Multiple sequence alignment - TraesCS1A01G252200

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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 TraesCS1A01G252200 chr1A 100.000 3761 0 0 1 3761 443869054 443872814 0.000000e+00 6946.0
1 TraesCS1A01G252200 chr1A 87.789 2031 197 24 757 2782 444421982 444419998 0.000000e+00 2329.0
2 TraesCS1A01G252200 chr1A 96.552 261 9 0 54 314 571583369 571583109 2.070000e-117 433.0
3 TraesCS1A01G252200 chr1A 96.198 263 10 0 54 316 447576925 447577187 7.460000e-117 431.0
4 TraesCS1A01G252200 chr1D 96.787 2303 72 2 472 2772 344283583 344285885 0.000000e+00 3842.0
5 TraesCS1A01G252200 chr1D 89.793 1881 169 14 919 2782 344676327 344674453 0.000000e+00 2388.0
6 TraesCS1A01G252200 chr1D 88.536 724 60 2 2990 3690 344301158 344301881 0.000000e+00 856.0
7 TraesCS1A01G252200 chr1D 77.176 1034 170 48 2777 3761 2639329 2640345 3.300000e-150 542.0
8 TraesCS1A01G252200 chr1D 95.890 219 9 0 2777 2995 344286348 344286566 4.620000e-94 355.0
9 TraesCS1A01G252200 chr1D 85.583 326 41 4 2777 3100 344365876 344366197 1.670000e-88 337.0
10 TraesCS1A01G252200 chr1D 93.413 167 10 1 307 472 344283234 344283400 2.900000e-61 246.0
11 TraesCS1A01G252200 chr1B 94.764 1967 57 10 816 2781 466288946 466287025 0.000000e+00 3020.0
12 TraesCS1A01G252200 chr1B 88.053 2034 195 28 757 2777 465964403 465966401 0.000000e+00 2366.0
13 TraesCS1A01G252200 chr1B 87.636 550 55 5 2866 3414 466282769 466282232 8.870000e-176 627.0
14 TraesCS1A01G252200 chr1B 85.115 262 34 2 473 729 466289206 466288945 2.880000e-66 263.0
15 TraesCS1A01G252200 chr1B 93.529 170 10 1 307 475 466289556 466289387 6.240000e-63 252.0
16 TraesCS1A01G252200 chr1B 84.375 256 34 5 471 720 1446929 1447184 2.900000e-61 246.0
17 TraesCS1A01G252200 chr1B 92.121 165 12 1 307 470 288173491 288173655 8.120000e-57 231.0
18 TraesCS1A01G252200 chr1B 91.579 95 7 1 2777 2871 466286988 466286895 3.050000e-26 130.0
19 TraesCS1A01G252200 chr7D 82.284 1716 279 20 1046 2742 84422149 84420440 0.000000e+00 1461.0
20 TraesCS1A01G252200 chr7D 81.834 1734 289 20 1029 2743 193935024 193936750 0.000000e+00 1434.0
21 TraesCS1A01G252200 chr5D 82.360 1712 268 23 1065 2760 424596974 424598667 0.000000e+00 1458.0
22 TraesCS1A01G252200 chr5D 85.370 622 87 4 1022 1641 124397909 124397290 3.170000e-180 641.0
23 TraesCS1A01G252200 chr5D 86.275 255 28 4 472 720 458109019 458108766 1.720000e-68 270.0
24 TraesCS1A01G252200 chr5D 86.056 251 32 3 473 720 535913621 535913371 2.230000e-67 267.0
25 TraesCS1A01G252200 chr5D 91.176 170 14 1 307 475 407010007 407009838 2.920000e-56 230.0
26 TraesCS1A01G252200 chr7B 82.270 1709 279 19 1052 2742 34168284 34169986 0.000000e+00 1456.0
27 TraesCS1A01G252200 chr7B 81.949 1734 287 20 1029 2743 157687796 157689522 0.000000e+00 1445.0
28 TraesCS1A01G252200 chr7B 81.526 498 69 2 3287 3761 719169325 719168828 4.560000e-104 388.0
29 TraesCS1A01G252200 chr7A 81.850 1708 288 16 1053 2743 203525556 203527258 0.000000e+00 1417.0
30 TraesCS1A01G252200 chr7A 96.198 263 10 0 52 314 535618668 535618930 7.460000e-117 431.0
31 TraesCS1A01G252200 chr7A 86.454 251 29 3 472 720 625373980 625373733 1.720000e-68 270.0
32 TraesCS1A01G252200 chr2A 77.027 1036 170 47 2777 3761 600679890 600680908 1.990000e-147 532.0
33 TraesCS1A01G252200 chr2A 96.212 264 10 0 51 314 653300493 653300230 2.070000e-117 433.0
34 TraesCS1A01G252200 chr6A 96.604 265 9 0 50 314 602321662 602321926 1.240000e-119 440.0
35 TraesCS1A01G252200 chr6A 81.325 498 67 10 3287 3761 46064781 46065275 7.620000e-102 381.0
36 TraesCS1A01G252200 chr6A 96.364 55 2 0 1 55 147980403 147980457 1.440000e-14 91.6
37 TraesCS1A01G252200 chr5A 96.255 267 9 1 48 314 448842456 448842191 1.600000e-118 436.0
38 TraesCS1A01G252200 chr5A 96.226 265 8 2 54 317 300648016 300647753 2.070000e-117 433.0
39 TraesCS1A01G252200 chr5A 82.875 327 50 5 2777 3100 11752109 11751786 4.750000e-74 289.0
40 TraesCS1A01G252200 chr5A 96.364 55 2 0 1 55 600472825 600472879 1.440000e-14 91.6
41 TraesCS1A01G252200 chr5A 94.545 55 3 0 1 55 365935529 365935583 6.690000e-13 86.1
42 TraesCS1A01G252200 chr4A 96.198 263 10 0 52 314 608002430 608002168 7.460000e-117 431.0
43 TraesCS1A01G252200 chr4A 95.506 267 11 1 50 316 54904413 54904148 3.470000e-115 425.0
44 TraesCS1A01G252200 chr4A 86.111 252 31 4 473 720 655620098 655620349 6.190000e-68 268.0
45 TraesCS1A01G252200 chr4A 92.727 55 4 0 1 55 477836012 477836066 3.110000e-11 80.5
46 TraesCS1A01G252200 chrUn 81.984 494 66 8 3287 3757 342375059 342374566 7.570000e-107 398.0
47 TraesCS1A01G252200 chrUn 82.077 491 65 8 3287 3754 381405531 381406021 7.570000e-107 398.0
48 TraesCS1A01G252200 chrUn 81.874 491 66 8 3287 3754 83638928 83639418 3.520000e-105 392.0
49 TraesCS1A01G252200 chrUn 86.454 251 30 4 473 720 171670713 171670464 4.790000e-69 272.0
50 TraesCS1A01G252200 chrUn 86.454 251 30 4 473 720 171735617 171735866 4.790000e-69 272.0
51 TraesCS1A01G252200 chrUn 92.121 165 12 1 307 470 86405567 86405731 8.120000e-57 231.0
52 TraesCS1A01G252200 chrUn 94.545 55 3 0 1 55 86405521 86405575 6.690000e-13 86.1
53 TraesCS1A01G252200 chr3D 81.325 498 70 8 3287 3761 593261868 593262365 2.120000e-102 383.0
54 TraesCS1A01G252200 chr3D 85.759 323 39 6 2782 3100 603679222 603678903 6.020000e-88 335.0
55 TraesCS1A01G252200 chr3D 86.111 252 31 3 472 719 333005580 333005329 6.190000e-68 268.0
56 TraesCS1A01G252200 chr3D 98.182 55 1 0 1 55 429309785 429309731 3.090000e-16 97.1
57 TraesCS1A01G252200 chr4B 84.818 303 38 6 2777 3076 167386746 167387043 7.900000e-77 298.0
58 TraesCS1A01G252200 chr4B 94.545 55 3 0 1 55 80165792 80165846 6.690000e-13 86.1
59 TraesCS1A01G252200 chr6B 93.333 165 8 3 307 469 504582717 504582880 1.350000e-59 241.0
60 TraesCS1A01G252200 chr6D 92.727 165 12 0 311 475 96638904 96638740 4.860000e-59 239.0
61 TraesCS1A01G252200 chr2B 91.813 171 12 2 307 475 799454727 799454557 1.750000e-58 237.0
62 TraesCS1A01G252200 chr2B 92.216 167 12 1 307 472 239641591 239641425 6.280000e-58 235.0
63 TraesCS1A01G252200 chr3A 98.000 50 1 0 1 50 670651124 670651173 1.860000e-13 87.9
64 TraesCS1A01G252200 chr3B 94.444 54 3 0 1 54 630577440 630577493 2.410000e-12 84.2


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 TraesCS1A01G252200 chr1A 443869054 443872814 3760 False 6946.00 6946 100.000000 1 3761 1 chr1A.!!$F1 3760
1 TraesCS1A01G252200 chr1A 444419998 444421982 1984 True 2329.00 2329 87.789000 757 2782 1 chr1A.!!$R1 2025
2 TraesCS1A01G252200 chr1D 344674453 344676327 1874 True 2388.00 2388 89.793000 919 2782 1 chr1D.!!$R1 1863
3 TraesCS1A01G252200 chr1D 344283234 344286566 3332 False 1481.00 3842 95.363333 307 2995 3 chr1D.!!$F4 2688
4 TraesCS1A01G252200 chr1D 344301158 344301881 723 False 856.00 856 88.536000 2990 3690 1 chr1D.!!$F2 700
5 TraesCS1A01G252200 chr1D 2639329 2640345 1016 False 542.00 542 77.176000 2777 3761 1 chr1D.!!$F1 984
6 TraesCS1A01G252200 chr1B 465964403 465966401 1998 False 2366.00 2366 88.053000 757 2777 1 chr1B.!!$F3 2020
7 TraesCS1A01G252200 chr1B 466286895 466289556 2661 True 916.25 3020 91.246750 307 2871 4 chr1B.!!$R2 2564
8 TraesCS1A01G252200 chr1B 466282232 466282769 537 True 627.00 627 87.636000 2866 3414 1 chr1B.!!$R1 548
9 TraesCS1A01G252200 chr7D 84420440 84422149 1709 True 1461.00 1461 82.284000 1046 2742 1 chr7D.!!$R1 1696
10 TraesCS1A01G252200 chr7D 193935024 193936750 1726 False 1434.00 1434 81.834000 1029 2743 1 chr7D.!!$F1 1714
11 TraesCS1A01G252200 chr5D 424596974 424598667 1693 False 1458.00 1458 82.360000 1065 2760 1 chr5D.!!$F1 1695
12 TraesCS1A01G252200 chr5D 124397290 124397909 619 True 641.00 641 85.370000 1022 1641 1 chr5D.!!$R1 619
13 TraesCS1A01G252200 chr7B 34168284 34169986 1702 False 1456.00 1456 82.270000 1052 2742 1 chr7B.!!$F1 1690
14 TraesCS1A01G252200 chr7B 157687796 157689522 1726 False 1445.00 1445 81.949000 1029 2743 1 chr7B.!!$F2 1714
15 TraesCS1A01G252200 chr7A 203525556 203527258 1702 False 1417.00 1417 81.850000 1053 2743 1 chr7A.!!$F1 1690
16 TraesCS1A01G252200 chr2A 600679890 600680908 1018 False 532.00 532 77.027000 2777 3761 1 chr2A.!!$F1 984

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
66 67 0.032714 GGGTAGTACTCCCTCCGGTT 60.033 60.000 18.19 0.0 41.58 4.44 F
68 69 1.064091 GGTAGTACTCCCTCCGGTTCT 60.064 57.143 0.00 0.0 0.00 3.01 F
306 307 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.0 0.00 5.14 F
337 338 1.171308 GGTCATGTCAGTGCTTGCAT 58.829 50.000 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2141 3.211288 GCTCCTCTGCGGCTCTTA 58.789 61.111 0.0 0.0 0.0 2.10 R
2172 2382 2.173519 CCGGAGTTGTACAGGAAGGTA 58.826 52.381 0.0 0.0 0.0 3.08 R
2416 2633 2.471818 CATCTGCTCAATCTCGTCCAG 58.528 52.381 0.0 0.0 0.0 3.86 R
2761 2978 1.267121 AACTAGTGGTGCCGTCATCT 58.733 50.000 0.0 0.0 0.0 2.90 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
18 19 2.682631 TAGACTGCATGCACTGGGA 58.317 52.632 18.46 0.00 0.00 4.37
19 20 0.538584 TAGACTGCATGCACTGGGAG 59.461 55.000 18.46 8.68 0.00 4.30
20 21 1.002868 GACTGCATGCACTGGGAGT 60.003 57.895 18.46 12.33 38.47 3.85
22 23 2.034532 TGCATGCACTGGGAGTGG 59.965 61.111 18.46 0.00 46.01 4.00
27 28 3.913855 TGCACTGGGAGTGGAAAAA 57.086 47.368 5.90 0.00 43.66 1.94
28 29 1.398692 TGCACTGGGAGTGGAAAAAC 58.601 50.000 5.90 0.00 43.66 2.43
29 30 1.064017 TGCACTGGGAGTGGAAAAACT 60.064 47.619 5.90 0.00 43.66 2.66
30 31 2.173782 TGCACTGGGAGTGGAAAAACTA 59.826 45.455 5.90 0.00 43.66 2.24
31 32 2.552743 GCACTGGGAGTGGAAAAACTAC 59.447 50.000 5.90 0.00 46.01 2.73
35 36 3.520691 GGGAGTGGAAAAACTACCCTT 57.479 47.619 0.00 0.00 44.48 3.95
36 37 3.418995 GGGAGTGGAAAAACTACCCTTC 58.581 50.000 0.00 0.00 44.48 3.46
37 38 3.074094 GGGAGTGGAAAAACTACCCTTCT 59.926 47.826 0.00 0.00 44.48 2.85
38 39 4.072839 GGAGTGGAAAAACTACCCTTCTG 58.927 47.826 0.00 0.00 0.00 3.02
39 40 3.487372 AGTGGAAAAACTACCCTTCTGC 58.513 45.455 0.00 0.00 0.00 4.26
40 41 3.138468 AGTGGAAAAACTACCCTTCTGCT 59.862 43.478 0.00 0.00 0.00 4.24
41 42 3.889538 GTGGAAAAACTACCCTTCTGCTT 59.110 43.478 0.00 0.00 0.00 3.91
42 43 3.888930 TGGAAAAACTACCCTTCTGCTTG 59.111 43.478 0.00 0.00 0.00 4.01
43 44 3.255888 GGAAAAACTACCCTTCTGCTTGG 59.744 47.826 0.00 0.00 0.00 3.61
44 45 1.911057 AAACTACCCTTCTGCTTGGC 58.089 50.000 0.00 0.00 0.00 4.52
45 46 0.771127 AACTACCCTTCTGCTTGGCA 59.229 50.000 0.00 0.00 36.92 4.92
46 47 0.771127 ACTACCCTTCTGCTTGGCAA 59.229 50.000 0.00 0.00 38.41 4.52
47 48 1.271597 ACTACCCTTCTGCTTGGCAAG 60.272 52.381 22.75 22.75 38.41 4.01
48 49 0.038166 TACCCTTCTGCTTGGCAAGG 59.962 55.000 27.25 13.06 38.41 3.61
49 50 1.980772 CCCTTCTGCTTGGCAAGGG 60.981 63.158 27.25 16.67 46.18 3.95
50 51 1.228675 CCTTCTGCTTGGCAAGGGT 60.229 57.895 27.25 0.00 38.41 4.34
51 52 0.038166 CCTTCTGCTTGGCAAGGGTA 59.962 55.000 27.25 3.25 38.41 3.69
52 53 1.457346 CTTCTGCTTGGCAAGGGTAG 58.543 55.000 27.25 13.05 38.41 3.18
53 54 0.771127 TTCTGCTTGGCAAGGGTAGT 59.229 50.000 27.25 0.00 38.41 2.73
54 55 1.651737 TCTGCTTGGCAAGGGTAGTA 58.348 50.000 27.25 1.44 38.41 1.82
55 56 1.278127 TCTGCTTGGCAAGGGTAGTAC 59.722 52.381 27.25 10.21 38.41 2.73
56 57 1.279271 CTGCTTGGCAAGGGTAGTACT 59.721 52.381 27.25 0.00 38.41 2.73
57 58 1.278127 TGCTTGGCAAGGGTAGTACTC 59.722 52.381 27.25 8.82 34.76 2.59
58 59 1.407025 GCTTGGCAAGGGTAGTACTCC 60.407 57.143 27.25 4.04 0.00 3.85
59 60 1.209747 CTTGGCAAGGGTAGTACTCCC 59.790 57.143 19.55 17.92 44.90 4.30
64 65 4.595031 GGGTAGTACTCCCTCCGG 57.405 66.667 18.19 0.00 41.58 5.14
65 66 1.617475 GGGTAGTACTCCCTCCGGT 59.383 63.158 18.19 0.00 41.58 5.28
66 67 0.032714 GGGTAGTACTCCCTCCGGTT 60.033 60.000 18.19 0.00 41.58 4.44
67 68 1.397672 GGTAGTACTCCCTCCGGTTC 58.602 60.000 0.00 0.00 0.00 3.62
68 69 1.064091 GGTAGTACTCCCTCCGGTTCT 60.064 57.143 0.00 0.00 0.00 3.01
69 70 2.622714 GGTAGTACTCCCTCCGGTTCTT 60.623 54.545 0.00 0.00 0.00 2.52
70 71 2.322339 AGTACTCCCTCCGGTTCTTT 57.678 50.000 0.00 0.00 0.00 2.52
71 72 2.617658 AGTACTCCCTCCGGTTCTTTT 58.382 47.619 0.00 0.00 0.00 2.27
72 73 2.977580 AGTACTCCCTCCGGTTCTTTTT 59.022 45.455 0.00 0.00 0.00 1.94
73 74 4.162651 AGTACTCCCTCCGGTTCTTTTTA 58.837 43.478 0.00 0.00 0.00 1.52
74 75 3.413846 ACTCCCTCCGGTTCTTTTTAC 57.586 47.619 0.00 0.00 0.00 2.01
75 76 2.977580 ACTCCCTCCGGTTCTTTTTACT 59.022 45.455 0.00 0.00 0.00 2.24
76 77 3.007723 ACTCCCTCCGGTTCTTTTTACTC 59.992 47.826 0.00 0.00 0.00 2.59
77 78 3.245441 TCCCTCCGGTTCTTTTTACTCT 58.755 45.455 0.00 0.00 0.00 3.24
78 79 3.007614 TCCCTCCGGTTCTTTTTACTCTG 59.992 47.826 0.00 0.00 0.00 3.35
79 80 2.742589 CCTCCGGTTCTTTTTACTCTGC 59.257 50.000 0.00 0.00 0.00 4.26
80 81 3.399330 CTCCGGTTCTTTTTACTCTGCA 58.601 45.455 0.00 0.00 0.00 4.41
81 82 4.003648 CTCCGGTTCTTTTTACTCTGCAT 58.996 43.478 0.00 0.00 0.00 3.96
82 83 5.155278 TCCGGTTCTTTTTACTCTGCATA 57.845 39.130 0.00 0.00 0.00 3.14
83 84 5.741011 TCCGGTTCTTTTTACTCTGCATAT 58.259 37.500 0.00 0.00 0.00 1.78
84 85 6.177610 TCCGGTTCTTTTTACTCTGCATATT 58.822 36.000 0.00 0.00 0.00 1.28
85 86 7.332557 TCCGGTTCTTTTTACTCTGCATATTA 58.667 34.615 0.00 0.00 0.00 0.98
86 87 7.494625 TCCGGTTCTTTTTACTCTGCATATTAG 59.505 37.037 0.00 0.00 0.00 1.73
87 88 7.494625 CCGGTTCTTTTTACTCTGCATATTAGA 59.505 37.037 0.00 0.00 0.00 2.10
88 89 8.879759 CGGTTCTTTTTACTCTGCATATTAGAA 58.120 33.333 0.00 0.00 0.00 2.10
99 100 9.678260 ACTCTGCATATTAGAATTCTTTGAAGT 57.322 29.630 14.36 8.33 0.00 3.01
101 102 9.671279 TCTGCATATTAGAATTCTTTGAAGTCA 57.329 29.630 14.36 3.90 0.00 3.41
126 127 6.445357 ACTTCACAAAGTTTGACCGTATTT 57.555 33.333 22.23 0.00 43.28 1.40
127 128 7.556733 ACTTCACAAAGTTTGACCGTATTTA 57.443 32.000 22.23 0.00 43.28 1.40
128 129 8.161699 ACTTCACAAAGTTTGACCGTATTTAT 57.838 30.769 22.23 0.00 43.28 1.40
129 130 9.275398 ACTTCACAAAGTTTGACCGTATTTATA 57.725 29.630 22.23 0.00 43.28 0.98
132 133 9.438228 TCACAAAGTTTGACCGTATTTATATGA 57.562 29.630 22.23 7.49 0.00 2.15
156 157 5.927281 AAAATATCAACATCTGCCAAGCT 57.073 34.783 0.00 0.00 0.00 3.74
157 158 7.408756 AAAAATATCAACATCTGCCAAGCTA 57.591 32.000 0.00 0.00 0.00 3.32
158 159 7.408756 AAAATATCAACATCTGCCAAGCTAA 57.591 32.000 0.00 0.00 0.00 3.09
159 160 7.408756 AAATATCAACATCTGCCAAGCTAAA 57.591 32.000 0.00 0.00 0.00 1.85
160 161 4.978083 ATCAACATCTGCCAAGCTAAAG 57.022 40.909 0.00 0.00 0.00 1.85
161 162 3.754965 TCAACATCTGCCAAGCTAAAGT 58.245 40.909 0.00 0.00 0.00 2.66
162 163 4.144297 TCAACATCTGCCAAGCTAAAGTT 58.856 39.130 0.00 0.00 0.00 2.66
163 164 5.312895 TCAACATCTGCCAAGCTAAAGTTA 58.687 37.500 0.00 0.00 0.00 2.24
164 165 5.945784 TCAACATCTGCCAAGCTAAAGTTAT 59.054 36.000 0.00 0.00 0.00 1.89
165 166 7.109501 TCAACATCTGCCAAGCTAAAGTTATA 58.890 34.615 0.00 0.00 0.00 0.98
166 167 6.927294 ACATCTGCCAAGCTAAAGTTATAC 57.073 37.500 0.00 0.00 0.00 1.47
167 168 6.414732 ACATCTGCCAAGCTAAAGTTATACA 58.585 36.000 0.00 0.00 0.00 2.29
168 169 6.884295 ACATCTGCCAAGCTAAAGTTATACAA 59.116 34.615 0.00 0.00 0.00 2.41
169 170 7.557719 ACATCTGCCAAGCTAAAGTTATACAAT 59.442 33.333 0.00 0.00 0.00 2.71
170 171 9.056005 CATCTGCCAAGCTAAAGTTATACAATA 57.944 33.333 0.00 0.00 0.00 1.90
171 172 9.799106 ATCTGCCAAGCTAAAGTTATACAATAT 57.201 29.630 0.00 0.00 0.00 1.28
172 173 9.056005 TCTGCCAAGCTAAAGTTATACAATATG 57.944 33.333 0.00 0.00 0.00 1.78
173 174 8.972458 TGCCAAGCTAAAGTTATACAATATGA 57.028 30.769 0.00 0.00 0.00 2.15
174 175 9.402320 TGCCAAGCTAAAGTTATACAATATGAA 57.598 29.630 0.00 0.00 0.00 2.57
195 196 8.627208 ATGAAACTTTAAGTCATGACACATCT 57.373 30.769 27.02 3.53 30.84 2.90
196 197 9.725019 ATGAAACTTTAAGTCATGACACATCTA 57.275 29.630 27.02 7.86 30.84 1.98
197 198 9.725019 TGAAACTTTAAGTCATGACACATCTAT 57.275 29.630 27.02 7.36 0.00 1.98
200 201 9.725019 AACTTTAAGTCATGACACATCTATTGA 57.275 29.630 27.02 5.47 0.00 2.57
201 202 9.896645 ACTTTAAGTCATGACACATCTATTGAT 57.103 29.630 27.02 0.00 0.00 2.57
229 230 9.906660 TTGATTTTAGATTGTGAATGTTGGTAC 57.093 29.630 0.00 0.00 0.00 3.34
230 231 9.072375 TGATTTTAGATTGTGAATGTTGGTACA 57.928 29.630 0.00 0.00 38.95 2.90
265 266 5.453567 GTTGGTCAAACTTTATGAGGCTT 57.546 39.130 0.00 0.00 35.75 4.35
266 267 5.222631 GTTGGTCAAACTTTATGAGGCTTG 58.777 41.667 0.00 0.00 35.75 4.01
267 268 4.724399 TGGTCAAACTTTATGAGGCTTGA 58.276 39.130 0.00 0.00 32.24 3.02
268 269 4.518970 TGGTCAAACTTTATGAGGCTTGAC 59.481 41.667 7.18 7.18 44.00 3.18
269 270 4.762251 GGTCAAACTTTATGAGGCTTGACT 59.238 41.667 13.22 0.00 44.08 3.41
270 271 5.241728 GGTCAAACTTTATGAGGCTTGACTT 59.758 40.000 13.22 0.00 44.08 3.01
271 272 6.239036 GGTCAAACTTTATGAGGCTTGACTTT 60.239 38.462 13.22 0.00 44.08 2.66
272 273 7.040686 GGTCAAACTTTATGAGGCTTGACTTTA 60.041 37.037 13.22 0.00 44.08 1.85
273 274 8.017946 GTCAAACTTTATGAGGCTTGACTTTAG 58.982 37.037 8.16 0.00 42.80 1.85
274 275 7.719633 TCAAACTTTATGAGGCTTGACTTTAGT 59.280 33.333 0.00 0.00 30.70 2.24
275 276 7.674471 AACTTTATGAGGCTTGACTTTAGTC 57.326 36.000 2.92 2.92 44.97 2.59
292 293 9.851043 GACTTTAGTCAAATCTTATATGCGAAC 57.149 33.333 5.04 0.00 44.18 3.95
293 294 9.601217 ACTTTAGTCAAATCTTATATGCGAACT 57.399 29.630 0.00 0.00 0.00 3.01
303 304 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
304 305 6.477688 TCTTATATGCGAACTAAAAAGGACCG 59.522 38.462 0.00 0.00 0.00 4.79
305 306 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
306 307 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
307 308 1.730612 GCGAACTAAAAAGGACCGGAG 59.269 52.381 9.46 0.00 0.00 4.63
337 338 1.171308 GGTCATGTCAGTGCTTGCAT 58.829 50.000 0.00 0.00 0.00 3.96
345 346 5.996669 TGTCAGTGCTTGCATTATCATAG 57.003 39.130 0.00 0.00 0.00 2.23
385 386 1.422531 GATCTCTGGATCTGGCACCT 58.577 55.000 0.00 0.00 43.55 4.00
433 434 5.643348 ACAATGATATCAACGTGCTTCAAGA 59.357 36.000 9.99 0.00 0.00 3.02
501 685 3.520290 GATGGGGCATCGTTCGATATA 57.480 47.619 7.38 0.00 31.01 0.86
504 688 5.597806 GATGGGGCATCGTTCGATATATTA 58.402 41.667 7.38 0.00 31.01 0.98
505 689 5.607939 TGGGGCATCGTTCGATATATTAT 57.392 39.130 7.38 0.00 0.00 1.28
531 717 4.689612 ACTTGAAGCACTAGGAAGTTGA 57.310 40.909 0.00 0.00 31.97 3.18
558 744 4.872124 GTGATGACTGCTTGTGTGATCATA 59.128 41.667 0.00 0.00 39.43 2.15
583 769 5.049336 CACAATACGATCGTAGAGGATGAGT 60.049 44.000 29.63 16.38 43.63 3.41
654 840 2.178890 GCCTGAGCATGAAGGAGCG 61.179 63.158 12.35 0.00 39.53 5.03
676 865 4.356289 GGCAACGTTTACACAGTTCATTT 58.644 39.130 0.00 0.00 0.00 2.32
684 873 9.228636 ACGTTTACACAGTTCATTTAATTTCAC 57.771 29.630 0.00 0.00 0.00 3.18
707 896 7.068103 TCACCATAAAATGCGTGATTAGGAAAT 59.932 33.333 6.95 0.00 36.35 2.17
720 909 1.471119 AGGAAATCACATGCAGCTGG 58.529 50.000 17.12 0.73 0.00 4.85
732 921 5.049198 CACATGCAGCTGGGTATAACAATAG 60.049 44.000 17.12 0.79 0.00 1.73
1628 1832 2.202987 CATGGTGAGGGAGCTCGC 60.203 66.667 22.44 22.44 0.00 5.03
2816 3491 3.932089 GCAAAATAAACGGCCATGTCAAT 59.068 39.130 2.24 0.00 0.00 2.57
2826 3501 1.635844 CCATGTCAATGTGTGCATGC 58.364 50.000 11.82 11.82 38.95 4.06
2893 3569 1.087771 GTGCGGCCGTTAGTAATGCT 61.088 55.000 28.70 0.00 0.00 3.79
2918 3594 0.179081 TAGCATGCAGAGCAGCTCAG 60.179 55.000 24.64 17.65 43.65 3.35
2999 3675 1.087501 GCGTGGTTGATCTTTCCCTC 58.912 55.000 0.00 0.00 0.00 4.30
3080 3757 3.796717 GCACAAAACACCTTAGTCTTTGC 59.203 43.478 0.00 0.00 31.60 3.68
3081 3758 4.440112 GCACAAAACACCTTAGTCTTTGCT 60.440 41.667 0.00 0.00 31.60 3.91
3092 3769 1.143684 AGTCTTTGCTTCCTTCTGGCA 59.856 47.619 0.00 0.00 0.00 4.92
3121 3823 1.308998 CTTGCAGGTGTCTTCGGTTT 58.691 50.000 0.00 0.00 0.00 3.27
3122 3824 1.676006 CTTGCAGGTGTCTTCGGTTTT 59.324 47.619 0.00 0.00 0.00 2.43
3141 3843 5.705905 GGTTTTAACAAGTGGTATGAGAGCT 59.294 40.000 0.00 0.00 0.00 4.09
3152 3854 2.507324 GAGAGCTGCGTCGTTCCC 60.507 66.667 0.00 0.00 0.00 3.97
3155 3857 3.282745 GAGCTGCGTCGTTCCCTGA 62.283 63.158 0.00 0.00 0.00 3.86
3208 3910 2.962786 CCGACAACCGTTGACGCA 60.963 61.111 24.47 0.00 45.01 5.24
3252 3955 0.540830 AGGAGGCTGACGACTCTTGT 60.541 55.000 0.00 0.00 45.12 3.16
3253 3956 0.109039 GGAGGCTGACGACTCTTGTC 60.109 60.000 0.00 0.00 45.12 3.18
3277 3980 1.738099 GGCGCGTGATCAGTGACTT 60.738 57.895 8.43 0.00 0.00 3.01
3279 3982 1.008875 GCGCGTGATCAGTGACTTCA 61.009 55.000 8.43 0.00 0.00 3.02
3282 3985 2.135139 GCGTGATCAGTGACTTCAACA 58.865 47.619 0.00 0.00 0.00 3.33
3285 3988 3.989817 CGTGATCAGTGACTTCAACATGA 59.010 43.478 0.00 0.00 0.00 3.07
3398 4107 2.012051 GCCAATACTCACCCCGACAAG 61.012 57.143 0.00 0.00 0.00 3.16
3482 4212 3.276091 CAACGACAAGGCGGCACA 61.276 61.111 13.08 0.00 35.12 4.57
3500 4230 0.389391 CAGGCGGTCATCCTACGATT 59.611 55.000 0.00 0.00 31.52 3.34
3639 4371 1.737008 GTTCGGAGTTCCAGGCGAC 60.737 63.158 0.00 0.00 35.14 5.19
3730 4462 1.153549 GCTCCGAGACACCATGGAC 60.154 63.158 21.47 9.43 0.00 4.02
3745 4477 0.894184 TGGACGAGGTGAGAGTGGTC 60.894 60.000 0.00 0.00 0.00 4.02
3751 4483 1.548269 GAGGTGAGAGTGGTCCAGAAG 59.452 57.143 0.00 0.00 0.00 2.85
3757 4489 3.711704 TGAGAGTGGTCCAGAAGTTTCTT 59.288 43.478 0.00 0.00 34.74 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.303074 CACTCCCAGTGCATGCAGT 60.303 57.895 23.41 22.90 39.62 4.40
6 7 0.895100 TTTCCACTCCCAGTGCATGC 60.895 55.000 11.82 11.82 44.63 4.06
7 8 1.619654 TTTTCCACTCCCAGTGCATG 58.380 50.000 0.00 0.00 44.63 4.06
8 9 1.963515 GTTTTTCCACTCCCAGTGCAT 59.036 47.619 0.00 0.00 44.63 3.96
10 11 1.692411 AGTTTTTCCACTCCCAGTGC 58.308 50.000 0.00 0.00 44.63 4.40
11 12 3.146847 GGTAGTTTTTCCACTCCCAGTG 58.853 50.000 0.00 0.00 45.53 3.66
12 13 2.107726 GGGTAGTTTTTCCACTCCCAGT 59.892 50.000 0.00 0.00 35.64 4.00
13 14 2.375509 AGGGTAGTTTTTCCACTCCCAG 59.624 50.000 0.00 0.00 36.94 4.45
14 15 2.424793 AGGGTAGTTTTTCCACTCCCA 58.575 47.619 0.00 0.00 36.94 4.37
15 16 3.074094 AGAAGGGTAGTTTTTCCACTCCC 59.926 47.826 0.00 0.00 35.72 4.30
16 17 4.072839 CAGAAGGGTAGTTTTTCCACTCC 58.927 47.826 0.00 0.00 0.00 3.85
17 18 3.502595 GCAGAAGGGTAGTTTTTCCACTC 59.497 47.826 0.00 0.00 0.00 3.51
18 19 3.138468 AGCAGAAGGGTAGTTTTTCCACT 59.862 43.478 0.00 0.00 0.00 4.00
19 20 3.487372 AGCAGAAGGGTAGTTTTTCCAC 58.513 45.455 0.00 0.00 0.00 4.02
20 21 3.876309 AGCAGAAGGGTAGTTTTTCCA 57.124 42.857 0.00 0.00 0.00 3.53
21 22 3.255888 CCAAGCAGAAGGGTAGTTTTTCC 59.744 47.826 0.00 0.00 0.00 3.13
22 23 3.305403 GCCAAGCAGAAGGGTAGTTTTTC 60.305 47.826 0.00 0.00 0.00 2.29
23 24 2.628178 GCCAAGCAGAAGGGTAGTTTTT 59.372 45.455 0.00 0.00 0.00 1.94
24 25 2.239400 GCCAAGCAGAAGGGTAGTTTT 58.761 47.619 0.00 0.00 0.00 2.43
25 26 1.144913 TGCCAAGCAGAAGGGTAGTTT 59.855 47.619 0.00 0.00 33.32 2.66
26 27 0.771127 TGCCAAGCAGAAGGGTAGTT 59.229 50.000 0.00 0.00 33.32 2.24
27 28 0.771127 TTGCCAAGCAGAAGGGTAGT 59.229 50.000 0.00 0.00 40.61 2.73
28 29 1.457346 CTTGCCAAGCAGAAGGGTAG 58.543 55.000 0.00 0.00 40.61 3.18
29 30 0.038166 CCTTGCCAAGCAGAAGGGTA 59.962 55.000 0.00 0.00 40.61 3.69
30 31 1.228675 CCTTGCCAAGCAGAAGGGT 60.229 57.895 0.00 0.00 40.61 4.34
31 32 1.980772 CCCTTGCCAAGCAGAAGGG 60.981 63.158 11.06 11.06 46.18 3.95
32 33 0.038166 TACCCTTGCCAAGCAGAAGG 59.962 55.000 0.00 0.00 40.61 3.46
33 34 1.271597 ACTACCCTTGCCAAGCAGAAG 60.272 52.381 0.00 0.00 40.61 2.85
34 35 0.771127 ACTACCCTTGCCAAGCAGAA 59.229 50.000 0.00 0.00 40.61 3.02
35 36 1.278127 GTACTACCCTTGCCAAGCAGA 59.722 52.381 0.00 0.00 40.61 4.26
36 37 1.279271 AGTACTACCCTTGCCAAGCAG 59.721 52.381 0.00 0.00 40.61 4.24
37 38 1.278127 GAGTACTACCCTTGCCAAGCA 59.722 52.381 0.00 0.00 36.47 3.91
38 39 1.407025 GGAGTACTACCCTTGCCAAGC 60.407 57.143 0.00 0.00 0.00 4.01
39 40 1.209747 GGGAGTACTACCCTTGCCAAG 59.790 57.143 13.90 0.00 43.65 3.61
40 41 1.282382 GGGAGTACTACCCTTGCCAA 58.718 55.000 13.90 0.00 43.65 4.52
41 42 3.001514 GGGAGTACTACCCTTGCCA 57.998 57.895 13.90 0.00 43.65 4.92
59 60 3.399330 TGCAGAGTAAAAAGAACCGGAG 58.601 45.455 9.46 0.00 0.00 4.63
60 61 3.478857 TGCAGAGTAAAAAGAACCGGA 57.521 42.857 9.46 0.00 0.00 5.14
61 62 6.436843 AATATGCAGAGTAAAAAGAACCGG 57.563 37.500 0.00 0.00 0.00 5.28
62 63 8.420374 TCTAATATGCAGAGTAAAAAGAACCG 57.580 34.615 0.00 0.00 0.00 4.44
73 74 9.678260 ACTTCAAAGAATTCTAATATGCAGAGT 57.322 29.630 8.75 7.81 0.00 3.24
75 76 9.671279 TGACTTCAAAGAATTCTAATATGCAGA 57.329 29.630 8.75 0.00 0.00 4.26
106 107 9.438228 TCATATAAATACGGTCAAACTTTGTGA 57.562 29.630 1.44 0.00 0.00 3.58
133 134 6.290294 AGCTTGGCAGATGTTGATATTTTT 57.710 33.333 0.00 0.00 0.00 1.94
134 135 5.927281 AGCTTGGCAGATGTTGATATTTT 57.073 34.783 0.00 0.00 0.00 1.82
135 136 7.123247 ACTTTAGCTTGGCAGATGTTGATATTT 59.877 33.333 0.00 0.00 0.00 1.40
136 137 6.604795 ACTTTAGCTTGGCAGATGTTGATATT 59.395 34.615 0.00 0.00 0.00 1.28
137 138 6.125029 ACTTTAGCTTGGCAGATGTTGATAT 58.875 36.000 0.00 0.00 0.00 1.63
138 139 5.500234 ACTTTAGCTTGGCAGATGTTGATA 58.500 37.500 0.00 0.00 0.00 2.15
139 140 4.338879 ACTTTAGCTTGGCAGATGTTGAT 58.661 39.130 0.00 0.00 0.00 2.57
140 141 3.754965 ACTTTAGCTTGGCAGATGTTGA 58.245 40.909 0.00 0.00 0.00 3.18
141 142 4.510038 AACTTTAGCTTGGCAGATGTTG 57.490 40.909 0.00 0.00 0.00 3.33
142 143 6.884295 TGTATAACTTTAGCTTGGCAGATGTT 59.116 34.615 0.00 0.00 0.00 2.71
143 144 6.414732 TGTATAACTTTAGCTTGGCAGATGT 58.585 36.000 0.00 0.00 0.00 3.06
144 145 6.925610 TGTATAACTTTAGCTTGGCAGATG 57.074 37.500 0.00 0.00 0.00 2.90
145 146 9.799106 ATATTGTATAACTTTAGCTTGGCAGAT 57.201 29.630 0.00 0.00 0.00 2.90
146 147 9.056005 CATATTGTATAACTTTAGCTTGGCAGA 57.944 33.333 0.00 0.00 0.00 4.26
147 148 9.056005 TCATATTGTATAACTTTAGCTTGGCAG 57.944 33.333 0.00 0.00 0.00 4.85
148 149 8.972458 TCATATTGTATAACTTTAGCTTGGCA 57.028 30.769 0.00 0.00 0.00 4.92
169 170 9.725019 AGATGTGTCATGACTTAAAGTTTCATA 57.275 29.630 25.55 1.27 0.00 2.15
170 171 8.627208 AGATGTGTCATGACTTAAAGTTTCAT 57.373 30.769 25.55 14.42 0.00 2.57
171 172 9.725019 ATAGATGTGTCATGACTTAAAGTTTCA 57.275 29.630 25.55 11.05 0.00 2.69
174 175 9.725019 TCAATAGATGTGTCATGACTTAAAGTT 57.275 29.630 25.55 10.34 0.00 2.66
175 176 9.896645 ATCAATAGATGTGTCATGACTTAAAGT 57.103 29.630 25.55 9.39 31.91 2.66
203 204 9.906660 GTACCAACATTCACAATCTAAAATCAA 57.093 29.630 0.00 0.00 0.00 2.57
204 205 9.072375 TGTACCAACATTCACAATCTAAAATCA 57.928 29.630 0.00 0.00 0.00 2.57
243 244 5.009610 TCAAGCCTCATAAAGTTTGACCAAC 59.990 40.000 0.00 0.00 35.32 3.77
244 245 5.009610 GTCAAGCCTCATAAAGTTTGACCAA 59.990 40.000 8.09 0.00 39.44 3.67
245 246 4.518970 GTCAAGCCTCATAAAGTTTGACCA 59.481 41.667 8.09 0.00 39.44 4.02
246 247 4.762251 AGTCAAGCCTCATAAAGTTTGACC 59.238 41.667 13.71 0.72 42.68 4.02
247 248 5.948992 AGTCAAGCCTCATAAAGTTTGAC 57.051 39.130 10.54 10.54 42.37 3.18
248 249 6.959639 AAAGTCAAGCCTCATAAAGTTTGA 57.040 33.333 0.00 0.00 0.00 2.69
249 250 7.875971 ACTAAAGTCAAGCCTCATAAAGTTTG 58.124 34.615 0.00 0.00 0.00 2.93
250 251 8.100508 GACTAAAGTCAAGCCTCATAAAGTTT 57.899 34.615 5.24 0.00 44.18 2.66
251 252 7.674471 GACTAAAGTCAAGCCTCATAAAGTT 57.326 36.000 5.24 0.00 44.18 2.66
266 267 9.851043 GTTCGCATATAAGATTTGACTAAAGTC 57.149 33.333 3.08 3.08 44.97 3.01
267 268 9.601217 AGTTCGCATATAAGATTTGACTAAAGT 57.399 29.630 0.00 0.00 0.00 2.66
277 278 8.837389 GGTCCTTTTTAGTTCGCATATAAGATT 58.163 33.333 0.00 0.00 0.00 2.40
278 279 7.170998 CGGTCCTTTTTAGTTCGCATATAAGAT 59.829 37.037 0.00 0.00 0.00 2.40
279 280 6.477688 CGGTCCTTTTTAGTTCGCATATAAGA 59.522 38.462 0.00 0.00 0.00 2.10
280 281 6.292703 CCGGTCCTTTTTAGTTCGCATATAAG 60.293 42.308 0.00 0.00 0.00 1.73
281 282 5.524646 CCGGTCCTTTTTAGTTCGCATATAA 59.475 40.000 0.00 0.00 0.00 0.98
282 283 5.051816 CCGGTCCTTTTTAGTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
283 284 3.875134 CCGGTCCTTTTTAGTTCGCATAT 59.125 43.478 0.00 0.00 0.00 1.78
284 285 3.055963 TCCGGTCCTTTTTAGTTCGCATA 60.056 43.478 0.00 0.00 0.00 3.14
285 286 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
286 287 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
287 288 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
288 289 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
289 290 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
290 291 2.305052 CTCCCTCCGGTCCTTTTTAGTT 59.695 50.000 0.00 0.00 0.00 2.24
291 292 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
292 293 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
293 294 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
294 295 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
295 296 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
296 297 3.306613 CTTATACTCCCTCCGGTCCTTT 58.693 50.000 0.00 0.00 0.00 3.11
297 298 2.425975 CCTTATACTCCCTCCGGTCCTT 60.426 54.545 0.00 0.00 0.00 3.36
298 299 1.147399 CCTTATACTCCCTCCGGTCCT 59.853 57.143 0.00 0.00 0.00 3.85
299 300 1.630223 CCTTATACTCCCTCCGGTCC 58.370 60.000 0.00 0.00 0.00 4.46
300 301 1.133231 ACCCTTATACTCCCTCCGGTC 60.133 57.143 0.00 0.00 0.00 4.79
301 302 0.939698 ACCCTTATACTCCCTCCGGT 59.060 55.000 0.00 0.00 0.00 5.28
302 303 1.133262 TGACCCTTATACTCCCTCCGG 60.133 57.143 0.00 0.00 0.00 5.14
303 304 2.376695 TGACCCTTATACTCCCTCCG 57.623 55.000 0.00 0.00 0.00 4.63
304 305 3.579151 GACATGACCCTTATACTCCCTCC 59.421 52.174 0.00 0.00 0.00 4.30
305 306 4.223953 TGACATGACCCTTATACTCCCTC 58.776 47.826 0.00 0.00 0.00 4.30
306 307 4.227197 CTGACATGACCCTTATACTCCCT 58.773 47.826 0.00 0.00 0.00 4.20
307 308 3.967987 ACTGACATGACCCTTATACTCCC 59.032 47.826 0.00 0.00 0.00 4.30
308 309 4.740934 GCACTGACATGACCCTTATACTCC 60.741 50.000 0.00 0.00 0.00 3.85
309 310 4.100189 AGCACTGACATGACCCTTATACTC 59.900 45.833 0.00 0.00 0.00 2.59
310 311 4.033709 AGCACTGACATGACCCTTATACT 58.966 43.478 0.00 0.00 0.00 2.12
337 338 2.484770 GCCACGGCCTCAACTATGATAA 60.485 50.000 0.00 0.00 34.37 1.75
433 434 1.447317 CCTTGCAAACACCAGCGAGT 61.447 55.000 0.00 0.00 40.01 4.18
501 685 9.606631 CTTCCTAGTGCTTCAAGTTCTAATAAT 57.393 33.333 0.00 0.00 0.00 1.28
504 688 7.010339 ACTTCCTAGTGCTTCAAGTTCTAAT 57.990 36.000 0.00 0.00 31.99 1.73
505 689 6.420913 ACTTCCTAGTGCTTCAAGTTCTAA 57.579 37.500 0.00 0.00 31.99 2.10
521 705 4.464244 CAGTCATCACCTCTCAACTTCCTA 59.536 45.833 0.00 0.00 0.00 2.94
523 707 3.594134 CAGTCATCACCTCTCAACTTCC 58.406 50.000 0.00 0.00 0.00 3.46
531 717 1.696336 ACACAAGCAGTCATCACCTCT 59.304 47.619 0.00 0.00 0.00 3.69
558 744 4.820173 TCATCCTCTACGATCGTATTGTGT 59.180 41.667 26.95 11.69 0.00 3.72
566 752 1.068885 GGCACTCATCCTCTACGATCG 60.069 57.143 14.88 14.88 0.00 3.69
583 769 1.729276 CGTAGATACGTTCCGGGCA 59.271 57.895 0.00 0.00 44.13 5.36
654 840 3.619233 ATGAACTGTGTAAACGTTGCC 57.381 42.857 0.00 0.00 0.00 4.52
676 865 9.729023 CTAATCACGCATTTTATGGTGAAATTA 57.271 29.630 11.97 8.31 40.88 1.40
684 873 7.424803 TGATTTCCTAATCACGCATTTTATGG 58.575 34.615 0.00 0.00 43.93 2.74
701 890 1.471119 CCAGCTGCATGTGATTTCCT 58.529 50.000 8.66 0.00 0.00 3.36
707 896 2.238395 TGTTATACCCAGCTGCATGTGA 59.762 45.455 8.66 0.00 0.00 3.58
720 909 9.649167 GTGTGTATGGGTATCTATTGTTATACC 57.351 37.037 0.00 0.00 44.64 2.73
732 921 8.732746 AGTATCTTTTTGTGTGTATGGGTATC 57.267 34.615 0.00 0.00 0.00 2.24
755 944 4.442192 GCAACTTCCTTGATCGAGGATAGT 60.442 45.833 28.99 27.11 44.98 2.12
864 1057 0.908910 TTAGACACATCGGGGTGCAT 59.091 50.000 7.19 0.27 42.55 3.96
964 1168 2.742348 TGAATGAATGAAGGCCTGCAT 58.258 42.857 21.76 21.76 0.00 3.96
1937 2141 3.211288 GCTCCTCTGCGGCTCTTA 58.789 61.111 0.00 0.00 0.00 2.10
2172 2382 2.173519 CCGGAGTTGTACAGGAAGGTA 58.826 52.381 0.00 0.00 0.00 3.08
2416 2633 2.471818 CATCTGCTCAATCTCGTCCAG 58.528 52.381 0.00 0.00 0.00 3.86
2761 2978 1.267121 AACTAGTGGTGCCGTCATCT 58.733 50.000 0.00 0.00 0.00 2.90
2816 3491 3.662153 CCAGCGTGCATGCACACA 61.662 61.111 40.95 11.58 46.47 3.72
2829 3504 3.757248 CTACCGGGCCACATCCAGC 62.757 68.421 6.32 0.00 0.00 4.85
2893 3569 0.547553 TGCTCTGCATGCTATCCCAA 59.452 50.000 20.33 0.00 31.71 4.12
3080 3757 3.613432 GCTCAACAATTGCCAGAAGGAAG 60.613 47.826 5.05 0.00 36.89 3.46
3081 3758 2.297033 GCTCAACAATTGCCAGAAGGAA 59.703 45.455 5.05 0.00 36.89 3.36
3092 3769 2.034124 ACACCTGCAAGCTCAACAATT 58.966 42.857 0.00 0.00 0.00 2.32
3121 3823 4.253685 GCAGCTCTCATACCACTTGTTAA 58.746 43.478 0.00 0.00 0.00 2.01
3122 3824 3.676049 CGCAGCTCTCATACCACTTGTTA 60.676 47.826 0.00 0.00 0.00 2.41
3152 3854 2.969238 GCCGGCCATGATCGTCAG 60.969 66.667 18.11 0.00 0.00 3.51
3155 3857 4.592192 CGAGCCGGCCATGATCGT 62.592 66.667 26.15 0.00 0.00 3.73
3265 3968 4.040829 ACCTCATGTTGAAGTCACTGATCA 59.959 41.667 0.00 0.00 0.00 2.92
3277 3980 1.596934 GGCTCCGACCTCATGTTGA 59.403 57.895 0.00 0.00 0.00 3.18
3279 3982 2.579201 CGGCTCCGACCTCATGTT 59.421 61.111 1.35 0.00 42.83 2.71
3282 3985 3.842923 CTGCGGCTCCGACCTCAT 61.843 66.667 13.11 0.00 42.83 2.90
3307 4016 2.586357 GACGATCTCCTTGCCGCC 60.586 66.667 0.00 0.00 0.00 6.13
3398 4107 0.099082 CTCCGACCACTCGAAGTAGC 59.901 60.000 0.00 0.00 43.06 3.58
3482 4212 0.674534 GAATCGTAGGATGACCGCCT 59.325 55.000 0.00 0.00 41.83 5.52
3488 4218 3.187842 CGACGGTATGAATCGTAGGATGA 59.812 47.826 0.00 0.00 39.88 2.92
3500 4230 1.951602 CCACCATCTACGACGGTATGA 59.048 52.381 0.00 0.00 0.00 2.15
3690 4422 2.243957 CGCAGGTTGTTGACGAGCA 61.244 57.895 3.64 0.00 0.00 4.26
3716 4448 1.139734 CCTCGTCCATGGTGTCTCG 59.860 63.158 12.58 10.10 0.00 4.04
3718 4450 1.975327 CACCTCGTCCATGGTGTCT 59.025 57.895 12.58 0.00 46.18 3.41
3730 4462 0.609406 TCTGGACCACTCTCACCTCG 60.609 60.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.