Multiple sequence alignment - TraesCS2B01G001000

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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 TraesCS2B01G001000 chr2B 100.000 4457 0 0 1 4457 469641 474097 0.000000e+00 8231.0
1 TraesCS2B01G001000 chr2B 85.646 1045 132 11 1694 2729 8567354 8568389 0.000000e+00 1083.0
2 TraesCS2B01G001000 chr2B 92.649 721 53 0 911 1631 8566388 8567108 0.000000e+00 1038.0
3 TraesCS2B01G001000 chr2B 86.584 723 92 5 189 908 8565480 8566200 0.000000e+00 793.0
4 TraesCS2B01G001000 chr2B 80.639 501 83 11 2218 2714 667790577 667791067 4.210000e-100 375.0
5 TraesCS2B01G001000 chr2B 84.718 373 43 10 3977 4344 8569726 8570089 1.180000e-95 361.0
6 TraesCS2B01G001000 chr2B 80.150 267 45 8 3865 4128 8597091 8597352 4.550000e-45 193.0
7 TraesCS2B01G001000 chr2D 96.619 1834 56 2 911 2738 1993014 1994847 0.000000e+00 3038.0
8 TraesCS2B01G001000 chr2D 95.820 909 37 1 1 908 1991918 1992826 0.000000e+00 1467.0
9 TraesCS2B01G001000 chr2D 91.295 965 51 14 3404 4347 1995631 1996583 0.000000e+00 1286.0
10 TraesCS2B01G001000 chr2D 84.560 1250 159 13 910 2125 2734900 2733651 0.000000e+00 1208.0
11 TraesCS2B01G001000 chr2D 96.500 600 21 0 2803 3402 1994981 1995580 0.000000e+00 992.0
12 TraesCS2B01G001000 chr2D 84.809 915 129 8 1 908 2735998 2735087 0.000000e+00 911.0
13 TraesCS2B01G001000 chr2D 89.073 723 75 4 188 908 22570846 22570126 0.000000e+00 894.0
14 TraesCS2B01G001000 chr2D 81.291 604 104 7 2806 3402 22567669 22567068 8.670000e-132 481.0
15 TraesCS2B01G001000 chr2D 81.589 516 90 3 2216 2730 2678349 2677838 5.330000e-114 422.0
16 TraesCS2B01G001000 chr2D 77.231 650 110 20 1 632 2358530 2359159 3.300000e-91 346.0
17 TraesCS2B01G001000 chr2D 83.962 106 6 2 2721 2815 1994863 1994968 1.710000e-14 91.6
18 TraesCS2B01G001000 chr2D 83.962 106 6 3 2721 2815 2539071 2538966 1.710000e-14 91.6
19 TraesCS2B01G001000 chr2D 94.286 35 2 0 2739 2773 2677669 2677635 2.000000e-03 54.7
20 TraesCS2B01G001000 chr2A 96.565 1834 57 2 911 2738 1872826 1874659 0.000000e+00 3033.0
21 TraesCS2B01G001000 chr2A 92.959 909 42 6 1 908 1871751 1872638 0.000000e+00 1304.0
22 TraesCS2B01G001000 chr2A 83.721 1333 178 17 910 2205 2364185 2365515 0.000000e+00 1223.0
23 TraesCS2B01G001000 chr2A 83.494 1345 181 18 910 2217 2882407 2883747 0.000000e+00 1216.0
24 TraesCS2B01G001000 chr2A 86.377 1035 134 4 1697 2729 2988341 2989370 0.000000e+00 1123.0
25 TraesCS2B01G001000 chr2A 96.333 600 22 0 2803 3402 1874793 1875392 0.000000e+00 987.0
26 TraesCS2B01G001000 chr2A 91.322 726 57 3 911 1630 2987369 2988094 0.000000e+00 987.0
27 TraesCS2B01G001000 chr2A 87.379 721 86 5 188 905 2915846 2916564 0.000000e+00 822.0
28 TraesCS2B01G001000 chr2A 89.298 570 34 11 3739 4302 1875811 1876359 0.000000e+00 689.0
29 TraesCS2B01G001000 chr2A 92.128 343 15 4 3404 3745 1875443 1875774 1.450000e-129 473.0
30 TraesCS2B01G001000 chr2A 81.431 517 82 13 2216 2725 2324199 2324708 1.150000e-110 411.0
31 TraesCS2B01G001000 chr2A 91.121 214 7 7 4168 4369 1906001 1906214 3.390000e-71 279.0
32 TraesCS2B01G001000 chr2A 80.344 407 41 17 3977 4369 2990704 2991085 5.680000e-69 272.0
33 TraesCS2B01G001000 chr2A 73.333 270 54 8 1 270 2881297 2881548 2.860000e-12 84.2
34 TraesCS2B01G001000 chr2A 78.814 118 25 0 1 118 2363075 2363192 3.700000e-11 80.5
35 TraesCS2B01G001000 chr5A 95.233 1846 70 5 911 2738 599782022 599780177 0.000000e+00 2905.0
36 TraesCS2B01G001000 chr5A 93.839 909 55 1 1 908 599783118 599782210 0.000000e+00 1367.0
37 TraesCS2B01G001000 chr5A 94.807 597 31 0 2806 3402 599780040 599779444 0.000000e+00 931.0
38 TraesCS2B01G001000 chr5A 92.507 347 18 7 4007 4347 599778792 599778448 1.440000e-134 490.0
39 TraesCS2B01G001000 chr5A 91.837 343 16 4 3404 3745 599779393 599779062 6.750000e-128 468.0
40 TraesCS2B01G001000 chr5A 90.336 238 18 2 3739 3974 599779025 599778791 1.560000e-79 307.0
41 TraesCS2B01G001000 chr5A 84.615 104 5 2 2721 2813 599780161 599780058 4.750000e-15 93.5
42 TraesCS2B01G001000 chr5D 95.256 1834 80 3 911 2738 480603380 480601548 0.000000e+00 2898.0
43 TraesCS2B01G001000 chr5D 94.389 909 49 2 1 908 480604475 480603568 0.000000e+00 1395.0
44 TraesCS2B01G001000 chr5D 94.975 597 30 0 2806 3402 480601411 480600815 0.000000e+00 937.0
45 TraesCS2B01G001000 chr5D 90.351 342 24 7 4011 4347 480600164 480599827 1.470000e-119 440.0
46 TraesCS2B01G001000 chr5D 90.769 325 13 9 3404 3728 480600764 480600457 6.900000e-113 418.0
47 TraesCS2B01G001000 chr5D 90.377 239 15 5 3739 3973 480600402 480600168 1.560000e-79 307.0
48 TraesCS2B01G001000 chr5D 83.654 104 6 2 2721 2813 480601532 480601429 2.210000e-13 87.9
49 TraesCS2B01G001000 chr5B 96.743 1566 51 0 910 2475 588941268 588939703 0.000000e+00 2610.0
50 TraesCS2B01G001000 chr5B 94.059 909 53 1 1 908 588942363 588941455 0.000000e+00 1378.0
51 TraesCS2B01G001000 chr5B 95.477 597 27 0 2806 3402 588934063 588933467 0.000000e+00 953.0
52 TraesCS2B01G001000 chr5B 87.195 492 33 12 3858 4347 588932777 588932314 2.360000e-147 532.0
53 TraesCS2B01G001000 chr5B 90.671 343 20 4 3404 3745 588933416 588933085 3.160000e-121 446.0
54 TraesCS2B01G001000 chr5B 90.377 239 16 4 3739 3973 588933048 588932813 1.560000e-79 307.0
55 TraesCS2B01G001000 chr5B 92.473 93 6 1 4365 4457 588932234 588932143 1.010000e-26 132.0
56 TraesCS2B01G001000 chrUn 84.662 1330 173 14 911 2212 15480404 15479078 0.000000e+00 1297.0
57 TraesCS2B01G001000 chrUn 81.313 594 111 0 2809 3402 15915677 15915084 2.410000e-132 483.0
58 TraesCS2B01G001000 chrUn 81.008 516 96 2 2216 2730 15916357 15915843 4.150000e-110 409.0
59 TraesCS2B01G001000 chrUn 78.856 402 57 20 3904 4289 15955512 15955123 3.440000e-61 246.0
60 TraesCS2B01G001000 chr3B 83.171 1337 185 14 911 2212 52919675 52918344 0.000000e+00 1186.0
61 TraesCS2B01G001000 chr3B 81.333 600 106 4 2806 3402 52917168 52916572 2.410000e-132 483.0
62 TraesCS2B01G001000 chr4B 83.503 588 94 2 2813 3400 634316824 634317408 3.030000e-151 545.0


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 TraesCS2B01G001000 chr2B 469641 474097 4456 False 8231.000000 8231 100.000000 1 4457 1 chr2B.!!$F1 4456
1 TraesCS2B01G001000 chr2B 8565480 8570089 4609 False 818.750000 1083 87.399250 189 4344 4 chr2B.!!$F4 4155
2 TraesCS2B01G001000 chr2D 1991918 1996583 4665 False 1374.920000 3038 92.839200 1 4347 5 chr2D.!!$F2 4346
3 TraesCS2B01G001000 chr2D 2733651 2735998 2347 True 1059.500000 1208 84.684500 1 2125 2 chr2D.!!$R3 2124
4 TraesCS2B01G001000 chr2D 22567068 22570846 3778 True 687.500000 894 85.182000 188 3402 2 chr2D.!!$R4 3214
5 TraesCS2B01G001000 chr2D 2358530 2359159 629 False 346.000000 346 77.231000 1 632 1 chr2D.!!$F1 631
6 TraesCS2B01G001000 chr2D 2677635 2678349 714 True 238.350000 422 87.937500 2216 2773 2 chr2D.!!$R2 557
7 TraesCS2B01G001000 chr2A 1871751 1876359 4608 False 1297.200000 3033 93.456600 1 4302 5 chr2A.!!$F4 4301
8 TraesCS2B01G001000 chr2A 2915846 2916564 718 False 822.000000 822 87.379000 188 905 1 chr2A.!!$F3 717
9 TraesCS2B01G001000 chr2A 2987369 2991085 3716 False 794.000000 1123 86.014333 911 4369 3 chr2A.!!$F7 3458
10 TraesCS2B01G001000 chr2A 2363075 2365515 2440 False 651.750000 1223 81.267500 1 2205 2 chr2A.!!$F5 2204
11 TraesCS2B01G001000 chr2A 2881297 2883747 2450 False 650.100000 1216 78.413500 1 2217 2 chr2A.!!$F6 2216
12 TraesCS2B01G001000 chr2A 2324199 2324708 509 False 411.000000 411 81.431000 2216 2725 1 chr2A.!!$F2 509
13 TraesCS2B01G001000 chr5A 599778448 599783118 4670 True 937.357143 2905 91.882000 1 4347 7 chr5A.!!$R1 4346
14 TraesCS2B01G001000 chr5D 480599827 480604475 4648 True 926.128571 2898 91.395857 1 4347 7 chr5D.!!$R1 4346
15 TraesCS2B01G001000 chr5B 588939703 588942363 2660 True 1994.000000 2610 95.401000 1 2475 2 chr5B.!!$R2 2474
16 TraesCS2B01G001000 chr5B 588932143 588934063 1920 True 474.000000 953 91.238600 2806 4457 5 chr5B.!!$R1 1651
17 TraesCS2B01G001000 chrUn 15479078 15480404 1326 True 1297.000000 1297 84.662000 911 2212 1 chrUn.!!$R1 1301
18 TraesCS2B01G001000 chrUn 15915084 15916357 1273 True 446.000000 483 81.160500 2216 3402 2 chrUn.!!$R3 1186
19 TraesCS2B01G001000 chr3B 52916572 52919675 3103 True 834.500000 1186 82.252000 911 3402 2 chr3B.!!$R1 2491
20 TraesCS2B01G001000 chr4B 634316824 634317408 584 False 545.000000 545 83.503000 2813 3400 1 chr4B.!!$F1 587

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
216 217 0.179037 GCAGATGCATGTCCAGCCTA 60.179 55.000 2.46 0.0 41.59 3.93 F
1320 1556 0.511653 GTCTTCGTTTTCGTCTGCCC 59.488 55.000 0.00 0.0 44.46 5.36 F
3055 4149 1.133407 GACTGCAGTCTCTCCTTACCG 59.867 57.143 34.54 0.0 41.65 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2454 0.742281 CTTCCACACCAGGCTCATCG 60.742 60.0 0.0 0.0 0.00 3.84 R
3138 4232 0.247736 CTCCTCCTTCAACACCCTCG 59.752 60.0 0.0 0.0 0.00 4.63 R
4369 5818 1.614996 ATCGGTGGCAAAACACATGA 58.385 45.0 0.0 0.0 43.08 3.07 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
144 145 3.499050 CAGCATGCTGAGCTCCAC 58.501 61.111 38.90 3.46 46.30 4.02
216 217 0.179037 GCAGATGCATGTCCAGCCTA 60.179 55.000 2.46 0.00 41.59 3.93
283 320 4.823442 GTGGTGATGAAGATCATGGCAATA 59.177 41.667 0.00 0.00 40.78 1.90
351 388 5.513094 CCAAAGGATGAAGGACACTGTAGAA 60.513 44.000 0.00 0.00 0.00 2.10
363 400 5.405873 GGACACTGTAGAACAACTAAAGCTC 59.594 44.000 0.00 0.00 39.40 4.09
464 502 2.289532 ACCTCAGAGTGCAGAGCCC 61.290 63.158 0.00 0.00 0.00 5.19
632 670 4.874970 ACCAACAAGTGCAGAATCATTTC 58.125 39.130 0.00 0.00 0.00 2.17
908 947 4.803613 GTCACAACTCGGCAAAAAGAAATT 59.196 37.500 0.00 0.00 0.00 1.82
957 1181 4.766891 CCTAGTTTGGCTCATTGGAAAAGA 59.233 41.667 0.00 0.00 0.00 2.52
960 1184 4.038402 AGTTTGGCTCATTGGAAAAGAGTG 59.962 41.667 0.00 0.00 43.19 3.51
1317 1553 3.113322 TGACTGTCTTCGTTTTCGTCTG 58.887 45.455 9.51 0.00 44.46 3.51
1320 1556 0.511653 GTCTTCGTTTTCGTCTGCCC 59.488 55.000 0.00 0.00 44.46 5.36
1495 1749 3.523157 TGGAGCAATGGATGAAGGTTCTA 59.477 43.478 0.00 0.00 0.00 2.10
1588 1842 5.728255 ATCCTGTGGAGTCCATGGTACATC 61.728 50.000 24.57 9.00 38.17 3.06
1624 1878 3.955551 TGTGCACCTACGATTCCTATGTA 59.044 43.478 15.69 0.00 0.00 2.29
1702 2139 1.827969 AGTCATGGTCTAGCAGTGGTC 59.172 52.381 0.00 0.00 0.00 4.02
1725 2162 2.839486 TTCCTGAAGACACGAGCAAT 57.161 45.000 0.00 0.00 0.00 3.56
1958 2398 3.314553 CAGCTCAAGCAAAACTGATTGG 58.685 45.455 4.59 0.00 45.16 3.16
2010 2454 4.785511 TTGGGATAGTAAGCGATCTAGC 57.214 45.455 0.00 0.00 37.41 3.42
2377 3103 4.169658 TGGAAATCATTGGATGGGGTGATA 59.830 41.667 0.00 0.00 32.92 2.15
2404 3130 6.659776 CAAAGCTTAGACCAAGTGTTAGTTC 58.340 40.000 0.00 0.00 36.55 3.01
2447 3173 4.282957 TGAGAAGCTGACACTTGAGAGATT 59.717 41.667 0.00 0.00 0.00 2.40
2489 3215 1.576356 CTTCTGATGCTAACCTCGCC 58.424 55.000 0.00 0.00 0.00 5.54
2503 3229 1.272781 CTCGCCGAAGACACTGATTC 58.727 55.000 0.00 0.00 0.00 2.52
2589 3333 2.014857 CCTGTTGAGCACATGGAGATG 58.985 52.381 0.00 0.00 33.76 2.90
2683 3430 5.187687 TGGAGATACGGGATTGTAAAAACC 58.812 41.667 0.00 0.00 0.00 3.27
2701 3508 6.872628 AAAACCTAAAACAGCTGGTAGTAC 57.127 37.500 19.93 0.00 31.82 2.73
2706 3513 2.220653 AACAGCTGGTAGTACGGGTA 57.779 50.000 19.93 0.00 0.00 3.69
3055 4149 1.133407 GACTGCAGTCTCTCCTTACCG 59.867 57.143 34.54 0.00 41.65 4.02
3059 4153 2.104530 GTCTCTCCTTACCGCCGC 59.895 66.667 0.00 0.00 0.00 6.53
3175 4269 0.250640 AGAAGAGCAGCCAACACAGG 60.251 55.000 0.00 0.00 0.00 4.00
3338 4432 2.436824 GCAAGAGGACGCCCTTCC 60.437 66.667 0.00 0.00 44.53 3.46
3598 4744 1.179174 GCCCTTTTCTTGCGACCCTT 61.179 55.000 0.00 0.00 0.00 3.95
3608 4754 4.178540 TCTTGCGACCCTTCTTAATAACG 58.821 43.478 0.00 0.00 0.00 3.18
3669 4815 3.612860 CGAGTTCCCTTGTACATTCTTCG 59.387 47.826 0.00 0.00 0.00 3.79
3670 4816 4.617530 CGAGTTCCCTTGTACATTCTTCGA 60.618 45.833 0.00 0.00 0.00 3.71
3671 4817 4.822026 AGTTCCCTTGTACATTCTTCGAG 58.178 43.478 0.00 0.00 0.00 4.04
3672 4818 4.283722 AGTTCCCTTGTACATTCTTCGAGT 59.716 41.667 0.00 0.00 0.00 4.18
3673 4819 4.884668 TCCCTTGTACATTCTTCGAGTT 57.115 40.909 0.00 0.00 0.00 3.01
3674 4820 4.817517 TCCCTTGTACATTCTTCGAGTTC 58.182 43.478 0.00 0.00 0.00 3.01
3675 4821 3.933332 CCCTTGTACATTCTTCGAGTTCC 59.067 47.826 0.00 0.00 0.00 3.62
3676 4822 3.933332 CCTTGTACATTCTTCGAGTTCCC 59.067 47.826 0.00 0.00 0.00 3.97
3677 4823 4.322801 CCTTGTACATTCTTCGAGTTCCCT 60.323 45.833 0.00 0.00 0.00 4.20
3678 4824 4.884668 TGTACATTCTTCGAGTTCCCTT 57.115 40.909 0.00 0.00 0.00 3.95
3679 4825 4.817517 TGTACATTCTTCGAGTTCCCTTC 58.182 43.478 0.00 0.00 0.00 3.46
3680 4826 2.960819 ACATTCTTCGAGTTCCCTTCG 58.039 47.619 0.00 0.00 39.33 3.79
3687 4833 1.035932 CGAGTTCCCTTCGAGCCCTA 61.036 60.000 0.00 0.00 40.36 3.53
3800 5002 5.042463 TCCATTTCCAGTTATATTCGCCA 57.958 39.130 0.00 0.00 0.00 5.69
3851 5057 3.921677 TCCCGCCGTATCAGATTTATTC 58.078 45.455 0.00 0.00 0.00 1.75
4040 5469 0.176910 TCTGTGCAGGTGTTCGTTCA 59.823 50.000 0.00 0.00 0.00 3.18
4099 5529 7.959658 TGGGTTATTGTCATTTCATCAAGAT 57.040 32.000 0.00 0.00 0.00 2.40
4116 5552 5.084519 TCAAGATGTGGTAGGTCTACTTGT 58.915 41.667 7.90 0.00 36.14 3.16
4131 5567 6.294342 GGTCTACTTGTGTAATTTGGGTTTCC 60.294 42.308 0.00 0.00 0.00 3.13
4181 5617 9.956640 AGAATATGAGTCAAGAACTGAAGAAAT 57.043 29.630 0.00 0.00 38.74 2.17
4247 5685 3.127548 GTCAATACCAGGTGTTGATGCAG 59.872 47.826 28.78 5.44 43.29 4.41
4307 5746 2.299993 TCGATGGCTTTCTGCTACTG 57.700 50.000 0.00 0.00 42.39 2.74
4369 5818 5.762179 TGATGGTGTATCTGGAAAGTTCT 57.238 39.130 0.00 0.00 36.71 3.01
4370 5819 5.734720 TGATGGTGTATCTGGAAAGTTCTC 58.265 41.667 0.00 0.00 36.71 2.87
4371 5820 5.248248 TGATGGTGTATCTGGAAAGTTCTCA 59.752 40.000 0.00 0.00 36.71 3.27
4447 5947 6.895756 ACTGATACAAGGTATCCAGTCTACAA 59.104 38.462 12.44 0.00 0.00 2.41
4451 5951 6.227298 ACAAGGTATCCAGTCTACAATCTG 57.773 41.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 1.747355 GAATTGCCATGTGACCTCTGG 59.253 52.381 0.00 0.00 0.00 3.86
194 195 1.725557 GCTGGACATGCATCTGCTGG 61.726 60.000 0.00 0.00 42.66 4.85
216 217 2.979678 TGAGGAAAGGAGCAGTTTACCT 59.020 45.455 0.00 0.00 35.36 3.08
283 320 0.527565 GGCATCGGTGTTTCTTGCAT 59.472 50.000 0.00 0.00 35.04 3.96
351 388 2.766313 TCACGCATGAGCTTTAGTTGT 58.234 42.857 0.00 0.00 39.10 3.32
363 400 6.732531 ATATCCTTAACATCATCACGCATG 57.267 37.500 0.00 0.00 0.00 4.06
464 502 1.633432 TGGTCCCTCCCATACAGTTTG 59.367 52.381 0.00 0.00 34.77 2.93
572 610 6.174720 TGTATCATAGTTGTCTTCCCCATC 57.825 41.667 0.00 0.00 0.00 3.51
632 670 5.526479 CACACATATCCAAATCCTGACTGAG 59.474 44.000 0.00 0.00 0.00 3.35
908 947 6.428083 TTGTCCTCAGTAATCTACCAACAA 57.572 37.500 0.00 0.00 0.00 2.83
1320 1556 6.564125 GCTTAATTTCTACCGATCCAACATCG 60.564 42.308 0.00 0.00 40.86 3.84
1495 1749 7.499232 CCCGAGAAAATCACCAAATATCTTAGT 59.501 37.037 0.00 0.00 0.00 2.24
1588 1842 3.068590 AGGTGCACAAGTCCTGAAAAATG 59.931 43.478 20.43 0.00 0.00 2.32
1624 1878 8.557450 AGAGATGTTAATTGGTAAACACCCTAT 58.443 33.333 0.00 0.00 38.35 2.57
1677 1955 4.081420 CCACTGCTAGACCATGACTTAAGT 60.081 45.833 8.13 8.13 0.00 2.24
1702 2139 2.807967 TGCTCGTGTCTTCAGGAAAATG 59.192 45.455 0.00 0.00 37.88 2.32
1971 2412 3.701040 CCCAATCCAATGTTAACCTCCTG 59.299 47.826 2.48 0.00 0.00 3.86
2010 2454 0.742281 CTTCCACACCAGGCTCATCG 60.742 60.000 0.00 0.00 0.00 3.84
2312 3038 7.370383 TGATTTTGAGTATGCAAACCTCTTTC 58.630 34.615 10.72 4.92 37.48 2.62
2377 3103 3.490348 ACACTTGGTCTAAGCTTTGCAT 58.510 40.909 3.20 0.00 40.16 3.96
2404 3130 6.390721 TCTCAAGACCTGTTTCTTTATCGAG 58.609 40.000 0.00 0.00 33.31 4.04
2447 3173 1.478654 GCTTCAACTCCAAAGGTGGGA 60.479 52.381 0.00 0.00 46.01 4.37
2489 3215 3.849911 TGCCTTAGAATCAGTGTCTTCG 58.150 45.455 0.00 0.00 0.00 3.79
2503 3229 2.706339 AGACCAGCTGAATGCCTTAG 57.294 50.000 17.39 0.00 44.23 2.18
2589 3333 5.393027 CCAACTATTACCATTCAAGTGGCAC 60.393 44.000 10.29 10.29 43.27 5.01
2683 3430 3.056322 ACCCGTACTACCAGCTGTTTTAG 60.056 47.826 13.81 12.11 0.00 1.85
2701 3508 1.278238 GTTTGTCGCAGATCTACCCG 58.722 55.000 0.00 0.00 40.67 5.28
2706 3513 2.005451 GATGCTGTTTGTCGCAGATCT 58.995 47.619 0.00 0.00 40.67 2.75
3059 4153 1.379044 AATTCCTTGAGCTGGCCGG 60.379 57.895 7.41 7.41 0.00 6.13
3137 4231 1.192146 TCCTCCTTCAACACCCTCGG 61.192 60.000 0.00 0.00 0.00 4.63
3138 4232 0.247736 CTCCTCCTTCAACACCCTCG 59.752 60.000 0.00 0.00 0.00 4.63
3175 4269 1.368850 GCAGCGTGGACGAAACAAC 60.369 57.895 2.73 0.00 43.02 3.32
3319 4413 1.743252 GAAGGGCGTCCTCTTGCTG 60.743 63.158 10.20 0.00 44.07 4.41
3338 4432 2.520741 GGAGGGAGGAGAGGAGCG 60.521 72.222 0.00 0.00 0.00 5.03
3436 4579 4.689612 TCTAGCTTTTCCAGTGACTTGT 57.310 40.909 0.00 0.00 0.00 3.16
3526 4672 5.102953 TGTTACCTTGGATCATCCTCTTG 57.897 43.478 4.96 0.00 37.46 3.02
3598 4744 6.544197 TGGGAATAAATGCAGCGTTATTAAGA 59.456 34.615 11.89 0.49 31.60 2.10
3608 4754 4.039488 TCATTGGATGGGAATAAATGCAGC 59.961 41.667 0.00 0.00 0.00 5.25
3647 4793 3.612860 CGAAGAATGTACAAGGGAACTCG 59.387 47.826 0.00 0.00 42.68 4.18
3669 4815 1.415200 ATAGGGCTCGAAGGGAACTC 58.585 55.000 0.00 0.00 42.68 3.01
3671 4817 2.036089 CACTATAGGGCTCGAAGGGAAC 59.964 54.545 4.43 0.00 0.00 3.62
3672 4818 2.317040 CACTATAGGGCTCGAAGGGAA 58.683 52.381 4.43 0.00 0.00 3.97
3673 4819 1.996798 CACTATAGGGCTCGAAGGGA 58.003 55.000 4.43 0.00 0.00 4.20
3674 4820 0.318762 GCACTATAGGGCTCGAAGGG 59.681 60.000 20.08 0.00 0.00 3.95
3675 4821 1.271102 GAGCACTATAGGGCTCGAAGG 59.729 57.143 34.90 1.65 46.01 3.46
3676 4822 2.715737 GAGCACTATAGGGCTCGAAG 57.284 55.000 34.90 0.00 46.01 3.79
3687 4833 4.406972 TGTATGGAAAGAGCAGAGCACTAT 59.593 41.667 0.00 0.00 0.00 2.12
3794 4996 7.596749 TTTCATTTTAACTTTTTGTGGCGAA 57.403 28.000 0.00 0.00 0.00 4.70
4040 5469 7.340232 TGCAAATATGAAGAAGCCTACAAGATT 59.660 33.333 0.00 0.00 0.00 2.40
4099 5529 6.675413 AATTACACAAGTAGACCTACCACA 57.325 37.500 3.74 0.00 36.75 4.17
4220 5658 6.677920 GCATCAACACCTGGTATTGACAATAC 60.678 42.308 21.82 24.34 42.36 1.89
4247 5685 4.397417 ACAGCAAGCCATCAGAAATTAGAC 59.603 41.667 0.00 0.00 0.00 2.59
4369 5818 1.614996 ATCGGTGGCAAAACACATGA 58.385 45.000 0.00 0.00 43.08 3.07
4370 5819 3.500982 CTTATCGGTGGCAAAACACATG 58.499 45.455 0.00 0.00 43.08 3.21
4371 5820 2.491693 CCTTATCGGTGGCAAAACACAT 59.508 45.455 0.00 0.00 43.08 3.21
4408 5908 9.696572 ACCTTGTATCAGTAGAATGTAGACTTA 57.303 33.333 0.00 0.00 0.00 2.24
4409 5909 8.596781 ACCTTGTATCAGTAGAATGTAGACTT 57.403 34.615 0.00 0.00 0.00 3.01
4430 5930 4.965532 AGCAGATTGTAGACTGGATACCTT 59.034 41.667 0.00 0.00 35.05 3.50
4433 5933 5.521906 TCAGCAGATTGTAGACTGGATAC 57.478 43.478 0.00 0.00 35.05 2.24


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

AutoCloner maintained by Alex Coulton.