Multiple sequence alignment - TraesCS2B01G352300

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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 TraesCS2B01G352300 chr2B 100.000 4805 0 0 1 4805 503447978 503452782 0.000000e+00 8874.0
1 TraesCS2B01G352300 chr2B 86.490 681 53 14 814 1492 503341649 503341006 0.000000e+00 712.0
2 TraesCS2B01G352300 chr2B 97.917 48 1 0 4391 4438 503452320 503452367 3.080000e-12 84.2
3 TraesCS2B01G352300 chr2B 97.917 48 1 0 4343 4390 503452368 503452415 3.080000e-12 84.2
4 TraesCS2B01G352300 chr2D 93.678 2768 101 34 641 3396 426429597 426432302 0.000000e+00 4074.0
5 TraesCS2B01G352300 chr2D 96.524 1352 39 5 3456 4805 426432332 426433677 0.000000e+00 2230.0
6 TraesCS2B01G352300 chr2D 93.388 605 31 5 1 603 426429001 426429598 0.000000e+00 887.0
7 TraesCS2B01G352300 chr2D 77.551 1225 130 60 1640 2823 611771567 611772687 5.320000e-169 604.0
8 TraesCS2B01G352300 chr2D 82.667 600 55 27 904 1502 611770933 611771484 2.010000e-133 486.0
9 TraesCS2B01G352300 chr2D 82.550 149 19 4 4657 4805 1819714 1819573 1.820000e-24 124.0
10 TraesCS2B01G352300 chr2D 100.000 48 0 0 4391 4438 426433215 426433262 6.620000e-14 89.8
11 TraesCS2B01G352300 chr2D 97.917 48 1 0 4343 4390 426433263 426433310 3.080000e-12 84.2
12 TraesCS2B01G352300 chr2A 91.372 2944 151 49 512 3396 562513646 562510747 0.000000e+00 3934.0
13 TraesCS2B01G352300 chr2A 96.804 1408 41 3 3401 4805 562510688 562509282 0.000000e+00 2348.0
14 TraesCS2B01G352300 chr2A 79.433 1128 112 46 954 2041 744244916 744245963 0.000000e+00 688.0
15 TraesCS2B01G352300 chr2A 91.361 463 24 12 1 454 562514124 562513669 1.900000e-173 619.0
16 TraesCS2B01G352300 chr2A 86.164 477 55 7 2297 2767 744246592 744247063 5.550000e-139 505.0
17 TraesCS2B01G352300 chr2A 97.917 48 1 0 4343 4390 562509696 562509649 3.080000e-12 84.2
18 TraesCS2B01G352300 chr1B 89.141 396 20 11 1 387 6412260 6412641 5.630000e-129 472.0
19 TraesCS2B01G352300 chr3A 87.500 392 25 12 5 387 227067205 227067581 9.550000e-117 431.0
20 TraesCS2B01G352300 chr4B 81.491 389 57 6 4418 4805 1766819 1767193 6.040000e-79 305.0
21 TraesCS2B01G352300 chr3B 80.402 398 52 16 4417 4805 825499261 825499641 3.660000e-71 279.0
22 TraesCS2B01G352300 chrUn 78.947 399 57 18 4417 4805 43079679 43079298 3.710000e-61 246.0


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 TraesCS2B01G352300 chr2B 503447978 503452782 4804 False 3014.133333 8874 98.611333 1 4805 3 chr2B.!!$F1 4804
1 TraesCS2B01G352300 chr2B 503341006 503341649 643 True 712.000000 712 86.490000 814 1492 1 chr2B.!!$R1 678
2 TraesCS2B01G352300 chr2D 426429001 426433677 4676 False 1473.000000 4074 96.301400 1 4805 5 chr2D.!!$F1 4804
3 TraesCS2B01G352300 chr2D 611770933 611772687 1754 False 545.000000 604 80.109000 904 2823 2 chr2D.!!$F2 1919
4 TraesCS2B01G352300 chr2A 562509282 562514124 4842 True 1746.300000 3934 94.363500 1 4805 4 chr2A.!!$R1 4804
5 TraesCS2B01G352300 chr2A 744244916 744247063 2147 False 596.500000 688 82.798500 954 2767 2 chr2A.!!$F1 1813

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
996 1068 0.881796 TGCCTACACTCACTCACTCG 59.118 55.0 0.00 0.00 0.00 4.18 F
1852 1977 0.798776 CATGAACAGCTTGACCGGAC 59.201 55.0 9.46 1.07 0.00 4.79 F
2880 3482 0.179059 TGAAGCGGCTGTTCAGTTCA 60.179 50.0 1.81 0.00 30.36 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2030 0.523968 CATTGCGCGACAAATCCAGG 60.524 55.0 12.1 0.0 42.86 4.45 R
3073 3675 0.550914 ACTCCCAGTGCAACCTTCAA 59.449 50.0 0.0 0.0 37.80 2.69 R
4780 5449 0.693622 TTGGGAGGAACAATGCGGTA 59.306 50.0 0.0 0.0 0.00 4.02 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
56 57 2.368548 CTGTCCATTGATCCGGGATGTA 59.631 50.000 15.70 1.98 32.43 2.29
97 102 8.345565 GCAGTGTACATATTTTATCCAAAGAGG 58.654 37.037 0.00 0.00 39.47 3.69
184 189 8.149973 TGTCTTACTGAAAGGTAACAAACATC 57.850 34.615 0.00 0.00 39.30 3.06
233 240 7.766278 GCTGAGTATTATTCTCTCTTGTTTGGA 59.234 37.037 0.87 0.00 33.59 3.53
255 262 3.515502 ACTAGACTTGTGGCTTATGCTGA 59.484 43.478 0.00 0.00 39.59 4.26
269 276 5.125097 GCTTATGCTGATAGGATTTCCATGG 59.875 44.000 4.97 4.97 35.73 3.66
272 279 3.202818 TGCTGATAGGATTTCCATGGTGT 59.797 43.478 12.58 0.00 38.89 4.16
360 367 7.957002 TGCCCAATAATTGAAGTTAACTTTCA 58.043 30.769 21.40 16.64 36.11 2.69
378 385 4.904895 TTCATTTGGGCCATGATTGAAA 57.095 36.364 7.26 0.00 30.63 2.69
399 408 5.813080 AAGTTAACTTTGTGACACTGGTC 57.187 39.130 15.22 0.00 37.45 4.02
427 436 2.362369 ACGCACTATCTGCCTGGCT 61.362 57.895 21.03 1.67 43.84 4.75
475 484 2.159653 CGAAAGCAAAATCCACTCTCCG 60.160 50.000 0.00 0.00 0.00 4.63
483 492 3.935818 AATCCACTCTCCGAGTAGAGA 57.064 47.619 14.01 3.24 44.93 3.10
484 493 2.695127 TCCACTCTCCGAGTAGAGAC 57.305 55.000 14.01 0.00 44.93 3.36
486 495 2.093394 TCCACTCTCCGAGTAGAGACTG 60.093 54.545 14.01 3.71 44.93 3.51
487 496 2.355310 CCACTCTCCGAGTAGAGACTGT 60.355 54.545 14.01 0.00 44.93 3.55
488 497 3.118702 CCACTCTCCGAGTAGAGACTGTA 60.119 52.174 14.01 0.00 44.93 2.74
489 498 4.116961 CACTCTCCGAGTAGAGACTGTAG 58.883 52.174 14.01 0.00 44.93 2.74
492 501 4.025360 TCTCCGAGTAGAGACTGTAGAGT 58.975 47.826 0.00 0.00 37.98 3.24
498 507 4.581868 AGTAGAGACTGTAGAGTGTGGTC 58.418 47.826 0.00 0.00 33.41 4.02
540 549 1.827969 CAGTCGAATCCTGACTTCCCT 59.172 52.381 0.00 0.00 44.00 4.20
626 656 3.599412 TTGACGGCAACTACCACTC 57.401 52.632 0.00 0.00 0.00 3.51
628 658 1.445582 GACGGCAACTACCACTCCG 60.446 63.158 0.00 0.00 45.04 4.63
629 659 2.654877 CGGCAACTACCACTCCGT 59.345 61.111 0.00 0.00 35.75 4.69
630 660 1.736645 CGGCAACTACCACTCCGTG 60.737 63.158 0.00 0.00 35.75 4.94
725 776 2.895372 CGTGCCCCGTCCAATAGC 60.895 66.667 0.00 0.00 0.00 2.97
732 783 1.227263 CCGTCCAATAGCTCCACGG 60.227 63.158 0.00 0.00 43.71 4.94
771 822 3.157680 CCCCGTCCAACCTGACTT 58.842 61.111 0.00 0.00 32.97 3.01
782 833 3.244770 CCAACCTGACTTAGCCTACCAAA 60.245 47.826 0.00 0.00 0.00 3.28
853 924 2.422479 CCTACGTGCTGCTACTCTACAA 59.578 50.000 0.00 0.00 0.00 2.41
868 939 4.943705 ACTCTACAATAAAGTCCGTCCGTA 59.056 41.667 0.00 0.00 0.00 4.02
941 1012 4.374702 GACCAGCAACAGCACGCG 62.375 66.667 3.53 3.53 0.00 6.01
980 1052 4.792804 GGCCACTCTGCTCCTGCC 62.793 72.222 0.00 0.00 38.71 4.85
996 1068 0.881796 TGCCTACACTCACTCACTCG 59.118 55.000 0.00 0.00 0.00 4.18
1000 1072 2.552743 CCTACACTCACTCACTCGTTCA 59.447 50.000 0.00 0.00 0.00 3.18
1043 1120 3.866582 CCCGGCTCCCTCCACATC 61.867 72.222 0.00 0.00 0.00 3.06
1044 1121 3.866582 CCGGCTCCCTCCACATCC 61.867 72.222 0.00 0.00 0.00 3.51
1045 1122 3.083349 CGGCTCCCTCCACATCCA 61.083 66.667 0.00 0.00 0.00 3.41
1046 1123 2.592308 GGCTCCCTCCACATCCAC 59.408 66.667 0.00 0.00 0.00 4.02
1063 1140 3.430862 CGTCCATGGCAACCACCG 61.431 66.667 6.96 0.00 35.80 4.94
1176 1272 1.972978 GGTACACGACCTCCTGCTT 59.027 57.895 0.00 0.00 45.89 3.91
1280 1381 2.716017 CCTGCACGGACTCCTCCTC 61.716 68.421 0.00 0.00 33.79 3.71
1281 1382 2.680352 TGCACGGACTCCTCCTCC 60.680 66.667 0.00 0.00 33.79 4.30
1282 1383 2.363147 GCACGGACTCCTCCTCCT 60.363 66.667 0.00 0.00 33.79 3.69
1293 1400 1.435515 CTCCTCCTCCGCTTCTTCG 59.564 63.158 0.00 0.00 0.00 3.79
1536 1645 1.913451 CTCTCACGTCGCTCGACCTT 61.913 60.000 15.64 1.61 41.76 3.50
1801 1926 3.746751 CGAGATACCCGAGACCTTCCTTA 60.747 52.174 0.00 0.00 0.00 2.69
1852 1977 0.798776 CATGAACAGCTTGACCGGAC 59.201 55.000 9.46 1.07 0.00 4.79
1896 2030 1.889545 AGTTTCAGAAGCTGCTGTCC 58.110 50.000 21.55 10.28 37.20 4.02
2295 2476 2.601966 ATCTCCGGCTCGATCCCC 60.602 66.667 0.00 0.00 0.00 4.81
2332 2920 1.008938 AGAGGCTGGTATCCTTGTCCT 59.991 52.381 0.00 0.00 33.24 3.85
2544 3141 0.882927 TTCCCGCCGTGTTTCTTGAG 60.883 55.000 0.00 0.00 0.00 3.02
2613 3210 1.407979 CCATTGAGAAAGCATCAGGGC 59.592 52.381 0.00 0.00 0.00 5.19
2658 3255 1.906574 TCCTTCGTTACAGGATTGGCT 59.093 47.619 0.00 0.00 35.34 4.75
2699 3296 1.009829 GCAGTTTGCAGGAGGATACG 58.990 55.000 0.00 0.00 44.26 3.06
2823 3425 3.532641 AGAGGAGCATTTGGAAAGGTT 57.467 42.857 0.00 0.00 0.00 3.50
2880 3482 0.179059 TGAAGCGGCTGTTCAGTTCA 60.179 50.000 1.81 0.00 30.36 3.18
2947 3549 2.096819 GCGAAAATCCGGCACAAGAATA 59.903 45.455 0.00 0.00 0.00 1.75
3073 3675 1.677552 GTGGGATGGAACGACAGGT 59.322 57.895 0.00 0.00 0.00 4.00
3144 3746 0.531532 ATACTCCTCGCATGCTGCAC 60.532 55.000 17.13 0.00 45.36 4.57
3198 3800 2.460669 GATGAATTTGAGCCCAGGGTT 58.539 47.619 7.55 0.00 0.00 4.11
3201 3803 0.178924 AATTTGAGCCCAGGGTTGCT 60.179 50.000 7.55 0.00 41.42 3.91
3301 3903 1.439353 CGCGCCAGGTATGCATTTCT 61.439 55.000 3.54 0.00 0.00 2.52
3302 3904 0.029834 GCGCCAGGTATGCATTTCTG 59.970 55.000 3.54 12.80 0.00 3.02
3303 3905 1.382522 CGCCAGGTATGCATTTCTGT 58.617 50.000 20.35 0.00 0.00 3.41
3304 3906 2.560504 CGCCAGGTATGCATTTCTGTA 58.439 47.619 20.35 0.00 0.00 2.74
3305 3907 2.545526 CGCCAGGTATGCATTTCTGTAG 59.454 50.000 20.35 13.28 0.00 2.74
3375 3982 2.144362 GCATTTGCAAGGTGTTCGC 58.856 52.632 13.36 1.73 41.59 4.70
3396 4003 6.750148 TCGCCTTGTTACCAATTTGTTTTAT 58.250 32.000 0.00 0.00 0.00 1.40
3397 4004 6.642950 TCGCCTTGTTACCAATTTGTTTTATG 59.357 34.615 0.00 0.00 0.00 1.90
3398 4005 6.128688 CGCCTTGTTACCAATTTGTTTTATGG 60.129 38.462 0.00 0.00 38.91 2.74
3399 4006 6.348132 GCCTTGTTACCAATTTGTTTTATGGC 60.348 38.462 0.00 0.00 36.37 4.40
3425 4086 6.644347 ACATATCAAGAAGGTAGAGTTGGTG 58.356 40.000 0.00 0.00 0.00 4.17
3568 4229 1.198713 GGTCATTCTCCTGGAGCTGA 58.801 55.000 19.08 19.00 0.00 4.26
3689 4350 3.727258 CGACCCCAGCATTCCCCA 61.727 66.667 0.00 0.00 0.00 4.96
3775 4436 0.034059 CCAGAGGCCGGACATGTATC 59.966 60.000 11.69 0.00 0.00 2.24
3851 4512 5.661312 ACCACCATACTCTGAAGTTGCTATA 59.339 40.000 0.00 0.00 36.92 1.31
3877 4538 2.154854 TTGACTGGAGAAGCACTTCG 57.845 50.000 4.81 0.00 43.97 3.79
3887 4548 3.994392 GAGAAGCACTTCGGTTTGTGATA 59.006 43.478 4.81 0.00 43.97 2.15
3912 4573 4.499183 CTGAGTTCAGACCATCTGTTACC 58.501 47.826 2.97 2.36 46.59 2.85
4096 4757 4.576463 ACAAAACGAGCTTCAGAAGAACAT 59.424 37.500 14.86 0.00 0.00 2.71
4130 4791 5.920273 ACAGCGATTAAACAACAATTCCAAG 59.080 36.000 0.00 0.00 0.00 3.61
4153 4814 7.105241 AGTTGCAAATATCTGAAAATCCTCC 57.895 36.000 0.00 0.00 0.00 4.30
4154 4815 6.894103 AGTTGCAAATATCTGAAAATCCTCCT 59.106 34.615 0.00 0.00 0.00 3.69
4155 4816 6.949352 TGCAAATATCTGAAAATCCTCCTC 57.051 37.500 0.00 0.00 0.00 3.71
4156 4817 6.666678 TGCAAATATCTGAAAATCCTCCTCT 58.333 36.000 0.00 0.00 0.00 3.69
4157 4818 6.769822 TGCAAATATCTGAAAATCCTCCTCTC 59.230 38.462 0.00 0.00 0.00 3.20
4229 4895 8.856153 ATTACATTACAGGACATAAACACACA 57.144 30.769 0.00 0.00 0.00 3.72
4352 5020 0.471617 ACTGCCAGTTCTTCAGTGCT 59.528 50.000 0.00 0.00 39.36 4.40
4563 5232 4.092968 CCGGGTCTGATAAACTTTTCTTCG 59.907 45.833 0.00 0.00 0.00 3.79
4738 5407 1.954146 CCCGCCGATCCAATACACG 60.954 63.158 0.00 0.00 0.00 4.49
4780 5449 4.993584 GGAACATCTTCAGCATACATCGAT 59.006 41.667 0.00 0.00 0.00 3.59
4783 5452 5.473931 ACATCTTCAGCATACATCGATACC 58.526 41.667 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.877097 TGGACAGGTGTTACATGCAT 57.123 45.000 0.00 0.00 32.34 3.96
56 57 2.637872 ACACTGCCACACCTACTACATT 59.362 45.455 0.00 0.00 0.00 2.71
97 102 4.843728 TGGTTCCAAGATGAGAATGTACC 58.156 43.478 0.00 0.00 0.00 3.34
184 189 4.876125 TGAAAGACAGTAAGACAGCAGAG 58.124 43.478 0.00 0.00 0.00 3.35
233 240 3.515502 TCAGCATAAGCCACAAGTCTAGT 59.484 43.478 0.00 0.00 43.56 2.57
255 262 4.536765 GGTCAACACCATGGAAATCCTAT 58.463 43.478 21.47 0.00 43.17 2.57
308 315 6.215495 ACAAGCAAGTAAAGGCAGTAAAAA 57.785 33.333 0.00 0.00 0.00 1.94
360 367 4.914177 AACTTTCAATCATGGCCCAAAT 57.086 36.364 0.00 0.00 0.00 2.32
378 385 5.099042 AGACCAGTGTCACAAAGTTAACT 57.901 39.130 1.12 1.12 44.33 2.24
399 408 3.439293 CAGATAGTGCGTGAGTGGTTAG 58.561 50.000 0.00 0.00 0.00 2.34
427 436 4.667573 AGATCTATCTGCCTCCGTCATAA 58.332 43.478 0.00 0.00 35.42 1.90
475 484 4.581868 ACCACACTCTACAGTCTCTACTC 58.418 47.826 0.00 0.00 31.97 2.59
482 491 2.662700 CAACGACCACACTCTACAGTC 58.337 52.381 0.00 0.00 0.00 3.51
483 492 1.269621 GCAACGACCACACTCTACAGT 60.270 52.381 0.00 0.00 0.00 3.55
484 493 1.269569 TGCAACGACCACACTCTACAG 60.270 52.381 0.00 0.00 0.00 2.74
486 495 1.000607 TCTGCAACGACCACACTCTAC 60.001 52.381 0.00 0.00 0.00 2.59
487 496 1.269723 CTCTGCAACGACCACACTCTA 59.730 52.381 0.00 0.00 0.00 2.43
488 497 0.032678 CTCTGCAACGACCACACTCT 59.967 55.000 0.00 0.00 0.00 3.24
489 498 0.946221 CCTCTGCAACGACCACACTC 60.946 60.000 0.00 0.00 0.00 3.51
492 501 2.280797 GCCTCTGCAACGACCACA 60.281 61.111 0.00 0.00 37.47 4.17
498 507 2.434884 ATCACGGCCTCTGCAACG 60.435 61.111 0.00 0.00 40.13 4.10
540 549 1.406887 GCTTTCCAGGATCGTTGCCTA 60.407 52.381 0.00 0.00 33.51 3.93
722 773 4.242475 CATTATTATTCGCCGTGGAGCTA 58.758 43.478 0.00 0.00 0.00 3.32
725 776 2.805671 TGCATTATTATTCGCCGTGGAG 59.194 45.455 0.00 0.00 0.00 3.86
782 833 1.070601 GGCTGTGCAGGGATTTGTTTT 59.929 47.619 1.11 0.00 0.00 2.43
806 877 2.094545 GGATTGACATGTGCTTTCCACC 60.095 50.000 1.15 0.00 44.01 4.61
853 924 4.464008 TGGACTATACGGACGGACTTTAT 58.536 43.478 0.00 0.00 0.00 1.40
868 939 0.469917 CTGCGGGTTGGATGGACTAT 59.530 55.000 0.00 0.00 0.00 2.12
941 1012 2.102553 GAGCTACGGACGGACAGC 59.897 66.667 0.00 7.00 0.00 4.40
944 1015 3.452024 GAGCGAGCTACGGACGGAC 62.452 68.421 0.00 0.00 42.83 4.79
945 1016 3.200593 GAGCGAGCTACGGACGGA 61.201 66.667 0.00 0.00 42.83 4.69
946 1017 4.592936 CGAGCGAGCTACGGACGG 62.593 72.222 0.00 0.00 42.83 4.79
980 1052 3.898517 TGAACGAGTGAGTGAGTGTAG 57.101 47.619 0.00 0.00 0.00 2.74
996 1068 2.870372 GAGGTGCGGTGCATGAAC 59.130 61.111 0.00 0.00 41.91 3.18
1041 1118 1.378514 GGTTGCCATGGACGTGGAT 60.379 57.895 18.40 0.00 42.02 3.41
1042 1119 2.033448 GGTTGCCATGGACGTGGA 59.967 61.111 18.40 0.00 42.02 4.02
1043 1120 2.282110 TGGTTGCCATGGACGTGG 60.282 61.111 18.40 6.19 42.35 4.94
1044 1121 2.625823 GGTGGTTGCCATGGACGTG 61.626 63.158 18.40 0.00 35.28 4.49
1045 1122 2.282180 GGTGGTTGCCATGGACGT 60.282 61.111 18.40 0.00 35.28 4.34
1046 1123 3.430862 CGGTGGTTGCCATGGACG 61.431 66.667 18.40 3.62 35.28 4.79
1136 1219 0.321387 CTGCTCTGCTTCTGCTTCCA 60.321 55.000 0.00 0.00 40.48 3.53
1176 1272 1.915078 GCAGGGAGGCCTTGAAGCTA 61.915 60.000 6.77 0.00 31.89 3.32
1281 1382 4.436998 ACGGGCGAAGAAGCGGAG 62.437 66.667 0.00 0.00 38.18 4.63
1282 1383 4.430765 GACGGGCGAAGAAGCGGA 62.431 66.667 0.00 0.00 38.18 5.54
1518 1625 0.671472 TAAGGTCGAGCGACGTGAGA 60.671 55.000 17.33 5.36 45.41 3.27
1536 1645 1.226575 CTCGATGTCGTTGCCGCTA 60.227 57.895 2.04 0.00 40.80 4.26
1896 2030 0.523968 CATTGCGCGACAAATCCAGG 60.524 55.000 12.10 0.00 42.86 4.45
2295 2476 2.478134 CCTCTTGCAGTTCTTGAAGTCG 59.522 50.000 0.00 0.00 0.00 4.18
2332 2920 0.531974 GTGAGACCGTTGCTGGACAA 60.532 55.000 0.00 0.00 35.33 3.18
2544 3141 4.366684 CACAGGCCTGGGTTCCCC 62.367 72.222 35.42 0.00 45.71 4.81
2568 3165 2.436646 CAATCGCTCGGCAACCCT 60.437 61.111 0.00 0.00 0.00 4.34
2823 3425 5.337554 CCGTCTTGTAACACGATCAGATAA 58.662 41.667 0.00 0.00 38.32 1.75
2880 3482 1.627329 TCTCTGAATGTCAGCTTGGCT 59.373 47.619 0.17 0.00 43.95 4.75
2882 3484 3.436015 CACTTCTCTGAATGTCAGCTTGG 59.564 47.826 0.17 0.00 43.95 3.61
2910 3512 2.705826 GCCAGCGCTTTCATCTCG 59.294 61.111 7.50 0.00 0.00 4.04
3073 3675 0.550914 ACTCCCAGTGCAACCTTCAA 59.449 50.000 0.00 0.00 37.80 2.69
3117 3719 4.221482 AGCATGCGAGGAGTATAATCATGA 59.779 41.667 13.01 0.00 33.64 3.07
3144 3746 1.941734 GCTCGACTTCAGATCGCGG 60.942 63.158 6.13 0.00 39.46 6.46
3198 3800 1.851304 GATGAATCCCAAACCCAGCA 58.149 50.000 0.00 0.00 0.00 4.41
3201 3803 1.074727 ACACGATGAATCCCAAACCCA 59.925 47.619 0.00 0.00 0.00 4.51
3301 3903 6.265876 TGGTGTACTGATTCAACTACACTACA 59.734 38.462 21.99 15.00 39.22 2.74
3302 3904 6.684686 TGGTGTACTGATTCAACTACACTAC 58.315 40.000 21.99 13.50 39.22 2.73
3303 3905 6.071560 CCTGGTGTACTGATTCAACTACACTA 60.072 42.308 21.99 18.34 39.22 2.74
3304 3906 5.279506 CCTGGTGTACTGATTCAACTACACT 60.280 44.000 21.99 0.00 39.22 3.55
3305 3907 4.929808 CCTGGTGTACTGATTCAACTACAC 59.070 45.833 18.07 18.07 38.74 2.90
3396 4003 6.136857 ACTCTACCTTCTTGATATGTAGCCA 58.863 40.000 0.00 0.00 31.24 4.75
3397 4004 6.658188 ACTCTACCTTCTTGATATGTAGCC 57.342 41.667 0.00 0.00 31.24 3.93
3398 4005 6.926272 CCAACTCTACCTTCTTGATATGTAGC 59.074 42.308 0.00 0.00 31.24 3.58
3399 4006 7.923344 CACCAACTCTACCTTCTTGATATGTAG 59.077 40.741 0.00 0.00 0.00 2.74
3449 4110 7.814587 AGAACTTCAGTAAAAATTTATGCAGCC 59.185 33.333 0.00 0.00 0.00 4.85
3487 4148 4.105486 GTGAAGTTTTGCTCTGGTTTCAC 58.895 43.478 0.00 0.00 37.06 3.18
3568 4229 3.329889 TGCTGGCCTTCCGGTGAT 61.330 61.111 3.32 0.00 40.99 3.06
3689 4350 3.196207 ATGCCCTGTTGCTCCGTGT 62.196 57.895 0.00 0.00 0.00 4.49
3775 4436 1.159713 TGCAGCGACCTCACAACTTG 61.160 55.000 0.00 0.00 0.00 3.16
3851 4512 4.019501 AGTGCTTCTCCAGTCAAAGATCAT 60.020 41.667 0.00 0.00 0.00 2.45
3912 4573 3.058293 ACACAACAGGCACGAAATACATG 60.058 43.478 0.00 0.00 0.00 3.21
4096 4757 4.633565 TGTTTAATCGCTGTATGCATGACA 59.366 37.500 10.16 8.91 43.06 3.58
4130 4791 7.067981 AGAGGAGGATTTTCAGATATTTGCAAC 59.932 37.037 0.00 0.00 0.00 4.17
4207 4873 7.575414 TTTGTGTGTTTATGTCCTGTAATGT 57.425 32.000 0.00 0.00 0.00 2.71
4229 4895 8.840200 TTGTACTCTAGTCCCTATCATCTTTT 57.160 34.615 0.00 0.00 0.00 2.27
4352 5020 5.183921 AGCAAGAGCCTCTCATATGGAGAA 61.184 45.833 17.78 0.00 45.56 2.87
4563 5232 5.569059 GTGAATAACTGCAACATAAGTGCAC 59.431 40.000 9.40 9.40 34.61 4.57
4732 5401 4.189231 GACTGAAGGGTAATTGCGTGTAT 58.811 43.478 0.00 0.00 0.00 2.29
4738 5407 2.026262 TCCAGGACTGAAGGGTAATTGC 60.026 50.000 0.00 0.00 0.00 3.56
4780 5449 0.693622 TTGGGAGGAACAATGCGGTA 59.306 50.000 0.00 0.00 0.00 4.02
4783 5452 0.958091 TTGTTGGGAGGAACAATGCG 59.042 50.000 0.00 0.00 40.18 4.73


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

AutoCloner maintained by Alex Coulton.