Multiple sequence alignment - TraesCS5B01G402300

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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 TraesCS5B01G402300 chr5B 100.000 3148 0 0 1 3148 578813982 578817129 0.000000e+00 5814.0
1 TraesCS5B01G402300 chr5B 93.327 1004 51 5 1138 2126 579003111 579004113 0.000000e+00 1469.0
2 TraesCS5B01G402300 chr5B 79.572 421 80 6 1748 2165 579150042 579150459 2.370000e-76 296.0
3 TraesCS5B01G402300 chr5B 74.844 481 102 16 1569 2038 652731026 652731498 1.910000e-47 200.0
4 TraesCS5B01G402300 chr5D 87.693 2722 221 47 2 2655 472397944 472400619 0.000000e+00 3066.0
5 TraesCS5B01G402300 chr5D 89.035 456 40 4 2660 3105 472400702 472401157 9.860000e-155 556.0
6 TraesCS5B01G402300 chr5D 74.895 474 107 8 1569 2036 519056342 519055875 4.120000e-49 206.0
7 TraesCS5B01G402300 chr5A 86.743 1139 81 31 1 1096 591672060 591673171 0.000000e+00 1203.0
8 TraesCS5B01G402300 chr5A 86.449 1070 87 22 1113 2153 591673240 591674280 0.000000e+00 1120.0
9 TraesCS5B01G402300 chr5A 74.668 1054 181 48 1140 2165 591976596 591977591 3.810000e-104 388.0
10 TraesCS5B01G402300 chr5A 76.757 185 33 6 2478 2660 632364323 632364499 9.300000e-16 95.3
11 TraesCS5B01G402300 chr2B 76.471 561 108 19 1566 2110 248690839 248691391 1.850000e-72 283.0
12 TraesCS5B01G402300 chr2B 83.824 136 15 3 2995 3123 76017128 76016993 4.260000e-24 122.0
13 TraesCS5B01G402300 chr2B 82.692 104 17 1 2496 2598 2080970 2081073 1.200000e-14 91.6
14 TraesCS5B01G402300 chr4D 75.868 576 113 23 1569 2134 489751225 489751784 1.440000e-68 270.0
15 TraesCS5B01G402300 chr4D 82.308 130 16 6 2521 2646 471425806 471425680 4.290000e-19 106.0
16 TraesCS5B01G402300 chr4B 75.350 572 123 17 1569 2134 628709645 628710204 3.110000e-65 259.0
17 TraesCS5B01G402300 chr4B 83.206 131 19 3 2489 2618 10586190 10586318 1.980000e-22 117.0
18 TraesCS5B01G402300 chr6A 74.633 477 102 15 1573 2038 594958890 594959358 3.200000e-45 193.0
19 TraesCS5B01G402300 chr6D 74.160 476 106 13 1573 2038 448810352 448810820 6.940000e-42 182.0
20 TraesCS5B01G402300 chr6D 80.952 126 23 1 2521 2646 429826943 429826819 7.190000e-17 99.0
21 TraesCS5B01G402300 chr6B 76.812 345 65 11 1573 1908 680725407 680725745 2.490000e-41 180.0
22 TraesCS5B01G402300 chr6B 85.496 131 16 2 2995 3123 22912089 22911960 1.970000e-27 134.0
23 TraesCS5B01G402300 chr6B 77.692 130 27 2 2518 2646 717633396 717633524 9.360000e-11 78.7
24 TraesCS5B01G402300 chr1A 85.000 140 18 2 2995 3131 440032891 440032752 4.230000e-29 139.0
25 TraesCS5B01G402300 chr3D 86.239 109 14 1 2490 2598 588831574 588831681 1.980000e-22 117.0
26 TraesCS5B01G402300 chr2A 91.566 83 7 0 3036 3118 67101219 67101301 7.130000e-22 115.0
27 TraesCS5B01G402300 chr7B 85.849 106 13 2 3018 3122 619133365 619133261 9.230000e-21 111.0
28 TraesCS5B01G402300 chr3B 78.613 173 32 3 2489 2660 787440580 787440748 3.320000e-20 110.0
29 TraesCS5B01G402300 chr3A 81.679 131 20 3 2995 3123 743803320 743803192 4.290000e-19 106.0
30 TraesCS5B01G402300 chr7A 82.727 110 15 2 3018 3123 617429667 617429776 9.300000e-16 95.3
31 TraesCS5B01G402300 chr4A 82.727 110 15 3 3018 3123 374450421 374450312 9.300000e-16 95.3


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 TraesCS5B01G402300 chr5B 578813982 578817129 3147 False 5814.0 5814 100.000 1 3148 1 chr5B.!!$F1 3147
1 TraesCS5B01G402300 chr5B 579003111 579004113 1002 False 1469.0 1469 93.327 1138 2126 1 chr5B.!!$F2 988
2 TraesCS5B01G402300 chr5D 472397944 472401157 3213 False 1811.0 3066 88.364 2 3105 2 chr5D.!!$F1 3103
3 TraesCS5B01G402300 chr5A 591672060 591674280 2220 False 1161.5 1203 86.596 1 2153 2 chr5A.!!$F3 2152
4 TraesCS5B01G402300 chr5A 591976596 591977591 995 False 388.0 388 74.668 1140 2165 1 chr5A.!!$F1 1025
5 TraesCS5B01G402300 chr2B 248690839 248691391 552 False 283.0 283 76.471 1566 2110 1 chr2B.!!$F2 544
6 TraesCS5B01G402300 chr4D 489751225 489751784 559 False 270.0 270 75.868 1569 2134 1 chr4D.!!$F1 565
7 TraesCS5B01G402300 chr4B 628709645 628710204 559 False 259.0 259 75.350 1569 2134 1 chr4B.!!$F2 565

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
665 725 0.180171 TGGGGAGCCATACATCGTTG 59.82 55.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2579 2781 0.268869 TCCCTATGAGCACCTCCCAT 59.731 55.0 0.0 0.0 0.0 4.0 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
30 31 2.561373 GCTTTCTCCGCCAAACCG 59.439 61.111 0.00 0.00 0.00 4.44
42 43 1.947456 GCCAAACCGACTTCAGTTTCT 59.053 47.619 0.00 0.00 34.02 2.52
56 57 3.627577 TCAGTTTCTTCAGTGAACCTTGC 59.372 43.478 0.08 0.00 0.00 4.01
76 77 2.616510 GCCTGCTCCTTTTCTTCAGCTA 60.617 50.000 0.00 0.00 32.76 3.32
83 84 4.256920 TCCTTTTCTTCAGCTACAGATGC 58.743 43.478 0.00 0.00 0.00 3.91
174 178 1.067495 GTGAGACGGACCTCTTCCTTG 60.067 57.143 0.00 0.00 43.25 3.61
177 181 1.203075 AGACGGACCTCTTCCTTGTCT 60.203 52.381 0.00 0.00 43.25 3.41
181 185 0.390472 GACCTCTTCCTTGTCTGCCG 60.390 60.000 0.00 0.00 0.00 5.69
224 252 2.442272 AGCCCCGTGTAGAGCGAT 60.442 61.111 0.00 0.00 0.00 4.58
253 281 2.801113 TTTTGCAGCATCGAAGGCGC 62.801 55.000 0.00 0.00 37.46 6.53
256 284 3.570638 CAGCATCGAAGGCGCCTG 61.571 66.667 33.60 19.62 37.46 4.85
282 310 1.982073 GCGCTGAAGGAAATCGTGGG 61.982 60.000 0.00 0.00 0.00 4.61
368 396 0.936600 TCGTCATCGCGAACCGTATA 59.063 50.000 15.24 0.00 37.99 1.47
369 397 1.040232 CGTCATCGCGAACCGTATAC 58.960 55.000 15.24 2.89 38.35 1.47
393 426 4.680237 TTGTGGGACGGAGCTGCG 62.680 66.667 26.95 26.95 0.00 5.18
436 469 4.795268 ACTATATCTCCATTACACGCACG 58.205 43.478 0.00 0.00 0.00 5.34
452 485 2.741985 CGCTCCCACGTCAATGCA 60.742 61.111 0.00 0.00 0.00 3.96
466 499 2.343475 AATGCAGCCCCGGTCTATGG 62.343 60.000 0.00 0.00 0.00 2.74
489 522 6.778069 TGGAAACCACAGTGGAAAATATTACA 59.222 34.615 27.39 13.54 40.96 2.41
507 549 6.737254 ATTACAAGTAACATTTCCGTCAGG 57.263 37.500 0.00 0.00 39.46 3.86
517 559 1.984570 TCCGTCAGGAAGGAGCCAG 60.985 63.158 0.00 0.00 45.12 4.85
645 705 7.358931 CGCGTGTCTTTTGTATTTAAGAGAAGA 60.359 37.037 0.00 0.00 31.45 2.87
646 706 8.443937 GCGTGTCTTTTGTATTTAAGAGAAGAT 58.556 33.333 0.00 0.00 31.45 2.40
647 707 9.746711 CGTGTCTTTTGTATTTAAGAGAAGATG 57.253 33.333 0.00 0.00 31.45 2.90
665 725 0.180171 TGGGGAGCCATACATCGTTG 59.820 55.000 0.00 0.00 0.00 4.10
668 728 2.480845 GGGAGCCATACATCGTTGTAC 58.519 52.381 8.45 0.00 41.02 2.90
669 729 2.480845 GGAGCCATACATCGTTGTACC 58.519 52.381 8.45 2.10 41.02 3.34
693 756 5.300752 CACTCCACTTGGCTAATATGGTAG 58.699 45.833 11.53 10.20 34.44 3.18
694 757 4.969359 ACTCCACTTGGCTAATATGGTAGT 59.031 41.667 11.53 10.65 34.44 2.73
695 758 6.041637 CACTCCACTTGGCTAATATGGTAGTA 59.958 42.308 11.53 0.00 34.44 1.82
696 759 6.267928 ACTCCACTTGGCTAATATGGTAGTAG 59.732 42.308 11.53 5.92 34.44 2.57
697 760 6.141083 TCCACTTGGCTAATATGGTAGTAGT 58.859 40.000 11.53 0.00 34.44 2.73
698 761 7.299896 TCCACTTGGCTAATATGGTAGTAGTA 58.700 38.462 11.53 0.00 34.44 1.82
821 885 5.968387 AATAACGAGTAGATTTTCGGCAG 57.032 39.130 0.00 0.00 40.93 4.85
832 896 4.631813 AGATTTTCGGCAGCTACTTGTAAG 59.368 41.667 0.00 0.00 0.00 2.34
871 936 2.111756 GTTTTCACAGCAACTTCAGCG 58.888 47.619 0.00 0.00 37.01 5.18
993 1063 2.096713 GGTCGATCAAAGCGCATCATAC 60.097 50.000 11.47 4.90 0.00 2.39
1004 1074 1.000274 CGCATCATACTGACCGATGGA 60.000 52.381 0.00 0.00 37.58 3.41
1101 1190 3.074412 CGTTATATGATCCAGCCAACCC 58.926 50.000 0.00 0.00 0.00 4.11
1193 1345 1.973281 CGCCTGCATGGTCAAAGGT 60.973 57.895 0.00 0.00 38.35 3.50
1530 1700 4.164664 CGTACGCGGCGGTAGACA 62.165 66.667 27.37 1.19 0.00 3.41
2092 2293 0.240945 CAGTGGTGGAAACCGAATGC 59.759 55.000 0.00 0.00 0.00 3.56
2193 2395 1.202336 GCAAGCTGTCAAGTGCAGTTT 60.202 47.619 3.38 0.00 37.78 2.66
2278 2480 9.601217 ACCAATTTAGCTATAGTGAGTTGTAAG 57.399 33.333 12.37 0.00 0.00 2.34
2279 2481 9.601217 CCAATTTAGCTATAGTGAGTTGTAAGT 57.399 33.333 12.37 0.00 0.00 2.24
2286 2488 7.931948 AGCTATAGTGAGTTGTAAGTTTTGTGT 59.068 33.333 0.84 0.00 0.00 3.72
2304 2506 6.841443 TTGTGTTAGAACAATTGCAAATGG 57.159 33.333 18.39 6.63 41.21 3.16
2385 2587 2.299582 CCACTGGATGCATTGGTTTGAA 59.700 45.455 14.54 0.00 0.00 2.69
2392 2594 2.037901 TGCATTGGTTTGAAAGAGGCA 58.962 42.857 0.00 0.00 0.00 4.75
2394 2596 2.680577 CATTGGTTTGAAAGAGGCAGC 58.319 47.619 0.00 0.00 0.00 5.25
2399 2601 2.063015 TTTGAAAGAGGCAGCGGGGA 62.063 55.000 0.00 0.00 0.00 4.81
2402 2604 2.543067 GAAAGAGGCAGCGGGGATGT 62.543 60.000 0.00 0.00 0.00 3.06
2441 2643 5.334260 CCATCCAACAATTGCAAATGACAAC 60.334 40.000 21.10 0.00 0.00 3.32
2451 2653 2.482864 CAAATGACAACCAACAAGGGC 58.517 47.619 0.00 0.00 43.89 5.19
2456 2658 4.531426 AACCAACAAGGGCGGCCA 62.531 61.111 31.59 0.00 43.89 5.36
2457 2659 3.826265 AACCAACAAGGGCGGCCAT 62.826 57.895 31.59 17.03 43.89 4.40
2477 2679 6.918067 CCATACATGGTTAGAGGAGACATA 57.082 41.667 0.00 0.00 43.05 2.29
2513 2715 3.119459 TGCGTTGAGTTAGAGGAGACATC 60.119 47.826 0.00 0.00 0.00 3.06
2535 2737 3.381908 CCTTGTAGACTATGAAGGCGTCT 59.618 47.826 9.28 0.00 40.74 4.18
2579 2781 5.037383 AGATGATGTACCGACTCAGTCTA 57.963 43.478 2.61 0.00 0.00 2.59
2581 2783 5.471797 AGATGATGTACCGACTCAGTCTATG 59.528 44.000 2.61 0.00 0.00 2.23
2586 2788 1.323412 CCGACTCAGTCTATGGGAGG 58.677 60.000 2.61 0.00 31.77 4.30
2594 2796 3.117131 TCAGTCTATGGGAGGTGCTCATA 60.117 47.826 0.00 0.00 38.96 2.15
2599 2801 0.691078 TGGGAGGTGCTCATAGGGAC 60.691 60.000 0.00 0.00 31.08 4.46
2600 2802 0.399233 GGGAGGTGCTCATAGGGACT 60.399 60.000 0.00 0.00 35.49 3.85
2611 2813 2.019249 CATAGGGACTTGGTGTGCATG 58.981 52.381 0.00 0.00 41.75 4.06
2630 2832 1.804151 TGCGTGCTTTTGTAGGATGAC 59.196 47.619 0.00 0.00 33.32 3.06
2639 2841 5.643777 GCTTTTGTAGGATGACTGTATGTGT 59.356 40.000 0.00 0.00 0.00 3.72
2640 2842 6.402550 GCTTTTGTAGGATGACTGTATGTGTG 60.403 42.308 0.00 0.00 0.00 3.82
2655 2857 3.600717 TGTGTGTTTGTTGTATGAGCG 57.399 42.857 0.00 0.00 0.00 5.03
2658 2860 2.546368 TGTGTTTGTTGTATGAGCGTCC 59.454 45.455 0.00 0.00 0.00 4.79
2685 2965 1.067495 GTGAAGTAGGCGTCAGCTTCT 60.067 52.381 19.28 0.00 44.37 2.85
2686 2966 1.202582 TGAAGTAGGCGTCAGCTTCTC 59.797 52.381 19.28 1.76 44.37 2.87
2719 2999 7.549488 ACTTCTCCAATCCTAAAATTAGTGTCG 59.451 37.037 0.00 0.00 0.00 4.35
2728 3008 6.876789 TCCTAAAATTAGTGTCGCTGATTTCA 59.123 34.615 14.45 2.26 40.92 2.69
2757 3037 3.924114 TGCTTATTTTCGGATGGAGGA 57.076 42.857 0.00 0.00 0.00 3.71
2779 3059 8.888579 AGGAAGTATTATGTACTTTGAATCCG 57.111 34.615 6.75 0.00 37.83 4.18
2835 3115 3.068024 ACTGTTTGGCATACAACAACTGG 59.932 43.478 11.83 1.66 39.19 4.00
2871 3151 8.762645 ACTTTATAGAGATTTGACTGGATGTGA 58.237 33.333 0.00 0.00 0.00 3.58
2889 3169 7.043565 GGATGTGAATGCAAAACAATCCTTAT 58.956 34.615 11.74 0.00 0.00 1.73
2968 3248 1.969064 AAACAATAGCGCCCGTGCA 60.969 52.632 2.29 0.00 37.32 4.57
2970 3250 1.714899 AACAATAGCGCCCGTGCATC 61.715 55.000 2.29 0.00 37.32 3.91
3014 3301 6.224584 TGAACATGATCACATTTTGTTGCAT 58.775 32.000 14.67 0.00 34.15 3.96
3016 3303 6.032956 ACATGATCACATTTTGTTGCATCT 57.967 33.333 0.00 0.00 34.15 2.90
3026 3315 8.618677 CACATTTTGTTGCATCTGAGATATACT 58.381 33.333 0.00 0.00 0.00 2.12
3085 3374 9.465985 TTTTAAACTCCGGAACATATTTGAAAC 57.534 29.630 5.23 0.00 0.00 2.78
3094 3383 7.035004 CGGAACATATTTGAAACCATGAACAT 58.965 34.615 7.97 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.119694 AGGTTCACTGAAGAAACTGAAGTC 58.880 41.667 4.80 0.00 43.59 3.01
42 43 0.183492 AGCAGGCAAGGTTCACTGAA 59.817 50.000 0.00 0.00 32.86 3.02
56 57 2.197283 AGCTGAAGAAAAGGAGCAGG 57.803 50.000 0.00 0.00 33.67 4.85
76 77 2.285969 AGGGGCTGGAGCATCTGT 60.286 61.111 0.20 0.00 44.36 3.41
181 185 4.681978 ACCTCTTGGCGCACGTCC 62.682 66.667 10.83 0.00 36.63 4.79
224 252 3.222855 CTGCAAAACCCGGCACCA 61.223 61.111 0.00 0.00 35.86 4.17
266 294 2.482326 GCCCCACGATTTCCTTCAG 58.518 57.895 0.00 0.00 0.00 3.02
329 357 1.228003 TTCGTCGTTGCCCCATGTT 60.228 52.632 0.00 0.00 0.00 2.71
333 361 2.029964 GAGTTCGTCGTTGCCCCA 59.970 61.111 0.00 0.00 0.00 4.96
368 396 0.834612 TCCGTCCCACAACTCAAAGT 59.165 50.000 0.00 0.00 0.00 2.66
369 397 1.512926 CTCCGTCCCACAACTCAAAG 58.487 55.000 0.00 0.00 0.00 2.77
393 426 2.158841 TCACTGAACTATTTTTCGCCGC 59.841 45.455 0.00 0.00 0.00 6.53
423 456 2.461110 GGGAGCGTGCGTGTAATGG 61.461 63.158 0.00 0.00 0.00 3.16
436 469 3.044059 GCTGCATTGACGTGGGAGC 62.044 63.158 0.00 0.00 38.78 4.70
452 485 1.632965 GGTTTCCATAGACCGGGGCT 61.633 60.000 7.95 7.95 0.00 5.19
466 499 8.357402 ACTTGTAATATTTTCCACTGTGGTTTC 58.643 33.333 25.15 10.25 39.03 2.78
507 549 0.813821 GGCAAATGACTGGCTCCTTC 59.186 55.000 0.00 0.00 38.77 3.46
517 559 0.775861 GTCGCGTTTTGGCAAATGAC 59.224 50.000 14.29 14.62 31.28 3.06
598 653 2.223805 GGCTTGTGTGTTTCTTCAAGGG 60.224 50.000 0.00 0.00 38.06 3.95
599 654 2.541588 CGGCTTGTGTGTTTCTTCAAGG 60.542 50.000 0.00 0.00 38.06 3.61
600 655 2.719798 CGGCTTGTGTGTTTCTTCAAG 58.280 47.619 0.00 0.00 39.83 3.02
601 656 1.202245 GCGGCTTGTGTGTTTCTTCAA 60.202 47.619 0.00 0.00 0.00 2.69
602 657 0.380378 GCGGCTTGTGTGTTTCTTCA 59.620 50.000 0.00 0.00 0.00 3.02
603 658 0.657368 CGCGGCTTGTGTGTTTCTTC 60.657 55.000 0.00 0.00 0.00 2.87
604 659 1.355210 CGCGGCTTGTGTGTTTCTT 59.645 52.632 0.00 0.00 0.00 2.52
646 706 2.521978 ACAACGATGTATGGCTCCCCA 61.522 52.381 0.00 0.00 38.24 4.96
647 707 0.180406 ACAACGATGTATGGCTCCCC 59.820 55.000 0.00 0.00 38.24 4.81
648 708 2.480845 GTACAACGATGTATGGCTCCC 58.519 52.381 8.88 0.00 43.60 4.30
665 725 1.272807 TAGCCAAGTGGAGTGGGTAC 58.727 55.000 0.18 0.00 44.94 3.34
668 728 3.480470 CATATTAGCCAAGTGGAGTGGG 58.520 50.000 0.18 0.00 36.58 4.61
669 729 3.117888 ACCATATTAGCCAAGTGGAGTGG 60.118 47.826 0.18 2.17 39.33 4.00
693 756 4.116961 TGCACGCAGAACCATAATACTAC 58.883 43.478 0.00 0.00 0.00 2.73
694 757 4.394439 TGCACGCAGAACCATAATACTA 57.606 40.909 0.00 0.00 0.00 1.82
695 758 3.260475 TGCACGCAGAACCATAATACT 57.740 42.857 0.00 0.00 0.00 2.12
696 759 3.621268 TCTTGCACGCAGAACCATAATAC 59.379 43.478 0.00 0.00 0.00 1.89
697 760 3.867857 TCTTGCACGCAGAACCATAATA 58.132 40.909 0.00 0.00 0.00 0.98
698 761 2.679837 CTCTTGCACGCAGAACCATAAT 59.320 45.455 0.00 0.00 0.00 1.28
821 885 9.719279 CTTATATATACTCCGCTTACAAGTAGC 57.281 37.037 0.00 0.00 0.00 3.58
832 896 8.221766 GTGAAAACTTGCTTATATATACTCCGC 58.778 37.037 0.00 0.00 0.00 5.54
871 936 4.164294 CTGAGCTTTACTGCTTTGATTGC 58.836 43.478 0.00 0.00 44.17 3.56
1004 1074 1.005394 ACGTTGAAGCGGTCCGAAT 60.005 52.632 17.49 1.41 35.98 3.34
1008 1078 1.445582 ATCGACGTTGAAGCGGTCC 60.446 57.895 10.11 0.00 35.98 4.46
1101 1190 5.714047 TCATCAGGCTATGCTACTAAATCG 58.286 41.667 0.00 0.00 0.00 3.34
1170 1322 3.188786 GACCATGCAGGCGACGAC 61.189 66.667 0.00 0.00 43.14 4.34
1193 1345 1.890894 GCTCTCCAGGACGTAAGCA 59.109 57.895 0.00 0.00 45.62 3.91
1516 1686 2.704342 AAGTTTGTCTACCGCCGCGT 62.704 55.000 12.58 2.59 0.00 6.01
1526 1696 3.627395 TCGCCATCCATAAGTTTGTCT 57.373 42.857 0.00 0.00 0.00 3.41
1619 1795 1.402896 GCCTCTCCATCATGTCCCGA 61.403 60.000 0.00 0.00 0.00 5.14
1795 1974 0.743701 CAGCTTCTCCATGCGCTTCT 60.744 55.000 9.73 0.00 0.00 2.85
1922 2113 1.412079 TGCTTGCAACACAGGGAAAT 58.588 45.000 0.00 0.00 0.00 2.17
2015 2208 2.202919 CACAGCATCGCCGATGGA 60.203 61.111 26.71 0.00 40.10 3.41
2193 2395 7.655236 TTTACAAGAAAACGTTCCGATGATA 57.345 32.000 0.00 0.00 33.92 2.15
2249 2451 7.985752 ACAACTCACTATAGCTAAATTGGTACC 59.014 37.037 4.43 4.43 0.00 3.34
2278 2480 7.639461 CCATTTGCAATTGTTCTAACACAAAAC 59.361 33.333 17.53 0.00 40.07 2.43
2279 2481 7.678218 GCCATTTGCAATTGTTCTAACACAAAA 60.678 33.333 17.53 3.35 38.92 2.44
2304 2506 9.229784 CATCATAATAAAGTGACTGTTGATTGC 57.770 33.333 0.00 0.00 0.00 3.56
2375 2577 1.270550 CGCTGCCTCTTTCAAACCAAT 59.729 47.619 0.00 0.00 0.00 3.16
2385 2587 2.606587 AACATCCCCGCTGCCTCTT 61.607 57.895 0.00 0.00 0.00 2.85
2392 2594 1.335132 ATCGGTACAACATCCCCGCT 61.335 55.000 0.00 0.00 40.23 5.52
2394 2596 2.032680 AAATCGGTACAACATCCCCG 57.967 50.000 0.00 0.00 41.75 5.73
2399 2601 4.398044 GGATGGACAAAATCGGTACAACAT 59.602 41.667 0.00 0.00 31.74 2.71
2402 2604 4.022413 TGGATGGACAAAATCGGTACAA 57.978 40.909 0.00 0.00 31.74 2.41
2441 2643 2.044451 TATGGCCGCCCTTGTTGG 60.044 61.111 7.03 0.00 0.00 3.77
2456 2658 6.495181 CAGGTATGTCTCCTCTAACCATGTAT 59.505 42.308 0.00 0.00 32.37 2.29
2457 2659 5.833667 CAGGTATGTCTCCTCTAACCATGTA 59.166 44.000 0.00 0.00 32.37 2.29
2477 2679 0.531974 AACGCACATTGTCGACAGGT 60.532 50.000 19.11 17.56 0.00 4.00
2487 2689 3.258372 TCTCCTCTAACTCAACGCACATT 59.742 43.478 0.00 0.00 0.00 2.71
2513 2715 3.381908 AGACGCCTTCATAGTCTACAAGG 59.618 47.826 12.51 12.51 42.71 3.61
2515 2717 3.428999 GCAGACGCCTTCATAGTCTACAA 60.429 47.826 0.00 0.00 42.65 2.41
2579 2781 0.268869 TCCCTATGAGCACCTCCCAT 59.731 55.000 0.00 0.00 0.00 4.00
2581 2783 0.399233 AGTCCCTATGAGCACCTCCC 60.399 60.000 0.00 0.00 0.00 4.30
2586 2788 1.279271 ACACCAAGTCCCTATGAGCAC 59.721 52.381 0.00 0.00 0.00 4.40
2594 2796 1.604593 GCATGCACACCAAGTCCCT 60.605 57.895 14.21 0.00 0.00 4.20
2611 2813 2.076863 AGTCATCCTACAAAAGCACGC 58.923 47.619 0.00 0.00 0.00 5.34
2621 2823 5.932303 ACAAACACACATACAGTCATCCTAC 59.068 40.000 0.00 0.00 0.00 3.18
2630 2832 6.079763 GCTCATACAACAAACACACATACAG 58.920 40.000 0.00 0.00 0.00 2.74
2639 2841 1.795872 CGGACGCTCATACAACAAACA 59.204 47.619 0.00 0.00 0.00 2.83
2640 2842 1.127951 CCGGACGCTCATACAACAAAC 59.872 52.381 0.00 0.00 0.00 2.93
2666 2946 1.202582 GAGAAGCTGACGCCTACTTCA 59.797 52.381 10.33 0.00 40.77 3.02
2671 2951 1.676746 ATACGAGAAGCTGACGCCTA 58.323 50.000 7.23 0.00 36.60 3.93
2672 2952 1.676746 TATACGAGAAGCTGACGCCT 58.323 50.000 7.23 0.00 36.60 5.52
2728 3008 8.527810 TCCATCCGAAAATAAGCAACTTTTTAT 58.472 29.630 0.00 0.00 0.00 1.40
2731 3011 6.339587 TCCATCCGAAAATAAGCAACTTTT 57.660 33.333 0.00 0.00 0.00 2.27
2747 3027 6.591750 AGTACATAATACTTCCTCCATCCG 57.408 41.667 0.00 0.00 0.00 4.18
2814 3094 3.317711 TCCAGTTGTTGTATGCCAAACAG 59.682 43.478 0.00 0.00 34.07 3.16
2821 3101 8.893727 AGTTTATCTATTCCAGTTGTTGTATGC 58.106 33.333 0.00 0.00 0.00 3.14
2862 3142 4.628333 GGATTGTTTTGCATTCACATCCAG 59.372 41.667 8.98 0.00 31.13 3.86
2871 3151 9.956640 TGGAATTTATAAGGATTGTTTTGCATT 57.043 25.926 0.00 0.00 0.00 3.56
2946 3226 0.955905 ACGGGCGCTATTGTTTGTTT 59.044 45.000 7.64 0.00 0.00 2.83
2947 3227 0.239879 CACGGGCGCTATTGTTTGTT 59.760 50.000 7.64 0.00 0.00 2.83
2950 3230 1.312371 ATGCACGGGCGCTATTGTTT 61.312 50.000 4.58 0.00 45.35 2.83
2987 3267 6.366604 GCAACAAAATGTGATCATGTTCATGA 59.633 34.615 16.19 16.19 34.19 3.07
2988 3268 6.146347 TGCAACAAAATGTGATCATGTTCATG 59.854 34.615 9.61 6.46 34.19 3.07
2991 3271 6.588756 AGATGCAACAAAATGTGATCATGTTC 59.411 34.615 8.35 0.00 34.19 3.18
2992 3272 6.367695 CAGATGCAACAAAATGTGATCATGTT 59.632 34.615 0.00 1.88 34.19 2.71
2993 3273 5.867174 CAGATGCAACAAAATGTGATCATGT 59.133 36.000 0.00 0.00 34.19 3.21
3068 3357 5.574891 TCATGGTTTCAAATATGTTCCGG 57.425 39.130 0.00 0.00 0.00 5.14
3069 3358 6.385843 TGTTCATGGTTTCAAATATGTTCCG 58.614 36.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.