Multiple sequence alignment - TraesCS1B01G006700

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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 TraesCS1B01G006700 chr1B 100.000 3839 0 0 1 3839 3951346 3955184 0.000000e+00 7090
1 TraesCS1B01G006700 chr1B 88.325 3332 377 7 1 3325 4483476 4480150 0.000000e+00 3988
2 TraesCS1B01G006700 chr1B 87.281 3373 413 13 1 3362 4095772 4099139 0.000000e+00 3838
3 TraesCS1B01G006700 chr1B 86.528 3318 421 20 1 3307 4114729 4118031 0.000000e+00 3627
4 TraesCS1B01G006700 chr1B 85.948 3366 461 9 4 3362 4510639 4507279 0.000000e+00 3585
5 TraesCS1B01G006700 chr1B 85.587 3372 461 17 1 3362 3964752 3968108 0.000000e+00 3511
6 TraesCS1B01G006700 chr1B 87.531 2863 333 20 4 2854 4150970 4153820 0.000000e+00 3288
7 TraesCS1B01G006700 chr1B 87.982 882 101 3 2485 3362 4842014 4841134 0.000000e+00 1037
8 TraesCS1B01G006700 chr1A 88.090 3854 417 30 4 3839 3503669 3499840 0.000000e+00 4536
9 TraesCS1B01G006700 chr1A 89.891 2651 234 16 809 3430 3656214 3653569 0.000000e+00 3380
10 TraesCS1B01G006700 chr1A 85.518 3204 453 9 4 3203 3672296 3669100 0.000000e+00 3336
11 TraesCS1B01G006700 chr1A 87.580 314 18 10 3484 3797 3653104 3652812 1.020000e-90 344
12 TraesCS1B01G006700 chr1D 86.802 3311 424 10 4 3307 620943 617639 0.000000e+00 3681
13 TraesCS1B01G006700 chr1D 92.324 482 25 7 3356 3835 651140 651611 0.000000e+00 675
14 TraesCS1B01G006700 chr1D 81.308 321 46 10 3523 3839 397748 398058 8.240000e-62 248


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 TraesCS1B01G006700 chr1B 3951346 3955184 3838 False 7090 7090 100.0000 1 3839 1 chr1B.!!$F1 3838
1 TraesCS1B01G006700 chr1B 4480150 4483476 3326 True 3988 3988 88.3250 1 3325 1 chr1B.!!$R1 3324
2 TraesCS1B01G006700 chr1B 4095772 4099139 3367 False 3838 3838 87.2810 1 3362 1 chr1B.!!$F3 3361
3 TraesCS1B01G006700 chr1B 4114729 4118031 3302 False 3627 3627 86.5280 1 3307 1 chr1B.!!$F4 3306
4 TraesCS1B01G006700 chr1B 4507279 4510639 3360 True 3585 3585 85.9480 4 3362 1 chr1B.!!$R2 3358
5 TraesCS1B01G006700 chr1B 3964752 3968108 3356 False 3511 3511 85.5870 1 3362 1 chr1B.!!$F2 3361
6 TraesCS1B01G006700 chr1B 4150970 4153820 2850 False 3288 3288 87.5310 4 2854 1 chr1B.!!$F5 2850
7 TraesCS1B01G006700 chr1B 4841134 4842014 880 True 1037 1037 87.9820 2485 3362 1 chr1B.!!$R3 877
8 TraesCS1B01G006700 chr1A 3499840 3503669 3829 True 4536 4536 88.0900 4 3839 1 chr1A.!!$R1 3835
9 TraesCS1B01G006700 chr1A 3669100 3672296 3196 True 3336 3336 85.5180 4 3203 1 chr1A.!!$R2 3199
10 TraesCS1B01G006700 chr1A 3652812 3656214 3402 True 1862 3380 88.7355 809 3797 2 chr1A.!!$R3 2988
11 TraesCS1B01G006700 chr1D 617639 620943 3304 True 3681 3681 86.8020 4 3307 1 chr1D.!!$R1 3303

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
984 986 0.625091 TAACCGGTTCCATCCCCCAT 60.625 55.0 26.16 0.0 0.00 4.00 F
1269 1271 0.617249 TGTTTGATGGCCCCATTCCC 60.617 55.0 0.00 0.0 36.70 3.97 F
1485 1487 0.703488 TGCTCATGGGTTCCATTCCA 59.297 50.0 0.00 0.0 42.23 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1843 0.881118 CCAAGTTGCTGCGGTAACAT 59.119 50.000 25.59 13.39 39.85 2.71 R
2345 2351 1.081442 GCCTTGTACACTTTGCCGC 60.081 57.895 0.00 0.00 0.00 6.53 R
3313 3341 0.252239 GGAACCCAAATTGGCCTCCT 60.252 55.000 18.13 0.00 35.21 3.69 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
136 137 3.042871 AGCTCAACTTCTCAGCTCTTG 57.957 47.619 0.00 0.00 39.37 3.02
525 526 8.076178 CAGCTAAATATTTTGTACCTGTATGGC 58.924 37.037 5.91 0.00 40.22 4.40
567 568 1.457346 CCCAAGAACTAGGCAAGCTG 58.543 55.000 0.00 0.00 0.00 4.24
571 572 1.352083 AGAACTAGGCAAGCTGGTCA 58.648 50.000 0.00 0.00 0.00 4.02
585 586 4.144297 AGCTGGTCAATTTGCAAAGTCTA 58.856 39.130 18.19 2.57 0.00 2.59
631 632 5.068636 CAGGTCCAATTCCAATCTCCATAG 58.931 45.833 0.00 0.00 0.00 2.23
666 667 6.625873 AAGATGAACACACTTTTTCTCTCC 57.374 37.500 0.00 0.00 0.00 3.71
675 676 6.183360 ACACACTTTTTCTCTCCAACAATCAG 60.183 38.462 0.00 0.00 0.00 2.90
686 687 2.674852 CCAACAATCAGATCACAGGTCG 59.325 50.000 0.00 0.00 0.00 4.79
687 688 2.674852 CAACAATCAGATCACAGGTCGG 59.325 50.000 0.00 0.00 0.00 4.79
744 745 5.248870 ACCAACTTGATCTCAACACAAAC 57.751 39.130 0.00 0.00 0.00 2.93
804 805 5.645067 CCTCACTATGCTCAATGAACTTTCA 59.355 40.000 0.00 0.00 42.14 2.69
807 808 6.712095 TCACTATGCTCAATGAACTTTCACTT 59.288 34.615 0.00 0.00 40.49 3.16
829 830 8.028354 CACTTTATGCAAATCAAATCACAGGTA 58.972 33.333 0.00 0.00 0.00 3.08
832 833 5.375417 TGCAAATCAAATCACAGGTACAG 57.625 39.130 0.00 0.00 0.00 2.74
856 857 5.796424 ACCTTCAAAATTGAGCATCTTGT 57.204 34.783 0.00 0.00 38.61 3.16
866 867 2.123342 GAGCATCTTGTCGAATCTCCG 58.877 52.381 0.00 0.00 0.00 4.63
879 880 5.061933 GTCGAATCTCCGGTTTTTAGACTTC 59.938 44.000 0.00 2.47 0.00 3.01
883 884 3.260128 TCTCCGGTTTTTAGACTTCTCCC 59.740 47.826 0.00 0.00 0.00 4.30
937 938 6.900194 AGCTTAGGAAATATAACCAAGCTGA 58.100 36.000 21.62 0.00 42.62 4.26
941 942 8.827177 TTAGGAAATATAACCAAGCTGATACG 57.173 34.615 0.00 0.00 0.00 3.06
984 986 0.625091 TAACCGGTTCCATCCCCCAT 60.625 55.000 26.16 0.00 0.00 4.00
1077 1079 1.413812 ACTTTTGGGAAGCTGCAAAGG 59.586 47.619 1.02 0.00 0.00 3.11
1080 1082 2.014010 TTGGGAAGCTGCAAAGGATT 57.986 45.000 1.02 0.00 0.00 3.01
1081 1083 2.897271 TGGGAAGCTGCAAAGGATTA 57.103 45.000 1.02 0.00 0.00 1.75
1082 1084 2.726821 TGGGAAGCTGCAAAGGATTAG 58.273 47.619 1.02 0.00 0.00 1.73
1129 1131 7.391833 ACAATTTATCAGGTTCTCTTCCTCAAC 59.608 37.037 0.00 0.00 32.37 3.18
1159 1161 5.113446 AGATCTCATCAGCCTTGTTGAAT 57.887 39.130 0.00 0.00 33.77 2.57
1165 1167 1.969923 TCAGCCTTGTTGAATTTGGGG 59.030 47.619 0.00 0.00 0.00 4.96
1191 1193 5.820947 GTCTAAAAACTCACTTTCAGGACCA 59.179 40.000 0.00 0.00 0.00 4.02
1245 1247 9.626045 AAACTTGAATATTTCGATGTTTCTTCC 57.374 29.630 0.00 0.00 0.00 3.46
1255 1257 8.741101 TTTCGATGTTTCTTCCAATATGTTTG 57.259 30.769 0.00 0.00 0.00 2.93
1269 1271 0.617249 TGTTTGATGGCCCCATTCCC 60.617 55.000 0.00 0.00 36.70 3.97
1287 1289 6.349363 CCATTCCCAGTAGTTTAAAGACTTGC 60.349 42.308 0.81 0.00 0.00 4.01
1291 1293 4.084013 CCAGTAGTTTAAAGACTTGCACGG 60.084 45.833 0.00 0.00 0.00 4.94
1297 1299 1.757682 AAAGACTTGCACGGGTTTGA 58.242 45.000 0.00 0.00 0.00 2.69
1298 1300 1.757682 AAGACTTGCACGGGTTTGAA 58.242 45.000 0.00 0.00 0.00 2.69
1299 1301 1.757682 AGACTTGCACGGGTTTGAAA 58.242 45.000 0.00 0.00 0.00 2.69
1303 1305 2.192624 CTTGCACGGGTTTGAAACAAG 58.807 47.619 10.53 5.51 0.00 3.16
1345 1347 7.952930 ACCAACTATCAGGTGATATATCTCAGT 59.047 37.037 13.79 6.59 33.95 3.41
1364 1366 4.932799 TCAGTATTTTGGTGTGTATCCACG 59.067 41.667 0.00 0.00 44.92 4.94
1371 1373 2.094234 TGGTGTGTATCCACGACTCATG 60.094 50.000 0.00 0.00 44.92 3.07
1373 1375 3.179830 GTGTGTATCCACGACTCATGAC 58.820 50.000 0.00 0.00 44.92 3.06
1378 1380 1.173913 TCCACGACTCATGACGATGT 58.826 50.000 12.18 0.00 35.52 3.06
1415 1417 2.244486 TTCTCTGGGCAGATCTCACT 57.756 50.000 0.00 0.00 36.76 3.41
1422 1424 4.015084 CTGGGCAGATCTCACTCAATTTT 58.985 43.478 0.00 0.00 0.00 1.82
1468 1470 6.073003 GGTCCTACATCTAGCACAAAATATGC 60.073 42.308 0.00 0.00 43.74 3.14
1482 1484 5.426185 ACAAAATATGCTCATGGGTTCCATT 59.574 36.000 0.00 0.00 42.23 3.16
1485 1487 0.703488 TGCTCATGGGTTCCATTCCA 59.297 50.000 0.00 0.00 42.23 3.53
1543 1546 5.132897 AGCACTCGATTCTAATCATCTCC 57.867 43.478 3.76 0.00 35.11 3.71
1544 1547 4.586421 AGCACTCGATTCTAATCATCTCCA 59.414 41.667 3.76 0.00 35.11 3.86
1550 1553 4.391216 CGATTCTAATCATCTCCATGGTGC 59.609 45.833 12.58 0.00 35.11 5.01
1577 1580 8.934023 ATTCCACCAGAAATCTGTAGTTTAAA 57.066 30.769 9.43 0.00 42.27 1.52
1578 1581 8.934023 TTCCACCAGAAATCTGTAGTTTAAAT 57.066 30.769 9.43 0.00 42.27 1.40
1621 1624 9.699410 ACTTATCATCAAACCAATTATCTGGAA 57.301 29.630 0.00 0.00 38.96 3.53
1657 1660 6.697892 ACAGATAGAAAAGCTACGCAATCTAC 59.302 38.462 0.00 0.00 0.00 2.59
1693 1696 1.801242 TGGGAACAGACTGAGTGGAA 58.199 50.000 10.08 0.00 35.01 3.53
1717 1720 0.790993 ACCTGAGGAACTAGGGACCA 59.209 55.000 4.99 0.00 41.55 4.02
1840 1843 4.824537 TGAGCAACAATAACTTAACTGGCA 59.175 37.500 0.00 0.00 0.00 4.92
2301 2307 5.048504 AGCATTTGATGATATTGTAAGGGCG 60.049 40.000 0.00 0.00 0.00 6.13
2345 2351 3.894759 ACATCATTGGAACAGGAGGATG 58.105 45.455 0.00 0.00 42.39 3.51
2437 2443 7.553402 CAGAAGAAGAGTTGGATGATGAAAGAT 59.447 37.037 0.00 0.00 0.00 2.40
2479 2485 6.262273 GGAAATCTTATTACAGATCCGCCAAA 59.738 38.462 0.00 0.00 31.87 3.28
2583 2589 4.085733 TCCACCGAACATTGGAAAATGAT 58.914 39.130 5.49 0.00 39.04 2.45
2592 2598 4.036027 ACATTGGAAAATGATGAGCTAGCG 59.964 41.667 9.55 0.00 34.39 4.26
2667 2673 5.207768 GCAATATCTTATTTGCACCACGAG 58.792 41.667 2.96 0.00 45.83 4.18
2864 2870 2.900546 ACCTTCCTTCTCACGTCTGAAT 59.099 45.455 0.00 0.00 0.00 2.57
3142 3157 0.037303 TCAAGCTGGCCTTCTCTTGG 59.963 55.000 19.20 7.76 37.21 3.61
3313 3341 1.202903 GGAGCCAGGGACTATCGTAGA 60.203 57.143 0.00 0.00 37.66 2.59
3326 3354 2.691409 TCGTAGAGGAGGCCAATTTG 57.309 50.000 5.01 0.00 0.00 2.32
3344 3372 4.986054 TTTGGGTTCCTGCTTTAGACTA 57.014 40.909 0.00 0.00 0.00 2.59
3464 3966 5.016831 GGACTTCCAGGAAAATTACCACAT 58.983 41.667 2.72 0.00 35.64 3.21
3465 3967 6.011981 AGGACTTCCAGGAAAATTACCACATA 60.012 38.462 2.72 0.00 38.89 2.29
3466 3968 6.095021 GGACTTCCAGGAAAATTACCACATAC 59.905 42.308 2.72 0.00 35.64 2.39
3467 3969 5.646360 ACTTCCAGGAAAATTACCACATACG 59.354 40.000 2.72 0.00 0.00 3.06
3469 3971 4.225492 TCCAGGAAAATTACCACATACGGA 59.775 41.667 0.00 0.00 0.00 4.69
3470 3972 4.574828 CCAGGAAAATTACCACATACGGAG 59.425 45.833 4.75 0.00 0.00 4.63
3471 3973 4.035208 CAGGAAAATTACCACATACGGAGC 59.965 45.833 4.75 0.00 0.00 4.70
3472 3974 4.080526 AGGAAAATTACCACATACGGAGCT 60.081 41.667 0.00 0.00 0.00 4.09
3473 3975 5.129815 AGGAAAATTACCACATACGGAGCTA 59.870 40.000 0.00 0.00 0.00 3.32
3474 3976 5.235831 GGAAAATTACCACATACGGAGCTAC 59.764 44.000 0.00 0.00 0.00 3.58
3475 3977 3.637998 ATTACCACATACGGAGCTACG 57.362 47.619 19.02 19.02 40.31 3.51
3476 3978 2.330440 TACCACATACGGAGCTACGA 57.670 50.000 28.55 9.37 37.61 3.43
3482 3984 1.173444 ATACGGAGCTACGAGCAGGG 61.173 60.000 28.55 0.00 45.56 4.45
3490 3992 2.158943 AGCTACGAGCAGGGAAATTACC 60.159 50.000 9.09 0.00 45.56 2.85
3517 4019 5.296780 CAGCAAGGAAAACTAGTTGACTCAA 59.703 40.000 9.34 0.00 0.00 3.02
3590 4092 9.065871 GTTTCTTGTATTTCATTGCTCACATAC 57.934 33.333 0.00 0.00 0.00 2.39
3673 4180 7.862372 TCAGATGCAATTGAAACAAAAGTAGAC 59.138 33.333 10.34 0.00 0.00 2.59
3688 4195 9.482627 ACAAAAGTAGACAGAAAAGATAGACAG 57.517 33.333 0.00 0.00 0.00 3.51
3724 4231 8.868522 ATCTTGAAAACATGAAGAATCTGGTA 57.131 30.769 0.00 0.00 29.78 3.25
3733 4240 7.425606 ACATGAAGAATCTGGTAAAACAACAC 58.574 34.615 0.00 0.00 0.00 3.32
3748 4255 3.530535 ACAACACGATGCTGCATACATA 58.469 40.909 16.23 0.00 0.00 2.29
3754 4261 9.248291 CAACACGATGCTGCATACATATATATA 57.752 33.333 16.23 0.00 0.00 0.86
3755 4262 9.987272 AACACGATGCTGCATACATATATATAT 57.013 29.630 16.23 0.00 0.00 0.86
3776 4283 3.664107 TCTTCAATCCTGACTGTTTCCG 58.336 45.455 0.00 0.00 0.00 4.30
3795 4302 3.012518 CCGTCATCCATTTCAGCTCTTT 58.987 45.455 0.00 0.00 0.00 2.52
3796 4303 4.081142 TCCGTCATCCATTTCAGCTCTTTA 60.081 41.667 0.00 0.00 0.00 1.85
3797 4304 4.635765 CCGTCATCCATTTCAGCTCTTTAA 59.364 41.667 0.00 0.00 0.00 1.52
3798 4305 5.297776 CCGTCATCCATTTCAGCTCTTTAAT 59.702 40.000 0.00 0.00 0.00 1.40
3822 4329 0.109597 GGCAGTTTTCCGCAGTCATG 60.110 55.000 0.00 0.00 0.00 3.07
3835 4342 4.616802 CCGCAGTCATGTGTTAAATGAAAC 59.383 41.667 0.00 0.00 35.87 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 6.233434 TGAGGTCAATATATGTGAGGAATGC 58.767 40.000 0.00 0.00 0.00 3.56
493 494 8.962679 CAGGTACAAAATATTTAGCTGGGTTAA 58.037 33.333 16.00 0.00 37.58 2.01
525 526 5.513267 GGGTATAGGCCCTGAAAGTAGATTG 60.513 48.000 0.00 0.00 45.22 2.67
567 568 4.457257 AGCTCTAGACTTTGCAAATTGACC 59.543 41.667 13.23 0.74 0.00 4.02
601 602 7.124147 GGAGATTGGAATTGGACCTGAAAAATA 59.876 37.037 0.00 0.00 0.00 1.40
631 632 4.937620 TGTGTTCATCTTAGTGAGATTGGC 59.062 41.667 0.00 0.00 42.55 4.52
666 667 2.674852 CCGACCTGTGATCTGATTGTTG 59.325 50.000 0.00 0.00 0.00 3.33
686 687 1.057471 GCCTAGTTCTGGGGGTATCC 58.943 60.000 4.49 0.00 0.00 2.59
687 688 1.802553 TGCCTAGTTCTGGGGGTATC 58.197 55.000 4.49 0.00 0.00 2.24
804 805 6.996509 ACCTGTGATTTGATTTGCATAAAGT 58.003 32.000 0.00 0.00 0.00 2.66
807 808 7.176515 ACTGTACCTGTGATTTGATTTGCATAA 59.823 33.333 0.00 0.00 0.00 1.90
829 830 6.006449 AGATGCTCAATTTTGAAGGTACTGT 58.994 36.000 0.00 0.00 40.86 3.55
832 833 6.681777 ACAAGATGCTCAATTTTGAAGGTAC 58.318 36.000 0.00 0.00 36.64 3.34
841 842 5.065731 GGAGATTCGACAAGATGCTCAATTT 59.934 40.000 0.00 0.00 33.61 1.82
847 848 1.202463 CCGGAGATTCGACAAGATGCT 60.202 52.381 0.00 0.00 0.00 3.79
856 857 4.796038 AGTCTAAAAACCGGAGATTCGA 57.204 40.909 9.46 0.00 0.00 3.71
866 867 4.277672 GGTTGTGGGAGAAGTCTAAAAACC 59.722 45.833 0.00 0.00 0.00 3.27
879 880 2.689983 GCCAGATATTTGGTTGTGGGAG 59.310 50.000 13.50 0.00 40.49 4.30
883 884 6.016777 GGAATAGAGCCAGATATTTGGTTGTG 60.017 42.308 13.50 0.00 40.49 3.33
937 938 7.232188 TGATTTACAGAGAGGGATAGTCGTAT 58.768 38.462 0.00 0.00 0.00 3.06
984 986 3.025978 GTTCATCAGATTGCCAATCCCA 58.974 45.455 13.69 1.24 38.71 4.37
986 988 3.294214 AGGTTCATCAGATTGCCAATCC 58.706 45.455 13.69 0.00 38.71 3.01
1129 1131 4.462133 AGGCTGATGAGATCTCCAAATTG 58.538 43.478 20.03 6.71 0.00 2.32
1159 1161 4.862371 AGTGAGTTTTTAGACACCCCAAA 58.138 39.130 0.00 0.00 34.33 3.28
1165 1167 6.238402 GGTCCTGAAAGTGAGTTTTTAGACAC 60.238 42.308 10.22 0.00 0.00 3.67
1231 1233 8.105097 TCAAACATATTGGAAGAAACATCGAA 57.895 30.769 0.00 0.00 0.00 3.71
1245 1247 4.503643 GGAATGGGGCCATCAAACATATTG 60.504 45.833 4.39 0.00 35.31 1.90
1254 1256 0.625980 TACTGGGAATGGGGCCATCA 60.626 55.000 4.39 2.02 35.31 3.07
1255 1257 0.111253 CTACTGGGAATGGGGCCATC 59.889 60.000 4.39 0.00 35.31 3.51
1269 1271 4.084013 CCCGTGCAAGTCTTTAAACTACTG 60.084 45.833 0.00 0.00 0.00 2.74
1287 1289 4.106909 GGTAAACTTGTTTCAAACCCGTG 58.893 43.478 1.72 0.00 0.00 4.94
1298 1300 7.789831 GTTGGTTCAACTCAAGGTAAACTTGTT 60.790 37.037 6.73 0.00 43.93 2.83
1299 1301 6.349860 GTTGGTTCAACTCAAGGTAAACTTGT 60.350 38.462 6.73 0.00 43.93 3.16
1316 1318 8.727100 AGATATATCACCTGATAGTTGGTTCA 57.273 34.615 15.08 0.00 40.04 3.18
1327 1329 9.159254 ACCAAAATACTGAGATATATCACCTGA 57.841 33.333 15.08 0.00 0.00 3.86
1364 1366 3.182967 GTCAAGGACATCGTCATGAGTC 58.817 50.000 0.00 0.00 33.13 3.36
1378 1380 4.748892 GAGAATCTGTTCGATGTCAAGGA 58.251 43.478 0.00 0.00 39.38 3.36
1415 1417 3.234353 TGGGTACATGCACCAAAATTGA 58.766 40.909 17.06 0.00 40.65 2.57
1422 1424 3.351740 CATTAGTTGGGTACATGCACCA 58.648 45.455 17.06 8.39 40.65 4.17
1468 1470 1.767759 GGTGGAATGGAACCCATGAG 58.232 55.000 0.00 0.00 44.40 2.90
1472 1474 0.254747 GATCGGTGGAATGGAACCCA 59.745 55.000 0.00 0.00 38.19 4.51
1482 1484 6.100569 TGGATAATTTAGAAAGGATCGGTGGA 59.899 38.462 0.00 0.00 0.00 4.02
1485 1487 6.771267 GGTTGGATAATTTAGAAAGGATCGGT 59.229 38.462 0.00 0.00 0.00 4.69
1522 1524 4.876125 TGGAGATGATTAGAATCGAGTGC 58.124 43.478 0.00 0.00 38.26 4.40
1543 1546 4.317359 TGGTGGAATCGCACCATG 57.683 55.556 16.15 0.00 45.54 3.66
1621 1624 5.745227 CTTTTCTATCTGTGTGGGTATGGT 58.255 41.667 0.00 0.00 0.00 3.55
1657 1660 8.597167 TCTGTTCCCAGATATATCAAGGTATTG 58.403 37.037 15.08 2.65 42.80 1.90
1693 1696 5.102783 TGGTCCCTAGTTCCTCAGGTATTAT 60.103 44.000 0.00 0.00 0.00 1.28
1717 1720 4.623932 TCAAGGACAGTAGTTTCATGCT 57.376 40.909 0.00 0.00 0.00 3.79
1840 1843 0.881118 CCAAGTTGCTGCGGTAACAT 59.119 50.000 25.59 13.39 39.85 2.71
1954 1957 5.106555 CCAAGTCATTGTAGGACACATCAAC 60.107 44.000 0.00 0.00 36.90 3.18
2301 2307 6.529125 TGTACTTATCATCGAAGTTTTCGGTC 59.471 38.462 10.84 0.00 44.45 4.79
2345 2351 1.081442 GCCTTGTACACTTTGCCGC 60.081 57.895 0.00 0.00 0.00 6.53
2437 2443 1.974265 TCCATTTCACTGCGAAACCA 58.026 45.000 0.00 0.00 46.22 3.67
2479 2485 6.839124 TCCATACATTTTGACAATGCTTCT 57.161 33.333 0.00 0.00 0.00 2.85
2583 2589 1.831106 TCCAATTCCTTCGCTAGCTCA 59.169 47.619 13.93 0.00 0.00 4.26
2592 2598 4.019174 TCTTCTGCCAATCCAATTCCTTC 58.981 43.478 0.00 0.00 0.00 3.46
2667 2673 4.393062 CGATGGATTATAGGTGGATTGCAC 59.607 45.833 0.00 0.00 0.00 4.57
2672 2678 9.883293 TTATATCTCGATGGATTATAGGTGGAT 57.117 33.333 0.00 0.00 0.00 3.41
3313 3341 0.252239 GGAACCCAAATTGGCCTCCT 60.252 55.000 18.13 0.00 35.21 3.69
3326 3354 3.770388 ACTCTAGTCTAAAGCAGGAACCC 59.230 47.826 0.00 0.00 0.00 4.11
3344 3372 2.159184 CGTGTGGCATATGAGTGACTCT 60.159 50.000 14.42 2.18 0.00 3.24
3416 3475 7.501225 CCTTTCACCGTGGTATTTTCCTATATT 59.499 37.037 0.00 0.00 0.00 1.28
3464 3966 1.822613 CCCTGCTCGTAGCTCCGTA 60.823 63.158 0.00 0.00 42.97 4.02
3465 3967 3.141488 CCCTGCTCGTAGCTCCGT 61.141 66.667 0.00 0.00 42.97 4.69
3466 3968 1.945354 TTTCCCTGCTCGTAGCTCCG 61.945 60.000 0.00 0.00 42.97 4.63
3467 3969 0.466124 ATTTCCCTGCTCGTAGCTCC 59.534 55.000 0.00 0.00 42.97 4.70
3469 3971 2.158943 GGTAATTTCCCTGCTCGTAGCT 60.159 50.000 8.07 0.00 42.97 3.32
3470 3972 2.210961 GGTAATTTCCCTGCTCGTAGC 58.789 52.381 0.58 0.58 42.82 3.58
3471 3973 3.536956 TGGTAATTTCCCTGCTCGTAG 57.463 47.619 0.00 0.00 0.00 3.51
3472 3974 3.008157 TGTTGGTAATTTCCCTGCTCGTA 59.992 43.478 0.00 0.00 0.00 3.43
3473 3975 2.224670 TGTTGGTAATTTCCCTGCTCGT 60.225 45.455 0.00 0.00 0.00 4.18
3474 3976 2.420022 CTGTTGGTAATTTCCCTGCTCG 59.580 50.000 0.00 0.00 0.00 5.03
3475 3977 2.164422 GCTGTTGGTAATTTCCCTGCTC 59.836 50.000 0.00 0.00 0.00 4.26
3476 3978 2.171003 GCTGTTGGTAATTTCCCTGCT 58.829 47.619 0.00 0.00 0.00 4.24
3482 3984 6.280643 AGTTTTCCTTGCTGTTGGTAATTTC 58.719 36.000 0.00 0.00 0.00 2.17
3490 3992 5.066505 AGTCAACTAGTTTTCCTTGCTGTTG 59.933 40.000 5.07 0.00 36.05 3.33
3517 4019 6.013032 CCCAGATTACATTGATGAGGAGGTAT 60.013 42.308 0.00 0.00 0.00 2.73
3559 4061 9.230122 TGAGCAATGAAATACAAGAAACTATCA 57.770 29.630 0.00 0.00 0.00 2.15
3590 4092 6.815142 TGCAATACGAGATGATGGATCTTATG 59.185 38.462 0.00 0.00 41.91 1.90
3625 4128 6.662755 TGAATCCATACCTGCTTCTGTATTT 58.337 36.000 0.00 0.00 0.00 1.40
3627 4130 5.604231 TCTGAATCCATACCTGCTTCTGTAT 59.396 40.000 0.00 0.00 0.00 2.29
3673 4180 8.768957 TCTCATTTGACTGTCTATCTTTTCTG 57.231 34.615 9.51 0.00 0.00 3.02
3688 4195 9.467258 TTCATGTTTTCAAGATTCTCATTTGAC 57.533 29.630 0.00 0.00 31.11 3.18
3724 4231 2.798976 ATGCAGCATCGTGTTGTTTT 57.201 40.000 0.52 0.00 30.85 2.43
3754 4261 4.256920 CGGAAACAGTCAGGATTGAAGAT 58.743 43.478 0.00 0.00 34.49 2.40
3755 4262 3.071023 ACGGAAACAGTCAGGATTGAAGA 59.929 43.478 0.00 0.00 34.49 2.87
3769 4276 2.487762 GCTGAAATGGATGACGGAAACA 59.512 45.455 0.00 0.00 0.00 2.83
3773 4280 1.833630 AGAGCTGAAATGGATGACGGA 59.166 47.619 0.00 0.00 0.00 4.69
3795 4302 4.461081 ACTGCGGAAAACTGCCAATAATTA 59.539 37.500 0.00 0.00 0.00 1.40
3796 4303 3.258123 ACTGCGGAAAACTGCCAATAATT 59.742 39.130 0.00 0.00 0.00 1.40
3797 4304 2.825532 ACTGCGGAAAACTGCCAATAAT 59.174 40.909 0.00 0.00 0.00 1.28
3798 4305 2.227865 GACTGCGGAAAACTGCCAATAA 59.772 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.