Multiple sequence alignment - TraesCS2B01G627200

Loading Multiple Alignment...

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 TraesCS2B01G627200 chr2B 100.000 3224 0 0 1 3224 799048611 799045388 0.000000e+00 5954.0
1 TraesCS2B01G627200 chr2B 80.176 1251 139 60 1289 2521 799029476 799030635 0.000000e+00 835.0
2 TraesCS2B01G627200 chr2B 84.186 860 94 20 1323 2179 798957996 798958816 0.000000e+00 797.0
3 TraesCS2B01G627200 chr2B 85.874 538 62 5 1748 2278 799106646 799106116 7.810000e-156 560.0
4 TraesCS2B01G627200 chr2B 92.593 378 20 3 1290 1664 799107342 799106970 1.320000e-148 536.0
5 TraesCS2B01G627200 chr2B 87.427 342 23 7 904 1231 798957609 798957944 3.040000e-100 375.0
6 TraesCS2B01G627200 chr2B 79.305 633 56 33 90 711 799108586 799108018 1.090000e-99 374.0
7 TraesCS2B01G627200 chr2B 86.905 336 27 6 904 1227 799029123 799029453 8.500000e-96 361.0
8 TraesCS2B01G627200 chr2B 86.970 330 28 7 2199 2514 798958803 798959131 1.100000e-94 357.0
9 TraesCS2B01G627200 chr2B 76.699 721 104 36 2517 3188 799030722 799031427 3.080000e-90 342.0
10 TraesCS2B01G627200 chr2B 78.268 635 61 36 90 711 799028270 799028840 1.430000e-88 337.0
11 TraesCS2B01G627200 chr2B 84.195 329 43 5 2518 2839 798959389 798959715 8.690000e-81 311.0
12 TraesCS2B01G627200 chr2B 85.246 305 29 13 701 999 799107986 799107692 1.880000e-77 300.0
13 TraesCS2B01G627200 chr2B 95.580 181 7 1 701 880 798957364 798957544 4.070000e-74 289.0
14 TraesCS2B01G627200 chr2B 78.405 514 53 23 217 706 798956848 798957327 6.810000e-72 281.0
15 TraesCS2B01G627200 chr2B 92.593 189 7 1 726 907 799028905 799029093 6.860000e-67 265.0
16 TraesCS2B01G627200 chr2B 87.395 238 21 6 997 1227 799107610 799107375 6.860000e-67 265.0
17 TraesCS2B01G627200 chr2B 75.043 577 86 26 2663 3213 799105903 799105359 7.010000e-52 215.0
18 TraesCS2B01G627200 chr2D 89.237 1626 123 24 906 2521 639746877 639745294 0.000000e+00 1986.0
19 TraesCS2B01G627200 chr2D 85.217 1292 117 31 901 2179 639821967 639820737 0.000000e+00 1260.0
20 TraesCS2B01G627200 chr2D 81.889 1408 148 50 904 2278 639733103 639734436 0.000000e+00 1088.0
21 TraesCS2B01G627200 chr2D 83.116 1072 110 32 2199 3222 639820750 639819702 0.000000e+00 911.0
22 TraesCS2B01G627200 chr2D 84.458 637 45 28 90 706 639822822 639822220 2.160000e-161 579.0
23 TraesCS2B01G627200 chr2D 87.110 481 46 9 90 563 639747701 639747230 6.120000e-147 531.0
24 TraesCS2B01G627200 chr2D 89.418 378 28 9 2518 2889 639745166 639744795 1.750000e-127 466.0
25 TraesCS2B01G627200 chr2D 81.034 464 57 17 217 672 639732193 639732633 1.110000e-89 340.0
26 TraesCS2B01G627200 chr2D 92.308 208 15 1 701 907 639732866 639733073 8.750000e-76 294.0
27 TraesCS2B01G627200 chr2D 83.766 308 22 5 416 711 639872789 639872498 1.910000e-67 267.0
28 TraesCS2B01G627200 chr2D 80.308 325 30 14 261 572 639891690 639891387 7.010000e-52 215.0
29 TraesCS2B01G627200 chr2D 83.422 187 16 3 721 907 639822166 639821995 3.330000e-35 159.0
30 TraesCS2B01G627200 chr2D 76.205 332 33 26 607 905 639747229 639746911 2.020000e-27 134.0
31 TraesCS2B01G627200 chr2D 90.476 63 5 1 98 159 639732108 639732170 7.410000e-12 82.4
32 TraesCS2B01G627200 chr2A 87.020 1641 148 26 912 2521 765393749 765392143 0.000000e+00 1790.0
33 TraesCS2B01G627200 chr2A 82.596 1402 125 49 904 2278 765373626 765374935 0.000000e+00 1127.0
34 TraesCS2B01G627200 chr2A 93.906 722 32 3 1 711 765394684 765393964 0.000000e+00 1079.0
35 TraesCS2B01G627200 chr2A 88.457 901 74 9 1290 2179 765441997 765441116 0.000000e+00 1061.0
36 TraesCS2B01G627200 chr2A 82.648 1216 100 56 90 1227 765443212 765442030 0.000000e+00 974.0
37 TraesCS2B01G627200 chr2A 78.670 872 155 21 1327 2190 765516081 765515233 4.700000e-153 551.0
38 TraesCS2B01G627200 chr2A 78.580 873 119 35 1357 2190 765278132 765278975 6.170000e-142 514.0
39 TraesCS2B01G627200 chr2A 89.067 375 33 5 2518 2889 765392054 765391685 2.930000e-125 459.0
40 TraesCS2B01G627200 chr2A 85.623 313 30 7 904 1204 765516443 765516134 6.710000e-82 315.0
41 TraesCS2B01G627200 chr2A 79.070 516 58 19 217 706 765372905 765373396 3.120000e-80 309.0
42 TraesCS2B01G627200 chr2A 84.424 321 28 13 2199 2511 765441129 765440823 2.430000e-76 296.0
43 TraesCS2B01G627200 chr2A 95.429 175 8 0 708 882 765393924 765393750 2.450000e-71 279.0
44 TraesCS2B01G627200 chr2A 77.419 496 52 18 2756 3223 765428772 765428309 1.160000e-59 241.0
45 TraesCS2B01G627200 chr2A 88.485 165 12 6 508 670 765517234 765517075 3.280000e-45 193.0
46 TraesCS2B01G627200 chr2A 77.570 321 28 20 418 711 765548530 765548227 1.550000e-33 154.0
47 TraesCS2B01G627200 chr2A 98.824 85 1 0 818 902 765373507 765373591 5.570000e-33 152.0
48 TraesCS2B01G627200 chr2A 89.706 68 4 3 701 765 765373445 765373512 2.060000e-12 84.2
49 TraesCS2B01G627200 chr2A 97.222 36 1 0 2427 2462 765279504 765279539 9.660000e-06 62.1
50 TraesCS2B01G627200 chr7B 88.966 145 16 0 1040 1184 426972986 426973130 2.560000e-41 180.0


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 TraesCS2B01G627200 chr2B 799045388 799048611 3223 True 5954.000000 5954 100.000000 1 3224 1 chr2B.!!$R1 3223
1 TraesCS2B01G627200 chr2B 799028270 799031427 3157 False 428.000000 835 82.928200 90 3188 5 chr2B.!!$F2 3098
2 TraesCS2B01G627200 chr2B 798956848 798959715 2867 False 401.666667 797 86.127167 217 2839 6 chr2B.!!$F1 2622
3 TraesCS2B01G627200 chr2B 799105359 799108586 3227 True 375.000000 560 84.242667 90 3213 6 chr2B.!!$R2 3123
4 TraesCS2B01G627200 chr2D 639744795 639747701 2906 True 779.250000 1986 85.492500 90 2889 4 chr2D.!!$R3 2799
5 TraesCS2B01G627200 chr2D 639819702 639822822 3120 True 727.250000 1260 84.053250 90 3222 4 chr2D.!!$R4 3132
6 TraesCS2B01G627200 chr2D 639732108 639734436 2328 False 451.100000 1088 86.426750 98 2278 4 chr2D.!!$F1 2180
7 TraesCS2B01G627200 chr2A 765391685 765394684 2999 True 901.750000 1790 91.355500 1 2889 4 chr2A.!!$R3 2888
8 TraesCS2B01G627200 chr2A 765440823 765443212 2389 True 777.000000 1061 85.176333 90 2511 3 chr2A.!!$R4 2421
9 TraesCS2B01G627200 chr2A 765372905 765374935 2030 False 418.050000 1127 87.549000 217 2278 4 chr2A.!!$F2 2061
10 TraesCS2B01G627200 chr2A 765515233 765517234 2001 True 353.000000 551 84.259333 508 2190 3 chr2A.!!$R5 1682
11 TraesCS2B01G627200 chr2A 765278132 765279539 1407 False 288.050000 514 87.901000 1357 2462 2 chr2A.!!$F1 1105

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
349 375 1.884579 CTGTGGTGTAGGTACGTGTCT 59.115 52.381 0.0 0.0 0.0 3.41 F
1566 2437 0.537188 AATCGGCATGAGGAAGACGT 59.463 50.000 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 2454 1.038681 TCCTACCATTAGGCGCACGA 61.039 55.0 10.83 0.0 44.46 4.35 R
3189 5160 0.168128 GATGTTGCGACGGGAAAAGG 59.832 55.0 0.00 0.0 0.00 3.11 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
75 86 3.883489 GGGGACAATATGCTAAAGTGACC 59.117 47.826 0.00 0.00 0.00 4.02
86 97 4.227300 TGCTAAAGTGACCACCATATTCCT 59.773 41.667 0.00 0.00 0.00 3.36
97 108 2.764010 ACCATATTCCTGCACGTACTCA 59.236 45.455 0.00 0.00 0.00 3.41
188 207 5.509163 CGATGTACCTCCGAAACCATATTCT 60.509 44.000 0.00 0.00 0.00 2.40
308 329 2.955660 TCCACCACAAAATTGACCAGAC 59.044 45.455 0.00 0.00 0.00 3.51
319 340 3.593442 TTGACCAGACACCCAATCTTT 57.407 42.857 0.00 0.00 0.00 2.52
330 351 6.271159 AGACACCCAATCTTTTCTCTCTAACT 59.729 38.462 0.00 0.00 0.00 2.24
333 354 6.148480 CACCCAATCTTTTCTCTCTAACTGTG 59.852 42.308 0.00 0.00 0.00 3.66
349 375 1.884579 CTGTGGTGTAGGTACGTGTCT 59.115 52.381 0.00 0.00 0.00 3.41
355 381 3.307242 GGTGTAGGTACGTGTCTAGTACG 59.693 52.174 16.71 16.71 43.81 3.67
475 518 2.234913 CTGGCTGGCCTTTGCATTCC 62.235 60.000 13.05 0.00 40.13 3.01
476 519 2.285024 GGCTGGCCTTTGCATTCCA 61.285 57.895 3.32 0.00 40.13 3.53
495 538 2.026262 CCAGCCCCTAAAAGCTTCACTA 60.026 50.000 0.00 0.00 37.18 2.74
503 546 4.937620 CCTAAAAGCTTCACTATCACAGCA 59.062 41.667 0.00 0.00 34.49 4.41
576 635 6.653320 TCCCACTTTACAAACAAGCTATACTG 59.347 38.462 0.00 0.00 0.00 2.74
716 1410 2.169769 GGGCTATATAGGGTGCGCATAA 59.830 50.000 15.91 0.00 38.10 1.90
882 1598 7.170151 GTCCACACGCATACAACATATATACAA 59.830 37.037 0.00 0.00 0.00 2.41
1077 1918 1.538876 CCACCCCACTGAGGAGGAA 60.539 63.158 5.84 0.00 41.22 3.36
1095 1936 2.292455 GGAACTGGTGGGGTACTACCTA 60.292 54.545 5.19 0.00 38.64 3.08
1161 2002 2.506444 GAGGTCGATCTCTACCGGATT 58.494 52.381 18.67 0.00 40.88 3.01
1325 2191 7.552687 GTGAGGTGGTGATTCAAGTTGAATATA 59.447 37.037 27.01 17.73 46.20 0.86
1326 2192 8.274322 TGAGGTGGTGATTCAAGTTGAATATAT 58.726 33.333 27.01 9.84 46.20 0.86
1505 2376 2.359975 GGGTTCTGGAAGGCCACG 60.360 66.667 5.01 0.00 39.92 4.94
1566 2437 0.537188 AATCGGCATGAGGAAGACGT 59.463 50.000 0.00 0.00 0.00 4.34
1738 2912 5.065090 TGAGAATTTCGCGTTGATGATGAAT 59.935 36.000 5.77 0.00 0.00 2.57
1739 2913 5.883661 AGAATTTCGCGTTGATGATGAATT 58.116 33.333 5.77 0.63 0.00 2.17
1740 2914 5.740569 AGAATTTCGCGTTGATGATGAATTG 59.259 36.000 5.77 0.00 0.00 2.32
1741 2915 4.676849 TTTCGCGTTGATGATGAATTGA 57.323 36.364 5.77 0.00 0.00 2.57
1742 2916 4.880886 TTCGCGTTGATGATGAATTGAT 57.119 36.364 5.77 0.00 0.00 2.57
1743 2917 4.199840 TCGCGTTGATGATGAATTGATG 57.800 40.909 5.77 0.00 0.00 3.07
1744 2918 3.870419 TCGCGTTGATGATGAATTGATGA 59.130 39.130 5.77 0.00 0.00 2.92
1843 3020 0.742505 CTACGTCTTCCCGGCATACA 59.257 55.000 0.00 0.00 0.00 2.29
1876 3053 1.186267 CCTCGGGGGCTACTATGACC 61.186 65.000 0.00 0.00 0.00 4.02
1921 3107 2.125106 GCGGCGACCTCCAATTCT 60.125 61.111 12.98 0.00 0.00 2.40
2064 3262 3.371063 GAGAGCCCACCGACGACA 61.371 66.667 0.00 0.00 0.00 4.35
2068 3266 4.309950 GCCCACCGACGACAACCT 62.310 66.667 0.00 0.00 0.00 3.50
2124 3331 4.477413 CAGCATGGAGAGATGGCC 57.523 61.111 0.00 0.00 0.00 5.36
2281 3517 9.454585 CGATTTCATTGTATACATGATTTGCTT 57.545 29.630 6.36 0.00 0.00 3.91
2371 3700 8.558713 TGGTTGTACCTAGATAGACTACTCTA 57.441 38.462 0.00 0.00 39.58 2.43
2416 3746 6.373216 GTGTCTACTGTAGATCACTCTGTTCT 59.627 42.308 25.94 0.00 37.13 3.01
2479 4083 6.939551 TTCACTTACTAATTTTCCGAGACG 57.060 37.500 0.00 0.00 0.00 4.18
2676 4594 7.686519 TCACGAACGGTTAAATAAATGTATGG 58.313 34.615 0.00 0.00 0.00 2.74
2721 4640 3.990318 TCGATCAAGCGTGATAGTGAT 57.010 42.857 15.36 0.00 44.83 3.06
2731 4650 7.171508 TCAAGCGTGATAGTGATTGGATTAATC 59.828 37.037 6.93 6.93 44.45 1.75
2811 4732 7.878477 TGTAGGTTTGAGTCGTAATTAAGTG 57.122 36.000 0.00 0.00 0.00 3.16
2816 4737 6.647895 GGTTTGAGTCGTAATTAAGTGGAGAA 59.352 38.462 0.00 0.00 0.00 2.87
2817 4738 7.172019 GGTTTGAGTCGTAATTAAGTGGAGAAA 59.828 37.037 0.00 0.00 0.00 2.52
2833 4754 1.079503 GAAACAGACAGACGGATGGC 58.920 55.000 0.00 0.00 0.00 4.40
2854 4799 4.011023 GCTCTCCTACTCGCCATCTATAA 58.989 47.826 0.00 0.00 0.00 0.98
2936 4904 7.538678 ACGTGCTGATCATTAAAATGTTCTTTC 59.461 33.333 12.58 5.23 36.53 2.62
2937 4905 7.752239 CGTGCTGATCATTAAAATGTTCTTTCT 59.248 33.333 12.58 0.00 36.53 2.52
2938 4906 9.070149 GTGCTGATCATTAAAATGTTCTTTCTC 57.930 33.333 12.58 3.21 36.53 2.87
2939 4907 8.795513 TGCTGATCATTAAAATGTTCTTTCTCA 58.204 29.630 12.58 4.13 36.53 3.27
2954 4923 2.315925 TCTCAACGGGATCAATCTGC 57.684 50.000 0.00 0.00 0.00 4.26
2964 4933 4.070716 GGGATCAATCTGCTGGTGAATAG 58.929 47.826 0.00 0.00 0.00 1.73
2971 4940 2.688446 TCTGCTGGTGAATAGGTACGAG 59.312 50.000 0.00 0.00 0.00 4.18
2972 4941 1.754803 TGCTGGTGAATAGGTACGAGG 59.245 52.381 0.00 0.00 0.00 4.63
2986 4955 1.771565 ACGAGGTCGATGGAATACCA 58.228 50.000 6.35 0.00 45.91 3.25
3003 4972 9.627123 TGGAATACCATCCTATTAAACAGAAAG 57.373 33.333 0.00 0.00 41.77 2.62
3005 4974 9.847224 GAATACCATCCTATTAAACAGAAAGGA 57.153 33.333 0.00 0.00 40.50 3.36
3007 4976 9.853177 ATACCATCCTATTAAACAGAAAGGAAG 57.147 33.333 0.00 0.00 39.68 3.46
3009 4978 6.547510 CCATCCTATTAAACAGAAAGGAAGGG 59.452 42.308 3.55 0.98 40.13 3.95
3017 4986 5.551305 AACAGAAAGGAAGGGGATTTTTG 57.449 39.130 0.00 0.00 0.00 2.44
3025 4994 1.644509 AGGGGATTTTTGGAACCTGC 58.355 50.000 0.00 0.00 0.00 4.85
3028 4997 2.496070 GGGGATTTTTGGAACCTGCTAC 59.504 50.000 0.00 0.00 0.00 3.58
3032 5001 5.656859 GGGATTTTTGGAACCTGCTACTATT 59.343 40.000 0.00 0.00 0.00 1.73
3034 5003 5.975693 TTTTTGGAACCTGCTACTATTGG 57.024 39.130 0.00 0.00 0.00 3.16
3099 5070 7.731882 TTTGAAAAATTCCGGGAAATAAACC 57.268 32.000 14.45 2.91 0.00 3.27
3183 5154 6.607735 TTTGCGTATAAGCCACTAATAACC 57.392 37.500 8.22 0.00 36.02 2.85
3189 5160 6.370718 CGTATAAGCCACTAATAACCAATCCC 59.629 42.308 0.00 0.00 0.00 3.85
3197 5168 5.362717 CACTAATAACCAATCCCCTTTTCCC 59.637 44.000 0.00 0.00 0.00 3.97
3217 5188 3.000925 CCCGTCGCAACATCACTAATTAC 59.999 47.826 0.00 0.00 0.00 1.89
3222 5193 3.369756 CGCAACATCACTAATTACCGTGT 59.630 43.478 5.14 0.00 33.07 4.49
3223 5194 4.563580 CGCAACATCACTAATTACCGTGTA 59.436 41.667 5.14 0.00 33.07 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.068103 CCTCCTCTTCCTGTATAGTAGCATATG 59.932 44.444 0.00 0.00 0.00 1.78
40 41 1.089978 TGTCCCCTCCTCTTCCTGTA 58.910 55.000 0.00 0.00 0.00 2.74
43 44 3.321950 CATATTGTCCCCTCCTCTTCCT 58.678 50.000 0.00 0.00 0.00 3.36
75 86 3.123804 GAGTACGTGCAGGAATATGGTG 58.876 50.000 14.38 0.00 0.00 4.17
86 97 2.134201 CTCAACAGTGAGTACGTGCA 57.866 50.000 6.38 0.00 45.44 4.57
97 108 3.825328 ACCTCAATTCAAGCTCAACAGT 58.175 40.909 0.00 0.00 0.00 3.55
308 329 6.148480 CACAGTTAGAGAGAAAAGATTGGGTG 59.852 42.308 0.00 0.00 0.00 4.61
319 340 4.737578 ACCTACACCACAGTTAGAGAGAA 58.262 43.478 0.00 0.00 0.00 2.87
330 351 1.985473 AGACACGTACCTACACCACA 58.015 50.000 0.00 0.00 0.00 4.17
333 354 3.307242 CGTACTAGACACGTACCTACACC 59.693 52.174 11.74 0.00 35.06 4.16
349 375 1.889105 CGCCGGCCTACTCGTACTA 60.889 63.158 23.46 0.00 0.00 1.82
475 518 2.206576 AGTGAAGCTTTTAGGGGCTG 57.793 50.000 0.00 0.00 38.91 4.85
476 519 3.523564 TGATAGTGAAGCTTTTAGGGGCT 59.476 43.478 0.00 0.00 40.85 5.19
495 538 2.174210 AGGTCCTGCATATTGCTGTGAT 59.826 45.455 0.00 0.00 45.31 3.06
503 546 5.522641 AGGAATGAAAAGGTCCTGCATATT 58.477 37.500 0.00 0.00 40.37 1.28
716 1410 1.470632 GCAGAGCAGAGCAGACGTATT 60.471 52.381 0.00 0.00 0.00 1.89
882 1598 1.153025 TCCACCGATCGACCGATCT 60.153 57.895 24.22 9.00 46.36 2.75
1077 1918 1.342774 GCTAGGTAGTACCCCACCAGT 60.343 57.143 16.05 0.00 39.75 4.00
1161 2002 1.541118 TTGGAGGTCCCATGGCTCA 60.541 57.895 16.76 3.96 46.10 4.26
1236 2093 7.823799 ACTTGTCATGGTTTCACTTCAAAATTT 59.176 29.630 0.00 0.00 0.00 1.82
1246 2103 6.744112 TCCAAAATACTTGTCATGGTTTCAC 58.256 36.000 0.00 0.00 0.00 3.18
1325 2191 7.062322 TCTCTGCACCATCCATTATTGTTAAT 58.938 34.615 0.00 0.00 0.00 1.40
1326 2192 6.422333 TCTCTGCACCATCCATTATTGTTAA 58.578 36.000 0.00 0.00 0.00 2.01
1583 2454 1.038681 TCCTACCATTAGGCGCACGA 61.039 55.000 10.83 0.00 44.46 4.35
1738 2912 5.183140 GCATCATCATCACCATGATCATCAA 59.817 40.000 4.86 0.00 45.26 2.57
1739 2913 4.700213 GCATCATCATCACCATGATCATCA 59.300 41.667 4.86 0.00 45.26 3.07
1740 2914 4.700213 TGCATCATCATCACCATGATCATC 59.300 41.667 4.86 0.00 45.26 2.92
1741 2915 4.662278 TGCATCATCATCACCATGATCAT 58.338 39.130 1.18 1.18 45.26 2.45
1742 2916 4.072131 CTGCATCATCATCACCATGATCA 58.928 43.478 0.00 0.00 45.26 2.92
1743 2917 3.440522 CCTGCATCATCATCACCATGATC 59.559 47.826 0.00 0.00 45.26 2.92
1917 3103 3.503363 GCGGCGCTCTGCAAGAAT 61.503 61.111 26.86 0.00 46.34 2.40
2104 3302 1.837789 CCATCTCTCCATGCTGGCT 59.162 57.895 0.00 0.00 37.47 4.75
2124 3331 2.125552 TTCCAGTCGATGCCAGCG 60.126 61.111 0.00 0.00 0.00 5.18
2225 3435 5.008415 GCTACGGTATGTCTGCTAACTCTAA 59.992 44.000 0.00 0.00 0.00 2.10
2310 3589 2.223377 CAGATGCACATGGACATCATCG 59.777 50.000 23.96 13.01 44.16 3.84
2371 3700 5.869579 ACACATGGACTCAGTAAGTGAAAT 58.130 37.500 0.00 0.00 38.74 2.17
2479 4083 1.063469 CATGCGGACGGTAAATCAACC 59.937 52.381 0.00 0.00 36.08 3.77
2489 4093 5.666969 TTATTAGAAAATCATGCGGACGG 57.333 39.130 0.00 0.00 0.00 4.79
2676 4594 1.296056 ACTAATTCGCGTGGGCACAC 61.296 55.000 9.72 9.72 44.23 3.82
2689 4607 6.533723 TCACGCTTGATCGATGTTAACTAATT 59.466 34.615 0.54 0.00 0.00 1.40
2721 4640 5.174037 ACAGGGAAACTCGATTAATCCAA 57.826 39.130 9.87 0.00 31.63 3.53
2731 4650 3.866651 AGATGATTGACAGGGAAACTCG 58.133 45.455 0.00 0.00 0.00 4.18
2811 4732 2.611518 CATCCGTCTGTCTGTTTCTCC 58.388 52.381 0.00 0.00 0.00 3.71
2816 4737 0.247736 GAGCCATCCGTCTGTCTGTT 59.752 55.000 0.00 0.00 0.00 3.16
2817 4738 0.613292 AGAGCCATCCGTCTGTCTGT 60.613 55.000 0.00 0.00 0.00 3.41
2833 4754 5.883115 TGATTATAGATGGCGAGTAGGAGAG 59.117 44.000 0.00 0.00 0.00 3.20
2854 4799 3.864789 AGTCCCTGTCACTTTGTTGAT 57.135 42.857 0.00 0.00 0.00 2.57
2912 4858 8.976986 AGAAAGAACATTTTAATGATCAGCAC 57.023 30.769 9.32 1.93 39.73 4.40
2936 4904 1.938577 CAGCAGATTGATCCCGTTGAG 59.061 52.381 0.00 0.00 0.00 3.02
2937 4905 1.407299 CCAGCAGATTGATCCCGTTGA 60.407 52.381 0.00 0.00 0.00 3.18
2938 4906 1.019673 CCAGCAGATTGATCCCGTTG 58.980 55.000 0.00 0.00 0.00 4.10
2939 4907 0.620556 ACCAGCAGATTGATCCCGTT 59.379 50.000 0.00 0.00 0.00 4.44
2954 4923 2.033049 CGACCTCGTACCTATTCACCAG 59.967 54.545 0.00 0.00 34.11 4.00
2964 4933 2.030451 GGTATTCCATCGACCTCGTACC 60.030 54.545 0.00 0.00 40.80 3.34
2986 4955 6.450352 TCCCCTTCCTTTCTGTTTAATAGGAT 59.550 38.462 0.00 0.00 35.11 3.24
2987 4956 5.793763 TCCCCTTCCTTTCTGTTTAATAGGA 59.206 40.000 0.00 0.00 33.34 2.94
2989 4958 8.595362 AAATCCCCTTCCTTTCTGTTTAATAG 57.405 34.615 0.00 0.00 0.00 1.73
2990 4959 8.966155 AAAATCCCCTTCCTTTCTGTTTAATA 57.034 30.769 0.00 0.00 0.00 0.98
2991 4960 7.872061 AAAATCCCCTTCCTTTCTGTTTAAT 57.128 32.000 0.00 0.00 0.00 1.40
2992 4961 7.419634 CCAAAAATCCCCTTCCTTTCTGTTTAA 60.420 37.037 0.00 0.00 0.00 1.52
2993 4962 6.042666 CCAAAAATCCCCTTCCTTTCTGTTTA 59.957 38.462 0.00 0.00 0.00 2.01
2994 4963 5.163205 CCAAAAATCCCCTTCCTTTCTGTTT 60.163 40.000 0.00 0.00 0.00 2.83
2997 4966 4.159557 TCCAAAAATCCCCTTCCTTTCTG 58.840 43.478 0.00 0.00 0.00 3.02
3000 4969 3.650942 GGTTCCAAAAATCCCCTTCCTTT 59.349 43.478 0.00 0.00 0.00 3.11
3003 4972 2.567169 CAGGTTCCAAAAATCCCCTTCC 59.433 50.000 0.00 0.00 0.00 3.46
3005 4974 1.977854 GCAGGTTCCAAAAATCCCCTT 59.022 47.619 0.00 0.00 0.00 3.95
3007 4976 1.644509 AGCAGGTTCCAAAAATCCCC 58.355 50.000 0.00 0.00 0.00 4.81
3009 4978 6.405842 CCAATAGTAGCAGGTTCCAAAAATCC 60.406 42.308 0.00 0.00 0.00 3.01
3017 4986 4.390264 GGAATCCAATAGTAGCAGGTTCC 58.610 47.826 0.00 0.00 0.00 3.62
3025 4994 7.657761 AGTTTATGAAGCGGAATCCAATAGTAG 59.342 37.037 0.00 0.00 0.00 2.57
3028 4997 6.867662 AGTTTATGAAGCGGAATCCAATAG 57.132 37.500 0.00 0.00 0.00 1.73
3032 5001 4.574828 GCTAAGTTTATGAAGCGGAATCCA 59.425 41.667 0.00 0.00 0.00 3.41
3034 5003 5.734855 TGCTAAGTTTATGAAGCGGAATC 57.265 39.130 0.00 0.00 37.80 2.52
3080 5050 5.221481 ACGTTGGTTTATTTCCCGGAATTTT 60.221 36.000 0.73 0.00 0.00 1.82
3144 5115 3.037431 GCAAAATACCATTGCCACACA 57.963 42.857 0.00 0.00 45.73 3.72
3165 5136 6.657966 GGGGATTGGTTATTAGTGGCTTATAC 59.342 42.308 0.00 0.00 0.00 1.47
3166 5137 6.564927 AGGGGATTGGTTATTAGTGGCTTATA 59.435 38.462 0.00 0.00 0.00 0.98
3183 5154 1.654023 GCGACGGGAAAAGGGGATTG 61.654 60.000 0.00 0.00 0.00 2.67
3189 5160 0.168128 GATGTTGCGACGGGAAAAGG 59.832 55.000 0.00 0.00 0.00 3.11
3197 5168 3.301579 CGGTAATTAGTGATGTTGCGACG 60.302 47.826 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.