Multiple sequence alignment - TraesCS2B01G198700

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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 TraesCS2B01G198700 chr2B 100.000 4335 0 0 1 4335 176405772 176410106 0.000000e+00 8006
1 TraesCS2B01G198700 chr2D 93.057 4422 194 49 1 4335 123802801 123807196 0.000000e+00 6360
2 TraesCS2B01G198700 chr2A 92.967 3000 130 43 1 2944 129096894 129099868 0.000000e+00 4296
3 TraesCS2B01G198700 chr2A 90.041 1446 73 26 2945 4335 129099907 129101336 0.000000e+00 1807
4 TraesCS2B01G198700 chr3A 94.218 882 34 5 1492 2369 729020131 729020999 0.000000e+00 1330
5 TraesCS2B01G198700 chr7B 92.383 407 14 5 1973 2369 504225081 504225480 8.140000e-157 564
6 TraesCS2B01G198700 chr7B 91.136 361 14 8 1467 1825 504224737 504225081 1.410000e-129 473
7 TraesCS2B01G198700 chr1B 92.383 407 14 5 1973 2369 101250658 101250259 8.140000e-157 564
8 TraesCS2B01G198700 chr1B 91.690 361 12 8 1467 1825 101251002 101250658 6.520000e-133 484


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 TraesCS2B01G198700 chr2B 176405772 176410106 4334 False 8006.0 8006 100.0000 1 4335 1 chr2B.!!$F1 4334
1 TraesCS2B01G198700 chr2D 123802801 123807196 4395 False 6360.0 6360 93.0570 1 4335 1 chr2D.!!$F1 4334
2 TraesCS2B01G198700 chr2A 129096894 129101336 4442 False 3051.5 4296 91.5040 1 4335 2 chr2A.!!$F1 4334
3 TraesCS2B01G198700 chr3A 729020131 729020999 868 False 1330.0 1330 94.2180 1492 2369 1 chr3A.!!$F1 877
4 TraesCS2B01G198700 chr7B 504224737 504225480 743 False 518.5 564 91.7595 1467 2369 2 chr7B.!!$F1 902
5 TraesCS2B01G198700 chr1B 101250259 101251002 743 True 524.0 564 92.0365 1467 2369 2 chr1B.!!$R1 902

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
53 54 0.865111 TTCTGTGCGAATTGTGACGG 59.135 50.000 0.0 0.00 0.00 4.79 F
611 616 1.426251 TTCCTGCTTGCTCCCTTGGA 61.426 55.000 0.0 0.00 0.00 3.53 F
766 774 1.933021 TATCTGTTCGTCTGGTGGGT 58.067 50.000 0.0 0.00 0.00 4.51 F
2357 2390 1.000607 CCTGCCAATGCACATGATAGC 60.001 52.381 0.0 0.68 44.23 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1199 2.027377 CAGACTTGGCTGATGAGGAGTT 60.027 50.000 0.00 0.00 38.14 3.01 R
1621 1639 2.837031 AATGGGGCTTCGGCGATGTT 62.837 55.000 21.59 7.12 42.91 2.71 R
2436 2470 3.825014 ACACGTTGATACAGACCACTAGT 59.175 43.478 0.00 0.00 0.00 2.57 R
3534 3647 0.469917 CTGGGATAATCAGGGTGCGT 59.530 55.000 0.00 0.00 0.00 5.24 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
41 42 3.119388 TGGCATGAAGCTAAATTCTGTGC 60.119 43.478 0.00 0.00 44.79 4.57
53 54 0.865111 TTCTGTGCGAATTGTGACGG 59.135 50.000 0.00 0.00 0.00 4.79
101 102 6.016777 GGAAAACAGATGCTAGTTCATATGGG 60.017 42.308 2.13 0.00 39.31 4.00
113 114 3.480505 TCATATGGGCAGTGTCTGATG 57.519 47.619 2.13 0.00 32.44 3.07
134 135 1.693606 AGGCCTTTGTTGGGTTTGATG 59.306 47.619 0.00 0.00 0.00 3.07
142 143 6.407525 CCTTTGTTGGGTTTGATGAGGTAAAA 60.408 38.462 0.00 0.00 0.00 1.52
167 168 9.598517 AATTCAAGAAAAATGCAGACACTTAAA 57.401 25.926 0.00 0.00 0.00 1.52
298 300 4.563786 GCTAGTGCTAGGGAAGAAAACTGT 60.564 45.833 8.16 0.00 36.03 3.55
373 375 2.450609 TAACACGCCTTCCTTGACTC 57.549 50.000 0.00 0.00 0.00 3.36
412 415 4.717877 TGTAGTATAAGCTAGGTACGCCA 58.282 43.478 0.00 0.00 37.19 5.69
506 509 6.946340 ACCTAAATTTGGAAATAAAGGGCAG 58.054 36.000 2.65 0.00 35.94 4.85
532 537 7.378461 GTGTGGTGTGTTGTGTATCTTTTTATG 59.622 37.037 0.00 0.00 0.00 1.90
565 570 6.647229 TGGATGATGCTAATTAGGCTAGATG 58.353 40.000 14.28 0.00 0.00 2.90
584 589 8.972127 GCTAGATGTGTCCCATTTCTAGATATA 58.028 37.037 8.95 0.00 33.10 0.86
611 616 1.426251 TTCCTGCTTGCTCCCTTGGA 61.426 55.000 0.00 0.00 0.00 3.53
652 657 6.883744 TGTATGCATGAATACTTGTGGTAGA 58.116 36.000 22.00 0.00 34.66 2.59
689 694 7.123355 TGTTGGAATGTTTCTTTTTCTGGAT 57.877 32.000 0.00 0.00 0.00 3.41
720 728 3.243839 ACATTTGTGACTCCATTGGCAAC 60.244 43.478 0.00 0.00 0.00 4.17
730 738 7.715249 GTGACTCCATTGGCAACTATCTATTTA 59.285 37.037 0.00 0.00 37.61 1.40
731 739 8.271458 TGACTCCATTGGCAACTATCTATTTAA 58.729 33.333 0.00 0.00 37.61 1.52
764 772 5.201713 ACATATATCTGTTCGTCTGGTGG 57.798 43.478 0.00 0.00 0.00 4.61
766 774 1.933021 TATCTGTTCGTCTGGTGGGT 58.067 50.000 0.00 0.00 0.00 4.51
921 929 6.952773 ATATAAGGCGCCATTTCAACTAAA 57.047 33.333 31.54 0.00 0.00 1.85
929 937 5.004726 GCGCCATTTCAACTAAAGCTAATTG 59.995 40.000 0.00 0.00 0.00 2.32
944 952 3.317430 GCTAATTGGAAATCCCTGCAGAG 59.683 47.826 17.39 0.39 35.38 3.35
1038 1047 4.520492 GGCCATCCTATTTCCAACTATGTG 59.480 45.833 0.00 0.00 0.00 3.21
1238 1249 2.689471 ACAACAAGAAGCATCTGCAACA 59.311 40.909 4.79 0.00 45.16 3.33
1245 1256 2.267174 AGCATCTGCAACAAGTGACT 57.733 45.000 4.79 0.00 45.16 3.41
1479 1496 5.009210 GCCTGTATTTTAATTATCGGCCACA 59.991 40.000 2.24 0.00 0.00 4.17
1517 1535 4.662278 TGCTCTTACCAATGCCTAAACTT 58.338 39.130 0.00 0.00 0.00 2.66
1621 1639 4.958581 TGGCTCTTCTCTCTGATGATGTTA 59.041 41.667 0.00 0.00 0.00 2.41
2093 2115 6.469595 CGTTTACGATTTGTTGAGTTTTGGAA 59.530 34.615 0.00 0.00 43.02 3.53
2313 2346 7.896383 TGGAAACAAATGGATAGGAAATAGG 57.104 36.000 0.00 0.00 37.44 2.57
2314 2347 7.647827 TGGAAACAAATGGATAGGAAATAGGA 58.352 34.615 0.00 0.00 37.44 2.94
2357 2390 1.000607 CCTGCCAATGCACATGATAGC 60.001 52.381 0.00 0.68 44.23 2.97
2429 2463 8.305046 CCCCCTTCTTGTCATATTTATCAAAA 57.695 34.615 0.00 0.00 0.00 2.44
2662 2700 9.931210 GAAGGTAATACAATACGGAAGAATTTG 57.069 33.333 0.00 0.00 0.00 2.32
2663 2701 9.457436 AAGGTAATACAATACGGAAGAATTTGT 57.543 29.630 0.00 0.00 35.99 2.83
2670 2708 8.980143 ACAATACGGAAGAATTTGTTATTTGG 57.020 30.769 0.00 0.00 31.02 3.28
2725 2763 4.713553 TGTGTTCTCTGGTATTTGCTGAA 58.286 39.130 0.00 0.00 0.00 3.02
2784 2822 2.851195 AGGCTGCCTTGGTAATATTCG 58.149 47.619 17.22 0.00 0.00 3.34
2818 2862 4.200874 TGACCCGTGAGTACATTTTTGTT 58.799 39.130 0.00 0.00 0.00 2.83
2891 2955 5.617609 CAGCATTCATTTGTTCAGCATTTG 58.382 37.500 0.00 0.00 0.00 2.32
2907 2971 3.366781 GCATTTGAGTTCCTGAAGGCTTC 60.367 47.826 20.27 20.27 34.44 3.86
2919 2983 2.693591 TGAAGGCTTCTACCCATCTACG 59.306 50.000 26.26 0.00 0.00 3.51
2922 2986 3.220940 AGGCTTCTACCCATCTACGTAC 58.779 50.000 0.00 0.00 0.00 3.67
2971 3072 2.304761 TGTTTCTAACATCGCCCCTTCT 59.695 45.455 0.00 0.00 36.25 2.85
3137 3238 3.582647 TGGCAAGAATACACTCCTTCAGA 59.417 43.478 0.00 0.00 0.00 3.27
3175 3276 1.684386 CTTCGGCATCAGCTCCCTCT 61.684 60.000 0.00 0.00 41.70 3.69
3206 3307 1.537990 GCTTTTCAACAACCGGCATGT 60.538 47.619 0.00 4.07 0.00 3.21
3257 3358 3.552384 TTGGCTTCCGTCCCACGT 61.552 61.111 0.00 0.00 40.58 4.49
3344 3445 4.418392 CATGATGAGGTAAAGCAAAGCAC 58.582 43.478 0.00 0.00 0.00 4.40
3418 3519 4.114794 GGAAATGTGGTTGCAATATCAGC 58.885 43.478 0.59 0.00 0.00 4.26
3432 3533 2.414994 ATCAGCTGGACCAAGACATG 57.585 50.000 15.13 0.00 0.00 3.21
3539 3652 7.686938 GTGTGTACTTATTCAAATAAGACGCAC 59.313 37.037 27.86 27.86 46.87 5.34
3545 3658 3.627395 TCAAATAAGACGCACCCTGAT 57.373 42.857 0.00 0.00 0.00 2.90
3570 3683 0.467384 CAGAGATCGGAGTTGGGCAT 59.533 55.000 0.00 0.00 0.00 4.40
3604 3717 2.119939 AGGCCTATCCTTCCTTACCC 57.880 55.000 1.29 0.00 44.75 3.69
3626 3739 4.566759 CCGTTGTGAATGTATCTGGTACTG 59.433 45.833 0.00 0.00 34.27 2.74
3627 3740 5.168569 CGTTGTGAATGTATCTGGTACTGT 58.831 41.667 0.00 0.00 34.27 3.55
3631 3744 7.476540 TGTGAATGTATCTGGTACTGTACTT 57.523 36.000 16.79 1.72 34.27 2.24
3632 3745 8.584063 TGTGAATGTATCTGGTACTGTACTTA 57.416 34.615 16.79 6.60 34.27 2.24
3665 3778 2.494870 AGCCTCAACCTTTGATGAATGC 59.505 45.455 0.00 0.00 39.30 3.56
3693 3806 4.685924 CAGTTCATCAACTTTGCAACCTT 58.314 39.130 0.00 0.00 41.24 3.50
3694 3807 4.505191 CAGTTCATCAACTTTGCAACCTTG 59.495 41.667 0.00 3.66 41.24 3.61
3713 3826 4.278170 CCTTGTTTGCCTGATTTCAGTACA 59.722 41.667 6.81 2.29 42.27 2.90
3741 3859 7.531534 GCAACTTTGTATCACATTTTGCATTTC 59.468 33.333 11.88 0.00 37.39 2.17
3755 3873 4.933505 TGCATTTCATTTGGTGACTTGA 57.066 36.364 0.00 0.00 36.32 3.02
3766 3884 2.746904 TGGTGACTTGACACAAACACAG 59.253 45.455 16.30 0.00 41.88 3.66
3815 3933 3.269538 TCCAAACGAACCTGAAAGTGA 57.730 42.857 0.00 0.00 0.00 3.41
3816 3934 3.815809 TCCAAACGAACCTGAAAGTGAT 58.184 40.909 0.00 0.00 0.00 3.06
3861 3981 8.946085 GTTTATGTTACATGAGTCAATGAGGAA 58.054 33.333 8.26 0.00 0.00 3.36
3866 3986 5.892160 ACATGAGTCAATGAGGAACAATG 57.108 39.130 0.00 0.00 0.00 2.82
3867 3987 4.157289 ACATGAGTCAATGAGGAACAATGC 59.843 41.667 0.00 0.00 30.26 3.56
3868 3988 4.025040 TGAGTCAATGAGGAACAATGCT 57.975 40.909 0.00 0.00 30.26 3.79
3869 3989 4.005650 TGAGTCAATGAGGAACAATGCTC 58.994 43.478 0.00 0.00 43.77 4.26
3870 3990 3.005554 AGTCAATGAGGAACAATGCTCG 58.994 45.455 0.00 0.00 46.23 5.03
3871 3991 2.744202 GTCAATGAGGAACAATGCTCGT 59.256 45.455 0.00 0.00 46.23 4.18
3872 3992 3.002791 TCAATGAGGAACAATGCTCGTC 58.997 45.455 0.00 0.00 46.23 4.20
3873 3993 3.005554 CAATGAGGAACAATGCTCGTCT 58.994 45.455 7.68 0.00 46.23 4.18
3874 3994 4.081697 TCAATGAGGAACAATGCTCGTCTA 60.082 41.667 7.68 0.00 46.23 2.59
3875 3995 3.510388 TGAGGAACAATGCTCGTCTAG 57.490 47.619 7.68 0.00 46.23 2.43
3975 4129 7.416213 GGTTGCATATTAGTTACTGGCAAATGA 60.416 37.037 0.00 0.00 40.87 2.57
3994 4148 7.927629 GCAAATGAAAATTCTGCCCTCAATATA 59.072 33.333 0.00 0.00 0.00 0.86
4002 4156 2.373169 CTGCCCTCAATATAGAAGGCCA 59.627 50.000 5.01 0.00 43.12 5.36
4005 4159 3.558109 GCCCTCAATATAGAAGGCCAGTC 60.558 52.174 5.01 0.93 38.85 3.51
4008 4162 4.590647 CCTCAATATAGAAGGCCAGTCAGA 59.409 45.833 5.01 0.00 0.00 3.27
4010 4164 6.408548 CCTCAATATAGAAGGCCAGTCAGAAA 60.409 42.308 5.01 0.00 0.00 2.52
4232 4391 2.186903 CGGCCTTGCGGTAGTCAT 59.813 61.111 0.00 0.00 0.00 3.06
4330 4489 5.584649 GGCTCTTACATTGTAGCAACATACA 59.415 40.000 11.16 0.00 36.68 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.531149 AGCAGAAACCGTCACAATTCG 59.469 47.619 0.00 0.00 0.00 3.34
101 102 0.035630 AAGGCCTCATCAGACACTGC 60.036 55.000 5.23 0.00 0.00 4.40
113 114 1.408969 TCAAACCCAACAAAGGCCTC 58.591 50.000 5.23 0.00 0.00 4.70
134 135 8.703336 GTCTGCATTTTTCTTGAATTTTACCTC 58.297 33.333 0.00 0.00 0.00 3.85
142 143 9.252962 CTTTAAGTGTCTGCATTTTTCTTGAAT 57.747 29.630 0.00 0.00 0.00 2.57
167 168 2.073776 AGTTCCAACCCCAGAATTCCT 58.926 47.619 0.65 0.00 0.00 3.36
298 300 8.146053 TGAATAGTCCTACCTTCAAGAAATGA 57.854 34.615 0.00 0.00 35.85 2.57
408 411 5.934043 TCATCCAACATTAGAATAGATGGCG 59.066 40.000 0.00 0.00 32.44 5.69
506 509 4.893424 AAAGATACACAACACACCACAC 57.107 40.909 0.00 0.00 0.00 3.82
532 537 5.841957 ATTAGCATCATCCAAGAACCAAC 57.158 39.130 0.00 0.00 0.00 3.77
584 589 0.403271 AGCAAGCAGGAATGTCCAGT 59.597 50.000 0.00 0.00 39.61 4.00
611 616 2.803030 ACAATCAAGAGCTGCCTGAT 57.197 45.000 0.00 0.00 0.00 2.90
652 657 3.951775 TTCCAACAAATAAGCGGCATT 57.048 38.095 1.45 0.00 0.00 3.56
703 708 3.264193 AGATAGTTGCCAATGGAGTCACA 59.736 43.478 2.05 0.00 0.00 3.58
731 739 9.764363 ACGAACAGATATATGTATGAACACATT 57.236 29.630 2.88 0.00 39.77 2.71
827 835 6.996282 ACCCCCTATCACTTTGTTTATAATCG 59.004 38.462 0.00 0.00 0.00 3.34
921 929 3.053395 TCTGCAGGGATTTCCAATTAGCT 60.053 43.478 15.13 0.00 38.24 3.32
929 937 3.359950 ACATTTCTCTGCAGGGATTTCC 58.640 45.455 19.11 0.00 0.00 3.13
944 952 4.216257 TCACTTAGCTCCAAGCAACATTTC 59.784 41.667 0.00 0.00 45.56 2.17
1188 1199 2.027377 CAGACTTGGCTGATGAGGAGTT 60.027 50.000 0.00 0.00 38.14 3.01
1245 1256 4.994852 GGTGTGTTGCTCATTTAGACTACA 59.005 41.667 0.00 0.00 0.00 2.74
1380 1393 4.476846 TCCCTCTGCCCAAAATATAAGACA 59.523 41.667 0.00 0.00 0.00 3.41
1479 1496 8.399529 TGGTAAGAGCATAGTAATAGGATAGGT 58.600 37.037 0.00 0.00 0.00 3.08
1621 1639 2.837031 AATGGGGCTTCGGCGATGTT 62.837 55.000 21.59 7.12 42.91 2.71
1887 1906 9.838339 GCAGTATAAGGAATATATGCCTGTAAT 57.162 33.333 13.49 9.77 34.00 1.89
1891 1910 7.559486 TCAGCAGTATAAGGAATATATGCCTG 58.441 38.462 13.49 1.65 34.72 4.85
2093 2115 7.039923 CCAAGCCATAGCAGAATGAATAAGATT 60.040 37.037 0.00 0.00 43.56 2.40
2357 2390 9.161629 TGAAACTATATGCCATAAATATGACCG 57.838 33.333 1.98 0.00 35.75 4.79
2435 2469 4.082895 ACACGTTGATACAGACCACTAGTC 60.083 45.833 0.00 0.00 46.71 2.59
2436 2470 3.825014 ACACGTTGATACAGACCACTAGT 59.175 43.478 0.00 0.00 0.00 2.57
2437 2471 4.436242 ACACGTTGATACAGACCACTAG 57.564 45.455 0.00 0.00 0.00 2.57
2438 2472 6.519679 AATACACGTTGATACAGACCACTA 57.480 37.500 0.00 0.00 0.00 2.74
2439 2473 5.401531 AATACACGTTGATACAGACCACT 57.598 39.130 0.00 0.00 0.00 4.00
2441 2475 9.304731 GTAAATAATACACGTTGATACAGACCA 57.695 33.333 0.00 0.00 0.00 4.02
2442 2476 8.758715 GGTAAATAATACACGTTGATACAGACC 58.241 37.037 0.00 0.00 0.00 3.85
2443 2477 8.758715 GGGTAAATAATACACGTTGATACAGAC 58.241 37.037 0.00 0.00 0.00 3.51
2444 2478 8.476447 TGGGTAAATAATACACGTTGATACAGA 58.524 33.333 0.00 0.00 0.00 3.41
2445 2479 8.651391 TGGGTAAATAATACACGTTGATACAG 57.349 34.615 0.00 0.00 0.00 2.74
2446 2480 7.711772 CCTGGGTAAATAATACACGTTGATACA 59.288 37.037 0.00 0.00 0.00 2.29
2447 2481 7.712205 ACCTGGGTAAATAATACACGTTGATAC 59.288 37.037 0.00 0.00 0.00 2.24
2448 2482 7.794041 ACCTGGGTAAATAATACACGTTGATA 58.206 34.615 0.00 0.00 0.00 2.15
2449 2483 6.655930 ACCTGGGTAAATAATACACGTTGAT 58.344 36.000 0.00 0.00 0.00 2.57
2450 2484 6.052405 ACCTGGGTAAATAATACACGTTGA 57.948 37.500 0.00 0.00 0.00 3.18
2451 2485 6.372103 TGAACCTGGGTAAATAATACACGTTG 59.628 38.462 0.00 0.00 0.00 4.10
2453 2487 6.052405 TGAACCTGGGTAAATAATACACGT 57.948 37.500 0.00 0.00 0.00 4.49
2454 2488 6.204108 GGATGAACCTGGGTAAATAATACACG 59.796 42.308 0.00 0.00 35.41 4.49
2652 2690 7.227049 TCAGGACCAAATAACAAATTCTTCC 57.773 36.000 0.00 0.00 0.00 3.46
2706 2744 4.666237 GCATTCAGCAAATACCAGAGAAC 58.334 43.478 0.00 0.00 44.79 3.01
2784 2822 1.409427 CACGGGTCAGATTAGTCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
2818 2862 5.046304 CCAGAGGTTCTCATCAAGGTTTAGA 60.046 44.000 0.00 0.00 32.06 2.10
2870 2934 5.407387 ACTCAAATGCTGAACAAATGAATGC 59.593 36.000 0.00 0.00 32.17 3.56
2891 2955 2.093394 GGGTAGAAGCCTTCAGGAACTC 60.093 54.545 7.29 0.00 37.39 3.01
2907 2971 8.388484 ACTTATAGTTGTACGTAGATGGGTAG 57.612 38.462 0.00 0.00 0.00 3.18
2971 3072 5.549228 AGATTCATGAAGGTATGGCTGGATA 59.451 40.000 14.54 0.00 0.00 2.59
3143 3244 4.735132 CGAAGGTGCGAAGGCGGA 62.735 66.667 0.00 0.00 44.10 5.54
3175 3276 6.039616 GGTTGTTGAAAAGCTTGACATGTTA 58.960 36.000 0.00 0.00 0.00 2.41
3206 3307 0.744414 GTGCGCTCCTGATTAGCCAA 60.744 55.000 9.73 0.00 36.60 4.52
3298 3399 4.041917 CGCTGGTGCATGCCGTTT 62.042 61.111 16.68 0.00 39.64 3.60
3432 3533 9.232473 AGATGAAACTCAAAAGGACTAATAACC 57.768 33.333 0.00 0.00 0.00 2.85
3438 3539 8.647796 TCAACTAGATGAAACTCAAAAGGACTA 58.352 33.333 0.00 0.00 0.00 2.59
3534 3647 0.469917 CTGGGATAATCAGGGTGCGT 59.530 55.000 0.00 0.00 0.00 5.24
3539 3652 2.499289 CCGATCTCTGGGATAATCAGGG 59.501 54.545 0.00 0.00 34.33 4.45
3545 3658 2.965831 CCAACTCCGATCTCTGGGATAA 59.034 50.000 0.00 0.00 34.33 1.75
3604 3717 5.168569 ACAGTACCAGATACATTCACAACG 58.831 41.667 0.00 0.00 36.09 4.10
3626 3739 5.105310 TGAGGCTCAACCATCTCTTAAGTAC 60.105 44.000 16.28 0.00 43.14 2.73
3627 3740 5.023452 TGAGGCTCAACCATCTCTTAAGTA 58.977 41.667 16.28 0.00 43.14 2.24
3652 3765 3.250744 CTGCAACAGCATTCATCAAAGG 58.749 45.455 0.00 0.00 37.69 3.11
3659 3772 2.885894 TGATGAACTGCAACAGCATTCA 59.114 40.909 13.48 13.48 38.67 2.57
3665 3778 3.488310 GCAAAGTTGATGAACTGCAACAG 59.512 43.478 0.00 0.00 45.08 3.16
3676 3789 5.146482 CAAACAAGGTTGCAAAGTTGATG 57.854 39.130 22.58 17.28 0.00 3.07
3713 3826 5.990386 TGCAAAATGTGATACAAAGTTGCAT 59.010 32.000 18.18 0.00 42.65 3.96
3741 3859 4.562394 GTGTTTGTGTCAAGTCACCAAATG 59.438 41.667 0.00 0.00 37.51 2.32
3755 3873 3.318839 CCCAATGTGATCTGTGTTTGTGT 59.681 43.478 0.00 0.00 0.00 3.72
3766 3884 3.507233 TGTTTCAGAAGCCCAATGTGATC 59.493 43.478 0.00 0.00 0.00 2.92
3861 3981 4.142816 GCATTGAAACTAGACGAGCATTGT 60.143 41.667 0.00 0.00 33.40 2.71
3866 3986 3.254060 TGAGCATTGAAACTAGACGAGC 58.746 45.455 0.00 0.00 0.00 5.03
3867 3987 5.105063 TGATGAGCATTGAAACTAGACGAG 58.895 41.667 0.00 0.00 0.00 4.18
3868 3988 5.072040 TGATGAGCATTGAAACTAGACGA 57.928 39.130 0.00 0.00 0.00 4.20
3869 3989 4.260132 GCTGATGAGCATTGAAACTAGACG 60.260 45.833 0.00 0.00 45.46 4.18
3870 3990 5.154215 GCTGATGAGCATTGAAACTAGAC 57.846 43.478 0.00 0.00 45.46 2.59
3936 4090 9.787435 ACTAATATGCAACCGATTTATTCCTAA 57.213 29.630 0.00 0.00 0.00 2.69
3948 4102 3.874543 TGCCAGTAACTAATATGCAACCG 59.125 43.478 0.00 0.00 0.00 4.44
3950 4104 7.479980 TCATTTGCCAGTAACTAATATGCAAC 58.520 34.615 0.00 0.00 37.01 4.17
3975 4129 7.830099 CCTTCTATATTGAGGGCAGAATTTT 57.170 36.000 2.53 0.00 0.00 1.82
4016 4170 4.141620 TGAGATATTTGAGGCCAGAACTCC 60.142 45.833 5.01 0.00 34.06 3.85
4075 4234 6.598525 TGTAAATTGATGTTGTGTCGCTAAG 58.401 36.000 0.00 0.00 0.00 2.18
4232 4391 2.104792 CTGTTGGAACCCTCACTGAGAA 59.895 50.000 7.69 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.