Multiple sequence alignment - TraesCS4B01G228100

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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 TraesCS4B01G228100 chr4B 100.000 3989 0 0 1 3989 477143860 477147848 0.000000e+00 7367.0
1 TraesCS4B01G228100 chr4B 96.907 97 3 0 3290 3386 477147245 477147149 3.190000e-36 163.0
2 TraesCS4B01G228100 chr4B 82.645 121 18 3 763 881 260063546 260063665 1.960000e-18 104.0
3 TraesCS4B01G228100 chr4A 96.259 2566 85 7 776 3337 69979341 69981899 0.000000e+00 4196.0
4 TraesCS4B01G228100 chr4A 96.580 614 15 4 3380 3987 69981900 69982513 0.000000e+00 1013.0
5 TraesCS4B01G228100 chr4A 83.769 727 82 16 6 724 69978496 69979194 0.000000e+00 656.0
6 TraesCS4B01G228100 chr4D 96.470 2351 75 5 948 3292 388821183 388823531 0.000000e+00 3875.0
7 TraesCS4B01G228100 chr4D 88.455 615 57 11 3384 3989 388823530 388824139 0.000000e+00 730.0
8 TraesCS4B01G228100 chr4D 91.473 258 13 5 651 902 388820924 388821178 2.950000e-91 346.0
9 TraesCS4B01G228100 chr4D 77.358 159 31 5 721 878 322890042 322889888 5.490000e-14 89.8
10 TraesCS4B01G228100 chr2B 94.545 110 3 3 3277 3386 206371289 206371183 2.470000e-37 167.0
11 TraesCS4B01G228100 chr2B 95.238 105 2 2 3285 3387 629108528 629108631 3.190000e-36 163.0
12 TraesCS4B01G228100 chr2B 93.458 107 5 1 3282 3386 629108638 629108532 1.480000e-34 158.0
13 TraesCS4B01G228100 chr2B 94.949 99 3 1 3290 3386 208229072 208229170 1.920000e-33 154.0
14 TraesCS4B01G228100 chr2B 88.608 79 8 1 602 680 53668656 53668579 1.180000e-15 95.3
15 TraesCS4B01G228100 chr6B 94.393 107 5 1 3288 3393 544667044 544666938 3.190000e-36 163.0
16 TraesCS4B01G228100 chr7A 93.519 108 4 2 3288 3393 505369779 505369885 1.480000e-34 158.0
17 TraesCS4B01G228100 chr2A 92.593 108 7 1 3285 3392 174332707 174332601 1.920000e-33 154.0
18 TraesCS4B01G228100 chr1A 87.786 131 9 6 3286 3411 561333799 561333671 3.210000e-31 147.0


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 TraesCS4B01G228100 chr4B 477143860 477147848 3988 False 7367.000000 7367 100.000000 1 3989 1 chr4B.!!$F2 3988
1 TraesCS4B01G228100 chr4A 69978496 69982513 4017 False 1955.000000 4196 92.202667 6 3987 3 chr4A.!!$F1 3981
2 TraesCS4B01G228100 chr4D 388820924 388824139 3215 False 1650.333333 3875 92.132667 651 3989 3 chr4D.!!$F1 3338

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
191 193 0.033306 GAACCTCCTCGGGGTAGAGT 60.033 60.0 0.0 0.00 35.83 3.24 F
510 517 0.104120 TACCGGCAATGATCACGAGG 59.896 55.0 0.0 2.69 0.00 4.63 F
1834 1956 0.037326 TAAGGCTGTGGAGCTGTTCG 60.037 55.0 0.0 0.00 45.44 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1427 0.183971 TAGAGGCGAAGAGGAGGAGG 59.816 60.000 0.0 0.0 0.00 4.30 R
2313 2435 0.459585 CGCTTATACACCCAGCACGT 60.460 55.000 0.0 0.0 32.71 4.49 R
3367 3491 3.269592 TCCTACTCCCTCTGTTCCAAA 57.730 47.619 0.0 0.0 0.00 3.28 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.252215 TACCGTGGCATTCGACTCCA 61.252 55.000 0.00 0.00 0.00 3.86
100 102 3.550842 GCAGAAGTGGCTCGACAATTTTT 60.551 43.478 0.00 0.00 0.00 1.94
135 137 2.505498 CCGCTCGCACATACGACAC 61.505 63.158 0.00 0.00 37.09 3.67
151 153 1.449601 CACGGTGGCATGGAGGTAC 60.450 63.158 0.00 0.00 0.00 3.34
183 185 2.492090 CGAGCTGAACCTCCTCGG 59.508 66.667 0.00 0.00 43.33 4.63
191 193 0.033306 GAACCTCCTCGGGGTAGAGT 60.033 60.000 0.00 0.00 35.83 3.24
192 194 1.213926 GAACCTCCTCGGGGTAGAGTA 59.786 57.143 0.00 0.00 35.83 2.59
193 195 0.845337 ACCTCCTCGGGGTAGAGTAG 59.155 60.000 0.00 0.00 36.56 2.57
194 196 0.110869 CCTCCTCGGGGTAGAGTAGG 59.889 65.000 0.00 0.00 37.89 3.18
195 197 0.845337 CTCCTCGGGGTAGAGTAGGT 59.155 60.000 0.00 0.00 36.56 3.08
196 198 0.842635 TCCTCGGGGTAGAGTAGGTC 59.157 60.000 0.00 0.00 36.56 3.85
197 199 0.534652 CCTCGGGGTAGAGTAGGTCG 60.535 65.000 0.00 0.00 36.56 4.79
198 200 0.467384 CTCGGGGTAGAGTAGGTCGA 59.533 60.000 0.00 0.00 33.75 4.20
199 201 0.467384 TCGGGGTAGAGTAGGTCGAG 59.533 60.000 0.00 0.00 0.00 4.04
204 206 1.767681 GGTAGAGTAGGTCGAGGAGGA 59.232 57.143 0.00 0.00 0.00 3.71
233 235 1.384643 GCCCCTCCTATGTGGACCT 60.385 63.158 0.00 0.00 40.56 3.85
275 277 2.697147 AAACCGCCTGGCTGATGTGT 62.697 55.000 17.38 0.94 39.70 3.72
277 279 1.522355 CCGCCTGGCTGATGTGTAG 60.522 63.158 17.92 0.00 0.00 2.74
279 281 2.176273 GCCTGGCTGATGTGTAGCG 61.176 63.158 12.43 0.00 42.03 4.26
280 282 1.219124 CCTGGCTGATGTGTAGCGT 59.781 57.895 0.00 0.00 42.03 5.07
285 287 1.536284 GGCTGATGTGTAGCGTACCTC 60.536 57.143 0.00 0.00 42.03 3.85
291 293 2.117156 TGTAGCGTACCTCCGAGGC 61.117 63.158 14.86 0.13 39.63 4.70
298 300 0.112801 GTACCTCCGAGGCTAGGGAT 59.887 60.000 14.86 2.46 39.63 3.85
301 303 1.834378 CTCCGAGGCTAGGGATGCA 60.834 63.158 14.03 0.00 0.00 3.96
307 309 2.772287 GAGGCTAGGGATGCATTGTAC 58.228 52.381 0.00 0.00 0.00 2.90
321 323 3.120199 GCATTGTACATGCAGAAGTTCGT 60.120 43.478 19.12 0.00 44.00 3.85
322 324 4.641954 CATTGTACATGCAGAAGTTCGTC 58.358 43.478 0.00 0.00 0.00 4.20
370 377 6.179040 AGCTTGCATTCTTTGTAGAGAAGAT 58.821 36.000 0.00 0.00 38.90 2.40
376 383 7.607607 TGCATTCTTTGTAGAGAAGATAAGCAA 59.392 33.333 0.00 0.00 38.90 3.91
377 384 8.121708 GCATTCTTTGTAGAGAAGATAAGCAAG 58.878 37.037 0.00 0.00 38.90 4.01
381 388 5.620738 TGTAGAGAAGATAAGCAAGGCAT 57.379 39.130 0.00 0.00 0.00 4.40
407 414 2.600769 AGGACGAGGAGCACCGTT 60.601 61.111 0.00 0.00 39.30 4.44
409 416 2.649034 GACGAGGAGCACCGTTCA 59.351 61.111 0.00 0.00 39.30 3.18
414 421 3.056328 GGAGCACCGTTCAAGGGC 61.056 66.667 0.00 0.00 35.02 5.19
416 423 3.842925 GAGCACCGTTCAAGGGCCA 62.843 63.158 6.18 0.00 35.02 5.36
422 429 2.032681 GTTCAAGGGCCAGCGTCT 59.967 61.111 6.18 0.00 0.00 4.18
425 432 1.899437 TTCAAGGGCCAGCGTCTAGG 61.899 60.000 6.18 0.00 0.00 3.02
448 455 4.212214 GTCGATGATTTATTCCACCAGCTC 59.788 45.833 0.00 0.00 0.00 4.09
460 467 1.227380 CCAGCTCGACAGGTATGGC 60.227 63.158 0.00 0.00 0.00 4.40
461 468 1.227380 CAGCTCGACAGGTATGGCC 60.227 63.158 0.00 0.00 37.58 5.36
467 474 2.285069 ACAGGTATGGCCGGGACA 60.285 61.111 4.28 4.28 43.70 4.02
471 478 2.372074 GGTATGGCCGGGACAAGGA 61.372 63.158 6.69 0.00 0.00 3.36
474 481 0.619255 TATGGCCGGGACAAGGAAGA 60.619 55.000 6.69 0.00 0.00 2.87
510 517 0.104120 TACCGGCAATGATCACGAGG 59.896 55.000 0.00 2.69 0.00 4.63
512 519 1.815003 CGGCAATGATCACGAGGCA 60.815 57.895 14.81 0.00 0.00 4.75
519 526 2.284625 ATCACGAGGCAGGTCCCA 60.285 61.111 0.00 0.00 34.51 4.37
548 555 2.233922 AGGGGTGAACTACATCGACTTG 59.766 50.000 0.00 0.00 0.00 3.16
551 558 3.251571 GGTGAACTACATCGACTTGGAC 58.748 50.000 0.00 0.00 0.00 4.02
557 564 1.475403 ACATCGACTTGGACGAGGAT 58.525 50.000 9.56 0.00 42.68 3.24
558 565 1.135139 ACATCGACTTGGACGAGGATG 59.865 52.381 9.56 0.00 42.68 3.51
559 566 1.405463 CATCGACTTGGACGAGGATGA 59.595 52.381 0.00 0.00 42.68 2.92
560 567 0.809385 TCGACTTGGACGAGGATGAC 59.191 55.000 0.00 0.00 34.85 3.06
561 568 0.811915 CGACTTGGACGAGGATGACT 59.188 55.000 0.00 0.00 0.00 3.41
562 569 1.202582 CGACTTGGACGAGGATGACTT 59.797 52.381 0.00 0.00 0.00 3.01
563 570 2.732597 CGACTTGGACGAGGATGACTTC 60.733 54.545 0.00 0.00 0.00 3.01
565 572 1.472878 CTTGGACGAGGATGACTTCGA 59.527 52.381 8.54 0.00 46.05 3.71
566 573 0.809385 TGGACGAGGATGACTTCGAC 59.191 55.000 8.54 2.79 46.05 4.20
567 574 0.248134 GGACGAGGATGACTTCGACG 60.248 60.000 8.54 0.00 46.05 5.12
573 580 2.015587 AGGATGACTTCGACGAGTACC 58.984 52.381 0.00 4.30 0.00 3.34
589 596 4.618965 GAGTACCGTGAAAAGAAGTGAGT 58.381 43.478 0.00 0.00 0.00 3.41
599 606 8.074972 CGTGAAAAGAAGTGAGTAGTAGTAGTT 58.925 37.037 0.00 0.00 0.00 2.24
600 607 9.396938 GTGAAAAGAAGTGAGTAGTAGTAGTTC 57.603 37.037 0.00 0.00 0.00 3.01
617 624 5.886474 AGTAGTTCGATGATCTAGTGTGGAA 59.114 40.000 0.00 0.00 0.00 3.53
618 625 5.000012 AGTTCGATGATCTAGTGTGGAAC 58.000 43.478 0.00 0.00 34.33 3.62
627 634 1.827969 CTAGTGTGGAACTGAGGAGGG 59.172 57.143 0.00 0.00 40.26 4.30
644 651 3.260380 GGAGGGAGTGTGATGATCTATGG 59.740 52.174 0.00 0.00 0.00 2.74
647 654 3.556633 GGGAGTGTGATGATCTATGGCAG 60.557 52.174 0.00 0.00 0.00 4.85
683 690 8.836268 TTATCTAGTGTGGTGTCGTTTTAATT 57.164 30.769 0.00 0.00 0.00 1.40
684 691 7.739498 ATCTAGTGTGGTGTCGTTTTAATTT 57.261 32.000 0.00 0.00 0.00 1.82
750 763 7.591006 ATGAATCATGTTCATGTTTGAAAGC 57.409 32.000 17.31 1.63 43.29 3.51
754 767 8.524870 AATCATGTTCATGTTTGAAAGCTTAC 57.475 30.769 0.00 0.00 43.29 2.34
768 781 3.577805 AGCTTACCAAGACACCAGTTT 57.422 42.857 0.00 0.00 0.00 2.66
770 783 5.043737 AGCTTACCAAGACACCAGTTTTA 57.956 39.130 0.00 0.00 0.00 1.52
919 1037 4.609947 GCCAAATTGCGAATATCATGTCA 58.390 39.130 0.00 0.00 0.00 3.58
920 1038 4.678287 GCCAAATTGCGAATATCATGTCAG 59.322 41.667 0.00 0.00 0.00 3.51
921 1039 4.678287 CCAAATTGCGAATATCATGTCAGC 59.322 41.667 0.00 0.00 0.00 4.26
922 1040 5.275494 CAAATTGCGAATATCATGTCAGCA 58.725 37.500 0.00 0.00 0.00 4.41
923 1041 3.950087 TTGCGAATATCATGTCAGCAC 57.050 42.857 0.00 0.00 32.57 4.40
924 1042 3.183793 TGCGAATATCATGTCAGCACT 57.816 42.857 0.00 0.00 0.00 4.40
925 1043 3.126073 TGCGAATATCATGTCAGCACTC 58.874 45.455 0.00 0.00 0.00 3.51
951 1069 1.219124 CTGCCGTAGCACCTCACAT 59.781 57.895 0.00 0.00 46.52 3.21
958 1076 2.610479 CGTAGCACCTCACATGTCAGTT 60.610 50.000 0.00 0.00 0.00 3.16
959 1077 1.888215 AGCACCTCACATGTCAGTTG 58.112 50.000 0.00 0.00 0.00 3.16
962 1080 2.618241 GCACCTCACATGTCAGTTGAAA 59.382 45.455 0.00 0.00 0.00 2.69
1013 1132 1.148310 AGTTTGATGAACCTGTCGCG 58.852 50.000 0.00 0.00 39.13 5.87
1068 1190 1.000019 CGGACTCCTCCACCTGGTA 60.000 63.158 0.00 0.00 36.12 3.25
1407 1529 2.266055 GCAGCGTCTGGTAGCCTT 59.734 61.111 8.57 0.00 31.21 4.35
1635 1757 3.824443 CCGTGGTAATTTTCAGGGAGTTT 59.176 43.478 11.62 0.00 40.27 2.66
1651 1773 0.821711 GTTTGTGGGGCTGCAGTGTA 60.822 55.000 16.64 0.00 0.00 2.90
1681 1803 3.136123 CTGGGACCATGGCAAGCG 61.136 66.667 13.04 0.00 0.00 4.68
1686 1808 1.675641 GACCATGGCAAGCGTCCTT 60.676 57.895 13.04 0.00 0.00 3.36
1751 1873 2.614057 GGGAGGTGTTTGATAAGATGCG 59.386 50.000 0.00 0.00 0.00 4.73
1834 1956 0.037326 TAAGGCTGTGGAGCTGTTCG 60.037 55.000 0.00 0.00 45.44 3.95
1852 1974 2.752030 TCGTGAGGATGGAGAAGGATT 58.248 47.619 0.00 0.00 0.00 3.01
1879 2001 5.735285 TGAGCCAGATAGGATGACATTAG 57.265 43.478 0.00 0.00 41.22 1.73
1931 2053 2.364970 CAGCATTTTCACTGGGGAAACA 59.635 45.455 0.00 0.00 36.56 2.83
1932 2054 3.007182 CAGCATTTTCACTGGGGAAACAT 59.993 43.478 0.00 0.00 36.56 2.71
1989 2111 3.872771 CCAATATGTTGCTGGAAAATGCC 59.127 43.478 0.00 0.00 33.90 4.40
2161 2283 0.467384 CATGCTAGGACAGGGTCTGG 59.533 60.000 0.00 0.00 35.51 3.86
2234 2356 2.669391 GCTTCTTGGATGTTGGAAAGCG 60.669 50.000 0.00 0.00 0.00 4.68
2274 2396 7.411808 TGACTAGTAGATATCAGATAACCCCC 58.588 42.308 3.59 0.00 0.00 5.40
2280 2402 4.916424 AGATATCAGATAACCCCCAAAGCT 59.084 41.667 5.32 0.00 0.00 3.74
2313 2435 3.026707 TGTATGGTGGATCTTCTCGGA 57.973 47.619 0.00 0.00 0.00 4.55
3221 3344 6.545298 GGGAGTGAGCATCTAATTTTCTGATT 59.455 38.462 0.00 0.00 34.92 2.57
3299 3423 1.293924 CAATGCAAGCTACTCCCTCG 58.706 55.000 0.00 0.00 0.00 4.63
3371 3495 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3372 3496 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3373 3497 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3374 3498 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3375 3499 8.352201 CAAAGTTGAGTCATCTATTTTGGAACA 58.648 33.333 4.14 0.00 35.65 3.18
3376 3500 7.678947 AGTTGAGTCATCTATTTTGGAACAG 57.321 36.000 1.70 0.00 42.39 3.16
3377 3501 7.453393 AGTTGAGTCATCTATTTTGGAACAGA 58.547 34.615 1.70 0.00 42.39 3.41
3378 3502 7.605691 AGTTGAGTCATCTATTTTGGAACAGAG 59.394 37.037 1.70 0.00 42.39 3.35
3417 3541 3.282021 TCTTTGATGTATGAAGGCAGGC 58.718 45.455 0.00 0.00 0.00 4.85
3485 3609 1.912043 CTCCCACCTGAACAAGATCCT 59.088 52.381 0.00 0.00 0.00 3.24
3555 3679 8.153550 GTGATTAATCAGGATCTCATACAGGTT 58.846 37.037 18.47 0.00 37.51 3.50
3815 3946 8.817100 CATGGTTTTGTTTTCCTCTTAGTTTTC 58.183 33.333 0.00 0.00 0.00 2.29
3848 3981 7.440523 AGCTGTGTAAGTCTTCCTTTTTATG 57.559 36.000 0.00 0.00 34.46 1.90
3882 4015 2.125461 TATGAGAACGATGCGCTGAG 57.875 50.000 9.73 1.49 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.739813 AGTCGAATGCCACGGTAAGC 60.740 55.000 0.00 0.00 0.00 3.09
14 15 0.108520 GGAGTCGAATGCCACGGTAA 60.109 55.000 0.00 0.00 0.00 2.85
34 35 1.078426 GCATAGTGGCCCGACAGTT 60.078 57.895 0.00 0.00 0.00 3.16
53 54 0.932123 CCTCGCACATGATCTCGACG 60.932 60.000 0.00 0.00 0.00 5.12
55 56 1.735973 CCCTCGCACATGATCTCGA 59.264 57.895 0.00 1.54 0.00 4.04
57 58 1.596477 GCCCCTCGCACATGATCTC 60.596 63.158 0.00 0.00 37.47 2.75
100 102 0.108804 CGGCAAGCTTCGGAGTCTAA 60.109 55.000 0.00 0.00 0.00 2.10
101 103 1.511305 CGGCAAGCTTCGGAGTCTA 59.489 57.895 0.00 0.00 0.00 2.59
102 104 2.262915 CGGCAAGCTTCGGAGTCT 59.737 61.111 0.00 0.00 0.00 3.24
103 105 3.491652 GCGGCAAGCTTCGGAGTC 61.492 66.667 9.31 0.00 44.04 3.36
127 129 1.153449 CCATGCCACCGTGTCGTAT 60.153 57.895 0.00 0.00 0.00 3.06
135 137 2.202878 CGTACCTCCATGCCACCG 60.203 66.667 0.00 0.00 0.00 4.94
172 174 0.033306 ACTCTACCCCGAGGAGGTTC 60.033 60.000 7.43 0.00 38.89 3.62
183 185 1.202794 CCTCCTCGACCTACTCTACCC 60.203 61.905 0.00 0.00 0.00 3.69
191 193 1.219824 AACCCCTCCTCCTCGACCTA 61.220 60.000 0.00 0.00 0.00 3.08
192 194 2.517582 GAACCCCTCCTCCTCGACCT 62.518 65.000 0.00 0.00 0.00 3.85
193 195 2.039137 AACCCCTCCTCCTCGACC 59.961 66.667 0.00 0.00 0.00 4.79
194 196 2.059190 GGAACCCCTCCTCCTCGAC 61.059 68.421 0.00 0.00 41.61 4.20
195 197 2.363361 GGAACCCCTCCTCCTCGA 59.637 66.667 0.00 0.00 41.61 4.04
233 235 3.832527 CCTTCTCCTTTTTGAGGGACAA 58.167 45.455 0.00 0.00 46.31 3.18
240 242 2.360801 CGGTTTGCCTTCTCCTTTTTGA 59.639 45.455 0.00 0.00 0.00 2.69
241 243 2.742774 CGGTTTGCCTTCTCCTTTTTG 58.257 47.619 0.00 0.00 0.00 2.44
265 267 0.460311 AGGTACGCTACACATCAGCC 59.540 55.000 0.00 0.00 35.53 4.85
275 277 0.250209 CTAGCCTCGGAGGTACGCTA 60.250 60.000 24.30 17.08 37.80 4.26
277 279 2.553727 CCTAGCCTCGGAGGTACGC 61.554 68.421 24.30 10.56 37.80 4.42
279 281 0.112801 ATCCCTAGCCTCGGAGGTAC 59.887 60.000 24.30 9.56 37.80 3.34
280 282 0.112606 CATCCCTAGCCTCGGAGGTA 59.887 60.000 24.30 14.17 37.80 3.08
285 287 0.604780 CAATGCATCCCTAGCCTCGG 60.605 60.000 0.00 0.00 0.00 4.63
301 303 3.367932 CGACGAACTTCTGCATGTACAAT 59.632 43.478 0.00 0.00 0.00 2.71
307 309 0.994995 CCTCGACGAACTTCTGCATG 59.005 55.000 0.00 0.00 0.00 4.06
321 323 2.593725 CGTCCGGATAGGCCTCGA 60.594 66.667 9.68 0.00 40.77 4.04
322 324 3.671411 CCGTCCGGATAGGCCTCG 61.671 72.222 9.68 7.02 40.77 4.63
341 348 0.524862 CAAAGAATGCAAGCTCCGCT 59.475 50.000 9.28 0.00 42.56 5.52
358 365 5.420725 TGCCTTGCTTATCTTCTCTACAA 57.579 39.130 0.00 0.00 0.00 2.41
359 366 5.129320 TCATGCCTTGCTTATCTTCTCTACA 59.871 40.000 0.00 0.00 0.00 2.74
361 368 5.876651 TCATGCCTTGCTTATCTTCTCTA 57.123 39.130 0.00 0.00 0.00 2.43
362 369 4.767578 TCATGCCTTGCTTATCTTCTCT 57.232 40.909 0.00 0.00 0.00 3.10
370 377 3.614092 CTCCTTCTTCATGCCTTGCTTA 58.386 45.455 0.00 0.00 0.00 3.09
376 383 0.539051 CGTCCTCCTTCTTCATGCCT 59.461 55.000 0.00 0.00 0.00 4.75
377 384 0.537188 TCGTCCTCCTTCTTCATGCC 59.463 55.000 0.00 0.00 0.00 4.40
381 388 1.840737 CTCCTCGTCCTCCTTCTTCA 58.159 55.000 0.00 0.00 0.00 3.02
407 414 2.359169 CCTAGACGCTGGCCCTTGA 61.359 63.158 0.00 0.00 0.00 3.02
409 416 2.284699 ACCTAGACGCTGGCCCTT 60.285 61.111 0.00 0.00 0.00 3.95
414 421 0.955178 ATCATCGACCTAGACGCTGG 59.045 55.000 11.08 0.00 0.00 4.85
416 423 5.455056 AATAAATCATCGACCTAGACGCT 57.545 39.130 0.00 0.00 0.00 5.07
422 429 5.741964 GCTGGTGGAATAAATCATCGACCTA 60.742 44.000 8.15 0.00 42.80 3.08
425 432 4.130118 AGCTGGTGGAATAAATCATCGAC 58.870 43.478 0.00 0.00 0.00 4.20
448 455 3.151710 TCCCGGCCATACCTGTCG 61.152 66.667 2.24 0.00 35.61 4.35
460 467 1.299976 CCCTTCTTCCTTGTCCCGG 59.700 63.158 0.00 0.00 0.00 5.73
461 468 1.299976 CCCCTTCTTCCTTGTCCCG 59.700 63.158 0.00 0.00 0.00 5.14
467 474 0.405973 GCTTCACCCCCTTCTTCCTT 59.594 55.000 0.00 0.00 0.00 3.36
471 478 2.125766 GACGGCTTCACCCCCTTCTT 62.126 60.000 0.00 0.00 33.26 2.52
474 481 1.229400 TAGACGGCTTCACCCCCTT 60.229 57.895 0.00 0.00 33.26 3.95
503 510 3.311110 GTGGGACCTGCCTCGTGA 61.311 66.667 0.00 0.00 36.66 4.35
510 517 1.222936 CTCCATCAGTGGGACCTGC 59.777 63.158 0.00 0.00 46.06 4.85
512 519 4.488303 CCTCCATCAGTGGGACCT 57.512 61.111 0.00 0.00 46.06 3.85
519 526 2.188817 GTAGTTCACCCCTCCATCAGT 58.811 52.381 0.00 0.00 0.00 3.41
532 539 2.815503 TCGTCCAAGTCGATGTAGTTCA 59.184 45.455 0.00 0.00 32.30 3.18
548 555 0.248134 CGTCGAAGTCATCCTCGTCC 60.248 60.000 0.00 0.00 0.00 4.79
551 558 0.727970 ACTCGTCGAAGTCATCCTCG 59.272 55.000 0.00 0.00 0.00 4.63
566 573 3.635331 TCACTTCTTTTCACGGTACTCG 58.365 45.455 0.00 0.00 45.88 4.18
567 574 4.618965 ACTCACTTCTTTTCACGGTACTC 58.381 43.478 0.00 0.00 0.00 2.59
573 580 7.583230 ACTACTACTACTCACTTCTTTTCACG 58.417 38.462 0.00 0.00 0.00 4.35
589 596 7.656542 CCACACTAGATCATCGAACTACTACTA 59.343 40.741 0.00 0.00 0.00 1.82
599 606 4.270008 TCAGTTCCACACTAGATCATCGA 58.730 43.478 0.00 0.00 32.76 3.59
600 607 4.498850 CCTCAGTTCCACACTAGATCATCG 60.499 50.000 0.00 0.00 32.76 3.84
617 624 1.077828 TCATCACACTCCCTCCTCAGT 59.922 52.381 0.00 0.00 0.00 3.41
618 625 1.857965 TCATCACACTCCCTCCTCAG 58.142 55.000 0.00 0.00 0.00 3.35
627 634 4.333913 ACTGCCATAGATCATCACACTC 57.666 45.455 0.00 0.00 0.00 3.51
710 717 9.661563 ACATGATTCATTGCATATTCAAAACTT 57.338 25.926 0.00 0.00 0.00 2.66
711 718 9.661563 AACATGATTCATTGCATATTCAAAACT 57.338 25.926 0.00 0.00 0.00 2.66
712 719 9.910511 GAACATGATTCATTGCATATTCAAAAC 57.089 29.630 0.00 0.00 30.44 2.43
714 721 9.825109 ATGAACATGATTCATTGCATATTCAAA 57.175 25.926 14.13 0.00 40.16 2.69
715 722 9.255304 CATGAACATGATTCATTGCATATTCAA 57.745 29.630 16.15 0.00 40.16 2.69
716 723 8.417884 ACATGAACATGATTCATTGCATATTCA 58.582 29.630 19.56 0.00 40.78 2.57
750 763 6.485313 TGATGTAAAACTGGTGTCTTGGTAAG 59.515 38.462 0.00 0.00 0.00 2.34
754 767 5.707298 AGATGATGTAAAACTGGTGTCTTGG 59.293 40.000 0.00 0.00 0.00 3.61
768 781 6.484364 TCTCTGCCATAACAGATGATGTAA 57.516 37.500 0.00 0.00 45.34 2.41
770 783 5.363562 TTCTCTGCCATAACAGATGATGT 57.636 39.130 0.00 0.00 45.34 3.06
910 1028 2.498885 ACTGCTGAGTGCTGACATGATA 59.501 45.455 0.00 0.00 42.27 2.15
911 1029 1.278413 ACTGCTGAGTGCTGACATGAT 59.722 47.619 0.00 0.00 42.27 2.45
912 1030 0.683412 ACTGCTGAGTGCTGACATGA 59.317 50.000 0.00 0.00 42.27 3.07
913 1031 0.796927 CACTGCTGAGTGCTGACATG 59.203 55.000 0.00 0.00 43.24 3.21
936 1054 0.246360 TGACATGTGAGGTGCTACGG 59.754 55.000 1.15 0.00 0.00 4.02
937 1055 1.067565 ACTGACATGTGAGGTGCTACG 60.068 52.381 16.98 0.00 0.00 3.51
940 1058 1.417517 TCAACTGACATGTGAGGTGCT 59.582 47.619 23.79 0.00 31.36 4.40
946 1064 4.398988 AGCAAACTTTCAACTGACATGTGA 59.601 37.500 1.15 0.00 0.00 3.58
951 1069 2.477694 CGCAGCAAACTTTCAACTGACA 60.478 45.455 0.00 0.00 0.00 3.58
1053 1175 1.006162 GAGTCTACCAGGTGGAGGAGT 59.994 57.143 5.75 3.33 38.94 3.85
1305 1427 0.183971 TAGAGGCGAAGAGGAGGAGG 59.816 60.000 0.00 0.00 0.00 4.30
1398 1520 1.303888 ACCGAGACGAAGGCTACCA 60.304 57.895 0.00 0.00 0.00 3.25
1407 1529 1.030488 GGATCTGGACACCGAGACGA 61.030 60.000 0.00 0.00 0.00 4.20
1513 1635 0.690762 AACACCTGGTAGGCATCGTT 59.309 50.000 0.00 0.00 39.63 3.85
1521 1643 3.063997 GCATTTCATCGAACACCTGGTAG 59.936 47.826 0.00 0.00 0.00 3.18
1635 1757 2.429930 GTACACTGCAGCCCCACA 59.570 61.111 15.27 0.00 0.00 4.17
1734 1856 3.438781 TGAACCGCATCTTATCAAACACC 59.561 43.478 0.00 0.00 0.00 4.16
1751 1873 5.805728 TCCAAGAAATAAGTCCTCTGAACC 58.194 41.667 0.00 0.00 0.00 3.62
1834 1956 2.158696 CCCAATCCTTCTCCATCCTCAC 60.159 54.545 0.00 0.00 0.00 3.51
1852 1974 1.770658 CATCCTATCTGGCTCAACCCA 59.229 52.381 0.00 0.00 37.83 4.51
1989 2111 2.612212 GTTGGCGTACATGTCCATTAGG 59.388 50.000 0.00 0.00 0.00 2.69
2161 2283 3.694566 ACAAAGGCAATAGAATCCGGTTC 59.305 43.478 0.00 4.94 37.08 3.62
2211 2333 1.533625 TTCCAACATCCAAGAAGCCG 58.466 50.000 0.00 0.00 0.00 5.52
2215 2337 2.582052 ACGCTTTCCAACATCCAAGAA 58.418 42.857 0.00 0.00 0.00 2.52
2274 2396 6.073385 CCATACATGTATAGTGCTCAGCTTTG 60.073 42.308 17.86 2.57 0.00 2.77
2280 2402 4.898861 TCCACCATACATGTATAGTGCTCA 59.101 41.667 28.60 16.81 35.03 4.26
2313 2435 0.459585 CGCTTATACACCCAGCACGT 60.460 55.000 0.00 0.00 32.71 4.49
2439 2561 1.945394 CTGAACAAACTGTCTGCTGCT 59.055 47.619 0.00 0.00 0.00 4.24
2998 3120 9.836864 TGTTAAGAATGCACTATGTGATAATCT 57.163 29.630 1.52 0.00 35.23 2.40
3221 3344 8.417106 TGTTGCTTTTACTGAACCAATAATCAA 58.583 29.630 0.00 0.00 0.00 2.57
3299 3423 7.454260 AAGTTGAGTCATCTATTTTGGAACC 57.546 36.000 4.14 0.00 0.00 3.62
3345 3469 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3346 3470 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3347 3471 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3348 3472 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3349 3473 8.352201 TGTTCCAAAATAGATGACTCAACTTTG 58.648 33.333 0.00 0.00 0.00 2.77
3350 3474 8.463930 TGTTCCAAAATAGATGACTCAACTTT 57.536 30.769 0.00 0.00 0.00 2.66
3351 3475 7.939039 TCTGTTCCAAAATAGATGACTCAACTT 59.061 33.333 0.00 0.00 28.72 2.66
3352 3476 7.453393 TCTGTTCCAAAATAGATGACTCAACT 58.547 34.615 0.00 0.00 28.72 3.16
3353 3477 7.148340 CCTCTGTTCCAAAATAGATGACTCAAC 60.148 40.741 0.00 0.00 32.88 3.18
3354 3478 6.881065 CCTCTGTTCCAAAATAGATGACTCAA 59.119 38.462 0.00 0.00 32.88 3.02
3355 3479 6.409704 CCTCTGTTCCAAAATAGATGACTCA 58.590 40.000 0.00 0.00 32.88 3.41
3356 3480 5.819901 CCCTCTGTTCCAAAATAGATGACTC 59.180 44.000 0.00 0.00 32.88 3.36
3357 3481 5.488919 TCCCTCTGTTCCAAAATAGATGACT 59.511 40.000 0.00 0.00 32.88 3.41
3358 3482 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
3359 3483 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
3360 3484 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
3361 3485 6.100424 CCTACTCCCTCTGTTCCAAAATAGAT 59.900 42.308 0.00 0.00 32.88 1.98
3362 3486 5.425539 CCTACTCCCTCTGTTCCAAAATAGA 59.574 44.000 0.00 0.00 32.42 1.98
3363 3487 5.425539 TCCTACTCCCTCTGTTCCAAAATAG 59.574 44.000 0.00 0.00 0.00 1.73
3364 3488 5.347124 TCCTACTCCCTCTGTTCCAAAATA 58.653 41.667 0.00 0.00 0.00 1.40
3365 3489 4.175962 TCCTACTCCCTCTGTTCCAAAAT 58.824 43.478 0.00 0.00 0.00 1.82
3366 3490 3.593942 TCCTACTCCCTCTGTTCCAAAA 58.406 45.455 0.00 0.00 0.00 2.44
3367 3491 3.269592 TCCTACTCCCTCTGTTCCAAA 57.730 47.619 0.00 0.00 0.00 3.28
3368 3492 3.491766 ATCCTACTCCCTCTGTTCCAA 57.508 47.619 0.00 0.00 0.00 3.53
3369 3493 4.834406 ATATCCTACTCCCTCTGTTCCA 57.166 45.455 0.00 0.00 0.00 3.53
3370 3494 6.316513 AGTTATATCCTACTCCCTCTGTTCC 58.683 44.000 0.00 0.00 0.00 3.62
3371 3495 7.842887 AAGTTATATCCTACTCCCTCTGTTC 57.157 40.000 0.00 0.00 0.00 3.18
3372 3496 8.068733 AGAAAGTTATATCCTACTCCCTCTGTT 58.931 37.037 0.00 0.00 0.00 3.16
3373 3497 7.597327 AGAAAGTTATATCCTACTCCCTCTGT 58.403 38.462 0.00 0.00 0.00 3.41
3374 3498 8.485578 AAGAAAGTTATATCCTACTCCCTCTG 57.514 38.462 0.00 0.00 0.00 3.35
3375 3499 8.929487 CAAAGAAAGTTATATCCTACTCCCTCT 58.071 37.037 0.00 0.00 0.00 3.69
3376 3500 8.925338 TCAAAGAAAGTTATATCCTACTCCCTC 58.075 37.037 0.00 0.00 0.00 4.30
3377 3501 8.855804 TCAAAGAAAGTTATATCCTACTCCCT 57.144 34.615 0.00 0.00 0.00 4.20
3378 3502 9.495572 CATCAAAGAAAGTTATATCCTACTCCC 57.504 37.037 0.00 0.00 0.00 4.30
3417 3541 3.819337 CCCAGAAAGCATGTATCCTGATG 59.181 47.826 0.00 0.00 0.00 3.07
3485 3609 4.316205 TCTGAAGAATCGCCGCTAATAA 57.684 40.909 0.00 0.00 0.00 1.40
3555 3679 4.457603 AGGTAGCATTGCAACGAAATACAA 59.542 37.500 11.91 0.00 0.00 2.41
3815 3946 4.926244 AGACTTACACAGCTATCGTGATG 58.074 43.478 9.47 2.41 37.80 3.07
3848 3981 6.755141 TCGTTCTCATAAATACTAACTGCACC 59.245 38.462 0.00 0.00 0.00 5.01
3882 4015 2.869897 CTGAACCGAGTAGAGTTGCTC 58.130 52.381 0.00 0.00 33.23 4.26
3890 4023 1.067565 TGAAGCTGCTGAACCGAGTAG 60.068 52.381 1.35 0.00 0.00 2.57
3962 4095 3.291584 CCTGAGCACTGTACAGAGGATA 58.708 50.000 29.30 11.04 34.07 2.59
3965 4098 0.108424 GCCTGAGCACTGTACAGAGG 60.108 60.000 29.30 23.31 39.53 3.69


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

AutoCloner maintained by Alex Coulton.