Multiple sequence alignment - TraesCS3A01G443000

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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 TraesCS3A01G443000 chr3A 100.000 2972 0 0 1 2972 684639239 684642210 0.000000e+00 5489.0
1 TraesCS3A01G443000 chr3A 90.378 1746 80 45 487 2182 684698489 684696782 0.000000e+00 2213.0
2 TraesCS3A01G443000 chr3A 89.379 885 50 14 1236 2103 13823439 13822582 0.000000e+00 1074.0
3 TraesCS3A01G443000 chr3A 98.592 568 7 1 2405 2972 80544047 80543481 0.000000e+00 1003.0
4 TraesCS3A01G443000 chr3A 89.189 148 12 1 21 168 684693068 684693211 6.540000e-42 182.0
5 TraesCS3A01G443000 chr3A 83.333 114 18 1 2267 2379 693197958 693197845 1.460000e-18 104.0
6 TraesCS3A01G443000 chr3D 90.514 2119 97 40 162 2215 547632160 547634239 0.000000e+00 2704.0
7 TraesCS3A01G443000 chr3D 91.855 1461 64 25 762 2199 547779451 547778023 0.000000e+00 1988.0
8 TraesCS3A01G443000 chr3D 92.903 155 11 0 14 168 547631982 547632136 2.980000e-55 226.0
9 TraesCS3A01G443000 chr3D 89.091 55 3 3 2362 2415 365398217 365398269 6.880000e-07 65.8
10 TraesCS3A01G443000 chr3B 89.279 2192 123 41 23 2123 725181252 725183422 0.000000e+00 2643.0
11 TraesCS3A01G443000 chr3B 90.526 1615 93 34 563 2150 725275741 725277322 0.000000e+00 2080.0
12 TraesCS3A01G443000 chr7A 96.975 595 17 1 2379 2972 654109765 654109171 0.000000e+00 998.0
13 TraesCS3A01G443000 chr7A 82.114 123 20 2 2267 2388 547107087 547106966 1.460000e-18 104.0
14 TraesCS3A01G443000 chr2D 96.465 594 18 3 2378 2970 322844664 322844073 0.000000e+00 977.0
15 TraesCS3A01G443000 chr2D 84.211 95 11 4 2267 2359 311543962 311544054 4.080000e-14 89.8
16 TraesCS3A01G443000 chr6B 95.798 595 23 2 2379 2972 4181434 4182027 0.000000e+00 959.0
17 TraesCS3A01G443000 chr6B 97.500 120 2 1 2376 2494 543677139 543677020 1.400000e-48 204.0
18 TraesCS3A01G443000 chr4B 88.870 602 46 12 2375 2970 314413631 314413045 0.000000e+00 721.0
19 TraesCS3A01G443000 chr7D 89.167 360 31 6 2376 2731 202384012 202384367 2.720000e-120 442.0
20 TraesCS3A01G443000 chr7D 87.500 376 39 6 2464 2832 565128828 565129202 7.610000e-116 427.0
21 TraesCS3A01G443000 chr7D 91.667 228 16 2 2729 2956 202384436 202384660 2.220000e-81 313.0
22 TraesCS3A01G443000 chr7D 91.398 93 7 1 2739 2830 624914239 624914147 3.110000e-25 126.0
23 TraesCS3A01G443000 chr7D 85.965 114 15 1 2267 2379 448866581 448866694 1.450000e-23 121.0
24 TraesCS3A01G443000 chrUn 89.286 252 18 4 2729 2972 30140652 30140402 1.030000e-79 307.0
25 TraesCS3A01G443000 chrUn 91.824 159 11 2 2370 2527 30147690 30147533 1.390000e-53 220.0
26 TraesCS3A01G443000 chrUn 87.586 145 13 4 2588 2731 30140873 30140733 2.370000e-36 163.0
27 TraesCS3A01G443000 chr2B 83.929 112 15 3 2270 2379 90418061 90417951 1.460000e-18 104.0
28 TraesCS3A01G443000 chr2B 84.112 107 14 3 2275 2379 90418530 90418425 1.880000e-17 100.0
29 TraesCS3A01G443000 chr5A 84.158 101 15 1 2280 2379 87891855 87891955 2.440000e-16 97.1
30 TraesCS3A01G443000 chr6A 81.579 114 20 1 2267 2379 180620887 180620774 3.150000e-15 93.5
31 TraesCS3A01G443000 chr1D 83.158 95 14 2 2282 2375 348009823 348009730 5.280000e-13 86.1


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 TraesCS3A01G443000 chr3A 684639239 684642210 2971 False 5489.0 5489 100.0000 1 2972 1 chr3A.!!$F1 2971
1 TraesCS3A01G443000 chr3A 684696782 684698489 1707 True 2213.0 2213 90.3780 487 2182 1 chr3A.!!$R3 1695
2 TraesCS3A01G443000 chr3A 13822582 13823439 857 True 1074.0 1074 89.3790 1236 2103 1 chr3A.!!$R1 867
3 TraesCS3A01G443000 chr3A 80543481 80544047 566 True 1003.0 1003 98.5920 2405 2972 1 chr3A.!!$R2 567
4 TraesCS3A01G443000 chr3D 547778023 547779451 1428 True 1988.0 1988 91.8550 762 2199 1 chr3D.!!$R1 1437
5 TraesCS3A01G443000 chr3D 547631982 547634239 2257 False 1465.0 2704 91.7085 14 2215 2 chr3D.!!$F2 2201
6 TraesCS3A01G443000 chr3B 725181252 725183422 2170 False 2643.0 2643 89.2790 23 2123 1 chr3B.!!$F1 2100
7 TraesCS3A01G443000 chr3B 725275741 725277322 1581 False 2080.0 2080 90.5260 563 2150 1 chr3B.!!$F2 1587
8 TraesCS3A01G443000 chr7A 654109171 654109765 594 True 998.0 998 96.9750 2379 2972 1 chr7A.!!$R2 593
9 TraesCS3A01G443000 chr2D 322844073 322844664 591 True 977.0 977 96.4650 2378 2970 1 chr2D.!!$R1 592
10 TraesCS3A01G443000 chr6B 4181434 4182027 593 False 959.0 959 95.7980 2379 2972 1 chr6B.!!$F1 593
11 TraesCS3A01G443000 chr4B 314413045 314413631 586 True 721.0 721 88.8700 2375 2970 1 chr4B.!!$R1 595
12 TraesCS3A01G443000 chr7D 202384012 202384660 648 False 377.5 442 90.4170 2376 2956 2 chr7D.!!$F3 580

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
782 887 0.179018 ATCCCCTAACCTTCATGCGC 60.179 55.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2479 0.037697 AATGCAAGTGCGTCGTCCTA 60.038 50.0 0.0 0.0 45.83 2.94 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
34 35 4.065088 GAGGTGTGATAAGACAAGTGCAA 58.935 43.478 0.00 0.00 0.00 4.08
42 43 1.972872 AGACAAGTGCAAGAAGGTGG 58.027 50.000 0.00 0.00 0.00 4.61
160 161 2.140792 TATCCAAGGCGAGGGAGGC 61.141 63.158 0.00 0.00 36.45 4.70
217 251 7.014615 GTCTGGAAATGCCTTGATATTTACCAT 59.985 37.037 0.00 0.00 37.63 3.55
220 254 7.147976 GGAAATGCCTTGATATTTACCATGAC 58.852 38.462 0.00 0.00 0.00 3.06
287 321 3.958147 CTACTGTGCCCACTGCCCG 62.958 68.421 5.37 0.00 40.16 6.13
574 646 7.543868 ACAGATTGTTCTTTCTTAGAGATGTCG 59.456 37.037 0.00 0.00 33.51 4.35
604 698 0.179084 ATACGCATTGAGGTCACCCG 60.179 55.000 0.00 0.00 35.12 5.28
613 707 3.434319 GGTCACCCGTGCATGCAG 61.434 66.667 23.41 12.59 0.00 4.41
676 777 6.071320 AGGTGCTAGTCATATGTAGTCATCA 58.929 40.000 1.90 0.00 35.70 3.07
685 786 8.791675 AGTCATATGTAGTCATCAGTATCTGTG 58.208 37.037 1.90 0.00 35.70 3.66
782 887 0.179018 ATCCCCTAACCTTCATGCGC 60.179 55.000 0.00 0.00 0.00 6.09
902 1017 1.304282 CACCCATCTCCAACCCCAG 59.696 63.158 0.00 0.00 0.00 4.45
934 1059 4.579869 TCCTCCTAGCTCATTGTTCAAAC 58.420 43.478 0.00 0.00 0.00 2.93
954 1079 9.868277 TTCAAACTTCAAACACATATTTTCTGT 57.132 25.926 0.00 0.00 0.00 3.41
955 1080 9.515020 TCAAACTTCAAACACATATTTTCTGTC 57.485 29.630 0.00 0.00 0.00 3.51
956 1081 9.520204 CAAACTTCAAACACATATTTTCTGTCT 57.480 29.630 0.00 0.00 0.00 3.41
959 1084 9.561069 ACTTCAAACACATATTTTCTGTCTACT 57.439 29.630 0.00 0.00 0.00 2.57
961 1086 9.778741 TTCAAACACATATTTTCTGTCTACTCT 57.221 29.630 0.00 0.00 0.00 3.24
962 1087 9.424319 TCAAACACATATTTTCTGTCTACTCTC 57.576 33.333 0.00 0.00 0.00 3.20
963 1088 9.429359 CAAACACATATTTTCTGTCTACTCTCT 57.571 33.333 0.00 0.00 0.00 3.10
1313 1493 3.222855 CAAGGCGGCCAACCACAA 61.223 61.111 23.09 0.00 34.57 3.33
1314 1494 3.223589 AAGGCGGCCAACCACAAC 61.224 61.111 23.09 0.00 34.57 3.32
1485 1674 2.124778 GAGAAGCAGCAGAGCCCC 60.125 66.667 0.00 0.00 34.23 5.80
1734 1935 0.753262 ATCGCACGAGCCCTAAGAAT 59.247 50.000 0.00 0.00 37.52 2.40
1920 2121 2.835705 CGCCGACATAGAGACCGCT 61.836 63.158 0.00 0.00 0.00 5.52
1988 2197 1.302033 GATCGATGGCGCCCAATCT 60.302 57.895 26.77 6.08 36.95 2.40
2046 2275 2.603173 CCTCTGCGTTGCTCTGTTTTTC 60.603 50.000 0.00 0.00 0.00 2.29
2050 2279 2.421775 TGCGTTGCTCTGTTTTTCTTGA 59.578 40.909 0.00 0.00 0.00 3.02
2191 2423 8.276252 TGTTCTTTATGGCTTATAAACAGACC 57.724 34.615 3.58 0.00 36.55 3.85
2206 2438 2.563179 ACAGACCGAACAAGCTCTGTAT 59.437 45.455 0.00 0.00 41.24 2.29
2231 2463 6.800072 TTTTCCCAAACAAATAAGGTCTGT 57.200 33.333 0.00 0.00 0.00 3.41
2232 2464 7.899648 TTTTCCCAAACAAATAAGGTCTGTA 57.100 32.000 0.00 0.00 0.00 2.74
2233 2465 8.485578 TTTTCCCAAACAAATAAGGTCTGTAT 57.514 30.769 0.00 0.00 0.00 2.29
2234 2466 8.485578 TTTCCCAAACAAATAAGGTCTGTATT 57.514 30.769 0.00 0.00 0.00 1.89
2235 2467 8.485578 TTCCCAAACAAATAAGGTCTGTATTT 57.514 30.769 0.00 0.00 32.58 1.40
2236 2468 8.485578 TCCCAAACAAATAAGGTCTGTATTTT 57.514 30.769 0.00 0.00 30.47 1.82
2237 2469 8.929487 TCCCAAACAAATAAGGTCTGTATTTTT 58.071 29.630 0.00 0.00 30.47 1.94
2257 2489 5.415415 TTTTAGATAGACTAGGACGACGC 57.585 43.478 0.00 0.00 32.30 5.19
2258 2490 2.616634 AGATAGACTAGGACGACGCA 57.383 50.000 0.00 0.00 0.00 5.24
2259 2491 2.211806 AGATAGACTAGGACGACGCAC 58.788 52.381 0.00 0.00 0.00 5.34
2260 2492 2.158928 AGATAGACTAGGACGACGCACT 60.159 50.000 0.00 0.00 0.00 4.40
2261 2493 2.105006 TAGACTAGGACGACGCACTT 57.895 50.000 0.00 0.00 0.00 3.16
2262 2494 0.522180 AGACTAGGACGACGCACTTG 59.478 55.000 0.00 0.00 0.00 3.16
2263 2495 1.071567 GACTAGGACGACGCACTTGC 61.072 60.000 0.00 0.00 37.78 4.01
2264 2496 1.080772 CTAGGACGACGCACTTGCA 60.081 57.895 1.48 0.00 42.21 4.08
2265 2497 0.458543 CTAGGACGACGCACTTGCAT 60.459 55.000 1.48 0.00 42.21 3.96
2266 2498 0.037697 TAGGACGACGCACTTGCATT 60.038 50.000 1.48 0.00 42.21 3.56
2267 2499 1.154413 GGACGACGCACTTGCATTG 60.154 57.895 1.48 0.00 42.21 2.82
2268 2500 1.793613 GACGACGCACTTGCATTGC 60.794 57.895 10.16 10.16 42.21 3.56
2273 2505 4.324424 GCACTTGCATTGCGTTGT 57.676 50.000 3.84 0.00 41.59 3.32
2274 2506 3.470520 GCACTTGCATTGCGTTGTA 57.529 47.368 3.84 0.00 41.59 2.41
2275 2507 1.764851 GCACTTGCATTGCGTTGTAA 58.235 45.000 3.84 0.00 41.59 2.41
2276 2508 1.451651 GCACTTGCATTGCGTTGTAAC 59.548 47.619 3.84 0.00 41.59 2.50
2320 2552 9.053135 GTATCTTAGTTCGTGATTTATCTAGCG 57.947 37.037 0.00 0.00 0.00 4.26
2321 2553 7.024340 TCTTAGTTCGTGATTTATCTAGCGT 57.976 36.000 0.00 0.00 0.00 5.07
2322 2554 7.478322 TCTTAGTTCGTGATTTATCTAGCGTT 58.522 34.615 0.00 0.00 0.00 4.84
2323 2555 8.615211 TCTTAGTTCGTGATTTATCTAGCGTTA 58.385 33.333 0.00 0.00 0.00 3.18
2324 2556 9.395707 CTTAGTTCGTGATTTATCTAGCGTTAT 57.604 33.333 0.00 0.00 0.00 1.89
2325 2557 7.854934 AGTTCGTGATTTATCTAGCGTTATC 57.145 36.000 0.00 0.00 0.00 1.75
2326 2558 7.423199 AGTTCGTGATTTATCTAGCGTTATCA 58.577 34.615 0.00 0.00 0.00 2.15
2327 2559 8.082852 AGTTCGTGATTTATCTAGCGTTATCAT 58.917 33.333 0.00 0.00 0.00 2.45
2328 2560 7.796958 TCGTGATTTATCTAGCGTTATCATG 57.203 36.000 0.00 0.00 32.81 3.07
2329 2561 7.368059 TCGTGATTTATCTAGCGTTATCATGT 58.632 34.615 0.00 0.00 33.15 3.21
2330 2562 7.326063 TCGTGATTTATCTAGCGTTATCATGTG 59.674 37.037 0.00 0.00 33.15 3.21
2331 2563 7.326063 CGTGATTTATCTAGCGTTATCATGTGA 59.674 37.037 0.00 0.00 0.00 3.58
2332 2564 9.144747 GTGATTTATCTAGCGTTATCATGTGAT 57.855 33.333 0.68 0.68 38.51 3.06
2333 2565 9.710900 TGATTTATCTAGCGTTATCATGTGATT 57.289 29.630 0.19 0.00 36.05 2.57
2334 2566 9.964253 GATTTATCTAGCGTTATCATGTGATTG 57.036 33.333 0.19 0.00 36.05 2.67
2335 2567 8.887036 TTTATCTAGCGTTATCATGTGATTGT 57.113 30.769 0.19 0.00 36.05 2.71
2336 2568 6.775939 ATCTAGCGTTATCATGTGATTGTG 57.224 37.500 0.19 0.00 36.05 3.33
2337 2569 5.660460 TCTAGCGTTATCATGTGATTGTGT 58.340 37.500 0.19 0.00 36.05 3.72
2338 2570 6.801575 TCTAGCGTTATCATGTGATTGTGTA 58.198 36.000 0.19 0.00 36.05 2.90
2339 2571 7.262048 TCTAGCGTTATCATGTGATTGTGTAA 58.738 34.615 0.19 0.00 36.05 2.41
2340 2572 6.735678 AGCGTTATCATGTGATTGTGTAAA 57.264 33.333 0.19 0.00 36.05 2.01
2341 2573 7.320443 AGCGTTATCATGTGATTGTGTAAAT 57.680 32.000 0.19 0.00 36.05 1.40
2342 2574 8.432110 AGCGTTATCATGTGATTGTGTAAATA 57.568 30.769 0.19 0.00 36.05 1.40
2343 2575 8.888716 AGCGTTATCATGTGATTGTGTAAATAA 58.111 29.630 0.19 0.00 36.05 1.40
2344 2576 9.497030 GCGTTATCATGTGATTGTGTAAATAAA 57.503 29.630 0.19 0.00 36.05 1.40
2519 2753 8.757789 CCATGTTGTATTATCAATGCATCAAAC 58.242 33.333 0.00 0.00 36.97 2.93
2670 2906 3.482156 TCCTCTCAGCCATTTAGATGC 57.518 47.619 0.00 0.00 31.67 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.204704 CTTATCACACCTCACCGCTGA 59.795 52.381 0.00 0.00 0.00 4.26
5 6 1.204704 TCTTATCACACCTCACCGCTG 59.795 52.381 0.00 0.00 0.00 5.18
6 7 1.204941 GTCTTATCACACCTCACCGCT 59.795 52.381 0.00 0.00 0.00 5.52
7 8 1.067142 TGTCTTATCACACCTCACCGC 60.067 52.381 0.00 0.00 0.00 5.68
8 9 3.254060 CTTGTCTTATCACACCTCACCG 58.746 50.000 0.00 0.00 0.00 4.94
9 10 3.997021 CACTTGTCTTATCACACCTCACC 59.003 47.826 0.00 0.00 0.00 4.02
10 11 3.433615 GCACTTGTCTTATCACACCTCAC 59.566 47.826 0.00 0.00 0.00 3.51
11 12 3.070878 TGCACTTGTCTTATCACACCTCA 59.929 43.478 0.00 0.00 0.00 3.86
12 13 3.664107 TGCACTTGTCTTATCACACCTC 58.336 45.455 0.00 0.00 0.00 3.85
18 19 4.756642 CACCTTCTTGCACTTGTCTTATCA 59.243 41.667 0.00 0.00 0.00 2.15
19 20 4.154918 CCACCTTCTTGCACTTGTCTTATC 59.845 45.833 0.00 0.00 0.00 1.75
34 35 1.071471 CACCTTCGTGCCACCTTCT 59.929 57.895 0.00 0.00 32.04 2.85
42 43 2.432628 CCCGAGTCACCTTCGTGC 60.433 66.667 0.00 0.00 40.04 5.34
65 66 0.389296 GCGGTGTTGTTTAATGCCCC 60.389 55.000 0.00 0.00 0.00 5.80
151 152 2.186384 CAAGAGCAGCCTCCCTCG 59.814 66.667 0.00 0.00 38.96 4.63
160 161 4.866486 GCCAAATCAAATTACCAAGAGCAG 59.134 41.667 0.00 0.00 0.00 4.24
163 164 4.866486 GCAGCCAAATCAAATTACCAAGAG 59.134 41.667 0.00 0.00 0.00 2.85
287 321 1.680249 CCTAGAGAAAAGGCTGGCACC 60.680 57.143 3.38 0.00 0.00 5.01
297 331 0.673644 GCACTGCGCCCTAGAGAAAA 60.674 55.000 4.18 0.00 32.94 2.29
392 438 7.276878 GGTTTTTGAATCCTCGAAACTCAAAAA 59.723 33.333 21.23 21.23 46.09 1.94
511 567 6.501453 TCCATGGTGGAGAATGTATATGATGA 59.499 38.462 12.58 0.00 42.67 2.92
537 609 4.874970 AGAACAATCTGTGGCAAAATGTC 58.125 39.130 0.00 0.00 33.59 3.06
574 646 2.290367 TCAATGCGTATTATGTGCCTGC 59.710 45.455 0.00 0.00 0.00 4.85
690 791 9.213799 ACAAGCTTTGATTTTGTTCTGTTTTTA 57.786 25.926 0.00 0.00 31.38 1.52
691 792 8.098220 ACAAGCTTTGATTTTGTTCTGTTTTT 57.902 26.923 0.00 0.00 31.38 1.94
711 812 6.760298 TCTCTTGTTATGATCATCAGACAAGC 59.240 38.462 30.89 13.97 44.83 4.01
782 887 0.172578 TGTGCGGTGATAGGAAGACG 59.827 55.000 0.00 0.00 0.00 4.18
881 996 1.000896 GGGTTGGAGATGGGTGTGG 60.001 63.158 0.00 0.00 0.00 4.17
902 1017 1.133482 AGCTAGGAGGAGAAGAGGAGC 60.133 57.143 0.00 0.00 0.00 4.70
954 1079 7.127405 TGAGGAAGTAGAGACTAGAGAGTAGA 58.873 42.308 0.00 0.00 35.45 2.59
955 1080 7.356089 TGAGGAAGTAGAGACTAGAGAGTAG 57.644 44.000 0.00 0.00 35.45 2.57
956 1081 7.924358 ATGAGGAAGTAGAGACTAGAGAGTA 57.076 40.000 0.00 0.00 35.45 2.59
957 1082 6.824958 ATGAGGAAGTAGAGACTAGAGAGT 57.175 41.667 0.00 0.00 39.20 3.24
958 1083 6.017109 GCAATGAGGAAGTAGAGACTAGAGAG 60.017 46.154 0.00 0.00 33.58 3.20
959 1084 5.825679 GCAATGAGGAAGTAGAGACTAGAGA 59.174 44.000 0.00 0.00 33.58 3.10
960 1085 5.009610 GGCAATGAGGAAGTAGAGACTAGAG 59.990 48.000 0.00 0.00 33.58 2.43
961 1086 4.890581 GGCAATGAGGAAGTAGAGACTAGA 59.109 45.833 0.00 0.00 33.58 2.43
962 1087 4.038642 GGGCAATGAGGAAGTAGAGACTAG 59.961 50.000 0.00 0.00 33.58 2.57
963 1088 3.961408 GGGCAATGAGGAAGTAGAGACTA 59.039 47.826 0.00 0.00 33.58 2.59
964 1089 2.769095 GGGCAATGAGGAAGTAGAGACT 59.231 50.000 0.00 0.00 37.59 3.24
965 1090 2.501723 TGGGCAATGAGGAAGTAGAGAC 59.498 50.000 0.00 0.00 0.00 3.36
1458 1647 1.192793 GCTGCTTCTCGTCGTCATAC 58.807 55.000 0.00 0.00 0.00 2.39
1461 1650 1.081175 CTGCTGCTTCTCGTCGTCA 60.081 57.895 0.00 0.00 0.00 4.35
1988 2197 1.841103 TCCTGCACCTACACTGGCA 60.841 57.895 0.00 0.00 34.66 4.92
2046 2275 3.873952 GGCCTATGAGCAACTACTTCAAG 59.126 47.826 0.00 0.00 0.00 3.02
2050 2279 1.139058 CCGGCCTATGAGCAACTACTT 59.861 52.381 0.00 0.00 0.00 2.24
2152 2381 9.423061 GCCATAAAGAACAAATCAATTAAGTGT 57.577 29.630 2.43 0.00 0.00 3.55
2153 2382 9.643693 AGCCATAAAGAACAAATCAATTAAGTG 57.356 29.630 0.00 0.00 0.00 3.16
2234 2466 5.355071 TGCGTCGTCCTAGTCTATCTAAAAA 59.645 40.000 0.00 0.00 0.00 1.94
2235 2467 4.877823 TGCGTCGTCCTAGTCTATCTAAAA 59.122 41.667 0.00 0.00 0.00 1.52
2236 2468 4.272018 GTGCGTCGTCCTAGTCTATCTAAA 59.728 45.833 0.00 0.00 0.00 1.85
2237 2469 3.806521 GTGCGTCGTCCTAGTCTATCTAA 59.193 47.826 0.00 0.00 0.00 2.10
2238 2470 3.069300 AGTGCGTCGTCCTAGTCTATCTA 59.931 47.826 0.00 0.00 0.00 1.98
2239 2471 2.158928 AGTGCGTCGTCCTAGTCTATCT 60.159 50.000 0.00 0.00 0.00 1.98
2240 2472 2.211806 AGTGCGTCGTCCTAGTCTATC 58.788 52.381 0.00 0.00 0.00 2.08
2241 2473 2.328819 AGTGCGTCGTCCTAGTCTAT 57.671 50.000 0.00 0.00 0.00 1.98
2242 2474 1.736126 CAAGTGCGTCGTCCTAGTCTA 59.264 52.381 0.00 0.00 0.00 2.59
2243 2475 0.522180 CAAGTGCGTCGTCCTAGTCT 59.478 55.000 0.00 0.00 0.00 3.24
2244 2476 1.071567 GCAAGTGCGTCGTCCTAGTC 61.072 60.000 0.00 0.00 0.00 2.59
2245 2477 1.080705 GCAAGTGCGTCGTCCTAGT 60.081 57.895 0.00 0.00 0.00 2.57
2246 2478 0.458543 ATGCAAGTGCGTCGTCCTAG 60.459 55.000 0.00 0.00 45.83 3.02
2247 2479 0.037697 AATGCAAGTGCGTCGTCCTA 60.038 50.000 0.00 0.00 45.83 2.94
2248 2480 1.301716 AATGCAAGTGCGTCGTCCT 60.302 52.632 0.00 0.00 45.83 3.85
2249 2481 1.154413 CAATGCAAGTGCGTCGTCC 60.154 57.895 0.00 0.00 45.83 4.79
2250 2482 4.422506 CAATGCAAGTGCGTCGTC 57.577 55.556 0.00 0.00 45.83 4.20
2257 2489 1.708158 CGTTACAACGCAATGCAAGTG 59.292 47.619 5.91 2.02 46.06 3.16
2258 2490 2.031037 CGTTACAACGCAATGCAAGT 57.969 45.000 5.91 2.66 46.06 3.16
2294 2526 9.053135 CGCTAGATAAATCACGAACTAAGATAC 57.947 37.037 0.00 0.00 0.00 2.24
2295 2527 8.781196 ACGCTAGATAAATCACGAACTAAGATA 58.219 33.333 0.00 0.00 0.00 1.98
2296 2528 7.649973 ACGCTAGATAAATCACGAACTAAGAT 58.350 34.615 0.00 0.00 0.00 2.40
2297 2529 7.024340 ACGCTAGATAAATCACGAACTAAGA 57.976 36.000 0.00 0.00 0.00 2.10
2298 2530 7.681125 AACGCTAGATAAATCACGAACTAAG 57.319 36.000 0.00 0.00 0.00 2.18
2299 2531 9.390795 GATAACGCTAGATAAATCACGAACTAA 57.609 33.333 0.00 0.00 0.00 2.24
2300 2532 8.562052 TGATAACGCTAGATAAATCACGAACTA 58.438 33.333 0.00 0.00 0.00 2.24
2301 2533 7.423199 TGATAACGCTAGATAAATCACGAACT 58.577 34.615 0.00 0.00 0.00 3.01
2302 2534 7.618964 TGATAACGCTAGATAAATCACGAAC 57.381 36.000 0.00 0.00 0.00 3.95
2303 2535 7.865889 ACATGATAACGCTAGATAAATCACGAA 59.134 33.333 0.00 0.00 0.00 3.85
2304 2536 7.326063 CACATGATAACGCTAGATAAATCACGA 59.674 37.037 0.00 0.00 0.00 4.35
2305 2537 7.326063 TCACATGATAACGCTAGATAAATCACG 59.674 37.037 0.00 0.00 0.00 4.35
2306 2538 8.520835 TCACATGATAACGCTAGATAAATCAC 57.479 34.615 0.00 0.00 0.00 3.06
2307 2539 9.710900 AATCACATGATAACGCTAGATAAATCA 57.289 29.630 0.00 0.00 33.73 2.57
2308 2540 9.964253 CAATCACATGATAACGCTAGATAAATC 57.036 33.333 0.00 0.00 33.73 2.17
2309 2541 9.494271 ACAATCACATGATAACGCTAGATAAAT 57.506 29.630 0.00 0.00 33.73 1.40
2310 2542 8.764287 CACAATCACATGATAACGCTAGATAAA 58.236 33.333 0.00 0.00 33.73 1.40
2311 2543 7.926018 ACACAATCACATGATAACGCTAGATAA 59.074 33.333 0.00 0.00 33.73 1.75
2312 2544 7.433680 ACACAATCACATGATAACGCTAGATA 58.566 34.615 0.00 0.00 33.73 1.98
2313 2545 6.283694 ACACAATCACATGATAACGCTAGAT 58.716 36.000 0.00 0.00 33.73 1.98
2314 2546 5.660460 ACACAATCACATGATAACGCTAGA 58.340 37.500 0.00 0.00 33.73 2.43
2315 2547 5.973651 ACACAATCACATGATAACGCTAG 57.026 39.130 0.00 0.00 33.73 3.42
2316 2548 7.835634 TTTACACAATCACATGATAACGCTA 57.164 32.000 0.00 0.00 33.73 4.26
2317 2549 6.735678 TTTACACAATCACATGATAACGCT 57.264 33.333 0.00 0.00 33.73 5.07
2318 2550 9.497030 TTTATTTACACAATCACATGATAACGC 57.503 29.630 0.00 0.00 33.73 4.84
2367 2599 9.740710 GGGGCATCATCTAGTTATAAAGTAAAT 57.259 33.333 0.00 0.00 0.00 1.40
2368 2600 7.876068 CGGGGCATCATCTAGTTATAAAGTAAA 59.124 37.037 0.00 0.00 0.00 2.01
2369 2601 7.383687 CGGGGCATCATCTAGTTATAAAGTAA 58.616 38.462 0.00 0.00 0.00 2.24
2370 2602 6.573680 GCGGGGCATCATCTAGTTATAAAGTA 60.574 42.308 0.00 0.00 0.00 2.24
2371 2603 5.794894 CGGGGCATCATCTAGTTATAAAGT 58.205 41.667 0.00 0.00 0.00 2.66
2372 2604 4.631813 GCGGGGCATCATCTAGTTATAAAG 59.368 45.833 0.00 0.00 0.00 1.85
2373 2605 4.575885 GCGGGGCATCATCTAGTTATAAA 58.424 43.478 0.00 0.00 0.00 1.40
2374 2606 3.368013 CGCGGGGCATCATCTAGTTATAA 60.368 47.826 0.00 0.00 0.00 0.98
2670 2906 7.087409 TCTATTTTGCACCAACATCTACATG 57.913 36.000 0.00 0.00 35.92 3.21
2710 2947 9.905713 ATGTAATACTAGGATTTGTGAATGTGT 57.094 29.630 5.27 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.