Multiple sequence alignment - TraesCS1B01G424500

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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 TraesCS1B01G424500 chr1B 100.000 3395 0 0 1 3395 648595362 648591968 0.000000e+00 6270.0
1 TraesCS1B01G424500 chr1B 77.680 569 89 29 77 623 434833759 434834311 2.540000e-81 313.0
2 TraesCS1B01G424500 chr1B 76.333 469 85 20 189 641 588792814 588793272 9.480000e-56 228.0
3 TraesCS1B01G424500 chr1A 88.400 1931 104 55 734 2578 562042013 562043909 0.000000e+00 2215.0
4 TraesCS1B01G424500 chr1A 90.307 423 34 5 2976 3395 562044847 562045265 6.400000e-152 547.0
5 TraesCS1B01G424500 chr1A 90.291 103 4 2 2877 2973 562044801 562044903 2.750000e-26 130.0
6 TraesCS1B01G424500 chr1A 95.122 41 1 1 558 598 12420163 12420202 2.830000e-06 63.9
7 TraesCS1B01G424500 chr1D 86.439 2050 125 76 780 2739 469052411 469054397 0.000000e+00 2104.0
8 TraesCS1B01G424500 chr1D 91.133 406 32 3 2991 3395 469054705 469055107 6.400000e-152 547.0
9 TraesCS1B01G424500 chrUn 77.698 695 127 21 1 681 452674693 452675373 1.900000e-107 399.0
10 TraesCS1B01G424500 chr5B 77.698 695 127 21 1 681 599989871 599989191 1.900000e-107 399.0
11 TraesCS1B01G424500 chr5B 77.554 695 128 21 1 681 600032760 600032080 8.830000e-106 394.0
12 TraesCS1B01G424500 chr5B 77.266 695 130 19 1 681 600011366 600010686 1.910000e-102 383.0
13 TraesCS1B01G424500 chr5B 81.250 176 30 1 1190 1362 27813083 27813258 4.570000e-29 139.0
14 TraesCS1B01G424500 chr5D 78.033 610 109 18 76 675 3519550 3520144 8.960000e-96 361.0
15 TraesCS1B01G424500 chr5D 76.110 473 87 19 1190 1649 37201849 37202308 1.230000e-54 224.0
16 TraesCS1B01G424500 chr5D 78.338 337 60 13 1788 2116 37202355 37202686 4.440000e-49 206.0
17 TraesCS1B01G424500 chr5D 93.902 82 4 1 1280 1361 508999696 508999776 4.600000e-24 122.0
18 TraesCS1B01G424500 chr6B 93.035 201 10 3 1456 1654 712103720 712103918 1.190000e-74 291.0
19 TraesCS1B01G424500 chr6B 91.589 107 7 2 1256 1361 712103523 712103628 2.730000e-31 147.0
20 TraesCS1B01G424500 chr6A 93.035 201 10 3 1456 1654 613237617 613237419 1.190000e-74 291.0
21 TraesCS1B01G424500 chr6A 73.899 636 109 31 2 626 87762475 87761886 5.740000e-48 202.0
22 TraesCS1B01G424500 chr3B 74.789 710 148 24 2 701 663057479 663058167 1.190000e-74 291.0
23 TraesCS1B01G424500 chr3B 73.714 350 83 6 1776 2125 74762765 74763105 9.890000e-26 128.0
24 TraesCS1B01G424500 chr6D 92.537 201 11 3 1456 1654 466908805 466908607 5.540000e-73 285.0
25 TraesCS1B01G424500 chr4B 75.507 641 108 36 4 629 500236314 500236920 5.580000e-68 268.0
26 TraesCS1B01G424500 chr7A 74.768 646 126 25 34 658 412722443 412723072 4.350000e-64 255.0
27 TraesCS1B01G424500 chr7A 77.317 410 76 15 1253 1649 31591886 31592291 3.410000e-55 226.0
28 TraesCS1B01G424500 chr7A 76.833 341 59 17 1788 2115 63378659 63378992 1.250000e-39 174.0
29 TraesCS1B01G424500 chr7A 79.891 184 34 3 1478 1659 620370839 620370657 7.640000e-27 132.0
30 TraesCS1B01G424500 chr7A 79.679 187 32 5 1460 1643 484395638 484395821 2.750000e-26 130.0
31 TraesCS1B01G424500 chr7A 79.058 191 36 4 1471 1659 620487458 620487646 9.890000e-26 128.0
32 TraesCS1B01G424500 chr7D 74.074 675 133 28 2 664 420293175 420293819 4.380000e-59 239.0
33 TraesCS1B01G424500 chr7D 78.324 346 63 9 1787 2123 58842626 58842284 2.650000e-51 213.0
34 TraesCS1B01G424500 chr7D 78.235 340 58 15 1788 2116 58830073 58830407 1.600000e-48 204.0
35 TraesCS1B01G424500 chr7D 78.894 199 37 5 1468 1664 538895324 538895129 2.750000e-26 130.0
36 TraesCS1B01G424500 chr2A 77.079 445 81 14 191 622 124661872 124662308 1.570000e-58 237.0
37 TraesCS1B01G424500 chr2A 81.481 108 17 3 524 629 101843101 101843207 6.040000e-13 86.1
38 TraesCS1B01G424500 chr4A 78.151 357 66 9 1776 2123 675954866 675954513 2.050000e-52 217.0
39 TraesCS1B01G424500 chr4A 77.233 347 65 13 1788 2124 675932852 675933194 1.240000e-44 191.0
40 TraesCS1B01G424500 chr7B 74.949 487 99 23 228 705 368424235 368424707 5.740000e-48 202.0


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 TraesCS1B01G424500 chr1B 648591968 648595362 3394 True 6270.0 6270 100.000 1 3395 1 chr1B.!!$R1 3394
1 TraesCS1B01G424500 chr1B 434833759 434834311 552 False 313.0 313 77.680 77 623 1 chr1B.!!$F1 546
2 TraesCS1B01G424500 chr1A 562042013 562045265 3252 False 964.0 2215 89.666 734 3395 3 chr1A.!!$F2 2661
3 TraesCS1B01G424500 chr1D 469052411 469055107 2696 False 1325.5 2104 88.786 780 3395 2 chr1D.!!$F1 2615
4 TraesCS1B01G424500 chrUn 452674693 452675373 680 False 399.0 399 77.698 1 681 1 chrUn.!!$F1 680
5 TraesCS1B01G424500 chr5B 599989191 599989871 680 True 399.0 399 77.698 1 681 1 chr5B.!!$R1 680
6 TraesCS1B01G424500 chr5B 600032080 600032760 680 True 394.0 394 77.554 1 681 1 chr5B.!!$R3 680
7 TraesCS1B01G424500 chr5B 600010686 600011366 680 True 383.0 383 77.266 1 681 1 chr5B.!!$R2 680
8 TraesCS1B01G424500 chr5D 3519550 3520144 594 False 361.0 361 78.033 76 675 1 chr5D.!!$F1 599
9 TraesCS1B01G424500 chr5D 37201849 37202686 837 False 215.0 224 77.224 1190 2116 2 chr5D.!!$F3 926
10 TraesCS1B01G424500 chr6A 87761886 87762475 589 True 202.0 202 73.899 2 626 1 chr6A.!!$R1 624
11 TraesCS1B01G424500 chr3B 663057479 663058167 688 False 291.0 291 74.789 2 701 1 chr3B.!!$F2 699
12 TraesCS1B01G424500 chr4B 500236314 500236920 606 False 268.0 268 75.507 4 629 1 chr4B.!!$F1 625
13 TraesCS1B01G424500 chr7A 412722443 412723072 629 False 255.0 255 74.768 34 658 1 chr7A.!!$F3 624
14 TraesCS1B01G424500 chr7D 420293175 420293819 644 False 239.0 239 74.074 2 664 1 chr7D.!!$F2 662

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
523 546 0.255033 GTGATGGGGTAGGGTTGTCC 59.745 60.0 0.00 0.00 0.0 4.02 F
807 845 0.387929 TATCCAAGACATCGCGGGTC 59.612 55.0 19.67 19.67 35.5 4.46 F
1016 1071 0.550914 AACACCACCATCACACCACT 59.449 50.0 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1812 0.107165 GTTAGGCTCGGGGCAAGATT 60.107 55.0 13.05 0.0 44.01 2.40 R
1712 1831 0.171903 CCGTGGGTAGGTACAGTTCG 59.828 60.0 0.00 0.0 0.00 3.95 R
2983 3222 0.109597 GCCACAAGTGATGCCTTTCG 60.110 55.0 0.94 0.0 0.00 3.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.195591 AACGAGCTGCGACGAGTGT 62.196 57.895 23.24 3.98 44.57 3.55
30 31 3.168604 CGAGCTGCGACGAGTGTG 61.169 66.667 14.67 0.00 44.57 3.82
32 33 1.371758 GAGCTGCGACGAGTGTGAA 60.372 57.895 0.00 0.00 0.00 3.18
64 65 2.388232 GCAACTACGTGGGCGGAAG 61.388 63.158 3.26 0.00 43.45 3.46
95 96 3.622826 CCCCAACTGGTCGTCGGT 61.623 66.667 0.00 0.00 36.31 4.69
196 205 2.610859 GAGTGGGGAGAGGGGCAA 60.611 66.667 0.00 0.00 0.00 4.52
257 272 4.504916 CTCTCTCGCTGCCGGTGG 62.505 72.222 1.90 0.00 34.56 4.61
304 320 3.777925 CTTGCACGACGAAGCCGG 61.778 66.667 0.00 0.00 40.78 6.13
305 321 4.595538 TTGCACGACGAAGCCGGT 62.596 61.111 1.90 0.00 40.78 5.28
309 325 3.598715 ACGACGAAGCCGGTGACA 61.599 61.111 1.90 0.00 40.78 3.58
345 361 2.490217 CGGACGCGACCTCAATCT 59.510 61.111 24.38 0.00 0.00 2.40
348 364 1.136984 GACGCGACCTCAATCTCGT 59.863 57.895 15.93 0.00 42.38 4.18
353 370 0.526211 CGACCTCAATCTCGTGGTCA 59.474 55.000 10.92 0.00 45.67 4.02
358 375 1.550524 CTCAATCTCGTGGTCAGGGAA 59.449 52.381 0.00 0.00 0.00 3.97
420 438 3.650950 GCTGGGAGCAAGGGTGGA 61.651 66.667 0.00 0.00 41.89 4.02
426 445 3.672295 GAGCAAGGGTGGAGGCGAG 62.672 68.421 0.00 0.00 0.00 5.03
428 447 4.101448 CAAGGGTGGAGGCGAGGG 62.101 72.222 0.00 0.00 0.00 4.30
441 460 3.532155 GAGGGCTCAGGCGTCGAT 61.532 66.667 5.03 0.00 39.81 3.59
442 461 3.781770 GAGGGCTCAGGCGTCGATG 62.782 68.421 5.03 0.00 39.81 3.84
469 491 0.551131 AGGTTGGAGGGAGGCAGAAT 60.551 55.000 0.00 0.00 0.00 2.40
472 494 1.213926 GTTGGAGGGAGGCAGAATGAT 59.786 52.381 0.00 0.00 39.69 2.45
474 496 0.842635 GGAGGGAGGCAGAATGATGT 59.157 55.000 0.00 0.00 39.69 3.06
523 546 0.255033 GTGATGGGGTAGGGTTGTCC 59.745 60.000 0.00 0.00 0.00 4.02
525 548 1.222567 GATGGGGTAGGGTTGTCCAT 58.777 55.000 0.00 0.00 40.52 3.41
588 623 6.676558 CCCCATATTTAGGCTGGATATGAAT 58.323 40.000 22.87 6.53 36.37 2.57
636 671 1.004918 CGTTTGAGGAGCCCGTCTT 60.005 57.895 0.00 0.00 0.00 3.01
644 679 3.991536 GAGCCCGTCTTGGTCGCTC 62.992 68.421 0.00 0.00 42.41 5.03
652 687 1.940613 GTCTTGGTCGCTCTTTTGTGT 59.059 47.619 0.00 0.00 0.00 3.72
690 725 2.883730 CCGCGTGGACGTATGTGG 60.884 66.667 10.20 0.00 42.22 4.17
701 736 2.049767 GTATGTGGCGGGTTTGGGG 61.050 63.158 0.00 0.00 0.00 4.96
702 737 3.948004 TATGTGGCGGGTTTGGGGC 62.948 63.158 0.00 0.00 0.00 5.80
709 744 4.354162 GGGTTTGGGGCGCTACCA 62.354 66.667 18.21 18.21 42.05 3.25
710 745 2.282603 GGTTTGGGGCGCTACCAA 60.283 61.111 25.86 25.86 45.73 3.67
711 746 2.632544 GGTTTGGGGCGCTACCAAC 61.633 63.158 28.25 22.74 46.94 3.77
712 747 2.670251 TTTGGGGCGCTACCAACG 60.670 61.111 28.25 0.00 46.94 4.10
713 748 3.479127 TTTGGGGCGCTACCAACGT 62.479 57.895 28.25 0.00 46.94 3.99
714 749 2.962142 TTTGGGGCGCTACCAACGTT 62.962 55.000 28.25 0.00 46.94 3.99
715 750 2.109517 TTGGGGCGCTACCAACGTTA 62.110 55.000 25.86 10.05 42.75 3.18
716 751 1.812507 GGGGCGCTACCAACGTTAG 60.813 63.158 7.64 0.00 42.05 2.34
717 752 1.216178 GGGCGCTACCAACGTTAGA 59.784 57.895 7.64 0.00 42.05 2.10
718 753 0.390209 GGGCGCTACCAACGTTAGAA 60.390 55.000 7.64 0.00 42.05 2.10
719 754 0.717784 GGCGCTACCAACGTTAGAAC 59.282 55.000 7.64 0.00 38.86 3.01
735 770 6.576551 GTTAGAACGATGAGGATTCAGTTC 57.423 41.667 0.00 0.00 38.12 3.01
759 794 6.485313 TCGACAGTATTTCAGGTGAAAACATT 59.515 34.615 9.13 0.00 45.81 2.71
760 795 6.578545 CGACAGTATTTCAGGTGAAAACATTG 59.421 38.462 9.13 9.35 45.81 2.82
762 797 6.183360 ACAGTATTTCAGGTGAAAACATTGCA 60.183 34.615 9.13 0.00 45.81 4.08
764 799 7.385752 CAGTATTTCAGGTGAAAACATTGCATT 59.614 33.333 9.13 0.00 45.81 3.56
765 800 7.933033 AGTATTTCAGGTGAAAACATTGCATTT 59.067 29.630 9.13 0.00 45.81 2.32
769 804 5.293814 TCAGGTGAAAACATTGCATTTGTTG 59.706 36.000 14.24 3.82 37.38 3.33
770 805 4.575645 AGGTGAAAACATTGCATTTGTTGG 59.424 37.500 14.24 0.00 37.38 3.77
772 807 5.525378 GGTGAAAACATTGCATTTGTTGGTA 59.475 36.000 14.24 3.84 37.38 3.25
773 808 6.292811 GGTGAAAACATTGCATTTGTTGGTAG 60.293 38.462 14.24 0.00 37.38 3.18
774 809 5.236047 TGAAAACATTGCATTTGTTGGTAGC 59.764 36.000 14.24 5.60 37.38 3.58
778 816 4.021280 ACATTGCATTTGTTGGTAGCATCA 60.021 37.500 1.56 1.56 34.87 3.07
803 841 4.997905 ATTGAATATCCAAGACATCGCG 57.002 40.909 0.00 0.00 0.00 5.87
804 842 2.754472 TGAATATCCAAGACATCGCGG 58.246 47.619 6.13 0.00 0.00 6.46
805 843 2.069273 GAATATCCAAGACATCGCGGG 58.931 52.381 6.13 0.81 0.00 6.13
806 844 1.048601 ATATCCAAGACATCGCGGGT 58.951 50.000 6.13 4.89 0.00 5.28
807 845 0.387929 TATCCAAGACATCGCGGGTC 59.612 55.000 19.67 19.67 35.50 4.46
808 846 2.629050 ATCCAAGACATCGCGGGTCG 62.629 60.000 20.60 11.13 40.20 4.79
864 907 1.229820 AGAGCACCATACCCACCCA 60.230 57.895 0.00 0.00 0.00 4.51
986 1030 2.893682 ATAAAGCTGCACCGGCTCCC 62.894 60.000 0.00 0.00 46.32 4.30
1002 1057 3.964875 CCGCACAGCACCAACACC 61.965 66.667 0.00 0.00 0.00 4.16
1003 1058 3.208383 CGCACAGCACCAACACCA 61.208 61.111 0.00 0.00 0.00 4.17
1004 1059 2.412937 GCACAGCACCAACACCAC 59.587 61.111 0.00 0.00 0.00 4.16
1005 1060 3.119193 CACAGCACCAACACCACC 58.881 61.111 0.00 0.00 0.00 4.61
1006 1061 1.752310 CACAGCACCAACACCACCA 60.752 57.895 0.00 0.00 0.00 4.17
1007 1062 1.108727 CACAGCACCAACACCACCAT 61.109 55.000 0.00 0.00 0.00 3.55
1011 1066 1.106351 GCACCAACACCACCATCACA 61.106 55.000 0.00 0.00 0.00 3.58
1012 1067 0.667993 CACCAACACCACCATCACAC 59.332 55.000 0.00 0.00 0.00 3.82
1016 1071 0.550914 AACACCACCATCACACCACT 59.449 50.000 0.00 0.00 0.00 4.00
1022 1077 1.055849 ACCATCACACCACTGCACTA 58.944 50.000 0.00 0.00 0.00 2.74
1043 1098 0.830444 ACTGGTGCGGTACAGAGGAA 60.830 55.000 0.00 0.00 38.09 3.36
1061 1117 3.797546 GCAGCAGAGGAGCAACGC 61.798 66.667 0.00 0.00 36.85 4.84
1062 1118 2.357881 CAGCAGAGGAGCAACGCA 60.358 61.111 0.00 0.00 36.85 5.24
1065 1121 2.049156 CAGAGGAGCAACGCACGA 60.049 61.111 0.00 0.00 0.00 4.35
1401 1484 2.191128 TCTTTTCAGAGGAGCAAGGC 57.809 50.000 0.00 0.00 0.00 4.35
1443 1530 1.222115 GGCTGTGGTTGACTCGTGTC 61.222 60.000 10.62 10.62 43.20 3.67
1449 1536 2.987149 GTGGTTGACTCGTGTCTGTATG 59.013 50.000 17.64 0.00 43.29 2.39
1465 1552 4.115516 CTGTATGCAAATAGCTGACGTCT 58.884 43.478 17.92 0.00 45.94 4.18
1684 1803 3.449737 CCATCTTGCATCCAAGTTCCATT 59.550 43.478 0.00 0.00 46.74 3.16
1685 1804 4.441079 CCATCTTGCATCCAAGTTCCATTC 60.441 45.833 0.00 0.00 46.74 2.67
1686 1805 3.765381 TCTTGCATCCAAGTTCCATTCA 58.235 40.909 0.00 0.00 46.74 2.57
1688 1807 2.170166 TGCATCCAAGTTCCATTCACC 58.830 47.619 0.00 0.00 0.00 4.02
1690 1809 2.562298 GCATCCAAGTTCCATTCACCAA 59.438 45.455 0.00 0.00 0.00 3.67
1693 1812 2.091610 TCCAAGTTCCATTCACCAACCA 60.092 45.455 0.00 0.00 0.00 3.67
1694 1813 2.697751 CCAAGTTCCATTCACCAACCAA 59.302 45.455 0.00 0.00 0.00 3.67
1695 1814 3.324556 CCAAGTTCCATTCACCAACCAAT 59.675 43.478 0.00 0.00 0.00 3.16
1697 1816 4.118168 AGTTCCATTCACCAACCAATCT 57.882 40.909 0.00 0.00 0.00 2.40
1699 1818 4.281688 AGTTCCATTCACCAACCAATCTTG 59.718 41.667 0.00 0.00 0.00 3.02
1700 1819 2.562298 TCCATTCACCAACCAATCTTGC 59.438 45.455 0.00 0.00 0.00 4.01
1701 1820 2.354003 CCATTCACCAACCAATCTTGCC 60.354 50.000 0.00 0.00 0.00 4.52
1702 1821 1.337118 TTCACCAACCAATCTTGCCC 58.663 50.000 0.00 0.00 0.00 5.36
1704 1823 1.606313 ACCAACCAATCTTGCCCCG 60.606 57.895 0.00 0.00 0.00 5.73
1706 1825 1.315257 CCAACCAATCTTGCCCCGAG 61.315 60.000 0.00 0.00 0.00 4.63
1708 1827 2.830370 CCAATCTTGCCCCGAGCC 60.830 66.667 0.00 0.00 42.71 4.70
1709 1828 2.273449 CAATCTTGCCCCGAGCCT 59.727 61.111 0.00 0.00 42.71 4.58
1711 1830 0.107214 CAATCTTGCCCCGAGCCTAA 60.107 55.000 0.00 0.00 42.71 2.69
1712 1831 0.107165 AATCTTGCCCCGAGCCTAAC 60.107 55.000 0.00 0.00 42.71 2.34
1713 1832 2.311688 ATCTTGCCCCGAGCCTAACG 62.312 60.000 0.00 0.00 42.71 3.18
1714 1833 2.998480 TTGCCCCGAGCCTAACGA 60.998 61.111 0.00 0.00 42.71 3.85
1715 1834 2.515996 CTTGCCCCGAGCCTAACGAA 62.516 60.000 0.00 0.00 42.71 3.85
1716 1835 2.510918 GCCCCGAGCCTAACGAAC 60.511 66.667 0.00 0.00 34.35 3.95
1717 1836 3.015312 GCCCCGAGCCTAACGAACT 62.015 63.158 0.00 0.00 34.35 3.01
1718 1837 1.153628 CCCCGAGCCTAACGAACTG 60.154 63.158 0.00 0.00 0.00 3.16
1719 1838 1.590147 CCCGAGCCTAACGAACTGT 59.410 57.895 0.00 0.00 0.00 3.55
1720 1839 0.813184 CCCGAGCCTAACGAACTGTA 59.187 55.000 0.00 0.00 0.00 2.74
1721 1840 1.468736 CCCGAGCCTAACGAACTGTAC 60.469 57.143 0.00 0.00 0.00 2.90
1722 1841 1.468736 CCGAGCCTAACGAACTGTACC 60.469 57.143 0.00 0.00 0.00 3.34
1723 1842 1.471684 CGAGCCTAACGAACTGTACCT 59.528 52.381 0.00 0.00 0.00 3.08
1724 1843 2.679837 CGAGCCTAACGAACTGTACCTA 59.320 50.000 0.00 0.00 0.00 3.08
1725 1844 3.486542 CGAGCCTAACGAACTGTACCTAC 60.487 52.174 0.00 0.00 0.00 3.18
1732 1851 0.533951 GAACTGTACCTACCCACGGG 59.466 60.000 0.00 0.00 42.03 5.28
1733 1852 1.547472 AACTGTACCTACCCACGGGC 61.547 60.000 0.69 0.00 39.32 6.13
1741 1860 0.531311 CTACCCACGGGCCGATTAAC 60.531 60.000 35.78 0.00 39.32 2.01
1755 1874 4.372656 CCGATTAACTCAGATTCCAGGTC 58.627 47.826 0.00 0.00 0.00 3.85
2006 2128 1.519455 GGATGAACACGGAGCTCGG 60.519 63.158 18.87 18.87 44.45 4.63
2145 2284 7.837689 TGATCCATCATCAATTTCTTCCTTTCT 59.162 33.333 0.00 0.00 38.68 2.52
2147 2286 8.426569 TCCATCATCAATTTCTTCCTTTCTTT 57.573 30.769 0.00 0.00 0.00 2.52
2149 2288 7.763071 CCATCATCAATTTCTTCCTTTCTTTCC 59.237 37.037 0.00 0.00 0.00 3.13
2155 2294 3.963428 TCTTCCTTTCTTTCCTCCTCG 57.037 47.619 0.00 0.00 0.00 4.63
2157 2311 3.258622 TCTTCCTTTCTTTCCTCCTCGTC 59.741 47.826 0.00 0.00 0.00 4.20
2158 2312 1.544691 TCCTTTCTTTCCTCCTCGTCG 59.455 52.381 0.00 0.00 0.00 5.12
2160 2314 2.288886 CCTTTCTTTCCTCCTCGTCGTT 60.289 50.000 0.00 0.00 0.00 3.85
2161 2315 2.433868 TTCTTTCCTCCTCGTCGTTG 57.566 50.000 0.00 0.00 0.00 4.10
2164 2321 2.059541 CTTTCCTCCTCGTCGTTGTTC 58.940 52.381 0.00 0.00 0.00 3.18
2188 2345 0.179207 TTCGATTCGAGACGGACACG 60.179 55.000 8.98 0.00 41.02 4.49
2284 2447 9.000486 AGTTACTGTTACAGAGAAAATTAAGGC 58.000 33.333 20.07 0.00 35.18 4.35
2286 2449 6.228258 ACTGTTACAGAGAAAATTAAGGCGA 58.772 36.000 20.07 0.00 35.18 5.54
2287 2450 6.147328 ACTGTTACAGAGAAAATTAAGGCGAC 59.853 38.462 20.07 0.00 35.18 5.19
2289 2452 6.367969 TGTTACAGAGAAAATTAAGGCGACTC 59.632 38.462 0.00 0.00 42.68 3.36
2290 2453 4.254492 ACAGAGAAAATTAAGGCGACTCC 58.746 43.478 0.00 0.00 42.68 3.85
2301 2464 2.457598 AGGCGACTCCTCTTGTGATTA 58.542 47.619 0.00 0.00 43.20 1.75
2303 2466 3.126831 GGCGACTCCTCTTGTGATTATG 58.873 50.000 0.00 0.00 0.00 1.90
2319 2482 3.815856 TTATGCTCTGCTTGGAGAGAG 57.184 47.619 20.62 4.27 41.95 3.20
2320 2483 1.570803 ATGCTCTGCTTGGAGAGAGT 58.429 50.000 20.62 7.03 41.95 3.24
2321 2484 2.222227 TGCTCTGCTTGGAGAGAGTA 57.778 50.000 20.62 5.49 41.95 2.59
2322 2485 1.821753 TGCTCTGCTTGGAGAGAGTAC 59.178 52.381 20.62 5.66 41.95 2.73
2349 2516 3.198068 AGTGCACATGTGATCGGTTATC 58.802 45.455 29.80 8.59 34.93 1.75
2356 2523 6.369890 GCACATGTGATCGGTTATCTATGAAT 59.630 38.462 29.80 0.00 35.36 2.57
2362 2529 9.825109 TGTGATCGGTTATCTATGAATAAAACA 57.175 29.630 0.00 0.00 35.45 2.83
2455 2640 8.641498 AGATATTGTTTTGGATTCTGTGAACT 57.359 30.769 0.00 0.00 0.00 3.01
2461 2646 6.071672 TGTTTTGGATTCTGTGAACTTGTTCA 60.072 34.615 11.62 11.62 0.00 3.18
2464 2649 6.317789 TGGATTCTGTGAACTTGTTCATTC 57.682 37.500 17.56 7.99 33.02 2.67
2503 2700 2.030946 GCTAGATGAATTGTCACCGTGC 59.969 50.000 0.00 0.00 36.31 5.34
2520 2717 2.856032 CGACGCAAGCAGACAAGG 59.144 61.111 0.00 0.00 45.62 3.61
2521 2718 1.664649 CGACGCAAGCAGACAAGGA 60.665 57.895 0.00 0.00 45.62 3.36
2560 2760 5.162075 GCTGTTCTAGTTTCAGTCGTACAT 58.838 41.667 0.00 0.00 0.00 2.29
2574 2774 1.864711 CGTACATATTGAACGGCCTGG 59.135 52.381 0.00 0.00 33.13 4.45
2575 2775 2.740580 CGTACATATTGAACGGCCTGGT 60.741 50.000 0.00 0.00 33.13 4.00
2576 2776 2.507407 ACATATTGAACGGCCTGGTT 57.493 45.000 0.00 0.00 0.00 3.67
2577 2777 2.802719 ACATATTGAACGGCCTGGTTT 58.197 42.857 0.00 0.00 0.00 3.27
2578 2778 3.161866 ACATATTGAACGGCCTGGTTTT 58.838 40.909 0.00 0.00 0.00 2.43
2579 2779 4.337145 ACATATTGAACGGCCTGGTTTTA 58.663 39.130 0.00 0.00 0.00 1.52
2580 2780 4.953579 ACATATTGAACGGCCTGGTTTTAT 59.046 37.500 0.00 0.00 0.00 1.40
2581 2781 5.420739 ACATATTGAACGGCCTGGTTTTATT 59.579 36.000 0.00 0.00 0.00 1.40
2582 2782 4.882842 ATTGAACGGCCTGGTTTTATTT 57.117 36.364 0.00 0.00 0.00 1.40
2583 2783 5.986501 ATTGAACGGCCTGGTTTTATTTA 57.013 34.783 0.00 0.00 0.00 1.40
2584 2784 5.986501 TTGAACGGCCTGGTTTTATTTAT 57.013 34.783 0.00 0.00 0.00 1.40
2585 2785 5.986501 TGAACGGCCTGGTTTTATTTATT 57.013 34.783 0.00 0.00 0.00 1.40
2586 2786 6.347859 TGAACGGCCTGGTTTTATTTATTT 57.652 33.333 0.00 0.00 0.00 1.40
2587 2787 7.463961 TGAACGGCCTGGTTTTATTTATTTA 57.536 32.000 0.00 0.00 0.00 1.40
2588 2788 8.068892 TGAACGGCCTGGTTTTATTTATTTAT 57.931 30.769 0.00 0.00 0.00 1.40
2625 2825 0.329261 TCTTCAAGATGGGCAGTGGG 59.671 55.000 0.00 0.00 0.00 4.61
2626 2826 1.304381 TTCAAGATGGGCAGTGGGC 60.304 57.895 0.00 0.00 43.74 5.36
2636 2836 4.320456 CAGTGGGCACGGTCAGCT 62.320 66.667 0.00 0.00 36.20 4.24
2637 2837 4.008933 AGTGGGCACGGTCAGCTC 62.009 66.667 0.00 0.00 36.20 4.09
2646 2846 4.577246 GGTCAGCTCGGCGGCTAG 62.577 72.222 19.67 6.80 41.00 3.42
2656 2856 1.411246 TCGGCGGCTAGTGTATTTCAT 59.589 47.619 7.21 0.00 0.00 2.57
2673 2873 9.952030 TGTATTTCATGTCAGTAAATTGGAGTA 57.048 29.630 0.00 0.00 0.00 2.59
2681 2881 6.878923 TGTCAGTAAATTGGAGTACATCTTGG 59.121 38.462 0.00 0.00 0.00 3.61
2682 2882 6.316390 GTCAGTAAATTGGAGTACATCTTGGG 59.684 42.308 0.00 0.00 0.00 4.12
2684 2884 3.737559 AATTGGAGTACATCTTGGGCA 57.262 42.857 0.00 0.00 0.00 5.36
2704 2905 4.152938 GGCAGGCTGAATTTGAATCAAAAC 59.847 41.667 20.86 10.23 36.90 2.43
2707 2908 4.984161 AGGCTGAATTTGAATCAAAACACG 59.016 37.500 12.75 10.32 36.90 4.49
2712 2913 0.665835 TTGAATCAAAACACGCCGCT 59.334 45.000 0.00 0.00 0.00 5.52
2713 2914 0.040514 TGAATCAAAACACGCCGCTG 60.041 50.000 0.00 0.00 0.00 5.18
2714 2915 0.237235 GAATCAAAACACGCCGCTGA 59.763 50.000 0.00 0.00 0.00 4.26
2715 2916 0.881118 AATCAAAACACGCCGCTGAT 59.119 45.000 0.00 0.00 0.00 2.90
2732 2933 5.220624 CCGCTGATTGATGAAAGAGAGAAAG 60.221 44.000 0.00 0.00 0.00 2.62
2749 2980 3.771479 AGAAAGGGAGGGCATTCAAATTC 59.229 43.478 0.00 0.00 0.00 2.17
2759 2995 7.255277 GGAGGGCATTCAAATTCAGAACTATAC 60.255 40.741 0.00 0.00 0.00 1.47
2762 2998 7.864379 GGGCATTCAAATTCAGAACTATACATG 59.136 37.037 0.00 0.00 0.00 3.21
2799 3035 9.489084 AATTAGAAAACCCAAAGCTTATGAAAC 57.511 29.630 0.00 0.00 0.00 2.78
2800 3036 5.528870 AGAAAACCCAAAGCTTATGAAACG 58.471 37.500 0.00 0.00 0.00 3.60
2807 3044 7.438564 ACCCAAAGCTTATGAAACGTAAAATT 58.561 30.769 0.00 0.00 0.00 1.82
2839 3078 7.511028 TCCATTTGTTAAAGTGTAAGGGGAAAT 59.489 33.333 0.00 0.00 0.00 2.17
2840 3079 8.808092 CCATTTGTTAAAGTGTAAGGGGAAATA 58.192 33.333 0.00 0.00 0.00 1.40
2851 3090 8.935741 AGTGTAAGGGGAAATATTTAGGACTAG 58.064 37.037 0.00 0.00 0.00 2.57
2871 3110 7.550196 GGACTAGTTTCCGTTTTATGATTGGTA 59.450 37.037 0.00 0.00 0.00 3.25
2872 3111 8.851541 ACTAGTTTCCGTTTTATGATTGGTAA 57.148 30.769 0.00 0.00 0.00 2.85
2873 3112 9.457436 ACTAGTTTCCGTTTTATGATTGGTAAT 57.543 29.630 0.00 0.00 0.00 1.89
2915 3154 6.939132 AGATCTTATGATTTGAGTTGGCAG 57.061 37.500 0.00 0.00 32.19 4.85
2917 3156 7.288560 AGATCTTATGATTTGAGTTGGCAGAT 58.711 34.615 0.00 0.00 32.19 2.90
2928 3167 4.460382 TGAGTTGGCAGATGAAAGAAATCC 59.540 41.667 0.00 0.00 0.00 3.01
2934 3173 4.463891 GGCAGATGAAAGAAATCCAAAGGA 59.536 41.667 0.00 0.00 35.55 3.36
2939 3178 7.974501 CAGATGAAAGAAATCCAAAGGAATCAG 59.025 37.037 0.00 0.00 34.34 2.90
2953 3192 4.330250 AGGAATCAGTTGTGGTCTGAATG 58.670 43.478 0.00 0.00 43.65 2.67
2973 3212 6.663523 TGAATGCGGAGTATATCAATCCTCTA 59.336 38.462 0.00 0.00 28.50 2.43
2974 3213 5.899120 TGCGGAGTATATCAATCCTCTAC 57.101 43.478 0.00 0.00 0.00 2.59
2975 3214 5.321927 TGCGGAGTATATCAATCCTCTACA 58.678 41.667 0.00 0.00 0.00 2.74
2976 3215 5.773176 TGCGGAGTATATCAATCCTCTACAA 59.227 40.000 0.00 0.00 0.00 2.41
2977 3216 6.266786 TGCGGAGTATATCAATCCTCTACAAA 59.733 38.462 0.00 0.00 0.00 2.83
2978 3217 7.152645 GCGGAGTATATCAATCCTCTACAAAA 58.847 38.462 0.00 0.00 0.00 2.44
2979 3218 7.656137 GCGGAGTATATCAATCCTCTACAAAAA 59.344 37.037 0.00 0.00 0.00 1.94
2981 3220 9.832445 GGAGTATATCAATCCTCTACAAAAACA 57.168 33.333 0.00 0.00 0.00 2.83
3002 3865 0.109597 CGAAAGGCATCACTTGTGGC 60.110 55.000 0.64 0.00 41.96 5.01
3023 3886 2.413765 CCTGAATACCGCGGAGTATACG 60.414 54.545 35.90 13.68 32.58 3.06
3025 3888 3.076621 TGAATACCGCGGAGTATACGAT 58.923 45.455 35.90 8.50 32.58 3.73
3026 3889 3.125829 TGAATACCGCGGAGTATACGATC 59.874 47.826 35.90 14.26 32.58 3.69
3028 3891 0.250640 ACCGCGGAGTATACGATCCT 60.251 55.000 35.90 0.00 33.12 3.24
3029 3892 0.447011 CCGCGGAGTATACGATCCTC 59.553 60.000 24.07 1.44 33.12 3.71
3030 3893 1.440708 CGCGGAGTATACGATCCTCT 58.559 55.000 0.00 0.00 33.12 3.69
3031 3894 1.805345 CGCGGAGTATACGATCCTCTT 59.195 52.381 0.00 0.00 33.12 2.85
3147 4010 7.226720 TGGAAGACGGAATAATGCTTATCTTTC 59.773 37.037 0.00 0.00 0.00 2.62
3255 4119 5.320549 ACAAGAATGGCATAAAGCTTCTG 57.679 39.130 0.00 1.66 44.79 3.02
3278 4142 5.588648 TGCCACTTGCCTAAGTAATGTATTC 59.411 40.000 0.00 0.00 45.12 1.75
3302 4167 9.573133 TTCTGTTTTTCAAGAAGAGAATTTCAC 57.427 29.630 0.00 0.00 33.20 3.18
3306 4171 8.595533 GTTTTTCAAGAAGAGAATTTCACCAAC 58.404 33.333 0.00 0.00 0.00 3.77
3322 4187 2.882137 ACCAACCATCACGTTAAAGTGG 59.118 45.455 19.37 8.09 42.10 4.00
3324 4189 4.066490 CCAACCATCACGTTAAAGTGGTA 58.934 43.478 19.37 3.83 42.05 3.25
3327 4192 4.706035 ACCATCACGTTAAAGTGGTACAA 58.294 39.130 19.37 2.47 44.16 2.41
3332 4197 8.291032 CCATCACGTTAAAGTGGTACAAAATTA 58.709 33.333 19.37 0.00 44.16 1.40
3333 4198 9.109533 CATCACGTTAAAGTGGTACAAAATTAC 57.890 33.333 19.37 0.00 44.16 1.89
3344 4209 7.446319 AGTGGTACAAAATTACCTAGTCCAAAC 59.554 37.037 0.00 0.00 44.16 2.93
3348 4213 4.645863 AAATTACCTAGTCCAAACCCGT 57.354 40.909 0.00 0.00 0.00 5.28
3350 4215 1.176527 TACCTAGTCCAAACCCGTCG 58.823 55.000 0.00 0.00 0.00 5.12
3359 4224 0.732571 CAAACCCGTCGCTGCATAAT 59.267 50.000 0.00 0.00 0.00 1.28
3362 4227 1.578583 ACCCGTCGCTGCATAATTAC 58.421 50.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 0.193574 AGGTTGGGACAGAGGAGGAA 59.806 55.000 0.00 0.00 42.39 3.36
127 130 1.674322 CCGCCACCGACAAGGATTT 60.674 57.895 0.00 0.00 45.00 2.17
175 178 4.400251 CCCTCTCCCCACTCCCGT 62.400 72.222 0.00 0.00 0.00 5.28
178 181 4.741239 TGCCCCTCTCCCCACTCC 62.741 72.222 0.00 0.00 0.00 3.85
179 182 2.610859 TTGCCCCTCTCCCCACTC 60.611 66.667 0.00 0.00 0.00 3.51
182 185 2.935481 CAGTTGCCCCTCTCCCCA 60.935 66.667 0.00 0.00 0.00 4.96
189 198 4.021925 GGACGAGCAGTTGCCCCT 62.022 66.667 0.00 0.00 43.38 4.79
196 205 2.573869 CGGACATGGACGAGCAGT 59.426 61.111 5.49 0.00 0.00 4.40
304 320 3.179265 CCGTCGGCGTCATGTCAC 61.179 66.667 9.28 0.00 36.15 3.67
305 321 3.366915 TCCGTCGGCGTCATGTCA 61.367 61.111 9.28 0.00 36.15 3.58
309 325 4.175489 CTCGTCCGTCGGCGTCAT 62.175 66.667 21.64 0.00 40.32 3.06
341 357 0.905357 CCTTCCCTGACCACGAGATT 59.095 55.000 0.00 0.00 0.00 2.40
342 358 0.978146 CCCTTCCCTGACCACGAGAT 60.978 60.000 0.00 0.00 0.00 2.75
345 361 3.319198 GCCCTTCCCTGACCACGA 61.319 66.667 0.00 0.00 0.00 4.35
348 364 2.935481 CCAGCCCTTCCCTGACCA 60.935 66.667 0.00 0.00 32.03 4.02
353 370 3.003763 GTCGTCCAGCCCTTCCCT 61.004 66.667 0.00 0.00 0.00 4.20
358 375 0.757188 CCTAGATGTCGTCCAGCCCT 60.757 60.000 0.00 0.00 0.00 5.19
396 413 2.530151 TTGCTCCCAGCCTCACCT 60.530 61.111 0.00 0.00 41.51 4.00
404 421 2.673523 CTCCACCCTTGCTCCCAG 59.326 66.667 0.00 0.00 0.00 4.45
435 454 1.296056 AACCTTTTCCGGCATCGACG 61.296 55.000 0.00 0.00 39.00 5.12
436 455 0.168128 CAACCTTTTCCGGCATCGAC 59.832 55.000 0.00 0.00 39.00 4.20
441 460 1.228429 CCTCCAACCTTTTCCGGCA 60.228 57.895 0.00 0.00 0.00 5.69
442 461 1.977009 CCCTCCAACCTTTTCCGGC 60.977 63.158 0.00 0.00 0.00 6.13
443 462 0.322546 CTCCCTCCAACCTTTTCCGG 60.323 60.000 0.00 0.00 0.00 5.14
447 466 0.113190 CTGCCTCCCTCCAACCTTTT 59.887 55.000 0.00 0.00 0.00 2.27
469 491 2.378208 TCCACCAAATCCTTCCACATCA 59.622 45.455 0.00 0.00 0.00 3.07
472 494 3.541242 AATCCACCAAATCCTTCCACA 57.459 42.857 0.00 0.00 0.00 4.17
474 496 4.125124 TCAAATCCACCAAATCCTTCCA 57.875 40.909 0.00 0.00 0.00 3.53
543 569 0.180406 GGTTATGTGAGTGCCCGGAT 59.820 55.000 0.73 0.00 0.00 4.18
544 570 1.600107 GGTTATGTGAGTGCCCGGA 59.400 57.895 0.73 0.00 0.00 5.14
553 579 3.586470 AAATATGGGGCGGTTATGTGA 57.414 42.857 0.00 0.00 0.00 3.58
555 581 3.812882 GCCTAAATATGGGGCGGTTATGT 60.813 47.826 0.00 0.00 36.37 2.29
623 658 2.579738 GACCAAGACGGGCTCCTC 59.420 66.667 0.00 0.00 41.26 3.71
636 671 0.878523 CGGACACAAAAGAGCGACCA 60.879 55.000 0.00 0.00 0.00 4.02
644 679 2.546789 GGTCACTAACCGGACACAAAAG 59.453 50.000 9.46 0.00 38.58 2.27
677 712 2.510691 CCCGCCACATACGTCCAC 60.511 66.667 0.00 0.00 0.00 4.02
683 718 2.049767 CCCCAAACCCGCCACATAC 61.050 63.158 0.00 0.00 0.00 2.39
701 736 0.364515 CGTTCTAACGTTGGTAGCGC 59.635 55.000 11.99 0.00 46.63 5.92
712 747 5.230306 CGAACTGAATCCTCATCGTTCTAAC 59.770 44.000 0.00 0.00 32.05 2.34
713 748 5.124936 TCGAACTGAATCCTCATCGTTCTAA 59.875 40.000 0.00 0.00 36.12 2.10
714 749 4.638865 TCGAACTGAATCCTCATCGTTCTA 59.361 41.667 0.00 0.00 36.12 2.10
715 750 3.444034 TCGAACTGAATCCTCATCGTTCT 59.556 43.478 0.00 0.00 36.12 3.01
716 751 3.548268 GTCGAACTGAATCCTCATCGTTC 59.452 47.826 0.00 0.00 36.12 3.95
717 752 3.056821 TGTCGAACTGAATCCTCATCGTT 60.057 43.478 0.00 0.00 36.12 3.85
718 753 2.492088 TGTCGAACTGAATCCTCATCGT 59.508 45.455 0.00 0.00 36.12 3.73
719 754 3.111838 CTGTCGAACTGAATCCTCATCG 58.888 50.000 0.00 0.00 36.05 3.84
720 755 4.116747 ACTGTCGAACTGAATCCTCATC 57.883 45.455 0.00 0.00 0.00 2.92
721 756 5.860941 ATACTGTCGAACTGAATCCTCAT 57.139 39.130 0.00 0.00 0.00 2.90
722 757 5.661056 AATACTGTCGAACTGAATCCTCA 57.339 39.130 0.00 0.00 0.00 3.86
723 758 6.100004 TGAAATACTGTCGAACTGAATCCTC 58.900 40.000 0.00 0.00 0.00 3.71
724 759 6.037786 TGAAATACTGTCGAACTGAATCCT 57.962 37.500 0.00 0.00 0.00 3.24
725 760 5.292101 CCTGAAATACTGTCGAACTGAATCC 59.708 44.000 0.00 0.00 0.00 3.01
726 761 5.869888 ACCTGAAATACTGTCGAACTGAATC 59.130 40.000 0.00 0.00 0.00 2.52
727 762 5.639506 CACCTGAAATACTGTCGAACTGAAT 59.360 40.000 0.00 0.00 0.00 2.57
728 763 4.988540 CACCTGAAATACTGTCGAACTGAA 59.011 41.667 0.00 0.00 0.00 3.02
729 764 4.279922 TCACCTGAAATACTGTCGAACTGA 59.720 41.667 0.00 0.00 0.00 3.41
730 765 4.556233 TCACCTGAAATACTGTCGAACTG 58.444 43.478 0.00 0.00 0.00 3.16
731 766 4.866508 TCACCTGAAATACTGTCGAACT 57.133 40.909 0.00 0.00 0.00 3.01
732 767 5.917541 TTTCACCTGAAATACTGTCGAAC 57.082 39.130 0.00 0.00 38.94 3.95
733 768 5.818336 TGTTTTCACCTGAAATACTGTCGAA 59.182 36.000 1.35 0.00 42.83 3.71
734 769 5.361427 TGTTTTCACCTGAAATACTGTCGA 58.639 37.500 1.35 0.00 42.83 4.20
735 770 5.666969 TGTTTTCACCTGAAATACTGTCG 57.333 39.130 1.35 0.00 42.83 4.35
759 794 4.597404 TTTGATGCTACCAACAAATGCA 57.403 36.364 0.00 0.00 38.36 3.96
760 795 5.921004 TTTTTGATGCTACCAACAAATGC 57.079 34.783 0.00 0.00 41.42 3.56
762 797 8.674263 TTCAATTTTTGATGCTACCAACAAAT 57.326 26.923 0.00 0.00 41.42 2.32
764 799 9.941325 ATATTCAATTTTTGATGCTACCAACAA 57.059 25.926 0.00 0.00 39.84 2.83
765 800 9.585099 GATATTCAATTTTTGATGCTACCAACA 57.415 29.630 0.00 0.00 39.84 3.33
769 804 9.252962 CTTGGATATTCAATTTTTGATGCTACC 57.747 33.333 0.00 0.00 39.84 3.18
772 807 8.533657 TGTCTTGGATATTCAATTTTTGATGCT 58.466 29.630 0.00 0.00 39.84 3.79
773 808 8.706492 TGTCTTGGATATTCAATTTTTGATGC 57.294 30.769 0.00 0.00 39.84 3.91
778 816 6.692681 CGCGATGTCTTGGATATTCAATTTTT 59.307 34.615 0.00 0.00 0.00 1.94
803 841 1.826487 GAGAGGAGAGGAGCGACCC 60.826 68.421 0.00 0.00 40.05 4.46
804 842 2.184167 CGAGAGGAGAGGAGCGACC 61.184 68.421 0.00 0.00 39.35 4.79
805 843 3.416490 CGAGAGGAGAGGAGCGAC 58.584 66.667 0.00 0.00 0.00 5.19
837 875 0.036105 TATGGTGCTCTGCTGGTGTG 60.036 55.000 0.00 0.00 0.00 3.82
864 907 0.909610 TTCCTTCGGATCTGGGCAGT 60.910 55.000 0.62 0.00 0.00 4.40
986 1030 3.208383 TGGTGTTGGTGCTGTGCG 61.208 61.111 0.00 0.00 0.00 5.34
1002 1057 0.535780 AGTGCAGTGGTGTGATGGTG 60.536 55.000 0.00 0.00 0.00 4.17
1003 1058 1.055849 TAGTGCAGTGGTGTGATGGT 58.944 50.000 3.69 0.00 0.00 3.55
1004 1059 1.270785 TGTAGTGCAGTGGTGTGATGG 60.271 52.381 3.69 0.00 0.00 3.51
1005 1060 1.800586 GTGTAGTGCAGTGGTGTGATG 59.199 52.381 3.69 0.00 0.00 3.07
1006 1061 1.694150 AGTGTAGTGCAGTGGTGTGAT 59.306 47.619 3.69 0.00 0.00 3.06
1007 1062 1.119684 AGTGTAGTGCAGTGGTGTGA 58.880 50.000 3.69 0.00 0.00 3.58
1022 1077 1.666011 CTCTGTACCGCACCAGTGT 59.334 57.895 0.00 0.00 0.00 3.55
1043 1098 2.047465 CGTTGCTCCTCTGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
1094 1150 1.383803 GGCAGAGGTGGAGGGAGAT 60.384 63.158 0.00 0.00 0.00 2.75
1425 1508 2.226269 GACACGAGTCAACCACAGC 58.774 57.895 8.20 0.00 44.34 4.40
1443 1530 4.026228 CAGACGTCAGCTATTTGCATACAG 60.026 45.833 19.50 0.00 45.94 2.74
1449 1536 1.009829 CCCAGACGTCAGCTATTTGC 58.990 55.000 19.50 0.00 43.29 3.68
1480 1567 1.264288 TCGATGTCGATCTCGTCATGG 59.736 52.381 15.15 13.89 45.15 3.66
1567 1654 2.849294 AGAACTGGTGCTCCTTCTTC 57.151 50.000 6.34 4.34 28.00 2.87
1684 1803 0.541764 GGGGCAAGATTGGTTGGTGA 60.542 55.000 0.00 0.00 0.00 4.02
1685 1804 1.876497 CGGGGCAAGATTGGTTGGTG 61.876 60.000 0.00 0.00 0.00 4.17
1686 1805 1.606313 CGGGGCAAGATTGGTTGGT 60.606 57.895 0.00 0.00 0.00 3.67
1688 1807 1.937546 GCTCGGGGCAAGATTGGTTG 61.938 60.000 0.00 0.00 41.35 3.77
1690 1809 2.044946 GCTCGGGGCAAGATTGGT 60.045 61.111 0.00 0.00 41.35 3.67
1693 1812 0.107165 GTTAGGCTCGGGGCAAGATT 60.107 55.000 13.05 0.00 44.01 2.40
1694 1813 1.527370 GTTAGGCTCGGGGCAAGAT 59.473 57.895 13.05 0.00 44.01 2.40
1695 1814 2.987125 GTTAGGCTCGGGGCAAGA 59.013 61.111 13.05 0.00 44.01 3.02
1697 1816 2.585341 TTCGTTAGGCTCGGGGCAA 61.585 57.895 13.05 0.00 44.01 4.52
1699 1818 2.510918 GTTCGTTAGGCTCGGGGC 60.511 66.667 0.00 0.00 40.90 5.80
1700 1819 1.153628 CAGTTCGTTAGGCTCGGGG 60.154 63.158 0.00 0.00 0.00 5.73
1701 1820 0.813184 TACAGTTCGTTAGGCTCGGG 59.187 55.000 0.00 0.00 0.00 5.14
1702 1821 1.468736 GGTACAGTTCGTTAGGCTCGG 60.469 57.143 0.00 0.00 0.00 4.63
1704 1823 3.181492 GGTAGGTACAGTTCGTTAGGCTC 60.181 52.174 0.00 0.00 0.00 4.70
1706 1825 2.159184 GGGTAGGTACAGTTCGTTAGGC 60.159 54.545 0.00 0.00 0.00 3.93
1708 1827 3.426695 CGTGGGTAGGTACAGTTCGTTAG 60.427 52.174 0.00 0.00 0.00 2.34
1709 1828 2.487762 CGTGGGTAGGTACAGTTCGTTA 59.512 50.000 0.00 0.00 0.00 3.18
1711 1830 0.883833 CGTGGGTAGGTACAGTTCGT 59.116 55.000 0.00 0.00 0.00 3.85
1712 1831 0.171903 CCGTGGGTAGGTACAGTTCG 59.828 60.000 0.00 0.00 0.00 3.95
1713 1832 0.533951 CCCGTGGGTAGGTACAGTTC 59.466 60.000 0.00 0.00 0.00 3.01
1714 1833 1.547472 GCCCGTGGGTAGGTACAGTT 61.547 60.000 6.82 0.00 37.65 3.16
1715 1834 1.986210 GCCCGTGGGTAGGTACAGT 60.986 63.158 6.82 0.00 37.65 3.55
1716 1835 2.728435 GGCCCGTGGGTAGGTACAG 61.728 68.421 6.82 0.00 37.65 2.74
1717 1836 2.684655 GGCCCGTGGGTAGGTACA 60.685 66.667 6.82 0.00 37.65 2.90
1718 1837 3.841758 CGGCCCGTGGGTAGGTAC 61.842 72.222 6.82 0.00 37.65 3.34
1719 1838 2.877089 AATCGGCCCGTGGGTAGGTA 62.877 60.000 1.63 0.00 37.65 3.08
1720 1839 2.877089 TAATCGGCCCGTGGGTAGGT 62.877 60.000 1.63 0.00 37.65 3.08
1721 1840 1.688269 TTAATCGGCCCGTGGGTAGG 61.688 60.000 1.63 0.00 37.65 3.18
1722 1841 0.531311 GTTAATCGGCCCGTGGGTAG 60.531 60.000 1.63 1.13 37.65 3.18
1723 1842 0.977108 AGTTAATCGGCCCGTGGGTA 60.977 55.000 1.63 0.00 37.65 3.69
1724 1843 2.248086 GAGTTAATCGGCCCGTGGGT 62.248 60.000 1.63 0.00 37.65 4.51
1725 1844 1.523032 GAGTTAATCGGCCCGTGGG 60.523 63.158 1.63 0.00 38.57 4.61
1732 1851 3.134458 CCTGGAATCTGAGTTAATCGGC 58.866 50.000 0.00 0.00 33.93 5.54
1733 1852 4.372656 GACCTGGAATCTGAGTTAATCGG 58.627 47.826 0.00 0.00 35.40 4.18
1741 1860 1.095600 TCGTCGACCTGGAATCTGAG 58.904 55.000 10.58 0.00 0.00 3.35
1902 2021 1.659262 CGCGGTAGTTGACGACGAAC 61.659 60.000 0.00 0.00 33.74 3.95
2145 2284 1.684983 AGAACAACGACGAGGAGGAAA 59.315 47.619 0.00 0.00 0.00 3.13
2147 2286 0.879765 GAGAACAACGACGAGGAGGA 59.120 55.000 0.00 0.00 0.00 3.71
2149 2288 0.596577 TGGAGAACAACGACGAGGAG 59.403 55.000 0.00 0.00 0.00 3.69
2155 2294 3.241678 CGAATCGAATGGAGAACAACGAC 60.242 47.826 0.00 0.00 41.75 4.34
2157 2311 2.921121 TCGAATCGAATGGAGAACAACG 59.079 45.455 1.57 0.00 35.40 4.10
2158 2312 4.031878 GTCTCGAATCGAATGGAGAACAAC 59.968 45.833 15.68 2.20 37.29 3.32
2160 2314 3.730963 CGTCTCGAATCGAATGGAGAACA 60.731 47.826 15.68 0.00 37.29 3.18
2161 2315 2.784380 CGTCTCGAATCGAATGGAGAAC 59.216 50.000 15.68 9.82 37.29 3.01
2164 2321 1.333931 TCCGTCTCGAATCGAATGGAG 59.666 52.381 18.07 6.18 34.74 3.86
2206 2363 4.465660 TGGTGAAATGTACATGGGAAATGG 59.534 41.667 9.63 0.00 0.00 3.16
2284 2447 4.047822 GAGCATAATCACAAGAGGAGTCG 58.952 47.826 0.00 0.00 0.00 4.18
2286 2449 4.682859 GCAGAGCATAATCACAAGAGGAGT 60.683 45.833 0.00 0.00 0.00 3.85
2287 2450 3.808726 GCAGAGCATAATCACAAGAGGAG 59.191 47.826 0.00 0.00 0.00 3.69
2289 2452 3.806380 AGCAGAGCATAATCACAAGAGG 58.194 45.455 0.00 0.00 0.00 3.69
2290 2453 4.035324 CCAAGCAGAGCATAATCACAAGAG 59.965 45.833 0.00 0.00 0.00 2.85
2301 2464 1.570803 ACTCTCTCCAAGCAGAGCAT 58.429 50.000 0.00 0.00 40.00 3.79
2303 2466 1.202245 CGTACTCTCTCCAAGCAGAGC 60.202 57.143 0.00 0.00 40.00 4.09
2319 2482 1.647213 CACATGTGCACTCGTACGTAC 59.353 52.381 19.41 15.90 0.00 3.67
2320 2483 1.536331 TCACATGTGCACTCGTACGTA 59.464 47.619 21.38 0.00 0.00 3.57
2321 2484 0.312729 TCACATGTGCACTCGTACGT 59.687 50.000 21.38 0.00 0.00 3.57
2322 2485 1.583856 GATCACATGTGCACTCGTACG 59.416 52.381 21.38 9.53 0.00 3.67
2401 2573 6.384305 AGAGATAAAAATCCCCTCTCGAAAGA 59.616 38.462 0.00 0.00 37.89 2.52
2402 2574 6.587273 AGAGATAAAAATCCCCTCTCGAAAG 58.413 40.000 0.00 0.00 37.89 2.62
2407 2579 6.553100 TCTCAGAGAGATAAAAATCCCCTCTC 59.447 42.308 0.00 0.00 46.10 3.20
2408 2580 6.448202 TCTCAGAGAGATAAAAATCCCCTCT 58.552 40.000 0.00 0.00 33.35 3.69
2409 2581 6.739331 TCTCAGAGAGATAAAAATCCCCTC 57.261 41.667 0.00 0.00 33.35 4.30
2455 2640 4.060038 GGATAGCTCCGAGAATGAACAA 57.940 45.455 0.00 0.00 0.00 2.83
2503 2700 1.221466 TTCCTTGTCTGCTTGCGTCG 61.221 55.000 0.00 0.00 0.00 5.12
2544 2741 6.748658 CCGTTCAATATGTACGACTGAAACTA 59.251 38.462 10.45 0.00 42.49 2.24
2545 2742 5.575606 CCGTTCAATATGTACGACTGAAACT 59.424 40.000 10.45 0.00 42.49 2.66
2546 2743 5.723135 GCCGTTCAATATGTACGACTGAAAC 60.723 44.000 10.45 0.00 42.49 2.78
2560 2760 5.986501 AAATAAAACCAGGCCGTTCAATA 57.013 34.783 0.00 0.00 0.00 1.90
2585 2785 9.733556 TGAAGATGGTAGAGCAAAGTAAAATAA 57.266 29.630 0.00 0.00 0.00 1.40
2586 2786 9.733556 TTGAAGATGGTAGAGCAAAGTAAAATA 57.266 29.630 0.00 0.00 0.00 1.40
2587 2787 8.635765 TTGAAGATGGTAGAGCAAAGTAAAAT 57.364 30.769 0.00 0.00 0.00 1.82
2588 2788 7.936847 TCTTGAAGATGGTAGAGCAAAGTAAAA 59.063 33.333 0.00 0.00 0.00 1.52
2607 2807 1.318158 GCCCACTGCCCATCTTGAAG 61.318 60.000 0.00 0.00 0.00 3.02
2619 2819 4.320456 AGCTGACCGTGCCCACTG 62.320 66.667 0.00 0.00 0.00 3.66
2629 2829 4.577246 CTAGCCGCCGAGCTGACC 62.577 72.222 9.82 0.00 44.67 4.02
2630 2830 3.827898 ACTAGCCGCCGAGCTGAC 61.828 66.667 9.82 0.00 44.67 3.51
2631 2831 3.826754 CACTAGCCGCCGAGCTGA 61.827 66.667 9.82 0.00 44.67 4.26
2632 2832 2.076622 ATACACTAGCCGCCGAGCTG 62.077 60.000 9.82 3.80 44.67 4.24
2634 2834 0.529992 AAATACACTAGCCGCCGAGC 60.530 55.000 0.00 0.00 0.00 5.03
2635 2835 1.202371 TGAAATACACTAGCCGCCGAG 60.202 52.381 0.00 0.00 0.00 4.63
2636 2836 0.818938 TGAAATACACTAGCCGCCGA 59.181 50.000 0.00 0.00 0.00 5.54
2637 2837 1.526887 CATGAAATACACTAGCCGCCG 59.473 52.381 0.00 0.00 0.00 6.46
2639 2839 3.194861 TGACATGAAATACACTAGCCGC 58.805 45.455 0.00 0.00 0.00 6.53
2640 2840 4.433615 ACTGACATGAAATACACTAGCCG 58.566 43.478 0.00 0.00 0.00 5.52
2641 2841 7.843490 TTTACTGACATGAAATACACTAGCC 57.157 36.000 0.00 0.00 0.00 3.93
2645 2845 8.862325 TCCAATTTACTGACATGAAATACACT 57.138 30.769 0.00 0.00 0.00 3.55
2646 2846 8.730680 ACTCCAATTTACTGACATGAAATACAC 58.269 33.333 0.00 0.00 0.00 2.90
2656 2856 6.878923 CCAAGATGTACTCCAATTTACTGACA 59.121 38.462 0.00 0.00 0.00 3.58
2673 2873 0.333993 ATTCAGCCTGCCCAAGATGT 59.666 50.000 0.00 0.00 0.00 3.06
2681 2881 3.598019 TTGATTCAAATTCAGCCTGCC 57.402 42.857 0.00 0.00 0.00 4.85
2682 2882 4.751098 TGTTTTGATTCAAATTCAGCCTGC 59.249 37.500 12.39 0.00 33.19 4.85
2684 2884 4.984161 CGTGTTTTGATTCAAATTCAGCCT 59.016 37.500 12.39 0.00 33.19 4.58
2704 2905 0.447406 TTTCATCAATCAGCGGCGTG 59.553 50.000 9.37 5.92 0.00 5.34
2707 2908 2.283298 TCTCTTTCATCAATCAGCGGC 58.717 47.619 0.00 0.00 0.00 6.53
2712 2913 6.378661 TCCCTTTCTCTCTTTCATCAATCA 57.621 37.500 0.00 0.00 0.00 2.57
2713 2914 5.821995 CCTCCCTTTCTCTCTTTCATCAATC 59.178 44.000 0.00 0.00 0.00 2.67
2714 2915 5.339861 CCCTCCCTTTCTCTCTTTCATCAAT 60.340 44.000 0.00 0.00 0.00 2.57
2715 2916 4.018960 CCCTCCCTTTCTCTCTTTCATCAA 60.019 45.833 0.00 0.00 0.00 2.57
2732 2933 2.738743 TCTGAATTTGAATGCCCTCCC 58.261 47.619 0.00 0.00 0.00 4.30
2781 3017 6.394025 TTTACGTTTCATAAGCTTTGGGTT 57.606 33.333 3.20 0.00 37.00 4.11
2825 3062 7.766736 AGTCCTAAATATTTCCCCTTACACT 57.233 36.000 3.39 0.00 0.00 3.55
2826 3063 8.712103 ACTAGTCCTAAATATTTCCCCTTACAC 58.288 37.037 3.39 0.00 0.00 2.90
2827 3064 8.865244 ACTAGTCCTAAATATTTCCCCTTACA 57.135 34.615 3.39 0.00 0.00 2.41
2840 3079 9.901172 ATCATAAAACGGAAACTAGTCCTAAAT 57.099 29.630 0.00 0.00 35.31 1.40
2842 3081 9.158233 CAATCATAAAACGGAAACTAGTCCTAA 57.842 33.333 0.00 0.00 35.31 2.69
2847 3086 8.851541 TTACCAATCATAAAACGGAAACTAGT 57.148 30.769 0.00 0.00 0.00 2.57
2890 3129 7.930325 TCTGCCAACTCAAATCATAAGATCTAG 59.070 37.037 0.00 0.00 31.90 2.43
2915 3154 7.834803 ACTGATTCCTTTGGATTTCTTTCATC 58.165 34.615 0.00 0.00 0.00 2.92
2917 3156 7.069826 ACAACTGATTCCTTTGGATTTCTTTCA 59.930 33.333 0.00 0.00 0.00 2.69
2928 3167 4.136796 TCAGACCACAACTGATTCCTTTG 58.863 43.478 0.00 0.00 39.10 2.77
2934 3173 2.485426 CGCATTCAGACCACAACTGATT 59.515 45.455 0.00 0.00 42.68 2.57
2939 3178 0.798776 CTCCGCATTCAGACCACAAC 59.201 55.000 0.00 0.00 0.00 3.32
2953 3192 5.899120 TGTAGAGGATTGATATACTCCGC 57.101 43.478 0.00 0.00 41.95 5.54
2973 3212 4.037923 AGTGATGCCTTTCGATGTTTTTGT 59.962 37.500 0.00 0.00 0.00 2.83
2974 3213 4.549458 AGTGATGCCTTTCGATGTTTTTG 58.451 39.130 0.00 0.00 0.00 2.44
2975 3214 4.853924 AGTGATGCCTTTCGATGTTTTT 57.146 36.364 0.00 0.00 0.00 1.94
2976 3215 4.037923 ACAAGTGATGCCTTTCGATGTTTT 59.962 37.500 0.00 0.00 0.00 2.43
2977 3216 3.569701 ACAAGTGATGCCTTTCGATGTTT 59.430 39.130 0.00 0.00 0.00 2.83
2978 3217 3.058016 CACAAGTGATGCCTTTCGATGTT 60.058 43.478 0.00 0.00 0.00 2.71
2979 3218 2.485426 CACAAGTGATGCCTTTCGATGT 59.515 45.455 0.00 0.00 0.00 3.06
2981 3220 2.086869 CCACAAGTGATGCCTTTCGAT 58.913 47.619 0.94 0.00 0.00 3.59
2983 3222 0.109597 GCCACAAGTGATGCCTTTCG 60.110 55.000 0.94 0.00 0.00 3.46
2984 3223 0.244721 GGCCACAAGTGATGCCTTTC 59.755 55.000 11.66 0.00 40.77 2.62
3002 3865 2.413765 CGTATACTCCGCGGTATTCAGG 60.414 54.545 27.15 10.72 34.65 3.86
3040 3903 4.645588 TCATTGCAACAGATGGCATATGAA 59.354 37.500 27.33 12.14 40.17 2.57
3043 3906 5.510690 CCAATCATTGCAACAGATGGCATAT 60.511 40.000 14.83 0.00 40.17 1.78
3045 3908 3.431626 CCAATCATTGCAACAGATGGCAT 60.432 43.478 14.83 0.00 40.17 4.40
3107 3970 1.895798 TCTTCCACTCGCTCAAGTCAT 59.104 47.619 0.00 0.00 0.00 3.06
3147 4010 1.380524 CCATTCTGGAAGCTGAGCTG 58.619 55.000 8.16 0.00 40.96 4.24
3207 4070 3.766691 GTGCAGCAATGGCCCCTG 61.767 66.667 0.00 2.65 42.56 4.45
3234 4098 4.110482 GCAGAAGCTTTATGCCATTCTTG 58.890 43.478 21.02 0.72 44.23 3.02
3255 4119 5.823045 AGAATACATTACTTAGGCAAGTGGC 59.177 40.000 11.08 0.00 44.81 5.01
3278 4142 7.975616 TGGTGAAATTCTCTTCTTGAAAAACAG 59.024 33.333 0.00 0.00 0.00 3.16
3288 4152 5.474876 GTGATGGTTGGTGAAATTCTCTTCT 59.525 40.000 0.00 0.00 0.00 2.85
3289 4153 5.617751 CGTGATGGTTGGTGAAATTCTCTTC 60.618 44.000 0.00 0.00 0.00 2.87
3302 4167 2.882137 ACCACTTTAACGTGATGGTTGG 59.118 45.455 13.31 0.00 40.86 3.77
3306 4171 5.676532 TTTGTACCACTTTAACGTGATGG 57.323 39.130 13.31 0.00 37.06 3.51
3322 4187 6.128200 CGGGTTTGGACTAGGTAATTTTGTAC 60.128 42.308 0.00 0.00 0.00 2.90
3324 4189 4.763279 CGGGTTTGGACTAGGTAATTTTGT 59.237 41.667 0.00 0.00 0.00 2.83
3327 4192 4.582869 GACGGGTTTGGACTAGGTAATTT 58.417 43.478 0.00 0.00 0.00 1.82
3332 4197 1.969862 CGACGGGTTTGGACTAGGT 59.030 57.895 0.00 0.00 0.00 3.08
3333 4198 1.447314 GCGACGGGTTTGGACTAGG 60.447 63.158 0.00 0.00 0.00 3.02
3344 4209 1.577468 TGTAATTATGCAGCGACGGG 58.423 50.000 0.00 0.00 0.00 5.28
3348 4213 5.112686 TGTGTACATGTAATTATGCAGCGA 58.887 37.500 7.25 0.00 0.00 4.93
3350 4215 9.729023 TTAATTGTGTACATGTAATTATGCAGC 57.271 29.630 7.25 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.