Multiple sequence alignment - TraesCS4D01G076000

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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 TraesCS4D01G076000 chr4D 100.000 4295 0 0 1 4295 50640292 50644586 0.000000e+00 7932.0
1 TraesCS4D01G076000 chr4A 93.505 3572 134 44 224 3734 546299628 546296094 0.000000e+00 5221.0
2 TraesCS4D01G076000 chr4A 88.889 540 35 13 3765 4295 546296093 546295570 3.620000e-180 641.0
3 TraesCS4D01G076000 chr4A 71.449 697 146 42 1373 2035 680451619 680452296 7.490000e-28 135.0
4 TraesCS4D01G076000 chr4A 93.590 78 4 1 2279 2356 568880943 568880867 9.760000e-22 115.0
5 TraesCS4D01G076000 chr4B 93.529 2936 113 38 941 3822 74441163 74444075 0.000000e+00 4298.0
6 TraesCS4D01G076000 chr4B 93.071 534 26 7 3765 4295 74444392 74444917 0.000000e+00 771.0
7 TraesCS4D01G076000 chr4B 86.957 552 23 18 434 944 74440585 74441128 3.720000e-160 575.0
8 TraesCS4D01G076000 chr4B 90.085 353 33 2 1 352 74440189 74440540 1.410000e-124 457.0
9 TraesCS4D01G076000 chr5D 77.037 1755 347 52 1158 2887 473117556 473115833 0.000000e+00 957.0
10 TraesCS4D01G076000 chr5D 73.409 707 153 30 1378 2062 326736067 326735374 9.290000e-57 231.0
11 TraesCS4D01G076000 chr5D 85.938 64 6 3 22 83 210680857 210680919 9.970000e-07 65.8
12 TraesCS4D01G076000 chr5B 76.629 1780 356 56 1158 2910 580515297 580513551 0.000000e+00 928.0
13 TraesCS4D01G076000 chr5B 91.667 48 4 0 28 75 224325490 224325537 2.770000e-07 67.6
14 TraesCS4D01G076000 chr5A 76.140 1777 370 50 1158 2910 593090091 593088345 0.000000e+00 883.0
15 TraesCS4D01G076000 chr5A 91.667 48 4 0 30 77 272950470 272950517 2.770000e-07 67.6
16 TraesCS4D01G076000 chr2A 73.637 899 187 42 1192 2062 652288604 652289480 6.980000e-78 302.0
17 TraesCS4D01G076000 chr2D 75.542 646 138 19 1378 2013 507749839 507750474 2.510000e-77 300.0
18 TraesCS4D01G076000 chr2B 74.576 649 139 22 1378 2013 596410843 596411478 1.180000e-65 261.0
19 TraesCS4D01G076000 chr6A 77.990 418 74 13 2481 2892 572572843 572572438 3.320000e-61 246.0
20 TraesCS4D01G076000 chr6B 77.262 409 75 13 2478 2880 643898439 643898835 1.550000e-54 224.0
21 TraesCS4D01G076000 chr6D 75.837 418 89 9 2478 2892 427569035 427568627 7.280000e-48 202.0
22 TraesCS4D01G076000 chr1D 83.594 128 17 3 2581 2706 366875450 366875575 2.710000e-22 117.0


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 TraesCS4D01G076000 chr4D 50640292 50644586 4294 False 7932.00 7932 100.0000 1 4295 1 chr4D.!!$F1 4294
1 TraesCS4D01G076000 chr4A 546295570 546299628 4058 True 2931.00 5221 91.1970 224 4295 2 chr4A.!!$R2 4071
2 TraesCS4D01G076000 chr4B 74440189 74444917 4728 False 1525.25 4298 90.9105 1 4295 4 chr4B.!!$F1 4294
3 TraesCS4D01G076000 chr5D 473115833 473117556 1723 True 957.00 957 77.0370 1158 2887 1 chr5D.!!$R2 1729
4 TraesCS4D01G076000 chr5D 326735374 326736067 693 True 231.00 231 73.4090 1378 2062 1 chr5D.!!$R1 684
5 TraesCS4D01G076000 chr5B 580513551 580515297 1746 True 928.00 928 76.6290 1158 2910 1 chr5B.!!$R1 1752
6 TraesCS4D01G076000 chr5A 593088345 593090091 1746 True 883.00 883 76.1400 1158 2910 1 chr5A.!!$R1 1752
7 TraesCS4D01G076000 chr2A 652288604 652289480 876 False 302.00 302 73.6370 1192 2062 1 chr2A.!!$F1 870
8 TraesCS4D01G076000 chr2D 507749839 507750474 635 False 300.00 300 75.5420 1378 2013 1 chr2D.!!$F1 635
9 TraesCS4D01G076000 chr2B 596410843 596411478 635 False 261.00 261 74.5760 1378 2013 1 chr2B.!!$F1 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
564 578 0.037326 TCCGGCAAAGACACAGCTAG 60.037 55.0 0.00 0.00 0.00 3.42 F
567 581 0.801251 GGCAAAGACACAGCTAGCAG 59.199 55.0 18.83 12.15 0.00 4.24 F
2490 2650 0.179001 TGATCACGCCGGAGATCCTA 60.179 55.0 13.83 0.31 38.89 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 2650 1.153168 CCCGATGATGTCCGGCTTT 60.153 57.895 0.00 0.0 44.07 3.51 R
2517 2677 3.803082 CACGCCGCCAGGATGTTG 61.803 66.667 0.00 0.0 41.02 3.33 R
3763 3967 0.469705 TTTCCTGCAGCACCAACCAT 60.470 50.000 8.66 0.0 0.00 3.55 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
23 24 5.484715 CATGGCAAATTCCTGACAATCTTT 58.515 37.500 0.00 0.00 38.03 2.52
29 30 7.983484 GGCAAATTCCTGACAATCTTTCAATAT 59.017 33.333 0.00 0.00 0.00 1.28
110 111 7.944729 ACATGATAATTTCAAGGTGTTAGCT 57.055 32.000 0.00 0.00 38.03 3.32
123 124 3.685272 GGTGTTAGCTAGGAGCAGTTTTC 59.315 47.826 0.64 0.00 45.56 2.29
139 140 3.459969 AGTTTTCAGAGGAAACACTCCCT 59.540 43.478 3.95 0.00 46.81 4.20
143 144 2.834549 TCAGAGGAAACACTCCCTGATC 59.165 50.000 7.48 0.00 46.81 2.92
198 199 1.726791 CCGTTCGTTCACTTGGATGAG 59.273 52.381 0.00 0.00 0.00 2.90
216 217 1.733399 GCTCCGTGAGTGAACGTCC 60.733 63.158 0.00 0.00 42.01 4.79
219 220 2.354188 CGTGAGTGAACGTCCGCA 60.354 61.111 0.00 0.00 38.74 5.69
290 291 3.124297 CCGAAACAGCAGCAAAAACAAAA 59.876 39.130 0.00 0.00 0.00 2.44
295 296 1.134128 AGCAGCAAAAACAAAAGGGGG 60.134 47.619 0.00 0.00 0.00 5.40
333 334 4.336713 TGTTTCACGTTTTCACATGGATCA 59.663 37.500 0.00 0.00 0.00 2.92
390 391 0.944311 CCGCCGTCCATAATCCGAAG 60.944 60.000 0.00 0.00 0.00 3.79
401 408 6.967767 GTCCATAATCCGAAGAGATACATACG 59.032 42.308 0.00 0.00 0.00 3.06
418 425 0.462789 ACGGAATATGGGACGGACAC 59.537 55.000 0.00 0.00 0.00 3.67
560 574 2.317609 CGGTCCGGCAAAGACACAG 61.318 63.158 2.34 0.00 35.89 3.66
561 575 2.617274 GGTCCGGCAAAGACACAGC 61.617 63.158 0.00 0.00 35.89 4.40
562 576 1.598130 GTCCGGCAAAGACACAGCT 60.598 57.895 0.00 0.00 34.27 4.24
563 577 0.320421 GTCCGGCAAAGACACAGCTA 60.320 55.000 0.00 0.00 34.27 3.32
564 578 0.037326 TCCGGCAAAGACACAGCTAG 60.037 55.000 0.00 0.00 0.00 3.42
565 579 1.639298 CCGGCAAAGACACAGCTAGC 61.639 60.000 6.62 6.62 0.00 3.42
566 580 0.950555 CGGCAAAGACACAGCTAGCA 60.951 55.000 18.83 0.00 0.00 3.49
567 581 0.801251 GGCAAAGACACAGCTAGCAG 59.199 55.000 18.83 12.15 0.00 4.24
587 603 3.681835 GGTCGACCGACTGGCAGT 61.682 66.667 22.26 22.26 44.04 4.40
648 672 2.995574 CCGTTCGTCCCACCCTCT 60.996 66.667 0.00 0.00 0.00 3.69
676 700 4.160635 GTGCGTGCGCCCACATAC 62.161 66.667 14.16 0.55 42.17 2.39
686 710 2.030274 GCGCCCACATACACTTTTTCTT 60.030 45.455 0.00 0.00 0.00 2.52
687 711 3.821841 CGCCCACATACACTTTTTCTTC 58.178 45.455 0.00 0.00 0.00 2.87
688 712 3.502211 CGCCCACATACACTTTTTCTTCT 59.498 43.478 0.00 0.00 0.00 2.85
689 713 4.613622 CGCCCACATACACTTTTTCTTCTG 60.614 45.833 0.00 0.00 0.00 3.02
690 714 4.518970 GCCCACATACACTTTTTCTTCTGA 59.481 41.667 0.00 0.00 0.00 3.27
692 716 6.460953 GCCCACATACACTTTTTCTTCTGAAA 60.461 38.462 0.00 0.00 40.08 2.69
694 718 8.143835 CCCACATACACTTTTTCTTCTGAAATT 58.856 33.333 0.00 0.00 41.24 1.82
732 797 3.389329 ACTCACACTCACCATCTTTCACT 59.611 43.478 0.00 0.00 0.00 3.41
734 799 3.070018 CACACTCACCATCTTTCACTCC 58.930 50.000 0.00 0.00 0.00 3.85
735 800 2.975489 ACACTCACCATCTTTCACTCCT 59.025 45.455 0.00 0.00 0.00 3.69
736 801 3.007398 ACACTCACCATCTTTCACTCCTC 59.993 47.826 0.00 0.00 0.00 3.71
737 802 2.569404 ACTCACCATCTTTCACTCCTCC 59.431 50.000 0.00 0.00 0.00 4.30
738 803 1.550524 TCACCATCTTTCACTCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
739 804 1.550524 CACCATCTTTCACTCCTCCGA 59.449 52.381 0.00 0.00 0.00 4.55
740 805 1.550976 ACCATCTTTCACTCCTCCGAC 59.449 52.381 0.00 0.00 0.00 4.79
741 806 1.469940 CCATCTTTCACTCCTCCGACG 60.470 57.143 0.00 0.00 0.00 5.12
742 807 0.818296 ATCTTTCACTCCTCCGACGG 59.182 55.000 7.84 7.84 0.00 4.79
743 808 1.215647 CTTTCACTCCTCCGACGGG 59.784 63.158 15.25 4.64 0.00 5.28
744 809 2.837371 CTTTCACTCCTCCGACGGGC 62.837 65.000 15.25 0.00 0.00 6.13
752 817 3.072468 TCCGACGGGCCTCGATTT 61.072 61.111 21.68 0.00 42.43 2.17
755 820 2.582436 GACGGGCCTCGATTTCCA 59.418 61.111 18.74 0.00 42.43 3.53
763 828 1.332997 GCCTCGATTTCCATCAAGCAG 59.667 52.381 0.00 0.00 0.00 4.24
804 869 7.015682 ACAAACTTCATCTCCTCTTCTTGTAGA 59.984 37.037 0.00 0.00 0.00 2.59
826 904 3.642141 ACCAACCAACTGTCCATCTTTT 58.358 40.909 0.00 0.00 0.00 2.27
947 1034 3.629883 TAACACTACCACGGCGGCG 62.630 63.158 31.06 31.06 39.03 6.46
1185 1330 3.446570 GCCGCTGCCAAGATGCTT 61.447 61.111 0.00 0.00 0.00 3.91
1218 1363 2.343758 GTCCTGCACGGCTTCTCA 59.656 61.111 0.00 0.00 0.00 3.27
1917 2077 2.279069 CGTCCTGGTGTCCTGCTCT 61.279 63.158 0.00 0.00 0.00 4.09
2136 2296 1.515521 CCAACTCCACCAGCGGAAAC 61.516 60.000 1.50 0.00 33.65 2.78
2232 2392 1.901650 GCGTCCAGAAAGGCTTCGTG 61.902 60.000 0.00 0.62 36.61 4.35
2490 2650 0.179001 TGATCACGCCGGAGATCCTA 60.179 55.000 13.83 0.31 38.89 2.94
2959 3119 0.243095 GAACAAGACCTACGCCGTCT 59.757 55.000 0.00 0.00 42.41 4.18
3136 3296 4.394078 CCGTCGACGTGAAGCCGA 62.394 66.667 33.49 0.00 37.74 5.54
3138 3298 3.164011 GTCGACGTGAAGCCGACG 61.164 66.667 10.40 0.00 44.84 5.12
3260 3420 1.445582 GGTCGGACGGTAAGCACAG 60.446 63.158 1.43 0.00 0.00 3.66
3295 3455 2.890808 AGCGATAACGTGGACATGAT 57.109 45.000 0.00 0.00 41.98 2.45
3381 3541 5.983118 CCAAAGGGTTCAGTGTGTAAAATTC 59.017 40.000 0.00 0.00 0.00 2.17
3399 3559 2.285868 GGGGGATTCGAGGGAGGA 59.714 66.667 0.00 0.00 0.00 3.71
3402 3562 1.141185 GGGGATTCGAGGGAGGAAAT 58.859 55.000 0.00 0.00 0.00 2.17
3408 3568 1.195115 TCGAGGGAGGAAATGGTGAG 58.805 55.000 0.00 0.00 0.00 3.51
3410 3570 1.765314 CGAGGGAGGAAATGGTGAGAT 59.235 52.381 0.00 0.00 0.00 2.75
3428 3597 5.582665 GTGAGATTTGGTGGTATCTCTCAAC 59.417 44.000 11.92 1.19 44.51 3.18
3436 3605 5.830457 TGGTGGTATCTCTCAACTATCTCAG 59.170 44.000 0.00 0.00 0.00 3.35
3438 3607 6.719370 GGTGGTATCTCTCAACTATCTCAGAT 59.281 42.308 0.00 0.00 0.00 2.90
3482 3654 8.748412 CATAACTTTTAGATTGTGATTTGGGGA 58.252 33.333 0.00 0.00 0.00 4.81
3488 3660 5.728637 AGATTGTGATTTGGGGAAGAAAC 57.271 39.130 0.00 0.00 0.00 2.78
3519 3691 2.110578 GAAAGGGATTTGGGTGATGGG 58.889 52.381 0.00 0.00 0.00 4.00
3531 3719 2.952310 GGGTGATGGGTATTGCTTTCTC 59.048 50.000 0.00 0.00 0.00 2.87
3546 3734 6.048073 TGCTTTCTCGGAATCAAATTATCG 57.952 37.500 0.00 0.00 0.00 2.92
3576 3765 1.005924 AGCTTGGGTAGTTGGATTGGG 59.994 52.381 0.00 0.00 0.00 4.12
3577 3766 1.272480 GCTTGGGTAGTTGGATTGGGT 60.272 52.381 0.00 0.00 0.00 4.51
3578 3767 2.723273 CTTGGGTAGTTGGATTGGGTC 58.277 52.381 0.00 0.00 0.00 4.46
3604 3793 4.592942 AGTTGGATCAGATTGCAGCTTTA 58.407 39.130 0.00 0.00 0.00 1.85
3614 3803 1.238439 TGCAGCTTTACAAGGACAGC 58.762 50.000 0.00 0.00 0.00 4.40
3616 3805 1.466558 GCAGCTTTACAAGGACAGCTC 59.533 52.381 0.00 0.00 40.75 4.09
3632 3821 2.952978 CAGCTCCACTGTAGTAGTAGGG 59.047 54.545 0.00 0.00 41.86 3.53
3633 3822 2.091775 AGCTCCACTGTAGTAGTAGGGG 60.092 54.545 0.00 0.00 37.60 4.79
3634 3823 2.357986 GCTCCACTGTAGTAGTAGGGGT 60.358 54.545 3.25 0.00 38.65 4.95
3635 3824 3.880914 GCTCCACTGTAGTAGTAGGGGTT 60.881 52.174 3.25 0.00 38.65 4.11
3636 3825 4.629694 GCTCCACTGTAGTAGTAGGGGTTA 60.630 50.000 3.25 0.00 38.65 2.85
3638 3827 5.699143 TCCACTGTAGTAGTAGGGGTTATC 58.301 45.833 3.25 0.00 38.65 1.75
3650 3854 3.118531 AGGGGTTATCTCAGTCAGCAAT 58.881 45.455 0.00 0.00 0.00 3.56
3651 3855 3.135530 AGGGGTTATCTCAGTCAGCAATC 59.864 47.826 0.00 0.00 0.00 2.67
3655 3859 5.288804 GGTTATCTCAGTCAGCAATCTCTC 58.711 45.833 0.00 0.00 0.00 3.20
3665 3869 3.587061 TCAGCAATCTCTCCCCTGTAAAA 59.413 43.478 0.00 0.00 0.00 1.52
3671 3875 4.569719 TCTCTCCCCTGTAAAATGTTCC 57.430 45.455 0.00 0.00 0.00 3.62
3679 3883 5.106436 CCCCTGTAAAATGTTCCGTCTAAAC 60.106 44.000 0.00 0.00 0.00 2.01
3756 3960 9.831737 AATGATTGAGTGAAGATAAAAGAAACG 57.168 29.630 0.00 0.00 0.00 3.60
3758 3962 8.712363 TGATTGAGTGAAGATAAAAGAAACGAG 58.288 33.333 0.00 0.00 0.00 4.18
3761 3965 7.214381 TGAGTGAAGATAAAAGAAACGAGGAA 58.786 34.615 0.00 0.00 0.00 3.36
3762 3966 7.385205 TGAGTGAAGATAAAAGAAACGAGGAAG 59.615 37.037 0.00 0.00 0.00 3.46
3763 3967 7.442656 AGTGAAGATAAAAGAAACGAGGAAGA 58.557 34.615 0.00 0.00 0.00 2.87
3791 4372 3.788333 TGCTGCAGGAAAGCATAATTC 57.212 42.857 17.12 0.00 45.50 2.17
3792 4373 3.090790 TGCTGCAGGAAAGCATAATTCA 58.909 40.909 17.12 0.00 45.50 2.57
3793 4374 3.129813 TGCTGCAGGAAAGCATAATTCAG 59.870 43.478 17.12 0.00 45.50 3.02
3827 4409 6.322712 ACTTGGAACTTGTGGCATTAAACTTA 59.677 34.615 0.00 0.00 0.00 2.24
3968 4551 1.897560 CAGGGAGGGTGTGAAAGTTC 58.102 55.000 0.00 0.00 0.00 3.01
4022 4612 1.668151 GACCGCTGGTTCTGGTGTC 60.668 63.158 1.80 0.00 35.25 3.67
4100 4690 6.594788 TGATAAAGCCTGAAATGAAAGCTT 57.405 33.333 0.00 0.00 45.28 3.74
4142 4732 3.267483 GCCGCTTAACAATAGAGTGGAA 58.733 45.455 6.38 0.00 42.32 3.53
4202 4792 2.949451 ATGTCTCTTCGCGATCTTGT 57.051 45.000 10.88 0.00 0.00 3.16
4207 4797 0.737367 TCTTCGCGATCTTGTGGCAG 60.737 55.000 10.88 0.00 0.00 4.85
4248 4838 0.894141 ACTGTCTGCTCTAGCCTGTG 59.106 55.000 0.00 0.00 41.18 3.66
4249 4839 0.459934 CTGTCTGCTCTAGCCTGTGC 60.460 60.000 0.00 0.00 41.18 4.57
4250 4840 1.153469 GTCTGCTCTAGCCTGTGCC 60.153 63.158 0.00 0.00 41.18 5.01
4251 4841 1.305633 TCTGCTCTAGCCTGTGCCT 60.306 57.895 0.00 0.00 41.18 4.75
4252 4842 1.153409 CTGCTCTAGCCTGTGCCTG 60.153 63.158 0.00 0.00 41.18 4.85
4253 4843 1.897225 CTGCTCTAGCCTGTGCCTGT 61.897 60.000 0.00 0.00 41.18 4.00
4258 4848 0.322975 CTAGCCTGTGCCTGTCTGTT 59.677 55.000 0.00 0.00 38.69 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.348476 TGCTATTGTATAAAGATTTGCCATGTA 57.652 29.630 0.00 0.00 0.00 2.29
45 46 9.734620 TTGTCATGCTATTGTATAAAGATTTGC 57.265 29.630 0.00 0.00 0.00 3.68
86 87 7.944729 AGCTAACACCTTGAAATTATCATGT 57.055 32.000 0.00 0.00 38.03 3.21
98 99 2.234908 ACTGCTCCTAGCTAACACCTTG 59.765 50.000 0.00 0.00 42.97 3.61
99 100 2.541466 ACTGCTCCTAGCTAACACCTT 58.459 47.619 0.00 0.00 42.97 3.50
100 101 2.239681 ACTGCTCCTAGCTAACACCT 57.760 50.000 0.00 0.00 42.97 4.00
101 102 3.336138 AAACTGCTCCTAGCTAACACC 57.664 47.619 0.00 0.00 42.97 4.16
103 104 4.283467 TCTGAAAACTGCTCCTAGCTAACA 59.717 41.667 0.00 0.00 42.97 2.41
107 108 2.235898 CCTCTGAAAACTGCTCCTAGCT 59.764 50.000 0.00 0.00 42.97 3.32
110 111 4.102524 TGTTTCCTCTGAAAACTGCTCCTA 59.897 41.667 6.54 0.00 41.92 2.94
123 124 2.568956 TGATCAGGGAGTGTTTCCTCTG 59.431 50.000 0.00 0.00 45.98 3.35
139 140 0.032815 TTGAGCGAACGGTGTGATCA 59.967 50.000 3.17 0.00 0.00 2.92
143 144 0.934496 TCTTTTGAGCGAACGGTGTG 59.066 50.000 3.17 0.00 0.00 3.82
179 180 1.126846 GCTCATCCAAGTGAACGAACG 59.873 52.381 0.00 0.00 0.00 3.95
198 199 1.733399 GGACGTTCACTCACGGAGC 60.733 63.158 0.00 0.00 44.82 4.70
208 209 1.656594 CAATAATCGTGCGGACGTTCA 59.343 47.619 28.49 14.76 46.20 3.18
216 217 1.091537 AACACCCCAATAATCGTGCG 58.908 50.000 0.00 0.00 0.00 5.34
219 220 6.490721 TGTTTCTTTAACACCCCAATAATCGT 59.509 34.615 0.00 0.00 41.73 3.73
290 291 2.149521 TTCCCTTCTTCTTTCCCCCT 57.850 50.000 0.00 0.00 0.00 4.79
295 296 5.008712 ACGTGAAACATTCCCTTCTTCTTTC 59.991 40.000 0.00 0.00 35.74 2.62
333 334 3.187700 GACACTCGCTAAAACGATGGAT 58.812 45.455 0.00 0.00 42.02 3.41
390 391 5.450137 CCGTCCCATATTCCGTATGTATCTC 60.450 48.000 0.00 0.00 38.83 2.75
401 408 1.485066 ACTGTGTCCGTCCCATATTCC 59.515 52.381 0.00 0.00 0.00 3.01
542 556 2.280524 TGTGTCTTTGCCGGACCG 60.281 61.111 5.05 6.99 33.22 4.79
560 574 3.851128 GGTCGACCCCCTGCTAGC 61.851 72.222 24.75 8.10 0.00 3.42
561 575 3.528370 CGGTCGACCCCCTGCTAG 61.528 72.222 28.52 8.24 0.00 3.42
562 576 4.051167 TCGGTCGACCCCCTGCTA 62.051 66.667 28.52 2.95 0.00 3.49
565 579 3.760035 CAGTCGGTCGACCCCCTG 61.760 72.222 28.52 26.63 45.59 4.45
587 603 1.118838 CCAACTTTGGGACTTTGGCA 58.881 50.000 0.00 0.00 44.70 4.92
686 710 8.647796 AGTGGTATCCGTATCAATAATTTCAGA 58.352 33.333 0.00 0.00 0.00 3.27
687 711 8.833231 AGTGGTATCCGTATCAATAATTTCAG 57.167 34.615 0.00 0.00 0.00 3.02
688 712 8.425703 TGAGTGGTATCCGTATCAATAATTTCA 58.574 33.333 0.00 0.00 0.00 2.69
689 713 8.709646 GTGAGTGGTATCCGTATCAATAATTTC 58.290 37.037 0.00 0.00 0.00 2.17
690 714 8.208224 TGTGAGTGGTATCCGTATCAATAATTT 58.792 33.333 0.00 0.00 0.00 1.82
692 716 7.015292 AGTGTGAGTGGTATCCGTATCAATAAT 59.985 37.037 0.00 0.00 0.00 1.28
694 718 5.831525 AGTGTGAGTGGTATCCGTATCAATA 59.168 40.000 0.00 0.00 0.00 1.90
697 721 3.628008 AGTGTGAGTGGTATCCGTATCA 58.372 45.455 0.00 0.00 0.00 2.15
698 722 3.630769 TGAGTGTGAGTGGTATCCGTATC 59.369 47.826 0.00 0.00 0.00 2.24
708 732 2.847327 AAGATGGTGAGTGTGAGTGG 57.153 50.000 0.00 0.00 0.00 4.00
734 799 2.955751 GAAATCGAGGCCCGTCGGAG 62.956 65.000 14.39 3.94 40.49 4.63
735 800 3.072468 AAATCGAGGCCCGTCGGA 61.072 61.111 14.39 2.45 40.49 4.55
736 801 2.585247 GAAATCGAGGCCCGTCGG 60.585 66.667 13.82 3.60 40.49 4.79
737 802 2.585247 GGAAATCGAGGCCCGTCG 60.585 66.667 8.05 8.05 41.51 5.12
738 803 0.880718 GATGGAAATCGAGGCCCGTC 60.881 60.000 12.46 6.31 39.75 4.79
739 804 1.146263 GATGGAAATCGAGGCCCGT 59.854 57.895 12.46 0.00 39.75 5.28
740 805 0.463654 TTGATGGAAATCGAGGCCCG 60.464 55.000 0.00 2.55 40.25 6.13
741 806 1.312815 CTTGATGGAAATCGAGGCCC 58.687 55.000 0.00 0.00 0.00 5.80
742 807 0.665298 GCTTGATGGAAATCGAGGCC 59.335 55.000 0.00 0.00 33.61 5.19
743 808 1.332997 CTGCTTGATGGAAATCGAGGC 59.667 52.381 5.36 0.00 33.61 4.70
744 809 2.611292 GACTGCTTGATGGAAATCGAGG 59.389 50.000 5.36 0.00 33.61 4.63
745 810 3.063180 GTGACTGCTTGATGGAAATCGAG 59.937 47.826 0.00 0.00 35.61 4.04
746 811 3.002791 GTGACTGCTTGATGGAAATCGA 58.997 45.455 0.00 0.00 0.00 3.59
747 812 3.005554 AGTGACTGCTTGATGGAAATCG 58.994 45.455 0.00 0.00 0.00 3.34
748 813 6.317857 GTTAAGTGACTGCTTGATGGAAATC 58.682 40.000 0.00 0.00 0.00 2.17
749 814 5.183904 GGTTAAGTGACTGCTTGATGGAAAT 59.816 40.000 0.00 0.00 0.00 2.17
752 817 3.072330 TGGTTAAGTGACTGCTTGATGGA 59.928 43.478 0.00 0.00 0.00 3.41
755 820 3.815401 GTGTGGTTAAGTGACTGCTTGAT 59.185 43.478 0.00 0.00 0.00 2.57
763 828 4.957759 AGTTTGTGTGTGGTTAAGTGAC 57.042 40.909 0.00 0.00 0.00 3.67
804 869 3.312736 AAGATGGACAGTTGGTTGGTT 57.687 42.857 0.00 0.00 0.00 3.67
826 904 3.244665 ACATGATTGGAAGAGTGTGAGCA 60.245 43.478 0.00 0.00 0.00 4.26
947 1034 3.982058 GCGTCAAGCTATATATATCCGGC 59.018 47.826 0.00 3.23 44.04 6.13
2136 2296 2.124403 GTCCCTGGCATGCAGAGG 60.124 66.667 21.36 22.04 0.00 3.69
2490 2650 1.153168 CCCGATGATGTCCGGCTTT 60.153 57.895 0.00 0.00 44.07 3.51
2517 2677 3.803082 CACGCCGCCAGGATGTTG 61.803 66.667 0.00 0.00 41.02 3.33
2959 3119 0.971386 GACGGGTAGTTGAGGTTGGA 59.029 55.000 0.00 0.00 0.00 3.53
3136 3296 2.651361 CGTGAACTCCAGCTCCGT 59.349 61.111 0.00 0.00 0.00 4.69
3138 3298 2.435059 GCCGTGAACTCCAGCTCC 60.435 66.667 0.00 0.00 0.00 4.70
3260 3420 2.353607 CTATCGGACTCGCCACGC 60.354 66.667 0.00 0.00 35.94 5.34
3295 3455 2.992689 TTCTGGGCGCCTGTCGTA 60.993 61.111 28.56 4.31 41.07 3.43
3381 3541 3.234730 CCTCCCTCGAATCCCCCG 61.235 72.222 0.00 0.00 0.00 5.73
3399 3559 5.831103 AGATACCACCAAATCTCACCATTT 58.169 37.500 0.00 0.00 0.00 2.32
3402 3562 4.104086 AGAGATACCACCAAATCTCACCA 58.896 43.478 13.22 0.00 46.99 4.17
3408 3568 7.731054 AGATAGTTGAGAGATACCACCAAATC 58.269 38.462 0.00 0.00 0.00 2.17
3410 3570 6.667848 TGAGATAGTTGAGAGATACCACCAAA 59.332 38.462 0.00 0.00 0.00 3.28
3428 3597 5.936956 GGGCCTTATTGACAATCTGAGATAG 59.063 44.000 3.36 0.00 0.00 2.08
3436 3605 5.796424 ATGATTGGGCCTTATTGACAATC 57.204 39.130 17.04 17.04 44.57 2.67
3438 3607 6.194235 AGTTATGATTGGGCCTTATTGACAA 58.806 36.000 4.53 0.00 0.00 3.18
3482 3654 3.758554 CCTTTCCATCATCACCGTTTCTT 59.241 43.478 0.00 0.00 0.00 2.52
3488 3660 2.645838 ATCCCTTTCCATCATCACCG 57.354 50.000 0.00 0.00 0.00 4.94
3519 3691 9.387123 GATAATTTGATTCCGAGAAAGCAATAC 57.613 33.333 0.00 0.00 34.78 1.89
3531 3719 4.554723 GCCAAGACCGATAATTTGATTCCG 60.555 45.833 0.00 0.00 0.00 4.30
3546 3734 0.909623 TACCCAAGCTAGCCAAGACC 59.090 55.000 12.13 0.00 0.00 3.85
3576 3765 2.941720 GCAATCTGATCCAACTCAGGAC 59.058 50.000 1.58 0.00 42.42 3.85
3577 3766 2.573009 TGCAATCTGATCCAACTCAGGA 59.427 45.455 1.58 0.00 42.42 3.86
3578 3767 2.943690 CTGCAATCTGATCCAACTCAGG 59.056 50.000 1.58 0.00 42.42 3.86
3579 3768 2.355132 GCTGCAATCTGATCCAACTCAG 59.645 50.000 0.00 0.00 43.33 3.35
3580 3769 2.026542 AGCTGCAATCTGATCCAACTCA 60.027 45.455 1.02 0.00 0.00 3.41
3581 3770 2.641305 AGCTGCAATCTGATCCAACTC 58.359 47.619 1.02 0.00 0.00 3.01
3582 3771 2.803030 AGCTGCAATCTGATCCAACT 57.197 45.000 1.02 0.00 0.00 3.16
3593 3782 2.229784 GCTGTCCTTGTAAAGCTGCAAT 59.770 45.455 1.02 0.00 44.44 3.56
3597 3786 2.079925 GGAGCTGTCCTTGTAAAGCTG 58.920 52.381 0.00 0.00 45.74 4.24
3599 3788 1.807142 GTGGAGCTGTCCTTGTAAAGC 59.193 52.381 0.00 0.00 44.44 3.51
3614 3803 3.666345 ACCCCTACTACTACAGTGGAG 57.334 52.381 0.00 0.00 37.96 3.86
3616 3805 5.703310 AGATAACCCCTACTACTACAGTGG 58.297 45.833 0.00 0.00 38.24 4.00
3623 3812 5.697067 CTGACTGAGATAACCCCTACTACT 58.303 45.833 0.00 0.00 0.00 2.57
3625 3814 4.079385 TGCTGACTGAGATAACCCCTACTA 60.079 45.833 0.00 0.00 0.00 1.82
3626 3815 3.301274 GCTGACTGAGATAACCCCTACT 58.699 50.000 0.00 0.00 0.00 2.57
3627 3816 3.031736 TGCTGACTGAGATAACCCCTAC 58.968 50.000 0.00 0.00 0.00 3.18
3628 3817 3.398318 TGCTGACTGAGATAACCCCTA 57.602 47.619 0.00 0.00 0.00 3.53
3629 3818 2.254152 TGCTGACTGAGATAACCCCT 57.746 50.000 0.00 0.00 0.00 4.79
3630 3819 3.135530 AGATTGCTGACTGAGATAACCCC 59.864 47.826 0.00 0.00 0.00 4.95
3632 3821 5.275067 AGAGATTGCTGACTGAGATAACC 57.725 43.478 0.00 0.00 0.00 2.85
3633 3822 5.288804 GGAGAGATTGCTGACTGAGATAAC 58.711 45.833 0.00 0.00 0.00 1.89
3634 3823 4.343526 GGGAGAGATTGCTGACTGAGATAA 59.656 45.833 0.00 0.00 0.00 1.75
3635 3824 3.894427 GGGAGAGATTGCTGACTGAGATA 59.106 47.826 0.00 0.00 0.00 1.98
3636 3825 2.699846 GGGAGAGATTGCTGACTGAGAT 59.300 50.000 0.00 0.00 0.00 2.75
3638 3827 1.138661 GGGGAGAGATTGCTGACTGAG 59.861 57.143 0.00 0.00 0.00 3.35
3650 3854 3.055385 CGGAACATTTTACAGGGGAGAGA 60.055 47.826 0.00 0.00 0.00 3.10
3651 3855 3.270877 CGGAACATTTTACAGGGGAGAG 58.729 50.000 0.00 0.00 0.00 3.20
3655 3859 3.067684 AGACGGAACATTTTACAGGGG 57.932 47.619 0.00 0.00 0.00 4.79
3665 3869 9.152595 GAAGAAAGAATAGTTTAGACGGAACAT 57.847 33.333 0.00 0.00 0.00 2.71
3700 3904 8.904834 CTTCAGAAGAAAAGATGATCCATTCAT 58.095 33.333 3.82 0.00 39.46 2.57
3719 3923 9.948964 TCTTCACTCAATCATTTATCTTCAGAA 57.051 29.630 0.00 0.00 0.00 3.02
3737 3941 7.599245 TCTTCCTCGTTTCTTTTATCTTCACTC 59.401 37.037 0.00 0.00 0.00 3.51
3756 3960 1.457346 CAGCACCAACCATCTTCCTC 58.543 55.000 0.00 0.00 0.00 3.71
3758 3962 0.895100 TGCAGCACCAACCATCTTCC 60.895 55.000 0.00 0.00 0.00 3.46
3761 3965 1.303888 CCTGCAGCACCAACCATCT 60.304 57.895 8.66 0.00 0.00 2.90
3762 3966 0.895100 TTCCTGCAGCACCAACCATC 60.895 55.000 8.66 0.00 0.00 3.51
3763 3967 0.469705 TTTCCTGCAGCACCAACCAT 60.470 50.000 8.66 0.00 0.00 3.55
3827 4409 8.562892 GCATAATGCGCCTAATATAGAAATGAT 58.437 33.333 4.18 0.00 31.71 2.45
3968 4551 6.128822 GCCTTTATTCGCCTTCTTTTCTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
4005 4595 2.426023 GACACCAGAACCAGCGGT 59.574 61.111 0.00 0.00 37.65 5.68
4022 4612 2.343426 GGCTTTGCCCCCTTTCTCG 61.343 63.158 0.00 0.00 44.06 4.04
4050 4640 6.879458 AGCGAGTGACAGGTCTAAATAATTTT 59.121 34.615 0.65 0.00 0.00 1.82
4151 4741 3.644966 TGCCGTCCATCTTTAATTCCT 57.355 42.857 0.00 0.00 0.00 3.36
4152 4742 4.672409 CTTTGCCGTCCATCTTTAATTCC 58.328 43.478 0.00 0.00 0.00 3.01
4207 4797 1.830847 AACAAAACTCACGGGCCCC 60.831 57.895 18.66 0.00 0.00 5.80
4248 4838 3.077359 AGCAATAGACAAACAGACAGGC 58.923 45.455 0.00 0.00 0.00 4.85
4249 4839 4.614535 GCAAGCAATAGACAAACAGACAGG 60.615 45.833 0.00 0.00 0.00 4.00
4250 4840 4.470462 GCAAGCAATAGACAAACAGACAG 58.530 43.478 0.00 0.00 0.00 3.51
4251 4841 3.253188 GGCAAGCAATAGACAAACAGACA 59.747 43.478 0.00 0.00 0.00 3.41
4252 4842 3.503748 AGGCAAGCAATAGACAAACAGAC 59.496 43.478 0.00 0.00 0.00 3.51
4253 4843 3.754965 AGGCAAGCAATAGACAAACAGA 58.245 40.909 0.00 0.00 0.00 3.41
4258 4848 5.420725 TCTAGAAGGCAAGCAATAGACAA 57.579 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.