAGTTTTTAGTCGAATTAGGGAG 60.220 44.000 0.00 0.00 0.00 4.30
3934 4862 5.526010 ACCGCAGTTTTTAGTCGAATTAG 57.474 39.130 0.00 0.00 0.00 1.73
3943 4871 3.963383 ACAGTGAACCGCAGTTTTTAG 57.037 42.857 0.00 0.00 35.94 1.85
3949 4877 1.525995 CCCAACAGTGAACCGCAGT 60.526 57.895 0.00 0.00 0.00 4.40
3950 4878 0.606401 ATCCCAACAGTGAACCGCAG 60.606 55.000 0.00 0.00 0.00 5.18
3951 4879 0.179004 AATCCCAACAGTGAACCGCA 60.179 50.000 0.00 0.00 0.00 5.69
3952 4880 0.958822 AAATCCCAACAGTGAACCGC 59.041 50.000 0.00 0.00 0.00 5.68
3953 4881 2.226330 TCAAATCCCAACAGTGAACCG 58.774 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.