Multiple sequence alignment - TraesCS1A01G387700

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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 TraesCS1A01G387700 chr1A 100.000 8382 0 0 1 8382 556306932 556298551 0.000000e+00 15479
1 TraesCS1A01G387700 chr1A 80.936 598 94 15 2 584 444242762 444242170 9.920000e-124 455
2 TraesCS1A01G387700 chr1A 78.544 261 33 14 5056 5300 556301746 556301493 5.240000e-32 150
3 TraesCS1A01G387700 chr1A 78.544 261 33 14 5187 5440 556301877 556301633 5.240000e-32 150
4 TraesCS1A01G387700 chr1D 93.082 7560 261 86 897 8382 464148045 464140674 0.000000e+00 10822
5 TraesCS1A01G387700 chr1D 80.412 485 70 16 2 467 344617172 344616694 6.230000e-91 346
6 TraesCS1A01G387700 chr1D 78.947 247 30 12 5069 5300 464143807 464143568 1.890000e-31 148
7 TraesCS1A01G387700 chr1B 93.798 2467 95 16 4342 6787 640159921 640157492 0.000000e+00 3655
8 TraesCS1A01G387700 chr1B 93.228 1462 66 8 2714 4173 640162005 640160575 0.000000e+00 2121
9 TraesCS1A01G387700 chr1B 93.030 1076 61 6 1672 2738 640163083 640162013 0.000000e+00 1559
10 TraesCS1A01G387700 chr1B 96.622 829 18 3 7557 8382 640156812 640155991 0.000000e+00 1367
11 TraesCS1A01G387700 chr1B 94.184 619 29 4 6810 7421 640157500 640156882 0.000000e+00 937
12 TraesCS1A01G387700 chr1B 86.280 656 76 9 5559 6205 679488532 679487882 0.000000e+00 701
13 TraesCS1A01G387700 chr1B 82.528 538 69 13 2 521 465980872 465981402 4.610000e-122 449
14 TraesCS1A01G387700 chr1B 81.748 515 48 25 1113 1599 640163784 640163288 1.020000e-103 388
15 TraesCS1A01G387700 chr1B 81.755 433 32 14 678 1075 640164210 640163790 1.360000e-82 318
16 TraesCS1A01G387700 chr1B 89.730 185 16 2 4162 4345 640160533 640160351 5.060000e-57 233
17 TraesCS1A01G387700 chr1B 79.608 255 29 13 5193 5440 640159201 640158963 2.420000e-35 161
18 TraesCS1A01G387700 chr5B 87.711 651 73 5 5559 6204 9581111 9580463 0.000000e+00 752
19 TraesCS1A01G387700 chr5B 85.100 651 89 6 5559 6204 326961072 326960425 0.000000e+00 658
20 TraesCS1A01G387700 chr7A 87.250 651 76 5 5559 6204 85734974 85734326 0.000000e+00 736
21 TraesCS1A01G387700 chr7A 85.351 669 73 11 5559 6204 176244295 176243629 0.000000e+00 669
22 TraesCS1A01G387700 chr7A 81.148 610 85 18 1 586 57694141 57693538 5.930000e-126 462
23 TraesCS1A01G387700 chr7A 87.791 172 17 4 6853 7023 85735161 85734993 1.850000e-46 198
24 TraesCS1A01G387700 chr3D 79.011 910 126 38 1 850 588129342 588128438 5.680000e-156 562
25 TraesCS1A01G387700 chr4A 78.475 892 131 36 1 841 628934552 628935433 2.070000e-145 527
26 TraesCS1A01G387700 chr6A 76.339 896 149 43 1 846 590210609 590209727 1.010000e-113 422
27 TraesCS1A01G387700 chr2A 77.606 710 110 32 1 676 167363769 167363075 1.320000e-102 385
28 TraesCS1A01G387700 chr4B 83.944 355 49 4 1 348 291802811 291803164 4.850000e-87 333


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 TraesCS1A01G387700 chr1A 556298551 556306932 8381 True 15479.000000 15479 100.000000 1 8382 1 chr1A.!!$R2 8381
1 TraesCS1A01G387700 chr1A 444242170 444242762 592 True 455.000000 455 80.936000 2 584 1 chr1A.!!$R1 582
2 TraesCS1A01G387700 chr1D 464140674 464148045 7371 True 10822.000000 10822 93.082000 897 8382 1 chr1D.!!$R2 7485
3 TraesCS1A01G387700 chr1B 640155991 640164210 8219 True 1193.222222 3655 89.300333 678 8382 9 chr1B.!!$R2 7704
4 TraesCS1A01G387700 chr1B 679487882 679488532 650 True 701.000000 701 86.280000 5559 6205 1 chr1B.!!$R1 646
5 TraesCS1A01G387700 chr1B 465980872 465981402 530 False 449.000000 449 82.528000 2 521 1 chr1B.!!$F1 519
6 TraesCS1A01G387700 chr5B 9580463 9581111 648 True 752.000000 752 87.711000 5559 6204 1 chr5B.!!$R1 645
7 TraesCS1A01G387700 chr5B 326960425 326961072 647 True 658.000000 658 85.100000 5559 6204 1 chr5B.!!$R2 645
8 TraesCS1A01G387700 chr7A 176243629 176244295 666 True 669.000000 669 85.351000 5559 6204 1 chr7A.!!$R2 645
9 TraesCS1A01G387700 chr7A 85734326 85735161 835 True 467.000000 736 87.520500 5559 7023 2 chr7A.!!$R3 1464
10 TraesCS1A01G387700 chr7A 57693538 57694141 603 True 462.000000 462 81.148000 1 586 1 chr7A.!!$R1 585
11 TraesCS1A01G387700 chr3D 588128438 588129342 904 True 562.000000 562 79.011000 1 850 1 chr3D.!!$R1 849
12 TraesCS1A01G387700 chr4A 628934552 628935433 881 False 527.000000 527 78.475000 1 841 1 chr4A.!!$F1 840
13 TraesCS1A01G387700 chr6A 590209727 590210609 882 True 422.000000 422 76.339000 1 846 1 chr6A.!!$R1 845
14 TraesCS1A01G387700 chr2A 167363075 167363769 694 True 385.000000 385 77.606000 1 676 1 chr2A.!!$R1 675

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
614 669 0.253044 CGGCTCTTGATGGGAGGAAA 59.747 55.000 0.00 0.0 0.00 3.13 F
1554 1705 0.250553 TTCCGTGGTTCGCTGGAATT 60.251 50.000 0.00 0.0 35.64 2.17 F
2420 2715 0.033781 GACAATTGGCCTGCAAAGCA 59.966 50.000 10.83 0.0 36.92 3.91 F
2763 3090 1.597027 GCCGTGTACTGTGTGCCTT 60.597 57.895 0.00 0.0 0.00 4.35 F
4263 4646 1.281867 TCCACCATCGATTGCCTCTTT 59.718 47.619 0.00 0.0 0.00 2.52 F
4357 5173 3.144506 CACTTTGAGTCCACAATCAGCT 58.855 45.455 0.00 0.0 0.00 4.24 F
5882 6717 3.149196 GTTGCTCTCTGATCCACCAAAA 58.851 45.455 0.00 0.0 0.00 2.44 F
6745 7611 0.028505 GCTGCTGGTGATGTAATGCG 59.971 55.000 0.00 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1710 0.032815 TAAGCACACACGCAGCTACA 59.967 50.000 0.00 0.0 37.70 2.74 R
2920 3247 1.619654 TGGATTTGCAGGAGTTGGTG 58.380 50.000 0.00 0.0 0.00 4.17 R
3996 4325 2.503895 AACCTGAGAAGGCAATCCAG 57.496 50.000 0.00 0.0 33.74 3.86 R
4758 5575 4.142795 GGCTGAAAAACGCAAAAGGAAAAA 60.143 37.500 0.00 0.0 0.00 1.94 R
5172 5990 1.300931 GCAGAGAGGACAACGCACA 60.301 57.895 0.00 0.0 0.00 4.57 R
6009 6865 1.322442 GGCCTGAAAGTTTCACAGCT 58.678 50.000 24.56 0.0 35.34 4.24 R
6862 7728 0.179009 AGCAAAGAACAGCTCCAGCA 60.179 50.000 0.48 0.0 45.16 4.41 R
7547 8420 0.458716 GGACCAGTTAGAGCTGCGAC 60.459 60.000 0.00 0.0 35.28 5.19 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
86 87 1.465794 GACTCGAAGTAGTCCTGCCT 58.534 55.000 0.00 0.00 40.06 4.75
110 112 2.780595 GCAATGGCCGCTCTCTTTA 58.219 52.632 0.00 0.00 0.00 1.85
137 144 1.451387 CAACAGTATGCCCCGGGAC 60.451 63.158 26.32 12.55 42.53 4.46
180 188 1.472728 GCCTAGTAACGTGGTCATGGG 60.473 57.143 0.00 0.00 0.00 4.00
209 217 1.088340 CAGCAGCCACAATCTCCTCG 61.088 60.000 0.00 0.00 0.00 4.63
256 265 5.903764 TCGCAAATGAAATTGTGGAAAAG 57.096 34.783 1.30 0.00 40.38 2.27
291 300 0.808755 GTCCATTTGTACCTTGCGGG 59.191 55.000 0.00 0.00 41.89 6.13
296 305 3.887335 TTGTACCTTGCGGGGCGAC 62.887 63.158 0.00 0.00 40.03 5.19
313 322 3.047877 CCCGTCGAACACCTTGCC 61.048 66.667 0.00 0.00 0.00 4.52
334 343 2.430367 GTGGTGGAAGAAGCCGGT 59.570 61.111 1.90 0.00 0.00 5.28
352 361 0.315568 GTCAGTGAAGAGCCTCGTGT 59.684 55.000 0.00 0.00 0.00 4.49
366 375 0.539669 TCGTGTCTCTCTGAGGCCAA 60.540 55.000 5.01 0.00 32.68 4.52
374 383 1.189752 CTCTGAGGCCAAGTAGCAGA 58.810 55.000 5.01 6.88 34.71 4.26
388 409 2.916052 GCAGACCTGTCGACGTGGA 61.916 63.158 27.09 0.00 34.09 4.02
423 446 3.788766 GTAGCCGCGCTTGTGTGG 61.789 66.667 5.56 9.19 40.44 4.17
472 499 3.218470 TCGACGTCGGGGTGTTGT 61.218 61.111 35.05 0.00 40.29 3.32
475 502 1.227321 GACGTCGGGGTGTTGTGAA 60.227 57.895 0.00 0.00 0.00 3.18
481 508 2.983592 GGGTGTTGTGAAGGCGGG 60.984 66.667 0.00 0.00 0.00 6.13
482 509 2.203294 GGTGTTGTGAAGGCGGGT 60.203 61.111 0.00 0.00 0.00 5.28
563 596 1.829222 AGGTATGTGGGTACGTTCAGG 59.171 52.381 0.00 0.00 0.00 3.86
614 669 0.253044 CGGCTCTTGATGGGAGGAAA 59.747 55.000 0.00 0.00 0.00 3.13
634 690 1.329913 GGGGAATGACCAATGTGCCC 61.330 60.000 0.00 0.00 41.20 5.36
636 692 0.324645 GGAATGACCAATGTGCCCCT 60.325 55.000 0.00 0.00 38.79 4.79
666 723 1.984570 CAGGAGAGGACAAGGGCGA 60.985 63.158 0.00 0.00 0.00 5.54
709 777 3.699411 AGCAAATGCAGCCCAAATTTA 57.301 38.095 8.28 0.00 45.16 1.40
730 800 3.083600 CTGAATGGGTCGCGCGAAC 62.084 63.158 38.41 38.41 0.00 3.95
761 832 2.325082 GCTGGTCCGTTTGCATCGT 61.325 57.895 10.11 0.00 0.00 3.73
776 848 2.737359 GCATCGTTCCGTTGGACTGATA 60.737 50.000 0.23 0.00 28.65 2.15
846 918 0.993746 GCGCGTTGAAGTTGCTCTTG 60.994 55.000 8.43 0.00 36.40 3.02
850 922 1.670811 CGTTGAAGTTGCTCTTGGTGT 59.329 47.619 0.00 0.00 36.40 4.16
851 923 2.869801 CGTTGAAGTTGCTCTTGGTGTA 59.130 45.455 0.00 0.00 36.40 2.90
858 950 0.898320 TGCTCTTGGTGTAGCCTCTC 59.102 55.000 0.00 0.00 37.97 3.20
869 961 0.462225 TAGCCTCTCGAGTCTCACGG 60.462 60.000 13.13 5.90 0.00 4.94
872 964 3.102107 CTCTCGAGTCTCACGGCGG 62.102 68.421 13.24 0.00 0.00 6.13
873 965 3.432588 CTCGAGTCTCACGGCGGT 61.433 66.667 13.24 0.00 0.00 5.68
976 1083 1.923395 ATCTGCCCCGGAACAAGGA 60.923 57.895 0.73 0.00 0.00 3.36
1036 1152 2.125350 CTTCTCCAGTCCAGCGCC 60.125 66.667 2.29 0.00 0.00 6.53
1075 1197 0.611896 CGTTCCCAAGCCAAATCCCT 60.612 55.000 0.00 0.00 0.00 4.20
1084 1206 0.472044 GCCAAATCCCTCTCCCTCTC 59.528 60.000 0.00 0.00 0.00 3.20
1088 1210 1.238896 AATCCCTCTCCCTCTCCCCA 61.239 60.000 0.00 0.00 0.00 4.96
1089 1211 1.967343 ATCCCTCTCCCTCTCCCCAC 61.967 65.000 0.00 0.00 0.00 4.61
1169 1301 1.150081 CAGCACCAGATGGATCCCC 59.850 63.158 9.90 0.68 38.94 4.81
1365 1502 2.722487 CCTGCTCGCCTACCTACG 59.278 66.667 0.00 0.00 0.00 3.51
1402 1539 1.687628 CGAGGAAATACGATCTCGGC 58.312 55.000 4.44 0.00 43.49 5.54
1410 1547 4.344474 CGATCTCGGCGGTAGGGC 62.344 72.222 7.21 0.00 35.37 5.19
1461 1598 1.459592 CCACAGTCGAACGATTTGGTC 59.540 52.381 0.00 0.00 0.00 4.02
1491 1628 2.887568 CCAGTGAGGATCGTGCGC 60.888 66.667 0.00 0.00 41.22 6.09
1525 1666 4.659172 TGGTTCAGCGCCTTGGGG 62.659 66.667 2.29 0.00 0.00 4.96
1529 1680 2.199652 TTCAGCGCCTTGGGGTTTG 61.200 57.895 2.29 0.00 34.45 2.93
1530 1681 2.912025 CAGCGCCTTGGGGTTTGT 60.912 61.111 2.29 0.00 34.45 2.83
1535 1686 2.028876 GCGCCTTGGGGTTTGTATTAT 58.971 47.619 0.00 0.00 34.45 1.28
1536 1687 2.429250 GCGCCTTGGGGTTTGTATTATT 59.571 45.455 0.00 0.00 34.45 1.40
1538 1689 3.067601 CGCCTTGGGGTTTGTATTATTCC 59.932 47.826 0.00 0.00 34.45 3.01
1541 1692 4.097286 CCTTGGGGTTTGTATTATTCCGTG 59.903 45.833 0.00 0.00 0.00 4.94
1554 1705 0.250553 TTCCGTGGTTCGCTGGAATT 60.251 50.000 0.00 0.00 35.64 2.17
1555 1706 0.672401 TCCGTGGTTCGCTGGAATTC 60.672 55.000 0.00 0.00 38.35 2.17
1559 1710 2.674177 CGTGGTTCGCTGGAATTCTAGT 60.674 50.000 18.80 0.00 34.05 2.57
1569 1720 2.496070 TGGAATTCTAGTGTAGCTGCGT 59.504 45.455 5.23 0.00 0.00 5.24
1600 1751 0.546122 TTCCCATCTCCGATGTTGGG 59.454 55.000 13.98 13.98 44.41 4.12
1601 1752 1.149174 CCCATCTCCGATGTTGGGG 59.851 63.158 12.91 0.00 41.16 4.96
1602 1753 1.635817 CCCATCTCCGATGTTGGGGT 61.636 60.000 12.91 0.00 41.16 4.95
1603 1754 0.255890 CCATCTCCGATGTTGGGGTT 59.744 55.000 3.47 0.00 0.00 4.11
1604 1755 1.340991 CCATCTCCGATGTTGGGGTTT 60.341 52.381 3.47 0.00 0.00 3.27
1605 1756 2.092646 CCATCTCCGATGTTGGGGTTTA 60.093 50.000 3.47 0.00 0.00 2.01
1607 1758 4.207165 CATCTCCGATGTTGGGGTTTAAT 58.793 43.478 0.00 0.00 0.00 1.40
1608 1759 3.881220 TCTCCGATGTTGGGGTTTAATC 58.119 45.455 0.00 0.00 0.00 1.75
1609 1760 2.949644 CTCCGATGTTGGGGTTTAATCC 59.050 50.000 0.00 0.00 0.00 3.01
1610 1761 2.028876 CCGATGTTGGGGTTTAATCCC 58.971 52.381 6.29 6.29 46.31 3.85
1620 1829 2.313643 GGGTTTAATCCCCTTCTCCCAA 59.686 50.000 10.18 0.00 41.54 4.12
1626 1835 2.899303 TCCCCTTCTCCCAACAAATC 57.101 50.000 0.00 0.00 0.00 2.17
1628 1837 1.004277 CCCCTTCTCCCAACAAATCGA 59.996 52.381 0.00 0.00 0.00 3.59
1631 1840 2.749621 CCTTCTCCCAACAAATCGAAGG 59.250 50.000 0.00 0.00 40.84 3.46
1633 1842 1.004277 TCTCCCAACAAATCGAAGGGG 59.996 52.381 0.00 0.00 40.02 4.79
1636 1845 1.750778 CCCAACAAATCGAAGGGGATG 59.249 52.381 0.00 0.00 37.80 3.51
1638 1847 1.094785 AACAAATCGAAGGGGATGCG 58.905 50.000 0.00 0.00 0.00 4.73
1639 1848 0.035439 ACAAATCGAAGGGGATGCGT 60.035 50.000 0.00 0.00 0.00 5.24
1640 1849 1.094785 CAAATCGAAGGGGATGCGTT 58.905 50.000 0.00 0.00 0.00 4.84
1642 1851 1.094785 AATCGAAGGGGATGCGTTTG 58.905 50.000 0.00 0.00 0.00 2.93
1643 1852 0.035439 ATCGAAGGGGATGCGTTTGT 60.035 50.000 0.00 0.00 0.00 2.83
1645 1854 0.953471 CGAAGGGGATGCGTTTGTGA 60.953 55.000 0.00 0.00 0.00 3.58
1646 1855 1.243902 GAAGGGGATGCGTTTGTGAA 58.756 50.000 0.00 0.00 0.00 3.18
1648 1857 1.463674 AGGGGATGCGTTTGTGAATC 58.536 50.000 0.00 0.00 0.00 2.52
1649 1858 0.455815 GGGGATGCGTTTGTGAATCC 59.544 55.000 0.00 0.00 38.30 3.01
1650 1859 1.173043 GGGATGCGTTTGTGAATCCA 58.827 50.000 3.28 0.00 40.38 3.41
1653 1862 1.812571 GATGCGTTTGTGAATCCAGGT 59.187 47.619 0.00 0.00 0.00 4.00
1654 1863 0.950836 TGCGTTTGTGAATCCAGGTG 59.049 50.000 0.00 0.00 0.00 4.00
1655 1864 0.240945 GCGTTTGTGAATCCAGGTGG 59.759 55.000 0.00 0.00 0.00 4.61
1656 1865 1.604604 CGTTTGTGAATCCAGGTGGT 58.395 50.000 0.00 0.00 36.34 4.16
1667 1876 1.897423 CAGGTGGTGGATCGCACTA 59.103 57.895 12.27 5.56 0.00 2.74
1668 1877 0.179100 CAGGTGGTGGATCGCACTAG 60.179 60.000 12.27 0.00 0.00 2.57
1669 1878 0.614979 AGGTGGTGGATCGCACTAGT 60.615 55.000 12.27 0.00 0.00 2.57
1670 1879 0.249398 GGTGGTGGATCGCACTAGTT 59.751 55.000 12.27 0.00 0.00 2.24
1671 1880 1.359848 GTGGTGGATCGCACTAGTTG 58.640 55.000 12.27 0.00 0.00 3.16
1687 1971 5.587844 CACTAGTTGCATTTAGAGAAGGCAT 59.412 40.000 10.88 0.00 34.03 4.40
1706 1990 4.380867 GGCATCAGGTAGTTGATTTGTTGG 60.381 45.833 0.00 0.00 35.67 3.77
1724 2008 0.839946 GGTGGGTGCTGACCTATCAT 59.160 55.000 0.00 0.00 42.66 2.45
1734 2018 3.223435 CTGACCTATCATCGTACCCTGT 58.777 50.000 0.00 0.00 33.22 4.00
1741 2025 6.553852 ACCTATCATCGTACCCTGTCTTTTAT 59.446 38.462 0.00 0.00 0.00 1.40
1815 2099 1.063190 TCTGCCTAAGCTGCTAGGGTA 60.063 52.381 19.73 15.25 39.20 3.69
1926 2214 2.490903 GCCTTGTCCTGTTCTAGTCGTA 59.509 50.000 0.00 0.00 0.00 3.43
1941 2229 3.525537 AGTCGTACCAATGCATCTCTTG 58.474 45.455 0.00 0.00 0.00 3.02
1945 2233 5.350365 GTCGTACCAATGCATCTCTTGTTTA 59.650 40.000 0.00 0.00 0.00 2.01
1958 2246 3.976169 TCTTGTTTACAGCAAATGCCAC 58.024 40.909 0.94 0.00 43.38 5.01
2017 2309 7.826690 ACTATTGTGATTGCCGTTTTAATTCT 58.173 30.769 0.00 0.00 0.00 2.40
2030 2322 6.077838 CGTTTTAATTCTTCTTCTTGGTCCG 58.922 40.000 0.00 0.00 0.00 4.79
2155 2447 4.127171 CAAGCTATGGTGTATGTGTACCC 58.873 47.826 0.00 0.00 36.10 3.69
2159 2451 4.262335 GCTATGGTGTATGTGTACCCTACC 60.262 50.000 0.00 0.00 36.10 3.18
2236 2528 1.912371 GCCTTGACCAGCGCAGTTAC 61.912 60.000 11.47 0.00 0.00 2.50
2240 2532 0.037697 TGACCAGCGCAGTTACGATT 60.038 50.000 11.47 0.00 34.06 3.34
2296 2588 4.857871 TGTATCGTATGCTCTTTTGTGC 57.142 40.909 0.00 0.00 39.19 4.57
2323 2618 2.465109 GCATTATGCGCTCGTTTGATTG 59.535 45.455 9.73 0.00 31.71 2.67
2326 2621 0.095245 ATGCGCTCGTTTGATTGTCG 59.905 50.000 9.73 0.00 0.00 4.35
2420 2715 0.033781 GACAATTGGCCTGCAAAGCA 59.966 50.000 10.83 0.00 36.92 3.91
2501 2796 9.073475 TGCTTTGTTTACTGTAATCATTTAGGT 57.927 29.630 11.03 0.00 0.00 3.08
2763 3090 1.597027 GCCGTGTACTGTGTGCCTT 60.597 57.895 0.00 0.00 0.00 4.35
2769 3096 1.763545 TGTACTGTGTGCCTTGTGGTA 59.236 47.619 0.00 0.00 35.27 3.25
2855 3182 3.069586 GCTGGTTTTTAACTCCTTTGCCT 59.930 43.478 0.00 0.00 0.00 4.75
2873 3200 5.730296 TGCCTTCTACTCTCTAATATGGC 57.270 43.478 0.00 0.00 37.38 4.40
2920 3247 4.201950 ACAAACAGAACACTGATGTGCTTC 60.202 41.667 0.00 0.00 42.77 3.86
3086 3415 6.183361 ACTTTCAAGTTCTATACCAGGTGGTT 60.183 38.462 7.04 0.00 40.21 3.67
3204 3533 8.657712 AGGGGTATCCTTATTATCACAAACTAC 58.342 37.037 0.00 0.00 45.47 2.73
3239 3568 3.224269 TGTCCCATGACATGCATTATGG 58.776 45.455 20.14 20.14 46.40 2.74
3648 3977 9.587772 TGTCTAAAGTAGTTTATCAATGAGCTC 57.412 33.333 6.82 6.82 0.00 4.09
3695 4024 2.682856 ACACGTGTTGAGATGCAAAGTT 59.317 40.909 17.22 0.00 38.44 2.66
3711 4040 7.165460 TGCAAAGTTGTAGCTATCTAGTGTA 57.835 36.000 0.00 0.00 0.00 2.90
3771 4100 6.920758 GCTATGAGTATGGTTCTGTACTTCTG 59.079 42.308 0.00 0.00 31.61 3.02
3959 4288 2.875296 TGCTTAAAACCCTGAGTGCAT 58.125 42.857 0.00 0.00 0.00 3.96
4254 4637 2.567169 TCACTTCAAGTCCACCATCGAT 59.433 45.455 0.00 0.00 0.00 3.59
4255 4638 3.007940 TCACTTCAAGTCCACCATCGATT 59.992 43.478 0.00 0.00 0.00 3.34
4263 4646 1.281867 TCCACCATCGATTGCCTCTTT 59.718 47.619 0.00 0.00 0.00 2.52
4357 5173 3.144506 CACTTTGAGTCCACAATCAGCT 58.855 45.455 0.00 0.00 0.00 4.24
4391 5207 9.601217 TCTATGTTTGCTAGGAGATCTTTTTAC 57.399 33.333 0.00 0.00 0.00 2.01
4430 5247 7.128976 TGAAACCAAATATTTTGCGCTTTTTC 58.871 30.769 9.73 1.65 0.00 2.29
4758 5575 5.133221 GCCTCCATAAGTCCATATTTGTGT 58.867 41.667 0.00 0.00 0.00 3.72
4770 5587 7.226523 AGTCCATATTTGTGTTTTTCCTTTTGC 59.773 33.333 0.00 0.00 0.00 3.68
4974 5791 8.001292 AGTCTATCAGCCCTGCTAAATATTTTT 58.999 33.333 5.91 0.00 36.40 1.94
5091 5908 5.290493 TCTGCTAAAGAGAAAGGTGTTGA 57.710 39.130 0.00 0.00 0.00 3.18
5172 5990 9.406113 AGCTTCTATGCTAAATTCTGATTTCTT 57.594 29.630 0.00 0.00 42.10 2.52
5180 5998 6.183359 GCTAAATTCTGATTTCTTGTGCGTTG 60.183 38.462 0.00 0.00 36.82 4.10
5281 6102 7.614124 AAAACATGATTTTGAACACAGCTTT 57.386 28.000 0.00 0.00 0.00 3.51
5284 6105 8.715191 AACATGATTTTGAACACAGCTTTTTA 57.285 26.923 0.00 0.00 0.00 1.52
5745 6580 9.998106 TCTTTCTTATAACTTTCTGCTGTACTT 57.002 29.630 0.00 0.00 0.00 2.24
5882 6717 3.149196 GTTGCTCTCTGATCCACCAAAA 58.851 45.455 0.00 0.00 0.00 2.44
5888 6723 4.410099 TCTCTGATCCACCAAAAATTGCT 58.590 39.130 0.00 0.00 0.00 3.91
5966 6821 9.360093 GTAAGTTCGTCTACTACTAACTCTGTA 57.640 37.037 0.00 0.00 41.78 2.74
5972 6827 7.543868 TCGTCTACTACTAACTCTGTAAGTCAC 59.456 40.741 0.00 0.00 37.17 3.67
5974 6829 9.218440 GTCTACTACTAACTCTGTAAGTCACTT 57.782 37.037 0.00 0.00 37.17 3.16
6000 6856 6.538945 AAGTCTCCAGAAACTATTCCTCTC 57.461 41.667 0.00 0.00 36.12 3.20
6001 6857 5.584913 AGTCTCCAGAAACTATTCCTCTCA 58.415 41.667 0.00 0.00 36.12 3.27
6009 6865 7.382110 CAGAAACTATTCCTCTCAAGAGTGAA 58.618 38.462 6.30 9.10 40.48 3.18
6073 6931 2.754472 TGTGGTGTTGATCGACAAGAG 58.246 47.619 17.55 0.00 39.30 2.85
6185 7043 5.459762 CCTTCAGTTAGTGCAACACAATTTG 59.540 40.000 0.00 0.00 41.43 2.32
6521 7384 5.758296 GCCAGAGATAATCGGAATTGTTACA 59.242 40.000 0.00 0.00 0.00 2.41
6602 7468 9.618890 AATGCAGTAACTATAGACATGTCATTT 57.381 29.630 27.02 13.46 0.00 2.32
6644 7510 7.697691 TCTGTCACTTCAAAGAAGATTTGTTC 58.302 34.615 13.23 2.09 0.00 3.18
6645 7511 6.795399 TGTCACTTCAAAGAAGATTTGTTCC 58.205 36.000 13.23 0.00 0.00 3.62
6646 7512 6.183360 TGTCACTTCAAAGAAGATTTGTTCCC 60.183 38.462 13.23 0.00 0.00 3.97
6647 7513 6.039829 GTCACTTCAAAGAAGATTTGTTCCCT 59.960 38.462 13.23 0.00 0.00 4.20
6648 7514 6.039717 TCACTTCAAAGAAGATTTGTTCCCTG 59.960 38.462 13.23 0.00 0.00 4.45
6649 7515 4.853924 TCAAAGAAGATTTGTTCCCTGC 57.146 40.909 0.74 0.00 0.00 4.85
6650 7516 3.573967 TCAAAGAAGATTTGTTCCCTGCC 59.426 43.478 0.74 0.00 0.00 4.85
6651 7517 2.978156 AGAAGATTTGTTCCCTGCCA 57.022 45.000 0.00 0.00 0.00 4.92
6652 7518 3.243359 AGAAGATTTGTTCCCTGCCAA 57.757 42.857 0.00 0.00 0.00 4.52
6653 7519 3.575805 AGAAGATTTGTTCCCTGCCAAA 58.424 40.909 0.00 0.00 35.25 3.28
6654 7520 3.575687 AGAAGATTTGTTCCCTGCCAAAG 59.424 43.478 0.00 0.00 34.35 2.77
6655 7521 2.962859 AGATTTGTTCCCTGCCAAAGT 58.037 42.857 0.00 0.00 34.35 2.66
6656 7522 3.308401 AGATTTGTTCCCTGCCAAAGTT 58.692 40.909 0.00 0.00 34.35 2.66
6657 7523 4.479158 AGATTTGTTCCCTGCCAAAGTTA 58.521 39.130 0.00 0.00 34.35 2.24
6658 7524 4.524328 AGATTTGTTCCCTGCCAAAGTTAG 59.476 41.667 0.00 0.00 34.35 2.34
6659 7525 3.306472 TTGTTCCCTGCCAAAGTTAGT 57.694 42.857 0.00 0.00 0.00 2.24
6660 7526 2.582052 TGTTCCCTGCCAAAGTTAGTG 58.418 47.619 0.00 0.00 0.00 2.74
6661 7527 2.092103 TGTTCCCTGCCAAAGTTAGTGT 60.092 45.455 0.00 0.00 0.00 3.55
6662 7528 2.270352 TCCCTGCCAAAGTTAGTGTG 57.730 50.000 0.00 0.00 0.00 3.82
6663 7529 0.598065 CCCTGCCAAAGTTAGTGTGC 59.402 55.000 0.00 0.00 0.00 4.57
6664 7530 1.609208 CCTGCCAAAGTTAGTGTGCT 58.391 50.000 0.00 0.00 0.00 4.40
6665 7531 1.267806 CCTGCCAAAGTTAGTGTGCTG 59.732 52.381 0.00 0.00 0.00 4.41
6727 7593 5.597813 ATCATAATTGATTCGGAGTTCGC 57.402 39.130 0.00 0.00 39.64 4.70
6731 7597 0.037326 TTGATTCGGAGTTCGCTGCT 60.037 50.000 0.00 0.00 39.05 4.24
6737 7603 1.078848 GGAGTTCGCTGCTGGTGAT 60.079 57.895 0.00 0.00 34.15 3.06
6738 7604 1.364626 GGAGTTCGCTGCTGGTGATG 61.365 60.000 0.00 0.00 34.15 3.07
6745 7611 0.028505 GCTGCTGGTGATGTAATGCG 59.971 55.000 0.00 0.00 0.00 4.73
6899 7765 3.538591 TGCTGCTAATCCAGTCATGAAG 58.461 45.455 0.00 0.00 35.28 3.02
7073 7939 3.852578 ACTCATTGGAAAGGTATGTCCCT 59.147 43.478 0.00 0.00 36.75 4.20
7117 7986 2.597505 CGTTTGAAGCGTGACTGTTGAG 60.598 50.000 0.00 0.00 0.00 3.02
7118 7987 2.309528 TTGAAGCGTGACTGTTGAGT 57.690 45.000 0.00 0.00 33.98 3.41
7252 8121 2.882761 GTTTTAAGGTGGCCTTTCGAGT 59.117 45.455 3.32 0.00 41.69 4.18
7351 8220 2.947448 TGTGTGACGAGGATGATGAG 57.053 50.000 0.00 0.00 0.00 2.90
7379 8251 3.699538 AGGTTCAGTTCTGTTGGGTTTTC 59.300 43.478 0.00 0.00 0.00 2.29
7388 8260 8.960591 CAGTTCTGTTGGGTTTTCTGATATAAT 58.039 33.333 0.00 0.00 0.00 1.28
7439 8312 7.822334 TCCATCTTACAATTACAGTTACCAGTG 59.178 37.037 0.00 0.00 0.00 3.66
7440 8313 7.065803 CCATCTTACAATTACAGTTACCAGTGG 59.934 40.741 7.91 7.91 0.00 4.00
7441 8314 7.305813 TCTTACAATTACAGTTACCAGTGGA 57.694 36.000 18.40 0.00 0.00 4.02
7442 8315 7.737869 TCTTACAATTACAGTTACCAGTGGAA 58.262 34.615 18.40 2.84 30.13 3.53
7443 8316 7.876068 TCTTACAATTACAGTTACCAGTGGAAG 59.124 37.037 18.40 3.64 28.97 3.46
7445 8318 6.362248 ACAATTACAGTTACCAGTGGAAGTT 58.638 36.000 18.40 0.00 28.97 2.66
7447 8320 7.994334 ACAATTACAGTTACCAGTGGAAGTTAA 59.006 33.333 18.40 0.39 28.97 2.01
7448 8321 8.842280 CAATTACAGTTACCAGTGGAAGTTAAA 58.158 33.333 18.40 2.17 28.97 1.52
7449 8322 8.983702 ATTACAGTTACCAGTGGAAGTTAAAA 57.016 30.769 18.40 2.98 28.97 1.52
7454 8327 3.208594 ACCAGTGGAAGTTAAAACGGAC 58.791 45.455 18.40 0.00 0.00 4.79
7471 8344 2.892640 CGACATCTTCGGCAGGGA 59.107 61.111 0.00 0.00 44.60 4.20
7488 8361 5.754890 GGCAGGGAAATATGCTTAAAATGTG 59.245 40.000 0.00 0.00 42.19 3.21
7489 8362 6.340522 GCAGGGAAATATGCTTAAAATGTGT 58.659 36.000 0.00 0.00 39.38 3.72
7490 8363 7.417342 GGCAGGGAAATATGCTTAAAATGTGTA 60.417 37.037 0.00 0.00 42.19 2.90
7531 8404 7.264373 ACTTTCGACAAATTTCAACATCTCT 57.736 32.000 0.00 0.00 0.00 3.10
7532 8405 7.707104 ACTTTCGACAAATTTCAACATCTCTT 58.293 30.769 0.00 0.00 0.00 2.85
7533 8406 8.190784 ACTTTCGACAAATTTCAACATCTCTTT 58.809 29.630 0.00 0.00 0.00 2.52
7534 8407 8.925161 TTTCGACAAATTTCAACATCTCTTTT 57.075 26.923 0.00 0.00 0.00 2.27
7536 8409 7.702386 TCGACAAATTTCAACATCTCTTTTCA 58.298 30.769 0.00 0.00 0.00 2.69
7537 8410 7.857389 TCGACAAATTTCAACATCTCTTTTCAG 59.143 33.333 0.00 0.00 0.00 3.02
7538 8411 7.857389 CGACAAATTTCAACATCTCTTTTCAGA 59.143 33.333 0.00 0.00 0.00 3.27
7540 8413 8.139989 ACAAATTTCAACATCTCTTTTCAGAGG 58.860 33.333 0.00 0.00 46.17 3.69
7541 8414 5.695851 TTTCAACATCTCTTTTCAGAGGC 57.304 39.130 0.00 0.00 46.17 4.70
7542 8415 4.630644 TCAACATCTCTTTTCAGAGGCT 57.369 40.909 0.00 0.00 46.17 4.58
7543 8416 4.573900 TCAACATCTCTTTTCAGAGGCTC 58.426 43.478 6.34 6.34 46.17 4.70
7544 8417 3.244033 ACATCTCTTTTCAGAGGCTCG 57.756 47.619 9.22 4.43 46.17 5.03
7545 8418 1.932511 CATCTCTTTTCAGAGGCTCGC 59.067 52.381 9.22 0.00 46.17 5.03
7546 8419 0.969149 TCTCTTTTCAGAGGCTCGCA 59.031 50.000 9.22 0.00 46.17 5.10
7547 8420 1.067283 TCTCTTTTCAGAGGCTCGCAG 60.067 52.381 9.22 3.57 46.17 5.18
7548 8421 0.681733 TCTTTTCAGAGGCTCGCAGT 59.318 50.000 9.22 0.00 0.00 4.40
7549 8422 1.074752 CTTTTCAGAGGCTCGCAGTC 58.925 55.000 9.22 0.00 0.00 3.51
7550 8423 0.667487 TTTTCAGAGGCTCGCAGTCG 60.667 55.000 9.22 0.00 0.00 4.18
7551 8424 3.633094 TTCAGAGGCTCGCAGTCGC 62.633 63.158 9.22 0.00 35.26 5.19
7552 8425 4.426112 CAGAGGCTCGCAGTCGCA 62.426 66.667 9.22 0.00 38.40 5.10
7553 8426 4.127040 AGAGGCTCGCAGTCGCAG 62.127 66.667 9.22 0.00 38.40 5.18
7603 8476 6.842437 TTGACAAGCACTCTCTAATCTACT 57.158 37.500 0.00 0.00 0.00 2.57
7604 8477 6.201226 TGACAAGCACTCTCTAATCTACTG 57.799 41.667 0.00 0.00 0.00 2.74
7605 8478 5.712446 TGACAAGCACTCTCTAATCTACTGT 59.288 40.000 0.00 0.00 0.00 3.55
7606 8479 6.884836 TGACAAGCACTCTCTAATCTACTGTA 59.115 38.462 0.00 0.00 0.00 2.74
7607 8480 7.090953 ACAAGCACTCTCTAATCTACTGTAC 57.909 40.000 0.00 0.00 0.00 2.90
7608 8481 6.887545 ACAAGCACTCTCTAATCTACTGTACT 59.112 38.462 0.00 0.00 0.00 2.73
7626 8499 7.688343 ACTGTACTAGTCTGTACTACCTCTTT 58.312 38.462 0.00 0.00 42.22 2.52
7672 8545 3.258228 TGTACACGATATGCACAACTGG 58.742 45.455 0.00 0.00 31.25 4.00
7830 8703 1.536766 TCCGTCGTGTCGATGTACTTT 59.463 47.619 9.84 0.00 40.74 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 112 2.358898 GGGCATACTGTTGAATCGCAAT 59.641 45.455 0.00 0.00 39.03 3.56
157 165 1.913778 TGACCACGTTACTAGGCAGA 58.086 50.000 0.00 0.00 0.00 4.26
165 173 3.919163 TCACCCATGACCACGTTAC 57.081 52.632 0.00 0.00 0.00 2.50
180 188 2.195567 TGGCTGCTGCTTTGGTCAC 61.196 57.895 15.64 0.00 39.59 3.67
256 265 2.983229 TGGACTCTAGTGACGAGTACC 58.017 52.381 0.00 2.74 40.83 3.34
296 305 3.047877 GGCAAGGTGTTCGACGGG 61.048 66.667 0.00 0.00 0.00 5.28
313 322 3.423154 GCTTCTTCCACCACGCCG 61.423 66.667 0.00 0.00 0.00 6.46
334 343 0.598562 GACACGAGGCTCTTCACTGA 59.401 55.000 13.50 0.00 0.00 3.41
352 361 1.272704 TGCTACTTGGCCTCAGAGAGA 60.273 52.381 3.32 0.00 0.00 3.10
362 371 0.737715 CGACAGGTCTGCTACTTGGC 60.738 60.000 6.79 2.99 39.83 4.52
366 375 0.605860 ACGTCGACAGGTCTGCTACT 60.606 55.000 17.16 0.00 0.00 2.57
374 383 2.338984 GCTTCCACGTCGACAGGT 59.661 61.111 17.16 3.02 0.00 4.00
388 409 2.177038 CTCGCTCGTCAGACGCTT 59.823 61.111 18.62 0.00 42.21 4.68
472 499 1.444836 CATCGTTTTACCCGCCTTCA 58.555 50.000 0.00 0.00 0.00 3.02
475 502 1.003112 TGCATCGTTTTACCCGCCT 60.003 52.632 0.00 0.00 0.00 5.52
481 508 1.711824 GCGTTTGGTGCATCGTTTTAC 59.288 47.619 0.00 0.00 0.00 2.01
482 509 1.335142 GGCGTTTGGTGCATCGTTTTA 60.335 47.619 0.00 0.00 0.00 1.52
529 557 0.995675 ATACCTCCCCCAGCAGCATT 60.996 55.000 0.00 0.00 0.00 3.56
530 558 1.386485 ATACCTCCCCCAGCAGCAT 60.386 57.895 0.00 0.00 0.00 3.79
595 650 0.253044 TTTCCTCCCATCAAGAGCCG 59.747 55.000 0.00 0.00 0.00 5.52
600 655 1.298953 TCCCCTTTCCTCCCATCAAG 58.701 55.000 0.00 0.00 0.00 3.02
602 657 1.570501 CATTCCCCTTTCCTCCCATCA 59.429 52.381 0.00 0.00 0.00 3.07
614 669 0.324645 GGCACATTGGTCATTCCCCT 60.325 55.000 0.00 0.00 34.77 4.79
636 692 2.997315 CTCCTGACCCGCCAGTCA 60.997 66.667 3.65 3.65 44.38 3.41
647 703 1.984570 CGCCCTTGTCCTCTCCTGA 60.985 63.158 0.00 0.00 0.00 3.86
652 708 3.764466 CGCTCGCCCTTGTCCTCT 61.764 66.667 0.00 0.00 0.00 3.69
761 832 4.647611 ACACAAATATCAGTCCAACGGAA 58.352 39.130 0.00 0.00 31.38 4.30
776 848 4.974368 TTGACTTGAAACGGACACAAAT 57.026 36.364 0.00 0.00 0.00 2.32
858 950 4.778415 CCACCGCCGTGAGACTCG 62.778 72.222 6.77 0.00 43.14 4.18
954 1050 4.506255 GTTCCGGGGCAGATGGGG 62.506 72.222 0.00 0.00 0.00 4.96
1013 1129 2.011046 GCTGGACTGGAGAAGTGATGC 61.011 57.143 0.00 0.00 40.07 3.91
1040 1156 4.084888 CGAAGTTGAACGCCGCCC 62.085 66.667 0.27 0.00 0.00 6.13
1075 1197 1.081092 CAAGGTGGGGAGAGGGAGA 59.919 63.158 0.00 0.00 0.00 3.71
1099 1221 3.462021 TGGGTTTTGATTTCGGCTTTTG 58.538 40.909 0.00 0.00 0.00 2.44
1100 1222 3.386402 TCTGGGTTTTGATTTCGGCTTTT 59.614 39.130 0.00 0.00 0.00 2.27
1103 1225 2.162681 CTCTGGGTTTTGATTTCGGCT 58.837 47.619 0.00 0.00 0.00 5.52
1104 1226 1.402852 GCTCTGGGTTTTGATTTCGGC 60.403 52.381 0.00 0.00 0.00 5.54
1105 1227 1.135689 CGCTCTGGGTTTTGATTTCGG 60.136 52.381 0.00 0.00 0.00 4.30
1106 1228 1.804151 TCGCTCTGGGTTTTGATTTCG 59.196 47.619 0.00 0.00 0.00 3.46
1107 1229 2.414691 GCTCGCTCTGGGTTTTGATTTC 60.415 50.000 0.00 0.00 0.00 2.17
1109 1231 1.168714 GCTCGCTCTGGGTTTTGATT 58.831 50.000 0.00 0.00 0.00 2.57
1110 1232 0.678048 GGCTCGCTCTGGGTTTTGAT 60.678 55.000 0.00 0.00 0.00 2.57
1111 1233 1.302511 GGCTCGCTCTGGGTTTTGA 60.303 57.895 0.00 0.00 0.00 2.69
1169 1301 2.657237 GGTATCCATCTCCGCCGG 59.343 66.667 0.00 0.00 0.00 6.13
1343 1476 2.444256 GGTAGGCGAGCAGGGGATT 61.444 63.158 0.00 0.00 0.00 3.01
1344 1477 2.020100 TAGGTAGGCGAGCAGGGGAT 62.020 60.000 0.00 0.00 0.00 3.85
1348 1481 2.061182 GACGTAGGTAGGCGAGCAGG 62.061 65.000 0.00 0.00 0.00 4.85
1365 1502 3.827898 CTCTCCCCGTCGCCAGAC 61.828 72.222 0.00 0.00 43.72 3.51
1410 1547 3.765257 ATCCCCCTCCAGGCTCGAG 62.765 68.421 8.45 8.45 0.00 4.04
1436 1573 1.183030 ATCGTTCGACTGTGGGGACA 61.183 55.000 0.00 0.00 38.70 4.02
1491 1628 0.107017 CCAGTGAGGCTGTATTGGGG 60.107 60.000 0.00 0.00 43.55 4.96
1510 1647 2.200337 AAACCCCAAGGCGCTGAAC 61.200 57.895 7.64 0.00 36.11 3.18
1525 1666 4.093850 AGCGAACCACGGAATAATACAAAC 59.906 41.667 0.00 0.00 42.83 2.93
1529 1680 2.542595 CCAGCGAACCACGGAATAATAC 59.457 50.000 0.00 0.00 42.83 1.89
1530 1681 2.431419 TCCAGCGAACCACGGAATAATA 59.569 45.455 0.00 0.00 42.83 0.98
1535 1686 0.250553 AATTCCAGCGAACCACGGAA 60.251 50.000 0.00 0.00 42.83 4.30
1536 1687 0.672401 GAATTCCAGCGAACCACGGA 60.672 55.000 0.00 0.00 42.83 4.69
1538 1689 1.927174 CTAGAATTCCAGCGAACCACG 59.073 52.381 0.65 0.00 45.66 4.94
1541 1692 2.973945 ACACTAGAATTCCAGCGAACC 58.026 47.619 0.65 0.00 0.00 3.62
1554 1705 1.068541 CACACACGCAGCTACACTAGA 60.069 52.381 0.00 0.00 0.00 2.43
1555 1706 1.340658 CACACACGCAGCTACACTAG 58.659 55.000 0.00 0.00 0.00 2.57
1559 1710 0.032815 TAAGCACACACGCAGCTACA 59.967 50.000 0.00 0.00 37.70 2.74
1569 1720 4.016444 GGAGATGGGAAAATAAGCACACA 58.984 43.478 0.00 0.00 0.00 3.72
1600 1751 3.245479 TGTTGGGAGAAGGGGATTAAACC 60.245 47.826 0.00 0.00 0.00 3.27
1601 1752 4.042271 TGTTGGGAGAAGGGGATTAAAC 57.958 45.455 0.00 0.00 0.00 2.01
1602 1753 4.750833 TTGTTGGGAGAAGGGGATTAAA 57.249 40.909 0.00 0.00 0.00 1.52
1603 1754 4.750833 TTTGTTGGGAGAAGGGGATTAA 57.249 40.909 0.00 0.00 0.00 1.40
1604 1755 4.627741 CGATTTGTTGGGAGAAGGGGATTA 60.628 45.833 0.00 0.00 0.00 1.75
1605 1756 3.713003 GATTTGTTGGGAGAAGGGGATT 58.287 45.455 0.00 0.00 0.00 3.01
1607 1758 1.004277 CGATTTGTTGGGAGAAGGGGA 59.996 52.381 0.00 0.00 0.00 4.81
1608 1759 1.004277 TCGATTTGTTGGGAGAAGGGG 59.996 52.381 0.00 0.00 0.00 4.79
1609 1760 2.489938 TCGATTTGTTGGGAGAAGGG 57.510 50.000 0.00 0.00 0.00 3.95
1610 1761 2.749621 CCTTCGATTTGTTGGGAGAAGG 59.250 50.000 7.52 7.52 45.56 3.46
1620 1829 0.035439 ACGCATCCCCTTCGATTTGT 60.035 50.000 0.00 0.00 0.00 2.83
1626 1835 0.953471 TCACAAACGCATCCCCTTCG 60.953 55.000 0.00 0.00 0.00 3.79
1628 1837 1.818674 GATTCACAAACGCATCCCCTT 59.181 47.619 0.00 0.00 0.00 3.95
1631 1840 1.133025 CTGGATTCACAAACGCATCCC 59.867 52.381 0.00 0.00 35.23 3.85
1633 1842 1.812571 ACCTGGATTCACAAACGCATC 59.187 47.619 0.00 0.00 0.00 3.91
1636 1845 0.240945 CCACCTGGATTCACAAACGC 59.759 55.000 0.00 0.00 37.39 4.84
1638 1847 1.613437 CCACCACCTGGATTCACAAAC 59.387 52.381 0.00 0.00 43.95 2.93
1639 1848 1.496857 TCCACCACCTGGATTCACAAA 59.503 47.619 0.00 0.00 44.99 2.83
1640 1849 1.144691 TCCACCACCTGGATTCACAA 58.855 50.000 0.00 0.00 44.99 3.33
1648 1857 1.613317 TAGTGCGATCCACCACCTGG 61.613 60.000 9.80 0.00 45.83 4.45
1649 1858 0.179100 CTAGTGCGATCCACCACCTG 60.179 60.000 9.80 0.00 45.83 4.00
1650 1859 0.614979 ACTAGTGCGATCCACCACCT 60.615 55.000 0.00 0.00 45.83 4.00
1653 1862 0.391130 GCAACTAGTGCGATCCACCA 60.391 55.000 0.00 0.00 45.10 4.17
1654 1863 2.384203 GCAACTAGTGCGATCCACC 58.616 57.895 0.00 0.00 45.10 4.61
1663 1872 4.937620 TGCCTTCTCTAAATGCAACTAGTG 59.062 41.667 0.00 0.00 0.00 2.74
1664 1873 5.165961 TGCCTTCTCTAAATGCAACTAGT 57.834 39.130 0.00 0.00 0.00 2.57
1665 1874 5.819379 TGATGCCTTCTCTAAATGCAACTAG 59.181 40.000 0.00 0.00 35.30 2.57
1667 1876 4.592942 TGATGCCTTCTCTAAATGCAACT 58.407 39.130 0.00 0.00 35.30 3.16
1668 1877 4.201990 CCTGATGCCTTCTCTAAATGCAAC 60.202 45.833 0.00 0.00 35.30 4.17
1669 1878 3.949754 CCTGATGCCTTCTCTAAATGCAA 59.050 43.478 0.00 0.00 35.30 4.08
1670 1879 3.054139 ACCTGATGCCTTCTCTAAATGCA 60.054 43.478 0.00 0.00 36.23 3.96
1671 1880 3.549794 ACCTGATGCCTTCTCTAAATGC 58.450 45.455 0.00 0.00 0.00 3.56
1672 1881 5.923204 ACTACCTGATGCCTTCTCTAAATG 58.077 41.667 0.00 0.00 0.00 2.32
1674 1883 5.483937 TCAACTACCTGATGCCTTCTCTAAA 59.516 40.000 0.00 0.00 0.00 1.85
1677 1886 3.445008 TCAACTACCTGATGCCTTCTCT 58.555 45.455 0.00 0.00 0.00 3.10
1678 1887 3.895232 TCAACTACCTGATGCCTTCTC 57.105 47.619 0.00 0.00 0.00 2.87
1684 1968 4.218417 ACCAACAAATCAACTACCTGATGC 59.782 41.667 0.00 0.00 36.16 3.91
1687 1971 4.141287 CCACCAACAAATCAACTACCTGA 58.859 43.478 0.00 0.00 0.00 3.86
1706 1990 1.539065 CGATGATAGGTCAGCACCCAC 60.539 57.143 0.00 0.00 45.12 4.61
1724 2008 7.232127 CCCTAGAATATAAAAGACAGGGTACGA 59.768 40.741 0.00 0.00 37.32 3.43
1734 2018 6.042781 ACCATGCGTCCCTAGAATATAAAAGA 59.957 38.462 0.00 0.00 0.00 2.52
1741 2025 2.628178 CTCACCATGCGTCCCTAGAATA 59.372 50.000 0.00 0.00 0.00 1.75
1745 2029 1.043116 TCCTCACCATGCGTCCCTAG 61.043 60.000 0.00 0.00 0.00 3.02
1750 2034 1.005037 TGTGTCCTCACCATGCGTC 60.005 57.895 0.00 0.00 43.26 5.19
1815 2099 2.144450 AGAGGAGGGGGAACAAAACTT 58.856 47.619 0.00 0.00 0.00 2.66
1926 2214 4.082571 GCTGTAAACAAGAGATGCATTGGT 60.083 41.667 0.00 0.00 0.00 3.67
1941 2229 2.697431 TCGTGGCATTTGCTGTAAAC 57.303 45.000 2.12 0.00 41.70 2.01
1945 2233 1.317613 TTCTTCGTGGCATTTGCTGT 58.682 45.000 2.12 0.00 41.70 4.40
1958 2246 4.728882 GCCAGTCAAAGCATACATTCTTCG 60.729 45.833 0.00 0.00 0.00 3.79
2017 2309 1.968493 ACACTAGCGGACCAAGAAGAA 59.032 47.619 0.00 0.00 0.00 2.52
2030 2322 2.208431 CTGGCTCTGCAATACACTAGC 58.792 52.381 0.00 0.00 33.32 3.42
2153 2445 1.076632 AGAGGCAGAGACGGTAGGG 60.077 63.158 0.00 0.00 0.00 3.53
2155 2447 1.440938 CGGAGAGGCAGAGACGGTAG 61.441 65.000 0.00 0.00 0.00 3.18
2296 2588 3.460362 ACGAGCGCATAATGCATAATG 57.540 42.857 11.47 0.00 45.36 1.90
2297 2589 4.024133 TCAAACGAGCGCATAATGCATAAT 60.024 37.500 11.47 0.00 45.36 1.28
2298 2590 3.311048 TCAAACGAGCGCATAATGCATAA 59.689 39.130 11.47 0.00 45.36 1.90
2299 2591 2.869192 TCAAACGAGCGCATAATGCATA 59.131 40.909 11.47 0.00 45.36 3.14
2300 2592 1.670295 TCAAACGAGCGCATAATGCAT 59.330 42.857 11.47 0.00 45.36 3.96
2301 2593 1.082690 TCAAACGAGCGCATAATGCA 58.917 45.000 11.47 0.00 45.36 3.96
2302 2594 2.389713 ATCAAACGAGCGCATAATGC 57.610 45.000 11.47 0.00 40.69 3.56
2303 2595 3.683989 ACAATCAAACGAGCGCATAATG 58.316 40.909 11.47 1.62 0.00 1.90
2323 2618 8.060020 TCAATTGACAATTCAACATTTTCGAC 57.940 30.769 10.52 0.00 44.66 4.20
2501 2796 7.174599 CCAATTGGTGCCAAATTTTCTAAATGA 59.825 33.333 16.90 0.00 39.55 2.57
2600 2895 6.311935 CAGCTAACATTTCAACATTGATTGGG 59.688 38.462 0.00 0.00 37.00 4.12
2824 3151 7.489160 AGGAGTTAAAAACCAGCTTAAACTTG 58.511 34.615 0.00 0.00 0.00 3.16
2855 3182 6.731292 TTGCTGCCATATTAGAGAGTAGAA 57.269 37.500 0.00 0.00 0.00 2.10
2873 3200 5.104374 ACACAAATTTCACTCTGTTTGCTG 58.896 37.500 0.00 0.00 35.53 4.41
2920 3247 1.619654 TGGATTTGCAGGAGTTGGTG 58.380 50.000 0.00 0.00 0.00 4.17
3020 3349 5.819991 AGACATTGGCTGAGAAAGGATTTA 58.180 37.500 0.00 0.00 39.27 1.40
3086 3415 2.639347 TCCAGCCTTGTCAAGAAGATGA 59.361 45.455 14.42 1.58 0.00 2.92
3642 3971 3.941483 GCCAGTATTAGCAAAAGAGCTCA 59.059 43.478 17.77 0.00 45.26 4.26
3648 3977 7.559590 AGTAATCTGCCAGTATTAGCAAAAG 57.440 36.000 0.00 0.00 38.82 2.27
3695 4024 8.657712 TCCTCTGTATTACACTAGATAGCTACA 58.342 37.037 0.00 0.00 0.00 2.74
3983 4312 6.763715 AGGCAATCCAGGTAAGACATATAA 57.236 37.500 0.00 0.00 33.74 0.98
3996 4325 2.503895 AACCTGAGAAGGCAATCCAG 57.496 50.000 0.00 0.00 33.74 3.86
4254 4637 8.956426 CCTAACAAACATAGATTAAAGAGGCAA 58.044 33.333 0.00 0.00 0.00 4.52
4255 4638 8.325787 TCCTAACAAACATAGATTAAAGAGGCA 58.674 33.333 0.00 0.00 0.00 4.75
4263 4646 7.989947 AGACCCTCCTAACAAACATAGATTA 57.010 36.000 0.00 0.00 0.00 1.75
4357 5173 4.164030 TCCTAGCAAACATAGATGGCTGAA 59.836 41.667 0.00 0.00 36.10 3.02
4401 5217 5.122082 AGCGCAAAATATTTGGTTTCAATGG 59.878 36.000 11.47 0.00 32.28 3.16
4430 5247 5.452078 TTAGGCAAATGAAGTGACAAAGG 57.548 39.130 0.00 0.00 0.00 3.11
4758 5575 4.142795 GGCTGAAAAACGCAAAAGGAAAAA 60.143 37.500 0.00 0.00 0.00 1.94
4770 5587 6.523676 ACAACATAAATTGGCTGAAAAACG 57.476 33.333 0.00 0.00 33.63 3.60
4923 5740 2.996621 GGTGTAGTAGCTGCAAGACAAG 59.003 50.000 4.12 0.00 34.07 3.16
5091 5908 8.860088 GGGGCTGTTCTTGAATTATTAATGTAT 58.140 33.333 0.00 0.00 0.00 2.29
5172 5990 1.300931 GCAGAGAGGACAACGCACA 60.301 57.895 0.00 0.00 0.00 4.57
5180 5998 3.568007 AGAGAATGATACGCAGAGAGGAC 59.432 47.826 0.00 0.00 0.00 3.85
5284 6105 9.601217 ACGTACTAGAAATCAGAATTTAGCATT 57.399 29.630 0.00 0.00 35.21 3.56
5738 6573 6.373779 CAAACAGATGCAGGTTTAAGTACAG 58.626 40.000 11.96 0.00 35.59 2.74
5745 6580 3.181434 ACTCCCAAACAGATGCAGGTTTA 60.181 43.478 11.96 0.03 35.59 2.01
5882 6717 6.886459 ACATTTCTACCACATGTCTAGCAATT 59.114 34.615 0.00 0.00 0.00 2.32
5888 6723 6.620877 AAGGACATTTCTACCACATGTCTA 57.379 37.500 10.49 0.00 44.25 2.59
5966 6821 5.359194 TTCTGGAGACTTTCAAGTGACTT 57.641 39.130 0.00 0.00 39.88 3.01
5972 6827 7.164803 AGGAATAGTTTCTGGAGACTTTCAAG 58.835 38.462 0.00 0.00 32.16 3.02
5974 6829 6.498651 AGAGGAATAGTTTCTGGAGACTTTCA 59.501 38.462 0.00 0.00 32.16 2.69
6000 6856 4.889832 AAGTTTCACAGCTTCACTCTTG 57.110 40.909 0.00 0.00 0.00 3.02
6001 6857 4.943705 TGAAAGTTTCACAGCTTCACTCTT 59.056 37.500 14.35 0.00 34.08 2.85
6009 6865 1.322442 GGCCTGAAAGTTTCACAGCT 58.678 50.000 24.56 0.00 35.34 4.24
6312 7174 5.560953 GCAACAAGTAGACTTTAACAGGCAG 60.561 44.000 0.00 0.00 33.11 4.85
6316 7178 6.844696 TCAGCAACAAGTAGACTTTAACAG 57.155 37.500 0.00 0.00 33.11 3.16
6406 7269 2.197792 TTCAATGCGATGCAATCAGC 57.802 45.000 0.00 0.00 45.97 4.26
6521 7384 6.729690 TTTGTTGTCTCCATTTTTGGATCT 57.270 33.333 0.00 0.00 37.34 2.75
6617 7483 8.908786 ACAAATCTTCTTTGAAGTGACAGATA 57.091 30.769 4.81 0.00 33.83 1.98
6639 7505 2.955660 CACTAACTTTGGCAGGGAACAA 59.044 45.455 0.00 0.00 0.00 2.83
6641 7507 2.293399 CACACTAACTTTGGCAGGGAAC 59.707 50.000 0.00 0.00 0.00 3.62
6644 7510 0.598065 GCACACTAACTTTGGCAGGG 59.402 55.000 0.00 0.00 0.00 4.45
6645 7511 1.267806 CAGCACACTAACTTTGGCAGG 59.732 52.381 0.00 0.00 0.00 4.85
6646 7512 1.335324 GCAGCACACTAACTTTGGCAG 60.335 52.381 0.00 0.00 0.00 4.85
6647 7513 0.667993 GCAGCACACTAACTTTGGCA 59.332 50.000 0.00 0.00 0.00 4.92
6648 7514 0.667993 TGCAGCACACTAACTTTGGC 59.332 50.000 0.00 0.00 0.00 4.52
6649 7515 2.405892 GTGCAGCACACTAACTTTGG 57.594 50.000 21.22 0.00 46.41 3.28
6718 7584 2.842394 ATCACCAGCAGCGAACTCCG 62.842 60.000 0.00 0.00 42.21 4.63
6727 7593 1.372582 ACGCATTACATCACCAGCAG 58.627 50.000 0.00 0.00 0.00 4.24
6731 7597 3.320673 TGTGTACGCATTACATCACCA 57.679 42.857 4.65 0.00 42.82 4.17
6762 7628 4.903045 TTTGGATCGAGGGAAGTTAAGT 57.097 40.909 0.00 0.00 0.00 2.24
6862 7728 0.179009 AGCAAAGAACAGCTCCAGCA 60.179 50.000 0.48 0.00 45.16 4.41
6899 7765 5.657470 TCAGTAAACAGAATATCGCATGC 57.343 39.130 7.91 7.91 0.00 4.06
6991 7857 1.080569 GGCCTTGTTGATTGCCACG 60.081 57.895 0.00 0.00 43.46 4.94
7073 7939 1.675310 CCAGCGGATGCAAGAACCA 60.675 57.895 0.00 0.00 46.23 3.67
7117 7986 3.305608 CCAAGAGGCATTTGTTTCCTCAC 60.306 47.826 9.80 0.00 46.71 3.51
7118 7987 2.892852 CCAAGAGGCATTTGTTTCCTCA 59.107 45.455 9.80 0.00 46.71 3.86
7252 8121 0.953727 TCGGTTTCTCGGACGAAGAA 59.046 50.000 0.00 0.00 31.79 2.52
7259 8128 2.654877 GGTGCTCGGTTTCTCGGA 59.345 61.111 0.00 0.00 0.00 4.55
7286 8155 2.871633 TGCACCTAATGTACATGCATCG 59.128 45.455 15.31 4.20 41.18 3.84
7351 8220 3.999663 CCAACAGAACTGAACCTCTGATC 59.000 47.826 8.87 0.00 41.38 2.92
7379 8251 4.633126 CCAGCATCCACCGAATTATATCAG 59.367 45.833 0.00 0.00 0.00 2.90
7388 8260 0.327924 ATGAACCAGCATCCACCGAA 59.672 50.000 0.00 0.00 0.00 4.30
7439 8312 3.992427 AGATGTCGTCCGTTTTAACTTCC 59.008 43.478 0.00 0.00 0.00 3.46
7440 8313 5.587033 AAGATGTCGTCCGTTTTAACTTC 57.413 39.130 0.00 0.00 0.00 3.01
7441 8314 4.149396 CGAAGATGTCGTCCGTTTTAACTT 59.851 41.667 0.00 0.00 45.09 2.66
7442 8315 3.671928 CGAAGATGTCGTCCGTTTTAACT 59.328 43.478 0.00 0.00 45.09 2.24
7443 8316 3.970225 CGAAGATGTCGTCCGTTTTAAC 58.030 45.455 0.00 0.00 45.09 2.01
7464 8337 5.754890 CACATTTTAAGCATATTTCCCTGCC 59.245 40.000 0.00 0.00 39.22 4.85
7512 8385 7.857389 TCTGAAAAGAGATGTTGAAATTTGTCG 59.143 33.333 0.00 0.00 0.00 4.35
7531 8404 0.667487 CGACTGCGAGCCTCTGAAAA 60.667 55.000 0.00 0.00 40.82 2.29
7532 8405 1.080501 CGACTGCGAGCCTCTGAAA 60.081 57.895 0.00 0.00 40.82 2.69
7533 8406 2.568612 CGACTGCGAGCCTCTGAA 59.431 61.111 0.00 0.00 40.82 3.02
7534 8407 4.121669 GCGACTGCGAGCCTCTGA 62.122 66.667 0.00 0.00 40.82 3.27
7544 8417 1.080995 CCAGTTAGAGCTGCGACTGC 61.081 60.000 17.08 0.00 38.48 4.40
7545 8418 0.244994 ACCAGTTAGAGCTGCGACTG 59.755 55.000 16.15 16.15 39.29 3.51
7546 8419 0.528470 GACCAGTTAGAGCTGCGACT 59.472 55.000 0.00 7.43 35.28 4.18
7547 8420 0.458716 GGACCAGTTAGAGCTGCGAC 60.459 60.000 0.00 0.00 35.28 5.19
7548 8421 0.612174 AGGACCAGTTAGAGCTGCGA 60.612 55.000 0.00 0.00 35.28 5.10
7549 8422 0.459237 CAGGACCAGTTAGAGCTGCG 60.459 60.000 0.00 0.00 35.28 5.18
7550 8423 0.898320 TCAGGACCAGTTAGAGCTGC 59.102 55.000 0.00 0.00 35.28 5.25
7551 8424 3.902881 AATCAGGACCAGTTAGAGCTG 57.097 47.619 0.00 0.00 36.31 4.24
7552 8425 4.777896 TGTAAATCAGGACCAGTTAGAGCT 59.222 41.667 0.00 0.00 0.00 4.09
7553 8426 5.086104 TGTAAATCAGGACCAGTTAGAGC 57.914 43.478 0.00 0.00 0.00 4.09
7554 8427 6.936279 TCTTGTAAATCAGGACCAGTTAGAG 58.064 40.000 0.00 0.00 0.00 2.43
7555 8428 6.928348 TCTTGTAAATCAGGACCAGTTAGA 57.072 37.500 0.00 0.00 0.00 2.10
7603 8476 7.683578 TCAAAGAGGTAGTACAGACTAGTACA 58.316 38.462 0.00 2.78 45.25 2.90
7604 8477 8.614346 CATCAAAGAGGTAGTACAGACTAGTAC 58.386 40.741 0.00 0.00 43.61 2.73
7605 8478 8.327271 ACATCAAAGAGGTAGTACAGACTAGTA 58.673 37.037 0.00 0.00 38.88 1.82
7606 8479 7.176490 ACATCAAAGAGGTAGTACAGACTAGT 58.824 38.462 0.00 0.00 38.88 2.57
7607 8480 7.633193 ACATCAAAGAGGTAGTACAGACTAG 57.367 40.000 2.06 0.00 38.88 2.57
7608 8481 9.121658 CATACATCAAAGAGGTAGTACAGACTA 57.878 37.037 2.06 0.00 37.10 2.59
7618 8491 3.194861 GCGCACATACATCAAAGAGGTA 58.805 45.455 0.30 0.00 33.44 3.08
7626 8499 1.066929 ACAGAGTGCGCACATACATCA 60.067 47.619 39.21 0.00 0.00 3.07
7672 8545 1.000496 AGAGGACGACGAGGTTTGAAC 60.000 52.381 0.00 0.00 0.00 3.18
7830 8703 2.046023 CCCGTGCAGAAGATGGCA 60.046 61.111 0.00 0.00 37.77 4.92


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

AutoCloner maintained by Alex Coulton.