Multiple sequence alignment - TraesCS2B01G614400

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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 TraesCS2B01G614400 chr2B 100.000 3301 0 0 1 3301 793170821 793167521 0.000000e+00 6096.0
1 TraesCS2B01G614400 chr2B 82.301 678 111 8 1665 2337 793141597 793140924 2.210000e-161 579.0
2 TraesCS2B01G614400 chr2B 78.354 559 119 2 1680 2237 792877160 792877717 8.710000e-96 361.0
3 TraesCS2B01G614400 chr2B 87.755 196 20 3 1331 1524 793141926 793141733 3.310000e-55 226.0
4 TraesCS2B01G614400 chr2B 83.721 215 35 0 1000 1214 793035076 793034862 1.550000e-48 204.0
5 TraesCS2B01G614400 chr2B 81.900 221 32 5 1001 1214 793142141 793141922 2.620000e-41 180.0
6 TraesCS2B01G614400 chr2B 93.023 86 4 2 1 85 649465276 649465360 1.240000e-24 124.0
7 TraesCS2B01G614400 chr2D 94.479 1123 49 6 1317 2438 643878747 643879857 0.000000e+00 1718.0
8 TraesCS2B01G614400 chr2D 85.987 942 72 33 300 1219 643877722 643878625 0.000000e+00 953.0
9 TraesCS2B01G614400 chr2D 82.484 805 86 30 2486 3250 643880147 643880936 0.000000e+00 654.0
10 TraesCS2B01G614400 chr2D 83.792 691 104 6 1651 2337 643901667 643902353 0.000000e+00 649.0
11 TraesCS2B01G614400 chr2D 80.678 590 114 0 1679 2268 644016788 644017377 3.000000e-125 459.0
12 TraesCS2B01G614400 chr2D 91.403 221 13 2 75 295 643877471 643877685 6.920000e-77 298.0
13 TraesCS2B01G614400 chr2D 80.631 222 33 7 1001 1214 643901092 643901311 2.640000e-36 163.0
14 TraesCS2B01G614400 chr2D 73.675 547 83 44 1001 1521 644220295 644219784 4.410000e-34 156.0
15 TraesCS2B01G614400 chr2A 89.437 1155 76 15 1298 2450 769003670 769004780 0.000000e+00 1415.0
16 TraesCS2B01G614400 chr2A 90.839 644 47 5 573 1216 769002694 769003325 0.000000e+00 852.0
17 TraesCS2B01G614400 chr2A 82.044 685 118 5 1656 2337 769020848 769021530 2.210000e-161 579.0
18 TraesCS2B01G614400 chr2A 79.831 590 119 0 1679 2268 769145322 769145911 6.540000e-117 431.0
19 TraesCS2B01G614400 chr2A 78.533 559 118 2 1680 2237 769473476 769472919 1.870000e-97 366.0
20 TraesCS2B01G614400 chr2A 75.672 781 105 34 2486 3216 769005012 769005757 8.890000e-81 311.0
21 TraesCS2B01G614400 chr2A 87.234 235 19 5 297 528 769002468 769002694 1.180000e-64 257.0
22 TraesCS2B01G614400 chr2A 83.721 215 35 0 1000 1214 769144924 769145138 1.550000e-48 204.0
23 TraesCS2B01G614400 chr2A 83.700 227 7 8 69 295 769002237 769002433 1.560000e-43 187.0
24 TraesCS2B01G614400 chr2A 80.631 222 33 8 1001 1214 769020358 769020577 2.640000e-36 163.0
25 TraesCS2B01G614400 chr2A 78.632 234 35 9 1001 1219 769473973 769473740 1.230000e-29 141.0
26 TraesCS2B01G614400 chr5B 97.297 74 1 1 1 73 207578947 207579020 1.240000e-24 124.0
27 TraesCS2B01G614400 chr7B 97.222 72 1 1 1 71 662929142 662929213 1.610000e-23 121.0
28 TraesCS2B01G614400 chr7B 94.595 74 3 1 1 73 553439609 553439682 2.690000e-21 113.0
29 TraesCS2B01G614400 chr6B 93.671 79 2 3 1 77 702917497 702917420 7.490000e-22 115.0
30 TraesCS2B01G614400 chr6B 93.421 76 2 3 4 77 702942919 702942845 3.480000e-20 110.0
31 TraesCS2B01G614400 chr6B 90.909 77 6 1 4 79 36133825 36133749 5.830000e-18 102.0
32 TraesCS2B01G614400 chr1B 94.366 71 3 1 4 73 571190744 571190814 1.250000e-19 108.0
33 TraesCS2B01G614400 chr1B 89.744 78 6 2 3 78 43379739 43379662 7.540000e-17 99.0
34 TraesCS2B01G614400 chr1B 82.353 68 7 4 47 112 503869551 503869615 2.000000e-03 54.7
35 TraesCS2B01G614400 chr3D 94.595 37 1 1 1328 1363 348912666 348912630 4.600000e-04 56.5
36 TraesCS2B01G614400 chr3B 94.286 35 1 1 1330 1363 448314246 448314212 6.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G614400 chr2B 793167521 793170821 3300 True 6096.000000 6096 100.000000 1 3301 1 chr2B.!!$R2 3300
1 TraesCS2B01G614400 chr2B 792877160 792877717 557 False 361.000000 361 78.354000 1680 2237 1 chr2B.!!$F2 557
2 TraesCS2B01G614400 chr2B 793140924 793142141 1217 True 328.333333 579 83.985333 1001 2337 3 chr2B.!!$R3 1336
3 TraesCS2B01G614400 chr2D 643877471 643880936 3465 False 905.750000 1718 88.588250 75 3250 4 chr2D.!!$F2 3175
4 TraesCS2B01G614400 chr2D 644016788 644017377 589 False 459.000000 459 80.678000 1679 2268 1 chr2D.!!$F1 589
5 TraesCS2B01G614400 chr2D 643901092 643902353 1261 False 406.000000 649 82.211500 1001 2337 2 chr2D.!!$F3 1336
6 TraesCS2B01G614400 chr2A 769002237 769005757 3520 False 604.400000 1415 85.376400 69 3216 5 chr2A.!!$F1 3147
7 TraesCS2B01G614400 chr2A 769020358 769021530 1172 False 371.000000 579 81.337500 1001 2337 2 chr2A.!!$F2 1336
8 TraesCS2B01G614400 chr2A 769144924 769145911 987 False 317.500000 431 81.776000 1000 2268 2 chr2A.!!$F3 1268
9 TraesCS2B01G614400 chr2A 769472919 769473973 1054 True 253.500000 366 78.582500 1001 2237 2 chr2A.!!$R1 1236

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
462 501 0.179129 AAACTATGCCCGACCGTACG 60.179 55.0 8.69 8.69 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 2846 0.035439 CCGGCACACAACCTCCTATT 60.035 55.0 0.0 0.0 0.0 1.73 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
23 24 6.994868 GAGTGTATCTAGGACTAAATTGCG 57.005 41.667 0.00 0.00 0.00 4.85
24 25 6.466885 AGTGTATCTAGGACTAAATTGCGT 57.533 37.500 0.00 0.00 0.00 5.24
25 26 6.505272 AGTGTATCTAGGACTAAATTGCGTC 58.495 40.000 0.00 0.05 0.00 5.19
26 27 6.321690 AGTGTATCTAGGACTAAATTGCGTCT 59.678 38.462 7.16 0.00 0.00 4.18
27 28 7.501559 AGTGTATCTAGGACTAAATTGCGTCTA 59.498 37.037 7.16 0.00 0.00 2.59
28 29 7.804129 GTGTATCTAGGACTAAATTGCGTCTAG 59.196 40.741 7.16 0.00 0.00 2.43
29 30 7.718314 TGTATCTAGGACTAAATTGCGTCTAGA 59.282 37.037 0.00 0.00 31.26 2.43
30 31 7.768807 ATCTAGGACTAAATTGCGTCTAGAT 57.231 36.000 0.00 0.00 32.35 1.98
31 32 8.865420 ATCTAGGACTAAATTGCGTCTAGATA 57.135 34.615 16.71 0.00 33.70 1.98
32 33 8.097078 TCTAGGACTAAATTGCGTCTAGATAC 57.903 38.462 0.00 0.00 0.00 2.24
33 34 6.710597 AGGACTAAATTGCGTCTAGATACA 57.289 37.500 0.00 0.00 0.00 2.29
34 35 7.291411 AGGACTAAATTGCGTCTAGATACAT 57.709 36.000 0.00 0.00 0.00 2.29
35 36 7.371936 AGGACTAAATTGCGTCTAGATACATC 58.628 38.462 0.00 0.00 0.00 3.06
36 37 7.231722 AGGACTAAATTGCGTCTAGATACATCT 59.768 37.037 0.00 0.00 40.86 2.90
37 38 8.512956 GGACTAAATTGCGTCTAGATACATCTA 58.487 37.037 0.00 0.00 38.32 1.98
42 43 9.935241 AAATTGCGTCTAGATACATCTATTCAT 57.065 29.630 0.00 0.00 38.60 2.57
43 44 9.579768 AATTGCGTCTAGATACATCTATTCATC 57.420 33.333 0.00 0.00 38.60 2.92
44 45 7.089770 TGCGTCTAGATACATCTATTCATCC 57.910 40.000 0.00 0.00 38.60 3.51
45 46 6.183360 TGCGTCTAGATACATCTATTCATCCG 60.183 42.308 0.00 0.00 38.60 4.18
46 47 6.195868 CGTCTAGATACATCTATTCATCCGC 58.804 44.000 0.00 0.00 38.60 5.54
47 48 6.183360 CGTCTAGATACATCTATTCATCCGCA 60.183 42.308 0.00 0.00 38.60 5.69
48 49 7.539436 GTCTAGATACATCTATTCATCCGCAA 58.461 38.462 0.00 0.00 38.60 4.85
49 50 7.700234 GTCTAGATACATCTATTCATCCGCAAG 59.300 40.741 0.00 0.00 38.60 4.01
50 51 6.352016 AGATACATCTATTCATCCGCAAGT 57.648 37.500 0.00 0.00 34.85 3.16
51 52 7.468141 AGATACATCTATTCATCCGCAAGTA 57.532 36.000 0.00 0.00 34.85 2.24
52 53 8.072321 AGATACATCTATTCATCCGCAAGTAT 57.928 34.615 0.00 0.00 34.85 2.12
53 54 8.535335 AGATACATCTATTCATCCGCAAGTATT 58.465 33.333 0.00 0.00 34.85 1.89
54 55 9.155975 GATACATCTATTCATCCGCAAGTATTT 57.844 33.333 0.00 0.00 0.00 1.40
55 56 7.807977 ACATCTATTCATCCGCAAGTATTTT 57.192 32.000 0.00 0.00 0.00 1.82
56 57 7.865707 ACATCTATTCATCCGCAAGTATTTTC 58.134 34.615 0.00 0.00 0.00 2.29
57 58 6.525121 TCTATTCATCCGCAAGTATTTTCG 57.475 37.500 0.00 0.00 0.00 3.46
58 59 4.552166 ATTCATCCGCAAGTATTTTCGG 57.448 40.909 2.67 2.67 41.37 4.30
61 62 1.352114 TCCGCAAGTATTTTCGGACG 58.648 50.000 7.62 0.00 43.03 4.79
62 63 0.372334 CCGCAAGTATTTTCGGACGG 59.628 55.000 2.95 0.00 42.23 4.79
63 64 1.352114 CGCAAGTATTTTCGGACGGA 58.648 50.000 0.00 0.00 0.00 4.69
64 65 1.323534 CGCAAGTATTTTCGGACGGAG 59.676 52.381 0.00 0.00 0.00 4.63
65 66 1.664151 GCAAGTATTTTCGGACGGAGG 59.336 52.381 0.00 0.00 0.00 4.30
66 67 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
67 68 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
72 73 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
135 136 3.564644 CAGATATGCAAAGAGGAGCCTTG 59.435 47.826 0.00 0.00 0.00 3.61
147 148 1.672145 GGAGCCTTGACTTCCGTGTAC 60.672 57.143 0.00 0.00 0.00 2.90
185 186 5.304101 ACTGGCTCCATCTAGTCTAGATTTG 59.696 44.000 18.16 12.91 42.70 2.32
189 190 7.149307 GGCTCCATCTAGTCTAGATTTGTAAC 58.851 42.308 18.16 7.47 42.70 2.50
192 193 9.126151 CTCCATCTAGTCTAGATTTGTAACTGA 57.874 37.037 18.16 3.81 42.70 3.41
194 195 7.858382 CCATCTAGTCTAGATTTGTAACTGACG 59.142 40.741 18.16 4.54 42.70 4.35
195 196 7.317842 TCTAGTCTAGATTTGTAACTGACGG 57.682 40.000 5.41 0.00 0.00 4.79
196 197 5.979288 AGTCTAGATTTGTAACTGACGGT 57.021 39.130 0.00 0.00 0.00 4.83
197 198 5.952033 AGTCTAGATTTGTAACTGACGGTC 58.048 41.667 0.00 0.00 0.00 4.79
198 199 5.475909 AGTCTAGATTTGTAACTGACGGTCA 59.524 40.000 10.88 10.88 0.00 4.02
199 200 5.572126 GTCTAGATTTGTAACTGACGGTCAC 59.428 44.000 6.76 0.00 0.00 3.67
200 201 4.602340 AGATTTGTAACTGACGGTCACT 57.398 40.909 6.76 0.00 0.00 3.41
201 202 5.717078 AGATTTGTAACTGACGGTCACTA 57.283 39.130 6.76 0.00 0.00 2.74
202 203 6.282199 AGATTTGTAACTGACGGTCACTAT 57.718 37.500 6.76 0.00 0.00 2.12
203 204 6.100004 AGATTTGTAACTGACGGTCACTATG 58.900 40.000 6.76 0.00 0.00 2.23
204 205 5.456548 TTTGTAACTGACGGTCACTATGA 57.543 39.130 6.76 0.00 0.00 2.15
259 260 4.192317 CCTAGCTAAGAATTTTCAGCGGT 58.808 43.478 0.00 0.00 39.04 5.68
263 264 5.222631 AGCTAAGAATTTTCAGCGGTTTTG 58.777 37.500 0.00 0.00 39.04 2.44
295 296 1.340889 TCTTGCAGGTGCCATTCAAAC 59.659 47.619 0.00 0.00 41.18 2.93
298 332 0.313672 GCAGGTGCCATTCAAACGAA 59.686 50.000 0.00 0.00 34.31 3.85
306 340 1.062002 CCATTCAAACGAACGATCCCG 59.938 52.381 0.14 0.00 42.50 5.14
330 369 6.208994 CGTCTCTAACCACCCTAGCTAATTAT 59.791 42.308 0.00 0.00 0.00 1.28
339 378 4.042934 ACCCTAGCTAATTATTCCGCCATT 59.957 41.667 0.00 0.00 0.00 3.16
369 408 2.703007 ACTCAACTCCTAGATGCCATCC 59.297 50.000 0.00 0.00 0.00 3.51
393 432 7.337436 TCCGAAACTATTCCAAAATCCGTTAAT 59.663 33.333 0.00 0.00 31.52 1.40
415 454 5.557576 TCATATCCAGGTCTCCATTCTTG 57.442 43.478 0.00 0.00 0.00 3.02
428 467 7.976734 GGTCTCCATTCTTGATAATATCCTACG 59.023 40.741 0.00 0.00 0.00 3.51
440 479 9.467796 TGATAATATCCTACGTGATCTTGATCT 57.532 33.333 11.31 0.00 0.00 2.75
442 481 7.531857 AATATCCTACGTGATCTTGATCTGT 57.468 36.000 11.31 11.44 0.00 3.41
457 496 2.973694 TCTGTAAACTATGCCCGACC 57.026 50.000 0.00 0.00 0.00 4.79
458 497 1.135527 TCTGTAAACTATGCCCGACCG 59.864 52.381 0.00 0.00 0.00 4.79
461 500 2.159254 TGTAAACTATGCCCGACCGTAC 60.159 50.000 0.00 0.00 0.00 3.67
462 501 0.179129 AAACTATGCCCGACCGTACG 60.179 55.000 8.69 8.69 0.00 3.67
466 505 0.463654 TATGCCCGACCGTACGTACT 60.464 55.000 22.55 5.64 0.00 2.73
467 506 1.996786 ATGCCCGACCGTACGTACTG 61.997 60.000 22.55 18.59 0.00 2.74
533 572 3.348647 TCCAAGGAATCAATCGAGCAA 57.651 42.857 0.00 0.00 0.00 3.91
536 575 2.749076 CAAGGAATCAATCGAGCAACCA 59.251 45.455 0.00 0.00 0.00 3.67
537 576 3.071874 AGGAATCAATCGAGCAACCAA 57.928 42.857 0.00 0.00 0.00 3.67
538 577 3.624777 AGGAATCAATCGAGCAACCAAT 58.375 40.909 0.00 0.00 0.00 3.16
543 582 6.238731 GGAATCAATCGAGCAACCAATAATCA 60.239 38.462 0.00 0.00 0.00 2.57
544 583 5.739752 TCAATCGAGCAACCAATAATCAG 57.260 39.130 0.00 0.00 0.00 2.90
547 586 3.186909 TCGAGCAACCAATAATCAGTCG 58.813 45.455 0.00 0.00 0.00 4.18
567 606 2.762745 GGCTTCACCGAGAAAACAGTA 58.237 47.619 0.00 0.00 35.40 2.74
571 611 3.299340 TCACCGAGAAAACAGTAGAGC 57.701 47.619 0.00 0.00 0.00 4.09
681 721 2.115052 TGTGCACGAAAGCCCCAT 59.885 55.556 13.13 0.00 0.00 4.00
691 731 1.586154 AAAGCCCCATGAAAGCGACG 61.586 55.000 0.00 0.00 0.00 5.12
713 753 2.223845 CCGTCGATGCATGCATTATCAA 59.776 45.455 32.60 14.50 36.70 2.57
716 756 3.976942 GTCGATGCATGCATTATCAAACC 59.023 43.478 32.60 16.71 36.70 3.27
736 776 2.681344 CCCTTTTATCACAACGGTAGGC 59.319 50.000 0.00 0.00 0.00 3.93
781 821 1.606224 GGTTCAAGCCATGCAACTTGG 60.606 52.381 20.72 12.72 42.82 3.61
796 836 1.623311 ACTTGGACATGTCGATCCACA 59.377 47.619 19.33 7.86 44.80 4.17
817 857 2.505628 TTGTAAGCAACGTACGTCCA 57.494 45.000 23.05 8.80 0.00 4.02
837 877 1.406970 GCTAGCTGCGACTTGTCGAC 61.407 60.000 24.65 9.11 34.64 4.20
851 891 1.414550 TGTCGACCTGTGTGGAATTGA 59.585 47.619 14.12 0.00 39.71 2.57
870 910 3.760738 TGAGGATCAGATCGAGCTATGT 58.239 45.455 1.25 0.00 42.56 2.29
886 926 6.225926 AGCTATGTGGCTAGCAAATTGCAC 62.226 45.833 20.82 14.16 45.35 4.57
956 997 4.779475 CTTGAGGAAGCCACACGT 57.221 55.556 0.00 0.00 0.00 4.49
957 998 3.906660 CTTGAGGAAGCCACACGTA 57.093 52.632 0.00 0.00 0.00 3.57
958 999 1.429463 CTTGAGGAAGCCACACGTAC 58.571 55.000 0.00 0.00 0.00 3.67
959 1000 0.319211 TTGAGGAAGCCACACGTACG 60.319 55.000 15.01 15.01 0.00 3.67
969 1010 0.856641 CACACGTACGACACCCTTTG 59.143 55.000 24.41 9.52 0.00 2.77
1239 1354 3.585748 GCGTACGCACATATGTCAAAT 57.414 42.857 33.90 0.00 41.49 2.32
1248 1363 8.153479 ACGCACATATGTCAAATTATGTACAT 57.847 30.769 13.93 13.93 37.02 2.29
1249 1364 8.069574 ACGCACATATGTCAAATTATGTACATG 58.930 33.333 18.81 2.68 37.02 3.21
1303 1495 9.881649 AGGAGTAATTATGTATGCATGAGTATG 57.118 33.333 10.16 0.00 36.58 2.39
1304 1496 9.875691 GGAGTAATTATGTATGCATGAGTATGA 57.124 33.333 10.16 0.00 36.36 2.15
1380 1725 2.558313 GAACAACAGCGAGCAGGC 59.442 61.111 0.00 0.00 0.00 4.85
1572 1917 4.152625 GCAGCACGCACGACCATC 62.153 66.667 0.00 0.00 41.79 3.51
1573 1918 2.738139 CAGCACGCACGACCATCA 60.738 61.111 0.00 0.00 0.00 3.07
1575 1920 1.375908 AGCACGCACGACCATCAAT 60.376 52.632 0.00 0.00 0.00 2.57
1576 1921 1.060937 GCACGCACGACCATCAATC 59.939 57.895 0.00 0.00 0.00 2.67
1577 1922 1.715585 CACGCACGACCATCAATCC 59.284 57.895 0.00 0.00 0.00 3.01
1579 1924 0.321210 ACGCACGACCATCAATCCAA 60.321 50.000 0.00 0.00 0.00 3.53
1580 1925 1.016627 CGCACGACCATCAATCCAAT 58.983 50.000 0.00 0.00 0.00 3.16
1597 1942 6.645790 ATCCAATTATCCAAATCTGAGTGC 57.354 37.500 0.00 0.00 0.00 4.40
1649 2039 5.206299 GTCGACATAGAGATTTACTGACGG 58.794 45.833 11.55 0.00 0.00 4.79
1859 2253 4.314440 TCTGGCGCGCACTCCTTT 62.314 61.111 34.42 0.00 0.00 3.11
1937 2331 0.530288 CGCCAATCGACCCCAATTTT 59.470 50.000 0.00 0.00 41.67 1.82
2093 2487 2.670148 GGACCAGGGCCTCATCGTT 61.670 63.158 2.89 0.00 0.00 3.85
2273 2667 2.588620 GAGGGTATCGAGACCATGAGT 58.411 52.381 29.08 9.03 41.73 3.41
2274 2668 3.752665 GAGGGTATCGAGACCATGAGTA 58.247 50.000 29.08 0.00 41.73 2.59
2338 2733 1.871772 GCTTGCTGAAGCGTGTGAT 59.128 52.632 0.00 0.00 45.12 3.06
2340 2736 1.150827 CTTGCTGAAGCGTGTGATCA 58.849 50.000 0.00 0.00 45.83 2.92
2341 2737 0.867746 TTGCTGAAGCGTGTGATCAC 59.132 50.000 19.27 19.27 45.83 3.06
2353 2749 1.068474 GTGATCACGTGTGTGCTACC 58.932 55.000 16.51 0.00 46.01 3.18
2357 2753 0.676736 TCACGTGTGTGCTACCATCA 59.323 50.000 16.51 0.00 46.01 3.07
2366 2762 2.224606 GTGCTACCATCATGTCATGGG 58.775 52.381 15.79 9.43 46.98 4.00
2370 2766 0.106369 ACCATCATGTCATGGGGCTG 60.106 55.000 18.74 9.95 46.98 4.85
2377 2773 1.678970 GTCATGGGGCTGGTGGTTC 60.679 63.158 0.00 0.00 0.00 3.62
2389 2785 4.069304 GCTGGTGGTTCTGTGTAATTGTA 58.931 43.478 0.00 0.00 0.00 2.41
2439 2835 4.041567 CAGACACCATGCCCCAAGTATATA 59.958 45.833 0.00 0.00 0.00 0.86
2440 2836 4.852118 AGACACCATGCCCCAAGTATATAT 59.148 41.667 0.00 0.00 0.00 0.86
2442 2838 3.696051 CACCATGCCCCAAGTATATATGC 59.304 47.826 0.00 0.00 0.00 3.14
2443 2839 3.593328 ACCATGCCCCAAGTATATATGCT 59.407 43.478 0.00 0.00 0.00 3.79
2444 2840 4.044571 ACCATGCCCCAAGTATATATGCTT 59.955 41.667 9.99 9.99 32.81 3.91
2445 2841 4.641989 CCATGCCCCAAGTATATATGCTTC 59.358 45.833 12.58 3.61 30.06 3.86
2446 2842 4.301072 TGCCCCAAGTATATATGCTTCC 57.699 45.455 12.58 3.88 30.06 3.46
2447 2843 3.916349 TGCCCCAAGTATATATGCTTCCT 59.084 43.478 12.58 0.00 30.06 3.36
2448 2844 5.097948 TGCCCCAAGTATATATGCTTCCTA 58.902 41.667 12.58 0.00 30.06 2.94
2449 2845 5.045869 TGCCCCAAGTATATATGCTTCCTAC 60.046 44.000 12.58 5.07 30.06 3.18
2450 2846 5.045869 GCCCCAAGTATATATGCTTCCTACA 60.046 44.000 12.58 0.00 30.06 2.74
2453 2849 8.768397 CCCCAAGTATATATGCTTCCTACAATA 58.232 37.037 12.58 0.00 30.06 1.90
2454 2850 9.823647 CCCAAGTATATATGCTTCCTACAATAG 57.176 37.037 12.58 0.17 30.06 1.73
2467 2863 2.200373 ACAATAGGAGGTTGTGTGCC 57.800 50.000 0.00 0.00 38.31 5.01
2468 2864 1.086696 CAATAGGAGGTTGTGTGCCG 58.913 55.000 0.00 0.00 0.00 5.69
2469 2865 0.035439 AATAGGAGGTTGTGTGCCGG 60.035 55.000 0.00 0.00 0.00 6.13
2470 2866 1.198759 ATAGGAGGTTGTGTGCCGGT 61.199 55.000 1.90 0.00 0.00 5.28
2472 2868 1.826487 GGAGGTTGTGTGCCGGTTT 60.826 57.895 1.90 0.00 0.00 3.27
2474 2870 1.077357 AGGTTGTGTGCCGGTTTGA 60.077 52.632 1.90 0.00 0.00 2.69
2475 2871 1.101049 AGGTTGTGTGCCGGTTTGAG 61.101 55.000 1.90 0.00 0.00 3.02
2476 2872 1.299089 GTTGTGTGCCGGTTTGAGC 60.299 57.895 1.90 0.00 0.00 4.26
2478 2874 1.106351 TTGTGTGCCGGTTTGAGCAT 61.106 50.000 1.90 0.00 41.86 3.79
2481 2877 1.268352 GTGTGCCGGTTTGAGCATTAA 59.732 47.619 1.90 0.00 41.86 1.40
2482 2878 2.094752 GTGTGCCGGTTTGAGCATTAAT 60.095 45.455 1.90 0.00 41.86 1.40
2483 2879 3.127895 GTGTGCCGGTTTGAGCATTAATA 59.872 43.478 1.90 0.00 41.86 0.98
2484 2880 3.951037 TGTGCCGGTTTGAGCATTAATAT 59.049 39.130 1.90 0.00 41.86 1.28
2485 2881 5.008217 GTGTGCCGGTTTGAGCATTAATATA 59.992 40.000 1.90 0.00 41.86 0.86
2486 2882 5.008217 TGTGCCGGTTTGAGCATTAATATAC 59.992 40.000 1.90 0.00 41.86 1.47
2487 2883 5.008217 GTGCCGGTTTGAGCATTAATATACA 59.992 40.000 1.90 0.00 41.86 2.29
2520 3165 4.855715 TCGATCTTAGCAGAAATCGGAT 57.144 40.909 10.35 0.00 33.88 4.18
2526 3171 2.787473 AGCAGAAATCGGATGGACAA 57.213 45.000 0.00 0.00 0.00 3.18
2527 3172 3.287867 AGCAGAAATCGGATGGACAAT 57.712 42.857 0.00 0.00 0.00 2.71
2528 3173 2.947652 AGCAGAAATCGGATGGACAATG 59.052 45.455 0.00 0.00 0.00 2.82
2529 3174 2.542411 GCAGAAATCGGATGGACAATGC 60.542 50.000 0.00 0.00 0.00 3.56
2536 3190 2.514592 ATGGACAATGCTCGCCGG 60.515 61.111 0.00 0.00 0.00 6.13
2538 3192 1.966901 ATGGACAATGCTCGCCGGTA 61.967 55.000 1.90 0.00 0.00 4.02
2565 3220 0.398381 GAGTGAGGCAGGGAGAGGAT 60.398 60.000 0.00 0.00 0.00 3.24
2572 3227 0.758123 GCAGGGAGAGGATGAGAAGG 59.242 60.000 0.00 0.00 0.00 3.46
2584 3239 3.071602 GGATGAGAAGGCATGCTACCTAA 59.928 47.826 18.92 5.52 36.14 2.69
2587 3242 4.517285 TGAGAAGGCATGCTACCTAAAAG 58.483 43.478 18.92 0.00 36.14 2.27
2591 3246 4.092116 AGGCATGCTACCTAAAAGATCC 57.908 45.455 18.92 0.00 35.10 3.36
2645 3306 8.992073 ACAGATAAAAATCAACAAAGATTTGCC 58.008 29.630 5.23 0.00 44.96 4.52
2659 3320 4.978863 TGCCGTGCGTTGCAGCTA 62.979 61.111 0.00 0.00 40.08 3.32
2670 3331 6.373779 GTGCGTTGCAGCTAAAATATCATAT 58.626 36.000 0.00 0.00 40.08 1.78
2671 3332 7.518161 GTGCGTTGCAGCTAAAATATCATATA 58.482 34.615 0.00 0.00 40.08 0.86
2672 3333 8.177663 GTGCGTTGCAGCTAAAATATCATATAT 58.822 33.333 0.00 0.00 40.08 0.86
2673 3334 9.377312 TGCGTTGCAGCTAAAATATCATATATA 57.623 29.630 0.00 0.00 38.13 0.86
2802 3469 4.338400 AGCTAGCGTCAAGGTTTTCTTTTT 59.662 37.500 9.55 0.00 32.41 1.94
2832 3499 2.619646 GTCTTTTTAACGAAGGTGCCCA 59.380 45.455 0.00 0.00 0.00 5.36
2874 3541 6.992715 AGGAATACGGGAAATCTCATGTTTAG 59.007 38.462 0.00 0.00 0.00 1.85
2878 3545 3.001330 CGGGAAATCTCATGTTTAGTCGC 59.999 47.826 0.00 0.00 0.00 5.19
2913 3592 4.143543 AGCAAAAATTTGTTGGGAATGGG 58.856 39.130 7.64 0.00 40.24 4.00
2934 3613 9.445973 AATGGGATAAATTTATTTAGGCCTTCA 57.554 29.630 12.58 0.00 35.88 3.02
2935 3614 9.619842 ATGGGATAAATTTATTTAGGCCTTCAT 57.380 29.630 12.58 6.02 35.88 2.57
2936 3615 9.088987 TGGGATAAATTTATTTAGGCCTTCATC 57.911 33.333 12.58 0.00 35.88 2.92
2963 3642 0.732880 CGCGTCAGTAGGAACCTGTG 60.733 60.000 0.00 1.65 0.00 3.66
3099 3809 8.199449 CAGGCACAAGATCCATTGTTTATATTT 58.801 33.333 0.00 0.00 41.41 1.40
3142 3853 6.100714 ACTTGACAGGGGAGTAAGAAACTTTA 59.899 38.462 0.00 0.00 39.07 1.85
3166 3884 0.396435 AAATCACAGGCACGAGACCA 59.604 50.000 0.00 0.00 0.00 4.02
3174 3892 4.079253 ACAGGCACGAGACCAATTTTTAT 58.921 39.130 0.00 0.00 0.00 1.40
3178 3896 4.857037 GGCACGAGACCAATTTTTATGTTC 59.143 41.667 0.00 0.00 0.00 3.18
3194 3912 7.510675 TTTATGTTCTTCTTCCTCATAGGGT 57.489 36.000 0.00 0.00 35.59 4.34
3217 3935 2.880890 ACTTGGCAGTGACAGTCAAATC 59.119 45.455 4.32 0.00 29.12 2.17
3218 3936 2.936919 TGGCAGTGACAGTCAAATCT 57.063 45.000 4.32 0.00 0.00 2.40
3219 3937 3.213206 TGGCAGTGACAGTCAAATCTT 57.787 42.857 4.32 0.00 0.00 2.40
3221 3939 3.316029 TGGCAGTGACAGTCAAATCTTTG 59.684 43.478 4.32 0.00 39.48 2.77
3222 3940 3.303406 GCAGTGACAGTCAAATCTTTGC 58.697 45.455 4.32 5.41 38.05 3.68
3223 3941 3.243168 GCAGTGACAGTCAAATCTTTGCA 60.243 43.478 4.32 0.00 38.05 4.08
3224 3942 4.734402 GCAGTGACAGTCAAATCTTTGCAA 60.734 41.667 4.32 0.00 38.05 4.08
3250 3968 3.963428 AGTCATAGACACAGGACCAAC 57.037 47.619 0.00 0.00 34.60 3.77
3251 3969 3.239449 AGTCATAGACACAGGACCAACA 58.761 45.455 0.00 0.00 34.60 3.33
3252 3970 3.840666 AGTCATAGACACAGGACCAACAT 59.159 43.478 0.00 0.00 34.60 2.71
3253 3971 5.023452 AGTCATAGACACAGGACCAACATA 58.977 41.667 0.00 0.00 34.60 2.29
3254 3972 5.663106 AGTCATAGACACAGGACCAACATAT 59.337 40.000 0.00 0.00 34.60 1.78
3255 3973 5.755375 GTCATAGACACAGGACCAACATATG 59.245 44.000 0.00 0.00 32.09 1.78
3256 3974 2.991250 AGACACAGGACCAACATATGC 58.009 47.619 1.58 0.00 0.00 3.14
3257 3975 2.573462 AGACACAGGACCAACATATGCT 59.427 45.455 1.58 0.00 0.00 3.79
3258 3976 3.774766 AGACACAGGACCAACATATGCTA 59.225 43.478 1.58 0.00 0.00 3.49
3259 3977 3.871594 GACACAGGACCAACATATGCTAC 59.128 47.826 1.58 0.00 0.00 3.58
3260 3978 3.206150 CACAGGACCAACATATGCTACC 58.794 50.000 1.58 0.10 0.00 3.18
3261 3979 2.172717 ACAGGACCAACATATGCTACCC 59.827 50.000 1.58 0.00 0.00 3.69
3262 3980 2.172505 CAGGACCAACATATGCTACCCA 59.827 50.000 1.58 0.00 0.00 4.51
3263 3981 2.849943 AGGACCAACATATGCTACCCAA 59.150 45.455 1.58 0.00 0.00 4.12
3264 3982 3.268334 AGGACCAACATATGCTACCCAAA 59.732 43.478 1.58 0.00 0.00 3.28
3265 3983 3.380320 GGACCAACATATGCTACCCAAAC 59.620 47.826 1.58 0.00 0.00 2.93
3266 3984 4.270008 GACCAACATATGCTACCCAAACT 58.730 43.478 1.58 0.00 0.00 2.66
3267 3985 4.672899 ACCAACATATGCTACCCAAACTT 58.327 39.130 1.58 0.00 0.00 2.66
3268 3986 4.462483 ACCAACATATGCTACCCAAACTTG 59.538 41.667 1.58 0.00 0.00 3.16
3269 3987 4.423732 CAACATATGCTACCCAAACTTGC 58.576 43.478 1.58 0.00 0.00 4.01
3270 3988 3.023832 ACATATGCTACCCAAACTTGCC 58.976 45.455 1.58 0.00 0.00 4.52
3271 3989 2.889170 TATGCTACCCAAACTTGCCA 57.111 45.000 0.00 0.00 0.00 4.92
3272 3990 2.236489 ATGCTACCCAAACTTGCCAT 57.764 45.000 0.00 0.00 0.00 4.40
3273 3991 2.008242 TGCTACCCAAACTTGCCATT 57.992 45.000 0.00 0.00 0.00 3.16
3274 3992 2.324541 TGCTACCCAAACTTGCCATTT 58.675 42.857 0.00 0.00 0.00 2.32
3275 3993 2.298729 TGCTACCCAAACTTGCCATTTC 59.701 45.455 0.00 0.00 0.00 2.17
3276 3994 2.298729 GCTACCCAAACTTGCCATTTCA 59.701 45.455 0.00 0.00 0.00 2.69
3277 3995 3.244044 GCTACCCAAACTTGCCATTTCAA 60.244 43.478 0.00 0.00 0.00 2.69
3278 3996 3.473923 ACCCAAACTTGCCATTTCAAG 57.526 42.857 2.33 2.33 46.57 3.02
3288 4006 6.140303 CTTGCCATTTCAAGTATATGCACT 57.860 37.500 0.00 0.00 38.81 4.40
3289 4007 5.503662 TGCCATTTCAAGTATATGCACTG 57.496 39.130 0.00 0.00 0.00 3.66
3290 4008 4.338964 TGCCATTTCAAGTATATGCACTGG 59.661 41.667 0.00 0.00 0.00 4.00
3291 4009 4.339247 GCCATTTCAAGTATATGCACTGGT 59.661 41.667 0.00 0.00 0.00 4.00
3292 4010 5.530915 GCCATTTCAAGTATATGCACTGGTA 59.469 40.000 0.00 0.00 0.00 3.25
3293 4011 6.207417 GCCATTTCAAGTATATGCACTGGTAT 59.793 38.462 0.00 0.00 0.00 2.73
3294 4012 7.390440 GCCATTTCAAGTATATGCACTGGTATA 59.610 37.037 0.00 0.00 0.00 1.47
3295 4013 9.453572 CCATTTCAAGTATATGCACTGGTATAT 57.546 33.333 0.00 0.00 36.46 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.505272 ACGCAATTTAGTCCTAGATACACTC 58.495 40.000 0.00 0.00 0.00 3.51
1 2 6.321690 AGACGCAATTTAGTCCTAGATACACT 59.678 38.462 6.47 0.00 38.08 3.55
2 3 6.505272 AGACGCAATTTAGTCCTAGATACAC 58.495 40.000 6.47 0.00 38.08 2.90
3 4 6.710597 AGACGCAATTTAGTCCTAGATACA 57.289 37.500 6.47 0.00 38.08 2.29
4 5 8.097078 TCTAGACGCAATTTAGTCCTAGATAC 57.903 38.462 6.47 0.00 38.08 2.24
5 6 8.865420 ATCTAGACGCAATTTAGTCCTAGATA 57.135 34.615 17.99 4.53 36.82 1.98
6 7 7.768807 ATCTAGACGCAATTTAGTCCTAGAT 57.231 36.000 0.00 16.08 38.08 1.98
7 8 7.718314 TGTATCTAGACGCAATTTAGTCCTAGA 59.282 37.037 0.00 0.00 38.08 2.43
8 9 7.872881 TGTATCTAGACGCAATTTAGTCCTAG 58.127 38.462 0.00 0.00 38.08 3.02
9 10 7.812690 TGTATCTAGACGCAATTTAGTCCTA 57.187 36.000 0.00 0.00 38.08 2.94
10 11 6.710597 TGTATCTAGACGCAATTTAGTCCT 57.289 37.500 0.00 0.00 38.08 3.85
11 12 7.371936 AGATGTATCTAGACGCAATTTAGTCC 58.628 38.462 0.00 0.00 38.08 3.85
16 17 9.935241 ATGAATAGATGTATCTAGACGCAATTT 57.065 29.630 0.00 0.00 42.20 1.82
17 18 9.579768 GATGAATAGATGTATCTAGACGCAATT 57.420 33.333 0.00 0.00 42.20 2.32
18 19 8.194104 GGATGAATAGATGTATCTAGACGCAAT 58.806 37.037 0.00 0.00 42.20 3.56
19 20 7.539436 GGATGAATAGATGTATCTAGACGCAA 58.461 38.462 0.00 0.00 42.20 4.85
20 21 6.183360 CGGATGAATAGATGTATCTAGACGCA 60.183 42.308 0.00 0.00 42.20 5.24
21 22 6.195868 CGGATGAATAGATGTATCTAGACGC 58.804 44.000 0.00 0.00 42.20 5.19
22 23 6.183360 TGCGGATGAATAGATGTATCTAGACG 60.183 42.308 0.00 6.55 42.20 4.18
23 24 7.089770 TGCGGATGAATAGATGTATCTAGAC 57.910 40.000 0.00 5.01 42.20 2.59
24 25 7.394641 ACTTGCGGATGAATAGATGTATCTAGA 59.605 37.037 7.57 0.00 42.20 2.43
25 26 7.542890 ACTTGCGGATGAATAGATGTATCTAG 58.457 38.462 7.57 0.00 42.20 2.43
26 27 7.468141 ACTTGCGGATGAATAGATGTATCTA 57.532 36.000 4.22 4.22 43.00 1.98
27 28 6.352016 ACTTGCGGATGAATAGATGTATCT 57.648 37.500 0.00 0.00 40.86 1.98
28 29 8.709386 AATACTTGCGGATGAATAGATGTATC 57.291 34.615 0.00 0.00 0.00 2.24
29 30 9.507329 AAAATACTTGCGGATGAATAGATGTAT 57.493 29.630 0.00 0.00 0.00 2.29
30 31 8.902540 AAAATACTTGCGGATGAATAGATGTA 57.097 30.769 0.00 0.00 0.00 2.29
31 32 7.307396 CGAAAATACTTGCGGATGAATAGATGT 60.307 37.037 0.00 0.00 29.05 3.06
32 33 7.011773 CGAAAATACTTGCGGATGAATAGATG 58.988 38.462 0.00 0.00 29.05 2.90
33 34 7.121974 CGAAAATACTTGCGGATGAATAGAT 57.878 36.000 0.00 0.00 29.05 1.98
34 35 6.525121 CGAAAATACTTGCGGATGAATAGA 57.475 37.500 0.00 0.00 29.05 1.98
44 45 1.323534 CTCCGTCCGAAAATACTTGCG 59.676 52.381 0.00 0.00 32.90 4.85
45 46 1.664151 CCTCCGTCCGAAAATACTTGC 59.336 52.381 0.00 0.00 0.00 4.01
46 47 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
47 48 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
48 49 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
49 50 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
50 51 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
51 52 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
52 53 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
53 54 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
54 55 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
55 56 0.839277 TATGTACTCCCTCCGTCCGA 59.161 55.000 0.00 0.00 0.00 4.55
56 57 1.236628 CTATGTACTCCCTCCGTCCG 58.763 60.000 0.00 0.00 0.00 4.79
57 58 2.361643 ACTATGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
58 59 2.813172 GCTACTATGTACTCCCTCCGTC 59.187 54.545 0.00 0.00 0.00 4.79
59 60 2.442502 AGCTACTATGTACTCCCTCCGT 59.557 50.000 0.00 0.00 0.00 4.69
60 61 3.143211 AGCTACTATGTACTCCCTCCG 57.857 52.381 0.00 0.00 0.00 4.63
61 62 4.011698 GCTAGCTACTATGTACTCCCTCC 58.988 52.174 7.70 0.00 0.00 4.30
62 63 4.913784 AGCTAGCTACTATGTACTCCCTC 58.086 47.826 17.69 0.00 0.00 4.30
63 64 5.786457 TCTAGCTAGCTACTATGTACTCCCT 59.214 44.000 20.67 0.00 0.00 4.20
64 65 6.052405 TCTAGCTAGCTACTATGTACTCCC 57.948 45.833 20.67 0.00 0.00 4.30
65 66 7.414762 GCATTCTAGCTAGCTACTATGTACTCC 60.415 44.444 26.65 15.18 0.00 3.85
66 67 7.414762 GGCATTCTAGCTAGCTACTATGTACTC 60.415 44.444 26.65 17.18 34.17 2.59
67 68 6.376018 GGCATTCTAGCTAGCTACTATGTACT 59.624 42.308 26.65 6.99 34.17 2.73
72 73 6.013379 TGAAGGCATTCTAGCTAGCTACTAT 58.987 40.000 20.67 13.16 36.33 2.12
147 148 1.970917 GCCAGTCATCCGCTTGTTCG 61.971 60.000 0.00 0.00 0.00 3.95
185 186 6.967135 TCATATCATAGTGACCGTCAGTTAC 58.033 40.000 14.05 0.00 35.23 2.50
189 190 7.094592 ACTGTATCATATCATAGTGACCGTCAG 60.095 40.741 0.08 0.00 0.00 3.51
192 193 6.715264 TCACTGTATCATATCATAGTGACCGT 59.285 38.462 0.00 0.00 39.46 4.83
194 195 8.031864 CCTTCACTGTATCATATCATAGTGACC 58.968 40.741 0.00 0.00 42.74 4.02
195 196 8.580720 ACCTTCACTGTATCATATCATAGTGAC 58.419 37.037 0.00 0.00 42.74 3.67
196 197 8.579863 CACCTTCACTGTATCATATCATAGTGA 58.420 37.037 0.00 0.00 41.73 3.41
197 198 7.330454 GCACCTTCACTGTATCATATCATAGTG 59.670 40.741 0.00 0.00 37.47 2.74
198 199 7.015584 TGCACCTTCACTGTATCATATCATAGT 59.984 37.037 0.00 0.00 0.00 2.12
199 200 7.381323 TGCACCTTCACTGTATCATATCATAG 58.619 38.462 0.00 0.00 0.00 2.23
200 201 7.301868 TGCACCTTCACTGTATCATATCATA 57.698 36.000 0.00 0.00 0.00 2.15
201 202 6.178607 TGCACCTTCACTGTATCATATCAT 57.821 37.500 0.00 0.00 0.00 2.45
202 203 5.612725 TGCACCTTCACTGTATCATATCA 57.387 39.130 0.00 0.00 0.00 2.15
203 204 6.146837 GTGATGCACCTTCACTGTATCATATC 59.853 42.308 10.94 0.00 41.12 1.63
204 205 5.994054 GTGATGCACCTTCACTGTATCATAT 59.006 40.000 10.94 0.00 41.12 1.78
259 260 3.750652 TGCAAGATCGACATGCTACAAAA 59.249 39.130 16.76 0.00 42.68 2.44
263 264 1.863454 CCTGCAAGATCGACATGCTAC 59.137 52.381 16.76 0.00 42.68 3.58
306 340 5.873146 AATTAGCTAGGGTGGTTAGAGAC 57.127 43.478 0.00 0.00 0.00 3.36
310 344 6.164176 CGGAATAATTAGCTAGGGTGGTTAG 58.836 44.000 0.00 0.00 0.00 2.34
312 346 4.745783 GCGGAATAATTAGCTAGGGTGGTT 60.746 45.833 0.00 0.00 0.00 3.67
313 347 3.244457 GCGGAATAATTAGCTAGGGTGGT 60.244 47.826 0.00 0.00 0.00 4.16
314 348 3.335579 GCGGAATAATTAGCTAGGGTGG 58.664 50.000 0.00 0.00 0.00 4.61
315 349 3.244422 TGGCGGAATAATTAGCTAGGGTG 60.244 47.826 0.00 0.00 0.00 4.61
316 350 2.976882 TGGCGGAATAATTAGCTAGGGT 59.023 45.455 0.00 0.00 0.00 4.34
330 369 1.003118 AGTGACAGCTTAATGGCGGAA 59.997 47.619 0.00 0.00 37.29 4.30
339 378 4.663334 TCTAGGAGTTGAGTGACAGCTTA 58.337 43.478 0.00 0.00 40.02 3.09
369 408 8.178964 TGATTAACGGATTTTGGAATAGTTTCG 58.821 33.333 0.00 0.00 32.26 3.46
393 432 5.218959 TCAAGAATGGAGACCTGGATATGA 58.781 41.667 0.00 0.00 0.00 2.15
415 454 9.729023 CAGATCAAGATCACGTAGGATATTATC 57.271 37.037 12.21 0.00 40.22 1.75
428 467 6.203723 GGGCATAGTTTACAGATCAAGATCAC 59.796 42.308 12.21 1.85 40.22 3.06
439 478 1.134907 ACGGTCGGGCATAGTTTACAG 60.135 52.381 0.00 0.00 0.00 2.74
440 479 0.896923 ACGGTCGGGCATAGTTTACA 59.103 50.000 0.00 0.00 0.00 2.41
442 481 1.065401 CGTACGGTCGGGCATAGTTTA 59.935 52.381 7.57 0.00 0.00 2.01
457 496 4.973396 TCACCTGTTAATCAGTACGTACG 58.027 43.478 19.49 15.01 42.19 3.67
458 497 7.823149 AATTCACCTGTTAATCAGTACGTAC 57.177 36.000 18.10 18.10 42.19 3.67
486 525 9.268282 TGGAGAAACCAGAAGATTAGTACTAAT 57.732 33.333 24.86 24.86 44.64 1.73
487 526 8.660295 TGGAGAAACCAGAAGATTAGTACTAA 57.340 34.615 17.41 17.41 44.64 2.24
533 572 3.270877 GTGAAGCCGACTGATTATTGGT 58.729 45.455 0.00 0.00 0.00 3.67
547 586 1.594331 ACTGTTTTCTCGGTGAAGCC 58.406 50.000 0.00 0.00 35.89 4.35
558 597 1.001633 TGACCGGGCTCTACTGTTTTC 59.998 52.381 9.82 0.00 0.00 2.29
571 611 3.121030 CGCAAAGAGCTGACCGGG 61.121 66.667 6.32 0.00 42.61 5.73
632 672 0.869068 TAACCAACGGCGACATGTTG 59.131 50.000 16.62 8.88 43.88 3.33
691 731 0.518636 ATAATGCATGCATCGACGGC 59.481 50.000 32.25 0.00 35.31 5.68
713 753 4.329392 CCTACCGTTGTGATAAAAGGGTT 58.671 43.478 5.92 0.00 41.73 4.11
716 756 2.681344 GGCCTACCGTTGTGATAAAAGG 59.319 50.000 0.00 0.00 35.12 3.11
781 821 5.727791 GCTTACAAATGTGGATCGACATGTC 60.728 44.000 22.13 16.21 36.66 3.06
796 836 3.391965 TGGACGTACGTTGCTTACAAAT 58.608 40.909 23.70 0.00 37.58 2.32
817 857 1.153939 CGACAAGTCGCAGCTAGCT 60.154 57.895 12.68 12.68 46.50 3.32
837 877 3.054875 TCTGATCCTCAATTCCACACAGG 60.055 47.826 0.00 0.00 39.47 4.00
851 891 2.824936 CCACATAGCTCGATCTGATCCT 59.175 50.000 11.84 6.17 0.00 3.24
870 910 1.594194 CCGGTGCAATTTGCTAGCCA 61.594 55.000 21.19 0.00 45.31 4.75
910 950 4.092968 CGCTCCAAGGTATTTATAATCGGC 59.907 45.833 0.00 0.00 0.00 5.54
969 1010 1.527844 GCAGCAGATGGATGGACCC 60.528 63.158 0.00 0.00 38.00 4.46
971 1012 0.179702 TCTGCAGCAGATGGATGGAC 59.820 55.000 21.85 0.00 35.39 4.02
1107 1184 1.338107 TGACGATGTGTTCCAGGTCT 58.662 50.000 0.00 0.00 33.71 3.85
1256 1371 9.363401 ACTCCTACATATACTTACATGCTAACA 57.637 33.333 0.00 0.00 0.00 2.41
1274 1389 8.870116 ACTCATGCATACATAATTACTCCTACA 58.130 33.333 0.00 0.00 33.67 2.74
1277 1392 9.881649 CATACTCATGCATACATAATTACTCCT 57.118 33.333 0.00 0.00 33.67 3.69
1278 1393 9.875691 TCATACTCATGCATACATAATTACTCC 57.124 33.333 0.00 0.00 33.67 3.85
1281 1473 9.926751 GCATCATACTCATGCATACATAATTAC 57.073 33.333 0.00 0.00 45.19 1.89
1298 1490 9.060347 CAGTAAATAAGGAACATGCATCATACT 57.940 33.333 0.00 0.00 0.00 2.12
1302 1494 7.176515 ACAACAGTAAATAAGGAACATGCATCA 59.823 33.333 0.00 0.00 0.00 3.07
1303 1495 7.538575 ACAACAGTAAATAAGGAACATGCATC 58.461 34.615 0.00 0.00 0.00 3.91
1304 1496 7.466746 ACAACAGTAAATAAGGAACATGCAT 57.533 32.000 0.00 0.00 0.00 3.96
1307 1499 7.144661 TGCAACAACAGTAAATAAGGAACATG 58.855 34.615 0.00 0.00 0.00 3.21
1311 1503 5.242838 CCCTGCAACAACAGTAAATAAGGAA 59.757 40.000 0.00 0.00 35.83 3.36
1313 1505 4.618227 GCCCTGCAACAACAGTAAATAAGG 60.618 45.833 0.00 0.00 35.83 2.69
1314 1506 4.218417 AGCCCTGCAACAACAGTAAATAAG 59.782 41.667 0.00 0.00 35.83 1.73
1380 1725 3.727258 TCAGGTTGGGCCCCATCG 61.727 66.667 22.27 5.42 38.26 3.84
1566 1911 8.086522 CAGATTTGGATAATTGGATTGATGGTC 58.913 37.037 0.00 0.00 0.00 4.02
1567 1912 7.785985 TCAGATTTGGATAATTGGATTGATGGT 59.214 33.333 0.00 0.00 0.00 3.55
1568 1913 8.185506 TCAGATTTGGATAATTGGATTGATGG 57.814 34.615 0.00 0.00 0.00 3.51
1570 1915 8.857098 CACTCAGATTTGGATAATTGGATTGAT 58.143 33.333 0.00 0.00 0.00 2.57
1571 1916 7.201848 GCACTCAGATTTGGATAATTGGATTGA 60.202 37.037 0.00 0.00 0.00 2.57
1572 1917 6.921857 GCACTCAGATTTGGATAATTGGATTG 59.078 38.462 0.00 0.00 0.00 2.67
1573 1918 6.837568 AGCACTCAGATTTGGATAATTGGATT 59.162 34.615 0.00 0.00 0.00 3.01
1575 1920 5.759059 AGCACTCAGATTTGGATAATTGGA 58.241 37.500 0.00 0.00 0.00 3.53
1576 1921 5.591472 TGAGCACTCAGATTTGGATAATTGG 59.409 40.000 0.00 0.00 34.14 3.16
1577 1922 6.688637 TGAGCACTCAGATTTGGATAATTG 57.311 37.500 0.00 0.00 34.14 2.32
1597 1942 5.068636 CCAGGAATAACCATCCAATCTGAG 58.931 45.833 0.00 0.00 42.04 3.35
1937 2331 3.061848 GCCTTTAGCTTGGCGGCA 61.062 61.111 7.97 7.97 39.71 5.69
2093 2487 4.920112 CGCGTGGTGTTGGGGTGA 62.920 66.667 0.00 0.00 0.00 4.02
2268 2662 0.179045 GCATGGCCCTCGTTACTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2269 2663 1.220749 GCATGGCCCTCGTTACTCA 59.779 57.895 0.00 0.00 0.00 3.41
2270 2664 1.523938 GGCATGGCCCTCGTTACTC 60.524 63.158 8.35 0.00 44.06 2.59
2338 2733 0.676736 TGATGGTAGCACACACGTGA 59.323 50.000 25.01 0.00 46.80 4.35
2340 2736 1.001974 ACATGATGGTAGCACACACGT 59.998 47.619 0.00 0.00 0.00 4.49
2341 2737 1.660607 GACATGATGGTAGCACACACG 59.339 52.381 0.00 0.00 0.00 4.49
2353 2749 0.106369 ACCAGCCCCATGACATGATG 60.106 55.000 17.24 8.22 0.00 3.07
2357 2753 1.803453 AACCACCAGCCCCATGACAT 61.803 55.000 0.00 0.00 0.00 3.06
2366 2762 2.200373 ATTACACAGAACCACCAGCC 57.800 50.000 0.00 0.00 0.00 4.85
2370 2766 6.569179 ACATTACAATTACACAGAACCACC 57.431 37.500 0.00 0.00 0.00 4.61
2406 2802 3.369892 GGCATGGTGTCTGATCACTTACT 60.370 47.826 0.00 0.00 38.28 2.24
2407 2803 2.939103 GGCATGGTGTCTGATCACTTAC 59.061 50.000 0.00 0.00 38.28 2.34
2408 2804 2.092968 GGGCATGGTGTCTGATCACTTA 60.093 50.000 0.00 2.41 38.28 2.24
2409 2805 1.340405 GGGCATGGTGTCTGATCACTT 60.340 52.381 0.00 0.00 38.28 3.16
2422 2818 4.240881 AGCATATATACTTGGGGCATGG 57.759 45.455 0.00 0.00 0.00 3.66
2446 2842 3.270877 GGCACACAACCTCCTATTGTAG 58.729 50.000 0.00 0.00 38.22 2.74
2447 2843 2.354303 CGGCACACAACCTCCTATTGTA 60.354 50.000 0.00 0.00 38.22 2.41
2448 2844 1.610624 CGGCACACAACCTCCTATTGT 60.611 52.381 0.00 0.00 40.95 2.71
2449 2845 1.086696 CGGCACACAACCTCCTATTG 58.913 55.000 0.00 0.00 0.00 1.90
2450 2846 0.035439 CCGGCACACAACCTCCTATT 60.035 55.000 0.00 0.00 0.00 1.73
2453 2849 2.279037 AAACCGGCACACAACCTCCT 62.279 55.000 0.00 0.00 0.00 3.69
2454 2850 1.826487 AAACCGGCACACAACCTCC 60.826 57.895 0.00 0.00 0.00 4.30
2456 2852 1.077357 TCAAACCGGCACACAACCT 60.077 52.632 0.00 0.00 0.00 3.50
2458 2854 1.299089 GCTCAAACCGGCACACAAC 60.299 57.895 0.00 0.00 0.00 3.32
2459 2855 1.106351 ATGCTCAAACCGGCACACAA 61.106 50.000 0.00 0.00 41.39 3.33
2460 2856 1.106351 AATGCTCAAACCGGCACACA 61.106 50.000 0.00 0.00 41.39 3.72
2461 2857 0.878416 TAATGCTCAAACCGGCACAC 59.122 50.000 0.00 0.00 41.39 3.82
2462 2858 1.610363 TTAATGCTCAAACCGGCACA 58.390 45.000 0.00 0.00 41.39 4.57
2463 2859 2.939460 ATTAATGCTCAAACCGGCAC 57.061 45.000 0.00 0.00 41.39 5.01
2464 2860 5.126779 TGTATATTAATGCTCAAACCGGCA 58.873 37.500 0.00 0.00 42.80 5.69
2465 2861 5.468746 TCTGTATATTAATGCTCAAACCGGC 59.531 40.000 0.00 0.00 0.00 6.13
2466 2862 6.346598 CGTCTGTATATTAATGCTCAAACCGG 60.347 42.308 0.00 0.00 0.00 5.28
2467 2863 6.200286 ACGTCTGTATATTAATGCTCAAACCG 59.800 38.462 0.00 0.00 0.00 4.44
2468 2864 7.478520 ACGTCTGTATATTAATGCTCAAACC 57.521 36.000 0.00 0.00 0.00 3.27
2469 2865 7.373441 GCAACGTCTGTATATTAATGCTCAAAC 59.627 37.037 0.00 0.00 0.00 2.93
2470 2866 7.065204 TGCAACGTCTGTATATTAATGCTCAAA 59.935 33.333 0.00 0.00 32.74 2.69
2472 2868 6.045955 TGCAACGTCTGTATATTAATGCTCA 58.954 36.000 0.00 0.00 32.74 4.26
2474 2870 6.280643 TCTGCAACGTCTGTATATTAATGCT 58.719 36.000 0.00 0.00 32.74 3.79
2475 2871 6.525121 TCTGCAACGTCTGTATATTAATGC 57.475 37.500 0.00 0.00 0.00 3.56
2476 2872 7.326063 TCGATCTGCAACGTCTGTATATTAATG 59.674 37.037 0.00 0.00 0.00 1.90
2478 2874 6.731164 TCGATCTGCAACGTCTGTATATTAA 58.269 36.000 0.00 0.00 0.00 1.40
2481 2877 4.830826 TCGATCTGCAACGTCTGTATAT 57.169 40.909 0.00 0.00 0.00 0.86
2482 2878 4.515567 AGATCGATCTGCAACGTCTGTATA 59.484 41.667 26.78 0.00 35.42 1.47
2483 2879 3.316588 AGATCGATCTGCAACGTCTGTAT 59.683 43.478 26.78 0.00 35.42 2.29
2484 2880 2.683362 AGATCGATCTGCAACGTCTGTA 59.317 45.455 26.78 0.00 35.42 2.74
2485 2881 1.474478 AGATCGATCTGCAACGTCTGT 59.526 47.619 26.78 0.00 35.42 3.41
2486 2882 2.200792 AGATCGATCTGCAACGTCTG 57.799 50.000 26.78 0.00 35.42 3.51
2487 2883 2.949451 AAGATCGATCTGCAACGTCT 57.051 45.000 27.93 7.42 37.19 4.18
2520 3165 2.572095 CTACCGGCGAGCATTGTCCA 62.572 60.000 9.30 0.00 0.00 4.02
2526 3171 4.227134 CAGGCTACCGGCGAGCAT 62.227 66.667 25.60 18.66 41.98 3.79
2536 3190 3.635510 CCTCACTCCCCAGGCTAC 58.364 66.667 0.00 0.00 0.00 3.58
2555 3209 0.341258 TGCCTTCTCATCCTCTCCCT 59.659 55.000 0.00 0.00 0.00 4.20
2572 3227 3.467803 ACGGATCTTTTAGGTAGCATGC 58.532 45.455 10.51 10.51 0.00 4.06
2591 3246 0.802994 TAAGTATTGTGGCCGCGACG 60.803 55.000 8.85 0.00 0.00 5.12
2637 3298 2.255252 GCAACGCACGGCAAATCT 59.745 55.556 0.00 0.00 0.00 2.40
2640 3301 4.921847 GCTGCAACGCACGGCAAA 62.922 61.111 0.00 0.00 39.93 3.68
2645 3306 2.519002 TATTTTAGCTGCAACGCACG 57.481 45.000 1.02 0.00 33.79 5.34
2670 3331 4.119556 AGCTAGCCAGAGGATGTGTATA 57.880 45.455 12.13 0.00 0.00 1.47
2671 3332 2.969628 AGCTAGCCAGAGGATGTGTAT 58.030 47.619 12.13 0.00 0.00 2.29
2672 3333 2.461300 AGCTAGCCAGAGGATGTGTA 57.539 50.000 12.13 0.00 0.00 2.90
2673 3334 2.035632 GTAGCTAGCCAGAGGATGTGT 58.964 52.381 12.13 0.00 0.00 3.72
2676 3337 3.827008 TTTGTAGCTAGCCAGAGGATG 57.173 47.619 12.13 0.00 0.00 3.51
2684 3345 5.220381 GGTTTGAAGTTTTTGTAGCTAGCC 58.780 41.667 12.13 0.00 0.00 3.93
2802 3469 6.038492 ACCTTCGTTAAAAAGACCGAAATGAA 59.962 34.615 0.00 0.00 38.66 2.57
2810 3477 3.278367 GGCACCTTCGTTAAAAAGACC 57.722 47.619 1.37 0.00 0.00 3.85
2851 3518 7.306632 CGACTAAACATGAGATTTCCCGTATTC 60.307 40.741 0.00 0.00 0.00 1.75
2892 3559 4.140536 TCCCATTCCCAACAAATTTTTGC 58.859 39.130 3.00 0.00 41.79 3.68
2905 3584 7.457852 AGGCCTAAATAAATTTATCCCATTCCC 59.542 37.037 1.29 6.65 32.36 3.97
2934 3613 1.966901 TACTGACGCGGCCCATTGAT 61.967 55.000 10.82 0.00 0.00 2.57
2935 3614 2.572095 CTACTGACGCGGCCCATTGA 62.572 60.000 10.82 0.00 0.00 2.57
2936 3615 2.125310 TACTGACGCGGCCCATTG 60.125 61.111 10.82 0.00 0.00 2.82
2963 3642 2.781646 CGAACTCGAAAGTTTGGCAAAC 59.218 45.455 30.67 30.67 45.80 2.93
3108 3818 0.400213 CCCTGTCAAGTGGCCTTACA 59.600 55.000 3.32 0.02 0.00 2.41
3112 3822 2.121963 TCCCCTGTCAAGTGGCCT 60.122 61.111 3.32 0.00 0.00 5.19
3161 3879 8.712228 AGGAAGAAGAACATAAAAATTGGTCT 57.288 30.769 0.00 0.00 42.90 3.85
3174 3892 4.223032 GTGACCCTATGAGGAAGAAGAACA 59.777 45.833 0.00 0.00 37.67 3.18
3178 3896 4.383552 CCAAGTGACCCTATGAGGAAGAAG 60.384 50.000 0.00 0.00 37.67 2.85
3229 3947 3.646162 TGTTGGTCCTGTGTCTATGACTT 59.354 43.478 0.00 0.00 33.15 3.01
3231 3949 3.678056 TGTTGGTCCTGTGTCTATGAC 57.322 47.619 0.00 0.00 0.00 3.06
3235 3953 3.774766 AGCATATGTTGGTCCTGTGTCTA 59.225 43.478 4.29 0.00 0.00 2.59
3242 3960 2.487775 TGGGTAGCATATGTTGGTCCT 58.512 47.619 4.29 0.00 37.26 3.85
3245 3963 4.316025 AGTTTGGGTAGCATATGTTGGT 57.684 40.909 4.29 0.00 39.88 3.67
3250 3968 3.023119 TGGCAAGTTTGGGTAGCATATG 58.977 45.455 0.00 0.00 0.00 1.78
3251 3969 3.380471 TGGCAAGTTTGGGTAGCATAT 57.620 42.857 0.00 0.00 0.00 1.78
3252 3970 2.889170 TGGCAAGTTTGGGTAGCATA 57.111 45.000 0.00 0.00 0.00 3.14
3253 3971 2.236489 ATGGCAAGTTTGGGTAGCAT 57.764 45.000 0.00 0.00 0.00 3.79
3254 3972 2.008242 AATGGCAAGTTTGGGTAGCA 57.992 45.000 0.00 0.00 0.00 3.49
3255 3973 2.298729 TGAAATGGCAAGTTTGGGTAGC 59.701 45.455 0.00 0.00 0.00 3.58
3256 3974 4.559153 CTTGAAATGGCAAGTTTGGGTAG 58.441 43.478 0.00 0.00 40.22 3.18
3257 3975 4.599047 CTTGAAATGGCAAGTTTGGGTA 57.401 40.909 0.00 0.00 40.22 3.69
3258 3976 3.473923 CTTGAAATGGCAAGTTTGGGT 57.526 42.857 0.00 0.00 40.22 4.51
3265 3983 9.238319 ACCAGTGCATATACTTGAAATGGCAAG 62.238 40.741 1.40 0.00 42.97 4.01
3266 3984 5.163530 CCAGTGCATATACTTGAAATGGCAA 60.164 40.000 0.00 0.00 33.85 4.52
3267 3985 4.338964 CCAGTGCATATACTTGAAATGGCA 59.661 41.667 0.00 0.00 33.85 4.92
3268 3986 4.339247 ACCAGTGCATATACTTGAAATGGC 59.661 41.667 1.40 0.00 42.97 4.40
3269 3987 7.750229 ATACCAGTGCATATACTTGAAATGG 57.250 36.000 0.11 0.11 44.43 3.16
3272 3990 9.634163 CGTATATACCAGTGCATATACTTGAAA 57.366 33.333 20.08 0.00 37.99 2.69
3273 3991 8.248253 CCGTATATACCAGTGCATATACTTGAA 58.752 37.037 20.08 0.00 37.99 2.69
3274 3992 7.612633 TCCGTATATACCAGTGCATATACTTGA 59.387 37.037 20.08 16.03 37.99 3.02
3275 3993 7.768240 TCCGTATATACCAGTGCATATACTTG 58.232 38.462 20.08 14.84 37.99 3.16
3276 3994 7.949690 TCCGTATATACCAGTGCATATACTT 57.050 36.000 20.08 3.24 37.99 2.24


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

AutoCloner maintained by Alex Coulton.