Multiple sequence alignment - TraesCS2A01G400600

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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 TraesCS2A01G400600 chr2A 100.000 5645 0 0 1 5645 654363640 654369284 0.000000e+00 10425.0
1 TraesCS2A01G400600 chr2D 91.973 2965 117 50 2716 5645 510616816 510619694 0.000000e+00 4045.0
2 TraesCS2A01G400600 chr2D 95.447 2438 101 8 257 2686 510614382 510616817 0.000000e+00 3879.0
3 TraesCS2A01G400600 chr2B 93.950 2694 94 30 1 2686 599998778 600001410 0.000000e+00 4008.0
4 TraesCS2A01G400600 chr2B 92.530 1834 94 29 3836 5645 600002670 600004484 0.000000e+00 2588.0
5 TraesCS2A01G400600 chr2B 96.584 849 27 2 2986 3833 600001777 600002624 0.000000e+00 1406.0
6 TraesCS2A01G400600 chr2B 91.930 285 8 8 2717 2989 600001416 600001697 8.870000e-103 385.0
7 TraesCS2A01G400600 chr2B 100.000 31 0 0 1926 1956 469524954 469524924 2.200000e-04 58.4
8 TraesCS2A01G400600 chr6A 87.425 334 40 2 1301 1633 474987120 474986788 3.190000e-102 383.0
9 TraesCS2A01G400600 chr6A 79.545 264 54 0 2197 2460 474986350 474986087 7.470000e-44 189.0
10 TraesCS2A01G400600 chr6B 87.126 334 41 2 1301 1633 485301965 485302297 1.480000e-100 377.0
11 TraesCS2A01G400600 chr6D 86.486 333 45 0 1301 1633 335339360 335339028 3.210000e-97 366.0


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 TraesCS2A01G400600 chr2A 654363640 654369284 5644 False 10425.00 10425 100.0000 1 5645 1 chr2A.!!$F1 5644
1 TraesCS2A01G400600 chr2D 510614382 510619694 5312 False 3962.00 4045 93.7100 257 5645 2 chr2D.!!$F1 5388
2 TraesCS2A01G400600 chr2B 599998778 600004484 5706 False 2096.75 4008 93.7485 1 5645 4 chr2B.!!$F1 5644
3 TraesCS2A01G400600 chr6A 474986087 474987120 1033 True 286.00 383 83.4850 1301 2460 2 chr6A.!!$R1 1159

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
218 221 0.107017 CCCGCAACAATCATCCCTCT 60.107 55.0 0.00 0.0 0.00 3.69 F
245 248 0.172578 TCCGTCGCACAATCTACCTG 59.827 55.0 0.00 0.0 0.00 4.00 F
420 423 0.179103 GTGCAGCAACAACAGGCTTT 60.179 50.0 0.00 0.0 38.56 3.51 F
2025 2051 0.322456 GGGTACATGTGAAGCCAGCA 60.322 55.0 9.11 0.0 33.37 4.41 F
3594 3743 0.373716 CGGTCTCGCCATTAAAGCAC 59.626 55.0 2.25 0.0 36.97 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 1665 0.103208 AGACCGCGAACTGGATCATC 59.897 55.000 8.23 0.0 0.00 2.92 R
1908 1927 1.515020 CTGCGGAAGAGACAGAGGG 59.485 63.158 0.00 0.0 33.10 4.30 R
2179 2231 2.037772 TGCACCACCGCCATTTATTTTT 59.962 40.909 0.00 0.0 0.00 1.94 R
3745 3898 0.446616 GAAGTTTCGGCGATGGTTCC 59.553 55.000 11.76 0.0 0.00 3.62 R
5380 5604 0.326264 AAGCCTCTGGACACCATCAC 59.674 55.000 0.00 0.0 30.82 3.06 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
34 35 4.955811 TCTGGCATACCGAATCAACTAT 57.044 40.909 0.00 0.00 39.70 2.12
46 48 6.127310 ACCGAATCAACTATCTATCATAGCCC 60.127 42.308 0.00 0.00 0.00 5.19
76 78 4.147321 AGATTGTTGACCTCACAAGCAAT 58.853 39.130 4.09 0.00 35.95 3.56
77 79 3.713858 TTGTTGACCTCACAAGCAATG 57.286 42.857 0.00 0.00 0.00 2.82
84 86 2.821969 ACCTCACAAGCAATGCCTTTAG 59.178 45.455 0.00 0.00 0.00 1.85
139 142 3.681835 ACTCCACGACGCCTCCAC 61.682 66.667 0.00 0.00 0.00 4.02
152 155 1.382522 CCTCCACCGAAATCACCATG 58.617 55.000 0.00 0.00 0.00 3.66
177 180 2.092592 CCTCTTTGGTTAACCGCCCTAT 60.093 50.000 19.65 0.00 39.43 2.57
188 191 2.182842 CGCCCTATGGTGCAAGAGC 61.183 63.158 0.00 0.00 42.57 4.09
191 194 1.957113 GCCCTATGGTGCAAGAGCTTT 60.957 52.381 0.00 0.00 42.74 3.51
212 215 0.251121 TGTCACCCCGCAACAATCAT 60.251 50.000 0.00 0.00 0.00 2.45
218 221 0.107017 CCCGCAACAATCATCCCTCT 60.107 55.000 0.00 0.00 0.00 3.69
244 247 0.892755 TTCCGTCGCACAATCTACCT 59.107 50.000 0.00 0.00 0.00 3.08
245 248 0.172578 TCCGTCGCACAATCTACCTG 59.827 55.000 0.00 0.00 0.00 4.00
284 287 1.002087 AGGACAATGACCTCGACCAAC 59.998 52.381 0.00 0.00 31.43 3.77
314 317 1.068921 GAAGCCCGGAGATGAGAGC 59.931 63.158 0.73 0.00 0.00 4.09
372 375 1.549203 CCACCATGGGGAGAAAACTG 58.451 55.000 18.14 0.19 38.05 3.16
390 393 2.124695 GAGGTCGTCCCCAATGGC 60.125 66.667 0.00 0.00 0.00 4.40
406 409 3.945434 GCGGCGATGGATGTGCAG 61.945 66.667 12.98 0.00 0.00 4.41
420 423 0.179103 GTGCAGCAACAACAGGCTTT 60.179 50.000 0.00 0.00 38.56 3.51
422 425 1.337703 TGCAGCAACAACAGGCTTTAG 59.662 47.619 0.00 0.00 38.56 1.85
423 426 1.608590 GCAGCAACAACAGGCTTTAGA 59.391 47.619 0.00 0.00 38.56 2.10
457 460 1.002134 CCTTCGGAGTTGCATGGGT 60.002 57.895 0.00 0.00 0.00 4.51
487 490 7.011389 GGCTTGAGATAAAACCATATTTTTGGC 59.989 37.037 0.00 0.00 40.68 4.52
563 566 8.986477 AGCATGACATGTCTTAAAATTAAACC 57.014 30.769 25.55 0.00 0.00 3.27
573 576 8.138712 TGTCTTAAAATTAAACCGCAACATCTT 58.861 29.630 0.00 0.00 0.00 2.40
585 588 5.934625 ACCGCAACATCTTATATCATCCTTC 59.065 40.000 0.00 0.00 0.00 3.46
598 601 9.895138 TTATATCATCCTTCCATGTGATATGTG 57.105 33.333 17.91 0.58 41.71 3.21
603 606 3.885297 CCTTCCATGTGATATGTGTTCCC 59.115 47.826 0.00 0.00 0.00 3.97
605 608 4.582973 TCCATGTGATATGTGTTCCCAA 57.417 40.909 0.00 0.00 0.00 4.12
611 614 5.517924 TGTGATATGTGTTCCCAATCCATT 58.482 37.500 0.00 0.00 0.00 3.16
674 677 6.519679 AAAAACCCCACCGAATAACTATTC 57.480 37.500 0.14 0.14 38.89 1.75
675 678 5.446260 AAACCCCACCGAATAACTATTCT 57.554 39.130 7.64 0.00 39.85 2.40
699 706 8.342634 TCTTTTACTACAATCAAGTTCAAGCAC 58.657 33.333 0.00 0.00 0.00 4.40
708 715 8.129211 ACAATCAAGTTCAAGCACTAACTAAAC 58.871 33.333 0.00 0.00 34.91 2.01
792 799 4.414846 AGTGAGATGAAAAGGGGCTCATAT 59.585 41.667 0.00 0.00 37.84 1.78
800 807 7.111247 TGAAAAGGGGCTCATATGTAAATTG 57.889 36.000 1.90 0.00 0.00 2.32
950 957 1.716028 AACCCACACAGAACCCCTCC 61.716 60.000 0.00 0.00 0.00 4.30
1298 1305 3.760035 CGTCCGGGACAGGGTGAG 61.760 72.222 25.80 4.87 32.09 3.51
1464 1471 2.126031 GACAACGTCGGCTCCCTC 60.126 66.667 0.00 0.00 0.00 4.30
1626 1633 3.382832 AAGGACGGGCTCTCCACG 61.383 66.667 5.08 0.00 34.36 4.94
1658 1665 4.794439 TCGATCACCACGCGCCAG 62.794 66.667 5.73 0.00 0.00 4.85
1669 1676 1.522355 CGCGCCAGATGATCCAGTT 60.522 57.895 0.00 0.00 0.00 3.16
1908 1927 0.740516 CACATTTCATTTGCCCGGCC 60.741 55.000 7.03 0.00 0.00 6.13
1952 1973 4.842029 GCAGCAGCTGTGAATTAATCTAC 58.158 43.478 23.60 0.00 37.91 2.59
1953 1974 4.333649 GCAGCAGCTGTGAATTAATCTACA 59.666 41.667 23.60 5.08 37.91 2.74
1954 1975 5.503683 GCAGCAGCTGTGAATTAATCTACAG 60.504 44.000 23.60 19.86 38.81 2.74
1995 2021 3.515330 ATAGCTTCAAATTGCACCTGC 57.485 42.857 0.00 0.00 42.50 4.85
2025 2051 0.322456 GGGTACATGTGAAGCCAGCA 60.322 55.000 9.11 0.00 33.37 4.41
2104 2153 3.075148 GCACTCCTTAAACCTCAAGGAC 58.925 50.000 2.30 0.00 45.25 3.85
2167 2219 2.553172 GACAGAGAGTGAACTGTACGGT 59.447 50.000 0.04 0.04 45.54 4.83
2501 2554 5.010112 CAGAGTTAATGAGAGGATTAGCCGA 59.990 44.000 0.00 0.00 43.43 5.54
2545 2598 3.181451 TGGAAATGAAGCAGACACTGACT 60.181 43.478 2.81 0.00 32.44 3.41
2550 2603 2.695147 TGAAGCAGACACTGACTGAGAA 59.305 45.455 12.04 0.00 37.54 2.87
2552 2605 4.202295 TGAAGCAGACACTGACTGAGAAAT 60.202 41.667 12.04 0.00 37.54 2.17
2672 2725 0.548510 GGTGAGCCTAGCCTGGATTT 59.451 55.000 0.00 0.00 0.00 2.17
2686 2739 3.435601 CCTGGATTTATGCACCCTAGCTT 60.436 47.826 0.00 0.00 34.99 3.74
2687 2740 4.202461 CCTGGATTTATGCACCCTAGCTTA 60.202 45.833 0.00 0.00 34.99 3.09
2688 2741 4.973168 TGGATTTATGCACCCTAGCTTAG 58.027 43.478 0.00 0.00 34.99 2.18
2689 2742 4.658435 TGGATTTATGCACCCTAGCTTAGA 59.342 41.667 0.00 0.00 34.99 2.10
2691 2744 6.500400 TGGATTTATGCACCCTAGCTTAGATA 59.500 38.462 0.00 0.00 34.99 1.98
2692 2745 7.044798 GGATTTATGCACCCTAGCTTAGATAG 58.955 42.308 0.00 0.00 34.99 2.08
2693 2746 6.996180 TTTATGCACCCTAGCTTAGATAGT 57.004 37.500 3.76 0.00 34.99 2.12
2694 2747 6.996180 TTATGCACCCTAGCTTAGATAGTT 57.004 37.500 3.76 0.00 34.99 2.24
2695 2748 5.896073 ATGCACCCTAGCTTAGATAGTTT 57.104 39.130 3.76 0.00 34.99 2.66
2696 2749 5.693769 TGCACCCTAGCTTAGATAGTTTT 57.306 39.130 3.76 0.00 34.99 2.43
2697 2750 5.671493 TGCACCCTAGCTTAGATAGTTTTC 58.329 41.667 3.76 0.00 34.99 2.29
2698 2751 5.057819 GCACCCTAGCTTAGATAGTTTTCC 58.942 45.833 3.76 0.00 0.00 3.13
2699 2752 5.290386 CACCCTAGCTTAGATAGTTTTCCG 58.710 45.833 3.76 0.00 0.00 4.30
2700 2753 5.068723 CACCCTAGCTTAGATAGTTTTCCGA 59.931 44.000 3.76 0.00 0.00 4.55
2701 2754 5.659971 ACCCTAGCTTAGATAGTTTTCCGAA 59.340 40.000 3.76 0.00 0.00 4.30
2702 2755 5.984323 CCCTAGCTTAGATAGTTTTCCGAAC 59.016 44.000 3.76 0.00 0.00 3.95
2703 2756 6.406624 CCCTAGCTTAGATAGTTTTCCGAACA 60.407 42.308 3.76 0.00 0.00 3.18
2704 2757 7.039882 CCTAGCTTAGATAGTTTTCCGAACAA 58.960 38.462 3.76 0.00 0.00 2.83
2705 2758 7.548075 CCTAGCTTAGATAGTTTTCCGAACAAA 59.452 37.037 3.76 0.00 0.00 2.83
2706 2759 7.739498 AGCTTAGATAGTTTTCCGAACAAAA 57.261 32.000 0.00 0.00 0.00 2.44
2707 2760 7.582352 AGCTTAGATAGTTTTCCGAACAAAAC 58.418 34.615 8.47 8.47 43.73 2.43
2708 2761 7.227910 AGCTTAGATAGTTTTCCGAACAAAACA 59.772 33.333 15.34 6.24 45.16 2.83
2709 2762 7.858879 GCTTAGATAGTTTTCCGAACAAAACAA 59.141 33.333 15.34 4.62 45.16 2.83
2710 2763 9.724839 CTTAGATAGTTTTCCGAACAAAACAAA 57.275 29.630 15.34 7.17 45.16 2.83
2712 2765 8.989653 AGATAGTTTTCCGAACAAAACAAAAA 57.010 26.923 15.34 0.00 45.16 1.94
2887 2940 2.287009 GCTTCAGAGTTTGTGTTTCCCG 60.287 50.000 0.00 0.00 0.00 5.14
2928 2981 5.126869 CCAATCTCCGATGCAGATAGATAGT 59.873 44.000 0.00 0.00 29.97 2.12
2929 2982 6.264832 CAATCTCCGATGCAGATAGATAGTC 58.735 44.000 0.00 0.00 29.97 2.59
2930 2983 5.172687 TCTCCGATGCAGATAGATAGTCT 57.827 43.478 0.00 0.00 0.00 3.24
2931 2984 5.565509 TCTCCGATGCAGATAGATAGTCTT 58.434 41.667 0.00 0.00 0.00 3.01
2933 2986 6.821160 TCTCCGATGCAGATAGATAGTCTTAG 59.179 42.308 0.00 0.00 0.00 2.18
2934 2987 6.477253 TCCGATGCAGATAGATAGTCTTAGT 58.523 40.000 0.00 0.00 0.00 2.24
2964 3028 6.332735 ACTAGAATTTTCTTGAACAAGCCC 57.667 37.500 9.38 0.00 38.70 5.19
2970 3034 5.523438 TTTTCTTGAACAAGCCCGTTTAT 57.477 34.783 9.38 0.00 38.28 1.40
2971 3035 6.636562 TTTTCTTGAACAAGCCCGTTTATA 57.363 33.333 9.38 0.00 38.28 0.98
2981 3045 5.105917 ACAAGCCCGTTTATAATTTCACCAG 60.106 40.000 0.00 0.00 0.00 4.00
3400 3549 1.473278 AGGTTCGTCCTCGATCTTCAC 59.527 52.381 0.00 0.00 44.42 3.18
3456 3605 1.086696 AAGTTGATGATGGCCGTTCG 58.913 50.000 0.00 0.00 0.00 3.95
3594 3743 0.373716 CGGTCTCGCCATTAAAGCAC 59.626 55.000 2.25 0.00 36.97 4.40
3639 3789 4.778534 ATCAACTGCAGAGTTCCAATTG 57.221 40.909 23.35 11.79 40.68 2.32
3694 3844 4.792068 TCTGATTCCAAGACCAAACTTGT 58.208 39.130 0.00 0.00 43.72 3.16
3699 3849 5.367945 TTCCAAGACCAAACTTGTCTACT 57.632 39.130 0.00 0.00 43.72 2.57
3745 3898 1.676746 CCCATGCAGGATGTGAGAAG 58.323 55.000 0.00 0.00 41.22 2.85
3823 3977 1.135139 AGATGCAGTAGTACGTGCCTG 59.865 52.381 16.88 1.50 39.04 4.85
3829 3983 2.030185 CAGTAGTACGTGCCTGTGTCTT 60.030 50.000 0.00 0.00 0.00 3.01
3859 4056 9.502091 ACAAGAAGTAAAAAGATATACACAGCA 57.498 29.630 0.00 0.00 0.00 4.41
3953 4153 5.844004 ACTGACAATATCTCAATCCGGTAC 58.156 41.667 0.00 0.00 0.00 3.34
3987 4187 4.178540 CTCATGTGCCATTTCACCATTTC 58.821 43.478 0.00 0.00 36.17 2.17
4003 4203 4.202781 ACCATTTCCCCAGTAAAAGGACAT 60.203 41.667 0.00 0.00 30.96 3.06
4041 4242 7.986889 ACAAAGTACAAGGCAAAATCTTCAAAT 59.013 29.630 0.00 0.00 0.00 2.32
4110 4311 2.624838 CAAGTTGCCATCAGGTTCACTT 59.375 45.455 0.00 0.00 37.19 3.16
4163 4364 6.019075 TGGCATTGTCGAGTAAATAAGATTCG 60.019 38.462 0.00 0.00 0.00 3.34
4169 4370 3.181774 CGAGTAAATAAGATTCGGTGGCG 59.818 47.826 0.00 0.00 0.00 5.69
4170 4371 4.117685 GAGTAAATAAGATTCGGTGGCGT 58.882 43.478 0.00 0.00 0.00 5.68
4457 4659 9.802039 AATACAGGTAAAATTTTGTCACCTCTA 57.198 29.630 17.37 12.50 37.52 2.43
4495 4701 4.974888 GCAAGCTTTCTTCAACTCTTTCTG 59.025 41.667 0.00 0.00 0.00 3.02
4498 4704 3.316308 GCTTTCTTCAACTCTTTCTGCCA 59.684 43.478 0.00 0.00 0.00 4.92
4499 4705 4.791088 GCTTTCTTCAACTCTTTCTGCCAC 60.791 45.833 0.00 0.00 0.00 5.01
4500 4706 2.851195 TCTTCAACTCTTTCTGCCACC 58.149 47.619 0.00 0.00 0.00 4.61
4501 4707 2.439507 TCTTCAACTCTTTCTGCCACCT 59.560 45.455 0.00 0.00 0.00 4.00
4508 4714 3.006247 CTCTTTCTGCCACCTTAAGCTC 58.994 50.000 0.00 0.00 0.00 4.09
4534 4740 3.701040 ACAGGCAAAATCTGAACAACTGT 59.299 39.130 0.00 0.00 36.22 3.55
4535 4741 4.887071 ACAGGCAAAATCTGAACAACTGTA 59.113 37.500 0.00 0.00 35.17 2.74
4542 4748 9.495754 GCAAAATCTGAACAACTGTATATCTTC 57.504 33.333 0.00 0.00 0.00 2.87
4560 4766 5.503634 TCTTCCTCATGTTCAGATGGAAA 57.496 39.130 0.00 0.00 37.23 3.13
4676 4883 6.806668 TGATGATATCTGGACAGTTTGGTA 57.193 37.500 3.98 0.00 0.00 3.25
4801 5010 4.951715 ACAGTCATATTACCGAGTACCACA 59.048 41.667 0.00 0.00 0.00 4.17
4868 5078 6.183360 CGTTTTCCATGTGGTTAGTCATCTAC 60.183 42.308 0.00 0.00 36.34 2.59
4927 5137 9.322773 CTCAAATGAGAAAGAGAGCATATTACA 57.677 33.333 4.37 0.00 44.74 2.41
5006 5225 6.945435 CAGACAGAGAGGAGAGGCTAATAATA 59.055 42.308 0.00 0.00 0.00 0.98
5007 5226 7.615365 CAGACAGAGAGGAGAGGCTAATAATAT 59.385 40.741 0.00 0.00 0.00 1.28
5008 5227 7.834181 AGACAGAGAGGAGAGGCTAATAATATC 59.166 40.741 0.00 0.00 0.00 1.63
5061 5280 1.518325 CGGTGACTGTTACAATGCCA 58.482 50.000 5.05 0.00 0.00 4.92
5188 5411 3.914984 TGTTACCTGACAGAGCAGC 57.085 52.632 3.32 0.00 34.56 5.25
5189 5412 0.321671 TGTTACCTGACAGAGCAGCC 59.678 55.000 3.32 0.00 34.56 4.85
5190 5413 0.391793 GTTACCTGACAGAGCAGCCC 60.392 60.000 3.32 0.00 34.56 5.19
5191 5414 1.553690 TTACCTGACAGAGCAGCCCC 61.554 60.000 3.32 0.00 34.56 5.80
5237 5460 0.689623 ACTGAGACCCAGAAGCCAAG 59.310 55.000 0.00 0.00 45.78 3.61
5538 5762 4.749310 CTCAGCCCAAGCGCGTCT 62.749 66.667 8.43 1.94 46.67 4.18
5573 5797 1.369625 GTGACCGGGCAATGAGTAAG 58.630 55.000 14.43 0.00 0.00 2.34
5574 5798 0.392461 TGACCGGGCAATGAGTAAGC 60.392 55.000 8.12 0.00 0.00 3.09
5615 5839 0.234884 GTACGCAACAGGCAACACTC 59.765 55.000 0.00 0.00 45.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.470709 AGTTGATTCGGTATGCCAGATG 58.529 45.455 0.00 0.00 34.09 2.90
25 26 7.364232 CCTTCGGGCTATGATAGATAGTTGATT 60.364 40.741 3.13 0.00 0.00 2.57
34 35 4.994282 TCTAACCTTCGGGCTATGATAGA 58.006 43.478 3.13 0.00 39.10 1.98
46 48 4.389077 GTGAGGTCAACAATCTAACCTTCG 59.611 45.833 0.00 0.00 42.15 3.79
84 86 1.528161 GCATGTGTGCCTTCTTTTTGC 59.472 47.619 0.00 0.00 45.76 3.68
109 112 2.029918 TCGTGGAGTGACTCATGAACAG 60.030 50.000 15.33 4.35 31.08 3.16
139 142 3.813443 AGAGGAATCATGGTGATTTCGG 58.187 45.455 6.63 0.00 46.20 4.30
152 155 2.422479 GGCGGTTAACCAAAGAGGAATC 59.578 50.000 24.14 0.37 41.22 2.52
177 180 1.024271 GACACAAAGCTCTTGCACCA 58.976 50.000 8.09 0.00 42.74 4.17
188 191 1.358759 GTTGCGGGGTGACACAAAG 59.641 57.895 8.08 0.00 0.00 2.77
191 194 1.152860 ATTGTTGCGGGGTGACACA 60.153 52.632 8.08 0.00 0.00 3.72
212 215 1.693627 GACGGAATCTAGCAGAGGGA 58.306 55.000 0.00 0.00 0.00 4.20
218 221 0.245266 TTGTGCGACGGAATCTAGCA 59.755 50.000 0.00 0.00 35.27 3.49
262 265 0.175989 GGTCGAGGTCATTGTCCTCC 59.824 60.000 19.94 9.90 46.09 4.30
284 287 2.124942 GGCTTCTCCTCCCTTGCG 60.125 66.667 0.00 0.00 0.00 4.85
372 375 2.590092 CCATTGGGGACGACCTCC 59.410 66.667 0.07 2.95 40.01 4.30
390 393 3.945434 GCTGCACATCCATCGCCG 61.945 66.667 0.00 0.00 0.00 6.46
406 409 1.871039 TCGTCTAAAGCCTGTTGTTGC 59.129 47.619 0.00 0.00 0.00 4.17
420 423 2.026169 AGGATCTCCACACACTCGTCTA 60.026 50.000 0.00 0.00 38.89 2.59
422 425 1.178276 AGGATCTCCACACACTCGTC 58.822 55.000 0.00 0.00 38.89 4.20
423 426 1.546476 GAAGGATCTCCACACACTCGT 59.454 52.381 0.00 0.00 38.89 4.18
457 460 8.593945 AAATATGGTTTTATCTCAAGCCTTCA 57.406 30.769 0.00 0.00 0.00 3.02
487 490 5.586243 CGCATGATCTTTATATTACAGGGGG 59.414 44.000 0.00 0.00 0.00 5.40
563 566 5.934043 TGGAAGGATGATATAAGATGTTGCG 59.066 40.000 0.00 0.00 0.00 4.85
573 576 9.050154 ACACATATCACATGGAAGGATGATATA 57.950 33.333 11.71 0.00 40.93 0.86
585 588 4.279169 GGATTGGGAACACATATCACATGG 59.721 45.833 0.00 0.00 42.67 3.66
595 598 3.944650 CGTGATAATGGATTGGGAACACA 59.055 43.478 0.00 0.00 42.67 3.72
598 601 4.703897 TCTCGTGATAATGGATTGGGAAC 58.296 43.478 0.00 0.00 0.00 3.62
603 606 6.612306 TCGACTATCTCGTGATAATGGATTG 58.388 40.000 8.42 0.00 43.45 2.67
605 608 6.819397 TTCGACTATCTCGTGATAATGGAT 57.181 37.500 8.42 0.00 43.45 3.41
611 614 5.238650 TGCTCAATTCGACTATCTCGTGATA 59.761 40.000 6.98 6.98 43.45 2.15
656 659 7.052248 AGTAAAAGAATAGTTATTCGGTGGGG 58.948 38.462 6.30 0.00 45.10 4.96
657 660 9.038803 GTAGTAAAAGAATAGTTATTCGGTGGG 57.961 37.037 6.30 0.00 45.10 4.61
674 677 8.345565 AGTGCTTGAACTTGATTGTAGTAAAAG 58.654 33.333 0.00 0.00 0.00 2.27
675 678 8.220755 AGTGCTTGAACTTGATTGTAGTAAAA 57.779 30.769 0.00 0.00 0.00 1.52
691 698 6.293955 GGCTCATTGTTTAGTTAGTGCTTGAA 60.294 38.462 0.00 0.00 0.00 2.69
695 702 4.911390 AGGCTCATTGTTTAGTTAGTGCT 58.089 39.130 0.00 0.00 0.00 4.40
708 715 4.178540 CCAGCAATGTTTTAGGCTCATTG 58.821 43.478 17.65 17.65 46.11 2.82
727 734 3.942829 TCTTGATGCAGTTTAGGACCAG 58.057 45.455 0.00 0.00 0.00 4.00
792 799 6.234177 CCCCCTTTATTGTTTGCAATTTACA 58.766 36.000 0.00 0.00 42.19 2.41
800 807 2.849294 TTGCCCCCTTTATTGTTTGC 57.151 45.000 0.00 0.00 0.00 3.68
950 957 1.261238 AAGCCAAGGAGGAGGAGACG 61.261 60.000 0.00 0.00 41.22 4.18
1298 1305 0.179081 GAACATGCTCCCGTACCTCC 60.179 60.000 0.00 0.00 0.00 4.30
1464 1471 2.386661 ACTTGTAGATGAAGCCGTGG 57.613 50.000 0.00 0.00 0.00 4.94
1658 1665 0.103208 AGACCGCGAACTGGATCATC 59.897 55.000 8.23 0.00 0.00 2.92
1686 1693 2.938956 ACCTGCATTAGCCATCTACC 57.061 50.000 0.00 0.00 41.13 3.18
1908 1927 1.515020 CTGCGGAAGAGACAGAGGG 59.485 63.158 0.00 0.00 33.10 4.30
1999 2025 2.484264 GCTTCACATGTACCCACTGTTC 59.516 50.000 0.00 0.00 0.00 3.18
2025 2051 5.411361 TCTGTGCGTGCTCATTAATTTAGTT 59.589 36.000 0.00 0.00 0.00 2.24
2114 2166 6.940430 AGGGAACTGAATTTGATGGAAATT 57.060 33.333 0.00 0.00 45.29 1.82
2179 2231 2.037772 TGCACCACCGCCATTTATTTTT 59.962 40.909 0.00 0.00 0.00 1.94
2423 2476 1.891616 GACGACTCTGGGGTTCTCC 59.108 63.158 0.00 0.00 0.00 3.71
2501 2554 7.274447 TCCAGTCAAATGAAAAGAAATTTGCT 58.726 30.769 0.00 0.00 41.47 3.91
2545 2598 3.554960 CCTCCTGTTCACGTGATTTCTCA 60.555 47.826 20.80 12.26 0.00 3.27
2550 2603 2.104111 TGTTCCTCCTGTTCACGTGATT 59.896 45.455 20.80 0.00 0.00 2.57
2552 2605 1.116308 TGTTCCTCCTGTTCACGTGA 58.884 50.000 15.76 15.76 0.00 4.35
2672 2725 6.996180 AAACTATCTAAGCTAGGGTGCATA 57.004 37.500 0.00 0.00 34.99 3.14
2687 2740 8.989653 TTTTTGTTTTGTTCGGAAAACTATCT 57.010 26.923 14.95 0.00 43.40 1.98
2710 2763 9.014297 ACAGTTGCAATATCTAAGCTAGTTTTT 57.986 29.630 0.59 0.00 0.00 1.94
2711 2764 8.567285 ACAGTTGCAATATCTAAGCTAGTTTT 57.433 30.769 0.59 0.00 0.00 2.43
2712 2765 9.099454 GTACAGTTGCAATATCTAAGCTAGTTT 57.901 33.333 0.59 0.00 0.00 2.66
2713 2766 8.258007 TGTACAGTTGCAATATCTAAGCTAGTT 58.742 33.333 0.59 0.00 0.00 2.24
2714 2767 7.782049 TGTACAGTTGCAATATCTAAGCTAGT 58.218 34.615 0.59 0.00 0.00 2.57
2715 2768 8.648557 TTGTACAGTTGCAATATCTAAGCTAG 57.351 34.615 0.59 0.00 0.00 3.42
2887 2940 6.350194 GGAGATTGGGACTTGGTTAAACAATC 60.350 42.308 6.36 6.74 41.61 2.67
2943 3007 4.825085 ACGGGCTTGTTCAAGAAAATTCTA 59.175 37.500 15.52 0.00 36.28 2.10
2948 3012 3.878160 AAACGGGCTTGTTCAAGAAAA 57.122 38.095 15.52 0.00 0.00 2.29
2971 3035 9.449719 CTACCTTATTACTTGTCTGGTGAAATT 57.550 33.333 0.00 0.00 0.00 1.82
2981 3045 6.600822 GGGGGTTTTCTACCTTATTACTTGTC 59.399 42.308 0.00 0.00 46.86 3.18
3199 3348 1.638529 AACAGAGGACCTGGTCTGAG 58.361 55.000 25.01 15.04 38.84 3.35
3400 3549 4.100653 TGCTATGGTTTCTGAGAGATGAGG 59.899 45.833 0.00 0.00 0.00 3.86
3437 3586 1.086696 CGAACGGCCATCATCAACTT 58.913 50.000 2.24 0.00 0.00 2.66
3456 3605 2.267961 GACCGGACACCATGACCC 59.732 66.667 9.46 0.00 0.00 4.46
3594 3743 3.997021 AGAGTACTGTTTCCTGCGATTTG 59.003 43.478 0.00 0.00 0.00 2.32
3678 3828 4.407621 TCAGTAGACAAGTTTGGTCTTGGA 59.592 41.667 10.44 0.00 46.11 3.53
3681 3831 5.871396 TCTCAGTAGACAAGTTTGGTCTT 57.129 39.130 0.00 0.00 42.77 3.01
3694 3844 5.220873 CGAATTCGTTCCTGATCTCAGTAGA 60.221 44.000 19.67 0.00 37.12 2.59
3699 3849 2.496070 ACCGAATTCGTTCCTGATCTCA 59.504 45.455 25.10 0.00 37.74 3.27
3714 3864 1.591183 GCATGGGCAACAACCGAAT 59.409 52.632 0.00 0.00 40.72 3.34
3745 3898 0.446616 GAAGTTTCGGCGATGGTTCC 59.553 55.000 11.76 0.00 0.00 3.62
3817 3970 2.682856 TCTTGTTCAAAGACACAGGCAC 59.317 45.455 0.00 0.00 0.00 5.01
3823 3977 9.788960 ATCTTTTTACTTCTTGTTCAAAGACAC 57.211 29.630 0.00 0.00 37.84 3.67
3850 4047 4.186926 CTGCAACTAGACATGCTGTGTAT 58.813 43.478 16.62 0.00 42.36 2.29
3857 4054 3.125316 GTGGTTACTGCAACTAGACATGC 59.875 47.826 0.00 4.85 42.86 4.06
3859 4056 4.617253 TGTGGTTACTGCAACTAGACAT 57.383 40.909 0.00 0.00 37.30 3.06
3887 4087 9.044150 CAAACATGAAAATAAACAATGGTCAGT 57.956 29.630 0.00 0.00 0.00 3.41
3891 4091 6.714356 CCCCAAACATGAAAATAAACAATGGT 59.286 34.615 0.00 0.00 0.00 3.55
3912 4112 1.151413 AGTCTAGAACCCTGAACCCCA 59.849 52.381 0.00 0.00 0.00 4.96
3953 4153 3.068165 TGGCACATGAGGTTCTATCTACG 59.932 47.826 0.00 0.00 0.00 3.51
3987 4187 7.660030 ATTTCATTATGTCCTTTTACTGGGG 57.340 36.000 0.00 0.00 0.00 4.96
4041 4242 0.914644 ATTGGCAAGGCAGCTCTCTA 59.085 50.000 5.96 0.00 34.17 2.43
4110 4311 3.821600 GACTCGATCACCTAGCAGGATAA 59.178 47.826 8.91 0.00 37.67 1.75
4163 4364 0.240945 CACAATCTTGGAACGCCACC 59.759 55.000 0.00 0.00 45.94 4.61
4169 4370 4.614535 GCACATCTCACACAATCTTGGAAC 60.615 45.833 0.00 0.00 0.00 3.62
4170 4371 3.503363 GCACATCTCACACAATCTTGGAA 59.497 43.478 0.00 0.00 0.00 3.53
4277 4479 3.428045 GCAAAGACCAAATCAGAATCCGG 60.428 47.826 0.00 0.00 0.00 5.14
4363 4565 3.110178 GTTCCGACGCAGAACCGG 61.110 66.667 0.00 0.00 44.22 5.28
4414 4616 6.708949 ACCTGTATTTCGTAACAAGATTGTGT 59.291 34.615 0.00 0.00 41.31 3.72
4451 4653 9.930693 GCTTGCTATATGTACTTATTTAGAGGT 57.069 33.333 6.59 0.00 0.00 3.85
4466 4672 7.551035 AGAGTTGAAGAAAGCTTGCTATATG 57.449 36.000 7.58 0.00 33.61 1.78
4495 4701 2.079925 CTGTTCAGAGCTTAAGGTGGC 58.920 52.381 12.82 0.00 0.00 5.01
4498 4704 1.699634 TGCCTGTTCAGAGCTTAAGGT 59.300 47.619 6.94 6.94 0.00 3.50
4499 4705 2.479566 TGCCTGTTCAGAGCTTAAGG 57.520 50.000 4.29 0.00 0.00 2.69
4500 4706 4.836125 TTTTGCCTGTTCAGAGCTTAAG 57.164 40.909 0.00 0.00 0.00 1.85
4501 4707 5.048504 CAGATTTTGCCTGTTCAGAGCTTAA 60.049 40.000 1.00 3.42 0.00 1.85
4508 4714 4.572985 TGTTCAGATTTTGCCTGTTCAG 57.427 40.909 0.00 0.00 33.57 3.02
4534 4740 8.496534 TTCCATCTGAACATGAGGAAGATATA 57.503 34.615 0.00 0.00 31.93 0.86
4535 4741 7.384524 TTCCATCTGAACATGAGGAAGATAT 57.615 36.000 0.00 0.00 31.93 1.63
4542 4748 3.127548 CCGTTTTCCATCTGAACATGAGG 59.872 47.826 0.00 0.00 31.05 3.86
4560 4766 0.841289 TGTTCCCTCCTTTGACCGTT 59.159 50.000 0.00 0.00 0.00 4.44
4676 4883 6.207691 ACAATCTTGTGTTTAACTGCAACT 57.792 33.333 0.00 0.00 40.49 3.16
4801 5010 3.333893 ACCCATTCTGGATCCATGAGAT 58.666 45.455 16.63 4.25 40.96 2.75
4868 5078 4.278170 ACTGATTTACACACAACACATGGG 59.722 41.667 0.00 0.00 38.89 4.00
4926 5136 3.317711 TGGCTCCACACAACAGTTTTATG 59.682 43.478 0.00 0.00 0.00 1.90
4927 5137 3.561143 TGGCTCCACACAACAGTTTTAT 58.439 40.909 0.00 0.00 0.00 1.40
4929 5139 1.846007 TGGCTCCACACAACAGTTTT 58.154 45.000 0.00 0.00 0.00 2.43
4930 5140 1.682854 CATGGCTCCACACAACAGTTT 59.317 47.619 0.00 0.00 0.00 2.66
4931 5141 1.321474 CATGGCTCCACACAACAGTT 58.679 50.000 0.00 0.00 0.00 3.16
4932 5142 1.174712 GCATGGCTCCACACAACAGT 61.175 55.000 0.00 0.00 0.00 3.55
4933 5143 1.582968 GCATGGCTCCACACAACAG 59.417 57.895 0.00 0.00 0.00 3.16
4934 5144 1.902918 GGCATGGCTCCACACAACA 60.903 57.895 12.86 0.00 0.00 3.33
4935 5145 1.604593 AGGCATGGCTCCACACAAC 60.605 57.895 17.44 0.00 0.00 3.32
4937 5147 2.034532 CAGGCATGGCTCCACACA 59.965 61.111 20.57 0.00 0.00 3.72
4938 5148 1.748122 CTCAGGCATGGCTCCACAC 60.748 63.158 20.57 0.00 0.00 3.82
5006 5225 0.548510 GGCTAGGCTGTTTGGGAGAT 59.451 55.000 9.46 0.00 0.00 2.75
5007 5226 1.562672 GGGCTAGGCTGTTTGGGAGA 61.563 60.000 16.80 0.00 0.00 3.71
5008 5227 1.077429 GGGCTAGGCTGTTTGGGAG 60.077 63.158 16.80 0.00 0.00 4.30
5046 5265 4.475944 GACACATTGGCATTGTAACAGTC 58.524 43.478 14.07 12.93 0.00 3.51
5082 5301 7.814587 GCTTTTCAATTATTAAGTGTGGCTCTT 59.185 33.333 4.01 0.00 0.00 2.85
5191 5414 4.547367 GGAATGGCGACCCGAGGG 62.547 72.222 6.63 6.63 42.03 4.30
5237 5460 6.348868 GGAAAAGGTGTCATTCAGAGATCAAC 60.349 42.308 0.00 0.00 0.00 3.18
5371 5595 6.127897 CCTCTGGACACCATCACTTTTAAATC 60.128 42.308 0.00 0.00 30.82 2.17
5380 5604 0.326264 AAGCCTCTGGACACCATCAC 59.674 55.000 0.00 0.00 30.82 3.06
5554 5778 1.369625 CTTACTCATTGCCCGGTCAC 58.630 55.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.