Multiple sequence alignment - TraesCS6D01G170400

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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 TraesCS6D01G170400 chr6D 100.000 3955 0 0 1 3955 157163068 157167022 0.000000e+00 7304
1 TraesCS6D01G170400 chr6A 95.264 2217 44 13 923 3104 215532076 215529886 0.000000e+00 3456
2 TraesCS6D01G170400 chr6A 94.326 564 19 6 3400 3955 215529605 215529047 0.000000e+00 852
3 TraesCS6D01G170400 chr6A 87.525 505 36 11 1 504 215533284 215532806 3.450000e-155 558
4 TraesCS6D01G170400 chr6A 88.235 391 28 12 552 925 215532810 215532421 6.030000e-123 451
5 TraesCS6D01G170400 chr6A 93.355 301 5 4 3104 3404 215529855 215529570 7.850000e-117 431
6 TraesCS6D01G170400 chr6A 85.311 177 23 1 358 534 215532015 215531842 3.140000e-41 180
7 TraesCS6D01G170400 chr6B 97.093 1789 35 3 923 2711 280045861 280047632 0.000000e+00 3000
8 TraesCS6D01G170400 chr6B 90.104 576 46 3 1 575 280033382 280033947 0.000000e+00 737
9 TraesCS6D01G170400 chr6B 91.521 401 9 4 2711 3104 280047659 280048041 2.710000e-146 529
10 TraesCS6D01G170400 chr6B 87.686 471 17 16 3457 3927 280048367 280048796 9.800000e-141 510
11 TraesCS6D01G170400 chr6B 89.247 372 19 4 578 928 280043966 280044337 2.800000e-121 446
12 TraesCS6D01G170400 chr6B 91.946 298 11 7 3104 3401 280048072 280048356 4.760000e-109 405
13 TraesCS6D01G170400 chr5A 81.416 226 31 8 2002 2222 329382457 329382238 1.460000e-39 174
14 TraesCS6D01G170400 chr5A 79.894 189 24 9 2002 2185 39046634 39046813 4.150000e-25 126
15 TraesCS6D01G170400 chr5A 79.894 189 24 9 2002 2185 39158263 39158442 4.150000e-25 126
16 TraesCS6D01G170400 chr5D 81.383 188 24 8 2002 2185 49699724 49699904 4.120000e-30 143
17 TraesCS6D01G170400 chr5B 81.383 188 24 8 2002 2185 52347473 52347653 4.120000e-30 143
18 TraesCS6D01G170400 chrUn 79.894 189 24 9 2002 2185 477859722 477859901 4.150000e-25 126


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 TraesCS6D01G170400 chr6D 157163068 157167022 3954 False 7304 7304 100.000000 1 3955 1 chr6D.!!$F1 3954
1 TraesCS6D01G170400 chr6A 215529047 215533284 4237 True 988 3456 90.669333 1 3955 6 chr6A.!!$R1 3954
2 TraesCS6D01G170400 chr6B 280043966 280048796 4830 False 978 3000 91.498600 578 3927 5 chr6B.!!$F2 3349
3 TraesCS6D01G170400 chr6B 280033382 280033947 565 False 737 737 90.104000 1 575 1 chr6B.!!$F1 574

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
530 531 0.105408 AGCGGGTACGAAACTTGTGT 59.895 50.0 0.0 0.0 44.60 3.72 F
1542 3101 0.178935 ACCCCCTGGTTGATTTGTGG 60.179 55.0 0.0 0.0 44.75 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 3233 1.248785 TACAGACCTCCACGCCTGAC 61.249 60.0 0.0 0.0 0.0 3.51 R
3422 5068 0.038709 GTCTGCTGCTCTCTTCGTGT 60.039 55.0 0.0 0.0 0.0 4.49 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
65 66 3.340814 CTGCAAGTGGAGTAGAATGGT 57.659 47.619 0.00 0.00 0.00 3.55
77 78 5.395435 GGAGTAGAATGGTCAGGGTTTAGTC 60.395 48.000 0.00 0.00 0.00 2.59
79 80 2.236395 AGAATGGTCAGGGTTTAGTCCG 59.764 50.000 0.00 0.00 0.00 4.79
195 196 0.467290 TGGACAAGTTTGGAGGGTGC 60.467 55.000 0.00 0.00 0.00 5.01
197 198 1.073284 GGACAAGTTTGGAGGGTGCTA 59.927 52.381 0.00 0.00 0.00 3.49
203 204 1.623811 GTTTGGAGGGTGCTAGACAGA 59.376 52.381 0.00 0.00 0.00 3.41
206 207 0.614979 GGAGGGTGCTAGACAGACCA 60.615 60.000 0.00 0.00 0.00 4.02
214 215 4.500545 GGTGCTAGACAGACCAGATGTATG 60.501 50.000 0.00 0.00 41.99 2.39
290 291 4.277672 CCGGACGTAATAGGAGATTTGAGA 59.722 45.833 0.00 0.00 0.00 3.27
332 333 6.189859 TCTTAGGGACGTTTCTATAACTCCA 58.810 40.000 0.00 0.00 0.00 3.86
333 334 6.837568 TCTTAGGGACGTTTCTATAACTCCAT 59.162 38.462 0.00 0.00 0.00 3.41
335 336 4.037684 AGGGACGTTTCTATAACTCCATCG 59.962 45.833 0.00 0.00 0.00 3.84
352 353 3.259064 CATCGTTCACCAATCGTACCTT 58.741 45.455 0.00 0.00 0.00 3.50
356 357 3.306166 CGTTCACCAATCGTACCTTCATC 59.694 47.826 0.00 0.00 0.00 2.92
432 433 4.888325 ATGGCCCCTCCTCCTCCG 62.888 72.222 0.00 0.00 35.26 4.63
514 515 2.827423 AGGGCATCCTCATCAGCG 59.173 61.111 0.00 0.00 39.80 5.18
515 516 2.281345 GGGCATCCTCATCAGCGG 60.281 66.667 0.00 0.00 0.00 5.52
516 517 2.281345 GGCATCCTCATCAGCGGG 60.281 66.667 0.00 0.00 0.00 6.13
517 518 2.507944 GCATCCTCATCAGCGGGT 59.492 61.111 0.00 0.00 0.00 5.28
518 519 1.748403 GCATCCTCATCAGCGGGTA 59.252 57.895 0.00 0.00 0.00 3.69
519 520 0.601311 GCATCCTCATCAGCGGGTAC 60.601 60.000 0.00 0.00 0.00 3.34
520 521 0.319040 CATCCTCATCAGCGGGTACG 60.319 60.000 0.00 0.00 44.63 3.67
521 522 0.467474 ATCCTCATCAGCGGGTACGA 60.467 55.000 0.00 0.00 44.60 3.43
522 523 0.681887 TCCTCATCAGCGGGTACGAA 60.682 55.000 0.00 0.00 44.60 3.85
523 524 0.174845 CCTCATCAGCGGGTACGAAA 59.825 55.000 0.00 0.00 44.60 3.46
524 525 1.278238 CTCATCAGCGGGTACGAAAC 58.722 55.000 0.00 0.00 44.60 2.78
525 526 0.892755 TCATCAGCGGGTACGAAACT 59.107 50.000 0.00 0.00 44.60 2.66
526 527 1.274167 TCATCAGCGGGTACGAAACTT 59.726 47.619 0.00 0.00 44.60 2.66
527 528 1.393539 CATCAGCGGGTACGAAACTTG 59.606 52.381 0.00 0.00 44.60 3.16
528 529 0.390124 TCAGCGGGTACGAAACTTGT 59.610 50.000 0.00 0.00 44.60 3.16
529 530 0.511221 CAGCGGGTACGAAACTTGTG 59.489 55.000 0.00 0.00 44.60 3.33
530 531 0.105408 AGCGGGTACGAAACTTGTGT 59.895 50.000 0.00 0.00 44.60 3.72
531 532 0.509929 GCGGGTACGAAACTTGTGTC 59.490 55.000 0.00 0.00 44.60 3.67
532 533 1.855513 CGGGTACGAAACTTGTGTCA 58.144 50.000 0.00 0.00 44.60 3.58
533 534 2.409975 CGGGTACGAAACTTGTGTCAT 58.590 47.619 0.00 0.00 44.60 3.06
534 535 2.156891 CGGGTACGAAACTTGTGTCATG 59.843 50.000 0.00 0.00 44.60 3.07
535 536 2.482721 GGGTACGAAACTTGTGTCATGG 59.517 50.000 0.00 0.00 0.00 3.66
536 537 2.482721 GGTACGAAACTTGTGTCATGGG 59.517 50.000 0.00 0.00 0.00 4.00
537 538 0.951558 ACGAAACTTGTGTCATGGGC 59.048 50.000 0.00 0.00 0.00 5.36
538 539 0.950836 CGAAACTTGTGTCATGGGCA 59.049 50.000 0.00 0.00 0.00 5.36
539 540 1.069022 CGAAACTTGTGTCATGGGCAG 60.069 52.381 0.00 0.00 0.00 4.85
540 541 2.229792 GAAACTTGTGTCATGGGCAGA 58.770 47.619 0.00 0.00 0.00 4.26
541 542 1.609208 AACTTGTGTCATGGGCAGAC 58.391 50.000 0.00 0.00 36.55 3.51
542 543 0.473755 ACTTGTGTCATGGGCAGACA 59.526 50.000 3.05 3.05 43.23 3.41
543 544 1.133823 ACTTGTGTCATGGGCAGACAA 60.134 47.619 8.00 0.00 46.50 3.18
544 545 1.267806 CTTGTGTCATGGGCAGACAAC 59.732 52.381 8.00 4.68 46.50 3.32
545 546 0.182299 TGTGTCATGGGCAGACAACA 59.818 50.000 8.00 6.67 46.50 3.33
546 547 0.593128 GTGTCATGGGCAGACAACAC 59.407 55.000 8.00 0.00 46.50 3.32
547 548 0.182299 TGTCATGGGCAGACAACACA 59.818 50.000 4.50 0.00 42.57 3.72
548 549 1.202915 TGTCATGGGCAGACAACACAT 60.203 47.619 4.50 0.00 42.57 3.21
549 550 1.888512 GTCATGGGCAGACAACACATT 59.111 47.619 0.00 0.00 36.06 2.71
550 551 2.297033 GTCATGGGCAGACAACACATTT 59.703 45.455 0.00 0.00 36.06 2.32
551 552 2.296752 TCATGGGCAGACAACACATTTG 59.703 45.455 0.00 0.00 0.00 2.32
552 553 1.039068 TGGGCAGACAACACATTTGG 58.961 50.000 0.00 0.00 0.00 3.28
553 554 0.319813 GGGCAGACAACACATTTGGC 60.320 55.000 0.00 0.00 0.00 4.52
554 555 0.675633 GGCAGACAACACATTTGGCT 59.324 50.000 0.00 0.00 38.56 4.75
581 582 1.094785 GCACGTGCACCTGGATTATT 58.905 50.000 34.52 0.00 41.59 1.40
700 701 5.375773 TGAATGACTTTCATGGTGTTCTGA 58.624 37.500 0.00 0.00 39.44 3.27
753 768 6.667414 TGTGCTTTTGGTCCCTGAATTATTAT 59.333 34.615 0.00 0.00 0.00 1.28
797 812 5.424757 GGTTTTTCCTTGGCTAAACTTGTT 58.575 37.500 12.58 0.00 32.53 2.83
1076 2635 1.526917 CCTCCCCAGCCATAAAGCG 60.527 63.158 0.00 0.00 38.01 4.68
1542 3101 0.178935 ACCCCCTGGTTGATTTGTGG 60.179 55.000 0.00 0.00 44.75 4.17
1674 3233 3.669023 GCGAGATCAAAAGGTTGAAGCTG 60.669 47.826 0.00 0.00 46.66 4.24
1697 3256 0.249398 GGCGTGGAGGTCTGTATGTT 59.751 55.000 0.00 0.00 0.00 2.71
1888 3447 2.749541 CGCAGACGTATTGAAGGCA 58.250 52.632 3.87 0.00 33.53 4.75
2035 3595 4.440880 AGCTGCTGTTATTTTGCAAACAA 58.559 34.783 12.39 6.34 35.32 2.83
2239 3799 2.360844 TCTGGATGACTCTGTCTCGAC 58.639 52.381 0.00 0.00 33.15 4.20
2282 3842 3.317993 GGCACATACACTTGTTTGAGGTT 59.682 43.478 6.79 0.00 32.50 3.50
2373 3933 7.260603 AGTGCTTATGCTTCCATTTATGTTTC 58.739 34.615 1.96 0.00 40.48 2.78
2562 4122 9.642343 GATTGAAGTCTATTTTACCCCCTTTAT 57.358 33.333 0.00 0.00 0.00 1.40
2676 4238 4.504858 ACGCAACCCTTTTATAGTCTGAG 58.495 43.478 0.00 0.00 0.00 3.35
2825 4419 3.964031 AGACATCCAGACCTATCCTTGTC 59.036 47.826 0.00 0.00 34.02 3.18
2961 4556 5.819991 TGAAAGAGGGCATCTGAAATTAGT 58.180 37.500 0.87 0.00 38.67 2.24
2968 4563 5.649831 AGGGCATCTGAAATTAGTTTGAGAC 59.350 40.000 2.12 0.00 39.76 3.36
3005 4600 6.889301 TCTTGTCTTCCGTCTAAACTAGAA 57.111 37.500 0.00 0.00 36.40 2.10
3034 4629 7.494298 ACAAAATGTCTGTATTTTTCACCCAAC 59.506 33.333 0.00 0.00 37.97 3.77
3167 4795 5.713792 TTGTGTTTGGTTGACAGAAGAAA 57.286 34.783 0.00 0.00 0.00 2.52
3304 4932 8.940768 ACAACATGCATGCGTATATGTATATA 57.059 30.769 26.53 0.00 32.64 0.86
3305 4933 9.546428 ACAACATGCATGCGTATATGTATATAT 57.454 29.630 26.53 3.70 32.64 0.86
3334 4980 4.770795 ACACAATTCCTATTTCCTCGGAG 58.229 43.478 0.00 0.00 0.00 4.63
3337 4983 4.101741 ACAATTCCTATTTCCTCGGAGGAG 59.898 45.833 24.81 14.24 46.73 3.69
3348 4994 2.729194 CTCGGAGGAGGAAGAAGAAGA 58.271 52.381 0.00 0.00 36.61 2.87
3349 4995 3.093057 CTCGGAGGAGGAAGAAGAAGAA 58.907 50.000 0.00 0.00 36.61 2.52
3350 4996 3.093057 TCGGAGGAGGAAGAAGAAGAAG 58.907 50.000 0.00 0.00 0.00 2.85
3351 4997 3.093057 CGGAGGAGGAAGAAGAAGAAGA 58.907 50.000 0.00 0.00 0.00 2.87
3352 4998 3.511934 CGGAGGAGGAAGAAGAAGAAGAA 59.488 47.826 0.00 0.00 0.00 2.52
3353 4999 4.381505 CGGAGGAGGAAGAAGAAGAAGAAG 60.382 50.000 0.00 0.00 0.00 2.85
3354 5000 4.775253 GGAGGAGGAAGAAGAAGAAGAAGA 59.225 45.833 0.00 0.00 0.00 2.87
3355 5001 5.105351 GGAGGAGGAAGAAGAAGAAGAAGAG 60.105 48.000 0.00 0.00 0.00 2.85
3356 5002 4.777366 AGGAGGAAGAAGAAGAAGAAGAGG 59.223 45.833 0.00 0.00 0.00 3.69
3357 5003 4.775253 GGAGGAAGAAGAAGAAGAAGAGGA 59.225 45.833 0.00 0.00 0.00 3.71
3399 5045 4.227512 ACGTACATTGACTACACGAACA 57.772 40.909 0.00 0.00 36.51 3.18
3400 5046 4.224433 ACGTACATTGACTACACGAACAG 58.776 43.478 0.00 0.00 36.51 3.16
3401 5047 4.224433 CGTACATTGACTACACGAACAGT 58.776 43.478 0.00 0.00 34.66 3.55
3414 5060 4.606457 ACGAACAGTGATAGGTACGTAC 57.394 45.455 17.56 17.56 0.00 3.67
3415 5061 4.002982 ACGAACAGTGATAGGTACGTACA 58.997 43.478 26.02 8.12 0.00 2.90
3416 5062 4.637534 ACGAACAGTGATAGGTACGTACAT 59.362 41.667 26.02 22.06 0.00 2.29
3417 5063 5.203370 CGAACAGTGATAGGTACGTACATC 58.797 45.833 26.02 20.22 0.00 3.06
3418 5064 4.808077 ACAGTGATAGGTACGTACATCG 57.192 45.455 26.02 11.48 46.00 3.84
3419 5065 4.445453 ACAGTGATAGGTACGTACATCGA 58.555 43.478 26.02 6.68 42.86 3.59
3420 5066 4.272018 ACAGTGATAGGTACGTACATCGAC 59.728 45.833 26.02 18.54 42.86 4.20
3421 5067 4.510711 CAGTGATAGGTACGTACATCGACT 59.489 45.833 26.02 19.98 42.86 4.18
3422 5068 5.693555 CAGTGATAGGTACGTACATCGACTA 59.306 44.000 26.02 17.20 42.86 2.59
3423 5069 5.694006 AGTGATAGGTACGTACATCGACTAC 59.306 44.000 26.02 14.40 42.86 2.73
3424 5070 5.463392 GTGATAGGTACGTACATCGACTACA 59.537 44.000 26.02 14.22 42.86 2.74
3425 5071 5.463392 TGATAGGTACGTACATCGACTACAC 59.537 44.000 26.02 14.54 42.86 2.90
3426 5072 2.604914 AGGTACGTACATCGACTACACG 59.395 50.000 26.02 8.57 42.86 4.49
3427 5073 2.603110 GGTACGTACATCGACTACACGA 59.397 50.000 26.02 0.00 46.04 4.35
3450 5096 3.125316 GAGAGCAGCAGACTGATGAATC 58.875 50.000 24.39 18.93 44.20 2.52
3520 5166 7.161404 TGTTGTCTAGTGTAGCATCAAAGATT 58.839 34.615 0.00 0.00 0.00 2.40
3599 5245 0.319900 GACGACATGCATATCCGGCT 60.320 55.000 15.65 0.00 0.00 5.52
3706 5357 0.324460 CCTCCTGACGTACTCCCCTT 60.324 60.000 0.00 0.00 0.00 3.95
3785 5436 1.988467 GGTGAAGTAGGCGTCGTTTAC 59.012 52.381 0.00 0.00 0.00 2.01
3884 5535 2.100023 CCATTCAATTCGCGCGCA 59.900 55.556 32.61 17.05 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.909623 CCGGACTAAACCCTGACCAT 59.090 55.000 0.00 0.00 0.00 3.55
65 66 1.200519 CATCCCGGACTAAACCCTGA 58.799 55.000 0.73 0.00 0.00 3.86
79 80 1.371558 GTGTCCCTATCCGCATCCC 59.628 63.158 0.00 0.00 0.00 3.85
195 196 4.038522 CCACCATACATCTGGTCTGTCTAG 59.961 50.000 0.00 0.00 46.79 2.43
197 198 2.768527 CCACCATACATCTGGTCTGTCT 59.231 50.000 0.00 0.00 46.79 3.41
206 207 2.774234 CTGAAGACCCCACCATACATCT 59.226 50.000 0.00 0.00 0.00 2.90
214 215 2.603652 GGACCCTGAAGACCCCACC 61.604 68.421 0.00 0.00 0.00 4.61
290 291 1.072331 AGAGCATCAACAACCGGAGTT 59.928 47.619 9.46 10.14 37.82 3.01
332 333 3.056393 TGAAGGTACGATTGGTGAACGAT 60.056 43.478 0.00 0.00 0.00 3.73
333 334 2.296752 TGAAGGTACGATTGGTGAACGA 59.703 45.455 0.00 0.00 0.00 3.85
335 336 3.621715 GGATGAAGGTACGATTGGTGAAC 59.378 47.826 0.00 0.00 0.00 3.18
470 471 3.073274 GGTACCACTCAATTTCCAGCT 57.927 47.619 7.15 0.00 0.00 4.24
504 505 0.174845 TTTCGTACCCGCTGATGAGG 59.825 55.000 0.00 0.00 0.00 3.86
505 506 1.135083 AGTTTCGTACCCGCTGATGAG 60.135 52.381 0.00 0.00 0.00 2.90
506 507 0.892755 AGTTTCGTACCCGCTGATGA 59.107 50.000 0.00 0.00 0.00 2.92
507 508 1.393539 CAAGTTTCGTACCCGCTGATG 59.606 52.381 0.00 0.00 0.00 3.07
508 509 1.001633 ACAAGTTTCGTACCCGCTGAT 59.998 47.619 0.00 0.00 0.00 2.90
509 510 0.390124 ACAAGTTTCGTACCCGCTGA 59.610 50.000 0.00 0.00 0.00 4.26
510 511 0.511221 CACAAGTTTCGTACCCGCTG 59.489 55.000 0.00 0.00 0.00 5.18
511 512 0.105408 ACACAAGTTTCGTACCCGCT 59.895 50.000 0.00 0.00 0.00 5.52
512 513 0.509929 GACACAAGTTTCGTACCCGC 59.490 55.000 0.00 0.00 0.00 6.13
513 514 1.855513 TGACACAAGTTTCGTACCCG 58.144 50.000 0.00 0.00 0.00 5.28
514 515 2.482721 CCATGACACAAGTTTCGTACCC 59.517 50.000 0.00 0.00 0.00 3.69
515 516 2.482721 CCCATGACACAAGTTTCGTACC 59.517 50.000 0.00 0.00 0.00 3.34
516 517 2.095919 GCCCATGACACAAGTTTCGTAC 60.096 50.000 0.00 0.00 0.00 3.67
517 518 2.147958 GCCCATGACACAAGTTTCGTA 58.852 47.619 0.00 0.00 0.00 3.43
518 519 0.951558 GCCCATGACACAAGTTTCGT 59.048 50.000 0.00 0.00 0.00 3.85
519 520 0.950836 TGCCCATGACACAAGTTTCG 59.049 50.000 0.00 0.00 0.00 3.46
520 521 2.030805 GTCTGCCCATGACACAAGTTTC 60.031 50.000 0.00 0.00 34.80 2.78
521 522 1.956477 GTCTGCCCATGACACAAGTTT 59.044 47.619 0.00 0.00 34.80 2.66
522 523 1.133823 TGTCTGCCCATGACACAAGTT 60.134 47.619 0.00 0.00 39.23 2.66
523 524 0.473755 TGTCTGCCCATGACACAAGT 59.526 50.000 0.00 0.00 39.23 3.16
524 525 1.267806 GTTGTCTGCCCATGACACAAG 59.732 52.381 0.00 0.00 43.13 3.16
525 526 1.317613 GTTGTCTGCCCATGACACAA 58.682 50.000 0.00 0.00 43.13 3.33
526 527 0.182299 TGTTGTCTGCCCATGACACA 59.818 50.000 0.00 0.00 43.13 3.72
527 528 0.593128 GTGTTGTCTGCCCATGACAC 59.407 55.000 0.00 0.00 43.13 3.67
528 529 0.182299 TGTGTTGTCTGCCCATGACA 59.818 50.000 0.00 0.00 41.94 3.58
529 530 1.538047 ATGTGTTGTCTGCCCATGAC 58.462 50.000 0.00 0.00 35.21 3.06
530 531 2.291209 AATGTGTTGTCTGCCCATGA 57.709 45.000 0.00 0.00 0.00 3.07
531 532 2.610976 CCAAATGTGTTGTCTGCCCATG 60.611 50.000 0.00 0.00 0.00 3.66
532 533 1.619827 CCAAATGTGTTGTCTGCCCAT 59.380 47.619 0.00 0.00 0.00 4.00
533 534 1.039068 CCAAATGTGTTGTCTGCCCA 58.961 50.000 0.00 0.00 0.00 5.36
534 535 0.319813 GCCAAATGTGTTGTCTGCCC 60.320 55.000 0.00 0.00 0.00 5.36
535 536 0.675633 AGCCAAATGTGTTGTCTGCC 59.324 50.000 0.00 0.00 0.00 4.85
536 537 2.514205 AAGCCAAATGTGTTGTCTGC 57.486 45.000 0.00 0.00 0.00 4.26
537 538 3.044986 CGAAAGCCAAATGTGTTGTCTG 58.955 45.455 0.00 0.00 0.00 3.51
538 539 2.034558 CCGAAAGCCAAATGTGTTGTCT 59.965 45.455 0.00 0.00 0.00 3.41
539 540 2.393764 CCGAAAGCCAAATGTGTTGTC 58.606 47.619 0.00 0.00 0.00 3.18
540 541 1.068434 CCCGAAAGCCAAATGTGTTGT 59.932 47.619 0.00 0.00 0.00 3.32
541 542 1.068434 ACCCGAAAGCCAAATGTGTTG 59.932 47.619 0.00 0.00 0.00 3.33
542 543 1.068434 CACCCGAAAGCCAAATGTGTT 59.932 47.619 0.00 0.00 0.00 3.32
543 544 0.673437 CACCCGAAAGCCAAATGTGT 59.327 50.000 0.00 0.00 0.00 3.72
544 545 0.667184 GCACCCGAAAGCCAAATGTG 60.667 55.000 0.00 0.00 0.00 3.21
545 546 1.112315 TGCACCCGAAAGCCAAATGT 61.112 50.000 0.00 0.00 0.00 2.71
546 547 0.667184 GTGCACCCGAAAGCCAAATG 60.667 55.000 5.22 0.00 0.00 2.32
547 548 1.665442 GTGCACCCGAAAGCCAAAT 59.335 52.632 5.22 0.00 0.00 2.32
548 549 2.840066 CGTGCACCCGAAAGCCAAA 61.840 57.895 12.15 0.00 0.00 3.28
549 550 3.283684 CGTGCACCCGAAAGCCAA 61.284 61.111 12.15 0.00 0.00 4.52
550 551 4.555709 ACGTGCACCCGAAAGCCA 62.556 61.111 12.15 0.00 0.00 4.75
551 552 4.025401 CACGTGCACCCGAAAGCC 62.025 66.667 12.15 0.00 0.00 4.35
552 553 4.683334 GCACGTGCACCCGAAAGC 62.683 66.667 34.52 3.22 41.59 3.51
731 746 9.448438 AAAAATAATAATTCAGGGACCAAAAGC 57.552 29.630 0.00 0.00 0.00 3.51
797 812 3.671008 ACCTTGTGTTGTACTCGCATA 57.329 42.857 0.00 0.00 0.00 3.14
920 942 5.279056 CGGAGATACAGAAAGGTCCCTTATC 60.279 48.000 0.00 0.00 34.84 1.75
984 2534 4.802051 ATGCCACCGCCGATGCTT 62.802 61.111 0.00 0.00 34.43 3.91
1542 3101 4.551702 ACCAAGCCATTGTAAAATTCCC 57.448 40.909 0.00 0.00 34.39 3.97
1674 3233 1.248785 TACAGACCTCCACGCCTGAC 61.249 60.000 0.00 0.00 0.00 3.51
1697 3256 8.058235 TCCTATGAAATATTGACATCCACCAAA 58.942 33.333 10.37 0.00 0.00 3.28
1888 3447 8.458843 CGTAATACCTCCATCACAAGAATTTTT 58.541 33.333 0.00 0.00 0.00 1.94
2035 3595 9.793259 TGAGTTTTTCCTAGATGTGATAAGTTT 57.207 29.630 0.00 0.00 0.00 2.66
2222 3782 2.354510 CTCAGTCGAGACAGAGTCATCC 59.645 54.545 14.88 0.00 42.34 3.51
2239 3799 2.557056 CCATATTCCCTTGCATGCTCAG 59.443 50.000 20.33 14.32 0.00 3.35
2373 3933 6.800408 GTGATTCGCAATCTGGAAATATCATG 59.200 38.462 9.34 0.00 38.72 3.07
2562 4122 3.067461 CGAAATTGGGATAAATCGGCCAA 59.933 43.478 2.24 0.00 34.25 4.52
2654 4216 4.504858 CTCAGACTATAAAAGGGTTGCGT 58.495 43.478 0.00 0.00 0.00 5.24
2676 4238 1.024271 TGTGCTTTGTCACAAGGAGC 58.976 50.000 3.33 5.53 43.27 4.70
2825 4419 7.696453 TCTGTCGCAGTTTTCTTTTTCTTTTAG 59.304 33.333 6.72 0.00 32.61 1.85
2961 4556 7.121168 ACAAGAAAAGTTGATCACTGTCTCAAA 59.879 33.333 0.00 0.00 35.12 2.69
2968 4563 6.433766 GGAAGACAAGAAAAGTTGATCACTG 58.566 40.000 0.00 0.00 35.12 3.66
3005 4600 7.926018 GGGTGAAAAATACAGACATTTTGTTCT 59.074 33.333 0.00 0.00 37.97 3.01
3034 4629 2.358898 GGCATACCATACAAGCAAGGTG 59.641 50.000 0.00 0.00 35.62 4.00
3305 4933 8.582437 CGAGGAAATAGGAATTGTGTACCTATA 58.418 37.037 0.00 0.00 43.49 1.31
3334 4980 4.775253 TCCTCTTCTTCTTCTTCTTCCTCC 59.225 45.833 0.00 0.00 0.00 4.30
3337 4983 7.521423 GCTTTTTCCTCTTCTTCTTCTTCTTCC 60.521 40.741 0.00 0.00 0.00 3.46
3345 4991 7.012799 CACTACTTGCTTTTTCCTCTTCTTCTT 59.987 37.037 0.00 0.00 0.00 2.52
3346 4992 6.484977 CACTACTTGCTTTTTCCTCTTCTTCT 59.515 38.462 0.00 0.00 0.00 2.85
3347 4993 6.483640 TCACTACTTGCTTTTTCCTCTTCTTC 59.516 38.462 0.00 0.00 0.00 2.87
3348 4994 6.357367 TCACTACTTGCTTTTTCCTCTTCTT 58.643 36.000 0.00 0.00 0.00 2.52
3349 4995 5.930135 TCACTACTTGCTTTTTCCTCTTCT 58.070 37.500 0.00 0.00 0.00 2.85
3350 4996 6.809630 ATCACTACTTGCTTTTTCCTCTTC 57.190 37.500 0.00 0.00 0.00 2.87
3351 4997 6.881602 CCTATCACTACTTGCTTTTTCCTCTT 59.118 38.462 0.00 0.00 0.00 2.85
3352 4998 6.013293 ACCTATCACTACTTGCTTTTTCCTCT 60.013 38.462 0.00 0.00 0.00 3.69
3353 4999 6.174049 ACCTATCACTACTTGCTTTTTCCTC 58.826 40.000 0.00 0.00 0.00 3.71
3354 5000 6.128138 ACCTATCACTACTTGCTTTTTCCT 57.872 37.500 0.00 0.00 0.00 3.36
3355 5001 6.035758 CGTACCTATCACTACTTGCTTTTTCC 59.964 42.308 0.00 0.00 0.00 3.13
3356 5002 6.589139 ACGTACCTATCACTACTTGCTTTTTC 59.411 38.462 0.00 0.00 0.00 2.29
3357 5003 6.461640 ACGTACCTATCACTACTTGCTTTTT 58.538 36.000 0.00 0.00 0.00 1.94
3399 5045 4.701765 AGTCGATGTACGTACCTATCACT 58.298 43.478 22.43 18.59 43.13 3.41
3400 5046 5.463392 TGTAGTCGATGTACGTACCTATCAC 59.537 44.000 22.43 17.11 43.13 3.06
3401 5047 5.463392 GTGTAGTCGATGTACGTACCTATCA 59.537 44.000 22.43 12.67 43.13 2.15
3402 5048 5.387855 CGTGTAGTCGATGTACGTACCTATC 60.388 48.000 22.43 17.34 43.13 2.08
3403 5049 4.445718 CGTGTAGTCGATGTACGTACCTAT 59.554 45.833 22.43 10.59 43.13 2.57
3404 5050 3.796717 CGTGTAGTCGATGTACGTACCTA 59.203 47.826 22.43 12.87 43.13 3.08
3405 5051 2.604914 CGTGTAGTCGATGTACGTACCT 59.395 50.000 22.43 13.31 43.13 3.08
3406 5052 2.603110 TCGTGTAGTCGATGTACGTACC 59.397 50.000 22.43 7.53 43.13 3.34
3407 5053 3.907178 TCGTGTAGTCGATGTACGTAC 57.093 47.619 18.90 18.90 43.13 3.67
3408 5054 4.173256 TCTTCGTGTAGTCGATGTACGTA 58.827 43.478 12.02 0.00 43.13 3.57
3409 5055 2.995939 TCTTCGTGTAGTCGATGTACGT 59.004 45.455 12.02 0.00 43.13 3.57
3410 5056 3.305361 TCTCTTCGTGTAGTCGATGTACG 59.695 47.826 7.76 7.76 39.57 3.67
3411 5057 4.782822 GCTCTCTTCGTGTAGTCGATGTAC 60.783 50.000 0.00 0.00 39.57 2.90
3412 5058 3.309138 GCTCTCTTCGTGTAGTCGATGTA 59.691 47.826 0.00 0.00 39.57 2.29
3413 5059 2.096174 GCTCTCTTCGTGTAGTCGATGT 59.904 50.000 0.00 0.00 39.57 3.06
3414 5060 2.096013 TGCTCTCTTCGTGTAGTCGATG 59.904 50.000 0.00 0.00 39.57 3.84
3415 5061 2.353269 CTGCTCTCTTCGTGTAGTCGAT 59.647 50.000 0.00 0.00 39.57 3.59
3416 5062 1.732809 CTGCTCTCTTCGTGTAGTCGA 59.267 52.381 0.00 0.00 38.08 4.20
3417 5063 1.792273 GCTGCTCTCTTCGTGTAGTCG 60.792 57.143 0.00 0.00 0.00 4.18
3418 5064 1.200252 TGCTGCTCTCTTCGTGTAGTC 59.800 52.381 0.00 0.00 0.00 2.59
3419 5065 1.201181 CTGCTGCTCTCTTCGTGTAGT 59.799 52.381 0.00 0.00 0.00 2.73
3420 5066 1.470494 TCTGCTGCTCTCTTCGTGTAG 59.530 52.381 0.00 0.00 0.00 2.74
3421 5067 1.200252 GTCTGCTGCTCTCTTCGTGTA 59.800 52.381 0.00 0.00 0.00 2.90
3422 5068 0.038709 GTCTGCTGCTCTCTTCGTGT 60.039 55.000 0.00 0.00 0.00 4.49
3423 5069 0.243365 AGTCTGCTGCTCTCTTCGTG 59.757 55.000 0.00 0.00 0.00 4.35
3424 5070 0.243365 CAGTCTGCTGCTCTCTTCGT 59.757 55.000 0.00 0.00 35.77 3.85
3425 5071 0.525311 TCAGTCTGCTGCTCTCTTCG 59.475 55.000 0.00 0.00 42.29 3.79
3426 5072 2.166050 TCATCAGTCTGCTGCTCTCTTC 59.834 50.000 0.00 0.00 42.29 2.87
3427 5073 2.177734 TCATCAGTCTGCTGCTCTCTT 58.822 47.619 0.00 0.00 42.29 2.85
3450 5096 2.325393 GAATGTAGGAGGGTGGCCGG 62.325 65.000 0.00 0.00 0.00 6.13
3520 5166 2.358125 CACGCGACAACCCATCCA 60.358 61.111 15.93 0.00 0.00 3.41
3599 5245 1.075525 ATACCTGCCAGGCGGAGTA 60.076 57.895 23.25 20.45 39.63 2.59
3652 5303 2.203280 CCCGTTGGACTGCAACCA 60.203 61.111 7.75 8.02 35.47 3.67
3706 5357 0.322816 GACCTCATCAAGCCCAAGCA 60.323 55.000 0.00 0.00 43.56 3.91
3785 5436 2.032860 ATCGGAAGGCGACCTGATGG 62.033 60.000 0.00 0.00 32.13 3.51
3806 5457 0.537371 GTGGAAGAACTGGGTGTGGG 60.537 60.000 0.00 0.00 0.00 4.61
3884 5535 5.957910 TTCAAATTCAAATTCAAACGCGT 57.042 30.435 5.58 5.58 0.00 6.01


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

AutoCloner maintained by Alex Coulton.