Multiple sequence alignment - TraesCS1A01G170200

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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 TraesCS1A01G170200 chr1A 100.000 6619 0 0 1 6619 303859348 303852730 0.000000e+00 12224.0
1 TraesCS1A01G170200 chr1D 95.358 4459 148 18 1345 5758 239810440 239805996 0.000000e+00 7033.0
2 TraesCS1A01G170200 chr1D 89.220 1308 89 25 1 1300 239811700 239810437 0.000000e+00 1587.0
3 TraesCS1A01G170200 chr1D 91.848 552 31 4 6058 6608 239805901 239805363 0.000000e+00 758.0
4 TraesCS1A01G170200 chr1B 94.357 2658 95 22 1999 4624 334245235 334242601 0.000000e+00 4026.0
5 TraesCS1A01G170200 chr1B 95.918 1225 47 2 4657 5879 334242605 334241382 0.000000e+00 1982.0
6 TraesCS1A01G170200 chr1B 89.255 1610 108 29 319 1908 334246980 334245416 0.000000e+00 1954.0
7 TraesCS1A01G170200 chr1B 87.385 325 34 6 1 319 334247983 334247660 3.770000e-97 366.0
8 TraesCS1A01G170200 chr1B 91.403 221 13 4 6310 6529 334241369 334241154 1.400000e-76 298.0
9 TraesCS1A01G170200 chr2B 83.438 1588 176 48 2745 4298 476397306 476398840 0.000000e+00 1395.0
10 TraesCS1A01G170200 chr2B 85.859 990 101 18 4661 5620 476399891 476400871 0.000000e+00 1016.0
11 TraesCS1A01G170200 chr2B 79.490 980 125 36 831 1769 476394922 476395866 1.570000e-175 627.0
12 TraesCS1A01G170200 chr2B 85.106 282 33 7 2318 2593 476395937 476396215 5.050000e-71 279.0
13 TraesCS1A01G170200 chr2B 82.407 324 37 12 116 434 219290291 219289983 1.420000e-66 265.0
14 TraesCS1A01G170200 chr2B 87.037 54 2 5 749 802 476394862 476394910 1.000000e-03 56.5
15 TraesCS1A01G170200 chr2D 85.442 996 100 19 4661 5620 402307682 402306696 0.000000e+00 994.0
16 TraesCS1A01G170200 chr2D 88.962 761 76 5 3541 4297 402308869 402308113 0.000000e+00 933.0
17 TraesCS1A01G170200 chr2D 79.373 989 129 41 831 1778 402312284 402311330 1.570000e-175 627.0
18 TraesCS1A01G170200 chr2D 81.312 701 84 23 2762 3461 402309644 402308990 5.880000e-145 525.0
19 TraesCS1A01G170200 chr2D 83.099 213 18 8 4393 4588 402307901 402307690 1.900000e-40 178.0
20 TraesCS1A01G170200 chr2D 87.037 54 2 5 749 802 402312344 402312296 1.000000e-03 56.5
21 TraesCS1A01G170200 chr2A 85.111 994 105 20 4661 5620 539394451 539393467 0.000000e+00 976.0
22 TraesCS1A01G170200 chr2A 88.084 814 82 10 3489 4298 539395558 539394756 0.000000e+00 952.0
23 TraesCS1A01G170200 chr2A 79.237 944 116 42 870 1769 539398874 539397967 9.560000e-163 584.0
24 TraesCS1A01G170200 chr2A 81.579 494 65 17 2969 3461 539396242 539395774 1.040000e-102 385.0
25 TraesCS1A01G170200 chr2A 83.883 273 34 8 2318 2585 539397904 539397637 1.100000e-62 252.0
26 TraesCS1A01G170200 chr2A 84.507 142 21 1 4447 4588 539394599 539394459 8.950000e-29 139.0
27 TraesCS1A01G170200 chr5A 77.435 811 152 23 4780 5571 641731049 641731847 7.820000e-124 455.0
28 TraesCS1A01G170200 chr5A 75.598 418 65 20 23 434 17431725 17432111 8.820000e-39 172.0
29 TraesCS1A01G170200 chr5A 75.185 270 56 8 1984 2250 168127039 168126778 4.190000e-22 117.0
30 TraesCS1A01G170200 chr5D 76.492 821 175 15 4780 5588 513975425 513976239 1.320000e-116 431.0
31 TraesCS1A01G170200 chr5D 76.905 420 59 23 23 434 152766219 152766608 3.130000e-48 204.0
32 TraesCS1A01G170200 chr5B 76.220 799 173 14 4780 5566 644887810 644888603 2.220000e-109 407.0
33 TraesCS1A01G170200 chr5B 75.540 417 64 25 23 433 571884791 571885175 3.170000e-38 171.0
34 TraesCS1A01G170200 chr4B 88.014 292 33 2 6248 6538 68119380 68119090 1.770000e-90 344.0
35 TraesCS1A01G170200 chr4B 79.535 215 17 14 5792 6002 68119816 68119625 1.940000e-25 128.0
36 TraesCS1A01G170200 chr4D 83.594 384 44 10 6253 6618 46622156 46621774 6.360000e-90 342.0
37 TraesCS1A01G170200 chr4A 82.857 385 46 12 6253 6618 533461603 533461220 1.780000e-85 327.0
38 TraesCS1A01G170200 chr4A 82.812 384 47 10 6253 6618 552256372 552256754 6.400000e-85 326.0
39 TraesCS1A01G170200 chr4A 93.103 87 2 4 5919 6002 533461981 533461896 2.510000e-24 124.0
40 TraesCS1A01G170200 chr6A 76.886 411 63 17 31 437 59504797 59504415 3.130000e-48 204.0


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 TraesCS1A01G170200 chr1A 303852730 303859348 6618 True 12224.00 12224 100.000000 1 6619 1 chr1A.!!$R1 6618
1 TraesCS1A01G170200 chr1D 239805363 239811700 6337 True 3126.00 7033 92.142000 1 6608 3 chr1D.!!$R1 6607
2 TraesCS1A01G170200 chr1B 334241154 334247983 6829 True 1725.20 4026 91.663600 1 6529 5 chr1B.!!$R1 6528
3 TraesCS1A01G170200 chr2B 476394862 476400871 6009 False 674.70 1395 84.186000 749 5620 5 chr2B.!!$F1 4871
4 TraesCS1A01G170200 chr2D 402306696 402312344 5648 True 552.25 994 84.204167 749 5620 6 chr2D.!!$R1 4871
5 TraesCS1A01G170200 chr2A 539393467 539398874 5407 True 548.00 976 83.733500 870 5620 6 chr2A.!!$R1 4750
6 TraesCS1A01G170200 chr5A 641731049 641731847 798 False 455.00 455 77.435000 4780 5571 1 chr5A.!!$F2 791
7 TraesCS1A01G170200 chr5D 513975425 513976239 814 False 431.00 431 76.492000 4780 5588 1 chr5D.!!$F2 808
8 TraesCS1A01G170200 chr5B 644887810 644888603 793 False 407.00 407 76.220000 4780 5566 1 chr5B.!!$F2 786
9 TraesCS1A01G170200 chr4B 68119090 68119816 726 True 236.00 344 83.774500 5792 6538 2 chr4B.!!$R1 746
10 TraesCS1A01G170200 chr4A 533461220 533461981 761 True 225.50 327 87.980000 5919 6618 2 chr4A.!!$R1 699

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
936 1652 0.033504 AACGCCGCAAGAGAAGAGAA 59.966 50.000 0.00 0.0 43.02 2.87 F
937 1653 0.389166 ACGCCGCAAGAGAAGAGAAG 60.389 55.000 0.00 0.0 43.02 2.85 F
1967 2891 0.679640 CGCAGCATCCCCAAAACCTA 60.680 55.000 0.00 0.0 0.00 3.08 F
2271 3231 0.609406 GGGCCAAAGGAGAAGTCACC 60.609 60.000 4.39 0.0 0.00 4.02 F
2841 5019 3.012502 TGAAGACCCACCTAGTATGACCT 59.987 47.826 0.00 0.0 0.00 3.85 F
3056 5301 4.097741 TCAAACCACCAGTTTTCATGACAG 59.902 41.667 0.00 0.0 46.79 3.51 F
4671 8060 4.202070 GGACAGAGGGAGTAGATTTCTTCG 60.202 50.000 0.00 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2949 0.110192 GCGGTTCCTTCTTGAAAGCG 60.110 55.000 0.00 0.00 37.41 4.68 R
2072 3021 0.677731 CAAAGATCTGCTTCGGGGCA 60.678 55.000 0.00 3.53 40.15 5.36 R
3462 5709 2.356135 ACACTCATGCCGGTATTTGAC 58.644 47.619 0.66 0.00 0.00 3.18 R
3568 6022 5.003804 TCTTCACTCTGCCAATAAGGAAAC 58.996 41.667 0.00 0.00 41.22 2.78 R
4737 8144 3.115390 CCTGGGAAAAGAGGAGGATACA 58.885 50.000 0.00 0.00 41.41 2.29 R
5195 8633 5.540337 AGTTGACTGAGGAATGACTGTAAGA 59.460 40.000 0.00 0.00 37.43 2.10 R
5896 9334 0.107848 CTCCGCCCCGAAATACTTGT 60.108 55.000 0.00 0.00 0.00 3.16 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
34 35 1.293062 AGCAGGGTCAACATGAGGAT 58.707 50.000 0.00 0.00 0.00 3.24
48 49 4.264352 ACATGAGGATAAAAAGGGAGGCAA 60.264 41.667 0.00 0.00 0.00 4.52
55 56 3.814504 AAAAAGGGAGGCAATGAGAGA 57.185 42.857 0.00 0.00 0.00 3.10
66 67 0.033699 AATGAGAGAAGGCAAGGGGC 60.034 55.000 0.00 0.00 43.74 5.80
68 69 2.607750 AGAGAAGGCAAGGGGCGA 60.608 61.111 0.00 0.00 46.16 5.54
69 70 1.977293 GAGAGAAGGCAAGGGGCGAT 61.977 60.000 0.00 0.00 46.16 4.58
82 85 0.468400 GGGCGATAGTGGGAGAGACT 60.468 60.000 0.00 0.00 39.35 3.24
87 90 2.761208 CGATAGTGGGAGAGACTGGTTT 59.239 50.000 0.00 0.00 0.00 3.27
92 95 0.036875 GGGAGAGACTGGTTTGTGGG 59.963 60.000 0.00 0.00 0.00 4.61
102 105 3.245229 ACTGGTTTGTGGGCAGAATATGA 60.245 43.478 0.00 0.00 0.00 2.15
104 107 4.352009 TGGTTTGTGGGCAGAATATGAAT 58.648 39.130 0.00 0.00 0.00 2.57
159 162 3.916035 AGAAAAGGGAAAGAAGTGGCTT 58.084 40.909 0.00 0.00 0.00 4.35
161 164 3.312736 AAAGGGAAAGAAGTGGCTTGA 57.687 42.857 0.00 0.00 0.00 3.02
233 236 7.708322 TGCTTGTATTTGCAATTTGTTTAGTGA 59.292 29.630 0.00 0.00 36.15 3.41
260 263 7.425577 TCATATGTGTAATAGTCAAGCATGC 57.574 36.000 10.51 10.51 0.00 4.06
408 1100 6.706055 TTTTGACACACGTGCAATTTTTAA 57.294 29.167 17.22 0.29 30.87 1.52
434 1126 9.142515 AGTGAATTTATGTGTGCATTATGTTTG 57.857 29.630 0.00 0.00 36.58 2.93
461 1164 1.202568 CGGCTTGACTGGCATGAGATA 60.203 52.381 0.00 0.00 0.00 1.98
467 1170 5.163581 GCTTGACTGGCATGAGATAAATTGT 60.164 40.000 0.00 0.00 0.00 2.71
470 1173 3.879295 ACTGGCATGAGATAAATTGTCCG 59.121 43.478 0.00 0.00 0.00 4.79
487 1190 3.499157 TGTCCGTGGTTGTAAGTTTATGC 59.501 43.478 0.00 0.00 0.00 3.14
495 1198 7.163520 CGTGGTTGTAAGTTTATGCGATATTTG 59.836 37.037 0.00 0.00 0.00 2.32
498 1201 9.349145 GGTTGTAAGTTTATGCGATATTTGTTT 57.651 29.630 0.00 0.00 0.00 2.83
546 1249 8.766493 TCGCGAATTACAATGATATCTTTTTG 57.234 30.769 6.20 7.92 0.00 2.44
683 1386 2.205911 GGACGGAAGAGAGCATTAAGC 58.794 52.381 0.00 0.00 46.19 3.09
703 1409 2.223044 GCAGCGCATTCAAGTAGTAACC 60.223 50.000 11.47 0.00 0.00 2.85
719 1425 8.076714 AGTAGTAACCGTAAAAACAAAGTAGC 57.923 34.615 0.00 0.00 0.00 3.58
725 1431 3.662186 CGTAAAAACAAAGTAGCGCAAGG 59.338 43.478 11.47 0.00 38.28 3.61
771 1481 2.811317 GCCGCTTGTGGTCTCTCG 60.811 66.667 2.01 0.00 0.00 4.04
772 1482 2.811317 CCGCTTGTGGTCTCTCGC 60.811 66.667 0.00 0.00 0.00 5.03
773 1483 2.259818 CGCTTGTGGTCTCTCGCT 59.740 61.111 0.00 0.00 0.00 4.93
867 1577 4.310769 CCTCACTCGATTCAGTTCAAGTT 58.689 43.478 0.00 0.00 0.00 2.66
868 1584 4.752101 CCTCACTCGATTCAGTTCAAGTTT 59.248 41.667 0.00 0.00 0.00 2.66
933 1649 1.374252 GGAACGCCGCAAGAGAAGA 60.374 57.895 0.00 0.00 43.02 2.87
934 1650 1.355066 GGAACGCCGCAAGAGAAGAG 61.355 60.000 0.00 0.00 43.02 2.85
935 1651 0.388649 GAACGCCGCAAGAGAAGAGA 60.389 55.000 0.00 0.00 43.02 3.10
936 1652 0.033504 AACGCCGCAAGAGAAGAGAA 59.966 50.000 0.00 0.00 43.02 2.87
937 1653 0.389166 ACGCCGCAAGAGAAGAGAAG 60.389 55.000 0.00 0.00 43.02 2.85
1196 1913 3.595758 CCGCGGCCATGGAATTCC 61.596 66.667 18.40 18.17 0.00 3.01
1230 1955 5.697067 TGGACCAGGTTTAGAAAGCTTTTA 58.303 37.500 14.05 5.19 43.61 1.52
1231 1956 6.311735 TGGACCAGGTTTAGAAAGCTTTTAT 58.688 36.000 14.05 8.06 43.61 1.40
1232 1957 7.463431 TGGACCAGGTTTAGAAAGCTTTTATA 58.537 34.615 14.05 7.04 43.61 0.98
1233 1958 7.392393 TGGACCAGGTTTAGAAAGCTTTTATAC 59.608 37.037 14.05 11.71 43.61 1.47
1234 1959 7.610692 GGACCAGGTTTAGAAAGCTTTTATACT 59.389 37.037 14.05 8.21 43.61 2.12
1235 1960 8.336801 ACCAGGTTTAGAAAGCTTTTATACTG 57.663 34.615 14.05 15.41 43.61 2.74
1292 2049 4.473477 ACTTAGAACGAGGAATCTTGGG 57.527 45.455 0.00 0.00 0.00 4.12
1339 2097 6.570672 TCAGTAAGACAACAATCTACTCGT 57.429 37.500 0.00 0.00 0.00 4.18
1342 2100 8.182227 TCAGTAAGACAACAATCTACTCGTATG 58.818 37.037 0.00 0.00 0.00 2.39
1343 2101 7.432545 CAGTAAGACAACAATCTACTCGTATGG 59.567 40.741 0.00 0.00 0.00 2.74
1476 2251 1.407936 TGGCCAAAAAGTAGCTGCAA 58.592 45.000 0.61 0.00 0.00 4.08
1658 2452 1.930371 GCACTTGGCGTTGACATTTCC 60.930 52.381 0.00 0.00 0.00 3.13
1818 2617 8.893563 TTCCCTGAAAAGTATGATAAACCATT 57.106 30.769 0.00 0.00 0.00 3.16
1894 2693 5.471556 TGATGATGCCAAACAAATCAACT 57.528 34.783 0.00 0.00 34.31 3.16
1940 2864 1.026718 CGAGGCCATCCACAAAGACC 61.027 60.000 5.01 0.00 33.74 3.85
1967 2891 0.679640 CGCAGCATCCCCAAAACCTA 60.680 55.000 0.00 0.00 0.00 3.08
1988 2937 2.412525 CCAAAGCTGTGCGCAACA 59.587 55.556 14.00 12.24 42.61 3.33
2000 2949 2.218530 GTGCGCAACATTCCAAGAAAAC 59.781 45.455 14.00 0.00 0.00 2.43
2026 2975 4.736896 GAAGGAACCGCCGCTCGT 62.737 66.667 0.00 0.00 43.43 4.18
2072 3021 3.118112 CAGATGTGAGACCAAGGGCTATT 60.118 47.826 0.00 0.00 0.00 1.73
2120 3076 3.471495 CCTTCAACAAGGTAACGATGC 57.529 47.619 0.00 0.00 44.11 3.91
2188 3145 2.479566 TCCACTTGGAGAGAATGCAC 57.520 50.000 0.00 0.00 39.78 4.57
2230 3187 1.798234 CGTCGTCCACCACACTACCA 61.798 60.000 0.00 0.00 0.00 3.25
2269 3229 1.374947 CGGGCCAAAGGAGAAGTCA 59.625 57.895 4.39 0.00 0.00 3.41
2270 3230 0.955919 CGGGCCAAAGGAGAAGTCAC 60.956 60.000 4.39 0.00 0.00 3.67
2271 3231 0.609406 GGGCCAAAGGAGAAGTCACC 60.609 60.000 4.39 0.00 0.00 4.02
2375 3339 5.346281 CGAACAGTAGTCTTCTGATTTCCAC 59.654 44.000 12.95 0.00 36.81 4.02
2470 3435 6.003326 TGCATTCCTCAAGAAAGTTGTGATA 58.997 36.000 0.00 0.00 38.21 2.15
2471 3436 6.489700 TGCATTCCTCAAGAAAGTTGTGATAA 59.510 34.615 0.00 0.00 38.21 1.75
2502 3467 6.019479 CGATCTTTTCTTGTATGTAGGTCTGC 60.019 42.308 0.00 0.00 0.00 4.26
2608 3578 8.090214 CCATTAACCCCATTATCATTGAATGAC 58.910 37.037 10.45 0.00 43.01 3.06
2626 3596 9.868277 TTGAATGACAAATTAAACTGTTGAACT 57.132 25.926 0.00 0.00 35.39 3.01
2651 4732 3.070476 TGTTGATTAGCCAGCACATCA 57.930 42.857 0.00 0.00 0.00 3.07
2841 5019 3.012502 TGAAGACCCACCTAGTATGACCT 59.987 47.826 0.00 0.00 0.00 3.85
3056 5301 4.097741 TCAAACCACCAGTTTTCATGACAG 59.902 41.667 0.00 0.00 46.79 3.51
3087 5332 5.297776 CCATATGTGTTGGAGATCTCAAACC 59.702 44.000 31.38 24.13 41.66 3.27
3215 5461 7.977789 TGCAGTACAGTTGATCTAAATGAAA 57.022 32.000 10.76 0.00 37.76 2.69
3252 5498 6.019779 TGAGGCACACAAATATTAAACACC 57.980 37.500 0.00 0.00 0.00 4.16
3282 5528 4.990543 TTTGAGTTGTGCAGTTATCTCG 57.009 40.909 0.00 0.00 0.00 4.04
3323 5569 5.221382 CCTCACATTCCATGATCCCAAAATC 60.221 44.000 0.00 0.00 0.00 2.17
3408 5655 7.470192 TGAAAGGAAGATTACCAAAAGAGGAT 58.530 34.615 0.00 0.00 0.00 3.24
3411 5658 9.822727 AAAGGAAGATTACCAAAAGAGGATTTA 57.177 29.630 0.00 0.00 0.00 1.40
3412 5659 9.822727 AAGGAAGATTACCAAAAGAGGATTTAA 57.177 29.630 0.00 0.00 0.00 1.52
3413 5660 9.822727 AGGAAGATTACCAAAAGAGGATTTAAA 57.177 29.630 0.00 0.00 0.00 1.52
3438 5685 8.467402 AAAAATTACAATCGTGTTCAACAACA 57.533 26.923 0.00 0.00 40.40 3.33
3453 5700 4.994852 TCAACAACAGAGGTGTAATAGTGC 59.005 41.667 0.00 0.00 35.08 4.40
3462 5709 6.199154 CAGAGGTGTAATAGTGCATACTTTCG 59.801 42.308 0.00 0.00 38.36 3.46
3466 5713 6.311935 GGTGTAATAGTGCATACTTTCGTCAA 59.688 38.462 0.00 0.00 38.36 3.18
3905 6360 5.767168 GGTTGCATTCTGGAGAGCTATAAAT 59.233 40.000 0.00 0.00 0.00 1.40
4139 6594 7.699812 GTCAGCTTCATAATTGGAATTCTTGTC 59.300 37.037 5.23 0.00 0.00 3.18
4585 7974 4.282873 GTCAGTGAAGCTTGTTAACTTGC 58.717 43.478 2.10 10.71 0.00 4.01
4671 8060 4.202070 GGACAGAGGGAGTAGATTTCTTCG 60.202 50.000 0.00 0.00 0.00 3.79
5195 8633 4.213513 GCATTCCTTTCTCATGGATCCTT 58.786 43.478 14.23 3.29 31.76 3.36
5201 8639 5.726308 TCCTTTCTCATGGATCCTTCTTACA 59.274 40.000 14.23 0.00 0.00 2.41
5369 8807 2.434774 GACCGGGCTTTTGAGGGT 59.565 61.111 6.32 0.00 0.00 4.34
5453 8891 1.804151 GCCAAGACTGTAAACATCGCA 59.196 47.619 0.00 0.00 0.00 5.10
5525 8963 6.552350 CCATGATGATCCTTCCTTTTGGTATT 59.448 38.462 0.00 0.00 41.38 1.89
5620 9058 3.454858 AGGACCAGGAGCTAATCTGAAA 58.545 45.455 11.41 0.00 33.11 2.69
5660 9098 6.510799 GCAGTGATGTTTCTGATAAGGATTCG 60.511 42.308 0.00 0.00 34.02 3.34
5692 9130 7.456684 TTGTGAATGTTTTGGTTGTAAATCG 57.543 32.000 0.00 0.00 0.00 3.34
5755 9193 5.438761 AGTTCTAACAAAGTGCCAACATC 57.561 39.130 0.00 0.00 0.00 3.06
5758 9196 4.460263 TCTAACAAAGTGCCAACATCACT 58.540 39.130 0.00 0.00 45.83 3.41
5759 9197 5.616270 TCTAACAAAGTGCCAACATCACTA 58.384 37.500 0.00 0.00 43.36 2.74
5760 9198 4.836125 AACAAAGTGCCAACATCACTAG 57.164 40.909 0.00 0.00 43.36 2.57
5761 9199 4.085357 ACAAAGTGCCAACATCACTAGA 57.915 40.909 0.00 0.00 43.36 2.43
5762 9200 4.655963 ACAAAGTGCCAACATCACTAGAT 58.344 39.130 0.00 0.00 43.36 1.98
5763 9201 5.804639 ACAAAGTGCCAACATCACTAGATA 58.195 37.500 0.00 0.00 43.36 1.98
5764 9202 6.237901 ACAAAGTGCCAACATCACTAGATAA 58.762 36.000 0.00 0.00 43.36 1.75
5765 9203 6.886459 ACAAAGTGCCAACATCACTAGATAAT 59.114 34.615 0.00 0.00 43.36 1.28
5766 9204 7.066284 ACAAAGTGCCAACATCACTAGATAATC 59.934 37.037 0.00 0.00 43.36 1.75
5767 9205 6.491714 AGTGCCAACATCACTAGATAATCT 57.508 37.500 0.00 0.00 42.45 2.40
5768 9206 6.286758 AGTGCCAACATCACTAGATAATCTG 58.713 40.000 0.00 0.00 42.45 2.90
5769 9207 6.098838 AGTGCCAACATCACTAGATAATCTGA 59.901 38.462 0.00 0.00 42.45 3.27
5770 9208 6.423302 GTGCCAACATCACTAGATAATCTGAG 59.577 42.308 0.00 0.00 31.88 3.35
5771 9209 5.407995 GCCAACATCACTAGATAATCTGAGC 59.592 44.000 0.00 0.00 31.88 4.26
5772 9210 6.519382 CCAACATCACTAGATAATCTGAGCA 58.481 40.000 0.00 0.00 31.88 4.26
5773 9211 6.423302 CCAACATCACTAGATAATCTGAGCAC 59.577 42.308 0.00 0.00 31.88 4.40
5774 9212 6.721704 ACATCACTAGATAATCTGAGCACA 57.278 37.500 0.00 0.00 31.88 4.57
5775 9213 7.300556 ACATCACTAGATAATCTGAGCACAT 57.699 36.000 0.00 0.00 31.88 3.21
5776 9214 7.733969 ACATCACTAGATAATCTGAGCACATT 58.266 34.615 0.00 0.00 31.88 2.71
5777 9215 7.656542 ACATCACTAGATAATCTGAGCACATTG 59.343 37.037 0.00 0.00 31.88 2.82
5778 9216 7.117285 TCACTAGATAATCTGAGCACATTGT 57.883 36.000 0.00 0.00 0.00 2.71
5779 9217 6.982724 TCACTAGATAATCTGAGCACATTGTG 59.017 38.462 12.54 12.54 36.51 3.33
5780 9218 6.760298 CACTAGATAATCTGAGCACATTGTGT 59.240 38.462 17.64 5.27 35.75 3.72
5781 9219 7.922811 CACTAGATAATCTGAGCACATTGTGTA 59.077 37.037 17.64 4.83 35.75 2.90
5782 9220 7.923344 ACTAGATAATCTGAGCACATTGTGTAC 59.077 37.037 17.64 12.14 35.75 2.90
5783 9221 6.882656 AGATAATCTGAGCACATTGTGTACT 58.117 36.000 17.64 7.56 35.75 2.73
5784 9222 7.334090 AGATAATCTGAGCACATTGTGTACTT 58.666 34.615 17.64 6.55 35.75 2.24
5785 9223 5.618056 AATCTGAGCACATTGTGTACTTG 57.382 39.130 17.64 5.82 35.75 3.16
5786 9224 4.071961 TCTGAGCACATTGTGTACTTGT 57.928 40.909 17.64 0.00 35.75 3.16
5787 9225 5.208463 TCTGAGCACATTGTGTACTTGTA 57.792 39.130 17.64 0.00 35.75 2.41
5788 9226 4.988540 TCTGAGCACATTGTGTACTTGTAC 59.011 41.667 17.64 4.14 35.75 2.90
5789 9227 4.698575 TGAGCACATTGTGTACTTGTACA 58.301 39.130 17.64 9.28 35.75 2.90
5808 9246 8.991243 TTGTACACGATAACTTAAACTGCTAT 57.009 30.769 0.00 0.00 0.00 2.97
5843 9281 4.998033 TCCACAACTGCATTTCGTGTATAA 59.002 37.500 13.89 0.00 0.00 0.98
5851 9289 8.319143 ACTGCATTTCGTGTATAACTAACTTT 57.681 30.769 0.00 0.00 0.00 2.66
5870 9308 5.364778 ACTTTAAAATGCACAAAGTTCCCC 58.635 37.500 10.25 0.00 38.94 4.81
5872 9310 1.408969 AAATGCACAAAGTTCCCCGT 58.591 45.000 0.00 0.00 0.00 5.28
5879 9317 3.118884 GCACAAAGTTCCCCGTCTAGATA 60.119 47.826 0.00 0.00 0.00 1.98
5880 9318 4.622220 GCACAAAGTTCCCCGTCTAGATAA 60.622 45.833 0.00 0.00 0.00 1.75
5881 9319 5.109903 CACAAAGTTCCCCGTCTAGATAAG 58.890 45.833 0.00 0.00 0.00 1.73
5882 9320 4.161754 ACAAAGTTCCCCGTCTAGATAAGG 59.838 45.833 0.00 0.07 0.00 2.69
5883 9321 3.967467 AGTTCCCCGTCTAGATAAGGA 57.033 47.619 11.89 8.09 0.00 3.36
5884 9322 3.834938 AGTTCCCCGTCTAGATAAGGAG 58.165 50.000 11.89 1.36 0.00 3.69
5889 9327 3.958798 CCCCGTCTAGATAAGGAGACAAA 59.041 47.826 11.89 0.00 41.87 2.83
5890 9328 4.589374 CCCCGTCTAGATAAGGAGACAAAT 59.411 45.833 11.89 0.00 41.87 2.32
5891 9329 5.279056 CCCCGTCTAGATAAGGAGACAAATC 60.279 48.000 11.89 0.00 41.87 2.17
5892 9330 5.536916 CCCGTCTAGATAAGGAGACAAATCT 59.463 44.000 11.89 0.00 41.87 2.40
5893 9331 6.715718 CCCGTCTAGATAAGGAGACAAATCTA 59.284 42.308 11.89 0.00 41.87 1.98
5895 9333 8.293867 CCGTCTAGATAAGGAGACAAATCTAAG 58.706 40.741 0.00 0.00 41.87 2.18
5896 9334 9.058174 CGTCTAGATAAGGAGACAAATCTAAGA 57.942 37.037 0.00 0.00 41.87 2.10
5898 9336 9.922477 TCTAGATAAGGAGACAAATCTAAGACA 57.078 33.333 0.00 0.00 36.49 3.41
5901 9339 9.041354 AGATAAGGAGACAAATCTAAGACAAGT 57.959 33.333 0.00 0.00 34.34 3.16
5906 9344 9.660180 AGGAGACAAATCTAAGACAAGTATTTC 57.340 33.333 0.00 0.00 34.34 2.17
5907 9345 8.596380 GGAGACAAATCTAAGACAAGTATTTCG 58.404 37.037 0.00 0.00 34.34 3.46
5908 9346 8.480643 AGACAAATCTAAGACAAGTATTTCGG 57.519 34.615 0.00 0.00 31.46 4.30
5909 9347 7.549488 AGACAAATCTAAGACAAGTATTTCGGG 59.451 37.037 0.00 0.00 31.46 5.14
5910 9348 6.598064 ACAAATCTAAGACAAGTATTTCGGGG 59.402 38.462 0.00 0.00 0.00 5.73
5911 9349 4.133013 TCTAAGACAAGTATTTCGGGGC 57.867 45.455 0.00 0.00 0.00 5.80
5912 9350 1.734163 AAGACAAGTATTTCGGGGCG 58.266 50.000 0.00 0.00 0.00 6.13
5913 9351 0.107848 AGACAAGTATTTCGGGGCGG 60.108 55.000 0.00 0.00 0.00 6.13
5914 9352 0.108041 GACAAGTATTTCGGGGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
5915 9353 0.107848 ACAAGTATTTCGGGGCGGAG 60.108 55.000 0.00 0.00 0.00 4.63
5916 9354 0.177141 CAAGTATTTCGGGGCGGAGA 59.823 55.000 0.00 0.00 0.00 3.71
5917 9355 1.129058 AAGTATTTCGGGGCGGAGAT 58.871 50.000 0.00 0.00 0.00 2.75
5991 9433 9.941664 CAATAACTATCAGTGATTCACATTTCC 57.058 33.333 18.57 0.00 36.74 3.13
6014 9456 5.361857 CCTTTTCTTCATATTGATGTGGGCT 59.638 40.000 0.00 0.00 34.41 5.19
6019 9461 5.951148 TCTTCATATTGATGTGGGCTTTTCA 59.049 36.000 0.00 0.00 34.41 2.69
6020 9462 5.581126 TCATATTGATGTGGGCTTTTCAC 57.419 39.130 0.00 0.00 34.41 3.18
6021 9463 5.263599 TCATATTGATGTGGGCTTTTCACT 58.736 37.500 0.00 0.00 36.21 3.41
6022 9464 5.357878 TCATATTGATGTGGGCTTTTCACTC 59.642 40.000 0.00 0.00 36.21 3.51
6023 9465 2.957402 TGATGTGGGCTTTTCACTCT 57.043 45.000 0.00 0.00 36.21 3.24
6024 9466 2.783135 TGATGTGGGCTTTTCACTCTC 58.217 47.619 0.00 0.00 36.21 3.20
6025 9467 2.106338 TGATGTGGGCTTTTCACTCTCA 59.894 45.455 0.00 0.00 36.21 3.27
6026 9468 2.260844 TGTGGGCTTTTCACTCTCAG 57.739 50.000 0.00 0.00 36.21 3.35
6027 9469 1.202806 TGTGGGCTTTTCACTCTCAGG 60.203 52.381 0.00 0.00 36.21 3.86
6028 9470 1.072331 GTGGGCTTTTCACTCTCAGGA 59.928 52.381 0.00 0.00 32.78 3.86
6029 9471 1.774254 TGGGCTTTTCACTCTCAGGAA 59.226 47.619 0.00 0.00 0.00 3.36
6030 9472 2.174639 TGGGCTTTTCACTCTCAGGAAA 59.825 45.455 0.00 0.00 0.00 3.13
6031 9473 3.181429 TGGGCTTTTCACTCTCAGGAAAT 60.181 43.478 0.00 0.00 33.43 2.17
6032 9474 3.829026 GGGCTTTTCACTCTCAGGAAATT 59.171 43.478 0.00 0.00 33.43 1.82
6033 9475 4.281941 GGGCTTTTCACTCTCAGGAAATTT 59.718 41.667 0.00 0.00 33.43 1.82
6034 9476 5.225642 GGCTTTTCACTCTCAGGAAATTTG 58.774 41.667 0.00 0.00 33.43 2.32
6035 9477 5.010012 GGCTTTTCACTCTCAGGAAATTTGA 59.990 40.000 0.00 0.00 33.43 2.69
6036 9478 5.917447 GCTTTTCACTCTCAGGAAATTTGAC 59.083 40.000 0.00 0.00 33.43 3.18
6037 9479 5.673337 TTTCACTCTCAGGAAATTTGACG 57.327 39.130 0.00 0.00 0.00 4.35
6038 9480 3.067106 TCACTCTCAGGAAATTTGACGC 58.933 45.455 0.00 0.00 0.00 5.19
6039 9481 2.160417 CACTCTCAGGAAATTTGACGCC 59.840 50.000 0.00 0.00 0.00 5.68
6040 9482 2.039084 ACTCTCAGGAAATTTGACGCCT 59.961 45.455 0.00 0.00 0.00 5.52
6041 9483 2.675348 CTCTCAGGAAATTTGACGCCTC 59.325 50.000 0.00 0.00 0.00 4.70
6042 9484 2.303022 TCTCAGGAAATTTGACGCCTCT 59.697 45.455 0.00 0.00 0.00 3.69
6043 9485 3.513912 TCTCAGGAAATTTGACGCCTCTA 59.486 43.478 0.00 0.00 0.00 2.43
6044 9486 4.020573 TCTCAGGAAATTTGACGCCTCTAA 60.021 41.667 0.00 0.00 0.00 2.10
6045 9487 4.843728 TCAGGAAATTTGACGCCTCTAAT 58.156 39.130 0.00 0.00 0.00 1.73
6046 9488 4.635765 TCAGGAAATTTGACGCCTCTAATG 59.364 41.667 0.00 0.00 0.00 1.90
6047 9489 4.635765 CAGGAAATTTGACGCCTCTAATGA 59.364 41.667 0.00 0.00 0.00 2.57
6050 9492 4.965119 AATTTGACGCCTCTAATGAACC 57.035 40.909 0.00 0.00 0.00 3.62
6053 9495 1.207089 TGACGCCTCTAATGAACCCTG 59.793 52.381 0.00 0.00 0.00 4.45
6056 9498 2.835764 ACGCCTCTAATGAACCCTGTTA 59.164 45.455 0.00 0.00 0.00 2.41
6238 9770 0.179124 CTGGAGAAGCGTAGTGAGCC 60.179 60.000 0.00 0.00 34.64 4.70
6239 9771 0.898326 TGGAGAAGCGTAGTGAGCCA 60.898 55.000 0.00 0.00 34.64 4.75
6241 9773 0.243907 GAGAAGCGTAGTGAGCCACA 59.756 55.000 7.86 0.00 36.74 4.17
6242 9774 0.679505 AGAAGCGTAGTGAGCCACAA 59.320 50.000 7.86 0.00 36.74 3.33
6243 9775 1.071605 GAAGCGTAGTGAGCCACAAG 58.928 55.000 7.86 0.94 36.74 3.16
6244 9776 0.951040 AAGCGTAGTGAGCCACAAGC 60.951 55.000 7.86 8.93 44.25 4.01
6251 9797 1.151668 GTGAGCCACAAGCACAGTAG 58.848 55.000 0.00 0.00 43.12 2.57
6261 9807 3.005554 CAAGCACAGTAGTTCCCTGATG 58.994 50.000 0.00 0.00 34.04 3.07
6282 9828 4.717877 TGTAAGACATAATCATGCCCTGG 58.282 43.478 0.00 0.00 35.39 4.45
6348 9894 2.816411 AGGAATGTCCTCGGTGTCTTA 58.184 47.619 0.00 0.00 45.66 2.10
6352 9898 3.821421 ATGTCCTCGGTGTCTTATTCC 57.179 47.619 0.00 0.00 0.00 3.01
6353 9899 2.816411 TGTCCTCGGTGTCTTATTCCT 58.184 47.619 0.00 0.00 0.00 3.36
6354 9900 2.496070 TGTCCTCGGTGTCTTATTCCTG 59.504 50.000 0.00 0.00 0.00 3.86
6355 9901 2.496470 GTCCTCGGTGTCTTATTCCTGT 59.504 50.000 0.00 0.00 0.00 4.00
6358 9904 3.254060 CTCGGTGTCTTATTCCTGTGTG 58.746 50.000 0.00 0.00 0.00 3.82
6359 9905 2.631062 TCGGTGTCTTATTCCTGTGTGT 59.369 45.455 0.00 0.00 0.00 3.72
6392 9938 9.423061 ACAGTGAAAACAGCATTAATAAAATCC 57.577 29.630 0.00 0.00 0.00 3.01
6434 9981 9.546909 GTGAACACATAATTCAGAAGTAATGTG 57.453 33.333 22.17 22.17 42.49 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.927267 TCTCTCATTGCCTCCCTTTTTA 57.073 40.909 0.00 0.00 0.00 1.52
48 49 1.611965 GCCCCTTGCCTTCTCTCAT 59.388 57.895 0.00 0.00 0.00 2.90
55 56 1.224592 CACTATCGCCCCTTGCCTT 59.775 57.895 0.00 0.00 36.24 4.35
66 67 2.060050 ACCAGTCTCTCCCACTATCG 57.940 55.000 0.00 0.00 0.00 2.92
68 69 3.261897 CACAAACCAGTCTCTCCCACTAT 59.738 47.826 0.00 0.00 0.00 2.12
69 70 2.632996 CACAAACCAGTCTCTCCCACTA 59.367 50.000 0.00 0.00 0.00 2.74
82 85 3.448093 TCATATTCTGCCCACAAACCA 57.552 42.857 0.00 0.00 0.00 3.67
87 90 3.947196 GTCACATTCATATTCTGCCCACA 59.053 43.478 0.00 0.00 0.00 4.17
92 95 4.637534 ACCACTGTCACATTCATATTCTGC 59.362 41.667 0.00 0.00 0.00 4.26
159 162 0.690192 TCTCTTTTCGGGGCACATCA 59.310 50.000 0.00 0.00 0.00 3.07
161 164 1.073923 ACTTCTCTTTTCGGGGCACAT 59.926 47.619 0.00 0.00 0.00 3.21
167 170 2.554032 ACAATGCACTTCTCTTTTCGGG 59.446 45.455 0.00 0.00 0.00 5.14
196 199 6.164876 TGCAAATACAAGCATGCTACAAAAT 58.835 32.000 23.00 7.82 39.49 1.82
205 208 8.497554 ACTAAACAAATTGCAAATACAAGCATG 58.502 29.630 1.71 0.00 40.94 4.06
239 242 4.749598 CGGCATGCTTGACTATTACACATA 59.250 41.667 18.92 0.00 0.00 2.29
240 243 3.561310 CGGCATGCTTGACTATTACACAT 59.439 43.478 18.92 0.00 0.00 3.21
258 261 2.143122 GCTATACATTGCTTAGCGGCA 58.857 47.619 1.45 0.00 40.74 5.69
260 263 6.727824 ATTAAGCTATACATTGCTTAGCGG 57.272 37.500 14.65 0.00 46.21 5.52
389 1077 5.031578 TCACTTAAAAATTGCACGTGTGTC 58.968 37.500 18.38 0.49 0.00 3.67
395 1087 9.514822 CACATAAATTCACTTAAAAATTGCACG 57.485 29.630 0.00 0.00 0.00 5.34
408 1100 9.142515 CAAACATAATGCACACATAAATTCACT 57.857 29.630 0.00 0.00 34.62 3.41
434 1126 2.633657 CAGTCAAGCCGCACACAC 59.366 61.111 0.00 0.00 0.00 3.82
461 1164 5.585820 AAACTTACAACCACGGACAATTT 57.414 34.783 0.00 0.00 0.00 1.82
467 1170 2.737783 CGCATAAACTTACAACCACGGA 59.262 45.455 0.00 0.00 0.00 4.69
470 1173 7.966204 ACAAATATCGCATAAACTTACAACCAC 59.034 33.333 0.00 0.00 0.00 4.16
498 1201 9.087424 GCGAGCATGTACTTATGAATATATCAA 57.913 33.333 0.00 0.00 42.54 2.57
499 1202 7.432252 CGCGAGCATGTACTTATGAATATATCA 59.568 37.037 0.00 0.00 43.67 2.15
509 1212 5.286438 TGTAATTCGCGAGCATGTACTTAT 58.714 37.500 9.59 0.00 0.00 1.73
514 1217 4.116238 TCATTGTAATTCGCGAGCATGTA 58.884 39.130 9.59 0.00 0.00 2.29
585 1288 9.685828 CAACCGTATTTATTTTGAAAAGAAGGA 57.314 29.630 7.68 0.00 32.98 3.36
647 1350 1.652124 CGTCCCGAACTAAATGTCACG 59.348 52.381 0.00 0.00 0.00 4.35
658 1361 1.153804 GCTCTCTTCCGTCCCGAAC 60.154 63.158 0.00 0.00 0.00 3.95
661 1364 0.744874 TAATGCTCTCTTCCGTCCCG 59.255 55.000 0.00 0.00 0.00 5.14
670 1373 0.107993 TGCGCTGCTTAATGCTCTCT 60.108 50.000 9.73 0.00 43.37 3.10
676 1379 3.141002 ACTTGAATGCGCTGCTTAATG 57.859 42.857 9.73 0.00 0.00 1.90
683 1386 2.029244 CGGTTACTACTTGAATGCGCTG 59.971 50.000 9.73 0.00 0.00 5.18
686 1389 5.766702 TTTACGGTTACTACTTGAATGCG 57.233 39.130 0.00 0.00 0.00 4.73
703 1409 3.662186 CCTTGCGCTACTTTGTTTTTACG 59.338 43.478 9.73 0.00 0.00 3.18
719 1425 0.941542 TTTTGTCGTCCTTCCTTGCG 59.058 50.000 0.00 0.00 0.00 4.85
725 1431 4.319549 GGTGAACAGATTTTGTCGTCCTTC 60.320 45.833 0.00 0.00 39.73 3.46
898 1614 2.680913 CCTTCTTTCCCACTGCGCG 61.681 63.158 0.00 0.00 0.00 6.86
986 1703 0.597377 CATCATGGCCGTCGATTCGA 60.597 55.000 4.29 4.29 0.00 3.71
1127 1844 3.919804 TGTAAATTTGCTTGCAGCGATTC 59.080 39.130 7.80 0.00 46.26 2.52
1148 1865 3.438087 AGAACTTCCAGCGAATTCACATG 59.562 43.478 6.22 0.00 0.00 3.21
1196 1913 3.080641 TGGTCCAGCCATCACCAG 58.919 61.111 0.00 0.00 43.61 4.00
1230 1955 9.030452 TCAAGGTGGCAAATAAATAAACAGTAT 57.970 29.630 0.00 0.00 0.00 2.12
1231 1956 8.410673 TCAAGGTGGCAAATAAATAAACAGTA 57.589 30.769 0.00 0.00 0.00 2.74
1232 1957 7.296628 TCAAGGTGGCAAATAAATAAACAGT 57.703 32.000 0.00 0.00 0.00 3.55
1233 1958 8.776376 ATTCAAGGTGGCAAATAAATAAACAG 57.224 30.769 0.00 0.00 0.00 3.16
1239 1964 8.458573 TCGTATATTCAAGGTGGCAAATAAAT 57.541 30.769 0.00 0.00 0.00 1.40
1292 2049 7.875554 TGAATAAATAAAGTGCCAAAAAGGACC 59.124 33.333 0.00 0.00 41.22 4.46
1476 2251 8.408043 TTGTCTCCAAATTACAGTGATGATTT 57.592 30.769 0.00 0.00 0.00 2.17
1555 2349 1.001641 ATCCCCTTGTGCTGTGCTC 60.002 57.895 0.00 0.00 0.00 4.26
1597 2391 1.904865 ACCAGGTTCCACGACGCTA 60.905 57.895 0.00 0.00 0.00 4.26
1658 2452 1.398390 GGAAAAGATAGTGTGCTGCGG 59.602 52.381 0.00 0.00 0.00 5.69
1807 2606 2.291475 TGCAGAGGCCAATGGTTTATCA 60.291 45.455 5.01 0.00 40.13 2.15
1818 2617 0.471191 ATCAATCGATGCAGAGGCCA 59.529 50.000 5.01 0.00 40.13 5.36
1866 2665 9.451002 TTGATTTGTTTGGCATCATCATTAATT 57.549 25.926 0.00 0.00 31.29 1.40
1904 2703 4.062991 GCCTCGAGTTCTTTCCTTTTACA 58.937 43.478 12.31 0.00 0.00 2.41
1911 2835 1.657822 GATGGCCTCGAGTTCTTTCC 58.342 55.000 12.31 3.25 0.00 3.13
1967 2891 3.595758 GCGCACAGCTTTGGTGGT 61.596 61.111 0.30 0.00 44.04 4.16
1988 2937 5.514274 TCTTGAAAGCGTTTTCTTGGAAT 57.486 34.783 22.71 0.00 42.56 3.01
2000 2949 0.110192 GCGGTTCCTTCTTGAAAGCG 60.110 55.000 0.00 0.00 37.41 4.68
2026 2975 1.473257 GGATGAGCCAACATCAGCGTA 60.473 52.381 14.80 0.00 45.68 4.42
2072 3021 0.677731 CAAAGATCTGCTTCGGGGCA 60.678 55.000 0.00 3.53 40.15 5.36
2120 3076 3.521220 GCAGCGTCGACGTACGTG 61.521 66.667 35.48 26.74 44.64 4.49
2197 3154 2.805546 GACGAGTATGGCGGCAGA 59.194 61.111 19.29 10.83 36.61 4.26
2230 3187 2.869636 GCTAGTTCTGTGTGAGCAAGCT 60.870 50.000 0.00 0.00 33.26 3.74
2269 3229 2.633509 CGACGTCTTCCCTTCCGGT 61.634 63.158 14.70 0.00 0.00 5.28
2270 3230 2.181021 CGACGTCTTCCCTTCCGG 59.819 66.667 14.70 0.00 0.00 5.14
2271 3231 1.154073 GACGACGTCTTCCCTTCCG 60.154 63.158 20.52 0.00 0.00 4.30
2398 3362 5.766670 TGAGATTCTTGCAACTGACAAATCT 59.233 36.000 0.00 3.91 30.80 2.40
2471 3436 9.751542 CCTACATACAAGAAAAGATCGAACTAT 57.248 33.333 0.00 0.00 0.00 2.12
2502 3467 5.395682 ACCTGAAATGAACATGATGGTTG 57.604 39.130 0.00 0.00 0.00 3.77
2626 3596 4.331108 TGTGCTGGCTAATCAACATGTTA 58.669 39.130 11.53 0.49 0.00 2.41
2651 4732 6.992063 ATCGTGATTTTCTAGCAAATGACT 57.008 33.333 13.51 0.00 30.50 3.41
2967 5152 8.079211 ACTAGTCCACATCATTAGTATGTTGT 57.921 34.615 0.00 0.00 42.57 3.32
2983 5228 7.981102 AAATTGGTAGAGAAAACTAGTCCAC 57.019 36.000 0.00 0.00 0.00 4.02
3056 5301 3.197766 TCTCCAACACATATGGACCAGTC 59.802 47.826 7.80 0.00 41.98 3.51
3087 5332 4.734854 GCAAAACATAGGCATAACATGACG 59.265 41.667 0.00 0.00 45.18 4.35
3178 5423 4.019321 ACTGTACTGCATACCAAACCTCAT 60.019 41.667 0.00 0.00 32.16 2.90
3215 5461 4.217118 GTGTGCCTCAAATTTCTCACAGAT 59.783 41.667 9.98 0.00 35.46 2.90
3252 5498 3.963665 TGCACAACTCAAATTTCCTTCG 58.036 40.909 0.00 0.00 0.00 3.79
3282 5528 7.929941 ATGTGAGGAATAAAAGAAGTCTTCC 57.070 36.000 9.04 0.00 34.61 3.46
3413 5660 8.467402 TGTTGTTGAACACGATTGTAATTTTT 57.533 26.923 0.00 0.00 37.15 1.94
3414 5661 7.971168 TCTGTTGTTGAACACGATTGTAATTTT 59.029 29.630 0.00 0.00 37.15 1.82
3438 5685 6.127423 ACGAAAGTATGCACTATTACACCTCT 60.127 38.462 0.00 0.00 46.88 3.69
3462 5709 2.356135 ACACTCATGCCGGTATTTGAC 58.644 47.619 0.66 0.00 0.00 3.18
3466 5713 5.801531 TCTATTACACTCATGCCGGTATT 57.198 39.130 0.66 0.00 0.00 1.89
3568 6022 5.003804 TCTTCACTCTGCCAATAAGGAAAC 58.996 41.667 0.00 0.00 41.22 2.78
4139 6594 9.307121 CTTCTTGGATCAGTACAATACAAGTAG 57.693 37.037 22.71 20.10 43.01 2.57
4150 6605 5.363939 CAGGGATTCTTCTTGGATCAGTAC 58.636 45.833 0.00 0.00 0.00 2.73
4585 7974 4.563337 CATCCCTAATGCAGTCACATTG 57.437 45.455 0.00 0.00 40.43 2.82
4737 8144 3.115390 CCTGGGAAAAGAGGAGGATACA 58.885 50.000 0.00 0.00 41.41 2.29
5195 8633 5.540337 AGTTGACTGAGGAATGACTGTAAGA 59.460 40.000 0.00 0.00 37.43 2.10
5453 8891 0.609131 CCCCTTGTGCTGATCCGTTT 60.609 55.000 0.00 0.00 0.00 3.60
5525 8963 1.071699 GGGCTGTAGAACAGGACACAA 59.928 52.381 8.99 0.00 46.01 3.33
5660 9098 7.224557 ACAACCAAAACATTCACAAATAAGCTC 59.775 33.333 0.00 0.00 0.00 4.09
5692 9130 8.327941 TGATAGCATATATTGTCTTTTGCTCC 57.672 34.615 0.00 0.00 40.60 4.70
5755 9193 6.760298 ACACAATGTGCTCAGATTATCTAGTG 59.240 38.462 14.01 0.00 36.98 2.74
5758 9196 8.011844 AGTACACAATGTGCTCAGATTATCTA 57.988 34.615 14.01 0.00 39.05 1.98
5759 9197 6.882656 AGTACACAATGTGCTCAGATTATCT 58.117 36.000 14.01 0.00 39.05 1.98
5760 9198 7.065085 ACAAGTACACAATGTGCTCAGATTATC 59.935 37.037 14.01 0.00 42.47 1.75
5761 9199 6.881065 ACAAGTACACAATGTGCTCAGATTAT 59.119 34.615 14.01 0.00 42.47 1.28
5762 9200 6.230472 ACAAGTACACAATGTGCTCAGATTA 58.770 36.000 14.01 0.00 42.47 1.75
5763 9201 5.065914 ACAAGTACACAATGTGCTCAGATT 58.934 37.500 14.01 0.00 42.47 2.40
5764 9202 4.645535 ACAAGTACACAATGTGCTCAGAT 58.354 39.130 14.01 0.00 42.47 2.90
5765 9203 4.071961 ACAAGTACACAATGTGCTCAGA 57.928 40.909 14.01 0.00 42.47 3.27
5766 9204 4.749598 TGTACAAGTACACAATGTGCTCAG 59.250 41.667 14.01 2.79 42.47 3.35
5767 9205 4.698575 TGTACAAGTACACAATGTGCTCA 58.301 39.130 14.01 0.00 42.47 4.26
5778 9216 9.184062 CAGTTTAAGTTATCGTGTACAAGTACA 57.816 33.333 8.88 8.88 43.14 2.90
5779 9217 8.158445 GCAGTTTAAGTTATCGTGTACAAGTAC 58.842 37.037 8.68 3.47 36.63 2.73
5780 9218 8.084073 AGCAGTTTAAGTTATCGTGTACAAGTA 58.916 33.333 8.68 0.00 0.00 2.24
5781 9219 6.927381 AGCAGTTTAAGTTATCGTGTACAAGT 59.073 34.615 8.68 0.00 0.00 3.16
5782 9220 7.347508 AGCAGTTTAAGTTATCGTGTACAAG 57.652 36.000 0.00 0.00 0.00 3.16
5783 9221 8.991243 ATAGCAGTTTAAGTTATCGTGTACAA 57.009 30.769 0.00 0.00 0.00 2.41
5784 9222 8.464404 AGATAGCAGTTTAAGTTATCGTGTACA 58.536 33.333 0.00 0.00 35.25 2.90
5785 9223 8.853469 AGATAGCAGTTTAAGTTATCGTGTAC 57.147 34.615 0.00 0.00 35.25 2.90
5808 9246 6.109156 TGCAGTTGTGGAAGTTCTATAAGA 57.891 37.500 2.25 0.00 0.00 2.10
5813 9251 4.213270 CGAAATGCAGTTGTGGAAGTTCTA 59.787 41.667 3.09 0.00 0.00 2.10
5814 9252 3.003689 CGAAATGCAGTTGTGGAAGTTCT 59.996 43.478 3.09 0.00 0.00 3.01
5822 9260 5.927030 AGTTATACACGAAATGCAGTTGTG 58.073 37.500 20.22 20.22 36.64 3.33
5851 9289 2.959707 ACGGGGAACTTTGTGCATTTTA 59.040 40.909 0.00 0.00 0.00 1.52
5857 9295 1.001633 TCTAGACGGGGAACTTTGTGC 59.998 52.381 0.00 0.00 0.00 4.57
5863 9301 3.462579 TCTCCTTATCTAGACGGGGAACT 59.537 47.826 0.00 0.00 0.00 3.01
5870 9308 9.058174 TCTTAGATTTGTCTCCTTATCTAGACG 57.942 37.037 0.00 0.00 44.14 4.18
5872 9310 9.922477 TGTCTTAGATTTGTCTCCTTATCTAGA 57.078 33.333 0.00 0.00 32.79 2.43
5880 9318 9.660180 GAAATACTTGTCTTAGATTTGTCTCCT 57.340 33.333 0.00 0.00 0.00 3.69
5881 9319 8.596380 CGAAATACTTGTCTTAGATTTGTCTCC 58.404 37.037 0.00 0.00 0.00 3.71
5882 9320 8.596380 CCGAAATACTTGTCTTAGATTTGTCTC 58.404 37.037 0.00 0.00 0.00 3.36
5883 9321 7.549488 CCCGAAATACTTGTCTTAGATTTGTCT 59.451 37.037 0.00 0.00 0.00 3.41
5884 9322 7.201617 CCCCGAAATACTTGTCTTAGATTTGTC 60.202 40.741 0.00 0.00 0.00 3.18
5889 9327 4.704965 GCCCCGAAATACTTGTCTTAGAT 58.295 43.478 0.00 0.00 0.00 1.98
5890 9328 3.429822 CGCCCCGAAATACTTGTCTTAGA 60.430 47.826 0.00 0.00 0.00 2.10
5891 9329 2.864343 CGCCCCGAAATACTTGTCTTAG 59.136 50.000 0.00 0.00 0.00 2.18
5892 9330 2.419021 CCGCCCCGAAATACTTGTCTTA 60.419 50.000 0.00 0.00 0.00 2.10
5893 9331 1.677820 CCGCCCCGAAATACTTGTCTT 60.678 52.381 0.00 0.00 0.00 3.01
5895 9333 0.108041 TCCGCCCCGAAATACTTGTC 60.108 55.000 0.00 0.00 0.00 3.18
5896 9334 0.107848 CTCCGCCCCGAAATACTTGT 60.108 55.000 0.00 0.00 0.00 3.16
5897 9335 0.177141 TCTCCGCCCCGAAATACTTG 59.823 55.000 0.00 0.00 0.00 3.16
5898 9336 1.129058 ATCTCCGCCCCGAAATACTT 58.871 50.000 0.00 0.00 0.00 2.24
5899 9337 2.005370 TATCTCCGCCCCGAAATACT 57.995 50.000 0.00 0.00 0.00 2.12
5900 9338 2.825861 TTATCTCCGCCCCGAAATAC 57.174 50.000 0.00 0.00 0.00 1.89
5901 9339 6.989155 ATATATTATCTCCGCCCCGAAATA 57.011 37.500 0.00 0.00 0.00 1.40
5902 9340 5.888982 ATATATTATCTCCGCCCCGAAAT 57.111 39.130 0.00 0.00 0.00 2.17
5903 9341 5.687166 AATATATTATCTCCGCCCCGAAA 57.313 39.130 0.00 0.00 0.00 3.46
5904 9342 5.687166 AAATATATTATCTCCGCCCCGAA 57.313 39.130 0.00 0.00 0.00 4.30
5905 9343 5.687166 AAAATATATTATCTCCGCCCCGA 57.313 39.130 0.00 0.00 0.00 5.14
5906 9344 6.579865 ACTAAAATATATTATCTCCGCCCCG 58.420 40.000 0.00 0.00 0.00 5.73
5907 9345 9.708092 GATACTAAAATATATTATCTCCGCCCC 57.292 37.037 0.00 0.00 0.00 5.80
5989 9431 5.360714 GCCCACATCAATATGAAGAAAAGGA 59.639 40.000 0.00 0.00 36.54 3.36
5991 9433 6.461110 AGCCCACATCAATATGAAGAAAAG 57.539 37.500 0.00 0.00 36.54 2.27
6014 9456 5.505654 GCGTCAAATTTCCTGAGAGTGAAAA 60.506 40.000 0.00 0.00 34.43 2.29
6019 9461 2.039084 AGGCGTCAAATTTCCTGAGAGT 59.961 45.455 0.00 0.00 0.00 3.24
6020 9462 2.675348 GAGGCGTCAAATTTCCTGAGAG 59.325 50.000 0.52 0.00 0.00 3.20
6021 9463 2.303022 AGAGGCGTCAAATTTCCTGAGA 59.697 45.455 9.41 0.00 0.00 3.27
6022 9464 2.704572 AGAGGCGTCAAATTTCCTGAG 58.295 47.619 9.41 0.00 0.00 3.35
6023 9465 2.859165 AGAGGCGTCAAATTTCCTGA 57.141 45.000 9.41 0.00 0.00 3.86
6024 9466 4.635765 TCATTAGAGGCGTCAAATTTCCTG 59.364 41.667 9.41 0.00 0.00 3.86
6025 9467 4.843728 TCATTAGAGGCGTCAAATTTCCT 58.156 39.130 9.41 0.00 0.00 3.36
6026 9468 5.332707 GTTCATTAGAGGCGTCAAATTTCC 58.667 41.667 9.41 0.00 0.00 3.13
6027 9469 5.332707 GGTTCATTAGAGGCGTCAAATTTC 58.667 41.667 9.41 0.00 0.00 2.17
6028 9470 4.157840 GGGTTCATTAGAGGCGTCAAATTT 59.842 41.667 9.41 0.00 0.00 1.82
6029 9471 3.694566 GGGTTCATTAGAGGCGTCAAATT 59.305 43.478 9.41 0.00 0.00 1.82
6030 9472 3.054361 AGGGTTCATTAGAGGCGTCAAAT 60.054 43.478 9.41 0.00 0.00 2.32
6031 9473 2.304761 AGGGTTCATTAGAGGCGTCAAA 59.695 45.455 9.41 0.00 0.00 2.69
6032 9474 1.906574 AGGGTTCATTAGAGGCGTCAA 59.093 47.619 9.41 1.75 0.00 3.18
6033 9475 1.207089 CAGGGTTCATTAGAGGCGTCA 59.793 52.381 9.41 0.00 0.00 4.35
6034 9476 1.207329 ACAGGGTTCATTAGAGGCGTC 59.793 52.381 0.00 0.00 0.00 5.19
6035 9477 1.276622 ACAGGGTTCATTAGAGGCGT 58.723 50.000 0.00 0.00 0.00 5.68
6036 9478 2.403252 AACAGGGTTCATTAGAGGCG 57.597 50.000 0.00 0.00 0.00 5.52
6037 9479 7.173390 GTGATTATAACAGGGTTCATTAGAGGC 59.827 40.741 0.00 0.00 0.00 4.70
6038 9480 7.385205 CGTGATTATAACAGGGTTCATTAGAGG 59.615 40.741 0.00 0.00 0.00 3.69
6039 9481 7.095607 GCGTGATTATAACAGGGTTCATTAGAG 60.096 40.741 0.00 0.00 0.00 2.43
6040 9482 6.704493 GCGTGATTATAACAGGGTTCATTAGA 59.296 38.462 0.00 0.00 0.00 2.10
6041 9483 6.706270 AGCGTGATTATAACAGGGTTCATTAG 59.294 38.462 0.00 0.00 31.54 1.73
6042 9484 6.588204 AGCGTGATTATAACAGGGTTCATTA 58.412 36.000 0.00 0.00 31.54 1.90
6043 9485 5.437060 AGCGTGATTATAACAGGGTTCATT 58.563 37.500 0.00 0.00 31.54 2.57
6044 9486 5.036117 AGCGTGATTATAACAGGGTTCAT 57.964 39.130 0.00 0.00 31.54 2.57
6045 9487 4.481368 AGCGTGATTATAACAGGGTTCA 57.519 40.909 0.00 0.00 31.54 3.18
6046 9488 6.220930 TGATAGCGTGATTATAACAGGGTTC 58.779 40.000 13.55 11.79 35.88 3.62
6047 9489 6.169557 TGATAGCGTGATTATAACAGGGTT 57.830 37.500 13.55 0.00 35.88 4.11
6174 9617 5.825679 TGTGCTCCTGTATGTTTTACTGTTT 59.174 36.000 0.00 0.00 0.00 2.83
6238 9770 2.146342 CAGGGAACTACTGTGCTTGTG 58.854 52.381 0.00 0.00 40.21 3.33
6239 9771 2.047061 TCAGGGAACTACTGTGCTTGT 58.953 47.619 0.00 0.00 40.21 3.16
6241 9773 2.639839 ACATCAGGGAACTACTGTGCTT 59.360 45.455 0.00 0.00 40.21 3.91
6242 9774 2.260822 ACATCAGGGAACTACTGTGCT 58.739 47.619 0.00 0.00 40.21 4.40
6243 9775 2.770164 ACATCAGGGAACTACTGTGC 57.230 50.000 0.00 0.00 40.21 4.57
6244 9776 5.047306 TGTCTTACATCAGGGAACTACTGTG 60.047 44.000 0.00 0.00 40.21 3.66
6245 9777 5.084519 TGTCTTACATCAGGGAACTACTGT 58.915 41.667 0.00 0.00 40.21 3.55
6251 9797 7.308229 GCATGATTATGTCTTACATCAGGGAAC 60.308 40.741 0.00 0.00 39.88 3.62
6261 9807 4.973168 TCCAGGGCATGATTATGTCTTAC 58.027 43.478 0.00 0.00 38.93 2.34
6282 9828 4.582656 AGCTAGATGATAGTCACACACCTC 59.417 45.833 0.00 0.00 0.00 3.85
6348 9894 4.756642 CACTGTTGACATACACACAGGAAT 59.243 41.667 8.65 0.00 39.50 3.01
6352 9898 5.733226 TTTCACTGTTGACATACACACAG 57.267 39.130 3.23 3.23 40.21 3.66
6353 9899 5.412904 TGTTTTCACTGTTGACATACACACA 59.587 36.000 0.00 0.00 0.00 3.72
6354 9900 5.874831 TGTTTTCACTGTTGACATACACAC 58.125 37.500 0.00 0.00 0.00 3.82
6355 9901 5.448496 GCTGTTTTCACTGTTGACATACACA 60.448 40.000 0.00 0.00 0.00 3.72
6358 9904 5.168526 TGCTGTTTTCACTGTTGACATAC 57.831 39.130 0.00 0.00 0.00 2.39
6359 9905 6.389830 AATGCTGTTTTCACTGTTGACATA 57.610 33.333 0.00 0.00 0.00 2.29
6434 9981 6.072838 TCACACTTTGATTCTCTTCTGCATTC 60.073 38.462 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.