Multiple sequence alignment - TraesCS1A01G322200

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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 TraesCS1A01G322200 chr1A 100.000 3841 0 0 1 3841 512872287 512876127 0.000000e+00 7094.0
1 TraesCS1A01G322200 chr1D 91.476 3144 220 20 2 3119 415401940 415405061 0.000000e+00 4277.0
2 TraesCS1A01G322200 chr1D 95.882 680 24 3 3162 3841 415413058 415413733 0.000000e+00 1098.0
3 TraesCS1A01G322200 chr1D 94.444 54 1 2 3117 3170 415405148 415405199 8.840000e-12 82.4
4 TraesCS1A01G322200 chr1B 92.107 1799 100 19 2070 3841 561701330 561703113 0.000000e+00 2497.0
5 TraesCS1A01G322200 chr1B 90.590 1764 143 11 154 1912 561699587 561701332 0.000000e+00 2316.0
6 TraesCS1A01G322200 chr5B 77.519 1290 252 32 838 2112 710344244 710345510 0.000000e+00 741.0
7 TraesCS1A01G322200 chr5B 76.183 1289 268 33 838 2112 695776975 695778238 0.000000e+00 643.0
8 TraesCS1A01G322200 chr5D 75.097 1550 331 48 778 2299 559982665 559984187 0.000000e+00 673.0
9 TraesCS1A01G322200 chr5D 76.084 1292 267 37 838 2112 559917479 559918745 1.510000e-178 636.0
10 TraesCS1A01G322200 chr4A 75.561 1293 271 40 838 2112 604774785 604776050 2.550000e-166 595.0
11 TraesCS1A01G322200 chr6D 75.589 1188 255 28 820 1992 458027309 458026142 4.340000e-154 555.0
12 TraesCS1A01G322200 chr6D 75.256 1172 257 27 828 1985 457697436 457696284 9.450000e-146 527.0
13 TraesCS1A01G322200 chr6B 74.448 1178 270 29 821 1985 696357385 696356226 2.680000e-131 479.0


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 TraesCS1A01G322200 chr1A 512872287 512876127 3840 False 7094.0 7094 100.0000 1 3841 1 chr1A.!!$F1 3840
1 TraesCS1A01G322200 chr1D 415401940 415405199 3259 False 2179.7 4277 92.9600 2 3170 2 chr1D.!!$F2 3168
2 TraesCS1A01G322200 chr1D 415413058 415413733 675 False 1098.0 1098 95.8820 3162 3841 1 chr1D.!!$F1 679
3 TraesCS1A01G322200 chr1B 561699587 561703113 3526 False 2406.5 2497 91.3485 154 3841 2 chr1B.!!$F1 3687
4 TraesCS1A01G322200 chr5B 710344244 710345510 1266 False 741.0 741 77.5190 838 2112 1 chr5B.!!$F2 1274
5 TraesCS1A01G322200 chr5B 695776975 695778238 1263 False 643.0 643 76.1830 838 2112 1 chr5B.!!$F1 1274
6 TraesCS1A01G322200 chr5D 559982665 559984187 1522 False 673.0 673 75.0970 778 2299 1 chr5D.!!$F2 1521
7 TraesCS1A01G322200 chr5D 559917479 559918745 1266 False 636.0 636 76.0840 838 2112 1 chr5D.!!$F1 1274
8 TraesCS1A01G322200 chr4A 604774785 604776050 1265 False 595.0 595 75.5610 838 2112 1 chr4A.!!$F1 1274
9 TraesCS1A01G322200 chr6D 458026142 458027309 1167 True 555.0 555 75.5890 820 1992 1 chr6D.!!$R2 1172
10 TraesCS1A01G322200 chr6D 457696284 457697436 1152 True 527.0 527 75.2560 828 1985 1 chr6D.!!$R1 1157
11 TraesCS1A01G322200 chr6B 696356226 696357385 1159 True 479.0 479 74.4480 821 1985 1 chr6B.!!$R1 1164

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
744 747 0.385029 GCACACACAATGTTCCTGCA 59.615 50.0 2.16 0.0 40.64 4.41 F
2413 2429 0.327591 ACGGAGAAGGGTCTACTCGT 59.672 55.0 0.00 0.0 31.69 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2524 2540 0.036952 CTCGGCTTCACCACTGATGT 60.037 55.000 0.0 0.0 39.03 3.06 R
3290 3420 2.450476 CCCAAGGCTGCAAATCTTAGT 58.550 47.619 0.5 0.0 0.00 2.24 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
25 26 2.223947 GGTTCAAGGGCGTTTTGATTGT 60.224 45.455 0.00 0.00 34.76 2.71
33 34 1.963747 CGTTTTGATTGTCGGGCTTC 58.036 50.000 0.00 0.00 0.00 3.86
43 44 3.627395 TGTCGGGCTTCTGTATCAATT 57.373 42.857 0.00 0.00 0.00 2.32
47 48 4.576463 GTCGGGCTTCTGTATCAATTTCAT 59.424 41.667 0.00 0.00 0.00 2.57
64 65 8.469200 TCAATTTCATAGAAGCCAAACATAAGG 58.531 33.333 0.00 0.00 0.00 2.69
106 107 1.293062 ACAGATTGCCTCACCCAGAT 58.707 50.000 0.00 0.00 0.00 2.90
120 121 0.881118 CCAGATGGGTTCACAAACGG 59.119 55.000 0.00 0.00 36.16 4.44
160 161 8.867112 ATGAAATTACATCTATTGCAAAGCTG 57.133 30.769 1.71 7.03 0.00 4.24
184 185 7.570132 TGAGAGAGCTACTACAAGATAAGAGT 58.430 38.462 0.00 0.00 0.00 3.24
221 222 7.397892 TTGTTTTCCTACAAAACATGACTCA 57.602 32.000 12.20 0.00 45.87 3.41
233 234 8.308931 ACAAAACATGACTCATGCATATTTCTT 58.691 29.630 17.50 1.03 44.80 2.52
244 245 9.745880 CTCATGCATATTTCTTTAGCATTTCTT 57.254 29.630 0.00 0.00 42.76 2.52
367 369 3.252215 TGAAGCATTTACAACGTTGGAGG 59.748 43.478 30.34 18.31 0.00 4.30
406 408 8.101309 TCCATTGGTTTCTTCCATATCTCTTA 57.899 34.615 1.86 0.00 37.33 2.10
413 415 8.510505 GGTTTCTTCCATATCTCTTATGCAATC 58.489 37.037 0.00 0.00 37.04 2.67
447 449 8.702438 CCATTTGTGATTATTTCAACAGACAAC 58.298 33.333 0.00 0.00 35.70 3.32
455 457 1.295792 TCAACAGACAACGTTGGAGC 58.704 50.000 30.34 19.10 43.18 4.70
457 459 1.003545 CAACAGACAACGTTGGAGCTG 60.004 52.381 29.82 29.82 40.05 4.24
469 471 2.496291 GGAGCTGCATGGCCCATTC 61.496 63.158 0.00 0.00 0.00 2.67
485 487 7.624549 TGGCCCATTCACTATATCTTCTATTC 58.375 38.462 0.00 0.00 0.00 1.75
534 536 5.528043 TTGTGACATAGTGTTGCCAAATT 57.472 34.783 0.00 0.00 0.00 1.82
540 542 9.072294 GTGACATAGTGTTGCCAAATTATAAAC 57.928 33.333 0.00 0.00 0.00 2.01
545 547 7.283625 AGTGTTGCCAAATTATAAACAGTGA 57.716 32.000 0.00 0.00 34.10 3.41
546 548 7.721402 AGTGTTGCCAAATTATAAACAGTGAA 58.279 30.769 0.00 0.00 34.10 3.18
549 551 9.553064 TGTTGCCAAATTATAAACAGTGAAAAT 57.447 25.926 0.00 0.00 0.00 1.82
608 610 9.014297 AGTCTCCTTTAGGTACAAAATTCAATG 57.986 33.333 0.00 0.00 36.34 2.82
609 611 9.010029 GTCTCCTTTAGGTACAAAATTCAATGA 57.990 33.333 0.00 0.00 36.34 2.57
610 612 9.581289 TCTCCTTTAGGTACAAAATTCAATGAA 57.419 29.630 0.00 0.00 36.34 2.57
611 613 9.846248 CTCCTTTAGGTACAAAATTCAATGAAG 57.154 33.333 1.10 0.00 36.34 3.02
612 614 9.362151 TCCTTTAGGTACAAAATTCAATGAAGT 57.638 29.630 1.10 0.00 36.34 3.01
613 615 9.410556 CCTTTAGGTACAAAATTCAATGAAGTG 57.589 33.333 1.10 2.54 0.00 3.16
614 616 9.410556 CTTTAGGTACAAAATTCAATGAAGTGG 57.589 33.333 1.10 0.00 0.00 4.00
615 617 8.698973 TTAGGTACAAAATTCAATGAAGTGGA 57.301 30.769 1.10 0.00 0.00 4.02
616 618 6.981722 AGGTACAAAATTCAATGAAGTGGAC 58.018 36.000 1.10 6.40 0.00 4.02
617 619 6.549364 AGGTACAAAATTCAATGAAGTGGACA 59.451 34.615 16.36 0.00 0.00 4.02
618 620 7.233348 AGGTACAAAATTCAATGAAGTGGACAT 59.767 33.333 16.36 9.88 0.00 3.06
741 744 2.653726 TGAAGCACACACAATGTTCCT 58.346 42.857 0.00 0.00 40.64 3.36
743 746 0.670162 AGCACACACAATGTTCCTGC 59.330 50.000 0.00 0.00 40.64 4.85
744 747 0.385029 GCACACACAATGTTCCTGCA 59.615 50.000 2.16 0.00 40.64 4.41
745 748 1.202394 GCACACACAATGTTCCTGCAA 60.202 47.619 0.00 0.00 40.64 4.08
746 749 2.738000 GCACACACAATGTTCCTGCAAA 60.738 45.455 0.00 0.00 40.64 3.68
747 750 3.519579 CACACACAATGTTCCTGCAAAA 58.480 40.909 0.00 0.00 40.64 2.44
748 751 3.931468 CACACACAATGTTCCTGCAAAAA 59.069 39.130 0.00 0.00 40.64 1.94
770 773 6.675413 AAATGGTCTATTTATGGCATGCAT 57.325 33.333 21.36 13.33 37.22 3.96
774 777 5.416639 TGGTCTATTTATGGCATGCATGATC 59.583 40.000 30.64 20.08 0.00 2.92
818 821 8.690203 TTCTTATCATAATTGGGTGGTGTATG 57.310 34.615 0.00 0.00 0.00 2.39
905 912 3.019564 GCAATATCAGGTGTGCTTTCCT 58.980 45.455 0.00 0.00 34.13 3.36
915 922 5.582665 CAGGTGTGCTTTCCTAGAGAATAAC 59.417 44.000 0.00 0.00 33.44 1.89
916 923 4.876679 GGTGTGCTTTCCTAGAGAATAACC 59.123 45.833 0.00 0.00 33.44 2.85
944 951 7.737869 TCTAGCAGAACTATAGCTACTACACT 58.262 38.462 0.00 0.00 39.68 3.55
966 973 6.584184 CACTCATTAGATATGTAGCAAGGTCG 59.416 42.308 0.00 0.00 0.00 4.79
978 985 0.944386 CAAGGTCGTGTTGTCCAAGG 59.056 55.000 0.00 0.00 0.00 3.61
1039 1046 3.077229 TGCACTCCAAAACATTGTTCG 57.923 42.857 1.83 0.00 0.00 3.95
1047 1054 4.564769 TCCAAAACATTGTTCGACAAAAGC 59.435 37.500 1.83 0.00 41.96 3.51
1081 1088 0.675633 GAACTGCTGCCCAAACATGT 59.324 50.000 0.00 0.00 0.00 3.21
1140 1148 5.594317 GTGGAGGTCTACCATTGCAATTATT 59.406 40.000 9.83 0.00 39.69 1.40
1212 1220 5.299531 GGAGAAGGTTAATAGGTCAATTGGC 59.700 44.000 5.42 2.83 0.00 4.52
1235 1243 7.669722 TGGCTCTACTTTGGAAAATAACAAGAT 59.330 33.333 0.00 0.00 0.00 2.40
1262 1271 7.040201 CCAAGAGGAATGAATAACATACCATGG 60.040 40.741 11.19 11.19 38.38 3.66
1319 1328 9.730420 AAGACATGTTTGTTGTATTTAAGTGTC 57.270 29.630 0.00 0.00 35.79 3.67
1351 1360 6.773638 AGGATTATGTGATTGATAGGGACAC 58.226 40.000 0.00 0.00 0.00 3.67
1352 1361 6.329986 AGGATTATGTGATTGATAGGGACACA 59.670 38.462 0.00 0.00 43.70 3.72
1396 1405 4.469227 AGAAGGCTTTATCTCTGAAGAGCA 59.531 41.667 0.00 0.00 41.80 4.26
1400 1409 3.814283 GCTTTATCTCTGAAGAGCATGGG 59.186 47.826 2.26 0.00 41.80 4.00
1408 1417 0.379669 GAAGAGCATGGGCAATGTCG 59.620 55.000 3.35 0.00 44.61 4.35
1437 1446 3.439476 GGTCGCTGAGAACTACTTCTACA 59.561 47.826 0.00 0.00 36.82 2.74
1445 1454 7.762159 GCTGAGAACTACTTCTACAAGCTTATT 59.238 37.037 0.00 0.00 36.82 1.40
1500 1509 2.710096 TGATGGCAAAGCTAGTACCC 57.290 50.000 0.00 0.00 0.00 3.69
1604 1613 0.920664 GACAAACGTGCTTGCCAAAC 59.079 50.000 0.00 0.00 0.00 2.93
1659 1668 0.597568 CATTGACCGGAAGCTTGCAA 59.402 50.000 18.65 4.86 0.00 4.08
1674 1683 2.616634 TGCAAATGTGTTGGCATGTT 57.383 40.000 0.00 0.00 39.34 2.71
1680 1689 5.409214 GCAAATGTGTTGGCATGTTTAGATT 59.591 36.000 0.00 0.00 34.25 2.40
1793 1802 7.855784 AGATTTTAAGGATTGTGAGGGTTTT 57.144 32.000 0.00 0.00 0.00 2.43
1799 1808 3.081804 GGATTGTGAGGGTTTTGACGAT 58.918 45.455 0.00 0.00 0.00 3.73
1810 1819 5.179368 AGGGTTTTGACGATTATGATATGCG 59.821 40.000 0.00 0.00 0.00 4.73
1861 1870 0.747255 CTCAGCTATAGGTGCACGGT 59.253 55.000 24.11 2.88 42.77 4.83
1958 1967 3.614092 AGAGTTGCCATGTGGAATAGTG 58.386 45.455 2.55 0.00 37.39 2.74
2162 2174 1.066358 GGACCCGAGGAGTACAAAAGG 60.066 57.143 0.00 0.00 0.00 3.11
2182 2197 7.481275 AAAGGCATGAACAAATGTTACTTTG 57.519 32.000 0.00 5.99 41.02 2.77
2206 2221 5.084818 TCACTATGCAAGCTTAGCAACTA 57.915 39.130 21.71 12.81 46.27 2.24
2225 2240 8.033038 AGCAACTATAAACTCATGTCTTTACGA 58.967 33.333 0.00 0.00 0.00 3.43
2292 2308 3.007831 TCCATTGCCATTTTCCCTTCAAC 59.992 43.478 0.00 0.00 0.00 3.18
2413 2429 0.327591 ACGGAGAAGGGTCTACTCGT 59.672 55.000 0.00 0.00 31.69 4.18
2424 2440 1.891150 GTCTACTCGTTGTTGGGGAGA 59.109 52.381 0.00 0.00 0.00 3.71
2456 2472 4.699925 ACTTTGCCTAGAACTGTGGTTA 57.300 40.909 0.00 0.00 35.58 2.85
2461 2477 5.499004 TGCCTAGAACTGTGGTTAAAGAT 57.501 39.130 0.00 0.00 35.58 2.40
2524 2540 3.045634 TCCCAAGTCTGAAGGAGTTCAA 58.954 45.455 0.00 0.00 42.27 2.69
2531 2547 4.346418 AGTCTGAAGGAGTTCAACATCAGT 59.654 41.667 10.55 0.00 42.27 3.41
2534 2550 3.136443 TGAAGGAGTTCAACATCAGTGGT 59.864 43.478 0.00 0.00 39.85 4.16
2550 2566 1.264749 TGGTGAAGCCGAGGCATACT 61.265 55.000 17.18 0.00 44.88 2.12
2583 2599 4.141144 GCGCTATGCCCAAGCTTA 57.859 55.556 0.00 0.00 40.80 3.09
2699 2715 0.467844 TGCTTGGCACAGATGGTTGT 60.468 50.000 0.00 0.00 42.39 3.32
2833 2866 0.883833 GGCAACACTGATGGAACCAG 59.116 55.000 0.00 0.00 37.64 4.00
3077 3119 7.771183 AGAAGATGAAAACTACAAGCACAAAA 58.229 30.769 0.00 0.00 0.00 2.44
3119 3161 4.750098 GTGCTTCAGTTTCTACTTGCTACA 59.250 41.667 0.00 0.00 30.26 2.74
3130 3260 6.294361 TCTACTTGCTACATACATGGTGTT 57.706 37.500 10.68 0.00 0.00 3.32
3197 3327 4.893608 TCTGTTTTCATTCAGGATCGTCA 58.106 39.130 0.00 0.00 33.13 4.35
3265 3395 3.249799 CACTGGTATTGCTTGTGTTTCGA 59.750 43.478 0.00 0.00 0.00 3.71
3274 3404 9.716507 GTATTGCTTGTGTTTCGATTATGTAAT 57.283 29.630 0.00 0.00 0.00 1.89
3393 3523 5.163683 TGAGCTCTAAAATGCATCAGCTTTC 60.164 40.000 16.19 7.30 42.74 2.62
3450 3580 5.137551 ACCATTAAAGTAGCACCACAAGTT 58.862 37.500 0.00 0.00 0.00 2.66
3455 3585 2.561569 AGTAGCACCACAAGTTCACAC 58.438 47.619 0.00 0.00 0.00 3.82
3670 3803 7.227049 ACTGTGGTCTGAAAAGAAAGAAAAA 57.773 32.000 0.00 0.00 0.00 1.94
3834 3967 5.333263 GCATACTGAAAATGTTGCAACAACC 60.333 40.000 34.06 22.05 43.03 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104120 AAAACGCCCTTGAACCTTGC 59.896 50.000 0.00 0.00 0.00 4.01
15 16 2.293399 ACAGAAGCCCGACAATCAAAAC 59.707 45.455 0.00 0.00 0.00 2.43
25 26 4.214986 TGAAATTGATACAGAAGCCCGA 57.785 40.909 0.00 0.00 0.00 5.14
33 34 8.461222 TGTTTGGCTTCTATGAAATTGATACAG 58.539 33.333 0.00 0.00 0.00 2.74
43 44 8.415950 TTTTCCTTATGTTTGGCTTCTATGAA 57.584 30.769 0.00 0.00 0.00 2.57
82 83 1.134371 GGGTGAGGCAATCTGTAGACC 60.134 57.143 0.00 0.00 0.00 3.85
83 84 1.555075 TGGGTGAGGCAATCTGTAGAC 59.445 52.381 0.00 0.00 0.00 2.59
90 91 3.106738 CCATCTGGGTGAGGCAATC 57.893 57.895 0.00 0.00 0.00 2.67
106 107 0.881159 CGCTACCGTTTGTGAACCCA 60.881 55.000 0.00 0.00 31.93 4.51
118 119 0.937304 CATCCCAAATGTCGCTACCG 59.063 55.000 0.00 0.00 0.00 4.02
119 120 2.325583 TCATCCCAAATGTCGCTACC 57.674 50.000 0.00 0.00 0.00 3.18
120 121 4.900635 ATTTCATCCCAAATGTCGCTAC 57.099 40.909 0.00 0.00 0.00 3.58
160 161 8.446599 AACTCTTATCTTGTAGTAGCTCTCTC 57.553 38.462 0.00 0.00 0.00 3.20
335 336 8.995220 ACGTTGTAAATGCTTCATAAACTCTTA 58.005 29.630 0.00 0.00 35.88 2.10
348 350 2.858745 ACCTCCAACGTTGTAAATGCT 58.141 42.857 25.63 0.00 35.88 3.79
359 361 7.214381 TGGAAGTTATATATGAACCTCCAACG 58.786 38.462 15.34 0.00 42.03 4.10
406 408 9.621629 AATCACAAATGGATTTATTGATTGCAT 57.378 25.926 14.58 0.00 38.68 3.96
447 449 3.818787 GGCCATGCAGCTCCAACG 61.819 66.667 0.00 0.00 0.00 4.10
455 457 1.991121 ATAGTGAATGGGCCATGCAG 58.009 50.000 28.00 0.00 28.85 4.41
457 459 3.960571 AGATATAGTGAATGGGCCATGC 58.039 45.455 22.01 20.09 0.00 4.06
557 559 8.253867 TCAACTCTAGTTACCTAACCAAAAGA 57.746 34.615 0.00 0.00 36.32 2.52
564 566 6.885918 AGGAGACTCAACTCTAGTTACCTAAC 59.114 42.308 4.53 0.00 35.83 2.34
567 569 5.523883 AGGAGACTCAACTCTAGTTACCT 57.476 43.478 4.53 0.00 35.83 3.08
580 582 7.741785 TGAATTTTGTACCTAAAGGAGACTCA 58.258 34.615 4.53 0.00 42.68 3.41
581 583 8.617290 TTGAATTTTGTACCTAAAGGAGACTC 57.383 34.615 2.23 0.00 42.68 3.36
585 587 9.846248 CTTCATTGAATTTTGTACCTAAAGGAG 57.154 33.333 2.23 0.00 38.94 3.69
608 610 7.154435 TCTACTTGTGTAGTATGTCCACTTC 57.846 40.000 3.58 0.00 44.74 3.01
609 611 7.534723 TTCTACTTGTGTAGTATGTCCACTT 57.465 36.000 3.58 0.00 44.74 3.16
610 612 7.719871 ATTCTACTTGTGTAGTATGTCCACT 57.280 36.000 3.58 0.00 44.74 4.00
611 613 9.865321 TTTATTCTACTTGTGTAGTATGTCCAC 57.135 33.333 3.58 0.00 44.74 4.02
612 614 9.865321 GTTTATTCTACTTGTGTAGTATGTCCA 57.135 33.333 3.58 0.00 44.74 4.02
641 643 9.849607 CATGCTCATTACTTAAGTTTACGTATG 57.150 33.333 14.49 9.98 0.00 2.39
745 748 6.887013 TGCATGCCATAAATAGACCATTTTT 58.113 32.000 16.68 0.00 37.93 1.94
746 749 6.482898 TGCATGCCATAAATAGACCATTTT 57.517 33.333 16.68 0.00 37.93 1.82
747 750 6.268158 TCATGCATGCCATAAATAGACCATTT 59.732 34.615 22.25 0.00 40.10 2.32
748 751 5.776208 TCATGCATGCCATAAATAGACCATT 59.224 36.000 22.25 0.00 31.47 3.16
770 773 6.899393 AATTGAACTAAAAGGTGCAGATCA 57.101 33.333 0.00 0.00 0.00 2.92
774 777 9.346725 GATAAGAAATTGAACTAAAAGGTGCAG 57.653 33.333 0.00 0.00 0.00 4.41
787 790 9.265862 ACCACCCAATTATGATAAGAAATTGAA 57.734 29.630 8.23 0.00 41.14 2.69
789 792 8.477256 ACACCACCCAATTATGATAAGAAATTG 58.523 33.333 0.00 0.00 39.31 2.32
887 894 5.211973 TCTCTAGGAAAGCACACCTGATAT 58.788 41.667 0.00 0.00 37.68 1.63
893 900 4.876679 GGTTATTCTCTAGGAAAGCACACC 59.123 45.833 0.00 0.00 37.49 4.16
905 912 6.793349 GTTCTGCTAGAACGGTTATTCTCTA 58.207 40.000 11.53 0.00 44.22 2.43
944 951 6.040504 ACACGACCTTGCTACATATCTAATGA 59.959 38.462 0.00 0.00 0.00 2.57
952 959 3.581755 GACAACACGACCTTGCTACATA 58.418 45.455 0.00 0.00 0.00 2.29
966 973 5.250200 TGGTCATAATACCTTGGACAACAC 58.750 41.667 0.00 0.00 40.44 3.32
998 1005 2.355010 ATCACTTAGGGCTTCCATGC 57.645 50.000 0.00 0.00 0.00 4.06
1031 1038 5.902981 CCAAAAATGCTTTTGTCGAACAATG 59.097 36.000 9.52 0.00 46.73 2.82
1039 1046 4.370917 TCAGAGCCAAAAATGCTTTTGTC 58.629 39.130 9.52 0.00 46.73 3.18
1047 1054 3.255149 AGCAGTTCTCAGAGCCAAAAATG 59.745 43.478 0.00 0.00 0.00 2.32
1081 1088 7.950124 AGGATTTTATCTGAAACCTCCTTCAAA 59.050 33.333 0.00 0.00 34.96 2.69
1212 1220 9.231297 TGGATCTTGTTATTTTCCAAAGTAGAG 57.769 33.333 0.00 0.00 33.66 2.43
1235 1243 7.206789 TGGTATGTTATTCATTCCTCTTGGA 57.793 36.000 5.41 0.00 42.21 3.53
1284 1293 9.725019 ATACAACAAACATGTCTTGAGATTAGA 57.275 29.630 20.41 6.14 32.27 2.10
1319 1328 4.067896 CAATCACATAATCCTCGGGGAAG 58.932 47.826 8.88 0.79 45.78 3.46
1351 1360 2.352225 GCTATCCATCGCCTCACTAGTG 60.352 54.545 17.17 17.17 0.00 2.74
1352 1361 1.889829 GCTATCCATCGCCTCACTAGT 59.110 52.381 0.00 0.00 0.00 2.57
1396 1405 1.001020 TCTTGCCGACATTGCCCAT 60.001 52.632 0.00 0.00 0.00 4.00
1400 1409 1.796796 GACCTCTTGCCGACATTGC 59.203 57.895 0.00 0.00 0.00 3.56
1408 1417 1.016653 GTTCTCAGCGACCTCTTGCC 61.017 60.000 0.00 0.00 0.00 4.52
1500 1509 0.249615 ATCATGTCATGGACTCGGCG 60.250 55.000 12.90 0.00 33.15 6.46
1571 1580 2.622436 GTTTGTCCTCCTTCTCCATCG 58.378 52.381 0.00 0.00 0.00 3.84
1604 1613 8.833231 ATAGTAGTCGAATAAAACCATGATGG 57.167 34.615 10.53 10.53 45.02 3.51
1624 1633 6.295632 CCGGTCAATGTATTGGATGGATAGTA 60.296 42.308 0.00 0.00 38.30 1.82
1659 1668 7.331687 GCTTAAATCTAAACATGCCAACACATT 59.668 33.333 0.00 0.00 0.00 2.71
1674 1683 7.047891 AGTGATCGAACATGGCTTAAATCTAA 58.952 34.615 0.00 0.00 0.00 2.10
1680 1689 5.580691 CAGTTAGTGATCGAACATGGCTTAA 59.419 40.000 0.00 0.00 32.88 1.85
1793 1802 6.018832 CCATATTGCGCATATCATAATCGTCA 60.019 38.462 12.75 0.00 0.00 4.35
1799 1808 7.446001 TTTGTCCATATTGCGCATATCATAA 57.554 32.000 12.75 0.00 0.00 1.90
1810 1819 6.165577 AGGTTGAACAATTTGTCCATATTGC 58.834 36.000 1.83 0.00 34.50 3.56
1861 1870 4.907269 TCCCTGATGGTAGCTTTGATATGA 59.093 41.667 0.00 0.00 34.77 2.15
1948 1957 5.355350 AGTTTAATGAGCTGCACTATTCCAC 59.645 40.000 1.02 0.82 0.00 4.02
1958 1967 4.455877 AGGTGTTGTAGTTTAATGAGCTGC 59.544 41.667 0.00 0.00 0.00 5.25
2136 2148 2.547640 TACTCCTCGGGTCCTCCACG 62.548 65.000 0.00 0.00 34.36 4.94
2162 2174 6.144577 GAGCAAAGTAACATTTGTTCATGC 57.855 37.500 10.05 6.83 44.83 4.06
2182 2197 2.283298 TGCTAAGCTTGCATAGTGAGC 58.717 47.619 9.86 7.95 35.31 4.26
2292 2308 7.369803 AGCAATCGCCAGACATATAAAATAG 57.630 36.000 0.00 0.00 39.83 1.73
2306 2322 2.017138 TCACGAAATAGCAATCGCCA 57.983 45.000 0.00 0.00 42.61 5.69
2307 2323 3.242739 ACATTCACGAAATAGCAATCGCC 60.243 43.478 0.00 0.00 42.61 5.54
2387 2403 6.183360 CGAGTAGACCCTTCTCCGTTAATTTA 60.183 42.308 0.00 0.00 32.75 1.40
2388 2404 5.393896 CGAGTAGACCCTTCTCCGTTAATTT 60.394 44.000 0.00 0.00 32.75 1.82
2424 2440 4.307259 TCTAGGCAAAGTAAGGATGGGAT 58.693 43.478 0.00 0.00 0.00 3.85
2430 2446 4.262894 CCACAGTTCTAGGCAAAGTAAGGA 60.263 45.833 0.00 0.00 0.00 3.36
2456 2472 6.582929 AGCCTATCTTTTGGTCCTATCTTT 57.417 37.500 0.00 0.00 0.00 2.52
2498 2514 2.573462 CTCCTTCAGACTTGGGAATCCA 59.427 50.000 0.09 0.00 42.25 3.41
2515 2531 2.705658 TCACCACTGATGTTGAACTCCT 59.294 45.455 0.00 0.00 0.00 3.69
2524 2540 0.036952 CTCGGCTTCACCACTGATGT 60.037 55.000 0.00 0.00 39.03 3.06
2531 2547 1.220749 GTATGCCTCGGCTTCACCA 59.779 57.895 9.65 0.00 42.51 4.17
2534 2550 2.737359 CGTTAAGTATGCCTCGGCTTCA 60.737 50.000 9.65 0.00 42.51 3.02
2550 2566 2.147958 AGCGCCTTTCATGAACGTTAA 58.852 42.857 7.89 0.00 0.00 2.01
2975 3014 9.078990 CACATCACCTTGACCTAGTAGAATATA 57.921 37.037 0.00 0.00 0.00 0.86
2976 3015 7.015682 CCACATCACCTTGACCTAGTAGAATAT 59.984 40.741 0.00 0.00 0.00 1.28
3119 3161 5.046663 GGGAATGACCAAAAACACCATGTAT 60.047 40.000 0.00 0.00 41.20 2.29
3130 3260 5.151454 AGTAACCAATGGGAATGACCAAAA 58.849 37.500 3.55 0.00 45.13 2.44
3220 3350 6.035005 GTGCTCAACAGAAAGAAACCTTTTTC 59.965 38.462 0.00 0.00 41.44 2.29
3221 3351 5.869344 GTGCTCAACAGAAAGAAACCTTTTT 59.131 36.000 0.00 0.00 34.27 1.94
3222 3352 5.185828 AGTGCTCAACAGAAAGAAACCTTTT 59.814 36.000 0.00 0.00 34.27 2.27
3223 3353 4.706962 AGTGCTCAACAGAAAGAAACCTTT 59.293 37.500 0.00 0.00 36.64 3.11
3290 3420 2.450476 CCCAAGGCTGCAAATCTTAGT 58.550 47.619 0.50 0.00 0.00 2.24
3393 3523 8.359642 TGGATTAGAACTTGTGATTCCAAAAAG 58.640 33.333 0.00 0.00 0.00 2.27
3450 3580 9.890629 AGCTCTTGTAAATAATATCTTGTGTGA 57.109 29.630 0.00 0.00 0.00 3.58
3455 3585 8.158169 TGGCAGCTCTTGTAAATAATATCTTG 57.842 34.615 0.00 0.00 0.00 3.02
3475 3608 3.745975 TGAAAATAGTGTTCGACTGGCAG 59.254 43.478 14.16 14.16 35.96 4.85
3512 3645 8.962679 TGGATAAATGGTTGTAATTTAGGTCAC 58.037 33.333 0.00 0.00 34.03 3.67
3670 3803 8.420222 TGTGTCCAAACATTTCACTAAATCAAT 58.580 29.630 0.00 0.00 37.81 2.57


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

AutoCloner maintained by Alex Coulton.