Multiple sequence alignment - TraesCS3A01G029200

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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 TraesCS3A01G029200 chr3A 100.000 7086 0 0 1 7086 15461390 15468475 0.000000e+00 13086.0
1 TraesCS3A01G029200 chr3A 85.672 1689 230 8 3266 4947 12163193 12164876 0.000000e+00 1768.0
2 TraesCS3A01G029200 chr3A 87.860 486 50 2 882 1367 12160732 12161208 4.800000e-156 562.0
3 TraesCS3A01G029200 chr3B 96.783 1772 55 1 3178 4949 27828401 27830170 0.000000e+00 2955.0
4 TraesCS3A01G029200 chr3B 96.727 1772 56 1 3178 4949 12088387 12086618 0.000000e+00 2950.0
5 TraesCS3A01G029200 chr3B 99.906 1064 1 0 4947 6010 172057050 172055987 0.000000e+00 1960.0
6 TraesCS3A01G029200 chr3B 93.929 1120 51 9 1819 2931 27831622 27832731 0.000000e+00 1676.0
7 TraesCS3A01G029200 chr3B 91.890 1159 66 15 1783 2934 12089850 12088713 0.000000e+00 1594.0
8 TraesCS3A01G029200 chr3B 91.782 1083 67 5 730 1801 27826072 27827143 0.000000e+00 1487.0
9 TraesCS3A01G029200 chr3B 91.705 1085 68 5 730 1802 12090943 12089869 0.000000e+00 1485.0
10 TraesCS3A01G029200 chr3B 92.903 944 49 7 1783 2720 27827168 27828099 0.000000e+00 1356.0
11 TraesCS3A01G029200 chr3B 95.052 768 34 3 3577 4344 27851599 27852362 0.000000e+00 1205.0
12 TraesCS3A01G029200 chr3B 94.037 654 30 3 1130 1774 27822539 27823192 0.000000e+00 983.0
13 TraesCS3A01G029200 chr3B 92.237 657 23 8 2931 3578 27832762 27833399 0.000000e+00 905.0
14 TraesCS3A01G029200 chr3B 90.694 591 44 10 6178 6764 27852358 27852941 0.000000e+00 776.0
15 TraesCS3A01G029200 chr3B 87.928 497 39 12 1 491 27825439 27825920 3.710000e-157 566.0
16 TraesCS3A01G029200 chr3B 96.096 333 13 0 6011 6343 27830163 27830495 1.740000e-150 544.0
17 TraesCS3A01G029200 chr3B 95.796 333 14 0 6011 6343 12086625 12086293 8.090000e-149 538.0
18 TraesCS3A01G029200 chr3B 93.548 248 15 1 2931 3177 12088680 12088433 1.120000e-97 368.0
19 TraesCS3A01G029200 chr3B 94.167 240 14 0 6748 6987 27855889 27856128 4.040000e-97 366.0
20 TraesCS3A01G029200 chr3B 94.318 176 8 2 6339 6512 12086013 12085838 1.170000e-67 268.0
21 TraesCS3A01G029200 chr3B 93.182 176 9 3 6339 6512 27830775 27830949 9.120000e-64 255.0
22 TraesCS3A01G029200 chr3B 93.525 139 7 2 601 737 586619709 586619847 9.320000e-49 206.0
23 TraesCS3A01G029200 chr3B 90.598 117 9 2 6972 7086 27856139 27856255 3.420000e-33 154.0
24 TraesCS3A01G029200 chr3B 85.246 122 17 1 6966 7086 804717878 804717999 2.680000e-24 124.0
25 TraesCS3A01G029200 chr3D 94.808 1772 89 1 3178 4949 5734966 5733198 0.000000e+00 2760.0
26 TraesCS3A01G029200 chr3D 85.501 1745 246 5 3213 4951 5792559 5794302 0.000000e+00 1814.0
27 TraesCS3A01G029200 chr3D 94.128 1090 49 5 726 1802 5737472 5736385 0.000000e+00 1644.0
28 TraesCS3A01G029200 chr3D 93.514 1033 51 10 1911 2934 5736316 5735291 0.000000e+00 1522.0
29 TraesCS3A01G029200 chr3D 87.363 546 54 6 859 1404 5790488 5791018 4.700000e-171 612.0
30 TraesCS3A01G029200 chr3D 92.435 423 28 4 6011 6429 5733205 5732783 1.020000e-167 601.0
31 TraesCS3A01G029200 chr3D 95.161 248 11 1 2931 3177 5735258 5735011 2.400000e-104 390.0
32 TraesCS3A01G029200 chr3D 86.944 337 35 8 6513 6845 5732777 5732446 3.120000e-98 370.0
33 TraesCS3A01G029200 chr3D 87.202 336 19 11 1 322 5750130 5749805 1.880000e-95 361.0
34 TraesCS3A01G029200 chr3D 84.887 311 10 10 321 597 5737779 5737472 5.410000e-71 279.0
35 TraesCS3A01G029200 chr3D 85.000 80 9 3 1783 1862 5736382 5736306 2.120000e-10 78.7
36 TraesCS3A01G029200 chr4B 100.000 1063 0 0 4950 6012 636683790 636684852 0.000000e+00 1964.0
37 TraesCS3A01G029200 chr2B 100.000 1062 0 0 4950 6011 630736034 630734973 0.000000e+00 1962.0
38 TraesCS3A01G029200 chr2B 93.688 301 18 1 5564 5863 74359078 74359378 3.900000e-122 449.0
39 TraesCS3A01G029200 chr2B 93.525 139 7 2 601 737 598742842 598742704 9.320000e-49 206.0
40 TraesCS3A01G029200 chr2B 85.833 120 15 2 6967 7085 542903484 542903366 7.460000e-25 126.0
41 TraesCS3A01G029200 chr5B 99.720 1071 1 2 4950 6020 418917811 418916743 0.000000e+00 1960.0
42 TraesCS3A01G029200 chr4A 100.000 1061 0 0 4949 6009 705546097 705545037 0.000000e+00 1960.0
43 TraesCS3A01G029200 chr7A 99.906 1062 1 0 4950 6011 122331661 122332722 0.000000e+00 1956.0
44 TraesCS3A01G029200 chr7A 93.525 139 7 2 601 737 454798565 454798703 9.320000e-49 206.0
45 TraesCS3A01G029200 chrUn 85.039 1778 243 14 3191 4951 28821595 28819824 0.000000e+00 1788.0
46 TraesCS3A01G029200 chrUn 92.806 139 8 2 601 737 254470450 254470588 4.330000e-47 200.0
47 TraesCS3A01G029200 chr1B 82.940 1442 233 10 3516 4951 590523541 590522107 0.000000e+00 1288.0
48 TraesCS3A01G029200 chr1B 82.322 1137 196 5 3818 4951 590647128 590645994 0.000000e+00 981.0
49 TraesCS3A01G029200 chr1B 82.146 1137 198 5 3818 4951 590666890 590665756 0.000000e+00 970.0
50 TraesCS3A01G029200 chr1B 82.704 636 96 7 3191 3813 590649886 590649252 2.890000e-153 553.0
51 TraesCS3A01G029200 chr1D 95.215 606 17 1 4946 5551 387192885 387192292 0.000000e+00 948.0
52 TraesCS3A01G029200 chr1D 93.525 139 7 2 601 737 320898499 320898361 9.320000e-49 206.0
53 TraesCS3A01G029200 chr1D 93.525 139 7 2 601 737 328991779 328991917 9.320000e-49 206.0
54 TraesCS3A01G029200 chr4D 92.904 606 31 5 4950 5551 418533812 418534409 0.000000e+00 870.0
55 TraesCS3A01G029200 chr4D 92.257 452 19 6 5564 6014 418534500 418534936 1.680000e-175 627.0
56 TraesCS3A01G029200 chr4D 93.525 139 7 2 601 737 279495459 279495321 9.320000e-49 206.0
57 TraesCS3A01G029200 chr7B 92.574 606 33 6 4948 5551 92126226 92125631 0.000000e+00 859.0
58 TraesCS3A01G029200 chr7B 94.137 307 18 0 5564 5870 92125540 92125234 1.080000e-127 468.0
59 TraesCS3A01G029200 chr7B 91.925 161 9 1 5855 6011 92125217 92125057 9.250000e-54 222.0
60 TraesCS3A01G029200 chr2D 76.579 1140 245 19 3377 4505 481962067 481963195 2.190000e-169 606.0
61 TraesCS3A01G029200 chr2D 86.567 67 9 0 6014 6080 156594511 156594577 2.740000e-09 75.0
62 TraesCS3A01G029200 chr2A 89.800 451 36 5 5564 6013 355516923 355517364 2.870000e-158 569.0
63 TraesCS3A01G029200 chr2A 88.889 63 7 0 6014 6076 166630150 166630212 2.120000e-10 78.7
64 TraesCS3A01G029200 chr7D 91.223 319 26 1 16 332 42153300 42152982 3.930000e-117 433.0
65 TraesCS3A01G029200 chr6D 85.470 351 51 0 1018 1368 300330436 300330086 4.040000e-97 366.0
66 TraesCS3A01G029200 chr6D 88.333 120 12 2 6967 7085 24591036 24591154 7.410000e-30 143.0
67 TraesCS3A01G029200 chr6D 93.151 73 5 0 6011 6083 300327361 300327289 2.700000e-19 108.0
68 TraesCS3A01G029200 chr6B 85.470 351 51 0 1018 1368 465151633 465151283 4.040000e-97 366.0
69 TraesCS3A01G029200 chr6B 90.000 120 10 2 6967 7085 31395878 31395760 3.420000e-33 154.0
70 TraesCS3A01G029200 chr6B 85.714 119 17 0 6967 7085 259713383 259713501 7.460000e-25 126.0
71 TraesCS3A01G029200 chr6B 93.151 73 5 0 6011 6083 465148499 465148427 2.700000e-19 108.0
72 TraesCS3A01G029200 chr6A 83.947 380 59 2 1000 1377 417442716 417443095 5.220000e-96 363.0
73 TraesCS3A01G029200 chr6A 92.857 140 8 2 600 737 551488833 551488694 1.210000e-47 202.0
74 TraesCS3A01G029200 chr6A 88.136 118 12 2 6967 7083 565385993 565385877 9.580000e-29 139.0
75 TraesCS3A01G029200 chr6A 94.286 70 4 0 6011 6080 417445835 417445904 2.700000e-19 108.0
76 TraesCS3A01G029200 chr6A 90.164 61 6 0 6016 6076 416658553 416658613 5.890000e-11 80.5
77 TraesCS3A01G029200 chr1A 93.525 139 7 2 601 737 401930117 401929979 9.320000e-49 206.0
78 TraesCS3A01G029200 chr5D 89.167 120 11 2 6967 7085 438599895 438599777 1.590000e-31 148.0
79 TraesCS3A01G029200 chr5A 84.496 129 15 4 6961 7086 144703916 144703790 9.650000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G029200 chr3A 15461390 15468475 7085 False 13086.000000 13086 100.000000 1 7086 1 chr3A.!!$F1 7085
1 TraesCS3A01G029200 chr3A 12160732 12164876 4144 False 1165.000000 1768 86.766000 882 4947 2 chr3A.!!$F2 4065
2 TraesCS3A01G029200 chr3B 172055987 172057050 1063 True 1960.000000 1960 99.906000 4947 6010 1 chr3B.!!$R1 1063
3 TraesCS3A01G029200 chr3B 12085838 12090943 5105 True 1200.500000 2950 93.997333 730 6512 6 chr3B.!!$R2 5782
4 TraesCS3A01G029200 chr3B 27822539 27833399 10860 False 1191.888889 2955 93.208556 1 6512 9 chr3B.!!$F3 6511
5 TraesCS3A01G029200 chr3B 27851599 27856255 4656 False 625.250000 1205 92.627750 3577 7086 4 chr3B.!!$F4 3509
6 TraesCS3A01G029200 chr3D 5790488 5794302 3814 False 1213.000000 1814 86.432000 859 4951 2 chr3D.!!$F1 4092
7 TraesCS3A01G029200 chr3D 5732446 5737779 5333 True 955.587500 2760 90.859625 321 6845 8 chr3D.!!$R2 6524
8 TraesCS3A01G029200 chr4B 636683790 636684852 1062 False 1964.000000 1964 100.000000 4950 6012 1 chr4B.!!$F1 1062
9 TraesCS3A01G029200 chr2B 630734973 630736034 1061 True 1962.000000 1962 100.000000 4950 6011 1 chr2B.!!$R3 1061
10 TraesCS3A01G029200 chr5B 418916743 418917811 1068 True 1960.000000 1960 99.720000 4950 6020 1 chr5B.!!$R1 1070
11 TraesCS3A01G029200 chr4A 705545037 705546097 1060 True 1960.000000 1960 100.000000 4949 6009 1 chr4A.!!$R1 1060
12 TraesCS3A01G029200 chr7A 122331661 122332722 1061 False 1956.000000 1956 99.906000 4950 6011 1 chr7A.!!$F1 1061
13 TraesCS3A01G029200 chrUn 28819824 28821595 1771 True 1788.000000 1788 85.039000 3191 4951 1 chrUn.!!$R1 1760
14 TraesCS3A01G029200 chr1B 590522107 590523541 1434 True 1288.000000 1288 82.940000 3516 4951 1 chr1B.!!$R1 1435
15 TraesCS3A01G029200 chr1B 590665756 590666890 1134 True 970.000000 970 82.146000 3818 4951 1 chr1B.!!$R2 1133
16 TraesCS3A01G029200 chr1B 590645994 590649886 3892 True 767.000000 981 82.513000 3191 4951 2 chr1B.!!$R3 1760
17 TraesCS3A01G029200 chr1D 387192292 387192885 593 True 948.000000 948 95.215000 4946 5551 1 chr1D.!!$R2 605
18 TraesCS3A01G029200 chr4D 418533812 418534936 1124 False 748.500000 870 92.580500 4950 6014 2 chr4D.!!$F1 1064
19 TraesCS3A01G029200 chr7B 92125057 92126226 1169 True 516.333333 859 92.878667 4948 6011 3 chr7B.!!$R1 1063
20 TraesCS3A01G029200 chr2D 481962067 481963195 1128 False 606.000000 606 76.579000 3377 4505 1 chr2D.!!$F2 1128
21 TraesCS3A01G029200 chr6D 300327289 300330436 3147 True 237.000000 366 89.310500 1018 6083 2 chr6D.!!$R1 5065
22 TraesCS3A01G029200 chr6B 465148427 465151633 3206 True 237.000000 366 89.310500 1018 6083 2 chr6B.!!$R2 5065
23 TraesCS3A01G029200 chr6A 417442716 417445904 3188 False 235.500000 363 89.116500 1000 6080 2 chr6A.!!$F2 5080

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
49 2946 0.029300 CACGGTGCCAAACTTCTGTG 59.971 55.000 0.00 0.00 0.00 3.66 F
959 3902 0.251341 GCTGTGTTCATCACCCCCTT 60.251 55.000 0.00 0.00 45.61 3.95 F
1802 5923 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57 F
3408 8053 0.321564 TTCGCATCAACACCCTCCTG 60.322 55.000 0.00 0.00 0.00 3.86 F
3642 8287 2.750350 GCCGGGATAGATGGTGGG 59.250 66.667 2.18 0.00 0.00 4.61 F
4575 11501 0.248825 CCAGCGTCGAGGAGATTCTG 60.249 60.000 9.75 6.05 33.64 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 5565 0.037232 ACCTCTTGCGCTCCACTAAC 60.037 55.000 9.73 0.0 0.00 2.34 R
2618 6846 1.051008 ATGTGCATCGGGAGCAGATA 58.949 50.000 5.71 0.0 43.19 1.98 R
3471 8116 0.979187 GGGGAATCCTCGGGTGTACA 60.979 60.000 0.00 0.0 0.00 2.90 R
4311 11076 1.427368 ACTGGGTTGGCAAGGTATTGA 59.573 47.619 0.00 0.0 38.83 2.57 R
4590 11516 2.354188 CTGAACACGTCCACGCGA 60.354 61.111 15.93 0.0 44.43 5.87 R
6434 13788 0.251354 ACCAGAAGCGCACATCTCAT 59.749 50.000 11.47 0.0 0.00 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
27 2924 8.958060 TTAGAGCTCTATATATGTTCACCCTT 57.042 34.615 23.81 0.00 0.00 3.95
28 2925 7.238486 AGAGCTCTATATATGTTCACCCTTG 57.762 40.000 16.50 0.00 0.00 3.61
41 2938 1.826054 CCCTTGACACGGTGCCAAA 60.826 57.895 11.00 1.58 0.00 3.28
49 2946 0.029300 CACGGTGCCAAACTTCTGTG 59.971 55.000 0.00 0.00 0.00 3.66
57 2954 5.356426 GTGCCAAACTTCTGTGGTTTAAAT 58.644 37.500 0.00 0.00 37.23 1.40
85 2982 8.962679 AGTTTTTGTACCTTGTGTAATTTGAGA 58.037 29.630 0.00 0.00 0.00 3.27
91 2988 7.771361 TGTACCTTGTGTAATTTGAGAACTTGA 59.229 33.333 0.00 0.00 0.00 3.02
92 2989 7.264373 ACCTTGTGTAATTTGAGAACTTGAG 57.736 36.000 0.00 0.00 0.00 3.02
116 3013 6.323739 AGGTTGATGTTTCCATTGTTGTTACT 59.676 34.615 0.00 0.00 0.00 2.24
118 3015 6.707440 TGATGTTTCCATTGTTGTTACTGT 57.293 33.333 0.00 0.00 0.00 3.55
123 3020 6.374613 TGTTTCCATTGTTGTTACTGTGTGTA 59.625 34.615 0.00 0.00 0.00 2.90
144 3041 6.146184 GTGTATGTATTCTCCGATGGATGTTG 59.854 42.308 0.00 0.00 0.00 3.33
174 3071 6.978343 TGATTGAAAGTTAGTATTGACCGG 57.022 37.500 0.00 0.00 0.00 5.28
175 3072 6.703319 TGATTGAAAGTTAGTATTGACCGGA 58.297 36.000 9.46 0.00 0.00 5.14
176 3073 6.592607 TGATTGAAAGTTAGTATTGACCGGAC 59.407 38.462 9.46 1.07 0.00 4.79
179 3076 4.877378 AAGTTAGTATTGACCGGACACA 57.123 40.909 9.46 2.00 0.00 3.72
192 3089 1.305930 GGACACAAATCCGGCTGGTC 61.306 60.000 12.43 0.00 36.30 4.02
245 3145 2.706190 GGATATTACTGGCTGGTCACCT 59.294 50.000 0.00 0.00 0.00 4.00
319 3219 8.452989 TCAAATATCGACGTATCAGAATCATG 57.547 34.615 0.00 0.00 0.00 3.07
357 3258 5.960113 AGACGGATACAATCATGAGCTATC 58.040 41.667 0.09 5.22 0.00 2.08
394 3295 3.487372 TGACACACTCTGTAGTAGTGCT 58.513 45.455 3.24 0.00 46.73 4.40
530 3454 1.399727 GGTCAAATTCGCCAAGTGACG 60.400 52.381 5.12 0.00 0.00 4.35
533 3457 1.002900 CAAATTCGCCAAGTGACGTGT 60.003 47.619 0.00 0.00 0.00 4.49
534 3458 1.305201 AATTCGCCAAGTGACGTGTT 58.695 45.000 0.00 0.00 0.00 3.32
535 3459 0.865769 ATTCGCCAAGTGACGTGTTC 59.134 50.000 0.00 0.00 0.00 3.18
536 3460 0.460459 TTCGCCAAGTGACGTGTTCA 60.460 50.000 0.00 0.00 0.00 3.18
537 3461 0.460459 TCGCCAAGTGACGTGTTCAA 60.460 50.000 0.00 0.00 35.39 2.69
538 3462 0.375454 CGCCAAGTGACGTGTTCAAA 59.625 50.000 0.00 0.00 35.39 2.69
581 3520 1.444836 CCATGCCAAAACCATGCAAG 58.555 50.000 0.00 0.00 38.93 4.01
603 3542 4.632538 GTGAAACCCATTATGCCTGTAC 57.367 45.455 0.00 0.00 0.00 2.90
604 3543 4.270008 GTGAAACCCATTATGCCTGTACT 58.730 43.478 0.00 0.00 0.00 2.73
605 3544 4.335594 GTGAAACCCATTATGCCTGTACTC 59.664 45.833 0.00 0.00 0.00 2.59
606 3545 3.577805 AACCCATTATGCCTGTACTCC 57.422 47.619 0.00 0.00 0.00 3.85
607 3546 1.774856 ACCCATTATGCCTGTACTCCC 59.225 52.381 0.00 0.00 0.00 4.30
608 3547 2.057922 CCCATTATGCCTGTACTCCCT 58.942 52.381 0.00 0.00 0.00 4.20
609 3548 2.039084 CCCATTATGCCTGTACTCCCTC 59.961 54.545 0.00 0.00 0.00 4.30
610 3549 2.039084 CCATTATGCCTGTACTCCCTCC 59.961 54.545 0.00 0.00 0.00 4.30
611 3550 1.410004 TTATGCCTGTACTCCCTCCG 58.590 55.000 0.00 0.00 0.00 4.63
612 3551 0.260816 TATGCCTGTACTCCCTCCGT 59.739 55.000 0.00 0.00 0.00 4.69
613 3552 0.617820 ATGCCTGTACTCCCTCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
614 3553 1.255667 TGCCTGTACTCCCTCCGTTC 61.256 60.000 0.00 0.00 0.00 3.95
615 3554 1.957765 GCCTGTACTCCCTCCGTTCC 61.958 65.000 0.00 0.00 0.00 3.62
616 3555 0.613853 CCTGTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 0.00 3.53
617 3556 1.263356 CTGTACTCCCTCCGTTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
618 3557 1.621814 CTGTACTCCCTCCGTTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
619 3558 2.038033 CTGTACTCCCTCCGTTCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
620 3559 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
621 3560 2.971901 ACTCCCTCCGTTCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
622 3561 2.791655 ACTCCCTCCGTTCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
623 3562 2.375509 ACTCCCTCCGTTCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
624 3563 3.181433 ACTCCCTCCGTTCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
625 3564 3.153919 TCCCTCCGTTCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
626 3565 2.890945 CCCTCCGTTCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
627 3566 3.057526 CCCTCCGTTCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
628 3567 3.821033 CCTCCGTTCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
629 3568 4.278419 CCTCCGTTCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
630 3569 5.472137 CCTCCGTTCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
631 3570 6.348540 CCTCCGTTCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
632 3571 6.292923 TCCGTTCCAAAATTCTTGTCTTAGA 58.707 36.000 0.00 0.00 0.00 2.10
633 3572 6.940298 TCCGTTCCAAAATTCTTGTCTTAGAT 59.060 34.615 0.00 0.00 0.00 1.98
634 3573 7.447238 TCCGTTCCAAAATTCTTGTCTTAGATT 59.553 33.333 0.00 0.00 0.00 2.40
635 3574 8.082242 CCGTTCCAAAATTCTTGTCTTAGATTT 58.918 33.333 0.00 0.00 0.00 2.17
636 3575 8.905702 CGTTCCAAAATTCTTGTCTTAGATTTG 58.094 33.333 0.00 0.00 29.84 2.32
637 3576 9.750125 GTTCCAAAATTCTTGTCTTAGATTTGT 57.250 29.630 0.00 0.00 28.79 2.83
638 3577 9.965824 TTCCAAAATTCTTGTCTTAGATTTGTC 57.034 29.630 0.00 0.00 28.79 3.18
639 3578 9.354673 TCCAAAATTCTTGTCTTAGATTTGTCT 57.645 29.630 0.00 0.00 28.79 3.41
660 3599 8.940397 TGTCTAGATATGGATGTATCAAGTCA 57.060 34.615 0.00 0.00 34.27 3.41
661 3600 8.797438 TGTCTAGATATGGATGTATCAAGTCAC 58.203 37.037 0.00 0.00 34.27 3.67
662 3601 8.797438 GTCTAGATATGGATGTATCAAGTCACA 58.203 37.037 0.00 0.00 34.27 3.58
663 3602 9.539194 TCTAGATATGGATGTATCAAGTCACAT 57.461 33.333 0.00 0.00 38.08 3.21
666 3605 9.857656 AGATATGGATGTATCAAGTCACATTTT 57.142 29.630 0.00 0.00 35.55 1.82
750 3689 8.035984 AGTATTAAACTAAGACAAGAGACCAGC 58.964 37.037 0.00 0.00 36.36 4.85
796 3736 8.218338 AGATTTAGGAAGTAATGTTCAGCATG 57.782 34.615 0.00 0.00 37.96 4.06
915 3855 3.085119 GCACCCCATCTGCCATTGC 62.085 63.158 0.00 0.00 38.26 3.56
930 3873 2.641305 CATTGCTCCCTCCAAGAGAAG 58.359 52.381 0.00 0.00 32.86 2.85
959 3902 0.251341 GCTGTGTTCATCACCCCCTT 60.251 55.000 0.00 0.00 45.61 3.95
960 3903 1.004277 GCTGTGTTCATCACCCCCTTA 59.996 52.381 0.00 0.00 45.61 2.69
981 3924 1.619654 CTCAGCCAATCAACCACCAA 58.380 50.000 0.00 0.00 0.00 3.67
997 3942 4.202388 ACCACCAACGTCCTACAAACTTAT 60.202 41.667 0.00 0.00 0.00 1.73
1038 3983 2.125350 GCTGAGAAGGACCCGCTG 60.125 66.667 0.00 0.00 0.00 5.18
1204 4149 2.315386 GGTTCGAAGGTCACCGTGC 61.315 63.158 0.00 0.00 0.00 5.34
1411 4358 2.422127 TGCATCTCGACATCTCAACGTA 59.578 45.455 0.00 0.00 0.00 3.57
1490 5565 6.476706 GCCTGTGCCTGCTAATTTAATTTAAG 59.523 38.462 0.00 0.00 0.00 1.85
1501 5576 9.434559 GCTAATTTAATTTAAGTTAGTGGAGCG 57.565 33.333 22.25 6.70 39.06 5.03
1658 5735 7.041098 GGTCATTAATGATTGTGTAGGGCTAAG 60.041 40.741 20.65 0.00 39.30 2.18
1665 5742 2.250031 TGTGTAGGGCTAAGACGGAAA 58.750 47.619 0.00 0.00 0.00 3.13
1666 5743 2.028748 TGTGTAGGGCTAAGACGGAAAC 60.029 50.000 0.00 0.00 0.00 2.78
1802 5923 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
1804 5925 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1885 6090 8.201242 TGACCACAAATCCATATATGCTACTA 57.799 34.615 7.24 0.00 0.00 1.82
1904 6109 9.991906 TGCTACTATTAAGTATTTATGTGGGTC 57.008 33.333 0.00 0.00 37.57 4.46
1943 6151 5.048083 TGGTATTTTTCTTCTGCATCCACAC 60.048 40.000 0.00 0.00 0.00 3.82
2084 6296 4.065321 ACTATCTTGCACTAGGTGATGC 57.935 45.455 1.57 0.00 42.40 3.91
2115 6327 4.213564 ACAAGCAGAGGGTAAGATTCAG 57.786 45.455 0.00 0.00 0.00 3.02
2197 6423 9.784680 GTTGTTGTAGAAGATATACTTTCGAGA 57.215 33.333 0.00 0.00 39.13 4.04
2495 6723 4.260985 TGGGCAACATGTAGTCACTAATG 58.739 43.478 0.00 0.00 39.74 1.90
2555 6783 2.553602 CAGTATGCCAGCACAGTCAAAA 59.446 45.455 0.00 0.00 0.00 2.44
2618 6846 5.440610 CAATCCATTACTAAGCCCAGACTT 58.559 41.667 0.00 0.00 0.00 3.01
2646 6890 4.439974 GCTCCCGATGCACATTAAATTCAA 60.440 41.667 0.00 0.00 0.00 2.69
2860 7109 0.529555 ACAAACGTTTGCATGCACCC 60.530 50.000 34.70 12.82 41.79 4.61
2872 7121 1.830587 ATGCACCCAGAGCACTCGAA 61.831 55.000 0.00 0.00 45.95 3.71
2908 7159 8.502387 TGCCAAATTGTTTGATATGTTTTTAGC 58.498 29.630 4.11 0.00 43.26 3.09
2985 7417 1.687123 CCTAGGTCCATACGAACCCTG 59.313 57.143 0.00 0.00 36.11 4.45
2987 7419 1.192428 AGGTCCATACGAACCCTGAC 58.808 55.000 0.00 0.00 36.11 3.51
2995 7427 2.649331 ACGAACCCTGACTCGTATTG 57.351 50.000 0.00 0.00 45.94 1.90
3183 7798 4.764679 TTTTGCACAGCTCGTATGAAAT 57.235 36.364 0.00 0.00 0.00 2.17
3216 7837 7.773224 CCAAATTATGACAAGTAGGTCCATGTA 59.227 37.037 0.00 0.00 36.97 2.29
3217 7838 9.342308 CAAATTATGACAAGTAGGTCCATGTAT 57.658 33.333 0.00 0.00 36.97 2.29
3280 7908 5.542779 CAGGACTTAAACTAGTCTGTTGCT 58.457 41.667 0.00 0.00 43.26 3.91
3408 8053 0.321564 TTCGCATCAACACCCTCCTG 60.322 55.000 0.00 0.00 0.00 3.86
3471 8116 3.953612 TCACAAAGCTCATCAACAAAGGT 59.046 39.130 0.00 0.00 0.00 3.50
3642 8287 2.750350 GCCGGGATAGATGGTGGG 59.250 66.667 2.18 0.00 0.00 4.61
4221 10985 4.901197 TGAGTTCTACAACAATGGGCTA 57.099 40.909 0.00 0.00 34.60 3.93
4311 11076 1.484038 CCTCCTACTGCTCTGAGCTT 58.516 55.000 28.04 18.00 42.97 3.74
4452 11351 3.628008 ACTCATGTCCTCCACGTACATA 58.372 45.455 0.77 0.00 32.70 2.29
4464 11363 1.337447 ACGTACATAGTGGCGCTTTGT 60.337 47.619 23.85 23.85 41.23 2.83
4545 11444 1.986882 CAGAGGTTGCCAAGAAGGTT 58.013 50.000 0.00 0.00 40.61 3.50
4575 11501 0.248825 CCAGCGTCGAGGAGATTCTG 60.249 60.000 9.75 6.05 33.64 3.02
4590 11516 4.552365 CTGATGGCCGCCACCGAT 62.552 66.667 16.16 0.00 35.80 4.18
6013 13077 1.372087 CTTGGATTCGTCCCTGCAGC 61.372 60.000 8.66 0.00 0.00 5.25
6015 13079 2.268920 GATTCGTCCCTGCAGCCA 59.731 61.111 8.66 0.00 0.00 4.75
6117 13181 2.632996 CTGGCCCGTTCTATCTCCATAA 59.367 50.000 0.00 0.00 0.00 1.90
6285 13353 4.636206 GTCTTTTGTCTGTTCTGGAACACT 59.364 41.667 11.53 0.00 45.42 3.55
6326 13394 3.306364 CCAAAACAAGTCACACAACCCAA 60.306 43.478 0.00 0.00 0.00 4.12
6349 13417 4.721776 AGAGCAACTAATTCAGGGGTATCA 59.278 41.667 0.00 0.00 0.00 2.15
6473 13827 3.381590 GGTCTTGGAGCAGTTTGTTCTTT 59.618 43.478 0.00 0.00 0.00 2.52
6476 13830 2.733956 TGGAGCAGTTTGTTCTTTGGT 58.266 42.857 0.00 0.00 0.00 3.67
6604 14876 8.758633 TTTTTACCGTTTTCATTTTGTTCTCA 57.241 26.923 0.00 0.00 0.00 3.27
6616 14888 7.703328 TCATTTTGTTCTCAACTTTACCTGTC 58.297 34.615 0.00 0.00 32.93 3.51
6618 14890 6.920569 TTTGTTCTCAACTTTACCTGTCTC 57.079 37.500 0.00 0.00 32.93 3.36
6619 14891 5.871396 TGTTCTCAACTTTACCTGTCTCT 57.129 39.130 0.00 0.00 0.00 3.10
6755 15711 4.857871 TCGCATGAAGCACAAGTTATAC 57.142 40.909 0.00 0.00 46.13 1.47
6768 18702 6.017440 GCACAAGTTATACTTCTGTGTTTCCA 60.017 38.462 11.26 0.00 38.53 3.53
6772 18706 8.567948 CAAGTTATACTTCTGTGTTTCCACATT 58.432 33.333 0.00 0.00 42.67 2.71
6815 18749 1.737838 TCCGCCTGAAGCATAAGTTG 58.262 50.000 0.00 0.00 44.04 3.16
6819 18753 1.135286 GCCTGAAGCATAAGTTGTGCC 60.135 52.381 19.64 7.35 43.50 5.01
6831 18765 0.308993 GTTGTGCCTCTGTGCTTCAC 59.691 55.000 0.00 0.00 34.56 3.18
6871 18805 1.878953 AAGTACAGTTGTGCTTCCCG 58.121 50.000 9.39 0.00 45.60 5.14
6993 18953 7.342769 TGAGTATCGTGATTAGCTAGGAAAA 57.657 36.000 0.00 0.00 38.61 2.29
7002 18962 9.706691 CGTGATTAGCTAGGAAAAATAGGATAA 57.293 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.588290 AGGGTGAACATATATAGAGCTCTAAG 57.412 38.462 26.62 15.79 31.39 2.18
2 3 8.807118 CAAGGGTGAACATATATAGAGCTCTAA 58.193 37.037 26.62 16.01 31.39 2.10
3 4 8.170730 TCAAGGGTGAACATATATAGAGCTCTA 58.829 37.037 25.23 25.23 0.00 2.43
4 5 7.013220 TCAAGGGTGAACATATATAGAGCTCT 58.987 38.462 22.17 22.17 0.00 4.09
6 7 6.554982 TGTCAAGGGTGAACATATATAGAGCT 59.445 38.462 0.00 0.00 34.87 4.09
9 10 6.239204 CCGTGTCAAGGGTGAACATATATAGA 60.239 42.308 0.00 0.00 34.87 1.98
11 12 5.364446 ACCGTGTCAAGGGTGAACATATATA 59.636 40.000 9.75 0.00 42.98 0.86
12 13 4.163458 ACCGTGTCAAGGGTGAACATATAT 59.837 41.667 9.75 0.00 42.98 0.86
13 14 3.516300 ACCGTGTCAAGGGTGAACATATA 59.484 43.478 9.75 0.00 42.98 0.86
14 15 2.304761 ACCGTGTCAAGGGTGAACATAT 59.695 45.455 9.75 0.00 42.98 1.78
22 2919 2.559922 TTTGGCACCGTGTCAAGGGT 62.560 55.000 17.51 0.32 43.41 4.34
24 2921 1.101049 AGTTTGGCACCGTGTCAAGG 61.101 55.000 17.51 2.91 43.41 3.61
27 2924 0.107410 AGAAGTTTGGCACCGTGTCA 60.107 50.000 0.47 0.47 0.00 3.58
28 2925 0.307760 CAGAAGTTTGGCACCGTGTC 59.692 55.000 0.00 0.00 0.00 3.67
41 2938 8.311109 ACAAAAACTCATTTAAACCACAGAAGT 58.689 29.630 0.00 0.00 0.00 3.01
49 2946 8.813282 CACAAGGTACAAAAACTCATTTAAACC 58.187 33.333 0.00 0.00 31.86 3.27
57 2954 8.740906 TCAAATTACACAAGGTACAAAAACTCA 58.259 29.630 0.00 0.00 0.00 3.41
116 3013 4.647399 TCCATCGGAGAATACATACACACA 59.353 41.667 0.00 0.00 43.58 3.72
118 3015 5.304357 ACATCCATCGGAGAATACATACACA 59.696 40.000 0.00 0.00 43.58 3.72
123 3020 5.163311 TGACAACATCCATCGGAGAATACAT 60.163 40.000 0.00 0.00 43.58 2.29
163 3060 3.606687 GGATTTGTGTCCGGTCAATACT 58.393 45.455 2.02 0.00 0.00 2.12
173 3070 1.303317 ACCAGCCGGATTTGTGTCC 60.303 57.895 5.05 0.00 35.59 4.02
174 3071 1.635663 CGACCAGCCGGATTTGTGTC 61.636 60.000 5.05 8.74 35.59 3.67
175 3072 1.671054 CGACCAGCCGGATTTGTGT 60.671 57.895 5.05 0.29 35.59 3.72
176 3073 3.177600 CGACCAGCCGGATTTGTG 58.822 61.111 5.05 0.00 35.59 3.33
192 3089 5.924475 AGAATAAAAACTGTGTCTCACCG 57.076 39.130 0.00 0.00 32.73 4.94
199 3096 8.630037 CCCTTTTCAGTAGAATAAAAACTGTGT 58.370 33.333 0.00 0.00 41.12 3.72
200 3097 8.846211 TCCCTTTTCAGTAGAATAAAAACTGTG 58.154 33.333 0.00 0.00 41.12 3.66
245 3145 2.225382 TCAGTGATAACTGACCGGGA 57.775 50.000 9.02 0.00 41.34 5.14
281 3181 6.464222 GTCGATATTTGATGTATCCTTGGGA 58.536 40.000 0.00 0.00 35.55 4.37
294 3194 7.542130 CCATGATTCTGATACGTCGATATTTGA 59.458 37.037 0.00 0.00 0.00 2.69
302 3202 4.860072 TCTTCCATGATTCTGATACGTCG 58.140 43.478 0.00 0.00 0.00 5.12
319 3219 0.784778 CGTCTTCACGTTGCTCTTCC 59.215 55.000 0.00 0.00 41.42 3.46
357 3258 2.674177 GTGTCATCACTAACCGGTCAGG 60.674 54.545 8.04 3.42 42.61 3.86
394 3295 2.027003 TGCAATCGATCATGCTCACA 57.973 45.000 19.80 0.62 42.97 3.58
425 3326 5.859648 GGTTTTTGTCTCGTTTCACAAGAAA 59.140 36.000 0.00 0.00 41.26 2.52
426 3327 5.048643 TGGTTTTTGTCTCGTTTCACAAGAA 60.049 36.000 0.00 0.00 34.07 2.52
530 3454 4.936891 AGTCTTGGAGCAAATTTGAACAC 58.063 39.130 22.31 8.69 0.00 3.32
533 3457 4.214310 TGGAGTCTTGGAGCAAATTTGAA 58.786 39.130 22.31 6.15 0.00 2.69
534 3458 3.831323 TGGAGTCTTGGAGCAAATTTGA 58.169 40.909 22.31 0.00 0.00 2.69
535 3459 4.038402 AGTTGGAGTCTTGGAGCAAATTTG 59.962 41.667 14.03 14.03 0.00 2.32
536 3460 4.218312 AGTTGGAGTCTTGGAGCAAATTT 58.782 39.130 0.00 0.00 0.00 1.82
537 3461 3.837355 AGTTGGAGTCTTGGAGCAAATT 58.163 40.909 0.00 0.00 0.00 1.82
538 3462 3.515602 AGTTGGAGTCTTGGAGCAAAT 57.484 42.857 0.00 0.00 0.00 2.32
581 3520 2.456577 ACAGGCATAATGGGTTTCACC 58.543 47.619 0.00 0.00 37.60 4.02
592 3531 1.342674 ACGGAGGGAGTACAGGCATAA 60.343 52.381 0.00 0.00 0.00 1.90
598 3537 1.263356 TTGGAACGGAGGGAGTACAG 58.737 55.000 0.00 0.00 0.00 2.74
603 3542 3.073274 AGAATTTTGGAACGGAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
604 3543 3.153919 CAAGAATTTTGGAACGGAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
605 3544 2.890945 ACAAGAATTTTGGAACGGAGGG 59.109 45.455 0.00 0.00 0.00 4.30
606 3545 3.821033 AGACAAGAATTTTGGAACGGAGG 59.179 43.478 0.00 0.00 0.00 4.30
607 3546 5.438761 AAGACAAGAATTTTGGAACGGAG 57.561 39.130 0.00 0.00 0.00 4.63
608 3547 6.292923 TCTAAGACAAGAATTTTGGAACGGA 58.707 36.000 0.00 0.00 0.00 4.69
609 3548 6.554334 TCTAAGACAAGAATTTTGGAACGG 57.446 37.500 0.00 0.00 0.00 4.44
610 3549 8.905702 CAAATCTAAGACAAGAATTTTGGAACG 58.094 33.333 5.68 0.00 28.49 3.95
611 3550 9.750125 ACAAATCTAAGACAAGAATTTTGGAAC 57.250 29.630 0.00 0.00 33.04 3.62
612 3551 9.965824 GACAAATCTAAGACAAGAATTTTGGAA 57.034 29.630 0.00 0.00 33.04 3.53
613 3552 9.354673 AGACAAATCTAAGACAAGAATTTTGGA 57.645 29.630 0.00 0.00 33.04 3.53
634 3573 9.367160 TGACTTGATACATCCATATCTAGACAA 57.633 33.333 0.00 0.00 36.75 3.18
635 3574 8.797438 GTGACTTGATACATCCATATCTAGACA 58.203 37.037 0.00 7.78 36.88 3.41
636 3575 8.797438 TGTGACTTGATACATCCATATCTAGAC 58.203 37.037 0.00 5.82 36.88 2.59
637 3576 8.940397 TGTGACTTGATACATCCATATCTAGA 57.060 34.615 10.02 0.00 36.88 2.43
640 3579 9.857656 AAAATGTGACTTGATACATCCATATCT 57.142 29.630 0.00 0.00 36.56 1.98
708 3647 9.588096 AGTTTAATACTCCCTCTGTTTCAAATT 57.412 29.630 0.00 0.00 28.23 1.82
711 3650 9.720769 CTTAGTTTAATACTCCCTCTGTTTCAA 57.279 33.333 0.00 0.00 38.33 2.69
712 3651 9.096823 TCTTAGTTTAATACTCCCTCTGTTTCA 57.903 33.333 0.00 0.00 38.33 2.69
713 3652 9.368674 GTCTTAGTTTAATACTCCCTCTGTTTC 57.631 37.037 0.00 0.00 38.33 2.78
714 3653 8.877195 TGTCTTAGTTTAATACTCCCTCTGTTT 58.123 33.333 0.00 0.00 38.33 2.83
715 3654 8.431910 TGTCTTAGTTTAATACTCCCTCTGTT 57.568 34.615 0.00 0.00 38.33 3.16
716 3655 8.431910 TTGTCTTAGTTTAATACTCCCTCTGT 57.568 34.615 0.00 0.00 38.33 3.41
717 3656 8.750298 TCTTGTCTTAGTTTAATACTCCCTCTG 58.250 37.037 0.00 0.00 38.33 3.35
718 3657 8.896722 TCTTGTCTTAGTTTAATACTCCCTCT 57.103 34.615 0.00 0.00 38.33 3.69
719 3658 8.968969 TCTCTTGTCTTAGTTTAATACTCCCTC 58.031 37.037 0.00 0.00 38.33 4.30
720 3659 8.751242 GTCTCTTGTCTTAGTTTAATACTCCCT 58.249 37.037 0.00 0.00 38.33 4.20
721 3660 7.980662 GGTCTCTTGTCTTAGTTTAATACTCCC 59.019 40.741 0.00 0.00 38.33 4.30
722 3661 8.529476 TGGTCTCTTGTCTTAGTTTAATACTCC 58.471 37.037 0.00 0.00 38.33 3.85
723 3662 9.575783 CTGGTCTCTTGTCTTAGTTTAATACTC 57.424 37.037 0.00 0.00 38.33 2.59
724 3663 8.035984 GCTGGTCTCTTGTCTTAGTTTAATACT 58.964 37.037 0.00 0.00 41.04 2.12
725 3664 7.817962 TGCTGGTCTCTTGTCTTAGTTTAATAC 59.182 37.037 0.00 0.00 0.00 1.89
726 3665 7.903145 TGCTGGTCTCTTGTCTTAGTTTAATA 58.097 34.615 0.00 0.00 0.00 0.98
727 3666 6.769512 TGCTGGTCTCTTGTCTTAGTTTAAT 58.230 36.000 0.00 0.00 0.00 1.40
728 3667 6.169557 TGCTGGTCTCTTGTCTTAGTTTAA 57.830 37.500 0.00 0.00 0.00 1.52
750 3689 6.932356 TCTAGGCTAAATGCTTTTCAGATG 57.068 37.500 0.11 0.00 42.39 2.90
796 3736 2.031508 GGACTGACTATCTGAGCGCTAC 60.032 54.545 11.50 4.70 0.00 3.58
915 3855 4.243793 TCTCTACTTCTCTTGGAGGGAG 57.756 50.000 0.00 0.00 33.72 4.30
930 3873 5.065704 TGATGAACACAGCTCTTCTCTAC 57.934 43.478 0.00 0.00 0.00 2.59
959 3902 1.004277 GGTGGTTGATTGGCTGAGGTA 59.996 52.381 0.00 0.00 0.00 3.08
960 3903 0.251341 GGTGGTTGATTGGCTGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
981 3924 4.634443 GCCATTGATAAGTTTGTAGGACGT 59.366 41.667 0.00 0.00 0.00 4.34
997 3942 0.820074 AACCCGTTGTTCGCCATTGA 60.820 50.000 0.00 0.00 38.35 2.57
1467 5542 8.986477 AACTTAAATTAAATTAGCAGGCACAG 57.014 30.769 0.00 0.00 0.00 3.66
1490 5565 0.037232 ACCTCTTGCGCTCCACTAAC 60.037 55.000 9.73 0.00 0.00 2.34
1501 5576 3.370061 GTGTGGACGTATAAACCTCTTGC 59.630 47.826 0.00 0.00 0.00 4.01
1658 5735 2.071540 CGGGGAAGTAAAGTTTCCGTC 58.928 52.381 0.00 0.00 44.08 4.79
1703 5780 7.672983 TTGAACTGATAGACCTTTTGCTTAG 57.327 36.000 0.00 0.00 0.00 2.18
1812 5933 1.835121 TGTTATACTGCTAGCGCACG 58.165 50.000 11.47 0.00 42.25 5.34
1816 5937 6.530913 ACATCATTTGTTATACTGCTAGCG 57.469 37.500 10.77 7.61 33.74 4.26
1943 6151 8.929827 TTTACTTAATTCATCATGCCACATTG 57.070 30.769 0.00 0.00 0.00 2.82
2084 6296 7.606456 TCTTACCCTCTGCTTGTTATTTAACTG 59.394 37.037 2.45 0.00 37.12 3.16
2555 6783 9.851686 TCCAACTATGCTAAACAGAAATATCAT 57.148 29.630 0.00 0.00 0.00 2.45
2618 6846 1.051008 ATGTGCATCGGGAGCAGATA 58.949 50.000 5.71 0.00 43.19 1.98
2663 6907 3.056607 TCAGCATCTTCGATGTGAACTCA 60.057 43.478 5.81 0.00 31.87 3.41
2664 6908 3.515630 TCAGCATCTTCGATGTGAACTC 58.484 45.455 5.81 0.00 31.87 3.01
2665 6909 3.599730 TCAGCATCTTCGATGTGAACT 57.400 42.857 5.81 0.00 31.87 3.01
2860 7109 3.320626 TCAAAGATGTTCGAGTGCTCTG 58.679 45.455 0.00 0.00 0.00 3.35
2872 7121 6.289834 TCAAACAATTTGGCATCAAAGATGT 58.710 32.000 8.60 0.00 44.87 3.06
2924 7176 7.106890 TCCAAACGTGGTGATTTAGATTCATA 58.893 34.615 0.00 0.00 46.11 2.15
2925 7177 5.943416 TCCAAACGTGGTGATTTAGATTCAT 59.057 36.000 0.00 0.00 46.11 2.57
2927 7179 5.873179 TCCAAACGTGGTGATTTAGATTC 57.127 39.130 0.00 0.00 46.11 2.52
2957 7389 3.756963 TCGTATGGACCTAGGATCATTCG 59.243 47.826 25.61 25.61 33.73 3.34
2985 7417 7.932120 ATGTTAGAGCATAACAATACGAGTC 57.068 36.000 15.75 0.00 40.32 3.36
2995 7427 8.662781 TGTTCTGGAATATGTTAGAGCATAAC 57.337 34.615 5.20 5.20 35.30 1.89
3086 7637 3.425625 CCGCTTTATAAAGTTTGCGCAGA 60.426 43.478 22.94 2.14 41.71 4.26
3183 7798 7.942341 ACCTACTTGTCATAATTTGGAAGAACA 59.058 33.333 0.00 0.00 0.00 3.18
3201 7822 9.052759 GTTTTGGTATATACATGGACCTACTTG 57.947 37.037 14.70 0.00 32.87 3.16
3216 7837 9.920946 ACACATAAATCTGGAGTTTTGGTATAT 57.079 29.630 6.29 0.00 0.00 0.86
3218 7839 9.747898 TTACACATAAATCTGGAGTTTTGGTAT 57.252 29.630 6.29 0.00 0.00 2.73
3280 7908 2.050836 ATATGGTCAATGCCGGCCGA 62.051 55.000 30.73 15.46 0.00 5.54
3408 8053 1.532868 CGTATGCCAGAATAGCCTTGC 59.467 52.381 0.00 0.00 0.00 4.01
3471 8116 0.979187 GGGGAATCCTCGGGTGTACA 60.979 60.000 0.00 0.00 0.00 2.90
3642 8287 1.981256 TGGGGTTCAGCTTGAAGAAC 58.019 50.000 0.00 6.18 42.51 3.01
4311 11076 1.427368 ACTGGGTTGGCAAGGTATTGA 59.573 47.619 0.00 0.00 38.83 2.57
4452 11351 2.980233 GCCTGACAAAGCGCCACT 60.980 61.111 2.29 0.00 0.00 4.00
4590 11516 2.354188 CTGAACACGTCCACGCGA 60.354 61.111 15.93 0.00 44.43 5.87
4780 11718 4.162690 GCCCTTCTCCACGGCGAT 62.163 66.667 16.62 0.00 31.92 4.58
6013 13077 1.817099 GTCGATGAGCTTGCCCTGG 60.817 63.158 0.00 0.00 0.00 4.45
6015 13079 2.586792 GGTCGATGAGCTTGCCCT 59.413 61.111 0.00 0.00 0.00 5.19
6117 13181 4.160329 TCAGTTATTCAGACAGGGACACT 58.840 43.478 0.00 0.00 0.00 3.55
6326 13394 4.721776 TGATACCCCTGAATTAGTTGCTCT 59.278 41.667 0.00 0.00 0.00 4.09
6349 13417 1.518572 CTGCGGCCTCGTTTCGTAT 60.519 57.895 0.00 0.00 38.89 3.06
6434 13788 0.251354 ACCAGAAGCGCACATCTCAT 59.749 50.000 11.47 0.00 0.00 2.90
6584 14066 5.961272 AGTTGAGAACAAAATGAAAACGGT 58.039 33.333 0.00 0.00 37.77 4.83
6673 15629 1.198713 AGCATACACTACTGCCAGCT 58.801 50.000 0.00 0.00 39.22 4.24
6768 18702 6.427547 CACAATTATGTTGCTTTTGGGAATGT 59.572 34.615 0.00 0.00 37.82 2.71
6772 18706 4.040217 AGCACAATTATGTTGCTTTTGGGA 59.960 37.500 0.00 0.00 39.35 4.37
6815 18749 0.819259 TTGGTGAAGCACAGAGGCAC 60.819 55.000 0.00 0.00 35.86 5.01
6831 18765 2.354510 TCACTCGTTGCTTCACTTTTGG 59.645 45.455 0.00 0.00 0.00 3.28
6871 18805 8.766493 AAAGCAAATTTGTATTTCGCTTTTTC 57.234 26.923 19.03 0.00 44.40 2.29
7064 19026 1.207089 TGTATTCCTTGAGCCTCGTGG 59.793 52.381 0.00 0.00 0.00 4.94
7065 19027 2.672961 TGTATTCCTTGAGCCTCGTG 57.327 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.