Multiple sequence alignment - TraesCS5D01G425300

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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 TraesCS5D01G425300 chr5D 100.000 3388 0 0 1 3388 483809014 483812401 0.000000e+00 6257.0
1 TraesCS5D01G425300 chr5D 78.200 1289 229 36 1117 2375 564759320 564758054 0.000000e+00 776.0
2 TraesCS5D01G425300 chr5D 75.549 1321 236 52 1121 2374 564748973 564747673 1.360000e-158 569.0
3 TraesCS5D01G425300 chr5D 85.488 379 41 7 267 639 210043178 210043548 1.910000e-102 383.0
4 TraesCS5D01G425300 chr5D 75.570 745 132 20 1121 1854 564752072 564751367 4.220000e-84 322.0
5 TraesCS5D01G425300 chr5D 74.078 976 163 51 1475 2374 557284049 557283088 5.460000e-83 318.0
6 TraesCS5D01G425300 chr5D 80.457 394 55 7 990 1373 483858399 483858018 7.160000e-72 281.0
7 TraesCS5D01G425300 chr5D 81.250 80 11 4 8 83 370108693 370108614 1.020000e-05 62.1
8 TraesCS5D01G425300 chr5A 92.639 1997 121 15 724 2711 605248722 605250701 0.000000e+00 2850.0
9 TraesCS5D01G425300 chr5A 89.552 871 55 15 2543 3388 605362568 605363427 0.000000e+00 1072.0
10 TraesCS5D01G425300 chr5A 92.126 635 48 2 1474 2107 605350359 605350992 0.000000e+00 894.0
11 TraesCS5D01G425300 chr5A 77.873 1288 230 35 1121 2376 656216542 656215278 0.000000e+00 749.0
12 TraesCS5D01G425300 chr5A 89.907 535 49 5 1294 1825 605349827 605350359 0.000000e+00 684.0
13 TraesCS5D01G425300 chr5A 85.057 696 63 21 2719 3386 605253570 605254252 0.000000e+00 671.0
14 TraesCS5D01G425300 chr5A 91.375 429 26 4 1 418 605248224 605248652 8.150000e-161 577.0
15 TraesCS5D01G425300 chr5A 90.461 304 27 2 2104 2407 605352650 605352951 1.890000e-107 399.0
16 TraesCS5D01G425300 chr5A 87.209 344 30 8 727 1064 605349490 605349825 2.470000e-101 379.0
17 TraesCS5D01G425300 chr5B 89.282 2006 134 23 700 2652 595017955 595019932 0.000000e+00 2438.0
18 TraesCS5D01G425300 chr5B 90.769 650 36 10 11 644 595015277 595015918 0.000000e+00 846.0
19 TraesCS5D01G425300 chr5B 86.370 763 68 20 2655 3384 595027384 595028143 0.000000e+00 800.0
20 TraesCS5D01G425300 chr5B 78.563 891 159 21 1501 2376 665002953 665002080 2.950000e-155 558.0
21 TraesCS5D01G425300 chr5B 81.498 681 80 20 2724 3361 595133548 595134225 5.010000e-143 518.0
22 TraesCS5D01G425300 chr5B 78.140 430 83 8 1958 2376 708532715 708532286 2.590000e-66 263.0
23 TraesCS5D01G425300 chr5B 81.923 260 41 6 274 528 301191947 301192205 7.360000e-52 215.0
24 TraesCS5D01G425300 chr5B 85.714 126 18 0 1613 1738 693687781 693687906 2.120000e-27 134.0
25 TraesCS5D01G425300 chr3A 77.117 992 176 38 1407 2376 744098548 744097586 8.330000e-146 527.0
26 TraesCS5D01G425300 chr3A 82.632 380 48 10 268 644 694024163 694023799 1.520000e-83 320.0
27 TraesCS5D01G425300 chr3A 74.740 768 135 44 1018 1749 742784776 742785520 4.280000e-74 289.0
28 TraesCS5D01G425300 chr7A 78.855 629 115 10 1784 2408 91497366 91497980 3.150000e-110 409.0
29 TraesCS5D01G425300 chr1A 85.637 369 47 3 267 635 218476708 218476346 1.910000e-102 383.0
30 TraesCS5D01G425300 chr2D 85.372 376 43 10 274 644 236159678 236159310 2.470000e-101 379.0
31 TraesCS5D01G425300 chr2D 82.065 368 61 5 274 638 187146124 187146489 3.280000e-80 309.0
32 TraesCS5D01G425300 chr2D 83.391 289 39 8 358 640 617049062 617049347 3.350000e-65 259.0
33 TraesCS5D01G425300 chr4A 78.211 615 106 21 1765 2370 606339752 606340347 5.340000e-98 368.0
34 TraesCS5D01G425300 chr4A 91.892 148 12 0 1112 1259 604667643 604667790 1.230000e-49 207.0
35 TraesCS5D01G425300 chr4A 80.000 165 24 6 1685 1844 605751020 605750860 2.760000e-21 113.0
36 TraesCS5D01G425300 chr7D 82.804 378 55 10 267 640 136401755 136402126 2.520000e-86 329.0
37 TraesCS5D01G425300 chr7D 87.607 234 25 3 1093 1324 89896750 89896981 5.570000e-68 268.0
38 TraesCS5D01G425300 chr4D 82.181 376 59 8 274 644 334663037 334662665 1.960000e-82 316.0
39 TraesCS5D01G425300 chr1B 81.283 374 61 8 267 634 175278783 175278413 9.190000e-76 294.0
40 TraesCS5D01G425300 chr3D 74.708 771 136 46 1015 1749 609232265 609233012 4.280000e-74 289.0
41 TraesCS5D01G425300 chr3D 79.592 98 14 4 8 100 591660785 591660689 7.850000e-07 65.8
42 TraesCS5D01G425300 chr7B 85.769 260 31 5 1100 1356 41039284 41039540 1.550000e-68 270.0
43 TraesCS5D01G425300 chr4B 83.838 99 9 5 8 100 427518859 427518762 1.670000e-13 87.9
44 TraesCS5D01G425300 chr3B 82.653 98 11 5 7 98 650054926 650054829 7.790000e-12 82.4
45 TraesCS5D01G425300 chr6B 82.105 95 12 4 8 98 143197306 143197399 3.630000e-10 76.8


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 TraesCS5D01G425300 chr5D 483809014 483812401 3387 False 6257.0 6257 100.000000 1 3388 1 chr5D.!!$F2 3387
1 TraesCS5D01G425300 chr5D 564758054 564759320 1266 True 776.0 776 78.200000 1117 2375 1 chr5D.!!$R4 1258
2 TraesCS5D01G425300 chr5D 564747673 564752072 4399 True 445.5 569 75.559500 1121 2374 2 chr5D.!!$R5 1253
3 TraesCS5D01G425300 chr5D 557283088 557284049 961 True 318.0 318 74.078000 1475 2374 1 chr5D.!!$R3 899
4 TraesCS5D01G425300 chr5A 605248224 605254252 6028 False 1366.0 2850 89.690333 1 3386 3 chr5A.!!$F2 3385
5 TraesCS5D01G425300 chr5A 605362568 605363427 859 False 1072.0 1072 89.552000 2543 3388 1 chr5A.!!$F1 845
6 TraesCS5D01G425300 chr5A 656215278 656216542 1264 True 749.0 749 77.873000 1121 2376 1 chr5A.!!$R1 1255
7 TraesCS5D01G425300 chr5A 605349490 605352951 3461 False 589.0 894 89.925750 727 2407 4 chr5A.!!$F3 1680
8 TraesCS5D01G425300 chr5B 595015277 595019932 4655 False 1642.0 2438 90.025500 11 2652 2 chr5B.!!$F5 2641
9 TraesCS5D01G425300 chr5B 595027384 595028143 759 False 800.0 800 86.370000 2655 3384 1 chr5B.!!$F2 729
10 TraesCS5D01G425300 chr5B 665002080 665002953 873 True 558.0 558 78.563000 1501 2376 1 chr5B.!!$R1 875
11 TraesCS5D01G425300 chr5B 595133548 595134225 677 False 518.0 518 81.498000 2724 3361 1 chr5B.!!$F3 637
12 TraesCS5D01G425300 chr3A 744097586 744098548 962 True 527.0 527 77.117000 1407 2376 1 chr3A.!!$R2 969
13 TraesCS5D01G425300 chr3A 742784776 742785520 744 False 289.0 289 74.740000 1018 1749 1 chr3A.!!$F1 731
14 TraesCS5D01G425300 chr7A 91497366 91497980 614 False 409.0 409 78.855000 1784 2408 1 chr7A.!!$F1 624
15 TraesCS5D01G425300 chr4A 606339752 606340347 595 False 368.0 368 78.211000 1765 2370 1 chr4A.!!$F2 605
16 TraesCS5D01G425300 chr3D 609232265 609233012 747 False 289.0 289 74.708000 1015 1749 1 chr3D.!!$F1 734

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
764 2764 0.250597 AGAAAGGGCCCGTTGTGTAC 60.251 55.0 28.83 12.73 0.00 2.90 F
1518 3574 0.034059 CTCTGGAGGACGTGCAACTT 59.966 55.0 10.52 0.00 31.75 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 9656 1.449353 GGCATGCCCACCAAAAACA 59.551 52.632 27.24 0.0 0.00 2.83 R
3257 13521 0.820871 TCTTTGTGCACAAACCCACC 59.179 50.000 35.10 0.0 40.55 4.61 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
99 103 8.402798 TGAACTATTTGAAATAAAGTGCTCCA 57.597 30.769 0.00 0.00 0.00 3.86
100 104 8.514594 TGAACTATTTGAAATAAAGTGCTCCAG 58.485 33.333 0.00 0.00 0.00 3.86
102 106 9.515226 AACTATTTGAAATAAAGTGCTCCAGTA 57.485 29.630 0.00 0.00 0.00 2.74
251 264 1.078426 AGCGGTAGAGCGGCAAAAT 60.078 52.632 1.45 0.00 44.64 1.82
309 322 4.696479 AGGGAACTAGGCATACATTCAG 57.304 45.455 0.00 0.00 40.61 3.02
314 327 4.946478 ACTAGGCATACATTCAGTCTCC 57.054 45.455 0.00 0.00 0.00 3.71
348 361 6.649141 ACTTTAGACTTGCAACGATAACATCA 59.351 34.615 0.00 0.00 0.00 3.07
388 401 7.959658 AACTTGGGTCAATTCAATATGATCA 57.040 32.000 0.00 0.00 0.00 2.92
418 431 9.725019 TTCTAACATCATACTCTCAATGTTGTT 57.275 29.630 13.79 13.79 43.97 2.83
419 432 9.371136 TCTAACATCATACTCTCAATGTTGTTC 57.629 33.333 13.05 0.00 42.22 3.18
420 433 9.376075 CTAACATCATACTCTCAATGTTGTTCT 57.624 33.333 13.05 0.00 42.22 3.01
421 434 8.627208 AACATCATACTCTCAATGTTGTTCTT 57.373 30.769 6.67 0.00 40.60 2.52
422 435 8.037382 ACATCATACTCTCAATGTTGTTCTTG 57.963 34.615 0.00 0.00 34.97 3.02
424 437 8.509690 CATCATACTCTCAATGTTGTTCTTGTT 58.490 33.333 0.00 0.00 0.00 2.83
425 438 8.450578 TCATACTCTCAATGTTGTTCTTGTTT 57.549 30.769 0.00 0.00 0.00 2.83
426 439 8.559536 TCATACTCTCAATGTTGTTCTTGTTTC 58.440 33.333 0.00 0.00 0.00 2.78
427 440 6.757897 ACTCTCAATGTTGTTCTTGTTTCA 57.242 33.333 0.00 0.00 0.00 2.69
430 443 7.552687 ACTCTCAATGTTGTTCTTGTTTCAGTA 59.447 33.333 0.00 0.00 0.00 2.74
431 444 7.693952 TCTCAATGTTGTTCTTGTTTCAGTAC 58.306 34.615 0.00 0.00 0.00 2.73
434 449 7.278203 TCAATGTTGTTCTTGTTTCAGTACGTA 59.722 33.333 0.00 0.00 0.00 3.57
458 473 2.943036 AAAAAGCCTACGACCAGGAA 57.057 45.000 0.00 0.00 38.00 3.36
467 482 4.272748 GCCTACGACCAGGAAAACATAATC 59.727 45.833 0.00 0.00 38.00 1.75
513 528 5.860941 CTAGAGGCAAGACTAGGAATCAA 57.139 43.478 0.00 0.00 34.32 2.57
545 560 7.064253 ACCATTTATTCTTCTACACGTGCTTAC 59.936 37.037 17.22 0.00 0.00 2.34
558 573 3.254166 ACGTGCTTACGAGTTTTCCTCTA 59.746 43.478 6.85 0.00 38.11 2.43
561 576 5.388164 CGTGCTTACGAGTTTTCCTCTAAAC 60.388 44.000 0.00 0.00 38.11 2.01
564 579 5.120363 GCTTACGAGTTTTCCTCTAAACCAG 59.880 44.000 0.00 0.00 38.49 4.00
655 2403 9.019764 GTAATACAAATGATTTCGGTTCATTGG 57.980 33.333 8.48 8.25 41.69 3.16
671 2419 4.097218 GGGAGGTTCTGCCCAAAC 57.903 61.111 0.00 0.00 44.07 2.93
676 2424 1.080569 GGTTCTGCCCAAACGCATG 60.081 57.895 0.00 0.00 38.30 4.06
681 2429 2.126888 GCCCAAACGCATGTGACG 60.127 61.111 14.43 0.85 0.00 4.35
683 2431 1.922135 GCCCAAACGCATGTGACGAT 61.922 55.000 14.43 0.00 0.00 3.73
687 2435 2.233355 CAAACGCATGTGACGATTGAC 58.767 47.619 14.43 0.00 43.42 3.18
716 2711 1.868498 CACCGAGCAAACCGAAGTTTA 59.132 47.619 0.00 0.00 44.47 2.01
763 2763 0.475044 AAGAAAGGGCCCGTTGTGTA 59.525 50.000 28.83 0.00 0.00 2.90
764 2764 0.250597 AGAAAGGGCCCGTTGTGTAC 60.251 55.000 28.83 12.73 0.00 2.90
765 2765 0.535553 GAAAGGGCCCGTTGTGTACA 60.536 55.000 28.83 0.00 0.00 2.90
766 2766 0.536460 AAAGGGCCCGTTGTGTACAG 60.536 55.000 23.24 0.00 0.00 2.74
767 2767 1.702022 AAGGGCCCGTTGTGTACAGT 61.702 55.000 18.44 0.00 0.00 3.55
774 2774 3.367703 GCCCGTTGTGTACAGTACAGTAT 60.368 47.826 14.03 0.00 39.77 2.12
807 2807 1.152652 ATCCGCCTCGTCTCCATCT 60.153 57.895 0.00 0.00 0.00 2.90
826 2826 0.614979 TTTCTCCCCTCACTCCCGAG 60.615 60.000 0.00 0.00 0.00 4.63
844 2848 3.356290 CGAGTCCAAGATCCCCAATTTT 58.644 45.455 0.00 0.00 0.00 1.82
884 2890 0.318955 ACAGCCGCAGACATTTTTGC 60.319 50.000 0.00 0.00 36.97 3.68
925 2931 2.846827 CCTTCTTCTCCCTACCACCATT 59.153 50.000 0.00 0.00 0.00 3.16
1076 3105 4.287781 TGGCGACGACGGAAGCAA 62.288 61.111 9.67 0.00 40.15 3.91
1201 3230 3.321648 AGATGGTGCGGACCTGCA 61.322 61.111 27.28 7.43 43.58 4.41
1313 3348 0.106769 TTCACCAGCAACCTTCTGCA 60.107 50.000 0.00 0.00 45.18 4.41
1315 3350 0.820891 CACCAGCAACCTTCTGCACT 60.821 55.000 0.00 0.00 45.18 4.40
1330 3365 2.512286 ACTGCCATGACATCGCGG 60.512 61.111 11.81 11.81 34.96 6.46
1428 3481 3.763671 CCTTGCCGGCTCAAAAGT 58.236 55.556 29.70 0.00 0.00 2.66
1443 3496 5.278169 GCTCAAAAGTTTGCATCTCTTCAGA 60.278 40.000 0.00 0.00 38.05 3.27
1518 3574 0.034059 CTCTGGAGGACGTGCAACTT 59.966 55.000 10.52 0.00 31.75 2.66
1530 3586 2.287915 CGTGCAACTTAGAAACTGCAGT 59.712 45.455 15.25 15.25 44.93 4.40
1534 3590 8.117595 CGTGCAACTTAGAAACTGCAGTTTTG 62.118 42.308 37.78 30.76 44.93 2.44
1564 3623 1.789464 GCAATGCTAAGATCGTCTCCG 59.211 52.381 0.00 0.00 0.00 4.63
1731 4175 0.036952 CCGTGCTGTCTCTTGTGGAT 60.037 55.000 0.00 0.00 0.00 3.41
1845 4308 2.096417 GCATTTCGCGGTCATGGTATAC 60.096 50.000 6.13 0.00 0.00 1.47
1951 4877 3.503748 GGTTTCAGCTGTTGTTCTATGCT 59.496 43.478 14.67 0.00 0.00 3.79
2000 4926 2.175878 TGAGAACCTGAGAAGCTTGC 57.824 50.000 2.10 0.00 0.00 4.01
2323 9656 2.623418 TCTGTCCACCTACTGGTCAT 57.377 50.000 0.00 0.00 46.60 3.06
2341 9674 0.036590 ATGTTTTTGGTGGGCATGCC 59.963 50.000 29.47 29.47 0.00 4.40
2444 9778 1.250154 TTGCTGATTTTCGCCCAGGG 61.250 55.000 0.00 0.00 0.00 4.45
2448 9782 1.678970 GATTTTCGCCCAGGGTGCT 60.679 57.895 15.13 0.00 32.51 4.40
2505 9841 9.539825 CTTTTACTAGTAGTTCATCATCTGCAT 57.460 33.333 8.40 0.00 0.00 3.96
2576 9912 6.339730 TGAAGCATGTCATTTCTGTTTGTTT 58.660 32.000 0.00 0.00 0.00 2.83
2589 9925 5.303971 TCTGTTTGTTTGGCAATTTATGGG 58.696 37.500 0.00 0.00 36.89 4.00
2618 9956 6.590234 AAAACTGAACAGGGGATTGATTAC 57.410 37.500 6.76 0.00 0.00 1.89
2702 10042 9.883142 TTTGATTTCACCAACTCATTACTTTTT 57.117 25.926 0.00 0.00 0.00 1.94
2754 12957 7.847711 AGTGGAAGTATCTTGTATCAGCTAT 57.152 36.000 0.00 0.00 0.00 2.97
2896 13115 2.288825 ACGTGTACAAGGGACATCAGTG 60.289 50.000 13.47 0.00 0.00 3.66
2940 13159 4.284490 ACATATCTTGCGGTCATACCTGAT 59.716 41.667 0.00 0.00 35.66 2.90
3004 13235 3.119388 TCGGACGAGGTGGTACAAAATAG 60.119 47.826 0.00 0.00 44.16 1.73
3033 13264 4.202556 TGGATGGTTCAGATGGTTTCTTGA 60.203 41.667 0.00 0.00 29.93 3.02
3065 13296 4.937201 AGTATGTTGTATCGCCTCATCA 57.063 40.909 0.00 0.00 0.00 3.07
3082 13313 5.092554 TCATCACGGTGATTTTAGGCTTA 57.907 39.130 20.52 0.00 34.28 3.09
3083 13314 5.116180 TCATCACGGTGATTTTAGGCTTAG 58.884 41.667 20.52 6.21 34.28 2.18
3084 13315 4.546829 TCACGGTGATTTTAGGCTTAGT 57.453 40.909 6.76 0.00 0.00 2.24
3180 13422 6.622896 GCGAAGGCAGTACTAAACATCAAAAT 60.623 38.462 0.00 0.00 39.62 1.82
3185 13427 7.867403 AGGCAGTACTAAACATCAAAATTGTTG 59.133 33.333 0.00 3.32 37.38 3.33
3257 13521 4.130118 GAGTGGAGTATTGCATTACTGGG 58.870 47.826 22.49 0.00 32.59 4.45
3275 13539 0.179086 GGGTGGGTTTGTGCACAAAG 60.179 55.000 38.24 0.00 45.36 2.77
3280 13544 3.129638 GTGGGTTTGTGCACAAAGAGTTA 59.870 43.478 38.24 22.48 45.36 2.24
3288 13552 2.948979 TGCACAAAGAGTTACAGTTGGG 59.051 45.455 0.00 0.00 0.00 4.12
3379 13645 2.373169 ACAAGGTCTGATTGGCTGAGAA 59.627 45.455 0.00 0.00 31.76 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 106 8.629158 TGCATGATGAAAGTGTACTTTTAAAGT 58.371 29.630 14.99 14.99 45.37 2.66
105 109 7.367285 GGTGCATGATGAAAGTGTACTTTTAA 58.633 34.615 10.98 4.36 45.37 1.52
106 110 6.072175 GGGTGCATGATGAAAGTGTACTTTTA 60.072 38.462 10.98 7.79 45.37 1.52
257 270 4.694339 AGAGTATTGAGTCAAATACGCCC 58.306 43.478 10.14 7.98 44.34 6.13
261 274 8.200792 AGACCATGAGAGTATTGAGTCAAATAC 58.799 37.037 10.14 12.21 41.41 1.89
307 320 7.536855 AGTCTAAAGTAATAACACGGAGACTG 58.463 38.462 0.00 0.00 36.31 3.51
309 322 7.201418 GCAAGTCTAAAGTAATAACACGGAGAC 60.201 40.741 0.00 0.00 31.72 3.36
314 327 6.730619 CGTTGCAAGTCTAAAGTAATAACACG 59.269 38.462 0.00 0.00 0.00 4.49
467 482 5.521735 GGACTAGCTCAAGTGTTGTATGATG 59.478 44.000 0.00 0.00 0.00 3.07
513 528 9.498176 ACGTGTAGAAGAATAAATGGTAAAACT 57.502 29.630 0.00 0.00 0.00 2.66
629 644 9.019764 CCAATGAACCGAAATCATTTGTATTAC 57.980 33.333 7.33 0.00 43.19 1.89
630 645 8.194104 CCCAATGAACCGAAATCATTTGTATTA 58.806 33.333 7.33 0.00 43.19 0.98
655 2403 2.626780 GCGTTTGGGCAGAACCTCC 61.627 63.158 0.00 0.00 39.10 4.30
671 2419 0.795698 TTGGTCAATCGTCACATGCG 59.204 50.000 0.00 0.00 0.00 4.73
681 2429 2.083774 TCGGTGCAAGATTGGTCAATC 58.916 47.619 14.01 14.01 45.66 2.67
683 2431 1.522668 CTCGGTGCAAGATTGGTCAA 58.477 50.000 0.00 0.00 0.00 3.18
710 2705 5.059404 CGAAAGGAACATGGCATAAACTT 57.941 39.130 0.00 0.00 0.00 2.66
763 2763 4.471548 CCTAGTGGGCTATACTGTACTGT 58.528 47.826 10.46 10.46 0.00 3.55
807 2807 0.614979 CTCGGGAGTGAGGGGAGAAA 60.615 60.000 0.00 0.00 32.18 2.52
826 2826 2.093500 GGCAAAATTGGGGATCTTGGAC 60.093 50.000 0.00 0.00 0.00 4.02
884 2890 0.598680 CTGCTAATTCGGAGGAGGCG 60.599 60.000 0.00 0.00 0.00 5.52
925 2931 0.736636 GCTTGTGCTCATATGCAGCA 59.263 50.000 19.49 19.49 44.80 4.41
1028 3036 2.819595 GATGCTTCGGCTTGGCGA 60.820 61.111 15.04 15.04 42.37 5.54
1197 3226 2.104859 CCTCGTGGACAGCATGCAG 61.105 63.158 21.98 15.38 42.53 4.41
1313 3348 2.512286 CCGCGATGTCATGGCAGT 60.512 61.111 18.43 0.00 33.19 4.40
1315 3350 2.511373 GACCGCGATGTCATGGCA 60.511 61.111 18.43 0.60 35.29 4.92
1428 3481 4.613925 AGACAGTCTGAAGAGATGCAAA 57.386 40.909 6.91 0.00 0.00 3.68
1443 3496 7.658525 ATCTGTCAGATTCAGATTAGACAGT 57.341 36.000 9.68 5.39 46.39 3.55
1495 3551 1.301716 GCACGTCCTCCAGAGCAAA 60.302 57.895 0.00 0.00 0.00 3.68
1496 3552 2.038814 TTGCACGTCCTCCAGAGCAA 62.039 55.000 1.99 1.99 40.52 3.91
1518 3574 3.944650 TGAGCACAAAACTGCAGTTTCTA 59.055 39.130 37.59 19.28 46.47 2.10
1564 3623 2.094854 CAGCCAATTTCTTGAGTGAGGC 60.095 50.000 0.00 0.00 41.08 4.70
1731 4175 1.805539 CGGAAGCTGAATCGACGCA 60.806 57.895 0.00 0.00 0.00 5.24
1830 4274 2.293677 AGAAGAGTATACCATGACCGCG 59.706 50.000 0.00 0.00 0.00 6.46
1845 4308 6.293004 AGGGTATGTCAAGAAGAAGAAGAG 57.707 41.667 0.00 0.00 0.00 2.85
1951 4877 3.367646 ACAGGAAGATCCTCACGAGTA 57.632 47.619 0.00 0.00 45.66 2.59
2000 4926 5.162794 GCTGATATGACACTCATCTAGCAG 58.837 45.833 0.00 0.00 38.26 4.24
2323 9656 1.449353 GGCATGCCCACCAAAAACA 59.551 52.632 27.24 0.00 0.00 2.83
2341 9674 4.513692 TCTTGTTGTTTGGTAGATTGGTCG 59.486 41.667 0.00 0.00 0.00 4.79
2345 9678 6.480524 TCGATCTTGTTGTTTGGTAGATTG 57.519 37.500 0.00 0.00 0.00 2.67
2444 9778 3.988379 TCAAATTGGTCAGACAAGCAC 57.012 42.857 2.17 0.00 33.23 4.40
2448 9782 7.177216 AGCTAATGATTCAAATTGGTCAGACAA 59.823 33.333 2.17 0.00 34.41 3.18
2558 9894 5.021033 TGCCAAACAAACAGAAATGACAT 57.979 34.783 0.00 0.00 0.00 3.06
2565 9901 5.762218 CCCATAAATTGCCAAACAAACAGAA 59.238 36.000 0.00 0.00 42.86 3.02
2599 9935 4.164988 AGAGGTAATCAATCCCCTGTTCAG 59.835 45.833 0.00 0.00 0.00 3.02
2618 9956 3.868077 CCTTGCGTCAAATAAGAGAGAGG 59.132 47.826 0.00 0.00 0.00 3.69
2654 9992 9.967451 TCAAACTACCTCAACCATCAAATATTA 57.033 29.630 0.00 0.00 0.00 0.98
2672 10011 8.784043 AGTAATGAGTTGGTGAAATCAAACTAC 58.216 33.333 1.54 0.00 39.48 2.73
2754 12957 7.981142 AGGTAACAACCTTAAATCACCTAGAA 58.019 34.615 0.00 0.00 36.56 2.10
2896 13115 2.728007 AGTAGGGCCTTTTGCTTCATC 58.272 47.619 13.45 0.00 40.92 2.92
3004 13235 7.721399 AGAAACCATCTGAACCATCCAATATAC 59.279 37.037 0.00 0.00 36.88 1.47
3019 13250 5.474532 TCCACTTCAATCAAGAAACCATCTG 59.525 40.000 0.00 0.00 38.79 2.90
3033 13264 6.037172 GCGATACAACATACTTCCACTTCAAT 59.963 38.462 0.00 0.00 0.00 2.57
3065 13296 3.518303 AGGACTAAGCCTAAAATCACCGT 59.482 43.478 0.00 0.00 36.22 4.83
3106 13340 5.127693 TGCCGCAAAATAGAGCTTAAAAA 57.872 34.783 0.00 0.00 0.00 1.94
3118 13352 4.972591 GCAAGACTGCCGCAAAAT 57.027 50.000 0.00 0.00 43.26 1.82
3180 13422 2.027073 CTAGCGTCGCTGCCAACAA 61.027 57.895 29.43 6.72 40.10 2.83
3185 13427 1.659954 CTGATCTAGCGTCGCTGCC 60.660 63.158 29.43 14.96 40.10 4.85
3235 13496 4.130118 CCCAGTAATGCAATACTCCACTC 58.870 47.826 11.59 0.00 33.90 3.51
3257 13521 0.820871 TCTTTGTGCACAAACCCACC 59.179 50.000 35.10 0.00 40.55 4.61
3275 13539 4.392138 GCTATCAACACCCAACTGTAACTC 59.608 45.833 0.00 0.00 0.00 3.01
3280 13544 2.504367 GTGCTATCAACACCCAACTGT 58.496 47.619 0.00 0.00 31.67 3.55


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

AutoCloner maintained by Alex Coulton.