Multiple sequence alignment - TraesCS4B01G125400

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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 TraesCS4B01G125400 chr4B 100.000 5314 0 0 1 5314 155371794 155377107 0.000000e+00 9814.0
1 TraesCS4B01G125400 chr4D 96.628 2966 68 16 1678 4638 168220266 168217328 0.000000e+00 4894.0
2 TraesCS4B01G125400 chr4D 96.465 990 24 5 694 1682 168221471 168220492 0.000000e+00 1624.0
3 TraesCS4B01G125400 chr4D 90.365 685 45 11 4631 5312 168200502 168199836 0.000000e+00 880.0
4 TraesCS4B01G125400 chr4D 92.625 339 12 5 1 326 168221815 168221477 4.820000e-130 475.0
5 TraesCS4B01G125400 chr4D 88.679 159 16 2 2622 2778 74079504 74079346 5.430000e-45 193.0
6 TraesCS4B01G125400 chr4D 98.000 50 1 0 304 353 19916070 19916021 2.640000e-13 87.9
7 TraesCS4B01G125400 chr4A 93.130 2329 118 18 2214 4537 363745099 363742808 0.000000e+00 3376.0
8 TraesCS4B01G125400 chr4A 94.085 1065 58 5 285 1346 363747726 363746664 0.000000e+00 1613.0
9 TraesCS4B01G125400 chr4A 95.256 801 33 4 1289 2087 363746218 363745421 0.000000e+00 1264.0
10 TraesCS4B01G125400 chr4A 93.213 442 26 4 512 949 363746663 363746222 0.000000e+00 647.0
11 TraesCS4B01G125400 chr4A 84.959 492 72 2 4819 5309 363719634 363719144 1.030000e-136 497.0
12 TraesCS4B01G125400 chr4A 92.857 294 14 4 1 287 363748100 363747807 2.290000e-113 420.0
13 TraesCS4B01G125400 chr4A 86.066 244 21 5 4695 4938 363719865 363719635 3.180000e-62 250.0
14 TraesCS4B01G125400 chr4A 90.698 129 12 0 4570 4698 363723063 363722935 7.080000e-39 172.0
15 TraesCS4B01G125400 chr4A 95.385 65 1 2 2082 2145 363745160 363745097 9.420000e-18 102.0
16 TraesCS4B01G125400 chr4A 94.872 39 1 1 2550 2588 212853323 212853360 5.750000e-05 60.2
17 TraesCS4B01G125400 chr1D 91.083 157 11 2 2621 2774 108261541 108261697 5.390000e-50 209.0
18 TraesCS4B01G125400 chr1D 89.610 154 15 1 2621 2774 7349703 7349855 1.510000e-45 195.0
19 TraesCS4B01G125400 chr1D 88.608 158 17 1 2620 2776 156133337 156133494 1.950000e-44 191.0
20 TraesCS4B01G125400 chr1D 93.651 63 4 0 4678 4740 422285219 422285157 1.580000e-15 95.3
21 TraesCS4B01G125400 chr1D 98.000 50 1 0 304 353 19957606 19957557 2.640000e-13 87.9
22 TraesCS4B01G125400 chr1D 98.000 50 1 0 304 353 206072266 206072315 2.640000e-13 87.9
23 TraesCS4B01G125400 chr1D 98.000 50 1 0 304 353 254497570 254497521 2.640000e-13 87.9
24 TraesCS4B01G125400 chr2D 90.196 153 15 0 2622 2774 122864111 122864263 3.250000e-47 200.0
25 TraesCS4B01G125400 chr5A 88.750 160 16 1 2622 2779 86662171 86662012 1.510000e-45 195.0
26 TraesCS4B01G125400 chr2A 88.608 158 18 0 2618 2775 141506314 141506471 5.430000e-45 193.0
27 TraesCS4B01G125400 chr2A 79.096 177 24 7 4606 4779 602118913 602118747 5.630000e-20 110.0
28 TraesCS4B01G125400 chr7D 98.000 50 1 0 304 353 336507508 336507557 2.640000e-13 87.9
29 TraesCS4B01G125400 chr5D 98.000 50 1 0 304 353 240137279 240137230 2.640000e-13 87.9
30 TraesCS4B01G125400 chr3D 98.000 50 1 0 304 353 21904198 21904149 2.640000e-13 87.9
31 TraesCS4B01G125400 chr1A 98.000 50 1 0 304 353 112776460 112776509 2.640000e-13 87.9
32 TraesCS4B01G125400 chr7B 84.507 71 11 0 4690 4760 77820884 77820814 2.660000e-08 71.3
33 TraesCS4B01G125400 chr6B 97.500 40 1 0 4690 4729 476031640 476031601 9.550000e-08 69.4
34 TraesCS4B01G125400 chr7A 88.679 53 3 3 2546 2597 405455820 405455770 1.600000e-05 62.1
35 TraesCS4B01G125400 chr5B 100.000 28 0 0 421 448 292749748 292749775 1.000000e-02 52.8
36 TraesCS4B01G125400 chr3A 96.875 32 0 1 2546 2577 705584512 705584482 1.000000e-02 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 TraesCS4B01G125400 chr4B 155371794 155377107 5313 False 9814.000000 9814 100.000000 1 5314 1 chr4B.!!$F1 5313
1 TraesCS4B01G125400 chr4D 168217328 168221815 4487 True 2331.000000 4894 95.239333 1 4638 3 chr4D.!!$R4 4637
2 TraesCS4B01G125400 chr4D 168199836 168200502 666 True 880.000000 880 90.365000 4631 5312 1 chr4D.!!$R3 681
3 TraesCS4B01G125400 chr4A 363742808 363748100 5292 True 1237.000000 3376 93.987667 1 4537 6 chr4A.!!$R2 4536
4 TraesCS4B01G125400 chr4A 363719144 363723063 3919 True 306.333333 497 87.241000 4570 5309 3 chr4A.!!$R1 739

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
605 700 0.539986 GCCCCGATTACTTGGTCTGA 59.460 55.000 0.00 0.0 0.00 3.27 F
652 748 0.663153 ACTGCCTGAGTGAAAAACGC 59.337 50.000 0.00 0.0 31.75 4.84 F
1049 1147 0.698238 ATGGCTGGCAGGTCAAGTTA 59.302 50.000 17.64 0.0 0.00 2.24 F
1287 1385 1.338674 TGAACCTGGATGCACTTACCG 60.339 52.381 0.00 0.0 0.00 4.02 F
2495 3592 3.001838 GTGCAGTACGTGTTCACAATTCA 59.998 43.478 0.00 0.0 0.00 2.57 F
3864 4964 2.145397 TACTACACTCAGAGCCCAGG 57.855 55.000 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 3653 0.179132 CAACAGCAACAGCAACAGCA 60.179 50.000 0.00 0.0 0.00 4.41 R
2558 3655 0.179132 TGCAACAGCAACAGCAACAG 60.179 50.000 0.00 0.0 34.85 3.16 R
2559 3656 0.460722 ATGCAACAGCAACAGCAACA 59.539 45.000 0.00 0.0 42.37 3.33 R
2561 3658 1.034356 AGATGCAACAGCAACAGCAA 58.966 45.000 0.00 0.0 42.37 3.91 R
3936 5036 1.141657 GCTGCTCCCTATTGGATGTGA 59.858 52.381 0.00 0.0 44.07 3.58 R
4783 8964 0.034896 GAGGTGGTCCACATCAACGT 59.965 55.000 27.65 0.9 43.43 3.99 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
73 74 3.309296 GAGATTCACTGGGGAGGTATGA 58.691 50.000 0.00 0.00 0.00 2.15
111 112 4.965119 ACAGCCCGAGATGATTTTTAAC 57.035 40.909 0.00 0.00 32.31 2.01
126 127 7.947282 TGATTTTTAACTGTTTCTTGTAGGGG 58.053 34.615 0.00 0.00 0.00 4.79
329 424 6.449830 ACATTTCTAGGTCCCAATATACCC 57.550 41.667 0.00 0.00 36.34 3.69
356 451 1.379044 ATCGCTGCCAAGAAAGGGG 60.379 57.895 0.00 0.00 0.00 4.79
388 483 7.875041 AGGTTATTGAAGTGATTGATAGGATCG 59.125 37.037 0.00 0.00 0.00 3.69
427 522 3.961477 TTGCCATGGAATTACGATTCG 57.039 42.857 18.40 4.14 42.12 3.34
433 528 2.201732 TGGAATTACGATTCGAGCAGC 58.798 47.619 13.95 0.00 42.12 5.25
455 550 1.218047 CGGCCAGTTCCTCGAATCA 59.782 57.895 2.24 0.00 0.00 2.57
477 572 1.841103 GGGGGAGAGGAGGATGAGC 60.841 68.421 0.00 0.00 0.00 4.26
524 619 2.204136 TGTGGGGTGGCTGGAGAT 60.204 61.111 0.00 0.00 0.00 2.75
541 636 0.734889 GATGTGCACGGGATGGAAAG 59.265 55.000 13.13 0.00 0.00 2.62
555 650 4.321974 GGATGGAAAGTTTGGGCTTTAGTG 60.322 45.833 0.00 0.00 38.64 2.74
580 675 3.056179 CCAAACCGGCATCCAAGTTAATT 60.056 43.478 0.00 0.00 0.00 1.40
585 680 2.923020 CGGCATCCAAGTTAATTGTTGC 59.077 45.455 8.39 8.39 41.72 4.17
589 684 1.271102 TCCAAGTTAATTGTTGCGCCC 59.729 47.619 4.18 0.00 37.17 6.13
605 700 0.539986 GCCCCGATTACTTGGTCTGA 59.460 55.000 0.00 0.00 0.00 3.27
616 711 2.301870 ACTTGGTCTGACAGCCGATAAA 59.698 45.455 10.38 0.00 0.00 1.40
632 727 3.056821 CGATAAATCGGTCTGATAGGCCA 60.057 47.826 5.01 0.00 40.96 5.36
634 729 2.622064 AATCGGTCTGATAGGCCAAC 57.378 50.000 5.01 0.00 40.96 3.77
635 730 1.794714 ATCGGTCTGATAGGCCAACT 58.205 50.000 5.01 0.00 40.96 3.16
636 731 0.824109 TCGGTCTGATAGGCCAACTG 59.176 55.000 5.01 0.00 40.96 3.16
637 732 0.811616 CGGTCTGATAGGCCAACTGC 60.812 60.000 5.01 0.00 40.96 4.40
646 742 4.481195 GCCAACTGCCTGAGTGAA 57.519 55.556 0.00 0.00 34.02 3.18
652 748 0.663153 ACTGCCTGAGTGAAAAACGC 59.337 50.000 0.00 0.00 31.75 4.84
661 757 3.120683 TGAGTGAAAAACGCAGCGAATAG 60.121 43.478 24.65 0.00 33.19 1.73
685 782 2.326773 TTTTCGAACCGGCACCCTCA 62.327 55.000 0.00 0.00 0.00 3.86
758 855 8.315482 GGAAGAGTAGTCTCCTGTAAAAAGAAT 58.685 37.037 0.00 0.00 41.26 2.40
1041 1139 0.744874 CAGATTCAATGGCTGGCAGG 59.255 55.000 17.64 4.71 0.00 4.85
1049 1147 0.698238 ATGGCTGGCAGGTCAAGTTA 59.302 50.000 17.64 0.00 0.00 2.24
1092 1190 6.053005 TGACAGGTTGGTCTTTAGTTACTTG 58.947 40.000 0.00 0.00 38.61 3.16
1287 1385 1.338674 TGAACCTGGATGCACTTACCG 60.339 52.381 0.00 0.00 0.00 4.02
1425 2026 8.715998 CAATAACAATAATCTTAGCGAGCATCT 58.284 33.333 0.00 0.00 0.00 2.90
1668 2269 4.218312 TCATCTGCTCCAATAGACTGCTA 58.782 43.478 0.00 0.00 0.00 3.49
1743 2574 6.659242 TCCAGTTATTTTGGATTCTGTTCTCC 59.341 38.462 0.00 0.00 39.74 3.71
1847 2678 6.844279 CGTTTCCTATACATGCGAACATAAAC 59.156 38.462 0.00 0.00 33.67 2.01
2388 3485 4.125703 CTCAACTTGGACTCATATGCCTC 58.874 47.826 0.00 0.00 0.00 4.70
2474 3571 6.070824 TGGTAGTGTTCATGTGTATCTGATGT 60.071 38.462 0.00 0.00 0.00 3.06
2495 3592 3.001838 GTGCAGTACGTGTTCACAATTCA 59.998 43.478 0.00 0.00 0.00 2.57
2552 3649 6.441093 TGATTCCTGTATTCAATTGTCTGC 57.559 37.500 5.13 0.00 0.00 4.26
2553 3650 6.182627 TGATTCCTGTATTCAATTGTCTGCT 58.817 36.000 5.13 0.00 0.00 4.24
2554 3651 7.337938 TGATTCCTGTATTCAATTGTCTGCTA 58.662 34.615 5.13 0.00 0.00 3.49
2555 3652 7.994911 TGATTCCTGTATTCAATTGTCTGCTAT 59.005 33.333 5.13 0.00 0.00 2.97
2556 3653 8.757982 ATTCCTGTATTCAATTGTCTGCTATT 57.242 30.769 5.13 0.00 0.00 1.73
2557 3654 7.558161 TCCTGTATTCAATTGTCTGCTATTG 57.442 36.000 5.13 0.00 38.54 1.90
2558 3655 6.038603 TCCTGTATTCAATTGTCTGCTATTGC 59.961 38.462 5.13 0.00 37.61 3.56
2559 3656 6.039047 CCTGTATTCAATTGTCTGCTATTGCT 59.961 38.462 5.13 0.00 37.61 3.91
2560 3657 6.788243 TGTATTCAATTGTCTGCTATTGCTG 58.212 36.000 5.13 0.00 37.61 4.41
2561 3658 5.909621 ATTCAATTGTCTGCTATTGCTGT 57.090 34.783 5.13 0.00 37.61 4.40
2562 3659 5.710513 TTCAATTGTCTGCTATTGCTGTT 57.289 34.783 5.13 0.00 37.61 3.16
2563 3660 5.050644 TCAATTGTCTGCTATTGCTGTTG 57.949 39.130 5.13 1.49 37.61 3.33
2564 3661 2.995466 TTGTCTGCTATTGCTGTTGC 57.005 45.000 0.00 0.00 40.48 4.17
2687 3784 9.265901 CAATATGGACTACATAAGGACTCAAAG 57.734 37.037 0.00 0.00 44.75 2.77
2716 3813 7.222611 GTGAACAAACACACTAAAATGCATCTT 59.777 33.333 0.00 0.00 40.11 2.40
3300 4397 3.000971 GCACGAGTACTGCGAGATTTAAC 60.001 47.826 17.67 0.00 0.00 2.01
3466 4565 9.874205 CCATGTTCCATAGATTATTGTGTTTTT 57.126 29.630 0.00 0.00 0.00 1.94
3479 4578 4.181309 TGTGTTTTTGAACAACAGGGAC 57.819 40.909 0.00 0.00 34.79 4.46
3709 4809 4.184629 CCATTAACGTCTCTCCTTTCCAG 58.815 47.826 0.00 0.00 0.00 3.86
3864 4964 2.145397 TACTACACTCAGAGCCCAGG 57.855 55.000 0.00 0.00 0.00 4.45
3931 5031 2.943199 GCCTGAATCTAAGCAGCCTTGT 60.943 50.000 0.00 0.00 32.47 3.16
3936 5036 0.764890 TCTAAGCAGCCTTGTGGTGT 59.235 50.000 0.00 0.00 44.44 4.16
4009 5109 2.551032 CGCATGATACATGGAGCAATGT 59.449 45.455 0.00 5.24 43.21 2.71
4029 5129 7.545265 GCAATGTTTCTAATTTAAGCACCATGA 59.455 33.333 0.00 0.00 0.00 3.07
4108 5208 1.251251 GCTTCTGGTCAGGTTGCATT 58.749 50.000 0.00 0.00 0.00 3.56
4268 5371 1.589716 CCCAAGAAGAAAGCAGCGGG 61.590 60.000 0.00 0.00 0.00 6.13
4317 5423 3.564225 AGAACGAAAAACCAGTTAGCCAG 59.436 43.478 0.00 0.00 0.00 4.85
4504 5610 6.995511 ATCTAGAACTCACTAGTCTGTGAC 57.004 41.667 0.00 0.00 41.43 3.67
4514 5620 4.745125 CACTAGTCTGTGACATGTTTTCGT 59.255 41.667 0.00 0.00 40.12 3.85
4541 5647 9.796120 CAAGGTTTTCAACTGTAATAAGAACAA 57.204 29.630 0.00 0.00 0.00 2.83
4543 5649 9.797556 AGGTTTTCAACTGTAATAAGAACAAAC 57.202 29.630 0.00 0.00 0.00 2.93
4556 5662 3.016736 AGAACAAACACAACTGGACTGG 58.983 45.455 0.00 0.00 0.00 4.00
4562 5668 0.466189 CACAACTGGACTGGGCAAGT 60.466 55.000 0.00 0.00 43.85 3.16
4609 5715 1.572941 CTCGGACAGTGTCGAACGA 59.427 57.895 16.89 17.60 34.87 3.85
4642 5748 0.474184 CTCTTGGACAACCACACCCT 59.526 55.000 0.00 0.00 46.80 4.34
4658 5764 4.080015 CACACCCTTCATATCCAAACCCTA 60.080 45.833 0.00 0.00 0.00 3.53
4686 5792 4.151689 ACATCGTGTAGAACAAATTCACCG 59.848 41.667 0.00 0.00 37.29 4.94
4705 8886 1.460359 CGCCAATTCAACAATGCAACC 59.540 47.619 0.00 0.00 0.00 3.77
4767 8948 4.647853 AGTACGACAATTCATAGGTAGGCA 59.352 41.667 0.00 0.00 0.00 4.75
4776 8957 8.052748 ACAATTCATAGGTAGGCAATACAAGAA 58.947 33.333 1.34 0.00 35.96 2.52
4777 8958 9.071276 CAATTCATAGGTAGGCAATACAAGAAT 57.929 33.333 1.34 0.00 35.96 2.40
4779 8960 9.950496 ATTCATAGGTAGGCAATACAAGAATAG 57.050 33.333 1.34 0.00 35.96 1.73
4780 8961 8.492415 TCATAGGTAGGCAATACAAGAATAGT 57.508 34.615 1.34 0.00 35.96 2.12
4781 8962 8.585881 TCATAGGTAGGCAATACAAGAATAGTC 58.414 37.037 1.34 0.00 35.96 2.59
4782 8963 6.176014 AGGTAGGCAATACAAGAATAGTCC 57.824 41.667 1.34 0.00 35.96 3.85
4783 8964 5.665812 AGGTAGGCAATACAAGAATAGTCCA 59.334 40.000 1.34 0.00 35.96 4.02
4784 8965 5.758784 GGTAGGCAATACAAGAATAGTCCAC 59.241 44.000 1.34 0.00 35.96 4.02
4785 8966 4.442706 AGGCAATACAAGAATAGTCCACG 58.557 43.478 0.00 0.00 0.00 4.94
4786 8967 4.081087 AGGCAATACAAGAATAGTCCACGT 60.081 41.667 0.00 0.00 0.00 4.49
4787 8968 4.634443 GGCAATACAAGAATAGTCCACGTT 59.366 41.667 0.00 0.00 0.00 3.99
4788 8969 5.447279 GGCAATACAAGAATAGTCCACGTTG 60.447 44.000 0.00 0.00 0.00 4.10
4814 9008 2.743718 CACCTCCTTGTCCGCAGT 59.256 61.111 0.00 0.00 0.00 4.40
4874 9068 1.221466 TTCCTGCTCACGTTGCTTCG 61.221 55.000 10.98 0.15 0.00 3.79
4884 9078 2.112297 TTGCTTCGTTCGCCCCTT 59.888 55.556 0.00 0.00 0.00 3.95
4901 9095 2.234908 CCCTTCCTCAGACGACATTCTT 59.765 50.000 0.00 0.00 0.00 2.52
4914 9108 2.742053 GACATTCTTCGCCTTGCAACTA 59.258 45.455 0.00 0.00 0.00 2.24
4919 9113 0.109723 TTCGCCTTGCAACTAACCCT 59.890 50.000 0.00 0.00 0.00 4.34
4947 9260 1.229625 AGCCCCACAGACTCCATCA 60.230 57.895 0.00 0.00 0.00 3.07
4991 9304 0.106116 GGGACAGGGTACTCGGAGAT 60.106 60.000 12.86 0.00 33.89 2.75
5007 9320 2.891580 GGAGATGTTATCTACGAGGGCA 59.108 50.000 0.00 0.00 40.38 5.36
5014 9327 4.227134 CTACGAGGGCAGCGGCAT 62.227 66.667 11.88 0.00 43.71 4.40
5038 9351 2.295602 GGACCAAGGGCGGAGGTTA 61.296 63.158 0.00 0.00 35.36 2.85
5049 9362 0.895530 CGGAGGTTAGTGAAGGCTCA 59.104 55.000 0.00 0.00 0.00 4.26
5050 9363 1.275291 CGGAGGTTAGTGAAGGCTCAA 59.725 52.381 0.00 0.00 31.88 3.02
5084 9397 2.995574 ACGGACACGGGAAGAGGG 60.996 66.667 0.00 0.00 46.48 4.30
5141 9454 5.633830 ATGTGGTGAGCAATTCAAACTAG 57.366 39.130 0.00 0.00 37.61 2.57
5146 9459 4.702131 GGTGAGCAATTCAAACTAGTCCAT 59.298 41.667 0.00 0.00 37.61 3.41
5147 9460 5.183904 GGTGAGCAATTCAAACTAGTCCATT 59.816 40.000 0.00 0.00 37.61 3.16
5173 9486 3.764237 TTGGTGGACTAGGTCAGTTTC 57.236 47.619 0.00 0.00 37.72 2.78
5179 9492 2.444421 GACTAGGTCAGTTTCGAGGGA 58.556 52.381 0.00 0.00 37.72 4.20
5189 9502 2.158519 AGTTTCGAGGGATTTTGGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
5193 9506 1.229177 AGGGATTTTGGGTGTGGCC 60.229 57.895 0.00 0.00 0.00 5.36
5216 9529 4.693283 GGTTTGTCGGATCTGATATGACA 58.307 43.478 16.18 16.18 37.76 3.58
5250 9563 1.622811 CTCCCCATATCAGCTCCAGAC 59.377 57.143 0.00 0.00 0.00 3.51
5312 9626 1.525995 CCGGTTTGAGGTGTGCAGT 60.526 57.895 0.00 0.00 0.00 4.40
5313 9627 1.101049 CCGGTTTGAGGTGTGCAGTT 61.101 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.984230 TGTTGGTGCTAAGCTAGGCT 59.016 50.000 11.27 0.00 42.56 4.58
111 112 4.698575 GAGATAGCCCCTACAAGAAACAG 58.301 47.826 0.00 0.00 0.00 3.16
126 127 4.389077 ACAACAAAAGCTACACGAGATAGC 59.611 41.667 8.62 8.62 44.56 2.97
307 402 6.448369 TGGGTATATTGGGACCTAGAAATG 57.552 41.667 0.00 0.00 35.91 2.32
356 451 5.880332 TCAATCACTTCAATAACCTACCTGC 59.120 40.000 0.00 0.00 0.00 4.85
357 452 9.265901 CTATCAATCACTTCAATAACCTACCTG 57.734 37.037 0.00 0.00 0.00 4.00
388 483 4.083271 GGCAATGAGTACCTTCACAGAAAC 60.083 45.833 0.00 0.00 0.00 2.78
455 550 0.193069 CATCCTCCTCTCCCCCTCAT 59.807 60.000 0.00 0.00 0.00 2.90
460 555 2.206536 CGCTCATCCTCCTCTCCCC 61.207 68.421 0.00 0.00 0.00 4.81
477 572 0.464554 GGAGGAAATTGAGGCTCCCG 60.465 60.000 12.86 0.00 0.00 5.14
514 609 2.046988 CGTGCACATCTCCAGCCA 60.047 61.111 18.64 0.00 0.00 4.75
524 619 0.179004 AACTTTCCATCCCGTGCACA 60.179 50.000 18.64 0.00 0.00 4.57
541 636 1.972198 GGCCCACTAAAGCCCAAAC 59.028 57.895 0.00 0.00 43.76 2.93
580 675 1.003112 AAGTAATCGGGGCGCAACA 60.003 52.632 10.83 0.00 0.00 3.33
585 680 0.810031 CAGACCAAGTAATCGGGGCG 60.810 60.000 0.00 0.00 33.85 6.13
589 684 2.271800 GCTGTCAGACCAAGTAATCGG 58.728 52.381 3.32 0.00 0.00 4.18
616 711 1.414181 CAGTTGGCCTATCAGACCGAT 59.586 52.381 3.32 0.00 38.21 4.18
632 727 1.065551 GCGTTTTTCACTCAGGCAGTT 59.934 47.619 0.00 0.00 30.26 3.16
634 729 0.662619 TGCGTTTTTCACTCAGGCAG 59.337 50.000 0.00 0.00 0.00 4.85
635 730 0.662619 CTGCGTTTTTCACTCAGGCA 59.337 50.000 0.00 0.00 34.95 4.75
636 731 0.661483 GCTGCGTTTTTCACTCAGGC 60.661 55.000 0.00 0.00 38.49 4.85
637 732 0.384725 CGCTGCGTTTTTCACTCAGG 60.385 55.000 14.93 0.00 38.49 3.86
638 733 0.581529 TCGCTGCGTTTTTCACTCAG 59.418 50.000 22.48 0.00 40.68 3.35
646 742 2.423577 ACTTCCTATTCGCTGCGTTTT 58.576 42.857 22.48 10.29 0.00 2.43
652 748 4.435651 GGTTCGAAAACTTCCTATTCGCTG 60.436 45.833 0.00 0.00 44.04 5.18
661 757 0.040692 GTGCCGGTTCGAAAACTTCC 60.041 55.000 1.90 0.00 35.61 3.46
685 782 3.907221 TCGGCCAGTTAATAGGTACTCT 58.093 45.455 2.24 0.00 41.75 3.24
758 855 3.244875 ACCACATGCATGGAACTACAGAA 60.245 43.478 29.41 0.00 43.02 3.02
1041 1139 3.492313 CTTTTCGGCAGCATAACTTGAC 58.508 45.455 0.00 0.00 0.00 3.18
1092 1190 7.965107 AGCAAATGAAAATGTATCGAAGAAGAC 59.035 33.333 0.00 0.00 43.58 3.01
1148 1246 8.333908 CAAAGCAACAAAGCAAAATGTATTACA 58.666 29.630 0.00 0.00 36.85 2.41
1743 2574 1.808945 AGCAAAGCCTGAGTCAATTCG 59.191 47.619 0.00 0.00 0.00 3.34
1847 2678 6.537453 TCAATTCTAGGAGTCTTCTTCTGG 57.463 41.667 0.00 0.00 31.07 3.86
1890 2721 1.016130 CAGGCGTCGAACTGCAGAAT 61.016 55.000 23.35 8.80 0.00 2.40
2474 3571 3.198872 TGAATTGTGAACACGTACTGCA 58.801 40.909 0.00 0.00 0.00 4.41
2495 3592 2.288825 CCCGTCGTGGCATCAATACTAT 60.289 50.000 0.00 0.00 35.87 2.12
2552 3649 2.030540 ACAGCAACAGCAACAGCAATAG 60.031 45.455 0.00 0.00 0.00 1.73
2553 3650 1.955778 ACAGCAACAGCAACAGCAATA 59.044 42.857 0.00 0.00 0.00 1.90
2554 3651 0.748450 ACAGCAACAGCAACAGCAAT 59.252 45.000 0.00 0.00 0.00 3.56
2555 3652 0.531657 AACAGCAACAGCAACAGCAA 59.468 45.000 0.00 0.00 0.00 3.91
2556 3653 0.179132 CAACAGCAACAGCAACAGCA 60.179 50.000 0.00 0.00 0.00 4.41
2557 3654 1.485032 GCAACAGCAACAGCAACAGC 61.485 55.000 0.00 0.00 0.00 4.40
2558 3655 0.179132 TGCAACAGCAACAGCAACAG 60.179 50.000 0.00 0.00 34.85 3.16
2559 3656 0.460722 ATGCAACAGCAACAGCAACA 59.539 45.000 0.00 0.00 42.37 3.33
2560 3657 1.134226 GATGCAACAGCAACAGCAAC 58.866 50.000 0.00 0.00 42.37 4.17
2561 3658 1.034356 AGATGCAACAGCAACAGCAA 58.966 45.000 0.00 0.00 42.37 3.91
2562 3659 1.034356 AAGATGCAACAGCAACAGCA 58.966 45.000 0.00 0.00 42.37 4.41
2563 3660 1.415374 CAAGATGCAACAGCAACAGC 58.585 50.000 0.00 0.00 42.37 4.40
2564 3661 1.415374 GCAAGATGCAACAGCAACAG 58.585 50.000 6.56 0.00 44.26 3.16
2683 3780 4.701956 AGTGTGTTTGTTCACTCCTTTG 57.298 40.909 0.00 0.00 40.28 2.77
2687 3784 5.458779 GCATTTTAGTGTGTTTGTTCACTCC 59.541 40.000 1.08 0.00 42.77 3.85
3054 4151 3.696281 TGGCATGATTTATTCAGCGTG 57.304 42.857 0.00 0.00 37.89 5.34
3198 4295 8.273780 AGCAGGACTATGTTTATCAGAAAAAG 57.726 34.615 0.00 0.00 0.00 2.27
3218 4315 5.804473 GTCGATCATGATCTGTAATAGCAGG 59.196 44.000 28.48 11.95 37.12 4.85
3300 4397 9.364989 CCTTTCTAAGAGATTCAACTTGAGTAG 57.635 37.037 0.00 0.00 0.00 2.57
3466 4565 8.328758 AGATCTATAAATTGTCCCTGTTGTTCA 58.671 33.333 0.00 0.00 0.00 3.18
3518 4617 6.979817 TGTTTGTGTTTGGAAGATCTTCATTG 59.020 34.615 31.29 0.00 41.20 2.82
3709 4809 2.337532 CAGGCAGCAACCACAAGC 59.662 61.111 0.00 0.00 0.00 4.01
3864 4964 6.411492 CGAAGCTCGTTCTGTAGTTCTATTAC 59.589 42.308 0.00 0.00 34.72 1.89
3931 5031 2.505407 CTCCCTATTGGATGTGACACCA 59.495 50.000 2.45 3.33 44.07 4.17
3936 5036 1.141657 GCTGCTCCCTATTGGATGTGA 59.858 52.381 0.00 0.00 44.07 3.58
4009 5109 6.832520 TGCTCATGGTGCTTAAATTAGAAA 57.167 33.333 11.66 0.00 0.00 2.52
4038 5138 1.815817 GATGGTGTGTTGGTTGGGGC 61.816 60.000 0.00 0.00 0.00 5.80
4108 5208 2.442272 GGAGCTCCTGAGGCCGTA 60.442 66.667 26.25 0.00 0.00 4.02
4274 5380 2.124901 CTATTTCCCGGTGCGCCA 60.125 61.111 18.18 0.00 34.09 5.69
4317 5423 4.035909 ACTGATTTGTTGTAACCCGTCAAC 59.964 41.667 0.00 0.00 42.62 3.18
4440 5546 6.347079 CCTGCTGCAAAATTGTATCAAAACAG 60.347 38.462 3.02 0.00 0.00 3.16
4451 5557 3.852286 TGATTAGCCTGCTGCAAAATTG 58.148 40.909 3.02 0.00 44.83 2.32
4504 5610 6.019896 GTTGAAAACCTTGACGAAAACATG 57.980 37.500 0.00 0.00 42.21 3.21
4541 5647 0.033601 TTGCCCAGTCCAGTTGTGTT 60.034 50.000 0.00 0.00 0.00 3.32
4543 5649 0.466189 ACTTGCCCAGTCCAGTTGTG 60.466 55.000 0.00 0.00 0.00 3.33
4572 5678 4.640855 ACACGTCTGGCGGTGTCG 62.641 66.667 6.61 0.12 46.52 4.35
4573 5679 2.733593 GACACGTCTGGCGGTGTC 60.734 66.667 16.87 16.87 46.52 3.67
4575 5681 3.916392 GAGGACACGTCTGGCGGTG 62.916 68.421 6.61 4.68 46.52 4.94
4576 5682 3.681835 GAGGACACGTCTGGCGGT 61.682 66.667 6.61 0.49 46.52 5.68
4577 5683 4.778415 CGAGGACACGTCTGGCGG 62.778 72.222 6.61 0.00 46.52 6.13
4609 5715 2.711009 TCCAAGAGGACAAATGAGGTGT 59.289 45.455 0.00 0.00 39.61 4.16
4642 5748 9.062524 CGATGTATTTTAGGGTTTGGATATGAA 57.937 33.333 0.00 0.00 0.00 2.57
4658 5764 9.607285 GTGAATTTGTTCTACACGATGTATTTT 57.393 29.630 0.00 0.00 31.66 1.82
4686 5792 2.492012 TGGTTGCATTGTTGAATTGGC 58.508 42.857 0.00 0.00 0.00 4.52
4705 8886 7.639461 GTGTTGAATTGTGGTTTATTTTGCTTG 59.361 33.333 0.00 0.00 0.00 4.01
4767 8948 7.064609 CACATCAACGTGGACTATTCTTGTATT 59.935 37.037 0.00 0.00 33.05 1.89
4782 8963 0.250295 AGGTGGTCCACATCAACGTG 60.250 55.000 23.48 0.00 35.86 4.49
4783 8964 0.034896 GAGGTGGTCCACATCAACGT 59.965 55.000 27.65 0.90 43.43 3.99
4784 8965 0.673644 GGAGGTGGTCCACATCAACG 60.674 60.000 31.73 0.00 45.37 4.10
4785 8966 3.249687 GGAGGTGGTCCACATCAAC 57.750 57.895 31.73 16.05 45.37 3.18
4874 9068 1.079057 GTCTGAGGAAGGGGCGAAC 60.079 63.158 0.00 0.00 0.00 3.95
4884 9078 1.135373 GCGAAGAATGTCGTCTGAGGA 60.135 52.381 0.00 0.00 43.06 3.71
4901 9095 0.978151 TAGGGTTAGTTGCAAGGCGA 59.022 50.000 0.00 0.00 0.00 5.54
4914 9108 2.070650 GGCTCCCATCCGTAGGGTT 61.071 63.158 0.53 0.00 39.56 4.11
4991 9304 0.384309 CGCTGCCCTCGTAGATAACA 59.616 55.000 0.00 0.00 33.89 2.41
5007 9320 2.045926 GGTCCTGTTCATGCCGCT 60.046 61.111 0.00 0.00 0.00 5.52
5014 9327 2.429930 CGCCCTTGGTCCTGTTCA 59.570 61.111 0.00 0.00 0.00 3.18
5016 9329 2.852075 TCCGCCCTTGGTCCTGTT 60.852 61.111 0.00 0.00 0.00 3.16
5038 9351 0.608640 CCTACCGTTGAGCCTTCACT 59.391 55.000 0.00 0.00 31.71 3.41
5049 9362 1.206371 CGTCCTCCATTTCCTACCGTT 59.794 52.381 0.00 0.00 0.00 4.44
5050 9363 0.822164 CGTCCTCCATTTCCTACCGT 59.178 55.000 0.00 0.00 0.00 4.83
5084 9397 3.763897 ACCTAGTCCACCAAATTGAATGC 59.236 43.478 0.00 0.00 0.00 3.56
5169 9482 2.030274 CACACCCAAAATCCCTCGAAAC 60.030 50.000 0.00 0.00 0.00 2.78
5173 9486 1.595093 GCCACACCCAAAATCCCTCG 61.595 60.000 0.00 0.00 0.00 4.63
5179 9492 1.051556 AAACCGGCCACACCCAAAAT 61.052 50.000 0.00 0.00 33.26 1.82
5193 9506 3.736252 GTCATATCAGATCCGACAAACCG 59.264 47.826 7.09 0.00 0.00 4.44
5211 9524 4.129737 CCCGGACGCGTCTGTCAT 62.130 66.667 37.95 4.94 40.72 3.06
5250 9563 2.297033 CACCTTTCAAACCCAGTCCATG 59.703 50.000 0.00 0.00 0.00 3.66
5292 9606 2.904866 GCACACCTCAAACCGGCA 60.905 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.