Multiple sequence alignment - TraesCS7D01G499600

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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 TraesCS7D01G499600 chr7D 100.000 5934 0 0 1 5934 606105900 606111833 0.000000e+00 10959.0
1 TraesCS7D01G499600 chr7D 94.186 4730 234 15 1223 5925 606011018 606015733 0.000000e+00 7173.0
2 TraesCS7D01G499600 chr7D 92.601 3798 244 18 2164 5934 605957465 605961252 0.000000e+00 5422.0
3 TraesCS7D01G499600 chr7D 90.651 3134 252 26 2203 5328 606182717 606185817 0.000000e+00 4126.0
4 TraesCS7D01G499600 chr7D 89.732 3019 248 23 1273 4275 606302028 606305000 0.000000e+00 3801.0
5 TraesCS7D01G499600 chr7D 94.121 1633 77 8 590 2214 606180815 606182436 0.000000e+00 2466.0
6 TraesCS7D01G499600 chr7D 93.862 896 48 2 1278 2172 605947619 605948508 0.000000e+00 1343.0
7 TraesCS7D01G499600 chr7D 88.878 1025 97 13 4309 5328 606305004 606306016 0.000000e+00 1245.0
8 TraesCS7D01G499600 chr7D 89.223 566 32 6 620 1164 605947013 605947570 0.000000e+00 680.0
9 TraesCS7D01G499600 chr7D 94.326 423 23 1 1 422 606179709 606180131 0.000000e+00 647.0
10 TraesCS7D01G499600 chr7D 90.930 430 30 5 1 422 606300548 606300976 2.400000e-158 569.0
11 TraesCS7D01G499600 chr7D 90.955 398 33 3 1 396 605969934 605970330 3.150000e-147 532.0
12 TraesCS7D01G499600 chr7D 88.084 428 38 8 1 422 605946029 605946449 4.130000e-136 496.0
13 TraesCS7D01G499600 chr7D 89.037 301 23 7 866 1164 606010719 606011011 1.220000e-96 364.0
14 TraesCS7D01G499600 chr7D 96.491 171 6 0 421 591 606180563 606180733 3.500000e-72 283.0
15 TraesCS7D01G499600 chr7D 90.909 143 9 2 695 836 606301570 606301709 7.850000e-44 189.0
16 TraesCS7D01G499600 chr7D 98.214 56 1 0 591 646 605946963 605947018 1.360000e-16 99.0
17 TraesCS7D01G499600 chr7A 92.302 4352 265 33 1223 5565 697823815 697828105 0.000000e+00 6117.0
18 TraesCS7D01G499600 chr7A 92.229 3603 233 22 1223 4816 697878462 697882026 0.000000e+00 5059.0
19 TraesCS7D01G499600 chr7A 92.112 3423 225 22 1223 4635 697976020 697979407 0.000000e+00 4783.0
20 TraesCS7D01G499600 chr7A 93.583 935 54 3 4631 5563 697981514 697982444 0.000000e+00 1389.0
21 TraesCS7D01G499600 chr7A 90.108 930 84 5 4478 5404 698131758 698132682 0.000000e+00 1201.0
22 TraesCS7D01G499600 chr7A 92.414 580 37 4 4986 5563 697882028 697882602 0.000000e+00 821.0
23 TraesCS7D01G499600 chr7A 89.286 588 42 13 590 1164 697877876 697878455 0.000000e+00 717.0
24 TraesCS7D01G499600 chr7A 88.644 590 42 15 590 1164 697975434 697976013 0.000000e+00 695.0
25 TraesCS7D01G499600 chr7A 89.945 547 35 5 620 1164 697823280 697823808 0.000000e+00 688.0
26 TraesCS7D01G499600 chr7A 89.421 397 19 2 5560 5934 697830345 697830740 4.160000e-131 479.0
27 TraesCS7D01G499600 chr7A 87.838 296 12 3 5560 5833 697984684 697984977 5.730000e-85 326.0
28 TraesCS7D01G499600 chr7A 95.536 112 5 0 5823 5934 697886045 697886156 4.720000e-41 180.0
29 TraesCS7D01G499600 chr7A 95.699 93 4 0 5842 5934 697985792 697985884 3.700000e-32 150.0
30 TraesCS7D01G499600 chr7B 89.172 4119 392 28 1223 5328 690094533 690098610 0.000000e+00 5086.0
31 TraesCS7D01G499600 chr7B 89.197 3962 375 28 1379 5328 690080898 690084818 0.000000e+00 4896.0
32 TraesCS7D01G499600 chr7B 88.892 3295 320 26 2044 5328 690031465 690034723 0.000000e+00 4015.0
33 TraesCS7D01G499600 chr7B 92.068 1185 82 5 1223 2401 690119994 690121172 0.000000e+00 1657.0
34 TraesCS7D01G499600 chr7B 88.683 1025 96 13 4309 5328 690202870 690203879 0.000000e+00 1232.0
35 TraesCS7D01G499600 chr7B 92.317 794 49 4 1223 2010 690030409 690031196 0.000000e+00 1118.0
36 TraesCS7D01G499600 chr7B 91.529 425 32 4 1 422 690183289 690183712 3.080000e-162 582.0
37 TraesCS7D01G499600 chr7B 91.121 428 34 4 1 425 690091811 690092237 1.430000e-160 577.0
38 TraesCS7D01G499600 chr7B 90.888 428 34 5 1 425 690117275 690117700 2.400000e-158 569.0
39 TraesCS7D01G499600 chr7B 89.499 419 41 3 1 417 690028787 690029204 1.460000e-145 527.0
40 TraesCS7D01G499600 chr7B 90.881 329 22 3 837 1164 690030081 690030402 9.130000e-118 435.0
41 TraesCS7D01G499600 chr7B 88.926 298 25 6 866 1162 690094234 690094524 1.570000e-95 361.0
42 TraesCS7D01G499600 chr7B 88.591 298 26 6 866 1162 690119695 690119985 7.310000e-94 355.0
43 TraesCS7D01G499600 chr7B 81.897 232 25 11 611 830 690094002 690094228 4.720000e-41 180.0
44 TraesCS7D01G499600 chr7B 81.897 232 25 11 611 830 690119463 690119689 4.720000e-41 180.0
45 TraesCS7D01G499600 chr7B 97.468 79 1 1 620 697 690030005 690030083 3.730000e-27 134.0
46 TraesCS7D01G499600 chr7B 95.833 72 3 0 420 491 690093935 690094006 3.760000e-22 117.0
47 TraesCS7D01G499600 chr7B 95.890 73 2 1 420 491 690119395 690119467 3.760000e-22 117.0
48 TraesCS7D01G499600 chr7B 98.113 53 1 0 591 643 690029934 690029986 6.330000e-15 93.5
49 TraesCS7D01G499600 chr3D 90.090 333 30 3 61 392 549371038 549371368 4.250000e-116 429.0
50 TraesCS7D01G499600 chr3A 89.720 321 30 3 61 380 686713290 686713608 1.990000e-109 407.0
51 TraesCS7D01G499600 chrUn 81.897 232 25 11 611 830 477661784 477662010 4.720000e-41 180.0
52 TraesCS7D01G499600 chrUn 94.595 37 2 0 455 491 477661752 477661788 2.310000e-04 58.4


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 TraesCS7D01G499600 chr7D 606105900 606111833 5933 False 10959.00 10959 100.000000 1 5934 1 chr7D.!!$F3 5933
1 TraesCS7D01G499600 chr7D 605957465 605961252 3787 False 5422.00 5422 92.601000 2164 5934 1 chr7D.!!$F1 3770
2 TraesCS7D01G499600 chr7D 606010719 606015733 5014 False 3768.50 7173 91.611500 866 5925 2 chr7D.!!$F5 5059
3 TraesCS7D01G499600 chr7D 606179709 606185817 6108 False 1880.50 4126 93.897250 1 5328 4 chr7D.!!$F6 5327
4 TraesCS7D01G499600 chr7D 606300548 606306016 5468 False 1451.00 3801 90.112250 1 5328 4 chr7D.!!$F7 5327
5 TraesCS7D01G499600 chr7D 605946029 605948508 2479 False 654.50 1343 92.345750 1 2172 4 chr7D.!!$F4 2171
6 TraesCS7D01G499600 chr7A 697823280 697830740 7460 False 2428.00 6117 90.556000 620 5934 3 chr7A.!!$F2 5314
7 TraesCS7D01G499600 chr7A 697877876 697886156 8280 False 1694.25 5059 92.366250 590 5934 4 chr7A.!!$F3 5344
8 TraesCS7D01G499600 chr7A 697975434 697985884 10450 False 1468.60 4783 91.575200 590 5934 5 chr7A.!!$F4 5344
9 TraesCS7D01G499600 chr7A 698131758 698132682 924 False 1201.00 1201 90.108000 4478 5404 1 chr7A.!!$F1 926
10 TraesCS7D01G499600 chr7B 690080898 690084818 3920 False 4896.00 4896 89.197000 1379 5328 1 chr7B.!!$F1 3949
11 TraesCS7D01G499600 chr7B 690091811 690098610 6799 False 1264.20 5086 89.389800 1 5328 5 chr7B.!!$F5 5327
12 TraesCS7D01G499600 chr7B 690202870 690203879 1009 False 1232.00 1232 88.683000 4309 5328 1 chr7B.!!$F3 1019
13 TraesCS7D01G499600 chr7B 690028787 690034723 5936 False 1053.75 4015 92.861667 1 5328 6 chr7B.!!$F4 5327
14 TraesCS7D01G499600 chr7B 690117275 690121172 3897 False 575.60 1657 89.866800 1 2401 5 chr7B.!!$F6 2400

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
234 237 0.039978 ACTCTTGTCGACTGCACTCG 60.040 55.000 17.92 9.2 34.83 4.18 F
1319 3401 0.320683 CTGTGACGGATGCCAAGACA 60.321 55.000 0.00 0.0 0.00 3.41 F
1409 3491 1.003233 GGACGGCTTCAAGCTCCTT 60.003 57.895 9.83 0.0 41.99 3.36 F
2251 4904 1.403116 CCACTACGTATGTGTTCGGCA 60.403 52.381 17.87 0.0 33.92 5.69 F
2647 5310 3.038788 TCTACAATCGTGCAGCTTTGA 57.961 42.857 8.87 0.0 0.00 2.69 F
4030 6706 1.205655 AGCGTGCATCTCACATACACT 59.794 47.619 0.00 0.0 45.92 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 3838 0.381089 CACTTCCGCTCTACTACCCG 59.619 60.000 0.00 0.0 0.00 5.28 R
2251 4904 0.034186 ACGTCCATCAATGCACCCAT 60.034 50.000 0.00 0.0 0.00 4.00 R
2780 5446 0.971386 CCCCAGCAATGTTTTGAGCT 59.029 50.000 0.00 0.0 37.95 4.09 R
3481 6154 0.667487 TCGCACTCTTGGCTTCTTCG 60.667 55.000 0.00 0.0 0.00 3.79 R
4418 7096 1.273048 GCTGCCATTGGAACATTGTCA 59.727 47.619 6.95 0.0 39.30 3.58 R
5727 14564 0.178068 TCCCGCAGCTAGATTGGAAC 59.822 55.000 0.00 0.0 0.00 3.62 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
71 74 4.507710 TGGAAGGACTCTCATTTCAATCG 58.492 43.478 0.00 0.00 0.00 3.34
98 101 5.870978 AGAAGTGAATTGCCAATTATTGTGC 59.129 36.000 1.95 7.64 0.00 4.57
223 226 8.961294 TTCGTAGAACTTGTATTACTCTTGTC 57.039 34.615 0.00 0.00 45.90 3.18
224 227 7.239271 TCGTAGAACTTGTATTACTCTTGTCG 58.761 38.462 0.00 0.00 0.00 4.35
234 237 0.039978 ACTCTTGTCGACTGCACTCG 60.040 55.000 17.92 9.20 34.83 4.18
252 255 7.324935 TGCACTCGAAATAAGGTTAGTGATAA 58.675 34.615 0.00 0.00 37.18 1.75
300 307 3.879892 GGAAGAACTATGACCTGGATTGC 59.120 47.826 0.00 0.00 0.00 3.56
417 427 7.228108 GGAAAAAGTATAGGTAACCTATGCACC 59.772 40.741 3.64 1.92 46.76 5.01
483 2398 1.040339 TGCCCGTGGTTTTGCTTTCT 61.040 50.000 0.00 0.00 0.00 2.52
999 3066 1.167781 TTCGGAAAACAACGGCCTCC 61.168 55.000 0.00 0.00 0.00 4.30
1104 3173 1.739562 CTGCGTCTGCCTCAAGGTC 60.740 63.158 0.00 0.00 41.78 3.85
1170 3245 5.884232 TCTTGAATCTTGATCCCTTGTGATG 59.116 40.000 0.00 0.00 0.00 3.07
1175 3250 6.923199 ATCTTGATCCCTTGTGATGTTTTT 57.077 33.333 0.00 0.00 0.00 1.94
1190 3265 9.955208 TGTGATGTTTTTGATATATGAATGCTC 57.045 29.630 0.00 0.00 0.00 4.26
1204 3279 6.630444 ATGAATGCTCTTTGCGATTAGAAT 57.370 33.333 0.00 0.00 46.63 2.40
1220 3295 9.076596 GCGATTAGAATAATGCTTTCTTTTTGT 57.923 29.630 0.00 0.00 35.19 2.83
1319 3401 0.320683 CTGTGACGGATGCCAAGACA 60.321 55.000 0.00 0.00 0.00 3.41
1321 3403 1.021390 GTGACGGATGCCAAGACAGG 61.021 60.000 0.00 0.00 0.00 4.00
1361 3443 1.402588 GGGAAGGAGAAGTTCGACGTC 60.403 57.143 5.18 5.18 0.00 4.34
1409 3491 1.003233 GGACGGCTTCAAGCTCCTT 60.003 57.895 9.83 0.00 41.99 3.36
1570 3657 4.874966 CACTGAGAGGACATTCATTCCTTC 59.125 45.833 0.00 0.00 44.03 3.46
1606 3693 7.860373 GTGAGATCCTATATATTCAGCACGATC 59.140 40.741 0.00 0.00 0.00 3.69
1621 3708 4.396166 AGCACGATCTTAGGAAACCAAATG 59.604 41.667 0.00 0.00 0.00 2.32
1652 3739 3.372822 CGCCACACTCACCGTATTTTTAT 59.627 43.478 0.00 0.00 0.00 1.40
1763 3854 2.123428 GCCGGGTAGTAGAGCGGAA 61.123 63.158 2.18 0.00 0.00 4.30
1922 4018 1.906574 GTGGACAGGGTAGGATGTGAA 59.093 52.381 0.00 0.00 0.00 3.18
1929 4025 6.352737 GGACAGGGTAGGATGTGAATTAAGAA 60.353 42.308 0.00 0.00 0.00 2.52
1991 4110 8.941995 TGTCTTTAGTATGCTAGAGATATGGT 57.058 34.615 13.05 0.00 39.58 3.55
1992 4111 9.015367 TGTCTTTAGTATGCTAGAGATATGGTC 57.985 37.037 13.05 2.13 39.58 4.02
2251 4904 1.403116 CCACTACGTATGTGTTCGGCA 60.403 52.381 17.87 0.00 33.92 5.69
2562 5217 8.667592 AAAACTACTTACTCCTGAGAATACCT 57.332 34.615 0.22 0.00 0.00 3.08
2621 5284 8.204836 AGATATGTTGAGTAGGTTAACCATGTC 58.795 37.037 26.26 17.85 38.89 3.06
2636 5299 9.395707 GTTAACCATGTCTAGTATCTACAATCG 57.604 37.037 0.00 0.00 0.00 3.34
2647 5310 3.038788 TCTACAATCGTGCAGCTTTGA 57.961 42.857 8.87 0.00 0.00 2.69
2757 5423 9.502091 AATAAAATACTTCAGATAATGGCGCTA 57.498 29.630 7.64 0.00 0.00 4.26
2883 5549 6.681729 TCTTCAGGTTCACCAGTACTTAAT 57.318 37.500 0.00 0.00 38.89 1.40
2933 5599 8.807948 ATAATATGGTGTTATGATGGGTTAGC 57.192 34.615 0.00 0.00 0.00 3.09
2955 5621 6.165577 AGCCATTGTGTCATGGTTATTTTTC 58.834 36.000 1.78 0.00 40.02 2.29
3018 5684 7.116819 GTGAATGTTTTTCCTTTTAGTTTGCG 58.883 34.615 0.00 0.00 0.00 4.85
3027 5693 4.641094 TCCTTTTAGTTTGCGTTGGAAAGA 59.359 37.500 0.00 0.00 0.00 2.52
3201 5874 6.176014 AGTACTGAACTCCAAAGCTAAGTT 57.824 37.500 0.00 0.00 36.00 2.66
3337 6010 3.425577 AAACATATGGCAGCATGTTCG 57.574 42.857 22.90 0.00 42.93 3.95
3481 6154 1.224592 CACAGGCATCCACTACCCC 59.775 63.158 0.00 0.00 0.00 4.95
3498 6171 1.301677 CCCGAAGAAGCCAAGAGTGC 61.302 60.000 0.00 0.00 0.00 4.40
3513 6186 2.234661 AGAGTGCGATGGACAATTGAGA 59.765 45.455 13.59 0.00 0.00 3.27
3702 6375 2.898729 ATGTCGATTGCCTCACTAGG 57.101 50.000 0.00 0.00 46.76 3.02
3838 6513 8.194769 AGCTTTTATTTTTGGGGTAACATATCG 58.805 33.333 0.00 0.00 39.74 2.92
3881 6556 4.212636 ACCTAGCATGAAAACGTGTGTAAC 59.787 41.667 0.00 0.00 37.35 2.50
3883 6558 4.893424 AGCATGAAAACGTGTGTAACTT 57.107 36.364 0.00 0.00 38.04 2.66
3967 6643 2.969821 TAACCCATGCAACACTTCCT 57.030 45.000 0.00 0.00 0.00 3.36
3977 6653 6.146021 CCATGCAACACTTCCTGTTATTTTTC 59.854 38.462 0.00 0.00 41.50 2.29
3990 6666 6.209391 CCTGTTATTTTTCTTCCCACATGTCT 59.791 38.462 0.00 0.00 0.00 3.41
4023 6699 1.434622 CCCATGAGCGTGCATCTCAC 61.435 60.000 19.56 0.00 42.63 3.51
4030 6706 1.205655 AGCGTGCATCTCACATACACT 59.794 47.619 0.00 0.00 45.92 3.55
4039 6715 9.065871 GTGCATCTCACATACACTTTTATTTTC 57.934 33.333 0.00 0.00 44.98 2.29
4122 6800 3.622612 TGATGCATGTGTAAGATGGAACG 59.377 43.478 2.46 0.00 42.14 3.95
4123 6801 3.326836 TGCATGTGTAAGATGGAACGA 57.673 42.857 0.00 0.00 34.33 3.85
4191 6869 1.841556 TGGGGTGTGTCCTCAGGTC 60.842 63.158 0.00 0.00 42.62 3.85
4249 6927 2.223829 CGGGTCACTTAGGTCAGCATAG 60.224 54.545 0.00 0.00 0.00 2.23
4401 7079 2.565841 CTGGCAACCCAAGCTCTATAC 58.434 52.381 0.00 0.00 41.58 1.47
4406 7084 4.040461 GGCAACCCAAGCTCTATACTGATA 59.960 45.833 0.00 0.00 0.00 2.15
4418 7096 9.736414 AGCTCTATACTGATATTGAATGCAAAT 57.264 29.630 0.00 0.00 37.59 2.32
4457 7135 2.102588 AGCACCTCAGTTCGTTTACAGT 59.897 45.455 0.00 0.00 0.00 3.55
4588 7266 2.867109 ACAGGAAGAACATCAGTGGG 57.133 50.000 0.00 0.00 0.00 4.61
4597 7275 1.153208 CATCAGTGGGAGAGGCTGC 60.153 63.158 0.00 0.00 0.00 5.25
4668 9457 0.604243 TGGTTTCGTCCCATTGACCG 60.604 55.000 0.00 0.00 41.18 4.79
4686 9475 1.575244 CGAGATGCATGATGTCGGTT 58.425 50.000 2.46 0.00 42.68 4.44
4735 9524 3.446442 AGGAACAATGGATCAGCAAGT 57.554 42.857 0.00 0.00 0.00 3.16
4955 9744 9.174166 GATAATGACACTTATGTTGGTTAACCT 57.826 33.333 24.78 7.74 39.95 3.50
5265 10062 3.073062 GTGCCCCTATCTATGACATGGTT 59.927 47.826 0.00 0.00 0.00 3.67
5405 10204 5.806366 AAATTAGAAATACCCGACCGTTG 57.194 39.130 0.00 0.00 0.00 4.10
5414 10213 7.935210 AGAAATACCCGACCGTTGATTTAATAT 59.065 33.333 0.00 0.00 0.00 1.28
5452 10251 7.714377 ACAGCCATTAGATCTGATTTAAGTGAG 59.286 37.037 5.18 0.00 0.00 3.51
5484 10283 7.807977 ATACAGCCATTAGTTTCGATTCAAT 57.192 32.000 0.00 0.00 0.00 2.57
5538 10337 1.696884 GAGATCCTCCTTCACCCCATC 59.303 57.143 0.00 0.00 0.00 3.51
5597 14411 2.071778 ACCCACCATGCCATTATGAC 57.928 50.000 0.00 0.00 0.00 3.06
5631 14445 1.720077 CCCCTCCCCTATTGCCTTCC 61.720 65.000 0.00 0.00 0.00 3.46
5716 14553 1.067060 TCACCGTCGGACATGATCATC 59.933 52.381 20.51 0.00 0.00 2.92
5727 14564 3.646946 ACATGATCATCGTTCCATCTCG 58.353 45.455 4.86 0.00 0.00 4.04
5925 15568 5.769484 TGTAAAGCACGGAAATACCAAAA 57.231 34.783 0.00 0.00 38.90 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 74 7.487189 CACAATAATTGGCAATTCACTTCTCTC 59.513 37.037 27.42 0.00 34.12 3.20
98 101 3.198635 ACAACTACCATGGAGTCCATCTG 59.801 47.826 22.36 17.60 43.15 2.90
223 226 2.607187 ACCTTATTTCGAGTGCAGTCG 58.393 47.619 33.09 33.09 41.51 4.18
224 227 5.062308 CACTAACCTTATTTCGAGTGCAGTC 59.938 44.000 11.77 11.77 0.00 3.51
252 255 4.576330 ACCCTTGCAAACTTAGCTAGAT 57.424 40.909 0.00 0.00 37.07 1.98
300 307 3.415457 AAGAAGCTGAAGGTCCTGAAG 57.585 47.619 0.00 0.00 0.00 3.02
399 409 5.900699 TGTTCTGGTGCATAGGTTACCTATA 59.099 40.000 22.03 6.69 44.19 1.31
417 427 8.464770 TTGTTCTTTTCTCAACAAATGTTCTG 57.535 30.769 0.00 0.00 39.10 3.02
483 2398 4.090588 GCCGTCGGTCCATGGGAA 62.091 66.667 13.02 0.00 31.38 3.97
563 2478 2.162319 TGTGTTCATGCGCTACTTGA 57.838 45.000 9.73 3.79 0.00 3.02
571 2486 1.082169 CCGTGGTTGTGTTCATGCG 60.082 57.895 0.00 0.00 0.00 4.73
999 3066 1.543944 GCCTTTTGTCCCCACCCATG 61.544 60.000 0.00 0.00 0.00 3.66
1104 3173 0.526524 CGCGCAAGAGGTTCTCTAGG 60.527 60.000 8.75 0.00 40.28 3.02
1170 3245 8.474577 CGCAAAGAGCATTCATATATCAAAAAC 58.525 33.333 0.00 0.00 46.13 2.43
1175 3250 7.677454 AATCGCAAAGAGCATTCATATATCA 57.323 32.000 0.00 0.00 46.13 2.15
1190 3265 8.847444 AAGAAAGCATTATTCTAATCGCAAAG 57.153 30.769 0.00 0.00 36.14 2.77
1192 3267 9.638239 AAAAAGAAAGCATTATTCTAATCGCAA 57.362 25.926 0.00 0.00 36.14 4.85
1204 3279 3.056304 GGCGCACAAAAAGAAAGCATTA 58.944 40.909 10.83 0.00 0.00 1.90
1220 3295 2.192664 TTCTAATGGACTTTGGCGCA 57.807 45.000 10.83 0.00 0.00 6.09
1319 3401 1.211456 CCCTGAGAATCTTCAGCCCT 58.789 55.000 4.80 0.00 42.58 5.19
1321 3403 0.813210 CGCCCTGAGAATCTTCAGCC 60.813 60.000 4.80 0.00 42.58 4.85
1549 3631 4.118410 CGAAGGAATGAATGTCCTCTCAG 58.882 47.826 0.00 0.00 45.12 3.35
1570 3657 2.887568 GATCTCACGTGCTGCCCG 60.888 66.667 11.67 2.26 0.00 6.13
1606 3693 3.928375 GCATGTGCATTTGGTTTCCTAAG 59.072 43.478 0.00 0.00 41.59 2.18
1621 3708 3.599792 GAGTGTGGCGTGCATGTGC 62.600 63.158 7.93 3.82 42.50 4.57
1643 3730 9.863845 TTTCGATTTCCCCAAAGATAAAAATAC 57.136 29.630 0.00 0.00 0.00 1.89
1652 3739 4.072131 CACTCTTTCGATTTCCCCAAAGA 58.928 43.478 0.00 0.00 34.47 2.52
1746 3837 0.750911 ACTTCCGCTCTACTACCCGG 60.751 60.000 0.00 0.00 41.97 5.73
1747 3838 0.381089 CACTTCCGCTCTACTACCCG 59.619 60.000 0.00 0.00 0.00 5.28
1748 3839 1.760192 TCACTTCCGCTCTACTACCC 58.240 55.000 0.00 0.00 0.00 3.69
1749 3840 3.548415 CGATTCACTTCCGCTCTACTACC 60.548 52.174 0.00 0.00 0.00 3.18
1763 3854 7.492669 CCTAATTCACTAATGTGTCGATTCACT 59.507 37.037 7.57 0.00 44.14 3.41
1890 3986 0.392998 CTGTCCACTTCCATTCCCCG 60.393 60.000 0.00 0.00 0.00 5.73
1970 4089 9.314133 ACATGACCATATCTCTAGCATACTAAA 57.686 33.333 0.00 0.00 0.00 1.85
1971 4090 8.743714 CACATGACCATATCTCTAGCATACTAA 58.256 37.037 0.00 0.00 0.00 2.24
1972 4091 7.890655 ACACATGACCATATCTCTAGCATACTA 59.109 37.037 0.00 0.00 0.00 1.82
1973 4092 6.723515 ACACATGACCATATCTCTAGCATACT 59.276 38.462 0.00 0.00 0.00 2.12
1974 4093 6.929625 ACACATGACCATATCTCTAGCATAC 58.070 40.000 0.00 0.00 0.00 2.39
1975 4094 7.122799 GGTACACATGACCATATCTCTAGCATA 59.877 40.741 0.00 0.00 36.91 3.14
1976 4095 6.071108 GGTACACATGACCATATCTCTAGCAT 60.071 42.308 0.00 0.00 36.91 3.79
1977 4096 5.243954 GGTACACATGACCATATCTCTAGCA 59.756 44.000 0.00 0.00 36.91 3.49
1978 4097 5.243954 TGGTACACATGACCATATCTCTAGC 59.756 44.000 0.00 0.00 42.15 3.42
1979 4098 6.901081 TGGTACACATGACCATATCTCTAG 57.099 41.667 0.00 0.00 42.15 2.43
2251 4904 0.034186 ACGTCCATCAATGCACCCAT 60.034 50.000 0.00 0.00 0.00 4.00
2600 5260 5.818678 AGACATGGTTAACCTACTCAACA 57.181 39.130 24.78 2.79 36.82 3.33
2621 5284 5.114785 AGCTGCACGATTGTAGATACTAG 57.885 43.478 1.02 0.00 37.65 2.57
2636 5299 3.631145 TCAAAGTCATCAAAGCTGCAC 57.369 42.857 1.02 0.00 0.00 4.57
2647 5310 7.986085 AATTAGTGTGCTAGTTCAAAGTCAT 57.014 32.000 0.00 0.00 0.00 3.06
2780 5446 0.971386 CCCCAGCAATGTTTTGAGCT 59.029 50.000 0.00 0.00 37.95 4.09
2912 5578 4.413851 TGGCTAACCCATCATAACACCATA 59.586 41.667 0.00 0.00 39.18 2.74
3007 5673 7.835634 ATTTTCTTTCCAACGCAAACTAAAA 57.164 28.000 0.00 0.00 0.00 1.52
3201 5874 3.130280 CACTGCATGCCATATGACCTA 57.870 47.619 16.68 0.00 0.00 3.08
3337 6010 3.189287 TGCTTCGGATTTTCTCTTGCTTC 59.811 43.478 0.00 0.00 0.00 3.86
3481 6154 0.667487 TCGCACTCTTGGCTTCTTCG 60.667 55.000 0.00 0.00 0.00 3.79
3498 6171 4.512571 TGTATGCATCTCAATTGTCCATCG 59.487 41.667 0.19 0.00 0.00 3.84
3513 6186 6.780457 AGCTTCCATAAACTTTGTATGCAT 57.220 33.333 3.79 3.79 0.00 3.96
3590 6263 8.462589 AATCCCAAATAGCAACAAATGTTTTT 57.537 26.923 0.00 0.00 35.83 1.94
3632 6305 3.890147 AGCCCCTAGAGTAACGTAATCAG 59.110 47.826 0.00 0.00 0.00 2.90
3670 6343 4.454847 GCAATCGACATTCATCATCTCCAT 59.545 41.667 0.00 0.00 0.00 3.41
3702 6375 4.796830 TGTAGATGACTCGATACGTTTTGC 59.203 41.667 0.00 0.00 0.00 3.68
3708 6381 4.815040 AACCTGTAGATGACTCGATACG 57.185 45.455 0.00 0.00 0.00 3.06
3838 6513 4.765339 AGGTGCATTACTAAACCTTTGACC 59.235 41.667 0.00 0.00 40.14 4.02
3872 6547 7.322699 GGACAAACATGATTAAAGTTACACACG 59.677 37.037 0.00 0.00 0.00 4.49
3947 6622 3.091545 CAGGAAGTGTTGCATGGGTTAT 58.908 45.455 0.00 0.00 0.00 1.89
3967 6643 7.175990 GGTAGACATGTGGGAAGAAAAATAACA 59.824 37.037 1.15 0.00 0.00 2.41
3977 6653 5.359194 AGTAATGGTAGACATGTGGGAAG 57.641 43.478 1.15 0.00 40.44 3.46
3990 6666 4.462834 CGCTCATGGGAGATAGTAATGGTA 59.537 45.833 0.00 0.00 44.26 3.25
4122 6800 6.998968 ACTCTCCTGAATGTTCATGAAATC 57.001 37.500 10.35 9.63 36.46 2.17
4123 6801 7.771927 AAACTCTCCTGAATGTTCATGAAAT 57.228 32.000 10.35 3.66 36.46 2.17
4191 6869 3.781770 GACTCCAGGAGGCGATGCG 62.782 68.421 21.31 0.00 33.35 4.73
4249 6927 3.003480 GACATACTGCTCTGGGTGTTTC 58.997 50.000 0.00 0.00 0.00 2.78
4401 7079 8.642908 ACATTGTCATTTGCATTCAATATCAG 57.357 30.769 0.00 0.00 31.33 2.90
4406 7084 6.231951 TGGAACATTGTCATTTGCATTCAAT 58.768 32.000 0.00 0.00 31.33 2.57
4418 7096 1.273048 GCTGCCATTGGAACATTGTCA 59.727 47.619 6.95 0.00 39.30 3.58
4457 7135 3.484953 ACTAAGGTAGTGATGGGGTCA 57.515 47.619 0.00 0.00 37.69 4.02
4588 7266 3.828875 AGTTAACCATAGCAGCCTCTC 57.171 47.619 0.88 0.00 0.00 3.20
4597 7275 7.994194 ACTAGTTCTTCCGTAGTTAACCATAG 58.006 38.462 0.88 0.00 0.00 2.23
4668 9457 3.120408 GCATAACCGACATCATGCATCTC 60.120 47.826 0.00 0.00 42.61 2.75
4735 9524 1.955778 CATTCAGTTGACCACCAAGCA 59.044 47.619 0.00 0.00 35.03 3.91
4894 9683 5.312708 AGCATCCTCTCCAATGAAATCCTAT 59.687 40.000 0.00 0.00 0.00 2.57
4984 9775 4.164221 TGGCCAATTAAAAGTTCCCAACAA 59.836 37.500 0.61 0.00 0.00 2.83
5265 10062 6.013379 TGTGTCTGATAAATTGGCCCTAAAA 58.987 36.000 0.00 0.00 0.00 1.52
5395 10194 8.592105 TTTAGTATATTAAATCAACGGTCGGG 57.408 34.615 0.00 0.00 0.00 5.14
5473 10272 8.144478 TGGGTTATTTTGTCAATTGAATCGAAA 58.856 29.630 10.35 11.24 0.00 3.46
5481 10280 5.163834 GCATGCTGGGTTATTTTGTCAATTG 60.164 40.000 11.37 0.00 0.00 2.32
5484 10283 3.306641 GGCATGCTGGGTTATTTTGTCAA 60.307 43.478 18.92 0.00 0.00 3.18
5494 10293 2.457813 TCATAATGGCATGCTGGGTT 57.542 45.000 18.92 9.74 0.00 4.11
5538 10337 6.038985 AGTCAAGTCTAATGATGATCACGTG 58.961 40.000 9.94 9.94 0.00 4.49
5575 14389 3.957497 GTCATAATGGCATGGTGGGTAAA 59.043 43.478 0.00 0.00 0.00 2.01
5631 14445 6.594788 TTTTCTCATCAATCTCAAAAGGGG 57.405 37.500 0.00 0.00 0.00 4.79
5716 14553 2.893637 AGATTGGAACGAGATGGAACG 58.106 47.619 0.00 0.00 0.00 3.95
5727 14564 0.178068 TCCCGCAGCTAGATTGGAAC 59.822 55.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.