Multiple sequence alignment - TraesCS5B01G427600

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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 TraesCS5B01G427600 chr5B 100.000 2963 0 0 1 2963 603832795 603829833 0.000000e+00 5472
1 TraesCS5B01G427600 chr5B 89.011 364 28 4 713 1076 603869292 603868941 9.750000e-120 440
2 TraesCS5B01G427600 chr5B 88.172 93 6 3 591 683 603871072 603870985 4.040000e-19 106
3 TraesCS5B01G427600 chrUn 88.153 2659 139 81 1 2587 68154101 68156655 0.000000e+00 3003
4 TraesCS5B01G427600 chrUn 84.545 330 28 12 2643 2963 68198167 68198482 3.710000e-79 305
5 TraesCS5B01G427600 chr5A 93.766 1171 50 8 939 2100 611128066 611126910 0.000000e+00 1736
6 TraesCS5B01G427600 chr5A 82.149 549 43 23 395 909 611128584 611128057 1.270000e-113 420
7 TraesCS5B01G427600 chr5A 85.357 280 11 11 2103 2379 611122784 611122532 2.260000e-66 263


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 TraesCS5B01G427600 chr5B 603829833 603832795 2962 True 5472 5472 100.0000 1 2963 1 chr5B.!!$R1 2962
1 TraesCS5B01G427600 chr5B 603868941 603871072 2131 True 273 440 88.5915 591 1076 2 chr5B.!!$R2 485
2 TraesCS5B01G427600 chrUn 68154101 68156655 2554 False 3003 3003 88.1530 1 2587 1 chrUn.!!$F1 2586
3 TraesCS5B01G427600 chr5A 611126910 611128584 1674 True 1078 1736 87.9575 395 2100 2 chr5A.!!$R2 1705

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
72 89 0.031917 TACCTACCCGGCAATGAGGA 60.032 55.0 0.0 0.0 35.61 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 3747 0.390124 CAACAACACCCAGCAAGCAT 59.61 50.0 0.0 0.0 0.0 3.79 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
42 45 1.443194 TCGCGCGAGACCTAACAAC 60.443 57.895 31.40 0.00 0.00 3.32
67 84 1.202604 CGAACATACCTACCCGGCAAT 60.203 52.381 0.00 0.00 35.61 3.56
68 85 2.218603 GAACATACCTACCCGGCAATG 58.781 52.381 0.00 0.00 36.19 2.82
70 87 1.416401 ACATACCTACCCGGCAATGAG 59.584 52.381 0.00 0.00 34.88 2.90
72 89 0.031917 TACCTACCCGGCAATGAGGA 60.032 55.000 0.00 0.00 35.61 3.71
74 91 1.447643 CTACCCGGCAATGAGGAGG 59.552 63.158 0.00 0.00 0.00 4.30
77 94 1.750399 CCCGGCAATGAGGAGGTTG 60.750 63.158 0.00 0.00 0.00 3.77
92 109 3.971245 AGGTTGCTCCTCTTCTTGTAG 57.029 47.619 0.00 0.00 44.42 2.74
100 117 3.511477 TCCTCTTCTTGTAGGCTTGACT 58.489 45.455 0.00 0.00 32.55 3.41
131 148 2.279120 CGATCAGCAGACCGAGCC 60.279 66.667 0.00 0.00 0.00 4.70
147 173 1.917787 GCCCCTCCATGCCCAAAAA 60.918 57.895 0.00 0.00 0.00 1.94
175 201 0.234884 GAAAAACAGACCGAGCACCG 59.765 55.000 0.00 0.00 38.18 4.94
202 228 1.462616 TGTGGAGTATGCATGTTGCC 58.537 50.000 10.16 6.13 44.23 4.52
209 235 4.559153 GAGTATGCATGTTGCCAACTTTT 58.441 39.130 10.16 0.00 44.23 2.27
215 241 4.035324 TGCATGTTGCCAACTTTTCATTTG 59.965 37.500 9.30 0.00 44.23 2.32
235 263 4.840401 TGATTTCTTAATGCGTGACTCG 57.160 40.909 0.00 0.00 43.12 4.18
249 277 1.303317 ACTCGGCCCATTTGGACAC 60.303 57.895 0.00 0.00 45.87 3.67
259 287 2.611518 CATTTGGACACGAGAGAGACC 58.388 52.381 0.00 0.00 37.09 3.85
260 288 0.966920 TTTGGACACGAGAGAGACCC 59.033 55.000 0.00 0.00 35.90 4.46
261 289 0.178973 TTGGACACGAGAGAGACCCA 60.179 55.000 0.00 0.00 35.90 4.51
313 341 3.011635 GCTCCTCTGCTTGCTCCGA 62.012 63.158 0.00 0.00 0.00 4.55
343 371 1.563173 GTCGAACACGACCAACAGC 59.437 57.895 10.96 0.00 46.91 4.40
346 374 0.586319 CGAACACGACCAACAGCATT 59.414 50.000 0.00 0.00 0.00 3.56
360 388 0.459899 AGCATTGCTACGACGGATGA 59.540 50.000 10.00 0.00 36.99 2.92
372 400 3.804325 ACGACGGATGAATGTTGATGATC 59.196 43.478 0.00 0.00 0.00 2.92
373 401 3.185188 CGACGGATGAATGTTGATGATCC 59.815 47.826 0.00 0.00 0.00 3.36
374 402 4.129380 GACGGATGAATGTTGATGATCCA 58.871 43.478 0.00 0.00 33.46 3.41
375 403 4.525996 ACGGATGAATGTTGATGATCCAA 58.474 39.130 0.00 0.00 33.46 3.53
376 404 4.577693 ACGGATGAATGTTGATGATCCAAG 59.422 41.667 0.00 0.00 33.46 3.61
377 405 4.556104 CGGATGAATGTTGATGATCCAAGC 60.556 45.833 0.00 0.00 33.46 4.01
378 406 4.340097 GGATGAATGTTGATGATCCAAGCA 59.660 41.667 0.00 0.00 33.96 3.91
393 434 4.179579 GCAGGAATTCACCGCCGC 62.180 66.667 7.93 0.00 34.73 6.53
397 438 3.508840 GAATTCACCGCCGCCCAG 61.509 66.667 0.00 0.00 0.00 4.45
431 477 4.451096 TCCAAGCAGTTCACGTAGAATTTC 59.549 41.667 0.00 0.00 38.76 2.17
441 487 2.168936 ACGTAGAATTTCCCGCCACATA 59.831 45.455 6.12 0.00 0.00 2.29
442 488 2.800544 CGTAGAATTTCCCGCCACATAG 59.199 50.000 0.00 0.00 0.00 2.23
448 494 0.742505 TTCCCGCCACATAGTACGAG 59.257 55.000 0.00 0.00 0.00 4.18
450 496 1.134128 TCCCGCCACATAGTACGAGTA 60.134 52.381 0.00 0.00 0.00 2.59
451 497 1.002033 CCCGCCACATAGTACGAGTAC 60.002 57.143 5.32 5.32 36.35 2.73
452 498 1.333524 CCGCCACATAGTACGAGTACG 60.334 57.143 7.64 0.00 45.75 3.67
454 500 2.222678 CGCCACATAGTACGAGTACGAT 59.777 50.000 7.64 5.61 42.66 3.73
458 504 4.143368 CCACATAGTACGAGTACGATCGAG 60.143 50.000 24.34 9.64 45.56 4.04
460 506 5.046529 ACATAGTACGAGTACGATCGAGTT 58.953 41.667 24.34 5.89 45.56 3.01
463 509 7.222805 ACATAGTACGAGTACGATCGAGTTTTA 59.777 37.037 24.34 0.00 45.56 1.52
464 510 5.790547 AGTACGAGTACGATCGAGTTTTAC 58.209 41.667 24.34 13.17 45.56 2.01
465 511 4.935885 ACGAGTACGATCGAGTTTTACT 57.064 40.909 24.34 17.86 45.56 2.24
466 512 6.752351 AGTACGAGTACGATCGAGTTTTACTA 59.248 38.462 24.34 1.15 45.56 1.82
467 513 6.595772 ACGAGTACGATCGAGTTTTACTAT 57.404 37.500 24.34 7.55 45.56 2.12
468 514 7.009568 ACGAGTACGATCGAGTTTTACTATT 57.990 36.000 24.34 6.06 45.56 1.73
527 575 4.857689 CGGTGCGCTGCAAAAATA 57.142 50.000 9.73 0.00 41.47 1.40
534 582 2.159254 TGCGCTGCAAAAATAGAATCCC 60.159 45.455 9.73 0.00 34.76 3.85
547 595 1.679559 GAATCCCTTGCACATGCCCC 61.680 60.000 0.49 0.00 41.18 5.80
549 597 4.387343 CCCTTGCACATGCCCCCT 62.387 66.667 0.49 0.00 41.18 4.79
550 598 3.072468 CCTTGCACATGCCCCCTG 61.072 66.667 0.49 0.00 41.18 4.45
551 599 3.766691 CTTGCACATGCCCCCTGC 61.767 66.667 0.49 0.00 41.18 4.85
567 615 0.511221 CTGCCCGTGAACTTTGTACG 59.489 55.000 0.00 0.00 37.55 3.67
634 685 4.868171 CGAGATTTCCGTTTTCCAGACATA 59.132 41.667 0.00 0.00 0.00 2.29
685 741 1.374252 CAAGGACCGAACCTGGACG 60.374 63.158 0.00 5.88 40.49 4.79
688 744 3.998672 GACCGAACCTGGACGCCA 61.999 66.667 0.00 0.00 0.00 5.69
689 745 3.524648 GACCGAACCTGGACGCCAA 62.525 63.158 0.00 0.00 30.80 4.52
740 2459 3.393360 CGCAGGGAGAAGAAGGGT 58.607 61.111 0.00 0.00 0.00 4.34
741 2460 1.219393 CGCAGGGAGAAGAAGGGTC 59.781 63.158 0.00 0.00 0.00 4.46
929 2651 3.147595 CAGGACCTCCGCCGATCA 61.148 66.667 0.00 0.00 42.08 2.92
1011 2736 0.242825 CAGCAGCCATGAACAACCTG 59.757 55.000 0.00 0.00 0.00 4.00
1521 3258 2.879462 CGGCGCTACTTCACCGTC 60.879 66.667 7.64 0.00 40.77 4.79
1728 3465 1.225376 TGTTCAACGACATGGCCGTC 61.225 55.000 14.25 0.00 39.57 4.79
1890 3627 2.583593 GGCATCCTGCTCGTCGTC 60.584 66.667 0.00 0.00 44.28 4.20
1893 3630 1.211818 GCATCCTGCTCGTCGTCATC 61.212 60.000 0.00 0.00 40.96 2.92
1896 3633 1.064946 CCTGCTCGTCGTCATCCTC 59.935 63.158 0.00 0.00 0.00 3.71
1963 3700 2.999331 ACAACAACAACCAGCAGTAGT 58.001 42.857 0.00 0.00 0.00 2.73
1964 3701 4.145365 ACAACAACAACCAGCAGTAGTA 57.855 40.909 0.00 0.00 0.00 1.82
1965 3702 4.127171 ACAACAACAACCAGCAGTAGTAG 58.873 43.478 0.00 0.00 0.00 2.57
1967 3704 2.969950 ACAACAACCAGCAGTAGTAGGA 59.030 45.455 0.00 0.00 0.00 2.94
1968 3705 3.389983 ACAACAACCAGCAGTAGTAGGAA 59.610 43.478 0.00 0.00 0.00 3.36
1969 3706 4.041691 ACAACAACCAGCAGTAGTAGGAAT 59.958 41.667 0.00 0.00 0.00 3.01
1971 3708 5.599999 ACAACCAGCAGTAGTAGGAATAG 57.400 43.478 0.00 0.00 0.00 1.73
1974 3711 4.290942 ACCAGCAGTAGTAGGAATAGCTT 58.709 43.478 0.00 0.00 0.00 3.74
1975 3712 4.100189 ACCAGCAGTAGTAGGAATAGCTTG 59.900 45.833 0.00 0.00 0.00 4.01
1976 3713 4.100189 CCAGCAGTAGTAGGAATAGCTTGT 59.900 45.833 0.00 0.00 0.00 3.16
1977 3714 5.046529 CAGCAGTAGTAGGAATAGCTTGTG 58.953 45.833 0.00 0.00 0.00 3.33
1978 3715 4.956700 AGCAGTAGTAGGAATAGCTTGTGA 59.043 41.667 0.00 0.00 0.00 3.58
1980 3717 5.694006 GCAGTAGTAGGAATAGCTTGTGATG 59.306 44.000 0.00 0.00 0.00 3.07
1981 3718 6.461648 GCAGTAGTAGGAATAGCTTGTGATGA 60.462 42.308 0.00 0.00 0.00 2.92
1982 3719 7.665690 CAGTAGTAGGAATAGCTTGTGATGAT 58.334 38.462 0.00 0.00 0.00 2.45
2002 3747 0.323999 ATGATCCTGGCTTGCTTGCA 60.324 50.000 4.13 0.00 34.04 4.08
2004 3749 0.102481 GATCCTGGCTTGCTTGCATG 59.898 55.000 0.00 0.00 34.04 4.06
2024 3769 1.336240 GCTTGCTGGGTGTTGTTGATC 60.336 52.381 0.00 0.00 0.00 2.92
2083 3828 2.203084 TGCGGTTCGTTGAGCCAA 60.203 55.556 0.66 0.00 32.31 4.52
2099 3844 9.083080 CGTTGAGCCAATCGATTATGTTATATA 57.917 33.333 10.97 0.00 0.00 0.86
2139 3884 6.072728 GGCGATTTATGAGTGGTAATTATGCA 60.073 38.462 0.00 0.00 0.00 3.96
2147 3892 7.087409 TGAGTGGTAATTATGCAGTTGATTG 57.913 36.000 0.00 0.00 0.00 2.67
2252 3997 3.554692 GGCGACGCACTCAATCGG 61.555 66.667 23.09 0.00 36.37 4.18
2260 4005 1.800655 CGCACTCAATCGGGAGAGAAG 60.801 57.143 6.66 1.16 45.48 2.85
2271 4016 4.605183 TCGGGAGAGAAGAAGAGAAGATT 58.395 43.478 0.00 0.00 0.00 2.40
2272 4017 4.642885 TCGGGAGAGAAGAAGAGAAGATTC 59.357 45.833 0.00 0.00 0.00 2.52
2273 4018 4.400884 CGGGAGAGAAGAAGAGAAGATTCA 59.599 45.833 0.00 0.00 0.00 2.57
2274 4019 5.068987 CGGGAGAGAAGAAGAGAAGATTCAT 59.931 44.000 0.00 0.00 0.00 2.57
2275 4020 6.406849 CGGGAGAGAAGAAGAGAAGATTCATT 60.407 42.308 0.00 0.00 0.00 2.57
2276 4021 6.986231 GGGAGAGAAGAAGAGAAGATTCATTC 59.014 42.308 0.00 0.00 0.00 2.67
2277 4022 7.364585 GGGAGAGAAGAAGAGAAGATTCATTCA 60.365 40.741 11.02 0.00 31.48 2.57
2278 4023 7.707893 GGAGAGAAGAAGAGAAGATTCATTCAG 59.292 40.741 11.02 0.00 31.48 3.02
2279 4024 7.558604 AGAGAAGAAGAGAAGATTCATTCAGG 58.441 38.462 11.02 0.00 31.48 3.86
2280 4025 7.180766 AGAGAAGAAGAGAAGATTCATTCAGGT 59.819 37.037 11.02 0.39 31.48 4.00
2281 4026 7.330262 AGAAGAAGAGAAGATTCATTCAGGTC 58.670 38.462 11.02 6.88 31.48 3.85
2282 4027 5.988287 AGAAGAGAAGATTCATTCAGGTCC 58.012 41.667 11.02 0.00 31.48 4.46
2283 4028 4.769345 AGAGAAGATTCATTCAGGTCCC 57.231 45.455 0.00 0.00 0.00 4.46
2284 4029 4.107072 AGAGAAGATTCATTCAGGTCCCA 58.893 43.478 0.00 0.00 0.00 4.37
2285 4030 4.537688 AGAGAAGATTCATTCAGGTCCCAA 59.462 41.667 0.00 0.00 0.00 4.12
2286 4031 4.593956 AGAAGATTCATTCAGGTCCCAAC 58.406 43.478 0.00 0.00 0.00 3.77
2287 4032 4.290722 AGAAGATTCATTCAGGTCCCAACT 59.709 41.667 0.00 0.00 0.00 3.16
2288 4033 5.488919 AGAAGATTCATTCAGGTCCCAACTA 59.511 40.000 0.00 0.00 0.00 2.24
2289 4034 5.104259 AGATTCATTCAGGTCCCAACTAC 57.896 43.478 0.00 0.00 0.00 2.73
2290 4035 3.713826 TTCATTCAGGTCCCAACTACC 57.286 47.619 0.00 0.00 37.27 3.18
2292 4037 2.838202 TCATTCAGGTCCCAACTACCTC 59.162 50.000 0.00 0.00 44.20 3.85
2293 4038 1.652947 TTCAGGTCCCAACTACCTCC 58.347 55.000 0.00 0.00 44.20 4.30
2294 4039 0.490017 TCAGGTCCCAACTACCTCCA 59.510 55.000 0.00 0.00 44.20 3.86
2295 4040 0.905357 CAGGTCCCAACTACCTCCAG 59.095 60.000 0.00 0.00 44.20 3.86
2296 4041 0.910088 AGGTCCCAACTACCTCCAGC 60.910 60.000 0.00 0.00 44.20 4.85
2297 4042 1.602771 GTCCCAACTACCTCCAGCC 59.397 63.158 0.00 0.00 0.00 4.85
2319 4064 2.894387 GCTCCAGATGCGAGGCAC 60.894 66.667 0.00 0.00 43.04 5.01
2402 4148 4.749323 CATGGACATGGTGGTGCT 57.251 55.556 4.39 0.00 35.24 4.40
2403 4149 3.880040 CATGGACATGGTGGTGCTA 57.120 52.632 4.39 0.00 35.24 3.49
2409 4155 1.553248 GACATGGTGGTGCTAGTGGTA 59.447 52.381 0.00 0.00 0.00 3.25
2410 4156 1.555075 ACATGGTGGTGCTAGTGGTAG 59.445 52.381 0.00 0.00 0.00 3.18
2423 4169 7.286316 GGTGCTAGTGGTAGTAGTAGGAAAATA 59.714 40.741 0.00 0.00 0.00 1.40
2459 4208 2.146342 CAAGCTTCTCGAAAGGCAGAA 58.854 47.619 0.00 0.00 0.00 3.02
2481 4230 0.669318 TCCGTGTCATTTCGAGGCAC 60.669 55.000 0.00 0.00 0.00 5.01
2490 4239 3.573772 TTCGAGGCACGCTGGACTG 62.574 63.158 0.00 0.00 42.26 3.51
2502 4251 0.445436 CTGGACTGCGACAAGATTGC 59.555 55.000 0.00 0.00 38.35 3.56
2515 4264 5.409643 ACAAGATTGCGATGCAGTAATAC 57.590 39.130 0.00 0.00 40.61 1.89
2555 4308 2.749621 CAAGATTAGCTGAACCACCACC 59.250 50.000 0.00 0.00 0.00 4.61
2564 4317 2.195123 GAACCACCACCGGAATTGCG 62.195 60.000 9.46 12.93 0.00 4.85
2565 4318 2.359354 CCACCACCGGAATTGCGA 60.359 61.111 21.76 0.00 0.00 5.10
2566 4319 1.748879 CCACCACCGGAATTGCGAT 60.749 57.895 21.76 0.00 0.00 4.58
2567 4320 1.429021 CACCACCGGAATTGCGATG 59.571 57.895 21.76 14.56 0.00 3.84
2587 4341 2.435234 GTCCGGTACATGGCGCAA 60.435 61.111 10.83 0.00 0.00 4.85
2588 4342 1.817941 GTCCGGTACATGGCGCAAT 60.818 57.895 10.83 0.00 0.00 3.56
2589 4343 1.078072 TCCGGTACATGGCGCAATT 60.078 52.632 10.83 0.00 0.00 2.32
2590 4344 0.178301 TCCGGTACATGGCGCAATTA 59.822 50.000 10.83 0.00 0.00 1.40
2591 4345 1.202710 TCCGGTACATGGCGCAATTAT 60.203 47.619 10.83 0.00 0.00 1.28
2592 4346 1.069296 CCGGTACATGGCGCAATTATG 60.069 52.381 10.83 10.53 0.00 1.90
2593 4347 1.601903 CGGTACATGGCGCAATTATGT 59.398 47.619 10.83 15.79 38.48 2.29
2594 4348 2.349438 CGGTACATGGCGCAATTATGTC 60.349 50.000 17.88 11.70 36.52 3.06
2595 4349 2.031157 GGTACATGGCGCAATTATGTCC 60.031 50.000 17.88 15.22 36.52 4.02
2596 4350 0.662619 ACATGGCGCAATTATGTCCG 59.337 50.000 10.83 0.00 29.55 4.79
2597 4351 0.662619 CATGGCGCAATTATGTCCGT 59.337 50.000 10.83 0.00 0.00 4.69
2598 4352 1.065401 CATGGCGCAATTATGTCCGTT 59.935 47.619 10.83 0.00 0.00 4.44
2599 4353 0.730265 TGGCGCAATTATGTCCGTTC 59.270 50.000 10.83 0.00 0.00 3.95
2600 4354 1.014352 GGCGCAATTATGTCCGTTCT 58.986 50.000 10.83 0.00 0.00 3.01
2601 4355 2.206750 GGCGCAATTATGTCCGTTCTA 58.793 47.619 10.83 0.00 0.00 2.10
2602 4356 2.610374 GGCGCAATTATGTCCGTTCTAA 59.390 45.455 10.83 0.00 0.00 2.10
2603 4357 3.303132 GGCGCAATTATGTCCGTTCTAAG 60.303 47.826 10.83 0.00 0.00 2.18
2604 4358 3.303132 GCGCAATTATGTCCGTTCTAAGG 60.303 47.826 0.30 0.00 0.00 2.69
2605 4359 3.247648 CGCAATTATGTCCGTTCTAAGGG 59.752 47.826 0.00 0.00 35.32 3.95
2606 4360 4.448210 GCAATTATGTCCGTTCTAAGGGA 58.552 43.478 0.05 0.05 40.40 4.20
2607 4361 4.879545 GCAATTATGTCCGTTCTAAGGGAA 59.120 41.667 5.75 0.00 43.82 3.97
2621 4375 4.963878 GGAACACATCCGCTCCAT 57.036 55.556 0.00 0.00 38.79 3.41
2623 4377 2.550830 GGAACACATCCGCTCCATAT 57.449 50.000 0.00 0.00 38.79 1.78
2624 4378 3.678056 GGAACACATCCGCTCCATATA 57.322 47.619 0.00 0.00 38.79 0.86
2625 4379 4.002906 GGAACACATCCGCTCCATATAA 57.997 45.455 0.00 0.00 38.79 0.98
2626 4380 4.385825 GGAACACATCCGCTCCATATAAA 58.614 43.478 0.00 0.00 38.79 1.40
2627 4381 4.452455 GGAACACATCCGCTCCATATAAAG 59.548 45.833 0.00 0.00 38.79 1.85
2628 4382 3.403038 ACACATCCGCTCCATATAAAGC 58.597 45.455 0.00 0.00 35.13 3.51
2629 4383 3.181455 ACACATCCGCTCCATATAAAGCA 60.181 43.478 8.69 0.00 38.45 3.91
2630 4384 3.814842 CACATCCGCTCCATATAAAGCAA 59.185 43.478 8.69 0.00 38.45 3.91
2631 4385 4.275689 CACATCCGCTCCATATAAAGCAAA 59.724 41.667 8.69 0.00 38.45 3.68
2632 4386 4.887071 ACATCCGCTCCATATAAAGCAAAA 59.113 37.500 8.69 0.00 38.45 2.44
2633 4387 5.359576 ACATCCGCTCCATATAAAGCAAAAA 59.640 36.000 8.69 0.00 38.45 1.94
2666 4420 1.938577 CTTCCATGAGAAGCACATCCG 59.061 52.381 9.94 0.00 45.38 4.18
2667 4421 0.462581 TCCATGAGAAGCACATCCGC 60.463 55.000 0.00 0.00 0.00 5.54
2668 4422 0.463295 CCATGAGAAGCACATCCGCT 60.463 55.000 0.00 0.00 46.67 5.52
2683 4437 4.522971 GCTTCCGCGAGAAAGGAT 57.477 55.556 8.23 0.00 36.28 3.24
2684 4438 3.661745 GCTTCCGCGAGAAAGGATA 57.338 52.632 8.23 0.00 36.28 2.59
2685 4439 1.935933 GCTTCCGCGAGAAAGGATAA 58.064 50.000 8.23 0.00 36.28 1.75
2686 4440 2.484889 GCTTCCGCGAGAAAGGATAAT 58.515 47.619 8.23 0.00 36.28 1.28
2687 4441 2.872858 GCTTCCGCGAGAAAGGATAATT 59.127 45.455 8.23 0.00 36.28 1.40
2688 4442 3.312697 GCTTCCGCGAGAAAGGATAATTT 59.687 43.478 8.23 0.00 36.28 1.82
2689 4443 4.786609 GCTTCCGCGAGAAAGGATAATTTG 60.787 45.833 8.23 0.00 36.28 2.32
2690 4444 3.869065 TCCGCGAGAAAGGATAATTTGT 58.131 40.909 8.23 0.00 0.00 2.83
2691 4445 3.621268 TCCGCGAGAAAGGATAATTTGTG 59.379 43.478 8.23 0.00 0.00 3.33
2692 4446 3.354397 CGCGAGAAAGGATAATTTGTGC 58.646 45.455 0.00 0.00 0.00 4.57
2693 4447 3.063997 CGCGAGAAAGGATAATTTGTGCT 59.936 43.478 0.00 0.00 0.00 4.40
2694 4448 4.437390 CGCGAGAAAGGATAATTTGTGCTT 60.437 41.667 0.00 0.00 0.00 3.91
2695 4449 5.030936 GCGAGAAAGGATAATTTGTGCTTC 58.969 41.667 0.63 0.00 0.00 3.86
2696 4450 5.573146 CGAGAAAGGATAATTTGTGCTTCC 58.427 41.667 0.63 0.00 0.00 3.46
2697 4451 5.123820 CGAGAAAGGATAATTTGTGCTTCCA 59.876 40.000 0.63 0.00 0.00 3.53
2698 4452 6.349280 CGAGAAAGGATAATTTGTGCTTCCAA 60.349 38.462 0.63 0.00 0.00 3.53
2699 4453 7.301868 AGAAAGGATAATTTGTGCTTCCAAA 57.698 32.000 0.63 0.00 38.58 3.28
2700 4454 7.734942 AGAAAGGATAATTTGTGCTTCCAAAA 58.265 30.769 0.63 0.00 37.81 2.44
2701 4455 8.210265 AGAAAGGATAATTTGTGCTTCCAAAAA 58.790 29.630 0.63 0.00 37.81 1.94
2728 4482 6.942532 AGAAGCACAACTATGTTTCTCAAA 57.057 33.333 0.00 0.00 44.09 2.69
2729 4483 7.333528 AGAAGCACAACTATGTTTCTCAAAA 57.666 32.000 0.00 0.00 44.09 2.44
2730 4484 7.771183 AGAAGCACAACTATGTTTCTCAAAAA 58.229 30.769 0.00 0.00 44.09 1.94
2753 4507 2.979814 AAAAACAGTTGTGCTTCCCC 57.020 45.000 0.00 0.00 0.00 4.81
2754 4508 0.744281 AAAACAGTTGTGCTTCCCCG 59.256 50.000 0.00 0.00 0.00 5.73
2755 4509 0.106918 AAACAGTTGTGCTTCCCCGA 60.107 50.000 0.00 0.00 0.00 5.14
2756 4510 0.106918 AACAGTTGTGCTTCCCCGAA 60.107 50.000 0.00 0.00 0.00 4.30
2757 4511 0.106918 ACAGTTGTGCTTCCCCGAAA 60.107 50.000 0.00 0.00 0.00 3.46
2758 4512 1.028905 CAGTTGTGCTTCCCCGAAAA 58.971 50.000 0.00 0.00 0.00 2.29
2759 4513 1.407258 CAGTTGTGCTTCCCCGAAAAA 59.593 47.619 0.00 0.00 0.00 1.94
2778 4532 3.436700 AAAAGAAAAGCACAACCGAGG 57.563 42.857 0.00 0.00 0.00 4.63
2779 4533 0.668535 AAGAAAAGCACAACCGAGGC 59.331 50.000 0.00 0.00 0.00 4.70
2780 4534 0.179018 AGAAAAGCACAACCGAGGCT 60.179 50.000 0.00 0.00 40.14 4.58
2782 4536 0.385390 AAAAGCACAACCGAGGCTTG 59.615 50.000 0.00 0.00 46.39 4.01
2783 4537 0.751643 AAAGCACAACCGAGGCTTGT 60.752 50.000 0.12 0.00 46.39 3.16
2784 4538 0.107831 AAGCACAACCGAGGCTTGTA 59.892 50.000 0.12 0.00 45.44 2.41
2785 4539 0.324943 AGCACAACCGAGGCTTGTAT 59.675 50.000 0.12 0.00 33.21 2.29
2786 4540 0.447801 GCACAACCGAGGCTTGTATG 59.552 55.000 0.12 1.95 30.48 2.39
2787 4541 1.943968 GCACAACCGAGGCTTGTATGA 60.944 52.381 10.11 0.00 30.48 2.15
2788 4542 2.422597 CACAACCGAGGCTTGTATGAA 58.577 47.619 10.11 0.00 30.48 2.57
2789 4543 2.811431 CACAACCGAGGCTTGTATGAAA 59.189 45.455 10.11 0.00 30.48 2.69
2790 4544 3.252215 CACAACCGAGGCTTGTATGAAAA 59.748 43.478 10.11 0.00 30.48 2.29
2791 4545 3.502211 ACAACCGAGGCTTGTATGAAAAG 59.498 43.478 10.11 0.00 29.81 2.27
2803 4557 7.935338 CTTGTATGAAAAGCACAAATGTTCT 57.065 32.000 0.00 0.00 32.16 3.01
2804 4558 8.356533 CTTGTATGAAAAGCACAAATGTTCTT 57.643 30.769 0.00 0.00 33.09 2.52
2805 4559 7.928908 TGTATGAAAAGCACAAATGTTCTTC 57.071 32.000 0.00 0.00 30.55 2.87
2806 4560 6.922957 TGTATGAAAAGCACAAATGTTCTTCC 59.077 34.615 0.00 0.00 30.55 3.46
2807 4561 4.358851 TGAAAAGCACAAATGTTCTTCCG 58.641 39.130 0.00 0.00 30.55 4.30
2808 4562 3.369546 AAAGCACAAATGTTCTTCCGG 57.630 42.857 0.00 0.00 30.55 5.14
2809 4563 1.247567 AGCACAAATGTTCTTCCGGG 58.752 50.000 0.00 0.00 0.00 5.73
2810 4564 0.958822 GCACAAATGTTCTTCCGGGT 59.041 50.000 0.00 0.00 0.00 5.28
2811 4565 1.339929 GCACAAATGTTCTTCCGGGTT 59.660 47.619 0.00 0.00 0.00 4.11
2812 4566 2.223947 GCACAAATGTTCTTCCGGGTTT 60.224 45.455 0.00 0.00 0.00 3.27
2813 4567 3.638484 CACAAATGTTCTTCCGGGTTTC 58.362 45.455 0.00 0.00 0.00 2.78
2814 4568 3.317993 CACAAATGTTCTTCCGGGTTTCT 59.682 43.478 0.00 0.00 0.00 2.52
2815 4569 4.517453 CACAAATGTTCTTCCGGGTTTCTA 59.483 41.667 0.00 0.00 0.00 2.10
2816 4570 5.183140 CACAAATGTTCTTCCGGGTTTCTAT 59.817 40.000 0.00 0.00 0.00 1.98
2817 4571 5.773176 ACAAATGTTCTTCCGGGTTTCTATT 59.227 36.000 0.00 0.00 0.00 1.73
2818 4572 6.266786 ACAAATGTTCTTCCGGGTTTCTATTT 59.733 34.615 0.00 0.21 0.00 1.40
2819 4573 6.911250 AATGTTCTTCCGGGTTTCTATTTT 57.089 33.333 0.00 0.00 0.00 1.82
2820 4574 6.911250 ATGTTCTTCCGGGTTTCTATTTTT 57.089 33.333 0.00 0.00 0.00 1.94
2869 4623 5.938438 TTTTTATTGCAGGGTTTTCATGC 57.062 34.783 0.00 0.00 40.40 4.06
2870 4624 4.888326 TTTATTGCAGGGTTTTCATGCT 57.112 36.364 4.38 0.00 40.62 3.79
2871 4625 4.888326 TTATTGCAGGGTTTTCATGCTT 57.112 36.364 4.38 0.00 40.62 3.91
2872 4626 3.775261 ATTGCAGGGTTTTCATGCTTT 57.225 38.095 4.38 0.00 40.62 3.51
2873 4627 3.557228 TTGCAGGGTTTTCATGCTTTT 57.443 38.095 4.38 0.00 40.62 2.27
2874 4628 3.557228 TGCAGGGTTTTCATGCTTTTT 57.443 38.095 4.38 0.00 40.62 1.94
2875 4629 4.679373 TGCAGGGTTTTCATGCTTTTTA 57.321 36.364 4.38 0.00 40.62 1.52
2876 4630 5.226194 TGCAGGGTTTTCATGCTTTTTAT 57.774 34.783 4.38 0.00 40.62 1.40
2877 4631 5.619220 TGCAGGGTTTTCATGCTTTTTATT 58.381 33.333 4.38 0.00 40.62 1.40
2878 4632 6.060788 TGCAGGGTTTTCATGCTTTTTATTT 58.939 32.000 4.38 0.00 40.62 1.40
2879 4633 6.545298 TGCAGGGTTTTCATGCTTTTTATTTT 59.455 30.769 4.38 0.00 40.62 1.82
2880 4634 7.067981 TGCAGGGTTTTCATGCTTTTTATTTTT 59.932 29.630 4.38 0.00 40.62 1.94
2920 4674 8.637281 TTTTTATTTCCGTTTTTCCTGACTTC 57.363 30.769 0.00 0.00 0.00 3.01
2921 4675 4.848562 ATTTCCGTTTTTCCTGACTTCC 57.151 40.909 0.00 0.00 0.00 3.46
2922 4676 3.284793 TTCCGTTTTTCCTGACTTCCA 57.715 42.857 0.00 0.00 0.00 3.53
2923 4677 2.846193 TCCGTTTTTCCTGACTTCCAG 58.154 47.619 0.00 0.00 42.55 3.86
2924 4678 2.171870 TCCGTTTTTCCTGACTTCCAGT 59.828 45.455 0.00 0.00 41.33 4.00
2925 4679 2.949644 CCGTTTTTCCTGACTTCCAGTT 59.050 45.455 0.00 0.00 41.33 3.16
2926 4680 3.380320 CCGTTTTTCCTGACTTCCAGTTT 59.620 43.478 0.00 0.00 41.33 2.66
2927 4681 4.497507 CCGTTTTTCCTGACTTCCAGTTTC 60.498 45.833 0.00 0.00 41.33 2.78
2928 4682 4.335594 CGTTTTTCCTGACTTCCAGTTTCT 59.664 41.667 0.00 0.00 41.33 2.52
2929 4683 5.163652 CGTTTTTCCTGACTTCCAGTTTCTT 60.164 40.000 0.00 0.00 41.33 2.52
2930 4684 6.266323 GTTTTTCCTGACTTCCAGTTTCTTC 58.734 40.000 0.00 0.00 41.33 2.87
2931 4685 3.386768 TCCTGACTTCCAGTTTCTTCG 57.613 47.619 0.00 0.00 41.33 3.79
2932 4686 2.963101 TCCTGACTTCCAGTTTCTTCGA 59.037 45.455 0.00 0.00 41.33 3.71
2933 4687 3.386726 TCCTGACTTCCAGTTTCTTCGAA 59.613 43.478 0.00 0.00 41.33 3.71
2934 4688 4.040461 TCCTGACTTCCAGTTTCTTCGAAT 59.960 41.667 0.00 0.00 41.33 3.34
2935 4689 4.757149 CCTGACTTCCAGTTTCTTCGAATT 59.243 41.667 0.00 0.00 41.33 2.17
2936 4690 5.239525 CCTGACTTCCAGTTTCTTCGAATTT 59.760 40.000 0.00 0.00 41.33 1.82
2937 4691 6.238759 CCTGACTTCCAGTTTCTTCGAATTTT 60.239 38.462 0.00 0.00 41.33 1.82
2938 4692 6.494842 TGACTTCCAGTTTCTTCGAATTTTG 58.505 36.000 0.00 0.00 0.00 2.44
2939 4693 6.094881 TGACTTCCAGTTTCTTCGAATTTTGT 59.905 34.615 0.00 0.00 0.00 2.83
2940 4694 6.863275 ACTTCCAGTTTCTTCGAATTTTGTT 58.137 32.000 0.00 0.00 0.00 2.83
2941 4695 6.972901 ACTTCCAGTTTCTTCGAATTTTGTTC 59.027 34.615 0.00 0.00 0.00 3.18
2942 4696 5.507077 TCCAGTTTCTTCGAATTTTGTTCG 58.493 37.500 0.00 3.96 42.74 3.95
2943 4697 5.065474 TCCAGTTTCTTCGAATTTTGTTCGT 59.935 36.000 0.00 0.00 42.09 3.85
2944 4698 5.171337 CCAGTTTCTTCGAATTTTGTTCGTG 59.829 40.000 0.00 5.26 42.09 4.35
2945 4699 5.963004 CAGTTTCTTCGAATTTTGTTCGTGA 59.037 36.000 0.00 7.14 42.09 4.35
2946 4700 6.467682 CAGTTTCTTCGAATTTTGTTCGTGAA 59.532 34.615 0.00 11.56 42.09 3.18
2947 4701 7.007905 CAGTTTCTTCGAATTTTGTTCGTGAAA 59.992 33.333 18.95 18.95 42.09 2.69
2948 4702 7.539366 AGTTTCTTCGAATTTTGTTCGTGAAAA 59.461 29.630 21.64 13.59 41.43 2.29
2949 4703 6.784068 TCTTCGAATTTTGTTCGTGAAAAC 57.216 33.333 0.00 0.00 42.09 2.43
2950 4704 6.315551 TCTTCGAATTTTGTTCGTGAAAACA 58.684 32.000 0.00 0.00 42.09 2.83
2951 4705 6.802348 TCTTCGAATTTTGTTCGTGAAAACAA 59.198 30.769 0.00 0.00 44.98 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.154093 TTGTTAGGTCTCGCGCGAG 60.154 57.895 45.23 45.23 43.21 5.03
25 26 2.442188 GGTTGTTAGGTCTCGCGCG 61.442 63.158 26.76 26.76 0.00 6.86
36 39 4.255833 AGGTATGTTCGTTCGGTTGTTA 57.744 40.909 0.00 0.00 0.00 2.41
40 43 2.094026 GGGTAGGTATGTTCGTTCGGTT 60.094 50.000 0.00 0.00 0.00 4.44
42 45 1.534595 CGGGTAGGTATGTTCGTTCGG 60.535 57.143 0.00 0.00 0.00 4.30
74 91 2.027653 AGCCTACAAGAAGAGGAGCAAC 60.028 50.000 0.00 0.00 34.46 4.17
77 94 2.234908 TCAAGCCTACAAGAAGAGGAGC 59.765 50.000 0.00 0.00 34.46 4.70
105 122 0.737367 TCTGCTGATCGCACGAAAGG 60.737 55.000 7.93 0.00 45.47 3.11
147 173 5.347635 GCTCGGTCTGTTTTTCTTTTTGTTT 59.652 36.000 0.00 0.00 0.00 2.83
150 176 4.265320 GTGCTCGGTCTGTTTTTCTTTTTG 59.735 41.667 0.00 0.00 0.00 2.44
152 178 3.181490 GGTGCTCGGTCTGTTTTTCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
175 201 1.303309 GCATACTCCACATGTGCTCC 58.697 55.000 20.81 0.27 31.98 4.70
199 225 8.954950 TTAAGAAATCAAATGAAAAGTTGGCA 57.045 26.923 0.00 0.00 0.00 4.92
202 228 9.519905 CGCATTAAGAAATCAAATGAAAAGTTG 57.480 29.630 10.79 0.00 33.38 3.16
209 235 7.144722 AGTCACGCATTAAGAAATCAAATGA 57.855 32.000 10.79 0.00 33.38 2.57
215 241 3.544244 GCCGAGTCACGCATTAAGAAATC 60.544 47.826 0.00 0.00 41.07 2.17
235 263 1.002624 TCTCGTGTCCAAATGGGCC 60.003 57.895 0.83 0.00 39.61 5.80
266 294 2.102578 AGCTTGACTGGCACACTTTTT 58.897 42.857 0.00 0.00 0.00 1.94
267 295 1.406539 CAGCTTGACTGGCACACTTTT 59.593 47.619 0.00 0.00 43.19 2.27
268 296 1.027357 CAGCTTGACTGGCACACTTT 58.973 50.000 0.00 0.00 43.19 2.66
269 297 2.711711 CAGCTTGACTGGCACACTT 58.288 52.632 0.00 0.00 43.19 3.16
270 298 4.469883 CAGCTTGACTGGCACACT 57.530 55.556 0.00 0.00 43.19 3.55
277 305 2.281070 ACGTGCCCAGCTTGACTG 60.281 61.111 0.00 0.00 46.77 3.51
278 306 2.281070 CACGTGCCCAGCTTGACT 60.281 61.111 0.82 0.00 0.00 3.41
289 317 2.358003 AAGCAGAGGAGCACGTGC 60.358 61.111 32.79 32.79 42.49 5.34
328 356 1.925946 GCAATGCTGTTGGTCGTGTTC 60.926 52.381 0.00 0.00 0.00 3.18
341 369 0.459899 TCATCCGTCGTAGCAATGCT 59.540 50.000 13.92 13.92 43.41 3.79
343 371 2.866156 ACATTCATCCGTCGTAGCAATG 59.134 45.455 0.00 0.00 0.00 2.82
346 374 2.094442 TCAACATTCATCCGTCGTAGCA 60.094 45.455 0.00 0.00 0.00 3.49
360 388 3.972133 TCCTGCTTGGATCATCAACATT 58.028 40.909 0.00 0.00 40.56 2.71
372 400 1.508088 GCGGTGAATTCCTGCTTGG 59.492 57.895 16.18 0.00 37.10 3.61
373 401 1.508088 GGCGGTGAATTCCTGCTTG 59.492 57.895 20.29 1.78 0.00 4.01
374 402 2.040544 CGGCGGTGAATTCCTGCTT 61.041 57.895 20.29 0.00 0.00 3.91
375 403 2.436646 CGGCGGTGAATTCCTGCT 60.437 61.111 20.29 0.00 0.00 4.24
376 404 4.179579 GCGGCGGTGAATTCCTGC 62.180 66.667 9.78 15.50 0.00 4.85
377 405 3.508840 GGCGGCGGTGAATTCCTG 61.509 66.667 9.78 0.87 0.00 3.86
378 406 4.796495 GGGCGGCGGTGAATTCCT 62.796 66.667 9.78 0.00 0.00 3.36
393 434 2.381911 CTTGGATTGGATTGGACTGGG 58.618 52.381 0.00 0.00 0.00 4.45
397 438 2.450476 ACTGCTTGGATTGGATTGGAC 58.550 47.619 0.00 0.00 0.00 4.02
431 477 1.002033 GTACTCGTACTATGTGGCGGG 60.002 57.143 0.12 0.00 33.45 6.13
441 487 4.935885 AAAACTCGATCGTACTCGTACT 57.064 40.909 15.94 0.00 39.62 2.73
442 488 5.790547 AGTAAAACTCGATCGTACTCGTAC 58.209 41.667 15.94 11.26 39.62 3.67
458 504 9.213819 CGCGGGTAAAATTAAGAATAGTAAAAC 57.786 33.333 0.00 0.00 0.00 2.43
460 506 7.467131 GCCGCGGGTAAAATTAAGAATAGTAAA 60.467 37.037 29.38 0.00 0.00 2.01
463 509 4.274214 GCCGCGGGTAAAATTAAGAATAGT 59.726 41.667 29.38 0.00 0.00 2.12
464 510 4.609783 CGCCGCGGGTAAAATTAAGAATAG 60.610 45.833 29.38 0.00 0.00 1.73
465 511 3.248125 CGCCGCGGGTAAAATTAAGAATA 59.752 43.478 29.38 0.00 0.00 1.75
466 512 2.032426 CGCCGCGGGTAAAATTAAGAAT 59.968 45.455 29.38 0.00 0.00 2.40
467 513 1.397692 CGCCGCGGGTAAAATTAAGAA 59.602 47.619 29.38 0.00 0.00 2.52
468 514 1.008329 CGCCGCGGGTAAAATTAAGA 58.992 50.000 29.38 0.00 0.00 2.10
522 570 4.141869 GGCATGTGCAAGGGATTCTATTTT 60.142 41.667 7.36 0.00 44.36 1.82
527 575 0.685458 GGGCATGTGCAAGGGATTCT 60.685 55.000 7.36 0.00 44.36 2.40
534 582 3.766691 GCAGGGGGCATGTGCAAG 61.767 66.667 7.36 0.00 44.36 4.01
547 595 0.872388 GTACAAAGTTCACGGGCAGG 59.128 55.000 0.00 0.00 0.00 4.85
549 597 2.607457 CGTACAAAGTTCACGGGCA 58.393 52.632 0.00 0.00 32.19 5.36
553 601 0.511221 CTGGCCGTACAAAGTTCACG 59.489 55.000 0.00 0.00 35.50 4.35
634 685 2.758327 TGGGTGCGTCGGCTATCT 60.758 61.111 0.00 0.00 40.82 1.98
659 710 0.739813 GTTCGGTCCTTGGATCACGG 60.740 60.000 0.55 0.00 0.00 4.94
685 741 3.830192 CCGATGGCTTGGCTTGGC 61.830 66.667 0.00 0.00 0.00 4.52
688 744 1.524621 CGATCCGATGGCTTGGCTT 60.525 57.895 0.00 0.00 0.00 4.35
689 745 2.109799 CGATCCGATGGCTTGGCT 59.890 61.111 0.00 0.00 0.00 4.75
735 2454 3.003763 GGCGACCCAGAGACCCTT 61.004 66.667 0.00 0.00 0.00 3.95
781 2503 4.813526 CCGTCTCGTCTCGTGCGG 62.814 72.222 10.41 10.41 35.40 5.69
922 2644 3.185246 TCTTGATTCTCCTTGATCGGC 57.815 47.619 0.00 0.00 0.00 5.54
929 2651 1.680249 GCCGGCTTCTTGATTCTCCTT 60.680 52.381 22.15 0.00 0.00 3.36
969 2691 3.706373 GGCTCAGGCAAGGGTCGA 61.706 66.667 0.00 0.00 40.87 4.20
971 2693 4.785453 CCGGCTCAGGCAAGGGTC 62.785 72.222 0.00 0.00 40.87 4.46
1011 2736 1.061485 GCTTCCACGAACTCGAGAAC 58.939 55.000 21.68 11.24 43.02 3.01
1077 2814 4.530857 GTCATCTCCACCCCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
1078 2815 4.530857 CGTCATCTCCACCCCGCC 62.531 72.222 0.00 0.00 0.00 6.13
1079 2816 4.530857 CCGTCATCTCCACCCCGC 62.531 72.222 0.00 0.00 0.00 6.13
1080 2817 4.530857 GCCGTCATCTCCACCCCG 62.531 72.222 0.00 0.00 0.00 5.73
1081 2818 4.530857 CGCCGTCATCTCCACCCC 62.531 72.222 0.00 0.00 0.00 4.95
1155 2892 4.094684 CGCAGGTCGTCCTTGATC 57.905 61.111 0.00 0.00 43.07 2.92
1752 3489 2.711922 GCCCTCGATGTCGTCCAGT 61.712 63.158 2.04 0.00 40.80 4.00
1890 3627 2.354503 GGGGATGACGATGATGAGGATG 60.355 54.545 0.00 0.00 0.00 3.51
1893 3630 1.051008 TGGGGATGACGATGATGAGG 58.949 55.000 0.00 0.00 0.00 3.86
1896 3633 1.001293 ACGATGGGGATGACGATGATG 59.999 52.381 0.00 0.00 0.00 3.07
1963 3700 8.481314 GGATCATATCATCACAAGCTATTCCTA 58.519 37.037 0.00 0.00 0.00 2.94
1964 3701 7.182387 AGGATCATATCATCACAAGCTATTCCT 59.818 37.037 0.00 0.00 0.00 3.36
1965 3702 7.280428 CAGGATCATATCATCACAAGCTATTCC 59.720 40.741 0.00 0.00 0.00 3.01
1967 3704 7.110810 CCAGGATCATATCATCACAAGCTATT 58.889 38.462 0.00 0.00 0.00 1.73
1968 3705 6.651086 CCAGGATCATATCATCACAAGCTAT 58.349 40.000 0.00 0.00 0.00 2.97
1969 3706 5.570236 GCCAGGATCATATCATCACAAGCTA 60.570 44.000 0.00 0.00 0.00 3.32
1971 3708 3.439476 GCCAGGATCATATCATCACAAGC 59.561 47.826 0.00 0.00 0.00 4.01
1974 3711 4.648651 CAAGCCAGGATCATATCATCACA 58.351 43.478 0.00 0.00 0.00 3.58
1975 3712 3.439476 GCAAGCCAGGATCATATCATCAC 59.561 47.826 0.00 0.00 0.00 3.06
1976 3713 3.329814 AGCAAGCCAGGATCATATCATCA 59.670 43.478 0.00 0.00 0.00 3.07
1977 3714 3.952931 AGCAAGCCAGGATCATATCATC 58.047 45.455 0.00 0.00 0.00 2.92
1978 3715 4.079970 CAAGCAAGCCAGGATCATATCAT 58.920 43.478 0.00 0.00 0.00 2.45
1980 3717 2.228343 GCAAGCAAGCCAGGATCATATC 59.772 50.000 0.00 0.00 0.00 1.63
1981 3718 2.236766 GCAAGCAAGCCAGGATCATAT 58.763 47.619 0.00 0.00 0.00 1.78
1982 3719 1.064537 TGCAAGCAAGCCAGGATCATA 60.065 47.619 0.00 0.00 0.00 2.15
2002 3747 0.390124 CAACAACACCCAGCAAGCAT 59.610 50.000 0.00 0.00 0.00 3.79
2004 3749 0.675633 ATCAACAACACCCAGCAAGC 59.324 50.000 0.00 0.00 0.00 4.01
2099 3844 9.701098 TCATAAATCGCCGAAAAGTATATAGTT 57.299 29.630 0.00 0.00 0.00 2.24
2101 3846 9.355215 ACTCATAAATCGCCGAAAAGTATATAG 57.645 33.333 0.00 0.00 0.00 1.31
2102 3847 9.135843 CACTCATAAATCGCCGAAAAGTATATA 57.864 33.333 0.00 0.00 0.00 0.86
2103 3848 7.117812 CCACTCATAAATCGCCGAAAAGTATAT 59.882 37.037 0.00 0.00 0.00 0.86
2123 3868 6.883756 TCAATCAACTGCATAATTACCACTCA 59.116 34.615 0.00 0.00 0.00 3.41
2124 3869 7.066284 ACTCAATCAACTGCATAATTACCACTC 59.934 37.037 0.00 0.00 0.00 3.51
2139 3884 3.891366 CTCCAACCCAAACTCAATCAACT 59.109 43.478 0.00 0.00 0.00 3.16
2147 3892 1.133915 TCCACACTCCAACCCAAACTC 60.134 52.381 0.00 0.00 0.00 3.01
2243 3988 3.699038 CTCTTCTTCTCTCCCGATTGAGT 59.301 47.826 0.00 0.00 33.93 3.41
2244 3989 3.951037 TCTCTTCTTCTCTCCCGATTGAG 59.049 47.826 0.00 0.00 0.00 3.02
2245 3990 3.969553 TCTCTTCTTCTCTCCCGATTGA 58.030 45.455 0.00 0.00 0.00 2.57
2246 3991 4.400884 TCTTCTCTTCTTCTCTCCCGATTG 59.599 45.833 0.00 0.00 0.00 2.67
2251 3996 5.930837 TGAATCTTCTCTTCTTCTCTCCC 57.069 43.478 0.00 0.00 0.00 4.30
2252 3997 7.555087 TGAATGAATCTTCTCTTCTTCTCTCC 58.445 38.462 7.09 0.00 0.00 3.71
2260 4005 5.122519 GGGACCTGAATGAATCTTCTCTTC 58.877 45.833 0.00 0.00 0.00 2.87
2271 4016 2.915869 AGGTAGTTGGGACCTGAATGA 58.084 47.619 0.00 0.00 45.90 2.57
2278 4023 1.602771 GCTGGAGGTAGTTGGGACC 59.397 63.158 0.00 0.00 37.22 4.46
2279 4024 0.910088 AGGCTGGAGGTAGTTGGGAC 60.910 60.000 0.00 0.00 0.00 4.46
2280 4025 0.617820 GAGGCTGGAGGTAGTTGGGA 60.618 60.000 0.00 0.00 0.00 4.37
2281 4026 0.909610 TGAGGCTGGAGGTAGTTGGG 60.910 60.000 0.00 0.00 0.00 4.12
2282 4027 0.539051 CTGAGGCTGGAGGTAGTTGG 59.461 60.000 0.00 0.00 0.00 3.77
2283 4028 0.539051 CCTGAGGCTGGAGGTAGTTG 59.461 60.000 0.00 0.00 0.00 3.16
2284 4029 1.268283 GCCTGAGGCTGGAGGTAGTT 61.268 60.000 17.96 0.00 46.69 2.24
2285 4030 1.687493 GCCTGAGGCTGGAGGTAGT 60.687 63.158 17.96 0.00 46.69 2.73
2286 4031 3.225235 GCCTGAGGCTGGAGGTAG 58.775 66.667 17.96 0.00 46.69 3.18
2296 4041 2.108566 CGCATCTGGAGCCTGAGG 59.891 66.667 0.00 0.00 0.00 3.86
2297 4042 1.067749 CTCGCATCTGGAGCCTGAG 59.932 63.158 2.58 0.00 0.00 3.35
2319 4064 0.320073 TTACTCCAACCAACGAGCGG 60.320 55.000 0.00 0.00 0.00 5.52
2328 4073 2.483188 CCTGCCGTAGATTACTCCAACC 60.483 54.545 0.00 0.00 0.00 3.77
2395 4141 3.631227 CCTACTACTACCACTAGCACCAC 59.369 52.174 0.00 0.00 0.00 4.16
2396 4142 3.524789 TCCTACTACTACCACTAGCACCA 59.475 47.826 0.00 0.00 0.00 4.17
2397 4143 4.162040 TCCTACTACTACCACTAGCACC 57.838 50.000 0.00 0.00 0.00 5.01
2398 4144 6.521151 TTTTCCTACTACTACCACTAGCAC 57.479 41.667 0.00 0.00 0.00 4.40
2399 4145 8.827832 TTATTTTCCTACTACTACCACTAGCA 57.172 34.615 0.00 0.00 0.00 3.49
2409 4155 9.836076 GCAACGAAATTTTATTTTCCTACTACT 57.164 29.630 0.00 0.00 33.02 2.57
2410 4156 9.836076 AGCAACGAAATTTTATTTTCCTACTAC 57.164 29.630 0.00 0.00 33.02 2.73
2490 4239 0.588233 CTGCATCGCAATCTTGTCGC 60.588 55.000 0.00 0.00 38.41 5.19
2515 4264 4.698780 TCTTGATTCCAGTGAGCAGAATTG 59.301 41.667 0.00 0.00 0.00 2.32
2527 4276 5.065731 GTGGTTCAGCTAATCTTGATTCCAG 59.934 44.000 0.00 0.00 0.00 3.86
2555 4308 1.353103 GGACTGCATCGCAATTCCG 59.647 57.895 0.00 0.00 38.41 4.30
2564 4317 1.160329 GCCATGTACCGGACTGCATC 61.160 60.000 9.46 0.00 0.00 3.91
2565 4318 1.153168 GCCATGTACCGGACTGCAT 60.153 57.895 9.46 0.00 0.00 3.96
2566 4319 2.267642 GCCATGTACCGGACTGCA 59.732 61.111 9.46 0.00 0.00 4.41
2567 4320 2.890474 CGCCATGTACCGGACTGC 60.890 66.667 9.46 6.14 0.00 4.40
2597 4351 1.906574 AGCGGATGTGTTCCCTTAGAA 59.093 47.619 0.00 0.00 42.06 2.10
2598 4352 1.480954 GAGCGGATGTGTTCCCTTAGA 59.519 52.381 0.00 0.00 42.06 2.10
2599 4353 1.473434 GGAGCGGATGTGTTCCCTTAG 60.473 57.143 0.00 0.00 42.06 2.18
2600 4354 0.539986 GGAGCGGATGTGTTCCCTTA 59.460 55.000 0.00 0.00 42.06 2.69
2601 4355 1.299976 GGAGCGGATGTGTTCCCTT 59.700 57.895 0.00 0.00 42.06 3.95
2602 4356 1.274703 ATGGAGCGGATGTGTTCCCT 61.275 55.000 0.00 0.00 42.06 4.20
2603 4357 0.468226 TATGGAGCGGATGTGTTCCC 59.532 55.000 0.00 0.00 42.06 3.97
2604 4358 2.550830 ATATGGAGCGGATGTGTTCC 57.449 50.000 0.00 0.00 41.59 3.62
2605 4359 4.083802 GCTTTATATGGAGCGGATGTGTTC 60.084 45.833 0.00 0.00 0.00 3.18
2606 4360 3.815401 GCTTTATATGGAGCGGATGTGTT 59.185 43.478 0.00 0.00 0.00 3.32
2607 4361 3.181455 TGCTTTATATGGAGCGGATGTGT 60.181 43.478 7.40 0.00 41.75 3.72
2608 4362 3.402110 TGCTTTATATGGAGCGGATGTG 58.598 45.455 7.40 0.00 41.75 3.21
2609 4363 3.769739 TGCTTTATATGGAGCGGATGT 57.230 42.857 7.40 0.00 41.75 3.06
2610 4364 5.437289 TTTTGCTTTATATGGAGCGGATG 57.563 39.130 7.40 0.00 41.75 3.51
2637 4391 4.092771 CTTCTCATGGAAGCACATGTTG 57.907 45.455 13.43 9.30 46.39 3.33
2647 4401 2.013563 GCGGATGTGCTTCTCATGGAA 61.014 52.381 0.00 0.00 0.00 3.53
2648 4402 0.462581 GCGGATGTGCTTCTCATGGA 60.463 55.000 0.00 0.00 0.00 3.41
2649 4403 0.463295 AGCGGATGTGCTTCTCATGG 60.463 55.000 0.00 0.00 44.46 3.66
2650 4404 3.076104 AGCGGATGTGCTTCTCATG 57.924 52.632 0.00 0.00 44.46 3.07
2667 4421 4.332819 ACAAATTATCCTTTCTCGCGGAAG 59.667 41.667 6.13 8.50 35.16 3.46
2668 4422 4.094294 CACAAATTATCCTTTCTCGCGGAA 59.906 41.667 6.13 6.05 32.12 4.30
2669 4423 3.621268 CACAAATTATCCTTTCTCGCGGA 59.379 43.478 6.13 0.00 0.00 5.54
2670 4424 3.788797 GCACAAATTATCCTTTCTCGCGG 60.789 47.826 6.13 0.00 0.00 6.46
2671 4425 3.063997 AGCACAAATTATCCTTTCTCGCG 59.936 43.478 0.00 0.00 0.00 5.87
2672 4426 4.622701 AGCACAAATTATCCTTTCTCGC 57.377 40.909 0.00 0.00 0.00 5.03
2673 4427 5.123820 TGGAAGCACAAATTATCCTTTCTCG 59.876 40.000 0.00 0.00 0.00 4.04
2674 4428 6.515272 TGGAAGCACAAATTATCCTTTCTC 57.485 37.500 0.00 0.00 0.00 2.87
2675 4429 6.916360 TTGGAAGCACAAATTATCCTTTCT 57.084 33.333 0.00 0.00 0.00 2.52
2676 4430 7.961325 TTTTGGAAGCACAAATTATCCTTTC 57.039 32.000 2.74 0.00 39.80 2.62
2699 4453 8.000780 AGAAACATAGTTGTGCTTCTCTTTTT 57.999 30.769 0.00 0.00 35.83 1.94
2700 4454 7.283127 TGAGAAACATAGTTGTGCTTCTCTTTT 59.717 33.333 17.22 0.00 43.70 2.27
2701 4455 6.767902 TGAGAAACATAGTTGTGCTTCTCTTT 59.232 34.615 17.22 0.00 43.70 2.52
2702 4456 6.291377 TGAGAAACATAGTTGTGCTTCTCTT 58.709 36.000 17.22 0.00 43.70 2.85
2703 4457 5.858381 TGAGAAACATAGTTGTGCTTCTCT 58.142 37.500 17.22 0.00 43.70 3.10
2704 4458 6.545504 TTGAGAAACATAGTTGTGCTTCTC 57.454 37.500 12.36 12.36 43.65 2.87
2705 4459 6.942532 TTTGAGAAACATAGTTGTGCTTCT 57.057 33.333 0.00 0.00 36.23 2.85
2706 4460 7.985634 TTTTTGAGAAACATAGTTGTGCTTC 57.014 32.000 0.00 0.00 35.83 3.86
2734 4488 1.136110 CGGGGAAGCACAACTGTTTTT 59.864 47.619 0.00 0.00 0.00 1.94
2735 4489 0.744281 CGGGGAAGCACAACTGTTTT 59.256 50.000 0.00 0.00 0.00 2.43
2736 4490 0.106918 TCGGGGAAGCACAACTGTTT 60.107 50.000 0.00 0.00 0.00 2.83
2737 4491 0.106918 TTCGGGGAAGCACAACTGTT 60.107 50.000 0.00 0.00 0.00 3.16
2738 4492 0.106918 TTTCGGGGAAGCACAACTGT 60.107 50.000 0.00 0.00 0.00 3.55
2739 4493 1.028905 TTTTCGGGGAAGCACAACTG 58.971 50.000 0.00 0.00 0.00 3.16
2740 4494 1.770294 TTTTTCGGGGAAGCACAACT 58.230 45.000 0.00 0.00 0.00 3.16
2757 4511 3.780902 CCTCGGTTGTGCTTTTCTTTTT 58.219 40.909 0.00 0.00 0.00 1.94
2758 4512 2.481276 GCCTCGGTTGTGCTTTTCTTTT 60.481 45.455 0.00 0.00 0.00 2.27
2759 4513 1.067060 GCCTCGGTTGTGCTTTTCTTT 59.933 47.619 0.00 0.00 0.00 2.52
2760 4514 0.668535 GCCTCGGTTGTGCTTTTCTT 59.331 50.000 0.00 0.00 0.00 2.52
2761 4515 0.179018 AGCCTCGGTTGTGCTTTTCT 60.179 50.000 0.00 0.00 29.17 2.52
2762 4516 0.668535 AAGCCTCGGTTGTGCTTTTC 59.331 50.000 0.00 0.00 42.37 2.29
2763 4517 0.385390 CAAGCCTCGGTTGTGCTTTT 59.615 50.000 0.00 0.00 42.37 2.27
2764 4518 2.032981 CAAGCCTCGGTTGTGCTTT 58.967 52.632 0.00 0.00 42.37 3.51
2765 4519 3.749981 CAAGCCTCGGTTGTGCTT 58.250 55.556 0.00 0.00 45.69 3.91
2770 4524 3.670627 GCTTTTCATACAAGCCTCGGTTG 60.671 47.826 2.20 2.20 45.13 3.77
2771 4525 2.488153 GCTTTTCATACAAGCCTCGGTT 59.512 45.455 0.00 0.00 40.79 4.44
2772 4526 2.084546 GCTTTTCATACAAGCCTCGGT 58.915 47.619 0.00 0.00 40.79 4.69
2773 4527 2.083774 TGCTTTTCATACAAGCCTCGG 58.916 47.619 2.34 0.00 45.25 4.63
2774 4528 2.483877 TGTGCTTTTCATACAAGCCTCG 59.516 45.455 2.34 0.00 45.25 4.63
2775 4529 4.503741 TTGTGCTTTTCATACAAGCCTC 57.496 40.909 2.34 0.00 45.25 4.70
2776 4530 4.935352 TTTGTGCTTTTCATACAAGCCT 57.065 36.364 2.34 0.00 45.25 4.58
2777 4531 4.990426 ACATTTGTGCTTTTCATACAAGCC 59.010 37.500 2.34 0.00 45.25 4.35
2778 4532 6.421801 AGAACATTTGTGCTTTTCATACAAGC 59.578 34.615 0.00 0.00 45.92 4.01
2779 4533 7.935338 AGAACATTTGTGCTTTTCATACAAG 57.065 32.000 0.00 0.00 35.91 3.16
2780 4534 7.437862 GGAAGAACATTTGTGCTTTTCATACAA 59.562 33.333 5.42 0.00 43.73 2.41
2781 4535 6.922957 GGAAGAACATTTGTGCTTTTCATACA 59.077 34.615 5.42 0.00 43.73 2.29
2782 4536 6.088085 CGGAAGAACATTTGTGCTTTTCATAC 59.912 38.462 5.42 0.00 43.73 2.39
2783 4537 6.148948 CGGAAGAACATTTGTGCTTTTCATA 58.851 36.000 5.42 0.00 43.73 2.15
2784 4538 4.984161 CGGAAGAACATTTGTGCTTTTCAT 59.016 37.500 5.42 0.00 43.73 2.57
2785 4539 4.358851 CGGAAGAACATTTGTGCTTTTCA 58.641 39.130 5.42 0.00 43.73 2.69
2786 4540 3.735746 CCGGAAGAACATTTGTGCTTTTC 59.264 43.478 5.42 1.65 43.73 2.29
2787 4541 3.492482 CCCGGAAGAACATTTGTGCTTTT 60.492 43.478 0.73 0.00 43.73 2.27
2788 4542 2.035832 CCCGGAAGAACATTTGTGCTTT 59.964 45.455 0.73 0.00 43.73 3.51
2789 4543 1.613437 CCCGGAAGAACATTTGTGCTT 59.387 47.619 0.73 3.52 46.27 3.91
2790 4544 1.247567 CCCGGAAGAACATTTGTGCT 58.752 50.000 0.73 0.00 34.75 4.40
2791 4545 0.958822 ACCCGGAAGAACATTTGTGC 59.041 50.000 0.73 0.00 0.00 4.57
2792 4546 3.317993 AGAAACCCGGAAGAACATTTGTG 59.682 43.478 0.73 0.00 0.00 3.33
2793 4547 3.562182 AGAAACCCGGAAGAACATTTGT 58.438 40.909 0.73 0.00 0.00 2.83
2794 4548 5.897377 ATAGAAACCCGGAAGAACATTTG 57.103 39.130 0.73 0.00 0.00 2.32
2795 4549 6.911250 AAATAGAAACCCGGAAGAACATTT 57.089 33.333 0.73 0.00 0.00 2.32
2796 4550 6.911250 AAAATAGAAACCCGGAAGAACATT 57.089 33.333 0.73 0.00 0.00 2.71
2797 4551 6.911250 AAAAATAGAAACCCGGAAGAACAT 57.089 33.333 0.73 0.00 0.00 2.71
2847 4601 5.619220 AGCATGAAAACCCTGCAATAAAAA 58.381 33.333 0.00 0.00 38.37 1.94
2848 4602 5.226194 AGCATGAAAACCCTGCAATAAAA 57.774 34.783 0.00 0.00 38.37 1.52
2849 4603 4.888326 AGCATGAAAACCCTGCAATAAA 57.112 36.364 0.00 0.00 38.37 1.40
2850 4604 4.888326 AAGCATGAAAACCCTGCAATAA 57.112 36.364 0.00 0.00 38.37 1.40
2851 4605 4.888326 AAAGCATGAAAACCCTGCAATA 57.112 36.364 0.00 0.00 38.37 1.90
2852 4606 3.775261 AAAGCATGAAAACCCTGCAAT 57.225 38.095 0.00 0.00 38.37 3.56
2853 4607 3.557228 AAAAGCATGAAAACCCTGCAA 57.443 38.095 0.00 0.00 38.37 4.08
2854 4608 3.557228 AAAAAGCATGAAAACCCTGCA 57.443 38.095 0.00 0.00 38.37 4.41
2855 4609 6.558771 AAATAAAAAGCATGAAAACCCTGC 57.441 33.333 0.00 0.00 36.15 4.85
2895 4649 7.707464 GGAAGTCAGGAAAAACGGAAATAAAAA 59.293 33.333 0.00 0.00 0.00 1.94
2896 4650 7.147880 TGGAAGTCAGGAAAAACGGAAATAAAA 60.148 33.333 0.00 0.00 0.00 1.52
2897 4651 6.321690 TGGAAGTCAGGAAAAACGGAAATAAA 59.678 34.615 0.00 0.00 0.00 1.40
2898 4652 5.828859 TGGAAGTCAGGAAAAACGGAAATAA 59.171 36.000 0.00 0.00 0.00 1.40
2899 4653 5.378332 TGGAAGTCAGGAAAAACGGAAATA 58.622 37.500 0.00 0.00 0.00 1.40
2900 4654 4.211920 TGGAAGTCAGGAAAAACGGAAAT 58.788 39.130 0.00 0.00 0.00 2.17
2901 4655 3.622630 TGGAAGTCAGGAAAAACGGAAA 58.377 40.909 0.00 0.00 0.00 3.13
2902 4656 3.211045 CTGGAAGTCAGGAAAAACGGAA 58.789 45.455 0.00 0.00 39.76 4.30
2903 4657 2.846193 CTGGAAGTCAGGAAAAACGGA 58.154 47.619 0.00 0.00 39.76 4.69
2917 4671 6.140737 CGAACAAAATTCGAAGAAACTGGAAG 59.859 38.462 3.35 0.00 45.90 3.46
2918 4672 5.968848 CGAACAAAATTCGAAGAAACTGGAA 59.031 36.000 3.35 0.00 45.90 3.53
2919 4673 5.065474 ACGAACAAAATTCGAAGAAACTGGA 59.935 36.000 15.35 0.00 45.90 3.86
2920 4674 5.171337 CACGAACAAAATTCGAAGAAACTGG 59.829 40.000 15.35 0.00 45.90 4.00
2921 4675 5.963004 TCACGAACAAAATTCGAAGAAACTG 59.037 36.000 15.35 2.33 45.90 3.16
2922 4676 6.114221 TCACGAACAAAATTCGAAGAAACT 57.886 33.333 15.35 0.00 45.90 2.66
2923 4677 6.784068 TTCACGAACAAAATTCGAAGAAAC 57.216 33.333 15.35 0.00 45.90 2.78
2924 4678 7.326305 TGTTTTCACGAACAAAATTCGAAGAAA 59.674 29.630 15.35 18.09 43.97 2.52
2925 4679 6.802348 TGTTTTCACGAACAAAATTCGAAGAA 59.198 30.769 15.35 14.19 43.97 2.52
2926 4680 6.315551 TGTTTTCACGAACAAAATTCGAAGA 58.684 32.000 15.35 9.69 43.97 2.87
2927 4681 6.547493 TGTTTTCACGAACAAAATTCGAAG 57.453 33.333 15.35 7.73 43.97 3.79
2928 4682 6.929587 TTGTTTTCACGAACAAAATTCGAA 57.070 29.167 15.35 0.00 44.13 3.71


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

AutoCloner maintained by Alex Coulton.