Multiple sequence alignment - TraesCS2D01G192800

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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 TraesCS2D01G192800 chr2D 100.000 3971 0 0 1 3971 136830655 136834625 0.000000e+00 7334.0
1 TraesCS2D01G192800 chr2D 87.952 249 20 6 2469 2710 634861289 634861534 6.490000e-73 285.0
2 TraesCS2D01G192800 chr2D 98.649 74 1 0 2 75 50951478 50951551 8.950000e-27 132.0
3 TraesCS2D01G192800 chr2D 97.333 75 2 0 1 75 563801053 563801127 1.160000e-25 128.0
4 TraesCS2D01G192800 chr2D 95.946 74 3 0 2 75 89199374 89199301 1.940000e-23 121.0
5 TraesCS2D01G192800 chr2A 92.830 2357 93 38 619 2934 164705890 164703569 0.000000e+00 3347.0
6 TraesCS2D01G192800 chr2A 86.004 493 33 15 97 564 164706555 164706074 2.760000e-136 496.0
7 TraesCS2D01G192800 chr2A 81.298 524 36 29 3484 3971 164703029 164702532 6.270000e-98 368.0
8 TraesCS2D01G192800 chr2A 100.000 40 0 0 557 596 164705926 164705887 1.530000e-09 75.0
9 TraesCS2D01G192800 chr2B 92.586 2320 88 26 649 2924 195528941 195531220 0.000000e+00 3254.0
10 TraesCS2D01G192800 chr2B 89.813 589 27 18 79 657 195521303 195521868 0.000000e+00 725.0
11 TraesCS2D01G192800 chr2B 92.804 403 15 6 3484 3874 195531766 195532166 4.450000e-159 571.0
12 TraesCS2D01G192800 chr2B 84.615 299 14 7 2931 3223 195531285 195531557 6.540000e-68 268.0
13 TraesCS2D01G192800 chr2B 85.156 128 12 6 3358 3485 195531617 195531737 1.500000e-24 124.0
14 TraesCS2D01G192800 chr2B 100.000 29 0 0 3943 3971 195532226 195532254 2.000000e-03 54.7
15 TraesCS2D01G192800 chr4A 82.353 442 74 4 2180 2619 546211461 546211900 8.050000e-102 381.0
16 TraesCS2D01G192800 chr4A 74.351 308 58 18 1290 1595 546210287 546210575 1.170000e-20 111.0
17 TraesCS2D01G192800 chr4D 81.064 470 83 6 2183 2649 50770604 50770138 1.740000e-98 370.0
18 TraesCS2D01G192800 chr4D 76.712 219 32 16 1381 1595 50771708 50771505 1.950000e-18 104.0
19 TraesCS2D01G192800 chr4B 80.810 469 86 4 2183 2649 74681863 74681397 8.110000e-97 364.0
20 TraesCS2D01G192800 chr4B 75.688 218 36 15 1381 1595 74682965 74682762 4.230000e-15 93.5
21 TraesCS2D01G192800 chr3D 98.667 75 1 0 1 75 571857113 571857039 2.490000e-27 134.0
22 TraesCS2D01G192800 chr3D 96.000 75 3 0 1 75 576210628 576210702 5.390000e-24 122.0
23 TraesCS2D01G192800 chr3D 98.333 60 1 0 16 75 170555542 170555601 5.430000e-19 106.0
24 TraesCS2D01G192800 chr3D 94.828 58 2 1 3246 3303 610326 610270 5.470000e-14 89.8
25 TraesCS2D01G192800 chr3D 75.132 189 40 6 2207 2391 414627690 414627505 9.150000e-12 82.4
26 TraesCS2D01G192800 chr7A 96.000 75 3 0 1 75 732909321 732909395 5.390000e-24 122.0
27 TraesCS2D01G192800 chr7A 91.045 67 5 1 3238 3303 646672630 646672696 5.470000e-14 89.8
28 TraesCS2D01G192800 chr5D 95.946 74 3 0 2 75 223229274 223229347 1.940000e-23 121.0
29 TraesCS2D01G192800 chr1B 94.667 75 4 0 1 75 677279087 677279161 2.510000e-22 117.0
30 TraesCS2D01G192800 chr7D 98.113 53 1 0 3251 3303 71352746 71352694 4.230000e-15 93.5
31 TraesCS2D01G192800 chrUn 98.077 52 1 0 3252 3303 111028710 111028761 1.520000e-14 91.6
32 TraesCS2D01G192800 chr1D 98.077 52 1 0 3252 3303 108802279 108802330 1.520000e-14 91.6
33 TraesCS2D01G192800 chr1D 98.077 52 1 0 3252 3303 439248240 439248291 1.520000e-14 91.6
34 TraesCS2D01G192800 chr1D 98.077 52 1 0 3252 3303 454511836 454511785 1.520000e-14 91.6
35 TraesCS2D01G192800 chr3A 94.828 58 2 1 3247 3303 739272441 739272384 5.470000e-14 89.8
36 TraesCS2D01G192800 chr5A 91.935 62 4 1 3243 3303 18060362 18060423 7.070000e-13 86.1
37 TraesCS2D01G192800 chr3B 75.132 189 40 6 2207 2391 540455246 540455061 9.150000e-12 82.4


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 TraesCS2D01G192800 chr2D 136830655 136834625 3970 False 7334.00 7334 100.0000 1 3971 1 chr2D.!!$F2 3970
1 TraesCS2D01G192800 chr2A 164702532 164706555 4023 True 1071.50 3347 90.0330 97 3971 4 chr2A.!!$R1 3874
2 TraesCS2D01G192800 chr2B 195528941 195532254 3313 False 854.34 3254 91.0322 649 3971 5 chr2B.!!$F2 3322
3 TraesCS2D01G192800 chr2B 195521303 195521868 565 False 725.00 725 89.8130 79 657 1 chr2B.!!$F1 578
4 TraesCS2D01G192800 chr4A 546210287 546211900 1613 False 246.00 381 78.3520 1290 2619 2 chr4A.!!$F1 1329
5 TraesCS2D01G192800 chr4D 50770138 50771708 1570 True 237.00 370 78.8880 1381 2649 2 chr4D.!!$R1 1268
6 TraesCS2D01G192800 chr4B 74681397 74682965 1568 True 228.75 364 78.2490 1381 2649 2 chr4B.!!$R1 1268

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
35 36 0.028242 GACGAGCGAGATCATGTCGT 59.972 55.0 6.02 10.89 46.02 4.34 F
62 63 0.239082 TCGTACGCACTGTTCATCGT 59.761 50.0 11.24 0.00 38.75 3.73 F
957 1175 0.250513 ACTCGCCTCACATCTTTCCC 59.749 55.0 0.00 0.00 0.00 3.97 F
1063 1285 0.315568 ATTAGAGCTCGTCATCCGCC 59.684 55.0 8.37 0.00 36.19 6.13 F
2792 3390 0.965439 GTGTGAGGAGCAGACTCAGT 59.035 55.0 5.41 0.00 44.90 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1285 0.820226 TCTCCTTCTCCATCGCACTG 59.180 55.0 0.0 0.0 0.00 3.66 R
1674 2046 1.084370 CGACTCCTGCGAATTCCCAC 61.084 60.0 0.0 0.0 0.00 4.61 R
2835 3444 0.108424 CTACCAGCAGGCAGACAGAC 60.108 60.0 0.0 0.0 39.06 3.51 R
2837 3446 0.175302 CTCTACCAGCAGGCAGACAG 59.825 60.0 0.0 0.0 39.06 3.51 R
3930 4760 0.301088 CGTCTACTACTGCGTCTCCG 59.699 60.0 0.0 0.0 37.07 4.63 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
21 22 3.710326 TCGATTAGTTGGATGGACGAG 57.290 47.619 0.00 0.00 0.00 4.18
22 23 2.128035 CGATTAGTTGGATGGACGAGC 58.872 52.381 0.00 0.00 0.00 5.03
23 24 2.128035 GATTAGTTGGATGGACGAGCG 58.872 52.381 0.00 0.00 0.00 5.03
24 25 1.179152 TTAGTTGGATGGACGAGCGA 58.821 50.000 0.00 0.00 0.00 4.93
25 26 0.738975 TAGTTGGATGGACGAGCGAG 59.261 55.000 0.00 0.00 0.00 5.03
26 27 0.965866 AGTTGGATGGACGAGCGAGA 60.966 55.000 0.00 0.00 0.00 4.04
27 28 0.103208 GTTGGATGGACGAGCGAGAT 59.897 55.000 0.00 0.00 0.00 2.75
28 29 0.385751 TTGGATGGACGAGCGAGATC 59.614 55.000 0.00 0.00 0.00 2.75
29 30 0.751643 TGGATGGACGAGCGAGATCA 60.752 55.000 0.00 0.00 0.00 2.92
30 31 0.600557 GGATGGACGAGCGAGATCAT 59.399 55.000 0.00 0.00 0.00 2.45
31 32 1.668337 GGATGGACGAGCGAGATCATG 60.668 57.143 0.00 0.00 0.00 3.07
32 33 1.000827 GATGGACGAGCGAGATCATGT 60.001 52.381 0.00 0.00 0.00 3.21
33 34 0.382158 TGGACGAGCGAGATCATGTC 59.618 55.000 0.00 0.00 0.00 3.06
34 35 0.658829 GGACGAGCGAGATCATGTCG 60.659 60.000 0.00 0.00 40.50 4.35
35 36 0.028242 GACGAGCGAGATCATGTCGT 59.972 55.000 6.02 10.89 46.02 4.34
36 37 1.260825 GACGAGCGAGATCATGTCGTA 59.739 52.381 6.02 0.00 43.55 3.43
37 38 1.003759 ACGAGCGAGATCATGTCGTAC 60.004 52.381 6.02 0.00 41.82 3.67
38 39 1.664629 GAGCGAGATCATGTCGTACG 58.335 55.000 9.53 9.53 39.69 3.67
39 40 1.260825 GAGCGAGATCATGTCGTACGA 59.739 52.381 15.28 15.28 39.69 3.43
40 41 1.669265 AGCGAGATCATGTCGTACGAA 59.331 47.619 21.39 10.90 39.69 3.85
41 42 2.096980 AGCGAGATCATGTCGTACGAAA 59.903 45.455 21.39 16.34 39.69 3.46
42 43 2.850060 GCGAGATCATGTCGTACGAAAA 59.150 45.455 21.39 12.05 39.69 2.29
43 44 3.486108 GCGAGATCATGTCGTACGAAAAT 59.514 43.478 21.39 13.93 39.69 1.82
44 45 4.374112 GCGAGATCATGTCGTACGAAAATC 60.374 45.833 21.39 15.11 39.69 2.17
45 46 4.144007 CGAGATCATGTCGTACGAAAATCG 60.144 45.833 21.39 17.26 38.03 3.34
56 57 2.848562 CGAAAATCGTACGCACTGTT 57.151 45.000 11.24 0.00 34.72 3.16
57 58 2.743172 CGAAAATCGTACGCACTGTTC 58.257 47.619 11.24 7.64 34.72 3.18
58 59 2.154198 CGAAAATCGTACGCACTGTTCA 59.846 45.455 11.24 0.00 34.72 3.18
59 60 3.181534 CGAAAATCGTACGCACTGTTCAT 60.182 43.478 11.24 0.00 34.72 2.57
60 61 3.991605 AAATCGTACGCACTGTTCATC 57.008 42.857 11.24 0.00 0.00 2.92
61 62 1.545759 ATCGTACGCACTGTTCATCG 58.454 50.000 11.24 0.00 0.00 3.84
62 63 0.239082 TCGTACGCACTGTTCATCGT 59.761 50.000 11.24 0.00 38.75 3.73
63 64 1.464219 TCGTACGCACTGTTCATCGTA 59.536 47.619 11.24 0.00 36.50 3.43
64 65 2.096335 TCGTACGCACTGTTCATCGTAT 59.904 45.455 11.24 0.00 39.21 3.06
65 66 2.213353 CGTACGCACTGTTCATCGTATG 59.787 50.000 0.52 0.00 39.21 2.39
66 67 0.999406 ACGCACTGTTCATCGTATGC 59.001 50.000 0.00 0.00 33.02 3.14
67 68 0.998669 CGCACTGTTCATCGTATGCA 59.001 50.000 0.00 0.00 33.27 3.96
68 69 1.267038 CGCACTGTTCATCGTATGCAC 60.267 52.381 0.00 0.00 33.27 4.57
69 70 1.731709 GCACTGTTCATCGTATGCACA 59.268 47.619 0.00 0.00 35.24 4.57
71 72 2.726555 CTGTTCATCGTATGCACAGC 57.273 50.000 11.98 0.00 44.88 4.40
72 73 2.001872 CTGTTCATCGTATGCACAGCA 58.998 47.619 11.98 0.00 44.88 4.41
73 74 2.416202 CTGTTCATCGTATGCACAGCAA 59.584 45.455 11.98 0.00 44.88 3.91
74 75 3.009026 TGTTCATCGTATGCACAGCAAT 58.991 40.909 0.00 0.00 43.62 3.56
75 76 3.063861 TGTTCATCGTATGCACAGCAATC 59.936 43.478 0.00 0.00 43.62 2.67
76 77 2.903798 TCATCGTATGCACAGCAATCA 58.096 42.857 0.00 0.00 43.62 2.57
77 78 3.469739 TCATCGTATGCACAGCAATCAT 58.530 40.909 0.00 0.00 43.62 2.45
83 84 5.702209 TCGTATGCACAGCAATCATATCAAT 59.298 36.000 0.00 0.00 43.62 2.57
95 96 6.587651 CAATCATATCAATGACACTGTAGCG 58.412 40.000 0.00 0.00 44.79 4.26
98 99 5.300792 TCATATCAATGACACTGTAGCGGTA 59.699 40.000 0.00 0.00 37.20 4.02
111 112 2.507102 CGGTAGTCGCCAGTGCTG 60.507 66.667 0.00 0.00 34.43 4.41
118 119 1.134965 AGTCGCCAGTGCTGATAAGTC 60.135 52.381 0.02 0.00 34.43 3.01
161 163 1.203313 GTACGTGCGTGCAAGAACC 59.797 57.895 14.53 0.00 0.00 3.62
177 179 2.813908 CCGTAGACAGGCGCAACC 60.814 66.667 10.83 0.00 39.61 3.77
178 180 3.179265 CGTAGACAGGCGCAACCG 61.179 66.667 10.83 0.00 46.52 4.44
179 181 2.048503 GTAGACAGGCGCAACCGT 60.049 61.111 10.83 0.00 46.52 4.83
180 182 1.666872 GTAGACAGGCGCAACCGTT 60.667 57.895 10.83 0.00 46.52 4.44
271 282 1.514014 GCGGTACTTGCAAATGCCG 60.514 57.895 29.18 29.18 41.18 5.69
437 457 1.164041 ACGGACCCTGAAGTTTTGCG 61.164 55.000 0.00 0.00 0.00 4.85
514 538 3.253838 TACCCACTGCCCCCACAC 61.254 66.667 0.00 0.00 0.00 3.82
663 851 8.324191 ACCTATCCAGATTCTAATTCTGTTCA 57.676 34.615 0.00 0.00 0.00 3.18
740 942 4.764896 TGCCATAGCATCGAGCAG 57.235 55.556 9.09 0.00 46.52 4.24
768 970 1.620822 AAGCCCAGACACACATTTCC 58.379 50.000 0.00 0.00 0.00 3.13
769 971 0.478072 AGCCCAGACACACATTTCCA 59.522 50.000 0.00 0.00 0.00 3.53
771 973 1.819305 GCCCAGACACACATTTCCACT 60.819 52.381 0.00 0.00 0.00 4.00
818 1032 1.002011 GCCTCTTTCCCTTTCGCCT 60.002 57.895 0.00 0.00 0.00 5.52
906 1120 1.956629 TTTCCCGTCTCATCTCGCCC 61.957 60.000 0.00 0.00 0.00 6.13
907 1121 3.917760 CCCGTCTCATCTCGCCCC 61.918 72.222 0.00 0.00 0.00 5.80
908 1122 3.917760 CCGTCTCATCTCGCCCCC 61.918 72.222 0.00 0.00 0.00 5.40
909 1123 4.271816 CGTCTCATCTCGCCCCCG 62.272 72.222 0.00 0.00 0.00 5.73
910 1124 4.593864 GTCTCATCTCGCCCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
957 1175 0.250513 ACTCGCCTCACATCTTTCCC 59.749 55.000 0.00 0.00 0.00 3.97
959 1177 1.198094 TCGCCTCACATCTTTCCCCA 61.198 55.000 0.00 0.00 0.00 4.96
960 1178 1.026718 CGCCTCACATCTTTCCCCAC 61.027 60.000 0.00 0.00 0.00 4.61
961 1179 0.329596 GCCTCACATCTTTCCCCACT 59.670 55.000 0.00 0.00 0.00 4.00
1027 1249 2.328099 CCCCGTGAAGCAAGCAGAC 61.328 63.158 0.00 0.00 0.00 3.51
1037 1259 1.784062 CAAGCAGACTCCTTTCGCG 59.216 57.895 0.00 0.00 0.00 5.87
1056 1278 2.605097 GCGTCCCTTATTAGAGCTCGTC 60.605 54.545 8.37 0.00 0.00 4.20
1063 1285 0.315568 ATTAGAGCTCGTCATCCGCC 59.684 55.000 8.37 0.00 36.19 6.13
1258 1480 1.153469 GGAGCAGCAGCAGTACCTC 60.153 63.158 3.17 0.00 45.49 3.85
1273 1495 2.420890 CTCCCGGAGCAGCTCATC 59.579 66.667 24.09 6.67 31.08 2.92
1674 2046 2.831333 ACTCACTTCACTTGACTGCTG 58.169 47.619 0.00 0.00 0.00 4.41
1702 2261 3.432588 CAGGAGTCGTCGTCCGCT 61.433 66.667 0.00 0.00 39.30 5.52
1843 2402 3.774702 GTCGTCAAGAACCGCGGC 61.775 66.667 28.58 10.42 0.00 6.53
1906 2465 4.227134 CTCTGGACGATGGCCCCG 62.227 72.222 12.37 12.37 0.00 5.73
2433 3019 1.395826 GCTCGTGCCTGGAGGACTAT 61.396 60.000 0.00 0.00 37.39 2.12
2792 3390 0.965439 GTGTGAGGAGCAGACTCAGT 59.035 55.000 5.41 0.00 44.90 3.41
2834 3443 2.094494 GCAGTTGCTAGCTAGTCAGTCA 60.094 50.000 21.62 8.16 38.21 3.41
2835 3444 3.768406 CAGTTGCTAGCTAGTCAGTCAG 58.232 50.000 21.62 10.06 0.00 3.51
2836 3445 3.192422 CAGTTGCTAGCTAGTCAGTCAGT 59.808 47.826 21.62 6.32 0.00 3.41
2837 3446 3.442273 AGTTGCTAGCTAGTCAGTCAGTC 59.558 47.826 21.62 8.08 0.00 3.51
2838 3447 3.358111 TGCTAGCTAGTCAGTCAGTCT 57.642 47.619 21.62 0.00 0.00 3.24
2839 3448 3.013219 TGCTAGCTAGTCAGTCAGTCTG 58.987 50.000 21.62 0.00 44.85 3.51
2840 3449 3.013921 GCTAGCTAGTCAGTCAGTCTGT 58.986 50.000 21.62 0.00 43.97 3.41
2841 3450 3.064820 GCTAGCTAGTCAGTCAGTCTGTC 59.935 52.174 21.62 0.00 43.97 3.51
2939 3651 1.069204 TGCCTAGCGATCATCTTGTCC 59.931 52.381 0.00 0.00 0.00 4.02
2980 3692 4.742201 TTCTGAGGCCGCTCGTGC 62.742 66.667 8.34 0.00 0.00 5.34
3040 3762 4.808364 TGCAGAAATTTTAGTGCAACCAAC 59.192 37.500 16.88 0.00 42.79 3.77
3042 3764 5.355596 CAGAAATTTTAGTGCAACCAACCA 58.644 37.500 0.00 0.00 37.80 3.67
3043 3765 5.814705 CAGAAATTTTAGTGCAACCAACCAA 59.185 36.000 0.00 0.00 37.80 3.67
3044 3766 6.018832 CAGAAATTTTAGTGCAACCAACCAAG 60.019 38.462 0.00 0.00 37.80 3.61
3108 3837 6.505272 GGAGCTGTACTACTACTAATTGTGG 58.495 44.000 0.00 0.00 0.00 4.17
3109 3838 5.903810 AGCTGTACTACTACTAATTGTGGC 58.096 41.667 0.00 0.00 0.00 5.01
3110 3839 5.048507 GCTGTACTACTACTAATTGTGGCC 58.951 45.833 0.00 0.00 0.00 5.36
3111 3840 5.394883 GCTGTACTACTACTAATTGTGGCCA 60.395 44.000 0.00 0.00 0.00 5.36
3112 3841 6.608539 TGTACTACTACTAATTGTGGCCAA 57.391 37.500 7.24 0.00 34.45 4.52
3113 3842 6.400568 TGTACTACTACTAATTGTGGCCAAC 58.599 40.000 7.24 2.03 32.26 3.77
3114 3843 4.840271 ACTACTACTAATTGTGGCCAACC 58.160 43.478 7.24 0.00 32.26 3.77
3115 3844 4.534897 ACTACTACTAATTGTGGCCAACCT 59.465 41.667 7.24 0.00 36.63 3.50
3116 3845 4.382386 ACTACTAATTGTGGCCAACCTT 57.618 40.909 7.24 3.27 36.63 3.50
3117 3846 4.736473 ACTACTAATTGTGGCCAACCTTT 58.264 39.130 7.24 1.41 36.63 3.11
3118 3847 4.765339 ACTACTAATTGTGGCCAACCTTTC 59.235 41.667 7.24 0.00 36.63 2.62
3119 3848 3.571590 ACTAATTGTGGCCAACCTTTCA 58.428 40.909 7.24 0.00 36.63 2.69
3120 3849 4.159557 ACTAATTGTGGCCAACCTTTCAT 58.840 39.130 7.24 0.00 36.63 2.57
3136 3865 0.319083 TCATGGTTCGTGTTACCGCT 59.681 50.000 0.00 0.00 38.55 5.52
3137 3866 0.442310 CATGGTTCGTGTTACCGCTG 59.558 55.000 0.00 0.00 38.55 5.18
3138 3867 0.672401 ATGGTTCGTGTTACCGCTGG 60.672 55.000 0.00 0.00 38.55 4.85
3139 3868 2.030958 GGTTCGTGTTACCGCTGGG 61.031 63.158 0.00 0.00 40.11 4.45
3140 3869 2.357760 TTCGTGTTACCGCTGGGC 60.358 61.111 0.00 0.00 36.48 5.36
3141 3870 2.874664 TTCGTGTTACCGCTGGGCT 61.875 57.895 0.00 0.00 36.48 5.19
3142 3871 3.118454 CGTGTTACCGCTGGGCTG 61.118 66.667 0.00 0.00 36.48 4.85
3143 3872 2.746277 GTGTTACCGCTGGGCTGG 60.746 66.667 0.00 0.00 36.48 4.85
3144 3873 4.715523 TGTTACCGCTGGGCTGGC 62.716 66.667 0.00 0.00 36.48 4.85
3182 3911 4.019860 AGTGCCACTTGACAGATGATACTT 60.020 41.667 0.00 0.00 0.00 2.24
3190 3919 7.437565 CACTTGACAGATGATACTTGATACCTG 59.562 40.741 0.00 0.00 0.00 4.00
3213 3942 5.945784 TGGTACTGATGCTTATTTTGAGCTT 59.054 36.000 0.00 0.00 40.75 3.74
3223 3952 1.321474 TTTTGAGCTTGGTGCCTCTG 58.679 50.000 0.00 0.00 44.23 3.35
3225 3954 2.060567 TTGAGCTTGGTGCCTCTGCT 62.061 55.000 0.00 0.00 44.23 4.24
3226 3955 1.744741 GAGCTTGGTGCCTCTGCTC 60.745 63.158 12.01 12.01 44.23 4.26
3228 3957 3.123620 CTTGGTGCCTCTGCTCGC 61.124 66.667 0.00 0.00 38.71 5.03
3229 3958 4.704833 TTGGTGCCTCTGCTCGCC 62.705 66.667 0.00 0.00 38.71 5.54
3231 3960 4.828925 GGTGCCTCTGCTCGCCTC 62.829 72.222 0.00 0.00 38.71 4.70
3232 3961 3.768922 GTGCCTCTGCTCGCCTCT 61.769 66.667 0.00 0.00 38.71 3.69
3233 3962 2.999648 TGCCTCTGCTCGCCTCTT 61.000 61.111 0.00 0.00 38.71 2.85
3234 3963 2.202864 GCCTCTGCTCGCCTCTTC 60.203 66.667 0.00 0.00 33.53 2.87
3235 3964 2.498726 CCTCTGCTCGCCTCTTCC 59.501 66.667 0.00 0.00 0.00 3.46
3236 3965 2.354401 CCTCTGCTCGCCTCTTCCA 61.354 63.158 0.00 0.00 0.00 3.53
3237 3966 1.593787 CTCTGCTCGCCTCTTCCAA 59.406 57.895 0.00 0.00 0.00 3.53
3238 3967 0.036952 CTCTGCTCGCCTCTTCCAAA 60.037 55.000 0.00 0.00 0.00 3.28
3239 3968 0.036952 TCTGCTCGCCTCTTCCAAAG 60.037 55.000 0.00 0.00 0.00 2.77
3240 3969 1.003355 TGCTCGCCTCTTCCAAAGG 60.003 57.895 0.00 0.00 36.95 3.11
3241 3970 1.296715 GCTCGCCTCTTCCAAAGGA 59.703 57.895 0.00 0.00 35.83 3.36
3242 3971 0.321653 GCTCGCCTCTTCCAAAGGAA 60.322 55.000 0.00 0.00 39.66 3.36
3243 3972 1.882352 GCTCGCCTCTTCCAAAGGAAA 60.882 52.381 0.00 0.00 41.54 3.13
3244 3973 2.079925 CTCGCCTCTTCCAAAGGAAAG 58.920 52.381 0.00 1.58 41.54 2.62
3245 3974 1.420138 TCGCCTCTTCCAAAGGAAAGT 59.580 47.619 0.00 0.00 41.54 2.66
3246 3975 1.537202 CGCCTCTTCCAAAGGAAAGTG 59.463 52.381 0.00 0.00 41.54 3.16
3247 3976 1.270826 GCCTCTTCCAAAGGAAAGTGC 59.729 52.381 0.00 0.00 41.54 4.40
3248 3977 2.868899 CCTCTTCCAAAGGAAAGTGCT 58.131 47.619 0.00 0.00 41.54 4.40
3249 3978 2.816672 CCTCTTCCAAAGGAAAGTGCTC 59.183 50.000 0.00 0.00 41.54 4.26
3250 3979 2.481952 CTCTTCCAAAGGAAAGTGCTCG 59.518 50.000 0.00 0.00 41.54 5.03
3251 3980 2.158813 TCTTCCAAAGGAAAGTGCTCGT 60.159 45.455 0.00 0.00 41.54 4.18
3252 3981 2.341846 TCCAAAGGAAAGTGCTCGTT 57.658 45.000 0.00 0.00 0.00 3.85
3253 3982 2.650322 TCCAAAGGAAAGTGCTCGTTT 58.350 42.857 0.00 0.00 34.58 3.60
3254 3983 3.020984 TCCAAAGGAAAGTGCTCGTTTT 58.979 40.909 0.00 0.00 32.55 2.43
3255 3984 3.445805 TCCAAAGGAAAGTGCTCGTTTTT 59.554 39.130 0.00 0.00 32.55 1.94
3273 4002 3.708563 TTTTTGGAACGAAGGCTCAAG 57.291 42.857 0.00 0.00 0.00 3.02
3274 4003 2.631160 TTTGGAACGAAGGCTCAAGA 57.369 45.000 0.00 0.00 0.00 3.02
3275 4004 2.631160 TTGGAACGAAGGCTCAAGAA 57.369 45.000 0.00 0.00 0.00 2.52
3276 4005 2.169832 TGGAACGAAGGCTCAAGAAG 57.830 50.000 0.00 0.00 0.00 2.85
3277 4006 1.691976 TGGAACGAAGGCTCAAGAAGA 59.308 47.619 0.00 0.00 0.00 2.87
3285 4014 2.985456 CTCAAGAAGAGCCCGGCT 59.015 61.111 13.16 13.16 43.88 5.52
3286 4015 1.298014 CTCAAGAAGAGCCCGGCTT 59.702 57.895 14.70 0.00 39.88 4.35
3287 4016 1.003355 TCAAGAAGAGCCCGGCTTG 60.003 57.895 14.70 7.58 39.88 4.01
3288 4017 2.042831 CAAGAAGAGCCCGGCTTGG 61.043 63.158 14.70 0.00 39.88 3.61
3289 4018 2.224159 AAGAAGAGCCCGGCTTGGA 61.224 57.895 14.70 0.00 39.88 3.53
3290 4019 1.779061 AAGAAGAGCCCGGCTTGGAA 61.779 55.000 14.70 0.00 39.88 3.53
3291 4020 1.077429 GAAGAGCCCGGCTTGGAAT 60.077 57.895 14.70 0.00 39.88 3.01
3292 4021 0.681243 GAAGAGCCCGGCTTGGAATT 60.681 55.000 14.70 4.04 39.88 2.17
3293 4022 0.623723 AAGAGCCCGGCTTGGAATTA 59.376 50.000 14.70 0.00 39.88 1.40
3294 4023 0.623723 AGAGCCCGGCTTGGAATTAA 59.376 50.000 14.70 0.00 39.88 1.40
3295 4024 0.738975 GAGCCCGGCTTGGAATTAAC 59.261 55.000 14.70 0.00 39.88 2.01
3296 4025 0.039035 AGCCCGGCTTGGAATTAACA 59.961 50.000 5.94 0.00 42.00 2.41
3297 4026 0.892063 GCCCGGCTTGGAATTAACAA 59.108 50.000 0.71 0.00 42.00 2.83
3298 4027 1.273886 GCCCGGCTTGGAATTAACAAA 59.726 47.619 0.71 0.00 42.00 2.83
3299 4028 2.673893 GCCCGGCTTGGAATTAACAAAG 60.674 50.000 0.71 0.00 42.00 2.77
3300 4029 2.606108 CCGGCTTGGAATTAACAAAGC 58.394 47.619 0.00 0.00 42.00 3.51
3301 4030 2.606108 CGGCTTGGAATTAACAAAGCC 58.394 47.619 13.17 13.17 38.06 4.35
3302 4031 2.029470 CGGCTTGGAATTAACAAAGCCA 60.029 45.455 20.02 1.59 39.71 4.75
3303 4032 3.553922 CGGCTTGGAATTAACAAAGCCAA 60.554 43.478 20.02 8.64 39.71 4.52
3304 4033 4.384940 GGCTTGGAATTAACAAAGCCAAA 58.615 39.130 16.82 0.00 39.61 3.28
3305 4034 4.819088 GGCTTGGAATTAACAAAGCCAAAA 59.181 37.500 16.82 0.00 39.61 2.44
3306 4035 5.298026 GGCTTGGAATTAACAAAGCCAAAAA 59.702 36.000 16.82 0.00 39.61 1.94
3307 4036 6.429624 GCTTGGAATTAACAAAGCCAAAAAG 58.570 36.000 0.00 0.00 38.08 2.27
3308 4037 6.038161 GCTTGGAATTAACAAAGCCAAAAAGT 59.962 34.615 0.00 0.00 38.08 2.66
3309 4038 6.917217 TGGAATTAACAAAGCCAAAAAGTG 57.083 33.333 0.00 0.00 0.00 3.16
3310 4039 5.295540 TGGAATTAACAAAGCCAAAAAGTGC 59.704 36.000 0.00 0.00 0.00 4.40
3311 4040 5.527214 GGAATTAACAAAGCCAAAAAGTGCT 59.473 36.000 0.00 0.00 40.17 4.40
3312 4041 6.292865 GGAATTAACAAAGCCAAAAAGTGCTC 60.293 38.462 0.00 0.00 36.66 4.26
3313 4042 2.208326 ACAAAGCCAAAAAGTGCTCG 57.792 45.000 0.00 0.00 36.66 5.03
3314 4043 1.476488 ACAAAGCCAAAAAGTGCTCGT 59.524 42.857 0.00 0.00 36.66 4.18
3315 4044 2.094234 ACAAAGCCAAAAAGTGCTCGTT 60.094 40.909 0.00 0.00 36.66 3.85
3316 4045 2.929398 CAAAGCCAAAAAGTGCTCGTTT 59.071 40.909 0.00 0.00 36.66 3.60
3317 4046 2.959507 AGCCAAAAAGTGCTCGTTTT 57.040 40.000 6.60 6.60 36.13 2.43
3318 4047 3.245518 AGCCAAAAAGTGCTCGTTTTT 57.754 38.095 9.25 4.41 37.54 1.94
3354 4103 5.437191 AAAAACCCTCTCTATGTACCCAG 57.563 43.478 0.00 0.00 0.00 4.45
3355 4104 4.348020 AAACCCTCTCTATGTACCCAGA 57.652 45.455 0.00 0.00 0.00 3.86
3356 4105 4.561254 AACCCTCTCTATGTACCCAGAT 57.439 45.455 0.00 0.00 0.00 2.90
3366 4115 8.425703 TCTCTATGTACCCAGATAGATAGATCG 58.574 40.741 2.16 0.00 37.02 3.69
3368 4117 4.270834 TGTACCCAGATAGATAGATCGGC 58.729 47.826 0.00 0.00 0.00 5.54
3376 4125 1.788258 AGATAGATCGGCGTGCATTG 58.212 50.000 6.85 0.00 0.00 2.82
3396 4145 1.806542 GGCACATTCGACATGACACTT 59.193 47.619 0.00 0.00 0.00 3.16
3421 4170 5.362556 TCTGAAAGATGCAACTTGCTAAC 57.637 39.130 15.16 6.36 40.94 2.34
3422 4171 5.065914 TCTGAAAGATGCAACTTGCTAACT 58.934 37.500 15.16 8.31 40.94 2.24
3424 4173 6.369890 TCTGAAAGATGCAACTTGCTAACTAG 59.630 38.462 15.16 4.75 40.94 2.57
3425 4174 6.230472 TGAAAGATGCAACTTGCTAACTAGA 58.770 36.000 15.16 0.00 45.31 2.43
3426 4175 6.881065 TGAAAGATGCAACTTGCTAACTAGAT 59.119 34.615 15.16 0.00 45.31 1.98
3427 4176 6.674694 AAGATGCAACTTGCTAACTAGATG 57.325 37.500 14.78 0.00 45.31 2.90
3432 4181 6.464222 TGCAACTTGCTAACTAGATGTACTT 58.536 36.000 14.78 0.00 45.31 2.24
3433 4182 7.608153 TGCAACTTGCTAACTAGATGTACTTA 58.392 34.615 14.78 0.00 45.31 2.24
3434 4183 7.759886 TGCAACTTGCTAACTAGATGTACTTAG 59.240 37.037 14.78 0.00 45.31 2.18
3435 4184 7.760340 GCAACTTGCTAACTAGATGTACTTAGT 59.240 37.037 6.50 0.00 40.96 2.24
3438 4187 9.683870 ACTTGCTAACTAGATGTACTTAGTAGT 57.316 33.333 0.00 0.00 38.44 2.73
3478 4228 7.389053 ACAGATCTTGCTTAGAAGTTAACCAAG 59.611 37.037 0.88 7.03 36.22 3.61
3503 4290 0.242017 GCATCTCTGGGTGTGTTTGC 59.758 55.000 0.00 0.00 0.00 3.68
3621 4416 1.985116 ACTTGGTCGCCTCCTCCTC 60.985 63.158 0.00 0.00 0.00 3.71
3623 4418 4.779733 TGGTCGCCTCCTCCTCCC 62.780 72.222 0.00 0.00 0.00 4.30
3811 4627 0.320421 ATTGACCAACGACCTGACGG 60.320 55.000 0.00 0.00 37.61 4.79
3851 4675 0.539207 TACACATGCAAGCCAAGCCA 60.539 50.000 0.00 0.00 0.00 4.75
3852 4676 1.368209 CACATGCAAGCCAAGCCAA 59.632 52.632 0.00 0.00 0.00 4.52
3853 4677 0.669318 CACATGCAAGCCAAGCCAAG 60.669 55.000 0.00 0.00 0.00 3.61
3854 4678 1.740296 CATGCAAGCCAAGCCAAGC 60.740 57.895 0.00 0.00 0.00 4.01
3855 4679 2.211410 ATGCAAGCCAAGCCAAGCA 61.211 52.632 0.00 0.00 35.38 3.91
3862 4686 1.904865 CCAAGCCAAGCAAGCCTGA 60.905 57.895 0.00 0.00 0.00 3.86
3863 4687 1.466025 CCAAGCCAAGCAAGCCTGAA 61.466 55.000 0.00 0.00 0.00 3.02
3865 4689 0.677842 AAGCCAAGCAAGCCTGAAAG 59.322 50.000 0.00 0.00 0.00 2.62
3874 4698 3.760684 AGCAAGCCTGAAAGAACTAATGG 59.239 43.478 0.00 0.00 34.07 3.16
3875 4699 3.758554 GCAAGCCTGAAAGAACTAATGGA 59.241 43.478 0.00 0.00 34.07 3.41
3913 4743 1.075979 TGTGTCCATCGATCGTTGCG 61.076 55.000 18.61 12.65 0.00 4.85
3916 4746 2.586079 CCATCGATCGTTGCGGCT 60.586 61.111 18.61 0.00 0.00 5.52
3919 4749 3.723235 ATCGATCGTTGCGGCTGCT 62.723 57.895 20.27 0.00 43.34 4.24
3920 4750 4.214383 CGATCGTTGCGGCTGCTG 62.214 66.667 20.27 3.55 43.34 4.41
3921 4751 4.527157 GATCGTTGCGGCTGCTGC 62.527 66.667 25.96 25.96 43.34 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.737047 GCTCGTCCATCCAACTAATCGAA 60.737 47.826 0.00 0.00 0.00 3.71
4 5 1.754803 TCGCTCGTCCATCCAACTAAT 59.245 47.619 0.00 0.00 0.00 1.73
5 6 1.134367 CTCGCTCGTCCATCCAACTAA 59.866 52.381 0.00 0.00 0.00 2.24
6 7 0.738975 CTCGCTCGTCCATCCAACTA 59.261 55.000 0.00 0.00 0.00 2.24
7 8 0.965866 TCTCGCTCGTCCATCCAACT 60.966 55.000 0.00 0.00 0.00 3.16
8 9 0.103208 ATCTCGCTCGTCCATCCAAC 59.897 55.000 0.00 0.00 0.00 3.77
9 10 0.385751 GATCTCGCTCGTCCATCCAA 59.614 55.000 0.00 0.00 0.00 3.53
10 11 0.751643 TGATCTCGCTCGTCCATCCA 60.752 55.000 0.00 0.00 0.00 3.41
11 12 0.600557 ATGATCTCGCTCGTCCATCC 59.399 55.000 0.00 0.00 0.00 3.51
12 13 1.000827 ACATGATCTCGCTCGTCCATC 60.001 52.381 0.00 0.00 0.00 3.51
13 14 1.000827 GACATGATCTCGCTCGTCCAT 60.001 52.381 0.00 0.00 0.00 3.41
14 15 0.382158 GACATGATCTCGCTCGTCCA 59.618 55.000 0.00 0.00 0.00 4.02
15 16 0.658829 CGACATGATCTCGCTCGTCC 60.659 60.000 0.00 0.00 0.00 4.79
16 17 0.028242 ACGACATGATCTCGCTCGTC 59.972 55.000 0.00 0.00 32.22 4.20
17 18 1.003759 GTACGACATGATCTCGCTCGT 60.004 52.381 0.00 5.02 40.51 4.18
18 19 1.664629 GTACGACATGATCTCGCTCG 58.335 55.000 0.00 0.00 34.34 5.03
19 20 1.260825 TCGTACGACATGATCTCGCTC 59.739 52.381 15.28 0.00 34.34 5.03
20 21 1.296727 TCGTACGACATGATCTCGCT 58.703 50.000 15.28 0.00 34.34 4.93
21 22 2.101053 TTCGTACGACATGATCTCGC 57.899 50.000 19.36 0.00 34.34 5.03
22 23 4.144007 CGATTTTCGTACGACATGATCTCG 60.144 45.833 19.36 14.64 34.72 4.04
23 24 5.225619 CGATTTTCGTACGACATGATCTC 57.774 43.478 19.36 7.19 34.72 2.75
37 38 2.154198 TGAACAGTGCGTACGATTTTCG 59.846 45.455 21.65 3.87 46.93 3.46
38 39 3.781341 TGAACAGTGCGTACGATTTTC 57.219 42.857 21.65 12.53 0.00 2.29
39 40 3.181534 CGATGAACAGTGCGTACGATTTT 60.182 43.478 21.65 3.00 0.00 1.82
40 41 2.344441 CGATGAACAGTGCGTACGATTT 59.656 45.455 21.65 3.15 0.00 2.17
41 42 1.917955 CGATGAACAGTGCGTACGATT 59.082 47.619 21.65 4.14 0.00 3.34
42 43 1.135489 ACGATGAACAGTGCGTACGAT 60.135 47.619 21.65 0.00 34.93 3.73
43 44 0.239082 ACGATGAACAGTGCGTACGA 59.761 50.000 21.65 0.80 34.93 3.43
44 45 1.886037 TACGATGAACAGTGCGTACG 58.114 50.000 11.84 11.84 38.09 3.67
45 46 2.034842 GCATACGATGAACAGTGCGTAC 60.035 50.000 0.00 0.00 41.29 3.67
46 47 2.190161 GCATACGATGAACAGTGCGTA 58.810 47.619 0.00 0.00 42.44 4.42
47 48 0.999406 GCATACGATGAACAGTGCGT 59.001 50.000 0.00 0.00 40.42 5.24
48 49 0.998669 TGCATACGATGAACAGTGCG 59.001 50.000 0.00 0.00 35.46 5.34
49 50 1.731709 TGTGCATACGATGAACAGTGC 59.268 47.619 4.99 0.00 43.79 4.40
53 54 2.091852 TGCTGTGCATACGATGAACA 57.908 45.000 7.98 7.98 46.41 3.18
54 55 3.063861 TGATTGCTGTGCATACGATGAAC 59.936 43.478 0.00 0.00 38.76 3.18
55 56 3.269178 TGATTGCTGTGCATACGATGAA 58.731 40.909 0.00 0.00 38.76 2.57
56 57 2.903798 TGATTGCTGTGCATACGATGA 58.096 42.857 0.00 0.00 38.76 2.92
57 58 3.891056 ATGATTGCTGTGCATACGATG 57.109 42.857 0.00 0.00 38.76 3.84
58 59 5.240121 TGATATGATTGCTGTGCATACGAT 58.760 37.500 0.00 0.00 38.76 3.73
59 60 4.630111 TGATATGATTGCTGTGCATACGA 58.370 39.130 0.00 0.00 38.76 3.43
60 61 4.996062 TGATATGATTGCTGTGCATACG 57.004 40.909 0.00 0.00 38.76 3.06
61 62 6.800408 GTCATTGATATGATTGCTGTGCATAC 59.200 38.462 0.00 0.00 42.49 2.39
62 63 6.487331 TGTCATTGATATGATTGCTGTGCATA 59.513 34.615 0.00 0.00 42.49 3.14
63 64 5.300792 TGTCATTGATATGATTGCTGTGCAT 59.699 36.000 0.00 0.00 42.49 3.96
64 65 4.641094 TGTCATTGATATGATTGCTGTGCA 59.359 37.500 0.00 0.00 42.49 4.57
65 66 4.974275 GTGTCATTGATATGATTGCTGTGC 59.026 41.667 0.00 0.00 42.49 4.57
66 67 6.183360 ACAGTGTCATTGATATGATTGCTGTG 60.183 38.462 1.83 3.41 41.99 3.66
67 68 5.884232 ACAGTGTCATTGATATGATTGCTGT 59.116 36.000 1.83 12.20 42.49 4.40
68 69 6.373186 ACAGTGTCATTGATATGATTGCTG 57.627 37.500 1.83 0.00 42.49 4.41
69 70 6.204301 GCTACAGTGTCATTGATATGATTGCT 59.796 38.462 0.00 0.00 42.49 3.91
70 71 6.369005 GCTACAGTGTCATTGATATGATTGC 58.631 40.000 0.00 0.00 42.49 3.56
71 72 6.347160 CCGCTACAGTGTCATTGATATGATTG 60.347 42.308 0.00 0.00 42.49 2.67
72 73 5.698089 CCGCTACAGTGTCATTGATATGATT 59.302 40.000 0.00 0.00 42.49 2.57
73 74 5.221521 ACCGCTACAGTGTCATTGATATGAT 60.222 40.000 0.00 0.00 42.49 2.45
74 75 4.099419 ACCGCTACAGTGTCATTGATATGA 59.901 41.667 0.00 0.00 38.45 2.15
75 76 4.371786 ACCGCTACAGTGTCATTGATATG 58.628 43.478 0.00 0.00 0.00 1.78
76 77 4.672587 ACCGCTACAGTGTCATTGATAT 57.327 40.909 0.00 0.00 0.00 1.63
77 78 4.643334 ACTACCGCTACAGTGTCATTGATA 59.357 41.667 0.00 0.00 0.00 2.15
83 84 0.800631 CGACTACCGCTACAGTGTCA 59.199 55.000 0.00 0.00 0.00 3.58
109 110 3.859961 GTGGACATGACACGACTTATCAG 59.140 47.826 0.00 0.00 0.00 2.90
110 111 3.845178 GTGGACATGACACGACTTATCA 58.155 45.455 0.00 0.00 0.00 2.15
152 154 0.320421 GCCTGTCTACGGTTCTTGCA 60.320 55.000 0.00 0.00 0.00 4.08
161 163 3.179265 CGGTTGCGCCTGTCTACG 61.179 66.667 4.18 0.00 34.25 3.51
178 180 5.409214 TGCAACAACTAATTCCTACGGTAAC 59.591 40.000 0.00 0.00 0.00 2.50
179 181 5.409214 GTGCAACAACTAATTCCTACGGTAA 59.591 40.000 0.00 0.00 36.32 2.85
180 182 4.931002 GTGCAACAACTAATTCCTACGGTA 59.069 41.667 0.00 0.00 36.32 4.02
238 240 1.197812 ACCGCTAAATACCGTTCCCT 58.802 50.000 0.00 0.00 0.00 4.20
244 246 2.542597 TGCAAGTACCGCTAAATACCG 58.457 47.619 6.45 0.00 0.00 4.02
374 389 5.584886 GCATGCTGCTCCTTGATTCAAGG 62.585 52.174 31.47 31.47 46.82 3.61
375 390 2.479730 GCATGCTGCTCCTTGATTCAAG 60.480 50.000 17.78 17.78 40.96 3.02
376 391 1.475280 GCATGCTGCTCCTTGATTCAA 59.525 47.619 11.37 0.00 40.96 2.69
401 421 3.806521 GTCCGTAGCTGTCGATCTTACTA 59.193 47.826 13.29 0.00 0.00 1.82
402 422 2.613133 GTCCGTAGCTGTCGATCTTACT 59.387 50.000 13.29 0.00 0.00 2.24
403 423 2.286891 GGTCCGTAGCTGTCGATCTTAC 60.287 54.545 13.29 5.05 0.00 2.34
514 538 2.195389 CATGTGGTGCCAAGATGGG 58.805 57.895 0.00 0.00 38.19 4.00
663 851 2.841160 GCCGGCCGAACAAACTGTT 61.841 57.895 30.73 0.00 44.37 3.16
709 899 0.742505 ATGGCATGGCTCGTGATTTG 59.257 50.000 21.08 0.00 0.00 2.32
713 903 1.227645 GCTATGGCATGGCTCGTGA 60.228 57.895 26.26 0.00 38.54 4.35
740 942 1.448717 GTCTGGGCTTTCTCTCGCC 60.449 63.158 0.00 0.00 45.55 5.54
757 959 2.975489 AGGAGAGAGTGGAAATGTGTGT 59.025 45.455 0.00 0.00 0.00 3.72
768 970 1.028905 GATGTCGGGAGGAGAGAGTG 58.971 60.000 0.00 0.00 0.00 3.51
769 971 0.106419 GGATGTCGGGAGGAGAGAGT 60.106 60.000 0.00 0.00 0.00 3.24
771 973 1.230497 GGGATGTCGGGAGGAGAGA 59.770 63.158 0.00 0.00 0.00 3.10
818 1032 1.966451 TCTGACGTGAGAGCGCTGA 60.966 57.895 18.48 0.00 34.88 4.26
913 1127 4.867599 GTAGAAGGCGACGGGCGG 62.868 72.222 4.96 0.00 44.92 6.13
914 1128 4.867599 GGTAGAAGGCGACGGGCG 62.868 72.222 0.00 0.00 44.92 6.13
915 1129 3.427598 GAGGTAGAAGGCGACGGGC 62.428 68.421 0.00 0.00 42.51 6.13
957 1175 1.689892 GGAGTAGAAGGAGGGGAGTGG 60.690 61.905 0.00 0.00 0.00 4.00
959 1177 1.007359 GTGGAGTAGAAGGAGGGGAGT 59.993 57.143 0.00 0.00 0.00 3.85
960 1178 1.289530 AGTGGAGTAGAAGGAGGGGAG 59.710 57.143 0.00 0.00 0.00 4.30
961 1179 1.288335 GAGTGGAGTAGAAGGAGGGGA 59.712 57.143 0.00 0.00 0.00 4.81
1027 1249 2.311124 AATAAGGGACGCGAAAGGAG 57.689 50.000 15.93 0.00 0.00 3.69
1037 1259 4.321378 GGATGACGAGCTCTAATAAGGGAC 60.321 50.000 12.85 0.00 0.00 4.46
1063 1285 0.820226 TCTCCTTCTCCATCGCACTG 59.180 55.000 0.00 0.00 0.00 3.66
1105 1327 1.986413 CACCACCTCCTCCTTCAGG 59.014 63.158 0.00 0.00 45.15 3.86
1183 1405 2.890109 GCGCGGGATCAGCATTCTG 61.890 63.158 8.83 0.00 41.67 3.02
1608 1848 1.798223 TCACTTGGAAGCGAATCAACG 59.202 47.619 0.00 0.00 0.00 4.10
1674 2046 1.084370 CGACTCCTGCGAATTCCCAC 61.084 60.000 0.00 0.00 0.00 4.61
1702 2261 1.269958 ACTGCTGCAGGATGTACTGA 58.730 50.000 31.00 0.00 40.97 3.41
1792 2351 1.375523 GAACTCGGACGCCACCATT 60.376 57.895 0.00 0.00 0.00 3.16
1906 2465 1.518572 CTCGACGTACCACATGCCC 60.519 63.158 0.00 0.00 0.00 5.36
2792 3390 3.429547 GCGGCTAATTCTTCACTCTGAGA 60.430 47.826 12.44 0.00 0.00 3.27
2834 3443 0.542938 TACCAGCAGGCAGACAGACT 60.543 55.000 0.00 0.00 39.06 3.24
2835 3444 0.108424 CTACCAGCAGGCAGACAGAC 60.108 60.000 0.00 0.00 39.06 3.51
2836 3445 0.251787 TCTACCAGCAGGCAGACAGA 60.252 55.000 0.00 0.00 39.06 3.41
2837 3446 0.175302 CTCTACCAGCAGGCAGACAG 59.825 60.000 0.00 0.00 39.06 3.51
2838 3447 0.251787 TCTCTACCAGCAGGCAGACA 60.252 55.000 0.00 0.00 39.06 3.41
2839 3448 1.118838 ATCTCTACCAGCAGGCAGAC 58.881 55.000 0.00 0.00 39.06 3.51
2840 3449 2.755952 TATCTCTACCAGCAGGCAGA 57.244 50.000 0.00 0.00 39.06 4.26
2841 3450 3.827008 TTTATCTCTACCAGCAGGCAG 57.173 47.619 0.00 0.00 39.06 4.85
2939 3651 9.599322 GAATCAACATTTATGCTCCTATTTACG 57.401 33.333 0.00 0.00 0.00 3.18
2980 3692 2.074948 ATCCAGGCTAGCCAGGTGG 61.075 63.158 36.32 31.70 42.61 4.61
2987 3699 4.940654 GGATAAAGATTCATCCAGGCTAGC 59.059 45.833 6.04 6.04 40.48 3.42
2988 3700 6.213195 AGAGGATAAAGATTCATCCAGGCTAG 59.787 42.308 3.61 0.00 42.78 3.42
2989 3701 6.013898 CAGAGGATAAAGATTCATCCAGGCTA 60.014 42.308 3.61 0.00 42.78 3.93
2990 3702 4.912744 AGAGGATAAAGATTCATCCAGGCT 59.087 41.667 3.61 0.00 42.78 4.58
3040 3762 1.475682 GGATGCAGAGAAAAGGCTTGG 59.524 52.381 0.00 0.00 0.00 3.61
3042 3764 1.844687 GGGATGCAGAGAAAAGGCTT 58.155 50.000 0.00 0.00 0.00 4.35
3043 3765 0.393537 CGGGATGCAGAGAAAAGGCT 60.394 55.000 0.00 0.00 0.00 4.58
3044 3766 0.392998 TCGGGATGCAGAGAAAAGGC 60.393 55.000 0.00 0.00 0.00 4.35
3112 3841 3.143728 GGTAACACGAACCATGAAAGGT 58.856 45.455 0.00 0.00 45.91 3.50
3113 3842 2.158841 CGGTAACACGAACCATGAAAGG 59.841 50.000 0.00 0.00 36.78 3.11
3114 3843 2.412325 GCGGTAACACGAACCATGAAAG 60.412 50.000 0.00 0.00 36.78 2.62
3115 3844 1.532007 GCGGTAACACGAACCATGAAA 59.468 47.619 0.00 0.00 36.78 2.69
3116 3845 1.149987 GCGGTAACACGAACCATGAA 58.850 50.000 0.00 0.00 36.78 2.57
3117 3846 0.319083 AGCGGTAACACGAACCATGA 59.681 50.000 0.00 0.00 36.78 3.07
3118 3847 0.442310 CAGCGGTAACACGAACCATG 59.558 55.000 0.00 0.00 36.78 3.66
3119 3848 0.672401 CCAGCGGTAACACGAACCAT 60.672 55.000 0.00 0.00 36.78 3.55
3120 3849 1.301087 CCAGCGGTAACACGAACCA 60.301 57.895 0.00 0.00 36.78 3.67
3139 3868 1.217244 CCAAGAAATGGCAGCCAGC 59.783 57.895 21.51 11.78 43.80 4.85
3182 3911 6.747414 AATAAGCATCAGTACCAGGTATCA 57.253 37.500 1.54 0.00 0.00 2.15
3190 3919 6.261118 CAAGCTCAAAATAAGCATCAGTACC 58.739 40.000 0.00 0.00 42.35 3.34
3223 3952 0.321653 TTCCTTTGGAAGAGGCGAGC 60.322 55.000 0.00 0.00 36.71 5.03
3225 3954 1.420138 ACTTTCCTTTGGAAGAGGCGA 59.580 47.619 0.00 0.00 43.06 5.54
3226 3955 1.537202 CACTTTCCTTTGGAAGAGGCG 59.463 52.381 0.00 0.00 43.06 5.52
3228 3957 2.816672 GAGCACTTTCCTTTGGAAGAGG 59.183 50.000 0.00 0.00 43.06 3.69
3229 3958 2.481952 CGAGCACTTTCCTTTGGAAGAG 59.518 50.000 0.00 3.86 43.06 2.85
3230 3959 2.158813 ACGAGCACTTTCCTTTGGAAGA 60.159 45.455 0.00 0.00 43.06 2.87
3231 3960 2.222027 ACGAGCACTTTCCTTTGGAAG 58.778 47.619 0.00 0.00 43.06 3.46
3232 3961 2.341846 ACGAGCACTTTCCTTTGGAA 57.658 45.000 0.00 0.00 40.27 3.53
3233 3962 2.341846 AACGAGCACTTTCCTTTGGA 57.658 45.000 0.00 0.00 0.00 3.53
3234 3963 3.436700 AAAACGAGCACTTTCCTTTGG 57.563 42.857 0.00 0.00 0.00 3.28
3253 3982 3.283751 TCTTGAGCCTTCGTTCCAAAAA 58.716 40.909 0.00 0.00 0.00 1.94
3254 3983 2.925724 TCTTGAGCCTTCGTTCCAAAA 58.074 42.857 0.00 0.00 0.00 2.44
3255 3984 2.631160 TCTTGAGCCTTCGTTCCAAA 57.369 45.000 0.00 0.00 0.00 3.28
3256 3985 2.104111 TCTTCTTGAGCCTTCGTTCCAA 59.896 45.455 0.00 0.00 0.00 3.53
3257 3986 1.691976 TCTTCTTGAGCCTTCGTTCCA 59.308 47.619 0.00 0.00 0.00 3.53
3258 3987 2.342179 CTCTTCTTGAGCCTTCGTTCC 58.658 52.381 0.00 0.00 35.84 3.62
3268 3997 1.023513 CAAGCCGGGCTCTTCTTGAG 61.024 60.000 24.08 1.42 45.33 3.02
3269 3998 1.003355 CAAGCCGGGCTCTTCTTGA 60.003 57.895 24.08 0.00 38.25 3.02
3270 3999 2.042831 CCAAGCCGGGCTCTTCTTG 61.043 63.158 24.08 16.12 38.25 3.02
3271 4000 1.779061 TTCCAAGCCGGGCTCTTCTT 61.779 55.000 24.08 2.52 38.25 2.52
3272 4001 1.566298 ATTCCAAGCCGGGCTCTTCT 61.566 55.000 24.08 2.98 38.25 2.85
3273 4002 0.681243 AATTCCAAGCCGGGCTCTTC 60.681 55.000 24.08 0.00 38.25 2.87
3274 4003 0.623723 TAATTCCAAGCCGGGCTCTT 59.376 50.000 24.08 12.92 38.25 2.85
3275 4004 0.623723 TTAATTCCAAGCCGGGCTCT 59.376 50.000 24.08 9.94 38.25 4.09
3276 4005 0.738975 GTTAATTCCAAGCCGGGCTC 59.261 55.000 24.08 1.99 38.25 4.70
3277 4006 0.039035 TGTTAATTCCAAGCCGGGCT 59.961 50.000 17.69 17.69 42.56 5.19
3278 4007 0.892063 TTGTTAATTCCAAGCCGGGC 59.108 50.000 12.11 12.11 34.36 6.13
3279 4008 2.673893 GCTTTGTTAATTCCAAGCCGGG 60.674 50.000 2.18 0.00 34.36 5.73
3280 4009 2.606108 GCTTTGTTAATTCCAAGCCGG 58.394 47.619 0.00 0.00 0.00 6.13
3281 4010 2.029470 TGGCTTTGTTAATTCCAAGCCG 60.029 45.455 15.23 3.90 38.16 5.52
3282 4011 3.676291 TGGCTTTGTTAATTCCAAGCC 57.324 42.857 13.75 13.75 36.99 4.35
3283 4012 6.038161 ACTTTTTGGCTTTGTTAATTCCAAGC 59.962 34.615 0.00 0.00 37.98 4.01
3284 4013 7.408910 CACTTTTTGGCTTTGTTAATTCCAAG 58.591 34.615 0.00 0.00 37.98 3.61
3285 4014 6.183360 GCACTTTTTGGCTTTGTTAATTCCAA 60.183 34.615 0.00 0.00 35.25 3.53
3286 4015 5.295540 GCACTTTTTGGCTTTGTTAATTCCA 59.704 36.000 0.00 0.00 0.00 3.53
3287 4016 5.527214 AGCACTTTTTGGCTTTGTTAATTCC 59.473 36.000 0.00 0.00 36.92 3.01
3288 4017 6.562086 CGAGCACTTTTTGGCTTTGTTAATTC 60.562 38.462 0.00 0.00 41.22 2.17
3289 4018 5.234116 CGAGCACTTTTTGGCTTTGTTAATT 59.766 36.000 0.00 0.00 41.22 1.40
3290 4019 4.744631 CGAGCACTTTTTGGCTTTGTTAAT 59.255 37.500 0.00 0.00 41.22 1.40
3291 4020 4.109050 CGAGCACTTTTTGGCTTTGTTAA 58.891 39.130 0.00 0.00 41.22 2.01
3292 4021 3.129638 ACGAGCACTTTTTGGCTTTGTTA 59.870 39.130 0.00 0.00 41.22 2.41
3293 4022 2.094234 ACGAGCACTTTTTGGCTTTGTT 60.094 40.909 0.00 0.00 41.22 2.83
3294 4023 1.476488 ACGAGCACTTTTTGGCTTTGT 59.524 42.857 0.00 0.00 41.22 2.83
3295 4024 2.208326 ACGAGCACTTTTTGGCTTTG 57.792 45.000 0.00 0.00 41.22 2.77
3296 4025 2.959507 AACGAGCACTTTTTGGCTTT 57.040 40.000 0.00 0.00 41.22 3.51
3297 4026 2.959507 AAACGAGCACTTTTTGGCTT 57.040 40.000 0.00 0.00 41.22 4.35
3298 4027 2.929398 CAAAAACGAGCACTTTTTGGCT 59.071 40.909 16.24 0.00 41.70 4.75
3299 4028 2.926838 TCAAAAACGAGCACTTTTTGGC 59.073 40.909 20.09 0.00 43.91 4.52
3300 4029 6.475402 ACTTATCAAAAACGAGCACTTTTTGG 59.525 34.615 20.09 10.79 43.91 3.28
3301 4030 7.449934 ACTTATCAAAAACGAGCACTTTTTG 57.550 32.000 17.14 17.14 44.60 2.44
3302 4031 9.575783 TTAACTTATCAAAAACGAGCACTTTTT 57.424 25.926 0.00 0.00 32.23 1.94
3303 4032 9.575783 TTTAACTTATCAAAAACGAGCACTTTT 57.424 25.926 0.00 0.00 0.00 2.27
3304 4033 9.575783 TTTTAACTTATCAAAAACGAGCACTTT 57.424 25.926 0.00 0.00 0.00 2.66
3305 4034 9.575783 TTTTTAACTTATCAAAAACGAGCACTT 57.424 25.926 0.00 0.00 30.72 3.16
3341 4070 7.659799 CCGATCTATCTATCTGGGTACATAGAG 59.340 44.444 6.74 0.00 35.53 2.43
3343 4072 6.205853 GCCGATCTATCTATCTGGGTACATAG 59.794 46.154 0.00 0.00 0.00 2.23
3351 4100 2.478709 GCACGCCGATCTATCTATCTGG 60.479 54.545 0.00 0.00 0.00 3.86
3352 4101 2.162408 TGCACGCCGATCTATCTATCTG 59.838 50.000 0.00 0.00 0.00 2.90
3354 4103 2.921634 TGCACGCCGATCTATCTATC 57.078 50.000 0.00 0.00 0.00 2.08
3355 4104 3.515630 CAATGCACGCCGATCTATCTAT 58.484 45.455 0.00 0.00 0.00 1.98
3356 4105 2.352715 CCAATGCACGCCGATCTATCTA 60.353 50.000 0.00 0.00 0.00 1.98
3376 4125 1.442769 AGTGTCATGTCGAATGTGCC 58.557 50.000 0.00 0.00 0.00 5.01
3383 4132 4.519540 TTCAGATGAAGTGTCATGTCGA 57.480 40.909 0.00 0.00 44.83 4.20
3384 4133 4.925646 TCTTTCAGATGAAGTGTCATGTCG 59.074 41.667 0.00 0.00 44.83 4.35
3432 4181 9.932207 GATCTGTACTGCTTCTCTATACTACTA 57.068 37.037 0.00 0.00 0.00 1.82
3433 4182 8.656806 AGATCTGTACTGCTTCTCTATACTACT 58.343 37.037 0.00 0.00 0.00 2.57
3434 4183 8.842358 AGATCTGTACTGCTTCTCTATACTAC 57.158 38.462 0.00 0.00 0.00 2.73
3435 4184 9.278978 CAAGATCTGTACTGCTTCTCTATACTA 57.721 37.037 0.00 0.00 0.00 1.82
3436 4185 7.255451 GCAAGATCTGTACTGCTTCTCTATACT 60.255 40.741 9.42 0.00 0.00 2.12
3438 4187 6.775142 AGCAAGATCTGTACTGCTTCTCTATA 59.225 38.462 12.84 0.00 0.00 1.31
3439 4188 5.598005 AGCAAGATCTGTACTGCTTCTCTAT 59.402 40.000 12.84 0.00 0.00 1.98
3445 4195 5.667539 TCTAAGCAAGATCTGTACTGCTT 57.332 39.130 27.02 27.02 43.70 3.91
3446 4196 5.186797 ACTTCTAAGCAAGATCTGTACTGCT 59.813 40.000 12.84 12.84 33.05 4.24
3478 4228 0.250901 ACACCCAGAGATGCCACAAC 60.251 55.000 0.00 0.00 0.00 3.32
3485 4235 1.901591 AGCAAACACACCCAGAGATG 58.098 50.000 0.00 0.00 0.00 2.90
3486 4236 2.233271 CAAGCAAACACACCCAGAGAT 58.767 47.619 0.00 0.00 0.00 2.75
3488 4238 0.670162 CCAAGCAAACACACCCAGAG 59.330 55.000 0.00 0.00 0.00 3.35
3489 4239 0.033601 ACCAAGCAAACACACCCAGA 60.034 50.000 0.00 0.00 0.00 3.86
3490 4240 0.385390 GACCAAGCAAACACACCCAG 59.615 55.000 0.00 0.00 0.00 4.45
3491 4241 1.040339 GGACCAAGCAAACACACCCA 61.040 55.000 0.00 0.00 0.00 4.51
3503 4290 1.484038 CTCTCCTCTCCTGGACCAAG 58.516 60.000 0.00 0.00 31.94 3.61
3621 4416 1.602605 GGTCCAACAGAAACGGGGG 60.603 63.158 0.00 0.00 0.00 5.40
3623 4418 1.165270 GATGGTCCAACAGAAACGGG 58.835 55.000 0.00 0.00 0.00 5.28
3851 4675 4.219288 CCATTAGTTCTTTCAGGCTTGCTT 59.781 41.667 0.00 0.00 0.00 3.91
3852 4676 3.760684 CCATTAGTTCTTTCAGGCTTGCT 59.239 43.478 0.00 0.00 0.00 3.91
3853 4677 3.758554 TCCATTAGTTCTTTCAGGCTTGC 59.241 43.478 0.00 0.00 0.00 4.01
3854 4678 5.006386 ACTCCATTAGTTCTTTCAGGCTTG 58.994 41.667 0.00 0.00 33.35 4.01
3855 4679 5.248380 ACTCCATTAGTTCTTTCAGGCTT 57.752 39.130 0.00 0.00 33.35 4.35
3884 4714 6.071896 ACGATCGATGGACACAGTATATCATT 60.072 38.462 24.34 0.00 0.00 2.57
3885 4715 5.416013 ACGATCGATGGACACAGTATATCAT 59.584 40.000 24.34 0.00 0.00 2.45
3887 4717 5.298197 ACGATCGATGGACACAGTATATC 57.702 43.478 24.34 0.00 0.00 1.63
3891 4721 2.734175 GCAACGATCGATGGACACAGTA 60.734 50.000 24.34 0.00 0.00 2.74
3892 4722 1.996292 CAACGATCGATGGACACAGT 58.004 50.000 24.34 0.00 0.00 3.55
3893 4723 0.647410 GCAACGATCGATGGACACAG 59.353 55.000 24.34 0.00 0.00 3.66
3896 4726 1.518352 CCGCAACGATCGATGGACA 60.518 57.895 24.34 0.00 0.00 4.02
3897 4727 2.871427 GCCGCAACGATCGATGGAC 61.871 63.158 24.34 7.51 0.00 4.02
3898 4728 2.584970 GCCGCAACGATCGATGGA 60.585 61.111 24.34 0.00 0.00 3.41
3924 4754 2.368131 CTACTGCGTCTCCGAGCGAG 62.368 65.000 13.99 10.86 40.30 5.03
3927 4757 0.305313 CTACTACTGCGTCTCCGAGC 59.695 60.000 0.00 0.00 35.63 5.03
3929 4759 1.649664 GTCTACTACTGCGTCTCCGA 58.350 55.000 0.00 0.00 35.63 4.55
3930 4760 0.301088 CGTCTACTACTGCGTCTCCG 59.699 60.000 0.00 0.00 37.07 4.63
3931 4761 0.656785 CCGTCTACTACTGCGTCTCC 59.343 60.000 0.00 0.00 0.00 3.71
3934 4764 0.522915 GTGCCGTCTACTACTGCGTC 60.523 60.000 0.00 0.00 40.90 5.19
3937 4767 0.729116 TACGTGCCGTCTACTACTGC 59.271 55.000 0.00 0.00 41.54 4.40
3938 4768 1.329906 CCTACGTGCCGTCTACTACTG 59.670 57.143 0.00 0.00 41.54 2.74
3939 4769 1.208052 TCCTACGTGCCGTCTACTACT 59.792 52.381 0.00 0.00 41.54 2.57
3940 4770 1.596727 CTCCTACGTGCCGTCTACTAC 59.403 57.143 0.00 0.00 41.54 2.73
3941 4771 1.473965 CCTCCTACGTGCCGTCTACTA 60.474 57.143 0.00 0.00 41.54 1.82


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

AutoCloner maintained by Alex Coulton.