Multiple sequence alignment - TraesCS3B01G354100

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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 TraesCS3B01G354100 chr3B 100.000 3130 0 0 1 3130 564758013 564761142 0.000000e+00 5781.0
1 TraesCS3B01G354100 chr3B 79.928 279 41 7 2833 3101 642065826 642065553 1.150000e-44 191.0
2 TraesCS3B01G354100 chr3D 94.102 1136 45 10 1001 2130 432513028 432514147 0.000000e+00 1707.0
3 TraesCS3B01G354100 chr3D 89.495 733 58 7 288 1015 432507379 432508097 0.000000e+00 909.0
4 TraesCS3B01G354100 chr3D 90.110 273 26 1 7 279 432501681 432501952 1.380000e-93 353.0
5 TraesCS3B01G354100 chr3D 87.129 303 17 13 2140 2430 432514197 432514489 1.080000e-84 324.0
6 TraesCS3B01G354100 chr3D 82.781 151 17 6 2539 2684 1663156 1663010 3.280000e-25 126.0
7 TraesCS3B01G354100 chr3D 86.598 97 11 2 2436 2530 105231486 105231390 4.270000e-19 106.0
8 TraesCS3B01G354100 chr3D 95.745 47 0 2 2823 2868 42347369 42347414 1.200000e-09 75.0
9 TraesCS3B01G354100 chr3A 93.988 815 36 7 955 1763 569890669 569891476 0.000000e+00 1221.0
10 TraesCS3B01G354100 chr3A 94.325 652 28 3 874 1525 570113794 570114436 0.000000e+00 990.0
11 TraesCS3B01G354100 chr3A 89.673 765 73 5 201 960 569889822 569890585 0.000000e+00 970.0
12 TraesCS3B01G354100 chr3A 87.707 846 85 8 7 850 569953166 569953994 0.000000e+00 968.0
13 TraesCS3B01G354100 chr3A 94.785 326 12 2 1807 2131 569891549 569891870 1.300000e-138 503.0
14 TraesCS3B01G354100 chr3A 94.444 324 15 1 1807 2130 570114814 570115134 2.170000e-136 496.0
15 TraesCS3B01G354100 chr3A 89.912 228 14 5 1567 1793 570114543 570114762 5.110000e-73 285.0
16 TraesCS3B01G354100 chr3A 90.640 203 18 1 3 205 569889316 569889517 5.150000e-68 268.0
17 TraesCS3B01G354100 chr3A 87.081 209 13 10 2229 2432 570115214 570115413 1.130000e-54 224.0
18 TraesCS3B01G354100 chr3A 78.671 286 39 10 2833 3101 732930444 732930164 1.490000e-38 171.0
19 TraesCS3B01G354100 chr3A 88.596 114 13 0 2712 2825 569892489 569892602 4.210000e-29 139.0
20 TraesCS3B01G354100 chr3A 86.607 112 10 3 2319 2429 569891985 569892092 5.480000e-23 119.0
21 TraesCS3B01G354100 chr3A 87.500 96 9 3 2436 2528 199695656 199695561 1.190000e-19 108.0
22 TraesCS3B01G354100 chr3A 96.970 33 0 1 2174 2206 569891874 569891905 2.000000e-03 54.7
23 TraesCS3B01G354100 chr4A 84.375 672 76 21 1094 1753 5122189 5122843 1.580000e-177 632.0
24 TraesCS3B01G354100 chr4A 91.500 400 32 1 1126 1525 5193109 5193506 1.640000e-152 549.0
25 TraesCS3B01G354100 chr4A 85.680 412 41 12 1816 2209 5122969 5123380 4.830000e-113 418.0
26 TraesCS3B01G354100 chr4A 88.923 325 34 2 1816 2139 5200516 5200839 1.750000e-107 399.0
27 TraesCS3B01G354100 chr4A 84.226 336 50 3 416 748 689667257 689666922 1.080000e-84 324.0
28 TraesCS3B01G354100 chr4A 79.038 291 40 8 2824 3103 629299891 629300171 2.480000e-41 180.0
29 TraesCS3B01G354100 chr4A 88.000 100 9 3 2431 2528 442937902 442937804 7.090000e-22 115.0
30 TraesCS3B01G354100 chr4A 91.525 59 4 1 910 967 5119580 5119638 2.590000e-11 80.5
31 TraesCS3B01G354100 chr4D 88.129 497 45 8 1034 1518 465352113 465351619 2.090000e-161 579.0
32 TraesCS3B01G354100 chr4D 90.750 400 35 1 1126 1525 465161972 465161575 1.650000e-147 532.0
33 TraesCS3B01G354100 chr4D 90.404 396 36 1 1130 1525 465185727 465185334 1.290000e-143 520.0
34 TraesCS3B01G354100 chr4D 85.496 393 48 8 1814 2197 465351285 465350893 4.860000e-108 401.0
35 TraesCS3B01G354100 chr4D 91.409 291 25 0 1840 2130 465183710 465183420 1.750000e-107 399.0
36 TraesCS3B01G354100 chr4D 90.000 300 29 1 1840 2139 465157641 465157343 1.360000e-103 387.0
37 TraesCS3B01G354100 chr4D 88.333 300 34 1 1840 2139 465161181 465160883 2.970000e-95 359.0
38 TraesCS3B01G354100 chr4D 93.377 151 9 1 1603 1752 465351561 465351411 4.060000e-54 222.0
39 TraesCS3B01G354100 chr4D 94.958 119 6 0 1634 1752 465161437 465161319 1.480000e-43 187.0
40 TraesCS3B01G354100 chr4D 79.688 256 42 8 495 744 467241441 467241692 3.210000e-40 176.0
41 TraesCS3B01G354100 chr4D 78.840 293 39 9 2823 3102 481181375 481181093 3.210000e-40 176.0
42 TraesCS3B01G354100 chr4D 80.978 184 27 5 2924 3103 386747624 386747445 4.210000e-29 139.0
43 TraesCS3B01G354100 chr4D 81.935 155 19 6 2548 2697 479687406 479687256 4.240000e-24 122.0
44 TraesCS3B01G354100 chr4B 90.215 419 35 1 1105 1517 582023717 582023299 2.750000e-150 542.0
45 TraesCS3B01G354100 chr4B 84.715 386 45 10 1816 2197 582022918 582022543 1.060000e-99 374.0
46 TraesCS3B01G354100 chr4B 83.575 207 27 5 2900 3103 115878952 115879154 1.480000e-43 187.0
47 TraesCS3B01G354100 chr4B 80.153 262 40 10 490 744 585029844 585030100 5.330000e-43 185.0
48 TraesCS3B01G354100 chr4B 80.864 162 25 5 556 715 624522963 624523120 4.240000e-24 122.0
49 TraesCS3B01G354100 chr4B 81.290 155 20 6 2548 2697 606916909 606916759 1.970000e-22 117.0
50 TraesCS3B01G354100 chr4B 84.685 111 9 6 860 967 582024574 582024469 1.540000e-18 104.0
51 TraesCS3B01G354100 chr4B 93.023 43 2 1 917 958 582023881 582023839 9.370000e-06 62.1
52 TraesCS3B01G354100 chr6A 93.029 373 17 5 1183 1553 166114362 166114727 1.280000e-148 536.0
53 TraesCS3B01G354100 chr6A 90.667 375 18 7 1569 1940 166114840 166115200 1.690000e-132 483.0
54 TraesCS3B01G354100 chr6A 76.180 466 89 17 279 732 421467973 421467518 3.140000e-55 226.0
55 TraesCS3B01G354100 chr1B 80.479 292 39 11 2824 3103 667011310 667011595 1.140000e-49 207.0
56 TraesCS3B01G354100 chr1B 78.598 271 38 8 2848 3103 303677980 303677715 8.980000e-36 161.0
57 TraesCS3B01G354100 chr7D 81.154 260 44 4 490 744 439237171 439237430 1.470000e-48 204.0
58 TraesCS3B01G354100 chr7D 80.288 208 29 6 2900 3105 571004157 571003960 2.520000e-31 147.0
59 TraesCS3B01G354100 chr7D 83.544 158 19 5 2532 2685 43386930 43386776 1.170000e-29 141.0
60 TraesCS3B01G354100 chr7D 83.007 153 15 8 2548 2694 390687492 390687345 9.110000e-26 128.0
61 TraesCS3B01G354100 chr2B 80.205 293 40 7 2824 3103 749821220 749820933 1.470000e-48 204.0
62 TraesCS3B01G354100 chr2B 79.863 293 41 8 2823 3103 749825120 749824834 6.850000e-47 198.0
63 TraesCS3B01G354100 chr2D 82.773 238 25 9 2904 3130 29015504 29015736 6.850000e-47 198.0
64 TraesCS3B01G354100 chr2D 77.778 297 37 14 2823 3103 83534219 83534502 4.180000e-34 156.0
65 TraesCS3B01G354100 chr2D 78.866 194 27 6 2832 3015 158246363 158246552 5.480000e-23 119.0
66 TraesCS3B01G354100 chr2D 88.889 90 8 2 2442 2529 17139230 17139141 3.300000e-20 110.0
67 TraesCS3B01G354100 chr2D 86.567 67 7 2 2477 2543 29260495 29260431 4.330000e-09 73.1
68 TraesCS3B01G354100 chr2D 93.182 44 1 2 2695 2737 648748661 648748703 2.610000e-06 63.9
69 TraesCS3B01G354100 chr6B 79.310 290 40 8 2824 3103 183596923 183596644 5.330000e-43 185.0
70 TraesCS3B01G354100 chr6B 81.761 159 18 8 2532 2685 36133505 36133657 4.240000e-24 122.0
71 TraesCS3B01G354100 chr6B 93.182 44 1 2 2695 2737 23818848 23818890 2.610000e-06 63.9
72 TraesCS3B01G354100 chr6B 86.441 59 6 2 2695 2752 606426979 606426922 2.610000e-06 63.9
73 TraesCS3B01G354100 chr1A 78.571 294 36 12 2824 3103 104377182 104376902 5.370000e-38 169.0
74 TraesCS3B01G354100 chr1A 91.304 46 2 2 2690 2734 50928453 50928497 9.370000e-06 62.1
75 TraesCS3B01G354100 chr1A 95.000 40 0 2 2696 2735 362059977 362059940 9.370000e-06 62.1
76 TraesCS3B01G354100 chr5D 80.000 250 29 9 2827 3065 520281102 520281341 6.940000e-37 165.0
77 TraesCS3B01G354100 chr5D 80.110 181 24 4 2902 3077 560224469 560224642 1.180000e-24 124.0
78 TraesCS3B01G354100 chr5D 92.857 42 2 1 2699 2740 543775557 543775517 3.370000e-05 60.2
79 TraesCS3B01G354100 chr7A 78.082 292 41 9 2823 3103 76126380 76126101 2.500000e-36 163.0
80 TraesCS3B01G354100 chr7A 82.822 163 15 10 2527 2682 1528800 1528644 1.960000e-27 134.0
81 TraesCS3B01G354100 chr7A 85.185 108 13 3 2425 2530 653596957 653597063 1.190000e-19 108.0
82 TraesCS3B01G354100 chr7B 83.799 179 15 11 2513 2685 663743398 663743568 1.160000e-34 158.0
83 TraesCS3B01G354100 chr7B 89.474 95 8 2 2436 2528 339685446 339685540 5.480000e-23 119.0
84 TraesCS3B01G354100 chr5B 76.147 327 46 15 2824 3128 708340014 708339698 3.250000e-30 143.0
85 TraesCS3B01G354100 chr5B 93.478 46 1 2 2695 2740 98836150 98836193 2.010000e-07 67.6
86 TraesCS3B01G354100 chr2A 77.211 294 34 15 2833 3102 715619363 715619079 1.170000e-29 141.0
87 TraesCS3B01G354100 chr2A 83.019 159 16 9 2532 2685 734269876 734270028 1.960000e-27 134.0
88 TraesCS3B01G354100 chr2A 88.421 95 9 2 2436 2528 742722139 742722233 2.550000e-21 113.0
89 TraesCS3B01G354100 chr2A 86.139 101 12 2 2430 2528 583840933 583841033 1.190000e-19 108.0
90 TraesCS3B01G354100 chr5A 82.822 163 19 7 2548 2702 585431625 585431786 1.510000e-28 137.0
91 TraesCS3B01G354100 chr5A 100.000 30 0 0 2712 2741 687682605 687682576 4.360000e-04 56.5
92 TraesCS3B01G354100 chr1D 83.099 142 18 4 2548 2685 473998924 473998785 1.180000e-24 124.0
93 TraesCS3B01G354100 chr1D 85.714 105 13 2 2428 2530 386474024 386474128 3.300000e-20 110.0
94 TraesCS3B01G354100 chr1D 95.122 41 2 0 2695 2735 69265997 69266037 7.250000e-07 65.8
95 TraesCS3B01G354100 chr1D 91.304 46 2 2 2690 2734 28820548 28820504 9.370000e-06 62.1


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 TraesCS3B01G354100 chr3B 564758013 564761142 3129 False 5781.000000 5781 100.000000 1 3130 1 chr3B.!!$F1 3129
1 TraesCS3B01G354100 chr3D 432513028 432514489 1461 False 1015.500000 1707 90.615500 1001 2430 2 chr3D.!!$F4 1429
2 TraesCS3B01G354100 chr3D 432507379 432508097 718 False 909.000000 909 89.495000 288 1015 1 chr3D.!!$F3 727
3 TraesCS3B01G354100 chr3A 569953166 569953994 828 False 968.000000 968 87.707000 7 850 1 chr3A.!!$F1 843
4 TraesCS3B01G354100 chr3A 570113794 570115413 1619 False 498.750000 990 91.440500 874 2432 4 chr3A.!!$F3 1558
5 TraesCS3B01G354100 chr3A 569889316 569892602 3286 False 467.814286 1221 91.608429 3 2825 7 chr3A.!!$F2 2822
6 TraesCS3B01G354100 chr4A 5119580 5123380 3800 False 376.833333 632 87.193333 910 2209 3 chr4A.!!$F4 1299
7 TraesCS3B01G354100 chr4D 465183420 465185727 2307 True 459.500000 520 90.906500 1130 2130 2 chr4D.!!$R5 1000
8 TraesCS3B01G354100 chr4D 465350893 465352113 1220 True 400.666667 579 89.000667 1034 2197 3 chr4D.!!$R6 1163
9 TraesCS3B01G354100 chr4D 465157343 465161972 4629 True 366.250000 532 91.010250 1126 2139 4 chr4D.!!$R4 1013
10 TraesCS3B01G354100 chr4B 582022543 582024574 2031 True 270.525000 542 88.159500 860 2197 4 chr4B.!!$R2 1337
11 TraesCS3B01G354100 chr6A 166114362 166115200 838 False 509.500000 536 91.848000 1183 1940 2 chr6A.!!$F1 757
12 TraesCS3B01G354100 chr2B 749820933 749825120 4187 True 201.000000 204 80.034000 2823 3103 2 chr2B.!!$R1 280

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
334 644 0.538746 TCCTCCCTTGGGTTTTTCGC 60.539 55.000 5.51 0.0 0.00 4.70 F
732 1046 1.501292 CATCCATTGCAACGCACGA 59.499 52.632 0.00 0.0 38.71 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 4470 1.004394 CCAGGAGTACAGGGGTTTTCC 59.996 57.143 0.0 0.0 39.75 3.13 R
2400 10358 0.442310 CCGGTCACAAGTTACATGCG 59.558 55.000 0.0 0.0 0.00 4.73 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
40 41 4.741928 ATAAGTGTGGAACCCTCCTTTT 57.258 40.909 0.00 0.00 42.94 2.27
44 45 2.623416 GTGTGGAACCCTCCTTTTTCTG 59.377 50.000 0.00 0.00 42.94 3.02
48 49 3.140144 TGGAACCCTCCTTTTTCTGTCAT 59.860 43.478 0.00 0.00 42.94 3.06
74 75 9.022884 TCATCAGGTTTTGTATGAAATGATTGA 57.977 29.630 0.00 0.00 0.00 2.57
93 94 8.454570 TGATTGATGCATACAATTCTACATGT 57.545 30.769 18.94 2.69 37.96 3.21
98 99 6.597262 TGCATACAATTCTACATGTTACCG 57.403 37.500 2.30 0.00 0.00 4.02
132 133 7.508687 AGGCCAATTTAGACAAAGAAAATGTT 58.491 30.769 5.01 0.00 0.00 2.71
173 174 2.099652 TTGTCTGAGGGAGCCACACG 62.100 60.000 0.00 0.00 0.00 4.49
187 188 2.292292 GCCACACGTAAAGGTGAATGTT 59.708 45.455 9.60 0.00 40.38 2.71
188 189 3.851838 GCCACACGTAAAGGTGAATGTTG 60.852 47.826 9.60 0.00 40.38 3.33
191 192 5.449314 CCACACGTAAAGGTGAATGTTGAAA 60.449 40.000 9.60 0.00 40.38 2.69
221 531 8.983702 AGTGTGTAACCCAACTTAAGATTTTA 57.016 30.769 10.09 0.00 34.36 1.52
222 532 8.843262 AGTGTGTAACCCAACTTAAGATTTTAC 58.157 33.333 10.09 9.20 34.36 2.01
238 548 1.774639 TTACTTGAACCGACTCGTGC 58.225 50.000 0.00 0.00 0.00 5.34
303 613 8.618702 TCTACTATTATAGAGGAGTTGGTTCG 57.381 38.462 6.21 0.00 0.00 3.95
334 644 0.538746 TCCTCCCTTGGGTTTTTCGC 60.539 55.000 5.51 0.00 0.00 4.70
354 664 2.039624 ACATGCGTCCCTCCCTCT 59.960 61.111 0.00 0.00 0.00 3.69
363 673 2.751816 CGTCCCTCCCTCTTTGGTTTTT 60.752 50.000 0.00 0.00 0.00 1.94
375 685 7.202001 CCCTCTTTGGTTTTTCTATTGACCTTT 60.202 37.037 0.00 0.00 33.33 3.11
413 723 5.051774 CGATGCCGCATAAAATTAAAACCAG 60.052 40.000 5.67 0.00 0.00 4.00
518 830 8.308931 TCAAATCAAATCTTCCCAAAATCTCAG 58.691 33.333 0.00 0.00 0.00 3.35
519 831 6.786967 ATCAAATCTTCCCAAAATCTCAGG 57.213 37.500 0.00 0.00 0.00 3.86
521 833 5.477984 TCAAATCTTCCCAAAATCTCAGGTG 59.522 40.000 0.00 0.00 0.00 4.00
615 928 8.815565 TCAATACTTTATTTGCATTCCCTACA 57.184 30.769 0.00 0.00 0.00 2.74
719 1033 8.596293 TGAATCACTAGAATATGTATGCATCCA 58.404 33.333 0.19 0.00 36.58 3.41
732 1046 1.501292 CATCCATTGCAACGCACGA 59.499 52.632 0.00 0.00 38.71 4.35
736 1050 1.794785 CATTGCAACGCACGAGCAG 60.795 57.895 0.00 0.37 38.71 4.24
809 1125 7.752695 ACACTAAATGAATACAAGCAACTAGC 58.247 34.615 0.00 0.00 46.19 3.42
835 1151 8.776470 CAAGTGCATTGGTTCAAAAATAAGATT 58.224 29.630 0.00 0.00 35.08 2.40
1108 3941 5.123027 GCTATAGCTCAAGCACAGAAAAACT 59.877 40.000 17.75 0.00 45.16 2.66
1163 4008 2.827642 GGGCCAAGCTAGCAGCAG 60.828 66.667 18.83 3.53 45.56 4.24
1383 4228 1.965219 CGAGAAGGTGGTCCTCGTT 59.035 57.895 0.00 0.00 44.35 3.85
1556 4470 5.061808 CGTGGAAGTAGTATTTCCTGAAACG 59.938 44.000 21.28 18.28 43.63 3.60
1576 5823 1.004394 GGAAAACCCCTGTACTCCTGG 59.996 57.143 0.00 0.00 0.00 4.45
1596 5847 2.474032 GGTTGTTTGCTCGCGATCTAAC 60.474 50.000 23.74 23.74 0.00 2.34
1604 5855 2.714985 GCTCGCGATCTAACTAGTTTCG 59.285 50.000 19.22 19.22 35.09 3.46
1761 6015 2.181021 CGGAGGTACAGTGTCCGC 59.819 66.667 8.05 7.39 46.18 5.54
2131 10029 3.076621 CTGTCAAGTATGCTGCCTGAAA 58.923 45.455 0.00 0.00 0.00 2.69
2134 10032 4.082625 TGTCAAGTATGCTGCCTGAAATTG 60.083 41.667 0.00 0.00 0.00 2.32
2135 10033 4.156556 GTCAAGTATGCTGCCTGAAATTGA 59.843 41.667 0.00 0.00 0.00 2.57
2138 10036 1.825090 ATGCTGCCTGAAATTGACGA 58.175 45.000 0.00 0.00 0.00 4.20
2157 10097 2.005537 CGCACGTTGCTTTGCTGAC 61.006 57.895 8.07 0.00 42.25 3.51
2202 10153 1.729131 CGTTGCCGGCATTTGTGAC 60.729 57.895 33.25 22.98 0.00 3.67
2223 10174 5.010617 TGACTTGTCACATCTACTGCTGTAA 59.989 40.000 4.91 0.00 0.00 2.41
2236 10190 6.893554 TCTACTGCTGTAATTACCTACCTCAA 59.106 38.462 13.01 0.00 0.00 3.02
2248 10202 4.397348 CCTCAAGGTTTGTCCCGG 57.603 61.111 0.00 0.00 36.75 5.73
2251 10205 0.605589 CTCAAGGTTTGTCCCGGTCC 60.606 60.000 0.00 0.00 36.75 4.46
2254 10208 0.179001 AAGGTTTGTCCCGGTCCTTG 60.179 55.000 0.00 0.00 37.17 3.61
2283 10237 5.820423 TCAGAGACTTCTACTGCACTCTATC 59.180 44.000 0.00 0.00 34.12 2.08
2284 10238 5.008613 CAGAGACTTCTACTGCACTCTATCC 59.991 48.000 0.00 0.00 34.12 2.59
2285 10239 4.861196 AGACTTCTACTGCACTCTATCCA 58.139 43.478 0.00 0.00 0.00 3.41
2286 10240 5.454062 AGACTTCTACTGCACTCTATCCAT 58.546 41.667 0.00 0.00 0.00 3.41
2287 10241 6.606069 AGACTTCTACTGCACTCTATCCATA 58.394 40.000 0.00 0.00 0.00 2.74
2288 10242 7.237982 AGACTTCTACTGCACTCTATCCATAT 58.762 38.462 0.00 0.00 0.00 1.78
2289 10243 8.387039 AGACTTCTACTGCACTCTATCCATATA 58.613 37.037 0.00 0.00 0.00 0.86
2291 10245 9.019656 ACTTCTACTGCACTCTATCCATATAAG 57.980 37.037 0.00 0.00 0.00 1.73
2292 10246 9.237187 CTTCTACTGCACTCTATCCATATAAGA 57.763 37.037 0.00 0.00 0.00 2.10
2293 10247 8.568676 TCTACTGCACTCTATCCATATAAGAC 57.431 38.462 0.00 0.00 0.00 3.01
2387 10345 2.350522 GTGAGCACCTATGTTGACAGG 58.649 52.381 0.00 0.00 37.97 4.00
2400 10358 2.928116 GTTGACAGGTACTAATCGTGGC 59.072 50.000 0.00 0.00 36.02 5.01
2434 10393 6.258230 TGTGACCGGAGTAATATAATACCG 57.742 41.667 9.46 0.00 40.03 4.02
2440 10735 4.400251 CGGAGTAATATAATACCGCCTCCA 59.600 45.833 0.00 0.00 34.36 3.86
2449 10744 9.975218 AATATAATACCGCCTCCATTTCTAAAT 57.025 29.630 0.00 0.00 0.00 1.40
2454 10749 9.449719 AATACCGCCTCCATTTCTAAATATAAG 57.550 33.333 0.00 0.00 0.00 1.73
2455 10750 6.838382 ACCGCCTCCATTTCTAAATATAAGT 58.162 36.000 0.00 0.00 0.00 2.24
2456 10751 7.287810 ACCGCCTCCATTTCTAAATATAAGTT 58.712 34.615 0.00 0.00 0.00 2.66
2457 10752 7.444487 ACCGCCTCCATTTCTAAATATAAGTTC 59.556 37.037 0.00 0.00 0.00 3.01
2459 10754 9.057089 CGCCTCCATTTCTAAATATAAGTTCTT 57.943 33.333 0.00 0.00 0.00 2.52
2477 10772 7.883391 AGTTCTTGAGAGATTCTAATACGGA 57.117 36.000 0.00 0.00 0.00 4.69
2478 10773 7.708998 AGTTCTTGAGAGATTCTAATACGGAC 58.291 38.462 0.00 0.00 0.00 4.79
2480 10775 8.838365 GTTCTTGAGAGATTCTAATACGGACTA 58.162 37.037 0.00 0.00 0.00 2.59
2481 10776 8.380743 TCTTGAGAGATTCTAATACGGACTAC 57.619 38.462 0.00 0.00 0.00 2.73
2483 10778 8.693120 TTGAGAGATTCTAATACGGACTACAT 57.307 34.615 0.00 0.00 0.00 2.29
2484 10779 9.788889 TTGAGAGATTCTAATACGGACTACATA 57.211 33.333 0.00 0.00 0.00 2.29
2486 10781 8.254178 AGAGATTCTAATACGGACTACATACG 57.746 38.462 0.00 0.00 0.00 3.06
2487 10782 7.333921 AGAGATTCTAATACGGACTACATACGG 59.666 40.741 0.00 0.00 0.00 4.02
2488 10783 7.164122 AGATTCTAATACGGACTACATACGGA 58.836 38.462 0.00 0.00 0.00 4.69
2489 10784 6.791887 TTCTAATACGGACTACATACGGAG 57.208 41.667 0.00 0.00 0.00 4.63
2507 10802 6.963049 ACGGAGTAAAATGAGTGAATGTAC 57.037 37.500 0.00 0.00 41.94 2.90
2508 10803 6.460781 ACGGAGTAAAATGAGTGAATGTACA 58.539 36.000 0.00 0.00 41.94 2.90
2509 10804 6.367969 ACGGAGTAAAATGAGTGAATGTACAC 59.632 38.462 0.00 0.00 41.94 2.90
2557 10852 9.495382 ACTCCCTCTCTGTCTTTAAATATAAGT 57.505 33.333 0.00 0.00 0.00 2.24
2592 10887 9.751542 AAGATTTCACTATAAAGACTACATCCG 57.248 33.333 0.00 0.00 0.00 4.18
2593 10888 8.361139 AGATTTCACTATAAAGACTACATCCGG 58.639 37.037 0.00 0.00 0.00 5.14
2594 10889 7.649533 TTTCACTATAAAGACTACATCCGGA 57.350 36.000 6.61 6.61 0.00 5.14
2595 10890 7.834881 TTCACTATAAAGACTACATCCGGAT 57.165 36.000 12.38 12.38 0.00 4.18
2596 10891 7.215719 TCACTATAAAGACTACATCCGGATG 57.784 40.000 37.23 37.23 44.15 3.51
2610 10905 6.531503 CATCCGGATGTATATAGACACCTT 57.468 41.667 32.39 0.00 34.23 3.50
2611 10906 6.936279 CATCCGGATGTATATAGACACCTTT 58.064 40.000 32.39 0.00 34.23 3.11
2612 10907 6.989155 TCCGGATGTATATAGACACCTTTT 57.011 37.500 0.00 0.00 30.52 2.27
2613 10908 8.528643 CATCCGGATGTATATAGACACCTTTTA 58.471 37.037 32.39 0.00 34.23 1.52
2614 10909 8.118976 TCCGGATGTATATAGACACCTTTTAG 57.881 38.462 0.00 0.00 30.52 1.85
2615 10910 7.946219 TCCGGATGTATATAGACACCTTTTAGA 59.054 37.037 0.00 0.00 30.52 2.10
2616 10911 8.244802 CCGGATGTATATAGACACCTTTTAGAG 58.755 40.741 1.52 0.00 30.52 2.43
2617 10912 8.794553 CGGATGTATATAGACACCTTTTAGAGT 58.205 37.037 1.52 0.00 30.52 3.24
2627 10922 8.779354 AGACACCTTTTAGAGTATGATTTCAC 57.221 34.615 0.00 0.00 0.00 3.18
2628 10923 8.598041 AGACACCTTTTAGAGTATGATTTCACT 58.402 33.333 0.00 0.00 0.00 3.41
2629 10924 9.220767 GACACCTTTTAGAGTATGATTTCACTT 57.779 33.333 0.00 0.00 0.00 3.16
2658 10953 9.944376 TTTGCTTAGTAGTCTATTGTGAAATCT 57.056 29.630 0.00 0.00 0.00 2.40
2659 10954 9.587772 TTGCTTAGTAGTCTATTGTGAAATCTC 57.412 33.333 0.00 0.00 0.00 2.75
2660 10955 8.972127 TGCTTAGTAGTCTATTGTGAAATCTCT 58.028 33.333 0.00 0.00 0.00 3.10
2668 10963 9.660180 AGTCTATTGTGAAATCTCTAAAAGGAC 57.340 33.333 0.00 0.00 0.00 3.85
2669 10964 9.660180 GTCTATTGTGAAATCTCTAAAAGGACT 57.340 33.333 0.00 0.00 0.00 3.85
2686 10981 8.515695 AAAAGGACTTATATTTAGAAACGGGG 57.484 34.615 0.00 0.00 0.00 5.73
2687 10982 6.819947 AGGACTTATATTTAGAAACGGGGT 57.180 37.500 0.00 0.00 0.00 4.95
2688 10983 6.589135 AGGACTTATATTTAGAAACGGGGTG 58.411 40.000 0.00 0.00 0.00 4.61
2689 10984 6.384886 AGGACTTATATTTAGAAACGGGGTGA 59.615 38.462 0.00 0.00 0.00 4.02
2690 10985 7.072076 AGGACTTATATTTAGAAACGGGGTGAT 59.928 37.037 0.00 0.00 0.00 3.06
2691 10986 7.718314 GGACTTATATTTAGAAACGGGGTGATT 59.282 37.037 0.00 0.00 0.00 2.57
2692 10987 9.768662 GACTTATATTTAGAAACGGGGTGATTA 57.231 33.333 0.00 0.00 0.00 1.75
2693 10988 9.551734 ACTTATATTTAGAAACGGGGTGATTAC 57.448 33.333 0.00 0.00 0.00 1.89
2694 10989 9.550406 CTTATATTTAGAAACGGGGTGATTACA 57.450 33.333 0.00 0.00 0.00 2.41
2696 10991 6.937436 ATTTAGAAACGGGGTGATTACATC 57.063 37.500 0.00 0.00 0.00 3.06
2697 10992 5.687166 TTAGAAACGGGGTGATTACATCT 57.313 39.130 0.00 0.00 0.00 2.90
2698 10993 4.569719 AGAAACGGGGTGATTACATCTT 57.430 40.909 0.00 0.00 0.00 2.40
2699 10994 5.687166 AGAAACGGGGTGATTACATCTTA 57.313 39.130 0.00 0.00 0.00 2.10
2700 10995 6.057321 AGAAACGGGGTGATTACATCTTAA 57.943 37.500 0.00 0.00 0.00 1.85
2701 10996 6.478129 AGAAACGGGGTGATTACATCTTAAA 58.522 36.000 0.00 0.00 0.00 1.52
2702 10997 6.943718 AGAAACGGGGTGATTACATCTTAAAA 59.056 34.615 0.00 0.00 0.00 1.52
2703 10998 6.753107 AACGGGGTGATTACATCTTAAAAG 57.247 37.500 0.00 0.00 0.00 2.27
2704 10999 6.057321 ACGGGGTGATTACATCTTAAAAGA 57.943 37.500 0.00 0.00 39.78 2.52
2705 11000 6.113411 ACGGGGTGATTACATCTTAAAAGAG 58.887 40.000 0.00 0.00 38.66 2.85
2706 11001 6.070424 ACGGGGTGATTACATCTTAAAAGAGA 60.070 38.462 0.00 0.00 38.66 3.10
2707 11002 6.258068 CGGGGTGATTACATCTTAAAAGAGAC 59.742 42.308 0.00 0.00 38.66 3.36
2708 11003 7.339482 GGGGTGATTACATCTTAAAAGAGACT 58.661 38.462 0.00 0.00 38.66 3.24
2709 11004 7.829706 GGGGTGATTACATCTTAAAAGAGACTT 59.170 37.037 0.00 0.00 38.66 3.01
2710 11005 8.669243 GGGTGATTACATCTTAAAAGAGACTTG 58.331 37.037 0.00 0.00 38.66 3.16
2711 11006 9.220767 GGTGATTACATCTTAAAAGAGACTTGT 57.779 33.333 0.00 1.09 38.66 3.16
2757 11052 7.798486 ATATAATCGCTATCAACTCGTTGTC 57.202 36.000 9.38 0.00 41.16 3.18
2768 11063 6.139048 TCAACTCGTTGTCGATCCATTATA 57.861 37.500 9.38 0.00 45.21 0.98
2777 11072 4.688879 TGTCGATCCATTATAATCAACGCC 59.311 41.667 0.00 0.00 0.00 5.68
2778 11073 4.688879 GTCGATCCATTATAATCAACGCCA 59.311 41.667 0.00 0.00 0.00 5.69
2806 11101 2.583024 TTCACCATTGCTCATCACCA 57.417 45.000 0.00 0.00 0.00 4.17
2816 11111 1.247567 CTCATCACCACCAACCAACC 58.752 55.000 0.00 0.00 0.00 3.77
2829 11124 0.178929 ACCAACCGGCCCCATTAAAA 60.179 50.000 0.00 0.00 34.57 1.52
2844 11139 5.851177 CCCATTAAAATCATTAAGCTACGCG 59.149 40.000 3.53 3.53 0.00 6.01
2850 11145 3.497297 TCATTAAGCTACGCGTGAAGA 57.503 42.857 24.59 0.00 0.00 2.87
2868 11163 2.438434 GCGGCCAACCAGCTATGT 60.438 61.111 2.24 0.00 34.11 2.29
2872 11167 0.322456 GGCCAACCAGCTATGTCACA 60.322 55.000 0.00 0.00 35.26 3.58
2875 11170 2.715046 CCAACCAGCTATGTCACATGT 58.285 47.619 0.00 0.00 0.00 3.21
2891 11186 2.980233 GTCGCAAGCTGGTTGGCT 60.980 61.111 19.87 0.00 45.30 4.75
2897 11192 0.537143 CAAGCTGGTTGGCTGTGGTA 60.537 55.000 11.59 0.00 42.24 3.25
2968 15169 2.193127 TCTTTTTAGATGGAGGCGGGA 58.807 47.619 0.00 0.00 0.00 5.14
2970 15171 3.202151 TCTTTTTAGATGGAGGCGGGAAT 59.798 43.478 0.00 0.00 0.00 3.01
2973 15174 1.633774 TAGATGGAGGCGGGAATCTC 58.366 55.000 0.00 0.00 31.90 2.75
2978 15179 1.144936 GAGGCGGGAATCTCTGGTG 59.855 63.158 0.00 0.00 0.00 4.17
2979 15180 1.613630 AGGCGGGAATCTCTGGTGT 60.614 57.895 0.00 0.00 0.00 4.16
3017 15218 2.246841 TGCAAAGTGGCACTCGATG 58.753 52.632 22.31 19.85 39.25 3.84
3018 15219 0.250252 TGCAAAGTGGCACTCGATGA 60.250 50.000 22.31 8.02 39.25 2.92
3021 15222 2.030946 GCAAAGTGGCACTCGATGATAC 59.969 50.000 22.31 4.79 0.00 2.24
3022 15223 3.261580 CAAAGTGGCACTCGATGATACA 58.738 45.455 22.31 0.00 0.00 2.29
3028 15229 1.193203 GCACTCGATGATACATTGCGG 59.807 52.381 0.00 0.00 0.00 5.69
3030 15231 2.219445 CACTCGATGATACATTGCGGTG 59.781 50.000 0.00 0.00 0.00 4.94
3034 15235 4.877282 TCGATGATACATTGCGGTGATAA 58.123 39.130 0.00 0.00 0.00 1.75
3035 15236 5.293560 TCGATGATACATTGCGGTGATAAA 58.706 37.500 0.00 0.00 0.00 1.40
3036 15237 5.755861 TCGATGATACATTGCGGTGATAAAA 59.244 36.000 0.00 0.00 0.00 1.52
3037 15238 6.258947 TCGATGATACATTGCGGTGATAAAAA 59.741 34.615 0.00 0.00 0.00 1.94
3103 15306 3.515901 AGATGTTTTTCTAGACCGAGGCT 59.484 43.478 0.00 0.00 0.00 4.58
3104 15307 4.710375 AGATGTTTTTCTAGACCGAGGCTA 59.290 41.667 0.00 0.00 0.00 3.93
3105 15308 5.364157 AGATGTTTTTCTAGACCGAGGCTAT 59.636 40.000 0.00 0.00 0.00 2.97
3106 15309 4.755411 TGTTTTTCTAGACCGAGGCTATG 58.245 43.478 0.00 0.00 0.00 2.23
3107 15310 4.222145 TGTTTTTCTAGACCGAGGCTATGT 59.778 41.667 0.00 0.00 0.00 2.29
3108 15311 5.419788 TGTTTTTCTAGACCGAGGCTATGTA 59.580 40.000 0.00 0.00 0.00 2.29
3109 15312 6.097839 TGTTTTTCTAGACCGAGGCTATGTAT 59.902 38.462 0.00 0.00 0.00 2.29
3110 15313 7.286087 TGTTTTTCTAGACCGAGGCTATGTATA 59.714 37.037 0.00 0.00 0.00 1.47
3111 15314 8.305317 GTTTTTCTAGACCGAGGCTATGTATAT 58.695 37.037 0.00 0.00 0.00 0.86
3112 15315 8.418597 TTTTCTAGACCGAGGCTATGTATATT 57.581 34.615 0.00 0.00 0.00 1.28
3113 15316 8.418597 TTTCTAGACCGAGGCTATGTATATTT 57.581 34.615 0.00 0.00 0.00 1.40
3114 15317 8.418597 TTCTAGACCGAGGCTATGTATATTTT 57.581 34.615 0.00 0.00 0.00 1.82
3115 15318 9.524496 TTCTAGACCGAGGCTATGTATATTTTA 57.476 33.333 0.00 0.00 0.00 1.52
3116 15319 9.524496 TCTAGACCGAGGCTATGTATATTTTAA 57.476 33.333 0.00 0.00 0.00 1.52
3119 15322 9.436957 AGACCGAGGCTATGTATATTTTAAATG 57.563 33.333 0.00 0.00 0.00 2.32
3120 15323 9.431887 GACCGAGGCTATGTATATTTTAAATGA 57.568 33.333 0.00 0.00 0.00 2.57
3121 15324 9.787435 ACCGAGGCTATGTATATTTTAAATGAA 57.213 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.036083 CACTTATACTTCAACATCCGGTGAAG 59.964 42.308 23.80 23.80 38.98 3.02
1 2 5.872617 CACTTATACTTCAACATCCGGTGAA 59.127 40.000 0.00 2.85 0.00 3.18
5 6 4.570772 CCACACTTATACTTCAACATCCGG 59.429 45.833 0.00 0.00 0.00 5.14
40 41 7.167535 TCATACAAAACCTGATGATGACAGAA 58.832 34.615 0.00 0.00 37.54 3.02
44 45 8.461222 TCATTTCATACAAAACCTGATGATGAC 58.539 33.333 0.00 0.00 0.00 3.06
48 49 9.022884 TCAATCATTTCATACAAAACCTGATGA 57.977 29.630 0.00 0.00 0.00 2.92
74 75 6.204688 CCGGTAACATGTAGAATTGTATGCAT 59.795 38.462 3.79 3.79 0.00 3.96
83 84 2.769663 TGGCTCCGGTAACATGTAGAAT 59.230 45.455 0.00 0.00 0.00 2.40
187 188 8.927675 AAGTTGGGTTACACACTTATATTTCA 57.072 30.769 0.00 0.00 32.48 2.69
216 526 3.185797 GCACGAGTCGGTTCAAGTAAAAT 59.814 43.478 18.30 0.00 0.00 1.82
221 531 0.033504 ATGCACGAGTCGGTTCAAGT 59.966 50.000 18.30 0.00 0.00 3.16
222 532 0.439985 CATGCACGAGTCGGTTCAAG 59.560 55.000 18.30 4.80 0.00 3.02
227 537 1.361668 GAATGCATGCACGAGTCGGT 61.362 55.000 25.37 0.38 0.00 4.69
291 601 4.699522 GCGCCCGAACCAACTCCT 62.700 66.667 0.00 0.00 0.00 3.69
309 619 2.692741 CCCAAGGGAGGAGGGGAC 60.693 72.222 0.00 0.00 43.57 4.46
334 644 4.489771 GGGAGGGACGCATGTGGG 62.490 72.222 11.65 0.00 0.00 4.61
337 647 1.201429 AAAGAGGGAGGGACGCATGT 61.201 55.000 0.00 0.00 0.00 3.21
340 650 2.592993 CCAAAGAGGGAGGGACGCA 61.593 63.158 0.00 0.00 0.00 5.24
363 673 8.529476 GGTTGAGACTACTAAAAGGTCAATAGA 58.471 37.037 0.00 0.00 30.70 1.98
375 685 2.098607 CGGCATCGGTTGAGACTACTAA 59.901 50.000 0.00 0.00 0.00 2.24
377 687 0.456221 CGGCATCGGTTGAGACTACT 59.544 55.000 0.00 0.00 0.00 2.57
381 691 0.529773 TATGCGGCATCGGTTGAGAC 60.530 55.000 20.34 0.00 36.79 3.36
459 771 9.237187 TGAGTTAATGCAGTATGTTATTTTGGA 57.763 29.630 0.00 0.00 39.31 3.53
467 779 9.410556 GATTTGTTTGAGTTAATGCAGTATGTT 57.589 29.630 0.00 0.00 39.31 2.71
472 784 8.891671 ATTTGATTTGTTTGAGTTAATGCAGT 57.108 26.923 0.00 0.00 0.00 4.40
518 830 3.190744 GGGAAGGAAAGTTTCGATTCACC 59.809 47.826 23.09 19.14 31.45 4.02
519 831 3.190744 GGGGAAGGAAAGTTTCGATTCAC 59.809 47.826 23.09 21.16 32.05 3.18
521 833 2.753452 GGGGGAAGGAAAGTTTCGATTC 59.247 50.000 17.57 17.57 0.00 2.52
600 913 5.754782 TGAGTATGTGTAGGGAATGCAAAT 58.245 37.500 0.00 0.00 0.00 2.32
719 1033 1.785041 AACTGCTCGTGCGTTGCAAT 61.785 50.000 0.59 4.30 41.47 3.56
809 1125 7.712264 TCTTATTTTTGAACCAATGCACTTG 57.288 32.000 0.00 0.00 34.42 3.16
835 1151 9.739276 CTTATATATGGAAAGTAATTGGAGGCA 57.261 33.333 0.00 0.00 0.00 4.75
1108 3941 2.870175 CATAGGTGGGGTTTTGTGACA 58.130 47.619 0.00 0.00 0.00 3.58
1556 4470 1.004394 CCAGGAGTACAGGGGTTTTCC 59.996 57.143 0.00 0.00 39.75 3.13
1576 5823 2.412089 AGTTAGATCGCGAGCAAACAAC 59.588 45.455 27.74 21.56 0.00 3.32
1596 5847 6.418819 TCCACGAACTTTTAAGACGAAACTAG 59.581 38.462 15.63 0.00 35.13 2.57
1604 5855 3.072211 CCCCTCCACGAACTTTTAAGAC 58.928 50.000 0.00 0.00 0.00 3.01
1760 6014 3.400054 AACAGGTAGGCGGAGGGC 61.400 66.667 0.00 0.00 42.51 5.19
1761 6015 2.584608 CAACAGGTAGGCGGAGGG 59.415 66.667 0.00 0.00 0.00 4.30
2007 9905 1.671054 CCACGGGGTAGTTGTGCAG 60.671 63.158 0.00 0.00 32.32 4.41
2151 10091 2.463752 AGGTAAACGGATAGGTCAGCA 58.536 47.619 0.00 0.00 0.00 4.41
2157 10097 4.986659 CGGTATCAAAGGTAAACGGATAGG 59.013 45.833 0.00 0.00 0.00 2.57
2202 10153 6.974932 AATTACAGCAGTAGATGTGACAAG 57.025 37.500 0.00 0.00 45.37 3.16
2236 10190 1.350310 ACAAGGACCGGGACAAACCT 61.350 55.000 6.32 1.42 38.98 3.50
2248 10202 4.698575 AGAAGTCTCTGAAACACAAGGAC 58.301 43.478 0.00 0.00 33.52 3.85
2251 10205 5.176590 GCAGTAGAAGTCTCTGAAACACAAG 59.823 44.000 10.22 0.00 32.70 3.16
2254 10208 4.446051 GTGCAGTAGAAGTCTCTGAAACAC 59.554 45.833 10.22 6.61 32.70 3.32
2283 10237 9.112725 TGTTGAAACATCATCTGTCTTATATGG 57.887 33.333 0.00 0.00 36.98 2.74
2381 10339 1.133598 CGCCACGATTAGTACCTGTCA 59.866 52.381 0.00 0.00 0.00 3.58
2387 10345 1.567504 ACATGCGCCACGATTAGTAC 58.432 50.000 4.18 0.00 0.00 2.73
2400 10358 0.442310 CCGGTCACAAGTTACATGCG 59.558 55.000 0.00 0.00 0.00 4.73
2451 10746 9.404848 TCCGTATTAGAATCTCTCAAGAACTTA 57.595 33.333 0.00 0.00 34.49 2.24
2454 10749 7.708998 AGTCCGTATTAGAATCTCTCAAGAAC 58.291 38.462 0.00 0.00 34.49 3.01
2455 10750 7.883391 AGTCCGTATTAGAATCTCTCAAGAA 57.117 36.000 0.00 0.00 34.49 2.52
2456 10751 7.991460 TGTAGTCCGTATTAGAATCTCTCAAGA 59.009 37.037 0.00 0.00 35.54 3.02
2457 10752 8.155821 TGTAGTCCGTATTAGAATCTCTCAAG 57.844 38.462 0.00 0.00 0.00 3.02
2459 10754 9.217278 GTATGTAGTCCGTATTAGAATCTCTCA 57.783 37.037 0.00 0.00 0.00 3.27
2460 10755 8.382130 CGTATGTAGTCCGTATTAGAATCTCTC 58.618 40.741 0.00 0.00 0.00 3.20
2461 10756 7.333921 CCGTATGTAGTCCGTATTAGAATCTCT 59.666 40.741 0.00 0.00 0.00 3.10
2462 10757 7.332926 TCCGTATGTAGTCCGTATTAGAATCTC 59.667 40.741 0.00 0.00 0.00 2.75
2463 10758 7.164122 TCCGTATGTAGTCCGTATTAGAATCT 58.836 38.462 0.00 0.00 0.00 2.40
2464 10759 7.118971 ACTCCGTATGTAGTCCGTATTAGAATC 59.881 40.741 0.00 0.00 0.00 2.52
2466 10761 6.291377 ACTCCGTATGTAGTCCGTATTAGAA 58.709 40.000 0.00 0.00 0.00 2.10
2467 10762 5.858381 ACTCCGTATGTAGTCCGTATTAGA 58.142 41.667 0.00 0.00 0.00 2.10
2468 10763 7.658179 TTACTCCGTATGTAGTCCGTATTAG 57.342 40.000 0.00 0.00 0.00 1.73
2471 10766 6.942532 TTTTACTCCGTATGTAGTCCGTAT 57.057 37.500 0.00 0.00 0.00 3.06
2474 10769 5.824429 TCATTTTACTCCGTATGTAGTCCG 58.176 41.667 0.00 0.00 0.00 4.79
2475 10770 6.696148 CACTCATTTTACTCCGTATGTAGTCC 59.304 42.308 0.00 0.00 0.00 3.85
2476 10771 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2477 10772 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2478 10773 8.755941 CATTCACTCATTTTACTCCGTATGTAG 58.244 37.037 0.00 0.00 0.00 2.74
2480 10775 7.103641 ACATTCACTCATTTTACTCCGTATGT 58.896 34.615 0.00 0.00 0.00 2.29
2481 10776 7.539712 ACATTCACTCATTTTACTCCGTATG 57.460 36.000 0.00 0.00 0.00 2.39
2483 10778 7.543172 GTGTACATTCACTCATTTTACTCCGTA 59.457 37.037 0.00 0.00 35.68 4.02
2484 10779 6.367969 GTGTACATTCACTCATTTTACTCCGT 59.632 38.462 0.00 0.00 35.68 4.69
2486 10781 7.907214 AGTGTACATTCACTCATTTTACTCC 57.093 36.000 0.00 0.00 44.07 3.85
2531 10826 9.495382 ACTTATATTTAAAGACAGAGAGGGAGT 57.505 33.333 0.00 0.00 0.00 3.85
2566 10861 9.751542 CGGATGTAGTCTTTATAGTGAAATCTT 57.248 33.333 0.00 0.00 0.00 2.40
2567 10862 8.361139 CCGGATGTAGTCTTTATAGTGAAATCT 58.639 37.037 0.00 0.00 0.00 2.40
2568 10863 8.358148 TCCGGATGTAGTCTTTATAGTGAAATC 58.642 37.037 0.00 0.00 0.00 2.17
2569 10864 8.246430 TCCGGATGTAGTCTTTATAGTGAAAT 57.754 34.615 0.00 0.00 0.00 2.17
2570 10865 7.649533 TCCGGATGTAGTCTTTATAGTGAAA 57.350 36.000 0.00 0.00 0.00 2.69
2571 10866 7.658261 CATCCGGATGTAGTCTTTATAGTGAA 58.342 38.462 32.39 0.00 34.23 3.18
2572 10867 7.215719 CATCCGGATGTAGTCTTTATAGTGA 57.784 40.000 32.39 0.00 34.23 3.41
2587 10882 6.531503 AAGGTGTCTATATACATCCGGATG 57.468 41.667 37.23 37.23 44.15 3.51
2588 10883 7.554959 AAAAGGTGTCTATATACATCCGGAT 57.445 36.000 12.38 12.38 30.33 4.18
2589 10884 6.989155 AAAAGGTGTCTATATACATCCGGA 57.011 37.500 6.61 6.61 30.33 5.14
2590 10885 8.118976 TCTAAAAGGTGTCTATATACATCCGG 57.881 38.462 0.00 0.00 30.33 5.14
2591 10886 8.794553 ACTCTAAAAGGTGTCTATATACATCCG 58.205 37.037 0.00 0.00 30.33 4.18
2601 10896 9.871238 GTGAAATCATACTCTAAAAGGTGTCTA 57.129 33.333 0.00 0.00 0.00 2.59
2602 10897 8.598041 AGTGAAATCATACTCTAAAAGGTGTCT 58.402 33.333 0.00 0.00 0.00 3.41
2603 10898 8.779354 AGTGAAATCATACTCTAAAAGGTGTC 57.221 34.615 0.00 0.00 0.00 3.67
2632 10927 9.944376 AGATTTCACAATAGACTACTAAGCAAA 57.056 29.630 0.00 0.00 32.04 3.68
2633 10928 9.587772 GAGATTTCACAATAGACTACTAAGCAA 57.412 33.333 0.00 0.00 32.04 3.91
2634 10929 8.972127 AGAGATTTCACAATAGACTACTAAGCA 58.028 33.333 0.00 0.00 32.04 3.91
2642 10937 9.660180 GTCCTTTTAGAGATTTCACAATAGACT 57.340 33.333 0.00 0.00 0.00 3.24
2643 10938 9.660180 AGTCCTTTTAGAGATTTCACAATAGAC 57.340 33.333 0.00 0.00 0.00 2.59
2660 10955 9.617523 CCCCGTTTCTAAATATAAGTCCTTTTA 57.382 33.333 0.00 0.00 0.00 1.52
2661 10956 8.111545 ACCCCGTTTCTAAATATAAGTCCTTTT 58.888 33.333 0.00 0.00 0.00 2.27
2662 10957 7.555195 CACCCCGTTTCTAAATATAAGTCCTTT 59.445 37.037 0.00 0.00 0.00 3.11
2663 10958 7.052248 CACCCCGTTTCTAAATATAAGTCCTT 58.948 38.462 0.00 0.00 0.00 3.36
2664 10959 6.384886 TCACCCCGTTTCTAAATATAAGTCCT 59.615 38.462 0.00 0.00 0.00 3.85
2665 10960 6.585416 TCACCCCGTTTCTAAATATAAGTCC 58.415 40.000 0.00 0.00 0.00 3.85
2666 10961 8.672823 AATCACCCCGTTTCTAAATATAAGTC 57.327 34.615 0.00 0.00 0.00 3.01
2667 10962 9.551734 GTAATCACCCCGTTTCTAAATATAAGT 57.448 33.333 0.00 0.00 0.00 2.24
2668 10963 9.550406 TGTAATCACCCCGTTTCTAAATATAAG 57.450 33.333 0.00 0.00 0.00 1.73
2670 10965 9.715121 GATGTAATCACCCCGTTTCTAAATATA 57.285 33.333 0.00 0.00 44.70 0.86
2671 10966 8.617290 GATGTAATCACCCCGTTTCTAAATAT 57.383 34.615 0.00 0.00 44.70 1.28
2699 10994 9.454859 CTCCATTCCTAAATACAAGTCTCTTTT 57.545 33.333 0.00 0.00 0.00 2.27
2700 10995 8.049721 CCTCCATTCCTAAATACAAGTCTCTTT 58.950 37.037 0.00 0.00 0.00 2.52
2701 10996 7.366011 CCCTCCATTCCTAAATACAAGTCTCTT 60.366 40.741 0.00 0.00 0.00 2.85
2702 10997 6.100424 CCCTCCATTCCTAAATACAAGTCTCT 59.900 42.308 0.00 0.00 0.00 3.10
2703 10998 6.099845 TCCCTCCATTCCTAAATACAAGTCTC 59.900 42.308 0.00 0.00 0.00 3.36
2704 10999 5.970640 TCCCTCCATTCCTAAATACAAGTCT 59.029 40.000 0.00 0.00 0.00 3.24
2705 11000 6.126739 ACTCCCTCCATTCCTAAATACAAGTC 60.127 42.308 0.00 0.00 0.00 3.01
2706 11001 5.731678 ACTCCCTCCATTCCTAAATACAAGT 59.268 40.000 0.00 0.00 0.00 3.16
2707 11002 6.253946 ACTCCCTCCATTCCTAAATACAAG 57.746 41.667 0.00 0.00 0.00 3.16
2708 11003 7.947782 ATACTCCCTCCATTCCTAAATACAA 57.052 36.000 0.00 0.00 0.00 2.41
2715 11010 9.809395 CGATTATATATACTCCCTCCATTCCTA 57.191 37.037 4.91 0.00 0.00 2.94
2716 11011 7.233757 GCGATTATATATACTCCCTCCATTCCT 59.766 40.741 4.91 0.00 0.00 3.36
2717 11012 7.233757 AGCGATTATATATACTCCCTCCATTCC 59.766 40.741 4.91 0.00 0.00 3.01
2718 11013 8.184304 AGCGATTATATATACTCCCTCCATTC 57.816 38.462 4.91 0.00 0.00 2.67
2719 11014 9.830186 ATAGCGATTATATATACTCCCTCCATT 57.170 33.333 4.91 0.00 0.00 3.16
2720 11015 9.469097 GATAGCGATTATATATACTCCCTCCAT 57.531 37.037 4.91 0.00 0.00 3.41
2721 11016 8.445588 TGATAGCGATTATATATACTCCCTCCA 58.554 37.037 4.91 2.09 0.00 3.86
2722 11017 8.865420 TGATAGCGATTATATATACTCCCTCC 57.135 38.462 4.91 0.12 0.00 4.30
2754 11049 4.688879 GGCGTTGATTATAATGGATCGACA 59.311 41.667 1.78 0.00 36.77 4.35
2757 11052 5.801350 ATGGCGTTGATTATAATGGATCG 57.199 39.130 1.78 4.05 0.00 3.69
2768 11063 4.036734 GTGAATCCACATATGGCGTTGATT 59.963 41.667 7.80 7.28 46.80 2.57
2790 11085 0.405198 TGGTGGTGATGAGCAATGGT 59.595 50.000 0.00 0.00 0.00 3.55
2799 11094 1.523154 CCGGTTGGTTGGTGGTGATG 61.523 60.000 0.00 0.00 0.00 3.07
2816 11111 4.039124 AGCTTAATGATTTTAATGGGGCCG 59.961 41.667 0.00 0.00 0.00 6.13
2844 11139 2.281484 TGGTTGGCCGCTCTTCAC 60.281 61.111 0.00 0.00 37.67 3.18
2850 11145 2.124570 CATAGCTGGTTGGCCGCT 60.125 61.111 7.28 7.28 43.35 5.52
2868 11163 0.534877 AACCAGCTTGCGACATGTGA 60.535 50.000 1.15 0.00 0.00 3.58
2872 11167 2.629656 GCCAACCAGCTTGCGACAT 61.630 57.895 0.00 0.00 0.00 3.06
2875 11170 2.979676 CAGCCAACCAGCTTGCGA 60.980 61.111 0.00 0.00 42.61 5.10
3081 15284 3.515901 AGCCTCGGTCTAGAAAAACATCT 59.484 43.478 0.00 0.00 0.00 2.90
3089 15292 8.418597 AAAATATACATAGCCTCGGTCTAGAA 57.581 34.615 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.