Multiple sequence alignment - TraesCS6A01G103400

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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 TraesCS6A01G103400 chr6A 100.000 4402 0 0 1 4402 72447286 72442885 0.000000e+00 8130.0
1 TraesCS6A01G103400 chr6A 88.889 72 6 2 4102 4172 549536916 549536846 2.180000e-13 87.9
2 TraesCS6A01G103400 chr6D 87.941 1559 118 35 8 1534 57473844 57472324 0.000000e+00 1773.0
3 TraesCS6A01G103400 chr6D 92.155 1211 75 16 1626 2824 57472249 57471047 0.000000e+00 1692.0
4 TraesCS6A01G103400 chr6D 92.691 1163 66 12 2862 4013 57471040 57469886 0.000000e+00 1659.0
5 TraesCS6A01G103400 chr6D 91.304 299 19 5 4106 4402 57469890 57469597 6.860000e-108 401.0
6 TraesCS6A01G103400 chr6D 84.590 305 31 10 3012 3310 94779230 94779524 5.570000e-74 289.0
7 TraesCS6A01G103400 chr6D 89.873 79 7 1 4099 4176 257923758 257923680 2.800000e-17 100.0
8 TraesCS6A01G103400 chr6B 95.000 920 40 3 1626 2544 129304059 129303145 0.000000e+00 1439.0
9 TraesCS6A01G103400 chr6B 89.365 724 42 16 803 1505 129304872 129304163 0.000000e+00 878.0
10 TraesCS6A01G103400 chr6B 91.255 526 23 10 3162 3686 129302426 129301923 0.000000e+00 695.0
11 TraesCS6A01G103400 chr6B 83.853 706 66 17 2198 2888 178011583 178010911 2.890000e-176 628.0
12 TraesCS6A01G103400 chr6B 91.071 224 17 3 2541 2762 129303033 129302811 2.570000e-77 300.0
13 TraesCS6A01G103400 chr6B 86.385 213 19 7 4181 4388 129300962 129300755 1.590000e-54 224.0
14 TraesCS6A01G103400 chr6B 86.154 195 22 2 599 788 34815626 34815820 5.770000e-49 206.0
15 TraesCS6A01G103400 chr6B 84.314 204 28 2 599 798 492857873 492858076 3.470000e-46 196.0
16 TraesCS6A01G103400 chr6B 90.435 115 4 2 3744 3858 129301490 129301383 1.280000e-30 145.0
17 TraesCS6A01G103400 chr6B 94.505 91 3 1 4018 4108 203685192 203685280 5.940000e-29 139.0
18 TraesCS6A01G103400 chr6B 87.387 111 8 4 4003 4113 49403880 49403984 5.980000e-24 122.0
19 TraesCS6A01G103400 chr6B 89.394 66 5 2 3938 4001 551188268 551188333 1.010000e-11 82.4
20 TraesCS6A01G103400 chr6B 89.394 66 5 2 3938 4001 551443286 551443351 1.010000e-11 82.4
21 TraesCS6A01G103400 chr6B 87.500 72 5 4 4102 4172 604077026 604076958 3.650000e-11 80.5
22 TraesCS6A01G103400 chr6B 87.879 66 6 2 3938 4001 551343661 551343726 4.720000e-10 76.8
23 TraesCS6A01G103400 chr6B 87.879 66 6 2 3938 4001 551589765 551589830 4.720000e-10 76.8
24 TraesCS6A01G103400 chr6B 87.879 66 6 2 3938 4001 551665749 551665814 4.720000e-10 76.8
25 TraesCS6A01G103400 chr6B 87.931 58 4 2 3938 3995 698143158 698143212 1.020000e-06 65.8
26 TraesCS6A01G103400 chr1D 86.603 209 18 4 599 797 246073016 246072808 5.730000e-54 222.0
27 TraesCS6A01G103400 chr1D 86.239 109 12 3 4018 4126 465077613 465077508 1.000000e-21 115.0
28 TraesCS6A01G103400 chr7B 85.294 204 20 5 599 797 153592630 153592828 7.470000e-48 202.0
29 TraesCS6A01G103400 chr7B 88.732 71 7 1 4102 4172 696077608 696077539 7.840000e-13 86.1
30 TraesCS6A01G103400 chr2B 82.673 202 29 4 599 796 716771979 716772178 1.630000e-39 174.0
31 TraesCS6A01G103400 chr2B 89.655 87 7 1 4018 4104 757524262 757524346 4.650000e-20 110.0
32 TraesCS6A01G103400 chr5A 83.246 191 27 3 610 795 585229066 585229256 2.110000e-38 171.0
33 TraesCS6A01G103400 chr5A 93.103 87 4 1 4018 4104 660190650 660190734 4.620000e-25 126.0
34 TraesCS6A01G103400 chr5A 86.111 108 10 4 4017 4123 19975727 19975830 1.290000e-20 111.0
35 TraesCS6A01G103400 chr5A 89.333 75 6 2 4099 4172 26532072 26532145 4.690000e-15 93.5
36 TraesCS6A01G103400 chr7D 85.430 151 21 1 631 780 66348981 66349131 5.890000e-34 156.0
37 TraesCS6A01G103400 chr7D 87.963 108 9 3 4013 4119 204732366 204732470 1.660000e-24 124.0
38 TraesCS6A01G103400 chr1B 91.837 98 5 2 4010 4107 652293771 652293677 2.760000e-27 134.0
39 TraesCS6A01G103400 chr1B 89.655 87 7 1 4018 4104 555953799 555953883 4.650000e-20 110.0
40 TraesCS6A01G103400 chr1B 86.076 79 9 2 703 780 585683723 585683800 2.820000e-12 84.2
41 TraesCS6A01G103400 chr1B 100.000 42 0 0 3938 3979 357594003 357594044 1.310000e-10 78.7
42 TraesCS6A01G103400 chr1B 93.478 46 2 1 3974 4019 533863082 533863126 2.840000e-07 67.6
43 TraesCS6A01G103400 chr3A 91.579 95 6 1 4016 4110 727583902 727583994 3.570000e-26 130.0
44 TraesCS6A01G103400 chr3B 87.850 107 11 1 4003 4109 739112763 739112867 1.660000e-24 124.0
45 TraesCS6A01G103400 chr3B 86.420 81 6 4 3938 4015 452282630 452282552 2.820000e-12 84.2
46 TraesCS6A01G103400 chr5D 85.124 121 14 3 3990 4108 386984074 386983956 2.150000e-23 121.0
47 TraesCS6A01G103400 chr4B 83.206 131 18 3 3974 4104 552019699 552019825 2.780000e-22 117.0
48 TraesCS6A01G103400 chr4B 100.000 39 0 0 3938 3976 180553918 180553956 6.110000e-09 73.1
49 TraesCS6A01G103400 chr1A 84.906 106 10 4 4015 4119 340408399 340408499 7.790000e-18 102.0
50 TraesCS6A01G103400 chr3D 82.203 118 13 6 4015 4131 134497614 134497504 1.300000e-15 95.3
51 TraesCS6A01G103400 chr4A 91.935 62 5 0 4102 4163 324519507 324519568 2.180000e-13 87.9


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 TraesCS6A01G103400 chr6A 72442885 72447286 4401 True 8130.00 8130 100.000000 1 4402 1 chr6A.!!$R1 4401
1 TraesCS6A01G103400 chr6D 57469597 57473844 4247 True 1381.25 1773 91.022750 8 4402 4 chr6D.!!$R2 4394
2 TraesCS6A01G103400 chr6B 178010911 178011583 672 True 628.00 628 83.853000 2198 2888 1 chr6B.!!$R1 690
3 TraesCS6A01G103400 chr6B 129300755 129304872 4117 True 613.50 1439 90.585167 803 4388 6 chr6B.!!$R3 3585

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
614 625 0.530744 TGCGTCTAATTGCGGACTCT 59.469 50.000 0.00 0.0 0.00 3.24 F
1098 1124 1.004044 TCTCTTCTTCTACCCGTCCGT 59.996 52.381 0.00 0.0 0.00 4.69 F
1538 1579 0.179000 GGCTGTGGACTGTGGGATAG 59.821 60.000 0.00 0.0 0.00 2.08 F
1561 1602 0.259938 GGGACTCCAATTCCAGGCAT 59.740 55.000 0.00 0.0 34.45 4.40 F
1562 1603 1.342374 GGGACTCCAATTCCAGGCATT 60.342 52.381 0.00 0.0 34.45 3.56 F
2439 2506 1.451387 CTGCGCGGGGATTAGGTTT 60.451 57.895 8.83 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1497 0.111061 TGCTTGGGCATCAGTTCACT 59.889 50.0 0.00 0.0 44.28 3.41 R
2357 2424 0.318762 AGAGCCGTCTTGAACTCCAC 59.681 55.0 0.00 0.0 0.00 4.02 R
3152 3498 0.108585 ATGAGGCGTCACAGTGGTTT 59.891 50.0 11.97 0.0 34.75 3.27 R
3154 3500 0.108585 AAATGAGGCGTCACAGTGGT 59.891 50.0 11.97 0.0 34.75 4.16 R
3157 3503 0.593128 GCAAAATGAGGCGTCACAGT 59.407 50.0 11.97 0.0 34.75 3.55 R
4268 5336 0.102120 TGTTTTGCTGGTTTGGCTCG 59.898 50.0 0.00 0.0 0.00 5.03 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
108 109 5.634439 CGGCAATGTTCATGATTTCTGAAAA 59.366 36.000 6.95 0.00 34.59 2.29
110 111 7.515643 GGCAATGTTCATGATTTCTGAAAAAG 58.484 34.615 6.95 0.00 34.59 2.27
256 257 5.350091 CCCCAATTTTAGTAAATGTTTGCCG 59.650 40.000 0.00 0.00 34.27 5.69
267 268 6.758886 AGTAAATGTTTGCCGATTCACAAAAA 59.241 30.769 4.04 0.41 37.50 1.94
358 359 7.144722 TCATGATTTCATAATAATGGTCGGC 57.855 36.000 0.00 0.00 34.52 5.54
375 376 5.124776 TGGTCGGCGAATCTGAAAAATATTT 59.875 36.000 12.92 0.00 0.00 1.40
434 435 8.417884 TGGAACTAAAATTAAGAACAAACAGGG 58.582 33.333 0.00 0.00 0.00 4.45
447 448 9.508642 AAGAACAAACAGGGAAAAATACAAAAA 57.491 25.926 0.00 0.00 0.00 1.94
448 449 8.941977 AGAACAAACAGGGAAAAATACAAAAAC 58.058 29.630 0.00 0.00 0.00 2.43
449 450 8.856153 AACAAACAGGGAAAAATACAAAAACT 57.144 26.923 0.00 0.00 0.00 2.66
450 451 8.856153 ACAAACAGGGAAAAATACAAAAACTT 57.144 26.923 0.00 0.00 0.00 2.66
451 452 8.726068 ACAAACAGGGAAAAATACAAAAACTTG 58.274 29.630 0.00 0.00 0.00 3.16
551 562 1.751924 GCCGGCCCAAAATGTACATAA 59.248 47.619 18.11 0.00 0.00 1.90
553 564 2.223386 CCGGCCCAAAATGTACATAACG 60.223 50.000 9.21 6.31 0.00 3.18
555 566 2.480587 GGCCCAAAATGTACATAACGCC 60.481 50.000 9.21 11.86 0.00 5.68
568 579 1.370587 TAACGCCTGCGGGTTTATGC 61.371 55.000 14.55 0.00 42.05 3.14
587 598 1.712977 CGCTCGGTCGCTAAGTAGGT 61.713 60.000 0.00 0.00 0.00 3.08
604 615 9.393512 CTAAGTAGGTACCTATATGCGTCTAAT 57.606 37.037 24.36 4.31 0.00 1.73
605 616 8.647256 AAGTAGGTACCTATATGCGTCTAATT 57.353 34.615 24.36 2.96 0.00 1.40
606 617 8.053026 AGTAGGTACCTATATGCGTCTAATTG 57.947 38.462 24.36 0.00 0.00 2.32
607 618 5.721232 AGGTACCTATATGCGTCTAATTGC 58.279 41.667 14.41 0.00 0.00 3.56
608 619 4.561606 GGTACCTATATGCGTCTAATTGCG 59.438 45.833 4.06 0.00 0.00 4.85
609 620 3.585862 ACCTATATGCGTCTAATTGCGG 58.414 45.455 0.00 0.00 0.00 5.69
610 621 3.257375 ACCTATATGCGTCTAATTGCGGA 59.743 43.478 0.00 0.00 0.00 5.54
611 622 3.612860 CCTATATGCGTCTAATTGCGGAC 59.387 47.826 0.00 0.00 0.00 4.79
612 623 2.882927 TATGCGTCTAATTGCGGACT 57.117 45.000 0.00 0.00 0.00 3.85
613 624 1.571919 ATGCGTCTAATTGCGGACTC 58.428 50.000 0.00 0.00 0.00 3.36
614 625 0.530744 TGCGTCTAATTGCGGACTCT 59.469 50.000 0.00 0.00 0.00 3.24
615 626 1.067142 TGCGTCTAATTGCGGACTCTT 60.067 47.619 0.00 0.00 0.00 2.85
616 627 2.000447 GCGTCTAATTGCGGACTCTTT 59.000 47.619 0.00 0.00 0.00 2.52
617 628 3.184541 GCGTCTAATTGCGGACTCTTTA 58.815 45.455 0.00 0.00 0.00 1.85
618 629 3.000022 GCGTCTAATTGCGGACTCTTTAC 60.000 47.826 0.00 0.00 0.00 2.01
619 630 4.421948 CGTCTAATTGCGGACTCTTTACT 58.578 43.478 0.00 0.00 0.00 2.24
635 646 7.435305 ACTCTTTACTGAAGTCTTTGGAGTAC 58.565 38.462 0.00 0.00 36.70 2.73
638 649 8.483758 TCTTTACTGAAGTCTTTGGAGTACTTT 58.516 33.333 0.00 0.00 36.70 2.66
661 672 1.933181 CGAGCAAAGATTGATACCGCA 59.067 47.619 0.00 0.00 0.00 5.69
685 696 9.476202 GCAAATAAGGTGTTTACAAGAGATTTT 57.524 29.630 0.00 0.00 0.00 1.82
824 840 3.380637 TCGAATAGGATTATCCGGCTAGC 59.619 47.826 6.04 6.04 42.75 3.42
827 843 4.744795 ATAGGATTATCCGGCTAGCAAG 57.255 45.455 18.24 9.78 42.75 4.01
832 848 3.620427 TTATCCGGCTAGCAAGTCAAA 57.380 42.857 18.24 0.26 0.00 2.69
844 860 2.029290 GCAAGTCAAAGACGGAGGTAGA 60.029 50.000 0.00 0.00 37.67 2.59
932 953 4.771127 GTCACGTGACACCACCAT 57.229 55.556 37.16 0.00 44.18 3.55
1098 1124 1.004044 TCTCTTCTTCTACCCGTCCGT 59.996 52.381 0.00 0.00 0.00 4.69
1160 1186 3.285484 TCTTAACGCTCCCGATTCTACT 58.715 45.455 0.00 0.00 38.29 2.57
1190 1221 1.433471 CCACTCTGATAGCGTCGCA 59.567 57.895 21.09 5.88 0.00 5.10
1208 1239 2.245096 GCATCGATTTATTCATGCCGC 58.755 47.619 0.00 0.00 35.03 6.53
1362 1393 2.247437 GCGCTCGGGCTAATCCTTG 61.247 63.158 5.36 0.00 36.09 3.61
1405 1436 1.218196 TCTTTGGGGTTTGGGTTGCTA 59.782 47.619 0.00 0.00 0.00 3.49
1417 1451 2.846206 TGGGTTGCTATGGACTCAAGAT 59.154 45.455 0.00 0.00 0.00 2.40
1427 1461 6.767902 GCTATGGACTCAAGATAACCAAATGA 59.232 38.462 0.00 0.00 34.28 2.57
1432 1466 7.669304 TGGACTCAAGATAACCAAATGAATTCA 59.331 33.333 11.26 11.26 0.00 2.57
1456 1497 7.231925 TCAGTCATGGTGTAAACTGTAGAGTTA 59.768 37.037 5.58 0.00 41.87 2.24
1473 1514 3.679389 AGTTAGTGAACTGATGCCCAAG 58.321 45.455 0.00 0.00 44.50 3.61
1500 1541 4.560035 CCAAATAGAGCATTGCGTTTCTTG 59.440 41.667 2.38 6.02 0.00 3.02
1503 1544 1.267806 AGAGCATTGCGTTTCTTGGTG 59.732 47.619 2.38 0.00 0.00 4.17
1508 1549 2.325583 TTGCGTTTCTTGGTGAGAGT 57.674 45.000 0.00 0.00 35.37 3.24
1511 1552 2.626266 TGCGTTTCTTGGTGAGAGTCTA 59.374 45.455 0.00 0.00 35.37 2.59
1534 1575 1.676635 CATGGCTGTGGACTGTGGG 60.677 63.158 0.00 0.00 0.00 4.61
1535 1576 1.847506 ATGGCTGTGGACTGTGGGA 60.848 57.895 0.00 0.00 0.00 4.37
1537 1578 0.546507 TGGCTGTGGACTGTGGGATA 60.547 55.000 0.00 0.00 0.00 2.59
1538 1579 0.179000 GGCTGTGGACTGTGGGATAG 59.821 60.000 0.00 0.00 0.00 2.08
1540 1581 1.765314 GCTGTGGACTGTGGGATAGAT 59.235 52.381 0.00 0.00 0.00 1.98
1542 1583 3.006323 GCTGTGGACTGTGGGATAGATAG 59.994 52.174 0.00 0.00 0.00 2.08
1543 1584 3.576118 CTGTGGACTGTGGGATAGATAGG 59.424 52.174 0.00 0.00 0.00 2.57
1544 1585 2.900546 GTGGACTGTGGGATAGATAGGG 59.099 54.545 0.00 0.00 0.00 3.53
1545 1586 2.795360 TGGACTGTGGGATAGATAGGGA 59.205 50.000 0.00 0.00 0.00 4.20
1546 1587 3.166679 GGACTGTGGGATAGATAGGGAC 58.833 54.545 0.00 0.00 0.00 4.46
1547 1588 3.181416 GGACTGTGGGATAGATAGGGACT 60.181 52.174 0.00 0.00 46.37 3.85
1549 1590 3.181416 ACTGTGGGATAGATAGGGACTCC 60.181 52.174 0.00 0.00 41.75 3.85
1551 1592 3.208922 TGTGGGATAGATAGGGACTCCAA 59.791 47.826 0.00 0.00 41.75 3.53
1553 1594 4.846940 GTGGGATAGATAGGGACTCCAATT 59.153 45.833 0.00 0.00 41.75 2.32
1554 1595 5.046231 GTGGGATAGATAGGGACTCCAATTC 60.046 48.000 0.00 0.00 41.75 2.17
1557 1598 5.188751 GGATAGATAGGGACTCCAATTCCAG 59.811 48.000 0.00 0.00 41.75 3.86
1558 1599 3.321950 AGATAGGGACTCCAATTCCAGG 58.678 50.000 0.00 0.00 41.75 4.45
1559 1600 1.213296 TAGGGACTCCAATTCCAGGC 58.787 55.000 0.00 0.00 41.75 4.85
1561 1602 0.259938 GGGACTCCAATTCCAGGCAT 59.740 55.000 0.00 0.00 34.45 4.40
1562 1603 1.342374 GGGACTCCAATTCCAGGCATT 60.342 52.381 0.00 0.00 34.45 3.56
1602 1643 4.278678 CTGGGCAGCTAAAATAAACGAG 57.721 45.455 0.00 0.00 0.00 4.18
1612 1653 5.446875 GCTAAAATAAACGAGGTTTCTCCCG 60.447 44.000 0.00 0.00 37.01 5.14
1617 1658 3.387947 GAGGTTTCTCCCGCCCGA 61.388 66.667 0.00 0.00 36.75 5.14
1680 1732 5.290158 CACAGCCATCATATTTTGAAGCAAC 59.710 40.000 0.00 0.00 39.15 4.17
1716 1769 6.208007 AGCATTTCAAGAGTGAATCACAATCA 59.792 34.615 16.38 0.00 44.67 2.57
1822 1879 4.466370 ACTGTGCTTTACTATCTGCCTGTA 59.534 41.667 0.00 0.00 0.00 2.74
1843 1900 7.308229 CCTGTATAATCTATGCCTGCAGAAAAC 60.308 40.741 17.39 1.95 0.00 2.43
1844 1901 7.282585 TGTATAATCTATGCCTGCAGAAAACT 58.717 34.615 17.39 0.00 0.00 2.66
1855 1912 1.792993 GCAGAAAACTGCGCATGCTAG 60.793 52.381 20.90 15.83 43.34 3.42
2076 2136 5.788450 AGTTGATGAAGAGAGACGTTTCAT 58.212 37.500 11.24 11.24 42.50 2.57
2086 2146 2.932614 GAGACGTTTCATGCTGTGCTAT 59.067 45.455 0.39 0.00 0.00 2.97
2224 2285 2.421424 GCAGATTGAATCGTTTGCTCCT 59.579 45.455 9.74 0.00 0.00 3.69
2371 2438 1.978542 CGGTAGTGGAGTTCAAGACG 58.021 55.000 0.00 0.00 0.00 4.18
2428 2495 2.744768 GGAGAAGAAAGCTGCGCGG 61.745 63.158 13.18 13.18 0.00 6.46
2439 2506 1.451387 CTGCGCGGGGATTAGGTTT 60.451 57.895 8.83 0.00 0.00 3.27
2462 2529 8.343366 GTTTATTTCTTCCCGTTCCTGATAATC 58.657 37.037 0.00 0.00 0.00 1.75
2568 2750 4.515404 GTGGTTAGGCCGCTACAG 57.485 61.111 0.00 0.00 44.20 2.74
2569 2751 1.595357 GTGGTTAGGCCGCTACAGT 59.405 57.895 0.00 0.00 44.20 3.55
2603 2790 8.754080 ACTAACTTGTAGAATAGCAGAATGTCT 58.246 33.333 0.00 0.00 39.31 3.41
2702 2894 4.708726 ACTCCTGCAAGCAATTGTATTC 57.291 40.909 7.40 0.00 0.00 1.75
2710 2902 3.370840 AGCAATTGTATTCCTGCTCCA 57.629 42.857 7.40 0.00 41.18 3.86
2734 2928 7.928167 CCATACTTGAATAGATTCTGTAGTGCA 59.072 37.037 4.02 0.00 37.67 4.57
2737 2931 4.682787 TGAATAGATTCTGTAGTGCACGG 58.317 43.478 12.01 3.58 37.67 4.94
2743 2937 3.610040 TTCTGTAGTGCACGGAATCAT 57.390 42.857 12.01 0.00 45.67 2.45
2756 2950 4.678287 CACGGAATCATAATGAGCAATTGC 59.322 41.667 23.05 23.05 42.49 3.56
2757 2951 4.338964 ACGGAATCATAATGAGCAATTGCA 59.661 37.500 30.89 13.06 45.16 4.08
2758 2952 4.678287 CGGAATCATAATGAGCAATTGCAC 59.322 41.667 30.89 25.14 45.16 4.57
2759 2953 4.678287 GGAATCATAATGAGCAATTGCACG 59.322 41.667 30.89 12.47 45.16 5.34
2760 2954 4.906065 ATCATAATGAGCAATTGCACGT 57.094 36.364 30.89 23.26 45.16 4.49
2761 2955 6.375945 AATCATAATGAGCAATTGCACGTA 57.624 33.333 30.89 20.03 45.16 3.57
2769 3084 5.656480 TGAGCAATTGCACGTAGAGTAATA 58.344 37.500 30.89 3.31 45.16 0.98
2776 3091 7.900782 ATTGCACGTAGAGTAATAAACTTGT 57.099 32.000 0.00 0.00 39.07 3.16
2825 3140 4.803329 ATAGATGGGGATTCTGCACTTT 57.197 40.909 0.00 0.00 0.00 2.66
2846 3161 5.557576 TTAGCTGTGCATGAGAGGATTAT 57.442 39.130 0.00 0.00 0.00 1.28
2847 3162 4.434545 AGCTGTGCATGAGAGGATTATT 57.565 40.909 0.00 0.00 0.00 1.40
2848 3163 5.557576 AGCTGTGCATGAGAGGATTATTA 57.442 39.130 0.00 0.00 0.00 0.98
2849 3164 6.124316 AGCTGTGCATGAGAGGATTATTAT 57.876 37.500 0.00 0.00 0.00 1.28
2850 3165 6.171921 AGCTGTGCATGAGAGGATTATTATC 58.828 40.000 0.00 0.00 0.00 1.75
2922 3237 8.846211 TGCATATACCAGGAATTACTTTTAAGC 58.154 33.333 0.00 0.00 0.00 3.09
2928 3243 8.107399 ACCAGGAATTACTTTTAAGCAAGTAC 57.893 34.615 0.00 0.00 38.68 2.73
2975 3318 9.593134 AGATTTATATCGACCTAGAATTGATGC 57.407 33.333 0.00 0.00 35.85 3.91
2977 3320 8.534333 TTTATATCGACCTAGAATTGATGCAC 57.466 34.615 0.00 0.00 0.00 4.57
2984 3327 4.411540 ACCTAGAATTGATGCACTCTCCAT 59.588 41.667 0.00 0.00 0.00 3.41
2990 3333 7.542025 AGAATTGATGCACTCTCCATTTTTAC 58.458 34.615 0.00 0.00 0.00 2.01
3030 3373 4.935205 GCCCTTGGAAAACATTACCATTTC 59.065 41.667 0.00 0.00 33.56 2.17
3052 3395 2.711009 TCTGTCCCCTTTGAACATCTGT 59.289 45.455 0.00 0.00 0.00 3.41
3087 3430 3.773860 TCCATGTGTGTGTGTTTGTTC 57.226 42.857 0.00 0.00 0.00 3.18
3123 3469 5.793817 TGTGCTTCATTTAGAGACAGCTTA 58.206 37.500 0.00 0.00 0.00 3.09
3124 3470 5.871524 TGTGCTTCATTTAGAGACAGCTTAG 59.128 40.000 0.00 0.00 0.00 2.18
3141 3487 8.919777 ACAGCTTAGACTAACCTTAATTGTTT 57.080 30.769 0.00 0.00 0.00 2.83
3144 3490 9.350951 AGCTTAGACTAACCTTAATTGTTTGTT 57.649 29.630 6.57 0.00 33.04 2.83
3145 3491 9.394477 GCTTAGACTAACCTTAATTGTTTGTTG 57.606 33.333 6.57 2.08 33.04 3.33
3146 3492 9.893305 CTTAGACTAACCTTAATTGTTTGTTGG 57.107 33.333 6.57 0.00 33.04 3.77
3147 3493 7.891498 AGACTAACCTTAATTGTTTGTTGGT 57.109 32.000 6.57 0.00 33.04 3.67
3151 3497 9.806203 ACTAACCTTAATTGTTTGTTGGTAAAC 57.194 29.630 0.00 0.00 40.18 2.01
3152 3498 9.804758 CTAACCTTAATTGTTTGTTGGTAAACA 57.195 29.630 0.00 0.00 45.78 2.83
3169 3515 0.814010 ACAAACCACTGTGACGCCTC 60.814 55.000 9.86 0.00 0.00 4.70
3180 3526 0.597568 TGACGCCTCATTTTGCTTGG 59.402 50.000 0.00 0.00 0.00 3.61
3186 3532 4.461081 ACGCCTCATTTTGCTTGGTATTTA 59.539 37.500 0.00 0.00 0.00 1.40
3421 3768 1.952133 CGCTCCGACGTTGTTGGAA 60.952 57.895 7.31 0.00 44.54 3.53
3441 3788 6.795399 TGGAAATCAAACACTCAACTTCTTC 58.205 36.000 0.00 0.00 0.00 2.87
3450 3797 4.896482 ACACTCAACTTCTTCCTACTGACT 59.104 41.667 0.00 0.00 0.00 3.41
3456 3803 5.652994 ACTTCTTCCTACTGACTGATCAC 57.347 43.478 0.00 0.00 0.00 3.06
3467 3814 2.685017 TGATCACGCCAGAGCCCT 60.685 61.111 0.00 0.00 34.57 5.19
3501 3848 3.365767 GCTTCTGATGTCAAGGTTGCTTC 60.366 47.826 0.00 0.00 0.00 3.86
3562 3909 6.038936 GTCTTTTAACTTGGTTGGAGCACTTA 59.961 38.462 0.00 0.00 0.00 2.24
3573 3920 5.402398 GTTGGAGCACTTAAATTGTCCATC 58.598 41.667 0.00 0.00 34.12 3.51
3638 3986 1.639298 GCATGTGCGGGTTCAGAGTC 61.639 60.000 0.00 0.00 0.00 3.36
3787 4510 3.754323 GACAGTGAGCAGTAGTGACTAGT 59.246 47.826 0.42 0.00 33.32 2.57
3792 4515 4.936411 GTGAGCAGTAGTGACTAGTGAGTA 59.064 45.833 26.93 11.40 39.10 2.59
3860 4583 0.528466 TCAGCGCCATCGAGACATTC 60.528 55.000 2.29 0.00 38.10 2.67
3925 4992 4.934001 AGCATCACTCTCTTACACATGTTG 59.066 41.667 0.00 0.00 0.00 3.33
3975 5042 3.890147 ACATTATGAGACGGAGGGAGTAC 59.110 47.826 0.00 0.00 0.00 2.73
3977 5044 2.526888 ATGAGACGGAGGGAGTACAA 57.473 50.000 0.00 0.00 0.00 2.41
3981 5048 1.355043 AGACGGAGGGAGTACAAGTCT 59.645 52.381 0.00 0.00 33.27 3.24
4013 5080 8.932791 AGAAATTTCAGTACAAACTACATACGG 58.067 33.333 19.99 0.00 33.48 4.02
4014 5081 8.836268 AAATTTCAGTACAAACTACATACGGA 57.164 30.769 0.00 0.00 33.48 4.69
4015 5082 9.444600 AAATTTCAGTACAAACTACATACGGAT 57.555 29.630 0.00 0.00 33.48 4.18
4016 5083 7.821595 TTTCAGTACAAACTACATACGGATG 57.178 36.000 5.94 5.94 34.67 3.51
4018 5085 7.628769 TCAGTACAAACTACATACGGATGTA 57.371 36.000 19.32 19.32 45.77 2.29
4019 5086 7.475015 TCAGTACAAACTACATACGGATGTAC 58.525 38.462 16.71 7.88 45.77 2.90
4020 5087 7.636150 AGTACAAACTACATACGGATGTACT 57.364 36.000 16.71 10.12 44.77 2.73
4021 5088 7.642978 CAGTACAAACTACATACGGATGTACTC 59.357 40.741 16.71 2.97 45.11 2.59
4022 5089 5.899299 ACAAACTACATACGGATGTACTCC 58.101 41.667 16.71 0.00 44.77 3.85
4023 5090 5.163478 ACAAACTACATACGGATGTACTCCC 60.163 44.000 16.71 0.00 44.77 4.30
4024 5091 4.450305 ACTACATACGGATGTACTCCCT 57.550 45.455 16.71 0.00 44.77 4.20
4025 5092 4.396522 ACTACATACGGATGTACTCCCTC 58.603 47.826 16.71 0.00 44.77 4.30
4026 5093 2.595238 ACATACGGATGTACTCCCTCC 58.405 52.381 12.79 0.00 44.77 4.30
4028 5095 4.254721 CGGATGTACTCCCTCCGT 57.745 61.111 14.50 0.00 45.30 4.69
4029 5096 3.409201 CGGATGTACTCCCTCCGTA 57.591 57.895 14.50 0.00 45.30 4.02
4030 5097 1.683943 CGGATGTACTCCCTCCGTAA 58.316 55.000 14.50 0.00 45.30 3.18
4031 5098 2.026641 CGGATGTACTCCCTCCGTAAA 58.973 52.381 14.50 0.00 45.30 2.01
4032 5099 2.223665 CGGATGTACTCCCTCCGTAAAC 60.224 54.545 14.50 0.00 45.30 2.01
4033 5100 3.029570 GGATGTACTCCCTCCGTAAACT 58.970 50.000 0.00 0.00 38.19 2.66
4034 5101 4.210331 GGATGTACTCCCTCCGTAAACTA 58.790 47.826 0.00 0.00 38.19 2.24
4035 5102 4.646492 GGATGTACTCCCTCCGTAAACTAA 59.354 45.833 0.00 0.00 38.19 2.24
4036 5103 5.303845 GGATGTACTCCCTCCGTAAACTAAT 59.696 44.000 0.00 0.00 38.19 1.73
4037 5104 6.491403 GGATGTACTCCCTCCGTAAACTAATA 59.509 42.308 0.00 0.00 38.19 0.98
4038 5105 7.178097 GGATGTACTCCCTCCGTAAACTAATAT 59.822 40.741 0.00 0.00 38.19 1.28
4039 5106 9.236006 GATGTACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
4040 5107 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
4041 5108 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
4042 5109 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
4043 5110 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4044 5111 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4045 5112 7.008941 TCCCTCCGTAAACTAATATAAGAGCT 58.991 38.462 0.00 0.00 0.00 4.09
4046 5113 7.508296 TCCCTCCGTAAACTAATATAAGAGCTT 59.492 37.037 0.00 0.00 0.00 3.74
4047 5114 8.148999 CCCTCCGTAAACTAATATAAGAGCTTT 58.851 37.037 0.00 0.00 0.00 3.51
4048 5115 9.543783 CCTCCGTAAACTAATATAAGAGCTTTT 57.456 33.333 0.00 0.00 0.00 2.27
4098 5165 9.543783 AAAAGCTCTTATATTAGTTTACGGAGG 57.456 33.333 0.00 0.00 0.00 4.30
4099 5166 7.229581 AGCTCTTATATTAGTTTACGGAGGG 57.770 40.000 0.00 0.00 0.00 4.30
4100 5167 7.008941 AGCTCTTATATTAGTTTACGGAGGGA 58.991 38.462 0.00 0.00 0.00 4.20
4101 5168 7.177041 AGCTCTTATATTAGTTTACGGAGGGAG 59.823 40.741 0.00 0.00 0.00 4.30
4102 5169 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4103 5170 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4114 5181 8.672815 GTTTACGGAGGGAGTATATAGTCATAC 58.327 40.741 17.44 6.95 0.00 2.39
4119 5186 9.111613 CGGAGGGAGTATATAGTCATACTTTAG 57.888 40.741 17.44 6.20 40.92 1.85
4134 5201 8.688151 GTCATACTTTAGAGTGTAGATCCACTT 58.312 37.037 6.14 0.98 45.46 3.16
4180 5247 8.074613 TCTTATTGAATTCTCTAGGAACGGAA 57.925 34.615 7.05 0.00 36.70 4.30
4230 5298 2.687935 AGTTGCACACAGGTTAACCTTG 59.312 45.455 24.99 24.27 46.09 3.61
4268 5336 7.801716 TTCCTAGCATGATACAATTGTTACC 57.198 36.000 17.78 6.97 0.00 2.85
4318 5386 4.390909 CGAGCCGAACTTTTTACTGGTTAT 59.609 41.667 0.00 0.00 0.00 1.89
4320 5388 6.091169 CGAGCCGAACTTTTTACTGGTTATTA 59.909 38.462 0.00 0.00 0.00 0.98
4322 5390 8.344446 AGCCGAACTTTTTACTGGTTATTAAT 57.656 30.769 0.00 0.00 0.00 1.40
4323 5391 8.456471 AGCCGAACTTTTTACTGGTTATTAATC 58.544 33.333 0.00 0.00 0.00 1.75
4324 5392 8.238631 GCCGAACTTTTTACTGGTTATTAATCA 58.761 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.236935 ACATTGCCGAATTCACAAACATC 58.763 39.130 13.19 0.00 0.00 3.06
108 109 7.001099 ACATTCTCTGGATTTTCAAATGCTT 57.999 32.000 5.51 0.00 37.58 3.91
110 111 7.662604 AAACATTCTCTGGATTTTCAAATGC 57.337 32.000 0.00 0.00 37.27 3.56
209 210 9.987272 GGGGAAATATTTAGGAAATTCATGAAG 57.013 33.333 14.54 0.00 32.38 3.02
228 229 9.008965 GCAAACATTTACTAAAATTGGGGAAAT 57.991 29.630 0.00 0.00 32.87 2.17
229 230 7.445707 GGCAAACATTTACTAAAATTGGGGAAA 59.554 33.333 0.00 0.00 32.87 3.13
232 233 5.350091 CGGCAAACATTTACTAAAATTGGGG 59.650 40.000 0.00 0.00 32.87 4.96
243 244 6.517914 TTTTGTGAATCGGCAAACATTTAC 57.482 33.333 3.06 0.00 34.77 2.01
335 336 6.023435 CGCCGACCATTATTATGAAATCATG 58.977 40.000 6.17 0.00 37.15 3.07
444 445 8.822855 CGCCCTTTACTTTATTTTTCAAGTTTT 58.177 29.630 0.00 0.00 34.92 2.43
445 446 8.198778 TCGCCCTTTACTTTATTTTTCAAGTTT 58.801 29.630 0.00 0.00 34.92 2.66
447 448 7.279750 TCGCCCTTTACTTTATTTTTCAAGT 57.720 32.000 0.00 0.00 37.08 3.16
448 449 8.582433 TTTCGCCCTTTACTTTATTTTTCAAG 57.418 30.769 0.00 0.00 0.00 3.02
449 450 8.943909 TTTTCGCCCTTTACTTTATTTTTCAA 57.056 26.923 0.00 0.00 0.00 2.69
450 451 8.943909 TTTTTCGCCCTTTACTTTATTTTTCA 57.056 26.923 0.00 0.00 0.00 2.69
525 536 2.340328 ATTTTGGGCCGGCTCGTTC 61.340 57.895 28.56 9.02 0.00 3.95
528 539 1.747367 TACATTTTGGGCCGGCTCG 60.747 57.895 28.56 12.01 0.00 5.03
530 541 0.324275 ATGTACATTTTGGGCCGGCT 60.324 50.000 28.56 6.02 0.00 5.52
568 579 1.009900 CCTACTTAGCGACCGAGCG 60.010 63.158 0.00 0.00 43.00 5.03
582 593 6.750963 GCAATTAGACGCATATAGGTACCTAC 59.249 42.308 24.07 10.26 0.00 3.18
587 598 4.460034 TCCGCAATTAGACGCATATAGGTA 59.540 41.667 0.00 0.00 0.00 3.08
604 615 3.321111 AGACTTCAGTAAAGAGTCCGCAA 59.679 43.478 0.00 0.00 38.44 4.85
605 616 2.891580 AGACTTCAGTAAAGAGTCCGCA 59.108 45.455 0.00 0.00 38.44 5.69
606 617 3.579335 AGACTTCAGTAAAGAGTCCGC 57.421 47.619 0.00 0.00 38.44 5.54
607 618 4.686554 CCAAAGACTTCAGTAAAGAGTCCG 59.313 45.833 0.00 0.00 38.44 4.79
608 619 5.855045 TCCAAAGACTTCAGTAAAGAGTCC 58.145 41.667 0.00 0.00 38.44 3.85
609 620 6.517605 ACTCCAAAGACTTCAGTAAAGAGTC 58.482 40.000 0.00 0.00 38.44 3.36
610 621 6.487299 ACTCCAAAGACTTCAGTAAAGAGT 57.513 37.500 0.00 0.00 38.44 3.24
611 622 7.662897 AGTACTCCAAAGACTTCAGTAAAGAG 58.337 38.462 0.00 0.00 38.44 2.85
612 623 7.598759 AGTACTCCAAAGACTTCAGTAAAGA 57.401 36.000 0.00 0.00 38.44 2.52
613 624 8.664211 AAAGTACTCCAAAGACTTCAGTAAAG 57.336 34.615 0.00 0.00 41.08 1.85
614 625 9.457436 AAAAAGTACTCCAAAGACTTCAGTAAA 57.543 29.630 0.00 0.00 32.27 2.01
615 626 9.106070 GAAAAAGTACTCCAAAGACTTCAGTAA 57.894 33.333 0.00 0.00 32.27 2.24
616 627 7.437267 CGAAAAAGTACTCCAAAGACTTCAGTA 59.563 37.037 0.00 0.00 32.27 2.74
617 628 6.258068 CGAAAAAGTACTCCAAAGACTTCAGT 59.742 38.462 0.00 0.00 32.27 3.41
618 629 6.479001 TCGAAAAAGTACTCCAAAGACTTCAG 59.521 38.462 0.00 0.00 32.27 3.02
619 630 6.342906 TCGAAAAAGTACTCCAAAGACTTCA 58.657 36.000 0.00 0.00 32.27 3.02
635 646 5.734498 CGGTATCAATCTTTGCTCGAAAAAG 59.266 40.000 12.08 12.08 36.22 2.27
638 649 3.063452 GCGGTATCAATCTTTGCTCGAAA 59.937 43.478 0.00 0.00 0.00 3.46
693 704 9.819267 ATACAAAGTAACTCTTATGGCTAAGAC 57.181 33.333 3.33 0.00 38.72 3.01
722 736 6.652481 ACACTGATGTGAACCTAAGATCAAAG 59.348 38.462 3.03 0.00 46.55 2.77
729 743 5.407407 AGGTACACTGATGTGAACCTAAG 57.593 43.478 3.03 0.00 43.30 2.18
824 840 3.936372 TCTACCTCCGTCTTTGACTTG 57.064 47.619 0.00 0.00 0.00 3.16
827 843 3.255149 TCAGTTCTACCTCCGTCTTTGAC 59.745 47.826 0.00 0.00 0.00 3.18
832 848 3.498334 AGTTTCAGTTCTACCTCCGTCT 58.502 45.455 0.00 0.00 0.00 4.18
932 953 2.204090 GAGTGGGGAACTGGGGGA 60.204 66.667 0.00 0.00 40.07 4.81
1160 1186 7.502561 ACGCTATCAGAGTGGCATATATGTATA 59.497 37.037 14.14 0.00 40.24 1.47
1190 1221 1.464608 CGGCGGCATGAATAAATCGAT 59.535 47.619 10.53 0.00 0.00 3.59
1253 1284 3.089874 CGATGAAGGGGCAGGGGA 61.090 66.667 0.00 0.00 0.00 4.81
1254 1285 4.195334 CCGATGAAGGGGCAGGGG 62.195 72.222 0.00 0.00 0.00 4.79
1294 1325 3.022401 GCATCGAGGTGCGCGAAAA 62.022 57.895 12.10 0.00 39.28 2.29
1307 1338 2.124193 TCCCCATTGCTGGCATCG 60.124 61.111 0.00 0.00 41.64 3.84
1316 1347 4.738998 TGCCACGCCTCCCCATTG 62.739 66.667 0.00 0.00 0.00 2.82
1317 1348 4.431131 CTGCCACGCCTCCCCATT 62.431 66.667 0.00 0.00 0.00 3.16
1362 1393 1.641577 GTTCGTACCTGGTGATCAGC 58.358 55.000 18.01 18.01 42.05 4.26
1405 1436 8.599624 AATTCATTTGGTTATCTTGAGTCCAT 57.400 30.769 0.00 0.00 0.00 3.41
1417 1451 6.493115 ACACCATGACTGAATTCATTTGGTTA 59.507 34.615 20.42 9.59 32.51 2.85
1427 1461 7.450074 TCTACAGTTTACACCATGACTGAATT 58.550 34.615 14.82 0.00 41.46 2.17
1432 1466 6.420913 AACTCTACAGTTTACACCATGACT 57.579 37.500 0.00 0.00 40.16 3.41
1456 1497 0.111061 TGCTTGGGCATCAGTTCACT 59.889 50.000 0.00 0.00 44.28 3.41
1473 1514 1.534595 CGCAATGCTCTATTTGGGTGC 60.535 52.381 2.94 0.00 0.00 5.01
1500 1541 3.133721 AGCCATGTTCATAGACTCTCACC 59.866 47.826 0.00 0.00 0.00 4.02
1503 1544 4.118410 CACAGCCATGTTCATAGACTCTC 58.882 47.826 0.00 0.00 37.65 3.20
1508 1549 2.840038 AGTCCACAGCCATGTTCATAGA 59.160 45.455 0.00 0.00 37.65 1.98
1511 1552 1.074405 ACAGTCCACAGCCATGTTCAT 59.926 47.619 0.00 0.00 37.65 2.57
1534 1575 5.188751 CCTGGAATTGGAGTCCCTATCTATC 59.811 48.000 6.74 0.00 33.89 2.08
1535 1576 5.097234 CCTGGAATTGGAGTCCCTATCTAT 58.903 45.833 6.74 0.00 33.89 1.98
1537 1578 3.321950 CCTGGAATTGGAGTCCCTATCT 58.678 50.000 6.74 0.00 33.89 1.98
1538 1579 2.224646 GCCTGGAATTGGAGTCCCTATC 60.225 54.545 6.74 1.63 33.89 2.08
1540 1581 1.213296 GCCTGGAATTGGAGTCCCTA 58.787 55.000 6.74 0.00 33.89 3.53
1542 1583 0.259938 ATGCCTGGAATTGGAGTCCC 59.740 55.000 6.74 0.00 33.89 4.46
1543 1584 1.753073 CAATGCCTGGAATTGGAGTCC 59.247 52.381 18.28 0.73 32.46 3.85
1581 1622 3.065371 CCTCGTTTATTTTAGCTGCCCAG 59.935 47.826 0.00 0.00 0.00 4.45
1582 1623 3.013921 CCTCGTTTATTTTAGCTGCCCA 58.986 45.455 0.00 0.00 0.00 5.36
1583 1624 3.014623 ACCTCGTTTATTTTAGCTGCCC 58.985 45.455 0.00 0.00 0.00 5.36
1587 1628 5.646793 GGGAGAAACCTCGTTTATTTTAGCT 59.353 40.000 0.00 0.00 35.77 3.32
1588 1629 5.446875 CGGGAGAAACCTCGTTTATTTTAGC 60.447 44.000 0.00 0.00 35.77 3.09
1594 1635 1.406477 GGCGGGAGAAACCTCGTTTAT 60.406 52.381 0.00 0.00 35.77 1.40
1597 1638 2.346365 GGCGGGAGAAACCTCGTT 59.654 61.111 0.00 0.00 38.98 3.85
1600 1641 3.372554 CTCGGGCGGGAGAAACCTC 62.373 68.421 0.00 0.00 36.08 3.85
1602 1643 4.468689 CCTCGGGCGGGAGAAACC 62.469 72.222 5.84 0.00 36.08 3.27
1617 1658 3.665675 GAACATGGCGCGTCTCCCT 62.666 63.158 13.81 0.00 0.00 4.20
1620 1661 1.421485 CAAGAACATGGCGCGTCTC 59.579 57.895 13.81 0.00 0.00 3.36
1640 1692 2.280797 TGTTCGCTGTGCTCCCAC 60.281 61.111 0.00 0.00 42.40 4.61
1680 1732 7.173218 TCACTCTTGAAATGCTACCACTAAAAG 59.827 37.037 0.00 0.00 0.00 2.27
1773 1830 1.713597 CAGAGCTGCATCACAACGTA 58.286 50.000 1.02 0.00 0.00 3.57
1822 1879 6.630444 CAGTTTTCTGCAGGCATAGATTAT 57.370 37.500 15.13 0.00 41.24 1.28
1843 1900 3.950254 GCAGGCTAGCATGCGCAG 61.950 66.667 35.14 16.61 43.66 5.18
1855 1912 0.386838 AACAGCAGTTTTCAGCAGGC 59.613 50.000 0.00 0.00 33.11 4.85
1919 1976 4.955811 ACTAGTTGGTTGACATGTCTCA 57.044 40.909 25.55 17.54 0.00 3.27
2224 2285 0.463654 CAGGCGCATAAGTAAGGCCA 60.464 55.000 10.83 0.00 46.12 5.36
2353 2420 1.672145 GCCGTCTTGAACTCCACTACC 60.672 57.143 0.00 0.00 0.00 3.18
2357 2424 0.318762 AGAGCCGTCTTGAACTCCAC 59.681 55.000 0.00 0.00 0.00 4.02
2428 2495 5.443283 ACGGGAAGAAATAAACCTAATCCC 58.557 41.667 0.00 0.00 41.51 3.85
2439 2506 7.131907 TGATTATCAGGAACGGGAAGAAATA 57.868 36.000 0.00 0.00 0.00 1.40
2462 2529 7.858382 ACAAAAACAATGTGATGCATGATTTTG 59.142 29.630 20.47 20.47 39.87 2.44
2568 2750 7.148623 GCTATTCTACAAGTTAGTCACCAACAC 60.149 40.741 0.00 0.00 0.00 3.32
2569 2751 6.872020 GCTATTCTACAAGTTAGTCACCAACA 59.128 38.462 0.00 0.00 0.00 3.33
2631 2818 5.010922 TGCAACCTAGCTGAAACAAAATCAT 59.989 36.000 0.00 0.00 34.99 2.45
2645 2832 1.555967 TGGGGAAAATGCAACCTAGC 58.444 50.000 0.00 0.00 0.00 3.42
2702 2894 6.649973 CAGAATCTATTCAAGTATGGAGCAGG 59.350 42.308 5.55 0.00 39.23 4.85
2710 2902 7.649705 CGTGCACTACAGAATCTATTCAAGTAT 59.350 37.037 16.19 0.00 39.23 2.12
2734 2928 4.338964 TGCAATTGCTCATTATGATTCCGT 59.661 37.500 29.37 0.00 42.66 4.69
2737 2931 5.276270 ACGTGCAATTGCTCATTATGATTC 58.724 37.500 29.37 0.00 42.66 2.52
2743 2937 4.503910 ACTCTACGTGCAATTGCTCATTA 58.496 39.130 29.37 17.92 42.66 1.90
2776 3091 9.403583 GGGACAAATAGGATGATGTTTTACTTA 57.596 33.333 0.00 0.00 0.00 2.24
2825 3140 5.557576 AATAATCCTCTCATGCACAGCTA 57.442 39.130 0.00 0.00 0.00 3.32
2846 3161 8.681486 AGCAAACATACATGCAGATAAGATAA 57.319 30.769 0.00 0.00 44.95 1.75
2847 3162 8.681486 AAGCAAACATACATGCAGATAAGATA 57.319 30.769 0.00 0.00 44.95 1.98
2848 3163 7.578310 AAGCAAACATACATGCAGATAAGAT 57.422 32.000 0.00 0.00 44.95 2.40
2849 3164 7.121020 TGAAAGCAAACATACATGCAGATAAGA 59.879 33.333 0.00 0.00 44.95 2.10
2850 3165 7.252708 TGAAAGCAAACATACATGCAGATAAG 58.747 34.615 0.00 0.00 44.95 1.73
2922 3237 9.803315 TGCTACTATACTTCAAATCAGTACTTG 57.197 33.333 0.00 0.00 29.39 3.16
2960 3302 4.141846 TGGAGAGTGCATCAATTCTAGGTC 60.142 45.833 0.00 0.00 0.00 3.85
2984 3327 7.757624 GGGCATCGAATTTCTGTTATGTAAAAA 59.242 33.333 0.00 0.00 0.00 1.94
2990 3333 5.276270 CAAGGGCATCGAATTTCTGTTATG 58.724 41.667 0.00 0.00 0.00 1.90
3003 3346 3.428862 GGTAATGTTTTCCAAGGGCATCG 60.429 47.826 0.00 0.00 0.00 3.84
3005 3348 3.515562 TGGTAATGTTTTCCAAGGGCAT 58.484 40.909 0.00 0.00 0.00 4.40
3008 3351 6.211384 AGAGAAATGGTAATGTTTTCCAAGGG 59.789 38.462 0.00 0.00 34.80 3.95
3030 3373 3.244700 ACAGATGTTCAAAGGGGACAGAG 60.245 47.826 0.00 0.00 0.00 3.35
3052 3395 6.013206 ACACACATGGAAAAGGTAGGTACATA 60.013 38.462 0.00 0.00 0.00 2.29
3123 3469 7.891498 ACCAACAAACAATTAAGGTTAGTCT 57.109 32.000 0.00 0.00 0.00 3.24
3144 3490 2.678836 CGTCACAGTGGTTTGTTTACCA 59.321 45.455 0.00 0.00 45.73 3.25
3145 3491 2.540157 GCGTCACAGTGGTTTGTTTACC 60.540 50.000 0.00 0.00 38.73 2.85
3146 3492 2.540157 GGCGTCACAGTGGTTTGTTTAC 60.540 50.000 0.00 0.00 0.00 2.01
3147 3493 1.671845 GGCGTCACAGTGGTTTGTTTA 59.328 47.619 0.00 0.00 0.00 2.01
3151 3497 0.813610 TGAGGCGTCACAGTGGTTTG 60.814 55.000 4.68 0.00 0.00 2.93
3152 3498 0.108585 ATGAGGCGTCACAGTGGTTT 59.891 50.000 11.97 0.00 34.75 3.27
3154 3500 0.108585 AAATGAGGCGTCACAGTGGT 59.891 50.000 11.97 0.00 34.75 4.16
3156 3502 1.664016 GCAAAATGAGGCGTCACAGTG 60.664 52.381 11.97 10.45 34.75 3.66
3157 3503 0.593128 GCAAAATGAGGCGTCACAGT 59.407 50.000 11.97 0.00 34.75 3.55
3158 3504 0.877071 AGCAAAATGAGGCGTCACAG 59.123 50.000 11.97 3.28 34.75 3.66
3164 3510 3.508744 AATACCAAGCAAAATGAGGCG 57.491 42.857 0.00 0.00 34.54 5.52
3180 3526 6.202954 AGTGATGCGCCTAAGACAATAAATAC 59.797 38.462 4.18 0.00 0.00 1.89
3186 3532 2.283298 CAGTGATGCGCCTAAGACAAT 58.717 47.619 4.18 0.00 0.00 2.71
3408 3754 3.480668 GTGTTTGATTTCCAACAACGTCG 59.519 43.478 0.00 0.00 33.85 5.12
3421 3768 7.227512 CAGTAGGAAGAAGTTGAGTGTTTGATT 59.772 37.037 0.00 0.00 0.00 2.57
3441 3788 0.817654 TGGCGTGATCAGTCAGTAGG 59.182 55.000 0.00 0.00 34.36 3.18
3450 3797 2.244117 GAAGGGCTCTGGCGTGATCA 62.244 60.000 0.00 0.00 39.81 2.92
3456 3803 4.394712 AACGGAAGGGCTCTGGCG 62.395 66.667 0.00 0.00 39.81 5.69
3467 3814 1.600636 CAGAAGCAGGGCAACGGAA 60.601 57.895 0.00 0.00 37.60 4.30
3501 3848 2.032030 CGTTTTCCGCCATATAGCAAGG 60.032 50.000 0.00 0.00 0.00 3.61
3510 3857 2.869503 ATCGGCTCGTTTTCCGCCAT 62.870 55.000 0.00 0.00 44.91 4.40
3562 3909 2.922283 AGGGACTCCTGATGGACAATTT 59.078 45.455 0.00 0.00 42.98 1.82
3573 3920 5.867151 ATACACAAGTAGAGAGGGACTCCTG 60.867 48.000 0.00 0.00 45.17 3.86
3787 4510 5.466819 CAACTGTTAGTCGACCATTACTCA 58.533 41.667 13.01 1.87 0.00 3.41
3792 4515 3.764237 ACCAACTGTTAGTCGACCATT 57.236 42.857 13.01 0.00 0.00 3.16
3860 4583 8.256611 AGTTTATACTGTACTTGCACTTGATG 57.743 34.615 0.00 0.00 31.99 3.07
3961 5028 1.355043 AGACTTGTACTCCCTCCGTCT 59.645 52.381 0.00 0.00 0.00 4.18
3991 5058 8.038944 ACATCCGTATGTAGTTTGTACTGAAAT 58.961 33.333 0.00 0.00 44.66 2.17
3994 5061 6.519679 ACATCCGTATGTAGTTTGTACTGA 57.480 37.500 0.00 0.00 44.66 3.41
4013 5080 5.841957 TTAGTTTACGGAGGGAGTACATC 57.158 43.478 0.00 0.00 0.00 3.06
4014 5081 9.592196 TTATATTAGTTTACGGAGGGAGTACAT 57.408 33.333 0.00 0.00 0.00 2.29
4015 5082 8.995027 TTATATTAGTTTACGGAGGGAGTACA 57.005 34.615 0.00 0.00 0.00 2.90
4016 5083 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
4017 5084 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4018 5085 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4019 5086 7.177041 AGCTCTTATATTAGTTTACGGAGGGAG 59.823 40.741 0.00 0.00 0.00 4.30
4020 5087 7.008941 AGCTCTTATATTAGTTTACGGAGGGA 58.991 38.462 0.00 0.00 0.00 4.20
4021 5088 7.229581 AGCTCTTATATTAGTTTACGGAGGG 57.770 40.000 0.00 0.00 0.00 4.30
4022 5089 9.543783 AAAAGCTCTTATATTAGTTTACGGAGG 57.456 33.333 0.00 0.00 0.00 4.30
4072 5139 9.543783 CCTCCGTAAACTAATATAAGAGCTTTT 57.456 33.333 0.00 0.00 0.00 2.27
4073 5140 8.148999 CCCTCCGTAAACTAATATAAGAGCTTT 58.851 37.037 0.00 0.00 0.00 3.51
4074 5141 7.508296 TCCCTCCGTAAACTAATATAAGAGCTT 59.492 37.037 0.00 0.00 0.00 3.74
4075 5142 7.008941 TCCCTCCGTAAACTAATATAAGAGCT 58.991 38.462 0.00 0.00 0.00 4.09
4076 5143 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4077 5144 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4084 5151 9.460019 GACTATATACTCCCTCCGTAAACTAAT 57.540 37.037 0.00 0.00 0.00 1.73
4085 5152 8.439971 TGACTATATACTCCCTCCGTAAACTAA 58.560 37.037 0.00 0.00 0.00 2.24
4086 5153 7.977818 TGACTATATACTCCCTCCGTAAACTA 58.022 38.462 0.00 0.00 0.00 2.24
4087 5154 6.845908 TGACTATATACTCCCTCCGTAAACT 58.154 40.000 0.00 0.00 0.00 2.66
4088 5155 7.700022 ATGACTATATACTCCCTCCGTAAAC 57.300 40.000 0.00 0.00 0.00 2.01
4089 5156 8.609483 AGTATGACTATATACTCCCTCCGTAAA 58.391 37.037 0.00 0.00 39.10 2.01
4090 5157 8.155620 AGTATGACTATATACTCCCTCCGTAA 57.844 38.462 0.00 0.00 39.10 3.18
4091 5158 7.746243 AGTATGACTATATACTCCCTCCGTA 57.254 40.000 0.00 0.00 39.10 4.02
4092 5159 6.639590 AGTATGACTATATACTCCCTCCGT 57.360 41.667 0.00 0.00 39.10 4.69
4093 5160 7.941431 AAAGTATGACTATATACTCCCTCCG 57.059 40.000 0.00 0.00 41.70 4.63
4106 5173 9.339850 GTGGATCTACACTCTAAAGTATGACTA 57.660 37.037 4.04 0.00 38.32 2.59
4107 5174 8.228035 GTGGATCTACACTCTAAAGTATGACT 57.772 38.462 4.04 0.00 38.32 3.41
4129 5196 6.671614 TTACATACGGAGCAAAATAAGTGG 57.328 37.500 0.00 0.00 0.00 4.00
4130 5197 8.142994 AGATTACATACGGAGCAAAATAAGTG 57.857 34.615 0.00 0.00 0.00 3.16
4140 5207 8.764524 ATTCAATAAGAGATTACATACGGAGC 57.235 34.615 0.00 0.00 0.00 4.70
4180 5247 7.309770 AGGACTGAAGAATTGAACTACTCTT 57.690 36.000 0.00 0.00 0.00 2.85
4250 5318 4.527564 GCTCGGTAACAATTGTATCATGC 58.472 43.478 12.39 8.79 0.00 4.06
4256 5324 3.502979 GGTTTGGCTCGGTAACAATTGTA 59.497 43.478 12.39 0.00 0.00 2.41
4268 5336 0.102120 TGTTTTGCTGGTTTGGCTCG 59.898 50.000 0.00 0.00 0.00 5.03
4320 5388 7.965107 GCTCGAACTCTGAAAAATACATTGATT 59.035 33.333 0.00 0.00 0.00 2.57
4322 5390 6.650807 AGCTCGAACTCTGAAAAATACATTGA 59.349 34.615 0.00 0.00 0.00 2.57
4323 5391 6.740002 CAGCTCGAACTCTGAAAAATACATTG 59.260 38.462 3.66 0.00 32.26 2.82
4324 5392 6.128172 CCAGCTCGAACTCTGAAAAATACATT 60.128 38.462 9.70 0.00 32.26 2.71
4325 5393 5.352569 CCAGCTCGAACTCTGAAAAATACAT 59.647 40.000 9.70 0.00 32.26 2.29
4326 5394 4.690748 CCAGCTCGAACTCTGAAAAATACA 59.309 41.667 9.70 0.00 32.26 2.29
4327 5395 4.691216 ACCAGCTCGAACTCTGAAAAATAC 59.309 41.667 9.70 0.00 32.26 1.89
4329 5397 3.744660 ACCAGCTCGAACTCTGAAAAAT 58.255 40.909 9.70 0.00 32.26 1.82


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

AutoCloner maintained by Alex Coulton.