Multiple sequence alignment - TraesCS6A01G380700

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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 TraesCS6A01G380700 chr6A 100.000 2870 0 0 1 2870 600914573 600911704 0.000000e+00 5301.0
1 TraesCS6A01G380700 chr6A 83.686 1183 115 28 694 1826 601146337 601147491 0.000000e+00 1044.0
2 TraesCS6A01G380700 chr6A 84.795 684 89 9 1157 1830 600978185 600977507 0.000000e+00 673.0
3 TraesCS6A01G380700 chr6A 80.176 681 105 25 1162 1829 601033115 601032452 1.550000e-132 483.0
4 TraesCS6A01G380700 chr6A 76.786 616 106 28 1228 1830 601166299 601165708 7.720000e-81 311.0
5 TraesCS6A01G380700 chr6A 92.857 182 13 0 1161 1342 601138329 601138148 6.100000e-67 265.0
6 TraesCS6A01G380700 chr6A 78.037 428 73 18 1416 1829 601211702 601211282 1.710000e-62 250.0
7 TraesCS6A01G380700 chr6A 90.184 163 11 2 685 847 601033405 601033248 1.040000e-49 207.0
8 TraesCS6A01G380700 chr6A 96.591 88 3 0 549 636 7983290 7983203 2.300000e-31 147.0
9 TraesCS6A01G380700 chr5A 96.378 1049 30 1 1830 2870 312255812 312254764 0.000000e+00 1720.0
10 TraesCS6A01G380700 chr1A 95.627 1052 35 4 1826 2868 292177148 292176099 0.000000e+00 1677.0
11 TraesCS6A01G380700 chr2B 95.048 1050 41 3 1830 2870 474892212 474891165 0.000000e+00 1640.0
12 TraesCS6A01G380700 chr2B 88.060 201 23 1 2670 2870 309502309 309502508 1.330000e-58 237.0
13 TraesCS6A01G380700 chr2B 82.692 104 17 1 185 287 471440974 471441077 1.100000e-14 91.6
14 TraesCS6A01G380700 chr6B 94.370 1048 48 4 1831 2870 438406041 438404997 0.000000e+00 1598.0
15 TraesCS6A01G380700 chr6B 93.727 829 42 3 1826 2646 229137190 229138016 0.000000e+00 1234.0
16 TraesCS6A01G380700 chr6B 90.842 677 58 3 1157 1830 691633460 691632785 0.000000e+00 904.0
17 TraesCS6A01G380700 chr6B 87.593 540 35 7 1 515 691636288 691635756 5.290000e-167 597.0
18 TraesCS6A01G380700 chr6B 82.916 679 88 23 1161 1829 691783873 691783213 1.150000e-163 586.0
19 TraesCS6A01G380700 chr6B 75.753 598 81 38 649 1221 691787589 691788147 2.860000e-60 243.0
20 TraesCS6A01G380700 chr6B 91.304 161 14 0 634 794 691633901 691633741 1.340000e-53 220.0
21 TraesCS6A01G380700 chr6B 82.703 185 10 9 855 1039 691633740 691633578 8.290000e-31 145.0
22 TraesCS6A01G380700 chr6B 97.500 40 1 0 510 549 691633942 691633903 5.130000e-08 69.4
23 TraesCS6A01G380700 chr7B 93.136 1049 62 4 1831 2870 402820548 402821595 0.000000e+00 1530.0
24 TraesCS6A01G380700 chr7B 95.652 92 4 0 550 641 742411890 742411981 6.410000e-32 148.0
25 TraesCS6A01G380700 chr4A 97.270 879 23 1 1993 2870 327513134 327512256 0.000000e+00 1489.0
26 TraesCS6A01G380700 chr4A 90.071 141 6 1 1830 1962 327513267 327513127 2.940000e-40 176.0
27 TraesCS6A01G380700 chr5B 88.740 1048 98 10 1830 2861 400933259 400932216 0.000000e+00 1264.0
28 TraesCS6A01G380700 chr3D 91.220 877 64 8 1830 2696 515232498 515233371 0.000000e+00 1181.0
29 TraesCS6A01G380700 chr6D 84.081 1137 114 37 727 1826 454825424 454826530 0.000000e+00 1035.0
30 TraesCS6A01G380700 chr6D 83.376 1161 119 53 694 1829 454659440 454658329 0.000000e+00 1007.0
31 TraesCS6A01G380700 chr6D 85.967 848 70 25 994 1830 454749669 454748860 0.000000e+00 861.0
32 TraesCS6A01G380700 chr6D 84.360 422 57 8 1406 1826 454673006 454673419 3.440000e-109 405.0
33 TraesCS6A01G380700 chr6D 78.013 614 104 23 1228 1830 454734289 454734882 9.780000e-95 357.0
34 TraesCS6A01G380700 chr6D 76.006 671 124 15 1828 2488 138911560 138910917 2.150000e-81 313.0
35 TraesCS6A01G380700 chr6D 83.768 345 23 12 663 997 454776630 454776309 2.160000e-76 296.0
36 TraesCS6A01G380700 chr6D 92.000 175 13 1 1161 1335 454662411 454662584 7.940000e-61 244.0
37 TraesCS6A01G380700 chr4D 91.716 338 17 2 1830 2159 365176338 365176004 2.610000e-125 459.0
38 TraesCS6A01G380700 chr7A 91.304 184 7 2 1827 2002 158648150 158647968 2.860000e-60 243.0
39 TraesCS6A01G380700 chr7A 92.929 99 6 1 550 647 675402117 675402019 2.980000e-30 143.0
40 TraesCS6A01G380700 chr7D 92.045 176 6 1 1830 1997 177876004 177876179 1.030000e-59 241.0
41 TraesCS6A01G380700 chr3A 95.745 94 2 2 543 634 638994347 638994440 1.780000e-32 150.0
42 TraesCS6A01G380700 chr1B 95.556 90 4 0 545 634 681293951 681293862 8.290000e-31 145.0
43 TraesCS6A01G380700 chr2A 93.684 95 6 0 550 644 691662399 691662305 2.980000e-30 143.0
44 TraesCS6A01G380700 chrUn 95.506 89 3 1 546 634 274220447 274220534 1.070000e-29 141.0
45 TraesCS6A01G380700 chrUn 95.506 89 3 1 546 634 274228217 274228304 1.070000e-29 141.0
46 TraesCS6A01G380700 chr1D 93.617 94 6 0 550 643 197821652 197821559 1.070000e-29 141.0


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 TraesCS6A01G380700 chr6A 600911704 600914573 2869 True 5301.00 5301 100.0000 1 2870 1 chr6A.!!$R2 2869
1 TraesCS6A01G380700 chr6A 601146337 601147491 1154 False 1044.00 1044 83.6860 694 1826 1 chr6A.!!$F1 1132
2 TraesCS6A01G380700 chr6A 600977507 600978185 678 True 673.00 673 84.7950 1157 1830 1 chr6A.!!$R3 673
3 TraesCS6A01G380700 chr6A 601032452 601033405 953 True 345.00 483 85.1800 685 1829 2 chr6A.!!$R7 1144
4 TraesCS6A01G380700 chr6A 601165708 601166299 591 True 311.00 311 76.7860 1228 1830 1 chr6A.!!$R5 602
5 TraesCS6A01G380700 chr5A 312254764 312255812 1048 True 1720.00 1720 96.3780 1830 2870 1 chr5A.!!$R1 1040
6 TraesCS6A01G380700 chr1A 292176099 292177148 1049 True 1677.00 1677 95.6270 1826 2868 1 chr1A.!!$R1 1042
7 TraesCS6A01G380700 chr2B 474891165 474892212 1047 True 1640.00 1640 95.0480 1830 2870 1 chr2B.!!$R1 1040
8 TraesCS6A01G380700 chr6B 438404997 438406041 1044 True 1598.00 1598 94.3700 1831 2870 1 chr6B.!!$R1 1039
9 TraesCS6A01G380700 chr6B 229137190 229138016 826 False 1234.00 1234 93.7270 1826 2646 1 chr6B.!!$F1 820
10 TraesCS6A01G380700 chr6B 691783213 691783873 660 True 586.00 586 82.9160 1161 1829 1 chr6B.!!$R2 668
11 TraesCS6A01G380700 chr6B 691632785 691636288 3503 True 387.08 904 89.9884 1 1830 5 chr6B.!!$R3 1829
12 TraesCS6A01G380700 chr6B 691787589 691788147 558 False 243.00 243 75.7530 649 1221 1 chr6B.!!$F2 572
13 TraesCS6A01G380700 chr7B 402820548 402821595 1047 False 1530.00 1530 93.1360 1831 2870 1 chr7B.!!$F1 1039
14 TraesCS6A01G380700 chr4A 327512256 327513267 1011 True 832.50 1489 93.6705 1830 2870 2 chr4A.!!$R1 1040
15 TraesCS6A01G380700 chr5B 400932216 400933259 1043 True 1264.00 1264 88.7400 1830 2861 1 chr5B.!!$R1 1031
16 TraesCS6A01G380700 chr3D 515232498 515233371 873 False 1181.00 1181 91.2200 1830 2696 1 chr3D.!!$F1 866
17 TraesCS6A01G380700 chr6D 454825424 454826530 1106 False 1035.00 1035 84.0810 727 1826 1 chr6D.!!$F4 1099
18 TraesCS6A01G380700 chr6D 454658329 454659440 1111 True 1007.00 1007 83.3760 694 1829 1 chr6D.!!$R2 1135
19 TraesCS6A01G380700 chr6D 454748860 454749669 809 True 861.00 861 85.9670 994 1830 1 chr6D.!!$R3 836
20 TraesCS6A01G380700 chr6D 454734289 454734882 593 False 357.00 357 78.0130 1228 1830 1 chr6D.!!$F3 602
21 TraesCS6A01G380700 chr6D 138910917 138911560 643 True 313.00 313 76.0060 1828 2488 1 chr6D.!!$R1 660

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
692 2537 0.606944 TACGGCGCAAGGAAAACCAT 60.607 50.0 10.83 0.0 38.28 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 4079 0.106708 GGGCGCTGACTTCCATCATA 59.893 55.0 7.64 0.0 0.0 2.15 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
92 93 8.593492 AAGAAAGAACATGGCTTCAAAAATAC 57.407 30.769 0.00 0.00 0.00 1.89
100 101 9.807649 AACATGGCTTCAAAAATACTATCATTC 57.192 29.630 0.00 0.00 0.00 2.67
101 102 9.193806 ACATGGCTTCAAAAATACTATCATTCT 57.806 29.630 0.00 0.00 0.00 2.40
131 132 4.939509 TTGAGATAGCTAACCGCAAAAC 57.060 40.909 11.30 0.00 42.61 2.43
175 176 6.584563 ACGAAAATATTTATTGCAAAGCACGT 59.415 30.769 1.71 2.48 38.71 4.49
177 178 7.949428 CGAAAATATTTATTGCAAAGCACGTTT 59.051 29.630 1.71 0.00 38.71 3.60
182 183 3.980646 ATTGCAAAGCACGTTTCAGTA 57.019 38.095 1.71 0.00 38.71 2.74
183 184 3.332761 TTGCAAAGCACGTTTCAGTAG 57.667 42.857 0.00 0.00 38.71 2.57
227 228 7.336396 ACCTCGTTATAATTTTTGCTACCTCT 58.664 34.615 0.00 0.00 0.00 3.69
237 238 6.861065 TTTTTGCTACCTCTAGTGTCTTTG 57.139 37.500 0.00 0.00 0.00 2.77
247 248 5.127194 CCTCTAGTGTCTTTGTACTGCCATA 59.873 44.000 0.00 0.00 0.00 2.74
392 394 8.697846 TTTAACACTTTATGATCCTGAGTACG 57.302 34.615 0.00 0.00 0.00 3.67
399 424 4.576216 ATGATCCTGAGTACGCACTTAG 57.424 45.455 0.60 0.60 37.97 2.18
428 453 1.200020 GCGTCAGTTTTCATCCCCTTG 59.800 52.381 0.00 0.00 0.00 3.61
457 482 3.566742 ACTTTAGTGGTTTTTGTAGCGGG 59.433 43.478 0.00 0.00 0.00 6.13
471 496 0.682852 AGCGGGCAAAGTACACTGTA 59.317 50.000 0.00 0.00 0.00 2.74
502 527 9.586435 GTTAATAAAGTTAGACCCGTTTAGCTA 57.414 33.333 0.00 0.00 0.00 3.32
539 2384 2.825861 TTACCTGAACGGGAAGTCAC 57.174 50.000 6.68 0.00 36.97 3.67
549 2394 3.486383 ACGGGAAGTCACATTCAAACAT 58.514 40.909 0.00 0.00 0.00 2.71
550 2395 4.647611 ACGGGAAGTCACATTCAAACATA 58.352 39.130 0.00 0.00 0.00 2.29
551 2396 4.454504 ACGGGAAGTCACATTCAAACATAC 59.545 41.667 0.00 0.00 0.00 2.39
552 2397 4.695455 CGGGAAGTCACATTCAAACATACT 59.305 41.667 0.00 0.00 0.00 2.12
553 2398 5.163854 CGGGAAGTCACATTCAAACATACTC 60.164 44.000 0.00 0.00 0.00 2.59
554 2399 5.123979 GGGAAGTCACATTCAAACATACTCC 59.876 44.000 0.00 0.00 0.00 3.85
555 2400 5.123979 GGAAGTCACATTCAAACATACTCCC 59.876 44.000 0.00 0.00 0.00 4.30
556 2401 5.505181 AGTCACATTCAAACATACTCCCT 57.495 39.130 0.00 0.00 0.00 4.20
557 2402 5.491982 AGTCACATTCAAACATACTCCCTC 58.508 41.667 0.00 0.00 0.00 4.30
558 2403 5.249393 AGTCACATTCAAACATACTCCCTCT 59.751 40.000 0.00 0.00 0.00 3.69
559 2404 5.352569 GTCACATTCAAACATACTCCCTCTG 59.647 44.000 0.00 0.00 0.00 3.35
560 2405 5.013079 TCACATTCAAACATACTCCCTCTGT 59.987 40.000 0.00 0.00 0.00 3.41
561 2406 6.212589 TCACATTCAAACATACTCCCTCTGTA 59.787 38.462 0.00 0.00 0.00 2.74
562 2407 6.878923 CACATTCAAACATACTCCCTCTGTAA 59.121 38.462 0.00 0.00 0.00 2.41
563 2408 7.390440 CACATTCAAACATACTCCCTCTGTAAA 59.610 37.037 0.00 0.00 0.00 2.01
564 2409 7.390718 ACATTCAAACATACTCCCTCTGTAAAC 59.609 37.037 0.00 0.00 0.00 2.01
565 2410 6.681729 TCAAACATACTCCCTCTGTAAACT 57.318 37.500 0.00 0.00 0.00 2.66
566 2411 7.786046 TCAAACATACTCCCTCTGTAAACTA 57.214 36.000 0.00 0.00 0.00 2.24
567 2412 8.197592 TCAAACATACTCCCTCTGTAAACTAA 57.802 34.615 0.00 0.00 0.00 2.24
568 2413 8.822805 TCAAACATACTCCCTCTGTAAACTAAT 58.177 33.333 0.00 0.00 0.00 1.73
628 2473 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
629 2474 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
630 2475 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
631 2476 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
632 2477 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
644 2489 2.418197 CGGAGGGAGTAGATCGCAAAAA 60.418 50.000 0.00 0.00 43.20 1.94
692 2537 0.606944 TACGGCGCAAGGAAAACCAT 60.607 50.000 10.83 0.00 38.28 3.55
794 2644 1.244019 AATTTGCCGTGCTCCAGTCC 61.244 55.000 0.00 0.00 0.00 3.85
795 2645 2.410322 ATTTGCCGTGCTCCAGTCCA 62.410 55.000 0.00 0.00 0.00 4.02
919 2791 4.689549 TCCCCTCGACTTCCCGCA 62.690 66.667 0.00 0.00 0.00 5.69
928 2800 3.716006 CTTCCCGCACACGCACTG 61.716 66.667 0.00 0.00 38.40 3.66
1056 2938 1.476085 ACAAGCTCTCGATCCACTGAG 59.524 52.381 0.00 0.00 0.00 3.35
1113 3000 2.570135 GTAGTACTAGCTAGCCCGTGT 58.430 52.381 20.91 7.85 0.00 4.49
1135 3025 6.591313 GTTAGTTAGCCAACTAGCAATCTC 57.409 41.667 12.65 0.00 45.62 2.75
1141 3037 2.554142 CCAACTAGCAATCTCGCATCA 58.446 47.619 0.00 0.00 0.00 3.07
1146 3042 3.806521 ACTAGCAATCTCGCATCAACATC 59.193 43.478 0.00 0.00 0.00 3.06
1147 3043 1.945394 AGCAATCTCGCATCAACATCC 59.055 47.619 0.00 0.00 0.00 3.51
1148 3044 1.672363 GCAATCTCGCATCAACATCCA 59.328 47.619 0.00 0.00 0.00 3.41
1149 3045 2.540361 GCAATCTCGCATCAACATCCAC 60.540 50.000 0.00 0.00 0.00 4.02
1152 3048 3.817709 TCTCGCATCAACATCCACATA 57.182 42.857 0.00 0.00 0.00 2.29
1153 3049 4.341366 TCTCGCATCAACATCCACATAT 57.659 40.909 0.00 0.00 0.00 1.78
1154 3050 4.707105 TCTCGCATCAACATCCACATATT 58.293 39.130 0.00 0.00 0.00 1.28
1155 3051 4.512571 TCTCGCATCAACATCCACATATTG 59.487 41.667 0.00 0.00 0.00 1.90
1159 3080 5.388111 GCATCAACATCCACATATTGATCG 58.612 41.667 0.00 0.00 39.25 3.69
1344 3269 3.744426 CCCGGTAAGTCACTGTTTACTTG 59.256 47.826 13.05 2.81 36.62 3.16
1371 3300 1.873270 CGGTCGGCCCATGATCGATA 61.873 60.000 5.94 0.00 42.42 2.92
1391 3348 0.737367 TCGCTGAATTCTGTGGCTCG 60.737 55.000 21.29 12.51 0.00 5.03
1396 3353 3.182967 CTGAATTCTGTGGCTCGTCTAC 58.817 50.000 7.05 0.00 0.00 2.59
1403 3370 2.184579 GGCTCGTCTACTGGTGGC 59.815 66.667 0.00 0.00 0.00 5.01
1440 3407 1.355210 CAAAAGAACGCGCACCTGT 59.645 52.632 5.73 0.00 0.00 4.00
1556 3523 3.920093 CTTCCACGTTGCCTCCCCC 62.920 68.421 0.00 0.00 0.00 5.40
1566 3533 2.606519 CCTCCCCCGTCTCCAACA 60.607 66.667 0.00 0.00 0.00 3.33
1567 3534 1.995626 CCTCCCCCGTCTCCAACAT 60.996 63.158 0.00 0.00 0.00 2.71
1587 3554 1.203087 TCCCCGTCAGTTCACTTCCTA 60.203 52.381 0.00 0.00 0.00 2.94
1598 3565 0.596083 CACTTCCTATGCTCCGCTCG 60.596 60.000 0.00 0.00 0.00 5.03
1786 3787 2.117206 GCACATGGACCCCAACCA 59.883 61.111 0.00 0.00 36.95 3.67
1816 3817 1.873863 CAGTGCTCCACGAGACGTA 59.126 57.895 0.00 0.00 38.32 3.57
1826 3827 0.743701 ACGAGACGTACTGGAGCGAT 60.744 55.000 0.00 0.00 38.73 4.58
1880 3881 9.947433 TTGCCATTTTCATTGAATAAGAAGAAT 57.053 25.926 0.00 0.00 0.00 2.40
1919 3930 1.135139 GCTACAATCCTCACTCTCGCA 59.865 52.381 0.00 0.00 0.00 5.10
1946 3957 9.097257 GCATTACATTACACAAATATTTTGCCT 57.903 29.630 0.00 0.00 0.00 4.75
1949 3960 7.151999 ACATTACACAAATATTTTGCCTCGA 57.848 32.000 0.00 0.00 0.00 4.04
2054 4065 5.450412 GCATTTCGCTCTTTCCATATTTCCA 60.450 40.000 0.00 0.00 37.77 3.53
2170 4181 3.856508 CAGTTCGCTGGGTGTACG 58.143 61.111 0.00 0.00 41.40 3.67
2193 4204 4.000988 TCTTGTAAACCGAGCCAAGATTC 58.999 43.478 0.00 0.00 38.61 2.52
2204 4215 4.213513 GAGCCAAGATTCAATCATTCCCT 58.786 43.478 0.00 0.00 0.00 4.20
2209 4220 5.008019 CCAAGATTCAATCATTCCCTACACG 59.992 44.000 0.00 0.00 0.00 4.49
2330 4346 0.320374 CCTGTCAGCCGTCCAAACTA 59.680 55.000 0.00 0.00 0.00 2.24
2663 4682 9.716507 TTTTTCTTGTAGAAAGTTCAAAGATCG 57.283 29.630 2.52 0.00 44.14 3.69
2667 4686 5.849510 TGTAGAAAGTTCAAAGATCGTGGA 58.150 37.500 0.33 0.00 0.00 4.02
2758 4778 1.476488 ACAACAACCTTTGTGGCAGAC 59.524 47.619 0.00 0.00 44.59 3.51
2791 4813 5.502079 TCTTTGTCCTTTTGTACACAAGGA 58.498 37.500 30.92 30.92 45.32 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.064706 TCGGGTTGTGTTTTGTAAAGAAATATA 57.935 29.630 0.00 0.00 0.00 0.86
10 11 6.037726 GTCGGGTTGTGTTTTGTAAAGAAAT 58.962 36.000 0.00 0.00 0.00 2.17
11 12 5.048224 TGTCGGGTTGTGTTTTGTAAAGAAA 60.048 36.000 0.00 0.00 0.00 2.52
14 15 4.099824 GTGTCGGGTTGTGTTTTGTAAAG 58.900 43.478 0.00 0.00 0.00 1.85
23 24 1.344065 TCTATGGTGTCGGGTTGTGT 58.656 50.000 0.00 0.00 0.00 3.72
151 152 6.977316 ACGTGCTTTGCAATAAATATTTTCG 58.023 32.000 5.91 0.00 41.47 3.46
157 158 6.442952 ACTGAAACGTGCTTTGCAATAAATA 58.557 32.000 0.00 0.00 41.47 1.40
160 161 4.300189 ACTGAAACGTGCTTTGCAATAA 57.700 36.364 0.00 0.00 41.47 1.40
175 176 2.490903 GACCACCTAGCGACTACTGAAA 59.509 50.000 0.00 0.00 0.00 2.69
177 178 1.681166 GGACCACCTAGCGACTACTGA 60.681 57.143 0.00 0.00 0.00 3.41
182 183 1.330655 CCATGGACCACCTAGCGACT 61.331 60.000 5.56 0.00 37.04 4.18
183 184 1.144057 CCATGGACCACCTAGCGAC 59.856 63.158 5.56 0.00 37.04 5.19
227 228 7.390823 TCAATTATGGCAGTACAAAGACACTA 58.609 34.615 0.00 0.00 0.00 2.74
257 258 5.119694 GCGGGAGAAACTTCTGATCTATTT 58.880 41.667 0.00 0.00 37.73 1.40
378 380 3.243569 GCTAAGTGCGTACTCAGGATCAT 60.244 47.826 6.63 0.00 35.69 2.45
435 460 3.566742 CCCGCTACAAAAACCACTAAAGT 59.433 43.478 0.00 0.00 0.00 2.66
471 496 9.565090 AAACGGGTCTAACTTTATTAACTCTTT 57.435 29.630 0.00 0.00 0.00 2.52
484 509 8.096414 TGTTTTTATAGCTAAACGGGTCTAACT 58.904 33.333 0.00 0.00 37.12 2.24
539 2384 7.607991 AGTTTACAGAGGGAGTATGTTTGAATG 59.392 37.037 0.00 0.00 31.40 2.67
602 2447 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
603 2448 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
604 2449 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
605 2450 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
606 2451 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
609 2454 9.866655 TCTACTCCCTCCGTAAACTAATATAAA 57.133 33.333 0.00 0.00 0.00 1.40
611 2456 9.678260 GATCTACTCCCTCCGTAAACTAATATA 57.322 37.037 0.00 0.00 0.00 0.86
612 2457 7.336427 CGATCTACTCCCTCCGTAAACTAATAT 59.664 40.741 0.00 0.00 0.00 1.28
613 2458 6.652481 CGATCTACTCCCTCCGTAAACTAATA 59.348 42.308 0.00 0.00 0.00 0.98
614 2459 5.472820 CGATCTACTCCCTCCGTAAACTAAT 59.527 44.000 0.00 0.00 0.00 1.73
615 2460 4.818546 CGATCTACTCCCTCCGTAAACTAA 59.181 45.833 0.00 0.00 0.00 2.24
616 2461 4.384056 CGATCTACTCCCTCCGTAAACTA 58.616 47.826 0.00 0.00 0.00 2.24
617 2462 3.212685 CGATCTACTCCCTCCGTAAACT 58.787 50.000 0.00 0.00 0.00 2.66
618 2463 2.287487 GCGATCTACTCCCTCCGTAAAC 60.287 54.545 0.00 0.00 0.00 2.01
619 2464 1.952296 GCGATCTACTCCCTCCGTAAA 59.048 52.381 0.00 0.00 0.00 2.01
620 2465 1.134007 TGCGATCTACTCCCTCCGTAA 60.134 52.381 0.00 0.00 0.00 3.18
621 2466 0.471191 TGCGATCTACTCCCTCCGTA 59.529 55.000 0.00 0.00 0.00 4.02
622 2467 0.395311 TTGCGATCTACTCCCTCCGT 60.395 55.000 0.00 0.00 0.00 4.69
623 2468 0.744874 TTTGCGATCTACTCCCTCCG 59.255 55.000 0.00 0.00 0.00 4.63
624 2469 2.981859 TTTTGCGATCTACTCCCTCC 57.018 50.000 0.00 0.00 0.00 4.30
644 2489 9.927081 ACTATTGAATTATGTCTTGGATTCCTT 57.073 29.630 3.95 0.00 0.00 3.36
692 2537 4.068599 TCGTTGCATGACAAAACCTATGA 58.931 39.130 0.00 0.00 40.82 2.15
778 2627 2.410322 ATTGGACTGGAGCACGGCAA 62.410 55.000 0.00 0.00 0.00 4.52
851 2706 1.077501 GATACAGCCAGCCAGCCAA 60.078 57.895 0.00 0.00 0.00 4.52
928 2800 0.107214 TGCAATACTACCTGGGCTGC 60.107 55.000 0.00 0.00 0.00 5.25
997 2869 3.317149 ACGCGCTCCACTATTTATACTGA 59.683 43.478 5.73 0.00 0.00 3.41
1056 2938 2.293399 TGATGCTTGCTGATGATGATGC 59.707 45.455 0.00 0.00 0.00 3.91
1065 2947 1.271379 CCTTTGCTTGATGCTTGCTGA 59.729 47.619 0.00 0.00 43.37 4.26
1096 2978 2.948315 ACTAACACGGGCTAGCTAGTAC 59.052 50.000 21.62 14.52 0.00 2.73
1113 3000 5.348986 CGAGATTGCTAGTTGGCTAACTAA 58.651 41.667 21.32 10.95 45.91 2.24
1135 3025 4.816786 TCAATATGTGGATGTTGATGCG 57.183 40.909 0.00 0.00 35.45 4.73
1141 3037 5.034852 TGGTCGATCAATATGTGGATGTT 57.965 39.130 0.00 0.00 0.00 2.71
1146 3042 2.485426 GGCATGGTCGATCAATATGTGG 59.515 50.000 0.60 0.00 0.00 4.17
1147 3043 2.158254 CGGCATGGTCGATCAATATGTG 59.842 50.000 0.60 0.00 29.41 3.21
1148 3044 2.224281 ACGGCATGGTCGATCAATATGT 60.224 45.455 0.60 0.00 33.65 2.29
1149 3045 2.413112 GACGGCATGGTCGATCAATATG 59.587 50.000 0.60 0.00 33.65 1.78
1152 3048 2.992089 GACGGCATGGTCGATCAAT 58.008 52.632 0.60 0.00 33.65 2.57
1153 3049 4.513519 GACGGCATGGTCGATCAA 57.486 55.556 0.60 0.00 33.65 2.57
1159 3080 0.739462 TGTCAATCGACGGCATGGTC 60.739 55.000 0.00 0.00 45.80 4.02
1221 3142 2.917227 TGACGCAGACCAGCTCCA 60.917 61.111 0.00 0.00 0.00 3.86
1353 3278 0.537188 ATATCGATCATGGGCCGACC 59.463 55.000 0.00 0.00 40.81 4.79
1371 3300 1.661341 GAGCCACAGAATTCAGCGAT 58.339 50.000 8.44 0.00 0.00 4.58
1391 3348 0.250166 AAACCACGCCACCAGTAGAC 60.250 55.000 0.00 0.00 0.00 2.59
1396 3353 2.908073 GCAGAAACCACGCCACCAG 61.908 63.158 0.00 0.00 0.00 4.00
1403 3370 1.571460 GTCAGCTGCAGAAACCACG 59.429 57.895 20.43 0.00 0.00 4.94
1531 3498 3.047877 CAACGTGGAAGACCCCGC 61.048 66.667 0.00 0.00 33.66 6.13
1535 3502 1.671379 GGAGGCAACGTGGAAGACC 60.671 63.158 0.00 0.00 46.39 3.85
1556 3523 1.153628 GACGGGGATGTTGGAGACG 60.154 63.158 0.00 0.00 0.00 4.18
1566 3533 0.613777 GGAAGTGAACTGACGGGGAT 59.386 55.000 0.00 0.00 0.00 3.85
1567 3534 0.471211 AGGAAGTGAACTGACGGGGA 60.471 55.000 0.00 0.00 0.00 4.81
1806 3807 1.226046 CGCTCCAGTACGTCTCGTG 60.226 63.158 0.00 0.00 41.39 4.35
1880 3881 1.337823 GCTGGCCTCGACTCTAAAACA 60.338 52.381 3.32 0.00 0.00 2.83
1919 3930 9.097257 GGCAAAATATTTGTGTAATGTAATGCT 57.903 29.630 0.39 0.00 33.47 3.79
1946 3957 1.817911 TTATGGTGGTGCCGTGTCGA 61.818 55.000 0.00 0.00 41.21 4.20
1949 3960 1.002624 CCTTATGGTGGTGCCGTGT 60.003 57.895 0.00 0.00 41.21 4.49
2054 4065 9.606631 GACTTCCATCATACTACTGATTTCTTT 57.393 33.333 0.00 0.00 33.59 2.52
2068 4079 0.106708 GGGCGCTGACTTCCATCATA 59.893 55.000 7.64 0.00 0.00 2.15
2170 4181 2.762745 TCTTGGCTCGGTTTACAAGAC 58.237 47.619 0.00 0.00 42.95 3.01
2193 4204 0.937304 CCGCGTGTAGGGAATGATTG 59.063 55.000 4.92 0.00 34.27 2.67
2204 4215 1.140161 GCTACACCATCCGCGTGTA 59.860 57.895 4.92 5.82 42.56 2.90
2209 4220 4.830765 TGCCGCTACACCATCCGC 62.831 66.667 0.00 0.00 0.00 5.54
2663 4682 0.600255 CCCAAGGATATCGCGTCCAC 60.600 60.000 15.70 2.80 38.25 4.02
2667 4686 0.674534 GAGACCCAAGGATATCGCGT 59.325 55.000 5.77 0.00 0.00 6.01
2758 4778 5.856455 ACAAAAGGACAAAGATATTTTCGCG 59.144 36.000 0.00 0.00 0.00 5.87
2791 4813 2.090775 ACCTTGGGTCAACTTGGGAAAT 60.091 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.