Multiple sequence alignment - TraesCS7A01G022300

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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 TraesCS7A01G022300 chr7A 100.000 3569 0 0 1 3569 8891871 8888303 0.000000e+00 6591
1 TraesCS7A01G022300 chr7A 90.347 259 23 2 2580 2837 730602989 730603246 4.410000e-89 339
2 TraesCS7A01G022300 chr7A 89.434 265 26 2 2580 2843 40783161 40783424 2.050000e-87 333
3 TraesCS7A01G022300 chr7D 91.306 2450 173 15 100 2541 8382828 8380411 0.000000e+00 3308
4 TraesCS7A01G022300 chr7D 91.358 1863 90 17 689 2541 8454527 8452726 0.000000e+00 2483
5 TraesCS7A01G022300 chr7D 89.698 398 33 5 3031 3423 8439909 8439515 5.320000e-138 501
6 TraesCS7A01G022300 chr7D 88.070 285 19 6 2842 3123 8380399 8380127 1.240000e-84 324
7 TraesCS7A01G022300 chr7D 97.030 101 3 0 1 101 8456412 8456312 1.700000e-38 171
8 TraesCS7A01G022300 chr7D 98.936 94 1 0 8 101 8382954 8382861 6.130000e-38 169
9 TraesCS7A01G022300 chr7D 84.733 131 6 7 3453 3569 8439513 8439383 6.260000e-23 119
10 TraesCS7A01G022300 chr5B 86.267 1551 176 26 1015 2533 503116630 503115085 0.000000e+00 1650
11 TraesCS7A01G022300 chr5B 81.086 608 107 6 147 749 311547866 311547262 2.490000e-131 479
12 TraesCS7A01G022300 chr5A 85.844 1547 181 24 1019 2533 529081004 529079464 0.000000e+00 1609
13 TraesCS7A01G022300 chr5A 89.209 278 27 3 2568 2843 356183986 356183710 9.490000e-91 344
14 TraesCS7A01G022300 chr5A 88.809 277 28 3 2576 2851 14917663 14917389 1.590000e-88 337
15 TraesCS7A01G022300 chr5D 85.530 1548 188 25 1019 2533 416259151 416257607 0.000000e+00 1585
16 TraesCS7A01G022300 chr5D 80.519 616 113 7 144 755 411155290 411155902 1.940000e-127 466
17 TraesCS7A01G022300 chr5D 80.414 628 103 19 123 739 446678415 446679033 9.030000e-126 460
18 TraesCS7A01G022300 chr4A 91.556 1125 69 7 1417 2541 731380457 731381555 0.000000e+00 1528
19 TraesCS7A01G022300 chr4A 80.560 607 113 5 146 748 162420410 162419805 2.510000e-126 462
20 TraesCS7A01G022300 chr4A 80.195 616 114 8 128 739 6818797 6819408 4.200000e-124 455
21 TraesCS7A01G022300 chr2D 76.635 1468 293 38 1026 2461 12556622 12558071 0.000000e+00 765
22 TraesCS7A01G022300 chr2D 81.250 592 102 9 147 734 619938845 619938259 1.500000e-128 470
23 TraesCS7A01G022300 chr2A 76.875 1427 275 40 1019 2406 12990405 12991815 0.000000e+00 756
24 TraesCS7A01G022300 chr2A 90.189 265 24 2 2580 2843 604000633 604000896 9.490000e-91 344
25 TraesCS7A01G022300 chr2B 76.414 1467 289 42 1026 2457 18950287 18948843 0.000000e+00 739
26 TraesCS7A01G022300 chr2B 74.821 1394 297 44 1025 2380 19102541 19101164 6.640000e-162 580
27 TraesCS7A01G022300 chr2B 81.399 629 102 10 130 748 162860199 162860822 1.910000e-137 499
28 TraesCS7A01G022300 chr2B 78.287 502 105 4 1019 1518 18913698 18914197 1.600000e-83 320
29 TraesCS7A01G022300 chr2B 75.681 477 99 13 1025 1491 405262345 405262814 4.640000e-54 222
30 TraesCS7A01G022300 chrUn 80.556 612 102 14 144 746 279318652 279319255 4.200000e-124 455
31 TraesCS7A01G022300 chr1A 90.189 265 24 2 2580 2843 329013677 329013940 9.490000e-91 344
32 TraesCS7A01G022300 chr6A 88.214 280 30 2 2564 2843 615710928 615711204 7.390000e-87 331
33 TraesCS7A01G022300 chr6A 89.057 265 27 2 2580 2843 503245993 503245730 9.550000e-86 327
34 TraesCS7A01G022300 chr6A 76.414 619 133 12 1769 2379 592817756 592817143 4.440000e-84 322
35 TraesCS7A01G022300 chr3B 89.057 265 26 3 2580 2843 706530186 706530448 3.440000e-85 326
36 TraesCS7A01G022300 chr3B 78.840 293 47 13 1019 1303 224961023 224960738 2.190000e-42 183
37 TraesCS7A01G022300 chr6D 74.274 758 176 18 1682 2428 446103453 446104202 5.790000e-78 302


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 TraesCS7A01G022300 chr7A 8888303 8891871 3568 True 6591 6591 100.000000 1 3569 1 chr7A.!!$R1 3568
1 TraesCS7A01G022300 chr7D 8452726 8456412 3686 True 1327 2483 94.194000 1 2541 2 chr7D.!!$R3 2540
2 TraesCS7A01G022300 chr7D 8380127 8382954 2827 True 1267 3308 92.770667 8 3123 3 chr7D.!!$R1 3115
3 TraesCS7A01G022300 chr7D 8439383 8439909 526 True 310 501 87.215500 3031 3569 2 chr7D.!!$R2 538
4 TraesCS7A01G022300 chr5B 503115085 503116630 1545 True 1650 1650 86.267000 1015 2533 1 chr5B.!!$R2 1518
5 TraesCS7A01G022300 chr5B 311547262 311547866 604 True 479 479 81.086000 147 749 1 chr5B.!!$R1 602
6 TraesCS7A01G022300 chr5A 529079464 529081004 1540 True 1609 1609 85.844000 1019 2533 1 chr5A.!!$R3 1514
7 TraesCS7A01G022300 chr5D 416257607 416259151 1544 True 1585 1585 85.530000 1019 2533 1 chr5D.!!$R1 1514
8 TraesCS7A01G022300 chr5D 411155290 411155902 612 False 466 466 80.519000 144 755 1 chr5D.!!$F1 611
9 TraesCS7A01G022300 chr5D 446678415 446679033 618 False 460 460 80.414000 123 739 1 chr5D.!!$F2 616
10 TraesCS7A01G022300 chr4A 731380457 731381555 1098 False 1528 1528 91.556000 1417 2541 1 chr4A.!!$F2 1124
11 TraesCS7A01G022300 chr4A 162419805 162420410 605 True 462 462 80.560000 146 748 1 chr4A.!!$R1 602
12 TraesCS7A01G022300 chr4A 6818797 6819408 611 False 455 455 80.195000 128 739 1 chr4A.!!$F1 611
13 TraesCS7A01G022300 chr2D 12556622 12558071 1449 False 765 765 76.635000 1026 2461 1 chr2D.!!$F1 1435
14 TraesCS7A01G022300 chr2D 619938259 619938845 586 True 470 470 81.250000 147 734 1 chr2D.!!$R1 587
15 TraesCS7A01G022300 chr2A 12990405 12991815 1410 False 756 756 76.875000 1019 2406 1 chr2A.!!$F1 1387
16 TraesCS7A01G022300 chr2B 18948843 18950287 1444 True 739 739 76.414000 1026 2457 1 chr2B.!!$R1 1431
17 TraesCS7A01G022300 chr2B 19101164 19102541 1377 True 580 580 74.821000 1025 2380 1 chr2B.!!$R2 1355
18 TraesCS7A01G022300 chr2B 162860199 162860822 623 False 499 499 81.399000 130 748 1 chr2B.!!$F2 618
19 TraesCS7A01G022300 chrUn 279318652 279319255 603 False 455 455 80.556000 144 746 1 chrUn.!!$F1 602
20 TraesCS7A01G022300 chr6A 592817143 592817756 613 True 322 322 76.414000 1769 2379 1 chr6A.!!$R2 610
21 TraesCS7A01G022300 chr6D 446103453 446104202 749 False 302 302 74.274000 1682 2428 1 chr6D.!!$F1 746

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
199 235 0.179097 GGTTCCGTCTCATCTCTGGC 60.179 60.000 0.00 0.0 0.00 4.85 F
413 449 0.530744 GCGTGTGGAGGTATGTCTCA 59.469 55.000 0.00 0.0 35.58 3.27 F
988 2216 1.002134 CCACGAACCATTGGAGCCT 60.002 57.895 10.37 0.0 34.46 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 3474 0.842467 CCTCCAAGAACTCAGGGGGT 60.842 60.0 0.00 0.0 38.32 4.95 R
2208 3561 0.530650 AGTGCGTCAGGAACACACAG 60.531 55.0 6.51 0.0 42.26 3.66 R
2982 4341 0.108329 GCCACGCCTACAGCTTCTAA 60.108 55.0 0.00 0.0 40.39 2.10 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 0.983467 TAGATGCTGAGTGCCCACAA 59.017 50.000 0.82 0.00 42.00 3.33
169 205 0.942252 GTTTTTCTGTCTTCCGCCGT 59.058 50.000 0.00 0.00 0.00 5.68
196 232 1.096416 GTCGGTTCCGTCTCATCTCT 58.904 55.000 11.04 0.00 0.00 3.10
199 235 0.179097 GGTTCCGTCTCATCTCTGGC 60.179 60.000 0.00 0.00 0.00 4.85
250 286 2.198426 CCCCTTGCTGGTGGTTGT 59.802 61.111 0.00 0.00 0.00 3.32
268 304 5.988561 TGGTTGTGCTCCATTTTTAAATGTC 59.011 36.000 12.70 4.31 43.24 3.06
406 442 3.315949 GGTGGGCGTGTGGAGGTA 61.316 66.667 0.00 0.00 0.00 3.08
413 449 0.530744 GCGTGTGGAGGTATGTCTCA 59.469 55.000 0.00 0.00 35.58 3.27
425 461 3.430929 GGTATGTCTCAAGCGGATCTGTT 60.431 47.826 2.89 0.00 0.00 3.16
503 546 2.317040 TGGATCCTTCCGATCTACACC 58.683 52.381 14.23 0.00 45.90 4.16
504 547 2.317040 GGATCCTTCCGATCTACACCA 58.683 52.381 3.84 0.00 45.90 4.17
505 548 2.036089 GGATCCTTCCGATCTACACCAC 59.964 54.545 3.84 0.00 45.90 4.16
512 555 1.743958 CCGATCTACACCACTCTTCGT 59.256 52.381 0.00 0.00 0.00 3.85
539 584 4.681978 GTTCCGGTGCGCTGGTCT 62.682 66.667 24.26 0.00 41.89 3.85
543 588 1.038681 TCCGGTGCGCTGGTCTTATA 61.039 55.000 24.26 1.06 41.89 0.98
552 597 4.100344 TGCGCTGGTCTTATATGGTCTTAA 59.900 41.667 9.73 0.00 0.00 1.85
603 648 2.528041 AGTTTTGTCTGACTCCGGTC 57.472 50.000 9.51 0.00 42.42 4.79
659 704 1.605712 GCTTCAGTGCTGGTAGTCGTT 60.606 52.381 0.00 0.00 0.00 3.85
687 732 5.247110 AGGTGGCCTGTGAATATAGATACAG 59.753 44.000 3.32 0.00 40.06 2.74
836 2064 7.512130 TGCATATAAGCATCCTATCTATTGGG 58.488 38.462 0.00 0.00 40.11 4.12
837 2065 7.127801 TGCATATAAGCATCCTATCTATTGGGT 59.872 37.037 0.00 0.00 40.11 4.51
838 2066 7.443575 GCATATAAGCATCCTATCTATTGGGTG 59.556 40.741 0.00 0.00 36.95 4.61
839 2067 4.647564 AAGCATCCTATCTATTGGGTGG 57.352 45.455 5.95 0.00 34.87 4.61
840 2068 2.307098 AGCATCCTATCTATTGGGTGGC 59.693 50.000 5.95 1.40 34.87 5.01
841 2069 2.307098 GCATCCTATCTATTGGGTGGCT 59.693 50.000 5.95 0.00 34.87 4.75
842 2070 3.871463 GCATCCTATCTATTGGGTGGCTG 60.871 52.174 5.95 0.00 34.87 4.85
843 2071 3.344535 TCCTATCTATTGGGTGGCTGA 57.655 47.619 0.00 0.00 0.00 4.26
844 2072 3.242867 TCCTATCTATTGGGTGGCTGAG 58.757 50.000 0.00 0.00 0.00 3.35
845 2073 3.116746 TCCTATCTATTGGGTGGCTGAGA 60.117 47.826 0.00 0.00 0.00 3.27
846 2074 3.648067 CCTATCTATTGGGTGGCTGAGAA 59.352 47.826 0.00 0.00 0.00 2.87
924 2152 2.959030 TCCGTGCATATAAGCTGTCTCT 59.041 45.455 1.16 0.00 34.99 3.10
925 2153 3.004839 TCCGTGCATATAAGCTGTCTCTC 59.995 47.826 1.16 0.00 34.99 3.20
926 2154 3.312828 CGTGCATATAAGCTGTCTCTCC 58.687 50.000 1.16 0.00 34.99 3.71
927 2155 3.005261 CGTGCATATAAGCTGTCTCTCCT 59.995 47.826 1.16 0.00 34.99 3.69
928 2156 4.305769 GTGCATATAAGCTGTCTCTCCTG 58.694 47.826 1.16 0.00 34.99 3.86
929 2157 3.244009 TGCATATAAGCTGTCTCTCCTGC 60.244 47.826 1.16 0.00 34.99 4.85
970 2198 6.286758 TGCTAGTTGAGATTCAGATCCAATC 58.713 40.000 6.83 6.83 32.44 2.67
978 2206 2.691409 TCAGATCCAATCCACGAACC 57.309 50.000 0.00 0.00 0.00 3.62
988 2216 1.002134 CCACGAACCATTGGAGCCT 60.002 57.895 10.37 0.00 34.46 4.58
1017 2245 2.927856 ATGGACACCGCTGGACCA 60.928 61.111 0.00 0.00 35.09 4.02
1242 2482 4.329545 GGCCTGCCCTCGTCACAA 62.330 66.667 0.00 0.00 0.00 3.33
1245 2485 3.114616 CTGCCCTCGTCACAAGCG 61.115 66.667 0.00 0.00 0.00 4.68
1579 2879 8.939201 TCAATCATGAGTCTCAATAACTTCTC 57.061 34.615 6.64 0.00 0.00 2.87
1584 2884 8.811017 TCATGAGTCTCAATAACTTCTCTTTCT 58.189 33.333 6.64 0.00 0.00 2.52
1585 2885 9.086336 CATGAGTCTCAATAACTTCTCTTTCTC 57.914 37.037 6.64 0.00 0.00 2.87
1589 2889 9.705290 AGTCTCAATAACTTCTCTTTCTCTTTC 57.295 33.333 0.00 0.00 0.00 2.62
1756 3076 1.079197 CTACACCATGTGGAGCGCA 60.079 57.895 11.47 0.00 37.70 6.09
1762 3082 3.381983 ATGTGGAGCGCACCGAGA 61.382 61.111 19.24 7.42 0.00 4.04
1764 3084 1.391933 ATGTGGAGCGCACCGAGATA 61.392 55.000 19.24 0.32 0.00 1.98
2112 3465 1.140589 CATCGTGAAGAGCGAGGCT 59.859 57.895 0.00 0.00 43.88 4.58
2530 3886 7.709182 TCAATGATGTGTTACTATCCGGTAAAG 59.291 37.037 0.00 0.00 34.11 1.85
2543 3899 9.159364 ACTATCCGGTAAAGAAAACATTTACTC 57.841 33.333 0.00 0.18 41.04 2.59
2544 3900 6.806388 TCCGGTAAAGAAAACATTTACTCC 57.194 37.500 0.00 0.00 41.04 3.85
2545 3901 6.297582 TCCGGTAAAGAAAACATTTACTCCA 58.702 36.000 0.00 0.00 41.04 3.86
2546 3902 6.205270 TCCGGTAAAGAAAACATTTACTCCAC 59.795 38.462 0.00 0.00 41.04 4.02
2547 3903 6.376177 CGGTAAAGAAAACATTTACTCCACC 58.624 40.000 8.10 0.00 41.04 4.61
2548 3904 6.016943 CGGTAAAGAAAACATTTACTCCACCA 60.017 38.462 8.10 0.00 41.04 4.17
2549 3905 7.368059 GGTAAAGAAAACATTTACTCCACCAG 58.632 38.462 8.10 0.00 41.04 4.00
2550 3906 7.013942 GGTAAAGAAAACATTTACTCCACCAGT 59.986 37.037 8.10 0.00 41.04 4.00
2551 3907 6.635030 AAGAAAACATTTACTCCACCAGTC 57.365 37.500 0.00 0.00 36.43 3.51
2552 3908 5.690865 AGAAAACATTTACTCCACCAGTCA 58.309 37.500 0.00 0.00 36.43 3.41
2553 3909 6.126409 AGAAAACATTTACTCCACCAGTCAA 58.874 36.000 0.00 0.00 36.43 3.18
2554 3910 5.767816 AAACATTTACTCCACCAGTCAAC 57.232 39.130 0.00 0.00 36.43 3.18
2555 3911 3.399330 ACATTTACTCCACCAGTCAACG 58.601 45.455 0.00 0.00 36.43 4.10
2556 3912 3.181458 ACATTTACTCCACCAGTCAACGT 60.181 43.478 0.00 0.00 36.43 3.99
2557 3913 2.519377 TTACTCCACCAGTCAACGTG 57.481 50.000 0.00 0.00 36.43 4.49
2558 3914 0.032952 TACTCCACCAGTCAACGTGC 59.967 55.000 0.00 0.00 36.43 5.34
2559 3915 2.279851 TCCACCAGTCAACGTGCG 60.280 61.111 0.00 0.00 0.00 5.34
2560 3916 3.345808 CCACCAGTCAACGTGCGG 61.346 66.667 0.00 0.00 0.00 5.69
2561 3917 4.012895 CACCAGTCAACGTGCGGC 62.013 66.667 0.00 0.00 0.00 6.53
2562 3918 4.235762 ACCAGTCAACGTGCGGCT 62.236 61.111 0.00 0.00 0.00 5.52
2563 3919 3.716006 CCAGTCAACGTGCGGCTG 61.716 66.667 11.82 11.82 0.00 4.85
2564 3920 2.661537 CAGTCAACGTGCGGCTGA 60.662 61.111 13.17 0.00 0.00 4.26
2565 3921 2.356313 AGTCAACGTGCGGCTGAG 60.356 61.111 0.00 0.00 0.00 3.35
2566 3922 2.661866 GTCAACGTGCGGCTGAGT 60.662 61.111 0.00 0.00 0.00 3.41
2567 3923 1.372499 GTCAACGTGCGGCTGAGTA 60.372 57.895 0.00 0.00 0.00 2.59
2568 3924 1.080772 TCAACGTGCGGCTGAGTAG 60.081 57.895 0.00 0.00 0.00 2.57
2569 3925 1.372997 CAACGTGCGGCTGAGTAGT 60.373 57.895 0.00 0.00 0.00 2.73
2570 3926 0.109458 CAACGTGCGGCTGAGTAGTA 60.109 55.000 0.00 0.00 0.00 1.82
2571 3927 0.599558 AACGTGCGGCTGAGTAGTAA 59.400 50.000 0.00 0.00 0.00 2.24
2572 3928 0.815734 ACGTGCGGCTGAGTAGTAAT 59.184 50.000 0.00 0.00 0.00 1.89
2573 3929 1.203994 ACGTGCGGCTGAGTAGTAATT 59.796 47.619 0.00 0.00 0.00 1.40
2574 3930 1.852895 CGTGCGGCTGAGTAGTAATTC 59.147 52.381 0.00 0.00 0.00 2.17
2575 3931 2.479730 CGTGCGGCTGAGTAGTAATTCT 60.480 50.000 0.00 0.00 0.00 2.40
2576 3932 2.860735 GTGCGGCTGAGTAGTAATTCTG 59.139 50.000 0.00 0.00 0.00 3.02
2577 3933 1.861575 GCGGCTGAGTAGTAATTCTGC 59.138 52.381 0.00 6.36 36.13 4.26
2578 3934 2.482142 GCGGCTGAGTAGTAATTCTGCT 60.482 50.000 0.00 0.00 41.62 4.24
2579 3935 3.786635 CGGCTGAGTAGTAATTCTGCTT 58.213 45.455 11.83 0.00 39.14 3.91
2580 3936 4.736759 GCGGCTGAGTAGTAATTCTGCTTA 60.737 45.833 0.00 0.00 39.14 3.09
2581 3937 4.740695 CGGCTGAGTAGTAATTCTGCTTAC 59.259 45.833 11.83 0.00 39.14 2.34
2582 3938 5.450688 CGGCTGAGTAGTAATTCTGCTTACT 60.451 44.000 11.83 2.17 42.89 2.24
2583 3939 5.980715 GGCTGAGTAGTAATTCTGCTTACTC 59.019 44.000 11.83 3.64 40.30 2.59
2584 3940 5.980715 GCTGAGTAGTAATTCTGCTTACTCC 59.019 44.000 0.00 0.00 40.30 3.85
2585 3941 6.466885 TGAGTAGTAATTCTGCTTACTCCC 57.533 41.667 0.00 0.00 40.30 4.30
2586 3942 6.195700 TGAGTAGTAATTCTGCTTACTCCCT 58.804 40.000 0.00 0.00 40.30 4.20
2587 3943 6.668283 TGAGTAGTAATTCTGCTTACTCCCTT 59.332 38.462 0.00 0.00 40.30 3.95
2588 3944 7.180408 TGAGTAGTAATTCTGCTTACTCCCTTT 59.820 37.037 0.00 0.00 40.30 3.11
2589 3945 7.331791 AGTAGTAATTCTGCTTACTCCCTTTG 58.668 38.462 0.00 0.00 40.30 2.77
2590 3946 6.128138 AGTAATTCTGCTTACTCCCTTTGT 57.872 37.500 0.00 0.00 37.36 2.83
2591 3947 6.174049 AGTAATTCTGCTTACTCCCTTTGTC 58.826 40.000 0.00 0.00 37.36 3.18
2592 3948 3.418684 TTCTGCTTACTCCCTTTGTCC 57.581 47.619 0.00 0.00 0.00 4.02
2593 3949 2.621070 TCTGCTTACTCCCTTTGTCCT 58.379 47.619 0.00 0.00 0.00 3.85
2594 3950 2.979678 TCTGCTTACTCCCTTTGTCCTT 59.020 45.455 0.00 0.00 0.00 3.36
2595 3951 3.008049 TCTGCTTACTCCCTTTGTCCTTC 59.992 47.826 0.00 0.00 0.00 3.46
2596 3952 2.708861 TGCTTACTCCCTTTGTCCTTCA 59.291 45.455 0.00 0.00 0.00 3.02
2597 3953 3.137544 TGCTTACTCCCTTTGTCCTTCAA 59.862 43.478 0.00 0.00 0.00 2.69
2598 3954 4.142038 GCTTACTCCCTTTGTCCTTCAAA 58.858 43.478 0.00 0.00 42.79 2.69
2599 3955 4.767409 GCTTACTCCCTTTGTCCTTCAAAT 59.233 41.667 0.00 0.00 43.78 2.32
2600 3956 5.944007 GCTTACTCCCTTTGTCCTTCAAATA 59.056 40.000 0.00 0.00 43.78 1.40
2601 3957 6.094186 GCTTACTCCCTTTGTCCTTCAAATAG 59.906 42.308 0.00 0.00 43.78 1.73
2602 3958 5.584551 ACTCCCTTTGTCCTTCAAATAGT 57.415 39.130 0.00 0.00 43.78 2.12
2603 3959 5.316987 ACTCCCTTTGTCCTTCAAATAGTG 58.683 41.667 0.00 0.00 43.78 2.74
2604 3960 5.163088 ACTCCCTTTGTCCTTCAAATAGTGT 60.163 40.000 0.00 0.00 43.78 3.55
2605 3961 6.043938 ACTCCCTTTGTCCTTCAAATAGTGTA 59.956 38.462 0.00 0.00 43.78 2.90
2606 3962 6.235664 TCCCTTTGTCCTTCAAATAGTGTAC 58.764 40.000 0.00 0.00 43.78 2.90
2607 3963 6.043938 TCCCTTTGTCCTTCAAATAGTGTACT 59.956 38.462 0.00 0.00 43.78 2.73
2608 3964 6.715264 CCCTTTGTCCTTCAAATAGTGTACTT 59.285 38.462 0.00 0.00 43.78 2.24
2609 3965 7.230712 CCCTTTGTCCTTCAAATAGTGTACTTT 59.769 37.037 0.00 0.00 43.78 2.66
2610 3966 8.630037 CCTTTGTCCTTCAAATAGTGTACTTTT 58.370 33.333 0.00 0.00 43.78 2.27
2682 4038 9.073475 ACAATAATACACCAATATTTATGCCGT 57.927 29.630 0.00 0.00 0.00 5.68
2683 4039 9.554724 CAATAATACACCAATATTTATGCCGTC 57.445 33.333 0.00 0.00 0.00 4.79
2684 4040 8.856153 ATAATACACCAATATTTATGCCGTCA 57.144 30.769 0.00 0.00 0.00 4.35
2685 4041 7.575414 AATACACCAATATTTATGCCGTCAA 57.425 32.000 0.00 0.00 0.00 3.18
2686 4042 5.906113 ACACCAATATTTATGCCGTCAAA 57.094 34.783 0.00 0.00 0.00 2.69
2687 4043 6.463995 ACACCAATATTTATGCCGTCAAAT 57.536 33.333 0.00 0.00 0.00 2.32
2688 4044 6.872920 ACACCAATATTTATGCCGTCAAATT 58.127 32.000 0.00 0.00 0.00 1.82
2689 4045 8.001881 ACACCAATATTTATGCCGTCAAATTA 57.998 30.769 0.00 0.00 0.00 1.40
2690 4046 8.134895 ACACCAATATTTATGCCGTCAAATTAG 58.865 33.333 0.00 0.00 0.00 1.73
2691 4047 8.134895 CACCAATATTTATGCCGTCAAATTAGT 58.865 33.333 0.00 0.00 0.00 2.24
2692 4048 9.344772 ACCAATATTTATGCCGTCAAATTAGTA 57.655 29.630 0.00 0.00 0.00 1.82
2693 4049 9.825972 CCAATATTTATGCCGTCAAATTAGTAG 57.174 33.333 0.00 0.00 0.00 2.57
2694 4050 9.329913 CAATATTTATGCCGTCAAATTAGTAGC 57.670 33.333 0.00 0.00 0.00 3.58
2695 4051 6.935741 ATTTATGCCGTCAAATTAGTAGCA 57.064 33.333 0.00 0.00 0.00 3.49
2696 4052 6.935741 TTTATGCCGTCAAATTAGTAGCAT 57.064 33.333 0.00 0.00 41.89 3.79
2697 4053 6.935741 TTATGCCGTCAAATTAGTAGCATT 57.064 33.333 0.00 0.00 39.89 3.56
2698 4054 4.875544 TGCCGTCAAATTAGTAGCATTC 57.124 40.909 0.00 0.00 0.00 2.67
2699 4055 3.308595 TGCCGTCAAATTAGTAGCATTCG 59.691 43.478 0.00 0.00 0.00 3.34
2700 4056 3.554324 GCCGTCAAATTAGTAGCATTCGA 59.446 43.478 0.00 0.00 0.00 3.71
2701 4057 4.211374 GCCGTCAAATTAGTAGCATTCGAT 59.789 41.667 0.00 0.00 0.00 3.59
2702 4058 5.277345 GCCGTCAAATTAGTAGCATTCGATT 60.277 40.000 0.00 0.00 0.00 3.34
2703 4059 6.715464 CCGTCAAATTAGTAGCATTCGATTT 58.285 36.000 0.00 0.00 0.00 2.17
2704 4060 7.517734 GCCGTCAAATTAGTAGCATTCGATTTA 60.518 37.037 0.00 0.00 0.00 1.40
2705 4061 8.495949 CCGTCAAATTAGTAGCATTCGATTTAT 58.504 33.333 0.00 0.00 0.00 1.40
2706 4062 9.306280 CGTCAAATTAGTAGCATTCGATTTATG 57.694 33.333 0.00 0.00 0.00 1.90
2767 4123 9.702494 TCACAAACATTGATATATTTTTGCACA 57.298 25.926 0.00 0.00 0.00 4.57
2773 4129 9.075519 ACATTGATATATTTTTGCACAAACTCG 57.924 29.630 0.00 0.00 0.00 4.18
2774 4130 9.288124 CATTGATATATTTTTGCACAAACTCGA 57.712 29.630 0.00 0.00 0.00 4.04
2776 4132 9.502145 TTGATATATTTTTGCACAAACTCGATC 57.498 29.630 0.00 3.02 0.00 3.69
2777 4133 8.672815 TGATATATTTTTGCACAAACTCGATCA 58.327 29.630 0.00 5.33 0.00 2.92
2778 4134 9.502145 GATATATTTTTGCACAAACTCGATCAA 57.498 29.630 0.00 0.00 0.00 2.57
2779 4135 9.853555 ATATATTTTTGCACAAACTCGATCAAA 57.146 25.926 0.00 0.00 0.00 2.69
2780 4136 8.761575 ATATTTTTGCACAAACTCGATCAAAT 57.238 26.923 0.00 0.00 0.00 2.32
2781 4137 6.900568 TTTTTGCACAAACTCGATCAAATT 57.099 29.167 0.00 0.00 0.00 1.82
2782 4138 6.900568 TTTTGCACAAACTCGATCAAATTT 57.099 29.167 0.00 0.00 0.00 1.82
2783 4139 6.900568 TTTGCACAAACTCGATCAAATTTT 57.099 29.167 0.00 0.00 0.00 1.82
2784 4140 7.993821 TTTGCACAAACTCGATCAAATTTTA 57.006 28.000 0.00 0.00 0.00 1.52
2785 4141 7.993821 TTGCACAAACTCGATCAAATTTTAA 57.006 28.000 0.00 0.00 0.00 1.52
2786 4142 7.993821 TGCACAAACTCGATCAAATTTTAAA 57.006 28.000 0.00 0.00 0.00 1.52
2787 4143 8.412608 TGCACAAACTCGATCAAATTTTAAAA 57.587 26.923 2.51 2.51 0.00 1.52
2788 4144 9.039870 TGCACAAACTCGATCAAATTTTAAAAT 57.960 25.926 7.64 7.64 0.00 1.82
2816 4172 9.788960 GTTTGACTCTTCAATAAAGTTGAAAGT 57.211 29.630 13.18 13.18 41.50 2.66
2819 4175 9.607988 TGACTCTTCAATAAAGTTGAAAGTACA 57.392 29.630 13.24 11.36 37.89 2.90
2820 4176 9.865484 GACTCTTCAATAAAGTTGAAAGTACAC 57.135 33.333 13.24 0.00 37.89 2.90
2821 4177 9.614792 ACTCTTCAATAAAGTTGAAAGTACACT 57.385 29.630 0.00 0.00 37.89 3.55
2834 4190 7.007313 TGAAAGTACACTTTTTCAAGTACGG 57.993 36.000 8.66 0.00 45.37 4.02
2835 4191 6.817641 TGAAAGTACACTTTTTCAAGTACGGA 59.182 34.615 8.66 0.00 45.37 4.69
2836 4192 6.839820 AAGTACACTTTTTCAAGTACGGAG 57.160 37.500 0.00 0.00 41.69 4.63
2837 4193 6.152932 AGTACACTTTTTCAAGTACGGAGA 57.847 37.500 0.00 0.00 41.69 3.71
2838 4194 6.214399 AGTACACTTTTTCAAGTACGGAGAG 58.786 40.000 0.00 0.00 41.69 3.20
2839 4195 5.272283 ACACTTTTTCAAGTACGGAGAGA 57.728 39.130 0.00 0.00 41.69 3.10
2840 4196 5.290386 ACACTTTTTCAAGTACGGAGAGAG 58.710 41.667 0.00 0.00 41.69 3.20
2854 4210 3.429135 CGGAGAGAGTAAGTACCAAAGGC 60.429 52.174 0.00 0.00 0.00 4.35
2863 4219 1.564348 AGTACCAAAGGCGATGGGATT 59.436 47.619 14.71 1.76 42.48 3.01
2865 4221 1.322538 ACCAAAGGCGATGGGATTGC 61.323 55.000 14.71 0.00 42.48 3.56
2869 4225 0.323725 AAGGCGATGGGATTGCTTGT 60.324 50.000 0.00 0.00 39.67 3.16
2876 4232 1.434555 TGGGATTGCTTGTAACGTCG 58.565 50.000 0.00 0.00 0.00 5.12
2881 4237 1.837538 TTGCTTGTAACGTCGCAGGC 61.838 55.000 15.90 15.90 38.06 4.85
2896 4255 0.318869 CAGGCAATGCAGCGTTTTGA 60.319 50.000 7.79 0.00 34.64 2.69
2903 4262 1.317613 TGCAGCGTTTTGAATGGACT 58.682 45.000 0.00 0.00 0.00 3.85
2933 4292 6.058183 AGATACCGATTGCTTGCTATTTCTT 58.942 36.000 0.00 0.00 0.00 2.52
2936 4295 4.641989 ACCGATTGCTTGCTATTTCTTGAT 59.358 37.500 0.00 0.00 0.00 2.57
2944 4303 2.158813 TGCTATTTCTTGATCCCGGACC 60.159 50.000 0.73 0.00 0.00 4.46
2949 4308 1.784358 TCTTGATCCCGGACCGTAAT 58.216 50.000 13.94 5.50 0.00 1.89
2957 4316 2.765135 TCCCGGACCGTAATATGTTTCA 59.235 45.455 13.94 0.00 0.00 2.69
2968 4327 8.516234 ACCGTAATATGTTTCATTGTTAGCAAA 58.484 29.630 0.00 0.00 38.21 3.68
2989 4348 9.196552 AGCAAAAACAATAGTTGATTTAGAAGC 57.803 29.630 0.00 1.86 38.17 3.86
2990 4349 9.196552 GCAAAAACAATAGTTGATTTAGAAGCT 57.803 29.630 0.00 0.00 38.17 3.74
2995 4354 8.723942 ACAATAGTTGATTTAGAAGCTGTAGG 57.276 34.615 0.00 0.00 0.00 3.18
2996 4355 7.281100 ACAATAGTTGATTTAGAAGCTGTAGGC 59.719 37.037 0.00 0.00 42.19 3.93
3021 4380 3.917985 GGCCTTAAAGTTGTTTATGTGCG 59.082 43.478 0.00 0.00 0.00 5.34
3075 4434 3.712907 GGGCAGTGGCGGACCTAA 61.713 66.667 10.99 0.00 42.47 2.69
3110 4471 1.282157 GGGTGCCAACCTTATCACTCT 59.718 52.381 0.00 0.00 46.70 3.24
3111 4472 2.633488 GGTGCCAACCTTATCACTCTC 58.367 52.381 0.00 0.00 43.84 3.20
3123 4484 5.447624 TTATCACTCTCACGACAGAAACA 57.552 39.130 0.00 0.00 0.00 2.83
3128 4489 3.181465 ACTCTCACGACAGAAACACCATT 60.181 43.478 0.00 0.00 0.00 3.16
3137 4498 5.253330 GACAGAAACACCATTTATCTCCCA 58.747 41.667 0.00 0.00 0.00 4.37
3138 4499 5.831103 ACAGAAACACCATTTATCTCCCAT 58.169 37.500 0.00 0.00 0.00 4.00
3174 4537 6.933521 AGAGCTAGAAATGCCATGTATGTAAG 59.066 38.462 0.00 0.00 0.00 2.34
3179 4542 2.682155 TGCCATGTATGTAAGCACGA 57.318 45.000 0.00 0.00 0.00 4.35
3193 4556 0.109226 GCACGACACTCCCACTAGAC 60.109 60.000 0.00 0.00 0.00 2.59
3197 4560 0.611340 GACACTCCCACTAGACCCGT 60.611 60.000 0.00 0.00 0.00 5.28
3235 4598 4.278419 ACAAATTCTTCCGTTCCCTTTCAG 59.722 41.667 0.00 0.00 0.00 3.02
3282 4645 4.207955 TGAGCATCTCGTAAGTGGATACT 58.792 43.478 0.00 0.00 35.36 2.12
3287 4650 5.505324 GCATCTCGTAAGTGGATACTAACGT 60.505 44.000 0.00 0.00 35.69 3.99
3296 4659 5.661458 AGTGGATACTAACGTCCAATTCAG 58.339 41.667 0.00 0.00 45.50 3.02
3304 4667 7.016361 ACTAACGTCCAATTCAGCAAATATC 57.984 36.000 0.00 0.00 0.00 1.63
3335 4698 6.593382 AGAGCAATTGAGAGTGATAACTGAAC 59.407 38.462 10.34 0.00 0.00 3.18
3343 4706 7.145985 TGAGAGTGATAACTGAACTAACACAC 58.854 38.462 0.00 0.00 0.00 3.82
3353 4716 6.101332 ACTGAACTAACACACTTGTTCGTTA 58.899 36.000 7.24 0.00 46.29 3.18
3363 4726 5.852229 CACACTTGTTCGTTAGTACTCTCTC 59.148 44.000 0.00 0.00 0.00 3.20
3364 4727 5.048852 ACACTTGTTCGTTAGTACTCTCTCC 60.049 44.000 0.00 0.00 0.00 3.71
3365 4728 5.048921 CACTTGTTCGTTAGTACTCTCTCCA 60.049 44.000 0.00 0.00 0.00 3.86
3368 4731 4.639310 TGTTCGTTAGTACTCTCTCCATCC 59.361 45.833 0.00 0.00 0.00 3.51
3383 4746 7.544650 TCTCTCCATCCCCTAATATAAGAACA 58.455 38.462 0.00 0.00 0.00 3.18
3411 4775 6.964807 TCAAGCTACAAGTCCCGTAATATA 57.035 37.500 0.00 0.00 0.00 0.86
3416 4780 7.432059 AGCTACAAGTCCCGTAATATAAGAAC 58.568 38.462 0.00 0.00 0.00 3.01
3417 4781 7.069085 AGCTACAAGTCCCGTAATATAAGAACA 59.931 37.037 0.00 0.00 0.00 3.18
3452 4816 9.907819 TTATGAAATAGAGGGAATACTAGGGAA 57.092 33.333 0.00 0.00 0.00 3.97
3453 4817 8.814448 ATGAAATAGAGGGAATACTAGGGAAA 57.186 34.615 0.00 0.00 0.00 3.13
3454 4818 8.263854 TGAAATAGAGGGAATACTAGGGAAAG 57.736 38.462 0.00 0.00 0.00 2.62
3508 4872 9.289303 CACATTAAAATAGAAACATGTACTGCC 57.711 33.333 0.00 0.00 0.00 4.85
3510 4874 9.507280 CATTAAAATAGAAACATGTACTGCCTG 57.493 33.333 0.00 0.00 0.00 4.85
3511 4875 5.567138 AAATAGAAACATGTACTGCCTGC 57.433 39.130 0.00 0.00 0.00 4.85
3512 4876 2.867109 AGAAACATGTACTGCCTGCT 57.133 45.000 0.00 0.00 0.00 4.24
3513 4877 3.981071 AGAAACATGTACTGCCTGCTA 57.019 42.857 0.00 0.00 0.00 3.49
3515 4879 5.614324 AGAAACATGTACTGCCTGCTATA 57.386 39.130 0.00 0.00 0.00 1.31
3516 4880 5.360591 AGAAACATGTACTGCCTGCTATAC 58.639 41.667 0.00 0.00 0.00 1.47
3519 4883 3.181465 ACATGTACTGCCTGCTATACCAC 60.181 47.826 0.00 0.00 0.00 4.16
3548 4925 3.061093 GCTTCCGGCTAGTGGTTAC 57.939 57.895 0.00 0.00 38.06 2.50
3553 4930 0.179145 CCGGCTAGTGGTTACTGACG 60.179 60.000 0.00 0.00 37.78 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.435428 GTCAGTTCACCGAATGTATTTTGTT 58.565 36.000 0.00 0.00 0.00 2.83
112 147 1.071385 CAGCTGGGTGAAGAGAGTGTT 59.929 52.381 5.57 0.00 0.00 3.32
406 442 3.340814 AAACAGATCCGCTTGAGACAT 57.659 42.857 0.00 0.00 0.00 3.06
413 449 1.613437 CCACCAAAAACAGATCCGCTT 59.387 47.619 0.00 0.00 0.00 4.68
425 461 1.988293 TCCGAGCAAATCCACCAAAA 58.012 45.000 0.00 0.00 0.00 2.44
504 547 2.396590 ACAACAACCACACGAAGAGT 57.603 45.000 0.00 0.00 0.00 3.24
505 548 2.031683 GGAACAACAACCACACGAAGAG 59.968 50.000 0.00 0.00 0.00 2.85
512 555 1.658686 GCACCGGAACAACAACCACA 61.659 55.000 9.46 0.00 0.00 4.17
539 584 8.692710 AGAAGTCATCGTGTTAAGACCATATAA 58.307 33.333 0.00 0.00 0.00 0.98
543 588 5.407407 AGAAGTCATCGTGTTAAGACCAT 57.593 39.130 0.00 0.00 0.00 3.55
552 597 1.880675 ACAGTCGAGAAGTCATCGTGT 59.119 47.619 0.00 0.00 40.95 4.49
603 648 1.263776 GACGTCATTGTCGCTCTCTG 58.736 55.000 11.55 0.00 0.00 3.35
659 704 1.578897 TATTCACAGGCCACCTAGCA 58.421 50.000 5.01 0.00 29.64 3.49
752 1980 2.096218 GTGCCGTTCAGTTCATCAGTTC 60.096 50.000 0.00 0.00 0.00 3.01
822 2050 3.843027 CTCAGCCACCCAATAGATAGGAT 59.157 47.826 0.00 0.00 0.00 3.24
823 2051 3.116746 TCTCAGCCACCCAATAGATAGGA 60.117 47.826 0.00 0.00 0.00 2.94
824 2052 3.242867 TCTCAGCCACCCAATAGATAGG 58.757 50.000 0.00 0.00 0.00 2.57
826 2054 4.037222 TGTTCTCAGCCACCCAATAGATA 58.963 43.478 0.00 0.00 0.00 1.98
828 2056 2.027192 GTGTTCTCAGCCACCCAATAGA 60.027 50.000 0.00 0.00 0.00 1.98
829 2057 2.290260 TGTGTTCTCAGCCACCCAATAG 60.290 50.000 0.00 0.00 0.00 1.73
831 2059 0.478072 TGTGTTCTCAGCCACCCAAT 59.522 50.000 0.00 0.00 0.00 3.16
832 2060 0.478072 ATGTGTTCTCAGCCACCCAA 59.522 50.000 0.00 0.00 0.00 4.12
833 2061 0.250858 CATGTGTTCTCAGCCACCCA 60.251 55.000 0.00 0.00 0.00 4.51
834 2062 0.250901 ACATGTGTTCTCAGCCACCC 60.251 55.000 0.00 0.00 0.00 4.61
835 2063 2.028112 TCTACATGTGTTCTCAGCCACC 60.028 50.000 9.11 0.00 0.00 4.61
836 2064 2.996621 GTCTACATGTGTTCTCAGCCAC 59.003 50.000 9.11 0.00 0.00 5.01
837 2065 2.632512 TGTCTACATGTGTTCTCAGCCA 59.367 45.455 9.11 0.00 0.00 4.75
838 2066 3.257393 CTGTCTACATGTGTTCTCAGCC 58.743 50.000 9.11 0.00 0.00 4.85
839 2067 2.670414 GCTGTCTACATGTGTTCTCAGC 59.330 50.000 9.11 15.88 36.88 4.26
840 2068 4.185467 AGCTGTCTACATGTGTTCTCAG 57.815 45.455 9.11 10.54 0.00 3.35
841 2069 4.380973 GCTAGCTGTCTACATGTGTTCTCA 60.381 45.833 9.11 0.16 0.00 3.27
842 2070 4.109050 GCTAGCTGTCTACATGTGTTCTC 58.891 47.826 9.11 0.00 0.00 2.87
843 2071 3.428180 CGCTAGCTGTCTACATGTGTTCT 60.428 47.826 13.93 0.00 0.00 3.01
844 2072 2.854777 CGCTAGCTGTCTACATGTGTTC 59.145 50.000 13.93 0.00 0.00 3.18
845 2073 2.492088 TCGCTAGCTGTCTACATGTGTT 59.508 45.455 13.93 0.00 0.00 3.32
846 2074 2.092323 TCGCTAGCTGTCTACATGTGT 58.908 47.619 13.93 0.00 0.00 3.72
924 2152 1.962402 GCCAAGACTAGAGAGGCAGGA 60.962 57.143 12.87 0.00 44.59 3.86
925 2153 0.463620 GCCAAGACTAGAGAGGCAGG 59.536 60.000 12.87 0.00 44.59 4.85
926 2154 0.463620 GGCCAAGACTAGAGAGGCAG 59.536 60.000 17.31 0.00 46.96 4.85
927 2155 0.041833 AGGCCAAGACTAGAGAGGCA 59.958 55.000 5.01 0.00 46.96 4.75
928 2156 0.463620 CAGGCCAAGACTAGAGAGGC 59.536 60.000 5.01 4.21 44.48 4.70
929 2157 0.463620 GCAGGCCAAGACTAGAGAGG 59.536 60.000 5.01 0.00 0.00 3.69
970 2198 1.002134 AGGCTCCAATGGTTCGTGG 60.002 57.895 0.00 0.00 36.13 4.94
978 2206 3.136123 CACCGGCAGGCTCCAATG 61.136 66.667 0.00 0.00 42.76 2.82
998 2226 2.436646 GTCCAGCGGTGTCCATGG 60.437 66.667 14.40 4.97 32.99 3.66
1598 2918 4.686091 CGTTTGTCAGTTGCTCTTCATCTA 59.314 41.667 0.00 0.00 0.00 1.98
1653 2973 1.035932 GCATGTGCTTGCTCATCCCT 61.036 55.000 7.13 0.00 39.57 4.20
1675 2995 4.803452 AGAATGGTTGGGAAGTCTTTCAA 58.197 39.130 0.00 0.00 34.90 2.69
1722 3042 1.148310 GTAGCTTGAAGTTCAGCGCA 58.852 50.000 23.01 12.80 30.37 6.09
1892 3215 2.141011 CTTGTGCAGGGGGTCCATGA 62.141 60.000 2.56 0.00 34.83 3.07
2121 3474 0.842467 CCTCCAAGAACTCAGGGGGT 60.842 60.000 0.00 0.00 38.32 4.95
2208 3561 0.530650 AGTGCGTCAGGAACACACAG 60.531 55.000 6.51 0.00 42.26 3.66
2232 3585 3.991999 TCGACCGTCGAGTTCCAT 58.008 55.556 19.51 0.00 44.82 3.41
2530 3886 6.206498 GTTGACTGGTGGAGTAAATGTTTTC 58.794 40.000 0.00 0.00 33.83 2.29
2541 3897 2.310233 CGCACGTTGACTGGTGGAG 61.310 63.158 0.00 0.00 34.76 3.86
2542 3898 2.279851 CGCACGTTGACTGGTGGA 60.280 61.111 0.00 0.00 34.76 4.02
2543 3899 3.345808 CCGCACGTTGACTGGTGG 61.346 66.667 0.00 0.00 34.76 4.61
2544 3900 4.012895 GCCGCACGTTGACTGGTG 62.013 66.667 0.00 0.00 37.22 4.17
2545 3901 4.235762 AGCCGCACGTTGACTGGT 62.236 61.111 0.00 0.00 0.00 4.00
2546 3902 3.716006 CAGCCGCACGTTGACTGG 61.716 66.667 0.00 0.00 0.00 4.00
2547 3903 2.661537 TCAGCCGCACGTTGACTG 60.662 61.111 0.00 0.00 0.00 3.51
2548 3904 1.802337 TACTCAGCCGCACGTTGACT 61.802 55.000 0.00 0.00 0.00 3.41
2549 3905 1.344942 CTACTCAGCCGCACGTTGAC 61.345 60.000 0.00 0.00 0.00 3.18
2550 3906 1.080772 CTACTCAGCCGCACGTTGA 60.081 57.895 0.00 0.00 0.00 3.18
2551 3907 0.109458 TACTACTCAGCCGCACGTTG 60.109 55.000 0.00 0.00 0.00 4.10
2552 3908 0.599558 TTACTACTCAGCCGCACGTT 59.400 50.000 0.00 0.00 0.00 3.99
2553 3909 0.815734 ATTACTACTCAGCCGCACGT 59.184 50.000 0.00 0.00 0.00 4.49
2554 3910 1.852895 GAATTACTACTCAGCCGCACG 59.147 52.381 0.00 0.00 0.00 5.34
2555 3911 2.860735 CAGAATTACTACTCAGCCGCAC 59.139 50.000 0.00 0.00 0.00 5.34
2556 3912 2.738643 GCAGAATTACTACTCAGCCGCA 60.739 50.000 0.00 0.00 0.00 5.69
2557 3913 1.861575 GCAGAATTACTACTCAGCCGC 59.138 52.381 0.00 0.00 0.00 6.53
2558 3914 3.444703 AGCAGAATTACTACTCAGCCG 57.555 47.619 0.00 0.00 0.00 5.52
2559 3915 5.908341 AGTAAGCAGAATTACTACTCAGCC 58.092 41.667 0.00 0.00 42.73 4.85
2560 3916 5.980715 GGAGTAAGCAGAATTACTACTCAGC 59.019 44.000 9.15 0.00 44.16 4.26
2561 3917 6.322712 AGGGAGTAAGCAGAATTACTACTCAG 59.677 42.308 8.36 0.00 44.16 3.35
2562 3918 6.195700 AGGGAGTAAGCAGAATTACTACTCA 58.804 40.000 8.36 0.00 44.16 3.41
2563 3919 6.718522 AGGGAGTAAGCAGAATTACTACTC 57.281 41.667 8.36 0.00 44.16 2.59
2564 3920 7.038231 ACAAAGGGAGTAAGCAGAATTACTACT 60.038 37.037 8.36 4.02 44.16 2.57
2565 3921 7.104290 ACAAAGGGAGTAAGCAGAATTACTAC 58.896 38.462 1.00 1.00 44.16 2.73
2566 3922 7.253905 ACAAAGGGAGTAAGCAGAATTACTA 57.746 36.000 0.00 0.00 44.16 1.82
2567 3923 6.128138 ACAAAGGGAGTAAGCAGAATTACT 57.872 37.500 0.00 0.00 46.23 2.24
2568 3924 5.354513 GGACAAAGGGAGTAAGCAGAATTAC 59.645 44.000 0.00 0.00 36.16 1.89
2569 3925 5.250774 AGGACAAAGGGAGTAAGCAGAATTA 59.749 40.000 0.00 0.00 0.00 1.40
2570 3926 4.043435 AGGACAAAGGGAGTAAGCAGAATT 59.957 41.667 0.00 0.00 0.00 2.17
2571 3927 3.589288 AGGACAAAGGGAGTAAGCAGAAT 59.411 43.478 0.00 0.00 0.00 2.40
2572 3928 2.979678 AGGACAAAGGGAGTAAGCAGAA 59.020 45.455 0.00 0.00 0.00 3.02
2573 3929 2.621070 AGGACAAAGGGAGTAAGCAGA 58.379 47.619 0.00 0.00 0.00 4.26
2574 3930 3.244561 TGAAGGACAAAGGGAGTAAGCAG 60.245 47.826 0.00 0.00 0.00 4.24
2575 3931 2.708861 TGAAGGACAAAGGGAGTAAGCA 59.291 45.455 0.00 0.00 0.00 3.91
2576 3932 3.418684 TGAAGGACAAAGGGAGTAAGC 57.581 47.619 0.00 0.00 0.00 3.09
2656 4012 9.073475 ACGGCATAAATATTGGTGTATTATTGT 57.927 29.630 0.00 0.00 0.00 2.71
2657 4013 9.554724 GACGGCATAAATATTGGTGTATTATTG 57.445 33.333 0.00 0.00 0.00 1.90
2658 4014 9.290988 TGACGGCATAAATATTGGTGTATTATT 57.709 29.630 0.00 0.00 0.00 1.40
2659 4015 8.856153 TGACGGCATAAATATTGGTGTATTAT 57.144 30.769 0.00 0.00 0.00 1.28
2660 4016 8.678593 TTGACGGCATAAATATTGGTGTATTA 57.321 30.769 0.00 0.00 0.00 0.98
2661 4017 7.575414 TTGACGGCATAAATATTGGTGTATT 57.425 32.000 0.00 0.00 0.00 1.89
2662 4018 7.575414 TTTGACGGCATAAATATTGGTGTAT 57.425 32.000 0.00 0.00 0.00 2.29
2663 4019 7.575414 ATTTGACGGCATAAATATTGGTGTA 57.425 32.000 0.00 0.00 0.00 2.90
2664 4020 5.906113 TTTGACGGCATAAATATTGGTGT 57.094 34.783 0.00 0.00 0.00 4.16
2665 4021 8.134895 ACTAATTTGACGGCATAAATATTGGTG 58.865 33.333 0.00 0.00 0.00 4.17
2666 4022 8.232913 ACTAATTTGACGGCATAAATATTGGT 57.767 30.769 0.00 0.00 0.00 3.67
2667 4023 9.825972 CTACTAATTTGACGGCATAAATATTGG 57.174 33.333 0.00 0.00 0.00 3.16
2668 4024 9.329913 GCTACTAATTTGACGGCATAAATATTG 57.670 33.333 0.00 0.00 0.00 1.90
2669 4025 9.062524 TGCTACTAATTTGACGGCATAAATATT 57.937 29.630 0.00 0.00 0.00 1.28
2670 4026 8.615878 TGCTACTAATTTGACGGCATAAATAT 57.384 30.769 0.00 0.00 0.00 1.28
2671 4027 8.615878 ATGCTACTAATTTGACGGCATAAATA 57.384 30.769 0.00 0.00 37.20 1.40
2672 4028 6.935741 TGCTACTAATTTGACGGCATAAAT 57.064 33.333 0.00 0.00 0.00 1.40
2673 4029 6.935741 ATGCTACTAATTTGACGGCATAAA 57.064 33.333 0.00 0.00 37.20 1.40
2674 4030 6.292649 CGAATGCTACTAATTTGACGGCATAA 60.293 38.462 0.00 0.00 37.85 1.90
2675 4031 5.176774 CGAATGCTACTAATTTGACGGCATA 59.823 40.000 0.00 0.00 37.85 3.14
2676 4032 4.024893 CGAATGCTACTAATTTGACGGCAT 60.025 41.667 0.00 10.67 40.04 4.40
2677 4033 3.308595 CGAATGCTACTAATTTGACGGCA 59.691 43.478 0.00 0.00 0.00 5.69
2678 4034 3.554324 TCGAATGCTACTAATTTGACGGC 59.446 43.478 0.00 0.00 0.00 5.68
2679 4035 5.907197 ATCGAATGCTACTAATTTGACGG 57.093 39.130 0.00 0.00 31.71 4.79
2680 4036 9.306280 CATAAATCGAATGCTACTAATTTGACG 57.694 33.333 0.00 0.00 31.71 4.35
2741 4097 9.702494 TGTGCAAAAATATATCAATGTTTGTGA 57.298 25.926 0.00 0.00 34.81 3.58
2747 4103 9.075519 CGAGTTTGTGCAAAAATATATCAATGT 57.924 29.630 5.11 0.00 31.33 2.71
2748 4104 9.288124 TCGAGTTTGTGCAAAAATATATCAATG 57.712 29.630 5.11 0.00 31.33 2.82
2750 4106 9.502145 GATCGAGTTTGTGCAAAAATATATCAA 57.498 29.630 5.11 0.00 31.33 2.57
2751 4107 8.672815 TGATCGAGTTTGTGCAAAAATATATCA 58.327 29.630 5.11 9.71 31.33 2.15
2752 4108 9.502145 TTGATCGAGTTTGTGCAAAAATATATC 57.498 29.630 5.11 7.47 31.33 1.63
2753 4109 9.853555 TTTGATCGAGTTTGTGCAAAAATATAT 57.146 25.926 5.11 0.00 31.33 0.86
2754 4110 9.853555 ATTTGATCGAGTTTGTGCAAAAATATA 57.146 25.926 5.11 0.00 31.33 0.86
2755 4111 8.761575 ATTTGATCGAGTTTGTGCAAAAATAT 57.238 26.923 5.11 0.00 31.33 1.28
2756 4112 8.586570 AATTTGATCGAGTTTGTGCAAAAATA 57.413 26.923 5.11 0.00 31.33 1.40
2757 4113 7.481275 AATTTGATCGAGTTTGTGCAAAAAT 57.519 28.000 5.11 0.00 31.33 1.82
2758 4114 6.900568 AATTTGATCGAGTTTGTGCAAAAA 57.099 29.167 0.00 0.00 31.33 1.94
2759 4115 6.900568 AAATTTGATCGAGTTTGTGCAAAA 57.099 29.167 2.79 0.00 31.33 2.44
2760 4116 6.900568 AAAATTTGATCGAGTTTGTGCAAA 57.099 29.167 4.33 0.00 0.00 3.68
2761 4117 7.993821 TTAAAATTTGATCGAGTTTGTGCAA 57.006 28.000 4.33 0.00 0.00 4.08
2762 4118 7.993821 TTTAAAATTTGATCGAGTTTGTGCA 57.006 28.000 4.33 0.00 0.00 4.57
2790 4146 9.788960 ACTTTCAACTTTATTGAAGAGTCAAAC 57.211 29.630 2.64 0.00 46.66 2.93
2793 4149 9.607988 TGTACTTTCAACTTTATTGAAGAGTCA 57.392 29.630 14.66 11.74 39.30 3.41
2794 4150 9.865484 GTGTACTTTCAACTTTATTGAAGAGTC 57.135 33.333 14.66 10.34 39.30 3.36
2795 4151 9.614792 AGTGTACTTTCAACTTTATTGAAGAGT 57.385 29.630 15.17 15.17 39.30 3.24
2806 4162 9.836076 GTACTTGAAAAAGTGTACTTTCAACTT 57.164 29.630 13.70 3.79 44.69 2.66
2807 4163 8.173130 CGTACTTGAAAAAGTGTACTTTCAACT 58.827 33.333 13.70 9.49 44.69 3.16
2808 4164 7.427318 CCGTACTTGAAAAAGTGTACTTTCAAC 59.573 37.037 13.70 7.28 44.69 3.18
2809 4165 7.333921 TCCGTACTTGAAAAAGTGTACTTTCAA 59.666 33.333 15.77 15.77 44.69 2.69
2810 4166 6.817641 TCCGTACTTGAAAAAGTGTACTTTCA 59.182 34.615 10.16 4.40 44.69 2.69
2811 4167 7.223387 TCTCCGTACTTGAAAAAGTGTACTTTC 59.777 37.037 10.16 0.74 44.69 2.62
2813 4169 6.576185 TCTCCGTACTTGAAAAAGTGTACTT 58.424 36.000 1.42 0.00 37.91 2.24
2814 4170 6.040166 TCTCTCCGTACTTGAAAAAGTGTACT 59.960 38.462 1.42 0.00 34.75 2.73
2815 4171 6.211515 TCTCTCCGTACTTGAAAAAGTGTAC 58.788 40.000 1.42 0.00 34.37 2.90
2816 4172 6.040166 ACTCTCTCCGTACTTGAAAAAGTGTA 59.960 38.462 1.42 0.00 34.37 2.90
2817 4173 5.163437 ACTCTCTCCGTACTTGAAAAAGTGT 60.163 40.000 1.42 0.00 34.37 3.55
2818 4174 5.290386 ACTCTCTCCGTACTTGAAAAAGTG 58.710 41.667 1.42 0.00 34.37 3.16
2819 4175 5.532664 ACTCTCTCCGTACTTGAAAAAGT 57.467 39.130 0.00 0.00 36.82 2.66
2820 4176 7.146648 ACTTACTCTCTCCGTACTTGAAAAAG 58.853 38.462 0.00 0.00 0.00 2.27
2821 4177 7.047460 ACTTACTCTCTCCGTACTTGAAAAA 57.953 36.000 0.00 0.00 0.00 1.94
2822 4178 6.645790 ACTTACTCTCTCCGTACTTGAAAA 57.354 37.500 0.00 0.00 0.00 2.29
2823 4179 6.150140 GGTACTTACTCTCTCCGTACTTGAAA 59.850 42.308 0.00 0.00 33.01 2.69
2824 4180 5.645497 GGTACTTACTCTCTCCGTACTTGAA 59.355 44.000 0.00 0.00 33.01 2.69
2825 4181 5.181748 GGTACTTACTCTCTCCGTACTTGA 58.818 45.833 0.00 0.00 33.01 3.02
2826 4182 4.940046 TGGTACTTACTCTCTCCGTACTTG 59.060 45.833 0.00 0.00 33.01 3.16
2827 4183 5.171339 TGGTACTTACTCTCTCCGTACTT 57.829 43.478 0.00 0.00 33.01 2.24
2828 4184 4.833478 TGGTACTTACTCTCTCCGTACT 57.167 45.455 0.00 0.00 33.01 2.73
2829 4185 5.163673 CCTTTGGTACTTACTCTCTCCGTAC 60.164 48.000 0.00 0.00 0.00 3.67
2830 4186 4.946157 CCTTTGGTACTTACTCTCTCCGTA 59.054 45.833 0.00 0.00 0.00 4.02
2831 4187 3.762823 CCTTTGGTACTTACTCTCTCCGT 59.237 47.826 0.00 0.00 0.00 4.69
2832 4188 3.429135 GCCTTTGGTACTTACTCTCTCCG 60.429 52.174 0.00 0.00 0.00 4.63
2833 4189 3.429135 CGCCTTTGGTACTTACTCTCTCC 60.429 52.174 0.00 0.00 0.00 3.71
2834 4190 3.442977 TCGCCTTTGGTACTTACTCTCTC 59.557 47.826 0.00 0.00 0.00 3.20
2835 4191 3.428532 TCGCCTTTGGTACTTACTCTCT 58.571 45.455 0.00 0.00 0.00 3.10
2836 4192 3.863142 TCGCCTTTGGTACTTACTCTC 57.137 47.619 0.00 0.00 0.00 3.20
2837 4193 3.118738 CCATCGCCTTTGGTACTTACTCT 60.119 47.826 0.00 0.00 0.00 3.24
2838 4194 3.195661 CCATCGCCTTTGGTACTTACTC 58.804 50.000 0.00 0.00 0.00 2.59
2839 4195 2.093128 CCCATCGCCTTTGGTACTTACT 60.093 50.000 0.00 0.00 31.99 2.24
2840 4196 2.093341 TCCCATCGCCTTTGGTACTTAC 60.093 50.000 0.00 0.00 31.99 2.34
2854 4210 2.006888 ACGTTACAAGCAATCCCATCG 58.993 47.619 0.00 0.00 0.00 3.84
2863 4219 2.314647 GCCTGCGACGTTACAAGCA 61.315 57.895 7.30 5.71 38.03 3.91
2865 4221 0.796312 ATTGCCTGCGACGTTACAAG 59.204 50.000 0.00 0.00 0.00 3.16
2869 4225 3.173853 GCATTGCCTGCGACGTTA 58.826 55.556 0.00 0.00 41.97 3.18
2881 4237 2.409378 GTCCATTCAAAACGCTGCATTG 59.591 45.455 0.00 2.00 0.00 2.82
2896 4255 6.038271 GCAATCGGTATCTACAAAAGTCCATT 59.962 38.462 0.00 0.00 0.00 3.16
2903 4262 4.941263 AGCAAGCAATCGGTATCTACAAAA 59.059 37.500 0.00 0.00 0.00 2.44
2933 4292 2.600790 ACATATTACGGTCCGGGATCA 58.399 47.619 17.28 0.00 0.00 2.92
2936 4295 2.765135 TGAAACATATTACGGTCCGGGA 59.235 45.455 17.28 3.54 0.00 5.14
2981 4340 1.674817 GCCACGCCTACAGCTTCTAAA 60.675 52.381 0.00 0.00 40.39 1.85
2982 4341 0.108329 GCCACGCCTACAGCTTCTAA 60.108 55.000 0.00 0.00 40.39 2.10
2983 4342 1.515954 GCCACGCCTACAGCTTCTA 59.484 57.895 0.00 0.00 40.39 2.10
2984 4343 2.266055 GCCACGCCTACAGCTTCT 59.734 61.111 0.00 0.00 40.39 2.85
2985 4344 2.820037 GGCCACGCCTACAGCTTC 60.820 66.667 0.00 0.00 46.69 3.86
2995 4354 2.502213 AAACAACTTTAAGGCCACGC 57.498 45.000 5.01 0.00 0.00 5.34
2996 4355 4.915085 CACATAAACAACTTTAAGGCCACG 59.085 41.667 5.01 0.00 0.00 4.94
2997 4356 4.684242 GCACATAAACAACTTTAAGGCCAC 59.316 41.667 5.01 0.00 0.00 5.01
2998 4357 4.557695 CGCACATAAACAACTTTAAGGCCA 60.558 41.667 5.01 0.00 0.00 5.36
3003 4362 5.209240 GCTCACGCACATAAACAACTTTAA 58.791 37.500 0.00 0.00 35.78 1.52
3021 4380 2.675348 GCATGACCTAGTCTTTGCTCAC 59.325 50.000 0.00 0.00 38.42 3.51
3075 4434 0.540365 CACCCCATGTGGTCAAGCTT 60.540 55.000 0.00 0.00 41.52 3.74
3110 4471 5.547465 AGATAAATGGTGTTTCTGTCGTGA 58.453 37.500 0.00 0.00 0.00 4.35
3111 4472 5.163854 GGAGATAAATGGTGTTTCTGTCGTG 60.164 44.000 0.00 0.00 0.00 4.35
3153 4516 6.564686 CGTGCTTACATACATGGCATTTCTAG 60.565 42.308 0.00 0.00 35.37 2.43
3162 4525 3.521560 AGTGTCGTGCTTACATACATGG 58.478 45.455 0.00 0.00 30.26 3.66
3174 4537 0.109226 GTCTAGTGGGAGTGTCGTGC 60.109 60.000 0.00 0.00 0.00 5.34
3179 4542 0.611340 GACGGGTCTAGTGGGAGTGT 60.611 60.000 0.00 0.00 0.00 3.55
3193 4556 0.828022 TACCCAAGCATAGTGACGGG 59.172 55.000 0.00 0.00 39.72 5.28
3197 4560 5.815581 AGAATTTGTACCCAAGCATAGTGA 58.184 37.500 0.00 0.00 0.00 3.41
3255 4618 2.346847 CACTTACGAGATGCTCAACTGC 59.653 50.000 0.00 0.00 0.00 4.40
3282 4645 6.821160 TCAGATATTTGCTGAATTGGACGTTA 59.179 34.615 0.00 0.00 39.29 3.18
3287 4650 9.281371 CTCTTATCAGATATTTGCTGAATTGGA 57.719 33.333 0.00 0.00 44.71 3.53
3296 4659 8.781196 TCTCAATTGCTCTTATCAGATATTTGC 58.219 33.333 0.00 0.00 0.00 3.68
3304 4667 8.763356 GTTATCACTCTCAATTGCTCTTATCAG 58.237 37.037 0.00 0.00 0.00 2.90
3343 4706 5.624344 TGGAGAGAGTACTAACGAACAAG 57.376 43.478 0.00 0.00 0.00 3.16
3348 4711 3.434739 GGGGATGGAGAGAGTACTAACGA 60.435 52.174 0.00 0.00 0.00 3.85
3353 4716 6.744802 ATATTAGGGGATGGAGAGAGTACT 57.255 41.667 0.00 0.00 0.00 2.73
3383 4746 4.142038 ACGGGACTTGTAGCTTGAAAAAT 58.858 39.130 0.00 0.00 0.00 1.82
3426 4790 9.907819 TTCCCTAGTATTCCCTCTATTTCATAA 57.092 33.333 0.00 0.00 0.00 1.90
3427 4791 9.907819 TTTCCCTAGTATTCCCTCTATTTCATA 57.092 33.333 0.00 0.00 0.00 2.15
3428 4792 8.814448 TTTCCCTAGTATTCCCTCTATTTCAT 57.186 34.615 0.00 0.00 0.00 2.57
3429 4793 7.849904 ACTTTCCCTAGTATTCCCTCTATTTCA 59.150 37.037 0.00 0.00 0.00 2.69
3430 4794 8.265108 ACTTTCCCTAGTATTCCCTCTATTTC 57.735 38.462 0.00 0.00 0.00 2.17
3431 4795 8.640033 AACTTTCCCTAGTATTCCCTCTATTT 57.360 34.615 0.00 0.00 0.00 1.40
3432 4796 7.292827 GGAACTTTCCCTAGTATTCCCTCTATT 59.707 40.741 0.00 0.00 41.62 1.73
3433 4797 6.788456 GGAACTTTCCCTAGTATTCCCTCTAT 59.212 42.308 0.00 0.00 41.62 1.98
3434 4798 6.141790 GGAACTTTCCCTAGTATTCCCTCTA 58.858 44.000 0.00 0.00 41.62 2.43
3435 4799 4.969999 GGAACTTTCCCTAGTATTCCCTCT 59.030 45.833 0.00 0.00 41.62 3.69
3436 4800 5.293319 GGAACTTTCCCTAGTATTCCCTC 57.707 47.826 0.00 0.00 41.62 4.30
3449 4813 8.919721 TTGTAGAGACATGGCTGGAACTTTCC 62.920 46.154 5.31 0.59 40.69 3.13
3450 4814 3.064900 AGAGACATGGCTGGAACTTTC 57.935 47.619 5.31 0.00 0.00 2.62
3451 4815 3.327757 TGTAGAGACATGGCTGGAACTTT 59.672 43.478 5.31 0.00 0.00 2.66
3452 4816 2.906389 TGTAGAGACATGGCTGGAACTT 59.094 45.455 5.31 0.00 0.00 2.66
3453 4817 2.540383 TGTAGAGACATGGCTGGAACT 58.460 47.619 5.31 0.00 0.00 3.01
3454 4818 3.265791 CTTGTAGAGACATGGCTGGAAC 58.734 50.000 5.31 1.05 34.86 3.62
3516 4880 0.961753 GGAAGCTCAAACCAAGGTGG 59.038 55.000 0.00 0.00 45.02 4.61
3519 4883 1.866853 GCCGGAAGCTCAAACCAAGG 61.867 60.000 5.05 0.00 38.99 3.61
3540 4917 3.259876 TCAATTAGGCGTCAGTAACCACT 59.740 43.478 0.00 0.00 34.42 4.00


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

AutoCloner maintained by Alex Coulton.