Multiple sequence alignment - TraesCS3D01G078000

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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 TraesCS3D01G078000 chr3D 100.000 2252 0 0 1 2252 38611801 38614052 0.000000e+00 4159
1 TraesCS3D01G078000 chr3D 94.423 771 41 2 1483 2252 450942536 450941767 0.000000e+00 1184
2 TraesCS3D01G078000 chr3D 87.571 177 19 3 1193 1368 1226777 1226603 3.790000e-48 202
3 TraesCS3D01G078000 chr3D 77.692 260 33 16 1117 1376 577026934 577027168 3.900000e-28 135
4 TraesCS3D01G078000 chr2D 95.319 769 33 2 1484 2252 609326559 609327324 0.000000e+00 1218
5 TraesCS3D01G078000 chr2D 89.055 603 55 8 6 599 448192161 448191561 0.000000e+00 737
6 TraesCS3D01G078000 chr6D 94.922 768 39 0 1485 2252 378322507 378323274 0.000000e+00 1203
7 TraesCS3D01G078000 chr6D 89.456 588 54 4 6 586 94777586 94778172 0.000000e+00 736
8 TraesCS3D01G078000 chr6D 92.016 501 34 4 611 1111 454745272 454744778 0.000000e+00 699
9 TraesCS3D01G078000 chr6D 90.780 282 18 6 1109 1384 454743137 454742858 9.820000e-99 370
10 TraesCS3D01G078000 chr4D 94.689 772 41 0 1481 2252 364618905 364619676 0.000000e+00 1199
11 TraesCS3D01G078000 chr4D 94.668 769 41 0 1484 2252 350489875 350489107 0.000000e+00 1194
12 TraesCS3D01G078000 chr4D 90.067 594 49 3 3 588 31018174 31017583 0.000000e+00 761
13 TraesCS3D01G078000 chr4D 87.722 619 63 9 6 614 351533808 351534423 0.000000e+00 710
14 TraesCS3D01G078000 chr1D 94.696 773 39 2 1482 2252 55682917 55683689 0.000000e+00 1199
15 TraesCS3D01G078000 chr1D 90.155 579 47 5 6 575 481494022 481493445 0.000000e+00 745
16 TraesCS3D01G078000 chr7D 94.661 768 40 1 1485 2252 262368796 262369562 0.000000e+00 1190
17 TraesCS3D01G078000 chr7D 94.545 770 41 1 1483 2252 427920364 427919596 0.000000e+00 1188
18 TraesCS3D01G078000 chr5D 94.531 768 42 0 1485 2252 268875982 268876749 0.000000e+00 1186
19 TraesCS3D01G078000 chr5D 89.394 594 52 9 7 592 9500216 9499626 0.000000e+00 737
20 TraesCS3D01G078000 chr5D 88.870 593 57 5 6 591 360902438 360903028 0.000000e+00 721
21 TraesCS3D01G078000 chr6A 90.886 801 50 9 605 1384 85254335 85253537 0.000000e+00 1053
22 TraesCS3D01G078000 chr1A 89.147 774 78 5 611 1378 535687470 535686697 0.000000e+00 959
23 TraesCS3D01G078000 chr5B 87.724 782 73 9 624 1384 192179634 192178855 0.000000e+00 891
24 TraesCS3D01G078000 chr3B 90.378 582 48 4 14 587 98994511 98993930 0.000000e+00 758
25 TraesCS3D01G078000 chr7B 90.877 570 41 5 814 1380 538049049 538049610 0.000000e+00 754
26 TraesCS3D01G078000 chrUn 89.527 592 52 6 7 590 73961066 73960477 0.000000e+00 741
27 TraesCS3D01G078000 chr7A 79.300 343 64 6 953 1292 233341056 233341394 1.340000e-57 233
28 TraesCS3D01G078000 chr7A 84.181 177 28 0 1186 1362 5392915 5392739 2.970000e-39 172
29 TraesCS3D01G078000 chr7A 76.019 417 53 25 982 1376 639294982 639295373 2.970000e-39 172
30 TraesCS3D01G078000 chr7A 81.421 183 30 4 1110 1292 3959122 3959300 1.800000e-31 147
31 TraesCS3D01G078000 chr4B 79.016 305 59 5 982 1284 661648832 661649133 1.050000e-48 204


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 TraesCS3D01G078000 chr3D 38611801 38614052 2251 False 4159.0 4159 100.000 1 2252 1 chr3D.!!$F1 2251
1 TraesCS3D01G078000 chr3D 450941767 450942536 769 True 1184.0 1184 94.423 1483 2252 1 chr3D.!!$R2 769
2 TraesCS3D01G078000 chr2D 609326559 609327324 765 False 1218.0 1218 95.319 1484 2252 1 chr2D.!!$F1 768
3 TraesCS3D01G078000 chr2D 448191561 448192161 600 True 737.0 737 89.055 6 599 1 chr2D.!!$R1 593
4 TraesCS3D01G078000 chr6D 378322507 378323274 767 False 1203.0 1203 94.922 1485 2252 1 chr6D.!!$F2 767
5 TraesCS3D01G078000 chr6D 94777586 94778172 586 False 736.0 736 89.456 6 586 1 chr6D.!!$F1 580
6 TraesCS3D01G078000 chr6D 454742858 454745272 2414 True 534.5 699 91.398 611 1384 2 chr6D.!!$R1 773
7 TraesCS3D01G078000 chr4D 364618905 364619676 771 False 1199.0 1199 94.689 1481 2252 1 chr4D.!!$F2 771
8 TraesCS3D01G078000 chr4D 350489107 350489875 768 True 1194.0 1194 94.668 1484 2252 1 chr4D.!!$R2 768
9 TraesCS3D01G078000 chr4D 31017583 31018174 591 True 761.0 761 90.067 3 588 1 chr4D.!!$R1 585
10 TraesCS3D01G078000 chr4D 351533808 351534423 615 False 710.0 710 87.722 6 614 1 chr4D.!!$F1 608
11 TraesCS3D01G078000 chr1D 55682917 55683689 772 False 1199.0 1199 94.696 1482 2252 1 chr1D.!!$F1 770
12 TraesCS3D01G078000 chr1D 481493445 481494022 577 True 745.0 745 90.155 6 575 1 chr1D.!!$R1 569
13 TraesCS3D01G078000 chr7D 262368796 262369562 766 False 1190.0 1190 94.661 1485 2252 1 chr7D.!!$F1 767
14 TraesCS3D01G078000 chr7D 427919596 427920364 768 True 1188.0 1188 94.545 1483 2252 1 chr7D.!!$R1 769
15 TraesCS3D01G078000 chr5D 268875982 268876749 767 False 1186.0 1186 94.531 1485 2252 1 chr5D.!!$F1 767
16 TraesCS3D01G078000 chr5D 9499626 9500216 590 True 737.0 737 89.394 7 592 1 chr5D.!!$R1 585
17 TraesCS3D01G078000 chr5D 360902438 360903028 590 False 721.0 721 88.870 6 591 1 chr5D.!!$F2 585
18 TraesCS3D01G078000 chr6A 85253537 85254335 798 True 1053.0 1053 90.886 605 1384 1 chr6A.!!$R1 779
19 TraesCS3D01G078000 chr1A 535686697 535687470 773 True 959.0 959 89.147 611 1378 1 chr1A.!!$R1 767
20 TraesCS3D01G078000 chr5B 192178855 192179634 779 True 891.0 891 87.724 624 1384 1 chr5B.!!$R1 760
21 TraesCS3D01G078000 chr3B 98993930 98994511 581 True 758.0 758 90.378 14 587 1 chr3B.!!$R1 573
22 TraesCS3D01G078000 chr7B 538049049 538049610 561 False 754.0 754 90.877 814 1380 1 chr7B.!!$F1 566
23 TraesCS3D01G078000 chrUn 73960477 73961066 589 True 741.0 741 89.527 7 590 1 chrUn.!!$R1 583

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
491 502 0.249447 GCAGGCAACCAAACAACTCC 60.249 55.0 0.0 0.0 37.17 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 3113 1.000385 TGGCACGCAGAAAATTGGAAG 60.0 47.619 0.0 0.0 0.0 3.46 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
94 97 1.175347 CGATCATCTCGGCCTCCTCA 61.175 60.000 0.00 0.00 43.82 3.86
99 102 4.200283 CTCGGCCTCCTCACTCGC 62.200 72.222 0.00 0.00 0.00 5.03
105 108 2.128507 CCTCCTCACTCGCCCTACC 61.129 68.421 0.00 0.00 0.00 3.18
106 109 1.379977 CTCCTCACTCGCCCTACCA 60.380 63.158 0.00 0.00 0.00 3.25
146 149 1.875576 CGAGCACTGCATTATCCTCCC 60.876 57.143 3.30 0.00 0.00 4.30
159 169 2.032528 CTCCCCTGTCTTTGCGCA 59.967 61.111 5.66 5.66 0.00 6.09
236 246 2.710902 CCCACGACTCCATGCTCGA 61.711 63.158 11.32 0.00 33.96 4.04
335 345 2.111384 CCTCTGCTAGCTCTTAACCCA 58.889 52.381 17.23 0.00 0.00 4.51
378 388 5.387113 AACTCTTAATCATACCCCATGCA 57.613 39.130 0.00 0.00 34.35 3.96
399 409 1.268845 GGCAACCAAACAACGTGTAGG 60.269 52.381 0.00 0.00 33.48 3.18
491 502 0.249447 GCAGGCAACCAAACAACTCC 60.249 55.000 0.00 0.00 37.17 3.85
553 564 2.831685 TGGAGAAGTGTATGCAACGT 57.168 45.000 0.00 0.00 0.00 3.99
556 567 3.508402 TGGAGAAGTGTATGCAACGTAGA 59.492 43.478 0.00 0.00 0.00 2.59
591 603 1.600023 CAACCAAACACGCCCTTAGA 58.400 50.000 0.00 0.00 0.00 2.10
597 609 2.616842 CAAACACGCCCTTAGAGTTTGT 59.383 45.455 0.00 0.00 41.68 2.83
599 611 2.490991 ACACGCCCTTAGAGTTTGTTC 58.509 47.619 0.00 0.00 0.00 3.18
602 614 4.020485 ACACGCCCTTAGAGTTTGTTCTAT 60.020 41.667 0.00 0.00 30.20 1.98
634 647 5.277925 GGAAAACGTTTACTTTCATCCGGAA 60.278 40.000 15.03 0.00 33.96 4.30
681 696 1.439228 CTGATCGACACGCATCCCT 59.561 57.895 0.00 0.00 0.00 4.20
682 697 0.596083 CTGATCGACACGCATCCCTC 60.596 60.000 0.00 0.00 0.00 4.30
705 720 4.473520 CCCATCCACCGCTTCGCT 62.474 66.667 0.00 0.00 0.00 4.93
779 796 0.250513 CCTTTCTCTTCCCCCGTCTG 59.749 60.000 0.00 0.00 0.00 3.51
787 804 1.125093 TTCCCCCGTCTGTGTCACAT 61.125 55.000 6.03 0.00 0.00 3.21
906 924 4.643387 AGGTGCTGCAACCCCGAC 62.643 66.667 15.18 0.00 41.54 4.79
1011 1030 1.743623 CGCGTCCATGGCCAAAGTA 60.744 57.895 10.96 0.00 0.00 2.24
1012 1031 1.095228 CGCGTCCATGGCCAAAGTAT 61.095 55.000 10.96 0.00 0.00 2.12
1018 1037 1.476085 CCATGGCCAAAGTATTGCGAA 59.524 47.619 10.96 0.00 35.10 4.70
1050 1069 1.443194 GGCGTTGCTGATGTTGCAG 60.443 57.895 0.00 0.00 41.71 4.41
1079 1098 2.437180 CGGAGCTGCATTGGAGCA 60.437 61.111 28.56 3.51 43.35 4.26
1233 2917 1.538047 GGAGTTGCAATGGAGCTTCA 58.462 50.000 0.59 0.00 34.99 3.02
1380 3064 4.505217 CGCCGACAATGCTGCGTC 62.505 66.667 0.00 0.00 41.95 5.19
1384 3068 3.799753 GACAATGCTGCGTCGGAT 58.200 55.556 0.00 0.00 0.00 4.18
1385 3069 2.089854 GACAATGCTGCGTCGGATT 58.910 52.632 0.00 0.00 0.00 3.01
1386 3070 0.447801 GACAATGCTGCGTCGGATTT 59.552 50.000 0.00 0.00 0.00 2.17
1387 3071 0.881118 ACAATGCTGCGTCGGATTTT 59.119 45.000 0.00 0.00 0.00 1.82
1388 3072 1.269448 ACAATGCTGCGTCGGATTTTT 59.731 42.857 0.00 0.00 0.00 1.94
1389 3073 2.486203 ACAATGCTGCGTCGGATTTTTA 59.514 40.909 0.00 0.00 0.00 1.52
1390 3074 3.100817 CAATGCTGCGTCGGATTTTTAG 58.899 45.455 0.00 0.00 0.00 1.85
1391 3075 1.803334 TGCTGCGTCGGATTTTTAGT 58.197 45.000 0.00 0.00 0.00 2.24
1392 3076 2.147958 TGCTGCGTCGGATTTTTAGTT 58.852 42.857 0.00 0.00 0.00 2.24
1393 3077 2.550606 TGCTGCGTCGGATTTTTAGTTT 59.449 40.909 0.00 0.00 0.00 2.66
1394 3078 2.908626 GCTGCGTCGGATTTTTAGTTTG 59.091 45.455 0.00 0.00 0.00 2.93
1395 3079 2.908626 CTGCGTCGGATTTTTAGTTTGC 59.091 45.455 0.00 0.00 0.00 3.68
1396 3080 2.550606 TGCGTCGGATTTTTAGTTTGCT 59.449 40.909 0.00 0.00 0.00 3.91
1397 3081 3.003897 TGCGTCGGATTTTTAGTTTGCTT 59.996 39.130 0.00 0.00 0.00 3.91
1398 3082 3.360758 GCGTCGGATTTTTAGTTTGCTTG 59.639 43.478 0.00 0.00 0.00 4.01
1399 3083 4.778904 CGTCGGATTTTTAGTTTGCTTGA 58.221 39.130 0.00 0.00 0.00 3.02
1400 3084 5.390613 CGTCGGATTTTTAGTTTGCTTGAT 58.609 37.500 0.00 0.00 0.00 2.57
1401 3085 5.856455 CGTCGGATTTTTAGTTTGCTTGATT 59.144 36.000 0.00 0.00 0.00 2.57
1402 3086 6.362283 CGTCGGATTTTTAGTTTGCTTGATTT 59.638 34.615 0.00 0.00 0.00 2.17
1403 3087 7.409343 CGTCGGATTTTTAGTTTGCTTGATTTC 60.409 37.037 0.00 0.00 0.00 2.17
1404 3088 7.595130 GTCGGATTTTTAGTTTGCTTGATTTCT 59.405 33.333 0.00 0.00 0.00 2.52
1405 3089 8.141268 TCGGATTTTTAGTTTGCTTGATTTCTT 58.859 29.630 0.00 0.00 0.00 2.52
1406 3090 8.216453 CGGATTTTTAGTTTGCTTGATTTCTTG 58.784 33.333 0.00 0.00 0.00 3.02
1407 3091 9.260002 GGATTTTTAGTTTGCTTGATTTCTTGA 57.740 29.630 0.00 0.00 0.00 3.02
1409 3093 8.994429 TTTTTAGTTTGCTTGATTTCTTGACA 57.006 26.923 0.00 0.00 0.00 3.58
1410 3094 8.994429 TTTTAGTTTGCTTGATTTCTTGACAA 57.006 26.923 0.00 0.00 0.00 3.18
1411 3095 9.598517 TTTTAGTTTGCTTGATTTCTTGACAAT 57.401 25.926 0.00 0.00 0.00 2.71
1412 3096 9.598517 TTTAGTTTGCTTGATTTCTTGACAATT 57.401 25.926 0.00 0.00 0.00 2.32
1413 3097 7.473027 AGTTTGCTTGATTTCTTGACAATTG 57.527 32.000 3.24 3.24 0.00 2.32
1414 3098 7.267128 AGTTTGCTTGATTTCTTGACAATTGA 58.733 30.769 13.59 0.00 0.00 2.57
1415 3099 7.765360 AGTTTGCTTGATTTCTTGACAATTGAA 59.235 29.630 13.59 0.00 0.00 2.69
1416 3100 8.553696 GTTTGCTTGATTTCTTGACAATTGAAT 58.446 29.630 13.59 0.00 0.00 2.57
1417 3101 8.665643 TTGCTTGATTTCTTGACAATTGAATT 57.334 26.923 13.59 0.00 0.00 2.17
1418 3102 8.665643 TGCTTGATTTCTTGACAATTGAATTT 57.334 26.923 13.59 0.00 0.00 1.82
1419 3103 9.111613 TGCTTGATTTCTTGACAATTGAATTTT 57.888 25.926 13.59 0.00 0.00 1.82
1420 3104 9.940166 GCTTGATTTCTTGACAATTGAATTTTT 57.060 25.926 13.59 0.00 0.00 1.94
1445 3129 3.578688 GAATGCTTCCAATTTTCTGCGT 58.421 40.909 0.00 0.00 0.00 5.24
1446 3130 2.420628 TGCTTCCAATTTTCTGCGTG 57.579 45.000 0.00 0.00 0.00 5.34
1447 3131 1.063031 GCTTCCAATTTTCTGCGTGC 58.937 50.000 0.00 0.00 0.00 5.34
1448 3132 1.701704 CTTCCAATTTTCTGCGTGCC 58.298 50.000 0.00 0.00 0.00 5.01
1449 3133 1.000385 CTTCCAATTTTCTGCGTGCCA 60.000 47.619 0.00 0.00 0.00 4.92
1450 3134 1.035923 TCCAATTTTCTGCGTGCCAA 58.964 45.000 0.00 0.00 0.00 4.52
1451 3135 1.410517 TCCAATTTTCTGCGTGCCAAA 59.589 42.857 0.00 0.00 0.00 3.28
1452 3136 2.036992 TCCAATTTTCTGCGTGCCAAAT 59.963 40.909 0.00 0.00 0.00 2.32
1453 3137 2.807392 CCAATTTTCTGCGTGCCAAATT 59.193 40.909 0.00 0.00 30.56 1.82
1454 3138 3.250521 CCAATTTTCTGCGTGCCAAATTT 59.749 39.130 4.61 0.00 28.44 1.82
1455 3139 4.450419 CCAATTTTCTGCGTGCCAAATTTA 59.550 37.500 0.00 0.00 28.44 1.40
1456 3140 5.389725 CCAATTTTCTGCGTGCCAAATTTAG 60.390 40.000 0.00 0.00 28.44 1.85
1457 3141 4.314740 TTTTCTGCGTGCCAAATTTAGT 57.685 36.364 0.00 0.00 0.00 2.24
1458 3142 4.314740 TTTCTGCGTGCCAAATTTAGTT 57.685 36.364 0.00 0.00 0.00 2.24
1459 3143 4.314740 TTCTGCGTGCCAAATTTAGTTT 57.685 36.364 0.00 0.00 0.00 2.66
1460 3144 3.896122 TCTGCGTGCCAAATTTAGTTTC 58.104 40.909 0.00 0.00 0.00 2.78
1461 3145 3.568007 TCTGCGTGCCAAATTTAGTTTCT 59.432 39.130 0.00 0.00 0.00 2.52
1462 3146 4.037446 TCTGCGTGCCAAATTTAGTTTCTT 59.963 37.500 0.00 0.00 0.00 2.52
1463 3147 4.295051 TGCGTGCCAAATTTAGTTTCTTC 58.705 39.130 0.00 0.00 0.00 2.87
1464 3148 4.202060 TGCGTGCCAAATTTAGTTTCTTCA 60.202 37.500 0.00 0.00 0.00 3.02
1465 3149 4.923281 GCGTGCCAAATTTAGTTTCTTCAT 59.077 37.500 0.00 0.00 0.00 2.57
1466 3150 5.405269 GCGTGCCAAATTTAGTTTCTTCATT 59.595 36.000 0.00 0.00 0.00 2.57
1467 3151 6.584563 GCGTGCCAAATTTAGTTTCTTCATTA 59.415 34.615 0.00 0.00 0.00 1.90
1468 3152 7.115663 GCGTGCCAAATTTAGTTTCTTCATTAA 59.884 33.333 0.00 0.00 0.00 1.40
1469 3153 8.973378 CGTGCCAAATTTAGTTTCTTCATTAAA 58.027 29.630 0.00 0.00 0.00 1.52
1471 3155 9.267084 TGCCAAATTTAGTTTCTTCATTAAACC 57.733 29.630 0.00 0.00 37.51 3.27
1472 3156 9.489084 GCCAAATTTAGTTTCTTCATTAAACCT 57.511 29.630 0.00 0.00 37.51 3.50
1481 3165 9.793259 AGTTTCTTCATTAAACCTCATAGTCAA 57.207 29.630 0.00 0.00 37.51 3.18
1490 3174 6.840780 AAACCTCATAGTCAAATTGAAGGG 57.159 37.500 13.39 5.88 0.00 3.95
1635 3321 2.890814 ACACAGTGTCCCTAGTAAGCT 58.109 47.619 0.00 0.00 0.00 3.74
1709 3395 6.707440 ACATGAGTTGTCATTTGGTAAACA 57.293 33.333 0.00 0.00 40.84 2.83
1731 3417 7.146715 ACAGGATCACATCATTAGGAGAATT 57.853 36.000 0.00 0.00 0.00 2.17
1755 3441 1.224592 ATGGACAAGACCCATCCGC 59.775 57.895 0.00 0.00 40.16 5.54
1804 3490 9.933723 AGTTTTATTGCTATTGCTTTCTTCATT 57.066 25.926 0.00 0.00 40.48 2.57
2080 3766 3.881795 GCAGGATGATGCATTACGAAAG 58.118 45.455 0.00 0.00 45.77 2.62
2093 3779 5.867716 GCATTACGAAAGGAGTAAAGAGACA 59.132 40.000 0.00 0.00 37.57 3.41
2159 3845 4.694339 GAATCTCGGGCAAGTAACATACT 58.306 43.478 0.00 0.00 41.73 2.12
2218 3904 6.532657 GGTTTGACCGATAAAGATCTTCGTAA 59.467 38.462 8.78 1.38 0.00 3.18
2241 3927 9.944376 GTAAAATATGTAGGAGCCAATATGAGA 57.056 33.333 0.00 0.00 0.00 3.27
2242 3928 8.854614 AAAATATGTAGGAGCCAATATGAGAC 57.145 34.615 0.00 0.00 0.00 3.36
2248 3934 2.968574 GGAGCCAATATGAGACTCCAGA 59.031 50.000 0.00 0.00 45.16 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 97 1.904865 TTCGTGTGGTAGGGCGAGT 60.905 57.895 0.00 0.00 34.78 4.18
99 102 1.202336 GGTATCGTTCGTGTGGTAGGG 60.202 57.143 0.00 0.00 0.00 3.53
105 108 0.650512 GCCATGGTATCGTTCGTGTG 59.349 55.000 14.67 0.00 0.00 3.82
106 109 0.804544 CGCCATGGTATCGTTCGTGT 60.805 55.000 14.67 0.00 0.00 4.49
139 142 1.604378 CGCAAAGACAGGGGAGGAT 59.396 57.895 0.00 0.00 0.00 3.24
146 149 3.033184 TGCTTGCGCAAAGACAGG 58.967 55.556 25.01 12.30 44.62 4.00
159 169 2.480845 GACGAACTAGTTGTGGTGCTT 58.519 47.619 14.14 0.00 0.00 3.91
166 176 0.947244 ACCGTCGACGAACTAGTTGT 59.053 50.000 37.65 21.28 43.02 3.32
236 246 3.353836 GCGCCGTGTCCAACATGT 61.354 61.111 0.00 0.00 33.37 3.21
300 310 2.486716 CAGAGGAAGGGGGAGAAGAAT 58.513 52.381 0.00 0.00 0.00 2.40
378 388 1.673920 CTACACGTTGTTTGGTTGCCT 59.326 47.619 0.00 0.00 0.00 4.75
399 409 0.301687 CATTGTCTCGGCGCATACAC 59.698 55.000 10.83 0.10 0.00 2.90
491 502 1.001746 AGCCTCATATGCGACATCTGG 59.998 52.381 0.00 0.00 0.00 3.86
533 544 3.334583 ACGTTGCATACACTTCTCCAT 57.665 42.857 0.00 0.00 0.00 3.41
553 564 2.371306 TGCCGTGTGCTACAGTATCTA 58.629 47.619 0.00 0.00 42.00 1.98
556 567 1.674817 GGTTGCCGTGTGCTACAGTAT 60.675 52.381 1.62 0.00 45.92 2.12
634 647 1.533129 GCTTGCGTCGGTTTGTTTTCT 60.533 47.619 0.00 0.00 0.00 2.52
705 720 2.558795 GACGAAGAGATATGGCTGGCTA 59.441 50.000 2.00 0.00 0.00 3.93
714 729 3.396276 TGAGAGAGGGGACGAAGAGATAT 59.604 47.826 0.00 0.00 0.00 1.63
779 796 1.824230 AGCTCTCCTCTCATGTGACAC 59.176 52.381 0.00 0.00 0.00 3.67
889 907 4.643387 GTCGGGGTTGCAGCACCT 62.643 66.667 20.50 0.00 36.97 4.00
1012 1031 1.667830 CCTCGAGGTTGCTTCGCAA 60.668 57.895 24.04 0.00 46.80 4.85
1079 1098 0.820871 GCTCCAATGACCGAGAGAGT 59.179 55.000 0.00 0.00 0.00 3.24
1370 3054 2.747446 ACTAAAAATCCGACGCAGCATT 59.253 40.909 0.00 0.00 0.00 3.56
1380 3064 7.873739 AGAAATCAAGCAAACTAAAAATCCG 57.126 32.000 0.00 0.00 0.00 4.18
1384 3068 8.994429 TGTCAAGAAATCAAGCAAACTAAAAA 57.006 26.923 0.00 0.00 0.00 1.94
1385 3069 8.994429 TTGTCAAGAAATCAAGCAAACTAAAA 57.006 26.923 0.00 0.00 0.00 1.52
1386 3070 9.598517 AATTGTCAAGAAATCAAGCAAACTAAA 57.401 25.926 0.00 0.00 0.00 1.85
1387 3071 9.033481 CAATTGTCAAGAAATCAAGCAAACTAA 57.967 29.630 0.00 0.00 0.00 2.24
1388 3072 8.412456 TCAATTGTCAAGAAATCAAGCAAACTA 58.588 29.630 5.13 0.00 0.00 2.24
1389 3073 7.267128 TCAATTGTCAAGAAATCAAGCAAACT 58.733 30.769 5.13 0.00 0.00 2.66
1390 3074 7.467557 TCAATTGTCAAGAAATCAAGCAAAC 57.532 32.000 5.13 0.00 0.00 2.93
1391 3075 8.665643 ATTCAATTGTCAAGAAATCAAGCAAA 57.334 26.923 5.13 0.00 0.00 3.68
1392 3076 8.665643 AATTCAATTGTCAAGAAATCAAGCAA 57.334 26.923 5.13 0.00 0.00 3.91
1393 3077 8.665643 AAATTCAATTGTCAAGAAATCAAGCA 57.334 26.923 5.13 0.00 0.00 3.91
1394 3078 9.940166 AAAAATTCAATTGTCAAGAAATCAAGC 57.060 25.926 5.13 0.00 0.00 4.01
1424 3108 3.365820 CACGCAGAAAATTGGAAGCATTC 59.634 43.478 0.00 0.00 46.67 2.67
1425 3109 3.319755 CACGCAGAAAATTGGAAGCATT 58.680 40.909 0.00 0.00 0.00 3.56
1426 3110 2.927871 GCACGCAGAAAATTGGAAGCAT 60.928 45.455 0.00 0.00 0.00 3.79
1427 3111 1.602668 GCACGCAGAAAATTGGAAGCA 60.603 47.619 0.00 0.00 0.00 3.91
1428 3112 1.063031 GCACGCAGAAAATTGGAAGC 58.937 50.000 0.00 0.00 0.00 3.86
1429 3113 1.000385 TGGCACGCAGAAAATTGGAAG 60.000 47.619 0.00 0.00 0.00 3.46
1430 3114 1.035923 TGGCACGCAGAAAATTGGAA 58.964 45.000 0.00 0.00 0.00 3.53
1431 3115 1.035923 TTGGCACGCAGAAAATTGGA 58.964 45.000 0.00 0.00 0.00 3.53
1432 3116 1.863267 TTTGGCACGCAGAAAATTGG 58.137 45.000 0.00 0.00 0.00 3.16
1433 3117 4.471157 AAATTTGGCACGCAGAAAATTG 57.529 36.364 8.93 0.00 33.65 2.32
1434 3118 5.296748 ACTAAATTTGGCACGCAGAAAATT 58.703 33.333 0.00 0.00 34.54 1.82
1435 3119 4.881920 ACTAAATTTGGCACGCAGAAAAT 58.118 34.783 0.00 0.00 0.00 1.82
1436 3120 4.314740 ACTAAATTTGGCACGCAGAAAA 57.685 36.364 0.00 0.00 0.00 2.29
1437 3121 4.314740 AACTAAATTTGGCACGCAGAAA 57.685 36.364 0.00 0.00 0.00 2.52
1438 3122 4.037446 AGAAACTAAATTTGGCACGCAGAA 59.963 37.500 0.00 0.00 0.00 3.02
1439 3123 3.568007 AGAAACTAAATTTGGCACGCAGA 59.432 39.130 0.00 0.00 0.00 4.26
1440 3124 3.900941 AGAAACTAAATTTGGCACGCAG 58.099 40.909 0.00 0.00 0.00 5.18
1441 3125 4.202060 TGAAGAAACTAAATTTGGCACGCA 60.202 37.500 0.00 0.00 0.00 5.24
1442 3126 4.295051 TGAAGAAACTAAATTTGGCACGC 58.705 39.130 0.00 0.00 0.00 5.34
1443 3127 8.514136 TTAATGAAGAAACTAAATTTGGCACG 57.486 30.769 0.00 0.00 0.00 5.34
1445 3129 9.267084 GGTTTAATGAAGAAACTAAATTTGGCA 57.733 29.630 0.00 0.00 37.05 4.92
1446 3130 9.489084 AGGTTTAATGAAGAAACTAAATTTGGC 57.511 29.630 0.00 0.00 37.05 4.52
1455 3139 9.793259 TTGACTATGAGGTTTAATGAAGAAACT 57.207 29.630 0.00 0.00 37.05 2.66
1463 3147 9.793252 CCTTCAATTTGACTATGAGGTTTAATG 57.207 33.333 0.00 0.00 0.00 1.90
1464 3148 8.971073 CCCTTCAATTTGACTATGAGGTTTAAT 58.029 33.333 11.37 0.00 0.00 1.40
1465 3149 8.167392 TCCCTTCAATTTGACTATGAGGTTTAA 58.833 33.333 11.37 0.00 0.00 1.52
1466 3150 7.695055 TCCCTTCAATTTGACTATGAGGTTTA 58.305 34.615 11.37 0.00 0.00 2.01
1467 3151 6.552008 TCCCTTCAATTTGACTATGAGGTTT 58.448 36.000 11.37 0.00 0.00 3.27
1468 3152 6.139679 TCCCTTCAATTTGACTATGAGGTT 57.860 37.500 11.37 0.00 0.00 3.50
1469 3153 5.779241 TCCCTTCAATTTGACTATGAGGT 57.221 39.130 11.37 0.00 0.00 3.85
1470 3154 8.790718 CATATTCCCTTCAATTTGACTATGAGG 58.209 37.037 0.00 3.05 0.00 3.86
1471 3155 8.295288 GCATATTCCCTTCAATTTGACTATGAG 58.705 37.037 0.00 0.00 0.00 2.90
1472 3156 7.231317 GGCATATTCCCTTCAATTTGACTATGA 59.769 37.037 0.00 0.00 0.00 2.15
1473 3157 7.373493 GGCATATTCCCTTCAATTTGACTATG 58.627 38.462 0.00 2.47 0.00 2.23
1474 3158 6.494835 GGGCATATTCCCTTCAATTTGACTAT 59.505 38.462 2.71 0.00 43.13 2.12
1475 3159 5.833131 GGGCATATTCCCTTCAATTTGACTA 59.167 40.000 2.71 0.00 43.13 2.59
1476 3160 4.651045 GGGCATATTCCCTTCAATTTGACT 59.349 41.667 2.71 0.00 43.13 3.41
1477 3161 4.948847 GGGCATATTCCCTTCAATTTGAC 58.051 43.478 2.71 0.00 43.13 3.18
1635 3321 8.728337 TTGATTAACGAGCTAGTCTAGTAGAA 57.272 34.615 8.68 0.00 30.15 2.10
1709 3395 8.888419 ACATAATTCTCCTAATGATGTGATCCT 58.112 33.333 0.81 0.00 31.99 3.24
1755 3441 8.749841 ACTTAACGATCATTATGCTAAGCTAG 57.250 34.615 0.00 0.00 0.00 3.42
1857 3543 5.472137 ACGTTTGATAGCACACAAGGTATTT 59.528 36.000 0.00 0.00 32.74 1.40
2077 3763 3.600388 CGGCATGTCTCTTTACTCCTTT 58.400 45.455 0.00 0.00 0.00 3.11
2080 3766 1.207329 ACCGGCATGTCTCTTTACTCC 59.793 52.381 0.00 0.00 0.00 3.85
2093 3779 2.093658 AGTTCAATCTCGTTACCGGCAT 60.094 45.455 0.00 0.00 33.95 4.40
2117 3803 4.923264 TCGATCGTCGGTATCTTCATAG 57.077 45.455 15.94 0.00 40.88 2.23
2159 3845 6.411376 ACATACGTTATTCCCTTTGTCATCA 58.589 36.000 0.00 0.00 0.00 3.07
2218 3904 8.212259 AGTCTCATATTGGCTCCTACATATTT 57.788 34.615 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.