Multiple sequence alignment - TraesCS2D01G299700

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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 TraesCS2D01G299700 chr2D 100.000 3233 0 0 1 3233 382129888 382126656 0.000000e+00 5971.0
1 TraesCS2D01G299700 chr2D 88.764 178 11 6 3014 3182 490798234 490798411 3.270000e-50 209.0
2 TraesCS2D01G299700 chr2D 85.714 98 12 2 2517 2613 32772441 32772345 5.710000e-18 102.0
3 TraesCS2D01G299700 chr2B 94.133 2318 100 15 1 2314 452913738 452911453 0.000000e+00 3494.0
4 TraesCS2D01G299700 chr2B 90.554 487 38 2 2668 3146 452910177 452909691 3.520000e-179 638.0
5 TraesCS2D01G299700 chr2B 92.929 396 21 5 2289 2681 452911449 452911058 1.300000e-158 569.0
6 TraesCS2D01G299700 chr2A 97.137 2026 37 8 461 2469 516309460 516307439 0.000000e+00 3400.0
7 TraesCS2D01G299700 chr2A 87.523 545 55 5 2612 3144 516307438 516306895 4.580000e-173 617.0
8 TraesCS2D01G299700 chr2A 87.643 437 53 1 1 436 779640395 779640831 1.030000e-139 507.0
9 TraesCS2D01G299700 chr2A 86.260 131 9 6 3014 3135 24296703 24296573 2.020000e-27 134.0
10 TraesCS2D01G299700 chr3D 91.176 442 36 2 1 439 303791983 303792424 5.970000e-167 597.0
11 TraesCS2D01G299700 chr3D 86.818 440 54 3 1 436 362043860 362044299 3.750000e-134 488.0
12 TraesCS2D01G299700 chr3D 89.394 132 14 0 2674 2805 581578603 581578734 2.000000e-37 167.0
13 TraesCS2D01G299700 chr3D 86.364 88 9 3 2527 2612 366808587 366808673 3.430000e-15 93.5
14 TraesCS2D01G299700 chr5D 88.315 445 39 3 1 436 341582539 341582979 3.700000e-144 521.0
15 TraesCS2D01G299700 chr1D 88.209 441 36 7 1 440 383475122 383475547 2.220000e-141 512.0
16 TraesCS2D01G299700 chr1A 87.356 435 53 2 1 434 373828275 373827842 6.230000e-137 497.0
17 TraesCS2D01G299700 chr5B 88.480 408 43 2 40 446 66019710 66019306 1.040000e-134 490.0
18 TraesCS2D01G299700 chr5B 88.202 178 12 6 3014 3182 611728724 611728901 1.520000e-48 204.0
19 TraesCS2D01G299700 chr5B 85.057 87 9 4 2517 2602 31140814 31140897 5.750000e-13 86.1
20 TraesCS2D01G299700 chr7A 86.788 439 54 4 1 438 167745052 167744617 1.350000e-133 486.0
21 TraesCS2D01G299700 chr7A 92.308 65 5 0 1210 1274 36630004 36629940 3.430000e-15 93.5
22 TraesCS2D01G299700 chr4D 86.905 420 49 3 1 414 488175236 488174817 1.760000e-127 466.0
23 TraesCS2D01G299700 chr4D 90.116 172 9 2 3019 3182 223447584 223447413 1.950000e-52 217.0
24 TraesCS2D01G299700 chr4D 86.316 95 11 2 2517 2610 476295401 476295494 5.710000e-18 102.0
25 TraesCS2D01G299700 chr7D 84.150 347 40 6 2674 3010 563365488 563365147 4.020000e-84 322.0
26 TraesCS2D01G299700 chr7D 90.960 177 7 3 3015 3182 563364812 563364636 2.510000e-56 230.0
27 TraesCS2D01G299700 chr7D 90.769 65 6 0 1210 1274 37234889 37234825 1.600000e-13 87.9
28 TraesCS2D01G299700 chr1B 83.929 336 45 6 2672 2998 231320689 231321024 2.420000e-81 313.0
29 TraesCS2D01G299700 chr1B 85.185 81 5 1 3032 3105 231321457 231321537 3.460000e-10 76.8
30 TraesCS2D01G299700 chr1B 93.333 45 2 1 2567 2611 474843750 474843793 7.490000e-07 65.8
31 TraesCS2D01G299700 chr6D 88.202 178 12 6 3014 3182 9012580 9012403 1.520000e-48 204.0
32 TraesCS2D01G299700 chr7B 89.542 153 16 0 2689 2841 726101159 726101007 9.150000e-46 195.0
33 TraesCS2D01G299700 chr7B 93.750 128 7 1 3056 3182 726100440 726100313 1.180000e-44 191.0
34 TraesCS2D01G299700 chr7B 88.660 97 9 2 2517 2612 411337227 411337322 2.040000e-22 117.0
35 TraesCS2D01G299700 chr5A 77.576 330 64 9 2664 2987 585000434 585000759 1.180000e-44 191.0
36 TraesCS2D01G299700 chr5A 85.000 100 13 2 2517 2615 637529252 637529154 2.050000e-17 100.0
37 TraesCS2D01G299700 chr5A 81.818 110 14 6 2517 2622 244451537 244451430 1.600000e-13 87.9
38 TraesCS2D01G299700 chr3B 87.023 131 8 3 3014 3135 421046120 421046250 4.350000e-29 139.0
39 TraesCS2D01G299700 chrUn 92.308 65 5 0 1210 1274 90726733 90726669 3.430000e-15 93.5
40 TraesCS2D01G299700 chrUn 92.308 65 5 0 1210 1274 90939278 90939214 3.430000e-15 93.5
41 TraesCS2D01G299700 chrUn 92.308 65 5 0 1210 1274 401026603 401026539 3.430000e-15 93.5
42 TraesCS2D01G299700 chr4A 90.769 65 6 0 1210 1274 689137570 689137506 1.600000e-13 87.9
43 TraesCS2D01G299700 chr4A 90.769 65 6 0 1210 1274 689190418 689190354 1.600000e-13 87.9


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 TraesCS2D01G299700 chr2D 382126656 382129888 3232 True 5971.0 5971 100.000000 1 3233 1 chr2D.!!$R2 3232
1 TraesCS2D01G299700 chr2B 452909691 452913738 4047 True 1567.0 3494 92.538667 1 3146 3 chr2B.!!$R1 3145
2 TraesCS2D01G299700 chr2A 516306895 516309460 2565 True 2008.5 3400 92.330000 461 3144 2 chr2A.!!$R2 2683
3 TraesCS2D01G299700 chr7D 563364636 563365488 852 True 276.0 322 87.555000 2674 3182 2 chr7D.!!$R2 508

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
377 379 0.038166 AAATCATGACCGGGCAGTGT 59.962 50.0 18.96 0.0 0.0 3.55 F
1462 1474 0.877071 GGTATGCAGCAATCCATCCG 59.123 55.0 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1641 0.038166 GGATGAGGTTGTTGGAGCCA 59.962 55.0 0.0 0.0 0.0 4.75 R
2851 3805 0.546122 AGGCGACAATGGATAAGGCA 59.454 50.0 0.0 0.0 0.0 4.75 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
17 18 3.659092 CTTGCAAGTCGCCGCCAA 61.659 61.111 18.65 0.00 41.33 4.52
21 22 3.118454 CAAGTCGCCGCCAACGAT 61.118 61.111 0.00 0.00 43.93 3.73
23 24 1.808390 AAGTCGCCGCCAACGATAC 60.808 57.895 0.00 0.00 43.93 2.24
25 26 4.858433 TCGCCGCCAACGATACCG 62.858 66.667 0.00 0.00 43.93 4.02
35 36 4.711980 CGATACCGTGCCTCTCAC 57.288 61.111 0.00 0.00 42.23 3.51
39 40 0.818296 ATACCGTGCCTCTCACAGAC 59.182 55.000 0.00 0.00 45.92 3.51
45 46 2.487428 CCTCTCACAGACGAGGCG 59.513 66.667 0.00 0.00 40.27 5.52
49 50 2.282251 TCACAGACGAGGCGGACT 60.282 61.111 0.00 0.00 0.00 3.85
50 51 2.126307 CACAGACGAGGCGGACTG 60.126 66.667 0.00 12.09 39.58 3.51
51 52 4.057428 ACAGACGAGGCGGACTGC 62.057 66.667 0.00 0.00 45.38 4.40
60 61 2.125512 GCGGACTGCGTCTCCATT 60.126 61.111 8.26 0.00 32.47 3.16
63 64 1.375908 GGACTGCGTCTCCATTGCA 60.376 57.895 8.26 0.00 37.07 4.08
73 74 0.538057 CTCCATTGCAGTGGTGTGGT 60.538 55.000 25.74 0.00 40.27 4.16
79 80 2.508928 CAGTGGTGTGGTTCGGGT 59.491 61.111 0.00 0.00 0.00 5.28
90 91 1.296056 GGTTCGGGTTGGACGACATG 61.296 60.000 0.00 0.00 40.45 3.21
132 133 0.622665 AGGTGAGGATTGGGAGCAAG 59.377 55.000 0.00 0.00 0.00 4.01
137 138 0.846427 AGGATTGGGAGCAAGGGTGA 60.846 55.000 0.00 0.00 0.00 4.02
179 180 2.674754 GAATGGTTGGAGGGCGGA 59.325 61.111 0.00 0.00 0.00 5.54
210 211 1.623311 GGAAGGGTTTGGTGGATTTGG 59.377 52.381 0.00 0.00 0.00 3.28
220 221 2.702478 TGGTGGATTTGGTGCAATTTGA 59.298 40.909 0.00 0.00 0.00 2.69
226 227 2.906691 TTGGTGCAATTTGAAGTGGG 57.093 45.000 0.00 0.00 0.00 4.61
279 281 4.008933 GGCGCTCCCATATCCGCT 62.009 66.667 7.64 0.00 45.21 5.52
289 291 3.054434 TCCCATATCCGCTCCATATTTGG 60.054 47.826 0.00 0.00 45.15 3.28
296 298 1.546323 CGCTCCATATTTGGGCTGGAT 60.546 52.381 2.06 0.00 43.81 3.41
352 354 1.535444 TTTGAGAGGCCCGTCTGGA 60.535 57.895 0.00 0.00 37.49 3.86
355 357 1.758514 GAGAGGCCCGTCTGGATCA 60.759 63.158 0.00 0.00 37.49 2.92
377 379 0.038166 AAATCATGACCGGGCAGTGT 59.962 50.000 18.96 0.00 0.00 3.55
380 382 2.927856 ATGACCGGGCAGTGTCCA 60.928 61.111 18.96 0.00 0.00 4.02
407 409 1.453745 GCCCGGGCATTTGAGATGA 60.454 57.895 40.73 0.00 41.49 2.92
422 424 0.902531 GATGAGTTTGAGGGGTCCGA 59.097 55.000 0.00 0.00 0.00 4.55
445 447 4.720649 TGTAGATGCTCTTAGTGACCAC 57.279 45.455 0.00 0.00 0.00 4.16
503 506 4.338012 TCATGAGGCATGTTTGTGAAGAT 58.662 39.130 7.23 0.00 41.98 2.40
928 940 2.206576 ACTCCTCAATCAAGCCAACC 57.793 50.000 0.00 0.00 0.00 3.77
1018 1030 3.848301 ATGGCGTTGCACTGGAGCA 62.848 57.895 0.00 0.00 43.99 4.26
1191 1203 1.377725 CAAGGAGCACGCCAAGGAT 60.378 57.895 0.00 0.00 0.00 3.24
1462 1474 0.877071 GGTATGCAGCAATCCATCCG 59.123 55.000 0.00 0.00 0.00 4.18
1474 1486 4.814234 GCAATCCATCCGACACACTAATAA 59.186 41.667 0.00 0.00 0.00 1.40
1483 1495 5.992829 TCCGACACACTAATAACAACACAAT 59.007 36.000 0.00 0.00 0.00 2.71
1548 1564 2.878526 GCCTTGATGAACTTTACCCGGT 60.879 50.000 0.00 0.00 0.00 5.28
1549 1565 2.747446 CCTTGATGAACTTTACCCGGTG 59.253 50.000 0.00 0.00 0.00 4.94
1550 1566 2.483014 TGATGAACTTTACCCGGTGG 57.517 50.000 0.00 0.00 37.80 4.61
1568 1584 4.988716 TCGGTGGAGCAGACGGGT 62.989 66.667 0.00 0.00 0.00 5.28
1625 1641 2.345244 CTGACCGCCAGCTTGAGT 59.655 61.111 0.00 0.00 35.89 3.41
1770 1786 5.012354 AGGTGTTTGATTTGATTGCCATTCT 59.988 36.000 0.00 0.00 0.00 2.40
1798 1816 3.642938 TGTAAGTGACATGGGGTGC 57.357 52.632 0.00 0.00 31.20 5.01
2297 2321 2.667473 AGCTCCTTGATTTGCAATGC 57.333 45.000 0.00 0.00 35.59 3.56
2362 2415 1.414378 GTGTTGCACCGTAAAATGGC 58.586 50.000 0.00 0.00 0.00 4.40
2440 2493 4.598062 GTGCTGAACTTGTACCAAGAAAC 58.402 43.478 10.73 2.95 0.00 2.78
2478 2531 1.485066 ACGAGTTGTCCCTGTCACTTT 59.515 47.619 0.00 0.00 0.00 2.66
2528 2582 8.912658 CATTCTACAATATATACGCTCGTTGTT 58.087 33.333 0.00 0.00 32.64 2.83
2530 2584 5.801176 ACAATATATACGCTCGTTGTTCG 57.199 39.130 0.00 0.00 41.41 3.95
2534 2588 1.355971 ATACGCTCGTTGTTCGCAAT 58.644 45.000 0.00 0.00 39.55 3.56
2537 2591 1.527736 ACGCTCGTTGTTCGCAATAAA 59.472 42.857 0.00 0.00 39.55 1.40
2539 2593 3.160545 CGCTCGTTGTTCGCAATAAATT 58.839 40.909 0.00 0.00 39.55 1.82
2543 2597 5.225129 GCTCGTTGTTCGCAATAAATTGTAG 59.775 40.000 4.71 0.48 39.55 2.74
2550 2604 9.522804 TTGTTCGCAATAAATTGTAGTCTTTTT 57.477 25.926 4.71 0.00 39.88 1.94
2655 2711 8.875168 CCATCTGTCTTTAAGATATACTCCCTT 58.125 37.037 0.00 0.00 33.03 3.95
2733 3684 1.202879 TGGAAACTTGCGACCCAATCT 60.203 47.619 0.00 0.00 31.91 2.40
2734 3685 1.886542 GGAAACTTGCGACCCAATCTT 59.113 47.619 0.00 0.00 31.91 2.40
2754 3705 7.781324 ATCTTTTGGATCTTTAACACATGGT 57.219 32.000 0.00 0.00 0.00 3.55
2763 3714 7.716998 GGATCTTTAACACATGGTGTAGATGAT 59.283 37.037 14.60 12.32 46.79 2.45
2904 3867 3.637273 GCTTCCGTCCCCCACTGT 61.637 66.667 0.00 0.00 0.00 3.55
2932 3895 1.152440 CGATGAGGCCTCCCCTACT 60.152 63.158 29.95 7.48 46.60 2.57
2953 3916 1.516365 CGATGACCTACGGCGGAGAT 61.516 60.000 23.26 1.24 0.00 2.75
2965 3928 2.721167 CGGAGATGAGCCGTTCCCA 61.721 63.158 0.00 0.00 43.66 4.37
2969 3932 1.002624 GATGAGCCGTTCCCAACCA 60.003 57.895 0.00 0.00 0.00 3.67
2978 3941 0.810823 GTTCCCAACCACGACGACAA 60.811 55.000 0.00 0.00 0.00 3.18
3110 4411 3.020274 TGTTTGCTCCAGTTTAGTGCAA 58.980 40.909 0.00 0.00 40.74 4.08
3182 4484 4.156455 ACTGAAGTGACTTGTTGGATGT 57.844 40.909 0.90 0.00 0.00 3.06
3183 4485 4.526970 ACTGAAGTGACTTGTTGGATGTT 58.473 39.130 0.90 0.00 0.00 2.71
3184 4486 4.336433 ACTGAAGTGACTTGTTGGATGTTG 59.664 41.667 0.90 0.00 0.00 3.33
3185 4487 4.269183 TGAAGTGACTTGTTGGATGTTGT 58.731 39.130 0.90 0.00 0.00 3.32
3186 4488 4.704540 TGAAGTGACTTGTTGGATGTTGTT 59.295 37.500 0.90 0.00 0.00 2.83
3187 4489 5.883115 TGAAGTGACTTGTTGGATGTTGTTA 59.117 36.000 0.90 0.00 0.00 2.41
3188 4490 6.038161 TGAAGTGACTTGTTGGATGTTGTTAG 59.962 38.462 0.90 0.00 0.00 2.34
3189 4491 5.680619 AGTGACTTGTTGGATGTTGTTAGA 58.319 37.500 0.00 0.00 0.00 2.10
3190 4492 6.119536 AGTGACTTGTTGGATGTTGTTAGAA 58.880 36.000 0.00 0.00 0.00 2.10
3191 4493 6.772716 AGTGACTTGTTGGATGTTGTTAGAAT 59.227 34.615 0.00 0.00 0.00 2.40
3192 4494 7.936847 AGTGACTTGTTGGATGTTGTTAGAATA 59.063 33.333 0.00 0.00 0.00 1.75
3193 4495 8.564574 GTGACTTGTTGGATGTTGTTAGAATAA 58.435 33.333 0.00 0.00 0.00 1.40
3194 4496 9.126151 TGACTTGTTGGATGTTGTTAGAATAAA 57.874 29.630 0.00 0.00 0.00 1.40
3210 4512 9.577003 GTTAGAATAAATTTAAGGCATACGTCG 57.423 33.333 1.21 0.00 0.00 5.12
3211 4513 9.531942 TTAGAATAAATTTAAGGCATACGTCGA 57.468 29.630 1.21 0.00 0.00 4.20
3212 4514 8.603242 AGAATAAATTTAAGGCATACGTCGAT 57.397 30.769 1.21 0.00 0.00 3.59
3213 4515 9.052759 AGAATAAATTTAAGGCATACGTCGATT 57.947 29.630 1.21 0.00 0.00 3.34
3217 4519 6.963049 ATTTAAGGCATACGTCGATTATCC 57.037 37.500 0.00 0.00 0.00 2.59
3218 4520 2.631418 AGGCATACGTCGATTATCCG 57.369 50.000 0.00 0.00 0.00 4.18
3219 4521 2.156917 AGGCATACGTCGATTATCCGA 58.843 47.619 0.00 0.00 36.06 4.55
3220 4522 2.161808 AGGCATACGTCGATTATCCGAG 59.838 50.000 0.00 0.00 39.43 4.63
3221 4523 2.516923 GCATACGTCGATTATCCGAGG 58.483 52.381 0.00 0.00 46.16 4.63
3222 4524 2.161012 GCATACGTCGATTATCCGAGGA 59.839 50.000 11.97 0.00 44.30 3.71
3223 4525 3.744987 CATACGTCGATTATCCGAGGAC 58.255 50.000 11.97 2.24 44.30 3.85
3224 4526 1.964552 ACGTCGATTATCCGAGGACT 58.035 50.000 11.97 0.00 44.30 3.85
3225 4527 3.117491 ACGTCGATTATCCGAGGACTA 57.883 47.619 11.97 0.00 44.30 2.59
3226 4528 3.470709 ACGTCGATTATCCGAGGACTAA 58.529 45.455 11.97 0.00 44.30 2.24
3227 4529 3.497640 ACGTCGATTATCCGAGGACTAAG 59.502 47.826 11.97 0.00 44.30 2.18
3228 4530 3.667430 CGTCGATTATCCGAGGACTAAGC 60.667 52.174 0.00 0.00 44.30 3.09
3229 4531 3.252701 GTCGATTATCCGAGGACTAAGCA 59.747 47.826 0.00 0.00 39.43 3.91
3230 4532 3.887110 TCGATTATCCGAGGACTAAGCAA 59.113 43.478 0.00 0.00 34.19 3.91
3231 4533 4.523173 TCGATTATCCGAGGACTAAGCAAT 59.477 41.667 0.00 0.00 34.19 3.56
3232 4534 4.859798 CGATTATCCGAGGACTAAGCAATC 59.140 45.833 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.214062 CCTCGTCTGTGAGAGGCAC 59.786 63.158 0.00 0.00 46.23 5.01
26 27 3.686760 CCTCGTCTGTGAGAGGCA 58.313 61.111 0.00 0.00 46.23 4.75
32 33 2.282251 AGTCCGCCTCGTCTGTGA 60.282 61.111 0.00 0.00 0.00 3.58
49 50 1.672030 CCACTGCAATGGAGACGCA 60.672 57.895 8.99 0.00 43.02 5.24
50 51 1.672356 ACCACTGCAATGGAGACGC 60.672 57.895 23.29 0.00 43.02 5.19
51 52 0.603707 ACACCACTGCAATGGAGACG 60.604 55.000 23.29 8.57 43.02 4.18
60 61 2.203139 CCGAACCACACCACTGCA 60.203 61.111 0.00 0.00 0.00 4.41
63 64 1.153046 CAACCCGAACCACACCACT 60.153 57.895 0.00 0.00 0.00 4.00
64 65 2.190841 CCAACCCGAACCACACCAC 61.191 63.158 0.00 0.00 0.00 4.16
65 66 2.193517 CCAACCCGAACCACACCA 59.806 61.111 0.00 0.00 0.00 4.17
73 74 0.320073 GACATGTCGTCCAACCCGAA 60.320 55.000 10.69 0.00 38.85 4.30
179 180 1.465189 AACCCTTCCTCCTCCTCCCT 61.465 60.000 0.00 0.00 0.00 4.20
210 211 0.667184 CGCCCCACTTCAAATTGCAC 60.667 55.000 0.00 0.00 0.00 4.57
262 264 3.941657 GAGCGGATATGGGAGCGCC 62.942 68.421 2.29 0.00 34.34 6.53
263 265 2.433318 GAGCGGATATGGGAGCGC 60.433 66.667 0.00 0.00 34.34 5.92
264 266 1.892819 ATGGAGCGGATATGGGAGCG 61.893 60.000 0.00 0.00 34.34 5.03
265 267 1.195115 TATGGAGCGGATATGGGAGC 58.805 55.000 0.00 0.00 0.00 4.70
266 268 4.194640 CAAATATGGAGCGGATATGGGAG 58.805 47.826 0.00 0.00 0.00 4.30
267 269 4.220693 CAAATATGGAGCGGATATGGGA 57.779 45.455 0.00 0.00 0.00 4.37
309 311 3.423154 CAAACGCTCGGGCTGACC 61.423 66.667 5.36 0.00 36.09 4.02
319 321 2.203294 AAACGGCCCTCAAACGCT 60.203 55.556 0.00 0.00 0.00 5.07
320 322 2.050442 CAAACGGCCCTCAAACGC 60.050 61.111 0.00 0.00 0.00 4.84
322 324 0.875059 CTCTCAAACGGCCCTCAAAC 59.125 55.000 0.00 0.00 0.00 2.93
363 365 2.927856 TGGACACTGCCCGGTCAT 60.928 61.111 0.00 0.00 35.74 3.06
389 391 1.450531 CTCATCTCAAATGCCCGGGC 61.451 60.000 39.40 39.40 42.35 6.13
391 393 1.755179 AACTCATCTCAAATGCCCGG 58.245 50.000 0.00 0.00 0.00 5.73
395 397 3.129988 CCCCTCAAACTCATCTCAAATGC 59.870 47.826 0.00 0.00 0.00 3.56
397 399 4.568592 GGACCCCTCAAACTCATCTCAAAT 60.569 45.833 0.00 0.00 0.00 2.32
405 407 1.003118 CAATCGGACCCCTCAAACTCA 59.997 52.381 0.00 0.00 0.00 3.41
407 409 1.064825 ACAATCGGACCCCTCAAACT 58.935 50.000 0.00 0.00 0.00 2.66
445 447 8.230486 GTCATCTTCAAGGTTATGTTGTACTTG 58.770 37.037 0.00 0.00 39.76 3.16
503 506 4.222588 CCTTGCCTTTGGGATGTTGAATTA 59.777 41.667 0.00 0.00 33.58 1.40
612 615 1.458639 GGCATGCATCCCCTTAGCAC 61.459 60.000 21.36 0.00 41.60 4.40
842 854 3.763360 TGCAACGGGATGATGAGAAATTT 59.237 39.130 0.00 0.00 0.00 1.82
928 940 5.233050 CACGATCAATAACAAGCTACTCTGG 59.767 44.000 0.00 0.00 0.00 3.86
1462 1474 8.742188 CAAACATTGTGTTGTTATTAGTGTGTC 58.258 33.333 0.00 0.00 40.14 3.67
1483 1495 6.397272 AGAAAGAAAACAATGCTCACAAACA 58.603 32.000 0.00 0.00 0.00 2.83
1548 1564 3.680786 CGTCTGCTCCACCGACCA 61.681 66.667 0.00 0.00 0.00 4.02
1549 1565 4.436998 CCGTCTGCTCCACCGACC 62.437 72.222 0.00 0.00 0.00 4.79
1550 1566 4.436998 CCCGTCTGCTCCACCGAC 62.437 72.222 0.00 0.00 0.00 4.79
1551 1567 4.988716 ACCCGTCTGCTCCACCGA 62.989 66.667 0.00 0.00 0.00 4.69
1589 1605 2.766229 GAGTCCCTCCTCCCCAGC 60.766 72.222 0.00 0.00 0.00 4.85
1625 1641 0.038166 GGATGAGGTTGTTGGAGCCA 59.962 55.000 0.00 0.00 0.00 4.75
1793 1811 2.273557 GATTGTTCATTGCATGCACCC 58.726 47.619 22.58 7.07 0.00 4.61
1798 1816 3.737047 GCTCCTGGATTGTTCATTGCATG 60.737 47.826 0.00 0.00 0.00 4.06
2297 2321 7.438160 TCACACACATACAGTACTTGAAAGAAG 59.562 37.037 0.00 0.00 0.00 2.85
2362 2415 1.126846 GAGGAACAAACACGATCGCAG 59.873 52.381 16.60 10.96 0.00 5.18
2440 2493 4.804139 ACTCGTAAGCACTTTATTGGATCG 59.196 41.667 0.00 0.00 37.18 3.69
2478 2531 6.173339 GTGGAACAGAGATATCCAGTTGAAA 58.827 40.000 9.07 0.00 43.59 2.69
2655 2711 5.761003 TCGCCATCGTATAATTAGAAACGA 58.239 37.500 17.49 17.49 46.98 3.85
2670 2726 3.349488 TCACTACATACTTCGCCATCG 57.651 47.619 0.00 0.00 0.00 3.84
2712 3663 1.818674 GATTGGGTCGCAAGTTTCCAT 59.181 47.619 8.42 0.00 39.48 3.41
2733 3684 6.723298 ACACCATGTGTTAAAGATCCAAAA 57.277 33.333 0.00 0.00 45.08 2.44
2734 3685 7.227873 TCTACACCATGTGTTAAAGATCCAAA 58.772 34.615 5.06 0.00 45.08 3.28
2754 3705 3.455910 AGCAAACCCAGCTATCATCTACA 59.544 43.478 0.00 0.00 41.32 2.74
2851 3805 0.546122 AGGCGACAATGGATAAGGCA 59.454 50.000 0.00 0.00 0.00 4.75
2904 3867 3.770040 CCTCATCGTGGGCCGTCA 61.770 66.667 0.00 0.00 37.94 4.35
2917 3880 2.365635 GCAGTAGGGGAGGCCTCA 60.366 66.667 33.29 11.02 0.00 3.86
2953 3916 2.112297 GTGGTTGGGAACGGCTCA 59.888 61.111 0.00 0.00 0.00 4.26
2965 3928 1.473857 CGTCGTTTGTCGTCGTGGTT 61.474 55.000 0.00 0.00 43.43 3.67
2969 3932 1.369689 CTCCGTCGTTTGTCGTCGT 60.370 57.895 6.24 0.00 45.89 4.34
3034 4328 1.265236 TCCACCATGGCCATTTTGAC 58.735 50.000 17.92 0.00 37.47 3.18
3110 4411 6.014840 AGGCAATGATTTCAACATCACTTCTT 60.015 34.615 0.00 0.00 35.97 2.52
3147 4448 7.952671 AGTCACTTCAGTACAAATACTCAGAA 58.047 34.615 0.00 0.00 39.80 3.02
3153 4454 7.225931 TCCAACAAGTCACTTCAGTACAAATAC 59.774 37.037 0.00 0.00 0.00 1.89
3184 4486 9.577003 CGACGTATGCCTTAAATTTATTCTAAC 57.423 33.333 0.00 0.00 0.00 2.34
3185 4487 9.531942 TCGACGTATGCCTTAAATTTATTCTAA 57.468 29.630 0.00 0.00 0.00 2.10
3186 4488 9.701098 ATCGACGTATGCCTTAAATTTATTCTA 57.299 29.630 0.00 0.00 0.00 2.10
3187 4489 8.603242 ATCGACGTATGCCTTAAATTTATTCT 57.397 30.769 0.00 0.00 0.00 2.40
3191 4493 8.928733 GGATAATCGACGTATGCCTTAAATTTA 58.071 33.333 0.00 0.00 0.00 1.40
3192 4494 7.359765 CGGATAATCGACGTATGCCTTAAATTT 60.360 37.037 0.00 0.00 0.00 1.82
3193 4495 6.090358 CGGATAATCGACGTATGCCTTAAATT 59.910 38.462 0.00 0.00 0.00 1.82
3194 4496 5.575606 CGGATAATCGACGTATGCCTTAAAT 59.424 40.000 0.00 0.00 0.00 1.40
3195 4497 4.919168 CGGATAATCGACGTATGCCTTAAA 59.081 41.667 0.00 0.00 0.00 1.52
3196 4498 4.216042 TCGGATAATCGACGTATGCCTTAA 59.784 41.667 0.00 0.00 33.92 1.85
3197 4499 3.752747 TCGGATAATCGACGTATGCCTTA 59.247 43.478 0.00 0.00 33.92 2.69
3198 4500 2.555325 TCGGATAATCGACGTATGCCTT 59.445 45.455 0.00 0.00 33.92 4.35
3199 4501 2.156917 TCGGATAATCGACGTATGCCT 58.843 47.619 0.00 0.00 33.92 4.75
3200 4502 2.516923 CTCGGATAATCGACGTATGCC 58.483 52.381 0.00 0.00 35.18 4.40
3201 4503 2.161012 TCCTCGGATAATCGACGTATGC 59.839 50.000 0.00 0.00 35.18 3.14
3202 4504 3.436015 AGTCCTCGGATAATCGACGTATG 59.564 47.826 0.00 0.00 35.18 2.39
3203 4505 3.672808 AGTCCTCGGATAATCGACGTAT 58.327 45.455 0.00 0.00 35.18 3.06
3204 4506 3.117491 AGTCCTCGGATAATCGACGTA 57.883 47.619 0.00 0.00 35.18 3.57
3205 4507 1.964552 AGTCCTCGGATAATCGACGT 58.035 50.000 0.00 0.00 35.18 4.34
3206 4508 3.667430 GCTTAGTCCTCGGATAATCGACG 60.667 52.174 0.00 0.00 35.18 5.12
3207 4509 3.252701 TGCTTAGTCCTCGGATAATCGAC 59.747 47.826 0.00 0.00 35.18 4.20
3208 4510 3.483421 TGCTTAGTCCTCGGATAATCGA 58.517 45.455 0.00 0.00 37.60 3.59
3209 4511 3.917329 TGCTTAGTCCTCGGATAATCG 57.083 47.619 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.