Multiple sequence alignment - TraesCS1A01G375300

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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 TraesCS1A01G375300 chr1A 100.000 4720 0 0 1 4720 550139109 550134390 0.000000e+00 8717.0
1 TraesCS1A01G375300 chr1A 84.763 1667 197 46 2396 4029 550217981 550219623 0.000000e+00 1618.0
2 TraesCS1A01G375300 chr1A 82.585 1872 197 52 1692 3494 550298585 550300396 0.000000e+00 1531.0
3 TraesCS1A01G375300 chr1A 82.486 708 85 21 2200 2887 550209993 550210681 6.810000e-163 584.0
4 TraesCS1A01G375300 chr1A 85.610 549 74 3 3227 3772 550210996 550211542 5.300000e-159 571.0
5 TraesCS1A01G375300 chr1A 87.568 370 29 12 1322 1676 550298128 550298495 3.400000e-111 412.0
6 TraesCS1A01G375300 chr1A 88.312 231 27 0 1457 1687 550216957 550217187 1.290000e-70 278.0
7 TraesCS1A01G375300 chr1A 84.328 268 42 0 1859 2126 550209382 550209649 3.620000e-66 263.0
8 TraesCS1A01G375300 chr1A 84.772 197 19 3 1692 1886 550217264 550217451 2.240000e-43 187.0
9 TraesCS1A01G375300 chr1A 85.027 187 22 2 4033 4214 361061675 361061490 8.070000e-43 185.0
10 TraesCS1A01G375300 chr1A 82.022 178 22 5 924 1098 550297414 550297584 4.920000e-30 143.0
11 TraesCS1A01G375300 chr1A 84.848 132 15 2 957 1085 550216569 550216698 1.380000e-25 128.0
12 TraesCS1A01G375300 chr1A 82.877 146 15 6 518 654 550196548 550196692 6.410000e-24 122.0
13 TraesCS1A01G375300 chr1D 95.086 3846 112 25 756 4560 457549159 457545350 0.000000e+00 5984.0
14 TraesCS1A01G375300 chr1D 82.796 2139 229 61 1876 3941 457844632 457846704 0.000000e+00 1783.0
15 TraesCS1A01G375300 chr1D 82.631 783 101 9 3267 4015 457584233 457585014 0.000000e+00 660.0
16 TraesCS1A01G375300 chr1D 82.254 710 84 20 2200 2887 457820592 457821281 4.100000e-160 575.0
17 TraesCS1A01G375300 chr1D 89.474 437 42 4 2396 2829 457583466 457583901 2.480000e-152 549.0
18 TraesCS1A01G375300 chr1D 81.997 661 79 27 3022 3654 457821365 457822013 4.180000e-145 525.0
19 TraesCS1A01G375300 chr1D 87.467 375 37 7 1322 1687 457582377 457582750 1.570000e-114 424.0
20 TraesCS1A01G375300 chr1D 86.704 361 21 12 55 395 457549881 457549528 4.460000e-100 375.0
21 TraesCS1A01G375300 chr1D 83.727 381 46 8 1985 2355 226467834 226468208 3.500000e-91 346.0
22 TraesCS1A01G375300 chr1D 81.560 423 44 17 1692 2088 457812513 457812927 7.620000e-83 318.0
23 TraesCS1A01G375300 chr1D 85.666 293 32 7 1404 1687 457812138 457812429 2.760000e-77 300.0
24 TraesCS1A01G375300 chr1D 85.714 287 32 6 1404 1682 457811626 457811911 1.280000e-75 294.0
25 TraesCS1A01G375300 chr1D 95.031 161 8 0 4560 4720 108260402 108260562 2.180000e-63 254.0
26 TraesCS1A01G375300 chr1D 95.031 161 8 0 4560 4720 143601057 143600897 2.180000e-63 254.0
27 TraesCS1A01G375300 chr1D 95.031 161 8 0 4560 4720 326148269 326148109 2.180000e-63 254.0
28 TraesCS1A01G375300 chr1D 84.889 225 25 6 845 1067 457581582 457581799 7.950000e-53 219.0
29 TraesCS1A01G375300 chr1D 86.432 199 15 7 1692 1886 457582829 457583019 1.720000e-49 207.0
30 TraesCS1A01G375300 chr1D 89.510 143 12 1 512 654 457549321 457549182 1.350000e-40 178.0
31 TraesCS1A01G375300 chr1D 85.915 142 17 3 3519 3657 457822013 457822154 1.060000e-31 148.0
32 TraesCS1A01G375300 chr1D 84.173 139 14 5 966 1098 457806983 457807119 1.380000e-25 128.0
33 TraesCS1A01G375300 chr1D 90.000 90 9 0 557 646 457581358 457581447 2.980000e-22 117.0
34 TraesCS1A01G375300 chr1B 94.436 1995 59 16 2107 4078 627157407 627155442 0.000000e+00 3022.0
35 TraesCS1A01G375300 chr1B 92.038 1369 60 16 756 2084 627158758 627157399 0.000000e+00 1879.0
36 TraesCS1A01G375300 chr1B 83.508 1049 114 28 1893 2894 627923420 627924456 0.000000e+00 924.0
37 TraesCS1A01G375300 chr1B 83.721 946 115 16 3024 3941 627924564 627925498 0.000000e+00 857.0
38 TraesCS1A01G375300 chr1B 85.795 704 81 8 3105 3793 627783225 627783924 0.000000e+00 728.0
39 TraesCS1A01G375300 chr1B 85.689 573 77 2 3203 3772 627887481 627888051 2.430000e-167 599.0
40 TraesCS1A01G375300 chr1B 87.382 531 53 10 2396 2919 627782560 627783083 8.740000e-167 597.0
41 TraesCS1A01G375300 chr1B 82.930 703 76 22 2200 2878 627886504 627887186 1.130000e-165 593.0
42 TraesCS1A01G375300 chr1B 85.000 580 60 12 1322 1886 627922876 627923443 8.870000e-157 564.0
43 TraesCS1A01G375300 chr1B 94.099 322 18 1 4084 4405 627154753 627154433 5.490000e-134 488.0
44 TraesCS1A01G375300 chr1B 86.149 296 31 7 1398 1684 627885354 627885648 1.280000e-80 311.0
45 TraesCS1A01G375300 chr1B 83.243 370 27 14 55 395 627159492 627159129 1.650000e-79 307.0
46 TraesCS1A01G375300 chr1B 80.896 424 42 12 1692 2092 627885894 627886301 9.930000e-77 298.0
47 TraesCS1A01G375300 chr1B 84.615 247 24 6 3780 4015 627888090 627888333 2.840000e-57 233.0
48 TraesCS1A01G375300 chr1B 78.157 293 42 16 822 1098 627884604 627884890 2.920000e-37 167.0
49 TraesCS1A01G375300 chr1B 89.908 109 4 5 422 526 627159048 627158943 2.960000e-27 134.0
50 TraesCS1A01G375300 chr1B 87.778 90 7 1 546 631 627884379 627884468 8.360000e-18 102.0
51 TraesCS1A01G375300 chr1B 91.379 58 5 0 2930 2987 627924453 627924510 3.920000e-11 80.5
52 TraesCS1A01G375300 chr3A 83.789 475 65 8 1891 2355 668583194 668583666 1.560000e-119 440.0
53 TraesCS1A01G375300 chr3A 84.000 350 47 5 2013 2355 668225506 668225853 1.270000e-85 327.0
54 TraesCS1A01G375300 chr3B 82.463 479 68 8 1891 2355 705148047 705148523 5.690000e-109 405.0
55 TraesCS1A01G375300 chr3B 94.512 164 8 1 4557 4720 541524031 541524193 7.840000e-63 252.0
56 TraesCS1A01G375300 chr7A 95.652 161 7 0 4560 4720 245981775 245981935 4.690000e-65 259.0
57 TraesCS1A01G375300 chr5D 94.643 168 8 1 4553 4720 443496137 443496303 4.690000e-65 259.0
58 TraesCS1A01G375300 chr5D 93.204 103 4 3 670 770 322375833 322375732 1.060000e-31 148.0
59 TraesCS1A01G375300 chr5A 95.652 161 7 0 4560 4720 638757494 638757654 4.690000e-65 259.0
60 TraesCS1A01G375300 chr7D 95.031 161 8 0 4560 4720 23081957 23081797 2.180000e-63 254.0
61 TraesCS1A01G375300 chr7D 90.826 109 9 1 660 768 34845547 34845654 1.370000e-30 145.0
62 TraesCS1A01G375300 chr7D 86.154 130 13 5 638 766 535305171 535305046 8.240000e-28 135.0
63 TraesCS1A01G375300 chr4D 95.031 161 8 0 4560 4720 43650412 43650572 2.180000e-63 254.0
64 TraesCS1A01G375300 chr2B 94.175 103 5 1 654 756 775395968 775396069 6.320000e-34 156.0
65 TraesCS1A01G375300 chr2B 95.833 96 1 2 659 754 31741623 31741715 8.180000e-33 152.0
66 TraesCS1A01G375300 chr3D 94.949 99 4 1 667 765 554346114 554346211 2.270000e-33 154.0
67 TraesCS1A01G375300 chr3D 100.000 30 0 0 576 605 332234911 332234882 6.600000e-04 56.5
68 TraesCS1A01G375300 chr2D 92.453 106 6 2 658 763 82187146 82187249 2.940000e-32 150.0
69 TraesCS1A01G375300 chr2A 87.705 122 10 5 660 781 777289160 777289276 2.290000e-28 137.0
70 TraesCS1A01G375300 chr2A 88.596 114 9 4 672 785 102901031 102900922 8.240000e-28 135.0


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 TraesCS1A01G375300 chr1A 550134390 550139109 4719 True 8717.000000 8717 100.000000 1 4720 1 chr1A.!!$R2 4719
1 TraesCS1A01G375300 chr1A 550297414 550300396 2982 False 695.333333 1531 84.058333 924 3494 3 chr1A.!!$F4 2570
2 TraesCS1A01G375300 chr1A 550216569 550219623 3054 False 552.750000 1618 85.673750 957 4029 4 chr1A.!!$F3 3072
3 TraesCS1A01G375300 chr1A 550209382 550211542 2160 False 472.666667 584 84.141333 1859 3772 3 chr1A.!!$F2 1913
4 TraesCS1A01G375300 chr1D 457545350 457549881 4531 True 2179.000000 5984 90.433333 55 4560 3 chr1D.!!$R3 4505
5 TraesCS1A01G375300 chr1D 457844632 457846704 2072 False 1783.000000 1783 82.796000 1876 3941 1 chr1D.!!$F4 2065
6 TraesCS1A01G375300 chr1D 457820592 457822154 1562 False 416.000000 575 83.388667 2200 3657 3 chr1D.!!$F7 1457
7 TraesCS1A01G375300 chr1D 457581358 457585014 3656 False 362.666667 660 86.815500 557 4015 6 chr1D.!!$F5 3458
8 TraesCS1A01G375300 chr1D 457811626 457812927 1301 False 304.000000 318 84.313333 1404 2088 3 chr1D.!!$F6 684
9 TraesCS1A01G375300 chr1B 627154433 627159492 5059 True 1166.000000 3022 90.744800 55 4405 5 chr1B.!!$R1 4350
10 TraesCS1A01G375300 chr1B 627782560 627783924 1364 False 662.500000 728 86.588500 2396 3793 2 chr1B.!!$F1 1397
11 TraesCS1A01G375300 chr1B 627922876 627925498 2622 False 606.375000 924 85.902000 1322 3941 4 chr1B.!!$F3 2619
12 TraesCS1A01G375300 chr1B 627884379 627888333 3954 False 329.000000 599 83.744857 546 4015 7 chr1B.!!$F2 3469

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
434 519 0.249489 GTCCAGATCCCGGAATCGTG 60.249 60.000 0.73 0.00 33.29 4.35 F
657 787 0.511653 GTTTCGACTTTCAGGGCGAC 59.488 55.000 0.00 0.00 31.91 5.19 F
1242 1752 1.074244 TGGTTAGGTGGGCCACTTTAC 59.926 52.381 33.87 28.91 37.19 2.01 F
2131 3609 1.270518 CCATCATCTTAGCTGGGACGG 60.271 57.143 0.00 0.00 38.10 4.79 F
3418 5426 0.390472 GAGTCCAGGAAGGTGCTTCG 60.390 60.000 0.00 0.00 40.99 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 3702 1.271054 ACTGGTGATGCAGTCAAGACC 60.271 52.381 0.00 0.0 38.90 3.85 R
2637 4432 2.609491 CCACGACAGACTTCATTTCGGA 60.609 50.000 0.00 0.0 33.97 4.55 R
2974 4850 1.875514 CATGACCATTGGCTATCGGTG 59.124 52.381 1.54 0.0 0.00 4.94 R
3620 5775 1.205893 AGATCGTGGAGTTCCTTGAGC 59.794 52.381 0.00 0.7 36.82 4.26 R
4568 7502 0.468226 TGTGGGCCTAGCTAAATCGG 59.532 55.000 4.53 0.0 0.00 4.18 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
25 26 8.922058 GACTCCGATTGTACATAGTTAAAGAA 57.078 34.615 0.00 0.00 0.00 2.52
26 27 9.362539 GACTCCGATTGTACATAGTTAAAGAAA 57.637 33.333 0.00 0.00 0.00 2.52
27 28 9.715121 ACTCCGATTGTACATAGTTAAAGAAAA 57.285 29.630 0.00 0.00 0.00 2.29
29 30 8.662141 TCCGATTGTACATAGTTAAAGAAAAGC 58.338 33.333 0.00 0.00 0.00 3.51
30 31 8.447833 CCGATTGTACATAGTTAAAGAAAAGCA 58.552 33.333 0.00 0.00 0.00 3.91
31 32 9.988350 CGATTGTACATAGTTAAAGAAAAGCAT 57.012 29.630 0.00 0.00 0.00 3.79
35 36 9.891828 TGTACATAGTTAAAGAAAAGCATTGTG 57.108 29.630 0.00 0.00 0.00 3.33
36 37 9.893305 GTACATAGTTAAAGAAAAGCATTGTGT 57.107 29.630 0.00 0.00 0.00 3.72
37 38 8.801715 ACATAGTTAAAGAAAAGCATTGTGTG 57.198 30.769 0.00 0.00 0.00 3.82
38 39 8.413229 ACATAGTTAAAGAAAAGCATTGTGTGT 58.587 29.630 0.00 0.00 0.00 3.72
39 40 8.693504 CATAGTTAAAGAAAAGCATTGTGTGTG 58.306 33.333 0.00 0.00 0.00 3.82
40 41 6.630071 AGTTAAAGAAAAGCATTGTGTGTGT 58.370 32.000 0.00 0.00 0.00 3.72
41 42 6.531240 AGTTAAAGAAAAGCATTGTGTGTGTG 59.469 34.615 0.00 0.00 0.00 3.82
42 43 4.454728 AAGAAAAGCATTGTGTGTGTGT 57.545 36.364 0.00 0.00 0.00 3.72
43 44 3.772932 AGAAAAGCATTGTGTGTGTGTG 58.227 40.909 0.00 0.00 0.00 3.82
44 45 3.193267 AGAAAAGCATTGTGTGTGTGTGT 59.807 39.130 0.00 0.00 0.00 3.72
45 46 2.565210 AAGCATTGTGTGTGTGTGTG 57.435 45.000 0.00 0.00 0.00 3.82
46 47 1.462616 AGCATTGTGTGTGTGTGTGT 58.537 45.000 0.00 0.00 0.00 3.72
47 48 1.132834 AGCATTGTGTGTGTGTGTGTG 59.867 47.619 0.00 0.00 0.00 3.82
48 49 1.135431 GCATTGTGTGTGTGTGTGTGT 60.135 47.619 0.00 0.00 0.00 3.72
49 50 2.517935 CATTGTGTGTGTGTGTGTGTG 58.482 47.619 0.00 0.00 0.00 3.82
50 51 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
51 52 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
52 53 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
53 54 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
58 59 2.675844 GTGTGTGTGTGTGTGTGTGTAT 59.324 45.455 0.00 0.00 0.00 2.29
113 121 3.581755 TGCTACATGTTACGAACTCACC 58.418 45.455 2.30 0.00 0.00 4.02
118 126 1.873698 TGTTACGAACTCACCAAGGC 58.126 50.000 0.00 0.00 0.00 4.35
129 137 2.124695 CCAAGGCGGGCTACCTTC 60.125 66.667 3.84 0.00 44.35 3.46
213 222 3.560896 ACGCGGCTTACAAAAGTAAGAAA 59.439 39.130 12.47 0.00 38.76 2.52
215 224 5.151389 CGCGGCTTACAAAAGTAAGAAATT 58.849 37.500 17.01 0.00 38.76 1.82
217 226 6.964934 CGCGGCTTACAAAAGTAAGAAATTAT 59.035 34.615 17.01 0.00 38.76 1.28
218 227 7.163682 CGCGGCTTACAAAAGTAAGAAATTATC 59.836 37.037 17.01 0.60 38.76 1.75
219 228 7.431376 GCGGCTTACAAAAGTAAGAAATTATCC 59.569 37.037 17.01 7.43 38.76 2.59
220 229 7.913821 CGGCTTACAAAAGTAAGAAATTATCCC 59.086 37.037 17.01 6.87 38.76 3.85
250 275 8.879342 ACATTTTTCTAGATTGATAGGTCTCG 57.121 34.615 0.00 0.00 0.00 4.04
251 276 8.696374 ACATTTTTCTAGATTGATAGGTCTCGA 58.304 33.333 0.00 0.00 0.00 4.04
277 302 5.420409 GCAATAAGGGAGATATAGGGTTCG 58.580 45.833 0.00 0.00 0.00 3.95
293 318 4.963428 CGCGCGGAATCCTACCCC 62.963 72.222 24.84 0.00 0.00 4.95
319 349 2.255554 GACGCTGAGTCGCTGACA 59.744 61.111 10.52 0.00 40.43 3.58
320 350 1.371758 GACGCTGAGTCGCTGACAA 60.372 57.895 10.52 0.00 40.43 3.18
386 416 4.556233 GACGATGGATCAAATCATCCGTA 58.444 43.478 8.01 0.00 45.03 4.02
387 417 4.560128 ACGATGGATCAAATCATCCGTAG 58.440 43.478 8.01 0.00 45.03 3.51
388 418 4.280929 ACGATGGATCAAATCATCCGTAGA 59.719 41.667 8.34 0.00 45.03 2.59
389 419 5.047021 ACGATGGATCAAATCATCCGTAGAT 60.047 40.000 8.34 0.00 45.03 1.98
391 421 6.183360 CGATGGATCAAATCATCCGTAGATTG 60.183 42.308 8.01 0.00 45.03 2.67
392 422 4.756642 TGGATCAAATCATCCGTAGATTGC 59.243 41.667 0.00 0.00 45.03 3.56
393 423 4.756642 GGATCAAATCATCCGTAGATTGCA 59.243 41.667 0.00 0.00 35.96 4.08
414 461 4.731773 GCAAATCCGTTTGAGATGGACATC 60.732 45.833 4.15 4.15 46.12 3.06
434 519 0.249489 GTCCAGATCCCGGAATCGTG 60.249 60.000 0.73 0.00 33.29 4.35
446 531 1.134610 GGAATCGTGTGGTTACCGGAT 60.135 52.381 9.46 0.00 0.00 4.18
481 567 5.503683 CGTCGTGATATATATCCCCGAGTTC 60.504 48.000 23.91 16.08 36.45 3.01
571 697 2.934886 AACCAAGCCATTGTGCAATT 57.065 40.000 0.00 0.00 34.39 2.32
574 700 2.158784 ACCAAGCCATTGTGCAATTTGT 60.159 40.909 0.00 0.00 34.39 2.83
655 785 1.574702 GGGTTTCGACTTTCAGGGCG 61.575 60.000 0.00 0.00 0.00 6.13
656 786 0.601841 GGTTTCGACTTTCAGGGCGA 60.602 55.000 0.00 0.00 0.00 5.54
657 787 0.511653 GTTTCGACTTTCAGGGCGAC 59.488 55.000 0.00 0.00 31.91 5.19
673 803 4.486574 GGCGACCTAGTATCAAGTACTC 57.513 50.000 0.00 0.00 42.63 2.59
674 804 3.252944 GGCGACCTAGTATCAAGTACTCC 59.747 52.174 0.00 0.00 42.63 3.85
678 808 5.064314 ACCTAGTATCAAGTACTCCCTCC 57.936 47.826 0.00 0.00 42.63 4.30
679 809 4.073549 CCTAGTATCAAGTACTCCCTCCG 58.926 52.174 0.00 0.00 42.63 4.63
680 810 3.666345 AGTATCAAGTACTCCCTCCGT 57.334 47.619 0.00 0.00 39.46 4.69
681 811 4.785346 AGTATCAAGTACTCCCTCCGTA 57.215 45.455 0.00 0.00 39.46 4.02
682 812 5.121380 AGTATCAAGTACTCCCTCCGTAA 57.879 43.478 0.00 0.00 39.46 3.18
683 813 5.513233 AGTATCAAGTACTCCCTCCGTAAA 58.487 41.667 0.00 0.00 39.46 2.01
684 814 4.732672 ATCAAGTACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
685 815 3.771216 TCAAGTACTCCCTCCGTAAACT 58.229 45.455 0.00 0.00 0.00 2.66
686 816 4.922206 TCAAGTACTCCCTCCGTAAACTA 58.078 43.478 0.00 0.00 0.00 2.24
687 817 5.324409 TCAAGTACTCCCTCCGTAAACTAA 58.676 41.667 0.00 0.00 0.00 2.24
688 818 5.954150 TCAAGTACTCCCTCCGTAAACTAAT 59.046 40.000 0.00 0.00 0.00 1.73
689 819 7.118723 TCAAGTACTCCCTCCGTAAACTAATA 58.881 38.462 0.00 0.00 0.00 0.98
690 820 7.781693 TCAAGTACTCCCTCCGTAAACTAATAT 59.218 37.037 0.00 0.00 0.00 1.28
691 821 9.071276 CAAGTACTCCCTCCGTAAACTAATATA 57.929 37.037 0.00 0.00 0.00 0.86
692 822 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
693 823 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
694 824 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
695 825 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
696 826 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
697 827 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
698 828 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
699 829 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
700 830 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
701 831 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
702 832 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
703 833 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
715 845 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
716 846 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
730 860 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
731 861 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
732 862 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
733 863 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
745 875 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
746 876 6.760161 AACGCTCTTATATTAGTTTACGGC 57.240 37.500 0.00 0.00 0.00 5.68
747 877 4.913924 ACGCTCTTATATTAGTTTACGGCG 59.086 41.667 4.80 4.80 42.65 6.46
748 878 4.322804 CGCTCTTATATTAGTTTACGGCGG 59.677 45.833 13.24 0.00 35.20 6.13
749 879 4.624452 GCTCTTATATTAGTTTACGGCGGG 59.376 45.833 13.24 0.00 0.00 6.13
750 880 5.565439 GCTCTTATATTAGTTTACGGCGGGA 60.565 44.000 13.24 0.00 0.00 5.14
751 881 6.017400 TCTTATATTAGTTTACGGCGGGAG 57.983 41.667 13.24 0.00 0.00 4.30
752 882 5.536161 TCTTATATTAGTTTACGGCGGGAGT 59.464 40.000 13.24 1.73 0.00 3.85
753 883 6.714810 TCTTATATTAGTTTACGGCGGGAGTA 59.285 38.462 13.24 0.67 0.00 2.59
754 884 2.939460 TTAGTTTACGGCGGGAGTAC 57.061 50.000 13.24 1.68 0.00 2.73
1117 1331 9.010029 CAACAATTAATCCCTTGTAAGTACACT 57.990 33.333 0.00 0.00 34.61 3.55
1242 1752 1.074244 TGGTTAGGTGGGCCACTTTAC 59.926 52.381 33.87 28.91 37.19 2.01
1363 1942 9.650539 CATCCATATAACCTGAACATAGAGAAG 57.349 37.037 0.00 0.00 0.00 2.85
1531 2638 2.586648 AGGAAAGACCCATGTTCCAC 57.413 50.000 12.97 0.00 42.81 4.02
1788 3144 7.394077 TGAGGATGCATCAAGTGAAGAAATTAA 59.606 33.333 27.25 0.00 0.00 1.40
1789 3145 8.125978 AGGATGCATCAAGTGAAGAAATTAAA 57.874 30.769 27.25 0.00 0.00 1.52
2084 3513 7.994425 ATGTGTTTGTTCAAGTACATCCATA 57.006 32.000 0.00 0.00 0.00 2.74
2129 3607 3.072184 ACATCCATCATCTTAGCTGGGAC 59.928 47.826 0.00 0.00 0.00 4.46
2130 3608 1.688735 TCCATCATCTTAGCTGGGACG 59.311 52.381 0.00 0.00 0.00 4.79
2131 3609 1.270518 CCATCATCTTAGCTGGGACGG 60.271 57.143 0.00 0.00 38.10 4.79
2132 3610 1.688735 CATCATCTTAGCTGGGACGGA 59.311 52.381 0.00 0.00 36.31 4.69
2356 4117 7.279981 AGAGTACATATGCATGTTCGCTTTTTA 59.720 33.333 10.16 0.00 42.98 1.52
2435 4228 5.476091 TGCGGGAAAAGGTTGATTATTTT 57.524 34.783 0.00 0.00 0.00 1.82
2674 4469 3.751698 GTCGTGGTTCAGAAAAAGGCTAT 59.248 43.478 0.00 0.00 0.00 2.97
2714 4509 4.226427 TGTCCAGAAGAAGGGATTCATG 57.774 45.455 0.00 0.00 35.25 3.07
2715 4510 3.054139 TGTCCAGAAGAAGGGATTCATGG 60.054 47.826 0.00 0.00 35.25 3.66
2985 4861 1.423584 ATGGACATCACCGATAGCCA 58.576 50.000 0.00 0.00 32.04 4.75
3059 4959 7.775053 TTAAGCATGGAACCAAATAACTCTT 57.225 32.000 0.00 0.00 0.00 2.85
3198 5123 0.539986 AATGGGTGTACCTGCCTACG 59.460 55.000 0.44 0.00 41.11 3.51
3222 5178 1.889545 AGCTCAGCCACAACTTTCTC 58.110 50.000 0.00 0.00 0.00 2.87
3418 5426 0.390472 GAGTCCAGGAAGGTGCTTCG 60.390 60.000 0.00 0.00 40.99 3.79
3452 5460 3.564133 CCATCCTGGACCAAAAGAATGGA 60.564 47.826 0.00 6.62 40.69 3.41
3461 5469 8.713708 TGGACCAAAAGAATGGAAAATACTTA 57.286 30.769 0.00 0.00 43.54 2.24
3620 5775 1.079127 ATGGTCCGACTTCTTGCCG 60.079 57.895 0.00 0.00 0.00 5.69
3644 5799 1.924731 AGGAACTCCACGATCTGTCA 58.075 50.000 0.00 0.00 38.89 3.58
3739 5894 2.125106 GCTTACCTCGTGGCCTGG 60.125 66.667 3.32 3.56 36.63 4.45
3864 6084 7.256756 AGTTCACAAGAAGTCAAGAAATGAG 57.743 36.000 0.00 0.00 39.19 2.90
3957 6204 6.128472 CGATCATGTCAGTTTGATGAGTTTCA 60.128 38.462 0.00 0.00 32.84 2.69
3988 6235 3.217626 GGTTCCATGATCCCATCTTCAC 58.782 50.000 0.00 0.00 0.00 3.18
4045 6292 5.408604 CGTTAGTGGACTTGCTACAAATTCT 59.591 40.000 0.00 0.00 0.00 2.40
4082 7012 6.096001 AGGCAATGATTTTGGTCTTCTATGTC 59.904 38.462 0.00 0.00 0.00 3.06
4192 7122 9.866655 TTACATCCATTTAATATTGCTTCCTCT 57.133 29.630 0.00 0.00 0.00 3.69
4207 7137 4.624882 GCTTCCTCTACATGATTATCTGCG 59.375 45.833 0.00 0.00 0.00 5.18
4284 7214 1.273327 GACTTCATTGGTTGCCCTTGG 59.727 52.381 0.00 0.00 0.00 3.61
4289 7219 0.105760 ATTGGTTGCCCTTGGTGTGA 60.106 50.000 0.00 0.00 0.00 3.58
4308 7238 2.741517 TGATGTGGTTTACGTGAGCATG 59.258 45.455 0.00 0.00 0.00 4.06
4313 7243 1.267532 GGTTTACGTGAGCATGCATCG 60.268 52.381 21.98 21.43 0.00 3.84
4319 7249 2.223947 ACGTGAGCATGCATCGGTTATA 60.224 45.455 21.98 0.00 0.00 0.98
4391 7321 2.289945 GCACTTCTTCCTGTCCTGTGAT 60.290 50.000 0.00 0.00 0.00 3.06
4399 7329 5.485353 TCTTCCTGTCCTGTGATAACATTCT 59.515 40.000 0.00 0.00 0.00 2.40
4503 7433 5.973565 GCTATCATAATTTGGTGACTGTTGC 59.026 40.000 0.00 0.00 0.00 4.17
4505 7435 6.594788 ATCATAATTTGGTGACTGTTGCTT 57.405 33.333 0.00 0.00 0.00 3.91
4532 7462 2.762875 GAGTGGTACCCCCTCCCG 60.763 72.222 10.07 0.00 0.00 5.14
4535 7465 3.931375 TGGTACCCCCTCCCGTGT 61.931 66.667 10.07 0.00 0.00 4.49
4563 7497 3.340814 TTTTTGGTGTGCAATGGTGTT 57.659 38.095 0.00 0.00 0.00 3.32
4564 7498 4.471904 TTTTTGGTGTGCAATGGTGTTA 57.528 36.364 0.00 0.00 0.00 2.41
4565 7499 4.679373 TTTTGGTGTGCAATGGTGTTAT 57.321 36.364 0.00 0.00 0.00 1.89
4566 7500 3.657015 TTGGTGTGCAATGGTGTTATG 57.343 42.857 0.00 0.00 0.00 1.90
4567 7501 1.891811 TGGTGTGCAATGGTGTTATGG 59.108 47.619 0.00 0.00 0.00 2.74
4568 7502 1.404047 GGTGTGCAATGGTGTTATGGC 60.404 52.381 0.00 0.00 0.00 4.40
4569 7503 0.894141 TGTGCAATGGTGTTATGGCC 59.106 50.000 0.00 0.00 0.00 5.36
4570 7504 0.179140 GTGCAATGGTGTTATGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
4571 7505 0.322906 TGCAATGGTGTTATGGCCGA 60.323 50.000 0.00 0.00 0.00 5.54
4572 7506 1.032014 GCAATGGTGTTATGGCCGAT 58.968 50.000 0.00 0.00 0.00 4.18
4573 7507 1.408702 GCAATGGTGTTATGGCCGATT 59.591 47.619 0.00 0.00 0.00 3.34
4574 7508 2.159114 GCAATGGTGTTATGGCCGATTT 60.159 45.455 0.00 0.00 0.00 2.17
4575 7509 3.067461 GCAATGGTGTTATGGCCGATTTA 59.933 43.478 0.00 0.00 0.00 1.40
4576 7510 4.792704 GCAATGGTGTTATGGCCGATTTAG 60.793 45.833 0.00 0.00 0.00 1.85
4577 7511 2.294074 TGGTGTTATGGCCGATTTAGC 58.706 47.619 0.00 0.00 0.00 3.09
4578 7512 2.092646 TGGTGTTATGGCCGATTTAGCT 60.093 45.455 0.00 0.00 0.00 3.32
4579 7513 3.134985 TGGTGTTATGGCCGATTTAGCTA 59.865 43.478 0.00 0.00 0.00 3.32
4580 7514 3.746492 GGTGTTATGGCCGATTTAGCTAG 59.254 47.826 0.00 0.00 0.00 3.42
4581 7515 3.746492 GTGTTATGGCCGATTTAGCTAGG 59.254 47.826 0.00 0.00 0.00 3.02
4584 7518 4.380980 GCCGATTTAGCTAGGCCC 57.619 61.111 10.00 0.00 43.54 5.80
4585 7519 1.450211 GCCGATTTAGCTAGGCCCA 59.550 57.895 10.00 0.00 43.54 5.36
4586 7520 0.885150 GCCGATTTAGCTAGGCCCAC 60.885 60.000 10.00 0.00 43.54 4.61
4587 7521 0.468226 CCGATTTAGCTAGGCCCACA 59.532 55.000 0.00 0.00 0.00 4.17
4588 7522 1.541233 CCGATTTAGCTAGGCCCACAG 60.541 57.143 0.00 0.00 0.00 3.66
4589 7523 1.541233 CGATTTAGCTAGGCCCACAGG 60.541 57.143 0.00 0.00 0.00 4.00
4600 7534 2.799176 CCCACAGGGCAATCTTAGC 58.201 57.895 0.00 0.00 35.35 3.09
4608 7542 1.839424 GGCAATCTTAGCCCACAAGT 58.161 50.000 0.00 0.00 46.50 3.16
4609 7543 2.171003 GGCAATCTTAGCCCACAAGTT 58.829 47.619 0.00 0.00 46.50 2.66
4610 7544 3.352648 GGCAATCTTAGCCCACAAGTTA 58.647 45.455 0.00 0.00 46.50 2.24
4611 7545 3.954258 GGCAATCTTAGCCCACAAGTTAT 59.046 43.478 0.00 0.00 46.50 1.89
4612 7546 4.036852 GGCAATCTTAGCCCACAAGTTATC 59.963 45.833 0.00 0.00 46.50 1.75
4613 7547 4.884164 GCAATCTTAGCCCACAAGTTATCT 59.116 41.667 0.00 0.00 0.00 1.98
4614 7548 5.358160 GCAATCTTAGCCCACAAGTTATCTT 59.642 40.000 0.00 0.00 0.00 2.40
4615 7549 6.542370 GCAATCTTAGCCCACAAGTTATCTTA 59.458 38.462 0.00 0.00 32.07 2.10
4616 7550 7.254932 GCAATCTTAGCCCACAAGTTATCTTAG 60.255 40.741 0.00 0.00 32.07 2.18
4617 7551 7.676683 ATCTTAGCCCACAAGTTATCTTAGA 57.323 36.000 0.00 0.00 32.07 2.10
4618 7552 7.676683 TCTTAGCCCACAAGTTATCTTAGAT 57.323 36.000 0.00 0.00 32.07 1.98
4619 7553 8.090788 TCTTAGCCCACAAGTTATCTTAGATT 57.909 34.615 0.00 0.00 32.07 2.40
4620 7554 9.209048 TCTTAGCCCACAAGTTATCTTAGATTA 57.791 33.333 0.00 0.00 32.07 1.75
4621 7555 9.832445 CTTAGCCCACAAGTTATCTTAGATTAA 57.168 33.333 0.00 0.00 32.07 1.40
4624 7558 9.343539 AGCCCACAAGTTATCTTAGATTAATTC 57.656 33.333 0.00 0.00 32.07 2.17
4625 7559 9.343539 GCCCACAAGTTATCTTAGATTAATTCT 57.656 33.333 0.00 0.00 38.57 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.922058 TTCTTTAACTATGTACAATCGGAGTC 57.078 34.615 0.00 0.00 0.00 3.36
1 2 9.715121 TTTTCTTTAACTATGTACAATCGGAGT 57.285 29.630 0.00 0.00 0.00 3.85
3 4 8.662141 GCTTTTCTTTAACTATGTACAATCGGA 58.338 33.333 0.00 0.00 0.00 4.55
4 5 8.447833 TGCTTTTCTTTAACTATGTACAATCGG 58.552 33.333 0.00 0.00 0.00 4.18
5 6 9.988350 ATGCTTTTCTTTAACTATGTACAATCG 57.012 29.630 0.00 0.00 0.00 3.34
9 10 9.891828 CACAATGCTTTTCTTTAACTATGTACA 57.108 29.630 0.00 0.00 0.00 2.90
10 11 9.893305 ACACAATGCTTTTCTTTAACTATGTAC 57.107 29.630 0.00 0.00 0.00 2.90
11 12 9.891828 CACACAATGCTTTTCTTTAACTATGTA 57.108 29.630 0.00 0.00 0.00 2.29
12 13 8.413229 ACACACAATGCTTTTCTTTAACTATGT 58.587 29.630 0.00 0.00 0.00 2.29
13 14 8.693504 CACACACAATGCTTTTCTTTAACTATG 58.306 33.333 0.00 0.00 0.00 2.23
14 15 8.413229 ACACACACAATGCTTTTCTTTAACTAT 58.587 29.630 0.00 0.00 0.00 2.12
15 16 7.700234 CACACACACAATGCTTTTCTTTAACTA 59.300 33.333 0.00 0.00 0.00 2.24
16 17 6.531240 CACACACACAATGCTTTTCTTTAACT 59.469 34.615 0.00 0.00 0.00 2.24
17 18 6.310224 ACACACACACAATGCTTTTCTTTAAC 59.690 34.615 0.00 0.00 0.00 2.01
18 19 6.309980 CACACACACACAATGCTTTTCTTTAA 59.690 34.615 0.00 0.00 0.00 1.52
19 20 5.804473 CACACACACACAATGCTTTTCTTTA 59.196 36.000 0.00 0.00 0.00 1.85
20 21 4.626604 CACACACACACAATGCTTTTCTTT 59.373 37.500 0.00 0.00 0.00 2.52
21 22 4.175516 CACACACACACAATGCTTTTCTT 58.824 39.130 0.00 0.00 0.00 2.52
22 23 3.193267 ACACACACACACAATGCTTTTCT 59.807 39.130 0.00 0.00 0.00 2.52
23 24 3.304026 CACACACACACACAATGCTTTTC 59.696 43.478 0.00 0.00 0.00 2.29
24 25 3.252400 CACACACACACACAATGCTTTT 58.748 40.909 0.00 0.00 0.00 2.27
25 26 2.230992 ACACACACACACACAATGCTTT 59.769 40.909 0.00 0.00 0.00 3.51
26 27 1.818060 ACACACACACACACAATGCTT 59.182 42.857 0.00 0.00 0.00 3.91
27 28 1.132834 CACACACACACACACAATGCT 59.867 47.619 0.00 0.00 0.00 3.79
28 29 1.135431 ACACACACACACACACAATGC 60.135 47.619 0.00 0.00 0.00 3.56
29 30 2.095314 ACACACACACACACACACAATG 60.095 45.455 0.00 0.00 0.00 2.82
30 31 2.095314 CACACACACACACACACACAAT 60.095 45.455 0.00 0.00 0.00 2.71
31 32 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
32 33 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
33 34 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
34 35 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
35 36 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
36 37 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
37 38 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
38 39 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
39 40 5.472320 TTTATACACACACACACACACAC 57.528 39.130 0.00 0.00 0.00 3.82
40 41 4.572795 CCTTTATACACACACACACACACA 59.427 41.667 0.00 0.00 0.00 3.72
41 42 4.812091 TCCTTTATACACACACACACACAC 59.188 41.667 0.00 0.00 0.00 3.82
42 43 5.024785 TCCTTTATACACACACACACACA 57.975 39.130 0.00 0.00 0.00 3.72
43 44 5.163992 CGATCCTTTATACACACACACACAC 60.164 44.000 0.00 0.00 0.00 3.82
44 45 4.926832 CGATCCTTTATACACACACACACA 59.073 41.667 0.00 0.00 0.00 3.72
45 46 4.927425 ACGATCCTTTATACACACACACAC 59.073 41.667 0.00 0.00 0.00 3.82
46 47 5.142061 ACGATCCTTTATACACACACACA 57.858 39.130 0.00 0.00 0.00 3.72
47 48 5.165676 TGACGATCCTTTATACACACACAC 58.834 41.667 0.00 0.00 0.00 3.82
48 49 5.394224 TGACGATCCTTTATACACACACA 57.606 39.130 0.00 0.00 0.00 3.72
49 50 6.715344 TTTGACGATCCTTTATACACACAC 57.285 37.500 0.00 0.00 0.00 3.82
50 51 7.731882 TTTTTGACGATCCTTTATACACACA 57.268 32.000 0.00 0.00 0.00 3.72
85 86 1.657094 CGTAACATGTAGCAACGTCCC 59.343 52.381 0.00 0.00 0.00 4.46
91 92 3.991773 GGTGAGTTCGTAACATGTAGCAA 59.008 43.478 0.00 0.00 0.00 3.91
113 121 2.511600 CGAAGGTAGCCCGCCTTG 60.512 66.667 8.53 0.00 45.51 3.61
133 141 4.796231 CGCTTCCGTGTCTCCCCG 62.796 72.222 0.00 0.00 0.00 5.73
188 197 0.533308 ACTTTTGTAAGCCGCGTCCA 60.533 50.000 4.92 0.00 34.60 4.02
215 224 9.973661 TCAATCTAGAAAAATGTTTGAGGGATA 57.026 29.630 0.00 0.00 0.00 2.59
217 226 8.884124 ATCAATCTAGAAAAATGTTTGAGGGA 57.116 30.769 0.00 0.00 0.00 4.20
248 273 5.299531 CCTATATCTCCCTTATTGCGATCGA 59.700 44.000 21.57 0.00 0.00 3.59
249 274 5.508153 CCCTATATCTCCCTTATTGCGATCG 60.508 48.000 11.69 11.69 0.00 3.69
250 275 5.364157 ACCCTATATCTCCCTTATTGCGATC 59.636 44.000 0.00 0.00 0.00 3.69
251 276 5.281314 ACCCTATATCTCCCTTATTGCGAT 58.719 41.667 0.00 0.00 0.00 4.58
277 302 4.620937 GGGGGTAGGATTCCGCGC 62.621 72.222 0.00 0.00 38.54 6.86
319 349 0.688487 TTTAGTAGCAGGCCCACGTT 59.312 50.000 0.00 0.00 0.00 3.99
320 350 0.688487 TTTTAGTAGCAGGCCCACGT 59.312 50.000 0.00 0.00 0.00 4.49
342 372 4.410228 TCCTTAATCCTGATAGCACTGCTT 59.590 41.667 9.30 0.00 40.44 3.91
343 373 3.969976 TCCTTAATCCTGATAGCACTGCT 59.030 43.478 8.95 8.95 43.41 4.24
386 416 4.142315 CCATCTCAAACGGATTTGCAATCT 60.142 41.667 0.00 0.00 44.22 2.40
387 417 4.107622 CCATCTCAAACGGATTTGCAATC 58.892 43.478 0.00 0.00 44.22 2.67
388 418 3.763360 TCCATCTCAAACGGATTTGCAAT 59.237 39.130 0.00 0.00 44.22 3.56
389 419 3.057596 GTCCATCTCAAACGGATTTGCAA 60.058 43.478 0.00 0.00 44.22 4.08
391 421 2.487762 TGTCCATCTCAAACGGATTTGC 59.512 45.455 0.00 0.00 44.22 3.68
392 422 4.494690 CGATGTCCATCTCAAACGGATTTG 60.495 45.833 5.79 0.00 38.14 2.32
393 423 3.623060 CGATGTCCATCTCAAACGGATTT 59.377 43.478 5.79 0.00 35.72 2.17
414 461 1.007271 CGATTCCGGGATCTGGACG 60.007 63.158 20.71 3.65 34.56 4.79
434 519 3.560105 AGGAGTAGTATCCGGTAACCAC 58.440 50.000 0.00 0.04 44.65 4.16
446 531 9.958234 GATATATATCACGACGTAGGAGTAGTA 57.042 37.037 16.41 0.00 32.98 1.82
524 650 2.654912 GACGGACGGCGTCTTGTTG 61.655 63.158 35.42 22.54 33.98 3.33
542 668 1.971695 GGCTTGGTTTCCTGGGTCG 60.972 63.158 0.00 0.00 0.00 4.79
543 669 0.251787 ATGGCTTGGTTTCCTGGGTC 60.252 55.000 0.00 0.00 0.00 4.46
544 670 0.190815 AATGGCTTGGTTTCCTGGGT 59.809 50.000 0.00 0.00 0.00 4.51
571 697 2.203480 GGCTGGACTTGGGCACAA 60.203 61.111 0.00 0.00 34.87 3.33
574 700 3.970410 CCTGGCTGGACTTGGGCA 61.970 66.667 4.05 0.00 38.35 5.36
655 785 5.072055 GGAGGGAGTACTTGATACTAGGTC 58.928 50.000 0.00 0.00 44.64 3.85
656 786 4.446023 CGGAGGGAGTACTTGATACTAGGT 60.446 50.000 0.00 0.00 44.64 3.08
657 787 4.073549 CGGAGGGAGTACTTGATACTAGG 58.926 52.174 0.00 0.00 44.64 3.02
671 801 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
673 803 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
674 804 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
689 819 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
690 820 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
691 821 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
692 822 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
706 836 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
707 837 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
719 849 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
720 850 8.423215 GCCGTAAACTAATATAAGAGCGTTTAG 58.577 37.037 0.00 0.00 30.36 1.85
721 851 7.113404 CGCCGTAAACTAATATAAGAGCGTTTA 59.887 37.037 0.00 0.00 34.42 2.01
722 852 6.074676 CGCCGTAAACTAATATAAGAGCGTTT 60.075 38.462 0.00 0.00 34.42 3.60
723 853 5.400485 CGCCGTAAACTAATATAAGAGCGTT 59.600 40.000 0.00 0.00 34.42 4.84
724 854 4.913924 CGCCGTAAACTAATATAAGAGCGT 59.086 41.667 0.00 0.00 34.42 5.07
725 855 4.322804 CCGCCGTAAACTAATATAAGAGCG 59.677 45.833 0.00 0.00 38.48 5.03
726 856 4.624452 CCCGCCGTAAACTAATATAAGAGC 59.376 45.833 0.00 0.00 0.00 4.09
727 857 6.017400 TCCCGCCGTAAACTAATATAAGAG 57.983 41.667 0.00 0.00 0.00 2.85
728 858 5.536161 ACTCCCGCCGTAAACTAATATAAGA 59.464 40.000 0.00 0.00 0.00 2.10
729 859 5.776744 ACTCCCGCCGTAAACTAATATAAG 58.223 41.667 0.00 0.00 0.00 1.73
730 860 5.789643 ACTCCCGCCGTAAACTAATATAA 57.210 39.130 0.00 0.00 0.00 0.98
731 861 6.003950 AGTACTCCCGCCGTAAACTAATATA 58.996 40.000 0.00 0.00 0.00 0.86
732 862 4.829492 AGTACTCCCGCCGTAAACTAATAT 59.171 41.667 0.00 0.00 0.00 1.28
733 863 4.207165 AGTACTCCCGCCGTAAACTAATA 58.793 43.478 0.00 0.00 0.00 0.98
734 864 3.026694 AGTACTCCCGCCGTAAACTAAT 58.973 45.455 0.00 0.00 0.00 1.73
735 865 2.446435 AGTACTCCCGCCGTAAACTAA 58.554 47.619 0.00 0.00 0.00 2.24
736 866 2.128771 AGTACTCCCGCCGTAAACTA 57.871 50.000 0.00 0.00 0.00 2.24
737 867 1.745653 GTAGTACTCCCGCCGTAAACT 59.254 52.381 0.00 0.00 0.00 2.66
738 868 1.745653 AGTAGTACTCCCGCCGTAAAC 59.254 52.381 0.00 0.00 0.00 2.01
739 869 1.745087 CAGTAGTACTCCCGCCGTAAA 59.255 52.381 0.00 0.00 0.00 2.01
740 870 1.340017 ACAGTAGTACTCCCGCCGTAA 60.340 52.381 0.00 0.00 0.00 3.18
741 871 0.253044 ACAGTAGTACTCCCGCCGTA 59.747 55.000 0.00 0.00 0.00 4.02
742 872 0.253044 TACAGTAGTACTCCCGCCGT 59.747 55.000 0.00 0.00 0.00 5.68
743 873 1.602311 ATACAGTAGTACTCCCGCCG 58.398 55.000 0.00 0.00 31.96 6.46
744 874 2.954318 TCAATACAGTAGTACTCCCGCC 59.046 50.000 0.00 0.00 31.96 6.13
745 875 3.631227 AGTCAATACAGTAGTACTCCCGC 59.369 47.826 0.00 0.00 31.96 6.13
746 876 5.831702 AAGTCAATACAGTAGTACTCCCG 57.168 43.478 0.00 0.00 31.96 5.14
747 877 7.407393 AGAAAGTCAATACAGTAGTACTCCC 57.593 40.000 0.00 0.00 31.96 4.30
748 878 8.305317 ACAAGAAAGTCAATACAGTAGTACTCC 58.695 37.037 0.00 0.00 31.96 3.85
749 879 9.130312 CACAAGAAAGTCAATACAGTAGTACTC 57.870 37.037 0.00 0.00 31.96 2.59
750 880 8.857098 TCACAAGAAAGTCAATACAGTAGTACT 58.143 33.333 0.00 0.00 31.96 2.73
751 881 9.640963 ATCACAAGAAAGTCAATACAGTAGTAC 57.359 33.333 0.00 0.00 31.96 2.73
752 882 9.856488 GATCACAAGAAAGTCAATACAGTAGTA 57.144 33.333 0.00 0.00 34.10 1.82
753 883 7.542477 CGATCACAAGAAAGTCAATACAGTAGT 59.458 37.037 0.00 0.00 0.00 2.73
754 884 7.542477 ACGATCACAAGAAAGTCAATACAGTAG 59.458 37.037 0.00 0.00 0.00 2.57
926 1116 3.806949 AGTAAGGGCACAATGAGGAAA 57.193 42.857 0.00 0.00 0.00 3.13
930 1120 5.300752 CCATAGTAGTAAGGGCACAATGAG 58.699 45.833 0.00 0.00 0.00 2.90
1363 1942 5.301555 GGAGAATAGAAGGGTGCAGAATAC 58.698 45.833 0.00 0.00 0.00 1.89
1531 2638 3.196039 TCATGCACCTTCCATTCCAAATG 59.804 43.478 0.00 0.00 0.00 2.32
2084 3513 9.990868 ATGTATTAGTTTTTGAGGGGAAATAGT 57.009 29.630 0.00 0.00 0.00 2.12
2129 3607 2.881074 CAGTCAAGACCATGTACTCCG 58.119 52.381 0.00 0.00 0.00 4.63
2130 3608 2.028112 TGCAGTCAAGACCATGTACTCC 60.028 50.000 0.00 0.00 0.00 3.85
2131 3609 3.319137 TGCAGTCAAGACCATGTACTC 57.681 47.619 0.00 0.00 0.00 2.59
2132 3610 3.261643 TGATGCAGTCAAGACCATGTACT 59.738 43.478 0.00 0.00 32.78 2.73
2139 3702 1.271054 ACTGGTGATGCAGTCAAGACC 60.271 52.381 0.00 0.00 38.90 3.85
2325 4082 5.698089 CGAACATGCATATGTACTCTGGAAT 59.302 40.000 0.00 0.00 46.54 3.01
2389 4150 9.034544 GCAAAAAGAATACAATCAACTGAGTTT 57.965 29.630 0.00 0.00 0.00 2.66
2637 4432 2.609491 CCACGACAGACTTCATTTCGGA 60.609 50.000 0.00 0.00 33.97 4.55
2674 4469 4.442706 GACAAAGAGGTTCTGAACTGTGA 58.557 43.478 19.05 0.00 0.00 3.58
2714 4509 2.355818 GGTCCAAGTGTATGTCCCTTCC 60.356 54.545 0.00 0.00 0.00 3.46
2715 4510 2.304761 TGGTCCAAGTGTATGTCCCTTC 59.695 50.000 0.00 0.00 0.00 3.46
2974 4850 1.875514 CATGACCATTGGCTATCGGTG 59.124 52.381 1.54 0.00 0.00 4.94
2985 4861 3.006110 CCTTGCACAAAGACATGACCATT 59.994 43.478 0.00 0.00 38.24 3.16
3198 5123 2.598394 TTGTGGCTGAGCTTGGGC 60.598 61.111 3.72 6.50 39.06 5.36
3461 5469 7.829706 AGAACAACTTAACCTGAAGTTCTTCTT 59.170 33.333 11.44 3.33 45.00 2.52
3485 5493 2.632996 ACTGCACTGGTAGTTGCTAAGA 59.367 45.455 0.00 0.00 36.49 2.10
3620 5775 1.205893 AGATCGTGGAGTTCCTTGAGC 59.794 52.381 0.00 0.70 36.82 4.26
3644 5799 8.519526 CAGTTCGATTCTATAAGATAGCCTCTT 58.480 37.037 4.70 4.70 46.16 2.85
3739 5894 7.445945 AGGATGAAGGCATATTAACTCTACAC 58.554 38.462 0.00 0.00 34.11 2.90
3957 6204 4.384427 GGGATCATGGAACCAAATGCAAAT 60.384 41.667 0.00 0.00 0.00 2.32
3988 6235 2.437200 TTTGAAAATGCTTGAGGCCG 57.563 45.000 0.00 0.00 40.92 6.13
4045 6292 9.868277 CCAAAATCATTGCCTTACAGTTTATAA 57.132 29.630 0.00 0.00 0.00 0.98
4061 6308 9.525826 AAGAAGACATAGAAGACCAAAATCATT 57.474 29.630 0.00 0.00 0.00 2.57
4062 6309 9.171877 GAAGAAGACATAGAAGACCAAAATCAT 57.828 33.333 0.00 0.00 0.00 2.45
4082 7012 4.111916 GGATCGCTCTCAAAGAGAAGAAG 58.888 47.826 8.14 0.00 45.07 2.85
4129 7059 8.154649 AGTGATACAGTGGTAAAAAGTGAAAG 57.845 34.615 0.00 0.00 32.19 2.62
4185 7115 5.632764 CACGCAGATAATCATGTAGAGGAAG 59.367 44.000 0.00 0.00 0.00 3.46
4192 7122 8.925700 GTGATAAATCACGCAGATAATCATGTA 58.074 33.333 7.31 0.00 46.46 2.29
4284 7214 2.096417 GCTCACGTAAACCACATCACAC 60.096 50.000 0.00 0.00 0.00 3.82
4289 7219 1.468520 GCATGCTCACGTAAACCACAT 59.531 47.619 11.37 0.00 0.00 3.21
4308 7238 3.122948 CAGCACCGTAATATAACCGATGC 59.877 47.826 0.88 0.88 0.00 3.91
4313 7243 3.463944 ACTGCAGCACCGTAATATAACC 58.536 45.455 15.27 0.00 0.00 2.85
4319 7249 0.874390 CACAACTGCAGCACCGTAAT 59.126 50.000 15.27 0.00 0.00 1.89
4391 7321 9.100197 TGCTCATCCTATATTACCAGAATGTTA 57.900 33.333 0.00 0.00 0.00 2.41
4431 7361 7.614192 ACGTACAAGGATCCCTCAAAATAAAAT 59.386 33.333 8.55 0.00 30.89 1.82
4436 7366 4.569719 ACGTACAAGGATCCCTCAAAAT 57.430 40.909 8.55 0.00 30.89 1.82
4437 7367 4.360951 AACGTACAAGGATCCCTCAAAA 57.639 40.909 8.55 0.00 30.89 2.44
4478 7408 6.183360 GCAACAGTCACCAAATTATGATAGCT 60.183 38.462 0.00 0.00 0.00 3.32
4491 7421 2.822561 TCAACAAAAGCAACAGTCACCA 59.177 40.909 0.00 0.00 0.00 4.17
4503 7433 4.813296 GGTACCACTCACTCAACAAAAG 57.187 45.455 7.15 0.00 0.00 2.27
4560 7494 3.805807 GCCTAGCTAAATCGGCCATAACA 60.806 47.826 10.00 0.00 36.56 2.41
4561 7495 2.742589 GCCTAGCTAAATCGGCCATAAC 59.257 50.000 10.00 0.00 36.56 1.89
4562 7496 3.053831 GCCTAGCTAAATCGGCCATAA 57.946 47.619 10.00 0.00 36.56 1.90
4563 7497 2.762535 GCCTAGCTAAATCGGCCATA 57.237 50.000 10.00 0.00 36.56 2.74
4564 7498 3.633361 GCCTAGCTAAATCGGCCAT 57.367 52.632 10.00 0.00 36.56 4.40
4567 7501 0.885150 GTGGGCCTAGCTAAATCGGC 60.885 60.000 12.25 12.25 41.75 5.54
4568 7502 0.468226 TGTGGGCCTAGCTAAATCGG 59.532 55.000 4.53 0.00 0.00 4.18
4569 7503 1.541233 CCTGTGGGCCTAGCTAAATCG 60.541 57.143 4.53 0.00 0.00 3.34
4570 7504 1.202818 CCCTGTGGGCCTAGCTAAATC 60.203 57.143 4.53 0.00 35.35 2.17
4571 7505 0.846693 CCCTGTGGGCCTAGCTAAAT 59.153 55.000 4.53 0.00 35.35 1.40
4572 7506 2.307153 CCCTGTGGGCCTAGCTAAA 58.693 57.895 4.53 0.00 35.35 1.85
4573 7507 4.066614 CCCTGTGGGCCTAGCTAA 57.933 61.111 4.53 0.00 35.35 3.09
4583 7517 2.799176 GGCTAAGATTGCCCTGTGG 58.201 57.895 0.00 0.00 44.32 4.17
4589 7523 7.582275 AAGATAACTTGTGGGCTAAGATTGCC 61.582 42.308 0.00 0.00 41.08 4.52
4590 7524 4.884164 AGATAACTTGTGGGCTAAGATTGC 59.116 41.667 0.00 0.00 0.00 3.56
4591 7525 7.987458 TCTAAGATAACTTGTGGGCTAAGATTG 59.013 37.037 0.00 0.00 37.53 2.67
4592 7526 8.090788 TCTAAGATAACTTGTGGGCTAAGATT 57.909 34.615 0.00 0.00 37.53 2.40
4593 7527 7.676683 TCTAAGATAACTTGTGGGCTAAGAT 57.323 36.000 0.00 0.00 37.53 2.40
4594 7528 7.676683 ATCTAAGATAACTTGTGGGCTAAGA 57.323 36.000 0.00 0.00 37.53 2.10
4595 7529 9.832445 TTAATCTAAGATAACTTGTGGGCTAAG 57.168 33.333 0.00 0.00 37.53 2.18
4598 7532 9.343539 GAATTAATCTAAGATAACTTGTGGGCT 57.656 33.333 0.00 0.00 37.53 5.19
4599 7533 9.343539 AGAATTAATCTAAGATAACTTGTGGGC 57.656 33.333 0.00 0.00 36.32 5.36


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

AutoCloner maintained by Alex Coulton.