Multiple sequence alignment - TraesCS2D01G019200

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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 TraesCS2D01G019200 chr2D 100.000 2437 0 0 1 2437 9007879 9010315 0.000000e+00 4501.0
1 TraesCS2D01G019200 chr2D 83.942 1507 218 12 852 2345 8670673 8672168 0.000000e+00 1421.0
2 TraesCS2D01G019200 chr2D 100.000 660 0 0 2670 3329 9010548 9011207 0.000000e+00 1219.0
3 TraesCS2D01G019200 chr2D 80.154 1562 259 30 851 2372 9642958 9644508 0.000000e+00 1120.0
4 TraesCS2D01G019200 chr2D 90.164 61 5 1 2919 2978 122036777 122036837 9.900000e-11 78.7
5 TraesCS2D01G019200 chr2B 95.389 1670 72 3 769 2437 11907203 11905538 0.000000e+00 2652.0
6 TraesCS2D01G019200 chr2B 79.910 1563 261 32 851 2372 11454244 11452694 0.000000e+00 1098.0
7 TraesCS2D01G019200 chr2B 80.349 1491 251 19 861 2331 11389552 11391020 0.000000e+00 1092.0
8 TraesCS2D01G019200 chr2B 95.095 367 16 2 2964 3329 9706495 9706860 8.010000e-161 577.0
9 TraesCS2D01G019200 chr2B 83.799 358 29 13 284 623 11913344 11912998 2.490000e-81 313.0
10 TraesCS2D01G019200 chr2B 88.306 248 18 5 2741 2981 11904862 11904619 1.510000e-73 287.0
11 TraesCS2D01G019200 chr2B 87.097 217 23 4 2 215 11913577 11913363 1.190000e-59 241.0
12 TraesCS2D01G019200 chr2B 92.920 113 6 1 621 733 11912803 11912693 2.660000e-36 163.0
13 TraesCS2D01G019200 chr2A 92.907 1847 96 22 619 2437 8412855 8414694 0.000000e+00 2652.0
14 TraesCS2D01G019200 chr2A 96.140 1114 40 3 1326 2437 8034405 8033293 0.000000e+00 1816.0
15 TraesCS2D01G019200 chr2A 80.000 1565 256 36 851 2372 8727294 8728844 0.000000e+00 1103.0
16 TraesCS2D01G019200 chr2A 80.293 1502 261 14 845 2331 7741594 7743075 0.000000e+00 1101.0
17 TraesCS2D01G019200 chr2A 79.612 1496 237 34 867 2331 9944092 9945550 0.000000e+00 1011.0
18 TraesCS2D01G019200 chr2A 93.960 596 21 6 2741 3329 8032814 8032227 0.000000e+00 887.0
19 TraesCS2D01G019200 chr2A 94.986 359 16 1 2973 3329 8023945 8023587 2.240000e-156 562.0
20 TraesCS2D01G019200 chr2A 90.299 268 25 1 17 284 8411889 8412155 1.900000e-92 350.0
21 TraesCS2D01G019200 chr2A 93.333 240 4 4 2741 2974 8026965 8026732 8.840000e-91 344.0
22 TraesCS2D01G019200 chr2A 82.029 345 17 12 284 623 8412427 8412731 5.510000e-63 252.0
23 TraesCS2D01G019200 chr2A 94.118 68 4 0 2670 2737 8027323 8027256 1.630000e-18 104.0
24 TraesCS2D01G019200 chr2A 90.141 71 3 4 2966 3034 179425768 179425836 4.570000e-14 89.8
25 TraesCS2D01G019200 chr3D 97.258 1532 41 1 906 2437 564053628 564055158 0.000000e+00 2595.0
26 TraesCS2D01G019200 chr3D 96.154 598 12 3 2738 3329 564055554 564056146 0.000000e+00 966.0
27 TraesCS2D01G019200 chr3D 85.131 343 34 9 284 618 564053249 564053582 5.320000e-88 335.0
28 TraesCS2D01G019200 chr3D 90.795 239 21 1 47 284 564052720 564052958 5.360000e-83 318.0
29 TraesCS2D01G019200 chr3D 92.169 166 8 4 3163 3324 15362527 15362691 2.580000e-56 230.0
30 TraesCS2D01G019200 chr3D 95.588 68 3 0 2670 2737 564055198 564055265 3.510000e-20 110.0
31 TraesCS2D01G019200 chr3D 87.671 73 5 4 2953 3022 17157723 17157652 7.650000e-12 82.4
32 TraesCS2D01G019200 chr3D 88.525 61 6 1 2919 2978 194687277 194687217 4.610000e-09 73.1
33 TraesCS2D01G019200 chrUn 97.035 1113 32 1 1326 2437 335085453 335086565 0.000000e+00 1871.0
34 TraesCS2D01G019200 chrUn 97.035 1113 32 1 1326 2437 416897230 416896118 0.000000e+00 1871.0
35 TraesCS2D01G019200 chrUn 83.117 154 20 5 849 999 310043599 310043749 5.790000e-28 135.0
36 TraesCS2D01G019200 chrUn 88.525 61 6 1 2919 2978 62694535 62694595 4.610000e-09 73.1
37 TraesCS2D01G019200 chr6B 85.714 84 8 4 2964 3045 2841879 2841798 5.920000e-13 86.1
38 TraesCS2D01G019200 chr6B 88.235 68 6 2 2955 3021 30511641 30511707 2.750000e-11 80.5
39 TraesCS2D01G019200 chr7A 84.270 89 9 5 2967 3052 68552503 68552589 7.650000e-12 82.4
40 TraesCS2D01G019200 chr6A 88.525 61 6 1 2919 2978 457604312 457604372 4.610000e-09 73.1
41 TraesCS2D01G019200 chr5D 88.525 61 6 1 2919 2978 46341084 46341144 4.610000e-09 73.1


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 TraesCS2D01G019200 chr2D 9007879 9011207 3328 False 2860.000000 4501 100.000000 1 3329 2 chr2D.!!$F4 3328
1 TraesCS2D01G019200 chr2D 8670673 8672168 1495 False 1421.000000 1421 83.942000 852 2345 1 chr2D.!!$F1 1493
2 TraesCS2D01G019200 chr2D 9642958 9644508 1550 False 1120.000000 1120 80.154000 851 2372 1 chr2D.!!$F2 1521
3 TraesCS2D01G019200 chr2B 11904619 11907203 2584 True 1469.500000 2652 91.847500 769 2981 2 chr2B.!!$R2 2212
4 TraesCS2D01G019200 chr2B 11452694 11454244 1550 True 1098.000000 1098 79.910000 851 2372 1 chr2B.!!$R1 1521
5 TraesCS2D01G019200 chr2B 11389552 11391020 1468 False 1092.000000 1092 80.349000 861 2331 1 chr2B.!!$F2 1470
6 TraesCS2D01G019200 chr2B 11912693 11913577 884 True 239.000000 313 87.938667 2 733 3 chr2B.!!$R3 731
7 TraesCS2D01G019200 chr2A 8032227 8034405 2178 True 1351.500000 1816 95.050000 1326 3329 2 chr2A.!!$R2 2003
8 TraesCS2D01G019200 chr2A 8727294 8728844 1550 False 1103.000000 1103 80.000000 851 2372 1 chr2A.!!$F2 1521
9 TraesCS2D01G019200 chr2A 7741594 7743075 1481 False 1101.000000 1101 80.293000 845 2331 1 chr2A.!!$F1 1486
10 TraesCS2D01G019200 chr2A 8411889 8414694 2805 False 1084.666667 2652 88.411667 17 2437 3 chr2A.!!$F5 2420
11 TraesCS2D01G019200 chr2A 9944092 9945550 1458 False 1011.000000 1011 79.612000 867 2331 1 chr2A.!!$F3 1464
12 TraesCS2D01G019200 chr2A 8023587 8027323 3736 True 336.666667 562 94.145667 2670 3329 3 chr2A.!!$R1 659
13 TraesCS2D01G019200 chr3D 564052720 564056146 3426 False 864.800000 2595 92.985200 47 3329 5 chr3D.!!$F2 3282
14 TraesCS2D01G019200 chrUn 335085453 335086565 1112 False 1871.000000 1871 97.035000 1326 2437 1 chrUn.!!$F3 1111
15 TraesCS2D01G019200 chrUn 416896118 416897230 1112 True 1871.000000 1871 97.035000 1326 2437 1 chrUn.!!$R1 1111

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
482 810 0.249120 CCATCGCTGTCACAGGGTTA 59.751 55.0 20.5 3.75 43.48 2.85 F
484 812 0.249398 ATCGCTGTCACAGGGTTACC 59.751 55.0 20.5 0.00 43.48 2.85 F
1150 1839 0.773644 AACCCTCCAAGACAGTGCAT 59.226 50.0 0.0 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 2245 0.676184 ACAGAAGAGAAGCACGAGCA 59.324 50.000 7.77 0.0 45.49 4.26 R
1839 2550 2.264480 CGTGGATGTTCTGCCGGA 59.736 61.111 5.05 0.0 0.00 5.14 R
2765 3899 1.763545 GCCCCCGAATTTCTAGAGACT 59.236 52.381 0.00 0.0 0.00 3.24 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
77 78 8.230486 ACAAATTACATGATCTTCGAACACTTC 58.770 33.333 0.00 0.00 0.00 3.01
102 103 7.806014 TCTTAGTGTGCGGTGAAAATTTTAATC 59.194 33.333 2.75 0.00 0.00 1.75
248 252 9.467258 CAGAAAACAATGAAATTTGCTCTCTTA 57.533 29.630 0.00 0.00 31.22 2.10
260 264 1.936547 GCTCTCTTATTTCTGCGGGTG 59.063 52.381 0.00 0.00 0.00 4.61
306 602 2.550830 TGTCAGCTTTTGAGGAGTCC 57.449 50.000 0.00 0.00 36.21 3.85
360 668 1.940613 GACCTGAGTTGCACGTTTCTT 59.059 47.619 0.00 0.00 0.00 2.52
374 682 3.095738 CGTTTCTTGAAACAACGTCCAC 58.904 45.455 21.31 0.00 38.75 4.02
376 684 4.095610 GTTTCTTGAAACAACGTCCACAG 58.904 43.478 18.05 0.00 33.08 3.66
380 688 4.638421 TCTTGAAACAACGTCCACAGATTT 59.362 37.500 0.00 0.00 0.00 2.17
382 690 3.314080 TGAAACAACGTCCACAGATTTCC 59.686 43.478 0.00 0.00 0.00 3.13
383 691 1.892209 ACAACGTCCACAGATTTCCC 58.108 50.000 0.00 0.00 0.00 3.97
384 692 1.420138 ACAACGTCCACAGATTTCCCT 59.580 47.619 0.00 0.00 0.00 4.20
386 694 0.613777 ACGTCCACAGATTTCCCTCC 59.386 55.000 0.00 0.00 0.00 4.30
387 695 0.613260 CGTCCACAGATTTCCCTCCA 59.387 55.000 0.00 0.00 0.00 3.86
388 696 1.406069 CGTCCACAGATTTCCCTCCAG 60.406 57.143 0.00 0.00 0.00 3.86
389 697 1.909302 GTCCACAGATTTCCCTCCAGA 59.091 52.381 0.00 0.00 0.00 3.86
390 698 1.909302 TCCACAGATTTCCCTCCAGAC 59.091 52.381 0.00 0.00 0.00 3.51
391 699 1.630369 CCACAGATTTCCCTCCAGACA 59.370 52.381 0.00 0.00 0.00 3.41
392 700 2.616510 CCACAGATTTCCCTCCAGACAC 60.617 54.545 0.00 0.00 0.00 3.67
393 701 1.276421 ACAGATTTCCCTCCAGACACG 59.724 52.381 0.00 0.00 0.00 4.49
394 702 0.905357 AGATTTCCCTCCAGACACGG 59.095 55.000 0.00 0.00 0.00 4.94
395 703 0.613777 GATTTCCCTCCAGACACGGT 59.386 55.000 0.00 0.00 0.00 4.83
396 704 0.324943 ATTTCCCTCCAGACACGGTG 59.675 55.000 6.58 6.58 0.00 4.94
397 705 2.391724 TTTCCCTCCAGACACGGTGC 62.392 60.000 8.30 1.14 0.00 5.01
398 706 3.314331 CCCTCCAGACACGGTGCT 61.314 66.667 8.30 3.65 0.00 4.40
399 707 2.743718 CCTCCAGACACGGTGCTT 59.256 61.111 8.30 0.00 0.00 3.91
400 708 1.374758 CCTCCAGACACGGTGCTTC 60.375 63.158 8.30 0.00 0.00 3.86
401 709 1.374758 CTCCAGACACGGTGCTTCC 60.375 63.158 8.30 0.00 0.00 3.46
458 786 2.758979 CCTCGTCTCCCTTTGTTAGCTA 59.241 50.000 0.00 0.00 0.00 3.32
464 792 1.280998 TCCCTTTGTTAGCTAGTGCCC 59.719 52.381 0.00 0.00 40.80 5.36
473 801 1.884926 GCTAGTGCCCATCGCTGTC 60.885 63.158 0.00 0.00 38.78 3.51
474 802 1.517361 CTAGTGCCCATCGCTGTCA 59.483 57.895 0.00 0.00 38.78 3.58
475 803 0.807667 CTAGTGCCCATCGCTGTCAC 60.808 60.000 2.01 2.01 38.78 3.67
476 804 1.540435 TAGTGCCCATCGCTGTCACA 61.540 55.000 10.21 0.00 38.78 3.58
477 805 2.046988 TGCCCATCGCTGTCACAG 60.047 61.111 0.00 0.00 38.78 3.66
478 806 2.821366 GCCCATCGCTGTCACAGG 60.821 66.667 7.00 0.00 31.21 4.00
479 807 2.124983 CCCATCGCTGTCACAGGG 60.125 66.667 15.71 15.71 44.21 4.45
480 808 2.665000 CCATCGCTGTCACAGGGT 59.335 61.111 20.50 6.46 43.48 4.34
481 809 1.003355 CCATCGCTGTCACAGGGTT 60.003 57.895 20.50 10.51 43.48 4.11
482 810 0.249120 CCATCGCTGTCACAGGGTTA 59.751 55.000 20.50 3.75 43.48 2.85
483 811 1.359848 CATCGCTGTCACAGGGTTAC 58.640 55.000 20.50 0.00 43.48 2.50
484 812 0.249398 ATCGCTGTCACAGGGTTACC 59.751 55.000 20.50 0.00 43.48 2.85
485 813 1.375523 CGCTGTCACAGGGTTACCC 60.376 63.158 13.56 13.56 45.90 3.69
528 873 2.290641 GTGGTTGCAACTACCAACTGAG 59.709 50.000 29.79 0.00 46.62 3.35
554 899 3.027974 ACGACTAGTTTGAAGTGGCTC 57.972 47.619 0.00 0.00 0.00 4.70
653 1323 1.204941 GACCGCTCCATAGTCAAGTGT 59.795 52.381 0.00 0.00 0.00 3.55
654 1324 1.066858 ACCGCTCCATAGTCAAGTGTG 60.067 52.381 0.00 0.00 0.00 3.82
686 1356 7.217200 TGGAAATATAAGCCACATAGACTGAC 58.783 38.462 0.00 0.00 0.00 3.51
698 1368 4.021016 ACATAGACTGACTGGGTTCTGAAC 60.021 45.833 12.05 12.05 0.00 3.18
729 1399 8.836413 CAAAGGAGAAGAACAAACATGTTACTA 58.164 33.333 12.39 0.00 31.35 1.82
739 1409 5.938125 ACAAACATGTTACTAGTGCCCTTAG 59.062 40.000 12.39 0.00 0.00 2.18
746 1422 7.108841 TGTTACTAGTGCCCTTAGATTACTG 57.891 40.000 5.39 0.00 0.00 2.74
772 1454 5.934625 AGTAATGAGCTGTTGTAACTCCAAG 59.065 40.000 0.00 0.00 0.00 3.61
782 1464 4.602340 TGTAACTCCAAGACAAGAGTCC 57.398 45.455 0.00 0.00 46.15 3.85
791 1473 1.346068 AGACAAGAGTCCCTGCAAGTC 59.654 52.381 0.00 0.00 46.15 3.01
823 1505 7.417456 GGAAGCCGGAATGGTAAATTATTTCTT 60.417 37.037 5.05 0.00 41.21 2.52
826 1508 7.123547 AGCCGGAATGGTAAATTATTTCTTCAA 59.876 33.333 5.05 0.00 41.21 2.69
833 1515 7.382898 TGGTAAATTATTTCTTCAAACAGCCC 58.617 34.615 0.00 0.00 0.00 5.19
837 1519 2.341846 TTTCTTCAAACAGCCCGACT 57.658 45.000 0.00 0.00 0.00 4.18
838 1520 2.341846 TTCTTCAAACAGCCCGACTT 57.658 45.000 0.00 0.00 0.00 3.01
839 1521 3.478857 TTCTTCAAACAGCCCGACTTA 57.521 42.857 0.00 0.00 0.00 2.24
841 1523 1.459592 CTTCAAACAGCCCGACTTACG 59.540 52.381 0.00 0.00 42.18 3.18
970 1659 1.888436 TTCACGCTCGGAGGCAGAAT 61.888 55.000 7.20 0.00 0.00 2.40
1150 1839 0.773644 AACCCTCCAAGACAGTGCAT 59.226 50.000 0.00 0.00 0.00 3.96
1398 2091 3.061322 CACCGACAACTTTATGTTCGGA 58.939 45.455 14.85 0.00 41.91 4.55
1516 2218 6.860790 AAGTTGGGAAGAAAACTTTGGTTA 57.139 33.333 0.00 0.00 42.51 2.85
1543 2245 1.153127 TGTGGCGACGAAAGGGTTT 60.153 52.632 0.00 0.00 0.00 3.27
1697 2408 8.519799 AACTTCCACTCATTTCTCTTAACAAA 57.480 30.769 0.00 0.00 0.00 2.83
1758 2469 4.713792 AAGATTAGCCCGATTTGGATCT 57.286 40.909 0.00 0.00 42.00 2.75
1839 2550 1.542030 CTAGCATTCGGGAGCGTAGAT 59.458 52.381 0.00 0.00 35.48 1.98
2097 2811 5.102953 ACTTTGCTATGCATCCACTTAGA 57.897 39.130 0.19 0.00 38.76 2.10
2239 2959 5.786121 ATCAAGGATACCCCCTCATAATG 57.214 43.478 0.00 0.00 34.95 1.90
2737 3579 7.241663 CACAATTGCATTAATCCTTGAATGG 57.758 36.000 5.05 0.00 34.29 3.16
2738 3580 6.259167 CACAATTGCATTAATCCTTGAATGGG 59.741 38.462 5.05 0.00 34.29 4.00
2739 3581 5.556006 ATTGCATTAATCCTTGAATGGGG 57.444 39.130 0.00 0.00 34.29 4.96
2762 3896 4.702131 GTCAAATCTTAAGTGACAGGGCAT 59.298 41.667 16.01 0.00 41.09 4.40
2763 3897 4.701651 TCAAATCTTAAGTGACAGGGCATG 59.298 41.667 1.63 0.00 0.00 4.06
2764 3898 2.113860 TCTTAAGTGACAGGGCATGC 57.886 50.000 9.90 9.90 0.00 4.06
2765 3899 1.350684 TCTTAAGTGACAGGGCATGCA 59.649 47.619 21.36 0.00 0.00 3.96
3160 7090 8.157476 TGACAGAAAAAGAGTCCTAGCTATTTT 58.843 33.333 0.00 0.00 40.32 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 7.807907 AGATTAAAATTTTCACCGCACACTAAG 59.192 33.333 6.72 0.00 0.00 2.18
248 252 1.745232 TATTTCGCACCCGCAGAAAT 58.255 45.000 15.82 15.82 45.06 2.17
306 602 4.447342 AGGGAAGGGGCAATGCGG 62.447 66.667 0.00 0.00 0.00 5.69
360 668 3.314080 GGAAATCTGTGGACGTTGTTTCA 59.686 43.478 0.00 0.00 0.00 2.69
374 682 1.406069 CCGTGTCTGGAGGGAAATCTG 60.406 57.143 0.00 0.00 0.00 2.90
376 684 0.613777 ACCGTGTCTGGAGGGAAATC 59.386 55.000 0.00 0.00 0.00 2.17
380 688 3.311110 GCACCGTGTCTGGAGGGA 61.311 66.667 0.00 0.00 0.00 4.20
382 690 1.374758 GAAGCACCGTGTCTGGAGG 60.375 63.158 0.00 0.00 0.00 4.30
383 691 1.374758 GGAAGCACCGTGTCTGGAG 60.375 63.158 0.00 0.00 0.00 3.86
384 692 1.480212 ATGGAAGCACCGTGTCTGGA 61.480 55.000 0.00 0.00 42.61 3.86
386 694 2.205074 GATATGGAAGCACCGTGTCTG 58.795 52.381 0.00 0.00 40.92 3.51
387 695 1.139058 GGATATGGAAGCACCGTGTCT 59.861 52.381 14.68 0.00 42.80 3.41
388 696 1.139058 AGGATATGGAAGCACCGTGTC 59.861 52.381 0.00 9.31 42.59 3.67
389 697 1.204146 AGGATATGGAAGCACCGTGT 58.796 50.000 0.00 0.00 42.61 4.49
390 698 2.628178 TCTAGGATATGGAAGCACCGTG 59.372 50.000 5.16 0.00 42.61 4.94
391 699 2.958818 TCTAGGATATGGAAGCACCGT 58.041 47.619 0.00 0.00 42.61 4.83
392 700 4.058817 GTTTCTAGGATATGGAAGCACCG 58.941 47.826 0.00 0.00 42.61 4.94
393 701 5.036117 TGTTTCTAGGATATGGAAGCACC 57.964 43.478 0.00 0.00 35.25 5.01
394 702 5.675538 ACTGTTTCTAGGATATGGAAGCAC 58.324 41.667 0.00 0.00 35.25 4.40
395 703 5.451937 CGACTGTTTCTAGGATATGGAAGCA 60.452 44.000 0.00 0.00 37.29 3.91
396 704 4.985409 CGACTGTTTCTAGGATATGGAAGC 59.015 45.833 0.00 0.00 31.44 3.86
397 705 6.392625 TCGACTGTTTCTAGGATATGGAAG 57.607 41.667 0.00 0.00 29.12 3.46
398 706 6.570692 GTTCGACTGTTTCTAGGATATGGAA 58.429 40.000 0.00 0.00 0.00 3.53
399 707 5.220989 CGTTCGACTGTTTCTAGGATATGGA 60.221 44.000 0.00 0.00 0.00 3.41
400 708 4.976731 CGTTCGACTGTTTCTAGGATATGG 59.023 45.833 0.00 0.00 0.00 2.74
401 709 5.681982 GTCGTTCGACTGTTTCTAGGATATG 59.318 44.000 16.50 0.00 32.82 1.78
437 750 1.550976 AGCTAACAAAGGGAGACGAGG 59.449 52.381 0.00 0.00 0.00 4.63
464 792 1.359848 GTAACCCTGTGACAGCGATG 58.640 55.000 7.16 0.00 0.00 3.84
479 807 0.457035 TATCGTCGGTGCTGGGTAAC 59.543 55.000 0.00 0.00 0.00 2.50
480 808 0.742505 CTATCGTCGGTGCTGGGTAA 59.257 55.000 0.00 0.00 0.00 2.85
481 809 0.394762 ACTATCGTCGGTGCTGGGTA 60.395 55.000 0.00 0.00 0.00 3.69
482 810 1.681327 ACTATCGTCGGTGCTGGGT 60.681 57.895 0.00 0.00 0.00 4.51
483 811 1.226974 CACTATCGTCGGTGCTGGG 60.227 63.158 0.00 0.00 0.00 4.45
484 812 1.226974 CCACTATCGTCGGTGCTGG 60.227 63.158 0.00 0.00 32.68 4.85
485 813 0.385751 ATCCACTATCGTCGGTGCTG 59.614 55.000 0.00 0.00 32.68 4.41
486 814 1.112113 AATCCACTATCGTCGGTGCT 58.888 50.000 0.00 0.00 32.68 4.40
487 815 2.034305 ACTAATCCACTATCGTCGGTGC 59.966 50.000 0.00 0.00 32.68 5.01
610 955 3.007979 TGTGCACTTGACACTACGTAG 57.992 47.619 20.97 20.97 38.86 3.51
653 1323 3.055021 TGGCTTATATTTCCACACGTCCA 60.055 43.478 0.00 0.00 0.00 4.02
654 1324 3.537580 TGGCTTATATTTCCACACGTCC 58.462 45.455 0.00 0.00 0.00 4.79
686 1356 3.181476 CCTTTGGTTTGTTCAGAACCCAG 60.181 47.826 10.93 1.11 44.73 4.45
698 1368 5.719173 TGTTTGTTCTTCTCCTTTGGTTTG 58.281 37.500 0.00 0.00 0.00 2.93
729 1399 6.869206 TTACTTCAGTAATCTAAGGGCACT 57.131 37.500 0.00 0.00 35.75 4.40
739 1409 7.602517 ACAACAGCTCATTACTTCAGTAATC 57.397 36.000 8.94 0.33 45.22 1.75
746 1422 5.932303 TGGAGTTACAACAGCTCATTACTTC 59.068 40.000 0.00 0.00 36.26 3.01
753 1429 3.133901 TGTCTTGGAGTTACAACAGCTCA 59.866 43.478 0.00 0.00 36.26 4.26
762 1438 3.579151 AGGGACTCTTGTCTTGGAGTTAC 59.421 47.826 0.00 0.00 42.06 2.50
764 1440 2.370189 CAGGGACTCTTGTCTTGGAGTT 59.630 50.000 0.00 0.00 42.06 3.01
765 1441 1.974236 CAGGGACTCTTGTCTTGGAGT 59.026 52.381 0.00 0.00 44.29 3.85
772 1454 1.346068 AGACTTGCAGGGACTCTTGTC 59.654 52.381 0.00 0.00 42.22 3.18
782 1464 1.580845 CTTCCGCCAAGACTTGCAGG 61.581 60.000 9.85 13.89 33.29 4.85
807 1489 8.040727 GGGCTGTTTGAAGAAATAATTTACCAT 58.959 33.333 0.00 0.00 0.00 3.55
808 1490 7.382898 GGGCTGTTTGAAGAAATAATTTACCA 58.617 34.615 0.00 0.00 0.00 3.25
823 1505 3.204505 CGTAAGTCGGGCTGTTTGA 57.795 52.632 0.00 0.00 35.71 2.69
833 1515 3.227810 AGGTAAAGCTTCCGTAAGTCG 57.772 47.619 0.00 0.00 34.99 4.18
837 1519 6.764560 GGATTGATTAGGTAAAGCTTCCGTAA 59.235 38.462 0.00 6.56 0.00 3.18
838 1520 6.099269 AGGATTGATTAGGTAAAGCTTCCGTA 59.901 38.462 0.00 0.00 33.99 4.02
839 1521 5.104485 AGGATTGATTAGGTAAAGCTTCCGT 60.104 40.000 0.00 0.00 33.99 4.69
841 1523 5.532779 CCAGGATTGATTAGGTAAAGCTTCC 59.467 44.000 0.00 0.00 30.91 3.46
842 1524 5.009110 GCCAGGATTGATTAGGTAAAGCTTC 59.991 44.000 0.00 0.00 0.00 3.86
843 1525 4.889995 GCCAGGATTGATTAGGTAAAGCTT 59.110 41.667 0.00 0.00 0.00 3.74
909 1592 1.902508 AGCAGGAAGGAGATGAAACGA 59.097 47.619 0.00 0.00 0.00 3.85
970 1659 2.363680 GCTGCAACCTCTCTATCAGCTA 59.636 50.000 4.95 0.00 42.41 3.32
1056 1745 3.119743 GCATCTTGAGCTGCAACAACATA 60.120 43.478 1.02 0.00 37.16 2.29
1150 1839 2.168313 TGATGCTAACCTCATCGAAGCA 59.832 45.455 8.05 8.05 46.30 3.91
1516 2218 1.664649 CGTCGCCACACACATGAGT 60.665 57.895 0.00 0.00 0.00 3.41
1543 2245 0.676184 ACAGAAGAGAAGCACGAGCA 59.324 50.000 7.77 0.00 45.49 4.26
1622 2333 5.283060 AGCAAACTCAATAACTACAAGCG 57.717 39.130 0.00 0.00 0.00 4.68
1758 2469 6.687081 ACACTAAGAAAAATCGGTTTCACA 57.313 33.333 0.00 0.00 39.52 3.58
1839 2550 2.264480 CGTGGATGTTCTGCCGGA 59.736 61.111 5.05 0.00 0.00 5.14
2355 3090 7.656707 ATGTTTGAAAATACATCAAAGTGCC 57.343 32.000 2.20 0.00 44.81 5.01
2737 3579 4.010349 CCCTGTCACTTAAGATTTGACCC 58.990 47.826 17.42 0.70 39.16 4.46
2738 3580 3.440522 GCCCTGTCACTTAAGATTTGACC 59.559 47.826 17.42 3.75 39.16 4.02
2739 3581 4.072131 TGCCCTGTCACTTAAGATTTGAC 58.928 43.478 10.09 12.96 40.14 3.18
2762 3896 2.168521 CCCCGAATTTCTAGAGACTGCA 59.831 50.000 0.00 0.00 0.00 4.41
2763 3897 2.483889 CCCCCGAATTTCTAGAGACTGC 60.484 54.545 0.00 0.00 0.00 4.40
2764 3898 2.483889 GCCCCCGAATTTCTAGAGACTG 60.484 54.545 0.00 0.00 0.00 3.51
2765 3899 1.763545 GCCCCCGAATTTCTAGAGACT 59.236 52.381 0.00 0.00 0.00 3.24
2995 6925 5.404946 TCTAGAATTAACGTGGAGGTTTCG 58.595 41.667 0.00 0.00 0.00 3.46
2999 6929 6.093633 GCATTTTCTAGAATTAACGTGGAGGT 59.906 38.462 5.89 0.00 0.00 3.85
3111 7041 9.127277 GTCACATAAGTAGAGAAATAGGACTCT 57.873 37.037 0.00 0.00 44.27 3.24
3160 7090 2.615447 GGTGTCTCGGACGTACATATGA 59.385 50.000 10.38 0.00 34.95 2.15
3294 7227 8.675705 CACAACTTGTGGATATTACATATGGA 57.324 34.615 13.36 0.00 44.27 3.41


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

AutoCloner maintained by Alex Coulton.