Multiple sequence alignment - TraesCS5A01G337900

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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 TraesCS5A01G337900 chr5A 100.000 3305 0 0 1 3305 546153217 546156521 0.000000e+00 6104.0
1 TraesCS5A01G337900 chr5A 87.985 2114 145 35 284 2322 546145464 546147543 0.000000e+00 2396.0
2 TraesCS5A01G337900 chr5A 95.192 1331 64 0 992 2322 545984611 545985941 0.000000e+00 2104.0
3 TraesCS5A01G337900 chr5A 90.689 1321 123 0 997 2317 545870668 545871988 0.000000e+00 1759.0
4 TraesCS5A01G337900 chr5A 81.279 219 35 6 1 216 546145236 546145451 4.380000e-39 172.0
5 TraesCS5A01G337900 chr5B 89.694 2416 194 28 13 2401 520045529 520047916 0.000000e+00 3031.0
6 TraesCS5A01G337900 chr5B 88.434 1686 134 25 643 2309 519660712 519662355 0.000000e+00 1977.0
7 TraesCS5A01G337900 chr5B 93.388 1331 85 1 989 2316 520036797 520038127 0.000000e+00 1967.0
8 TraesCS5A01G337900 chr5B 81.910 890 95 33 1 863 520035845 520036695 0.000000e+00 691.0
9 TraesCS5A01G337900 chr5B 87.574 507 48 6 2809 3302 520059250 520059754 1.030000e-159 573.0
10 TraesCS5A01G337900 chr5B 87.126 435 32 14 2396 2810 520048237 520048667 3.860000e-129 472.0
11 TraesCS5A01G337900 chr5B 78.613 173 24 11 162 328 272674824 272674989 5.830000e-18 102.0
12 TraesCS5A01G337900 chr5B 91.304 46 4 0 901 946 520036700 520036745 2.750000e-06 63.9
13 TraesCS5A01G337900 chr5D 90.708 2077 138 19 372 2424 430511027 430513072 0.000000e+00 2715.0
14 TraesCS5A01G337900 chr5D 87.908 1687 140 27 645 2322 430445235 430446866 0.000000e+00 1927.0
15 TraesCS5A01G337900 chr5D 90.310 1321 128 0 997 2317 430164059 430165379 0.000000e+00 1731.0
16 TraesCS5A01G337900 chr5D 90.234 512 37 6 2806 3305 430520365 430520875 0.000000e+00 656.0
17 TraesCS5A01G337900 chr5D 90.476 63 6 0 1 63 430510807 430510869 2.110000e-12 84.2
18 TraesCS5A01G337900 chr6D 77.014 422 79 12 79 495 397032472 397032064 3.320000e-55 226.0
19 TraesCS5A01G337900 chr6B 94.444 36 2 0 443 478 612193669 612193704 4.610000e-04 56.5


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 TraesCS5A01G337900 chr5A 546153217 546156521 3304 False 6104.0 6104 100.000000 1 3305 1 chr5A.!!$F3 3304
1 TraesCS5A01G337900 chr5A 545984611 545985941 1330 False 2104.0 2104 95.192000 992 2322 1 chr5A.!!$F2 1330
2 TraesCS5A01G337900 chr5A 545870668 545871988 1320 False 1759.0 1759 90.689000 997 2317 1 chr5A.!!$F1 1320
3 TraesCS5A01G337900 chr5A 546145236 546147543 2307 False 1284.0 2396 84.632000 1 2322 2 chr5A.!!$F4 2321
4 TraesCS5A01G337900 chr5B 519660712 519662355 1643 False 1977.0 1977 88.434000 643 2309 1 chr5B.!!$F2 1666
5 TraesCS5A01G337900 chr5B 520045529 520048667 3138 False 1751.5 3031 88.410000 13 2810 2 chr5B.!!$F5 2797
6 TraesCS5A01G337900 chr5B 520035845 520038127 2282 False 907.3 1967 88.867333 1 2316 3 chr5B.!!$F4 2315
7 TraesCS5A01G337900 chr5B 520059250 520059754 504 False 573.0 573 87.574000 2809 3302 1 chr5B.!!$F3 493
8 TraesCS5A01G337900 chr5D 430445235 430446866 1631 False 1927.0 1927 87.908000 645 2322 1 chr5D.!!$F2 1677
9 TraesCS5A01G337900 chr5D 430164059 430165379 1320 False 1731.0 1731 90.310000 997 2317 1 chr5D.!!$F1 1320
10 TraesCS5A01G337900 chr5D 430510807 430513072 2265 False 1399.6 2715 90.592000 1 2424 2 chr5D.!!$F4 2423
11 TraesCS5A01G337900 chr5D 430520365 430520875 510 False 656.0 656 90.234000 2806 3305 1 chr5D.!!$F3 499


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
979 1089 0.1078 TCTCCGGTCTCGTCCTACAG 60.108 60.0 0.0 0.0 33.95 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 3044 0.031721 AGTGTTCAAGTCGGACGGAC 59.968 55.0 5.05 5.05 46.45 4.79 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
29 30 1.202114 CTGAGCTTCTTCTCTGTCGCT 59.798 52.381 0.00 0.00 34.29 4.93
109 110 1.006102 ACAACTTCCGTCTCCAGCG 60.006 57.895 0.00 0.00 0.00 5.18
137 138 3.829044 CGGGTCCATGCGTCGGTA 61.829 66.667 0.00 0.00 0.00 4.02
168 176 1.705745 AGAAGAGTGGGGGAAAAGGAC 59.294 52.381 0.00 0.00 0.00 3.85
175 183 1.272258 TGGGGGAAAAGGACGGAATTC 60.272 52.381 0.00 0.00 0.00 2.17
209 219 6.288294 CACGGGATGATGGAAGAAAATAGTA 58.712 40.000 0.00 0.00 0.00 1.82
220 231 5.857517 GGAAGAAAATAGTAGGAGATACGCG 59.142 44.000 3.53 3.53 39.55 6.01
272 283 2.417933 CGAGCTCCATCTCAGTTTTTGG 59.582 50.000 8.47 0.00 33.41 3.28
276 287 3.754965 CTCCATCTCAGTTTTTGGTGGA 58.245 45.455 0.00 0.00 34.42 4.02
278 289 3.138283 TCCATCTCAGTTTTTGGTGGACT 59.862 43.478 0.00 0.00 32.26 3.85
282 293 1.286553 TCAGTTTTTGGTGGACTGGGT 59.713 47.619 3.24 0.00 40.80 4.51
313 324 2.629050 CTACGTGGCTCATGTCCGGG 62.629 65.000 0.00 0.00 35.12 5.73
319 330 3.083349 CTCATGTCCGGGCTCCCA 61.083 66.667 7.97 0.00 35.37 4.37
324 335 2.075355 ATGTCCGGGCTCCCACAAAA 62.075 55.000 7.97 0.00 35.37 2.44
333 348 1.001974 GCTCCCACAAAACCCCATTTC 59.998 52.381 0.00 0.00 0.00 2.17
345 362 3.930035 ACCCCATTTCCCAGTTTGTTTA 58.070 40.909 0.00 0.00 0.00 2.01
346 363 4.299485 ACCCCATTTCCCAGTTTGTTTAA 58.701 39.130 0.00 0.00 0.00 1.52
431 448 3.702048 GGTGTCCGGGCAGCTACA 61.702 66.667 30.14 9.31 34.39 2.74
457 474 2.165030 GACGGATAAGGACGGTTTGAGA 59.835 50.000 0.00 0.00 0.00 3.27
468 486 0.599204 GGTTTGAGAGTCGGCGTTGA 60.599 55.000 6.85 0.00 0.00 3.18
499 534 8.322091 GCCCTAACTAGTCAAACATCCATATAT 58.678 37.037 0.00 0.00 0.00 0.86
516 554 5.337089 CCATATATGGGACTAGCAGTCAGTG 60.337 48.000 22.31 0.00 46.79 3.66
624 665 2.071778 AGCAGGCAAAGGAGTGAAAA 57.928 45.000 0.00 0.00 0.00 2.29
625 666 2.601905 AGCAGGCAAAGGAGTGAAAAT 58.398 42.857 0.00 0.00 0.00 1.82
626 667 3.766545 AGCAGGCAAAGGAGTGAAAATA 58.233 40.909 0.00 0.00 0.00 1.40
627 668 3.760684 AGCAGGCAAAGGAGTGAAAATAG 59.239 43.478 0.00 0.00 0.00 1.73
630 671 5.006386 CAGGCAAAGGAGTGAAAATAGAGT 58.994 41.667 0.00 0.00 0.00 3.24
680 722 2.154567 TCTAGGTAACAGCCGGTCAT 57.845 50.000 1.90 0.00 41.41 3.06
698 741 5.335127 GGTCATTAGTCAAACACATGCATC 58.665 41.667 0.00 0.00 0.00 3.91
713 760 1.153449 CATCGTTTAGAGGCGGGCA 60.153 57.895 3.78 0.00 0.00 5.36
734 783 4.697514 CAGTCCAAGTCTCAAGTCTCAAA 58.302 43.478 0.00 0.00 0.00 2.69
735 784 5.118990 CAGTCCAAGTCTCAAGTCTCAAAA 58.881 41.667 0.00 0.00 0.00 2.44
736 785 5.007136 CAGTCCAAGTCTCAAGTCTCAAAAC 59.993 44.000 0.00 0.00 0.00 2.43
737 786 4.876107 GTCCAAGTCTCAAGTCTCAAAACA 59.124 41.667 0.00 0.00 0.00 2.83
739 788 5.586243 TCCAAGTCTCAAGTCTCAAAACAAG 59.414 40.000 0.00 0.00 0.00 3.16
740 789 5.220931 CCAAGTCTCAAGTCTCAAAACAAGG 60.221 44.000 0.00 0.00 0.00 3.61
810 883 1.729838 GCGAGCGTGTTCGAGACTT 60.730 57.895 10.34 0.00 43.03 3.01
829 905 7.427989 AGACTTCCAATACCGTCCTATAAAA 57.572 36.000 0.00 0.00 0.00 1.52
856 932 1.526686 CAGCAGCAGGACAACCACA 60.527 57.895 0.00 0.00 38.94 4.17
863 939 2.624838 AGCAGGACAACCACAAAATCAG 59.375 45.455 0.00 0.00 38.94 2.90
893 980 2.221055 CACAAGAGTACAAGACCGCAAC 59.779 50.000 0.00 0.00 0.00 4.17
901 988 3.469863 AAGACCGCAACGCCTCCAA 62.470 57.895 0.00 0.00 0.00 3.53
911 998 0.396811 ACGCCTCCAAGTACAAGCTT 59.603 50.000 0.00 0.00 0.00 3.74
913 1000 1.878102 CGCCTCCAAGTACAAGCTTGT 60.878 52.381 32.97 32.97 43.03 3.16
970 1080 1.619332 AGAAACCACTTCTCCGGTCTC 59.381 52.381 0.00 0.00 40.61 3.36
971 1081 0.317479 AAACCACTTCTCCGGTCTCG 59.683 55.000 0.00 0.00 33.17 4.04
972 1082 0.826672 AACCACTTCTCCGGTCTCGT 60.827 55.000 0.00 0.00 33.17 4.18
974 1084 1.507174 CACTTCTCCGGTCTCGTCC 59.493 63.158 0.00 0.00 33.95 4.79
975 1085 0.961358 CACTTCTCCGGTCTCGTCCT 60.961 60.000 0.00 0.00 33.95 3.85
976 1086 0.617413 ACTTCTCCGGTCTCGTCCTA 59.383 55.000 0.00 0.00 33.95 2.94
977 1087 1.015868 CTTCTCCGGTCTCGTCCTAC 58.984 60.000 0.00 0.00 33.95 3.18
978 1088 0.325933 TTCTCCGGTCTCGTCCTACA 59.674 55.000 0.00 0.00 33.95 2.74
979 1089 0.107800 TCTCCGGTCTCGTCCTACAG 60.108 60.000 0.00 0.00 33.95 2.74
980 1090 0.107800 CTCCGGTCTCGTCCTACAGA 60.108 60.000 0.00 0.00 33.95 3.41
981 1091 0.107800 TCCGGTCTCGTCCTACAGAG 60.108 60.000 0.00 0.00 35.91 3.35
982 1092 0.107800 CCGGTCTCGTCCTACAGAGA 60.108 60.000 0.00 0.00 40.78 3.10
983 1093 1.678123 CCGGTCTCGTCCTACAGAGAA 60.678 57.143 0.00 0.00 44.07 2.87
984 1094 2.082231 CGGTCTCGTCCTACAGAGAAA 58.918 52.381 0.00 0.00 44.07 2.52
985 1095 2.159544 CGGTCTCGTCCTACAGAGAAAC 60.160 54.545 0.00 0.00 44.07 2.78
986 1096 2.164017 GGTCTCGTCCTACAGAGAAACC 59.836 54.545 0.00 0.00 44.07 3.27
987 1097 2.818432 GTCTCGTCCTACAGAGAAACCA 59.182 50.000 0.00 0.00 44.07 3.67
1043 1180 3.882025 GCTCGTCAAGCCTTCCTG 58.118 61.111 0.00 0.00 45.92 3.86
1200 1337 2.046023 CTTGCCATGGTCCTCGCA 60.046 61.111 14.67 0.09 0.00 5.10
1551 1688 4.935495 CCAGTGCACCACCACGCT 62.935 66.667 14.63 0.00 40.59 5.07
1686 1823 2.743752 CGTCATCCACAAGGCGCAG 61.744 63.158 10.83 0.00 33.74 5.18
1837 1974 2.903404 GAGACCTCCAAGATCCGGT 58.097 57.895 0.00 0.00 0.00 5.28
2256 2393 1.838073 ATGCCTTCGTCCCCGTCTTT 61.838 55.000 0.00 0.00 35.01 2.52
2343 2483 7.453126 AGAATCGGTAGATTGATAACTGAGGAT 59.547 37.037 0.00 0.00 46.30 3.24
2344 2484 6.576662 TCGGTAGATTGATAACTGAGGATC 57.423 41.667 0.00 0.00 0.00 3.36
2345 2485 6.721668 ATCGGTAGATTGATAACTGAGGATCA 59.278 38.462 0.00 0.00 36.77 2.92
2424 2891 6.338146 TGAGAATTGTATGGTGCTACTGTAC 58.662 40.000 0.00 0.00 0.00 2.90
2453 2930 5.818678 AGGTTCTGATGTACCAGTAACAA 57.181 39.130 0.26 0.00 36.27 2.83
2455 2932 4.935808 GGTTCTGATGTACCAGTAACAAGG 59.064 45.833 12.09 0.00 34.30 3.61
2512 2990 7.654520 CCAATGTATGCCTAATCTTTTTGATGG 59.345 37.037 0.00 0.00 35.21 3.51
2537 3017 9.962759 GGTATGTTAGTACGTTAAATTGAACAG 57.037 33.333 6.49 1.94 0.00 3.16
2564 3044 8.854979 TGTTCAATTTTGACACTGAAGTATTG 57.145 30.769 0.00 0.00 36.83 1.90
2568 3051 5.666969 TTTTGACACTGAAGTATTGTCCG 57.333 39.130 0.00 0.00 37.97 4.79
2572 3055 2.259618 CACTGAAGTATTGTCCGTCCG 58.740 52.381 0.00 0.00 0.00 4.79
2579 3062 2.559668 AGTATTGTCCGTCCGACTTGAA 59.440 45.455 0.00 0.00 42.49 2.69
2608 3091 7.656707 AAACAATGAAAGTATGAAACCATGC 57.343 32.000 0.00 0.00 0.00 4.06
2679 3163 5.107375 GCAAAACGGAATTGTACGAGTCTTA 60.107 40.000 10.25 0.00 0.00 2.10
2687 3171 8.106348 CGGAATTGTACGAGTCTTACAAAATAC 58.894 37.037 21.78 14.89 41.55 1.89
2689 3173 8.524870 AATTGTACGAGTCTTACAAAATACGT 57.475 30.769 21.78 5.94 41.55 3.57
2690 3174 9.624697 AATTGTACGAGTCTTACAAAATACGTA 57.375 29.630 21.78 0.00 41.55 3.57
2699 3183 6.034256 GTCTTACAAAATACGTAGATGCGTGT 59.966 38.462 6.22 0.00 45.33 4.49
2719 3203 7.295952 CGTGTAATGCTAAGAAATGAGAAGT 57.704 36.000 0.00 0.00 0.00 3.01
2738 3222 7.719193 TGAGAAGTGACAAAATAACCATCAAGA 59.281 33.333 0.00 0.00 0.00 3.02
2812 3297 8.352201 TGTCTTTTTGTCTTCTGTATGGAAATG 58.648 33.333 0.00 0.00 0.00 2.32
2955 3441 6.905578 TGAATCACTGAATTGATGAACACTG 58.094 36.000 0.00 0.00 36.31 3.66
2960 3446 6.870439 TCACTGAATTGATGAACACTGTCTAG 59.130 38.462 0.00 0.00 0.00 2.43
2961 3447 6.648310 CACTGAATTGATGAACACTGTCTAGT 59.352 38.462 0.00 0.00 37.75 2.57
3036 3533 2.028748 CAGGTTCAATTTTGGCTCTGGG 60.029 50.000 0.00 0.00 0.00 4.45
3071 3568 7.967890 AAGCTTGAATTGAAAAATACCAAGG 57.032 32.000 0.00 0.00 32.56 3.61
3073 3570 5.122239 GCTTGAATTGAAAAATACCAAGGCC 59.878 40.000 0.00 0.00 32.56 5.19
3074 3571 5.815233 TGAATTGAAAAATACCAAGGCCA 57.185 34.783 5.01 0.00 0.00 5.36
3104 3601 1.824852 CCCGAGCAAAGGCCTAAAAAT 59.175 47.619 5.16 0.00 42.56 1.82
3108 3605 4.381932 CCGAGCAAAGGCCTAAAAATTCAT 60.382 41.667 5.16 0.00 42.56 2.57
3115 3612 9.558648 GCAAAGGCCTAAAAATTCATTAATTTG 57.441 29.630 5.16 1.51 43.04 2.32
3141 3638 9.810231 GATAACAAATGTTAAACCAATTTGCAG 57.190 29.630 9.82 0.00 42.93 4.41
3172 3669 8.868522 AAATGAATTATTGTCTCTGTTCTCCA 57.131 30.769 0.00 0.00 0.00 3.86
3205 3702 9.423061 ACAATATTTTACACATTTCAGGCTTTC 57.577 29.630 0.00 0.00 0.00 2.62
3221 3718 3.494924 GGCTTTCATTTTGGGCTTCAAGT 60.495 43.478 0.00 0.00 36.62 3.16
3234 3731 0.107831 TTCAAGTCCGACCAACAGGG 59.892 55.000 0.00 0.00 44.81 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.543802 CGACAGAGAAGAAGCTCAGGT 59.456 52.381 0.00 0.00 37.37 4.00
29 30 5.299279 GGAGAGGTTTGACTTGTTGATGAAA 59.701 40.000 0.00 0.00 0.00 2.69
137 138 0.610687 CACTCTTCTTTCCTCCCGCT 59.389 55.000 0.00 0.00 0.00 5.52
146 147 2.789399 TCCTTTTCCCCCACTCTTCTTT 59.211 45.455 0.00 0.00 0.00 2.52
168 176 2.962253 GCTCTCCGCCGAATTCCG 60.962 66.667 0.00 0.00 38.18 4.30
178 186 1.300465 CATCATCCCGTGCTCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
186 195 5.373812 ACTATTTTCTTCCATCATCCCGT 57.626 39.130 0.00 0.00 0.00 5.28
192 202 8.577296 CGTATCTCCTACTATTTTCTTCCATCA 58.423 37.037 0.00 0.00 0.00 3.07
209 219 1.200716 TGTTTTCGTCGCGTATCTCCT 59.799 47.619 5.77 0.00 0.00 3.69
216 226 1.634225 CACACTGTTTTCGTCGCGT 59.366 52.632 5.77 0.00 0.00 6.01
217 227 1.083657 CCACACTGTTTTCGTCGCG 60.084 57.895 0.00 0.00 0.00 5.87
220 231 0.307760 CTGGCCACACTGTTTTCGTC 59.692 55.000 0.00 0.00 0.00 4.20
259 270 3.490348 CCAGTCCACCAAAAACTGAGAT 58.510 45.455 3.42 0.00 42.37 2.75
260 271 2.422803 CCCAGTCCACCAAAAACTGAGA 60.423 50.000 3.42 0.00 42.37 3.27
272 283 2.030562 CCGACACACCCAGTCCAC 59.969 66.667 0.00 0.00 32.41 4.02
276 287 2.207924 GGACTCCGACACACCCAGT 61.208 63.158 0.00 0.00 0.00 4.00
278 289 0.896940 GTAGGACTCCGACACACCCA 60.897 60.000 3.55 0.00 0.00 4.51
282 293 1.239296 CCACGTAGGACTCCGACACA 61.239 60.000 8.84 0.00 41.22 3.72
313 324 1.001974 GAAATGGGGTTTTGTGGGAGC 59.998 52.381 0.00 0.00 0.00 4.70
319 330 2.487746 ACTGGGAAATGGGGTTTTGT 57.512 45.000 0.00 0.00 0.00 2.83
324 335 2.487746 AACAAACTGGGAAATGGGGT 57.512 45.000 0.00 0.00 0.00 4.95
333 348 3.553917 CGGCAAAGTTTAAACAAACTGGG 59.446 43.478 20.06 3.97 41.76 4.45
345 362 3.202097 CCACAATTTTCCGGCAAAGTTT 58.798 40.909 5.32 0.00 0.00 2.66
346 363 2.169561 ACCACAATTTTCCGGCAAAGTT 59.830 40.909 5.32 3.77 0.00 2.66
391 408 3.622206 GCAAGTCATCCATAACTGACCCA 60.622 47.826 0.00 0.00 42.18 4.51
400 417 1.134521 GGACACCGCAAGTCATCCATA 60.135 52.381 0.00 0.00 37.74 2.74
401 418 0.392998 GGACACCGCAAGTCATCCAT 60.393 55.000 0.00 0.00 37.74 3.41
423 440 1.816537 TCCGTCTGGATGTAGCTGC 59.183 57.895 0.00 0.00 40.17 5.25
457 474 1.579429 GGCATTTTCAACGCCGACT 59.421 52.632 0.00 0.00 35.79 4.18
468 486 6.152831 GGATGTTTGACTAGTTAGGGCATTTT 59.847 38.462 0.00 0.00 0.00 1.82
499 534 1.717032 AACACTGACTGCTAGTCCCA 58.283 50.000 11.99 0.00 44.44 4.37
502 537 3.670991 CGAGAAAACACTGACTGCTAGTC 59.329 47.826 8.75 8.75 45.26 2.59
503 538 3.068307 ACGAGAAAACACTGACTGCTAGT 59.932 43.478 0.00 0.00 0.00 2.57
504 539 3.426859 CACGAGAAAACACTGACTGCTAG 59.573 47.826 0.00 0.00 0.00 3.42
505 540 3.381045 CACGAGAAAACACTGACTGCTA 58.619 45.455 0.00 0.00 0.00 3.49
506 541 2.205074 CACGAGAAAACACTGACTGCT 58.795 47.619 0.00 0.00 0.00 4.24
507 542 1.261619 CCACGAGAAAACACTGACTGC 59.738 52.381 0.00 0.00 0.00 4.40
508 543 2.540101 GTCCACGAGAAAACACTGACTG 59.460 50.000 0.00 0.00 0.00 3.51
511 546 2.971660 TGTCCACGAGAAAACACTGA 57.028 45.000 0.00 0.00 0.00 3.41
624 665 6.432162 TCACAAGTCTAAACCGTACACTCTAT 59.568 38.462 0.00 0.00 0.00 1.98
625 666 5.764686 TCACAAGTCTAAACCGTACACTCTA 59.235 40.000 0.00 0.00 0.00 2.43
626 667 4.581824 TCACAAGTCTAAACCGTACACTCT 59.418 41.667 0.00 0.00 0.00 3.24
627 668 4.678742 GTCACAAGTCTAAACCGTACACTC 59.321 45.833 0.00 0.00 0.00 3.51
630 671 4.652421 TGTCACAAGTCTAAACCGTACA 57.348 40.909 0.00 0.00 0.00 2.90
680 722 5.431420 AAACGATGCATGTGTTTGACTAA 57.569 34.783 20.20 0.00 34.73 2.24
698 741 1.810030 GACTGCCCGCCTCTAAACG 60.810 63.158 0.00 0.00 0.00 3.60
713 760 5.119694 GTTTTGAGACTTGAGACTTGGACT 58.880 41.667 0.00 0.00 0.00 3.85
810 883 8.076910 TGTACTTTTTATAGGACGGTATTGGA 57.923 34.615 0.00 0.00 31.19 3.53
829 905 0.764890 TCCTGCTGCTGGTTGTACTT 59.235 50.000 22.62 0.00 0.00 2.24
856 932 5.415701 ACTCTTGTGTTGTGTGTCTGATTTT 59.584 36.000 0.00 0.00 0.00 1.82
863 939 4.868171 TCTTGTACTCTTGTGTTGTGTGTC 59.132 41.667 0.00 0.00 0.00 3.67
893 980 0.798776 CAAGCTTGTACTTGGAGGCG 59.201 55.000 18.65 0.00 42.73 5.52
970 1080 2.296471 ACTGTGGTTTCTCTGTAGGACG 59.704 50.000 0.00 0.00 0.00 4.79
971 1081 4.280174 TGTACTGTGGTTTCTCTGTAGGAC 59.720 45.833 0.00 0.00 0.00 3.85
972 1082 4.280174 GTGTACTGTGGTTTCTCTGTAGGA 59.720 45.833 0.00 0.00 0.00 2.94
974 1084 5.196341 TGTGTACTGTGGTTTCTCTGTAG 57.804 43.478 0.00 0.00 0.00 2.74
975 1085 4.500887 GCTGTGTACTGTGGTTTCTCTGTA 60.501 45.833 0.00 0.00 0.00 2.74
976 1086 3.741388 GCTGTGTACTGTGGTTTCTCTGT 60.741 47.826 0.00 0.00 0.00 3.41
977 1087 2.802816 GCTGTGTACTGTGGTTTCTCTG 59.197 50.000 0.00 0.00 0.00 3.35
978 1088 2.434336 TGCTGTGTACTGTGGTTTCTCT 59.566 45.455 0.00 0.00 0.00 3.10
979 1089 2.833794 TGCTGTGTACTGTGGTTTCTC 58.166 47.619 0.00 0.00 0.00 2.87
980 1090 3.275617 TTGCTGTGTACTGTGGTTTCT 57.724 42.857 0.00 0.00 0.00 2.52
981 1091 3.304659 CCATTGCTGTGTACTGTGGTTTC 60.305 47.826 0.00 0.00 0.00 2.78
982 1092 2.622942 CCATTGCTGTGTACTGTGGTTT 59.377 45.455 0.00 0.00 0.00 3.27
983 1093 2.158682 TCCATTGCTGTGTACTGTGGTT 60.159 45.455 0.00 0.00 0.00 3.67
984 1094 1.419762 TCCATTGCTGTGTACTGTGGT 59.580 47.619 0.00 0.00 0.00 4.16
985 1095 2.079158 CTCCATTGCTGTGTACTGTGG 58.921 52.381 0.00 0.00 0.00 4.17
986 1096 2.079158 CCTCCATTGCTGTGTACTGTG 58.921 52.381 0.00 0.00 0.00 3.66
987 1097 1.699634 ACCTCCATTGCTGTGTACTGT 59.300 47.619 0.00 0.00 0.00 3.55
1158 1295 3.432051 CTCGATGGAGGCCGTGGTC 62.432 68.421 0.00 0.00 36.61 4.02
1200 1337 3.047877 GCAAAGGCGCGGTACTGT 61.048 61.111 8.83 0.00 0.00 3.55
1245 1382 1.826921 GAGGATGACGGAGGGCGTA 60.827 63.158 0.00 0.00 0.00 4.42
1601 1738 1.070957 GGCAGGTAGTATTCCCGGC 59.929 63.158 0.00 0.00 40.65 6.13
1603 1740 0.031721 GACGGCAGGTAGTATTCCCG 59.968 60.000 0.00 0.00 41.31 5.14
1608 1745 2.496291 GGGCGACGGCAGGTAGTAT 61.496 63.158 23.66 0.00 42.47 2.12
1659 1796 4.697514 CCTTGTGGATGACGATGTTATCT 58.302 43.478 0.00 0.00 30.74 1.98
1662 1799 2.627945 GCCTTGTGGATGACGATGTTA 58.372 47.619 0.00 0.00 34.57 2.41
1686 1823 2.003301 GCGATGAAGTCCTTGGAGAAC 58.997 52.381 0.00 0.00 0.00 3.01
2256 2393 1.078918 CGCCTGGAGATTGTGCTCA 60.079 57.895 0.00 0.00 36.62 4.26
2343 2483 4.011966 TCTTTTCTCTGCTGAATGCTGA 57.988 40.909 0.00 0.00 45.30 4.26
2344 2484 4.761235 TTCTTTTCTCTGCTGAATGCTG 57.239 40.909 0.00 0.00 43.37 4.41
2345 2485 4.765856 ACATTCTTTTCTCTGCTGAATGCT 59.234 37.500 12.17 0.74 44.34 3.79
2346 2486 5.056894 ACATTCTTTTCTCTGCTGAATGC 57.943 39.130 12.17 0.00 44.34 3.56
2347 2487 6.675026 TCAACATTCTTTTCTCTGCTGAATG 58.325 36.000 11.06 11.06 45.32 2.67
2348 2488 6.889301 TCAACATTCTTTTCTCTGCTGAAT 57.111 33.333 0.00 0.00 0.00 2.57
2349 2489 6.889301 ATCAACATTCTTTTCTCTGCTGAA 57.111 33.333 0.00 0.00 0.00 3.02
2412 2879 2.806244 CCTTTGTGTGTACAGTAGCACC 59.194 50.000 10.75 0.00 38.23 5.01
2424 2891 4.133820 TGGTACATCAGAACCTTTGTGTG 58.866 43.478 0.00 0.00 36.67 3.82
2483 2961 9.420118 TCAAAAAGATTAGGCATACATTGGTAT 57.580 29.630 0.00 0.00 40.86 2.73
2484 2962 8.815565 TCAAAAAGATTAGGCATACATTGGTA 57.184 30.769 0.00 0.00 0.00 3.25
2485 2963 7.716799 TCAAAAAGATTAGGCATACATTGGT 57.283 32.000 0.00 0.00 0.00 3.67
2486 2964 7.654520 CCATCAAAAAGATTAGGCATACATTGG 59.345 37.037 0.00 0.00 33.72 3.16
2488 2966 8.310122 ACCATCAAAAAGATTAGGCATACATT 57.690 30.769 0.00 0.00 33.72 2.71
2490 2968 8.849168 CATACCATCAAAAAGATTAGGCATACA 58.151 33.333 0.00 0.00 33.72 2.29
2491 2969 8.850156 ACATACCATCAAAAAGATTAGGCATAC 58.150 33.333 0.00 0.00 33.72 2.39
2495 2973 8.903820 ACTAACATACCATCAAAAAGATTAGGC 58.096 33.333 0.00 0.00 33.72 3.93
2537 3017 9.683069 AATACTTCAGTGTCAAAATTGAACATC 57.317 29.630 0.00 0.00 39.21 3.06
2540 3020 8.856490 ACAATACTTCAGTGTCAAAATTGAAC 57.144 30.769 0.00 0.00 39.21 3.18
2564 3044 0.031721 AGTGTTCAAGTCGGACGGAC 59.968 55.000 5.05 5.05 46.45 4.79
2568 3051 5.235616 TCATTGTTTAGTGTTCAAGTCGGAC 59.764 40.000 0.00 0.00 0.00 4.79
2579 3062 8.908903 TGGTTTCATACTTTCATTGTTTAGTGT 58.091 29.630 0.00 0.00 0.00 3.55
2679 3163 6.701937 CATTACACGCATCTACGTATTTTGT 58.298 36.000 0.00 0.00 46.34 2.83
2687 3171 4.287720 TCTTAGCATTACACGCATCTACG 58.712 43.478 0.00 0.00 39.50 3.51
2689 3173 6.983890 TCATTTCTTAGCATTACACGCATCTA 59.016 34.615 0.00 0.00 0.00 1.98
2690 3174 5.817296 TCATTTCTTAGCATTACACGCATCT 59.183 36.000 0.00 0.00 0.00 2.90
2699 3183 8.846943 TTGTCACTTCTCATTTCTTAGCATTA 57.153 30.769 0.00 0.00 0.00 1.90
2707 3191 8.463930 TGGTTATTTTGTCACTTCTCATTTCT 57.536 30.769 0.00 0.00 0.00 2.52
2711 3195 8.408043 TTGATGGTTATTTTGTCACTTCTCAT 57.592 30.769 0.00 0.00 0.00 2.90
2783 3267 8.463930 TCCATACAGAAGACAAAAAGACAATT 57.536 30.769 0.00 0.00 0.00 2.32
2784 3268 8.463930 TTCCATACAGAAGACAAAAAGACAAT 57.536 30.769 0.00 0.00 0.00 2.71
2832 3317 6.934645 TCCGATTTGTCTTCTTTGTACAGAAT 59.065 34.615 0.00 0.00 32.21 2.40
2853 3339 9.739276 AAATGGCAAGAGATTAATATATTCCGA 57.261 29.630 0.00 0.00 0.00 4.55
2955 3441 7.553044 ACCTTCAACCATGCTTAAATACTAGAC 59.447 37.037 0.00 0.00 0.00 2.59
2960 3446 8.301002 TGTTTACCTTCAACCATGCTTAAATAC 58.699 33.333 0.00 0.00 0.00 1.89
2961 3447 8.410673 TGTTTACCTTCAACCATGCTTAAATA 57.589 30.769 0.00 0.00 0.00 1.40
3055 3552 4.263287 GGGTTGGCCTTGGTATTTTTCAAT 60.263 41.667 3.32 0.00 34.45 2.57
3071 3568 4.629523 TCGGGTTGTCGGGTTGGC 62.630 66.667 0.00 0.00 0.00 4.52
3073 3570 3.047877 GCTCGGGTTGTCGGGTTG 61.048 66.667 0.00 0.00 32.39 3.77
3074 3571 2.612095 TTTGCTCGGGTTGTCGGGTT 62.612 55.000 0.00 0.00 32.39 4.11
3115 3612 9.810231 CTGCAAATTGGTTTAACATTTGTTATC 57.190 29.630 16.68 6.24 39.89 1.75
3120 3617 6.259608 TGTCCTGCAAATTGGTTTAACATTTG 59.740 34.615 13.26 13.26 35.87 2.32
3125 3622 6.670077 TTTTGTCCTGCAAATTGGTTTAAC 57.330 33.333 0.00 0.00 45.38 2.01
3134 3631 9.287373 ACAATAATTCATTTTTGTCCTGCAAAT 57.713 25.926 3.35 0.00 45.38 2.32
3179 3676 9.423061 GAAAGCCTGAAATGTGTAAAATATTGT 57.577 29.630 0.00 0.00 0.00 2.71
3205 3702 1.885887 TCGGACTTGAAGCCCAAAATG 59.114 47.619 0.00 0.00 33.76 2.32



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

AutoCloner maintained by Alex Coulton.