Multiple sequence alignment - TraesCS5D01G401800

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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 TraesCS5D01G401800 chr5D 100.000 3010 0 0 1 3010 467596897 467599906 0.000000e+00 5559.0
1 TraesCS5D01G401800 chr5D 94.872 39 2 0 2703 2741 460647555 460647593 9.010000e-06 62.1
2 TraesCS5D01G401800 chr5B 91.915 2647 148 22 1 2611 574670712 574673328 0.000000e+00 3642.0
3 TraesCS5D01G401800 chr5B 92.132 394 23 3 2613 3005 574673364 574673750 1.580000e-152 549.0
4 TraesCS5D01G401800 chr5B 77.301 163 26 9 446 602 569309468 569309625 5.350000e-13 86.1
5 TraesCS5D01G401800 chr5A 94.064 1196 53 4 1434 2611 588372217 588373412 0.000000e+00 1799.0
6 TraesCS5D01G401800 chr5A 92.557 524 24 5 818 1341 588371681 588372189 0.000000e+00 737.0
7 TraesCS5D01G401800 chr5A 94.977 219 11 0 2792 3010 588373577 588373795 7.990000e-91 344.0
8 TraesCS5D01G401800 chr5A 92.233 103 7 1 2613 2715 588373448 588373549 8.700000e-31 145.0
9 TraesCS5D01G401800 chr5A 92.045 88 4 3 742 829 588371579 588371663 1.470000e-23 121.0
10 TraesCS5D01G401800 chr3D 84.906 159 22 2 446 602 612268610 612268452 3.110000e-35 159.0
11 TraesCS5D01G401800 chr7A 81.421 183 30 4 444 623 689378118 689378299 2.420000e-31 147.0
12 TraesCS5D01G401800 chr4B 81.143 175 29 3 442 612 663936157 663935983 1.460000e-28 137.0
13 TraesCS5D01G401800 chr7D 81.988 161 25 4 442 598 499909128 499909288 1.880000e-27 134.0
14 TraesCS5D01G401800 chr2B 81.366 161 28 2 444 602 76097834 76097994 2.440000e-26 130.0
15 TraesCS5D01G401800 chr2D 80.892 157 29 1 443 598 524398503 524398659 4.070000e-24 122.0
16 TraesCS5D01G401800 chr2D 81.250 144 25 1 454 597 138701079 138701220 6.820000e-22 115.0
17 TraesCS5D01G401800 chr6B 87.500 72 8 1 2662 2732 688308024 688307953 6.920000e-12 82.4


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 TraesCS5D01G401800 chr5D 467596897 467599906 3009 False 5559.0 5559 100.0000 1 3010 1 chr5D.!!$F2 3009
1 TraesCS5D01G401800 chr5B 574670712 574673750 3038 False 2095.5 3642 92.0235 1 3005 2 chr5B.!!$F2 3004
2 TraesCS5D01G401800 chr5A 588371579 588373795 2216 False 629.2 1799 93.1752 742 3010 5 chr5A.!!$F1 2268

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
105 106 0.648441 GTTTCAAGACGTGTGTGCGA 59.352 50.0 0.0 0.0 35.59 5.10 F
213 214 1.073964 TCGTTCGTCTCCTACTCACG 58.926 55.0 0.0 0.0 34.27 4.35 F
1574 1631 0.321919 ATTGTGTGGCGAGCTCATGT 60.322 50.0 15.4 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1436 0.250295 CACAACTGTCCCACGACCAT 60.250 55.0 0.0 0.0 38.32 3.55 R
1752 1816 0.468226 TCGGTGCCATCCATACCTTC 59.532 55.0 0.0 0.0 32.28 3.46 R
2825 2942 0.394192 CCAAGTGAGACCTCTGCACA 59.606 55.0 0.0 0.0 35.08 4.57 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
35 36 4.510711 TCTTGTGGTCGACGATAGAGATAC 59.489 45.833 9.92 0.00 41.38 2.24
38 39 3.059051 GTGGTCGACGATAGAGATACCAC 60.059 52.174 9.92 13.34 44.62 4.16
57 58 3.780902 CACTGAAAGGGGTTGTGAAAAC 58.219 45.455 0.00 0.00 39.30 2.43
60 61 2.164624 TGAAAGGGGTTGTGAAAACACG 59.835 45.455 0.00 0.00 0.00 4.49
66 67 2.604614 GGGTTGTGAAAACACGCAGATC 60.605 50.000 0.00 0.00 0.00 2.75
76 77 4.671569 CGCAGATCTAGGGGGCGC 62.672 72.222 10.89 0.00 41.27 6.53
101 102 2.286184 GCGAATGTTTCAAGACGTGTGT 60.286 45.455 0.00 0.00 0.00 3.72
105 106 0.648441 GTTTCAAGACGTGTGTGCGA 59.352 50.000 0.00 0.00 35.59 5.10
108 109 3.327754 AAGACGTGTGTGCGACGC 61.328 61.111 14.19 14.19 40.56 5.19
139 140 2.034376 AGGTCCTCGACGCAGAGT 59.966 61.111 6.93 0.00 36.56 3.24
167 168 4.752879 GCTAGGGTTGCCGTCGCA 62.753 66.667 0.00 0.00 45.49 5.10
209 210 1.792941 GCGTCGTTCGTCTCCTACT 59.207 57.895 0.00 0.00 42.13 2.57
213 214 1.073964 TCGTTCGTCTCCTACTCACG 58.926 55.000 0.00 0.00 34.27 4.35
244 245 3.351885 AGAGGAGGGAGGAGGCGT 61.352 66.667 0.00 0.00 0.00 5.68
258 259 4.752879 GCGTTGGTGGCCTAGCGA 62.753 66.667 3.32 0.00 0.00 4.93
273 274 3.770040 CGATGCGGAGGTGACCCA 61.770 66.667 0.00 0.00 0.00 4.51
315 316 2.608090 GCGGCTCCTCTTAAATACACAC 59.392 50.000 0.00 0.00 0.00 3.82
338 339 9.120538 ACACTGTTGATATAATTATGGTGGTTC 57.879 33.333 8.28 0.00 0.00 3.62
339 340 8.567948 CACTGTTGATATAATTATGGTGGTTCC 58.432 37.037 8.28 0.00 0.00 3.62
342 343 8.430431 TGTTGATATAATTATGGTGGTTCCGTA 58.570 33.333 8.28 0.00 39.52 4.02
384 385 6.389830 ACACTTTTGCTTGTGATATGACAA 57.610 33.333 7.54 7.54 37.59 3.18
544 545 7.853377 TTAGAGCGTAGATTCATACATTTCG 57.147 36.000 0.00 0.00 0.00 3.46
545 546 4.681942 AGAGCGTAGATTCATACATTTCGC 59.318 41.667 0.00 0.00 41.11 4.70
546 547 4.368315 AGCGTAGATTCATACATTTCGCA 58.632 39.130 0.00 0.00 42.79 5.10
549 550 6.017934 AGCGTAGATTCATACATTTCGCATTT 60.018 34.615 0.00 0.00 42.79 2.32
566 567 5.989168 TCGCATTTTATGTAGTCCATAGTGG 59.011 40.000 0.00 0.00 37.34 4.00
581 582 7.605410 TCCATAGTGGAATCTTTAAAACGAC 57.395 36.000 0.00 0.00 45.00 4.34
598 617 7.543947 AAAACGACTTATATTTAGGAACGGG 57.456 36.000 0.00 0.00 0.00 5.28
599 618 5.205759 ACGACTTATATTTAGGAACGGGG 57.794 43.478 0.00 0.00 0.00 5.73
675 695 1.707427 AGCAAACATCCCTCTGTTCCT 59.293 47.619 0.00 0.00 38.38 3.36
725 746 2.528564 CGGGATATGGGCCATCAATTT 58.471 47.619 25.07 0.09 0.00 1.82
812 833 3.018805 TCCCCGAAATCCCCACCC 61.019 66.667 0.00 0.00 0.00 4.61
814 835 2.767352 CCCGAAATCCCCACCCAA 59.233 61.111 0.00 0.00 0.00 4.12
815 836 1.379843 CCCGAAATCCCCACCCAAG 60.380 63.158 0.00 0.00 0.00 3.61
855 903 4.842091 GCAAGCGGCGGCAGATTG 62.842 66.667 23.35 23.35 43.41 2.67
860 908 2.398554 GCGGCGGCAGATTGAAGAA 61.399 57.895 9.78 0.00 39.62 2.52
893 941 1.421646 CCAGAATCCAGATACCCACCC 59.578 57.143 0.00 0.00 0.00 4.61
895 943 2.370189 CAGAATCCAGATACCCACCCTC 59.630 54.545 0.00 0.00 0.00 4.30
933 981 1.994463 GGGCAGATTCACCCACTCT 59.006 57.895 9.34 0.00 46.22 3.24
953 1001 1.136305 TGTACAGCAGTATTCCCTCGC 59.864 52.381 0.00 0.00 31.84 5.03
956 1004 2.111251 GCAGTATTCCCTCGCCCC 59.889 66.667 0.00 0.00 0.00 5.80
1059 1107 2.347490 CTCCACAACACCCCCGAG 59.653 66.667 0.00 0.00 0.00 4.63
1184 1232 4.972999 AGGTAGGTTGGTAGGTAGGTAA 57.027 45.455 0.00 0.00 0.00 2.85
1384 1436 3.195396 GGCAATGCAAGGTTTAATCCTCA 59.805 43.478 7.79 1.53 36.74 3.86
1385 1437 4.141869 GGCAATGCAAGGTTTAATCCTCAT 60.142 41.667 7.79 3.72 36.74 2.90
1386 1438 4.807304 GCAATGCAAGGTTTAATCCTCATG 59.193 41.667 5.54 3.18 36.74 3.07
1387 1439 5.353938 CAATGCAAGGTTTAATCCTCATGG 58.646 41.667 5.54 0.89 36.74 3.66
1388 1440 4.046286 TGCAAGGTTTAATCCTCATGGT 57.954 40.909 5.54 0.00 36.74 3.55
1389 1441 4.016444 TGCAAGGTTTAATCCTCATGGTC 58.984 43.478 5.54 0.00 36.74 4.02
1482 1534 2.276732 CTCTGTTGAGGGCTTTGGAA 57.723 50.000 0.00 0.00 36.70 3.53
1515 1571 5.826601 TTGTGTCAGCAGAGAGTAGATAG 57.173 43.478 0.00 0.00 0.00 2.08
1546 1603 6.546034 ACAATACTACTTGGCAATATGTTCCC 59.454 38.462 0.00 0.00 0.00 3.97
1574 1631 0.321919 ATTGTGTGGCGAGCTCATGT 60.322 50.000 15.40 0.00 0.00 3.21
1669 1726 1.291877 GCTTGCCGTGACTGGTACTG 61.292 60.000 0.00 0.00 0.00 2.74
1676 1733 1.542030 CGTGACTGGTACTGCTTCTCT 59.458 52.381 0.00 0.00 0.00 3.10
1681 1745 1.754226 CTGGTACTGCTTCTCTCCTCC 59.246 57.143 0.00 0.00 0.00 4.30
1697 1761 5.694995 TCTCCTCCTGTTTTCATGTTCTTT 58.305 37.500 0.00 0.00 0.00 2.52
1702 1766 7.041107 CCTCCTGTTTTCATGTTCTTTTTCAA 58.959 34.615 0.00 0.00 0.00 2.69
1704 1768 6.529829 TCCTGTTTTCATGTTCTTTTTCAACG 59.470 34.615 0.00 0.00 0.00 4.10
1719 1783 9.528018 TCTTTTTCAACGCATTTTATTTTCTCT 57.472 25.926 0.00 0.00 0.00 3.10
1736 1800 2.429971 TCTCTTAGGCTGTCTGCTCATG 59.570 50.000 0.00 0.00 42.39 3.07
1737 1801 2.168106 CTCTTAGGCTGTCTGCTCATGT 59.832 50.000 0.00 0.00 42.39 3.21
1746 1810 6.212187 AGGCTGTCTGCTCATGTATGATAATA 59.788 38.462 1.44 0.00 42.39 0.98
1747 1811 6.312426 GGCTGTCTGCTCATGTATGATAATAC 59.688 42.308 1.44 0.00 42.39 1.89
1752 1816 8.217115 GTCTGCTCATGTATGATAATACGTTTG 58.783 37.037 0.00 0.00 36.02 2.93
2240 2315 5.163290 TGTGTGTGATGTAAACCCTCTTACA 60.163 40.000 0.00 0.00 43.89 2.41
2292 2367 5.823861 TCCATGCCATTACTGCTTCTATA 57.176 39.130 0.00 0.00 0.00 1.31
2296 2371 7.391554 TCCATGCCATTACTGCTTCTATATTTC 59.608 37.037 0.00 0.00 0.00 2.17
2299 2374 8.158169 TGCCATTACTGCTTCTATATTTCTTG 57.842 34.615 0.00 0.00 0.00 3.02
2313 2388 3.363341 TTTCTTGTTTTCGTGGGATGC 57.637 42.857 0.00 0.00 0.00 3.91
2330 2405 1.107945 TGCGCCACAGTACTGCTATA 58.892 50.000 22.90 2.11 0.00 1.31
2405 2480 8.965986 AAGACTTTTGTGTAACTTGTTCTTTC 57.034 30.769 0.00 0.00 38.04 2.62
2425 2500 6.910433 TCTTTCGTAACTTTCAAGATGCAAAC 59.090 34.615 0.00 0.00 0.00 2.93
2429 2504 5.277779 CGTAACTTTCAAGATGCAAACTGGA 60.278 40.000 0.00 0.00 0.00 3.86
2489 2564 0.454957 CTTCCCGTGCAAGCATTTCG 60.455 55.000 0.00 0.00 0.00 3.46
2537 2612 0.401738 CCCCTTGTGTCACCTCACAT 59.598 55.000 0.00 0.00 45.73 3.21
2568 2643 2.300437 AGTTGGGCAGTAGACTTCAGAC 59.700 50.000 0.00 0.00 0.00 3.51
2611 2686 3.749226 GCCCCCTCTCTTGATATTTCTG 58.251 50.000 0.00 0.00 0.00 3.02
2641 2750 9.013229 TGAAGAAATTTTATCATGTGCTACTGT 57.987 29.630 0.00 0.00 0.00 3.55
2673 2783 0.249398 CCTAGGACCTGGGTTTGACG 59.751 60.000 15.79 0.00 0.00 4.35
2714 2831 0.036010 TGCAGAGTAAGGCTTGCCTC 60.036 55.000 15.10 14.38 33.41 4.70
2723 2840 4.589374 AGTAAGGCTTGCCTCGTATAATCT 59.411 41.667 15.10 0.00 0.00 2.40
2726 2843 4.781934 AGGCTTGCCTCGTATAATCTTTT 58.218 39.130 8.56 0.00 0.00 2.27
2732 2849 4.407621 TGCCTCGTATAATCTTTTCCCAGA 59.592 41.667 0.00 0.00 0.00 3.86
2747 2864 1.121407 CCAGACCTCACCTGGTGTCA 61.121 60.000 25.15 7.37 44.66 3.58
2771 2888 2.933056 GCTTCTAGCACTTGGTCTGTCC 60.933 54.545 0.00 0.00 41.89 4.02
2772 2889 2.009681 TCTAGCACTTGGTCTGTCCA 57.990 50.000 0.00 0.00 45.60 4.02
2822 2939 6.442564 TGGAAATGTACACCTTACCTGATAGT 59.557 38.462 0.00 0.00 0.00 2.12
2823 2940 7.620491 TGGAAATGTACACCTTACCTGATAGTA 59.380 37.037 0.00 0.00 0.00 1.82
2824 2941 8.648693 GGAAATGTACACCTTACCTGATAGTAT 58.351 37.037 0.00 0.00 0.00 2.12
2826 2943 9.832445 AAATGTACACCTTACCTGATAGTATTG 57.168 33.333 0.00 0.00 0.00 1.90
2836 2958 4.100189 ACCTGATAGTATTGTGCAGAGGTC 59.900 45.833 0.00 0.00 0.00 3.85
2854 2976 2.019984 GTCTCACTTGGAATGGATGGC 58.980 52.381 0.00 0.00 0.00 4.40
2902 3024 0.700564 ATGTGGAAGGTGGTGCTGAT 59.299 50.000 0.00 0.00 0.00 2.90
2972 3094 0.824759 GCTACGGGTGAACCATCTCT 59.175 55.000 1.16 0.00 40.22 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.079578 TCGTCGACCACAAGATAGTCTT 58.920 45.455 10.58 0.00 37.14 3.01
11 12 3.542648 TCTCTATCGTCGACCACAAGAT 58.457 45.455 10.58 8.92 0.00 2.40
35 36 2.065899 TTCACAACCCCTTTCAGTGG 57.934 50.000 0.00 0.00 0.00 4.00
50 51 2.673368 CCCTAGATCTGCGTGTTTTCAC 59.327 50.000 5.18 0.00 46.33 3.18
57 58 2.423446 GCCCCCTAGATCTGCGTG 59.577 66.667 5.18 0.00 0.00 5.34
60 61 2.330924 AAAGCGCCCCCTAGATCTGC 62.331 60.000 2.29 0.00 0.00 4.26
76 77 3.418619 CACGTCTTGAAACATTCGCAAAG 59.581 43.478 0.00 0.00 0.00 2.77
185 186 3.684315 GACGAACGACGCGTGCAA 61.684 61.111 20.70 0.00 46.94 4.08
213 214 2.892425 CTCTCCCAATCGTGCGCC 60.892 66.667 4.18 0.00 0.00 6.53
244 245 2.124736 GCATCGCTAGGCCACCAA 60.125 61.111 5.01 0.00 0.00 3.67
253 254 2.782222 GGTCACCTCCGCATCGCTA 61.782 63.158 0.00 0.00 0.00 4.26
258 259 1.852157 ATGTTGGGTCACCTCCGCAT 61.852 55.000 0.00 0.00 37.76 4.73
263 264 0.609131 CCACCATGTTGGGTCACCTC 60.609 60.000 0.25 0.00 43.37 3.85
290 291 0.530870 ATTTAAGAGGAGCCGCTCGC 60.531 55.000 14.21 8.81 37.98 5.03
292 293 3.124560 GTGTATTTAAGAGGAGCCGCTC 58.875 50.000 12.27 12.27 0.00 5.03
296 297 4.833390 ACAGTGTGTATTTAAGAGGAGCC 58.167 43.478 0.00 0.00 0.00 4.70
315 316 7.444183 ACGGAACCACCATAATTATATCAACAG 59.556 37.037 0.00 0.00 38.90 3.16
329 330 4.913784 AGTAAAATGTACGGAACCACCAT 58.086 39.130 0.00 0.00 38.90 3.55
477 478 4.718774 ACATGTAGTCCATGATGGAGTCTT 59.281 41.667 24.28 11.72 46.94 3.01
479 480 4.375272 CACATGTAGTCCATGATGGAGTC 58.625 47.826 24.28 15.98 46.94 3.36
522 523 4.681942 GCGAAATGTATGAATCTACGCTCT 59.318 41.667 0.00 0.00 40.28 4.09
523 524 4.444388 TGCGAAATGTATGAATCTACGCTC 59.556 41.667 0.00 0.00 43.07 5.03
526 527 9.811655 ATAAAATGCGAAATGTATGAATCTACG 57.188 29.630 0.00 0.00 0.00 3.51
543 544 5.989168 TCCACTATGGACTACATAAAATGCG 59.011 40.000 0.00 0.00 42.67 4.73
572 573 9.097257 CCCGTTCCTAAATATAAGTCGTTTTAA 57.903 33.333 0.00 0.00 0.00 1.52
574 575 6.539826 CCCCGTTCCTAAATATAAGTCGTTTT 59.460 38.462 0.00 0.00 0.00 2.43
581 582 6.430000 CACATTCCCCCGTTCCTAAATATAAG 59.570 42.308 0.00 0.00 0.00 1.73
648 668 5.385198 ACAGAGGGATGTTTGCTAGAAAAA 58.615 37.500 0.00 0.00 0.00 1.94
649 669 4.985538 ACAGAGGGATGTTTGCTAGAAAA 58.014 39.130 0.00 0.00 0.00 2.29
650 670 4.640771 ACAGAGGGATGTTTGCTAGAAA 57.359 40.909 0.00 0.00 0.00 2.52
651 671 4.565652 GGAACAGAGGGATGTTTGCTAGAA 60.566 45.833 0.00 0.00 43.32 2.10
652 672 3.055094 GGAACAGAGGGATGTTTGCTAGA 60.055 47.826 0.00 0.00 43.32 2.43
653 673 3.054802 AGGAACAGAGGGATGTTTGCTAG 60.055 47.826 0.00 0.00 43.32 3.42
665 685 0.107312 CTGATGGGCAGGAACAGAGG 60.107 60.000 0.00 0.00 41.07 3.69
753 774 0.324943 CGTGGGCCTAGGATAATGGG 59.675 60.000 14.75 0.00 0.00 4.00
812 833 3.058363 GCAGAGAAAGAAGAACTGCCTTG 60.058 47.826 0.00 0.00 45.19 3.61
814 835 2.777094 GCAGAGAAAGAAGAACTGCCT 58.223 47.619 0.00 0.00 45.19 4.75
855 903 3.769844 TCTGGACCAGGTATCTGTTCTTC 59.230 47.826 21.56 0.00 39.31 2.87
860 908 3.041946 GGATTCTGGACCAGGTATCTGT 58.958 50.000 21.56 0.31 39.31 3.41
893 941 1.678425 GGCTTGCAGAGGAAGAAGGAG 60.678 57.143 2.32 0.00 0.00 3.69
895 943 1.023513 CGGCTTGCAGAGGAAGAAGG 61.024 60.000 2.32 0.00 0.00 3.46
933 981 1.136305 GCGAGGGAATACTGCTGTACA 59.864 52.381 5.50 0.00 0.00 2.90
998 1046 3.982372 TTCGTCAGCGTCGGCATCC 62.982 63.158 0.00 0.00 43.41 3.51
1059 1107 1.226717 GACGACGATCCAGCAGTCC 60.227 63.158 0.00 0.00 0.00 3.85
1184 1232 1.153628 GAAGCGCGTCCATACACCT 60.154 57.895 12.67 0.00 0.00 4.00
1234 1286 1.278238 CATTCGGTCGAACAGGCTAC 58.722 55.000 8.00 0.00 36.91 3.58
1384 1436 0.250295 CACAACTGTCCCACGACCAT 60.250 55.000 0.00 0.00 38.32 3.55
1385 1437 1.145156 CACAACTGTCCCACGACCA 59.855 57.895 0.00 0.00 38.32 4.02
1386 1438 2.251642 GCACAACTGTCCCACGACC 61.252 63.158 0.00 0.00 38.32 4.79
1387 1439 1.227556 AGCACAACTGTCCCACGAC 60.228 57.895 0.00 0.00 39.66 4.34
1388 1440 1.227527 CAGCACAACTGTCCCACGA 60.228 57.895 0.00 0.00 41.86 4.35
1389 1441 2.253758 CCAGCACAACTGTCCCACG 61.254 63.158 0.00 0.00 45.68 4.94
1480 1532 7.362662 TCTGCTGACACAAATTCTATTTGTTC 58.637 34.615 13.49 13.78 40.30 3.18
1482 1534 6.712095 TCTCTGCTGACACAAATTCTATTTGT 59.288 34.615 11.01 11.01 42.75 2.83
1515 1571 5.828299 TTGCCAAGTAGTATTGTAATGCC 57.172 39.130 0.00 0.00 0.00 4.40
1546 1603 1.204704 TCGCCACACAATCAGAGTAGG 59.795 52.381 0.00 0.00 0.00 3.18
1574 1631 5.499313 TCTGCATTGTATTCATCAACAGGA 58.501 37.500 0.00 0.00 0.00 3.86
1669 1726 3.409026 TGAAAACAGGAGGAGAGAAGC 57.591 47.619 0.00 0.00 0.00 3.86
1676 1733 6.379703 TGAAAAAGAACATGAAAACAGGAGGA 59.620 34.615 0.00 0.00 0.00 3.71
1681 1745 6.177822 GCGTTGAAAAAGAACATGAAAACAG 58.822 36.000 0.00 0.00 0.00 3.16
1697 1761 9.405587 CCTAAGAGAAAATAAAATGCGTTGAAA 57.594 29.630 0.00 0.00 0.00 2.69
1702 1766 6.151144 ACAGCCTAAGAGAAAATAAAATGCGT 59.849 34.615 0.00 0.00 0.00 5.24
1704 1768 7.699812 CAGACAGCCTAAGAGAAAATAAAATGC 59.300 37.037 0.00 0.00 0.00 3.56
1736 1800 9.701098 TCCATACCTTCAAACGTATTATCATAC 57.299 33.333 0.00 0.00 33.05 2.39
1746 1810 2.290641 TGCCATCCATACCTTCAAACGT 60.291 45.455 0.00 0.00 0.00 3.99
1747 1811 2.097466 GTGCCATCCATACCTTCAAACG 59.903 50.000 0.00 0.00 0.00 3.60
1752 1816 0.468226 TCGGTGCCATCCATACCTTC 59.532 55.000 0.00 0.00 32.28 3.46
1838 1902 2.158667 AGGTGTTTCGTCCAAGTCCAAT 60.159 45.455 0.00 0.00 0.00 3.16
2185 2260 6.774170 CAGGTCTTGAAATGAATCCATCCATA 59.226 38.462 0.00 0.00 31.40 2.74
2240 2315 2.033757 CAGCAGCTGCCTCAAGGT 59.966 61.111 34.39 12.11 43.38 3.50
2292 2367 3.611530 CGCATCCCACGAAAACAAGAAAT 60.612 43.478 0.00 0.00 0.00 2.17
2296 2371 0.729140 GCGCATCCCACGAAAACAAG 60.729 55.000 0.30 0.00 0.00 3.16
2299 2374 2.178273 GGCGCATCCCACGAAAAC 59.822 61.111 10.83 0.00 0.00 2.43
2313 2388 3.253432 TCAGATATAGCAGTACTGTGGCG 59.747 47.826 23.44 0.00 0.00 5.69
2405 2480 4.911610 CCAGTTTGCATCTTGAAAGTTACG 59.088 41.667 0.00 0.00 0.00 3.18
2425 2500 0.897621 GAGGGGCCAACAAATTCCAG 59.102 55.000 4.39 0.00 0.00 3.86
2429 2504 2.106338 CAAAAGGAGGGGCCAACAAATT 59.894 45.455 4.39 0.00 40.02 1.82
2537 2612 2.546899 ACTGCCCAACTATCTACACCA 58.453 47.619 0.00 0.00 0.00 4.17
2588 2663 1.807814 AATATCAAGAGAGGGGGCGT 58.192 50.000 0.00 0.00 0.00 5.68
2611 2686 8.976986 AGCACATGATAAAATTTCTTCAACTC 57.023 30.769 0.00 0.17 0.00 3.01
2641 2750 4.222145 CAGGTCCTAGGTTACTAAGCACAA 59.778 45.833 9.08 0.00 0.00 3.33
2669 2779 2.543641 CAATGCATAGAGACTGCGTCA 58.456 47.619 0.00 0.00 42.62 4.35
2714 2831 5.753921 GTGAGGTCTGGGAAAAGATTATACG 59.246 44.000 0.00 0.00 0.00 3.06
2723 2840 0.771127 CCAGGTGAGGTCTGGGAAAA 59.229 55.000 2.40 0.00 45.95 2.29
2732 2849 1.476007 GCTCTGACACCAGGTGAGGT 61.476 60.000 27.39 3.30 44.48 3.85
2747 2864 2.233431 CAGACCAAGTGCTAGAAGCTCT 59.767 50.000 0.00 0.00 45.84 4.09
2779 2896 7.722285 ACATTTCCAGGTTACTAAGCAGTAAAA 59.278 33.333 0.00 0.00 46.30 1.52
2780 2897 7.228590 ACATTTCCAGGTTACTAAGCAGTAAA 58.771 34.615 0.00 0.00 46.30 2.01
2781 2898 6.775708 ACATTTCCAGGTTACTAAGCAGTAA 58.224 36.000 1.00 0.00 43.46 2.24
2822 2939 3.306989 CCAAGTGAGACCTCTGCACAATA 60.307 47.826 0.00 0.00 35.08 1.90
2823 2940 2.551721 CCAAGTGAGACCTCTGCACAAT 60.552 50.000 0.00 0.00 35.08 2.71
2824 2941 1.202687 CCAAGTGAGACCTCTGCACAA 60.203 52.381 0.00 0.00 35.08 3.33
2825 2942 0.394192 CCAAGTGAGACCTCTGCACA 59.606 55.000 0.00 0.00 35.08 4.57
2826 2943 0.681733 TCCAAGTGAGACCTCTGCAC 59.318 55.000 0.00 0.00 0.00 4.57
2836 2958 1.019673 CGCCATCCATTCCAAGTGAG 58.980 55.000 0.00 0.00 0.00 3.51
2854 2976 2.863153 CTCCGCCTTCAAGCAACG 59.137 61.111 0.00 0.00 0.00 4.10
2881 3003 1.604593 AGCACCACCTTCCACATGC 60.605 57.895 0.00 0.00 0.00 4.06
2902 3024 2.868504 AAGCCCCAGGTTGAGAAGA 58.131 52.632 0.00 0.00 30.94 2.87
2972 3094 1.277273 CAGTGCAGTGGAAGGATCAGA 59.723 52.381 14.08 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.