Multiple sequence alignment - TraesCS6A01G223800

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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 TraesCS6A01G223800 chr6A 100.000 3602 0 0 1 3602 420823417 420819816 0.000000e+00 6652
1 TraesCS6A01G223800 chr6D 95.707 2632 91 14 25 2646 298923518 298926137 0.000000e+00 4215
2 TraesCS6A01G223800 chr6D 88.343 712 75 6 2894 3602 298955678 298956384 0.000000e+00 848
3 TraesCS6A01G223800 chr6D 90.129 233 22 1 3370 3602 298956547 298956778 5.840000e-78 302
4 TraesCS6A01G223800 chr6D 87.349 166 9 6 2730 2895 298954105 298954258 2.860000e-41 180
5 TraesCS6A01G223800 chr6B 95.138 2468 93 12 455 2914 462034569 462037017 0.000000e+00 3868
6 TraesCS6A01G223800 chr6B 89.292 551 55 2 3055 3602 462063229 462063778 0.000000e+00 688
7 TraesCS6A01G223800 chr6B 87.255 102 10 3 288 387 462034343 462034443 2.940000e-21 113
8 TraesCS6A01G223800 chr5D 76.474 1560 321 42 1015 2552 537088077 537089612 0.000000e+00 806
9 TraesCS6A01G223800 chr5D 75.882 1559 331 41 1015 2552 537162874 537161340 0.000000e+00 754
10 TraesCS6A01G223800 chr4A 76.399 1555 322 38 1015 2548 632999852 632998322 0.000000e+00 797
11 TraesCS6A01G223800 chr4A 76.276 1568 322 42 1009 2552 632989700 632991241 0.000000e+00 789
12 TraesCS6A01G223800 chr4A 75.789 1425 293 45 993 2389 685834791 685836191 0.000000e+00 673
13 TraesCS6A01G223800 chr4D 74.762 1573 334 49 1012 2552 479540665 479542206 0.000000e+00 647
14 TraesCS6A01G223800 chr4B 74.680 1564 342 43 1012 2548 606764719 606766255 0.000000e+00 645


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 TraesCS6A01G223800 chr6A 420819816 420823417 3601 True 6652.000000 6652 100.0000 1 3602 1 chr6A.!!$R1 3601
1 TraesCS6A01G223800 chr6D 298923518 298926137 2619 False 4215.000000 4215 95.7070 25 2646 1 chr6D.!!$F1 2621
2 TraesCS6A01G223800 chr6D 298954105 298956778 2673 False 443.333333 848 88.6070 2730 3602 3 chr6D.!!$F2 872
3 TraesCS6A01G223800 chr6B 462034343 462037017 2674 False 1990.500000 3868 91.1965 288 2914 2 chr6B.!!$F2 2626
4 TraesCS6A01G223800 chr6B 462063229 462063778 549 False 688.000000 688 89.2920 3055 3602 1 chr6B.!!$F1 547
5 TraesCS6A01G223800 chr5D 537088077 537089612 1535 False 806.000000 806 76.4740 1015 2552 1 chr5D.!!$F1 1537
6 TraesCS6A01G223800 chr5D 537161340 537162874 1534 True 754.000000 754 75.8820 1015 2552 1 chr5D.!!$R1 1537
7 TraesCS6A01G223800 chr4A 632998322 632999852 1530 True 797.000000 797 76.3990 1015 2548 1 chr4A.!!$R1 1533
8 TraesCS6A01G223800 chr4A 632989700 632991241 1541 False 789.000000 789 76.2760 1009 2552 1 chr4A.!!$F1 1543
9 TraesCS6A01G223800 chr4A 685834791 685836191 1400 False 673.000000 673 75.7890 993 2389 1 chr4A.!!$F2 1396
10 TraesCS6A01G223800 chr4D 479540665 479542206 1541 False 647.000000 647 74.7620 1012 2552 1 chr4D.!!$F1 1540
11 TraesCS6A01G223800 chr4B 606764719 606766255 1536 False 645.000000 645 74.6800 1012 2548 1 chr4B.!!$F1 1536

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
747 814 0.039764 CCCCTTTGTTCCTTCTCCCC 59.96 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 2801 0.105964 CCCCTCCGCGATAATTGTCA 59.894 55.0 8.23 0.0 0.0 3.58 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
21 22 4.406648 TTGATAGAGCCATCGACAATGT 57.593 40.909 0.00 0.00 33.13 2.71
22 23 3.721035 TGATAGAGCCATCGACAATGTG 58.279 45.455 0.00 0.00 33.13 3.21
23 24 2.602257 TAGAGCCATCGACAATGTGG 57.398 50.000 0.00 0.00 33.13 4.17
24 25 0.904649 AGAGCCATCGACAATGTGGA 59.095 50.000 6.18 0.00 34.94 4.02
25 26 1.278985 AGAGCCATCGACAATGTGGAA 59.721 47.619 6.18 0.00 34.94 3.53
26 27 2.092753 AGAGCCATCGACAATGTGGAAT 60.093 45.455 6.18 0.00 34.94 3.01
27 28 2.019249 AGCCATCGACAATGTGGAATG 58.981 47.619 6.18 2.22 34.94 2.67
28 29 1.745087 GCCATCGACAATGTGGAATGT 59.255 47.619 6.18 0.00 34.94 2.71
29 30 2.478370 GCCATCGACAATGTGGAATGTG 60.478 50.000 6.18 0.00 34.94 3.21
34 35 1.269448 GACAATGTGGAATGTGCCGTT 59.731 47.619 0.00 0.00 0.00 4.44
66 67 7.187824 TGATCTAAAAGTAGTCATGGAAGCT 57.812 36.000 0.00 0.00 0.00 3.74
82 83 3.712218 GGAAGCTTGTAGATAGGAGGGTT 59.288 47.826 2.10 0.00 0.00 4.11
89 90 4.404640 TGTAGATAGGAGGGTTGTATCCG 58.595 47.826 0.00 0.00 40.73 4.18
91 92 4.194678 AGATAGGAGGGTTGTATCCGAA 57.805 45.455 0.00 0.00 40.73 4.30
92 93 4.153411 AGATAGGAGGGTTGTATCCGAAG 58.847 47.826 0.00 0.00 40.73 3.79
122 123 0.855349 GACGATGATGATGACACGGC 59.145 55.000 0.00 0.00 0.00 5.68
132 133 1.735571 GATGACACGGCGGTTTTATGT 59.264 47.619 13.24 4.82 0.00 2.29
174 175 4.104696 TGCTTTGTGATTCATGCTCATG 57.895 40.909 3.55 3.55 40.09 3.07
185 186 2.623416 TCATGCTCATGGGTAGAGTACG 59.377 50.000 9.69 0.00 39.24 3.67
202 204 1.603456 ACGTGGTTGATGATGTTGCA 58.397 45.000 0.00 0.00 0.00 4.08
238 240 4.436986 CGATTTTCTAGCCGGGTTTTCTTC 60.437 45.833 13.43 1.74 0.00 2.87
278 280 6.589139 GGTCGAGTACTAGCTAAACAACATTT 59.411 38.462 0.00 0.00 0.00 2.32
279 281 7.117379 GGTCGAGTACTAGCTAAACAACATTTT 59.883 37.037 0.00 0.00 0.00 1.82
280 282 8.493547 GTCGAGTACTAGCTAAACAACATTTTT 58.506 33.333 0.00 0.00 0.00 1.94
310 312 9.943163 CCTAAAAAGAAAGAAGCTAGCATATTC 57.057 33.333 18.83 12.12 0.00 1.75
341 344 2.923121 CGGGATTCTCACCAATCATGT 58.077 47.619 0.00 0.00 34.84 3.21
344 347 4.683129 CGGGATTCTCACCAATCATGTACA 60.683 45.833 0.00 0.00 34.84 2.90
348 351 4.529109 TCTCACCAATCATGTACACGAA 57.471 40.909 0.00 0.00 0.00 3.85
349 352 4.888917 TCTCACCAATCATGTACACGAAA 58.111 39.130 0.00 0.00 0.00 3.46
390 419 7.481275 TTTGGTCGGTTATATTAATTCGGAC 57.519 36.000 0.00 3.28 0.00 4.79
505 567 4.771590 ATCGACTGAAAACACATGCAAT 57.228 36.364 0.00 0.00 0.00 3.56
563 625 9.619316 CAAATCACAAAGTAATAAAATGGACGA 57.381 29.630 0.00 0.00 0.00 4.20
571 633 8.658499 AAGTAATAAAATGGACGATACCAGAC 57.342 34.615 0.00 0.00 43.49 3.51
588 652 8.779354 ATACCAGACTTAACTGAAAGCTAAAG 57.221 34.615 0.00 0.00 39.94 1.85
590 654 6.931840 ACCAGACTTAACTGAAAGCTAAAGAG 59.068 38.462 0.00 0.00 39.94 2.85
625 689 4.035792 CACAAATCAAACCGGTTAGTCACA 59.964 41.667 22.60 1.12 0.00 3.58
637 701 3.568007 GGTTAGTCACACCTGCATTCAAA 59.432 43.478 0.00 0.00 0.00 2.69
655 719 5.512942 TCAAAAAGACACTATCATCCCCA 57.487 39.130 0.00 0.00 0.00 4.96
747 814 0.039764 CCCCTTTGTTCCTTCTCCCC 59.960 60.000 0.00 0.00 0.00 4.81
865 932 4.720090 CACATCTAGACAAAGCAAAGCAG 58.280 43.478 0.00 0.00 0.00 4.24
882 949 3.604065 GCAGTAAGCCGGCTTTTATAC 57.396 47.619 43.93 33.92 37.47 1.47
968 1038 3.438017 TTGCTTTGCACCGGCCAAC 62.438 57.895 0.00 0.00 38.71 3.77
983 1053 1.896660 CAACAAGTGTGGACGGGGG 60.897 63.158 0.00 0.00 0.00 5.40
984 1054 2.073716 AACAAGTGTGGACGGGGGA 61.074 57.895 0.00 0.00 0.00 4.81
985 1055 2.052047 AACAAGTGTGGACGGGGGAG 62.052 60.000 0.00 0.00 0.00 4.30
986 1056 2.203182 AAGTGTGGACGGGGGAGA 59.797 61.111 0.00 0.00 0.00 3.71
987 1057 2.214920 AAGTGTGGACGGGGGAGAC 61.215 63.158 0.00 0.00 0.00 3.36
1295 1366 2.345991 CAAGGTCGGCCGGAAGAA 59.654 61.111 27.83 1.12 40.50 2.52
2612 2689 0.678048 CCCTTGTAGAACCTGCCTGC 60.678 60.000 0.00 0.00 0.00 4.85
2625 2702 2.343758 CCTGCACGTAGGCTGTGT 59.656 61.111 0.00 0.00 39.53 3.72
2650 2727 3.499918 ACCACTCGATGAAAAAGAAGCTG 59.500 43.478 0.00 0.00 0.00 4.24
2662 2739 6.873076 TGAAAAAGAAGCTGTTTGAATGTGTT 59.127 30.769 0.00 0.00 0.00 3.32
2697 2774 2.291153 CCGGGATTGGGATTAGATGCAT 60.291 50.000 0.00 0.00 0.00 3.96
2711 2788 2.441001 AGATGCATTCCAAGGACCCTAG 59.559 50.000 0.00 0.00 0.00 3.02
2718 2795 1.720533 TCCAAGGACCCTAGGTACACT 59.279 52.381 8.29 0.00 39.47 3.55
2724 2801 1.274447 GACCCTAGGTACACTGCGTTT 59.726 52.381 8.29 0.00 35.25 3.60
2726 2803 1.274167 CCCTAGGTACACTGCGTTTGA 59.726 52.381 8.29 0.00 0.00 2.69
2785 2862 7.435784 GGAAGGAATTGTCGAGATTAGACTTAC 59.564 40.741 0.00 0.00 39.24 2.34
2809 2886 8.997621 ACGATTTCTCATTTTACTAGTAAGCA 57.002 30.769 14.73 7.16 0.00 3.91
2837 2914 5.339611 GTGTGCAACTTATGTTTTGATCGAC 59.660 40.000 0.00 0.00 38.04 4.20
2845 2922 7.963981 ACTTATGTTTTGATCGACACACATAG 58.036 34.615 4.02 5.19 36.79 2.23
2923 4421 0.530211 TGCAAGCCAAATGTGCACAC 60.530 50.000 24.37 9.18 43.09 3.82
2944 4442 7.923344 GCACACATCAATACTATTCTAGTGTCT 59.077 37.037 0.00 0.00 39.81 3.41
2955 4453 8.288689 ACTATTCTAGTGTCTCTTCTTTCTCC 57.711 38.462 0.00 0.00 37.69 3.71
3000 4498 5.882000 CCTCTTTGATATTGATCACACCACA 59.118 40.000 0.00 0.00 41.92 4.17
3004 4502 7.830697 TCTTTGATATTGATCACACCACATCTT 59.169 33.333 0.00 0.00 41.92 2.40
3015 4513 1.774254 ACCACATCTTCCTCCACAACA 59.226 47.619 0.00 0.00 0.00 3.33
3016 4514 2.174639 ACCACATCTTCCTCCACAACAA 59.825 45.455 0.00 0.00 0.00 2.83
3017 4515 2.554032 CCACATCTTCCTCCACAACAAC 59.446 50.000 0.00 0.00 0.00 3.32
3018 4516 3.480470 CACATCTTCCTCCACAACAACT 58.520 45.455 0.00 0.00 0.00 3.16
3019 4517 3.499918 CACATCTTCCTCCACAACAACTC 59.500 47.826 0.00 0.00 0.00 3.01
3020 4518 2.930826 TCTTCCTCCACAACAACTCC 57.069 50.000 0.00 0.00 0.00 3.85
3021 4519 2.408565 TCTTCCTCCACAACAACTCCT 58.591 47.619 0.00 0.00 0.00 3.69
3039 4537 4.067896 CTCCTATCACCATATGCAACCAC 58.932 47.826 0.00 0.00 0.00 4.16
3049 4547 0.178981 ATGCAACCACTTGTGCTCCT 60.179 50.000 0.00 0.00 0.00 3.69
3050 4548 0.819259 TGCAACCACTTGTGCTCCTC 60.819 55.000 0.00 0.00 0.00 3.71
3066 4564 0.179062 CCTCTCGAGGCCCATCTTTG 60.179 60.000 13.56 0.00 42.44 2.77
3074 4572 2.000048 AGGCCCATCTTTGTTCCCTTA 59.000 47.619 0.00 0.00 0.00 2.69
3093 4591 5.340027 CCCTTATTGTTATGTCTCCCACCTT 60.340 44.000 0.00 0.00 0.00 3.50
3106 4604 2.645297 TCCCACCTTGTTAGCCACAATA 59.355 45.455 0.00 0.00 44.72 1.90
3112 4610 5.882557 CACCTTGTTAGCCACAATAGAATCT 59.117 40.000 0.00 0.00 44.72 2.40
3117 4615 7.859325 TGTTAGCCACAATAGAATCTTAACC 57.141 36.000 0.00 0.00 29.87 2.85
3122 4620 5.353123 GCCACAATAGAATCTTAACCGTTGA 59.647 40.000 0.00 0.00 0.00 3.18
3133 4631 9.834628 GAATCTTAACCGTTGATACAAATTTGA 57.165 29.630 24.64 8.78 0.00 2.69
3158 4656 9.535270 GAACGATGAAAGAAAAGATGTAGAAAG 57.465 33.333 0.00 0.00 0.00 2.62
3160 4658 9.273016 ACGATGAAAGAAAAGATGTAGAAAGAA 57.727 29.630 0.00 0.00 0.00 2.52
3188 4686 9.681692 GAACATACATAATTGCAGCATATTTGA 57.318 29.630 0.00 0.00 0.00 2.69
3197 4695 3.119388 TGCAGCATATTTGACAGCCTTTC 60.119 43.478 0.00 0.00 0.00 2.62
3203 4701 3.904136 ATTTGACAGCCTTTCGACTTG 57.096 42.857 0.00 0.00 0.00 3.16
3221 4719 8.475331 TCGACTTGTGTAGAATATTCCTTTTC 57.525 34.615 11.92 0.96 0.00 2.29
3223 4721 7.549488 CGACTTGTGTAGAATATTCCTTTTCCT 59.451 37.037 11.92 0.00 0.00 3.36
3264 4765 7.500141 AGAAAATGGTACTCAAATTTGCAACT 58.500 30.769 13.54 0.00 0.00 3.16
3274 4776 6.366877 ACTCAAATTTGCAACTCATTACATGC 59.633 34.615 13.54 0.00 39.22 4.06
3315 4817 8.506437 CAACAAAAGCTTATCAGTTGATCACTA 58.494 33.333 19.87 0.00 38.80 2.74
3367 4869 9.358406 ACAGATAGCATCAAATAAATTCATCCA 57.642 29.630 0.00 0.00 0.00 3.41
3392 4894 7.812309 TCGTACTTCAAGTAATCAACATCAG 57.188 36.000 0.00 0.00 31.62 2.90
3437 4939 5.741011 ACAAAAGTCAAGACTAGTCAACCA 58.259 37.500 24.44 2.87 41.58 3.67
3449 4951 6.209788 AGACTAGTCAACCAGAGTCTAAAAGG 59.790 42.308 24.44 0.00 45.28 3.11
3477 4979 1.289160 AGTCCAAGCAAGCTCCCATA 58.711 50.000 0.00 0.00 0.00 2.74
3494 4996 1.926426 ATAGGTCCAGGCAAGCCACC 61.926 60.000 14.40 12.08 38.92 4.61
3505 5007 1.151450 AAGCCACCCCAGTCAACAG 59.849 57.895 0.00 0.00 0.00 3.16
3517 5019 3.062763 CAGTCAACAGTAGTCCAAGCTG 58.937 50.000 0.00 0.00 36.41 4.24
3519 5021 2.037251 GTCAACAGTAGTCCAAGCTGGA 59.963 50.000 0.00 0.00 45.98 3.86
3541 5438 6.071108 TGGATTTCAAGGTCAACAAGTCAAAA 60.071 34.615 0.00 0.00 0.00 2.44
3550 5447 7.840931 AGGTCAACAAGTCAAAAGAAAAAGAT 58.159 30.769 0.00 0.00 0.00 2.40
3594 5491 5.309638 AGGAGAAGGCAAGAGTAAAGAAAC 58.690 41.667 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.122046 CACATTGTCGATGGCTCTATCAA 58.878 43.478 5.04 0.00 40.21 2.57
1 2 3.493176 CCACATTGTCGATGGCTCTATCA 60.493 47.826 5.04 0.00 40.21 2.15
2 3 3.062763 CCACATTGTCGATGGCTCTATC 58.937 50.000 5.04 0.00 40.21 2.08
3 4 2.700371 TCCACATTGTCGATGGCTCTAT 59.300 45.455 5.04 0.00 40.21 1.98
4 5 2.107366 TCCACATTGTCGATGGCTCTA 58.893 47.619 5.04 0.00 40.21 2.43
6 7 1.737838 TTCCACATTGTCGATGGCTC 58.262 50.000 5.04 0.00 40.21 4.70
7 8 2.019249 CATTCCACATTGTCGATGGCT 58.981 47.619 5.04 0.00 40.21 4.75
8 9 1.745087 ACATTCCACATTGTCGATGGC 59.255 47.619 5.04 0.00 40.21 4.40
9 10 2.478370 GCACATTCCACATTGTCGATGG 60.478 50.000 5.04 0.00 40.21 3.51
10 11 2.478370 GGCACATTCCACATTGTCGATG 60.478 50.000 0.00 0.00 41.71 3.84
11 12 1.745087 GGCACATTCCACATTGTCGAT 59.255 47.619 0.00 0.00 0.00 3.59
12 13 1.164411 GGCACATTCCACATTGTCGA 58.836 50.000 0.00 0.00 0.00 4.20
13 14 0.179192 CGGCACATTCCACATTGTCG 60.179 55.000 0.00 0.00 0.00 4.35
14 15 0.881118 ACGGCACATTCCACATTGTC 59.119 50.000 0.00 0.00 0.00 3.18
15 16 1.000385 CAACGGCACATTCCACATTGT 60.000 47.619 0.00 0.00 0.00 2.71
16 17 1.269174 TCAACGGCACATTCCACATTG 59.731 47.619 0.00 0.00 0.00 2.82
17 18 1.614996 TCAACGGCACATTCCACATT 58.385 45.000 0.00 0.00 0.00 2.71
18 19 1.745087 GATCAACGGCACATTCCACAT 59.255 47.619 0.00 0.00 0.00 3.21
19 20 1.164411 GATCAACGGCACATTCCACA 58.836 50.000 0.00 0.00 0.00 4.17
20 21 1.453155 AGATCAACGGCACATTCCAC 58.547 50.000 0.00 0.00 0.00 4.02
21 22 2.198827 AAGATCAACGGCACATTCCA 57.801 45.000 0.00 0.00 0.00 3.53
22 23 3.876914 TCATAAGATCAACGGCACATTCC 59.123 43.478 0.00 0.00 0.00 3.01
23 24 5.679734 ATCATAAGATCAACGGCACATTC 57.320 39.130 0.00 0.00 0.00 2.67
66 67 4.831155 CGGATACAACCCTCCTATCTACAA 59.169 45.833 0.00 0.00 0.00 2.41
89 90 2.026301 CGTCGCCGAGATCCCTTC 59.974 66.667 0.00 0.00 35.63 3.46
101 102 0.500178 CGTGTCATCATCATCGTCGC 59.500 55.000 0.00 0.00 0.00 5.19
122 123 3.628942 GGGCCTAAACCTACATAAAACCG 59.371 47.826 0.84 0.00 0.00 4.44
132 133 4.647399 GCAACATAAATGGGCCTAAACCTA 59.353 41.667 4.53 0.00 0.00 3.08
174 175 2.756760 TCATCAACCACGTACTCTACCC 59.243 50.000 0.00 0.00 0.00 3.69
185 186 3.173599 CGAATGCAACATCATCAACCAC 58.826 45.455 0.00 0.00 0.00 4.16
202 204 6.967199 GGCTAGAAAATCGATTGAAAACGAAT 59.033 34.615 12.25 0.00 41.65 3.34
238 240 2.283388 ACCATGGCCCAACTGCAG 60.283 61.111 13.04 13.48 0.00 4.41
278 280 9.961265 GCTAGCTTCTTTCTTTTTAGGTAAAAA 57.039 29.630 7.70 7.30 41.36 1.94
279 281 9.127277 TGCTAGCTTCTTTCTTTTTAGGTAAAA 57.873 29.630 17.23 0.00 34.64 1.52
280 282 8.685838 TGCTAGCTTCTTTCTTTTTAGGTAAA 57.314 30.769 17.23 0.00 0.00 2.01
281 283 8.863872 ATGCTAGCTTCTTTCTTTTTAGGTAA 57.136 30.769 17.23 0.00 0.00 2.85
341 344 0.391228 TGGCTCACAGCTTTCGTGTA 59.609 50.000 2.92 0.00 41.99 2.90
344 347 1.166531 GGTTGGCTCACAGCTTTCGT 61.167 55.000 0.00 0.00 41.99 3.85
348 351 0.178953 AATGGGTTGGCTCACAGCTT 60.179 50.000 0.00 0.00 41.99 3.74
349 352 0.178953 AAATGGGTTGGCTCACAGCT 60.179 50.000 0.00 0.00 41.99 4.24
385 388 2.429930 CCAGCCCTTTGTGTCCGA 59.570 61.111 0.00 0.00 0.00 4.55
390 419 1.463553 GGTCAACCCAGCCCTTTGTG 61.464 60.000 0.00 0.00 0.00 3.33
505 567 2.124507 GAGCACCTGGTTGGCTGGTA 62.125 60.000 15.58 0.00 38.15 3.25
531 593 8.500837 TTTTATTACTTTGTGATTTGTGCTCG 57.499 30.769 0.00 0.00 0.00 5.03
563 625 8.594550 TCTTTAGCTTTCAGTTAAGTCTGGTAT 58.405 33.333 0.00 0.00 36.25 2.73
625 689 5.769662 TGATAGTGTCTTTTTGAATGCAGGT 59.230 36.000 0.00 0.00 0.00 4.00
637 701 3.435601 GGCATGGGGATGATAGTGTCTTT 60.436 47.826 0.00 0.00 0.00 2.52
655 719 3.826221 ATGCGCAACATACGGCAT 58.174 50.000 17.11 0.00 41.01 4.40
747 814 2.912967 GACAATGAACTTGCTGAATGCG 59.087 45.455 0.00 0.00 46.63 4.73
968 1038 2.214216 TCTCCCCCGTCCACACTTG 61.214 63.158 0.00 0.00 0.00 3.16
1295 1366 1.899814 TGATGGTCTTGCCGTAGAACT 59.100 47.619 0.00 0.00 41.21 3.01
1591 1662 3.752339 GGGGTCTTCCGCGTACGT 61.752 66.667 17.90 0.00 36.95 3.57
2526 2603 2.283966 CCGGACACCTCCTCCAGT 60.284 66.667 0.00 0.00 33.79 4.00
2612 2689 2.317609 GGTGCACACAGCCTACGTG 61.318 63.158 20.43 0.00 44.83 4.49
2625 2702 2.844946 TCTTTTTCATCGAGTGGTGCA 58.155 42.857 0.00 0.00 0.00 4.57
2650 2727 3.309410 CCCAGCACAAAACACATTCAAAC 59.691 43.478 0.00 0.00 0.00 2.93
2662 2739 2.203422 CCGGGTTCCCAGCACAAA 60.203 61.111 8.70 0.00 0.00 2.83
2684 2761 3.823304 GTCCTTGGAATGCATCTAATCCC 59.177 47.826 11.74 2.87 0.00 3.85
2685 2762 3.823304 GGTCCTTGGAATGCATCTAATCC 59.177 47.826 0.00 3.60 0.00 3.01
2686 2763 3.823304 GGGTCCTTGGAATGCATCTAATC 59.177 47.826 0.00 0.00 0.00 1.75
2687 2764 3.464833 AGGGTCCTTGGAATGCATCTAAT 59.535 43.478 0.00 0.00 0.00 1.73
2688 2765 2.852449 AGGGTCCTTGGAATGCATCTAA 59.148 45.455 0.00 0.00 0.00 2.10
2689 2766 2.492025 AGGGTCCTTGGAATGCATCTA 58.508 47.619 0.00 0.00 0.00 1.98
2697 2774 2.113052 AGTGTACCTAGGGTCCTTGGAA 59.887 50.000 21.20 6.41 40.55 3.53
2711 2788 3.619233 AATTGTCAAACGCAGTGTACC 57.381 42.857 0.00 0.00 45.00 3.34
2718 2795 1.201976 CCGCGATAATTGTCAAACGCA 60.202 47.619 8.23 0.00 44.96 5.24
2724 2801 0.105964 CCCCTCCGCGATAATTGTCA 59.894 55.000 8.23 0.00 0.00 3.58
2726 2803 0.834612 TTCCCCTCCGCGATAATTGT 59.165 50.000 8.23 0.00 0.00 2.71
2785 2862 9.855361 CATGCTTACTAGTAAAATGAGAAATCG 57.145 33.333 22.33 8.25 0.00 3.34
2823 2900 7.899178 AACTATGTGTGTCGATCAAAACATA 57.101 32.000 15.66 15.66 37.08 2.29
2825 2902 6.612247 AAACTATGTGTGTCGATCAAAACA 57.388 33.333 0.00 0.00 32.15 2.83
2882 2959 6.827762 TGCATACTTGTGATATGTCCAATTGA 59.172 34.615 7.12 0.00 33.35 2.57
2891 2968 5.503662 TTGGCTTGCATACTTGTGATATG 57.496 39.130 0.00 0.00 33.84 1.78
2895 4393 3.573538 ACATTTGGCTTGCATACTTGTGA 59.426 39.130 0.00 0.00 0.00 3.58
2937 4435 5.105554 GCATCAGGAGAAAGAAGAGACACTA 60.106 44.000 0.00 0.00 0.00 2.74
2938 4436 4.322650 GCATCAGGAGAAAGAAGAGACACT 60.323 45.833 0.00 0.00 0.00 3.55
2944 4442 4.897509 TCAAGCATCAGGAGAAAGAAGA 57.102 40.909 0.00 0.00 0.00 2.87
2955 4453 6.766944 AGAGGAGAAACAATATCAAGCATCAG 59.233 38.462 0.00 0.00 0.00 2.90
2991 4489 1.347707 GTGGAGGAAGATGTGGTGTGA 59.652 52.381 0.00 0.00 0.00 3.58
3000 4498 2.982488 AGGAGTTGTTGTGGAGGAAGAT 59.018 45.455 0.00 0.00 0.00 2.40
3004 4502 3.260884 GTGATAGGAGTTGTTGTGGAGGA 59.739 47.826 0.00 0.00 0.00 3.71
3015 4513 4.165950 TGGTTGCATATGGTGATAGGAGTT 59.834 41.667 4.56 0.00 0.00 3.01
3016 4514 3.716353 TGGTTGCATATGGTGATAGGAGT 59.284 43.478 4.56 0.00 0.00 3.85
3017 4515 4.067896 GTGGTTGCATATGGTGATAGGAG 58.932 47.826 4.56 0.00 0.00 3.69
3018 4516 3.716353 AGTGGTTGCATATGGTGATAGGA 59.284 43.478 4.56 0.00 0.00 2.94
3019 4517 4.090761 AGTGGTTGCATATGGTGATAGG 57.909 45.455 4.56 0.00 0.00 2.57
3020 4518 4.883585 ACAAGTGGTTGCATATGGTGATAG 59.116 41.667 4.56 0.00 37.14 2.08
3021 4519 4.639755 CACAAGTGGTTGCATATGGTGATA 59.360 41.667 4.56 0.00 37.14 2.15
3049 4547 0.984230 AACAAAGATGGGCCTCGAGA 59.016 50.000 15.71 0.00 0.00 4.04
3050 4548 1.373570 GAACAAAGATGGGCCTCGAG 58.626 55.000 5.13 5.13 0.00 4.04
3066 4564 5.589050 GTGGGAGACATAACAATAAGGGAAC 59.411 44.000 0.00 0.00 0.00 3.62
3074 4572 4.657814 ACAAGGTGGGAGACATAACAAT 57.342 40.909 0.00 0.00 0.00 2.71
3093 4591 6.537301 CGGTTAAGATTCTATTGTGGCTAACA 59.463 38.462 0.00 0.00 36.85 2.41
3106 4604 9.840427 CAAATTTGTATCAACGGTTAAGATTCT 57.160 29.630 10.15 0.00 0.00 2.40
3112 4610 7.637229 TCGTTCAAATTTGTATCAACGGTTAA 58.363 30.769 28.05 15.30 33.76 2.01
3117 4615 7.774224 TTCATCGTTCAAATTTGTATCAACG 57.226 32.000 25.27 25.27 0.00 4.10
3133 4631 9.273016 TCTTTCTACATCTTTTCTTTCATCGTT 57.727 29.630 0.00 0.00 0.00 3.85
3158 4656 9.903682 ATATGCTGCAATTATGTATGTTCTTTC 57.096 29.630 6.36 0.00 0.00 2.62
3165 4663 9.124807 CTGTCAAATATGCTGCAATTATGTATG 57.875 33.333 6.36 2.66 0.00 2.39
3197 4695 7.549488 AGGAAAAGGAATATTCTACACAAGTCG 59.451 37.037 14.95 0.00 0.00 4.18
3274 4776 6.534793 AGCTTTTGTTGTTTCCTATGTGTTTG 59.465 34.615 0.00 0.00 0.00 2.93
3278 4780 8.081633 TGATAAGCTTTTGTTGTTTCCTATGTG 58.918 33.333 3.20 0.00 0.00 3.21
3344 4846 9.499585 CGATGGATGAATTTATTTGATGCTATC 57.500 33.333 0.00 0.00 0.00 2.08
3365 4867 6.961359 TGTTGATTACTTGAAGTACGATGG 57.039 37.500 4.23 0.00 28.93 3.51
3367 4869 7.010552 GCTGATGTTGATTACTTGAAGTACGAT 59.989 37.037 4.23 0.00 28.93 3.73
3399 4901 8.445275 TTGACTTTTGTTGACTACATATGTGT 57.555 30.769 18.81 13.63 42.39 3.72
3437 4939 9.268282 TGGACTATTATTGACCTTTTAGACTCT 57.732 33.333 0.00 0.00 0.00 3.24
3449 4951 5.008118 GGAGCTTGCTTGGACTATTATTGAC 59.992 44.000 0.00 0.00 0.00 3.18
3477 4979 3.971702 GGTGGCTTGCCTGGACCT 61.972 66.667 13.18 0.00 0.00 3.85
3494 4996 2.872038 GCTTGGACTACTGTTGACTGGG 60.872 54.545 0.00 0.00 0.00 4.45
3517 5019 5.514274 TTGACTTGTTGACCTTGAAATCC 57.486 39.130 0.00 0.00 0.00 3.01
3519 5021 7.169158 TCTTTTGACTTGTTGACCTTGAAAT 57.831 32.000 0.00 0.00 0.00 2.17
3562 5459 5.013599 ACTCTTGCCTTCTCCTTTGACTTAT 59.986 40.000 0.00 0.00 0.00 1.73
3563 5460 4.348168 ACTCTTGCCTTCTCCTTTGACTTA 59.652 41.667 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.