Multiple sequence alignment - TraesCS4A01G463100

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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 TraesCS4A01G463100 chr4A 100.000 3540 0 0 1 3540 726977905 726981444 0.000000e+00 6538.0
1 TraesCS4A01G463100 chr4A 94.295 1560 80 5 1063 2615 727054991 727056548 0.000000e+00 2379.0
2 TraesCS4A01G463100 chr4A 91.260 389 26 7 2613 2998 727056758 727057141 1.130000e-144 523.0
3 TraesCS4A01G463100 chr7D 93.194 2013 115 6 611 2615 11072213 11070215 0.000000e+00 2939.0
4 TraesCS4A01G463100 chr7D 85.223 494 52 6 2613 3105 11069911 11069438 4.110000e-134 488.0
5 TraesCS4A01G463100 chr7D 90.625 160 12 3 590 746 11254082 11253923 3.580000e-50 209.0
6 TraesCS4A01G463100 chr7A 92.582 2049 141 9 569 2615 10255611 10253572 0.000000e+00 2931.0
7 TraesCS4A01G463100 chr7A 91.752 2061 139 23 570 2615 10353557 10351513 0.000000e+00 2835.0
8 TraesCS4A01G463100 chr7A 92.298 1571 89 15 844 2410 10608851 10610393 0.000000e+00 2202.0
9 TraesCS4A01G463100 chr7A 94.235 850 46 2 1768 2615 10279846 10278998 0.000000e+00 1295.0
10 TraesCS4A01G463100 chr7A 92.655 708 43 5 1063 1766 10280632 10279930 0.000000e+00 1011.0
11 TraesCS4A01G463100 chr7A 92.047 591 40 5 2031 2615 10208388 10207799 0.000000e+00 824.0
12 TraesCS4A01G463100 chr7A 89.818 658 35 11 30 665 641529942 641529295 0.000000e+00 815.0
13 TraesCS4A01G463100 chr7A 89.514 658 37 11 30 665 646921436 646920789 0.000000e+00 804.0
14 TraesCS4A01G463100 chr7A 89.418 567 32 13 1 545 10255887 10255327 0.000000e+00 689.0
15 TraesCS4A01G463100 chr7A 88.770 561 42 11 1 545 10608127 10608682 0.000000e+00 667.0
16 TraesCS4A01G463100 chr7A 85.639 571 46 18 1 545 10353831 10353271 5.130000e-158 568.0
17 TraesCS4A01G463100 chr7A 89.948 388 32 6 2613 2998 10253261 10252879 8.830000e-136 494.0
18 TraesCS4A01G463100 chr7A 83.806 494 59 6 2613 3105 10207487 10207014 1.940000e-122 449.0
19 TraesCS4A01G463100 chr7A 88.235 340 30 9 2769 3106 10278393 10278062 7.120000e-107 398.0
20 TraesCS4A01G463100 chr7A 90.175 285 28 0 569 853 10608398 10608682 4.320000e-99 372.0
21 TraesCS4A01G463100 chr7A 82.798 436 54 13 3107 3535 10350894 10350473 1.550000e-98 370.0
22 TraesCS4A01G463100 chr7A 93.860 228 9 3 3318 3540 10206552 10206325 4.380000e-89 339.0
23 TraesCS4A01G463100 chr7A 87.361 269 33 1 2613 2881 10351209 10350942 1.230000e-79 307.0
24 TraesCS4A01G463100 chr7A 91.406 128 6 3 3 129 10286698 10286575 1.690000e-38 171.0
25 TraesCS4A01G463100 chr7A 92.958 71 5 0 2700 2770 10278568 10278498 1.740000e-18 104.0
26 TraesCS4A01G463100 chr5A 89.514 658 37 12 30 665 579649715 579649068 0.000000e+00 804.0
27 TraesCS4A01G463100 chr6A 88.956 661 41 11 27 665 409920133 409920783 0.000000e+00 787.0
28 TraesCS4A01G463100 chr3A 88.906 658 41 11 30 665 19077743 19077096 0.000000e+00 782.0
29 TraesCS4A01G463100 chr2A 96.875 32 1 0 213 244 17418332 17418301 2.000000e-03 54.7


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 TraesCS4A01G463100 chr4A 726977905 726981444 3539 False 6538.000000 6538 100.000000 1 3540 1 chr4A.!!$F1 3539
1 TraesCS4A01G463100 chr4A 727054991 727057141 2150 False 1451.000000 2379 92.777500 1063 2998 2 chr4A.!!$F2 1935
2 TraesCS4A01G463100 chr7D 11069438 11072213 2775 True 1713.500000 2939 89.208500 611 3105 2 chr7D.!!$R2 2494
3 TraesCS4A01G463100 chr7A 10252879 10255887 3008 True 1371.333333 2931 90.649333 1 2998 3 chr7A.!!$R5 2997
4 TraesCS4A01G463100 chr7A 10608127 10610393 2266 False 1080.333333 2202 90.414333 1 2410 3 chr7A.!!$F1 2409
5 TraesCS4A01G463100 chr7A 10350473 10353831 3358 True 1020.000000 2835 86.887500 1 3535 4 chr7A.!!$R7 3534
6 TraesCS4A01G463100 chr7A 641529295 641529942 647 True 815.000000 815 89.818000 30 665 1 chr7A.!!$R2 635
7 TraesCS4A01G463100 chr7A 646920789 646921436 647 True 804.000000 804 89.514000 30 665 1 chr7A.!!$R3 635
8 TraesCS4A01G463100 chr7A 10278062 10280632 2570 True 702.000000 1295 92.020750 1063 3106 4 chr7A.!!$R6 2043
9 TraesCS4A01G463100 chr7A 10206325 10208388 2063 True 537.333333 824 89.904333 2031 3540 3 chr7A.!!$R4 1509
10 TraesCS4A01G463100 chr5A 579649068 579649715 647 True 804.000000 804 89.514000 30 665 1 chr5A.!!$R1 635
11 TraesCS4A01G463100 chr6A 409920133 409920783 650 False 787.000000 787 88.956000 27 665 1 chr6A.!!$F1 638
12 TraesCS4A01G463100 chr3A 19077096 19077743 647 True 782.000000 782 88.906000 30 665 1 chr3A.!!$R1 635

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
746 779 0.395686 ATGCTGTCTCTGCTGTGTGT 59.604 50.0 0.00 0.0 0.0 3.72 F
1270 1494 0.237235 TGCGCGTTGAACCAGATTTC 59.763 50.0 8.43 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1899 2.624838 CAGAAAAGCAAGAAAGCCTGGA 59.375 45.455 0.0 0.0 34.23 3.86 R
3080 3932 1.144936 GCAGTAGAGGGCGAGCAAT 59.855 57.895 0.0 0.0 0.00 3.56 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
43 44 1.592223 CCACCCTCTTCGACCTCAC 59.408 63.158 0.00 0.00 0.00 3.51
124 132 4.076394 GCCTGTACCTGAAAATGTACCAA 58.924 43.478 0.00 0.00 37.19 3.67
125 133 4.082949 GCCTGTACCTGAAAATGTACCAAC 60.083 45.833 0.00 0.00 37.19 3.77
126 134 5.067273 CCTGTACCTGAAAATGTACCAACA 58.933 41.667 0.00 0.00 40.69 3.33
128 136 6.882140 CCTGTACCTGAAAATGTACCAACATA 59.118 38.462 0.00 0.00 45.79 2.29
129 137 7.148306 CCTGTACCTGAAAATGTACCAACATAC 60.148 40.741 0.00 0.00 45.79 2.39
130 138 7.225011 TGTACCTGAAAATGTACCAACATACA 58.775 34.615 0.00 0.00 45.79 2.29
147 173 7.975058 CCAACATACAATTGCATCAATCTGTAA 59.025 33.333 5.05 0.00 34.53 2.41
184 210 6.996509 TCAAGCTTTGGATGCTAAATTTCTT 58.003 32.000 0.00 0.00 40.22 2.52
185 211 7.444299 TCAAGCTTTGGATGCTAAATTTCTTT 58.556 30.769 0.00 0.00 40.22 2.52
233 259 1.820581 GCATCTGCATTGCCATGGT 59.179 52.632 14.67 0.00 41.59 3.55
444 475 2.024918 CTGCTGTGTGCGGTTTCTT 58.975 52.632 0.00 0.00 46.63 2.52
454 485 2.228822 GTGCGGTTTCTTGGATGTCATT 59.771 45.455 0.00 0.00 0.00 2.57
455 486 3.438781 GTGCGGTTTCTTGGATGTCATTA 59.561 43.478 0.00 0.00 0.00 1.90
456 487 3.438781 TGCGGTTTCTTGGATGTCATTAC 59.561 43.478 0.00 0.00 0.00 1.89
495 526 4.655649 TCCATTCAGCTATCTGTACCATGT 59.344 41.667 0.00 0.00 41.10 3.21
551 582 8.157476 CCTCTATTAAGTTATTACCATGGTGCT 58.843 37.037 28.17 16.15 0.00 4.40
552 583 8.902540 TCTATTAAGTTATTACCATGGTGCTG 57.097 34.615 28.17 5.65 0.00 4.41
553 584 5.828299 TTAAGTTATTACCATGGTGCTGC 57.172 39.130 28.17 13.05 0.00 5.25
554 585 3.652057 AGTTATTACCATGGTGCTGCT 57.348 42.857 28.17 15.02 0.00 4.24
555 586 3.545703 AGTTATTACCATGGTGCTGCTC 58.454 45.455 28.17 12.71 0.00 4.26
556 587 3.200825 AGTTATTACCATGGTGCTGCTCT 59.799 43.478 28.17 14.64 0.00 4.09
595 626 3.362870 TTGGTCACCACATATGCATCA 57.637 42.857 0.19 0.00 30.78 3.07
732 765 5.006844 GCTCATCTTGCTGCTATATATGCTG 59.993 44.000 0.00 3.13 0.00 4.41
746 779 0.395686 ATGCTGTCTCTGCTGTGTGT 59.604 50.000 0.00 0.00 0.00 3.72
755 788 3.323115 TCTCTGCTGTGTGTGATTTCTCT 59.677 43.478 0.00 0.00 0.00 3.10
785 818 7.058525 TCATTCTCATCTATGCACTTCCATTT 58.941 34.615 0.00 0.00 0.00 2.32
798 831 5.125417 GCACTTCCATTTGGCTTATCTGTAA 59.875 40.000 0.00 0.00 34.44 2.41
872 1089 7.990541 TTCCATAAAATCATTGCGAGATTTG 57.009 32.000 10.37 1.92 42.98 2.32
876 1093 3.705043 AATCATTGCGAGATTTGAGCC 57.295 42.857 0.00 0.00 31.99 4.70
885 1102 3.726607 CGAGATTTGAGCCTAGCAAGAT 58.273 45.455 0.00 0.00 0.00 2.40
892 1109 9.061435 AGATTTGAGCCTAGCAAGATAAATTAC 57.939 33.333 0.00 0.00 0.00 1.89
903 1120 4.162040 AGATAAATTACAGCTGCAGCCT 57.838 40.909 34.39 22.09 43.38 4.58
924 1141 5.115480 CCTCTTACTTTCTGATTCTGCTCC 58.885 45.833 0.00 0.00 0.00 4.70
925 1142 5.337894 CCTCTTACTTTCTGATTCTGCTCCA 60.338 44.000 0.00 0.00 0.00 3.86
939 1156 3.324846 TCTGCTCCATGTTAGACAGTTGT 59.675 43.478 12.26 0.00 0.00 3.32
992 1210 1.470632 CGCTGCTTCGATTTCCTCTCT 60.471 52.381 0.00 0.00 0.00 3.10
1080 1298 2.619849 CCTGATCTTCCTGCCACATGTT 60.620 50.000 0.00 0.00 0.00 2.71
1086 1304 2.885135 TCCTGCCACATGTTCATTCT 57.115 45.000 0.00 0.00 0.00 2.40
1180 1399 0.948623 CAAGATGGTGCGTGTCCGAA 60.949 55.000 0.00 0.00 35.63 4.30
1256 1480 3.425713 AGCCACAGATTGTGCGCG 61.426 61.111 0.00 0.00 46.51 6.86
1270 1494 0.237235 TGCGCGTTGAACCAGATTTC 59.763 50.000 8.43 0.00 0.00 2.17
1546 1775 6.346477 TGTGGGATAGCTAACTGTATGATC 57.654 41.667 0.00 0.00 0.00 2.92
1667 1899 8.416329 GCAGATATTTTTCTGTATCCAATGGTT 58.584 33.333 0.00 0.00 44.10 3.67
1763 1996 7.573968 ATGGTCCTTGCTATGAACTAATTTC 57.426 36.000 0.00 0.00 34.41 2.17
1766 2081 4.574828 TCCTTGCTATGAACTAATTTCGCC 59.425 41.667 0.00 0.00 36.97 5.54
2040 2357 3.255642 TGAATTGCCTACAAAGAAGGTGC 59.744 43.478 0.00 0.00 39.77 5.01
2044 2361 1.453155 CCTACAAAGAAGGTGCGCAT 58.547 50.000 15.91 0.00 0.00 4.73
2047 2364 1.317613 ACAAAGAAGGTGCGCATTCA 58.682 45.000 24.73 0.00 37.82 2.57
2106 2423 3.132289 GGCCCAAATACCCTTAGCTTTTC 59.868 47.826 0.00 0.00 0.00 2.29
2165 2482 4.374843 TGCTGTTTCATTATGCACCATC 57.625 40.909 0.00 0.00 0.00 3.51
2335 2654 3.534554 TGCTGTACTATGATTGTGCAGG 58.465 45.455 21.40 8.11 44.45 4.85
2540 2866 6.114187 TGCAGGTTTCCGAGATATTATGAT 57.886 37.500 0.00 0.00 0.00 2.45
2586 2919 4.868067 ACTGTTACACTTCAGGACTAACG 58.132 43.478 0.00 0.00 36.17 3.18
2610 2943 5.091552 ACTCCAGTTTCTATTGGTCCTACA 58.908 41.667 0.00 0.00 35.89 2.74
2650 3301 3.181445 TGTTAGAATTGGTGTGCCTCAGT 60.181 43.478 0.00 0.00 35.27 3.41
2733 3462 4.648762 ACACTAGATGTTGAGAGGGATCTG 59.351 45.833 0.00 0.00 38.98 2.90
2746 3475 3.034635 AGGGATCTGCTCGTACAATTCT 58.965 45.455 0.00 0.00 0.00 2.40
2749 3478 3.487574 GGATCTGCTCGTACAATTCTTCG 59.512 47.826 0.00 0.00 0.00 3.79
2844 3679 8.388656 TGTAAAAGATAAATAGAGTGTCCCCT 57.611 34.615 0.00 0.00 0.00 4.79
2865 3700 5.221185 CCCTTGCATCCATCTTTTATGTCTG 60.221 44.000 0.00 0.00 0.00 3.51
2866 3701 5.359009 CCTTGCATCCATCTTTTATGTCTGT 59.641 40.000 0.00 0.00 0.00 3.41
3000 3852 8.739039 CAATAATTACATGAAAGTTGGACAGGA 58.261 33.333 0.00 0.00 0.00 3.86
3005 3857 4.895297 ACATGAAAGTTGGACAGGAAACAT 59.105 37.500 0.00 0.00 0.00 2.71
3006 3858 4.916983 TGAAAGTTGGACAGGAAACATG 57.083 40.909 0.00 0.00 0.00 3.21
3021 3873 6.581171 GGAAACATGTCAGATTTTCCTTCT 57.419 37.500 14.77 0.00 42.53 2.85
3023 3875 8.110860 GGAAACATGTCAGATTTTCCTTCTAA 57.889 34.615 14.77 0.00 42.53 2.10
3026 3878 9.793259 AAACATGTCAGATTTTCCTTCTAACTA 57.207 29.630 0.00 0.00 0.00 2.24
3080 3932 4.920112 CAACGTGGTGCCCGGTGA 62.920 66.667 0.00 0.00 45.59 4.02
3146 4262 6.650427 TTACATAGGCTTCATACTGATCGT 57.350 37.500 0.00 0.00 0.00 3.73
3171 4287 1.407618 GACTTCGGCCCTGTTTGTTTT 59.592 47.619 0.00 0.00 0.00 2.43
3178 4294 3.390135 GGCCCTGTTTGTTTTAGCTTTC 58.610 45.455 0.00 0.00 0.00 2.62
3198 4314 5.801531 TTCGGCAGCTAATTCTATTAGGA 57.198 39.130 8.15 0.00 0.00 2.94
3217 4333 7.581213 TTAGGAAAAATCAGAAGCTGAAACA 57.419 32.000 0.78 0.00 44.04 2.83
3220 4336 7.330262 AGGAAAAATCAGAAGCTGAAACAAAA 58.670 30.769 0.78 0.00 44.04 2.44
3222 4338 7.904977 GGAAAAATCAGAAGCTGAAACAAAAAC 59.095 33.333 0.78 0.00 44.04 2.43
3234 4377 7.657354 AGCTGAAACAAAAACCTATTTGGAATC 59.343 33.333 4.96 1.41 43.10 2.52
3245 4388 4.100498 CCTATTTGGAATCTGCTTTGCCAT 59.900 41.667 0.00 0.00 38.35 4.40
3247 4390 1.927487 TGGAATCTGCTTTGCCATGT 58.073 45.000 0.00 0.00 0.00 3.21
3248 4391 2.250031 TGGAATCTGCTTTGCCATGTT 58.750 42.857 0.00 0.00 0.00 2.71
3249 4392 2.633967 TGGAATCTGCTTTGCCATGTTT 59.366 40.909 0.00 0.00 0.00 2.83
3250 4393 3.831333 TGGAATCTGCTTTGCCATGTTTA 59.169 39.130 0.00 0.00 0.00 2.01
3251 4394 4.176271 GGAATCTGCTTTGCCATGTTTAC 58.824 43.478 0.00 0.00 0.00 2.01
3252 4395 4.082026 GGAATCTGCTTTGCCATGTTTACT 60.082 41.667 0.00 0.00 0.00 2.24
3253 4396 5.473039 GAATCTGCTTTGCCATGTTTACTT 58.527 37.500 0.00 0.00 0.00 2.24
3254 4397 4.503741 TCTGCTTTGCCATGTTTACTTC 57.496 40.909 0.00 0.00 0.00 3.01
3302 4445 1.881973 GTGAATCAGCTTTGCCAGTGA 59.118 47.619 0.00 0.00 0.00 3.41
3305 4448 0.886563 ATCAGCTTTGCCAGTGAAGC 59.113 50.000 6.89 6.89 46.57 3.86
3308 4451 1.208614 GCTTTGCCAGTGAAGCGAG 59.791 57.895 0.00 0.00 38.89 5.03
3312 4455 1.758440 TTGCCAGTGAAGCGAGTCCT 61.758 55.000 0.00 0.00 0.00 3.85
3313 4456 0.898326 TGCCAGTGAAGCGAGTCCTA 60.898 55.000 0.00 0.00 0.00 2.94
3314 4457 0.246635 GCCAGTGAAGCGAGTCCTAA 59.753 55.000 0.00 0.00 0.00 2.69
3315 4458 1.997669 CCAGTGAAGCGAGTCCTAAC 58.002 55.000 0.00 0.00 0.00 2.34
3316 4459 1.618861 CAGTGAAGCGAGTCCTAACG 58.381 55.000 0.00 0.00 0.00 3.18
3323 4466 0.735287 GCGAGTCCTAACGTGGTTCC 60.735 60.000 0.00 0.00 0.00 3.62
3405 4548 7.062749 TCTTTCTCCTACTAGAAACAAAGCA 57.937 36.000 0.00 0.00 39.86 3.91
3453 4600 8.450964 CGCTAATTATGTGAAGAAGAAAAAGGA 58.549 33.333 0.00 0.00 0.00 3.36
3454 4601 9.561270 GCTAATTATGTGAAGAAGAAAAAGGAC 57.439 33.333 0.00 0.00 0.00 3.85
3463 4610 9.880064 GTGAAGAAGAAAAAGGACTTTACATAC 57.120 33.333 0.00 0.00 30.97 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.266055 CGAAGAGGGTGGCCTGTC 59.734 66.667 3.32 0.00 0.00 3.51
96 104 4.816385 ACATTTTCAGGTACAGGCATATCG 59.184 41.667 0.00 0.00 0.00 2.92
125 133 9.338291 GCTATTACAGATTGATGCAATTGTATG 57.662 33.333 14.16 2.50 33.90 2.39
126 134 9.293404 AGCTATTACAGATTGATGCAATTGTAT 57.707 29.630 8.93 8.93 33.90 2.29
128 136 7.283807 TGAGCTATTACAGATTGATGCAATTGT 59.716 33.333 7.40 0.00 33.90 2.71
129 137 7.645402 TGAGCTATTACAGATTGATGCAATTG 58.355 34.615 0.00 0.00 33.90 2.32
130 138 7.812690 TGAGCTATTACAGATTGATGCAATT 57.187 32.000 0.00 0.00 33.90 2.32
147 173 3.710209 AAGCTTGAGGTGTTGAGCTAT 57.290 42.857 0.00 0.00 44.17 2.97
184 210 5.523188 CACAAAAACTAATCAAGCAGCCAAA 59.477 36.000 0.00 0.00 0.00 3.28
185 211 5.049167 CACAAAAACTAATCAAGCAGCCAA 58.951 37.500 0.00 0.00 0.00 4.52
382 413 3.564027 GCACGCCCACGCTCATAC 61.564 66.667 0.00 0.00 45.53 2.39
383 414 3.770040 AGCACGCCCACGCTCATA 61.770 61.111 0.00 0.00 45.53 2.15
444 475 6.268387 TGCATAGATGAGAGTAATGACATCCA 59.732 38.462 0.00 0.00 39.61 3.41
454 485 6.324770 TGAATGGAAGTGCATAGATGAGAGTA 59.675 38.462 0.00 0.00 0.00 2.59
455 486 5.129980 TGAATGGAAGTGCATAGATGAGAGT 59.870 40.000 0.00 0.00 0.00 3.24
456 487 5.608449 TGAATGGAAGTGCATAGATGAGAG 58.392 41.667 0.00 0.00 0.00 3.20
595 626 9.603921 CCCAATCAAATGATAAATACTTGCTTT 57.396 29.630 0.00 0.00 33.73 3.51
613 644 5.163205 CCTGTACCATCATCTACCCAATCAA 60.163 44.000 0.00 0.00 0.00 2.57
684 717 6.233434 CACACCCATGCTCATACTACATAAT 58.767 40.000 0.00 0.00 0.00 1.28
685 718 5.610398 CACACCCATGCTCATACTACATAA 58.390 41.667 0.00 0.00 0.00 1.90
688 721 2.419990 GCACACCCATGCTCATACTACA 60.420 50.000 0.00 0.00 42.62 2.74
690 723 2.620251 GCACACCCATGCTCATACTA 57.380 50.000 0.00 0.00 42.62 1.82
701 734 0.607217 CAGCAAGATGAGCACACCCA 60.607 55.000 0.00 0.00 0.00 4.51
713 746 5.479724 AGAGACAGCATATATAGCAGCAAGA 59.520 40.000 0.00 0.00 0.00 3.02
714 747 5.577554 CAGAGACAGCATATATAGCAGCAAG 59.422 44.000 0.00 3.02 0.00 4.01
732 765 3.397482 AGAAATCACACACAGCAGAGAC 58.603 45.455 0.00 0.00 0.00 3.36
755 788 8.039538 GGAAGTGCATAGATGAGAATGATATCA 58.960 37.037 8.10 8.10 0.00 2.15
785 818 2.093181 ACGGCATGTTACAGATAAGCCA 60.093 45.455 13.06 0.00 40.58 4.75
798 831 6.759272 AGAGTGATATGTATTAACGGCATGT 58.241 36.000 0.00 0.00 0.00 3.21
853 1070 5.357878 AGGCTCAAATCTCGCAATGATTTTA 59.642 36.000 6.01 0.12 40.76 1.52
856 1073 3.285484 AGGCTCAAATCTCGCAATGATT 58.715 40.909 0.00 0.00 35.88 2.57
872 1089 5.994668 AGCTGTAATTTATCTTGCTAGGCTC 59.005 40.000 0.00 0.00 0.00 4.70
876 1093 6.609237 TGCAGCTGTAATTTATCTTGCTAG 57.391 37.500 16.64 0.00 0.00 3.42
885 1102 3.634397 AGAGGCTGCAGCTGTAATTTA 57.366 42.857 35.82 0.00 41.70 1.40
892 1109 1.736681 GAAAGTAAGAGGCTGCAGCTG 59.263 52.381 35.82 10.11 41.70 4.24
903 1120 5.745312 TGGAGCAGAATCAGAAAGTAAGA 57.255 39.130 0.00 0.00 0.00 2.10
939 1156 0.887836 CCTCAGCAAGAACAGCAGCA 60.888 55.000 0.00 0.00 0.00 4.41
1080 1298 4.517285 GGTTCATAAGCAGGACAGAATGA 58.483 43.478 0.00 0.00 39.69 2.57
1086 1304 2.551270 AGAGGGTTCATAAGCAGGACA 58.449 47.619 0.00 0.00 0.00 4.02
1180 1399 2.507407 AATGCACGGTAACAGGGATT 57.493 45.000 0.00 0.00 0.00 3.01
1256 1480 8.099364 TCACAAGAATAGAAATCTGGTTCAAC 57.901 34.615 10.82 0.00 28.32 3.18
1270 1494 4.821805 ACAACCACAGGTTCACAAGAATAG 59.178 41.667 0.00 0.00 43.05 1.73
1546 1775 9.502145 AATTAACAGTGCAAATTGTGTATATCG 57.498 29.630 0.00 0.00 0.00 2.92
1667 1899 2.624838 CAGAAAAGCAAGAAAGCCTGGA 59.375 45.455 0.00 0.00 34.23 3.86
1763 1996 7.387673 TCCACAGATTGATATTATTAACTGGCG 59.612 37.037 0.00 0.00 0.00 5.69
2106 2423 5.634859 GCACTGAAAGGTAAAATTGACCATG 59.365 40.000 1.76 0.00 39.65 3.66
2156 2473 4.016444 ACAAATTAGAACCGATGGTGCAT 58.984 39.130 0.00 0.00 35.34 3.96
2165 2482 9.490663 GACAAAATGATCTACAAATTAGAACCG 57.509 33.333 0.00 0.00 0.00 4.44
2335 2654 4.142902 CCACCATATTAATCACGATTCCGC 60.143 45.833 0.00 0.00 39.95 5.54
2470 2794 7.942990 ACCACAAGAGCTCACTATATTACTAC 58.057 38.462 17.77 0.00 0.00 2.73
2479 2803 4.833380 AGTTTAGACCACAAGAGCTCACTA 59.167 41.667 17.77 4.95 0.00 2.74
2540 2866 3.610040 TTCTGAAGCGAATTGAGGCTA 57.390 42.857 0.00 0.00 38.88 3.93
2586 2919 4.828072 AGGACCAATAGAAACTGGAGTC 57.172 45.455 0.00 0.00 36.49 3.36
2610 2943 3.396260 ACAAAGCTGCAGCATTTCAAT 57.604 38.095 38.24 15.14 45.16 2.57
2693 3344 8.826710 CATCTAGTGTTTTCAAGTGTAACAGAA 58.173 33.333 0.00 0.00 41.43 3.02
2733 3462 5.041940 AGGATAACGAAGAATTGTACGAGC 58.958 41.667 0.00 0.00 0.00 5.03
2840 3675 3.962718 ACATAAAAGATGGATGCAAGGGG 59.037 43.478 0.00 0.00 0.00 4.79
2844 3679 5.393352 GCACAGACATAAAAGATGGATGCAA 60.393 40.000 0.00 0.00 0.00 4.08
3000 3852 8.697507 AGTTAGAAGGAAAATCTGACATGTTT 57.302 30.769 0.00 0.00 36.26 2.83
3039 3891 7.471721 TGAAATGAACAATGTCATATTCCGTC 58.528 34.615 7.10 3.90 37.25 4.79
3050 3902 4.358851 CACCACGTTGAAATGAACAATGT 58.641 39.130 0.00 0.00 44.73 2.71
3080 3932 1.144936 GCAGTAGAGGGCGAGCAAT 59.855 57.895 0.00 0.00 0.00 3.56
3146 4262 1.415672 AACAGGGCCGAAGTCTCCAA 61.416 55.000 0.00 0.00 0.00 3.53
3178 4294 6.861065 TTTTCCTAATAGAATTAGCTGCCG 57.139 37.500 0.00 0.00 0.00 5.69
3193 4309 7.581213 TGTTTCAGCTTCTGATTTTTCCTAA 57.419 32.000 0.00 0.00 40.39 2.69
3198 4314 7.607607 AGGTTTTTGTTTCAGCTTCTGATTTTT 59.392 29.630 0.00 0.00 40.39 1.94
3210 4326 8.981647 CAGATTCCAAATAGGTTTTTGTTTCAG 58.018 33.333 0.00 0.00 39.02 3.02
3217 4333 6.427853 GCAAAGCAGATTCCAAATAGGTTTTT 59.572 34.615 0.00 0.00 39.02 1.94
3220 4336 4.081476 GGCAAAGCAGATTCCAAATAGGTT 60.081 41.667 0.00 0.00 39.02 3.50
3222 4338 3.448301 TGGCAAAGCAGATTCCAAATAGG 59.552 43.478 0.00 0.00 39.47 2.57
3234 4377 4.232221 CTGAAGTAAACATGGCAAAGCAG 58.768 43.478 0.00 0.00 0.00 4.24
3248 4391 8.148351 ACAGTATCAACTTTACTGCTGAAGTAA 58.852 33.333 4.06 4.06 46.81 2.24
3249 4392 7.667557 ACAGTATCAACTTTACTGCTGAAGTA 58.332 34.615 10.02 0.00 46.81 2.24
3250 4393 6.525629 ACAGTATCAACTTTACTGCTGAAGT 58.474 36.000 10.02 0.00 46.81 3.01
3251 4394 7.171508 TCAACAGTATCAACTTTACTGCTGAAG 59.828 37.037 12.17 0.00 46.81 3.02
3252 4395 6.989759 TCAACAGTATCAACTTTACTGCTGAA 59.010 34.615 12.17 0.99 46.81 3.02
3253 4396 6.521162 TCAACAGTATCAACTTTACTGCTGA 58.479 36.000 11.05 11.05 46.81 4.26
3254 4397 6.785488 TCAACAGTATCAACTTTACTGCTG 57.215 37.500 10.02 8.72 46.81 4.41
3265 4408 8.707938 CTGATTCACAGTATCAACAGTATCAA 57.292 34.615 0.00 0.00 41.30 2.57
3281 4424 1.610038 CACTGGCAAAGCTGATTCACA 59.390 47.619 0.00 0.00 0.00 3.58
3282 4425 1.881973 TCACTGGCAAAGCTGATTCAC 59.118 47.619 0.00 0.00 0.00 3.18
3298 4441 1.068472 CACGTTAGGACTCGCTTCACT 60.068 52.381 0.00 0.00 0.00 3.41
3302 4445 0.677842 AACCACGTTAGGACTCGCTT 59.322 50.000 0.00 0.00 0.00 4.68
3305 4448 0.599558 TGGAACCACGTTAGGACTCG 59.400 55.000 0.00 0.00 0.00 4.18
3308 4451 1.154197 GCTTGGAACCACGTTAGGAC 58.846 55.000 0.00 0.00 0.00 3.85
3312 4455 1.310904 GTTGGCTTGGAACCACGTTA 58.689 50.000 0.00 0.00 36.76 3.18
3313 4456 1.388837 GGTTGGCTTGGAACCACGTT 61.389 55.000 0.00 0.00 42.26 3.99
3314 4457 1.826487 GGTTGGCTTGGAACCACGT 60.826 57.895 0.00 0.00 42.26 4.49
3315 4458 2.903547 CGGTTGGCTTGGAACCACG 61.904 63.158 5.45 0.00 42.75 4.94
3316 4459 1.104577 TTCGGTTGGCTTGGAACCAC 61.105 55.000 5.45 0.00 42.75 4.16
3405 4548 8.526667 AGCGTACTATATCACCATTGATCTAT 57.473 34.615 0.00 0.00 41.87 1.98
3426 4573 8.237267 CCTTTTTCTTCTTCACATAATTAGCGT 58.763 33.333 0.00 0.00 0.00 5.07
3453 4600 8.770828 CCGAATTGAATTATCCGTATGTAAAGT 58.229 33.333 0.00 0.00 0.00 2.66
3454 4601 8.770828 ACCGAATTGAATTATCCGTATGTAAAG 58.229 33.333 0.00 0.00 0.00 1.85
3455 4602 8.552865 CACCGAATTGAATTATCCGTATGTAAA 58.447 33.333 0.00 0.00 0.00 2.01
3456 4603 7.711772 ACACCGAATTGAATTATCCGTATGTAA 59.288 33.333 0.00 0.00 0.00 2.41
3457 4604 7.211573 ACACCGAATTGAATTATCCGTATGTA 58.788 34.615 0.00 0.00 0.00 2.29
3463 4610 4.552767 GCAGACACCGAATTGAATTATCCG 60.553 45.833 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.