Multiple sequence alignment - TraesCS2A01G021000

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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 TraesCS2A01G021000 chr2A 100.000 3455 0 0 1 3455 9943094 9946548 0.000000e+00 6381.0
1 TraesCS2A01G021000 chr2A 82.055 1538 250 19 999 2521 8630958 8632484 0.000000e+00 1288.0
2 TraesCS2A01G021000 chr2A 80.384 1509 274 16 999 2499 9982951 9984445 0.000000e+00 1127.0
3 TraesCS2A01G021000 chr2A 80.290 1517 274 19 999 2502 9111118 9109614 0.000000e+00 1122.0
4 TraesCS2A01G021000 chr2A 100.000 29 0 0 2693 2721 32881039 32881011 2.000000e-03 54.7
5 TraesCS2A01G021000 chr2B 94.604 1742 74 12 1725 3455 13345697 13343965 0.000000e+00 2678.0
6 TraesCS2A01G021000 chr2B 95.521 960 36 6 740 1696 13346647 13345692 0.000000e+00 1528.0
7 TraesCS2A01G021000 chr2B 82.189 1718 273 18 777 2480 11400420 11402118 0.000000e+00 1447.0
8 TraesCS2A01G021000 chr2B 80.231 1558 286 11 982 2525 12942406 12943955 0.000000e+00 1151.0
9 TraesCS2A01G021000 chr2B 85.986 735 95 6 9 739 774540302 774539572 0.000000e+00 780.0
10 TraesCS2A01G021000 chr2B 85.933 718 95 4 21 735 774478007 774477293 0.000000e+00 761.0
11 TraesCS2A01G021000 chr2B 85.124 121 9 4 2862 2973 175630184 175630304 7.840000e-22 115.0
12 TraesCS2A01G021000 chr4D 81.736 1555 257 16 975 2512 464204577 464206121 0.000000e+00 1273.0
13 TraesCS2A01G021000 chr4D 86.443 745 91 8 1 742 464994499 464993762 0.000000e+00 808.0
14 TraesCS2A01G021000 chr2D 81.539 1533 266 5 982 2500 9588273 9589802 0.000000e+00 1247.0
15 TraesCS2A01G021000 chr2D 81.356 1534 266 13 999 2520 9380445 9381970 0.000000e+00 1230.0
16 TraesCS2A01G021000 chr2D 80.996 1405 228 19 957 2349 8479388 8478011 0.000000e+00 1079.0
17 TraesCS2A01G021000 chr2D 85.210 737 102 3 1 735 66853623 66852892 0.000000e+00 750.0
18 TraesCS2A01G021000 chr5A 86.549 736 92 4 2 735 708702808 708702078 0.000000e+00 804.0
19 TraesCS2A01G021000 chr3D 86.431 737 95 3 1 735 587396298 587397031 0.000000e+00 802.0
20 TraesCS2A01G021000 chr3D 85.714 70 10 0 2651 2720 318419275 318419206 1.330000e-09 75.0
21 TraesCS2A01G021000 chr3D 100.000 28 0 0 2693 2720 582611955 582611982 6.000000e-03 52.8
22 TraesCS2A01G021000 chr1A 86.486 740 88 7 1 735 534141488 534142220 0.000000e+00 802.0
23 TraesCS2A01G021000 chr1A 81.579 114 12 5 2870 2975 137872547 137872435 6.140000e-13 86.1
24 TraesCS2A01G021000 chr7D 86.024 737 97 4 1 735 131825979 131826711 0.000000e+00 785.0
25 TraesCS2A01G021000 chr7D 78.205 156 17 12 2839 2980 41281498 41281346 2.210000e-12 84.2
26 TraesCS2A01G021000 chr3B 85.638 745 100 5 1 743 42493295 42492556 0.000000e+00 776.0
27 TraesCS2A01G021000 chr3B 100.000 34 0 0 2651 2684 566987202 566987169 2.880000e-06 63.9
28 TraesCS2A01G021000 chr3B 92.857 42 3 0 2894 2935 667217200 667217159 1.040000e-05 62.1
29 TraesCS2A01G021000 chr3B 94.286 35 1 1 2687 2721 737092718 737092751 6.000000e-03 52.8
30 TraesCS2A01G021000 chr5D 87.379 103 9 2 2837 2935 254521511 254521613 7.840000e-22 115.0
31 TraesCS2A01G021000 chr7A 80.882 136 15 3 2839 2963 105506525 105506390 2.840000e-16 97.1
32 TraesCS2A01G021000 chr7A 87.500 64 8 0 2870 2933 279189838 279189775 1.330000e-09 75.0
33 TraesCS2A01G021000 chr7A 81.319 91 7 5 2650 2731 514710343 514710254 8.000000e-07 65.8
34 TraesCS2A01G021000 chr7A 94.286 35 1 1 2687 2721 274388297 274388264 6.000000e-03 52.8
35 TraesCS2A01G021000 chr3A 85.915 71 10 0 2865 2935 8650281 8650351 3.700000e-10 76.8
36 TraesCS2A01G021000 chr6B 100.000 34 0 0 2651 2684 558925819 558925852 2.880000e-06 63.9
37 TraesCS2A01G021000 chr6B 100.000 28 0 0 2694 2721 131695066 131695039 6.000000e-03 52.8
38 TraesCS2A01G021000 chr4A 100.000 34 0 0 2651 2684 737859042 737859075 2.880000e-06 63.9
39 TraesCS2A01G021000 chr4A 94.444 36 1 1 2687 2722 691154794 691154828 2.000000e-03 54.7


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 TraesCS2A01G021000 chr2A 9943094 9946548 3454 False 6381 6381 100.0000 1 3455 1 chr2A.!!$F2 3454
1 TraesCS2A01G021000 chr2A 8630958 8632484 1526 False 1288 1288 82.0550 999 2521 1 chr2A.!!$F1 1522
2 TraesCS2A01G021000 chr2A 9982951 9984445 1494 False 1127 1127 80.3840 999 2499 1 chr2A.!!$F3 1500
3 TraesCS2A01G021000 chr2A 9109614 9111118 1504 True 1122 1122 80.2900 999 2502 1 chr2A.!!$R1 1503
4 TraesCS2A01G021000 chr2B 13343965 13346647 2682 True 2103 2678 95.0625 740 3455 2 chr2B.!!$R3 2715
5 TraesCS2A01G021000 chr2B 11400420 11402118 1698 False 1447 1447 82.1890 777 2480 1 chr2B.!!$F1 1703
6 TraesCS2A01G021000 chr2B 12942406 12943955 1549 False 1151 1151 80.2310 982 2525 1 chr2B.!!$F2 1543
7 TraesCS2A01G021000 chr2B 774539572 774540302 730 True 780 780 85.9860 9 739 1 chr2B.!!$R2 730
8 TraesCS2A01G021000 chr2B 774477293 774478007 714 True 761 761 85.9330 21 735 1 chr2B.!!$R1 714
9 TraesCS2A01G021000 chr4D 464204577 464206121 1544 False 1273 1273 81.7360 975 2512 1 chr4D.!!$F1 1537
10 TraesCS2A01G021000 chr4D 464993762 464994499 737 True 808 808 86.4430 1 742 1 chr4D.!!$R1 741
11 TraesCS2A01G021000 chr2D 9588273 9589802 1529 False 1247 1247 81.5390 982 2500 1 chr2D.!!$F2 1518
12 TraesCS2A01G021000 chr2D 9380445 9381970 1525 False 1230 1230 81.3560 999 2520 1 chr2D.!!$F1 1521
13 TraesCS2A01G021000 chr2D 8478011 8479388 1377 True 1079 1079 80.9960 957 2349 1 chr2D.!!$R1 1392
14 TraesCS2A01G021000 chr2D 66852892 66853623 731 True 750 750 85.2100 1 735 1 chr2D.!!$R2 734
15 TraesCS2A01G021000 chr5A 708702078 708702808 730 True 804 804 86.5490 2 735 1 chr5A.!!$R1 733
16 TraesCS2A01G021000 chr3D 587396298 587397031 733 False 802 802 86.4310 1 735 1 chr3D.!!$F2 734
17 TraesCS2A01G021000 chr1A 534141488 534142220 732 False 802 802 86.4860 1 735 1 chr1A.!!$F1 734
18 TraesCS2A01G021000 chr7D 131825979 131826711 732 False 785 785 86.0240 1 735 1 chr7D.!!$F1 734
19 TraesCS2A01G021000 chr3B 42492556 42493295 739 True 776 776 85.6380 1 743 1 chr3B.!!$R1 742

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
763 768 0.033504 GAGGTCGTTGAGTCCAGCAA 59.966 55.000 0.0 0.0 0.0 3.91 F
1454 1488 1.280710 ACTTATGGGCGGATGTGAACA 59.719 47.619 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2033 0.842635 TGCAACCCCTTGGCAAATTT 59.157 45.000 0.0 0.0 34.05 1.82 R
2793 2842 1.484653 TGCATTACTGAGTGGCGGTAT 59.515 47.619 0.0 0.0 38.14 2.73 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
57 58 4.344968 CCTCCCAGACAAAAGTCCAAAATT 59.655 41.667 0.00 0.00 0.00 1.82
125 127 1.613630 AGATGCCGTCTTGGGAGGT 60.614 57.895 0.00 0.00 43.72 3.85
136 138 0.930726 TTGGGAGGTTTGGGTGTTCT 59.069 50.000 0.00 0.00 0.00 3.01
148 150 0.765510 GGTGTTCTGGGGAGAGTTGT 59.234 55.000 0.00 0.00 0.00 3.32
159 161 1.947456 GGAGAGTTGTTGTGGGTGAAC 59.053 52.381 0.00 0.00 0.00 3.18
160 162 2.639065 GAGAGTTGTTGTGGGTGAACA 58.361 47.619 0.00 0.00 0.00 3.18
216 218 2.129555 GAGGTTGGCAGGAGGAGCAA 62.130 60.000 0.00 0.00 0.00 3.91
265 267 5.163405 GCCTGGTAAGAGATGTCAAGTCATA 60.163 44.000 0.00 0.00 0.00 2.15
286 288 4.065281 GGCCGACAGGTGCTACGT 62.065 66.667 0.00 0.00 40.50 3.57
296 298 1.070134 AGGTGCTACGTTGTGTCATGT 59.930 47.619 0.00 0.00 0.00 3.21
302 304 2.325583 ACGTTGTGTCATGTCTGGTT 57.674 45.000 0.00 0.00 0.00 3.67
319 321 1.339631 GGTTGGCAGGTGCTACACATA 60.340 52.381 1.26 0.00 41.70 2.29
322 324 1.006832 GGCAGGTGCTACACATAACG 58.993 55.000 1.26 0.00 41.70 3.18
344 346 1.996798 TCTTCCAGAGTCTCCACGTT 58.003 50.000 0.00 0.00 0.00 3.99
356 358 1.004320 CCACGTTGGGATGGACGAA 60.004 57.895 2.69 0.00 41.53 3.85
384 386 3.565214 TGGAGTCTTTGGGCGCCA 61.565 61.111 30.85 12.04 32.30 5.69
433 437 4.104420 AGGCAAGGATTATGCAGATCTCTT 59.896 41.667 11.35 10.07 45.60 2.85
487 491 2.413796 CGGCTTCTAAAACGTGTGCATA 59.586 45.455 0.00 0.00 0.00 3.14
497 501 1.067425 ACGTGTGCATATGGTGTACGT 60.067 47.619 7.63 0.00 45.25 3.57
503 507 5.349270 GTGTGCATATGGTGTACGTTTTAGA 59.651 40.000 4.56 0.00 45.25 2.10
528 532 0.965866 TGCACCGGTTGTTTGTTCCA 60.966 50.000 2.97 0.00 0.00 3.53
532 536 3.305744 GCACCGGTTGTTTGTTCCAATAT 60.306 43.478 2.97 0.00 0.00 1.28
551 555 7.127186 TCCAATATGTTATATGGATGGATCGGT 59.873 37.037 0.00 0.00 37.05 4.69
617 621 8.372459 ACATTATCAAGTTTGTAGGTGTGAGTA 58.628 33.333 0.00 0.00 0.00 2.59
619 623 4.628074 TCAAGTTTGTAGGTGTGAGTAGC 58.372 43.478 0.00 0.00 0.00 3.58
643 647 0.463654 TCGGGTGGCTTGATGTATGC 60.464 55.000 0.00 0.00 0.00 3.14
652 657 3.587923 GCTTGATGTATGCTTTTGCCAA 58.412 40.909 0.00 0.00 46.87 4.52
708 713 3.109044 CATCGATTGATGCAGAGGACT 57.891 47.619 10.05 0.00 45.06 3.85
728 733 3.465966 ACTGGGGTTTAACCTCCTTTTCT 59.534 43.478 11.97 0.00 38.22 2.52
763 768 0.033504 GAGGTCGTTGAGTCCAGCAA 59.966 55.000 0.00 0.00 0.00 3.91
794 799 5.514500 AATAGAAAGTTGGCCTGTCCTTA 57.486 39.130 3.32 0.00 35.26 2.69
806 811 3.445096 GCCTGTCCTTATCAGCATGTTTT 59.555 43.478 0.00 0.00 37.40 2.43
819 824 7.609760 TCAGCATGTTTTGACGTTTAGATAT 57.390 32.000 0.00 0.00 37.40 1.63
874 880 4.745649 ACTCGTCTAGTCAATGGTTTAGC 58.254 43.478 0.00 0.00 30.33 3.09
1081 1103 3.782656 TGAAAAAGTACCACTCCTCCC 57.217 47.619 0.00 0.00 0.00 4.30
1107 1135 6.267699 TCCATGCGAAATTAGAGGAGAAGATA 59.732 38.462 0.00 0.00 0.00 1.98
1110 1138 7.818997 TGCGAAATTAGAGGAGAAGATAGTA 57.181 36.000 0.00 0.00 0.00 1.82
1277 1305 1.477295 GAGGTACCGAACTCTCCAAGG 59.523 57.143 6.18 0.00 0.00 3.61
1330 1361 4.056740 CTCATCTACCAGCTGCTTGTATG 58.943 47.826 13.23 11.05 0.00 2.39
1438 1472 7.701539 AACATGGCAGAATTCATTGTACTTA 57.298 32.000 8.44 0.00 0.00 2.24
1452 1486 2.502130 TGTACTTATGGGCGGATGTGAA 59.498 45.455 0.00 0.00 0.00 3.18
1454 1488 1.280710 ACTTATGGGCGGATGTGAACA 59.719 47.619 0.00 0.00 0.00 3.18
1508 1542 3.275143 ACACCGACAACTTCATGTTCAA 58.725 40.909 0.00 0.00 36.63 2.69
1560 1594 3.859627 GCTTCTTGTTGCAGCACAATGAT 60.860 43.478 1.37 0.00 41.27 2.45
1603 1637 5.144832 TGGATGTTCTTCCGATCATAGGTA 58.855 41.667 0.00 0.00 38.74 3.08
1652 1686 2.356913 TCATGTGTGTGGCGACGG 60.357 61.111 0.00 0.00 0.00 4.79
1887 1921 1.737793 GCTCGATTTGGAACGGTGAAT 59.262 47.619 0.00 0.00 0.00 2.57
1926 1960 7.925483 AGTGTTCTATCTTATGATGAGTTGAGC 59.075 37.037 1.45 0.00 34.32 4.26
2057 2093 4.216257 ACTTCTCGCAGCAAATATGTTTGT 59.784 37.500 15.30 1.43 45.14 2.83
2349 2392 8.765488 TTATGCTAATTTCATGGGAATCAAGA 57.235 30.769 0.00 0.00 31.93 3.02
2399 2442 2.426522 TGTTACAAGTCATGCTCAGGC 58.573 47.619 0.00 0.00 39.26 4.85
2553 2601 2.632028 TGTGGGGAAACAAATGGATGTG 59.368 45.455 0.00 0.00 32.81 3.21
2585 2633 5.528043 AACACTGAACCAAATGTATTGCA 57.472 34.783 0.00 0.00 0.00 4.08
2642 2690 2.293677 CTGTCCGGATATACTTGTCGCT 59.706 50.000 7.81 0.00 0.00 4.93
2644 2692 2.292569 GTCCGGATATACTTGTCGCTCA 59.707 50.000 7.81 0.00 0.00 4.26
2704 2752 3.810941 TCGGTTTGAGCGACAAGTATTTT 59.189 39.130 0.00 0.00 43.66 1.82
2705 2753 4.084223 TCGGTTTGAGCGACAAGTATTTTC 60.084 41.667 0.00 0.00 43.66 2.29
2710 2758 2.991190 GAGCGACAAGTATTTTCGGACA 59.009 45.455 0.00 0.00 33.28 4.02
2712 2760 2.991190 GCGACAAGTATTTTCGGACAGA 59.009 45.455 0.00 0.00 33.28 3.41
2714 2762 3.612860 CGACAAGTATTTTCGGACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
2716 2764 5.223449 ACAAGTATTTTCGGACAGAGGAA 57.777 39.130 0.00 0.00 0.00 3.36
2717 2765 5.238583 ACAAGTATTTTCGGACAGAGGAAG 58.761 41.667 0.00 0.00 0.00 3.46
2747 2796 6.867519 TTATCAGATCAAACAGTCCACCTA 57.132 37.500 0.00 0.00 0.00 3.08
2761 2810 7.355101 ACAGTCCACCTACTCATCTTAGATAA 58.645 38.462 0.00 0.00 0.00 1.75
2793 2842 1.419381 TGTGAAGTGGCACTACCTGA 58.581 50.000 22.37 0.00 39.49 3.86
2835 2884 5.747248 GCAGCTTATAATGGATCAGGAAGGT 60.747 44.000 0.00 0.00 0.00 3.50
2901 2950 4.032960 TGGGCTACATGTGAACTGAAAT 57.967 40.909 9.11 0.00 0.00 2.17
2902 2951 3.758023 TGGGCTACATGTGAACTGAAATG 59.242 43.478 9.11 0.00 0.00 2.32
2926 2976 1.319079 GAACAAACACACCAAAACGCG 59.681 47.619 3.53 3.53 0.00 6.01
2989 3045 8.237267 AGTGAACAGAGAAAGTAAACAAACAAG 58.763 33.333 0.00 0.00 0.00 3.16
3055 3111 8.604035 GCTATACGTGTATTATAAGCATGCAAT 58.396 33.333 21.98 15.14 0.00 3.56
3065 3121 2.088950 AGCATGCAATTTGACCAAGC 57.911 45.000 21.98 0.00 0.00 4.01
3177 3233 3.165058 CGGAGCAATTGAGCTAGTACA 57.835 47.619 10.34 0.00 46.75 2.90
3205 3261 8.402472 GTTTTGTGCATTATAGTATAGTGCCAA 58.598 33.333 26.06 24.21 35.03 4.52
3224 3280 5.102313 GCCAACACACAGGATAAATTAAGC 58.898 41.667 0.00 0.00 0.00 3.09
3268 3324 4.458989 GCCAAGTACCAACTCATCATTTCA 59.541 41.667 0.00 0.00 33.75 2.69
3283 3339 5.448926 TCATTTCATATCACAACGTCACG 57.551 39.130 0.00 0.00 0.00 4.35
3355 3411 7.438757 TCAAACATGTGTTTTGAGAATTCCATG 59.561 33.333 8.32 8.41 45.07 3.66
3356 3412 6.653526 ACATGTGTTTTGAGAATTCCATGA 57.346 33.333 18.10 2.11 34.17 3.07
3357 3413 7.235935 ACATGTGTTTTGAGAATTCCATGAT 57.764 32.000 18.10 5.70 34.17 2.45
3359 3415 6.028146 TGTGTTTTGAGAATTCCATGATGG 57.972 37.500 4.74 4.74 39.43 3.51
3360 3416 5.539574 TGTGTTTTGAGAATTCCATGATGGT 59.460 36.000 11.87 0.00 39.03 3.55
3362 3418 5.774184 TGTTTTGAGAATTCCATGATGGTGA 59.226 36.000 11.87 2.00 39.03 4.02
3363 3419 6.438108 TGTTTTGAGAATTCCATGATGGTGAT 59.562 34.615 11.87 4.41 39.03 3.06
3366 3422 5.128205 TGAGAATTCCATGATGGTGATGTC 58.872 41.667 11.87 7.24 39.03 3.06
3367 3423 4.467769 AGAATTCCATGATGGTGATGTCC 58.532 43.478 11.87 1.81 39.03 4.02
3378 3434 2.295253 GTGATGTCCACCCTTAGTCG 57.705 55.000 0.00 0.00 39.86 4.18
3379 3435 1.549170 GTGATGTCCACCCTTAGTCGT 59.451 52.381 0.00 0.00 39.86 4.34
3380 3436 2.028385 GTGATGTCCACCCTTAGTCGTT 60.028 50.000 0.00 0.00 39.86 3.85
3418 3474 3.616956 TCTGCTATGACCCAAGAACAG 57.383 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.607299 TCTGGGAGGGGGTCGGAA 61.607 66.667 0.00 0.00 0.00 4.30
92 94 3.900855 TCTCCACGGAGAGTACGC 58.099 61.111 11.87 0.00 45.26 4.42
103 105 1.450312 CCCAAGACGGCATCTCCAC 60.450 63.158 0.00 0.00 36.27 4.02
109 111 0.609131 CAAACCTCCCAAGACGGCAT 60.609 55.000 0.00 0.00 0.00 4.40
125 127 0.771127 CTCTCCCCAGAACACCCAAA 59.229 55.000 0.00 0.00 0.00 3.28
136 138 0.991355 ACCCACAACAACTCTCCCCA 60.991 55.000 0.00 0.00 0.00 4.96
148 150 0.546122 ACAGAGCTGTTCACCCACAA 59.454 50.000 0.00 0.00 41.83 3.33
186 188 1.047801 GCCAACCTCCACACCATTTT 58.952 50.000 0.00 0.00 0.00 1.82
187 189 0.105760 TGCCAACCTCCACACCATTT 60.106 50.000 0.00 0.00 0.00 2.32
216 218 1.329906 CTGACGCGGTAGATAGAACGT 59.670 52.381 12.47 0.00 36.30 3.99
242 244 4.808414 TGACTTGACATCTCTTACCAGG 57.192 45.455 0.00 0.00 0.00 4.45
286 288 1.317613 GCCAACCAGACATGACACAA 58.682 50.000 0.00 0.00 0.00 3.33
296 298 1.374947 GTAGCACCTGCCAACCAGA 59.625 57.895 0.00 0.00 44.64 3.86
302 304 1.674519 CGTTATGTGTAGCACCTGCCA 60.675 52.381 0.00 0.00 43.38 4.92
319 321 2.104170 GGAGACTCTGGAAGATCCGTT 58.896 52.381 1.74 0.00 45.62 4.44
322 324 1.407258 CGTGGAGACTCTGGAAGATCC 59.593 57.143 1.74 0.00 45.62 3.36
344 346 2.264480 CTGCGTTCGTCCATCCCA 59.736 61.111 0.00 0.00 0.00 4.37
384 386 1.227645 CATCCATCGACGCCACCAT 60.228 57.895 0.00 0.00 0.00 3.55
409 411 4.842948 AGAGATCTGCATAATCCTTGCCTA 59.157 41.667 0.00 0.00 39.39 3.93
410 412 3.651904 AGAGATCTGCATAATCCTTGCCT 59.348 43.478 0.00 0.00 39.39 4.75
433 437 0.904865 ACCGCTGTCCCATCTTCAGA 60.905 55.000 0.00 0.00 0.00 3.27
487 491 4.870426 CAGCAGATCTAAAACGTACACCAT 59.130 41.667 0.00 0.00 0.00 3.55
497 501 1.003118 ACCGGTGCAGCAGATCTAAAA 59.997 47.619 17.33 0.00 0.00 1.52
503 507 0.823356 AAACAACCGGTGCAGCAGAT 60.823 50.000 17.33 0.00 0.00 2.90
528 532 7.987458 GTCACCGATCCATCCATATAACATATT 59.013 37.037 0.00 0.00 0.00 1.28
532 536 4.321675 CGTCACCGATCCATCCATATAACA 60.322 45.833 0.00 0.00 35.63 2.41
551 555 5.048013 CCCATATCTATAGCTGTTGTCGTCA 60.048 44.000 0.00 0.00 0.00 4.35
559 563 5.015710 TCTCACTCCCCATATCTATAGCTGT 59.984 44.000 0.00 0.00 0.00 4.40
619 623 3.976701 ATCAAGCCACCCGAAGCCG 62.977 63.158 0.00 0.00 0.00 5.52
643 647 1.969923 TCCATGAGGGTTTGGCAAAAG 59.030 47.619 15.29 0.00 38.11 2.27
706 711 3.465966 AGAAAAGGAGGTTAAACCCCAGT 59.534 43.478 0.00 0.00 39.75 4.00
708 713 5.666474 TTAGAAAAGGAGGTTAAACCCCA 57.334 39.130 0.00 0.00 39.75 4.96
735 740 6.598503 TGGACTCAACGACCTCTAGAATATA 58.401 40.000 0.00 0.00 0.00 0.86
763 768 7.893833 ACAGGCCAACTTTCTATTATTACCTTT 59.106 33.333 5.01 0.00 0.00 3.11
794 799 5.940192 TCTAAACGTCAAAACATGCTGAT 57.060 34.783 0.00 0.00 0.00 2.90
883 889 7.118680 TGGCTCGTCGAAATATAGAAAAGTTTT 59.881 33.333 0.00 0.00 0.00 2.43
1081 1103 4.327982 TCTCCTCTAATTTCGCATGGAG 57.672 45.455 0.00 0.00 40.47 3.86
1107 1135 2.047061 TGTTGCAACCTCTCCACTACT 58.953 47.619 26.14 0.00 0.00 2.57
1110 1138 0.179018 GGTGTTGCAACCTCTCCACT 60.179 55.000 26.14 0.00 37.24 4.00
1218 1246 0.398522 ATCCTCGGTACATGGCCTCA 60.399 55.000 3.32 0.00 0.00 3.86
1277 1305 4.389576 CGTTGAAGCCTGCACCGC 62.390 66.667 0.00 0.00 0.00 5.68
1330 1361 1.131883 TGTCCGAGAACGCTTAGCTAC 59.868 52.381 1.76 0.00 38.29 3.58
1335 1366 1.610038 TCAGTTGTCCGAGAACGCTTA 59.390 47.619 2.96 0.00 38.29 3.09
1438 1472 0.034186 ATGTGTTCACATCCGCCCAT 60.034 50.000 11.97 0.00 0.00 4.00
1452 1486 1.198759 AGGGCCTACGAACCATGTGT 61.199 55.000 2.82 0.00 0.00 3.72
1454 1488 1.416401 CATAGGGCCTACGAACCATGT 59.584 52.381 17.19 0.00 0.00 3.21
1508 1542 2.437359 GCTTCTCAGCATGCCGGT 60.437 61.111 15.66 0.00 46.49 5.28
1560 1594 0.036765 GTGCATGACCACCGGTAAGA 60.037 55.000 6.87 0.00 35.25 2.10
1603 1637 3.297134 TTTCTTCCCAGTTGCAGAAGT 57.703 42.857 11.19 0.00 38.50 3.01
1729 1763 1.488390 AACATCATCCCAACCATGGC 58.512 50.000 13.04 0.00 46.09 4.40
1926 1960 4.008074 TGCCAGAGTCTTGAAAAGGTAG 57.992 45.455 0.00 0.00 46.24 3.18
1999 2033 0.842635 TGCAACCCCTTGGCAAATTT 59.157 45.000 0.00 0.00 34.05 1.82
2057 2093 5.243060 TCGAGTTTCCTTCTCAACACATCTA 59.757 40.000 0.00 0.00 32.79 1.98
2349 2392 4.142093 GCAAATGAGTTATGAGGTGGCATT 60.142 41.667 0.00 0.00 0.00 3.56
2399 2442 2.513753 TGGCACTACCTTCAAATGTGG 58.486 47.619 0.00 0.00 40.22 4.17
2428 2471 1.807573 GCACTCCTCTTCGCTTCCG 60.808 63.158 0.00 0.00 0.00 4.30
2553 2601 8.296713 ACATTTGGTTCAGTGTTATACATGAAC 58.703 33.333 17.28 17.28 41.01 3.18
2567 2615 7.092079 TGAGATTTGCAATACATTTGGTTCAG 58.908 34.615 0.00 0.00 0.00 3.02
2613 2661 6.553852 ACAAGTATATCCGGACAGAGGTAATT 59.446 38.462 6.12 0.00 0.00 1.40
2668 2716 5.005779 GCTCAAACCGATGTATCTACAACTG 59.994 44.000 0.00 0.00 39.99 3.16
2677 2725 2.665649 TGTCGCTCAAACCGATGTAT 57.334 45.000 0.00 0.00 37.04 2.29
2684 2732 4.148891 CGAAAATACTTGTCGCTCAAACC 58.851 43.478 0.00 0.00 35.48 3.27
2697 2745 6.574350 CATACTTCCTCTGTCCGAAAATACT 58.426 40.000 0.00 0.00 0.00 2.12
2704 2752 2.145397 AGCATACTTCCTCTGTCCGA 57.855 50.000 0.00 0.00 0.00 4.55
2705 2753 2.969628 AAGCATACTTCCTCTGTCCG 57.030 50.000 0.00 0.00 0.00 4.79
2710 2758 7.609097 TGATCTGATAAAGCATACTTCCTCT 57.391 36.000 0.00 0.00 34.05 3.69
2712 2760 8.049117 TGTTTGATCTGATAAAGCATACTTCCT 58.951 33.333 0.54 0.00 34.05 3.36
2714 2762 8.887717 ACTGTTTGATCTGATAAAGCATACTTC 58.112 33.333 4.93 0.00 34.05 3.01
2716 2764 7.497249 GGACTGTTTGATCTGATAAAGCATACT 59.503 37.037 4.93 0.00 0.00 2.12
2717 2765 7.280876 TGGACTGTTTGATCTGATAAAGCATAC 59.719 37.037 4.93 3.29 0.00 2.39
2761 2810 4.094887 GCCACTTCACATGATGTTATTCGT 59.905 41.667 0.00 0.00 31.13 3.85
2773 2822 1.977854 TCAGGTAGTGCCACTTCACAT 59.022 47.619 1.02 0.00 39.35 3.21
2775 2824 2.770164 ATCAGGTAGTGCCACTTCAC 57.230 50.000 1.02 0.00 40.61 3.18
2793 2842 1.484653 TGCATTACTGAGTGGCGGTAT 59.515 47.619 0.00 0.00 38.14 2.73
2835 2884 3.726557 TCGGAACAGAGGGAGTAGTTA 57.273 47.619 0.00 0.00 0.00 2.24
2890 2939 6.251376 GTGTTTGTTCACTCATTTCAGTTCAC 59.749 38.462 0.00 0.00 35.68 3.18
2901 2950 4.551388 GTTTTGGTGTGTTTGTTCACTCA 58.449 39.130 0.00 0.00 38.90 3.41
2902 2951 3.606346 CGTTTTGGTGTGTTTGTTCACTC 59.394 43.478 0.00 0.00 38.90 3.51
2961 3017 9.391006 TGTTTGTTTACTTTCTCTGTTCACTAT 57.609 29.630 0.00 0.00 0.00 2.12
3001 3057 5.654497 TGCTAGACTATTATGCGATGATGG 58.346 41.667 0.00 0.00 0.00 3.51
3055 3111 8.892723 CATATATAGAGTTGTTGCTTGGTCAAA 58.107 33.333 0.00 0.00 0.00 2.69
3065 3121 7.495606 TGGAGTTGCACATATATAGAGTTGTTG 59.504 37.037 0.00 0.00 0.00 3.33
3113 3169 3.604582 GATGGTTCTGGGACTTCTCTTG 58.395 50.000 0.00 0.00 0.00 3.02
3177 3233 7.228706 GGCACTATACTATAATGCACAAAACCT 59.771 37.037 10.78 0.00 38.05 3.50
3205 3261 6.128282 CGTTGAGCTTAATTTATCCTGTGTGT 60.128 38.462 0.00 0.00 0.00 3.72
3224 3280 3.304257 CTGATTCCTCGCTATCGTTGAG 58.696 50.000 0.00 0.00 36.96 3.02
3268 3324 2.905959 TCGACGTGACGTTGTGATAT 57.094 45.000 23.12 0.00 41.37 1.63
3308 3364 5.974108 TGAGGCTGTATTTGTCTACCTAAC 58.026 41.667 0.00 0.00 0.00 2.34
3313 3369 6.149474 ACATGTTTGAGGCTGTATTTGTCTAC 59.851 38.462 0.00 0.00 0.00 2.59
3359 3415 1.549170 ACGACTAAGGGTGGACATCAC 59.451 52.381 0.00 0.00 45.34 3.06
3360 3416 1.933021 ACGACTAAGGGTGGACATCA 58.067 50.000 0.00 0.00 0.00 3.07
3362 3418 3.134081 CCATAACGACTAAGGGTGGACAT 59.866 47.826 0.00 0.00 0.00 3.06
3363 3419 2.498481 CCATAACGACTAAGGGTGGACA 59.502 50.000 0.00 0.00 0.00 4.02
3366 3422 2.498481 TCACCATAACGACTAAGGGTGG 59.502 50.000 8.58 0.00 44.48 4.61
3367 3423 3.880047 TCACCATAACGACTAAGGGTG 57.120 47.619 0.00 0.00 45.45 4.61
3370 3426 4.060038 AGCATCACCATAACGACTAAGG 57.940 45.455 0.00 0.00 0.00 2.69
3371 3427 5.833082 AGTAGCATCACCATAACGACTAAG 58.167 41.667 0.00 0.00 0.00 2.18
3372 3428 5.847111 AGTAGCATCACCATAACGACTAA 57.153 39.130 0.00 0.00 0.00 2.24
3374 3430 4.737855 AAGTAGCATCACCATAACGACT 57.262 40.909 0.00 0.00 0.00 4.18
3375 3431 6.924060 AGATTAAGTAGCATCACCATAACGAC 59.076 38.462 0.00 0.00 0.00 4.34
3376 3432 6.923508 CAGATTAAGTAGCATCACCATAACGA 59.076 38.462 0.00 0.00 0.00 3.85
3377 3433 6.346919 GCAGATTAAGTAGCATCACCATAACG 60.347 42.308 0.00 0.00 0.00 3.18
3378 3434 6.708054 AGCAGATTAAGTAGCATCACCATAAC 59.292 38.462 0.00 0.00 0.00 1.89
3379 3435 6.830912 AGCAGATTAAGTAGCATCACCATAA 58.169 36.000 0.00 0.00 0.00 1.90
3380 3436 6.425210 AGCAGATTAAGTAGCATCACCATA 57.575 37.500 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.