Multiple sequence alignment - TraesCS7D01G248600

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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 TraesCS7D01G248600 chr7D 100.000 3820 0 0 1 3820 220280144 220276325 0.000000e+00 7055.0
1 TraesCS7D01G248600 chr7D 96.708 243 8 0 3307 3549 194552616 194552374 4.600000e-109 405.0
2 TraesCS7D01G248600 chr7D 95.935 246 10 0 3306 3551 155292554 155292309 2.140000e-107 399.0
3 TraesCS7D01G248600 chr7D 93.822 259 15 1 3291 3548 210295508 210295766 4.630000e-104 388.0
4 TraesCS7D01G248600 chr7A 93.860 3290 133 32 68 3307 232591598 232588328 0.000000e+00 4892.0
5 TraesCS7D01G248600 chr7A 92.336 274 14 4 3548 3820 232588326 232588059 2.150000e-102 383.0
6 TraesCS7D01G248600 chr7A 100.000 50 0 0 1 50 232591627 232591578 4.060000e-15 93.5
7 TraesCS7D01G248600 chr7B 95.962 2922 78 19 406 3307 179253234 179256135 0.000000e+00 4706.0
8 TraesCS7D01G248600 chr7B 98.864 264 3 0 3557 3820 179256182 179256445 4.470000e-129 472.0
9 TraesCS7D01G248600 chr2D 96.721 244 7 1 3307 3550 347496683 347496441 4.600000e-109 405.0
10 TraesCS7D01G248600 chr2B 96.327 245 9 0 3308 3552 464038559 464038315 1.650000e-108 403.0
11 TraesCS7D01G248600 chr5B 96.680 241 8 0 3306 3546 131080942 131081182 5.940000e-108 401.0
12 TraesCS7D01G248600 chr5B 89.796 98 10 0 3607 3704 457123291 457123194 4.010000e-25 126.0
13 TraesCS7D01G248600 chr4A 95.951 247 9 1 3306 3551 150384041 150384287 2.140000e-107 399.0
14 TraesCS7D01G248600 chr6B 95.918 245 10 0 3306 3550 427455465 427455709 7.690000e-107 398.0
15 TraesCS7D01G248600 chr4D 95.918 245 9 1 3306 3550 338268363 338268120 2.770000e-106 396.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G248600 chr7D 220276325 220280144 3819 True 7055.0 7055 100.000000 1 3820 1 chr7D.!!$R3 3819
1 TraesCS7D01G248600 chr7A 232588059 232591627 3568 True 1789.5 4892 95.398667 1 3820 3 chr7A.!!$R1 3819
2 TraesCS7D01G248600 chr7B 179253234 179256445 3211 False 2589.0 4706 97.413000 406 3820 2 chr7B.!!$F1 3414

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
685 698 0.032615 TACCCAATTCCCACCATGCC 60.033 55.0 0.00 0.00 0.00 4.40 F
923 952 0.321919 GCTGAATGAGTGCACCAGGA 60.322 55.0 14.63 0.00 32.09 3.86 F
1708 1743 0.106769 TTTGGTGTTCCTGCAGAGCA 60.107 50.0 17.39 8.22 36.92 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1743 2.842496 TCTGATCCTTGCTGAATCCAGT 59.158 45.455 0.00 0.0 42.35 4.00 R
1845 1880 3.704566 GGTGAAAGAATTGGGGGTAATCC 59.295 47.826 0.00 0.0 0.00 3.01 R
2944 3007 0.029433 GGCGCTAACAAGCTAATGGC 59.971 55.000 7.64 0.0 42.19 4.40 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
46 47 4.047822 GACTGAGAAATATCGCTGTCAGG 58.952 47.826 12.27 0.00 46.30 3.86
47 48 3.181471 ACTGAGAAATATCGCTGTCAGGG 60.181 47.826 10.59 10.59 36.54 4.45
48 49 3.031013 TGAGAAATATCGCTGTCAGGGA 58.969 45.455 20.64 20.64 41.55 4.20
49 50 3.181475 TGAGAAATATCGCTGTCAGGGAC 60.181 47.826 20.77 8.74 40.09 4.46
50 51 3.034635 AGAAATATCGCTGTCAGGGACT 58.965 45.455 20.77 10.77 40.09 3.85
64 65 3.742433 AGGGACTGAGAAATATCGCTG 57.258 47.619 0.00 0.00 37.18 5.18
65 66 3.034635 AGGGACTGAGAAATATCGCTGT 58.965 45.455 0.00 0.00 39.54 4.40
66 67 3.068873 AGGGACTGAGAAATATCGCTGTC 59.931 47.826 9.81 9.81 46.32 3.51
69 70 4.926244 GACTGAGAAATATCGCTGTCAGA 58.074 43.478 3.32 0.00 46.30 3.27
70 71 5.330455 ACTGAGAAATATCGCTGTCAGAA 57.670 39.130 3.32 0.00 33.46 3.02
71 72 5.724328 ACTGAGAAATATCGCTGTCAGAAA 58.276 37.500 3.32 0.00 33.46 2.52
72 73 6.344500 ACTGAGAAATATCGCTGTCAGAAAT 58.656 36.000 3.32 0.00 33.46 2.17
73 74 7.492524 ACTGAGAAATATCGCTGTCAGAAATA 58.507 34.615 3.32 0.68 33.46 1.40
74 75 7.651304 ACTGAGAAATATCGCTGTCAGAAATAG 59.349 37.037 3.32 0.00 33.46 1.73
75 76 7.716612 TGAGAAATATCGCTGTCAGAAATAGA 58.283 34.615 3.32 0.00 0.00 1.98
76 77 7.864882 TGAGAAATATCGCTGTCAGAAATAGAG 59.135 37.037 3.32 0.00 0.00 2.43
77 78 6.644592 AGAAATATCGCTGTCAGAAATAGAGC 59.355 38.462 3.32 0.00 0.00 4.09
78 79 5.720371 ATATCGCTGTCAGAAATAGAGCT 57.280 39.130 3.32 0.00 0.00 4.09
79 80 3.156511 TCGCTGTCAGAAATAGAGCTG 57.843 47.619 3.32 0.00 0.00 4.24
143 144 1.933181 CACTTCACGACAAGTTGAGCA 59.067 47.619 10.54 0.00 34.17 4.26
324 325 4.691685 CGCTATAGACTACAGTAGACAGGG 59.308 50.000 14.94 6.58 0.00 4.45
325 326 5.005094 GCTATAGACTACAGTAGACAGGGG 58.995 50.000 14.94 2.52 0.00 4.79
351 352 9.257651 GTTTTTAGACACAACTACAGTAGACAT 57.742 33.333 14.94 0.00 0.00 3.06
364 365 6.680874 ACAGTAGACATGTAGCTACAGTAC 57.319 41.667 29.05 23.90 39.92 2.73
367 368 6.990939 CAGTAGACATGTAGCTACAGTACCTA 59.009 42.308 29.05 21.98 39.92 3.08
436 437 6.084326 ACTGGTTAAATCCAAATCACACAC 57.916 37.500 0.00 0.00 37.01 3.82
437 438 5.596361 ACTGGTTAAATCCAAATCACACACA 59.404 36.000 0.00 0.00 37.01 3.72
438 439 5.837437 TGGTTAAATCCAAATCACACACAC 58.163 37.500 0.00 0.00 34.24 3.82
439 440 5.360999 TGGTTAAATCCAAATCACACACACA 59.639 36.000 0.00 0.00 34.24 3.72
581 585 3.857549 TCACATCTCCGTCTTCTTCTG 57.142 47.619 0.00 0.00 0.00 3.02
603 607 2.653702 CCGCCTCGATCTGGATCC 59.346 66.667 4.20 4.20 34.40 3.36
627 637 2.845659 AGGTGGGTTACATCCTCATCA 58.154 47.619 0.00 0.00 0.00 3.07
634 644 7.227156 GTGGGTTACATCCTCATCAAATATCT 58.773 38.462 0.00 0.00 0.00 1.98
657 667 1.860950 CTCCGCTGTGTTCGATTATGG 59.139 52.381 0.00 0.00 0.00 2.74
658 668 1.206132 TCCGCTGTGTTCGATTATGGT 59.794 47.619 0.00 0.00 0.00 3.55
659 669 2.427812 TCCGCTGTGTTCGATTATGGTA 59.572 45.455 0.00 0.00 0.00 3.25
660 670 2.538449 CCGCTGTGTTCGATTATGGTAC 59.462 50.000 0.00 0.00 0.00 3.34
661 671 2.538449 CGCTGTGTTCGATTATGGTACC 59.462 50.000 4.43 4.43 0.00 3.34
685 698 0.032615 TACCCAATTCCCACCATGCC 60.033 55.000 0.00 0.00 0.00 4.40
716 731 3.239449 GGGGGAAGAAAAACCATCTGTT 58.761 45.455 0.00 0.00 39.43 3.16
725 740 4.734398 AAAACCATCTGTTGACAGCAAA 57.266 36.364 6.27 0.00 43.46 3.68
765 781 1.141858 GCTCCCCTTTAGCACTGCTAT 59.858 52.381 11.61 0.00 41.01 2.97
804 824 1.004595 CCATCAGATCAGTGTGTGCG 58.995 55.000 0.00 0.00 0.00 5.34
811 831 4.338118 TCAGATCAGTGTGTGCGTATGATA 59.662 41.667 0.00 0.00 30.98 2.15
923 952 0.321919 GCTGAATGAGTGCACCAGGA 60.322 55.000 14.63 0.00 32.09 3.86
947 976 2.100252 CCAAACTGATAGCCTGGCATTG 59.900 50.000 22.65 12.60 0.00 2.82
948 977 1.396653 AACTGATAGCCTGGCATTGC 58.603 50.000 22.65 7.64 0.00 3.56
977 1012 3.476295 TGCTTCATCGCATTTCAGTTC 57.524 42.857 0.00 0.00 34.44 3.01
990 1025 5.629097 CATTTCAGTTCTTGTGCAGAGATC 58.371 41.667 0.88 1.26 31.12 2.75
1078 1113 1.680989 TTCGACGAGGAGGCCATCA 60.681 57.895 5.01 0.00 0.00 3.07
1176 1211 0.454620 ACGACGTCAAGATCGAGCAC 60.455 55.000 17.16 0.00 40.86 4.40
1257 1292 2.966732 GCTCATCCCCACGGTCCAA 61.967 63.158 0.00 0.00 0.00 3.53
1306 1341 3.797225 GAGATCGCGCAGGCCATCA 62.797 63.158 8.75 0.00 39.00 3.07
1512 1547 1.866015 TCGACAGGGAGGTCATGATT 58.134 50.000 0.00 0.00 37.66 2.57
1569 1604 1.519234 CAGCATCGACAAGCGGCTA 60.519 57.895 1.35 0.00 41.33 3.93
1708 1743 0.106769 TTTGGTGTTCCTGCAGAGCA 60.107 50.000 17.39 8.22 36.92 4.26
1845 1880 2.358737 GACAAGGGCGAGGTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
1947 1982 1.622312 TGCAGTCTCAGTGAGATGCTT 59.378 47.619 33.24 18.81 40.98 3.91
2115 2151 6.602410 TGAACATTTTGGGCATTGAGAATA 57.398 33.333 0.00 0.00 0.00 1.75
2288 2325 7.816411 ACTTTACTCCCCTAAAATGCTATCAT 58.184 34.615 0.00 0.00 33.53 2.45
2292 2329 9.610104 TTACTCCCCTAAAATGCTATCATAGTA 57.390 33.333 0.00 0.00 31.46 1.82
2746 2809 5.412594 TGTACAGTCAAATGCAGAGATTTCC 59.587 40.000 0.00 0.00 0.00 3.13
2753 2816 6.150140 GTCAAATGCAGAGATTTCCTACAGTT 59.850 38.462 0.00 0.00 0.00 3.16
3197 3260 7.669427 TGACAATAGAGCCATTCAAATTTTGT 58.331 30.769 8.89 0.00 0.00 2.83
3307 3374 3.311596 GCCATTACGGGTTAGACATGAAC 59.688 47.826 0.00 0.00 34.06 3.18
3308 3375 4.766375 CCATTACGGGTTAGACATGAACT 58.234 43.478 0.00 0.72 0.00 3.01
3309 3376 5.682990 GCCATTACGGGTTAGACATGAACTA 60.683 44.000 0.00 0.00 34.06 2.24
3310 3377 5.983720 CCATTACGGGTTAGACATGAACTAG 59.016 44.000 0.00 0.00 0.00 2.57
3311 3378 3.521947 ACGGGTTAGACATGAACTAGC 57.478 47.619 0.00 4.98 0.00 3.42
3312 3379 2.829720 ACGGGTTAGACATGAACTAGCA 59.170 45.455 0.00 0.00 0.00 3.49
3313 3380 3.259876 ACGGGTTAGACATGAACTAGCAA 59.740 43.478 0.00 0.00 0.00 3.91
3314 3381 3.865745 CGGGTTAGACATGAACTAGCAAG 59.134 47.826 0.00 0.13 0.00 4.01
3315 3382 4.381612 CGGGTTAGACATGAACTAGCAAGA 60.382 45.833 0.00 0.00 0.00 3.02
3316 3383 5.675538 GGGTTAGACATGAACTAGCAAGAT 58.324 41.667 0.00 0.00 0.00 2.40
3317 3384 5.525378 GGGTTAGACATGAACTAGCAAGATG 59.475 44.000 0.00 0.00 0.00 2.90
3318 3385 5.007136 GGTTAGACATGAACTAGCAAGATGC 59.993 44.000 0.00 0.00 45.46 3.91
3319 3386 3.539604 AGACATGAACTAGCAAGATGCC 58.460 45.455 0.00 0.00 46.52 4.40
3320 3387 2.615912 GACATGAACTAGCAAGATGCCC 59.384 50.000 0.00 0.00 46.52 5.36
3321 3388 1.600957 CATGAACTAGCAAGATGCCCG 59.399 52.381 0.00 0.00 46.52 6.13
3322 3389 0.613260 TGAACTAGCAAGATGCCCGT 59.387 50.000 0.00 0.00 46.52 5.28
3323 3390 1.009829 GAACTAGCAAGATGCCCGTG 58.990 55.000 0.00 0.00 46.52 4.94
3324 3391 1.026718 AACTAGCAAGATGCCCGTGC 61.027 55.000 6.11 6.11 46.52 5.34
3327 3394 3.737172 GCAAGATGCCCGTGCGTT 61.737 61.111 0.00 0.00 40.20 4.84
3328 3395 2.176546 CAAGATGCCCGTGCGTTG 59.823 61.111 0.00 0.00 41.78 4.10
3329 3396 3.737172 AAGATGCCCGTGCGTTGC 61.737 61.111 0.00 0.00 41.78 4.17
3339 3406 2.942879 TGCGTTGCACGGAACATC 59.057 55.556 10.02 0.00 39.47 3.06
3340 3407 1.889573 TGCGTTGCACGGAACATCA 60.890 52.632 10.02 0.00 39.47 3.07
3341 3408 1.281353 GCGTTGCACGGAACATCAA 59.719 52.632 10.02 0.00 42.82 2.57
3342 3409 0.725784 GCGTTGCACGGAACATCAAG 60.726 55.000 10.02 0.00 42.82 3.02
3343 3410 0.865111 CGTTGCACGGAACATCAAGA 59.135 50.000 2.31 0.00 38.08 3.02
3344 3411 1.464608 CGTTGCACGGAACATCAAGAT 59.535 47.619 2.31 0.00 38.08 2.40
3345 3412 2.725759 CGTTGCACGGAACATCAAGATG 60.726 50.000 8.45 8.45 40.19 2.90
3346 3413 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
3347 3414 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
3348 3415 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
3349 3416 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
3350 3417 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
3351 3418 3.855379 CACGGAACATCAAGATGCATTTG 59.145 43.478 9.85 7.88 42.39 2.32
3352 3419 3.507233 ACGGAACATCAAGATGCATTTGT 59.493 39.130 9.85 0.00 42.39 2.83
3353 3420 4.699735 ACGGAACATCAAGATGCATTTGTA 59.300 37.500 9.85 0.00 42.39 2.41
3354 3421 5.357878 ACGGAACATCAAGATGCATTTGTAT 59.642 36.000 9.85 1.80 42.39 2.29
3355 3422 5.684184 CGGAACATCAAGATGCATTTGTATG 59.316 40.000 9.85 13.57 42.39 2.39
3356 3423 6.458615 CGGAACATCAAGATGCATTTGTATGA 60.459 38.462 22.17 15.31 42.39 2.15
3357 3424 6.916387 GGAACATCAAGATGCATTTGTATGAG 59.084 38.462 22.17 12.56 42.39 2.90
3358 3425 7.400599 AACATCAAGATGCATTTGTATGAGT 57.599 32.000 22.17 12.92 42.39 3.41
3359 3426 8.510243 AACATCAAGATGCATTTGTATGAGTA 57.490 30.769 22.17 8.59 42.39 2.59
3360 3427 8.151141 ACATCAAGATGCATTTGTATGAGTAG 57.849 34.615 22.17 12.72 42.39 2.57
3361 3428 7.772292 ACATCAAGATGCATTTGTATGAGTAGT 59.228 33.333 22.17 13.08 42.39 2.73
3362 3429 8.618677 CATCAAGATGCATTTGTATGAGTAGTT 58.381 33.333 0.00 0.00 33.37 2.24
3363 3430 8.565896 TCAAGATGCATTTGTATGAGTAGTTT 57.434 30.769 0.00 0.00 33.37 2.66
3364 3431 9.665719 TCAAGATGCATTTGTATGAGTAGTTTA 57.334 29.630 0.00 0.00 33.37 2.01
3370 3437 9.448438 TGCATTTGTATGAGTAGTTTATCTTGT 57.552 29.630 0.00 0.00 33.37 3.16
3388 3455 7.602517 ATCTTGTAAGAGAAAAGGATGAACG 57.397 36.000 0.51 0.00 38.66 3.95
3389 3456 6.755206 TCTTGTAAGAGAAAAGGATGAACGA 58.245 36.000 0.00 0.00 0.00 3.85
3390 3457 6.868864 TCTTGTAAGAGAAAAGGATGAACGAG 59.131 38.462 0.00 0.00 0.00 4.18
3391 3458 5.479306 TGTAAGAGAAAAGGATGAACGAGG 58.521 41.667 0.00 0.00 0.00 4.63
3392 3459 3.618690 AGAGAAAAGGATGAACGAGGG 57.381 47.619 0.00 0.00 0.00 4.30
3393 3460 3.173965 AGAGAAAAGGATGAACGAGGGA 58.826 45.455 0.00 0.00 0.00 4.20
3394 3461 3.583086 AGAGAAAAGGATGAACGAGGGAA 59.417 43.478 0.00 0.00 0.00 3.97
3395 3462 3.935828 GAGAAAAGGATGAACGAGGGAAG 59.064 47.826 0.00 0.00 0.00 3.46
3396 3463 2.789409 AAAGGATGAACGAGGGAAGG 57.211 50.000 0.00 0.00 0.00 3.46
3397 3464 0.253327 AAGGATGAACGAGGGAAGGC 59.747 55.000 0.00 0.00 0.00 4.35
3398 3465 1.153147 GGATGAACGAGGGAAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
3411 3478 3.183793 GGAAGGCCCTATTTGCAAATG 57.816 47.619 30.43 20.32 0.00 2.32
3412 3479 2.501316 GGAAGGCCCTATTTGCAAATGT 59.499 45.455 30.43 12.33 0.00 2.71
3413 3480 3.524541 GAAGGCCCTATTTGCAAATGTG 58.475 45.455 30.43 22.20 0.00 3.21
3414 3481 1.832998 AGGCCCTATTTGCAAATGTGG 59.167 47.619 30.43 27.81 0.00 4.17
3415 3482 1.830477 GGCCCTATTTGCAAATGTGGA 59.170 47.619 30.70 15.82 0.00 4.02
3416 3483 2.159057 GGCCCTATTTGCAAATGTGGAG 60.159 50.000 30.70 22.03 0.00 3.86
3417 3484 2.760092 GCCCTATTTGCAAATGTGGAGA 59.240 45.455 30.70 14.94 0.00 3.71
3418 3485 3.181483 GCCCTATTTGCAAATGTGGAGAG 60.181 47.826 30.70 21.21 0.00 3.20
3419 3486 3.382546 CCCTATTTGCAAATGTGGAGAGG 59.617 47.826 30.80 26.61 0.00 3.69
3420 3487 3.382546 CCTATTTGCAAATGTGGAGAGGG 59.617 47.826 30.43 15.92 0.00 4.30
3421 3488 1.631405 TTTGCAAATGTGGAGAGGGG 58.369 50.000 8.05 0.00 0.00 4.79
3422 3489 0.482446 TTGCAAATGTGGAGAGGGGT 59.518 50.000 0.00 0.00 0.00 4.95
3423 3490 0.251297 TGCAAATGTGGAGAGGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
3424 3491 0.251341 GCAAATGTGGAGAGGGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
3425 3492 1.538047 CAAATGTGGAGAGGGGTGTG 58.462 55.000 0.00 0.00 0.00 3.82
3426 3493 0.405585 AAATGTGGAGAGGGGTGTGG 59.594 55.000 0.00 0.00 0.00 4.17
3427 3494 1.500783 AATGTGGAGAGGGGTGTGGG 61.501 60.000 0.00 0.00 0.00 4.61
3428 3495 2.529389 GTGGAGAGGGGTGTGGGT 60.529 66.667 0.00 0.00 0.00 4.51
3429 3496 1.229400 GTGGAGAGGGGTGTGGGTA 60.229 63.158 0.00 0.00 0.00 3.69
3430 3497 0.620700 GTGGAGAGGGGTGTGGGTAT 60.621 60.000 0.00 0.00 0.00 2.73
3431 3498 0.326238 TGGAGAGGGGTGTGGGTATC 60.326 60.000 0.00 0.00 0.00 2.24
3432 3499 1.054978 GGAGAGGGGTGTGGGTATCC 61.055 65.000 0.00 0.00 0.00 2.59
3433 3500 0.031010 GAGAGGGGTGTGGGTATCCT 60.031 60.000 0.00 0.00 0.00 3.24
3434 3501 0.421904 AGAGGGGTGTGGGTATCCTT 59.578 55.000 0.00 0.00 0.00 3.36
3435 3502 1.203570 AGAGGGGTGTGGGTATCCTTT 60.204 52.381 0.00 0.00 0.00 3.11
3436 3503 1.639108 GAGGGGTGTGGGTATCCTTTT 59.361 52.381 0.00 0.00 0.00 2.27
3437 3504 2.848071 GAGGGGTGTGGGTATCCTTTTA 59.152 50.000 0.00 0.00 0.00 1.52
3438 3505 2.579400 AGGGGTGTGGGTATCCTTTTAC 59.421 50.000 0.00 0.00 0.00 2.01
3439 3506 2.309458 GGGGTGTGGGTATCCTTTTACA 59.691 50.000 0.00 0.00 0.00 2.41
3440 3507 3.245336 GGGGTGTGGGTATCCTTTTACAA 60.245 47.826 0.00 0.00 0.00 2.41
3441 3508 4.409187 GGGTGTGGGTATCCTTTTACAAA 58.591 43.478 0.00 0.00 0.00 2.83
3442 3509 4.833938 GGGTGTGGGTATCCTTTTACAAAA 59.166 41.667 0.00 0.00 0.00 2.44
3443 3510 5.482526 GGGTGTGGGTATCCTTTTACAAAAT 59.517 40.000 0.00 0.00 0.00 1.82
3444 3511 6.014070 GGGTGTGGGTATCCTTTTACAAAATT 60.014 38.462 0.00 0.00 0.00 1.82
3445 3512 6.871492 GGTGTGGGTATCCTTTTACAAAATTG 59.129 38.462 0.00 0.00 0.00 2.32
3446 3513 6.367695 GTGTGGGTATCCTTTTACAAAATTGC 59.632 38.462 0.00 0.00 0.00 3.56
3447 3514 5.872617 GTGGGTATCCTTTTACAAAATTGCC 59.127 40.000 0.00 0.00 0.00 4.52
3448 3515 5.544176 TGGGTATCCTTTTACAAAATTGCCA 59.456 36.000 0.00 0.00 0.00 4.92
3449 3516 6.214412 TGGGTATCCTTTTACAAAATTGCCAT 59.786 34.615 0.00 0.00 0.00 4.40
3450 3517 7.400339 TGGGTATCCTTTTACAAAATTGCCATA 59.600 33.333 0.00 0.00 0.00 2.74
3451 3518 7.926018 GGGTATCCTTTTACAAAATTGCCATAG 59.074 37.037 0.00 0.00 0.00 2.23
3452 3519 8.474831 GGTATCCTTTTACAAAATTGCCATAGT 58.525 33.333 0.00 0.00 0.00 2.12
3453 3520 9.869757 GTATCCTTTTACAAAATTGCCATAGTT 57.130 29.630 0.00 0.00 0.00 2.24
3455 3522 8.825667 TCCTTTTACAAAATTGCCATAGTTTC 57.174 30.769 0.00 0.00 0.00 2.78
3456 3523 7.875554 TCCTTTTACAAAATTGCCATAGTTTCC 59.124 33.333 0.00 0.00 0.00 3.13
3457 3524 7.877612 CCTTTTACAAAATTGCCATAGTTTCCT 59.122 33.333 0.00 0.00 0.00 3.36
3458 3525 9.271828 CTTTTACAAAATTGCCATAGTTTCCTT 57.728 29.630 0.00 0.00 0.00 3.36
3459 3526 8.825667 TTTACAAAATTGCCATAGTTTCCTTC 57.174 30.769 0.00 0.00 0.00 3.46
3460 3527 5.793817 ACAAAATTGCCATAGTTTCCTTCC 58.206 37.500 0.00 0.00 0.00 3.46
3461 3528 5.543790 ACAAAATTGCCATAGTTTCCTTCCT 59.456 36.000 0.00 0.00 0.00 3.36
3462 3529 6.723977 ACAAAATTGCCATAGTTTCCTTCCTA 59.276 34.615 0.00 0.00 0.00 2.94
3463 3530 7.400052 ACAAAATTGCCATAGTTTCCTTCCTAT 59.600 33.333 0.00 0.00 0.00 2.57
3464 3531 7.588497 AAATTGCCATAGTTTCCTTCCTATC 57.412 36.000 0.00 0.00 0.00 2.08
3465 3532 4.706842 TGCCATAGTTTCCTTCCTATCC 57.293 45.455 0.00 0.00 0.00 2.59
3466 3533 3.071023 TGCCATAGTTTCCTTCCTATCCG 59.929 47.826 0.00 0.00 0.00 4.18
3467 3534 3.071167 GCCATAGTTTCCTTCCTATCCGT 59.929 47.826 0.00 0.00 0.00 4.69
3468 3535 4.799917 GCCATAGTTTCCTTCCTATCCGTC 60.800 50.000 0.00 0.00 0.00 4.79
3469 3536 4.344102 CCATAGTTTCCTTCCTATCCGTCA 59.656 45.833 0.00 0.00 0.00 4.35
3470 3537 5.509840 CCATAGTTTCCTTCCTATCCGTCAG 60.510 48.000 0.00 0.00 0.00 3.51
3471 3538 3.709587 AGTTTCCTTCCTATCCGTCAGA 58.290 45.455 0.00 0.00 0.00 3.27
3472 3539 4.290942 AGTTTCCTTCCTATCCGTCAGAT 58.709 43.478 0.00 0.00 39.15 2.90
3473 3540 4.717280 AGTTTCCTTCCTATCCGTCAGATT 59.283 41.667 0.00 0.00 36.33 2.40
3474 3541 5.189934 AGTTTCCTTCCTATCCGTCAGATTT 59.810 40.000 0.00 0.00 36.33 2.17
3475 3542 6.383147 AGTTTCCTTCCTATCCGTCAGATTTA 59.617 38.462 0.00 0.00 36.33 1.40
3476 3543 6.801718 TTCCTTCCTATCCGTCAGATTTAA 57.198 37.500 0.00 0.00 36.33 1.52
3477 3544 6.801718 TCCTTCCTATCCGTCAGATTTAAA 57.198 37.500 0.00 0.00 36.33 1.52
3478 3545 7.374975 TCCTTCCTATCCGTCAGATTTAAAT 57.625 36.000 0.00 0.00 36.33 1.40
3479 3546 7.442656 TCCTTCCTATCCGTCAGATTTAAATC 58.557 38.462 18.70 18.70 36.33 2.17
3480 3547 6.366332 CCTTCCTATCCGTCAGATTTAAATCG 59.634 42.308 19.86 15.23 40.35 3.34
3481 3548 5.779922 TCCTATCCGTCAGATTTAAATCGG 58.220 41.667 19.86 19.33 40.35 4.18
3486 3553 3.587403 GTCAGATTTAAATCGGACGGC 57.413 47.619 31.74 18.20 45.64 5.68
3487 3554 2.287103 GTCAGATTTAAATCGGACGGCC 59.713 50.000 31.74 17.93 45.64 6.13
3488 3555 2.169769 TCAGATTTAAATCGGACGGCCT 59.830 45.455 22.22 2.40 40.35 5.19
3489 3556 3.385433 TCAGATTTAAATCGGACGGCCTA 59.615 43.478 22.22 0.00 40.35 3.93
3490 3557 4.039973 TCAGATTTAAATCGGACGGCCTAT 59.960 41.667 22.22 0.00 40.35 2.57
3491 3558 5.244402 TCAGATTTAAATCGGACGGCCTATA 59.756 40.000 22.22 2.64 40.35 1.31
3492 3559 6.070995 TCAGATTTAAATCGGACGGCCTATAT 60.071 38.462 22.22 0.00 40.35 0.86
3493 3560 6.594159 CAGATTTAAATCGGACGGCCTATATT 59.406 38.462 19.84 0.00 40.35 1.28
3494 3561 6.594159 AGATTTAAATCGGACGGCCTATATTG 59.406 38.462 19.86 0.00 40.35 1.90
3495 3562 2.094762 AATCGGACGGCCTATATTGC 57.905 50.000 5.33 0.00 0.00 3.56
3496 3563 0.973632 ATCGGACGGCCTATATTGCA 59.026 50.000 5.33 0.00 0.00 4.08
3497 3564 0.317160 TCGGACGGCCTATATTGCAG 59.683 55.000 5.33 0.00 0.00 4.41
3498 3565 0.670546 CGGACGGCCTATATTGCAGG 60.671 60.000 5.33 0.00 36.16 4.85
3499 3566 0.685097 GGACGGCCTATATTGCAGGA 59.315 55.000 0.00 0.00 34.91 3.86
3500 3567 1.279271 GGACGGCCTATATTGCAGGAT 59.721 52.381 0.00 0.00 34.91 3.24
3501 3568 2.350522 GACGGCCTATATTGCAGGATG 58.649 52.381 0.00 0.00 34.91 3.51
3502 3569 1.003580 ACGGCCTATATTGCAGGATGG 59.996 52.381 0.00 0.00 34.91 3.51
3503 3570 1.467920 GGCCTATATTGCAGGATGGC 58.532 55.000 0.00 10.13 34.91 4.40
3504 3571 1.272092 GGCCTATATTGCAGGATGGCA 60.272 52.381 17.22 0.00 43.19 4.92
3505 3572 2.089980 GCCTATATTGCAGGATGGCAG 58.910 52.381 12.68 0.00 45.88 4.85
3506 3573 2.719739 CCTATATTGCAGGATGGCAGG 58.280 52.381 0.00 0.00 45.88 4.85
3507 3574 2.089980 CTATATTGCAGGATGGCAGGC 58.910 52.381 0.00 0.00 45.88 4.85
3508 3575 0.186630 ATATTGCAGGATGGCAGGCA 59.813 50.000 0.00 0.00 45.88 4.75
3509 3576 0.752743 TATTGCAGGATGGCAGGCAC 60.753 55.000 0.00 0.00 45.88 5.01
3510 3577 2.791613 ATTGCAGGATGGCAGGCACA 62.792 55.000 0.00 0.00 45.88 4.57
3511 3578 3.446570 GCAGGATGGCAGGCACAC 61.447 66.667 0.00 0.00 35.86 3.82
3512 3579 2.753043 CAGGATGGCAGGCACACC 60.753 66.667 12.37 12.37 0.00 4.16
3513 3580 3.259314 AGGATGGCAGGCACACCA 61.259 61.111 19.51 0.00 41.01 4.17
3516 3583 2.765279 ATGGCAGGCACACCATCA 59.235 55.556 0.00 0.00 42.69 3.07
3517 3584 1.308666 ATGGCAGGCACACCATCAT 59.691 52.632 0.00 0.00 42.69 2.45
3518 3585 0.754217 ATGGCAGGCACACCATCATC 60.754 55.000 0.00 0.00 42.69 2.92
3519 3586 1.378911 GGCAGGCACACCATCATCA 60.379 57.895 0.00 0.00 39.06 3.07
3520 3587 1.660560 GGCAGGCACACCATCATCAC 61.661 60.000 0.00 0.00 39.06 3.06
3521 3588 1.660560 GCAGGCACACCATCATCACC 61.661 60.000 0.00 0.00 39.06 4.02
3522 3589 0.322726 CAGGCACACCATCATCACCA 60.323 55.000 0.00 0.00 39.06 4.17
3523 3590 0.405198 AGGCACACCATCATCACCAA 59.595 50.000 0.00 0.00 39.06 3.67
3524 3591 0.527565 GGCACACCATCATCACCAAC 59.472 55.000 0.00 0.00 35.26 3.77
3525 3592 1.538047 GCACACCATCATCACCAACT 58.462 50.000 0.00 0.00 0.00 3.16
3526 3593 1.470098 GCACACCATCATCACCAACTC 59.530 52.381 0.00 0.00 0.00 3.01
3527 3594 2.877300 GCACACCATCATCACCAACTCT 60.877 50.000 0.00 0.00 0.00 3.24
3528 3595 2.745821 CACACCATCATCACCAACTCTG 59.254 50.000 0.00 0.00 0.00 3.35
3529 3596 2.373169 ACACCATCATCACCAACTCTGT 59.627 45.455 0.00 0.00 0.00 3.41
3530 3597 3.181440 ACACCATCATCACCAACTCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
3531 3598 3.822735 CACCATCATCACCAACTCTGTTT 59.177 43.478 0.00 0.00 0.00 2.83
3532 3599 4.279169 CACCATCATCACCAACTCTGTTTT 59.721 41.667 0.00 0.00 0.00 2.43
3533 3600 4.895297 ACCATCATCACCAACTCTGTTTTT 59.105 37.500 0.00 0.00 0.00 1.94
3578 3646 7.557724 TCCGAGGTTAACATGAACATATGTAA 58.442 34.615 9.21 0.88 40.24 2.41
3579 3647 7.709182 TCCGAGGTTAACATGAACATATGTAAG 59.291 37.037 9.21 2.24 40.24 2.34
3580 3648 7.042051 CCGAGGTTAACATGAACATATGTAAGG 60.042 40.741 9.21 5.23 40.24 2.69
3581 3649 7.494625 CGAGGTTAACATGAACATATGTAAGGT 59.505 37.037 9.21 5.89 40.24 3.50
3730 3835 1.879380 TGAGACCAAGACAAAATGCGG 59.121 47.619 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.034635 ACAGCGATATTTCTCAGTCCCT 58.965 45.455 0.00 0.00 0.00 4.20
45 46 3.181475 TGACAGCGATATTTCTCAGTCCC 60.181 47.826 0.00 0.00 0.00 4.46
46 47 4.046938 TGACAGCGATATTTCTCAGTCC 57.953 45.455 0.00 0.00 0.00 3.85
47 48 4.926244 TCTGACAGCGATATTTCTCAGTC 58.074 43.478 0.00 0.00 0.00 3.51
48 49 4.991153 TCTGACAGCGATATTTCTCAGT 57.009 40.909 0.00 0.00 0.00 3.41
49 50 6.841443 ATTTCTGACAGCGATATTTCTCAG 57.159 37.500 0.00 0.00 0.00 3.35
50 51 7.716612 TCTATTTCTGACAGCGATATTTCTCA 58.283 34.615 0.00 0.00 0.00 3.27
51 52 7.148820 GCTCTATTTCTGACAGCGATATTTCTC 60.149 40.741 0.00 0.00 0.00 2.87
52 53 6.644592 GCTCTATTTCTGACAGCGATATTTCT 59.355 38.462 0.00 0.00 0.00 2.52
53 54 6.644592 AGCTCTATTTCTGACAGCGATATTTC 59.355 38.462 0.00 0.00 35.14 2.17
54 55 6.423302 CAGCTCTATTTCTGACAGCGATATTT 59.577 38.462 0.00 0.00 35.14 1.40
55 56 5.925397 CAGCTCTATTTCTGACAGCGATATT 59.075 40.000 0.00 0.00 35.14 1.28
56 57 5.242615 TCAGCTCTATTTCTGACAGCGATAT 59.757 40.000 0.00 0.00 34.69 1.63
57 58 4.580580 TCAGCTCTATTTCTGACAGCGATA 59.419 41.667 0.00 0.00 34.69 2.92
58 59 3.382865 TCAGCTCTATTTCTGACAGCGAT 59.617 43.478 0.00 0.00 34.69 4.58
59 60 2.755103 TCAGCTCTATTTCTGACAGCGA 59.245 45.455 0.00 0.00 34.69 4.93
60 61 3.114809 CTCAGCTCTATTTCTGACAGCG 58.885 50.000 0.00 0.00 35.66 5.18
61 62 3.456280 CCTCAGCTCTATTTCTGACAGC 58.544 50.000 0.00 0.00 35.66 4.40
62 63 3.703556 TCCCTCAGCTCTATTTCTGACAG 59.296 47.826 0.00 0.00 35.66 3.51
63 64 3.449018 GTCCCTCAGCTCTATTTCTGACA 59.551 47.826 0.00 0.00 35.66 3.58
64 65 3.449018 TGTCCCTCAGCTCTATTTCTGAC 59.551 47.826 0.00 0.00 35.66 3.51
65 66 3.713003 TGTCCCTCAGCTCTATTTCTGA 58.287 45.455 0.00 0.00 37.70 3.27
66 67 4.478206 TTGTCCCTCAGCTCTATTTCTG 57.522 45.455 0.00 0.00 0.00 3.02
67 68 5.045286 ACATTTGTCCCTCAGCTCTATTTCT 60.045 40.000 0.00 0.00 0.00 2.52
68 69 5.189180 ACATTTGTCCCTCAGCTCTATTTC 58.811 41.667 0.00 0.00 0.00 2.17
69 70 5.184892 ACATTTGTCCCTCAGCTCTATTT 57.815 39.130 0.00 0.00 0.00 1.40
70 71 4.851639 ACATTTGTCCCTCAGCTCTATT 57.148 40.909 0.00 0.00 0.00 1.73
71 72 4.521146 CAACATTTGTCCCTCAGCTCTAT 58.479 43.478 0.00 0.00 0.00 1.98
72 73 3.869912 GCAACATTTGTCCCTCAGCTCTA 60.870 47.826 0.00 0.00 0.00 2.43
73 74 2.787994 CAACATTTGTCCCTCAGCTCT 58.212 47.619 0.00 0.00 0.00 4.09
74 75 1.200948 GCAACATTTGTCCCTCAGCTC 59.799 52.381 0.00 0.00 0.00 4.09
75 76 1.251251 GCAACATTTGTCCCTCAGCT 58.749 50.000 0.00 0.00 0.00 4.24
76 77 0.109597 CGCAACATTTGTCCCTCAGC 60.110 55.000 0.00 0.00 0.00 4.26
77 78 0.109597 GCGCAACATTTGTCCCTCAG 60.110 55.000 0.30 0.00 0.00 3.35
78 79 1.523154 GGCGCAACATTTGTCCCTCA 61.523 55.000 10.83 0.00 0.00 3.86
79 80 1.212751 GGCGCAACATTTGTCCCTC 59.787 57.895 10.83 0.00 0.00 4.30
128 129 3.607422 TTCATTGCTCAACTTGTCGTG 57.393 42.857 0.00 0.00 0.00 4.35
324 325 7.707893 TGTCTACTGTAGTTGTGTCTAAAAACC 59.292 37.037 14.11 0.00 0.00 3.27
325 326 8.638685 TGTCTACTGTAGTTGTGTCTAAAAAC 57.361 34.615 14.11 1.92 0.00 2.43
351 352 3.657398 TGGCTAGGTACTGTAGCTACA 57.343 47.619 24.63 24.63 42.27 2.74
436 437 0.316442 GCATCAATCGACGGCATGTG 60.316 55.000 0.00 0.00 0.00 3.21
437 438 0.744057 TGCATCAATCGACGGCATGT 60.744 50.000 0.00 0.00 31.75 3.21
438 439 0.377905 TTGCATCAATCGACGGCATG 59.622 50.000 0.00 0.00 35.44 4.06
439 440 1.093972 TTTGCATCAATCGACGGCAT 58.906 45.000 0.00 0.00 35.44 4.40
581 585 2.356793 CAGATCGAGGCGGGATGC 60.357 66.667 0.00 0.00 45.38 3.91
603 607 2.039746 TGAGGATGTAACCCACCTTGTG 59.960 50.000 0.00 0.00 32.53 3.33
627 637 2.119495 ACACAGCGGAGGGAGATATTT 58.881 47.619 0.00 0.00 0.00 1.40
634 644 1.541310 AATCGAACACAGCGGAGGGA 61.541 55.000 0.00 0.00 0.00 4.20
657 667 2.765699 TGGGAATTGGGTACTACGGTAC 59.234 50.000 0.00 0.00 45.38 3.34
658 668 2.765699 GTGGGAATTGGGTACTACGGTA 59.234 50.000 0.00 0.00 0.00 4.02
659 669 1.556451 GTGGGAATTGGGTACTACGGT 59.444 52.381 0.00 0.00 0.00 4.83
660 670 1.134310 GGTGGGAATTGGGTACTACGG 60.134 57.143 0.00 0.00 0.00 4.02
661 671 1.555992 TGGTGGGAATTGGGTACTACG 59.444 52.381 0.00 0.00 0.00 3.51
675 688 1.024271 CAAATCTACGGCATGGTGGG 58.976 55.000 0.00 0.00 0.00 4.61
725 740 5.237344 GGAGCAGTCGCAAAATTATAGACAT 59.763 40.000 0.00 0.00 42.27 3.06
730 745 3.118038 AGGGGAGCAGTCGCAAAATTATA 60.118 43.478 0.00 0.00 42.27 0.98
733 748 0.251341 AGGGGAGCAGTCGCAAAATT 60.251 50.000 0.00 0.00 42.27 1.82
734 749 0.251341 AAGGGGAGCAGTCGCAAAAT 60.251 50.000 0.00 0.00 42.27 1.82
765 781 3.002102 GGTACGAAAAAGGCGTAATCCA 58.998 45.455 0.00 0.00 44.62 3.41
804 824 9.561069 AGGTTCAGTTGGTTCATATTATCATAC 57.439 33.333 0.00 0.00 0.00 2.39
811 831 6.777580 ACAAGAAGGTTCAGTTGGTTCATATT 59.222 34.615 0.00 0.00 0.00 1.28
923 952 2.025037 TGCCAGGCTATCAGTTTGGAAT 60.025 45.455 14.15 0.00 0.00 3.01
947 976 2.224784 TGCGATGAAGCATCATACATGC 59.775 45.455 4.06 7.54 46.30 4.06
977 1012 0.252479 AGGGCTGATCTCTGCACAAG 59.748 55.000 12.92 0.00 45.20 3.16
1257 1292 4.334118 TGCAGCGTGGTGAGGCAT 62.334 61.111 2.76 0.00 35.31 4.40
1306 1341 1.120530 AGTATCGGCGGGAACTTGAT 58.879 50.000 7.21 0.00 0.00 2.57
1512 1547 3.963733 CTTGGTCAGGATCTTGCCA 57.036 52.632 14.17 14.17 0.00 4.92
1536 1571 3.928992 CGATGCTGTATCCCATGATGTAC 59.071 47.826 0.00 0.00 31.82 2.90
1708 1743 2.842496 TCTGATCCTTGCTGAATCCAGT 59.158 45.455 0.00 0.00 42.35 4.00
1845 1880 3.704566 GGTGAAAGAATTGGGGGTAATCC 59.295 47.826 0.00 0.00 0.00 3.01
1947 1982 5.470098 GGCAAACTTCTTCTGATTACAGTCA 59.530 40.000 0.00 0.00 43.81 3.41
2288 2325 8.084073 GTGTGTGACTGTGTAATTAGGTTACTA 58.916 37.037 0.00 0.00 42.58 1.82
2292 2329 5.526111 GTGTGTGTGACTGTGTAATTAGGTT 59.474 40.000 0.00 0.00 0.00 3.50
2753 2816 7.744087 ACTGCAAAATGAACACATTACTCTA 57.256 32.000 0.00 0.00 34.38 2.43
2944 3007 0.029433 GGCGCTAACAAGCTAATGGC 59.971 55.000 7.64 0.00 42.19 4.40
3168 3231 7.834881 ATTTGAATGGCTCTATTGTCATCAT 57.165 32.000 0.00 0.00 0.00 2.45
3307 3374 2.528743 CGCACGGGCATCTTGCTAG 61.529 63.158 11.77 0.00 44.28 3.42
3308 3375 2.511373 CGCACGGGCATCTTGCTA 60.511 61.111 11.77 0.00 44.28 3.49
3309 3376 4.704833 ACGCACGGGCATCTTGCT 62.705 61.111 11.77 0.00 44.28 3.91
3310 3377 3.737172 AACGCACGGGCATCTTGC 61.737 61.111 11.77 0.00 44.08 4.01
3311 3378 2.176546 CAACGCACGGGCATCTTG 59.823 61.111 11.77 3.62 41.24 3.02
3312 3379 3.737172 GCAACGCACGGGCATCTT 61.737 61.111 11.77 0.00 41.24 2.40
3325 3392 2.855180 CATCTTGATGTTCCGTGCAAC 58.145 47.619 0.00 0.00 0.00 4.17
3326 3393 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
3327 3394 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
3328 3395 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
3329 3396 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
3330 3397 3.507233 ACAAATGCATCTTGATGTTCCGT 59.493 39.130 20.96 2.07 0.00 4.69
3331 3398 4.100707 ACAAATGCATCTTGATGTTCCG 57.899 40.909 20.96 1.56 0.00 4.30
3332 3399 6.798482 TCATACAAATGCATCTTGATGTTCC 58.202 36.000 20.96 0.00 32.76 3.62
3333 3400 7.478322 ACTCATACAAATGCATCTTGATGTTC 58.522 34.615 20.96 0.00 32.76 3.18
3334 3401 7.400599 ACTCATACAAATGCATCTTGATGTT 57.599 32.000 20.96 1.04 32.76 2.71
3335 3402 7.772292 ACTACTCATACAAATGCATCTTGATGT 59.228 33.333 20.96 14.21 32.76 3.06
3336 3403 8.151141 ACTACTCATACAAATGCATCTTGATG 57.849 34.615 20.96 18.39 32.76 3.07
3337 3404 8.743085 AACTACTCATACAAATGCATCTTGAT 57.257 30.769 20.96 11.48 32.76 2.57
3338 3405 8.565896 AAACTACTCATACAAATGCATCTTGA 57.434 30.769 20.96 10.81 32.76 3.02
3344 3411 9.448438 ACAAGATAAACTACTCATACAAATGCA 57.552 29.630 0.00 0.00 32.76 3.96
3362 3429 9.151471 CGTTCATCCTTTTCTCTTACAAGATAA 57.849 33.333 0.00 0.00 33.93 1.75
3363 3430 8.528643 TCGTTCATCCTTTTCTCTTACAAGATA 58.471 33.333 0.00 0.00 33.93 1.98
3364 3431 7.386851 TCGTTCATCCTTTTCTCTTACAAGAT 58.613 34.615 0.00 0.00 33.93 2.40
3365 3432 6.755206 TCGTTCATCCTTTTCTCTTACAAGA 58.245 36.000 0.00 0.00 0.00 3.02
3366 3433 6.091441 CCTCGTTCATCCTTTTCTCTTACAAG 59.909 42.308 0.00 0.00 0.00 3.16
3367 3434 5.932303 CCTCGTTCATCCTTTTCTCTTACAA 59.068 40.000 0.00 0.00 0.00 2.41
3368 3435 5.479306 CCTCGTTCATCCTTTTCTCTTACA 58.521 41.667 0.00 0.00 0.00 2.41
3369 3436 4.870991 CCCTCGTTCATCCTTTTCTCTTAC 59.129 45.833 0.00 0.00 0.00 2.34
3370 3437 4.775780 TCCCTCGTTCATCCTTTTCTCTTA 59.224 41.667 0.00 0.00 0.00 2.10
3371 3438 3.583086 TCCCTCGTTCATCCTTTTCTCTT 59.417 43.478 0.00 0.00 0.00 2.85
3372 3439 3.173965 TCCCTCGTTCATCCTTTTCTCT 58.826 45.455 0.00 0.00 0.00 3.10
3373 3440 3.611766 TCCCTCGTTCATCCTTTTCTC 57.388 47.619 0.00 0.00 0.00 2.87
3374 3441 3.307762 CCTTCCCTCGTTCATCCTTTTCT 60.308 47.826 0.00 0.00 0.00 2.52
3375 3442 3.010420 CCTTCCCTCGTTCATCCTTTTC 58.990 50.000 0.00 0.00 0.00 2.29
3376 3443 2.880167 GCCTTCCCTCGTTCATCCTTTT 60.880 50.000 0.00 0.00 0.00 2.27
3377 3444 1.340114 GCCTTCCCTCGTTCATCCTTT 60.340 52.381 0.00 0.00 0.00 3.11
3378 3445 0.253327 GCCTTCCCTCGTTCATCCTT 59.747 55.000 0.00 0.00 0.00 3.36
3379 3446 1.627297 GGCCTTCCCTCGTTCATCCT 61.627 60.000 0.00 0.00 0.00 3.24
3380 3447 1.153147 GGCCTTCCCTCGTTCATCC 60.153 63.158 0.00 0.00 0.00 3.51
3381 3448 4.542075 GGCCTTCCCTCGTTCATC 57.458 61.111 0.00 0.00 0.00 2.92
3391 3458 2.501316 ACATTTGCAAATAGGGCCTTCC 59.499 45.455 23.69 0.00 0.00 3.46
3392 3459 3.524541 CACATTTGCAAATAGGGCCTTC 58.475 45.455 23.69 0.00 0.00 3.46
3393 3460 2.236893 CCACATTTGCAAATAGGGCCTT 59.763 45.455 23.69 0.00 0.00 4.35
3394 3461 1.832998 CCACATTTGCAAATAGGGCCT 59.167 47.619 23.69 12.58 0.00 5.19
3395 3462 1.830477 TCCACATTTGCAAATAGGGCC 59.170 47.619 28.64 0.00 0.00 5.80
3396 3463 2.760092 TCTCCACATTTGCAAATAGGGC 59.240 45.455 28.64 0.00 0.00 5.19
3397 3464 3.382546 CCTCTCCACATTTGCAAATAGGG 59.617 47.826 28.64 26.83 0.00 3.53
3398 3465 3.382546 CCCTCTCCACATTTGCAAATAGG 59.617 47.826 23.69 24.96 0.00 2.57
3399 3466 3.382546 CCCCTCTCCACATTTGCAAATAG 59.617 47.826 23.69 17.07 0.00 1.73
3400 3467 3.245586 ACCCCTCTCCACATTTGCAAATA 60.246 43.478 23.69 8.18 0.00 1.40
3401 3468 2.181975 CCCCTCTCCACATTTGCAAAT 58.818 47.619 18.99 18.99 0.00 2.32
3402 3469 1.133199 ACCCCTCTCCACATTTGCAAA 60.133 47.619 15.44 15.44 0.00 3.68
3403 3470 0.482446 ACCCCTCTCCACATTTGCAA 59.518 50.000 0.00 0.00 0.00 4.08
3404 3471 0.251297 CACCCCTCTCCACATTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
3405 3472 0.251341 ACACCCCTCTCCACATTTGC 60.251 55.000 0.00 0.00 0.00 3.68
3406 3473 1.538047 CACACCCCTCTCCACATTTG 58.462 55.000 0.00 0.00 0.00 2.32
3407 3474 0.405585 CCACACCCCTCTCCACATTT 59.594 55.000 0.00 0.00 0.00 2.32
3408 3475 1.500783 CCCACACCCCTCTCCACATT 61.501 60.000 0.00 0.00 0.00 2.71
3409 3476 1.925455 CCCACACCCCTCTCCACAT 60.925 63.158 0.00 0.00 0.00 3.21
3410 3477 2.038545 TACCCACACCCCTCTCCACA 62.039 60.000 0.00 0.00 0.00 4.17
3411 3478 0.620700 ATACCCACACCCCTCTCCAC 60.621 60.000 0.00 0.00 0.00 4.02
3412 3479 0.326238 GATACCCACACCCCTCTCCA 60.326 60.000 0.00 0.00 0.00 3.86
3413 3480 1.054978 GGATACCCACACCCCTCTCC 61.055 65.000 0.00 0.00 0.00 3.71
3414 3481 0.031010 AGGATACCCACACCCCTCTC 60.031 60.000 0.00 0.00 33.88 3.20
3415 3482 0.421904 AAGGATACCCACACCCCTCT 59.578 55.000 0.00 0.00 33.88 3.69
3416 3483 1.296002 AAAGGATACCCACACCCCTC 58.704 55.000 0.00 0.00 33.88 4.30
3417 3484 1.768265 AAAAGGATACCCACACCCCT 58.232 50.000 0.00 0.00 33.88 4.79
3418 3485 2.309458 TGTAAAAGGATACCCACACCCC 59.691 50.000 0.00 0.00 33.88 4.95
3419 3486 3.724732 TGTAAAAGGATACCCACACCC 57.275 47.619 0.00 0.00 33.88 4.61
3420 3487 6.599356 ATTTTGTAAAAGGATACCCACACC 57.401 37.500 0.00 0.00 33.88 4.16
3421 3488 6.367695 GCAATTTTGTAAAAGGATACCCACAC 59.632 38.462 0.00 0.00 33.88 3.82
3422 3489 6.459923 GCAATTTTGTAAAAGGATACCCACA 58.540 36.000 0.00 0.00 33.88 4.17
3423 3490 5.872617 GGCAATTTTGTAAAAGGATACCCAC 59.127 40.000 0.00 0.00 33.88 4.61
3424 3491 5.544176 TGGCAATTTTGTAAAAGGATACCCA 59.456 36.000 0.00 0.00 33.88 4.51
3425 3492 6.043854 TGGCAATTTTGTAAAAGGATACCC 57.956 37.500 0.00 0.00 37.17 3.69
3426 3493 8.474831 ACTATGGCAATTTTGTAAAAGGATACC 58.525 33.333 0.00 0.00 37.17 2.73
3427 3494 9.869757 AACTATGGCAATTTTGTAAAAGGATAC 57.130 29.630 0.00 0.00 0.00 2.24
3429 3496 9.435688 GAAACTATGGCAATTTTGTAAAAGGAT 57.564 29.630 0.00 0.00 0.00 3.24
3430 3497 7.875554 GGAAACTATGGCAATTTTGTAAAAGGA 59.124 33.333 0.00 0.00 0.00 3.36
3431 3498 7.877612 AGGAAACTATGGCAATTTTGTAAAAGG 59.122 33.333 0.00 0.00 40.61 3.11
3432 3499 8.831715 AGGAAACTATGGCAATTTTGTAAAAG 57.168 30.769 0.00 0.00 40.61 2.27
3433 3500 9.267084 GAAGGAAACTATGGCAATTTTGTAAAA 57.733 29.630 0.00 0.00 42.68 1.52
3434 3501 7.875554 GGAAGGAAACTATGGCAATTTTGTAAA 59.124 33.333 0.00 0.00 42.68 2.01
3435 3502 7.234577 AGGAAGGAAACTATGGCAATTTTGTAA 59.765 33.333 0.00 0.00 42.68 2.41
3436 3503 6.723977 AGGAAGGAAACTATGGCAATTTTGTA 59.276 34.615 0.00 0.00 42.68 2.41
3437 3504 5.543790 AGGAAGGAAACTATGGCAATTTTGT 59.456 36.000 0.00 0.00 42.68 2.83
3438 3505 6.041423 AGGAAGGAAACTATGGCAATTTTG 57.959 37.500 0.00 0.00 42.68 2.44
3439 3506 7.069950 GGATAGGAAGGAAACTATGGCAATTTT 59.930 37.037 0.00 0.00 42.68 1.82
3440 3507 6.551227 GGATAGGAAGGAAACTATGGCAATTT 59.449 38.462 0.00 0.00 42.68 1.82
3441 3508 6.071320 GGATAGGAAGGAAACTATGGCAATT 58.929 40.000 0.00 0.00 42.68 2.32
3442 3509 5.635120 GGATAGGAAGGAAACTATGGCAAT 58.365 41.667 0.00 0.00 42.68 3.56
3443 3510 4.444306 CGGATAGGAAGGAAACTATGGCAA 60.444 45.833 0.00 0.00 42.68 4.52
3444 3511 3.071023 CGGATAGGAAGGAAACTATGGCA 59.929 47.826 0.00 0.00 42.68 4.92
3445 3512 3.071167 ACGGATAGGAAGGAAACTATGGC 59.929 47.826 0.00 0.00 42.68 4.40
3446 3513 4.344102 TGACGGATAGGAAGGAAACTATGG 59.656 45.833 0.00 0.00 42.68 2.74
3447 3514 5.302059 TCTGACGGATAGGAAGGAAACTATG 59.698 44.000 0.00 0.00 42.68 2.23
3448 3515 5.455872 TCTGACGGATAGGAAGGAAACTAT 58.544 41.667 0.00 0.00 42.68 2.12
3449 3516 4.863548 TCTGACGGATAGGAAGGAAACTA 58.136 43.478 0.00 0.00 42.68 2.24
3450 3517 4.290942 ATCTGACGGATAGGAAGGAAACT 58.709 43.478 0.00 0.00 35.69 2.66
3451 3518 4.674281 ATCTGACGGATAGGAAGGAAAC 57.326 45.455 0.00 0.00 32.04 2.78
3452 3519 5.693769 AAATCTGACGGATAGGAAGGAAA 57.306 39.130 0.00 0.00 33.71 3.13
3453 3520 6.801718 TTAAATCTGACGGATAGGAAGGAA 57.198 37.500 0.00 0.00 33.71 3.36
3454 3521 6.801718 TTTAAATCTGACGGATAGGAAGGA 57.198 37.500 0.00 0.00 33.71 3.36
3455 3522 6.366332 CGATTTAAATCTGACGGATAGGAAGG 59.634 42.308 22.52 1.49 33.71 3.46
3456 3523 6.366332 CCGATTTAAATCTGACGGATAGGAAG 59.634 42.308 22.52 5.18 42.40 3.46
3457 3524 6.041182 TCCGATTTAAATCTGACGGATAGGAA 59.959 38.462 22.52 3.51 43.30 3.36
3458 3525 5.537295 TCCGATTTAAATCTGACGGATAGGA 59.463 40.000 22.52 15.81 43.30 2.94
3459 3526 5.779922 TCCGATTTAAATCTGACGGATAGG 58.220 41.667 22.52 14.11 43.30 2.57
3466 3533 2.287103 GGCCGTCCGATTTAAATCTGAC 59.713 50.000 28.94 28.94 42.58 3.51
3467 3534 2.169769 AGGCCGTCCGATTTAAATCTGA 59.830 45.455 22.52 19.16 37.47 3.27
3468 3535 2.561569 AGGCCGTCCGATTTAAATCTG 58.438 47.619 22.52 17.39 37.47 2.90
3469 3536 4.618920 ATAGGCCGTCCGATTTAAATCT 57.381 40.909 22.52 7.00 37.47 2.40
3470 3537 6.674760 GCAATATAGGCCGTCCGATTTAAATC 60.675 42.308 16.79 16.79 37.47 2.17
3471 3538 5.123344 GCAATATAGGCCGTCCGATTTAAAT 59.877 40.000 0.00 0.00 37.47 1.40
3472 3539 4.453136 GCAATATAGGCCGTCCGATTTAAA 59.547 41.667 0.00 0.00 37.47 1.52
3473 3540 3.998341 GCAATATAGGCCGTCCGATTTAA 59.002 43.478 0.00 0.00 37.47 1.52
3474 3541 3.007074 TGCAATATAGGCCGTCCGATTTA 59.993 43.478 0.00 0.00 37.47 1.40
3475 3542 2.224426 TGCAATATAGGCCGTCCGATTT 60.224 45.455 0.00 0.00 37.47 2.17
3476 3543 1.346395 TGCAATATAGGCCGTCCGATT 59.654 47.619 0.00 0.00 37.47 3.34
3477 3544 0.973632 TGCAATATAGGCCGTCCGAT 59.026 50.000 0.00 0.00 37.47 4.18
3478 3545 0.317160 CTGCAATATAGGCCGTCCGA 59.683 55.000 0.00 0.00 37.47 4.55
3479 3546 0.670546 CCTGCAATATAGGCCGTCCG 60.671 60.000 0.00 0.00 37.47 4.79
3480 3547 0.685097 TCCTGCAATATAGGCCGTCC 59.315 55.000 0.00 0.00 35.23 4.79
3481 3548 2.350522 CATCCTGCAATATAGGCCGTC 58.649 52.381 0.00 0.00 35.23 4.79
3482 3549 1.003580 CCATCCTGCAATATAGGCCGT 59.996 52.381 0.00 0.00 35.23 5.68
3483 3550 1.742761 CCATCCTGCAATATAGGCCG 58.257 55.000 0.00 0.00 35.23 6.13
3484 3551 1.272092 TGCCATCCTGCAATATAGGCC 60.272 52.381 12.50 0.00 38.56 5.19
3485 3552 2.089980 CTGCCATCCTGCAATATAGGC 58.910 52.381 9.23 9.23 41.51 3.93
3486 3553 2.719739 CCTGCCATCCTGCAATATAGG 58.280 52.381 0.00 0.00 41.51 2.57
3487 3554 2.089980 GCCTGCCATCCTGCAATATAG 58.910 52.381 0.00 0.00 41.51 1.31
3488 3555 1.424684 TGCCTGCCATCCTGCAATATA 59.575 47.619 0.00 0.00 41.51 0.86
3489 3556 0.186630 TGCCTGCCATCCTGCAATAT 59.813 50.000 0.00 0.00 41.51 1.28
3490 3557 0.752743 GTGCCTGCCATCCTGCAATA 60.753 55.000 0.00 0.00 41.51 1.90
3491 3558 2.056223 GTGCCTGCCATCCTGCAAT 61.056 57.895 0.00 0.00 41.51 3.56
3492 3559 2.677524 GTGCCTGCCATCCTGCAA 60.678 61.111 0.00 0.00 41.51 4.08
3493 3560 3.969119 TGTGCCTGCCATCCTGCA 61.969 61.111 0.00 0.00 39.37 4.41
3494 3561 3.446570 GTGTGCCTGCCATCCTGC 61.447 66.667 0.00 0.00 0.00 4.85
3495 3562 2.753043 GGTGTGCCTGCCATCCTG 60.753 66.667 0.00 0.00 0.00 3.86
3496 3563 2.619446 ATGGTGTGCCTGCCATCCT 61.619 57.895 0.00 0.00 41.24 3.24
3497 3564 2.043652 ATGGTGTGCCTGCCATCC 60.044 61.111 0.00 0.00 41.24 3.51
3500 3567 1.378911 GATGATGGTGTGCCTGCCA 60.379 57.895 0.00 0.00 39.33 4.92
3501 3568 1.378911 TGATGATGGTGTGCCTGCC 60.379 57.895 0.00 0.00 35.27 4.85
3502 3569 1.660560 GGTGATGATGGTGTGCCTGC 61.661 60.000 0.00 0.00 35.27 4.85
3503 3570 0.322726 TGGTGATGATGGTGTGCCTG 60.323 55.000 0.00 0.00 35.27 4.85
3504 3571 0.405198 TTGGTGATGATGGTGTGCCT 59.595 50.000 0.00 0.00 35.27 4.75
3505 3572 0.527565 GTTGGTGATGATGGTGTGCC 59.472 55.000 0.00 0.00 0.00 5.01
3506 3573 1.470098 GAGTTGGTGATGATGGTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
3507 3574 2.745821 CAGAGTTGGTGATGATGGTGTG 59.254 50.000 0.00 0.00 0.00 3.82
3508 3575 2.373169 ACAGAGTTGGTGATGATGGTGT 59.627 45.455 0.00 0.00 0.00 4.16
3509 3576 3.063510 ACAGAGTTGGTGATGATGGTG 57.936 47.619 0.00 0.00 0.00 4.17
3510 3577 3.795688 AACAGAGTTGGTGATGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
3511 3578 5.458041 AAAAACAGAGTTGGTGATGATGG 57.542 39.130 0.00 0.00 0.00 3.51
3535 3602 8.943594 ACCTCGGAAAATATCTCTACTCTTAT 57.056 34.615 0.00 0.00 0.00 1.73
3536 3603 8.763984 AACCTCGGAAAATATCTCTACTCTTA 57.236 34.615 0.00 0.00 0.00 2.10
3537 3604 7.663043 AACCTCGGAAAATATCTCTACTCTT 57.337 36.000 0.00 0.00 0.00 2.85
3538 3605 8.631797 GTTAACCTCGGAAAATATCTCTACTCT 58.368 37.037 0.00 0.00 0.00 3.24
3539 3606 8.411683 TGTTAACCTCGGAAAATATCTCTACTC 58.588 37.037 2.48 0.00 0.00 2.59
3540 3607 8.302515 TGTTAACCTCGGAAAATATCTCTACT 57.697 34.615 2.48 0.00 0.00 2.57
3541 3608 8.979574 CATGTTAACCTCGGAAAATATCTCTAC 58.020 37.037 2.48 0.00 0.00 2.59
3542 3609 8.920174 TCATGTTAACCTCGGAAAATATCTCTA 58.080 33.333 2.48 0.00 0.00 2.43
3543 3610 7.792032 TCATGTTAACCTCGGAAAATATCTCT 58.208 34.615 2.48 0.00 0.00 3.10
3544 3611 8.336080 GTTCATGTTAACCTCGGAAAATATCTC 58.664 37.037 2.48 0.00 0.00 2.75
3545 3612 7.827236 TGTTCATGTTAACCTCGGAAAATATCT 59.173 33.333 2.48 0.00 0.00 1.98
3546 3613 7.981142 TGTTCATGTTAACCTCGGAAAATATC 58.019 34.615 2.48 0.00 0.00 1.63
3547 3614 7.931578 TGTTCATGTTAACCTCGGAAAATAT 57.068 32.000 2.48 0.00 0.00 1.28
3578 3646 8.784043 GTTCAACATTGATAACAACTCTTACCT 58.216 33.333 0.00 0.00 38.90 3.08
3579 3647 8.784043 AGTTCAACATTGATAACAACTCTTACC 58.216 33.333 0.00 0.00 38.90 2.85
3730 3835 8.345565 ACAATAAACAACTCTTCATCTCAACAC 58.654 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.