Multiple sequence alignment - TraesCS3A01G350200

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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 TraesCS3A01G350200 chr3A 100.000 4260 0 0 1 4260 598905138 598900879 0.000000e+00 7867.0
1 TraesCS3A01G350200 chr3D 92.739 3443 143 48 878 4257 456010896 456007498 0.000000e+00 4874.0
2 TraesCS3A01G350200 chr3D 91.152 712 43 10 101 806 456011741 456011044 0.000000e+00 948.0
3 TraesCS3A01G350200 chr3D 89.362 47 3 2 49 94 79188796 79188751 1.650000e-04 58.4
4 TraesCS3A01G350200 chr3B 89.838 3828 225 65 512 4260 602472585 602468843 0.000000e+00 4763.0
5 TraesCS3A01G350200 chr3B 90.837 251 15 3 97 347 602473071 602472829 3.180000e-86 329.0
6 TraesCS3A01G350200 chr3B 89.781 137 10 2 377 509 602472831 602472695 5.660000e-39 172.0
7 TraesCS3A01G350200 chr3B 100.000 45 0 0 2603 2647 602470509 602470465 2.730000e-12 84.2
8 TraesCS3A01G350200 chr3B 100.000 31 0 0 14 44 52898684 52898654 1.650000e-04 58.4
9 TraesCS3A01G350200 chr5D 92.029 1104 54 14 2262 3352 491583644 491584726 0.000000e+00 1520.0
10 TraesCS3A01G350200 chr5D 87.727 717 48 24 290 994 491582947 491583635 0.000000e+00 800.0
11 TraesCS3A01G350200 chr5D 93.750 144 7 2 97 240 491582793 491582934 9.280000e-52 215.0
12 TraesCS3A01G350200 chr1A 100.000 31 0 0 14 44 347625642 347625612 1.650000e-04 58.4


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 TraesCS3A01G350200 chr3A 598900879 598905138 4259 True 7867.00 7867 100.000000 1 4260 1 chr3A.!!$R1 4259
1 TraesCS3A01G350200 chr3D 456007498 456011741 4243 True 2911.00 4874 91.945500 101 4257 2 chr3D.!!$R2 4156
2 TraesCS3A01G350200 chr3B 602468843 602473071 4228 True 1337.05 4763 92.614000 97 4260 4 chr3B.!!$R2 4163
3 TraesCS3A01G350200 chr5D 491582793 491584726 1933 False 845.00 1520 91.168667 97 3352 3 chr5D.!!$F1 3255

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
261 262 0.458543 TCGAGCTCGAAGGTCAATGC 60.459 55.000 35.16 0.00 46.30 3.56 F
550 663 0.784778 GCCATCGCGCAAGTATACTC 59.215 55.000 8.75 0.00 41.68 2.59 F
1314 1522 1.515954 CGACGTGGGCTACTTCCAT 59.484 57.895 0.00 0.00 36.58 3.41 F
2352 2567 1.471487 GAAAATTGGCGCGCGGATTC 61.471 55.000 33.06 19.37 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2258 0.101040 GGCGCTCAATGCAAGCATAA 59.899 50.000 7.64 0.0 43.06 1.90 R
2057 2267 1.133025 CTTTTGGTAGGGCGCTCAATG 59.867 52.381 11.40 0.0 0.00 2.82 R
2711 2975 0.106894 GCGGCCTAATTAGCTGACCT 59.893 55.000 15.63 0.0 39.03 3.85 R
4155 4480 0.687920 TTCCAACCACATAGTCGGCA 59.312 50.000 0.00 0.0 0.00 5.69 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
28 29 9.802039 AAACCTGTTTAGTTTAATATCAGACCA 57.198 29.630 0.00 0.00 35.71 4.02
29 30 9.449719 AACCTGTTTAGTTTAATATCAGACCAG 57.550 33.333 0.00 0.00 0.00 4.00
30 31 8.822805 ACCTGTTTAGTTTAATATCAGACCAGA 58.177 33.333 0.00 0.00 0.00 3.86
31 32 9.838339 CCTGTTTAGTTTAATATCAGACCAGAT 57.162 33.333 0.00 0.00 0.00 2.90
45 46 7.630242 TCAGACCAGATAGCATTTTTAAAGG 57.370 36.000 0.00 0.00 0.00 3.11
46 47 7.175104 TCAGACCAGATAGCATTTTTAAAGGT 58.825 34.615 0.00 0.00 0.00 3.50
47 48 7.336931 TCAGACCAGATAGCATTTTTAAAGGTC 59.663 37.037 0.00 0.00 41.49 3.85
48 49 7.406104 AGACCAGATAGCATTTTTAAAGGTCT 58.594 34.615 10.88 10.88 45.18 3.85
49 50 8.056407 GACCAGATAGCATTTTTAAAGGTCTT 57.944 34.615 0.00 0.00 38.90 3.01
50 51 8.422577 ACCAGATAGCATTTTTAAAGGTCTTT 57.577 30.769 1.43 1.43 36.63 2.52
51 52 8.870116 ACCAGATAGCATTTTTAAAGGTCTTTT 58.130 29.630 1.04 0.00 34.23 2.27
52 53 9.358872 CCAGATAGCATTTTTAAAGGTCTTTTC 57.641 33.333 1.04 0.00 34.23 2.29
55 56 9.914131 GATAGCATTTTTAAAGGTCTTTTCTGT 57.086 29.630 1.04 0.00 34.23 3.41
56 57 9.914131 ATAGCATTTTTAAAGGTCTTTTCTGTC 57.086 29.630 1.04 0.00 34.23 3.51
57 58 7.781056 AGCATTTTTAAAGGTCTTTTCTGTCA 58.219 30.769 1.04 0.00 34.23 3.58
58 59 8.257306 AGCATTTTTAAAGGTCTTTTCTGTCAA 58.743 29.630 1.04 0.00 34.23 3.18
59 60 9.045223 GCATTTTTAAAGGTCTTTTCTGTCAAT 57.955 29.630 1.04 0.00 34.23 2.57
67 68 7.133891 AGGTCTTTTCTGTCAATTATGTTCG 57.866 36.000 0.00 0.00 0.00 3.95
68 69 6.149474 AGGTCTTTTCTGTCAATTATGTTCGG 59.851 38.462 0.00 0.00 0.00 4.30
69 70 5.795441 GTCTTTTCTGTCAATTATGTTCGGC 59.205 40.000 0.00 0.00 0.00 5.54
70 71 5.471797 TCTTTTCTGTCAATTATGTTCGGCA 59.528 36.000 0.00 0.00 0.00 5.69
71 72 5.697473 TTTCTGTCAATTATGTTCGGCAA 57.303 34.783 0.00 0.00 0.00 4.52
72 73 4.944962 TCTGTCAATTATGTTCGGCAAG 57.055 40.909 0.00 0.00 0.00 4.01
73 74 4.323417 TCTGTCAATTATGTTCGGCAAGT 58.677 39.130 0.00 0.00 0.00 3.16
74 75 4.154015 TCTGTCAATTATGTTCGGCAAGTG 59.846 41.667 0.00 0.00 0.00 3.16
75 76 3.190327 TGTCAATTATGTTCGGCAAGTGG 59.810 43.478 0.00 0.00 0.00 4.00
76 77 3.190535 GTCAATTATGTTCGGCAAGTGGT 59.809 43.478 0.00 0.00 0.00 4.16
77 78 3.438781 TCAATTATGTTCGGCAAGTGGTC 59.561 43.478 0.00 0.00 0.00 4.02
78 79 2.851263 TTATGTTCGGCAAGTGGTCT 57.149 45.000 0.00 0.00 0.00 3.85
79 80 2.851263 TATGTTCGGCAAGTGGTCTT 57.149 45.000 0.00 0.00 0.00 3.01
80 81 1.981256 ATGTTCGGCAAGTGGTCTTT 58.019 45.000 0.00 0.00 0.00 2.52
81 82 1.757682 TGTTCGGCAAGTGGTCTTTT 58.242 45.000 0.00 0.00 0.00 2.27
82 83 2.096248 TGTTCGGCAAGTGGTCTTTTT 58.904 42.857 0.00 0.00 0.00 1.94
83 84 3.280295 TGTTCGGCAAGTGGTCTTTTTA 58.720 40.909 0.00 0.00 0.00 1.52
84 85 3.314080 TGTTCGGCAAGTGGTCTTTTTAG 59.686 43.478 0.00 0.00 0.00 1.85
85 86 3.478857 TCGGCAAGTGGTCTTTTTAGA 57.521 42.857 0.00 0.00 0.00 2.10
86 87 3.135994 TCGGCAAGTGGTCTTTTTAGAC 58.864 45.455 0.00 0.00 38.04 2.59
87 88 2.875933 CGGCAAGTGGTCTTTTTAGACA 59.124 45.455 7.52 0.00 40.38 3.41
88 89 3.314080 CGGCAAGTGGTCTTTTTAGACAA 59.686 43.478 7.52 0.00 40.38 3.18
89 90 4.201970 CGGCAAGTGGTCTTTTTAGACAAA 60.202 41.667 7.52 0.00 40.38 2.83
90 91 5.656480 GGCAAGTGGTCTTTTTAGACAAAA 58.344 37.500 7.52 0.00 40.38 2.44
91 92 6.103330 GGCAAGTGGTCTTTTTAGACAAAAA 58.897 36.000 7.52 0.00 40.47 1.94
173 174 1.732405 CGTGACGCTGCACTCTATTCA 60.732 52.381 0.00 0.00 36.65 2.57
233 234 1.080093 GAATGGCACGTGTCCTCGA 60.080 57.895 19.06 0.00 34.70 4.04
234 235 1.078759 GAATGGCACGTGTCCTCGAG 61.079 60.000 19.06 5.13 34.70 4.04
235 236 3.649277 ATGGCACGTGTCCTCGAGC 62.649 63.158 19.06 0.00 44.04 5.03
261 262 0.458543 TCGAGCTCGAAGGTCAATGC 60.459 55.000 35.16 0.00 46.30 3.56
277 278 3.774702 GCGTCGAACGACTTGCCC 61.775 66.667 21.67 4.97 46.05 5.36
298 299 1.685517 TGATCAGGCTCGATCAGAAGG 59.314 52.381 19.14 0.00 45.31 3.46
335 336 1.470494 TGTGAGATGTCTCGTGCTCTC 59.530 52.381 5.62 0.00 45.72 3.20
345 347 1.522355 CGTGCTCTCGCCATCCAAT 60.522 57.895 0.00 0.00 34.43 3.16
347 349 1.820906 TGCTCTCGCCATCCAATGC 60.821 57.895 0.00 0.00 34.43 3.56
349 351 1.170919 GCTCTCGCCATCCAATGCAT 61.171 55.000 0.00 0.00 0.00 3.96
373 375 2.823628 GAGTCGTTCTCGGTTTGGG 58.176 57.895 0.00 0.00 37.69 4.12
389 391 2.388232 GGGTGATGGACGCAACGAC 61.388 63.158 0.00 0.00 37.46 4.34
395 397 3.400590 GGACGCAACGACACCGAC 61.401 66.667 0.00 0.00 39.50 4.79
439 445 2.463876 GTTGTGAACAAAAGGCTCTGC 58.536 47.619 0.00 0.00 37.63 4.26
446 452 1.683385 ACAAAAGGCTCTGCTGTTTCC 59.317 47.619 0.00 0.00 0.00 3.13
477 483 4.314440 TGCACGTGTGGGCTCTCC 62.314 66.667 18.38 0.00 0.00 3.71
506 512 1.000274 GGCCAACGATTTGCTTTCTGT 60.000 47.619 0.00 0.00 0.00 3.41
529 642 7.431249 TGTAGCTATTATGACTTTCTTACCGG 58.569 38.462 0.00 0.00 0.00 5.28
546 659 2.591715 GGGCCATCGCGCAAGTAT 60.592 61.111 8.75 0.00 46.77 2.12
547 660 1.301401 GGGCCATCGCGCAAGTATA 60.301 57.895 8.75 0.00 46.77 1.47
550 663 0.784778 GCCATCGCGCAAGTATACTC 59.215 55.000 8.75 0.00 41.68 2.59
551 664 1.868109 GCCATCGCGCAAGTATACTCA 60.868 52.381 8.75 0.00 41.68 3.41
586 699 2.202690 CGGAGCCGCACGTGATAA 60.203 61.111 22.23 0.00 0.00 1.75
595 708 3.181510 GCCGCACGTGATAATTTTCTTCT 60.182 43.478 22.23 0.00 0.00 2.85
596 709 4.671766 GCCGCACGTGATAATTTTCTTCTT 60.672 41.667 22.23 0.00 0.00 2.52
660 778 5.180868 AGCGCTGATATCAAATCAAATCTCC 59.819 40.000 10.39 0.00 0.00 3.71
764 887 2.125912 CGAGGGAGTGGTTCTGCG 60.126 66.667 0.00 0.00 35.27 5.18
774 897 2.626780 GGTTCTGCGGGCCTTTGTC 61.627 63.158 0.84 0.00 0.00 3.18
775 898 1.600916 GTTCTGCGGGCCTTTGTCT 60.601 57.895 0.84 0.00 0.00 3.41
1133 1341 4.431131 CCACATGCCGCTCCCCTT 62.431 66.667 0.00 0.00 0.00 3.95
1148 1356 4.847516 CTTCATCGCCGACGCCGA 62.848 66.667 2.52 2.52 39.84 5.54
1227 1435 4.475135 GCCCCCTCTCGCCTCAAC 62.475 72.222 0.00 0.00 0.00 3.18
1314 1522 1.515954 CGACGTGGGCTACTTCCAT 59.484 57.895 0.00 0.00 36.58 3.41
1336 1544 3.877450 TCGGCCATGGCATCCCTC 61.877 66.667 36.56 17.93 44.11 4.30
1362 1570 2.202987 CCATCCTCTGCACTCGCC 60.203 66.667 0.00 0.00 37.32 5.54
1404 1612 4.064491 GCTATGCGCGCGTCCATC 62.064 66.667 31.81 14.83 0.00 3.51
1599 1807 1.689412 GGTGGGTTTCGGGGAGAAT 59.311 57.895 0.00 0.00 38.86 2.40
1745 1953 3.335356 ATTGCGAGTGGGAGCAGGG 62.335 63.158 0.00 0.00 44.72 4.45
1877 2085 4.702131 GCAACACCCATCTCTATTGACTTT 59.298 41.667 0.00 0.00 0.00 2.66
1962 2170 7.610692 AGATGTGTAGTGTAGTGTAGTGTGTAT 59.389 37.037 0.00 0.00 0.00 2.29
2048 2258 7.701539 TGCACAACTATTTCATTCATAAGGT 57.298 32.000 0.00 0.00 0.00 3.50
2057 2267 9.403110 CTATTTCATTCATAAGGTTATGCTTGC 57.597 33.333 5.04 0.00 40.19 4.01
2094 2306 6.879400 ACCAAAAGTTTAGCATAACCAAACA 58.121 32.000 0.00 0.00 35.17 2.83
2223 2436 8.489559 GCAAATAACCAACATACATGCATATTG 58.510 33.333 0.00 0.00 0.00 1.90
2278 2491 1.719246 GCTTTTTCCGCCGTCATTTTC 59.281 47.619 0.00 0.00 0.00 2.29
2352 2567 1.471487 GAAAATTGGCGCGCGGATTC 61.471 55.000 33.06 19.37 0.00 2.52
2711 2975 3.572642 TCACTCTACTCAACCTGAACCA 58.427 45.455 0.00 0.00 0.00 3.67
2744 3008 2.738139 CCGCGTGTCTGCATCACA 60.738 61.111 17.90 8.38 35.79 3.58
2819 3095 4.142249 ACGTCTTTTGAAAACAAAGAGGGG 60.142 41.667 15.67 4.29 44.75 4.79
3277 3564 6.346919 GCATATGATTAAGCTCGTTCGTCATT 60.347 38.462 6.97 0.00 0.00 2.57
3300 3587 3.729163 GCTCTCTAGCGTTGGATTTTTGC 60.729 47.826 0.00 0.00 39.39 3.68
3420 3733 5.217474 GTCAGAACGACTTTGGGTAAACCA 61.217 45.833 0.81 0.00 44.27 3.67
3524 3837 8.912988 TGAGAAGATTGTTTTCCTTATGTTTGT 58.087 29.630 0.00 0.00 0.00 2.83
3531 3844 6.173339 TGTTTTCCTTATGTTTGTTGGCAAA 58.827 32.000 0.00 0.00 41.77 3.68
3537 3850 5.990996 CCTTATGTTTGTTGGCAAATCAACT 59.009 36.000 0.00 0.00 45.11 3.16
3538 3851 6.146021 CCTTATGTTTGTTGGCAAATCAACTC 59.854 38.462 0.00 0.43 45.11 3.01
3544 3857 3.565482 TGTTGGCAAATCAACTCTGTCTC 59.435 43.478 0.00 0.00 45.15 3.36
3581 3897 6.042437 GGAGGCATTTCATCTAAAAATGGGAT 59.958 38.462 9.79 0.00 42.00 3.85
3582 3898 7.419403 GGAGGCATTTCATCTAAAAATGGGATT 60.419 37.037 9.79 0.00 42.00 3.01
3587 3903 9.880157 CATTTCATCTAAAAATGGGATTGTCTT 57.120 29.630 0.00 0.00 39.39 3.01
3627 3943 4.417437 ACACTAAAAGCAGTAGGAGAGGA 58.583 43.478 0.00 0.00 0.00 3.71
3662 3980 9.049523 TGATGCATTCAAACATATAGAAGAGTC 57.950 33.333 0.00 0.00 0.00 3.36
3685 4003 3.265791 CGACAAGCCTTAGAAGCAGAAT 58.734 45.455 0.00 0.00 0.00 2.40
3696 4015 6.699642 CCTTAGAAGCAGAATAGAAGCTACAC 59.300 42.308 0.00 0.00 37.70 2.90
3712 4031 3.858238 GCTACACGGAGTTGACAATAGAC 59.142 47.826 0.00 0.00 41.61 2.59
3796 4119 9.110502 GGTTCTAATACCCTTAAGTTGAGATTG 57.889 37.037 0.97 0.00 31.71 2.67
3823 4146 4.635765 TGCTCCAATCTCCAAGAATAAACG 59.364 41.667 0.00 0.00 0.00 3.60
3956 4280 3.657015 ATGCTCGATGATCTGTTCGAT 57.343 42.857 13.64 1.19 42.84 3.59
4048 4373 3.640029 GCCATCAATCCCTGTCAATCAAT 59.360 43.478 0.00 0.00 0.00 2.57
4092 4417 2.746904 AGCACATGTTTAGCGCACATTA 59.253 40.909 11.47 0.00 32.25 1.90
4155 4480 3.932822 TGACATTGCACGTACTAACCAT 58.067 40.909 0.00 0.00 0.00 3.55
4250 4589 5.057149 ACGACTTAATAAAGCTAGCCATGG 58.943 41.667 12.13 7.63 36.05 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.802039 TGGTCTGATATTAAACTAAACAGGTTT 57.198 29.630 2.66 2.66 39.70 3.27
3 4 9.449719 CTGGTCTGATATTAAACTAAACAGGTT 57.550 33.333 0.00 0.00 0.00 3.50
4 5 8.822805 TCTGGTCTGATATTAAACTAAACAGGT 58.177 33.333 0.00 0.00 0.00 4.00
5 6 9.838339 ATCTGGTCTGATATTAAACTAAACAGG 57.162 33.333 0.00 0.00 0.00 4.00
19 20 9.342308 CCTTTAAAAATGCTATCTGGTCTGATA 57.658 33.333 0.00 0.00 0.00 2.15
20 21 7.836183 ACCTTTAAAAATGCTATCTGGTCTGAT 59.164 33.333 0.00 0.00 0.00 2.90
21 22 7.175104 ACCTTTAAAAATGCTATCTGGTCTGA 58.825 34.615 0.00 0.00 0.00 3.27
22 23 7.337942 AGACCTTTAAAAATGCTATCTGGTCTG 59.662 37.037 14.27 0.00 45.76 3.51
23 24 7.406104 AGACCTTTAAAAATGCTATCTGGTCT 58.594 34.615 10.88 10.88 43.67 3.85
24 25 7.631717 AGACCTTTAAAAATGCTATCTGGTC 57.368 36.000 0.00 0.00 40.11 4.02
25 26 8.422577 AAAGACCTTTAAAAATGCTATCTGGT 57.577 30.769 0.00 0.00 0.00 4.00
26 27 9.358872 GAAAAGACCTTTAAAAATGCTATCTGG 57.641 33.333 0.00 0.00 31.63 3.86
29 30 9.914131 ACAGAAAAGACCTTTAAAAATGCTATC 57.086 29.630 0.00 0.00 31.63 2.08
30 31 9.914131 GACAGAAAAGACCTTTAAAAATGCTAT 57.086 29.630 0.00 0.00 31.63 2.97
31 32 8.908903 TGACAGAAAAGACCTTTAAAAATGCTA 58.091 29.630 0.00 0.00 31.63 3.49
32 33 7.781056 TGACAGAAAAGACCTTTAAAAATGCT 58.219 30.769 0.00 0.00 31.63 3.79
33 34 8.419076 TTGACAGAAAAGACCTTTAAAAATGC 57.581 30.769 0.00 0.00 31.63 3.56
41 42 8.076178 CGAACATAATTGACAGAAAAGACCTTT 58.924 33.333 0.00 0.00 0.00 3.11
42 43 7.308589 CCGAACATAATTGACAGAAAAGACCTT 60.309 37.037 0.00 0.00 0.00 3.50
43 44 6.149474 CCGAACATAATTGACAGAAAAGACCT 59.851 38.462 0.00 0.00 0.00 3.85
44 45 6.314784 CCGAACATAATTGACAGAAAAGACC 58.685 40.000 0.00 0.00 0.00 3.85
45 46 5.795441 GCCGAACATAATTGACAGAAAAGAC 59.205 40.000 0.00 0.00 0.00 3.01
46 47 5.471797 TGCCGAACATAATTGACAGAAAAGA 59.528 36.000 0.00 0.00 0.00 2.52
47 48 5.698832 TGCCGAACATAATTGACAGAAAAG 58.301 37.500 0.00 0.00 0.00 2.27
48 49 5.697473 TGCCGAACATAATTGACAGAAAA 57.303 34.783 0.00 0.00 0.00 2.29
49 50 5.240623 ACTTGCCGAACATAATTGACAGAAA 59.759 36.000 0.00 0.00 0.00 2.52
50 51 4.759693 ACTTGCCGAACATAATTGACAGAA 59.240 37.500 0.00 0.00 0.00 3.02
51 52 4.154015 CACTTGCCGAACATAATTGACAGA 59.846 41.667 0.00 0.00 0.00 3.41
52 53 4.406069 CACTTGCCGAACATAATTGACAG 58.594 43.478 0.00 0.00 0.00 3.51
53 54 3.190327 CCACTTGCCGAACATAATTGACA 59.810 43.478 0.00 0.00 0.00 3.58
54 55 3.190535 ACCACTTGCCGAACATAATTGAC 59.809 43.478 0.00 0.00 0.00 3.18
55 56 3.417101 ACCACTTGCCGAACATAATTGA 58.583 40.909 0.00 0.00 0.00 2.57
56 57 3.440173 AGACCACTTGCCGAACATAATTG 59.560 43.478 0.00 0.00 0.00 2.32
57 58 3.686016 AGACCACTTGCCGAACATAATT 58.314 40.909 0.00 0.00 0.00 1.40
58 59 3.350219 AGACCACTTGCCGAACATAAT 57.650 42.857 0.00 0.00 0.00 1.28
59 60 2.851263 AGACCACTTGCCGAACATAA 57.149 45.000 0.00 0.00 0.00 1.90
60 61 2.851263 AAGACCACTTGCCGAACATA 57.149 45.000 0.00 0.00 34.80 2.29
61 62 1.981256 AAAGACCACTTGCCGAACAT 58.019 45.000 0.00 0.00 36.39 2.71
62 63 1.757682 AAAAGACCACTTGCCGAACA 58.242 45.000 0.00 0.00 36.39 3.18
63 64 2.863401 AAAAAGACCACTTGCCGAAC 57.137 45.000 0.00 0.00 36.39 3.95
64 65 3.562557 GTCTAAAAAGACCACTTGCCGAA 59.437 43.478 0.00 0.00 36.39 4.30
65 66 3.135994 GTCTAAAAAGACCACTTGCCGA 58.864 45.455 0.00 0.00 36.39 5.54
66 67 2.875933 TGTCTAAAAAGACCACTTGCCG 59.124 45.455 3.25 0.00 37.99 5.69
67 68 4.911514 TTGTCTAAAAAGACCACTTGCC 57.088 40.909 3.25 0.00 37.99 4.52
88 89 7.018487 TGGATCATGGAAATGTGGAATTTTT 57.982 32.000 0.00 0.00 0.00 1.94
89 90 6.623979 TGGATCATGGAAATGTGGAATTTT 57.376 33.333 0.00 0.00 0.00 1.82
90 91 6.441284 TCTTGGATCATGGAAATGTGGAATTT 59.559 34.615 0.00 0.00 0.00 1.82
91 92 5.959594 TCTTGGATCATGGAAATGTGGAATT 59.040 36.000 0.00 0.00 0.00 2.17
92 93 5.521696 TCTTGGATCATGGAAATGTGGAAT 58.478 37.500 0.00 0.00 0.00 3.01
93 94 4.933134 TCTTGGATCATGGAAATGTGGAA 58.067 39.130 0.00 0.00 0.00 3.53
94 95 4.529897 CTCTTGGATCATGGAAATGTGGA 58.470 43.478 0.00 0.00 0.00 4.02
95 96 3.067742 GCTCTTGGATCATGGAAATGTGG 59.932 47.826 0.00 0.00 0.00 4.17
131 132 4.455877 CGCTTTTTCTCACTTTATGGACCT 59.544 41.667 0.00 0.00 0.00 3.85
135 136 5.147162 GTCACGCTTTTTCTCACTTTATGG 58.853 41.667 0.00 0.00 0.00 2.74
136 137 4.840772 CGTCACGCTTTTTCTCACTTTATG 59.159 41.667 0.00 0.00 0.00 1.90
173 174 2.756760 TCGATCCGGTTAAACTACTGCT 59.243 45.455 0.00 0.00 0.00 4.24
177 178 4.925646 ACTTTGTCGATCCGGTTAAACTAC 59.074 41.667 0.00 0.00 0.00 2.73
261 262 2.049433 AGGGCAAGTCGTTCGACG 60.049 61.111 17.46 7.58 44.19 5.12
298 299 3.521560 TCACATCTGTAGCACGGATTTC 58.478 45.455 7.60 0.00 41.19 2.17
335 336 0.309922 GAGTCATGCATTGGATGGCG 59.690 55.000 15.74 0.00 30.39 5.69
345 347 0.881796 AGAACGACTCGAGTCATGCA 59.118 50.000 37.14 0.00 44.99 3.96
373 375 1.491563 GTGTCGTTGCGTCCATCAC 59.508 57.895 0.00 0.00 0.00 3.06
389 391 2.100631 GCTGAACCATCGGTCGGTG 61.101 63.158 0.00 0.00 36.67 4.94
395 397 1.817099 GCTGGAGCTGAACCATCGG 60.817 63.158 0.00 0.00 36.79 4.18
461 467 4.314440 TGGAGAGCCCACACGTGC 62.314 66.667 17.22 0.41 40.82 5.34
477 483 0.957395 AATCGTTGGCCTCAGCTGTG 60.957 55.000 14.67 11.58 39.73 3.66
506 512 6.014840 CCCCGGTAAGAAAGTCATAATAGCTA 60.015 42.308 0.00 0.00 0.00 3.32
529 642 1.301401 TATACTTGCGCGATGGCCC 60.301 57.895 12.10 0.00 35.02 5.80
542 655 6.711277 TCACTGCAAATTTCCTGAGTATACT 58.289 36.000 4.68 4.68 0.00 2.12
546 659 5.885230 CATCACTGCAAATTTCCTGAGTA 57.115 39.130 0.00 0.00 0.00 2.59
547 660 4.778534 CATCACTGCAAATTTCCTGAGT 57.221 40.909 0.00 0.00 0.00 3.41
660 778 2.437200 GATCTCGCAGGATCTTCTGG 57.563 55.000 8.19 0.00 39.06 3.86
688 807 7.127405 TGCAATGGAGGCCATAATGAATATAT 58.873 34.615 5.01 0.00 44.40 0.86
689 808 6.492274 TGCAATGGAGGCCATAATGAATATA 58.508 36.000 5.01 0.00 44.40 0.86
764 887 3.062466 GCCGGAAGACAAAGGCCC 61.062 66.667 5.05 0.00 43.54 5.80
774 897 2.511600 CGGTAAGCAGGCCGGAAG 60.512 66.667 5.05 0.00 43.85 3.46
986 1194 2.941025 CCATGGAGGTGGTGGGGT 60.941 66.667 5.56 0.00 34.46 4.95
989 1197 0.394352 GTAAGCCATGGAGGTGGTGG 60.394 60.000 18.40 0.00 41.47 4.61
991 1199 0.912486 GAGTAAGCCATGGAGGTGGT 59.088 55.000 18.40 0.00 41.47 4.16
1314 1522 3.445518 GATGCCATGGCCGACGAGA 62.446 63.158 33.44 13.93 41.09 4.04
1336 1544 3.095163 AGAGGATGGCAGCTGGGG 61.095 66.667 17.12 0.00 0.00 4.96
1404 1612 2.032071 AACCCGAGCGTGGAAAGG 59.968 61.111 0.00 0.00 0.00 3.11
1432 1640 2.990479 GGCGTCCACTCCCTGATT 59.010 61.111 0.00 0.00 0.00 2.57
1433 1641 3.461773 CGGCGTCCACTCCCTGAT 61.462 66.667 0.00 0.00 0.00 2.90
1877 2085 3.576550 GCACTTCCCAGGGAATAAAAACA 59.423 43.478 22.21 0.00 41.23 2.83
1935 2143 6.086871 CACACTACACTACACTACACATCTG 58.913 44.000 0.00 0.00 0.00 2.90
1936 2144 5.768662 ACACACTACACTACACTACACATCT 59.231 40.000 0.00 0.00 0.00 2.90
1937 2145 6.010294 ACACACTACACTACACTACACATC 57.990 41.667 0.00 0.00 0.00 3.06
1938 2146 7.698506 ATACACACTACACTACACTACACAT 57.301 36.000 0.00 0.00 0.00 3.21
1939 2147 7.661027 TGTATACACACTACACTACACTACACA 59.339 37.037 0.08 0.00 0.00 3.72
1940 2148 8.032952 TGTATACACACTACACTACACTACAC 57.967 38.462 0.08 0.00 0.00 2.90
1941 2149 7.879677 ACTGTATACACACTACACTACACTACA 59.120 37.037 0.08 0.00 0.00 2.74
1942 2150 8.261492 ACTGTATACACACTACACTACACTAC 57.739 38.462 0.08 0.00 0.00 2.73
1943 2151 7.276438 CGACTGTATACACACTACACTACACTA 59.724 40.741 0.08 0.00 0.00 2.74
1944 2152 6.091849 CGACTGTATACACACTACACTACACT 59.908 42.308 0.08 0.00 0.00 3.55
1962 2170 2.745102 TGAACGATTTGCACGACTGTA 58.255 42.857 1.86 0.00 34.70 2.74
2048 2258 0.101040 GGCGCTCAATGCAAGCATAA 59.899 50.000 7.64 0.00 43.06 1.90
2053 2263 1.718757 GGTAGGGCGCTCAATGCAAG 61.719 60.000 11.40 0.00 43.06 4.01
2057 2267 1.133025 CTTTTGGTAGGGCGCTCAATG 59.867 52.381 11.40 0.00 0.00 2.82
2123 2336 9.371136 TCTAGAGTTACAATCAAACAAGCTATG 57.629 33.333 0.00 0.00 0.00 2.23
2259 2472 2.324860 GGAAAATGACGGCGGAAAAAG 58.675 47.619 13.24 0.00 0.00 2.27
2278 2491 2.202703 ATTTTTACCAACGCGCGGGG 62.203 55.000 35.22 33.59 0.00 5.73
2502 2717 9.305925 CCTCTTATTGGCTAAATCATGTTTTTC 57.694 33.333 7.05 1.09 0.00 2.29
2711 2975 0.106894 GCGGCCTAATTAGCTGACCT 59.893 55.000 15.63 0.00 39.03 3.85
2772 3048 5.354234 TGGTCTTTGTGACTTTGTCTCTTTC 59.646 40.000 0.00 0.00 44.74 2.62
2819 3095 9.681692 TTGCAGCAAAAATATATACATGATGAC 57.318 29.630 4.99 6.00 0.00 3.06
3300 3587 7.060059 CAGCTATAACGAATCGAACATGTCTAG 59.940 40.741 10.55 0.00 0.00 2.43
3376 3672 1.498865 AACTCAAGTCAACGGCAGCG 61.499 55.000 0.00 0.00 0.00 5.18
3387 3683 2.822764 GTCGTTCTGACCAACTCAAGT 58.177 47.619 0.00 0.00 42.04 3.16
3524 3837 4.090761 AGAGACAGAGTTGATTTGCCAA 57.909 40.909 0.00 0.00 0.00 4.52
3531 3844 7.418827 CCAATTCCATCTAGAGACAGAGTTGAT 60.419 40.741 15.10 0.00 32.64 2.57
3537 3850 4.898265 CCTCCAATTCCATCTAGAGACAGA 59.102 45.833 0.00 0.00 0.00 3.41
3538 3851 4.502950 GCCTCCAATTCCATCTAGAGACAG 60.503 50.000 0.00 0.00 0.00 3.51
3544 3857 5.135383 TGAAATGCCTCCAATTCCATCTAG 58.865 41.667 0.00 0.00 31.29 2.43
3598 3914 7.012044 TCTCCTACTGCTTTTAGTGTCAAAAAC 59.988 37.037 0.00 0.00 32.19 2.43
3614 3930 4.037446 CACAGTAAGATCCTCTCCTACTGC 59.963 50.000 12.62 0.00 39.59 4.40
3627 3943 6.822667 TGTTTGAATGCATCACAGTAAGAT 57.177 33.333 0.00 0.00 37.92 2.40
3630 3948 9.612066 TCTATATGTTTGAATGCATCACAGTAA 57.388 29.630 0.00 0.00 37.92 2.24
3638 3956 7.307632 GCGACTCTTCTATATGTTTGAATGCAT 60.308 37.037 0.00 0.00 0.00 3.96
3662 3980 1.014044 TGCTTCTAAGGCTTGTCGCG 61.014 55.000 10.69 0.00 40.44 5.87
3685 4003 3.151554 TGTCAACTCCGTGTAGCTTCTA 58.848 45.455 0.00 0.00 0.00 2.10
3696 4015 8.570096 TTATATTTCGTCTATTGTCAACTCCG 57.430 34.615 0.00 0.00 0.00 4.63
3764 4087 7.563724 ACTTAAGGGTATTAGAACCTTGTGA 57.436 36.000 6.42 0.00 43.98 3.58
3796 4119 7.807977 TTATTCTTGGAGATTGGAGCATAAC 57.192 36.000 0.00 0.00 0.00 1.89
3823 4146 2.919228 ACCAAGGTCACTTTCTGTCAC 58.081 47.619 0.00 0.00 33.81 3.67
3998 4323 9.183368 GAGATTAGTTGGATCTTCTTTTTGGAT 57.817 33.333 0.00 0.00 34.13 3.41
3999 4324 8.163408 TGAGATTAGTTGGATCTTCTTTTTGGA 58.837 33.333 0.00 0.00 34.13 3.53
4001 4326 7.967303 GCTGAGATTAGTTGGATCTTCTTTTTG 59.033 37.037 0.00 0.00 34.13 2.44
4006 4331 4.718774 TGGCTGAGATTAGTTGGATCTTCT 59.281 41.667 0.00 0.00 34.13 2.85
4008 4333 5.131642 TGATGGCTGAGATTAGTTGGATCTT 59.868 40.000 0.00 0.00 34.13 2.40
4048 4373 5.508567 TCAATATTGGAGCAATTCAGGTCA 58.491 37.500 15.36 0.00 37.74 4.02
4155 4480 0.687920 TTCCAACCACATAGTCGGCA 59.312 50.000 0.00 0.00 0.00 5.69
4186 4525 4.102210 TCAATGAGGATAGGCAGAAGGAAG 59.898 45.833 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.