Multiple sequence alignment - TraesCS4B01G083700

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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 TraesCS4B01G083700 chr4B 100.000 5137 0 0 1 5137 82313319 82308183 0.000000e+00 9487
1 TraesCS4B01G083700 chr4A 91.516 5186 325 41 1 5137 541782879 541787998 0.000000e+00 7033
2 TraesCS4B01G083700 chr4A 92.672 1733 114 6 2317 4049 541800962 541802681 0.000000e+00 2484
3 TraesCS4B01G083700 chr4A 94.143 1400 75 3 2784 4183 541876660 541878052 0.000000e+00 2124
4 TraesCS4B01G083700 chr4A 86.282 831 71 14 4338 5137 541878071 541878889 0.000000e+00 863
5 TraesCS4B01G083700 chr4A 85.739 589 50 7 4576 5137 541866138 541866719 4.430000e-165 592
6 TraesCS4B01G083700 chr4A 79.540 435 51 23 4310 4714 541800006 541800432 5.070000e-70 276
7 TraesCS4B01G083700 chr4A 90.419 167 8 5 4338 4503 541865971 541866130 4.030000e-51 213
8 TraesCS4B01G083700 chr4D 94.565 2723 142 4 1444 4166 55286679 55283963 0.000000e+00 4204
9 TraesCS4B01G083700 chr4D 92.625 461 29 4 962 1419 55287132 55286674 0.000000e+00 658
10 TraesCS4B01G083700 chr4D 83.264 484 35 18 27 483 55287902 55287438 2.230000e-108 403
11 TraesCS4B01G083700 chr4D 90.789 228 11 6 4292 4518 55283397 55283179 3.890000e-76 296
12 TraesCS4B01G083700 chr3A 72.769 2185 520 59 1980 4125 7472138 7469990 0.000000e+00 669
13 TraesCS4B01G083700 chr3D 72.643 2270 524 77 1901 4120 1636299 1634077 0.000000e+00 662
14 TraesCS4B01G083700 chr3B 72.013 2419 574 78 1761 4125 5172534 5174903 5.650000e-174 621


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 TraesCS4B01G083700 chr4B 82308183 82313319 5136 True 9487.00 9487 100.00000 1 5137 1 chr4B.!!$R1 5136
1 TraesCS4B01G083700 chr4A 541782879 541787998 5119 False 7033.00 7033 91.51600 1 5137 1 chr4A.!!$F1 5136
2 TraesCS4B01G083700 chr4A 541876660 541878889 2229 False 1493.50 2124 90.21250 2784 5137 2 chr4A.!!$F4 2353
3 TraesCS4B01G083700 chr4A 541800006 541802681 2675 False 1380.00 2484 86.10600 2317 4714 2 chr4A.!!$F2 2397
4 TraesCS4B01G083700 chr4A 541865971 541866719 748 False 402.50 592 88.07900 4338 5137 2 chr4A.!!$F3 799
5 TraesCS4B01G083700 chr4D 55283179 55287902 4723 True 1390.25 4204 90.31075 27 4518 4 chr4D.!!$R1 4491
6 TraesCS4B01G083700 chr3A 7469990 7472138 2148 True 669.00 669 72.76900 1980 4125 1 chr3A.!!$R1 2145
7 TraesCS4B01G083700 chr3D 1634077 1636299 2222 True 662.00 662 72.64300 1901 4120 1 chr3D.!!$R1 2219
8 TraesCS4B01G083700 chr3B 5172534 5174903 2369 False 621.00 621 72.01300 1761 4125 1 chr3B.!!$F1 2364

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
69 70 0.487325 TCAAGGAGGAGTGGAGTGGA 59.513 55.0 0.00 0.0 0.00 4.02 F
1140 1212 0.537188 TCAAGAAGGCCATCGTCCTC 59.463 55.0 5.01 0.0 32.45 3.71 F
2452 2553 0.042581 TCATGGTAGGGTGCCAGAGA 59.957 55.0 0.00 0.0 39.65 3.10 F
2673 2774 0.101219 GCAACATCCCCGCTTCATTC 59.899 55.0 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1316 0.614812 TAAACCCCGGTTGACTAGGC 59.385 55.000 0.0 0.0 38.47 3.93 R
2727 2828 1.272490 CCAAGAGACGCTGGTACTGAA 59.728 52.381 0.0 0.0 0.00 3.02 R
4070 4205 0.178767 CCTCCTCCATGTTGATGCGA 59.821 55.000 0.0 0.0 0.00 5.10 R
4634 5305 1.150567 CTGGCTCGGAATGCTTCTCG 61.151 60.000 0.0 0.0 0.00 4.04 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
68 69 1.209019 CATCAAGGAGGAGTGGAGTGG 59.791 57.143 0.00 0.00 0.00 4.00
69 70 0.487325 TCAAGGAGGAGTGGAGTGGA 59.513 55.000 0.00 0.00 0.00 4.02
70 71 0.610687 CAAGGAGGAGTGGAGTGGAC 59.389 60.000 0.00 0.00 0.00 4.02
108 109 5.735766 ACCCAAGCTAAACAGAGAGAATAC 58.264 41.667 0.00 0.00 0.00 1.89
163 165 5.874810 GTCCAGACTAGCATTAATGTTGTGA 59.125 40.000 16.61 5.16 0.00 3.58
191 193 1.149148 GGTGTTTCCTTGACTCGAGC 58.851 55.000 13.61 6.11 0.00 5.03
212 222 1.098050 GTTCTATGCAGCCACCTTGG 58.902 55.000 0.00 0.00 41.55 3.61
217 227 1.495579 ATGCAGCCACCTTGGAGACT 61.496 55.000 0.00 0.00 40.96 3.24
253 278 2.808206 GGCGTCCCTATCCAGGTGG 61.808 68.421 0.00 0.00 40.79 4.61
255 280 1.823295 CGTCCCTATCCAGGTGGTG 59.177 63.158 0.00 0.00 40.79 4.17
288 315 4.199310 TCCAGTGTAATATTCTTGCAGGC 58.801 43.478 0.00 0.00 0.00 4.85
297 324 3.795623 ATTCTTGCAGGCATCATTGAC 57.204 42.857 0.00 0.00 0.00 3.18
299 326 1.089112 CTTGCAGGCATCATTGACGA 58.911 50.000 0.00 0.00 35.32 4.20
301 328 1.753930 TGCAGGCATCATTGACGAAT 58.246 45.000 0.00 0.00 35.32 3.34
303 330 2.874086 TGCAGGCATCATTGACGAATAG 59.126 45.455 0.00 0.00 35.32 1.73
393 425 1.226018 CGGCCGATTGCGAAGAAAC 60.226 57.895 24.07 0.00 42.61 2.78
400 432 3.125146 CCGATTGCGAAGAAACTGATCAA 59.875 43.478 0.00 0.00 40.82 2.57
411 443 2.859165 ACTGATCAACATTCGGGTGT 57.141 45.000 0.00 0.00 0.00 4.16
419 451 1.900981 CATTCGGGTGTGCCAACCA 60.901 57.895 9.55 0.00 42.24 3.67
427 459 2.978010 GTGCCAACCACTCCACGG 60.978 66.667 0.00 0.00 41.35 4.94
444 476 1.076549 GGGTCCATGGGCAAGTGAA 59.923 57.895 20.13 0.00 0.00 3.18
512 557 5.241506 TGAGTTTTGAATAGAGTTGCCTTGG 59.758 40.000 0.00 0.00 0.00 3.61
569 620 2.951229 AAAACGAGAGAACCCATGGT 57.049 45.000 11.73 0.00 37.65 3.55
582 633 2.485677 CATGGTCATGGGCACTCAC 58.514 57.895 3.17 0.00 35.24 3.51
602 653 1.142748 CTCTGCTCACCCCATCGTC 59.857 63.158 0.00 0.00 0.00 4.20
705 774 5.239306 CCTCACTTGTTTAAGCATCTGTTCA 59.761 40.000 0.00 0.00 37.43 3.18
711 780 6.000891 TGTTTAAGCATCTGTTCATGTCAC 57.999 37.500 0.00 0.00 0.00 3.67
719 788 5.990386 GCATCTGTTCATGTCACTCATCTAT 59.010 40.000 0.00 0.00 34.09 1.98
720 789 7.015001 AGCATCTGTTCATGTCACTCATCTATA 59.985 37.037 0.00 0.00 34.09 1.31
742 811 3.774066 GCTTTTGCTTCTCACAAACTGT 58.226 40.909 0.00 0.00 43.35 3.55
777 846 6.600032 TCATGTTCTCCTCTTCTACTCTACAC 59.400 42.308 0.00 0.00 0.00 2.90
864 933 3.636764 GCCCAAGAACCTTGAGAAAAGAA 59.363 43.478 8.16 0.00 0.00 2.52
884 953 9.946165 AAAAGAAACGACTCTAAATAACTTTGG 57.054 29.630 0.00 0.00 0.00 3.28
906 975 6.919721 TGGAGGTAAGCAACATACAAAAATC 58.080 36.000 0.00 0.00 27.17 2.17
909 978 7.363793 GGAGGTAAGCAACATACAAAAATCCAT 60.364 37.037 0.00 0.00 0.00 3.41
913 982 5.969423 AGCAACATACAAAAATCCATCCTG 58.031 37.500 0.00 0.00 0.00 3.86
914 983 5.716228 AGCAACATACAAAAATCCATCCTGA 59.284 36.000 0.00 0.00 0.00 3.86
915 984 5.807011 GCAACATACAAAAATCCATCCTGAC 59.193 40.000 0.00 0.00 0.00 3.51
916 985 6.332630 CAACATACAAAAATCCATCCTGACC 58.667 40.000 0.00 0.00 0.00 4.02
917 986 5.579047 ACATACAAAAATCCATCCTGACCA 58.421 37.500 0.00 0.00 0.00 4.02
919 988 6.322201 ACATACAAAAATCCATCCTGACCATC 59.678 38.462 0.00 0.00 0.00 3.51
920 989 4.939255 ACAAAAATCCATCCTGACCATCT 58.061 39.130 0.00 0.00 0.00 2.90
922 991 6.125029 ACAAAAATCCATCCTGACCATCTAG 58.875 40.000 0.00 0.00 0.00 2.43
923 992 5.983333 AAAATCCATCCTGACCATCTAGT 57.017 39.130 0.00 0.00 0.00 2.57
924 993 5.983333 AAATCCATCCTGACCATCTAGTT 57.017 39.130 0.00 0.00 0.00 2.24
926 995 3.041211 TCCATCCTGACCATCTAGTTGG 58.959 50.000 16.86 16.86 42.82 3.77
927 996 3.041211 CCATCCTGACCATCTAGTTGGA 58.959 50.000 23.87 4.01 39.25 3.53
928 997 3.455910 CCATCCTGACCATCTAGTTGGAA 59.544 47.826 23.87 11.86 39.25 3.53
929 998 4.446371 CATCCTGACCATCTAGTTGGAAC 58.554 47.826 23.87 16.90 39.25 3.62
930 999 3.516586 TCCTGACCATCTAGTTGGAACA 58.483 45.455 23.87 19.69 39.25 3.18
973 1042 5.608437 TGACCATCTAAATTCCCTCTGCTAT 59.392 40.000 0.00 0.00 0.00 2.97
1056 1125 2.202797 ATAGCAGCGTCCAGTGCG 60.203 61.111 0.00 0.00 44.78 5.34
1104 1176 1.127951 CACAGTAATGAAACGGACCGC 59.872 52.381 15.39 0.00 0.00 5.68
1140 1212 0.537188 TCAAGAAGGCCATCGTCCTC 59.463 55.000 5.01 0.00 32.45 3.71
1189 1261 1.821061 CGAGAGCACCCACCTCTGTT 61.821 60.000 0.00 0.00 39.66 3.16
1191 1263 1.834263 GAGAGCACCCACCTCTGTTAT 59.166 52.381 0.00 0.00 39.66 1.89
1223 1295 2.121963 TTGCAGGACCAGGGACCT 60.122 61.111 3.38 3.38 40.68 3.85
1244 1316 2.276743 CCGCGTCGTCTCTCTTCG 60.277 66.667 4.92 0.00 0.00 3.79
1250 1322 1.371595 GTCGTCTCTCTTCGCCTAGT 58.628 55.000 0.00 0.00 0.00 2.57
1325 1397 2.233676 TCAGAAATCTAGCACTGCCGAA 59.766 45.455 0.00 0.00 0.00 4.30
1326 1398 3.002791 CAGAAATCTAGCACTGCCGAAA 58.997 45.455 0.00 0.00 0.00 3.46
1338 1410 2.108700 CTGCCGAAAAACACTTTCACG 58.891 47.619 0.00 0.00 0.00 4.35
1384 1456 3.685214 CTTCGTCGCCTCCAGACCG 62.685 68.421 0.00 0.00 35.33 4.79
1387 1459 4.131088 GTCGCCTCCAGACCGTCC 62.131 72.222 0.00 0.00 32.78 4.79
1392 1464 1.913762 CCTCCAGACCGTCCACCTT 60.914 63.158 0.00 0.00 0.00 3.50
1398 1470 1.066143 CAGACCGTCCACCTTAGCAAT 60.066 52.381 0.00 0.00 0.00 3.56
1403 1475 3.054655 ACCGTCCACCTTAGCAATAACAT 60.055 43.478 0.00 0.00 0.00 2.71
1579 1651 2.622452 CCTCCTTCCATTGCCAATGTCT 60.622 50.000 15.83 0.00 37.18 3.41
1645 1717 1.078848 ATCCCTGACGAGCTTGCAC 60.079 57.895 0.00 0.00 0.00 4.57
1725 1797 2.305009 CCAGCCATCCTCAATCTTTCC 58.695 52.381 0.00 0.00 0.00 3.13
1823 1895 7.371936 CCTAATCTCCAGATACTTTCGTTAGG 58.628 42.308 0.00 0.00 33.73 2.69
1870 1942 2.500888 CGCATTCATTCGTAAACGCAA 58.499 42.857 0.00 0.00 39.60 4.85
2095 2167 2.229792 GTCAGGTGCCAAGTTCATTGA 58.770 47.619 0.00 0.00 41.83 2.57
2113 2185 7.395190 TCATTGAGTAACCTTTCCATTCATG 57.605 36.000 0.00 0.00 0.00 3.07
2247 2319 3.957586 CCACACTGGCTGGGAGCA 61.958 66.667 0.00 0.00 44.75 4.26
2445 2546 8.163408 TCCAATAATAATCTTCATGGTAGGGTG 58.837 37.037 0.00 0.00 0.00 4.61
2452 2553 0.042581 TCATGGTAGGGTGCCAGAGA 59.957 55.000 0.00 0.00 39.65 3.10
2673 2774 0.101219 GCAACATCCCCGCTTCATTC 59.899 55.000 0.00 0.00 0.00 2.67
2727 2828 8.625786 ATTTGTCTTACAATAACTTAACCGGT 57.374 30.769 0.00 0.00 38.00 5.28
2770 2876 4.219288 GGAACCTTCAGCATCTTGAACAAT 59.781 41.667 0.00 0.00 33.71 2.71
2887 2993 0.916086 TGGTGGGGCATCGAACTTAT 59.084 50.000 0.00 0.00 0.00 1.73
2958 3064 6.990349 GGCTACCTGTAATATTCAAAGTAGCA 59.010 38.462 25.81 5.18 42.71 3.49
3198 3304 4.998671 TCAAGAAGAAAATGTGGTTGCA 57.001 36.364 0.00 0.00 0.00 4.08
3210 3316 4.566545 TGTGGTTGCAGTGAAAGTATTG 57.433 40.909 0.00 0.00 0.00 1.90
3346 3452 6.173339 TCTAGAGGAAATGATTTCAAAGCGT 58.827 36.000 18.55 1.12 41.43 5.07
3349 3455 7.396540 AGAGGAAATGATTTCAAAGCGTTAT 57.603 32.000 18.55 0.00 41.43 1.89
3455 3561 6.872920 ACATTTCACTTGCTCAAAGGTTAAA 58.127 32.000 0.00 0.00 40.51 1.52
3560 3666 5.813672 CCAGCAACATTCTTTTGGATAATGG 59.186 40.000 0.00 0.00 35.40 3.16
3785 3914 5.294734 TGCAATCTACAGAATATGGAGCA 57.705 39.130 0.00 0.00 40.06 4.26
3821 3950 1.270839 ACCGCTGCAGATGTTTACAGT 60.271 47.619 20.43 0.00 32.65 3.55
3871 4000 1.347707 ACGAAAGAGCCCAACAGATGA 59.652 47.619 0.00 0.00 0.00 2.92
3940 4069 2.082231 CCCTGACAAGATGTTGCAGAG 58.918 52.381 20.73 9.93 38.80 3.35
4070 4205 2.304180 CACCAAGTCCTCTCCAAGTGAT 59.696 50.000 0.00 0.00 0.00 3.06
4078 4213 2.419159 CCTCTCCAAGTGATCGCATCAA 60.419 50.000 9.33 0.00 41.69 2.57
4236 4906 8.803799 GCTTAACATTATTTTGTATTGAACCGG 58.196 33.333 0.00 0.00 0.00 5.28
4290 4960 5.067805 GTGCTATAGGGGAAGAAAACAATGG 59.932 44.000 1.04 0.00 0.00 3.16
4317 4987 6.984474 GCCATACTTAATGTACAACTAGAGCA 59.016 38.462 0.00 0.00 33.45 4.26
4354 5024 1.033746 CCATTCAATCCGCTGGTGCT 61.034 55.000 0.00 0.00 36.97 4.40
4376 5046 3.181434 TGGATCTGGTTTTACCACAGCTT 60.181 43.478 0.00 0.00 44.79 3.74
4377 5047 3.191371 GGATCTGGTTTTACCACAGCTTG 59.809 47.826 0.00 0.00 44.79 4.01
4415 5085 5.799435 TGCAAATGTGTAAAGTCATAATGCG 59.201 36.000 0.00 0.00 38.57 4.73
4543 5214 5.354234 AGCCAATGGTATTAAACACGAAGAG 59.646 40.000 0.00 0.00 0.00 2.85
4580 5251 7.778382 TGAGTCACCACTATATAGCAGACTTTA 59.222 37.037 19.38 13.12 35.45 1.85
4597 5268 7.225538 GCAGACTTTACATATGTTGCTAGTGAT 59.774 37.037 14.77 1.91 0.00 3.06
4627 5298 4.572795 TCGTGCAAACTTACTCAACAATGA 59.427 37.500 0.00 0.00 0.00 2.57
4634 5305 8.125448 GCAAACTTACTCAACAATGATAGGATC 58.875 37.037 0.00 0.00 34.37 3.36
4674 5345 3.008049 AGTCAAGGCGTTCCTCTAAATGT 59.992 43.478 0.00 0.00 43.40 2.71
4734 5426 3.689872 ACCTATGCTCTACCTTCCAGA 57.310 47.619 0.00 0.00 0.00 3.86
4743 5435 3.960102 CTCTACCTTCCAGAGCTGAATCT 59.040 47.826 0.00 0.00 33.60 2.40
4745 5437 3.625649 ACCTTCCAGAGCTGAATCTTC 57.374 47.619 0.00 0.00 0.00 2.87
4757 5449 3.791245 CTGAATCTTCCTGGAGTACAGC 58.209 50.000 0.00 0.00 46.14 4.40
4814 5506 5.990120 AGATTCCTGAAAATCCCACAAAG 57.010 39.130 0.00 0.00 36.49 2.77
4815 5507 5.644188 AGATTCCTGAAAATCCCACAAAGA 58.356 37.500 0.00 0.00 36.49 2.52
4816 5508 6.077322 AGATTCCTGAAAATCCCACAAAGAA 58.923 36.000 0.00 0.00 36.49 2.52
4817 5509 6.554605 AGATTCCTGAAAATCCCACAAAGAAA 59.445 34.615 0.00 0.00 36.49 2.52
4818 5510 5.789643 TCCTGAAAATCCCACAAAGAAAG 57.210 39.130 0.00 0.00 0.00 2.62
4868 5568 4.625972 TGCATGAATGACAAGTGCATAG 57.374 40.909 0.00 0.00 38.88 2.23
4879 5579 6.054941 TGACAAGTGCATAGAACTTCTTTCA 58.945 36.000 0.00 0.00 35.70 2.69
4881 5581 5.239525 ACAAGTGCATAGAACTTCTTTCACC 59.760 40.000 0.00 0.00 35.70 4.02
4883 5583 6.360370 AGTGCATAGAACTTCTTTCACCTA 57.640 37.500 0.00 0.00 36.57 3.08
4890 5592 3.141767 ACTTCTTTCACCTAAGGCCAC 57.858 47.619 5.01 0.00 0.00 5.01
4894 5596 2.154462 CTTTCACCTAAGGCCACAGTG 58.846 52.381 5.01 7.23 0.00 3.66
4917 5619 2.260743 GCAGAAAGCAAGGCTGGC 59.739 61.111 5.50 5.50 44.79 4.85
4921 5623 4.238062 AAAGCAAGGCTGGCCCCA 62.238 61.111 11.06 0.00 39.62 4.96
4934 5636 3.642141 CTGGCCCCATATGGTAGTTTTT 58.358 45.455 20.46 0.00 0.00 1.94
4935 5637 3.370104 TGGCCCCATATGGTAGTTTTTG 58.630 45.455 20.46 2.37 0.00 2.44
4944 5646 7.201785 CCCATATGGTAGTTTTTGTGTATGGTC 60.202 40.741 20.46 0.00 36.96 4.02
4985 5687 8.107095 TCTTTCTGTATGTTTTATGCTTAGGGT 58.893 33.333 0.00 0.00 0.00 4.34
5060 5762 5.059833 GGCATCTCCTTAGTGAGGTTATTG 58.940 45.833 0.11 0.00 46.39 1.90
5088 5790 2.110213 GTTCACGGCCAGGTGACA 59.890 61.111 12.47 3.08 45.97 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.658799 CCCAATATATCTTGTAGATAACACCTG 57.341 37.037 0.91 0.00 40.28 4.00
56 57 1.476007 GCACAGTCCACTCCACTCCT 61.476 60.000 0.00 0.00 0.00 3.69
68 69 0.952984 GGTCCAAGCTCTGCACAGTC 60.953 60.000 0.00 0.00 0.00 3.51
69 70 1.072159 GGTCCAAGCTCTGCACAGT 59.928 57.895 0.00 0.00 0.00 3.55
70 71 1.673665 GGGTCCAAGCTCTGCACAG 60.674 63.158 0.00 0.00 0.00 3.66
180 182 2.857152 GCATAGAACAGCTCGAGTCAAG 59.143 50.000 15.13 4.26 0.00 3.02
191 193 1.741706 CAAGGTGGCTGCATAGAACAG 59.258 52.381 0.50 0.00 38.22 3.16
217 227 0.250234 CCAGGATCTCCTTCACGCAA 59.750 55.000 0.00 0.00 46.09 4.85
253 278 0.393537 CACTGGAGCTCCCATTCCAC 60.394 60.000 29.95 2.66 45.57 4.02
255 280 1.204146 TACACTGGAGCTCCCATTCC 58.796 55.000 29.95 5.27 45.57 3.01
260 285 4.965200 AGAATATTACACTGGAGCTCCC 57.035 45.455 29.95 12.55 34.29 4.30
297 324 2.009774 CTGCCCAACCTTGACTATTCG 58.990 52.381 0.00 0.00 0.00 3.34
299 326 5.450818 TTATCTGCCCAACCTTGACTATT 57.549 39.130 0.00 0.00 0.00 1.73
301 328 6.763715 ATATTATCTGCCCAACCTTGACTA 57.236 37.500 0.00 0.00 0.00 2.59
303 330 6.534634 ACTATATTATCTGCCCAACCTTGAC 58.465 40.000 0.00 0.00 0.00 3.18
305 332 5.639506 CGACTATATTATCTGCCCAACCTTG 59.360 44.000 0.00 0.00 0.00 3.61
307 334 5.084519 TCGACTATATTATCTGCCCAACCT 58.915 41.667 0.00 0.00 0.00 3.50
308 335 5.401531 TCGACTATATTATCTGCCCAACC 57.598 43.478 0.00 0.00 0.00 3.77
309 336 7.148407 CCATTTCGACTATATTATCTGCCCAAC 60.148 40.741 0.00 0.00 0.00 3.77
310 337 6.878923 CCATTTCGACTATATTATCTGCCCAA 59.121 38.462 0.00 0.00 0.00 4.12
311 338 6.406370 CCATTTCGACTATATTATCTGCCCA 58.594 40.000 0.00 0.00 0.00 5.36
312 339 5.294552 GCCATTTCGACTATATTATCTGCCC 59.705 44.000 0.00 0.00 0.00 5.36
313 340 6.109359 AGCCATTTCGACTATATTATCTGCC 58.891 40.000 0.00 0.00 0.00 4.85
393 425 1.131126 GCACACCCGAATGTTGATCAG 59.869 52.381 0.00 0.00 0.00 2.90
400 432 1.901464 GGTTGGCACACCCGAATGT 60.901 57.895 7.39 0.00 39.29 2.71
411 443 4.263572 CCCGTGGAGTGGTTGGCA 62.264 66.667 0.00 0.00 0.00 4.92
427 459 0.038166 TCTTCACTTGCCCATGGACC 59.962 55.000 15.22 4.18 0.00 4.46
444 476 1.705873 AGTTGACTCCAGGTTCGTCT 58.294 50.000 7.49 0.00 0.00 4.18
512 557 7.712205 ACTGTCTCTAGCTACTAACTAGTAAGC 59.288 40.741 0.00 3.60 38.24 3.09
569 620 0.322648 CAGAGTGTGAGTGCCCATGA 59.677 55.000 0.00 0.00 0.00 3.07
582 633 1.153489 CGATGGGGTGAGCAGAGTG 60.153 63.158 0.00 0.00 0.00 3.51
610 661 0.662619 TGAAGCAAAACTGGTCAGCG 59.337 50.000 0.00 0.00 0.00 5.18
650 701 1.003839 CTTACGGCTGCCTTGGTCA 60.004 57.895 17.92 0.00 0.00 4.02
705 774 6.590068 AGCAAAAGCTATAGATGAGTGACAT 58.410 36.000 3.21 0.00 42.47 3.06
711 780 6.760298 TGTGAGAAGCAAAAGCTATAGATGAG 59.240 38.462 3.21 0.00 0.00 2.90
719 788 4.640201 ACAGTTTGTGAGAAGCAAAAGCTA 59.360 37.500 0.00 0.00 33.51 3.32
720 789 3.445096 ACAGTTTGTGAGAAGCAAAAGCT 59.555 39.130 0.00 0.00 35.87 3.74
742 811 9.152327 AGAAGAGGAGAACATGAATGATGTATA 57.848 33.333 0.00 0.00 45.12 1.47
777 846 3.513119 TCAGAGTTCTCTTCACATCCCTG 59.487 47.826 0.00 0.00 0.00 4.45
838 907 1.228124 TCAAGGTTCTTGGGCACGG 60.228 57.895 7.67 0.00 0.00 4.94
864 933 6.766429 ACCTCCAAAGTTATTTAGAGTCGTT 58.234 36.000 0.00 0.00 33.74 3.85
879 948 5.957842 TTGTATGTTGCTTACCTCCAAAG 57.042 39.130 0.00 0.00 0.00 2.77
883 952 6.071616 TGGATTTTTGTATGTTGCTTACCTCC 60.072 38.462 0.00 0.00 0.00 4.30
884 953 6.919721 TGGATTTTTGTATGTTGCTTACCTC 58.080 36.000 0.00 0.00 0.00 3.85
906 975 3.041211 TCCAACTAGATGGTCAGGATGG 58.959 50.000 17.77 0.00 41.46 3.51
909 978 3.260884 GTGTTCCAACTAGATGGTCAGGA 59.739 47.826 17.77 0.00 41.46 3.86
913 982 4.393062 CACATGTGTTCCAACTAGATGGTC 59.607 45.833 18.03 12.71 41.46 4.02
914 983 4.326826 CACATGTGTTCCAACTAGATGGT 58.673 43.478 18.03 0.00 41.46 3.55
915 984 3.691118 CCACATGTGTTCCAACTAGATGG 59.309 47.826 23.79 12.74 42.12 3.51
916 985 3.127548 GCCACATGTGTTCCAACTAGATG 59.872 47.826 23.79 5.42 0.00 2.90
917 986 3.347216 GCCACATGTGTTCCAACTAGAT 58.653 45.455 23.79 0.00 0.00 1.98
919 988 1.812571 GGCCACATGTGTTCCAACTAG 59.187 52.381 23.79 6.82 0.00 2.57
920 989 1.143889 TGGCCACATGTGTTCCAACTA 59.856 47.619 25.75 10.03 31.47 2.24
922 991 0.749649 TTGGCCACATGTGTTCCAAC 59.250 50.000 30.35 14.80 36.82 3.77
923 992 0.749649 GTTGGCCACATGTGTTCCAA 59.250 50.000 30.35 30.35 38.26 3.53
924 993 1.451337 CGTTGGCCACATGTGTTCCA 61.451 55.000 24.75 24.75 32.18 3.53
926 995 0.383949 AACGTTGGCCACATGTGTTC 59.616 50.000 23.79 15.35 0.00 3.18
927 996 0.820871 AAACGTTGGCCACATGTGTT 59.179 45.000 23.79 7.39 0.00 3.32
928 997 0.383949 GAAACGTTGGCCACATGTGT 59.616 50.000 23.79 3.59 0.00 3.72
929 998 0.318614 GGAAACGTTGGCCACATGTG 60.319 55.000 19.31 19.31 0.00 3.21
930 999 0.467290 AGGAAACGTTGGCCACATGT 60.467 50.000 19.12 5.91 0.00 3.21
973 1042 6.821665 GTGTTATACTCTGGCCAAATCTACAA 59.178 38.462 7.01 0.00 0.00 2.41
1104 1176 0.979665 TGAACTCAAGCAGGGAGAGG 59.020 55.000 6.33 0.00 36.26 3.69
1189 1261 1.406887 GCAAGAGACGCCTTCCCAATA 60.407 52.381 0.00 0.00 0.00 1.90
1191 1263 1.302511 GCAAGAGACGCCTTCCCAA 60.303 57.895 0.00 0.00 0.00 4.12
1244 1316 0.614812 TAAACCCCGGTTGACTAGGC 59.385 55.000 0.00 0.00 38.47 3.93
1250 1322 1.762471 CCCACTAAACCCCGGTTGA 59.238 57.895 0.00 0.00 38.47 3.18
1325 1397 1.213430 TCTCCCCCGTGAAAGTGTTTT 59.787 47.619 0.00 0.00 0.00 2.43
1326 1398 0.841289 TCTCCCCCGTGAAAGTGTTT 59.159 50.000 0.00 0.00 0.00 2.83
1352 1424 4.344865 GAAGGCGGCCAAGGGACA 62.345 66.667 23.09 0.00 0.00 4.02
1384 1456 5.449177 GCAGAATGTTATTGCTAAGGTGGAC 60.449 44.000 0.00 0.00 39.31 4.02
1387 1459 5.449588 CCTGCAGAATGTTATTGCTAAGGTG 60.450 44.000 17.39 0.00 39.31 4.00
1392 1464 2.951642 GCCCTGCAGAATGTTATTGCTA 59.048 45.455 17.39 0.00 39.31 3.49
1419 1491 2.523902 TTTGCAAGGCTGGTGGGG 60.524 61.111 0.00 0.00 0.00 4.96
1509 1581 2.033141 TGCAGCTGCTGGAGGTTC 59.967 61.111 36.61 12.98 42.66 3.62
1579 1651 1.678123 GCTGAGCTTCCTCATTGCTGA 60.678 52.381 0.00 0.00 46.44 4.26
1823 1895 1.821136 CCCCATGAAAGAAGTTCTGGC 59.179 52.381 6.06 2.26 37.13 4.85
1870 1942 1.612463 GTCCAAGACACGTAGACTGGT 59.388 52.381 0.00 0.00 32.09 4.00
2095 2167 6.306987 ACTGAACATGAATGGAAAGGTTACT 58.693 36.000 0.00 0.00 0.00 2.24
2113 2185 6.385649 TTGTCCCAAAAACAGATACTGAAC 57.614 37.500 5.76 0.00 35.18 3.18
2247 2319 7.764331 AGCTCAGTTTTTGCAAATTTTTGAAT 58.236 26.923 13.65 4.44 40.55 2.57
2445 2546 3.767902 ATGCTAAAGATCCTCTCTGGC 57.232 47.619 0.00 0.00 33.29 4.85
2452 2553 7.286316 CCTTATTGTTGGAATGCTAAAGATCCT 59.714 37.037 0.00 0.00 33.02 3.24
2460 2561 7.364585 CCAATTTCCCTTATTGTTGGAATGCTA 60.365 37.037 0.00 0.00 38.65 3.49
2673 2774 1.757682 TTAGGCCAAATAGGTTGCCG 58.242 50.000 5.01 0.00 38.03 5.69
2727 2828 1.272490 CCAAGAGACGCTGGTACTGAA 59.728 52.381 0.00 0.00 0.00 3.02
2770 2876 6.708502 TCAAGATGGTTGAACGACAAATCTAA 59.291 34.615 11.42 4.97 40.36 2.10
2887 2993 3.788227 AACAGAACATGAAGGCAGGTA 57.212 42.857 0.00 0.00 38.21 3.08
2958 3064 1.660560 GCATGCAAGCGAGTGGGATT 61.661 55.000 14.21 0.00 0.00 3.01
3198 3304 6.759272 TGTCTCTAAGCACAATACTTTCACT 58.241 36.000 0.00 0.00 0.00 3.41
3210 3316 1.406205 GCTCCCCTTGTCTCTAAGCAC 60.406 57.143 0.00 0.00 0.00 4.40
3318 3424 7.854916 GCTTTGAAATCATTTCCTCTAGAATCG 59.145 37.037 7.68 0.00 38.90 3.34
3346 3452 6.000246 TCCTGGCATGAACTCATACAATAA 58.000 37.500 0.00 0.00 34.26 1.40
3349 3455 3.370846 CCTCCTGGCATGAACTCATACAA 60.371 47.826 0.00 0.00 34.26 2.41
3390 3496 2.432444 CCATTGCCTTCCGTTGAGTAA 58.568 47.619 0.00 0.00 0.00 2.24
3455 3561 5.311265 CATCTGCTATATCCACCACAATGT 58.689 41.667 0.00 0.00 0.00 2.71
3560 3666 1.945394 CTCCAACATGAGCTACCATGC 59.055 52.381 13.78 0.00 45.79 4.06
3760 3878 7.101700 TGCTCCATATTCTGTAGATTGCATAG 58.898 38.462 0.00 0.00 0.00 2.23
3785 3914 1.270678 GCGGTAGAAACTTGACCACCT 60.271 52.381 0.00 0.00 32.39 4.00
3821 3950 1.491332 TCAAGGAGAACGACCCCAAAA 59.509 47.619 0.00 0.00 0.00 2.44
3871 4000 3.689649 GCTTAATCCGTCCTTGAACATGT 59.310 43.478 0.00 0.00 0.00 3.21
4070 4205 0.178767 CCTCCTCCATGTTGATGCGA 59.821 55.000 0.00 0.00 0.00 5.10
4078 4213 2.304056 CCAGCCACCTCCTCCATGT 61.304 63.158 0.00 0.00 0.00 3.21
4110 4245 4.521146 CCTCCAATATATGCATCCCTGAC 58.479 47.826 0.19 0.00 0.00 3.51
4186 4856 2.630580 GACCATACTTTTGCACCCCAAA 59.369 45.455 0.00 0.00 41.48 3.28
4187 4857 2.158385 AGACCATACTTTTGCACCCCAA 60.158 45.455 0.00 0.00 0.00 4.12
4290 4960 7.042658 GCTCTAGTTGTACATTAAGTATGGCAC 60.043 40.741 0.00 0.00 38.64 5.01
4317 4987 3.788227 TGGCAAGAGAGTACATTTGGT 57.212 42.857 0.00 0.00 0.00 3.67
4376 5046 4.141413 ACATTTGCATATGCTCCTAGTCCA 60.141 41.667 27.13 1.78 42.66 4.02
4377 5047 4.214971 CACATTTGCATATGCTCCTAGTCC 59.785 45.833 27.13 0.00 42.66 3.85
4378 5048 4.818546 ACACATTTGCATATGCTCCTAGTC 59.181 41.667 27.13 0.00 42.66 2.59
4379 5049 4.785301 ACACATTTGCATATGCTCCTAGT 58.215 39.130 27.13 16.12 42.66 2.57
4380 5050 6.866010 TTACACATTTGCATATGCTCCTAG 57.134 37.500 27.13 15.54 42.66 3.02
4381 5051 6.828273 ACTTTACACATTTGCATATGCTCCTA 59.172 34.615 27.13 10.95 42.66 2.94
4382 5052 5.653769 ACTTTACACATTTGCATATGCTCCT 59.346 36.000 27.13 9.61 42.66 3.69
4383 5053 5.894807 ACTTTACACATTTGCATATGCTCC 58.105 37.500 27.13 0.43 42.66 4.70
4415 5085 6.314896 GCTGCTCATCCTTTACATCATATACC 59.685 42.308 0.00 0.00 0.00 2.73
4515 5186 5.065859 TCGTGTTTAATACCATTGGCTCATG 59.934 40.000 1.54 0.00 0.00 3.07
4580 5251 8.982685 CGAGAAATTATCACTAGCAACATATGT 58.017 33.333 1.41 1.41 0.00 2.29
4597 5268 7.011576 TGTTGAGTAAGTTTGCACGAGAAATTA 59.988 33.333 0.00 0.00 0.00 1.40
4627 5298 3.157881 TCGGAATGCTTCTCGATCCTAT 58.842 45.455 0.00 0.00 30.97 2.57
4634 5305 1.150567 CTGGCTCGGAATGCTTCTCG 61.151 60.000 0.00 0.00 0.00 4.04
4674 5345 2.047061 CGGATTCCTCCCAATCCTACA 58.953 52.381 9.90 0.00 46.95 2.74
4734 5426 3.445008 TGTACTCCAGGAAGATTCAGCT 58.555 45.455 0.00 0.00 0.00 4.24
4743 5435 0.895530 CCTTCGCTGTACTCCAGGAA 59.104 55.000 0.00 0.00 41.81 3.36
4745 5437 0.173708 GACCTTCGCTGTACTCCAGG 59.826 60.000 0.00 0.00 41.81 4.45
4757 5449 3.731867 GCTTTATGCACAATGGACCTTCG 60.732 47.826 0.00 0.00 42.31 3.79
4814 5506 7.948278 TCAACTACAAGTAGAAGAAGCTTTC 57.052 36.000 13.79 0.00 36.97 2.62
4815 5507 8.371770 CTTCAACTACAAGTAGAAGAAGCTTT 57.628 34.615 21.21 0.00 38.85 3.51
4816 5508 7.954788 CTTCAACTACAAGTAGAAGAAGCTT 57.045 36.000 21.21 0.00 38.85 3.74
4860 5560 5.234466 AGGTGAAAGAAGTTCTATGCACT 57.766 39.130 21.79 10.97 37.13 4.40
4868 5568 3.502595 GTGGCCTTAGGTGAAAGAAGTTC 59.497 47.826 3.32 0.00 36.70 3.01
4879 5579 2.583143 GAAAACACTGTGGCCTTAGGT 58.417 47.619 13.09 0.04 0.00 3.08
4881 5581 1.069227 GCGAAAACACTGTGGCCTTAG 60.069 52.381 13.09 4.61 0.00 2.18
4883 5583 1.034838 TGCGAAAACACTGTGGCCTT 61.035 50.000 13.09 2.00 0.00 4.35
4890 5592 2.473530 TGCTTTCTGCGAAAACACTG 57.526 45.000 5.49 0.00 46.63 3.66
4894 5596 1.131771 GCCTTGCTTTCTGCGAAAAC 58.868 50.000 5.49 2.54 46.63 2.43
4917 5619 6.040391 CCATACACAAAAACTACCATATGGGG 59.960 42.308 25.55 18.75 42.91 4.96
4921 5623 9.528489 AAAGACCATACACAAAAACTACCATAT 57.472 29.630 0.00 0.00 0.00 1.78
4934 5636 3.973206 ACCGATCAAAGACCATACACA 57.027 42.857 0.00 0.00 0.00 3.72
4935 5637 5.416947 AGTAACCGATCAAAGACCATACAC 58.583 41.667 0.00 0.00 0.00 2.90
4944 5646 6.787085 ACAGAAAGAAGTAACCGATCAAAG 57.213 37.500 0.00 0.00 0.00 2.77
4985 5687 3.820467 CAGAACTATTGGACACCAGCAAA 59.180 43.478 0.00 0.00 33.81 3.68
5060 5762 1.450312 CCGTGAACCTGATCAGCCC 60.450 63.158 17.76 8.51 0.00 5.19
5088 5790 2.222445 GGACGAACGTTTAATGCAGTGT 59.778 45.455 0.46 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.