Multiple sequence alignment - TraesCS3A01G053100

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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 TraesCS3A01G053100 chr3A 100.000 2518 0 0 1 2518 29353062 29350545 0.000000e+00 4650.0
1 TraesCS3A01G053100 chr3A 97.110 1834 52 1 686 2518 29048195 29050028 0.000000e+00 3092.0
2 TraesCS3A01G053100 chr3A 92.044 905 51 4 1563 2446 29065215 29066119 0.000000e+00 1253.0
3 TraesCS3A01G053100 chr3A 97.652 511 12 0 688 1198 29064711 29065221 0.000000e+00 878.0
4 TraesCS3A01G053100 chr3A 93.417 319 11 1 31 349 29064401 29064709 4.910000e-127 464.0
5 TraesCS3A01G053100 chr3A 94.774 287 15 0 31 317 29037896 29038182 4.940000e-122 448.0
6 TraesCS3A01G053100 chrUn 84.323 842 118 9 952 1783 43664696 43665533 0.000000e+00 811.0
7 TraesCS3A01G053100 chrUn 85.290 707 95 7 951 1651 43770372 43771075 0.000000e+00 721.0
8 TraesCS3A01G053100 chrUn 79.777 717 132 11 966 1671 44529588 44528874 2.230000e-140 508.0
9 TraesCS3A01G053100 chrUn 79.224 722 135 13 963 1671 44271226 44271945 2.910000e-134 488.0
10 TraesCS3A01G053100 chrUn 79.144 724 134 15 963 1671 44297060 44297781 3.770000e-133 484.0
11 TraesCS3A01G053100 chrUn 83.462 520 79 6 945 1458 168641904 168641386 6.300000e-131 477.0
12 TraesCS3A01G053100 chrUn 90.196 51 3 2 2266 2315 215334736 215334785 5.810000e-07 65.8
13 TraesCS3A01G053100 chrUn 90.196 51 3 2 2266 2315 286307538 286307489 5.810000e-07 65.8
14 TraesCS3A01G053100 chrUn 90.196 51 3 2 2266 2315 286313821 286313772 5.810000e-07 65.8
15 TraesCS3A01G053100 chrUn 90.196 51 3 2 2266 2315 295782734 295782783 5.810000e-07 65.8
16 TraesCS3A01G053100 chr6D 94.379 338 14 4 351 686 302369803 302369469 4.800000e-142 514.0
17 TraesCS3A01G053100 chr6D 92.878 337 18 5 351 686 113673940 113673609 3.770000e-133 484.0
18 TraesCS3A01G053100 chr6D 85.882 85 11 1 1910 1994 361545838 361545921 3.450000e-14 89.8
19 TraesCS3A01G053100 chr6D 85.714 56 7 1 1785 1839 445614928 445614983 9.730000e-05 58.4
20 TraesCS3A01G053100 chr3B 84.462 502 74 4 945 1443 35212259 35212759 2.250000e-135 492.0
21 TraesCS3A01G053100 chr3B 84.462 502 74 4 945 1443 35288443 35288943 2.250000e-135 492.0
22 TraesCS3A01G053100 chr3B 90.741 54 5 0 1788 1841 822840810 822840757 3.470000e-09 73.1
23 TraesCS3A01G053100 chr2A 92.711 343 18 5 346 686 663358023 663357686 2.910000e-134 488.0
24 TraesCS3A01G053100 chr2A 92.308 338 20 5 351 686 116228067 116228400 2.270000e-130 475.0
25 TraesCS3A01G053100 chr2A 76.485 404 76 12 1933 2331 128477541 128477930 4.250000e-48 202.0
26 TraesCS3A01G053100 chr2A 91.935 62 4 1 1780 1841 666033960 666034020 4.460000e-13 86.1
27 TraesCS3A01G053100 chr2A 91.379 58 4 1 1785 1841 306178117 306178174 7.470000e-11 78.7
28 TraesCS3A01G053100 chr2A 90.164 61 5 1 1781 1841 651511830 651511889 7.470000e-11 78.7
29 TraesCS3A01G053100 chr4D 92.857 336 19 4 351 685 379622977 379622646 1.350000e-132 483.0
30 TraesCS3A01G053100 chr4D 92.308 338 21 4 351 686 352211938 352211604 2.270000e-130 475.0
31 TraesCS3A01G053100 chr4D 76.490 604 124 11 1913 2510 49161373 49160782 1.880000e-81 313.0
32 TraesCS3A01G053100 chr4D 75.526 523 108 14 1916 2430 150975157 150974647 3.240000e-59 239.0
33 TraesCS3A01G053100 chr4D 84.043 94 15 0 2279 2372 62306865 62306958 9.590000e-15 91.6
34 TraesCS3A01G053100 chr4D 88.333 60 5 2 1783 1841 94985288 94985230 1.250000e-08 71.3
35 TraesCS3A01G053100 chr1A 92.878 337 16 5 351 686 442216218 442215889 1.350000e-132 483.0
36 TraesCS3A01G053100 chr5A 92.582 337 18 5 351 686 501690658 501690988 6.300000e-131 477.0
37 TraesCS3A01G053100 chr1D 92.082 341 19 4 351 686 299496386 299496049 8.150000e-130 473.0
38 TraesCS3A01G053100 chr1D 100.000 34 0 0 2282 2315 422672963 422672930 2.090000e-06 63.9
39 TraesCS3A01G053100 chr1D 85.455 55 5 3 1784 1837 37415342 37415394 1.000000e-03 54.7
40 TraesCS3A01G053100 chr5D 77.905 611 129 6 1913 2518 565513250 565512641 2.360000e-100 375.0
41 TraesCS3A01G053100 chr5D 84.536 97 13 2 2276 2371 102271528 102271623 7.420000e-16 95.3
42 TraesCS3A01G053100 chr5D 92.727 55 4 0 1788 1842 27853053 27852999 2.080000e-11 80.5
43 TraesCS3A01G053100 chr5D 78.512 121 24 2 2285 2404 327125010 327125129 7.470000e-11 78.7
44 TraesCS3A01G053100 chr3D 79.174 557 105 11 1935 2485 488885752 488886303 2.360000e-100 375.0
45 TraesCS3A01G053100 chr3D 80.196 409 77 4 2104 2509 590126134 590126541 1.130000e-78 303.0
46 TraesCS3A01G053100 chr3D 87.500 64 4 4 1785 1845 524645198 524645136 1.250000e-08 71.3
47 TraesCS3A01G053100 chr2D 76.611 543 111 12 1965 2502 569945508 569946039 4.100000e-73 285.0
48 TraesCS3A01G053100 chr2D 93.220 59 3 1 1785 1842 215848445 215848503 4.460000e-13 86.1
49 TraesCS3A01G053100 chr2D 94.444 54 3 0 1788 1841 481447191 481447138 1.610000e-12 84.2
50 TraesCS3A01G053100 chr1B 76.122 557 121 12 1934 2481 575412148 575411595 5.300000e-72 281.0
51 TraesCS3A01G053100 chr1B 92.157 51 4 0 1790 1840 137616777 137616727 3.470000e-09 73.1
52 TraesCS3A01G053100 chr7B 77.363 402 75 10 1935 2331 495161515 495161905 9.060000e-55 224.0
53 TraesCS3A01G053100 chr6B 77.330 397 73 11 1940 2331 26888200 26888584 4.220000e-53 219.0
54 TraesCS3A01G053100 chr7A 91.026 78 7 0 1920 1997 229277660 229277583 3.430000e-19 106.0
55 TraesCS3A01G053100 chr7A 89.286 56 6 0 1786 1841 684111700 684111755 1.250000e-08 71.3
56 TraesCS3A01G053100 chr7D 74.823 282 41 17 2077 2353 17176351 17176095 1.590000e-17 100.0
57 TraesCS3A01G053100 chr7D 91.228 57 4 1 1787 1842 34751268 34751212 2.690000e-10 76.8
58 TraesCS3A01G053100 chr7D 95.455 44 1 1 1800 1842 478369844 478369801 4.490000e-08 69.4
59 TraesCS3A01G053100 chr2B 89.655 58 5 1 1785 1841 223156585 223156642 3.470000e-09 73.1
60 TraesCS3A01G053100 chr5B 88.889 54 5 1 1792 1844 69806153 69806206 5.810000e-07 65.8


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 TraesCS3A01G053100 chr3A 29350545 29353062 2517 True 4650 4650 100.000 1 2518 1 chr3A.!!$R1 2517
1 TraesCS3A01G053100 chr3A 29048195 29050028 1833 False 3092 3092 97.110 686 2518 1 chr3A.!!$F2 1832
2 TraesCS3A01G053100 chr3A 29064401 29066119 1718 False 865 1253 94.371 31 2446 3 chr3A.!!$F3 2415
3 TraesCS3A01G053100 chrUn 43664696 43665533 837 False 811 811 84.323 952 1783 1 chrUn.!!$F1 831
4 TraesCS3A01G053100 chrUn 43770372 43771075 703 False 721 721 85.290 951 1651 1 chrUn.!!$F2 700
5 TraesCS3A01G053100 chrUn 44528874 44529588 714 True 508 508 79.777 966 1671 1 chrUn.!!$R1 705
6 TraesCS3A01G053100 chrUn 44271226 44271945 719 False 488 488 79.224 963 1671 1 chrUn.!!$F3 708
7 TraesCS3A01G053100 chrUn 44297060 44297781 721 False 484 484 79.144 963 1671 1 chrUn.!!$F4 708
8 TraesCS3A01G053100 chrUn 168641386 168641904 518 True 477 477 83.462 945 1458 1 chrUn.!!$R2 513
9 TraesCS3A01G053100 chr3B 35212259 35212759 500 False 492 492 84.462 945 1443 1 chr3B.!!$F1 498
10 TraesCS3A01G053100 chr3B 35288443 35288943 500 False 492 492 84.462 945 1443 1 chr3B.!!$F2 498
11 TraesCS3A01G053100 chr4D 49160782 49161373 591 True 313 313 76.490 1913 2510 1 chr4D.!!$R1 597
12 TraesCS3A01G053100 chr4D 150974647 150975157 510 True 239 239 75.526 1916 2430 1 chr4D.!!$R3 514
13 TraesCS3A01G053100 chr5D 565512641 565513250 609 True 375 375 77.905 1913 2518 1 chr5D.!!$R2 605
14 TraesCS3A01G053100 chr3D 488885752 488886303 551 False 375 375 79.174 1935 2485 1 chr3D.!!$F1 550
15 TraesCS3A01G053100 chr2D 569945508 569946039 531 False 285 285 76.611 1965 2502 1 chr2D.!!$F2 537
16 TraesCS3A01G053100 chr1B 575411595 575412148 553 True 281 281 76.122 1934 2481 1 chr1B.!!$R2 547

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
619 620 0.17899 GTCAGGGGTGCTTGGAACTT 60.179 55.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1874 0.680921 CATTGGATGGCGTTCCCTGT 60.681 55.0 4.07 0.0 34.67 4.0 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
17 18 4.592192 ATGCTCGGTCGATGGCGG 62.592 66.667 0.00 0.00 38.28 6.13
20 21 4.933064 CTCGGTCGATGGCGGCTC 62.933 72.222 11.43 4.41 42.88 4.70
23 24 3.224324 GGTCGATGGCGGCTCCTA 61.224 66.667 11.43 0.00 42.88 2.94
24 25 2.027751 GTCGATGGCGGCTCCTAC 59.972 66.667 11.43 0.00 39.48 3.18
25 26 3.592814 TCGATGGCGGCTCCTACG 61.593 66.667 11.43 8.80 38.28 3.51
26 27 3.592814 CGATGGCGGCTCCTACGA 61.593 66.667 11.43 0.00 36.67 3.43
27 28 2.812499 GATGGCGGCTCCTACGAA 59.188 61.111 11.43 0.00 35.26 3.85
28 29 1.367840 GATGGCGGCTCCTACGAAT 59.632 57.895 11.43 0.00 35.26 3.34
29 30 0.601558 GATGGCGGCTCCTACGAATA 59.398 55.000 11.43 0.00 35.26 1.75
63 64 6.199342 CCAAAATTAATTAATACCCCGCAACG 59.801 38.462 11.07 0.00 0.00 4.10
79 80 3.730662 CGCAACGGATTCCAACATAAAGG 60.731 47.826 3.09 0.00 0.00 3.11
80 81 3.442273 GCAACGGATTCCAACATAAAGGA 59.558 43.478 3.09 0.00 0.00 3.36
181 182 6.128007 CGGCAAATTTACCTGAAAGATACTGT 60.128 38.462 5.90 0.00 34.07 3.55
182 183 7.251281 GGCAAATTTACCTGAAAGATACTGTC 58.749 38.462 0.00 0.00 34.07 3.51
183 184 7.121315 GGCAAATTTACCTGAAAGATACTGTCT 59.879 37.037 0.00 0.00 39.43 3.41
186 187 9.793259 AAATTTACCTGAAAGATACTGTCTTCA 57.207 29.630 0.00 0.00 46.39 3.02
187 188 9.965902 AATTTACCTGAAAGATACTGTCTTCAT 57.034 29.630 0.00 0.00 46.39 2.57
227 228 7.636150 ACTAGTTAAAATGCAGCTCATGATT 57.364 32.000 0.00 0.00 35.13 2.57
296 297 0.457853 TAGTTGATCGCCGACAGTGC 60.458 55.000 0.00 0.00 0.00 4.40
329 330 4.142049 TGCGTCATCATATGGTGTAGTTCA 60.142 41.667 15.54 5.67 0.00 3.18
349 350 3.258372 TCACTAGTCGAGCTCACCAAATT 59.742 43.478 15.40 0.00 0.00 1.82
351 352 4.800993 CACTAGTCGAGCTCACCAAATTAG 59.199 45.833 15.40 10.16 0.00 1.73
352 353 4.705507 ACTAGTCGAGCTCACCAAATTAGA 59.294 41.667 15.40 0.00 0.00 2.10
353 354 4.116747 AGTCGAGCTCACCAAATTAGAG 57.883 45.455 15.40 0.00 0.00 2.43
354 355 3.764434 AGTCGAGCTCACCAAATTAGAGA 59.236 43.478 15.40 0.00 0.00 3.10
355 356 4.109050 GTCGAGCTCACCAAATTAGAGAG 58.891 47.826 15.40 0.00 0.00 3.20
356 357 3.764434 TCGAGCTCACCAAATTAGAGAGT 59.236 43.478 15.40 0.00 0.00 3.24
357 358 3.862267 CGAGCTCACCAAATTAGAGAGTG 59.138 47.826 15.40 0.00 0.00 3.51
358 359 3.604582 AGCTCACCAAATTAGAGAGTGC 58.395 45.455 0.00 0.00 0.00 4.40
359 360 3.262915 AGCTCACCAAATTAGAGAGTGCT 59.737 43.478 0.00 0.00 0.00 4.40
360 361 4.006319 GCTCACCAAATTAGAGAGTGCTT 58.994 43.478 0.00 0.00 0.00 3.91
361 362 4.142730 GCTCACCAAATTAGAGAGTGCTTG 60.143 45.833 0.00 0.00 0.00 4.01
362 363 4.326826 TCACCAAATTAGAGAGTGCTTGG 58.673 43.478 0.00 0.00 39.38 3.61
363 364 4.041567 TCACCAAATTAGAGAGTGCTTGGA 59.958 41.667 5.69 0.00 37.38 3.53
364 365 4.946157 CACCAAATTAGAGAGTGCTTGGAT 59.054 41.667 5.69 0.00 37.38 3.41
365 366 6.070251 TCACCAAATTAGAGAGTGCTTGGATA 60.070 38.462 5.69 0.00 37.38 2.59
366 367 6.037610 CACCAAATTAGAGAGTGCTTGGATAC 59.962 42.308 5.69 0.00 37.38 2.24
367 368 5.235186 CCAAATTAGAGAGTGCTTGGATACG 59.765 44.000 0.00 0.00 36.26 3.06
368 369 5.599999 AATTAGAGAGTGCTTGGATACGT 57.400 39.130 0.00 0.00 42.51 3.57
369 370 5.599999 ATTAGAGAGTGCTTGGATACGTT 57.400 39.130 0.00 0.00 42.51 3.99
370 371 3.963428 AGAGAGTGCTTGGATACGTTT 57.037 42.857 0.00 0.00 42.51 3.60
371 372 4.273148 AGAGAGTGCTTGGATACGTTTT 57.727 40.909 0.00 0.00 42.51 2.43
372 373 5.401531 AGAGAGTGCTTGGATACGTTTTA 57.598 39.130 0.00 0.00 42.51 1.52
373 374 5.411781 AGAGAGTGCTTGGATACGTTTTAG 58.588 41.667 0.00 0.00 42.51 1.85
374 375 5.047235 AGAGAGTGCTTGGATACGTTTTAGT 60.047 40.000 0.00 0.00 42.51 2.24
375 376 5.169295 AGAGTGCTTGGATACGTTTTAGTC 58.831 41.667 0.00 0.00 42.51 2.59
376 377 4.251268 AGTGCTTGGATACGTTTTAGTCC 58.749 43.478 0.00 0.00 42.51 3.85
377 378 3.373130 GTGCTTGGATACGTTTTAGTCCC 59.627 47.826 0.00 0.00 42.51 4.46
378 379 3.008157 TGCTTGGATACGTTTTAGTCCCA 59.992 43.478 0.00 0.00 42.51 4.37
379 380 4.196971 GCTTGGATACGTTTTAGTCCCAT 58.803 43.478 0.00 0.00 42.51 4.00
380 381 4.035208 GCTTGGATACGTTTTAGTCCCATG 59.965 45.833 0.00 0.00 42.51 3.66
381 382 5.423704 TTGGATACGTTTTAGTCCCATGA 57.576 39.130 0.00 0.00 42.51 3.07
382 383 4.761975 TGGATACGTTTTAGTCCCATGAC 58.238 43.478 0.00 0.00 40.25 3.06
384 385 5.657745 TGGATACGTTTTAGTCCCATGACTA 59.342 40.000 0.00 0.00 45.97 2.59
398 399 7.793036 GTCCCATGACTAAAATTAGTAGGACT 58.207 38.462 22.03 0.00 43.64 3.85
399 400 8.921205 GTCCCATGACTAAAATTAGTAGGACTA 58.079 37.037 22.03 8.87 43.64 2.59
400 401 9.496710 TCCCATGACTAAAATTAGTAGGACTAA 57.503 33.333 15.19 1.75 43.64 2.24
411 412 8.664211 AATTAGTAGGACTAAAACATGCTAGC 57.336 34.615 8.10 8.10 43.16 3.42
412 413 5.024785 AGTAGGACTAAAACATGCTAGCC 57.975 43.478 13.29 0.00 0.00 3.93
413 414 4.717280 AGTAGGACTAAAACATGCTAGCCT 59.283 41.667 13.29 0.00 0.00 4.58
414 415 4.143986 AGGACTAAAACATGCTAGCCTC 57.856 45.455 13.29 0.00 0.00 4.70
415 416 3.519510 AGGACTAAAACATGCTAGCCTCA 59.480 43.478 13.29 0.00 0.00 3.86
416 417 4.164988 AGGACTAAAACATGCTAGCCTCAT 59.835 41.667 13.29 0.00 0.00 2.90
417 418 4.513318 GGACTAAAACATGCTAGCCTCATC 59.487 45.833 13.29 0.00 0.00 2.92
418 419 4.455606 ACTAAAACATGCTAGCCTCATCC 58.544 43.478 13.29 0.00 0.00 3.51
419 420 3.370840 AAAACATGCTAGCCTCATCCA 57.629 42.857 13.29 0.00 0.00 3.41
420 421 3.589951 AAACATGCTAGCCTCATCCAT 57.410 42.857 13.29 0.00 0.00 3.41
421 422 2.563261 ACATGCTAGCCTCATCCATG 57.437 50.000 13.29 9.71 39.23 3.66
422 423 1.773052 ACATGCTAGCCTCATCCATGT 59.227 47.619 13.29 10.38 40.99 3.21
423 424 2.174210 ACATGCTAGCCTCATCCATGTT 59.826 45.455 13.29 0.00 42.58 2.71
424 425 3.220110 CATGCTAGCCTCATCCATGTTT 58.780 45.455 13.29 0.00 0.00 2.83
425 426 2.646930 TGCTAGCCTCATCCATGTTTG 58.353 47.619 13.29 0.00 0.00 2.93
426 427 1.952296 GCTAGCCTCATCCATGTTTGG 59.048 52.381 2.29 0.00 45.15 3.28
486 487 7.919385 ATGCATTTATTATCCTTCAAACCCT 57.081 32.000 0.00 0.00 0.00 4.34
487 488 7.346751 TGCATTTATTATCCTTCAAACCCTC 57.653 36.000 0.00 0.00 0.00 4.30
488 489 6.323739 TGCATTTATTATCCTTCAAACCCTCC 59.676 38.462 0.00 0.00 0.00 4.30
489 490 6.551227 GCATTTATTATCCTTCAAACCCTCCT 59.449 38.462 0.00 0.00 0.00 3.69
490 491 7.724061 GCATTTATTATCCTTCAAACCCTCCTA 59.276 37.037 0.00 0.00 0.00 2.94
491 492 9.813826 CATTTATTATCCTTCAAACCCTCCTAT 57.186 33.333 0.00 0.00 0.00 2.57
493 494 5.906772 TTATCCTTCAAACCCTCCTATCC 57.093 43.478 0.00 0.00 0.00 2.59
494 495 3.214694 TCCTTCAAACCCTCCTATCCA 57.785 47.619 0.00 0.00 0.00 3.41
495 496 3.115390 TCCTTCAAACCCTCCTATCCAG 58.885 50.000 0.00 0.00 0.00 3.86
496 497 3.115390 CCTTCAAACCCTCCTATCCAGA 58.885 50.000 0.00 0.00 0.00 3.86
497 498 3.523564 CCTTCAAACCCTCCTATCCAGAA 59.476 47.826 0.00 0.00 0.00 3.02
498 499 4.518249 CTTCAAACCCTCCTATCCAGAAC 58.482 47.826 0.00 0.00 0.00 3.01
499 500 3.803340 TCAAACCCTCCTATCCAGAACT 58.197 45.455 0.00 0.00 0.00 3.01
500 501 3.775316 TCAAACCCTCCTATCCAGAACTC 59.225 47.826 0.00 0.00 0.00 3.01
501 502 2.074729 ACCCTCCTATCCAGAACTCG 57.925 55.000 0.00 0.00 0.00 4.18
502 503 0.676736 CCCTCCTATCCAGAACTCGC 59.323 60.000 0.00 0.00 0.00 5.03
503 504 0.676736 CCTCCTATCCAGAACTCGCC 59.323 60.000 0.00 0.00 0.00 5.54
504 505 1.698506 CTCCTATCCAGAACTCGCCT 58.301 55.000 0.00 0.00 0.00 5.52
505 506 1.339610 CTCCTATCCAGAACTCGCCTG 59.660 57.143 0.00 0.00 0.00 4.85
506 507 1.115467 CCTATCCAGAACTCGCCTGT 58.885 55.000 0.00 0.00 0.00 4.00
507 508 1.202463 CCTATCCAGAACTCGCCTGTG 60.202 57.143 0.00 0.00 0.00 3.66
508 509 1.478510 CTATCCAGAACTCGCCTGTGT 59.521 52.381 0.00 0.00 0.00 3.72
509 510 0.687354 ATCCAGAACTCGCCTGTGTT 59.313 50.000 0.00 0.00 34.68 3.32
510 511 1.334160 TCCAGAACTCGCCTGTGTTA 58.666 50.000 0.00 0.00 32.29 2.41
511 512 1.689813 TCCAGAACTCGCCTGTGTTAA 59.310 47.619 0.00 0.00 32.29 2.01
512 513 2.103432 TCCAGAACTCGCCTGTGTTAAA 59.897 45.455 0.00 0.00 32.29 1.52
513 514 2.480419 CCAGAACTCGCCTGTGTTAAAG 59.520 50.000 0.00 0.00 32.29 1.85
514 515 3.390135 CAGAACTCGCCTGTGTTAAAGA 58.610 45.455 0.00 0.00 32.29 2.52
515 516 3.430218 CAGAACTCGCCTGTGTTAAAGAG 59.570 47.826 0.00 0.00 32.29 2.85
516 517 3.321111 AGAACTCGCCTGTGTTAAAGAGA 59.679 43.478 0.00 0.00 32.29 3.10
517 518 3.305398 ACTCGCCTGTGTTAAAGAGAG 57.695 47.619 0.00 0.00 0.00 3.20
518 519 2.028930 ACTCGCCTGTGTTAAAGAGAGG 60.029 50.000 0.00 0.00 0.00 3.69
519 520 2.231478 CTCGCCTGTGTTAAAGAGAGGA 59.769 50.000 3.68 0.00 0.00 3.71
520 521 2.231478 TCGCCTGTGTTAAAGAGAGGAG 59.769 50.000 3.68 0.99 0.00 3.69
521 522 2.028930 CGCCTGTGTTAAAGAGAGGAGT 60.029 50.000 3.68 0.00 0.00 3.85
522 523 3.555168 CGCCTGTGTTAAAGAGAGGAGTT 60.555 47.826 3.68 0.00 0.00 3.01
523 524 4.321750 CGCCTGTGTTAAAGAGAGGAGTTA 60.322 45.833 3.68 0.00 0.00 2.24
524 525 5.548406 GCCTGTGTTAAAGAGAGGAGTTAA 58.452 41.667 3.68 0.00 0.00 2.01
525 526 5.995897 GCCTGTGTTAAAGAGAGGAGTTAAA 59.004 40.000 3.68 0.00 0.00 1.52
526 527 6.655425 GCCTGTGTTAAAGAGAGGAGTTAAAT 59.345 38.462 3.68 0.00 0.00 1.40
527 528 7.361286 GCCTGTGTTAAAGAGAGGAGTTAAATG 60.361 40.741 3.68 0.00 0.00 2.32
528 529 7.878127 CCTGTGTTAAAGAGAGGAGTTAAATGA 59.122 37.037 0.00 0.00 0.00 2.57
529 530 8.833231 TGTGTTAAAGAGAGGAGTTAAATGAG 57.167 34.615 0.00 0.00 0.00 2.90
530 531 8.429641 TGTGTTAAAGAGAGGAGTTAAATGAGT 58.570 33.333 0.00 0.00 0.00 3.41
531 532 9.924650 GTGTTAAAGAGAGGAGTTAAATGAGTA 57.075 33.333 0.00 0.00 0.00 2.59
535 536 8.887264 AAAGAGAGGAGTTAAATGAGTAGAGA 57.113 34.615 0.00 0.00 0.00 3.10
536 537 8.519799 AAGAGAGGAGTTAAATGAGTAGAGAG 57.480 38.462 0.00 0.00 0.00 3.20
537 538 7.867921 AGAGAGGAGTTAAATGAGTAGAGAGA 58.132 38.462 0.00 0.00 0.00 3.10
538 539 7.993183 AGAGAGGAGTTAAATGAGTAGAGAGAG 59.007 40.741 0.00 0.00 0.00 3.20
539 540 7.060421 AGAGGAGTTAAATGAGTAGAGAGAGG 58.940 42.308 0.00 0.00 0.00 3.69
540 541 6.975949 AGGAGTTAAATGAGTAGAGAGAGGA 58.024 40.000 0.00 0.00 0.00 3.71
541 542 6.831868 AGGAGTTAAATGAGTAGAGAGAGGAC 59.168 42.308 0.00 0.00 0.00 3.85
542 543 6.831868 GGAGTTAAATGAGTAGAGAGAGGACT 59.168 42.308 0.00 0.00 0.00 3.85
543 544 7.994334 GGAGTTAAATGAGTAGAGAGAGGACTA 59.006 40.741 0.00 0.00 0.00 2.59
544 545 9.398538 GAGTTAAATGAGTAGAGAGAGGACTAA 57.601 37.037 0.00 0.00 0.00 2.24
545 546 9.930158 AGTTAAATGAGTAGAGAGAGGACTAAT 57.070 33.333 0.00 0.00 0.00 1.73
547 548 7.833285 AAATGAGTAGAGAGAGGACTAATCC 57.167 40.000 0.00 0.00 46.69 3.01
562 563 6.296803 GGACTAATCCACATTTTAGTAGGGG 58.703 44.000 0.00 0.00 45.47 4.79
563 564 6.126565 GGACTAATCCACATTTTAGTAGGGGT 60.127 42.308 0.00 0.00 45.47 4.95
564 565 7.071572 GGACTAATCCACATTTTAGTAGGGGTA 59.928 40.741 0.00 0.00 45.47 3.69
565 566 7.799081 ACTAATCCACATTTTAGTAGGGGTAC 58.201 38.462 0.00 0.00 36.99 3.34
566 567 7.147426 ACTAATCCACATTTTAGTAGGGGTACC 60.147 40.741 2.17 2.17 41.38 3.34
601 602 8.951614 AAAAATTTAGTTAGCCCCTCTTTAGT 57.048 30.769 0.00 0.00 0.00 2.24
602 603 8.577048 AAAATTTAGTTAGCCCCTCTTTAGTC 57.423 34.615 0.00 0.00 0.00 2.59
603 604 6.886178 ATTTAGTTAGCCCCTCTTTAGTCA 57.114 37.500 0.00 0.00 0.00 3.41
604 605 5.934402 TTAGTTAGCCCCTCTTTAGTCAG 57.066 43.478 0.00 0.00 0.00 3.51
605 606 3.108376 AGTTAGCCCCTCTTTAGTCAGG 58.892 50.000 0.00 0.00 0.00 3.86
610 611 0.253327 CCCTCTTTAGTCAGGGGTGC 59.747 60.000 0.00 0.00 45.39 5.01
611 612 1.280457 CCTCTTTAGTCAGGGGTGCT 58.720 55.000 0.00 0.00 28.24 4.40
612 613 1.630878 CCTCTTTAGTCAGGGGTGCTT 59.369 52.381 0.00 0.00 28.24 3.91
613 614 2.616510 CCTCTTTAGTCAGGGGTGCTTG 60.617 54.545 0.00 0.00 28.24 4.01
614 615 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
615 616 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
616 617 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
617 618 0.690762 TAGTCAGGGGTGCTTGGAAC 59.309 55.000 0.00 0.00 0.00 3.62
618 619 1.062488 AGTCAGGGGTGCTTGGAACT 61.062 55.000 0.00 0.00 0.00 3.01
619 620 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.000 0.00 0.00 0.00 2.66
620 621 0.555769 TCAGGGGTGCTTGGAACTTT 59.444 50.000 0.00 0.00 0.00 2.66
621 622 1.777878 TCAGGGGTGCTTGGAACTTTA 59.222 47.619 0.00 0.00 0.00 1.85
622 623 2.162681 CAGGGGTGCTTGGAACTTTAG 58.837 52.381 0.00 0.00 0.00 1.85
623 624 0.888619 GGGGTGCTTGGAACTTTAGC 59.111 55.000 0.00 0.00 35.50 3.09
624 625 0.888619 GGGTGCTTGGAACTTTAGCC 59.111 55.000 0.00 0.00 34.03 3.93
625 626 1.547901 GGGTGCTTGGAACTTTAGCCT 60.548 52.381 0.00 0.00 34.03 4.58
626 627 1.813178 GGTGCTTGGAACTTTAGCCTC 59.187 52.381 0.00 0.00 34.03 4.70
627 628 2.553247 GGTGCTTGGAACTTTAGCCTCT 60.553 50.000 0.00 0.00 34.03 3.69
628 629 3.149981 GTGCTTGGAACTTTAGCCTCTT 58.850 45.455 0.00 0.00 34.03 2.85
629 630 4.324267 GTGCTTGGAACTTTAGCCTCTTA 58.676 43.478 0.00 0.00 34.03 2.10
630 631 4.760204 GTGCTTGGAACTTTAGCCTCTTAA 59.240 41.667 0.00 0.00 34.03 1.85
631 632 5.240844 GTGCTTGGAACTTTAGCCTCTTAAA 59.759 40.000 0.00 0.00 34.03 1.52
632 633 5.473504 TGCTTGGAACTTTAGCCTCTTAAAG 59.526 40.000 4.46 4.46 43.21 1.85
633 634 5.705905 GCTTGGAACTTTAGCCTCTTAAAGA 59.294 40.000 11.30 0.00 41.17 2.52
634 635 6.128145 GCTTGGAACTTTAGCCTCTTAAAGAG 60.128 42.308 11.30 0.56 41.17 2.85
635 636 6.681729 TGGAACTTTAGCCTCTTAAAGAGA 57.318 37.500 11.30 0.00 45.07 3.10
672 673 9.942526 ATTCAGACTAAAATAAATCCCTTGGAT 57.057 29.630 0.00 0.00 45.46 3.41
673 674 8.980481 TCAGACTAAAATAAATCCCTTGGATC 57.020 34.615 0.00 0.00 42.27 3.36
674 675 7.998964 TCAGACTAAAATAAATCCCTTGGATCC 59.001 37.037 4.20 4.20 42.27 3.36
675 676 7.779798 CAGACTAAAATAAATCCCTTGGATCCA 59.220 37.037 11.44 11.44 42.27 3.41
676 677 8.343787 AGACTAAAATAAATCCCTTGGATCCAA 58.656 33.333 25.53 25.53 42.27 3.53
684 685 3.181526 CTTGGATCCAAGCACCCTC 57.818 57.895 35.47 0.00 45.38 4.30
838 839 2.088423 GCCGAATACAACATCCAACCA 58.912 47.619 0.00 0.00 0.00 3.67
1049 1051 1.859703 GTCATCTCATCTTCTGCAGCG 59.140 52.381 9.47 2.34 0.00 5.18
1154 1156 1.842562 ACAATGCTCCTCATAGCCACT 59.157 47.619 0.00 0.00 42.05 4.00
1181 1183 0.531532 CCATCTCATGCGGTCAGGTC 60.532 60.000 0.00 0.00 0.00 3.85
1380 1382 2.233566 ATCCCCTCCAAGTGCAGCA 61.234 57.895 0.00 0.00 0.00 4.41
1412 1414 2.685999 GCCATCAGCCCTTCCCTT 59.314 61.111 0.00 0.00 34.35 3.95
1651 1686 5.100943 GGAGACACGAGACTTTATTGTACC 58.899 45.833 0.00 0.00 0.00 3.34
1688 1727 7.773149 ACACTTCTAGTATGTGGATTGTACTC 58.227 38.462 13.70 0.00 37.52 2.59
1728 1767 6.090358 CAGGTACTTTACTCCACATAACAACG 59.910 42.308 0.00 0.00 34.60 4.10
1861 1900 1.228063 CGCCATCCAATGCTAGCCT 60.228 57.895 13.29 0.00 0.00 4.58
1883 1922 6.033966 CCTTATAAAACGAGCCAACAATTCC 58.966 40.000 0.00 0.00 0.00 3.01
2098 2146 0.536460 CTTGGGCTTAACGTGGTGGT 60.536 55.000 0.00 0.00 0.00 4.16
2192 2256 3.671971 GCTCCGTCATTATCTCGATCTGG 60.672 52.174 0.00 0.00 0.00 3.86
2237 2302 2.928396 CCACCTTGAGGGGTCGGT 60.928 66.667 1.54 0.00 36.70 4.69
2511 2595 4.040198 GAAGGGGGAGGGGAGGGT 62.040 72.222 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.592192 CCGCCATCGACCGAGCAT 62.592 66.667 3.83 0.00 38.10 3.79
3 4 4.933064 GAGCCGCCATCGACCGAG 62.933 72.222 3.83 0.00 38.10 4.63
6 7 3.224324 TAGGAGCCGCCATCGACC 61.224 66.667 0.00 0.00 40.02 4.79
7 8 2.027751 GTAGGAGCCGCCATCGAC 59.972 66.667 0.00 0.00 40.02 4.20
8 9 3.592814 CGTAGGAGCCGCCATCGA 61.593 66.667 0.00 0.00 40.02 3.59
9 10 2.421877 ATTCGTAGGAGCCGCCATCG 62.422 60.000 0.00 0.00 40.02 3.84
10 11 0.601558 TATTCGTAGGAGCCGCCATC 59.398 55.000 0.00 0.00 40.02 3.51
11 12 1.045407 TTATTCGTAGGAGCCGCCAT 58.955 50.000 0.00 0.00 40.02 4.40
12 13 0.825410 TTTATTCGTAGGAGCCGCCA 59.175 50.000 0.00 0.00 40.02 5.69
13 14 1.215244 GTTTATTCGTAGGAGCCGCC 58.785 55.000 0.00 0.00 0.00 6.13
14 15 1.215244 GGTTTATTCGTAGGAGCCGC 58.785 55.000 0.00 0.00 0.00 6.53
15 16 1.202336 ACGGTTTATTCGTAGGAGCCG 60.202 52.381 0.00 0.00 43.05 5.52
16 17 2.100418 AGACGGTTTATTCGTAGGAGCC 59.900 50.000 0.00 0.00 41.22 4.70
17 18 3.370276 GAGACGGTTTATTCGTAGGAGC 58.630 50.000 0.00 0.00 41.22 4.70
18 19 3.379372 TGGAGACGGTTTATTCGTAGGAG 59.621 47.826 0.00 0.00 41.22 3.69
19 20 3.355378 TGGAGACGGTTTATTCGTAGGA 58.645 45.455 0.00 0.00 41.22 2.94
20 21 3.788333 TGGAGACGGTTTATTCGTAGG 57.212 47.619 0.00 0.00 41.22 3.18
21 22 6.657836 ATTTTGGAGACGGTTTATTCGTAG 57.342 37.500 0.00 0.00 41.22 3.51
22 23 8.545229 TTAATTTTGGAGACGGTTTATTCGTA 57.455 30.769 0.00 0.00 41.22 3.43
23 24 5.952526 AATTTTGGAGACGGTTTATTCGT 57.047 34.783 0.00 0.00 44.03 3.85
24 25 8.905103 AATTAATTTTGGAGACGGTTTATTCG 57.095 30.769 0.00 0.00 0.00 3.34
63 64 4.770010 TGTGGTTCCTTTATGTTGGAATCC 59.230 41.667 0.00 0.00 41.45 3.01
66 67 6.739331 AATTGTGGTTCCTTTATGTTGGAA 57.261 33.333 0.00 0.00 39.73 3.53
76 77 4.021192 CCAGTGCATAAATTGTGGTTCCTT 60.021 41.667 0.00 0.00 0.00 3.36
79 80 3.056607 AGCCAGTGCATAAATTGTGGTTC 60.057 43.478 0.00 0.00 41.13 3.62
80 81 2.899256 AGCCAGTGCATAAATTGTGGTT 59.101 40.909 0.00 0.00 41.13 3.67
195 196 8.567285 AGCTGCATTTTAACTAGTATTGACTT 57.433 30.769 1.02 0.00 37.10 3.01
197 198 7.974675 TGAGCTGCATTTTAACTAGTATTGAC 58.025 34.615 1.02 0.00 0.00 3.18
216 217 3.306917 TTGTTGCCAAATCATGAGCTG 57.693 42.857 0.09 0.47 0.00 4.24
296 297 2.048222 ATGACGCAGGTGGTCGTG 60.048 61.111 0.00 0.00 39.22 4.35
329 330 3.963428 AATTTGGTGAGCTCGACTAGT 57.037 42.857 9.64 0.00 0.00 2.57
349 350 5.401531 AAAACGTATCCAAGCACTCTCTA 57.598 39.130 0.00 0.00 0.00 2.43
351 352 5.169295 ACTAAAACGTATCCAAGCACTCTC 58.831 41.667 0.00 0.00 0.00 3.20
352 353 5.148651 ACTAAAACGTATCCAAGCACTCT 57.851 39.130 0.00 0.00 0.00 3.24
353 354 4.329256 GGACTAAAACGTATCCAAGCACTC 59.671 45.833 0.00 0.00 0.00 3.51
354 355 4.251268 GGACTAAAACGTATCCAAGCACT 58.749 43.478 0.00 0.00 0.00 4.40
355 356 3.373130 GGGACTAAAACGTATCCAAGCAC 59.627 47.826 0.00 0.00 32.45 4.40
356 357 3.008157 TGGGACTAAAACGTATCCAAGCA 59.992 43.478 0.00 0.00 32.45 3.91
357 358 3.602483 TGGGACTAAAACGTATCCAAGC 58.398 45.455 0.00 0.00 32.45 4.01
358 359 5.293569 GTCATGGGACTAAAACGTATCCAAG 59.706 44.000 0.00 0.00 40.99 3.61
359 360 5.180271 GTCATGGGACTAAAACGTATCCAA 58.820 41.667 0.00 0.00 40.99 3.53
360 361 4.761975 GTCATGGGACTAAAACGTATCCA 58.238 43.478 0.00 0.00 40.99 3.41
373 374 7.793036 AGTCCTACTAATTTTAGTCATGGGAC 58.207 38.462 21.36 21.36 42.66 4.46
374 375 7.989947 AGTCCTACTAATTTTAGTCATGGGA 57.010 36.000 6.26 7.83 42.66 4.37
385 386 9.110502 GCTAGCATGTTTTAGTCCTACTAATTT 57.889 33.333 10.63 0.00 40.08 1.82
386 387 7.715686 GGCTAGCATGTTTTAGTCCTACTAATT 59.284 37.037 18.24 0.00 40.08 1.40
387 388 7.071321 AGGCTAGCATGTTTTAGTCCTACTAAT 59.929 37.037 18.24 0.00 40.08 1.73
388 389 6.383147 AGGCTAGCATGTTTTAGTCCTACTAA 59.617 38.462 18.24 0.00 38.79 2.24
389 390 5.897824 AGGCTAGCATGTTTTAGTCCTACTA 59.102 40.000 18.24 0.00 0.00 1.82
390 391 4.717280 AGGCTAGCATGTTTTAGTCCTACT 59.283 41.667 18.24 0.00 0.00 2.57
391 392 5.024785 AGGCTAGCATGTTTTAGTCCTAC 57.975 43.478 18.24 0.00 0.00 3.18
392 393 4.714802 TGAGGCTAGCATGTTTTAGTCCTA 59.285 41.667 18.24 0.00 0.00 2.94
393 394 3.519510 TGAGGCTAGCATGTTTTAGTCCT 59.480 43.478 18.24 0.00 0.00 3.85
394 395 3.873910 TGAGGCTAGCATGTTTTAGTCC 58.126 45.455 18.24 0.00 0.00 3.85
395 396 4.513318 GGATGAGGCTAGCATGTTTTAGTC 59.487 45.833 18.24 0.00 0.00 2.59
396 397 4.080356 TGGATGAGGCTAGCATGTTTTAGT 60.080 41.667 18.24 0.00 0.00 2.24
397 398 4.454678 TGGATGAGGCTAGCATGTTTTAG 58.545 43.478 18.24 0.00 0.00 1.85
398 399 4.502105 TGGATGAGGCTAGCATGTTTTA 57.498 40.909 18.24 0.00 0.00 1.52
399 400 3.370840 TGGATGAGGCTAGCATGTTTT 57.629 42.857 18.24 0.00 0.00 2.43
400 401 3.220110 CATGGATGAGGCTAGCATGTTT 58.780 45.455 18.24 0.00 0.00 2.83
401 402 2.174210 ACATGGATGAGGCTAGCATGTT 59.826 45.455 18.24 0.00 0.00 2.71
402 403 1.773052 ACATGGATGAGGCTAGCATGT 59.227 47.619 18.24 12.54 0.00 3.21
403 404 2.563261 ACATGGATGAGGCTAGCATG 57.437 50.000 18.24 11.88 0.00 4.06
404 405 3.220110 CAAACATGGATGAGGCTAGCAT 58.780 45.455 18.24 10.08 0.00 3.79
405 406 2.646930 CAAACATGGATGAGGCTAGCA 58.353 47.619 18.24 0.00 0.00 3.49
406 407 1.952296 CCAAACATGGATGAGGCTAGC 59.048 52.381 6.04 6.04 0.00 3.42
407 408 3.565764 TCCAAACATGGATGAGGCTAG 57.434 47.619 0.00 0.00 32.09 3.42
416 417 8.657387 TTTTAGTATTTGGATCCAAACATGGA 57.343 30.769 36.31 21.62 46.80 3.41
460 461 9.605951 AGGGTTTGAAGGATAATAAATGCATAT 57.394 29.630 0.00 0.00 0.00 1.78
461 462 9.077885 GAGGGTTTGAAGGATAATAAATGCATA 57.922 33.333 0.00 0.00 0.00 3.14
462 463 7.015584 GGAGGGTTTGAAGGATAATAAATGCAT 59.984 37.037 0.00 0.00 0.00 3.96
463 464 6.323739 GGAGGGTTTGAAGGATAATAAATGCA 59.676 38.462 0.00 0.00 0.00 3.96
464 465 6.551227 AGGAGGGTTTGAAGGATAATAAATGC 59.449 38.462 0.00 0.00 0.00 3.56
465 466 9.813826 ATAGGAGGGTTTGAAGGATAATAAATG 57.186 33.333 0.00 0.00 0.00 2.32
467 468 8.445588 GGATAGGAGGGTTTGAAGGATAATAAA 58.554 37.037 0.00 0.00 0.00 1.40
468 469 7.574750 TGGATAGGAGGGTTTGAAGGATAATAA 59.425 37.037 0.00 0.00 0.00 1.40
469 470 7.086260 TGGATAGGAGGGTTTGAAGGATAATA 58.914 38.462 0.00 0.00 0.00 0.98
470 471 5.917087 TGGATAGGAGGGTTTGAAGGATAAT 59.083 40.000 0.00 0.00 0.00 1.28
471 472 5.293643 TGGATAGGAGGGTTTGAAGGATAA 58.706 41.667 0.00 0.00 0.00 1.75
472 473 4.903149 TGGATAGGAGGGTTTGAAGGATA 58.097 43.478 0.00 0.00 0.00 2.59
473 474 3.718956 CTGGATAGGAGGGTTTGAAGGAT 59.281 47.826 0.00 0.00 0.00 3.24
474 475 3.115390 CTGGATAGGAGGGTTTGAAGGA 58.885 50.000 0.00 0.00 0.00 3.36
475 476 3.115390 TCTGGATAGGAGGGTTTGAAGG 58.885 50.000 0.00 0.00 0.00 3.46
476 477 4.226168 AGTTCTGGATAGGAGGGTTTGAAG 59.774 45.833 0.00 0.00 0.00 3.02
477 478 4.175962 AGTTCTGGATAGGAGGGTTTGAA 58.824 43.478 0.00 0.00 0.00 2.69
478 479 3.775316 GAGTTCTGGATAGGAGGGTTTGA 59.225 47.826 0.00 0.00 0.00 2.69
479 480 3.430929 CGAGTTCTGGATAGGAGGGTTTG 60.431 52.174 0.00 0.00 0.00 2.93
480 481 2.766828 CGAGTTCTGGATAGGAGGGTTT 59.233 50.000 0.00 0.00 0.00 3.27
481 482 2.389715 CGAGTTCTGGATAGGAGGGTT 58.610 52.381 0.00 0.00 0.00 4.11
482 483 2.030045 GCGAGTTCTGGATAGGAGGGT 61.030 57.143 0.00 0.00 0.00 4.34
483 484 0.676736 GCGAGTTCTGGATAGGAGGG 59.323 60.000 0.00 0.00 0.00 4.30
484 485 0.676736 GGCGAGTTCTGGATAGGAGG 59.323 60.000 0.00 0.00 0.00 4.30
485 486 1.339610 CAGGCGAGTTCTGGATAGGAG 59.660 57.143 0.00 0.00 0.00 3.69
486 487 1.342076 ACAGGCGAGTTCTGGATAGGA 60.342 52.381 0.00 0.00 36.62 2.94
487 488 1.115467 ACAGGCGAGTTCTGGATAGG 58.885 55.000 0.00 0.00 36.62 2.57
488 489 1.478510 ACACAGGCGAGTTCTGGATAG 59.521 52.381 0.00 0.00 36.62 2.08
489 490 1.557099 ACACAGGCGAGTTCTGGATA 58.443 50.000 0.00 0.00 36.62 2.59
490 491 0.687354 AACACAGGCGAGTTCTGGAT 59.313 50.000 0.00 0.00 36.62 3.41
491 492 1.334160 TAACACAGGCGAGTTCTGGA 58.666 50.000 0.00 0.00 36.62 3.86
492 493 2.163818 TTAACACAGGCGAGTTCTGG 57.836 50.000 0.00 0.00 36.62 3.86
493 494 3.390135 TCTTTAACACAGGCGAGTTCTG 58.610 45.455 0.00 0.00 38.16 3.02
494 495 3.321111 TCTCTTTAACACAGGCGAGTTCT 59.679 43.478 0.00 0.00 0.00 3.01
495 496 3.650139 TCTCTTTAACACAGGCGAGTTC 58.350 45.455 0.00 0.00 0.00 3.01
496 497 3.555168 CCTCTCTTTAACACAGGCGAGTT 60.555 47.826 0.00 0.00 0.00 3.01
497 498 2.028930 CCTCTCTTTAACACAGGCGAGT 60.029 50.000 0.00 0.00 0.00 4.18
498 499 2.231478 TCCTCTCTTTAACACAGGCGAG 59.769 50.000 0.00 0.00 0.00 5.03
499 500 2.231478 CTCCTCTCTTTAACACAGGCGA 59.769 50.000 0.00 0.00 0.00 5.54
500 501 2.028930 ACTCCTCTCTTTAACACAGGCG 60.029 50.000 0.00 0.00 0.00 5.52
501 502 3.686916 ACTCCTCTCTTTAACACAGGC 57.313 47.619 0.00 0.00 0.00 4.85
502 503 7.878127 TCATTTAACTCCTCTCTTTAACACAGG 59.122 37.037 0.00 0.00 0.00 4.00
503 504 8.833231 TCATTTAACTCCTCTCTTTAACACAG 57.167 34.615 0.00 0.00 0.00 3.66
504 505 8.429641 ACTCATTTAACTCCTCTCTTTAACACA 58.570 33.333 0.00 0.00 0.00 3.72
505 506 8.834749 ACTCATTTAACTCCTCTCTTTAACAC 57.165 34.615 0.00 0.00 0.00 3.32
509 510 9.976776 TCTCTACTCATTTAACTCCTCTCTTTA 57.023 33.333 0.00 0.00 0.00 1.85
510 511 8.887264 TCTCTACTCATTTAACTCCTCTCTTT 57.113 34.615 0.00 0.00 0.00 2.52
511 512 8.333235 TCTCTCTACTCATTTAACTCCTCTCTT 58.667 37.037 0.00 0.00 0.00 2.85
512 513 7.867921 TCTCTCTACTCATTTAACTCCTCTCT 58.132 38.462 0.00 0.00 0.00 3.10
513 514 7.228706 CCTCTCTCTACTCATTTAACTCCTCTC 59.771 44.444 0.00 0.00 0.00 3.20
514 515 7.060421 CCTCTCTCTACTCATTTAACTCCTCT 58.940 42.308 0.00 0.00 0.00 3.69
515 516 7.012989 GTCCTCTCTCTACTCATTTAACTCCTC 59.987 44.444 0.00 0.00 0.00 3.71
516 517 6.831868 GTCCTCTCTCTACTCATTTAACTCCT 59.168 42.308 0.00 0.00 0.00 3.69
517 518 6.831868 AGTCCTCTCTCTACTCATTTAACTCC 59.168 42.308 0.00 0.00 0.00 3.85
518 519 7.875327 AGTCCTCTCTCTACTCATTTAACTC 57.125 40.000 0.00 0.00 0.00 3.01
519 520 9.930158 ATTAGTCCTCTCTCTACTCATTTAACT 57.070 33.333 0.00 0.00 0.00 2.24
521 522 9.357161 GGATTAGTCCTCTCTCTACTCATTTAA 57.643 37.037 0.00 0.00 41.60 1.52
522 523 8.503573 TGGATTAGTCCTCTCTCTACTCATTTA 58.496 37.037 5.79 0.00 45.32 1.40
523 524 7.286775 GTGGATTAGTCCTCTCTCTACTCATTT 59.713 40.741 5.79 0.00 45.32 2.32
524 525 6.775629 GTGGATTAGTCCTCTCTCTACTCATT 59.224 42.308 5.79 0.00 45.32 2.57
525 526 6.126332 TGTGGATTAGTCCTCTCTCTACTCAT 60.126 42.308 5.79 0.00 45.32 2.90
526 527 5.191921 TGTGGATTAGTCCTCTCTCTACTCA 59.808 44.000 5.79 0.00 45.32 3.41
527 528 5.686753 TGTGGATTAGTCCTCTCTCTACTC 58.313 45.833 5.79 0.00 45.32 2.59
528 529 5.718801 TGTGGATTAGTCCTCTCTCTACT 57.281 43.478 5.79 0.00 45.32 2.57
529 530 6.969993 AATGTGGATTAGTCCTCTCTCTAC 57.030 41.667 5.79 0.00 45.32 2.59
530 531 7.979786 AAAATGTGGATTAGTCCTCTCTCTA 57.020 36.000 5.79 0.00 45.32 2.43
531 532 6.882768 AAAATGTGGATTAGTCCTCTCTCT 57.117 37.500 5.79 0.00 45.32 3.10
532 533 7.787028 ACTAAAATGTGGATTAGTCCTCTCTC 58.213 38.462 5.79 0.00 45.32 3.20
533 534 7.741554 ACTAAAATGTGGATTAGTCCTCTCT 57.258 36.000 5.79 0.00 45.32 3.10
534 535 8.145122 CCTACTAAAATGTGGATTAGTCCTCTC 58.855 40.741 5.79 0.00 45.32 3.20
535 536 7.071321 CCCTACTAAAATGTGGATTAGTCCTCT 59.929 40.741 5.79 0.00 45.32 3.69
536 537 7.217906 CCCTACTAAAATGTGGATTAGTCCTC 58.782 42.308 5.79 2.58 45.32 3.71
537 538 6.101296 CCCCTACTAAAATGTGGATTAGTCCT 59.899 42.308 5.79 0.00 45.32 3.85
538 539 6.126565 ACCCCTACTAAAATGTGGATTAGTCC 60.127 42.308 0.00 0.00 40.53 3.85
539 540 6.896883 ACCCCTACTAAAATGTGGATTAGTC 58.103 40.000 1.78 0.00 40.53 2.59
540 541 6.903340 ACCCCTACTAAAATGTGGATTAGT 57.097 37.500 3.93 3.93 43.05 2.24
541 542 7.222161 GGTACCCCTACTAAAATGTGGATTAG 58.778 42.308 0.00 0.00 35.67 1.73
542 543 7.140522 GGTACCCCTACTAAAATGTGGATTA 57.859 40.000 0.00 0.00 0.00 1.75
543 544 6.009908 GGTACCCCTACTAAAATGTGGATT 57.990 41.667 0.00 0.00 0.00 3.01
544 545 5.641789 GGTACCCCTACTAAAATGTGGAT 57.358 43.478 0.00 0.00 0.00 3.41
576 577 8.951614 ACTAAAGAGGGGCTAACTAAATTTTT 57.048 30.769 0.00 0.00 0.00 1.94
577 578 8.168058 TGACTAAAGAGGGGCTAACTAAATTTT 58.832 33.333 0.00 0.00 0.00 1.82
578 579 7.696017 TGACTAAAGAGGGGCTAACTAAATTT 58.304 34.615 0.00 0.00 0.00 1.82
579 580 7.266905 TGACTAAAGAGGGGCTAACTAAATT 57.733 36.000 0.00 0.00 0.00 1.82
580 581 6.126739 CCTGACTAAAGAGGGGCTAACTAAAT 60.127 42.308 0.00 0.00 0.00 1.40
581 582 5.189145 CCTGACTAAAGAGGGGCTAACTAAA 59.811 44.000 0.00 0.00 0.00 1.85
582 583 4.715297 CCTGACTAAAGAGGGGCTAACTAA 59.285 45.833 0.00 0.00 0.00 2.24
583 584 4.287552 CCTGACTAAAGAGGGGCTAACTA 58.712 47.826 0.00 0.00 0.00 2.24
584 585 3.108376 CCTGACTAAAGAGGGGCTAACT 58.892 50.000 0.00 0.00 0.00 2.24
585 586 2.170817 CCCTGACTAAAGAGGGGCTAAC 59.829 54.545 0.00 0.00 44.88 2.34
586 587 2.478292 CCCTGACTAAAGAGGGGCTAA 58.522 52.381 0.00 0.00 44.88 3.09
587 588 2.176247 CCCTGACTAAAGAGGGGCTA 57.824 55.000 0.00 0.00 44.88 3.93
588 589 3.013682 CCCTGACTAAAGAGGGGCT 57.986 57.895 0.00 0.00 44.88 5.19
592 593 1.280457 AGCACCCCTGACTAAAGAGG 58.720 55.000 0.00 0.00 0.00 3.69
593 594 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
594 595 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
595 596 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
596 597 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
597 598 1.073284 GTTCCAAGCACCCCTGACTAA 59.927 52.381 0.00 0.00 0.00 2.24
598 599 0.690762 GTTCCAAGCACCCCTGACTA 59.309 55.000 0.00 0.00 0.00 2.59
599 600 1.062488 AGTTCCAAGCACCCCTGACT 61.062 55.000 0.00 0.00 0.00 3.41
600 601 0.178990 AAGTTCCAAGCACCCCTGAC 60.179 55.000 0.00 0.00 0.00 3.51
601 602 0.555769 AAAGTTCCAAGCACCCCTGA 59.444 50.000 0.00 0.00 0.00 3.86
602 603 2.162681 CTAAAGTTCCAAGCACCCCTG 58.837 52.381 0.00 0.00 0.00 4.45
603 604 1.547901 GCTAAAGTTCCAAGCACCCCT 60.548 52.381 0.00 0.00 36.26 4.79
604 605 0.888619 GCTAAAGTTCCAAGCACCCC 59.111 55.000 0.00 0.00 36.26 4.95
605 606 0.888619 GGCTAAAGTTCCAAGCACCC 59.111 55.000 7.02 0.00 38.01 4.61
606 607 1.813178 GAGGCTAAAGTTCCAAGCACC 59.187 52.381 0.00 0.00 38.01 5.01
607 608 2.784347 AGAGGCTAAAGTTCCAAGCAC 58.216 47.619 0.00 2.09 38.01 4.40
608 609 3.508845 AAGAGGCTAAAGTTCCAAGCA 57.491 42.857 0.00 0.00 38.01 3.91
609 610 5.705905 TCTTTAAGAGGCTAAAGTTCCAAGC 59.294 40.000 7.84 0.00 39.12 4.01
610 611 7.162082 TCTCTTTAAGAGGCTAAAGTTCCAAG 58.838 38.462 20.29 0.00 42.54 3.61
611 612 7.074653 TCTCTTTAAGAGGCTAAAGTTCCAA 57.925 36.000 20.29 0.00 42.54 3.53
612 613 6.681729 TCTCTTTAAGAGGCTAAAGTTCCA 57.318 37.500 20.29 0.00 42.54 3.53
646 647 9.942526 ATCCAAGGGATTTATTTTAGTCTGAAT 57.057 29.630 0.00 0.00 39.79 2.57
647 648 9.408648 GATCCAAGGGATTTATTTTAGTCTGAA 57.591 33.333 0.00 0.00 43.27 3.02
648 649 7.998964 GGATCCAAGGGATTTATTTTAGTCTGA 59.001 37.037 6.95 0.00 43.27 3.27
649 650 7.779798 TGGATCCAAGGGATTTATTTTAGTCTG 59.220 37.037 13.46 0.00 43.27 3.51
650 651 7.882755 TGGATCCAAGGGATTTATTTTAGTCT 58.117 34.615 13.46 0.00 43.27 3.24
651 652 8.533569 TTGGATCCAAGGGATTTATTTTAGTC 57.466 34.615 23.63 0.00 43.27 2.59
652 653 8.539117 CTTGGATCCAAGGGATTTATTTTAGT 57.461 34.615 37.26 0.00 46.88 2.24
667 668 1.075601 AAGAGGGTGCTTGGATCCAA 58.924 50.000 25.53 25.53 0.00 3.53
668 669 1.965414 TAAGAGGGTGCTTGGATCCA 58.035 50.000 11.44 11.44 0.00 3.41
669 670 3.117888 TCAATAAGAGGGTGCTTGGATCC 60.118 47.826 4.20 4.20 0.00 3.36
670 671 4.156455 TCAATAAGAGGGTGCTTGGATC 57.844 45.455 0.00 0.00 0.00 3.36
671 672 4.166725 TGATCAATAAGAGGGTGCTTGGAT 59.833 41.667 0.00 0.00 0.00 3.41
672 673 3.523157 TGATCAATAAGAGGGTGCTTGGA 59.477 43.478 0.00 0.00 0.00 3.53
673 674 3.889815 TGATCAATAAGAGGGTGCTTGG 58.110 45.455 0.00 0.00 0.00 3.61
674 675 4.946157 AGTTGATCAATAAGAGGGTGCTTG 59.054 41.667 12.12 0.00 0.00 4.01
675 676 5.184892 AGTTGATCAATAAGAGGGTGCTT 57.815 39.130 12.12 0.00 0.00 3.91
676 677 4.851639 AGTTGATCAATAAGAGGGTGCT 57.148 40.909 12.12 0.00 0.00 4.40
677 678 5.675538 AGTAGTTGATCAATAAGAGGGTGC 58.324 41.667 12.12 0.00 0.00 5.01
678 679 6.127054 TGGAGTAGTTGATCAATAAGAGGGTG 60.127 42.308 12.12 0.00 0.00 4.61
679 680 5.964477 TGGAGTAGTTGATCAATAAGAGGGT 59.036 40.000 12.12 0.00 0.00 4.34
680 681 6.463614 CCTGGAGTAGTTGATCAATAAGAGGG 60.464 46.154 12.12 4.49 0.00 4.30
681 682 6.325028 TCCTGGAGTAGTTGATCAATAAGAGG 59.675 42.308 12.12 10.55 0.00 3.69
682 683 7.353414 TCCTGGAGTAGTTGATCAATAAGAG 57.647 40.000 12.12 2.22 0.00 2.85
683 684 7.255625 CGATCCTGGAGTAGTTGATCAATAAGA 60.256 40.741 12.12 0.00 33.14 2.10
684 685 6.865726 CGATCCTGGAGTAGTTGATCAATAAG 59.134 42.308 12.12 2.38 33.14 1.73
930 931 2.897350 TGTACCACCTACTGTGTCCAT 58.103 47.619 0.00 0.00 43.85 3.41
1049 1051 1.848652 TAGTAGTGGTGGTGAGCTCC 58.151 55.000 12.15 2.19 0.00 4.70
1154 1156 2.202919 CATGAGATGGCCGCGTCA 60.203 61.111 4.92 3.20 0.00 4.35
1181 1183 2.747855 GGGCTCAAGGCGGAGTTG 60.748 66.667 10.23 0.00 42.94 3.16
1380 1382 0.694771 ATGGCGTATGGGATGCTGAT 59.305 50.000 0.00 0.00 40.25 2.90
1412 1414 5.531287 TGATTAGCGAATAGTAGAGCAGTCA 59.469 40.000 0.00 0.00 0.00 3.41
1728 1767 6.590292 TCACTTTATTTTCATCGTCTCTCACC 59.410 38.462 0.00 0.00 0.00 4.02
1835 1874 0.680921 CATTGGATGGCGTTCCCTGT 60.681 55.000 4.07 0.00 34.67 4.00
1861 1900 6.383415 GTGGAATTGTTGGCTCGTTTTATAA 58.617 36.000 0.00 0.00 0.00 0.98
1883 1922 3.904136 AGAATTTCGTGAGCTTTGGTG 57.096 42.857 0.00 0.00 0.00 4.17
2052 2092 3.610040 TCCACGCTACATCAATGAAGT 57.390 42.857 0.00 0.00 0.00 3.01
2378 2461 4.293494 AGCTCATCCTCTGATGGTTCTTA 58.707 43.478 2.97 0.00 46.92 2.10


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

AutoCloner maintained by Alex Coulton.