Multiple sequence alignment - TraesCS5B01G306500

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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 TraesCS5B01G306500 chr5B 100.000 3020 0 0 1 3020 490100588 490103607 0.000000e+00 5578.0
1 TraesCS5B01G306500 chr5B 91.176 68 6 0 1573 1640 10514064 10514131 3.210000e-15 93.5
2 TraesCS5B01G306500 chr5A 90.810 2557 145 39 219 2739 514451172 514453674 0.000000e+00 3338.0
3 TraesCS5B01G306500 chr5A 74.038 208 48 6 54 258 112092064 112091860 2.500000e-11 80.5
4 TraesCS5B01G306500 chr5D 90.715 2477 147 28 1 2440 408545606 408548036 0.000000e+00 3223.0
5 TraesCS5B01G306500 chr5D 87.643 526 18 18 2522 3020 408555351 408555856 4.370000e-158 568.0
6 TraesCS5B01G306500 chr5D 97.436 39 1 0 2487 2525 408548065 408548103 1.940000e-07 67.6
7 TraesCS5B01G306500 chr3B 91.576 368 24 3 1881 2246 778546415 778546053 4.490000e-138 501.0
8 TraesCS5B01G306500 chrUn 91.530 366 25 3 1881 2245 421058938 421059298 1.620000e-137 499.0
9 TraesCS5B01G306500 chrUn 88.559 236 23 2 1847 2082 47704252 47704021 1.770000e-72 283.0
10 TraesCS5B01G306500 chr7A 82.598 408 52 7 985 1392 193120792 193121180 2.880000e-90 342.0
11 TraesCS5B01G306500 chr7A 90.594 202 19 0 1433 1634 193121189 193121390 4.960000e-68 268.0
12 TraesCS5B01G306500 chr7A 94.118 68 4 0 1573 1640 623459539 623459606 1.480000e-18 104.0
13 TraesCS5B01G306500 chr7A 92.647 68 5 0 1573 1640 717180659 717180726 6.890000e-17 99.0
14 TraesCS5B01G306500 chr7D 91.632 239 16 2 1844 2082 73561262 73561496 8.070000e-86 327.0
15 TraesCS5B01G306500 chr7D 81.295 417 47 15 985 1401 185357503 185357888 2.920000e-80 309.0
16 TraesCS5B01G306500 chr7D 91.045 201 18 0 1435 1635 185357890 185358090 3.840000e-69 272.0
17 TraesCS5B01G306500 chr7D 88.506 87 9 1 126 211 123322426 123322512 1.480000e-18 104.0
18 TraesCS5B01G306500 chr3D 90.678 236 17 3 1847 2082 443423645 443423415 2.920000e-80 309.0
19 TraesCS5B01G306500 chr4D 78.899 218 44 1 147 364 433702654 433702439 2.430000e-31 147.0
20 TraesCS5B01G306500 chr4B 77.966 236 51 1 48 282 40418470 40418705 2.430000e-31 147.0
21 TraesCS5B01G306500 chr6D 96.552 58 2 0 1583 1640 27404348 27404405 2.480000e-16 97.1
22 TraesCS5B01G306500 chr7B 92.727 55 4 0 1586 1640 727672447 727672501 2.500000e-11 80.5
23 TraesCS5B01G306500 chr4A 75.625 160 29 8 29 178 665662718 665662559 1.500000e-08 71.3


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 TraesCS5B01G306500 chr5B 490100588 490103607 3019 False 5578.0 5578 100.0000 1 3020 1 chr5B.!!$F2 3019
1 TraesCS5B01G306500 chr5A 514451172 514453674 2502 False 3338.0 3338 90.8100 219 2739 1 chr5A.!!$F1 2520
2 TraesCS5B01G306500 chr5D 408545606 408548103 2497 False 1645.3 3223 94.0755 1 2525 2 chr5D.!!$F2 2524
3 TraesCS5B01G306500 chr5D 408555351 408555856 505 False 568.0 568 87.6430 2522 3020 1 chr5D.!!$F1 498
4 TraesCS5B01G306500 chr7A 193120792 193121390 598 False 305.0 342 86.5960 985 1634 2 chr7A.!!$F3 649
5 TraesCS5B01G306500 chr7D 185357503 185358090 587 False 290.5 309 86.1700 985 1635 2 chr7D.!!$F3 650

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
347 348 0.172578 CATCGCTAGGTGGTCAACGA 59.827 55.0 0.0 0.0 0.00 3.85 F
1086 1141 0.329596 GGGTCACAGCCTTCCTGATT 59.670 55.0 0.0 0.0 44.64 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1375 1.663702 CGTCTTCACCACGTCCACC 60.664 63.158 0.0 0.0 32.41 4.61 R
2883 2992 0.605589 GTCCGGGGTTCCTGACTTTG 60.606 60.000 0.0 0.0 42.00 2.77 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 2.423446 CCTACTCGCATGGCTCCC 59.577 66.667 0.00 0.00 0.00 4.30
18 19 2.028190 CTACTCGCATGGCTCCCG 59.972 66.667 0.00 0.00 0.00 5.14
19 20 2.758327 TACTCGCATGGCTCCCGT 60.758 61.111 0.00 0.00 0.00 5.28
40 41 2.202171 GCAATGCGTCCAACGTCG 60.202 61.111 1.14 0.00 44.73 5.12
41 42 2.950172 GCAATGCGTCCAACGTCGT 61.950 57.895 0.00 0.00 44.73 4.34
42 43 1.129809 CAATGCGTCCAACGTCGTC 59.870 57.895 0.00 0.00 44.73 4.20
49 50 2.431942 CCAACGTCGTCGAAGGGG 60.432 66.667 9.47 9.47 40.62 4.79
50 51 2.337532 CAACGTCGTCGAAGGGGT 59.662 61.111 9.47 0.00 40.62 4.95
57 58 1.189524 TCGTCGAAGGGGTTGTGGAT 61.190 55.000 0.00 0.00 0.00 3.41
58 59 1.019278 CGTCGAAGGGGTTGTGGATG 61.019 60.000 0.00 0.00 0.00 3.51
62 63 1.247567 GAAGGGGTTGTGGATGTGTG 58.752 55.000 0.00 0.00 0.00 3.82
66 67 1.523758 GGGTTGTGGATGTGTGTCTC 58.476 55.000 0.00 0.00 0.00 3.36
78 79 2.599281 TGTCTCCGGCGGAACTCA 60.599 61.111 30.59 23.52 0.00 3.41
82 83 2.682136 TCCGGCGGAACTCATGGA 60.682 61.111 29.11 0.00 0.00 3.41
83 84 2.238847 CTCCGGCGGAACTCATGGAA 62.239 60.000 30.59 2.94 0.00 3.53
84 85 1.153168 CCGGCGGAACTCATGGAAT 60.153 57.895 24.41 0.00 0.00 3.01
86 87 1.094785 CGGCGGAACTCATGGAATTT 58.905 50.000 0.00 0.00 0.00 1.82
87 88 1.202177 CGGCGGAACTCATGGAATTTG 60.202 52.381 0.00 0.00 0.00 2.32
89 90 1.818674 GCGGAACTCATGGAATTTGGT 59.181 47.619 0.00 0.00 0.00 3.67
94 95 3.992943 ACTCATGGAATTTGGTCGGTA 57.007 42.857 0.00 0.00 0.00 4.02
106 107 1.092348 GGTCGGTATTGGTCTTTGGC 58.908 55.000 0.00 0.00 0.00 4.52
110 111 1.745827 CGGTATTGGTCTTTGGCGGAT 60.746 52.381 0.00 0.00 0.00 4.18
114 115 1.821216 TTGGTCTTTGGCGGATCTTC 58.179 50.000 0.00 0.00 0.00 2.87
130 131 3.900966 TCTTCATGGATCCAGTCTGTG 57.099 47.619 21.33 13.10 0.00 3.66
136 137 1.000843 TGGATCCAGTCTGTGTTCGTG 59.999 52.381 11.44 0.00 0.00 4.35
144 145 2.041966 GTCTGTGTTCGTGTGTCTACG 58.958 52.381 0.00 0.00 44.98 3.51
159 160 3.322541 TGTCTACGTGTTGGATCCTTTCA 59.677 43.478 14.23 6.65 0.00 2.69
179 180 7.498239 CCTTTCAATCTATGCTTCTCTTCATCA 59.502 37.037 0.00 0.00 0.00 3.07
182 183 5.548181 ATCTATGCTTCTCTTCATCAGCA 57.452 39.130 0.00 0.00 46.02 4.41
201 202 3.363341 CAACGGTTGCTATTTTGGTGT 57.637 42.857 8.09 0.00 0.00 4.16
212 213 1.604604 TTTTGGTGTGCTAGTCCTGC 58.395 50.000 0.00 0.00 0.00 4.85
214 215 2.125512 GGTGTGCTAGTCCTGCCG 60.126 66.667 0.00 0.00 0.00 5.69
217 218 3.391382 GTGCTAGTCCTGCCGGGT 61.391 66.667 2.18 0.00 36.25 5.28
225 226 1.689233 TCCTGCCGGGTCTTAGCAT 60.689 57.895 2.18 0.00 35.64 3.79
233 234 1.799181 CGGGTCTTAGCATGACGACTG 60.799 57.143 0.00 0.00 35.45 3.51
237 238 1.818674 TCTTAGCATGACGACTGCTCA 59.181 47.619 12.89 4.06 46.79 4.26
239 240 2.967599 TAGCATGACGACTGCTCAAT 57.032 45.000 12.89 0.00 46.79 2.57
243 244 2.095567 GCATGACGACTGCTCAATTGTT 60.096 45.455 5.13 0.00 36.68 2.83
265 266 8.439993 TGTTTACTACAACAAAGTATGCTCAA 57.560 30.769 0.00 0.00 33.60 3.02
273 274 2.386661 AAGTATGCTCAACTCCGGTG 57.613 50.000 0.00 0.00 0.00 4.94
290 291 2.408565 GGTGAGGGAGGGATGATAACA 58.591 52.381 0.00 0.00 0.00 2.41
294 295 1.048601 GGGAGGGATGATAACAGCGA 58.951 55.000 0.00 0.00 32.75 4.93
295 296 1.625818 GGGAGGGATGATAACAGCGAT 59.374 52.381 0.00 0.00 32.75 4.58
296 297 2.613977 GGGAGGGATGATAACAGCGATG 60.614 54.545 0.00 0.00 32.75 3.84
303 304 2.193447 TGATAACAGCGATGCGTCTTC 58.807 47.619 0.00 0.00 0.00 2.87
307 308 4.135153 AGCGATGCGTCTTCGGCT 62.135 61.111 4.05 2.21 37.10 5.52
311 312 2.507102 ATGCGTCTTCGGCTCGTG 60.507 61.111 0.00 0.00 37.56 4.35
312 313 3.282745 ATGCGTCTTCGGCTCGTGT 62.283 57.895 0.00 0.00 37.56 4.49
313 314 2.733593 GCGTCTTCGGCTCGTGTT 60.734 61.111 0.00 0.00 37.56 3.32
314 315 2.717809 GCGTCTTCGGCTCGTGTTC 61.718 63.158 0.00 0.00 37.56 3.18
315 316 2.087009 CGTCTTCGGCTCGTGTTCC 61.087 63.158 0.00 0.00 0.00 3.62
316 317 1.737008 GTCTTCGGCTCGTGTTCCC 60.737 63.158 0.00 0.00 0.00 3.97
343 344 2.430248 TAGTCATCGCTAGGTGGTCA 57.570 50.000 0.00 0.00 0.00 4.02
347 348 0.172578 CATCGCTAGGTGGTCAACGA 59.827 55.000 0.00 0.00 0.00 3.85
359 360 6.650120 AGGTGGTCAACGAATCTAAATGTAT 58.350 36.000 0.00 0.00 0.00 2.29
360 361 7.110155 AGGTGGTCAACGAATCTAAATGTATT 58.890 34.615 0.00 0.00 0.00 1.89
361 362 7.610305 AGGTGGTCAACGAATCTAAATGTATTT 59.390 33.333 0.00 0.00 0.00 1.40
389 390 8.654230 TCTATCACTTCTGATGAATAGTTTGC 57.346 34.615 0.00 0.00 37.70 3.68
401 402 7.652909 TGATGAATAGTTTGCAAGTTTTTCCTG 59.347 33.333 0.00 0.00 0.00 3.86
457 469 6.256757 GCAGTGAGGTTATGAAGAAGTACATC 59.743 42.308 0.00 0.00 0.00 3.06
483 495 2.897326 TGAGCTAGTTGCACCTTCACTA 59.103 45.455 0.00 0.00 45.94 2.74
532 544 1.308216 ATTCTCCAGGGACCAGGGG 60.308 63.158 0.00 0.00 0.00 4.79
535 547 4.024984 TCCAGGGACCAGGGGAGG 62.025 72.222 0.00 0.00 0.00 4.30
587 600 3.795688 TTCTCTTTTCCTGCCACAGAT 57.204 42.857 0.00 0.00 32.44 2.90
636 649 2.422597 TGCACGAAATTCCACTACCTG 58.577 47.619 0.00 0.00 0.00 4.00
637 650 2.037902 TGCACGAAATTCCACTACCTGA 59.962 45.455 0.00 0.00 0.00 3.86
638 651 3.270877 GCACGAAATTCCACTACCTGAT 58.729 45.455 0.00 0.00 0.00 2.90
639 652 3.063997 GCACGAAATTCCACTACCTGATG 59.936 47.826 0.00 0.00 0.00 3.07
640 653 3.063997 CACGAAATTCCACTACCTGATGC 59.936 47.826 0.00 0.00 0.00 3.91
641 654 3.055094 ACGAAATTCCACTACCTGATGCT 60.055 43.478 0.00 0.00 0.00 3.79
642 655 3.941483 CGAAATTCCACTACCTGATGCTT 59.059 43.478 0.00 0.00 0.00 3.91
643 656 4.396166 CGAAATTCCACTACCTGATGCTTT 59.604 41.667 0.00 0.00 0.00 3.51
644 657 5.106157 CGAAATTCCACTACCTGATGCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
645 658 5.904362 AATTCCACTACCTGATGCTTTTC 57.096 39.130 0.00 0.00 0.00 2.29
646 659 4.640771 TTCCACTACCTGATGCTTTTCT 57.359 40.909 0.00 0.00 0.00 2.52
702 739 2.067605 ACACCTCACCAACCCGTCA 61.068 57.895 0.00 0.00 0.00 4.35
830 885 0.821711 CCGAAACAAGGGGAGCACAA 60.822 55.000 0.00 0.00 0.00 3.33
831 886 0.593128 CGAAACAAGGGGAGCACAAG 59.407 55.000 0.00 0.00 0.00 3.16
949 1004 5.627135 AGAAAGTTGAGATTTTCCCGGTTA 58.373 37.500 0.00 0.00 33.38 2.85
1074 1129 2.879233 GCACCTTCCTCGGGTCACA 61.879 63.158 0.00 0.00 34.44 3.58
1086 1141 0.329596 GGGTCACAGCCTTCCTGATT 59.670 55.000 0.00 0.00 44.64 2.57
1101 1156 1.472878 CTGATTGTCTTCTCCGTCGGA 59.527 52.381 14.54 14.54 0.00 4.55
1581 1642 4.899239 CCGGCCATCCTCTGCGTC 62.899 72.222 2.24 0.00 0.00 5.19
2192 2258 4.016706 CGCCTTGTCCCCGGTCTT 62.017 66.667 0.00 0.00 0.00 3.01
2202 2270 0.537371 CCCCGGTCTTTGAACTTGCT 60.537 55.000 0.00 0.00 0.00 3.91
2233 2301 2.598985 TTCGTTTGGGCCGCCATT 60.599 55.556 12.58 0.00 0.00 3.16
2258 2326 3.815809 TCTTTTCTCCACCAAACGACAT 58.184 40.909 0.00 0.00 0.00 3.06
2267 2335 5.175859 TCCACCAAACGACATATTCTTCTC 58.824 41.667 0.00 0.00 0.00 2.87
2290 2360 3.207419 CACGACGAGAAATCAACAAACG 58.793 45.455 0.00 0.00 0.00 3.60
2326 2396 4.215399 CACGTCCATTGTACATCAAAGGTT 59.785 41.667 0.00 0.00 43.10 3.50
2414 2490 8.918202 TTATCTTCTGGTAAAGAAAAAGCAGA 57.082 30.769 0.42 0.42 44.38 4.26
2455 2531 2.178764 AGATGGAGGGATAGACTGCAGA 59.821 50.000 23.35 0.00 39.67 4.26
2458 2534 2.324541 GGAGGGATAGACTGCAGATGT 58.675 52.381 23.35 6.69 0.00 3.06
2464 2540 4.444022 GGGATAGACTGCAGATGTTGATGT 60.444 45.833 23.35 0.00 0.00 3.06
2476 2552 6.016527 GCAGATGTTGATGTTGATGGTGATAT 60.017 38.462 0.00 0.00 0.00 1.63
2628 2710 0.451783 CTTAGCGTGGGAATGGCAAC 59.548 55.000 0.00 0.00 0.00 4.17
2639 2721 0.178975 AATGGCAACGGTGGGAAAGA 60.179 50.000 0.90 0.00 42.51 2.52
2640 2722 0.609131 ATGGCAACGGTGGGAAAGAG 60.609 55.000 0.90 0.00 42.51 2.85
2641 2723 1.072505 GGCAACGGTGGGAAAGAGA 59.927 57.895 0.90 0.00 0.00 3.10
2642 2724 0.955919 GGCAACGGTGGGAAAGAGAG 60.956 60.000 0.90 0.00 0.00 3.20
2643 2725 0.034896 GCAACGGTGGGAAAGAGAGA 59.965 55.000 0.90 0.00 0.00 3.10
2644 2726 1.941668 GCAACGGTGGGAAAGAGAGAG 60.942 57.143 0.90 0.00 0.00 3.20
2645 2727 1.618837 CAACGGTGGGAAAGAGAGAGA 59.381 52.381 0.00 0.00 0.00 3.10
2646 2728 1.551452 ACGGTGGGAAAGAGAGAGAG 58.449 55.000 0.00 0.00 0.00 3.20
2647 2729 1.075698 ACGGTGGGAAAGAGAGAGAGA 59.924 52.381 0.00 0.00 0.00 3.10
2648 2730 1.748493 CGGTGGGAAAGAGAGAGAGAG 59.252 57.143 0.00 0.00 0.00 3.20
2649 2731 2.619332 CGGTGGGAAAGAGAGAGAGAGA 60.619 54.545 0.00 0.00 0.00 3.10
2650 2732 3.023832 GGTGGGAAAGAGAGAGAGAGAG 58.976 54.545 0.00 0.00 0.00 3.20
2651 2733 3.308832 GGTGGGAAAGAGAGAGAGAGAGA 60.309 52.174 0.00 0.00 0.00 3.10
2654 2736 4.080356 TGGGAAAGAGAGAGAGAGAGAGAG 60.080 50.000 0.00 0.00 0.00 3.20
2657 2739 5.129485 GGAAAGAGAGAGAGAGAGAGAGAGA 59.871 48.000 0.00 0.00 0.00 3.10
2690 2772 2.036387 GCCAAACTGGTTAGGTGGTTT 58.964 47.619 5.08 0.00 40.46 3.27
2706 2788 6.988522 AGGTGGTTTCGTTAATAAATTTGCT 58.011 32.000 0.00 0.00 0.00 3.91
2777 2859 4.988716 TGGTCGAGCCCACGGAGT 62.989 66.667 12.85 0.00 36.52 3.85
2783 2892 0.747283 CGAGCCCACGGAGTAGTACT 60.747 60.000 1.37 1.37 41.61 2.73
2819 2928 1.599047 CTGGACGGATGCAGGTTCT 59.401 57.895 0.00 0.00 40.47 3.01
2883 2992 2.551270 CGCTGAACCTCACGCAAC 59.449 61.111 0.00 0.00 0.00 4.17
2896 3005 1.021968 ACGCAACAAAGTCAGGAACC 58.978 50.000 0.00 0.00 0.00 3.62
2898 3007 0.673985 GCAACAAAGTCAGGAACCCC 59.326 55.000 0.00 0.00 0.00 4.95
2919 3028 4.887071 CCCGGACTGAAATCCATTTGATAA 59.113 41.667 0.73 0.00 38.87 1.75
2922 3031 7.417797 CCCGGACTGAAATCCATTTGATAATTT 60.418 37.037 0.73 0.00 38.87 1.82
2943 3052 1.208259 GTTTTTGCTTGGCTGTTCCG 58.792 50.000 0.00 0.00 37.80 4.30
2973 3082 2.304092 TCGCTACCCGAATATGTCAGT 58.696 47.619 0.00 0.00 44.21 3.41
2981 3090 6.726490 ACCCGAATATGTCAGTATTACACT 57.274 37.500 0.00 0.00 38.32 3.55
2998 3107 1.365999 CTGGCGTGCCCGTGATATA 59.634 57.895 8.69 0.00 35.87 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.731969 CCCTTCGACGACGTTGGAC 60.732 63.158 15.12 0.00 40.69 4.02
33 34 1.300388 AACCCCTTCGACGACGTTG 60.300 57.895 9.05 9.05 40.69 4.10
35 36 2.337532 CAACCCCTTCGACGACGT 59.662 61.111 0.00 0.00 40.69 4.34
40 41 0.036306 ACATCCACAACCCCTTCGAC 59.964 55.000 0.00 0.00 0.00 4.20
41 42 0.036164 CACATCCACAACCCCTTCGA 59.964 55.000 0.00 0.00 0.00 3.71
42 43 0.250727 ACACATCCACAACCCCTTCG 60.251 55.000 0.00 0.00 0.00 3.79
49 50 1.148310 CGGAGACACACATCCACAAC 58.852 55.000 0.00 0.00 35.14 3.32
50 51 0.034756 CCGGAGACACACATCCACAA 59.965 55.000 0.00 0.00 35.14 3.33
57 58 3.228017 TTCCGCCGGAGACACACA 61.228 61.111 5.05 0.00 31.21 3.72
58 59 2.737376 GTTCCGCCGGAGACACAC 60.737 66.667 5.05 0.00 31.21 3.82
62 63 1.519455 CATGAGTTCCGCCGGAGAC 60.519 63.158 5.05 8.10 31.21 3.36
66 67 0.748005 AATTCCATGAGTTCCGCCGG 60.748 55.000 0.00 0.00 0.00 6.13
78 79 3.951680 GACCAATACCGACCAAATTCCAT 59.048 43.478 0.00 0.00 0.00 3.41
82 83 4.219725 CCAAAGACCAATACCGACCAAATT 59.780 41.667 0.00 0.00 0.00 1.82
83 84 3.761752 CCAAAGACCAATACCGACCAAAT 59.238 43.478 0.00 0.00 0.00 2.32
84 85 3.150767 CCAAAGACCAATACCGACCAAA 58.849 45.455 0.00 0.00 0.00 3.28
86 87 1.612199 GCCAAAGACCAATACCGACCA 60.612 52.381 0.00 0.00 0.00 4.02
87 88 1.092348 GCCAAAGACCAATACCGACC 58.908 55.000 0.00 0.00 0.00 4.79
89 90 0.391927 CCGCCAAAGACCAATACCGA 60.392 55.000 0.00 0.00 0.00 4.69
94 95 2.290896 TGAAGATCCGCCAAAGACCAAT 60.291 45.455 0.00 0.00 0.00 3.16
110 111 3.176411 ACACAGACTGGATCCATGAAGA 58.824 45.455 16.63 0.00 0.00 2.87
114 115 2.274437 CGAACACAGACTGGATCCATG 58.726 52.381 16.63 13.68 0.00 3.66
128 129 1.831343 ACACGTAGACACACGAACAC 58.169 50.000 2.26 0.00 44.69 3.32
130 131 1.519758 CCAACACGTAGACACACGAAC 59.480 52.381 2.26 0.00 44.69 3.95
136 137 3.314541 AAGGATCCAACACGTAGACAC 57.685 47.619 15.82 0.00 0.00 3.67
144 145 5.591877 AGCATAGATTGAAAGGATCCAACAC 59.408 40.000 15.82 2.97 0.00 3.32
159 160 5.926663 TGCTGATGAAGAGAAGCATAGATT 58.073 37.500 0.00 0.00 40.59 2.40
182 183 2.544903 GCACACCAAAATAGCAACCGTT 60.545 45.455 0.00 0.00 0.00 4.44
201 202 3.075005 GACCCGGCAGGACTAGCA 61.075 66.667 3.68 0.00 41.02 3.49
212 213 0.527817 GTCGTCATGCTAAGACCCGG 60.528 60.000 0.00 0.00 32.41 5.73
214 215 1.927895 CAGTCGTCATGCTAAGACCC 58.072 55.000 0.00 0.00 34.41 4.46
225 226 4.377021 AGTAAACAATTGAGCAGTCGTCA 58.623 39.130 13.59 0.00 0.00 4.35
239 240 8.439993 TGAGCATACTTTGTTGTAGTAAACAA 57.560 30.769 0.00 0.00 45.77 2.83
243 244 7.386848 GGAGTTGAGCATACTTTGTTGTAGTAA 59.613 37.037 0.00 0.00 32.28 2.24
255 256 1.478510 CTCACCGGAGTTGAGCATACT 59.521 52.381 9.46 0.00 36.36 2.12
258 259 1.599047 CCTCACCGGAGTTGAGCAT 59.401 57.895 9.46 0.00 39.64 3.79
262 263 4.113617 CTCCCTCACCGGAGTTGA 57.886 61.111 9.46 0.00 43.94 3.18
273 274 1.001406 CGCTGTTATCATCCCTCCCTC 59.999 57.143 0.00 0.00 0.00 4.30
282 283 2.515926 AGACGCATCGCTGTTATCAT 57.484 45.000 0.00 0.00 0.00 2.45
290 291 4.135153 AGCCGAAGACGCATCGCT 62.135 61.111 0.11 0.00 38.93 4.93
294 295 2.507102 CACGAGCCGAAGACGCAT 60.507 61.111 1.50 0.00 38.29 4.73
295 296 3.493830 AACACGAGCCGAAGACGCA 62.494 57.895 1.50 0.00 38.29 5.24
296 297 2.717809 GAACACGAGCCGAAGACGC 61.718 63.158 1.50 0.00 38.29 5.19
303 304 3.642778 ATCACGGGAACACGAGCCG 62.643 63.158 2.83 0.00 37.61 5.52
307 308 3.695556 TGACTATAATCACGGGAACACGA 59.304 43.478 2.83 0.00 37.61 4.35
311 312 3.673809 GCGATGACTATAATCACGGGAAC 59.326 47.826 0.00 0.00 0.00 3.62
312 313 3.572682 AGCGATGACTATAATCACGGGAA 59.427 43.478 0.00 0.00 0.00 3.97
313 314 3.154710 AGCGATGACTATAATCACGGGA 58.845 45.455 0.00 0.00 0.00 5.14
314 315 3.577649 AGCGATGACTATAATCACGGG 57.422 47.619 7.78 0.00 0.00 5.28
315 316 4.156190 ACCTAGCGATGACTATAATCACGG 59.844 45.833 7.78 0.00 0.00 4.94
316 317 5.089411 CACCTAGCGATGACTATAATCACG 58.911 45.833 0.00 0.00 0.00 4.35
369 370 6.906659 ACTTGCAAACTATTCATCAGAAGTG 58.093 36.000 0.00 0.00 37.14 3.16
442 445 6.552725 AGCTCATCTGGATGTACTTCTTCATA 59.447 38.462 9.94 0.00 39.72 2.15
457 469 1.209019 AGGTGCAACTAGCTCATCTGG 59.791 52.381 0.00 0.00 45.94 3.86
535 547 5.349260 TGGATACTCTGTCACTCACTGACC 61.349 50.000 0.00 0.00 43.13 4.02
636 649 5.356470 AGTTTAGGAGCATCAGAAAAGCATC 59.644 40.000 0.00 0.00 36.25 3.91
637 650 5.259632 AGTTTAGGAGCATCAGAAAAGCAT 58.740 37.500 0.00 0.00 36.25 3.79
638 651 4.655963 AGTTTAGGAGCATCAGAAAAGCA 58.344 39.130 0.00 0.00 36.25 3.91
639 652 6.403746 GGTTAGTTTAGGAGCATCAGAAAAGC 60.404 42.308 0.00 0.00 36.25 3.51
640 653 6.183360 CGGTTAGTTTAGGAGCATCAGAAAAG 60.183 42.308 0.00 0.00 36.25 2.27
641 654 5.642063 CGGTTAGTTTAGGAGCATCAGAAAA 59.358 40.000 0.00 0.00 36.25 2.29
642 655 5.175859 CGGTTAGTTTAGGAGCATCAGAAA 58.824 41.667 0.00 0.00 36.25 2.52
643 656 4.222145 ACGGTTAGTTTAGGAGCATCAGAA 59.778 41.667 0.00 0.00 36.25 3.02
644 657 3.767673 ACGGTTAGTTTAGGAGCATCAGA 59.232 43.478 0.00 0.00 36.25 3.27
645 658 3.865745 CACGGTTAGTTTAGGAGCATCAG 59.134 47.826 0.00 0.00 36.25 2.90
646 659 3.512329 TCACGGTTAGTTTAGGAGCATCA 59.488 43.478 0.00 0.00 36.25 3.07
702 739 0.395686 TGACTGCTCTGCTCTGCTTT 59.604 50.000 0.00 0.00 0.00 3.51
830 885 2.434359 GCCGTTAGCTTGACGCCT 60.434 61.111 14.66 0.00 40.39 5.52
831 886 3.497031 GGCCGTTAGCTTGACGCC 61.497 66.667 14.66 14.70 43.05 5.68
949 1004 2.101582 CCTGCTGTAGGCTCGTATTCTT 59.898 50.000 0.00 0.00 40.38 2.52
1062 1117 2.203788 AAGGCTGTGACCCGAGGA 60.204 61.111 0.00 0.00 0.00 3.71
1065 1120 2.203788 AGGAAGGCTGTGACCCGA 60.204 61.111 0.00 0.00 0.00 5.14
1068 1123 1.271597 ACAATCAGGAAGGCTGTGACC 60.272 52.381 0.00 0.00 0.00 4.02
1074 1129 2.238395 GGAGAAGACAATCAGGAAGGCT 59.762 50.000 0.00 0.00 0.00 4.58
1083 1138 2.873133 ATCCGACGGAGAAGACAATC 57.127 50.000 22.99 0.00 34.05 2.67
1086 1141 2.286872 GAGTATCCGACGGAGAAGACA 58.713 52.381 22.99 0.00 34.05 3.41
1101 1156 1.167155 AGACGATGCCGAGCGAGTAT 61.167 55.000 0.00 0.00 39.50 2.12
1197 1252 4.194720 GTGACGCCGCTCGAGGAT 62.195 66.667 15.58 0.00 41.67 3.24
1314 1375 1.663702 CGTCTTCACCACGTCCACC 60.664 63.158 0.00 0.00 32.41 4.61
1316 1377 2.023414 AAGCGTCTTCACCACGTCCA 62.023 55.000 0.00 0.00 39.54 4.02
1830 1891 1.746615 CCAGGCCAGGTTGATGTCG 60.747 63.158 5.01 0.00 0.00 4.35
1947 2008 4.760047 CGGACGGTGAGCCCCTTG 62.760 72.222 0.00 0.00 0.00 3.61
2052 2113 4.415501 GACAAGCACGAGCACGCG 62.416 66.667 3.53 3.53 45.49 6.01
2192 2258 3.678056 ACACCTCGATAGCAAGTTCAA 57.322 42.857 0.00 0.00 0.00 2.69
2233 2301 5.047943 TGTCGTTTGGTGGAGAAAAGAAAAA 60.048 36.000 0.00 0.00 0.00 1.94
2253 2321 3.478874 CGTCGTGTGAGAAGAATATGTCG 59.521 47.826 0.00 0.00 0.00 4.35
2254 2322 4.659088 TCGTCGTGTGAGAAGAATATGTC 58.341 43.478 0.00 0.00 0.00 3.06
2267 2335 3.852471 TTGTTGATTTCTCGTCGTGTG 57.148 42.857 0.00 0.00 0.00 3.82
2326 2396 5.518848 AACATGACAACAGCTTTTCATCA 57.481 34.783 0.00 0.00 0.00 3.07
2414 2490 1.080298 CGTACCGCGAAGAACCCTT 60.080 57.895 8.23 0.00 44.77 3.95
2424 2500 2.331805 CTCCATCTCCGTACCGCG 59.668 66.667 0.00 0.00 40.95 6.46
2464 2540 9.471084 CGTACACAACTTATATATCACCATCAA 57.529 33.333 0.00 0.00 0.00 2.57
2476 2552 6.179756 TCCTCCACTACGTACACAACTTATA 58.820 40.000 0.00 0.00 0.00 0.98
2546 2622 3.242936 CGTCACCTTCTTCTAGCTCTAGC 60.243 52.174 0.00 0.00 42.49 3.42
2547 2623 3.314080 CCGTCACCTTCTTCTAGCTCTAG 59.686 52.174 0.00 0.00 34.56 2.43
2548 2624 3.280295 CCGTCACCTTCTTCTAGCTCTA 58.720 50.000 0.00 0.00 0.00 2.43
2549 2625 2.096248 CCGTCACCTTCTTCTAGCTCT 58.904 52.381 0.00 0.00 0.00 4.09
2550 2626 1.819903 ACCGTCACCTTCTTCTAGCTC 59.180 52.381 0.00 0.00 0.00 4.09
2628 2710 1.748493 CTCTCTCTCTCTTTCCCACCG 59.252 57.143 0.00 0.00 0.00 4.94
2639 2721 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2640 2722 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2641 2723 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2642 2724 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
2643 2725 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
2644 2726 5.830991 ACTACTCTCTCTCTCTCTCTCTCTC 59.169 48.000 0.00 0.00 0.00 3.20
2645 2727 5.596361 CACTACTCTCTCTCTCTCTCTCTCT 59.404 48.000 0.00 0.00 0.00 3.10
2646 2728 5.221342 CCACTACTCTCTCTCTCTCTCTCTC 60.221 52.000 0.00 0.00 0.00 3.20
2647 2729 4.651503 CCACTACTCTCTCTCTCTCTCTCT 59.348 50.000 0.00 0.00 0.00 3.10
2648 2730 4.740934 GCCACTACTCTCTCTCTCTCTCTC 60.741 54.167 0.00 0.00 0.00 3.20
2649 2731 3.134804 GCCACTACTCTCTCTCTCTCTCT 59.865 52.174 0.00 0.00 0.00 3.10
2650 2732 3.467803 GCCACTACTCTCTCTCTCTCTC 58.532 54.545 0.00 0.00 0.00 3.20
2651 2733 2.172717 GGCCACTACTCTCTCTCTCTCT 59.827 54.545 0.00 0.00 0.00 3.10
2654 2736 2.428544 TGGCCACTACTCTCTCTCTC 57.571 55.000 0.00 0.00 0.00 3.20
2657 2739 2.564947 CAGTTTGGCCACTACTCTCTCT 59.435 50.000 3.88 0.00 0.00 3.10
2690 2772 7.113684 CGAACCAACAAGCAAATTTATTAACGA 59.886 33.333 0.00 0.00 0.00 3.85
2706 2788 4.329801 CGAAGATGATGATCGAACCAACAA 59.670 41.667 5.51 0.00 38.82 2.83
2760 2842 3.572447 TACTCCGTGGGCTCGACCA 62.572 63.158 6.41 0.00 42.05 4.02
2788 2897 2.103094 TCCGTCCAGCAGATTAATCCAG 59.897 50.000 11.92 6.50 0.00 3.86
2819 2928 5.048083 CACTCCCAGATCGAAAAATCCAAAA 60.048 40.000 0.00 0.00 0.00 2.44
2883 2992 0.605589 GTCCGGGGTTCCTGACTTTG 60.606 60.000 0.00 0.00 42.00 2.77
2896 3005 2.722094 TCAAATGGATTTCAGTCCGGG 58.278 47.619 0.00 0.00 41.35 5.73
2898 3007 7.376866 CGAAATTATCAAATGGATTTCAGTCCG 59.623 37.037 8.00 0.00 41.35 4.79
2919 3028 3.177997 ACAGCCAAGCAAAAACGAAAT 57.822 38.095 0.00 0.00 0.00 2.17
2922 3031 1.202359 GGAACAGCCAAGCAAAAACGA 60.202 47.619 0.00 0.00 36.34 3.85
2981 3090 1.068417 GTATATCACGGGCACGCCA 59.932 57.895 9.12 0.00 46.04 5.69
2998 3107 4.913335 ATGTATGTATTGACCGAGTCGT 57.087 40.909 12.31 0.00 34.95 4.34


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

AutoCloner maintained by Alex Coulton.