Multiple sequence alignment - TraesCS2A01G250400

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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 TraesCS2A01G250400 chr2A 100.000 3472 0 0 1 3472 377569107 377572578 0.000000e+00 6412
1 TraesCS2A01G250400 chr2A 94.925 867 42 2 2605 3470 281103586 281102721 0.000000e+00 1356
2 TraesCS2A01G250400 chr2A 94.489 871 46 2 2603 3472 638138633 638139502 0.000000e+00 1341
3 TraesCS2A01G250400 chr2A 96.471 85 2 1 2511 2595 230764755 230764838 4.670000e-29 139
4 TraesCS2A01G250400 chr4D 94.911 2515 119 7 1 2512 426266277 426263769 0.000000e+00 3927
5 TraesCS2A01G250400 chr6D 94.559 2463 122 10 55 2510 249264292 249266749 0.000000e+00 3795
6 TraesCS2A01G250400 chr3A 93.879 2516 148 6 1 2512 204342958 204340445 0.000000e+00 3788
7 TraesCS2A01G250400 chr3A 93.556 2514 159 3 1 2512 204308729 204306217 0.000000e+00 3742
8 TraesCS2A01G250400 chr3A 92.874 2526 161 16 1 2512 174072938 174070418 0.000000e+00 3650
9 TraesCS2A01G250400 chr3A 95.046 868 42 1 2606 3472 333776101 333775234 0.000000e+00 1363
10 TraesCS2A01G250400 chr3A 94.598 870 45 2 2604 3472 643443127 643442259 0.000000e+00 1345
11 TraesCS2A01G250400 chr3A 94.737 95 2 2 2511 2605 204279029 204278938 1.000000e-30 145
12 TraesCS2A01G250400 chr3A 93.684 95 4 1 2511 2605 698802556 698802648 1.300000e-29 141
13 TraesCS2A01G250400 chr3D 93.872 2513 146 7 2 2512 254419840 254417334 0.000000e+00 3781
14 TraesCS2A01G250400 chr1D 93.646 2518 144 9 2 2512 285939050 285941558 0.000000e+00 3749
15 TraesCS2A01G250400 chr7A 93.564 2517 151 9 1 2511 421609607 421612118 0.000000e+00 3740
16 TraesCS2A01G250400 chr7A 95.392 868 38 2 2606 3472 511131807 511130941 0.000000e+00 1380
17 TraesCS2A01G250400 chr7A 95.282 869 39 2 2605 3472 234790743 234791610 0.000000e+00 1376
18 TraesCS2A01G250400 chr7A 96.842 95 2 1 2511 2605 421622917 421623010 1.290000e-34 158
19 TraesCS2A01G250400 chr6A 93.064 2523 161 12 1 2513 118303833 118306351 0.000000e+00 3677
20 TraesCS2A01G250400 chr6A 94.828 870 44 1 2604 3472 153770180 153769311 0.000000e+00 1356
21 TraesCS2A01G250400 chr1A 94.276 891 50 1 2583 3472 415377126 415378016 0.000000e+00 1362
22 TraesCS2A01G250400 chr1A 94.483 870 47 1 2604 3472 72967768 72968637 0.000000e+00 1339
23 TraesCS2A01G250400 chr5A 94.937 869 43 1 2605 3472 345997369 345996501 0.000000e+00 1360
24 TraesCS2A01G250400 chr5A 93.684 95 4 2 2511 2605 625234515 625234607 1.300000e-29 141
25 TraesCS2A01G250400 chr5A 93.548 93 1 2 2513 2605 649066221 649066308 2.170000e-27 134
26 TraesCS2A01G250400 chr5A 91.000 100 6 3 2511 2608 628615551 628615453 7.820000e-27 132
27 TraesCS2A01G250400 chr5A 91.579 95 5 2 2511 2605 649019261 649019352 1.010000e-25 128
28 TraesCS2A01G250400 chr4A 94.394 874 46 3 2601 3472 504510689 504511561 0.000000e+00 1339
29 TraesCS2A01G250400 chr4A 93.684 95 5 1 2511 2605 554025627 554025720 1.300000e-29 141
30 TraesCS2A01G250400 chr5D 93.684 95 1 2 2511 2605 205341184 205341273 1.680000e-28 137


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 TraesCS2A01G250400 chr2A 377569107 377572578 3471 False 6412 6412 100.000 1 3472 1 chr2A.!!$F2 3471
1 TraesCS2A01G250400 chr2A 281102721 281103586 865 True 1356 1356 94.925 2605 3470 1 chr2A.!!$R1 865
2 TraesCS2A01G250400 chr2A 638138633 638139502 869 False 1341 1341 94.489 2603 3472 1 chr2A.!!$F3 869
3 TraesCS2A01G250400 chr4D 426263769 426266277 2508 True 3927 3927 94.911 1 2512 1 chr4D.!!$R1 2511
4 TraesCS2A01G250400 chr6D 249264292 249266749 2457 False 3795 3795 94.559 55 2510 1 chr6D.!!$F1 2455
5 TraesCS2A01G250400 chr3A 204340445 204342958 2513 True 3788 3788 93.879 1 2512 1 chr3A.!!$R4 2511
6 TraesCS2A01G250400 chr3A 204306217 204308729 2512 True 3742 3742 93.556 1 2512 1 chr3A.!!$R3 2511
7 TraesCS2A01G250400 chr3A 174070418 174072938 2520 True 3650 3650 92.874 1 2512 1 chr3A.!!$R1 2511
8 TraesCS2A01G250400 chr3A 333775234 333776101 867 True 1363 1363 95.046 2606 3472 1 chr3A.!!$R5 866
9 TraesCS2A01G250400 chr3A 643442259 643443127 868 True 1345 1345 94.598 2604 3472 1 chr3A.!!$R6 868
10 TraesCS2A01G250400 chr3D 254417334 254419840 2506 True 3781 3781 93.872 2 2512 1 chr3D.!!$R1 2510
11 TraesCS2A01G250400 chr1D 285939050 285941558 2508 False 3749 3749 93.646 2 2512 1 chr1D.!!$F1 2510
12 TraesCS2A01G250400 chr7A 421609607 421612118 2511 False 3740 3740 93.564 1 2511 1 chr7A.!!$F2 2510
13 TraesCS2A01G250400 chr7A 511130941 511131807 866 True 1380 1380 95.392 2606 3472 1 chr7A.!!$R1 866
14 TraesCS2A01G250400 chr7A 234790743 234791610 867 False 1376 1376 95.282 2605 3472 1 chr7A.!!$F1 867
15 TraesCS2A01G250400 chr6A 118303833 118306351 2518 False 3677 3677 93.064 1 2513 1 chr6A.!!$F1 2512
16 TraesCS2A01G250400 chr6A 153769311 153770180 869 True 1356 1356 94.828 2604 3472 1 chr6A.!!$R1 868
17 TraesCS2A01G250400 chr1A 415377126 415378016 890 False 1362 1362 94.276 2583 3472 1 chr1A.!!$F2 889
18 TraesCS2A01G250400 chr1A 72967768 72968637 869 False 1339 1339 94.483 2604 3472 1 chr1A.!!$F1 868
19 TraesCS2A01G250400 chr5A 345996501 345997369 868 True 1360 1360 94.937 2605 3472 1 chr5A.!!$R1 867
20 TraesCS2A01G250400 chr4A 504510689 504511561 872 False 1339 1339 94.394 2601 3472 1 chr4A.!!$F1 871

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
942 957 1.340405 ACCATTGCCGCTTCAATCTCT 60.340 47.619 0.0 0.0 34.68 3.10 F
1141 1156 0.179045 GCTCCACGGCAAGGATATGT 60.179 55.000 0.0 0.0 33.99 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2258 0.179156 CTGCAACATCGGCCAATGAC 60.179 55.0 11.59 0.0 0.0 3.06 R
2779 2815 0.393944 GGGCTAGGGTTACACAAGGC 60.394 60.0 0.00 0.0 0.0 4.35 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
376 389 4.274950 ACCACTACGACACCAAATTTCAAG 59.725 41.667 0.00 0.00 0.00 3.02
387 400 1.803334 AATTTCAAGACCGCACGCTA 58.197 45.000 0.00 0.00 0.00 4.26
597 612 4.866508 ACAAGACTTAACATCCTCACGA 57.133 40.909 0.00 0.00 0.00 4.35
630 645 8.121305 TCAAAAAGCATATGTCACCTAAACAT 57.879 30.769 4.29 0.00 40.37 2.71
717 732 2.984562 TGACAAGACAAGTCAGTGCAA 58.015 42.857 2.72 0.00 40.80 4.08
766 781 3.579302 CTTCCAGGCCACCACCCA 61.579 66.667 5.01 0.00 0.00 4.51
778 793 3.632080 CACCCACGCCACCCACTA 61.632 66.667 0.00 0.00 0.00 2.74
862 877 3.716195 CCGCCTCCCACACATCCA 61.716 66.667 0.00 0.00 0.00 3.41
910 925 1.552337 TGTCTTCCATCTCTGCCTCAC 59.448 52.381 0.00 0.00 0.00 3.51
942 957 1.340405 ACCATTGCCGCTTCAATCTCT 60.340 47.619 0.00 0.00 34.68 3.10
1012 1027 0.181350 GAAGGCGATGGTGGAGGAAT 59.819 55.000 0.00 0.00 0.00 3.01
1074 1089 2.743664 CAGCAACCTCATCGATGTTCAA 59.256 45.455 24.09 4.84 0.00 2.69
1137 1152 1.841302 TTGAGCTCCACGGCAAGGAT 61.841 55.000 12.15 0.00 33.99 3.24
1141 1156 0.179045 GCTCCACGGCAAGGATATGT 60.179 55.000 0.00 0.00 33.99 2.29
1152 1167 4.130118 GCAAGGATATGTTGGAGATCGTT 58.870 43.478 0.00 0.00 32.00 3.85
1168 1183 3.926003 TTTGCACCAGCGAACCAA 58.074 50.000 0.00 0.00 46.23 3.67
1170 1185 0.749649 TTTGCACCAGCGAACCAAAT 59.250 45.000 0.00 0.00 46.23 2.32
1180 1195 1.444836 CGAACCAAATAAGGCCGACA 58.555 50.000 0.00 0.00 32.10 4.35
1222 1237 1.000896 AAGGGCAGCGGCTTGTATT 60.001 52.632 9.17 0.00 40.87 1.89
1238 1253 2.055100 GTATTCGAGCTTCATCGGAGC 58.945 52.381 0.00 0.00 42.93 4.70
1260 1275 0.987294 ATGTGGAGTTCACCAGGGAG 59.013 55.000 0.00 0.00 45.48 4.30
1576 1595 9.638239 GAACTTGATGCACCAAATTAATTTCTA 57.362 29.630 10.53 0.00 0.00 2.10
1619 1638 6.282167 AGATTCTGATCTTGATGCACTAGTG 58.718 40.000 18.93 18.93 39.63 2.74
1770 1790 7.553044 GCACTGGTATAGGTCTTTTATTCAACT 59.447 37.037 0.00 0.00 0.00 3.16
1817 1839 8.851541 TCAAGCAGCACATATATCATTGAATA 57.148 30.769 0.00 0.00 0.00 1.75
1977 2005 5.873712 GCATCTACCTCATGGATTATCACTG 59.126 44.000 0.00 0.00 37.04 3.66
2045 2074 1.774254 ACCTTCAATGTGTGTCTCCCA 59.226 47.619 0.00 0.00 0.00 4.37
2130 2159 1.421268 TCAGCATTGGAGGTGACAAGT 59.579 47.619 0.00 0.00 40.73 3.16
2171 2200 4.935352 TTTGGAGATCAAACCCAACAAG 57.065 40.909 7.95 0.00 40.14 3.16
2189 2222 1.527034 AGTTCATCAACATGCAGCGT 58.473 45.000 0.00 0.00 34.60 5.07
2225 2258 3.067106 ACACACCAGCAAATACTTCGAG 58.933 45.455 0.00 0.00 0.00 4.04
2228 2261 3.244078 ACACCAGCAAATACTTCGAGTCA 60.244 43.478 0.00 0.00 0.00 3.41
2285 2318 5.819991 TCCTACAAAGGCATGAAGAAGAAT 58.180 37.500 0.00 0.00 43.31 2.40
2409 2445 4.024893 AGACAATTGACAACATCGTGACAC 60.025 41.667 13.59 0.00 0.00 3.67
2415 2451 0.934496 CAACATCGTGACACGTTGGT 59.066 50.000 31.56 26.83 43.38 3.67
2420 2456 4.109766 ACATCGTGACACGTTGGTATATG 58.890 43.478 31.56 24.44 43.38 1.78
2435 2471 5.428253 TGGTATATGTCAAAAGAGCAGGAC 58.572 41.667 0.00 0.00 0.00 3.85
2458 2494 1.273609 TGACCCCTACTACCACTGCAT 60.274 52.381 0.00 0.00 0.00 3.96
2513 2549 0.041839 GTGTTGCTCGCACTTCTGTG 60.042 55.000 0.00 0.00 46.37 3.66
2514 2550 0.461870 TGTTGCTCGCACTTCTGTGT 60.462 50.000 0.00 0.00 45.44 3.72
2515 2551 0.233332 GTTGCTCGCACTTCTGTGTC 59.767 55.000 0.00 0.00 45.44 3.67
2516 2552 0.179086 TTGCTCGCACTTCTGTGTCA 60.179 50.000 0.00 0.00 45.44 3.58
2517 2553 0.598419 TGCTCGCACTTCTGTGTCAG 60.598 55.000 0.00 0.00 45.44 3.51
2518 2554 0.598680 GCTCGCACTTCTGTGTCAGT 60.599 55.000 0.00 0.00 45.44 3.41
2519 2555 1.335964 GCTCGCACTTCTGTGTCAGTA 60.336 52.381 0.00 0.00 45.44 2.74
2520 2556 2.320367 CTCGCACTTCTGTGTCAGTAC 58.680 52.381 0.00 0.00 45.44 2.73
2521 2557 1.679153 TCGCACTTCTGTGTCAGTACA 59.321 47.619 0.00 0.00 45.44 2.90
2522 2558 2.100087 TCGCACTTCTGTGTCAGTACAA 59.900 45.455 0.00 0.00 45.44 2.41
2523 2559 2.218759 CGCACTTCTGTGTCAGTACAAC 59.781 50.000 0.00 0.00 45.44 3.32
2524 2560 3.458189 GCACTTCTGTGTCAGTACAACT 58.542 45.455 0.00 0.00 45.44 3.16
2525 2561 4.617959 GCACTTCTGTGTCAGTACAACTA 58.382 43.478 0.00 0.00 45.44 2.24
2526 2562 5.230942 GCACTTCTGTGTCAGTACAACTAT 58.769 41.667 0.00 0.00 45.44 2.12
2527 2563 5.119279 GCACTTCTGTGTCAGTACAACTATG 59.881 44.000 0.00 0.00 45.44 2.23
2528 2564 5.119279 CACTTCTGTGTCAGTACAACTATGC 59.881 44.000 0.00 0.00 37.36 3.14
2529 2565 4.864704 TCTGTGTCAGTACAACTATGCA 57.135 40.909 0.00 0.00 37.36 3.96
2530 2566 4.556233 TCTGTGTCAGTACAACTATGCAC 58.444 43.478 0.00 0.00 37.36 4.57
2531 2567 3.659786 TGTGTCAGTACAACTATGCACC 58.340 45.455 0.00 0.00 37.36 5.01
2532 2568 2.666508 GTGTCAGTACAACTATGCACCG 59.333 50.000 0.00 0.00 37.36 4.94
2533 2569 2.559231 TGTCAGTACAACTATGCACCGA 59.441 45.455 0.00 0.00 30.91 4.69
2534 2570 3.179830 GTCAGTACAACTATGCACCGAG 58.820 50.000 0.00 0.00 0.00 4.63
2535 2571 2.165641 TCAGTACAACTATGCACCGAGG 59.834 50.000 0.00 0.00 0.00 4.63
2536 2572 1.480954 AGTACAACTATGCACCGAGGG 59.519 52.381 0.00 0.00 0.00 4.30
2537 2573 0.828022 TACAACTATGCACCGAGGGG 59.172 55.000 0.00 0.00 40.11 4.79
2538 2574 1.819632 CAACTATGCACCGAGGGGC 60.820 63.158 9.87 9.87 36.48 5.80
2539 2575 2.297895 AACTATGCACCGAGGGGCA 61.298 57.895 22.32 22.32 45.23 5.36
2540 2576 2.109799 CTATGCACCGAGGGGCAG 59.890 66.667 24.15 8.19 44.24 4.85
2541 2577 2.687200 TATGCACCGAGGGGCAGT 60.687 61.111 24.15 14.32 44.24 4.40
2542 2578 2.930385 CTATGCACCGAGGGGCAGTG 62.930 65.000 24.15 14.86 44.24 3.66
2548 2584 4.077184 CGAGGGGCAGTGCGGTTA 62.077 66.667 9.45 0.00 0.00 2.85
2549 2585 2.590092 GAGGGGCAGTGCGGTTAT 59.410 61.111 9.45 0.00 0.00 1.89
2550 2586 1.077716 GAGGGGCAGTGCGGTTATT 60.078 57.895 9.45 0.00 0.00 1.40
2551 2587 1.077716 AGGGGCAGTGCGGTTATTC 60.078 57.895 9.45 0.00 0.00 1.75
2552 2588 1.077716 GGGGCAGTGCGGTTATTCT 60.078 57.895 9.45 0.00 0.00 2.40
2553 2589 1.376609 GGGGCAGTGCGGTTATTCTG 61.377 60.000 9.45 0.00 0.00 3.02
2554 2590 0.676782 GGGCAGTGCGGTTATTCTGT 60.677 55.000 9.45 0.00 0.00 3.41
2555 2591 1.165270 GGCAGTGCGGTTATTCTGTT 58.835 50.000 9.45 0.00 0.00 3.16
2556 2592 1.539827 GGCAGTGCGGTTATTCTGTTT 59.460 47.619 9.45 0.00 0.00 2.83
2557 2593 2.414161 GGCAGTGCGGTTATTCTGTTTC 60.414 50.000 9.45 0.00 0.00 2.78
2558 2594 2.414161 GCAGTGCGGTTATTCTGTTTCC 60.414 50.000 0.00 0.00 0.00 3.13
2559 2595 2.161609 CAGTGCGGTTATTCTGTTTCCC 59.838 50.000 0.00 0.00 0.00 3.97
2560 2596 1.471287 GTGCGGTTATTCTGTTTCCCC 59.529 52.381 0.00 0.00 0.00 4.81
2561 2597 1.353022 TGCGGTTATTCTGTTTCCCCT 59.647 47.619 0.00 0.00 0.00 4.79
2562 2598 2.014857 GCGGTTATTCTGTTTCCCCTC 58.985 52.381 0.00 0.00 0.00 4.30
2563 2599 2.640184 CGGTTATTCTGTTTCCCCTCC 58.360 52.381 0.00 0.00 0.00 4.30
2564 2600 2.682858 CGGTTATTCTGTTTCCCCTCCC 60.683 54.545 0.00 0.00 0.00 4.30
2565 2601 2.357881 GGTTATTCTGTTTCCCCTCCCC 60.358 54.545 0.00 0.00 0.00 4.81
2566 2602 1.603634 TATTCTGTTTCCCCTCCCCC 58.396 55.000 0.00 0.00 0.00 5.40
2590 2626 3.632080 CGCACCCACACACCCCTA 61.632 66.667 0.00 0.00 0.00 3.53
2591 2627 2.840576 GCACCCACACACCCCTAA 59.159 61.111 0.00 0.00 0.00 2.69
2592 2628 1.303317 GCACCCACACACCCCTAAG 60.303 63.158 0.00 0.00 0.00 2.18
2593 2629 1.774894 GCACCCACACACCCCTAAGA 61.775 60.000 0.00 0.00 0.00 2.10
2594 2630 0.991920 CACCCACACACCCCTAAGAT 59.008 55.000 0.00 0.00 0.00 2.40
2595 2631 2.193127 CACCCACACACCCCTAAGATA 58.807 52.381 0.00 0.00 0.00 1.98
2596 2632 2.170607 CACCCACACACCCCTAAGATAG 59.829 54.545 0.00 0.00 0.00 2.08
2597 2633 2.045326 ACCCACACACCCCTAAGATAGA 59.955 50.000 0.00 0.00 0.00 1.98
2598 2634 3.311402 ACCCACACACCCCTAAGATAGAT 60.311 47.826 0.00 0.00 0.00 1.98
2599 2635 4.078219 ACCCACACACCCCTAAGATAGATA 60.078 45.833 0.00 0.00 0.00 1.98
2638 2674 0.267960 ATTAGGGGGTCTCCGGACAT 59.732 55.000 0.00 0.00 43.77 3.06
2660 2696 1.809684 GGACTATATCCTTTGGCCGC 58.190 55.000 0.00 0.00 45.22 6.53
2749 2785 3.443681 GTGGAAGGCAAGCTAAGCAATAA 59.556 43.478 12.48 0.00 0.00 1.40
2779 2815 4.957684 ATATCTCCTCCTTTGTAACCGG 57.042 45.455 0.00 0.00 0.00 5.28
2995 3033 2.553466 CCCGAACCTGGGTAAAACATCA 60.553 50.000 0.00 0.00 44.76 3.07
3004 3042 3.076785 TGGGTAAAACATCATGTCCCCTT 59.923 43.478 9.34 0.00 31.60 3.95
3035 3073 0.739462 CATCCGCCTTAGACGCACAA 60.739 55.000 0.00 0.00 0.00 3.33
3277 3315 3.249189 TGGCCACCAGGTCAGGTC 61.249 66.667 0.00 0.00 46.77 3.85
3411 3450 1.153745 GTGTTCAGGAGATCGCGCT 60.154 57.895 5.56 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 224 6.925718 CAGATCGTTCATTGAGGTATGTACAT 59.074 38.462 13.93 13.93 0.00 2.29
224 231 3.181490 CGACCAGATCGTTCATTGAGGTA 60.181 47.826 0.00 0.00 46.25 3.08
376 389 4.446385 TGTAATTTCATATAGCGTGCGGTC 59.554 41.667 0.00 0.00 0.00 4.79
561 574 8.671028 GTTAAGTCTTGTTTTTCCACTGAAGTA 58.329 33.333 0.00 0.00 0.00 2.24
617 632 5.510520 GGCATTTTGGAATGTTTAGGTGACA 60.511 40.000 1.63 0.00 43.67 3.58
630 645 3.055963 GTGGTGATGATGGCATTTTGGAA 60.056 43.478 0.00 0.00 34.11 3.53
717 732 6.212955 CGTCCAATTCAAATGGTTTTACTGT 58.787 36.000 0.00 0.00 39.09 3.55
766 781 4.388499 CCGCTTAGTGGGTGGCGT 62.388 66.667 3.47 0.00 45.11 5.68
778 793 2.912025 CCCTTGTGGCAACCGCTT 60.912 61.111 0.00 0.00 38.60 4.68
862 877 1.213094 CTTTGAAGGTGCGTCGACGT 61.213 55.000 35.48 18.40 42.22 4.34
910 925 0.890683 GCAATGGTGGTTTCTGGGAG 59.109 55.000 0.00 0.00 0.00 4.30
942 957 3.085533 AGTTTGTGGTTTGTGTGCAGTA 58.914 40.909 0.00 0.00 0.00 2.74
1074 1089 3.764466 CGCTTCTCGCTGGGGACT 61.764 66.667 0.00 0.00 36.13 3.85
1137 1152 3.006940 GGTGCAAACGATCTCCAACATA 58.993 45.455 0.00 0.00 0.00 2.29
1141 1156 1.522668 CTGGTGCAAACGATCTCCAA 58.477 50.000 0.00 0.00 0.00 3.53
1152 1167 1.610363 TATTTGGTTCGCTGGTGCAA 58.390 45.000 0.00 0.00 39.64 4.08
1168 1183 2.238646 TCATCACCTTGTCGGCCTTATT 59.761 45.455 0.00 0.00 35.61 1.40
1170 1185 1.207089 CTCATCACCTTGTCGGCCTTA 59.793 52.381 0.00 0.00 35.61 2.69
1180 1195 2.380365 TGAGCCTGCTCATCACCTT 58.620 52.632 17.46 0.00 46.80 3.50
1210 1225 0.108138 AAGCTCGAATACAAGCCGCT 60.108 50.000 0.00 0.00 39.39 5.52
1222 1237 1.032114 TCAGCTCCGATGAAGCTCGA 61.032 55.000 0.00 0.00 41.12 4.04
1576 1595 7.012138 CAGAATCTATGCTAGCACATCAAGTTT 59.988 37.037 22.07 12.83 0.00 2.66
1789 1811 8.173542 TCAATGATATATGTGCTGCTTGATTT 57.826 30.769 0.00 0.00 0.00 2.17
2130 2159 1.421268 ACCAGACTTGTTCAGCATCCA 59.579 47.619 0.00 0.00 0.00 3.41
2171 2200 3.120199 ACTTACGCTGCATGTTGATGAAC 60.120 43.478 0.00 0.00 0.00 3.18
2225 2258 0.179156 CTGCAACATCGGCCAATGAC 60.179 55.000 11.59 0.00 0.00 3.06
2228 2261 2.713967 GCCTGCAACATCGGCCAAT 61.714 57.895 2.24 0.00 37.86 3.16
2256 2289 2.311542 TCATGCCTTTGTAGGATGGGTT 59.688 45.455 0.00 0.00 45.05 4.11
2285 2318 2.626785 TGGTGTTCTCCCTTGTCCATA 58.373 47.619 0.00 0.00 0.00 2.74
2367 2403 2.631062 TCTTCCATGACTTGTACGTGGT 59.369 45.455 0.00 0.00 42.85 4.16
2409 2445 5.220662 CCTGCTCTTTTGACATATACCAACG 60.221 44.000 0.00 0.00 0.00 4.10
2415 2451 4.119862 GCGTCCTGCTCTTTTGACATATA 58.880 43.478 0.00 0.00 41.73 0.86
2435 2471 0.683504 AGTGGTAGTAGGGGTCAGCG 60.684 60.000 0.00 0.00 0.00 5.18
2513 2549 3.179830 CTCGGTGCATAGTTGTACTGAC 58.820 50.000 0.00 0.00 45.40 3.51
2515 2551 2.540515 CCTCGGTGCATAGTTGTACTG 58.459 52.381 0.00 0.00 43.81 2.74
2516 2552 1.480954 CCCTCGGTGCATAGTTGTACT 59.519 52.381 0.00 0.00 38.40 2.73
2517 2553 1.472728 CCCCTCGGTGCATAGTTGTAC 60.473 57.143 0.00 0.00 37.70 2.90
2518 2554 0.828022 CCCCTCGGTGCATAGTTGTA 59.172 55.000 0.00 0.00 0.00 2.41
2519 2555 1.602237 CCCCTCGGTGCATAGTTGT 59.398 57.895 0.00 0.00 0.00 3.32
2520 2556 1.819632 GCCCCTCGGTGCATAGTTG 60.820 63.158 0.00 0.00 0.00 3.16
2521 2557 2.257409 CTGCCCCTCGGTGCATAGTT 62.257 60.000 0.00 0.00 36.79 2.24
2522 2558 2.687200 TGCCCCTCGGTGCATAGT 60.687 61.111 0.00 0.00 31.31 2.12
2523 2559 2.109799 CTGCCCCTCGGTGCATAG 59.890 66.667 0.00 0.00 36.79 2.23
2524 2560 2.687200 ACTGCCCCTCGGTGCATA 60.687 61.111 0.00 0.00 36.79 3.14
2525 2561 4.415150 CACTGCCCCTCGGTGCAT 62.415 66.667 0.00 0.00 44.30 3.96
2531 2567 2.869503 AATAACCGCACTGCCCCTCG 62.870 60.000 0.00 0.00 0.00 4.63
2532 2568 1.077716 AATAACCGCACTGCCCCTC 60.078 57.895 0.00 0.00 0.00 4.30
2533 2569 1.077716 GAATAACCGCACTGCCCCT 60.078 57.895 0.00 0.00 0.00 4.79
2534 2570 1.077716 AGAATAACCGCACTGCCCC 60.078 57.895 0.00 0.00 0.00 5.80
2535 2571 0.676782 ACAGAATAACCGCACTGCCC 60.677 55.000 0.00 0.00 34.25 5.36
2536 2572 1.165270 AACAGAATAACCGCACTGCC 58.835 50.000 0.00 0.00 34.25 4.85
2537 2573 2.414161 GGAAACAGAATAACCGCACTGC 60.414 50.000 0.00 0.00 34.25 4.40
2538 2574 2.161609 GGGAAACAGAATAACCGCACTG 59.838 50.000 0.00 0.00 36.58 3.66
2539 2575 2.433436 GGGAAACAGAATAACCGCACT 58.567 47.619 0.00 0.00 0.00 4.40
2540 2576 1.471287 GGGGAAACAGAATAACCGCAC 59.529 52.381 0.00 0.00 34.48 5.34
2541 2577 1.353022 AGGGGAAACAGAATAACCGCA 59.647 47.619 0.00 0.00 36.31 5.69
2542 2578 2.014857 GAGGGGAAACAGAATAACCGC 58.985 52.381 0.00 0.00 0.00 5.68
2543 2579 2.640184 GGAGGGGAAACAGAATAACCG 58.360 52.381 0.00 0.00 0.00 4.44
2544 2580 2.357881 GGGGAGGGGAAACAGAATAACC 60.358 54.545 0.00 0.00 0.00 2.85
2545 2581 2.357881 GGGGGAGGGGAAACAGAATAAC 60.358 54.545 0.00 0.00 0.00 1.89
2546 2582 1.927371 GGGGGAGGGGAAACAGAATAA 59.073 52.381 0.00 0.00 0.00 1.40
2547 2583 1.603634 GGGGGAGGGGAAACAGAATA 58.396 55.000 0.00 0.00 0.00 1.75
2548 2584 2.410039 GGGGGAGGGGAAACAGAAT 58.590 57.895 0.00 0.00 0.00 2.40
2549 2585 3.931707 GGGGGAGGGGAAACAGAA 58.068 61.111 0.00 0.00 0.00 3.02
2573 2609 3.185299 TTAGGGGTGTGTGGGTGCG 62.185 63.158 0.00 0.00 0.00 5.34
2574 2610 1.303317 CTTAGGGGTGTGTGGGTGC 60.303 63.158 0.00 0.00 0.00 5.01
2575 2611 0.991920 ATCTTAGGGGTGTGTGGGTG 59.008 55.000 0.00 0.00 0.00 4.61
2576 2612 2.045326 TCTATCTTAGGGGTGTGTGGGT 59.955 50.000 0.00 0.00 0.00 4.51
2577 2613 2.759355 TCTATCTTAGGGGTGTGTGGG 58.241 52.381 0.00 0.00 0.00 4.61
2578 2614 6.467677 CATTATCTATCTTAGGGGTGTGTGG 58.532 44.000 0.00 0.00 0.00 4.17
2579 2615 6.467677 CCATTATCTATCTTAGGGGTGTGTG 58.532 44.000 0.00 0.00 0.00 3.82
2580 2616 5.548056 CCCATTATCTATCTTAGGGGTGTGT 59.452 44.000 0.00 0.00 0.00 3.72
2581 2617 5.548056 ACCCATTATCTATCTTAGGGGTGTG 59.452 44.000 0.00 0.00 45.47 3.82
2582 2618 5.738401 ACCCATTATCTATCTTAGGGGTGT 58.262 41.667 0.00 0.00 45.47 4.16
2585 2621 5.426833 CCTCACCCATTATCTATCTTAGGGG 59.573 48.000 0.00 0.00 39.15 4.79
2586 2622 5.426833 CCCTCACCCATTATCTATCTTAGGG 59.573 48.000 0.00 0.00 40.66 3.53
2587 2623 6.264528 TCCCTCACCCATTATCTATCTTAGG 58.735 44.000 0.00 0.00 0.00 2.69
2588 2624 6.957020 ACTCCCTCACCCATTATCTATCTTAG 59.043 42.308 0.00 0.00 0.00 2.18
2589 2625 6.875469 ACTCCCTCACCCATTATCTATCTTA 58.125 40.000 0.00 0.00 0.00 2.10
2590 2626 5.731924 ACTCCCTCACCCATTATCTATCTT 58.268 41.667 0.00 0.00 0.00 2.40
2591 2627 5.337788 GACTCCCTCACCCATTATCTATCT 58.662 45.833 0.00 0.00 0.00 1.98
2592 2628 4.468153 GGACTCCCTCACCCATTATCTATC 59.532 50.000 0.00 0.00 0.00 2.08
2593 2629 4.110426 AGGACTCCCTCACCCATTATCTAT 59.890 45.833 0.00 0.00 38.86 1.98
2594 2630 3.471306 AGGACTCCCTCACCCATTATCTA 59.529 47.826 0.00 0.00 38.86 1.98
2595 2631 2.251338 AGGACTCCCTCACCCATTATCT 59.749 50.000 0.00 0.00 38.86 1.98
2596 2632 2.370189 CAGGACTCCCTCACCCATTATC 59.630 54.545 0.00 0.00 42.02 1.75
2597 2633 2.412591 CAGGACTCCCTCACCCATTAT 58.587 52.381 0.00 0.00 42.02 1.28
2598 2634 1.625228 CCAGGACTCCCTCACCCATTA 60.625 57.143 0.00 0.00 42.02 1.90
2599 2635 0.916358 CCAGGACTCCCTCACCCATT 60.916 60.000 0.00 0.00 42.02 3.16
2660 2696 5.891451 TCGTATCTTCATAGTCCAACAGTG 58.109 41.667 0.00 0.00 0.00 3.66
2779 2815 0.393944 GGGCTAGGGTTACACAAGGC 60.394 60.000 0.00 0.00 0.00 4.35
2833 2869 6.097129 TGGTATGATTGTATGTTGTCCTACGA 59.903 38.462 0.00 0.00 0.00 3.43
2927 2963 7.939039 CCCTATGTCCTGCTTGATTTATTCTTA 59.061 37.037 0.00 0.00 0.00 2.10
2995 3033 2.197465 GTAACAGGAGGAAGGGGACAT 58.803 52.381 0.00 0.00 0.00 3.06
3178 3216 3.653344 CCGAACACAAAGATCTGTCTGA 58.347 45.455 0.00 0.00 34.13 3.27
3180 3218 2.417719 GCCGAACACAAAGATCTGTCT 58.582 47.619 0.00 0.00 35.82 3.41
3277 3315 2.415512 GCCGTGTAGTTTAAGCTTCCAG 59.584 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.