Multiple sequence alignment - TraesCS4A01G087000

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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 TraesCS4A01G087000 chr4A 100.000 4627 0 0 1 4627 91468852 91473478 0.000000e+00 8545.0
1 TraesCS4A01G087000 chr4A 90.196 51 4 1 4123 4173 590945768 590945817 1.070000e-06 65.8
2 TraesCS4A01G087000 chr4D 93.535 4068 114 70 1 4000 373211345 373207359 0.000000e+00 5917.0
3 TraesCS4A01G087000 chr4D 89.050 484 32 7 4002 4478 373207191 373206722 8.630000e-162 580.0
4 TraesCS4A01G087000 chr4D 96.552 116 4 0 4512 4627 373206720 373206605 4.720000e-45 193.0
5 TraesCS4A01G087000 chr4B 93.980 3538 111 34 685 4191 458460306 458456840 0.000000e+00 5260.0
6 TraesCS4A01G087000 chr4B 90.832 709 27 19 1 692 458461022 458460335 0.000000e+00 915.0
7 TraesCS4A01G087000 chr4B 85.802 324 13 11 4304 4627 458456460 458456170 3.480000e-81 313.0
8 TraesCS4A01G087000 chr4B 93.966 116 6 1 4193 4307 458456808 458456693 1.710000e-39 174.0
9 TraesCS4A01G087000 chr4B 91.803 61 3 1 4108 4168 633752685 633752743 2.970000e-12 84.2
10 TraesCS4A01G087000 chr5A 88.889 144 16 0 1556 1699 445392218 445392361 1.320000e-40 178.0
11 TraesCS4A01G087000 chr5D 88.435 147 15 2 1554 1699 345848407 345848262 4.760000e-40 176.0
12 TraesCS4A01G087000 chr5B 88.194 144 17 0 1556 1699 405768065 405768208 6.150000e-39 172.0
13 TraesCS4A01G087000 chrUn 84.112 107 10 4 4070 4169 50620858 50620964 3.810000e-16 97.1
14 TraesCS4A01G087000 chr2A 90.476 63 6 0 4106 4168 726091546 726091484 2.970000e-12 84.2
15 TraesCS4A01G087000 chr7D 100.000 37 0 0 816 852 185418984 185419020 8.310000e-08 69.4
16 TraesCS4A01G087000 chr6B 97.500 40 1 0 816 855 353088544 353088505 8.310000e-08 69.4
17 TraesCS4A01G087000 chr7B 100.000 35 0 0 4135 4169 125522976 125523010 1.070000e-06 65.8
18 TraesCS4A01G087000 chr3B 91.667 48 2 2 4123 4169 527155608 527155562 1.070000e-06 65.8
19 TraesCS4A01G087000 chr7A 97.222 36 1 0 4135 4170 164402562 164402597 1.390000e-05 62.1
20 TraesCS4A01G087000 chr3A 92.683 41 3 0 4118 4158 208512 208472 5.000000e-05 60.2


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 TraesCS4A01G087000 chr4A 91468852 91473478 4626 False 8545.0 8545 100.000000 1 4627 1 chr4A.!!$F1 4626
1 TraesCS4A01G087000 chr4D 373206605 373211345 4740 True 2230.0 5917 93.045667 1 4627 3 chr4D.!!$R1 4626
2 TraesCS4A01G087000 chr4B 458456170 458461022 4852 True 1665.5 5260 91.145000 1 4627 4 chr4B.!!$R1 4626

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
138 139 0.179936 CCCCGGTCTAGACTAGTCGT 59.820 60.0 21.88 8.42 34.09 4.34 F
355 376 0.449345 CATACACATACGCGCGCATG 60.449 55.0 34.82 34.82 0.00 4.06 F
692 754 0.482887 TCCTCCCTCTCTGTGTGTGA 59.517 55.0 0.00 0.00 0.00 3.58 F
2143 2228 0.533085 GCGCCCTACTCCCAAGAATC 60.533 60.0 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2209 0.106894 GGATTCTTGGGAGTAGGGCG 59.893 60.0 0.00 0.00 0.0 6.13 R
2126 2210 1.512735 AGGATTCTTGGGAGTAGGGC 58.487 55.0 0.00 0.00 0.0 5.19 R
2465 2619 0.685097 TCCATGGATTACGGGCTAGC 59.315 55.0 11.44 6.04 0.0 3.42 R
3943 4132 0.037232 GAAGCCTTGTACTGACCGCT 60.037 55.0 0.00 0.00 0.0 5.52 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
133 134 2.194056 CGGCCCCGGTCTAGACTA 59.806 66.667 21.88 0.00 35.56 2.59
134 135 1.897615 CGGCCCCGGTCTAGACTAG 60.898 68.421 21.88 15.57 35.56 2.57
135 136 1.229643 GGCCCCGGTCTAGACTAGT 59.770 63.158 21.88 0.00 0.00 2.57
136 137 0.822944 GGCCCCGGTCTAGACTAGTC 60.823 65.000 21.88 15.41 0.00 2.59
137 138 1.165284 GCCCCGGTCTAGACTAGTCG 61.165 65.000 21.88 15.96 34.09 4.18
138 139 0.179936 CCCCGGTCTAGACTAGTCGT 59.820 60.000 21.88 8.42 34.09 4.34
139 140 1.414181 CCCCGGTCTAGACTAGTCGTA 59.586 57.143 21.88 9.08 34.09 3.43
140 141 2.478831 CCCGGTCTAGACTAGTCGTAC 58.521 57.143 21.88 15.07 34.09 3.67
145 146 4.975502 CGGTCTAGACTAGTCGTACAGTAG 59.024 50.000 21.88 11.80 34.47 2.57
162 163 9.563898 CGTACAGTAGTAACAAGATTGATTACA 57.436 33.333 14.61 0.00 32.32 2.41
167 168 9.804758 AGTAGTAACAAGATTGATTACACTAGC 57.195 33.333 14.61 0.00 32.32 3.42
168 169 9.804758 GTAGTAACAAGATTGATTACACTAGCT 57.195 33.333 14.61 0.00 32.32 3.32
169 170 8.934507 AGTAACAAGATTGATTACACTAGCTC 57.065 34.615 0.00 0.00 32.32 4.09
170 171 8.754080 AGTAACAAGATTGATTACACTAGCTCT 58.246 33.333 0.00 0.00 32.32 4.09
173 174 8.299990 ACAAGATTGATTACACTAGCTCTAGT 57.700 34.615 3.84 3.84 46.52 2.57
204 213 2.891936 TGCTAATCGCTGCGGCAG 60.892 61.111 25.21 25.21 40.11 4.85
349 370 0.937699 CCGACCCATACACATACGCG 60.938 60.000 3.53 3.53 0.00 6.01
350 371 1.545614 CGACCCATACACATACGCGC 61.546 60.000 5.73 0.00 0.00 6.86
352 373 2.544359 CCATACACATACGCGCGC 59.456 61.111 32.58 23.91 0.00 6.86
353 374 2.234335 CCATACACATACGCGCGCA 61.234 57.895 32.58 20.08 0.00 6.09
354 375 1.556591 CCATACACATACGCGCGCAT 61.557 55.000 32.58 21.80 0.00 4.73
355 376 0.449345 CATACACATACGCGCGCATG 60.449 55.000 34.82 34.82 0.00 4.06
356 377 1.556591 ATACACATACGCGCGCATGG 61.557 55.000 37.69 29.31 0.00 3.66
357 378 4.943591 CACATACGCGCGCATGGC 62.944 66.667 37.69 1.00 38.69 4.40
359 380 4.943591 CATACGCGCGCATGGCAC 62.944 66.667 30.66 0.00 43.84 5.01
395 416 8.983724 CGTACAAAGGTATACTACTACTACTCC 58.016 40.741 2.25 0.00 0.00 3.85
476 497 2.512515 GCCTGGTGTCGATCAGCC 60.513 66.667 12.45 3.48 43.10 4.85
479 500 3.723235 CTGGTGTCGATCAGCCCCG 62.723 68.421 12.45 0.00 43.10 5.73
674 695 3.769300 AGCCTTTTCTCTTCCTCTCTCTC 59.231 47.826 0.00 0.00 0.00 3.20
692 754 0.482887 TCCTCCCTCTCTGTGTGTGA 59.517 55.000 0.00 0.00 0.00 3.58
883 945 2.785258 GATCGCCCACGCAAACTC 59.215 61.111 0.00 0.00 39.84 3.01
897 959 0.746563 AAACTCACACCACACCACCG 60.747 55.000 0.00 0.00 0.00 4.94
915 990 3.065095 CACCGTAGCTAGACTAGAACCAC 59.935 52.174 13.91 3.90 0.00 4.16
916 991 3.276857 CCGTAGCTAGACTAGAACCACA 58.723 50.000 13.91 0.00 0.00 4.17
917 992 3.693085 CCGTAGCTAGACTAGAACCACAA 59.307 47.826 13.91 0.00 0.00 3.33
918 993 4.438472 CCGTAGCTAGACTAGAACCACAAC 60.438 50.000 13.91 0.00 0.00 3.32
919 994 4.395542 CGTAGCTAGACTAGAACCACAACT 59.604 45.833 13.91 0.99 0.00 3.16
920 995 5.583854 CGTAGCTAGACTAGAACCACAACTA 59.416 44.000 13.91 0.08 0.00 2.24
921 996 6.238157 CGTAGCTAGACTAGAACCACAACTAG 60.238 46.154 13.91 0.00 41.01 2.57
922 997 5.817784 AGCTAGACTAGAACCACAACTAGA 58.182 41.667 13.91 0.00 39.25 2.43
923 998 6.246919 AGCTAGACTAGAACCACAACTAGAA 58.753 40.000 13.91 0.00 39.25 2.10
924 999 6.151480 AGCTAGACTAGAACCACAACTAGAAC 59.849 42.308 13.91 0.00 39.25 3.01
925 1000 6.151480 GCTAGACTAGAACCACAACTAGAACT 59.849 42.308 13.91 0.00 39.25 3.01
926 1001 6.980416 AGACTAGAACCACAACTAGAACTT 57.020 37.500 0.00 0.00 39.25 2.66
927 1002 9.228949 CTAGACTAGAACCACAACTAGAACTTA 57.771 37.037 3.13 0.00 39.25 2.24
928 1003 8.113173 AGACTAGAACCACAACTAGAACTTAG 57.887 38.462 0.00 0.00 39.25 2.18
929 1004 7.943447 AGACTAGAACCACAACTAGAACTTAGA 59.057 37.037 0.00 0.00 39.25 2.10
930 1005 8.474710 ACTAGAACCACAACTAGAACTTAGAA 57.525 34.615 0.00 0.00 39.25 2.10
1338 1413 1.377333 CCCCTTCTTCCCGTTGCTC 60.377 63.158 0.00 0.00 0.00 4.26
1452 1527 4.517703 GCGTCGTCCTCGTCCGAG 62.518 72.222 9.68 9.68 41.63 4.63
1659 1734 3.084579 CGCATCAACTCGCACCTC 58.915 61.111 0.00 0.00 0.00 3.85
1777 1852 5.107568 CGTATCTTCAACTCTAGCATGCATG 60.108 44.000 22.70 22.70 0.00 4.06
1862 1937 2.494059 CGAACTCCAACACTCCATTGT 58.506 47.619 0.00 0.00 0.00 2.71
2124 2208 1.883084 GATCCTGCTGGTTACCGCG 60.883 63.158 9.73 0.00 34.23 6.46
2125 2209 4.752879 TCCTGCTGGTTACCGCGC 62.753 66.667 9.73 0.00 34.23 6.86
2143 2228 0.533085 GCGCCCTACTCCCAAGAATC 60.533 60.000 0.00 0.00 0.00 2.52
2146 2231 2.690840 GCCCTACTCCCAAGAATCCTA 58.309 52.381 0.00 0.00 0.00 2.94
2178 2268 5.277857 TCCTTCTACATGCCTTTAGCTAC 57.722 43.478 0.00 0.00 44.23 3.58
2247 2337 7.190335 TCCATGCTAGTTAACCTTAAGCTAA 57.810 36.000 16.20 0.00 0.00 3.09
2248 2338 7.802117 TCCATGCTAGTTAACCTTAAGCTAAT 58.198 34.615 16.20 4.95 0.00 1.73
2249 2339 8.930527 TCCATGCTAGTTAACCTTAAGCTAATA 58.069 33.333 16.20 2.53 0.00 0.98
2250 2340 9.209175 CCATGCTAGTTAACCTTAAGCTAATAG 57.791 37.037 16.20 4.80 0.00 1.73
2251 2341 8.713271 CATGCTAGTTAACCTTAAGCTAATAGC 58.287 37.037 3.66 3.66 42.84 2.97
2279 2369 7.041644 AGTCGTGCTATAGTACTCTTTCATCTC 60.042 40.741 17.42 0.00 0.00 2.75
2327 2475 2.817844 AGTCGGTTTTAGATTTGCACCC 59.182 45.455 0.00 0.00 0.00 4.61
2360 2508 1.425412 GTCAAAAGGCAGCAATGCAG 58.575 50.000 8.35 0.00 36.33 4.41
2399 2547 7.812690 TCTGTTGACTGTTCTAGTAGTGTTA 57.187 36.000 0.00 0.00 40.53 2.41
2400 2548 8.405418 TCTGTTGACTGTTCTAGTAGTGTTAT 57.595 34.615 0.00 0.00 40.53 1.89
2401 2549 8.857098 TCTGTTGACTGTTCTAGTAGTGTTATT 58.143 33.333 0.00 0.00 40.53 1.40
2413 2561 9.649167 TCTAGTAGTGTTATTAGGTTCAAAAGC 57.351 33.333 0.00 0.00 0.00 3.51
2433 2581 4.151883 AGCTTTTTGGTTTCTGGATGCTA 58.848 39.130 0.00 0.00 0.00 3.49
2434 2582 4.219288 AGCTTTTTGGTTTCTGGATGCTAG 59.781 41.667 0.00 0.00 0.00 3.42
2435 2583 4.218417 GCTTTTTGGTTTCTGGATGCTAGA 59.782 41.667 0.00 0.00 0.00 2.43
2436 2584 5.105595 GCTTTTTGGTTTCTGGATGCTAGAT 60.106 40.000 0.00 0.00 0.00 1.98
2437 2585 6.573094 GCTTTTTGGTTTCTGGATGCTAGATT 60.573 38.462 0.00 0.00 0.00 2.40
2438 2586 7.362920 GCTTTTTGGTTTCTGGATGCTAGATTA 60.363 37.037 0.00 0.00 0.00 1.75
2439 2587 7.630242 TTTTGGTTTCTGGATGCTAGATTAG 57.370 36.000 0.00 0.00 0.00 1.73
2440 2588 6.560003 TTGGTTTCTGGATGCTAGATTAGA 57.440 37.500 0.00 0.00 0.00 2.10
2441 2589 5.918608 TGGTTTCTGGATGCTAGATTAGAC 58.081 41.667 0.00 0.00 0.00 2.59
2442 2590 5.425217 TGGTTTCTGGATGCTAGATTAGACA 59.575 40.000 0.00 0.00 0.00 3.41
2443 2591 5.988561 GGTTTCTGGATGCTAGATTAGACAG 59.011 44.000 0.00 0.00 0.00 3.51
2444 2592 4.862902 TCTGGATGCTAGATTAGACAGC 57.137 45.455 0.00 0.00 35.82 4.40
2445 2593 4.478203 TCTGGATGCTAGATTAGACAGCT 58.522 43.478 0.00 0.00 36.26 4.24
2448 2596 6.015856 TCTGGATGCTAGATTAGACAGCTTAC 60.016 42.308 0.00 0.00 36.26 2.34
2465 2619 9.186323 GACAGCTTACAATGACATATACTACTG 57.814 37.037 0.00 0.00 0.00 2.74
2488 2642 4.384208 GCTAGCCCGTAATCCATGGATAAT 60.384 45.833 27.54 15.49 34.93 1.28
2543 2707 4.320456 CCAGGAGCACTGCACCGT 62.320 66.667 11.37 0.00 46.14 4.83
2554 2718 1.746220 ACTGCACCGTCTAGCTAAGAG 59.254 52.381 0.00 0.00 33.88 2.85
2583 2747 1.153706 ACGGGCGTGATAACGGAAG 60.154 57.895 4.40 0.00 0.00 3.46
2675 2839 1.800805 AACACAGATCGCTTGTGGAG 58.199 50.000 15.62 0.00 37.83 3.86
2896 3060 1.003718 AAGCCGGACCTCCTTTTCG 60.004 57.895 5.05 0.00 0.00 3.46
3185 3368 1.841103 GGAGATCAGGGAGGAGGCC 60.841 68.421 0.00 0.00 0.00 5.19
3503 3686 2.042537 ATCCAGGAGGCGCTCAGA 60.043 61.111 7.64 2.04 33.74 3.27
3527 3710 4.796231 ATGGAGCGCACGTCGTCC 62.796 66.667 11.47 7.24 41.07 4.79
3724 3912 3.181504 CGAAACGGAAGGAAACAACAGTT 60.182 43.478 0.00 0.00 0.00 3.16
3913 4102 2.713895 TTGTTTGTGTGGTGTGTGTG 57.286 45.000 0.00 0.00 0.00 3.82
3914 4103 1.610363 TGTTTGTGTGGTGTGTGTGT 58.390 45.000 0.00 0.00 0.00 3.72
3943 4132 2.108952 TCTCTCCATGGGATCGATCTCA 59.891 50.000 29.29 29.29 42.36 3.27
4023 4378 6.158695 ACCCATATACATTCAACTTCTCAGGT 59.841 38.462 0.00 0.00 0.00 4.00
4025 4380 7.557719 CCCATATACATTCAACTTCTCAGGTTT 59.442 37.037 0.00 0.00 0.00 3.27
4028 4383 4.145052 ACATTCAACTTCTCAGGTTTCCC 58.855 43.478 0.00 0.00 0.00 3.97
4057 4412 2.002505 ACCTGCAGATACCGCTAGAT 57.997 50.000 17.39 0.00 0.00 1.98
4084 4439 5.531122 TGTTTATTACTCCCTCCGATCTG 57.469 43.478 0.00 0.00 0.00 2.90
4093 4448 5.950023 ACTCCCTCCGATCTGTATTACTTA 58.050 41.667 0.00 0.00 0.00 2.24
4160 4522 5.912892 TGAGCGACAAGTAATATGGATTGA 58.087 37.500 0.00 0.00 0.00 2.57
4200 4592 8.731275 TTGACATGTAAGTATGAAAGTATGGG 57.269 34.615 0.00 0.00 0.00 4.00
4302 4695 6.660521 ACATTAATGCATGTTCCAGAAGAGAA 59.339 34.615 15.48 0.00 33.29 2.87
4325 4954 4.397420 ACTATGAATGTCCTGTTTGCACA 58.603 39.130 0.00 0.00 0.00 4.57
4328 4957 5.571784 ATGAATGTCCTGTTTGCACATAG 57.428 39.130 0.00 0.00 30.37 2.23
4380 5009 4.305989 TGCATCCAGTTCACAAAAAGTC 57.694 40.909 0.00 0.00 0.00 3.01
4521 5150 8.749841 TTATTATTTGTTGGTGTTGTGCATAC 57.250 30.769 0.00 0.00 0.00 2.39
4579 5208 3.959943 ACAGTGTTAATGTCCAAAACGC 58.040 40.909 0.00 0.00 34.60 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 3.779759 ACTGTACGACTAGTCTAGACCG 58.220 50.000 19.38 16.90 0.00 4.79
128 129 7.382110 TCTTGTTACTACTGTACGACTAGTCT 58.618 38.462 20.34 10.13 0.00 3.24
129 130 7.588143 TCTTGTTACTACTGTACGACTAGTC 57.412 40.000 13.18 13.18 0.00 2.59
130 131 8.449397 CAATCTTGTTACTACTGTACGACTAGT 58.551 37.037 0.00 0.00 0.00 2.57
132 133 8.552083 TCAATCTTGTTACTACTGTACGACTA 57.448 34.615 0.00 0.00 0.00 2.59
133 134 7.444629 TCAATCTTGTTACTACTGTACGACT 57.555 36.000 0.00 0.00 0.00 4.18
134 135 8.684973 AATCAATCTTGTTACTACTGTACGAC 57.315 34.615 0.00 0.00 0.00 4.34
135 136 9.778993 GTAATCAATCTTGTTACTACTGTACGA 57.221 33.333 0.00 0.00 0.00 3.43
136 137 9.563898 TGTAATCAATCTTGTTACTACTGTACG 57.436 33.333 12.37 0.00 31.77 3.67
145 146 8.934507 AGAGCTAGTGTAATCAATCTTGTTAC 57.065 34.615 0.00 7.71 0.00 2.50
162 163 6.885376 ACTTGTATACACACACTAGAGCTAGT 59.115 38.462 4.68 4.38 46.52 2.57
163 164 7.190191 CACTTGTATACACACACTAGAGCTAG 58.810 42.308 4.68 3.06 35.33 3.42
164 165 6.404403 GCACTTGTATACACACACTAGAGCTA 60.404 42.308 4.68 0.00 33.73 3.32
167 168 5.955488 AGCACTTGTATACACACACTAGAG 58.045 41.667 4.68 0.14 33.30 2.43
168 169 5.977489 AGCACTTGTATACACACACTAGA 57.023 39.130 4.68 0.00 33.30 2.43
169 170 7.165977 CGATTAGCACTTGTATACACACACTAG 59.834 40.741 4.68 1.66 33.30 2.57
170 171 6.970613 CGATTAGCACTTGTATACACACACTA 59.029 38.462 4.68 3.21 33.30 2.74
171 172 5.805486 CGATTAGCACTTGTATACACACACT 59.195 40.000 4.68 4.17 33.30 3.55
172 173 6.021055 CGATTAGCACTTGTATACACACAC 57.979 41.667 4.68 0.00 33.30 3.82
204 213 0.258774 ACTCCTCCCTCTCTCTCTGC 59.741 60.000 0.00 0.00 0.00 4.26
274 295 3.090532 AATCCACGCCTCCTCCCC 61.091 66.667 0.00 0.00 0.00 4.81
349 370 1.792949 GTAGTAGTATGTGCCATGCGC 59.207 52.381 0.00 0.00 39.75 6.09
350 371 2.051423 CGTAGTAGTATGTGCCATGCG 58.949 52.381 0.00 0.00 0.00 4.73
476 497 2.596338 GTGGGGTGTGGAAACGGG 60.596 66.667 0.00 0.00 0.00 5.28
479 500 3.292159 GCCGTGGGGTGTGGAAAC 61.292 66.667 0.00 0.00 34.97 2.78
648 669 4.006989 GAGAGGAAGAGAAAAGGCTTTCC 58.993 47.826 13.76 9.10 41.72 3.13
649 670 4.905429 AGAGAGGAAGAGAAAAGGCTTTC 58.095 43.478 13.76 7.09 41.19 2.62
650 671 4.597075 AGAGAGAGGAAGAGAAAAGGCTTT 59.403 41.667 6.68 6.68 0.00 3.51
651 672 4.167319 AGAGAGAGGAAGAGAAAAGGCTT 58.833 43.478 0.00 0.00 0.00 4.35
674 695 0.894141 CTCACACACAGAGAGGGAGG 59.106 60.000 0.00 0.00 35.04 4.30
692 754 2.587060 TCCTCTCTCCCTCTCTCTCT 57.413 55.000 0.00 0.00 0.00 3.10
883 945 1.959226 GCTACGGTGGTGTGGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
897 959 5.900865 AGTTGTGGTTCTAGTCTAGCTAC 57.099 43.478 1.60 3.23 0.00 3.58
915 990 9.710979 CGATCTAGTTCTTCTAAGTTCTAGTTG 57.289 37.037 15.77 9.10 34.94 3.16
916 991 9.669887 TCGATCTAGTTCTTCTAAGTTCTAGTT 57.330 33.333 15.77 11.46 34.94 2.24
917 992 9.841295 ATCGATCTAGTTCTTCTAAGTTCTAGT 57.159 33.333 15.77 9.06 34.94 2.57
919 994 9.275398 GGATCGATCTAGTTCTTCTAAGTTCTA 57.725 37.037 23.96 0.00 0.00 2.10
920 995 7.229907 GGGATCGATCTAGTTCTTCTAAGTTCT 59.770 40.741 23.96 0.00 0.00 3.01
921 996 7.364970 GGGATCGATCTAGTTCTTCTAAGTTC 58.635 42.308 23.96 1.99 0.00 3.01
922 997 6.016943 CGGGATCGATCTAGTTCTTCTAAGTT 60.017 42.308 23.96 0.00 39.00 2.66
923 998 5.470777 CGGGATCGATCTAGTTCTTCTAAGT 59.529 44.000 23.96 0.00 39.00 2.24
924 999 5.618195 GCGGGATCGATCTAGTTCTTCTAAG 60.618 48.000 23.96 3.70 39.00 2.18
925 1000 4.215827 GCGGGATCGATCTAGTTCTTCTAA 59.784 45.833 23.96 0.00 39.00 2.10
926 1001 3.752222 GCGGGATCGATCTAGTTCTTCTA 59.248 47.826 23.96 0.00 39.00 2.10
927 1002 2.554893 GCGGGATCGATCTAGTTCTTCT 59.445 50.000 23.96 0.00 39.00 2.85
928 1003 2.293677 TGCGGGATCGATCTAGTTCTTC 59.706 50.000 23.96 5.51 39.00 2.87
929 1004 2.034812 GTGCGGGATCGATCTAGTTCTT 59.965 50.000 23.96 0.00 39.00 2.52
930 1005 1.609555 GTGCGGGATCGATCTAGTTCT 59.390 52.381 23.96 0.00 39.00 3.01
997 1072 3.723235 CTCCGTGAGCACCCATCGG 62.723 68.421 0.00 0.00 42.12 4.18
1191 1266 2.433145 ATGGTCGCACTCACGCTG 60.433 61.111 0.00 0.00 0.00 5.18
1569 1644 0.977627 TGGCGTCCATGATCTCCTGT 60.978 55.000 0.00 0.00 0.00 4.00
1754 1829 5.757320 ACATGCATGCTAGAGTTGAAGATAC 59.243 40.000 26.53 0.00 0.00 2.24
1760 1835 3.528532 CAGACATGCATGCTAGAGTTGA 58.471 45.455 26.53 0.00 0.00 3.18
1862 1937 1.078490 TGAAATGGAATGGGGAGCCAA 59.922 47.619 0.00 0.00 34.95 4.52
2124 2208 0.533085 GATTCTTGGGAGTAGGGCGC 60.533 60.000 0.00 0.00 0.00 6.53
2125 2209 0.106894 GGATTCTTGGGAGTAGGGCG 59.893 60.000 0.00 0.00 0.00 6.13
2126 2210 1.512735 AGGATTCTTGGGAGTAGGGC 58.487 55.000 0.00 0.00 0.00 5.19
2127 2211 3.071747 GCTTAGGATTCTTGGGAGTAGGG 59.928 52.174 0.00 0.00 0.00 3.53
2143 2228 1.813102 AGAAGGATCTGGGGCTTAGG 58.187 55.000 0.00 0.00 33.59 2.69
2146 2231 2.270434 TGTAGAAGGATCTGGGGCTT 57.730 50.000 0.00 0.00 37.10 4.35
2178 2268 2.019984 GCATGGTTTGGAAGAGCTAGG 58.980 52.381 0.00 0.00 0.00 3.02
2249 2339 5.217978 AGAGTACTATAGCACGACTAGCT 57.782 43.478 0.00 0.00 45.77 3.32
2250 2340 5.927954 AAGAGTACTATAGCACGACTAGC 57.072 43.478 0.00 0.00 33.29 3.42
2251 2341 7.479897 TGAAAGAGTACTATAGCACGACTAG 57.520 40.000 0.00 0.00 33.29 2.57
2252 2342 7.932491 AGATGAAAGAGTACTATAGCACGACTA 59.068 37.037 0.00 0.00 34.64 2.59
2253 2343 6.768861 AGATGAAAGAGTACTATAGCACGACT 59.231 38.462 0.00 0.27 0.00 4.18
2327 2475 4.791734 GCCTTTTGACCGTAAAGACTTTGG 60.792 45.833 10.80 6.72 35.16 3.28
2360 2508 5.180117 AGTCAACAGATCAGTAACAATGCAC 59.820 40.000 0.00 0.00 0.00 4.57
2399 2547 8.046708 AGAAACCAAAAAGCTTTTGAACCTAAT 58.953 29.630 24.50 3.97 0.00 1.73
2400 2548 7.333174 CAGAAACCAAAAAGCTTTTGAACCTAA 59.667 33.333 24.50 0.00 0.00 2.69
2401 2549 6.816140 CAGAAACCAAAAAGCTTTTGAACCTA 59.184 34.615 24.50 0.00 0.00 3.08
2402 2550 5.643348 CAGAAACCAAAAAGCTTTTGAACCT 59.357 36.000 24.50 13.70 0.00 3.50
2413 2561 5.964958 TCTAGCATCCAGAAACCAAAAAG 57.035 39.130 0.00 0.00 0.00 2.27
2438 2586 9.137459 AGTAGTATATGTCATTGTAAGCTGTCT 57.863 33.333 0.00 0.00 0.00 3.41
2439 2587 9.186323 CAGTAGTATATGTCATTGTAAGCTGTC 57.814 37.037 0.00 0.00 0.00 3.51
2440 2588 7.653713 GCAGTAGTATATGTCATTGTAAGCTGT 59.346 37.037 0.00 0.00 0.00 4.40
2441 2589 7.869937 AGCAGTAGTATATGTCATTGTAAGCTG 59.130 37.037 0.00 0.00 0.00 4.24
2442 2590 7.957002 AGCAGTAGTATATGTCATTGTAAGCT 58.043 34.615 0.00 0.00 0.00 3.74
2443 2591 9.347934 CTAGCAGTAGTATATGTCATTGTAAGC 57.652 37.037 0.00 0.00 0.00 3.09
2444 2592 9.347934 GCTAGCAGTAGTATATGTCATTGTAAG 57.652 37.037 10.63 0.00 0.00 2.34
2445 2593 8.304596 GGCTAGCAGTAGTATATGTCATTGTAA 58.695 37.037 18.24 0.00 0.00 2.41
2448 2596 6.102663 GGGCTAGCAGTAGTATATGTCATTG 58.897 44.000 18.24 0.00 0.00 2.82
2465 2619 0.685097 TCCATGGATTACGGGCTAGC 59.315 55.000 11.44 6.04 0.00 3.42
2488 2642 1.686587 CTAGCCGGTGGATGATGTGTA 59.313 52.381 1.90 0.00 0.00 2.90
2543 2707 4.406003 GTGGTCAAATCCCTCTTAGCTAGA 59.594 45.833 0.00 0.00 0.00 2.43
2554 2718 3.131478 CGCCCGTGGTCAAATCCC 61.131 66.667 0.00 0.00 0.00 3.85
2608 2772 1.468520 CAAACCATCGATCACCACCAC 59.531 52.381 0.00 0.00 0.00 4.16
2609 2773 1.612991 CCAAACCATCGATCACCACCA 60.613 52.381 0.00 0.00 0.00 4.17
2610 2774 1.094785 CCAAACCATCGATCACCACC 58.905 55.000 0.00 0.00 0.00 4.61
2720 2884 1.886313 CTAGTGCATGGCTCGCCTG 60.886 63.158 9.65 6.30 36.94 4.85
2773 2937 2.032528 CGAGGGGAGCACAAGCAA 59.967 61.111 0.00 0.00 45.49 3.91
2883 3047 2.041115 GCAGGCGAAAAGGAGGTCC 61.041 63.158 0.00 0.00 0.00 4.46
2884 3048 0.678048 ATGCAGGCGAAAAGGAGGTC 60.678 55.000 0.00 0.00 0.00 3.85
2885 3049 0.962356 CATGCAGGCGAAAAGGAGGT 60.962 55.000 0.00 0.00 0.00 3.85
2999 3174 2.099921 CGAGCTGCCAGTAGTAGTTGAT 59.900 50.000 0.00 0.00 0.00 2.57
3001 3176 1.914634 CGAGCTGCCAGTAGTAGTTG 58.085 55.000 0.00 0.00 0.00 3.16
3003 3178 1.810532 GCGAGCTGCCAGTAGTAGT 59.189 57.895 0.00 0.00 37.76 2.73
3724 3912 3.002451 GTGGTGCATGTACGTTGTGTTTA 59.998 43.478 7.89 0.00 0.00 2.01
3913 4102 5.049060 CGATCCCATGGAGAGATATCGATAC 60.049 48.000 15.22 2.24 34.05 2.24
3914 4103 5.066593 CGATCCCATGGAGAGATATCGATA 58.933 45.833 15.22 7.75 34.05 2.92
3943 4132 0.037232 GAAGCCTTGTACTGACCGCT 60.037 55.000 0.00 0.00 0.00 5.52
4057 4412 4.080807 TCGGAGGGAGTAATAAACATGCAA 60.081 41.667 0.00 0.00 0.00 4.08
4121 4483 6.873656 TGTCGCTCAAACGAATATATTTAGC 58.126 36.000 0.00 2.57 44.93 3.09
4122 4484 8.540492 ACTTGTCGCTCAAACGAATATATTTAG 58.460 33.333 0.00 0.30 44.93 1.85
4125 4487 6.903883 ACTTGTCGCTCAAACGAATATATT 57.096 33.333 0.00 0.00 44.93 1.28
4129 4491 7.042992 CCATATTACTTGTCGCTCAAACGAATA 60.043 37.037 0.00 0.00 44.93 1.75
4132 4494 4.565166 CCATATTACTTGTCGCTCAAACGA 59.435 41.667 0.00 0.00 40.36 3.85
4160 4522 5.880901 ACATGTCAAATCAGTTACTCCCTT 58.119 37.500 0.00 0.00 0.00 3.95
4191 4553 6.712547 GCTAAGACATAATGAGCCCATACTTT 59.287 38.462 0.00 0.00 31.59 2.66
4200 4592 4.679197 CAGACGAGCTAAGACATAATGAGC 59.321 45.833 0.00 0.00 0.00 4.26
4302 4695 4.826733 TGTGCAAACAGGACATTCATAGTT 59.173 37.500 0.00 0.00 44.19 2.24
4328 4957 8.799091 GTGCATGTATAGACATTGATCGTATAC 58.201 37.037 0.00 0.00 44.18 1.47
4380 5009 4.276678 ACATGAGACACTGTCCAAAACATG 59.723 41.667 18.43 18.43 37.23 3.21
4415 5044 4.591498 ACAACAATACTGGTGGTCAGAGTA 59.409 41.667 0.00 0.00 45.26 2.59
4423 5052 6.817765 AAGTATTCACAACAATACTGGTGG 57.182 37.500 6.62 0.00 45.14 4.61
4490 5119 9.474920 CACAACACCAACAAATAATAAGAACAT 57.525 29.630 0.00 0.00 0.00 2.71
4491 5120 7.436673 GCACAACACCAACAAATAATAAGAACA 59.563 33.333 0.00 0.00 0.00 3.18
4492 5121 7.436673 TGCACAACACCAACAAATAATAAGAAC 59.563 33.333 0.00 0.00 0.00 3.01
4493 5122 7.492524 TGCACAACACCAACAAATAATAAGAA 58.507 30.769 0.00 0.00 0.00 2.52
4494 5123 7.043961 TGCACAACACCAACAAATAATAAGA 57.956 32.000 0.00 0.00 0.00 2.10
4495 5124 7.887996 ATGCACAACACCAACAAATAATAAG 57.112 32.000 0.00 0.00 0.00 1.73
4496 5125 8.360390 TGTATGCACAACACCAACAAATAATAA 58.640 29.630 0.00 0.00 0.00 1.40
4497 5126 7.886338 TGTATGCACAACACCAACAAATAATA 58.114 30.769 0.00 0.00 0.00 0.98
4498 5127 6.753180 TGTATGCACAACACCAACAAATAAT 58.247 32.000 0.00 0.00 0.00 1.28
4499 5128 6.149129 TGTATGCACAACACCAACAAATAA 57.851 33.333 0.00 0.00 0.00 1.40
4500 5129 5.774498 TGTATGCACAACACCAACAAATA 57.226 34.783 0.00 0.00 0.00 1.40
4501 5130 4.662468 TGTATGCACAACACCAACAAAT 57.338 36.364 0.00 0.00 0.00 2.32
4502 5131 4.662468 ATGTATGCACAACACCAACAAA 57.338 36.364 5.89 0.00 38.42 2.83
4503 5132 4.366586 CAATGTATGCACAACACCAACAA 58.633 39.130 5.89 0.00 38.42 2.83
4504 5133 3.974912 CAATGTATGCACAACACCAACA 58.025 40.909 5.89 0.00 38.42 3.33
4521 5150 8.801715 AATTGTGACTAGTTTTAACTGCAATG 57.198 30.769 0.00 0.00 40.07 2.82
4579 5208 5.076873 TCCCTCTTGTTAATGAAAAGGTGG 58.923 41.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.