Multiple sequence alignment - TraesCS1B01G275900

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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 TraesCS1B01G275900 chr1B 100.000 2754 0 0 1 2754 483463516 483460763 0.000000e+00 5086
1 TraesCS1B01G275900 chr1B 80.762 525 88 12 2238 2754 253766711 253767230 5.530000e-107 398
2 TraesCS1B01G275900 chr1D 91.685 1395 78 18 469 1842 361129245 361127868 0.000000e+00 1899
3 TraesCS1B01G275900 chr1D 93.069 404 15 6 1 392 361129792 361129390 1.840000e-161 579
4 TraesCS1B01G275900 chr1D 87.032 347 40 4 1838 2181 361127762 361127418 1.200000e-103 387
5 TraesCS1B01G275900 chr1D 96.154 104 3 1 376 479 361129375 361129273 4.720000e-38 169
6 TraesCS1B01G275900 chr1D 80.882 204 35 4 14 214 417894034 417894236 1.020000e-34 158
7 TraesCS1B01G275900 chr1A 93.717 955 59 1 488 1441 460846658 460845704 0.000000e+00 1430
8 TraesCS1B01G275900 chr1A 88.639 757 61 11 1436 2182 460844832 460844091 0.000000e+00 898
9 TraesCS1B01G275900 chr1A 86.829 410 41 13 1 404 460847214 460846812 1.950000e-121 446
10 TraesCS1B01G275900 chr1A 88.321 137 12 4 345 479 460846830 460846696 7.890000e-36 161
11 TraesCS1B01G275900 chr7A 85.651 453 63 2 2304 2754 357723535 357723987 2.480000e-130 475
12 TraesCS1B01G275900 chr7A 82.960 446 70 6 2313 2754 248316972 248316529 5.530000e-107 398
13 TraesCS1B01G275900 chr7A 80.385 520 90 7 2238 2754 380523698 380523188 4.300000e-103 385
14 TraesCS1B01G275900 chr7A 75.466 322 66 10 65 379 62553242 62553557 7.950000e-31 145
15 TraesCS1B01G275900 chr5D 80.998 521 87 8 2238 2753 103633016 103632503 1.190000e-108 403
16 TraesCS1B01G275900 chr5D 80.497 523 85 14 2238 2754 317758594 317759105 4.300000e-103 385
17 TraesCS1B01G275900 chr3D 80.962 520 89 6 2238 2754 253741871 253741359 1.190000e-108 403
18 TraesCS1B01G275900 chr7D 80.190 525 93 7 2234 2754 321978684 321979201 1.550000e-102 383
19 TraesCS1B01G275900 chr4D 82.327 447 68 11 2314 2754 136484191 136484632 7.200000e-101 377
20 TraesCS1B01G275900 chr5B 77.841 352 59 13 52 392 670301600 670301257 1.670000e-47 200
21 TraesCS1B01G275900 chr5B 86.076 158 16 6 65 220 657274633 657274786 6.100000e-37 165
22 TraesCS1B01G275900 chr6B 79.801 302 38 18 15 307 689992141 689992428 6.020000e-47 198
23 TraesCS1B01G275900 chr5A 76.829 328 52 20 61 379 491100622 491100310 2.190000e-36 163
24 TraesCS1B01G275900 chr7B 81.347 193 30 6 26 215 23268206 23268395 4.750000e-33 152
25 TraesCS1B01G275900 chr2D 77.186 263 42 16 39 287 14345241 14344983 1.330000e-28 137


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 TraesCS1B01G275900 chr1B 483460763 483463516 2753 True 5086.00 5086 100.0000 1 2754 1 chr1B.!!$R1 2753
1 TraesCS1B01G275900 chr1B 253766711 253767230 519 False 398.00 398 80.7620 2238 2754 1 chr1B.!!$F1 516
2 TraesCS1B01G275900 chr1D 361127418 361129792 2374 True 758.50 1899 91.9850 1 2181 4 chr1D.!!$R1 2180
3 TraesCS1B01G275900 chr1A 460844091 460847214 3123 True 733.75 1430 89.3765 1 2182 4 chr1A.!!$R1 2181
4 TraesCS1B01G275900 chr7A 380523188 380523698 510 True 385.00 385 80.3850 2238 2754 1 chr7A.!!$R2 516
5 TraesCS1B01G275900 chr5D 103632503 103633016 513 True 403.00 403 80.9980 2238 2753 1 chr5D.!!$R1 515
6 TraesCS1B01G275900 chr5D 317758594 317759105 511 False 385.00 385 80.4970 2238 2754 1 chr5D.!!$F1 516
7 TraesCS1B01G275900 chr3D 253741359 253741871 512 True 403.00 403 80.9620 2238 2754 1 chr3D.!!$R1 516
8 TraesCS1B01G275900 chr7D 321978684 321979201 517 False 383.00 383 80.1900 2234 2754 1 chr7D.!!$F1 520

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
853 948 0.734253 CGAGTCCCACTTTCTCAGCG 60.734 60.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2649 3774 0.035317 AGCTTCTGGTCATGACGCAA 59.965 50.0 19.33 10.49 32.17 4.85 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
532 626 5.532406 TCTTGAAGGGTCAGTTGATTTTCTG 59.468 40.000 0.00 0.00 34.49 3.02
554 648 3.706086 GGTCCCGTTTATACTGGGAAGTA 59.294 47.826 14.16 0.00 43.69 2.24
557 651 5.303845 GTCCCGTTTATACTGGGAAGTAGAT 59.696 44.000 14.16 0.00 43.69 1.98
561 655 7.226128 CCCGTTTATACTGGGAAGTAGATTTTC 59.774 40.741 7.21 0.00 39.17 2.29
583 678 1.730851 GTCCCCTAATTCCCGATCCT 58.269 55.000 0.00 0.00 0.00 3.24
637 732 1.966451 CGGGACCAAGCACACCTTC 60.966 63.158 0.00 0.00 0.00 3.46
638 733 1.150536 GGGACCAAGCACACCTTCA 59.849 57.895 0.00 0.00 0.00 3.02
705 800 4.162690 GCCGCCTTCGTGAGGGAT 62.163 66.667 1.67 0.00 46.40 3.85
709 804 1.450312 GCCTTCGTGAGGGATGGTG 60.450 63.158 1.67 0.00 46.40 4.17
799 894 1.634702 GCTCTACCTCTTCAAGTGCG 58.365 55.000 0.00 0.00 0.00 5.34
841 936 1.000385 CAGATGCAGATCTCGAGTCCC 60.000 57.143 13.13 2.94 36.75 4.46
853 948 0.734253 CGAGTCCCACTTTCTCAGCG 60.734 60.000 0.00 0.00 0.00 5.18
922 1017 2.777972 CCGAGCGATTACCACCGGA 61.778 63.158 9.46 0.00 39.31 5.14
975 1070 1.721664 CCGTCGGATCAGCGACCTAA 61.722 60.000 4.91 0.00 32.11 2.69
1043 1138 1.849976 GAGCAGCAGAAGCACCACAC 61.850 60.000 0.00 0.00 45.49 3.82
1146 1242 2.108566 CTGCTGCTCCTGATCGGG 59.891 66.667 15.09 15.09 0.00 5.14
1222 1318 3.686726 GCTCTTGGAATTCGTCTGTTCAT 59.313 43.478 0.00 0.00 0.00 2.57
1339 1435 1.877576 GCTTTACTTGGCAGGGGTGC 61.878 60.000 0.44 0.00 0.00 5.01
1342 1438 3.567579 TACTTGGCAGGGGTGCTGC 62.568 63.158 0.44 0.00 46.20 5.25
1429 1525 3.127533 GTGTGGTGGATGCGAGCC 61.128 66.667 0.00 0.00 0.00 4.70
1431 1527 1.987306 TGTGGTGGATGCGAGCCTA 60.987 57.895 0.00 0.00 0.00 3.93
1441 1537 1.289109 TGCGAGCCTAACGTTCTTGC 61.289 55.000 16.87 16.87 37.66 4.01
1445 2418 0.955919 AGCCTAACGTTCTTGCTGCC 60.956 55.000 15.65 0.00 0.00 4.85
1473 2446 0.472734 AGGAGGTGCTCTCTGTTGGT 60.473 55.000 7.40 0.00 42.10 3.67
1485 2458 0.802494 CTGTTGGTAATGTGACCGGC 59.198 55.000 0.00 0.00 42.99 6.13
1509 2482 4.742201 TTCGCGTGCAGGGAGAGC 62.742 66.667 5.77 0.00 42.94 4.09
1592 2571 4.680171 GCTTATTGCGTTTCTACCTTGT 57.320 40.909 0.00 0.00 0.00 3.16
1660 2642 3.114065 GACCTCCATTCGATCGTTGTAC 58.886 50.000 15.94 0.00 0.00 2.90
1705 2702 2.435372 TGGAGGTAAATGCACCATCC 57.565 50.000 0.00 0.00 41.40 3.51
1720 2717 1.608590 CCATCCGTGCTTGAACTTGTT 59.391 47.619 0.00 0.00 0.00 2.83
1730 2727 6.623549 CGTGCTTGAACTTGTTATGGATGATT 60.624 38.462 0.00 0.00 0.00 2.57
1742 2739 7.715657 TGTTATGGATGATTATTTTGGTGCTC 58.284 34.615 0.00 0.00 0.00 4.26
1797 2794 3.259876 ACTTGGCTCTTACGACCAATACA 59.740 43.478 0.00 0.00 42.35 2.29
1798 2795 3.520290 TGGCTCTTACGACCAATACAG 57.480 47.619 0.00 0.00 0.00 2.74
1847 2954 3.274288 GGCACTGTATTTCCTTCTGAGG 58.726 50.000 0.00 0.00 45.02 3.86
1854 2961 5.794894 TGTATTTCCTTCTGAGGTGAAGTC 58.205 41.667 0.00 0.00 43.97 3.01
1861 2968 0.244994 CTGAGGTGAAGTCTGTCCCG 59.755 60.000 0.00 0.00 0.00 5.14
1883 2990 3.022406 GTGACGACCTAACTCACCCTAT 58.978 50.000 0.00 0.00 0.00 2.57
1884 2991 3.066481 GTGACGACCTAACTCACCCTATC 59.934 52.174 0.00 0.00 0.00 2.08
1897 3004 6.807789 ACTCACCCTATCGAGAGTTTTTATC 58.192 40.000 6.28 0.00 38.08 1.75
1932 3039 2.811431 CAAACGCTACCCACATGAAAGA 59.189 45.455 0.00 0.00 0.00 2.52
1945 3052 5.504665 CCACATGAAAGAAGAAGTGTGACAC 60.505 44.000 7.83 7.83 39.30 3.67
1977 3084 3.649981 AGCTAGAATCATACCATGTGCCT 59.350 43.478 0.00 0.00 0.00 4.75
1980 3087 6.669591 AGCTAGAATCATACCATGTGCCTATA 59.330 38.462 0.00 0.00 0.00 1.31
2007 3114 5.978814 TCCTTCGGAGAAGATTTAAGGAAG 58.021 41.667 11.00 0.00 45.90 3.46
2015 3122 6.715264 GGAGAAGATTTAAGGAAGAAACCACA 59.285 38.462 0.00 0.00 0.00 4.17
2036 3143 2.443255 AGACCAAGGGTTCATGAACTGT 59.557 45.455 31.81 21.80 40.94 3.55
2051 3158 6.705381 TCATGAACTGTAATTTTTGCCCAAAG 59.295 34.615 0.00 0.00 0.00 2.77
2063 3173 1.202879 TGCCCAAAGACGATGTTTCCT 60.203 47.619 0.00 0.00 0.00 3.36
2072 3182 3.499918 AGACGATGTTTCCTTTCTGCAAG 59.500 43.478 0.00 0.00 0.00 4.01
2167 3278 6.267699 TGATCTTTTATCTAGCGGAAGATCCA 59.732 38.462 21.71 13.87 46.06 3.41
2168 3279 6.672266 TCTTTTATCTAGCGGAAGATCCAT 57.328 37.500 3.00 0.00 37.41 3.41
2182 3293 5.163152 GGAAGATCCATCACTCTAACCCAAT 60.163 44.000 0.00 0.00 36.28 3.16
2183 3294 5.983333 AGATCCATCACTCTAACCCAATT 57.017 39.130 0.00 0.00 0.00 2.32
2184 3295 6.332976 AGATCCATCACTCTAACCCAATTT 57.667 37.500 0.00 0.00 0.00 1.82
2185 3296 6.735556 AGATCCATCACTCTAACCCAATTTT 58.264 36.000 0.00 0.00 0.00 1.82
2186 3297 7.184862 AGATCCATCACTCTAACCCAATTTTT 58.815 34.615 0.00 0.00 0.00 1.94
2187 3298 8.336235 AGATCCATCACTCTAACCCAATTTTTA 58.664 33.333 0.00 0.00 0.00 1.52
2188 3299 7.938140 TCCATCACTCTAACCCAATTTTTAG 57.062 36.000 0.00 0.00 0.00 1.85
2189 3300 6.889722 TCCATCACTCTAACCCAATTTTTAGG 59.110 38.462 0.00 0.00 0.00 2.69
2197 3308 2.723273 CCCAATTTTTAGGGCTCGTCT 58.277 47.619 0.00 0.00 38.44 4.18
2198 3309 3.881220 CCCAATTTTTAGGGCTCGTCTA 58.119 45.455 0.00 0.00 38.44 2.59
2199 3310 4.461198 CCCAATTTTTAGGGCTCGTCTAT 58.539 43.478 0.00 0.00 38.44 1.98
2200 3311 4.275936 CCCAATTTTTAGGGCTCGTCTATG 59.724 45.833 0.00 0.00 38.44 2.23
2201 3312 5.123227 CCAATTTTTAGGGCTCGTCTATGA 58.877 41.667 0.00 0.00 0.00 2.15
2202 3313 5.007724 CCAATTTTTAGGGCTCGTCTATGAC 59.992 44.000 0.00 0.00 0.00 3.06
2219 3330 7.852516 GTCTATGACGATTAAACCAAATCTCC 58.147 38.462 0.00 0.00 34.34 3.71
2220 3331 7.494625 GTCTATGACGATTAAACCAAATCTCCA 59.505 37.037 0.00 0.00 34.34 3.86
2221 3332 6.683974 ATGACGATTAAACCAAATCTCCAG 57.316 37.500 0.00 0.00 34.34 3.86
2222 3333 5.800296 TGACGATTAAACCAAATCTCCAGA 58.200 37.500 0.00 0.00 34.34 3.86
2223 3334 5.874810 TGACGATTAAACCAAATCTCCAGAG 59.125 40.000 0.00 0.00 34.34 3.35
2224 3335 6.049955 ACGATTAAACCAAATCTCCAGAGA 57.950 37.500 0.00 0.00 42.37 3.10
2225 3336 5.875359 ACGATTAAACCAAATCTCCAGAGAC 59.125 40.000 0.00 0.00 40.75 3.36
2226 3337 6.109359 CGATTAAACCAAATCTCCAGAGACT 58.891 40.000 0.00 0.00 40.75 3.24
2227 3338 6.595716 CGATTAAACCAAATCTCCAGAGACTT 59.404 38.462 0.00 0.00 40.75 3.01
2228 3339 7.119846 CGATTAAACCAAATCTCCAGAGACTTT 59.880 37.037 0.00 0.31 40.75 2.66
2229 3340 7.745620 TTAAACCAAATCTCCAGAGACTTTC 57.254 36.000 0.00 0.00 40.75 2.62
2230 3341 4.293662 ACCAAATCTCCAGAGACTTTCC 57.706 45.455 0.00 0.00 40.75 3.13
2231 3342 3.913163 ACCAAATCTCCAGAGACTTTCCT 59.087 43.478 0.00 0.00 40.75 3.36
2232 3343 4.019771 ACCAAATCTCCAGAGACTTTCCTC 60.020 45.833 0.00 0.00 40.75 3.71
2233 3344 4.224818 CCAAATCTCCAGAGACTTTCCTCT 59.775 45.833 0.00 0.00 43.84 3.69
2234 3345 5.280419 CCAAATCTCCAGAGACTTTCCTCTT 60.280 44.000 0.00 0.00 41.29 2.85
2235 3346 6.237154 CAAATCTCCAGAGACTTTCCTCTTT 58.763 40.000 0.00 0.00 41.29 2.52
2236 3347 4.881019 TCTCCAGAGACTTTCCTCTTTG 57.119 45.455 0.00 0.00 41.29 2.77
2249 3360 2.565391 TCCTCTTTGTGTCGGCATTCTA 59.435 45.455 0.00 0.00 0.00 2.10
2253 3364 2.380084 TTGTGTCGGCATTCTAGGAC 57.620 50.000 0.00 0.00 0.00 3.85
2259 3370 1.107538 CGGCATTCTAGGACTCGGGA 61.108 60.000 0.00 0.00 0.00 5.14
2329 3440 4.587189 GCCTAGTACGGCCCAGCG 62.587 72.222 0.00 0.00 44.41 5.18
2333 3451 2.337749 CTAGTACGGCCCAGCGACAG 62.338 65.000 0.00 0.00 0.00 3.51
2358 3476 1.738099 CAAGACAAGACCCTCGCGG 60.738 63.158 6.13 0.00 37.81 6.46
2386 3506 3.425578 CTCGCGAGGAGAACAACAT 57.574 52.632 28.40 0.00 46.23 2.71
2397 3517 3.244561 GGAGAACAACATCAAGACCTCCA 60.245 47.826 0.00 0.00 38.91 3.86
2521 3646 0.318275 CGCGGCAGAGGAGATAGTTC 60.318 60.000 0.00 0.00 0.00 3.01
2529 3654 4.409247 GCAGAGGAGATAGTTCCCCTTTTA 59.591 45.833 0.00 0.00 38.02 1.52
2548 3673 5.514500 TTTAGTGCTAAGGGAACAAGGAT 57.486 39.130 0.00 0.00 0.00 3.24
2561 3686 0.036010 CAAGGATGGACGCAGGTTCT 60.036 55.000 0.00 0.00 0.00 3.01
2569 3694 0.456995 GACGCAGGTTCTCGAGGAAG 60.457 60.000 13.56 0.00 34.23 3.46
2570 3695 1.153745 CGCAGGTTCTCGAGGAAGG 60.154 63.158 13.56 0.00 34.23 3.46
2592 3717 1.276138 CCCAAAGGTTTCCATTCTGGC 59.724 52.381 0.00 0.00 37.47 4.85
2599 3724 1.861542 TTTCCATTCTGGCGCAACGG 61.862 55.000 10.83 0.00 37.47 4.44
2643 3768 4.148825 GGGTGTCATCGCCGAGCT 62.149 66.667 0.00 0.00 44.47 4.09
2649 3774 4.498520 CATCGCCGAGCTCACCGT 62.499 66.667 15.40 3.81 0.00 4.83
2657 3782 1.738099 GAGCTCACCGTTGCGTCAT 60.738 57.895 9.40 0.00 0.00 3.06
2710 3835 8.537858 ACCTTTCGTTAGGATTAGATGTACTTT 58.462 33.333 11.63 0.00 38.73 2.66
2726 3851 5.968254 TGTACTTTTTGTCCCCTTTCAAAC 58.032 37.500 0.00 0.00 34.05 2.93
2728 3853 6.890814 TGTACTTTTTGTCCCCTTTCAAACTA 59.109 34.615 0.00 0.00 34.05 2.24
2730 3855 6.192044 ACTTTTTGTCCCCTTTCAAACTAGA 58.808 36.000 0.00 0.00 34.05 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 104 5.683876 AGTATTGTTCAGCCTACATCACT 57.316 39.130 0.00 0.00 0.00 3.41
380 404 5.917447 GCTGTTTCATCTCTTTTCTGTTTCC 59.083 40.000 0.00 0.00 0.00 3.13
387 411 4.377841 CGTGAGGCTGTTTCATCTCTTTTC 60.378 45.833 0.00 0.00 0.00 2.29
532 626 2.502947 ACTTCCCAGTATAAACGGGACC 59.497 50.000 4.85 0.00 43.54 4.46
583 678 3.770040 CATGGCCGTCGTCTCCCA 61.770 66.667 0.00 0.00 0.00 4.37
589 684 1.066430 ACACTTTATCATGGCCGTCGT 60.066 47.619 0.00 0.00 0.00 4.34
637 732 1.536766 TGGCAAAGCTTCAAGATCGTG 59.463 47.619 0.00 1.76 0.00 4.35
638 733 1.808945 CTGGCAAAGCTTCAAGATCGT 59.191 47.619 0.00 0.00 0.00 3.73
697 792 0.329596 AGAAAGGCACCATCCCTCAC 59.670 55.000 0.00 0.00 0.00 3.51
841 936 2.171940 GTGCGCGCTGAGAAAGTG 59.828 61.111 33.29 0.00 39.57 3.16
853 948 2.703409 GATGTCCATGTCGTGCGC 59.297 61.111 0.00 0.00 0.00 6.09
1043 1138 4.120755 GCAGGAAGGAGGGCAGGG 62.121 72.222 0.00 0.00 0.00 4.45
1140 1236 1.884926 CTCAAGCGCTTCCCCGATC 60.885 63.158 22.21 0.00 0.00 3.69
1141 1237 1.690219 ATCTCAAGCGCTTCCCCGAT 61.690 55.000 22.21 15.66 0.00 4.18
1146 1242 0.307146 GATGCATCTCAAGCGCTTCC 59.693 55.000 22.21 5.17 33.85 3.46
1342 1438 3.126514 AGCAAAATCGCTGTTCTGATCAG 59.873 43.478 17.07 17.07 41.85 2.90
1429 1525 1.873591 ACTTGGCAGCAAGAACGTTAG 59.126 47.619 0.00 0.00 36.16 2.34
1431 1527 0.381801 CACTTGGCAGCAAGAACGTT 59.618 50.000 0.00 0.00 36.16 3.99
1445 2418 0.595095 GAGCACCTCCTTTGCACTTG 59.405 55.000 0.00 0.00 42.83 3.16
1473 2446 3.065786 CGAAGTAGTAGCCGGTCACATTA 59.934 47.826 1.90 0.00 0.00 1.90
1485 2458 0.525668 CCCTGCACGCGAAGTAGTAG 60.526 60.000 15.93 5.78 0.00 2.57
1509 2482 0.248825 CGTCCTTCTCCTGCTCATCG 60.249 60.000 0.00 0.00 0.00 3.84
1592 2571 9.777297 ACCAAGGTAGAAACGTAATAAACTTAA 57.223 29.630 0.00 0.00 0.00 1.85
1625 2604 6.428771 CGAATGGAGGTCCTTTACTAAAAACA 59.571 38.462 0.00 0.00 34.04 2.83
1641 2623 2.159156 TGGTACAACGATCGAATGGAGG 60.159 50.000 24.34 5.10 31.92 4.30
1686 2683 1.408127 CGGATGGTGCATTTACCTCCA 60.408 52.381 0.00 0.00 41.43 3.86
1705 2702 4.154015 TCATCCATAACAAGTTCAAGCACG 59.846 41.667 0.00 0.00 0.00 5.34
1720 2717 5.048782 GCGAGCACCAAAATAATCATCCATA 60.049 40.000 0.00 0.00 0.00 2.74
1730 2727 0.519519 CAACCGCGAGCACCAAAATA 59.480 50.000 8.23 0.00 0.00 1.40
1742 2739 5.788531 CACTTTTCTTTATTCTACAACCGCG 59.211 40.000 0.00 0.00 0.00 6.46
1797 2794 5.536161 AGGCAACATATGACAAGAACAAACT 59.464 36.000 10.38 0.00 40.75 2.66
1798 2795 5.772521 AGGCAACATATGACAAGAACAAAC 58.227 37.500 10.38 0.00 40.75 2.93
1847 2954 0.319641 GTCACCGGGACAGACTTCAC 60.320 60.000 6.32 0.00 46.19 3.18
1911 3018 2.811431 TCTTTCATGTGGGTAGCGTTTG 59.189 45.455 0.00 0.00 0.00 2.93
1945 3052 9.941325 ATGGTATGATTCTAGCTATGAGAAAAG 57.059 33.333 1.64 0.00 36.54 2.27
2007 3114 1.954382 GAACCCTTGGTCTGTGGTTTC 59.046 52.381 0.00 0.00 41.03 2.78
2015 3122 2.443255 ACAGTTCATGAACCCTTGGTCT 59.557 45.455 30.34 10.47 42.06 3.85
2036 3143 5.461032 ACATCGTCTTTGGGCAAAAATTA 57.539 34.783 0.00 0.00 0.00 1.40
2051 3158 3.814945 CTTGCAGAAAGGAAACATCGTC 58.185 45.455 0.00 0.00 31.68 4.20
2063 3173 2.821969 GAGAAAGATGGGCTTGCAGAAA 59.178 45.455 0.00 0.00 36.80 2.52
2072 3182 0.036388 TGACGTGGAGAAAGATGGGC 60.036 55.000 0.00 0.00 0.00 5.36
2167 3278 5.656859 GCCCTAAAAATTGGGTTAGAGTGAT 59.343 40.000 0.00 0.00 45.06 3.06
2168 3279 5.014202 GCCCTAAAAATTGGGTTAGAGTGA 58.986 41.667 0.00 0.00 45.06 3.41
2194 3305 7.494625 TGGAGATTTGGTTTAATCGTCATAGAC 59.505 37.037 0.00 0.00 39.09 2.59
2195 3306 7.561251 TGGAGATTTGGTTTAATCGTCATAGA 58.439 34.615 0.00 0.00 39.09 1.98
2196 3307 7.710907 TCTGGAGATTTGGTTTAATCGTCATAG 59.289 37.037 0.00 0.00 39.09 2.23
2197 3308 7.561251 TCTGGAGATTTGGTTTAATCGTCATA 58.439 34.615 0.00 0.00 39.09 2.15
2198 3309 6.414732 TCTGGAGATTTGGTTTAATCGTCAT 58.585 36.000 0.00 0.00 39.09 3.06
2199 3310 5.800296 TCTGGAGATTTGGTTTAATCGTCA 58.200 37.500 0.00 0.00 39.09 4.35
2200 3311 6.036191 GTCTCTGGAGATTTGGTTTAATCGTC 59.964 42.308 3.52 0.00 39.97 4.20
2201 3312 5.875359 GTCTCTGGAGATTTGGTTTAATCGT 59.125 40.000 3.52 0.00 39.97 3.73
2202 3313 6.109359 AGTCTCTGGAGATTTGGTTTAATCG 58.891 40.000 3.52 0.00 39.97 3.34
2203 3314 7.929941 AAGTCTCTGGAGATTTGGTTTAATC 57.070 36.000 7.41 0.00 39.97 1.75
2204 3315 7.394641 GGAAAGTCTCTGGAGATTTGGTTTAAT 59.605 37.037 8.68 0.00 37.44 1.40
2205 3316 6.715264 GGAAAGTCTCTGGAGATTTGGTTTAA 59.285 38.462 8.68 0.00 37.44 1.52
2206 3317 6.044404 AGGAAAGTCTCTGGAGATTTGGTTTA 59.956 38.462 8.68 0.00 37.44 2.01
2207 3318 5.073428 GGAAAGTCTCTGGAGATTTGGTTT 58.927 41.667 8.68 3.17 37.44 3.27
2208 3319 4.352298 AGGAAAGTCTCTGGAGATTTGGTT 59.648 41.667 8.68 0.00 37.44 3.67
2209 3320 3.913163 AGGAAAGTCTCTGGAGATTTGGT 59.087 43.478 8.68 0.00 37.44 3.67
2210 3321 4.224818 AGAGGAAAGTCTCTGGAGATTTGG 59.775 45.833 8.68 0.00 42.05 3.28
2211 3322 5.419239 AGAGGAAAGTCTCTGGAGATTTG 57.581 43.478 8.68 0.00 42.05 2.32
2212 3323 6.183361 ACAAAGAGGAAAGTCTCTGGAGATTT 60.183 38.462 3.52 3.30 42.75 2.17
2213 3324 5.309282 ACAAAGAGGAAAGTCTCTGGAGATT 59.691 40.000 3.52 0.00 42.75 2.40
2214 3325 4.843516 ACAAAGAGGAAAGTCTCTGGAGAT 59.156 41.667 3.52 0.00 42.75 2.75
2215 3326 4.039730 CACAAAGAGGAAAGTCTCTGGAGA 59.960 45.833 0.00 0.00 42.75 3.71
2216 3327 4.202305 ACACAAAGAGGAAAGTCTCTGGAG 60.202 45.833 0.00 0.00 42.75 3.86
2217 3328 3.711704 ACACAAAGAGGAAAGTCTCTGGA 59.288 43.478 0.00 0.00 42.75 3.86
2218 3329 4.061596 GACACAAAGAGGAAAGTCTCTGG 58.938 47.826 0.00 0.00 42.75 3.86
2219 3330 3.738282 CGACACAAAGAGGAAAGTCTCTG 59.262 47.826 0.00 0.00 42.75 3.35
2220 3331 3.243907 CCGACACAAAGAGGAAAGTCTCT 60.244 47.826 0.00 0.00 45.22 3.10
2221 3332 3.060602 CCGACACAAAGAGGAAAGTCTC 58.939 50.000 0.00 0.00 0.00 3.36
2222 3333 2.807108 GCCGACACAAAGAGGAAAGTCT 60.807 50.000 0.00 0.00 0.00 3.24
2223 3334 1.531578 GCCGACACAAAGAGGAAAGTC 59.468 52.381 0.00 0.00 0.00 3.01
2224 3335 1.134220 TGCCGACACAAAGAGGAAAGT 60.134 47.619 0.00 0.00 0.00 2.66
2225 3336 1.593196 TGCCGACACAAAGAGGAAAG 58.407 50.000 0.00 0.00 0.00 2.62
2226 3337 2.270352 ATGCCGACACAAAGAGGAAA 57.730 45.000 0.00 0.00 0.00 3.13
2227 3338 2.151202 GAATGCCGACACAAAGAGGAA 58.849 47.619 0.00 0.00 0.00 3.36
2228 3339 1.347707 AGAATGCCGACACAAAGAGGA 59.652 47.619 0.00 0.00 0.00 3.71
2229 3340 1.813513 AGAATGCCGACACAAAGAGG 58.186 50.000 0.00 0.00 0.00 3.69
2230 3341 2.932614 CCTAGAATGCCGACACAAAGAG 59.067 50.000 0.00 0.00 0.00 2.85
2231 3342 2.565391 TCCTAGAATGCCGACACAAAGA 59.435 45.455 0.00 0.00 0.00 2.52
2232 3343 2.673368 GTCCTAGAATGCCGACACAAAG 59.327 50.000 0.00 0.00 0.00 2.77
2233 3344 2.301870 AGTCCTAGAATGCCGACACAAA 59.698 45.455 0.00 0.00 0.00 2.83
2234 3345 1.899814 AGTCCTAGAATGCCGACACAA 59.100 47.619 0.00 0.00 0.00 3.33
2235 3346 1.476891 GAGTCCTAGAATGCCGACACA 59.523 52.381 0.00 0.00 0.00 3.72
2236 3347 1.534175 CGAGTCCTAGAATGCCGACAC 60.534 57.143 0.00 0.00 0.00 3.67
2259 3370 1.073444 CATGCAGGCTGATCTGGGTAT 59.927 52.381 20.86 0.00 35.43 2.73
2303 3414 2.487532 CGTACTAGGCTGTCGGGGG 61.488 68.421 0.00 0.00 0.00 5.40
2304 3415 2.487532 CCGTACTAGGCTGTCGGGG 61.488 68.421 0.00 0.00 37.92 5.73
2329 3440 0.322008 CTTGTCTTGGAGGCCCTGTC 60.322 60.000 0.00 0.00 0.00 3.51
2333 3451 1.002011 GGTCTTGTCTTGGAGGCCC 60.002 63.158 0.00 0.00 31.37 5.80
2338 3456 1.671742 GCGAGGGTCTTGTCTTGGA 59.328 57.895 0.00 0.00 0.00 3.53
2377 3497 3.648067 TCTGGAGGTCTTGATGTTGTTCT 59.352 43.478 0.00 0.00 0.00 3.01
2471 3593 0.246360 TCGTCATGGCTCACGTCATT 59.754 50.000 0.00 0.00 31.91 2.57
2504 3626 0.676736 GGGAACTATCTCCTCTGCCG 59.323 60.000 0.00 0.00 35.63 5.69
2529 3654 2.025887 CCATCCTTGTTCCCTTAGCACT 60.026 50.000 0.00 0.00 0.00 4.40
2541 3666 0.321653 GAACCTGCGTCCATCCTTGT 60.322 55.000 0.00 0.00 0.00 3.16
2548 3673 2.636412 CCTCGAGAACCTGCGTCCA 61.636 63.158 15.71 0.00 0.00 4.02
2561 3686 2.602676 CCTTTGGGGCCTTCCTCGA 61.603 63.158 0.84 0.00 34.77 4.04
2569 3694 0.613260 GAATGGAAACCTTTGGGGCC 59.387 55.000 0.00 0.00 39.10 5.80
2570 3695 1.276138 CAGAATGGAAACCTTTGGGGC 59.724 52.381 0.00 0.00 39.10 5.80
2592 3717 3.047877 GGTCTTGGTCCCGTTGCG 61.048 66.667 0.00 0.00 0.00 4.85
2599 3724 1.079750 GAGCTCGTGGTCTTGGTCC 60.080 63.158 9.30 0.00 37.68 4.46
2628 3753 2.161486 GTGAGCTCGGCGATGACAC 61.161 63.158 11.27 16.21 0.00 3.67
2643 3768 1.666553 GGTCATGACGCAACGGTGA 60.667 57.895 19.33 0.00 0.00 4.02
2649 3774 0.035317 AGCTTCTGGTCATGACGCAA 59.965 50.000 19.33 10.49 32.17 4.85
2657 3782 1.174712 GCCTGCAAAGCTTCTGGTCA 61.175 55.000 0.00 0.00 0.00 4.02
2710 3835 5.118729 TGTCTAGTTTGAAAGGGGACAAA 57.881 39.130 4.94 0.00 34.33 2.83
2726 3851 3.181450 GGAAGGGATCCCACAATGTCTAG 60.181 52.174 32.69 0.00 43.00 2.43
2728 3853 1.566231 GGAAGGGATCCCACAATGTCT 59.434 52.381 32.69 6.30 43.00 3.41


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

AutoCloner maintained by Alex Coulton.