Multiple sequence alignment - TraesCS6B01G011600

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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 TraesCS6B01G011600 chr6B 100.000 3388 0 0 1 3388 6816710 6813323 0.000000e+00 6257.0
1 TraesCS6B01G011600 chr6B 91.282 1193 59 19 1 1160 7178898 7180078 0.000000e+00 1587.0
2 TraesCS6B01G011600 chr6B 96.110 797 29 2 366 1160 7221481 7222277 0.000000e+00 1299.0
3 TraesCS6B01G011600 chr6B 94.743 799 30 4 1210 1999 7180067 7180862 0.000000e+00 1232.0
4 TraesCS6B01G011600 chr6B 94.618 799 31 4 1210 1999 7222266 7223061 0.000000e+00 1227.0
5 TraesCS6B01G011600 chr6B 93.014 730 49 2 2660 3388 7223657 7224385 0.000000e+00 1064.0
6 TraesCS6B01G011600 chr6B 92.966 725 49 2 2665 3388 7181722 7182445 0.000000e+00 1055.0
7 TraesCS6B01G011600 chr6B 86.096 374 27 13 2211 2559 7181007 7181380 2.470000e-101 379.0
8 TraesCS6B01G011600 chr6B 86.096 374 27 13 2211 2559 7223206 7223579 2.470000e-101 379.0
9 TraesCS6B01G011600 chr6B 97.674 215 5 0 1505 1719 6814716 6814502 1.480000e-98 370.0
10 TraesCS6B01G011600 chr6B 97.674 215 5 0 1995 2209 6815206 6814992 1.480000e-98 370.0
11 TraesCS6B01G011600 chr6B 97.664 214 5 0 1995 2208 7180364 7180577 5.340000e-98 368.0
12 TraesCS6B01G011600 chr6B 97.664 214 5 0 1995 2208 7222563 7222776 5.340000e-98 368.0
13 TraesCS6B01G011600 chr6B 85.324 293 22 9 1 284 7220867 7221147 1.990000e-72 283.0
14 TraesCS6B01G011600 chr6B 97.619 42 1 0 3347 3388 35946253 35946294 4.690000e-09 73.1
15 TraesCS6B01G011600 chrUn 95.452 1583 54 4 424 1999 322770860 322769289 0.000000e+00 2508.0
16 TraesCS6B01G011600 chrUn 88.257 1107 101 14 2211 3295 322769144 322768045 0.000000e+00 1297.0
17 TraesCS6B01G011600 chrUn 89.147 774 67 11 2522 3282 126987530 126988299 0.000000e+00 948.0
18 TraesCS6B01G011600 chrUn 93.699 365 12 7 1 355 415038547 415038910 1.380000e-148 536.0
19 TraesCS6B01G011600 chrUn 95.349 215 10 0 1995 2209 322769789 322769575 3.240000e-90 342.0
20 TraesCS6B01G011600 chrUn 95.146 103 5 0 2114 2216 406474828 406474726 2.710000e-36 163.0
21 TraesCS6B01G011600 chrUn 95.146 103 5 0 2114 2216 452334956 452335058 2.710000e-36 163.0
22 TraesCS6B01G011600 chrUn 100.000 52 0 0 1571 1622 217899188 217899239 2.780000e-16 97.1
23 TraesCS6B01G011600 chrUn 100.000 52 0 0 2061 2112 217899188 217899239 2.780000e-16 97.1
24 TraesCS6B01G011600 chr6A 89.102 1358 130 10 654 1999 2264184 2262833 0.000000e+00 1672.0
25 TraesCS6B01G011600 chr6A 93.088 217 10 4 1995 2209 2263333 2263120 2.540000e-81 313.0
26 TraesCS6B01G011600 chr6A 95.556 135 6 0 2211 2345 2262660 2262526 2.050000e-52 217.0
27 TraesCS6B01G011600 chr6A 95.146 103 5 0 2114 2216 84403103 84403001 2.710000e-36 163.0
28 TraesCS6B01G011600 chr6D 85.939 1145 129 18 376 1519 3472163 3471050 0.000000e+00 1194.0
29 TraesCS6B01G011600 chr6D 88.312 924 81 15 2431 3346 21590861 21589957 0.000000e+00 1083.0
30 TraesCS6B01G011600 chr6D 94.183 361 7 5 1 355 3485898 3485546 3.850000e-149 538.0
31 TraesCS6B01G011600 chr6D 83.534 249 25 7 1766 1999 3470916 3470669 5.690000e-53 219.0
32 TraesCS6B01G011600 chr6D 95.690 116 5 0 1624 1739 389251282 389251167 1.610000e-43 187.0
33 TraesCS6B01G011600 chr6D 98.182 55 1 0 2061 2115 458949838 458949784 2.780000e-16 97.1
34 TraesCS6B01G011600 chr6D 98.182 55 1 0 1571 1625 458949838 458949784 2.780000e-16 97.1
35 TraesCS6B01G011600 chr2B 90.447 827 67 10 2522 3345 759514205 759515022 0.000000e+00 1079.0
36 TraesCS6B01G011600 chr2B 97.674 43 1 0 3346 3388 750025423 750025465 1.300000e-09 75.0
37 TraesCS6B01G011600 chr5B 90.097 828 72 7 2522 3346 689872610 689873430 0.000000e+00 1066.0
38 TraesCS6B01G011600 chr5B 84.698 281 34 6 2379 2654 591728388 591728112 4.310000e-69 272.0
39 TraesCS6B01G011600 chr5B 84.838 277 32 6 2379 2654 689872428 689872695 1.550000e-68 270.0
40 TraesCS6B01G011600 chr5B 92.857 42 3 0 3347 3388 14344175 14344134 1.020000e-05 62.1
41 TraesCS6B01G011600 chr7B 89.467 826 86 1 2522 3346 742758963 742759788 0.000000e+00 1042.0
42 TraesCS6B01G011600 chr7B 95.349 43 1 1 3346 3388 635322041 635322000 2.180000e-07 67.6
43 TraesCS6B01G011600 chr3D 86.743 958 98 21 2380 3327 565460425 565459487 0.000000e+00 1038.0
44 TraesCS6B01G011600 chr3D 86.325 117 12 2 1225 1341 142480945 142480833 1.280000e-24 124.0
45 TraesCS6B01G011600 chr2A 88.875 782 78 8 2522 3300 31017545 31018320 0.000000e+00 953.0
46 TraesCS6B01G011600 chr2A 95.000 120 5 1 1620 1739 160870185 160870067 1.610000e-43 187.0
47 TraesCS6B01G011600 chr2A 97.143 35 1 0 2342 2376 653556635 653556669 3.650000e-05 60.2
48 TraesCS6B01G011600 chr7D 88.496 791 84 7 2522 3308 573266507 573267294 0.000000e+00 950.0
49 TraesCS6B01G011600 chr7D 89.873 711 64 5 2522 3230 634270151 634270855 0.000000e+00 907.0
50 TraesCS6B01G011600 chr4B 86.716 271 34 2 2380 2650 660872796 660872528 1.980000e-77 300.0
51 TraesCS6B01G011600 chr4B 95.146 103 5 0 2114 2216 209112966 209113068 2.710000e-36 163.0
52 TraesCS6B01G011600 chr5D 85.921 277 33 4 2379 2651 322575334 322575060 1.190000e-74 291.0
53 TraesCS6B01G011600 chr5D 95.690 116 5 0 1624 1739 503229608 503229493 1.610000e-43 187.0
54 TraesCS6B01G011600 chr5D 98.182 55 1 0 2061 2115 79827282 79827228 2.780000e-16 97.1
55 TraesCS6B01G011600 chr4D 100.000 52 0 0 1571 1622 87365269 87365320 2.780000e-16 97.1
56 TraesCS6B01G011600 chr4D 100.000 52 0 0 2061 2112 87365269 87365320 2.780000e-16 97.1
57 TraesCS6B01G011600 chr4D 94.872 39 2 0 2337 2375 11304366 11304404 1.020000e-05 62.1
58 TraesCS6B01G011600 chr7A 93.023 43 3 0 3346 3388 18056853 18056895 2.820000e-06 63.9
59 TraesCS6B01G011600 chr4A 95.000 40 2 0 2340 2379 428324141 428324102 2.820000e-06 63.9
60 TraesCS6B01G011600 chr4A 97.143 35 1 0 2342 2376 367481640 367481674 3.650000e-05 60.2
61 TraesCS6B01G011600 chr3A 93.023 43 3 0 3346 3388 512213544 512213502 2.820000e-06 63.9
62 TraesCS6B01G011600 chr1B 97.297 37 1 0 3346 3382 638047891 638047855 2.820000e-06 63.9
63 TraesCS6B01G011600 chr1B 94.737 38 2 0 2342 2379 31742299 31742262 3.650000e-05 60.2
64 TraesCS6B01G011600 chr3B 90.909 44 3 1 2337 2379 698882395 698882352 1.310000e-04 58.4


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 TraesCS6B01G011600 chr6B 6813323 6816710 3387 True 2332.333333 6257 98.449333 1 3388 3 chr6B.!!$R1 3387
1 TraesCS6B01G011600 chr6B 7178898 7182445 3547 False 924.200000 1587 92.550200 1 3388 5 chr6B.!!$F2 3387
2 TraesCS6B01G011600 chr6B 7220867 7224385 3518 False 770.000000 1299 92.137667 1 3388 6 chr6B.!!$F3 3387
3 TraesCS6B01G011600 chrUn 322768045 322770860 2815 True 1382.333333 2508 93.019333 424 3295 3 chrUn.!!$R2 2871
4 TraesCS6B01G011600 chrUn 126987530 126988299 769 False 948.000000 948 89.147000 2522 3282 1 chrUn.!!$F1 760
5 TraesCS6B01G011600 chr6A 2262526 2264184 1658 True 734.000000 1672 92.582000 654 2345 3 chr6A.!!$R2 1691
6 TraesCS6B01G011600 chr6D 21589957 21590861 904 True 1083.000000 1083 88.312000 2431 3346 1 chr6D.!!$R2 915
7 TraesCS6B01G011600 chr6D 3470669 3472163 1494 True 706.500000 1194 84.736500 376 1999 2 chr6D.!!$R4 1623
8 TraesCS6B01G011600 chr2B 759514205 759515022 817 False 1079.000000 1079 90.447000 2522 3345 1 chr2B.!!$F2 823
9 TraesCS6B01G011600 chr5B 689872428 689873430 1002 False 668.000000 1066 87.467500 2379 3346 2 chr5B.!!$F1 967
10 TraesCS6B01G011600 chr7B 742758963 742759788 825 False 1042.000000 1042 89.467000 2522 3346 1 chr7B.!!$F1 824
11 TraesCS6B01G011600 chr3D 565459487 565460425 938 True 1038.000000 1038 86.743000 2380 3327 1 chr3D.!!$R2 947
12 TraesCS6B01G011600 chr2A 31017545 31018320 775 False 953.000000 953 88.875000 2522 3300 1 chr2A.!!$F1 778
13 TraesCS6B01G011600 chr7D 573266507 573267294 787 False 950.000000 950 88.496000 2522 3308 1 chr7D.!!$F1 786
14 TraesCS6B01G011600 chr7D 634270151 634270855 704 False 907.000000 907 89.873000 2522 3230 1 chr7D.!!$F2 708

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
157 163 0.400670 GAGGGGATAAGAGGGCTGGT 60.401 60.0 0.0 0.0 0.00 4.00 F
1080 1388 1.015109 CGAGATCGTCTTCCTTCGGA 58.985 55.0 0.0 0.0 34.11 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2184 1.134220 AGTGGGTCAGAGCGAACAAAA 60.134 47.619 6.79 0.0 30.31 2.44 R
2416 2869 0.802494 GCAACCGGGACTAATGTGTG 59.198 55.000 6.32 0.0 0.00 3.82 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
63 64 9.358872 GAAAATAATGGAAAATGTTCTGAGACC 57.641 33.333 0.00 0.00 33.92 3.85
64 65 8.421249 AAATAATGGAAAATGTTCTGAGACCA 57.579 30.769 0.00 0.00 33.92 4.02
65 66 8.599624 AATAATGGAAAATGTTCTGAGACCAT 57.400 30.769 0.00 0.00 38.32 3.55
66 67 9.699410 AATAATGGAAAATGTTCTGAGACCATA 57.301 29.630 0.00 0.00 36.13 2.74
67 68 9.699410 ATAATGGAAAATGTTCTGAGACCATAA 57.301 29.630 0.00 0.00 36.13 1.90
68 69 8.599624 AATGGAAAATGTTCTGAGACCATAAT 57.400 30.769 0.00 0.00 36.13 1.28
70 71 8.055279 TGGAAAATGTTCTGAGACCATAATTC 57.945 34.615 8.81 8.81 33.92 2.17
71 72 7.669304 TGGAAAATGTTCTGAGACCATAATTCA 59.331 33.333 15.28 2.75 33.92 2.57
72 73 8.689972 GGAAAATGTTCTGAGACCATAATTCAT 58.310 33.333 15.28 0.00 33.92 2.57
73 74 9.512435 GAAAATGTTCTGAGACCATAATTCATG 57.488 33.333 11.12 0.00 0.00 3.07
75 76 9.685276 AAATGTTCTGAGACCATAATTCATGTA 57.315 29.630 0.00 0.00 32.21 2.29
76 77 9.857656 AATGTTCTGAGACCATAATTCATGTAT 57.142 29.630 0.00 0.00 32.21 2.29
77 78 8.893219 TGTTCTGAGACCATAATTCATGTATC 57.107 34.615 0.00 0.00 32.21 2.24
78 79 8.708378 TGTTCTGAGACCATAATTCATGTATCT 58.292 33.333 0.00 0.00 33.16 1.98
79 80 9.553064 GTTCTGAGACCATAATTCATGTATCTT 57.447 33.333 0.00 0.00 31.51 2.40
80 81 9.770097 TTCTGAGACCATAATTCATGTATCTTC 57.230 33.333 0.00 0.00 31.51 2.87
81 82 9.152327 TCTGAGACCATAATTCATGTATCTTCT 57.848 33.333 0.00 0.00 31.51 2.85
102 103 6.381481 TCTGCATGCTTGGTCAATTAATAG 57.619 37.500 20.33 2.29 0.00 1.73
124 125 6.512514 AGGAATGATAAGAGGAGATTGCTT 57.487 37.500 0.00 0.00 0.00 3.91
125 126 6.909076 AGGAATGATAAGAGGAGATTGCTTT 58.091 36.000 0.00 0.00 0.00 3.51
126 127 7.352738 AGGAATGATAAGAGGAGATTGCTTTT 58.647 34.615 0.00 0.00 0.00 2.27
127 128 7.838193 AGGAATGATAAGAGGAGATTGCTTTTT 59.162 33.333 0.00 0.00 0.00 1.94
128 129 8.134261 GGAATGATAAGAGGAGATTGCTTTTTC 58.866 37.037 0.00 0.00 0.00 2.29
157 163 0.400670 GAGGGGATAAGAGGGCTGGT 60.401 60.000 0.00 0.00 0.00 4.00
179 185 8.306313 TGGTCACATATATTGAAGTACTCTGT 57.694 34.615 0.00 0.00 0.00 3.41
214 220 9.884299 CATGTGCGTTTGTTACAAATTATTATG 57.116 29.630 13.84 11.71 0.00 1.90
250 256 7.611855 TCAGATTTAGATATCCTATCTCGCACA 59.388 37.037 0.00 0.00 0.00 4.57
263 269 3.466836 TCTCGCACATGTTTTCTCTGTT 58.533 40.909 0.00 0.00 0.00 3.16
265 271 3.951306 TCGCACATGTTTTCTCTGTTTG 58.049 40.909 0.00 0.00 0.00 2.93
296 305 5.450818 AATTTACCAGGTAAGAGGCATGA 57.549 39.130 12.03 0.00 29.41 3.07
299 308 5.546621 TTACCAGGTAAGAGGCATGATAC 57.453 43.478 8.09 0.00 0.00 2.24
305 314 7.147302 ACCAGGTAAGAGGCATGATACTTTTAT 60.147 37.037 0.00 0.00 0.00 1.40
337 346 3.604582 CTTTGGCTGGAAGAAGAGGTAG 58.395 50.000 0.00 0.00 34.07 3.18
349 358 6.829811 GGAAGAAGAGGTAGCTAGAAAGTCTA 59.170 42.308 0.00 0.00 0.00 2.59
350 359 7.201758 GGAAGAAGAGGTAGCTAGAAAGTCTAC 60.202 44.444 0.00 0.00 34.38 2.59
351 360 6.723339 AGAAGAGGTAGCTAGAAAGTCTACA 58.277 40.000 0.00 0.00 35.65 2.74
352 361 7.351166 AGAAGAGGTAGCTAGAAAGTCTACAT 58.649 38.462 0.00 0.00 35.65 2.29
353 362 6.952773 AGAGGTAGCTAGAAAGTCTACATG 57.047 41.667 0.00 0.00 35.65 3.21
354 363 6.428295 AGAGGTAGCTAGAAAGTCTACATGT 58.572 40.000 2.69 2.69 35.65 3.21
355 364 6.893005 AGAGGTAGCTAGAAAGTCTACATGTT 59.107 38.462 2.30 0.00 35.65 2.71
356 365 6.868622 AGGTAGCTAGAAAGTCTACATGTTG 58.131 40.000 2.30 1.19 35.65 3.33
358 367 7.343316 AGGTAGCTAGAAAGTCTACATGTTGAT 59.657 37.037 13.09 0.00 35.65 2.57
362 371 9.757227 AGCTAGAAAGTCTACATGTTGATTATC 57.243 33.333 13.09 10.91 0.00 1.75
363 372 9.757227 GCTAGAAAGTCTACATGTTGATTATCT 57.243 33.333 13.09 16.27 0.00 1.98
372 633 4.164221 ACATGTTGATTATCTCGAGGGGTT 59.836 41.667 13.56 0.00 0.00 4.11
408 669 8.523658 AGAGGCTGGAAATAAACATTACTTTTC 58.476 33.333 0.00 0.00 0.00 2.29
410 671 8.870116 AGGCTGGAAATAAACATTACTTTTCTT 58.130 29.630 0.00 0.00 0.00 2.52
531 792 4.681978 ACGTTCGCTGGGGAGCAC 62.682 66.667 0.00 0.00 34.41 4.40
645 906 4.002316 GGATTTGCCATGCTTGCTAAAAA 58.998 39.130 0.00 0.00 36.34 1.94
718 979 3.248266 GTTTGATAAGTCCGTACGCACT 58.752 45.455 5.89 5.89 0.00 4.40
984 1292 2.696893 GGCTCCCTCCTACTCCCA 59.303 66.667 0.00 0.00 0.00 4.37
1050 1358 2.124193 TCCGCCTCCGTTATCCGA 60.124 61.111 0.00 0.00 39.56 4.55
1075 1383 2.482333 CCGGCGAGATCGTCTTCCT 61.482 63.158 9.30 0.00 42.59 3.36
1080 1388 1.015109 CGAGATCGTCTTCCTTCGGA 58.985 55.000 0.00 0.00 34.11 4.55
1406 1714 7.530010 TCTTGTTCAAATGTCTAGCTAATTGC 58.470 34.615 0.00 0.00 43.29 3.56
1477 1785 2.355716 CCGCCATAGGTCTTCCTTTTGA 60.356 50.000 0.00 0.00 42.12 2.69
1494 1802 4.635699 TTTGACCCTTTTAGGACCTCTC 57.364 45.455 0.00 0.00 37.67 3.20
1814 2184 5.579753 ATTTCTATGCATCTCACATCCCT 57.420 39.130 0.19 0.00 0.00 4.20
1877 2254 2.820059 ATCTCAAGAACACACGCTCA 57.180 45.000 0.00 0.00 0.00 4.26
2000 2387 9.225436 TCAAACTGATTACAATGCTTACATACA 57.775 29.630 0.00 0.00 34.62 2.29
2005 2392 9.454585 CTGATTACAATGCTTACATACAAATGG 57.545 33.333 0.00 0.00 37.43 3.16
2006 2393 9.183368 TGATTACAATGCTTACATACAAATGGA 57.817 29.630 0.00 0.00 37.43 3.41
2011 2398 9.153721 ACAATGCTTACATACAAATGGAAAATG 57.846 29.630 0.00 0.00 35.45 2.32
2012 2399 9.153721 CAATGCTTACATACAAATGGAAAATGT 57.846 29.630 0.00 0.00 35.45 2.71
2029 2416 9.703892 TGGAAAATGTATATGTTTGGTTCAAAG 57.296 29.630 0.00 0.00 33.82 2.77
2030 2417 9.150348 GGAAAATGTATATGTTTGGTTCAAAGG 57.850 33.333 0.00 0.00 33.82 3.11
2037 2424 9.797556 GTATATGTTTGGTTCAAAGGAATAACC 57.202 33.333 0.00 0.00 42.49 2.85
2040 2427 5.536916 TGTTTGGTTCAAAGGAATAACCGAT 59.463 36.000 0.00 0.00 44.62 4.18
2041 2428 5.637006 TTGGTTCAAAGGAATAACCGATG 57.363 39.130 0.00 0.00 44.62 3.84
2042 2429 4.013728 TGGTTCAAAGGAATAACCGATGG 58.986 43.478 0.00 0.00 44.62 3.51
2044 2431 4.703093 GGTTCAAAGGAATAACCGATGGAA 59.297 41.667 0.00 0.00 44.74 3.53
2045 2432 5.359860 GGTTCAAAGGAATAACCGATGGAAT 59.640 40.000 0.00 0.00 44.74 3.01
2046 2433 6.127451 GGTTCAAAGGAATAACCGATGGAATT 60.127 38.462 0.00 0.00 44.74 2.17
2047 2434 7.067737 GGTTCAAAGGAATAACCGATGGAATTA 59.932 37.037 0.00 0.00 44.74 1.40
2048 2435 8.630037 GTTCAAAGGAATAACCGATGGAATTAT 58.370 33.333 0.00 0.00 44.74 1.28
2049 2436 8.391075 TCAAAGGAATAACCGATGGAATTATC 57.609 34.615 0.00 0.00 44.74 1.75
2050 2437 7.447238 TCAAAGGAATAACCGATGGAATTATCC 59.553 37.037 0.00 0.00 44.34 2.59
2051 2438 6.704056 AGGAATAACCGATGGAATTATCCT 57.296 37.500 0.00 0.00 44.37 3.24
2053 2440 7.526918 AGGAATAACCGATGGAATTATCCTTT 58.473 34.615 0.00 0.00 44.37 3.11
2054 2441 7.448469 AGGAATAACCGATGGAATTATCCTTTG 59.552 37.037 0.00 0.00 44.37 2.77
2056 2443 4.170468 ACCGATGGAATTATCCTTTGCT 57.830 40.909 0.00 0.00 46.70 3.91
2057 2444 4.137543 ACCGATGGAATTATCCTTTGCTC 58.862 43.478 0.00 0.00 46.70 4.26
2058 2445 4.141390 ACCGATGGAATTATCCTTTGCTCT 60.141 41.667 0.00 0.00 46.70 4.09
2059 2446 4.823989 CCGATGGAATTATCCTTTGCTCTT 59.176 41.667 0.00 0.00 46.70 2.85
2060 2447 5.997746 CCGATGGAATTATCCTTTGCTCTTA 59.002 40.000 0.00 0.00 46.70 2.10
2061 2448 6.148480 CCGATGGAATTATCCTTTGCTCTTAG 59.852 42.308 0.00 0.00 46.70 2.18
2062 2449 6.148480 CGATGGAATTATCCTTTGCTCTTAGG 59.852 42.308 0.00 0.00 46.70 2.69
2063 2450 5.694995 TGGAATTATCCTTTGCTCTTAGGG 58.305 41.667 0.00 0.00 46.70 3.53
2065 2452 6.000840 GGAATTATCCTTTGCTCTTAGGGAG 58.999 44.000 0.00 0.00 42.93 4.30
2066 2453 6.409810 GGAATTATCCTTTGCTCTTAGGGAGT 60.410 42.308 0.00 0.00 42.93 3.85
2067 2454 3.922171 ATCCTTTGCTCTTAGGGAGTG 57.078 47.619 0.00 0.00 43.62 3.51
2068 2455 1.909302 TCCTTTGCTCTTAGGGAGTGG 59.091 52.381 0.00 0.00 43.62 4.00
2069 2456 1.630878 CCTTTGCTCTTAGGGAGTGGT 59.369 52.381 0.00 0.00 43.62 4.16
2070 2457 2.355209 CCTTTGCTCTTAGGGAGTGGTC 60.355 54.545 0.00 0.00 43.62 4.02
2071 2458 2.327325 TTGCTCTTAGGGAGTGGTCT 57.673 50.000 0.00 0.00 43.62 3.85
2072 2459 2.327325 TGCTCTTAGGGAGTGGTCTT 57.673 50.000 0.00 0.00 43.62 3.01
2073 2460 3.468071 TGCTCTTAGGGAGTGGTCTTA 57.532 47.619 0.00 0.00 43.62 2.10
2074 2461 3.786553 TGCTCTTAGGGAGTGGTCTTAA 58.213 45.455 0.00 0.00 43.62 1.85
2075 2462 4.362677 TGCTCTTAGGGAGTGGTCTTAAT 58.637 43.478 0.00 0.00 43.62 1.40
2076 2463 5.525484 TGCTCTTAGGGAGTGGTCTTAATA 58.475 41.667 0.00 0.00 43.62 0.98
2077 2464 5.363005 TGCTCTTAGGGAGTGGTCTTAATAC 59.637 44.000 0.00 0.00 43.62 1.89
2078 2465 5.221481 GCTCTTAGGGAGTGGTCTTAATACC 60.221 48.000 3.09 3.09 43.62 2.73
2079 2466 4.891756 TCTTAGGGAGTGGTCTTAATACCG 59.108 45.833 5.63 0.00 42.91 4.02
2080 2467 3.393426 AGGGAGTGGTCTTAATACCGA 57.607 47.619 5.63 0.00 42.91 4.69
2081 2468 3.924922 AGGGAGTGGTCTTAATACCGAT 58.075 45.455 5.63 0.00 42.91 4.18
2082 2469 3.641906 AGGGAGTGGTCTTAATACCGATG 59.358 47.826 5.63 0.00 42.91 3.84
2083 2470 3.387050 GGGAGTGGTCTTAATACCGATGT 59.613 47.826 5.63 0.00 42.91 3.06
2084 2471 4.501058 GGGAGTGGTCTTAATACCGATGTC 60.501 50.000 5.63 0.41 42.91 3.06
2085 2472 4.341520 GGAGTGGTCTTAATACCGATGTCT 59.658 45.833 5.63 0.09 42.91 3.41
2086 2473 5.163437 GGAGTGGTCTTAATACCGATGTCTT 60.163 44.000 5.63 0.00 42.91 3.01
2087 2474 6.295719 AGTGGTCTTAATACCGATGTCTTT 57.704 37.500 5.63 0.00 42.91 2.52
2088 2475 6.338937 AGTGGTCTTAATACCGATGTCTTTC 58.661 40.000 5.63 0.00 42.91 2.62
2089 2476 6.154706 AGTGGTCTTAATACCGATGTCTTTCT 59.845 38.462 5.63 0.00 42.91 2.52
2090 2477 6.817140 GTGGTCTTAATACCGATGTCTTTCTT 59.183 38.462 5.63 0.00 42.91 2.52
2091 2478 7.333672 GTGGTCTTAATACCGATGTCTTTCTTT 59.666 37.037 5.63 0.00 42.91 2.52
2092 2479 8.533657 TGGTCTTAATACCGATGTCTTTCTTTA 58.466 33.333 5.63 0.00 42.91 1.85
2093 2480 9.374838 GGTCTTAATACCGATGTCTTTCTTTAA 57.625 33.333 0.00 0.00 0.00 1.52
2095 2482 9.374838 TCTTAATACCGATGTCTTTCTTTAACC 57.625 33.333 0.00 0.00 0.00 2.85
2096 2483 9.379791 CTTAATACCGATGTCTTTCTTTAACCT 57.620 33.333 0.00 0.00 0.00 3.50
2097 2484 9.729281 TTAATACCGATGTCTTTCTTTAACCTT 57.271 29.630 0.00 0.00 0.00 3.50
2098 2485 8.631480 AATACCGATGTCTTTCTTTAACCTTT 57.369 30.769 0.00 0.00 0.00 3.11
2099 2486 6.313744 ACCGATGTCTTTCTTTAACCTTTG 57.686 37.500 0.00 0.00 0.00 2.77
2100 2487 5.240844 ACCGATGTCTTTCTTTAACCTTTGG 59.759 40.000 0.00 0.00 0.00 3.28
2101 2488 5.335661 CCGATGTCTTTCTTTAACCTTTGGG 60.336 44.000 0.00 0.00 38.88 4.12
2102 2489 5.472137 CGATGTCTTTCTTTAACCTTTGGGA 59.528 40.000 0.00 0.00 36.25 4.37
2103 2490 6.348540 CGATGTCTTTCTTTAACCTTTGGGAG 60.349 42.308 0.00 0.00 36.25 4.30
2111 2498 4.716003 CCTTTGGGAGGTCGAACC 57.284 61.111 0.00 0.00 40.95 3.62
2128 2515 3.614806 CTCTCTCGAGGGCTTGCT 58.385 61.111 13.56 0.00 33.51 3.91
2129 2516 1.896694 CTCTCTCGAGGGCTTGCTT 59.103 57.895 13.56 0.00 33.51 3.91
2130 2517 1.107114 CTCTCTCGAGGGCTTGCTTA 58.893 55.000 13.56 0.00 33.51 3.09
2131 2518 1.478510 CTCTCTCGAGGGCTTGCTTAA 59.521 52.381 13.56 0.00 33.51 1.85
2132 2519 1.478510 TCTCTCGAGGGCTTGCTTAAG 59.521 52.381 13.56 0.00 0.00 1.85
2133 2520 1.478510 CTCTCGAGGGCTTGCTTAAGA 59.521 52.381 13.56 0.00 0.00 2.10
2134 2521 1.899814 TCTCGAGGGCTTGCTTAAGAA 59.100 47.619 13.56 0.00 0.00 2.52
2135 2522 2.501723 TCTCGAGGGCTTGCTTAAGAAT 59.498 45.455 13.56 0.00 0.00 2.40
2136 2523 3.704566 TCTCGAGGGCTTGCTTAAGAATA 59.295 43.478 13.56 0.00 0.00 1.75
2137 2524 4.161565 TCTCGAGGGCTTGCTTAAGAATAA 59.838 41.667 13.56 0.00 0.00 1.40
2138 2525 4.442706 TCGAGGGCTTGCTTAAGAATAAG 58.557 43.478 6.67 8.23 41.27 1.73
2139 2526 4.161565 TCGAGGGCTTGCTTAAGAATAAGA 59.838 41.667 6.67 0.00 40.90 2.10
2140 2527 4.876107 CGAGGGCTTGCTTAAGAATAAGAA 59.124 41.667 6.67 0.00 40.90 2.52
2141 2528 5.354234 CGAGGGCTTGCTTAAGAATAAGAAA 59.646 40.000 6.67 0.00 40.90 2.52
2163 2550 9.911788 AGAAAGAAGAATCTTATGGAAATAGCA 57.088 29.630 0.00 0.00 45.19 3.49
2166 2553 9.857656 AAGAAGAATCTTATGGAAATAGCATGA 57.142 29.630 0.00 0.00 44.11 3.07
2167 2554 9.857656 AGAAGAATCTTATGGAAATAGCATGAA 57.142 29.630 0.00 0.00 29.15 2.57
2169 2556 9.638176 AAGAATCTTATGGAAATAGCATGAAGT 57.362 29.630 0.00 0.00 0.00 3.01
2173 2560 8.908786 TCTTATGGAAATAGCATGAAGTAAGG 57.091 34.615 0.00 0.00 0.00 2.69
2174 2561 8.494433 TCTTATGGAAATAGCATGAAGTAAGGT 58.506 33.333 0.00 0.00 0.00 3.50
2175 2562 9.125026 CTTATGGAAATAGCATGAAGTAAGGTT 57.875 33.333 0.00 0.00 0.00 3.50
2185 2572 7.349598 AGCATGAAGTAAGGTTTGATCCTATT 58.650 34.615 0.00 0.00 36.74 1.73
2186 2573 7.500559 AGCATGAAGTAAGGTTTGATCCTATTC 59.499 37.037 0.00 0.00 36.74 1.75
2187 2574 7.283127 GCATGAAGTAAGGTTTGATCCTATTCA 59.717 37.037 0.00 0.00 38.16 2.57
2188 2575 9.177608 CATGAAGTAAGGTTTGATCCTATTCAA 57.822 33.333 9.98 0.00 37.76 2.69
2189 2576 8.792830 TGAAGTAAGGTTTGATCCTATTCAAG 57.207 34.615 0.00 0.00 36.97 3.02
2191 2578 6.663734 AGTAAGGTTTGATCCTATTCAAGGG 58.336 40.000 0.00 0.00 46.55 3.95
2192 2579 4.526438 AGGTTTGATCCTATTCAAGGGG 57.474 45.455 0.00 0.00 46.55 4.79
2193 2580 4.119155 AGGTTTGATCCTATTCAAGGGGA 58.881 43.478 0.00 0.00 46.55 4.81
2194 2581 4.733988 AGGTTTGATCCTATTCAAGGGGAT 59.266 41.667 0.00 0.00 46.55 3.85
2196 2583 5.536538 GGTTTGATCCTATTCAAGGGGATTC 59.463 44.000 0.00 0.00 46.55 2.52
2197 2584 5.324832 TTGATCCTATTCAAGGGGATTCC 57.675 43.478 0.00 0.00 46.55 3.01
2199 2586 2.771688 TCCTATTCAAGGGGATTCCGT 58.228 47.619 0.00 0.00 46.55 4.69
2200 2587 3.931317 TCCTATTCAAGGGGATTCCGTA 58.069 45.455 0.00 0.00 46.55 4.02
2201 2588 4.300345 TCCTATTCAAGGGGATTCCGTAA 58.700 43.478 0.00 0.00 46.55 3.18
2203 2590 5.371472 TCCTATTCAAGGGGATTCCGTAAAT 59.629 40.000 0.00 0.00 46.55 1.40
2204 2591 6.559539 TCCTATTCAAGGGGATTCCGTAAATA 59.440 38.462 0.00 0.00 46.55 1.40
2205 2592 7.238933 TCCTATTCAAGGGGATTCCGTAAATAT 59.761 37.037 0.00 0.00 46.55 1.28
2207 2594 5.237236 TCAAGGGGATTCCGTAAATATCC 57.763 43.478 0.00 0.00 41.52 2.59
2231 2684 3.549873 GCTTCTACAGCTCGTTGATCTTC 59.450 47.826 0.00 0.00 46.27 2.87
2287 2740 7.432869 AGTGCTAACATAGTTTTCATTGCAAA 58.567 30.769 1.71 0.00 0.00 3.68
2324 2777 2.691409 TGCATGTTAGCTACCCTGTC 57.309 50.000 0.00 0.00 34.99 3.51
2348 2801 5.280830 CCATGACATCCATCCATCTAATCCA 60.281 44.000 0.00 0.00 31.94 3.41
2351 2804 5.789054 TGACATCCATCCATCTAATCCATCT 59.211 40.000 0.00 0.00 0.00 2.90
2394 2847 9.915629 CTTTCTAGTGACACTAGTAGAAAACAT 57.084 33.333 32.02 2.02 46.31 2.71
2416 2869 2.951726 GCTTTGGTTGAAGCTCAATCC 58.048 47.619 2.57 7.92 46.55 3.01
2445 2923 0.322322 TCCCGGTTGCATTACGAACT 59.678 50.000 0.00 0.00 0.00 3.01
2486 2989 1.381928 CCCAGTTCGAGCGGCTAGTA 61.382 60.000 0.60 0.00 0.00 1.82
2543 3133 2.610438 TTAGTCCCGGTAGGTGTCTT 57.390 50.000 0.00 0.00 36.75 3.01
2547 3137 1.553704 GTCCCGGTAGGTGTCTTCAAT 59.446 52.381 0.00 0.00 36.75 2.57
2561 3151 5.520649 GTGTCTTCAATCGGGACTAAAGATC 59.479 44.000 0.00 0.00 0.00 2.75
2771 3622 8.614469 TCAAAATTTTGTCCAGTTTCTGTTTT 57.386 26.923 25.98 0.00 39.18 2.43
2841 3692 4.519540 TTTGCTTCAAACCCTAGATTGC 57.480 40.909 0.00 0.00 0.00 3.56
3080 3932 5.877012 ACATTGTGGTATGCTTCTGTTAGAG 59.123 40.000 0.00 0.00 0.00 2.43
3230 4096 4.629200 CACTTCAATAGAACCTGACTCTGC 59.371 45.833 0.00 0.00 0.00 4.26
3240 4106 2.441750 ACCTGACTCTGCCTTGGTTAAA 59.558 45.455 0.00 0.00 0.00 1.52
3284 4154 1.405463 CGGTGCTAGCAGATGTAGTCA 59.595 52.381 20.03 0.00 0.00 3.41
3288 4158 2.492088 TGCTAGCAGATGTAGTCAACGT 59.508 45.455 14.93 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.933097 CTGATGTGCCGCATGTAGTC 59.067 55.000 0.00 0.00 38.06 2.59
22 23 7.025365 CCATTATTTTCATATCTGATGTGCCG 58.975 38.462 9.28 0.00 0.00 5.69
54 55 9.770097 GAAGATACATGAATTATGGTCTCAGAA 57.230 33.333 0.00 0.00 41.25 3.02
55 56 9.152327 AGAAGATACATGAATTATGGTCTCAGA 57.848 33.333 0.00 0.00 41.25 3.27
56 57 9.205719 CAGAAGATACATGAATTATGGTCTCAG 57.794 37.037 0.00 0.00 41.25 3.35
57 58 7.658982 GCAGAAGATACATGAATTATGGTCTCA 59.341 37.037 0.00 0.00 41.25 3.27
58 59 7.658982 TGCAGAAGATACATGAATTATGGTCTC 59.341 37.037 0.00 0.00 41.25 3.36
59 60 7.512130 TGCAGAAGATACATGAATTATGGTCT 58.488 34.615 0.00 0.00 41.25 3.85
60 61 7.734924 TGCAGAAGATACATGAATTATGGTC 57.265 36.000 0.00 0.00 41.25 4.02
61 62 7.309012 GCATGCAGAAGATACATGAATTATGGT 60.309 37.037 14.21 0.00 43.04 3.55
63 64 7.817641 AGCATGCAGAAGATACATGAATTATG 58.182 34.615 21.98 0.00 43.04 1.90
64 65 7.997773 AGCATGCAGAAGATACATGAATTAT 57.002 32.000 21.98 0.00 43.04 1.28
65 66 7.255346 CCAAGCATGCAGAAGATACATGAATTA 60.255 37.037 21.98 0.00 43.04 1.40
66 67 6.461092 CCAAGCATGCAGAAGATACATGAATT 60.461 38.462 21.98 0.00 43.04 2.17
67 68 5.009710 CCAAGCATGCAGAAGATACATGAAT 59.990 40.000 21.98 0.00 43.04 2.57
68 69 4.337274 CCAAGCATGCAGAAGATACATGAA 59.663 41.667 21.98 0.00 43.04 2.57
70 71 3.630769 ACCAAGCATGCAGAAGATACATG 59.369 43.478 21.98 0.00 43.21 3.21
71 72 3.881688 GACCAAGCATGCAGAAGATACAT 59.118 43.478 21.98 0.00 0.00 2.29
72 73 3.273434 GACCAAGCATGCAGAAGATACA 58.727 45.455 21.98 0.00 0.00 2.29
73 74 3.273434 TGACCAAGCATGCAGAAGATAC 58.727 45.455 21.98 4.01 0.00 2.24
75 76 2.502142 TGACCAAGCATGCAGAAGAT 57.498 45.000 21.98 0.00 0.00 2.40
76 77 2.275134 TTGACCAAGCATGCAGAAGA 57.725 45.000 21.98 0.00 0.00 2.87
77 78 3.587797 AATTGACCAAGCATGCAGAAG 57.412 42.857 21.98 7.97 0.00 2.85
78 79 5.664294 ATTAATTGACCAAGCATGCAGAA 57.336 34.783 21.98 3.01 0.00 3.02
79 80 5.300034 CCTATTAATTGACCAAGCATGCAGA 59.700 40.000 21.98 0.00 0.00 4.26
80 81 5.300034 TCCTATTAATTGACCAAGCATGCAG 59.700 40.000 21.98 11.91 0.00 4.41
81 82 5.199723 TCCTATTAATTGACCAAGCATGCA 58.800 37.500 21.98 0.00 0.00 3.96
102 103 7.579761 AAAAGCAATCTCCTCTTATCATTCC 57.420 36.000 0.00 0.00 0.00 3.01
141 142 0.470341 GTGACCAGCCCTCTTATCCC 59.530 60.000 0.00 0.00 0.00 3.85
143 144 4.899352 ATATGTGACCAGCCCTCTTATC 57.101 45.455 0.00 0.00 0.00 1.75
179 185 0.103208 AAACGCACATGGCCGAAAAA 59.897 45.000 13.16 0.00 40.31 1.94
184 190 0.727793 GTAACAAACGCACATGGCCG 60.728 55.000 0.00 1.26 40.31 6.13
230 236 7.468141 AACATGTGCGAGATAGGATATCTAA 57.532 36.000 0.00 0.00 0.00 2.10
233 239 6.870965 AGAAAACATGTGCGAGATAGGATATC 59.129 38.462 0.00 0.00 0.00 1.63
241 247 3.668447 ACAGAGAAAACATGTGCGAGAT 58.332 40.909 0.00 0.00 0.00 2.75
277 286 5.216622 AGTATCATGCCTCTTACCTGGTAA 58.783 41.667 17.82 17.82 0.00 2.85
296 305 7.387673 GCCAAAGCAACCTTTTGATAAAAGTAT 59.612 33.333 11.70 0.00 41.62 2.12
299 308 5.759763 AGCCAAAGCAACCTTTTGATAAAAG 59.240 36.000 6.99 6.99 43.68 2.27
305 314 1.138661 CCAGCCAAAGCAACCTTTTGA 59.861 47.619 0.00 0.00 43.56 2.69
337 346 9.757227 AGATAATCAACATGTAGACTTTCTAGC 57.243 33.333 0.00 0.00 28.01 3.42
349 358 3.711704 ACCCCTCGAGATAATCAACATGT 59.288 43.478 15.71 0.00 0.00 3.21
350 359 4.342862 ACCCCTCGAGATAATCAACATG 57.657 45.455 15.71 0.00 0.00 3.21
351 360 5.126067 CAAACCCCTCGAGATAATCAACAT 58.874 41.667 15.71 0.00 0.00 2.71
352 361 4.513442 CAAACCCCTCGAGATAATCAACA 58.487 43.478 15.71 0.00 0.00 3.33
353 362 3.877508 CCAAACCCCTCGAGATAATCAAC 59.122 47.826 15.71 0.00 0.00 3.18
354 363 3.778075 TCCAAACCCCTCGAGATAATCAA 59.222 43.478 15.71 0.00 0.00 2.57
355 364 3.380393 TCCAAACCCCTCGAGATAATCA 58.620 45.455 15.71 0.00 0.00 2.57
356 365 4.417426 TTCCAAACCCCTCGAGATAATC 57.583 45.455 15.71 0.00 0.00 1.75
358 367 4.855298 AATTCCAAACCCCTCGAGATAA 57.145 40.909 15.71 0.00 0.00 1.75
360 369 4.855298 TTAATTCCAAACCCCTCGAGAT 57.145 40.909 15.71 0.00 0.00 2.75
361 370 4.287585 TCTTTAATTCCAAACCCCTCGAGA 59.712 41.667 15.71 0.00 0.00 4.04
362 371 4.585879 TCTTTAATTCCAAACCCCTCGAG 58.414 43.478 5.13 5.13 0.00 4.04
363 372 4.566907 CCTCTTTAATTCCAAACCCCTCGA 60.567 45.833 0.00 0.00 0.00 4.04
364 373 3.694566 CCTCTTTAATTCCAAACCCCTCG 59.305 47.826 0.00 0.00 0.00 4.63
372 633 8.311109 GTTTATTTCCAGCCTCTTTAATTCCAA 58.689 33.333 0.00 0.00 0.00 3.53
531 792 1.124839 GAAAAGCTTTCGCATTTGCCG 59.875 47.619 13.10 0.00 37.20 5.69
546 807 4.555116 GCCAACACAAATTGCCATGAAAAG 60.555 41.667 0.00 0.00 0.00 2.27
645 906 7.874940 TGAGACAGAATGACAAATCGATTTTT 58.125 30.769 20.56 14.88 39.69 1.94
718 979 4.753516 AAGTACCCATGATTCGTCATCA 57.246 40.909 0.00 3.08 46.41 3.07
950 1248 2.409651 CCTACCGAGACGCTGCTC 59.590 66.667 0.00 0.00 0.00 4.26
1050 1358 3.910490 GATCTCGCCGGAGCAGCT 61.910 66.667 5.05 0.00 40.26 4.24
1075 1383 3.332493 GACGCGCACCTACTCCGAA 62.332 63.158 5.73 0.00 0.00 4.30
1080 1388 2.572284 GAAGGACGCGCACCTACT 59.428 61.111 22.34 10.61 36.67 2.57
1343 1651 7.879677 TGCGGTATCAATTATCTTCAATGATCT 59.120 33.333 0.00 0.00 0.00 2.75
1371 1679 6.150140 AGACATTTGAACAAGAGATAGGTTGC 59.850 38.462 0.00 0.00 0.00 4.17
1376 1684 9.809096 TTAGCTAGACATTTGAACAAGAGATAG 57.191 33.333 0.00 0.00 0.00 2.08
1406 1714 4.778904 CACACCAAGTTTACACAATACGG 58.221 43.478 0.00 0.00 0.00 4.02
1477 1785 2.552367 CCAGAGAGGTCCTAAAAGGGT 58.448 52.381 0.00 0.00 35.59 4.34
1494 1802 8.430801 TTTTCCATTTGTATGTTTTGAACCAG 57.569 30.769 0.00 0.00 0.00 4.00
1539 1909 8.134895 GCAAAGGATAATTTCATCGGTTATTCA 58.865 33.333 0.00 0.00 0.00 2.57
1814 2184 1.134220 AGTGGGTCAGAGCGAACAAAA 60.134 47.619 6.79 0.00 30.31 2.44
1877 2254 5.012664 TCCTTGGTGAAGTGTGTGTACATAT 59.987 40.000 0.00 0.00 39.39 1.78
2003 2390 9.703892 CTTTGAACCAAACATATACATTTTCCA 57.296 29.630 0.00 0.00 0.00 3.53
2004 2391 9.150348 CCTTTGAACCAAACATATACATTTTCC 57.850 33.333 0.00 0.00 0.00 3.13
2005 2392 9.921637 TCCTTTGAACCAAACATATACATTTTC 57.078 29.630 0.00 0.00 0.00 2.29
2011 2398 9.797556 GGTTATTCCTTTGAACCAAACATATAC 57.202 33.333 0.00 0.00 41.93 1.47
2012 2399 8.679100 CGGTTATTCCTTTGAACCAAACATATA 58.321 33.333 4.09 0.00 42.36 0.86
2014 2401 6.715718 TCGGTTATTCCTTTGAACCAAACATA 59.284 34.615 4.09 0.00 42.36 2.29
2016 2403 4.888239 TCGGTTATTCCTTTGAACCAAACA 59.112 37.500 4.09 0.00 42.36 2.83
2017 2404 5.441709 TCGGTTATTCCTTTGAACCAAAC 57.558 39.130 4.09 0.00 42.36 2.93
2020 2407 4.013728 CCATCGGTTATTCCTTTGAACCA 58.986 43.478 4.09 0.00 42.36 3.67
2021 2408 4.266714 TCCATCGGTTATTCCTTTGAACC 58.733 43.478 0.00 0.00 39.44 3.62
2022 2409 5.890424 TTCCATCGGTTATTCCTTTGAAC 57.110 39.130 0.00 0.00 32.13 3.18
2023 2410 8.760980 ATAATTCCATCGGTTATTCCTTTGAA 57.239 30.769 0.00 0.00 34.33 2.69
2024 2411 7.447238 GGATAATTCCATCGGTTATTCCTTTGA 59.553 37.037 0.00 0.00 42.12 2.69
2025 2412 7.448469 AGGATAATTCCATCGGTTATTCCTTTG 59.552 37.037 0.00 0.00 45.30 2.77
2026 2413 7.526918 AGGATAATTCCATCGGTTATTCCTTT 58.473 34.615 0.00 0.00 45.30 3.11
2027 2414 7.091533 AGGATAATTCCATCGGTTATTCCTT 57.908 36.000 0.00 0.00 45.30 3.36
2029 2416 7.593825 CAAAGGATAATTCCATCGGTTATTCC 58.406 38.462 0.00 0.00 45.30 3.01
2030 2417 7.040409 AGCAAAGGATAATTCCATCGGTTATTC 60.040 37.037 0.00 0.00 45.30 1.75
2032 2419 6.306987 AGCAAAGGATAATTCCATCGGTTAT 58.693 36.000 0.00 0.00 45.30 1.89
2033 2420 5.690865 AGCAAAGGATAATTCCATCGGTTA 58.309 37.500 0.00 0.00 45.30 2.85
2034 2421 4.536765 AGCAAAGGATAATTCCATCGGTT 58.463 39.130 0.00 0.00 45.30 4.44
2035 2422 4.137543 GAGCAAAGGATAATTCCATCGGT 58.862 43.478 0.00 0.00 45.30 4.69
2037 2424 6.148480 CCTAAGAGCAAAGGATAATTCCATCG 59.852 42.308 0.00 0.00 45.30 3.84
2040 2427 5.431731 TCCCTAAGAGCAAAGGATAATTCCA 59.568 40.000 0.00 0.00 45.30 3.53
2041 2428 5.941788 TCCCTAAGAGCAAAGGATAATTCC 58.058 41.667 0.00 0.00 42.96 3.01
2054 2441 8.398200 CGGTATTAAGACCACTCCCTAAGAGC 62.398 50.000 18.92 0.00 38.69 4.09
2056 2443 4.891756 CGGTATTAAGACCACTCCCTAAGA 59.108 45.833 18.92 0.00 39.72 2.10
2057 2444 4.891756 TCGGTATTAAGACCACTCCCTAAG 59.108 45.833 18.92 0.00 39.72 2.18
2058 2445 4.870636 TCGGTATTAAGACCACTCCCTAA 58.129 43.478 18.92 0.00 39.72 2.69
2059 2446 4.524802 TCGGTATTAAGACCACTCCCTA 57.475 45.455 18.92 0.00 39.72 3.53
2060 2447 3.393426 TCGGTATTAAGACCACTCCCT 57.607 47.619 18.92 0.00 39.72 4.20
2061 2448 3.387050 ACATCGGTATTAAGACCACTCCC 59.613 47.826 18.92 0.00 39.72 4.30
2062 2449 4.341520 AGACATCGGTATTAAGACCACTCC 59.658 45.833 18.92 4.23 39.72 3.85
2063 2450 5.517322 AGACATCGGTATTAAGACCACTC 57.483 43.478 18.92 7.12 39.72 3.51
2065 2452 6.338937 AGAAAGACATCGGTATTAAGACCAC 58.661 40.000 18.92 5.03 39.72 4.16
2066 2453 6.540438 AGAAAGACATCGGTATTAAGACCA 57.460 37.500 18.92 6.93 39.72 4.02
2067 2454 7.845066 AAAGAAAGACATCGGTATTAAGACC 57.155 36.000 9.32 9.32 36.00 3.85
2069 2456 9.374838 GGTTAAAGAAAGACATCGGTATTAAGA 57.625 33.333 0.00 0.00 0.00 2.10
2070 2457 9.379791 AGGTTAAAGAAAGACATCGGTATTAAG 57.620 33.333 0.00 0.00 0.00 1.85
2071 2458 9.729281 AAGGTTAAAGAAAGACATCGGTATTAA 57.271 29.630 0.00 0.00 0.00 1.40
2072 2459 9.729281 AAAGGTTAAAGAAAGACATCGGTATTA 57.271 29.630 0.00 0.00 0.00 0.98
2073 2460 8.512138 CAAAGGTTAAAGAAAGACATCGGTATT 58.488 33.333 0.00 0.00 0.00 1.89
2074 2461 7.120726 CCAAAGGTTAAAGAAAGACATCGGTAT 59.879 37.037 0.00 0.00 0.00 2.73
2075 2462 6.428771 CCAAAGGTTAAAGAAAGACATCGGTA 59.571 38.462 0.00 0.00 0.00 4.02
2076 2463 5.240844 CCAAAGGTTAAAGAAAGACATCGGT 59.759 40.000 0.00 0.00 0.00 4.69
2077 2464 5.335661 CCCAAAGGTTAAAGAAAGACATCGG 60.336 44.000 0.00 0.00 0.00 4.18
2078 2465 5.472137 TCCCAAAGGTTAAAGAAAGACATCG 59.528 40.000 0.00 0.00 0.00 3.84
2079 2466 6.071896 CCTCCCAAAGGTTAAAGAAAGACATC 60.072 42.308 0.00 0.00 40.67 3.06
2080 2467 5.775195 CCTCCCAAAGGTTAAAGAAAGACAT 59.225 40.000 0.00 0.00 40.67 3.06
2081 2468 5.137551 CCTCCCAAAGGTTAAAGAAAGACA 58.862 41.667 0.00 0.00 40.67 3.41
2082 2469 5.707242 CCTCCCAAAGGTTAAAGAAAGAC 57.293 43.478 0.00 0.00 40.67 3.01
2112 2499 1.478510 CTTAAGCAAGCCCTCGAGAGA 59.521 52.381 15.71 0.00 39.12 3.10
2113 2500 1.478510 TCTTAAGCAAGCCCTCGAGAG 59.521 52.381 15.71 0.16 0.00 3.20
2114 2501 1.557099 TCTTAAGCAAGCCCTCGAGA 58.443 50.000 15.71 0.00 0.00 4.04
2115 2502 2.386661 TTCTTAAGCAAGCCCTCGAG 57.613 50.000 5.13 5.13 0.00 4.04
2116 2503 4.161565 TCTTATTCTTAAGCAAGCCCTCGA 59.838 41.667 0.00 0.00 35.72 4.04
2117 2504 4.442706 TCTTATTCTTAAGCAAGCCCTCG 58.557 43.478 0.00 0.00 35.72 4.63
2118 2505 6.599638 TCTTTCTTATTCTTAAGCAAGCCCTC 59.400 38.462 0.00 0.00 38.09 4.30
2119 2506 6.485171 TCTTTCTTATTCTTAAGCAAGCCCT 58.515 36.000 0.00 0.00 38.09 5.19
2120 2507 6.759497 TCTTTCTTATTCTTAAGCAAGCCC 57.241 37.500 0.00 0.00 38.09 5.19
2121 2508 8.045176 TCTTCTTTCTTATTCTTAAGCAAGCC 57.955 34.615 0.00 0.00 38.09 4.35
2137 2524 9.911788 TGCTATTTCCATAAGATTCTTCTTTCT 57.088 29.630 1.27 0.00 42.29 2.52
2140 2527 9.857656 TCATGCTATTTCCATAAGATTCTTCTT 57.142 29.630 1.27 0.00 44.44 2.52
2141 2528 9.857656 TTCATGCTATTTCCATAAGATTCTTCT 57.142 29.630 1.27 0.00 0.00 2.85
2143 2530 9.638176 ACTTCATGCTATTTCCATAAGATTCTT 57.362 29.630 4.03 4.03 0.00 2.52
2147 2534 9.512588 CCTTACTTCATGCTATTTCCATAAGAT 57.487 33.333 0.00 0.00 0.00 2.40
2148 2535 8.494433 ACCTTACTTCATGCTATTTCCATAAGA 58.506 33.333 0.00 0.00 0.00 2.10
2149 2536 8.682936 ACCTTACTTCATGCTATTTCCATAAG 57.317 34.615 0.00 0.00 0.00 1.73
2150 2537 9.474313 AAACCTTACTTCATGCTATTTCCATAA 57.526 29.630 0.00 0.00 0.00 1.90
2151 2538 8.902806 CAAACCTTACTTCATGCTATTTCCATA 58.097 33.333 0.00 0.00 0.00 2.74
2152 2539 7.615365 TCAAACCTTACTTCATGCTATTTCCAT 59.385 33.333 0.00 0.00 0.00 3.41
2153 2540 6.945435 TCAAACCTTACTTCATGCTATTTCCA 59.055 34.615 0.00 0.00 0.00 3.53
2154 2541 7.391148 TCAAACCTTACTTCATGCTATTTCC 57.609 36.000 0.00 0.00 0.00 3.13
2155 2542 8.131731 GGATCAAACCTTACTTCATGCTATTTC 58.868 37.037 0.00 0.00 0.00 2.17
2156 2543 7.836183 AGGATCAAACCTTACTTCATGCTATTT 59.164 33.333 0.00 0.00 36.86 1.40
2157 2544 7.349598 AGGATCAAACCTTACTTCATGCTATT 58.650 34.615 0.00 0.00 36.86 1.73
2158 2545 6.904626 AGGATCAAACCTTACTTCATGCTAT 58.095 36.000 0.00 0.00 36.86 2.97
2159 2546 6.313519 AGGATCAAACCTTACTTCATGCTA 57.686 37.500 0.00 0.00 36.86 3.49
2160 2547 5.184892 AGGATCAAACCTTACTTCATGCT 57.815 39.130 0.00 0.00 36.86 3.79
2161 2548 7.283127 TGAATAGGATCAAACCTTACTTCATGC 59.717 37.037 0.00 0.00 41.00 4.06
2162 2549 8.737168 TGAATAGGATCAAACCTTACTTCATG 57.263 34.615 0.00 0.00 41.00 3.07
2163 2550 9.401058 CTTGAATAGGATCAAACCTTACTTCAT 57.599 33.333 0.00 0.00 38.75 2.57
2164 2551 8.792830 CTTGAATAGGATCAAACCTTACTTCA 57.207 34.615 0.00 0.00 38.75 3.02
2185 2572 5.237236 GGATATTTACGGAATCCCCTTGA 57.763 43.478 0.00 0.00 34.30 3.02
2191 2578 3.329929 AGCGGGATATTTACGGAATCC 57.670 47.619 0.00 0.00 38.79 3.01
2192 2579 4.566987 AGAAGCGGGATATTTACGGAATC 58.433 43.478 0.00 0.00 0.00 2.52
2193 2580 4.618920 AGAAGCGGGATATTTACGGAAT 57.381 40.909 0.00 0.00 0.00 3.01
2194 2581 4.341806 TGTAGAAGCGGGATATTTACGGAA 59.658 41.667 0.00 0.00 0.00 4.30
2196 2583 4.235360 CTGTAGAAGCGGGATATTTACGG 58.765 47.826 0.00 0.00 0.00 4.02
2197 2584 3.673809 GCTGTAGAAGCGGGATATTTACG 59.326 47.826 0.00 0.00 43.45 3.18
2231 2684 5.180117 GGTATTATTATCAGTGCAGGTGCTG 59.820 44.000 3.18 0.00 42.66 4.41
2287 2740 6.003950 ACATGCATACTTACCAACTGACTTT 58.996 36.000 0.00 0.00 0.00 2.66
2324 2777 5.191426 GGATTAGATGGATGGATGTCATGG 58.809 45.833 0.00 0.00 35.97 3.66
2376 2829 5.483685 AGCCATGTTTTCTACTAGTGTCA 57.516 39.130 5.39 0.00 0.00 3.58
2416 2869 0.802494 GCAACCGGGACTAATGTGTG 59.198 55.000 6.32 0.00 0.00 3.82
2470 2973 1.720301 CGTACTAGCCGCTCGAACT 59.280 57.895 0.00 0.00 0.00 3.01
2543 3133 4.099573 GGTCTGATCTTTAGTCCCGATTGA 59.900 45.833 0.00 0.00 0.00 2.57
2547 3137 3.383698 AGGTCTGATCTTTAGTCCCGA 57.616 47.619 0.00 0.00 0.00 5.14
2561 3151 1.338769 CCAACCGGGACTAAAGGTCTG 60.339 57.143 6.32 0.00 43.97 3.51
2638 3254 2.735259 TCAGAACCCCTTTAGTCCCT 57.265 50.000 0.00 0.00 0.00 4.20
2724 3573 8.761575 TTGAATCTAATGCAAAAAGAATCACC 57.238 30.769 11.49 0.00 30.82 4.02
2879 3730 7.168219 TCTAACATGTGACTAGGAGCAAAAAT 58.832 34.615 0.00 0.00 0.00 1.82
3057 3909 6.108687 TCTCTAACAGAAGCATACCACAATG 58.891 40.000 0.00 0.00 0.00 2.82
3058 3910 6.299805 TCTCTAACAGAAGCATACCACAAT 57.700 37.500 0.00 0.00 0.00 2.71
3212 4078 3.902881 AGGCAGAGTCAGGTTCTATTG 57.097 47.619 0.00 0.00 0.00 1.90
3230 4096 6.937436 AGTGACAACTAAGTTTAACCAAGG 57.063 37.500 0.00 0.00 33.79 3.61
3240 4106 3.055094 CCCAGCCATAGTGACAACTAAGT 60.055 47.826 0.00 0.00 42.17 2.24
3284 4154 4.007659 GGTGTCCATCCAATTCTAACGTT 58.992 43.478 5.88 5.88 0.00 3.99


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

AutoCloner maintained by Alex Coulton.