Multiple sequence alignment - TraesCS3B01G177900

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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 TraesCS3B01G177900 chr3B 100.000 2897 0 0 1 2897 182202449 182205345 0.000000e+00 5350
1 TraesCS3B01G177900 chr3B 82.862 1663 243 18 555 2192 113983187 113984832 0.000000e+00 1454
2 TraesCS3B01G177900 chr3B 74.684 316 61 13 782 1080 116390562 116390249 3.920000e-24 122
3 TraesCS3B01G177900 chr3D 90.428 1870 148 18 1042 2897 127904076 127905928 0.000000e+00 2433
4 TraesCS3B01G177900 chr3D 83.305 1737 240 26 520 2220 68037649 68035927 0.000000e+00 1555
5 TraesCS3B01G177900 chr3D 90.947 950 75 6 153 1094 127903134 127904080 0.000000e+00 1267
6 TraesCS3B01G177900 chr3D 84.861 469 58 7 2326 2784 478787200 478787665 7.310000e-126 460
7 TraesCS3B01G177900 chr3D 83.224 459 62 7 2336 2781 585107170 585107626 9.660000e-110 407
8 TraesCS3B01G177900 chr3D 86.452 155 20 1 1 154 127902947 127903101 4.960000e-38 169
9 TraesCS3B01G177900 chr3D 74.528 318 62 13 782 1082 71116345 71116030 1.410000e-23 121
10 TraesCS3B01G177900 chr3A 82.957 1725 258 18 492 2192 79876212 79874500 0.000000e+00 1524
11 TraesCS3B01G177900 chr3A 82.296 1751 250 33 492 2199 79802979 79801246 0.000000e+00 1461
12 TraesCS3B01G177900 chr3A 82.567 1675 253 20 553 2199 79905711 79904048 0.000000e+00 1439
13 TraesCS3B01G177900 chr3A 91.473 903 76 1 1042 1943 138807345 138808247 0.000000e+00 1240
14 TraesCS3B01G177900 chr3A 89.062 960 85 11 153 1094 138806392 138807349 0.000000e+00 1173
15 TraesCS3B01G177900 chr3A 88.782 936 81 17 1972 2893 138808247 138809172 0.000000e+00 1125
16 TraesCS3B01G177900 chr3A 74.168 511 113 18 1502 2002 80103143 80103644 8.190000e-46 195
17 TraesCS3B01G177900 chr2B 84.778 473 54 12 2326 2786 538960331 538959865 2.630000e-125 459
18 TraesCS3B01G177900 chr2B 83.149 451 63 6 2336 2783 605178660 605179100 1.620000e-107 399
19 TraesCS3B01G177900 chr5A 83.441 465 66 5 2326 2781 146646654 146646192 3.450000e-114 422
20 TraesCS3B01G177900 chr1B 82.150 493 70 7 2308 2784 490054147 490053657 9.660000e-110 407
21 TraesCS3B01G177900 chr1B 81.290 465 58 12 2326 2781 277432301 277431857 1.650000e-92 350
22 TraesCS3B01G177900 chr4B 81.764 499 71 9 2301 2781 210597357 210597853 1.620000e-107 399
23 TraesCS3B01G177900 chr4B 81.818 495 73 6 2304 2782 423891149 423890656 1.620000e-107 399
24 TraesCS3B01G177900 chr2A 82.403 466 69 9 2326 2781 38984014 38983552 7.520000e-106 394
25 TraesCS3B01G177900 chr2A 77.647 255 52 5 1076 1328 545800445 545800696 1.800000e-32 150
26 TraesCS3B01G177900 chr1D 81.744 493 71 8 2306 2782 408990591 408991080 7.520000e-106 394
27 TraesCS3B01G177900 chr7D 82.571 459 65 7 2336 2781 13595053 13594597 9.730000e-105 390
28 TraesCS3B01G177900 chr7B 85.714 350 39 4 2439 2781 379500949 379501294 2.740000e-95 359


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 TraesCS3B01G177900 chr3B 182202449 182205345 2896 False 5350.000000 5350 100.000000 1 2897 1 chr3B.!!$F2 2896
1 TraesCS3B01G177900 chr3B 113983187 113984832 1645 False 1454.000000 1454 82.862000 555 2192 1 chr3B.!!$F1 1637
2 TraesCS3B01G177900 chr3D 68035927 68037649 1722 True 1555.000000 1555 83.305000 520 2220 1 chr3D.!!$R1 1700
3 TraesCS3B01G177900 chr3D 127902947 127905928 2981 False 1289.666667 2433 89.275667 1 2897 3 chr3D.!!$F3 2896
4 TraesCS3B01G177900 chr3A 79874500 79876212 1712 True 1524.000000 1524 82.957000 492 2192 1 chr3A.!!$R2 1700
5 TraesCS3B01G177900 chr3A 79801246 79802979 1733 True 1461.000000 1461 82.296000 492 2199 1 chr3A.!!$R1 1707
6 TraesCS3B01G177900 chr3A 79904048 79905711 1663 True 1439.000000 1439 82.567000 553 2199 1 chr3A.!!$R3 1646
7 TraesCS3B01G177900 chr3A 138806392 138809172 2780 False 1179.333333 1240 89.772333 153 2893 3 chr3A.!!$F2 2740

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
244 281 0.035630 ATGAAGCCTGCACTCACTCC 60.036 55.000 0.0 0.0 0.00 3.85 F
480 517 1.338294 TGCCTGCCTTGCATCAAAATG 60.338 47.619 0.0 0.0 38.13 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1196 1380 0.612744 TTCTCGTGGTGCATGGATGA 59.387 50.0 0.00 0.0 0.00 2.92 R
2344 2549 0.249489 CGGCCACACTATGAGTAGCC 60.249 60.0 2.24 0.0 35.76 3.93 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
59 61 4.701956 ATGCGTATTTTCTTCCTTGTGG 57.298 40.909 0.00 0.00 0.00 4.17
60 62 2.817258 TGCGTATTTTCTTCCTTGTGGG 59.183 45.455 0.00 0.00 0.00 4.61
89 91 9.790344 CTAATGGATCACAATTATTTCTCCTCT 57.210 33.333 0.00 0.00 0.00 3.69
115 117 2.128290 ACTGGGCATGCTACAGTGCA 62.128 55.000 32.63 8.48 43.29 4.57
133 135 6.710744 ACAGTGCAGCTACTAAAAGTTATTGT 59.289 34.615 0.00 0.00 0.00 2.71
134 136 7.017645 CAGTGCAGCTACTAAAAGTTATTGTG 58.982 38.462 0.00 0.00 0.00 3.33
137 139 6.148811 TGCAGCTACTAAAAGTTATTGTGGAC 59.851 38.462 0.00 0.00 0.00 4.02
143 145 4.483476 AAAAGTTATTGTGGACGAGTGC 57.517 40.909 0.00 0.00 0.00 4.40
146 148 1.017177 TTATTGTGGACGAGTGCCGC 61.017 55.000 0.00 0.00 43.32 6.53
147 149 1.884075 TATTGTGGACGAGTGCCGCT 61.884 55.000 0.00 0.00 43.32 5.52
183 219 8.296713 TGATCATTTCATATGATTGACATGCAG 58.703 33.333 16.77 0.00 38.73 4.41
206 243 7.009540 GCAGTTTTTGTATATCAAGGTGATTGC 59.990 37.037 0.00 0.00 38.26 3.56
211 248 8.846943 TTTGTATATCAAGGTGATTGCGATAT 57.153 30.769 0.00 0.00 38.26 1.63
214 251 6.974932 ATATCAAGGTGATTGCGATATGTC 57.025 37.500 0.00 0.00 38.26 3.06
221 258 6.582636 AGGTGATTGCGATATGTCTTCTTTA 58.417 36.000 0.00 0.00 0.00 1.85
235 272 5.182001 TGTCTTCTTTAAGAATGAAGCCTGC 59.818 40.000 7.92 0.00 43.30 4.85
244 281 0.035630 ATGAAGCCTGCACTCACTCC 60.036 55.000 0.00 0.00 0.00 3.85
259 296 3.036026 CTCCAATCGAGTGTCACGG 57.964 57.895 12.41 0.00 33.51 4.94
283 320 4.521256 CCTATCCTCCTCCTAGAAAGAACG 59.479 50.000 0.00 0.00 0.00 3.95
293 330 4.624024 TCCTAGAAAGAACGCACATAAACG 59.376 41.667 0.00 0.00 0.00 3.60
303 340 3.002246 ACGCACATAAACGCATAGATTGG 59.998 43.478 0.00 0.00 0.00 3.16
312 349 9.371136 CATAAACGCATAGATTGGTATATGTCT 57.629 33.333 0.00 0.00 33.18 3.41
346 383 4.150897 ACTACTTTGGTGCTTGACTTGA 57.849 40.909 0.00 0.00 0.00 3.02
356 393 3.681897 GTGCTTGACTTGATGACCTACAG 59.318 47.826 0.00 0.00 0.00 2.74
359 396 4.322349 GCTTGACTTGATGACCTACAGAGT 60.322 45.833 0.00 0.00 0.00 3.24
364 401 4.021016 ACTTGATGACCTACAGAGTTGACC 60.021 45.833 0.00 0.00 0.00 4.02
375 412 2.027745 CAGAGTTGACCCACTATGCAGT 60.028 50.000 0.00 0.00 29.62 4.40
376 413 2.234908 AGAGTTGACCCACTATGCAGTC 59.765 50.000 0.00 0.00 30.46 3.51
408 445 3.627577 CCCTACGGAAAACATTGAGGATG 59.372 47.826 0.00 0.00 41.71 3.51
472 509 1.620739 TTTTGGTTGCCTGCCTTGCA 61.621 50.000 0.00 0.00 36.84 4.08
474 511 1.818959 TTGGTTGCCTGCCTTGCATC 61.819 55.000 0.00 0.00 38.13 3.91
480 517 1.338294 TGCCTGCCTTGCATCAAAATG 60.338 47.619 0.00 0.00 38.13 2.32
482 519 2.872842 GCCTGCCTTGCATCAAAATGTT 60.873 45.455 0.00 0.00 38.13 2.71
510 547 6.549736 TCCACGAGAGAAAGACATATATGGAA 59.450 38.462 16.96 0.00 0.00 3.53
539 586 6.446909 TTGCTCTCTCCATCTCTCTATCTA 57.553 41.667 0.00 0.00 0.00 1.98
774 854 3.161866 GGTTTTATGAAAGCAGGTGGGA 58.838 45.455 7.23 0.00 41.65 4.37
797 877 7.702348 GGGAAGATCAAATTTACCAAAAGATCG 59.298 37.037 0.00 0.00 34.87 3.69
988 1068 4.558538 AATCTCCATAAGCATCAAACGC 57.441 40.909 0.00 0.00 0.00 4.84
1028 1116 8.093927 GCATTCCATTCTCTATAGCTTCTACTT 58.906 37.037 0.00 0.00 0.00 2.24
1127 1311 3.490759 CACGACAGCCATGCCGAC 61.491 66.667 0.00 0.00 35.65 4.79
1165 1349 2.690632 GCCCTTGAATCCCCATCATCAA 60.691 50.000 0.00 0.00 0.00 2.57
1181 1365 7.286087 CCCATCATCAAATTCACCTTCAATAGA 59.714 37.037 0.00 0.00 0.00 1.98
1196 1380 7.675619 ACCTTCAATAGAAAATTCCTCACCAAT 59.324 33.333 0.00 0.00 32.35 3.16
1211 1395 0.382873 CCAATCATCCATGCACCACG 59.617 55.000 0.00 0.00 0.00 4.94
1219 1403 0.957395 CCATGCACCACGAGAAGCTT 60.957 55.000 0.00 0.00 0.00 3.74
1220 1404 1.675714 CCATGCACCACGAGAAGCTTA 60.676 52.381 0.00 0.00 0.00 3.09
1229 1413 3.935203 CCACGAGAAGCTTATGTGATGTT 59.065 43.478 20.67 0.00 32.39 2.71
1407 1592 3.306613 TGACTCATCTCATCAGAGGCAT 58.693 45.455 0.00 0.00 42.22 4.40
1411 1596 6.723052 TGACTCATCTCATCAGAGGCATAATA 59.277 38.462 0.00 0.00 42.22 0.98
1413 1598 8.148437 ACTCATCTCATCAGAGGCATAATATT 57.852 34.615 0.00 0.00 42.34 1.28
1422 1607 6.851318 TCAGAGGCATAATATTTCCATGGAA 58.149 36.000 23.63 23.63 0.00 3.53
1434 1619 3.744940 TCCATGGAAGCTTCATCCTTT 57.255 42.857 27.02 1.32 37.85 3.11
1457 1642 4.699637 ACATCGTTACTCCAAACAGAACA 58.300 39.130 0.00 0.00 0.00 3.18
1494 1679 1.523758 CCCAAGTTATCGCTATGGGC 58.476 55.000 0.00 0.00 43.89 5.36
1512 1697 4.033894 GAGCCGGATGATGGTTCG 57.966 61.111 5.05 0.00 0.00 3.95
1517 1702 1.937108 GCCGGATGATGGTTCGATCTC 60.937 57.143 5.05 0.00 0.00 2.75
1565 1752 7.609056 TCAAAGGTAAACTCACTACCATCTAC 58.391 38.462 2.10 0.00 41.23 2.59
1615 1803 3.263425 CCCCTTCACACCAAGTACTATGT 59.737 47.826 0.00 0.00 0.00 2.29
1617 1805 5.046159 CCCCTTCACACCAAGTACTATGTAA 60.046 44.000 0.00 0.00 0.00 2.41
1647 1835 6.118170 ACAGAACATACAAGATGGGAGATTG 58.882 40.000 0.00 0.00 0.00 2.67
1741 1929 7.569240 AGAAGATAAAATCCCTCTAGTTGGTG 58.431 38.462 0.00 0.00 0.00 4.17
1748 1936 1.474077 CCCTCTAGTTGGTGCAAATGC 59.526 52.381 0.00 0.00 42.50 3.56
1749 1937 2.440409 CCTCTAGTTGGTGCAAATGCT 58.560 47.619 6.97 0.00 42.66 3.79
1786 1974 5.815740 GGTATTACACATGGTCCTACAACAG 59.184 44.000 0.00 0.00 0.00 3.16
1899 2087 5.705609 TGAAAAGCCTACAAAGTTGATCC 57.294 39.130 0.00 0.00 0.00 3.36
1904 2092 2.009774 CCTACAAAGTTGATCCTGCCG 58.990 52.381 0.00 0.00 0.00 5.69
1909 2097 2.418368 AAGTTGATCCTGCCGCATAA 57.582 45.000 0.00 0.00 0.00 1.90
1917 2105 4.526650 TGATCCTGCCGCATAACTAGATAA 59.473 41.667 0.00 0.00 0.00 1.75
2206 2404 4.847198 AGGTGCATCAGTATTCATGTCAA 58.153 39.130 0.00 0.00 0.00 3.18
2306 2504 1.064166 CCTCCACATTCTTCTGGCCAT 60.064 52.381 5.51 0.00 0.00 4.40
2325 2523 3.627577 CCATTGTTCAAGTATTCTCCCGG 59.372 47.826 0.00 0.00 0.00 5.73
2334 2532 5.659525 TCAAGTATTCTCCCGGTTAATCAGA 59.340 40.000 0.00 0.00 0.00 3.27
2344 2549 4.574828 CCCGGTTAATCAGACCAGTTAATG 59.425 45.833 0.00 0.00 36.99 1.90
2398 2604 3.615496 CCTATTCCCGTGTTAACTTGTCG 59.385 47.826 7.22 6.62 0.00 4.35
2399 2605 2.886862 TTCCCGTGTTAACTTGTCGA 57.113 45.000 7.22 0.00 0.00 4.20
2400 2606 2.138596 TCCCGTGTTAACTTGTCGAC 57.861 50.000 9.11 9.11 0.00 4.20
2403 2610 0.780002 CGTGTTAACTTGTCGACCGG 59.220 55.000 14.12 0.00 0.00 5.28
2405 2612 1.788886 GTGTTAACTTGTCGACCGGTC 59.211 52.381 25.28 25.28 0.00 4.79
2411 2618 1.069513 ACTTGTCGACCGGTCAATTGA 59.930 47.619 32.80 19.41 0.00 2.57
2435 2642 9.005777 TGACCAGTTACAACCATTAATTACTTC 57.994 33.333 0.00 0.00 0.00 3.01
2442 2649 6.485171 ACAACCATTAATTACTTCTCAGGCT 58.515 36.000 0.00 0.00 0.00 4.58
2444 2651 6.313519 ACCATTAATTACTTCTCAGGCTGA 57.686 37.500 17.68 17.68 0.00 4.26
2485 2692 0.396974 TCAGGTGGGCAAACAAAGCT 60.397 50.000 0.00 0.00 0.00 3.74
2511 2718 1.154430 TTTGGCCTGTAACCCCTTCT 58.846 50.000 3.32 0.00 0.00 2.85
2523 2730 1.385915 CCCTTCTAGCCCCATCCCA 60.386 63.158 0.00 0.00 0.00 4.37
2580 2788 8.449397 CCTCATCTCTATGCTTTTAATATGTGC 58.551 37.037 0.00 0.00 32.76 4.57
2583 2791 7.177498 TCTCTATGCTTTTAATATGTGCACG 57.823 36.000 13.13 0.00 36.44 5.34
2584 2792 6.983890 TCTCTATGCTTTTAATATGTGCACGA 59.016 34.615 13.13 2.60 36.44 4.35
2602 2810 4.095782 GCACGACAACATGTTTGGGTATAT 59.904 41.667 8.77 0.00 0.00 0.86
2604 2812 6.027131 CACGACAACATGTTTGGGTATATTG 58.973 40.000 8.77 0.00 0.00 1.90
2632 2840 2.965831 TGGGAGCATGAGAGTATGGTAC 59.034 50.000 0.00 0.00 38.76 3.34
2752 2960 0.245539 CTCCTAAACCGACCGAGCAA 59.754 55.000 0.00 0.00 0.00 3.91
2786 2994 6.076981 ACGATTTCTTGAACATTGCTTCTT 57.923 33.333 0.00 0.00 0.00 2.52
2806 3014 4.826733 TCTTGCAACTCTTGGCTAATTGAA 59.173 37.500 0.00 0.00 0.00 2.69
2808 3016 5.125100 TGCAACTCTTGGCTAATTGAAAG 57.875 39.130 0.00 0.00 0.00 2.62
2893 3102 2.025793 TCGGGTTTTGCAGGATGGATTA 60.026 45.455 0.00 0.00 35.22 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 2.043980 ACATCCGCGGGCGAATTTT 61.044 52.632 27.83 0.00 42.83 1.82
27 29 1.136690 AATACGCATACGCACATCCG 58.863 50.000 0.00 0.00 45.53 4.18
42 44 8.674607 CATTAGTACCCACAAGGAAGAAAATAC 58.325 37.037 0.00 0.00 39.89 1.89
46 48 5.311121 TCCATTAGTACCCACAAGGAAGAAA 59.689 40.000 0.00 0.00 39.89 2.52
48 50 4.431378 TCCATTAGTACCCACAAGGAAGA 58.569 43.478 0.00 0.00 39.89 2.87
49 51 4.837093 TCCATTAGTACCCACAAGGAAG 57.163 45.455 0.00 0.00 39.89 3.46
53 55 5.097742 TGTGATCCATTAGTACCCACAAG 57.902 43.478 0.00 0.00 31.21 3.16
89 91 3.947196 CTGTAGCATGCCCAGTAATCAAA 59.053 43.478 21.17 0.00 0.00 2.69
99 101 2.768492 GCTGCACTGTAGCATGCCC 61.768 63.158 15.66 5.99 44.68 5.36
115 117 6.694447 TCGTCCACAATAACTTTTAGTAGCT 58.306 36.000 0.00 0.00 0.00 3.32
133 135 2.449031 AATCAAGCGGCACTCGTCCA 62.449 55.000 1.45 0.00 41.72 4.02
134 136 1.696832 GAATCAAGCGGCACTCGTCC 61.697 60.000 1.45 0.00 41.72 4.79
137 139 1.712081 CTGAATCAAGCGGCACTCG 59.288 57.895 1.45 0.00 42.76 4.18
146 148 8.784043 TCATATGAAATGATCAGCTGAATCAAG 58.216 33.333 22.50 13.16 42.53 3.02
147 149 8.685838 TCATATGAAATGATCAGCTGAATCAA 57.314 30.769 22.50 9.95 42.53 2.57
183 219 7.247728 TCGCAATCACCTTGATATACAAAAAC 58.752 34.615 0.00 0.00 35.76 2.43
206 243 8.279103 GGCTTCATTCTTAAAGAAGACATATCG 58.721 37.037 8.39 0.00 44.80 2.92
214 251 5.182760 AGTGCAGGCTTCATTCTTAAAGAAG 59.817 40.000 0.67 0.67 37.69 2.85
221 258 2.157738 GTGAGTGCAGGCTTCATTCTT 58.842 47.619 10.59 0.00 0.00 2.52
244 281 0.172578 TAGGCCGTGACACTCGATTG 59.827 55.000 3.68 0.55 0.00 2.67
259 296 4.120946 TCTTTCTAGGAGGAGGATAGGC 57.879 50.000 0.00 0.00 0.00 3.93
283 320 4.552166 ACCAATCTATGCGTTTATGTGC 57.448 40.909 0.00 0.00 0.00 4.57
346 383 2.567615 GTGGGTCAACTCTGTAGGTCAT 59.432 50.000 0.00 0.00 0.00 3.06
356 393 2.234908 AGACTGCATAGTGGGTCAACTC 59.765 50.000 4.57 0.00 37.25 3.01
359 396 2.497675 GAGAGACTGCATAGTGGGTCAA 59.502 50.000 4.57 0.00 37.25 3.18
364 401 1.474478 ACACGAGAGACTGCATAGTGG 59.526 52.381 0.00 0.00 37.25 4.00
375 412 4.631773 CGTAGGGGACACGAGAGA 57.368 61.111 0.00 0.00 41.91 3.10
408 445 1.593196 TGCTGCAGACTACCAAACAC 58.407 50.000 20.43 0.00 0.00 3.32
436 473 1.119684 AAAGGTCCAAAGTTGCACCC 58.880 50.000 0.31 0.00 0.00 4.61
474 511 5.611796 TTCTCTCGTGGATCAACATTTTG 57.388 39.130 0.13 0.00 0.00 2.44
480 517 3.914312 TGTCTTTCTCTCGTGGATCAAC 58.086 45.455 0.00 0.00 0.00 3.18
482 519 7.309438 CCATATATGTCTTTCTCTCGTGGATCA 60.309 40.741 11.73 0.00 0.00 2.92
484 521 6.721668 TCCATATATGTCTTTCTCTCGTGGAT 59.278 38.462 11.73 0.00 0.00 3.41
510 547 5.426185 AGAGAGATGGAGAGAGCAAAGATTT 59.574 40.000 0.00 0.00 0.00 2.17
539 586 8.161640 TGGATCTGTGAGAGATAGAGATAGAT 57.838 38.462 0.00 0.00 41.91 1.98
676 754 8.463930 TGTATGTTCTCTTTTGTTGGAAGAAT 57.536 30.769 0.00 0.00 33.10 2.40
699 779 6.896860 TGATTATTGAAGAATTGGTCCCATGT 59.103 34.615 0.00 0.00 0.00 3.21
965 1045 5.444122 GCGTTTGATGCTTATGGAGATTAC 58.556 41.667 0.00 0.00 0.00 1.89
968 1048 2.880890 GGCGTTTGATGCTTATGGAGAT 59.119 45.455 0.00 0.00 0.00 2.75
969 1049 2.288666 GGCGTTTGATGCTTATGGAGA 58.711 47.619 0.00 0.00 0.00 3.71
988 1068 3.959293 TGGAATGCATATGCTAGGATGG 58.041 45.455 27.13 0.23 42.66 3.51
1028 1116 6.881065 AGCTACTAGCAAGATCAACAATTTGA 59.119 34.615 10.73 0.00 45.56 2.69
1127 1311 9.657419 ATTCAAGGGCTACAAAATCTTTTAATG 57.343 29.630 0.00 0.00 0.00 1.90
1165 1349 9.312904 TGAGGAATTTTCTATTGAAGGTGAATT 57.687 29.630 0.00 0.00 33.28 2.17
1181 1365 5.395990 GCATGGATGATTGGTGAGGAATTTT 60.396 40.000 0.00 0.00 0.00 1.82
1196 1380 0.612744 TTCTCGTGGTGCATGGATGA 59.387 50.000 0.00 0.00 0.00 2.92
1211 1395 7.834068 TTGACTAACATCACATAAGCTTCTC 57.166 36.000 0.00 0.00 0.00 2.87
1220 1404 8.654094 TGGATCTATCATTGACTAACATCACAT 58.346 33.333 0.00 0.00 0.00 3.21
1229 1413 8.439964 TGGAATCATGGATCTATCATTGACTA 57.560 34.615 0.00 0.00 0.00 2.59
1304 1488 6.044404 GTCCAAGGATAAAGGATTAGGGATCA 59.956 42.308 0.00 0.00 36.43 2.92
1407 1592 7.529555 AGGATGAAGCTTCCATGGAAATATTA 58.470 34.615 26.87 14.28 35.59 0.98
1411 1596 4.261411 AGGATGAAGCTTCCATGGAAAT 57.739 40.909 26.87 17.27 35.59 2.17
1413 1598 3.744940 AAGGATGAAGCTTCCATGGAA 57.255 42.857 25.53 25.53 35.59 3.53
1422 1607 5.978814 AGTAACGATGTAAAGGATGAAGCT 58.021 37.500 0.00 0.00 0.00 3.74
1434 1619 5.845103 TGTTCTGTTTGGAGTAACGATGTA 58.155 37.500 0.00 0.00 0.00 2.29
1462 1647 7.285401 AGCGATAACTTGGGAATGAACAATTAT 59.715 33.333 0.00 0.00 0.00 1.28
1494 1679 1.951130 CGAACCATCATCCGGCTCG 60.951 63.158 0.00 0.00 35.96 5.03
1512 1697 5.851720 TGCTTGATGTCCATCTTAGAGATC 58.148 41.667 8.61 0.00 38.60 2.75
1565 1752 9.118236 GAATCTTTTCAGGATAACAAAGAAACG 57.882 33.333 0.00 0.00 38.44 3.60
1615 1803 6.878923 CCATCTTGTATGTTCTGTTCCTGTTA 59.121 38.462 0.00 0.00 0.00 2.41
1617 1805 5.248640 CCATCTTGTATGTTCTGTTCCTGT 58.751 41.667 0.00 0.00 0.00 4.00
1647 1835 8.784043 GGTACACCATAAGGATCATCAAATAAC 58.216 37.037 0.00 0.00 38.69 1.89
1741 1929 6.382869 ACCACTATCAGAAATAGCATTTGC 57.617 37.500 0.00 0.00 42.49 3.68
1749 1937 9.996554 CCATGTGTAATACCACTATCAGAAATA 57.003 33.333 0.00 0.00 36.30 1.40
1786 1974 1.715519 CTTGCATTTGTACTTGCGTGC 59.284 47.619 10.12 6.84 41.80 5.34
1899 2087 3.244078 TGGGTTATCTAGTTATGCGGCAG 60.244 47.826 9.25 0.00 0.00 4.85
1917 2105 7.774713 TGGTCCCAATAATATTAATCATGGGT 58.225 34.615 24.06 0.00 45.04 4.51
1967 2158 4.367450 TGCTAAAACCTTTGTGCATTCAC 58.633 39.130 0.00 0.00 43.40 3.18
2055 2249 5.059161 CACACCCACATAACATATCTCCAG 58.941 45.833 0.00 0.00 0.00 3.86
2058 2252 6.823689 AGTTTCACACCCACATAACATATCTC 59.176 38.462 0.00 0.00 0.00 2.75
2104 2299 4.037089 AGGGAAACAACAACGGAAACATAC 59.963 41.667 0.00 0.00 0.00 2.39
2112 2307 5.008811 TGTTTACATAGGGAAACAACAACGG 59.991 40.000 15.28 0.00 41.37 4.44
2113 2308 6.062434 TGTTTACATAGGGAAACAACAACG 57.938 37.500 15.28 0.00 41.37 4.10
2217 2415 6.720112 ATTTGGTCATGGGATGAAACATAG 57.280 37.500 0.00 0.00 41.69 2.23
2225 2423 5.597182 AGAGATTGAATTTGGTCATGGGATG 59.403 40.000 0.00 0.00 0.00 3.51
2229 2427 7.395190 TTGTAGAGATTGAATTTGGTCATGG 57.605 36.000 0.00 0.00 0.00 3.66
2262 2460 6.071616 GGTGCCATTGTTAAGTAGGATGAAAA 60.072 38.462 0.00 0.00 0.00 2.29
2263 2461 5.417580 GGTGCCATTGTTAAGTAGGATGAAA 59.582 40.000 0.00 0.00 0.00 2.69
2264 2462 4.947388 GGTGCCATTGTTAAGTAGGATGAA 59.053 41.667 0.00 0.00 0.00 2.57
2306 2504 4.360951 AACCGGGAGAATACTTGAACAA 57.639 40.909 6.32 0.00 0.00 2.83
2344 2549 0.249489 CGGCCACACTATGAGTAGCC 60.249 60.000 2.24 0.00 35.76 3.93
2356 2561 1.742831 GTGCTATTTGATTCGGCCACA 59.257 47.619 2.24 0.00 0.00 4.17
2357 2562 1.065551 GGTGCTATTTGATTCGGCCAC 59.934 52.381 2.24 0.00 0.00 5.01
2403 2610 5.705609 ATGGTTGTAACTGGTCAATTGAC 57.294 39.130 27.16 27.16 44.04 3.18
2411 2618 9.227777 GAGAAGTAATTAATGGTTGTAACTGGT 57.772 33.333 0.00 0.00 0.00 4.00
2435 2642 4.262808 CCAGTAGGGATTAATCAGCCTGAG 60.263 50.000 18.52 10.55 40.01 3.35
2459 2666 2.225242 TGTTTGCCCACCTGATAATGGT 60.225 45.455 0.00 0.00 38.53 3.55
2468 2675 0.396974 TGAGCTTTGTTTGCCCACCT 60.397 50.000 0.00 0.00 0.00 4.00
2485 2692 3.161866 GGGTTACAGGCCAAAATCTTGA 58.838 45.455 5.01 0.00 34.14 3.02
2511 2718 0.645496 TAAGGAGTGGGATGGGGCTA 59.355 55.000 0.00 0.00 0.00 3.93
2558 2766 7.657354 TCGTGCACATATTAAAAGCATAGAGAT 59.343 33.333 18.64 0.00 37.56 2.75
2580 2788 5.811399 ATATACCCAAACATGTTGTCGTG 57.189 39.130 12.82 6.43 36.71 4.35
2583 2791 5.960113 TGCAATATACCCAAACATGTTGTC 58.040 37.500 12.82 0.00 0.00 3.18
2584 2792 5.991933 TGCAATATACCCAAACATGTTGT 57.008 34.783 12.82 8.53 0.00 3.32
2602 2810 0.547553 TCATGCTCCCAGCTATGCAA 59.452 50.000 0.00 0.00 42.97 4.08
2604 2812 0.395686 TCTCATGCTCCCAGCTATGC 59.604 55.000 0.00 0.00 42.97 3.14
2661 2869 8.275040 AGTTGGTATATTGAATAGGAACTTGCT 58.725 33.333 0.00 0.00 41.75 3.91
2752 2960 6.987992 TGTTCAAGAAATCGTTAACAGGTAGT 59.012 34.615 6.39 0.00 0.00 2.73
2786 2994 4.826733 TCTTTCAATTAGCCAAGAGTTGCA 59.173 37.500 0.00 0.00 0.00 4.08
2806 3014 5.149239 GGGTAGGCTAAATCTAGAGGTCTT 58.851 45.833 0.00 0.00 0.00 3.01
2808 3016 3.833650 GGGGTAGGCTAAATCTAGAGGTC 59.166 52.174 0.00 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.