Multiple sequence alignment - TraesCS5D01G103900

Loading Multiple Alignment...

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 TraesCS5D01G103900 chr5D 100.000 6634 0 0 1 6634 117745615 117738982 0.000000e+00 12251.0
1 TraesCS5D01G103900 chr5D 93.590 78 4 1 6244 6321 117739294 117739218 1.510000e-21 115.0
2 TraesCS5D01G103900 chr5D 93.590 78 4 1 6322 6398 117739372 117739295 1.510000e-21 115.0
3 TraesCS5D01G103900 chr5B 96.593 3258 83 10 2575 5815 129325574 129328820 0.000000e+00 5376.0
4 TraesCS5D01G103900 chr5B 93.386 2026 74 15 645 2651 129323589 129325573 0.000000e+00 2944.0
5 TraesCS5D01G103900 chr5B 92.208 616 25 8 1 608 129322724 129323324 0.000000e+00 850.0
6 TraesCS5D01G103900 chr5B 92.308 182 13 1 6138 6318 454486875 454486694 2.370000e-64 257.0
7 TraesCS5D01G103900 chr5B 91.758 182 14 1 6138 6318 454368767 454368586 1.100000e-62 252.0
8 TraesCS5D01G103900 chr5B 90.909 110 7 1 1 110 314297351 314297457 1.930000e-30 145.0
9 TraesCS5D01G103900 chr5A 94.776 3484 125 20 692 4136 126698346 126694881 0.000000e+00 5373.0
10 TraesCS5D01G103900 chr5A 98.620 1739 17 1 4224 5962 126694457 126692726 0.000000e+00 3072.0
11 TraesCS5D01G103900 chr5A 97.644 679 15 1 5957 6634 126692569 126691891 0.000000e+00 1164.0
12 TraesCS5D01G103900 chr5A 94.253 261 11 3 135 392 126699389 126699130 4.820000e-106 396.0
13 TraesCS5D01G103900 chr5A 94.656 131 7 0 6138 6268 478924282 478924152 3.140000e-48 204.0
14 TraesCS5D01G103900 chr5A 92.079 101 7 1 4134 4233 126694576 126694476 2.490000e-29 141.0
15 TraesCS5D01G103900 chr5A 88.182 110 8 5 1 109 7114073 7114178 6.980000e-25 126.0
16 TraesCS5D01G103900 chr5A 94.872 78 3 1 6244 6321 126692203 126692127 3.250000e-23 121.0
17 TraesCS5D01G103900 chr5A 93.590 78 4 1 6322 6398 126692281 126692204 1.510000e-21 115.0
18 TraesCS5D01G103900 chr5A 75.090 277 39 23 2331 2595 56732477 56732735 1.180000e-17 102.0
19 TraesCS5D01G103900 chr4D 80.144 277 36 14 6138 6414 40207324 40207067 8.780000e-44 189.0
20 TraesCS5D01G103900 chr4D 91.736 121 9 1 2330 2450 5677295 5677176 4.110000e-37 167.0
21 TraesCS5D01G103900 chr4D 90.426 94 5 4 2330 2421 361037267 361037358 3.250000e-23 121.0
22 TraesCS5D01G103900 chr4D 88.525 61 6 1 6261 6321 40207142 40207083 9.230000e-09 73.1
23 TraesCS5D01G103900 chr6B 90.909 121 10 1 2330 2450 625888674 625888555 1.910000e-35 161.0
24 TraesCS5D01G103900 chr6B 93.878 49 3 0 2713 2761 378287140 378287092 2.570000e-09 75.0
25 TraesCS5D01G103900 chr6B 92.683 41 3 0 2713 2753 70745792 70745752 7.180000e-05 60.2
26 TraesCS5D01G103900 chr7A 83.815 173 19 3 6469 6632 20969656 20969484 8.910000e-34 156.0
27 TraesCS5D01G103900 chr7A 88.182 110 10 1 1 110 699736028 699736134 1.940000e-25 128.0
28 TraesCS5D01G103900 chr6D 90.000 110 8 1 1 110 348087717 348087611 8.970000e-29 139.0
29 TraesCS5D01G103900 chr6D 88.393 112 8 3 1 110 445836715 445836823 5.400000e-26 130.0
30 TraesCS5D01G103900 chr6D 97.222 36 1 0 2720 2755 468016174 468016209 2.000000e-05 62.1
31 TraesCS5D01G103900 chr3A 90.000 110 8 2 1 110 256916740 256916846 8.970000e-29 139.0
32 TraesCS5D01G103900 chr3A 88.182 110 10 1 1 110 624858128 624858022 1.940000e-25 128.0
33 TraesCS5D01G103900 chr3A 88.073 109 12 1 3 110 721931441 721931333 1.940000e-25 128.0
34 TraesCS5D01G103900 chr3B 81.503 173 20 5 2330 2490 782841697 782841525 1.500000e-26 132.0
35 TraesCS5D01G103900 chr1D 86.957 115 10 3 1 113 465131003 465130892 2.510000e-24 124.0
36 TraesCS5D01G103900 chr1D 91.250 80 7 0 2332 2411 37215051 37214972 7.030000e-20 110.0
37 TraesCS5D01G103900 chr1A 92.500 80 5 1 2332 2411 36563567 36563489 5.440000e-21 113.0
38 TraesCS5D01G103900 chr6A 97.222 36 1 0 2720 2755 614097534 614097569 2.000000e-05 62.1
39 TraesCS5D01G103900 chrUn 100.000 32 0 0 2724 2755 79584458 79584427 7.180000e-05 60.2
40 TraesCS5D01G103900 chrUn 100.000 32 0 0 2724 2755 268074391 268074360 7.180000e-05 60.2
41 TraesCS5D01G103900 chr4B 92.308 39 3 0 2713 2751 564786349 564786311 1.000000e-03 56.5


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 TraesCS5D01G103900 chr5D 117738982 117745615 6633 True 12251.000000 12251 100.000000 1 6634 1 chr5D.!!$R1 6633
1 TraesCS5D01G103900 chr5B 129322724 129328820 6096 False 3056.666667 5376 94.062333 1 5815 3 chr5B.!!$F2 5814
2 TraesCS5D01G103900 chr5A 126691891 126699389 7498 True 1483.142857 5373 95.119143 135 6634 7 chr5A.!!$R2 6499

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
620 650 0.178935 CTCCTCCATCCTCCCTCTCC 60.179 65.0 0.00 0.0 0.00 3.71 F
887 1381 0.744874 TCTTCATCCCGACCTAAGCG 59.255 55.0 0.00 0.0 0.00 4.68 F
2556 3071 0.743345 CTTTTTACCGCCTCCTCCCG 60.743 60.0 0.00 0.0 0.00 5.14 F
3026 3635 0.531974 GGCTGCATCCATTTGGCATG 60.532 55.0 0.55 0.0 36.87 4.06 F
4221 5148 1.335145 GGCCCCCATGATGAATGAAG 58.665 55.0 0.00 0.0 38.72 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2521 1.546476 GTGATCCAAGAGGTCACGAGT 59.454 52.381 0.0 0.0 36.73 4.18 R
2859 3465 0.543749 ATCCTGTGGTTCTGCCTAGC 59.456 55.000 0.0 0.0 38.35 3.42 R
4181 5107 0.545071 AGCCTCCCCCAAAAACATGG 60.545 55.000 0.0 0.0 40.35 3.66 R
4321 5276 1.557443 CCGTCAAGTCTCAACACGGC 61.557 60.000 0.0 0.0 43.22 5.68 R
5955 6918 0.320374 CACCCGTGAAAGCTAGTCCA 59.680 55.000 0.0 0.0 0.00 4.02 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
24 25 4.584874 TGGTATTGACTTGGTGGTGTATG 58.415 43.478 0.00 0.00 0.00 2.39
215 217 0.870307 GACCGCGCGAGACATATGTT 60.870 55.000 34.63 2.25 0.00 2.71
216 218 0.459585 ACCGCGCGAGACATATGTTT 60.460 50.000 34.63 3.79 0.00 2.83
275 279 5.426833 ACAGGTTAGTAGCATCTTCCAGAAT 59.573 40.000 0.00 0.00 0.00 2.40
311 315 0.447801 CGGAAGGAAAACGATGCCAG 59.552 55.000 0.00 0.00 0.00 4.85
332 336 0.465460 AACATGACCACACCGCACTT 60.465 50.000 0.00 0.00 0.00 3.16
464 490 1.332375 CTGCCGTCGAAAAGAAAACCA 59.668 47.619 0.00 0.00 0.00 3.67
465 491 1.743958 TGCCGTCGAAAAGAAAACCAA 59.256 42.857 0.00 0.00 0.00 3.67
466 492 2.114056 GCCGTCGAAAAGAAAACCAAC 58.886 47.619 0.00 0.00 0.00 3.77
467 493 2.723209 CCGTCGAAAAGAAAACCAACC 58.277 47.619 0.00 0.00 0.00 3.77
468 494 2.542205 CCGTCGAAAAGAAAACCAACCC 60.542 50.000 0.00 0.00 0.00 4.11
469 495 2.097791 CGTCGAAAAGAAAACCAACCCA 59.902 45.455 0.00 0.00 0.00 4.51
534 564 0.687354 TCTTCCTTGGTCTCAGGTGC 59.313 55.000 0.00 0.00 0.00 5.01
605 635 3.729108 TCCACATCTCCATCTTTCTCCT 58.271 45.455 0.00 0.00 0.00 3.69
606 636 3.708631 TCCACATCTCCATCTTTCTCCTC 59.291 47.826 0.00 0.00 0.00 3.71
608 638 3.453717 CACATCTCCATCTTTCTCCTCCA 59.546 47.826 0.00 0.00 0.00 3.86
609 639 4.102838 CACATCTCCATCTTTCTCCTCCAT 59.897 45.833 0.00 0.00 0.00 3.41
612 642 3.051496 TCTCCATCTTTCTCCTCCATCCT 60.051 47.826 0.00 0.00 0.00 3.24
613 643 3.312890 TCCATCTTTCTCCTCCATCCTC 58.687 50.000 0.00 0.00 0.00 3.71
614 644 2.371510 CCATCTTTCTCCTCCATCCTCC 59.628 54.545 0.00 0.00 0.00 4.30
615 645 2.182516 TCTTTCTCCTCCATCCTCCC 57.817 55.000 0.00 0.00 0.00 4.30
616 646 1.653918 TCTTTCTCCTCCATCCTCCCT 59.346 52.381 0.00 0.00 0.00 4.20
617 647 2.046292 CTTTCTCCTCCATCCTCCCTC 58.954 57.143 0.00 0.00 0.00 4.30
618 648 1.324014 TTCTCCTCCATCCTCCCTCT 58.676 55.000 0.00 0.00 0.00 3.69
619 649 0.856982 TCTCCTCCATCCTCCCTCTC 59.143 60.000 0.00 0.00 0.00 3.20
620 650 0.178935 CTCCTCCATCCTCCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
621 651 1.152139 CCTCCATCCTCCCTCTCCC 60.152 68.421 0.00 0.00 0.00 4.30
622 652 1.152139 CTCCATCCTCCCTCTCCCC 60.152 68.421 0.00 0.00 0.00 4.81
623 653 2.122189 CCATCCTCCCTCTCCCCC 60.122 72.222 0.00 0.00 0.00 5.40
637 667 3.966543 CCCCCACTCCACACCCAC 61.967 72.222 0.00 0.00 0.00 4.61
638 668 3.966543 CCCCACTCCACACCCACC 61.967 72.222 0.00 0.00 0.00 4.61
639 669 2.854032 CCCACTCCACACCCACCT 60.854 66.667 0.00 0.00 0.00 4.00
640 670 2.460853 CCCACTCCACACCCACCTT 61.461 63.158 0.00 0.00 0.00 3.50
641 671 1.073199 CCACTCCACACCCACCTTC 59.927 63.158 0.00 0.00 0.00 3.46
642 672 1.073199 CACTCCACACCCACCTTCC 59.927 63.158 0.00 0.00 0.00 3.46
643 673 1.073706 ACTCCACACCCACCTTCCT 60.074 57.895 0.00 0.00 0.00 3.36
694 953 2.124487 CGTCGCCTCTCCTCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
699 1190 1.528309 GCCTCTCCTCTCCTCTCCG 60.528 68.421 0.00 0.00 0.00 4.63
887 1381 0.744874 TCTTCATCCCGACCTAAGCG 59.255 55.000 0.00 0.00 0.00 4.68
1593 2092 1.590238 CGTGAAATCTCTGACATCGGC 59.410 52.381 0.00 0.00 0.00 5.54
1686 2187 5.181009 CCATATGAGCTGTTGAACTCTTCA 58.819 41.667 3.65 0.00 38.04 3.02
1696 2197 6.691754 TGTTGAACTCTTCACTTTATGCAA 57.308 33.333 0.00 0.00 39.87 4.08
1706 2207 6.267471 TCTTCACTTTATGCAATGGAAAGGTT 59.733 34.615 14.48 0.00 35.02 3.50
1714 2215 4.219115 TGCAATGGAAAGGTTTAGGTTCA 58.781 39.130 0.00 0.00 0.00 3.18
1762 2263 5.447818 CCTTGATAAACAGGAGAAACGATGC 60.448 44.000 0.00 0.00 0.00 3.91
1763 2264 3.938963 TGATAAACAGGAGAAACGATGCC 59.061 43.478 0.00 0.00 0.00 4.40
1780 2281 0.801067 GCCGCGACGAATACAGAGTT 60.801 55.000 8.23 0.00 0.00 3.01
1783 2284 2.031314 CCGCGACGAATACAGAGTTAGA 59.969 50.000 8.23 0.00 0.00 2.10
1784 2285 3.281601 CGCGACGAATACAGAGTTAGAG 58.718 50.000 0.00 0.00 0.00 2.43
1785 2286 3.242349 CGCGACGAATACAGAGTTAGAGT 60.242 47.826 0.00 0.00 0.00 3.24
1840 2341 6.550854 ACCCAGAAAATGTCAAAGAGATTTGA 59.449 34.615 3.34 0.00 36.04 2.69
1924 2436 4.658901 AGGGTACTATGGGTCAACTTATGG 59.341 45.833 0.00 0.00 0.00 2.74
2143 2658 9.347240 GTACTGGTATGTATTGTAGGAGTTAGA 57.653 37.037 0.00 0.00 0.00 2.10
2144 2659 8.466617 ACTGGTATGTATTGTAGGAGTTAGAG 57.533 38.462 0.00 0.00 0.00 2.43
2170 2685 4.081476 GGAAAAGATGGATTTTGACCTGGG 60.081 45.833 0.00 0.00 32.62 4.45
2174 2689 3.464833 AGATGGATTTTGACCTGGGCTAT 59.535 43.478 0.00 0.00 0.00 2.97
2227 2742 2.876550 GCGTTGGTTGAAGTTTACCTCT 59.123 45.455 8.91 0.00 35.41 3.69
2384 2899 3.310193 GGGGTAGGCTAGAGATGAAACT 58.690 50.000 0.00 0.00 0.00 2.66
2556 3071 0.743345 CTTTTTACCGCCTCCTCCCG 60.743 60.000 0.00 0.00 0.00 5.14
2573 3088 1.674817 CCCGTATCAACTTTGGTCGCT 60.675 52.381 0.00 0.00 0.00 4.93
2683 3275 1.610522 ACTGAAAGGAACTGCATGTGC 59.389 47.619 0.00 0.00 40.86 4.57
2717 3323 5.643777 GTGCCATGTTGTTCAGTATTACTCT 59.356 40.000 0.00 0.00 0.00 3.24
2800 3406 4.413928 CCGACCCTTTTGGCATGA 57.586 55.556 0.00 0.00 37.83 3.07
2859 3465 4.547671 TCTAGGTAATTGAGTGGGAGAGG 58.452 47.826 0.00 0.00 0.00 3.69
2885 3491 3.451178 GGCAGAACCACAGGATAGACTAA 59.549 47.826 0.00 0.00 38.86 2.24
2886 3492 4.101741 GGCAGAACCACAGGATAGACTAAT 59.898 45.833 0.00 0.00 38.86 1.73
2993 3602 5.052693 TGCATCTTAGGGAATGCTATTGT 57.947 39.130 8.59 0.00 40.41 2.71
2994 3603 5.448654 TGCATCTTAGGGAATGCTATTGTT 58.551 37.500 8.59 0.00 40.41 2.83
3026 3635 0.531974 GGCTGCATCCATTTGGCATG 60.532 55.000 0.55 0.00 36.87 4.06
3090 3699 5.019498 CGTCCAACGAAAATCTTAAATCGG 58.981 41.667 0.00 0.00 46.05 4.18
3277 3896 9.643693 AAGGAAGTAGCATTTGTTAATCAATTG 57.356 29.630 0.00 0.00 39.17 2.32
3299 3918 6.403866 TGATGGTGCAATTTCTTACAAACT 57.596 33.333 0.00 0.00 0.00 2.66
3382 4001 7.814107 GCATTTGGTTAGTTCTGAATTTCATCA 59.186 33.333 0.00 0.00 0.00 3.07
3457 4076 4.872691 ACTGCTGTTGGAAATTATCTCGAG 59.127 41.667 5.93 5.93 0.00 4.04
3620 4239 7.016957 AGCAATGAGTCCCTTAGATCAATATCA 59.983 37.037 0.00 0.00 34.28 2.15
3816 4435 3.614616 GGCTTACTCTCTCGTCAAACATG 59.385 47.826 0.00 0.00 0.00 3.21
3850 4469 3.503891 TGATTTTGTCTCATGCGCATTG 58.496 40.909 22.81 16.65 0.00 2.82
3883 4502 9.390795 CTTTGATCATCCGAAATTATTGCTTAG 57.609 33.333 0.00 0.00 0.00 2.18
3923 4542 3.441101 ACTGGATAGGTCTAGTGTGCAA 58.559 45.455 0.00 0.00 43.60 4.08
4126 4745 5.789643 AGTTTGCATGTGAGTTGGTATTT 57.210 34.783 0.00 0.00 0.00 1.40
4181 5107 6.414987 GGCTGTACTTTTCGATAAAATGATGC 59.585 38.462 0.00 0.00 34.18 3.91
4221 5148 1.335145 GGCCCCCATGATGAATGAAG 58.665 55.000 0.00 0.00 38.72 3.02
4321 5276 1.402787 AACACTGAAGGCAACCTTGG 58.597 50.000 3.02 0.00 44.82 3.61
4682 5637 5.408299 TGAATGACGAAGGTTTGTGATACTG 59.592 40.000 0.00 0.00 0.00 2.74
4683 5638 3.064207 TGACGAAGGTTTGTGATACTGC 58.936 45.455 0.00 0.00 0.00 4.40
4684 5639 3.064207 GACGAAGGTTTGTGATACTGCA 58.936 45.455 0.00 0.00 0.00 4.41
4685 5640 3.674997 ACGAAGGTTTGTGATACTGCAT 58.325 40.909 0.00 0.00 0.00 3.96
4686 5641 4.827692 ACGAAGGTTTGTGATACTGCATA 58.172 39.130 0.00 0.00 0.00 3.14
4687 5642 4.630069 ACGAAGGTTTGTGATACTGCATAC 59.370 41.667 0.00 0.00 0.00 2.39
4688 5643 4.870426 CGAAGGTTTGTGATACTGCATACT 59.130 41.667 0.00 0.00 0.00 2.12
5175 6130 2.803956 TCGGAATTTCTTCGGTTGTCAC 59.196 45.455 0.00 0.00 34.34 3.67
5305 6260 6.418101 TGGTATGCAGAATTTAGCTTCTTCT 58.582 36.000 0.00 0.00 33.18 2.85
5866 6829 3.024784 CGCAGCAGAGTTGTGCAA 58.975 55.556 4.01 0.00 46.60 4.08
5923 6886 4.389374 TGCTGTAAAAGAAGGAACCTGAG 58.611 43.478 0.00 0.00 0.00 3.35
5955 6918 9.733556 TGATTTTGTATATTGTACCTCTGTTGT 57.266 29.630 0.00 0.00 0.00 3.32
5957 6920 7.915293 TTTGTATATTGTACCTCTGTTGTGG 57.085 36.000 0.00 0.00 0.00 4.17
5962 6925 4.866508 TTGTACCTCTGTTGTGGACTAG 57.133 45.455 0.00 0.00 0.00 2.57
5963 6926 2.561419 TGTACCTCTGTTGTGGACTAGC 59.439 50.000 0.00 0.00 0.00 3.42
5964 6927 2.016905 ACCTCTGTTGTGGACTAGCT 57.983 50.000 0.00 0.00 0.00 3.32
5965 6928 2.330216 ACCTCTGTTGTGGACTAGCTT 58.670 47.619 0.00 0.00 0.00 3.74
5966 6929 2.706190 ACCTCTGTTGTGGACTAGCTTT 59.294 45.455 0.00 0.00 0.00 3.51
5967 6930 3.244249 ACCTCTGTTGTGGACTAGCTTTC 60.244 47.826 0.00 0.00 0.00 2.62
5971 7097 1.798813 GTTGTGGACTAGCTTTCACGG 59.201 52.381 0.00 0.00 33.25 4.94
6037 7163 7.824289 TGACTGATTTTCCAATCGTCTATTCTT 59.176 33.333 14.87 0.00 41.77 2.52
6084 7210 3.678289 TCATCACAAACAGGATCCACAG 58.322 45.455 15.82 5.90 0.00 3.66
6121 7247 7.504924 AAATTCAACCATCTTCAAAGTCGTA 57.495 32.000 0.00 0.00 0.00 3.43
6128 7254 5.469084 ACCATCTTCAAAGTCGTAGTTTTCC 59.531 40.000 0.00 0.00 0.00 3.13
6346 7472 6.541641 CAGAAGATAATTTTGGAGGTCTGGAG 59.458 42.308 0.00 0.00 0.00 3.86
6400 7526 8.680903 CAAAGAGAAATTTCTGCACATAGGTAT 58.319 33.333 25.12 0.00 37.73 2.73
6515 7641 3.503363 TCAGCATCAACTAAAGGCAACAG 59.497 43.478 0.00 0.00 41.41 3.16
6554 7680 8.194104 CGATGAAAATGAATACCCCAACAATAA 58.806 33.333 0.00 0.00 0.00 1.40
6581 7707 6.934048 TGAAATCCCAAACCAAATGTTTTC 57.066 33.333 0.00 0.00 44.80 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.958119 ATATTAGTAACACATACACCACCAAG 57.042 34.615 0.00 0.00 36.94 3.61
74 75 7.769044 ACTCCGCATGTTATATTTGTCTAAAGT 59.231 33.333 0.00 0.00 0.00 2.66
87 88 9.174166 ACTCTTTTTATTTACTCCGCATGTTAT 57.826 29.630 0.00 0.00 0.00 1.89
91 92 7.970384 TGTACTCTTTTTATTTACTCCGCATG 58.030 34.615 0.00 0.00 0.00 4.06
183 184 2.738521 CGGTCACGCTCCACTTGG 60.739 66.667 0.00 0.00 0.00 3.61
216 218 2.688958 CGTAGGGGTGTTTGTGGAAAAA 59.311 45.455 0.00 0.00 0.00 1.94
275 279 3.277133 GCTGGAGCGCAATTTGGA 58.723 55.556 11.47 0.00 0.00 3.53
297 301 3.057596 TCATGTTTCTGGCATCGTTTTCC 60.058 43.478 0.00 0.00 0.00 3.13
311 315 0.040425 GTGCGGTGTGGTCATGTTTC 60.040 55.000 0.00 0.00 0.00 2.78
353 357 8.297426 CGTACTGCTCTACATTAATCTATGGAA 58.703 37.037 0.00 0.00 0.00 3.53
467 493 2.661997 CCCGCCCATGGTTTTTGG 59.338 61.111 11.73 4.57 0.00 3.28
468 494 2.047370 GCCCGCCCATGGTTTTTG 60.047 61.111 11.73 0.00 0.00 2.44
469 495 3.690280 CGCCCGCCCATGGTTTTT 61.690 61.111 11.73 0.00 0.00 1.94
500 526 3.701664 AGGAAGATGACCAAAATGTCCC 58.298 45.455 0.00 0.00 34.25 4.46
534 564 3.528370 CGGCCGAGGTGGAGGTAG 61.528 72.222 24.07 0.00 42.00 3.18
605 635 2.727071 GGGGGAGAGGGAGGATGGA 61.727 68.421 0.00 0.00 0.00 3.41
606 636 2.122189 GGGGGAGAGGGAGGATGG 60.122 72.222 0.00 0.00 0.00 3.51
620 650 3.966543 GTGGGTGTGGAGTGGGGG 61.967 72.222 0.00 0.00 0.00 5.40
621 651 3.966543 GGTGGGTGTGGAGTGGGG 61.967 72.222 0.00 0.00 0.00 4.96
622 652 2.411765 GAAGGTGGGTGTGGAGTGGG 62.412 65.000 0.00 0.00 0.00 4.61
623 653 1.073199 GAAGGTGGGTGTGGAGTGG 59.927 63.158 0.00 0.00 0.00 4.00
624 654 1.073199 GGAAGGTGGGTGTGGAGTG 59.927 63.158 0.00 0.00 0.00 3.51
625 655 1.073706 AGGAAGGTGGGTGTGGAGT 60.074 57.895 0.00 0.00 0.00 3.85
626 656 1.679898 GAGGAAGGTGGGTGTGGAG 59.320 63.158 0.00 0.00 0.00 3.86
627 657 1.846124 GGAGGAAGGTGGGTGTGGA 60.846 63.158 0.00 0.00 0.00 4.02
628 658 2.757077 GGAGGAAGGTGGGTGTGG 59.243 66.667 0.00 0.00 0.00 4.17
629 659 1.189524 TACGGAGGAAGGTGGGTGTG 61.190 60.000 0.00 0.00 0.00 3.82
630 660 1.156803 TACGGAGGAAGGTGGGTGT 59.843 57.895 0.00 0.00 0.00 4.16
631 661 1.595357 GTACGGAGGAAGGTGGGTG 59.405 63.158 0.00 0.00 0.00 4.61
632 662 1.611556 GGTACGGAGGAAGGTGGGT 60.612 63.158 0.00 0.00 0.00 4.51
633 663 0.908180 AAGGTACGGAGGAAGGTGGG 60.908 60.000 0.00 0.00 0.00 4.61
634 664 0.535797 GAAGGTACGGAGGAAGGTGG 59.464 60.000 0.00 0.00 0.00 4.61
635 665 0.535797 GGAAGGTACGGAGGAAGGTG 59.464 60.000 0.00 0.00 0.00 4.00
636 666 0.616964 GGGAAGGTACGGAGGAAGGT 60.617 60.000 0.00 0.00 0.00 3.50
637 667 1.335882 GGGGAAGGTACGGAGGAAGG 61.336 65.000 0.00 0.00 0.00 3.46
638 668 1.335882 GGGGGAAGGTACGGAGGAAG 61.336 65.000 0.00 0.00 0.00 3.46
639 669 1.306397 GGGGGAAGGTACGGAGGAA 60.306 63.158 0.00 0.00 0.00 3.36
640 670 2.365764 GGGGGAAGGTACGGAGGA 59.634 66.667 0.00 0.00 0.00 3.71
641 671 2.039951 TGGGGGAAGGTACGGAGG 59.960 66.667 0.00 0.00 0.00 4.30
642 672 2.364780 GGTGGGGGAAGGTACGGAG 61.365 68.421 0.00 0.00 0.00 4.63
643 673 2.284847 GGTGGGGGAAGGTACGGA 60.285 66.667 0.00 0.00 0.00 4.69
758 1249 0.250640 GCCTCAGCATGGTAGGATGG 60.251 60.000 18.69 9.39 39.53 3.51
841 1335 4.828296 GGACGGCGAGGTAGGGGA 62.828 72.222 16.62 0.00 0.00 4.81
1593 2092 1.982612 TCTTCACAAGCAGATCGACG 58.017 50.000 0.00 0.00 0.00 5.12
1686 2187 6.496911 ACCTAAACCTTTCCATTGCATAAAGT 59.503 34.615 0.00 0.00 0.00 2.66
1696 2197 3.431415 GGCTGAACCTAAACCTTTCCAT 58.569 45.455 0.00 0.00 34.51 3.41
1762 2263 2.031314 TCTAACTCTGTATTCGTCGCGG 59.969 50.000 6.13 0.00 0.00 6.46
1763 2264 3.242349 ACTCTAACTCTGTATTCGTCGCG 60.242 47.826 0.00 0.00 0.00 5.87
1780 2281 9.739276 AATCAATAAACATCAAAGTCCACTCTA 57.261 29.630 0.00 0.00 0.00 2.43
1783 2284 7.039504 AGCAATCAATAAACATCAAAGTCCACT 60.040 33.333 0.00 0.00 0.00 4.00
1784 2285 7.092716 AGCAATCAATAAACATCAAAGTCCAC 58.907 34.615 0.00 0.00 0.00 4.02
1785 2286 7.230849 AGCAATCAATAAACATCAAAGTCCA 57.769 32.000 0.00 0.00 0.00 4.02
1864 2365 3.056107 TCTCTAAACTGGATGAACCACCG 60.056 47.826 0.00 0.00 44.64 4.94
1939 2451 2.560105 GTTTCCTCTTCCAGCTGCATTT 59.440 45.455 8.66 0.00 0.00 2.32
1953 2465 9.606631 AGAACAGATATGTAAGAATGTTTCCTC 57.393 33.333 0.00 0.00 31.44 3.71
2009 2521 1.546476 GTGATCCAAGAGGTCACGAGT 59.454 52.381 0.00 0.00 36.73 4.18
2143 2658 4.528206 GGTCAAAATCCATCTTTTCCACCT 59.472 41.667 0.00 0.00 31.27 4.00
2144 2659 4.528206 AGGTCAAAATCCATCTTTTCCACC 59.472 41.667 0.00 0.00 32.72 4.61
2227 2742 8.615211 GCAACAGATTCAGATTCAACATATACA 58.385 33.333 0.00 0.00 0.00 2.29
2384 2899 2.940410 GGTTCTCACGGTTTTCTGTTGA 59.060 45.455 0.00 0.00 37.30 3.18
2556 3071 2.973945 AGGAGCGACCAAAGTTGATAC 58.026 47.619 5.84 0.00 42.04 2.24
2573 3088 5.492565 TGAAAATACTAGGAGGGGTAGGA 57.507 43.478 0.00 0.00 0.00 2.94
2800 3406 1.304713 CACCCCTTTCCAGCAGCAT 60.305 57.895 0.00 0.00 0.00 3.79
2855 3461 0.545309 TGTGGTTCTGCCTAGCCTCT 60.545 55.000 0.00 0.00 38.35 3.69
2859 3465 0.543749 ATCCTGTGGTTCTGCCTAGC 59.456 55.000 0.00 0.00 38.35 3.42
2993 3602 4.503817 GGATGCAGCCATGTCTACTCATAA 60.504 45.833 18.08 0.00 0.00 1.90
2994 3603 3.007290 GGATGCAGCCATGTCTACTCATA 59.993 47.826 18.08 0.00 0.00 2.15
3026 3635 5.047377 ACATGGATTCCAAAACATACACCAC 60.047 40.000 9.98 0.00 36.95 4.16
3090 3699 1.858458 GTTGGCAAAAACTTTCCTCGC 59.142 47.619 0.00 0.00 0.00 5.03
3277 3896 8.986477 AATAGTTTGTAAGAAATTGCACCATC 57.014 30.769 0.00 0.00 0.00 3.51
3310 3929 7.066284 ACTCCTCACATTAATACTTTGATGCAC 59.934 37.037 0.00 0.00 33.33 4.57
3382 4001 4.040461 TGCTGCTACTTCCTTTCAGTAGTT 59.960 41.667 0.00 0.00 43.96 2.24
3457 4076 6.261603 TGCTCATGAGTATGTTCAATCCATTC 59.738 38.462 23.38 1.75 35.73 2.67
3576 4195 1.949525 GCTCACCTGCAACAGAAAAGA 59.050 47.619 0.00 0.00 32.44 2.52
3620 4239 3.135530 ACTCCTCAAGCTTCTCAAGTGTT 59.864 43.478 0.00 0.00 0.00 3.32
3745 4364 8.045507 ACATGATAATATGCAAGAGTATCCCTG 58.954 37.037 13.66 13.02 33.66 4.45
3850 4469 5.801350 TTTCGGATGATCAAAGACATGAC 57.199 39.130 0.00 0.00 30.82 3.06
3883 4502 4.444720 CCAGTTTAAAGTGTGACGAGAGAC 59.555 45.833 19.25 0.00 0.00 3.36
3923 4542 8.254508 TCAAACAGTAAAAATTGCAGGTAAACT 58.745 29.630 0.00 0.00 0.00 2.66
4126 4745 6.083098 TGCAGCAAAGCAAGTAAAATTAGA 57.917 33.333 0.00 0.00 42.46 2.10
4181 5107 0.545071 AGCCTCCCCCAAAAACATGG 60.545 55.000 0.00 0.00 40.35 3.66
4321 5276 1.557443 CCGTCAAGTCTCAACACGGC 61.557 60.000 0.00 0.00 43.22 5.68
4966 5921 6.112058 AGAACTGCAGCTTTAGGATAGAAAG 58.888 40.000 15.27 0.00 37.04 2.62
5251 6206 6.016192 CCTGTCTAAGGTTTAGAGCATATCGA 60.016 42.308 0.00 0.00 41.74 3.59
5305 6260 2.101750 TGCCTCGTCAGAACTTGTACAA 59.898 45.455 8.28 8.28 0.00 2.41
5866 6829 8.207545 GGTTCATATCAAATAGAGAACTCCACT 58.792 37.037 0.00 0.00 35.64 4.00
5955 6918 0.320374 CACCCGTGAAAGCTAGTCCA 59.680 55.000 0.00 0.00 0.00 4.02
5957 6920 1.997669 CTCACCCGTGAAAGCTAGTC 58.002 55.000 0.00 0.00 39.39 2.59
5962 6925 0.383949 TTTTGCTCACCCGTGAAAGC 59.616 50.000 0.00 0.94 39.39 3.51
5963 6926 1.946768 TCTTTTGCTCACCCGTGAAAG 59.053 47.619 0.00 0.52 39.39 2.62
5964 6927 2.045561 TCTTTTGCTCACCCGTGAAA 57.954 45.000 0.00 0.00 39.39 2.69
5965 6928 2.045561 TTCTTTTGCTCACCCGTGAA 57.954 45.000 0.00 0.00 39.39 3.18
5966 6929 2.270352 ATTCTTTTGCTCACCCGTGA 57.730 45.000 0.00 0.00 38.06 4.35
5967 6930 3.502211 ACTTATTCTTTTGCTCACCCGTG 59.498 43.478 0.00 0.00 0.00 4.94
5971 7097 6.072112 TGACAACTTATTCTTTTGCTCACC 57.928 37.500 0.00 0.00 0.00 4.02
6084 7210 4.516698 TGGTTGAATTTTGTCAGCTCTCTC 59.483 41.667 0.00 0.00 0.00 3.20
6121 7247 3.332034 GTGTACCTATGTGCGGAAAACT 58.668 45.455 0.00 0.00 0.00 2.66
6200 7326 9.814899 CCAAGAAGCCTCTCATAGTATTATATG 57.185 37.037 0.00 0.00 34.96 1.78
6346 7472 3.084039 TGATCATGCCTGAACTGAAACC 58.916 45.455 0.00 0.00 34.37 3.27
6515 7641 5.584649 TCATTTTCATCGTCATCTGGTAACC 59.415 40.000 0.00 0.00 0.00 2.85
6581 7707 3.181503 ACTCATTTCAGCGCTGCTAAATG 60.182 43.478 35.74 35.74 38.86 2.32
6591 7717 2.238245 GCTGTGAACTCATTTCAGCG 57.762 50.000 5.39 0.00 45.23 5.18
6593 7719 3.004002 TGCTTGCTGTGAACTCATTTCAG 59.996 43.478 0.00 0.00 45.23 3.02


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

AutoCloner maintained by Alex Coulton.