Multiple sequence alignment - TraesCS4D01G184000

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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 TraesCS4D01G184000 chr4D 100.000 3819 0 0 1 3819 322229250 322225432 0.000000e+00 7053.0
1 TraesCS4D01G184000 chr4D 97.573 618 14 1 1 617 419162833 419162216 0.000000e+00 1057.0
2 TraesCS4D01G184000 chr4D 79.351 339 43 20 2040 2366 322227133 322226810 2.990000e-51 213.0
3 TraesCS4D01G184000 chr4D 79.290 338 45 18 2118 2441 322227211 322226885 2.990000e-51 213.0
4 TraesCS4D01G184000 chr5D 95.272 994 19 8 2849 3819 480810382 480809394 0.000000e+00 1550.0
5 TraesCS4D01G184000 chr4B 89.119 1158 55 40 1341 2449 399036174 399037309 0.000000e+00 1375.0
6 TraesCS4D01G184000 chr4B 89.227 854 47 17 2040 2848 399036939 399037792 0.000000e+00 1026.0
7 TraesCS4D01G184000 chr4B 81.074 391 37 21 984 1359 399035790 399036158 1.040000e-70 278.0
8 TraesCS4D01G184000 chr4B 90.132 152 13 2 2216 2366 399037220 399037370 3.010000e-46 196.0
9 TraesCS4D01G184000 chr4B 89.552 67 3 1 838 904 399035600 399035662 8.790000e-12 82.4
10 TraesCS4D01G184000 chr7B 90.807 979 55 18 2850 3817 616897335 616898289 0.000000e+00 1277.0
11 TraesCS4D01G184000 chr7B 76.517 890 115 59 2936 3754 746624851 746623985 2.140000e-107 399.0
12 TraesCS4D01G184000 chr6B 90.361 996 54 20 2846 3819 704862518 704863493 0.000000e+00 1269.0
13 TraesCS4D01G184000 chr6B 95.082 61 2 1 2849 2909 22756164 22756105 1.130000e-15 95.3
14 TraesCS4D01G184000 chr6B 82.353 85 3 5 3586 3658 703460876 703460792 3.180000e-06 63.9
15 TraesCS4D01G184000 chr4A 93.832 843 22 14 1341 2175 150658144 150658964 0.000000e+00 1242.0
16 TraesCS4D01G184000 chr4A 96.934 685 21 0 2164 2848 150658986 150659670 0.000000e+00 1149.0
17 TraesCS4D01G184000 chr4A 83.127 403 38 20 929 1322 150657567 150657948 1.310000e-89 340.0
18 TraesCS4D01G184000 chr4A 78.883 573 54 25 3050 3596 66763305 66763836 3.680000e-85 326.0
19 TraesCS4D01G184000 chr4A 78.883 573 54 24 3050 3596 66777107 66777638 3.680000e-85 326.0
20 TraesCS4D01G184000 chr4A 82.429 387 22 20 614 963 150657179 150657556 2.880000e-76 296.0
21 TraesCS4D01G184000 chr4A 90.909 165 9 4 2291 2449 150659038 150659202 2.310000e-52 217.0
22 TraesCS4D01G184000 chr4A 78.223 349 45 17 2040 2357 150658907 150659255 1.080000e-45 195.0
23 TraesCS4D01G184000 chr4A 94.643 56 3 0 2118 2173 150658829 150658884 1.890000e-13 87.9
24 TraesCS4D01G184000 chr6D 98.358 609 10 0 1 609 11162802 11163410 0.000000e+00 1070.0
25 TraesCS4D01G184000 chr6D 97.876 612 13 0 1 612 290248725 290248114 0.000000e+00 1059.0
26 TraesCS4D01G184000 chr6D 83.152 825 82 28 3031 3819 61008934 61008131 0.000000e+00 701.0
27 TraesCS4D01G184000 chr6D 79.915 468 68 20 3138 3594 437346176 437346628 1.710000e-83 320.0
28 TraesCS4D01G184000 chr3D 98.203 612 11 0 1 612 297448411 297447800 0.000000e+00 1070.0
29 TraesCS4D01G184000 chr3D 98.194 609 11 0 1 609 288046171 288046779 0.000000e+00 1064.0
30 TraesCS4D01G184000 chr3D 93.939 66 4 0 2846 2911 2776349 2776414 2.430000e-17 100.0
31 TraesCS4D01G184000 chr3D 91.667 48 3 1 3773 3819 435691577 435691624 8.860000e-07 65.8
32 TraesCS4D01G184000 chr7D 98.039 612 12 0 1 612 7724477 7723866 0.000000e+00 1064.0
33 TraesCS4D01G184000 chr7D 98.194 609 11 0 1 609 568762005 568762613 0.000000e+00 1064.0
34 TraesCS4D01G184000 chr7D 89.308 636 29 17 3221 3819 60117711 60117078 0.000000e+00 761.0
35 TraesCS4D01G184000 chr7D 90.179 336 17 5 2851 3184 60130260 60129939 1.270000e-114 424.0
36 TraesCS4D01G184000 chr7D 95.238 63 3 0 2848 2910 582297246 582297308 2.430000e-17 100.0
37 TraesCS4D01G184000 chr2D 98.194 609 11 0 1 609 402548731 402549339 0.000000e+00 1064.0
38 TraesCS4D01G184000 chr2D 96.975 628 16 3 1 627 407655527 407654902 0.000000e+00 1051.0
39 TraesCS4D01G184000 chr2D 91.667 48 3 1 3773 3819 54003163 54003116 8.860000e-07 65.8
40 TraesCS4D01G184000 chr1A 88.132 910 43 27 2933 3819 39653556 39654423 0.000000e+00 1022.0
41 TraesCS4D01G184000 chr1D 76.049 405 57 24 3181 3559 377779722 377779332 1.410000e-39 174.0
42 TraesCS4D01G184000 chr3B 75.811 339 49 17 3374 3704 206162236 206161923 1.430000e-29 141.0
43 TraesCS4D01G184000 chr3B 76.735 245 34 16 3374 3616 820775538 820775761 8.670000e-22 115.0
44 TraesCS4D01G184000 chr7A 92.754 69 4 1 2847 2915 13776926 13776993 8.730000e-17 99.0
45 TraesCS4D01G184000 chr6A 91.549 71 5 1 2840 2910 68503308 68503239 3.140000e-16 97.1


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 TraesCS4D01G184000 chr4D 322225432 322229250 3818 True 2493.000000 7053 86.213667 1 3819 3 chr4D.!!$R2 3818
1 TraesCS4D01G184000 chr4D 419162216 419162833 617 True 1057.000000 1057 97.573000 1 617 1 chr4D.!!$R1 616
2 TraesCS4D01G184000 chr5D 480809394 480810382 988 True 1550.000000 1550 95.272000 2849 3819 1 chr5D.!!$R1 970
3 TraesCS4D01G184000 chr4B 399035600 399037792 2192 False 591.480000 1375 87.820800 838 2848 5 chr4B.!!$F1 2010
4 TraesCS4D01G184000 chr7B 616897335 616898289 954 False 1277.000000 1277 90.807000 2850 3817 1 chr7B.!!$F1 967
5 TraesCS4D01G184000 chr7B 746623985 746624851 866 True 399.000000 399 76.517000 2936 3754 1 chr7B.!!$R1 818
6 TraesCS4D01G184000 chr6B 704862518 704863493 975 False 1269.000000 1269 90.361000 2846 3819 1 chr6B.!!$F1 973
7 TraesCS4D01G184000 chr4A 150657179 150659670 2491 False 503.842857 1242 88.585286 614 2848 7 chr4A.!!$F3 2234
8 TraesCS4D01G184000 chr4A 66763305 66763836 531 False 326.000000 326 78.883000 3050 3596 1 chr4A.!!$F1 546
9 TraesCS4D01G184000 chr4A 66777107 66777638 531 False 326.000000 326 78.883000 3050 3596 1 chr4A.!!$F2 546
10 TraesCS4D01G184000 chr6D 11162802 11163410 608 False 1070.000000 1070 98.358000 1 609 1 chr6D.!!$F1 608
11 TraesCS4D01G184000 chr6D 290248114 290248725 611 True 1059.000000 1059 97.876000 1 612 1 chr6D.!!$R2 611
12 TraesCS4D01G184000 chr6D 61008131 61008934 803 True 701.000000 701 83.152000 3031 3819 1 chr6D.!!$R1 788
13 TraesCS4D01G184000 chr3D 297447800 297448411 611 True 1070.000000 1070 98.203000 1 612 1 chr3D.!!$R1 611
14 TraesCS4D01G184000 chr3D 288046171 288046779 608 False 1064.000000 1064 98.194000 1 609 1 chr3D.!!$F2 608
15 TraesCS4D01G184000 chr7D 7723866 7724477 611 True 1064.000000 1064 98.039000 1 612 1 chr7D.!!$R1 611
16 TraesCS4D01G184000 chr7D 568762005 568762613 608 False 1064.000000 1064 98.194000 1 609 1 chr7D.!!$F1 608
17 TraesCS4D01G184000 chr7D 60117078 60117711 633 True 761.000000 761 89.308000 3221 3819 1 chr7D.!!$R2 598
18 TraesCS4D01G184000 chr2D 402548731 402549339 608 False 1064.000000 1064 98.194000 1 609 1 chr2D.!!$F1 608
19 TraesCS4D01G184000 chr2D 407654902 407655527 625 True 1051.000000 1051 96.975000 1 627 1 chr2D.!!$R2 626
20 TraesCS4D01G184000 chr1A 39653556 39654423 867 False 1022.000000 1022 88.132000 2933 3819 1 chr1A.!!$F1 886

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
930 968 0.034896 GAACCTTGCCTGACGGAAGA 59.965 55.0 0.0 0.0 0.0 2.87 F
1635 1949 0.394352 ATTGACGGGATGGAGTTGCC 60.394 55.0 0.0 0.0 37.1 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2306 0.419459 ACCCTCCTCTTCCATGACCT 59.581 55.000 0.0 0.0 0.0 3.85 R
3481 4021 1.742831 GGTGTGATGAGCCGCAAAATA 59.257 47.619 0.0 0.0 0.0 1.40 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
347 348 2.072487 GGAGCTATGGTGAGGGCCA 61.072 63.158 6.18 0.00 43.48 5.36
538 539 3.679980 GGTGCGGCATACAAGAGTATATG 59.320 47.826 5.72 0.00 38.88 1.78
579 580 4.116113 TGGGATAGGGGTACAAAACTGAT 58.884 43.478 0.00 0.00 0.00 2.90
609 610 7.804712 ACTAGAAGTCGTATACCATAATGACG 58.195 38.462 0.00 0.00 36.85 4.35
678 679 1.943293 GCGTCGTGCCTTTGGTTTA 59.057 52.632 0.00 0.00 37.76 2.01
681 682 2.073816 CGTCGTGCCTTTGGTTTATCT 58.926 47.619 0.00 0.00 0.00 1.98
682 683 2.159707 CGTCGTGCCTTTGGTTTATCTG 60.160 50.000 0.00 0.00 0.00 2.90
683 684 1.810151 TCGTGCCTTTGGTTTATCTGC 59.190 47.619 0.00 0.00 0.00 4.26
684 685 1.812571 CGTGCCTTTGGTTTATCTGCT 59.187 47.619 0.00 0.00 0.00 4.24
732 760 1.826054 CCGCCCACCAACAAACAGA 60.826 57.895 0.00 0.00 0.00 3.41
733 761 1.178534 CCGCCCACCAACAAACAGAT 61.179 55.000 0.00 0.00 0.00 2.90
752 780 2.619697 TGCCCCATTCAATTCCTTCA 57.380 45.000 0.00 0.00 0.00 3.02
795 833 1.027792 GGACCGCGTCTCTCTCTCTT 61.028 60.000 4.92 0.00 32.47 2.85
798 836 1.091537 CCGCGTCTCTCTCTCTTTCT 58.908 55.000 4.92 0.00 0.00 2.52
800 838 2.006888 CGCGTCTCTCTCTCTTTCTCT 58.993 52.381 0.00 0.00 0.00 3.10
805 843 4.142902 CGTCTCTCTCTCTTTCTCTCACAC 60.143 50.000 0.00 0.00 0.00 3.82
809 847 4.277174 TCTCTCTCTTTCTCTCACACACAC 59.723 45.833 0.00 0.00 0.00 3.82
821 859 2.106131 ACACACACAGCGCTTCGA 59.894 55.556 7.50 0.00 0.00 3.71
868 906 3.195698 GATCGAGCGTGTTGGCCC 61.196 66.667 0.00 0.00 0.00 5.80
891 929 1.269726 CGTGACAAAAAGCAAGGCCAT 60.270 47.619 5.01 0.00 0.00 4.40
892 930 2.030363 CGTGACAAAAAGCAAGGCCATA 60.030 45.455 5.01 0.00 0.00 2.74
897 935 1.571955 AAAAGCAAGGCCATAAGGGG 58.428 50.000 5.01 0.00 37.04 4.79
930 968 0.034896 GAACCTTGCCTGACGGAAGA 59.965 55.000 0.00 0.00 0.00 2.87
949 1030 2.022035 AGAGGGGAGAGAGAGAGAGAGA 60.022 54.545 0.00 0.00 0.00 3.10
950 1031 2.370189 GAGGGGAGAGAGAGAGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
952 1033 3.051341 AGGGGAGAGAGAGAGAGAGAGTA 60.051 52.174 0.00 0.00 0.00 2.59
960 1041 0.465460 AGAGAGAGAGTAGCAGCGGG 60.465 60.000 0.00 0.00 0.00 6.13
1018 1132 1.144503 CCATGGGGAAGGAGAGATTGG 59.855 57.143 2.85 0.00 35.59 3.16
1056 1170 1.153823 CCACCGCTTCTTCGTCGAT 60.154 57.895 0.00 0.00 0.00 3.59
1130 1244 2.103153 TCCACCCACTCTCAACTCTT 57.897 50.000 0.00 0.00 0.00 2.85
1131 1245 3.254093 TCCACCCACTCTCAACTCTTA 57.746 47.619 0.00 0.00 0.00 2.10
1132 1246 3.583228 TCCACCCACTCTCAACTCTTAA 58.417 45.455 0.00 0.00 0.00 1.85
1133 1247 4.168101 TCCACCCACTCTCAACTCTTAAT 58.832 43.478 0.00 0.00 0.00 1.40
1134 1248 4.223032 TCCACCCACTCTCAACTCTTAATC 59.777 45.833 0.00 0.00 0.00 1.75
1135 1249 4.223923 CCACCCACTCTCAACTCTTAATCT 59.776 45.833 0.00 0.00 0.00 2.40
1136 1250 5.415221 CACCCACTCTCAACTCTTAATCTC 58.585 45.833 0.00 0.00 0.00 2.75
1137 1251 5.047021 CACCCACTCTCAACTCTTAATCTCA 60.047 44.000 0.00 0.00 0.00 3.27
1138 1252 5.723887 ACCCACTCTCAACTCTTAATCTCAT 59.276 40.000 0.00 0.00 0.00 2.90
1139 1253 6.127196 ACCCACTCTCAACTCTTAATCTCATC 60.127 42.308 0.00 0.00 0.00 2.92
1140 1254 6.098124 CCCACTCTCAACTCTTAATCTCATCT 59.902 42.308 0.00 0.00 0.00 2.90
1141 1255 7.364585 CCCACTCTCAACTCTTAATCTCATCTT 60.365 40.741 0.00 0.00 0.00 2.40
1142 1256 7.706179 CCACTCTCAACTCTTAATCTCATCTTC 59.294 40.741 0.00 0.00 0.00 2.87
1143 1257 8.469200 CACTCTCAACTCTTAATCTCATCTTCT 58.531 37.037 0.00 0.00 0.00 2.85
1144 1258 9.034800 ACTCTCAACTCTTAATCTCATCTTCTT 57.965 33.333 0.00 0.00 0.00 2.52
1145 1259 9.874205 CTCTCAACTCTTAATCTCATCTTCTTT 57.126 33.333 0.00 0.00 0.00 2.52
1190 1305 5.482908 TCATCTGCTTCTCTAGTTTTGGTC 58.517 41.667 0.00 0.00 0.00 4.02
1202 1317 2.949644 AGTTTTGGTCCCAACTTTCTCG 59.050 45.455 0.00 0.00 35.46 4.04
1223 1349 2.932614 GTTGATCGTCCATGTTCCTGAG 59.067 50.000 0.00 0.00 0.00 3.35
1231 1357 4.442052 CGTCCATGTTCCTGAGTGTATGAT 60.442 45.833 0.00 0.00 0.00 2.45
1234 1360 4.102210 CCATGTTCCTGAGTGTATGATCCT 59.898 45.833 0.00 0.00 0.00 3.24
1257 1383 5.938322 TGCCGTTCTTCTTTCATGTATTTC 58.062 37.500 0.00 0.00 0.00 2.17
1258 1384 5.471797 TGCCGTTCTTCTTTCATGTATTTCA 59.528 36.000 0.00 0.00 0.00 2.69
1261 1387 7.542130 GCCGTTCTTCTTTCATGTATTTCATTT 59.458 33.333 0.00 0.00 34.09 2.32
1295 1425 6.749118 GGGATTGATCTTTCATGTCTTTTTCG 59.251 38.462 0.00 0.00 0.00 3.46
1318 1450 6.092122 TCGCCATGTTTAACTGAATCTGTTAG 59.908 38.462 11.53 2.80 31.51 2.34
1323 1464 6.235664 TGTTTAACTGAATCTGTTAGTCCCC 58.764 40.000 11.53 2.85 31.51 4.81
1330 1471 4.844085 TGAATCTGTTAGTCCCCTCTTTCA 59.156 41.667 0.00 0.00 0.00 2.69
1377 1684 8.605325 ACTAGGTGGTACTACTGAATATTGTT 57.395 34.615 9.41 0.00 0.00 2.83
1378 1685 8.693625 ACTAGGTGGTACTACTGAATATTGTTC 58.306 37.037 9.41 0.00 0.00 3.18
1379 1686 7.735326 AGGTGGTACTACTGAATATTGTTCT 57.265 36.000 9.41 0.00 0.00 3.01
1635 1949 0.394352 ATTGACGGGATGGAGTTGCC 60.394 55.000 0.00 0.00 37.10 4.52
1992 2306 1.201429 GCCAAGGTGAAGGAGGAGGA 61.201 60.000 0.00 0.00 0.00 3.71
2233 2580 4.785453 CCACCAGGCTTCGGCTCC 62.785 72.222 0.00 0.00 41.44 4.70
2255 2677 2.825836 CGGAACCATGCAGGAGCC 60.826 66.667 0.00 4.30 41.22 4.70
2725 3162 2.676471 ATGAGGCCGTTTGCACCC 60.676 61.111 0.00 0.00 43.89 4.61
2865 3302 3.186817 TGTTACGGGTTTGCTATTTCACG 59.813 43.478 0.00 0.00 0.00 4.35
2873 3310 6.278363 GGGTTTGCTATTTCACGTCTAGATA 58.722 40.000 0.00 0.00 0.00 1.98
3106 3561 6.183360 GCTGTCTTTGTCTGTTTTCTTCTTCT 60.183 38.462 0.00 0.00 0.00 2.85
3160 3618 3.128589 TCGCTACATCCTTTGCATTTTCC 59.871 43.478 0.00 0.00 0.00 3.13
3178 3636 4.569719 TTCCGAGGCCTTTTATCTTCTT 57.430 40.909 6.77 0.00 0.00 2.52
3179 3637 4.569719 TCCGAGGCCTTTTATCTTCTTT 57.430 40.909 6.77 0.00 0.00 2.52
3180 3638 4.918588 TCCGAGGCCTTTTATCTTCTTTT 58.081 39.130 6.77 0.00 0.00 2.27
3181 3639 5.321927 TCCGAGGCCTTTTATCTTCTTTTT 58.678 37.500 6.77 0.00 0.00 1.94
3328 3817 9.618410 GTTTCGATTTTTGTGTTCATTTAAGTG 57.382 29.630 0.00 0.00 0.00 3.16
3338 3827 9.891828 TTGTGTTCATTTAAGTGAATCATGTAC 57.108 29.630 15.45 3.74 39.99 2.90
3481 4021 0.320771 GTGTCACTCGCCCATTGTCT 60.321 55.000 0.00 0.00 0.00 3.41
3622 4168 4.442612 GCTGGCTCATCAGTTCTTCTCATA 60.443 45.833 0.00 0.00 37.12 2.15
3773 4357 7.788026 TCTTTTCTTGTCCTACTTTGTGAGTA 58.212 34.615 0.00 0.00 39.86 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
347 348 4.803426 CGCGGCCGCTTCTCTCTT 62.803 66.667 43.60 0.00 39.32 2.85
538 539 3.004002 CCCAAGTCGGTTTGTACCTTTTC 59.996 47.826 0.00 0.00 42.66 2.29
579 580 8.523915 TTATGGTATACGACTTCTAGTCCAAA 57.476 34.615 0.00 0.00 42.12 3.28
609 610 0.543174 AGGTCAGGTCAGGTCAGGTC 60.543 60.000 0.00 0.00 0.00 3.85
612 613 1.480137 GATCAGGTCAGGTCAGGTCAG 59.520 57.143 0.00 0.00 0.00 3.51
636 637 5.280945 TGTTCCATTTCTCTTTTGCTTTCG 58.719 37.500 0.00 0.00 0.00 3.46
653 654 2.933878 AAAGGCACGACGCTGTTCCA 62.934 55.000 0.00 0.00 41.91 3.53
655 656 1.082756 CAAAGGCACGACGCTGTTC 60.083 57.895 0.00 0.00 41.91 3.18
732 760 3.119009 TGAAGGAATTGAATGGGGCAT 57.881 42.857 0.00 0.00 0.00 4.40
733 761 2.619697 TGAAGGAATTGAATGGGGCA 57.380 45.000 0.00 0.00 0.00 5.36
777 815 0.806241 AAAGAGAGAGAGACGCGGTC 59.194 55.000 12.47 6.87 0.00 4.79
795 833 1.802508 CGCTGTGTGTGTGTGAGAGAA 60.803 52.381 0.00 0.00 0.00 2.87
798 836 1.882625 GCGCTGTGTGTGTGTGAGA 60.883 57.895 0.00 0.00 0.00 3.27
800 838 1.428370 GAAGCGCTGTGTGTGTGTGA 61.428 55.000 12.58 0.00 0.00 3.58
805 843 2.661566 CCTCGAAGCGCTGTGTGTG 61.662 63.158 12.58 2.01 0.00 3.82
809 847 3.485431 CTGCCTCGAAGCGCTGTG 61.485 66.667 12.58 6.77 34.65 3.66
868 906 0.934436 CCTTGCTTTTTGTCACGGCG 60.934 55.000 4.80 4.80 0.00 6.46
869 907 1.215014 GCCTTGCTTTTTGTCACGGC 61.215 55.000 0.00 0.00 39.79 5.68
870 908 0.597377 GGCCTTGCTTTTTGTCACGG 60.597 55.000 0.00 0.00 0.00 4.94
871 909 0.102120 TGGCCTTGCTTTTTGTCACG 59.898 50.000 3.32 0.00 0.00 4.35
897 935 3.412408 GTTCCCCTGCCCTCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
906 944 1.303643 GTCAGGCAAGGTTCCCCTG 60.304 63.158 6.37 6.37 45.88 4.45
921 959 0.033991 CTCTCTCCCCTCTTCCGTCA 60.034 60.000 0.00 0.00 0.00 4.35
930 968 2.293856 ACTCTCTCTCTCTCTCTCCCCT 60.294 54.545 0.00 0.00 0.00 4.79
949 1030 2.060980 CCTTCCTCCCGCTGCTACT 61.061 63.158 0.00 0.00 0.00 2.57
950 1031 2.022240 CTCCTTCCTCCCGCTGCTAC 62.022 65.000 0.00 0.00 0.00 3.58
952 1033 3.080121 CTCCTTCCTCCCGCTGCT 61.080 66.667 0.00 0.00 0.00 4.24
960 1041 1.107945 CTTCTCCGTCCTCCTTCCTC 58.892 60.000 0.00 0.00 0.00 3.71
1004 1118 0.182299 CAGGGCCAATCTCTCCTTCC 59.818 60.000 6.18 0.00 0.00 3.46
1018 1132 4.154347 CCTCTCCAGCGTCAGGGC 62.154 72.222 0.00 0.00 0.00 5.19
1082 1196 0.249573 ACGTACGTTGTTGAGGTGGG 60.250 55.000 16.72 0.00 0.00 4.61
1149 1263 9.404848 AGCAGATGAGATTGAGAATATTTTTCA 57.595 29.630 0.00 0.00 0.00 2.69
1152 1266 9.629878 AGAAGCAGATGAGATTGAGAATATTTT 57.370 29.630 0.00 0.00 0.00 1.82
1153 1267 9.275398 GAGAAGCAGATGAGATTGAGAATATTT 57.725 33.333 0.00 0.00 0.00 1.40
1154 1268 8.653191 AGAGAAGCAGATGAGATTGAGAATATT 58.347 33.333 0.00 0.00 0.00 1.28
1155 1269 8.197592 AGAGAAGCAGATGAGATTGAGAATAT 57.802 34.615 0.00 0.00 0.00 1.28
1156 1270 7.600231 AGAGAAGCAGATGAGATTGAGAATA 57.400 36.000 0.00 0.00 0.00 1.75
1157 1271 6.488769 AGAGAAGCAGATGAGATTGAGAAT 57.511 37.500 0.00 0.00 0.00 2.40
1158 1272 5.936187 AGAGAAGCAGATGAGATTGAGAA 57.064 39.130 0.00 0.00 0.00 2.87
1159 1273 6.128486 ACTAGAGAAGCAGATGAGATTGAGA 58.872 40.000 0.00 0.00 0.00 3.27
1160 1274 6.395426 ACTAGAGAAGCAGATGAGATTGAG 57.605 41.667 0.00 0.00 0.00 3.02
1161 1275 6.788598 AACTAGAGAAGCAGATGAGATTGA 57.211 37.500 0.00 0.00 0.00 2.57
1202 1317 2.932614 CTCAGGAACATGGACGATCAAC 59.067 50.000 0.00 0.00 0.00 3.18
1223 1349 2.604046 AGAACGGCAGGATCATACAC 57.396 50.000 0.00 0.00 0.00 2.90
1231 1357 2.224523 ACATGAAAGAAGAACGGCAGGA 60.225 45.455 0.00 0.00 0.00 3.86
1234 1360 5.471797 TGAAATACATGAAAGAAGAACGGCA 59.528 36.000 0.00 0.00 0.00 5.69
1266 1392 9.484806 AAAAGACATGAAAGATCAATCCCTAAT 57.515 29.630 0.00 0.00 39.49 1.73
1268 1394 8.884124 AAAAAGACATGAAAGATCAATCCCTA 57.116 30.769 0.00 0.00 39.49 3.53
1269 1395 7.362401 CGAAAAAGACATGAAAGATCAATCCCT 60.362 37.037 0.00 0.00 39.49 4.20
1272 1401 6.252228 GGCGAAAAAGACATGAAAGATCAATC 59.748 38.462 0.00 0.00 39.49 2.67
1284 1413 5.920273 CAGTTAAACATGGCGAAAAAGACAT 59.080 36.000 0.00 0.00 41.31 3.06
1295 1425 7.145932 ACTAACAGATTCAGTTAAACATGGC 57.854 36.000 0.00 0.00 31.66 4.40
1318 1450 6.413783 TTGGTTAAAAATGAAAGAGGGGAC 57.586 37.500 0.00 0.00 0.00 4.46
1349 1490 9.352191 CAATATTCAGTAGTACCACCTAGTAGT 57.648 37.037 0.00 0.00 0.00 2.73
1350 1491 9.352191 ACAATATTCAGTAGTACCACCTAGTAG 57.648 37.037 0.00 0.00 0.00 2.57
1351 1492 9.705103 AACAATATTCAGTAGTACCACCTAGTA 57.295 33.333 0.00 0.00 0.00 1.82
1353 1494 8.915036 AGAACAATATTCAGTAGTACCACCTAG 58.085 37.037 0.00 0.00 0.00 3.02
1354 1495 8.834004 AGAACAATATTCAGTAGTACCACCTA 57.166 34.615 0.00 0.00 0.00 3.08
1355 1496 7.735326 AGAACAATATTCAGTAGTACCACCT 57.265 36.000 0.00 0.00 0.00 4.00
1356 1497 8.258708 AGAAGAACAATATTCAGTAGTACCACC 58.741 37.037 0.00 0.00 0.00 4.61
1357 1498 9.654663 AAGAAGAACAATATTCAGTAGTACCAC 57.345 33.333 0.00 0.00 0.00 4.16
1358 1499 9.871238 GAAGAAGAACAATATTCAGTAGTACCA 57.129 33.333 0.00 0.00 0.00 3.25
1362 1669 9.660180 GGAAGAAGAAGAACAATATTCAGTAGT 57.340 33.333 0.00 0.00 0.00 2.73
1363 1670 9.658799 TGGAAGAAGAAGAACAATATTCAGTAG 57.341 33.333 0.00 0.00 0.00 2.57
1377 1684 9.184523 TCAGTTAACAAAAATGGAAGAAGAAGA 57.815 29.630 8.61 0.00 0.00 2.87
1378 1685 9.801873 TTCAGTTAACAAAAATGGAAGAAGAAG 57.198 29.630 8.61 0.00 0.00 2.85
1450 1757 9.006839 GGAAACACATCACATATATCATCACAT 57.993 33.333 0.00 0.00 0.00 3.21
1453 1760 8.654094 AGAGGAAACACATCACATATATCATCA 58.346 33.333 0.00 0.00 0.00 3.07
1454 1761 9.149225 GAGAGGAAACACATCACATATATCATC 57.851 37.037 0.00 0.00 0.00 2.92
1455 1762 8.099537 GGAGAGGAAACACATCACATATATCAT 58.900 37.037 0.00 0.00 0.00 2.45
1456 1763 7.290948 AGGAGAGGAAACACATCACATATATCA 59.709 37.037 0.00 0.00 0.00 2.15
1457 1764 7.675062 AGGAGAGGAAACACATCACATATATC 58.325 38.462 0.00 0.00 0.00 1.63
1458 1765 7.512058 AGAGGAGAGGAAACACATCACATATAT 59.488 37.037 0.00 0.00 0.00 0.86
1474 1781 2.826287 CGCGCAGAGAGGAGAGGA 60.826 66.667 8.75 0.00 0.00 3.71
1635 1949 1.676746 CATGATCTGGGACTGCAAGG 58.323 55.000 0.00 0.00 39.30 3.61
1953 2267 4.680237 TGTTGGACGCGGCAGAGG 62.680 66.667 17.00 0.00 0.00 3.69
1954 2268 3.414700 GTGTTGGACGCGGCAGAG 61.415 66.667 17.00 0.00 0.00 3.35
1992 2306 0.419459 ACCCTCCTCTTCCATGACCT 59.581 55.000 0.00 0.00 0.00 3.85
2273 2695 2.852075 TGGTGGTGTGGGGAGGAC 60.852 66.667 0.00 0.00 0.00 3.85
3328 3817 7.472543 AGTTTTAGCAATTCGGTACATGATTC 58.527 34.615 0.00 0.00 0.00 2.52
3338 3827 9.208022 TCATCTATATGAGTTTTAGCAATTCGG 57.792 33.333 0.00 0.00 37.20 4.30
3481 4021 1.742831 GGTGTGATGAGCCGCAAAATA 59.257 47.619 0.00 0.00 0.00 1.40
3622 4168 6.197168 AGACAAAGAGGAATGAGAGAGAGAT 58.803 40.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.