Multiple sequence alignment - TraesCS3D01G337200

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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 TraesCS3D01G337200 chr3D 100.000 2835 0 0 1 2835 449112288 449115122 0.000000e+00 5236.0
1 TraesCS3D01G337200 chr3D 100.000 2189 0 0 2995 5183 449115282 449117470 0.000000e+00 4043.0
2 TraesCS3D01G337200 chr3D 91.093 247 21 1 2589 2835 449114743 449114988 2.990000e-87 333.0
3 TraesCS3D01G337200 chr3D 91.093 247 21 1 2456 2701 449114876 449115122 2.990000e-87 333.0
4 TraesCS3D01G337200 chr3D 93.694 222 13 1 2995 3215 449114883 449115104 1.080000e-86 331.0
5 TraesCS3D01G337200 chr3D 90.233 215 20 1 3001 3214 449114756 449114970 3.950000e-71 279.0
6 TraesCS3D01G337200 chr3D 90.233 215 20 1 2469 2683 449115288 449115501 3.950000e-71 279.0
7 TraesCS3D01G337200 chr3A 89.569 2924 162 58 2 2835 591575862 591578732 0.000000e+00 3578.0
8 TraesCS3D01G337200 chr3A 91.900 1642 78 20 3252 4884 591579174 591580769 0.000000e+00 2244.0
9 TraesCS3D01G337200 chr3A 89.501 381 37 3 2456 2835 591578486 591578864 3.630000e-131 479.0
10 TraesCS3D01G337200 chr3A 87.696 382 43 4 2456 2835 591578619 591578998 4.760000e-120 442.0
11 TraesCS3D01G337200 chr3A 87.603 363 41 3 2456 2817 591578753 591579112 8.030000e-113 418.0
12 TraesCS3D01G337200 chr3A 90.370 270 15 7 2995 3260 591578892 591579154 1.380000e-90 344.0
13 TraesCS3D01G337200 chr3A 91.129 248 20 2 2589 2835 591578352 591578598 8.320000e-88 335.0
14 TraesCS3D01G337200 chr3A 93.488 215 14 0 2995 3209 591578760 591578974 2.330000e-83 320.0
15 TraesCS3D01G337200 chr3A 92.342 222 16 1 2995 3215 591578493 591578714 1.080000e-81 315.0
16 TraesCS3D01G337200 chr3A 90.278 216 18 3 2995 3208 591578626 591578840 3.950000e-71 279.0
17 TraesCS3D01G337200 chr3A 89.862 217 20 2 3001 3215 591578365 591578581 1.420000e-70 278.0
18 TraesCS3D01G337200 chr3B 89.640 1583 93 27 1 1537 590290388 590291945 0.000000e+00 1949.0
19 TraesCS3D01G337200 chr3B 90.951 1304 82 17 1504 2791 590291960 590293243 0.000000e+00 1722.0
20 TraesCS3D01G337200 chr3B 96.382 995 33 2 3252 4244 590293902 590294895 0.000000e+00 1635.0
21 TraesCS3D01G337200 chr3B 88.366 361 36 5 2456 2815 590293478 590293833 3.710000e-116 429.0
22 TraesCS3D01G337200 chr3B 92.542 295 13 3 4896 5183 590298492 590298784 1.040000e-111 414.0
23 TraesCS3D01G337200 chr3B 91.481 270 15 7 2995 3260 590293617 590293882 1.060000e-96 364.0
24 TraesCS3D01G337200 chr3B 88.814 295 27 5 2542 2835 590293432 590293721 1.770000e-94 357.0
25 TraesCS3D01G337200 chr3B 86.246 349 21 4 4376 4722 590294977 590295300 2.300000e-93 353.0
26 TraesCS3D01G337200 chr3B 93.953 215 11 1 2995 3209 590293485 590293697 1.800000e-84 324.0
27 TraesCS3D01G337200 chr3B 87.805 123 11 3 4918 5037 658387338 658387459 1.950000e-29 141.0
28 TraesCS3D01G337200 chr4B 88.235 119 12 1 4921 5037 175904523 175904405 1.950000e-29 141.0
29 TraesCS3D01G337200 chr7B 88.393 112 11 1 4928 5037 97914684 97914573 3.260000e-27 134.0
30 TraesCS3D01G337200 chr5A 86.585 82 11 0 4921 5002 6263159 6263078 1.990000e-14 91.6


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 TraesCS3D01G337200 chr3D 449112288 449117470 5182 False 1547.714286 5236 93.763714 1 5183 7 chr3D.!!$F1 5182
1 TraesCS3D01G337200 chr3A 591575862 591580769 4907 False 821.090909 3578 90.339818 2 4884 11 chr3A.!!$F1 4882
2 TraesCS3D01G337200 chr3B 590290388 590298784 8396 False 838.555556 1949 90.930556 1 5183 9 chr3B.!!$F2 5182

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
799 853 0.036875 GAGGTCCTGTTTGGTGGGAG 59.963 60.0 0.00 0.0 37.07 4.30 F
1364 1418 0.322726 TGGATGTGGACGACGAGGTA 60.323 55.0 0.00 0.0 0.00 3.08 F
1541 1661 0.464735 ACGATGACGAGGAGGAGGAG 60.465 60.0 0.00 0.0 42.66 3.69 F
2438 2595 0.695347 AGTAGGCCTTCTTTGCAGCT 59.305 50.0 12.58 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1959 0.319405 GGCTGCAGGTTGAGCAAAAT 59.681 50.000 17.12 0.00 42.17 1.82 R
3244 3708 0.249447 TGACACAACAGCCTCTCACG 60.249 55.000 0.00 0.00 0.00 4.35 R
3302 3797 3.904339 AGCCCGTTTAGGACATATCTGAT 59.096 43.478 0.00 0.00 45.00 2.90 R
4369 4870 0.106469 TGTTACAAGGCTTGGCACCA 60.106 50.000 29.26 17.19 34.12 4.17 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
62 63 2.092598 GGGTACCGGATCTCCCTTTA 57.907 55.000 9.46 0.00 40.86 1.85
67 68 2.829023 ACCGGATCTCCCTTTAGTCAA 58.171 47.619 9.46 0.00 0.00 3.18
95 96 3.748568 GCGAAACAAACAGAGAAGGATCT 59.251 43.478 0.00 0.00 39.10 2.75
258 260 1.658686 GGAGTGACCGAGCGACAGAT 61.659 60.000 0.00 0.00 0.00 2.90
285 289 2.170607 ACCCATTAGCTAGCACAACGAT 59.829 45.455 18.83 0.00 0.00 3.73
287 291 3.990469 CCCATTAGCTAGCACAACGATAG 59.010 47.826 18.83 0.00 46.19 2.08
302 306 3.369835 CGATAGGTTTCGTGCAAGTTC 57.630 47.619 0.00 0.00 34.46 3.01
573 621 9.487790 TTGTTCATAAAATGGTCAAGAATTTCC 57.512 29.630 0.00 0.00 0.00 3.13
574 622 8.869109 TGTTCATAAAATGGTCAAGAATTTCCT 58.131 29.630 0.00 0.00 0.00 3.36
655 703 9.636879 CAAAATTTGTTCACTTTTCCCAAAAAT 57.363 25.926 0.00 0.00 34.00 1.82
681 729 7.555087 TGGTCAAAATCTTCAATTGTTGTTCT 58.445 30.769 5.13 0.00 0.00 3.01
787 841 6.687350 CAAAATTTTGTTCCCAGGAGGTCCT 61.687 44.000 20.57 0.00 39.00 3.85
799 853 0.036875 GAGGTCCTGTTTGGTGGGAG 59.963 60.000 0.00 0.00 37.07 4.30
800 854 1.603739 GGTCCTGTTTGGTGGGAGC 60.604 63.158 0.00 0.00 39.81 4.70
810 864 2.202987 GTGGGAGCTGCGATGGAG 60.203 66.667 0.00 0.00 0.00 3.86
823 877 1.135575 CGATGGAGTTTCCTTTGCTGC 60.136 52.381 0.00 0.00 37.46 5.25
836 890 1.234615 TTGCTGCGTGGGCTAACTTC 61.235 55.000 0.00 0.00 40.82 3.01
845 899 3.618997 CGTGGGCTAACTTCTGGTTACAT 60.619 47.826 0.00 0.00 39.17 2.29
846 900 4.382254 CGTGGGCTAACTTCTGGTTACATA 60.382 45.833 0.00 0.00 39.17 2.29
852 906 6.598064 GGCTAACTTCTGGTTACATATGTGTT 59.402 38.462 18.81 12.73 39.77 3.32
868 922 2.292016 TGTGTTTAACGCAACCATCTGG 59.708 45.455 9.02 0.00 35.42 3.86
888 942 0.465642 GGGATGGGCCTAAAGAACGG 60.466 60.000 4.53 0.00 36.66 4.44
1042 1096 2.202756 GATCCTCCGCCACGTCAC 60.203 66.667 0.00 0.00 0.00 3.67
1358 1412 1.375523 GGTGGTGGATGTGGACGAC 60.376 63.158 0.00 0.00 0.00 4.34
1363 1417 1.605451 TGGATGTGGACGACGAGGT 60.605 57.895 0.00 0.00 0.00 3.85
1364 1418 0.322726 TGGATGTGGACGACGAGGTA 60.323 55.000 0.00 0.00 0.00 3.08
1367 1439 1.948145 GATGTGGACGACGAGGTAGAT 59.052 52.381 0.00 0.00 0.00 1.98
1370 1442 1.741706 GTGGACGACGAGGTAGATGAA 59.258 52.381 0.00 0.00 0.00 2.57
1466 1538 2.204090 GGGGTGGAGGGTGAGGAA 60.204 66.667 0.00 0.00 0.00 3.36
1538 1658 1.090625 ACGACGATGACGAGGAGGAG 61.091 60.000 0.00 0.00 42.66 3.69
1541 1661 0.464735 ACGATGACGAGGAGGAGGAG 60.465 60.000 0.00 0.00 42.66 3.69
1654 1774 4.692228 ACTTTCGGTTACGTTTACTCCAA 58.308 39.130 0.00 0.00 41.85 3.53
1735 1855 4.218312 ACATGCTTTCCTCAAAGAAACCT 58.782 39.130 0.00 0.00 41.60 3.50
1775 1895 8.038351 TGTCGATTAATGTGTTTAGATCTGGAA 58.962 33.333 5.18 0.00 0.00 3.53
1926 2048 2.148768 CGTTCAACCTTTACCTGTCCC 58.851 52.381 0.00 0.00 0.00 4.46
1950 2072 4.797471 CCATTGTGTGGTAGTTGACATTG 58.203 43.478 0.00 0.00 43.44 2.82
1958 2080 4.218417 GTGGTAGTTGACATTGAATTGGCT 59.782 41.667 0.00 0.00 0.00 4.75
2047 2169 4.451629 TCCGAGAATAGTCAAGGACAAC 57.548 45.455 3.06 0.00 34.60 3.32
2143 2268 5.282055 TCCATCTGAGCTGTTAACCTATG 57.718 43.478 2.48 0.00 0.00 2.23
2153 2278 3.935203 CTGTTAACCTATGAGCCACACAG 59.065 47.826 2.48 0.00 0.00 3.66
2215 2340 2.359214 CTGTACTAGATCTGCCTTGCGA 59.641 50.000 5.18 0.00 0.00 5.10
2266 2391 8.884124 AAATCTCACTATTTCCCAAAATCTCA 57.116 30.769 0.00 0.00 36.49 3.27
2267 2392 7.872113 ATCTCACTATTTCCCAAAATCTCAC 57.128 36.000 0.00 0.00 36.49 3.51
2268 2393 7.020827 TCTCACTATTTCCCAAAATCTCACT 57.979 36.000 0.00 0.00 36.49 3.41
2269 2394 8.146053 TCTCACTATTTCCCAAAATCTCACTA 57.854 34.615 0.00 0.00 36.49 2.74
2270 2395 8.772250 TCTCACTATTTCCCAAAATCTCACTAT 58.228 33.333 0.00 0.00 36.49 2.12
2271 2396 9.401058 CTCACTATTTCCCAAAATCTCACTATT 57.599 33.333 0.00 0.00 36.49 1.73
2272 2397 9.753674 TCACTATTTCCCAAAATCTCACTATTT 57.246 29.630 0.00 0.00 36.49 1.40
2339 2464 6.538021 GTGCAGATCTGTCAGATTTGATAGTT 59.462 38.462 28.75 2.41 38.65 2.24
2341 2466 6.538021 GCAGATCTGTCAGATTTGATAGTTGT 59.462 38.462 28.75 1.23 38.65 3.32
2433 2590 7.011857 GTCAGATTTGATAGTAGGCCTTCTTTG 59.988 40.741 17.92 4.40 35.39 2.77
2438 2595 0.695347 AGTAGGCCTTCTTTGCAGCT 59.305 50.000 12.58 0.00 0.00 4.24
2489 2647 1.620819 TCAGAGGCTGTTTCTGAGGAC 59.379 52.381 0.00 0.00 44.47 3.85
2558 2716 3.745975 TGATCCAAAGCACTAGTCAAACG 59.254 43.478 0.00 0.00 0.00 3.60
2683 2842 3.054139 TGCCTATCTGATCCAAAGCACTT 60.054 43.478 0.00 0.00 0.00 3.16
2695 2854 3.859386 CCAAAGCACTTGTCAAACACTTC 59.141 43.478 0.00 0.00 32.65 3.01
2718 2877 9.882996 CTTCCATTTTCTTTTCTTTATTTTGCC 57.117 29.630 0.00 0.00 0.00 4.52
2720 2879 7.713073 TCCATTTTCTTTTCTTTATTTTGCCGT 59.287 29.630 0.00 0.00 0.00 5.68
3049 3380 4.569966 CCAGAGCTCTACTATGTTGCAAAG 59.430 45.833 17.75 0.00 35.76 2.77
3076 3407 6.870769 ACTGATTTGCCTATTTGATCCAAAG 58.129 36.000 0.00 0.00 36.76 2.77
3081 3412 7.775053 TTTGCCTATTTGATCCAAAGTACTT 57.225 32.000 1.12 1.12 36.76 2.24
3219 3682 6.491745 CCTATCTGATCCAAAGCACTACTAGA 59.508 42.308 0.00 0.00 0.00 2.43
3370 3865 2.311463 CGTCAGTCTGATCCCCTATGT 58.689 52.381 5.68 0.00 0.00 2.29
3508 4003 9.227777 GATCCCAAACTGTAGTTAAACTGTTAT 57.772 33.333 0.00 0.00 39.65 1.89
3629 4127 0.033920 AGCATCGTTGTGAGCAGTCA 59.966 50.000 0.00 0.00 0.00 3.41
3638 4136 4.905866 CGTTGTGAGCAGTCAAAACTAATG 59.094 41.667 7.26 0.00 45.54 1.90
3640 4138 6.265577 GTTGTGAGCAGTCAAAACTAATGTT 58.734 36.000 2.50 0.00 44.66 2.71
3688 4188 6.046168 AGGAGGAGCTAGGAACTGAATATCTA 59.954 42.308 0.00 0.00 41.52 1.98
3715 4215 2.042831 GCTTGGCCGTGCTGAAGAT 61.043 57.895 11.89 0.00 0.00 2.40
3742 4242 1.466167 CATTCCAGTGACTTTGAGCCG 59.534 52.381 0.00 0.00 0.00 5.52
3769 4269 1.219773 ATGGTGATGGTGCTGAGGAT 58.780 50.000 0.00 0.00 0.00 3.24
3818 4318 2.479566 TGGTGAGGATTCTGTCAAGC 57.520 50.000 0.00 0.00 0.00 4.01
4250 4750 8.842358 ACTAGCTTGCTGTTATTTTACTGTTA 57.158 30.769 5.26 0.00 0.00 2.41
4319 4820 5.554636 CGCTTAGAAGACATTTGCTGTTAG 58.445 41.667 0.00 0.00 38.54 2.34
4320 4821 5.348724 CGCTTAGAAGACATTTGCTGTTAGA 59.651 40.000 0.00 0.00 38.54 2.10
4359 4860 0.776810 TGGATTCCCTCAACAAGCCA 59.223 50.000 0.00 0.00 35.69 4.75
4360 4861 1.146774 TGGATTCCCTCAACAAGCCAA 59.853 47.619 0.00 0.00 35.13 4.52
4361 4862 1.821136 GGATTCCCTCAACAAGCCAAG 59.179 52.381 0.00 0.00 0.00 3.61
4362 4863 2.555227 GGATTCCCTCAACAAGCCAAGA 60.555 50.000 0.00 0.00 0.00 3.02
4363 4864 2.978156 TTCCCTCAACAAGCCAAGAT 57.022 45.000 0.00 0.00 0.00 2.40
4364 4865 4.526970 GATTCCCTCAACAAGCCAAGATA 58.473 43.478 0.00 0.00 0.00 1.98
4365 4866 3.350219 TCCCTCAACAAGCCAAGATAC 57.650 47.619 0.00 0.00 0.00 2.24
4366 4867 2.026262 TCCCTCAACAAGCCAAGATACC 60.026 50.000 0.00 0.00 0.00 2.73
4367 4868 2.290896 CCCTCAACAAGCCAAGATACCA 60.291 50.000 0.00 0.00 0.00 3.25
4368 4869 3.624777 CCTCAACAAGCCAAGATACCAT 58.375 45.455 0.00 0.00 0.00 3.55
4369 4870 4.019174 CCTCAACAAGCCAAGATACCATT 58.981 43.478 0.00 0.00 0.00 3.16
4370 4871 4.142315 CCTCAACAAGCCAAGATACCATTG 60.142 45.833 0.00 0.00 0.00 2.82
4376 4877 2.142356 CCAAGATACCATTGGTGCCA 57.858 50.000 18.83 0.00 41.94 4.92
4377 4878 2.455557 CCAAGATACCATTGGTGCCAA 58.544 47.619 18.83 6.08 41.94 4.52
4378 4879 2.428171 CCAAGATACCATTGGTGCCAAG 59.572 50.000 18.83 5.64 41.94 3.61
4379 4880 1.767759 AGATACCATTGGTGCCAAGC 58.232 50.000 18.83 0.79 39.47 4.01
4380 4881 0.746659 GATACCATTGGTGCCAAGCC 59.253 55.000 18.83 0.00 39.47 4.35
4381 4882 0.336048 ATACCATTGGTGCCAAGCCT 59.664 50.000 18.83 0.00 39.47 4.58
4382 4883 0.114168 TACCATTGGTGCCAAGCCTT 59.886 50.000 18.83 0.00 39.47 4.35
4383 4884 1.294138 CCATTGGTGCCAAGCCTTG 59.706 57.895 9.65 0.00 39.47 3.61
4419 4920 5.762825 ATTCTATAACAGTGCCATTGCTG 57.237 39.130 0.00 0.00 38.71 4.41
4443 4944 2.867109 AGTGTCATGGCTGTTAGCTT 57.133 45.000 0.00 0.00 41.99 3.74
4562 5064 1.561643 TTGGAGATTGAGAGCTCGGT 58.438 50.000 8.37 0.00 39.20 4.69
4587 5089 9.450807 GTGTACACAGATAAAATAAATGGATGC 57.549 33.333 21.14 0.00 0.00 3.91
4588 5090 8.341903 TGTACACAGATAAAATAAATGGATGCG 58.658 33.333 0.00 0.00 0.00 4.73
4598 5100 7.581213 AAATAAATGGATGCGAATTAGGACA 57.419 32.000 0.00 0.00 0.00 4.02
4600 5102 3.845781 ATGGATGCGAATTAGGACACT 57.154 42.857 0.00 0.00 0.00 3.55
4650 5152 3.808036 GCGTCCGGCATGTTATGT 58.192 55.556 0.00 0.00 42.87 2.29
4651 5153 1.641677 GCGTCCGGCATGTTATGTC 59.358 57.895 0.00 0.00 42.87 3.06
4656 5160 0.940126 CCGGCATGTTATGTCAGAGC 59.060 55.000 0.00 0.00 33.60 4.09
4674 5178 1.959848 CTCACGAGTGCACTGGAGA 59.040 57.895 32.20 27.38 0.00 3.71
4694 5198 5.588246 GGAGAAATCCACAGAAATCCTTCTC 59.412 44.000 0.00 0.00 40.05 2.87
4741 5245 3.163594 GTCCTTTGTTTCAATCGCGATG 58.836 45.455 24.47 16.43 0.00 3.84
4748 5252 0.742990 TTCAATCGCGATGGTCACCC 60.743 55.000 24.47 0.00 0.00 4.61
4823 5327 6.397272 AGCATCGATCTCAAATCTAGGATTC 58.603 40.000 0.00 0.00 0.00 2.52
4837 5341 2.472029 AGGATTCGAACTCTGATGGGT 58.528 47.619 0.00 0.00 0.00 4.51
4839 5343 4.030913 AGGATTCGAACTCTGATGGGTTA 58.969 43.478 0.00 0.00 0.00 2.85
4863 5367 1.635817 TACCAGCCAGCCTCCCAATC 61.636 60.000 0.00 0.00 0.00 2.67
4878 8408 5.163519 CCTCCCAATCATTTAACCACATGTC 60.164 44.000 0.00 0.00 0.00 3.06
4886 8416 4.655440 TTTAACCACATGTCGATTCACG 57.345 40.909 0.00 0.00 44.09 4.35
4888 8418 0.391130 ACCACATGTCGATTCACGGG 60.391 55.000 0.00 0.00 42.82 5.28
4926 8491 5.096521 TGGAGATATAGATCAACATGCCCT 58.903 41.667 0.00 0.00 34.17 5.19
4933 8498 2.025981 AGATCAACATGCCCTTGCTACA 60.026 45.455 0.00 0.00 38.71 2.74
4938 8503 1.290203 CATGCCCTTGCTACACTACG 58.710 55.000 0.00 0.00 38.71 3.51
4942 8507 2.005560 GCCCTTGCTACACTACGGAAC 61.006 57.143 0.00 0.00 33.53 3.62
4964 8529 5.617252 ACGAGGAAAGATAAGGAACAACAA 58.383 37.500 0.00 0.00 0.00 2.83
5028 8593 6.986817 AGTTGATAGGTACACATAGCACAATC 59.013 38.462 0.00 0.00 27.86 2.67
5038 8603 5.163764 ACACATAGCACAATCAAACATACGG 60.164 40.000 0.00 0.00 0.00 4.02
5070 8635 4.548346 CGATAAAACGCTTCTTCTAAGCCG 60.548 45.833 4.28 2.90 40.02 5.52
5090 8655 5.694910 AGCCGAACATTTAGAACATATACCG 59.305 40.000 0.00 0.00 0.00 4.02
5111 8676 5.591067 ACCGAATTCTTGTCAAACCTACAAA 59.409 36.000 3.52 0.00 36.46 2.83
5170 8735 7.539712 ACGATGTTGGTCAAATAGTAATCAG 57.460 36.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.690762 GCCTTAGTGGTCTGGGTTGA 59.309 55.000 0.00 0.00 38.35 3.18
50 51 2.158943 CGGGTTGACTAAAGGGAGATCC 60.159 54.545 0.00 0.00 0.00 3.36
62 63 0.179067 TTGTTTCGCTCGGGTTGACT 60.179 50.000 0.00 0.00 0.00 3.41
67 68 0.179067 TCTGTTTGTTTCGCTCGGGT 60.179 50.000 0.00 0.00 0.00 5.28
95 96 5.610791 AGACCTTTCTTTCCCCCTTATCTA 58.389 41.667 0.00 0.00 0.00 1.98
139 141 2.841442 AGGGTTTCTTGTTCCTCTCG 57.159 50.000 0.00 0.00 0.00 4.04
285 289 4.448210 AGAAAGAACTTGCACGAAACCTA 58.552 39.130 0.00 0.00 0.00 3.08
287 291 3.692791 AGAAAGAACTTGCACGAAACC 57.307 42.857 0.00 0.00 0.00 3.27
296 300 5.335661 CCCCAAAACCGATAGAAAGAACTTG 60.336 44.000 0.00 0.00 39.76 3.16
298 302 4.042435 TCCCCAAAACCGATAGAAAGAACT 59.958 41.667 0.00 0.00 39.76 3.01
302 306 3.014623 GGTCCCCAAAACCGATAGAAAG 58.985 50.000 0.00 0.00 39.76 2.62
329 336 9.757227 CATTAAAAACACCATTCAAGAACCTTA 57.243 29.630 0.00 0.00 0.00 2.69
655 703 8.040132 AGAACAACAATTGAAGATTTTGACCAA 58.960 29.630 13.59 0.00 0.00 3.67
787 841 2.410322 ATCGCAGCTCCCACCAAACA 62.410 55.000 0.00 0.00 0.00 2.83
799 853 1.135575 CAAAGGAAACTCCATCGCAGC 60.136 52.381 0.00 0.00 42.68 5.25
800 854 1.135575 GCAAAGGAAACTCCATCGCAG 60.136 52.381 0.00 0.00 42.68 5.18
810 864 1.007387 CCCACGCAGCAAAGGAAAC 60.007 57.895 0.00 0.00 0.00 2.78
823 877 2.289195 TGTAACCAGAAGTTAGCCCACG 60.289 50.000 0.00 0.00 41.63 4.94
836 890 6.171932 TGCGTTAAACACATATGTAACCAG 57.828 37.500 8.32 0.00 38.45 4.00
845 899 4.155099 CCAGATGGTTGCGTTAAACACATA 59.845 41.667 0.00 0.00 39.17 2.29
846 900 3.057596 CCAGATGGTTGCGTTAAACACAT 60.058 43.478 0.00 0.00 39.17 3.21
852 906 0.322997 CCCCCAGATGGTTGCGTTAA 60.323 55.000 0.00 0.00 0.00 2.01
868 922 0.465642 CGTTCTTTAGGCCCATCCCC 60.466 60.000 0.00 0.00 34.51 4.81
1337 1391 1.079127 GTCCACATCCACCACCTCG 60.079 63.158 0.00 0.00 0.00 4.63
1358 1412 1.611491 GCCTCCTCTTCATCTACCTCG 59.389 57.143 0.00 0.00 0.00 4.63
1363 1417 1.757118 CAACCGCCTCCTCTTCATCTA 59.243 52.381 0.00 0.00 0.00 1.98
1364 1418 0.539051 CAACCGCCTCCTCTTCATCT 59.461 55.000 0.00 0.00 0.00 2.90
1367 1439 1.671742 GTCAACCGCCTCCTCTTCA 59.328 57.895 0.00 0.00 0.00 3.02
1370 1442 3.382832 CCGTCAACCGCCTCCTCT 61.383 66.667 0.00 0.00 34.38 3.69
1538 1658 1.424635 CTCGTCGACTTCGTCCTCC 59.575 63.158 14.70 0.00 40.80 4.30
1541 1661 1.424635 CTCCTCGTCGACTTCGTCC 59.575 63.158 14.70 0.00 40.80 4.79
1599 1719 5.394443 GGCATACATTTGAGATGGCAAGAAA 60.394 40.000 14.27 0.00 43.58 2.52
1602 1722 3.973657 GGCATACATTTGAGATGGCAAG 58.026 45.455 14.27 0.00 43.58 4.01
1606 1726 5.067954 TGAGATGGCATACATTTGAGATGG 58.932 41.667 0.00 0.00 40.72 3.51
1617 1737 4.051922 CCGAAAGTACTGAGATGGCATAC 58.948 47.826 0.00 0.00 0.00 2.39
1708 1828 4.191544 TCTTTGAGGAAAGCATGTATCGG 58.808 43.478 0.00 0.00 38.83 4.18
1735 1855 2.432206 TCGACAGCAACGAGAAATCA 57.568 45.000 0.00 0.00 34.85 2.57
1746 1866 7.010460 CAGATCTAAACACATTAATCGACAGCA 59.990 37.037 0.00 0.00 0.00 4.41
1837 1959 0.319405 GGCTGCAGGTTGAGCAAAAT 59.681 50.000 17.12 0.00 42.17 1.82
2047 2169 6.939132 AGTATATCGAAGGGGACATATACG 57.061 41.667 0.00 0.00 38.73 3.06
2143 2268 1.137872 CCCATCTCTACTGTGTGGCTC 59.862 57.143 0.00 0.00 0.00 4.70
2153 2278 4.202305 GGCATATCATAGCCCCATCTCTAC 60.202 50.000 0.00 0.00 45.18 2.59
2188 2313 6.500041 CAAGGCAGATCTAGTACAGTAAGAC 58.500 44.000 0.00 0.00 0.00 3.01
2256 2381 5.945784 TGAGTGGGAAATAGTGAGATTTTGG 59.054 40.000 0.00 0.00 0.00 3.28
2257 2382 6.881065 TCTGAGTGGGAAATAGTGAGATTTTG 59.119 38.462 0.00 0.00 0.00 2.44
2258 2383 7.020827 TCTGAGTGGGAAATAGTGAGATTTT 57.979 36.000 0.00 0.00 0.00 1.82
2259 2384 6.627087 TCTGAGTGGGAAATAGTGAGATTT 57.373 37.500 0.00 0.00 0.00 2.17
2260 2385 6.183361 GGATCTGAGTGGGAAATAGTGAGATT 60.183 42.308 0.00 0.00 0.00 2.40
2261 2386 5.306678 GGATCTGAGTGGGAAATAGTGAGAT 59.693 44.000 0.00 0.00 0.00 2.75
2262 2387 4.651503 GGATCTGAGTGGGAAATAGTGAGA 59.348 45.833 0.00 0.00 0.00 3.27
2263 2388 4.406972 TGGATCTGAGTGGGAAATAGTGAG 59.593 45.833 0.00 0.00 0.00 3.51
2264 2389 4.361783 TGGATCTGAGTGGGAAATAGTGA 58.638 43.478 0.00 0.00 0.00 3.41
2265 2390 4.760530 TGGATCTGAGTGGGAAATAGTG 57.239 45.455 0.00 0.00 0.00 2.74
2266 2391 5.749462 CTTTGGATCTGAGTGGGAAATAGT 58.251 41.667 0.00 0.00 0.00 2.12
2267 2392 4.578105 GCTTTGGATCTGAGTGGGAAATAG 59.422 45.833 0.00 0.00 0.00 1.73
2268 2393 4.526970 GCTTTGGATCTGAGTGGGAAATA 58.473 43.478 0.00 0.00 0.00 1.40
2269 2394 3.359950 GCTTTGGATCTGAGTGGGAAAT 58.640 45.455 0.00 0.00 0.00 2.17
2270 2395 2.555227 GGCTTTGGATCTGAGTGGGAAA 60.555 50.000 0.00 0.00 0.00 3.13
2271 2396 1.004745 GGCTTTGGATCTGAGTGGGAA 59.995 52.381 0.00 0.00 0.00 3.97
2272 2397 0.620556 GGCTTTGGATCTGAGTGGGA 59.379 55.000 0.00 0.00 0.00 4.37
2273 2398 0.329261 TGGCTTTGGATCTGAGTGGG 59.671 55.000 0.00 0.00 0.00 4.61
2339 2464 4.142790 AGTGAGAAACGAGAACTAGGACA 58.857 43.478 0.00 0.00 0.00 4.02
2341 2466 4.395625 TGAGTGAGAAACGAGAACTAGGA 58.604 43.478 0.00 0.00 0.00 2.94
2433 2590 0.321034 TCACACATGGACAGAGCTGC 60.321 55.000 0.00 0.00 0.00 5.25
2438 2595 2.905736 TCTCCAATCACACATGGACAGA 59.094 45.455 0.00 0.00 40.74 3.41
2558 2716 9.333497 GCAAAATAAAGAAATGAAAATGGAAGC 57.667 29.630 0.00 0.00 0.00 3.86
2683 2842 7.610865 AGAAAAGAAAATGGAAGTGTTTGACA 58.389 30.769 0.00 0.00 0.00 3.58
2695 2854 7.798052 CACGGCAAAATAAAGAAAAGAAAATGG 59.202 33.333 0.00 0.00 0.00 3.16
2718 2877 5.409211 CCTCTGATATTCATCATCTCCACG 58.591 45.833 0.00 0.00 40.40 4.94
2720 2879 5.046520 CAGCCTCTGATATTCATCATCTCCA 60.047 44.000 0.00 0.00 40.40 3.86
3049 3380 7.333528 TGGATCAAATAGGCAAATCAGTTAC 57.666 36.000 0.00 0.00 0.00 2.50
3066 3397 8.062065 AGTGTTTGAAAAGTACTTTGGATCAA 57.938 30.769 21.22 21.53 32.36 2.57
3102 3433 6.122277 TCATCTCCTCGGCAAAATAAAGAAT 58.878 36.000 0.00 0.00 0.00 2.40
3244 3708 0.249447 TGACACAACAGCCTCTCACG 60.249 55.000 0.00 0.00 0.00 4.35
3302 3797 3.904339 AGCCCGTTTAGGACATATCTGAT 59.096 43.478 0.00 0.00 45.00 2.90
3539 4037 7.988599 CCAATTATTTGGTGGACAATCATCAAT 59.011 33.333 8.03 0.00 46.27 2.57
3629 4127 6.035843 CAGTGCAAGTGTCAACATTAGTTTT 58.964 36.000 0.00 0.00 31.34 2.43
3644 4142 0.894141 TGCCAAACAACAGTGCAAGT 59.106 45.000 0.00 0.00 0.00 3.16
3715 4215 3.777106 AAGTCACTGGAATGCTCTTCA 57.223 42.857 2.71 0.00 0.00 3.02
3742 4242 2.827921 AGCACCATCACCATTTTCTTCC 59.172 45.455 0.00 0.00 0.00 3.46
3769 4269 4.262938 GCATCATCATCCTCAATCTCCTCA 60.263 45.833 0.00 0.00 0.00 3.86
3818 4318 1.495878 CTCTTCGATGAGGATTGCGG 58.504 55.000 18.20 0.00 0.00 5.69
3984 4484 4.599041 CATTTACCAACAATCCTCTCCCA 58.401 43.478 0.00 0.00 0.00 4.37
3985 4485 3.381590 GCATTTACCAACAATCCTCTCCC 59.618 47.826 0.00 0.00 0.00 4.30
4107 4607 9.702494 CATATCTAATGCTCATACAGAAGTTCA 57.298 33.333 5.50 0.00 0.00 3.18
4250 4750 3.580458 AGAACTGTAGGTCAAGCAGTGAT 59.420 43.478 0.00 0.00 41.94 3.06
4326 4827 3.947834 GGGAATCCAAAGACCATACTGTG 59.052 47.826 0.09 0.00 0.00 3.66
4327 4828 3.852578 AGGGAATCCAAAGACCATACTGT 59.147 43.478 0.09 0.00 34.83 3.55
4328 4829 4.080356 TGAGGGAATCCAAAGACCATACTG 60.080 45.833 0.09 0.00 34.83 2.74
4329 4830 4.111577 TGAGGGAATCCAAAGACCATACT 58.888 43.478 0.09 0.00 34.83 2.12
4330 4831 4.503714 TGAGGGAATCCAAAGACCATAC 57.496 45.455 0.09 0.00 34.83 2.39
4333 4834 2.445145 TGTTGAGGGAATCCAAAGACCA 59.555 45.455 0.09 0.00 34.83 4.02
4334 4835 3.154827 TGTTGAGGGAATCCAAAGACC 57.845 47.619 0.09 0.00 34.83 3.85
4335 4836 3.057245 GCTTGTTGAGGGAATCCAAAGAC 60.057 47.826 0.09 0.00 34.83 3.01
4359 4860 2.102578 GCTTGGCACCAATGGTATCTT 58.897 47.619 3.85 0.00 35.20 2.40
4360 4861 1.686115 GGCTTGGCACCAATGGTATCT 60.686 52.381 3.85 0.00 35.20 1.98
4361 4862 0.746659 GGCTTGGCACCAATGGTATC 59.253 55.000 3.85 0.50 35.20 2.24
4362 4863 0.336048 AGGCTTGGCACCAATGGTAT 59.664 50.000 3.85 0.00 35.20 2.73
4363 4864 0.114168 AAGGCTTGGCACCAATGGTA 59.886 50.000 3.85 0.00 35.20 3.25
4364 4865 1.152269 AAGGCTTGGCACCAATGGT 60.152 52.632 0.00 0.00 35.20 3.55
4365 4866 1.294138 CAAGGCTTGGCACCAATGG 59.706 57.895 19.55 0.00 35.20 3.16
4366 4867 1.255882 TACAAGGCTTGGCACCAATG 58.744 50.000 29.26 3.80 35.20 2.82
4367 4868 1.618343 GTTACAAGGCTTGGCACCAAT 59.382 47.619 29.26 10.50 35.20 3.16
4368 4869 1.036707 GTTACAAGGCTTGGCACCAA 58.963 50.000 29.26 12.86 34.12 3.67
4369 4870 0.106469 TGTTACAAGGCTTGGCACCA 60.106 50.000 29.26 17.19 34.12 4.17
4370 4871 1.256812 ATGTTACAAGGCTTGGCACC 58.743 50.000 29.26 15.01 34.12 5.01
4371 4872 4.513198 TTAATGTTACAAGGCTTGGCAC 57.487 40.909 29.26 23.56 34.12 5.01
4372 4873 5.736951 ATTTAATGTTACAAGGCTTGGCA 57.263 34.783 29.26 23.24 34.12 4.92
4373 4874 8.716646 ATTAATTTAATGTTACAAGGCTTGGC 57.283 30.769 29.26 18.96 34.12 4.52
4419 4920 1.826385 AACAGCCATGACACTAAGCC 58.174 50.000 0.00 0.00 0.00 4.35
4443 4944 4.081531 GGGATTGTGAAATCATGAAGCCAA 60.082 41.667 0.00 0.00 31.89 4.52
4562 5064 8.341903 CGCATCCATTTATTTTATCTGTGTACA 58.658 33.333 0.00 0.00 0.00 2.90
4587 5089 4.196193 TGGCCATTTAGTGTCCTAATTCG 58.804 43.478 0.00 0.00 33.27 3.34
4588 5090 5.297029 GTCTGGCCATTTAGTGTCCTAATTC 59.703 44.000 5.51 0.00 33.27 2.17
4598 5100 0.625849 CCCCTGTCTGGCCATTTAGT 59.374 55.000 5.51 0.00 0.00 2.24
4600 5102 2.006748 CCCCCTGTCTGGCCATTTA 58.993 57.895 5.51 0.00 0.00 1.40
4622 5124 4.700365 CGGACGCTGCGACAGTGA 62.700 66.667 30.47 0.00 43.78 3.41
4631 5133 1.089481 ACATAACATGCCGGACGCTG 61.089 55.000 5.05 0.00 38.78 5.18
4647 5149 0.108898 GCACTCGTGAGCTCTGACAT 60.109 55.000 16.19 0.00 0.00 3.06
4648 5150 1.287191 GCACTCGTGAGCTCTGACA 59.713 57.895 16.19 0.00 0.00 3.58
4649 5151 1.006314 GTGCACTCGTGAGCTCTGAC 61.006 60.000 16.19 4.59 0.00 3.51
4650 5152 1.175347 AGTGCACTCGTGAGCTCTGA 61.175 55.000 15.25 11.83 33.66 3.27
4651 5153 1.007848 CAGTGCACTCGTGAGCTCTG 61.008 60.000 18.64 19.13 41.85 3.35
4656 5160 0.315251 TTCTCCAGTGCACTCGTGAG 59.685 55.000 18.64 21.29 0.00 3.51
4674 5178 5.527026 AGGAGAAGGATTTCTGTGGATTT 57.473 39.130 0.00 0.00 43.63 2.17
4694 5198 1.234821 TTGCCTTTTGCGACTGTAGG 58.765 50.000 0.00 0.00 45.60 3.18
4748 5252 2.659897 GCATCTAGCAGACGGCCG 60.660 66.667 26.86 26.86 46.50 6.13
4805 5309 7.594758 CAGAGTTCGAATCCTAGATTTGAGATC 59.405 40.741 0.00 9.01 0.00 2.75
4823 5327 5.753921 GGTATTTCTAACCCATCAGAGTTCG 59.246 44.000 0.00 0.00 0.00 3.95
4837 5341 2.172717 GGAGGCTGGCTGGTATTTCTAA 59.827 50.000 9.06 0.00 0.00 2.10
4839 5343 0.548510 GGAGGCTGGCTGGTATTTCT 59.451 55.000 9.06 0.00 0.00 2.52
4863 5367 5.021389 CGTGAATCGACATGTGGTTAAATG 58.979 41.667 1.15 0.00 42.86 2.32
4878 8408 1.651987 ATTGTGCTACCCGTGAATCG 58.348 50.000 0.00 0.00 39.52 3.34
4886 8416 5.546621 TCTCCAACTATATTGTGCTACCC 57.453 43.478 0.00 0.00 0.00 3.69
4926 8491 1.200716 CCTCGTTCCGTAGTGTAGCAA 59.799 52.381 0.00 0.00 0.00 3.91
4933 8498 4.097589 CCTTATCTTTCCTCGTTCCGTAGT 59.902 45.833 0.00 0.00 0.00 2.73
4938 8503 4.828829 TGTTCCTTATCTTTCCTCGTTCC 58.171 43.478 0.00 0.00 0.00 3.62
4942 8507 6.554334 TTTGTTGTTCCTTATCTTTCCTCG 57.446 37.500 0.00 0.00 0.00 4.63
4950 8515 9.612620 CAGTACATTCTTTTGTTGTTCCTTATC 57.387 33.333 0.00 0.00 0.00 1.75
4951 8516 9.349713 TCAGTACATTCTTTTGTTGTTCCTTAT 57.650 29.630 0.00 0.00 0.00 1.73
4952 8517 8.740123 TCAGTACATTCTTTTGTTGTTCCTTA 57.260 30.769 0.00 0.00 0.00 2.69
4964 8529 8.853077 TTGATCAATGTCTCAGTACATTCTTT 57.147 30.769 3.38 0.00 44.79 2.52
4974 8539 6.600246 ACATCGATTTGATCAATGTCTCAG 57.400 37.500 9.40 5.83 31.59 3.35
5038 8603 2.285977 AGCGTTTTATCGGATGGGAAC 58.714 47.619 0.00 2.42 0.00 3.62
5142 8707 4.794169 ACTATTTGACCAACATCGTTTGC 58.206 39.130 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.