Multiple sequence alignment - TraesCS2B01G035700

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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 TraesCS2B01G035700 chr2B 100.000 7856 0 0 1 7856 17143067 17150922 0.000000e+00 14508.0
1 TraesCS2B01G035700 chr2B 90.275 1090 104 2 6533 7622 17444683 17445770 0.000000e+00 1424.0
2 TraesCS2B01G035700 chr2B 88.144 1164 108 16 6533 7693 17502660 17501524 0.000000e+00 1358.0
3 TraesCS2B01G035700 chr2B 86.414 1163 131 11 6533 7694 17514683 17513547 0.000000e+00 1247.0
4 TraesCS2B01G035700 chr2B 86.114 893 113 5 6533 7422 17439609 17438725 0.000000e+00 952.0
5 TraesCS2B01G035700 chr2B 90.062 644 54 8 850 1485 17503297 17502656 0.000000e+00 826.0
6 TraesCS2B01G035700 chr2B 86.916 642 68 12 852 1485 17515312 17514679 0.000000e+00 706.0
7 TraesCS2B01G035700 chr2B 86.356 601 72 7 890 1485 17440200 17439605 0.000000e+00 647.0
8 TraesCS2B01G035700 chr2B 87.525 505 49 7 6940 7443 17094640 17094149 9.430000e-159 571.0
9 TraesCS2B01G035700 chr2B 87.119 427 55 0 1059 1485 17444261 17444687 1.260000e-132 484.0
10 TraesCS2B01G035700 chr2B 100.000 205 0 0 8174 8378 17151240 17151444 6.140000e-101 379.0
11 TraesCS2B01G035700 chr2B 96.020 201 8 0 8178 8378 17445943 17446143 2.250000e-85 327.0
12 TraesCS2B01G035700 chr2B 92.857 140 10 0 7717 7856 17445793 17445932 3.960000e-48 204.0
13 TraesCS2B01G035700 chr5D 93.414 5071 276 28 1486 6532 515096299 515101335 0.000000e+00 7461.0
14 TraesCS2B01G035700 chr5D 94.712 851 41 4 5 852 282856717 282855868 0.000000e+00 1319.0
15 TraesCS2B01G035700 chr6B 92.928 5076 304 29 1486 6541 55691816 55686776 0.000000e+00 7334.0
16 TraesCS2B01G035700 chr6B 93.006 4990 263 33 1486 6457 718911895 718916816 0.000000e+00 7203.0
17 TraesCS2B01G035700 chr3D 92.691 5076 304 31 1486 6535 569837310 569842344 0.000000e+00 7256.0
18 TraesCS2B01G035700 chr4A 92.326 5082 309 34 1486 6543 641519222 641514198 0.000000e+00 7149.0
19 TraesCS2B01G035700 chr4A 75.036 685 134 26 6707 7365 712446394 712447067 4.950000e-72 283.0
20 TraesCS2B01G035700 chr4A 74.892 693 133 28 6707 7371 712112313 712111634 2.300000e-70 278.0
21 TraesCS2B01G035700 chr4A 73.598 731 158 23 6657 7365 687627405 687626688 1.810000e-61 248.0
22 TraesCS2B01G035700 chr4A 73.461 731 159 23 6657 7365 687661228 687660511 8.400000e-60 243.0
23 TraesCS2B01G035700 chr4A 73.324 731 160 22 6657 7365 687706943 687706226 3.910000e-58 237.0
24 TraesCS2B01G035700 chr1A 91.168 5084 370 33 1486 6532 100004427 100009468 0.000000e+00 6828.0
25 TraesCS2B01G035700 chr1A 91.951 3044 194 24 1486 4510 575873909 575876920 0.000000e+00 4217.0
26 TraesCS2B01G035700 chr1A 81.882 861 94 37 3 854 489447555 489448362 0.000000e+00 669.0
27 TraesCS2B01G035700 chr7D 90.999 5066 404 27 1486 6532 581264644 581269676 0.000000e+00 6782.0
28 TraesCS2B01G035700 chr7D 91.928 3543 233 26 3016 6536 636817104 636813593 0.000000e+00 4909.0
29 TraesCS2B01G035700 chr7D 85.198 858 100 18 3 854 53374996 53375832 0.000000e+00 856.0
30 TraesCS2B01G035700 chr7D 90.303 165 15 1 688 852 334924781 334924618 1.830000e-51 215.0
31 TraesCS2B01G035700 chr7D 91.111 45 3 1 7566 7610 568233170 568233213 9.080000e-05 60.2
32 TraesCS2B01G035700 chr2A 92.168 4022 263 24 1478 5477 720557786 720561777 0.000000e+00 5635.0
33 TraesCS2B01G035700 chr2A 93.107 2974 192 10 3564 6532 104993786 104990821 0.000000e+00 4344.0
34 TraesCS2B01G035700 chr2A 93.764 2678 158 6 3858 6532 17215074 17217745 0.000000e+00 4012.0
35 TraesCS2B01G035700 chr2A 93.876 1992 102 8 1486 3460 104997972 104995984 0.000000e+00 2985.0
36 TraesCS2B01G035700 chr2A 94.690 1902 92 6 1486 3383 17213179 17215075 0.000000e+00 2944.0
37 TraesCS2B01G035700 chr2A 89.394 924 86 7 6533 7454 11982735 11981822 0.000000e+00 1153.0
38 TraesCS2B01G035700 chr2A 88.906 649 59 13 847 1485 11983376 11982731 0.000000e+00 787.0
39 TraesCS2B01G035700 chr2A 87.391 460 44 7 6998 7454 11782637 11782189 4.480000e-142 516.0
40 TraesCS2B01G035700 chr2A 85.575 409 48 10 454 856 726976479 726976882 1.300000e-112 418.0
41 TraesCS2B01G035700 chr5B 88.954 4101 379 38 2476 6553 669885627 669889676 0.000000e+00 4996.0
42 TraesCS2B01G035700 chr2D 89.479 922 89 4 6533 7454 11327164 11326251 0.000000e+00 1158.0
43 TraesCS2B01G035700 chr2D 87.063 572 67 7 920 1485 11327730 11327160 2.550000e-179 640.0
44 TraesCS2B01G035700 chr6A 88.235 561 59 5 297 852 522416121 522416679 0.000000e+00 664.0
45 TraesCS2B01G035700 chr6A 87.805 369 38 6 5 369 146482473 146482838 7.770000e-115 425.0
46 TraesCS2B01G035700 chr6A 88.571 315 31 5 539 852 146483177 146483487 2.210000e-100 377.0
47 TraesCS2B01G035700 chr7B 87.569 362 38 7 496 854 743630910 743630553 6.050000e-111 412.0
48 TraesCS2B01G035700 chr3B 83.853 353 52 4 15 364 683022850 683023200 1.740000e-86 331.0
49 TraesCS2B01G035700 chr3B 89.552 201 18 2 652 850 683023552 683023751 1.400000e-62 252.0
50 TraesCS2B01G035700 chr3B 78.498 293 49 13 1006 1287 13905514 13905225 6.680000e-41 180.0
51 TraesCS2B01G035700 chr7A 74.674 691 129 28 6707 7365 22198755 22199431 1.790000e-66 265.0
52 TraesCS2B01G035700 chr1D 80.263 152 22 7 7550 7698 476593406 476593552 3.200000e-19 108.0


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 TraesCS2B01G035700 chr2B 17143067 17151444 8377 False 7443.50 14508 100.00000 1 8378 2 chr2B.!!$F1 8377
1 TraesCS2B01G035700 chr2B 17501524 17503297 1773 True 1092.00 1358 89.10300 850 7693 2 chr2B.!!$R3 6843
2 TraesCS2B01G035700 chr2B 17513547 17515312 1765 True 976.50 1247 86.66500 852 7694 2 chr2B.!!$R4 6842
3 TraesCS2B01G035700 chr2B 17438725 17440200 1475 True 799.50 952 86.23500 890 7422 2 chr2B.!!$R2 6532
4 TraesCS2B01G035700 chr2B 17444261 17446143 1882 False 609.75 1424 91.56775 1059 8378 4 chr2B.!!$F2 7319
5 TraesCS2B01G035700 chr5D 515096299 515101335 5036 False 7461.00 7461 93.41400 1486 6532 1 chr5D.!!$F1 5046
6 TraesCS2B01G035700 chr5D 282855868 282856717 849 True 1319.00 1319 94.71200 5 852 1 chr5D.!!$R1 847
7 TraesCS2B01G035700 chr6B 55686776 55691816 5040 True 7334.00 7334 92.92800 1486 6541 1 chr6B.!!$R1 5055
8 TraesCS2B01G035700 chr6B 718911895 718916816 4921 False 7203.00 7203 93.00600 1486 6457 1 chr6B.!!$F1 4971
9 TraesCS2B01G035700 chr3D 569837310 569842344 5034 False 7256.00 7256 92.69100 1486 6535 1 chr3D.!!$F1 5049
10 TraesCS2B01G035700 chr4A 641514198 641519222 5024 True 7149.00 7149 92.32600 1486 6543 1 chr4A.!!$R1 5057
11 TraesCS2B01G035700 chr4A 712446394 712447067 673 False 283.00 283 75.03600 6707 7365 1 chr4A.!!$F1 658
12 TraesCS2B01G035700 chr4A 712111634 712112313 679 True 278.00 278 74.89200 6707 7371 1 chr4A.!!$R5 664
13 TraesCS2B01G035700 chr4A 687626688 687627405 717 True 248.00 248 73.59800 6657 7365 1 chr4A.!!$R2 708
14 TraesCS2B01G035700 chr4A 687660511 687661228 717 True 243.00 243 73.46100 6657 7365 1 chr4A.!!$R3 708
15 TraesCS2B01G035700 chr4A 687706226 687706943 717 True 237.00 237 73.32400 6657 7365 1 chr4A.!!$R4 708
16 TraesCS2B01G035700 chr1A 100004427 100009468 5041 False 6828.00 6828 91.16800 1486 6532 1 chr1A.!!$F1 5046
17 TraesCS2B01G035700 chr1A 575873909 575876920 3011 False 4217.00 4217 91.95100 1486 4510 1 chr1A.!!$F3 3024
18 TraesCS2B01G035700 chr1A 489447555 489448362 807 False 669.00 669 81.88200 3 854 1 chr1A.!!$F2 851
19 TraesCS2B01G035700 chr7D 581264644 581269676 5032 False 6782.00 6782 90.99900 1486 6532 1 chr7D.!!$F3 5046
20 TraesCS2B01G035700 chr7D 636813593 636817104 3511 True 4909.00 4909 91.92800 3016 6536 1 chr7D.!!$R2 3520
21 TraesCS2B01G035700 chr7D 53374996 53375832 836 False 856.00 856 85.19800 3 854 1 chr7D.!!$F1 851
22 TraesCS2B01G035700 chr2A 720557786 720561777 3991 False 5635.00 5635 92.16800 1478 5477 1 chr2A.!!$F1 3999
23 TraesCS2B01G035700 chr2A 104990821 104997972 7151 True 3664.50 4344 93.49150 1486 6532 2 chr2A.!!$R3 5046
24 TraesCS2B01G035700 chr2A 17213179 17217745 4566 False 3478.00 4012 94.22700 1486 6532 2 chr2A.!!$F3 5046
25 TraesCS2B01G035700 chr2A 11981822 11983376 1554 True 970.00 1153 89.15000 847 7454 2 chr2A.!!$R2 6607
26 TraesCS2B01G035700 chr5B 669885627 669889676 4049 False 4996.00 4996 88.95400 2476 6553 1 chr5B.!!$F1 4077
27 TraesCS2B01G035700 chr2D 11326251 11327730 1479 True 899.00 1158 88.27100 920 7454 2 chr2D.!!$R1 6534
28 TraesCS2B01G035700 chr6A 522416121 522416679 558 False 664.00 664 88.23500 297 852 1 chr6A.!!$F1 555
29 TraesCS2B01G035700 chr6A 146482473 146483487 1014 False 401.00 425 88.18800 5 852 2 chr6A.!!$F2 847
30 TraesCS2B01G035700 chr3B 683022850 683023751 901 False 291.50 331 86.70250 15 850 2 chr3B.!!$F1 835
31 TraesCS2B01G035700 chr7A 22198755 22199431 676 False 265.00 265 74.67400 6707 7365 1 chr7A.!!$F1 658

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
913 1117 0.106335 AGCTCGAGCAGATCAATGGG 59.894 55.000 36.87 0.0 45.16 4.00 F
940 1146 0.172352 CTCTGTCCTCACGCTTCTCC 59.828 60.000 0.00 0.0 0.00 3.71 F
2312 2531 0.333993 AGGTGGGAGCATGCAAGAAT 59.666 50.000 21.98 0.0 0.00 2.40 F
3014 3233 2.104792 AGTAGCTGCTTTCACAACAGGA 59.895 45.455 7.79 0.0 31.94 3.86 F
3468 5831 0.107508 CCAAGGTGGATCATGTCGCT 60.108 55.000 0.00 0.0 40.96 4.93 F
4371 6745 0.605860 GGCATGGAGGCATGAGCTAG 60.606 60.000 0.00 0.0 43.51 3.42 F
5608 8004 0.252012 CAGAGGAGTGGGAGGACTGT 60.252 60.000 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2498 0.318120 CCACCTTTGCACATTGGACC 59.682 55.000 0.00 0.00 0.00 4.46 R
2779 2998 3.034635 AGAGCATGGTACTCTAGGTTGG 58.965 50.000 0.00 0.00 42.69 3.77 R
3271 3492 1.202290 CGTTTTGCTGGTCTTGCTGTT 60.202 47.619 0.00 0.00 0.00 3.16 R
4984 7360 1.002502 GAAAACCCTCCTCCACGGG 60.003 63.158 0.00 0.00 46.26 5.28 R
5434 7830 1.152881 AGGCCGCAATGATCTTCCC 60.153 57.895 0.00 0.00 0.00 3.97 R
5656 8052 0.034960 AGGTGAGCGAGCTCTACTCA 60.035 55.000 24.53 24.53 46.63 3.41 R
7493 9939 0.865769 CCGAAGACAGTTGAAACCGG 59.134 55.000 0.00 0.00 0.00 5.28 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
30 31 2.288458 GTGTTCGGTTCGTGGAATCAAA 59.712 45.455 0.00 0.00 0.00 2.69
101 102 2.181021 CGAACGAGAGGGAACGGG 59.819 66.667 0.00 0.00 0.00 5.28
269 271 4.897357 CATGCCGCCGAGCTAGCA 62.897 66.667 18.83 10.96 39.15 3.49
291 293 4.489771 CTCCCAATCCCGCCGCTT 62.490 66.667 0.00 0.00 0.00 4.68
369 372 1.605753 GCCGTTGTTCCTTTCCTCTT 58.394 50.000 0.00 0.00 0.00 2.85
370 373 2.774687 GCCGTTGTTCCTTTCCTCTTA 58.225 47.619 0.00 0.00 0.00 2.10
380 383 6.183361 TGTTCCTTTCCTCTTATTCCCTTTCA 60.183 38.462 0.00 0.00 0.00 2.69
392 395 3.269592 TCCCTTTCACTCCTCCTTACA 57.730 47.619 0.00 0.00 0.00 2.41
401 412 0.398098 TCCTCCTTACATCCCGACCC 60.398 60.000 0.00 0.00 0.00 4.46
513 524 3.998672 GGCGTTCGGTCTCCACCA 61.999 66.667 0.00 0.00 44.02 4.17
526 537 1.600636 CCACCAATGGTCACAGCGT 60.601 57.895 0.00 0.00 41.64 5.07
597 784 2.625314 CCAGCGAGATCCTTGTCTGATA 59.375 50.000 0.00 0.00 0.00 2.15
710 912 3.491342 TGAACAAATCCATTCGGTTCCA 58.509 40.909 11.39 0.00 35.17 3.53
752 954 5.189539 CCCAAATGTAACCATTCCATTCCTT 59.810 40.000 0.00 0.00 40.42 3.36
862 1064 5.479027 ACCAAACACACCCTAAATATCCAAC 59.521 40.000 0.00 0.00 0.00 3.77
875 1077 8.137437 CCTAAATATCCAACCACACAATCATTC 58.863 37.037 0.00 0.00 0.00 2.67
880 1082 0.523072 ACCACACAATCATTCGCAGC 59.477 50.000 0.00 0.00 0.00 5.25
913 1117 0.106335 AGCTCGAGCAGATCAATGGG 59.894 55.000 36.87 0.00 45.16 4.00
924 1128 1.767681 GATCAATGGGTCAGCTCCTCT 59.232 52.381 0.00 0.00 0.00 3.69
925 1129 0.907486 TCAATGGGTCAGCTCCTCTG 59.093 55.000 0.00 0.00 44.21 3.35
931 1137 0.613292 GGTCAGCTCCTCTGTCCTCA 60.613 60.000 0.00 0.00 44.36 3.86
940 1146 0.172352 CTCTGTCCTCACGCTTCTCC 59.828 60.000 0.00 0.00 0.00 3.71
952 1158 2.604686 TTCTCCTGTGCGGCCTCT 60.605 61.111 0.00 0.00 0.00 3.69
966 1172 4.856607 CTCTTCGCCGTCCTCCGC 62.857 72.222 0.00 0.00 34.38 5.54
991 1200 1.949847 CTGTGCTCCTACTCCACCCG 61.950 65.000 0.00 0.00 0.00 5.28
1074 1283 4.388499 GCCTTCTCGAACCGCCCA 62.388 66.667 0.00 0.00 0.00 5.36
1132 1341 2.551270 GCCAGCAGAACACGAACG 59.449 61.111 0.00 0.00 0.00 3.95
1144 1353 2.244382 CGAACGTCAACACCGTGC 59.756 61.111 0.00 0.00 38.77 5.34
1260 1469 3.785859 GTCCAGGGCCTCATCGCA 61.786 66.667 0.95 0.00 0.00 5.10
1346 1555 2.250485 CGTGTTCTCGGTCGTCGT 59.750 61.111 0.00 0.00 40.32 4.34
1543 1752 4.150980 GCGTTGCGTGTTATATATAGCCAA 59.849 41.667 4.36 0.00 0.00 4.52
1560 1770 2.290705 GCCAAAGGCTAGGGTTTACAGA 60.291 50.000 7.88 0.00 46.69 3.41
1574 1785 4.564199 GGTTTACAGAATCCGGTAGTTGGT 60.564 45.833 0.00 0.00 0.00 3.67
1579 1790 4.529377 ACAGAATCCGGTAGTTGGTTTAGA 59.471 41.667 0.00 0.00 0.00 2.10
1617 1829 9.422681 AGTTAGCTAACTACAAGATAAGGATCA 57.577 33.333 32.78 0.00 44.18 2.92
1640 1852 3.054875 AGGCTTTAAACCTAACTACCGGG 60.055 47.826 6.32 0.00 35.10 5.73
1641 1853 3.055167 GGCTTTAAACCTAACTACCGGGA 60.055 47.826 6.32 0.00 0.00 5.14
1648 1860 5.963214 AACCTAACTACCGGGATACAATT 57.037 39.130 6.32 0.00 39.74 2.32
1649 1861 5.286267 ACCTAACTACCGGGATACAATTG 57.714 43.478 6.32 3.24 39.74 2.32
1651 1863 5.898972 ACCTAACTACCGGGATACAATTGTA 59.101 40.000 20.14 20.14 39.74 2.41
1666 1881 2.127906 GTAACGCACGCAACACCG 60.128 61.111 0.00 0.00 0.00 4.94
1668 1883 2.587679 TAACGCACGCAACACCGAC 61.588 57.895 0.00 0.00 0.00 4.79
1769 1986 6.433766 CAAGTTGAGATTGTTCTTGAACTCC 58.566 40.000 13.65 4.35 35.49 3.85
1843 2060 7.287061 TCATTAGTGGGAATGAACCGAATATT 58.713 34.615 0.00 0.00 41.70 1.28
1886 2103 7.821846 ACTCTTTCTCTGACAAAGTGATAATCC 59.178 37.037 12.35 0.00 33.32 3.01
2141 2360 2.765699 TCCAAAGAAAACAGCAAAGCCT 59.234 40.909 0.00 0.00 0.00 4.58
2153 2372 1.742268 GCAAAGCCTCCTGTTGATCTC 59.258 52.381 0.00 0.00 0.00 2.75
2279 2498 4.997905 TCTGAAGATTCTTTTCACTGCG 57.002 40.909 0.00 0.00 31.66 5.18
2312 2531 0.333993 AGGTGGGAGCATGCAAGAAT 59.666 50.000 21.98 0.00 0.00 2.40
2478 2697 5.809001 AGAGAGGCATATTTGACACTTTGA 58.191 37.500 0.00 0.00 31.20 2.69
2497 2716 6.888632 ACTTTGAAATTCATCATACCTGCTCT 59.111 34.615 0.00 0.00 0.00 4.09
2555 2774 7.268586 TCAAGACTATGCCATCTTTAACTCTC 58.731 38.462 0.00 0.00 32.77 3.20
2768 2987 3.360867 TGGCTGAAAACCAAGTCTTTGA 58.639 40.909 0.00 0.00 36.36 2.69
2779 2998 4.157840 ACCAAGTCTTTGAAGTTTCACACC 59.842 41.667 0.00 0.00 36.83 4.16
2879 3098 3.246203 TGTCCTTTACCTCATACCCAGGA 60.246 47.826 0.00 0.00 34.75 3.86
2987 3206 5.582269 TGATACTGCAATAGACAGAACAAGC 59.418 40.000 0.00 0.00 38.55 4.01
3014 3233 2.104792 AGTAGCTGCTTTCACAACAGGA 59.895 45.455 7.79 0.00 31.94 3.86
3074 3293 2.568623 ACCCCTTTGCAACTAGTCTG 57.431 50.000 0.00 0.00 0.00 3.51
3099 3318 5.755861 GCCTTGTATCTGTCTATTTCTCCAC 59.244 44.000 0.00 0.00 0.00 4.02
3104 3323 5.690464 ATCTGTCTATTTCTCCACTTGCT 57.310 39.130 0.00 0.00 0.00 3.91
3226 3446 5.726397 TCTTCATCCATTGCATTTTTCCAG 58.274 37.500 0.00 0.00 0.00 3.86
3295 3516 0.655733 CAAGACCAGCAAAACGACGT 59.344 50.000 0.00 0.00 0.00 4.34
3296 3517 1.862201 CAAGACCAGCAAAACGACGTA 59.138 47.619 0.00 0.00 0.00 3.57
3312 3533 4.157289 ACGACGTACTTTGTCATACCTGAT 59.843 41.667 0.00 0.00 36.11 2.90
3426 3671 1.525923 CCTGCACAGAGGATCCAGG 59.474 63.158 15.82 6.06 37.35 4.45
3433 3678 1.293458 ACAGAGGATCCAGGACCTGAT 59.707 52.381 23.77 13.83 36.57 2.90
3468 5831 0.107508 CCAAGGTGGATCATGTCGCT 60.108 55.000 0.00 0.00 40.96 4.93
3469 5832 1.012086 CAAGGTGGATCATGTCGCTG 58.988 55.000 0.00 0.00 0.00 5.18
3470 5833 0.745845 AAGGTGGATCATGTCGCTGC 60.746 55.000 0.00 0.00 0.00 5.25
3474 5837 1.332889 TGGATCATGTCGCTGCCTCT 61.333 55.000 0.00 0.00 0.00 3.69
3545 5908 3.414700 CCTGTGACGCGCCTGTTC 61.415 66.667 5.73 0.00 0.00 3.18
3568 5931 2.587194 GCGTGCGATGCTCCTGAT 60.587 61.111 0.00 0.00 0.00 2.90
3569 5932 2.176273 GCGTGCGATGCTCCTGATT 61.176 57.895 0.00 0.00 0.00 2.57
3570 5933 1.640069 CGTGCGATGCTCCTGATTG 59.360 57.895 0.00 0.00 0.00 2.67
3571 5934 1.769098 CGTGCGATGCTCCTGATTGG 61.769 60.000 0.00 0.00 37.10 3.16
3572 5935 1.820906 TGCGATGCTCCTGATTGGC 60.821 57.895 0.00 0.00 35.26 4.52
3573 5936 2.550101 GCGATGCTCCTGATTGGCC 61.550 63.158 0.00 0.00 35.26 5.36
3574 5937 1.895707 CGATGCTCCTGATTGGCCC 60.896 63.158 0.00 0.00 35.26 5.80
3575 5938 1.895707 GATGCTCCTGATTGGCCCG 60.896 63.158 0.00 0.00 35.26 6.13
3576 5939 4.802051 TGCTCCTGATTGGCCCGC 62.802 66.667 0.00 0.00 35.26 6.13
3577 5940 4.802051 GCTCCTGATTGGCCCGCA 62.802 66.667 0.00 0.00 35.26 5.69
3578 5941 2.194056 CTCCTGATTGGCCCGCAT 59.806 61.111 0.00 0.00 35.26 4.73
3583 5946 3.219198 GATTGGCCCGCATCACCC 61.219 66.667 0.00 0.00 0.00 4.61
3584 5947 4.059304 ATTGGCCCGCATCACCCA 62.059 61.111 0.00 0.00 0.00 4.51
3662 6025 4.379243 CCGACCCTGAGTGCGCTT 62.379 66.667 9.73 0.00 0.00 4.68
3719 6082 4.530857 GTGGGGACGCTGGATCGG 62.531 72.222 0.00 0.00 38.02 4.18
3850 6220 1.227556 GTGTTCCACGCCTGTCTGT 60.228 57.895 0.00 0.00 0.00 3.41
3863 6233 4.168760 GCCTGTCTGTTGCATAAAATCAC 58.831 43.478 0.00 0.00 0.00 3.06
3874 6245 5.363101 TGCATAAAATCACAGCCAAAAACA 58.637 33.333 0.00 0.00 0.00 2.83
3875 6246 5.466058 TGCATAAAATCACAGCCAAAAACAG 59.534 36.000 0.00 0.00 0.00 3.16
3876 6247 5.106987 GCATAAAATCACAGCCAAAAACAGG 60.107 40.000 0.00 0.00 0.00 4.00
3903 6274 5.606348 TTTCCACCAAAATTTACAGCAGT 57.394 34.783 0.00 0.00 0.00 4.40
3908 6279 7.151308 TCCACCAAAATTTACAGCAGTATTTG 58.849 34.615 6.78 6.78 31.89 2.32
4045 6416 5.185635 TGGATTTAGTGAGGCAAATGGAAAG 59.814 40.000 0.00 0.00 0.00 2.62
4069 6440 8.649973 AGATAGTTTCGTCAAAGATAACATCC 57.350 34.615 0.00 0.00 0.00 3.51
4071 6442 5.805728 AGTTTCGTCAAAGATAACATCCCT 58.194 37.500 0.00 0.00 0.00 4.20
4093 6464 5.644636 CCTAGAGATATAGACACGTCCTTCC 59.355 48.000 0.00 0.00 0.00 3.46
4186 6557 6.959639 AACTCTAGTTTCTTGGCATGAAAA 57.040 33.333 24.65 13.02 35.54 2.29
4257 6631 7.961351 TGATAGTTGGGTTTTTCATGAAACAT 58.039 30.769 20.35 4.50 40.44 2.71
4342 6716 1.740718 GCTAGAAAAGCCTCGTCCCAG 60.741 57.143 0.00 0.00 46.25 4.45
4371 6745 0.605860 GGCATGGAGGCATGAGCTAG 60.606 60.000 0.00 0.00 43.51 3.42
4447 6821 1.983481 TTGATGGGCATGTGGGCAC 60.983 57.895 0.00 0.00 45.66 5.01
4480 6854 4.202274 TGTGTGATCCCTACTTGACGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
4504 6878 2.731976 GGAATTTAGGCGCTCATACTCG 59.268 50.000 7.64 0.00 0.00 4.18
4570 6944 5.057149 AGTCGTTCAACTAGTGCTTGAAAT 58.943 37.500 9.51 0.00 38.92 2.17
4638 7014 9.923143 ATATATCCATGTGAATTTGCTGAAATG 57.077 29.630 0.00 0.00 31.83 2.32
4641 7017 6.703319 TCCATGTGAATTTGCTGAAATGATT 58.297 32.000 0.00 0.00 31.83 2.57
4713 7089 5.631481 GCCCCCATACATCAGAGAAAACTAA 60.631 44.000 0.00 0.00 0.00 2.24
4733 7109 7.971183 ACTAACTCTAAAGGAGCTTTTGAAG 57.029 36.000 0.00 0.00 45.48 3.02
4810 7186 6.126863 TCACACACTCCCTCTTTATTCAAT 57.873 37.500 0.00 0.00 0.00 2.57
4984 7360 0.896226 AGAGCCCGTTTCTACACCTC 59.104 55.000 0.00 0.00 0.00 3.85
5130 7508 5.104859 TGGGCACATGCAGAATATTTTTGAT 60.105 36.000 6.15 0.00 44.36 2.57
5434 7830 2.005451 CAGATTTGGCAGAAGACCTCG 58.995 52.381 0.00 0.00 0.00 4.63
5608 8004 0.252012 CAGAGGAGTGGGAGGACTGT 60.252 60.000 0.00 0.00 0.00 3.55
5686 8082 0.877071 CGCTCACCTTGATTTGCTGT 59.123 50.000 0.00 0.00 0.00 4.40
5701 8099 1.746727 GCTGTGTACGAGCGCAGATG 61.747 60.000 21.67 0.00 46.58 2.90
5737 8135 3.196463 CACATAGTCGTAGTCGAGTCCT 58.804 50.000 0.00 0.00 45.07 3.85
5802 8200 1.126488 ACCGATGCCATCTCATCACT 58.874 50.000 2.75 0.00 42.15 3.41
5804 8202 1.202615 CCGATGCCATCTCATCACTGT 60.203 52.381 2.75 0.00 42.15 3.55
5882 8280 1.002134 AGGGCGATTCTGGTGTTGG 60.002 57.895 0.00 0.00 0.00 3.77
5927 8325 1.043816 GAAGATCTCCCTGATGGCGA 58.956 55.000 0.00 0.00 35.14 5.54
5932 8330 3.391665 CTCCCTGATGGCGACCCAC 62.392 68.421 0.00 0.00 45.77 4.61
5974 8372 1.003355 CGCCACCTGAACCATGACT 60.003 57.895 0.00 0.00 0.00 3.41
6013 8411 0.252479 AGATGAAGCTCAGCACCTGG 59.748 55.000 0.00 0.00 34.77 4.45
6016 8414 1.078567 GAAGCTCAGCACCTGGGAG 60.079 63.158 0.00 0.00 32.95 4.30
6025 8423 1.680651 CACCTGGGAGTCTCGAGCT 60.681 63.158 7.81 8.39 0.00 4.09
6052 8450 1.451387 GTCGTATGCAGGGTTGGGG 60.451 63.158 0.00 0.00 0.00 4.96
6063 8461 3.618750 GTTGGGGACGTCCGTGGA 61.619 66.667 27.68 11.17 36.71 4.02
6111 8509 2.588314 CGGCTGCTCCTGATCTGC 60.588 66.667 0.00 0.00 0.00 4.26
6254 8652 1.453379 CTTGAGGAGGCCATGGCTG 60.453 63.158 34.70 11.82 38.98 4.85
6353 8752 4.150980 GCGTTGCGTGTTATATATAGCCAA 59.849 41.667 4.36 0.00 0.00 4.52
6370 8770 2.290705 GCCAAAGGCTAGGGTTTACAGA 60.291 50.000 7.88 0.00 46.69 3.41
6384 8785 4.564199 GGTTTACAGAATCCGGTAGTTGGT 60.564 45.833 0.00 0.00 0.00 3.67
6389 8790 4.529377 ACAGAATCCGGTAGTTGGTTTAGA 59.471 41.667 0.00 0.00 0.00 2.10
6427 8831 9.422681 AGTTAGCTAACTACAAGATAAGGATCA 57.577 33.333 32.78 0.00 44.18 2.92
6434 8839 6.963322 ACTACAAGATAAGGATCAAGGCTTT 58.037 36.000 0.00 0.00 34.17 3.51
6450 8855 3.054875 AGGCTTTAAACCTAACTACCGGG 60.055 47.826 6.32 0.00 35.10 5.73
6451 8856 3.055167 GGCTTTAAACCTAACTACCGGGA 60.055 47.826 6.32 0.00 0.00 5.14
6461 8870 5.898972 ACCTAACTACCGGGATACAATTGTA 59.101 40.000 20.14 20.14 39.74 2.41
6476 8885 2.127906 GTAACGCACGCAACACCG 60.128 61.111 0.00 0.00 0.00 4.94
6478 8887 2.587679 TAACGCACGCAACACCGAC 61.588 57.895 0.00 0.00 0.00 4.79
6489 8898 3.609879 CGCAACACCGACCATATATACGA 60.610 47.826 0.00 0.00 0.00 3.43
6564 8976 3.181367 CGCAAGCTCTTCGCCATT 58.819 55.556 0.00 0.00 40.39 3.16
6576 8988 2.114670 CGCCATTGATGTCCGGCTT 61.115 57.895 0.00 0.00 42.59 4.35
6578 8990 0.947244 GCCATTGATGTCCGGCTTAG 59.053 55.000 0.00 0.00 41.50 2.18
6601 9013 1.224120 AGCTATTCCTCCCTCCCATCA 59.776 52.381 0.00 0.00 0.00 3.07
6648 9060 0.386858 CTCGACCACGTGACGACAAT 60.387 55.000 25.06 0.00 40.69 2.71
6654 9066 4.147322 CGTGACGACAATGGCCGC 62.147 66.667 0.00 0.00 0.00 6.53
6655 9067 2.742372 GTGACGACAATGGCCGCT 60.742 61.111 0.00 0.00 0.00 5.52
6759 9174 2.562635 CGACTGATCTCGGAGTTCCTA 58.437 52.381 12.32 0.00 0.00 2.94
6873 9297 1.814586 CGACTACGGCGAGGTCTCT 60.815 63.158 16.62 0.00 35.72 3.10
6934 9370 1.154205 GGAGACGCTACGCATGCATT 61.154 55.000 19.57 6.25 0.00 3.56
7001 9437 1.274703 ATGCTGGTCGGAGGAATGGT 61.275 55.000 0.00 0.00 0.00 3.55
7006 9442 1.590147 GTCGGAGGAATGGTCGTGT 59.410 57.895 0.00 0.00 0.00 4.49
7245 9684 1.376553 GAAGAGCTTCTTGGCCGCT 60.377 57.895 1.28 1.28 36.73 5.52
7344 9789 1.078709 TGATGAAGAAGCCGCTTTCG 58.921 50.000 7.16 0.00 32.33 3.46
7371 9816 3.773630 ACGCGACGCACCAAATCG 61.774 61.111 21.35 2.95 38.87 3.34
7372 9817 4.499023 CGCGACGCACCAAATCGG 62.499 66.667 21.35 0.00 42.50 4.18
7392 9837 6.531503 TCGGTCTAAAGATCTCAACATCTT 57.468 37.500 0.00 0.00 43.70 2.40
7394 9839 6.152831 TCGGTCTAAAGATCTCAACATCTTGA 59.847 38.462 0.00 0.00 41.45 3.02
7395 9840 6.254589 CGGTCTAAAGATCTCAACATCTTGAC 59.745 42.308 0.00 2.00 41.45 3.18
7463 9909 3.150335 CAGCCGAGCCTAGAGCCA 61.150 66.667 0.00 0.00 45.47 4.75
7476 9922 1.267121 AGAGCCACGGAAAGCTTCTA 58.733 50.000 0.00 0.00 40.11 2.10
7493 9939 4.673841 GCTTCTACTTCTGCCATTTTCTGC 60.674 45.833 0.00 0.00 0.00 4.26
7502 9948 1.270041 GCCATTTTCTGCCGGTTTCAA 60.270 47.619 1.90 0.00 0.00 2.69
7504 9950 2.035832 CCATTTTCTGCCGGTTTCAACT 59.964 45.455 1.90 0.00 0.00 3.16
7509 9955 1.134220 TCTGCCGGTTTCAACTGTCTT 60.134 47.619 1.90 0.00 33.38 3.01
7515 9961 1.264288 GGTTTCAACTGTCTTCGGCAG 59.736 52.381 0.00 0.00 39.67 4.85
7560 10006 4.634012 TGCTATCTAGTTTTGGTGTGGT 57.366 40.909 0.00 0.00 0.00 4.16
7662 10108 5.691305 CAGAAAGAAAATTTTGCACGGATCA 59.309 36.000 8.47 0.00 0.00 2.92
7665 10111 3.320541 AGAAAATTTTGCACGGATCACCA 59.679 39.130 8.47 0.00 35.59 4.17
7694 10140 6.625362 AGATACCACGAATATAGCATGACTG 58.375 40.000 0.00 0.00 0.00 3.51
7695 10141 4.937201 ACCACGAATATAGCATGACTGA 57.063 40.909 0.00 0.00 0.00 3.41
7696 10142 4.876125 ACCACGAATATAGCATGACTGAG 58.124 43.478 0.00 0.00 0.00 3.35
7697 10143 4.584743 ACCACGAATATAGCATGACTGAGA 59.415 41.667 0.00 0.00 0.00 3.27
7698 10144 5.244851 ACCACGAATATAGCATGACTGAGAT 59.755 40.000 0.00 0.00 0.00 2.75
7699 10145 6.162079 CCACGAATATAGCATGACTGAGATT 58.838 40.000 0.00 0.00 0.00 2.40
7700 10146 6.648310 CCACGAATATAGCATGACTGAGATTT 59.352 38.462 0.00 0.00 0.00 2.17
7701 10147 7.814587 CCACGAATATAGCATGACTGAGATTTA 59.185 37.037 0.00 0.00 0.00 1.40
7702 10148 8.858186 CACGAATATAGCATGACTGAGATTTAG 58.142 37.037 0.00 0.00 0.00 1.85
7703 10149 7.543868 ACGAATATAGCATGACTGAGATTTAGC 59.456 37.037 0.00 0.00 0.00 3.09
7704 10150 7.543520 CGAATATAGCATGACTGAGATTTAGCA 59.456 37.037 0.00 0.00 0.00 3.49
7705 10151 9.212641 GAATATAGCATGACTGAGATTTAGCAA 57.787 33.333 0.00 0.00 0.00 3.91
7706 10152 9.736414 AATATAGCATGACTGAGATTTAGCAAT 57.264 29.630 0.00 0.00 0.00 3.56
7707 10153 7.670009 ATAGCATGACTGAGATTTAGCAATC 57.330 36.000 0.00 0.00 39.45 2.67
7733 10179 5.183140 CGATCTAGTTTTGGTCCCACAAATT 59.817 40.000 0.00 0.00 39.80 1.82
7737 10183 3.120041 GTTTTGGTCCCACAAATTGTCG 58.880 45.455 0.00 0.00 39.80 4.35
7739 10185 0.183971 TGGTCCCACAAATTGTCGGT 59.816 50.000 9.49 0.00 30.27 4.69
7758 10204 4.121317 CGGTTCACCAGTGTAAACTAACA 58.879 43.478 0.00 0.00 35.14 2.41
7759 10205 4.571580 CGGTTCACCAGTGTAAACTAACAA 59.428 41.667 0.00 0.00 35.14 2.83
7788 10234 2.713877 ACACTTACGGGTTGTTTGTGT 58.286 42.857 0.00 0.00 39.39 3.72
7791 10237 0.377554 TTACGGGTTGTTTGTGTGCG 59.622 50.000 0.00 0.00 0.00 5.34
7793 10239 2.473760 CGGGTTGTTTGTGTGCGGA 61.474 57.895 0.00 0.00 0.00 5.54
7803 10249 3.455990 TTGTGTGCGGAAGTAGTTACA 57.544 42.857 0.00 0.00 0.00 2.41
7846 10292 2.925706 TTAGTGGTGGGCGCCTCA 60.926 61.111 28.56 19.91 0.00 3.86
8261 10707 0.955919 GGTTCCTGTCCGGCAAAGAG 60.956 60.000 0.00 0.00 0.00 2.85
8268 10714 4.115199 CCGGCAAAGAGGGGGAGG 62.115 72.222 0.00 0.00 0.00 4.30
8363 10809 0.676466 TGGGCATGACGATGGTGAAC 60.676 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.562298 ACGAACCGAACACACCCTTATA 59.438 45.455 0.00 0.00 0.00 0.98
30 31 2.478890 CCGACCCGTGACGCTCTAT 61.479 63.158 0.00 0.00 0.00 1.98
59 60 1.672356 AAACGCTGGAATCGCTGCT 60.672 52.632 0.00 0.00 0.00 4.24
269 271 3.090532 GCGGGATTGGGAGGAGGT 61.091 66.667 0.00 0.00 0.00 3.85
291 293 1.486145 GGAACCTCGGGAACAAGGGA 61.486 60.000 0.00 0.00 0.00 4.20
357 360 6.045577 AGTGAAAGGGAATAAGAGGAAAGGAA 59.954 38.462 0.00 0.00 0.00 3.36
369 372 5.347124 TGTAAGGAGGAGTGAAAGGGAATA 58.653 41.667 0.00 0.00 0.00 1.75
370 373 4.175962 TGTAAGGAGGAGTGAAAGGGAAT 58.824 43.478 0.00 0.00 0.00 3.01
380 383 1.688627 GGTCGGGATGTAAGGAGGAGT 60.689 57.143 0.00 0.00 0.00 3.85
392 395 2.444140 CGGAAGGAGGGTCGGGAT 60.444 66.667 0.00 0.00 0.00 3.85
513 524 1.298667 GGGGTACGCTGTGACCATT 59.701 57.895 10.04 0.00 37.47 3.16
589 776 9.396022 GAAATTCAGGAGGTAAAATATCAGACA 57.604 33.333 0.00 0.00 0.00 3.41
597 784 9.547279 AATACAAGGAAATTCAGGAGGTAAAAT 57.453 29.630 0.00 0.00 0.00 1.82
635 831 8.032952 ACAAACAACACACATATACAGAGATG 57.967 34.615 0.00 0.00 0.00 2.90
636 832 9.890629 ATACAAACAACACACATATACAGAGAT 57.109 29.630 0.00 0.00 0.00 2.75
637 833 9.719355 AATACAAACAACACACATATACAGAGA 57.281 29.630 0.00 0.00 0.00 3.10
710 912 6.739331 TTTGGGTGTTTGGTTTATGAGATT 57.261 33.333 0.00 0.00 0.00 2.40
752 954 6.428771 CCTTACGTTTGGTAGAAGGAATTCAA 59.571 38.462 7.93 0.00 32.84 2.69
862 1064 0.179156 GGCTGCGAATGATTGTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
880 1082 3.138930 GAGCTGCTGCATGGCATGG 62.139 63.158 27.48 13.79 41.63 3.66
886 1088 2.814238 CTGCTCGAGCTGCTGCATG 61.814 63.158 35.27 12.86 42.74 4.06
887 1089 2.313051 ATCTGCTCGAGCTGCTGCAT 62.313 55.000 35.27 21.41 42.74 3.96
888 1090 2.902759 GATCTGCTCGAGCTGCTGCA 62.903 60.000 35.27 20.19 42.74 4.41
889 1091 2.202905 ATCTGCTCGAGCTGCTGC 60.203 61.111 35.27 12.08 42.66 5.25
890 1092 0.459759 TTGATCTGCTCGAGCTGCTG 60.460 55.000 35.27 22.29 42.66 4.41
892 1094 0.582482 CATTGATCTGCTCGAGCTGC 59.418 55.000 35.27 22.97 42.66 5.25
893 1095 1.218763 CCATTGATCTGCTCGAGCTG 58.781 55.000 35.27 33.38 42.66 4.24
899 1101 1.134159 AGCTGACCCATTGATCTGCTC 60.134 52.381 13.06 0.00 44.07 4.26
924 1128 0.827925 ACAGGAGAAGCGTGAGGACA 60.828 55.000 0.00 0.00 36.29 4.02
925 1129 0.389166 CACAGGAGAAGCGTGAGGAC 60.389 60.000 0.00 0.00 36.29 3.85
970 1176 1.153745 GTGGAGTAGGAGCACAGCG 60.154 63.158 0.00 0.00 0.00 5.18
973 1179 1.982395 CGGGTGGAGTAGGAGCACA 60.982 63.158 0.00 0.00 0.00 4.57
991 1200 1.094073 ATCTTGAGCATGGCGAGTGC 61.094 55.000 0.00 1.65 42.81 4.40
1004 1213 1.219124 GCTGGGTCGCTGATCTTGA 59.781 57.895 0.00 0.00 0.00 3.02
1121 1330 1.283736 GGTGTTGACGTTCGTGTTCT 58.716 50.000 1.74 0.00 0.00 3.01
1126 1335 2.519175 GCACGGTGTTGACGTTCGT 61.519 57.895 10.24 0.00 43.58 3.85
1127 1336 2.244382 GCACGGTGTTGACGTTCG 59.756 61.111 10.24 0.00 43.58 3.95
1132 1341 2.713154 GTGTGGCACGGTGTTGAC 59.287 61.111 13.77 0.00 0.00 3.18
1371 1580 4.039357 CGCACGTGGTCCTCGTCT 62.039 66.667 18.88 0.00 39.55 4.18
1405 1614 1.537202 GGCAAGCTGGAAGTGTTGTAG 59.463 52.381 0.00 0.00 33.97 2.74
1461 1670 0.534412 CCACGAGCTTCTCCATGACT 59.466 55.000 0.00 0.00 0.00 3.41
1464 1673 0.534412 ACTCCACGAGCTTCTCCATG 59.466 55.000 0.00 0.00 32.04 3.66
1543 1752 3.118371 CGGATTCTGTAAACCCTAGCCTT 60.118 47.826 0.00 0.00 0.00 4.35
1560 1770 5.012354 TCAAGTCTAAACCAACTACCGGATT 59.988 40.000 9.46 0.00 0.00 3.01
1617 1829 4.566278 CCCGGTAGTTAGGTTTAAAGCCTT 60.566 45.833 13.60 0.00 37.54 4.35
1619 1831 3.055167 TCCCGGTAGTTAGGTTTAAAGCC 60.055 47.826 13.60 6.29 0.00 4.35
1640 1852 3.377434 TGCGTGCGTTACAATTGTATC 57.623 42.857 18.69 16.21 0.00 2.24
1641 1853 3.058846 TGTTGCGTGCGTTACAATTGTAT 60.059 39.130 18.69 0.00 0.00 2.29
1648 1860 2.872515 CGGTGTTGCGTGCGTTACA 61.873 57.895 0.00 0.00 0.00 2.41
1649 1861 2.127906 CGGTGTTGCGTGCGTTAC 60.128 61.111 0.00 0.00 0.00 2.50
1651 1863 3.932313 GTCGGTGTTGCGTGCGTT 61.932 61.111 0.00 0.00 0.00 4.84
1769 1986 3.496130 CCTTATCATGGCGCAAGTTAGAG 59.504 47.826 10.83 0.00 41.68 2.43
1870 2087 5.497464 TGAGGTGGATTATCACTTTGTCA 57.503 39.130 0.00 0.00 37.75 3.58
1871 2088 6.375455 ACATTGAGGTGGATTATCACTTTGTC 59.625 38.462 0.00 0.00 37.75 3.18
1886 2103 5.215160 GCTAGAACAAAACACATTGAGGTG 58.785 41.667 0.00 0.00 44.35 4.00
2045 2262 3.475566 ACAGAAGCTGAGTACAAAGCA 57.524 42.857 18.61 1.09 42.06 3.91
2198 2417 5.067153 CACAAGGTCAATGTCAACTTTGGTA 59.933 40.000 8.40 0.00 36.94 3.25
2261 2480 3.120165 GGACCGCAGTGAAAAGAATCTTC 60.120 47.826 0.00 0.00 0.00 2.87
2279 2498 0.318120 CCACCTTTGCACATTGGACC 59.682 55.000 0.00 0.00 0.00 4.46
2503 2722 7.171508 GTCAAGAAAAGTATGTGTCAGATGTGA 59.828 37.037 0.00 0.00 0.00 3.58
2654 2873 7.812690 TGATGATATTATTGTTGCAAGCTCT 57.187 32.000 0.00 0.00 0.00 4.09
2768 2987 3.458487 ACTCTAGGTTGGGTGTGAAACTT 59.542 43.478 0.00 0.00 38.04 2.66
2779 2998 3.034635 AGAGCATGGTACTCTAGGTTGG 58.965 50.000 0.00 0.00 42.69 3.77
2879 3098 5.511545 GGAAGAAGTGTACATGAGACAACCT 60.512 44.000 0.00 0.00 0.00 3.50
2987 3206 3.664107 TGTGAAAGCAGCTACTGTTAGG 58.336 45.455 0.00 0.00 33.43 2.69
3053 3272 2.814336 CAGACTAGTTGCAAAGGGGTTC 59.186 50.000 0.00 0.00 0.00 3.62
3074 3293 5.163301 TGGAGAAATAGACAGATACAAGGCC 60.163 44.000 0.00 0.00 0.00 5.19
3205 3425 5.486735 ACTGGAAAAATGCAATGGATGAA 57.513 34.783 0.00 0.00 0.00 2.57
3210 3430 9.747293 AAAATAAAAACTGGAAAAATGCAATGG 57.253 25.926 0.00 0.00 0.00 3.16
3226 3446 7.382898 TGGTAGAGGCATTGGAAAATAAAAAC 58.617 34.615 0.00 0.00 0.00 2.43
3271 3492 1.202290 CGTTTTGCTGGTCTTGCTGTT 60.202 47.619 0.00 0.00 0.00 3.16
3295 3516 5.653330 TGGTACGATCAGGTATGACAAAGTA 59.347 40.000 0.00 0.00 38.57 2.24
3296 3517 4.464951 TGGTACGATCAGGTATGACAAAGT 59.535 41.667 0.00 0.00 38.57 2.66
3417 3662 3.567902 GGATCAGGTCCTGGATCCT 57.432 57.895 27.07 7.62 44.16 3.24
3426 3671 2.512515 GTGCGGCTGGATCAGGTC 60.513 66.667 0.00 0.00 31.21 3.85
3433 3678 3.785859 GGATCTGGTGCGGCTGGA 61.786 66.667 0.00 0.00 0.00 3.86
3555 5918 2.550101 GGCCAATCAGGAGCATCGC 61.550 63.158 0.00 0.00 41.22 4.58
3556 5919 1.895707 GGGCCAATCAGGAGCATCG 60.896 63.158 4.39 0.00 41.22 3.84
3557 5920 1.895707 CGGGCCAATCAGGAGCATC 60.896 63.158 4.39 0.00 41.22 3.91
3558 5921 2.194056 CGGGCCAATCAGGAGCAT 59.806 61.111 4.39 0.00 41.22 3.79
3559 5922 4.802051 GCGGGCCAATCAGGAGCA 62.802 66.667 4.39 0.00 41.22 4.26
3560 5923 4.802051 TGCGGGCCAATCAGGAGC 62.802 66.667 4.39 0.00 41.22 4.70
3561 5924 1.895707 GATGCGGGCCAATCAGGAG 60.896 63.158 4.39 0.00 41.22 3.69
3562 5925 2.192979 GATGCGGGCCAATCAGGA 59.807 61.111 4.39 0.00 41.22 3.86
3563 5926 2.124193 TGATGCGGGCCAATCAGG 60.124 61.111 13.43 0.00 41.84 3.86
3564 5927 2.484062 GGTGATGCGGGCCAATCAG 61.484 63.158 16.90 0.00 0.00 2.90
3565 5928 2.440065 GGTGATGCGGGCCAATCA 60.440 61.111 13.43 13.43 0.00 2.57
3566 5929 3.219198 GGGTGATGCGGGCCAATC 61.219 66.667 4.39 6.81 0.00 2.67
3567 5930 4.059304 TGGGTGATGCGGGCCAAT 62.059 61.111 4.39 0.00 0.00 3.16
3568 5931 4.738998 CTGGGTGATGCGGGCCAA 62.739 66.667 4.39 0.00 0.00 4.52
3575 5938 2.825836 CCCTTCGCTGGGTGATGC 60.826 66.667 4.63 0.00 42.25 3.91
3576 5939 2.124570 CCCCTTCGCTGGGTGATG 60.125 66.667 10.86 0.00 45.70 3.07
3577 5940 2.285368 TCCCCTTCGCTGGGTGAT 60.285 61.111 10.86 0.00 45.70 3.06
3578 5941 3.319198 GTCCCCTTCGCTGGGTGA 61.319 66.667 10.86 5.94 45.70 4.02
3583 5946 4.452733 GTCCGGTCCCCTTCGCTG 62.453 72.222 0.00 0.00 0.00 5.18
3588 5951 2.122099 AAGTGGTCCGGTCCCCTT 60.122 61.111 15.53 12.42 0.00 3.95
3646 6009 2.811317 GAAGCGCACTCAGGGTCG 60.811 66.667 11.47 0.00 0.00 4.79
3661 6024 2.112297 GTGGGGACAGGCGTTGAA 59.888 61.111 0.00 0.00 44.46 2.69
3662 6025 4.308458 CGTGGGGACAGGCGTTGA 62.308 66.667 0.00 0.00 44.46 3.18
3850 6220 5.819379 TGTTTTTGGCTGTGATTTTATGCAA 59.181 32.000 0.00 0.00 0.00 4.08
3863 6233 4.202243 TGGAAATTCTCCTGTTTTTGGCTG 60.202 41.667 7.78 0.00 45.64 4.85
3874 6245 7.610580 TGTAAATTTTGGTGGAAATTCTCCT 57.389 32.000 0.00 0.00 45.64 3.69
3875 6246 6.368791 GCTGTAAATTTTGGTGGAAATTCTCC 59.631 38.462 0.00 0.00 45.64 3.71
3876 6247 6.928492 TGCTGTAAATTTTGGTGGAAATTCTC 59.072 34.615 0.00 0.00 38.04 2.87
3908 6279 6.146347 GCTGATCCTTCGGTTAATCTTCATAC 59.854 42.308 0.00 0.00 0.00 2.39
4045 6416 7.711339 AGGGATGTTATCTTTGACGAAACTATC 59.289 37.037 0.00 0.00 0.00 2.08
4069 6440 5.644636 GGAAGGACGTGTCTATATCTCTAGG 59.355 48.000 0.00 0.00 0.00 3.02
4071 6442 6.436738 AGGAAGGACGTGTCTATATCTCTA 57.563 41.667 0.00 0.00 0.00 2.43
4093 6464 4.932200 GGGTTCAAGTGTCTAGATGTCAAG 59.068 45.833 0.00 0.00 0.00 3.02
4195 6569 3.423162 TTGTGCGTGCTGGCCAAAC 62.423 57.895 7.01 7.60 0.00 2.93
4234 6608 9.625747 AAAATGTTTCATGAAAAACCCAACTAT 57.374 25.926 22.07 0.00 38.16 2.12
4342 6716 2.765699 TGCCTCCATGCCCTTAAAATTC 59.234 45.455 0.00 0.00 0.00 2.17
4371 6745 1.902508 TGGATGTGGGTCTCTCACTTC 59.097 52.381 6.99 6.99 38.07 3.01
4447 6821 1.393539 GGGATCACACATCACGTTTCG 59.606 52.381 0.00 0.00 0.00 3.46
4480 6854 4.781934 AGTATGAGCGCCTAAATTCCTTT 58.218 39.130 2.29 0.00 0.00 3.11
4486 6860 1.784525 GCGAGTATGAGCGCCTAAAT 58.215 50.000 2.29 0.00 46.93 1.40
4504 6878 4.128388 CAAACGGATTGGGGCGGC 62.128 66.667 0.00 0.00 35.27 6.53
4570 6944 8.303156 TCAGAAGTTTTCAAAGTGTTTCATGAA 58.697 29.630 3.38 3.38 0.00 2.57
4713 7089 7.068686 AGTACTTCAAAAGCTCCTTTAGAGT 57.931 36.000 0.00 0.00 45.21 3.24
4733 7109 7.344093 ACTTCCCTACCCAAATTCTAGTAGTAC 59.656 40.741 0.00 0.00 32.12 2.73
4984 7360 1.002502 GAAAACCCTCCTCCACGGG 60.003 63.158 0.00 0.00 46.26 5.28
5130 7508 5.237996 CGTACCCTTACTCGTGATCTTCATA 59.762 44.000 0.00 0.00 0.00 2.15
5139 7517 2.995466 TGTTCGTACCCTTACTCGTG 57.005 50.000 0.00 0.00 0.00 4.35
5147 7525 3.494398 GGTCATGCATATGTTCGTACCCT 60.494 47.826 0.00 0.00 35.73 4.34
5209 7587 6.149973 ACAAGTACAATGGACATGATCAAGTG 59.850 38.462 8.58 1.08 0.00 3.16
5370 7766 1.201343 GGAGTGCTATCGTCGCTTTC 58.799 55.000 0.00 0.00 0.00 2.62
5434 7830 1.152881 AGGCCGCAATGATCTTCCC 60.153 57.895 0.00 0.00 0.00 3.97
5608 8004 0.322456 CCATGTTTGAAGGCGGAGGA 60.322 55.000 0.00 0.00 0.00 3.71
5656 8052 0.034960 AGGTGAGCGAGCTCTACTCA 60.035 55.000 24.53 24.53 46.63 3.41
5686 8082 1.153842 CACCATCTGCGCTCGTACA 60.154 57.895 9.73 0.00 0.00 2.90
5701 8099 0.608640 ATGTGTCCTTCGTCTCCACC 59.391 55.000 0.00 0.00 0.00 4.61
5737 8135 0.546507 TGGTGTCCTACATCCTGGCA 60.547 55.000 0.00 0.00 0.00 4.92
5956 8354 1.003355 AGTCATGGTTCAGGTGGCG 60.003 57.895 0.00 0.00 0.00 5.69
5974 8372 1.942776 TCAACTCCATCTCAGCTCCA 58.057 50.000 0.00 0.00 0.00 3.86
6013 8411 0.522180 TCGACAAAGCTCGAGACTCC 59.478 55.000 18.75 0.00 37.76 3.85
6016 8414 1.914700 GACATCGACAAAGCTCGAGAC 59.085 52.381 18.75 7.74 45.50 3.36
6025 8423 2.267426 CCTGCATACGACATCGACAAA 58.733 47.619 8.54 0.00 43.02 2.83
6063 8461 2.665185 GCGACAAGGACGGCAAGT 60.665 61.111 0.00 0.00 0.00 3.16
6104 8502 2.158608 TCTCCTACCTCGATGCAGATCA 60.159 50.000 0.00 0.00 0.00 2.92
6111 8509 0.589223 GCTCGTCTCCTACCTCGATG 59.411 60.000 0.00 0.00 0.00 3.84
6139 8537 4.881440 GCCATGGCAGCCATCCGA 62.881 66.667 32.08 0.00 43.15 4.55
6254 8652 2.863137 CCTCTAAAAGCACATCTCTCGC 59.137 50.000 0.00 0.00 0.00 5.03
6353 8752 3.118371 CGGATTCTGTAAACCCTAGCCTT 60.118 47.826 0.00 0.00 0.00 4.35
6370 8770 5.012354 TCAAGTCTAAACCAACTACCGGATT 59.988 40.000 9.46 0.00 0.00 3.01
6427 8831 4.566278 CCCGGTAGTTAGGTTTAAAGCCTT 60.566 45.833 13.60 0.00 37.54 4.35
6429 8833 3.055167 TCCCGGTAGTTAGGTTTAAAGCC 60.055 47.826 13.60 6.29 0.00 4.35
6434 8839 7.092935 ACAATTGTATCCCGGTAGTTAGGTTTA 60.093 37.037 9.97 0.00 0.00 2.01
6450 8855 3.377434 TGCGTGCGTTACAATTGTATC 57.623 42.857 18.69 16.21 0.00 2.24
6451 8856 3.058846 TGTTGCGTGCGTTACAATTGTAT 60.059 39.130 18.69 0.00 0.00 2.29
6461 8870 3.932313 GTCGGTGTTGCGTGCGTT 61.932 61.111 0.00 0.00 0.00 4.84
6564 8976 1.686325 GCTCCCTAAGCCGGACATCA 61.686 60.000 5.05 0.00 45.92 3.07
6648 9060 3.365291 GACATACGGACAGCGGCCA 62.365 63.158 2.24 0.00 0.00 5.36
6654 9066 1.738350 AGTGACTCGACATACGGACAG 59.262 52.381 0.00 0.00 42.82 3.51
6655 9067 1.736126 GAGTGACTCGACATACGGACA 59.264 52.381 0.00 0.00 42.82 4.02
6982 9418 1.274703 ACCATTCCTCCGACCAGCAT 61.275 55.000 0.00 0.00 0.00 3.79
7231 9670 2.267324 GAGAGCGGCCAAGAAGCT 59.733 61.111 2.24 1.70 44.80 3.74
7371 9816 7.099764 TGTCAAGATGTTGAGATCTTTAGACC 58.900 38.462 5.37 0.00 43.55 3.85
7372 9817 8.539770 TTGTCAAGATGTTGAGATCTTTAGAC 57.460 34.615 5.37 11.33 43.55 2.59
7463 9909 2.613223 GGCAGAAGTAGAAGCTTTCCGT 60.613 50.000 0.00 0.00 0.00 4.69
7493 9939 0.865769 CCGAAGACAGTTGAAACCGG 59.134 55.000 0.00 0.00 0.00 5.28
7502 9948 1.841556 TTCCCCTGCCGAAGACAGT 60.842 57.895 0.00 0.00 33.09 3.55
7504 9950 2.747686 GTTCCCCTGCCGAAGACA 59.252 61.111 0.00 0.00 0.00 3.41
7515 9961 2.638363 GTGTATAGATCTGGGGTTCCCC 59.362 54.545 19.35 19.35 44.67 4.81
7529 9975 9.547753 ACCAAAACTAGATAGCAATGTGTATAG 57.452 33.333 0.00 0.00 0.00 1.31
7538 9984 4.980573 ACCACACCAAAACTAGATAGCAA 58.019 39.130 0.00 0.00 0.00 3.91
7552 9998 3.392947 TCAATTGAGACCTAACCACACCA 59.607 43.478 3.38 0.00 0.00 4.17
7560 10006 9.924650 GTTAAGTCTTAGTCAATTGAGACCTAA 57.075 33.333 17.38 15.36 39.39 2.69
7632 10078 8.711457 CCGTGCAAAATTTTCTTTCTGATATTT 58.289 29.630 0.00 0.00 0.00 1.40
7635 10081 6.976088 TCCGTGCAAAATTTTCTTTCTGATA 58.024 32.000 0.00 0.00 0.00 2.15
7637 10083 5.255710 TCCGTGCAAAATTTTCTTTCTGA 57.744 34.783 0.00 0.00 0.00 3.27
7638 10084 5.691305 TGATCCGTGCAAAATTTTCTTTCTG 59.309 36.000 0.00 0.00 0.00 3.02
7639 10085 5.691754 GTGATCCGTGCAAAATTTTCTTTCT 59.308 36.000 0.00 0.00 0.00 2.52
7640 10086 5.107491 GGTGATCCGTGCAAAATTTTCTTTC 60.107 40.000 0.00 0.00 0.00 2.62
7644 10090 3.648009 TGGTGATCCGTGCAAAATTTTC 58.352 40.909 0.00 0.00 36.30 2.29
7645 10091 3.742433 TGGTGATCCGTGCAAAATTTT 57.258 38.095 0.00 0.00 36.30 1.82
7646 10092 3.587923 CATGGTGATCCGTGCAAAATTT 58.412 40.909 0.00 0.00 42.77 1.82
7647 10093 3.235157 CATGGTGATCCGTGCAAAATT 57.765 42.857 0.00 0.00 42.77 1.82
7648 10094 2.945447 CATGGTGATCCGTGCAAAAT 57.055 45.000 0.00 0.00 42.77 1.82
7662 10108 7.039293 TGCTATATTCGTGGTATCTTACATGGT 60.039 37.037 0.00 0.00 0.00 3.55
7665 10111 8.749354 TCATGCTATATTCGTGGTATCTTACAT 58.251 33.333 0.00 0.00 0.00 2.29
7696 10142 8.279103 CCAAAACTAGATCGAGATTGCTAAATC 58.721 37.037 10.07 0.00 42.26 2.17
7697 10143 7.770897 ACCAAAACTAGATCGAGATTGCTAAAT 59.229 33.333 10.07 0.00 0.00 1.40
7698 10144 7.103641 ACCAAAACTAGATCGAGATTGCTAAA 58.896 34.615 10.07 0.00 0.00 1.85
7699 10145 6.640518 ACCAAAACTAGATCGAGATTGCTAA 58.359 36.000 10.07 0.00 0.00 3.09
7700 10146 6.222038 ACCAAAACTAGATCGAGATTGCTA 57.778 37.500 10.07 0.00 0.00 3.49
7701 10147 5.091261 ACCAAAACTAGATCGAGATTGCT 57.909 39.130 10.07 0.11 0.00 3.91
7702 10148 4.271291 GGACCAAAACTAGATCGAGATTGC 59.729 45.833 10.07 3.48 0.00 3.56
7703 10149 4.811557 GGGACCAAAACTAGATCGAGATTG 59.188 45.833 10.07 12.81 0.00 2.67
7704 10150 4.469945 TGGGACCAAAACTAGATCGAGATT 59.530 41.667 10.07 0.89 0.00 2.40
7705 10151 4.030913 TGGGACCAAAACTAGATCGAGAT 58.969 43.478 10.07 0.00 0.00 2.75
7706 10152 3.194968 GTGGGACCAAAACTAGATCGAGA 59.805 47.826 10.07 0.00 0.00 4.04
7707 10153 3.056107 TGTGGGACCAAAACTAGATCGAG 60.056 47.826 0.00 0.70 0.00 4.04
7708 10154 2.901192 TGTGGGACCAAAACTAGATCGA 59.099 45.455 0.00 0.00 0.00 3.59
7709 10155 3.328382 TGTGGGACCAAAACTAGATCG 57.672 47.619 0.00 0.00 0.00 3.69
7710 10156 6.015434 ACAATTTGTGGGACCAAAACTAGATC 60.015 38.462 0.15 0.00 37.81 2.75
7711 10157 5.838521 ACAATTTGTGGGACCAAAACTAGAT 59.161 36.000 0.15 0.00 37.81 1.98
7712 10158 5.205056 ACAATTTGTGGGACCAAAACTAGA 58.795 37.500 0.15 0.00 37.81 2.43
7713 10159 5.528870 GACAATTTGTGGGACCAAAACTAG 58.471 41.667 6.80 0.00 37.81 2.57
7714 10160 4.036971 CGACAATTTGTGGGACCAAAACTA 59.963 41.667 6.80 0.00 37.81 2.24
7715 10161 3.181480 CGACAATTTGTGGGACCAAAACT 60.181 43.478 6.80 0.00 37.81 2.66
7733 10179 2.168936 AGTTTACACTGGTGAACCGACA 59.831 45.455 7.78 0.00 42.66 4.35
7737 10183 6.316890 TCTTTGTTAGTTTACACTGGTGAACC 59.683 38.462 7.78 0.00 42.66 3.62
7739 10185 7.925043 TTCTTTGTTAGTTTACACTGGTGAA 57.075 32.000 7.78 0.00 34.06 3.18
7758 10204 4.281898 ACCCGTAAGTGTAGCATTCTTT 57.718 40.909 0.00 0.00 0.00 2.52
7759 10205 3.975168 ACCCGTAAGTGTAGCATTCTT 57.025 42.857 0.00 0.00 0.00 2.52
7788 10234 1.067142 CAGCCTGTAACTACTTCCGCA 60.067 52.381 0.00 0.00 0.00 5.69
7791 10237 5.246307 ACAATTCAGCCTGTAACTACTTCC 58.754 41.667 0.00 0.00 0.00 3.46
7793 10239 7.094762 GCTTTACAATTCAGCCTGTAACTACTT 60.095 37.037 0.00 0.00 37.66 2.24
7803 10249 3.270877 CCGTAGCTTTACAATTCAGCCT 58.729 45.455 0.00 0.00 33.73 4.58
8173 10619 3.995048 GTCTGCGCCTTATTAATCTACCC 59.005 47.826 4.18 0.00 0.00 3.69
8174 10620 4.448060 GTGTCTGCGCCTTATTAATCTACC 59.552 45.833 4.18 0.00 0.00 3.18
8175 10621 4.148348 CGTGTCTGCGCCTTATTAATCTAC 59.852 45.833 4.18 0.00 0.00 2.59
8176 10622 4.202080 ACGTGTCTGCGCCTTATTAATCTA 60.202 41.667 4.18 0.00 34.88 1.98
8256 10702 3.009714 GACGCCCTCCCCCTCTTT 61.010 66.667 0.00 0.00 0.00 2.52
8284 10730 0.107312 CCTGATCTGCTTGGGTCCTG 60.107 60.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.