Multiple sequence alignment - TraesCS2D01G180900

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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 TraesCS2D01G180900 chr2D 100.000 3236 0 0 1 3236 125345950 125342715 0.000000e+00 5976.0
1 TraesCS2D01G180900 chr2D 77.946 331 52 18 1691 2012 37245727 37245409 1.530000e-43 187.0
2 TraesCS2D01G180900 chr2B 91.234 1791 101 32 1172 2954 178731949 178730207 0.000000e+00 2386.0
3 TraesCS2D01G180900 chr2B 82.463 536 77 9 434 957 583108266 583107736 1.370000e-123 453.0
4 TraesCS2D01G180900 chr2B 78.443 334 48 16 1691 2012 64863763 64864084 2.550000e-46 196.0
5 TraesCS2D01G180900 chr2A 94.461 1372 46 13 968 2334 131712460 131711114 0.000000e+00 2085.0
6 TraesCS2D01G180900 chr2A 86.976 906 73 22 2341 3236 131711003 131710133 0.000000e+00 977.0
7 TraesCS2D01G180900 chr2A 74.651 860 171 37 1219 2059 24003220 24002389 1.440000e-88 337.0
8 TraesCS2D01G180900 chr2A 80.147 272 49 4 1744 2011 679971485 679971755 7.080000e-47 198.0
9 TraesCS2D01G180900 chr2A 80.000 275 42 10 1746 2012 42027189 42027458 1.180000e-44 191.0
10 TraesCS2D01G180900 chr2A 83.962 106 15 2 3131 3235 718839856 718839960 2.050000e-17 100.0
11 TraesCS2D01G180900 chr7B 93.548 558 24 7 418 964 363231831 363232387 0.000000e+00 821.0
12 TraesCS2D01G180900 chr7B 97.381 420 9 1 1 420 363231374 363231791 0.000000e+00 713.0
13 TraesCS2D01G180900 chr3D 93.548 558 24 7 418 964 570538470 570537914 0.000000e+00 821.0
14 TraesCS2D01G180900 chr3D 92.832 558 28 7 418 964 478426410 478426966 0.000000e+00 798.0
15 TraesCS2D01G180900 chr3D 95.952 420 15 1 1 420 478425953 478426370 0.000000e+00 680.0
16 TraesCS2D01G180900 chr3D 95.952 420 15 1 1 420 570538927 570538510 0.000000e+00 680.0
17 TraesCS2D01G180900 chr3D 83.240 537 74 11 434 957 584682701 584682168 2.260000e-131 479.0
18 TraesCS2D01G180900 chr5D 91.039 558 38 7 418 964 564237719 564237163 0.000000e+00 743.0
19 TraesCS2D01G180900 chr5D 97.143 420 10 1 1 420 564238176 564237759 0.000000e+00 708.0
20 TraesCS2D01G180900 chr5D 95.952 420 14 2 1 420 399974009 399974425 0.000000e+00 678.0
21 TraesCS2D01G180900 chr7A 96.190 420 14 1 1 420 640368696 640368279 0.000000e+00 686.0
22 TraesCS2D01G180900 chr7A 90.952 420 36 1 1 420 418712570 418712153 6.060000e-157 564.0
23 TraesCS2D01G180900 chr7A 81.495 535 85 10 434 957 380509718 380509187 8.300000e-116 427.0
24 TraesCS2D01G180900 chr7A 75.121 824 161 32 1213 2019 46911803 46911007 2.390000e-91 346.0
25 TraesCS2D01G180900 chr7A 74.142 379 87 9 1205 1579 163916284 163915913 2.600000e-31 147.0
26 TraesCS2D01G180900 chr3B 95.000 420 17 3 1 420 664535688 664535273 0.000000e+00 656.0
27 TraesCS2D01G180900 chr6B 91.727 411 32 1 1 411 705858713 705859121 1.300000e-158 569.0
28 TraesCS2D01G180900 chr4D 82.276 536 78 11 434 957 297376489 297375959 6.370000e-122 448.0
29 TraesCS2D01G180900 chr6A 83.298 467 68 8 418 875 23217770 23218235 3.860000e-114 422.0
30 TraesCS2D01G180900 chr6A 82.075 106 18 1 3131 3235 455318981 455318876 4.450000e-14 89.8
31 TraesCS2D01G180900 chr1A 79.852 541 93 7 425 954 27317456 27317991 6.550000e-102 381.0
32 TraesCS2D01G180900 chr1A 77.152 639 122 20 1380 2009 11531069 11530446 1.850000e-92 350.0
33 TraesCS2D01G180900 chr7D 74.858 879 180 29 1205 2070 163011470 163010620 8.530000e-96 361.0


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 TraesCS2D01G180900 chr2D 125342715 125345950 3235 True 5976.0 5976 100.0000 1 3236 1 chr2D.!!$R2 3235
1 TraesCS2D01G180900 chr2B 178730207 178731949 1742 True 2386.0 2386 91.2340 1172 2954 1 chr2B.!!$R1 1782
2 TraesCS2D01G180900 chr2B 583107736 583108266 530 True 453.0 453 82.4630 434 957 1 chr2B.!!$R2 523
3 TraesCS2D01G180900 chr2A 131710133 131712460 2327 True 1531.0 2085 90.7185 968 3236 2 chr2A.!!$R2 2268
4 TraesCS2D01G180900 chr2A 24002389 24003220 831 True 337.0 337 74.6510 1219 2059 1 chr2A.!!$R1 840
5 TraesCS2D01G180900 chr7B 363231374 363232387 1013 False 767.0 821 95.4645 1 964 2 chr7B.!!$F1 963
6 TraesCS2D01G180900 chr3D 570537914 570538927 1013 True 750.5 821 94.7500 1 964 2 chr3D.!!$R2 963
7 TraesCS2D01G180900 chr3D 478425953 478426966 1013 False 739.0 798 94.3920 1 964 2 chr3D.!!$F1 963
8 TraesCS2D01G180900 chr3D 584682168 584682701 533 True 479.0 479 83.2400 434 957 1 chr3D.!!$R1 523
9 TraesCS2D01G180900 chr5D 564237163 564238176 1013 True 725.5 743 94.0910 1 964 2 chr5D.!!$R1 963
10 TraesCS2D01G180900 chr7A 380509187 380509718 531 True 427.0 427 81.4950 434 957 1 chr7A.!!$R3 523
11 TraesCS2D01G180900 chr7A 46911007 46911803 796 True 346.0 346 75.1210 1213 2019 1 chr7A.!!$R1 806
12 TraesCS2D01G180900 chr4D 297375959 297376489 530 True 448.0 448 82.2760 434 957 1 chr4D.!!$R1 523
13 TraesCS2D01G180900 chr1A 27317456 27317991 535 False 381.0 381 79.8520 425 954 1 chr1A.!!$F1 529
14 TraesCS2D01G180900 chr1A 11530446 11531069 623 True 350.0 350 77.1520 1380 2009 1 chr1A.!!$R1 629
15 TraesCS2D01G180900 chr7D 163010620 163011470 850 True 361.0 361 74.8580 1205 2070 1 chr7D.!!$R1 865


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
420 421 0.259356 AAACTCGGGTTGGGTTGGAA 59.741 50.0 0.00 0.0 35.63 3.53 F
1189 1247 0.321475 TCACGCATGCAGATTGTCCA 60.321 50.0 19.57 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2282 1.228367 ATCTCCAATGGCCGCCATC 60.228 57.895 25.27 0.0 44.4 3.51 R
3123 3322 0.240945 CTCCGAAACTTGGCGCAATT 59.759 50.000 10.83 0.0 0.0 2.32 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
57 58 5.296151 AGCGGATTTATTCTCATCTTGGA 57.704 39.130 0.00 0.00 0.00 3.53
75 76 4.609018 CAGCCCCATAGACCGCGG 62.609 72.222 26.86 26.86 0.00 6.46
332 333 3.860717 TGCTCTCGCACACAATCG 58.139 55.556 0.00 0.00 42.25 3.34
338 339 4.483683 CGCACACAATCGCCGACG 62.484 66.667 0.00 0.00 42.01 5.12
339 340 3.411351 GCACACAATCGCCGACGT 61.411 61.111 0.00 0.00 41.18 4.34
342 343 1.593209 ACACAATCGCCGACGTGTT 60.593 52.632 15.99 3.87 39.49 3.32
420 421 0.259356 AAACTCGGGTTGGGTTGGAA 59.741 50.000 0.00 0.00 35.63 3.53
421 422 0.481128 AACTCGGGTTGGGTTGGAAT 59.519 50.000 0.00 0.00 33.96 3.01
422 423 1.364269 ACTCGGGTTGGGTTGGAATA 58.636 50.000 0.00 0.00 0.00 1.75
428 471 3.380320 CGGGTTGGGTTGGAATAAGATTC 59.620 47.826 0.00 0.00 0.00 2.52
535 578 2.283529 TGGGAGAGAAGCGGACCAC 61.284 63.158 0.00 0.00 0.00 4.16
536 579 1.985116 GGGAGAGAAGCGGACCACT 60.985 63.158 0.00 0.00 0.00 4.00
578 624 0.981183 TCAGTTTCAGGGTACGGCAT 59.019 50.000 0.00 0.00 0.00 4.40
764 813 2.756760 GTGTACCTATCGGTGAGTCCAA 59.243 50.000 0.00 0.00 45.18 3.53
770 819 4.049186 CCTATCGGTGAGTCCAAATTACG 58.951 47.826 0.00 0.00 35.57 3.18
821 870 1.473278 GAGAATTCTCGTCCGTGGTCT 59.527 52.381 19.31 0.00 32.78 3.85
825 874 0.679002 TTCTCGTCCGTGGTCTAGGG 60.679 60.000 0.00 0.00 35.61 3.53
966 1020 2.364579 CAGGCCCCGGTGGTAGTA 60.365 66.667 0.00 0.00 36.04 1.82
995 1049 1.136891 GGGCTTGTGCACCAATAATCC 59.863 52.381 15.69 6.68 41.91 3.01
1041 1095 5.074430 ACGAAACAAACGTGTCACTTATC 57.926 39.130 0.65 0.00 42.37 1.75
1066 1120 4.616381 TCAAAATGTTGCAATCGACAATCG 59.384 37.500 0.59 0.00 39.85 3.34
1136 1193 9.214953 GAACAGCATCTTTATTCTAAATCAACG 57.785 33.333 0.00 0.00 0.00 4.10
1138 1195 7.134815 CAGCATCTTTATTCTAAATCAACGGG 58.865 38.462 0.00 0.00 0.00 5.28
1139 1196 5.915196 GCATCTTTATTCTAAATCAACGGGC 59.085 40.000 0.00 0.00 0.00 6.13
1140 1197 6.459573 GCATCTTTATTCTAAATCAACGGGCA 60.460 38.462 0.00 0.00 0.00 5.36
1189 1247 0.321475 TCACGCATGCAGATTGTCCA 60.321 50.000 19.57 0.00 0.00 4.02
1501 1565 2.746359 GTGTCCAGCAGCAGGTCT 59.254 61.111 3.35 0.00 0.00 3.85
1528 1592 0.471780 TGAGGAAGAGCACCCTGTCA 60.472 55.000 0.00 0.00 31.84 3.58
1711 1775 1.198408 CTGCAGACGTACACGACCTTA 59.802 52.381 8.42 0.00 43.02 2.69
1722 1786 2.508663 GACCTTACAGCCGGCGAC 60.509 66.667 23.20 0.00 0.00 5.19
1986 2068 2.278013 GAGGATCACGTCGTCGGC 60.278 66.667 7.05 0.00 41.85 5.54
2134 2216 1.377856 GAACTCCTCCTTGGCTGGC 60.378 63.158 0.00 0.00 35.26 4.85
2188 2270 2.046217 GGAACAGGGCCGGAAGTC 60.046 66.667 11.67 4.52 0.00 3.01
2189 2271 2.046217 GAACAGGGCCGGAAGTCC 60.046 66.667 11.67 0.00 0.00 3.85
2190 2272 2.852075 AACAGGGCCGGAAGTCCA 60.852 61.111 11.67 0.00 35.14 4.02
2191 2273 3.192103 AACAGGGCCGGAAGTCCAC 62.192 63.158 11.67 0.00 35.14 4.02
2222 2304 1.228367 GCGGCCATTGGAGATGGAT 60.228 57.895 6.95 0.00 41.64 3.41
2223 2305 1.521450 GCGGCCATTGGAGATGGATG 61.521 60.000 6.95 1.67 41.64 3.51
2224 2306 0.892358 CGGCCATTGGAGATGGATGG 60.892 60.000 6.95 0.00 41.64 3.51
2225 2307 0.479815 GGCCATTGGAGATGGATGGA 59.520 55.000 6.95 0.00 42.31 3.41
2315 2398 0.321122 CAGGCTGACACTTCCACTCC 60.321 60.000 9.42 0.00 0.00 3.85
2323 2406 0.771127 CACTTCCACTCCTTTGGGGA 59.229 55.000 0.00 0.00 42.77 4.81
2334 2417 7.237679 TCCACTCCTTTGGGGAAGAATATATAG 59.762 40.741 0.00 0.00 44.58 1.31
2336 2419 9.101325 CACTCCTTTGGGGAAGAATATATAGTA 57.899 37.037 0.00 0.00 44.58 1.82
2337 2420 9.327731 ACTCCTTTGGGGAAGAATATATAGTAG 57.672 37.037 0.00 0.00 44.58 2.57
2338 2421 9.327731 CTCCTTTGGGGAAGAATATATAGTAGT 57.672 37.037 0.00 0.00 44.58 2.73
2383 2570 3.549827 CGCATGTGCCTTTTGTTCACTTA 60.550 43.478 0.00 0.00 37.91 2.24
2418 2605 7.925483 ACGATGGATCAAATTTTGACTTTGAAA 59.075 29.630 13.80 0.00 43.61 2.69
2480 2670 0.257039 AGACCCCAACCTCATCATGC 59.743 55.000 0.00 0.00 0.00 4.06
2483 2673 1.077663 ACCCCAACCTCATCATGCTTT 59.922 47.619 0.00 0.00 0.00 3.51
2484 2674 2.311542 ACCCCAACCTCATCATGCTTTA 59.688 45.455 0.00 0.00 0.00 1.85
2485 2675 2.954318 CCCCAACCTCATCATGCTTTAG 59.046 50.000 0.00 0.00 0.00 1.85
2486 2676 3.624777 CCCAACCTCATCATGCTTTAGT 58.375 45.455 0.00 0.00 0.00 2.24
2487 2677 4.019174 CCCAACCTCATCATGCTTTAGTT 58.981 43.478 0.00 0.00 0.00 2.24
2488 2678 4.463891 CCCAACCTCATCATGCTTTAGTTT 59.536 41.667 0.00 0.00 0.00 2.66
2489 2679 5.047092 CCCAACCTCATCATGCTTTAGTTTT 60.047 40.000 0.00 0.00 0.00 2.43
2490 2680 5.865552 CCAACCTCATCATGCTTTAGTTTTG 59.134 40.000 0.00 0.00 0.00 2.44
2496 2686 7.116805 CCTCATCATGCTTTAGTTTTGTTTTCC 59.883 37.037 0.00 0.00 0.00 3.13
2501 2691 7.504238 TCATGCTTTAGTTTTGTTTTCCTCCTA 59.496 33.333 0.00 0.00 0.00 2.94
2504 2694 8.194769 TGCTTTAGTTTTGTTTTCCTCCTAAAG 58.805 33.333 0.00 0.00 40.98 1.85
2511 2701 5.656549 TGTTTTCCTCCTAAAGAAAGGGA 57.343 39.130 0.00 0.00 37.24 4.20
2512 2702 6.214177 TGTTTTCCTCCTAAAGAAAGGGAT 57.786 37.500 0.00 0.00 37.24 3.85
2513 2703 6.620429 TGTTTTCCTCCTAAAGAAAGGGATT 58.380 36.000 0.00 0.00 37.24 3.01
2514 2704 7.761608 TGTTTTCCTCCTAAAGAAAGGGATTA 58.238 34.615 0.00 0.00 37.24 1.75
2515 2705 8.398743 TGTTTTCCTCCTAAAGAAAGGGATTAT 58.601 33.333 0.00 0.00 37.24 1.28
2517 2707 5.941788 TCCTCCTAAAGAAAGGGATTATGC 58.058 41.667 0.00 0.00 37.24 3.14
2518 2708 5.431731 TCCTCCTAAAGAAAGGGATTATGCA 59.568 40.000 0.00 0.00 37.24 3.96
2519 2709 6.103205 TCCTCCTAAAGAAAGGGATTATGCAT 59.897 38.462 3.79 3.79 37.24 3.96
2520 2710 7.294720 TCCTCCTAAAGAAAGGGATTATGCATA 59.705 37.037 1.16 1.16 37.24 3.14
2521 2711 7.609532 CCTCCTAAAGAAAGGGATTATGCATAG 59.390 40.741 6.50 0.00 37.24 2.23
2522 2712 8.045720 TCCTAAAGAAAGGGATTATGCATAGT 57.954 34.615 6.50 3.64 37.24 2.12
2523 2713 8.502738 TCCTAAAGAAAGGGATTATGCATAGTT 58.497 33.333 6.50 0.00 37.24 2.24
2524 2714 8.571336 CCTAAAGAAAGGGATTATGCATAGTTG 58.429 37.037 6.50 0.00 32.55 3.16
2542 2732 7.986562 CATAGTTGCAGTCTTGTAGTACTAGA 58.013 38.462 9.97 9.97 0.00 2.43
2544 2734 7.469537 AGTTGCAGTCTTGTAGTACTAGAAT 57.530 36.000 14.79 11.67 32.19 2.40
2546 2736 8.679100 AGTTGCAGTCTTGTAGTACTAGAATAG 58.321 37.037 14.79 10.22 46.50 1.73
2615 2805 8.015185 AGGGTTATAAATACGAGTTTAGCTCA 57.985 34.615 0.00 0.00 44.33 4.26
2654 2845 9.267084 GTTAGGAAATGCAAATTGAAAAAGGTA 57.733 29.630 0.00 0.00 0.00 3.08
2709 2902 4.812403 ATGTGGGGATGAATATTGTGGA 57.188 40.909 0.00 0.00 0.00 4.02
2714 2907 4.915809 TGGGGATGAATATTGTGGATCTCT 59.084 41.667 0.00 0.00 0.00 3.10
2715 2908 5.221986 TGGGGATGAATATTGTGGATCTCTG 60.222 44.000 0.00 0.00 0.00 3.35
2764 2958 4.303794 ACCCTAGTATGTTATCTTGGGCA 58.696 43.478 10.55 0.00 45.75 5.36
2793 2988 7.303634 TGAAAATCCTAGTATGTTCTTTCGC 57.696 36.000 0.46 0.00 0.00 4.70
2794 2989 7.103641 TGAAAATCCTAGTATGTTCTTTCGCT 58.896 34.615 0.46 0.00 0.00 4.93
2796 2991 5.854010 ATCCTAGTATGTTCTTTCGCTCA 57.146 39.130 0.00 0.00 0.00 4.26
2797 2992 5.250235 TCCTAGTATGTTCTTTCGCTCAG 57.750 43.478 0.00 0.00 0.00 3.35
2834 3031 0.703488 TCATCACATTCTTGGGGGCA 59.297 50.000 0.00 0.00 0.00 5.36
2839 3036 1.205417 CACATTCTTGGGGGCATTGTC 59.795 52.381 0.00 0.00 0.00 3.18
2863 3060 0.394565 AGCTCGGATGCCTATTGGTC 59.605 55.000 0.00 0.00 35.27 4.02
2864 3061 0.106708 GCTCGGATGCCTATTGGTCA 59.893 55.000 0.00 0.00 35.27 4.02
2905 3103 1.135199 GCATGCTTTGATCCTGGTGTG 60.135 52.381 11.37 0.00 0.00 3.82
2961 3159 3.006110 TGTCTCCTACCTTTTACACGTGG 59.994 47.826 21.57 2.73 0.00 4.94
2966 3164 2.934886 ACCTTTTACACGTGGCCTTA 57.065 45.000 21.57 0.00 0.00 2.69
2986 3185 1.144057 GGTCATCGTTCTCGGGCAT 59.856 57.895 0.00 0.00 37.69 4.40
2999 3198 2.936498 CTCGGGCATTACTGTTTGTAGG 59.064 50.000 0.00 0.00 32.08 3.18
3001 3200 2.442413 GGGCATTACTGTTTGTAGGCA 58.558 47.619 0.00 0.00 35.99 4.75
3016 3215 1.895707 GGCAGGATTGATGCTCCGG 60.896 63.158 0.00 0.00 43.35 5.14
3027 3226 2.043953 GCTCCGGGGCCTGAAATT 60.044 61.111 18.17 0.00 0.00 1.82
3056 3255 0.954449 GTGACCCTCTCAGACGACGA 60.954 60.000 0.00 0.00 0.00 4.20
3058 3257 1.646624 GACCCTCTCAGACGACGACC 61.647 65.000 0.00 0.00 0.00 4.79
3069 3268 0.746063 ACGACGACCTGGTGTGTTTA 59.254 50.000 2.82 0.00 0.00 2.01
3091 3290 0.454196 GCAACAACGTCCAGTGGTTT 59.546 50.000 9.54 0.00 44.28 3.27
3092 3291 1.671845 GCAACAACGTCCAGTGGTTTA 59.328 47.619 9.54 0.00 44.28 2.01
3093 3292 2.292292 GCAACAACGTCCAGTGGTTTAT 59.708 45.455 9.54 0.00 44.28 1.40
3098 3297 2.423577 ACGTCCAGTGGTTTATCAAGC 58.576 47.619 9.54 0.00 0.00 4.01
3104 3303 3.308117 CCAGTGGTTTATCAAGCAGGGTA 60.308 47.826 0.00 0.00 41.08 3.69
3106 3305 2.676342 GTGGTTTATCAAGCAGGGTACG 59.324 50.000 0.00 0.00 41.08 3.67
3112 3311 2.961526 TCAAGCAGGGTACGATCTTC 57.038 50.000 0.00 0.00 0.00 2.87
3123 3322 6.204301 CAGGGTACGATCTTCGAGTTATTCTA 59.796 42.308 3.62 0.00 43.74 2.10
3138 3337 6.322491 AGTTATTCTAATTGCGCCAAGTTTC 58.678 36.000 4.18 0.00 0.00 2.78
3139 3338 2.892373 TCTAATTGCGCCAAGTTTCG 57.108 45.000 4.18 0.00 0.00 3.46
3148 3347 0.599204 GCCAAGTTTCGGAGTCGTCA 60.599 55.000 0.00 0.00 37.69 4.35
3165 3364 5.897377 TCGTCAAGACACTCATCAGAATA 57.103 39.130 0.72 0.00 0.00 1.75
3173 3372 4.922206 ACACTCATCAGAATAAAGCCCAA 58.078 39.130 0.00 0.00 0.00 4.12
3175 3374 4.701651 CACTCATCAGAATAAAGCCCAACA 59.298 41.667 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.893270 CCTGCGGGAATTGGTGAACA 60.893 55.000 5.28 0.00 33.58 3.18
57 58 3.849951 CGCGGTCTATGGGGCTGT 61.850 66.667 0.00 0.00 0.00 4.40
75 76 6.514048 GCTGATAATTTTACATGGAGTCTGGC 60.514 42.308 0.00 0.00 0.00 4.85
139 140 7.227049 ACCATGGAATTGTTATCTTTTTCGT 57.773 32.000 21.47 0.00 0.00 3.85
332 333 3.600786 GCTAAACATAAAAACACGTCGGC 59.399 43.478 0.00 0.00 0.00 5.54
338 339 7.422399 TCAGACTTGGCTAAACATAAAAACAC 58.578 34.615 0.00 0.00 0.00 3.32
339 340 7.575414 TCAGACTTGGCTAAACATAAAAACA 57.425 32.000 0.00 0.00 0.00 2.83
342 343 8.349983 GTCTTTCAGACTTGGCTAAACATAAAA 58.650 33.333 0.00 0.00 41.88 1.52
420 421 5.972382 GTCTTCGCGTAAGTCTGAATCTTAT 59.028 40.000 5.77 0.00 41.68 1.73
421 422 5.330295 GTCTTCGCGTAAGTCTGAATCTTA 58.670 41.667 5.77 0.00 41.68 2.10
422 423 4.167268 GTCTTCGCGTAAGTCTGAATCTT 58.833 43.478 5.77 0.00 41.68 2.40
465 508 1.267574 ATGATGCACGACCAGGGTCT 61.268 55.000 15.95 1.31 42.54 3.85
535 578 3.508840 GGAATCGGCGGCCACAAG 61.509 66.667 20.71 2.16 0.00 3.16
536 579 3.969250 GAGGAATCGGCGGCCACAA 62.969 63.158 20.71 3.83 0.00 3.33
578 624 1.351017 CTCCTAAGTGTTCAAGCCCCA 59.649 52.381 0.00 0.00 0.00 4.96
615 661 2.223340 GGCGCTAAAACACATGGAGATG 60.223 50.000 7.64 0.00 35.49 2.90
700 746 8.441312 TTTTCTTCTGGTACTCGTATTTGTTT 57.559 30.769 0.00 0.00 0.00 2.83
805 854 1.390565 CCTAGACCACGGACGAGAAT 58.609 55.000 0.00 0.00 0.00 2.40
821 870 2.759973 CTCTGCTGACGGGCCCTA 60.760 66.667 22.43 5.02 0.00 3.53
825 874 2.570582 CTTCTCCTCTGCTGACGGGC 62.571 65.000 8.49 0.00 0.00 6.13
964 1018 0.312729 CACAAGCCCCACGGTTTTAC 59.687 55.000 0.00 0.00 28.42 2.01
965 1019 1.457009 GCACAAGCCCCACGGTTTTA 61.457 55.000 0.00 0.00 28.42 1.52
966 1020 2.791868 GCACAAGCCCCACGGTTTT 61.792 57.895 0.00 0.00 28.42 2.43
995 1049 2.549754 ACCGAACTTGTCAGCATCAAAG 59.450 45.455 0.00 0.00 0.00 2.77
1030 1084 5.339611 GCAACATTTTGACGATAAGTGACAC 59.660 40.000 0.00 0.00 34.24 3.67
1041 1095 3.295785 TGTCGATTGCAACATTTTGACG 58.704 40.909 0.00 0.00 34.24 4.35
1093 1148 0.035317 TTCTCGGCACAATCACTGCT 59.965 50.000 0.00 0.00 34.84 4.24
1138 1195 2.048023 TATGCTTGGCTGCTGGTGC 61.048 57.895 0.00 0.19 40.20 5.01
1139 1196 0.961857 TGTATGCTTGGCTGCTGGTG 60.962 55.000 0.00 0.00 0.00 4.17
1140 1197 0.679002 CTGTATGCTTGGCTGCTGGT 60.679 55.000 0.00 0.00 0.00 4.00
1345 1403 1.699634 CTGGAGGTGAACAAGAAGGGA 59.300 52.381 0.00 0.00 0.00 4.20
1501 1565 1.544691 GTGCTCTTCCTCAGGTACGAA 59.455 52.381 0.00 0.00 0.00 3.85
1732 1796 3.450115 CTCCCCGAGTCGGTCACC 61.450 72.222 28.98 0.00 46.80 4.02
1733 1797 4.131088 GCTCCCCGAGTCGGTCAC 62.131 72.222 28.98 12.47 46.80 3.67
2104 2186 2.182030 GAGTTCGGGAGCCTCGTG 59.818 66.667 0.00 0.00 0.00 4.35
2112 2194 2.291043 GCCAAGGAGGAGTTCGGGA 61.291 63.158 0.00 0.00 41.22 5.14
2189 2271 3.803082 CGCCATCGCCACCAAGTG 61.803 66.667 0.00 0.00 0.00 3.16
2200 2282 1.228367 ATCTCCAATGGCCGCCATC 60.228 57.895 25.27 0.00 44.40 3.51
2418 2605 2.676342 GGTACCATTTCGCTTTCGACAT 59.324 45.455 7.15 0.00 45.43 3.06
2483 2673 8.909923 CCTTTCTTTAGGAGGAAAACAAAACTA 58.090 33.333 0.00 0.00 37.50 2.24
2484 2674 7.147724 CCCTTTCTTTAGGAGGAAAACAAAACT 60.148 37.037 0.00 0.00 37.50 2.66
2485 2675 6.984474 CCCTTTCTTTAGGAGGAAAACAAAAC 59.016 38.462 0.00 0.00 37.50 2.43
2486 2676 6.898521 TCCCTTTCTTTAGGAGGAAAACAAAA 59.101 34.615 0.00 0.00 37.50 2.44
2487 2677 6.436890 TCCCTTTCTTTAGGAGGAAAACAAA 58.563 36.000 0.00 0.00 37.50 2.83
2488 2678 6.020881 TCCCTTTCTTTAGGAGGAAAACAA 57.979 37.500 0.00 0.00 37.50 2.83
2489 2679 5.656549 TCCCTTTCTTTAGGAGGAAAACA 57.343 39.130 0.00 0.00 37.50 2.83
2490 2680 8.687242 CATAATCCCTTTCTTTAGGAGGAAAAC 58.313 37.037 0.00 0.00 37.50 2.43
2496 2686 8.160106 ACTATGCATAATCCCTTTCTTTAGGAG 58.840 37.037 8.00 0.00 37.50 3.69
2517 2707 7.986562 TCTAGTACTACAAGACTGCAACTATG 58.013 38.462 0.00 0.00 0.00 2.23
2518 2708 8.577048 TTCTAGTACTACAAGACTGCAACTAT 57.423 34.615 0.00 0.00 0.00 2.12
2519 2709 7.991084 TTCTAGTACTACAAGACTGCAACTA 57.009 36.000 0.00 0.00 0.00 2.24
2520 2710 6.896021 TTCTAGTACTACAAGACTGCAACT 57.104 37.500 0.00 0.00 0.00 3.16
2521 2711 8.460428 ACTATTCTAGTACTACAAGACTGCAAC 58.540 37.037 0.00 0.00 37.23 4.17
2522 2712 8.577048 ACTATTCTAGTACTACAAGACTGCAA 57.423 34.615 0.00 0.00 37.23 4.08
2537 2727 9.688091 TCATTCTCACTCTTGTACTATTCTAGT 57.312 33.333 0.00 0.00 42.68 2.57
2546 2736 9.371136 TGTATTTCATCATTCTCACTCTTGTAC 57.629 33.333 0.00 0.00 0.00 2.90
2689 2882 4.416513 AGATCCACAATATTCATCCCCACA 59.583 41.667 0.00 0.00 0.00 4.17
2692 2885 5.013495 TCAGAGATCCACAATATTCATCCCC 59.987 44.000 0.00 0.00 0.00 4.81
2695 2888 7.714377 ACAAGTCAGAGATCCACAATATTCATC 59.286 37.037 0.00 0.00 0.00 2.92
2696 2889 7.571919 ACAAGTCAGAGATCCACAATATTCAT 58.428 34.615 0.00 0.00 0.00 2.57
2757 2951 1.134610 GGATTTTCAGCCATGCCCAAG 60.135 52.381 0.00 0.00 0.00 3.61
2764 2958 6.904626 AGAACATACTAGGATTTTCAGCCAT 58.095 36.000 14.84 0.00 0.00 4.40
2793 2988 2.096565 CACAACATGACAAGACGCTGAG 60.097 50.000 0.00 0.00 0.00 3.35
2794 2989 1.866601 CACAACATGACAAGACGCTGA 59.133 47.619 0.00 0.00 0.00 4.26
2796 2991 1.867233 GACACAACATGACAAGACGCT 59.133 47.619 0.00 0.00 0.00 5.07
2797 2992 1.597195 TGACACAACATGACAAGACGC 59.403 47.619 0.00 0.00 29.61 5.19
2834 3031 1.762460 ATCCGAGCTCCCCGACAAT 60.762 57.895 8.47 0.00 0.00 2.71
2863 3060 2.462255 AAAGCCACAGACGCGCATTG 62.462 55.000 5.73 4.56 0.00 2.82
2864 3061 2.260869 AAAGCCACAGACGCGCATT 61.261 52.632 5.73 0.00 0.00 3.56
2905 3103 3.067106 TCATGCCAGTCGAAGAAGTTTC 58.933 45.455 0.00 0.00 39.69 2.78
2961 3159 2.128035 CGAGAACGATGACCATAAGGC 58.872 52.381 0.00 0.00 42.66 4.35
2966 3164 1.144057 GCCCGAGAACGATGACCAT 59.856 57.895 0.00 0.00 42.66 3.55
2972 3170 1.480954 ACAGTAATGCCCGAGAACGAT 59.519 47.619 0.00 0.00 42.66 3.73
2974 3172 1.722011 AACAGTAATGCCCGAGAACG 58.278 50.000 0.00 0.00 39.43 3.95
2986 3185 5.235850 TCAATCCTGCCTACAAACAGTAA 57.764 39.130 0.00 0.00 30.92 2.24
2999 3198 1.895707 CCCGGAGCATCAATCCTGC 60.896 63.158 0.73 0.00 39.97 4.85
3001 3200 3.125376 GCCCCGGAGCATCAATCCT 62.125 63.158 1.65 0.00 36.25 3.24
3016 3215 0.393808 TGCCGTCTAATTTCAGGCCC 60.394 55.000 0.00 0.00 46.67 5.80
3056 3255 3.027412 TGTTGCAATAAACACACCAGGT 58.973 40.909 0.59 0.00 35.16 4.00
3058 3257 3.485378 CGTTGTTGCAATAAACACACCAG 59.515 43.478 21.05 6.42 39.70 4.00
3069 3268 0.667993 CCACTGGACGTTGTTGCAAT 59.332 50.000 0.59 0.00 0.00 3.56
3091 3290 3.004419 CGAAGATCGTACCCTGCTTGATA 59.996 47.826 0.00 0.00 34.72 2.15
3092 3291 2.223829 CGAAGATCGTACCCTGCTTGAT 60.224 50.000 0.00 0.00 34.72 2.57
3093 3292 1.134367 CGAAGATCGTACCCTGCTTGA 59.866 52.381 0.00 0.00 34.72 3.02
3098 3297 4.832590 ATAACTCGAAGATCGTACCCTG 57.167 45.455 0.00 0.00 41.35 4.45
3104 3303 6.142480 CGCAATTAGAATAACTCGAAGATCGT 59.858 38.462 0.00 0.00 41.35 3.73
3106 3305 6.292873 GCGCAATTAGAATAACTCGAAGATC 58.707 40.000 0.30 0.00 33.89 2.75
3112 3311 4.034048 ACTTGGCGCAATTAGAATAACTCG 59.966 41.667 10.83 0.00 0.00 4.18
3123 3322 0.240945 CTCCGAAACTTGGCGCAATT 59.759 50.000 10.83 0.00 0.00 2.32
3138 3337 0.591659 TGAGTGTCTTGACGACTCCG 59.408 55.000 19.94 0.00 43.25 4.63
3139 3338 2.229062 TGATGAGTGTCTTGACGACTCC 59.771 50.000 19.94 12.16 43.25 3.85
3148 3347 5.189180 GGGCTTTATTCTGATGAGTGTCTT 58.811 41.667 0.00 0.00 0.00 3.01
3153 3352 4.922206 TGTTGGGCTTTATTCTGATGAGT 58.078 39.130 0.00 0.00 0.00 3.41
3165 3364 4.088634 TGCAAAGATAGATGTTGGGCTTT 58.911 39.130 0.00 0.00 0.00 3.51



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

AutoCloner maintained by Alex Coulton.