Multiple sequence alignment - TraesCS6B01G352600

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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 TraesCS6B01G352600 chr6B 100.000 2975 0 0 1 2975 618332395 618329421 0.000000e+00 5494.0
1 TraesCS6B01G352600 chr6B 94.028 1055 42 5 1172 2222 618143072 618142035 0.000000e+00 1580.0
2 TraesCS6B01G352600 chr6B 90.026 762 65 8 2222 2975 618141776 618141018 0.000000e+00 976.0
3 TraesCS6B01G352600 chr6B 88.910 523 37 6 644 1146 618143592 618143071 2.520000e-175 625.0
4 TraesCS6B01G352600 chr6B 95.804 286 9 1 1 286 618325238 618324956 2.700000e-125 459.0
5 TraesCS6B01G352600 chr6B 83.957 374 57 3 2603 2975 111549631 111550002 3.650000e-94 355.0
6 TraesCS6B01G352600 chr6B 83.690 374 59 2 2603 2975 111350399 111350771 4.720000e-93 351.0
7 TraesCS6B01G352600 chr6B 83.646 373 58 3 2603 2974 111337736 111338106 6.100000e-92 348.0
8 TraesCS6B01G352600 chr6B 90.511 137 5 5 293 428 618300067 618299938 1.100000e-39 174.0
9 TraesCS6B01G352600 chr6D 92.973 1295 66 11 776 2050 411222382 411221093 0.000000e+00 1864.0
10 TraesCS6B01G352600 chr6D 85.828 501 27 17 43 528 411402243 411401772 2.660000e-135 492.0
11 TraesCS6B01G352600 chr6A 93.470 1026 53 7 992 2013 555980565 555979550 0.000000e+00 1511.0
12 TraesCS6B01G352600 chr6A 90.317 537 31 9 1 528 555984017 555983493 0.000000e+00 684.0
13 TraesCS6B01G352600 chr6A 84.300 414 45 10 573 971 555981041 555980633 1.290000e-103 387.0
14 TraesCS6B01G352600 chr6A 80.363 331 60 4 2258 2585 425052210 425051882 2.290000e-61 246.0
15 TraesCS6B01G352600 chr5B 82.385 738 88 21 2258 2967 212188510 212189233 3.280000e-169 604.0
16 TraesCS6B01G352600 chr5B 87.726 277 34 0 2272 2548 592294251 592294527 1.030000e-84 324.0
17 TraesCS6B01G352600 chr2B 82.029 690 110 10 2265 2950 539698098 539697419 2.570000e-160 575.0
18 TraesCS6B01G352600 chr2B 79.238 761 102 21 2265 2973 754345078 754345834 2.070000e-131 479.0
19 TraesCS6B01G352600 chr5D 80.938 661 84 23 2258 2884 500124103 500124755 4.460000e-133 484.0
20 TraesCS6B01G352600 chr5D 85.867 375 52 1 2601 2975 296361163 296361536 5.980000e-107 398.0
21 TraesCS6B01G352600 chr1D 86.721 369 47 2 2608 2975 204083165 204082798 2.760000e-110 409.0
22 TraesCS6B01G352600 chr1D 93.548 62 4 0 581 642 462909621 462909560 3.160000e-15 93.5
23 TraesCS6B01G352600 chr1D 93.548 62 4 0 581 642 462916849 462916788 3.160000e-15 93.5
24 TraesCS6B01G352600 chr2D 86.327 373 49 2 2601 2973 496375553 496375923 3.570000e-109 405.0
25 TraesCS6B01G352600 chr2D 84.437 302 43 3 2258 2559 496357835 496358132 8.060000e-76 294.0
26 TraesCS6B01G352600 chr1B 86.059 373 52 0 2603 2975 9872764 9873136 4.620000e-108 401.0
27 TraesCS6B01G352600 chr1B 87.500 80 8 2 565 643 336392083 336392161 1.140000e-14 91.6
28 TraesCS6B01G352600 chr1B 86.076 79 10 1 563 640 49642070 49642148 1.900000e-12 84.2
29 TraesCS6B01G352600 chr3B 83.914 373 59 1 2601 2973 317606929 317606558 3.650000e-94 355.0
30 TraesCS6B01G352600 chr3B 82.301 113 16 4 532 641 367454176 367454287 8.780000e-16 95.3
31 TraesCS6B01G352600 chr3A 84.308 325 45 3 2270 2591 283092848 283092527 2.230000e-81 313.0
32 TraesCS6B01G352600 chr7D 91.429 70 4 2 571 639 631181377 631181309 8.780000e-16 95.3
33 TraesCS6B01G352600 chr7D 85.897 78 7 2 571 646 181597898 181597823 2.460000e-11 80.5
34 TraesCS6B01G352600 chr2A 91.667 60 5 0 580 639 768981319 768981378 1.900000e-12 84.2


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 TraesCS6B01G352600 chr6B 618329421 618332395 2974 True 5494.000000 5494 100.000000 1 2975 1 chr6B.!!$R3 2974
1 TraesCS6B01G352600 chr6B 618141018 618143592 2574 True 1060.333333 1580 90.988000 644 2975 3 chr6B.!!$R4 2331
2 TraesCS6B01G352600 chr6D 411221093 411222382 1289 True 1864.000000 1864 92.973000 776 2050 1 chr6D.!!$R1 1274
3 TraesCS6B01G352600 chr6A 555979550 555984017 4467 True 860.666667 1511 89.362333 1 2013 3 chr6A.!!$R2 2012
4 TraesCS6B01G352600 chr5B 212188510 212189233 723 False 604.000000 604 82.385000 2258 2967 1 chr5B.!!$F1 709
5 TraesCS6B01G352600 chr2B 539697419 539698098 679 True 575.000000 575 82.029000 2265 2950 1 chr2B.!!$R1 685
6 TraesCS6B01G352600 chr2B 754345078 754345834 756 False 479.000000 479 79.238000 2265 2973 1 chr2B.!!$F1 708
7 TraesCS6B01G352600 chr5D 500124103 500124755 652 False 484.000000 484 80.938000 2258 2884 1 chr5D.!!$F2 626

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
204 205 0.600255 GTACACTGTTCAGGCGCAGT 60.6 55.0 10.83 0.0 45.69 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 4582 1.286257 TCTGAGAGCTCTTCTAGGCCA 59.714 52.381 19.36 8.26 35.87 5.36 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
32 33 2.701107 GAGAGCTGTTGGGAAAGGTAC 58.299 52.381 0.00 0.00 0.00 3.34
38 39 5.930135 AGCTGTTGGGAAAGGTACATATAG 58.070 41.667 0.00 0.00 0.00 1.31
39 40 5.428783 AGCTGTTGGGAAAGGTACATATAGT 59.571 40.000 0.00 0.00 0.00 2.12
40 41 6.614087 AGCTGTTGGGAAAGGTACATATAGTA 59.386 38.462 0.00 0.00 0.00 1.82
72 73 2.752030 TGCAGGCTAGTGAAGGAGTAT 58.248 47.619 0.00 0.00 0.00 2.12
77 78 5.112686 CAGGCTAGTGAAGGAGTATCAAAC 58.887 45.833 0.00 0.00 36.25 2.93
81 82 4.899352 AGTGAAGGAGTATCAAACAGCT 57.101 40.909 0.00 0.00 36.25 4.24
82 83 4.573900 AGTGAAGGAGTATCAAACAGCTG 58.426 43.478 13.48 13.48 36.25 4.24
86 87 5.877012 TGAAGGAGTATCAAACAGCTGATTC 59.123 40.000 23.35 2.67 37.27 2.52
88 89 4.472833 AGGAGTATCAAACAGCTGATTCCT 59.527 41.667 23.35 14.46 37.87 3.36
105 106 6.730447 TGATTCCTGATCCCACTAAATCAAA 58.270 36.000 0.00 0.00 33.60 2.69
137 138 4.903010 AGTGAACCGCAACGCCGT 62.903 61.111 0.00 0.00 0.00 5.68
148 149 4.712425 ACGCCGTCCTTCGTTCCG 62.712 66.667 0.00 0.00 35.09 4.30
204 205 0.600255 GTACACTGTTCAGGCGCAGT 60.600 55.000 10.83 0.00 45.69 4.40
206 207 1.595109 CACTGTTCAGGCGCAGTCA 60.595 57.895 10.83 4.85 43.27 3.41
242 243 0.790814 GGAAAGGTGCTCGAAAGACG 59.209 55.000 0.00 0.00 44.09 4.18
264 273 4.045783 GAGCGTCAAAGATAGGTAGCTTC 58.954 47.826 0.00 0.00 33.51 3.86
291 300 3.837146 TCTGATGGAGGATTATGGAGCTC 59.163 47.826 4.71 4.71 0.00 4.09
312 321 3.942130 CCATCTTGGGGAACAGTTTTC 57.058 47.619 0.00 0.00 32.67 2.29
313 322 2.562738 CCATCTTGGGGAACAGTTTTCC 59.437 50.000 0.00 0.00 37.86 3.13
314 323 3.230134 CATCTTGGGGAACAGTTTTCCA 58.770 45.455 10.20 6.68 40.32 3.53
324 333 5.946377 GGGAACAGTTTTCCATGATACTTCT 59.054 40.000 10.20 0.00 40.32 2.85
325 334 7.110155 GGGAACAGTTTTCCATGATACTTCTA 58.890 38.462 10.20 0.00 40.32 2.10
337 346 9.083422 TCCATGATACTTCTATAAAGAGGACTG 57.917 37.037 0.00 0.00 33.20 3.51
338 347 8.310382 CCATGATACTTCTATAAAGAGGACTGG 58.690 40.741 0.00 0.00 33.20 4.00
353 362 3.713650 TGGCAGTACCAGAGAGGC 58.286 61.111 0.00 0.00 46.36 4.70
357 366 1.513158 CAGTACCAGAGAGGCGGTG 59.487 63.158 0.00 0.00 43.14 4.94
358 367 0.965866 CAGTACCAGAGAGGCGGTGA 60.966 60.000 0.00 0.00 43.14 4.02
395 404 2.819608 GCAACCTTGATGCTTTGGAGTA 59.180 45.455 0.00 0.00 40.64 2.59
397 406 2.699954 ACCTTGATGCTTTGGAGTACG 58.300 47.619 0.00 0.00 0.00 3.67
403 412 2.335316 TGCTTTGGAGTACGGTTTGT 57.665 45.000 0.00 0.00 0.00 2.83
404 413 2.645802 TGCTTTGGAGTACGGTTTGTT 58.354 42.857 0.00 0.00 0.00 2.83
405 414 3.018149 TGCTTTGGAGTACGGTTTGTTT 58.982 40.909 0.00 0.00 0.00 2.83
406 415 3.444388 TGCTTTGGAGTACGGTTTGTTTT 59.556 39.130 0.00 0.00 0.00 2.43
407 416 3.794564 GCTTTGGAGTACGGTTTGTTTTG 59.205 43.478 0.00 0.00 0.00 2.44
408 417 4.675933 GCTTTGGAGTACGGTTTGTTTTGT 60.676 41.667 0.00 0.00 0.00 2.83
425 434 1.840737 TGTCTCTAGAGGACACTGGC 58.159 55.000 19.67 0.00 38.57 4.85
448 457 2.708051 CATGACATGAGACTGCCAGTT 58.292 47.619 10.03 0.00 0.00 3.16
480 490 2.105821 AGTCCGGATTTTCACAACCTGA 59.894 45.455 7.81 0.00 0.00 3.86
528 538 5.599999 AGATACGATTGGTCTAACAGCTT 57.400 39.130 0.00 0.00 0.00 3.74
530 540 3.678056 ACGATTGGTCTAACAGCTTGA 57.322 42.857 0.00 0.00 0.00 3.02
531 541 4.002906 ACGATTGGTCTAACAGCTTGAA 57.997 40.909 0.00 0.00 0.00 2.69
532 542 4.385825 ACGATTGGTCTAACAGCTTGAAA 58.614 39.130 0.00 0.00 0.00 2.69
533 543 4.819630 ACGATTGGTCTAACAGCTTGAAAA 59.180 37.500 0.00 0.00 0.00 2.29
555 2957 9.550811 GAAAAGTATCCGGTTTAATTAGTTGTG 57.449 33.333 0.00 0.00 0.00 3.33
556 2958 8.851541 AAAGTATCCGGTTTAATTAGTTGTGA 57.148 30.769 0.00 0.00 0.00 3.58
557 2959 8.488651 AAGTATCCGGTTTAATTAGTTGTGAG 57.511 34.615 0.00 0.00 0.00 3.51
558 2960 7.618137 AGTATCCGGTTTAATTAGTTGTGAGT 58.382 34.615 0.00 0.00 0.00 3.41
560 2962 5.613329 TCCGGTTTAATTAGTTGTGAGTGT 58.387 37.500 0.00 0.00 0.00 3.55
561 2963 5.467399 TCCGGTTTAATTAGTTGTGAGTGTG 59.533 40.000 0.00 0.00 0.00 3.82
562 2964 5.467399 CCGGTTTAATTAGTTGTGAGTGTGA 59.533 40.000 0.00 0.00 0.00 3.58
563 2965 6.347402 CCGGTTTAATTAGTTGTGAGTGTGAG 60.347 42.308 0.00 0.00 0.00 3.51
564 2966 6.202188 CGGTTTAATTAGTTGTGAGTGTGAGT 59.798 38.462 0.00 0.00 0.00 3.41
565 2967 7.254658 CGGTTTAATTAGTTGTGAGTGTGAGTT 60.255 37.037 0.00 0.00 0.00 3.01
568 2970 9.781834 TTTAATTAGTTGTGAGTGTGAGTTTTG 57.218 29.630 0.00 0.00 0.00 2.44
569 2971 5.811399 TTAGTTGTGAGTGTGAGTTTTGG 57.189 39.130 0.00 0.00 0.00 3.28
570 2972 3.686016 AGTTGTGAGTGTGAGTTTTGGT 58.314 40.909 0.00 0.00 0.00 3.67
571 2973 3.440173 AGTTGTGAGTGTGAGTTTTGGTG 59.560 43.478 0.00 0.00 0.00 4.17
577 2994 5.010933 TGAGTGTGAGTTTTGGTGGTTTTA 58.989 37.500 0.00 0.00 0.00 1.52
581 2998 6.014925 AGTGTGAGTTTTGGTGGTTTTAAAGT 60.015 34.615 0.00 0.00 0.00 2.66
586 3003 6.403049 AGTTTTGGTGGTTTTAAAGTTGAGG 58.597 36.000 0.00 0.00 0.00 3.86
587 3004 5.346181 TTTGGTGGTTTTAAAGTTGAGGG 57.654 39.130 0.00 0.00 0.00 4.30
589 3006 3.955551 TGGTGGTTTTAAAGTTGAGGGAC 59.044 43.478 0.00 0.00 0.00 4.46
590 3007 3.319972 GGTGGTTTTAAAGTTGAGGGACC 59.680 47.826 0.00 0.00 0.00 4.46
595 3012 6.183360 TGGTTTTAAAGTTGAGGGACCATTTC 60.183 38.462 0.00 0.00 31.47 2.17
604 3021 6.839134 AGTTGAGGGACCATTTCTAAACTTTT 59.161 34.615 0.00 0.00 0.00 2.27
605 3022 6.648879 TGAGGGACCATTTCTAAACTTTTG 57.351 37.500 0.00 0.00 0.00 2.44
611 3028 6.642540 GGACCATTTCTAAACTTTTGCAAGAG 59.357 38.462 15.05 15.05 33.72 2.85
614 3031 7.706607 ACCATTTCTAAACTTTTGCAAGAGTTC 59.293 33.333 29.23 0.00 35.17 3.01
615 3032 7.096477 CCATTTCTAAACTTTTGCAAGAGTTCG 60.096 37.037 29.23 23.15 35.17 3.95
653 3070 5.539842 ACTTATCCCTTTCCTAAGCTAGGT 58.460 41.667 8.51 0.00 46.32 3.08
668 3086 2.683768 CTAGGTTAGGCTCCATCAGGT 58.316 52.381 0.00 0.00 35.89 4.00
673 3091 2.016393 TAGGCTCCATCAGGTTCGCG 62.016 60.000 0.00 0.00 35.89 5.87
724 3144 1.079503 GGCTGAGCGTAGGAACTTTG 58.920 55.000 0.00 0.00 41.75 2.77
725 3145 1.608283 GGCTGAGCGTAGGAACTTTGT 60.608 52.381 0.00 0.00 41.75 2.83
745 3165 3.680786 CGTCACGGACAGGCCAGA 61.681 66.667 5.01 0.00 35.94 3.86
746 3166 2.048127 GTCACGGACAGGCCAGAC 60.048 66.667 5.01 0.00 35.17 3.51
767 3187 2.159382 GTGCCGGAGATTTCCTTCAAA 58.841 47.619 5.05 0.00 41.67 2.69
781 3201 1.019278 TTCAAAGTCTCCCGCGATGC 61.019 55.000 8.23 0.00 0.00 3.91
844 3264 4.947147 GGCTGCACCCCGTGTCAA 62.947 66.667 0.50 0.00 35.75 3.18
845 3265 2.672996 GCTGCACCCCGTGTCAAT 60.673 61.111 0.00 0.00 35.75 2.57
939 3380 1.819288 TCTTCAACTCGATCGCTCCTT 59.181 47.619 11.09 0.00 0.00 3.36
946 3387 1.884926 CGATCGCTCCTTTCTGCCC 60.885 63.158 0.26 0.00 0.00 5.36
973 3414 0.972983 ACTGACCACCGATCTCCCTG 60.973 60.000 0.00 0.00 0.00 4.45
999 3487 4.388080 CGCACCGACGTACGTCCA 62.388 66.667 35.47 0.00 41.76 4.02
1016 3504 2.904866 AATGCACGTGTTGGCGGT 60.905 55.556 18.38 0.00 35.98 5.68
1097 3585 5.105752 CGTCCACAAGAGGAATAAGAAGAG 58.894 45.833 0.00 0.00 39.92 2.85
1409 3903 2.048222 CGGCTTCTGCTCGGACAA 60.048 61.111 0.00 0.00 39.59 3.18
1594 4088 1.444250 GACGTCAAGACCACCACCA 59.556 57.895 11.55 0.00 0.00 4.17
1635 4129 1.374758 CGCCAAGCTCTCGGACTTT 60.375 57.895 1.09 0.00 0.00 2.66
1666 4160 3.803082 CCAAGCACGCCACGATGG 61.803 66.667 0.00 0.00 41.55 3.51
1938 4435 3.451178 TGCTATGGAACCTAGAGTTGTCC 59.549 47.826 0.00 0.00 39.40 4.02
2025 4522 3.081445 CAAAATATTCGTCGTGTCGTGC 58.919 45.455 0.00 0.00 0.00 5.34
2042 4539 4.615541 GTCGTGCTTTTGGTGCTAAATTAC 59.384 41.667 0.00 0.00 0.00 1.89
2050 4547 5.715434 TTGGTGCTAAATTACTTTCCCAC 57.285 39.130 0.00 0.00 0.00 4.61
2085 4582 0.748005 GTGCGCCCACCATAGTTCAT 60.748 55.000 4.18 0.00 35.92 2.57
2086 4583 0.747644 TGCGCCCACCATAGTTCATG 60.748 55.000 4.18 0.00 0.00 3.07
2112 4609 6.638610 CCTAGAAGAGCTCTCAGATGAAAAA 58.361 40.000 18.55 0.00 35.41 1.94
2127 4624 9.708092 TCAGATGAAAAATGTAAATCATTGCAA 57.292 25.926 0.00 0.00 44.85 4.08
2206 4707 4.085357 AGGAGCACAACACATGAACTTA 57.915 40.909 0.00 0.00 0.00 2.24
2218 4719 7.218228 ACACATGAACTTATTTGAGCAATGA 57.782 32.000 0.00 0.00 0.00 2.57
2240 5000 4.536765 ACATAGTTTTCATCCATGACCCC 58.463 43.478 0.00 0.00 36.36 4.95
2245 5005 4.845796 AGTTTTCATCCATGACCCCAAAAT 59.154 37.500 0.00 0.00 36.36 1.82
2253 5013 4.955450 TCCATGACCCCAAAATAACTCATG 59.045 41.667 0.00 0.00 36.37 3.07
2260 5020 7.038729 TGACCCCAAAATAACTCATGCAAAATA 60.039 33.333 0.00 0.00 0.00 1.40
2285 5045 2.868583 CGATCGAGGCTTGATCAATGTT 59.131 45.455 33.39 8.31 41.85 2.71
2339 5099 1.270274 GGCAGTCACATCATGCAAACA 59.730 47.619 0.00 0.00 41.78 2.83
2356 5116 4.550639 GCAAACATGCGCTATAATTTTGCC 60.551 41.667 21.16 10.73 0.00 4.52
2377 5138 4.217118 GCCTCACAAGTCAAGAACAATCAT 59.783 41.667 0.00 0.00 0.00 2.45
2511 5279 2.125552 CTCTTGCGGTGGCGATCA 60.126 61.111 0.00 0.00 44.10 2.92
2562 5334 1.906333 TTTTTGCCCGCCTTCCCTC 60.906 57.895 0.00 0.00 0.00 4.30
2570 5342 2.285743 GCCTTCCCTCTCACCCCT 60.286 66.667 0.00 0.00 0.00 4.79
2596 5368 2.610433 CTTGTGCATCTTCACTAGCGA 58.390 47.619 0.00 0.00 37.81 4.93
2602 5374 2.402305 CATCTTCACTAGCGAGATGGC 58.598 52.381 16.86 0.00 41.80 4.40
2604 5376 0.596083 CTTCACTAGCGAGATGGCGG 60.596 60.000 0.00 0.00 38.18 6.13
2636 5435 3.691342 CGTGCCTTCTCGGGGACA 61.691 66.667 6.04 0.00 46.04 4.02
2682 5481 4.586235 AGTTGCCCTGGCGCTTGT 62.586 61.111 7.64 0.00 45.51 3.16
2703 5502 4.864334 GATGGGCGGTGGAGGCTG 62.864 72.222 0.00 0.00 36.85 4.85
2780 5601 0.034756 CCATGACTTCCACGGTGACA 59.965 55.000 10.28 2.49 0.00 3.58
2792 5613 2.643272 GTGACAGGCGACGACTGA 59.357 61.111 36.35 13.25 42.14 3.41
2796 5617 1.299562 GACAGGCGACGACTGAGAGA 61.300 60.000 36.35 0.00 42.14 3.10
2809 5630 0.541998 TGAGAGACGTCCATGGTGGT 60.542 55.000 13.01 10.90 39.03 4.16
2816 5637 0.321210 CGTCCATGGTGGTGCTACAA 60.321 55.000 12.58 0.00 39.03 2.41
2887 5709 0.686769 GGAAGGGAGAGCGGGAACTA 60.687 60.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.035458 ACCTTTCCCAACAGCTCTCG 59.965 55.000 0.00 0.00 0.00 4.04
32 33 7.307989 GCCTGCAAAATGGTACTGTACTATATG 60.308 40.741 15.84 17.03 0.00 1.78
38 39 3.081804 AGCCTGCAAAATGGTACTGTAC 58.918 45.455 9.46 9.46 0.00 2.90
39 40 3.433306 AGCCTGCAAAATGGTACTGTA 57.567 42.857 0.00 0.00 0.00 2.74
40 41 2.292828 AGCCTGCAAAATGGTACTGT 57.707 45.000 0.00 0.00 0.00 3.55
42 43 3.009033 TCACTAGCCTGCAAAATGGTACT 59.991 43.478 0.00 0.00 0.00 2.73
43 44 3.343617 TCACTAGCCTGCAAAATGGTAC 58.656 45.455 0.00 0.00 0.00 3.34
44 45 3.712016 TCACTAGCCTGCAAAATGGTA 57.288 42.857 0.00 0.00 0.00 3.25
72 73 3.614092 GGATCAGGAATCAGCTGTTTGA 58.386 45.455 14.65 11.59 35.96 2.69
77 78 1.489649 AGTGGGATCAGGAATCAGCTG 59.510 52.381 7.63 7.63 35.96 4.24
81 82 5.974156 TGATTTAGTGGGATCAGGAATCA 57.026 39.130 0.00 0.00 35.96 2.57
82 83 7.830099 ATTTGATTTAGTGGGATCAGGAATC 57.170 36.000 0.00 0.00 34.10 2.52
86 87 6.660949 GGGATATTTGATTTAGTGGGATCAGG 59.339 42.308 0.00 0.00 34.10 3.86
88 89 6.335311 AGGGGATATTTGATTTAGTGGGATCA 59.665 38.462 0.00 0.00 0.00 2.92
105 106 2.171448 GTTCACTGCACAGAGGGGATAT 59.829 50.000 4.31 0.00 0.00 1.63
148 149 1.404035 GGAGCCTCTCGAGAAGTTCTC 59.596 57.143 22.30 21.00 40.06 2.87
191 192 1.005748 CTCTGACTGCGCCTGAACA 60.006 57.895 4.18 3.80 0.00 3.18
212 213 1.903404 ACCTTTCCCAGCCGCTTTG 60.903 57.895 0.00 0.00 0.00 2.77
242 243 3.719173 AGCTACCTATCTTTGACGCTC 57.281 47.619 0.00 0.00 0.00 5.03
264 273 5.872963 TCCATAATCCTCCATCAGAACATG 58.127 41.667 0.00 0.00 0.00 3.21
312 321 8.310382 CCAGTCCTCTTTATAGAAGTATCATGG 58.690 40.741 0.00 0.00 0.00 3.66
313 322 7.816995 GCCAGTCCTCTTTATAGAAGTATCATG 59.183 40.741 0.00 0.00 0.00 3.07
314 323 7.510685 TGCCAGTCCTCTTTATAGAAGTATCAT 59.489 37.037 0.00 0.00 0.00 2.45
324 333 4.616553 TGGTACTGCCAGTCCTCTTTATA 58.383 43.478 0.00 0.00 43.61 0.98
325 334 3.450904 TGGTACTGCCAGTCCTCTTTAT 58.549 45.455 0.00 0.00 43.61 1.40
337 346 2.496817 CGCCTCTCTGGTACTGCC 59.503 66.667 0.00 0.00 38.35 4.85
338 347 2.352032 ACCGCCTCTCTGGTACTGC 61.352 63.158 0.00 0.00 36.50 4.40
353 362 1.813513 ACTTGAGAAGCCATTCACCG 58.186 50.000 0.00 0.00 37.94 4.94
357 366 3.311966 GTTGCAACTTGAGAAGCCATTC 58.688 45.455 22.36 0.00 35.52 2.67
358 367 2.036346 GGTTGCAACTTGAGAAGCCATT 59.964 45.455 27.64 0.00 0.00 3.16
395 404 4.100498 TCCTCTAGAGACAAAACAAACCGT 59.900 41.667 21.76 0.00 0.00 4.83
397 406 5.236695 GTGTCCTCTAGAGACAAAACAAACC 59.763 44.000 21.76 5.69 38.63 3.27
403 412 3.006967 GCCAGTGTCCTCTAGAGACAAAA 59.993 47.826 21.76 0.00 41.24 2.44
404 413 2.563179 GCCAGTGTCCTCTAGAGACAAA 59.437 50.000 21.76 0.00 41.24 2.83
405 414 2.171840 GCCAGTGTCCTCTAGAGACAA 58.828 52.381 21.76 3.40 41.24 3.18
406 415 1.840737 GCCAGTGTCCTCTAGAGACA 58.159 55.000 21.76 18.51 41.24 3.41
407 416 0.736053 CGCCAGTGTCCTCTAGAGAC 59.264 60.000 21.76 16.33 39.07 3.36
408 417 0.394488 CCGCCAGTGTCCTCTAGAGA 60.394 60.000 21.76 4.61 0.00 3.10
425 434 1.434622 GGCAGTCTCATGTCATGCCG 61.435 60.000 8.03 2.14 46.19 5.69
448 457 1.568504 ATCCGGACTAGCCTGAAACA 58.431 50.000 6.12 0.00 33.30 2.83
457 467 3.684788 CAGGTTGTGAAAATCCGGACTAG 59.315 47.826 6.12 0.00 0.00 2.57
480 490 2.432146 ACGTATCATGGTCAGATGTGCT 59.568 45.455 0.00 0.00 0.00 4.40
528 538 9.287373 ACAACTAATTAAACCGGATACTTTTCA 57.713 29.630 9.46 0.00 0.00 2.69
530 540 9.287373 TCACAACTAATTAAACCGGATACTTTT 57.713 29.630 9.46 0.00 0.00 2.27
531 541 8.851541 TCACAACTAATTAAACCGGATACTTT 57.148 30.769 9.46 0.00 0.00 2.66
532 542 8.098912 ACTCACAACTAATTAAACCGGATACTT 58.901 33.333 9.46 4.19 0.00 2.24
533 543 7.548075 CACTCACAACTAATTAAACCGGATACT 59.452 37.037 9.46 0.00 0.00 2.12
535 545 7.332430 CACACTCACAACTAATTAAACCGGATA 59.668 37.037 9.46 0.00 0.00 2.59
550 2952 3.427503 CCACCAAAACTCACACTCACAAC 60.428 47.826 0.00 0.00 0.00 3.32
553 2955 2.365582 ACCACCAAAACTCACACTCAC 58.634 47.619 0.00 0.00 0.00 3.51
555 2957 4.450082 AAAACCACCAAAACTCACACTC 57.550 40.909 0.00 0.00 0.00 3.51
556 2958 5.986501 TTAAAACCACCAAAACTCACACT 57.013 34.783 0.00 0.00 0.00 3.55
557 2959 6.160684 ACTTTAAAACCACCAAAACTCACAC 58.839 36.000 0.00 0.00 0.00 3.82
558 2960 6.347859 ACTTTAAAACCACCAAAACTCACA 57.652 33.333 0.00 0.00 0.00 3.58
560 2962 6.994221 TCAACTTTAAAACCACCAAAACTCA 58.006 32.000 0.00 0.00 0.00 3.41
561 2963 6.533723 CCTCAACTTTAAAACCACCAAAACTC 59.466 38.462 0.00 0.00 0.00 3.01
562 2964 6.403049 CCTCAACTTTAAAACCACCAAAACT 58.597 36.000 0.00 0.00 0.00 2.66
563 2965 5.583061 CCCTCAACTTTAAAACCACCAAAAC 59.417 40.000 0.00 0.00 0.00 2.43
564 2966 5.484290 TCCCTCAACTTTAAAACCACCAAAA 59.516 36.000 0.00 0.00 0.00 2.44
565 2967 5.024118 TCCCTCAACTTTAAAACCACCAAA 58.976 37.500 0.00 0.00 0.00 3.28
568 2970 3.319972 GGTCCCTCAACTTTAAAACCACC 59.680 47.826 0.00 0.00 0.00 4.61
569 2971 3.955551 TGGTCCCTCAACTTTAAAACCAC 59.044 43.478 0.95 0.00 30.91 4.16
570 2972 4.252570 TGGTCCCTCAACTTTAAAACCA 57.747 40.909 0.95 0.95 33.35 3.67
571 2973 5.801531 AATGGTCCCTCAACTTTAAAACC 57.198 39.130 0.00 0.00 0.00 3.27
577 2994 6.373759 AGTTTAGAAATGGTCCCTCAACTTT 58.626 36.000 0.00 0.00 0.00 2.66
581 2998 6.462347 GCAAAAGTTTAGAAATGGTCCCTCAA 60.462 38.462 0.00 0.00 0.00 3.02
586 3003 6.512297 TCTTGCAAAAGTTTAGAAATGGTCC 58.488 36.000 0.00 0.00 0.00 4.46
587 3004 7.203218 ACTCTTGCAAAAGTTTAGAAATGGTC 58.797 34.615 0.00 0.00 0.00 4.02
589 3006 7.096477 CGAACTCTTGCAAAAGTTTAGAAATGG 60.096 37.037 18.78 0.00 35.90 3.16
590 3007 7.643764 TCGAACTCTTGCAAAAGTTTAGAAATG 59.356 33.333 18.78 4.72 35.90 2.32
595 3012 6.629252 GTCTTCGAACTCTTGCAAAAGTTTAG 59.371 38.462 18.78 15.39 35.90 1.85
614 3031 8.813643 AGGGATAAGTATATTTTTCGTCTTCG 57.186 34.615 0.00 0.00 38.55 3.79
646 3063 2.324541 CTGATGGAGCCTAACCTAGCT 58.675 52.381 0.00 0.00 43.55 3.32
653 3070 0.178068 GCGAACCTGATGGAGCCTAA 59.822 55.000 0.00 0.00 37.04 2.69
668 3086 2.350388 GCATTTTTGAGTTCTCCGCGAA 60.350 45.455 8.23 0.00 0.00 4.70
673 3091 2.226437 TCGCAGCATTTTTGAGTTCTCC 59.774 45.455 0.00 0.00 0.00 3.71
680 3098 2.881513 TGGTTACTCGCAGCATTTTTGA 59.118 40.909 0.00 0.00 0.00 2.69
840 3260 1.063174 GCGAATCAGTCTGCCATTGAC 59.937 52.381 0.00 0.00 34.88 3.18
841 3261 1.372582 GCGAATCAGTCTGCCATTGA 58.627 50.000 0.00 0.00 0.00 2.57
843 3263 0.749454 GGGCGAATCAGTCTGCCATT 60.749 55.000 9.58 0.00 43.52 3.16
844 3264 1.153086 GGGCGAATCAGTCTGCCAT 60.153 57.895 9.58 0.00 43.52 4.40
845 3265 1.913951 ATGGGCGAATCAGTCTGCCA 61.914 55.000 9.58 0.00 43.52 4.92
939 3380 2.038557 GGTCAGTTAGTCTTGGGCAGAA 59.961 50.000 0.00 0.00 31.28 3.02
946 3387 3.193691 AGATCGGTGGTCAGTTAGTCTTG 59.806 47.826 0.00 0.00 0.00 3.02
999 3487 2.904866 ACCGCCAACACGTGCATT 60.905 55.556 17.22 0.00 0.00 3.56
1097 3585 1.690985 CTGGTCTCCCCCTTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
1585 4079 1.990060 CGAGGAGGATGGTGGTGGT 60.990 63.158 0.00 0.00 0.00 4.16
1594 4088 1.384525 CAGTTCTCGTCGAGGAGGAT 58.615 55.000 29.20 15.80 34.74 3.24
1666 4160 1.736612 AAGGAGTAGACGTCGGACTC 58.263 55.000 30.35 30.35 39.12 3.36
1806 4303 3.754530 TCCTTGATCGCCGCGTCA 61.755 61.111 13.39 12.64 0.00 4.35
2008 4505 2.273370 AAGCACGACACGACGAATAT 57.727 45.000 0.00 0.00 37.03 1.28
2025 4522 6.645003 GTGGGAAAGTAATTTAGCACCAAAAG 59.355 38.462 0.00 0.00 0.00 2.27
2042 4539 1.446907 CTGTGCTGCTAGTGGGAAAG 58.553 55.000 0.00 0.00 0.00 2.62
2085 4582 1.286257 TCTGAGAGCTCTTCTAGGCCA 59.714 52.381 19.36 8.26 35.87 5.36
2086 4583 2.065899 TCTGAGAGCTCTTCTAGGCC 57.934 55.000 19.36 3.34 35.87 5.19
2112 4609 4.986034 CCATCGCATTGCAATGATTTACAT 59.014 37.500 37.36 17.84 41.45 2.29
2147 4644 7.618907 TCTTTCATATCCATCATTTTTGACCCA 59.381 33.333 0.00 0.00 0.00 4.51
2187 4688 6.437928 TCAAATAAGTTCATGTGTTGTGCTC 58.562 36.000 0.00 0.00 0.00 4.26
2206 4707 7.977853 GGATGAAAACTATGTCATTGCTCAAAT 59.022 33.333 0.00 0.00 34.61 2.32
2218 4719 4.017591 TGGGGTCATGGATGAAAACTATGT 60.018 41.667 0.00 0.00 38.75 2.29
2240 5000 9.288124 TCGATGTATTTTGCATGAGTTATTTTG 57.712 29.630 0.00 0.00 0.00 2.44
2245 5005 6.699642 TCGATCGATGTATTTTGCATGAGTTA 59.300 34.615 15.15 0.00 0.00 2.24
2253 5013 2.802816 AGCCTCGATCGATGTATTTTGC 59.197 45.455 19.78 10.78 0.00 3.68
2260 5020 1.683385 TGATCAAGCCTCGATCGATGT 59.317 47.619 19.78 3.07 41.85 3.06
2339 5099 3.631686 TGTGAGGCAAAATTATAGCGCAT 59.368 39.130 11.47 3.63 0.00 4.73
2356 5116 7.966753 CCATTATGATTGTTCTTGACTTGTGAG 59.033 37.037 0.00 0.00 0.00 3.51
2377 5138 5.897050 AGTTGTTTTCACTTTTCGCCATTA 58.103 33.333 0.00 0.00 0.00 1.90
2560 5332 2.227036 AAGGTGGCAGGGGTGAGAG 61.227 63.158 0.00 0.00 0.00 3.20
2562 5334 2.034687 CAAGGTGGCAGGGGTGAG 59.965 66.667 0.00 0.00 0.00 3.51
2570 5342 0.178995 TGAAGATGCACAAGGTGGCA 60.179 50.000 0.00 0.00 45.23 4.92
2732 5552 0.539051 CCCCTCAAGCAGATCTCGTT 59.461 55.000 0.00 0.00 0.00 3.85
2780 5601 2.392181 CGTCTCTCAGTCGTCGCCT 61.392 63.158 0.00 0.00 0.00 5.52
2792 5613 1.975327 CACCACCATGGACGTCTCT 59.025 57.895 21.47 0.00 40.96 3.10
2796 5617 1.295423 GTAGCACCACCATGGACGT 59.705 57.895 21.47 10.84 40.96 4.34
2809 5630 1.077787 CTTCCCCGGCATTGTAGCA 60.078 57.895 0.00 0.00 35.83 3.49
2816 5637 3.728373 GACCACCTTCCCCGGCAT 61.728 66.667 0.00 0.00 0.00 4.40
2865 5686 2.689034 CCCGCTCTCCCTTCCCTT 60.689 66.667 0.00 0.00 0.00 3.95
2887 5709 2.359478 GGGACATTTCCGCGTGGT 60.359 61.111 16.01 0.00 43.94 4.16
2951 5773 0.449388 CTTCAGAAACATGAGGCGGC 59.551 55.000 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.