Multiple sequence alignment - TraesCS7D01G503200

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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 TraesCS7D01G503200 chr7D 100.000 3215 0 0 1 3215 608421527 608424741 0.000000e+00 5938.0
1 TraesCS7D01G503200 chr7D 90.970 897 67 3 1547 2443 607622322 607621440 0.000000e+00 1195.0
2 TraesCS7D01G503200 chr7D 76.382 597 127 11 1033 1625 607933286 607933872 3.110000e-80 309.0
3 TraesCS7D01G503200 chr7D 90.000 230 20 2 2438 2667 610204480 610204706 8.720000e-76 294.0
4 TraesCS7D01G503200 chr1B 91.834 3233 165 47 1 3215 455355337 455358488 0.000000e+00 4416.0
5 TraesCS7D01G503200 chr1B 100.000 29 0 0 751 779 193469282 193469310 2.000000e-03 54.7
6 TraesCS7D01G503200 chr7A 91.739 2421 101 31 812 3212 700421543 700423884 0.000000e+00 3271.0
7 TraesCS7D01G503200 chr7A 89.017 1475 130 16 956 2426 699865867 699864421 0.000000e+00 1797.0
8 TraesCS7D01G503200 chrUn 94.007 1652 68 8 812 2447 83447978 83446342 0.000000e+00 2473.0
9 TraesCS7D01G503200 chr7B 87.814 1592 159 15 869 2447 693258771 693257202 0.000000e+00 1832.0
10 TraesCS7D01G503200 chr7B 89.210 1177 110 8 1269 2443 697265105 697263944 0.000000e+00 1454.0
11 TraesCS7D01G503200 chr7B 89.318 983 83 7 988 1968 696909509 696908547 0.000000e+00 1214.0
12 TraesCS7D01G503200 chr7B 86.957 644 73 4 1580 2219 700731675 700732311 0.000000e+00 713.0
13 TraesCS7D01G503200 chr7B 86.861 548 62 6 1580 2125 700679183 700679722 3.550000e-169 604.0
14 TraesCS7D01G503200 chr7B 88.260 477 51 3 1971 2447 696906809 696906338 1.670000e-157 566.0
15 TraesCS7D01G503200 chr7B 89.487 409 37 4 2488 2894 693256912 693256508 2.210000e-141 512.0
16 TraesCS7D01G503200 chr7B 89.487 409 35 6 2488 2894 696906047 696905645 7.960000e-141 510.0
17 TraesCS7D01G503200 chr7B 81.784 527 57 16 2691 3215 693954269 693953780 3.860000e-109 405.0
18 TraesCS7D01G503200 chr7B 87.952 332 37 3 950 1279 697277402 697277072 3.890000e-104 388.0
19 TraesCS7D01G503200 chr7B 90.574 244 20 2 2438 2681 693954566 693954326 1.440000e-83 320.0
20 TraesCS7D01G503200 chr7B 77.486 533 102 15 1089 1614 697402262 697402783 1.450000e-78 303.0
21 TraesCS7D01G503200 chr7B 89.868 227 22 1 2434 2660 700731322 700731097 1.130000e-74 291.0
22 TraesCS7D01G503200 chr7B 89.823 226 21 2 2435 2660 696905208 696904985 4.060000e-74 289.0
23 TraesCS7D01G503200 chr7B 88.333 240 23 4 2438 2676 697263666 697263431 1.890000e-72 283.0
24 TraesCS7D01G503200 chr7B 75.318 628 133 16 1033 1648 695502277 695501660 6.790000e-72 281.0
25 TraesCS7D01G503200 chr7B 86.047 258 29 6 2514 2770 700730733 700730482 1.470000e-68 270.0
26 TraesCS7D01G503200 chr7B 74.468 611 142 6 1033 1640 697615773 697615174 5.320000e-63 252.0
27 TraesCS7D01G503200 chr7B 85.380 171 19 4 2729 2894 697263432 697263263 4.260000e-39 172.0
28 TraesCS7D01G503200 chr4D 91.525 236 19 1 1 235 327653472 327653707 1.110000e-84 324.0
29 TraesCS7D01G503200 chr4D 100.000 29 0 0 752 780 83274753 83274725 2.000000e-03 54.7
30 TraesCS7D01G503200 chr3D 90.948 232 17 4 7 236 328214650 328214421 3.110000e-80 309.0
31 TraesCS7D01G503200 chr3D 90.741 54 4 1 726 778 520728024 520727971 1.600000e-08 71.3
32 TraesCS7D01G503200 chr2D 89.831 236 22 2 1 236 596801566 596801333 5.210000e-78 302.0
33 TraesCS7D01G503200 chr6D 89.496 238 24 1 1 237 273274427 273274190 1.870000e-77 300.0
34 TraesCS7D01G503200 chr1D 89.362 235 23 2 2 235 172038777 172039010 8.720000e-76 294.0
35 TraesCS7D01G503200 chr1D 82.031 256 39 7 466 716 141717156 141717409 9.040000e-51 211.0
36 TraesCS7D01G503200 chr6B 88.987 227 23 2 11 236 470044085 470044310 2.440000e-71 279.0
37 TraesCS7D01G503200 chr6B 88.261 230 23 4 7 235 470109635 470109861 4.090000e-69 272.0
38 TraesCS7D01G503200 chr3A 87.446 231 24 5 7 235 281437680 281437453 8.850000e-66 261.0
39 TraesCS7D01G503200 chr5D 89.091 55 5 1 726 779 316794165 316794111 2.070000e-07 67.6
40 TraesCS7D01G503200 chr5D 94.286 35 0 2 752 786 416263958 416263926 6.000000e-03 52.8
41 TraesCS7D01G503200 chr4B 85.484 62 6 3 723 783 338450359 338450418 9.630000e-06 62.1
42 TraesCS7D01G503200 chr1A 77.477 111 20 4 672 778 82151003 82151112 9.630000e-06 62.1
43 TraesCS7D01G503200 chr1A 100.000 28 0 0 752 779 314426659 314426686 6.000000e-03 52.8
44 TraesCS7D01G503200 chr6A 75.397 126 22 7 658 778 607813275 607813154 6.000000e-03 52.8


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 TraesCS7D01G503200 chr7D 608421527 608424741 3214 False 5938.000000 5938 100.0000 1 3215 1 chr7D.!!$F2 3214
1 TraesCS7D01G503200 chr7D 607621440 607622322 882 True 1195.000000 1195 90.9700 1547 2443 1 chr7D.!!$R1 896
2 TraesCS7D01G503200 chr7D 607933286 607933872 586 False 309.000000 309 76.3820 1033 1625 1 chr7D.!!$F1 592
3 TraesCS7D01G503200 chr1B 455355337 455358488 3151 False 4416.000000 4416 91.8340 1 3215 1 chr1B.!!$F2 3214
4 TraesCS7D01G503200 chr7A 700421543 700423884 2341 False 3271.000000 3271 91.7390 812 3212 1 chr7A.!!$F1 2400
5 TraesCS7D01G503200 chr7A 699864421 699865867 1446 True 1797.000000 1797 89.0170 956 2426 1 chr7A.!!$R1 1470
6 TraesCS7D01G503200 chrUn 83446342 83447978 1636 True 2473.000000 2473 94.0070 812 2447 1 chrUn.!!$R1 1635
7 TraesCS7D01G503200 chr7B 693256508 693258771 2263 True 1172.000000 1832 88.6505 869 2894 2 chr7B.!!$R4 2025
8 TraesCS7D01G503200 chr7B 700731675 700732311 636 False 713.000000 713 86.9570 1580 2219 1 chr7B.!!$F3 639
9 TraesCS7D01G503200 chr7B 696904985 696909509 4524 True 644.750000 1214 89.2220 988 2894 4 chr7B.!!$R6 1906
10 TraesCS7D01G503200 chr7B 697263263 697265105 1842 True 636.333333 1454 87.6410 1269 2894 3 chr7B.!!$R7 1625
11 TraesCS7D01G503200 chr7B 700679183 700679722 539 False 604.000000 604 86.8610 1580 2125 1 chr7B.!!$F2 545
12 TraesCS7D01G503200 chr7B 693953780 693954566 786 True 362.500000 405 86.1790 2438 3215 2 chr7B.!!$R5 777
13 TraesCS7D01G503200 chr7B 697402262 697402783 521 False 303.000000 303 77.4860 1089 1614 1 chr7B.!!$F1 525
14 TraesCS7D01G503200 chr7B 695501660 695502277 617 True 281.000000 281 75.3180 1033 1648 1 chr7B.!!$R1 615
15 TraesCS7D01G503200 chr7B 700730482 700731322 840 True 280.500000 291 87.9575 2434 2770 2 chr7B.!!$R8 336
16 TraesCS7D01G503200 chr7B 697615174 697615773 599 True 252.000000 252 74.4680 1033 1640 1 chr7B.!!$R3 607

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
140 141 0.170339 CATCTCGTGTCACGCACCTA 59.830 55.0 20.56 1.94 44.97 3.08 F
1285 1316 0.043334 CTTCTCCTTCCTCCCCTCCA 59.957 60.0 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 1755 0.179124 GAGTCCCAGTAGAAGCAGCG 60.179 60.000 0.0 0.0 0.00 5.18 R
2296 4123 1.069049 GGCCAATTGCAACACTGAACT 59.931 47.619 0.0 0.0 43.89 3.01 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
18 19 1.228094 GCCTAGCCCATCTTGCTCC 60.228 63.158 0.00 0.00 40.23 4.70
50 51 3.733709 CTCAAGGAGCAACCCTGTT 57.266 52.632 0.00 0.00 40.05 3.16
83 84 6.681616 GCATATCATCCATTCGGTAGGACTAG 60.682 46.154 0.00 0.00 36.60 2.57
140 141 0.170339 CATCTCGTGTCACGCACCTA 59.830 55.000 20.56 1.94 44.97 3.08
142 143 1.167781 TCTCGTGTCACGCACCTACA 61.168 55.000 20.56 0.43 44.97 2.74
243 245 3.626924 ACCACGACAGGCCTCCAC 61.627 66.667 0.00 0.00 0.00 4.02
262 264 2.260434 GTCGCCACCGCTTCACTA 59.740 61.111 0.00 0.00 0.00 2.74
281 283 3.188786 CAACGAGCCACTAGCCGC 61.189 66.667 0.00 0.00 45.47 6.53
316 318 4.740235 GCTTCTAGCTAGCCACCG 57.260 61.111 16.35 3.47 38.45 4.94
408 410 3.159984 GCAAGGAGCGAGAACACG 58.840 61.111 0.00 0.00 0.00 4.49
412 414 2.804368 AAGGAGCGAGAACACGAGCG 62.804 60.000 0.00 0.00 35.09 5.03
453 455 3.736100 CAAAGCATGGCGGTCGCA 61.736 61.111 17.21 4.04 44.11 5.10
454 456 3.434319 AAAGCATGGCGGTCGCAG 61.434 61.111 17.21 7.40 44.11 5.18
492 494 3.539107 GGCTTCGTCGCCGTTACG 61.539 66.667 0.00 0.00 40.79 3.18
536 538 4.250305 AGAGTTGCCGGGCGTTGT 62.250 61.111 15.40 0.00 0.00 3.32
540 542 4.572571 TTGCCGGGCGTTGTCCTT 62.573 61.111 15.40 0.00 0.00 3.36
572 575 3.488090 GTGCGTTGCGGTAGCTCC 61.488 66.667 0.00 0.00 45.42 4.70
573 576 4.752879 TGCGTTGCGGTAGCTCCC 62.753 66.667 0.00 0.00 45.42 4.30
593 596 4.271816 CGACGGCGCAGGAGCTAT 62.272 66.667 13.26 0.00 39.10 2.97
606 609 1.410083 GGAGCTATGGGCAATTCACCA 60.410 52.381 0.40 0.40 44.79 4.17
607 610 1.678101 GAGCTATGGGCAATTCACCAC 59.322 52.381 0.00 0.00 44.79 4.16
608 611 0.746659 GCTATGGGCAATTCACCACC 59.253 55.000 0.00 0.00 40.05 4.61
647 651 2.088423 GGGCGGACATGACACAAAATA 58.912 47.619 0.00 0.00 0.00 1.40
653 657 5.562917 CGGACATGACACAAAATATGTCTG 58.437 41.667 13.77 11.79 45.58 3.51
654 658 5.122239 CGGACATGACACAAAATATGTCTGT 59.878 40.000 13.94 7.90 45.30 3.41
702 706 4.544001 AAAAACGGACACGGCAGA 57.456 50.000 0.00 0.00 46.48 4.26
703 707 2.317230 AAAAACGGACACGGCAGAG 58.683 52.632 0.00 0.00 46.48 3.35
704 708 1.782028 AAAAACGGACACGGCAGAGC 61.782 55.000 0.00 0.00 46.48 4.09
716 720 3.680786 CAGAGCGGACGGGTGACA 61.681 66.667 0.00 0.00 0.00 3.58
717 721 2.680352 AGAGCGGACGGGTGACAT 60.680 61.111 0.00 0.00 0.00 3.06
726 730 2.879646 GGACGGGTGACATACAAACAAA 59.120 45.455 0.00 0.00 0.00 2.83
760 764 0.606401 AACATCTGGTTGGGTCAGCG 60.606 55.000 0.00 0.00 38.60 5.18
761 765 2.045926 ATCTGGTTGGGTCAGCGC 60.046 61.111 0.00 0.00 32.63 5.92
762 766 3.958147 ATCTGGTTGGGTCAGCGCG 62.958 63.158 0.00 0.00 32.63 6.86
763 767 4.988598 CTGGTTGGGTCAGCGCGT 62.989 66.667 8.43 0.00 0.00 6.01
764 768 4.555709 TGGTTGGGTCAGCGCGTT 62.556 61.111 8.43 0.00 0.00 4.84
765 769 4.025401 GGTTGGGTCAGCGCGTTG 62.025 66.667 17.58 17.58 0.00 4.10
766 770 4.025401 GTTGGGTCAGCGCGTTGG 62.025 66.667 22.99 5.26 0.00 3.77
767 771 4.243008 TTGGGTCAGCGCGTTGGA 62.243 61.111 22.99 7.75 0.00 3.53
768 772 4.680237 TGGGTCAGCGCGTTGGAG 62.680 66.667 22.99 0.00 0.00 3.86
769 773 4.681978 GGGTCAGCGCGTTGGAGT 62.682 66.667 22.99 0.00 0.00 3.85
770 774 2.665185 GGTCAGCGCGTTGGAGTT 60.665 61.111 22.99 0.00 0.00 3.01
771 775 2.551270 GTCAGCGCGTTGGAGTTG 59.449 61.111 22.99 0.00 0.00 3.16
772 776 3.345808 TCAGCGCGTTGGAGTTGC 61.346 61.111 22.99 0.00 0.00 4.17
773 777 3.349006 CAGCGCGTTGGAGTTGCT 61.349 61.111 15.84 0.00 36.05 3.91
774 778 3.044305 AGCGCGTTGGAGTTGCTC 61.044 61.111 8.43 0.00 0.00 4.26
775 779 3.044305 GCGCGTTGGAGTTGCTCT 61.044 61.111 8.43 0.00 0.00 4.09
776 780 2.607892 GCGCGTTGGAGTTGCTCTT 61.608 57.895 8.43 0.00 0.00 2.85
777 781 1.289109 GCGCGTTGGAGTTGCTCTTA 61.289 55.000 8.43 0.00 0.00 2.10
778 782 0.716108 CGCGTTGGAGTTGCTCTTAG 59.284 55.000 0.00 0.00 0.00 2.18
779 783 1.797025 GCGTTGGAGTTGCTCTTAGT 58.203 50.000 0.00 0.00 0.00 2.24
788 792 1.127582 GTTGCTCTTAGTGCTCAAGCG 59.872 52.381 7.78 0.00 45.83 4.68
789 793 0.603065 TGCTCTTAGTGCTCAAGCGA 59.397 50.000 7.78 0.00 45.83 4.93
793 797 3.673594 GCTCTTAGTGCTCAAGCGACTAA 60.674 47.826 17.85 17.85 45.83 2.24
799 803 1.362406 GCTCAAGCGACTAACAGCCC 61.362 60.000 0.00 0.00 0.00 5.19
848 857 6.524101 TTCATTTTGTAACCCTATTCAGCC 57.476 37.500 0.00 0.00 0.00 4.85
855 864 2.496899 ACCCTATTCAGCCAACACAG 57.503 50.000 0.00 0.00 0.00 3.66
958 984 4.065281 CTTCCGTTCCCGTCGGCT 62.065 66.667 5.50 0.00 46.49 5.52
1285 1316 0.043334 CTTCTCCTTCCTCCCCTCCA 59.957 60.000 0.00 0.00 0.00 3.86
1478 1515 4.157120 GACCCCCGTGCTACGCAT 62.157 66.667 3.56 0.00 41.91 4.73
1500 1537 1.751162 CTCCGACGAGCCTCTCCTT 60.751 63.158 0.00 0.00 0.00 3.36
1733 1783 4.069312 TCTACTGGGACTCCACCAATAA 57.931 45.455 0.00 0.00 38.32 1.40
1749 1799 6.940298 CCACCAATAACAAGAGGAAAGAGTTA 59.060 38.462 0.00 0.00 0.00 2.24
1910 1960 1.884579 CAGCAAACATGACCTCTGCTT 59.115 47.619 0.00 0.00 41.30 3.91
1942 1995 3.006217 GCAGAACAAAGGCAAGAATTCCT 59.994 43.478 0.65 0.00 0.00 3.36
2224 4012 4.986034 CGCCGACAATATGAAGTGGTATAA 59.014 41.667 0.00 0.00 0.00 0.98
2284 4111 7.253422 CCTTCATAGTTTTCACATGGATTGTC 58.747 38.462 0.00 0.00 36.00 3.18
2285 4112 7.121759 CCTTCATAGTTTTCACATGGATTGTCT 59.878 37.037 0.00 0.00 36.00 3.41
2286 4113 9.166173 CTTCATAGTTTTCACATGGATTGTCTA 57.834 33.333 0.00 0.00 36.00 2.59
2287 4114 9.513906 TTCATAGTTTTCACATGGATTGTCTAA 57.486 29.630 0.00 0.00 36.00 2.10
2288 4115 9.685276 TCATAGTTTTCACATGGATTGTCTAAT 57.315 29.630 0.00 0.00 36.00 1.73
2289 4116 9.726232 CATAGTTTTCACATGGATTGTCTAATG 57.274 33.333 0.00 0.00 36.00 1.90
2290 4117 6.624423 AGTTTTCACATGGATTGTCTAATGC 58.376 36.000 0.00 0.00 36.00 3.56
2291 4118 6.435277 AGTTTTCACATGGATTGTCTAATGCT 59.565 34.615 0.00 0.00 36.00 3.79
2292 4119 6.839124 TTTCACATGGATTGTCTAATGCTT 57.161 33.333 0.00 0.00 36.00 3.91
2293 4120 7.936496 TTTCACATGGATTGTCTAATGCTTA 57.064 32.000 0.00 0.00 36.00 3.09
2294 4121 7.936496 TTCACATGGATTGTCTAATGCTTAA 57.064 32.000 0.00 0.00 36.00 1.85
2295 4122 7.320443 TCACATGGATTGTCTAATGCTTAAC 57.680 36.000 0.00 0.00 36.00 2.01
2296 4123 6.883756 TCACATGGATTGTCTAATGCTTAACA 59.116 34.615 0.00 0.00 36.00 2.41
2297 4124 7.066163 TCACATGGATTGTCTAATGCTTAACAG 59.934 37.037 0.00 0.00 36.00 3.16
2298 4125 6.886459 ACATGGATTGTCTAATGCTTAACAGT 59.114 34.615 0.00 0.00 35.83 3.55
2454 4578 7.905493 CGTACAAAAGAAAATCTCTGCCTAATC 59.095 37.037 0.00 0.00 33.37 1.75
2723 5146 6.198966 GCTGGTTTCTTTTGTGTACATTTCTG 59.801 38.462 0.00 0.00 0.00 3.02
2947 5817 2.304180 CCAAATGTCTCCTCTGGTCTGT 59.696 50.000 0.00 0.00 0.00 3.41
3055 5925 2.288729 CGTGGATGTAGCATCATTGTGG 59.711 50.000 10.71 0.00 0.00 4.17
3094 5964 1.204941 AGACGTCATCACCTTGCCTAC 59.795 52.381 19.50 0.00 0.00 3.18
3119 5989 7.499232 ACAGGATGGTACTATTTACATTGCTTC 59.501 37.037 0.00 0.00 43.62 3.86
3155 6025 9.995957 TCGTCATGTATATGTTTTGGTTAATTG 57.004 29.630 0.00 0.00 35.73 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.075601 TTTGGGTGGAGGAGCAAGAT 58.924 50.000 0.00 0.00 0.00 2.40
18 19 1.242076 CTTGAGCTGTTTGGGTGGAG 58.758 55.000 0.00 0.00 0.00 3.86
50 51 5.105351 CCGAATGGATGATATGCACTAGGTA 60.105 44.000 0.00 0.00 37.49 3.08
140 141 2.742372 GGCGAGATTGGCACGTGT 60.742 61.111 18.38 0.00 32.93 4.49
142 143 2.125512 GAGGCGAGATTGGCACGT 60.126 61.111 0.00 0.00 36.77 4.49
221 223 2.125106 GGCCTGTCGTGGTGATCC 60.125 66.667 0.00 0.00 0.00 3.36
246 248 2.571757 CTAGTGAAGCGGTGGCGA 59.428 61.111 0.00 0.00 46.35 5.54
261 263 1.515954 GGCTAGTGGCTCGTTGCTA 59.484 57.895 0.00 0.00 42.39 3.49
262 264 2.266055 GGCTAGTGGCTCGTTGCT 59.734 61.111 0.00 0.00 42.39 3.91
265 267 4.452733 GGCGGCTAGTGGCTCGTT 62.453 66.667 0.00 0.00 41.46 3.85
302 304 3.217017 CGGCGGTGGCTAGCTAGA 61.217 66.667 25.15 0.90 39.81 2.43
303 305 4.286320 CCGGCGGTGGCTAGCTAG 62.286 72.222 19.97 16.84 39.81 3.42
363 365 3.860605 CGCCCATGATCCGGGTCA 61.861 66.667 22.11 22.11 46.40 4.02
394 396 2.569134 GCTCGTGTTCTCGCTCCT 59.431 61.111 0.00 0.00 0.00 3.69
436 438 3.672255 CTGCGACCGCCATGCTTTG 62.672 63.158 12.08 0.00 41.09 2.77
437 439 3.434319 CTGCGACCGCCATGCTTT 61.434 61.111 12.08 0.00 41.09 3.51
536 538 4.069232 CCTGCTCGCGGACAAGGA 62.069 66.667 6.13 0.00 0.00 3.36
540 542 4.056125 CACTCCTGCTCGCGGACA 62.056 66.667 6.13 3.71 0.00 4.02
578 581 4.227134 CCATAGCTCCTGCGCCGT 62.227 66.667 4.18 0.00 45.42 5.68
584 587 1.952296 GTGAATTGCCCATAGCTCCTG 59.048 52.381 0.00 0.00 44.23 3.86
593 596 0.105760 ACTTGGTGGTGAATTGCCCA 60.106 50.000 0.00 0.00 0.00 5.36
606 609 1.265905 GGCATTTCGTCGAAACTTGGT 59.734 47.619 21.91 3.80 34.23 3.67
607 610 1.963747 GGCATTTCGTCGAAACTTGG 58.036 50.000 21.91 12.85 34.23 3.61
699 703 1.663379 TATGTCACCCGTCCGCTCTG 61.663 60.000 0.00 0.00 0.00 3.35
700 704 1.379443 TATGTCACCCGTCCGCTCT 60.379 57.895 0.00 0.00 0.00 4.09
701 705 1.226888 GTATGTCACCCGTCCGCTC 60.227 63.158 0.00 0.00 0.00 5.03
702 706 1.537814 TTGTATGTCACCCGTCCGCT 61.538 55.000 0.00 0.00 0.00 5.52
703 707 0.671163 TTTGTATGTCACCCGTCCGC 60.671 55.000 0.00 0.00 0.00 5.54
704 708 1.073177 GTTTGTATGTCACCCGTCCG 58.927 55.000 0.00 0.00 0.00 4.79
705 709 2.172851 TGTTTGTATGTCACCCGTCC 57.827 50.000 0.00 0.00 0.00 4.79
706 710 4.555348 TTTTGTTTGTATGTCACCCGTC 57.445 40.909 0.00 0.00 0.00 4.79
707 711 4.985538 TTTTTGTTTGTATGTCACCCGT 57.014 36.364 0.00 0.00 0.00 5.28
726 730 5.366477 ACCAGATGTTGATTTTGTCCCTTTT 59.634 36.000 0.00 0.00 0.00 2.27
730 734 4.871933 AACCAGATGTTGATTTTGTCCC 57.128 40.909 0.00 0.00 35.31 4.46
744 748 2.045926 GCGCTGACCCAACCAGAT 60.046 61.111 0.00 0.00 33.65 2.90
748 752 4.025401 CAACGCGCTGACCCAACC 62.025 66.667 5.73 0.00 0.00 3.77
758 762 1.289109 TAAGAGCAACTCCAACGCGC 61.289 55.000 5.73 0.00 0.00 6.86
760 764 1.461127 CACTAAGAGCAACTCCAACGC 59.539 52.381 0.00 0.00 0.00 4.84
761 765 1.461127 GCACTAAGAGCAACTCCAACG 59.539 52.381 0.00 0.00 0.00 4.10
762 766 2.739379 GAGCACTAAGAGCAACTCCAAC 59.261 50.000 0.00 0.00 0.00 3.77
763 767 2.368548 TGAGCACTAAGAGCAACTCCAA 59.631 45.455 0.00 0.00 0.00 3.53
764 768 1.970640 TGAGCACTAAGAGCAACTCCA 59.029 47.619 0.00 0.00 0.00 3.86
765 769 2.751166 TGAGCACTAAGAGCAACTCC 57.249 50.000 0.00 0.00 0.00 3.85
766 770 2.414825 GCTTGAGCACTAAGAGCAACTC 59.585 50.000 0.00 0.00 41.59 3.01
767 771 2.421619 GCTTGAGCACTAAGAGCAACT 58.578 47.619 0.00 0.00 41.59 3.16
768 772 1.127582 CGCTTGAGCACTAAGAGCAAC 59.872 52.381 3.65 0.00 42.21 4.17
769 773 1.000843 TCGCTTGAGCACTAAGAGCAA 59.999 47.619 3.65 0.00 42.21 3.91
770 774 0.603065 TCGCTTGAGCACTAAGAGCA 59.397 50.000 3.65 0.00 42.21 4.26
771 775 0.995728 GTCGCTTGAGCACTAAGAGC 59.004 55.000 3.65 0.00 42.21 4.09
772 776 2.645730 AGTCGCTTGAGCACTAAGAG 57.354 50.000 3.65 0.00 42.21 2.85
773 777 3.254903 TGTTAGTCGCTTGAGCACTAAGA 59.745 43.478 19.11 16.92 41.04 2.10
774 778 3.575630 TGTTAGTCGCTTGAGCACTAAG 58.424 45.455 19.11 0.00 41.04 2.18
775 779 3.575630 CTGTTAGTCGCTTGAGCACTAA 58.424 45.455 16.71 16.71 39.68 2.24
776 780 2.671351 GCTGTTAGTCGCTTGAGCACTA 60.671 50.000 3.65 7.33 42.21 2.74
777 781 1.937108 GCTGTTAGTCGCTTGAGCACT 60.937 52.381 3.65 8.20 42.21 4.40
778 782 0.440371 GCTGTTAGTCGCTTGAGCAC 59.560 55.000 3.65 1.28 42.21 4.40
779 783 0.670546 GGCTGTTAGTCGCTTGAGCA 60.671 55.000 3.65 0.00 42.21 4.26
788 792 2.165319 AACTTCACGGGCTGTTAGTC 57.835 50.000 10.49 0.00 0.00 2.59
789 793 2.366266 TGTAACTTCACGGGCTGTTAGT 59.634 45.455 0.00 0.13 0.00 2.24
793 797 2.552315 CAAATGTAACTTCACGGGCTGT 59.448 45.455 0.00 0.00 0.00 4.40
841 845 2.612972 CGAGTACCTGTGTTGGCTGAAT 60.613 50.000 0.00 0.00 0.00 2.57
848 857 0.250124 TTGGCCGAGTACCTGTGTTG 60.250 55.000 0.00 0.00 0.00 3.33
855 864 1.448013 GCAGTCTTGGCCGAGTACC 60.448 63.158 19.96 9.13 0.00 3.34
958 984 0.324091 GTCGAGGAGGGGAAGTGGTA 60.324 60.000 0.00 0.00 0.00 3.25
1285 1316 4.473520 CGGGATCCAGCGGCAGTT 62.474 66.667 15.23 0.00 0.00 3.16
1500 1537 1.595993 CGTTCTCGCTGAGGGGAAGA 61.596 60.000 0.00 0.00 34.03 2.87
1705 1755 0.179124 GAGTCCCAGTAGAAGCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
1733 1783 4.796618 GCACGAGTAACTCTTTCCTCTTGT 60.797 45.833 0.00 0.00 0.00 3.16
1749 1799 2.826128 TCTCTGGATGTTAAGCACGAGT 59.174 45.455 0.00 0.00 0.00 4.18
1910 1960 2.143122 CTTTGTTCTGCCTAACGCTGA 58.857 47.619 0.00 0.00 43.04 4.26
1942 1995 0.764271 TTCACCATCTGCCACTGACA 59.236 50.000 0.00 0.00 0.00 3.58
2224 4012 7.944729 ACATAACTGGAAATGCAGTAGAAAT 57.055 32.000 8.04 0.00 0.00 2.17
2284 4111 5.853282 GCAACACTGAACTGTTAAGCATTAG 59.147 40.000 4.76 0.00 32.90 1.73
2285 4112 5.298026 TGCAACACTGAACTGTTAAGCATTA 59.702 36.000 4.76 0.00 31.56 1.90
2286 4113 4.097741 TGCAACACTGAACTGTTAAGCATT 59.902 37.500 4.76 0.00 31.56 3.56
2287 4114 3.631686 TGCAACACTGAACTGTTAAGCAT 59.368 39.130 4.76 0.00 31.56 3.79
2288 4115 3.013219 TGCAACACTGAACTGTTAAGCA 58.987 40.909 4.76 0.00 33.16 3.91
2289 4116 3.691049 TGCAACACTGAACTGTTAAGC 57.309 42.857 4.76 0.00 32.90 3.09
2290 4117 5.459762 CCAATTGCAACACTGAACTGTTAAG 59.540 40.000 0.00 3.25 32.90 1.85
2291 4118 5.347342 CCAATTGCAACACTGAACTGTTAA 58.653 37.500 0.00 0.00 32.90 2.01
2292 4119 4.736168 GCCAATTGCAACACTGAACTGTTA 60.736 41.667 0.00 0.00 40.77 2.41
2293 4120 3.784338 CCAATTGCAACACTGAACTGTT 58.216 40.909 0.00 0.00 34.56 3.16
2294 4121 2.481795 GCCAATTGCAACACTGAACTGT 60.482 45.455 0.00 0.00 40.77 3.55
2295 4122 2.129607 GCCAATTGCAACACTGAACTG 58.870 47.619 0.00 0.00 40.77 3.16
2296 4123 1.069049 GGCCAATTGCAACACTGAACT 59.931 47.619 0.00 0.00 43.89 3.01
2297 4124 1.202510 TGGCCAATTGCAACACTGAAC 60.203 47.619 0.61 0.00 43.89 3.18
2298 4125 1.117994 TGGCCAATTGCAACACTGAA 58.882 45.000 0.61 0.00 43.89 3.02
2723 5146 1.860676 TGGAGCACGTAACAAGACAC 58.139 50.000 0.00 0.00 0.00 3.67
2936 5806 3.835395 AGAAGTTTAGGACAGACCAGAGG 59.165 47.826 0.00 0.00 42.04 3.69
2947 5817 6.882140 TGAACAAACAAGACAGAAGTTTAGGA 59.118 34.615 0.00 0.00 34.03 2.94
3055 5925 3.243177 GTCTACCGCGAATTGAGAACATC 59.757 47.826 8.23 0.00 0.00 3.06
3094 5964 7.307396 CGAAGCAATGTAAATAGTACCATCCTG 60.307 40.741 0.00 0.00 0.00 3.86
3155 6025 6.624423 AGAACATCCAAAATGATGCTACAAC 58.376 36.000 1.12 0.00 44.84 3.32


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

AutoCloner maintained by Alex Coulton.