Multiple sequence alignment - TraesCS5A01G494700

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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 TraesCS5A01G494700 chr5A 100.000 4112 0 0 1 4112 663212299 663216410 0.000000e+00 7594.0
1 TraesCS5A01G494700 chr4B 91.584 2935 152 58 1 2871 613154359 613157262 0.000000e+00 3964.0
2 TraesCS5A01G494700 chr4B 93.291 1252 67 9 2870 4110 613157422 613158667 0.000000e+00 1831.0
3 TraesCS5A01G494700 chr4D 92.173 1878 106 27 2256 4110 483064372 483066231 0.000000e+00 2615.0
4 TraesCS5A01G494700 chr4D 84.480 1933 154 70 208 2071 483062329 483064184 0.000000e+00 1773.0
5 TraesCS5A01G494700 chr4D 85.185 135 18 2 3972 4105 483036518 483036385 1.990000e-28 137.0
6 TraesCS5A01G494700 chr4D 83.824 136 20 2 3972 4106 482967616 482967482 1.200000e-25 128.0
7 TraesCS5A01G494700 chr2A 86.029 544 56 11 766 1297 23479419 23478884 2.150000e-157 566.0
8 TraesCS5A01G494700 chr2A 84.946 93 8 1 105 197 121224098 121224012 5.660000e-14 89.8
9 TraesCS5A01G494700 chr2A 92.453 53 3 1 2192 2243 34328145 34328197 1.590000e-09 75.0
10 TraesCS5A01G494700 chr7D 87.912 91 5 2 107 197 289566353 289566437 7.270000e-18 102.0
11 TraesCS5A01G494700 chr5B 87.234 94 6 2 107 200 664024318 664024231 7.270000e-18 102.0
12 TraesCS5A01G494700 chr5B 84.211 95 8 3 107 200 142660041 142660129 7.320000e-13 86.1
13 TraesCS5A01G494700 chr3D 85.859 99 9 1 104 197 7263887 7263985 2.620000e-17 100.0
14 TraesCS5A01G494700 chr5D 86.957 92 6 3 106 197 46043533 46043618 9.410000e-17 99.0
15 TraesCS5A01G494700 chr5D 89.333 75 5 2 2186 2257 288588435 288588509 1.570000e-14 91.6
16 TraesCS5A01G494700 chr5D 86.486 74 7 3 2193 2263 324375065 324374992 1.230000e-10 78.7
17 TraesCS5A01G494700 chr5D 86.765 68 6 2 2193 2257 546651473 546651540 5.700000e-09 73.1
18 TraesCS5A01G494700 chr2B 85.417 96 8 3 102 197 523089955 523090044 1.220000e-15 95.3
19 TraesCS5A01G494700 chr1D 84.615 91 8 3 107 197 416034188 416034104 7.320000e-13 86.1
20 TraesCS5A01G494700 chr7A 86.957 69 6 2 2192 2257 593451919 593451987 1.590000e-09 75.0
21 TraesCS5A01G494700 chr6B 86.957 69 5 4 2188 2253 435313256 435313189 1.590000e-09 75.0
22 TraesCS5A01G494700 chrUn 85.507 69 7 2 2193 2258 50872433 50872365 7.380000e-08 69.4
23 TraesCS5A01G494700 chrUn 85.507 69 7 2 2193 2258 50890345 50890277 7.380000e-08 69.4
24 TraesCS5A01G494700 chrUn 89.286 56 5 1 2189 2243 134112285 134112340 7.380000e-08 69.4


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 TraesCS5A01G494700 chr5A 663212299 663216410 4111 False 7594.0 7594 100.0000 1 4112 1 chr5A.!!$F1 4111
1 TraesCS5A01G494700 chr4B 613154359 613158667 4308 False 2897.5 3964 92.4375 1 4110 2 chr4B.!!$F1 4109
2 TraesCS5A01G494700 chr4D 483062329 483066231 3902 False 2194.0 2615 88.3265 208 4110 2 chr4D.!!$F1 3902
3 TraesCS5A01G494700 chr2A 23478884 23479419 535 True 566.0 566 86.0290 766 1297 1 chr2A.!!$R1 531

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
665 685 0.038159 CGTGGGAGAAGACAGGTGAC 60.038 60.0 0.00 0.0 0.00 3.67 F
1161 1221 0.122435 TGGTAACCTCCCTTCCCCAT 59.878 55.0 0.00 0.0 0.00 4.00 F
1200 1265 0.757561 TCCCACGTGTCTTCTGACCA 60.758 55.0 15.65 0.0 42.28 4.02 F
2908 3297 0.752658 CCGGCACATGGATGAGACTA 59.247 55.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1578 0.959553 ATATCCTACGGGCACTCGTG 59.040 55.0 5.68 0.0 43.70 4.35 R
2889 3278 0.752658 TAGTCTCATCCATGTGCCGG 59.247 55.0 0.00 0.0 0.00 6.13 R
2935 3324 1.463674 GTGGGGACAATAACAGCAGG 58.536 55.0 0.00 0.0 46.06 4.85 R
3835 4241 0.171231 CCATCTTCGACGAGCAGACA 59.829 55.0 1.46 0.0 0.00 3.41 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 4.876107 CCATTAGCATGAAGTAACGAAGGT 59.124 41.667 0.00 0.00 31.07 3.50
44 45 6.244552 AGGTCTCAGATTCATGAAATGCTA 57.755 37.500 13.09 3.65 46.21 3.49
69 70 3.469739 ACATGAATCACATCGCAGCATA 58.530 40.909 0.00 0.00 37.07 3.14
78 79 2.483106 ACATCGCAGCATATCAATCAGC 59.517 45.455 0.00 0.00 0.00 4.26
79 80 2.243602 TCGCAGCATATCAATCAGCA 57.756 45.000 0.00 0.00 0.00 4.41
116 117 6.262496 GCACAAAAATATTACTACTCCCTCCC 59.738 42.308 0.00 0.00 0.00 4.30
119 120 7.147355 ACAAAAATATTACTACTCCCTCCCTCC 60.147 40.741 0.00 0.00 0.00 4.30
120 121 4.696040 ATATTACTACTCCCTCCCTCCC 57.304 50.000 0.00 0.00 0.00 4.30
144 145 7.250569 CCACAATATAAGAGCGTTTTTGACAT 58.749 34.615 0.00 0.00 0.00 3.06
175 176 3.050619 ACTAGTGTCGAAAACGCTCTTG 58.949 45.455 0.00 0.00 45.69 3.02
187 191 1.346395 ACGCTCTTGTATTGTGGGACA 59.654 47.619 0.00 0.00 0.00 4.02
330 337 3.795150 GCGAAGTCAAATCAACCTGCAAA 60.795 43.478 0.00 0.00 0.00 3.68
331 338 4.358851 CGAAGTCAAATCAACCTGCAAAA 58.641 39.130 0.00 0.00 0.00 2.44
343 350 0.164647 CTGCAAAACGCGAGAGAAGG 59.835 55.000 15.93 0.00 46.97 3.46
376 383 0.809385 TCAGATCCGAGACGTCAACC 59.191 55.000 19.50 5.45 0.00 3.77
404 411 0.548510 TCCTGAGATCTGAGGAGCGA 59.451 55.000 25.30 5.04 38.07 4.93
455 475 1.697284 CCCTGGAGATGACGAGATCA 58.303 55.000 0.00 0.00 43.13 2.92
496 516 4.225340 CGCGACGAGGACGAGGAG 62.225 72.222 0.00 0.00 42.66 3.69
497 517 3.878519 GCGACGAGGACGAGGAGG 61.879 72.222 0.00 0.00 42.66 4.30
498 518 2.125229 CGACGAGGACGAGGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
616 636 2.195741 AAGGCTTTAAACCCTCGTCC 57.804 50.000 2.46 0.00 0.00 4.79
660 680 2.266055 GCCCGTGGGAGAAGACAG 59.734 66.667 9.72 0.00 37.50 3.51
662 682 1.913762 CCCGTGGGAGAAGACAGGT 60.914 63.158 0.00 0.00 37.50 4.00
664 684 1.185618 CCGTGGGAGAAGACAGGTGA 61.186 60.000 0.00 0.00 0.00 4.02
665 685 0.038159 CGTGGGAGAAGACAGGTGAC 60.038 60.000 0.00 0.00 0.00 3.67
667 687 1.273886 GTGGGAGAAGACAGGTGACTC 59.726 57.143 0.00 0.00 40.21 3.36
674 713 1.004440 GACAGGTGACTCACTGGGC 60.004 63.158 9.08 0.42 40.21 5.36
869 926 0.814410 CCGTAGGCGCTAGAGTCAGA 60.814 60.000 7.64 0.00 46.14 3.27
871 928 1.807000 CGTAGGCGCTAGAGTCAGAGA 60.807 57.143 7.64 0.00 0.00 3.10
876 933 0.465460 CGCTAGAGTCAGAGAGGGCT 60.465 60.000 0.00 0.00 0.00 5.19
884 941 1.988956 CAGAGAGGGCTGCCTGTCT 60.989 63.158 19.68 19.71 40.39 3.41
885 942 1.685421 AGAGAGGGCTGCCTGTCTC 60.685 63.158 29.18 29.18 35.92 3.36
887 944 1.958902 GAGAGGGCTGCCTGTCTCTG 61.959 65.000 29.12 0.00 36.80 3.35
888 945 3.007920 AGGGCTGCCTGTCTCTGG 61.008 66.667 19.68 0.00 0.00 3.86
955 1015 2.310233 CGTCGGTCAGCACCAACAG 61.310 63.158 0.00 0.00 44.02 3.16
966 1026 1.458777 ACCAACAGTCCCACCTCGA 60.459 57.895 0.00 0.00 0.00 4.04
969 1029 0.320771 CAACAGTCCCACCTCGAAGG 60.321 60.000 0.00 0.00 42.49 3.46
981 1041 2.096248 CCTCGAAGGCAGACTAGACTT 58.904 52.381 0.00 0.00 40.27 3.01
1033 1093 2.587194 CCCAGATCAGCGCCTTCG 60.587 66.667 2.29 0.00 39.07 3.79
1147 1207 2.036098 TCCGCCTCCTCGTGGTAA 59.964 61.111 2.99 0.00 34.83 2.85
1161 1221 0.122435 TGGTAACCTCCCTTCCCCAT 59.878 55.000 0.00 0.00 0.00 4.00
1162 1222 0.844660 GGTAACCTCCCTTCCCCATC 59.155 60.000 0.00 0.00 0.00 3.51
1200 1265 0.757561 TCCCACGTGTCTTCTGACCA 60.758 55.000 15.65 0.00 42.28 4.02
1218 1283 1.740025 CCAGGACGGATGCTTTTTCTC 59.260 52.381 0.00 0.00 36.56 2.87
1317 1383 4.508461 CATCAACTGCTTCCAAACATCA 57.492 40.909 0.00 0.00 0.00 3.07
1318 1384 5.068234 CATCAACTGCTTCCAAACATCAT 57.932 39.130 0.00 0.00 0.00 2.45
1319 1385 6.198650 CATCAACTGCTTCCAAACATCATA 57.801 37.500 0.00 0.00 0.00 2.15
1320 1386 6.802608 CATCAACTGCTTCCAAACATCATAT 58.197 36.000 0.00 0.00 0.00 1.78
1333 1422 8.637099 TCCAAACATCATATTTTTGTTCAGTGA 58.363 29.630 0.00 0.00 32.66 3.41
1334 1423 9.426837 CCAAACATCATATTTTTGTTCAGTGAT 57.573 29.630 0.00 0.00 32.66 3.06
1378 1469 2.027192 TCGATTGCAGTTCCTTAAGGCT 60.027 45.455 17.32 6.23 34.44 4.58
1436 1527 1.455402 TCCTTGCTGCCTTTGCACA 60.455 52.632 0.00 0.00 44.23 4.57
1439 1530 1.425412 CTTGCTGCCTTTGCACATTC 58.575 50.000 0.00 0.00 44.23 2.67
1455 1546 0.881118 ATTCATCCGTTGCGTTTGCT 59.119 45.000 0.00 0.00 43.34 3.91
1457 1548 1.509787 CATCCGTTGCGTTTGCTCG 60.510 57.895 0.00 0.00 43.34 5.03
1460 1551 2.307309 CCGTTGCGTTTGCTCGAGA 61.307 57.895 18.75 0.00 43.34 4.04
1461 1552 1.128611 CGTTGCGTTTGCTCGAGAG 59.871 57.895 18.75 2.27 43.34 3.20
1476 1567 1.198713 GAGAGCCTTCTGTCCATCCA 58.801 55.000 0.00 0.00 32.53 3.41
1477 1568 1.556911 GAGAGCCTTCTGTCCATCCAA 59.443 52.381 0.00 0.00 32.53 3.53
1487 1578 4.326826 TCTGTCCATCCAATGTGAAGAAC 58.673 43.478 0.00 0.00 0.00 3.01
1564 1655 7.011295 AGTCATTAGCTAGTACTCACGACTTAC 59.989 40.741 0.00 0.00 0.00 2.34
1570 1661 8.364129 AGCTAGTACTCACGACTTACTAATAC 57.636 38.462 0.00 0.00 29.90 1.89
1590 1681 9.941664 CTAATACATGTTGATTTGCTCTTTAGG 57.058 33.333 2.30 0.00 0.00 2.69
1592 1683 6.899393 ACATGTTGATTTGCTCTTTAGGAA 57.101 33.333 0.00 0.00 0.00 3.36
1593 1684 7.472334 ACATGTTGATTTGCTCTTTAGGAAT 57.528 32.000 0.00 0.00 32.57 3.01
1605 1697 2.425143 TTAGGAATGCAAGAGGCCAG 57.575 50.000 5.01 0.00 43.89 4.85
1751 1850 4.069304 TGTTGGAATCAAGTAAGTTCCCG 58.931 43.478 0.00 0.00 40.51 5.14
1872 1972 3.963428 ATAATACCTCATCTGACGGGC 57.037 47.619 0.00 0.00 0.00 6.13
1959 2059 4.708726 AAACTAATGCCTTGTCTGATGC 57.291 40.909 0.00 0.00 0.00 3.91
2016 2116 7.492669 ACAATCTATTGGTCAAGTCTTATGTCG 59.507 37.037 7.56 0.00 41.96 4.35
2025 2125 3.660501 AGTCTTATGTCGCTGTTCACA 57.339 42.857 0.00 0.00 0.00 3.58
2134 2343 4.318332 TGGTCTTGTGCTCATACTTCTTG 58.682 43.478 0.00 0.00 0.00 3.02
2135 2344 4.040339 TGGTCTTGTGCTCATACTTCTTGA 59.960 41.667 0.00 0.00 0.00 3.02
2137 2346 4.991056 GTCTTGTGCTCATACTTCTTGACA 59.009 41.667 0.00 0.00 0.00 3.58
2138 2347 5.466728 GTCTTGTGCTCATACTTCTTGACAA 59.533 40.000 0.00 0.00 0.00 3.18
2145 2354 8.596380 GTGCTCATACTTCTTGACAATTACTAC 58.404 37.037 0.00 0.00 0.00 2.73
2166 2375 8.219546 ACTACCTCCGTAAGTAAATAGAAGAC 57.780 38.462 0.00 0.00 0.00 3.01
2167 2376 7.831193 ACTACCTCCGTAAGTAAATAGAAGACA 59.169 37.037 0.00 0.00 0.00 3.41
2220 2430 7.846644 AAGATGTTTTTGCAGTTCAAATTGA 57.153 28.000 0.00 0.00 43.53 2.57
2221 2431 7.846644 AGATGTTTTTGCAGTTCAAATTGAA 57.153 28.000 4.03 4.03 43.53 2.69
2238 2456 6.763303 AATTGAACGGCAAAAATGTCTTAC 57.237 33.333 0.00 0.00 40.48 2.34
2306 2524 2.424601 GAGGCATGACAAGCTAAATGCA 59.575 45.455 18.71 0.00 45.72 3.96
2368 2586 2.730550 CCAAAGTGGATTGGCAGAAC 57.269 50.000 0.00 0.00 43.11 3.01
2381 2599 0.999406 GCAGAACGCGCTTTCTCATA 59.001 50.000 24.61 0.00 33.31 2.15
2444 2669 7.984050 TGATGAGTTCATTCCATAGAGAGTTTC 59.016 37.037 0.00 0.00 36.57 2.78
2679 2905 1.099295 ACGACCGGACGAGCATCATA 61.099 55.000 31.92 0.00 37.03 2.15
2908 3297 0.752658 CCGGCACATGGATGAGACTA 59.247 55.000 0.00 0.00 0.00 2.59
2935 3324 2.813754 TCTGTGCCTTACAATTGACTGC 59.186 45.455 13.59 9.44 39.20 4.40
2941 3330 2.163010 CCTTACAATTGACTGCCTGCTG 59.837 50.000 13.59 0.00 0.00 4.41
2993 3390 7.015584 ACTCATGCCTGTTTCCTTTTATCTTTT 59.984 33.333 0.00 0.00 0.00 2.27
2994 3391 7.153985 TCATGCCTGTTTCCTTTTATCTTTTG 58.846 34.615 0.00 0.00 0.00 2.44
3082 3479 3.726607 CTGATCCTCATAGTTGCTCACC 58.273 50.000 0.00 0.00 0.00 4.02
3161 3558 7.925993 TCCTTTAATGATTTACGCAGGTTATG 58.074 34.615 0.00 0.00 0.00 1.90
3221 3618 5.551233 TGGTTAGATTTCCAGTTGAGTCAG 58.449 41.667 0.00 0.00 0.00 3.51
3280 3686 3.773560 CACTCATTTACCTTTTGGGGGA 58.226 45.455 0.00 0.00 46.08 4.81
3345 3751 8.761689 AGACTGATTGCCATTTGGTATTTTTAT 58.238 29.630 0.00 0.00 37.57 1.40
3346 3752 9.382275 GACTGATTGCCATTTGGTATTTTTATT 57.618 29.630 0.00 0.00 37.57 1.40
3532 3938 3.157217 GATGTCGGCATCGAGGGCT 62.157 63.158 21.54 2.06 46.91 5.19
3535 3941 2.839632 TCGGCATCGAGGGCTGAT 60.840 61.111 21.54 0.00 41.51 2.90
3577 3983 3.324846 TGTCAGCAGGATTTAGTCTGTGT 59.675 43.478 0.00 0.00 33.81 3.72
3580 3986 4.526650 TCAGCAGGATTTAGTCTGTGTACA 59.473 41.667 0.00 0.00 33.81 2.90
3643 4049 3.692406 GTCCTTGGCGAGGTCGGT 61.692 66.667 20.33 0.00 46.39 4.69
3661 4067 3.838271 GCGCTCTGGGGATCGTCA 61.838 66.667 0.00 0.00 34.14 4.35
3679 4085 2.124695 GACCGTCCCATGCCCTTC 60.125 66.667 0.00 0.00 0.00 3.46
3742 4148 4.643387 GTGCCTCGGCTGGGTGTT 62.643 66.667 9.65 0.00 42.51 3.32
3835 4241 4.269523 TTGGTCAGCGCCTTGGCT 62.270 61.111 2.29 0.00 46.13 4.75
3881 4287 2.291365 TCATGTTTGATCCCATCTGCG 58.709 47.619 0.00 0.00 0.00 5.18
3882 4288 2.019249 CATGTTTGATCCCATCTGCGT 58.981 47.619 0.00 0.00 0.00 5.24
3883 4289 3.118445 TCATGTTTGATCCCATCTGCGTA 60.118 43.478 0.00 0.00 0.00 4.42
3885 4291 2.027653 TGTTTGATCCCATCTGCGTACA 60.028 45.455 0.00 0.00 0.00 2.90
3887 4293 3.342377 TTGATCCCATCTGCGTACAAA 57.658 42.857 0.00 0.00 0.00 2.83
3888 4294 2.905075 TGATCCCATCTGCGTACAAAG 58.095 47.619 0.00 0.00 0.00 2.77
3889 4295 1.599542 GATCCCATCTGCGTACAAAGC 59.400 52.381 0.00 0.00 0.00 3.51
3892 4298 0.729116 CCATCTGCGTACAAAGCCAG 59.271 55.000 0.00 0.00 0.00 4.85
3895 4301 3.651480 CTGCGTACAAAGCCAGCGC 62.651 63.158 0.00 0.00 47.00 5.92
3896 4302 3.722295 GCGTACAAAGCCAGCGCA 61.722 61.111 11.47 0.00 46.23 6.09
3897 4303 2.173382 CGTACAAAGCCAGCGCAC 59.827 61.111 11.47 0.00 37.52 5.34
3900 4306 1.524849 TACAAAGCCAGCGCACACA 60.525 52.632 11.47 0.00 37.52 3.72
3901 4307 1.506309 TACAAAGCCAGCGCACACAG 61.506 55.000 11.47 0.00 37.52 3.66
3947 4353 3.008330 CTCCCAGAGCAATTGTTCAGAG 58.992 50.000 22.26 19.04 0.00 3.35
3962 4368 4.021104 TGTTCAGAGATCTTCATCAACGGT 60.021 41.667 0.00 0.00 0.00 4.83
3980 4386 4.964593 ACGGTTTTATTACCTGTGTGACT 58.035 39.130 0.00 0.00 35.97 3.41
4004 4410 0.753262 CGTAGAGGGGGAAGGTGATG 59.247 60.000 0.00 0.00 0.00 3.07
4013 4419 1.373570 GGAAGGTGATGTAGCTGCAC 58.626 55.000 6.66 4.51 37.17 4.57
4066 4472 0.182061 ATGATGCTCAGCCCGATGTT 59.818 50.000 0.00 0.00 0.00 2.71
4079 4485 2.810274 CCCGATGTTCATATGGAAGCAG 59.190 50.000 2.13 0.00 35.82 4.24
4081 4487 3.496130 CCGATGTTCATATGGAAGCAGTC 59.504 47.826 2.13 0.00 35.82 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.260114 TGTAGTTAGCATTTCATGAATCTGAGA 58.740 33.333 18.02 0.93 0.00 3.27
44 45 3.310774 GCTGCGATGTGATTCATGTAGTT 59.689 43.478 0.00 0.00 36.83 2.24
55 56 3.731089 TGATTGATATGCTGCGATGTGA 58.269 40.909 0.00 0.00 0.00 3.58
69 70 3.606846 CGTGTCACGTTTTGCTGATTGAT 60.607 43.478 17.30 0.00 36.74 2.57
99 100 4.002050 TGGGAGGGAGGGAGTAGTAATAT 58.998 47.826 0.00 0.00 0.00 1.28
100 101 3.141649 GTGGGAGGGAGGGAGTAGTAATA 59.858 52.174 0.00 0.00 0.00 0.98
106 107 0.722676 ATTGTGGGAGGGAGGGAGTA 59.277 55.000 0.00 0.00 0.00 2.59
116 117 6.093495 TCAAAAACGCTCTTATATTGTGGGAG 59.907 38.462 0.00 0.00 0.00 4.30
119 120 6.607689 TGTCAAAAACGCTCTTATATTGTGG 58.392 36.000 0.00 0.00 0.00 4.17
120 121 8.577939 CAATGTCAAAAACGCTCTTATATTGTG 58.422 33.333 0.00 0.00 0.00 3.33
163 164 3.500680 TCCCACAATACAAGAGCGTTTTC 59.499 43.478 0.00 0.00 0.00 2.29
167 168 1.346395 TGTCCCACAATACAAGAGCGT 59.654 47.619 0.00 0.00 0.00 5.07
175 176 2.188817 ACTCCCTCTGTCCCACAATAC 58.811 52.381 0.00 0.00 0.00 1.89
187 191 3.829728 ACCTACACAAGTACTCCCTCT 57.170 47.619 0.00 0.00 0.00 3.69
330 337 2.126424 GCGACCTTCTCTCGCGTT 60.126 61.111 5.77 0.00 46.32 4.84
343 350 1.929836 GATCTGATGGTCTTGTGCGAC 59.070 52.381 0.00 0.00 0.00 5.19
412 419 2.936032 GGAAGGTCAGTGGGCCCT 60.936 66.667 25.70 0.00 0.00 5.19
413 420 4.410400 CGGAAGGTCAGTGGGCCC 62.410 72.222 17.59 17.59 0.00 5.80
415 422 1.153349 GATCGGAAGGTCAGTGGGC 60.153 63.158 0.00 0.00 42.10 5.36
416 423 1.522569 GGATCGGAAGGTCAGTGGG 59.477 63.158 0.00 0.00 45.13 4.61
660 680 3.626924 ACCGCCCAGTGAGTCACC 61.627 66.667 19.71 3.48 34.49 4.02
662 682 4.314440 GCACCGCCCAGTGAGTCA 62.314 66.667 0.00 0.00 40.34 3.41
854 911 0.465460 CCTCTCTGACTCTAGCGCCT 60.465 60.000 2.29 0.00 0.00 5.52
857 914 0.465460 AGCCCTCTCTGACTCTAGCG 60.465 60.000 0.00 0.00 0.00 4.26
859 916 1.032014 GCAGCCCTCTCTGACTCTAG 58.968 60.000 0.00 0.00 36.19 2.43
869 926 1.988956 CAGAGACAGGCAGCCCTCT 60.989 63.158 8.22 10.46 40.33 3.69
871 928 3.007920 CCAGAGACAGGCAGCCCT 61.008 66.667 8.22 0.00 44.25 5.19
920 977 4.874977 GGCGAGCTAGGTCGTGGC 62.875 72.222 36.30 23.84 42.17 5.01
955 1015 2.266055 CTGCCTTCGAGGTGGGAC 59.734 66.667 0.00 0.00 37.80 4.46
966 1026 2.028930 CGTGGAAAGTCTAGTCTGCCTT 60.029 50.000 9.44 0.00 0.00 4.35
969 1029 1.351153 GCGTGGAAAGTCTAGTCTGC 58.649 55.000 0.00 0.00 0.00 4.26
1147 1207 0.030603 GAGAGATGGGGAAGGGAGGT 60.031 60.000 0.00 0.00 0.00 3.85
1161 1221 1.070786 GCGTTGTTGGGGTGAGAGA 59.929 57.895 0.00 0.00 0.00 3.10
1162 1222 0.535102 AAGCGTTGTTGGGGTGAGAG 60.535 55.000 0.00 0.00 0.00 3.20
1200 1265 3.118592 CCTAGAGAAAAAGCATCCGTCCT 60.119 47.826 0.00 0.00 0.00 3.85
1218 1283 2.496817 GGCGCCTCACAGACCTAG 59.503 66.667 22.15 0.00 0.00 3.02
1305 1371 9.480053 ACTGAACAAAAATATGATGTTTGGAAG 57.520 29.630 6.97 4.24 37.41 3.46
1334 1423 9.878667 TCGAAGAAACACAATCACCTTATTATA 57.121 29.630 0.00 0.00 0.00 0.98
1335 1424 8.786826 TCGAAGAAACACAATCACCTTATTAT 57.213 30.769 0.00 0.00 0.00 1.28
1336 1425 8.786826 ATCGAAGAAACACAATCACCTTATTA 57.213 30.769 0.00 0.00 43.58 0.98
1337 1426 7.687941 ATCGAAGAAACACAATCACCTTATT 57.312 32.000 0.00 0.00 43.58 1.40
1378 1469 3.866379 AAGCAATCCCCGTGCAGCA 62.866 57.895 0.00 0.00 44.74 4.41
1436 1527 0.881118 AGCAAACGCAACGGATGAAT 59.119 45.000 0.00 0.00 0.00 2.57
1439 1530 1.509787 CGAGCAAACGCAACGGATG 60.510 57.895 0.00 0.00 0.00 3.51
1455 1546 1.107114 GATGGACAGAAGGCTCTCGA 58.893 55.000 0.00 0.00 0.00 4.04
1457 1548 1.198713 TGGATGGACAGAAGGCTCTC 58.801 55.000 0.00 0.00 0.00 3.20
1460 1551 1.637553 ACATTGGATGGACAGAAGGCT 59.362 47.619 0.00 0.00 33.60 4.58
1461 1552 1.747355 CACATTGGATGGACAGAAGGC 59.253 52.381 0.00 0.00 33.60 4.35
1462 1553 3.354948 TCACATTGGATGGACAGAAGG 57.645 47.619 0.00 0.00 33.60 3.46
1463 1554 4.582869 TCTTCACATTGGATGGACAGAAG 58.417 43.478 0.00 0.00 33.94 2.85
1464 1555 4.639078 TCTTCACATTGGATGGACAGAA 57.361 40.909 0.00 0.00 33.60 3.02
1465 1556 4.202451 TGTTCTTCACATTGGATGGACAGA 60.202 41.667 0.00 0.00 29.78 3.41
1468 1559 3.120199 CGTGTTCTTCACATTGGATGGAC 60.120 47.826 0.00 0.00 46.44 4.02
1471 1562 3.748048 ACTCGTGTTCTTCACATTGGATG 59.252 43.478 0.00 0.00 46.44 3.51
1476 1567 1.873591 GGCACTCGTGTTCTTCACATT 59.126 47.619 0.00 0.00 46.44 2.71
1477 1568 1.512926 GGCACTCGTGTTCTTCACAT 58.487 50.000 0.00 0.00 46.44 3.21
1487 1578 0.959553 ATATCCTACGGGCACTCGTG 59.040 55.000 5.68 0.00 43.70 4.35
1489 1580 1.068472 GTGATATCCTACGGGCACTCG 60.068 57.143 0.00 0.00 0.00 4.18
1491 1582 0.959553 CGTGATATCCTACGGGCACT 59.040 55.000 7.52 0.00 36.71 4.40
1496 1587 1.002142 TGAACGCGTGATATCCTACGG 60.002 52.381 14.98 9.08 40.43 4.02
1521 1612 5.965033 ATGACTAGGATCCAACATTGAGT 57.035 39.130 15.82 5.04 0.00 3.41
1529 1620 7.527796 AGTACTAGCTAATGACTAGGATCCAA 58.472 38.462 15.82 0.00 41.22 3.53
1532 1623 7.148540 CGTGAGTACTAGCTAATGACTAGGATC 60.149 44.444 0.00 0.00 41.22 3.36
1536 1627 6.702723 AGTCGTGAGTACTAGCTAATGACTAG 59.297 42.308 12.10 0.00 41.88 2.57
1537 1628 6.580788 AGTCGTGAGTACTAGCTAATGACTA 58.419 40.000 12.10 0.00 41.88 2.59
1564 1655 9.941664 CCTAAAGAGCAAATCAACATGTATTAG 57.058 33.333 0.00 0.00 0.00 1.73
1570 1661 6.255020 GCATTCCTAAAGAGCAAATCAACATG 59.745 38.462 0.00 0.00 0.00 3.21
1588 1679 1.305623 CCTGGCCTCTTGCATTCCT 59.694 57.895 3.32 0.00 43.89 3.36
1590 1681 1.379576 AGCCTGGCCTCTTGCATTC 60.380 57.895 16.57 0.00 43.89 2.67
1592 1683 2.044252 CAGCCTGGCCTCTTGCAT 60.044 61.111 16.57 0.00 43.89 3.96
1593 1684 3.251509 TCAGCCTGGCCTCTTGCA 61.252 61.111 16.57 0.00 43.89 4.08
1605 1697 3.628032 GCAGGTCCTAAAATAACTCAGCC 59.372 47.826 0.00 0.00 0.00 4.85
1662 1761 3.118847 TGGCAGAGAGAAGAAGCATGTAG 60.119 47.826 0.00 0.00 0.00 2.74
1711 1810 3.183259 GGCGCGCCAAGAACAATA 58.817 55.556 43.55 0.00 35.81 1.90
1751 1850 2.991250 ACCATACATGACCTTGTCAGC 58.009 47.619 0.00 0.00 46.04 4.26
1847 1946 6.147328 GCCCGTCAGATGAGGTATTATAAAAC 59.853 42.308 2.24 0.00 0.00 2.43
1872 1972 8.863049 GTTTAAATTGACATATCCTTGTGCAAG 58.137 33.333 5.03 5.03 38.14 4.01
1919 2019 4.094442 AGTTTTTGACGAAGGACAAGACAC 59.906 41.667 0.00 0.00 31.16 3.67
1959 2059 7.812648 TCCAGTACCTAAAAATGTGAAAATCG 58.187 34.615 0.00 0.00 0.00 3.34
2025 2125 1.270550 GCACAGCAAATGCCACTTACT 59.729 47.619 0.94 0.00 43.38 2.24
2145 2354 8.943909 AAATGTCTTCTATTTACTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
2161 2370 6.198966 ACGAATTGAACTGCAAAAATGTCTTC 59.801 34.615 0.00 0.00 40.48 2.87
2166 2375 7.393551 AGTTACGAATTGAACTGCAAAAATG 57.606 32.000 0.00 0.00 40.48 2.32
2167 2376 9.522804 TTTAGTTACGAATTGAACTGCAAAAAT 57.477 25.926 0.00 0.00 40.48 1.82
2216 2426 5.837437 TGTAAGACATTTTTGCCGTTCAAT 58.163 33.333 0.00 0.00 34.12 2.57
2217 2427 5.250235 TGTAAGACATTTTTGCCGTTCAA 57.750 34.783 0.00 0.00 0.00 2.69
2218 2428 4.902443 TGTAAGACATTTTTGCCGTTCA 57.098 36.364 0.00 0.00 0.00 3.18
2306 2524 1.693062 TGGAACAAACTGCAATGCCAT 59.307 42.857 1.53 0.00 31.92 4.40
2368 2586 7.043986 GGAATATACATAGTATGAGAAAGCGCG 60.044 40.741 17.13 0.00 0.00 6.86
2404 2622 7.776933 TGAACTCATCACAATAGCACTTATC 57.223 36.000 0.00 0.00 31.50 1.75
2444 2669 2.857592 GCACAGGGCAATGACAATAG 57.142 50.000 0.00 0.00 43.97 1.73
2673 2899 7.210174 TCTACAAGATCCCGTCTTTTATGATG 58.790 38.462 0.00 0.00 44.80 3.07
2679 2905 5.187967 ACATCTCTACAAGATCCCGTCTTTT 59.812 40.000 0.00 0.00 44.80 2.27
2889 3278 0.752658 TAGTCTCATCCATGTGCCGG 59.247 55.000 0.00 0.00 0.00 6.13
2908 3297 4.892934 TCAATTGTAAGGCACAGAAAAGGT 59.107 37.500 5.13 0.00 38.72 3.50
2935 3324 1.463674 GTGGGGACAATAACAGCAGG 58.536 55.000 0.00 0.00 46.06 4.85
2941 3330 2.215942 AGCAAGGTGGGGACAATAAC 57.784 50.000 0.00 0.00 46.06 1.89
2974 3363 8.404107 TCCTACAAAAGATAAAAGGAAACAGG 57.596 34.615 0.00 0.00 30.34 4.00
2977 3366 9.639601 CCATTCCTACAAAAGATAAAAGGAAAC 57.360 33.333 5.77 0.00 44.06 2.78
2993 3390 4.080072 TGACACATATTGGCCATTCCTACA 60.080 41.667 6.09 0.00 35.26 2.74
2994 3391 4.275936 GTGACACATATTGGCCATTCCTAC 59.724 45.833 6.09 0.00 35.26 3.18
3082 3479 2.713895 TTGACACGAGCTCTTCTCTG 57.286 50.000 12.85 0.00 39.70 3.35
3161 3558 7.489435 GCTTTTTGGGAAGAAACAATCTATAGC 59.511 37.037 0.00 0.00 37.42 2.97
3345 3751 5.656416 ACAAACAAAAACCCTCTCATCTCAA 59.344 36.000 0.00 0.00 0.00 3.02
3346 3752 5.067674 CACAAACAAAAACCCTCTCATCTCA 59.932 40.000 0.00 0.00 0.00 3.27
3430 3836 6.149973 CCAATGTATAGCCAACATAGGATGTG 59.850 42.308 0.00 0.00 44.07 3.21
3529 3935 0.179097 GGTCGGTCTCTTCATCAGCC 60.179 60.000 0.00 0.00 0.00 4.85
3532 3938 1.475403 GGAGGTCGGTCTCTTCATCA 58.525 55.000 6.04 0.00 34.39 3.07
3535 3941 2.341101 GCGGAGGTCGGTCTCTTCA 61.341 63.158 6.04 0.00 39.69 3.02
3577 3983 2.118233 TTGTGGTGGCGCATCCTGTA 62.118 55.000 10.83 0.00 35.26 2.74
3580 3986 2.672996 GTTGTGGTGGCGCATCCT 60.673 61.111 10.83 0.00 35.26 3.24
3661 4067 2.610859 AAGGGCATGGGACGGTCT 60.611 61.111 8.23 0.00 0.00 3.85
3679 4085 3.052082 CCGGTGCACCTGCTTCAG 61.052 66.667 32.28 15.38 42.66 3.02
3835 4241 0.171231 CCATCTTCGACGAGCAGACA 59.829 55.000 1.46 0.00 0.00 3.41
3881 4287 1.082104 GTGTGCGCTGGCTTTGTAC 60.082 57.895 9.73 0.00 40.82 2.90
3882 4288 1.506309 CTGTGTGCGCTGGCTTTGTA 61.506 55.000 9.73 0.00 40.82 2.41
3883 4289 2.828095 TGTGTGCGCTGGCTTTGT 60.828 55.556 9.73 0.00 40.82 2.83
3885 4291 1.601759 ATCTGTGTGCGCTGGCTTT 60.602 52.632 9.73 0.00 40.82 3.51
3887 4293 2.532465 ATCATCTGTGTGCGCTGGCT 62.532 55.000 9.73 0.00 40.82 4.75
3888 4294 1.651240 AATCATCTGTGTGCGCTGGC 61.651 55.000 9.73 0.00 40.52 4.85
3889 4295 1.655484 TAATCATCTGTGTGCGCTGG 58.345 50.000 9.73 0.00 0.00 4.85
3892 4298 1.268234 GCCTTAATCATCTGTGTGCGC 60.268 52.381 0.00 0.00 0.00 6.09
3895 4301 3.064958 CAGCAGCCTTAATCATCTGTGTG 59.935 47.826 0.00 0.00 0.00 3.82
3896 4302 3.276857 CAGCAGCCTTAATCATCTGTGT 58.723 45.455 0.00 0.00 0.00 3.72
3897 4303 3.276857 ACAGCAGCCTTAATCATCTGTG 58.723 45.455 0.00 0.00 32.77 3.66
3900 4306 4.853007 AGAAACAGCAGCCTTAATCATCT 58.147 39.130 0.00 0.00 0.00 2.90
3901 4307 4.036144 GGAGAAACAGCAGCCTTAATCATC 59.964 45.833 0.00 0.00 0.00 2.92
3947 4353 8.122952 CAGGTAATAAAACCGTTGATGAAGATC 58.877 37.037 0.00 0.00 44.77 2.75
3962 4368 4.628333 GCGCTAGTCACACAGGTAATAAAA 59.372 41.667 0.00 0.00 0.00 1.52
3980 4386 1.826921 CTTCCCCCTCTACGCGCTA 60.827 63.158 5.73 0.00 0.00 4.26
4004 4410 0.321671 TCCAGTTCCTGTGCAGCTAC 59.678 55.000 0.00 0.00 0.00 3.58
4022 4428 4.792804 GTGCTGGGGCTGGCTCTC 62.793 72.222 1.76 0.00 39.59 3.20
4079 4485 4.699522 ACGCCCGGCTTGAAGGAC 62.700 66.667 8.05 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.