Multiple sequence alignment - TraesCS7D01G235300

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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 TraesCS7D01G235300 chr7D 100.000 2630 0 0 1 2630 197917568 197914939 0.000000e+00 4857
1 TraesCS7D01G235300 chr7D 90.293 1535 126 14 3 1516 349039377 349040909 0.000000e+00 1988
2 TraesCS7D01G235300 chr7D 92.866 813 51 5 1505 2311 431845075 431844264 0.000000e+00 1173
3 TraesCS7D01G235300 chr7D 99.060 319 3 0 2312 2630 61254230 61254548 8.170000e-160 573
4 TraesCS7D01G235300 chr7D 98.746 319 4 0 2312 2630 618095252 618095570 3.800000e-158 568
5 TraesCS7D01G235300 chr7D 88.710 372 31 9 3 363 198898967 198898596 6.680000e-121 444
6 TraesCS7D01G235300 chr5D 90.933 1533 118 10 3 1516 129684346 129685876 0.000000e+00 2041
7 TraesCS7D01G235300 chr5D 89.494 1542 129 11 3 1516 193499004 193497468 0.000000e+00 1919
8 TraesCS7D01G235300 chr5D 98.746 319 4 0 2312 2630 472423697 472423379 3.800000e-158 568
9 TraesCS7D01G235300 chr5D 97.598 333 5 2 2298 2630 552595883 552596212 3.800000e-158 568
10 TraesCS7D01G235300 chr3D 90.085 1533 132 6 3 1516 363920517 363922048 0.000000e+00 1971
11 TraesCS7D01G235300 chr3D 89.725 1528 137 9 7 1516 104492780 104494305 0.000000e+00 1934
12 TraesCS7D01G235300 chr3D 89.808 1511 134 9 25 1516 324823037 324824546 0.000000e+00 1919
13 TraesCS7D01G235300 chr3D 92.355 811 58 2 1505 2311 465572035 465572845 0.000000e+00 1151
14 TraesCS7D01G235300 chr3D 92.193 807 58 3 1505 2311 462520559 462519758 0.000000e+00 1136
15 TraesCS7D01G235300 chr3D 87.621 517 51 3 3 508 471668834 471669348 2.920000e-164 588
16 TraesCS7D01G235300 chr3D 98.746 319 4 0 2312 2630 614960647 614960329 3.800000e-158 568
17 TraesCS7D01G235300 chr3D 98.142 323 6 0 2308 2630 581261088 581261410 4.910000e-157 564
18 TraesCS7D01G235300 chr6D 89.765 1534 134 10 3 1516 210561625 210560095 0.000000e+00 1941
19 TraesCS7D01G235300 chr6D 89.940 1511 128 11 3 1493 218569588 218571094 0.000000e+00 1927
20 TraesCS7D01G235300 chr6D 85.122 531 55 17 3 524 309213288 309213803 3.000000e-144 521
21 TraesCS7D01G235300 chr6D 88.204 373 33 1 3 364 50981161 50981533 4.020000e-118 435
22 TraesCS7D01G235300 chr6D 91.509 318 16 1 3 309 65077950 65077633 6.730000e-116 427
23 TraesCS7D01G235300 chr6D 81.517 211 30 7 3 209 337103555 337103760 5.820000e-37 165
24 TraesCS7D01G235300 chr1D 88.197 1525 158 14 3 1515 297638228 297639742 0.000000e+00 1799
25 TraesCS7D01G235300 chr1D 91.862 811 62 4 1505 2311 205348306 205349116 0.000000e+00 1129
26 TraesCS7D01G235300 chr1D 98.438 320 5 0 2311 2630 431748725 431749044 4.910000e-157 564
27 TraesCS7D01G235300 chr1D 90.323 372 25 2 3 363 431240893 431241264 6.590000e-131 477
28 TraesCS7D01G235300 chr2D 94.431 808 45 0 1504 2311 284454651 284455458 0.000000e+00 1243
29 TraesCS7D01G235300 chr2D 98.746 319 4 0 2312 2630 633508397 633508715 3.800000e-158 568
30 TraesCS7D01G235300 chr2D 97.590 332 7 1 2299 2630 648855375 648855705 3.800000e-158 568
31 TraesCS7D01G235300 chr4D 93.185 807 55 0 1505 2311 160018155 160017349 0.000000e+00 1186
32 TraesCS7D01G235300 chr4D 93.078 809 53 3 1505 2311 287040014 287040821 0.000000e+00 1181
33 TraesCS7D01G235300 chr4D 92.365 812 59 2 1503 2311 301211082 301211893 0.000000e+00 1153
34 TraesCS7D01G235300 chr4D 92.193 807 60 3 1505 2311 236293929 236293126 0.000000e+00 1138
35 TraesCS7D01G235300 chr7A 86.264 364 19 9 3 353 556826458 556826113 1.490000e-97 366


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 TraesCS7D01G235300 chr7D 197914939 197917568 2629 True 4857 4857 100.000 1 2630 1 chr7D.!!$R1 2629
1 TraesCS7D01G235300 chr7D 349039377 349040909 1532 False 1988 1988 90.293 3 1516 1 chr7D.!!$F2 1513
2 TraesCS7D01G235300 chr7D 431844264 431845075 811 True 1173 1173 92.866 1505 2311 1 chr7D.!!$R3 806
3 TraesCS7D01G235300 chr5D 129684346 129685876 1530 False 2041 2041 90.933 3 1516 1 chr5D.!!$F1 1513
4 TraesCS7D01G235300 chr5D 193497468 193499004 1536 True 1919 1919 89.494 3 1516 1 chr5D.!!$R1 1513
5 TraesCS7D01G235300 chr3D 363920517 363922048 1531 False 1971 1971 90.085 3 1516 1 chr3D.!!$F3 1513
6 TraesCS7D01G235300 chr3D 104492780 104494305 1525 False 1934 1934 89.725 7 1516 1 chr3D.!!$F1 1509
7 TraesCS7D01G235300 chr3D 324823037 324824546 1509 False 1919 1919 89.808 25 1516 1 chr3D.!!$F2 1491
8 TraesCS7D01G235300 chr3D 465572035 465572845 810 False 1151 1151 92.355 1505 2311 1 chr3D.!!$F4 806
9 TraesCS7D01G235300 chr3D 462519758 462520559 801 True 1136 1136 92.193 1505 2311 1 chr3D.!!$R1 806
10 TraesCS7D01G235300 chr3D 471668834 471669348 514 False 588 588 87.621 3 508 1 chr3D.!!$F5 505
11 TraesCS7D01G235300 chr6D 210560095 210561625 1530 True 1941 1941 89.765 3 1516 1 chr6D.!!$R2 1513
12 TraesCS7D01G235300 chr6D 218569588 218571094 1506 False 1927 1927 89.940 3 1493 1 chr6D.!!$F2 1490
13 TraesCS7D01G235300 chr6D 309213288 309213803 515 False 521 521 85.122 3 524 1 chr6D.!!$F3 521
14 TraesCS7D01G235300 chr1D 297638228 297639742 1514 False 1799 1799 88.197 3 1515 1 chr1D.!!$F2 1512
15 TraesCS7D01G235300 chr1D 205348306 205349116 810 False 1129 1129 91.862 1505 2311 1 chr1D.!!$F1 806
16 TraesCS7D01G235300 chr2D 284454651 284455458 807 False 1243 1243 94.431 1504 2311 1 chr2D.!!$F1 807
17 TraesCS7D01G235300 chr4D 160017349 160018155 806 True 1186 1186 93.185 1505 2311 1 chr4D.!!$R1 806
18 TraesCS7D01G235300 chr4D 287040014 287040821 807 False 1181 1181 93.078 1505 2311 1 chr4D.!!$F1 806
19 TraesCS7D01G235300 chr4D 301211082 301211893 811 False 1153 1153 92.365 1503 2311 1 chr4D.!!$F2 808
20 TraesCS7D01G235300 chr4D 236293126 236293929 803 True 1138 1138 92.193 1505 2311 1 chr4D.!!$R2 806

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
536 598 0.106918 ACCTGCCCGTCTGACAAAAA 60.107 50.0 8.73 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2415 0.035056 AACTGCCCTGTGACCTATGC 60.035 55.0 0.0 0.0 0.0 3.14 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
25 26 2.027653 TGGTCTTGTTGCACCGATATGA 60.028 45.455 0.00 0.00 35.15 2.15
84 85 2.656947 TGCCTCTTTAGCACCAAAGT 57.343 45.000 5.66 0.00 36.94 2.66
88 89 3.077359 CCTCTTTAGCACCAAAGTGGAG 58.923 50.000 15.81 0.00 45.63 3.86
138 170 1.802508 CGTCATGGCTTGCGTCATAGA 60.803 52.381 0.00 0.00 32.69 1.98
175 207 1.110442 CTCGCCTTGATCTCTCCACT 58.890 55.000 0.00 0.00 0.00 4.00
536 598 0.106918 ACCTGCCCGTCTGACAAAAA 60.107 50.000 8.73 0.00 0.00 1.94
642 704 3.626729 CCAGATCTGCTTCAATCCCCTTT 60.627 47.826 17.76 0.00 0.00 3.11
746 809 0.891373 CTCAGAGAAGAACCTCGCCA 59.109 55.000 0.00 0.00 38.19 5.69
852 915 1.208293 GAGCACCTTCTACCCCTTCTG 59.792 57.143 0.00 0.00 0.00 3.02
1040 1119 0.321671 CGCCACTTCTTCTTCCTCCA 59.678 55.000 0.00 0.00 0.00 3.86
1140 1219 3.394836 GCCGAGGGCTTCAGGAGT 61.395 66.667 10.68 0.00 46.69 3.85
1176 1255 2.978010 GCCAAGTGTGTCCACCCG 60.978 66.667 0.00 0.00 42.88 5.28
1195 1274 2.357034 GGTTGAAGCTGCCGACGA 60.357 61.111 0.00 0.00 0.00 4.20
1335 1414 2.041762 AGGGCCATGCTCCTGAGA 59.958 61.111 6.18 0.00 30.35 3.27
1614 1693 3.210012 ATCCCTTGCAGCCAACGGT 62.210 57.895 0.00 0.00 31.49 4.83
1664 1746 2.160205 GGTGGCTCCTTTCCTGTTTAC 58.840 52.381 0.00 0.00 0.00 2.01
1717 1799 3.178228 GCGTTTAAACTTGCGTTTGGTAC 59.822 43.478 16.01 0.00 42.94 3.34
1760 1844 9.142515 CTTGTAATATTTGCTTGAGATTTTGCA 57.857 29.630 0.00 0.00 0.00 4.08
1914 1998 2.046285 TCGCGATGCTCAGGAGTCA 61.046 57.895 3.71 0.00 0.00 3.41
1920 2004 2.111384 GATGCTCAGGAGTCACCCTTA 58.889 52.381 0.00 0.00 40.05 2.69
1927 2011 2.431942 AGTCACCCTTAACGCGCG 60.432 61.111 30.96 30.96 0.00 6.86
1958 2043 7.362920 GCTTACAGAAAGGAAATGCAGGAATAA 60.363 37.037 0.00 0.00 35.58 1.40
1963 2048 6.950619 AGAAAGGAAATGCAGGAATAAGTCTT 59.049 34.615 0.00 0.00 0.00 3.01
1975 2060 6.645415 CAGGAATAAGTCTTGTGTTCTACGTT 59.355 38.462 0.00 0.00 0.00 3.99
1976 2061 7.811236 CAGGAATAAGTCTTGTGTTCTACGTTA 59.189 37.037 0.00 0.00 0.00 3.18
2113 2198 0.322546 GTCCCCCTTGACGCTCAAAT 60.323 55.000 2.82 0.00 35.73 2.32
2199 2284 4.473520 CCTGGCTGGGTGGCGTAG 62.474 72.222 1.84 0.00 45.14 3.51
2311 2398 3.334054 AGGGCTCCCTGAGGTTGC 61.334 66.667 6.68 0.63 46.22 4.17
2312 2399 3.650950 GGGCTCCCTGAGGTTGCA 61.651 66.667 13.47 0.00 36.10 4.08
2313 2400 2.360475 GGCTCCCTGAGGTTGCAC 60.360 66.667 13.47 1.87 36.10 4.57
2314 2401 2.753029 GCTCCCTGAGGTTGCACT 59.247 61.111 7.87 0.00 35.07 4.40
2315 2402 1.553690 GGCTCCCTGAGGTTGCACTA 61.554 60.000 13.47 0.00 36.10 2.74
2316 2403 0.107945 GCTCCCTGAGGTTGCACTAG 60.108 60.000 7.87 0.00 35.07 2.57
2317 2404 1.270907 CTCCCTGAGGTTGCACTAGT 58.729 55.000 0.00 0.00 0.00 2.57
2318 2405 2.457598 CTCCCTGAGGTTGCACTAGTA 58.542 52.381 0.00 0.00 0.00 1.82
2319 2406 2.428890 CTCCCTGAGGTTGCACTAGTAG 59.571 54.545 0.00 0.00 0.00 2.57
2320 2407 2.042569 TCCCTGAGGTTGCACTAGTAGA 59.957 50.000 3.59 0.00 0.00 2.59
2321 2408 2.832129 CCCTGAGGTTGCACTAGTAGAA 59.168 50.000 3.59 0.00 0.00 2.10
2322 2409 3.260884 CCCTGAGGTTGCACTAGTAGAAA 59.739 47.826 3.59 0.00 0.00 2.52
2323 2410 4.262894 CCCTGAGGTTGCACTAGTAGAAAA 60.263 45.833 3.59 0.00 0.00 2.29
2324 2411 4.691216 CCTGAGGTTGCACTAGTAGAAAAC 59.309 45.833 3.59 5.20 0.00 2.43
2325 2412 5.284861 TGAGGTTGCACTAGTAGAAAACA 57.715 39.130 3.59 0.00 0.00 2.83
2326 2413 5.297547 TGAGGTTGCACTAGTAGAAAACAG 58.702 41.667 3.59 0.00 0.00 3.16
2327 2414 4.642429 AGGTTGCACTAGTAGAAAACAGG 58.358 43.478 3.59 0.00 0.00 4.00
2328 2415 3.751698 GGTTGCACTAGTAGAAAACAGGG 59.248 47.826 3.59 0.00 0.00 4.45
2329 2416 3.053831 TGCACTAGTAGAAAACAGGGC 57.946 47.619 3.59 0.00 36.65 5.19
2330 2417 2.370519 TGCACTAGTAGAAAACAGGGCA 59.629 45.455 3.59 0.00 40.80 5.36
2331 2418 3.009033 TGCACTAGTAGAAAACAGGGCAT 59.991 43.478 3.59 0.00 39.30 4.40
2332 2419 4.224147 TGCACTAGTAGAAAACAGGGCATA 59.776 41.667 3.59 0.00 39.30 3.14
2333 2420 4.811557 GCACTAGTAGAAAACAGGGCATAG 59.188 45.833 3.59 0.00 36.35 2.23
2334 2421 5.360591 CACTAGTAGAAAACAGGGCATAGG 58.639 45.833 3.59 0.00 0.00 2.57
2335 2422 5.030820 ACTAGTAGAAAACAGGGCATAGGT 58.969 41.667 3.59 0.00 0.00 3.08
2336 2423 4.489306 AGTAGAAAACAGGGCATAGGTC 57.511 45.455 0.00 0.00 0.00 3.85
2337 2424 3.844211 AGTAGAAAACAGGGCATAGGTCA 59.156 43.478 0.00 0.00 0.00 4.02
2338 2425 3.073274 AGAAAACAGGGCATAGGTCAC 57.927 47.619 0.00 0.00 0.00 3.67
2339 2426 2.375174 AGAAAACAGGGCATAGGTCACA 59.625 45.455 0.00 0.00 0.00 3.58
2340 2427 2.496899 AAACAGGGCATAGGTCACAG 57.503 50.000 0.00 0.00 0.00 3.66
2341 2428 0.620556 AACAGGGCATAGGTCACAGG 59.379 55.000 0.00 0.00 0.00 4.00
2342 2429 1.274703 ACAGGGCATAGGTCACAGGG 61.275 60.000 0.00 0.00 0.00 4.45
2343 2430 2.193248 GGGCATAGGTCACAGGGC 59.807 66.667 0.00 0.00 0.00 5.19
2344 2431 2.679342 GGGCATAGGTCACAGGGCA 61.679 63.158 0.00 0.00 0.00 5.36
2345 2432 1.153086 GGCATAGGTCACAGGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
2346 2433 1.604378 GCATAGGTCACAGGGCAGT 59.396 57.895 0.00 0.00 0.00 4.40
2347 2434 0.035056 GCATAGGTCACAGGGCAGTT 60.035 55.000 0.00 0.00 0.00 3.16
2348 2435 1.614317 GCATAGGTCACAGGGCAGTTT 60.614 52.381 0.00 0.00 0.00 2.66
2349 2436 2.795329 CATAGGTCACAGGGCAGTTTT 58.205 47.619 0.00 0.00 0.00 2.43
2350 2437 2.561478 TAGGTCACAGGGCAGTTTTC 57.439 50.000 0.00 0.00 0.00 2.29
2351 2438 0.550914 AGGTCACAGGGCAGTTTTCA 59.449 50.000 0.00 0.00 0.00 2.69
2352 2439 0.668535 GGTCACAGGGCAGTTTTCAC 59.331 55.000 0.00 0.00 0.00 3.18
2353 2440 1.388547 GTCACAGGGCAGTTTTCACA 58.611 50.000 0.00 0.00 0.00 3.58
2354 2441 1.956477 GTCACAGGGCAGTTTTCACAT 59.044 47.619 0.00 0.00 0.00 3.21
2355 2442 2.362077 GTCACAGGGCAGTTTTCACATT 59.638 45.455 0.00 0.00 0.00 2.71
2356 2443 3.568007 GTCACAGGGCAGTTTTCACATTA 59.432 43.478 0.00 0.00 0.00 1.90
2357 2444 3.820467 TCACAGGGCAGTTTTCACATTAG 59.180 43.478 0.00 0.00 0.00 1.73
2358 2445 2.558359 ACAGGGCAGTTTTCACATTAGC 59.442 45.455 0.00 0.00 0.00 3.09
2359 2446 2.094545 CAGGGCAGTTTTCACATTAGCC 60.095 50.000 0.00 0.00 39.86 3.93
2360 2447 2.654749 GGCAGTTTTCACATTAGCCC 57.345 50.000 0.00 0.00 34.71 5.19
2361 2448 1.204704 GGCAGTTTTCACATTAGCCCC 59.795 52.381 0.00 0.00 34.71 5.80
2362 2449 1.135402 GCAGTTTTCACATTAGCCCCG 60.135 52.381 0.00 0.00 0.00 5.73
2363 2450 1.472480 CAGTTTTCACATTAGCCCCGG 59.528 52.381 0.00 0.00 0.00 5.73
2364 2451 1.074889 AGTTTTCACATTAGCCCCGGT 59.925 47.619 0.00 0.00 0.00 5.28
2365 2452 1.890489 GTTTTCACATTAGCCCCGGTT 59.110 47.619 0.00 0.00 0.00 4.44
2366 2453 1.828979 TTTCACATTAGCCCCGGTTC 58.171 50.000 0.00 0.00 0.00 3.62
2367 2454 0.693622 TTCACATTAGCCCCGGTTCA 59.306 50.000 0.00 0.00 0.00 3.18
2368 2455 0.251916 TCACATTAGCCCCGGTTCAG 59.748 55.000 0.00 0.00 0.00 3.02
2369 2456 0.035439 CACATTAGCCCCGGTTCAGT 60.035 55.000 0.00 0.00 0.00 3.41
2370 2457 0.252197 ACATTAGCCCCGGTTCAGTC 59.748 55.000 0.00 0.00 0.00 3.51
2371 2458 0.251916 CATTAGCCCCGGTTCAGTCA 59.748 55.000 0.00 0.00 0.00 3.41
2372 2459 1.134098 CATTAGCCCCGGTTCAGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
2373 2460 0.251916 TTAGCCCCGGTTCAGTCATG 59.748 55.000 0.00 0.00 0.00 3.07
2374 2461 0.616395 TAGCCCCGGTTCAGTCATGA 60.616 55.000 0.00 0.00 0.00 3.07
2375 2462 1.002624 GCCCCGGTTCAGTCATGAA 60.003 57.895 0.00 0.00 43.20 2.57
2382 2469 3.927555 TTCAGTCATGAACCGGGAC 57.072 52.632 6.32 2.53 40.54 4.46
2383 2470 0.323629 TTCAGTCATGAACCGGGACC 59.676 55.000 6.32 0.00 40.54 4.46
2384 2471 1.078426 CAGTCATGAACCGGGACCC 60.078 63.158 6.32 0.00 31.99 4.46
2385 2472 1.537889 AGTCATGAACCGGGACCCA 60.538 57.895 12.15 0.00 31.99 4.51
2386 2473 0.914417 AGTCATGAACCGGGACCCAT 60.914 55.000 12.15 0.00 31.99 4.00
2387 2474 0.748005 GTCATGAACCGGGACCCATG 60.748 60.000 12.15 13.18 38.12 3.66
2388 2475 1.453745 CATGAACCGGGACCCATGG 60.454 63.158 12.15 4.14 34.39 3.66
2389 2476 2.689691 ATGAACCGGGACCCATGGG 61.690 63.158 30.23 30.23 42.03 4.00
2400 2487 2.519302 CCATGGGGGCATTCGTCC 60.519 66.667 2.85 0.00 35.48 4.79
2406 2493 2.822701 GGGCATTCGTCCCGGTTC 60.823 66.667 0.00 0.00 33.43 3.62
2407 2494 3.192922 GGCATTCGTCCCGGTTCG 61.193 66.667 0.00 4.79 0.00 3.95
2408 2495 2.433664 GCATTCGTCCCGGTTCGT 60.434 61.111 13.60 0.00 0.00 3.85
2409 2496 2.736682 GCATTCGTCCCGGTTCGTG 61.737 63.158 13.60 8.10 0.00 4.35
2410 2497 1.080366 CATTCGTCCCGGTTCGTGA 60.080 57.895 13.60 6.24 0.00 4.35
2411 2498 1.076533 CATTCGTCCCGGTTCGTGAG 61.077 60.000 13.60 3.53 0.00 3.51
2412 2499 2.830704 ATTCGTCCCGGTTCGTGAGC 62.831 60.000 13.60 0.00 0.00 4.26
2413 2500 4.351938 CGTCCCGGTTCGTGAGCA 62.352 66.667 0.00 0.00 0.00 4.26
2414 2501 2.737376 GTCCCGGTTCGTGAGCAC 60.737 66.667 0.00 0.00 0.00 4.40
2415 2502 3.228017 TCCCGGTTCGTGAGCACA 61.228 61.111 0.00 0.00 0.00 4.57
2416 2503 2.738521 CCCGGTTCGTGAGCACAG 60.739 66.667 0.00 0.00 0.00 3.66
2417 2504 2.738521 CCGGTTCGTGAGCACAGG 60.739 66.667 0.00 0.00 36.26 4.00
2418 2505 2.738521 CGGTTCGTGAGCACAGGG 60.739 66.667 4.02 0.00 33.41 4.45
2419 2506 2.358737 GGTTCGTGAGCACAGGGG 60.359 66.667 4.02 0.00 33.41 4.79
2420 2507 2.358737 GTTCGTGAGCACAGGGGG 60.359 66.667 4.02 0.00 33.41 5.40
2421 2508 4.329545 TTCGTGAGCACAGGGGGC 62.330 66.667 4.02 0.00 33.41 5.80
2448 2535 2.438434 CCTCGTGGGCATTGGTCC 60.438 66.667 0.00 0.00 40.08 4.46
2449 2536 2.438434 CTCGTGGGCATTGGTCCC 60.438 66.667 0.00 0.00 44.17 4.46
2450 2537 4.402528 TCGTGGGCATTGGTCCCG 62.403 66.667 0.00 0.00 46.92 5.14
2452 2539 4.360405 GTGGGCATTGGTCCCGGT 62.360 66.667 0.00 0.00 46.92 5.28
2453 2540 3.585428 TGGGCATTGGTCCCGGTT 61.585 61.111 0.00 0.00 46.92 4.44
2454 2541 2.754254 GGGCATTGGTCCCGGTTC 60.754 66.667 0.00 0.00 33.43 3.62
2455 2542 3.131478 GGCATTGGTCCCGGTTCG 61.131 66.667 0.00 0.00 0.00 3.95
2456 2543 2.359478 GCATTGGTCCCGGTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
2457 2544 1.078988 GCATTGGTCCCGGTTCGTA 60.079 57.895 0.00 0.00 0.00 3.43
2458 2545 0.463116 GCATTGGTCCCGGTTCGTAT 60.463 55.000 0.00 0.00 0.00 3.06
2459 2546 1.295792 CATTGGTCCCGGTTCGTATG 58.704 55.000 0.00 0.00 0.00 2.39
2460 2547 0.179468 ATTGGTCCCGGTTCGTATGG 59.821 55.000 0.00 0.00 0.00 2.74
2461 2548 0.903924 TTGGTCCCGGTTCGTATGGA 60.904 55.000 0.00 0.00 0.00 3.41
2462 2549 0.903924 TGGTCCCGGTTCGTATGGAA 60.904 55.000 0.00 0.00 0.00 3.53
2473 2560 2.993937 TCGTATGGAACCATTTGTCCC 58.006 47.619 11.68 0.00 37.82 4.46
2474 2561 1.668751 CGTATGGAACCATTTGTCCCG 59.331 52.381 11.68 2.53 37.82 5.14
2475 2562 2.021457 GTATGGAACCATTTGTCCCGG 58.979 52.381 11.68 0.00 37.82 5.73
2476 2563 0.407918 ATGGAACCATTTGTCCCGGT 59.592 50.000 0.00 0.00 31.82 5.28
2477 2564 0.186386 TGGAACCATTTGTCCCGGTT 59.814 50.000 0.00 0.00 45.64 4.44
2479 2566 0.519961 GAACCATTTGTCCCGGTTCG 59.480 55.000 0.00 0.00 46.63 3.95
2480 2567 0.108963 AACCATTTGTCCCGGTTCGA 59.891 50.000 0.00 0.00 38.69 3.71
2481 2568 0.321298 ACCATTTGTCCCGGTTCGAG 60.321 55.000 0.00 0.00 0.00 4.04
2482 2569 1.644786 CCATTTGTCCCGGTTCGAGC 61.645 60.000 0.00 0.00 0.00 5.03
2483 2570 1.376812 ATTTGTCCCGGTTCGAGCC 60.377 57.895 8.48 8.48 0.00 4.70
2484 2571 2.119484 ATTTGTCCCGGTTCGAGCCA 62.119 55.000 19.03 0.00 0.00 4.75
2485 2572 2.999739 TTTGTCCCGGTTCGAGCCAC 63.000 60.000 19.03 9.54 0.00 5.01
2496 2583 3.692406 GAGCCACGAACCGGGACT 61.692 66.667 6.32 0.00 28.17 3.85
2497 2584 2.283388 AGCCACGAACCGGGACTA 60.283 61.111 6.32 0.00 28.17 2.59
2498 2585 1.880819 GAGCCACGAACCGGGACTAA 61.881 60.000 6.32 0.00 28.17 2.24
2499 2586 1.219935 GCCACGAACCGGGACTAAT 59.780 57.895 6.32 0.00 28.17 1.73
2500 2587 1.087771 GCCACGAACCGGGACTAATG 61.088 60.000 6.32 0.00 28.17 1.90
2501 2588 0.461339 CCACGAACCGGGACTAATGG 60.461 60.000 6.32 1.45 28.17 3.16
2502 2589 0.248289 CACGAACCGGGACTAATGGT 59.752 55.000 6.32 0.00 37.68 3.55
2503 2590 0.533951 ACGAACCGGGACTAATGGTC 59.466 55.000 6.32 0.00 43.79 4.02
2511 2598 3.969995 GACTAATGGTCCTCGCTCC 57.030 57.895 0.00 0.00 38.93 4.70
2512 2599 1.404843 GACTAATGGTCCTCGCTCCT 58.595 55.000 0.00 0.00 38.93 3.69
2513 2600 1.067821 GACTAATGGTCCTCGCTCCTG 59.932 57.143 0.00 0.00 38.93 3.86
2514 2601 0.390860 CTAATGGTCCTCGCTCCTGG 59.609 60.000 0.00 0.00 0.00 4.45
2515 2602 1.686325 TAATGGTCCTCGCTCCTGGC 61.686 60.000 0.00 0.00 37.64 4.85
2521 2608 4.020617 CTCGCTCCTGGCCCACAA 62.021 66.667 0.00 0.00 37.74 3.33
2522 2609 4.329545 TCGCTCCTGGCCCACAAC 62.330 66.667 0.00 0.00 37.74 3.32
2524 2611 4.284550 GCTCCTGGCCCACAACCA 62.285 66.667 0.00 0.00 35.40 3.67
2525 2612 2.765969 CTCCTGGCCCACAACCAT 59.234 61.111 0.00 0.00 36.36 3.55
2526 2613 1.077265 CTCCTGGCCCACAACCATT 59.923 57.895 0.00 0.00 36.36 3.16
2527 2614 0.542702 CTCCTGGCCCACAACCATTT 60.543 55.000 0.00 0.00 36.36 2.32
2528 2615 0.831288 TCCTGGCCCACAACCATTTG 60.831 55.000 0.00 0.00 36.36 2.32
2530 2617 0.318120 CTGGCCCACAACCATTTGTC 59.682 55.000 0.00 0.00 44.57 3.18
2531 2618 1.118356 TGGCCCACAACCATTTGTCC 61.118 55.000 0.00 0.00 44.57 4.02
2532 2619 1.671166 GCCCACAACCATTTGTCCC 59.329 57.895 0.00 0.00 44.57 4.46
2533 2620 1.963679 CCCACAACCATTTGTCCCG 59.036 57.895 0.00 0.00 44.57 5.14
2534 2621 1.531739 CCCACAACCATTTGTCCCGG 61.532 60.000 0.00 0.00 44.57 5.73
2535 2622 0.825840 CCACAACCATTTGTCCCGGT 60.826 55.000 0.00 0.00 44.57 5.28
2536 2623 1.036707 CACAACCATTTGTCCCGGTT 58.963 50.000 0.00 0.00 44.57 4.44
2537 2624 1.000717 CACAACCATTTGTCCCGGTTC 60.001 52.381 0.00 0.00 44.57 3.62
2538 2625 1.133606 ACAACCATTTGTCCCGGTTCT 60.134 47.619 0.00 0.00 42.67 3.01
2539 2626 1.960689 CAACCATTTGTCCCGGTTCTT 59.039 47.619 0.00 0.00 41.07 2.52
2540 2627 1.905637 ACCATTTGTCCCGGTTCTTC 58.094 50.000 0.00 0.00 0.00 2.87
2541 2628 0.802494 CCATTTGTCCCGGTTCTTCG 59.198 55.000 0.00 0.00 0.00 3.79
2542 2629 0.168128 CATTTGTCCCGGTTCTTCGC 59.832 55.000 0.00 0.00 0.00 4.70
2543 2630 0.250553 ATTTGTCCCGGTTCTTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
2544 2631 0.250553 TTTGTCCCGGTTCTTCGCAT 60.251 50.000 0.00 0.00 0.00 4.73
2545 2632 0.953471 TTGTCCCGGTTCTTCGCATG 60.953 55.000 0.00 0.00 0.00 4.06
2546 2633 1.079405 GTCCCGGTTCTTCGCATGA 60.079 57.895 0.00 0.00 0.00 3.07
2547 2634 0.672401 GTCCCGGTTCTTCGCATGAA 60.672 55.000 0.00 0.00 0.00 2.57
2548 2635 0.672401 TCCCGGTTCTTCGCATGAAC 60.672 55.000 0.00 5.29 42.00 3.18
2552 2639 1.794222 GTTCTTCGCATGAACCGGG 59.206 57.895 6.32 0.00 38.19 5.73
2553 2640 0.672401 GTTCTTCGCATGAACCGGGA 60.672 55.000 6.32 0.00 38.19 5.14
2554 2641 0.672401 TTCTTCGCATGAACCGGGAC 60.672 55.000 6.32 0.00 0.00 4.46
2555 2642 1.375396 CTTCGCATGAACCGGGACA 60.375 57.895 6.32 5.75 0.00 4.02
2556 2643 1.361668 CTTCGCATGAACCGGGACAG 61.362 60.000 6.32 1.30 0.00 3.51
2557 2644 1.822114 TTCGCATGAACCGGGACAGA 61.822 55.000 6.32 0.00 0.00 3.41
2558 2645 1.375396 CGCATGAACCGGGACAGAA 60.375 57.895 6.32 0.00 0.00 3.02
2559 2646 1.361668 CGCATGAACCGGGACAGAAG 61.362 60.000 6.32 1.42 0.00 2.85
2560 2647 1.026718 GCATGAACCGGGACAGAAGG 61.027 60.000 6.32 0.00 0.00 3.46
2561 2648 1.026718 CATGAACCGGGACAGAAGGC 61.027 60.000 6.32 0.00 0.00 4.35
2562 2649 1.201429 ATGAACCGGGACAGAAGGCT 61.201 55.000 6.32 0.00 0.00 4.58
2563 2650 1.079057 GAACCGGGACAGAAGGCTC 60.079 63.158 6.32 0.00 0.00 4.70
2564 2651 2.837371 GAACCGGGACAGAAGGCTCG 62.837 65.000 6.32 0.00 0.00 5.03
2565 2652 4.148825 CCGGGACAGAAGGCTCGG 62.149 72.222 0.00 0.00 0.00 4.63
2566 2653 3.068691 CGGGACAGAAGGCTCGGA 61.069 66.667 0.00 0.00 0.00 4.55
2567 2654 2.427245 CGGGACAGAAGGCTCGGAT 61.427 63.158 0.00 0.00 0.00 4.18
2568 2655 1.908483 GGGACAGAAGGCTCGGATT 59.092 57.895 0.00 0.00 0.00 3.01
2569 2656 0.253327 GGGACAGAAGGCTCGGATTT 59.747 55.000 0.00 0.00 0.00 2.17
2570 2657 1.485066 GGGACAGAAGGCTCGGATTTA 59.515 52.381 0.00 0.00 0.00 1.40
2571 2658 2.483889 GGGACAGAAGGCTCGGATTTAG 60.484 54.545 0.00 0.00 0.00 1.85
2572 2659 2.168728 GGACAGAAGGCTCGGATTTAGT 59.831 50.000 0.00 0.00 0.00 2.24
2573 2660 3.383825 GGACAGAAGGCTCGGATTTAGTA 59.616 47.826 0.00 0.00 0.00 1.82
2574 2661 4.361420 GACAGAAGGCTCGGATTTAGTAC 58.639 47.826 0.00 0.00 0.00 2.73
2575 2662 3.132467 ACAGAAGGCTCGGATTTAGTACC 59.868 47.826 0.00 0.00 0.00 3.34
2584 2671 2.542595 CGGATTTAGTACCGGTTCATGC 59.457 50.000 15.04 1.59 44.59 4.06
2585 2672 2.876550 GGATTTAGTACCGGTTCATGCC 59.123 50.000 15.04 2.33 0.00 4.40
2586 2673 3.537580 GATTTAGTACCGGTTCATGCCA 58.462 45.455 15.04 0.00 0.00 4.92
2587 2674 2.389962 TTAGTACCGGTTCATGCCAC 57.610 50.000 15.04 1.99 0.00 5.01
2588 2675 0.173935 TAGTACCGGTTCATGCCACG 59.826 55.000 15.04 0.00 0.00 4.94
2589 2676 1.079681 GTACCGGTTCATGCCACGA 60.080 57.895 15.04 0.00 0.00 4.35
2590 2677 0.671163 GTACCGGTTCATGCCACGAA 60.671 55.000 15.04 0.00 0.00 3.85
2591 2678 0.671163 TACCGGTTCATGCCACGAAC 60.671 55.000 15.04 0.00 41.66 3.95
2594 2681 2.867472 GTTCATGCCACGAACCGG 59.133 61.111 0.00 0.00 37.40 5.28
2595 2682 2.359354 TTCATGCCACGAACCGGG 60.359 61.111 6.32 0.00 0.00 5.73
2596 2683 2.884980 TTCATGCCACGAACCGGGA 61.885 57.895 6.32 0.00 28.17 5.14
2597 2684 3.124921 CATGCCACGAACCGGGAC 61.125 66.667 6.32 0.00 28.17 4.46
2598 2685 4.404098 ATGCCACGAACCGGGACC 62.404 66.667 6.32 0.00 28.17 4.46
2600 2687 4.629523 GCCACGAACCGGGACCAA 62.630 66.667 6.32 0.00 28.17 3.67
2601 2688 2.349755 CCACGAACCGGGACCAAT 59.650 61.111 6.32 0.00 28.17 3.16
2602 2689 2.038269 CCACGAACCGGGACCAATG 61.038 63.158 6.32 0.00 28.17 2.82
2603 2690 1.004320 CACGAACCGGGACCAATGA 60.004 57.895 6.32 0.00 28.17 2.57
2604 2691 1.019278 CACGAACCGGGACCAATGAG 61.019 60.000 6.32 0.00 28.17 2.90
2605 2692 1.449601 CGAACCGGGACCAATGAGG 60.450 63.158 6.32 0.00 45.67 3.86
2620 2707 5.930135 CCAATGAGGTGCCTATATATACCC 58.070 45.833 0.00 0.00 33.67 3.69
2621 2708 5.163195 CCAATGAGGTGCCTATATATACCCC 60.163 48.000 0.00 0.00 33.67 4.95
2622 2709 4.986591 TGAGGTGCCTATATATACCCCT 57.013 45.455 0.00 0.00 33.67 4.79
2623 2710 4.880164 TGAGGTGCCTATATATACCCCTC 58.120 47.826 11.73 11.73 38.16 4.30
2624 2711 3.890147 GAGGTGCCTATATATACCCCTCG 59.110 52.174 0.00 0.00 33.67 4.63
2625 2712 2.364647 GGTGCCTATATATACCCCTCGC 59.635 54.545 0.00 0.00 0.00 5.03
2626 2713 2.364647 GTGCCTATATATACCCCTCGCC 59.635 54.545 0.00 0.00 0.00 5.54
2627 2714 1.969208 GCCTATATATACCCCTCGCCC 59.031 57.143 0.00 0.00 0.00 6.13
2628 2715 2.236766 CCTATATATACCCCTCGCCCG 58.763 57.143 0.00 0.00 0.00 6.13
2629 2716 1.612463 CTATATATACCCCTCGCCCGC 59.388 57.143 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.817634 TCGGTGCAACAAGACCAAGG 60.818 55.000 0.98 0.00 39.98 3.61
84 85 2.626780 CGCAGTGTCCTCGTCTCCA 61.627 63.158 0.00 0.00 0.00 3.86
107 108 2.512286 CATGACGACTGGCGCCAT 60.512 61.111 32.87 20.35 44.13 4.40
518 580 0.593128 CTTTTTGTCAGACGGGCAGG 59.407 55.000 0.00 0.00 0.00 4.85
552 614 1.274447 GGAAAGCAATGAAGGCAAGCT 59.726 47.619 0.00 0.00 39.97 3.74
642 704 1.218047 CCATTGGTCGGAAGCTCGA 59.782 57.895 0.00 0.00 36.76 4.04
817 880 1.003233 GCTCTTTGAAGCCTCCGGT 60.003 57.895 0.00 0.00 36.22 5.28
852 915 1.134075 CAGACAACGCTGCTCATGC 59.866 57.895 0.00 0.00 40.20 4.06
1040 1119 3.074412 GAGGTGTGACCGTCATTGATTT 58.926 45.455 4.13 0.00 44.90 2.17
1140 1219 2.158623 GGCATCCATCATGACCCACTTA 60.159 50.000 0.00 0.00 33.74 2.24
1176 1255 4.090057 GTCGGCAGCTTCAACCGC 62.090 66.667 8.90 0.00 46.49 5.68
1195 1274 0.904865 TCGTCAGACTGGGGCATCTT 60.905 55.000 1.81 0.00 0.00 2.40
1318 1397 2.041762 TCTCAGGAGCATGGCCCT 59.958 61.111 0.00 0.00 31.30 5.19
1335 1414 1.004745 ACCCGCAACATCAGGAATTCT 59.995 47.619 5.23 0.00 0.00 2.40
1495 1574 0.599204 GGAACGAAGGCACTCGACAA 60.599 55.000 14.80 0.00 38.49 3.18
1496 1575 1.006571 GGAACGAAGGCACTCGACA 60.007 57.895 14.80 0.00 38.49 4.35
1560 1639 1.445582 GTCGCCTTCACCTGTACCG 60.446 63.158 0.00 0.00 0.00 4.02
1609 1688 0.250727 CATCCTTGGACACCACCGTT 60.251 55.000 0.00 0.00 30.78 4.44
1614 1693 1.676968 CCGTCATCCTTGGACACCA 59.323 57.895 0.00 0.00 34.97 4.17
1623 1705 0.179000 GCAAGTCATCCCGTCATCCT 59.821 55.000 0.00 0.00 0.00 3.24
1664 1746 2.997986 GCATGGTCCATTTTGCAGAAAG 59.002 45.455 10.49 0.00 35.22 2.62
1717 1799 9.784531 ATATTACAAGACATATTGTTCTCCCAG 57.215 33.333 0.00 0.00 40.47 4.45
1760 1844 5.011635 ACGTAAAGCAAATGGGAAGGAAATT 59.988 36.000 0.00 0.00 0.00 1.82
1813 1897 1.445582 CCAACGACGGCTGAGGTAC 60.446 63.158 0.00 0.00 0.00 3.34
1914 1998 2.025418 CTGTTCGCGCGTTAAGGGT 61.025 57.895 30.98 0.00 34.93 4.34
1920 2004 1.886861 CTGTAAGCTGTTCGCGCGTT 61.887 55.000 30.98 17.79 45.59 4.84
1927 2011 5.157067 GCATTTCCTTTCTGTAAGCTGTTC 58.843 41.667 0.00 0.00 32.19 3.18
1958 2043 4.547532 CTGCTAACGTAGAACACAAGACT 58.452 43.478 0.00 0.00 0.00 3.24
1963 2048 1.337447 GCCCTGCTAACGTAGAACACA 60.337 52.381 0.00 0.00 0.00 3.72
2067 2152 2.780094 ATCGCGACTCAGGAGCCTG 61.780 63.158 12.93 10.29 44.86 4.85
2113 2198 1.992557 AGGGCAAAGGTATGAAGGTCA 59.007 47.619 0.00 0.00 0.00 4.02
2311 2398 5.104900 ACCTATGCCCTGTTTTCTACTAGTG 60.105 44.000 5.39 0.00 0.00 2.74
2312 2399 5.030820 ACCTATGCCCTGTTTTCTACTAGT 58.969 41.667 0.00 0.00 0.00 2.57
2313 2400 5.128827 TGACCTATGCCCTGTTTTCTACTAG 59.871 44.000 0.00 0.00 0.00 2.57
2314 2401 5.027460 TGACCTATGCCCTGTTTTCTACTA 58.973 41.667 0.00 0.00 0.00 1.82
2315 2402 3.844211 TGACCTATGCCCTGTTTTCTACT 59.156 43.478 0.00 0.00 0.00 2.57
2316 2403 3.939592 GTGACCTATGCCCTGTTTTCTAC 59.060 47.826 0.00 0.00 0.00 2.59
2317 2404 3.585289 TGTGACCTATGCCCTGTTTTCTA 59.415 43.478 0.00 0.00 0.00 2.10
2318 2405 2.375174 TGTGACCTATGCCCTGTTTTCT 59.625 45.455 0.00 0.00 0.00 2.52
2319 2406 2.749621 CTGTGACCTATGCCCTGTTTTC 59.250 50.000 0.00 0.00 0.00 2.29
2320 2407 2.555227 CCTGTGACCTATGCCCTGTTTT 60.555 50.000 0.00 0.00 0.00 2.43
2321 2408 1.004745 CCTGTGACCTATGCCCTGTTT 59.995 52.381 0.00 0.00 0.00 2.83
2322 2409 0.620556 CCTGTGACCTATGCCCTGTT 59.379 55.000 0.00 0.00 0.00 3.16
2323 2410 1.274703 CCCTGTGACCTATGCCCTGT 61.275 60.000 0.00 0.00 0.00 4.00
2324 2411 1.528824 CCCTGTGACCTATGCCCTG 59.471 63.158 0.00 0.00 0.00 4.45
2325 2412 2.378634 GCCCTGTGACCTATGCCCT 61.379 63.158 0.00 0.00 0.00 5.19
2326 2413 2.193248 GCCCTGTGACCTATGCCC 59.807 66.667 0.00 0.00 0.00 5.36
2327 2414 1.153086 CTGCCCTGTGACCTATGCC 60.153 63.158 0.00 0.00 0.00 4.40
2328 2415 0.035056 AACTGCCCTGTGACCTATGC 60.035 55.000 0.00 0.00 0.00 3.14
2329 2416 2.496899 AAACTGCCCTGTGACCTATG 57.503 50.000 0.00 0.00 0.00 2.23
2330 2417 2.375174 TGAAAACTGCCCTGTGACCTAT 59.625 45.455 0.00 0.00 0.00 2.57
2331 2418 1.771854 TGAAAACTGCCCTGTGACCTA 59.228 47.619 0.00 0.00 0.00 3.08
2332 2419 0.550914 TGAAAACTGCCCTGTGACCT 59.449 50.000 0.00 0.00 0.00 3.85
2333 2420 0.668535 GTGAAAACTGCCCTGTGACC 59.331 55.000 0.00 0.00 0.00 4.02
2334 2421 1.388547 TGTGAAAACTGCCCTGTGAC 58.611 50.000 0.00 0.00 0.00 3.67
2335 2422 2.363306 ATGTGAAAACTGCCCTGTGA 57.637 45.000 0.00 0.00 0.00 3.58
2336 2423 3.612479 GCTAATGTGAAAACTGCCCTGTG 60.612 47.826 0.00 0.00 0.00 3.66
2337 2424 2.558359 GCTAATGTGAAAACTGCCCTGT 59.442 45.455 0.00 0.00 0.00 4.00
2338 2425 2.094545 GGCTAATGTGAAAACTGCCCTG 60.095 50.000 0.00 0.00 33.45 4.45
2339 2426 2.171003 GGCTAATGTGAAAACTGCCCT 58.829 47.619 0.00 0.00 33.45 5.19
2340 2427 2.654749 GGCTAATGTGAAAACTGCCC 57.345 50.000 0.00 0.00 33.45 5.36
2341 2428 1.204704 GGGGCTAATGTGAAAACTGCC 59.795 52.381 0.00 0.00 38.28 4.85
2342 2429 1.135402 CGGGGCTAATGTGAAAACTGC 60.135 52.381 0.00 0.00 0.00 4.40
2343 2430 1.472480 CCGGGGCTAATGTGAAAACTG 59.528 52.381 0.00 0.00 0.00 3.16
2344 2431 1.074889 ACCGGGGCTAATGTGAAAACT 59.925 47.619 6.32 0.00 0.00 2.66
2345 2432 1.541379 ACCGGGGCTAATGTGAAAAC 58.459 50.000 6.32 0.00 0.00 2.43
2346 2433 2.164338 GAACCGGGGCTAATGTGAAAA 58.836 47.619 6.32 0.00 0.00 2.29
2347 2434 1.074084 TGAACCGGGGCTAATGTGAAA 59.926 47.619 6.32 0.00 0.00 2.69
2348 2435 0.693622 TGAACCGGGGCTAATGTGAA 59.306 50.000 6.32 0.00 0.00 3.18
2349 2436 0.251916 CTGAACCGGGGCTAATGTGA 59.748 55.000 6.32 0.00 0.00 3.58
2350 2437 0.035439 ACTGAACCGGGGCTAATGTG 60.035 55.000 6.32 0.00 0.00 3.21
2351 2438 0.252197 GACTGAACCGGGGCTAATGT 59.748 55.000 6.32 0.00 0.00 2.71
2352 2439 0.251916 TGACTGAACCGGGGCTAATG 59.748 55.000 6.32 0.00 0.00 1.90
2353 2440 1.134098 CATGACTGAACCGGGGCTAAT 60.134 52.381 6.32 0.00 0.00 1.73
2354 2441 0.251916 CATGACTGAACCGGGGCTAA 59.748 55.000 6.32 0.00 0.00 3.09
2355 2442 0.616395 TCATGACTGAACCGGGGCTA 60.616 55.000 6.32 0.00 0.00 3.93
2356 2443 1.488705 TTCATGACTGAACCGGGGCT 61.489 55.000 6.32 0.00 36.46 5.19
2357 2444 1.002624 TTCATGACTGAACCGGGGC 60.003 57.895 6.32 0.00 36.46 5.80
2364 2451 0.323629 GGTCCCGGTTCATGACTGAA 59.676 55.000 0.00 0.00 39.07 3.02
2365 2452 1.550130 GGGTCCCGGTTCATGACTGA 61.550 60.000 0.00 0.00 36.72 3.41
2366 2453 1.078426 GGGTCCCGGTTCATGACTG 60.078 63.158 0.00 0.00 0.00 3.51
2367 2454 0.914417 ATGGGTCCCGGTTCATGACT 60.914 55.000 2.65 0.00 0.00 3.41
2368 2455 0.748005 CATGGGTCCCGGTTCATGAC 60.748 60.000 14.43 8.13 39.27 3.06
2369 2456 1.607071 CATGGGTCCCGGTTCATGA 59.393 57.895 14.43 0.00 39.27 3.07
2370 2457 1.453745 CCATGGGTCCCGGTTCATG 60.454 63.158 2.85 8.47 37.37 3.07
2371 2458 2.689691 CCCATGGGTCCCGGTTCAT 61.690 63.158 23.93 0.00 0.00 2.57
2372 2459 3.334891 CCCATGGGTCCCGGTTCA 61.335 66.667 23.93 0.00 0.00 3.18
2373 2460 4.123545 CCCCATGGGTCCCGGTTC 62.124 72.222 29.33 0.00 38.25 3.62
2383 2470 2.519302 GGACGAATGCCCCCATGG 60.519 66.667 4.14 4.14 37.09 3.66
2384 2471 2.519302 GGGACGAATGCCCCCATG 60.519 66.667 0.00 0.00 39.81 3.66
2397 2484 2.737376 GTGCTCACGAACCGGGAC 60.737 66.667 6.32 0.00 32.99 4.46
2398 2485 3.220999 CTGTGCTCACGAACCGGGA 62.221 63.158 6.32 0.00 36.75 5.14
2399 2486 2.738521 CTGTGCTCACGAACCGGG 60.739 66.667 6.32 0.00 0.00 5.73
2400 2487 2.738521 CCTGTGCTCACGAACCGG 60.739 66.667 0.00 0.00 0.00 5.28
2401 2488 2.738521 CCCTGTGCTCACGAACCG 60.739 66.667 0.00 0.00 0.00 4.44
2402 2489 2.358737 CCCCTGTGCTCACGAACC 60.359 66.667 0.00 0.00 0.00 3.62
2403 2490 2.358737 CCCCCTGTGCTCACGAAC 60.359 66.667 0.00 0.00 0.00 3.95
2404 2491 4.329545 GCCCCCTGTGCTCACGAA 62.330 66.667 0.00 0.00 0.00 3.85
2431 2518 2.438434 GGACCAATGCCCACGAGG 60.438 66.667 0.00 0.00 39.47 4.63
2432 2519 2.438434 GGGACCAATGCCCACGAG 60.438 66.667 0.00 0.00 45.31 4.18
2433 2520 4.402528 CGGGACCAATGCCCACGA 62.403 66.667 0.00 0.00 46.36 4.35
2435 2522 3.879180 AACCGGGACCAATGCCCAC 62.879 63.158 6.32 0.00 46.36 4.61
2436 2523 3.577334 GAACCGGGACCAATGCCCA 62.577 63.158 6.32 0.00 46.36 5.36
2437 2524 2.754254 GAACCGGGACCAATGCCC 60.754 66.667 6.32 0.00 42.41 5.36
2438 2525 2.524951 TACGAACCGGGACCAATGCC 62.525 60.000 6.32 0.00 0.00 4.40
2439 2526 0.463116 ATACGAACCGGGACCAATGC 60.463 55.000 6.32 0.00 0.00 3.56
2440 2527 1.295792 CATACGAACCGGGACCAATG 58.704 55.000 6.32 0.00 0.00 2.82
2441 2528 0.179468 CCATACGAACCGGGACCAAT 59.821 55.000 6.32 0.00 0.00 3.16
2442 2529 0.903924 TCCATACGAACCGGGACCAA 60.904 55.000 6.32 0.00 0.00 3.67
2443 2530 0.903924 TTCCATACGAACCGGGACCA 60.904 55.000 6.32 0.00 0.00 4.02
2444 2531 0.460811 GTTCCATACGAACCGGGACC 60.461 60.000 6.32 0.00 44.46 4.46
2445 2532 3.055144 GTTCCATACGAACCGGGAC 57.945 57.895 6.32 0.00 44.46 4.46
2451 2538 3.128068 GGGACAAATGGTTCCATACGAAC 59.872 47.826 4.67 0.00 45.54 3.95
2452 2539 3.349022 GGGACAAATGGTTCCATACGAA 58.651 45.455 4.67 0.00 45.54 3.85
2453 2540 2.678479 CGGGACAAATGGTTCCATACGA 60.678 50.000 4.67 0.00 46.73 3.43
2454 2541 1.668751 CGGGACAAATGGTTCCATACG 59.331 52.381 4.67 2.38 46.73 3.06
2455 2542 2.021457 CCGGGACAAATGGTTCCATAC 58.979 52.381 4.67 0.00 46.73 2.39
2456 2543 1.636519 ACCGGGACAAATGGTTCCATA 59.363 47.619 6.32 0.00 46.73 2.74
2457 2544 0.407918 ACCGGGACAAATGGTTCCAT 59.592 50.000 6.32 0.00 46.73 3.41
2458 2545 0.186386 AACCGGGACAAATGGTTCCA 59.814 50.000 6.32 0.00 46.73 3.53
2459 2546 3.045518 AACCGGGACAAATGGTTCC 57.954 52.632 6.32 0.00 42.11 3.62
2462 2549 0.321298 CTCGAACCGGGACAAATGGT 60.321 55.000 6.32 0.00 37.68 3.55
2463 2550 1.644786 GCTCGAACCGGGACAAATGG 61.645 60.000 6.32 0.00 0.00 3.16
2464 2551 1.644786 GGCTCGAACCGGGACAAATG 61.645 60.000 6.32 0.00 34.24 2.32
2465 2552 1.376812 GGCTCGAACCGGGACAAAT 60.377 57.895 6.32 0.00 34.24 2.32
2466 2553 2.031465 GGCTCGAACCGGGACAAA 59.969 61.111 6.32 0.00 34.24 2.83
2467 2554 3.235481 TGGCTCGAACCGGGACAA 61.235 61.111 6.32 0.00 44.95 3.18
2468 2555 3.998672 GTGGCTCGAACCGGGACA 61.999 66.667 6.32 0.00 46.14 4.02
2479 2566 1.880819 TTAGTCCCGGTTCGTGGCTC 61.881 60.000 0.00 0.00 0.00 4.70
2480 2567 1.262640 ATTAGTCCCGGTTCGTGGCT 61.263 55.000 0.00 0.00 0.00 4.75
2481 2568 1.087771 CATTAGTCCCGGTTCGTGGC 61.088 60.000 0.00 0.00 0.00 5.01
2482 2569 0.461339 CCATTAGTCCCGGTTCGTGG 60.461 60.000 0.00 0.00 0.00 4.94
2483 2570 0.248289 ACCATTAGTCCCGGTTCGTG 59.752 55.000 0.00 0.00 0.00 4.35
2484 2571 0.533951 GACCATTAGTCCCGGTTCGT 59.466 55.000 0.00 0.00 39.84 3.85
2485 2572 3.357504 GACCATTAGTCCCGGTTCG 57.642 57.895 0.00 0.00 39.84 3.95
2493 2580 1.067821 CAGGAGCGAGGACCATTAGTC 59.932 57.143 0.00 0.00 45.51 2.59
2494 2581 1.115467 CAGGAGCGAGGACCATTAGT 58.885 55.000 0.00 0.00 0.00 2.24
2495 2582 0.390860 CCAGGAGCGAGGACCATTAG 59.609 60.000 0.00 0.00 0.00 1.73
2496 2583 1.686325 GCCAGGAGCGAGGACCATTA 61.686 60.000 0.00 0.00 0.00 1.90
2497 2584 3.036429 GCCAGGAGCGAGGACCATT 62.036 63.158 0.00 0.00 0.00 3.16
2498 2585 3.474570 GCCAGGAGCGAGGACCAT 61.475 66.667 0.00 0.00 0.00 3.55
2504 2591 4.020617 TTGTGGGCCAGGAGCGAG 62.021 66.667 6.40 0.00 45.17 5.03
2505 2592 4.329545 GTTGTGGGCCAGGAGCGA 62.330 66.667 6.40 0.00 45.17 4.93
2507 2594 3.590466 ATGGTTGTGGGCCAGGAGC 62.590 63.158 6.40 9.05 39.65 4.70
2508 2595 0.542702 AAATGGTTGTGGGCCAGGAG 60.543 55.000 6.40 0.00 39.65 3.69
2509 2596 0.831288 CAAATGGTTGTGGGCCAGGA 60.831 55.000 6.40 0.00 39.65 3.86
2510 2597 1.120795 ACAAATGGTTGTGGGCCAGG 61.121 55.000 6.40 0.00 46.40 4.45
2511 2598 2.439837 ACAAATGGTTGTGGGCCAG 58.560 52.632 6.40 0.00 46.40 4.85
2512 2599 4.716025 ACAAATGGTTGTGGGCCA 57.284 50.000 0.00 0.00 46.40 5.36
2519 2606 1.616159 AGAACCGGGACAAATGGTTG 58.384 50.000 6.32 0.00 45.63 3.77
2521 2608 1.880646 CGAAGAACCGGGACAAATGGT 60.881 52.381 6.32 0.00 37.68 3.55
2522 2609 0.802494 CGAAGAACCGGGACAAATGG 59.198 55.000 6.32 0.00 0.00 3.16
2523 2610 0.168128 GCGAAGAACCGGGACAAATG 59.832 55.000 6.32 0.00 0.00 2.32
2524 2611 0.250553 TGCGAAGAACCGGGACAAAT 60.251 50.000 6.32 0.00 0.00 2.32
2525 2612 0.250553 ATGCGAAGAACCGGGACAAA 60.251 50.000 6.32 0.00 0.00 2.83
2526 2613 0.953471 CATGCGAAGAACCGGGACAA 60.953 55.000 6.32 0.00 0.00 3.18
2527 2614 1.375396 CATGCGAAGAACCGGGACA 60.375 57.895 6.32 0.00 0.00 4.02
2528 2615 0.672401 TTCATGCGAAGAACCGGGAC 60.672 55.000 6.32 0.00 0.00 4.46
2529 2616 0.672401 GTTCATGCGAAGAACCGGGA 60.672 55.000 6.32 0.00 39.48 5.14
2530 2617 1.794222 GTTCATGCGAAGAACCGGG 59.206 57.895 6.32 0.00 39.48 5.73
2534 2621 0.672401 TCCCGGTTCATGCGAAGAAC 60.672 55.000 0.00 7.07 43.49 3.01
2535 2622 0.672401 GTCCCGGTTCATGCGAAGAA 60.672 55.000 0.00 0.00 0.00 2.52
2536 2623 1.079405 GTCCCGGTTCATGCGAAGA 60.079 57.895 0.00 0.00 0.00 2.87
2537 2624 1.361668 CTGTCCCGGTTCATGCGAAG 61.362 60.000 0.00 0.00 0.00 3.79
2538 2625 1.375396 CTGTCCCGGTTCATGCGAA 60.375 57.895 0.00 0.00 0.00 4.70
2539 2626 1.822114 TTCTGTCCCGGTTCATGCGA 61.822 55.000 0.00 0.00 0.00 5.10
2540 2627 1.361668 CTTCTGTCCCGGTTCATGCG 61.362 60.000 0.00 0.00 0.00 4.73
2541 2628 1.026718 CCTTCTGTCCCGGTTCATGC 61.027 60.000 0.00 0.00 0.00 4.06
2542 2629 1.026718 GCCTTCTGTCCCGGTTCATG 61.027 60.000 0.00 0.00 0.00 3.07
2543 2630 1.201429 AGCCTTCTGTCCCGGTTCAT 61.201 55.000 0.00 0.00 0.00 2.57
2544 2631 1.827399 GAGCCTTCTGTCCCGGTTCA 61.827 60.000 0.00 0.00 0.00 3.18
2545 2632 1.079057 GAGCCTTCTGTCCCGGTTC 60.079 63.158 0.00 0.00 0.00 3.62
2546 2633 2.943978 CGAGCCTTCTGTCCCGGTT 61.944 63.158 0.00 0.00 0.00 4.44
2547 2634 3.382832 CGAGCCTTCTGTCCCGGT 61.383 66.667 0.00 0.00 0.00 5.28
2548 2635 4.148825 CCGAGCCTTCTGTCCCGG 62.149 72.222 0.00 0.00 0.00 5.73
2549 2636 1.961180 AATCCGAGCCTTCTGTCCCG 61.961 60.000 0.00 0.00 0.00 5.14
2550 2637 0.253327 AAATCCGAGCCTTCTGTCCC 59.747 55.000 0.00 0.00 0.00 4.46
2551 2638 2.168728 ACTAAATCCGAGCCTTCTGTCC 59.831 50.000 0.00 0.00 0.00 4.02
2552 2639 3.528597 ACTAAATCCGAGCCTTCTGTC 57.471 47.619 0.00 0.00 0.00 3.51
2553 2640 3.132467 GGTACTAAATCCGAGCCTTCTGT 59.868 47.826 0.00 0.00 0.00 3.41
2554 2641 3.718815 GGTACTAAATCCGAGCCTTCTG 58.281 50.000 0.00 0.00 0.00 3.02
2563 2650 2.542595 GCATGAACCGGTACTAAATCCG 59.457 50.000 8.00 0.00 45.42 4.18
2564 2651 2.876550 GGCATGAACCGGTACTAAATCC 59.123 50.000 8.00 0.00 0.00 3.01
2565 2652 3.311596 GTGGCATGAACCGGTACTAAATC 59.688 47.826 8.00 0.00 0.00 2.17
2566 2653 3.275999 GTGGCATGAACCGGTACTAAAT 58.724 45.455 8.00 0.00 0.00 1.40
2567 2654 2.702261 GTGGCATGAACCGGTACTAAA 58.298 47.619 8.00 0.00 0.00 1.85
2568 2655 1.404449 CGTGGCATGAACCGGTACTAA 60.404 52.381 8.00 0.00 0.00 2.24
2569 2656 0.173935 CGTGGCATGAACCGGTACTA 59.826 55.000 8.00 0.00 0.00 1.82
2570 2657 1.079405 CGTGGCATGAACCGGTACT 60.079 57.895 8.00 0.00 0.00 2.73
2571 2658 0.671163 TTCGTGGCATGAACCGGTAC 60.671 55.000 17.86 0.00 0.00 3.34
2572 2659 0.671163 GTTCGTGGCATGAACCGGTA 60.671 55.000 32.65 6.85 37.98 4.02
2573 2660 1.964373 GTTCGTGGCATGAACCGGT 60.964 57.895 32.65 0.00 37.98 5.28
2574 2661 2.867472 GTTCGTGGCATGAACCGG 59.133 61.111 32.65 0.00 37.98 5.28
2577 2664 2.686816 CCCGGTTCGTGGCATGAAC 61.687 63.158 34.08 34.08 42.00 3.18
2578 2665 2.359354 CCCGGTTCGTGGCATGAA 60.359 61.111 17.86 17.86 0.00 2.57
2579 2666 3.315140 TCCCGGTTCGTGGCATGA 61.315 61.111 5.03 5.03 0.00 3.07
2580 2667 3.124921 GTCCCGGTTCGTGGCATG 61.125 66.667 0.00 0.00 0.00 4.06
2581 2668 4.404098 GGTCCCGGTTCGTGGCAT 62.404 66.667 0.00 0.00 0.00 4.40
2583 2670 3.912745 ATTGGTCCCGGTTCGTGGC 62.913 63.158 0.00 0.00 0.00 5.01
2584 2671 2.038269 CATTGGTCCCGGTTCGTGG 61.038 63.158 0.00 0.00 0.00 4.94
2585 2672 1.004320 TCATTGGTCCCGGTTCGTG 60.004 57.895 0.00 0.00 0.00 4.35
2586 2673 1.295423 CTCATTGGTCCCGGTTCGT 59.705 57.895 0.00 0.00 0.00 3.85
2587 2674 1.449601 CCTCATTGGTCCCGGTTCG 60.450 63.158 0.00 0.00 0.00 3.95
2588 2675 4.637771 CCTCATTGGTCCCGGTTC 57.362 61.111 0.00 0.00 0.00 3.62
2597 2684 5.163195 GGGGTATATATAGGCACCTCATTGG 60.163 48.000 0.00 0.00 42.93 3.16
2598 2685 5.667626 AGGGGTATATATAGGCACCTCATTG 59.332 44.000 11.48 0.00 33.69 2.82
2599 2686 5.866346 AGGGGTATATATAGGCACCTCATT 58.134 41.667 11.48 0.00 33.69 2.57
2600 2687 5.468658 GAGGGGTATATATAGGCACCTCAT 58.531 45.833 22.80 8.48 42.10 2.90
2601 2688 4.630430 CGAGGGGTATATATAGGCACCTCA 60.630 50.000 25.16 0.00 42.52 3.86
2602 2689 3.890147 CGAGGGGTATATATAGGCACCTC 59.110 52.174 19.90 19.90 39.80 3.85
2603 2690 3.912248 CGAGGGGTATATATAGGCACCT 58.088 50.000 9.22 9.22 0.00 4.00
2604 2691 2.364647 GCGAGGGGTATATATAGGCACC 59.635 54.545 0.00 0.00 0.00 5.01
2605 2692 2.364647 GGCGAGGGGTATATATAGGCAC 59.635 54.545 0.00 0.00 0.00 5.01
2606 2693 2.674420 GGCGAGGGGTATATATAGGCA 58.326 52.381 0.00 0.00 0.00 4.75
2607 2694 1.969208 GGGCGAGGGGTATATATAGGC 59.031 57.143 0.00 0.00 0.00 3.93
2608 2695 2.236766 CGGGCGAGGGGTATATATAGG 58.763 57.143 0.00 0.00 0.00 2.57
2609 2696 1.612463 GCGGGCGAGGGGTATATATAG 59.388 57.143 0.00 0.00 0.00 1.31
2610 2697 1.696063 GCGGGCGAGGGGTATATATA 58.304 55.000 0.00 0.00 0.00 0.86
2611 2698 2.512973 GCGGGCGAGGGGTATATAT 58.487 57.895 0.00 0.00 0.00 0.86
2612 2699 4.023137 GCGGGCGAGGGGTATATA 57.977 61.111 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.