Multiple sequence alignment - TraesCS7B01G415200

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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 TraesCS7B01G415200 chr7B 100.000 3377 0 0 1 3377 682928474 682925098 0.000000e+00 6237.0
1 TraesCS7B01G415200 chr7B 91.870 1636 122 3 688 2314 682967908 682966275 0.000000e+00 2274.0
2 TraesCS7B01G415200 chr7B 95.516 669 26 3 2710 3377 729144587 729145252 0.000000e+00 1066.0
3 TraesCS7B01G415200 chr7B 95.366 669 27 3 2710 3377 729077065 729077730 0.000000e+00 1061.0
4 TraesCS7B01G415200 chr7B 95.217 669 28 3 2710 3377 729212099 729212764 0.000000e+00 1055.0
5 TraesCS7B01G415200 chr7B 89.058 658 59 5 1506 2152 682840698 682840043 0.000000e+00 804.0
6 TraesCS7B01G415200 chr7B 77.753 1362 254 26 955 2285 681619424 681620767 0.000000e+00 791.0
7 TraesCS7B01G415200 chr7B 77.646 1266 223 39 1014 2252 680911961 680913193 0.000000e+00 715.0
8 TraesCS7B01G415200 chr7B 85.824 649 87 5 2709 3355 733717223 733717868 0.000000e+00 684.0
9 TraesCS7B01G415200 chr7B 86.549 565 62 10 2 557 682968514 682967955 8.010000e-171 610.0
10 TraesCS7B01G415200 chr7B 94.937 237 11 1 2474 2710 682966214 682965979 1.480000e-98 370.0
11 TraesCS7B01G415200 chr7B 92.405 237 13 3 2474 2710 682839974 682839743 1.940000e-87 333.0
12 TraesCS7B01G415200 chr7B 92.500 200 13 2 670 869 682974467 682974270 5.520000e-73 285.0
13 TraesCS7B01G415200 chr7B 85.965 228 31 1 955 1181 681518858 681519085 3.370000e-60 243.0
14 TraesCS7B01G415200 chr7B 94.000 50 3 0 2397 2446 682966262 682966213 3.610000e-10 76.8
15 TraesCS7B01G415200 chr7A 92.388 1445 103 3 870 2308 694097589 694096146 0.000000e+00 2052.0
16 TraesCS7B01G415200 chr7A 77.042 1298 230 45 987 2250 693492704 693493967 0.000000e+00 684.0
17 TraesCS7B01G415200 chr7A 93.671 237 13 2 2474 2710 694096100 694095866 1.490000e-93 353.0
18 TraesCS7B01G415200 chr7A 97.143 35 1 0 2150 2184 47155214 47155180 3.640000e-05 60.2
19 TraesCS7B01G415200 chr7D 89.527 1566 108 21 754 2308 602437711 602436191 0.000000e+00 1932.0
20 TraesCS7B01G415200 chr7D 77.786 1355 258 21 955 2283 602018962 602020299 0.000000e+00 795.0
21 TraesCS7B01G415200 chr7D 77.506 1267 223 40 1014 2252 601914894 601916126 0.000000e+00 704.0
22 TraesCS7B01G415200 chr7D 88.703 478 45 9 90 562 602438335 602437862 2.920000e-160 575.0
23 TraesCS7B01G415200 chr7D 88.889 315 27 5 2397 2711 602436169 602435863 6.840000e-102 381.0
24 TraesCS7B01G415200 chr7D 73.138 1195 232 61 1083 2232 601494306 601493156 2.490000e-91 346.0
25 TraesCS7B01G415200 chr7D 95.000 80 4 0 2318 2397 600948436 600948515 3.540000e-25 126.0
26 TraesCS7B01G415200 chr5B 95.970 670 24 2 2709 3377 559152631 559151964 0.000000e+00 1085.0
27 TraesCS7B01G415200 chr5B 95.373 670 28 2 2709 3377 571179654 571178987 0.000000e+00 1062.0
28 TraesCS7B01G415200 chr5B 93.750 80 5 0 2318 2397 522041043 522040964 1.650000e-23 121.0
29 TraesCS7B01G415200 chr2B 95.224 670 28 3 2709 3377 117786923 117787589 0.000000e+00 1057.0
30 TraesCS7B01G415200 chr2B 91.311 610 50 3 2768 3377 859171 858565 0.000000e+00 830.0
31 TraesCS7B01G415200 chr3D 90.702 484 41 3 2710 3192 349670418 349669938 2.840000e-180 641.0
32 TraesCS7B01G415200 chr2D 91.218 353 30 1 3026 3377 5441364 5441716 2.360000e-131 479.0
33 TraesCS7B01G415200 chr6D 76.224 286 64 2 1912 2195 1374014 1374297 7.550000e-32 148.0
34 TraesCS7B01G415200 chr3B 97.500 80 2 0 2318 2397 263803257 263803336 1.630000e-28 137.0
35 TraesCS7B01G415200 chr5A 94.118 85 3 2 2318 2400 74706839 74706923 9.840000e-26 128.0
36 TraesCS7B01G415200 chrUn 95.000 80 4 0 2318 2397 108422555 108422476 3.540000e-25 126.0
37 TraesCS7B01G415200 chrUn 93.333 45 3 0 2147 2191 48887085 48887041 2.170000e-07 67.6
38 TraesCS7B01G415200 chr3A 95.000 80 4 0 2318 2397 737582600 737582679 3.540000e-25 126.0
39 TraesCS7B01G415200 chr1D 95.000 80 4 0 2318 2397 270277185 270277106 3.540000e-25 126.0
40 TraesCS7B01G415200 chr6B 93.750 80 5 0 2318 2397 544084341 544084420 1.650000e-23 121.0
41 TraesCS7B01G415200 chr5D 93.750 80 5 0 2318 2397 430156987 430156908 1.650000e-23 121.0
42 TraesCS7B01G415200 chr4A 94.737 38 2 0 2144 2181 655474974 655475011 3.640000e-05 60.2


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 TraesCS7B01G415200 chr7B 682925098 682928474 3376 True 6237.000000 6237 100.000000 1 3377 1 chr7B.!!$R1 3376
1 TraesCS7B01G415200 chr7B 729144587 729145252 665 False 1066.000000 1066 95.516000 2710 3377 1 chr7B.!!$F5 667
2 TraesCS7B01G415200 chr7B 729077065 729077730 665 False 1061.000000 1061 95.366000 2710 3377 1 chr7B.!!$F4 667
3 TraesCS7B01G415200 chr7B 729212099 729212764 665 False 1055.000000 1055 95.217000 2710 3377 1 chr7B.!!$F6 667
4 TraesCS7B01G415200 chr7B 682965979 682968514 2535 True 832.700000 2274 91.839000 2 2710 4 chr7B.!!$R4 2708
5 TraesCS7B01G415200 chr7B 681619424 681620767 1343 False 791.000000 791 77.753000 955 2285 1 chr7B.!!$F3 1330
6 TraesCS7B01G415200 chr7B 680911961 680913193 1232 False 715.000000 715 77.646000 1014 2252 1 chr7B.!!$F1 1238
7 TraesCS7B01G415200 chr7B 733717223 733717868 645 False 684.000000 684 85.824000 2709 3355 1 chr7B.!!$F7 646
8 TraesCS7B01G415200 chr7B 682839743 682840698 955 True 568.500000 804 90.731500 1506 2710 2 chr7B.!!$R3 1204
9 TraesCS7B01G415200 chr7A 694095866 694097589 1723 True 1202.500000 2052 93.029500 870 2710 2 chr7A.!!$R2 1840
10 TraesCS7B01G415200 chr7A 693492704 693493967 1263 False 684.000000 684 77.042000 987 2250 1 chr7A.!!$F1 1263
11 TraesCS7B01G415200 chr7D 602435863 602438335 2472 True 962.666667 1932 89.039667 90 2711 3 chr7D.!!$R2 2621
12 TraesCS7B01G415200 chr7D 602018962 602020299 1337 False 795.000000 795 77.786000 955 2283 1 chr7D.!!$F3 1328
13 TraesCS7B01G415200 chr7D 601914894 601916126 1232 False 704.000000 704 77.506000 1014 2252 1 chr7D.!!$F2 1238
14 TraesCS7B01G415200 chr7D 601493156 601494306 1150 True 346.000000 346 73.138000 1083 2232 1 chr7D.!!$R1 1149
15 TraesCS7B01G415200 chr5B 559151964 559152631 667 True 1085.000000 1085 95.970000 2709 3377 1 chr5B.!!$R2 668
16 TraesCS7B01G415200 chr5B 571178987 571179654 667 True 1062.000000 1062 95.373000 2709 3377 1 chr5B.!!$R3 668
17 TraesCS7B01G415200 chr2B 117786923 117787589 666 False 1057.000000 1057 95.224000 2709 3377 1 chr2B.!!$F1 668
18 TraesCS7B01G415200 chr2B 858565 859171 606 True 830.000000 830 91.311000 2768 3377 1 chr2B.!!$R1 609

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
992 1040 0.109226 AGCGTACGTGCCTCTTCTTC 60.109 55.0 17.9 0.0 34.65 2.87 F
1701 1782 0.032403 GTGTGCTGCTGATGCCAAAA 59.968 50.0 0.0 0.0 38.71 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2442 0.180406 ATGATGAGTAACACCCGGCC 59.820 55.0 0.00 0.00 0.0 6.13 R
3010 3135 0.179134 CAGTGGACGCAGCTACCTAC 60.179 60.0 6.35 3.85 0.0 3.18 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 43 2.519771 ATGGATGACATGGTTGCAGT 57.480 45.000 0.00 0.00 38.70 4.40
57 58 6.851609 TGGTTGCAGTGTGATCATATAAAAC 58.148 36.000 0.00 0.44 0.00 2.43
83 84 6.919158 TCCTCCTCAAGTTTACTAGCCTATA 58.081 40.000 0.00 0.00 0.00 1.31
118 119 6.469410 AGGTGACTTACGTTTTGATTGGATA 58.531 36.000 0.00 0.00 37.44 2.59
297 298 9.041354 AGTAGAGGATTTATGGATGAAGATACC 57.959 37.037 0.00 0.00 0.00 2.73
350 352 8.137437 TCTTTCTTTTGAAAAGGATACTGCAAG 58.863 33.333 16.79 2.08 46.42 4.01
443 451 4.965200 TCGTTTGGAAATTTGGGGAATT 57.035 36.364 0.00 0.00 39.63 2.17
480 488 8.514136 TGGTGATCATTTTTAAAATCACGAAC 57.486 30.769 18.96 10.74 45.69 3.95
482 490 8.424731 GGTGATCATTTTTAAAATCACGAACAC 58.575 33.333 18.96 16.58 45.69 3.32
483 491 9.180678 GTGATCATTTTTAAAATCACGAACACT 57.819 29.630 13.70 0.00 38.81 3.55
538 554 4.155826 TGAGCATTTCCGAAATTCGTGAAT 59.844 37.500 14.58 10.45 38.40 2.57
636 677 1.202722 ACCGTCCCATCGTTCTGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
637 678 1.877443 CCGTCCCATCGTTCTGTTTTT 59.123 47.619 0.00 0.00 0.00 1.94
668 709 8.638685 TGAAACTACGTTCTGTTTATATAGCC 57.361 34.615 11.91 2.55 36.64 3.93
676 717 4.806330 TCTGTTTATATAGCCGCAGTAGC 58.194 43.478 0.00 0.00 37.42 3.58
697 738 8.195436 AGTAGCACGCTATACAGAAAATAGAAA 58.805 33.333 1.43 0.00 0.00 2.52
739 780 3.366396 CTGGCCCACTTAGAGTCTAAGA 58.634 50.000 35.83 17.92 0.00 2.10
740 781 3.964031 CTGGCCCACTTAGAGTCTAAGAT 59.036 47.826 35.83 21.78 0.00 2.40
743 784 4.038642 GGCCCACTTAGAGTCTAAGATCTG 59.961 50.000 35.83 25.71 0.00 2.90
746 787 6.681865 GCCCACTTAGAGTCTAAGATCTGAAC 60.682 46.154 35.83 19.28 0.00 3.18
751 792 8.058847 ACTTAGAGTCTAAGATCTGAACCATCT 58.941 37.037 35.83 13.82 31.51 2.90
992 1040 0.109226 AGCGTACGTGCCTCTTCTTC 60.109 55.000 17.90 0.00 34.65 2.87
1040 1088 4.570663 CCGGGTAAGAGAGGCGCG 62.571 72.222 0.00 0.00 38.11 6.86
1080 1128 1.025041 TCCAGAGGACATCATCGACG 58.975 55.000 0.00 0.00 0.00 5.12
1326 1374 3.367025 CGAACACCGTAAAGATGAGGTTC 59.633 47.826 0.00 0.00 34.25 3.62
1421 1475 0.036010 GCAAGCAAGCTCTCCTACCA 60.036 55.000 0.00 0.00 0.00 3.25
1423 1477 1.277557 CAAGCAAGCTCTCCTACCACT 59.722 52.381 0.00 0.00 0.00 4.00
1424 1478 1.190643 AGCAAGCTCTCCTACCACTC 58.809 55.000 0.00 0.00 0.00 3.51
1434 1488 0.635009 CCTACCACTCCCTGGGTCTA 59.365 60.000 13.56 0.00 45.78 2.59
1443 1497 1.234529 CCTGGGTCTAGGCTAGGCT 59.765 63.158 24.19 23.67 0.00 4.58
1445 1499 1.501582 CTGGGTCTAGGCTAGGCTTT 58.498 55.000 25.37 3.38 0.00 3.51
1508 1562 4.478686 AGAGAATATAGGGTGCTTTGGGTT 59.521 41.667 0.00 0.00 0.00 4.11
1521 1575 3.259123 GCTTTGGGTTTCAGGATCACAAT 59.741 43.478 0.00 0.00 0.00 2.71
1522 1576 4.262592 GCTTTGGGTTTCAGGATCACAATT 60.263 41.667 0.00 0.00 0.00 2.32
1523 1577 5.047377 GCTTTGGGTTTCAGGATCACAATTA 60.047 40.000 0.00 0.00 0.00 1.40
1571 1627 0.321564 CAGTTGGATCGGACAAGCCA 60.322 55.000 0.00 0.00 35.94 4.75
1584 1640 2.754946 CAAGCCAAGGCATGTCAAAT 57.245 45.000 14.40 0.00 44.88 2.32
1598 1654 2.948979 TGTCAAATTCAGAACGCCAACT 59.051 40.909 0.00 0.00 0.00 3.16
1612 1668 1.876416 GCCAACTGTCTTGTCGGCTTA 60.876 52.381 0.00 0.00 36.58 3.09
1670 1742 0.821711 CACCAATCCAACACCGTGGT 60.822 55.000 3.03 0.00 43.38 4.16
1686 1758 1.806542 GTGGTAGTCTGCATTGGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
1701 1782 0.032403 GTGTGCTGCTGATGCCAAAA 59.968 50.000 0.00 0.00 38.71 2.44
2233 2357 1.668101 GACGAGCCTCCATTCTCCGT 61.668 60.000 0.00 0.00 0.00 4.69
2314 2438 2.638480 TTGGATGGCCATAGTAGCAC 57.362 50.000 20.84 3.70 45.46 4.40
2316 2440 0.393077 GGATGGCCATAGTAGCACGT 59.607 55.000 20.84 0.00 0.00 4.49
2318 2442 2.352814 GGATGGCCATAGTAGCACGTAG 60.353 54.545 20.84 0.00 0.00 3.51
2319 2443 1.037493 TGGCCATAGTAGCACGTAGG 58.963 55.000 0.00 0.00 0.00 3.18
2320 2444 0.319641 GGCCATAGTAGCACGTAGGC 60.320 60.000 0.00 0.00 39.86 3.93
2321 2445 0.319641 GCCATAGTAGCACGTAGGCC 60.320 60.000 0.00 0.00 34.71 5.19
2322 2446 0.039437 CCATAGTAGCACGTAGGCCG 60.039 60.000 0.00 0.00 44.03 6.13
2324 2448 1.177256 ATAGTAGCACGTAGGCCGGG 61.177 60.000 2.18 0.00 45.00 5.73
2328 2452 4.692475 GCACGTAGGCCGGGTGTT 62.692 66.667 20.12 0.00 43.72 3.32
2329 2453 2.972267 CACGTAGGCCGGGTGTTA 59.028 61.111 2.18 0.00 42.24 2.41
2330 2454 1.446618 CACGTAGGCCGGGTGTTAC 60.447 63.158 2.18 2.22 42.24 2.50
2331 2455 1.607467 ACGTAGGCCGGGTGTTACT 60.607 57.895 2.18 0.00 42.24 2.24
2332 2456 1.140375 CGTAGGCCGGGTGTTACTC 59.860 63.158 2.18 0.00 0.00 2.59
2333 2457 1.597797 CGTAGGCCGGGTGTTACTCA 61.598 60.000 2.18 0.00 0.00 3.41
2334 2458 0.828677 GTAGGCCGGGTGTTACTCAT 59.171 55.000 2.18 0.00 0.00 2.90
2335 2459 1.117150 TAGGCCGGGTGTTACTCATC 58.883 55.000 2.18 0.00 0.00 2.92
2336 2460 0.907704 AGGCCGGGTGTTACTCATCA 60.908 55.000 2.18 0.00 0.00 3.07
2337 2461 0.180406 GGCCGGGTGTTACTCATCAT 59.820 55.000 2.18 0.00 0.00 2.45
2338 2462 1.299541 GCCGGGTGTTACTCATCATG 58.700 55.000 2.18 0.00 0.00 3.07
2339 2463 1.134521 GCCGGGTGTTACTCATCATGA 60.135 52.381 2.18 0.00 0.00 3.07
2340 2464 2.485479 GCCGGGTGTTACTCATCATGAT 60.485 50.000 2.18 1.18 0.00 2.45
2341 2465 3.808728 CCGGGTGTTACTCATCATGATT 58.191 45.455 5.16 0.00 0.00 2.57
2342 2466 4.199310 CCGGGTGTTACTCATCATGATTT 58.801 43.478 5.16 0.00 0.00 2.17
2343 2467 4.035558 CCGGGTGTTACTCATCATGATTTG 59.964 45.833 5.16 4.34 0.00 2.32
2344 2468 4.635765 CGGGTGTTACTCATCATGATTTGT 59.364 41.667 5.16 10.18 0.00 2.83
2345 2469 5.815222 CGGGTGTTACTCATCATGATTTGTA 59.185 40.000 5.16 9.20 0.00 2.41
2346 2470 6.483307 CGGGTGTTACTCATCATGATTTGTAT 59.517 38.462 5.16 0.00 0.00 2.29
2347 2471 7.307396 CGGGTGTTACTCATCATGATTTGTATC 60.307 40.741 5.16 11.01 0.00 2.24
2348 2472 7.716998 GGGTGTTACTCATCATGATTTGTATCT 59.283 37.037 5.16 0.00 0.00 1.98
2349 2473 9.113838 GGTGTTACTCATCATGATTTGTATCTT 57.886 33.333 5.16 0.00 0.00 2.40
2429 2553 6.655078 ATAGCACATTGTGAACCTTTCTTT 57.345 33.333 20.77 0.00 35.23 2.52
2434 2558 7.039504 AGCACATTGTGAACCTTTCTTTCATAT 60.040 33.333 20.77 0.00 35.47 1.78
2449 2573 7.558161 TCTTTCATATGCTGATTGTTCGATT 57.442 32.000 0.00 0.00 32.72 3.34
2477 2601 3.126831 GTTCAGTATGCAATCTCTCCCG 58.873 50.000 0.00 0.00 34.76 5.14
2531 2655 3.187022 TGATGTCTCATCAACTTTGTGCG 59.813 43.478 9.55 0.00 0.00 5.34
2538 2662 2.772568 TCAACTTTGTGCGAACATGG 57.227 45.000 0.00 0.00 0.00 3.66
2547 2671 2.223456 TGTGCGAACATGGTTTCTTGTG 60.223 45.455 0.00 0.00 32.53 3.33
2556 2680 5.783111 ACATGGTTTCTTGTGCCTTAATTC 58.217 37.500 0.00 0.00 31.23 2.17
2705 2829 3.733684 GCGTTTTGAGGCAGAAAGAAACA 60.734 43.478 0.00 0.00 0.00 2.83
2934 3059 2.093288 TCCTGATCTGATCAACCAGCAC 60.093 50.000 19.95 0.00 39.11 4.40
2971 3096 4.573900 GATCTCTGTCCACTGTTGTGATT 58.426 43.478 0.00 0.00 46.55 2.57
2985 3110 8.506437 CACTGTTGTGATTATCTTAAGAGCAAA 58.494 33.333 11.53 5.83 46.55 3.68
2986 3111 9.066892 ACTGTTGTGATTATCTTAAGAGCAAAA 57.933 29.630 11.53 5.36 0.00 2.44
2996 3121 6.371809 TCTTAAGAGCAAAACACGACAATT 57.628 33.333 0.00 0.00 0.00 2.32
3008 3133 3.945285 ACACGACAATTTGTCTCCACTTT 59.055 39.130 23.29 2.53 44.85 2.66
3010 3135 5.236478 ACACGACAATTTGTCTCCACTTTAG 59.764 40.000 23.29 9.88 44.85 1.85
3058 3183 1.478654 GGTTCAAACCCTCCAAGCAGA 60.479 52.381 0.10 0.00 43.43 4.26
3356 3482 0.327924 TGGATGCCCACGAGTGAATT 59.672 50.000 4.59 0.00 37.58 2.17
3366 3492 4.439153 CCCACGAGTGAATTAACGTAGCTA 60.439 45.833 4.59 0.00 37.22 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.777106 TCATGCTCCATAAGACCCATC 57.223 47.619 0.00 0.00 0.00 3.51
2 3 3.047857 TGATCATGCTCCATAAGACCCA 58.952 45.455 0.00 0.00 0.00 4.51
5 6 4.903054 TCCATGATCATGCTCCATAAGAC 58.097 43.478 27.24 0.00 37.49 3.01
11 12 2.440253 TGTCATCCATGATCATGCTCCA 59.560 45.455 27.24 15.99 39.30 3.86
35 36 7.698130 GGAAGTTTTATATGATCACACTGCAAC 59.302 37.037 0.00 0.00 0.00 4.17
40 41 8.095452 AGGAGGAAGTTTTATATGATCACACT 57.905 34.615 0.00 0.00 0.00 3.55
42 43 8.089625 TGAGGAGGAAGTTTTATATGATCACA 57.910 34.615 0.00 0.00 0.00 3.58
57 58 4.468153 AGGCTAGTAAACTTGAGGAGGAAG 59.532 45.833 0.00 0.00 0.00 3.46
83 84 4.268359 CGTAAGTCACCTACCTAGGAAGT 58.732 47.826 17.98 6.53 46.63 3.01
196 197 8.153550 TGGCTTTGTAAACATAATCCAAATGTT 58.846 29.630 0.00 0.00 46.77 2.71
343 345 7.759489 TTCTAATTGTACAAATCCTTGCAGT 57.241 32.000 13.23 0.00 35.84 4.40
423 431 6.262049 AGAAAAATTCCCCAAATTTCCAAACG 59.738 34.615 0.00 0.00 44.88 3.60
501 515 8.527810 TCGGAAATGCTCAGGTATTTTAATTTT 58.472 29.630 0.00 0.00 37.75 1.82
503 517 7.639113 TCGGAAATGCTCAGGTATTTTAATT 57.361 32.000 0.00 0.00 37.75 1.40
504 518 7.639113 TTCGGAAATGCTCAGGTATTTTAAT 57.361 32.000 0.00 0.00 37.75 1.40
507 523 5.975693 TTTCGGAAATGCTCAGGTATTTT 57.024 34.783 0.00 0.00 37.75 1.82
574 597 3.132925 CTGTGGTTTGCTCCCAAAATTG 58.867 45.455 0.00 0.00 42.19 2.32
581 604 4.599036 AACCTGTGGTTTGCTCCC 57.401 55.556 0.00 0.00 44.33 4.30
610 643 2.764572 AGAACGATGGGACGGTTTAGAT 59.235 45.455 0.00 0.00 37.61 1.98
648 689 5.217393 TGCGGCTATATAAACAGAACGTAG 58.783 41.667 0.00 0.00 0.00 3.51
649 690 5.185668 TGCGGCTATATAAACAGAACGTA 57.814 39.130 0.00 0.00 0.00 3.57
650 691 4.049186 CTGCGGCTATATAAACAGAACGT 58.951 43.478 0.00 0.00 0.00 3.99
651 692 4.049186 ACTGCGGCTATATAAACAGAACG 58.951 43.478 0.00 0.00 0.00 3.95
652 693 5.118817 GCTACTGCGGCTATATAAACAGAAC 59.881 44.000 0.00 0.00 0.00 3.01
653 694 5.221362 TGCTACTGCGGCTATATAAACAGAA 60.221 40.000 0.00 0.00 43.34 3.02
654 695 4.279922 TGCTACTGCGGCTATATAAACAGA 59.720 41.667 0.00 0.00 43.34 3.41
655 696 4.386049 GTGCTACTGCGGCTATATAAACAG 59.614 45.833 0.00 0.00 43.34 3.16
656 697 4.304110 GTGCTACTGCGGCTATATAAACA 58.696 43.478 0.00 0.00 43.34 2.83
657 698 3.364023 CGTGCTACTGCGGCTATATAAAC 59.636 47.826 0.00 0.00 43.34 2.01
658 699 3.571571 CGTGCTACTGCGGCTATATAAA 58.428 45.455 0.00 0.00 43.34 1.40
659 700 2.670229 GCGTGCTACTGCGGCTATATAA 60.670 50.000 0.00 0.00 43.34 0.98
660 701 1.135489 GCGTGCTACTGCGGCTATATA 60.135 52.381 0.00 0.00 43.34 0.86
668 709 1.002792 TCTGTATAGCGTGCTACTGCG 60.003 52.381 3.26 0.00 43.34 5.18
697 738 5.009010 CCAGCTCAGTTATGTCAGTTGTTTT 59.991 40.000 0.00 0.00 0.00 2.43
701 742 2.417933 GCCAGCTCAGTTATGTCAGTTG 59.582 50.000 0.00 0.00 0.00 3.16
706 747 0.253044 TGGGCCAGCTCAGTTATGTC 59.747 55.000 0.00 0.00 0.00 3.06
746 787 1.204704 TGAGTTGTGCGACCTAGATGG 59.795 52.381 0.00 0.00 42.93 3.51
751 792 1.292223 GGCTGAGTTGTGCGACCTA 59.708 57.895 0.00 0.00 0.00 3.08
848 889 4.421479 CAGGGACGACGCGAGCTT 62.421 66.667 15.93 0.00 0.00 3.74
1080 1128 1.594331 GGCAACCGGATGAGTATTCC 58.406 55.000 17.00 1.75 0.00 3.01
1147 1195 0.324614 TTCAGGCGTGGATGTGACAT 59.675 50.000 6.56 0.00 0.00 3.06
1262 1310 1.757306 CTGCTGACTGGTGGTCCTT 59.243 57.895 0.00 0.00 43.89 3.36
1421 1475 0.558712 CTAGCCTAGACCCAGGGAGT 59.441 60.000 14.54 0.17 36.10 3.85
1423 1477 1.939113 CCTAGCCTAGACCCAGGGA 59.061 63.158 14.54 0.00 36.10 4.20
1424 1478 1.839296 GCCTAGCCTAGACCCAGGG 60.839 68.421 2.85 2.85 36.10 4.45
1443 1497 2.080693 AGCAATTACGATGGTGCGAAA 58.919 42.857 0.00 0.00 41.90 3.46
1445 1499 1.732941 AAGCAATTACGATGGTGCGA 58.267 45.000 0.00 0.00 41.90 5.10
1522 1576 9.909644 GGACGTATAAGCTAGATTCAAGAAATA 57.090 33.333 0.00 0.00 0.00 1.40
1523 1577 8.643324 AGGACGTATAAGCTAGATTCAAGAAAT 58.357 33.333 0.00 0.00 0.00 2.17
1571 1627 3.612479 GCGTTCTGAATTTGACATGCCTT 60.612 43.478 0.00 0.00 0.00 4.35
1584 1640 1.939934 CAAGACAGTTGGCGTTCTGAA 59.060 47.619 9.63 0.00 35.84 3.02
1598 1654 1.621317 TCCATGTAAGCCGACAAGACA 59.379 47.619 0.00 0.00 31.83 3.41
1612 1668 4.324563 CCTCCACTAACTTCCATTCCATGT 60.325 45.833 0.00 0.00 0.00 3.21
1686 1758 2.667473 ATCTTTTTGGCATCAGCAGC 57.333 45.000 0.00 0.00 44.61 5.25
1701 1782 5.485353 TGTCTTCACCATCTCCTGTAATCTT 59.515 40.000 0.00 0.00 0.00 2.40
2314 2438 1.140375 GAGTAACACCCGGCCTACG 59.860 63.158 0.00 0.00 43.80 3.51
2316 2440 1.117150 GATGAGTAACACCCGGCCTA 58.883 55.000 0.00 0.00 0.00 3.93
2318 2442 0.180406 ATGATGAGTAACACCCGGCC 59.820 55.000 0.00 0.00 0.00 6.13
2319 2443 1.134521 TCATGATGAGTAACACCCGGC 60.135 52.381 0.00 0.00 0.00 6.13
2320 2444 2.979814 TCATGATGAGTAACACCCGG 57.020 50.000 0.00 0.00 0.00 5.73
2321 2445 4.635765 ACAAATCATGATGAGTAACACCCG 59.364 41.667 9.46 0.00 0.00 5.28
2322 2446 7.716998 AGATACAAATCATGATGAGTAACACCC 59.283 37.037 18.78 9.81 34.28 4.61
2453 2577 4.943705 GGGAGAGATTGCATACTGAACAAA 59.056 41.667 0.00 0.00 0.00 2.83
2531 2655 3.733443 AAGGCACAAGAAACCATGTTC 57.267 42.857 0.00 0.00 0.00 3.18
2538 2662 3.896122 TGCGAATTAAGGCACAAGAAAC 58.104 40.909 0.00 0.00 33.52 2.78
2547 2671 7.196331 AGAAACAAATCTATGCGAATTAAGGC 58.804 34.615 0.00 0.00 0.00 4.35
2721 2845 5.946377 AGTGATGAATAAAACTCCCTTCCAC 59.054 40.000 0.00 0.00 0.00 4.02
2724 2848 7.607991 TCTTGAGTGATGAATAAAACTCCCTTC 59.392 37.037 0.00 0.00 38.61 3.46
2800 2925 0.675208 AATGCCGCACGGTTGTATGA 60.675 50.000 11.27 0.00 37.65 2.15
2934 3059 1.197264 GAGATCGATCCCGTTACTCCG 59.803 57.143 21.66 0.00 37.05 4.63
2971 3096 7.667043 ATTGTCGTGTTTTGCTCTTAAGATA 57.333 32.000 5.44 0.00 0.00 1.98
2996 3121 5.185249 CAGCTACCTACTAAAGTGGAGACAA 59.815 44.000 0.00 0.00 46.06 3.18
3008 3133 1.064906 AGTGGACGCAGCTACCTACTA 60.065 52.381 6.35 0.00 0.00 1.82
3010 3135 0.179134 CAGTGGACGCAGCTACCTAC 60.179 60.000 6.35 3.85 0.00 3.18
3189 3315 3.074412 GTGGACCAAACTCAATGTCGAT 58.926 45.455 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.