Multiple sequence alignment - TraesCS5D01G492800

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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 TraesCS5D01G492800 chr5D 100.000 2807 0 0 1 2807 525760312 525763118 0.000000e+00 5184.0
1 TraesCS5D01G492800 chr5D 90.649 1433 81 24 499 1901 525731667 525733076 0.000000e+00 1855.0
2 TraesCS5D01G492800 chr5B 93.603 1532 69 11 444 1949 660209081 660210609 0.000000e+00 2259.0
3 TraesCS5D01G492800 chr5B 89.153 1429 92 28 505 1901 660185836 660187233 0.000000e+00 1722.0
4 TraesCS5D01G492800 chr5B 88.309 479 31 9 2347 2801 660218469 660218946 4.090000e-153 551.0
5 TraesCS5D01G492800 chr5B 82.787 366 29 16 2463 2798 660272181 660272542 2.110000e-76 296.0
6 TraesCS5D01G492800 chr5B 89.172 157 11 5 2154 2307 660218323 660218476 1.030000e-44 191.0
7 TraesCS5D01G492800 chr5B 97.468 79 2 0 2003 2081 660210612 660210690 4.880000e-28 135.0
8 TraesCS5D01G492800 chr5B 97.015 67 2 0 2081 2147 660217982 660218048 2.290000e-21 113.0
9 TraesCS5D01G492800 chr5A 95.098 1326 35 10 615 1910 652064031 652065356 0.000000e+00 2061.0
10 TraesCS5D01G492800 chr5A 88.456 1386 96 36 668 2029 652050012 652051357 0.000000e+00 1615.0
11 TraesCS5D01G492800 chr5A 87.053 587 71 4 1 586 652063448 652064030 0.000000e+00 658.0
12 TraesCS5D01G492800 chr5A 86.804 485 62 2 1 484 437173932 437174415 8.850000e-150 540.0
13 TraesCS5D01G492800 chr5A 86.186 485 65 2 1 484 633002759 633003242 8.910000e-145 523.0
14 TraesCS5D01G492800 chr5A 97.682 302 7 0 2004 2305 652065380 652065681 1.150000e-143 520.0
15 TraesCS5D01G492800 chr5A 91.860 258 20 1 2544 2801 652066289 652066545 2.660000e-95 359.0
16 TraesCS5D01G492800 chr5A 97.902 143 2 1 2301 2443 652066055 652066196 2.160000e-61 246.0
17 TraesCS5D01G492800 chr5A 83.000 100 6 7 2427 2518 652118516 652118612 2.320000e-11 80.5
18 TraesCS5D01G492800 chr2A 87.010 485 61 2 1 484 17556622 17557105 1.900000e-151 545.0
19 TraesCS5D01G492800 chr2A 82.474 97 13 1 543 639 757956529 757956621 6.440000e-12 82.4
20 TraesCS5D01G492800 chr1A 86.804 485 62 2 1 484 539290998 539291481 8.850000e-150 540.0
21 TraesCS5D01G492800 chr4A 86.327 490 64 3 1 488 173648761 173648273 5.320000e-147 531.0
22 TraesCS5D01G492800 chr2D 86.151 491 66 2 1 490 565931486 565930997 1.910000e-146 529.0
23 TraesCS5D01G492800 chr4B 86.186 485 65 2 1 484 2449616 2450099 8.910000e-145 523.0
24 TraesCS5D01G492800 chr7D 85.979 485 66 2 1 484 636588532 636589015 4.140000e-143 518.0
25 TraesCS5D01G492800 chr1B 94.828 58 3 0 2144 2201 633788846 633788903 1.070000e-14 91.6
26 TraesCS5D01G492800 chr1B 94.828 58 3 0 2144 2201 633794182 633794239 1.070000e-14 91.6
27 TraesCS5D01G492800 chr3B 92.453 53 4 0 571 623 687067574 687067522 3.000000e-10 76.8


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 TraesCS5D01G492800 chr5D 525760312 525763118 2806 False 5184.0 5184 100.000000 1 2807 1 chr5D.!!$F2 2806
1 TraesCS5D01G492800 chr5D 525731667 525733076 1409 False 1855.0 1855 90.649000 499 1901 1 chr5D.!!$F1 1402
2 TraesCS5D01G492800 chr5B 660185836 660187233 1397 False 1722.0 1722 89.153000 505 1901 1 chr5B.!!$F1 1396
3 TraesCS5D01G492800 chr5B 660209081 660210690 1609 False 1197.0 2259 95.535500 444 2081 2 chr5B.!!$F3 1637
4 TraesCS5D01G492800 chr5B 660217982 660218946 964 False 285.0 551 91.498667 2081 2801 3 chr5B.!!$F4 720
5 TraesCS5D01G492800 chr5A 652050012 652051357 1345 False 1615.0 1615 88.456000 668 2029 1 chr5A.!!$F3 1361
6 TraesCS5D01G492800 chr5A 652063448 652066545 3097 False 768.8 2061 93.919000 1 2801 5 chr5A.!!$F5 2800

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
121 123 0.174162 GTCATGGCAAAGGGTGATGC 59.826 55.0 0.0 0.0 41.82 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2017 1.064621 CGTATGCATGCTGGCCAAC 59.935 57.895 20.33 1.82 0.0 3.77 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
25 26 8.839310 GCATATAATGGTCTACAACTTCATCT 57.161 34.615 0.00 0.00 0.00 2.90
26 27 9.929180 GCATATAATGGTCTACAACTTCATCTA 57.071 33.333 0.00 0.00 0.00 1.98
41 42 6.109359 ACTTCATCTACAGCTATGGTTTGTC 58.891 40.000 0.00 0.00 0.00 3.18
42 43 5.939764 TCATCTACAGCTATGGTTTGTCT 57.060 39.130 0.00 0.00 0.00 3.41
52 53 4.260375 GCTATGGTTTGTCTGATAAGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
53 54 2.422597 TGGTTTGTCTGATAAGTGCGG 58.577 47.619 0.00 0.00 0.00 5.69
55 56 2.415512 GGTTTGTCTGATAAGTGCGGAC 59.584 50.000 0.00 0.00 41.06 4.79
83 85 5.464030 AGGTAGACGTTTACAATCTGTGT 57.536 39.130 17.04 0.00 44.82 3.72
84 86 5.850614 AGGTAGACGTTTACAATCTGTGTT 58.149 37.500 17.04 0.00 41.98 3.32
88 90 4.024893 AGACGTTTACAATCTGTGTTGCAG 60.025 41.667 0.00 0.00 46.34 4.41
102 104 4.276678 TGTGTTGCAGAGAGAAAATGAAGG 59.723 41.667 0.00 0.00 0.00 3.46
107 109 4.698780 TGCAGAGAGAAAATGAAGGTCATG 59.301 41.667 0.00 0.00 37.15 3.07
121 123 0.174162 GTCATGGCAAAGGGTGATGC 59.826 55.000 0.00 0.00 41.82 3.91
127 129 0.807496 GCAAAGGGTGATGCTGAGAC 59.193 55.000 0.00 0.00 39.46 3.36
156 158 3.549794 GGCATTATGAGGAGCAGAAAGT 58.450 45.455 0.00 0.00 30.49 2.66
197 199 6.586463 TCTTCTTTGAGTACGTGCTTGATAAG 59.414 38.462 7.83 9.14 0.00 1.73
201 203 5.339008 TGAGTACGTGCTTGATAAGGAAT 57.661 39.130 7.83 0.00 0.00 3.01
209 211 2.223572 GCTTGATAAGGAATGGCGGTTG 60.224 50.000 0.00 0.00 0.00 3.77
230 232 3.195610 TGAAGAGTATGTTCTGGTGCGAT 59.804 43.478 0.00 0.00 39.45 4.58
252 254 1.825474 CACAGTCACGGAGGGACTATT 59.175 52.381 4.49 0.00 43.47 1.73
260 262 4.353191 TCACGGAGGGACTATTAGGACTAT 59.647 45.833 0.00 0.00 41.55 2.12
272 274 9.169592 GACTATTAGGACTATAGAGATGTGGTC 57.830 40.741 6.78 2.38 0.00 4.02
275 277 4.138290 AGGACTATAGAGATGTGGTCGTG 58.862 47.826 6.78 0.00 0.00 4.35
283 285 2.869801 GAGATGTGGTCGTGTTTGACAA 59.130 45.455 0.00 0.00 40.72 3.18
284 286 3.275143 AGATGTGGTCGTGTTTGACAAA 58.725 40.909 0.00 0.00 40.72 2.83
323 325 1.981256 ATGGTATTGCCGTTCATCCC 58.019 50.000 0.00 0.00 41.21 3.85
328 330 1.185315 ATTGCCGTTCATCCCCTTTG 58.815 50.000 0.00 0.00 0.00 2.77
329 331 0.178975 TTGCCGTTCATCCCCTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
331 333 1.644786 GCCGTTCATCCCCTTTGTCG 61.645 60.000 0.00 0.00 0.00 4.35
344 346 4.329392 CCCTTTGTCGGTGTTAATAACCT 58.671 43.478 0.18 0.00 35.39 3.50
347 349 3.235157 TGTCGGTGTTAATAACCTCCG 57.765 47.619 21.63 21.63 43.83 4.63
350 352 4.219507 TGTCGGTGTTAATAACCTCCGTTA 59.780 41.667 24.31 16.63 43.35 3.18
351 353 5.105392 TGTCGGTGTTAATAACCTCCGTTAT 60.105 40.000 24.31 0.00 45.25 1.89
369 371 5.221087 CCGTTATACCACTGTTTTTGGTTGT 60.221 40.000 0.00 0.00 45.62 3.32
370 372 5.683743 CGTTATACCACTGTTTTTGGTTGTG 59.316 40.000 0.00 0.00 45.62 3.33
373 375 1.276415 CACTGTTTTTGGTTGTGCCG 58.724 50.000 0.00 0.00 41.21 5.69
382 384 2.039818 TGGTTGTGCCGTTGTTTCTA 57.960 45.000 0.00 0.00 41.21 2.10
414 416 0.673644 GGACATACGTGTGGCTGCTT 60.674 55.000 18.27 0.00 39.09 3.91
427 429 1.872313 GGCTGCTTCAGACATCTATGC 59.128 52.381 0.00 0.00 39.71 3.14
429 431 1.526041 CTGCTTCAGACATCTATGCGC 59.474 52.381 0.00 0.00 32.44 6.09
457 459 1.534595 GTCAGCAGAAGCCAAAGTCAG 59.465 52.381 0.00 0.00 43.56 3.51
464 466 4.397417 GCAGAAGCCAAAGTCAGTAATCAT 59.603 41.667 0.00 0.00 33.58 2.45
487 489 3.586039 GGTGACGATGCAATGTTCG 57.414 52.632 5.91 5.91 41.04 3.95
503 505 0.239879 TTCGGAAACCTGCGCAAATC 59.760 50.000 13.05 7.20 36.15 2.17
595 599 6.335471 TCAAATGGTGTAGAAGTTAGACGA 57.665 37.500 0.00 0.00 0.00 4.20
599 603 4.392047 TGGTGTAGAAGTTAGACGAGACA 58.608 43.478 0.00 0.00 0.00 3.41
852 880 5.722021 TTGACTAGCACAGTAGATGAACA 57.278 39.130 0.00 0.00 37.72 3.18
1430 1492 3.782443 GTTCCTCATCGGGGGCGT 61.782 66.667 0.00 0.00 0.00 5.68
1696 1760 6.715264 TCTCTCCAAATATGATCTAGCGTACA 59.285 38.462 0.00 0.00 0.00 2.90
1853 1918 4.425772 TCTCCTTAATCCCAGACAGAACA 58.574 43.478 0.00 0.00 0.00 3.18
1870 1935 8.345565 AGACAGAACAAAACTATTTCATGTGAC 58.654 33.333 0.00 0.00 0.00 3.67
1968 2033 1.971481 CTAGTTGGCCAGCATGCATA 58.029 50.000 22.64 3.87 31.97 3.14
1970 2035 1.064621 GTTGGCCAGCATGCATACG 59.935 57.895 21.98 4.93 31.97 3.06
1974 2047 1.230635 GGCCAGCATGCATACGTAGG 61.231 60.000 21.98 2.16 31.97 3.18
1977 2050 0.532640 CAGCATGCATACGTAGGGCA 60.533 55.000 21.98 22.12 42.43 5.36
1986 2059 2.700722 TACGTAGGGCATGCAATTCA 57.299 45.000 21.36 0.00 0.00 2.57
1992 2065 1.276989 AGGGCATGCAATTCAACTTGG 59.723 47.619 21.36 0.00 0.00 3.61
2288 2632 9.931210 GATCCCTACAAAATGATAAAGTAAACG 57.069 33.333 0.00 0.00 0.00 3.60
2299 2643 7.801547 TGATAAAGTAAACGGTCGAGTAAAG 57.198 36.000 0.00 0.00 0.00 1.85
2313 3035 4.157289 TCGAGTAAAGCTTAGACAACCGAT 59.843 41.667 0.00 0.00 0.00 4.18
2317 3039 7.222224 CGAGTAAAGCTTAGACAACCGATAAAT 59.778 37.037 0.00 0.00 0.00 1.40
2438 3196 1.079875 AGCGCGTACGTGGTAAATGG 61.080 55.000 29.89 3.84 42.83 3.16
2439 3197 1.077645 GCGCGTACGTGGTAAATGGA 61.078 55.000 28.26 0.00 42.83 3.41
2440 3198 1.563111 CGCGTACGTGGTAAATGGAT 58.437 50.000 20.84 0.00 33.53 3.41
2441 3199 1.256895 CGCGTACGTGGTAAATGGATG 59.743 52.381 20.84 0.00 33.53 3.51
2442 3200 2.273557 GCGTACGTGGTAAATGGATGT 58.726 47.619 17.90 0.00 0.00 3.06
2443 3201 2.674357 GCGTACGTGGTAAATGGATGTT 59.326 45.455 17.90 0.00 0.00 2.71
2444 3202 3.125658 GCGTACGTGGTAAATGGATGTTT 59.874 43.478 17.90 0.00 0.00 2.83
2445 3203 4.725737 GCGTACGTGGTAAATGGATGTTTC 60.726 45.833 17.90 0.00 0.00 2.78
2446 3204 4.628333 CGTACGTGGTAAATGGATGTTTCT 59.372 41.667 7.22 0.00 0.00 2.52
2447 3205 5.445407 CGTACGTGGTAAATGGATGTTTCTG 60.445 44.000 7.22 0.00 0.00 3.02
2448 3206 3.190535 ACGTGGTAAATGGATGTTTCTGC 59.809 43.478 0.00 0.00 0.00 4.26
2449 3207 3.190327 CGTGGTAAATGGATGTTTCTGCA 59.810 43.478 0.00 0.00 0.00 4.41
2450 3208 4.320861 CGTGGTAAATGGATGTTTCTGCAA 60.321 41.667 0.00 0.00 0.00 4.08
2451 3209 5.163513 GTGGTAAATGGATGTTTCTGCAAG 58.836 41.667 0.00 0.00 0.00 4.01
2452 3210 4.220382 TGGTAAATGGATGTTTCTGCAAGG 59.780 41.667 0.00 0.00 0.00 3.61
2453 3211 4.462483 GGTAAATGGATGTTTCTGCAAGGA 59.538 41.667 0.00 0.00 0.00 3.36
2454 3212 4.796038 AAATGGATGTTTCTGCAAGGAG 57.204 40.909 0.00 0.00 0.00 3.69
2455 3213 3.726557 ATGGATGTTTCTGCAAGGAGA 57.273 42.857 0.00 0.00 0.00 3.71
2456 3214 3.726557 TGGATGTTTCTGCAAGGAGAT 57.273 42.857 0.00 0.00 0.00 2.75
2457 3215 4.038271 TGGATGTTTCTGCAAGGAGATT 57.962 40.909 0.00 0.00 0.00 2.40
2458 3216 4.012374 TGGATGTTTCTGCAAGGAGATTC 58.988 43.478 0.00 0.00 0.00 2.52
2459 3217 4.012374 GGATGTTTCTGCAAGGAGATTCA 58.988 43.478 0.00 0.00 0.00 2.57
2460 3218 4.643784 GGATGTTTCTGCAAGGAGATTCAT 59.356 41.667 8.04 8.04 0.00 2.57
2461 3219 5.450137 GGATGTTTCTGCAAGGAGATTCATG 60.450 44.000 11.35 0.00 0.00 3.07
2462 3220 4.654915 TGTTTCTGCAAGGAGATTCATGA 58.345 39.130 0.00 0.00 0.00 3.07
2463 3221 4.456911 TGTTTCTGCAAGGAGATTCATGAC 59.543 41.667 0.00 0.00 0.00 3.06
2464 3222 3.986996 TCTGCAAGGAGATTCATGACA 57.013 42.857 0.00 0.00 0.00 3.58
2465 3223 3.603532 TCTGCAAGGAGATTCATGACAC 58.396 45.455 0.00 0.00 0.00 3.67
2466 3224 2.349590 TGCAAGGAGATTCATGACACG 58.650 47.619 0.00 0.00 0.00 4.49
2467 3225 2.289631 TGCAAGGAGATTCATGACACGT 60.290 45.455 0.00 0.00 0.00 4.49
2468 3226 3.056179 TGCAAGGAGATTCATGACACGTA 60.056 43.478 0.00 0.00 0.00 3.57
2469 3227 3.307242 GCAAGGAGATTCATGACACGTAC 59.693 47.826 0.00 0.00 0.00 3.67
2470 3228 3.802948 AGGAGATTCATGACACGTACC 57.197 47.619 0.00 0.00 0.00 3.34
2471 3229 2.431057 AGGAGATTCATGACACGTACCC 59.569 50.000 0.00 0.00 0.00 3.69
2472 3230 2.167693 GGAGATTCATGACACGTACCCA 59.832 50.000 0.00 0.00 0.00 4.51
2473 3231 3.448686 GAGATTCATGACACGTACCCAG 58.551 50.000 0.00 0.00 0.00 4.45
2509 3267 3.054875 AGAGATCAGTAAATGCACTGCCA 60.055 43.478 0.00 0.00 44.62 4.92
2517 3284 1.409251 AATGCACTGCCAGCCCAAAA 61.409 50.000 0.00 0.00 0.00 2.44
2526 3297 1.207811 GCCAGCCCAAAAGCATGTAAT 59.792 47.619 0.00 0.00 34.23 1.89
2538 3309 3.800826 ATGTAATGAACCGGAGCCC 57.199 52.632 9.46 0.00 0.00 5.19
2539 3310 0.916086 ATGTAATGAACCGGAGCCCA 59.084 50.000 9.46 0.00 0.00 5.36
2540 3311 0.693622 TGTAATGAACCGGAGCCCAA 59.306 50.000 9.46 0.00 0.00 4.12
2541 3312 1.074084 TGTAATGAACCGGAGCCCAAA 59.926 47.619 9.46 0.00 0.00 3.28
2603 3397 3.000925 GCACGACACGACCAATAAATAGG 59.999 47.826 0.00 0.00 0.00 2.57
2622 3416 1.287730 GGAGATCGATCCATGTGCGC 61.288 60.000 21.66 0.00 39.34 6.09
2721 3516 4.201679 CGCCCGCCATAGTCGTCA 62.202 66.667 0.00 0.00 0.00 4.35
2724 3519 2.423898 CCCGCCATAGTCGTCACCT 61.424 63.158 0.00 0.00 0.00 4.00
2727 3522 0.172578 CGCCATAGTCGTCACCTTGA 59.827 55.000 0.00 0.00 0.00 3.02
2737 3532 2.047274 CACCTTGATCGCCACCGT 60.047 61.111 0.00 0.00 35.54 4.83
2744 3539 3.099619 GATCGCCACCGTCGTCGTA 62.100 63.158 0.71 0.00 35.54 3.43
2748 3543 2.949106 CCACCGTCGTCGTACTGT 59.051 61.111 0.71 0.00 35.01 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.791867 ACCATAGCTGTAGATGAAGTTGTA 57.208 37.500 0.00 0.00 0.00 2.41
21 22 5.664457 TCAGACAAACCATAGCTGTAGATG 58.336 41.667 0.00 0.00 0.00 2.90
25 26 7.041721 CACTTATCAGACAAACCATAGCTGTA 58.958 38.462 0.00 0.00 0.00 2.74
26 27 5.877012 CACTTATCAGACAAACCATAGCTGT 59.123 40.000 0.00 0.00 0.00 4.40
52 53 9.242477 GATTGTAAACGTCTACCTAATAAGTCC 57.758 37.037 0.00 0.00 0.00 3.85
55 56 9.798994 ACAGATTGTAAACGTCTACCTAATAAG 57.201 33.333 0.00 0.00 0.00 1.73
83 85 4.717877 TGACCTTCATTTTCTCTCTGCAA 58.282 39.130 0.00 0.00 0.00 4.08
84 86 4.356405 TGACCTTCATTTTCTCTCTGCA 57.644 40.909 0.00 0.00 0.00 4.41
88 90 4.012374 TGCCATGACCTTCATTTTCTCTC 58.988 43.478 0.00 0.00 34.28 3.20
102 104 0.174162 GCATCACCCTTTGCCATGAC 59.826 55.000 0.00 0.00 32.66 3.06
107 109 0.322816 TCTCAGCATCACCCTTTGCC 60.323 55.000 0.00 0.00 39.72 4.52
121 123 2.809861 AATGCCCACTGCCGTCTCAG 62.810 60.000 0.00 0.00 40.16 3.35
127 129 1.168407 CCTCATAATGCCCACTGCCG 61.168 60.000 0.00 0.00 40.16 5.69
145 147 1.673329 GGTCCTTCGACTTTCTGCTCC 60.673 57.143 0.00 0.00 39.15 4.70
156 158 1.893801 GAAGAAGTCAGGGTCCTTCGA 59.106 52.381 0.00 0.00 41.51 3.71
197 199 2.396590 TACTCTTCAACCGCCATTCC 57.603 50.000 0.00 0.00 0.00 3.01
201 203 2.301870 AGAACATACTCTTCAACCGCCA 59.698 45.455 0.00 0.00 0.00 5.69
209 211 3.232213 TCGCACCAGAACATACTCTTC 57.768 47.619 0.00 0.00 0.00 2.87
230 232 2.523168 TCCCTCCGTGACTGTGCA 60.523 61.111 0.00 0.00 0.00 4.57
252 254 5.163227 ACACGACCACATCTCTATAGTCCTA 60.163 44.000 0.00 0.00 0.00 2.94
260 262 3.319689 TGTCAAACACGACCACATCTCTA 59.680 43.478 0.00 0.00 34.88 2.43
298 300 6.462347 GGGATGAACGGCAATACCATATTTTT 60.462 38.462 0.00 0.00 39.03 1.94
302 304 3.561313 GGGGATGAACGGCAATACCATAT 60.561 47.826 0.00 0.00 39.03 1.78
303 305 2.224670 GGGGATGAACGGCAATACCATA 60.225 50.000 0.00 0.00 39.03 2.74
304 306 1.478654 GGGGATGAACGGCAATACCAT 60.479 52.381 0.00 0.00 39.03 3.55
305 307 0.106918 GGGGATGAACGGCAATACCA 60.107 55.000 0.00 0.00 39.03 3.25
307 309 2.052782 AAGGGGATGAACGGCAATAC 57.947 50.000 0.00 0.00 0.00 1.89
308 310 2.291282 ACAAAGGGGATGAACGGCAATA 60.291 45.455 0.00 0.00 0.00 1.90
309 311 1.185315 CAAAGGGGATGAACGGCAAT 58.815 50.000 0.00 0.00 0.00 3.56
314 316 0.321298 ACCGACAAAGGGGATGAACG 60.321 55.000 0.00 0.00 35.02 3.95
318 320 2.483014 TAACACCGACAAAGGGGATG 57.517 50.000 0.00 0.00 38.30 3.51
323 325 4.393990 GGAGGTTATTAACACCGACAAAGG 59.606 45.833 8.73 0.00 39.56 3.11
328 330 5.351458 ATAACGGAGGTTATTAACACCGAC 58.649 41.667 31.39 10.09 44.89 4.79
329 331 5.596836 ATAACGGAGGTTATTAACACCGA 57.403 39.130 31.39 20.00 44.89 4.69
331 333 6.479990 GTGGTATAACGGAGGTTATTAACACC 59.520 42.308 8.73 9.57 44.89 4.16
373 375 3.427863 CCTTCGGTCTCGTTAGAAACAAC 59.572 47.826 0.00 0.00 37.69 3.32
382 384 1.475682 GTATGTCCCTTCGGTCTCGTT 59.524 52.381 0.00 0.00 37.69 3.85
388 390 0.245539 CACACGTATGTCCCTTCGGT 59.754 55.000 0.00 0.00 36.72 4.69
389 391 0.459585 CCACACGTATGTCCCTTCGG 60.460 60.000 0.00 0.00 36.72 4.30
396 398 0.721718 GAAGCAGCCACACGTATGTC 59.278 55.000 0.00 0.00 36.72 3.06
399 401 0.608130 TCTGAAGCAGCCACACGTAT 59.392 50.000 0.00 0.00 0.00 3.06
402 404 0.952497 ATGTCTGAAGCAGCCACACG 60.952 55.000 0.00 0.00 0.00 4.49
414 416 0.179113 TTGCGCGCATAGATGTCTGA 60.179 50.000 36.83 13.31 0.00 3.27
422 424 0.247419 CTGACAGTTTGCGCGCATAG 60.247 55.000 36.83 25.15 0.00 2.23
427 429 2.104770 TTCTGCTGACAGTTTGCGCG 62.105 55.000 0.00 0.00 44.77 6.86
429 431 0.385223 GCTTCTGCTGACAGTTTGCG 60.385 55.000 3.99 0.00 44.77 4.85
457 459 3.669122 GCATCGTCACCGTCTATGATTAC 59.331 47.826 0.00 0.00 35.01 1.89
464 466 1.203758 ACATTGCATCGTCACCGTCTA 59.796 47.619 0.00 0.00 35.01 2.59
476 478 1.067635 GCAGGTTTCCGAACATTGCAT 60.068 47.619 10.89 0.00 42.54 3.96
484 486 0.239879 GATTTGCGCAGGTTTCCGAA 59.760 50.000 11.31 0.00 0.00 4.30
487 489 0.171231 GAGGATTTGCGCAGGTTTCC 59.829 55.000 11.31 15.21 0.00 3.13
503 505 2.644676 TGACGTAGGAGTCAGATGAGG 58.355 52.381 0.00 0.00 45.18 3.86
553 556 4.511617 TGATTTTACGCCAAGATTTGCA 57.488 36.364 0.00 0.00 0.00 4.08
593 597 5.464722 CCAGATGAGAATTAACCATGTCTCG 59.535 44.000 4.79 0.00 39.52 4.04
595 599 6.566079 TCCAGATGAGAATTAACCATGTCT 57.434 37.500 0.00 0.00 0.00 3.41
664 670 6.534634 AGTTGAGGTAAATGCTCTAGTTTGT 58.465 36.000 0.00 0.00 0.00 2.83
705 732 3.857052 CTTAGTTTCAGCACCGTCCATA 58.143 45.455 0.00 0.00 0.00 2.74
852 880 6.382608 CCGTGCGAGCTATATATATGCTTAT 58.617 40.000 16.02 0.00 37.16 1.73
880 922 0.804933 GGTGTGATACTCGTTCGGCC 60.805 60.000 0.00 0.00 0.00 6.13
1696 1760 7.238486 AGCTCCTCGTTAAAGATATCATCAT 57.762 36.000 5.32 0.00 0.00 2.45
1853 1918 8.299570 GGAATCAGTGTCACATGAAATAGTTTT 58.700 33.333 5.62 0.00 0.00 2.43
1870 1935 3.504906 AGCACACAAATCTGGAATCAGTG 59.495 43.478 0.00 0.00 41.59 3.66
1949 2014 1.605710 GTATGCATGCTGGCCAACTAG 59.394 52.381 20.33 0.00 0.00 2.57
1952 2017 1.064621 CGTATGCATGCTGGCCAAC 59.935 57.895 20.33 1.82 0.00 3.77
1968 2033 1.472480 GTTGAATTGCATGCCCTACGT 59.528 47.619 16.68 0.00 0.00 3.57
1970 2035 3.514645 CAAGTTGAATTGCATGCCCTAC 58.485 45.455 16.68 8.78 0.00 3.18
1974 2047 1.729284 CCCAAGTTGAATTGCATGCC 58.271 50.000 16.68 0.00 0.00 4.40
1977 2050 3.706600 ATTGCCCAAGTTGAATTGCAT 57.293 38.095 3.87 0.00 0.00 3.96
1986 2059 1.616159 ACACGCTAATTGCCCAAGTT 58.384 45.000 0.00 0.00 38.78 2.66
1992 2065 3.691498 GATAACCAACACGCTAATTGCC 58.309 45.455 0.00 0.00 38.78 4.52
2121 2194 9.916397 GTAAATTACCAACTGAATAATCTGTCG 57.084 33.333 0.00 0.00 36.81 4.35
2288 2632 3.925299 GGTTGTCTAAGCTTTACTCGACC 59.075 47.826 3.20 8.97 31.21 4.79
2299 2643 6.598753 TTGCTATTTATCGGTTGTCTAAGC 57.401 37.500 0.00 0.00 0.00 3.09
2317 3039 7.053316 TGTACCTACAGTAACAGTTTTGCTA 57.947 36.000 0.00 0.00 31.05 3.49
2438 3196 5.356190 TCATGAATCTCCTTGCAGAAACATC 59.644 40.000 0.00 0.00 0.00 3.06
2439 3197 5.125097 GTCATGAATCTCCTTGCAGAAACAT 59.875 40.000 0.00 0.00 0.00 2.71
2440 3198 4.456911 GTCATGAATCTCCTTGCAGAAACA 59.543 41.667 0.00 0.00 0.00 2.83
2441 3199 4.456911 TGTCATGAATCTCCTTGCAGAAAC 59.543 41.667 0.00 0.00 0.00 2.78
2442 3200 4.456911 GTGTCATGAATCTCCTTGCAGAAA 59.543 41.667 0.00 0.00 0.00 2.52
2443 3201 4.005650 GTGTCATGAATCTCCTTGCAGAA 58.994 43.478 0.00 0.00 0.00 3.02
2444 3202 3.603532 GTGTCATGAATCTCCTTGCAGA 58.396 45.455 0.00 0.00 0.00 4.26
2445 3203 2.350804 CGTGTCATGAATCTCCTTGCAG 59.649 50.000 0.00 0.00 0.00 4.41
2446 3204 2.289631 ACGTGTCATGAATCTCCTTGCA 60.290 45.455 0.00 0.00 0.00 4.08
2447 3205 2.350522 ACGTGTCATGAATCTCCTTGC 58.649 47.619 0.00 0.00 0.00 4.01
2448 3206 3.865745 GGTACGTGTCATGAATCTCCTTG 59.134 47.826 0.00 0.00 0.00 3.61
2449 3207 3.118738 GGGTACGTGTCATGAATCTCCTT 60.119 47.826 0.00 0.00 0.00 3.36
2450 3208 2.431057 GGGTACGTGTCATGAATCTCCT 59.569 50.000 0.00 0.00 0.00 3.69
2451 3209 2.167693 TGGGTACGTGTCATGAATCTCC 59.832 50.000 0.00 0.00 0.00 3.71
2452 3210 3.448686 CTGGGTACGTGTCATGAATCTC 58.551 50.000 0.00 0.00 0.00 2.75
2453 3211 2.168521 CCTGGGTACGTGTCATGAATCT 59.831 50.000 0.00 0.00 0.00 2.40
2454 3212 2.093658 ACCTGGGTACGTGTCATGAATC 60.094 50.000 0.00 0.00 0.00 2.52
2455 3213 1.906574 ACCTGGGTACGTGTCATGAAT 59.093 47.619 0.00 0.00 0.00 2.57
2456 3214 1.001520 CACCTGGGTACGTGTCATGAA 59.998 52.381 0.00 0.00 0.00 2.57
2457 3215 0.606096 CACCTGGGTACGTGTCATGA 59.394 55.000 0.00 0.00 0.00 3.07
2458 3216 0.320374 ACACCTGGGTACGTGTCATG 59.680 55.000 0.00 0.00 38.90 3.07
2459 3217 2.754648 ACACCTGGGTACGTGTCAT 58.245 52.632 0.00 0.00 38.90 3.06
2460 3218 4.281102 ACACCTGGGTACGTGTCA 57.719 55.556 0.00 0.00 38.90 3.58
2462 3220 0.468585 TCAGACACCTGGGTACGTGT 60.469 55.000 0.00 4.22 45.67 4.49
2463 3221 0.677288 TTCAGACACCTGGGTACGTG 59.323 55.000 0.00 0.00 40.76 4.49
2464 3222 1.069668 GTTTCAGACACCTGGGTACGT 59.930 52.381 0.00 0.00 40.76 3.57
2465 3223 1.792006 GTTTCAGACACCTGGGTACG 58.208 55.000 0.00 0.00 40.76 3.67
2466 3224 1.607251 CCGTTTCAGACACCTGGGTAC 60.607 57.143 0.00 0.00 40.76 3.34
2467 3225 0.682852 CCGTTTCAGACACCTGGGTA 59.317 55.000 0.00 0.00 40.76 3.69
2468 3226 1.052124 TCCGTTTCAGACACCTGGGT 61.052 55.000 0.00 0.00 40.76 4.51
2469 3227 0.320771 CTCCGTTTCAGACACCTGGG 60.321 60.000 0.00 0.00 40.76 4.45
2470 3228 0.679505 TCTCCGTTTCAGACACCTGG 59.320 55.000 0.00 0.00 40.76 4.45
2471 3229 1.613925 TCTCTCCGTTTCAGACACCTG 59.386 52.381 0.00 0.00 41.74 4.00
2472 3230 1.996798 TCTCTCCGTTTCAGACACCT 58.003 50.000 0.00 0.00 0.00 4.00
2473 3231 2.231478 TGATCTCTCCGTTTCAGACACC 59.769 50.000 0.00 0.00 0.00 4.16
2509 3267 3.055891 GGTTCATTACATGCTTTTGGGCT 60.056 43.478 0.00 0.00 0.00 5.19
2517 3284 1.668419 GCTCCGGTTCATTACATGCT 58.332 50.000 0.00 0.00 0.00 3.79
2526 3297 2.281208 CGTTTGGGCTCCGGTTCA 60.281 61.111 0.00 0.00 0.00 3.18
2527 3298 3.733960 GCGTTTGGGCTCCGGTTC 61.734 66.667 0.00 0.00 0.00 3.62
2528 3299 3.860930 ATGCGTTTGGGCTCCGGTT 62.861 57.895 0.00 0.00 0.00 4.44
2529 3300 4.344865 ATGCGTTTGGGCTCCGGT 62.345 61.111 0.00 0.00 0.00 5.28
2530 3301 3.814268 CATGCGTTTGGGCTCCGG 61.814 66.667 0.00 0.00 0.00 5.14
2531 3302 4.481112 GCATGCGTTTGGGCTCCG 62.481 66.667 0.00 0.00 0.00 4.63
2533 3304 2.126346 GTGCATGCGTTTGGGCTC 60.126 61.111 14.09 0.00 0.00 4.70
2534 3305 4.041917 CGTGCATGCGTTTGGGCT 62.042 61.111 14.09 0.00 0.00 5.19
2535 3306 4.341502 ACGTGCATGCGTTTGGGC 62.342 61.111 14.09 0.00 43.04 5.36
2603 3397 1.287730 GCGCACATGGATCGATCTCC 61.288 60.000 23.96 11.68 35.74 3.71
2622 3416 2.105528 GCCGGGAATGCAATGCAG 59.894 61.111 14.98 0.00 43.65 4.41
2721 3516 2.264794 GACGGTGGCGATCAAGGT 59.735 61.111 0.00 0.00 0.00 3.50
2724 3519 2.126228 GACGACGGTGGCGATCAA 60.126 61.111 0.00 0.00 0.00 2.57
2727 3522 3.126879 TACGACGACGGTGGCGAT 61.127 61.111 11.54 0.00 44.46 4.58
2737 3532 0.392193 GAGAGGGGACAGTACGACGA 60.392 60.000 0.00 0.00 0.00 4.20
2744 3539 2.284995 GCTGGGAGAGGGGACAGT 60.285 66.667 0.00 0.00 33.62 3.55
2769 3564 3.656045 CGCCGGTGGGTGTTGTTC 61.656 66.667 7.26 0.00 39.07 3.18


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

AutoCloner maintained by Alex Coulton.