Multiple sequence alignment - TraesCS4B01G187000

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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 TraesCS4B01G187000 chr4B 100.000 3805 0 0 1 3805 407059534 407055730 0.000000e+00 7027.0
1 TraesCS4B01G187000 chr4B 95.122 41 2 0 3081 3121 407056416 407056376 8.820000e-07 65.8
2 TraesCS4B01G187000 chr4B 95.122 41 2 0 3119 3159 407056454 407056414 8.820000e-07 65.8
3 TraesCS4B01G187000 chr4D 96.006 3130 77 17 1 3121 327721960 327718870 0.000000e+00 5044.0
4 TraesCS4B01G187000 chr4A 94.920 2362 68 11 1 2357 143249749 143252063 0.000000e+00 3650.0
5 TraesCS4B01G187000 chr4A 95.302 1043 38 8 2342 3376 143252079 143253118 0.000000e+00 1644.0
6 TraesCS4B01G187000 chr4A 91.558 154 10 3 3482 3635 143253223 143253373 3.850000e-50 209.0
7 TraesCS4B01G187000 chr4A 98.000 100 2 0 3706 3805 143254324 143254423 1.410000e-39 174.0
8 TraesCS4B01G187000 chr4A 100.000 38 0 0 3119 3156 143252823 143252860 1.900000e-08 71.3
9 TraesCS4B01G187000 chr4A 97.368 38 1 0 3081 3118 143252861 143252898 8.820000e-07 65.8
10 TraesCS4B01G187000 chr3B 95.856 724 10 10 1958 2676 554899968 554900676 0.000000e+00 1153.0
11 TraesCS4B01G187000 chr3B 95.021 723 16 10 1958 2676 303334400 303333694 0.000000e+00 1118.0
12 TraesCS4B01G187000 chr5B 95.297 723 14 7 1958 2676 299679337 299680043 0.000000e+00 1129.0
13 TraesCS4B01G187000 chr2B 95.159 723 16 9 1958 2676 188856425 188855718 0.000000e+00 1123.0
14 TraesCS4B01G187000 chr6A 85.946 185 21 4 3493 3675 203595645 203595826 3.880000e-45 193.0
15 TraesCS4B01G187000 chr3A 80.519 231 35 9 2563 2786 434069283 434069056 6.540000e-38 169.0
16 TraesCS4B01G187000 chr3A 88.889 72 8 0 3527 3598 170737606 170737535 5.240000e-14 89.8
17 TraesCS4B01G187000 chr1D 81.481 216 29 8 2569 2777 477480552 477480763 2.350000e-37 167.0
18 TraesCS4B01G187000 chr1D 80.269 223 31 7 2563 2777 477435963 477436180 5.090000e-34 156.0
19 TraesCS4B01G187000 chr1B 81.106 217 30 8 2569 2778 665061697 665061909 3.040000e-36 163.0
20 TraesCS4B01G187000 chr1B 80.717 223 30 8 2563 2777 665049843 665050060 1.090000e-35 161.0
21 TraesCS4B01G187000 chr1A 80.269 223 31 7 2563 2777 573818415 573818632 5.090000e-34 156.0
22 TraesCS4B01G187000 chr3D 79.372 223 37 8 2563 2779 301414176 301414395 8.520000e-32 148.0


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 TraesCS4B01G187000 chr4B 407055730 407059534 3804 True 2386.200000 7027 96.748000 1 3805 3 chr4B.!!$R1 3804
1 TraesCS4B01G187000 chr4D 327718870 327721960 3090 True 5044.000000 5044 96.006000 1 3121 1 chr4D.!!$R1 3120
2 TraesCS4B01G187000 chr4A 143249749 143254423 4674 False 969.016667 3650 96.191333 1 3805 6 chr4A.!!$F1 3804
3 TraesCS4B01G187000 chr3B 554899968 554900676 708 False 1153.000000 1153 95.856000 1958 2676 1 chr3B.!!$F1 718
4 TraesCS4B01G187000 chr3B 303333694 303334400 706 True 1118.000000 1118 95.021000 1958 2676 1 chr3B.!!$R1 718
5 TraesCS4B01G187000 chr5B 299679337 299680043 706 False 1129.000000 1129 95.297000 1958 2676 1 chr5B.!!$F1 718
6 TraesCS4B01G187000 chr2B 188855718 188856425 707 True 1123.000000 1123 95.159000 1958 2676 1 chr2B.!!$R1 718

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
542 543 0.756294 TGTGATGTCCAACGGTGACT 59.244 50.000 0.0 0.0 33.83 3.41 F
641 642 1.627329 AGAAAAGTCGGTTCTACCCCC 59.373 52.381 0.0 0.0 33.75 5.40 F
1952 1954 0.898320 TTCCACTACAGAGGCAGAGC 59.102 55.000 0.0 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1390 0.461693 GAGGAGAGACAGGTGCATGC 60.462 60.0 11.82 11.82 0.00 4.06 R
2358 2396 2.937469 TTGCCAACAAATAGCCGATG 57.063 45.0 0.00 0.00 31.21 3.84 R
3411 3482 0.093026 GACTGCACGATCGAAAACCG 59.907 55.0 24.34 7.19 40.25 4.44 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
150 151 1.917273 GTGCAATGCATGATGTGACC 58.083 50.000 12.38 0.00 41.91 4.02
204 205 3.125316 CGAGTTGAAACTAACCGTTCCA 58.875 45.455 0.00 0.00 39.88 3.53
286 287 1.071699 TGCTAACACCCTCACCTGAAC 59.928 52.381 0.00 0.00 0.00 3.18
368 369 2.092699 ACCCTAGCTCTGATTTCTTGCC 60.093 50.000 0.00 0.00 0.00 4.52
527 528 1.206849 TGCGGCATAGATTCTGTGTGA 59.793 47.619 11.47 0.00 0.00 3.58
542 543 0.756294 TGTGATGTCCAACGGTGACT 59.244 50.000 0.00 0.00 33.83 3.41
565 566 4.580167 TGAATGCAGTGCTCTTTACTGTTT 59.420 37.500 17.60 2.21 45.60 2.83
599 600 5.275974 CGCTCTAAACGAAATGAAGCTACTC 60.276 44.000 0.00 0.00 0.00 2.59
640 641 2.354503 GGAGAAAAGTCGGTTCTACCCC 60.355 54.545 0.00 0.00 35.46 4.95
641 642 1.627329 AGAAAAGTCGGTTCTACCCCC 59.373 52.381 0.00 0.00 33.75 5.40
710 711 7.750458 TCATTTTCACTTGATTCATTTCTACGC 59.250 33.333 0.00 0.00 0.00 4.42
711 712 6.552859 TTTCACTTGATTCATTTCTACGCA 57.447 33.333 0.00 0.00 0.00 5.24
712 713 5.784750 TCACTTGATTCATTTCTACGCAG 57.215 39.130 0.00 0.00 0.00 5.18
713 714 4.093408 TCACTTGATTCATTTCTACGCAGC 59.907 41.667 0.00 0.00 0.00 5.25
714 715 4.002982 ACTTGATTCATTTCTACGCAGCA 58.997 39.130 0.00 0.00 0.00 4.41
715 716 4.142816 ACTTGATTCATTTCTACGCAGCAC 60.143 41.667 0.00 0.00 0.00 4.40
716 717 3.599343 TGATTCATTTCTACGCAGCACT 58.401 40.909 0.00 0.00 0.00 4.40
717 718 3.371898 TGATTCATTTCTACGCAGCACTG 59.628 43.478 0.00 0.00 0.00 3.66
718 719 2.455674 TCATTTCTACGCAGCACTGT 57.544 45.000 0.00 0.00 0.00 3.55
719 720 2.766313 TCATTTCTACGCAGCACTGTT 58.234 42.857 0.00 0.00 0.00 3.16
720 721 3.138304 TCATTTCTACGCAGCACTGTTT 58.862 40.909 0.00 0.00 0.00 2.83
721 722 3.186409 TCATTTCTACGCAGCACTGTTTC 59.814 43.478 0.00 0.00 0.00 2.78
722 723 2.526304 TTCTACGCAGCACTGTTTCT 57.474 45.000 0.00 0.00 0.00 2.52
723 724 3.653539 TTCTACGCAGCACTGTTTCTA 57.346 42.857 0.00 0.00 0.00 2.10
724 725 2.942710 TCTACGCAGCACTGTTTCTAC 58.057 47.619 0.00 0.00 0.00 2.59
818 820 2.094182 TGGTCTTAGTGAGATGAACGGC 60.094 50.000 0.00 0.00 36.61 5.68
853 855 2.507484 CAGGGCAATCAAGTCACTTCA 58.493 47.619 0.00 0.00 0.00 3.02
856 858 2.622942 GGGCAATCAAGTCACTTCAACA 59.377 45.455 0.00 0.00 0.00 3.33
867 869 5.295950 AGTCACTTCAACATGTCTCTCAAG 58.704 41.667 0.00 0.00 0.00 3.02
869 871 3.811497 CACTTCAACATGTCTCTCAAGCA 59.189 43.478 0.00 0.00 0.00 3.91
910 912 4.367023 TTCCGAACCCGACAGGCG 62.367 66.667 0.00 0.00 40.58 5.52
913 915 4.351938 CGAACCCGACAGGCGACA 62.352 66.667 0.00 0.00 44.57 4.35
914 916 2.432628 GAACCCGACAGGCGACAG 60.433 66.667 0.00 0.00 44.57 3.51
915 917 3.934391 GAACCCGACAGGCGACAGG 62.934 68.421 0.00 0.00 44.57 4.00
1222 1224 2.046988 TCTCCGACGACCGCTACA 60.047 61.111 0.00 0.00 36.84 2.74
1233 1235 2.278857 CGCTACATCTCGCCGCTT 60.279 61.111 0.00 0.00 0.00 4.68
1716 1718 1.673168 AATCTGCGCTGAATTCCTCC 58.327 50.000 21.22 0.00 0.00 4.30
1724 1726 1.200948 GCTGAATTCCTCCAACACAGC 59.799 52.381 2.27 0.00 38.47 4.40
1937 1939 1.344065 TACTCTGCTTTCGGGTTCCA 58.656 50.000 0.00 0.00 0.00 3.53
1952 1954 0.898320 TTCCACTACAGAGGCAGAGC 59.102 55.000 0.00 0.00 0.00 4.09
2367 2405 6.701340 TCAGAAATAGTATTGCATCGGCTAT 58.299 36.000 3.62 0.00 41.91 2.97
2858 2899 0.098376 CGTCTCCTACTGCCGTGTAC 59.902 60.000 0.00 0.00 0.00 2.90
2923 2964 1.306148 CGCATGTCTGATGCCTTCAT 58.694 50.000 0.00 0.00 41.71 2.57
2942 2983 2.281070 AGGGACTGCTTGCGTGTG 60.281 61.111 0.00 0.00 37.18 3.82
3239 3284 2.671396 GCAAGTGTATCATCGGTTCGTT 59.329 45.455 0.00 0.00 0.00 3.85
3240 3285 3.483574 GCAAGTGTATCATCGGTTCGTTG 60.484 47.826 0.00 0.00 0.00 4.10
3262 3307 8.376203 CGTTGTTATCTTGTTGATCAGAACTAG 58.624 37.037 0.00 0.00 33.20 2.57
3267 3312 3.616956 TGTTGATCAGAACTAGCCCAG 57.383 47.619 0.00 0.00 0.00 4.45
3300 3345 9.919416 TTTGTATATATGGTGGATGGATATTGG 57.081 33.333 0.00 0.00 0.00 3.16
3302 3347 8.937835 TGTATATATGGTGGATGGATATTGGAG 58.062 37.037 0.00 0.00 0.00 3.86
3341 3386 5.971202 CCAACATTTATATGCCGAAGTGTTC 59.029 40.000 0.00 0.00 34.43 3.18
3360 3405 7.152645 AGTGTTCTTATGTTTCGAGAAAGCTA 58.847 34.615 0.00 0.00 31.79 3.32
3371 3416 3.056393 TCGAGAAAGCTATTTTCCGACCA 60.056 43.478 0.00 0.00 45.15 4.02
3372 3417 3.871594 CGAGAAAGCTATTTTCCGACCAT 59.128 43.478 0.00 0.00 45.15 3.55
3374 3419 5.502544 CGAGAAAGCTATTTTCCGACCATTC 60.503 44.000 0.00 0.00 45.15 2.67
3375 3420 5.501156 AGAAAGCTATTTTCCGACCATTCT 58.499 37.500 0.00 0.00 45.15 2.40
3376 3421 5.355350 AGAAAGCTATTTTCCGACCATTCTG 59.645 40.000 0.00 0.00 45.15 3.02
3377 3422 4.487714 AGCTATTTTCCGACCATTCTGA 57.512 40.909 0.00 0.00 0.00 3.27
3380 3425 5.888161 AGCTATTTTCCGACCATTCTGATTT 59.112 36.000 0.00 0.00 0.00 2.17
3381 3426 6.378280 AGCTATTTTCCGACCATTCTGATTTT 59.622 34.615 0.00 0.00 0.00 1.82
3382 3427 7.035612 GCTATTTTCCGACCATTCTGATTTTT 58.964 34.615 0.00 0.00 0.00 1.94
3401 3472 9.550406 TGATTTTTATTATAGATCCGAACGGTT 57.450 29.630 12.93 4.82 36.47 4.44
3412 3483 2.650163 GAACGGTTCGGAGTCATCG 58.350 57.895 4.94 0.00 0.00 3.84
3427 3499 4.657502 TCGGTTTTCGATCGTGCA 57.342 50.000 15.94 0.00 43.74 4.57
3435 3507 3.308008 CGATCGTGCAGTCTCGCG 61.308 66.667 7.03 0.00 40.91 5.87
3453 3525 0.951040 CGCGAGCCTCCCATAATTCC 60.951 60.000 0.00 0.00 0.00 3.01
3454 3526 0.951040 GCGAGCCTCCCATAATTCCG 60.951 60.000 0.00 0.00 0.00 4.30
3455 3527 0.320771 CGAGCCTCCCATAATTCCGG 60.321 60.000 0.00 0.00 0.00 5.14
3456 3528 0.765510 GAGCCTCCCATAATTCCGGT 59.234 55.000 0.00 0.00 0.00 5.28
3457 3529 1.143073 GAGCCTCCCATAATTCCGGTT 59.857 52.381 0.00 0.00 0.00 4.44
3458 3530 1.569072 AGCCTCCCATAATTCCGGTTT 59.431 47.619 0.00 0.00 0.00 3.27
3459 3531 1.954382 GCCTCCCATAATTCCGGTTTC 59.046 52.381 0.00 0.00 0.00 2.78
3460 3532 2.218603 CCTCCCATAATTCCGGTTTCG 58.781 52.381 0.00 0.00 0.00 3.46
3470 3542 3.057337 CGGTTTCGGGTGTCTCCT 58.943 61.111 0.00 0.00 36.25 3.69
3471 3543 1.370064 CGGTTTCGGGTGTCTCCTT 59.630 57.895 0.00 0.00 36.25 3.36
3472 3544 0.604578 CGGTTTCGGGTGTCTCCTTA 59.395 55.000 0.00 0.00 36.25 2.69
3473 3545 1.001181 CGGTTTCGGGTGTCTCCTTAA 59.999 52.381 0.00 0.00 36.25 1.85
3474 3546 2.354403 CGGTTTCGGGTGTCTCCTTAAT 60.354 50.000 0.00 0.00 36.25 1.40
3475 3547 3.682696 GGTTTCGGGTGTCTCCTTAATT 58.317 45.455 0.00 0.00 36.25 1.40
3476 3548 4.621274 CGGTTTCGGGTGTCTCCTTAATTA 60.621 45.833 0.00 0.00 36.25 1.40
3477 3549 5.247862 GGTTTCGGGTGTCTCCTTAATTAA 58.752 41.667 0.00 0.00 36.25 1.40
3478 3550 5.122869 GGTTTCGGGTGTCTCCTTAATTAAC 59.877 44.000 0.00 0.00 36.25 2.01
3479 3551 4.114058 TCGGGTGTCTCCTTAATTAACG 57.886 45.455 0.00 0.00 36.25 3.18
3480 3552 2.606272 CGGGTGTCTCCTTAATTAACGC 59.394 50.000 0.00 0.00 36.25 4.84
3496 3568 4.400410 GCGATTTCAATTGCGGGG 57.600 55.556 0.00 0.00 36.19 5.73
3510 3582 6.153680 TCAATTGCGGGGTTTATTAATTGACT 59.846 34.615 0.00 0.00 38.72 3.41
3513 3585 3.002965 GCGGGGTTTATTAATTGACTCGG 59.997 47.826 0.00 0.00 0.00 4.63
3514 3586 4.193865 CGGGGTTTATTAATTGACTCGGT 58.806 43.478 0.00 0.00 0.00 4.69
3544 3616 6.920758 GTCTCATGACTCTTAATTAGCACGAT 59.079 38.462 0.00 0.00 39.94 3.73
3553 3625 8.837389 ACTCTTAATTAGCACGATTTAATTCCC 58.163 33.333 0.00 0.00 33.06 3.97
3554 3626 8.974060 TCTTAATTAGCACGATTTAATTCCCT 57.026 30.769 0.00 0.00 33.06 4.20
3614 3686 4.630069 ACGTGTACTGCCATTTAAAGCTAG 59.370 41.667 0.00 0.00 0.00 3.42
3621 3693 6.159293 ACTGCCATTTAAAGCTAGCTTTTTC 58.841 36.000 39.47 23.73 42.93 2.29
3622 3694 5.160641 TGCCATTTAAAGCTAGCTTTTTCG 58.839 37.500 39.47 26.28 42.93 3.46
3630 4485 9.791820 TTTAAAGCTAGCTTTTTCGTTTTAAGT 57.208 25.926 39.47 18.77 42.93 2.24
3659 4514 1.098050 GTGTGCATGGGACAGGAATC 58.902 55.000 0.00 0.00 46.40 2.52
3677 4532 4.103785 GGAATCAATCTCTTCCCCTCATCA 59.896 45.833 0.00 0.00 35.83 3.07
3683 4538 2.091278 TCTCTTCCCCTCATCATACGGT 60.091 50.000 0.00 0.00 0.00 4.83
3697 4552 7.213678 TCATCATACGGTACATGCAAGATTAA 58.786 34.615 0.00 0.00 0.00 1.40
3698 4553 6.838198 TCATACGGTACATGCAAGATTAAC 57.162 37.500 0.00 0.00 0.00 2.01
3699 4554 5.756347 TCATACGGTACATGCAAGATTAACC 59.244 40.000 0.00 0.00 0.00 2.85
3700 4555 3.945346 ACGGTACATGCAAGATTAACCA 58.055 40.909 0.00 0.00 0.00 3.67
3701 4556 4.328536 ACGGTACATGCAAGATTAACCAA 58.671 39.130 0.00 0.00 0.00 3.67
3702 4557 4.155280 ACGGTACATGCAAGATTAACCAAC 59.845 41.667 0.00 0.00 0.00 3.77
3703 4558 4.394920 CGGTACATGCAAGATTAACCAACT 59.605 41.667 0.00 0.00 0.00 3.16
3704 4559 5.447279 CGGTACATGCAAGATTAACCAACTC 60.447 44.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 3.067461 GCTCTACCAGTGTCTTCATCGAT 59.933 47.826 0.00 0.00 0.00 3.59
150 151 1.206132 TGGAGTACATAACACAGGGCG 59.794 52.381 0.00 0.00 0.00 6.13
204 205 1.333177 ACGACTTCTCAAGGAGCTGT 58.667 50.000 0.00 0.00 0.00 4.40
368 369 6.020995 GGTATTGTTGTTCTGTTGTTGAAACG 60.021 38.462 0.00 0.00 0.00 3.60
421 422 7.223582 CAGTAATATTGAGCACTGAACTACTGG 59.776 40.741 9.57 0.00 40.67 4.00
527 528 2.426522 CATTCAGTCACCGTTGGACAT 58.573 47.619 0.00 0.00 37.74 3.06
542 543 3.743521 ACAGTAAAGAGCACTGCATTCA 58.256 40.909 3.30 0.00 45.96 2.57
565 566 2.555325 TCGTTTAGAGCGTTCCTGAAGA 59.445 45.455 0.00 0.00 0.00 2.87
599 600 6.698380 TCTCCCAGTTACTGCTAAAAAGTAG 58.302 40.000 6.88 0.00 31.96 2.57
640 641 1.400629 CGCATGCTCAACTCAACAAGG 60.401 52.381 17.13 0.00 0.00 3.61
641 642 1.959747 CGCATGCTCAACTCAACAAG 58.040 50.000 17.13 0.00 0.00 3.16
710 711 0.320771 AGGCCGTAGAAACAGTGCTG 60.321 55.000 0.00 0.00 0.00 4.41
711 712 0.396811 AAGGCCGTAGAAACAGTGCT 59.603 50.000 0.00 0.00 0.00 4.40
712 713 2.088950 TAAGGCCGTAGAAACAGTGC 57.911 50.000 0.00 0.00 0.00 4.40
713 714 5.007385 AGTATAAGGCCGTAGAAACAGTG 57.993 43.478 4.31 0.00 0.00 3.66
714 715 5.046807 ACAAGTATAAGGCCGTAGAAACAGT 60.047 40.000 4.31 3.53 0.00 3.55
715 716 5.416947 ACAAGTATAAGGCCGTAGAAACAG 58.583 41.667 4.31 3.00 0.00 3.16
716 717 5.410355 ACAAGTATAAGGCCGTAGAAACA 57.590 39.130 4.31 0.00 0.00 2.83
717 718 7.547019 AGTTAACAAGTATAAGGCCGTAGAAAC 59.453 37.037 8.61 2.87 0.00 2.78
718 719 7.614494 AGTTAACAAGTATAAGGCCGTAGAAA 58.386 34.615 8.61 0.00 0.00 2.52
719 720 7.174107 AGTTAACAAGTATAAGGCCGTAGAA 57.826 36.000 8.61 0.00 0.00 2.10
720 721 6.780457 AGTTAACAAGTATAAGGCCGTAGA 57.220 37.500 8.61 0.00 0.00 2.59
721 722 8.193438 ACTAAGTTAACAAGTATAAGGCCGTAG 58.807 37.037 8.61 0.00 0.00 3.51
722 723 7.975616 CACTAAGTTAACAAGTATAAGGCCGTA 59.024 37.037 8.61 0.00 0.00 4.02
723 724 6.815142 CACTAAGTTAACAAGTATAAGGCCGT 59.185 38.462 8.61 0.00 0.00 5.68
724 725 6.238022 GCACTAAGTTAACAAGTATAAGGCCG 60.238 42.308 8.61 0.00 0.00 6.13
818 820 1.134670 GCCCTGCCTTATATAGAGCCG 60.135 57.143 4.22 0.00 0.00 5.52
853 855 2.551459 GTTGCTGCTTGAGAGACATGTT 59.449 45.455 0.00 0.00 0.00 2.71
856 858 2.424557 CAGTTGCTGCTTGAGAGACAT 58.575 47.619 0.00 0.00 0.00 3.06
910 912 0.038892 TTACCTTCGTGTCGCCTGTC 60.039 55.000 0.00 0.00 0.00 3.51
911 913 0.319297 GTTACCTTCGTGTCGCCTGT 60.319 55.000 0.00 0.00 0.00 4.00
912 914 1.012486 GGTTACCTTCGTGTCGCCTG 61.012 60.000 0.00 0.00 0.00 4.85
913 915 1.291272 GGTTACCTTCGTGTCGCCT 59.709 57.895 0.00 0.00 0.00 5.52
914 916 2.090524 CGGTTACCTTCGTGTCGCC 61.091 63.158 0.00 0.00 0.00 5.54
915 917 2.723719 GCGGTTACCTTCGTGTCGC 61.724 63.158 0.00 0.00 35.12 5.19
916 918 2.090524 GGCGGTTACCTTCGTGTCG 61.091 63.158 0.00 0.00 0.00 4.35
1214 1216 4.570663 GCGGCGAGATGTAGCGGT 62.571 66.667 12.98 0.00 36.31 5.68
1388 1390 0.461693 GAGGAGAGACAGGTGCATGC 60.462 60.000 11.82 11.82 0.00 4.06
1479 1481 3.006756 GCGTGCTGCTACCTCCTCA 62.007 63.158 0.00 0.00 41.73 3.86
1716 1718 4.067896 ACTGGAACTATTGAGCTGTGTTG 58.932 43.478 0.00 0.00 0.00 3.33
1875 1877 8.732746 AAATTAGCTAATTCAACATACTCCGT 57.267 30.769 27.56 8.42 35.00 4.69
2358 2396 2.937469 TTGCCAACAAATAGCCGATG 57.063 45.000 0.00 0.00 31.21 3.84
2367 2405 7.335422 ACTTTGTAACATGAAATTGCCAACAAA 59.665 29.630 0.00 0.00 39.77 2.83
2827 2868 0.889638 AGGAGACGACGAGCAGTTGA 60.890 55.000 0.00 0.00 37.67 3.18
2858 2899 1.380515 TCGGAGGAGAGGAAGCCAG 60.381 63.158 0.00 0.00 0.00 4.85
2863 2904 1.682684 GCAGGTCGGAGGAGAGGAA 60.683 63.158 0.00 0.00 0.00 3.36
2923 2964 2.031012 CACGCAAGCAGTCCCTGA 59.969 61.111 0.00 0.00 45.62 3.86
2941 2982 8.290325 CGTAATGCTACTACTGATTCTATGACA 58.710 37.037 0.00 0.00 0.00 3.58
2942 2983 7.271653 GCGTAATGCTACTACTGATTCTATGAC 59.728 40.741 0.00 0.00 41.73 3.06
3084 3129 0.593128 CTGTTTTCCTGCCCTGAACG 59.407 55.000 0.00 0.00 0.00 3.95
3229 3274 4.992319 TCAACAAGATAACAACGAACCGAT 59.008 37.500 0.00 0.00 0.00 4.18
3239 3284 6.818644 GGCTAGTTCTGATCAACAAGATAACA 59.181 38.462 0.00 0.00 37.00 2.41
3240 3285 6.258947 GGGCTAGTTCTGATCAACAAGATAAC 59.741 42.308 0.00 0.00 37.00 1.89
3262 3307 7.066284 CACCATATATACAAAGCTTATCTGGGC 59.934 40.741 0.00 0.00 0.00 5.36
3267 3312 9.113838 CCATCCACCATATATACAAAGCTTATC 57.886 37.037 0.00 0.00 0.00 1.75
3341 3386 7.636359 CGGAAAATAGCTTTCTCGAAACATAAG 59.364 37.037 0.00 0.00 42.73 1.73
3374 3419 9.204570 ACCGTTCGGATCTATAATAAAAATCAG 57.795 33.333 18.28 0.00 0.00 2.90
3375 3420 9.550406 AACCGTTCGGATCTATAATAAAAATCA 57.450 29.630 18.28 0.00 0.00 2.57
3401 3472 0.883153 TCGAAAACCGATGACTCCGA 59.117 50.000 0.00 0.00 43.23 4.55
3402 3473 3.411808 TCGAAAACCGATGACTCCG 57.588 52.632 0.00 0.00 43.23 4.63
3411 3482 0.093026 GACTGCACGATCGAAAACCG 59.907 55.000 24.34 7.19 40.25 4.44
3412 3483 1.390463 GAGACTGCACGATCGAAAACC 59.610 52.381 24.34 6.12 0.00 3.27
3435 3507 0.951040 CGGAATTATGGGAGGCTCGC 60.951 60.000 23.32 23.32 0.00 5.03
3453 3525 0.604578 TAAGGAGACACCCGAAACCG 59.395 55.000 0.00 0.00 40.05 4.44
3454 3526 2.845363 TTAAGGAGACACCCGAAACC 57.155 50.000 0.00 0.00 40.05 3.27
3455 3527 5.163923 CGTTAATTAAGGAGACACCCGAAAC 60.164 44.000 11.62 0.00 40.05 2.78
3456 3528 4.931002 CGTTAATTAAGGAGACACCCGAAA 59.069 41.667 11.62 0.00 40.05 3.46
3457 3529 4.497300 CGTTAATTAAGGAGACACCCGAA 58.503 43.478 11.62 0.00 40.05 4.30
3458 3530 3.676873 GCGTTAATTAAGGAGACACCCGA 60.677 47.826 19.43 0.00 40.05 5.14
3459 3531 2.606272 GCGTTAATTAAGGAGACACCCG 59.394 50.000 19.43 8.06 40.05 5.28
3460 3532 2.606272 CGCGTTAATTAAGGAGACACCC 59.394 50.000 19.43 1.85 40.05 4.61
3461 3533 3.514645 TCGCGTTAATTAAGGAGACACC 58.485 45.455 19.43 2.45 39.35 4.16
3462 3534 5.713822 AATCGCGTTAATTAAGGAGACAC 57.286 39.130 21.34 4.94 33.92 3.67
3463 3535 5.870433 TGAAATCGCGTTAATTAAGGAGACA 59.130 36.000 21.34 14.41 33.92 3.41
3464 3536 6.340537 TGAAATCGCGTTAATTAAGGAGAC 57.659 37.500 21.34 12.55 33.92 3.36
3465 3537 6.971527 TTGAAATCGCGTTAATTAAGGAGA 57.028 33.333 21.22 21.22 35.16 3.71
3466 3538 7.305418 GCAATTGAAATCGCGTTAATTAAGGAG 60.305 37.037 19.43 16.35 0.00 3.69
3467 3539 6.470877 GCAATTGAAATCGCGTTAATTAAGGA 59.529 34.615 19.43 8.59 0.00 3.36
3468 3540 6.557711 CGCAATTGAAATCGCGTTAATTAAGG 60.558 38.462 10.34 12.51 42.66 2.69
3469 3541 6.328828 CGCAATTGAAATCGCGTTAATTAAG 58.671 36.000 10.34 0.00 42.66 1.85
3470 3542 5.228220 CCGCAATTGAAATCGCGTTAATTAA 59.772 36.000 10.34 0.00 46.02 1.40
3471 3543 4.731000 CCGCAATTGAAATCGCGTTAATTA 59.269 37.500 10.34 0.00 46.02 1.40
3472 3544 3.545873 CCGCAATTGAAATCGCGTTAATT 59.454 39.130 10.34 0.00 46.02 1.40
3473 3545 3.105203 CCGCAATTGAAATCGCGTTAAT 58.895 40.909 10.34 0.00 46.02 1.40
3474 3546 2.510874 CCGCAATTGAAATCGCGTTAA 58.489 42.857 10.34 0.00 46.02 2.01
3475 3547 1.202087 CCCGCAATTGAAATCGCGTTA 60.202 47.619 10.34 0.00 46.02 3.18
3476 3548 0.455972 CCCGCAATTGAAATCGCGTT 60.456 50.000 10.34 0.00 46.02 4.84
3477 3549 1.136565 CCCGCAATTGAAATCGCGT 59.863 52.632 10.34 0.00 46.02 6.01
3478 3550 1.586042 CCCCGCAATTGAAATCGCG 60.586 57.895 10.34 0.00 46.96 5.87
3479 3551 0.108851 AACCCCGCAATTGAAATCGC 60.109 50.000 10.34 0.00 0.00 4.58
3480 3552 2.362169 AAACCCCGCAATTGAAATCG 57.638 45.000 10.34 2.73 0.00 3.34
3495 3567 9.764870 GACTAAAACCGAGTCAATTAATAAACC 57.235 33.333 0.00 0.00 42.47 3.27
3567 3639 5.605540 ATTAGGACCCCATTAATCATGCT 57.394 39.130 0.00 0.00 0.00 3.79
3575 3647 5.898972 AGTACACGTAATTAGGACCCCATTA 59.101 40.000 11.96 0.00 0.00 1.90
3638 4493 0.250858 TTCCTGTCCCATGCACACAG 60.251 55.000 9.09 9.09 37.81 3.66
3639 4494 0.405198 ATTCCTGTCCCATGCACACA 59.595 50.000 0.00 0.00 0.00 3.72
3640 4495 1.098050 GATTCCTGTCCCATGCACAC 58.902 55.000 0.00 0.00 0.00 3.82
3659 4514 4.562347 CCGTATGATGAGGGGAAGAGATTG 60.562 50.000 0.00 0.00 0.00 2.67
3677 4532 5.676552 TGGTTAATCTTGCATGTACCGTAT 58.323 37.500 0.00 0.00 0.00 3.06
3683 4538 5.123820 GCTGAGTTGGTTAATCTTGCATGTA 59.876 40.000 0.00 0.00 0.00 2.29
3697 4552 2.040278 TCCAATTGCTAGCTGAGTTGGT 59.960 45.455 25.64 3.02 37.82 3.67
3698 4553 2.715046 TCCAATTGCTAGCTGAGTTGG 58.285 47.619 23.21 23.21 37.91 3.77
3699 4554 3.693085 ACATCCAATTGCTAGCTGAGTTG 59.307 43.478 17.23 14.00 0.00 3.16
3700 4555 3.693085 CACATCCAATTGCTAGCTGAGTT 59.307 43.478 17.23 2.61 0.00 3.01
3701 4556 3.276857 CACATCCAATTGCTAGCTGAGT 58.723 45.455 17.23 0.72 0.00 3.41
3702 4557 3.276857 ACACATCCAATTGCTAGCTGAG 58.723 45.455 17.23 5.09 0.00 3.35
3703 4558 3.354948 ACACATCCAATTGCTAGCTGA 57.645 42.857 17.23 4.98 0.00 4.26
3704 4559 4.818005 TCATACACATCCAATTGCTAGCTG 59.182 41.667 17.23 5.84 0.00 4.24


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

AutoCloner maintained by Alex Coulton.