Multiple sequence alignment - TraesCS3A01G353400

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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 TraesCS3A01G353400 chr3A 100.000 2144 0 0 1 2144 601343611 601341468 0.000000e+00 3960.0
1 TraesCS3A01G353400 chr3A 83.425 543 42 24 718 1217 601368630 601368093 5.390000e-126 460.0
2 TraesCS3A01G353400 chr3A 83.824 136 22 0 992 1127 601380663 601380528 1.730000e-26 130.0
3 TraesCS3A01G353400 chr3A 76.515 264 41 15 863 1118 601374683 601374433 8.030000e-25 124.0
4 TraesCS3A01G353400 chr2A 97.318 895 20 2 1250 2144 718926344 718925454 0.000000e+00 1517.0
5 TraesCS3A01G353400 chr5B 93.857 879 54 0 1266 2144 392100224 392101102 0.000000e+00 1325.0
6 TraesCS3A01G353400 chr5B 93.743 879 55 0 1266 2144 392041363 392042241 0.000000e+00 1319.0
7 TraesCS3A01G353400 chr5B 93.515 879 57 0 1266 2144 392056384 392057262 0.000000e+00 1308.0
8 TraesCS3A01G353400 chrUn 93.515 879 57 0 1266 2144 429314774 429313896 0.000000e+00 1308.0
9 TraesCS3A01G353400 chrUn 95.190 499 24 0 1646 2144 426443589 426444087 0.000000e+00 789.0
10 TraesCS3A01G353400 chrUn 95.190 499 24 0 1646 2144 426444890 426445388 0.000000e+00 789.0
11 TraesCS3A01G353400 chrUn 91.850 319 26 0 1266 1584 435173092 435173410 1.510000e-121 446.0
12 TraesCS3A01G353400 chrUn 84.466 103 15 1 178 280 28617211 28617110 1.350000e-17 100.0
13 TraesCS3A01G353400 chr4A 84.015 807 105 13 1339 2144 722138936 722139719 0.000000e+00 754.0
14 TraesCS3A01G353400 chr3B 84.717 530 51 20 718 1219 606380447 606379920 8.830000e-139 503.0
15 TraesCS3A01G353400 chr3B 89.753 283 25 4 224 504 606274522 606274242 2.020000e-95 359.0
16 TraesCS3A01G353400 chr3B 88.973 263 19 4 788 1040 606224236 606223974 1.230000e-82 316.0
17 TraesCS3A01G353400 chr3B 89.617 183 17 2 6 187 606274703 606274522 4.600000e-57 231.0
18 TraesCS3A01G353400 chr3B 87.047 193 22 3 552 743 606274235 606274045 4.630000e-52 215.0
19 TraesCS3A01G353400 chr3B 90.598 117 11 0 1110 1226 606223742 606223626 2.850000e-34 156.0
20 TraesCS3A01G353400 chr3B 82.803 157 25 2 981 1137 606558829 606558675 2.870000e-29 139.0
21 TraesCS3A01G353400 chr3B 72.780 518 80 33 734 1202 606421222 606420717 3.740000e-23 119.0
22 TraesCS3A01G353400 chr3B 96.491 57 1 1 504 559 773166010 773165954 2.270000e-15 93.5
23 TraesCS3A01G353400 chr3B 97.727 44 1 0 735 778 606274011 606273968 2.280000e-10 76.8
24 TraesCS3A01G353400 chr7A 77.690 883 153 21 1266 2144 500180634 500181476 1.140000e-137 499.0
25 TraesCS3A01G353400 chr3D 85.124 363 40 7 552 903 459088639 459088280 2.020000e-95 359.0
26 TraesCS3A01G353400 chr3D 80.503 477 47 18 788 1219 459105145 459104670 7.380000e-85 324.0
27 TraesCS3A01G353400 chr3D 88.525 244 17 3 6 248 459090303 459090070 3.480000e-73 285.0
28 TraesCS3A01G353400 chr3D 87.160 257 20 8 250 504 459088891 459088646 1.620000e-71 279.0
29 TraesCS3A01G353400 chr3D 94.574 129 7 0 1098 1226 459088280 459088152 1.300000e-47 200.0
30 TraesCS3A01G353400 chr3D 77.258 299 43 14 863 1137 459195037 459194740 3.690000e-33 152.0
31 TraesCS3A01G353400 chr3D 96.429 56 2 0 504 559 134554612 134554557 2.270000e-15 93.5
32 TraesCS3A01G353400 chr3D 94.915 59 2 1 504 561 555317352 555317410 8.150000e-15 91.6
33 TraesCS3A01G353400 chr5D 96.429 56 2 0 504 559 34047538 34047483 2.270000e-15 93.5
34 TraesCS3A01G353400 chr5D 94.828 58 2 1 503 559 398523158 398523101 2.930000e-14 89.8
35 TraesCS3A01G353400 chr1D 96.429 56 2 0 504 559 432549943 432549888 2.270000e-15 93.5
36 TraesCS3A01G353400 chr5A 96.429 56 1 1 505 559 622536829 622536884 8.150000e-15 91.6
37 TraesCS3A01G353400 chr5A 93.443 61 2 2 501 559 680718575 680718515 2.930000e-14 89.8
38 TraesCS3A01G353400 chr4D 92.063 63 3 2 504 564 53754803 53754741 1.050000e-13 87.9


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 TraesCS3A01G353400 chr3A 601341468 601343611 2143 True 3960.00 3960 100.00000 1 2144 1 chr3A.!!$R1 2143
1 TraesCS3A01G353400 chr3A 601368093 601368630 537 True 460.00 460 83.42500 718 1217 1 chr3A.!!$R2 499
2 TraesCS3A01G353400 chr2A 718925454 718926344 890 True 1517.00 1517 97.31800 1250 2144 1 chr2A.!!$R1 894
3 TraesCS3A01G353400 chr5B 392100224 392101102 878 False 1325.00 1325 93.85700 1266 2144 1 chr5B.!!$F3 878
4 TraesCS3A01G353400 chr5B 392041363 392042241 878 False 1319.00 1319 93.74300 1266 2144 1 chr5B.!!$F1 878
5 TraesCS3A01G353400 chr5B 392056384 392057262 878 False 1308.00 1308 93.51500 1266 2144 1 chr5B.!!$F2 878
6 TraesCS3A01G353400 chrUn 429313896 429314774 878 True 1308.00 1308 93.51500 1266 2144 1 chrUn.!!$R2 878
7 TraesCS3A01G353400 chrUn 426443589 426445388 1799 False 789.00 789 95.19000 1646 2144 2 chrUn.!!$F2 498
8 TraesCS3A01G353400 chr4A 722138936 722139719 783 False 754.00 754 84.01500 1339 2144 1 chr4A.!!$F1 805
9 TraesCS3A01G353400 chr3B 606379920 606380447 527 True 503.00 503 84.71700 718 1219 1 chr3B.!!$R1 501
10 TraesCS3A01G353400 chr3B 606223626 606224236 610 True 236.00 316 89.78550 788 1226 2 chr3B.!!$R5 438
11 TraesCS3A01G353400 chr3B 606273968 606274703 735 True 220.45 359 91.03600 6 778 4 chr3B.!!$R6 772
12 TraesCS3A01G353400 chr7A 500180634 500181476 842 False 499.00 499 77.69000 1266 2144 1 chr7A.!!$F1 878
13 TraesCS3A01G353400 chr3D 459088152 459090303 2151 True 280.75 359 88.84575 6 1226 4 chr3D.!!$R4 1220

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
839 2109 0.106918 AACTTGTTCCCAGACCGCAA 60.107 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 3415 1.429148 GGAGCTTAATGGACGCCACG 61.429 60.0 0.5 0.0 35.8 4.94 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
34 36 1.663643 GCATTCTGAATTGCCGACGTA 59.336 47.619 0.00 0.00 0.00 3.57
36 38 3.493129 GCATTCTGAATTGCCGACGTATA 59.507 43.478 0.00 0.00 0.00 1.47
38 40 5.334105 GCATTCTGAATTGCCGACGTATATT 60.334 40.000 0.00 0.00 0.00 1.28
55 57 6.927381 ACGTATATTTAATCCCTTGTTCTCCG 59.073 38.462 0.00 0.00 0.00 4.63
71 73 1.133598 CTCCGATACGCCACACTAACA 59.866 52.381 0.00 0.00 0.00 2.41
165 167 3.503748 AGCTAAGCTGGTGTTGATCAAAC 59.496 43.478 10.35 10.44 37.57 2.93
166 168 3.667960 GCTAAGCTGGTGTTGATCAAACG 60.668 47.826 10.35 0.00 42.10 3.60
208 238 6.712241 TTTGTTTTTGCGAGAAAATTGTCA 57.288 29.167 0.00 0.00 31.80 3.58
209 239 6.712241 TTGTTTTTGCGAGAAAATTGTCAA 57.288 29.167 0.00 0.00 31.80 3.18
210 240 6.900568 TGTTTTTGCGAGAAAATTGTCAAT 57.099 29.167 0.00 0.00 31.80 2.57
211 241 6.932051 TGTTTTTGCGAGAAAATTGTCAATC 58.068 32.000 0.00 0.00 31.80 2.67
213 243 7.918033 TGTTTTTGCGAGAAAATTGTCAATCTA 59.082 29.630 0.00 0.00 31.80 1.98
214 244 8.915654 GTTTTTGCGAGAAAATTGTCAATCTAT 58.084 29.630 0.00 0.00 31.80 1.98
215 245 9.474920 TTTTTGCGAGAAAATTGTCAATCTATT 57.525 25.926 0.00 0.00 0.00 1.73
216 246 8.673626 TTTGCGAGAAAATTGTCAATCTATTC 57.326 30.769 0.00 4.87 0.00 1.75
217 247 7.376435 TGCGAGAAAATTGTCAATCTATTCA 57.624 32.000 15.46 2.45 0.00 2.57
218 248 7.466805 TGCGAGAAAATTGTCAATCTATTCAG 58.533 34.615 15.46 11.67 0.00 3.02
221 251 7.964559 CGAGAAAATTGTCAATCTATTCAGCAA 59.035 33.333 15.46 0.00 0.00 3.91
222 252 8.976986 AGAAAATTGTCAATCTATTCAGCAAC 57.023 30.769 15.46 0.00 0.00 4.17
223 253 8.800332 AGAAAATTGTCAATCTATTCAGCAACT 58.200 29.630 15.46 0.00 0.00 3.16
248 1455 1.985159 AGGTAGTGCCAAGACCATCAA 59.015 47.619 0.00 0.00 40.61 2.57
386 1594 6.484977 TGAAACAAAGGCAAAAGTTTTGTCTT 59.515 30.769 32.51 32.51 45.21 3.01
435 1643 9.869757 AGTTGCAAATTAATACATAGAAAACCC 57.130 29.630 0.00 0.00 0.00 4.11
453 1661 1.133025 CCCGATGAAAACTGTGATGGC 59.867 52.381 0.00 0.00 0.00 4.40
470 1678 7.622713 TGTGATGGCCTTTAAATTTGATCAAT 58.377 30.769 9.40 0.00 0.00 2.57
471 1679 7.765360 TGTGATGGCCTTTAAATTTGATCAATC 59.235 33.333 9.40 0.00 0.00 2.67
479 1687 8.863049 CCTTTAAATTTGATCAATCCTCAAACG 58.137 33.333 9.40 0.00 43.31 3.60
492 1700 5.523438 TCCTCAAACGGCTAATTGTTTTT 57.477 34.783 0.00 0.00 36.22 1.94
504 1712 6.280643 GCTAATTGTTTTTGGAGTGAACCTT 58.719 36.000 0.00 0.00 0.00 3.50
505 1713 6.761242 GCTAATTGTTTTTGGAGTGAACCTTT 59.239 34.615 0.00 0.00 0.00 3.11
507 1715 7.994425 AATTGTTTTTGGAGTGAACCTTTTT 57.006 28.000 0.00 0.00 0.00 1.94
508 1716 7.609760 ATTGTTTTTGGAGTGAACCTTTTTC 57.390 32.000 0.00 0.00 0.00 2.29
510 1718 5.047943 TGTTTTTGGAGTGAACCTTTTTCGA 60.048 36.000 0.00 0.00 0.00 3.71
511 1719 4.625972 TTTGGAGTGAACCTTTTTCGAC 57.374 40.909 0.00 0.00 0.00 4.20
512 1720 3.269538 TGGAGTGAACCTTTTTCGACA 57.730 42.857 0.00 0.00 0.00 4.35
513 1721 3.611970 TGGAGTGAACCTTTTTCGACAA 58.388 40.909 0.00 0.00 0.00 3.18
514 1722 4.011023 TGGAGTGAACCTTTTTCGACAAA 58.989 39.130 0.00 0.00 0.00 2.83
515 1723 4.095782 TGGAGTGAACCTTTTTCGACAAAG 59.904 41.667 15.59 15.59 34.06 2.77
520 1728 2.793278 CCTTTTTCGACAAAGGGTGG 57.207 50.000 28.14 9.78 46.49 4.61
521 1729 2.303175 CCTTTTTCGACAAAGGGTGGA 58.697 47.619 28.14 0.00 46.49 4.02
522 1730 2.890945 CCTTTTTCGACAAAGGGTGGAT 59.109 45.455 28.14 0.00 46.49 3.41
523 1731 3.320826 CCTTTTTCGACAAAGGGTGGATT 59.679 43.478 28.14 0.00 46.49 3.01
524 1732 4.202212 CCTTTTTCGACAAAGGGTGGATTT 60.202 41.667 28.14 0.00 46.49 2.17
525 1733 5.346181 TTTTTCGACAAAGGGTGGATTTT 57.654 34.783 0.00 0.00 34.00 1.82
526 1734 6.461788 CCTTTTTCGACAAAGGGTGGATTTTA 60.462 38.462 28.14 0.00 46.49 1.52
527 1735 6.658188 TTTTCGACAAAGGGTGGATTTTAT 57.342 33.333 0.00 0.00 34.00 1.40
528 1736 6.658188 TTTCGACAAAGGGTGGATTTTATT 57.342 33.333 0.00 0.00 34.00 1.40
529 1737 7.762588 TTTCGACAAAGGGTGGATTTTATTA 57.237 32.000 0.00 0.00 34.00 0.98
530 1738 7.762588 TTCGACAAAGGGTGGATTTTATTAA 57.237 32.000 0.00 0.00 34.00 1.40
531 1739 7.148355 TCGACAAAGGGTGGATTTTATTAAC 57.852 36.000 0.00 0.00 28.37 2.01
532 1740 6.943718 TCGACAAAGGGTGGATTTTATTAACT 59.056 34.615 0.00 0.00 28.37 2.24
533 1741 7.120138 TCGACAAAGGGTGGATTTTATTAACTC 59.880 37.037 0.00 0.00 28.37 3.01
534 1742 7.094549 CGACAAAGGGTGGATTTTATTAACTCA 60.095 37.037 0.00 0.00 0.00 3.41
535 1743 8.485578 ACAAAGGGTGGATTTTATTAACTCAA 57.514 30.769 0.00 0.00 0.00 3.02
536 1744 8.929487 ACAAAGGGTGGATTTTATTAACTCAAA 58.071 29.630 0.00 0.00 0.00 2.69
537 1745 9.771534 CAAAGGGTGGATTTTATTAACTCAAAA 57.228 29.630 0.00 0.00 0.00 2.44
539 1747 9.942850 AAGGGTGGATTTTATTAACTCAAAATG 57.057 29.630 8.29 0.00 35.14 2.32
540 1748 9.320295 AGGGTGGATTTTATTAACTCAAAATGA 57.680 29.630 8.29 0.00 35.14 2.57
541 1749 9.936759 GGGTGGATTTTATTAACTCAAAATGAA 57.063 29.630 8.29 0.00 35.14 2.57
551 1759 8.752766 ATTAACTCAAAATGAAGCATCAAGTG 57.247 30.769 0.00 0.00 39.49 3.16
552 1760 6.395426 AACTCAAAATGAAGCATCAAGTGA 57.605 33.333 0.00 0.00 39.49 3.41
553 1761 6.585695 ACTCAAAATGAAGCATCAAGTGAT 57.414 33.333 0.00 0.00 39.49 3.06
554 1762 7.692460 ACTCAAAATGAAGCATCAAGTGATA 57.308 32.000 0.00 0.00 39.49 2.15
576 1784 9.691362 TGATAAAAAGAAATCCACTTAGCAAAC 57.309 29.630 0.00 0.00 0.00 2.93
578 1786 9.696917 ATAAAAAGAAATCCACTTAGCAAACTG 57.303 29.630 0.00 0.00 0.00 3.16
580 1788 3.507622 AGAAATCCACTTAGCAAACTGGC 59.492 43.478 0.00 0.00 0.00 4.85
584 1792 1.895131 CCACTTAGCAAACTGGCCATT 59.105 47.619 5.51 0.00 0.00 3.16
586 1794 3.509575 CCACTTAGCAAACTGGCCATTAA 59.490 43.478 5.51 0.00 0.00 1.40
594 1802 4.680172 GCAAACTGGCCATTAATGTGCATA 60.680 41.667 22.31 13.72 0.00 3.14
604 1812 7.548780 GGCCATTAATGTGCATAAGAAAAGAAA 59.451 33.333 22.31 0.00 0.00 2.52
617 1825 1.055849 AAAGAAAATGGTGGGGTGGC 58.944 50.000 0.00 0.00 0.00 5.01
618 1826 0.190815 AAGAAAATGGTGGGGTGGCT 59.809 50.000 0.00 0.00 0.00 4.75
637 1850 1.682344 GGGTGGGTGCTTCCAATCC 60.682 63.158 0.27 0.00 38.72 3.01
658 1871 2.096496 CGCAGGATCTGAATGTTTGTCC 59.904 50.000 0.00 0.00 32.44 4.02
663 1876 6.409704 CAGGATCTGAATGTTTGTCCTCTAA 58.590 40.000 0.00 0.00 34.00 2.10
703 1916 4.365514 TCACTTCATTAGGGTTGCTTCA 57.634 40.909 0.00 0.00 0.00 3.02
706 1919 5.774690 TCACTTCATTAGGGTTGCTTCAAAT 59.225 36.000 0.00 0.00 0.00 2.32
720 1936 4.231890 TGCTTCAAATATACCCCTTCCCTT 59.768 41.667 0.00 0.00 0.00 3.95
800 2070 3.746940 AGCAAATACTAACCCACGTGTT 58.253 40.909 15.65 5.69 0.00 3.32
804 2074 5.179929 GCAAATACTAACCCACGTGTTACTT 59.820 40.000 15.65 2.38 0.00 2.24
831 2101 0.468226 AGCGAGTCAACTTGTTCCCA 59.532 50.000 0.00 0.00 0.00 4.37
836 2106 1.202651 AGTCAACTTGTTCCCAGACCG 60.203 52.381 0.00 0.00 0.00 4.79
839 2109 0.106918 AACTTGTTCCCAGACCGCAA 60.107 50.000 0.00 0.00 0.00 4.85
883 2171 0.882474 AGAAGAACGCGCAGTCTAGT 59.118 50.000 5.73 0.00 0.00 2.57
960 2251 1.484444 AAACCAGCTCTCGCCTTCCT 61.484 55.000 0.00 0.00 36.60 3.36
977 2286 2.175202 TCCTTGCAACACAAACCAAGT 58.825 42.857 0.00 0.00 37.96 3.16
978 2287 2.564947 TCCTTGCAACACAAACCAAGTT 59.435 40.909 0.00 0.00 37.96 2.66
983 2292 2.808244 CAACACAAACCAAGTTCGCAT 58.192 42.857 0.00 0.00 0.00 4.73
998 2312 0.897863 CGCATAGGAGGAGGAGGAGG 60.898 65.000 0.00 0.00 0.00 4.30
1011 2325 1.411216 GGAGGAGGAATGGAGTACGGA 60.411 57.143 0.00 0.00 0.00 4.69
1024 2338 2.141448 TACGGACACCCCTGCAACA 61.141 57.895 0.00 0.00 0.00 3.33
1025 2339 1.697082 TACGGACACCCCTGCAACAA 61.697 55.000 0.00 0.00 0.00 2.83
1026 2340 2.551912 CGGACACCCCTGCAACAAC 61.552 63.158 0.00 0.00 0.00 3.32
1033 2485 2.620112 CCCTGCAACAACAGCTCCG 61.620 63.158 0.00 0.00 36.29 4.63
1090 2542 0.457443 GCTCAAGGTGCAAATAGCCC 59.543 55.000 0.00 0.00 44.83 5.19
1120 2572 2.904866 GCCTTGTTGTGCCGGTCA 60.905 61.111 1.90 0.00 0.00 4.02
1130 2609 2.112297 GCCGGTCACCAGGAACAA 59.888 61.111 1.90 0.00 30.31 2.83
1226 2705 4.637534 GTGCTTGATATGCATACATAGGGG 59.362 45.833 8.99 0.00 41.97 4.79
1227 2706 4.289410 TGCTTGATATGCATACATAGGGGT 59.711 41.667 8.99 0.00 41.97 4.95
1228 2707 4.637534 GCTTGATATGCATACATAGGGGTG 59.362 45.833 8.99 0.00 41.97 4.61
1229 2708 4.842531 TGATATGCATACATAGGGGTGG 57.157 45.455 8.99 0.00 41.97 4.61
1230 2709 4.434195 TGATATGCATACATAGGGGTGGA 58.566 43.478 8.99 0.00 41.97 4.02
1231 2710 5.038962 TGATATGCATACATAGGGGTGGAT 58.961 41.667 8.99 0.00 41.97 3.41
1232 2711 3.726557 ATGCATACATAGGGGTGGATG 57.273 47.619 0.00 0.00 42.26 3.51
1233 2712 2.700354 TGCATACATAGGGGTGGATGA 58.300 47.619 3.38 0.00 41.99 2.92
1234 2713 3.052329 TGCATACATAGGGGTGGATGAA 58.948 45.455 3.38 0.00 41.99 2.57
1235 2714 3.072915 TGCATACATAGGGGTGGATGAAG 59.927 47.826 3.38 0.00 41.99 3.02
1236 2715 3.327757 GCATACATAGGGGTGGATGAAGA 59.672 47.826 3.38 0.00 41.99 2.87
1237 2716 4.018960 GCATACATAGGGGTGGATGAAGAT 60.019 45.833 3.38 0.00 41.99 2.40
1238 2717 5.738909 CATACATAGGGGTGGATGAAGATC 58.261 45.833 0.00 0.00 41.99 2.75
1245 2724 4.055654 GGATGAAGATCCTGCGGC 57.944 61.111 0.00 0.00 44.58 6.53
1246 2725 1.146930 GGATGAAGATCCTGCGGCA 59.853 57.895 1.29 1.29 44.58 5.69
1247 2726 1.162800 GGATGAAGATCCTGCGGCAC 61.163 60.000 0.00 0.00 44.58 5.01
1510 2989 1.935327 GACTCGGAGTTCGTCCCTGG 61.935 65.000 12.67 0.00 43.47 4.45
1936 3415 0.247695 GCTCGCGGTTGCAAGAATAC 60.248 55.000 6.13 0.00 42.97 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.490079 GCAATTCAGAATGCAATATCTTCACAA 59.510 33.333 0.00 0.00 42.12 3.33
2 3 6.976349 GCAATTCAGAATGCAATATCTTCACA 59.024 34.615 0.00 0.00 42.12 3.58
4 5 6.509656 GGCAATTCAGAATGCAATATCTTCA 58.490 36.000 15.28 0.00 44.32 3.02
11 12 2.478370 CGTCGGCAATTCAGAATGCAAT 60.478 45.455 15.28 0.00 44.32 3.56
34 36 7.817962 CGTATCGGAGAACAAGGGATTAAATAT 59.182 37.037 0.00 0.00 43.58 1.28
36 38 5.989777 CGTATCGGAGAACAAGGGATTAAAT 59.010 40.000 0.00 0.00 43.58 1.40
38 40 4.738541 GCGTATCGGAGAACAAGGGATTAA 60.739 45.833 0.00 0.00 43.58 1.40
55 57 4.243270 GGGATATGTTAGTGTGGCGTATC 58.757 47.826 0.00 0.00 32.98 2.24
71 73 7.921304 TCTTATGTAACAGCATGATGGGATAT 58.079 34.615 16.55 8.62 39.69 1.63
186 216 6.712241 TTGACAATTTTCTCGCAAAAACAA 57.288 29.167 0.00 0.00 31.35 2.83
187 217 6.756074 AGATTGACAATTTTCTCGCAAAAACA 59.244 30.769 1.39 0.00 31.35 2.83
188 218 7.165427 AGATTGACAATTTTCTCGCAAAAAC 57.835 32.000 1.39 0.00 31.35 2.43
190 220 9.128107 GAATAGATTGACAATTTTCTCGCAAAA 57.872 29.630 1.39 0.00 0.00 2.44
191 221 8.296000 TGAATAGATTGACAATTTTCTCGCAAA 58.704 29.630 1.39 0.00 0.00 3.68
192 222 7.815641 TGAATAGATTGACAATTTTCTCGCAA 58.184 30.769 1.39 0.00 0.00 4.85
193 223 7.376435 TGAATAGATTGACAATTTTCTCGCA 57.624 32.000 1.39 0.00 0.00 5.10
194 224 6.413235 GCTGAATAGATTGACAATTTTCTCGC 59.587 38.462 1.39 9.20 0.00 5.03
195 225 7.466805 TGCTGAATAGATTGACAATTTTCTCG 58.533 34.615 1.39 4.41 0.00 4.04
197 227 8.800332 AGTTGCTGAATAGATTGACAATTTTCT 58.200 29.630 1.39 0.00 0.00 2.52
198 228 8.857216 CAGTTGCTGAATAGATTGACAATTTTC 58.143 33.333 1.39 7.19 32.44 2.29
199 229 8.362639 ACAGTTGCTGAATAGATTGACAATTTT 58.637 29.630 1.39 0.00 35.18 1.82
200 230 7.889469 ACAGTTGCTGAATAGATTGACAATTT 58.111 30.769 1.39 0.00 35.18 1.82
201 231 7.175467 TGACAGTTGCTGAATAGATTGACAATT 59.825 33.333 1.39 0.00 35.18 2.32
203 233 5.997129 TGACAGTTGCTGAATAGATTGACAA 59.003 36.000 2.91 0.00 35.18 3.18
204 234 5.550290 TGACAGTTGCTGAATAGATTGACA 58.450 37.500 2.91 0.00 35.18 3.58
205 235 6.402983 CCTTGACAGTTGCTGAATAGATTGAC 60.403 42.308 2.91 0.00 35.18 3.18
206 236 5.645067 CCTTGACAGTTGCTGAATAGATTGA 59.355 40.000 2.91 0.00 35.18 2.57
207 237 5.413833 ACCTTGACAGTTGCTGAATAGATTG 59.586 40.000 2.91 0.00 35.18 2.67
208 238 5.564550 ACCTTGACAGTTGCTGAATAGATT 58.435 37.500 2.91 0.00 35.18 2.40
209 239 5.171339 ACCTTGACAGTTGCTGAATAGAT 57.829 39.130 2.91 0.00 35.18 1.98
210 240 4.623932 ACCTTGACAGTTGCTGAATAGA 57.376 40.909 2.91 0.00 35.18 1.98
211 241 5.349817 CACTACCTTGACAGTTGCTGAATAG 59.650 44.000 2.91 0.00 35.18 1.73
213 243 4.067896 CACTACCTTGACAGTTGCTGAAT 58.932 43.478 2.91 0.00 35.18 2.57
214 244 3.466836 CACTACCTTGACAGTTGCTGAA 58.533 45.455 2.91 0.00 35.18 3.02
215 245 2.806745 GCACTACCTTGACAGTTGCTGA 60.807 50.000 2.91 0.00 35.18 4.26
216 246 1.532868 GCACTACCTTGACAGTTGCTG 59.467 52.381 0.00 0.00 37.52 4.41
217 247 1.543429 GGCACTACCTTGACAGTTGCT 60.543 52.381 0.00 0.00 34.51 3.91
218 248 0.875059 GGCACTACCTTGACAGTTGC 59.125 55.000 0.00 0.00 34.51 4.17
221 251 2.047061 TCTTGGCACTACCTTGACAGT 58.953 47.619 0.00 0.00 35.36 3.55
222 252 2.417719 GTCTTGGCACTACCTTGACAG 58.582 52.381 0.00 0.00 35.36 3.51
223 253 1.071699 GGTCTTGGCACTACCTTGACA 59.928 52.381 9.64 0.00 40.64 3.58
272 1479 6.157645 AGTCTAGACAAGATTTGATGGTCCAT 59.842 38.462 24.44 3.26 36.36 3.41
274 1481 5.814705 CAGTCTAGACAAGATTTGATGGTCC 59.185 44.000 24.44 0.00 36.36 4.46
356 1564 9.617975 CAAAACTTTTGCCTTTGTTTCAAAATA 57.382 25.926 1.30 0.00 38.51 1.40
357 1565 8.140628 ACAAAACTTTTGCCTTTGTTTCAAAAT 58.859 25.926 13.22 0.00 39.61 1.82
361 1569 5.994668 AGACAAAACTTTTGCCTTTGTTTCA 59.005 32.000 13.22 0.00 41.95 2.69
362 1570 6.480524 AGACAAAACTTTTGCCTTTGTTTC 57.519 33.333 13.22 2.59 41.95 2.78
421 1629 7.610305 ACAGTTTTCATCGGGTTTTCTATGTAT 59.390 33.333 0.00 0.00 0.00 2.29
426 1634 5.369833 TCACAGTTTTCATCGGGTTTTCTA 58.630 37.500 0.00 0.00 0.00 2.10
435 1643 2.086869 AGGCCATCACAGTTTTCATCG 58.913 47.619 5.01 0.00 0.00 3.84
453 1661 8.863049 CGTTTGAGGATTGATCAAATTTAAAGG 58.137 33.333 13.09 11.51 45.54 3.11
470 1678 5.285651 CAAAAACAATTAGCCGTTTGAGGA 58.714 37.500 0.00 0.00 35.57 3.71
471 1679 4.447389 CCAAAAACAATTAGCCGTTTGAGG 59.553 41.667 0.00 0.00 35.57 3.86
479 1687 4.988540 GGTTCACTCCAAAAACAATTAGCC 59.011 41.667 0.00 0.00 0.00 3.93
492 1700 3.269538 TGTCGAAAAAGGTTCACTCCA 57.730 42.857 0.00 0.00 0.00 3.86
504 1712 6.658188 ATAAAATCCACCCTTTGTCGAAAA 57.342 33.333 0.00 0.00 0.00 2.29
505 1713 6.658188 AATAAAATCCACCCTTTGTCGAAA 57.342 33.333 0.00 0.00 0.00 3.46
507 1715 6.943718 AGTTAATAAAATCCACCCTTTGTCGA 59.056 34.615 0.00 0.00 0.00 4.20
508 1716 7.094549 TGAGTTAATAAAATCCACCCTTTGTCG 60.095 37.037 0.00 0.00 0.00 4.35
510 1718 8.485578 TTGAGTTAATAAAATCCACCCTTTGT 57.514 30.769 0.00 0.00 0.00 2.83
511 1719 9.771534 TTTTGAGTTAATAAAATCCACCCTTTG 57.228 29.630 0.00 0.00 0.00 2.77
513 1721 9.942850 CATTTTGAGTTAATAAAATCCACCCTT 57.057 29.630 0.00 0.00 35.07 3.95
514 1722 9.320295 TCATTTTGAGTTAATAAAATCCACCCT 57.680 29.630 0.00 0.00 35.07 4.34
515 1723 9.936759 TTCATTTTGAGTTAATAAAATCCACCC 57.063 29.630 0.00 0.00 35.07 4.61
525 1733 9.844790 CACTTGATGCTTCATTTTGAGTTAATA 57.155 29.630 2.75 0.00 0.00 0.98
526 1734 8.579006 TCACTTGATGCTTCATTTTGAGTTAAT 58.421 29.630 2.75 0.00 0.00 1.40
527 1735 7.939782 TCACTTGATGCTTCATTTTGAGTTAA 58.060 30.769 2.75 0.00 0.00 2.01
528 1736 7.509141 TCACTTGATGCTTCATTTTGAGTTA 57.491 32.000 2.75 0.00 0.00 2.24
529 1737 6.395426 TCACTTGATGCTTCATTTTGAGTT 57.605 33.333 2.75 0.00 0.00 3.01
530 1738 6.585695 ATCACTTGATGCTTCATTTTGAGT 57.414 33.333 2.75 0.90 32.68 3.41
531 1739 8.975410 TTTATCACTTGATGCTTCATTTTGAG 57.025 30.769 2.75 0.28 36.05 3.02
532 1740 9.761504 TTTTTATCACTTGATGCTTCATTTTGA 57.238 25.926 2.75 6.89 36.05 2.69
534 1742 9.985730 TCTTTTTATCACTTGATGCTTCATTTT 57.014 25.926 2.75 0.00 36.05 1.82
535 1743 9.985730 TTCTTTTTATCACTTGATGCTTCATTT 57.014 25.926 2.75 0.00 36.05 2.32
536 1744 9.985730 TTTCTTTTTATCACTTGATGCTTCATT 57.014 25.926 2.75 0.00 36.05 2.57
538 1746 9.630098 GATTTCTTTTTATCACTTGATGCTTCA 57.370 29.630 1.77 0.00 36.05 3.02
539 1747 9.080915 GGATTTCTTTTTATCACTTGATGCTTC 57.919 33.333 1.77 0.00 36.05 3.86
540 1748 8.587608 TGGATTTCTTTTTATCACTTGATGCTT 58.412 29.630 1.77 0.00 36.05 3.91
541 1749 8.031277 GTGGATTTCTTTTTATCACTTGATGCT 58.969 33.333 1.77 0.00 36.05 3.79
542 1750 8.031277 AGTGGATTTCTTTTTATCACTTGATGC 58.969 33.333 1.77 0.00 36.05 3.91
543 1751 9.918630 AAGTGGATTTCTTTTTATCACTTGATG 57.081 29.630 1.77 0.00 36.05 3.07
546 1754 9.346725 GCTAAGTGGATTTCTTTTTATCACTTG 57.653 33.333 13.81 7.03 33.28 3.16
547 1755 9.077885 TGCTAAGTGGATTTCTTTTTATCACTT 57.922 29.630 0.00 0.00 35.08 3.16
548 1756 8.635765 TGCTAAGTGGATTTCTTTTTATCACT 57.364 30.769 0.00 0.00 0.00 3.41
549 1757 9.691362 TTTGCTAAGTGGATTTCTTTTTATCAC 57.309 29.630 0.00 0.00 0.00 3.06
550 1758 9.691362 GTTTGCTAAGTGGATTTCTTTTTATCA 57.309 29.630 0.00 0.00 0.00 2.15
551 1759 9.914131 AGTTTGCTAAGTGGATTTCTTTTTATC 57.086 29.630 0.00 0.00 0.00 1.75
552 1760 9.696917 CAGTTTGCTAAGTGGATTTCTTTTTAT 57.303 29.630 7.73 0.00 32.16 1.40
570 1778 2.354003 GCACATTAATGGCCAGTTTGCT 60.354 45.455 12.70 0.00 0.00 3.91
576 1784 5.518848 TTCTTATGCACATTAATGGCCAG 57.481 39.130 19.37 13.77 0.00 4.85
578 1786 6.572519 TCTTTTCTTATGCACATTAATGGCC 58.427 36.000 19.37 9.98 0.00 5.36
584 1792 9.421806 CACCATTTTCTTTTCTTATGCACATTA 57.578 29.630 0.00 0.00 0.00 1.90
586 1794 6.875195 CCACCATTTTCTTTTCTTATGCACAT 59.125 34.615 0.00 0.00 0.00 3.21
594 1802 3.390967 CCACCCCACCATTTTCTTTTCTT 59.609 43.478 0.00 0.00 0.00 2.52
604 1812 3.996621 CCCAGCCACCCCACCATT 61.997 66.667 0.00 0.00 0.00 3.16
617 1825 0.967380 GATTGGAAGCACCCACCCAG 60.967 60.000 0.00 0.00 35.62 4.45
618 1826 1.076549 GATTGGAAGCACCCACCCA 59.923 57.895 0.00 0.00 35.62 4.51
637 1850 2.096496 GGACAAACATTCAGATCCTGCG 59.904 50.000 0.00 0.00 0.00 5.18
658 1871 9.231297 TGAACCTTTTTATCCATGAACTTAGAG 57.769 33.333 0.00 0.00 0.00 2.43
663 1876 7.505585 TGAAGTGAACCTTTTTATCCATGAACT 59.494 33.333 0.00 0.00 32.03 3.01
703 1916 9.021747 ACACTAATTAAGGGAAGGGGTATATTT 57.978 33.333 0.00 0.00 30.77 1.40
706 1919 7.140990 TCACACTAATTAAGGGAAGGGGTATA 58.859 38.462 0.00 0.00 30.77 1.47
720 1936 6.040955 CCTGGCTCTCACTATCACACTAATTA 59.959 42.308 0.00 0.00 0.00 1.40
800 2070 7.225931 ACAAGTTGACTCGCTTTATTTGAAGTA 59.774 33.333 10.54 0.00 0.00 2.24
804 2074 6.371809 AACAAGTTGACTCGCTTTATTTGA 57.628 33.333 10.54 0.00 0.00 2.69
831 2101 1.599047 CCCATCTCTGTTGCGGTCT 59.401 57.895 0.00 0.00 0.00 3.85
836 2106 3.350219 TTAACTCCCCATCTCTGTTGC 57.650 47.619 0.00 0.00 0.00 4.17
839 2109 7.989947 TTACTAATTAACTCCCCATCTCTGT 57.010 36.000 0.00 0.00 0.00 3.41
883 2171 2.243602 AAGTTTTCGGGCACGTTCTA 57.756 45.000 8.89 0.00 41.85 2.10
935 2223 3.129792 CGAGAGCTGGTTTGAGGAC 57.870 57.895 0.00 0.00 0.00 3.85
960 2251 2.600731 CGAACTTGGTTTGTGTTGCAA 58.399 42.857 0.00 0.00 34.87 4.08
977 2286 0.556258 TCCTCCTCCTCCTATGCGAA 59.444 55.000 0.00 0.00 0.00 4.70
978 2287 0.111446 CTCCTCCTCCTCCTATGCGA 59.889 60.000 0.00 0.00 0.00 5.10
983 2292 1.505538 CCATTCCTCCTCCTCCTCCTA 59.494 57.143 0.00 0.00 0.00 2.94
998 2312 0.177373 GGGGTGTCCGTACTCCATTC 59.823 60.000 1.53 0.00 41.08 2.67
1011 2325 2.127232 GCTGTTGTTGCAGGGGTGT 61.127 57.895 0.00 0.00 37.00 4.16
1024 2338 1.898574 CCTTGTTGCCGGAGCTGTT 60.899 57.895 5.05 0.00 40.80 3.16
1025 2339 2.281761 CCTTGTTGCCGGAGCTGT 60.282 61.111 5.05 0.00 40.80 4.40
1026 2340 2.032528 TCCTTGTTGCCGGAGCTG 59.967 61.111 5.05 0.00 40.80 4.24
1033 2485 0.962855 GGCCTCTTCTCCTTGTTGCC 60.963 60.000 0.00 0.00 0.00 4.52
1090 2542 3.655211 AAGGCTGCCCAGGGTCTG 61.655 66.667 16.57 4.96 0.00 3.51
1120 2572 2.408565 TCTCCTGAAGTTGTTCCTGGT 58.591 47.619 0.00 0.00 31.09 4.00
1130 2609 1.767681 GGCCATCTCATCTCCTGAAGT 59.232 52.381 0.00 0.00 32.14 3.01
1243 2722 2.491022 ATAGGTCTCGCTCCGTGCC 61.491 63.158 0.00 0.00 38.78 5.01
1244 2723 1.299468 CATAGGTCTCGCTCCGTGC 60.299 63.158 0.00 0.00 38.57 5.34
1245 2724 0.309302 CTCATAGGTCTCGCTCCGTG 59.691 60.000 0.00 0.00 0.00 4.94
1246 2725 1.448922 GCTCATAGGTCTCGCTCCGT 61.449 60.000 0.00 0.00 0.00 4.69
1247 2726 1.284408 GCTCATAGGTCTCGCTCCG 59.716 63.158 0.00 0.00 0.00 4.63
1248 2727 1.663173 GGCTCATAGGTCTCGCTCC 59.337 63.158 0.00 0.00 0.00 4.70
1249 2728 1.109920 TGGGCTCATAGGTCTCGCTC 61.110 60.000 0.00 0.00 0.00 5.03
1250 2729 1.075970 TGGGCTCATAGGTCTCGCT 60.076 57.895 0.00 0.00 0.00 4.93
1251 2730 1.068250 GTGGGCTCATAGGTCTCGC 59.932 63.158 0.00 0.00 0.00 5.03
1252 2731 1.742768 GGTGGGCTCATAGGTCTCG 59.257 63.158 0.00 0.00 0.00 4.04
1253 2732 1.742768 CGGTGGGCTCATAGGTCTC 59.257 63.158 0.00 0.00 0.00 3.36
1254 2733 2.435693 GCGGTGGGCTCATAGGTCT 61.436 63.158 0.00 0.00 39.11 3.85
1321 2800 4.738998 CAGGTTGGCCGGCATGGA 62.739 66.667 30.85 7.55 42.00 3.41
1936 3415 1.429148 GGAGCTTAATGGACGCCACG 61.429 60.000 0.50 0.00 35.80 4.94
2046 3525 4.814041 GAGGAGAGGCCAGCCCCT 62.814 72.222 5.01 5.50 40.02 4.79


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

AutoCloner maintained by Alex Coulton.