Multiple sequence alignment - TraesCS2A01G460500

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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 TraesCS2A01G460500 chr2A 100.000 2231 0 0 1 2231 706918368 706920598 0.000000e+00 4120
1 TraesCS2A01G460500 chr2A 88.641 493 44 9 891 1372 706903553 706904044 6.860000e-165 590
2 TraesCS2A01G460500 chr2A 93.231 325 18 2 568 892 706902949 706903269 2.000000e-130 475
3 TraesCS2A01G460500 chr2A 87.156 436 29 8 1358 1782 706904056 706904475 9.330000e-129 470
4 TraesCS2A01G460500 chr2A 79.422 554 71 21 926 1463 707040186 707040712 3.520000e-93 351
5 TraesCS2A01G460500 chr2A 77.310 617 71 38 808 1373 707077283 707077881 1.290000e-77 300
6 TraesCS2A01G460500 chr2A 78.436 422 49 19 981 1373 707235801 707236209 1.030000e-58 237
7 TraesCS2A01G460500 chr2A 77.855 429 42 20 982 1373 707222102 707222514 1.340000e-52 217
8 TraesCS2A01G460500 chr2A 84.810 158 24 0 2070 2227 590628969 590628812 2.290000e-35 159
9 TraesCS2A01G460500 chr2B 86.007 1072 92 23 592 1629 680062915 680063962 0.000000e+00 1096
10 TraesCS2A01G460500 chr2B 78.582 677 74 40 865 1514 680221227 680221859 4.500000e-102 381
11 TraesCS2A01G460500 chr2B 76.552 435 45 19 983 1373 680446066 680446487 3.780000e-43 185
12 TraesCS2A01G460500 chr2B 90.265 113 4 2 1660 1765 680063962 680064074 8.310000e-30 141
13 TraesCS2A01G460500 chr2D 90.187 856 52 6 1358 2213 567051997 567052820 0.000000e+00 1086
14 TraesCS2A01G460500 chr2D 89.163 812 58 15 592 1381 567051186 567051989 0.000000e+00 985
15 TraesCS2A01G460500 chr2D 80.417 623 65 28 865 1463 567568880 567569469 2.650000e-114 422
16 TraesCS2A01G460500 chr2D 76.593 722 79 41 797 1457 567594647 567595339 4.620000e-82 315
17 TraesCS2A01G460500 chr2D 77.910 421 43 22 981 1373 567677886 567678284 1.340000e-52 217
18 TraesCS2A01G460500 chr2D 90.909 132 10 1 981 1110 567806006 567806137 2.280000e-40 176
19 TraesCS2A01G460500 chr2D 83.465 127 19 2 2106 2231 55710046 55709921 1.400000e-22 117
20 TraesCS2A01G460500 chr3D 94.553 514 23 2 3 511 594757215 594756702 0.000000e+00 789
21 TraesCS2A01G460500 chr3D 94.163 514 25 2 3 511 61653031 61652518 0.000000e+00 778
22 TraesCS2A01G460500 chr1D 94.542 513 23 2 3 510 461347948 461347436 0.000000e+00 787
23 TraesCS2A01G460500 chr1D 93.957 513 25 3 3 510 470867636 470867125 0.000000e+00 771
24 TraesCS2A01G460500 chr5D 94.358 514 24 2 3 511 552486358 552485845 0.000000e+00 784
25 TraesCS2A01G460500 chr6D 94.141 512 26 3 3 510 254957507 254958018 0.000000e+00 776
26 TraesCS2A01G460500 chr6D 93.957 513 26 2 3 510 470581744 470581232 0.000000e+00 771
27 TraesCS2A01G460500 chr7D 93.774 514 26 3 3 511 32538472 32538984 0.000000e+00 767
28 TraesCS2A01G460500 chr7D 93.462 520 25 5 3 517 583995183 583994668 0.000000e+00 763
29 TraesCS2A01G460500 chr7D 79.528 254 41 5 1965 2216 39672309 39672065 1.060000e-38 171
30 TraesCS2A01G460500 chr5B 80.519 308 54 4 1929 2231 128850683 128850377 4.790000e-57 231
31 TraesCS2A01G460500 chr5A 80.602 299 50 5 1921 2213 127535189 127535485 8.020000e-55 224
32 TraesCS2A01G460500 chrUn 78.175 252 40 8 995 1235 155033223 155033470 1.790000e-31 147
33 TraesCS2A01G460500 chr3B 78.175 252 40 8 995 1235 792434456 792434209 1.790000e-31 147
34 TraesCS2A01G460500 chr3B 77.778 252 41 8 995 1235 792344135 792343888 8.310000e-30 141
35 TraesCS2A01G460500 chr4A 82.759 145 23 2 2070 2214 47284653 47284795 6.470000e-26 128


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 TraesCS2A01G460500 chr2A 706918368 706920598 2230 False 4120.000000 4120 100.000 1 2231 1 chr2A.!!$F1 2230
1 TraesCS2A01G460500 chr2A 706902949 706904475 1526 False 511.666667 590 89.676 568 1782 3 chr2A.!!$F6 1214
2 TraesCS2A01G460500 chr2A 707040186 707040712 526 False 351.000000 351 79.422 926 1463 1 chr2A.!!$F2 537
3 TraesCS2A01G460500 chr2A 707077283 707077881 598 False 300.000000 300 77.310 808 1373 1 chr2A.!!$F3 565
4 TraesCS2A01G460500 chr2B 680062915 680064074 1159 False 618.500000 1096 88.136 592 1765 2 chr2B.!!$F3 1173
5 TraesCS2A01G460500 chr2B 680221227 680221859 632 False 381.000000 381 78.582 865 1514 1 chr2B.!!$F1 649
6 TraesCS2A01G460500 chr2D 567051186 567052820 1634 False 1035.500000 1086 89.675 592 2213 2 chr2D.!!$F5 1621
7 TraesCS2A01G460500 chr2D 567568880 567569469 589 False 422.000000 422 80.417 865 1463 1 chr2D.!!$F1 598
8 TraesCS2A01G460500 chr2D 567594647 567595339 692 False 315.000000 315 76.593 797 1457 1 chr2D.!!$F2 660
9 TraesCS2A01G460500 chr3D 594756702 594757215 513 True 789.000000 789 94.553 3 511 1 chr3D.!!$R2 508
10 TraesCS2A01G460500 chr3D 61652518 61653031 513 True 778.000000 778 94.163 3 511 1 chr3D.!!$R1 508
11 TraesCS2A01G460500 chr1D 461347436 461347948 512 True 787.000000 787 94.542 3 510 1 chr1D.!!$R1 507
12 TraesCS2A01G460500 chr1D 470867125 470867636 511 True 771.000000 771 93.957 3 510 1 chr1D.!!$R2 507
13 TraesCS2A01G460500 chr5D 552485845 552486358 513 True 784.000000 784 94.358 3 511 1 chr5D.!!$R1 508
14 TraesCS2A01G460500 chr6D 254957507 254958018 511 False 776.000000 776 94.141 3 510 1 chr6D.!!$F1 507
15 TraesCS2A01G460500 chr6D 470581232 470581744 512 True 771.000000 771 93.957 3 510 1 chr6D.!!$R1 507
16 TraesCS2A01G460500 chr7D 32538472 32538984 512 False 767.000000 767 93.774 3 511 1 chr7D.!!$F1 508
17 TraesCS2A01G460500 chr7D 583994668 583995183 515 True 763.000000 763 93.462 3 517 1 chr7D.!!$R2 514

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
546 552 0.026803 CAAGCTTATCGCCAGTTCGC 59.973 55.0 0.0 0.0 40.39 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2709 0.108138 CCAGTCGGTCACCCATCTTC 60.108 60.0 0.0 0.0 0.0 2.87 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
35 36 1.814248 GCCGTGGAGAAGAAACAACCT 60.814 52.381 0.00 0.00 0.00 3.50
157 159 1.817099 GCAATAGCTCTGCCGCTGT 60.817 57.895 9.12 0.00 41.12 4.40
175 177 0.737715 GTCGAGAAATGCGCTCCACT 60.738 55.000 9.73 2.96 0.00 4.00
270 272 1.520564 GCACGGTCACACAGTCACA 60.521 57.895 0.00 0.00 0.00 3.58
283 285 0.534427 AGTCACAGGTCGAGTCGTGA 60.534 55.000 13.12 5.53 36.09 4.35
309 311 2.860009 TGACTCTTGACTACGTGACCT 58.140 47.619 0.00 0.00 0.00 3.85
313 315 4.649692 ACTCTTGACTACGTGACCTTAGA 58.350 43.478 0.00 0.00 0.00 2.10
344 346 1.556911 CAGTCAGAGCACATAACCCCT 59.443 52.381 0.00 0.00 0.00 4.79
363 365 3.329814 CCCTAGTGTCCTAACCAAACCTT 59.670 47.826 0.00 0.00 0.00 3.50
366 368 5.247792 CCTAGTGTCCTAACCAAACCTTAGT 59.752 44.000 0.00 0.00 0.00 2.24
450 456 2.874701 GTCGCATGAGAGCCATTACAAT 59.125 45.455 0.00 0.00 31.94 2.71
465 471 1.144969 ACAATCAACGACGTCGCATT 58.855 45.000 35.92 26.35 44.43 3.56
512 518 4.259952 GGGAGCTATTTGCCCCAC 57.740 61.111 10.27 0.00 45.59 4.61
513 519 1.615262 GGGAGCTATTTGCCCCACT 59.385 57.895 10.27 0.00 45.59 4.00
514 520 0.753111 GGGAGCTATTTGCCCCACTG 60.753 60.000 10.27 0.00 45.59 3.66
515 521 0.753111 GGAGCTATTTGCCCCACTGG 60.753 60.000 0.00 0.00 39.61 4.00
524 530 4.619320 CCCCACTGGCCCAAAGCA 62.619 66.667 0.00 0.00 46.50 3.91
525 531 2.523902 CCCACTGGCCCAAAGCAA 60.524 61.111 0.00 0.00 46.50 3.91
526 532 2.736531 CCACTGGCCCAAAGCAAC 59.263 61.111 0.00 0.00 46.50 4.17
527 533 2.736531 CACTGGCCCAAAGCAACC 59.263 61.111 0.00 0.00 46.50 3.77
528 534 2.132996 CACTGGCCCAAAGCAACCA 61.133 57.895 0.00 0.00 46.50 3.67
529 535 1.382420 ACTGGCCCAAAGCAACCAA 60.382 52.632 0.00 0.00 46.50 3.67
530 536 1.368579 CTGGCCCAAAGCAACCAAG 59.631 57.895 0.00 0.00 46.50 3.61
531 537 2.031012 GGCCCAAAGCAACCAAGC 59.969 61.111 0.00 0.00 46.50 4.01
539 545 2.482326 AGCAACCAAGCTTATCGCC 58.518 52.632 0.00 0.00 43.70 5.54
540 546 0.322456 AGCAACCAAGCTTATCGCCA 60.322 50.000 0.00 0.00 43.70 5.69
541 547 0.099436 GCAACCAAGCTTATCGCCAG 59.901 55.000 0.00 0.00 40.39 4.85
542 548 1.453155 CAACCAAGCTTATCGCCAGT 58.547 50.000 0.00 0.00 40.39 4.00
543 549 1.812571 CAACCAAGCTTATCGCCAGTT 59.187 47.619 0.00 0.00 40.39 3.16
544 550 1.739067 ACCAAGCTTATCGCCAGTTC 58.261 50.000 0.00 0.00 40.39 3.01
545 551 0.652592 CCAAGCTTATCGCCAGTTCG 59.347 55.000 0.00 0.00 40.39 3.95
546 552 0.026803 CAAGCTTATCGCCAGTTCGC 59.973 55.000 0.00 0.00 40.39 4.70
547 553 1.090052 AAGCTTATCGCCAGTTCGCC 61.090 55.000 0.00 0.00 40.39 5.54
548 554 2.871427 GCTTATCGCCAGTTCGCCG 61.871 63.158 0.00 0.00 0.00 6.46
549 555 2.871427 CTTATCGCCAGTTCGCCGC 61.871 63.158 0.00 0.00 0.00 6.53
550 556 4.884257 TATCGCCAGTTCGCCGCC 62.884 66.667 0.00 0.00 0.00 6.13
563 569 4.974721 CCGCCAAGGCACCAACCT 62.975 66.667 12.19 0.00 43.91 3.50
564 570 2.033448 CGCCAAGGCACCAACCTA 59.967 61.111 12.19 0.00 39.93 3.08
565 571 2.332654 CGCCAAGGCACCAACCTAC 61.333 63.158 12.19 0.00 39.93 3.18
566 572 1.074951 GCCAAGGCACCAACCTACT 59.925 57.895 6.14 0.00 39.93 2.57
588 594 1.132267 ACATATCCAGGAGCCTCCCAT 60.132 52.381 7.26 0.00 37.19 4.00
589 595 1.281287 CATATCCAGGAGCCTCCCATG 59.719 57.143 7.26 0.00 37.19 3.66
590 596 0.567687 TATCCAGGAGCCTCCCATGA 59.432 55.000 7.26 1.79 37.19 3.07
603 609 1.776667 TCCCATGATCCCATCCTTGAC 59.223 52.381 0.00 0.00 0.00 3.18
645 654 4.111916 ACTGAAGAAACGCAAACCAATTG 58.888 39.130 0.00 0.00 42.21 2.32
708 725 4.954970 CATCCGGCCCCCATTCCG 62.955 72.222 0.00 0.00 44.89 4.30
754 777 5.802465 CCCATACATGCATATGTCTCTCTT 58.198 41.667 0.00 0.00 44.00 2.85
772 795 1.990160 TTCCAGCCCTTGACCGTGTT 61.990 55.000 0.00 0.00 0.00 3.32
787 810 1.984570 TGTTCTCGAGCAGGAGGGG 60.985 63.158 7.81 0.00 34.74 4.79
917 1225 4.382831 CAACGTACACGATGCTAACAAAG 58.617 43.478 9.04 0.00 43.02 2.77
924 1259 4.021368 ACACGATGCTAACAAAGTACCTCT 60.021 41.667 0.00 0.00 0.00 3.69
960 1307 1.824230 CAAGCTAGACTGCTCCTCACT 59.176 52.381 0.00 0.00 43.24 3.41
966 1314 2.442413 AGACTGCTCCTCACTAGTCAC 58.558 52.381 0.00 0.00 41.44 3.67
1012 1371 3.311106 CAGTTAGCAATGGCAAAGTGTG 58.689 45.455 0.00 0.00 44.61 3.82
1020 1379 2.713154 GCAAAGTGTGTCGCCGTT 59.287 55.556 0.00 0.00 0.00 4.44
1089 1448 1.298014 CCAGAAGGACCAGGCACTC 59.702 63.158 0.00 0.00 33.19 3.51
1090 1449 1.483595 CCAGAAGGACCAGGCACTCA 61.484 60.000 0.00 0.00 33.19 3.41
1254 1650 6.214191 TCATCTCTAGTTCATGTTCTGACC 57.786 41.667 0.00 0.00 32.17 4.02
1315 1728 2.030717 ACTTCTATAGCTGACATCGCCG 60.031 50.000 0.00 0.00 0.00 6.46
1395 1884 5.127845 TCTGTATTTCCTCTCAGTCCATGTC 59.872 44.000 0.00 0.00 0.00 3.06
1397 1888 4.751767 ATTTCCTCTCAGTCCATGTCTC 57.248 45.455 0.00 0.00 0.00 3.36
1407 1898 4.870426 TCAGTCCATGTCTCTATTTTTCGC 59.130 41.667 0.00 0.00 0.00 4.70
1465 1962 7.996551 CGTAATACATAATACTTTGTCAGTGCG 59.003 37.037 0.00 0.00 35.97 5.34
1466 1963 9.027129 GTAATACATAATACTTTGTCAGTGCGA 57.973 33.333 0.00 0.00 35.97 5.10
1467 1964 8.487313 AATACATAATACTTTGTCAGTGCGAA 57.513 30.769 0.00 0.00 35.97 4.70
1468 1965 6.985188 ACATAATACTTTGTCAGTGCGAAT 57.015 33.333 0.00 0.00 35.97 3.34
1469 1966 6.775088 ACATAATACTTTGTCAGTGCGAATG 58.225 36.000 0.00 0.00 35.97 2.67
1470 1967 6.371548 ACATAATACTTTGTCAGTGCGAATGT 59.628 34.615 0.00 0.00 35.97 2.71
1471 1968 4.668576 ATACTTTGTCAGTGCGAATGTG 57.331 40.909 0.00 0.00 35.97 3.21
1472 1969 2.288666 ACTTTGTCAGTGCGAATGTGT 58.711 42.857 0.00 0.00 32.83 3.72
1489 1986 5.791367 ATGTGTGATCGTCTTCTTGAATG 57.209 39.130 0.00 0.00 0.00 2.67
1496 2001 7.063426 TGTGATCGTCTTCTTGAATGAACATAC 59.937 37.037 0.00 0.00 0.00 2.39
1527 2032 1.792949 GGTTGCATCATCGATCGTACC 59.207 52.381 15.94 7.21 0.00 3.34
1615 2123 5.127845 TGAGGTAACACCAATGCTTTGAAAA 59.872 36.000 13.58 0.00 41.95 2.29
1643 2151 6.590656 AAGGTGATTGGATTAATAGGGACA 57.409 37.500 0.00 0.00 0.00 4.02
1644 2152 6.786843 AGGTGATTGGATTAATAGGGACAT 57.213 37.500 0.00 0.00 0.00 3.06
1645 2153 6.546484 AGGTGATTGGATTAATAGGGACATG 58.454 40.000 0.00 0.00 0.00 3.21
1646 2154 5.183904 GGTGATTGGATTAATAGGGACATGC 59.816 44.000 0.00 0.00 0.00 4.06
1647 2155 5.769662 GTGATTGGATTAATAGGGACATGCA 59.230 40.000 0.00 0.00 0.00 3.96
1648 2156 6.435277 GTGATTGGATTAATAGGGACATGCAT 59.565 38.462 0.00 0.00 0.00 3.96
1649 2157 7.011994 TGATTGGATTAATAGGGACATGCATT 58.988 34.615 0.00 0.00 0.00 3.56
1650 2158 6.653526 TTGGATTAATAGGGACATGCATTG 57.346 37.500 0.00 0.00 0.00 2.82
1682 2190 3.876274 TCTCTCATCAACTCTTTCGGG 57.124 47.619 0.00 0.00 0.00 5.14
1719 2227 1.364626 CTGCGTGGATGGAGCTTCAC 61.365 60.000 0.00 0.00 0.00 3.18
1900 2423 5.160607 TCAAATTGGTATCAGAACCGACT 57.839 39.130 0.00 0.00 42.91 4.18
1901 2424 5.556915 TCAAATTGGTATCAGAACCGACTT 58.443 37.500 0.00 0.00 42.91 3.01
1961 2484 1.163420 GCACGTGTGGTCCATTGTGA 61.163 55.000 18.38 0.00 35.47 3.58
2006 2529 1.336887 ACTGGATGCACAGACGTGTAC 60.337 52.381 11.03 0.00 45.50 2.90
2025 2548 5.046520 GTGTACTAAGAGGGAACATTCCTGT 60.047 44.000 10.45 0.00 46.72 4.00
2029 2552 1.355720 AGAGGGAACATTCCTGTTGGG 59.644 52.381 10.45 0.00 45.57 4.12
2059 2582 1.412710 ACGTCAAGCTCCTTTGAGTGA 59.587 47.619 0.00 0.00 40.95 3.41
2075 2598 7.364232 CCTTTGAGTGAAGGTGTATATGAGAGT 60.364 40.741 0.00 0.00 41.06 3.24
2093 2616 8.774546 ATGAGAGTCTGACTTAATAGGAATGA 57.225 34.615 12.27 0.00 0.00 2.57
2104 2627 8.343168 ACTTAATAGGAATGATAGACCTCTCG 57.657 38.462 0.00 0.00 35.52 4.04
2117 2640 7.759886 TGATAGACCTCTCGTATCAACAAAAAG 59.240 37.037 0.00 0.00 31.66 2.27
2140 2663 0.969149 CTTCTTTTTGGGGAGGCCAC 59.031 55.000 5.01 0.00 0.00 5.01
2153 2676 0.603975 AGGCCACTCGCAAAGAACTC 60.604 55.000 5.01 0.00 40.31 3.01
2180 2703 0.955919 AAGCGTGCTAGGTTTGGAGC 60.956 55.000 0.00 0.00 39.25 4.70
2186 2709 2.083774 TGCTAGGTTTGGAGCGATTTG 58.916 47.619 0.00 0.00 41.83 2.32
2188 2711 2.747446 GCTAGGTTTGGAGCGATTTGAA 59.253 45.455 0.00 0.00 0.00 2.69
2213 2736 1.226746 GTGACCGACTGGAAAGTTGG 58.773 55.000 10.10 10.10 46.37 3.77
2217 2740 2.256117 CCGACTGGAAAGTTGGTCTT 57.744 50.000 4.24 0.00 38.30 3.01
2218 2741 1.873591 CCGACTGGAAAGTTGGTCTTG 59.126 52.381 4.24 0.00 38.30 3.02
2219 2742 2.484770 CCGACTGGAAAGTTGGTCTTGA 60.485 50.000 4.24 0.00 38.30 3.02
2220 2743 2.802816 CGACTGGAAAGTTGGTCTTGAG 59.197 50.000 0.00 0.00 36.40 3.02
2221 2744 3.741388 CGACTGGAAAGTTGGTCTTGAGT 60.741 47.826 0.00 0.00 36.40 3.41
2222 2745 3.545703 ACTGGAAAGTTGGTCTTGAGTG 58.454 45.455 0.00 0.00 36.40 3.51
2223 2746 2.291741 CTGGAAAGTTGGTCTTGAGTGC 59.708 50.000 0.00 0.00 36.40 4.40
2224 2747 1.264288 GGAAAGTTGGTCTTGAGTGCG 59.736 52.381 0.00 0.00 36.40 5.34
2225 2748 0.663153 AAAGTTGGTCTTGAGTGCGC 59.337 50.000 0.00 0.00 36.40 6.09
2226 2749 0.463654 AAGTTGGTCTTGAGTGCGCA 60.464 50.000 5.66 5.66 34.77 6.09
2227 2750 1.160329 AGTTGGTCTTGAGTGCGCAC 61.160 55.000 32.79 32.79 0.00 5.34
2228 2751 1.153269 TTGGTCTTGAGTGCGCACA 60.153 52.632 39.21 19.97 0.00 4.57
2229 2752 1.159713 TTGGTCTTGAGTGCGCACAG 61.160 55.000 39.21 28.07 0.00 3.66
2230 2753 1.595382 GGTCTTGAGTGCGCACAGT 60.595 57.895 39.21 22.58 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.554036 GGCCCGATGGTGGAGCTC 62.554 72.222 4.71 4.71 0.00 4.09
11 12 2.211410 TTTCTTCTCCACGGCCCGA 61.211 57.895 11.71 0.00 0.00 5.14
35 36 2.598565 AGAATCTCGATTGGATCCGGA 58.401 47.619 6.61 6.61 0.00 5.14
157 159 0.815095 TAGTGGAGCGCATTTCTCGA 59.185 50.000 11.47 0.00 0.00 4.04
175 177 1.213537 CGGTTTCTTCTCCGCGGTA 59.786 57.895 27.15 12.33 40.28 4.02
270 272 1.450531 AACCGTTCACGACTCGACCT 61.451 55.000 5.20 0.00 43.02 3.85
283 285 2.360165 ACGTAGTCAAGAGTCAACCGTT 59.640 45.455 0.00 0.00 29.74 4.44
323 325 1.555075 GGGGTTATGTGCTCTGACTGA 59.445 52.381 0.00 0.00 0.00 3.41
344 346 6.080009 AGACTAAGGTTTGGTTAGGACACTA 58.920 40.000 0.00 0.00 32.61 2.74
363 365 4.568359 CGCGACTAGTTGGTAGTTAGACTA 59.432 45.833 12.18 0.00 42.48 2.59
366 368 3.338249 ACGCGACTAGTTGGTAGTTAGA 58.662 45.455 15.93 0.00 42.48 2.10
450 456 1.465777 TCTCTAATGCGACGTCGTTGA 59.534 47.619 35.48 21.66 42.22 3.18
465 471 9.521503 CGATATCTTTGAGTTGAATTGTCTCTA 57.478 33.333 0.34 0.00 0.00 2.43
488 494 1.242076 GCAAATAGCTCCCATGCGAT 58.758 50.000 0.00 0.00 41.15 4.58
511 517 1.382420 TTGGTTGCTTTGGGCCAGT 60.382 52.632 6.23 0.00 40.92 4.00
512 518 1.368579 CTTGGTTGCTTTGGGCCAG 59.631 57.895 6.23 0.00 40.92 4.85
513 519 2.806009 GCTTGGTTGCTTTGGGCCA 61.806 57.895 0.00 0.00 40.92 5.36
514 520 2.031012 GCTTGGTTGCTTTGGGCC 59.969 61.111 0.00 0.00 40.92 5.80
515 521 3.141449 AGCTTGGTTGCTTTGGGC 58.859 55.556 0.00 0.00 40.93 5.36
546 552 3.561120 TAGGTTGGTGCCTTGGCGG 62.561 63.158 7.18 0.00 39.94 6.13
547 553 2.033448 TAGGTTGGTGCCTTGGCG 59.967 61.111 7.18 0.00 39.94 5.69
548 554 0.960861 GAGTAGGTTGGTGCCTTGGC 60.961 60.000 4.43 4.43 39.94 4.52
549 555 0.400213 TGAGTAGGTTGGTGCCTTGG 59.600 55.000 0.00 0.00 39.94 3.61
550 556 1.202758 TGTGAGTAGGTTGGTGCCTTG 60.203 52.381 0.00 0.00 39.94 3.61
551 557 1.136828 TGTGAGTAGGTTGGTGCCTT 58.863 50.000 0.00 0.00 39.94 4.35
552 558 1.362224 ATGTGAGTAGGTTGGTGCCT 58.638 50.000 0.00 0.00 42.43 4.75
553 559 3.467803 GATATGTGAGTAGGTTGGTGCC 58.532 50.000 0.00 0.00 0.00 5.01
554 560 3.118408 TGGATATGTGAGTAGGTTGGTGC 60.118 47.826 0.00 0.00 0.00 5.01
555 561 4.443457 CCTGGATATGTGAGTAGGTTGGTG 60.443 50.000 0.00 0.00 0.00 4.17
556 562 3.711704 CCTGGATATGTGAGTAGGTTGGT 59.288 47.826 0.00 0.00 0.00 3.67
557 563 3.967326 TCCTGGATATGTGAGTAGGTTGG 59.033 47.826 0.00 0.00 0.00 3.77
558 564 4.502259 GCTCCTGGATATGTGAGTAGGTTG 60.502 50.000 0.00 0.00 0.00 3.77
559 565 3.643792 GCTCCTGGATATGTGAGTAGGTT 59.356 47.826 0.00 0.00 0.00 3.50
560 566 3.235200 GCTCCTGGATATGTGAGTAGGT 58.765 50.000 0.00 0.00 0.00 3.08
561 567 2.564947 GGCTCCTGGATATGTGAGTAGG 59.435 54.545 0.00 0.00 0.00 3.18
562 568 3.505386 AGGCTCCTGGATATGTGAGTAG 58.495 50.000 0.00 0.00 0.00 2.57
563 569 3.501349 GAGGCTCCTGGATATGTGAGTA 58.499 50.000 2.15 0.00 0.00 2.59
564 570 2.324541 GAGGCTCCTGGATATGTGAGT 58.675 52.381 2.15 0.00 0.00 3.41
565 571 1.622811 GGAGGCTCCTGGATATGTGAG 59.377 57.143 26.44 0.00 32.53 3.51
566 572 1.722034 GGAGGCTCCTGGATATGTGA 58.278 55.000 26.44 0.00 32.53 3.58
588 594 1.344953 CCCGGTCAAGGATGGGATCA 61.345 60.000 0.00 0.00 44.88 2.92
589 595 1.054406 TCCCGGTCAAGGATGGGATC 61.054 60.000 0.00 0.00 45.66 3.36
590 596 1.004230 TCCCGGTCAAGGATGGGAT 59.996 57.895 0.00 0.00 45.66 3.85
603 609 5.938125 TCAGTAGATCTTTTTCTTTTCCCGG 59.062 40.000 0.00 0.00 0.00 5.73
680 689 4.883354 CCGGATGCCTTCCCCTGC 62.883 72.222 0.00 0.00 42.06 4.85
697 706 3.219198 GTGCATCGGAATGGGGGC 61.219 66.667 0.00 0.00 33.19 5.80
708 725 1.491563 GTGTCAACGTCGGTGCATC 59.508 57.895 5.10 0.00 0.00 3.91
747 764 1.270907 GTCAAGGGCTGGAAGAGAGA 58.729 55.000 0.00 0.00 34.07 3.10
754 777 2.391724 GAACACGGTCAAGGGCTGGA 62.392 60.000 0.00 0.00 0.00 3.86
879 902 2.128035 CGTTGCTTCTTATAGGCGAGG 58.872 52.381 0.00 0.00 0.00 4.63
913 1221 4.261197 GGCTGTGTTTGAAGAGGTACTTTG 60.261 45.833 0.00 0.00 41.55 2.77
917 1225 2.548480 GTGGCTGTGTTTGAAGAGGTAC 59.452 50.000 0.00 0.00 0.00 3.34
924 1259 1.135141 GCTTGTGTGGCTGTGTTTGAA 60.135 47.619 0.00 0.00 0.00 2.69
960 1307 9.909644 GTTCTGAACTTTTGATACTAGTGACTA 57.090 33.333 13.13 0.00 0.00 2.59
966 1314 6.819146 GGGAGGTTCTGAACTTTTGATACTAG 59.181 42.308 19.05 0.00 0.00 2.57
1315 1728 1.284715 CGCCGGTGTTTTTCTTCCC 59.715 57.895 6.91 0.00 0.00 3.97
1395 1884 5.385617 CACACAAAGGAGCGAAAAATAGAG 58.614 41.667 0.00 0.00 0.00 2.43
1397 1888 3.914364 GCACACAAAGGAGCGAAAAATAG 59.086 43.478 0.00 0.00 0.00 1.73
1407 1898 3.367932 CGTACATGTAGCACACAAAGGAG 59.632 47.826 5.62 0.00 41.55 3.69
1465 1962 5.845985 TTCAAGAAGACGATCACACATTC 57.154 39.130 0.00 0.00 0.00 2.67
1466 1963 5.934043 TCATTCAAGAAGACGATCACACATT 59.066 36.000 0.00 0.00 0.00 2.71
1467 1964 5.482006 TCATTCAAGAAGACGATCACACAT 58.518 37.500 0.00 0.00 0.00 3.21
1468 1965 4.881920 TCATTCAAGAAGACGATCACACA 58.118 39.130 0.00 0.00 0.00 3.72
1469 1966 5.177511 TGTTCATTCAAGAAGACGATCACAC 59.822 40.000 0.00 0.00 0.00 3.82
1470 1967 5.296748 TGTTCATTCAAGAAGACGATCACA 58.703 37.500 0.00 0.00 0.00 3.58
1471 1968 5.845985 TGTTCATTCAAGAAGACGATCAC 57.154 39.130 0.00 0.00 0.00 3.06
1472 1969 6.535150 GGTATGTTCATTCAAGAAGACGATCA 59.465 38.462 0.00 0.00 0.00 2.92
1489 1986 4.335594 GCAACCTGTTGATAGGGTATGTTC 59.664 45.833 13.94 0.00 42.93 3.18
1496 2001 3.003394 TGATGCAACCTGTTGATAGGG 57.997 47.619 13.94 0.00 42.93 3.53
1527 2032 5.152623 TGGGACTTTGTGATTAGAGAGTG 57.847 43.478 0.00 0.00 0.00 3.51
1615 2123 7.352522 TCCCTATTAATCCAATCACCTTACCTT 59.647 37.037 0.00 0.00 0.00 3.50
1646 2154 6.430000 TGATGAGAGATAACCATGCATCAATG 59.570 38.462 0.00 0.00 38.06 2.82
1647 2155 6.540083 TGATGAGAGATAACCATGCATCAAT 58.460 36.000 0.00 0.00 38.06 2.57
1648 2156 5.932455 TGATGAGAGATAACCATGCATCAA 58.068 37.500 0.00 0.00 38.06 2.57
1649 2157 5.556006 TGATGAGAGATAACCATGCATCA 57.444 39.130 0.00 0.00 38.51 3.07
1650 2158 5.996513 AGTTGATGAGAGATAACCATGCATC 59.003 40.000 0.00 0.00 33.24 3.91
1682 2190 3.706698 GCAGACCAAGAAAACTCCAAAC 58.293 45.455 0.00 0.00 0.00 2.93
1719 2227 5.750547 ACACTGATTGCTCACTATAATGTCG 59.249 40.000 0.00 0.00 0.00 4.35
1821 2344 8.112822 TGGTTGGGGTTTACATATATCATATGG 58.887 37.037 2.13 0.00 0.00 2.74
1961 2484 2.042259 CGTGTGCCATGCCATGAGT 61.042 57.895 6.18 0.00 0.00 3.41
2059 2582 8.824756 TTAAGTCAGACTCTCATATACACCTT 57.175 34.615 2.72 0.00 0.00 3.50
2075 2598 9.303116 GAGGTCTATCATTCCTATTAAGTCAGA 57.697 37.037 0.00 0.00 0.00 3.27
2093 2616 7.612677 ACTTTTTGTTGATACGAGAGGTCTAT 58.387 34.615 0.00 0.00 0.00 1.98
2098 2621 5.701290 AGGAACTTTTTGTTGATACGAGAGG 59.299 40.000 0.00 0.00 39.30 3.69
2117 2640 1.618837 GCCTCCCCAAAAAGAAGGAAC 59.381 52.381 0.00 0.00 0.00 3.62
2132 2655 1.302511 TTCTTTGCGAGTGGCCTCC 60.303 57.895 3.32 0.00 42.61 4.30
2140 2663 3.971032 AACTTTGGAGTTCTTTGCGAG 57.029 42.857 0.00 0.00 42.35 5.03
2153 2676 2.423577 ACCTAGCACGCTTAACTTTGG 58.576 47.619 0.00 0.00 0.00 3.28
2180 2703 1.665679 CGGTCACCCATCTTCAAATCG 59.334 52.381 0.00 0.00 0.00 3.34
2186 2709 0.108138 CCAGTCGGTCACCCATCTTC 60.108 60.000 0.00 0.00 0.00 2.87
2188 2711 0.544357 TTCCAGTCGGTCACCCATCT 60.544 55.000 0.00 0.00 0.00 2.90
2213 2736 4.033894 ACTGTGCGCACTCAAGAC 57.966 55.556 37.59 13.47 0.00 3.01


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

AutoCloner maintained by Alex Coulton.