Multiple sequence alignment - TraesCS7A01G388900

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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 TraesCS7A01G388900 chr7A 100.000 3937 0 0 1 3937 564607177 564611113 0.000000e+00 7271.0
1 TraesCS7A01G388900 chr7D 95.616 1688 53 5 455 2126 498711294 498712976 0.000000e+00 2687.0
2 TraesCS7A01G388900 chr7D 91.685 1864 78 32 2129 3937 498713022 498714863 0.000000e+00 2512.0
3 TraesCS7A01G388900 chr7D 100.000 32 0 0 3 34 498711063 498711094 4.250000e-05 60.2
4 TraesCS7A01G388900 chr7B 91.831 1873 74 31 2129 3937 527037543 527039400 0.000000e+00 2538.0
5 TraesCS7A01G388900 chr7B 93.421 1672 72 13 455 2111 527035834 527037482 0.000000e+00 2444.0
6 TraesCS7A01G388900 chr7B 100.000 35 0 0 1 35 527034587 527034621 9.130000e-07 65.8
7 TraesCS7A01G388900 chr7B 100.000 30 0 0 3 32 527023571 527023600 5.500000e-04 56.5
8 TraesCS7A01G388900 chr4D 97.297 37 1 0 238 274 363928432 363928396 3.280000e-06 63.9
9 TraesCS7A01G388900 chr2B 93.182 44 2 1 266 309 683784068 683784026 3.280000e-06 63.9
10 TraesCS7A01G388900 chr2A 76.984 126 20 6 124 241 678036010 678036134 3.280000e-06 63.9
11 TraesCS7A01G388900 chr6B 80.822 73 12 2 238 309 623079610 623079681 5.500000e-04 56.5


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 TraesCS7A01G388900 chr7A 564607177 564611113 3936 False 7271.000000 7271 100.000 1 3937 1 chr7A.!!$F1 3936
1 TraesCS7A01G388900 chr7D 498711063 498714863 3800 False 1753.066667 2687 95.767 3 3937 3 chr7D.!!$F1 3934
2 TraesCS7A01G388900 chr7B 527034587 527039400 4813 False 1682.600000 2538 95.084 1 3937 3 chr7B.!!$F2 3936

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
576 1681 0.107456 CCATTAGCTGCCCGAGATGT 59.893 55.0 0.00 0.0 0.00 3.06 F
618 1726 0.107945 GCCACTAGGTCCAAGCTGAG 60.108 60.0 0.00 0.0 37.19 3.35 F
921 2041 0.255033 TCCACTACTCGAGCTAGCCA 59.745 55.0 13.61 0.0 0.00 4.75 F
2375 3584 0.614979 GTCAGGCTCTACCACCCTCA 60.615 60.0 0.00 0.0 43.14 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 3162 0.035458 AGTGGTCTGGTAGCTTGTGC 59.965 55.000 0.00 0.00 40.05 4.57 R
2473 3682 0.258194 ACGTAGAATCTCCTCCCGGT 59.742 55.000 0.00 0.00 0.00 5.28 R
2502 3711 1.078143 GGTGATCTTGGCGCCTTCT 60.078 57.895 29.70 9.69 33.20 2.85 R
3470 4740 1.073897 AGTCAGAGGGCTGCCAAAC 59.926 57.895 22.05 10.72 42.01 2.93 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
65 1170 8.250143 ACAAAATATGTTTGTCCTTCTCCTTT 57.750 30.769 9.04 0.00 40.06 3.11
66 1171 8.143835 ACAAAATATGTTTGTCCTTCTCCTTTG 58.856 33.333 9.04 0.00 40.06 2.77
68 1173 8.934023 AAATATGTTTGTCCTTCTCCTTTGTA 57.066 30.769 0.00 0.00 0.00 2.41
69 1174 7.923414 ATATGTTTGTCCTTCTCCTTTGTAC 57.077 36.000 0.00 0.00 0.00 2.90
70 1175 5.367945 TGTTTGTCCTTCTCCTTTGTACT 57.632 39.130 0.00 0.00 0.00 2.73
71 1176 6.488769 TGTTTGTCCTTCTCCTTTGTACTA 57.511 37.500 0.00 0.00 0.00 1.82
72 1177 7.074653 TGTTTGTCCTTCTCCTTTGTACTAT 57.925 36.000 0.00 0.00 0.00 2.12
73 1178 8.197592 TGTTTGTCCTTCTCCTTTGTACTATA 57.802 34.615 0.00 0.00 0.00 1.31
74 1179 8.822805 TGTTTGTCCTTCTCCTTTGTACTATAT 58.177 33.333 0.00 0.00 0.00 0.86
102 1207 9.570468 TTACTAAGACTACTATACCTGGTCATG 57.430 37.037 0.63 0.00 0.00 3.07
103 1208 7.005296 ACTAAGACTACTATACCTGGTCATGG 58.995 42.308 0.63 0.54 0.00 3.66
104 1209 4.742012 AGACTACTATACCTGGTCATGGG 58.258 47.826 0.63 0.00 0.00 4.00
105 1210 4.419200 AGACTACTATACCTGGTCATGGGA 59.581 45.833 0.63 0.00 0.00 4.37
106 1211 5.076598 AGACTACTATACCTGGTCATGGGAT 59.923 44.000 0.63 0.00 32.00 3.85
107 1212 6.277283 AGACTACTATACCTGGTCATGGGATA 59.723 42.308 0.63 0.00 29.52 2.59
108 1213 7.035764 AGACTACTATACCTGGTCATGGGATAT 60.036 40.741 0.63 0.00 30.61 1.63
109 1214 7.126733 ACTACTATACCTGGTCATGGGATATC 58.873 42.308 0.63 0.00 30.61 1.63
110 1215 5.281314 ACTATACCTGGTCATGGGATATCC 58.719 45.833 13.87 13.87 30.61 2.59
121 1226 2.358322 GGGATATCCAGCCCGAAAAA 57.642 50.000 23.27 0.00 41.57 1.94
122 1227 2.230660 GGGATATCCAGCCCGAAAAAG 58.769 52.381 23.27 0.00 41.57 2.27
123 1228 1.609072 GGATATCCAGCCCGAAAAAGC 59.391 52.381 17.34 0.00 35.64 3.51
124 1229 1.609072 GATATCCAGCCCGAAAAAGCC 59.391 52.381 0.00 0.00 0.00 4.35
125 1230 0.395173 TATCCAGCCCGAAAAAGCCC 60.395 55.000 0.00 0.00 0.00 5.19
126 1231 3.747976 CCAGCCCGAAAAAGCCCG 61.748 66.667 0.00 0.00 0.00 6.13
127 1232 2.671619 CAGCCCGAAAAAGCCCGA 60.672 61.111 0.00 0.00 0.00 5.14
128 1233 2.046285 CAGCCCGAAAAAGCCCGAT 61.046 57.895 0.00 0.00 0.00 4.18
129 1234 1.749258 AGCCCGAAAAAGCCCGATC 60.749 57.895 0.00 0.00 0.00 3.69
130 1235 1.749258 GCCCGAAAAAGCCCGATCT 60.749 57.895 0.00 0.00 0.00 2.75
131 1236 1.993369 GCCCGAAAAAGCCCGATCTG 61.993 60.000 0.00 0.00 0.00 2.90
132 1237 0.392461 CCCGAAAAAGCCCGATCTGA 60.392 55.000 0.00 0.00 0.00 3.27
133 1238 0.727398 CCGAAAAAGCCCGATCTGAC 59.273 55.000 0.00 0.00 0.00 3.51
134 1239 0.727398 CGAAAAAGCCCGATCTGACC 59.273 55.000 0.00 0.00 0.00 4.02
135 1240 1.095600 GAAAAAGCCCGATCTGACCC 58.904 55.000 0.00 0.00 0.00 4.46
136 1241 0.676782 AAAAAGCCCGATCTGACCCG 60.677 55.000 0.00 0.00 0.00 5.28
137 1242 2.536997 AAAAGCCCGATCTGACCCGG 62.537 60.000 11.89 11.89 44.94 5.73
155 1260 4.820744 CCCGGTCTTGCCCATGGG 62.821 72.222 27.87 27.87 38.57 4.00
156 1261 4.047125 CCGGTCTTGCCCATGGGT 62.047 66.667 31.58 0.00 37.65 4.51
157 1262 2.751436 CGGTCTTGCCCATGGGTG 60.751 66.667 31.58 20.94 37.65 4.61
158 1263 2.362889 GGTCTTGCCCATGGGTGG 60.363 66.667 31.58 20.50 45.61 4.61
195 1300 5.452078 TTTTAGCCTGAAGAACACATTGG 57.548 39.130 0.00 0.00 0.00 3.16
196 1301 1.251251 AGCCTGAAGAACACATTGGC 58.749 50.000 0.00 0.00 36.68 4.52
197 1302 0.244721 GCCTGAAGAACACATTGGCC 59.755 55.000 0.00 0.00 32.27 5.36
198 1303 0.523072 CCTGAAGAACACATTGGCCG 59.477 55.000 0.00 0.00 0.00 6.13
199 1304 0.523072 CTGAAGAACACATTGGCCGG 59.477 55.000 0.00 0.00 0.00 6.13
200 1305 0.893270 TGAAGAACACATTGGCCGGG 60.893 55.000 2.18 0.00 0.00 5.73
201 1306 2.212900 GAAGAACACATTGGCCGGGC 62.213 60.000 23.42 23.42 0.00 6.13
217 1322 3.150949 GCCTGGGCTTGGCTTTTT 58.849 55.556 12.64 0.00 46.38 1.94
236 1341 5.748670 TTTTTACATTTTAGGGAAGGGGC 57.251 39.130 0.00 0.00 0.00 5.80
237 1342 3.391799 TTACATTTTAGGGAAGGGGCC 57.608 47.619 0.00 0.00 0.00 5.80
316 1421 6.998802 ACAGATGGCCAGATATAACTAAGAC 58.001 40.000 13.05 0.00 0.00 3.01
324 1429 8.254508 GGCCAGATATAACTAAGACTAATCCAG 58.745 40.741 0.00 0.00 0.00 3.86
364 1469 5.904630 TGTTCGTCATGAAAATACAACAACG 59.095 36.000 0.00 0.00 38.60 4.10
365 1470 5.024768 TCGTCATGAAAATACAACAACGG 57.975 39.130 0.00 0.00 0.00 4.44
366 1471 4.512198 TCGTCATGAAAATACAACAACGGT 59.488 37.500 0.00 0.00 0.00 4.83
369 1474 6.344624 CGTCATGAAAATACAACAACGGTTTG 60.345 38.462 0.00 0.00 34.21 2.93
371 1476 5.000012 TGAAAATACAACAACGGTTTGCT 58.000 34.783 0.00 0.00 36.00 3.91
372 1477 5.038033 TGAAAATACAACAACGGTTTGCTC 58.962 37.500 0.00 0.00 36.00 4.26
373 1478 3.636282 AATACAACAACGGTTTGCTCC 57.364 42.857 0.00 0.00 36.00 4.70
385 1490 3.076999 TGCTCCGGCAGAAATGGA 58.923 55.556 0.00 0.00 44.28 3.41
386 1491 1.378378 TGCTCCGGCAGAAATGGAA 59.622 52.632 0.00 0.00 44.28 3.53
393 1498 2.614057 CCGGCAGAAATGGAAGATACAC 59.386 50.000 0.00 0.00 0.00 2.90
409 1514 3.361977 ACGCGCCGGCAGAAATTT 61.362 55.556 28.98 0.00 39.92 1.82
418 1523 3.491447 GCCGGCAGAAATTTGCAGAATAT 60.491 43.478 24.80 0.00 45.86 1.28
419 1524 4.261572 GCCGGCAGAAATTTGCAGAATATA 60.262 41.667 24.80 0.00 45.86 0.86
433 1538 6.573434 TGCAGAATATAATGACGTCTCTTGT 58.427 36.000 17.92 10.87 0.00 3.16
434 1539 6.697455 TGCAGAATATAATGACGTCTCTTGTC 59.303 38.462 17.92 5.73 36.88 3.18
435 1540 6.144724 GCAGAATATAATGACGTCTCTTGTCC 59.855 42.308 17.92 0.34 35.46 4.02
436 1541 6.360947 CAGAATATAATGACGTCTCTTGTCCG 59.639 42.308 17.92 0.00 35.46 4.79
437 1542 5.769484 ATATAATGACGTCTCTTGTCCGT 57.231 39.130 17.92 0.00 35.46 4.69
438 1543 6.872628 ATATAATGACGTCTCTTGTCCGTA 57.127 37.500 17.92 0.00 35.46 4.02
439 1544 5.769484 ATAATGACGTCTCTTGTCCGTAT 57.231 39.130 17.92 0.00 35.46 3.06
440 1545 6.872628 ATAATGACGTCTCTTGTCCGTATA 57.127 37.500 17.92 0.00 35.46 1.47
441 1546 5.769484 AATGACGTCTCTTGTCCGTATAT 57.231 39.130 17.92 0.00 35.46 0.86
442 1547 6.872628 AATGACGTCTCTTGTCCGTATATA 57.127 37.500 17.92 0.00 35.46 0.86
443 1548 7.450124 AATGACGTCTCTTGTCCGTATATAT 57.550 36.000 17.92 0.00 35.46 0.86
444 1549 8.557592 AATGACGTCTCTTGTCCGTATATATA 57.442 34.615 17.92 0.00 35.46 0.86
445 1550 7.592439 TGACGTCTCTTGTCCGTATATATAG 57.408 40.000 17.92 0.00 35.46 1.31
446 1551 7.381323 TGACGTCTCTTGTCCGTATATATAGA 58.619 38.462 17.92 0.00 35.46 1.98
447 1552 8.039538 TGACGTCTCTTGTCCGTATATATAGAT 58.960 37.037 17.92 0.00 35.46 1.98
448 1553 8.422973 ACGTCTCTTGTCCGTATATATAGATC 57.577 38.462 0.00 0.00 32.22 2.75
449 1554 8.259411 ACGTCTCTTGTCCGTATATATAGATCT 58.741 37.037 0.00 0.00 32.22 2.75
450 1555 9.747293 CGTCTCTTGTCCGTATATATAGATCTA 57.253 37.037 4.57 4.57 0.00 1.98
453 1558 9.833917 CTCTTGTCCGTATATATAGATCTACCA 57.166 37.037 4.10 0.00 0.00 3.25
572 1677 4.766970 CTCCATTAGCTGCCCGAG 57.233 61.111 0.00 0.00 0.00 4.63
573 1678 2.127839 CTCCATTAGCTGCCCGAGA 58.872 57.895 0.00 0.00 0.00 4.04
574 1679 0.683973 CTCCATTAGCTGCCCGAGAT 59.316 55.000 0.00 0.00 0.00 2.75
576 1681 0.107456 CCATTAGCTGCCCGAGATGT 59.893 55.000 0.00 0.00 0.00 3.06
582 1687 2.037620 GCTGCCCGAGATGTCCAGAT 62.038 60.000 0.00 0.00 0.00 2.90
595 1700 1.329906 GTCCAGATCAGATGCAAAGCG 59.670 52.381 0.00 0.00 0.00 4.68
618 1726 0.107945 GCCACTAGGTCCAAGCTGAG 60.108 60.000 0.00 0.00 37.19 3.35
788 1905 4.090588 CGGTCCTTTGCCGCCCTA 62.091 66.667 0.00 0.00 42.82 3.53
825 1942 3.435566 TCGATCACGACATGCTAAAGAC 58.564 45.455 0.00 0.00 43.81 3.01
920 2040 1.335496 CTTCCACTACTCGAGCTAGCC 59.665 57.143 13.61 1.79 0.00 3.93
921 2041 0.255033 TCCACTACTCGAGCTAGCCA 59.745 55.000 13.61 0.00 0.00 4.75
1083 2203 2.747460 CTGTCGTCGGGGTCGGTA 60.747 66.667 0.00 0.00 36.95 4.02
1363 2483 4.821589 CGTGGAGGAAGGCGAGCC 62.822 72.222 5.89 5.89 0.00 4.70
1733 2856 2.774044 TGCTCACGTGCAAAACTCA 58.226 47.368 11.67 0.00 40.29 3.41
1986 3109 1.001706 GAGGCTGTCAAAAACGGGTTC 60.002 52.381 0.00 0.00 34.56 3.62
2039 3162 2.569059 CATGCATTACCTCTGGTGGAG 58.431 52.381 0.00 0.00 41.51 3.86
2095 3222 2.221749 CACTGCATGCGTCGCTAATTAT 59.778 45.455 19.50 0.00 0.00 1.28
2114 3241 6.710597 ATTATCTCTGCAAGCAACAATGAT 57.289 33.333 0.00 0.00 0.00 2.45
2116 3243 3.682696 TCTCTGCAAGCAACAATGATCT 58.317 40.909 0.00 0.00 0.00 2.75
2119 3246 1.265568 GCAAGCAACAATGATCTGCG 58.734 50.000 0.00 0.00 41.05 5.18
2158 3367 1.666700 GTGTGCGTGTGGTTACTGAAA 59.333 47.619 0.00 0.00 0.00 2.69
2159 3368 1.937223 TGTGCGTGTGGTTACTGAAAG 59.063 47.619 0.00 0.00 42.29 2.62
2160 3369 0.941542 TGCGTGTGGTTACTGAAAGC 59.058 50.000 0.00 0.00 37.60 3.51
2161 3370 1.226746 GCGTGTGGTTACTGAAAGCT 58.773 50.000 0.00 0.00 37.60 3.74
2177 3386 4.637534 TGAAAGCTTATTCTCTGACATGGC 59.362 41.667 0.00 0.00 0.00 4.40
2366 3575 1.356059 AGGTCAGTCAGTCAGGCTCTA 59.644 52.381 0.00 0.00 0.00 2.43
2375 3584 0.614979 GTCAGGCTCTACCACCCTCA 60.615 60.000 0.00 0.00 43.14 3.86
2543 3752 2.163613 GGATGATCAACCGGAAAACCAC 59.836 50.000 9.46 0.00 0.00 4.16
2721 3933 2.195922 GTTCAGCAAAACTGCAACCAG 58.804 47.619 0.00 0.00 46.76 4.00
2728 3940 4.006026 CAAAACTGCAACCAGCTTTTTG 57.994 40.909 10.69 10.69 43.65 2.44
3200 4442 3.188460 ACAGCGTGCTTAAACCATTGTAG 59.812 43.478 0.00 0.00 0.00 2.74
3201 4443 3.435327 CAGCGTGCTTAAACCATTGTAGA 59.565 43.478 0.00 0.00 0.00 2.59
3206 4460 4.076394 TGCTTAAACCATTGTAGACACCC 58.924 43.478 0.00 0.00 0.00 4.61
3215 4469 5.487488 ACCATTGTAGACACCCTTTCTCATA 59.513 40.000 0.00 0.00 0.00 2.15
3276 4531 5.048364 TGCTTTACGCATGTAAAAGATTGGT 60.048 36.000 16.03 0.00 46.80 3.67
3292 4547 6.362210 AGATTGGTTTTGCATTGTTTTCAC 57.638 33.333 0.00 0.00 0.00 3.18
3293 4548 6.114767 AGATTGGTTTTGCATTGTTTTCACT 58.885 32.000 0.00 0.00 0.00 3.41
3294 4549 6.598850 AGATTGGTTTTGCATTGTTTTCACTT 59.401 30.769 0.00 0.00 0.00 3.16
3295 4550 6.566197 TTGGTTTTGCATTGTTTTCACTTT 57.434 29.167 0.00 0.00 0.00 2.66
3296 4551 6.566197 TGGTTTTGCATTGTTTTCACTTTT 57.434 29.167 0.00 0.00 0.00 2.27
3297 4552 6.606768 TGGTTTTGCATTGTTTTCACTTTTC 58.393 32.000 0.00 0.00 0.00 2.29
3298 4553 6.205464 TGGTTTTGCATTGTTTTCACTTTTCA 59.795 30.769 0.00 0.00 0.00 2.69
3299 4554 7.080724 GGTTTTGCATTGTTTTCACTTTTCAA 58.919 30.769 0.00 0.00 0.00 2.69
3303 4558 5.121454 TGCATTGTTTTCACTTTTCAACCAC 59.879 36.000 0.00 0.00 0.00 4.16
3416 4685 0.508641 CGTTCGAGGTTGCAGTTCAG 59.491 55.000 0.00 0.00 0.00 3.02
3470 4740 4.021016 ACAGAGGTAGTAGCTTTGAACAGG 60.021 45.833 22.59 0.14 32.85 4.00
3485 4755 1.975407 CAGGTTTGGCAGCCCTCTG 60.975 63.158 9.64 7.46 43.16 3.35
3486 4756 2.156098 AGGTTTGGCAGCCCTCTGA 61.156 57.895 9.64 0.00 42.95 3.27
3501 4773 4.330250 CCCTCTGACTGACATTGTTGAAT 58.670 43.478 0.00 0.00 0.00 2.57
3527 4810 2.218603 GTCAACTCAGCCTTCGGAAAA 58.781 47.619 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 1181 9.570468 CATGACCAGGTATAGTAGTCTTAGTAA 57.430 37.037 0.00 0.00 0.00 2.24
77 1182 8.162085 CCATGACCAGGTATAGTAGTCTTAGTA 58.838 40.741 0.00 0.00 0.00 1.82
78 1183 7.005296 CCATGACCAGGTATAGTAGTCTTAGT 58.995 42.308 0.00 0.00 0.00 2.24
79 1184 6.434652 CCCATGACCAGGTATAGTAGTCTTAG 59.565 46.154 0.00 0.00 0.00 2.18
80 1185 6.103649 TCCCATGACCAGGTATAGTAGTCTTA 59.896 42.308 0.00 0.00 0.00 2.10
81 1186 5.103215 TCCCATGACCAGGTATAGTAGTCTT 60.103 44.000 0.00 0.00 0.00 3.01
82 1187 4.419200 TCCCATGACCAGGTATAGTAGTCT 59.581 45.833 0.00 0.00 0.00 3.24
83 1188 4.737578 TCCCATGACCAGGTATAGTAGTC 58.262 47.826 0.00 0.00 0.00 2.59
84 1189 4.827036 TCCCATGACCAGGTATAGTAGT 57.173 45.455 0.00 0.00 0.00 2.73
85 1190 6.551601 GGATATCCCATGACCAGGTATAGTAG 59.448 46.154 11.02 0.00 34.14 2.57
86 1191 6.010201 TGGATATCCCATGACCAGGTATAGTA 60.010 42.308 19.34 0.00 40.82 1.82
87 1192 5.222758 TGGATATCCCATGACCAGGTATAGT 60.223 44.000 19.34 0.00 40.82 2.12
88 1193 5.280499 TGGATATCCCATGACCAGGTATAG 58.720 45.833 19.34 0.00 40.82 1.31
89 1194 5.280499 CTGGATATCCCATGACCAGGTATA 58.720 45.833 19.34 0.00 45.57 1.47
90 1195 4.107072 CTGGATATCCCATGACCAGGTAT 58.893 47.826 19.34 0.00 45.57 2.73
91 1196 3.520696 CTGGATATCCCATGACCAGGTA 58.479 50.000 19.34 0.00 45.57 3.08
92 1197 2.342659 CTGGATATCCCATGACCAGGT 58.657 52.381 19.34 0.00 45.57 4.00
93 1198 1.004044 GCTGGATATCCCATGACCAGG 59.996 57.143 19.34 0.00 45.57 4.45
94 1199 1.004044 GGCTGGATATCCCATGACCAG 59.996 57.143 19.34 9.41 45.57 4.00
95 1200 1.067295 GGCTGGATATCCCATGACCA 58.933 55.000 19.34 0.00 45.57 4.02
96 1201 0.329596 GGGCTGGATATCCCATGACC 59.670 60.000 19.34 16.03 45.57 4.02
97 1202 0.036010 CGGGCTGGATATCCCATGAC 60.036 60.000 19.34 11.05 45.57 3.06
98 1203 0.178906 TCGGGCTGGATATCCCATGA 60.179 55.000 19.34 7.17 45.57 3.07
99 1204 0.692476 TTCGGGCTGGATATCCCATG 59.308 55.000 19.34 10.24 45.57 3.66
100 1205 1.444933 TTTCGGGCTGGATATCCCAT 58.555 50.000 19.34 0.00 45.57 4.00
101 1206 1.217916 TTTTCGGGCTGGATATCCCA 58.782 50.000 19.34 6.52 42.75 4.37
102 1207 2.230660 CTTTTTCGGGCTGGATATCCC 58.769 52.381 19.34 4.37 39.17 3.85
103 1208 1.609072 GCTTTTTCGGGCTGGATATCC 59.391 52.381 15.39 15.39 0.00 2.59
104 1209 1.609072 GGCTTTTTCGGGCTGGATATC 59.391 52.381 0.00 0.00 0.00 1.63
105 1210 1.692411 GGCTTTTTCGGGCTGGATAT 58.308 50.000 0.00 0.00 0.00 1.63
106 1211 0.395173 GGGCTTTTTCGGGCTGGATA 60.395 55.000 0.00 0.00 0.00 2.59
107 1212 1.682344 GGGCTTTTTCGGGCTGGAT 60.682 57.895 0.00 0.00 0.00 3.41
108 1213 2.282887 GGGCTTTTTCGGGCTGGA 60.283 61.111 0.00 0.00 0.00 3.86
109 1214 3.747976 CGGGCTTTTTCGGGCTGG 61.748 66.667 0.00 0.00 32.87 4.85
110 1215 1.993369 GATCGGGCTTTTTCGGGCTG 61.993 60.000 0.00 0.00 37.03 4.85
111 1216 1.749258 GATCGGGCTTTTTCGGGCT 60.749 57.895 0.00 0.00 0.00 5.19
112 1217 1.749258 AGATCGGGCTTTTTCGGGC 60.749 57.895 0.00 0.00 0.00 6.13
113 1218 0.392461 TCAGATCGGGCTTTTTCGGG 60.392 55.000 0.00 0.00 0.00 5.14
114 1219 0.727398 GTCAGATCGGGCTTTTTCGG 59.273 55.000 0.00 0.00 0.00 4.30
115 1220 0.727398 GGTCAGATCGGGCTTTTTCG 59.273 55.000 0.00 0.00 0.00 3.46
116 1221 1.095600 GGGTCAGATCGGGCTTTTTC 58.904 55.000 0.00 0.00 0.00 2.29
117 1222 0.676782 CGGGTCAGATCGGGCTTTTT 60.677 55.000 0.00 0.00 0.00 1.94
118 1223 1.078426 CGGGTCAGATCGGGCTTTT 60.078 57.895 0.00 0.00 0.00 2.27
119 1224 2.584608 CGGGTCAGATCGGGCTTT 59.415 61.111 0.00 0.00 0.00 3.51
120 1225 3.470888 CCGGGTCAGATCGGGCTT 61.471 66.667 0.00 0.00 42.32 4.35
138 1243 4.820744 CCCATGGGCAAGACCGGG 62.821 72.222 20.41 0.00 40.62 5.73
139 1244 4.047125 ACCCATGGGCAAGACCGG 62.047 66.667 31.73 0.00 40.62 5.28
140 1245 2.751436 CACCCATGGGCAAGACCG 60.751 66.667 31.73 4.61 40.62 4.79
141 1246 2.362889 CCACCCATGGGCAAGACC 60.363 66.667 31.73 0.00 43.04 3.85
172 1277 5.738783 GCCAATGTGTTCTTCAGGCTAAAAA 60.739 40.000 0.00 0.00 37.67 1.94
173 1278 4.261994 GCCAATGTGTTCTTCAGGCTAAAA 60.262 41.667 0.00 0.00 37.67 1.52
174 1279 3.255642 GCCAATGTGTTCTTCAGGCTAAA 59.744 43.478 0.00 0.00 37.67 1.85
175 1280 2.819608 GCCAATGTGTTCTTCAGGCTAA 59.180 45.455 0.00 0.00 37.67 3.09
176 1281 2.436417 GCCAATGTGTTCTTCAGGCTA 58.564 47.619 0.00 0.00 37.67 3.93
177 1282 1.251251 GCCAATGTGTTCTTCAGGCT 58.749 50.000 0.00 0.00 37.67 4.58
178 1283 0.244721 GGCCAATGTGTTCTTCAGGC 59.755 55.000 0.00 0.00 39.86 4.85
179 1284 0.523072 CGGCCAATGTGTTCTTCAGG 59.477 55.000 2.24 0.00 0.00 3.86
180 1285 0.523072 CCGGCCAATGTGTTCTTCAG 59.477 55.000 2.24 0.00 0.00 3.02
181 1286 0.893270 CCCGGCCAATGTGTTCTTCA 60.893 55.000 2.24 0.00 0.00 3.02
182 1287 1.883021 CCCGGCCAATGTGTTCTTC 59.117 57.895 2.24 0.00 0.00 2.87
183 1288 2.275380 GCCCGGCCAATGTGTTCTT 61.275 57.895 2.24 0.00 0.00 2.52
184 1289 2.676471 GCCCGGCCAATGTGTTCT 60.676 61.111 2.24 0.00 0.00 3.01
214 1319 4.532916 GGCCCCTTCCCTAAAATGTAAAAA 59.467 41.667 0.00 0.00 0.00 1.94
215 1320 4.098155 GGCCCCTTCCCTAAAATGTAAAA 58.902 43.478 0.00 0.00 0.00 1.52
216 1321 3.566997 GGGCCCCTTCCCTAAAATGTAAA 60.567 47.826 12.23 0.00 43.13 2.01
217 1322 2.023791 GGGCCCCTTCCCTAAAATGTAA 60.024 50.000 12.23 0.00 43.13 2.41
218 1323 1.571936 GGGCCCCTTCCCTAAAATGTA 59.428 52.381 12.23 0.00 43.13 2.29
219 1324 0.338467 GGGCCCCTTCCCTAAAATGT 59.662 55.000 12.23 0.00 43.13 2.71
220 1325 0.755327 CGGGCCCCTTCCCTAAAATG 60.755 60.000 18.66 0.00 44.30 2.32
221 1326 1.618586 CGGGCCCCTTCCCTAAAAT 59.381 57.895 18.66 0.00 44.30 1.82
222 1327 2.618449 CCGGGCCCCTTCCCTAAAA 61.618 63.158 18.66 0.00 44.30 1.52
223 1328 3.018805 CCGGGCCCCTTCCCTAAA 61.019 66.667 18.66 0.00 44.30 1.85
289 1394 3.259374 AGTTATATCTGGCCATCTGTCGG 59.741 47.826 5.51 0.00 0.00 4.79
290 1395 4.527509 AGTTATATCTGGCCATCTGTCG 57.472 45.455 5.51 0.00 0.00 4.35
291 1396 7.039363 AGTCTTAGTTATATCTGGCCATCTGTC 60.039 40.741 5.51 0.00 0.00 3.51
292 1397 6.784969 AGTCTTAGTTATATCTGGCCATCTGT 59.215 38.462 5.51 0.00 0.00 3.41
293 1398 7.238486 AGTCTTAGTTATATCTGGCCATCTG 57.762 40.000 5.51 0.00 0.00 2.90
294 1399 8.958060 TTAGTCTTAGTTATATCTGGCCATCT 57.042 34.615 5.51 0.00 0.00 2.90
295 1400 9.810545 GATTAGTCTTAGTTATATCTGGCCATC 57.189 37.037 5.51 0.00 0.00 3.51
296 1401 8.763601 GGATTAGTCTTAGTTATATCTGGCCAT 58.236 37.037 5.51 0.00 0.00 4.40
297 1402 7.733047 TGGATTAGTCTTAGTTATATCTGGCCA 59.267 37.037 4.71 4.71 0.00 5.36
298 1403 8.135382 TGGATTAGTCTTAGTTATATCTGGCC 57.865 38.462 0.00 0.00 0.00 5.36
299 1404 9.026121 TCTGGATTAGTCTTAGTTATATCTGGC 57.974 37.037 0.00 0.00 0.00 4.85
328 1433 6.252967 TCATGACGAACATAGCACATTTTT 57.747 33.333 0.00 0.00 37.46 1.94
330 1435 5.878332 TTCATGACGAACATAGCACATTT 57.122 34.783 0.00 0.00 37.46 2.32
331 1436 5.878332 TTTCATGACGAACATAGCACATT 57.122 34.783 0.00 0.00 37.46 2.71
336 1441 7.240674 TGTTGTATTTTCATGACGAACATAGC 58.759 34.615 0.00 0.00 37.46 2.97
338 1443 7.742525 CGTTGTTGTATTTTCATGACGAACATA 59.257 33.333 0.00 0.00 37.46 2.29
344 1449 4.778904 ACCGTTGTTGTATTTTCATGACG 58.221 39.130 0.00 0.00 0.00 4.35
345 1450 6.561350 GCAAACCGTTGTTGTATTTTCATGAC 60.561 38.462 0.00 0.00 37.06 3.06
369 1474 0.392998 TCTTCCATTTCTGCCGGAGC 60.393 55.000 5.05 0.00 40.48 4.70
371 1476 2.503765 TGTATCTTCCATTTCTGCCGGA 59.496 45.455 5.05 0.00 0.00 5.14
372 1477 2.614057 GTGTATCTTCCATTTCTGCCGG 59.386 50.000 0.00 0.00 0.00 6.13
373 1478 2.285220 CGTGTATCTTCCATTTCTGCCG 59.715 50.000 0.00 0.00 0.00 5.69
374 1479 2.032178 GCGTGTATCTTCCATTTCTGCC 59.968 50.000 0.00 0.00 0.00 4.85
378 1483 1.003866 GGCGCGTGTATCTTCCATTTC 60.004 52.381 8.43 0.00 0.00 2.17
379 1484 1.014352 GGCGCGTGTATCTTCCATTT 58.986 50.000 8.43 0.00 0.00 2.32
380 1485 1.151777 CGGCGCGTGTATCTTCCATT 61.152 55.000 8.43 0.00 0.00 3.16
381 1486 1.591594 CGGCGCGTGTATCTTCCAT 60.592 57.895 8.43 0.00 0.00 3.41
382 1487 2.202690 CGGCGCGTGTATCTTCCA 60.203 61.111 8.43 0.00 0.00 3.53
383 1488 2.960129 CCGGCGCGTGTATCTTCC 60.960 66.667 8.43 0.00 0.00 3.46
385 1490 4.444838 TGCCGGCGCGTGTATCTT 62.445 61.111 23.90 0.00 38.08 2.40
386 1491 4.873129 CTGCCGGCGCGTGTATCT 62.873 66.667 23.90 0.00 38.08 1.98
393 1498 2.875711 CAAATTTCTGCCGGCGCG 60.876 61.111 23.90 15.91 38.08 6.86
409 1514 6.573434 ACAAGAGACGTCATTATATTCTGCA 58.427 36.000 19.50 0.00 0.00 4.41
418 1523 6.872628 ATATACGGACAAGAGACGTCATTA 57.127 37.500 19.50 0.00 41.53 1.90
419 1524 5.769484 ATATACGGACAAGAGACGTCATT 57.231 39.130 19.50 9.31 41.53 2.57
433 1538 5.693555 CGCGTGGTAGATCTATATATACGGA 59.306 44.000 19.24 0.00 31.75 4.69
434 1539 5.614231 GCGCGTGGTAGATCTATATATACGG 60.614 48.000 8.43 13.85 31.75 4.02
435 1540 5.372445 GCGCGTGGTAGATCTATATATACG 58.628 45.833 8.43 12.61 31.75 3.06
436 1541 5.372445 CGCGCGTGGTAGATCTATATATAC 58.628 45.833 24.19 0.00 0.00 1.47
437 1542 4.084171 GCGCGCGTGGTAGATCTATATATA 60.084 45.833 32.35 0.00 0.00 0.86
438 1543 3.303857 GCGCGCGTGGTAGATCTATATAT 60.304 47.826 32.35 0.00 0.00 0.86
439 1544 2.031314 GCGCGCGTGGTAGATCTATATA 59.969 50.000 32.35 0.00 0.00 0.86
440 1545 1.202154 GCGCGCGTGGTAGATCTATAT 60.202 52.381 32.35 0.00 0.00 0.86
441 1546 0.167470 GCGCGCGTGGTAGATCTATA 59.833 55.000 32.35 0.00 0.00 1.31
442 1547 1.081376 GCGCGCGTGGTAGATCTAT 60.081 57.895 32.35 0.00 0.00 1.98
443 1548 2.330393 GCGCGCGTGGTAGATCTA 59.670 61.111 32.35 0.00 0.00 1.98
444 1549 4.570663 GGCGCGCGTGGTAGATCT 62.571 66.667 32.35 0.00 0.00 2.75
445 1550 2.672908 TTAGGCGCGCGTGGTAGATC 62.673 60.000 34.10 13.24 0.00 2.75
446 1551 2.679132 CTTAGGCGCGCGTGGTAGAT 62.679 60.000 34.10 11.70 0.00 1.98
447 1552 3.405592 CTTAGGCGCGCGTGGTAGA 62.406 63.158 34.10 12.96 0.00 2.59
448 1553 2.954868 CTTAGGCGCGCGTGGTAG 60.955 66.667 34.10 23.11 0.00 3.18
487 1592 3.669344 CGCTCTTTTGGCCGGCAA 61.669 61.111 30.85 16.59 0.00 4.52
570 1675 3.747854 TGCATCTGATCTGGACATCTC 57.252 47.619 0.00 0.00 0.00 2.75
571 1676 4.452825 CTTTGCATCTGATCTGGACATCT 58.547 43.478 0.00 0.00 0.00 2.90
572 1677 3.003482 GCTTTGCATCTGATCTGGACATC 59.997 47.826 0.00 0.00 0.00 3.06
573 1678 2.950309 GCTTTGCATCTGATCTGGACAT 59.050 45.455 0.00 0.00 0.00 3.06
574 1679 2.362736 GCTTTGCATCTGATCTGGACA 58.637 47.619 0.00 0.00 0.00 4.02
576 1681 1.207811 TCGCTTTGCATCTGATCTGGA 59.792 47.619 0.00 0.00 0.00 3.86
582 1687 0.523072 GGCTTTCGCTTTGCATCTGA 59.477 50.000 0.00 0.00 36.09 3.27
595 1700 1.003696 AGCTTGGACCTAGTGGCTTTC 59.996 52.381 4.81 0.00 36.63 2.62
618 1726 2.159747 CGGAGCAAAACCGTTAGTTAGC 60.160 50.000 0.00 0.00 44.57 3.09
981 2101 4.437587 TCGACCCCTCCCTCCGTC 62.438 72.222 0.00 0.00 0.00 4.79
982 2102 4.444081 CTCGACCCCTCCCTCCGT 62.444 72.222 0.00 0.00 0.00 4.69
983 2103 3.438615 ATCTCGACCCCTCCCTCCG 62.439 68.421 0.00 0.00 0.00 4.63
984 2104 1.834822 CATCTCGACCCCTCCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
1570 2690 1.600916 ACCGCAGAAAGTTCCAGGC 60.601 57.895 0.00 0.00 0.00 4.85
1691 2814 3.850095 GAGAGGTATGAGGCGCGGC 62.850 68.421 27.06 27.06 0.00 6.53
1692 2815 2.196925 AGAGAGGTATGAGGCGCGG 61.197 63.158 8.83 0.00 0.00 6.46
1693 2816 1.007964 CAGAGAGGTATGAGGCGCG 60.008 63.158 0.00 0.00 0.00 6.86
1730 2853 6.363357 TCATTGATCAACGTAGCGATAATGAG 59.637 38.462 11.07 0.00 30.11 2.90
1733 2856 6.868339 TGATCATTGATCAACGTAGCGATAAT 59.132 34.615 23.72 0.00 44.70 1.28
1848 2971 2.079925 ACGCCTCTGAAAGCTGAATTC 58.920 47.619 0.00 0.00 0.00 2.17
1850 2973 1.277557 AGACGCCTCTGAAAGCTGAAT 59.722 47.619 0.00 0.00 0.00 2.57
1986 3109 1.031235 TGACCACCACATGTTGCTTG 58.969 50.000 0.00 0.00 0.00 4.01
2039 3162 0.035458 AGTGGTCTGGTAGCTTGTGC 59.965 55.000 0.00 0.00 40.05 4.57
2095 3222 3.439129 CAGATCATTGTTGCTTGCAGAGA 59.561 43.478 0.00 0.00 0.00 3.10
2114 3241 2.288579 ACACGGTGTAATCTTTCGCAGA 60.289 45.455 12.96 0.00 35.33 4.26
2116 3243 2.063266 GACACGGTGTAATCTTTCGCA 58.937 47.619 14.74 0.00 0.00 5.10
2119 3246 4.647291 CACTGACACGGTGTAATCTTTC 57.353 45.455 14.74 0.16 36.14 2.62
2158 3367 2.776536 AGGCCATGTCAGAGAATAAGCT 59.223 45.455 5.01 0.00 0.00 3.74
2159 3368 2.877168 CAGGCCATGTCAGAGAATAAGC 59.123 50.000 5.01 0.00 0.00 3.09
2160 3369 4.125703 GTCAGGCCATGTCAGAGAATAAG 58.874 47.826 5.01 0.00 0.00 1.73
2161 3370 3.430790 CGTCAGGCCATGTCAGAGAATAA 60.431 47.826 5.01 0.00 0.00 1.40
2190 3399 1.301087 TGCTGCAATGCAAAGCACC 60.301 52.632 16.54 7.13 43.04 5.01
2366 3575 1.354368 CAGTGGGTTTATGAGGGTGGT 59.646 52.381 0.00 0.00 0.00 4.16
2375 3584 2.969821 TGTTCAGGCAGTGGGTTTAT 57.030 45.000 0.00 0.00 0.00 1.40
2473 3682 0.258194 ACGTAGAATCTCCTCCCGGT 59.742 55.000 0.00 0.00 0.00 5.28
2502 3711 1.078143 GGTGATCTTGGCGCCTTCT 60.078 57.895 29.70 9.69 33.20 2.85
2559 3768 4.351054 CCCTTGCCCTTGCCGTCT 62.351 66.667 0.00 0.00 36.33 4.18
2583 3792 2.654079 CCAGCTCTTGAGGCTCCGT 61.654 63.158 12.86 0.00 38.03 4.69
2735 3949 2.568956 CTCCCTGATGAACCTGTCAAGA 59.431 50.000 0.00 0.00 40.50 3.02
2881 4095 4.864334 CGATGAGCACCAGCCCCC 62.864 72.222 0.00 0.00 43.56 5.40
3073 4292 4.331968 CAAGCCTATAAACACCACTCCAA 58.668 43.478 0.00 0.00 0.00 3.53
3074 4293 3.872240 GCAAGCCTATAAACACCACTCCA 60.872 47.826 0.00 0.00 0.00 3.86
3075 4294 2.683362 GCAAGCCTATAAACACCACTCC 59.317 50.000 0.00 0.00 0.00 3.85
3206 4460 7.410120 AAGCCAACCCTTTTATATGAGAAAG 57.590 36.000 0.00 0.00 33.67 2.62
3215 4469 4.202451 ACAATGCAAAGCCAACCCTTTTAT 60.202 37.500 0.00 0.00 32.97 1.40
3260 4514 5.921004 TGCAAAACCAATCTTTTACATGC 57.079 34.783 0.00 0.00 0.00 4.06
3276 4531 7.080724 GGTTGAAAAGTGAAAACAATGCAAAA 58.919 30.769 0.00 0.00 0.00 2.44
3292 4547 6.700960 TGTGAAAAGCATATGTGGTTGAAAAG 59.299 34.615 7.70 0.00 44.74 2.27
3293 4548 6.577103 TGTGAAAAGCATATGTGGTTGAAAA 58.423 32.000 7.70 0.00 44.74 2.29
3294 4549 6.154203 TGTGAAAAGCATATGTGGTTGAAA 57.846 33.333 7.70 0.00 44.74 2.69
3295 4550 5.781210 TGTGAAAAGCATATGTGGTTGAA 57.219 34.783 7.70 0.00 44.74 2.69
3296 4551 5.712004 CATGTGAAAAGCATATGTGGTTGA 58.288 37.500 7.70 0.00 44.74 3.18
3416 4685 4.582441 CAAGGTGTTTTTGCAGTTCAAC 57.418 40.909 0.00 0.00 33.73 3.18
3432 4702 3.074538 ACCTCTGTTCCTAAATGCAAGGT 59.925 43.478 2.88 0.00 35.48 3.50
3433 4703 3.690460 ACCTCTGTTCCTAAATGCAAGG 58.310 45.455 0.00 0.00 35.26 3.61
3470 4740 1.073897 AGTCAGAGGGCTGCCAAAC 59.926 57.895 22.05 10.72 42.01 2.93
3485 4755 6.145534 TGACGACTTATTCAACAATGTCAGTC 59.854 38.462 0.00 0.00 33.38 3.51
3486 4756 5.989168 TGACGACTTATTCAACAATGTCAGT 59.011 36.000 0.00 0.00 31.00 3.41
3501 4773 2.351447 CGAAGGCTGAGTTGACGACTTA 60.351 50.000 0.00 0.00 39.19 2.24
3631 4916 7.753309 ATAAGCTTGTCGATATGTCTAGTCT 57.247 36.000 9.86 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.