Multiple sequence alignment - TraesCS2B01G473900

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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 TraesCS2B01G473900 chr2B 100.000 3255 0 0 1 3255 670852257 670855511 0.000000e+00 6011.0
1 TraesCS2B01G473900 chr2B 89.992 1289 94 20 1001 2262 671040074 671038794 0.000000e+00 1633.0
2 TraesCS2B01G473900 chr2B 82.263 327 38 11 2434 2753 682342096 682342409 6.920000e-67 265.0
3 TraesCS2B01G473900 chr2D 94.043 2535 87 23 549 3050 561851163 561853666 0.000000e+00 3786.0
4 TraesCS2B01G473900 chr2D 89.860 1282 93 22 1001 2266 561909159 561907899 0.000000e+00 1613.0
5 TraesCS2B01G473900 chr2D 85.767 541 61 7 1 529 561850420 561850956 2.840000e-155 558.0
6 TraesCS2B01G473900 chr2D 92.754 138 1 1 3114 3251 561855879 561856007 1.190000e-44 191.0
7 TraesCS2B01G473900 chr2D 97.674 43 1 0 3187 3229 180996928 180996886 1.250000e-09 75.0
8 TraesCS2B01G473900 chr2A 93.268 1827 75 17 557 2355 701496677 701498483 0.000000e+00 2649.0
9 TraesCS2B01G473900 chr2A 89.330 1284 105 19 1001 2265 701868361 701867091 0.000000e+00 1583.0
10 TraesCS2B01G473900 chr2A 85.752 379 40 10 1154 1519 628063372 628062995 3.940000e-104 388.0
11 TraesCS2B01G473900 chr4A 93.987 765 41 4 2355 3117 564696056 564695295 0.000000e+00 1153.0
12 TraesCS2B01G473900 chr4A 92.735 468 27 4 2352 2813 635361154 635360688 0.000000e+00 669.0
13 TraesCS2B01G473900 chr4A 93.204 309 18 3 2811 3117 635354926 635354619 4.950000e-123 451.0
14 TraesCS2B01G473900 chr4A 95.000 140 6 1 3114 3253 635354344 635354206 5.470000e-53 219.0
15 TraesCS2B01G473900 chr4A 93.571 140 8 1 3114 3253 564695020 564694882 1.180000e-49 207.0
16 TraesCS2B01G473900 chr3A 92.699 767 43 8 2355 3117 713317771 713318528 0.000000e+00 1094.0
17 TraesCS2B01G473900 chr3A 97.143 140 4 0 3114 3253 713318781 713318920 1.510000e-58 237.0
18 TraesCS2B01G473900 chr7A 81.971 771 98 18 2354 3115 626327224 626326486 1.660000e-172 616.0
19 TraesCS2B01G473900 chr7A 89.296 355 31 6 2767 3115 63572895 63573248 3.860000e-119 438.0
20 TraesCS2B01G473900 chr7B 88.764 356 29 9 2767 3115 25661982 25661631 3.000000e-115 425.0
21 TraesCS2B01G473900 chr7B 95.455 132 6 0 1542 1673 506596659 506596790 9.150000e-51 211.0
22 TraesCS2B01G473900 chr6D 88.451 355 33 7 2767 3115 76066902 76066550 3.880000e-114 422.0
23 TraesCS2B01G473900 chr6D 79.412 204 38 4 2550 2752 452131010 452131210 1.220000e-29 141.0
24 TraesCS2B01G473900 chr5B 88.451 355 33 7 2767 3115 476171861 476172213 3.880000e-114 422.0
25 TraesCS2B01G473900 chr5D 92.308 104 8 0 1303 1406 436205412 436205515 7.280000e-32 148.0
26 TraesCS2B01G473900 chr4D 100.000 31 0 0 3198 3228 365178327 365178357 1.260000e-04 58.4
27 TraesCS2B01G473900 chr5A 100.000 28 0 0 3187 3214 705153167 705153194 6.000000e-03 52.8


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 TraesCS2B01G473900 chr2B 670852257 670855511 3254 False 6011.000000 6011 100.000000 1 3255 1 chr2B.!!$F1 3254
1 TraesCS2B01G473900 chr2B 671038794 671040074 1280 True 1633.000000 1633 89.992000 1001 2262 1 chr2B.!!$R1 1261
2 TraesCS2B01G473900 chr2D 561907899 561909159 1260 True 1613.000000 1613 89.860000 1001 2266 1 chr2D.!!$R2 1265
3 TraesCS2B01G473900 chr2D 561850420 561856007 5587 False 1511.666667 3786 90.854667 1 3251 3 chr2D.!!$F1 3250
4 TraesCS2B01G473900 chr2A 701496677 701498483 1806 False 2649.000000 2649 93.268000 557 2355 1 chr2A.!!$F1 1798
5 TraesCS2B01G473900 chr2A 701867091 701868361 1270 True 1583.000000 1583 89.330000 1001 2265 1 chr2A.!!$R2 1264
6 TraesCS2B01G473900 chr4A 564694882 564696056 1174 True 680.000000 1153 93.779000 2355 3253 2 chr4A.!!$R2 898
7 TraesCS2B01G473900 chr4A 635354206 635354926 720 True 335.000000 451 94.102000 2811 3253 2 chr4A.!!$R3 442
8 TraesCS2B01G473900 chr3A 713317771 713318920 1149 False 665.500000 1094 94.921000 2355 3253 2 chr3A.!!$F1 898
9 TraesCS2B01G473900 chr7A 626326486 626327224 738 True 616.000000 616 81.971000 2354 3115 1 chr7A.!!$R1 761

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
832 1033 0.107703 TAGCTAGCGCCATTGTTGCT 60.108 50.0 9.55 5.71 42.58 3.91 F
1814 2081 0.453950 CGACACCTTCTACGACGTGG 60.454 60.0 11.56 8.10 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2361 1.229529 ACCTTCACCCCGTCCATCT 60.230 57.895 0.0 0.0 0.0 2.90 R
3150 5608 7.202016 TCACTAATTTGACACACTGATTTCC 57.798 36.000 0.0 0.0 0.0 3.13 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
38 41 2.746277 ACCGGTGCTCGAAATGGC 60.746 61.111 6.12 0.00 42.43 4.40
41 44 2.034879 CGGTGCTCGAAATGGCAGT 61.035 57.895 0.00 0.00 42.43 4.40
58 61 3.220658 TCACCTGACGTGCGACCA 61.221 61.111 0.00 0.00 42.69 4.02
80 83 1.378882 GCGAGGCATGCTGGAATCAA 61.379 55.000 18.92 0.00 0.00 2.57
89 92 2.745884 TGGAATCAACCGCCAGCG 60.746 61.111 4.75 4.75 39.44 5.18
111 114 2.593148 TGCAACCGCGACAACCAT 60.593 55.556 8.23 0.00 42.97 3.55
135 138 4.241555 GAGCCATGCCCCGACGAT 62.242 66.667 0.00 0.00 0.00 3.73
170 173 3.799755 GCGATGTTGGACCACGCC 61.800 66.667 14.51 0.00 42.79 5.68
173 176 1.302511 GATGTTGGACCACGCCTGT 60.303 57.895 0.00 0.00 0.00 4.00
182 185 2.433145 CACGCCTGTCGATGCTGT 60.433 61.111 0.00 0.00 41.67 4.40
190 193 0.673437 TGTCGATGCTGTGACTGACA 59.327 50.000 0.00 0.00 36.10 3.58
201 204 2.225117 TGTGACTGACAGAGAGGGATGA 60.225 50.000 10.08 0.00 0.00 2.92
229 232 1.130561 GGCGACACCAAAAGCTATGAC 59.869 52.381 1.14 0.00 38.86 3.06
233 236 1.073284 ACACCAAAAGCTATGACCGGT 59.927 47.619 6.92 6.92 0.00 5.28
235 238 2.556622 CACCAAAAGCTATGACCGGTTT 59.443 45.455 9.42 1.66 33.93 3.27
236 239 2.556622 ACCAAAAGCTATGACCGGTTTG 59.443 45.455 9.42 6.46 32.96 2.93
239 242 2.851263 AAGCTATGACCGGTTTGACA 57.149 45.000 9.42 1.27 0.00 3.58
254 257 1.109609 TGACAACAATGCTGCAACCA 58.890 45.000 6.36 0.00 0.00 3.67
255 258 1.202394 TGACAACAATGCTGCAACCAC 60.202 47.619 6.36 0.00 0.00 4.16
256 259 0.248990 ACAACAATGCTGCAACCACG 60.249 50.000 6.36 0.00 0.00 4.94
268 280 1.077357 AACCACGTGCTGGAAACCA 60.077 52.632 10.91 0.00 43.95 3.67
269 281 1.381165 AACCACGTGCTGGAAACCAC 61.381 55.000 10.91 0.00 43.95 4.16
276 288 3.047877 CTGGAAACCACGACGCCC 61.048 66.667 0.00 0.00 0.00 6.13
277 289 3.818121 CTGGAAACCACGACGCCCA 62.818 63.158 0.00 0.00 0.00 5.36
298 310 1.262950 TCGTTGTCAATGCTGAAACCG 59.737 47.619 0.00 0.00 31.88 4.44
300 312 0.313672 TTGTCAATGCTGAAACCGGC 59.686 50.000 0.00 0.00 36.49 6.13
319 332 3.205815 AGCACCAAAGCTGAAACCA 57.794 47.368 0.00 0.00 44.66 3.67
320 333 1.484038 AGCACCAAAGCTGAAACCAA 58.516 45.000 0.00 0.00 44.66 3.67
333 346 0.827368 AAACCAACAACGGCCATTGT 59.173 45.000 12.30 12.30 44.76 2.71
338 351 2.642129 CAACGGCCATTGTTGCGA 59.358 55.556 2.64 0.00 40.11 5.10
342 355 2.495866 GGCCATTGTTGCGATGGG 59.504 61.111 15.07 0.00 43.68 4.00
377 390 1.866237 GTTGTCGCCGCTGATTTGA 59.134 52.632 0.00 0.00 0.00 2.69
384 397 1.131126 CGCCGCTGATTTGATGAAACT 59.869 47.619 0.00 0.00 0.00 2.66
391 404 4.439289 GCTGATTTGATGAAACTGGGTAGC 60.439 45.833 0.00 0.00 0.00 3.58
392 405 4.922206 TGATTTGATGAAACTGGGTAGCT 58.078 39.130 0.00 0.00 0.00 3.32
394 407 6.115446 TGATTTGATGAAACTGGGTAGCTAG 58.885 40.000 3.46 3.46 0.00 3.42
395 408 3.543680 TGATGAAACTGGGTAGCTAGC 57.456 47.619 14.67 14.67 0.00 3.42
396 409 2.159099 TGATGAAACTGGGTAGCTAGCG 60.159 50.000 16.33 6.57 0.00 4.26
397 410 1.552578 TGAAACTGGGTAGCTAGCGA 58.447 50.000 16.33 11.94 0.00 4.93
398 411 2.108168 TGAAACTGGGTAGCTAGCGAT 58.892 47.619 16.33 1.87 0.00 4.58
424 437 2.579787 GACGGGCGTCATGACTCG 60.580 66.667 22.95 22.63 44.02 4.18
426 439 1.985447 GACGGGCGTCATGACTCGTA 61.985 60.000 26.55 0.00 44.02 3.43
430 443 1.470979 GGGCGTCATGACTCGTAATGT 60.471 52.381 22.95 0.00 0.00 2.71
437 450 3.435327 TCATGACTCGTAATGTTGCAACC 59.565 43.478 26.14 10.11 0.00 3.77
438 451 2.147958 TGACTCGTAATGTTGCAACCC 58.852 47.619 26.14 10.74 0.00 4.11
458 471 3.489059 CCCGGATGCACAATTGTTATGAC 60.489 47.826 8.77 0.00 0.00 3.06
465 478 1.472480 ACAATTGTTATGACCGGCAGC 59.528 47.619 4.92 0.00 0.00 5.25
490 503 2.182030 GTTGGCGACGAGGAGGAG 59.818 66.667 0.00 0.00 0.00 3.69
491 504 2.282958 TTGGCGACGAGGAGGAGT 60.283 61.111 0.00 0.00 0.00 3.85
495 508 2.995872 GCGACGAGGAGGAGTGCTT 61.996 63.158 0.00 0.00 0.00 3.91
498 511 2.507992 CGAGGAGGAGTGCTTGCG 60.508 66.667 0.00 0.00 0.00 4.85
531 544 3.151022 GGGAGAGGGAGGTGCGAG 61.151 72.222 0.00 0.00 0.00 5.03
532 545 3.844090 GGAGAGGGAGGTGCGAGC 61.844 72.222 0.00 0.00 0.00 5.03
533 546 2.757917 GAGAGGGAGGTGCGAGCT 60.758 66.667 0.00 0.00 0.00 4.09
534 547 3.073735 AGAGGGAGGTGCGAGCTG 61.074 66.667 0.00 0.00 0.00 4.24
535 548 4.828925 GAGGGAGGTGCGAGCTGC 62.829 72.222 0.00 0.00 46.70 5.25
554 754 3.391382 AGCGGAGGTCGGAAAGGG 61.391 66.667 0.00 0.00 39.69 3.95
577 777 3.121030 ATGCGGCTGTGCGTTCTC 61.121 61.111 0.00 0.00 37.81 2.87
582 782 2.661866 GCTGTGCGTTCTCCGTGT 60.662 61.111 0.00 0.00 39.32 4.49
588 788 2.658707 GCGTTCTCCGTGTGCTGTC 61.659 63.158 0.00 0.00 39.32 3.51
602 802 0.737715 GCTGTCGAATCAACGGCTCT 60.738 55.000 0.00 0.00 44.04 4.09
609 809 1.410882 GAATCAACGGCTCTCTAGGCT 59.589 52.381 0.00 0.00 45.93 4.58
656 857 2.895865 CGCCTAGGTCGCTCTCGA 60.896 66.667 11.31 0.00 43.28 4.04
657 858 2.887889 CGCCTAGGTCGCTCTCGAG 61.888 68.421 11.31 5.93 46.46 4.04
658 859 1.820481 GCCTAGGTCGCTCTCGAGT 60.820 63.158 13.13 0.00 46.46 4.18
728 929 0.114364 TTCCTTTTCTCCAAGGGCCC 59.886 55.000 16.46 16.46 43.40 5.80
729 930 1.678970 CCTTTTCTCCAAGGGCCCG 60.679 63.158 18.44 2.08 39.95 6.13
730 931 1.678970 CTTTTCTCCAAGGGCCCGG 60.679 63.158 18.44 13.48 0.00 5.73
731 932 3.218386 TTTTCTCCAAGGGCCCGGG 62.218 63.158 25.23 25.23 0.00 5.73
732 933 4.667935 TTCTCCAAGGGCCCGGGA 62.668 66.667 29.64 29.64 0.00 5.14
733 934 4.667935 TCTCCAAGGGCCCGGGAA 62.668 66.667 30.67 21.19 0.00 3.97
734 935 3.657350 CTCCAAGGGCCCGGGAAA 61.657 66.667 30.67 15.63 0.00 3.13
735 936 3.186680 TCCAAGGGCCCGGGAAAA 61.187 61.111 29.66 12.48 0.00 2.29
775 976 1.373748 GCTCAACGGTGCCGAGTTA 60.374 57.895 18.16 0.00 42.83 2.24
782 983 1.068474 CGGTGCCGAGTTAAGTCAAG 58.932 55.000 10.83 2.47 42.83 3.02
783 984 0.796927 GGTGCCGAGTTAAGTCAAGC 59.203 55.000 10.83 12.08 0.00 4.01
810 1011 2.826428 TGACTGCAGATTTAGATCCGC 58.174 47.619 23.35 0.00 36.44 5.54
832 1033 0.107703 TAGCTAGCGCCATTGTTGCT 60.108 50.000 9.55 5.71 42.58 3.91
849 1050 4.137543 GTTGCTACTATTGCCTGCCTTAT 58.862 43.478 0.00 0.00 0.00 1.73
866 1067 7.310072 TGCCTTATTTTTATTCAATCGACGA 57.690 32.000 0.00 0.00 0.00 4.20
867 1068 7.753659 TGCCTTATTTTTATTCAATCGACGAA 58.246 30.769 0.00 1.88 0.00 3.85
870 1071 7.376072 CCTTATTTTTATTCAATCGACGAAGGC 59.624 37.037 0.00 0.00 0.00 4.35
871 1072 3.918258 TTTATTCAATCGACGAAGGCG 57.082 42.857 0.00 0.00 44.79 5.52
872 1073 2.855660 TATTCAATCGACGAAGGCGA 57.144 45.000 0.00 0.00 42.48 5.54
874 1075 1.277326 TTCAATCGACGAAGGCGATG 58.723 50.000 11.76 6.48 46.67 3.84
875 1076 1.145759 TCAATCGACGAAGGCGATGC 61.146 55.000 11.76 0.00 46.67 3.91
996 1224 1.671328 TCCTCGTGACACAGATCGATC 59.329 52.381 17.91 17.91 0.00 3.69
1014 1242 2.903855 GACATGGGCGATGCTGGG 60.904 66.667 9.58 0.00 35.15 4.45
1024 1252 1.948104 CGATGCTGGGGAAATTCGTA 58.052 50.000 0.00 0.00 0.00 3.43
1065 1293 5.655488 TCTCGTTCTCCATCTTGAATTCTC 58.345 41.667 7.05 0.00 0.00 2.87
1071 1299 6.090483 TCTCCATCTTGAATTCTCGATACC 57.910 41.667 7.05 0.00 0.00 2.73
1136 1364 3.908081 GGACTAATCGGCCGGCGA 61.908 66.667 27.83 20.18 0.00 5.54
1137 1365 2.338984 GACTAATCGGCCGGCGAT 59.661 61.111 27.83 22.97 0.00 4.58
1138 1366 2.022129 GACTAATCGGCCGGCGATG 61.022 63.158 28.16 19.28 0.00 3.84
1139 1367 3.414700 CTAATCGGCCGGCGATGC 61.415 66.667 28.16 11.76 0.00 3.91
1390 1651 2.416432 GCTCCTCTACTTCCGGCGT 61.416 63.158 6.01 0.00 0.00 5.68
1511 1778 1.077930 TACGCGCTCCTCTACCTGT 60.078 57.895 5.73 0.00 0.00 4.00
1814 2081 0.453950 CGACACCTTCTACGACGTGG 60.454 60.000 11.56 8.10 0.00 4.94
1918 2185 2.561956 CGGCGAGATGGACGGGTAT 61.562 63.158 0.00 0.00 33.92 2.73
2094 2361 0.108804 GTGATCTTCTTCGGCGACCA 60.109 55.000 10.16 0.00 0.00 4.02
2267 2540 8.194769 TCAATACAGAGTGAATAGAATACGCAA 58.805 33.333 0.00 0.00 0.00 4.85
2297 2570 0.320697 GTGCTCACCCCGTTCTTAGT 59.679 55.000 0.00 0.00 0.00 2.24
2413 2686 2.045926 ATCCACCGTTCAGCTGCC 60.046 61.111 9.47 0.46 0.00 4.85
2418 2691 1.453155 CACCGTTCAGCTGCCTTATT 58.547 50.000 9.47 0.00 0.00 1.40
2419 2692 1.131126 CACCGTTCAGCTGCCTTATTG 59.869 52.381 9.47 0.00 0.00 1.90
2522 2797 3.718434 AGATCAATAAGACCCATGGCAGA 59.282 43.478 6.09 0.00 0.00 4.26
2554 2829 4.964593 ACTTTTTGTAGTGGGATGTACGT 58.035 39.130 0.00 0.00 0.00 3.57
2576 2852 1.417288 GCATGGGGCATCTCTCCTCT 61.417 60.000 0.00 0.00 43.97 3.69
2577 2853 0.686224 CATGGGGCATCTCTCCTCTC 59.314 60.000 0.00 0.00 0.00 3.20
2591 2871 4.588899 TCTCCTCTCTCTCTCTCAAACAG 58.411 47.826 0.00 0.00 0.00 3.16
2879 3161 9.865321 ATGATTGAAACCACTTTTCTGAATATG 57.135 29.630 0.00 0.00 43.70 1.78
3058 3343 9.683069 GTAATGTGTTTTCTGAAATGAGTGAAT 57.317 29.630 3.31 0.00 0.00 2.57
3150 5608 5.566016 TGTTTTTCTTTCAGTTGAAACGACG 59.434 36.000 3.28 0.00 38.94 5.12
3253 5711 7.099266 TCACTCATTTGACACAACTGATTTT 57.901 32.000 0.00 0.00 0.00 1.82
3254 5712 8.219546 TCACTCATTTGACACAACTGATTTTA 57.780 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.036875 GGTGGCCTAGTTGAAGCACT 59.963 55.000 3.32 0.00 0.00 4.40
67 70 1.314534 TGGCGGTTGATTCCAGCATG 61.315 55.000 0.00 0.00 0.00 4.06
73 76 1.819632 ATCGCTGGCGGTTGATTCC 60.820 57.895 14.94 0.00 40.25 3.01
89 92 2.965147 TTGTCGCGGTTGCAGCATC 61.965 57.895 6.13 0.00 42.97 3.91
100 103 4.444024 CCGCACATGGTTGTCGCG 62.444 66.667 0.00 0.00 45.00 5.87
130 133 0.037326 TTGTCAGTCCCAGCATCGTC 60.037 55.000 0.00 0.00 0.00 4.20
135 138 0.321919 GCTGATTGTCAGTCCCAGCA 60.322 55.000 0.00 0.00 45.94 4.41
170 173 1.336240 TGTCAGTCACAGCATCGACAG 60.336 52.381 0.00 0.00 34.48 3.51
173 176 3.800628 CTGTCAGTCACAGCATCGA 57.199 52.632 0.00 0.00 46.30 3.59
182 185 2.907458 TCATCCCTCTCTGTCAGTCA 57.093 50.000 0.00 0.00 0.00 3.41
190 193 2.406559 CCACTTCCATCATCCCTCTCT 58.593 52.381 0.00 0.00 0.00 3.10
193 196 0.533755 CGCCACTTCCATCATCCCTC 60.534 60.000 0.00 0.00 0.00 4.30
201 204 3.156714 TGGTGTCGCCACTTCCAT 58.843 55.556 0.00 0.00 43.61 3.41
229 232 1.769733 CAGCATTGTTGTCAAACCGG 58.230 50.000 0.00 0.00 37.11 5.28
233 236 2.093816 TGGTTGCAGCATTGTTGTCAAA 60.094 40.909 2.05 0.00 37.11 2.69
235 238 1.109609 TGGTTGCAGCATTGTTGTCA 58.890 45.000 2.05 0.00 0.00 3.58
236 239 1.490621 GTGGTTGCAGCATTGTTGTC 58.509 50.000 2.05 0.00 0.00 3.18
239 242 0.248990 CACGTGGTTGCAGCATTGTT 60.249 50.000 7.95 0.00 0.00 2.83
256 259 2.935955 CGTCGTGGTTTCCAGCAC 59.064 61.111 0.00 0.00 46.27 4.40
276 288 3.236816 GGTTTCAGCATTGACAACGATG 58.763 45.455 0.00 0.00 40.00 3.84
277 289 2.095768 CGGTTTCAGCATTGACAACGAT 60.096 45.455 0.00 0.00 44.77 3.73
281 293 0.313672 GCCGGTTTCAGCATTGACAA 59.686 50.000 1.90 0.00 31.71 3.18
282 294 0.821301 TGCCGGTTTCAGCATTGACA 60.821 50.000 1.90 0.00 33.08 3.58
301 313 1.136891 GTTGGTTTCAGCTTTGGTGCT 59.863 47.619 0.00 0.00 45.18 4.40
320 333 1.523154 ATCGCAACAATGGCCGTTGT 61.523 50.000 33.21 33.21 44.49 3.32
333 346 2.045708 ATGCTTTCGCCCATCGCAA 61.046 52.632 0.00 0.00 37.30 4.85
338 351 1.033746 CAGACCATGCTTTCGCCCAT 61.034 55.000 0.00 0.00 34.43 4.00
370 383 4.922206 AGCTACCCAGTTTCATCAAATCA 58.078 39.130 0.00 0.00 0.00 2.57
377 390 2.108168 TCGCTAGCTACCCAGTTTCAT 58.892 47.619 13.93 0.00 0.00 2.57
384 397 2.028125 GCACCATCGCTAGCTACCCA 62.028 60.000 13.93 0.00 0.00 4.51
391 404 1.878522 GTCACCGCACCATCGCTAG 60.879 63.158 0.00 0.00 0.00 3.42
392 405 2.183300 GTCACCGCACCATCGCTA 59.817 61.111 0.00 0.00 0.00 4.26
411 424 1.922570 ACATTACGAGTCATGACGCC 58.077 50.000 21.83 15.60 36.20 5.68
424 437 1.469079 GCATCCGGGTTGCAACATTAC 60.469 52.381 29.55 15.57 39.90 1.89
426 439 1.184322 TGCATCCGGGTTGCAACATT 61.184 50.000 29.55 7.44 46.48 2.71
437 450 3.489059 GGTCATAACAATTGTGCATCCGG 60.489 47.826 12.82 0.00 0.00 5.14
438 451 3.694734 GGTCATAACAATTGTGCATCCG 58.305 45.455 12.82 0.00 0.00 4.18
473 486 2.182030 CTCCTCCTCGTCGCCAAC 59.818 66.667 0.00 0.00 0.00 3.77
484 497 2.811317 CGTCGCAAGCACTCCTCC 60.811 66.667 0.00 0.00 37.18 4.30
490 503 3.764049 GTCGTCCGTCGCAAGCAC 61.764 66.667 0.00 0.00 39.67 4.40
516 529 2.757917 AGCTCGCACCTCCCTCTC 60.758 66.667 0.00 0.00 0.00 3.20
529 542 4.828925 GACCTCCGCTGGCAGCTC 62.829 72.222 34.17 21.83 39.60 4.09
534 547 4.388499 TTTCCGACCTCCGCTGGC 62.388 66.667 0.00 0.00 36.84 4.85
535 548 2.125512 CTTTCCGACCTCCGCTGG 60.126 66.667 0.00 0.00 36.84 4.85
536 549 2.125512 CCTTTCCGACCTCCGCTG 60.126 66.667 0.00 0.00 36.84 5.18
537 550 3.391382 CCCTTTCCGACCTCCGCT 61.391 66.667 0.00 0.00 36.84 5.52
539 552 4.468689 GGCCCTTTCCGACCTCCG 62.469 72.222 0.00 0.00 38.18 4.63
540 553 2.610532 GATGGCCCTTTCCGACCTCC 62.611 65.000 0.00 0.00 0.00 4.30
541 554 1.153147 GATGGCCCTTTCCGACCTC 60.153 63.158 0.00 0.00 0.00 3.85
542 555 1.281925 ATGATGGCCCTTTCCGACCT 61.282 55.000 0.00 0.00 0.00 3.85
543 556 1.103398 CATGATGGCCCTTTCCGACC 61.103 60.000 0.00 0.00 0.00 4.79
544 557 1.728490 GCATGATGGCCCTTTCCGAC 61.728 60.000 0.00 0.00 0.00 4.79
545 558 1.453745 GCATGATGGCCCTTTCCGA 60.454 57.895 0.00 0.00 0.00 4.55
546 559 2.837883 CGCATGATGGCCCTTTCCG 61.838 63.158 0.00 0.00 0.00 4.30
547 560 2.492773 CCGCATGATGGCCCTTTCC 61.493 63.158 0.00 0.00 0.00 3.13
555 755 4.246206 CGCACAGCCGCATGATGG 62.246 66.667 0.00 0.00 0.00 3.51
577 777 0.163788 GTTGATTCGACAGCACACGG 59.836 55.000 0.00 0.00 0.00 4.94
578 778 0.179275 CGTTGATTCGACAGCACACG 60.179 55.000 4.94 0.00 0.00 4.49
582 782 1.005037 AGCCGTTGATTCGACAGCA 60.005 52.632 13.47 0.00 0.00 4.41
588 788 1.866063 GCCTAGAGAGCCGTTGATTCG 60.866 57.143 0.00 0.00 0.00 3.34
602 802 1.899054 CGCCAGATCGGAGCCTAGA 60.899 63.158 7.64 0.00 36.56 2.43
646 847 1.426223 GTGGAGACTCGAGAGCGAC 59.574 63.158 21.68 10.89 42.51 5.19
647 848 1.745864 GGTGGAGACTCGAGAGCGA 60.746 63.158 21.68 1.94 45.71 4.93
648 849 1.587043 TTGGTGGAGACTCGAGAGCG 61.587 60.000 21.68 0.00 39.35 5.03
649 850 0.603569 TTTGGTGGAGACTCGAGAGC 59.396 55.000 21.68 10.70 0.00 4.09
650 851 1.401670 CGTTTGGTGGAGACTCGAGAG 60.402 57.143 21.68 0.00 0.00 3.20
651 852 0.596577 CGTTTGGTGGAGACTCGAGA 59.403 55.000 21.68 0.00 0.00 4.04
653 854 1.201647 GATCGTTTGGTGGAGACTCGA 59.798 52.381 0.00 0.00 0.00 4.04
654 855 1.067846 TGATCGTTTGGTGGAGACTCG 60.068 52.381 0.00 0.00 0.00 4.18
655 856 2.737252 GTTGATCGTTTGGTGGAGACTC 59.263 50.000 0.00 0.00 0.00 3.36
656 857 2.767505 GTTGATCGTTTGGTGGAGACT 58.232 47.619 0.00 0.00 0.00 3.24
657 858 1.459592 CGTTGATCGTTTGGTGGAGAC 59.540 52.381 0.00 0.00 34.52 3.36
658 859 1.606994 CCGTTGATCGTTTGGTGGAGA 60.607 52.381 0.00 0.00 37.94 3.71
728 929 1.818060 TGCCATGAGTCAATTTTCCCG 59.182 47.619 0.00 0.00 0.00 5.14
729 930 3.091545 TCTGCCATGAGTCAATTTTCCC 58.908 45.455 0.00 0.00 0.00 3.97
730 931 4.741342 CTTCTGCCATGAGTCAATTTTCC 58.259 43.478 0.00 0.00 0.00 3.13
731 932 4.171754 GCTTCTGCCATGAGTCAATTTTC 58.828 43.478 0.00 0.00 0.00 2.29
732 933 3.366679 CGCTTCTGCCATGAGTCAATTTT 60.367 43.478 0.00 0.00 35.36 1.82
733 934 2.163010 CGCTTCTGCCATGAGTCAATTT 59.837 45.455 0.00 0.00 35.36 1.82
734 935 1.741706 CGCTTCTGCCATGAGTCAATT 59.258 47.619 0.00 0.00 35.36 2.32
735 936 1.339438 ACGCTTCTGCCATGAGTCAAT 60.339 47.619 0.00 0.00 35.36 2.57
769 970 6.526222 GTCAACATTAGCTTGACTTAACTCG 58.474 40.000 8.01 0.00 42.85 4.18
782 983 6.668541 TCTAAATCTGCAGTCAACATTAGC 57.331 37.500 14.67 0.00 0.00 3.09
783 984 7.307042 CGGATCTAAATCTGCAGTCAACATTAG 60.307 40.741 14.67 13.13 31.65 1.73
832 1033 9.415008 TGAATAAAAATAAGGCAGGCAATAGTA 57.585 29.630 0.00 0.00 0.00 1.82
849 1050 4.389382 TCGCCTTCGTCGATTGAATAAAAA 59.611 37.500 0.00 0.00 36.96 1.94
866 1067 3.213206 TGATCCTATTTGCATCGCCTT 57.787 42.857 0.00 0.00 0.00 4.35
867 1068 2.936919 TGATCCTATTTGCATCGCCT 57.063 45.000 0.00 0.00 0.00 5.52
870 1071 7.225538 GGGAATACTATGATCCTATTTGCATCG 59.774 40.741 0.00 0.00 33.61 3.84
871 1072 7.500559 GGGGAATACTATGATCCTATTTGCATC 59.499 40.741 0.00 0.00 33.61 3.91
872 1073 7.349598 GGGGAATACTATGATCCTATTTGCAT 58.650 38.462 0.00 0.00 33.61 3.96
873 1074 6.576244 CGGGGAATACTATGATCCTATTTGCA 60.576 42.308 0.00 0.00 33.61 4.08
874 1075 5.817816 CGGGGAATACTATGATCCTATTTGC 59.182 44.000 0.00 0.00 33.61 3.68
875 1076 6.070194 ACCGGGGAATACTATGATCCTATTTG 60.070 42.308 6.32 0.00 33.61 2.32
962 1190 0.037882 CGAGGATGTGCACAGACAGT 60.038 55.000 25.84 7.75 0.00 3.55
974 1202 1.401905 TCGATCTGTGTCACGAGGATG 59.598 52.381 9.57 4.67 0.00 3.51
996 1224 3.274586 CCAGCATCGCCCATGTCG 61.275 66.667 0.00 0.00 34.56 4.35
1014 1242 3.174799 GCGATCTGCATACGAATTTCC 57.825 47.619 10.57 0.00 45.45 3.13
1065 1293 2.030457 GCACAACAAGATTCCGGTATCG 59.970 50.000 14.59 5.12 0.00 2.92
1071 1299 1.197721 GGTCAGCACAACAAGATTCCG 59.802 52.381 0.00 0.00 0.00 4.30
1136 1364 0.182061 CCTCCTGTACCTGCATGCAT 59.818 55.000 22.97 10.26 0.00 3.96
1137 1365 1.603842 CCTCCTGTACCTGCATGCA 59.396 57.895 21.29 21.29 0.00 3.96
1138 1366 1.821332 GCCTCCTGTACCTGCATGC 60.821 63.158 11.82 11.82 0.00 4.06
1139 1367 1.522355 CGCCTCCTGTACCTGCATG 60.522 63.158 0.00 0.00 0.00 4.06
1273 1534 4.441695 CTGCCGAGGAAGCTCGCA 62.442 66.667 0.00 0.00 44.60 5.10
1814 2081 2.011046 GCTCCAGAACTGCATCTCCAC 61.011 57.143 0.00 0.00 0.00 4.02
1918 2185 1.382629 GGCCACCTTGCCCTTCTTA 59.617 57.895 0.00 0.00 46.11 2.10
2094 2361 1.229529 ACCTTCACCCCGTCCATCT 60.230 57.895 0.00 0.00 0.00 2.90
2267 2540 1.896465 GGGTGAGCACAGTCTAAGTCT 59.104 52.381 2.75 0.00 0.00 3.24
2297 2570 5.068460 CCACACAGGGATGAACAAAGTTTTA 59.932 40.000 0.00 0.00 0.00 1.52
2389 2662 1.473257 GCTGAACGGTGGATGCTATGA 60.473 52.381 0.00 0.00 0.00 2.15
2413 2686 5.992217 GGGCCTATTAGACACAGACAATAAG 59.008 44.000 0.84 0.00 0.00 1.73
2418 2691 2.116238 GGGGCCTATTAGACACAGACA 58.884 52.381 0.84 0.00 0.00 3.41
2419 2692 2.116238 TGGGGCCTATTAGACACAGAC 58.884 52.381 0.84 0.00 0.00 3.51
2522 2797 6.322712 TCCCACTACAAAAAGTACTGCATTTT 59.677 34.615 0.00 0.00 0.00 1.82
2540 2815 3.006430 CCATGCATACGTACATCCCACTA 59.994 47.826 0.00 0.00 0.00 2.74
2576 2852 4.141981 GCATGGATCTGTTTGAGAGAGAGA 60.142 45.833 0.00 0.00 32.80 3.10
2577 2853 4.121317 GCATGGATCTGTTTGAGAGAGAG 58.879 47.826 0.00 0.00 32.80 3.20
2879 3161 8.141268 TGGAATATGAAACTCACAAAGAAAACC 58.859 33.333 0.00 0.00 0.00 3.27
3150 5608 7.202016 TCACTAATTTGACACACTGATTTCC 57.798 36.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.