Multiple sequence alignment - TraesCS4D01G328600

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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 TraesCS4D01G328600 chr4D 100.000 5479 0 0 515 5993 487102864 487097386 0.000000e+00 10118.0
1 TraesCS4D01G328600 chr4D 100.000 237 0 0 1 237 487103378 487103142 7.130000e-119 438.0
2 TraesCS4D01G328600 chr4B 95.460 2643 83 20 2655 5281 622114876 622112255 0.000000e+00 4181.0
3 TraesCS4D01G328600 chr4B 92.293 1609 85 17 874 2463 622116711 622115123 0.000000e+00 2248.0
4 TraesCS4D01G328600 chr4B 93.715 716 41 4 5280 5992 622112203 622111489 0.000000e+00 1070.0
5 TraesCS4D01G328600 chr4B 92.405 237 16 1 1 237 622117548 622117314 2.680000e-88 337.0
6 TraesCS4D01G328600 chr4B 94.355 124 7 0 2389 2512 622115164 622115041 2.200000e-44 191.0
7 TraesCS4D01G328600 chr4B 88.235 68 2 4 817 878 622116815 622116748 6.440000e-10 76.8
8 TraesCS4D01G328600 chr5A 89.691 1940 133 26 521 2430 668163415 668161513 0.000000e+00 2412.0
9 TraesCS4D01G328600 chr5A 93.893 1490 51 15 2422 3884 668161553 668160077 0.000000e+00 2211.0
10 TraesCS4D01G328600 chr5A 94.297 1245 40 8 3883 5105 668159953 668158718 0.000000e+00 1877.0
11 TraesCS4D01G328600 chr5A 88.549 751 43 21 5248 5991 668158718 668158004 0.000000e+00 870.0


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 TraesCS4D01G328600 chr4D 487097386 487103378 5992 True 5278.000000 10118 100.000000 1 5993 2 chr4D.!!$R1 5992
1 TraesCS4D01G328600 chr4B 622111489 622117548 6059 True 1350.633333 4181 92.743833 1 5992 6 chr4B.!!$R1 5991
2 TraesCS4D01G328600 chr5A 668158004 668163415 5411 True 1842.500000 2412 91.607500 521 5991 4 chr5A.!!$R1 5470

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
710 712 0.035881 CTGCTCAACCTGGCTTCTCA 59.964 55.000 0.00 0.00 0.00 3.27 F
759 761 0.107214 GAGCGATGGGGTGGAATGAA 60.107 55.000 0.00 0.00 0.00 2.57 F
827 829 1.136446 GGTTGTATGTCGACGTGTTGC 60.136 52.381 20.52 8.25 0.00 4.17 F
1096 1145 1.319799 CTCCCCTTCTCCTCCCCAT 59.680 63.158 0.00 0.00 0.00 4.00 F
1818 1891 1.519455 CGAGACGGAGGATGGCAAC 60.519 63.158 0.00 0.00 0.00 4.17 F
2066 2163 2.002586 CTGTCATTGAACAGTAGGCGG 58.997 52.381 7.62 0.00 41.43 6.13 F
2445 2576 2.099098 CCAAACGCTTCAAAGTTGGTCT 59.901 45.455 0.00 0.00 0.00 3.85 F
2582 2731 2.173519 CCATGGGATGTTTTGACTGCT 58.826 47.619 2.85 0.00 0.00 4.24 F
4462 4887 0.109342 GCCTCCGATTGGGTCATGAT 59.891 55.000 0.00 0.00 37.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2550 1.208259 CTTTGAAGCGTTTGGGCAAC 58.792 50.000 0.00 0.0 34.64 4.17 R
2561 2692 1.895131 GCAGTCAAAACATCCCATGGT 59.105 47.619 11.73 0.0 33.60 3.55 R
2563 2694 3.947910 AAGCAGTCAAAACATCCCATG 57.052 42.857 0.00 0.0 0.00 3.66 R
2565 2696 6.267471 AGAATTTAAGCAGTCAAAACATCCCA 59.733 34.615 0.00 0.0 0.00 4.37 R
3135 3415 6.861065 TGACTGTTCCTAAAACTGAATGAC 57.139 37.500 2.42 0.0 0.00 3.06 R
4024 4434 3.244215 ACGTCATCTGGGCGATTGATATT 60.244 43.478 0.00 0.0 0.00 1.28 R
4044 4454 9.469807 AGAGATAATTCTTGAGCTTAACATACG 57.530 33.333 0.00 0.0 30.30 3.06 R
4501 4926 5.613360 CGAGTTATGCTGCTTTGATATTCGG 60.613 44.000 0.00 0.0 0.00 4.30 R
5395 5881 0.813184 CTGCGCATGGAACCTGAATT 59.187 50.000 12.24 0.0 0.00 2.17 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
44 45 2.768698 TGCAAAAATGTTGAGGCATGG 58.231 42.857 0.00 0.00 0.00 3.66
45 46 2.078392 GCAAAAATGTTGAGGCATGGG 58.922 47.619 0.00 0.00 0.00 4.00
50 51 1.176527 ATGTTGAGGCATGGGAAACG 58.823 50.000 0.00 0.00 0.00 3.60
73 74 6.151985 ACGTAGATACAATTTTTCCATGGCAA 59.848 34.615 6.96 0.00 0.00 4.52
106 107 1.937191 TGGGAAAATTTGAGGGAGCC 58.063 50.000 0.00 0.00 0.00 4.70
118 119 0.906775 AGGGAGCCATGGCAATTTTG 59.093 50.000 37.18 0.00 44.88 2.44
145 146 4.101114 TCTACTGGAATGTAAGGGAGCAA 58.899 43.478 0.00 0.00 0.00 3.91
149 150 4.280929 ACTGGAATGTAAGGGAGCAAAAAC 59.719 41.667 0.00 0.00 0.00 2.43
195 196 1.079197 TGGTGTGCCTCTATGTGCG 60.079 57.895 0.00 0.00 35.27 5.34
196 197 1.079127 GGTGTGCCTCTATGTGCGT 60.079 57.895 0.00 0.00 0.00 5.24
197 198 1.361668 GGTGTGCCTCTATGTGCGTG 61.362 60.000 0.00 0.00 0.00 5.34
227 228 0.039346 CGCATGCATGTGGTGTGAAA 60.039 50.000 28.76 0.00 34.78 2.69
230 231 1.996898 CATGCATGTGGTGTGAAATGC 59.003 47.619 18.91 0.00 44.49 3.56
537 538 0.677288 CTTACGTGGACAGTGACCCA 59.323 55.000 9.22 7.01 0.00 4.51
538 539 0.677288 TTACGTGGACAGTGACCCAG 59.323 55.000 9.22 5.65 32.28 4.45
583 585 0.326264 GGTGGTGTCTGCTCCATCTT 59.674 55.000 0.00 0.00 39.99 2.40
584 586 1.446907 GTGGTGTCTGCTCCATCTTG 58.553 55.000 0.00 0.00 39.99 3.02
593 595 1.074405 TGCTCCATCTTGTCTTTGGCT 59.926 47.619 0.00 0.00 0.00 4.75
596 598 3.127721 GCTCCATCTTGTCTTTGGCTAAC 59.872 47.826 0.00 0.00 0.00 2.34
597 599 4.326826 CTCCATCTTGTCTTTGGCTAACA 58.673 43.478 0.00 0.00 0.00 2.41
625 627 1.291877 GAAGACAACGCCACTCGCAT 61.292 55.000 0.00 0.00 43.23 4.73
663 665 2.371259 GCACCTCCTCCCCCTTCTC 61.371 68.421 0.00 0.00 0.00 2.87
698 700 1.203237 ACCTCCTTCTCCTCTGCTCAA 60.203 52.381 0.00 0.00 0.00 3.02
702 704 1.066286 CCTTCTCCTCTGCTCAACCTG 60.066 57.143 0.00 0.00 0.00 4.00
710 712 0.035881 CTGCTCAACCTGGCTTCTCA 59.964 55.000 0.00 0.00 0.00 3.27
711 713 0.250467 TGCTCAACCTGGCTTCTCAC 60.250 55.000 0.00 0.00 0.00 3.51
716 718 1.345741 CAACCTGGCTTCTCACAGAGA 59.654 52.381 0.00 0.00 36.86 3.10
729 731 2.356695 TCACAGAGAAGAACAACGACGA 59.643 45.455 0.00 0.00 0.00 4.20
759 761 0.107214 GAGCGATGGGGTGGAATGAA 60.107 55.000 0.00 0.00 0.00 2.57
766 768 2.293246 TGGGGTGGAATGAAATAGGGT 58.707 47.619 0.00 0.00 0.00 4.34
769 771 3.565670 GGGGTGGAATGAAATAGGGTGTT 60.566 47.826 0.00 0.00 0.00 3.32
777 779 5.983333 ATGAAATAGGGTGTTCTGGAGAT 57.017 39.130 0.00 0.00 0.00 2.75
794 796 4.228010 GGAGATAGGGGATAAGGATAGGC 58.772 52.174 0.00 0.00 0.00 3.93
795 797 4.078278 GGAGATAGGGGATAAGGATAGGCT 60.078 50.000 0.00 0.00 0.00 4.58
796 798 4.889780 AGATAGGGGATAAGGATAGGCTG 58.110 47.826 0.00 0.00 0.00 4.85
798 800 1.203492 AGGGGATAAGGATAGGCTGGG 60.203 57.143 0.00 0.00 0.00 4.45
800 802 1.290134 GGATAAGGATAGGCTGGGGG 58.710 60.000 0.00 0.00 0.00 5.40
827 829 1.136446 GGTTGTATGTCGACGTGTTGC 60.136 52.381 20.52 8.25 0.00 4.17
887 936 4.137543 AGAGCCAACTACTTCCTTTGTTG 58.862 43.478 0.00 0.00 39.35 3.33
923 972 2.897207 CGGCCCTCACGTCCATAA 59.103 61.111 0.00 0.00 0.00 1.90
941 990 4.958581 CCATAAGAAATCTGGGCTCCTTTT 59.041 41.667 0.00 0.00 0.00 2.27
942 991 5.163478 CCATAAGAAATCTGGGCTCCTTTTG 60.163 44.000 0.00 0.00 0.00 2.44
963 1012 3.073798 TGAGCCCACCTAAATCACTTTCA 59.926 43.478 0.00 0.00 0.00 2.69
1096 1145 1.319799 CTCCCCTTCTCCTCCCCAT 59.680 63.158 0.00 0.00 0.00 4.00
1139 1197 4.292178 CTCCCGCCTCCGCAGATC 62.292 72.222 0.00 0.00 34.03 2.75
1143 1201 4.292178 CGCCTCCGCAGATCCCTC 62.292 72.222 0.00 0.00 34.03 4.30
1590 1663 3.677648 AAGTCCCGCGCGTACAGT 61.678 61.111 29.95 14.79 0.00 3.55
1818 1891 1.519455 CGAGACGGAGGATGGCAAC 60.519 63.158 0.00 0.00 0.00 4.17
1855 1928 4.947388 AGTTCCACAACTTCTGTTTTGCTA 59.053 37.500 0.00 0.00 40.16 3.49
1986 2066 3.788227 ATCAACCCTGTGCTAGAAACA 57.212 42.857 0.00 0.00 0.00 2.83
2045 2125 4.021719 AGGATGGTTTGCTGAAAATGTGAG 60.022 41.667 0.00 0.00 0.00 3.51
2048 2145 3.054878 GGTTTGCTGAAAATGTGAGCTG 58.945 45.455 0.00 0.00 33.66 4.24
2066 2163 2.002586 CTGTCATTGAACAGTAGGCGG 58.997 52.381 7.62 0.00 41.43 6.13
2191 2289 8.692110 TTGACTATTGCAAATTTATTCTGCTG 57.308 30.769 1.71 0.00 37.00 4.41
2369 2467 6.801539 AATGCTCAGAATAACACTTCGAAA 57.198 33.333 0.00 0.00 0.00 3.46
2413 2511 4.142816 CCCAAACGCTTCAAAGATAGTCAG 60.143 45.833 0.00 0.00 0.00 3.51
2419 2550 4.027295 CGCTTCAAAGATAGTCAGCTTACG 60.027 45.833 0.00 0.00 28.03 3.18
2445 2576 2.099098 CCAAACGCTTCAAAGTTGGTCT 59.901 45.455 0.00 0.00 0.00 3.85
2483 2614 7.917505 CCAAACTCATGATATAAAACCTTGAGC 59.082 37.037 0.00 0.00 36.28 4.26
2517 2648 7.781548 ATTGTTATTGGTAAGTATCCGTGAC 57.218 36.000 0.00 0.00 0.00 3.67
2564 2695 8.818622 TCTTAACTTCTAGTTAGCTGATACCA 57.181 34.615 0.00 0.00 41.23 3.25
2565 2696 9.422681 TCTTAACTTCTAGTTAGCTGATACCAT 57.577 33.333 0.00 0.00 41.23 3.55
2568 2717 5.305644 ACTTCTAGTTAGCTGATACCATGGG 59.694 44.000 18.09 0.00 0.00 4.00
2582 2731 2.173519 CCATGGGATGTTTTGACTGCT 58.826 47.619 2.85 0.00 0.00 4.24
2604 2753 8.093659 TGCTTAAATTCTTTGGCCAATAAAAC 57.906 30.769 21.26 9.05 0.00 2.43
2616 2765 8.918961 TTGGCCAATAAAACTACAATTAATCG 57.081 30.769 16.05 0.00 0.00 3.34
2659 2809 9.300681 AGTTATACAAATTGATACCATGGGATG 57.699 33.333 16.38 2.19 0.00 3.51
2773 3048 3.847037 GCACTGTGCATTTTGAAACAG 57.153 42.857 26.70 0.00 44.26 3.16
2774 3049 3.446799 GCACTGTGCATTTTGAAACAGA 58.553 40.909 26.70 0.00 44.26 3.41
2775 3050 3.488310 GCACTGTGCATTTTGAAACAGAG 59.512 43.478 26.70 2.13 44.26 3.35
2776 3051 4.675510 CACTGTGCATTTTGAAACAGAGT 58.324 39.130 8.54 0.00 42.09 3.24
2777 3052 5.733091 GCACTGTGCATTTTGAAACAGAGTA 60.733 40.000 26.70 0.00 44.26 2.59
2778 3053 6.264832 CACTGTGCATTTTGAAACAGAGTAA 58.735 36.000 8.54 0.00 42.09 2.24
2819 3094 7.175104 ACAATTTTAGAGGCTATTCCAACTCA 58.825 34.615 0.00 0.00 37.29 3.41
2826 3101 5.190528 AGAGGCTATTCCAACTCATTTGAGA 59.809 40.000 14.29 0.00 40.01 3.27
2862 3140 8.883731 CACTTCCAGTGTGGTATATTAGAAAAG 58.116 37.037 0.00 0.00 41.19 2.27
2921 3201 4.080919 TCTGGCACAACTTCTATATGCTGT 60.081 41.667 0.00 0.00 38.70 4.40
3135 3415 4.651994 CTGCTGTTAAGTCATTTTAGCCG 58.348 43.478 0.00 0.00 0.00 5.52
3199 3479 4.122776 AGCCTTGCTAACATATTGTCTCG 58.877 43.478 0.00 0.00 36.99 4.04
3206 3486 7.694388 TGCTAACATATTGTCTCGTAACATC 57.306 36.000 0.00 0.00 0.00 3.06
3429 3712 7.336931 TGCACTTGATAAGGTAATTTCTTCTCC 59.663 37.037 0.00 0.00 0.00 3.71
3752 4035 4.933505 TGTTGTTTGCTTTCATGATGGA 57.066 36.364 0.00 0.00 0.00 3.41
3797 4080 9.444534 GTTTGATGTTGTTTGTTTTCAGTTTTT 57.555 25.926 0.00 0.00 0.00 1.94
4008 4418 7.642978 GCATGCAATCAGACTATAAAAACTCTG 59.357 37.037 14.21 0.00 32.86 3.35
4024 4434 7.801716 AAAACTCTGTTGCTCTACAATGTTA 57.198 32.000 0.00 0.00 41.27 2.41
4044 4454 5.700832 TGTTAATATCAATCGCCCAGATGAC 59.299 40.000 0.00 0.00 40.02 3.06
4462 4887 0.109342 GCCTCCGATTGGGTCATGAT 59.891 55.000 0.00 0.00 37.00 2.45
4648 5073 3.455910 TGCTTCCAGTTGCAGATAGGTAT 59.544 43.478 0.00 0.00 34.84 2.73
4649 5074 3.812053 GCTTCCAGTTGCAGATAGGTATG 59.188 47.826 0.00 0.00 0.00 2.39
4652 5077 5.474578 TCCAGTTGCAGATAGGTATGATC 57.525 43.478 0.00 0.00 0.00 2.92
4653 5078 4.901250 TCCAGTTGCAGATAGGTATGATCA 59.099 41.667 0.00 0.00 0.00 2.92
4655 5080 6.043590 TCCAGTTGCAGATAGGTATGATCAAT 59.956 38.462 0.00 0.00 0.00 2.57
4656 5081 6.370994 CCAGTTGCAGATAGGTATGATCAATC 59.629 42.308 0.00 0.00 0.00 2.67
4657 5082 6.932960 CAGTTGCAGATAGGTATGATCAATCA 59.067 38.462 0.00 0.00 41.70 2.57
4658 5083 6.933521 AGTTGCAGATAGGTATGATCAATCAC 59.066 38.462 0.00 0.00 40.03 3.06
4659 5084 6.423776 TGCAGATAGGTATGATCAATCACA 57.576 37.500 0.00 0.00 40.03 3.58
4821 5251 7.114754 AGGTTGATGATGCAGAAAGATTAGAA 58.885 34.615 0.00 0.00 0.00 2.10
4833 5263 5.721960 AGAAAGATTAGAAGTAGCCACTGGA 59.278 40.000 0.00 0.00 34.36 3.86
4991 5423 8.652810 ACCAATATTCATAAAAATCTTGCTGC 57.347 30.769 0.00 0.00 0.00 5.25
5133 5565 4.961099 TGATGGTGATCTGAGACATCTTCT 59.039 41.667 10.77 0.00 38.88 2.85
5153 5585 6.500751 TCTTCTACCCTAGGAACAATTCAAGT 59.499 38.462 11.48 0.00 0.00 3.16
5156 5588 8.388656 TCTACCCTAGGAACAATTCAAGTTAT 57.611 34.615 11.48 0.00 0.00 1.89
5178 5610 3.508744 ATTAATTCAGTTTGCCTGCCG 57.491 42.857 0.00 0.00 41.25 5.69
5229 5661 1.002069 ATCAACAGGGAGCCCATCAA 58.998 50.000 8.53 0.00 38.92 2.57
5304 5790 9.784531 ATAAGATATAACAGTAAAGCAGCACAT 57.215 29.630 0.00 0.00 0.00 3.21
5337 5823 6.563422 TCTGAAAAGTTTGGTGAACAGATTG 58.437 36.000 0.00 0.00 40.84 2.67
5372 5858 2.042464 ACTCTCAGACAGTTTCAGGCA 58.958 47.619 0.00 0.00 0.00 4.75
5387 5873 2.745492 GCAGCTCCAGCACAGGTC 60.745 66.667 0.48 0.00 45.16 3.85
5395 5881 0.320683 CCAGCACAGGTCGTTGATCA 60.321 55.000 0.00 0.00 0.00 2.92
5465 5953 4.159099 AGCAAGGCTCCAGGATGA 57.841 55.556 0.00 0.00 31.86 2.92
5473 5961 3.000819 TCCAGGATGAACGCCGGT 61.001 61.111 1.90 0.00 39.69 5.28
5505 5993 3.834489 GGAAGATCTCCATGAGCTGAA 57.166 47.619 0.00 0.00 41.05 3.02
5514 6002 1.648504 CATGAGCTGAACATGCGAGA 58.351 50.000 0.00 0.00 38.58 4.04
5534 6022 3.691342 TTAGCAGGCCACTCGCGT 61.691 61.111 5.01 0.00 38.94 6.01
5545 6033 0.778815 CACTCGCGTTCTTCAGTGAC 59.221 55.000 15.93 0.00 38.90 3.67
5550 6038 1.401670 CGCGTTCTTCAGTGACTAGCT 60.402 52.381 0.00 0.00 0.00 3.32
5614 6102 2.224475 GGCCAGCATCATCATGTAGACT 60.224 50.000 0.00 0.00 31.86 3.24
5724 6213 4.082190 GGCTTTTCCAATTCCTGGTAGTTC 60.082 45.833 0.00 0.00 46.51 3.01
5741 6230 4.213564 AGTTCTCAGAATTAGCCACCAG 57.786 45.455 0.00 0.00 0.00 4.00
5766 6255 2.010497 GCTTAAGGTCAAGCCAGCTAC 58.990 52.381 4.29 0.00 44.22 3.58
5795 6284 6.835488 TGTTATACCGTTCCTATACTTCCAGT 59.165 38.462 0.00 0.00 0.00 4.00
5837 6330 6.200665 CAGTAATAGAGTTCAGAAGAGCATGC 59.799 42.308 10.51 10.51 0.00 4.06
5852 6346 2.369532 AGCATGCCTTTTGTTGTCCAAT 59.630 40.909 15.66 0.00 31.81 3.16
5900 6394 4.576463 GTGCTCCCAATATGTCTACCAAAG 59.424 45.833 0.00 0.00 0.00 2.77
5987 6481 8.908786 TTCTAGTTCAGAACAGAAATCACAAT 57.091 30.769 15.85 0.00 38.39 2.71
5988 6482 8.539770 TCTAGTTCAGAACAGAAATCACAATC 57.460 34.615 15.85 0.00 0.00 2.67
5990 6484 7.814264 AGTTCAGAACAGAAATCACAATCTT 57.186 32.000 15.85 0.00 0.00 2.40
5991 6485 7.869800 AGTTCAGAACAGAAATCACAATCTTC 58.130 34.615 15.85 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.700656 CCATGGAAAAATTGTATCTACGTTTCC 59.299 37.037 5.56 5.51 0.00 3.13
45 46 7.220108 GCCATGGAAAAATTGTATCTACGTTTC 59.780 37.037 18.40 0.00 0.00 2.78
50 51 8.770438 TTTTGCCATGGAAAAATTGTATCTAC 57.230 30.769 24.51 0.00 28.44 2.59
73 74 6.405278 AATTTTCCCATGTCTCGAGTTTTT 57.595 33.333 13.13 0.00 0.00 1.94
80 81 3.129287 CCCTCAAATTTTCCCATGTCTCG 59.871 47.826 0.00 0.00 0.00 4.04
90 91 2.419159 GCCATGGCTCCCTCAAATTTTC 60.419 50.000 29.98 0.00 38.26 2.29
95 96 0.041535 ATTGCCATGGCTCCCTCAAA 59.958 50.000 35.53 20.70 42.51 2.69
118 119 4.137543 CCCTTACATTCCAGTAGATTGGC 58.862 47.826 0.00 0.00 38.16 4.52
124 125 4.487714 TTGCTCCCTTACATTCCAGTAG 57.512 45.455 0.00 0.00 0.00 2.57
145 146 2.224185 GCAAAATTGGACCTCCGGTTTT 60.224 45.455 0.00 0.00 35.25 2.43
149 150 0.897863 TGGCAAAATTGGACCTCCGG 60.898 55.000 0.00 0.00 39.43 5.14
181 182 0.670546 ACACACGCACATAGAGGCAC 60.671 55.000 0.00 0.00 0.00 5.01
514 515 0.032952 TCACTGTCCACGTAAGCCAC 59.967 55.000 0.00 0.00 45.62 5.01
515 516 0.032952 GTCACTGTCCACGTAAGCCA 59.967 55.000 0.00 0.00 45.62 4.75
516 517 0.669625 GGTCACTGTCCACGTAAGCC 60.670 60.000 0.00 0.00 45.62 4.35
517 518 0.669625 GGGTCACTGTCCACGTAAGC 60.670 60.000 0.00 0.00 45.62 3.09
519 520 0.677288 CTGGGTCACTGTCCACGTAA 59.323 55.000 0.00 0.00 0.00 3.18
560 562 2.348998 GAGCAGACACCACCCTGG 59.651 66.667 0.00 0.00 45.02 4.45
565 567 1.271054 ACAAGATGGAGCAGACACCAC 60.271 52.381 0.00 0.00 39.53 4.16
583 585 1.139256 TGTCCGTGTTAGCCAAAGACA 59.861 47.619 0.00 0.00 35.88 3.41
584 586 1.873698 TGTCCGTGTTAGCCAAAGAC 58.126 50.000 0.00 0.00 0.00 3.01
593 595 3.491639 CGTTGTCTTCAATGTCCGTGTTA 59.508 43.478 0.00 0.00 36.25 2.41
596 598 1.398451 GCGTTGTCTTCAATGTCCGTG 60.398 52.381 0.00 0.00 41.20 4.94
597 599 0.865769 GCGTTGTCTTCAATGTCCGT 59.134 50.000 0.00 0.00 41.20 4.69
640 642 4.106925 GGGGAGGAGGTGCAGCAG 62.107 72.222 19.63 0.00 0.00 4.24
647 649 1.869452 AGGAGAAGGGGGAGGAGGT 60.869 63.158 0.00 0.00 0.00 3.85
663 665 4.785453 GGTTGCCGGAGCCAGAGG 62.785 72.222 5.05 0.00 38.69 3.69
698 700 1.722034 TTCTCTGTGAGAAGCCAGGT 58.278 50.000 5.97 0.00 42.78 4.00
710 712 2.543238 GGTCGTCGTTGTTCTTCTCTGT 60.543 50.000 0.00 0.00 0.00 3.41
711 713 2.052157 GGTCGTCGTTGTTCTTCTCTG 58.948 52.381 0.00 0.00 0.00 3.35
716 718 1.952635 GCCGGTCGTCGTTGTTCTT 60.953 57.895 1.90 0.00 37.11 2.52
722 724 4.974989 GGGTTGCCGGTCGTCGTT 62.975 66.667 1.90 0.00 37.11 3.85
746 748 2.024464 CACCCTATTTCATTCCACCCCA 60.024 50.000 0.00 0.00 0.00 4.96
748 750 3.382083 ACACCCTATTTCATTCCACCC 57.618 47.619 0.00 0.00 0.00 4.61
754 756 5.779241 TCTCCAGAACACCCTATTTCATT 57.221 39.130 0.00 0.00 0.00 2.57
759 761 4.235372 CCCTATCTCCAGAACACCCTATT 58.765 47.826 0.00 0.00 0.00 1.73
766 768 4.172041 TCCTTATCCCCTATCTCCAGAACA 59.828 45.833 0.00 0.00 0.00 3.18
769 771 5.196779 CCTATCCTTATCCCCTATCTCCAGA 59.803 48.000 0.00 0.00 0.00 3.86
777 779 2.045885 CCCAGCCTATCCTTATCCCCTA 59.954 54.545 0.00 0.00 0.00 3.53
804 806 0.738412 CACGTCGACATACAACCCCC 60.738 60.000 17.16 0.00 0.00 5.40
805 807 0.037975 ACACGTCGACATACAACCCC 60.038 55.000 17.16 0.00 0.00 4.95
806 808 1.458064 CAACACGTCGACATACAACCC 59.542 52.381 17.16 0.00 0.00 4.11
807 809 1.136446 GCAACACGTCGACATACAACC 60.136 52.381 17.16 0.00 0.00 3.77
808 810 1.136446 GGCAACACGTCGACATACAAC 60.136 52.381 17.16 0.07 0.00 3.32
809 811 1.141645 GGCAACACGTCGACATACAA 58.858 50.000 17.16 0.00 0.00 2.41
810 812 0.032267 TGGCAACACGTCGACATACA 59.968 50.000 17.16 1.35 46.17 2.29
811 813 2.817035 TGGCAACACGTCGACATAC 58.183 52.632 17.16 0.00 46.17 2.39
827 829 2.609737 GGTACTTCTTGACACCGAGTGG 60.610 54.545 8.57 0.00 37.94 4.00
868 873 4.607955 GAACAACAAAGGAAGTAGTTGGC 58.392 43.478 8.72 0.00 44.10 4.52
869 874 4.261031 CCGAACAACAAAGGAAGTAGTTGG 60.261 45.833 8.72 0.00 44.10 3.77
870 875 4.261031 CCCGAACAACAAAGGAAGTAGTTG 60.261 45.833 0.00 0.00 45.02 3.16
872 877 3.473625 CCCGAACAACAAAGGAAGTAGT 58.526 45.455 0.00 0.00 0.00 2.73
923 972 3.694926 CTCAAAAGGAGCCCAGATTTCT 58.305 45.455 0.00 0.00 36.69 2.52
941 990 3.073798 TGAAAGTGATTTAGGTGGGCTCA 59.926 43.478 0.00 0.00 0.00 4.26
942 991 3.686016 TGAAAGTGATTTAGGTGGGCTC 58.314 45.455 0.00 0.00 0.00 4.70
963 1012 1.492599 GGGCTCTTATCTTCTGGGCTT 59.507 52.381 0.00 0.00 0.00 4.35
1096 1145 2.454941 GGGGAGAGGGTGGAGGAA 59.545 66.667 0.00 0.00 0.00 3.36
1138 1196 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1139 1197 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
1140 1198 1.541672 GGAGAGGGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
1141 1199 1.541672 GGGAGAGGGAGAGGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
1142 1200 2.015726 GGGGAGAGGGAGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1143 1201 2.612251 GGGGAGAGGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1224 1282 1.585668 ACATCGTCGTCGTAGTCGTAG 59.414 52.381 1.33 0.00 40.43 3.51
1590 1663 2.574018 CGTGTCCAGCCTCACCTCA 61.574 63.158 0.00 0.00 0.00 3.86
1750 1823 1.519455 CCGCGATGTCCTCAAGACC 60.519 63.158 8.23 0.00 45.68 3.85
1779 1852 2.039418 CCTGGCACATACTGGCTACTA 58.961 52.381 0.00 0.00 45.96 1.82
1818 1891 1.347817 GGAACTCACTTCTCGCGCTG 61.348 60.000 5.56 0.00 0.00 5.18
1868 1941 6.748132 TCAACAATGGAAAGGATTCTGAAAC 58.252 36.000 0.00 0.00 35.79 2.78
1962 2042 5.472137 TGTTTCTAGCACAGGGTTGATTTAC 59.528 40.000 0.00 0.00 0.00 2.01
1986 2066 8.958119 TCAGTATATTTACTTCATTCGGCTTT 57.042 30.769 0.00 0.00 36.50 3.51
2048 2145 1.338769 ACCCGCCTACTGTTCAATGAC 60.339 52.381 0.00 0.00 0.00 3.06
2066 2163 5.390461 GGAAAATTCCGCTTGCAAAATAACC 60.390 40.000 0.00 0.00 37.65 2.85
2143 2241 6.902224 AACAACATGCTTGTTTTTACTTCC 57.098 33.333 14.80 0.00 43.57 3.46
2191 2289 1.376037 GTACTGTGCCCTCTGGTGC 60.376 63.158 0.00 0.00 0.00 5.01
2224 2322 6.322201 GGGATAAGAGATTGCAAATTTCTCCA 59.678 38.462 20.01 11.84 33.48 3.86
2233 2331 4.018506 TCAACCAGGGATAAGAGATTGCAA 60.019 41.667 0.00 0.00 0.00 4.08
2419 2550 1.208259 CTTTGAAGCGTTTGGGCAAC 58.792 50.000 0.00 0.00 34.64 4.17
2445 2576 5.565509 TCATGAGTTTGGGCAATGTAAGTA 58.434 37.500 0.00 0.00 0.00 2.24
2541 2672 8.421784 CCATGGTATCAGCTAACTAGAAGTTAA 58.578 37.037 2.57 0.00 39.89 2.01
2542 2673 7.015292 CCCATGGTATCAGCTAACTAGAAGTTA 59.985 40.741 11.73 0.03 39.51 2.24
2546 2677 5.464069 TCCCATGGTATCAGCTAACTAGAA 58.536 41.667 11.73 0.00 0.00 2.10
2556 2687 5.066893 CAGTCAAAACATCCCATGGTATCAG 59.933 44.000 11.73 0.00 33.60 2.90
2561 2692 1.895131 GCAGTCAAAACATCCCATGGT 59.105 47.619 11.73 0.00 33.60 3.55
2563 2694 3.947910 AAGCAGTCAAAACATCCCATG 57.052 42.857 0.00 0.00 0.00 3.66
2564 2695 6.610075 ATTTAAGCAGTCAAAACATCCCAT 57.390 33.333 0.00 0.00 0.00 4.00
2565 2696 6.267471 AGAATTTAAGCAGTCAAAACATCCCA 59.733 34.615 0.00 0.00 0.00 4.37
2568 2717 8.490355 CCAAAGAATTTAAGCAGTCAAAACATC 58.510 33.333 0.00 0.00 35.03 3.06
2695 2970 6.926280 TTGCGCTAGTGATTACAAAATTTG 57.074 33.333 9.73 3.89 0.00 2.32
2707 2982 7.307160 GCACTTGTTATAATATTGCGCTAGTGA 60.307 37.037 9.73 0.00 32.82 3.41
2710 2985 6.887368 TGCACTTGTTATAATATTGCGCTAG 58.113 36.000 9.73 0.00 0.00 3.42
2730 3005 8.003784 GTGCATTTTGATAGTTAAAGTTTGCAC 58.996 33.333 0.00 0.00 39.72 4.57
2771 3046 8.719560 TGTAGTACTATCAGTCTGTTACTCTG 57.280 38.462 5.75 0.00 35.76 3.35
2772 3047 9.908747 ATTGTAGTACTATCAGTCTGTTACTCT 57.091 33.333 5.75 0.00 35.76 3.24
2811 3086 8.102676 TGACATAGATTTCTCAAATGAGTTGGA 58.897 33.333 10.06 0.00 42.60 3.53
2819 3094 8.503458 CTGGAAGTGACATAGATTTCTCAAAT 57.497 34.615 0.00 0.00 0.00 2.32
2862 3140 7.156876 TGATCCCAAATACATCACACTTTTC 57.843 36.000 0.00 0.00 0.00 2.29
3135 3415 6.861065 TGACTGTTCCTAAAACTGAATGAC 57.139 37.500 2.42 0.00 0.00 3.06
3797 4080 9.995003 AAGAACCAATGCAAATATGTAAAGAAA 57.005 25.926 0.00 0.00 0.00 2.52
4008 4418 9.586150 CGATTGATATTAACATTGTAGAGCAAC 57.414 33.333 0.00 0.00 40.28 4.17
4024 4434 3.244215 ACGTCATCTGGGCGATTGATATT 60.244 43.478 0.00 0.00 0.00 1.28
4044 4454 9.469807 AGAGATAATTCTTGAGCTTAACATACG 57.530 33.333 0.00 0.00 30.30 3.06
4462 4887 6.484364 TTGATAAGCTCATATGTCCTCACA 57.516 37.500 1.90 0.53 33.02 3.58
4501 4926 5.613360 CGAGTTATGCTGCTTTGATATTCGG 60.613 44.000 0.00 0.00 0.00 4.30
4648 5073 8.499967 CAAAAATGCTTCAAATGTGATTGATCA 58.500 29.630 0.00 0.00 38.98 2.92
4649 5074 7.480542 GCAAAAATGCTTCAAATGTGATTGATC 59.519 33.333 0.00 0.00 38.98 2.92
4652 5077 6.664515 AGCAAAAATGCTTCAAATGTGATTG 58.335 32.000 0.00 0.00 43.52 2.67
4653 5078 6.870971 AGCAAAAATGCTTCAAATGTGATT 57.129 29.167 0.00 0.00 43.52 2.57
4655 5080 7.966246 AATAGCAAAAATGCTTCAAATGTGA 57.034 28.000 8.79 0.00 43.52 3.58
4656 5081 8.897809 CAAAATAGCAAAAATGCTTCAAATGTG 58.102 29.630 8.79 0.00 43.52 3.21
4657 5082 8.623030 ACAAAATAGCAAAAATGCTTCAAATGT 58.377 25.926 8.79 6.02 43.52 2.71
4658 5083 9.453325 AACAAAATAGCAAAAATGCTTCAAATG 57.547 25.926 8.79 5.47 43.52 2.32
4659 5084 9.453325 CAACAAAATAGCAAAAATGCTTCAAAT 57.547 25.926 8.79 0.00 43.52 2.32
4821 5251 1.228769 TGACGGTCCAGTGGCTACT 60.229 57.895 3.51 0.00 37.75 2.57
4833 5263 5.889853 TGGTCTATCTATAGTTTGTGACGGT 59.110 40.000 0.00 0.00 0.00 4.83
4991 5423 8.807118 TGACATAAAGGAGATAAGCCTGTATAG 58.193 37.037 0.00 0.00 34.40 1.31
5304 5790 2.872245 CAAACTTTTCAGAGGAGCGACA 59.128 45.455 0.00 0.00 0.00 4.35
5337 5823 4.400884 TCTGAGAGTTCTCTCCTGTATTGC 59.599 45.833 22.07 1.22 43.25 3.56
5372 5858 2.511452 AACGACCTGTGCTGGAGCT 61.511 57.895 0.00 0.00 42.66 4.09
5387 5873 4.665212 CATGGAACCTGAATTGATCAACG 58.335 43.478 11.07 0.00 37.67 4.10
5395 5881 0.813184 CTGCGCATGGAACCTGAATT 59.187 50.000 12.24 0.00 0.00 2.17
5505 5993 2.009042 GCCTGCTAACTTCTCGCATGT 61.009 52.381 0.00 0.00 32.62 3.21
5514 6002 1.376037 GCGAGTGGCCTGCTAACTT 60.376 57.895 3.32 0.00 34.80 2.66
5534 6022 4.100963 TCCAAACAGCTAGTCACTGAAGAA 59.899 41.667 3.21 0.00 38.55 2.52
5545 6033 3.772060 GGAAATGCTCCAAACAGCTAG 57.228 47.619 0.00 0.00 44.67 3.42
5614 6102 1.993653 CCCTCACAGCTGGAATGGA 59.006 57.895 19.93 6.41 0.00 3.41
5638 6126 2.112380 TCGCATCTTCCATTTGCTGA 57.888 45.000 0.00 0.00 34.23 4.26
5673 6162 1.414181 GGAGAGCATGATCCCTTCGAA 59.586 52.381 7.49 0.00 0.00 3.71
5724 6213 2.503356 AGGTCTGGTGGCTAATTCTGAG 59.497 50.000 0.00 0.00 0.00 3.35
5795 6284 2.309613 ACTGCTTGCATTCTTTGGTCA 58.690 42.857 0.00 0.00 0.00 4.02
5837 6330 7.542130 GCTACATTCTAATTGGACAACAAAAGG 59.458 37.037 0.00 0.00 43.46 3.11
5852 6346 9.851686 ACTTATGAATCCATTGCTACATTCTAA 57.148 29.630 0.00 0.00 34.31 2.10
5900 6394 5.412594 TGCATTTGGAACAGTCTCTGAATAC 59.587 40.000 3.70 0.00 42.39 1.89


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

AutoCloner maintained by Alex Coulton.