Multiple sequence alignment - TraesCS5B01G381500

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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 TraesCS5B01G381500 chr5B 100.000 3518 0 0 1 3518 559762476 559765993 0.000000e+00 6497
1 TraesCS5B01G381500 chr5B 78.085 1264 246 23 1109 2358 65279495 65278249 0.000000e+00 771
2 TraesCS5B01G381500 chr5D 92.681 2555 114 33 58 2580 457662853 457665366 0.000000e+00 3615
3 TraesCS5B01G381500 chr5D 90.418 814 42 11 2614 3426 457665367 457666145 0.000000e+00 1038
4 TraesCS5B01G381500 chr5D 78.355 1289 238 33 1074 2343 65753744 65755010 0.000000e+00 797
5 TraesCS5B01G381500 chr5D 93.333 105 2 4 3414 3518 457666167 457666266 2.190000e-32 150
6 TraesCS5B01G381500 chr5A 93.521 2238 84 30 792 2990 575594131 575596346 0.000000e+00 3273
7 TraesCS5B01G381500 chr5A 90.734 518 43 2 1413 1926 33001989 33001473 0.000000e+00 686
8 TraesCS5B01G381500 chr5A 91.617 501 30 8 3019 3518 575596415 575596904 0.000000e+00 682
9 TraesCS5B01G381500 chr3B 91.141 824 31 14 107 924 779641403 779640616 0.000000e+00 1079
10 TraesCS5B01G381500 chr2B 90.787 521 45 3 1405 1923 666078733 666079252 0.000000e+00 693
11 TraesCS5B01G381500 chr2B 87.586 145 18 0 1438 1582 243356336 243356480 6.040000e-38 169
12 TraesCS5B01G381500 chr1A 90.267 524 48 3 1405 1926 21481607 21482129 0.000000e+00 682
13 TraesCS5B01G381500 chr1A 91.611 453 37 1 1413 1865 575504585 575504134 2.980000e-175 625
14 TraesCS5B01G381500 chr1A 77.570 642 114 23 1090 1722 521629138 521629758 9.280000e-96 361
15 TraesCS5B01G381500 chr1B 89.883 514 43 2 1413 1926 494066560 494066056 0.000000e+00 652
16 TraesCS5B01G381500 chrUn 90.909 396 35 1 1531 1926 213610249 213609855 6.690000e-147 531
17 TraesCS5B01G381500 chr1D 77.564 624 110 23 1108 1722 426586991 426587593 2.010000e-92 350
18 TraesCS5B01G381500 chr7B 84.127 189 24 4 1033 1218 494219643 494219828 1.000000e-40 178
19 TraesCS5B01G381500 chr4B 96.000 75 3 0 2290 2364 639238543 639238469 4.770000e-24 122


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 TraesCS5B01G381500 chr5B 559762476 559765993 3517 False 6497.0 6497 100.000 1 3518 1 chr5B.!!$F1 3517
1 TraesCS5B01G381500 chr5B 65278249 65279495 1246 True 771.0 771 78.085 1109 2358 1 chr5B.!!$R1 1249
2 TraesCS5B01G381500 chr5D 457662853 457666266 3413 False 1601.0 3615 92.144 58 3518 3 chr5D.!!$F2 3460
3 TraesCS5B01G381500 chr5D 65753744 65755010 1266 False 797.0 797 78.355 1074 2343 1 chr5D.!!$F1 1269
4 TraesCS5B01G381500 chr5A 575594131 575596904 2773 False 1977.5 3273 92.569 792 3518 2 chr5A.!!$F1 2726
5 TraesCS5B01G381500 chr5A 33001473 33001989 516 True 686.0 686 90.734 1413 1926 1 chr5A.!!$R1 513
6 TraesCS5B01G381500 chr3B 779640616 779641403 787 True 1079.0 1079 91.141 107 924 1 chr3B.!!$R1 817
7 TraesCS5B01G381500 chr2B 666078733 666079252 519 False 693.0 693 90.787 1405 1923 1 chr2B.!!$F2 518
8 TraesCS5B01G381500 chr1A 21481607 21482129 522 False 682.0 682 90.267 1405 1926 1 chr1A.!!$F1 521
9 TraesCS5B01G381500 chr1A 521629138 521629758 620 False 361.0 361 77.570 1090 1722 1 chr1A.!!$F2 632
10 TraesCS5B01G381500 chr1B 494066056 494066560 504 True 652.0 652 89.883 1413 1926 1 chr1B.!!$R1 513
11 TraesCS5B01G381500 chr1D 426586991 426587593 602 False 350.0 350 77.564 1108 1722 1 chr1D.!!$F1 614

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
758 785 0.105964 TTCGGCCGGACCATATCTTG 59.894 55.0 27.83 0.0 39.03 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2609 2695 1.202806 ACTTGGTGCATGCAGTGTACT 60.203 47.619 23.41 0.0 42.36 2.73 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
17 18 2.893398 GATCGGCGTGGTTCTCCT 59.107 61.111 6.85 0.00 34.23 3.69
18 19 1.519455 GATCGGCGTGGTTCTCCTG 60.519 63.158 6.85 0.00 34.23 3.86
19 20 1.945354 GATCGGCGTGGTTCTCCTGA 61.945 60.000 6.85 0.00 34.23 3.86
20 21 1.330655 ATCGGCGTGGTTCTCCTGAT 61.331 55.000 6.85 0.00 34.23 2.90
21 22 0.681887 TCGGCGTGGTTCTCCTGATA 60.682 55.000 6.85 0.00 34.23 2.15
22 23 0.389391 CGGCGTGGTTCTCCTGATAT 59.611 55.000 0.00 0.00 34.23 1.63
23 24 1.202533 CGGCGTGGTTCTCCTGATATT 60.203 52.381 0.00 0.00 34.23 1.28
24 25 2.741878 CGGCGTGGTTCTCCTGATATTT 60.742 50.000 0.00 0.00 34.23 1.40
25 26 2.872858 GGCGTGGTTCTCCTGATATTTC 59.127 50.000 0.00 0.00 34.23 2.17
26 27 3.432326 GGCGTGGTTCTCCTGATATTTCT 60.432 47.826 0.00 0.00 34.23 2.52
27 28 3.557595 GCGTGGTTCTCCTGATATTTCTG 59.442 47.826 0.00 0.00 34.23 3.02
28 29 3.557595 CGTGGTTCTCCTGATATTTCTGC 59.442 47.826 0.00 0.00 34.23 4.26
29 30 3.557595 GTGGTTCTCCTGATATTTCTGCG 59.442 47.826 0.00 0.00 34.23 5.18
30 31 2.545946 GGTTCTCCTGATATTTCTGCGC 59.454 50.000 0.00 0.00 0.00 6.09
31 32 2.533266 TCTCCTGATATTTCTGCGCC 57.467 50.000 4.18 0.00 0.00 6.53
32 33 1.070758 TCTCCTGATATTTCTGCGCCC 59.929 52.381 4.18 0.00 0.00 6.13
33 34 0.108585 TCCTGATATTTCTGCGCCCC 59.891 55.000 4.18 0.00 0.00 5.80
34 35 0.109342 CCTGATATTTCTGCGCCCCT 59.891 55.000 4.18 0.00 0.00 4.79
35 36 1.477558 CCTGATATTTCTGCGCCCCTT 60.478 52.381 4.18 0.00 0.00 3.95
36 37 1.876156 CTGATATTTCTGCGCCCCTTC 59.124 52.381 4.18 0.00 0.00 3.46
37 38 1.239347 GATATTTCTGCGCCCCTTCC 58.761 55.000 4.18 0.00 0.00 3.46
38 39 0.178990 ATATTTCTGCGCCCCTTCCC 60.179 55.000 4.18 0.00 0.00 3.97
39 40 1.279025 TATTTCTGCGCCCCTTCCCT 61.279 55.000 4.18 0.00 0.00 4.20
40 41 2.155197 ATTTCTGCGCCCCTTCCCTT 62.155 55.000 4.18 0.00 0.00 3.95
41 42 2.764637 TTTCTGCGCCCCTTCCCTTC 62.765 60.000 4.18 0.00 0.00 3.46
42 43 4.803908 CTGCGCCCCTTCCCTTCC 62.804 72.222 4.18 0.00 0.00 3.46
44 45 4.491409 GCGCCCCTTCCCTTCCTC 62.491 72.222 0.00 0.00 0.00 3.71
45 46 2.689034 CGCCCCTTCCCTTCCTCT 60.689 66.667 0.00 0.00 0.00 3.69
46 47 2.736826 CGCCCCTTCCCTTCCTCTC 61.737 68.421 0.00 0.00 0.00 3.20
47 48 2.379459 GCCCCTTCCCTTCCTCTCC 61.379 68.421 0.00 0.00 0.00 3.71
48 49 2.066999 CCCCTTCCCTTCCTCTCCG 61.067 68.421 0.00 0.00 0.00 4.63
49 50 2.736826 CCCTTCCCTTCCTCTCCGC 61.737 68.421 0.00 0.00 0.00 5.54
50 51 2.496817 CTTCCCTTCCTCTCCGCG 59.503 66.667 0.00 0.00 0.00 6.46
51 52 2.283676 TTCCCTTCCTCTCCGCGT 60.284 61.111 4.92 0.00 0.00 6.01
52 53 2.286127 CTTCCCTTCCTCTCCGCGTC 62.286 65.000 4.92 0.00 0.00 5.19
53 54 3.839432 CCCTTCCTCTCCGCGTCC 61.839 72.222 4.92 0.00 0.00 4.79
54 55 3.068691 CCTTCCTCTCCGCGTCCA 61.069 66.667 4.92 0.00 0.00 4.02
55 56 2.182030 CTTCCTCTCCGCGTCCAC 59.818 66.667 4.92 0.00 0.00 4.02
56 57 2.282958 TTCCTCTCCGCGTCCACT 60.283 61.111 4.92 0.00 0.00 4.00
59 60 1.749638 CCTCTCCGCGTCCACTAGT 60.750 63.158 4.92 0.00 0.00 2.57
83 84 4.643387 AAGCCCAGCTTCGCGGTT 62.643 61.111 6.13 0.00 46.77 4.44
90 91 3.508840 GCTTCGCGGTTCATGGGG 61.509 66.667 6.13 0.00 0.00 4.96
111 112 1.273886 GATGATTCCCTCCTACGCTCC 59.726 57.143 0.00 0.00 0.00 4.70
135 142 3.720601 CAGCCCCACCAGCAGCTA 61.721 66.667 0.00 0.00 33.33 3.32
200 212 3.247411 TGCCGATATACGTGCAAATTGAG 59.753 43.478 0.00 0.00 41.97 3.02
221 233 3.636231 CACCAGCAGGGACGGGAA 61.636 66.667 0.00 0.00 41.15 3.97
282 295 2.366533 CCGGTAGCTTCTACAGTGAGA 58.633 52.381 0.00 0.00 0.00 3.27
283 296 2.952978 CCGGTAGCTTCTACAGTGAGAT 59.047 50.000 0.00 0.00 0.00 2.75
284 297 3.003897 CCGGTAGCTTCTACAGTGAGATC 59.996 52.174 0.00 0.00 0.00 2.75
285 298 3.880490 CGGTAGCTTCTACAGTGAGATCT 59.120 47.826 0.00 0.00 0.00 2.75
384 402 8.532977 TTTCCAAATAAAGCTATTTTCACTGC 57.467 30.769 0.00 0.00 35.88 4.40
387 405 6.867816 CCAAATAAAGCTATTTTCACTGCACA 59.132 34.615 0.00 0.00 35.88 4.57
700 727 7.986085 AATATATATCCAGGTGAAAGCACAC 57.014 36.000 0.00 0.00 46.96 3.82
758 785 0.105964 TTCGGCCGGACCATATCTTG 59.894 55.000 27.83 0.00 39.03 3.02
898 945 5.412594 TCTTCTGCCAGCACTAATACAAAAG 59.587 40.000 0.00 0.00 0.00 2.27
899 946 3.440173 TCTGCCAGCACTAATACAAAAGC 59.560 43.478 0.00 0.00 0.00 3.51
919 968 4.565022 AGCTAGAGACAAAAACAGAGAGC 58.435 43.478 0.00 0.00 0.00 4.09
956 1005 2.358737 GTGAGGAGCCCAACCACG 60.359 66.667 0.00 0.00 0.00 4.94
1913 1987 2.357517 AAACGGTCGCTCAGCCTG 60.358 61.111 0.00 0.00 0.00 4.85
2177 2251 2.510238 GTAGAGCGGCTGCCACTG 60.510 66.667 20.29 3.35 44.31 3.66
2273 2347 4.504916 CTGGAGGCAGGCGACGAG 62.505 72.222 0.00 0.00 0.00 4.18
2561 2639 8.824159 AAGGTCTGAATCTGATGATAATAACG 57.176 34.615 0.00 0.00 31.70 3.18
2577 2655 9.344772 TGATAATAACGTTGCCCTTATAATTGT 57.655 29.630 11.99 0.00 0.00 2.71
2607 2693 9.817809 GATCTTTTGACTATAACCATACACTGA 57.182 33.333 0.00 0.00 0.00 3.41
2628 2714 1.527034 AGTACACTGCATGCACCAAG 58.473 50.000 18.46 9.91 0.00 3.61
2637 2728 1.039068 CATGCACCAAGTTGGAACCA 58.961 50.000 28.80 19.75 40.96 3.67
2699 2791 6.506500 AGTCCATTCAATCAAAGTGATGTC 57.493 37.500 0.00 0.00 37.15 3.06
2702 2794 6.005823 TCCATTCAATCAAAGTGATGTCTGT 58.994 36.000 0.00 0.00 37.15 3.41
2753 2846 4.811908 TGAACCATGATTTGTGATGCTTG 58.188 39.130 0.00 0.00 0.00 4.01
2783 2876 6.721318 ACTTGAAGGCTTGAATCTAATGGTA 58.279 36.000 3.46 0.00 0.00 3.25
2784 2877 6.599638 ACTTGAAGGCTTGAATCTAATGGTAC 59.400 38.462 3.46 0.00 0.00 3.34
2785 2878 6.313519 TGAAGGCTTGAATCTAATGGTACT 57.686 37.500 3.46 0.00 0.00 2.73
2842 2935 3.743521 TCAGGTTGGAACATTGTCTGAG 58.256 45.455 0.00 0.00 39.30 3.35
2847 2940 3.049708 TGGAACATTGTCTGAGCTCTG 57.950 47.619 16.19 15.06 0.00 3.35
2865 2958 2.832129 TCTGTGGAAGGTAGCCTACTTG 59.168 50.000 1.24 0.00 31.13 3.16
2868 2961 3.393278 TGTGGAAGGTAGCCTACTTGTTT 59.607 43.478 1.24 0.00 31.13 2.83
2869 2962 4.001652 GTGGAAGGTAGCCTACTTGTTTC 58.998 47.826 1.24 2.06 31.13 2.78
2870 2963 3.908103 TGGAAGGTAGCCTACTTGTTTCT 59.092 43.478 1.24 0.00 31.13 2.52
2871 2964 4.349930 TGGAAGGTAGCCTACTTGTTTCTT 59.650 41.667 1.24 0.00 31.13 2.52
2872 2965 4.695928 GGAAGGTAGCCTACTTGTTTCTTG 59.304 45.833 1.24 0.00 31.13 3.02
2932 3026 4.321974 GGGCTTTCCAAAGACAATTAGTGG 60.322 45.833 7.22 0.00 46.07 4.00
2934 3028 5.475564 GGCTTTCCAAAGACAATTAGTGGTA 59.524 40.000 3.11 0.00 43.66 3.25
2935 3029 6.015772 GGCTTTCCAAAGACAATTAGTGGTAA 60.016 38.462 3.11 0.00 43.66 2.85
2936 3030 7.309805 GGCTTTCCAAAGACAATTAGTGGTAAT 60.310 37.037 3.11 0.00 43.66 1.89
2959 3053 5.520376 AATAAATTAGTGCCATGACAGCC 57.480 39.130 0.00 0.00 0.00 4.85
2971 3065 0.250295 TGACAGCCACTACAAGGTGC 60.250 55.000 0.00 0.00 36.03 5.01
2986 3080 2.357881 TGCTTCCTGCGAGCACAG 60.358 61.111 0.00 0.00 44.63 3.66
3015 3109 0.539051 CTTCCCTGGCAGGTACTCTG 59.461 60.000 30.68 15.19 46.03 3.35
3073 3207 2.113774 CTGCCTGCAACTGTCCCA 59.886 61.111 0.00 0.00 0.00 4.37
3074 3208 2.203337 TGCCTGCAACTGTCCCAC 60.203 61.111 0.00 0.00 0.00 4.61
3075 3209 3.357079 GCCTGCAACTGTCCCACG 61.357 66.667 0.00 0.00 0.00 4.94
3076 3210 2.425592 CCTGCAACTGTCCCACGA 59.574 61.111 0.00 0.00 0.00 4.35
3077 3211 1.669115 CCTGCAACTGTCCCACGAG 60.669 63.158 0.00 0.00 0.00 4.18
3078 3212 1.669115 CTGCAACTGTCCCACGAGG 60.669 63.158 0.00 0.00 0.00 4.63
3079 3213 3.050275 GCAACTGTCCCACGAGGC 61.050 66.667 0.00 0.00 34.51 4.70
3080 3214 2.358737 CAACTGTCCCACGAGGCC 60.359 66.667 0.00 0.00 34.51 5.19
3085 3219 4.436998 GTCCCACGAGGCCACGAG 62.437 72.222 29.67 20.98 37.03 4.18
3093 3227 1.217585 CGAGGCCACGAGTATGCATG 61.218 60.000 18.51 0.00 35.09 4.06
3107 3245 1.358877 TGCATGTGTAGCTGCTTACG 58.641 50.000 7.79 0.00 39.16 3.18
3114 3252 3.369756 TGTGTAGCTGCTTACGCATTAAC 59.630 43.478 7.79 0.00 46.74 2.01
3170 3308 4.647399 TGAAAAGGACCAAGGAACGAATTT 59.353 37.500 0.00 0.00 0.00 1.82
3234 3372 0.951558 GTGCTGGTCGTTTTCCATGT 59.048 50.000 0.00 0.00 34.26 3.21
3235 3373 1.069227 GTGCTGGTCGTTTTCCATGTC 60.069 52.381 0.00 0.00 34.26 3.06
3236 3374 1.234821 GCTGGTCGTTTTCCATGTCA 58.765 50.000 0.00 0.00 34.26 3.58
3237 3375 1.197721 GCTGGTCGTTTTCCATGTCAG 59.802 52.381 0.00 0.00 34.26 3.51
3238 3376 2.494059 CTGGTCGTTTTCCATGTCAGT 58.506 47.619 0.00 0.00 34.26 3.41
3239 3377 2.878406 CTGGTCGTTTTCCATGTCAGTT 59.122 45.455 0.00 0.00 34.26 3.16
3240 3378 2.875933 TGGTCGTTTTCCATGTCAGTTC 59.124 45.455 0.00 0.00 0.00 3.01
3241 3379 2.875933 GGTCGTTTTCCATGTCAGTTCA 59.124 45.455 0.00 0.00 0.00 3.18
3242 3380 3.502211 GGTCGTTTTCCATGTCAGTTCAT 59.498 43.478 0.00 0.00 0.00 2.57
3243 3381 4.023193 GGTCGTTTTCCATGTCAGTTCATT 60.023 41.667 0.00 0.00 0.00 2.57
3244 3382 5.147162 GTCGTTTTCCATGTCAGTTCATTC 58.853 41.667 0.00 0.00 0.00 2.67
3245 3383 4.819088 TCGTTTTCCATGTCAGTTCATTCA 59.181 37.500 0.00 0.00 0.00 2.57
3246 3384 5.473162 TCGTTTTCCATGTCAGTTCATTCAT 59.527 36.000 0.00 0.00 0.00 2.57
3247 3385 5.570206 CGTTTTCCATGTCAGTTCATTCATG 59.430 40.000 0.00 0.00 37.83 3.07
3298 3450 3.307339 GCCCAGATATGGAAGAGTCATCC 60.307 52.174 8.28 7.49 37.48 3.51
3328 3480 2.159448 CCGTTTGAAGCGCCAATGAATA 60.159 45.455 2.29 0.00 0.00 1.75
3340 3492 3.552273 GCCAATGAATATGCCTTGCTGAG 60.552 47.826 0.00 0.00 0.00 3.35
3376 3528 2.115595 CGCTTTTCATGACGCACAAAA 58.884 42.857 0.00 0.00 0.00 2.44
3387 3539 0.594796 CGCACAAAAGTTGGCAGGAC 60.595 55.000 0.00 0.00 34.12 3.85
3399 3551 0.539986 GGCAGGACGATTGGAACCTA 59.460 55.000 0.00 0.00 0.00 3.08
3429 3581 6.770746 AGTAAGCATCTCGGTAAAAGTAGA 57.229 37.500 0.00 0.00 0.00 2.59
3430 3582 6.562518 AGTAAGCATCTCGGTAAAAGTAGAC 58.437 40.000 0.00 0.00 0.00 2.59
3435 3587 5.972382 GCATCTCGGTAAAAGTAGACTAGTG 59.028 44.000 0.00 0.00 0.00 2.74
3436 3588 5.557891 TCTCGGTAAAAGTAGACTAGTGC 57.442 43.478 0.00 0.00 0.00 4.40
3437 3589 5.005740 TCTCGGTAAAAGTAGACTAGTGCA 58.994 41.667 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.519455 CAGGAGAACCACGCCGATC 60.519 63.158 0.00 0.00 43.25 3.69
1 2 1.330655 ATCAGGAGAACCACGCCGAT 61.331 55.000 0.00 0.00 43.25 4.18
2 3 0.681887 TATCAGGAGAACCACGCCGA 60.682 55.000 0.00 0.00 43.25 5.54
5 6 3.557595 CAGAAATATCAGGAGAACCACGC 59.442 47.826 0.00 0.00 38.94 5.34
7 8 3.557595 CGCAGAAATATCAGGAGAACCAC 59.442 47.826 0.00 0.00 38.94 4.16
8 9 3.797039 CGCAGAAATATCAGGAGAACCA 58.203 45.455 0.00 0.00 38.94 3.67
9 10 2.545946 GCGCAGAAATATCAGGAGAACC 59.454 50.000 0.30 0.00 0.00 3.62
10 11 2.545946 GGCGCAGAAATATCAGGAGAAC 59.454 50.000 10.83 0.00 0.00 3.01
11 12 2.485479 GGGCGCAGAAATATCAGGAGAA 60.485 50.000 10.83 0.00 0.00 2.87
12 13 1.070758 GGGCGCAGAAATATCAGGAGA 59.929 52.381 10.83 0.00 0.00 3.71
13 14 1.517242 GGGCGCAGAAATATCAGGAG 58.483 55.000 10.83 0.00 0.00 3.69
14 15 0.108585 GGGGCGCAGAAATATCAGGA 59.891 55.000 10.83 0.00 0.00 3.86
15 16 0.109342 AGGGGCGCAGAAATATCAGG 59.891 55.000 10.83 0.00 0.00 3.86
16 17 1.876156 GAAGGGGCGCAGAAATATCAG 59.124 52.381 10.83 0.00 0.00 2.90
17 18 1.476833 GGAAGGGGCGCAGAAATATCA 60.477 52.381 10.83 0.00 0.00 2.15
18 19 1.239347 GGAAGGGGCGCAGAAATATC 58.761 55.000 10.83 0.00 0.00 1.63
19 20 0.178990 GGGAAGGGGCGCAGAAATAT 60.179 55.000 10.83 0.00 0.00 1.28
20 21 1.226262 GGGAAGGGGCGCAGAAATA 59.774 57.895 10.83 0.00 0.00 1.40
21 22 2.043953 GGGAAGGGGCGCAGAAAT 60.044 61.111 10.83 0.00 0.00 2.17
22 23 2.764637 GAAGGGAAGGGGCGCAGAAA 62.765 60.000 10.83 0.00 0.00 2.52
23 24 3.256960 AAGGGAAGGGGCGCAGAA 61.257 61.111 10.83 0.00 0.00 3.02
24 25 3.717294 GAAGGGAAGGGGCGCAGA 61.717 66.667 10.83 0.00 0.00 4.26
25 26 4.803908 GGAAGGGAAGGGGCGCAG 62.804 72.222 10.83 0.00 0.00 5.18
27 28 4.491409 GAGGAAGGGAAGGGGCGC 62.491 72.222 0.00 0.00 0.00 6.53
28 29 2.689034 AGAGGAAGGGAAGGGGCG 60.689 66.667 0.00 0.00 0.00 6.13
29 30 2.379459 GGAGAGGAAGGGAAGGGGC 61.379 68.421 0.00 0.00 0.00 5.80
30 31 2.066999 CGGAGAGGAAGGGAAGGGG 61.067 68.421 0.00 0.00 0.00 4.79
31 32 2.736826 GCGGAGAGGAAGGGAAGGG 61.737 68.421 0.00 0.00 0.00 3.95
32 33 2.904131 GCGGAGAGGAAGGGAAGG 59.096 66.667 0.00 0.00 0.00 3.46
33 34 2.286127 GACGCGGAGAGGAAGGGAAG 62.286 65.000 12.47 0.00 0.00 3.46
34 35 2.283676 ACGCGGAGAGGAAGGGAA 60.284 61.111 12.47 0.00 0.00 3.97
35 36 2.754658 GACGCGGAGAGGAAGGGA 60.755 66.667 12.47 0.00 0.00 4.20
36 37 3.839432 GGACGCGGAGAGGAAGGG 61.839 72.222 12.47 0.00 0.00 3.95
37 38 3.068691 TGGACGCGGAGAGGAAGG 61.069 66.667 12.47 0.00 0.00 3.46
38 39 1.030488 TAGTGGACGCGGAGAGGAAG 61.030 60.000 12.47 0.00 0.00 3.46
39 40 1.001764 TAGTGGACGCGGAGAGGAA 60.002 57.895 12.47 0.00 0.00 3.36
40 41 1.451567 CTAGTGGACGCGGAGAGGA 60.452 63.158 12.47 0.00 0.00 3.71
41 42 0.463295 TACTAGTGGACGCGGAGAGG 60.463 60.000 12.47 0.00 0.00 3.69
42 43 0.656785 GTACTAGTGGACGCGGAGAG 59.343 60.000 12.47 0.85 0.00 3.20
43 44 0.036105 TGTACTAGTGGACGCGGAGA 60.036 55.000 12.47 0.00 0.00 3.71
44 45 0.377554 CTGTACTAGTGGACGCGGAG 59.622 60.000 12.47 0.00 0.00 4.63
45 46 1.651240 GCTGTACTAGTGGACGCGGA 61.651 60.000 12.47 0.00 0.00 5.54
46 47 1.226603 GCTGTACTAGTGGACGCGG 60.227 63.158 12.47 0.00 0.00 6.46
47 48 0.109458 TTGCTGTACTAGTGGACGCG 60.109 55.000 3.53 3.53 0.00 6.01
48 49 1.993370 CTTTGCTGTACTAGTGGACGC 59.007 52.381 5.39 5.77 0.00 5.19
49 50 1.993370 GCTTTGCTGTACTAGTGGACG 59.007 52.381 5.39 0.00 0.00 4.79
50 51 2.347731 GGCTTTGCTGTACTAGTGGAC 58.652 52.381 5.39 0.00 0.00 4.02
51 52 1.278127 GGGCTTTGCTGTACTAGTGGA 59.722 52.381 5.39 0.00 0.00 4.02
52 53 1.003118 TGGGCTTTGCTGTACTAGTGG 59.997 52.381 5.39 0.00 0.00 4.00
53 54 2.350522 CTGGGCTTTGCTGTACTAGTG 58.649 52.381 5.39 0.00 0.00 2.74
54 55 1.339151 GCTGGGCTTTGCTGTACTAGT 60.339 52.381 0.00 0.00 0.00 2.57
55 56 1.065854 AGCTGGGCTTTGCTGTACTAG 60.066 52.381 0.00 0.00 33.89 2.57
56 57 0.984230 AGCTGGGCTTTGCTGTACTA 59.016 50.000 0.00 0.00 33.89 1.82
90 91 1.273886 GAGCGTAGGAGGGAATCATCC 59.726 57.143 0.00 0.00 43.71 3.51
135 142 3.641017 GCCAAGAGAGAAAGGCAGT 57.359 52.632 0.00 0.00 46.26 4.40
200 212 2.357517 CGTCCCTGCTGGTGTCAC 60.358 66.667 9.00 0.00 34.77 3.67
221 233 4.677151 GTGGGGAGGGGGAGGTGT 62.677 72.222 0.00 0.00 0.00 4.16
229 242 0.397816 TTGTTGGTTTGTGGGGAGGG 60.398 55.000 0.00 0.00 0.00 4.30
294 308 3.871594 GTGTTGCTGTGTAGTGAGAAGTT 59.128 43.478 0.00 0.00 0.00 2.66
296 310 3.722147 AGTGTTGCTGTGTAGTGAGAAG 58.278 45.455 0.00 0.00 0.00 2.85
299 313 2.224042 TGGAGTGTTGCTGTGTAGTGAG 60.224 50.000 0.00 0.00 0.00 3.51
363 377 7.872163 TGTGCAGTGAAAATAGCTTTATTTG 57.128 32.000 0.00 0.00 30.77 2.32
432 450 4.973663 ACATAAATAAATAAAGGCGCACGC 59.026 37.500 10.83 6.46 41.06 5.34
560 587 7.444183 CCAAGTTGTCTTTTACCTCATCAAGTA 59.556 37.037 1.45 0.00 0.00 2.24
688 715 0.308993 GCTGTCAGTGTGCTTTCACC 59.691 55.000 0.93 0.00 42.46 4.02
742 769 0.886490 CAGCAAGATATGGTCCGGCC 60.886 60.000 0.00 1.41 37.77 6.13
758 785 4.450053 ACTAGATCTTCTTCATTGGCAGC 58.550 43.478 0.00 0.00 0.00 5.25
825 857 7.201617 CCTCGGAGAAACAAATAGTAATTGGAC 60.202 40.741 6.58 0.00 34.09 4.02
898 945 3.682377 GGCTCTCTGTTTTTGTCTCTAGC 59.318 47.826 0.00 0.00 0.00 3.42
899 946 4.249661 GGGCTCTCTGTTTTTGTCTCTAG 58.750 47.826 0.00 0.00 0.00 2.43
2273 2347 3.003763 AACGCCTGGACCTCCTCC 61.004 66.667 0.00 0.00 39.97 4.30
2302 2379 1.519455 CCAAGCTCCGTCCTAAGCG 60.519 63.158 0.00 0.00 43.37 4.68
2468 2546 9.545105 ACAAAATTTCTAATCACAAGCATCAAA 57.455 25.926 0.00 0.00 0.00 2.69
2561 2639 7.100458 AGATCAACACAATTATAAGGGCAAC 57.900 36.000 0.00 0.00 0.00 4.17
2577 2655 9.952030 TGTATGGTTATAGTCAAAAGATCAACA 57.048 29.630 0.00 0.00 0.00 3.33
2607 2693 3.273434 CTTGGTGCATGCAGTGTACTAT 58.727 45.455 23.41 0.00 42.36 2.12
2608 2694 2.038426 ACTTGGTGCATGCAGTGTACTA 59.962 45.455 23.41 3.58 42.36 1.82
2609 2695 1.202806 ACTTGGTGCATGCAGTGTACT 60.203 47.619 23.41 0.00 42.36 2.73
2628 2714 7.278868 TGTCATTGTGTTAATTTTGGTTCCAAC 59.721 33.333 3.56 0.00 0.00 3.77
2842 2935 1.137282 GTAGGCTACCTTCCACAGAGC 59.863 57.143 13.82 0.00 34.61 4.09
2847 2940 3.697619 AACAAGTAGGCTACCTTCCAC 57.302 47.619 20.67 0.00 34.61 4.02
2865 2958 7.317390 TGTGGAGTTTTTAAAGGACAAGAAAC 58.683 34.615 6.58 0.00 0.00 2.78
2868 2961 6.460953 GCATGTGGAGTTTTTAAAGGACAAGA 60.461 38.462 0.00 0.00 0.00 3.02
2869 2962 5.691754 GCATGTGGAGTTTTTAAAGGACAAG 59.308 40.000 0.00 0.00 0.00 3.16
2870 2963 5.127845 TGCATGTGGAGTTTTTAAAGGACAA 59.872 36.000 0.00 0.00 0.00 3.18
2871 2964 4.646945 TGCATGTGGAGTTTTTAAAGGACA 59.353 37.500 0.00 0.00 0.00 4.02
2872 2965 5.195001 TGCATGTGGAGTTTTTAAAGGAC 57.805 39.130 0.00 0.00 0.00 3.85
2932 3026 9.612620 GCTGTCATGGCACTAATTTATTATTAC 57.387 33.333 0.00 0.00 0.00 1.89
2934 3028 7.287466 TGGCTGTCATGGCACTAATTTATTATT 59.713 33.333 0.00 0.00 37.59 1.40
2935 3029 6.777091 TGGCTGTCATGGCACTAATTTATTAT 59.223 34.615 0.00 0.00 37.59 1.28
2936 3030 6.125719 TGGCTGTCATGGCACTAATTTATTA 58.874 36.000 0.00 0.00 37.59 0.98
2971 3065 1.461127 GTTTACTGTGCTCGCAGGAAG 59.539 52.381 14.09 3.41 40.09 3.46
2986 3080 3.339141 CTGCCAGGGAAGAAGAGTTTAC 58.661 50.000 0.00 0.00 0.00 2.01
3015 3109 0.787183 GTTCAGACGTTCAGCAGAGC 59.213 55.000 0.00 0.00 0.00 4.09
3073 3207 1.676678 ATGCATACTCGTGGCCTCGT 61.677 55.000 25.10 11.00 0.00 4.18
3074 3208 1.068083 ATGCATACTCGTGGCCTCG 59.932 57.895 20.92 20.92 0.00 4.63
3075 3209 0.179073 ACATGCATACTCGTGGCCTC 60.179 55.000 3.32 0.00 0.00 4.70
3076 3210 0.462581 CACATGCATACTCGTGGCCT 60.463 55.000 3.32 0.00 0.00 5.19
3077 3211 0.744414 ACACATGCATACTCGTGGCC 60.744 55.000 16.57 0.00 33.62 5.36
3078 3212 1.860950 CTACACATGCATACTCGTGGC 59.139 52.381 16.57 0.00 33.62 5.01
3079 3213 1.860950 GCTACACATGCATACTCGTGG 59.139 52.381 16.57 7.59 33.62 4.94
3080 3214 2.537214 CAGCTACACATGCATACTCGTG 59.463 50.000 12.07 12.07 35.48 4.35
3085 3219 3.060272 CGTAAGCAGCTACACATGCATAC 60.060 47.826 0.00 1.63 45.01 2.39
3107 3245 8.403606 ACAGTAATTACAGTAGTCGTTAATGC 57.596 34.615 17.65 0.00 31.59 3.56
3114 3252 6.432607 TCCTGACAGTAATTACAGTAGTCG 57.567 41.667 17.65 13.30 0.00 4.18
3170 3308 3.462483 TTGTTGCGAGTTAAGACAGGA 57.538 42.857 0.00 0.00 0.00 3.86
3234 3372 4.897509 AGGACAGACATGAATGAACTGA 57.102 40.909 19.96 0.00 38.23 3.41
3235 3373 4.999311 TGAAGGACAGACATGAATGAACTG 59.001 41.667 0.00 15.08 39.47 3.16
3236 3374 5.233083 TGAAGGACAGACATGAATGAACT 57.767 39.130 0.00 0.00 0.00 3.01
3298 3450 2.995450 CTTCAAACGGACGGACGCG 61.995 63.158 3.53 3.53 37.37 6.01
3328 3480 2.236766 GCATATTCCTCAGCAAGGCAT 58.763 47.619 0.33 0.00 45.78 4.40
3340 3492 2.094762 AGCGATTACGGGCATATTCC 57.905 50.000 0.00 0.00 40.15 3.01
3348 3500 2.285602 CGTCATGAAAAGCGATTACGGG 60.286 50.000 0.00 0.00 40.15 5.28
3376 3528 0.400213 TTCCAATCGTCCTGCCAACT 59.600 50.000 0.00 0.00 0.00 3.16
3387 3539 2.033049 ACTCGTCGATAGGTTCCAATCG 59.967 50.000 0.00 0.00 44.88 3.34
3429 3581 1.037493 TGACCACGACTTGCACTAGT 58.963 50.000 0.00 0.00 0.00 2.57
3430 3582 2.148916 TTGACCACGACTTGCACTAG 57.851 50.000 0.00 0.00 0.00 2.57
3435 3587 1.295792 TCTGTTTGACCACGACTTGC 58.704 50.000 0.00 0.00 0.00 4.01
3436 3588 2.286418 GCTTCTGTTTGACCACGACTTG 60.286 50.000 0.00 0.00 0.00 3.16
3437 3589 1.940613 GCTTCTGTTTGACCACGACTT 59.059 47.619 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.