Multiple sequence alignment - TraesCS2A01G121900

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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 TraesCS2A01G121900 chr2A 100.000 2603 0 0 1 2603 71448651 71446049 0.000000e+00 4807.0
1 TraesCS2A01G121900 chr2A 94.040 151 9 0 2453 2603 611168256 611168106 2.010000e-56 230.0
2 TraesCS2A01G121900 chr2B 91.857 1621 92 13 1 1587 110141545 110139931 0.000000e+00 2226.0
3 TraesCS2A01G121900 chr2B 90.887 406 35 2 54 458 247031780 247032184 6.340000e-151 544.0
4 TraesCS2A01G121900 chr2B 90.686 408 34 4 60 464 677671731 677671325 8.200000e-150 540.0
5 TraesCS2A01G121900 chr2B 94.304 158 8 1 2447 2603 208618491 208618648 9.310000e-60 241.0
6 TraesCS2A01G121900 chr2B 93.464 153 9 1 2452 2603 754627747 754627595 2.610000e-55 226.0
7 TraesCS2A01G121900 chr2B 92.857 154 11 0 2450 2603 512301092 512300939 9.370000e-55 224.0
8 TraesCS2A01G121900 chr2B 92.810 153 10 1 2452 2603 5019213 5019365 1.210000e-53 220.0
9 TraesCS2A01G121900 chr2B 100.000 29 0 0 1567 1595 608946329 608946301 1.000000e-03 54.7
10 TraesCS2A01G121900 chr2B 100.000 28 0 0 1582 1609 110139948 110139921 5.000000e-03 52.8
11 TraesCS2A01G121900 chr2D 93.564 839 42 5 1 829 72967019 72966183 0.000000e+00 1240.0
12 TraesCS2A01G121900 chr2D 93.578 654 30 4 933 1583 72966118 72965474 0.000000e+00 965.0
13 TraesCS2A01G121900 chr2D 92.606 568 42 0 1020 1587 72954963 72954396 0.000000e+00 817.0
14 TraesCS2A01G121900 chr2D 81.591 440 53 16 1767 2193 72964972 72964548 3.210000e-89 339.0
15 TraesCS2A01G121900 chr2D 97.500 40 1 0 826 865 72966171 72966132 4.650000e-08 69.4
16 TraesCS2A01G121900 chr4B 91.457 398 32 2 63 459 450115965 450115569 1.760000e-151 545.0
17 TraesCS2A01G121900 chr4B 90.909 407 35 2 54 459 514592322 514592727 1.760000e-151 545.0
18 TraesCS2A01G121900 chr4B 100.000 30 0 0 499 528 404460658 404460687 3.620000e-04 56.5
19 TraesCS2A01G121900 chr3B 90.663 407 35 3 54 459 659538264 659538668 2.950000e-149 538.0
20 TraesCS2A01G121900 chr7B 90.819 403 33 4 60 460 221308651 221308251 1.060000e-148 536.0
21 TraesCS2A01G121900 chr6D 90.819 403 34 3 60 460 380719183 380718782 1.060000e-148 536.0
22 TraesCS2A01G121900 chrUn 87.065 402 47 3 1206 1605 262807913 262808311 1.420000e-122 449.0
23 TraesCS2A01G121900 chr5A 83.403 476 71 6 1120 1587 8918102 8917627 3.980000e-118 435.0
24 TraesCS2A01G121900 chr6B 94.079 152 9 0 2452 2603 688761953 688761802 5.600000e-57 231.0
25 TraesCS2A01G121900 chr6B 92.258 155 10 1 2451 2603 430866746 430866900 4.360000e-53 219.0
26 TraesCS2A01G121900 chr4A 93.421 152 10 0 2452 2603 714555508 714555659 2.610000e-55 226.0
27 TraesCS2A01G121900 chr4A 75.851 323 67 11 1251 1569 41946428 41946113 1.250000e-33 154.0
28 TraesCS2A01G121900 chr4A 91.489 47 2 1 503 549 571048095 571048051 2.160000e-06 63.9
29 TraesCS2A01G121900 chr1B 92.208 154 12 0 2450 2603 374311599 374311446 4.360000e-53 219.0
30 TraesCS2A01G121900 chr4D 74.593 307 70 8 1251 1554 422536003 422536304 7.560000e-26 128.0
31 TraesCS2A01G121900 chr5D 95.238 42 2 0 498 539 27095073 27095032 1.670000e-07 67.6
32 TraesCS2A01G121900 chr7A 94.737 38 2 0 503 540 690127598 690127561 2.800000e-05 60.2


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 TraesCS2A01G121900 chr2A 71446049 71448651 2602 True 4807.00 4807 100.00000 1 2603 1 chr2A.!!$R1 2602
1 TraesCS2A01G121900 chr2B 110139921 110141545 1624 True 1139.40 2226 95.92850 1 1609 2 chr2B.!!$R5 1608
2 TraesCS2A01G121900 chr2D 72954396 72954963 567 True 817.00 817 92.60600 1020 1587 1 chr2D.!!$R1 567
3 TraesCS2A01G121900 chr2D 72964548 72967019 2471 True 653.35 1240 91.55825 1 2193 4 chr2D.!!$R2 2192

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
494 503 0.105964 CGTCCAGTGTGTTTGAGGGA 59.894 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2680 0.178903 TGGGTGCTCCTGGACTAGTT 60.179 55.0 4.53 0.0 34.78 2.24 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
133 134 1.493854 TTCCGCTTGGCCCTCCTTTA 61.494 55.000 0.00 0.00 0.00 1.85
134 135 1.452108 CCGCTTGGCCCTCCTTTAG 60.452 63.158 0.00 0.00 0.00 1.85
189 190 3.354678 GGCACGCCAAACAGACAT 58.645 55.556 2.36 0.00 35.81 3.06
243 244 3.244579 GGACAATATGGAACGAGCGTAAC 59.755 47.826 0.00 0.00 0.00 2.50
271 272 7.964604 AGAGTTTTTAAACATAAGAGCGTCT 57.035 32.000 7.97 0.00 41.30 4.18
375 376 0.966179 TGTGTGAGTAGTCCGCATGT 59.034 50.000 0.00 0.00 0.00 3.21
410 411 6.148976 GGGTGACTTGTAACAAACTCTATTCC 59.851 42.308 0.00 0.00 0.00 3.01
494 503 0.105964 CGTCCAGTGTGTTTGAGGGA 59.894 55.000 0.00 0.00 0.00 4.20
501 510 6.657541 GTCCAGTGTGTTTGAGGGATAATTTA 59.342 38.462 0.00 0.00 0.00 1.40
556 568 2.290008 TGGTGGATATTGAAGTGCGTGT 60.290 45.455 0.00 0.00 0.00 4.49
575 587 8.225107 GTGCGTGTGTATAAAAAGTTCTTATGA 58.775 33.333 0.00 0.00 0.00 2.15
662 674 1.166531 AGCGAGTTGGAGGCACAAAC 61.167 55.000 0.00 0.00 31.17 2.93
663 675 1.569493 CGAGTTGGAGGCACAAACG 59.431 57.895 0.00 3.33 31.17 3.60
685 697 1.000060 GAACCCGCGGCATATGTAGTA 60.000 52.381 22.85 0.00 0.00 1.82
769 781 7.472334 AGTAATGATCAGAAGTGCCAAAATT 57.528 32.000 0.09 0.00 0.00 1.82
772 784 5.138125 TGATCAGAAGTGCCAAAATTTCC 57.862 39.130 0.00 0.00 0.00 3.13
773 785 4.834496 TGATCAGAAGTGCCAAAATTTCCT 59.166 37.500 0.00 0.00 0.00 3.36
867 896 5.405269 GGTTTATGGTCAAATCAAACACAGC 59.595 40.000 0.00 0.00 32.11 4.40
869 898 1.336440 TGGTCAAATCAAACACAGCCG 59.664 47.619 0.00 0.00 0.00 5.52
884 913 3.245315 CCGTACAGCGCGTGTAGC 61.245 66.667 17.75 12.89 42.56 3.58
908 937 1.731720 GGAGCAGGTCTGTGATCAAC 58.268 55.000 0.00 0.00 0.00 3.18
933 972 2.529632 ACAGAGCATAGTGTCTGACCA 58.470 47.619 5.17 0.00 42.49 4.02
942 981 1.160137 GTGTCTGACCAACCATCTGC 58.840 55.000 5.17 0.00 0.00 4.26
952 991 0.744414 AACCATCTGCGCGTGCTATT 60.744 50.000 23.16 3.30 43.34 1.73
993 1037 2.821969 AGCACACCTCAACAATTCATCC 59.178 45.455 0.00 0.00 0.00 3.51
1045 1089 0.108567 GAGCACCCTCTTCGTCTTCC 60.109 60.000 0.00 0.00 35.16 3.46
1062 1106 1.919240 TCCTGTACTTCGCCTCTTCA 58.081 50.000 0.00 0.00 0.00 3.02
1275 1319 4.831307 GACGACGCGCTCACGGAT 62.831 66.667 5.73 2.65 40.57 4.18
1408 1452 2.005960 CTACTCCGGGAGCACCTTCG 62.006 65.000 23.84 0.00 36.97 3.79
1563 1607 2.527100 CTCGACCTGGACGTGTTTATC 58.473 52.381 17.38 0.00 0.00 1.75
1564 1608 2.163815 CTCGACCTGGACGTGTTTATCT 59.836 50.000 17.38 0.00 0.00 1.98
1565 1609 3.346315 TCGACCTGGACGTGTTTATCTA 58.654 45.455 17.38 0.00 0.00 1.98
1566 1610 3.127548 TCGACCTGGACGTGTTTATCTAC 59.872 47.826 17.38 0.00 0.00 2.59
1567 1611 3.432782 GACCTGGACGTGTTTATCTACG 58.567 50.000 0.00 0.00 45.19 3.51
1574 1618 1.580704 CGTGTTTATCTACGTCCACGC 59.419 52.381 0.00 0.00 44.43 5.34
1611 1655 4.152644 CATGCATGATGGACGGCT 57.847 55.556 22.59 0.00 0.00 5.52
1612 1656 1.947013 CATGCATGATGGACGGCTC 59.053 57.895 22.59 0.00 0.00 4.70
1620 1664 2.852075 TGGACGGCTCCAACCCTT 60.852 61.111 3.59 0.00 44.26 3.95
1622 1666 1.128809 TGGACGGCTCCAACCCTTTA 61.129 55.000 3.59 0.00 44.26 1.85
1623 1667 0.255033 GGACGGCTCCAACCCTTTAT 59.745 55.000 0.00 0.00 36.42 1.40
1624 1668 1.340697 GGACGGCTCCAACCCTTTATT 60.341 52.381 0.00 0.00 36.42 1.40
1625 1669 2.443416 GACGGCTCCAACCCTTTATTT 58.557 47.619 0.00 0.00 0.00 1.40
1626 1670 2.823747 GACGGCTCCAACCCTTTATTTT 59.176 45.455 0.00 0.00 0.00 1.82
1627 1671 4.011698 GACGGCTCCAACCCTTTATTTTA 58.988 43.478 0.00 0.00 0.00 1.52
1628 1672 4.606210 ACGGCTCCAACCCTTTATTTTAT 58.394 39.130 0.00 0.00 0.00 1.40
1629 1673 4.401202 ACGGCTCCAACCCTTTATTTTATG 59.599 41.667 0.00 0.00 0.00 1.90
1631 1675 5.660460 GGCTCCAACCCTTTATTTTATGTG 58.340 41.667 0.00 0.00 0.00 3.21
1632 1676 5.109210 GCTCCAACCCTTTATTTTATGTGC 58.891 41.667 0.00 0.00 0.00 4.57
1634 1678 5.337788 TCCAACCCTTTATTTTATGTGCCT 58.662 37.500 0.00 0.00 0.00 4.75
1636 1680 6.271159 TCCAACCCTTTATTTTATGTGCCTTT 59.729 34.615 0.00 0.00 0.00 3.11
1637 1681 6.593770 CCAACCCTTTATTTTATGTGCCTTTC 59.406 38.462 0.00 0.00 0.00 2.62
1638 1682 6.926630 ACCCTTTATTTTATGTGCCTTTCA 57.073 33.333 0.00 0.00 0.00 2.69
1639 1683 7.494922 ACCCTTTATTTTATGTGCCTTTCAT 57.505 32.000 0.00 0.00 0.00 2.57
1640 1684 7.917003 ACCCTTTATTTTATGTGCCTTTCATT 58.083 30.769 0.00 0.00 0.00 2.57
1642 1686 9.230122 CCCTTTATTTTATGTGCCTTTCATTTT 57.770 29.630 0.00 0.00 0.00 1.82
1648 1692 8.770438 TTTTATGTGCCTTTCATTTTATGTCC 57.230 30.769 0.00 0.00 0.00 4.02
1649 1693 4.799564 TGTGCCTTTCATTTTATGTCCC 57.200 40.909 0.00 0.00 0.00 4.46
1651 1695 4.837860 TGTGCCTTTCATTTTATGTCCCTT 59.162 37.500 0.00 0.00 0.00 3.95
1652 1696 5.047377 TGTGCCTTTCATTTTATGTCCCTTC 60.047 40.000 0.00 0.00 0.00 3.46
1663 1707 9.316730 CATTTTATGTCCCTTCCATTTTATGTG 57.683 33.333 0.00 0.00 0.00 3.21
1665 1709 9.535170 TTTTATGTCCCTTCCATTTTATGTGTA 57.465 29.630 0.00 0.00 0.00 2.90
1669 1713 9.881773 ATGTCCCTTCCATTTTATGTGTATTAT 57.118 29.630 0.00 0.00 0.00 1.28
1671 1715 9.131791 GTCCCTTCCATTTTATGTGTATTATGT 57.868 33.333 0.00 0.00 0.00 2.29
1672 1716 9.349713 TCCCTTCCATTTTATGTGTATTATGTC 57.650 33.333 0.00 0.00 0.00 3.06
1673 1717 8.576442 CCCTTCCATTTTATGTGTATTATGTCC 58.424 37.037 0.00 0.00 0.00 4.02
1674 1718 8.576442 CCTTCCATTTTATGTGTATTATGTCCC 58.424 37.037 0.00 0.00 0.00 4.46
1790 2180 9.474920 GGAATTGTGATAAGAAATTTTGTGACA 57.525 29.630 0.00 0.00 0.00 3.58
1869 2264 4.069304 ACATTTTAGAAGTTGCTACGCCA 58.931 39.130 0.00 0.00 0.00 5.69
1885 2280 1.153369 CCATCCGGTGCACCAGTAG 60.153 63.158 34.16 20.31 35.14 2.57
1886 2281 1.596934 CATCCGGTGCACCAGTAGT 59.403 57.895 34.16 13.02 35.14 2.73
1905 2300 4.476628 AGTATTACAAGGGTGGGTTACG 57.523 45.455 0.00 0.00 0.00 3.18
1906 2301 4.095946 AGTATTACAAGGGTGGGTTACGA 58.904 43.478 0.00 0.00 0.00 3.43
1907 2302 3.622166 ATTACAAGGGTGGGTTACGAG 57.378 47.619 0.00 0.00 0.00 4.18
1908 2303 2.307496 TACAAGGGTGGGTTACGAGA 57.693 50.000 0.00 0.00 0.00 4.04
1915 2310 3.387050 AGGGTGGGTTACGAGATACATTC 59.613 47.826 0.00 0.00 0.00 2.67
1917 2312 3.493873 GGTGGGTTACGAGATACATTCCC 60.494 52.174 0.00 0.00 34.77 3.97
1919 2314 3.971305 TGGGTTACGAGATACATTCCCAT 59.029 43.478 0.00 0.00 38.70 4.00
1920 2315 5.011329 GTGGGTTACGAGATACATTCCCATA 59.989 44.000 0.00 0.00 44.14 2.74
1925 2320 4.742012 ACGAGATACATTCCCATAGGAGT 58.258 43.478 0.00 0.00 45.19 3.85
1926 2321 5.148502 ACGAGATACATTCCCATAGGAGTT 58.851 41.667 0.00 0.00 45.19 3.01
1927 2322 5.602978 ACGAGATACATTCCCATAGGAGTTT 59.397 40.000 0.00 0.00 45.19 2.66
1928 2323 6.099845 ACGAGATACATTCCCATAGGAGTTTT 59.900 38.462 0.00 0.00 45.19 2.43
1929 2324 6.992715 CGAGATACATTCCCATAGGAGTTTTT 59.007 38.462 0.00 0.00 45.19 1.94
1987 2383 5.876357 TCTTCTAGTAAAATTGTGGCCTGT 58.124 37.500 3.32 0.00 0.00 4.00
2000 2396 1.143889 TGGCCTGTCCACATGTAACAA 59.856 47.619 3.32 0.00 40.72 2.83
2001 2397 2.224992 TGGCCTGTCCACATGTAACAAT 60.225 45.455 3.32 0.00 40.72 2.71
2004 2400 4.461081 GGCCTGTCCACATGTAACAATTTA 59.539 41.667 12.71 0.00 34.01 1.40
2005 2401 5.127031 GGCCTGTCCACATGTAACAATTTAT 59.873 40.000 12.71 0.00 34.01 1.40
2008 2404 7.275560 GCCTGTCCACATGTAACAATTTATTTC 59.724 37.037 12.71 0.00 0.00 2.17
2130 2528 9.707957 ATTACCATGGTTAATAAGAATGTTGGA 57.292 29.630 25.38 0.00 0.00 3.53
2157 2555 9.965824 TTTCTCTCAATGAAAAATCTAACCAAC 57.034 29.630 0.00 0.00 31.45 3.77
2158 2556 8.110860 TCTCTCAATGAAAAATCTAACCAACC 57.889 34.615 0.00 0.00 0.00 3.77
2166 2564 5.584551 AAAATCTAACCAACCTGGAGACT 57.415 39.130 0.00 0.00 40.96 3.24
2169 2567 2.158219 TCTAACCAACCTGGAGACTCCA 60.158 50.000 22.97 22.97 45.98 3.86
2187 2585 8.635765 AGACTCCAAAAGAATGCAACTAATTA 57.364 30.769 0.00 0.00 0.00 1.40
2188 2586 9.247861 AGACTCCAAAAGAATGCAACTAATTAT 57.752 29.630 0.00 0.00 0.00 1.28
2255 2653 8.836268 TTACTAAGCGTTTCTCTCCATAAAAA 57.164 30.769 0.00 0.00 0.00 1.94
2273 2671 3.851458 AAAACAAACTAGTCCTCCCGT 57.149 42.857 0.00 0.00 0.00 5.28
2274 2672 4.961438 AAAACAAACTAGTCCTCCCGTA 57.039 40.909 0.00 0.00 0.00 4.02
2275 2673 4.532314 AAACAAACTAGTCCTCCCGTAG 57.468 45.455 0.00 0.00 0.00 3.51
2276 2674 3.446442 ACAAACTAGTCCTCCCGTAGA 57.554 47.619 0.00 0.00 0.00 2.59
2277 2675 3.771216 ACAAACTAGTCCTCCCGTAGAA 58.229 45.455 0.00 0.00 0.00 2.10
2278 2676 4.154942 ACAAACTAGTCCTCCCGTAGAAA 58.845 43.478 0.00 0.00 0.00 2.52
2279 2677 4.590222 ACAAACTAGTCCTCCCGTAGAAAA 59.410 41.667 0.00 0.00 0.00 2.29
2280 2678 5.070847 ACAAACTAGTCCTCCCGTAGAAAAA 59.929 40.000 0.00 0.00 0.00 1.94
2299 2697 2.861147 AAAACTAGTCCAGGAGCACC 57.139 50.000 0.00 0.00 0.00 5.01
2300 2698 0.984995 AAACTAGTCCAGGAGCACCC 59.015 55.000 0.00 0.00 36.73 4.61
2301 2699 0.178903 AACTAGTCCAGGAGCACCCA 60.179 55.000 0.00 0.00 37.41 4.51
2302 2700 0.905337 ACTAGTCCAGGAGCACCCAC 60.905 60.000 0.00 0.00 37.41 4.61
2303 2701 0.904865 CTAGTCCAGGAGCACCCACA 60.905 60.000 0.00 0.00 37.41 4.17
2304 2702 0.472925 TAGTCCAGGAGCACCCACAA 60.473 55.000 0.00 0.00 37.41 3.33
2305 2703 1.150536 GTCCAGGAGCACCCACAAA 59.849 57.895 0.00 0.00 37.41 2.83
2306 2704 0.467290 GTCCAGGAGCACCCACAAAA 60.467 55.000 0.00 0.00 37.41 2.44
2307 2705 0.482446 TCCAGGAGCACCCACAAAAT 59.518 50.000 0.00 0.00 37.41 1.82
2308 2706 1.707989 TCCAGGAGCACCCACAAAATA 59.292 47.619 0.00 0.00 37.41 1.40
2309 2707 2.094675 CCAGGAGCACCCACAAAATAG 58.905 52.381 0.00 0.00 37.41 1.73
2310 2708 1.474077 CAGGAGCACCCACAAAATAGC 59.526 52.381 0.00 0.00 37.41 2.97
2311 2709 1.075374 AGGAGCACCCACAAAATAGCA 59.925 47.619 0.00 0.00 37.41 3.49
2312 2710 1.202348 GGAGCACCCACAAAATAGCAC 59.798 52.381 0.00 0.00 34.14 4.40
2313 2711 1.885887 GAGCACCCACAAAATAGCACA 59.114 47.619 0.00 0.00 0.00 4.57
2314 2712 2.493278 GAGCACCCACAAAATAGCACAT 59.507 45.455 0.00 0.00 0.00 3.21
2315 2713 3.694072 GAGCACCCACAAAATAGCACATA 59.306 43.478 0.00 0.00 0.00 2.29
2316 2714 4.280819 AGCACCCACAAAATAGCACATAT 58.719 39.130 0.00 0.00 0.00 1.78
2317 2715 4.711355 AGCACCCACAAAATAGCACATATT 59.289 37.500 0.00 0.00 35.51 1.28
2318 2716 5.187576 AGCACCCACAAAATAGCACATATTT 59.812 36.000 0.00 0.00 44.34 1.40
2319 2717 6.379703 AGCACCCACAAAATAGCACATATTTA 59.620 34.615 0.00 0.00 42.14 1.40
2320 2718 7.069826 AGCACCCACAAAATAGCACATATTTAT 59.930 33.333 0.00 0.00 42.14 1.40
2321 2719 8.356657 GCACCCACAAAATAGCACATATTTATA 58.643 33.333 0.00 0.00 42.14 0.98
2390 2788 3.051210 GAACCTTGGGTTGCTGCC 58.949 61.111 6.69 0.00 46.95 4.85
2391 2789 1.832167 GAACCTTGGGTTGCTGCCA 60.832 57.895 6.69 0.00 46.95 4.92
2392 2790 1.152269 AACCTTGGGTTGCTGCCAT 60.152 52.632 0.77 0.00 45.07 4.40
2393 2791 1.187567 AACCTTGGGTTGCTGCCATC 61.188 55.000 0.77 0.00 45.07 3.51
2394 2792 1.304713 CCTTGGGTTGCTGCCATCT 60.305 57.895 0.00 0.00 0.00 2.90
2395 2793 1.318158 CCTTGGGTTGCTGCCATCTC 61.318 60.000 0.00 0.00 0.00 2.75
2396 2794 1.651240 CTTGGGTTGCTGCCATCTCG 61.651 60.000 0.00 0.00 0.00 4.04
2397 2795 3.512516 GGGTTGCTGCCATCTCGC 61.513 66.667 0.00 0.00 0.00 5.03
2398 2796 3.512516 GGTTGCTGCCATCTCGCC 61.513 66.667 0.00 0.00 0.00 5.54
2399 2797 3.869272 GTTGCTGCCATCTCGCCG 61.869 66.667 0.00 0.00 0.00 6.46
2400 2798 4.393155 TTGCTGCCATCTCGCCGT 62.393 61.111 0.00 0.00 0.00 5.68
2401 2799 4.819761 TGCTGCCATCTCGCCGTC 62.820 66.667 0.00 0.00 0.00 4.79
2403 2801 4.147449 CTGCCATCTCGCCGTCCA 62.147 66.667 0.00 0.00 0.00 4.02
2404 2802 4.451150 TGCCATCTCGCCGTCCAC 62.451 66.667 0.00 0.00 0.00 4.02
2406 2804 3.770040 CCATCTCGCCGTCCACCA 61.770 66.667 0.00 0.00 0.00 4.17
2407 2805 2.509336 CATCTCGCCGTCCACCAC 60.509 66.667 0.00 0.00 0.00 4.16
2408 2806 2.994995 ATCTCGCCGTCCACCACA 60.995 61.111 0.00 0.00 0.00 4.17
2409 2807 3.006756 ATCTCGCCGTCCACCACAG 62.007 63.158 0.00 0.00 0.00 3.66
2413 2811 4.927782 GCCGTCCACCACAGCACA 62.928 66.667 0.00 0.00 0.00 4.57
2414 2812 2.032528 CCGTCCACCACAGCACAT 59.967 61.111 0.00 0.00 0.00 3.21
2415 2813 2.327343 CCGTCCACCACAGCACATG 61.327 63.158 0.00 0.00 0.00 3.21
2416 2814 2.956987 GTCCACCACAGCACATGC 59.043 61.111 0.00 0.00 42.49 4.06
2417 2815 2.282391 TCCACCACAGCACATGCC 60.282 61.111 0.00 0.00 43.38 4.40
2418 2816 3.376078 CCACCACAGCACATGCCC 61.376 66.667 0.00 0.00 43.38 5.36
2419 2817 3.740397 CACCACAGCACATGCCCG 61.740 66.667 0.00 0.00 43.38 6.13
2420 2818 4.269523 ACCACAGCACATGCCCGT 62.270 61.111 0.00 0.00 43.38 5.28
2421 2819 3.434319 CCACAGCACATGCCCGTC 61.434 66.667 0.00 0.00 43.38 4.79
2422 2820 3.792047 CACAGCACATGCCCGTCG 61.792 66.667 0.00 0.00 43.38 5.12
2425 2823 3.770040 AGCACATGCCCGTCGCTA 61.770 61.111 0.00 0.00 43.38 4.26
2426 2824 2.588877 GCACATGCCCGTCGCTAT 60.589 61.111 0.00 0.00 38.78 2.97
2427 2825 1.300620 GCACATGCCCGTCGCTATA 60.301 57.895 0.00 0.00 38.78 1.31
2428 2826 1.557443 GCACATGCCCGTCGCTATAC 61.557 60.000 0.00 0.00 38.78 1.47
2429 2827 0.944311 CACATGCCCGTCGCTATACC 60.944 60.000 0.00 0.00 38.78 2.73
2430 2828 1.113517 ACATGCCCGTCGCTATACCT 61.114 55.000 0.00 0.00 38.78 3.08
2431 2829 0.033504 CATGCCCGTCGCTATACCTT 59.966 55.000 0.00 0.00 38.78 3.50
2432 2830 0.756903 ATGCCCGTCGCTATACCTTT 59.243 50.000 0.00 0.00 38.78 3.11
2433 2831 0.538118 TGCCCGTCGCTATACCTTTT 59.462 50.000 0.00 0.00 38.78 2.27
2434 2832 1.065998 TGCCCGTCGCTATACCTTTTT 60.066 47.619 0.00 0.00 38.78 1.94
2476 2874 4.759516 TTTTAAGGAAAGCCGTCATGAC 57.240 40.909 16.21 16.21 39.96 3.06
2477 2875 3.695830 TTAAGGAAAGCCGTCATGACT 57.304 42.857 22.95 4.18 39.96 3.41
2478 2876 1.813513 AAGGAAAGCCGTCATGACTG 58.186 50.000 22.95 17.76 39.96 3.51
2479 2877 0.687354 AGGAAAGCCGTCATGACTGT 59.313 50.000 22.95 5.05 39.96 3.55
2480 2878 1.072331 AGGAAAGCCGTCATGACTGTT 59.928 47.619 22.95 12.33 39.96 3.16
2481 2879 1.880027 GGAAAGCCGTCATGACTGTTT 59.120 47.619 22.95 17.45 0.00 2.83
2482 2880 3.071479 GGAAAGCCGTCATGACTGTTTA 58.929 45.455 22.95 0.00 0.00 2.01
2483 2881 3.689649 GGAAAGCCGTCATGACTGTTTAT 59.310 43.478 22.95 11.37 0.00 1.40
2484 2882 4.873827 GGAAAGCCGTCATGACTGTTTATA 59.126 41.667 22.95 0.00 0.00 0.98
2485 2883 5.527582 GGAAAGCCGTCATGACTGTTTATAT 59.472 40.000 22.95 6.74 0.00 0.86
2486 2884 6.038271 GGAAAGCCGTCATGACTGTTTATATT 59.962 38.462 22.95 6.41 0.00 1.28
2487 2885 7.391148 AAAGCCGTCATGACTGTTTATATTT 57.609 32.000 22.95 9.65 0.00 1.40
2488 2886 6.604735 AGCCGTCATGACTGTTTATATTTC 57.395 37.500 22.95 1.55 0.00 2.17
2489 2887 6.112734 AGCCGTCATGACTGTTTATATTTCA 58.887 36.000 22.95 0.00 0.00 2.69
2490 2888 6.767902 AGCCGTCATGACTGTTTATATTTCAT 59.232 34.615 22.95 0.00 0.00 2.57
2491 2889 6.852853 GCCGTCATGACTGTTTATATTTCATG 59.147 38.462 22.95 3.91 43.25 3.07
2492 2890 6.852853 CCGTCATGACTGTTTATATTTCATGC 59.147 38.462 22.95 1.29 42.15 4.06
2493 2891 6.571154 CGTCATGACTGTTTATATTTCATGCG 59.429 38.462 22.95 8.09 42.15 4.73
2494 2892 6.358030 GTCATGACTGTTTATATTTCATGCGC 59.642 38.462 18.83 0.00 42.15 6.09
2495 2893 5.809719 TGACTGTTTATATTTCATGCGCA 57.190 34.783 14.96 14.96 0.00 6.09
2496 2894 6.188400 TGACTGTTTATATTTCATGCGCAA 57.812 33.333 17.11 0.00 0.00 4.85
2497 2895 6.616017 TGACTGTTTATATTTCATGCGCAAA 58.384 32.000 17.11 4.38 0.00 3.68
2498 2896 7.087007 TGACTGTTTATATTTCATGCGCAAAA 58.913 30.769 17.11 12.58 0.00 2.44
2499 2897 7.596621 TGACTGTTTATATTTCATGCGCAAAAA 59.403 29.630 17.11 18.70 0.00 1.94
2537 2935 9.895138 TTTGTTAATACATCTACTAGAAACCCC 57.105 33.333 0.00 0.00 33.44 4.95
2538 2936 7.719483 TGTTAATACATCTACTAGAAACCCCG 58.281 38.462 0.00 0.00 0.00 5.73
2539 2937 5.803237 AATACATCTACTAGAAACCCCGG 57.197 43.478 0.00 0.00 0.00 5.73
2540 2938 3.393426 ACATCTACTAGAAACCCCGGA 57.607 47.619 0.73 0.00 0.00 5.14
2541 2939 3.297736 ACATCTACTAGAAACCCCGGAG 58.702 50.000 0.73 0.00 0.00 4.63
2556 2954 3.569873 GGAGGCTCCGATTTCCAAA 57.430 52.632 19.53 0.00 0.00 3.28
2557 2955 1.095600 GGAGGCTCCGATTTCCAAAC 58.904 55.000 19.53 0.00 0.00 2.93
2558 2956 1.613255 GGAGGCTCCGATTTCCAAACA 60.613 52.381 19.53 0.00 0.00 2.83
2559 2957 2.159382 GAGGCTCCGATTTCCAAACAA 58.841 47.619 2.15 0.00 0.00 2.83
2560 2958 2.755103 GAGGCTCCGATTTCCAAACAAT 59.245 45.455 2.15 0.00 0.00 2.71
2561 2959 3.165071 AGGCTCCGATTTCCAAACAATT 58.835 40.909 0.00 0.00 0.00 2.32
2562 2960 3.056607 AGGCTCCGATTTCCAAACAATTG 60.057 43.478 3.24 3.24 36.25 2.32
2563 2961 3.306019 GGCTCCGATTTCCAAACAATTGT 60.306 43.478 4.92 4.92 34.60 2.71
2564 2962 4.082463 GGCTCCGATTTCCAAACAATTGTA 60.082 41.667 12.39 0.00 34.60 2.41
2565 2963 5.394115 GGCTCCGATTTCCAAACAATTGTAT 60.394 40.000 12.39 0.00 34.60 2.29
2566 2964 5.516339 GCTCCGATTTCCAAACAATTGTATG 59.484 40.000 12.39 3.61 34.60 2.39
2567 2965 6.624861 GCTCCGATTTCCAAACAATTGTATGA 60.625 38.462 12.39 6.04 34.60 2.15
2568 2966 6.851609 TCCGATTTCCAAACAATTGTATGAG 58.148 36.000 12.39 1.60 34.60 2.90
2569 2967 6.657117 TCCGATTTCCAAACAATTGTATGAGA 59.343 34.615 12.39 4.07 34.60 3.27
2570 2968 6.968904 CCGATTTCCAAACAATTGTATGAGAG 59.031 38.462 12.39 0.00 34.60 3.20
2571 2969 7.148255 CCGATTTCCAAACAATTGTATGAGAGA 60.148 37.037 12.39 2.87 34.60 3.10
2572 2970 8.236586 CGATTTCCAAACAATTGTATGAGAGAA 58.763 33.333 12.39 6.87 34.60 2.87
2573 2971 9.346725 GATTTCCAAACAATTGTATGAGAGAAC 57.653 33.333 12.39 0.00 34.60 3.01
2574 2972 8.463930 TTTCCAAACAATTGTATGAGAGAACT 57.536 30.769 12.39 0.00 34.60 3.01
2575 2973 7.672983 TCCAAACAATTGTATGAGAGAACTC 57.327 36.000 12.39 0.00 37.95 3.01
2576 2974 6.655003 TCCAAACAATTGTATGAGAGAACTCC 59.345 38.462 12.39 0.00 37.30 3.85
2577 2975 6.402550 CCAAACAATTGTATGAGAGAACTCCG 60.403 42.308 12.39 0.00 37.30 4.63
2578 2976 5.661056 ACAATTGTATGAGAGAACTCCGA 57.339 39.130 9.97 0.00 41.99 4.55
2579 2977 5.655488 ACAATTGTATGAGAGAACTCCGAG 58.345 41.667 9.97 0.00 41.99 4.63
2580 2978 5.186021 ACAATTGTATGAGAGAACTCCGAGT 59.814 40.000 9.97 0.00 41.99 4.18
2581 2979 5.923733 ATTGTATGAGAGAACTCCGAGTT 57.076 39.130 13.75 13.75 41.95 3.01
2582 2980 5.723672 TTGTATGAGAGAACTCCGAGTTT 57.276 39.130 14.96 5.60 38.80 2.66
2583 2981 5.060662 TGTATGAGAGAACTCCGAGTTTG 57.939 43.478 14.96 0.00 38.80 2.93
2584 2982 4.523173 TGTATGAGAGAACTCCGAGTTTGT 59.477 41.667 14.96 6.07 38.80 2.83
2585 2983 5.708697 TGTATGAGAGAACTCCGAGTTTGTA 59.291 40.000 14.96 2.02 38.80 2.41
2586 2984 4.768130 TGAGAGAACTCCGAGTTTGTAG 57.232 45.455 14.96 0.00 38.80 2.74
2587 2985 3.057456 TGAGAGAACTCCGAGTTTGTAGC 60.057 47.826 14.96 2.36 38.80 3.58
2588 2986 2.231721 AGAGAACTCCGAGTTTGTAGCC 59.768 50.000 14.96 1.68 38.80 3.93
2589 2987 1.067776 AGAACTCCGAGTTTGTAGCCG 60.068 52.381 14.96 0.00 38.80 5.52
2590 2988 0.963962 AACTCCGAGTTTGTAGCCGA 59.036 50.000 8.03 0.00 34.11 5.54
2591 2989 1.183549 ACTCCGAGTTTGTAGCCGAT 58.816 50.000 0.00 0.00 0.00 4.18
2592 2990 2.372264 ACTCCGAGTTTGTAGCCGATA 58.628 47.619 0.00 0.00 0.00 2.92
2593 2991 2.756760 ACTCCGAGTTTGTAGCCGATAA 59.243 45.455 0.00 0.00 0.00 1.75
2594 2992 3.194116 ACTCCGAGTTTGTAGCCGATAAA 59.806 43.478 0.00 0.00 0.00 1.40
2595 2993 4.142004 ACTCCGAGTTTGTAGCCGATAAAT 60.142 41.667 0.00 0.00 0.00 1.40
2596 2994 4.761975 TCCGAGTTTGTAGCCGATAAATT 58.238 39.130 0.00 0.00 0.00 1.82
2597 2995 5.180271 TCCGAGTTTGTAGCCGATAAATTT 58.820 37.500 0.00 0.00 0.00 1.82
2598 2996 5.064198 TCCGAGTTTGTAGCCGATAAATTTG 59.936 40.000 0.00 0.00 0.00 2.32
2599 2997 4.728608 CGAGTTTGTAGCCGATAAATTTGC 59.271 41.667 0.00 0.00 0.00 3.68
2600 2998 4.993905 AGTTTGTAGCCGATAAATTTGCC 58.006 39.130 0.00 0.00 0.00 4.52
2601 2999 3.684103 TTGTAGCCGATAAATTTGCCG 57.316 42.857 0.00 4.13 0.00 5.69
2602 3000 1.332375 TGTAGCCGATAAATTTGCCGC 59.668 47.619 0.00 0.04 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.410912 TCTCTTGGAATTTTTCATGATGCTATG 58.589 33.333 0.00 0.00 0.00 2.23
133 134 4.360951 TCCACCAATCTTTAACCGAACT 57.639 40.909 0.00 0.00 0.00 3.01
134 135 4.698304 TCATCCACCAATCTTTAACCGAAC 59.302 41.667 0.00 0.00 0.00 3.95
189 190 2.356278 GTGAGGGATGCCTTGGCA 59.644 61.111 17.19 17.19 0.00 4.92
243 244 6.031417 CGCTCTTATGTTTAAAAACTCTTGCG 59.969 38.462 7.09 10.37 39.59 4.85
246 247 8.379457 AGACGCTCTTATGTTTAAAAACTCTT 57.621 30.769 7.09 0.00 39.59 2.85
271 272 1.066858 GGAGAGCAAGATTGTCGGTGA 60.067 52.381 0.00 0.00 0.00 4.02
358 359 0.170339 CGACATGCGGACTACTCACA 59.830 55.000 0.00 0.00 36.03 3.58
375 376 3.478857 ACAAGTCACCCAATTACACGA 57.521 42.857 0.00 0.00 0.00 4.35
410 411 4.739793 TGCCTCATCCATTAAATAAGGGG 58.260 43.478 4.22 0.00 37.70 4.79
536 548 2.095853 CACACGCACTTCAATATCCACC 59.904 50.000 0.00 0.00 0.00 4.61
575 587 7.698163 ATCCTCTTCTACCCAAACTCATATT 57.302 36.000 0.00 0.00 0.00 1.28
651 663 2.265904 GGTTCCCGTTTGTGCCTCC 61.266 63.158 0.00 0.00 0.00 4.30
663 675 2.386064 TACATATGCCGCGGGTTCCC 62.386 60.000 29.38 10.37 0.00 3.97
685 697 2.281070 CACTCCCGTGTGCTTGCT 60.281 61.111 0.00 0.00 36.39 3.91
769 781 4.593206 TCTTCAAAGCCTCTCTAACAGGAA 59.407 41.667 0.00 0.00 31.91 3.36
772 784 4.502962 CCTCTTCAAAGCCTCTCTAACAG 58.497 47.826 0.00 0.00 0.00 3.16
773 785 3.307059 GCCTCTTCAAAGCCTCTCTAACA 60.307 47.826 0.00 0.00 0.00 2.41
867 896 3.245315 GCTACACGCGCTGTACGG 61.245 66.667 5.73 0.00 43.93 4.02
884 913 3.699894 ACAGACCTGCTCCGCCAG 61.700 66.667 0.00 0.00 0.00 4.85
886 915 2.914777 GATCACAGACCTGCTCCGCC 62.915 65.000 0.00 0.00 0.00 6.13
898 927 2.341257 CTCTGTTCGGGTTGATCACAG 58.659 52.381 0.00 0.00 36.97 3.66
908 937 1.478510 AGACACTATGCTCTGTTCGGG 59.521 52.381 0.00 0.00 0.00 5.14
933 972 0.744414 AATAGCACGCGCAGATGGTT 60.744 50.000 5.73 0.00 42.27 3.67
942 981 3.241091 TGTTGACGTATAAATAGCACGCG 59.759 43.478 3.53 3.53 39.23 6.01
1045 1089 1.067565 TGCTGAAGAGGCGAAGTACAG 60.068 52.381 0.00 0.00 0.00 2.74
1389 1433 1.817209 GAAGGTGCTCCCGGAGTAG 59.183 63.158 16.09 0.00 38.74 2.57
1470 1514 2.370445 CGCCATCCTGAACCTCCCT 61.370 63.158 0.00 0.00 0.00 4.20
1609 1653 5.109210 GCACATAAAATAAAGGGTTGGAGC 58.891 41.667 0.00 0.00 0.00 4.70
1611 1655 5.337788 AGGCACATAAAATAAAGGGTTGGA 58.662 37.500 0.00 0.00 0.00 3.53
1612 1656 5.675684 AGGCACATAAAATAAAGGGTTGG 57.324 39.130 0.00 0.00 0.00 3.77
1614 1658 7.309770 TGAAAGGCACATAAAATAAAGGGTT 57.690 32.000 0.00 0.00 0.00 4.11
1615 1659 6.926630 TGAAAGGCACATAAAATAAAGGGT 57.073 33.333 0.00 0.00 0.00 4.34
1616 1660 8.791327 AAATGAAAGGCACATAAAATAAAGGG 57.209 30.769 0.00 0.00 0.00 3.95
1622 1666 9.382275 GGACATAAAATGAAAGGCACATAAAAT 57.618 29.630 0.00 0.00 0.00 1.82
1623 1667 7.821846 GGGACATAAAATGAAAGGCACATAAAA 59.178 33.333 0.00 0.00 0.00 1.52
1624 1668 7.180051 AGGGACATAAAATGAAAGGCACATAAA 59.820 33.333 0.00 0.00 0.00 1.40
1625 1669 6.667414 AGGGACATAAAATGAAAGGCACATAA 59.333 34.615 0.00 0.00 0.00 1.90
1626 1670 6.194235 AGGGACATAAAATGAAAGGCACATA 58.806 36.000 0.00 0.00 0.00 2.29
1627 1671 5.025453 AGGGACATAAAATGAAAGGCACAT 58.975 37.500 0.00 0.00 0.00 3.21
1628 1672 4.415596 AGGGACATAAAATGAAAGGCACA 58.584 39.130 0.00 0.00 0.00 4.57
1629 1673 5.405935 AAGGGACATAAAATGAAAGGCAC 57.594 39.130 0.00 0.00 0.00 5.01
1631 1675 4.466015 TGGAAGGGACATAAAATGAAAGGC 59.534 41.667 0.00 0.00 0.00 4.35
1632 1676 6.796785 ATGGAAGGGACATAAAATGAAAGG 57.203 37.500 0.00 0.00 0.00 3.11
1636 1680 9.265862 ACATAAAATGGAAGGGACATAAAATGA 57.734 29.630 0.00 0.00 33.60 2.57
1637 1681 9.316730 CACATAAAATGGAAGGGACATAAAATG 57.683 33.333 0.00 0.00 33.60 2.32
1638 1682 9.045745 ACACATAAAATGGAAGGGACATAAAAT 57.954 29.630 0.00 0.00 33.60 1.82
1639 1683 8.429237 ACACATAAAATGGAAGGGACATAAAA 57.571 30.769 0.00 0.00 33.60 1.52
1640 1684 9.707957 ATACACATAAAATGGAAGGGACATAAA 57.292 29.630 0.00 0.00 33.60 1.40
1643 1687 9.881773 ATAATACACATAAAATGGAAGGGACAT 57.118 29.630 0.00 0.00 33.60 3.06
1645 1689 9.131791 ACATAATACACATAAAATGGAAGGGAC 57.868 33.333 0.00 0.00 33.60 4.46
1647 1691 8.576442 GGACATAATACACATAAAATGGAAGGG 58.424 37.037 0.00 0.00 33.60 3.95
1648 1692 8.576442 GGGACATAATACACATAAAATGGAAGG 58.424 37.037 0.00 0.00 33.60 3.46
1649 1693 9.354673 AGGGACATAATACACATAAAATGGAAG 57.645 33.333 0.00 0.00 33.60 3.46
1651 1695 9.707957 AAAGGGACATAATACACATAAAATGGA 57.292 29.630 0.00 0.00 33.60 3.41
1652 1696 9.965824 GAAAGGGACATAATACACATAAAATGG 57.034 33.333 0.00 0.00 33.60 3.16
1753 1798 9.823647 TTCTTATCACAATTCCATCTACTCTTC 57.176 33.333 0.00 0.00 0.00 2.87
1763 1808 9.474920 GTCACAAAATTTCTTATCACAATTCCA 57.525 29.630 0.00 0.00 0.00 3.53
1764 1809 9.474920 TGTCACAAAATTTCTTATCACAATTCC 57.525 29.630 0.00 0.00 0.00 3.01
1843 2238 6.236017 CGTAGCAACTTCTAAAATGTTGGA 57.764 37.500 0.00 0.00 40.72 3.53
1869 2264 1.789523 ATACTACTGGTGCACCGGAT 58.210 50.000 44.14 30.66 45.36 4.18
1881 2276 5.127682 CGTAACCCACCCTTGTAATACTACT 59.872 44.000 0.00 0.00 0.00 2.57
1885 2280 4.160252 TCTCGTAACCCACCCTTGTAATAC 59.840 45.833 0.00 0.00 0.00 1.89
1886 2281 4.352009 TCTCGTAACCCACCCTTGTAATA 58.648 43.478 0.00 0.00 0.00 0.98
2105 2503 9.707957 ATCCAACATTCTTATTAACCATGGTAA 57.292 29.630 20.12 13.02 0.00 2.85
2106 2504 9.707957 AATCCAACATTCTTATTAACCATGGTA 57.292 29.630 20.12 3.19 0.00 3.25
2108 2506 9.533253 GAAATCCAACATTCTTATTAACCATGG 57.467 33.333 11.19 11.19 0.00 3.66
2111 2509 9.753674 AGAGAAATCCAACATTCTTATTAACCA 57.246 29.630 0.00 0.00 36.08 3.67
2120 2518 8.413309 TTTCATTGAGAGAAATCCAACATTCT 57.587 30.769 0.00 0.00 38.56 2.40
2229 2627 9.444600 TTTTTATGGAGAGAAACGCTTAGTAAT 57.555 29.630 0.00 0.00 0.00 1.89
2230 2628 8.836268 TTTTTATGGAGAGAAACGCTTAGTAA 57.164 30.769 0.00 0.00 0.00 2.24
2252 2650 4.160642 ACGGGAGGACTAGTTTGTTTTT 57.839 40.909 0.00 0.00 0.00 1.94
2253 2651 3.851458 ACGGGAGGACTAGTTTGTTTT 57.149 42.857 0.00 0.00 0.00 2.43
2254 2652 4.154942 TCTACGGGAGGACTAGTTTGTTT 58.845 43.478 0.00 0.00 0.00 2.83
2255 2653 3.771216 TCTACGGGAGGACTAGTTTGTT 58.229 45.455 0.00 0.00 0.00 2.83
2256 2654 3.446442 TCTACGGGAGGACTAGTTTGT 57.554 47.619 0.00 0.00 0.00 2.83
2257 2655 4.796038 TTTCTACGGGAGGACTAGTTTG 57.204 45.455 0.00 0.00 0.00 2.93
2258 2656 5.813513 TTTTTCTACGGGAGGACTAGTTT 57.186 39.130 0.00 0.00 0.00 2.66
2279 2677 2.224793 GGGTGCTCCTGGACTAGTTTTT 60.225 50.000 4.53 0.00 34.78 1.94
2280 2678 1.351350 GGGTGCTCCTGGACTAGTTTT 59.649 52.381 4.53 0.00 34.78 2.43
2281 2679 0.984995 GGGTGCTCCTGGACTAGTTT 59.015 55.000 4.53 0.00 34.78 2.66
2282 2680 0.178903 TGGGTGCTCCTGGACTAGTT 60.179 55.000 4.53 0.00 34.78 2.24
2283 2681 0.905337 GTGGGTGCTCCTGGACTAGT 60.905 60.000 4.53 0.00 34.78 2.57
2284 2682 0.904865 TGTGGGTGCTCCTGGACTAG 60.905 60.000 4.53 0.00 34.78 2.57
2285 2683 0.472925 TTGTGGGTGCTCCTGGACTA 60.473 55.000 4.53 0.00 34.78 2.59
2286 2684 1.352622 TTTGTGGGTGCTCCTGGACT 61.353 55.000 4.53 0.00 34.78 3.85
2287 2685 0.467290 TTTTGTGGGTGCTCCTGGAC 60.467 55.000 4.53 0.51 36.20 4.02
2288 2686 0.482446 ATTTTGTGGGTGCTCCTGGA 59.518 50.000 4.53 0.00 36.20 3.86
2289 2687 2.094675 CTATTTTGTGGGTGCTCCTGG 58.905 52.381 4.53 0.00 36.20 4.45
2290 2688 1.474077 GCTATTTTGTGGGTGCTCCTG 59.526 52.381 4.53 0.00 36.20 3.86
2291 2689 1.075374 TGCTATTTTGTGGGTGCTCCT 59.925 47.619 4.53 0.00 36.20 3.69
2292 2690 1.202348 GTGCTATTTTGTGGGTGCTCC 59.798 52.381 0.00 0.00 0.00 4.70
2293 2691 1.885887 TGTGCTATTTTGTGGGTGCTC 59.114 47.619 0.00 0.00 0.00 4.26
2294 2692 1.993956 TGTGCTATTTTGTGGGTGCT 58.006 45.000 0.00 0.00 0.00 4.40
2295 2693 4.654091 ATATGTGCTATTTTGTGGGTGC 57.346 40.909 0.00 0.00 0.00 5.01
2356 2754 9.112658 CCCAAGGTTCCCTTATATAAGATAAGA 57.887 37.037 21.75 10.91 42.67 2.10
2357 2755 8.891501 ACCCAAGGTTCCCTTATATAAGATAAG 58.108 37.037 21.75 6.75 42.67 1.73
2358 2756 8.823810 ACCCAAGGTTCCCTTATATAAGATAA 57.176 34.615 21.75 12.91 42.67 1.75
2359 2757 8.665906 CAACCCAAGGTTCCCTTATATAAGATA 58.334 37.037 21.75 8.07 43.05 1.98
2360 2758 7.526918 CAACCCAAGGTTCCCTTATATAAGAT 58.473 38.462 21.75 0.60 43.05 2.40
2361 2759 6.636336 GCAACCCAAGGTTCCCTTATATAAGA 60.636 42.308 21.75 2.49 43.05 2.10
2362 2760 5.535030 GCAACCCAAGGTTCCCTTATATAAG 59.465 44.000 14.56 14.56 43.05 1.73
2363 2761 5.194942 AGCAACCCAAGGTTCCCTTATATAA 59.805 40.000 0.00 0.00 43.05 0.98
2364 2762 4.729881 AGCAACCCAAGGTTCCCTTATATA 59.270 41.667 0.00 0.00 43.05 0.86
2365 2763 3.531814 AGCAACCCAAGGTTCCCTTATAT 59.468 43.478 0.00 0.00 43.05 0.86
2366 2764 2.923629 AGCAACCCAAGGTTCCCTTATA 59.076 45.455 0.00 0.00 43.05 0.98
2367 2765 1.716503 AGCAACCCAAGGTTCCCTTAT 59.283 47.619 0.00 0.00 43.05 1.73
2368 2766 1.154430 AGCAACCCAAGGTTCCCTTA 58.846 50.000 0.00 0.00 43.05 2.69
2369 2767 0.469892 CAGCAACCCAAGGTTCCCTT 60.470 55.000 0.00 0.00 43.05 3.95
2370 2768 1.153756 CAGCAACCCAAGGTTCCCT 59.846 57.895 0.00 0.00 43.05 4.20
2371 2769 2.574018 GCAGCAACCCAAGGTTCCC 61.574 63.158 0.00 0.00 43.05 3.97
2372 2770 2.574018 GGCAGCAACCCAAGGTTCC 61.574 63.158 0.00 0.00 43.05 3.62
2373 2771 1.187567 ATGGCAGCAACCCAAGGTTC 61.188 55.000 0.00 0.00 43.05 3.62
2375 2773 1.607467 GATGGCAGCAACCCAAGGT 60.607 57.895 0.00 0.00 37.65 3.50
2376 2774 1.304713 AGATGGCAGCAACCCAAGG 60.305 57.895 5.19 0.00 35.67 3.61
2377 2775 1.651240 CGAGATGGCAGCAACCCAAG 61.651 60.000 5.19 0.00 35.67 3.61
2378 2776 1.675310 CGAGATGGCAGCAACCCAA 60.675 57.895 5.19 0.00 35.67 4.12
2379 2777 2.046023 CGAGATGGCAGCAACCCA 60.046 61.111 5.19 0.00 36.66 4.51
2380 2778 3.512516 GCGAGATGGCAGCAACCC 61.513 66.667 5.19 0.00 0.00 4.11
2381 2779 3.512516 GGCGAGATGGCAGCAACC 61.513 66.667 5.19 0.00 44.08 3.77
2382 2780 3.869272 CGGCGAGATGGCAGCAAC 61.869 66.667 5.19 0.00 45.16 4.17
2383 2781 4.393155 ACGGCGAGATGGCAGCAA 62.393 61.111 16.62 0.00 45.16 3.91
2384 2782 4.819761 GACGGCGAGATGGCAGCA 62.820 66.667 16.62 0.00 45.16 4.41
2386 2784 4.147449 TGGACGGCGAGATGGCAG 62.147 66.667 16.62 0.00 45.16 4.85
2387 2785 4.451150 GTGGACGGCGAGATGGCA 62.451 66.667 16.62 0.00 45.16 4.92
2389 2787 3.770040 TGGTGGACGGCGAGATGG 61.770 66.667 16.62 0.00 0.00 3.51
2390 2788 2.509336 GTGGTGGACGGCGAGATG 60.509 66.667 16.62 0.00 0.00 2.90
2391 2789 2.994995 TGTGGTGGACGGCGAGAT 60.995 61.111 16.62 0.00 0.00 2.75
2392 2790 3.680786 CTGTGGTGGACGGCGAGA 61.681 66.667 16.62 0.00 0.00 4.04
2397 2795 2.032528 ATGTGCTGTGGTGGACGG 59.967 61.111 0.00 0.00 0.00 4.79
2398 2796 2.969806 GCATGTGCTGTGGTGGACG 61.970 63.158 0.00 0.00 38.21 4.79
2399 2797 2.629656 GGCATGTGCTGTGGTGGAC 61.630 63.158 4.84 0.00 41.70 4.02
2400 2798 2.282391 GGCATGTGCTGTGGTGGA 60.282 61.111 4.84 0.00 41.70 4.02
2401 2799 3.376078 GGGCATGTGCTGTGGTGG 61.376 66.667 4.84 0.00 41.70 4.61
2402 2800 3.740397 CGGGCATGTGCTGTGGTG 61.740 66.667 4.84 0.00 41.70 4.17
2403 2801 4.269523 ACGGGCATGTGCTGTGGT 62.270 61.111 4.84 0.00 41.70 4.16
2404 2802 3.434319 GACGGGCATGTGCTGTGG 61.434 66.667 4.84 0.00 41.70 4.17
2405 2803 3.792047 CGACGGGCATGTGCTGTG 61.792 66.667 4.84 0.00 41.70 3.66
2415 2813 1.660167 AAAAAGGTATAGCGACGGGC 58.340 50.000 0.00 0.00 44.05 6.13
2454 2852 4.825085 AGTCATGACGGCTTTCCTTAAAAA 59.175 37.500 19.85 0.00 36.20 1.94
2455 2853 4.215399 CAGTCATGACGGCTTTCCTTAAAA 59.785 41.667 19.85 0.00 36.20 1.52
2456 2854 3.751175 CAGTCATGACGGCTTTCCTTAAA 59.249 43.478 19.85 0.00 36.20 1.52
2457 2855 3.244422 ACAGTCATGACGGCTTTCCTTAA 60.244 43.478 23.58 0.00 36.20 1.85
2458 2856 2.301870 ACAGTCATGACGGCTTTCCTTA 59.698 45.455 23.58 0.00 36.20 2.69
2459 2857 1.072331 ACAGTCATGACGGCTTTCCTT 59.928 47.619 23.58 1.83 36.20 3.36
2460 2858 0.687354 ACAGTCATGACGGCTTTCCT 59.313 50.000 23.58 2.53 36.20 3.36
2461 2859 1.523758 AACAGTCATGACGGCTTTCC 58.476 50.000 23.58 0.00 36.20 3.13
2462 2860 4.946784 ATAAACAGTCATGACGGCTTTC 57.053 40.909 23.58 0.00 36.20 2.62
2463 2861 7.120579 TGAAATATAAACAGTCATGACGGCTTT 59.879 33.333 23.58 21.78 36.20 3.51
2464 2862 6.597672 TGAAATATAAACAGTCATGACGGCTT 59.402 34.615 23.58 20.00 36.20 4.35
2465 2863 6.112734 TGAAATATAAACAGTCATGACGGCT 58.887 36.000 23.58 10.84 36.20 5.52
2466 2864 6.358118 TGAAATATAAACAGTCATGACGGC 57.642 37.500 23.58 6.69 36.20 5.68
2467 2865 6.852853 GCATGAAATATAAACAGTCATGACGG 59.147 38.462 22.31 22.31 45.44 4.79
2468 2866 6.571154 CGCATGAAATATAAACAGTCATGACG 59.429 38.462 19.85 16.37 45.44 4.35
2469 2867 6.358030 GCGCATGAAATATAAACAGTCATGAC 59.642 38.462 18.47 18.47 45.44 3.06
2470 2868 6.038050 TGCGCATGAAATATAAACAGTCATGA 59.962 34.615 5.66 0.00 45.44 3.07
2471 2869 6.200808 TGCGCATGAAATATAAACAGTCATG 58.799 36.000 5.66 7.43 45.40 3.07
2472 2870 6.375945 TGCGCATGAAATATAAACAGTCAT 57.624 33.333 5.66 0.00 0.00 3.06
2473 2871 5.809719 TGCGCATGAAATATAAACAGTCA 57.190 34.783 5.66 0.00 0.00 3.41
2474 2872 7.504922 TTTTGCGCATGAAATATAAACAGTC 57.495 32.000 12.75 0.00 0.00 3.51
2475 2873 7.881643 TTTTTGCGCATGAAATATAAACAGT 57.118 28.000 12.75 0.00 0.00 3.55
2511 2909 9.895138 GGGGTTTCTAGTAGATGTATTAACAAA 57.105 33.333 0.00 0.00 39.58 2.83
2512 2910 8.199449 CGGGGTTTCTAGTAGATGTATTAACAA 58.801 37.037 0.00 0.00 39.58 2.83
2513 2911 7.201938 CCGGGGTTTCTAGTAGATGTATTAACA 60.202 40.741 0.00 0.00 40.69 2.41
2514 2912 7.014615 TCCGGGGTTTCTAGTAGATGTATTAAC 59.985 40.741 0.00 1.44 0.00 2.01
2515 2913 7.068702 TCCGGGGTTTCTAGTAGATGTATTAA 58.931 38.462 0.00 0.00 0.00 1.40
2516 2914 6.613699 TCCGGGGTTTCTAGTAGATGTATTA 58.386 40.000 0.00 0.00 0.00 0.98
2517 2915 5.461327 TCCGGGGTTTCTAGTAGATGTATT 58.539 41.667 0.00 0.00 0.00 1.89
2518 2916 5.070823 TCCGGGGTTTCTAGTAGATGTAT 57.929 43.478 0.00 0.00 0.00 2.29
2519 2917 4.467769 CTCCGGGGTTTCTAGTAGATGTA 58.532 47.826 0.00 0.00 0.00 2.29
2520 2918 3.297736 CTCCGGGGTTTCTAGTAGATGT 58.702 50.000 0.00 0.00 0.00 3.06
2521 2919 2.628657 CCTCCGGGGTTTCTAGTAGATG 59.371 54.545 0.00 0.00 0.00 2.90
2522 2920 2.960163 CCTCCGGGGTTTCTAGTAGAT 58.040 52.381 0.00 0.00 0.00 1.98
2523 2921 1.687368 GCCTCCGGGGTTTCTAGTAGA 60.687 57.143 0.00 0.00 37.43 2.59
2524 2922 0.751452 GCCTCCGGGGTTTCTAGTAG 59.249 60.000 0.00 0.00 37.43 2.57
2525 2923 0.337428 AGCCTCCGGGGTTTCTAGTA 59.663 55.000 0.00 0.00 40.98 1.82
2526 2924 0.976590 GAGCCTCCGGGGTTTCTAGT 60.977 60.000 0.00 0.00 44.22 2.57
2527 2925 1.687297 GGAGCCTCCGGGGTTTCTAG 61.687 65.000 0.00 0.00 44.22 2.43
2528 2926 1.688187 GGAGCCTCCGGGGTTTCTA 60.688 63.158 0.00 0.00 44.22 2.10
2529 2927 3.009714 GGAGCCTCCGGGGTTTCT 61.010 66.667 0.00 0.00 44.22 2.52
2538 2936 1.095600 GTTTGGAAATCGGAGCCTCC 58.904 55.000 0.00 0.00 0.00 4.30
2539 2937 1.821216 TGTTTGGAAATCGGAGCCTC 58.179 50.000 0.00 0.00 0.00 4.70
2540 2938 2.286365 TTGTTTGGAAATCGGAGCCT 57.714 45.000 0.00 0.00 0.00 4.58
2541 2939 3.253230 CAATTGTTTGGAAATCGGAGCC 58.747 45.455 0.00 0.00 0.00 4.70
2542 2940 3.913089 ACAATTGTTTGGAAATCGGAGC 58.087 40.909 4.92 0.00 37.15 4.70
2543 2941 6.851609 TCATACAATTGTTTGGAAATCGGAG 58.148 36.000 23.35 0.66 37.15 4.63
2544 2942 6.657117 TCTCATACAATTGTTTGGAAATCGGA 59.343 34.615 23.35 11.02 37.15 4.55
2545 2943 6.851609 TCTCATACAATTGTTTGGAAATCGG 58.148 36.000 23.35 9.48 37.15 4.18
2546 2944 7.751732 TCTCTCATACAATTGTTTGGAAATCG 58.248 34.615 23.35 11.14 37.15 3.34
2547 2945 9.346725 GTTCTCTCATACAATTGTTTGGAAATC 57.653 33.333 23.35 9.04 37.15 2.17
2548 2946 9.082313 AGTTCTCTCATACAATTGTTTGGAAAT 57.918 29.630 23.35 16.56 37.15 2.17
2549 2947 8.463930 AGTTCTCTCATACAATTGTTTGGAAA 57.536 30.769 23.35 12.70 37.15 3.13
2550 2948 7.174946 GGAGTTCTCTCATACAATTGTTTGGAA 59.825 37.037 23.35 17.22 42.05 3.53
2551 2949 6.655003 GGAGTTCTCTCATACAATTGTTTGGA 59.345 38.462 23.35 18.45 42.05 3.53
2552 2950 6.402550 CGGAGTTCTCTCATACAATTGTTTGG 60.403 42.308 23.35 16.01 42.05 3.28
2553 2951 6.368791 TCGGAGTTCTCTCATACAATTGTTTG 59.631 38.462 17.78 18.75 42.05 2.93
2554 2952 6.464222 TCGGAGTTCTCTCATACAATTGTTT 58.536 36.000 17.78 5.99 42.05 2.83
2555 2953 6.037786 TCGGAGTTCTCTCATACAATTGTT 57.962 37.500 17.78 1.87 42.05 2.83
2556 2954 5.186021 ACTCGGAGTTCTCTCATACAATTGT 59.814 40.000 16.68 16.68 42.05 2.71
2557 2955 5.655488 ACTCGGAGTTCTCTCATACAATTG 58.345 41.667 4.45 3.24 42.05 2.32
2558 2956 5.923733 ACTCGGAGTTCTCTCATACAATT 57.076 39.130 4.45 0.00 42.05 2.32
2559 2957 5.923733 AACTCGGAGTTCTCTCATACAAT 57.076 39.130 17.38 0.00 42.05 2.71
2560 2958 5.010719 ACAAACTCGGAGTTCTCTCATACAA 59.989 40.000 22.62 0.00 37.47 2.41
2561 2959 4.523173 ACAAACTCGGAGTTCTCTCATACA 59.477 41.667 22.62 0.00 37.47 2.29
2562 2960 5.061920 ACAAACTCGGAGTTCTCTCATAC 57.938 43.478 22.62 0.00 37.47 2.39
2563 2961 5.163642 GCTACAAACTCGGAGTTCTCTCATA 60.164 44.000 22.62 8.94 37.47 2.15
2564 2962 4.381079 GCTACAAACTCGGAGTTCTCTCAT 60.381 45.833 22.62 4.36 37.47 2.90
2565 2963 3.057456 GCTACAAACTCGGAGTTCTCTCA 60.057 47.826 22.62 7.05 37.47 3.27
2566 2964 3.503891 GCTACAAACTCGGAGTTCTCTC 58.496 50.000 22.62 8.63 37.47 3.20
2567 2965 2.231721 GGCTACAAACTCGGAGTTCTCT 59.768 50.000 22.62 11.01 37.47 3.10
2568 2966 2.608268 GGCTACAAACTCGGAGTTCTC 58.392 52.381 22.62 10.45 37.47 2.87
2569 2967 1.067776 CGGCTACAAACTCGGAGTTCT 60.068 52.381 22.62 13.56 37.47 3.01
2570 2968 1.068055 TCGGCTACAAACTCGGAGTTC 60.068 52.381 22.62 10.38 37.47 3.01
2571 2969 0.963962 TCGGCTACAAACTCGGAGTT 59.036 50.000 17.38 17.38 40.80 3.01
2572 2970 1.183549 ATCGGCTACAAACTCGGAGT 58.816 50.000 4.45 4.45 0.00 3.85
2573 2971 3.431922 TTATCGGCTACAAACTCGGAG 57.568 47.619 2.83 2.83 0.00 4.63
2574 2972 3.872511 TTTATCGGCTACAAACTCGGA 57.127 42.857 0.00 0.00 0.00 4.55
2575 2973 5.263185 CAAATTTATCGGCTACAAACTCGG 58.737 41.667 0.00 0.00 0.00 4.63
2576 2974 4.728608 GCAAATTTATCGGCTACAAACTCG 59.271 41.667 0.00 0.00 0.00 4.18
2577 2975 5.034797 GGCAAATTTATCGGCTACAAACTC 58.965 41.667 0.00 0.00 0.00 3.01
2578 2976 4.438200 CGGCAAATTTATCGGCTACAAACT 60.438 41.667 0.00 0.00 0.00 2.66
2579 2977 3.789224 CGGCAAATTTATCGGCTACAAAC 59.211 43.478 0.00 0.00 0.00 2.93
2580 2978 3.732471 GCGGCAAATTTATCGGCTACAAA 60.732 43.478 12.26 0.00 0.00 2.83
2581 2979 2.223386 GCGGCAAATTTATCGGCTACAA 60.223 45.455 12.26 0.00 0.00 2.41
2582 2980 1.332375 GCGGCAAATTTATCGGCTACA 59.668 47.619 12.26 0.00 0.00 2.74
2583 2981 2.032414 GCGGCAAATTTATCGGCTAC 57.968 50.000 12.26 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.