Multiple sequence alignment - TraesCS1D01G321000

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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 TraesCS1D01G321000 chr1D 100.000 3221 0 0 1 3221 414569394 414566174 0.000000e+00 5949.0
1 TraesCS1D01G321000 chr1D 95.349 43 1 1 8 50 389866807 389866766 2.070000e-07 67.6
2 TraesCS1D01G321000 chr1B 91.577 2505 143 32 773 3221 560020498 560018006 0.000000e+00 3395.0
3 TraesCS1D01G321000 chr1B 84.473 702 42 23 53 706 560021207 560020525 5.860000e-177 630.0
4 TraesCS1D01G321000 chr1B 94.845 97 5 0 2862 2958 337573637 337573733 5.570000e-33 152.0
5 TraesCS1D01G321000 chr1A 87.728 1206 78 27 1725 2872 511450304 511449111 0.000000e+00 1343.0
6 TraesCS1D01G321000 chr1A 87.260 730 58 17 575 1295 511451962 511451259 0.000000e+00 800.0
7 TraesCS1D01G321000 chr1A 86.979 384 30 6 2858 3221 511449092 511448709 6.430000e-112 414.0
8 TraesCS1D01G321000 chr1A 96.078 51 2 0 117 167 511452373 511452323 2.060000e-12 84.2
9 TraesCS1D01G321000 chr2D 81.785 1389 193 39 888 2238 33544437 33545803 0.000000e+00 1109.0
10 TraesCS1D01G321000 chr2D 81.432 1341 200 32 928 2238 33340632 33341953 0.000000e+00 1051.0
11 TraesCS1D01G321000 chr7D 79.036 1369 247 24 899 2244 601494461 601493110 0.000000e+00 902.0
12 TraesCS1D01G321000 chr7D 79.396 1291 232 20 958 2228 601787082 601785806 0.000000e+00 880.0
13 TraesCS1D01G321000 chr7D 79.348 1288 236 20 962 2228 601699824 601698546 0.000000e+00 878.0
14 TraesCS1D01G321000 chr7D 74.376 1323 260 45 971 2226 576606663 576607973 2.890000e-135 492.0
15 TraesCS1D01G321000 chr7D 82.353 289 36 5 192 478 629828939 629829214 1.490000e-58 237.0
16 TraesCS1D01G321000 chr7B 79.407 1316 235 21 952 2244 680541731 680540429 0.000000e+00 896.0
17 TraesCS1D01G321000 chr7B 79.073 1295 237 18 960 2228 680854497 680853211 0.000000e+00 859.0
18 TraesCS1D01G321000 chr7B 80.757 925 130 26 1310 2226 732713329 732712445 0.000000e+00 678.0
19 TraesCS1D01G321000 chr7B 77.019 322 54 9 931 1234 732713668 732713349 1.990000e-37 167.0
20 TraesCS1D01G321000 chr7B 88.235 51 4 2 1 50 61126475 61126524 3.470000e-05 60.2
21 TraesCS1D01G321000 chr7B 85.484 62 3 3 2895 2953 732711759 732711701 3.470000e-05 60.2
22 TraesCS1D01G321000 chr7A 79.457 1290 232 18 959 2228 693399006 693397730 0.000000e+00 883.0
23 TraesCS1D01G321000 chr7A 72.606 1274 285 40 979 2211 693492717 693493967 8.490000e-96 361.0
24 TraesCS1D01G321000 chr7A 83.945 218 17 6 1004 1221 725925506 725925705 3.280000e-45 193.0
25 TraesCS1D01G321000 chr7A 77.647 170 25 10 2992 3156 726003427 726003266 1.230000e-14 91.6
26 TraesCS1D01G321000 chr6A 93.814 97 6 0 2862 2958 11915237 11915333 2.590000e-31 147.0
27 TraesCS1D01G321000 chr3A 93.814 97 6 0 2862 2958 233469952 233470048 2.590000e-31 147.0
28 TraesCS1D01G321000 chr4B 91.753 97 8 0 2862 2958 6833954 6833858 5.610000e-28 135.0
29 TraesCS1D01G321000 chr2B 85.227 88 8 4 470 556 773735761 773735844 5.730000e-13 86.1
30 TraesCS1D01G321000 chr3D 93.182 44 2 1 8 50 593644775 593644732 2.680000e-06 63.9
31 TraesCS1D01G321000 chr4A 86.275 51 5 2 1 50 88258501 88258452 2.000000e-03 54.7


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 TraesCS1D01G321000 chr1D 414566174 414569394 3220 True 5949.000000 5949 100.000000 1 3221 1 chr1D.!!$R2 3220
1 TraesCS1D01G321000 chr1B 560018006 560021207 3201 True 2012.500000 3395 88.025000 53 3221 2 chr1B.!!$R1 3168
2 TraesCS1D01G321000 chr1A 511448709 511452373 3664 True 660.300000 1343 89.511250 117 3221 4 chr1A.!!$R1 3104
3 TraesCS1D01G321000 chr2D 33544437 33545803 1366 False 1109.000000 1109 81.785000 888 2238 1 chr2D.!!$F2 1350
4 TraesCS1D01G321000 chr2D 33340632 33341953 1321 False 1051.000000 1051 81.432000 928 2238 1 chr2D.!!$F1 1310
5 TraesCS1D01G321000 chr7D 601493110 601494461 1351 True 902.000000 902 79.036000 899 2244 1 chr7D.!!$R1 1345
6 TraesCS1D01G321000 chr7D 601785806 601787082 1276 True 880.000000 880 79.396000 958 2228 1 chr7D.!!$R3 1270
7 TraesCS1D01G321000 chr7D 601698546 601699824 1278 True 878.000000 878 79.348000 962 2228 1 chr7D.!!$R2 1266
8 TraesCS1D01G321000 chr7D 576606663 576607973 1310 False 492.000000 492 74.376000 971 2226 1 chr7D.!!$F1 1255
9 TraesCS1D01G321000 chr7B 680540429 680541731 1302 True 896.000000 896 79.407000 952 2244 1 chr7B.!!$R1 1292
10 TraesCS1D01G321000 chr7B 680853211 680854497 1286 True 859.000000 859 79.073000 960 2228 1 chr7B.!!$R2 1268
11 TraesCS1D01G321000 chr7B 732711701 732713668 1967 True 301.733333 678 81.086667 931 2953 3 chr7B.!!$R3 2022
12 TraesCS1D01G321000 chr7A 693397730 693399006 1276 True 883.000000 883 79.457000 959 2228 1 chr7A.!!$R1 1269
13 TraesCS1D01G321000 chr7A 693492717 693493967 1250 False 361.000000 361 72.606000 979 2211 1 chr7A.!!$F1 1232

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
50 51 0.179124 GGTCCGCTAGAGTTGCTCTG 60.179 60.0 8.75 1.26 41.37 3.35 F
749 878 0.239613 TGCAACACACACACACACAC 59.760 50.0 0.00 0.00 0.00 3.82 F
1848 2862 0.035152 TGGATGTCTGGGTGATGCAC 60.035 55.0 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 2150 0.321564 AATGACGCCAGTGCAAGCTA 60.322 50.000 0.00 0.00 37.32 3.32 R
2176 3207 0.757188 GGAGAATGGAGGCTCCTCGA 60.757 60.000 32.28 14.76 45.72 4.04 R
2927 4367 1.210155 GCTGATGGTTCACCGTTGC 59.790 57.895 0.00 0.00 39.43 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
17 18 2.986290 CCGGAATTTTTGGGGGCC 59.014 61.111 0.00 0.00 0.00 5.80
18 19 2.665089 CCGGAATTTTTGGGGGCCC 61.665 63.158 15.76 15.76 0.00 5.80
19 20 2.986290 GGAATTTTTGGGGGCCCG 59.014 61.111 17.79 0.00 39.42 6.13
20 21 2.665089 GGAATTTTTGGGGGCCCGG 61.665 63.158 17.79 0.00 39.42 5.73
21 22 3.323758 GAATTTTTGGGGGCCCGGC 62.324 63.158 17.79 3.76 39.42 6.13
45 46 2.494918 CGGGGTCCGCTAGAGTTG 59.505 66.667 4.18 0.00 41.17 3.16
46 47 2.187163 GGGGTCCGCTAGAGTTGC 59.813 66.667 0.00 0.00 0.00 4.17
47 48 2.359967 GGGGTCCGCTAGAGTTGCT 61.360 63.158 0.00 0.00 0.00 3.91
48 49 1.142097 GGGTCCGCTAGAGTTGCTC 59.858 63.158 0.00 0.00 0.00 4.26
49 50 1.324005 GGGTCCGCTAGAGTTGCTCT 61.324 60.000 4.02 4.02 43.83 4.09
50 51 0.179124 GGTCCGCTAGAGTTGCTCTG 60.179 60.000 8.75 1.26 41.37 3.35
51 52 0.179124 GTCCGCTAGAGTTGCTCTGG 60.179 60.000 8.75 6.99 41.37 3.86
57 58 2.430332 GCTAGAGTTGCTCTGGATGTCT 59.570 50.000 12.63 0.00 40.77 3.41
64 65 1.620739 GCTCTGGATGTCTGCCCTGA 61.621 60.000 0.00 0.00 0.00 3.86
98 101 1.388531 GTCCTCACCCTCTCCCTCA 59.611 63.158 0.00 0.00 0.00 3.86
113 116 1.379176 CTCACTCGAGCTCTCCCCA 60.379 63.158 13.61 0.00 31.00 4.96
114 117 0.967887 CTCACTCGAGCTCTCCCCAA 60.968 60.000 13.61 0.00 31.00 4.12
115 118 0.541998 TCACTCGAGCTCTCCCCAAA 60.542 55.000 13.61 0.00 0.00 3.28
165 168 3.844090 GCACCTCGAGCTCTCCCC 61.844 72.222 12.85 0.00 0.00 4.81
169 172 2.837291 CTCGAGCTCTCCCCCTGG 60.837 72.222 12.85 0.00 0.00 4.45
230 233 2.737376 GGCACGGTTCGACCACTC 60.737 66.667 5.15 0.00 38.47 3.51
231 234 2.028484 GCACGGTTCGACCACTCA 59.972 61.111 5.15 0.00 38.47 3.41
232 235 1.593209 GCACGGTTCGACCACTCAA 60.593 57.895 5.15 0.00 38.47 3.02
295 313 4.695560 CCGCCTTCTTCGGTTCTT 57.304 55.556 0.00 0.00 41.85 2.52
296 314 2.457080 CCGCCTTCTTCGGTTCTTC 58.543 57.895 0.00 0.00 41.85 2.87
381 424 3.008375 CCCTCTTCATGTTTCTCTCCACA 59.992 47.826 0.00 0.00 0.00 4.17
382 425 4.324099 CCCTCTTCATGTTTCTCTCCACAT 60.324 45.833 0.00 0.00 33.72 3.21
591 701 1.128507 CAGACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
652 770 9.832445 TTCTTCTTTTCAACTGTAACAGATACT 57.168 29.630 0.00 0.00 35.42 2.12
654 772 7.421530 TCTTTTCAACTGTAACAGATACTGC 57.578 36.000 0.00 0.00 37.05 4.40
655 773 6.989759 TCTTTTCAACTGTAACAGATACTGCA 59.010 34.615 0.00 0.00 37.05 4.41
656 774 7.497579 TCTTTTCAACTGTAACAGATACTGCAA 59.502 33.333 0.00 0.00 37.05 4.08
657 775 6.785488 TTCAACTGTAACAGATACTGCAAG 57.215 37.500 0.00 0.00 37.05 4.01
658 776 5.853936 TCAACTGTAACAGATACTGCAAGT 58.146 37.500 0.00 0.00 42.40 3.16
659 777 6.288294 TCAACTGTAACAGATACTGCAAGTT 58.712 36.000 0.00 0.00 40.92 2.66
660 778 6.765989 TCAACTGTAACAGATACTGCAAGTTT 59.234 34.615 0.00 0.00 40.92 2.66
661 779 6.787085 ACTGTAACAGATACTGCAAGTTTC 57.213 37.500 0.00 0.00 44.00 2.78
700 818 8.369462 CAACGAATGCTACAACTCTAATTTTC 57.631 34.615 0.00 0.00 0.00 2.29
704 822 8.869897 CGAATGCTACAACTCTAATTTTCTACA 58.130 33.333 0.00 0.00 0.00 2.74
707 825 8.029642 TGCTACAACTCTAATTTTCTACAAGC 57.970 34.615 0.00 0.00 0.00 4.01
708 826 7.878127 TGCTACAACTCTAATTTTCTACAAGCT 59.122 33.333 0.00 0.00 0.00 3.74
709 827 8.722394 GCTACAACTCTAATTTTCTACAAGCTT 58.278 33.333 0.00 0.00 0.00 3.74
723 852 4.959399 GCTTCTCAGCAGCCTCAT 57.041 55.556 0.00 0.00 46.49 2.90
739 868 3.735746 GCCTCATTTTTACTGCAACACAC 59.264 43.478 0.00 0.00 0.00 3.82
743 872 5.098893 TCATTTTTACTGCAACACACACAC 58.901 37.500 0.00 0.00 0.00 3.82
747 876 0.521291 ACTGCAACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
748 877 0.520847 CTGCAACACACACACACACA 59.479 50.000 0.00 0.00 0.00 3.72
749 878 0.239613 TGCAACACACACACACACAC 59.760 50.000 0.00 0.00 0.00 3.82
750 879 0.239613 GCAACACACACACACACACA 59.760 50.000 0.00 0.00 0.00 3.72
753 882 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
754 883 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
756 885 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
757 886 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
758 887 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
759 888 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
760 889 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
761 890 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
762 891 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
763 892 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
764 893 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
765 894 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
766 895 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
767 896 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
768 897 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
769 898 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
770 899 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
771 900 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
787 916 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
875 1008 9.438291 CACAAACAACTCTTTAACTACAATCAG 57.562 33.333 0.00 0.00 0.00 2.90
897 1030 5.602458 GGTGTAAGCTAACAGTTTGTACC 57.398 43.478 0.00 0.00 0.00 3.34
929 1068 4.084287 TCTTGATTTCAGCTGCTCCAAAT 58.916 39.130 9.47 9.83 0.00 2.32
964 1107 1.202710 TGGACGAACTAAAGCTTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
999 1149 2.987547 GGACTCCGACGGACCACA 60.988 66.667 13.88 0.00 0.00 4.17
1044 1195 2.569354 GCTCGAGGATCTGCCGGAT 61.569 63.158 15.58 0.00 43.43 4.18
1056 1216 3.109928 TCTGCCGGATGATATCATGGAT 58.890 45.455 22.86 0.00 36.57 3.41
1086 1252 1.002134 CAGGTTGCCGTCCAAGGAT 60.002 57.895 0.00 0.00 33.21 3.24
1467 1673 0.639392 ATAGGGTGCTCTGGGTCTCT 59.361 55.000 0.00 0.00 0.00 3.10
1557 1771 1.620819 AGAGTCAGAATGCCGACAGTT 59.379 47.619 0.00 0.00 34.48 3.16
1670 2657 1.358725 CGTCATTGTGGTACCAGCGG 61.359 60.000 16.93 5.63 0.00 5.52
1708 2695 4.500703 GGAGACATTATTGTGTTCGACG 57.499 45.455 0.00 0.00 35.79 5.12
1848 2862 0.035152 TGGATGTCTGGGTGATGCAC 60.035 55.000 0.00 0.00 0.00 4.57
1989 3015 3.242284 CGGTGCGATTGTTGAACGATATT 60.242 43.478 0.00 0.00 0.00 1.28
1990 3016 4.026393 CGGTGCGATTGTTGAACGATATTA 60.026 41.667 0.00 0.00 0.00 0.98
2176 3207 5.221382 GGCCATGATATGATGCAAGAAAAGT 60.221 40.000 0.00 0.00 0.00 2.66
2253 3300 3.348119 CCTTTTGTCCTTAGCTCTTCCC 58.652 50.000 0.00 0.00 0.00 3.97
2292 3378 5.707764 TCATTTTGGATGTGATCGTTTGGTA 59.292 36.000 0.00 0.00 0.00 3.25
2297 3383 4.250464 GGATGTGATCGTTTGGTACTTGA 58.750 43.478 0.00 0.00 0.00 3.02
2298 3384 4.330074 GGATGTGATCGTTTGGTACTTGAG 59.670 45.833 0.00 0.00 0.00 3.02
2338 3522 7.178983 TCAATGATCTTTGGCAAGGTTAAGATT 59.821 33.333 18.33 2.40 37.44 2.40
2346 3530 5.324409 TGGCAAGGTTAAGATTCACAGATT 58.676 37.500 0.00 0.00 0.00 2.40
2395 3628 5.568685 TCTAGATCTCTTACATATGCCGC 57.431 43.478 0.00 0.00 0.00 6.53
2538 3778 1.304547 ACTCGGGAGCACTGCTAGT 60.305 57.895 2.71 0.64 39.88 2.57
2806 4204 2.423892 CTCTAGCTTCGCACAAGTAGGA 59.576 50.000 0.00 0.00 0.00 2.94
2892 4325 3.045601 AGTAGACACTGACAACCATGC 57.954 47.619 0.00 0.00 32.25 4.06
2927 4367 0.518636 CACAGATGCCACAGAAACGG 59.481 55.000 0.00 0.00 0.00 4.44
2972 4429 5.178096 TCTGATACAGAATTGGGAGCAAA 57.822 39.130 0.00 0.00 37.57 3.68
3018 4475 3.903090 AGGAATCCTTGCAAAAATGTCCA 59.097 39.130 14.68 0.00 0.00 4.02
3044 4501 3.439857 TCCAGGGAAAATGGTCTCAAG 57.560 47.619 0.00 0.00 39.01 3.02
3051 4508 6.647895 CAGGGAAAATGGTCTCAAGAAATTTG 59.352 38.462 0.00 0.00 0.00 2.32
3053 4510 6.424812 GGGAAAATGGTCTCAAGAAATTTGTG 59.575 38.462 0.00 0.00 0.00 3.33
3113 4570 3.513119 AGATACTTCAGCTCACAGCAAGA 59.487 43.478 0.00 0.00 45.56 3.02
3121 4578 2.620585 AGCTCACAGCAAGAAAAGTTCC 59.379 45.455 0.00 0.00 45.56 3.62
3122 4579 2.358898 GCTCACAGCAAGAAAAGTTCCA 59.641 45.455 0.00 0.00 41.89 3.53
3123 4580 3.181487 GCTCACAGCAAGAAAAGTTCCAA 60.181 43.478 0.00 0.00 41.89 3.53
3158 4615 9.166173 CACATATACACAAGGAAGAAAGAATGA 57.834 33.333 0.00 0.00 0.00 2.57
3168 4625 7.660030 AGGAAGAAAGAATGAAAGGAAACAA 57.340 32.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.986290 GGGCCCCCAAAAATTCCG 59.014 61.111 12.23 0.00 35.81 4.30
3 4 2.986290 CCGGGCCCCCAAAAATTC 59.014 61.111 18.66 0.00 35.37 2.17
4 5 3.326578 GCCGGGCCCCCAAAAATT 61.327 61.111 18.66 0.00 35.37 1.82
29 30 2.187163 GCAACTCTAGCGGACCCC 59.813 66.667 0.00 0.00 0.00 4.95
30 31 1.142097 GAGCAACTCTAGCGGACCC 59.858 63.158 0.00 0.00 37.01 4.46
31 32 0.179124 CAGAGCAACTCTAGCGGACC 60.179 60.000 0.00 0.00 38.99 4.46
32 33 0.179124 CCAGAGCAACTCTAGCGGAC 60.179 60.000 0.00 0.00 38.99 4.79
33 34 0.323451 TCCAGAGCAACTCTAGCGGA 60.323 55.000 0.00 0.00 38.99 5.54
34 35 0.749649 ATCCAGAGCAACTCTAGCGG 59.250 55.000 0.00 0.00 38.99 5.52
35 36 1.135915 ACATCCAGAGCAACTCTAGCG 59.864 52.381 0.00 0.00 38.99 4.26
36 37 2.430332 AGACATCCAGAGCAACTCTAGC 59.570 50.000 0.00 0.00 38.99 3.42
37 38 3.737663 GCAGACATCCAGAGCAACTCTAG 60.738 52.174 0.00 0.00 38.99 2.43
38 39 2.167281 GCAGACATCCAGAGCAACTCTA 59.833 50.000 0.00 0.00 38.99 2.43
39 40 1.066286 GCAGACATCCAGAGCAACTCT 60.066 52.381 0.00 0.00 42.11 3.24
40 41 1.367659 GCAGACATCCAGAGCAACTC 58.632 55.000 0.00 0.00 0.00 3.01
41 42 0.035630 GGCAGACATCCAGAGCAACT 60.036 55.000 0.00 0.00 0.00 3.16
42 43 1.028868 GGGCAGACATCCAGAGCAAC 61.029 60.000 0.00 0.00 0.00 4.17
43 44 1.203441 AGGGCAGACATCCAGAGCAA 61.203 55.000 0.00 0.00 0.00 3.91
44 45 1.614525 AGGGCAGACATCCAGAGCA 60.615 57.895 0.00 0.00 0.00 4.26
45 46 1.153208 CAGGGCAGACATCCAGAGC 60.153 63.158 0.00 0.00 0.00 4.09
46 47 0.464870 CTCAGGGCAGACATCCAGAG 59.535 60.000 0.00 0.00 0.00 3.35
47 48 0.041684 TCTCAGGGCAGACATCCAGA 59.958 55.000 0.00 0.00 0.00 3.86
48 49 0.177604 GTCTCAGGGCAGACATCCAG 59.822 60.000 0.00 0.00 42.25 3.86
49 50 0.545071 TGTCTCAGGGCAGACATCCA 60.545 55.000 2.31 0.00 46.43 3.41
50 51 2.290847 TGTCTCAGGGCAGACATCC 58.709 57.895 2.31 0.00 46.43 3.51
64 65 0.391263 GGACGGCGAATTTCCTGTCT 60.391 55.000 16.62 0.00 32.09 3.41
98 101 1.261238 CCTTTGGGGAGAGCTCGAGT 61.261 60.000 15.13 0.23 37.23 4.18
113 116 1.309876 GGATCCCCTTCCCTTCCTTT 58.690 55.000 0.00 0.00 0.00 3.11
114 117 0.123266 TGGATCCCCTTCCCTTCCTT 59.877 55.000 9.90 0.00 34.67 3.36
115 118 0.327964 CTGGATCCCCTTCCCTTCCT 60.328 60.000 9.90 0.00 34.67 3.36
214 217 1.593209 TTGAGTGGTCGAACCGTGC 60.593 57.895 0.00 0.00 42.58 5.34
226 229 3.114616 CAGCGGCTCGGTTGAGTG 61.115 66.667 0.00 0.00 44.48 3.51
253 259 1.249407 GAGAAGGTGTCTGTCGGAGT 58.751 55.000 0.00 0.00 36.41 3.85
289 307 2.434359 CTGCGTCGGGGAAGAACC 60.434 66.667 0.00 0.00 38.08 3.62
290 308 2.434359 CCTGCGTCGGGGAAGAAC 60.434 66.667 0.00 0.00 0.00 3.01
291 309 2.920912 ACCTGCGTCGGGGAAGAA 60.921 61.111 9.14 0.00 33.40 2.52
292 310 3.691342 CACCTGCGTCGGGGAAGA 61.691 66.667 9.14 0.00 33.40 2.87
293 311 3.649277 CTCACCTGCGTCGGGGAAG 62.649 68.421 9.14 3.03 35.69 3.46
294 312 3.691342 CTCACCTGCGTCGGGGAA 61.691 66.667 9.14 0.00 35.69 3.97
381 424 1.066573 GCGTAGGCCAGATGCAGATAT 60.067 52.381 15.14 0.00 43.89 1.63
382 425 0.318441 GCGTAGGCCAGATGCAGATA 59.682 55.000 15.14 0.00 43.89 1.98
591 701 1.063806 CGTCGCCTGAAAACTCTCTG 58.936 55.000 0.00 0.00 0.00 3.35
617 727 8.972262 ACAGTTGAAAAGAAGAAAAGAGAAAC 57.028 30.769 0.00 0.00 0.00 2.78
658 776 1.949525 GTTGCTCAGCTCAGTTGGAAA 59.050 47.619 0.00 0.00 0.00 3.13
659 777 1.597742 GTTGCTCAGCTCAGTTGGAA 58.402 50.000 0.00 0.00 0.00 3.53
660 778 0.601046 CGTTGCTCAGCTCAGTTGGA 60.601 55.000 0.00 0.00 0.00 3.53
661 779 0.601046 TCGTTGCTCAGCTCAGTTGG 60.601 55.000 0.00 0.00 0.00 3.77
700 818 1.066286 AGGCTGCTGAGAAGCTTGTAG 60.066 52.381 13.03 0.00 40.64 2.74
704 822 0.619505 ATGAGGCTGCTGAGAAGCTT 59.380 50.000 13.03 4.07 40.64 3.74
707 825 4.699257 AGTAAAAATGAGGCTGCTGAGAAG 59.301 41.667 0.00 0.00 0.00 2.85
708 826 4.456911 CAGTAAAAATGAGGCTGCTGAGAA 59.543 41.667 0.00 0.00 0.00 2.87
709 827 4.005650 CAGTAAAAATGAGGCTGCTGAGA 58.994 43.478 0.00 0.00 0.00 3.27
723 852 4.230657 GTGTGTGTGTGTTGCAGTAAAAA 58.769 39.130 0.00 0.00 0.00 1.94
739 868 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
743 872 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
747 876 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
748 877 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
749 878 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
750 879 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
753 882 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
754 883 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
756 885 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
757 886 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
758 887 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
759 888 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
760 889 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
761 890 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
762 891 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
763 892 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
764 893 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
765 894 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
766 895 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
767 896 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
768 897 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
769 898 2.916089 CAATTGTGTGTGTGTGTGTGTG 59.084 45.455 0.00 0.00 0.00 3.82
770 899 2.670789 GCAATTGTGTGTGTGTGTGTGT 60.671 45.455 7.40 0.00 0.00 3.72
771 900 1.919263 GCAATTGTGTGTGTGTGTGTG 59.081 47.619 7.40 0.00 0.00 3.82
787 916 0.318955 GCTGCAAAGTTGACGGCAAT 60.319 50.000 7.13 0.00 36.92 3.56
875 1008 5.178809 CAGGTACAAACTGTTAGCTTACACC 59.821 44.000 0.43 0.00 0.00 4.16
897 1030 4.215827 AGCTGAAATCAAGAAGACAAGCAG 59.784 41.667 0.00 0.00 0.00 4.24
929 1068 1.534476 TCCACCCACGGCTAACTCA 60.534 57.895 0.00 0.00 0.00 3.41
964 1107 0.600255 CCGGTCAGCTGAAAAGACGT 60.600 55.000 20.19 0.00 33.18 4.34
999 1149 2.273449 CCTCTTCTGCCCGGCATT 59.727 61.111 13.86 0.00 38.13 3.56
1019 1170 0.820226 CAGATCCTCGAGCAAGGTCA 59.180 55.000 6.99 0.00 37.69 4.02
1024 1175 2.496341 CGGCAGATCCTCGAGCAA 59.504 61.111 6.99 0.00 0.00 3.91
1056 1216 3.704566 ACGGCAACCTGATGAGTATCTTA 59.295 43.478 0.00 0.00 34.92 2.10
1335 1521 3.369471 GGTTGCAGATGTAGAGCTGGTTA 60.369 47.826 7.30 0.00 36.03 2.85
1482 1694 5.326069 AGGACGTATAAGCTGGATGTAGAT 58.674 41.667 0.00 0.00 0.00 1.98
1638 2150 0.321564 AATGACGCCAGTGCAAGCTA 60.322 50.000 0.00 0.00 37.32 3.32
1670 2657 3.357079 CGCCGCCTCCCATAATGC 61.357 66.667 0.00 0.00 0.00 3.56
1708 2695 1.005340 CGGAATGACTCTGCTTCTGC 58.995 55.000 0.00 0.00 40.20 4.26
1848 2862 4.379186 GCCCAGATTTCAGCATCATAATCG 60.379 45.833 0.00 0.00 33.38 3.34
1989 3015 3.807622 GCTCACACTTGTTTAGCACAGTA 59.192 43.478 8.10 0.00 36.48 2.74
1990 3016 2.614057 GCTCACACTTGTTTAGCACAGT 59.386 45.455 8.10 0.00 36.48 3.55
2176 3207 0.757188 GGAGAATGGAGGCTCCTCGA 60.757 60.000 32.28 14.76 45.72 4.04
2253 3300 5.009510 TCCAAAATGACATGTGGTACAAGTG 59.990 40.000 1.15 0.00 44.16 3.16
2292 3378 8.262933 TCATTGATCAAGACATCATACTCAAGT 58.737 33.333 14.54 0.00 32.69 3.16
2297 3383 9.848710 AAAGATCATTGATCAAGACATCATACT 57.151 29.630 24.71 0.79 41.12 2.12
2298 3384 9.880064 CAAAGATCATTGATCAAGACATCATAC 57.120 33.333 24.71 0.00 41.12 2.39
2338 3522 5.247862 ACAACATAGCATGACAATCTGTGA 58.752 37.500 0.00 0.00 0.00 3.58
2346 3530 4.766373 ACATTCCAACAACATAGCATGACA 59.234 37.500 0.00 0.00 0.00 3.58
2395 3628 3.367292 CCGGACATTTGGAATCAAACAGG 60.367 47.826 0.00 0.00 44.53 4.00
2469 3704 7.449247 AGGATTTCTTAGATCATAGAAGCACC 58.551 38.462 8.84 11.85 32.43 5.01
2565 3808 6.304356 TCAGCAAGTTTCTTTCTACACATG 57.696 37.500 0.00 0.00 0.00 3.21
2566 3809 6.767902 TCTTCAGCAAGTTTCTTTCTACACAT 59.232 34.615 0.00 0.00 0.00 3.21
2611 3854 6.656632 TGAACAGAGGACCATCATATCTAC 57.343 41.667 0.00 0.00 0.00 2.59
2676 4073 2.738587 TGGCTACAAACTGGACCAAA 57.261 45.000 0.00 0.00 0.00 3.28
2806 4204 4.452455 CGTAGAGCCAGTGAAAATTGACTT 59.548 41.667 0.00 0.00 0.00 3.01
2875 4308 1.230635 GCGCATGGTTGTCAGTGTCT 61.231 55.000 0.30 0.00 0.00 3.41
2892 4325 1.462283 CTGTGATGTGTTCCTTCTGCG 59.538 52.381 0.00 0.00 0.00 5.18
2927 4367 1.210155 GCTGATGGTTCACCGTTGC 59.790 57.895 0.00 0.00 39.43 4.17
2958 4398 4.751767 TGTTTTGTTTGCTCCCAATTCT 57.248 36.364 0.00 0.00 0.00 2.40
2972 4429 2.302733 GGAATTGGGAGCCATGTTTTGT 59.697 45.455 0.00 0.00 31.53 2.83
3018 4475 4.492646 AGACCATTTTCCCTGGATGTTTT 58.507 39.130 0.00 0.00 37.22 2.43
3027 4484 6.327365 ACAAATTTCTTGAGACCATTTTCCCT 59.673 34.615 0.00 0.00 0.00 4.20
3113 4570 4.016444 TGTGCTCTTCACTTGGAACTTTT 58.984 39.130 0.00 0.00 45.81 2.27
3121 4578 6.183360 CCTTGTGTATATGTGCTCTTCACTTG 60.183 42.308 0.00 0.00 45.81 3.16
3122 4579 5.877012 CCTTGTGTATATGTGCTCTTCACTT 59.123 40.000 0.00 0.00 45.81 3.16
3123 4580 5.187772 TCCTTGTGTATATGTGCTCTTCACT 59.812 40.000 0.00 0.00 45.81 3.41
3137 4594 7.944554 TCCTTTCATTCTTTCTTCCTTGTGTAT 59.055 33.333 0.00 0.00 0.00 2.29
3158 4615 9.225436 TGTTAGCATTTTCTTTTTGTTTCCTTT 57.775 25.926 0.00 0.00 0.00 3.11
3168 4625 7.271511 TGTCCATGTTGTTAGCATTTTCTTTT 58.728 30.769 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.