Multiple sequence alignment - TraesCS1D01G102600

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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 TraesCS1D01G102600 chr1D 100.000 4100 0 0 1 4100 91229813 91233912 0.000000e+00 7572.0
1 TraesCS1D01G102600 chr1D 82.955 176 30 0 340 515 455126665 455126490 4.240000e-35 159.0
2 TraesCS1D01G102600 chr1A 96.610 3392 68 19 726 4100 87198054 87201415 0.000000e+00 5583.0
3 TraesCS1D01G102600 chr1B 97.732 1587 33 2 1695 3278 145718939 145720525 0.000000e+00 2728.0
4 TraesCS1D01G102600 chr1B 97.694 1084 24 1 627 1709 145717842 145718925 0.000000e+00 1862.0
5 TraesCS1D01G102600 chr1B 96.031 655 13 3 3295 3949 145720901 145721542 0.000000e+00 1053.0
6 TraesCS1D01G102600 chr1B 94.366 426 15 6 1 426 145714153 145714569 0.000000e+00 645.0
7 TraesCS1D01G102600 chr2D 84.639 319 31 10 3 320 643815178 643815479 6.660000e-78 302.0
8 TraesCS1D01G102600 chr5A 92.638 163 11 1 1 163 503932888 503932727 2.460000e-57 233.0
9 TraesCS1D01G102600 chr5A 85.833 120 12 3 46 163 503929093 503928977 5.570000e-24 122.0
10 TraesCS1D01G102600 chr5D 90.798 163 14 1 1 163 398868819 398868658 2.480000e-52 217.0
11 TraesCS1D01G102600 chr6B 79.233 313 32 13 170 458 123019886 123019583 1.950000e-43 187.0
12 TraesCS1D01G102600 chr6B 86.093 151 19 2 366 515 548954023 548953874 1.180000e-35 161.0
13 TraesCS1D01G102600 chr6B 86.093 151 19 2 366 515 549034543 549034394 1.180000e-35 161.0
14 TraesCS1D01G102600 chr6B 88.525 61 7 0 730 790 226364953 226365013 1.580000e-09 75.0
15 TraesCS1D01G102600 chr7B 86.093 151 19 2 366 515 69854974 69854825 1.180000e-35 161.0
16 TraesCS1D01G102600 chr7B 86.093 151 19 2 366 515 69921489 69921340 1.180000e-35 161.0
17 TraesCS1D01G102600 chr7B 84.906 159 22 2 358 515 70353308 70353151 4.240000e-35 159.0
18 TraesCS1D01G102600 chr7B 84.314 153 18 4 366 515 69998133 69997984 1.190000e-30 145.0
19 TraesCS1D01G102600 chr4A 88.710 124 10 2 338 457 526555970 526555847 9.180000e-32 148.0
20 TraesCS1D01G102600 chr4D 82.022 178 23 3 165 341 154933732 154933901 4.270000e-30 143.0
21 TraesCS1D01G102600 chr5B 91.262 103 6 3 62 163 479036322 479036222 1.990000e-28 137.0
22 TraesCS1D01G102600 chr5B 86.555 119 13 3 46 163 479032171 479032055 1.200000e-25 128.0
23 TraesCS1D01G102600 chr6D 84.848 99 12 2 410 508 441541154 441541059 3.370000e-16 97.1
24 TraesCS1D01G102600 chr6D 84.270 89 8 4 707 790 127199067 127199154 9.450000e-12 82.4


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 TraesCS1D01G102600 chr1D 91229813 91233912 4099 False 7572 7572 100.00000 1 4100 1 chr1D.!!$F1 4099
1 TraesCS1D01G102600 chr1A 87198054 87201415 3361 False 5583 5583 96.61000 726 4100 1 chr1A.!!$F1 3374
2 TraesCS1D01G102600 chr1B 145714153 145721542 7389 False 1572 2728 96.45575 1 3949 4 chr1B.!!$F1 3948

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
513 2421 0.036388 ATGAACGCAACGGGTCATCT 60.036 50.0 3.49 0.00 32.94 2.90 F
514 2422 0.604073 TGAACGCAACGGGTCATCTA 59.396 50.0 0.00 0.00 0.00 1.98 F
1317 4420 1.019278 CACGCAACCGCTACATCCTT 61.019 55.0 0.00 0.00 38.22 3.36 F
2997 6138 1.021390 CATGTTCCCAGTGGAGCGAC 61.021 60.0 11.95 4.06 44.36 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 5386 1.670811 GGAACATACGACAAGGCATGG 59.329 52.381 0.00 0.00 0.00 3.66 R
2380 5521 2.985139 GCACTTTTTCAGATCTGCAAGC 59.015 45.455 18.36 9.31 0.00 4.01 R
3066 6207 0.174162 ATTTTGCGCCAGAATCTGCC 59.826 50.000 4.18 0.00 0.00 4.85 R
3980 7480 0.036577 CAGCCTCAGAACTGTCCCAG 60.037 60.000 1.73 0.00 37.52 4.45 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
35 36 4.812626 CCTTGTTGCAAGCTTGAGAAAATT 59.187 37.500 30.39 0.00 0.00 1.82
98 99 1.202867 TGTTGCAGGCATACAACCTCA 60.203 47.619 11.67 0.00 44.38 3.86
106 107 2.679837 GGCATACAACCTCATGTCACAG 59.320 50.000 0.00 0.00 34.75 3.66
129 130 3.895656 TCTACCACTTTGGATATCCCTCG 59.104 47.826 19.34 9.20 40.96 4.63
134 135 2.330216 CTTTGGATATCCCTCGGTCCT 58.670 52.381 19.34 0.00 35.38 3.85
136 137 2.489528 TGGATATCCCTCGGTCCTTT 57.510 50.000 19.34 0.00 35.38 3.11
202 203 7.538678 AGTTGCTTAAACGATGAAATCATGTTC 59.461 33.333 0.00 0.00 45.97 3.18
213 214 7.095899 CGATGAAATCATGTTCGATACTGATGT 60.096 37.037 0.00 0.86 45.97 3.06
319 320 5.793030 AGGTTAAGAGACAAGCGCTATAT 57.207 39.130 12.05 0.00 0.00 0.86
325 326 5.966742 AGAGACAAGCGCTATATATGTGA 57.033 39.130 15.95 0.00 0.00 3.58
326 327 6.522625 AGAGACAAGCGCTATATATGTGAT 57.477 37.500 15.95 5.00 0.00 3.06
350 351 4.994220 GCATCTCTGCTATCATCAAGTG 57.006 45.455 0.00 0.00 45.32 3.16
351 352 4.629092 GCATCTCTGCTATCATCAAGTGA 58.371 43.478 0.00 0.00 45.32 3.41
353 354 5.050227 GCATCTCTGCTATCATCAAGTGAAC 60.050 44.000 0.00 0.00 45.32 3.18
354 355 5.929058 TCTCTGCTATCATCAAGTGAACT 57.071 39.130 0.00 0.00 40.97 3.01
355 356 5.900425 TCTCTGCTATCATCAAGTGAACTC 58.100 41.667 0.00 0.00 40.97 3.01
356 357 5.420104 TCTCTGCTATCATCAAGTGAACTCA 59.580 40.000 0.00 0.00 40.97 3.41
357 358 6.097981 TCTCTGCTATCATCAAGTGAACTCAT 59.902 38.462 0.00 0.00 40.97 2.90
358 359 7.286316 TCTCTGCTATCATCAAGTGAACTCATA 59.714 37.037 0.00 0.00 40.97 2.15
359 360 7.785033 TCTGCTATCATCAAGTGAACTCATAA 58.215 34.615 0.00 0.00 40.97 1.90
360 361 7.708322 TCTGCTATCATCAAGTGAACTCATAAC 59.292 37.037 0.00 0.00 40.97 1.89
361 362 7.559486 TGCTATCATCAAGTGAACTCATAACT 58.441 34.615 0.00 0.00 40.97 2.24
426 427 6.782988 AGCACCATGTGTACCTAAGTATCTAT 59.217 38.462 0.00 0.00 35.75 1.98
428 429 8.582437 GCACCATGTGTACCTAAGTATCTATTA 58.418 37.037 0.00 0.00 35.75 0.98
489 2397 3.808095 CTCTGCTCGCTTTCTCTTTTTG 58.192 45.455 0.00 0.00 0.00 2.44
490 2398 3.206150 TCTGCTCGCTTTCTCTTTTTGT 58.794 40.909 0.00 0.00 0.00 2.83
491 2399 3.002656 TCTGCTCGCTTTCTCTTTTTGTG 59.997 43.478 0.00 0.00 0.00 3.33
492 2400 2.047040 GCTCGCTTTCTCTTTTTGTGC 58.953 47.619 0.00 0.00 0.00 4.57
494 2402 2.020720 TCGCTTTCTCTTTTTGTGCCA 58.979 42.857 0.00 0.00 0.00 4.92
495 2403 2.622942 TCGCTTTCTCTTTTTGTGCCAT 59.377 40.909 0.00 0.00 0.00 4.40
496 2404 2.727798 CGCTTTCTCTTTTTGTGCCATG 59.272 45.455 0.00 0.00 0.00 3.66
497 2405 3.550639 CGCTTTCTCTTTTTGTGCCATGA 60.551 43.478 0.00 0.00 0.00 3.07
498 2406 4.370917 GCTTTCTCTTTTTGTGCCATGAA 58.629 39.130 0.00 0.00 0.00 2.57
499 2407 4.209911 GCTTTCTCTTTTTGTGCCATGAAC 59.790 41.667 0.00 0.00 0.00 3.18
500 2408 3.624326 TCTCTTTTTGTGCCATGAACG 57.376 42.857 0.00 0.00 0.00 3.95
501 2409 2.053627 CTCTTTTTGTGCCATGAACGC 58.946 47.619 0.00 0.00 0.00 4.84
502 2410 1.406898 TCTTTTTGTGCCATGAACGCA 59.593 42.857 0.00 0.00 0.00 5.24
504 2412 1.565305 TTTTGTGCCATGAACGCAAC 58.435 45.000 12.43 2.52 38.13 4.17
505 2413 0.593518 TTTGTGCCATGAACGCAACG 60.594 50.000 12.43 0.00 38.13 4.10
507 2415 3.361158 TGCCATGAACGCAACGGG 61.361 61.111 0.00 0.00 32.05 5.28
508 2416 3.361977 GCCATGAACGCAACGGGT 61.362 61.111 0.00 0.00 0.00 5.28
509 2417 2.867472 CCATGAACGCAACGGGTC 59.133 61.111 0.00 0.00 0.00 4.46
510 2418 1.963855 CCATGAACGCAACGGGTCA 60.964 57.895 0.00 0.00 31.74 4.02
511 2419 1.305219 CCATGAACGCAACGGGTCAT 61.305 55.000 0.00 3.49 36.61 3.06
512 2420 0.096976 CATGAACGCAACGGGTCATC 59.903 55.000 5.72 0.00 34.95 2.92
513 2421 0.036388 ATGAACGCAACGGGTCATCT 60.036 50.000 3.49 0.00 32.94 2.90
514 2422 0.604073 TGAACGCAACGGGTCATCTA 59.396 50.000 0.00 0.00 0.00 1.98
515 2423 1.206132 TGAACGCAACGGGTCATCTAT 59.794 47.619 0.00 0.00 0.00 1.98
516 2424 2.277084 GAACGCAACGGGTCATCTATT 58.723 47.619 0.00 0.00 0.00 1.73
517 2425 1.651987 ACGCAACGGGTCATCTATTG 58.348 50.000 0.00 0.00 0.00 1.90
518 2426 1.066430 ACGCAACGGGTCATCTATTGT 60.066 47.619 0.00 0.00 0.00 2.71
519 2427 2.006888 CGCAACGGGTCATCTATTGTT 58.993 47.619 0.00 0.00 0.00 2.83
520 2428 2.418628 CGCAACGGGTCATCTATTGTTT 59.581 45.455 0.00 0.00 0.00 2.83
521 2429 3.619483 CGCAACGGGTCATCTATTGTTTA 59.381 43.478 0.00 0.00 0.00 2.01
522 2430 4.272504 CGCAACGGGTCATCTATTGTTTAT 59.727 41.667 0.00 0.00 0.00 1.40
523 2431 5.464057 CGCAACGGGTCATCTATTGTTTATA 59.536 40.000 0.00 0.00 0.00 0.98
524 2432 6.018588 CGCAACGGGTCATCTATTGTTTATAA 60.019 38.462 0.00 0.00 0.00 0.98
525 2433 7.466185 CGCAACGGGTCATCTATTGTTTATAAA 60.466 37.037 0.00 0.00 0.00 1.40
526 2434 7.642586 GCAACGGGTCATCTATTGTTTATAAAC 59.357 37.037 19.44 19.44 39.33 2.01
527 2435 7.473027 ACGGGTCATCTATTGTTTATAAACG 57.527 36.000 20.51 8.75 41.74 3.60
528 2436 6.480981 ACGGGTCATCTATTGTTTATAAACGG 59.519 38.462 20.51 11.98 41.74 4.44
529 2437 6.073440 CGGGTCATCTATTGTTTATAAACGGG 60.073 42.308 20.51 11.70 41.74 5.28
530 2438 6.293790 GGGTCATCTATTGTTTATAAACGGGC 60.294 42.308 20.51 7.64 41.74 6.13
531 2439 6.485648 GGTCATCTATTGTTTATAAACGGGCT 59.514 38.462 20.51 9.48 41.74 5.19
550 2458 3.103289 TGTCGTGTTAGCAGCGCG 61.103 61.111 0.00 0.00 40.68 6.86
565 2473 2.324330 CGCGCCACACTTCCATGAA 61.324 57.895 0.00 0.00 0.00 2.57
582 2490 4.388469 CCATGAAACAAATTGCTAAACGGG 59.612 41.667 0.00 0.00 0.00 5.28
618 2526 2.885644 CACGCGTGCTATTCGGCT 60.886 61.111 28.16 0.00 0.00 5.52
631 2539 5.822519 TGCTATTCGGCTTATTTCTGACATT 59.177 36.000 0.00 0.00 0.00 2.71
815 3918 2.557056 CCAGTCACTTCTCCGACAACTA 59.443 50.000 0.00 0.00 34.48 2.24
1317 4420 1.019278 CACGCAACCGCTACATCCTT 61.019 55.000 0.00 0.00 38.22 3.36
1522 4625 2.663196 CCGACTGGGACTGGTTCC 59.337 66.667 0.00 0.00 45.00 3.62
1659 4762 4.056050 GGTCTTTCGTTTCTCAGCAGTAA 58.944 43.478 0.00 0.00 0.00 2.24
1698 4801 3.727726 TCGGCAGGTACATGTTCATATG 58.272 45.455 2.30 0.00 0.00 1.78
1827 4958 1.337728 TGCCTGTTGTCACGGATGTAG 60.338 52.381 0.00 0.00 0.00 2.74
1875 5010 4.159377 AGTGTTATTGCAATTGTCCACG 57.841 40.909 18.75 0.00 0.00 4.94
1963 5098 7.775093 TCTTGGTTTTGATATATCTGAAGTGGG 59.225 37.037 13.79 0.46 0.00 4.61
1989 5126 1.980844 GTGCACATTTCAGAACATGCG 59.019 47.619 13.17 0.79 33.67 4.73
2101 5238 2.281761 CTCGTGCTGGCCTTTGGT 60.282 61.111 3.32 0.00 0.00 3.67
2148 5285 3.909732 TCCAGTTTCTGTCCCAAACATT 58.090 40.909 0.00 0.00 37.23 2.71
2246 5386 4.771590 TTGTCCTGTTGCAGATTTGATC 57.228 40.909 0.00 0.00 32.44 2.92
2515 5656 6.259550 AGTTCTTCACAGGCATTTATTGTC 57.740 37.500 0.00 0.00 0.00 3.18
2997 6138 1.021390 CATGTTCCCAGTGGAGCGAC 61.021 60.000 11.95 4.06 44.36 5.19
3052 6193 7.924412 CCTTGAAGTTGCAGCAATATATCAATT 59.076 33.333 11.96 0.00 0.00 2.32
3066 6207 8.790718 CAATATATCAATTGGACCTTGGAAGAG 58.209 37.037 5.42 0.00 33.95 2.85
3087 6228 1.818850 CAGATTCTGGCGCAAAATCG 58.181 50.000 10.83 7.68 35.14 3.34
3156 6297 4.672801 GCTTAAAGCTTCGAGGTTTCCATG 60.673 45.833 0.00 0.00 41.56 3.66
3262 6412 1.483004 GAGTGCTCTTTCTAGACCCCC 59.517 57.143 0.00 0.00 0.00 5.40
3263 6413 1.203313 AGTGCTCTTTCTAGACCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
3338 6838 8.049117 GGAATCTATATTTGTGGCTCCATCATA 58.951 37.037 0.00 0.00 0.00 2.15
3351 6851 4.498682 GCTCCATCATAACATTGAAGGCAC 60.499 45.833 0.00 0.00 35.06 5.01
3656 7156 7.548075 AGTTCACTAAAATATCAACAGTACCGG 59.452 37.037 0.00 0.00 0.00 5.28
3802 7302 4.746535 TCTGGGACATGCGAGTTTTATA 57.253 40.909 0.00 0.00 38.20 0.98
3980 7480 7.320443 TGACTACATGATTATCACAAAAGGC 57.680 36.000 0.00 0.00 0.00 4.35
3998 7498 4.648007 TGGGACAGTTCTGAGGCT 57.352 55.556 6.83 0.00 0.00 4.58
3999 7499 2.061220 TGGGACAGTTCTGAGGCTG 58.939 57.895 6.83 8.96 38.58 4.85
4043 7544 6.899393 AAAGCAAATCACTTAGGTCAATCA 57.101 33.333 0.00 0.00 0.00 2.57
4073 7574 7.717568 TCCTAACAGATTCATCTAGTTAGTGC 58.282 38.462 21.90 0.00 41.09 4.40
4083 7584 4.569761 TCTAGTTAGTGCGACCATCATC 57.430 45.455 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.615289 TGATCGAGATCAGACATCAGAGTA 58.385 41.667 11.37 0.00 42.42 2.59
79 80 1.533625 TGAGGTTGTATGCCTGCAAC 58.466 50.000 13.19 13.19 44.45 4.17
98 99 3.646162 TCCAAAGTGGTAGACTGTGACAT 59.354 43.478 0.00 0.00 42.04 3.06
106 107 4.262079 CGAGGGATATCCAAAGTGGTAGAC 60.262 50.000 23.27 1.31 39.03 2.59
134 135 3.006110 AGTCCGTTGTATTCGTCCTGAAA 59.994 43.478 0.00 0.00 40.71 2.69
136 137 2.094906 CAGTCCGTTGTATTCGTCCTGA 60.095 50.000 0.00 0.00 0.00 3.86
202 203 4.610945 TGCTACATGTCACATCAGTATCG 58.389 43.478 0.00 0.00 0.00 2.92
213 214 4.711846 AGGTAGAGTCATTGCTACATGTCA 59.288 41.667 0.00 0.00 38.93 3.58
319 320 7.414222 TGATAGCAGAGATGCATATCACATA 57.586 36.000 22.54 11.85 33.91 2.29
325 326 6.819146 CACTTGATGATAGCAGAGATGCATAT 59.181 38.462 0.00 0.00 37.25 1.78
326 327 6.014840 TCACTTGATGATAGCAGAGATGCATA 60.015 38.462 0.00 0.00 32.24 3.14
368 369 2.113807 ACATGGTAGCATGAGAGCTCA 58.886 47.619 35.01 2.23 45.26 4.26
402 403 5.277857 AGATACTTAGGTACACATGGTGC 57.722 43.478 0.00 0.00 36.98 5.01
430 431 9.793259 TGAAAGTGAGAGTAATTTAGAACCAAT 57.207 29.630 0.00 0.00 0.00 3.16
459 2367 0.671781 AGCGAGCAGAGCGTTCAAAT 60.672 50.000 1.01 0.00 40.04 2.32
466 2374 0.735632 AAGAGAAAGCGAGCAGAGCG 60.736 55.000 0.00 0.00 40.04 5.03
489 2397 2.126888 CCGTTGCGTTCATGGCAC 60.127 61.111 0.00 0.00 40.71 5.01
490 2398 3.361158 CCCGTTGCGTTCATGGCA 61.361 61.111 0.00 0.00 38.93 4.92
491 2399 3.322706 GACCCGTTGCGTTCATGGC 62.323 63.158 0.00 0.00 0.00 4.40
492 2400 1.305219 ATGACCCGTTGCGTTCATGG 61.305 55.000 0.00 0.00 30.26 3.66
494 2402 0.036388 AGATGACCCGTTGCGTTCAT 60.036 50.000 3.56 3.56 32.79 2.57
495 2403 0.604073 TAGATGACCCGTTGCGTTCA 59.396 50.000 0.00 0.00 0.00 3.18
496 2404 1.935933 ATAGATGACCCGTTGCGTTC 58.064 50.000 0.00 0.00 0.00 3.95
497 2405 2.006888 CAATAGATGACCCGTTGCGTT 58.993 47.619 0.00 0.00 0.00 4.84
498 2406 1.066430 ACAATAGATGACCCGTTGCGT 60.066 47.619 0.00 0.00 0.00 5.24
499 2407 1.651987 ACAATAGATGACCCGTTGCG 58.348 50.000 0.00 0.00 0.00 4.85
500 2408 5.751243 ATAAACAATAGATGACCCGTTGC 57.249 39.130 0.00 0.00 0.00 4.17
501 2409 7.849026 CGTTTATAAACAATAGATGACCCGTTG 59.151 37.037 24.27 2.32 38.81 4.10
502 2410 7.011669 CCGTTTATAAACAATAGATGACCCGTT 59.988 37.037 24.27 0.00 38.81 4.44
504 2412 6.073440 CCCGTTTATAAACAATAGATGACCCG 60.073 42.308 24.27 8.57 38.81 5.28
505 2413 6.293790 GCCCGTTTATAAACAATAGATGACCC 60.294 42.308 24.27 0.00 38.81 4.46
507 2415 7.012044 ACAGCCCGTTTATAAACAATAGATGAC 59.988 37.037 24.27 6.40 38.81 3.06
508 2416 7.011950 CACAGCCCGTTTATAAACAATAGATGA 59.988 37.037 24.27 0.00 38.81 2.92
509 2417 7.132213 CACAGCCCGTTTATAAACAATAGATG 58.868 38.462 24.27 19.08 38.81 2.90
510 2418 6.826741 ACACAGCCCGTTTATAAACAATAGAT 59.173 34.615 24.27 8.50 38.81 1.98
511 2419 6.174760 ACACAGCCCGTTTATAAACAATAGA 58.825 36.000 24.27 0.00 38.81 1.98
512 2420 6.431198 ACACAGCCCGTTTATAAACAATAG 57.569 37.500 24.27 13.60 38.81 1.73
513 2421 5.063691 CGACACAGCCCGTTTATAAACAATA 59.936 40.000 24.27 0.00 38.81 1.90
514 2422 4.142773 CGACACAGCCCGTTTATAAACAAT 60.143 41.667 24.27 7.29 38.81 2.71
515 2423 3.186817 CGACACAGCCCGTTTATAAACAA 59.813 43.478 24.27 0.00 38.81 2.83
516 2424 2.737783 CGACACAGCCCGTTTATAAACA 59.262 45.455 24.27 0.00 38.81 2.83
517 2425 2.738314 ACGACACAGCCCGTTTATAAAC 59.262 45.455 16.87 16.87 35.21 2.01
518 2426 2.737783 CACGACACAGCCCGTTTATAAA 59.262 45.455 0.00 0.00 36.83 1.40
519 2427 2.288948 ACACGACACAGCCCGTTTATAA 60.289 45.455 0.00 0.00 36.83 0.98
520 2428 1.273048 ACACGACACAGCCCGTTTATA 59.727 47.619 0.00 0.00 36.83 0.98
521 2429 0.034337 ACACGACACAGCCCGTTTAT 59.966 50.000 0.00 0.00 36.83 1.40
522 2430 0.179078 AACACGACACAGCCCGTTTA 60.179 50.000 0.00 0.00 36.83 2.01
523 2431 0.179078 TAACACGACACAGCCCGTTT 60.179 50.000 0.00 0.00 36.83 3.60
524 2432 0.599204 CTAACACGACACAGCCCGTT 60.599 55.000 0.00 0.00 36.83 4.44
525 2433 1.006571 CTAACACGACACAGCCCGT 60.007 57.895 0.00 0.00 39.88 5.28
526 2434 2.380410 GCTAACACGACACAGCCCG 61.380 63.158 0.00 0.00 0.00 6.13
527 2435 1.291877 CTGCTAACACGACACAGCCC 61.292 60.000 0.00 0.00 32.97 5.19
528 2436 1.901650 GCTGCTAACACGACACAGCC 61.902 60.000 1.93 0.00 46.21 4.85
529 2437 1.493311 GCTGCTAACACGACACAGC 59.507 57.895 0.00 0.00 45.95 4.40
530 2438 1.775344 CGCTGCTAACACGACACAG 59.225 57.895 0.00 0.00 0.00 3.66
531 2439 2.307309 GCGCTGCTAACACGACACA 61.307 57.895 0.00 0.00 0.00 3.72
550 2458 3.451141 TTTGTTTCATGGAAGTGTGGC 57.549 42.857 0.00 0.00 0.00 5.01
553 2461 5.280654 AGCAATTTGTTTCATGGAAGTGT 57.719 34.783 0.00 0.00 0.00 3.55
565 2473 2.030628 CCGACCCGTTTAGCAATTTGTT 60.031 45.455 0.00 0.00 0.00 2.83
618 2526 7.984050 TGAAACAGCCAAAAATGTCAGAAATAA 59.016 29.630 0.00 0.00 0.00 1.40
815 3918 3.719883 TTTGTCGCGTGTCGGTGGT 62.720 57.895 5.77 0.00 39.05 4.16
1063 4166 1.036707 GAGAGGAAGAGGATCCACCG 58.963 60.000 15.82 0.00 42.27 4.94
1698 4801 8.758715 GGCAATTTGATGTTAATTAGAAGATGC 58.241 33.333 0.00 0.00 0.00 3.91
1852 4987 5.163663 CCGTGGACAATTGCAATAACACTAT 60.164 40.000 13.39 0.00 0.00 2.12
1875 5010 6.529220 ACAGACAATAATGGAGCTCTATTCC 58.471 40.000 26.48 12.79 35.20 3.01
1963 5098 6.484540 CATGTTCTGAAATGTGCACTATCTC 58.515 40.000 19.41 9.77 0.00 2.75
2084 5221 2.281761 ACCAAAGGCCAGCACGAG 60.282 61.111 5.01 0.00 0.00 4.18
2101 5238 4.399618 TGTCATCTGGAAAACCGAAAAACA 59.600 37.500 0.00 0.00 0.00 2.83
2246 5386 1.670811 GGAACATACGACAAGGCATGG 59.329 52.381 0.00 0.00 0.00 3.66
2380 5521 2.985139 GCACTTTTTCAGATCTGCAAGC 59.015 45.455 18.36 9.31 0.00 4.01
2515 5656 7.147949 ACCAATGAAATTAAATCAGAGCAGAGG 60.148 37.037 0.00 0.00 32.46 3.69
2567 5708 6.100424 CCATGGAGAACCTAGTAAGAAGGAAT 59.900 42.308 5.56 0.00 37.57 3.01
2824 5965 3.587061 TGTCCACTGTCCACCATCTTATT 59.413 43.478 0.00 0.00 0.00 1.40
2997 6138 2.357637 ACCAGGTTTCACAACATTCACG 59.642 45.455 0.00 0.00 34.15 4.35
3052 6193 0.473694 TCTGCCTCTTCCAAGGTCCA 60.474 55.000 0.00 0.00 38.79 4.02
3066 6207 0.174162 ATTTTGCGCCAGAATCTGCC 59.826 50.000 4.18 0.00 0.00 4.85
3087 6228 4.863707 TGCAGCTATAGCCTGCAC 57.136 55.556 30.94 16.07 44.17 4.57
3136 6277 2.747446 GCATGGAAACCTCGAAGCTTTA 59.253 45.455 0.00 0.00 0.00 1.85
3156 6297 1.093159 CAGAGAACCTTGATGCTGGC 58.907 55.000 0.00 0.00 0.00 4.85
3275 6425 5.584551 ACTTAGGAGCCAATATTAAGGGG 57.415 43.478 0.00 0.00 0.00 4.79
3338 6838 4.008330 CTCATCTCTGTGCCTTCAATGTT 58.992 43.478 0.00 0.00 0.00 2.71
3351 6851 5.298347 TCAATTAGCATGCTCTCATCTCTG 58.702 41.667 26.57 11.18 0.00 3.35
3656 7156 9.135843 GTGGCATAAAGTACAAATTTAAAGACC 57.864 33.333 0.00 0.00 0.00 3.85
3802 7302 6.593770 TGTTTGTGATTGTCATAGCGAACTAT 59.406 34.615 0.00 0.00 39.82 2.12
3980 7480 0.036577 CAGCCTCAGAACTGTCCCAG 60.037 60.000 1.73 0.00 37.52 4.45
3990 7490 1.216444 GACATGTCGCAGCCTCAGA 59.784 57.895 10.69 0.00 0.00 3.27
4073 7574 4.489679 TCAAGTAGATCGATGATGGTCG 57.510 45.455 0.54 0.00 42.74 4.79


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

AutoCloner maintained by Alex Coulton.