Multiple sequence alignment - TraesCS7D01G264900

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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 TraesCS7D01G264900 chr7D 100.000 6317 0 0 1 6317 246028090 246034406 0.000000e+00 11666.0
1 TraesCS7D01G264900 chr7D 88.462 364 40 2 3015 3377 390684915 390685277 7.520000e-119 438.0
2 TraesCS7D01G264900 chr7B 95.199 3374 97 26 2 3349 222303797 222307131 0.000000e+00 5273.0
3 TraesCS7D01G264900 chr7B 98.017 1715 25 2 3350 5055 222307466 222309180 0.000000e+00 2970.0
4 TraesCS7D01G264900 chr7B 94.027 1172 43 10 5056 6203 222309259 222310427 0.000000e+00 1751.0
5 TraesCS7D01G264900 chr7B 89.256 363 34 2 3015 3377 387155704 387156061 3.470000e-122 449.0
6 TraesCS7D01G264900 chr7A 95.159 2458 86 10 1 2426 262463416 262465872 0.000000e+00 3849.0
7 TraesCS7D01G264900 chr7A 96.855 1113 35 0 3694 4806 262467088 262468200 0.000000e+00 1862.0
8 TraesCS7D01G264900 chr7A 89.954 1095 48 21 5061 6130 262468411 262469468 0.000000e+00 1356.0
9 TraesCS7D01G264900 chr7A 85.992 257 16 6 3383 3619 262466699 262466955 2.260000e-64 257.0
10 TraesCS7D01G264900 chr7A 96.063 127 5 0 4929 5055 262468195 262468321 2.310000e-49 207.0
11 TraesCS7D01G264900 chr7A 90.385 156 10 4 2433 2586 262465951 262466103 3.860000e-47 200.0
12 TraesCS7D01G264900 chr5A 91.257 366 29 1 3015 3377 365931082 365930717 4.400000e-136 496.0
13 TraesCS7D01G264900 chr5A 81.935 155 24 3 6045 6197 279116410 279116562 1.850000e-25 128.0
14 TraesCS7D01G264900 chr3D 90.515 369 28 5 3015 3377 263812252 263812619 1.230000e-131 481.0
15 TraesCS7D01G264900 chr1B 90.331 362 32 1 3019 3377 440279960 440280321 7.410000e-129 472.0
16 TraesCS7D01G264900 chr1B 85.714 147 19 2 6045 6191 484008328 484008472 3.050000e-33 154.0
17 TraesCS7D01G264900 chr5D 89.071 366 37 1 3015 3377 485614829 485615194 9.660000e-123 451.0
18 TraesCS7D01G264900 chr5D 82.051 156 21 6 6045 6197 213956737 213956888 6.650000e-25 126.0
19 TraesCS7D01G264900 chr3B 88.889 369 34 2 3015 3377 333460480 333460113 1.250000e-121 448.0
20 TraesCS7D01G264900 chr3A 88.767 365 34 2 3019 3377 353160537 353160900 2.090000e-119 440.0
21 TraesCS7D01G264900 chr2D 81.944 144 25 1 6058 6200 594646025 594646168 3.090000e-23 121.0
22 TraesCS7D01G264900 chr5B 82.963 135 19 3 6045 6177 228506917 228507049 1.110000e-22 119.0
23 TraesCS7D01G264900 chr1A 80.952 147 27 1 6045 6191 460998233 460998378 1.440000e-21 115.0
24 TraesCS7D01G264900 chr1D 80.741 135 23 3 6045 6178 361359166 361359298 1.120000e-17 102.0
25 TraesCS7D01G264900 chrUn 79.710 138 25 3 6058 6194 16392679 16392814 5.210000e-16 97.1


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 TraesCS7D01G264900 chr7D 246028090 246034406 6316 False 11666.000000 11666 100.000000 1 6317 1 chr7D.!!$F1 6316
1 TraesCS7D01G264900 chr7B 222303797 222310427 6630 False 3331.333333 5273 95.747667 2 6203 3 chr7B.!!$F2 6201
2 TraesCS7D01G264900 chr7A 262463416 262469468 6052 False 1288.500000 3849 92.401333 1 6130 6 chr7A.!!$F1 6129

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
70 71 1.478654 CGGCCAGCCCATAATAAACCT 60.479 52.381 2.24 0.0 0.00 3.50 F
1103 1121 1.022735 GATCCGGTGCTTCTCGTAGA 58.977 55.000 0.00 0.0 0.00 2.59 F
1477 1496 0.802494 CTTCATGGTTTTCGGTCCGG 59.198 55.000 12.29 0.0 0.00 5.14 F
3136 3476 0.176680 CGGACTCCTCCCATGTCAAG 59.823 60.000 0.00 0.0 31.93 3.02 F
3351 4025 0.108138 AACATGCACCTCTCCGCTAC 60.108 55.000 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1481 0.178984 AAACCCGGACCGAAAACCAT 60.179 50.000 17.49 0.00 0.00 3.55 R
2996 3336 2.030335 GCGAAAAAGGCTTTGTTGTTGG 59.970 45.455 14.19 6.52 0.00 3.77 R
3331 3671 0.108186 TAGCGGAGAGGTGCATGTTG 60.108 55.000 0.00 0.00 0.00 3.33 R
4901 5650 1.468520 GCTAGTTTCCGAGCAATGCAA 59.531 47.619 8.35 0.00 38.97 4.08 R
5353 6190 1.651240 CTGAAGGCATGAGCAACGGG 61.651 60.000 0.00 0.00 44.61 5.28 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
70 71 1.478654 CGGCCAGCCCATAATAAACCT 60.479 52.381 2.24 0.00 0.00 3.50
144 145 3.701532 TCAAACGACAATTGACCAACC 57.298 42.857 13.59 0.00 32.10 3.77
193 194 3.436704 CAGAACCAACATTCGCATACTGT 59.563 43.478 0.00 0.00 33.57 3.55
199 200 4.985413 CAACATTCGCATACTGTTGGATT 58.015 39.130 9.96 0.00 43.71 3.01
298 311 5.595885 CCAATTGTACCACATGAACAAACA 58.404 37.500 0.00 0.00 36.75 2.83
398 416 4.717313 GGCTTGTGGTCGGGGTCC 62.717 72.222 0.00 0.00 0.00 4.46
866 884 3.547868 CCTTCATGATGTACTTCGTGACG 59.452 47.826 25.40 23.23 40.45 4.35
929 947 5.204409 TCAGGAAGTTAACGCTGTTTCTA 57.796 39.130 0.00 0.00 0.00 2.10
1031 1049 4.424711 GGGACCCGCATTCTGGCA 62.425 66.667 0.00 0.00 0.00 4.92
1103 1121 1.022735 GATCCGGTGCTTCTCGTAGA 58.977 55.000 0.00 0.00 0.00 2.59
1135 1153 2.261671 GCGGTCATGTGGTCGACT 59.738 61.111 16.46 0.00 32.57 4.18
1295 1313 2.203070 CCGACCTGCCATACCAGC 60.203 66.667 0.00 0.00 0.00 4.85
1462 1481 0.819259 GTGAGGCCTTGTGTGCTTCA 60.819 55.000 6.77 0.00 41.78 3.02
1475 1494 1.068541 GTGCTTCATGGTTTTCGGTCC 60.069 52.381 0.00 0.00 0.00 4.46
1477 1496 0.802494 CTTCATGGTTTTCGGTCCGG 59.198 55.000 12.29 0.00 0.00 5.14
1662 1684 6.879458 TGGAGTAAGACTTCCTTTTCTTATGC 59.121 38.462 0.00 0.00 36.84 3.14
1771 1793 7.656137 TGATTTAGCTTTAGGAAATAGGTAGCG 59.344 37.037 0.00 0.00 32.68 4.26
1805 1827 2.798009 GCAGTGGTGTGCGTTGTT 59.202 55.556 0.00 0.00 32.74 2.83
1820 1842 4.397730 TGCGTTGTTGATTGGCTATGTTAT 59.602 37.500 0.00 0.00 0.00 1.89
2333 2357 7.490402 CCTGAAATCTGCTTTCCATTTTCATAC 59.510 37.037 1.93 0.00 42.23 2.39
2335 2359 8.030692 TGAAATCTGCTTTCCATTTTCATACTG 58.969 33.333 1.93 0.00 42.23 2.74
2336 2360 7.472334 AATCTGCTTTCCATTTTCATACTGT 57.528 32.000 0.00 0.00 0.00 3.55
2339 2363 6.660521 TCTGCTTTCCATTTTCATACTGTCAT 59.339 34.615 0.00 0.00 0.00 3.06
2454 2576 2.489938 TAAGGCTGGCGATGAAGTTT 57.510 45.000 0.00 0.00 0.00 2.66
2600 2760 6.095432 AGCAGATTCCATGAGACATAGTAC 57.905 41.667 0.00 0.00 0.00 2.73
2922 3262 9.995003 ACTTTGTTTAATTAAGATGGCAATTCA 57.005 25.926 0.00 0.00 0.00 2.57
2996 3336 9.048446 TGACTAAATTACTAACTCCAACAACAC 57.952 33.333 0.00 0.00 0.00 3.32
3014 3354 4.014569 ACACCAACAACAAAGCCTTTTT 57.985 36.364 0.00 0.00 0.00 1.94
3058 3398 3.397482 CACATGGATAGCTAGCTTCCAC 58.603 50.000 32.71 19.75 42.09 4.02
3068 3408 4.643387 GCTTCCACGCACCCCTGT 62.643 66.667 0.00 0.00 0.00 4.00
3091 3431 3.751175 CCATGGCTAGTTCTTTCGTGAAA 59.249 43.478 0.00 0.00 0.00 2.69
3136 3476 0.176680 CGGACTCCTCCCATGTCAAG 59.823 60.000 0.00 0.00 31.93 3.02
3146 3486 4.506625 CCTCCCATGTCAAGTTTGGTCTAA 60.507 45.833 0.00 0.00 0.00 2.10
3173 3513 6.350864 CCGACCTCTCTTGATATAATCAGCAT 60.351 42.308 0.00 0.00 40.94 3.79
3201 3541 4.529219 TCCGCTATGCACTGGCCG 62.529 66.667 0.00 0.00 40.13 6.13
3235 3575 3.894759 CCCAAACCATCTCAGATGATGT 58.105 45.455 16.90 3.40 41.47 3.06
3331 3671 2.785868 GTGGCCACACATCCATCTC 58.214 57.895 31.23 0.00 46.90 2.75
3351 4025 0.108138 AACATGCACCTCTCCGCTAC 60.108 55.000 0.00 0.00 0.00 3.58
3378 4052 0.865111 TGTTGAACATGTCGCCTTCG 59.135 50.000 0.00 0.00 0.00 3.79
3429 4103 7.870445 TCAAATTACCTAAACCTGATTTGTTGC 59.130 33.333 0.00 0.00 36.43 4.17
3486 4160 4.941263 TGTGCTGGGTTCTGTTATAATGAC 59.059 41.667 0.00 0.00 0.00 3.06
3673 4409 6.992063 ATTGCTGACTTCTGTCGATTTTAT 57.008 33.333 0.00 0.00 45.70 1.40
4069 4818 4.616553 TCCAAGCACTAGGTATTCCTACA 58.383 43.478 0.00 0.00 44.58 2.74
4510 5259 6.213600 CCCATATAACACAAGGGCTAGTCTAT 59.786 42.308 0.00 0.00 31.81 1.98
4603 5352 2.810852 CCCAGTCTTCAGAAGAAACTGC 59.189 50.000 19.88 7.72 39.67 4.40
4697 5446 3.061369 TGGCCTCTCCTCCTGTATACTA 58.939 50.000 3.32 0.00 35.26 1.82
4770 5519 5.983540 ACCTAGAGAATCATTCTGGTGTTC 58.016 41.667 4.06 0.00 40.87 3.18
5343 6180 1.297664 GGTGCTGAGCATGTGATCTC 58.702 55.000 11.58 0.00 41.91 2.75
5353 6190 6.743110 TGAGCATGTGATCTCTAACTGTATC 58.257 40.000 0.00 0.00 0.00 2.24
5498 6337 1.293924 ATACGCAGACTGATGCAAGC 58.706 50.000 6.65 0.00 46.87 4.01
5550 6389 0.174845 GCACGTACTAGTGGCCATCA 59.825 55.000 9.72 0.00 42.09 3.07
5557 6396 4.394920 CGTACTAGTGGCCATCATTTTGTT 59.605 41.667 9.72 0.00 0.00 2.83
5558 6397 4.789012 ACTAGTGGCCATCATTTTGTTG 57.211 40.909 9.72 0.00 0.00 3.33
5559 6398 2.460757 AGTGGCCATCATTTTGTTGC 57.539 45.000 9.72 0.00 0.00 4.17
5690 6537 0.387929 TGTGTGAACACCGAGGACTC 59.612 55.000 10.92 0.00 45.88 3.36
5742 6589 1.464997 GATGCAACTTCCTCGTGGTTC 59.535 52.381 2.99 0.00 34.23 3.62
5792 6639 0.108585 AAGGCGGTTGCTTTCTGAGA 59.891 50.000 0.00 0.00 35.10 3.27
5804 6651 7.225341 GGTTGCTTTCTGAGATTGTTTTTGATT 59.775 33.333 0.00 0.00 0.00 2.57
5999 6857 7.495901 AGCTGATACCAGTATATGCACATATC 58.504 38.462 6.42 0.52 42.35 1.63
6003 6861 8.527810 TGATACCAGTATATGCACATATCGAAA 58.472 33.333 6.42 0.00 35.71 3.46
6036 6894 9.602568 TTAACATGACACTTACTTTTGTCTACA 57.397 29.630 0.00 0.00 42.31 2.74
6038 6896 8.142994 ACATGACACTTACTTTTGTCTACAAG 57.857 34.615 0.00 0.00 42.31 3.16
6040 6898 8.491152 CATGACACTTACTTTTGTCTACAAGAG 58.509 37.037 10.82 10.82 42.31 2.85
6133 7006 1.196200 ACAAACGCATCAAAACACGC 58.804 45.000 0.00 0.00 0.00 5.34
6151 7024 9.772973 AAAACACGCCTATATACATTCTATTCA 57.227 29.630 0.00 0.00 0.00 2.57
6226 7099 9.790297 ACTACTTGATATTCATATCCCATACCT 57.210 33.333 4.66 0.00 38.66 3.08
6228 7101 7.341805 ACTTGATATTCATATCCCATACCTGC 58.658 38.462 4.66 0.00 38.66 4.85
6229 7102 6.252599 TGATATTCATATCCCATACCTGCC 57.747 41.667 4.66 0.00 38.66 4.85
6230 7103 5.730697 TGATATTCATATCCCATACCTGCCA 59.269 40.000 4.66 0.00 38.66 4.92
6231 7104 6.390758 TGATATTCATATCCCATACCTGCCAT 59.609 38.462 4.66 0.00 38.66 4.40
6232 7105 4.305539 TTCATATCCCATACCTGCCATG 57.694 45.455 0.00 0.00 0.00 3.66
6233 7106 2.025981 TCATATCCCATACCTGCCATGC 60.026 50.000 0.00 0.00 0.00 4.06
6234 7107 1.746157 TATCCCATACCTGCCATGCT 58.254 50.000 0.00 0.00 0.00 3.79
6235 7108 0.855598 ATCCCATACCTGCCATGCTT 59.144 50.000 0.00 0.00 0.00 3.91
6236 7109 0.106569 TCCCATACCTGCCATGCTTG 60.107 55.000 0.00 0.00 0.00 4.01
6237 7110 0.396139 CCCATACCTGCCATGCTTGT 60.396 55.000 0.00 0.00 0.00 3.16
6238 7111 1.133823 CCCATACCTGCCATGCTTGTA 60.134 52.381 0.00 0.00 0.00 2.41
6239 7112 2.489619 CCCATACCTGCCATGCTTGTAT 60.490 50.000 0.00 0.00 0.00 2.29
6240 7113 3.244875 CCCATACCTGCCATGCTTGTATA 60.245 47.826 0.00 0.00 29.86 1.47
6241 7114 3.753272 CCATACCTGCCATGCTTGTATAC 59.247 47.826 0.00 0.00 29.86 1.47
6242 7115 4.388485 CATACCTGCCATGCTTGTATACA 58.612 43.478 0.08 0.08 29.86 2.29
6243 7116 3.582998 ACCTGCCATGCTTGTATACAT 57.417 42.857 6.36 0.00 0.00 2.29
6244 7117 3.216800 ACCTGCCATGCTTGTATACATG 58.783 45.455 6.36 10.32 42.67 3.21
6251 7124 3.838244 TGCTTGTATACATGGAGGACC 57.162 47.619 17.67 3.72 0.00 4.46
6265 7138 5.645056 TGGAGGACCAAGCATATGATTAA 57.355 39.130 5.78 0.00 43.91 1.40
6266 7139 5.624159 TGGAGGACCAAGCATATGATTAAG 58.376 41.667 5.78 3.75 43.91 1.85
6267 7140 5.132648 TGGAGGACCAAGCATATGATTAAGT 59.867 40.000 5.78 7.06 43.91 2.24
6268 7141 5.471456 GGAGGACCAAGCATATGATTAAGTG 59.529 44.000 5.78 0.00 35.97 3.16
6269 7142 4.823989 AGGACCAAGCATATGATTAAGTGC 59.176 41.667 15.37 15.37 37.84 4.40
6271 7144 5.278169 GGACCAAGCATATGATTAAGTGCTG 60.278 44.000 15.69 1.24 46.37 4.41
6272 7145 5.195940 ACCAAGCATATGATTAAGTGCTGT 58.804 37.500 5.78 0.00 46.37 4.40
6273 7146 5.066893 ACCAAGCATATGATTAAGTGCTGTG 59.933 40.000 5.78 0.00 46.37 3.66
6274 7147 5.297527 CCAAGCATATGATTAAGTGCTGTGA 59.702 40.000 5.78 0.00 46.37 3.58
6275 7148 6.183360 CCAAGCATATGATTAAGTGCTGTGAA 60.183 38.462 5.78 0.00 46.37 3.18
6276 7149 7.423199 CAAGCATATGATTAAGTGCTGTGAAT 58.577 34.615 5.78 0.00 46.37 2.57
6277 7150 8.562052 CAAGCATATGATTAAGTGCTGTGAATA 58.438 33.333 5.78 0.00 46.37 1.75
6278 7151 8.681486 AGCATATGATTAAGTGCTGTGAATAA 57.319 30.769 6.97 0.00 45.44 1.40
6279 7152 8.562892 AGCATATGATTAAGTGCTGTGAATAAC 58.437 33.333 6.97 0.00 45.44 1.89
6280 7153 7.805071 GCATATGATTAAGTGCTGTGAATAACC 59.195 37.037 6.97 0.00 34.85 2.85
6281 7154 8.839343 CATATGATTAAGTGCTGTGAATAACCA 58.161 33.333 0.00 0.00 0.00 3.67
6282 7155 6.494893 TGATTAAGTGCTGTGAATAACCAC 57.505 37.500 0.00 0.00 37.55 4.16
6283 7156 5.414454 TGATTAAGTGCTGTGAATAACCACC 59.586 40.000 0.00 0.00 36.26 4.61
6284 7157 2.949177 AGTGCTGTGAATAACCACCA 57.051 45.000 0.00 0.00 36.26 4.17
6285 7158 3.439857 AGTGCTGTGAATAACCACCAT 57.560 42.857 0.00 0.00 36.26 3.55
6286 7159 3.084039 AGTGCTGTGAATAACCACCATG 58.916 45.455 0.00 0.00 36.26 3.66
6287 7160 2.164219 GTGCTGTGAATAACCACCATGG 59.836 50.000 11.19 11.19 45.02 3.66
6288 7161 1.750778 GCTGTGAATAACCACCATGGG 59.249 52.381 18.09 4.89 43.37 4.00
6289 7162 1.750778 CTGTGAATAACCACCATGGGC 59.249 52.381 18.09 0.00 43.37 5.36
6290 7163 1.357420 TGTGAATAACCACCATGGGCT 59.643 47.619 18.09 0.00 43.37 5.19
6291 7164 2.578480 TGTGAATAACCACCATGGGCTA 59.422 45.455 18.09 1.71 43.37 3.93
6292 7165 3.204158 TGTGAATAACCACCATGGGCTAT 59.796 43.478 18.09 4.13 43.37 2.97
6293 7166 4.413851 TGTGAATAACCACCATGGGCTATA 59.586 41.667 18.09 4.38 43.37 1.31
6294 7167 5.074377 TGTGAATAACCACCATGGGCTATAT 59.926 40.000 18.09 6.63 43.37 0.86
6295 7168 5.415701 GTGAATAACCACCATGGGCTATATG 59.584 44.000 18.09 3.54 43.37 1.78
6297 7170 2.132303 ACCACCATGGGCTATATGGA 57.868 50.000 20.58 0.00 46.42 3.41
6298 7171 1.988107 ACCACCATGGGCTATATGGAG 59.012 52.381 20.58 11.48 46.42 3.86
6299 7172 1.340405 CCACCATGGGCTATATGGAGC 60.340 57.143 18.09 0.00 46.42 4.70
6300 7173 0.615331 ACCATGGGCTATATGGAGCG 59.385 55.000 18.09 0.00 46.42 5.03
6301 7174 0.615331 CCATGGGCTATATGGAGCGT 59.385 55.000 2.85 0.00 46.42 5.07
6302 7175 1.406069 CCATGGGCTATATGGAGCGTC 60.406 57.143 2.85 0.00 46.42 5.19
6303 7176 1.552337 CATGGGCTATATGGAGCGTCT 59.448 52.381 0.00 0.00 43.83 4.18
6304 7177 2.597578 TGGGCTATATGGAGCGTCTA 57.402 50.000 0.00 0.00 43.83 2.59
6305 7178 2.447443 TGGGCTATATGGAGCGTCTAG 58.553 52.381 0.00 0.00 43.83 2.43
6306 7179 1.751924 GGGCTATATGGAGCGTCTAGG 59.248 57.143 0.00 0.00 43.83 3.02
6307 7180 2.448453 GGCTATATGGAGCGTCTAGGT 58.552 52.381 0.00 0.00 43.83 3.08
6308 7181 3.618351 GGCTATATGGAGCGTCTAGGTA 58.382 50.000 0.00 0.00 43.83 3.08
6309 7182 3.377798 GGCTATATGGAGCGTCTAGGTAC 59.622 52.174 0.00 0.00 43.83 3.34
6310 7183 3.063725 GCTATATGGAGCGTCTAGGTACG 59.936 52.174 0.00 0.00 45.58 3.67
6311 7184 1.888215 TATGGAGCGTCTAGGTACGG 58.112 55.000 6.16 0.00 43.06 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.769739 ATCTTCTGGTGTGCAGTACAA 57.230 42.857 0.00 0.00 41.89 2.41
144 145 9.659830 GTTACTGTTGTACTGGAATTTAGTTTG 57.340 33.333 0.00 0.00 0.00 2.93
193 194 8.972458 TTGTTGATTCGATCCTATTAATCCAA 57.028 30.769 0.00 0.00 0.00 3.53
199 200 7.054124 AGGCTTTTGTTGATTCGATCCTATTA 58.946 34.615 0.00 0.00 0.00 0.98
298 311 1.802880 CGCAGTCGCTATAGGCTTGTT 60.803 52.381 1.04 0.00 39.13 2.83
317 330 1.680735 CTCCACTCCTCTCTCATTCCG 59.319 57.143 0.00 0.00 0.00 4.30
866 884 2.042831 GTCAGCCCCACATGTCAGC 61.043 63.158 0.00 0.00 0.00 4.26
929 947 1.615424 AGTAGGGCGGTGGTCCAAT 60.615 57.895 0.00 0.00 41.80 3.16
1031 1049 3.336122 ACGGAAGTACGACCTGTCT 57.664 52.632 9.08 0.00 46.88 3.41
1089 1107 1.335142 CCGCTATCTACGAGAAGCACC 60.335 57.143 0.00 0.00 32.02 5.01
1164 1182 3.391382 CCGGGAGAAGGAGGCGTT 61.391 66.667 0.00 0.00 0.00 4.84
1462 1481 0.178984 AAACCCGGACCGAAAACCAT 60.179 50.000 17.49 0.00 0.00 3.55
1475 1494 2.017049 CTCAAGCCAATCCTAAACCCG 58.983 52.381 0.00 0.00 0.00 5.28
1477 1496 3.826729 ACAACTCAAGCCAATCCTAAACC 59.173 43.478 0.00 0.00 0.00 3.27
1662 1684 5.634859 GCCAAATGATCCAAGTTTAACAGTG 59.365 40.000 0.00 0.00 0.00 3.66
1771 1793 7.065803 ACACCACTGCATAACATTCTATACAAC 59.934 37.037 0.00 0.00 0.00 3.32
1786 1808 1.383456 AACAACGCACACCACTGCAT 61.383 50.000 0.00 0.00 36.94 3.96
1805 1827 4.349048 AGGAGCTCATAACATAGCCAATCA 59.651 41.667 17.19 0.00 39.64 2.57
1820 1842 5.128827 AGAATAATTACAACCGAGGAGCTCA 59.871 40.000 17.19 0.00 0.00 4.26
1984 2006 3.555966 AGCAACAACAGTAGAAGCCTTT 58.444 40.909 0.00 0.00 0.00 3.11
2454 2576 4.973168 ACACAAGAATTCTAGCAGTGGAA 58.027 39.130 22.91 0.00 0.00 3.53
2559 2685 7.661536 ATCTGCTTCATAGTACAAGGAACTA 57.338 36.000 0.00 0.00 38.49 2.24
2600 2760 5.885230 TGATTTTCTACACTGCTTGATGG 57.115 39.130 0.00 0.00 0.00 3.51
2713 2874 9.515226 GGCTAATTAACATATTCACTCCCAATA 57.485 33.333 0.00 0.00 0.00 1.90
2921 3261 3.124560 TGTTGTTGTCTTGCATTGCATG 58.875 40.909 12.95 14.85 38.76 4.06
2922 3262 3.455990 TGTTGTTGTCTTGCATTGCAT 57.544 38.095 12.95 0.00 38.76 3.96
2923 3263 2.955477 TGTTGTTGTCTTGCATTGCA 57.045 40.000 7.38 7.38 36.47 4.08
2924 3264 3.864583 TCTTTGTTGTTGTCTTGCATTGC 59.135 39.130 0.46 0.46 0.00 3.56
2925 3265 4.027458 CGTCTTTGTTGTTGTCTTGCATTG 60.027 41.667 0.00 0.00 0.00 2.82
2996 3336 2.030335 GCGAAAAAGGCTTTGTTGTTGG 59.970 45.455 14.19 6.52 0.00 3.77
3068 3408 2.565391 TCACGAAAGAACTAGCCATGGA 59.435 45.455 18.40 0.00 0.00 3.41
3091 3431 4.882559 AGAGAGATCTGAAGGACTGGAAT 58.117 43.478 0.00 0.00 0.00 3.01
3146 3486 5.394738 TGATTATATCAAGAGAGGTCGGGT 58.605 41.667 0.00 0.00 36.11 5.28
3201 3541 0.249031 GTTTGGGCATATTCAGCGCC 60.249 55.000 2.29 0.00 45.47 6.53
3204 3544 2.961062 AGATGGTTTGGGCATATTCAGC 59.039 45.455 0.00 0.00 0.00 4.26
3235 3575 4.279169 CCAATTGAAGAGAAGCTTGTCCAA 59.721 41.667 19.26 16.61 36.83 3.53
3331 3671 0.108186 TAGCGGAGAGGTGCATGTTG 60.108 55.000 0.00 0.00 0.00 3.33
3351 4025 3.363970 GCGACATGTTCAACAGTAAGGTG 60.364 47.826 0.00 0.00 35.78 4.00
3378 4052 3.211045 TGTTGGAGTTGGTAAAGAGTGC 58.789 45.455 0.00 0.00 0.00 4.40
3429 4103 2.609459 GGTCATCGTATCACAAAGCAGG 59.391 50.000 0.00 0.00 0.00 4.85
3569 4259 8.192110 GCAAAGAGCTAACTATAGAGTAACACT 58.808 37.037 6.78 0.00 41.15 3.55
3673 4409 1.136305 GCCTCACCACAGCGATAAGTA 59.864 52.381 0.00 0.00 0.00 2.24
4069 4818 7.362401 CCAGCAGCTAAATAAATGTTTGTCTCT 60.362 37.037 0.00 0.00 0.00 3.10
4510 5259 5.304686 CTACCAATTGGAAGGTGGCTATA 57.695 43.478 31.22 7.64 38.87 1.31
4563 5312 2.359107 ATGACGCCCACTGCAGTG 60.359 61.111 35.15 35.15 45.23 3.66
4697 5446 6.043411 GCTACTATCTGAACTCACCGAAAAT 58.957 40.000 0.00 0.00 0.00 1.82
4770 5519 5.291971 GCAATATATCCAGTTGCAAAAGGG 58.708 41.667 16.04 11.22 45.57 3.95
4901 5650 1.468520 GCTAGTTTCCGAGCAATGCAA 59.531 47.619 8.35 0.00 38.97 4.08
5353 6190 1.651240 CTGAAGGCATGAGCAACGGG 61.651 60.000 0.00 0.00 44.61 5.28
5550 6389 3.052036 GTCGACATTGCAGCAACAAAAT 58.948 40.909 10.85 0.00 32.27 1.82
5557 6396 2.670210 CGCAGTCGACATTGCAGCA 61.670 57.895 24.22 0.00 40.28 4.41
5558 6397 2.097160 CGCAGTCGACATTGCAGC 59.903 61.111 24.22 14.14 40.28 5.25
5559 6398 0.451628 CAACGCAGTCGACATTGCAG 60.452 55.000 24.22 19.21 45.00 4.41
5655 6502 6.427853 TGTTCACACAAGGTCAAGATAATCTG 59.572 38.462 0.00 0.00 0.00 2.90
5742 6589 2.299297 ACAGAAAGTACGGAACTCAGGG 59.701 50.000 0.00 0.00 37.50 4.45
5792 6639 4.039124 AGAAGCCCGTGAATCAAAAACAAT 59.961 37.500 0.00 0.00 0.00 2.71
5804 6651 1.367471 CAGTCACAGAAGCCCGTGA 59.633 57.895 0.00 0.00 39.77 4.35
5983 6836 8.748380 TTCTCTTTCGATATGTGCATATACTG 57.252 34.615 5.18 1.74 34.36 2.74
5999 6857 9.530129 GTAAGTGTCATGTTAATTTCTCTTTCG 57.470 33.333 0.00 0.00 0.00 3.46
6040 6898 2.502142 ATTCAAAACGGAGGTACCCC 57.498 50.000 8.74 8.83 34.64 4.95
6093 6966 6.753107 TGTTCACTCATCTCAGTTCGTATA 57.247 37.500 0.00 0.00 0.00 1.47
6094 6967 5.644977 TGTTCACTCATCTCAGTTCGTAT 57.355 39.130 0.00 0.00 0.00 3.06
6097 6970 4.375405 CGTTTGTTCACTCATCTCAGTTCG 60.375 45.833 0.00 0.00 0.00 3.95
6099 6972 3.248602 GCGTTTGTTCACTCATCTCAGTT 59.751 43.478 0.00 0.00 0.00 3.16
6203 7076 7.341805 GCAGGTATGGGATATGAATATCAAGT 58.658 38.462 11.45 1.05 40.67 3.16
6204 7077 6.769822 GGCAGGTATGGGATATGAATATCAAG 59.230 42.308 11.45 0.00 40.67 3.02
6205 7078 6.217280 TGGCAGGTATGGGATATGAATATCAA 59.783 38.462 11.45 1.34 40.67 2.57
6206 7079 5.730697 TGGCAGGTATGGGATATGAATATCA 59.269 40.000 11.45 0.00 40.67 2.15
6207 7080 6.252599 TGGCAGGTATGGGATATGAATATC 57.747 41.667 2.23 2.23 38.70 1.63
6208 7081 6.607970 CATGGCAGGTATGGGATATGAATAT 58.392 40.000 0.00 0.00 0.00 1.28
6209 7082 5.632190 GCATGGCAGGTATGGGATATGAATA 60.632 44.000 0.00 0.00 0.00 1.75
6210 7083 4.863548 CATGGCAGGTATGGGATATGAAT 58.136 43.478 0.00 0.00 0.00 2.57
6211 7084 3.561960 GCATGGCAGGTATGGGATATGAA 60.562 47.826 0.00 0.00 0.00 2.57
6212 7085 2.025981 GCATGGCAGGTATGGGATATGA 60.026 50.000 0.00 0.00 0.00 2.15
6213 7086 2.025605 AGCATGGCAGGTATGGGATATG 60.026 50.000 0.00 0.00 0.00 1.78
6214 7087 2.281966 AGCATGGCAGGTATGGGATAT 58.718 47.619 0.00 0.00 0.00 1.63
6215 7088 1.746157 AGCATGGCAGGTATGGGATA 58.254 50.000 0.00 0.00 0.00 2.59
6216 7089 0.855598 AAGCATGGCAGGTATGGGAT 59.144 50.000 0.00 0.00 0.00 3.85
6217 7090 0.106569 CAAGCATGGCAGGTATGGGA 60.107 55.000 0.00 0.00 0.00 4.37
6218 7091 0.396139 ACAAGCATGGCAGGTATGGG 60.396 55.000 0.00 0.00 0.00 4.00
6219 7092 2.346766 TACAAGCATGGCAGGTATGG 57.653 50.000 0.00 0.00 0.00 2.74
6220 7093 4.388485 TGTATACAAGCATGGCAGGTATG 58.612 43.478 2.20 2.88 0.00 2.39
6221 7094 4.705110 TGTATACAAGCATGGCAGGTAT 57.295 40.909 2.20 2.88 0.00 2.73
6222 7095 4.388485 CATGTATACAAGCATGGCAGGTA 58.612 43.478 10.14 0.00 38.90 3.08
6223 7096 3.216800 CATGTATACAAGCATGGCAGGT 58.783 45.455 10.14 0.00 38.90 4.00
6224 7097 3.909776 CATGTATACAAGCATGGCAGG 57.090 47.619 10.14 0.00 38.90 4.85
6229 7102 4.067896 GGTCCTCCATGTATACAAGCATG 58.932 47.826 10.14 3.42 41.37 4.06
6230 7103 3.716353 TGGTCCTCCATGTATACAAGCAT 59.284 43.478 10.14 0.00 39.03 3.79
6231 7104 3.111484 TGGTCCTCCATGTATACAAGCA 58.889 45.455 10.14 5.25 39.03 3.91
6232 7105 3.838244 TGGTCCTCCATGTATACAAGC 57.162 47.619 10.14 2.50 39.03 4.01
6233 7106 4.130118 GCTTGGTCCTCCATGTATACAAG 58.870 47.826 10.14 5.28 43.91 3.16
6234 7107 3.521531 TGCTTGGTCCTCCATGTATACAA 59.478 43.478 10.14 0.00 43.91 2.41
6235 7108 3.111484 TGCTTGGTCCTCCATGTATACA 58.889 45.455 8.27 8.27 43.91 2.29
6236 7109 3.838244 TGCTTGGTCCTCCATGTATAC 57.162 47.619 0.00 0.00 43.91 1.47
6237 7110 5.784906 TCATATGCTTGGTCCTCCATGTATA 59.215 40.000 0.00 11.07 44.06 1.47
6238 7111 4.598807 TCATATGCTTGGTCCTCCATGTAT 59.401 41.667 0.00 8.24 43.91 2.29
6239 7112 3.973305 TCATATGCTTGGTCCTCCATGTA 59.027 43.478 0.00 0.00 43.91 2.29
6240 7113 2.779430 TCATATGCTTGGTCCTCCATGT 59.221 45.455 0.00 0.00 43.91 3.21
6241 7114 3.497103 TCATATGCTTGGTCCTCCATG 57.503 47.619 0.00 0.00 43.91 3.66
6242 7115 4.736611 AATCATATGCTTGGTCCTCCAT 57.263 40.909 0.00 0.00 43.91 3.41
6243 7116 5.132648 ACTTAATCATATGCTTGGTCCTCCA 59.867 40.000 2.03 0.00 42.66 3.86
6244 7117 5.471456 CACTTAATCATATGCTTGGTCCTCC 59.529 44.000 2.03 0.00 0.00 4.30
6245 7118 5.049129 GCACTTAATCATATGCTTGGTCCTC 60.049 44.000 2.03 0.00 35.16 3.71
6246 7119 4.823989 GCACTTAATCATATGCTTGGTCCT 59.176 41.667 2.03 0.00 35.16 3.85
6247 7120 4.823989 AGCACTTAATCATATGCTTGGTCC 59.176 41.667 2.03 0.00 46.06 4.46
6248 7121 5.297776 ACAGCACTTAATCATATGCTTGGTC 59.702 40.000 2.03 0.00 46.06 4.02
6249 7122 5.066893 CACAGCACTTAATCATATGCTTGGT 59.933 40.000 2.03 0.00 46.06 3.67
6250 7123 5.297527 TCACAGCACTTAATCATATGCTTGG 59.702 40.000 2.03 0.00 46.06 3.61
6251 7124 6.367686 TCACAGCACTTAATCATATGCTTG 57.632 37.500 2.03 0.00 46.06 4.01
6252 7125 7.578310 ATTCACAGCACTTAATCATATGCTT 57.422 32.000 0.00 0.00 46.06 3.91
6254 7127 7.805071 GGTTATTCACAGCACTTAATCATATGC 59.195 37.037 0.00 0.00 38.39 3.14
6255 7128 8.839343 TGGTTATTCACAGCACTTAATCATATG 58.161 33.333 0.00 0.00 0.00 1.78
6256 7129 8.840321 GTGGTTATTCACAGCACTTAATCATAT 58.160 33.333 0.00 0.00 39.18 1.78
6257 7130 7.282224 GGTGGTTATTCACAGCACTTAATCATA 59.718 37.037 2.60 0.00 41.48 2.15
6258 7131 6.095440 GGTGGTTATTCACAGCACTTAATCAT 59.905 38.462 2.60 0.00 41.48 2.45
6259 7132 5.414454 GGTGGTTATTCACAGCACTTAATCA 59.586 40.000 2.60 0.00 41.48 2.57
6260 7133 5.414454 TGGTGGTTATTCACAGCACTTAATC 59.586 40.000 2.60 0.00 41.48 1.75
6261 7134 5.321102 TGGTGGTTATTCACAGCACTTAAT 58.679 37.500 2.60 0.00 41.48 1.40
6262 7135 4.720046 TGGTGGTTATTCACAGCACTTAA 58.280 39.130 2.60 0.00 41.48 1.85
6263 7136 4.359434 TGGTGGTTATTCACAGCACTTA 57.641 40.909 2.60 0.00 41.48 2.24
6264 7137 3.222173 TGGTGGTTATTCACAGCACTT 57.778 42.857 2.60 0.00 41.48 3.16
6265 7138 2.949177 TGGTGGTTATTCACAGCACT 57.051 45.000 2.60 0.00 41.48 4.40
6266 7139 2.164219 CCATGGTGGTTATTCACAGCAC 59.836 50.000 2.57 0.00 46.28 4.40
6268 7141 1.750778 CCCATGGTGGTTATTCACAGC 59.249 52.381 11.73 0.00 39.27 4.40
6269 7142 1.750778 GCCCATGGTGGTTATTCACAG 59.249 52.381 11.73 0.00 39.27 3.66
6270 7143 1.357420 AGCCCATGGTGGTTATTCACA 59.643 47.619 11.73 0.00 39.27 3.58
6271 7144 2.143876 AGCCCATGGTGGTTATTCAC 57.856 50.000 11.73 0.00 35.17 3.18
6272 7145 5.516415 CCATATAGCCCATGGTGGTTATTCA 60.516 44.000 11.73 0.00 38.53 2.57
6273 7146 4.949856 CCATATAGCCCATGGTGGTTATTC 59.050 45.833 11.73 0.00 38.53 1.75
6274 7147 4.605813 TCCATATAGCCCATGGTGGTTATT 59.394 41.667 11.73 0.35 43.03 1.40
6275 7148 4.183116 TCCATATAGCCCATGGTGGTTAT 58.817 43.478 11.73 6.78 43.03 1.89
6276 7149 3.587061 CTCCATATAGCCCATGGTGGTTA 59.413 47.826 11.73 0.00 43.03 2.85
6277 7150 2.376518 CTCCATATAGCCCATGGTGGTT 59.623 50.000 11.73 0.00 43.03 3.67
6278 7151 1.988107 CTCCATATAGCCCATGGTGGT 59.012 52.381 11.73 10.37 43.03 4.16
6279 7152 1.340405 GCTCCATATAGCCCATGGTGG 60.340 57.143 11.73 10.73 43.03 4.61
6280 7153 1.676916 CGCTCCATATAGCCCATGGTG 60.677 57.143 11.73 3.26 43.03 4.17
6281 7154 0.615331 CGCTCCATATAGCCCATGGT 59.385 55.000 11.73 0.00 43.03 3.55
6282 7155 0.615331 ACGCTCCATATAGCCCATGG 59.385 55.000 4.14 4.14 43.74 3.66
6283 7156 1.552337 AGACGCTCCATATAGCCCATG 59.448 52.381 0.00 0.00 39.43 3.66
6284 7157 1.944177 AGACGCTCCATATAGCCCAT 58.056 50.000 0.00 0.00 39.43 4.00
6285 7158 2.447443 CTAGACGCTCCATATAGCCCA 58.553 52.381 0.00 0.00 39.43 5.36
6286 7159 1.751924 CCTAGACGCTCCATATAGCCC 59.248 57.143 0.00 0.00 39.43 5.19
6287 7160 2.448453 ACCTAGACGCTCCATATAGCC 58.552 52.381 0.00 0.00 39.43 3.93
6288 7161 3.063725 CGTACCTAGACGCTCCATATAGC 59.936 52.174 0.00 0.00 39.21 2.97
6289 7162 3.622163 CCGTACCTAGACGCTCCATATAG 59.378 52.174 0.00 0.00 41.56 1.31
6290 7163 3.008375 ACCGTACCTAGACGCTCCATATA 59.992 47.826 0.00 0.00 41.56 0.86
6291 7164 2.224719 ACCGTACCTAGACGCTCCATAT 60.225 50.000 0.00 0.00 41.56 1.78
6292 7165 1.141657 ACCGTACCTAGACGCTCCATA 59.858 52.381 0.00 0.00 41.56 2.74
6293 7166 0.106819 ACCGTACCTAGACGCTCCAT 60.107 55.000 0.00 0.00 41.56 3.41
6294 7167 1.028330 CACCGTACCTAGACGCTCCA 61.028 60.000 0.00 0.00 41.56 3.86
6295 7168 1.028868 ACACCGTACCTAGACGCTCC 61.029 60.000 0.00 0.00 41.56 4.70
6296 7169 1.656652 TACACCGTACCTAGACGCTC 58.343 55.000 0.00 0.00 41.56 5.03
6297 7170 2.338577 ATACACCGTACCTAGACGCT 57.661 50.000 0.00 0.00 41.56 5.07


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

AutoCloner maintained by Alex Coulton.