Multiple sequence alignment - TraesCS5D01G172500

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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 TraesCS5D01G172500 chr5D 100.000 5224 0 0 1 5224 269344959 269339736 0.000000e+00 9648.0
1 TraesCS5D01G172500 chr5D 98.913 92 1 0 2662 2753 269342209 269342118 1.160000e-36 165.0
2 TraesCS5D01G172500 chr5D 98.913 92 1 0 2751 2842 269342298 269342207 1.160000e-36 165.0
3 TraesCS5D01G172500 chr5D 92.683 82 6 0 5020 5101 269339859 269339940 9.190000e-23 119.0
4 TraesCS5D01G172500 chr5D 80.488 123 22 2 472 593 489314555 489314434 5.570000e-15 93.5
5 TraesCS5D01G172500 chr5A 98.058 2111 35 5 2662 4768 358049503 358047395 0.000000e+00 3666.0
6 TraesCS5D01G172500 chr5A 95.054 2123 42 17 769 2842 358051520 358049412 0.000000e+00 3280.0
7 TraesCS5D01G172500 chr5A 92.073 328 15 3 4700 5019 358047412 358047088 7.980000e-123 451.0
8 TraesCS5D01G172500 chr5A 80.500 600 101 11 3 593 550636233 550636825 3.710000e-121 446.0
9 TraesCS5D01G172500 chr5A 92.623 122 5 3 5103 5224 358047085 358046968 6.950000e-39 172.0
10 TraesCS5D01G172500 chr5A 88.136 118 10 3 617 733 358051619 358051505 2.540000e-28 137.0
11 TraesCS5D01G172500 chr5A 93.878 49 3 0 5011 5059 361911652 361911604 2.020000e-09 75.0
12 TraesCS5D01G172500 chr5B 95.635 2016 66 9 2751 4757 305055416 305053414 0.000000e+00 3216.0
13 TraesCS5D01G172500 chr5B 93.585 2042 65 13 769 2753 305057357 305055325 0.000000e+00 2985.0
14 TraesCS5D01G172500 chr5B 90.462 650 58 4 1 649 305058302 305057656 0.000000e+00 854.0
15 TraesCS5D01G172500 chr5B 89.362 141 2 5 4881 5019 305053153 305053024 1.160000e-36 165.0
16 TraesCS5D01G172500 chr5B 91.860 86 7 0 648 733 305057427 305057342 2.560000e-23 121.0
17 TraesCS5D01G172500 chr7D 89.505 1534 134 14 2755 4265 45655987 45654458 0.000000e+00 1916.0
18 TraesCS5D01G172500 chr7D 86.316 570 58 6 1745 2303 45656775 45656215 2.080000e-168 603.0
19 TraesCS5D01G172500 chr7D 90.764 314 26 1 2443 2753 45656213 45655900 2.910000e-112 416.0
20 TraesCS5D01G172500 chr7D 90.598 234 19 1 2022 2252 45570444 45570677 1.830000e-79 307.0
21 TraesCS5D01G172500 chr7D 83.333 246 27 8 1745 1976 45570179 45570424 1.140000e-51 215.0
22 TraesCS5D01G172500 chr7D 88.435 147 14 3 4134 4279 45570686 45570830 1.930000e-39 174.0
23 TraesCS5D01G172500 chr7D 88.764 89 10 0 5016 5104 608441707 608441619 5.530000e-20 110.0
24 TraesCS5D01G172500 chr4A 89.498 1533 134 13 2755 4265 658224727 658223200 0.000000e+00 1914.0
25 TraesCS5D01G172500 chr4A 89.090 1549 135 17 2755 4277 657889286 657890826 0.000000e+00 1893.0
26 TraesCS5D01G172500 chr4A 88.411 535 47 9 1731 2251 657888190 657888723 9.550000e-177 630.0
27 TraesCS5D01G172500 chr4A 87.449 486 38 5 1832 2303 658225431 658224955 5.950000e-149 538.0
28 TraesCS5D01G172500 chr4A 92.357 314 21 2 2443 2753 658224953 658224640 1.330000e-120 444.0
29 TraesCS5D01G172500 chr4A 90.441 272 26 0 2482 2753 657889102 657889373 4.970000e-95 359.0
30 TraesCS5D01G172500 chr4A 85.000 160 15 6 4410 4564 658223146 658222991 2.520000e-33 154.0
31 TraesCS5D01G172500 chr4A 91.071 56 5 0 5018 5073 42785090 42785035 5.610000e-10 76.8
32 TraesCS5D01G172500 chr4A 89.655 58 6 0 5048 5105 42785035 42785092 2.020000e-09 75.0
33 TraesCS5D01G172500 chr7A 88.730 1535 132 19 2755 4265 47696085 47697602 0.000000e+00 1838.0
34 TraesCS5D01G172500 chr7A 88.315 1472 138 14 2755 4205 47796635 47795177 0.000000e+00 1735.0
35 TraesCS5D01G172500 chr7A 85.787 591 56 12 1731 2303 47797443 47796863 7.490000e-168 601.0
36 TraesCS5D01G172500 chr7A 85.114 571 68 10 1745 2303 47695313 47695878 7.590000e-158 568.0
37 TraesCS5D01G172500 chr7A 90.446 314 27 1 2443 2753 47796861 47796548 1.350000e-110 411.0
38 TraesCS5D01G172500 chr7A 85.350 314 22 7 2443 2753 47695880 47696172 2.360000e-78 303.0
39 TraesCS5D01G172500 chr2B 87.475 503 52 5 1811 2303 275457196 275456695 2.110000e-158 569.0
40 TraesCS5D01G172500 chr2B 88.462 104 12 0 2443 2546 275456693 275456590 5.490000e-25 126.0
41 TraesCS5D01G172500 chr2B 81.944 144 26 0 450 593 25405134 25404991 7.100000e-24 122.0
42 TraesCS5D01G172500 chr2B 94.595 37 2 0 5065 5101 737625524 737625560 2.030000e-04 58.4
43 TraesCS5D01G172500 chr4D 74.951 507 109 14 108 603 1363030 1362531 3.170000e-52 217.0
44 TraesCS5D01G172500 chr4D 85.714 84 6 2 5018 5101 85535465 85535542 3.350000e-12 84.2
45 TraesCS5D01G172500 chr3D 73.441 497 122 7 110 599 436229400 436229893 1.490000e-40 178.0
46 TraesCS5D01G172500 chr3D 87.931 116 11 2 4408 4522 566397754 566397867 3.280000e-27 134.0
47 TraesCS5D01G172500 chr3D 78.808 151 25 5 4457 4601 566112217 566112366 1.550000e-15 95.3
48 TraesCS5D01G172500 chr2D 72.855 571 129 21 43 598 537303205 537302646 6.950000e-39 172.0
49 TraesCS5D01G172500 chrUn 73.291 468 113 10 131 590 153373647 153374110 1.510000e-35 161.0
50 TraesCS5D01G172500 chr3B 88.525 122 11 2 4408 4528 755606978 755606859 1.520000e-30 145.0
51 TraesCS5D01G172500 chr3B 80.729 192 27 7 4417 4601 754723117 754722929 1.960000e-29 141.0
52 TraesCS5D01G172500 chr3B 80.000 205 27 9 4408 4601 754772735 754772534 7.050000e-29 139.0
53 TraesCS5D01G172500 chr3B 95.349 43 2 0 5017 5059 257211128 257211086 9.390000e-08 69.4
54 TraesCS5D01G172500 chr3A 72.391 460 115 8 136 587 725408845 725409300 9.120000e-28 135.0
55 TraesCS5D01G172500 chr6D 80.247 162 32 0 465 626 335323324 335323163 7.100000e-24 122.0
56 TraesCS5D01G172500 chr1B 79.104 134 28 0 472 605 617812164 617812297 5.570000e-15 93.5
57 TraesCS5D01G172500 chr7B 90.141 71 5 2 5015 5084 610556396 610556327 2.000000e-14 91.6
58 TraesCS5D01G172500 chr7B 89.394 66 5 2 5037 5101 610556327 610556391 1.210000e-11 82.4
59 TraesCS5D01G172500 chr7B 93.333 45 3 0 5015 5059 680190559 680190603 3.380000e-07 67.6
60 TraesCS5D01G172500 chr7B 70.710 338 83 13 263 590 117151007 117151338 1.570000e-05 62.1
61 TraesCS5D01G172500 chr1D 71.512 344 86 7 264 599 452247523 452247184 1.210000e-11 82.4


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 TraesCS5D01G172500 chr5D 269339736 269344959 5223 True 3326.000000 9648 99.275333 1 5224 3 chr5D.!!$R2 5223
1 TraesCS5D01G172500 chr5A 358046968 358051619 4651 True 1541.200000 3666 93.188800 617 5224 5 chr5A.!!$R2 4607
2 TraesCS5D01G172500 chr5A 550636233 550636825 592 False 446.000000 446 80.500000 3 593 1 chr5A.!!$F1 590
3 TraesCS5D01G172500 chr5B 305053024 305058302 5278 True 1468.200000 3216 92.180800 1 5019 5 chr5B.!!$R1 5018
4 TraesCS5D01G172500 chr7D 45654458 45656775 2317 True 978.333333 1916 88.861667 1745 4265 3 chr7D.!!$R2 2520
5 TraesCS5D01G172500 chr7D 45570179 45570830 651 False 232.000000 307 87.455333 1745 4279 3 chr7D.!!$F1 2534
6 TraesCS5D01G172500 chr4A 657888190 657890826 2636 False 960.666667 1893 89.314000 1731 4277 3 chr4A.!!$F2 2546
7 TraesCS5D01G172500 chr4A 658222991 658225431 2440 True 762.500000 1914 88.576000 1832 4564 4 chr4A.!!$R2 2732
8 TraesCS5D01G172500 chr7A 47795177 47797443 2266 True 915.666667 1735 88.182667 1731 4205 3 chr7A.!!$R1 2474
9 TraesCS5D01G172500 chr7A 47695313 47697602 2289 False 903.000000 1838 86.398000 1745 4265 3 chr7A.!!$F1 2520
10 TraesCS5D01G172500 chr2B 275456590 275457196 606 True 347.500000 569 87.968500 1811 2546 2 chr2B.!!$R2 735

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
777 1012 0.108041 ACCACGTGTGAACCGACTTT 60.108 50.0 15.65 0.0 0.00 2.66 F
2075 2395 0.171903 ACTGCAAATTCATCCGCTGC 59.828 50.0 0.00 0.0 0.00 5.25 F
2566 3061 0.251077 CTGCCAAGGCTCCTGTTCTT 60.251 55.0 12.96 0.0 42.51 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 3029 2.556114 CCTTGGCAGGTCTTTGAGGAAT 60.556 50.000 0.00 0.0 35.06 3.01 R
2908 3584 1.971481 TGATGCCCATCCTTTCATCG 58.029 50.000 5.86 0.0 38.43 3.84 R
4315 5038 2.090524 GTCGGTCCAGTAAACGGCG 61.091 63.158 4.80 4.8 0.00 6.46 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 1.321474 CTTGCAAGAAGGCCTTCACA 58.679 50.000 39.84 31.43 41.84 3.58
38 40 3.837355 AGAAGGCCTTCACATTCTGTTT 58.163 40.909 39.84 17.88 41.84 2.83
40 42 5.385198 AGAAGGCCTTCACATTCTGTTTAA 58.615 37.500 39.84 0.00 41.84 1.52
41 43 5.833131 AGAAGGCCTTCACATTCTGTTTAAA 59.167 36.000 39.84 0.00 41.84 1.52
99 101 5.906838 TGATTTATCACGATTAATGCGTTGC 59.093 36.000 0.08 0.00 40.44 4.17
103 105 1.135546 CACGATTAATGCGTTGCCCAA 60.136 47.619 0.08 0.00 40.44 4.12
105 107 1.917303 CGATTAATGCGTTGCCCAAAC 59.083 47.619 0.08 0.00 35.25 2.93
106 108 2.669670 CGATTAATGCGTTGCCCAAACA 60.670 45.455 0.08 0.00 38.84 2.83
110 112 2.027460 GCGTTGCCCAAACACCTG 59.973 61.111 0.00 0.00 38.84 4.00
164 166 3.944476 CTCCACTAGCACTTGCCTT 57.056 52.632 0.00 0.00 43.38 4.35
178 180 5.466393 GCACTTGCCTTGAAAAACAATATGT 59.534 36.000 0.00 0.00 37.88 2.29
199 201 6.403333 TGTTGTCATCTGCGAATAGTAAAC 57.597 37.500 0.00 0.00 0.00 2.01
254 256 5.134725 AGCCCATTTAGATTGGATGACTT 57.865 39.130 0.00 0.00 36.26 3.01
290 292 1.122019 AGGCACGAAAGACCCTCTGT 61.122 55.000 0.00 0.00 31.46 3.41
316 318 6.156949 TGCTATCAAGAAAAGGTATGGAGAGT 59.843 38.462 0.00 0.00 0.00 3.24
336 338 3.231298 GGGTCTCCCAATCCCTCG 58.769 66.667 0.00 0.00 44.65 4.63
338 340 0.764752 GGGTCTCCCAATCCCTCGAT 60.765 60.000 0.00 0.00 44.65 3.59
340 342 2.541466 GGTCTCCCAATCCCTCGATAT 58.459 52.381 0.00 0.00 0.00 1.63
354 356 1.933181 TCGATATGCTTTGAACCGCTG 59.067 47.619 0.00 0.00 0.00 5.18
357 359 3.002656 CGATATGCTTTGAACCGCTGAAT 59.997 43.478 0.00 0.00 0.00 2.57
360 365 3.011949 TGCTTTGAACCGCTGAATTTC 57.988 42.857 0.00 0.00 0.00 2.17
427 432 5.626578 GCCCATTACAATATGCACCAACTTT 60.627 40.000 0.00 0.00 0.00 2.66
456 461 6.926630 AAAAACCCAGCCTGAACATTATTA 57.073 33.333 0.00 0.00 0.00 0.98
518 523 2.408271 TATCAAGCTTCAGGGCACAG 57.592 50.000 0.00 0.00 34.17 3.66
574 579 3.641434 ATGAAGGCACTCATAAGCTGT 57.359 42.857 0.66 0.00 38.49 4.40
605 610 9.634021 ATGTTGTCAGTAATGAGTCTATCTAGA 57.366 33.333 0.00 0.00 0.00 2.43
612 617 8.994170 CAGTAATGAGTCTATCTAGAACGATGA 58.006 37.037 0.00 0.00 33.47 2.92
640 645 8.258007 AGATTGTTCCTCTCGTATAATGTTTGA 58.742 33.333 0.00 0.00 0.00 2.69
641 646 8.964476 ATTGTTCCTCTCGTATAATGTTTGAT 57.036 30.769 0.00 0.00 0.00 2.57
699 934 2.124151 GGCAAGTCCCGCATCCAT 60.124 61.111 0.00 0.00 0.00 3.41
733 968 3.810310 TGGCAACCGACTTTGATTTTT 57.190 38.095 0.00 0.00 0.00 1.94
764 999 7.916914 AAATTGTTTAGATAGCTTACCACGT 57.083 32.000 0.00 0.00 0.00 4.49
765 1000 6.903883 ATTGTTTAGATAGCTTACCACGTG 57.096 37.500 9.08 9.08 0.00 4.49
766 1001 5.395682 TGTTTAGATAGCTTACCACGTGT 57.604 39.130 15.65 5.35 0.00 4.49
767 1002 5.165676 TGTTTAGATAGCTTACCACGTGTG 58.834 41.667 15.65 8.62 0.00 3.82
768 1003 5.047872 TGTTTAGATAGCTTACCACGTGTGA 60.048 40.000 15.65 0.00 0.00 3.58
769 1004 5.648178 TTAGATAGCTTACCACGTGTGAA 57.352 39.130 15.65 6.99 0.00 3.18
770 1005 3.846360 AGATAGCTTACCACGTGTGAAC 58.154 45.455 15.65 0.00 0.00 3.18
771 1006 2.443887 TAGCTTACCACGTGTGAACC 57.556 50.000 15.65 0.00 0.00 3.62
772 1007 0.599204 AGCTTACCACGTGTGAACCG 60.599 55.000 15.65 0.00 0.00 4.44
773 1008 0.598158 GCTTACCACGTGTGAACCGA 60.598 55.000 15.65 0.00 0.00 4.69
774 1009 1.134226 CTTACCACGTGTGAACCGAC 58.866 55.000 15.65 0.00 0.00 4.79
775 1010 0.746063 TTACCACGTGTGAACCGACT 59.254 50.000 15.65 0.00 0.00 4.18
776 1011 0.746063 TACCACGTGTGAACCGACTT 59.254 50.000 15.65 0.00 0.00 3.01
777 1012 0.108041 ACCACGTGTGAACCGACTTT 60.108 50.000 15.65 0.00 0.00 2.66
778 1013 0.303493 CCACGTGTGAACCGACTTTG 59.697 55.000 15.65 0.00 0.00 2.77
779 1014 1.282817 CACGTGTGAACCGACTTTGA 58.717 50.000 7.58 0.00 0.00 2.69
780 1015 1.864711 CACGTGTGAACCGACTTTGAT 59.135 47.619 7.58 0.00 0.00 2.57
781 1016 2.286833 CACGTGTGAACCGACTTTGATT 59.713 45.455 7.58 0.00 0.00 2.57
782 1017 2.940410 ACGTGTGAACCGACTTTGATTT 59.060 40.909 0.00 0.00 0.00 2.17
783 1018 3.375922 ACGTGTGAACCGACTTTGATTTT 59.624 39.130 0.00 0.00 0.00 1.82
856 1093 3.832490 ACAGGCCTCATAGCATTCGTATA 59.168 43.478 0.00 0.00 0.00 1.47
982 1224 3.382832 CCCGTCTGAAGCCGACCT 61.383 66.667 0.00 0.00 0.00 3.85
985 1227 1.513158 CGTCTGAAGCCGACCTCAT 59.487 57.895 0.00 0.00 0.00 2.90
1351 1611 2.432628 GGAAGGACCACGACAGCG 60.433 66.667 0.00 0.00 44.79 5.18
1352 1612 2.432628 GAAGGACCACGACAGCGG 60.433 66.667 0.00 0.00 43.17 5.52
1353 1613 3.222354 GAAGGACCACGACAGCGGT 62.222 63.158 0.00 0.00 43.17 5.68
1354 1614 3.515316 AAGGACCACGACAGCGGTG 62.515 63.158 14.13 14.13 43.17 4.94
1522 1788 1.205460 TAAGGGGGACAAGGGCAGTC 61.205 60.000 0.00 0.00 35.29 3.51
1554 1844 1.198713 ATGGAGATTCACAGAGCGGT 58.801 50.000 0.00 0.00 0.00 5.68
1581 1871 7.361713 GCAGCCACTAATGTAAGTATTTTGTGA 60.362 37.037 0.00 0.00 31.23 3.58
1640 1934 5.163322 TGTTTCTGAATTGGGCAAGTGATTT 60.163 36.000 0.00 0.00 0.00 2.17
1650 1944 3.774066 GGCAAGTGATTTCTAATGTGCC 58.226 45.455 0.00 0.00 43.10 5.01
1796 2101 6.178324 AGCCCAATAAGTACTTCTGTTTACC 58.822 40.000 12.39 0.00 0.00 2.85
1887 2200 3.632643 TCCTATGCTGACTTTGCATCA 57.367 42.857 4.42 0.00 46.80 3.07
2075 2395 0.171903 ACTGCAAATTCATCCGCTGC 59.828 50.000 0.00 0.00 0.00 5.25
2534 3029 4.412843 TGGTACATCCAGTGAACTGACTA 58.587 43.478 12.05 0.00 46.59 2.59
2566 3061 0.251077 CTGCCAAGGCTCCTGTTCTT 60.251 55.000 12.96 0.00 42.51 2.52
2733 3409 6.183360 CCACTACTTTTGGTTCATCCTTTGTT 60.183 38.462 0.00 0.00 37.07 2.83
2734 3410 7.013846 CCACTACTTTTGGTTCATCCTTTGTTA 59.986 37.037 0.00 0.00 37.07 2.41
2735 3411 8.076178 CACTACTTTTGGTTCATCCTTTGTTAG 58.924 37.037 0.00 0.00 37.07 2.34
2736 3412 6.405278 ACTTTTGGTTCATCCTTTGTTAGG 57.595 37.500 0.00 0.00 46.27 2.69
2737 3413 5.897250 ACTTTTGGTTCATCCTTTGTTAGGT 59.103 36.000 0.00 0.00 45.03 3.08
2738 3414 6.040504 ACTTTTGGTTCATCCTTTGTTAGGTC 59.959 38.462 0.00 0.00 45.03 3.85
2739 3415 4.715534 TGGTTCATCCTTTGTTAGGTCA 57.284 40.909 0.00 0.00 45.03 4.02
2740 3416 5.055265 TGGTTCATCCTTTGTTAGGTCAA 57.945 39.130 0.00 0.00 45.03 3.18
2741 3417 4.825085 TGGTTCATCCTTTGTTAGGTCAAC 59.175 41.667 0.00 0.00 45.03 3.18
2742 3418 4.825085 GGTTCATCCTTTGTTAGGTCAACA 59.175 41.667 0.00 0.00 45.49 3.33
2743 3419 5.476945 GGTTCATCCTTTGTTAGGTCAACAT 59.523 40.000 0.00 0.00 46.38 2.71
2744 3420 6.015434 GGTTCATCCTTTGTTAGGTCAACATT 60.015 38.462 0.00 0.00 46.38 2.71
2745 3421 7.175990 GGTTCATCCTTTGTTAGGTCAACATTA 59.824 37.037 0.00 0.00 46.38 1.90
2746 3422 8.573035 GTTCATCCTTTGTTAGGTCAACATTAA 58.427 33.333 0.00 0.00 46.38 1.40
2747 3423 8.106247 TCATCCTTTGTTAGGTCAACATTAAC 57.894 34.615 0.00 0.00 46.38 2.01
2748 3424 7.721842 TCATCCTTTGTTAGGTCAACATTAACA 59.278 33.333 5.77 5.77 46.38 2.41
2749 3425 7.883391 TCCTTTGTTAGGTCAACATTAACAA 57.117 32.000 13.59 13.59 46.38 2.83
2750 3426 7.936584 TCCTTTGTTAGGTCAACATTAACAAG 58.063 34.615 15.51 12.06 46.38 3.16
2751 3427 6.640907 CCTTTGTTAGGTCAACATTAACAAGC 59.359 38.462 15.51 0.00 46.38 4.01
2752 3428 6.701145 TTGTTAGGTCAACATTAACAAGCA 57.299 33.333 13.59 0.26 46.38 3.91
2753 3429 6.892658 TGTTAGGTCAACATTAACAAGCAT 57.107 33.333 6.89 0.00 42.29 3.79
2754 3430 6.908825 TGTTAGGTCAACATTAACAAGCATC 58.091 36.000 6.89 0.00 42.29 3.91
2755 3431 6.714810 TGTTAGGTCAACATTAACAAGCATCT 59.285 34.615 6.89 0.00 42.29 2.90
2756 3432 7.230510 TGTTAGGTCAACATTAACAAGCATCTT 59.769 33.333 6.89 0.00 42.29 2.40
2757 3433 8.726988 GTTAGGTCAACATTAACAAGCATCTTA 58.273 33.333 0.00 0.00 37.09 2.10
2758 3434 7.759489 AGGTCAACATTAACAAGCATCTTAA 57.241 32.000 0.00 0.00 0.00 1.85
2759 3435 7.593825 AGGTCAACATTAACAAGCATCTTAAC 58.406 34.615 0.00 0.00 0.00 2.01
2760 3436 7.230510 AGGTCAACATTAACAAGCATCTTAACA 59.769 33.333 0.00 0.00 0.00 2.41
2761 3437 8.028938 GGTCAACATTAACAAGCATCTTAACAT 58.971 33.333 0.00 0.00 0.00 2.71
2772 3448 9.851686 ACAAGCATCTTAACATATATTTCAGGA 57.148 29.630 0.00 0.00 0.00 3.86
2792 3468 8.712228 TCAGGATGATATGTAGTTCTGTACAT 57.288 34.615 0.00 2.34 42.56 2.29
2793 3469 9.147732 TCAGGATGATATGTAGTTCTGTACATT 57.852 33.333 0.00 0.00 42.56 2.71
2794 3470 9.201127 CAGGATGATATGTAGTTCTGTACATTG 57.799 37.037 0.00 0.00 40.47 2.82
2795 3471 9.147732 AGGATGATATGTAGTTCTGTACATTGA 57.852 33.333 0.00 0.00 40.09 2.57
2796 3472 9.197694 GGATGATATGTAGTTCTGTACATTGAC 57.802 37.037 0.00 0.00 40.09 3.18
2797 3473 9.197694 GATGATATGTAGTTCTGTACATTGACC 57.802 37.037 0.00 0.00 40.09 4.02
2798 3474 7.497595 TGATATGTAGTTCTGTACATTGACCC 58.502 38.462 0.00 0.00 40.09 4.46
2799 3475 5.755409 ATGTAGTTCTGTACATTGACCCA 57.245 39.130 0.00 0.00 40.09 4.51
2800 3476 4.890088 TGTAGTTCTGTACATTGACCCAC 58.110 43.478 0.00 0.00 0.00 4.61
2801 3477 4.591498 TGTAGTTCTGTACATTGACCCACT 59.409 41.667 0.00 0.00 0.00 4.00
2802 3478 5.776208 TGTAGTTCTGTACATTGACCCACTA 59.224 40.000 0.00 0.00 0.00 2.74
2803 3479 5.148651 AGTTCTGTACATTGACCCACTAC 57.851 43.478 0.00 0.00 0.00 2.73
2804 3480 4.838986 AGTTCTGTACATTGACCCACTACT 59.161 41.667 0.00 0.00 0.00 2.57
2805 3481 5.307196 AGTTCTGTACATTGACCCACTACTT 59.693 40.000 0.00 0.00 0.00 2.24
2806 3482 5.818678 TCTGTACATTGACCCACTACTTT 57.181 39.130 0.00 0.00 0.00 2.66
2807 3483 6.182507 TCTGTACATTGACCCACTACTTTT 57.817 37.500 0.00 0.00 0.00 2.27
2808 3484 5.995282 TCTGTACATTGACCCACTACTTTTG 59.005 40.000 0.00 0.00 0.00 2.44
2809 3485 5.067273 TGTACATTGACCCACTACTTTTGG 58.933 41.667 0.00 0.00 0.00 3.28
2810 3486 4.178956 ACATTGACCCACTACTTTTGGT 57.821 40.909 0.00 0.00 31.46 3.67
2811 3487 4.542697 ACATTGACCCACTACTTTTGGTT 58.457 39.130 0.00 0.00 31.46 3.67
2812 3488 4.583073 ACATTGACCCACTACTTTTGGTTC 59.417 41.667 0.00 0.00 31.46 3.62
2813 3489 3.935818 TGACCCACTACTTTTGGTTCA 57.064 42.857 0.00 0.00 33.44 3.18
2814 3490 4.447138 TGACCCACTACTTTTGGTTCAT 57.553 40.909 0.00 0.00 31.06 2.57
2815 3491 4.394729 TGACCCACTACTTTTGGTTCATC 58.605 43.478 0.00 0.00 31.06 2.92
2816 3492 3.756963 GACCCACTACTTTTGGTTCATCC 59.243 47.826 0.00 0.00 31.46 3.51
2817 3493 3.397955 ACCCACTACTTTTGGTTCATCCT 59.602 43.478 0.00 0.00 37.07 3.24
2818 3494 4.141018 ACCCACTACTTTTGGTTCATCCTT 60.141 41.667 0.00 0.00 37.07 3.36
2819 3495 4.832823 CCCACTACTTTTGGTTCATCCTTT 59.167 41.667 0.00 0.00 37.07 3.11
2820 3496 5.278957 CCCACTACTTTTGGTTCATCCTTTG 60.279 44.000 0.00 0.00 37.07 2.77
2821 3497 5.301805 CCACTACTTTTGGTTCATCCTTTGT 59.698 40.000 0.00 0.00 37.07 2.83
2908 3584 5.107722 GCTTGCAAAAGCTACTGTTCATTTC 60.108 40.000 0.00 0.00 42.32 2.17
3026 3702 4.074970 ACTGCAGAGGATTAAGGTTTGTG 58.925 43.478 23.35 0.00 0.00 3.33
3311 3997 4.988540 CCTCACTCTGTTGATCGTTTGTAA 59.011 41.667 0.00 0.00 0.00 2.41
3776 4469 1.067974 TCAGAACGCCGTGAGAAGAAA 59.932 47.619 0.00 0.00 0.00 2.52
4315 5038 1.137872 AGACTGCTGTATGCTAGCACC 59.862 52.381 22.07 14.35 45.52 5.01
4344 5070 4.451629 ACTGGACCGACTACTTTGTATG 57.548 45.455 0.00 0.00 0.00 2.39
4562 5296 1.338105 TGCTAGCACGATGAAGTTGCT 60.338 47.619 14.93 0.42 39.36 3.91
4589 5323 4.021719 TCCGATCTAAACTTTTCCGTCACT 60.022 41.667 0.00 0.00 0.00 3.41
4596 5330 7.211573 TCTAAACTTTTCCGTCACTGAACATA 58.788 34.615 0.00 0.00 0.00 2.29
4626 5361 1.944709 AGGTTAGTCGTGCAAAACCAC 59.055 47.619 14.73 5.50 43.14 4.16
4671 5414 3.635591 CCCCAAATCAATCTAACTGGCT 58.364 45.455 0.00 0.00 0.00 4.75
4672 5415 4.026052 CCCCAAATCAATCTAACTGGCTT 58.974 43.478 0.00 0.00 0.00 4.35
4673 5416 4.467438 CCCCAAATCAATCTAACTGGCTTT 59.533 41.667 0.00 0.00 0.00 3.51
4674 5417 5.413499 CCCAAATCAATCTAACTGGCTTTG 58.587 41.667 0.00 0.00 0.00 2.77
4675 5418 5.413499 CCAAATCAATCTAACTGGCTTTGG 58.587 41.667 0.00 0.00 36.51 3.28
4676 5419 4.725790 AATCAATCTAACTGGCTTTGGC 57.274 40.909 0.00 0.00 37.82 4.52
4715 5458 5.105146 TCAGGTGTGGTTTGTGCTAATTTTT 60.105 36.000 0.00 0.00 0.00 1.94
4768 5560 4.662468 TGAGGTTTGTGCTAATTTTGCA 57.338 36.364 1.26 1.26 38.19 4.08
4790 5582 3.287867 AAGCCGGACAATCTCATTGAT 57.712 42.857 5.05 0.00 42.83 2.57
4800 5592 4.100529 CAATCTCATTGATGAACAACGGC 58.899 43.478 0.00 0.00 42.83 5.68
4855 5647 0.621571 TGTCATGCCCCTAGCCTCTT 60.622 55.000 0.00 0.00 42.71 2.85
4856 5648 0.107643 GTCATGCCCCTAGCCTCTTC 59.892 60.000 0.00 0.00 42.71 2.87
4862 5654 1.348775 CCCCTAGCCTCTTCCCCAAG 61.349 65.000 0.00 0.00 0.00 3.61
4889 5681 1.134560 CCTTGCAGAGTAGTACCCGTC 59.865 57.143 0.00 0.00 0.00 4.79
4910 5791 2.508361 GGGCATGATTGTTCCCCAG 58.492 57.895 0.00 0.00 35.75 4.45
5019 5909 7.745022 TTTGCACATAAGTCATACGTACTAC 57.255 36.000 0.00 0.00 0.00 2.73
5021 5911 6.722301 TGCACATAAGTCATACGTACTACTC 58.278 40.000 11.03 1.03 0.00 2.59
5022 5912 6.541278 TGCACATAAGTCATACGTACTACTCT 59.459 38.462 11.03 5.91 0.00 3.24
5023 5913 7.070798 GCACATAAGTCATACGTACTACTCTC 58.929 42.308 11.03 0.00 0.00 3.20
5024 5914 7.041916 GCACATAAGTCATACGTACTACTCTCT 60.042 40.741 11.03 1.16 0.00 3.10
5025 5915 8.489559 CACATAAGTCATACGTACTACTCTCTC 58.510 40.741 11.03 0.00 0.00 3.20
5026 5916 7.656948 ACATAAGTCATACGTACTACTCTCTCC 59.343 40.741 11.03 0.00 0.00 3.71
5027 5917 5.611128 AGTCATACGTACTACTCTCTCCA 57.389 43.478 0.00 0.00 0.00 3.86
5028 5918 6.177310 AGTCATACGTACTACTCTCTCCAT 57.823 41.667 0.00 0.00 0.00 3.41
5029 5919 6.225318 AGTCATACGTACTACTCTCTCCATC 58.775 44.000 0.00 0.00 0.00 3.51
5030 5920 5.409214 GTCATACGTACTACTCTCTCCATCC 59.591 48.000 0.00 0.00 0.00 3.51
5031 5921 3.211718 ACGTACTACTCTCTCCATCCC 57.788 52.381 0.00 0.00 0.00 3.85
5032 5922 2.508716 ACGTACTACTCTCTCCATCCCA 59.491 50.000 0.00 0.00 0.00 4.37
5033 5923 3.053842 ACGTACTACTCTCTCCATCCCAA 60.054 47.826 0.00 0.00 0.00 4.12
5034 5924 3.952323 CGTACTACTCTCTCCATCCCAAA 59.048 47.826 0.00 0.00 0.00 3.28
5035 5925 4.401519 CGTACTACTCTCTCCATCCCAAAA 59.598 45.833 0.00 0.00 0.00 2.44
5036 5926 5.069251 CGTACTACTCTCTCCATCCCAAAAT 59.931 44.000 0.00 0.00 0.00 1.82
5037 5927 6.264744 CGTACTACTCTCTCCATCCCAAAATA 59.735 42.308 0.00 0.00 0.00 1.40
5038 5928 7.201884 CGTACTACTCTCTCCATCCCAAAATAA 60.202 40.741 0.00 0.00 0.00 1.40
5039 5929 7.130681 ACTACTCTCTCCATCCCAAAATAAG 57.869 40.000 0.00 0.00 0.00 1.73
5040 5930 6.674419 ACTACTCTCTCCATCCCAAAATAAGT 59.326 38.462 0.00 0.00 0.00 2.24
5041 5931 5.749462 ACTCTCTCCATCCCAAAATAAGTG 58.251 41.667 0.00 0.00 0.00 3.16
5042 5932 5.488919 ACTCTCTCCATCCCAAAATAAGTGA 59.511 40.000 0.00 0.00 0.00 3.41
5043 5933 5.745227 TCTCTCCATCCCAAAATAAGTGAC 58.255 41.667 0.00 0.00 0.00 3.67
5044 5934 5.488919 TCTCTCCATCCCAAAATAAGTGACT 59.511 40.000 0.00 0.00 0.00 3.41
5045 5935 5.745227 TCTCCATCCCAAAATAAGTGACTC 58.255 41.667 0.00 0.00 0.00 3.36
5046 5936 4.513442 TCCATCCCAAAATAAGTGACTCG 58.487 43.478 0.00 0.00 0.00 4.18
5047 5937 4.224147 TCCATCCCAAAATAAGTGACTCGA 59.776 41.667 0.00 0.00 0.00 4.04
5048 5938 5.104527 TCCATCCCAAAATAAGTGACTCGAT 60.105 40.000 0.00 0.00 0.00 3.59
5049 5939 5.590259 CCATCCCAAAATAAGTGACTCGATT 59.410 40.000 0.00 0.00 0.00 3.34
5050 5940 6.095440 CCATCCCAAAATAAGTGACTCGATTT 59.905 38.462 0.00 0.00 0.00 2.17
5051 5941 7.362920 CCATCCCAAAATAAGTGACTCGATTTT 60.363 37.037 10.62 10.62 32.97 1.82
5052 5942 6.908825 TCCCAAAATAAGTGACTCGATTTTG 58.091 36.000 24.49 24.49 43.82 2.44
5053 5943 6.488683 TCCCAAAATAAGTGACTCGATTTTGT 59.511 34.615 26.72 7.57 43.18 2.83
5054 5944 7.662258 TCCCAAAATAAGTGACTCGATTTTGTA 59.338 33.333 26.72 18.74 43.18 2.41
5055 5945 7.749126 CCCAAAATAAGTGACTCGATTTTGTAC 59.251 37.037 26.72 0.00 43.18 2.90
5056 5946 8.504005 CCAAAATAAGTGACTCGATTTTGTACT 58.496 33.333 26.72 6.58 43.18 2.73
5061 5951 9.924650 ATAAGTGACTCGATTTTGTACTAAAGT 57.075 29.630 8.41 0.92 0.00 2.66
5062 5952 8.658499 AAGTGACTCGATTTTGTACTAAAGTT 57.342 30.769 8.41 0.00 0.00 2.66
5063 5953 9.754382 AAGTGACTCGATTTTGTACTAAAGTTA 57.246 29.630 8.41 0.00 0.00 2.24
5064 5954 9.754382 AGTGACTCGATTTTGTACTAAAGTTAA 57.246 29.630 8.41 0.00 0.00 2.01
5091 5981 8.801882 ATAAAATCGAGTCACTTATTTTGGGA 57.198 30.769 16.52 3.75 34.37 4.37
5092 5982 7.703058 AAAATCGAGTCACTTATTTTGGGAT 57.297 32.000 9.78 0.00 31.99 3.85
5093 5983 6.683974 AATCGAGTCACTTATTTTGGGATG 57.316 37.500 0.00 0.00 0.00 3.51
5094 5984 4.513442 TCGAGTCACTTATTTTGGGATGG 58.487 43.478 0.00 0.00 0.00 3.51
5095 5985 4.224147 TCGAGTCACTTATTTTGGGATGGA 59.776 41.667 0.00 0.00 0.00 3.41
5096 5986 4.572389 CGAGTCACTTATTTTGGGATGGAG 59.428 45.833 0.00 0.00 0.00 3.86
5097 5987 5.626809 CGAGTCACTTATTTTGGGATGGAGA 60.627 44.000 0.00 0.00 0.00 3.71
5098 5988 5.749462 AGTCACTTATTTTGGGATGGAGAG 58.251 41.667 0.00 0.00 0.00 3.20
5099 5989 5.488919 AGTCACTTATTTTGGGATGGAGAGA 59.511 40.000 0.00 0.00 0.00 3.10
5100 5990 5.819901 GTCACTTATTTTGGGATGGAGAGAG 59.180 44.000 0.00 0.00 0.00 3.20
5101 5991 4.578105 CACTTATTTTGGGATGGAGAGAGC 59.422 45.833 0.00 0.00 0.00 4.09
5120 6010 1.334869 GCATTATTCTCTGCAACCCCG 59.665 52.381 0.00 0.00 38.28 5.73
5134 6024 2.342279 CCCGTCTCTCCGTTTGCA 59.658 61.111 0.00 0.00 0.00 4.08
5148 6038 3.173599 CGTTTGCAGCATGGAGTTTATG 58.826 45.455 0.00 0.00 38.09 1.90
5185 6075 4.437587 CCCCTGCTGCTCCCTTGG 62.438 72.222 0.00 0.00 0.00 3.61
5187 6077 4.044439 CCTGCTGCTCCCTTGGCT 62.044 66.667 0.00 0.00 0.00 4.75
5188 6078 2.035312 CTGCTGCTCCCTTGGCTT 59.965 61.111 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.725844 AGGTGTCCAGAGAATTTTAAACAGAAT 59.274 33.333 0.00 0.00 0.00 2.40
38 40 9.581289 TCAATAAAAGGTGTCCAGAGAATTTTA 57.419 29.630 0.00 0.00 0.00 1.52
40 42 8.477419 TTCAATAAAAGGTGTCCAGAGAATTT 57.523 30.769 0.00 0.00 0.00 1.82
41 43 7.944554 TCTTCAATAAAAGGTGTCCAGAGAATT 59.055 33.333 0.00 0.00 0.00 2.17
61 63 8.998377 TCGTGATAAATCAGTCATTTTCTTCAA 58.002 29.630 0.00 0.00 37.51 2.69
85 87 1.917303 GTTTGGGCAACGCATTAATCG 59.083 47.619 5.96 5.96 37.60 3.34
99 101 6.989169 TGAATTTTTATTGTCAGGTGTTTGGG 59.011 34.615 0.00 0.00 0.00 4.12
103 105 7.494298 GGTGTTGAATTTTTATTGTCAGGTGTT 59.506 33.333 0.00 0.00 0.00 3.32
105 107 7.169645 CAGGTGTTGAATTTTTATTGTCAGGTG 59.830 37.037 0.00 0.00 0.00 4.00
106 108 7.209475 CAGGTGTTGAATTTTTATTGTCAGGT 58.791 34.615 0.00 0.00 0.00 4.00
110 112 8.432110 AAACCAGGTGTTGAATTTTTATTGTC 57.568 30.769 0.00 0.00 37.23 3.18
178 180 4.565166 CCGTTTACTATTCGCAGATGACAA 59.435 41.667 0.00 0.00 35.04 3.18
234 236 6.039047 CAGACAAGTCATCCAATCTAAATGGG 59.961 42.308 2.72 0.00 38.54 4.00
254 256 4.072131 GTGCCTCCTAAAATCAACAGACA 58.928 43.478 0.00 0.00 0.00 3.41
290 292 6.957631 TCTCCATACCTTTTCTTGATAGCAA 58.042 36.000 0.00 0.00 0.00 3.91
336 338 4.558538 ATTCAGCGGTTCAAAGCATATC 57.441 40.909 0.00 0.00 35.48 1.63
338 340 4.380444 GGAAATTCAGCGGTTCAAAGCATA 60.380 41.667 0.00 0.00 35.48 3.14
340 342 2.288152 GGAAATTCAGCGGTTCAAAGCA 60.288 45.455 0.00 0.00 35.48 3.91
354 356 6.151817 AGTGCTCTTCAATGGTAAGGAAATTC 59.848 38.462 0.00 0.00 0.00 2.17
357 359 4.761739 CAGTGCTCTTCAATGGTAAGGAAA 59.238 41.667 0.00 0.00 37.14 3.13
360 365 3.942829 TCAGTGCTCTTCAATGGTAAGG 58.057 45.455 0.00 0.00 40.85 2.69
470 475 7.330262 TGAAAGCATATGACATAGTTGAGTGA 58.670 34.615 6.97 0.00 0.00 3.41
518 523 3.684788 ACACAACGATGAGAAATAGGCAC 59.315 43.478 0.00 0.00 0.00 5.01
600 605 5.419155 AGGAACAATCTGTCATCGTTCTAGA 59.581 40.000 0.00 0.00 36.91 2.43
603 608 4.221703 AGAGGAACAATCTGTCATCGTTCT 59.778 41.667 0.00 0.00 36.91 3.01
604 609 4.499183 AGAGGAACAATCTGTCATCGTTC 58.501 43.478 0.00 0.00 36.17 3.95
605 610 4.499183 GAGAGGAACAATCTGTCATCGTT 58.501 43.478 0.00 0.00 0.00 3.85
612 617 7.113658 ACATTATACGAGAGGAACAATCTGT 57.886 36.000 0.00 0.00 0.00 3.41
669 904 0.251787 ACTTGCCAACAGGGATTCCC 60.252 55.000 14.42 14.42 45.90 3.97
670 905 1.177401 GACTTGCCAACAGGGATTCC 58.823 55.000 0.00 0.00 40.01 3.01
671 906 1.177401 GGACTTGCCAACAGGGATTC 58.823 55.000 0.00 0.00 40.01 2.52
699 934 1.201181 GTTGCCATGATTAACCACGCA 59.799 47.619 0.00 0.00 0.00 5.24
738 973 9.439500 ACGTGGTAAGCTATCTAAACAATTTTA 57.561 29.630 0.00 0.00 0.00 1.52
739 974 8.234546 CACGTGGTAAGCTATCTAAACAATTTT 58.765 33.333 7.95 0.00 0.00 1.82
740 975 7.389607 ACACGTGGTAAGCTATCTAAACAATTT 59.610 33.333 21.57 0.00 0.00 1.82
741 976 6.877322 ACACGTGGTAAGCTATCTAAACAATT 59.123 34.615 21.57 0.00 0.00 2.32
742 977 6.312918 CACACGTGGTAAGCTATCTAAACAAT 59.687 38.462 21.57 0.00 0.00 2.71
743 978 5.636121 CACACGTGGTAAGCTATCTAAACAA 59.364 40.000 21.57 0.00 0.00 2.83
744 979 5.047872 TCACACGTGGTAAGCTATCTAAACA 60.048 40.000 21.57 0.00 0.00 2.83
745 980 5.404946 TCACACGTGGTAAGCTATCTAAAC 58.595 41.667 21.57 0.00 0.00 2.01
746 981 5.648178 TCACACGTGGTAAGCTATCTAAA 57.352 39.130 21.57 0.00 0.00 1.85
747 982 5.404946 GTTCACACGTGGTAAGCTATCTAA 58.595 41.667 21.57 0.00 0.00 2.10
748 983 4.142315 GGTTCACACGTGGTAAGCTATCTA 60.142 45.833 21.57 0.00 0.00 1.98
749 984 3.368116 GGTTCACACGTGGTAAGCTATCT 60.368 47.826 21.57 0.00 0.00 1.98
750 985 2.928116 GGTTCACACGTGGTAAGCTATC 59.072 50.000 21.57 1.34 0.00 2.08
751 986 2.673043 CGGTTCACACGTGGTAAGCTAT 60.673 50.000 21.57 0.00 0.00 2.97
752 987 1.336148 CGGTTCACACGTGGTAAGCTA 60.336 52.381 21.57 0.00 0.00 3.32
753 988 0.599204 CGGTTCACACGTGGTAAGCT 60.599 55.000 21.57 0.00 0.00 3.74
754 989 0.598158 TCGGTTCACACGTGGTAAGC 60.598 55.000 21.57 19.83 0.00 3.09
755 990 1.134226 GTCGGTTCACACGTGGTAAG 58.866 55.000 21.57 6.86 0.00 2.34
756 991 0.746063 AGTCGGTTCACACGTGGTAA 59.254 50.000 21.57 10.61 0.00 2.85
757 992 0.746063 AAGTCGGTTCACACGTGGTA 59.254 50.000 21.57 4.01 0.00 3.25
758 993 0.108041 AAAGTCGGTTCACACGTGGT 60.108 50.000 21.57 2.37 0.00 4.16
759 994 0.303493 CAAAGTCGGTTCACACGTGG 59.697 55.000 21.57 9.11 0.00 4.94
760 995 1.282817 TCAAAGTCGGTTCACACGTG 58.717 50.000 15.48 15.48 0.00 4.49
761 996 2.234300 ATCAAAGTCGGTTCACACGT 57.766 45.000 0.00 0.00 0.00 4.49
762 997 3.602390 AAATCAAAGTCGGTTCACACG 57.398 42.857 0.00 0.00 0.00 4.49
763 998 4.733405 GTCAAAATCAAAGTCGGTTCACAC 59.267 41.667 0.00 0.00 0.00 3.82
764 999 4.201970 GGTCAAAATCAAAGTCGGTTCACA 60.202 41.667 0.00 0.00 0.00 3.58
765 1000 4.287720 GGTCAAAATCAAAGTCGGTTCAC 58.712 43.478 0.00 0.00 0.00 3.18
766 1001 3.002862 CGGTCAAAATCAAAGTCGGTTCA 59.997 43.478 0.00 0.00 0.00 3.18
767 1002 3.551551 CGGTCAAAATCAAAGTCGGTTC 58.448 45.455 0.00 0.00 0.00 3.62
768 1003 2.292292 CCGGTCAAAATCAAAGTCGGTT 59.708 45.455 0.00 0.00 0.00 4.44
769 1004 1.877443 CCGGTCAAAATCAAAGTCGGT 59.123 47.619 0.00 0.00 0.00 4.69
770 1005 2.147958 TCCGGTCAAAATCAAAGTCGG 58.852 47.619 0.00 0.00 37.82 4.79
771 1006 2.806244 ACTCCGGTCAAAATCAAAGTCG 59.194 45.455 0.00 0.00 0.00 4.18
772 1007 4.406001 GACTCCGGTCAAAATCAAAGTC 57.594 45.455 0.00 0.00 41.75 3.01
794 1029 0.811915 CGGAACAGAGAGGTGACGAT 59.188 55.000 0.00 0.00 0.00 3.73
944 1181 3.164269 ATGGGAGCGCCGGAGATT 61.164 61.111 10.31 0.00 33.83 2.40
982 1224 4.492303 GGGAGGGGACGGGGATGA 62.492 72.222 0.00 0.00 0.00 2.92
985 1227 4.815973 CATGGGAGGGGACGGGGA 62.816 72.222 0.00 0.00 0.00 4.81
1236 1496 4.508128 GACCGATCCCGCTTCGCA 62.508 66.667 0.00 0.00 35.31 5.10
1326 1586 1.368579 GTGGTCCTTCCGTTTCCGA 59.631 57.895 0.00 0.00 39.52 4.55
1461 1727 4.626287 GCATCAACATCCTCAAACCTCCTA 60.626 45.833 0.00 0.00 0.00 2.94
1522 1788 3.834489 ATCTCCATTAGCACCAGACTG 57.166 47.619 0.00 0.00 0.00 3.51
1554 1844 6.432783 ACAAAATACTTACATTAGTGGCTGCA 59.567 34.615 0.50 0.00 0.00 4.41
1640 1934 5.435686 AATTGGTACTCAGGCACATTAGA 57.564 39.130 0.00 0.00 0.00 2.10
1650 1944 6.875726 TCTGAGTTCATCAAATTGGTACTCAG 59.124 38.462 23.42 23.42 45.59 3.35
1796 2101 6.840780 ACCATAGACCAAATTTCTTCCAAG 57.159 37.500 0.00 0.00 0.00 3.61
1887 2200 3.891366 GAGCACCACCCTGCAAAATATAT 59.109 43.478 0.00 0.00 39.86 0.86
2075 2395 9.360093 CATCAAGACTTAAGTTACTACTTCTGG 57.640 37.037 10.02 0.00 43.45 3.86
2534 3029 2.556114 CCTTGGCAGGTCTTTGAGGAAT 60.556 50.000 0.00 0.00 35.06 3.01
2733 3409 8.726988 GTTAAGATGCTTGTTAATGTTGACCTA 58.273 33.333 5.41 0.00 0.00 3.08
2734 3410 7.230510 TGTTAAGATGCTTGTTAATGTTGACCT 59.769 33.333 5.41 0.00 0.00 3.85
2735 3411 7.367285 TGTTAAGATGCTTGTTAATGTTGACC 58.633 34.615 5.41 0.00 0.00 4.02
2736 3412 8.970691 ATGTTAAGATGCTTGTTAATGTTGAC 57.029 30.769 5.41 0.00 0.00 3.18
2746 3422 9.851686 TCCTGAAATATATGTTAAGATGCTTGT 57.148 29.630 0.00 0.00 0.00 3.16
2764 3440 9.988815 GTACAGAACTACATATCATCCTGAAAT 57.011 33.333 0.00 0.00 0.00 2.17
2765 3441 8.977412 TGTACAGAACTACATATCATCCTGAAA 58.023 33.333 0.00 0.00 0.00 2.69
2766 3442 8.533569 TGTACAGAACTACATATCATCCTGAA 57.466 34.615 0.00 0.00 0.00 3.02
2767 3443 8.712228 ATGTACAGAACTACATATCATCCTGA 57.288 34.615 0.33 0.00 35.89 3.86
2768 3444 9.201127 CAATGTACAGAACTACATATCATCCTG 57.799 37.037 0.33 0.00 36.50 3.86
2769 3445 9.147732 TCAATGTACAGAACTACATATCATCCT 57.852 33.333 0.33 0.00 36.50 3.24
2770 3446 9.197694 GTCAATGTACAGAACTACATATCATCC 57.802 37.037 0.33 0.00 36.50 3.51
2771 3447 9.197694 GGTCAATGTACAGAACTACATATCATC 57.802 37.037 0.33 0.00 36.50 2.92
2772 3448 8.150945 GGGTCAATGTACAGAACTACATATCAT 58.849 37.037 0.33 0.00 36.50 2.45
2773 3449 7.125053 TGGGTCAATGTACAGAACTACATATCA 59.875 37.037 0.33 0.00 36.50 2.15
2774 3450 7.438459 GTGGGTCAATGTACAGAACTACATATC 59.562 40.741 10.57 0.00 36.50 1.63
2775 3451 7.125811 AGTGGGTCAATGTACAGAACTACATAT 59.874 37.037 15.83 0.00 36.50 1.78
2776 3452 6.439375 AGTGGGTCAATGTACAGAACTACATA 59.561 38.462 15.83 0.00 36.50 2.29
2777 3453 5.248477 AGTGGGTCAATGTACAGAACTACAT 59.752 40.000 15.83 2.67 38.72 2.29
2778 3454 4.591498 AGTGGGTCAATGTACAGAACTACA 59.409 41.667 15.83 8.32 35.65 2.74
2779 3455 5.148651 AGTGGGTCAATGTACAGAACTAC 57.851 43.478 8.16 8.16 33.66 2.73
2780 3456 6.014647 AGTAGTGGGTCAATGTACAGAACTA 58.985 40.000 0.33 0.00 0.00 2.24
2781 3457 4.838986 AGTAGTGGGTCAATGTACAGAACT 59.161 41.667 0.33 0.00 0.00 3.01
2782 3458 5.148651 AGTAGTGGGTCAATGTACAGAAC 57.851 43.478 0.33 0.00 0.00 3.01
2783 3459 5.818678 AAGTAGTGGGTCAATGTACAGAA 57.181 39.130 0.33 0.00 0.00 3.02
2784 3460 5.818678 AAAGTAGTGGGTCAATGTACAGA 57.181 39.130 0.33 0.00 0.00 3.41
2785 3461 5.181245 CCAAAAGTAGTGGGTCAATGTACAG 59.819 44.000 0.33 0.00 32.03 2.74
2786 3462 5.067273 CCAAAAGTAGTGGGTCAATGTACA 58.933 41.667 0.00 0.00 32.03 2.90
2787 3463 5.067954 ACCAAAAGTAGTGGGTCAATGTAC 58.932 41.667 0.00 0.00 40.75 2.90
2788 3464 5.313280 ACCAAAAGTAGTGGGTCAATGTA 57.687 39.130 0.00 0.00 40.75 2.29
2789 3465 4.178956 ACCAAAAGTAGTGGGTCAATGT 57.821 40.909 0.00 0.00 40.75 2.71
2795 3471 3.397955 AGGATGAACCAAAAGTAGTGGGT 59.602 43.478 0.00 0.00 39.40 4.51
2796 3472 4.034285 AGGATGAACCAAAAGTAGTGGG 57.966 45.455 0.00 0.00 40.75 4.61
2797 3473 5.301805 ACAAAGGATGAACCAAAAGTAGTGG 59.698 40.000 0.00 0.00 42.04 4.00
2798 3474 6.391227 ACAAAGGATGAACCAAAAGTAGTG 57.609 37.500 0.00 0.00 42.04 2.74
2799 3475 8.166422 CTAACAAAGGATGAACCAAAAGTAGT 57.834 34.615 0.00 0.00 42.04 2.73
2820 3496 6.554334 TCTGCTTGTTAATGTTGACCTAAC 57.446 37.500 0.00 0.00 39.80 2.34
2821 3497 6.995686 TCTTCTGCTTGTTAATGTTGACCTAA 59.004 34.615 0.00 0.00 0.00 2.69
2908 3584 1.971481 TGATGCCCATCCTTTCATCG 58.029 50.000 5.86 0.00 38.43 3.84
3053 3734 9.569122 AGGTACAATAAACTAAAACATGACTGT 57.431 29.630 0.00 0.00 37.12 3.55
3178 3864 2.100989 GGGTTCATGTCTACCTCGACT 58.899 52.381 12.04 0.00 35.00 4.18
3311 3997 4.724798 TGCTGTATACTGATAAAGGGGGTT 59.275 41.667 13.44 0.00 0.00 4.11
3776 4469 5.192176 GGATCATCAAAAAGCTTCCTCTCT 58.808 41.667 0.00 0.00 0.00 3.10
4315 5038 2.090524 GTCGGTCCAGTAAACGGCG 61.091 63.158 4.80 4.80 0.00 6.46
4344 5070 2.739913 TCCGAAAATGACATTCGTGACC 59.260 45.455 0.05 0.00 46.11 4.02
4562 5296 6.029346 ACGGAAAAGTTTAGATCGGAGTTA 57.971 37.500 0.00 0.00 0.00 2.24
4596 5330 8.500753 TTTGCACGACTAACCTCATTTAATAT 57.499 30.769 0.00 0.00 0.00 1.28
4626 5361 3.183574 TCGTTGTGAAAGCAGATAACACG 59.816 43.478 0.00 0.00 34.72 4.49
4627 5362 4.702392 CTCGTTGTGAAAGCAGATAACAC 58.298 43.478 0.00 0.00 0.00 3.32
4715 5458 0.110486 AGGGAAAGAAGCTTCGGCAA 59.890 50.000 20.43 0.00 44.74 4.52
4716 5459 0.321653 GAGGGAAAGAAGCTTCGGCA 60.322 55.000 20.43 0.00 44.74 5.69
4768 5560 3.420893 TCAATGAGATTGTCCGGCTTTT 58.579 40.909 0.00 0.00 41.02 2.27
4790 5582 1.669760 GTCCATCGGCCGTTGTTCA 60.670 57.895 29.18 13.83 0.00 3.18
4800 5592 1.811266 CTGAAGCCACGTCCATCGG 60.811 63.158 0.00 0.00 44.69 4.18
4855 5647 1.531365 CAAGGCAAGTGCTTGGGGA 60.531 57.895 13.07 0.00 40.74 4.81
4856 5648 3.053828 CAAGGCAAGTGCTTGGGG 58.946 61.111 13.07 0.00 40.74 4.96
4862 5654 0.801251 CTACTCTGCAAGGCAAGTGC 59.199 55.000 12.84 0.00 38.41 4.40
4889 5681 2.508361 GGGAACAATCATGCCCCAG 58.492 57.895 0.00 0.00 40.57 4.45
4910 5791 3.356529 TCATTTGCTCTTTCTCCCCTC 57.643 47.619 0.00 0.00 0.00 4.30
4918 5799 1.838112 TCGCCCATCATTTGCTCTTT 58.162 45.000 0.00 0.00 0.00 2.52
5019 5909 5.819901 GTCACTTATTTTGGGATGGAGAGAG 59.180 44.000 0.00 0.00 0.00 3.20
5021 5911 5.749462 AGTCACTTATTTTGGGATGGAGAG 58.251 41.667 0.00 0.00 0.00 3.20
5022 5912 5.626809 CGAGTCACTTATTTTGGGATGGAGA 60.627 44.000 0.00 0.00 0.00 3.71
5023 5913 4.572389 CGAGTCACTTATTTTGGGATGGAG 59.428 45.833 0.00 0.00 0.00 3.86
5024 5914 4.224147 TCGAGTCACTTATTTTGGGATGGA 59.776 41.667 0.00 0.00 0.00 3.41
5025 5915 4.513442 TCGAGTCACTTATTTTGGGATGG 58.487 43.478 0.00 0.00 0.00 3.51
5026 5916 6.683974 AATCGAGTCACTTATTTTGGGATG 57.316 37.500 0.00 0.00 0.00 3.51
5027 5917 7.176690 ACAAAATCGAGTCACTTATTTTGGGAT 59.823 33.333 26.90 14.19 46.31 3.85
5028 5918 6.488683 ACAAAATCGAGTCACTTATTTTGGGA 59.511 34.615 26.90 1.76 46.31 4.37
5029 5919 6.677913 ACAAAATCGAGTCACTTATTTTGGG 58.322 36.000 26.90 14.19 46.31 4.12
5030 5920 8.504005 AGTACAAAATCGAGTCACTTATTTTGG 58.496 33.333 26.90 16.87 46.31 3.28
5035 5925 9.924650 ACTTTAGTACAAAATCGAGTCACTTAT 57.075 29.630 0.00 0.00 0.00 1.73
5036 5926 9.754382 AACTTTAGTACAAAATCGAGTCACTTA 57.246 29.630 0.00 0.00 0.00 2.24
5037 5927 8.658499 AACTTTAGTACAAAATCGAGTCACTT 57.342 30.769 0.00 0.00 0.00 3.16
5038 5928 9.754382 TTAACTTTAGTACAAAATCGAGTCACT 57.246 29.630 0.00 0.00 0.00 3.41
5065 5955 9.893634 TCCCAAAATAAGTGACTCGATTTTATA 57.106 29.630 14.20 4.79 31.86 0.98
5066 5956 8.801882 TCCCAAAATAAGTGACTCGATTTTAT 57.198 30.769 14.20 0.00 31.86 1.40
5067 5957 8.673711 CATCCCAAAATAAGTGACTCGATTTTA 58.326 33.333 14.20 4.47 31.86 1.52
5068 5958 7.362920 CCATCCCAAAATAAGTGACTCGATTTT 60.363 37.037 10.62 10.62 32.97 1.82
5069 5959 6.095440 CCATCCCAAAATAAGTGACTCGATTT 59.905 38.462 0.00 0.00 0.00 2.17
5070 5960 5.590259 CCATCCCAAAATAAGTGACTCGATT 59.410 40.000 0.00 0.00 0.00 3.34
5071 5961 5.104527 TCCATCCCAAAATAAGTGACTCGAT 60.105 40.000 0.00 0.00 0.00 3.59
5072 5962 4.224147 TCCATCCCAAAATAAGTGACTCGA 59.776 41.667 0.00 0.00 0.00 4.04
5073 5963 4.513442 TCCATCCCAAAATAAGTGACTCG 58.487 43.478 0.00 0.00 0.00 4.18
5074 5964 5.745227 TCTCCATCCCAAAATAAGTGACTC 58.255 41.667 0.00 0.00 0.00 3.36
5075 5965 5.488919 TCTCTCCATCCCAAAATAAGTGACT 59.511 40.000 0.00 0.00 0.00 3.41
5076 5966 5.745227 TCTCTCCATCCCAAAATAAGTGAC 58.255 41.667 0.00 0.00 0.00 3.67
5077 5967 5.630069 GCTCTCTCCATCCCAAAATAAGTGA 60.630 44.000 0.00 0.00 0.00 3.41
5078 5968 4.578105 GCTCTCTCCATCCCAAAATAAGTG 59.422 45.833 0.00 0.00 0.00 3.16
5079 5969 4.228210 TGCTCTCTCCATCCCAAAATAAGT 59.772 41.667 0.00 0.00 0.00 2.24
5080 5970 4.785301 TGCTCTCTCCATCCCAAAATAAG 58.215 43.478 0.00 0.00 0.00 1.73
5081 5971 4.860802 TGCTCTCTCCATCCCAAAATAA 57.139 40.909 0.00 0.00 0.00 1.40
5082 5972 5.393068 AATGCTCTCTCCATCCCAAAATA 57.607 39.130 0.00 0.00 0.00 1.40
5083 5973 3.967467 ATGCTCTCTCCATCCCAAAAT 57.033 42.857 0.00 0.00 0.00 1.82
5084 5974 3.744940 AATGCTCTCTCCATCCCAAAA 57.255 42.857 0.00 0.00 0.00 2.44
5085 5975 5.133322 AGAATAATGCTCTCTCCATCCCAAA 59.867 40.000 0.00 0.00 0.00 3.28
5086 5976 4.662179 AGAATAATGCTCTCTCCATCCCAA 59.338 41.667 0.00 0.00 0.00 4.12
5087 5977 4.237843 AGAATAATGCTCTCTCCATCCCA 58.762 43.478 0.00 0.00 0.00 4.37
5088 5978 4.531732 AGAGAATAATGCTCTCTCCATCCC 59.468 45.833 0.00 0.00 45.24 3.85
5089 5979 5.481105 CAGAGAATAATGCTCTCTCCATCC 58.519 45.833 0.00 0.00 45.24 3.51
5090 5980 4.931002 GCAGAGAATAATGCTCTCTCCATC 59.069 45.833 0.00 0.00 45.24 3.51
5091 5981 4.347292 TGCAGAGAATAATGCTCTCTCCAT 59.653 41.667 0.00 0.00 45.24 3.41
5092 5982 3.708121 TGCAGAGAATAATGCTCTCTCCA 59.292 43.478 0.00 0.00 45.24 3.86
5093 5983 4.333913 TGCAGAGAATAATGCTCTCTCC 57.666 45.455 0.00 0.00 45.24 3.71
5094 5984 4.511082 GGTTGCAGAGAATAATGCTCTCTC 59.489 45.833 0.00 0.00 45.24 3.20
5096 5986 3.563390 GGGTTGCAGAGAATAATGCTCTC 59.437 47.826 0.00 0.00 40.60 3.20
5097 5987 3.549794 GGGTTGCAGAGAATAATGCTCT 58.450 45.455 0.00 0.00 43.21 4.09
5098 5988 2.620585 GGGGTTGCAGAGAATAATGCTC 59.379 50.000 0.00 0.00 42.98 4.26
5099 5989 2.659428 GGGGTTGCAGAGAATAATGCT 58.341 47.619 0.00 0.00 42.98 3.79
5100 5990 1.334869 CGGGGTTGCAGAGAATAATGC 59.665 52.381 0.00 0.00 42.86 3.56
5101 5991 2.614057 GACGGGGTTGCAGAGAATAATG 59.386 50.000 0.00 0.00 0.00 1.90
5120 6010 0.445436 CATGCTGCAAACGGAGAGAC 59.555 55.000 6.36 0.00 0.00 3.36
5134 6024 5.351465 CGTTTCTGTACATAAACTCCATGCT 59.649 40.000 25.39 0.00 34.21 3.79
5148 6038 0.714439 GCTTCTCGGCGTTTCTGTAC 59.286 55.000 6.85 0.00 0.00 2.90
5192 6082 4.380444 GGAGCAGTTTCTCAACAACAACAA 60.380 41.667 0.00 0.00 35.05 2.83
5194 6084 3.489229 GGGAGCAGTTTCTCAACAACAAC 60.489 47.826 0.00 0.00 35.05 3.32
5197 6087 2.576615 AGGGAGCAGTTTCTCAACAAC 58.423 47.619 0.00 0.00 35.05 3.32
5200 6090 1.882623 CCAAGGGAGCAGTTTCTCAAC 59.117 52.381 0.00 0.00 34.84 3.18


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

AutoCloner maintained by Alex Coulton.