Multiple sequence alignment - TraesCS2B01G324100

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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 TraesCS2B01G324100 chr2B 100.000 3784 0 0 1 3784 463212866 463209083 0.000000e+00 6988
1 TraesCS2B01G324100 chr2A 93.012 2991 143 34 503 3452 528269651 528266686 0.000000e+00 4305
2 TraesCS2B01G324100 chr2A 93.208 265 15 3 3516 3779 528266490 528266228 1.650000e-103 387
3 TraesCS2B01G324100 chr2A 81.050 438 54 13 1 421 528270373 528269948 4.720000e-84 322
4 TraesCS2B01G324100 chr2D 86.326 2428 217 54 1 2371 391464274 391461905 0.000000e+00 2538
5 TraesCS2B01G324100 chr2D 91.192 1317 72 11 2387 3689 391461362 391460076 0.000000e+00 1749


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 TraesCS2B01G324100 chr2B 463209083 463212866 3783 True 6988.000000 6988 100.000 1 3784 1 chr2B.!!$R1 3783
1 TraesCS2B01G324100 chr2A 528266228 528270373 4145 True 1671.333333 4305 89.090 1 3779 3 chr2A.!!$R1 3778
2 TraesCS2B01G324100 chr2D 391460076 391464274 4198 True 2143.500000 2538 88.759 1 3689 2 chr2D.!!$R1 3688

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
707 969 0.107654 GACAGTACATGAGGGTGGCC 60.108 60.000 0.00 0.0 0.00 5.36 F
755 1026 0.768221 GGGGTCCATGGCTCCATCTA 60.768 60.000 21.55 0.0 33.90 1.98 F
1233 1508 1.067250 GAGCGTCCTGATCCTGCTC 59.933 63.158 0.00 0.0 44.37 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 3351 0.840288 TAGCTGGGGTGCCTGAGAAA 60.840 55.0 0.0 0.0 0.00 2.52 R
2633 3441 1.726853 GAAGAGGTCCAACACATCCG 58.273 55.0 0.0 0.0 36.38 4.18 R
3177 3995 0.108585 AAGCTCCTGCCTCGAAAACA 59.891 50.0 0.0 0.0 40.80 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.565764 TCATAGGTTGAGAATGCCAGG 57.434 47.619 0.00 0.00 0.00 4.45
38 39 0.255890 TAGGTTGAGAATGCCAGGCC 59.744 55.000 9.64 0.00 0.00 5.19
87 88 1.076265 GTAGGGCCCAATGTTCCCC 60.076 63.158 27.56 0.00 40.97 4.81
91 92 0.264657 GGGCCCAATGTTCCCCTAAT 59.735 55.000 19.95 0.00 34.59 1.73
93 94 2.090999 GGGCCCAATGTTCCCCTAATAA 60.091 50.000 19.95 0.00 34.59 1.40
100 101 2.294074 TGTTCCCCTAATAACATGCGC 58.706 47.619 0.00 0.00 30.88 6.09
102 103 2.685897 GTTCCCCTAATAACATGCGCAA 59.314 45.455 17.11 0.00 0.00 4.85
135 137 5.339530 GGATCCCCAAGTCATATTCCATAGG 60.340 48.000 0.00 0.00 0.00 2.57
171 189 6.930164 TCATGAAATTGTCCAAAAATGACCAG 59.070 34.615 0.00 0.00 31.60 4.00
223 241 1.285962 AGTTGGTCCAATGGCATAGCT 59.714 47.619 7.77 0.00 0.00 3.32
230 248 4.159506 GGTCCAATGGCATAGCTAAAAACA 59.840 41.667 0.00 0.00 0.00 2.83
231 249 5.337169 GGTCCAATGGCATAGCTAAAAACAA 60.337 40.000 0.00 0.00 0.00 2.83
257 283 6.916360 AGAAGCAATACAAAATGGAGGAAA 57.084 33.333 0.00 0.00 0.00 3.13
258 284 7.301868 AGAAGCAATACAAAATGGAGGAAAA 57.698 32.000 0.00 0.00 0.00 2.29
259 285 7.734942 AGAAGCAATACAAAATGGAGGAAAAA 58.265 30.769 0.00 0.00 0.00 1.94
260 286 8.377799 AGAAGCAATACAAAATGGAGGAAAAAT 58.622 29.630 0.00 0.00 0.00 1.82
261 287 8.922931 AAGCAATACAAAATGGAGGAAAAATT 57.077 26.923 0.00 0.00 0.00 1.82
262 288 8.326680 AGCAATACAAAATGGAGGAAAAATTG 57.673 30.769 0.00 0.00 0.00 2.32
263 289 7.938490 AGCAATACAAAATGGAGGAAAAATTGT 59.062 29.630 0.00 0.00 34.31 2.71
264 290 9.213799 GCAATACAAAATGGAGGAAAAATTGTA 57.786 29.630 0.00 0.00 36.55 2.41
309 335 0.615331 GAACTGGATCTGGGCAGACA 59.385 55.000 4.00 0.00 40.75 3.41
319 345 4.479993 GGCAGACAGGGCGCTGAT 62.480 66.667 34.63 20.34 34.06 2.90
335 361 2.598394 ATGCTGCCCGTGCTTGTT 60.598 55.556 0.00 0.00 38.71 2.83
339 365 3.136345 CTGCCCGTGCTTGTTTGCA 62.136 57.895 0.00 0.00 41.05 4.08
340 366 2.339712 GCCCGTGCTTGTTTGCAT 59.660 55.556 0.00 0.00 45.23 3.96
344 370 0.244450 CCGTGCTTGTTTGCATCCAT 59.756 50.000 0.00 0.00 45.23 3.41
350 376 3.008157 TGCTTGTTTGCATCCATTGGATT 59.992 39.130 15.75 0.00 39.79 3.01
361 387 0.171007 CATTGGATTTGCGGCGAGTT 59.829 50.000 12.98 0.00 0.00 3.01
362 388 0.171007 ATTGGATTTGCGGCGAGTTG 59.829 50.000 12.98 0.00 0.00 3.16
363 389 1.169661 TTGGATTTGCGGCGAGTTGT 61.170 50.000 12.98 0.00 0.00 3.32
375 401 1.354337 CGAGTTGTGCACCATCTCCG 61.354 60.000 15.69 6.72 36.82 4.63
382 408 2.670148 GCACCATCTCCGGACCCTT 61.670 63.158 0.00 0.00 0.00 3.95
384 410 1.080354 ACCATCTCCGGACCCTTCA 59.920 57.895 0.00 0.00 0.00 3.02
386 412 0.978146 CCATCTCCGGACCCTTCAGT 60.978 60.000 0.00 0.00 0.00 3.41
388 414 0.905357 ATCTCCGGACCCTTCAGTTG 59.095 55.000 0.00 0.00 0.00 3.16
392 418 1.597027 CGGACCCTTCAGTTGCGTT 60.597 57.895 0.00 0.00 0.00 4.84
394 420 1.566018 GGACCCTTCAGTTGCGTTCG 61.566 60.000 0.00 0.00 0.00 3.95
416 442 4.872574 TCCGGAATCCCCTCCCCG 62.873 72.222 0.00 0.00 41.47 5.73
421 447 2.039951 AATCCCCTCCCCGTTCGA 59.960 61.111 0.00 0.00 0.00 3.71
443 469 1.591158 CGACGGATCGTTATTGGTTGG 59.409 52.381 0.00 0.00 43.66 3.77
450 476 0.621609 CGTTATTGGTTGGGGGAGGA 59.378 55.000 0.00 0.00 0.00 3.71
451 477 1.408266 CGTTATTGGTTGGGGGAGGAG 60.408 57.143 0.00 0.00 0.00 3.69
453 479 0.626277 TATTGGTTGGGGGAGGAGGG 60.626 60.000 0.00 0.00 0.00 4.30
478 504 2.405191 GCGATGGCGGCTTTCTTC 59.595 61.111 11.43 0.00 38.16 2.87
479 505 2.109126 GCGATGGCGGCTTTCTTCT 61.109 57.895 11.43 0.00 38.16 2.85
480 506 2.009888 CGATGGCGGCTTTCTTCTC 58.990 57.895 11.43 0.00 0.00 2.87
482 508 0.460284 GATGGCGGCTTTCTTCTCGA 60.460 55.000 11.43 0.00 0.00 4.04
483 509 0.741221 ATGGCGGCTTTCTTCTCGAC 60.741 55.000 11.43 0.00 0.00 4.20
484 510 2.445438 GGCGGCTTTCTTCTCGACG 61.445 63.158 0.00 0.00 0.00 5.12
485 511 1.443872 GCGGCTTTCTTCTCGACGA 60.444 57.895 0.00 0.00 0.00 4.20
486 512 1.675524 GCGGCTTTCTTCTCGACGAC 61.676 60.000 0.00 0.00 0.00 4.34
487 513 0.386858 CGGCTTTCTTCTCGACGACA 60.387 55.000 0.00 0.00 0.00 4.35
488 514 1.779569 GGCTTTCTTCTCGACGACAA 58.220 50.000 0.00 0.00 0.00 3.18
489 515 2.132762 GGCTTTCTTCTCGACGACAAA 58.867 47.619 0.00 0.00 0.00 2.83
490 516 2.155924 GGCTTTCTTCTCGACGACAAAG 59.844 50.000 0.00 1.07 0.00 2.77
491 517 2.410389 GCTTTCTTCTCGACGACAAAGC 60.410 50.000 16.70 16.70 39.09 3.51
522 763 2.689983 GGGGCCAACAATCACAATAGAG 59.310 50.000 4.39 0.00 0.00 2.43
557 798 1.348064 TCGATGTTGACCACCTCCTT 58.652 50.000 0.00 0.00 0.00 3.36
558 799 1.275291 TCGATGTTGACCACCTCCTTC 59.725 52.381 0.00 0.00 0.00 3.46
563 804 3.692406 GACCACCTCCTTCGCCGT 61.692 66.667 0.00 0.00 0.00 5.68
580 821 2.104859 GTAACTTCCTTCGCCGCCC 61.105 63.158 0.00 0.00 0.00 6.13
581 822 2.288025 TAACTTCCTTCGCCGCCCT 61.288 57.895 0.00 0.00 0.00 5.19
618 859 0.508641 CTTCGTCTTGCAGTTCACCG 59.491 55.000 0.00 0.00 0.00 4.94
619 860 1.495584 TTCGTCTTGCAGTTCACCGC 61.496 55.000 0.00 0.00 0.00 5.68
622 878 1.073025 TCTTGCAGTTCACCGCCAT 59.927 52.632 0.00 0.00 0.00 4.40
658 914 4.521639 GGCATCATCCATATTGCTCTTTGA 59.478 41.667 0.00 0.00 35.46 2.69
659 915 5.335740 GGCATCATCCATATTGCTCTTTGAG 60.336 44.000 0.00 0.00 35.46 3.02
663 921 4.156455 TCCATATTGCTCTTTGAGGGAC 57.844 45.455 0.00 0.00 0.00 4.46
668 926 1.448717 GCTCTTTGAGGGACGAGGC 60.449 63.158 0.00 0.00 0.00 4.70
681 939 2.278013 GAGGCATCCGACGACGAC 60.278 66.667 9.28 0.00 42.66 4.34
688 950 2.575363 CATCCGACGACGACATCTATG 58.425 52.381 9.28 0.00 42.66 2.23
691 953 1.329599 CCGACGACGACATCTATGACA 59.670 52.381 9.28 0.00 42.66 3.58
695 957 4.516359 GACGACGACATCTATGACAGTAC 58.484 47.826 0.00 0.00 0.00 2.73
700 962 6.066054 ACGACATCTATGACAGTACATGAG 57.934 41.667 0.00 0.00 0.00 2.90
706 968 0.613260 TGACAGTACATGAGGGTGGC 59.387 55.000 0.00 0.00 0.00 5.01
707 969 0.107654 GACAGTACATGAGGGTGGCC 60.108 60.000 0.00 0.00 0.00 5.36
709 971 2.513897 GTACATGAGGGTGGCCGC 60.514 66.667 8.12 8.12 0.00 6.53
725 988 2.361104 GCGGGATGGGTGAGCAAA 60.361 61.111 0.00 0.00 0.00 3.68
729 992 1.632589 GGGATGGGTGAGCAAAGTTT 58.367 50.000 0.00 0.00 0.00 2.66
736 999 1.264288 GGTGAGCAAAGTTTGAGGACG 59.736 52.381 19.82 0.00 0.00 4.79
738 1001 0.875059 GAGCAAAGTTTGAGGACGGG 59.125 55.000 19.82 0.00 0.00 5.28
755 1026 0.768221 GGGGTCCATGGCTCCATCTA 60.768 60.000 21.55 0.00 33.90 1.98
780 1051 4.563184 CACGAAGTAGCCAACTATCTGAAC 59.437 45.833 0.00 0.00 41.61 3.18
786 1057 2.766263 AGCCAACTATCTGAACCATCGA 59.234 45.455 0.00 0.00 0.00 3.59
820 1091 1.145119 AGACTTTTTCCCCTCCACCAC 59.855 52.381 0.00 0.00 0.00 4.16
824 1095 1.432023 TTTTCCCCTCCACCACCCTC 61.432 60.000 0.00 0.00 0.00 4.30
834 1105 3.396570 CCACCCTCCACGGTACCC 61.397 72.222 6.25 0.00 33.67 3.69
841 1112 3.387947 CCACGGTACCCTCGCCTT 61.388 66.667 6.25 0.00 0.00 4.35
865 1136 5.950544 TTTTTCCTCGATCCCTTCTATCA 57.049 39.130 0.00 0.00 0.00 2.15
886 1157 2.202987 CCCACGCTGCTCTGATCC 60.203 66.667 0.00 0.00 0.00 3.36
934 1209 2.549754 CGATCCAATGCCGCTCTAAATT 59.450 45.455 0.00 0.00 0.00 1.82
943 1218 2.364002 GCCGCTCTAAATTCTCTCCTCT 59.636 50.000 0.00 0.00 0.00 3.69
1230 1505 1.227205 GCTGAGCGTCCTGATCCTG 60.227 63.158 0.00 0.00 29.76 3.86
1233 1508 1.067250 GAGCGTCCTGATCCTGCTC 59.933 63.158 0.00 0.00 44.37 4.26
1249 1524 1.303799 GCTCTCCGTGTACGAGACCA 61.304 60.000 5.91 0.00 43.02 4.02
1332 1607 4.082523 CTCGTCATGGTGGCCGGT 62.083 66.667 1.90 0.00 0.00 5.28
1707 1982 5.164051 CGATTGTTCGTCATATGTATCCTGC 60.164 44.000 1.90 0.00 40.53 4.85
1713 1988 4.099419 TCGTCATATGTATCCTGCACTTGT 59.901 41.667 1.90 0.00 0.00 3.16
1759 2037 8.643324 ACAATTACTTTCTGAGTTCTGACTACT 58.357 33.333 0.00 0.00 39.86 2.57
1762 2040 8.687292 TTACTTTCTGAGTTCTGACTACTACA 57.313 34.615 0.00 0.00 39.86 2.74
1763 2041 7.768807 ACTTTCTGAGTTCTGACTACTACAT 57.231 36.000 0.00 0.00 35.88 2.29
1764 2042 8.865420 ACTTTCTGAGTTCTGACTACTACATA 57.135 34.615 0.00 0.00 35.88 2.29
1765 2043 9.298250 ACTTTCTGAGTTCTGACTACTACATAA 57.702 33.333 0.00 0.00 35.88 1.90
1896 2176 8.817100 GTGGAAGTAAATAATTAAAATGGCTGC 58.183 33.333 0.00 0.00 0.00 5.25
1946 2226 1.338389 ACATTTTGCAGAGGCCATTGC 60.338 47.619 20.91 20.91 40.13 3.56
2001 2281 9.665719 TCAAACATGTAGTTCAGCTCATAAATA 57.334 29.630 0.00 0.00 40.26 1.40
2066 2347 5.415701 GGTTGATGCTTCCTGAAGTTTATCA 59.584 40.000 8.57 11.95 40.45 2.15
2101 2382 7.347252 TCTCATCTCAGTACAGTATTACCACT 58.653 38.462 0.00 0.00 0.00 4.00
2145 2426 6.148150 TCGAGTTCGTTAGTTATTTTGGCAAT 59.852 34.615 0.00 0.00 40.80 3.56
2366 2647 5.705609 TTCTGCTGAAACCTTATTTCACC 57.294 39.130 3.21 0.00 34.96 4.02
2401 3209 8.673711 GTTGGTAATGCATTTATCTGTACTTCA 58.326 33.333 18.75 0.00 0.00 3.02
2431 3239 5.125100 TCTTGAATGTCTGTTGATTTGCC 57.875 39.130 0.00 0.00 0.00 4.52
2492 3300 9.614792 GTAAGCTATGATTTTAAGGAGGAAAGA 57.385 33.333 0.00 0.00 0.00 2.52
2633 3441 6.045955 GTCTCAGTTCCAAGAAGATCCATAC 58.954 44.000 0.00 0.00 0.00 2.39
2646 3454 2.684001 TCCATACGGATGTGTTGGAC 57.316 50.000 6.92 0.00 37.02 4.02
2696 3504 1.338389 CCGTTTCACCGTACCATTCCT 60.338 52.381 0.00 0.00 0.00 3.36
2784 3592 3.261818 ACCTTCCTTGGACTCAGTAGT 57.738 47.619 0.00 0.00 39.21 2.73
2806 3618 5.781818 AGTGGAAAAAGGATGTTTGGATCAT 59.218 36.000 0.00 0.00 0.00 2.45
2819 3631 7.718334 TGTTTGGATCATACTTCTACTCTCA 57.282 36.000 0.00 0.00 0.00 3.27
2845 3658 6.825610 TGTAAAATCCCAGCATTCTTGTTTT 58.174 32.000 0.00 0.00 0.00 2.43
2865 3678 1.635487 TGCCCCTGTTTCTAAGCTGAT 59.365 47.619 0.00 0.00 0.00 2.90
2948 3761 6.361481 CACTAGTTAGATTGTTTTCGTCACGA 59.639 38.462 0.00 0.00 0.00 4.35
2979 3792 5.571454 GCCCACATGCTCCATATATACAGAA 60.571 44.000 0.00 0.00 0.00 3.02
2983 3796 9.017509 CCACATGCTCCATATATACAGAATTTT 57.982 33.333 0.00 0.00 0.00 1.82
3037 3853 6.668323 ACTGTGAATTTGTTAGTACACATGC 58.332 36.000 0.00 0.00 37.56 4.06
3129 3945 5.964958 ACTGGAAACCTTATGAACATGTG 57.035 39.130 0.00 0.00 0.00 3.21
3238 4056 1.361668 ATGTGCTCGCTACTTTGCCG 61.362 55.000 0.00 0.00 0.00 5.69
3294 4112 4.101898 TGTGTCCATGGTTGTGTACTAACT 59.898 41.667 12.58 0.00 0.00 2.24
3558 4536 6.798959 ACAATCTTACGAGTTACGAGTGTTAC 59.201 38.462 0.00 0.00 45.77 2.50
3568 4546 9.713740 CGAGTTACGAGTGTTACTTTATAATCT 57.286 33.333 0.00 0.00 45.77 2.40
3708 4693 0.543277 CCAGCTATTGGTCCAGAGCA 59.457 55.000 23.07 0.00 42.41 4.26
3727 4712 5.072040 AGCACCAAAGTATTTTGTATGCC 57.928 39.130 22.64 12.14 45.91 4.40
3739 4724 3.634397 TTGTATGCCTTCCTTCCTCAG 57.366 47.619 0.00 0.00 0.00 3.35
3746 4731 3.181429 TGCCTTCCTTCCTCAGAAAATGT 60.181 43.478 0.00 0.00 0.00 2.71
3748 4733 5.196695 GCCTTCCTTCCTCAGAAAATGTAT 58.803 41.667 0.00 0.00 0.00 2.29
3776 4761 7.094205 CCCTCTGTAAACTATGAACTGCAAAAT 60.094 37.037 0.00 0.00 0.00 1.82
3779 4764 7.172532 TCTGTAAACTATGAACTGCAAAATCGT 59.827 33.333 0.00 0.00 0.00 3.73
3780 4765 7.295201 TGTAAACTATGAACTGCAAAATCGTC 58.705 34.615 0.00 0.00 0.00 4.20
3781 4766 6.560253 AAACTATGAACTGCAAAATCGTCT 57.440 33.333 0.00 0.00 0.00 4.18
3782 4767 6.560253 AACTATGAACTGCAAAATCGTCTT 57.440 33.333 0.00 0.00 0.00 3.01
3783 4768 7.667043 AACTATGAACTGCAAAATCGTCTTA 57.333 32.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.462759 AGATACGCAAGGCAAGAGGC 60.463 55.000 0.00 0.00 46.39 4.70
38 39 2.476854 GCAAAGATACGCAAGGCAAGAG 60.477 50.000 0.00 0.00 46.39 2.85
74 75 3.637769 TGTTATTAGGGGAACATTGGGC 58.362 45.455 0.00 0.00 30.72 5.36
87 88 5.456497 CCAATTGTCTTGCGCATGTTATTAG 59.544 40.000 21.14 9.75 0.00 1.73
91 92 2.094803 CCCAATTGTCTTGCGCATGTTA 60.095 45.455 21.14 10.00 0.00 2.41
93 94 0.244450 CCCAATTGTCTTGCGCATGT 59.756 50.000 21.14 0.89 0.00 3.21
129 131 2.602257 TGACGAACATGAGCCTATGG 57.398 50.000 0.00 0.00 32.32 2.74
160 178 7.237471 AGTTTATTTGGGATCCTGGTCATTTTT 59.763 33.333 12.58 0.00 0.00 1.94
171 189 6.670695 ATGCCATTAGTTTATTTGGGATCC 57.329 37.500 1.92 1.92 35.66 3.36
230 248 7.734942 TCCTCCATTTTGTATTGCTTCTTTTT 58.265 30.769 0.00 0.00 0.00 1.94
231 249 7.301868 TCCTCCATTTTGTATTGCTTCTTTT 57.698 32.000 0.00 0.00 0.00 2.27
257 283 3.424829 CGCAGCAAGACACGATACAATTT 60.425 43.478 0.00 0.00 0.00 1.82
258 284 2.094258 CGCAGCAAGACACGATACAATT 59.906 45.455 0.00 0.00 0.00 2.32
259 285 1.660607 CGCAGCAAGACACGATACAAT 59.339 47.619 0.00 0.00 0.00 2.71
260 286 1.067693 CGCAGCAAGACACGATACAA 58.932 50.000 0.00 0.00 0.00 2.41
261 287 0.242555 TCGCAGCAAGACACGATACA 59.757 50.000 0.00 0.00 0.00 2.29
262 288 0.640768 GTCGCAGCAAGACACGATAC 59.359 55.000 0.00 0.00 38.42 2.24
263 289 0.242555 TGTCGCAGCAAGACACGATA 59.757 50.000 5.07 0.00 42.91 2.92
264 290 1.006220 TGTCGCAGCAAGACACGAT 60.006 52.632 5.07 0.00 42.91 3.73
265 291 2.415426 TGTCGCAGCAAGACACGA 59.585 55.556 5.07 0.00 42.91 4.35
315 341 2.749044 AAGCACGGGCAGCATCAG 60.749 61.111 14.57 0.00 44.61 2.90
316 342 3.057548 CAAGCACGGGCAGCATCA 61.058 61.111 14.57 0.00 44.61 3.07
319 345 2.832661 AAACAAGCACGGGCAGCA 60.833 55.556 14.57 0.00 44.61 4.41
335 361 1.134759 CCGCAAATCCAATGGATGCAA 60.135 47.619 22.95 0.00 42.27 4.08
339 365 0.751277 TCGCCGCAAATCCAATGGAT 60.751 50.000 9.36 9.36 45.46 3.41
340 366 1.375853 CTCGCCGCAAATCCAATGGA 61.376 55.000 3.67 3.67 35.55 3.41
344 370 1.169661 ACAACTCGCCGCAAATCCAA 61.170 50.000 0.00 0.00 0.00 3.53
350 376 3.947841 GTGCACAACTCGCCGCAA 61.948 61.111 13.17 0.00 35.87 4.85
361 387 2.662596 GTCCGGAGATGGTGCACA 59.337 61.111 20.43 5.24 0.00 4.57
362 388 2.125106 GGTCCGGAGATGGTGCAC 60.125 66.667 3.06 8.80 0.00 4.57
363 389 3.399181 GGGTCCGGAGATGGTGCA 61.399 66.667 3.06 0.00 0.00 4.57
369 395 0.905357 CAACTGAAGGGTCCGGAGAT 59.095 55.000 3.06 0.00 0.00 2.75
375 401 1.566018 CGAACGCAACTGAAGGGTCC 61.566 60.000 0.00 0.00 0.00 4.46
382 408 4.595538 ACGGCCGAACGCAACTGA 62.596 61.111 35.90 0.00 40.31 3.41
432 458 1.063942 CCTCCTCCCCCAACCAATAAC 60.064 57.143 0.00 0.00 0.00 1.89
435 461 1.935931 CCCTCCTCCCCCAACCAAT 60.936 63.158 0.00 0.00 0.00 3.16
437 463 4.693915 CCCCTCCTCCCCCAACCA 62.694 72.222 0.00 0.00 0.00 3.67
462 488 1.756375 CGAGAAGAAAGCCGCCATCG 61.756 60.000 0.00 0.00 0.00 3.84
464 490 0.741221 GTCGAGAAGAAAGCCGCCAT 60.741 55.000 0.00 0.00 0.00 4.40
466 492 2.445438 CGTCGAGAAGAAAGCCGCC 61.445 63.158 0.00 0.00 0.00 6.13
467 493 1.443872 TCGTCGAGAAGAAAGCCGC 60.444 57.895 0.00 0.00 0.00 6.53
469 495 1.779569 TTGTCGTCGAGAAGAAAGCC 58.220 50.000 0.00 0.00 0.00 4.35
470 496 2.410389 GCTTTGTCGTCGAGAAGAAAGC 60.410 50.000 19.34 19.34 43.41 3.51
471 497 2.160091 CGCTTTGTCGTCGAGAAGAAAG 60.160 50.000 17.85 13.65 35.36 2.62
473 499 1.002142 TCGCTTTGTCGTCGAGAAGAA 60.002 47.619 17.85 0.51 0.00 2.52
474 500 0.589708 TCGCTTTGTCGTCGAGAAGA 59.410 50.000 17.85 5.70 0.00 2.87
475 501 0.703466 GTCGCTTTGTCGTCGAGAAG 59.297 55.000 4.90 8.99 32.54 2.85
477 503 1.439858 CGTCGCTTTGTCGTCGAGA 60.440 57.895 0.00 0.00 41.87 4.04
478 504 3.044114 GCGTCGCTTTGTCGTCGAG 62.044 63.158 10.68 0.00 41.87 4.04
479 505 3.095278 GCGTCGCTTTGTCGTCGA 61.095 61.111 10.68 0.00 41.87 4.20
480 506 4.449161 CGCGTCGCTTTGTCGTCG 62.449 66.667 16.36 0.00 42.11 5.12
482 508 3.688330 CACGCGTCGCTTTGTCGT 61.688 61.111 9.86 1.14 0.00 4.34
510 751 3.189606 TGTGTCCCCCTCTATTGTGATT 58.810 45.455 0.00 0.00 0.00 2.57
511 752 2.845659 TGTGTCCCCCTCTATTGTGAT 58.154 47.619 0.00 0.00 0.00 3.06
522 763 1.153168 CGATGTGGATGTGTCCCCC 60.153 63.158 0.00 0.00 44.41 5.40
557 798 1.444895 GCGAAGGAAGTTACGGCGA 60.445 57.895 16.62 0.00 0.00 5.54
558 799 2.450345 GGCGAAGGAAGTTACGGCG 61.450 63.158 4.80 4.80 40.82 6.46
563 804 1.833787 AAGGGCGGCGAAGGAAGTTA 61.834 55.000 12.98 0.00 0.00 2.24
611 852 1.745489 GGAGTCCATGGCGGTGAAC 60.745 63.158 6.96 0.00 35.57 3.18
618 859 2.825836 CTTGGCGGAGTCCATGGC 60.826 66.667 6.96 6.83 34.07 4.40
619 860 2.124570 CCTTGGCGGAGTCCATGG 60.125 66.667 10.49 4.97 40.39 3.66
622 878 3.329542 GATGCCTTGGCGGAGTCCA 62.330 63.158 10.49 0.00 33.16 4.02
658 914 3.148279 GTCGGATGCCTCGTCCCT 61.148 66.667 0.00 0.00 36.26 4.20
659 915 4.570663 CGTCGGATGCCTCGTCCC 62.571 72.222 0.00 0.00 36.26 4.46
663 921 3.872728 TCGTCGTCGGATGCCTCG 61.873 66.667 1.55 0.00 37.69 4.63
668 926 2.223377 TCATAGATGTCGTCGTCGGATG 59.777 50.000 1.55 11.03 37.69 3.51
681 939 5.510349 CCACCCTCATGTACTGTCATAGATG 60.510 48.000 0.00 0.00 0.00 2.90
688 950 0.107654 GGCCACCCTCATGTACTGTC 60.108 60.000 0.00 0.00 0.00 3.51
691 953 3.031417 GCGGCCACCCTCATGTACT 62.031 63.158 2.24 0.00 0.00 2.73
707 969 4.776322 TTGCTCACCCATCCCGCG 62.776 66.667 0.00 0.00 0.00 6.46
709 971 0.609131 AACTTTGCTCACCCATCCCG 60.609 55.000 0.00 0.00 0.00 5.14
717 980 1.264288 CCGTCCTCAAACTTTGCTCAC 59.736 52.381 0.00 0.00 0.00 3.51
718 981 1.593196 CCGTCCTCAAACTTTGCTCA 58.407 50.000 0.00 0.00 0.00 4.26
736 999 0.768221 TAGATGGAGCCATGGACCCC 60.768 60.000 18.40 13.06 36.70 4.95
738 1001 0.398318 GGTAGATGGAGCCATGGACC 59.602 60.000 18.40 18.08 36.70 4.46
755 1026 3.097614 AGATAGTTGGCTACTTCGTGGT 58.902 45.455 6.96 0.00 38.33 4.16
780 1051 0.179073 AGCCGTGGAAGATTCGATGG 60.179 55.000 10.53 10.53 42.79 3.51
786 1057 3.983044 AAAGTCTAGCCGTGGAAGATT 57.017 42.857 0.00 0.00 0.00 2.40
845 1116 5.398236 AGATGATAGAAGGGATCGAGGAAA 58.602 41.667 0.00 0.00 0.00 3.13
847 1118 4.568804 GGAGATGATAGAAGGGATCGAGGA 60.569 50.000 0.00 0.00 0.00 3.71
849 1120 3.699038 GGGAGATGATAGAAGGGATCGAG 59.301 52.174 0.00 0.00 0.00 4.04
850 1121 3.076032 TGGGAGATGATAGAAGGGATCGA 59.924 47.826 0.00 0.00 0.00 3.59
853 1124 3.169099 CGTGGGAGATGATAGAAGGGAT 58.831 50.000 0.00 0.00 0.00 3.85
865 1136 1.047596 ATCAGAGCAGCGTGGGAGAT 61.048 55.000 0.00 0.00 0.00 2.75
934 1209 1.285373 GGTGGTGGAGTAGAGGAGAGA 59.715 57.143 0.00 0.00 0.00 3.10
943 1218 2.358932 GGATCTAGGTGGTGGTGGAGTA 60.359 54.545 0.00 0.00 0.00 2.59
1230 1505 1.303799 TGGTCTCGTACACGGAGAGC 61.304 60.000 16.78 16.78 40.65 4.09
1233 1508 0.959372 ACCTGGTCTCGTACACGGAG 60.959 60.000 1.39 0.00 40.29 4.63
1249 1524 1.479709 CTCCTCATCGTCCTGAACCT 58.520 55.000 0.00 0.00 0.00 3.50
1332 1607 2.672714 GCGCTGGTGTATATCGAATGA 58.327 47.619 0.00 0.00 0.00 2.57
1653 1928 4.009675 GACTAATCAGCACCACATTTCCA 58.990 43.478 0.00 0.00 0.00 3.53
1713 1988 5.748670 TGTACATCTAGGCCTTGTTGTTA 57.251 39.130 28.10 18.16 0.00 2.41
1832 2112 9.749340 TTCCTAAATCTATGATCATGCATCAAT 57.251 29.630 18.72 0.00 45.06 2.57
1869 2149 9.868277 CAGCCATTTTAATTATTTACTTCCACA 57.132 29.630 0.00 0.00 0.00 4.17
1896 2176 4.384846 GCTTGCTGTCAATGATGTTTTCTG 59.615 41.667 0.00 0.00 0.00 3.02
1946 2226 6.748333 TTAGAGAACTCATCAGCCATTTTG 57.252 37.500 4.64 0.00 0.00 2.44
2001 2281 6.382282 TCTGACTATCCATGTTTCAGAGATGT 59.618 38.462 0.00 0.00 38.20 3.06
2066 2347 8.589338 ACTGTACTGAGATGAGAAAGTAAACAT 58.411 33.333 6.77 0.00 0.00 2.71
2145 2426 4.464008 AGTGAGAAGTTTTTGCCAGATGA 58.536 39.130 0.00 0.00 0.00 2.92
2328 2609 4.045636 GCAGAAAGCCTTGACAAAAAGA 57.954 40.909 0.00 0.00 37.23 2.52
2408 3216 5.068855 TGGCAAATCAACAGACATTCAAGAA 59.931 36.000 0.00 0.00 0.00 2.52
2422 3230 3.005684 AGAGTCGCAAATTGGCAAATCAA 59.994 39.130 3.01 0.00 0.00 2.57
2424 3232 2.919229 CAGAGTCGCAAATTGGCAAATC 59.081 45.455 3.01 0.00 0.00 2.17
2425 3233 2.557924 TCAGAGTCGCAAATTGGCAAAT 59.442 40.909 3.01 0.00 0.00 2.32
2431 3239 5.459762 ACAAAATGTTCAGAGTCGCAAATTG 59.540 36.000 0.00 0.00 0.00 2.32
2543 3351 0.840288 TAGCTGGGGTGCCTGAGAAA 60.840 55.000 0.00 0.00 0.00 2.52
2633 3441 1.726853 GAAGAGGTCCAACACATCCG 58.273 55.000 0.00 0.00 36.38 4.18
2696 3504 2.245379 AGGGCAGCCATTGGGGTAA 61.245 57.895 15.19 0.00 44.97 2.85
2784 3592 6.953520 AGTATGATCCAAACATCCTTTTTCCA 59.046 34.615 0.00 0.00 0.00 3.53
2806 3618 7.672660 TGGGATTTTACAGTGAGAGTAGAAGTA 59.327 37.037 0.00 0.00 0.00 2.24
2819 3631 5.079643 ACAAGAATGCTGGGATTTTACAGT 58.920 37.500 0.00 0.00 37.07 3.55
2845 3658 1.064003 TCAGCTTAGAAACAGGGGCA 58.936 50.000 0.00 0.00 0.00 5.36
2865 3678 7.723382 AGACAGGAATGGGGATATCTATTCTA 58.277 38.462 18.44 2.92 31.83 2.10
2953 3766 4.227982 TGTATATATGGAGCATGTGGGCAT 59.772 41.667 0.00 0.00 35.83 4.40
2956 3769 5.682234 TCTGTATATATGGAGCATGTGGG 57.318 43.478 0.00 0.00 0.00 4.61
2983 3796 2.764572 GAGACCCGGGATAAGTGAGAAA 59.235 50.000 32.02 0.00 0.00 2.52
2993 3809 0.546747 TTTCAGTGGAGACCCGGGAT 60.547 55.000 32.02 16.23 34.29 3.85
3037 3853 3.929610 GCTTCCACTGCTAGTTTACAGAG 59.070 47.826 2.53 0.00 37.35 3.35
3129 3945 6.599638 GGAAGAATACCAGGATATTACATGGC 59.400 42.308 0.00 0.00 44.23 4.40
3177 3995 0.108585 AAGCTCCTGCCTCGAAAACA 59.891 50.000 0.00 0.00 40.80 2.83
3226 4044 2.412325 CCAGTAAAACGGCAAAGTAGCG 60.412 50.000 0.00 0.00 34.64 4.26
3381 4199 9.819267 AAGGTCATGTATTTAAAAACGGAAAAA 57.181 25.926 0.00 0.00 0.00 1.94
3385 4203 7.513371 ACAAGGTCATGTATTTAAAAACGGA 57.487 32.000 0.00 0.00 0.00 4.69
3448 4266 9.860898 AGGGTACTAACATTTTTACGTACTAAG 57.139 33.333 0.00 0.00 0.00 2.18
3708 4693 6.016555 AGGAAGGCATACAAAATACTTTGGT 58.983 36.000 1.28 0.00 45.30 3.67
3712 4697 6.494059 AGGAAGGAAGGCATACAAAATACTT 58.506 36.000 0.00 0.00 0.00 2.24
3727 4712 6.319911 GGGAATACATTTTCTGAGGAAGGAAG 59.680 42.308 0.00 0.00 32.61 3.46
3746 4731 7.093068 TGCAGTTCATAGTTTACAGAGGGAATA 60.093 37.037 0.00 0.00 0.00 1.75
3748 4733 5.012664 TGCAGTTCATAGTTTACAGAGGGAA 59.987 40.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.