Multiple sequence alignment - TraesCS1B01G061700

Loading Multiple Alignment...

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 TraesCS1B01G061700 chr1B 100.000 3464 0 0 1 3464 46831004 46827541 0.000000e+00 6397.0
1 TraesCS1B01G061700 chr1B 87.546 2971 242 51 454 3378 4597760 4594872 0.000000e+00 3319.0
2 TraesCS1B01G061700 chr1B 89.117 2389 166 37 631 2978 4110160 4112495 0.000000e+00 2885.0
3 TraesCS1B01G061700 chr1B 87.905 2406 203 43 626 2984 4954499 4952135 0.000000e+00 2750.0
4 TraesCS1B01G061700 chr1B 89.586 2055 166 21 652 2688 70232782 70234806 0.000000e+00 2566.0
5 TraesCS1B01G061700 chr1B 90.133 1206 93 7 1812 2997 4798955 4797756 0.000000e+00 1544.0
6 TraesCS1B01G061700 chr1B 82.060 903 73 39 1 825 46690818 46691709 0.000000e+00 688.0
7 TraesCS1B01G061700 chr1B 83.358 679 52 20 2482 3123 46693720 46694374 3.880000e-159 571.0
8 TraesCS1B01G061700 chr1B 80.750 587 49 17 2482 3037 4933204 4932651 1.940000e-107 399.0
9 TraesCS1B01G061700 chr1B 89.226 297 16 9 3178 3460 4797653 4797359 1.180000e-94 357.0
10 TraesCS1B01G061700 chr1B 88.514 296 18 9 3178 3460 4112608 4112900 9.200000e-91 344.0
11 TraesCS1B01G061700 chr1B 80.943 488 33 25 1 437 4955657 4955179 7.170000e-87 331.0
12 TraesCS1B01G061700 chr1B 92.857 140 7 1 464 600 4109416 4109555 2.110000e-47 200.0
13 TraesCS1B01G061700 chr1B 82.213 253 19 9 450 689 4955100 4954861 9.810000e-46 195.0
14 TraesCS1B01G061700 chr1B 84.653 202 8 4 3033 3233 4516594 4516415 2.750000e-41 180.0
15 TraesCS1B01G061700 chr1B 81.690 213 22 7 179 376 4598478 4598268 9.950000e-36 161.0
16 TraesCS1B01G061700 chr1B 92.784 97 5 2 3029 3123 4112505 4112601 4.660000e-29 139.0
17 TraesCS1B01G061700 chr1B 92.784 97 5 2 3029 3123 4797756 4797660 4.660000e-29 139.0
18 TraesCS1B01G061700 chr1B 80.137 146 15 8 443 586 4542871 4542738 2.850000e-16 97.1
19 TraesCS1B01G061700 chr1B 84.043 94 5 3 3323 3416 4912603 4912520 7.970000e-12 82.4
20 TraesCS1B01G061700 chr1B 86.567 67 1 3 469 535 70232629 70232687 2.230000e-07 67.6
21 TraesCS1B01G061700 chr1B 93.182 44 2 1 544 586 46691880 46691923 2.890000e-06 63.9
22 TraesCS1B01G061700 chr6A 90.014 2854 156 43 645 3458 613493623 613496387 0.000000e+00 3572.0
23 TraesCS1B01G061700 chr6A 85.397 2383 231 64 661 3023 64167849 64165564 0.000000e+00 2364.0
24 TraesCS1B01G061700 chr6A 81.875 320 39 9 2710 3017 64172812 64172500 5.740000e-63 252.0
25 TraesCS1B01G061700 chr6A 74.886 438 60 32 173 585 613492552 613492964 1.660000e-33 154.0
26 TraesCS1B01G061700 chr5B 87.956 2574 203 46 645 3168 60826000 60823484 0.000000e+00 2937.0
27 TraesCS1B01G061700 chr5B 78.049 492 44 26 2543 3001 617172519 617172979 5.740000e-63 252.0
28 TraesCS1B01G061700 chr5B 91.429 105 5 3 3037 3139 617173104 617173206 1.300000e-29 141.0
29 TraesCS1B01G061700 chr5B 89.888 89 3 2 498 586 60826243 60826161 3.660000e-20 110.0
30 TraesCS1B01G061700 chr5B 79.355 155 14 8 224 372 60826563 60826421 3.680000e-15 93.5
31 TraesCS1B01G061700 chr5B 90.909 44 4 0 400 443 505452631 505452674 3.730000e-05 60.2
32 TraesCS1B01G061700 chr3D 87.476 2635 206 47 626 3217 560024908 560022355 0.000000e+00 2924.0
33 TraesCS1B01G061700 chr3D 77.052 658 70 43 1 608 560026154 560025528 1.560000e-78 303.0
34 TraesCS1B01G061700 chr1A 87.579 2375 206 31 693 3034 2943269 2945587 0.000000e+00 2669.0
35 TraesCS1B01G061700 chr1A 91.158 1787 142 10 970 2755 3013316 3015087 0.000000e+00 2410.0
36 TraesCS1B01G061700 chr1A 84.201 538 51 9 2702 3217 3015085 3015610 3.110000e-135 492.0
37 TraesCS1B01G061700 chr1A 89.764 254 25 1 2852 3104 3520959 3520706 1.200000e-84 324.0
38 TraesCS1B01G061700 chr1A 87.059 255 24 7 3188 3438 3520666 3520417 2.630000e-71 279.0
39 TraesCS1B01G061700 chr1A 76.066 422 37 36 192 581 2942229 2942618 9.950000e-36 161.0
40 TraesCS1B01G061700 chr1A 90.678 118 7 1 708 825 3542277 3542164 1.660000e-33 154.0
41 TraesCS1B01G061700 chr1A 93.204 103 6 1 3309 3411 32548113 32548214 2.150000e-32 150.0
42 TraesCS1B01G061700 chr1A 88.333 60 5 2 370 427 2942888 2942947 1.720000e-08 71.3
43 TraesCS1B01G061700 chr6D 88.479 1953 168 29 691 2640 51348854 51350752 0.000000e+00 2307.0
44 TraesCS1B01G061700 chr6D 87.402 2040 189 33 661 2693 50956360 50958338 0.000000e+00 2281.0
45 TraesCS1B01G061700 chr6D 87.916 1953 182 28 691 2640 50949155 50951056 0.000000e+00 2250.0
46 TraesCS1B01G061700 chr6D 93.182 44 3 0 502 545 51342725 51342768 8.020000e-07 65.8
47 TraesCS1B01G061700 chr1D 86.233 937 64 20 2511 3406 387236 388148 0.000000e+00 955.0
48 TraesCS1B01G061700 chr1D 92.466 146 8 1 2948 3090 665751 665896 4.530000e-49 206.0
49 TraesCS1B01G061700 chr1D 93.204 103 6 1 3309 3411 33988264 33988365 2.150000e-32 150.0
50 TraesCS1B01G061700 chr1D 95.604 91 3 1 3033 3122 33988075 33988165 1.000000e-30 145.0
51 TraesCS1B01G061700 chr1D 90.909 44 4 0 400 443 361672967 361673010 3.730000e-05 60.2
52 TraesCS1B01G061700 chr5D 95.050 101 3 2 3037 3136 497870076 497870175 1.290000e-34 158.0
53 TraesCS1B01G061700 chr5D 86.395 147 15 5 180 324 535498790 535498647 4.630000e-34 156.0
54 TraesCS1B01G061700 chr5D 80.000 155 14 9 224 372 57818967 57819110 7.910000e-17 99.0
55 TraesCS1B01G061700 chr7A 84.756 164 5 11 612 756 725598549 725598387 2.790000e-31 147.0
56 TraesCS1B01G061700 chr7A 83.636 165 6 11 612 756 123593902 123594065 6.030000e-28 135.0
57 TraesCS1B01G061700 chr7A 82.424 165 8 10 612 756 74733358 74733521 1.310000e-24 124.0
58 TraesCS1B01G061700 chr5A 84.848 165 4 10 612 756 72758660 72758497 2.790000e-31 147.0
59 TraesCS1B01G061700 chr5A 83.030 165 7 8 612 756 216621754 216621917 2.810000e-26 130.0
60 TraesCS1B01G061700 chr4A 84.242 165 5 8 612 756 78431724 78431561 1.300000e-29 141.0
61 TraesCS1B01G061700 chr2A 84.242 165 5 10 612 756 27942851 27943014 1.300000e-29 141.0
62 TraesCS1B01G061700 chr2A 84.242 165 5 11 612 756 31069565 31069402 1.300000e-29 141.0
63 TraesCS1B01G061700 chr3A 83.636 165 6 11 612 756 475549336 475549173 6.030000e-28 135.0
64 TraesCS1B01G061700 chr7D 89.412 85 4 2 502 586 548230852 548230931 6.120000e-18 102.0
65 TraesCS1B01G061700 chrUn 88.333 60 5 2 370 427 361631293 361631352 1.720000e-08 71.3
66 TraesCS1B01G061700 chr6B 93.182 44 3 0 502 545 120595628 120595585 8.020000e-07 65.8


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 TraesCS1B01G061700 chr1B 46827541 46831004 3463 True 6397.000000 6397 100.000000 1 3464 1 chr1B.!!$R5 3463
1 TraesCS1B01G061700 chr1B 4594872 4598478 3606 True 1740.000000 3319 84.618000 179 3378 2 chr1B.!!$R6 3199
2 TraesCS1B01G061700 chr1B 70232629 70234806 2177 False 1316.800000 2566 88.076500 469 2688 2 chr1B.!!$F3 2219
3 TraesCS1B01G061700 chr1B 4952135 4955657 3522 True 1092.000000 2750 83.687000 1 2984 3 chr1B.!!$R8 2983
4 TraesCS1B01G061700 chr1B 4109416 4112900 3484 False 892.000000 2885 90.818000 464 3460 4 chr1B.!!$F1 2996
5 TraesCS1B01G061700 chr1B 4797359 4798955 1596 True 680.000000 1544 90.714333 1812 3460 3 chr1B.!!$R7 1648
6 TraesCS1B01G061700 chr1B 46690818 46694374 3556 False 440.966667 688 86.200000 1 3123 3 chr1B.!!$F2 3122
7 TraesCS1B01G061700 chr1B 4932651 4933204 553 True 399.000000 399 80.750000 2482 3037 1 chr1B.!!$R4 555
8 TraesCS1B01G061700 chr6A 64165564 64167849 2285 True 2364.000000 2364 85.397000 661 3023 1 chr6A.!!$R1 2362
9 TraesCS1B01G061700 chr6A 613492552 613496387 3835 False 1863.000000 3572 82.450000 173 3458 2 chr6A.!!$F1 3285
10 TraesCS1B01G061700 chr5B 60823484 60826563 3079 True 1046.833333 2937 85.733000 224 3168 3 chr5B.!!$R1 2944
11 TraesCS1B01G061700 chr3D 560022355 560026154 3799 True 1613.500000 2924 82.264000 1 3217 2 chr3D.!!$R1 3216
12 TraesCS1B01G061700 chr1A 3013316 3015610 2294 False 1451.000000 2410 87.679500 970 3217 2 chr1A.!!$F3 2247
13 TraesCS1B01G061700 chr1A 2942229 2945587 3358 False 967.100000 2669 83.992667 192 3034 3 chr1A.!!$F2 2842
14 TraesCS1B01G061700 chr1A 3520417 3520959 542 True 301.500000 324 88.411500 2852 3438 2 chr1A.!!$R2 586
15 TraesCS1B01G061700 chr6D 51348854 51350752 1898 False 2307.000000 2307 88.479000 691 2640 1 chr6D.!!$F4 1949
16 TraesCS1B01G061700 chr6D 50956360 50958338 1978 False 2281.000000 2281 87.402000 661 2693 1 chr6D.!!$F2 2032
17 TraesCS1B01G061700 chr6D 50949155 50951056 1901 False 2250.000000 2250 87.916000 691 2640 1 chr6D.!!$F1 1949
18 TraesCS1B01G061700 chr1D 387236 388148 912 False 955.000000 955 86.233000 2511 3406 1 chr1D.!!$F1 895

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
540 718 0.250553 TTGCCCAACCAAGACCTACG 60.251 55.000 0.00 0.00 0.0 3.51 F
700 2309 0.523335 GATGTGGCCGCGTCATTTTC 60.523 55.000 29.60 5.30 0.0 2.29 F
1392 3053 1.615883 GTGTCTCTCAGGCTGAACTCA 59.384 52.381 19.29 12.04 0.0 3.41 F
1543 3205 2.069273 CGTTGGAAGAGCTTGTAGTGG 58.931 52.381 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 3777 1.011968 CGAGAACACGAATCGGGCAA 61.012 55.000 4.18 0.0 31.12 4.52 R
2249 3926 1.869767 CGAGATTACTCAAGCATGGGC 59.130 52.381 0.00 0.0 42.72 5.36 R
2269 3946 2.029244 CGTTATGACACATCCGAAGTGC 59.971 50.000 3.67 0.0 40.59 4.40 R
3424 5281 1.755179 AAGGCGCATGTTAGCTCAAT 58.245 45.000 10.83 0.0 0.00 2.57 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
24 25 1.012234 GCCGAAAATAGCGCTCGTG 60.012 57.895 16.34 6.65 0.00 4.35
78 80 0.547471 TGAGCCCACATCTTCCTCCA 60.547 55.000 0.00 0.00 0.00 3.86
109 113 2.853731 AATTACAGAGACGAGCGAGG 57.146 50.000 0.00 0.00 0.00 4.63
135 141 3.677424 GCTAGGGTTTACACTCTGCTCTG 60.677 52.174 0.00 0.00 33.23 3.35
147 153 3.760035 GCTCTGTTCCTCCGCCGA 61.760 66.667 0.00 0.00 0.00 5.54
148 154 2.492090 CTCTGTTCCTCCGCCGAG 59.508 66.667 0.00 0.00 35.72 4.63
211 245 1.017701 CAAGGAAGGTACCGCCGTTC 61.018 60.000 17.72 11.09 43.70 3.95
213 247 1.153686 GGAAGGTACCGCCGTTCTC 60.154 63.158 6.18 0.00 43.70 2.87
233 287 1.691196 CGCTTCTCCTCTCCTGAGAT 58.309 55.000 0.00 0.00 42.73 2.75
237 291 3.689858 GCTTCTCCTCTCCTGAGATACCA 60.690 52.174 0.00 0.00 42.73 3.25
249 307 2.225522 TGAGATACCACTCCCTGTTCCA 60.226 50.000 0.00 0.00 36.22 3.53
273 338 1.673009 GCGTTGGTTCCCCGATTCA 60.673 57.895 2.95 0.00 0.00 2.57
373 459 7.765695 AATCATCATCCACAAACTTAGTTGT 57.234 32.000 0.00 0.00 42.48 3.32
375 461 8.862325 ATCATCATCCACAAACTTAGTTGTTA 57.138 30.769 0.00 0.00 39.73 2.41
376 462 8.684386 TCATCATCCACAAACTTAGTTGTTAA 57.316 30.769 0.00 0.00 39.73 2.01
378 464 9.559958 CATCATCCACAAACTTAGTTGTTAATC 57.440 33.333 0.00 0.00 39.73 1.75
379 465 8.684386 TCATCCACAAACTTAGTTGTTAATCA 57.316 30.769 0.00 0.00 39.73 2.57
394 499 6.726490 TGTTAATCATCTCCTAGGTACCAC 57.274 41.667 15.94 0.00 0.00 4.16
427 538 0.969149 GCTTTTTGCCTAGGGTTGCT 59.031 50.000 11.72 0.00 35.15 3.91
429 540 2.238521 CTTTTTGCCTAGGGTTGCTGA 58.761 47.619 11.72 0.00 0.00 4.26
433 544 1.616159 TGCCTAGGGTTGCTGAAAAC 58.384 50.000 11.72 0.00 0.00 2.43
441 574 2.949644 GGGTTGCTGAAAACACTACAGT 59.050 45.455 0.00 0.00 34.60 3.55
461 594 5.181748 CAGTAGATATTAGATTGGCCCTGC 58.818 45.833 0.00 0.00 0.00 4.85
488 662 4.100084 TCATCGGCTGTGGCTGGG 62.100 66.667 0.00 0.00 44.44 4.45
540 718 0.250553 TTGCCCAACCAAGACCTACG 60.251 55.000 0.00 0.00 0.00 3.51
589 767 3.415212 TCCTCTGCTTTTCATGTTCAGG 58.585 45.455 0.00 0.00 0.00 3.86
608 786 4.695455 TCAGGTTCAGCAATTTGTAGTAGC 59.305 41.667 0.00 0.00 0.00 3.58
633 851 4.331168 AGTTTGCGTCAATTCTAGCTCATC 59.669 41.667 0.00 0.00 0.00 2.92
639 857 5.007039 GCGTCAATTCTAGCTCATCATTCAA 59.993 40.000 0.00 0.00 0.00 2.69
640 858 6.417327 CGTCAATTCTAGCTCATCATTCAAC 58.583 40.000 0.00 0.00 0.00 3.18
700 2309 0.523335 GATGTGGCCGCGTCATTTTC 60.523 55.000 29.60 5.30 0.00 2.29
740 2352 4.148838 AGACAGATAAGGTGCTAGCTAGG 58.851 47.826 22.10 4.48 0.00 3.02
767 2386 8.388484 AGCTACTTTAATAAATCTCCATGCTG 57.612 34.615 0.00 0.00 0.00 4.41
811 2436 2.977914 TGGACAGATACAGCAGAAAGC 58.022 47.619 0.00 0.00 46.19 3.51
838 2474 9.591404 GCTCAAACTTCATCATTATATTCTTCG 57.409 33.333 0.00 0.00 0.00 3.79
881 2523 5.539979 CCAGTGTGATCTCCATCTATCTTG 58.460 45.833 0.00 0.00 0.00 3.02
927 2579 9.831737 GTATATCATAATTTTGATGACTGGTGC 57.168 33.333 18.34 2.10 36.97 5.01
1075 2736 6.092396 CAGGACAAGTGATCTGAATTCTCTTG 59.908 42.308 15.93 15.93 44.40 3.02
1083 2744 4.104383 TCTGAATTCTCTTGCCCTTGTT 57.896 40.909 7.05 0.00 0.00 2.83
1089 2750 5.813513 ATTCTCTTGCCCTTGTTTCAAAT 57.186 34.783 0.00 0.00 0.00 2.32
1392 3053 1.615883 GTGTCTCTCAGGCTGAACTCA 59.384 52.381 19.29 12.04 0.00 3.41
1543 3205 2.069273 CGTTGGAAGAGCTTGTAGTGG 58.931 52.381 0.00 0.00 0.00 4.00
1573 3235 5.419471 TGCAAAGGAATCAATCATCATGACA 59.581 36.000 0.00 0.00 0.00 3.58
2100 3777 3.777106 TTTCTGGTGCTCATTCAGTCT 57.223 42.857 0.00 0.00 0.00 3.24
2269 3946 1.869767 GCCCATGCTTGAGTAATCTCG 59.130 52.381 0.22 0.00 37.76 4.04
2509 4193 7.117199 CAGTATGAATTTGCTGCTGAAGCCT 62.117 44.000 4.91 0.00 46.71 4.58
2532 4219 6.857964 CCTTTAAGTTGTTTAGTGTGCATCAG 59.142 38.462 0.00 0.00 0.00 2.90
2594 4284 6.036577 TCTGAACTTTTTGTTGCCTTCTTT 57.963 33.333 0.00 0.00 39.30 2.52
2595 4285 6.099341 TCTGAACTTTTTGTTGCCTTCTTTC 58.901 36.000 0.00 0.00 39.30 2.62
2596 4286 6.036577 TGAACTTTTTGTTGCCTTCTTTCT 57.963 33.333 0.00 0.00 39.30 2.52
2597 4287 5.868801 TGAACTTTTTGTTGCCTTCTTTCTG 59.131 36.000 0.00 0.00 39.30 3.02
2611 4306 5.279156 CCTTCTTTCTGCCTTTACTGCAATT 60.279 40.000 0.00 0.00 38.46 2.32
2708 4423 7.358066 CACTCGTGTATTACTATCAACCGTAT 58.642 38.462 0.00 0.00 0.00 3.06
2810 4577 2.037772 CTGTGGAGGCACTATATGACCC 59.962 54.545 0.00 0.00 41.55 4.46
2955 4779 7.360113 AGTTTCAATGGACATTTACAAAGGT 57.640 32.000 0.00 0.00 35.37 3.50
3123 4954 7.288852 AGTGACTCTGAAGGCATATAACATAGT 59.711 37.037 0.00 0.00 44.23 2.12
3132 4963 5.760253 AGGCATATAACATAGTTGTGTGCTC 59.240 40.000 20.79 14.03 35.83 4.26
3148 4985 3.132289 TGTGCTCATTACAGGTAGGTAGC 59.868 47.826 0.00 0.00 0.00 3.58
3286 5135 3.439857 TTGAGGGGTTCAGATTTCTGG 57.560 47.619 7.68 0.00 43.91 3.86
3344 5199 3.639538 TCAGTTCAGCTCGTAGAAACAC 58.360 45.455 0.00 0.00 34.09 3.32
3368 5223 5.126061 CCATTTGCCTTGTATTTGTAGCTCT 59.874 40.000 0.00 0.00 0.00 4.09
3399 5254 3.555586 CCAACTTTGCTTTGCTGGCTATT 60.556 43.478 0.00 0.00 0.00 1.73
3416 5271 8.455682 GCTGGCTATTTAATTTGTGTTGTACTA 58.544 33.333 0.00 0.00 0.00 1.82
3447 5311 0.035056 AGCTAACATGCGCCTTTCCT 60.035 50.000 4.18 0.00 38.13 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 1.906574 TCTGTAATTTCCAGCGGGAGT 59.093 47.619 5.52 0.00 46.01 3.85
109 113 3.738590 GCAGAGTGTAAACCCTAGCTAGC 60.739 52.174 15.74 6.62 0.00 3.42
188 216 1.551019 GGCGGTACCTTCCTTGACCT 61.551 60.000 10.90 0.00 34.51 3.85
211 245 0.395036 TCAGGAGAGGAGAAGCGGAG 60.395 60.000 0.00 0.00 0.00 4.63
213 247 0.395036 TCTCAGGAGAGGAGAAGCGG 60.395 60.000 0.00 0.00 42.34 5.52
350 422 7.765695 AACAACTAAGTTTGTGGATGATGAT 57.234 32.000 0.00 0.00 39.70 2.45
351 423 8.684386 TTAACAACTAAGTTTGTGGATGATGA 57.316 30.769 0.00 0.00 39.70 2.92
352 424 9.559958 GATTAACAACTAAGTTTGTGGATGATG 57.440 33.333 0.00 0.00 39.70 3.07
353 425 9.295825 TGATTAACAACTAAGTTTGTGGATGAT 57.704 29.630 0.00 0.00 39.70 2.45
354 426 8.684386 TGATTAACAACTAAGTTTGTGGATGA 57.316 30.769 0.00 0.00 39.70 2.92
373 459 7.823635 ACTAGTGGTACCTAGGAGATGATTAA 58.176 38.462 17.98 0.00 39.01 1.40
375 461 6.282568 ACTAGTGGTACCTAGGAGATGATT 57.717 41.667 17.98 0.00 39.01 2.57
376 462 5.933846 ACTAGTGGTACCTAGGAGATGAT 57.066 43.478 17.98 0.00 39.01 2.45
378 464 6.436738 TCTACTAGTGGTACCTAGGAGATG 57.563 45.833 17.98 6.66 45.83 2.90
394 499 7.674471 AGGCAAAAAGCTTACTTTCTACTAG 57.326 36.000 0.00 0.00 45.48 2.57
433 544 7.179338 AGGGCCAATCTAATATCTACTGTAGTG 59.821 40.741 14.11 2.66 0.00 2.74
441 574 4.093743 TCGCAGGGCCAATCTAATATCTA 58.906 43.478 6.18 0.00 0.00 1.98
461 594 0.994995 CAGCCGATGAGTTGAGTTCG 59.005 55.000 0.00 0.00 0.00 3.95
569 747 3.152341 ACCTGAACATGAAAAGCAGAGG 58.848 45.455 0.00 0.00 0.00 3.69
589 767 6.969828 ACTAGCTACTACAAATTGCTGAAC 57.030 37.500 0.00 0.00 35.47 3.18
608 786 4.864806 TGAGCTAGAATTGACGCAAACTAG 59.135 41.667 19.46 19.46 37.41 2.57
633 851 8.562892 CCATAATTAAGTAGCAGAGGTTGAATG 58.437 37.037 0.00 0.00 0.00 2.67
639 857 5.428783 ACCACCATAATTAAGTAGCAGAGGT 59.571 40.000 0.00 0.00 0.00 3.85
640 858 5.930135 ACCACCATAATTAAGTAGCAGAGG 58.070 41.667 0.00 0.00 0.00 3.69
675 897 0.944386 GACGCGGCCACATCATTAAT 59.056 50.000 12.47 0.00 0.00 1.40
700 2309 7.873719 TCTGTCTCTAGATTGTTAGGAAGAG 57.126 40.000 0.00 0.00 33.37 2.85
740 2352 9.495572 AGCATGGAGATTTATTAAAGTAGCTAC 57.504 33.333 16.43 16.43 0.00 3.58
767 2386 7.306749 CCAAAACTTAATTGTGTGCTGTTCATC 60.307 37.037 0.00 0.00 0.00 2.92
775 2394 5.587289 TCTGTCCAAAACTTAATTGTGTGC 58.413 37.500 0.00 0.00 0.00 4.57
811 2436 9.591404 GAAGAATATAATGATGAAGTTTGAGCG 57.409 33.333 0.00 0.00 0.00 5.03
856 2492 1.576577 AGATGGAGATCACACTGGCA 58.423 50.000 0.00 0.00 0.00 4.92
901 2547 9.831737 GCACCAGTCATCAAAATTATGATATAC 57.168 33.333 0.00 0.00 37.96 1.47
912 2563 0.874390 GAGCGCACCAGTCATCAAAA 59.126 50.000 11.47 0.00 0.00 2.44
923 2575 1.782028 AACAACCGAAAGAGCGCACC 61.782 55.000 11.47 0.00 0.00 5.01
924 2576 0.028902 AAACAACCGAAAGAGCGCAC 59.971 50.000 11.47 2.25 0.00 5.34
925 2577 0.736053 AAAACAACCGAAAGAGCGCA 59.264 45.000 11.47 0.00 0.00 6.09
926 2578 1.002792 AGAAAACAACCGAAAGAGCGC 60.003 47.619 0.00 0.00 0.00 5.92
927 2579 2.286833 TGAGAAAACAACCGAAAGAGCG 59.713 45.455 0.00 0.00 0.00 5.03
1021 2682 4.313282 CTGTTGAGAATCTCTGTCAGCAA 58.687 43.478 11.92 0.00 32.00 3.91
1075 2736 2.560105 AGAGCTGATTTGAAACAAGGGC 59.440 45.455 0.00 0.00 0.00 5.19
1083 2744 7.418368 CCCTCTATCTTGTAGAGCTGATTTGAA 60.418 40.741 0.00 0.00 39.66 2.69
1089 2750 3.463704 TCCCCTCTATCTTGTAGAGCTGA 59.536 47.826 0.00 3.23 39.66 4.26
1392 3053 5.278758 CCCAATCGAAGTTATTTGTGGTGTT 60.279 40.000 0.00 0.00 0.00 3.32
1543 3205 7.262772 TGATGATTGATTCCTTTGCAATTCTC 58.737 34.615 0.00 0.00 32.80 2.87
1573 3235 4.325344 CCATCCTGGACCAAACTTTAGGAT 60.325 45.833 0.00 3.83 43.77 3.24
2100 3777 1.011968 CGAGAACACGAATCGGGCAA 61.012 55.000 4.18 0.00 31.12 4.52
2249 3926 1.869767 CGAGATTACTCAAGCATGGGC 59.130 52.381 0.00 0.00 42.72 5.36
2269 3946 2.029244 CGTTATGACACATCCGAAGTGC 59.971 50.000 3.67 0.00 40.59 4.40
2509 4193 7.328277 ACTGATGCACACTAAACAACTTAAA 57.672 32.000 0.00 0.00 0.00 1.52
2532 4219 2.099141 TGATGCACAGCCTTGTCTAC 57.901 50.000 0.00 0.00 34.62 2.59
2594 4284 6.437162 AGGAAAATAATTGCAGTAAAGGCAGA 59.563 34.615 0.00 0.00 43.05 4.26
2595 4285 6.633856 AGGAAAATAATTGCAGTAAAGGCAG 58.366 36.000 0.00 0.00 43.05 4.85
2596 4286 6.603940 AGGAAAATAATTGCAGTAAAGGCA 57.396 33.333 0.00 0.00 40.00 4.75
2597 4287 7.905604 AAAGGAAAATAATTGCAGTAAAGGC 57.094 32.000 0.00 0.00 0.00 4.35
2626 4321 7.164122 GCCATCCAAAGATCATCATTAGACTA 58.836 38.462 0.00 0.00 0.00 2.59
2708 4423 9.555727 AGTAGAAACTAAGCAACAAGAATTACA 57.444 29.630 0.00 0.00 32.84 2.41
2810 4577 9.269415 GCTTAAGTAATACAAATAACACCAACG 57.731 33.333 4.02 0.00 0.00 4.10
2838 4616 7.572523 TGTCTTCAAAATCACTTCTGACATT 57.427 32.000 0.00 0.00 0.00 2.71
2928 4752 7.925483 CCTTTGTAAATGTCCATTGAAACTTGA 59.075 33.333 0.00 0.00 0.00 3.02
2955 4779 2.975732 TCAACAAAACAAGCATGCCA 57.024 40.000 15.66 0.00 0.00 4.92
3123 4954 3.326588 ACCTACCTGTAATGAGCACACAA 59.673 43.478 0.00 0.00 0.00 3.33
3132 4963 4.100963 TGATGTGGCTACCTACCTGTAATG 59.899 45.833 0.00 0.00 0.00 1.90
3148 4985 2.422479 CCAGAGCAAAGACATGATGTGG 59.578 50.000 1.23 0.00 42.63 4.17
3344 5199 5.126061 AGAGCTACAAATACAAGGCAAATGG 59.874 40.000 0.00 0.00 0.00 3.16
3368 5223 4.121317 CAAAGCAAAGTTGGCATCTTGAA 58.879 39.130 11.35 0.00 0.00 2.69
3416 5271 6.863126 GGCGCATGTTAGCTCAATTATAAAAT 59.137 34.615 10.83 0.00 0.00 1.82
3417 5272 6.039270 AGGCGCATGTTAGCTCAATTATAAAA 59.961 34.615 10.83 0.00 0.00 1.52
3418 5273 5.530915 AGGCGCATGTTAGCTCAATTATAAA 59.469 36.000 10.83 0.00 0.00 1.40
3424 5281 1.755179 AAGGCGCATGTTAGCTCAAT 58.245 45.000 10.83 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.