Multiple sequence alignment - TraesCS4B01G198800

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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 TraesCS4B01G198800 chr4B 100.000 4194 0 0 1 4194 427499974 427495781 0.000000e+00 7745.0
1 TraesCS4B01G198800 chr4B 92.308 104 6 2 4091 4194 24837286 24837387 3.380000e-31 147.0
2 TraesCS4B01G198800 chr4B 79.412 170 15 11 1042 1205 385957548 385957703 7.420000e-18 102.0
3 TraesCS4B01G198800 chr4D 93.377 1676 89 9 1565 3223 346453736 346452066 0.000000e+00 2460.0
4 TraesCS4B01G198800 chr4D 87.381 1363 64 35 1 1293 346455224 346453900 0.000000e+00 1465.0
5 TraesCS4B01G198800 chr4D 94.278 734 26 7 3381 4106 346451837 346451112 0.000000e+00 1109.0
6 TraesCS4B01G198800 chr4D 89.634 164 10 2 1313 1469 346453908 346453745 7.110000e-48 202.0
7 TraesCS4B01G198800 chr4D 90.714 140 9 2 3318 3453 346451969 346451830 2.580000e-42 183.0
8 TraesCS4B01G198800 chr4D 91.549 71 3 2 3250 3317 346452070 346452000 1.240000e-15 95.3
9 TraesCS4B01G198800 chr4A 93.121 1541 94 9 1688 3222 119081288 119082822 0.000000e+00 2248.0
10 TraesCS4B01G198800 chr4A 92.686 793 35 6 3318 4106 119083080 119083853 0.000000e+00 1122.0
11 TraesCS4B01G198800 chr4A 85.714 945 55 33 112 989 119079765 119080696 0.000000e+00 924.0
12 TraesCS4B01G198800 chr4A 83.770 382 33 20 1016 1376 119080753 119081126 6.720000e-88 335.0
13 TraesCS4B01G198800 chr4A 86.441 118 11 1 1 118 119079630 119079742 1.580000e-24 124.0
14 TraesCS4B01G198800 chr4A 92.857 70 5 0 1406 1475 119081187 119081256 7.420000e-18 102.0
15 TraesCS4B01G198800 chr4A 79.651 172 11 11 1042 1205 538908630 538908475 7.420000e-18 102.0
16 TraesCS4B01G198800 chr1B 98.864 88 1 0 4102 4189 571173431 571173344 1.560000e-34 158.0
17 TraesCS4B01G198800 chr1B 92.105 76 1 2 3203 3277 480973022 480972951 7.420000e-18 102.0
18 TraesCS4B01G198800 chr2B 96.774 93 3 0 4102 4194 662898919 662899011 5.610000e-34 156.0
19 TraesCS4B01G198800 chr2B 91.429 105 7 2 4090 4194 245933509 245933611 4.370000e-30 143.0
20 TraesCS4B01G198800 chr2B 80.000 170 14 8 1042 1205 17219896 17219741 1.590000e-19 108.0
21 TraesCS4B01G198800 chr2B 80.000 170 14 8 1042 1205 414953270 414953425 1.590000e-19 108.0
22 TraesCS4B01G198800 chr2B 79.412 170 15 8 1042 1205 127202947 127203102 7.420000e-18 102.0
23 TraesCS4B01G198800 chr7B 93.939 99 5 1 4091 4189 157681774 157681677 9.390000e-32 148.0
24 TraesCS4B01G198800 chr7B 92.308 104 6 2 4091 4193 715360301 715360403 3.380000e-31 147.0
25 TraesCS4B01G198800 chr7B 90.278 72 2 2 3207 3277 616828768 616828835 5.780000e-14 89.8
26 TraesCS4B01G198800 chr7B 89.189 74 3 2 3205 3277 616756865 616756934 2.080000e-13 87.9
27 TraesCS4B01G198800 chr5B 92.453 106 5 3 4089 4194 547451073 547451175 9.390000e-32 148.0
28 TraesCS4B01G198800 chr6D 93.000 100 7 0 4095 4194 132853883 132853784 3.380000e-31 147.0
29 TraesCS4B01G198800 chr3B 90.741 108 8 2 4087 4194 452550879 452550774 4.370000e-30 143.0
30 TraesCS4B01G198800 chr3B 88.158 76 3 2 3205 3279 776359627 776359557 7.470000e-13 86.1
31 TraesCS4B01G198800 chr3B 93.182 44 3 0 3270 3313 11069993 11070036 9.730000e-07 65.8
32 TraesCS4B01G198800 chr1D 92.000 75 1 2 3204 3277 358222551 358222621 2.670000e-17 100.0
33 TraesCS4B01G198800 chr7A 88.889 81 3 3 3199 3277 652009235 652009311 1.240000e-15 95.3
34 TraesCS4B01G198800 chr7A 93.182 44 1 2 1473 1516 227094703 227094662 3.500000e-06 63.9
35 TraesCS4B01G198800 chr7A 94.872 39 2 0 3276 3314 664381484 664381522 1.260000e-05 62.1
36 TraesCS4B01G198800 chr2D 89.474 76 3 3 3206 3280 23305960 23306031 1.610000e-14 91.6
37 TraesCS4B01G198800 chr2D 97.561 41 0 1 1473 1513 318557770 318557731 7.520000e-08 69.4
38 TraesCS4B01G198800 chr2D 94.737 38 2 0 3276 3313 72772530 72772567 4.530000e-05 60.2
39 TraesCS4B01G198800 chr2D 100.000 29 0 0 3270 3298 262614617 262614645 2.000000e-03 54.7
40 TraesCS4B01G198800 chr2A 89.474 76 3 3 3206 3280 25484392 25484321 1.610000e-14 91.6
41 TraesCS4B01G198800 chr3A 86.842 76 4 2 3205 3279 716368713 716368643 3.480000e-11 80.5
42 TraesCS4B01G198800 chr5D 97.561 41 0 1 1473 1513 430447378 430447417 7.520000e-08 69.4
43 TraesCS4B01G198800 chr3D 93.023 43 3 0 3271 3313 27936566 27936608 3.500000e-06 63.9
44 TraesCS4B01G198800 chr3D 90.476 42 0 4 1488 1527 26681249 26681210 8.000000e-03 52.8
45 TraesCS4B01G198800 chr7D 85.000 60 7 2 3271 3330 518794525 518794468 4.530000e-05 60.2
46 TraesCS4B01G198800 chr6B 92.500 40 3 0 3274 3313 599054938 599054977 1.630000e-04 58.4


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 TraesCS4B01G198800 chr4B 427495781 427499974 4193 True 7745.000000 7745 100.000000 1 4194 1 chr4B.!!$R1 4193
1 TraesCS4B01G198800 chr4D 346451112 346455224 4112 True 919.050000 2460 91.155500 1 4106 6 chr4D.!!$R1 4105
2 TraesCS4B01G198800 chr4A 119079630 119083853 4223 False 809.166667 2248 89.098167 1 4106 6 chr4A.!!$F1 4105

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
745 820 0.038435 AGACGAGACGAGACGACTCA 60.038 55.0 14.99 0.0 45.49 3.41 F
1509 1720 0.258484 TACGTTATGGGACGGAGGGA 59.742 55.0 0.00 0.0 46.77 4.20 F
2923 3149 0.614979 TCTACCCAGGGAGCAGACAC 60.615 60.0 14.54 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2460 0.389166 CTCCACCACTCTCTGAACGC 60.389 60.000 0.00 0.0 0.0 4.84 R
3044 3270 0.965439 CAAATCCTGAACCGGGCAAA 59.035 50.000 6.32 0.0 0.0 3.68 R
3739 4241 1.998315 CCAAGCAGAAGACAGATGACG 59.002 52.381 0.00 0.0 0.0 4.35 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
37 38 4.303257 GGTTTCAGGGCCGAGAAG 57.697 61.111 12.94 0.00 0.00 2.85
38 39 1.677552 GGTTTCAGGGCCGAGAAGA 59.322 57.895 12.94 4.35 0.00 2.87
39 40 0.391793 GGTTTCAGGGCCGAGAAGAG 60.392 60.000 12.94 0.00 0.00 2.85
40 41 0.608640 GTTTCAGGGCCGAGAAGAGA 59.391 55.000 12.94 0.00 0.00 3.10
41 42 1.002087 GTTTCAGGGCCGAGAAGAGAA 59.998 52.381 12.94 1.78 0.00 2.87
42 43 0.898320 TTCAGGGCCGAGAAGAGAAG 59.102 55.000 9.90 0.00 0.00 2.85
51 52 2.478134 CCGAGAAGAGAAGCACACTTTG 59.522 50.000 0.00 0.00 35.82 2.77
58 59 1.208642 GAAGCACACTTTGTTGGCGC 61.209 55.000 0.00 0.00 35.82 6.53
60 61 1.945662 GCACACTTTGTTGGCGCAG 60.946 57.895 10.83 0.00 0.00 5.18
76 77 2.921754 GCGCAGTCAGTTACTTAATCGT 59.078 45.455 0.30 0.00 35.76 3.73
86 87 8.922676 GTCAGTTACTTAATCGTGAAGAAATGA 58.077 33.333 0.00 0.00 0.00 2.57
89 90 8.718734 AGTTACTTAATCGTGAAGAAATGAACC 58.281 33.333 1.67 0.00 0.00 3.62
91 92 9.932207 TTACTTAATCGTGAAGAAATGAACCTA 57.068 29.630 1.67 0.00 0.00 3.08
118 119 5.507985 CGAAATCCTAATTCCCAAGAATGCC 60.508 44.000 0.00 0.00 42.03 4.40
126 156 4.720775 TTCCCAAGAATGCCCAAAAATT 57.279 36.364 0.00 0.00 0.00 1.82
127 157 4.018484 TCCCAAGAATGCCCAAAAATTG 57.982 40.909 0.00 0.00 0.00 2.32
145 175 2.276868 CGAGAAAGCATTGCGGCG 60.277 61.111 0.51 0.51 39.27 6.46
166 196 1.533731 TCGCAAATTGAGGGAACGAAC 59.466 47.619 0.00 0.00 0.00 3.95
204 234 1.512926 GCCATGGCACTATTCCGTAG 58.487 55.000 32.08 0.00 41.49 3.51
276 328 0.809385 CATAGACCACCGACGTCAGT 59.191 55.000 17.16 7.63 32.41 3.41
280 332 0.387750 GACCACCGACGTCAGTAACC 60.388 60.000 17.16 0.00 0.00 2.85
290 342 2.056577 CGTCAGTAACCAACCGAGAAC 58.943 52.381 0.00 0.00 0.00 3.01
298 350 0.460284 CCAACCGAGAACCCGATCAG 60.460 60.000 0.00 0.00 0.00 2.90
346 398 2.675075 GCGGGGCCAAACTAGCAA 60.675 61.111 4.39 0.00 0.00 3.91
376 447 2.556287 GCAAAGAACCGGCGTCAG 59.444 61.111 6.01 0.00 0.00 3.51
377 448 2.966309 GCAAAGAACCGGCGTCAGG 61.966 63.158 6.01 0.00 0.00 3.86
516 587 1.443828 GATCTGGGACGGCTTCTCC 59.556 63.158 0.00 0.00 32.53 3.71
632 704 2.041405 GTGAGGGAGGGAGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
745 820 0.038435 AGACGAGACGAGACGACTCA 60.038 55.000 14.99 0.00 45.49 3.41
901 993 4.814294 GGTCGATGCGCCTTCGGT 62.814 66.667 23.95 0.00 37.22 4.69
910 1002 1.804326 CGCCTTCGGTCCTACGTTG 60.804 63.158 0.00 0.00 34.94 4.10
918 1010 1.666888 CGGTCCTACGTTGCGTACTTT 60.667 52.381 0.00 0.00 41.54 2.66
945 1037 2.074576 GTACGCCTTCCTTTGGACTTC 58.925 52.381 0.00 0.00 0.00 3.01
947 1043 1.876664 GCCTTCCTTTGGACTTCGC 59.123 57.895 0.00 0.00 0.00 4.70
1200 1344 4.069232 CTCGCGCACCCCTTCTCA 62.069 66.667 8.75 0.00 0.00 3.27
1235 1379 1.134788 CCTCCGAAAGATGGTAAGCGT 60.135 52.381 0.00 0.00 0.00 5.07
1257 1434 1.878775 GTGCTTGCTACCAGCCTTG 59.121 57.895 0.00 0.00 41.51 3.61
1283 1460 1.254026 CCTAACCACGGTCTCTGTCA 58.746 55.000 0.00 0.00 0.00 3.58
1293 1470 1.134818 GGTCTCTGTCACACACACACA 60.135 52.381 0.00 0.00 0.00 3.72
1294 1471 1.927174 GTCTCTGTCACACACACACAC 59.073 52.381 0.00 0.00 0.00 3.82
1295 1472 1.548269 TCTCTGTCACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
1296 1473 1.660607 CTCTGTCACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
1297 1474 1.001406 TCTGTCACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
1298 1475 1.128507 CTGTCACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
1299 1476 1.152510 GTCACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
1300 1477 1.136085 GTCACACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
1301 1478 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1302 1479 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1303 1480 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1304 1481 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1305 1482 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1306 1483 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1307 1484 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1308 1485 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1309 1486 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1310 1487 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1311 1488 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1351 1528 6.434652 ACTTAGTGAGTACTGCAGAGTTGTAT 59.565 38.462 23.35 3.83 37.78 2.29
1352 1529 5.065704 AGTGAGTACTGCAGAGTTGTATG 57.934 43.478 23.35 0.00 35.34 2.39
1353 1530 4.524714 AGTGAGTACTGCAGAGTTGTATGT 59.475 41.667 23.35 0.00 35.34 2.29
1354 1531 4.859798 GTGAGTACTGCAGAGTTGTATGTC 59.140 45.833 23.35 4.81 33.21 3.06
1359 1539 4.822026 ACTGCAGAGTTGTATGTCCTTAC 58.178 43.478 23.35 0.00 0.00 2.34
1422 1633 9.354673 AGTAATCATCTGTAAATAAATGGGTGG 57.645 33.333 0.00 0.00 0.00 4.61
1425 1636 6.135454 TCATCTGTAAATAAATGGGTGGCAT 58.865 36.000 0.00 0.00 0.00 4.40
1471 1682 6.378848 GGTGATCTGGGTATAGAATCTACTCC 59.621 46.154 0.00 0.00 0.00 3.85
1475 1686 7.891825 TCTGGGTATAGAATCTACTCCTAGT 57.108 40.000 17.96 0.00 0.00 2.57
1476 1687 7.691213 TCTGGGTATAGAATCTACTCCTAGTG 58.309 42.308 17.96 3.88 0.00 2.74
1477 1688 7.295196 TCTGGGTATAGAATCTACTCCTAGTGT 59.705 40.741 17.96 0.00 0.00 3.55
1478 1689 7.460071 TGGGTATAGAATCTACTCCTAGTGTC 58.540 42.308 10.73 0.00 0.00 3.67
1480 1691 7.943447 GGGTATAGAATCTACTCCTAGTGTCAA 59.057 40.741 10.73 0.00 0.00 3.18
1481 1692 9.352191 GGTATAGAATCTACTCCTAGTGTCAAA 57.648 37.037 0.00 0.00 0.00 2.69
1505 1716 3.901087 TCCTACGTTATGGGACGGA 57.099 52.632 0.00 0.00 46.77 4.69
1508 1719 2.811307 TACGTTATGGGACGGAGGG 58.189 57.895 0.00 0.00 46.77 4.30
1509 1720 0.258484 TACGTTATGGGACGGAGGGA 59.742 55.000 0.00 0.00 46.77 4.20
1510 1721 1.041447 ACGTTATGGGACGGAGGGAG 61.041 60.000 2.39 0.00 46.77 4.30
1511 1722 1.041447 CGTTATGGGACGGAGGGAGT 61.041 60.000 0.00 0.00 39.27 3.85
1512 1723 1.751733 CGTTATGGGACGGAGGGAGTA 60.752 57.143 0.00 0.00 39.27 2.59
1513 1724 1.962100 GTTATGGGACGGAGGGAGTAG 59.038 57.143 0.00 0.00 0.00 2.57
1514 1725 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
1515 1726 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
1516 1727 1.229131 TGGGACGGAGGGAGTAGTAT 58.771 55.000 0.00 0.00 0.00 2.12
1517 1728 2.421725 TGGGACGGAGGGAGTAGTATA 58.578 52.381 0.00 0.00 0.00 1.47
1518 1729 2.107204 TGGGACGGAGGGAGTAGTATAC 59.893 54.545 0.00 0.00 43.47 1.47
1519 1730 2.107204 GGGACGGAGGGAGTAGTATACA 59.893 54.545 5.50 0.00 46.26 2.29
1520 1731 3.245193 GGGACGGAGGGAGTAGTATACAT 60.245 52.174 5.50 0.00 46.26 2.29
1521 1732 4.018960 GGGACGGAGGGAGTAGTATACATA 60.019 50.000 5.50 0.00 46.26 2.29
1522 1733 5.515534 GGGACGGAGGGAGTAGTATACATAA 60.516 48.000 5.50 0.00 46.26 1.90
1523 1734 5.647225 GGACGGAGGGAGTAGTATACATAAG 59.353 48.000 5.50 0.00 46.26 1.73
1524 1735 6.198237 ACGGAGGGAGTAGTATACATAAGT 57.802 41.667 5.50 0.00 46.26 2.24
1525 1736 7.321717 ACGGAGGGAGTAGTATACATAAGTA 57.678 40.000 5.50 0.00 46.26 2.24
1526 1737 7.926705 ACGGAGGGAGTAGTATACATAAGTAT 58.073 38.462 5.50 0.00 46.26 2.12
1527 1738 9.051259 ACGGAGGGAGTAGTATACATAAGTATA 57.949 37.037 5.50 0.00 46.26 1.47
1528 1739 9.896645 CGGAGGGAGTAGTATACATAAGTATAA 57.103 37.037 5.50 0.00 46.26 0.98
1572 1783 9.607285 TCTTTCTTTTTGCGAAAGATACATAAC 57.393 29.630 13.73 0.00 46.71 1.89
1597 1808 6.753913 TTGCTCTAATCTGAATATGGGACT 57.246 37.500 0.00 0.00 0.00 3.85
1624 1835 4.873827 TCCCATACTAAACAATCGCACTTC 59.126 41.667 0.00 0.00 0.00 3.01
1642 1853 6.518736 CGCACTTCGAAAGTTTAAATAGGTTC 59.481 38.462 0.00 0.00 40.46 3.62
1707 1918 2.230508 TGGAAGTCGCTGTCGTAAATCT 59.769 45.455 0.00 0.00 36.96 2.40
1806 2017 1.391157 TTGTGTTGCCAGGAAGCCAC 61.391 55.000 0.00 0.00 0.00 5.01
1809 2020 0.698238 TGTTGCCAGGAAGCCACTAT 59.302 50.000 0.00 0.00 30.06 2.12
1844 2055 3.062323 GCAATAGCTCAATGTCTGTGC 57.938 47.619 0.00 0.00 43.49 4.57
1865 2076 4.887071 TGCCACTTCAGTATTTCAACAACT 59.113 37.500 0.00 0.00 0.00 3.16
1882 2093 3.265791 CAACTAGCTCATCCAGAACCAC 58.734 50.000 0.00 0.00 0.00 4.16
1935 2146 6.116806 TCTAACTTTGTTTACTGCACTGGAA 58.883 36.000 0.00 0.00 0.00 3.53
2013 2224 3.915437 ACTTTAAATGTTGGACGGCTG 57.085 42.857 0.00 0.00 0.00 4.85
2052 2263 4.871933 AATTTTCCAGGGCTGTAACTTG 57.128 40.909 0.00 0.00 0.00 3.16
2113 2324 3.249189 AGGCGTTCCCAGGCAAGA 61.249 61.111 0.00 0.00 35.34 3.02
2114 2325 3.056328 GGCGTTCCCAGGCAAGAC 61.056 66.667 0.00 0.00 35.34 3.01
2239 2460 3.648009 GCTTAGCTCAGCTGTATAGTGG 58.352 50.000 10.31 1.61 40.10 4.00
2240 2461 3.648009 CTTAGCTCAGCTGTATAGTGGC 58.352 50.000 10.31 7.89 40.10 5.01
2268 2489 2.043115 AGAGTGGTGGAGACATACAGGA 59.957 50.000 0.00 0.00 46.14 3.86
2269 2490 2.428890 GAGTGGTGGAGACATACAGGAG 59.571 54.545 0.00 0.00 46.14 3.69
2335 2556 0.879765 CTCTTGGAAGTTGCTGCCAG 59.120 55.000 0.00 0.00 40.80 4.85
2375 2596 5.335897 TGTCTTGGACTTCTTGCATTATTGC 60.336 40.000 2.60 2.60 40.24 3.56
2452 2673 6.712095 ACTCTTTCTTCACAGCATATTCACAA 59.288 34.615 0.00 0.00 0.00 3.33
2707 2933 6.933521 AGCCACTATAGATAGCTGTGAATTTG 59.066 38.462 6.78 0.00 33.68 2.32
2766 2992 4.039852 ACTTGGCACCGTCCATTTTATTTT 59.960 37.500 0.00 0.00 35.77 1.82
2793 3019 5.743872 AGTTGACAAGCGTTTCATTCTTTTC 59.256 36.000 0.00 0.00 0.00 2.29
2809 3035 5.276461 TCTTTTCTCAACAGCTGTCAGTA 57.724 39.130 21.95 10.21 0.00 2.74
2810 3036 5.670485 TCTTTTCTCAACAGCTGTCAGTAA 58.330 37.500 21.95 15.44 0.00 2.24
2845 3071 4.408821 ATCGAGCAAAGGCCGGCA 62.409 61.111 30.85 3.80 42.56 5.69
2923 3149 0.614979 TCTACCCAGGGAGCAGACAC 60.615 60.000 14.54 0.00 0.00 3.67
2935 3161 3.330267 GAGCAGACACTAGAACTTTGGG 58.670 50.000 0.00 0.00 0.00 4.12
2951 3177 2.690778 GGGCACCGTAAAGCTGCAG 61.691 63.158 10.11 10.11 40.86 4.41
3001 3227 1.343821 GCGTCGCTCGTTATGTTGG 59.656 57.895 10.68 0.00 42.13 3.77
3022 3248 3.255888 GGAAGTTGCCCTGTTTTAAGGAG 59.744 47.826 0.00 0.00 40.02 3.69
3023 3249 2.239400 AGTTGCCCTGTTTTAAGGAGC 58.761 47.619 0.00 0.00 40.02 4.70
3039 3265 3.359950 AGGAGCATCATGGAAAGGAAAC 58.640 45.455 0.00 0.00 36.25 2.78
3043 3269 2.827921 GCATCATGGAAAGGAAACCAGT 59.172 45.455 0.00 0.00 39.62 4.00
3044 3270 3.259123 GCATCATGGAAAGGAAACCAGTT 59.741 43.478 0.00 0.00 39.62 3.16
3060 3286 0.112412 AGTTTTGCCCGGTTCAGGAT 59.888 50.000 0.00 0.00 0.00 3.24
3071 3297 2.415893 CGGTTCAGGATTTGCATGGTTC 60.416 50.000 0.00 0.00 0.00 3.62
3077 3303 3.449737 CAGGATTTGCATGGTTCCATCTT 59.550 43.478 0.86 0.00 0.00 2.40
3126 3352 6.767456 TGTGTTGCCTTTATTCATTGGAAAT 58.233 32.000 0.00 0.00 36.43 2.17
3137 3363 4.879295 TCATTGGAAATGGGGATGTACT 57.121 40.909 0.00 0.00 0.00 2.73
3139 3365 4.478317 TCATTGGAAATGGGGATGTACTCT 59.522 41.667 0.00 0.00 0.00 3.24
3158 3384 9.431887 TGTACTCTACATTGTAAACCTTTGATC 57.568 33.333 0.00 0.00 32.89 2.92
3165 3394 8.877864 ACATTGTAAACCTTTGATCTGGATTA 57.122 30.769 6.91 3.73 0.00 1.75
3181 3410 3.052869 TGGATTAGAGCAGACACTAGGGA 60.053 47.826 0.00 0.00 0.00 4.20
3194 3423 1.293924 CTAGGGAGAACTGCAATGCG 58.706 55.000 0.00 0.00 0.00 4.73
3222 3451 8.890410 AACATAAGTACTCCCTCTGTAAAGTA 57.110 34.615 0.00 0.00 0.00 2.24
3223 3452 8.890410 ACATAAGTACTCCCTCTGTAAAGTAA 57.110 34.615 0.00 0.00 0.00 2.24
3224 3453 9.317827 ACATAAGTACTCCCTCTGTAAAGTAAA 57.682 33.333 0.00 0.00 0.00 2.01
3229 3458 9.765295 AGTACTCCCTCTGTAAAGTAAATAAGA 57.235 33.333 0.00 0.00 0.00 2.10
3230 3459 9.800433 GTACTCCCTCTGTAAAGTAAATAAGAC 57.200 37.037 0.00 0.00 0.00 3.01
3231 3460 7.849160 ACTCCCTCTGTAAAGTAAATAAGACC 58.151 38.462 0.00 0.00 0.00 3.85
3232 3461 7.679025 ACTCCCTCTGTAAAGTAAATAAGACCT 59.321 37.037 0.00 0.00 0.00 3.85
3233 3462 8.445361 TCCCTCTGTAAAGTAAATAAGACCTT 57.555 34.615 0.00 0.00 0.00 3.50
3234 3463 8.887393 TCCCTCTGTAAAGTAAATAAGACCTTT 58.113 33.333 0.00 0.00 0.00 3.11
3235 3464 9.516546 CCCTCTGTAAAGTAAATAAGACCTTTT 57.483 33.333 0.00 0.00 0.00 2.27
3363 3788 5.184096 TGCAACCTTTTGACTTTAGAACACA 59.816 36.000 0.00 0.00 34.24 3.72
3409 3834 7.353414 TGGTCAAGGTTGAATGATTTAACAA 57.647 32.000 13.68 0.00 39.21 2.83
3560 4058 1.140052 CGAGGGGTAACATGCATGGTA 59.860 52.381 29.41 25.24 39.74 3.25
3739 4241 3.003763 ACCAGAAGGGAGGGTCGC 61.004 66.667 0.00 0.00 41.15 5.19
3840 4342 0.383949 CGGCTAGTCTCTTCCTGCTC 59.616 60.000 0.00 0.00 0.00 4.26
3868 4370 1.468054 GCACCTGAAAATAGCCAAGCG 60.468 52.381 0.00 0.00 0.00 4.68
3948 4450 2.092212 ACTCCCCAAGGCACTATCAATG 60.092 50.000 0.00 0.00 38.49 2.82
3961 4463 5.050091 GCACTATCAATGACATTTCCTACGG 60.050 44.000 0.00 0.00 0.00 4.02
4027 4529 3.829886 TGGAAGCAACATAAAAGCTCG 57.170 42.857 0.00 0.00 37.70 5.03
4040 4542 4.329462 AAAAGCTCGTGTTTCTCTCTCT 57.671 40.909 0.00 0.00 0.00 3.10
4050 4552 5.619086 CGTGTTTCTCTCTCTCTCTTTCTCC 60.619 48.000 0.00 0.00 0.00 3.71
4067 4569 8.532977 TCTTTCTCCTTTTGTTTTGTTTTGAG 57.467 30.769 0.00 0.00 0.00 3.02
4106 4608 9.968870 TTCTCTCTTTCAGAAGTAAGAAGTTAC 57.031 33.333 0.00 0.00 39.17 2.50
4108 4610 9.620660 CTCTCTTTCAGAAGTAAGAAGTTACTC 57.379 37.037 0.00 0.00 46.88 2.59
4109 4611 8.578151 TCTCTTTCAGAAGTAAGAAGTTACTCC 58.422 37.037 0.00 0.00 46.88 3.85
4110 4612 7.668492 TCTTTCAGAAGTAAGAAGTTACTCCC 58.332 38.462 0.00 0.00 46.88 4.30
4111 4613 7.509659 TCTTTCAGAAGTAAGAAGTTACTCCCT 59.490 37.037 0.00 0.00 46.88 4.20
4112 4614 6.837471 TCAGAAGTAAGAAGTTACTCCCTC 57.163 41.667 0.00 0.00 46.88 4.30
4113 4615 5.715753 TCAGAAGTAAGAAGTTACTCCCTCC 59.284 44.000 0.00 0.00 46.88 4.30
4114 4616 4.705991 AGAAGTAAGAAGTTACTCCCTCCG 59.294 45.833 0.00 0.00 46.88 4.63
4115 4617 4.044946 AGTAAGAAGTTACTCCCTCCGT 57.955 45.455 0.00 0.00 44.81 4.69
4116 4618 4.015764 AGTAAGAAGTTACTCCCTCCGTC 58.984 47.826 0.00 0.00 44.81 4.79
4117 4619 1.849977 AGAAGTTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
4118 4620 0.822811 GAAGTTACTCCCTCCGTCCC 59.177 60.000 0.00 0.00 0.00 4.46
4119 4621 0.115745 AAGTTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
4120 4622 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
4121 4623 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
4122 4624 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
4123 4625 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
4124 4626 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
4125 4627 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4126 4628 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4127 4629 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4128 4630 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4129 4631 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4130 4632 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
4131 4633 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
4132 4634 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
4133 4635 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
4134 4636 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
4135 4637 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
4136 4638 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
4137 4639 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
4138 4640 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
4139 4641 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
4140 4642 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
4141 4643 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
4142 4644 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4148 4650 9.701098 ATATAAGAACGTTTTTGACACTAGTGA 57.299 29.630 29.30 4.89 0.00 3.41
4149 4651 6.730960 AAGAACGTTTTTGACACTAGTGAA 57.269 33.333 29.30 13.84 0.00 3.18
4150 4652 6.345920 AGAACGTTTTTGACACTAGTGAAG 57.654 37.500 29.30 10.27 0.00 3.02
4151 4653 5.873164 AGAACGTTTTTGACACTAGTGAAGT 59.127 36.000 29.30 10.91 39.81 3.01
4164 4666 6.103222 ACTAGTGAAGTGTCAAAAACGTTC 57.897 37.500 0.00 0.00 36.93 3.95
4165 4667 5.873164 ACTAGTGAAGTGTCAAAAACGTTCT 59.127 36.000 0.00 0.00 36.93 3.01
4166 4668 5.622770 AGTGAAGTGTCAAAAACGTTCTT 57.377 34.783 0.00 0.00 34.87 2.52
4167 4669 6.730960 AGTGAAGTGTCAAAAACGTTCTTA 57.269 33.333 0.00 0.00 34.87 2.10
4168 4670 7.316544 AGTGAAGTGTCAAAAACGTTCTTAT 57.683 32.000 0.00 0.00 34.87 1.73
4169 4671 8.428186 AGTGAAGTGTCAAAAACGTTCTTATA 57.572 30.769 0.00 0.00 34.87 0.98
4170 4672 9.052759 AGTGAAGTGTCAAAAACGTTCTTATAT 57.947 29.630 0.00 0.00 34.87 0.86
4171 4673 9.659830 GTGAAGTGTCAAAAACGTTCTTATATT 57.340 29.630 0.00 0.00 34.87 1.28
4176 4678 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
4177 4679 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
4178 4680 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.489329 CCTGAAACCGCACAAGATTCAT 59.511 45.455 0.00 0.00 30.39 2.57
37 38 1.597937 CGCCAACAAAGTGTGCTTCTC 60.598 52.381 0.00 0.00 33.01 2.87
38 39 0.381801 CGCCAACAAAGTGTGCTTCT 59.618 50.000 0.00 0.00 33.01 2.85
39 40 1.208642 GCGCCAACAAAGTGTGCTTC 61.209 55.000 0.00 0.00 33.01 3.86
40 41 1.226945 GCGCCAACAAAGTGTGCTT 60.227 52.632 0.00 0.00 36.30 3.91
41 42 2.340453 CTGCGCCAACAAAGTGTGCT 62.340 55.000 4.18 0.00 0.00 4.40
42 43 1.945662 CTGCGCCAACAAAGTGTGC 60.946 57.895 4.18 0.00 0.00 4.57
51 52 1.226746 AAGTAACTGACTGCGCCAAC 58.773 50.000 4.18 0.00 38.87 3.77
58 59 7.869016 TTCTTCACGATTAAGTAACTGACTG 57.131 36.000 0.00 0.00 38.87 3.51
60 61 8.922676 TCATTTCTTCACGATTAAGTAACTGAC 58.077 33.333 0.00 0.00 0.00 3.51
64 65 8.718734 AGGTTCATTTCTTCACGATTAAGTAAC 58.281 33.333 0.00 0.00 0.00 2.50
76 77 6.148811 GGATTTCGTGTAGGTTCATTTCTTCA 59.851 38.462 0.00 0.00 0.00 3.02
86 87 5.045432 TGGGAATTAGGATTTCGTGTAGGTT 60.045 40.000 0.00 0.00 0.00 3.50
89 90 6.346096 TCTTGGGAATTAGGATTTCGTGTAG 58.654 40.000 0.00 0.00 0.00 2.74
91 92 5.174037 TCTTGGGAATTAGGATTTCGTGT 57.826 39.130 0.00 0.00 0.00 4.49
118 119 4.704457 CAATGCTTTCTCGCAATTTTTGG 58.296 39.130 0.00 0.00 44.06 3.28
126 156 2.869646 CCGCAATGCTTTCTCGCA 59.130 55.556 2.94 0.00 45.10 5.10
127 157 2.577911 GCCGCAATGCTTTCTCGC 60.578 61.111 2.94 0.00 0.00 5.03
145 175 1.153353 TCGTTCCCTCAATTTGCGAC 58.847 50.000 0.00 0.00 0.00 5.19
156 186 3.552384 TGCCCGTGTTCGTTCCCT 61.552 61.111 0.00 0.00 35.01 4.20
204 234 4.854399 TGATGTTTGGTTCGTGAAATGTC 58.146 39.130 0.00 0.00 0.00 3.06
276 328 1.205417 GATCGGGTTCTCGGTTGGTTA 59.795 52.381 0.00 0.00 0.00 2.85
280 332 1.084370 GCTGATCGGGTTCTCGGTTG 61.084 60.000 3.14 0.00 0.00 3.77
290 342 3.207547 TATCGTGCGGCTGATCGGG 62.208 63.158 10.74 0.00 0.00 5.14
298 350 1.141019 TCTCTTGGTATCGTGCGGC 59.859 57.895 0.00 0.00 0.00 6.53
359 411 2.556287 CTGACGCCGGTTCTTTGC 59.444 61.111 1.90 0.00 0.00 3.68
360 412 2.325082 CCCTGACGCCGGTTCTTTG 61.325 63.158 1.90 0.00 0.00 2.77
361 413 2.032071 CCCTGACGCCGGTTCTTT 59.968 61.111 1.90 0.00 0.00 2.52
364 416 4.452733 CTCCCCTGACGCCGGTTC 62.453 72.222 1.90 0.00 0.00 3.62
376 447 3.445987 TCTCCTTCTTCTTCTTCTCCCC 58.554 50.000 0.00 0.00 0.00 4.81
377 448 4.775253 TCTTCTCCTTCTTCTTCTTCTCCC 59.225 45.833 0.00 0.00 0.00 4.30
516 587 3.854669 ATGAGGAAGGAGCCCGCG 61.855 66.667 0.00 0.00 0.00 6.46
601 672 1.300971 CCTCACCACTGCATTCCGTG 61.301 60.000 0.00 0.00 0.00 4.94
602 673 1.003355 CCTCACCACTGCATTCCGT 60.003 57.895 0.00 0.00 0.00 4.69
632 704 0.548510 CACTTCCCTTCCATCCCTCC 59.451 60.000 0.00 0.00 0.00 4.30
745 820 0.396811 CGTGGACAAAAGGGAGGACT 59.603 55.000 0.00 0.00 0.00 3.85
779 854 1.517242 CTGACAGTTGAGCAGTTCCC 58.483 55.000 0.00 0.00 0.00 3.97
790 869 1.069765 CAGACGGCACCTGACAGTT 59.930 57.895 0.93 0.00 33.65 3.16
901 993 2.095059 GGAGAAAGTACGCAACGTAGGA 60.095 50.000 0.00 0.00 43.06 2.94
918 1010 1.640917 AAGGAAGGCGTACTTGGAGA 58.359 50.000 0.00 0.00 40.21 3.71
945 1037 3.312421 TCACAGAGACCAAAGAAAAAGCG 59.688 43.478 0.00 0.00 0.00 4.68
947 1043 6.634436 CGAATTCACAGAGACCAAAGAAAAAG 59.366 38.462 6.22 0.00 0.00 2.27
980 1077 0.254462 CCAAGGAAGGAGAAGGAGGC 59.746 60.000 0.00 0.00 0.00 4.70
1235 1379 2.662596 CTGGTAGCAAGCACGGGA 59.337 61.111 0.00 0.00 0.00 5.14
1257 1434 1.208776 AGACCGTGGTTAGGTTATGGC 59.791 52.381 0.00 0.00 43.01 4.40
1283 1460 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1293 1470 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1294 1471 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1295 1472 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1296 1473 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1297 1474 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1298 1475 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1299 1476 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1300 1477 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1301 1478 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1302 1479 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
1303 1480 1.535028 CAAGTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
1304 1481 1.535028 ACAAGTGTGTGTGTGTGTGTG 59.465 47.619 0.00 0.00 36.31 3.82
1305 1482 1.890876 ACAAGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 36.31 3.72
1306 1483 2.987413 AACAAGTGTGTGTGTGTGTG 57.013 45.000 0.00 0.00 38.27 3.82
1307 1484 3.670625 AGTAACAAGTGTGTGTGTGTGT 58.329 40.909 0.00 0.00 38.27 3.72
1308 1485 4.678509 AAGTAACAAGTGTGTGTGTGTG 57.321 40.909 0.00 0.00 38.27 3.82
1309 1486 5.350365 CACTAAGTAACAAGTGTGTGTGTGT 59.650 40.000 0.00 0.00 38.27 3.72
1310 1487 5.579119 TCACTAAGTAACAAGTGTGTGTGTG 59.421 40.000 2.72 0.00 42.96 3.82
1311 1488 5.726397 TCACTAAGTAACAAGTGTGTGTGT 58.274 37.500 2.72 0.00 42.96 3.72
1381 1561 4.252878 TGATTACTCGAAGCAAGCATGAA 58.747 39.130 0.00 0.00 28.17 2.57
1422 1633 6.091713 CCTTGTCAAATTTTCTGATGGAATGC 59.908 38.462 0.00 0.00 33.53 3.56
1425 1636 6.323482 TCACCTTGTCAAATTTTCTGATGGAA 59.677 34.615 0.00 0.00 0.00 3.53
1486 1697 1.336125 CTCCGTCCCATAACGTAGGAC 59.664 57.143 13.98 13.98 45.49 3.85
1487 1698 1.683943 CTCCGTCCCATAACGTAGGA 58.316 55.000 3.41 0.00 41.01 2.94
1488 1699 0.672342 CCTCCGTCCCATAACGTAGG 59.328 60.000 0.00 0.00 41.46 3.18
1489 1700 0.672342 CCCTCCGTCCCATAACGTAG 59.328 60.000 0.00 0.00 41.01 3.51
1490 1701 0.258484 TCCCTCCGTCCCATAACGTA 59.742 55.000 0.00 0.00 41.01 3.57
1491 1702 1.000739 TCCCTCCGTCCCATAACGT 59.999 57.895 0.00 0.00 41.01 3.99
1492 1703 1.041447 ACTCCCTCCGTCCCATAACG 61.041 60.000 0.00 0.00 42.24 3.18
1493 1704 1.962100 CTACTCCCTCCGTCCCATAAC 59.038 57.143 0.00 0.00 0.00 1.89
1494 1705 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1495 1706 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1496 1707 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1497 1708 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
1498 1709 2.107204 TGTATACTACTCCCTCCGTCCC 59.893 54.545 4.17 0.00 0.00 4.46
1499 1710 3.498774 TGTATACTACTCCCTCCGTCC 57.501 52.381 4.17 0.00 0.00 4.79
1500 1711 6.237154 ACTTATGTATACTACTCCCTCCGTC 58.763 44.000 4.17 0.00 0.00 4.79
1501 1712 6.198237 ACTTATGTATACTACTCCCTCCGT 57.802 41.667 4.17 0.00 0.00 4.69
1502 1713 9.896645 TTATACTTATGTATACTACTCCCTCCG 57.103 37.037 4.17 0.00 40.24 4.63
1548 1759 9.959749 AAGTTATGTATCTTTCGCAAAAAGAAA 57.040 25.926 13.48 0.35 39.43 2.52
1549 1760 9.959749 AAAGTTATGTATCTTTCGCAAAAAGAA 57.040 25.926 13.48 1.05 39.43 2.52
1550 1761 9.393249 CAAAGTTATGTATCTTTCGCAAAAAGA 57.607 29.630 12.24 12.24 40.17 2.52
1551 1762 8.155923 GCAAAGTTATGTATCTTTCGCAAAAAG 58.844 33.333 2.83 2.83 32.52 2.27
1552 1763 7.865385 AGCAAAGTTATGTATCTTTCGCAAAAA 59.135 29.630 13.77 0.00 34.05 1.94
1553 1764 7.367285 AGCAAAGTTATGTATCTTTCGCAAAA 58.633 30.769 13.77 0.00 34.05 2.44
1554 1765 6.908825 AGCAAAGTTATGTATCTTTCGCAAA 58.091 32.000 13.77 0.00 34.05 3.68
1555 1766 6.371548 AGAGCAAAGTTATGTATCTTTCGCAA 59.628 34.615 13.77 0.00 34.05 4.85
1556 1767 5.874810 AGAGCAAAGTTATGTATCTTTCGCA 59.125 36.000 13.77 0.00 34.05 5.10
1557 1768 6.351327 AGAGCAAAGTTATGTATCTTTCGC 57.649 37.500 0.00 0.00 32.52 4.70
1572 1783 7.172875 CAGTCCCATATTCAGATTAGAGCAAAG 59.827 40.741 0.00 0.00 0.00 2.77
1597 1808 5.295787 GTGCGATTGTTTAGTATGGGATTCA 59.704 40.000 0.00 0.00 0.00 2.57
1624 1835 6.401796 CCCAGTCGAACCTATTTAAACTTTCG 60.402 42.308 12.61 12.61 37.72 3.46
1660 1871 5.635280 CAGTGAAACATCATCAGTCGTAACT 59.365 40.000 0.00 0.00 41.43 2.24
1665 1876 2.998670 AGCAGTGAAACATCATCAGTCG 59.001 45.455 0.00 0.00 41.43 4.18
1806 2017 4.707030 TTGCTGCCAGTTCATTCAATAG 57.293 40.909 0.00 0.00 0.00 1.73
1809 2020 3.119388 GCTATTGCTGCCAGTTCATTCAA 60.119 43.478 0.00 0.00 36.03 2.69
1844 2055 6.428159 AGCTAGTTGTTGAAATACTGAAGTGG 59.572 38.462 0.00 0.00 0.00 4.00
1865 2076 2.237143 CCTTGTGGTTCTGGATGAGCTA 59.763 50.000 0.00 0.00 0.00 3.32
1921 2132 1.419762 TCCAGCTTCCAGTGCAGTAAA 59.580 47.619 0.00 0.00 0.00 2.01
1924 2135 1.072159 GTCCAGCTTCCAGTGCAGT 59.928 57.895 0.00 0.00 0.00 4.40
2013 2224 8.526147 TGGAAAATTTCAGGAGAAGAAATCATC 58.474 33.333 8.09 0.00 42.98 2.92
2052 2263 3.386078 TCTCACTCTTCCTATGCATGGAC 59.614 47.826 12.26 0.00 32.65 4.02
2113 2324 4.165372 TGGAGAAACAAGGTACTCAAAGGT 59.835 41.667 0.00 0.00 38.49 3.50
2114 2325 4.714632 TGGAGAAACAAGGTACTCAAAGG 58.285 43.478 0.00 0.00 38.49 3.11
2239 2460 0.389166 CTCCACCACTCTCTGAACGC 60.389 60.000 0.00 0.00 0.00 4.84
2240 2461 1.068194 GTCTCCACCACTCTCTGAACG 60.068 57.143 0.00 0.00 0.00 3.95
2268 2489 1.611673 CCGACCTGCATTTTCTCCACT 60.612 52.381 0.00 0.00 0.00 4.00
2269 2490 0.804989 CCGACCTGCATTTTCTCCAC 59.195 55.000 0.00 0.00 0.00 4.02
2335 2556 2.983229 AGACATCATCTGCAGAACCAC 58.017 47.619 22.50 10.27 35.81 4.16
2492 2714 7.969536 AATATCCTCATGAATAAGAACCACG 57.030 36.000 0.00 0.00 0.00 4.94
2525 2747 0.984230 GAAGTCCCACACCATCCTCA 59.016 55.000 0.00 0.00 0.00 3.86
2766 2992 4.814234 AGAATGAAACGCTTGTCAACTGTA 59.186 37.500 0.00 0.00 0.00 2.74
2793 3019 6.785488 TGTTTATTACTGACAGCTGTTGAG 57.215 37.500 22.65 21.02 0.00 3.02
2809 3035 6.757897 TCGATGAGCATTCCTTTGTTTATT 57.242 33.333 0.00 0.00 0.00 1.40
2810 3036 6.369059 CTCGATGAGCATTCCTTTGTTTAT 57.631 37.500 0.00 0.00 0.00 1.40
2845 3071 1.783071 TCCAAACTTTCCGCCCTTTT 58.217 45.000 0.00 0.00 0.00 2.27
2923 3149 2.754946 TACGGTGCCCAAAGTTCTAG 57.245 50.000 0.00 0.00 0.00 2.43
2965 3191 2.190161 CGCATCAAATGGCATCACTTG 58.810 47.619 0.00 1.87 32.01 3.16
2966 3192 1.820519 ACGCATCAAATGGCATCACTT 59.179 42.857 0.00 0.00 0.00 3.16
2977 3203 1.323235 CATAACGAGCGACGCATCAAA 59.677 47.619 23.70 4.57 46.94 2.69
3001 3227 3.305403 GCTCCTTAAAACAGGGCAACTTC 60.305 47.826 0.00 0.00 34.24 3.01
3022 3248 2.827921 ACTGGTTTCCTTTCCATGATGC 59.172 45.455 0.00 0.00 33.01 3.91
3023 3249 5.473066 AAACTGGTTTCCTTTCCATGATG 57.527 39.130 0.00 0.00 33.01 3.07
3039 3265 1.659794 CTGAACCGGGCAAAACTGG 59.340 57.895 6.32 0.00 42.81 4.00
3043 3269 1.342819 CAAATCCTGAACCGGGCAAAA 59.657 47.619 6.32 0.00 0.00 2.44
3044 3270 0.965439 CAAATCCTGAACCGGGCAAA 59.035 50.000 6.32 0.00 0.00 3.68
3087 3313 3.305608 GCAACACAAGCTGCCTAGAAAAT 60.306 43.478 0.00 0.00 30.67 1.82
3097 3323 4.241590 TGAATAAAGGCAACACAAGCTG 57.758 40.909 0.00 0.00 41.41 4.24
3100 3326 5.782047 TCCAATGAATAAAGGCAACACAAG 58.218 37.500 0.00 0.00 41.41 3.16
3137 3363 7.685481 TCCAGATCAAAGGTTTACAATGTAGA 58.315 34.615 0.00 0.00 0.00 2.59
3139 3365 8.877864 AATCCAGATCAAAGGTTTACAATGTA 57.122 30.769 0.00 0.00 0.00 2.29
3149 3375 4.718774 TCTGCTCTAATCCAGATCAAAGGT 59.281 41.667 0.00 0.00 33.44 3.50
3153 3379 4.713814 AGTGTCTGCTCTAATCCAGATCAA 59.286 41.667 0.00 0.00 39.95 2.57
3158 3384 3.320541 CCCTAGTGTCTGCTCTAATCCAG 59.679 52.174 0.00 0.00 0.00 3.86
3165 3394 2.042433 AGTTCTCCCTAGTGTCTGCTCT 59.958 50.000 0.00 0.00 0.00 4.09
3174 3403 1.406069 CGCATTGCAGTTCTCCCTAGT 60.406 52.381 9.69 0.00 0.00 2.57
3181 3410 3.648339 ATGTTTTCGCATTGCAGTTCT 57.352 38.095 9.69 0.00 0.00 3.01
3194 3423 9.152595 CTTTACAGAGGGAGTACTTATGTTTTC 57.847 37.037 0.00 0.00 0.00 2.29
3324 3749 3.388024 AGGTTGCACTTCACTTCTACTCA 59.612 43.478 0.00 0.00 0.00 3.41
3363 3788 5.882557 CCAAGCTGATATAACTGACAAGGTT 59.117 40.000 0.00 0.00 0.00 3.50
3425 3850 7.395525 AGTTGTCACTCCTATCTATCTAGGA 57.604 40.000 0.27 0.27 44.01 2.94
3426 3851 7.040062 CCAAGTTGTCACTCCTATCTATCTAGG 60.040 44.444 1.45 0.00 39.81 3.02
3427 3852 7.523052 GCCAAGTTGTCACTCCTATCTATCTAG 60.523 44.444 1.45 0.00 30.45 2.43
3438 3926 2.417719 CAGTAGCCAAGTTGTCACTCC 58.582 52.381 1.45 0.00 30.45 3.85
3560 4058 3.624861 CCATCCGTCGTAGTAAGTACAGT 59.375 47.826 0.00 0.00 0.00 3.55
3561 4059 3.547613 GCCATCCGTCGTAGTAAGTACAG 60.548 52.174 0.00 0.00 0.00 2.74
3562 4060 2.355756 GCCATCCGTCGTAGTAAGTACA 59.644 50.000 0.00 0.00 0.00 2.90
3563 4061 2.287248 GGCCATCCGTCGTAGTAAGTAC 60.287 54.545 0.00 0.00 0.00 2.73
3739 4241 1.998315 CCAAGCAGAAGACAGATGACG 59.002 52.381 0.00 0.00 0.00 4.35
3825 4327 2.909504 ACCAGAGCAGGAAGAGACTA 57.090 50.000 0.00 0.00 0.00 2.59
3961 4463 2.606725 CGGAATAGCATAGCAGCATAGC 59.393 50.000 0.00 0.00 36.85 2.97
4027 4529 5.476945 AGGAGAAAGAGAGAGAGAGAAACAC 59.523 44.000 0.00 0.00 0.00 3.32
4040 4542 8.364142 TCAAAACAAAACAAAAGGAGAAAGAGA 58.636 29.630 0.00 0.00 0.00 3.10
4067 4569 9.057089 TCTGAAAGAGAGAAACACTTAATTTCC 57.943 33.333 0.00 0.00 38.67 3.13
4106 4608 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4107 4609 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
4108 4610 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
4109 4611 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
4110 4612 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
4111 4613 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
4112 4614 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
4113 4615 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
4114 4616 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
4115 4617 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
4116 4618 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
4122 4624 9.701098 TCACTAGTGTCAAAAACGTTCTTATAT 57.299 29.630 21.99 0.00 0.00 0.86
4123 4625 9.531942 TTCACTAGTGTCAAAAACGTTCTTATA 57.468 29.630 21.99 0.00 0.00 0.98
4124 4626 8.428186 TTCACTAGTGTCAAAAACGTTCTTAT 57.572 30.769 21.99 0.00 0.00 1.73
4125 4627 7.546667 ACTTCACTAGTGTCAAAAACGTTCTTA 59.453 33.333 21.99 0.00 35.19 2.10
4126 4628 6.370718 ACTTCACTAGTGTCAAAAACGTTCTT 59.629 34.615 21.99 0.00 35.19 2.52
4127 4629 5.873164 ACTTCACTAGTGTCAAAAACGTTCT 59.127 36.000 21.99 0.00 35.19 3.01
4128 4630 6.103222 ACTTCACTAGTGTCAAAAACGTTC 57.897 37.500 21.99 0.00 35.19 3.95
4141 4643 5.873164 AGAACGTTTTTGACACTTCACTAGT 59.127 36.000 0.46 0.00 37.68 2.57
4142 4644 6.345920 AGAACGTTTTTGACACTTCACTAG 57.654 37.500 0.46 0.00 0.00 2.57
4143 4645 6.730960 AAGAACGTTTTTGACACTTCACTA 57.269 33.333 0.46 0.00 0.00 2.74
4144 4646 5.622770 AAGAACGTTTTTGACACTTCACT 57.377 34.783 0.46 0.00 0.00 3.41
4145 4647 9.659830 AATATAAGAACGTTTTTGACACTTCAC 57.340 29.630 13.87 0.00 0.00 3.18
4150 4652 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4151 4653 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
4152 4654 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
4153 4655 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
4154 4656 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
4155 4657 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
4156 4658 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
4157 4659 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
4158 4660 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
4159 4661 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
4160 4662 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
4161 4663 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
4162 4664 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
4163 4665 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
4164 4666 8.666129 TTACTCCCTCTGTCCCATAATATAAG 57.334 38.462 0.00 0.00 0.00 1.73
4167 4669 9.805204 AATATTACTCCCTCTGTCCCATAATAT 57.195 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.