Multiple sequence alignment - TraesCS1B01G062800

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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 TraesCS1B01G062800 chr1B 100.000 3706 0 0 1 3706 47627612 47623907 0.000000e+00 6844.0
1 TraesCS1B01G062800 chr1B 76.961 1606 278 58 1124 2679 542628511 542626948 0.000000e+00 832.0
2 TraesCS1B01G062800 chr1B 77.283 1391 253 41 1323 2688 542767923 542766571 0.000000e+00 760.0
3 TraesCS1B01G062800 chr1B 75.606 1402 265 56 1319 2679 542715648 542714283 1.130000e-174 623.0
4 TraesCS1B01G062800 chr1B 78.058 1030 181 27 1319 2322 542762680 542761670 3.160000e-170 608.0
5 TraesCS1B01G062800 chr1B 86.705 173 23 0 1108 1280 542768102 542767930 3.780000e-45 193.0
6 TraesCS1B01G062800 chr1B 87.342 158 18 2 1108 1264 542762855 542762699 2.940000e-41 180.0
7 TraesCS1B01G062800 chr1B 84.431 167 26 0 1109 1275 542715822 542715656 8.230000e-37 165.0
8 TraesCS1B01G062800 chr1D 92.464 2508 140 17 1203 3706 29812230 29814692 0.000000e+00 3539.0
9 TraesCS1B01G062800 chr1D 89.690 2289 158 36 996 3265 30078213 30075984 0.000000e+00 2848.0
10 TraesCS1B01G062800 chr1D 78.594 1294 239 27 1410 2689 403338928 403337659 0.000000e+00 821.0
11 TraesCS1B01G062800 chr1D 77.509 1405 250 45 1322 2688 403517873 403516497 0.000000e+00 784.0
12 TraesCS1B01G062800 chr1D 78.376 1133 209 16 1576 2688 403550412 403549296 0.000000e+00 702.0
13 TraesCS1B01G062800 chr1D 86.737 475 36 11 3244 3706 30075672 30075213 1.540000e-138 503.0
14 TraesCS1B01G062800 chr1D 83.034 613 43 22 33 593 30079129 30078526 1.990000e-137 499.0
15 TraesCS1B01G062800 chr1D 93.182 220 15 0 988 1207 29806771 29806990 1.280000e-84 324.0
16 TraesCS1B01G062800 chr1D 80.215 465 41 25 255 671 29806221 29806682 6.020000e-78 302.0
17 TraesCS1B01G062800 chr1D 89.545 220 22 1 740 959 30078531 30078313 1.010000e-70 278.0
18 TraesCS1B01G062800 chr1D 86.869 198 20 5 762 959 29806488 29806679 2.240000e-52 217.0
19 TraesCS1B01G062800 chr1D 89.714 175 8 4 89 263 29805885 29806049 8.060000e-52 215.0
20 TraesCS1B01G062800 chr1D 86.857 175 21 2 1108 1281 403554288 403554115 1.050000e-45 195.0
21 TraesCS1B01G062800 chr1D 81.513 238 31 9 1035 1264 403518127 403517895 2.270000e-42 183.0
22 TraesCS1B01G062800 chr1D 93.966 116 7 0 407 522 30078694 30078579 3.800000e-40 176.0
23 TraesCS1B01G062800 chr1D 86.538 156 21 0 1108 1263 403349775 403349620 4.920000e-39 172.0
24 TraesCS1B01G062800 chr1D 96.939 98 3 0 320 417 29806259 29806356 8.230000e-37 165.0
25 TraesCS1B01G062800 chr1D 81.592 201 22 3 486 671 30078510 30078310 6.410000e-33 152.0
26 TraesCS1B01G062800 chr1D 90.278 72 7 0 413 484 29806373 29806444 1.100000e-15 95.3
27 TraesCS1B01G062800 chr1D 91.803 61 5 0 1322 1382 403554110 403554050 6.590000e-13 86.1
28 TraesCS1B01G062800 chr1D 100.000 44 0 0 955 998 30078284 30078241 8.530000e-12 82.4
29 TraesCS1B01G062800 chr1D 92.982 57 1 3 815 871 30078583 30078530 3.070000e-11 80.5
30 TraesCS1B01G062800 chr1D 97.727 44 1 0 955 998 29806708 29806751 3.970000e-10 76.8
31 TraesCS1B01G062800 chr1A 91.612 2289 130 25 992 3265 30132109 30129868 0.000000e+00 3107.0
32 TraesCS1B01G062800 chr1A 78.107 1384 252 33 1322 2689 498797054 498795706 0.000000e+00 830.0
33 TraesCS1B01G062800 chr1A 75.301 1413 273 53 1319 2688 498668324 498666945 1.140000e-169 606.0
34 TraesCS1B01G062800 chr1A 87.045 494 28 10 33 501 30132905 30132423 3.280000e-145 525.0
35 TraesCS1B01G062800 chr1A 87.226 274 26 2 407 671 30132475 30132202 1.670000e-78 303.0
36 TraesCS1B01G062800 chr1A 89.055 201 14 3 762 961 30132396 30132203 3.700000e-60 243.0
37 TraesCS1B01G062800 chr1A 78.363 342 74 0 2348 2689 498599363 498599022 4.820000e-54 222.0
38 TraesCS1B01G062800 chr1A 97.674 43 1 0 951 993 30132180 30132138 1.430000e-09 75.0
39 TraesCS1B01G062800 chr1A 95.652 46 2 0 2143 2188 589871533 589871578 1.430000e-09 75.0
40 TraesCS1B01G062800 chr6B 75.854 1317 251 39 1392 2689 117494789 117493521 3.160000e-170 608.0


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 TraesCS1B01G062800 chr1B 47623907 47627612 3705 True 6844.0000 6844 100.000000 1 3706 1 chr1B.!!$R1 3705
1 TraesCS1B01G062800 chr1B 542626948 542628511 1563 True 832.0000 832 76.961000 1124 2679 1 chr1B.!!$R2 1555
2 TraesCS1B01G062800 chr1B 542761670 542768102 6432 True 435.2500 760 82.347000 1108 2688 4 chr1B.!!$R4 1580
3 TraesCS1B01G062800 chr1B 542714283 542715822 1539 True 394.0000 623 80.018500 1109 2679 2 chr1B.!!$R3 1570
4 TraesCS1B01G062800 chr1D 29812230 29814692 2462 False 3539.0000 3539 92.464000 1203 3706 1 chr1D.!!$F1 2503
5 TraesCS1B01G062800 chr1D 403337659 403338928 1269 True 821.0000 821 78.594000 1410 2689 1 chr1D.!!$R1 1279
6 TraesCS1B01G062800 chr1D 30075213 30079129 3916 True 577.3625 2848 89.693250 33 3706 8 chr1D.!!$R3 3673
7 TraesCS1B01G062800 chr1D 403516497 403518127 1630 True 483.5000 784 79.511000 1035 2688 2 chr1D.!!$R4 1653
8 TraesCS1B01G062800 chr1D 403549296 403554288 4992 True 327.7000 702 85.678667 1108 2688 3 chr1D.!!$R5 1580
9 TraesCS1B01G062800 chr1A 30129868 30132905 3037 True 850.6000 3107 90.522400 33 3265 5 chr1A.!!$R4 3232
10 TraesCS1B01G062800 chr1A 498795706 498797054 1348 True 830.0000 830 78.107000 1322 2689 1 chr1A.!!$R3 1367
11 TraesCS1B01G062800 chr1A 498666945 498668324 1379 True 606.0000 606 75.301000 1319 2688 1 chr1A.!!$R2 1369
12 TraesCS1B01G062800 chr6B 117493521 117494789 1268 True 608.0000 608 75.854000 1392 2689 1 chr6B.!!$R1 1297

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
79 80 0.041238 ACCCTCTTCCTCACCATCGA 59.959 55.0 0.0 0.0 0.0 3.59 F
761 832 0.105964 CAGACGATGGGGGCGATAAA 59.894 55.0 0.0 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 5065 0.106967 GGGGATGAGCTGAAACTCCC 60.107 60.000 1.89 1.89 44.11 4.30 R
2749 6580 1.202710 TCGCCAGGCTAGAACAAAACA 60.203 47.619 10.54 0.00 0.00 2.83 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
26 27 3.334751 CGTTCACGGCTTCACGCA 61.335 61.111 0.00 0.00 41.67 5.24
27 28 2.876879 CGTTCACGGCTTCACGCAA 61.877 57.895 0.00 0.00 41.67 4.85
28 29 1.368850 GTTCACGGCTTCACGCAAC 60.369 57.895 0.00 0.00 41.67 4.17
29 30 2.539338 TTCACGGCTTCACGCAACC 61.539 57.895 0.00 0.00 41.67 3.77
30 31 4.025401 CACGGCTTCACGCAACCC 62.025 66.667 0.00 0.00 41.67 4.11
31 32 4.250305 ACGGCTTCACGCAACCCT 62.250 61.111 0.00 0.00 41.67 4.34
78 79 0.461961 GACCCTCTTCCTCACCATCG 59.538 60.000 0.00 0.00 0.00 3.84
79 80 0.041238 ACCCTCTTCCTCACCATCGA 59.959 55.000 0.00 0.00 0.00 3.59
86 87 0.323816 TCCTCACCATCGAGCAGAGT 60.324 55.000 0.00 0.00 0.00 3.24
190 194 2.612251 CCTCCCCTCCTCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
275 283 2.603776 AAACCCTCCCGCGTCTCT 60.604 61.111 4.92 0.00 0.00 3.10
419 448 4.269523 TGCAAAGGAGGCGGCTGT 62.270 61.111 19.63 0.00 0.00 4.40
584 655 1.295423 AGCGTAGGTTTGCGGATGT 59.705 52.632 0.00 0.00 35.87 3.06
590 661 3.053291 GTTTGCGGATGTGGCGGA 61.053 61.111 0.00 0.00 0.00 5.54
591 662 2.745884 TTTGCGGATGTGGCGGAG 60.746 61.111 0.00 0.00 0.00 4.63
592 663 4.776322 TTGCGGATGTGGCGGAGG 62.776 66.667 0.00 0.00 0.00 4.30
594 665 4.899239 GCGGATGTGGCGGAGGAG 62.899 72.222 0.00 0.00 0.00 3.69
595 666 4.227134 CGGATGTGGCGGAGGAGG 62.227 72.222 0.00 0.00 0.00 4.30
596 667 4.554036 GGATGTGGCGGAGGAGGC 62.554 72.222 0.00 0.00 37.19 4.70
597 668 3.785859 GATGTGGCGGAGGAGGCA 61.786 66.667 0.00 0.00 44.68 4.75
680 751 4.821589 GGCGGCGACCCAGAAGAG 62.822 72.222 12.98 0.00 0.00 2.85
681 752 4.070552 GCGGCGACCCAGAAGAGT 62.071 66.667 12.98 0.00 0.00 3.24
682 753 2.707849 GCGGCGACCCAGAAGAGTA 61.708 63.158 12.98 0.00 0.00 2.59
683 754 1.433879 CGGCGACCCAGAAGAGTAG 59.566 63.158 0.00 0.00 0.00 2.57
684 755 1.817209 GGCGACCCAGAAGAGTAGG 59.183 63.158 0.00 0.00 0.00 3.18
685 756 0.971447 GGCGACCCAGAAGAGTAGGT 60.971 60.000 0.00 0.00 34.57 3.08
686 757 0.896226 GCGACCCAGAAGAGTAGGTT 59.104 55.000 0.00 0.00 31.10 3.50
687 758 1.275573 GCGACCCAGAAGAGTAGGTTT 59.724 52.381 0.00 0.00 31.10 3.27
688 759 2.931320 GCGACCCAGAAGAGTAGGTTTG 60.931 54.545 0.00 0.00 31.10 2.93
689 760 2.701107 GACCCAGAAGAGTAGGTTTGC 58.299 52.381 0.00 0.00 31.10 3.68
690 761 1.002087 ACCCAGAAGAGTAGGTTTGCG 59.998 52.381 0.00 0.00 0.00 4.85
691 762 1.676014 CCCAGAAGAGTAGGTTTGCGG 60.676 57.143 0.00 0.00 0.00 5.69
692 763 1.275291 CCAGAAGAGTAGGTTTGCGGA 59.725 52.381 0.00 0.00 0.00 5.54
693 764 2.093447 CCAGAAGAGTAGGTTTGCGGAT 60.093 50.000 0.00 0.00 0.00 4.18
694 765 2.932614 CAGAAGAGTAGGTTTGCGGATG 59.067 50.000 0.00 0.00 0.00 3.51
695 766 1.666189 GAAGAGTAGGTTTGCGGATGC 59.334 52.381 0.00 0.00 43.20 3.91
705 776 2.203070 GCGGATGCGGAGTTGGAT 60.203 61.111 9.20 0.00 0.00 3.41
706 777 2.537560 GCGGATGCGGAGTTGGATG 61.538 63.158 9.20 0.00 0.00 3.51
707 778 2.537560 CGGATGCGGAGTTGGATGC 61.538 63.158 0.00 0.00 0.00 3.91
708 779 2.189499 GGATGCGGAGTTGGATGCC 61.189 63.158 0.00 0.00 0.00 4.40
713 784 3.309582 GGAGTTGGATGCCGAGGA 58.690 61.111 0.00 0.00 0.00 3.71
714 785 1.144936 GGAGTTGGATGCCGAGGAG 59.855 63.158 0.00 0.00 0.00 3.69
715 786 1.144936 GAGTTGGATGCCGAGGAGG 59.855 63.158 0.00 0.00 44.97 4.30
734 805 4.996434 AGCGCCTGTGCTGGTGAC 62.996 66.667 2.29 4.54 45.28 3.67
735 806 4.996434 GCGCCTGTGCTGGTGACT 62.996 66.667 11.92 0.00 39.82 3.41
736 807 3.046087 CGCCTGTGCTGGTGACTG 61.046 66.667 3.02 0.00 39.82 3.51
758 829 4.241555 GCAGACGATGGGGGCGAT 62.242 66.667 0.00 0.00 0.00 4.58
759 830 2.867855 GCAGACGATGGGGGCGATA 61.868 63.158 0.00 0.00 0.00 2.92
760 831 1.745890 CAGACGATGGGGGCGATAA 59.254 57.895 0.00 0.00 0.00 1.75
761 832 0.105964 CAGACGATGGGGGCGATAAA 59.894 55.000 0.00 0.00 0.00 1.40
762 833 1.056660 AGACGATGGGGGCGATAAAT 58.943 50.000 0.00 0.00 0.00 1.40
763 834 1.156736 GACGATGGGGGCGATAAATG 58.843 55.000 0.00 0.00 0.00 2.32
764 835 0.889186 ACGATGGGGGCGATAAATGC 60.889 55.000 0.00 0.00 0.00 3.56
772 843 0.798776 GGCGATAAATGCCGATGAGG 59.201 55.000 0.00 0.00 43.70 3.86
942 1013 1.620822 GGCCAATAAATGCCGAGGAT 58.379 50.000 0.00 0.00 38.00 3.24
1024 1158 3.114616 CTGCAGTTGAGGCGACGG 61.115 66.667 5.25 0.00 0.00 4.79
1165 1305 0.317938 CGCCGTACTCTGCAGTATCC 60.318 60.000 14.67 0.00 37.45 2.59
1257 1397 0.605589 CAGCTCCTCTCAACCTCGTT 59.394 55.000 0.00 0.00 0.00 3.85
1285 1425 2.042686 AGAACTCAACAGCAGCAACA 57.957 45.000 0.00 0.00 0.00 3.33
1289 1429 1.402968 ACTCAACAGCAGCAACAACAG 59.597 47.619 0.00 0.00 0.00 3.16
1297 1437 1.135141 GCAGCAACAACAGTTTGGTCA 60.135 47.619 0.00 0.00 37.00 4.02
1407 5027 6.570672 AATAGCAACTATCATGGCAAGATG 57.429 37.500 15.03 7.80 0.00 2.90
1445 5065 0.798776 CAAGCCTTGGACAAGCTACG 59.201 55.000 6.54 0.00 37.11 3.51
1561 5190 2.343018 CCAAATTTGGCGGCTGCA 59.657 55.556 23.81 2.32 45.35 4.41
1778 5419 3.885358 GCTTTTGCACTAACTGGTGTAC 58.115 45.455 0.00 0.00 46.58 2.90
1890 5546 0.683828 TACGGGTAATCTCGGCACCA 60.684 55.000 0.00 0.00 33.78 4.17
1896 5552 3.602483 GGTAATCTCGGCACCAAAACTA 58.398 45.455 0.00 0.00 32.32 2.24
1908 5564 4.629634 GCACCAAAACTAAACATATTGGGC 59.370 41.667 7.65 4.68 43.77 5.36
1919 5578 2.036475 ACATATTGGGCACGCTCTCTAG 59.964 50.000 0.00 0.00 0.00 2.43
1957 5616 2.689983 CAGCTTGGAACCACAGTTTTCT 59.310 45.455 0.00 0.00 35.94 2.52
2116 5809 2.105993 GGGTGTTGGTTCTTGACTACCT 59.894 50.000 0.00 0.00 35.41 3.08
2149 5842 4.704965 ACAGTGGTTAACTTCCTCAAGTC 58.295 43.478 5.42 0.00 42.45 3.01
2561 6284 0.107703 TGCTGCGGACCAAAGATAGG 60.108 55.000 0.00 0.00 0.00 2.57
2714 6545 2.899975 TCCCCATTTTGAAGATTGCCA 58.100 42.857 0.00 0.00 0.00 4.92
2749 6580 2.446435 AGCCCAACTTTTATGTCGCAT 58.554 42.857 0.00 0.00 0.00 4.73
2762 6593 3.536158 TGTCGCATGTTTTGTTCTAGC 57.464 42.857 0.00 0.00 0.00 3.42
2765 6596 2.483877 TCGCATGTTTTGTTCTAGCCTG 59.516 45.455 0.00 0.00 0.00 4.85
2826 6657 4.214310 TCAGTGATGGAATGTTTTGTGGT 58.786 39.130 0.00 0.00 0.00 4.16
2902 6801 1.152756 AACTTGCGGCTTGAAGGGT 60.153 52.632 0.00 0.00 0.00 4.34
2924 6823 7.039270 GGGTTTGGCCAGTAGTTTATTTTATG 58.961 38.462 5.11 0.00 39.65 1.90
3007 6917 6.183360 TGTTTGGTCTTGTAATTTAAGCTGCA 60.183 34.615 1.02 0.00 0.00 4.41
3036 6949 5.871524 GCAGCAGCTACTATATTTATCTGCA 59.128 40.000 16.29 0.00 45.45 4.41
3037 6950 6.369890 GCAGCAGCTACTATATTTATCTGCAA 59.630 38.462 16.29 0.00 45.45 4.08
3086 7085 9.853177 ATTATCTGCCTTATAACTTGCTTTAGT 57.147 29.630 0.00 0.00 0.00 2.24
3089 7088 9.681062 ATCTGCCTTATAACTTGCTTTAGTAAA 57.319 29.630 0.00 0.00 0.00 2.01
3148 7412 6.272318 CAGAATGTTTGCAACCTTGTTTCTA 58.728 36.000 0.00 0.00 0.00 2.10
3362 8351 3.685139 TTTGGTGTGATCTGAGACTCC 57.315 47.619 0.00 0.00 0.00 3.85
3398 8387 6.389091 TCATTTAATGAACACATGCCACTTC 58.611 36.000 5.03 0.00 36.11 3.01
3511 10843 6.399249 CCATGCATCGAATTATTCATTTTCGC 60.399 38.462 0.00 0.00 41.38 4.70
3543 10875 6.879993 TCCTATCTATACTGCAGCACTAGTAC 59.120 42.308 15.27 0.00 32.68 2.73
3544 10876 6.655425 CCTATCTATACTGCAGCACTAGTACA 59.345 42.308 15.27 0.00 32.68 2.90
3547 10879 8.815565 ATCTATACTGCAGCACTAGTACATAT 57.184 34.615 15.27 2.54 32.68 1.78
3562 11100 6.102897 AGTACATATATGCTCTGTGGGAAC 57.897 41.667 12.79 0.00 0.00 3.62
3564 11102 3.388024 ACATATATGCTCTGTGGGAACGT 59.612 43.478 12.79 0.00 0.00 3.99
3566 11104 2.851263 TATGCTCTGTGGGAACGTTT 57.149 45.000 0.46 0.00 0.00 3.60
3637 11175 9.383519 TGATTTTCTTCTAGTATTAACCAGCAG 57.616 33.333 0.00 0.00 0.00 4.24
3673 11211 1.144057 CATGGTAGGGTCGAGGCAC 59.856 63.158 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.035458 AGGAAGAGGGTTGCGTGAAG 59.965 55.000 0.00 0.00 0.00 3.02
19 20 0.034896 GAGGAAGAGGGTTGCGTGAA 59.965 55.000 0.00 0.00 0.00 3.18
20 21 1.118965 TGAGGAAGAGGGTTGCGTGA 61.119 55.000 0.00 0.00 0.00 4.35
21 22 0.951040 GTGAGGAAGAGGGTTGCGTG 60.951 60.000 0.00 0.00 0.00 5.34
22 23 1.122019 AGTGAGGAAGAGGGTTGCGT 61.122 55.000 0.00 0.00 0.00 5.24
23 24 0.035458 AAGTGAGGAAGAGGGTTGCG 59.965 55.000 0.00 0.00 0.00 4.85
24 25 1.611936 GGAAGTGAGGAAGAGGGTTGC 60.612 57.143 0.00 0.00 0.00 4.17
25 26 1.003696 GGGAAGTGAGGAAGAGGGTTG 59.996 57.143 0.00 0.00 0.00 3.77
26 27 1.132365 AGGGAAGTGAGGAAGAGGGTT 60.132 52.381 0.00 0.00 0.00 4.11
27 28 0.494095 AGGGAAGTGAGGAAGAGGGT 59.506 55.000 0.00 0.00 0.00 4.34
28 29 2.552093 TAGGGAAGTGAGGAAGAGGG 57.448 55.000 0.00 0.00 0.00 4.30
29 30 4.910458 TTTTAGGGAAGTGAGGAAGAGG 57.090 45.455 0.00 0.00 0.00 3.69
53 54 3.181443 TGGTGAGGAAGAGGGTCTTTTTC 60.181 47.826 0.00 0.00 36.73 2.29
55 56 2.418669 TGGTGAGGAAGAGGGTCTTTT 58.581 47.619 0.00 0.00 36.73 2.27
56 57 2.118403 TGGTGAGGAAGAGGGTCTTT 57.882 50.000 0.00 0.00 36.73 2.52
57 58 2.192263 GATGGTGAGGAAGAGGGTCTT 58.808 52.381 0.00 0.00 39.87 3.01
58 59 1.872773 GATGGTGAGGAAGAGGGTCT 58.127 55.000 0.00 0.00 0.00 3.85
59 60 0.461961 CGATGGTGAGGAAGAGGGTC 59.538 60.000 0.00 0.00 0.00 4.46
60 61 0.041238 TCGATGGTGAGGAAGAGGGT 59.959 55.000 0.00 0.00 0.00 4.34
142 146 2.975536 CGGCGGTACTTGAGGGAA 59.024 61.111 0.00 0.00 0.00 3.97
171 175 2.204705 AGAGGAGGAGGGGAGGGT 60.205 66.667 0.00 0.00 0.00 4.34
179 183 1.118356 CCGGGAATGGAGAGGAGGAG 61.118 65.000 0.00 0.00 0.00 3.69
180 184 1.075226 CCGGGAATGGAGAGGAGGA 60.075 63.158 0.00 0.00 0.00 3.71
181 185 2.812619 GCCGGGAATGGAGAGGAGG 61.813 68.421 2.18 0.00 0.00 4.30
182 186 2.812619 GGCCGGGAATGGAGAGGAG 61.813 68.421 2.18 0.00 0.00 3.69
275 283 3.473647 CCTCCATGGCTGGCGAGA 61.474 66.667 6.96 0.00 42.80 4.04
393 401 1.597854 CTCCTTTGCAGTCACCGCA 60.598 57.895 0.00 0.00 37.68 5.69
554 625 0.179097 CCTACGCTTCTGGGAAGCTC 60.179 60.000 23.70 3.62 40.94 4.09
578 649 4.227134 CCTCCTCCGCCACATCCG 62.227 72.222 0.00 0.00 0.00 4.18
628 699 3.042560 GGCATTTATCGCCCCAGC 58.957 61.111 0.00 0.00 44.22 4.85
634 705 1.941812 CCACCTCGGCATTTATCGC 59.058 57.895 0.00 0.00 0.00 4.58
665 736 1.433879 CTACTCTTCTGGGTCGCCG 59.566 63.158 0.00 0.00 0.00 6.46
666 737 0.971447 ACCTACTCTTCTGGGTCGCC 60.971 60.000 0.00 0.00 0.00 5.54
667 738 0.896226 AACCTACTCTTCTGGGTCGC 59.104 55.000 0.00 0.00 0.00 5.19
668 739 2.931320 GCAAACCTACTCTTCTGGGTCG 60.931 54.545 0.00 0.00 0.00 4.79
669 740 2.701107 GCAAACCTACTCTTCTGGGTC 58.299 52.381 0.00 0.00 0.00 4.46
670 741 1.002087 CGCAAACCTACTCTTCTGGGT 59.998 52.381 0.00 0.00 0.00 4.51
671 742 1.676014 CCGCAAACCTACTCTTCTGGG 60.676 57.143 0.00 0.00 0.00 4.45
672 743 1.275291 TCCGCAAACCTACTCTTCTGG 59.725 52.381 0.00 0.00 0.00 3.86
673 744 2.743636 TCCGCAAACCTACTCTTCTG 57.256 50.000 0.00 0.00 0.00 3.02
674 745 2.678190 GCATCCGCAAACCTACTCTTCT 60.678 50.000 0.00 0.00 38.36 2.85
675 746 1.666189 GCATCCGCAAACCTACTCTTC 59.334 52.381 0.00 0.00 38.36 2.87
676 747 1.739067 GCATCCGCAAACCTACTCTT 58.261 50.000 0.00 0.00 38.36 2.85
677 748 0.460284 CGCATCCGCAAACCTACTCT 60.460 55.000 0.00 0.00 38.40 3.24
678 749 1.429148 CCGCATCCGCAAACCTACTC 61.429 60.000 0.00 0.00 38.40 2.59
679 750 1.449601 CCGCATCCGCAAACCTACT 60.450 57.895 0.00 0.00 38.40 2.57
680 751 1.429148 CTCCGCATCCGCAAACCTAC 61.429 60.000 0.00 0.00 38.40 3.18
681 752 1.153449 CTCCGCATCCGCAAACCTA 60.153 57.895 0.00 0.00 38.40 3.08
682 753 2.436646 CTCCGCATCCGCAAACCT 60.437 61.111 0.00 0.00 38.40 3.50
683 754 2.332654 AACTCCGCATCCGCAAACC 61.333 57.895 0.00 0.00 38.40 3.27
684 755 1.154225 CAACTCCGCATCCGCAAAC 60.154 57.895 0.00 0.00 38.40 2.93
685 756 2.331893 CCAACTCCGCATCCGCAAA 61.332 57.895 0.00 0.00 38.40 3.68
686 757 2.535485 ATCCAACTCCGCATCCGCAA 62.535 55.000 0.00 0.00 38.40 4.85
687 758 3.030168 ATCCAACTCCGCATCCGCA 62.030 57.895 0.00 0.00 38.40 5.69
688 759 2.203070 ATCCAACTCCGCATCCGC 60.203 61.111 0.00 0.00 0.00 5.54
689 760 2.537560 GCATCCAACTCCGCATCCG 61.538 63.158 0.00 0.00 0.00 4.18
690 761 2.189499 GGCATCCAACTCCGCATCC 61.189 63.158 0.00 0.00 0.00 3.51
691 762 2.537560 CGGCATCCAACTCCGCATC 61.538 63.158 0.00 0.00 36.53 3.91
692 763 2.514592 CGGCATCCAACTCCGCAT 60.515 61.111 0.00 0.00 36.53 4.73
693 764 3.664025 CTCGGCATCCAACTCCGCA 62.664 63.158 0.00 0.00 42.65 5.69
694 765 2.892425 CTCGGCATCCAACTCCGC 60.892 66.667 0.00 0.00 42.65 5.54
695 766 2.202932 CCTCGGCATCCAACTCCG 60.203 66.667 0.00 0.00 44.16 4.63
696 767 1.144936 CTCCTCGGCATCCAACTCC 59.855 63.158 0.00 0.00 0.00 3.85
697 768 1.144936 CCTCCTCGGCATCCAACTC 59.855 63.158 0.00 0.00 0.00 3.01
698 769 3.313874 CCTCCTCGGCATCCAACT 58.686 61.111 0.00 0.00 0.00 3.16
720 791 3.360340 GCAGTCACCAGCACAGGC 61.360 66.667 0.00 0.00 41.61 4.85
721 792 2.111669 TGCAGTCACCAGCACAGG 59.888 61.111 0.00 0.00 35.51 4.00
735 806 4.758251 CCCATCGTCTGCCGTGCA 62.758 66.667 0.00 0.00 37.94 4.57
737 808 4.838152 CCCCCATCGTCTGCCGTG 62.838 72.222 0.00 0.00 37.94 4.94
741 812 2.377628 TTATCGCCCCCATCGTCTGC 62.378 60.000 0.00 0.00 0.00 4.26
742 813 0.105964 TTTATCGCCCCCATCGTCTG 59.894 55.000 0.00 0.00 0.00 3.51
743 814 1.056660 ATTTATCGCCCCCATCGTCT 58.943 50.000 0.00 0.00 0.00 4.18
744 815 1.156736 CATTTATCGCCCCCATCGTC 58.843 55.000 0.00 0.00 0.00 4.20
745 816 0.889186 GCATTTATCGCCCCCATCGT 60.889 55.000 0.00 0.00 0.00 3.73
746 817 1.586154 GGCATTTATCGCCCCCATCG 61.586 60.000 0.00 0.00 44.22 3.84
747 818 2.267045 GGCATTTATCGCCCCCATC 58.733 57.895 0.00 0.00 44.22 3.51
748 819 4.519610 GGCATTTATCGCCCCCAT 57.480 55.556 0.00 0.00 44.22 4.00
753 824 0.798776 CCTCATCGGCATTTATCGCC 59.201 55.000 0.00 0.00 46.62 5.54
778 849 3.947132 CTGCAGTCTCCGCCACAGG 62.947 68.421 5.25 0.00 0.00 4.00
779 850 2.433838 CTGCAGTCTCCGCCACAG 60.434 66.667 5.25 0.00 0.00 3.66
780 851 4.007644 CCTGCAGTCTCCGCCACA 62.008 66.667 13.81 0.00 0.00 4.17
785 856 4.463879 CCTGGCCTGCAGTCTCCG 62.464 72.222 13.81 7.22 0.00 4.63
830 901 2.094675 GCTTCTGGGAAGCTTGCATTA 58.905 47.619 20.27 4.58 40.01 1.90
860 931 2.823593 CATCCAACGCCGCATCCA 60.824 61.111 0.00 0.00 0.00 3.41
1001 1135 1.227943 GCCTCAACTGCAGTCACCA 60.228 57.895 21.95 3.30 0.00 4.17
1088 1222 1.251527 ATCGACGTCTGTGCTCCCTT 61.252 55.000 14.70 0.00 0.00 3.95
1097 1231 1.946156 CCCGCATCATCGACGTCTG 60.946 63.158 14.70 6.21 0.00 3.51
1165 1305 1.830477 CTTGGTGGGGAGAAGAGAGAG 59.170 57.143 0.00 0.00 0.00 3.20
1239 1379 0.605589 CAACGAGGTTGAGAGGAGCT 59.394 55.000 2.40 0.00 45.28 4.09
1257 1397 2.821546 CTGTTGAGTTCTTCGTCCACA 58.178 47.619 0.00 0.00 0.00 4.17
1289 1429 6.476706 CCTCTTTGAAATCAAGTTGACCAAAC 59.523 38.462 18.30 7.62 37.15 2.93
1297 1437 4.515567 GTCGTCCCTCTTTGAAATCAAGTT 59.484 41.667 0.00 0.00 37.15 2.66
1407 5027 1.271926 TGGGAACTAAGCCAGCCTTTC 60.272 52.381 0.00 0.00 34.95 2.62
1432 5052 1.053424 AACTCCCGTAGCTTGTCCAA 58.947 50.000 0.00 0.00 0.00 3.53
1445 5065 0.106967 GGGGATGAGCTGAAACTCCC 60.107 60.000 1.89 1.89 44.11 4.30
1561 5190 4.336889 TCACAATCAAGTCGGAGAAACT 57.663 40.909 0.00 0.00 39.69 2.66
1778 5419 2.951642 TCTTGCAAAGGGACACTTTCTG 59.048 45.455 0.00 0.00 46.20 3.02
1890 5546 4.219725 AGCGTGCCCAATATGTTTAGTTTT 59.780 37.500 0.00 0.00 0.00 2.43
1896 5552 2.017049 GAGAGCGTGCCCAATATGTTT 58.983 47.619 0.00 0.00 0.00 2.83
1908 5564 3.717400 TTTATGCCTCTAGAGAGCGTG 57.283 47.619 25.82 11.65 40.75 5.34
1919 5578 5.397326 CAAGCTGAAGTTCTTTTATGCCTC 58.603 41.667 4.17 0.00 0.00 4.70
1971 5642 3.673902 TGAATGAGCAACGGATGAAGAA 58.326 40.909 0.00 0.00 0.00 2.52
2009 5693 6.039717 ACAAGTGCATTCATAAGAACAACAGT 59.960 34.615 0.00 0.00 36.39 3.55
2043 5729 5.258456 ACAGCAATCATATTCTGCAAAGG 57.742 39.130 0.00 0.00 38.58 3.11
2116 5809 9.016438 GGAAGTTAACCACTGTATCCAAATTAA 57.984 33.333 0.88 0.00 35.12 1.40
2149 5842 3.826282 TCTCCAAGCAGGGGAAGG 58.174 61.111 0.00 0.00 46.57 3.46
2561 6284 6.355397 TCAATTCGAGCATCTTGAGAAATC 57.645 37.500 0.00 0.00 0.00 2.17
2714 6545 3.228188 TGGGCTTTGAACAGAAGACAT 57.772 42.857 0.00 0.00 33.68 3.06
2749 6580 1.202710 TCGCCAGGCTAGAACAAAACA 60.203 47.619 10.54 0.00 0.00 2.83
2762 6593 2.076863 AGAAAATCGAAACTCGCCAGG 58.923 47.619 0.00 0.00 40.21 4.45
2765 6596 3.806316 TCAAGAAAATCGAAACTCGCC 57.194 42.857 0.00 0.00 40.21 5.54
2826 6657 4.523173 CGCCCAGGTATAATTCTGACTAGA 59.477 45.833 0.00 0.00 33.11 2.43
2902 6801 7.039363 AGCACATAAAATAAACTACTGGCCAAA 60.039 33.333 7.01 0.00 0.00 3.28
2924 6823 6.314896 ACAGATCTAAACAAGAGCAATAGCAC 59.685 38.462 0.00 0.00 43.38 4.40
2934 6835 9.944376 AACTAAGCATTACAGATCTAAACAAGA 57.056 29.630 0.00 0.00 39.02 3.02
3063 7062 9.681062 TTTACTAAAGCAAGTTATAAGGCAGAT 57.319 29.630 6.50 0.00 0.00 2.90
3064 7063 9.509956 TTTTACTAAAGCAAGTTATAAGGCAGA 57.490 29.630 6.50 0.00 0.00 4.26
3072 7071 9.923143 GGGACAAATTTTACTAAAGCAAGTTAT 57.077 29.630 0.00 0.00 0.00 1.89
3073 7072 8.915036 TGGGACAAATTTTACTAAAGCAAGTTA 58.085 29.630 0.00 0.00 31.92 2.24
3075 7074 7.354751 TGGGACAAATTTTACTAAAGCAAGT 57.645 32.000 0.00 0.00 31.92 3.16
3097 7096 8.948145 TCATGAATTGCAAAGGAATAAATTTGG 58.052 29.630 1.71 0.00 36.99 3.28
3148 7412 6.763355 AGATGTGTCATTCACTGAAACTAGT 58.237 36.000 0.00 0.00 46.27 2.57
3347 8336 2.087646 CACTCGGAGTCTCAGATCACA 58.912 52.381 7.89 0.00 0.00 3.58
3398 8387 5.947228 TTTTCAAGCCTGTATGACTTCAG 57.053 39.130 0.00 0.00 0.00 3.02
3481 10809 1.896220 TAATTCGATGCATGGCCCTC 58.104 50.000 2.46 0.00 0.00 4.30
3482 10810 2.592102 ATAATTCGATGCATGGCCCT 57.408 45.000 2.46 0.00 0.00 5.19
3484 10812 3.921119 TGAATAATTCGATGCATGGCC 57.079 42.857 2.46 0.00 0.00 5.36
3486 10814 6.399249 GCGAAAATGAATAATTCGATGCATGG 60.399 38.462 2.46 2.00 46.50 3.66
3488 10816 5.630680 GGCGAAAATGAATAATTCGATGCAT 59.369 36.000 0.00 0.00 46.50 3.96
3511 10843 6.105333 GCTGCAGTATAGATAGGAATGAAGG 58.895 44.000 16.64 0.00 0.00 3.46
3543 10875 3.995199 ACGTTCCCACAGAGCATATATG 58.005 45.455 8.45 8.45 0.00 1.78
3544 10876 4.689612 AACGTTCCCACAGAGCATATAT 57.310 40.909 0.00 0.00 0.00 0.86
3547 10879 2.851263 AAACGTTCCCACAGAGCATA 57.149 45.000 0.00 0.00 0.00 3.14
3673 11211 1.659601 CTCTGAATTCGCACTGCTCAG 59.340 52.381 10.41 10.41 35.82 3.35


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

AutoCloner maintained by Alex Coulton.