Multiple sequence alignment - TraesCS6A01G382900

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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 TraesCS6A01G382900 chr6A 100.000 2900 0 0 1 2900 602074560 602077459 0.000000e+00 5356
1 TraesCS6A01G382900 chr6A 84.511 1175 103 42 880 2019 602131293 602132423 0.000000e+00 1088
2 TraesCS6A01G382900 chr6A 96.449 535 18 1 2366 2900 36435092 36435625 0.000000e+00 881
3 TraesCS6A01G382900 chr6A 82.490 1028 141 27 1048 2058 601264698 601263693 0.000000e+00 865
4 TraesCS6A01G382900 chr6A 79.739 1224 201 37 843 2058 601257220 601256036 0.000000e+00 843
5 TraesCS6A01G382900 chr6A 86.164 159 16 3 285 437 602130620 602130778 1.790000e-37 167
6 TraesCS6A01G382900 chr6D 88.215 1782 116 35 616 2345 455421433 455423172 0.000000e+00 2041
7 TraesCS6A01G382900 chr6D 88.578 858 76 16 1048 1891 455425276 455426125 0.000000e+00 1022
8 TraesCS6A01G382900 chr6D 81.278 1330 163 49 761 2058 454996822 454995547 0.000000e+00 998
9 TraesCS6A01G382900 chr6D 79.513 1108 166 39 964 2059 454962832 454961774 0.000000e+00 732
10 TraesCS6A01G382900 chr6D 90.155 386 21 9 72 443 455418796 455419178 1.210000e-133 486
11 TraesCS6A01G382900 chr6D 87.179 156 14 3 288 437 455424432 455424587 3.840000e-39 172
12 TraesCS6A01G382900 chr6B 84.778 1511 125 45 574 2030 692570217 692571676 0.000000e+00 1419
13 TraesCS6A01G382900 chr6B 86.660 967 89 28 952 1901 692574350 692575293 0.000000e+00 1035
14 TraesCS6A01G382900 chr6B 81.625 1083 147 36 957 2025 691944808 691945852 0.000000e+00 850
15 TraesCS6A01G382900 chr6B 79.694 1241 184 46 843 2059 691975976 691977172 0.000000e+00 833
16 TraesCS6A01G382900 chr6B 79.661 1239 188 42 843 2059 692044928 692043732 0.000000e+00 833
17 TraesCS6A01G382900 chr6B 85.542 415 38 14 72 470 692569817 692570225 5.780000e-112 414
18 TraesCS6A01G382900 chr6B 92.281 285 21 1 2073 2356 692571892 692572176 1.250000e-108 403
19 TraesCS6A01G382900 chr6B 82.586 379 26 13 83 443 692549522 692549878 6.080000e-77 298
20 TraesCS6A01G382900 chr6B 80.797 276 31 15 171 437 692573300 692573562 2.280000e-46 196
21 TraesCS6A01G382900 chr6B 89.655 87 2 2 576 655 692549905 692549991 1.420000e-18 104
22 TraesCS6A01G382900 chr1B 96.822 535 17 0 2366 2900 634323576 634324110 0.000000e+00 894
23 TraesCS6A01G382900 chr7B 96.636 535 18 0 2366 2900 657620051 657619517 0.000000e+00 889
24 TraesCS6A01G382900 chr7B 88.462 104 11 1 471 573 275706795 275706898 1.090000e-24 124
25 TraesCS6A01G382900 chr2B 96.408 529 19 0 2372 2900 772475631 772475103 0.000000e+00 872
26 TraesCS6A01G382900 chr5B 90.858 536 45 4 2366 2900 59931359 59930827 0.000000e+00 715
27 TraesCS6A01G382900 chr5A 90.654 535 49 1 2366 2900 45374988 45374455 0.000000e+00 710
28 TraesCS6A01G382900 chr2D 90.654 535 48 2 2366 2900 272353069 272353601 0.000000e+00 710
29 TraesCS6A01G382900 chr5D 93.501 477 30 1 2366 2842 56956898 56956423 0.000000e+00 708
30 TraesCS6A01G382900 chr2A 90.737 529 49 0 2372 2900 350393859 350393331 0.000000e+00 706


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 TraesCS6A01G382900 chr6A 602074560 602077459 2899 False 5356.00 5356 100.00000 1 2900 1 chr6A.!!$F2 2899
1 TraesCS6A01G382900 chr6A 36435092 36435625 533 False 881.00 881 96.44900 2366 2900 1 chr6A.!!$F1 534
2 TraesCS6A01G382900 chr6A 601263693 601264698 1005 True 865.00 865 82.49000 1048 2058 1 chr6A.!!$R2 1010
3 TraesCS6A01G382900 chr6A 601256036 601257220 1184 True 843.00 843 79.73900 843 2058 1 chr6A.!!$R1 1215
4 TraesCS6A01G382900 chr6A 602130620 602132423 1803 False 627.50 1088 85.33750 285 2019 2 chr6A.!!$F3 1734
5 TraesCS6A01G382900 chr6D 454995547 454996822 1275 True 998.00 998 81.27800 761 2058 1 chr6D.!!$R2 1297
6 TraesCS6A01G382900 chr6D 455418796 455426125 7329 False 930.25 2041 88.53175 72 2345 4 chr6D.!!$F1 2273
7 TraesCS6A01G382900 chr6D 454961774 454962832 1058 True 732.00 732 79.51300 964 2059 1 chr6D.!!$R1 1095
8 TraesCS6A01G382900 chr6B 691944808 691945852 1044 False 850.00 850 81.62500 957 2025 1 chr6B.!!$F1 1068
9 TraesCS6A01G382900 chr6B 691975976 691977172 1196 False 833.00 833 79.69400 843 2059 1 chr6B.!!$F2 1216
10 TraesCS6A01G382900 chr6B 692043732 692044928 1196 True 833.00 833 79.66100 843 2059 1 chr6B.!!$R1 1216
11 TraesCS6A01G382900 chr6B 692569817 692575293 5476 False 693.40 1419 86.01160 72 2356 5 chr6B.!!$F4 2284
12 TraesCS6A01G382900 chr1B 634323576 634324110 534 False 894.00 894 96.82200 2366 2900 1 chr1B.!!$F1 534
13 TraesCS6A01G382900 chr7B 657619517 657620051 534 True 889.00 889 96.63600 2366 2900 1 chr7B.!!$R1 534
14 TraesCS6A01G382900 chr2B 772475103 772475631 528 True 872.00 872 96.40800 2372 2900 1 chr2B.!!$R1 528
15 TraesCS6A01G382900 chr5B 59930827 59931359 532 True 715.00 715 90.85800 2366 2900 1 chr5B.!!$R1 534
16 TraesCS6A01G382900 chr5A 45374455 45374988 533 True 710.00 710 90.65400 2366 2900 1 chr5A.!!$R1 534
17 TraesCS6A01G382900 chr2D 272353069 272353601 532 False 710.00 710 90.65400 2366 2900 1 chr2D.!!$F1 534
18 TraesCS6A01G382900 chr2A 350393331 350393859 528 True 706.00 706 90.73700 2372 2900 1 chr2A.!!$R1 528

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
567 1539 0.030908 GGCGTAAGTCAGGAGATCCG 59.969 60.0 0.0 0.0 45.31 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 8370 0.178915 TCCCGGTTTTCCCTCTCTCA 60.179 55.0 0.0 0.0 36.42 3.27 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
17 18 4.154613 CGATTCTATCGCCGGCTC 57.845 61.111 26.68 12.39 46.55 4.70
18 19 1.797933 CGATTCTATCGCCGGCTCG 60.798 63.158 26.68 20.74 46.55 5.03
19 20 2.049063 ATTCTATCGCCGGCTCGC 60.049 61.111 26.68 0.00 0.00 5.03
20 21 3.575351 ATTCTATCGCCGGCTCGCC 62.575 63.158 26.68 0.00 0.00 5.54
34 35 4.609247 CGCCCTCCGACGACGATC 62.609 72.222 9.28 0.00 42.66 3.69
35 36 3.210528 GCCCTCCGACGACGATCT 61.211 66.667 9.28 0.00 42.66 2.75
36 37 2.772691 GCCCTCCGACGACGATCTT 61.773 63.158 9.28 0.00 42.66 2.40
37 38 1.807886 CCCTCCGACGACGATCTTT 59.192 57.895 9.28 0.00 42.66 2.52
38 39 1.019673 CCCTCCGACGACGATCTTTA 58.980 55.000 9.28 0.00 42.66 1.85
39 40 1.607628 CCCTCCGACGACGATCTTTAT 59.392 52.381 9.28 0.00 42.66 1.40
40 41 2.604855 CCCTCCGACGACGATCTTTATG 60.605 54.545 9.28 0.00 42.66 1.90
41 42 2.033049 CCTCCGACGACGATCTTTATGT 59.967 50.000 9.28 0.00 42.66 2.29
42 43 3.289911 CTCCGACGACGATCTTTATGTC 58.710 50.000 9.28 0.00 42.66 3.06
43 44 2.941064 TCCGACGACGATCTTTATGTCT 59.059 45.455 9.28 0.00 42.66 3.41
44 45 3.002042 TCCGACGACGATCTTTATGTCTC 59.998 47.826 9.28 0.00 42.66 3.36
45 46 3.002451 CCGACGACGATCTTTATGTCTCT 59.998 47.826 9.28 0.00 42.66 3.10
46 47 4.496010 CCGACGACGATCTTTATGTCTCTT 60.496 45.833 9.28 0.00 42.66 2.85
47 48 4.434909 CGACGACGATCTTTATGTCTCTTG 59.565 45.833 0.00 0.00 42.66 3.02
48 49 5.562506 ACGACGATCTTTATGTCTCTTGA 57.437 39.130 0.00 0.00 0.00 3.02
49 50 5.950883 ACGACGATCTTTATGTCTCTTGAA 58.049 37.500 0.00 0.00 0.00 2.69
50 51 6.030849 ACGACGATCTTTATGTCTCTTGAAG 58.969 40.000 0.00 0.00 0.00 3.02
51 52 5.457148 CGACGATCTTTATGTCTCTTGAAGG 59.543 44.000 0.00 0.00 0.00 3.46
52 53 5.665459 ACGATCTTTATGTCTCTTGAAGGG 58.335 41.667 0.00 0.00 0.00 3.95
53 54 5.187967 ACGATCTTTATGTCTCTTGAAGGGT 59.812 40.000 0.00 0.00 0.00 4.34
54 55 5.751028 CGATCTTTATGTCTCTTGAAGGGTC 59.249 44.000 0.00 0.00 0.00 4.46
55 56 6.627087 ATCTTTATGTCTCTTGAAGGGTCA 57.373 37.500 0.00 0.00 0.00 4.02
56 57 6.433847 TCTTTATGTCTCTTGAAGGGTCAA 57.566 37.500 0.00 0.00 41.57 3.18
57 58 7.020827 TCTTTATGTCTCTTGAAGGGTCAAT 57.979 36.000 0.00 0.00 42.85 2.57
58 59 6.881065 TCTTTATGTCTCTTGAAGGGTCAATG 59.119 38.462 0.00 0.00 42.85 2.82
59 60 3.423539 TGTCTCTTGAAGGGTCAATGG 57.576 47.619 0.00 0.00 42.85 3.16
60 61 2.087646 GTCTCTTGAAGGGTCAATGGC 58.912 52.381 0.00 0.00 42.85 4.40
61 62 1.988107 TCTCTTGAAGGGTCAATGGCT 59.012 47.619 0.00 0.00 42.85 4.75
62 63 2.089980 CTCTTGAAGGGTCAATGGCTG 58.910 52.381 0.00 0.00 42.85 4.85
63 64 1.180029 CTTGAAGGGTCAATGGCTGG 58.820 55.000 0.00 0.00 42.85 4.85
64 65 0.776810 TTGAAGGGTCAATGGCTGGA 59.223 50.000 0.00 0.00 38.88 3.86
65 66 0.329261 TGAAGGGTCAATGGCTGGAG 59.671 55.000 0.00 0.00 0.00 3.86
66 67 0.620556 GAAGGGTCAATGGCTGGAGA 59.379 55.000 0.00 0.00 0.00 3.71
67 68 1.213926 GAAGGGTCAATGGCTGGAGAT 59.786 52.381 0.00 0.00 0.00 2.75
68 69 0.549950 AGGGTCAATGGCTGGAGATG 59.450 55.000 0.00 0.00 0.00 2.90
69 70 1.105759 GGGTCAATGGCTGGAGATGC 61.106 60.000 0.00 0.00 0.00 3.91
70 71 0.106819 GGTCAATGGCTGGAGATGCT 60.107 55.000 0.00 0.00 0.00 3.79
115 123 2.999331 TGCTTTGGCATAAGTCTACCC 58.001 47.619 9.90 0.00 44.28 3.69
116 124 2.576191 TGCTTTGGCATAAGTCTACCCT 59.424 45.455 9.90 0.00 44.28 4.34
117 125 2.945668 GCTTTGGCATAAGTCTACCCTG 59.054 50.000 9.90 0.00 38.54 4.45
118 126 3.622455 GCTTTGGCATAAGTCTACCCTGT 60.622 47.826 9.90 0.00 38.54 4.00
119 127 4.589908 CTTTGGCATAAGTCTACCCTGTT 58.410 43.478 0.00 0.00 0.00 3.16
120 128 3.627395 TGGCATAAGTCTACCCTGTTG 57.373 47.619 0.00 0.00 0.00 3.33
148 162 2.488891 CCCTCGCCCCAATTGAATATGA 60.489 50.000 7.12 0.00 0.00 2.15
173 195 2.575993 CTGAGTGCTCGGTGGGAG 59.424 66.667 0.04 0.00 46.06 4.30
216 238 0.106819 AAGTCTCTGATGGGGCATGC 60.107 55.000 9.90 9.90 0.00 4.06
250 272 5.523916 ACGTGATTTCCAGCATCATTAGTAC 59.476 40.000 0.00 0.00 33.22 2.73
283 305 7.204243 TCTATAGTACATCTAATCGCCCCTA 57.796 40.000 0.00 0.00 31.94 3.53
420 448 3.013921 GTGGAATTGATTAGTGGCGGAA 58.986 45.455 0.00 0.00 0.00 4.30
438 466 2.357569 GGAAACAGCTCCCCATCAATCT 60.358 50.000 0.00 0.00 0.00 2.40
443 471 0.178970 GCTCCCCATCAATCTGGCAT 60.179 55.000 0.00 0.00 34.77 4.40
445 473 2.787994 CTCCCCATCAATCTGGCATAC 58.212 52.381 0.00 0.00 34.77 2.39
446 474 2.107031 CTCCCCATCAATCTGGCATACA 59.893 50.000 0.00 0.00 34.77 2.29
450 1422 5.015497 TCCCCATCAATCTGGCATACATTAT 59.985 40.000 0.00 0.00 34.77 1.28
453 1425 6.605995 CCCATCAATCTGGCATACATTATCAT 59.394 38.462 0.00 0.00 34.77 2.45
465 1437 7.909641 GGCATACATTATCATTTTTGTTTTGGC 59.090 33.333 0.00 0.00 0.00 4.52
466 1438 8.449397 GCATACATTATCATTTTTGTTTTGGCA 58.551 29.630 0.00 0.00 0.00 4.92
469 1441 7.647228 ACATTATCATTTTTGTTTTGGCAACC 58.353 30.769 0.00 0.00 0.00 3.77
470 1442 4.809815 ATCATTTTTGTTTTGGCAACCG 57.190 36.364 0.00 0.00 0.00 4.44
471 1443 2.939103 TCATTTTTGTTTTGGCAACCGG 59.061 40.909 0.00 0.00 0.00 5.28
472 1444 2.762535 TTTTTGTTTTGGCAACCGGA 57.237 40.000 9.46 0.00 0.00 5.14
473 1445 2.011540 TTTTGTTTTGGCAACCGGAC 57.988 45.000 9.46 0.00 0.00 4.79
474 1446 0.179134 TTTGTTTTGGCAACCGGACG 60.179 50.000 9.46 0.00 0.00 4.79
475 1447 2.354188 GTTTTGGCAACCGGACGC 60.354 61.111 9.46 10.32 0.00 5.19
476 1448 3.955101 TTTTGGCAACCGGACGCG 61.955 61.111 9.46 3.53 0.00 6.01
490 1462 4.156622 CGCGGCTCGTCTGACGTA 62.157 66.667 27.16 14.42 43.14 3.57
491 1463 2.576317 GCGGCTCGTCTGACGTAC 60.576 66.667 27.16 19.93 43.14 3.67
492 1464 2.276493 CGGCTCGTCTGACGTACG 60.276 66.667 27.16 23.69 43.14 3.67
493 1465 2.099831 GGCTCGTCTGACGTACGG 59.900 66.667 27.16 16.97 43.14 4.02
494 1466 2.684843 GGCTCGTCTGACGTACGGT 61.685 63.158 27.16 5.07 43.14 4.83
495 1467 1.225963 GCTCGTCTGACGTACGGTC 60.226 63.158 27.16 14.53 46.27 4.79
496 1468 1.423056 CTCGTCTGACGTACGGTCC 59.577 63.158 27.16 8.82 45.46 4.46
497 1469 1.293963 CTCGTCTGACGTACGGTCCA 61.294 60.000 27.16 12.94 45.46 4.02
498 1470 1.154338 CGTCTGACGTACGGTCCAC 60.154 63.158 21.30 9.64 45.46 4.02
499 1471 1.154338 GTCTGACGTACGGTCCACG 60.154 63.158 21.06 2.12 45.46 4.94
515 1487 2.027605 CGCACTGACGTGTGGACT 59.972 61.111 7.98 0.00 45.54 3.85
516 1488 2.016704 CGCACTGACGTGTGGACTC 61.017 63.158 7.98 0.00 45.54 3.36
517 1489 2.016704 GCACTGACGTGTGGACTCG 61.017 63.158 7.98 0.00 43.16 4.18
518 1490 1.371758 CACTGACGTGTGGACTCGG 60.372 63.158 0.00 0.00 37.19 4.63
519 1491 1.527611 ACTGACGTGTGGACTCGGA 60.528 57.895 0.00 0.00 37.19 4.55
520 1492 1.081376 CTGACGTGTGGACTCGGAC 60.081 63.158 0.00 1.37 37.19 4.79
521 1493 2.257676 GACGTGTGGACTCGGACC 59.742 66.667 0.00 0.00 37.19 4.46
522 1494 3.278592 GACGTGTGGACTCGGACCC 62.279 68.421 0.00 0.00 37.19 4.46
523 1495 3.299977 CGTGTGGACTCGGACCCA 61.300 66.667 0.00 0.00 0.00 4.51
526 1498 4.736896 GTGGACTCGGACCCACGC 62.737 72.222 8.50 0.00 42.73 5.34
529 1501 4.773117 GACTCGGACCCACGCGTC 62.773 72.222 9.86 0.00 40.66 5.19
531 1503 4.778415 CTCGGACCCACGCGTCAG 62.778 72.222 9.86 6.05 34.24 3.51
566 1538 3.969995 GGCGTAAGTCAGGAGATCC 57.030 57.895 0.00 0.00 45.31 3.36
567 1539 0.030908 GGCGTAAGTCAGGAGATCCG 59.969 60.000 0.00 0.00 45.31 4.18
568 1540 0.030908 GCGTAAGTCAGGAGATCCGG 59.969 60.000 0.00 0.00 39.96 5.14
569 1541 0.030908 CGTAAGTCAGGAGATCCGGC 59.969 60.000 0.00 0.00 42.08 6.13
570 1542 1.404843 GTAAGTCAGGAGATCCGGCT 58.595 55.000 0.00 0.00 42.08 5.52
571 1543 1.338655 GTAAGTCAGGAGATCCGGCTC 59.661 57.143 0.00 0.00 42.08 4.70
585 1557 3.365265 GCTCCTTGGCAACCACCG 61.365 66.667 0.00 0.00 30.78 4.94
661 2892 0.608130 TGTGCAACTACTCGAGCCAT 59.392 50.000 13.61 0.00 38.04 4.40
667 2898 0.107116 ACTACTCGAGCCATCCGTCT 60.107 55.000 13.61 0.00 0.00 4.18
668 2899 1.140452 ACTACTCGAGCCATCCGTCTA 59.860 52.381 13.61 0.00 0.00 2.59
669 2900 1.801771 CTACTCGAGCCATCCGTCTAG 59.198 57.143 13.61 0.00 0.00 2.43
753 2997 0.103208 ATACACAGCTAGCCTCGTGC 59.897 55.000 22.62 0.00 41.71 5.34
770 6802 0.034756 TGCCGGTAATGGATGGATCG 59.965 55.000 1.90 0.00 0.00 3.69
771 6803 0.034896 GCCGGTAATGGATGGATCGT 59.965 55.000 1.90 0.00 0.00 3.73
772 6804 1.274167 GCCGGTAATGGATGGATCGTA 59.726 52.381 1.90 0.00 0.00 3.43
773 6805 2.929592 GCCGGTAATGGATGGATCGTAC 60.930 54.545 1.90 0.00 0.00 3.67
774 6806 2.592194 CGGTAATGGATGGATCGTACG 58.408 52.381 9.53 9.53 0.00 3.67
829 6873 2.749621 AGCCTGCATAAACAACTGCTAC 59.250 45.455 0.00 0.00 39.16 3.58
841 6885 2.428171 CAACTGCTACATCCCCATTTGG 59.572 50.000 0.00 0.00 0.00 3.28
890 6936 1.673665 AGGCTCTTGCTTGCTTCCG 60.674 57.895 0.00 0.00 39.59 4.30
928 6977 3.423154 CTCGTCGCAGCCAAACCC 61.423 66.667 0.00 0.00 0.00 4.11
940 6989 0.392706 CCAAACCCCTTTGACCTTGC 59.607 55.000 0.00 0.00 39.43 4.01
1019 7097 1.377725 CACCCAAGAAGCGCTCCAT 60.378 57.895 12.06 0.00 0.00 3.41
1033 7111 1.473434 GCTCCATAGCTACACCACCAC 60.473 57.143 0.00 0.00 45.85 4.16
1034 7112 1.139058 CTCCATAGCTACACCACCACC 59.861 57.143 0.00 0.00 0.00 4.61
1035 7113 0.908910 CCATAGCTACACCACCACCA 59.091 55.000 0.00 0.00 0.00 4.17
1036 7114 1.280710 CCATAGCTACACCACCACCAA 59.719 52.381 0.00 0.00 0.00 3.67
1038 7116 0.323629 TAGCTACACCACCACCAAGC 59.676 55.000 0.00 0.00 0.00 4.01
1040 7118 1.237285 GCTACACCACCACCAAGCTG 61.237 60.000 0.00 0.00 0.00 4.24
1041 7119 0.396435 CTACACCACCACCAAGCTGA 59.604 55.000 0.00 0.00 0.00 4.26
1042 7120 1.003580 CTACACCACCACCAAGCTGAT 59.996 52.381 0.00 0.00 0.00 2.90
1043 7121 1.064003 ACACCACCACCAAGCTGATA 58.936 50.000 0.00 0.00 0.00 2.15
1044 7122 1.003580 ACACCACCACCAAGCTGATAG 59.996 52.381 0.00 0.00 0.00 2.08
1045 7123 0.035056 ACCACCACCAAGCTGATAGC 60.035 55.000 0.00 0.00 42.84 2.97
1046 7124 0.035152 CCACCACCAAGCTGATAGCA 60.035 55.000 3.43 0.00 45.56 3.49
1203 7281 1.134098 CCTGGCATCCCGTGAGTTATT 60.134 52.381 0.00 0.00 0.00 1.40
1206 7285 2.158957 TGGCATCCCGTGAGTTATTCTC 60.159 50.000 0.00 0.00 43.03 2.87
1219 7299 7.225538 CGTGAGTTATTCTCCTGCTGAATTATT 59.774 37.037 0.00 0.00 42.12 1.40
1225 7305 4.686972 TCTCCTGCTGAATTATTCACTCG 58.313 43.478 3.20 0.00 35.46 4.18
1254 7338 3.069872 TCAACTTCCTTGTTGCATTGCAT 59.930 39.130 12.95 0.00 44.83 3.96
1266 7350 1.346365 CATTGCATCTTGTGTGCTGC 58.654 50.000 0.00 0.00 42.92 5.25
1531 7644 2.586079 CGCGCCACCGAGATCATT 60.586 61.111 0.00 0.00 36.29 2.57
1595 7708 2.485814 GCCAACAAGCTCTTCACTAAGG 59.514 50.000 0.00 0.00 33.22 2.69
1630 7743 2.049802 GTGTTCGTCTTCCCGCGA 60.050 61.111 8.23 0.00 35.17 5.87
1660 7773 1.676967 CTTCCAGCAGAACAGGGGC 60.677 63.158 0.00 0.00 0.00 5.80
1661 7774 2.416107 CTTCCAGCAGAACAGGGGCA 62.416 60.000 0.00 0.00 0.00 5.36
1667 7780 1.228367 CAGAACAGGGGCAACTGCT 60.228 57.895 8.16 0.00 42.21 4.24
1669 7782 1.073897 GAACAGGGGCAACTGCTCT 59.926 57.895 0.82 0.00 42.36 4.09
1678 7791 1.739562 CAACTGCTCTGCCTCCGTC 60.740 63.158 0.00 0.00 0.00 4.79
1825 7938 1.515521 CCGTCAAGGCCAGGTTCAAC 61.516 60.000 5.01 0.00 0.00 3.18
1833 7946 0.393132 GCCAGGTTCAACTAGGGAGC 60.393 60.000 0.00 0.00 0.00 4.70
1922 8036 7.621428 AATGGTAATCAAGTCATCAAGTGAG 57.379 36.000 0.00 0.00 37.56 3.51
1967 8082 8.988064 TGTTGTTGTGTATGTTACATTTGTTT 57.012 26.923 2.23 0.00 41.34 2.83
2000 8115 9.267096 GAGATAATAAAACTTGCTTCTGTTTCG 57.733 33.333 0.00 0.00 35.63 3.46
2004 8119 1.014352 ACTTGCTTCTGTTTCGCGTT 58.986 45.000 5.77 0.00 0.00 4.84
2005 8120 1.268032 ACTTGCTTCTGTTTCGCGTTG 60.268 47.619 5.77 0.00 0.00 4.10
2007 8122 0.303493 TGCTTCTGTTTCGCGTTGTC 59.697 50.000 5.77 0.00 0.00 3.18
2035 8153 3.670625 ACATTTTAGTAGTGCGCCTTGA 58.329 40.909 4.18 0.00 0.00 3.02
2054 8172 7.254898 CGCCTTGATGTCTTGATGTGTTATTAT 60.255 37.037 0.00 0.00 0.00 1.28
2055 8173 9.056005 GCCTTGATGTCTTGATGTGTTATTATA 57.944 33.333 0.00 0.00 0.00 0.98
2103 8221 9.559958 CAAATCTATAACTTGGCAGTAGTTTTG 57.440 33.333 9.66 10.50 37.12 2.44
2106 8224 3.436700 AACTTGGCAGTAGTTTTGCAC 57.563 42.857 0.00 0.00 43.28 4.57
2124 8242 4.980590 TGCACGCTACATTTTTCATAAGG 58.019 39.130 0.00 0.00 0.00 2.69
2125 8243 4.697828 TGCACGCTACATTTTTCATAAGGA 59.302 37.500 0.00 0.00 0.00 3.36
2126 8244 5.028375 GCACGCTACATTTTTCATAAGGAC 58.972 41.667 0.00 0.00 0.00 3.85
2127 8245 5.255596 CACGCTACATTTTTCATAAGGACG 58.744 41.667 0.00 0.00 0.00 4.79
2143 8261 2.081462 GGACGAACCACCCAAATACAG 58.919 52.381 0.00 0.00 38.79 2.74
2148 8266 3.610911 GAACCACCCAAATACAGGAGAG 58.389 50.000 0.00 0.00 0.00 3.20
2198 8317 0.251209 AAGCGGGAGAGGAAAAACCC 60.251 55.000 0.00 0.00 40.05 4.11
2204 8323 1.338864 GGAGAGGAAAAACCCGGAGAC 60.339 57.143 0.73 0.00 40.05 3.36
2206 8325 1.071857 AGAGGAAAAACCCGGAGACAC 59.928 52.381 0.73 0.00 40.05 3.67
2238 8357 3.473625 ACCACCCACGTAAAGAAGAAAG 58.526 45.455 0.00 0.00 0.00 2.62
2251 8370 7.095187 CGTAAAGAAGAAAGCCAACTGATAAGT 60.095 37.037 0.00 0.00 0.00 2.24
2304 8423 3.123621 CGAAGCGTTTGAGTAGCAAGATT 59.876 43.478 0.00 0.00 37.87 2.40
2319 8438 9.643693 AGTAGCAAGATTAAAATTGGAATGTTG 57.356 29.630 13.82 13.82 38.61 3.33
2338 8457 4.159506 TGTTGGCATATAGCTTTTGGGAAC 59.840 41.667 0.00 0.00 44.79 3.62
2345 8464 6.127619 GCATATAGCTTTTGGGAACAGAACTT 60.128 38.462 0.00 0.00 40.72 2.66
2346 8465 5.712152 ATAGCTTTTGGGAACAGAACTTG 57.288 39.130 0.00 0.00 44.54 3.16
2348 8467 4.532834 AGCTTTTGGGAACAGAACTTGTA 58.467 39.130 0.00 0.00 44.54 2.41
2349 8468 4.580580 AGCTTTTGGGAACAGAACTTGTAG 59.419 41.667 0.00 0.00 44.54 2.74
2350 8469 4.338400 GCTTTTGGGAACAGAACTTGTAGT 59.662 41.667 0.00 0.00 44.54 2.73
2351 8470 5.529800 GCTTTTGGGAACAGAACTTGTAGTA 59.470 40.000 0.00 0.00 44.54 1.82
2352 8471 6.512903 GCTTTTGGGAACAGAACTTGTAGTAC 60.513 42.308 0.00 0.00 44.54 2.73
2353 8472 5.617528 TTGGGAACAGAACTTGTAGTACA 57.382 39.130 0.00 0.00 44.54 2.90
2354 8473 5.617528 TGGGAACAGAACTTGTAGTACAA 57.382 39.130 14.85 14.85 39.73 2.41
2356 8475 5.995282 TGGGAACAGAACTTGTAGTACAATG 59.005 40.000 15.91 13.23 39.73 2.82
2357 8476 6.183361 TGGGAACAGAACTTGTAGTACAATGA 60.183 38.462 15.91 0.00 39.73 2.57
2358 8477 6.708949 GGGAACAGAACTTGTAGTACAATGAA 59.291 38.462 15.91 0.00 39.73 2.57
2359 8478 7.307811 GGGAACAGAACTTGTAGTACAATGAAC 60.308 40.741 15.91 10.15 39.73 3.18
2361 8480 8.732746 AACAGAACTTGTAGTACAATGAACTT 57.267 30.769 15.91 3.61 39.73 2.66
2362 8481 8.142994 ACAGAACTTGTAGTACAATGAACTTG 57.857 34.615 15.91 11.75 37.48 3.16
2363 8482 7.769044 ACAGAACTTGTAGTACAATGAACTTGT 59.231 33.333 15.91 12.27 43.81 3.16
2364 8483 9.256477 CAGAACTTGTAGTACAATGAACTTGTA 57.744 33.333 15.91 0.00 46.30 2.41
2409 8528 2.467880 CAACTAGGGGCCTAAGACAGA 58.532 52.381 0.84 0.00 0.00 3.41
2440 8623 7.071321 TCCCCTATCTCCTTATCTCTTTTTGAC 59.929 40.741 0.00 0.00 0.00 3.18
2565 9838 4.701651 TGTTTGCGGATGATTCTTTGATCT 59.298 37.500 0.00 0.00 0.00 2.75
2652 10192 0.974383 AGGGCAGCGTGTAAGTACTT 59.026 50.000 13.68 13.68 0.00 2.24
2836 11370 5.815233 AGAGTTTGTCAGAGATTGAAGGA 57.185 39.130 0.00 0.00 37.61 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.089349 GCGAGCCGGCGATAGAATC 61.089 63.158 23.20 10.39 39.76 2.52
2 3 2.049063 GCGAGCCGGCGATAGAAT 60.049 61.111 23.20 0.00 39.76 2.40
3 4 4.280494 GGCGAGCCGGCGATAGAA 62.280 66.667 23.20 0.00 43.33 2.10
17 18 4.609247 GATCGTCGTCGGAGGGCG 62.609 72.222 17.60 17.60 37.69 6.13
18 19 2.280823 AAAGATCGTCGTCGGAGGGC 62.281 60.000 1.55 0.00 37.69 5.19
19 20 1.019673 TAAAGATCGTCGTCGGAGGG 58.980 55.000 1.55 0.00 37.69 4.30
20 21 2.033049 ACATAAAGATCGTCGTCGGAGG 59.967 50.000 1.55 0.00 37.69 4.30
21 22 3.002451 AGACATAAAGATCGTCGTCGGAG 59.998 47.826 1.55 0.00 37.69 4.63
22 23 2.941064 AGACATAAAGATCGTCGTCGGA 59.059 45.455 1.55 0.00 37.69 4.55
23 24 3.002451 AGAGACATAAAGATCGTCGTCGG 59.998 47.826 1.55 0.00 37.69 4.79
24 25 4.198473 AGAGACATAAAGATCGTCGTCG 57.802 45.455 0.00 0.00 34.80 5.12
25 26 5.570344 TCAAGAGACATAAAGATCGTCGTC 58.430 41.667 0.00 0.00 34.80 4.20
26 27 5.562506 TCAAGAGACATAAAGATCGTCGT 57.437 39.130 0.00 0.00 34.80 4.34
27 28 5.457148 CCTTCAAGAGACATAAAGATCGTCG 59.543 44.000 0.00 0.00 34.80 5.12
28 29 5.751028 CCCTTCAAGAGACATAAAGATCGTC 59.249 44.000 0.00 0.00 0.00 4.20
29 30 5.187967 ACCCTTCAAGAGACATAAAGATCGT 59.812 40.000 0.00 0.00 0.00 3.73
30 31 5.665459 ACCCTTCAAGAGACATAAAGATCG 58.335 41.667 0.00 0.00 0.00 3.69
31 32 6.644347 TGACCCTTCAAGAGACATAAAGATC 58.356 40.000 0.00 0.00 0.00 2.75
32 33 6.627087 TGACCCTTCAAGAGACATAAAGAT 57.373 37.500 0.00 0.00 0.00 2.40
33 34 6.433847 TTGACCCTTCAAGAGACATAAAGA 57.566 37.500 0.00 0.00 36.79 2.52
34 35 6.094603 CCATTGACCCTTCAAGAGACATAAAG 59.905 42.308 0.00 0.00 45.07 1.85
35 36 5.945784 CCATTGACCCTTCAAGAGACATAAA 59.054 40.000 0.00 0.00 45.07 1.40
36 37 5.500234 CCATTGACCCTTCAAGAGACATAA 58.500 41.667 0.00 0.00 45.07 1.90
37 38 4.626287 GCCATTGACCCTTCAAGAGACATA 60.626 45.833 0.00 0.00 45.07 2.29
38 39 3.875369 GCCATTGACCCTTCAAGAGACAT 60.875 47.826 0.00 0.00 45.07 3.06
39 40 2.553028 GCCATTGACCCTTCAAGAGACA 60.553 50.000 0.00 0.00 45.07 3.41
40 41 2.087646 GCCATTGACCCTTCAAGAGAC 58.912 52.381 0.00 0.00 45.07 3.36
41 42 1.988107 AGCCATTGACCCTTCAAGAGA 59.012 47.619 0.00 0.00 45.07 3.10
42 43 2.089980 CAGCCATTGACCCTTCAAGAG 58.910 52.381 0.00 0.00 45.07 2.85
43 44 1.272092 CCAGCCATTGACCCTTCAAGA 60.272 52.381 0.00 0.00 45.07 3.02
44 45 1.180029 CCAGCCATTGACCCTTCAAG 58.820 55.000 0.00 0.00 45.07 3.02
45 46 0.776810 TCCAGCCATTGACCCTTCAA 59.223 50.000 0.00 0.00 45.93 2.69
46 47 0.329261 CTCCAGCCATTGACCCTTCA 59.671 55.000 0.00 0.00 0.00 3.02
47 48 0.620556 TCTCCAGCCATTGACCCTTC 59.379 55.000 0.00 0.00 0.00 3.46
48 49 1.064166 CATCTCCAGCCATTGACCCTT 60.064 52.381 0.00 0.00 0.00 3.95
49 50 0.549950 CATCTCCAGCCATTGACCCT 59.450 55.000 0.00 0.00 0.00 4.34
50 51 1.105759 GCATCTCCAGCCATTGACCC 61.106 60.000 0.00 0.00 0.00 4.46
51 52 0.106819 AGCATCTCCAGCCATTGACC 60.107 55.000 0.00 0.00 0.00 4.02
52 53 1.307097 GAGCATCTCCAGCCATTGAC 58.693 55.000 0.00 0.00 0.00 3.18
53 54 3.794737 GAGCATCTCCAGCCATTGA 57.205 52.632 0.00 0.00 0.00 2.57
61 62 5.750943 TCCTGGTGGTTAGAGCATCTCCA 62.751 52.174 0.00 0.00 36.83 3.86
62 63 3.220066 TCCTGGTGGTTAGAGCATCTCC 61.220 54.545 0.00 0.00 39.77 3.71
63 64 2.111384 TCCTGGTGGTTAGAGCATCTC 58.889 52.381 0.00 0.00 39.77 2.75
64 65 2.237392 GTTCCTGGTGGTTAGAGCATCT 59.763 50.000 0.00 0.00 41.35 2.90
65 66 2.633488 GTTCCTGGTGGTTAGAGCATC 58.367 52.381 0.00 0.00 34.23 3.91
66 67 1.282157 GGTTCCTGGTGGTTAGAGCAT 59.718 52.381 0.00 0.00 34.23 3.79
67 68 0.690762 GGTTCCTGGTGGTTAGAGCA 59.309 55.000 0.00 0.00 34.23 4.26
68 69 0.391263 CGGTTCCTGGTGGTTAGAGC 60.391 60.000 0.00 0.00 34.23 4.09
69 70 0.391263 GCGGTTCCTGGTGGTTAGAG 60.391 60.000 0.00 0.00 34.23 2.43
70 71 1.122632 TGCGGTTCCTGGTGGTTAGA 61.123 55.000 0.00 0.00 34.23 2.10
114 122 4.785453 GAGGGCGAGGGCAACAGG 62.785 72.222 0.00 0.00 42.47 4.00
136 144 6.262496 ACTCAGCCACTGATCATATTCAATTG 59.738 38.462 0.00 0.00 39.92 2.32
216 238 0.109597 GAAATCACGTTGCCCAGCAG 60.110 55.000 0.00 0.00 40.61 4.24
277 299 1.621317 GAACAGCTCTCCTATAGGGGC 59.379 57.143 18.97 18.49 35.00 5.80
352 378 8.055279 TGGTCAATAACTTCATCCTGATTTTC 57.945 34.615 0.00 0.00 0.00 2.29
392 420 5.625197 GCCACTAATCAATTCCACTTGCATT 60.625 40.000 0.00 0.00 0.00 3.56
420 448 1.064166 CCAGATTGATGGGGAGCTGTT 60.064 52.381 0.00 0.00 36.64 3.16
438 466 8.944029 CCAAAACAAAAATGATAATGTATGCCA 58.056 29.630 0.00 0.00 0.00 4.92
443 471 8.778358 GGTTGCCAAAACAAAAATGATAATGTA 58.222 29.630 0.00 0.00 0.00 2.29
445 473 6.796072 CGGTTGCCAAAACAAAAATGATAATG 59.204 34.615 0.00 0.00 0.00 1.90
446 474 6.072783 CCGGTTGCCAAAACAAAAATGATAAT 60.073 34.615 0.00 0.00 0.00 1.28
450 1422 2.939103 CCGGTTGCCAAAACAAAAATGA 59.061 40.909 0.00 0.00 0.00 2.57
453 1425 2.347731 GTCCGGTTGCCAAAACAAAAA 58.652 42.857 0.00 0.00 0.00 1.94
473 1445 4.156622 TACGTCAGACGAGCCGCG 62.157 66.667 29.53 0.00 46.05 6.46
474 1446 2.576317 GTACGTCAGACGAGCCGC 60.576 66.667 29.53 10.01 46.05 6.53
475 1447 2.276493 CGTACGTCAGACGAGCCG 60.276 66.667 29.53 21.16 46.05 5.52
476 1448 2.099831 CCGTACGTCAGACGAGCC 59.900 66.667 29.53 14.28 46.05 4.70
477 1449 1.225963 GACCGTACGTCAGACGAGC 60.226 63.158 29.53 18.40 46.05 5.03
478 1450 1.293963 TGGACCGTACGTCAGACGAG 61.294 60.000 29.53 18.07 46.05 4.18
479 1451 1.301637 TGGACCGTACGTCAGACGA 60.302 57.895 29.53 10.29 46.05 4.20
481 1453 1.154338 CGTGGACCGTACGTCAGAC 60.154 63.158 15.21 10.61 43.95 3.51
482 1454 2.969806 GCGTGGACCGTACGTCAGA 61.970 63.158 15.21 0.44 43.95 3.27
483 1455 2.503375 GCGTGGACCGTACGTCAG 60.503 66.667 15.21 1.10 43.95 3.51
484 1456 3.285982 TGCGTGGACCGTACGTCA 61.286 61.111 15.21 6.80 43.95 4.35
485 1457 2.802414 GTGCGTGGACCGTACGTC 60.802 66.667 15.21 11.40 42.19 4.34
489 1461 2.646719 GTCAGTGCGTGGACCGTA 59.353 61.111 0.00 0.00 39.32 4.02
490 1462 4.640855 CGTCAGTGCGTGGACCGT 62.641 66.667 0.00 0.00 39.32 4.83
491 1463 4.640855 ACGTCAGTGCGTGGACCG 62.641 66.667 11.00 0.00 43.99 4.79
501 1473 1.527611 TCCGAGTCCACACGTCAGT 60.528 57.895 0.00 0.00 0.00 3.41
502 1474 1.081376 GTCCGAGTCCACACGTCAG 60.081 63.158 0.00 0.00 0.00 3.51
503 1475 2.558286 GGTCCGAGTCCACACGTCA 61.558 63.158 0.00 0.00 0.00 4.35
504 1476 2.257676 GGTCCGAGTCCACACGTC 59.742 66.667 0.00 0.00 0.00 4.34
505 1477 3.300765 GGGTCCGAGTCCACACGT 61.301 66.667 0.00 0.00 0.00 4.49
506 1478 3.299977 TGGGTCCGAGTCCACACG 61.300 66.667 0.00 0.00 0.00 4.49
514 1486 4.778415 CTGACGCGTGGGTCCGAG 62.778 72.222 20.70 0.00 36.07 4.63
537 1509 4.708386 TTACGCCCCCTGCCGTTG 62.708 66.667 0.00 0.00 36.24 4.10
538 1510 4.404098 CTTACGCCCCCTGCCGTT 62.404 66.667 0.00 0.00 36.24 4.44
540 1512 4.832608 GACTTACGCCCCCTGCCG 62.833 72.222 0.00 0.00 36.24 5.69
541 1513 3.682292 CTGACTTACGCCCCCTGCC 62.682 68.421 0.00 0.00 36.24 4.85
542 1514 2.125106 CTGACTTACGCCCCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
543 1515 1.961180 CTCCTGACTTACGCCCCCTG 61.961 65.000 0.00 0.00 0.00 4.45
544 1516 1.686110 CTCCTGACTTACGCCCCCT 60.686 63.158 0.00 0.00 0.00 4.79
545 1517 1.049289 ATCTCCTGACTTACGCCCCC 61.049 60.000 0.00 0.00 0.00 5.40
546 1518 0.389757 GATCTCCTGACTTACGCCCC 59.610 60.000 0.00 0.00 0.00 5.80
547 1519 0.389757 GGATCTCCTGACTTACGCCC 59.610 60.000 0.00 0.00 0.00 6.13
548 1520 0.030908 CGGATCTCCTGACTTACGCC 59.969 60.000 0.00 0.00 0.00 5.68
549 1521 0.030908 CCGGATCTCCTGACTTACGC 59.969 60.000 0.00 0.00 0.00 4.42
550 1522 0.030908 GCCGGATCTCCTGACTTACG 59.969 60.000 5.05 0.00 0.00 3.18
551 1523 1.338655 GAGCCGGATCTCCTGACTTAC 59.661 57.143 13.71 0.00 0.00 2.34
552 1524 1.693627 GAGCCGGATCTCCTGACTTA 58.306 55.000 13.71 0.00 0.00 2.24
553 1525 2.510664 GAGCCGGATCTCCTGACTT 58.489 57.895 13.71 0.00 0.00 3.01
554 1526 4.268720 GAGCCGGATCTCCTGACT 57.731 61.111 13.71 0.00 0.00 3.41
560 1532 2.110006 GCCAAGGAGCCGGATCTC 59.890 66.667 20.86 10.21 0.00 2.75
561 1533 2.300967 TTGCCAAGGAGCCGGATCT 61.301 57.895 20.86 0.00 0.00 2.75
562 1534 2.115291 GTTGCCAAGGAGCCGGATC 61.115 63.158 12.38 12.38 0.00 3.36
563 1535 2.044946 GTTGCCAAGGAGCCGGAT 60.045 61.111 5.05 0.00 0.00 4.18
564 1536 4.344865 GGTTGCCAAGGAGCCGGA 62.345 66.667 5.05 0.00 0.00 5.14
565 1537 4.659172 TGGTTGCCAAGGAGCCGG 62.659 66.667 0.00 0.00 0.00 6.13
566 1538 3.365265 GTGGTTGCCAAGGAGCCG 61.365 66.667 0.00 0.00 34.18 5.52
567 1539 2.991540 GGTGGTTGCCAAGGAGCC 60.992 66.667 0.00 0.00 34.18 4.70
568 1540 3.365265 CGGTGGTTGCCAAGGAGC 61.365 66.667 0.00 0.00 34.18 4.70
569 1541 3.365265 GCGGTGGTTGCCAAGGAG 61.365 66.667 0.00 0.00 34.18 3.69
570 1542 4.196778 TGCGGTGGTTGCCAAGGA 62.197 61.111 0.00 0.00 34.18 3.36
571 1543 3.673484 CTGCGGTGGTTGCCAAGG 61.673 66.667 0.00 0.00 34.18 3.61
572 1544 2.594303 TCTGCGGTGGTTGCCAAG 60.594 61.111 0.00 0.00 34.18 3.61
573 1545 2.594303 CTCTGCGGTGGTTGCCAA 60.594 61.111 0.00 0.00 34.18 4.52
574 1546 3.555324 TCTCTGCGGTGGTTGCCA 61.555 61.111 0.00 0.00 0.00 4.92
575 1547 3.050275 GTCTCTGCGGTGGTTGCC 61.050 66.667 0.00 0.00 0.00 4.52
576 1548 2.280797 TGTCTCTGCGGTGGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
585 1557 3.249559 CCAAGTTGAGTTTCTGTCTCTGC 59.750 47.826 3.87 0.00 33.59 4.26
753 2997 2.670229 CGTACGATCCATCCATTACCGG 60.670 54.545 10.44 0.00 0.00 5.28
770 6802 5.127371 GTTTTCGAATCAGATCCACGTAC 57.873 43.478 0.00 0.00 0.00 3.67
823 6867 2.428171 CAACCAAATGGGGATGTAGCAG 59.572 50.000 4.17 0.00 42.91 4.24
824 6868 2.455557 CAACCAAATGGGGATGTAGCA 58.544 47.619 4.17 0.00 42.91 3.49
825 6869 1.756538 CCAACCAAATGGGGATGTAGC 59.243 52.381 4.17 0.00 42.91 3.58
829 6873 0.826062 GAGCCAACCAAATGGGGATG 59.174 55.000 4.17 0.30 42.91 3.51
841 6885 3.588955 GTTCCATGAATTTGGAGCCAAC 58.411 45.455 0.50 0.00 46.22 3.77
855 6899 2.823593 TGCGCATCCGGTTCCATG 60.824 61.111 5.66 0.00 34.32 3.66
862 6906 4.845580 AAGAGCCTGCGCATCCGG 62.846 66.667 12.24 10.73 37.52 5.14
890 6936 2.687566 ACTGGGTCGGATGGGGAC 60.688 66.667 0.00 0.00 0.00 4.46
923 6971 0.106419 TCGCAAGGTCAAAGGGGTTT 60.106 50.000 0.00 0.00 38.47 3.27
925 6974 0.609131 CATCGCAAGGTCAAAGGGGT 60.609 55.000 0.00 0.00 38.47 4.95
928 6977 1.508088 GCCATCGCAAGGTCAAAGG 59.492 57.895 0.00 0.00 38.47 3.11
929 6978 1.135315 CGCCATCGCAAGGTCAAAG 59.865 57.895 0.00 0.00 38.47 2.77
940 6989 1.202568 GATTCGTGCATCGCCATCG 59.797 57.895 0.00 0.00 39.67 3.84
977 7054 0.466124 AATGAGCGAAGGTAGGAGCC 59.534 55.000 0.00 0.00 39.88 4.70
1019 7097 0.323629 GCTTGGTGGTGGTGTAGCTA 59.676 55.000 0.00 0.00 0.00 3.32
1033 7111 1.202268 GCTTGCTTGCTATCAGCTTGG 60.202 52.381 0.00 0.00 42.97 3.61
1034 7112 1.471287 TGCTTGCTTGCTATCAGCTTG 59.529 47.619 0.00 0.00 42.97 4.01
1035 7113 1.830279 TGCTTGCTTGCTATCAGCTT 58.170 45.000 0.00 0.00 42.97 3.74
1036 7114 1.743958 CTTGCTTGCTTGCTATCAGCT 59.256 47.619 0.00 0.00 42.97 4.24
1038 7116 1.471287 TGCTTGCTTGCTTGCTATCAG 59.529 47.619 10.35 0.00 0.00 2.90
1040 7118 2.858344 CAATGCTTGCTTGCTTGCTATC 59.142 45.455 10.35 0.00 0.00 2.08
1041 7119 2.494471 TCAATGCTTGCTTGCTTGCTAT 59.506 40.909 10.35 2.76 0.00 2.97
1042 7120 1.887854 TCAATGCTTGCTTGCTTGCTA 59.112 42.857 10.35 0.00 0.00 3.49
1043 7121 0.677288 TCAATGCTTGCTTGCTTGCT 59.323 45.000 10.35 0.00 0.00 3.91
1044 7122 0.788391 GTCAATGCTTGCTTGCTTGC 59.212 50.000 3.47 0.00 0.00 4.01
1045 7123 1.269883 TGGTCAATGCTTGCTTGCTTG 60.270 47.619 3.47 5.61 0.00 4.01
1046 7124 1.042229 TGGTCAATGCTTGCTTGCTT 58.958 45.000 3.47 0.00 0.00 3.91
1203 7281 4.160439 ACGAGTGAATAATTCAGCAGGAGA 59.840 41.667 0.00 0.00 41.01 3.71
1206 7285 4.437239 AGACGAGTGAATAATTCAGCAGG 58.563 43.478 0.00 0.00 41.01 4.85
1219 7299 3.132289 AGGAAGTTGACAAAGACGAGTGA 59.868 43.478 0.00 0.00 0.00 3.41
1266 7350 3.805267 GGTCAGCAAGATCCAGCG 58.195 61.111 1.78 0.00 35.48 5.18
1425 7538 1.848431 TTCACCCCGGGGAATGACA 60.848 57.895 46.68 24.46 38.96 3.58
1561 7674 0.466372 TGTTGGCGGTGGTGATGAAA 60.466 50.000 0.00 0.00 0.00 2.69
1630 7743 3.241530 TGGAAGTGCACGAGCCCT 61.242 61.111 12.01 0.00 41.13 5.19
1660 7773 1.739562 GACGGAGGCAGAGCAGTTG 60.740 63.158 0.00 0.00 0.00 3.16
1661 7774 1.548357 ATGACGGAGGCAGAGCAGTT 61.548 55.000 0.00 0.00 0.00 3.16
1667 7780 3.838271 GGCGATGACGGAGGCAGA 61.838 66.667 0.00 0.00 40.15 4.26
1678 7791 2.787249 CTGTTGAAGGCGGCGATG 59.213 61.111 12.98 0.00 0.00 3.84
1686 7799 0.879765 CTGAAGCTGGCTGTTGAAGG 59.120 55.000 0.00 0.00 0.00 3.46
1816 7929 1.208293 GAGGCTCCCTAGTTGAACCTG 59.792 57.143 2.15 0.00 31.76 4.00
1860 7973 7.611213 ACAGACGATTATTTTCTTCCGAAAT 57.389 32.000 0.00 0.00 38.81 2.17
1905 8019 4.283363 ACAGCTCACTTGATGACTTGAT 57.717 40.909 0.00 0.00 32.37 2.57
1922 8036 3.432252 ACAAATCAACTACACGCTACAGC 59.568 43.478 0.00 0.00 37.78 4.40
1936 8050 9.809096 AATGTAACATACACAACAACAAATCAA 57.191 25.926 0.00 0.00 42.23 2.57
1978 8093 5.849081 CGCGAAACAGAAGCAAGTTTTATTA 59.151 36.000 0.00 0.00 38.01 0.98
2000 8115 8.866956 ACTACTAAAATGTAACATAGACAACGC 58.133 33.333 0.00 0.00 0.00 4.84
2004 8119 7.009815 GCGCACTACTAAAATGTAACATAGACA 59.990 37.037 0.30 0.00 0.00 3.41
2005 8120 7.335491 GCGCACTACTAAAATGTAACATAGAC 58.665 38.462 0.30 0.00 0.00 2.59
2007 8122 6.479001 AGGCGCACTACTAAAATGTAACATAG 59.521 38.462 10.83 0.00 0.00 2.23
2068 8186 7.230510 TGCCAAGTTATAGATTTGTTGACTTGT 59.769 33.333 11.07 0.00 40.29 3.16
2070 8188 7.448469 ACTGCCAAGTTATAGATTTGTTGACTT 59.552 33.333 0.00 0.00 30.14 3.01
2071 8189 6.942576 ACTGCCAAGTTATAGATTTGTTGACT 59.057 34.615 0.00 0.00 30.14 3.41
2075 8193 8.863872 AACTACTGCCAAGTTATAGATTTGTT 57.136 30.769 0.00 0.00 37.88 2.83
2088 8206 1.925946 GCGTGCAAAACTACTGCCAAG 60.926 52.381 0.00 0.00 39.13 3.61
2103 8221 5.028375 GTCCTTATGAAAAATGTAGCGTGC 58.972 41.667 0.00 0.00 0.00 5.34
2106 8224 5.712217 TCGTCCTTATGAAAAATGTAGCG 57.288 39.130 0.00 0.00 0.00 4.26
2124 8242 2.081462 CCTGTATTTGGGTGGTTCGTC 58.919 52.381 0.00 0.00 0.00 4.20
2125 8243 1.700739 TCCTGTATTTGGGTGGTTCGT 59.299 47.619 0.00 0.00 0.00 3.85
2126 8244 2.027561 TCTCCTGTATTTGGGTGGTTCG 60.028 50.000 0.00 0.00 0.00 3.95
2127 8245 3.610911 CTCTCCTGTATTTGGGTGGTTC 58.389 50.000 0.00 0.00 0.00 3.62
2143 8261 3.784701 TCTCATACGACAAAGCTCTCC 57.215 47.619 0.00 0.00 0.00 3.71
2179 8298 0.251209 GGGTTTTTCCTCTCCCGCTT 60.251 55.000 0.00 0.00 36.25 4.68
2214 8333 3.888583 TCTTCTTTACGTGGGTGGTTTT 58.111 40.909 0.00 0.00 0.00 2.43
2238 8357 3.431486 CCCTCTCTCACTTATCAGTTGGC 60.431 52.174 0.00 0.00 0.00 4.52
2251 8370 0.178915 TCCCGGTTTTCCCTCTCTCA 60.179 55.000 0.00 0.00 36.42 3.27
2294 8413 8.872845 CCAACATTCCAATTTTAATCTTGCTAC 58.127 33.333 0.00 0.00 0.00 3.58
2304 8423 8.248904 AGCTATATGCCAACATTCCAATTTTA 57.751 30.769 0.00 0.00 44.23 1.52
2319 8438 4.207165 TCTGTTCCCAAAAGCTATATGCC 58.793 43.478 0.00 0.00 44.23 4.40
2325 8444 4.532834 ACAAGTTCTGTTCCCAAAAGCTA 58.467 39.130 0.00 0.00 32.99 3.32
2326 8445 3.365472 ACAAGTTCTGTTCCCAAAAGCT 58.635 40.909 0.00 0.00 32.99 3.74
2327 8446 3.801114 ACAAGTTCTGTTCCCAAAAGC 57.199 42.857 0.00 0.00 32.99 3.51
2353 8472 9.737427 CGTCTGTCTCTATATTACAAGTTCATT 57.263 33.333 0.00 0.00 0.00 2.57
2354 8473 9.121658 TCGTCTGTCTCTATATTACAAGTTCAT 57.878 33.333 0.00 0.00 0.00 2.57
2356 8475 9.953697 ATTCGTCTGTCTCTATATTACAAGTTC 57.046 33.333 0.00 0.00 0.00 3.01
2364 8483 8.692710 TGGTGTAAATTCGTCTGTCTCTATATT 58.307 33.333 0.00 0.00 0.00 1.28
2409 8528 5.559545 AGAGATAAGGAGATAGGGGATCACT 59.440 44.000 0.00 0.00 36.98 3.41
2440 8623 5.188434 TGCTTGATAATCCTTCAGAACAGG 58.812 41.667 0.00 0.00 0.00 4.00
2565 9838 3.617284 TCTGTACCGTAGCTCTCATGAA 58.383 45.455 0.00 0.00 0.00 2.57
2652 10192 7.038017 AGGACTGAAGAAGATACTGGATTTTGA 60.038 37.037 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.