Multiple sequence alignment - TraesCS5B01G313300

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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 TraesCS5B01G313300 chr5B 100.000 2681 0 0 1 2681 495474580 495471900 0.000000e+00 4951
1 TraesCS5B01G313300 chr5B 82.099 162 29 0 1079 1240 93212469 93212308 3.600000e-29 139
2 TraesCS5B01G313300 chr5A 91.401 1570 69 21 536 2062 523880141 523878595 0.000000e+00 2091
3 TraesCS5B01G313300 chr5A 93.279 491 25 3 1 483 523880644 523880154 0.000000e+00 717
4 TraesCS5B01G313300 chr5A 83.505 388 34 16 2076 2453 523878522 523878155 4.280000e-88 335
5 TraesCS5B01G313300 chr5A 88.085 235 19 6 2448 2681 523868093 523867867 1.220000e-68 270
6 TraesCS5B01G313300 chr5A 82.099 162 29 0 1079 1240 80155793 80155632 3.600000e-29 139
7 TraesCS5B01G313300 chr5D 93.799 1274 61 13 528 1785 412148298 412147027 0.000000e+00 1899
8 TraesCS5B01G313300 chr5D 87.965 914 48 18 1784 2681 412147001 412146134 0.000000e+00 1022
9 TraesCS5B01G313300 chr5D 94.835 484 24 1 1 483 412148785 412148302 0.000000e+00 754
10 TraesCS5B01G313300 chr5D 82.099 162 29 0 1079 1240 87173735 87173574 3.600000e-29 139
11 TraesCS5B01G313300 chr3D 86.035 981 110 17 709 1682 322682257 322683217 0.000000e+00 1027
12 TraesCS5B01G313300 chr2B 88.868 521 47 8 773 1291 769581327 769581838 4.870000e-177 630
13 TraesCS5B01G313300 chr2B 82.353 170 30 0 1073 1242 211614104 211614273 5.980000e-32 148
14 TraesCS5B01G313300 chr6A 86.139 606 51 10 709 1301 420552954 420552369 8.150000e-175 623
15 TraesCS5B01G313300 chr6A 83.710 221 23 7 1497 1717 420541058 420540851 2.110000e-46 196
16 TraesCS5B01G313300 chr1A 85.432 556 54 13 1067 1622 585231637 585231109 1.080000e-153 553
17 TraesCS5B01G313300 chr1A 84.746 354 44 7 681 1031 585231989 585231643 1.980000e-91 346
18 TraesCS5B01G313300 chr7D 86.505 289 39 0 1421 1709 292242948 292242660 4.310000e-83 318
19 TraesCS5B01G313300 chr7D 90.385 208 20 0 822 1029 292243286 292243079 9.460000e-70 274
20 TraesCS5B01G313300 chr7D 91.549 142 11 1 1067 1208 292243079 292242939 7.570000e-46 195
21 TraesCS5B01G313300 chr7B 86.879 282 11 8 709 981 50603009 50602745 2.610000e-75 292
22 TraesCS5B01G313300 chr7B 80.308 325 31 23 974 1296 50601050 50600757 5.810000e-52 215
23 TraesCS5B01G313300 chr1B 93.103 116 4 1 916 1031 489693773 489693884 1.650000e-37 167
24 TraesCS5B01G313300 chr1B 75.875 257 29 16 681 918 489693240 489693482 1.700000e-17 100


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 TraesCS5B01G313300 chr5B 495471900 495474580 2680 True 4951.000000 4951 100.000000 1 2681 1 chr5B.!!$R2 2680
1 TraesCS5B01G313300 chr5A 523878155 523880644 2489 True 1047.666667 2091 89.395000 1 2453 3 chr5A.!!$R3 2452
2 TraesCS5B01G313300 chr5D 412146134 412148785 2651 True 1225.000000 1899 92.199667 1 2681 3 chr5D.!!$R2 2680
3 TraesCS5B01G313300 chr3D 322682257 322683217 960 False 1027.000000 1027 86.035000 709 1682 1 chr3D.!!$F1 973
4 TraesCS5B01G313300 chr2B 769581327 769581838 511 False 630.000000 630 88.868000 773 1291 1 chr2B.!!$F2 518
5 TraesCS5B01G313300 chr6A 420552369 420552954 585 True 623.000000 623 86.139000 709 1301 1 chr6A.!!$R2 592
6 TraesCS5B01G313300 chr1A 585231109 585231989 880 True 449.500000 553 85.089000 681 1622 2 chr1A.!!$R1 941
7 TraesCS5B01G313300 chr7D 292242660 292243286 626 True 262.333333 318 89.479667 822 1709 3 chr7D.!!$R1 887
8 TraesCS5B01G313300 chr7B 50600757 50603009 2252 True 253.500000 292 83.593500 709 1296 2 chr7B.!!$R1 587

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
31 32 0.179045 ATGCCGCTCCCATTGAGTAC 60.179 55.0 0.0 0.0 43.48 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 3492 0.318614 AATTGCAAACGAACTGCCCG 60.319 50.0 1.71 0.0 39.13 6.13 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
31 32 0.179045 ATGCCGCTCCCATTGAGTAC 60.179 55.000 0.00 0.00 43.48 2.73
80 81 5.885449 AAATCCCTTCGATCTCATCTCTT 57.115 39.130 0.00 0.00 0.00 2.85
83 84 6.985653 ATCCCTTCGATCTCATCTCTTTTA 57.014 37.500 0.00 0.00 0.00 1.52
139 140 3.951332 CGAGGAAAGCGCTGAACA 58.049 55.556 12.58 0.00 0.00 3.18
152 153 2.412421 CTGAACAACAGCTTTCTGGC 57.588 50.000 0.00 0.00 44.54 4.85
166 167 2.570415 TCTGGCCACGGAATGTTTAA 57.430 45.000 0.00 0.00 0.00 1.52
377 386 4.742201 GCGAGCTGAAGTGGCGGA 62.742 66.667 0.00 0.00 34.52 5.54
430 439 2.202756 GAGGCGATCGTGGTGGAC 60.203 66.667 17.81 0.00 0.00 4.02
483 492 1.103803 GTCCTCGTGTGGAGCATCTA 58.896 55.000 0.00 0.00 41.71 1.98
513 522 0.392336 TTTTTGCATGGGTGTGGAGC 59.608 50.000 0.00 0.00 0.00 4.70
514 523 0.758310 TTTTGCATGGGTGTGGAGCA 60.758 50.000 0.00 0.00 0.00 4.26
515 524 0.542467 TTTGCATGGGTGTGGAGCAT 60.542 50.000 0.00 0.00 34.87 3.79
516 525 0.966875 TTGCATGGGTGTGGAGCATC 60.967 55.000 0.00 0.00 34.87 3.91
517 526 1.077212 GCATGGGTGTGGAGCATCT 60.077 57.895 0.00 0.00 33.73 2.90
518 527 0.181114 GCATGGGTGTGGAGCATCTA 59.819 55.000 0.00 0.00 33.73 1.98
528 537 3.194062 GTGGAGCATCTACTTGAAGAGC 58.806 50.000 0.00 0.00 43.99 4.09
529 538 2.169352 TGGAGCATCTACTTGAAGAGCC 59.831 50.000 0.00 0.00 33.73 4.70
530 539 2.433970 GGAGCATCTACTTGAAGAGCCT 59.566 50.000 0.00 0.00 33.73 4.58
531 540 3.492482 GGAGCATCTACTTGAAGAGCCTC 60.492 52.174 0.00 0.00 33.73 4.70
534 543 3.620821 GCATCTACTTGAAGAGCCTCAAC 59.379 47.826 0.00 0.00 32.00 3.18
542 551 2.289882 TGAAGAGCCTCAACATGACAGG 60.290 50.000 0.00 2.14 0.00 4.00
548 557 1.065854 CCTCAACATGACAGGGGTCTC 60.066 57.143 0.00 0.00 44.61 3.36
596 609 4.696402 AGTGACCACGTTAAACAAAAGTGA 59.304 37.500 5.55 0.00 46.69 3.41
659 672 4.693538 TTGCAGCGCAATAATGAACTTA 57.306 36.364 11.47 0.00 43.99 2.24
661 674 5.247507 TGCAGCGCAATAATGAACTTATT 57.752 34.783 11.47 0.00 40.02 1.40
664 677 5.516339 GCAGCGCAATAATGAACTTATTTGT 59.484 36.000 11.47 0.00 37.84 2.83
692 705 4.389890 TCCAAATGCCTAATGATTGCAC 57.610 40.909 0.00 0.00 37.92 4.57
695 708 1.321474 ATGCCTAATGATTGCACGGG 58.679 50.000 0.00 0.00 37.92 5.28
700 713 2.878406 CCTAATGATTGCACGGGGTTAG 59.122 50.000 0.00 0.00 0.00 2.34
703 716 0.906066 TGATTGCACGGGGTTAGCTA 59.094 50.000 0.00 0.00 0.00 3.32
706 719 1.745232 TTGCACGGGGTTAGCTATTG 58.255 50.000 0.00 0.00 0.00 1.90
707 720 0.616371 TGCACGGGGTTAGCTATTGT 59.384 50.000 0.00 0.00 0.00 2.71
743 758 0.324614 TGTCCATGTCACGGCAATCT 59.675 50.000 0.00 0.00 0.00 2.40
766 782 3.618855 AAGCCGGGTAGAGCTCCCA 62.619 63.158 6.57 0.00 44.81 4.37
820 854 0.560688 AAAAGACAAAGGGGCCAGGA 59.439 50.000 4.39 0.00 0.00 3.86
870 904 0.322008 CCTCTTTGGTGGAGTGGAGC 60.322 60.000 0.00 0.00 31.08 4.70
1128 2891 0.614697 TGGCCGAGATCAAGGACTCA 60.615 55.000 12.71 4.40 36.23 3.41
1541 3341 2.752238 CGGAGGAGCTGGAGACGT 60.752 66.667 0.00 0.00 0.00 4.34
1557 3357 3.597728 GTTGTTTGGGCCGCGGAA 61.598 61.111 33.48 12.33 0.00 4.30
1632 3432 1.213013 GTCGTCTGTGATCGTGCCT 59.787 57.895 0.00 0.00 0.00 4.75
1650 3450 1.153066 TTCCAAGTTCGGTGCAGCA 60.153 52.632 17.33 0.00 0.00 4.41
1689 3489 2.762745 GACGGTTTCTAGCAAGGAACA 58.237 47.619 0.00 0.00 42.32 3.18
1692 3492 2.678336 CGGTTTCTAGCAAGGAACATCC 59.322 50.000 0.00 0.00 42.32 3.51
1774 3574 1.070821 CGCGAGCAGTGAAATGAAGA 58.929 50.000 0.00 0.00 0.00 2.87
1775 3575 1.662629 CGCGAGCAGTGAAATGAAGAT 59.337 47.619 0.00 0.00 0.00 2.40
1776 3576 2.094894 CGCGAGCAGTGAAATGAAGATT 59.905 45.455 0.00 0.00 0.00 2.40
1777 3577 3.678662 GCGAGCAGTGAAATGAAGATTC 58.321 45.455 0.00 0.00 0.00 2.52
1778 3578 3.373439 GCGAGCAGTGAAATGAAGATTCT 59.627 43.478 0.00 0.00 0.00 2.40
1779 3579 4.142730 GCGAGCAGTGAAATGAAGATTCTT 60.143 41.667 0.00 0.00 0.00 2.52
1781 3581 6.020372 CGAGCAGTGAAATGAAGATTCTTTC 58.980 40.000 0.00 0.00 0.00 2.62
1782 3582 6.264841 AGCAGTGAAATGAAGATTCTTTCC 57.735 37.500 0.00 0.00 0.00 3.13
1783 3583 5.771666 AGCAGTGAAATGAAGATTCTTTCCA 59.228 36.000 0.00 0.00 0.00 3.53
1784 3584 6.266103 AGCAGTGAAATGAAGATTCTTTCCAA 59.734 34.615 0.00 0.00 0.00 3.53
1788 3617 7.673082 AGTGAAATGAAGATTCTTTCCAAGGAT 59.327 33.333 0.00 0.00 0.00 3.24
1832 3661 4.841246 AGTTGACCTGAAGTCCTGAATAGT 59.159 41.667 0.00 0.00 45.68 2.12
1906 3735 1.519408 ACGAAAACCATTCGAGTGGG 58.481 50.000 28.24 14.00 43.77 4.61
1909 3738 0.112412 AAAACCATTCGAGTGGGCCT 59.888 50.000 28.24 11.56 43.77 5.19
1954 3785 8.485976 AACAAAATTTGACTGGATTTTCGAAA 57.514 26.923 13.19 6.47 34.25 3.46
1991 3822 9.247861 AGCAATAGTGGAAAAACTAAGATCAAT 57.752 29.630 0.00 0.00 36.28 2.57
2062 3893 6.393990 TGGCAACATAACAATACAATTCCAC 58.606 36.000 0.00 0.00 46.17 4.02
2114 4004 4.050553 ACCAAAATCAACATTGTTCAGCG 58.949 39.130 0.00 0.00 0.00 5.18
2129 4019 3.513462 TCAGCGTCAACGTAACATTTG 57.487 42.857 4.29 0.00 42.22 2.32
2176 4066 6.220930 AGAACATAGAGCAACGAAGTAAACA 58.779 36.000 0.00 0.00 45.00 2.83
2178 4068 8.033038 AGAACATAGAGCAACGAAGTAAACATA 58.967 33.333 0.00 0.00 45.00 2.29
2226 4129 7.875971 ACAGTCCAACAATCTAACAAAAGATC 58.124 34.615 0.00 0.00 35.10 2.75
2227 4130 7.502226 ACAGTCCAACAATCTAACAAAAGATCA 59.498 33.333 0.00 0.00 35.10 2.92
2228 4131 8.019669 CAGTCCAACAATCTAACAAAAGATCAG 58.980 37.037 0.00 0.00 35.10 2.90
2229 4132 7.939039 AGTCCAACAATCTAACAAAAGATCAGA 59.061 33.333 0.00 0.00 35.10 3.27
2230 4133 8.567948 GTCCAACAATCTAACAAAAGATCAGAA 58.432 33.333 0.00 0.00 35.10 3.02
2231 4134 9.130661 TCCAACAATCTAACAAAAGATCAGAAA 57.869 29.630 0.00 0.00 35.10 2.52
2232 4135 9.748708 CCAACAATCTAACAAAAGATCAGAAAA 57.251 29.630 0.00 0.00 35.10 2.29
2234 4137 9.750125 AACAATCTAACAAAAGATCAGAAAACC 57.250 29.630 0.00 0.00 35.10 3.27
2235 4138 8.912988 ACAATCTAACAAAAGATCAGAAAACCA 58.087 29.630 0.00 0.00 35.10 3.67
2236 4139 9.918630 CAATCTAACAAAAGATCAGAAAACCAT 57.081 29.630 0.00 0.00 35.10 3.55
2242 4145 8.463930 ACAAAAGATCAGAAAACCATAACAGA 57.536 30.769 0.00 0.00 0.00 3.41
2243 4146 8.352942 ACAAAAGATCAGAAAACCATAACAGAC 58.647 33.333 0.00 0.00 0.00 3.51
2247 4150 7.102346 AGATCAGAAAACCATAACAGACTGAG 58.898 38.462 10.08 0.00 36.76 3.35
2303 4206 3.117745 TCACCATCCATCATCTTCACCT 58.882 45.455 0.00 0.00 0.00 4.00
2337 4240 3.025322 AGGTTCCAACACATCACCAAA 57.975 42.857 0.00 0.00 0.00 3.28
2348 4251 8.356657 CCAACACATCACCAAAATAGTCTTTTA 58.643 33.333 0.00 0.00 0.00 1.52
2356 4259 8.956426 TCACCAAAATAGTCTTTTACCATCATC 58.044 33.333 0.00 0.00 0.00 2.92
2357 4260 7.910162 CACCAAAATAGTCTTTTACCATCATCG 59.090 37.037 0.00 0.00 0.00 3.84
2358 4261 7.610305 ACCAAAATAGTCTTTTACCATCATCGT 59.390 33.333 0.00 0.00 0.00 3.73
2412 4315 5.763204 AGTTAACAACAATGTCAGATCGGTT 59.237 36.000 8.61 0.00 39.40 4.44
2456 4361 2.747446 CAAAGTGATGGTACTTTCCCCG 59.253 50.000 0.00 0.00 45.15 5.73
2458 4363 1.831736 AGTGATGGTACTTTCCCCGAG 59.168 52.381 0.00 0.00 0.00 4.63
2465 4370 3.839490 TGGTACTTTCCCCGAGAATTGTA 59.161 43.478 0.00 0.00 33.44 2.41
2476 4381 8.842358 TCCCCGAGAATTGTATTGAATAATAC 57.158 34.615 0.00 0.00 45.71 1.89
2477 4382 7.881232 TCCCCGAGAATTGTATTGAATAATACC 59.119 37.037 7.48 0.00 45.19 2.73
2511 4416 8.779354 TTACCTCTTCTTGAAGAAATAAGCTC 57.221 34.615 9.15 0.00 33.19 4.09
2525 4430 6.763135 AGAAATAAGCTCGAGCAAACATCATA 59.237 34.615 36.87 16.70 45.16 2.15
2526 4431 6.536731 AATAAGCTCGAGCAAACATCATAG 57.463 37.500 36.87 0.00 45.16 2.23
2527 4432 3.533606 AGCTCGAGCAAACATCATAGT 57.466 42.857 36.87 10.86 45.16 2.12
2545 4450 3.059352 AGTAAGCACAACCATCCTCAC 57.941 47.619 0.00 0.00 0.00 3.51
2579 4484 3.058016 ACGATCATCAACAAAAGCACCTG 60.058 43.478 0.00 0.00 0.00 4.00
2582 4487 2.034939 TCATCAACAAAAGCACCTGCAG 59.965 45.455 6.78 6.78 45.16 4.41
2589 4494 1.152694 AAGCACCTGCAGGCTTCAA 60.153 52.632 33.06 0.00 46.82 2.69
2595 4501 0.538057 CCTGCAGGCTTCAACCTCAA 60.538 55.000 22.33 0.00 38.26 3.02
2608 4514 4.016444 TCAACCTCAAGAACAAAAGCACT 58.984 39.130 0.00 0.00 0.00 4.40
2619 4525 6.856895 AGAACAAAAGCACTAGCAAATATCC 58.143 36.000 0.00 0.00 45.49 2.59
2644 4550 1.544724 ACCATCATCACCAAAACCCG 58.455 50.000 0.00 0.00 0.00 5.28
2667 4573 5.696724 CGCCATCCGTAAGAAAATAGAATCT 59.303 40.000 0.00 0.00 43.02 2.40
2671 4577 9.632807 CCATCCGTAAGAAAATAGAATCTAGAG 57.367 37.037 0.00 0.00 43.02 2.43
2675 4581 9.615295 CCGTAAGAAAATAGAATCTAGAGCTAC 57.385 37.037 0.00 0.00 43.02 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.436646 GCGGGGATGGTCACAGTG 60.437 66.667 0.00 0.00 0.00 3.66
64 65 5.344665 GGCGATAAAAGAGATGAGATCGAAG 59.655 44.000 6.28 0.00 38.71 3.79
134 135 1.032014 GGCCAGAAAGCTGTTGTTCA 58.968 50.000 0.00 0.00 40.63 3.18
139 140 1.898574 CCGTGGCCAGAAAGCTGTT 60.899 57.895 5.11 0.00 40.63 3.16
166 167 2.970987 AGGGCCTTGTTTGTTTACCAT 58.029 42.857 0.00 0.00 0.00 3.55
199 200 4.631131 CAAATGGATGGCGACTAGTATGA 58.369 43.478 0.00 0.00 0.00 2.15
244 245 3.057033 GGAATATACCGGTGATGTACGCT 60.057 47.826 19.93 0.00 0.00 5.07
385 394 2.095919 GCCACAATTGTCCTACGTGTTC 60.096 50.000 8.48 0.00 0.00 3.18
430 439 3.851845 TTTGCGTCAGGTCGACCCG 62.852 63.158 30.82 26.14 42.07 5.28
434 443 1.952133 CCGTTTTGCGTCAGGTCGA 60.952 57.895 0.00 0.00 39.32 4.20
494 503 0.392336 GCTCCACACCCATGCAAAAA 59.608 50.000 0.00 0.00 0.00 1.94
495 504 0.758310 TGCTCCACACCCATGCAAAA 60.758 50.000 0.00 0.00 0.00 2.44
496 505 0.542467 ATGCTCCACACCCATGCAAA 60.542 50.000 0.00 0.00 37.20 3.68
497 506 0.966875 GATGCTCCACACCCATGCAA 60.967 55.000 0.00 0.00 37.20 4.08
498 507 1.378911 GATGCTCCACACCCATGCA 60.379 57.895 0.00 0.00 38.05 3.96
499 508 0.181114 TAGATGCTCCACACCCATGC 59.819 55.000 0.00 0.00 0.00 4.06
500 509 1.487976 AGTAGATGCTCCACACCCATG 59.512 52.381 0.00 0.00 0.00 3.66
501 510 1.885049 AGTAGATGCTCCACACCCAT 58.115 50.000 0.00 0.00 0.00 4.00
502 511 1.278985 CAAGTAGATGCTCCACACCCA 59.721 52.381 0.00 0.00 0.00 4.51
503 512 1.555075 TCAAGTAGATGCTCCACACCC 59.445 52.381 0.00 0.00 0.00 4.61
504 513 3.055819 TCTTCAAGTAGATGCTCCACACC 60.056 47.826 0.00 0.00 0.00 4.16
505 514 4.180057 CTCTTCAAGTAGATGCTCCACAC 58.820 47.826 0.00 0.00 0.00 3.82
506 515 3.368843 GCTCTTCAAGTAGATGCTCCACA 60.369 47.826 0.00 0.00 0.00 4.17
507 516 3.194062 GCTCTTCAAGTAGATGCTCCAC 58.806 50.000 0.00 0.00 0.00 4.02
508 517 2.169352 GGCTCTTCAAGTAGATGCTCCA 59.831 50.000 0.00 0.00 0.00 3.86
509 518 2.433970 AGGCTCTTCAAGTAGATGCTCC 59.566 50.000 0.00 0.00 0.00 4.70
510 519 3.131933 TGAGGCTCTTCAAGTAGATGCTC 59.868 47.826 16.72 0.00 0.00 4.26
511 520 3.102972 TGAGGCTCTTCAAGTAGATGCT 58.897 45.455 16.72 0.00 0.00 3.79
512 521 3.533606 TGAGGCTCTTCAAGTAGATGC 57.466 47.619 16.72 0.00 0.00 3.91
513 522 4.825422 TGTTGAGGCTCTTCAAGTAGATG 58.175 43.478 16.72 0.00 37.72 2.90
514 523 5.188555 TCATGTTGAGGCTCTTCAAGTAGAT 59.811 40.000 16.72 0.00 37.72 1.98
515 524 4.528206 TCATGTTGAGGCTCTTCAAGTAGA 59.472 41.667 16.72 8.87 37.72 2.59
516 525 4.629200 GTCATGTTGAGGCTCTTCAAGTAG 59.371 45.833 16.72 7.04 37.72 2.57
517 526 4.040339 TGTCATGTTGAGGCTCTTCAAGTA 59.960 41.667 16.72 2.73 37.72 2.24
518 527 3.181451 TGTCATGTTGAGGCTCTTCAAGT 60.181 43.478 16.72 0.00 37.72 3.16
519 528 3.405831 TGTCATGTTGAGGCTCTTCAAG 58.594 45.455 16.72 11.35 37.72 3.02
520 529 3.405831 CTGTCATGTTGAGGCTCTTCAA 58.594 45.455 16.72 0.00 34.83 2.69
521 530 2.289882 CCTGTCATGTTGAGGCTCTTCA 60.290 50.000 16.72 14.36 0.00 3.02
522 531 2.354259 CCTGTCATGTTGAGGCTCTTC 58.646 52.381 16.72 9.10 0.00 2.87
523 532 1.004044 CCCTGTCATGTTGAGGCTCTT 59.996 52.381 16.72 0.00 0.00 2.85
524 533 0.617413 CCCTGTCATGTTGAGGCTCT 59.383 55.000 16.72 0.00 0.00 4.09
525 534 0.393537 CCCCTGTCATGTTGAGGCTC 60.394 60.000 7.79 7.79 0.00 4.70
526 535 1.136329 ACCCCTGTCATGTTGAGGCT 61.136 55.000 0.00 0.00 0.00 4.58
527 536 0.678048 GACCCCTGTCATGTTGAGGC 60.678 60.000 0.00 0.00 41.37 4.70
528 537 0.987294 AGACCCCTGTCATGTTGAGG 59.013 55.000 0.00 0.00 44.33 3.86
529 538 1.404717 CGAGACCCCTGTCATGTTGAG 60.405 57.143 0.00 0.00 44.33 3.02
530 539 0.608130 CGAGACCCCTGTCATGTTGA 59.392 55.000 0.00 0.00 44.33 3.18
531 540 0.608130 TCGAGACCCCTGTCATGTTG 59.392 55.000 0.00 0.00 44.33 3.33
534 543 1.114627 TGATCGAGACCCCTGTCATG 58.885 55.000 0.00 0.00 44.33 3.07
579 592 5.227184 GTGCTCTTCACTTTTGTTTAACGTG 59.773 40.000 0.00 0.00 42.38 4.49
580 593 5.329493 GTGCTCTTCACTTTTGTTTAACGT 58.671 37.500 0.00 0.00 42.38 3.99
596 609 2.564553 GATCGCCCACTCGTGCTCTT 62.565 60.000 0.00 0.00 0.00 2.85
692 705 6.053005 TCTTGATTAACAATAGCTAACCCCG 58.947 40.000 0.00 0.00 37.88 5.73
695 708 7.126398 CGCTTCTTGATTAACAATAGCTAACC 58.874 38.462 0.00 0.00 40.56 2.85
700 713 4.201910 TGCCGCTTCTTGATTAACAATAGC 60.202 41.667 0.00 0.00 39.96 2.97
703 716 4.158394 ACATGCCGCTTCTTGATTAACAAT 59.842 37.500 0.00 0.00 37.88 2.71
706 719 3.487544 GGACATGCCGCTTCTTGATTAAC 60.488 47.826 0.00 0.00 0.00 2.01
707 720 2.682856 GGACATGCCGCTTCTTGATTAA 59.317 45.455 0.00 0.00 0.00 1.40
743 758 2.656069 GCTCTACCCGGCTTGGTCA 61.656 63.158 0.00 0.00 39.91 4.02
766 782 2.596851 ATGACGCCTTGCTGGGAGT 61.597 57.895 4.86 4.86 41.87 3.85
820 854 4.381292 GCATCTGGCACTTGCTAAATTCTT 60.381 41.667 9.12 0.00 43.97 2.52
870 904 8.943002 TCCATACGTACATATATACACACAGAG 58.057 37.037 0.00 0.00 0.00 3.35
1541 3341 3.291383 CTTCCGCGGCCCAAACAA 61.291 61.111 23.51 6.64 0.00 2.83
1557 3357 1.371558 GCCGTCCAACTCCAAGACT 59.628 57.895 0.00 0.00 0.00 3.24
1591 3391 1.004918 CCTTGAACGCCTTCTCCGT 60.005 57.895 0.00 0.00 41.24 4.69
1632 3432 1.153066 TGCTGCACCGAACTTGGAA 60.153 52.632 0.00 0.00 0.00 3.53
1650 3450 3.236003 GAGGCCAAACGACTCCGGT 62.236 63.158 5.01 0.00 40.78 5.28
1689 3489 2.332654 GCAAACGAACTGCCCGGAT 61.333 57.895 0.73 0.00 33.51 4.18
1692 3492 0.318614 AATTGCAAACGAACTGCCCG 60.319 50.000 1.71 0.00 39.13 6.13
1737 3537 2.052157 GCGCGATATCTACACTGTTCC 58.948 52.381 12.10 0.00 0.00 3.62
1777 3577 4.162040 ACTAGGCATCATCCTTGGAAAG 57.838 45.455 0.00 0.00 45.69 2.62
1778 3578 4.591321 AACTAGGCATCATCCTTGGAAA 57.409 40.909 0.00 0.00 37.66 3.13
1779 3579 4.263905 ACAAACTAGGCATCATCCTTGGAA 60.264 41.667 0.00 0.00 37.66 3.53
1781 3581 3.624777 ACAAACTAGGCATCATCCTTGG 58.375 45.455 0.00 0.00 37.66 3.61
1782 3582 5.431765 AGTACAAACTAGGCATCATCCTTG 58.568 41.667 0.00 0.00 37.66 3.61
1783 3583 5.700402 AGTACAAACTAGGCATCATCCTT 57.300 39.130 0.00 0.00 37.66 3.36
1784 3584 5.900123 AGTAGTACAAACTAGGCATCATCCT 59.100 40.000 2.52 0.00 38.89 3.24
1832 3661 1.275291 TGCAAACCGAAACCCAAAACA 59.725 42.857 0.00 0.00 0.00 2.83
1944 3773 8.736751 TTGCTACCTGTTAAATTTCGAAAATC 57.263 30.769 15.66 4.71 0.00 2.17
1949 3778 7.065324 CCACTATTGCTACCTGTTAAATTTCGA 59.935 37.037 0.00 0.00 0.00 3.71
1950 3779 7.065324 TCCACTATTGCTACCTGTTAAATTTCG 59.935 37.037 0.00 0.00 0.00 3.46
1954 3785 8.644374 TTTTCCACTATTGCTACCTGTTAAAT 57.356 30.769 0.00 0.00 0.00 1.40
2129 4019 7.186804 TCTCTTTGAACTTTTGAAATCGTGAC 58.813 34.615 0.00 0.00 0.00 3.67
2176 4066 0.456221 CTGAGGACCGCTGACGTTAT 59.544 55.000 0.00 0.00 37.70 1.89
2178 4068 2.143594 GACTGAGGACCGCTGACGTT 62.144 60.000 9.08 0.00 37.70 3.99
2226 4129 5.308825 ACCTCAGTCTGTTATGGTTTTCTG 58.691 41.667 0.00 0.00 0.00 3.02
2227 4130 5.568620 ACCTCAGTCTGTTATGGTTTTCT 57.431 39.130 0.00 0.00 0.00 2.52
2228 4131 5.531287 ACAACCTCAGTCTGTTATGGTTTTC 59.469 40.000 14.67 0.00 35.86 2.29
2229 4132 5.445964 ACAACCTCAGTCTGTTATGGTTTT 58.554 37.500 14.67 9.42 35.86 2.43
2230 4133 5.048846 ACAACCTCAGTCTGTTATGGTTT 57.951 39.130 14.67 8.05 35.86 3.27
2231 4134 4.706842 ACAACCTCAGTCTGTTATGGTT 57.293 40.909 12.79 12.79 38.18 3.67
2232 4135 4.591498 TGTACAACCTCAGTCTGTTATGGT 59.409 41.667 0.00 2.28 0.00 3.55
2233 4136 5.147330 TGTACAACCTCAGTCTGTTATGG 57.853 43.478 0.00 1.69 0.00 2.74
2234 4137 6.634805 AGATGTACAACCTCAGTCTGTTATG 58.365 40.000 0.00 0.00 0.00 1.90
2235 4138 6.859112 AGATGTACAACCTCAGTCTGTTAT 57.141 37.500 0.00 0.00 0.00 1.89
2236 4139 6.665992 AAGATGTACAACCTCAGTCTGTTA 57.334 37.500 0.00 0.00 0.00 2.41
2237 4140 5.552870 AAGATGTACAACCTCAGTCTGTT 57.447 39.130 0.00 0.00 0.00 3.16
2238 4141 5.300752 CAAAGATGTACAACCTCAGTCTGT 58.699 41.667 0.00 0.00 0.00 3.41
2239 4142 4.153117 GCAAAGATGTACAACCTCAGTCTG 59.847 45.833 0.00 0.00 0.00 3.51
2240 4143 4.202357 TGCAAAGATGTACAACCTCAGTCT 60.202 41.667 0.00 0.00 0.00 3.24
2241 4144 4.065088 TGCAAAGATGTACAACCTCAGTC 58.935 43.478 0.00 0.00 0.00 3.51
2242 4145 4.085357 TGCAAAGATGTACAACCTCAGT 57.915 40.909 0.00 0.00 0.00 3.41
2243 4146 4.516698 AGTTGCAAAGATGTACAACCTCAG 59.483 41.667 0.00 0.00 42.61 3.35
2247 4150 5.682943 TGTAGTTGCAAAGATGTACAACC 57.317 39.130 0.00 0.00 42.61 3.77
2303 4206 2.706723 TGGAACCTACTGTGGTGCTTTA 59.293 45.455 7.16 0.00 40.73 1.85
2337 4240 6.761714 GGTGACGATGATGGTAAAAGACTATT 59.238 38.462 0.00 0.00 27.45 1.73
2348 4251 3.320359 GGGGGTGACGATGATGGT 58.680 61.111 0.00 0.00 0.00 3.55
2439 4342 1.829222 TCTCGGGGAAAGTACCATCAC 59.171 52.381 0.00 0.00 0.00 3.06
2490 4395 6.237808 GCTCGAGCTTATTTCTTCAAGAAGAG 60.238 42.308 29.88 2.61 41.99 2.85
2492 4397 5.349817 TGCTCGAGCTTATTTCTTCAAGAAG 59.650 40.000 35.27 3.43 42.66 2.85
2496 4401 5.238432 TGTTTGCTCGAGCTTATTTCTTCAA 59.762 36.000 35.27 16.16 42.66 2.69
2498 4403 5.283060 TGTTTGCTCGAGCTTATTTCTTC 57.717 39.130 35.27 16.13 42.66 2.87
2499 4404 5.412594 TGATGTTTGCTCGAGCTTATTTCTT 59.587 36.000 35.27 17.57 42.66 2.52
2511 4416 4.329801 TGTGCTTACTATGATGTTTGCTCG 59.670 41.667 0.00 0.00 0.00 5.03
2525 4430 2.290323 GGTGAGGATGGTTGTGCTTACT 60.290 50.000 0.00 0.00 0.00 2.24
2526 4431 2.084546 GGTGAGGATGGTTGTGCTTAC 58.915 52.381 0.00 0.00 0.00 2.34
2527 4432 1.702401 TGGTGAGGATGGTTGTGCTTA 59.298 47.619 0.00 0.00 0.00 3.09
2579 4484 1.268079 GTTCTTGAGGTTGAAGCCTGC 59.732 52.381 0.00 0.00 39.34 4.85
2582 4487 4.363138 CTTTTGTTCTTGAGGTTGAAGCC 58.637 43.478 0.00 0.00 0.00 4.35
2589 4494 3.565902 GCTAGTGCTTTTGTTCTTGAGGT 59.434 43.478 0.00 0.00 36.03 3.85
2595 4501 6.660949 AGGATATTTGCTAGTGCTTTTGTTCT 59.339 34.615 0.00 0.00 40.48 3.01
2608 4514 6.012337 TGATGGTTTGGAGGATATTTGCTA 57.988 37.500 0.00 0.00 0.00 3.49
2619 4525 4.559153 GTTTTGGTGATGATGGTTTGGAG 58.441 43.478 0.00 0.00 0.00 3.86
2644 4550 8.088981 TCTAGATTCTATTTTCTTACGGATGGC 58.911 37.037 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.