Multiple sequence alignment - TraesCS1B01G207400

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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 TraesCS1B01G207400 chr1B 100.000 5761 0 0 1 5761 374850031 374855791 0.000000e+00 10639.0
1 TraesCS1B01G207400 chr1B 73.901 2594 607 55 2205 4761 205878253 205875693 0.000000e+00 976.0
2 TraesCS1B01G207400 chr1B 96.648 358 10 2 1 358 374851574 374851219 1.380000e-165 593.0
3 TraesCS1B01G207400 chr1B 74.020 1428 319 40 3354 4761 675253660 675255055 8.500000e-148 534.0
4 TraesCS1B01G207400 chr1B 89.474 57 4 1 4705 4761 210180465 210180411 2.880000e-08 71.3
5 TraesCS1B01G207400 chr3D 91.884 2957 204 11 1828 4761 341258044 341255101 0.000000e+00 4098.0
6 TraesCS1B01G207400 chr3D 73.146 3102 761 60 1627 4701 552411659 552414715 0.000000e+00 1048.0
7 TraesCS1B01G207400 chr3D 74.799 2234 506 43 2559 4761 51731377 51733584 0.000000e+00 953.0
8 TraesCS1B01G207400 chr3D 74.807 909 208 14 3416 4318 120099017 120098124 1.950000e-104 390.0
9 TraesCS1B01G207400 chr3D 94.595 37 2 0 4704 4740 451376163 451376199 2.240000e-04 58.4
10 TraesCS1B01G207400 chr7D 95.145 1792 79 6 2976 4766 509906346 509908130 0.000000e+00 2820.0
11 TraesCS1B01G207400 chr7D 93.700 1381 80 2 1600 2979 509900350 509901724 0.000000e+00 2061.0
12 TraesCS1B01G207400 chr7D 90.458 765 71 2 4997 5761 623370572 623369810 0.000000e+00 1007.0
13 TraesCS1B01G207400 chr7D 88.366 765 80 4 4998 5761 336628652 336627896 0.000000e+00 911.0
14 TraesCS1B01G207400 chr4A 97.690 1602 21 6 1 1587 453032443 453034043 0.000000e+00 2739.0
15 TraesCS1B01G207400 chr4A 96.648 358 10 2 1 358 453034000 453033645 1.380000e-165 593.0
16 TraesCS1B01G207400 chr2A 97.505 1603 22 5 1 1587 558945626 558947226 0.000000e+00 2723.0
17 TraesCS1B01G207400 chr2A 96.239 1542 36 9 1 1522 642980177 642978638 0.000000e+00 2507.0
18 TraesCS1B01G207400 chr2A 96.927 358 9 2 1 358 558947183 558946828 2.970000e-167 599.0
19 TraesCS1B01G207400 chr2A 90.000 370 36 1 3527 3896 209403794 209404162 1.450000e-130 477.0
20 TraesCS1B01G207400 chr4B 95.503 1601 31 15 2 1587 386222174 386220600 0.000000e+00 2519.0
21 TraesCS1B01G207400 chr4B 97.690 736 14 3 855 1587 386217693 386216958 0.000000e+00 1262.0
22 TraesCS1B01G207400 chr4B 83.639 764 124 1 4998 5761 558626003 558625241 0.000000e+00 717.0
23 TraesCS1B01G207400 chr4B 71.889 2451 601 82 2353 4761 66871830 66869426 3.790000e-176 628.0
24 TraesCS1B01G207400 chr4B 95.822 359 13 2 1 358 386218822 386219179 3.870000e-161 579.0
25 TraesCS1B01G207400 chr7B 96.599 1529 27 7 74 1587 567612771 567611253 0.000000e+00 2512.0
26 TraesCS1B01G207400 chr7B 88.366 765 87 2 4998 5761 252237108 252237871 0.000000e+00 918.0
27 TraesCS1B01G207400 chr7B 84.856 766 112 3 4998 5761 557202150 557202913 0.000000e+00 769.0
28 TraesCS1B01G207400 chr7B 84.375 768 107 8 4998 5761 605915509 605914751 0.000000e+00 741.0
29 TraesCS1B01G207400 chr6B 95.208 1565 41 22 1 1561 477690183 477691717 0.000000e+00 2444.0
30 TraesCS1B01G207400 chr6B 84.020 1796 250 25 2996 4765 181956863 181955079 0.000000e+00 1692.0
31 TraesCS1B01G207400 chr6B 92.506 774 45 4 4000 4766 713502015 713501248 0.000000e+00 1096.0
32 TraesCS1B01G207400 chr6B 90.707 764 71 0 4998 5761 716339937 716339174 0.000000e+00 1018.0
33 TraesCS1B01G207400 chr6B 93.142 452 26 3 4316 4767 58849577 58850023 0.000000e+00 658.0
34 TraesCS1B01G207400 chr2B 95.990 1197 20 5 1 1182 776065515 776066698 0.000000e+00 1919.0
35 TraesCS1B01G207400 chr2B 92.995 1242 69 14 359 1587 799052181 799053417 0.000000e+00 1796.0
36 TraesCS1B01G207400 chr2B 93.997 1166 54 12 434 1587 183313112 183311951 0.000000e+00 1751.0
37 TraesCS1B01G207400 chr3B 93.793 1176 71 1 3592 4767 758726887 758725714 0.000000e+00 1766.0
38 TraesCS1B01G207400 chr3B 88.482 764 88 0 4998 5761 405729752 405728989 0.000000e+00 924.0
39 TraesCS1B01G207400 chr3B 76.917 1265 258 24 3509 4761 787601111 787602353 0.000000e+00 688.0
40 TraesCS1B01G207400 chr7A 93.085 1128 69 6 2699 3824 32780945 32782065 0.000000e+00 1642.0
41 TraesCS1B01G207400 chr7A 91.480 892 51 4 3820 4710 32795415 32796282 0.000000e+00 1203.0
42 TraesCS1B01G207400 chr7A 82.768 766 128 2 4997 5761 50363651 50364413 0.000000e+00 680.0
43 TraesCS1B01G207400 chr7A 97.059 34 0 1 5193 5225 537793210 537793243 8.060000e-04 56.5
44 TraesCS1B01G207400 chr6A 91.445 1204 83 15 359 1549 210790732 210791928 0.000000e+00 1635.0
45 TraesCS1B01G207400 chr6A 83.654 832 122 11 3221 4047 116702691 116701869 0.000000e+00 771.0
46 TraesCS1B01G207400 chr6A 97.765 358 7 1 1 358 573150979 573150623 2.950000e-172 616.0
47 TraesCS1B01G207400 chr6A 75.476 787 169 22 3966 4738 600761774 600762550 4.240000e-96 363.0
48 TraesCS1B01G207400 chr6A 87.692 65 6 1 4703 4767 7118654 7118592 2.230000e-09 75.0
49 TraesCS1B01G207400 chr6A 100.000 31 0 0 4704 4734 59791423 59791453 2.240000e-04 58.4
50 TraesCS1B01G207400 chr2D 90.464 1185 106 6 3527 4709 194801304 194802483 0.000000e+00 1555.0
51 TraesCS1B01G207400 chr2D 91.375 429 32 3 4334 4761 544578427 544578851 2.990000e-162 582.0
52 TraesCS1B01G207400 chr2D 97.222 36 1 0 4705 4740 533885585 533885620 1.730000e-05 62.1
53 TraesCS1B01G207400 chr1A 90.977 1075 88 5 3642 4712 561767005 561765936 0.000000e+00 1439.0
54 TraesCS1B01G207400 chr1A 76.699 1030 203 30 3748 4761 412271998 412270990 6.570000e-149 538.0
55 TraesCS1B01G207400 chr1A 89.238 223 18 4 4766 4983 347917482 347917703 2.050000e-69 274.0
56 TraesCS1B01G207400 chrUn 97.554 736 15 3 855 1587 414075111 414074376 0.000000e+00 1256.0
57 TraesCS1B01G207400 chrUn 95.349 86 3 1 4658 4742 225030513 225030598 1.010000e-27 135.0
58 TraesCS1B01G207400 chr5B 96.893 708 22 0 3989 4696 532105777 532105070 0.000000e+00 1186.0
59 TraesCS1B01G207400 chr1D 91.116 484 38 1 4998 5481 484370480 484370002 0.000000e+00 651.0
60 TraesCS1B01G207400 chr1D 76.511 1175 253 21 3567 4728 383697668 383698832 2.280000e-173 619.0
61 TraesCS1B01G207400 chr1D 70.745 2779 714 86 2022 4761 75530066 75527348 2.360000e-148 536.0
62 TraesCS1B01G207400 chr1D 76.730 954 204 16 3751 4696 434596197 434597140 3.080000e-142 516.0
63 TraesCS1B01G207400 chr1D 90.813 283 26 0 5479 5761 484333038 484332756 4.210000e-101 379.0
64 TraesCS1B01G207400 chr1D 90.000 220 19 3 4766 4983 275596755 275596973 1.220000e-71 281.0
65 TraesCS1B01G207400 chr5A 75.643 1244 279 21 3431 4665 554597026 554598254 1.070000e-166 597.0
66 TraesCS1B01G207400 chr5D 73.062 1058 238 39 3515 4551 564768761 564767730 1.200000e-86 331.0
67 TraesCS1B01G207400 chr5D 73.166 954 232 18 3380 4318 434562253 434563197 7.200000e-84 322.0
68 TraesCS1B01G207400 chr6D 76.323 359 79 6 3963 4318 295041206 295041561 2.740000e-43 187.0
69 TraesCS1B01G207400 chr6D 78.114 297 59 5 3963 4256 294959565 294959858 3.550000e-42 183.0


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 TraesCS1B01G207400 chr1B 374850031 374855791 5760 False 10639.0 10639 100.0000 1 5761 1 chr1B.!!$F1 5760
1 TraesCS1B01G207400 chr1B 205875693 205878253 2560 True 976.0 976 73.9010 2205 4761 1 chr1B.!!$R1 2556
2 TraesCS1B01G207400 chr1B 675253660 675255055 1395 False 534.0 534 74.0200 3354 4761 1 chr1B.!!$F2 1407
3 TraesCS1B01G207400 chr3D 341255101 341258044 2943 True 4098.0 4098 91.8840 1828 4761 1 chr3D.!!$R2 2933
4 TraesCS1B01G207400 chr3D 552411659 552414715 3056 False 1048.0 1048 73.1460 1627 4701 1 chr3D.!!$F3 3074
5 TraesCS1B01G207400 chr3D 51731377 51733584 2207 False 953.0 953 74.7990 2559 4761 1 chr3D.!!$F1 2202
6 TraesCS1B01G207400 chr3D 120098124 120099017 893 True 390.0 390 74.8070 3416 4318 1 chr3D.!!$R1 902
7 TraesCS1B01G207400 chr7D 509906346 509908130 1784 False 2820.0 2820 95.1450 2976 4766 1 chr7D.!!$F2 1790
8 TraesCS1B01G207400 chr7D 509900350 509901724 1374 False 2061.0 2061 93.7000 1600 2979 1 chr7D.!!$F1 1379
9 TraesCS1B01G207400 chr7D 623369810 623370572 762 True 1007.0 1007 90.4580 4997 5761 1 chr7D.!!$R2 764
10 TraesCS1B01G207400 chr7D 336627896 336628652 756 True 911.0 911 88.3660 4998 5761 1 chr7D.!!$R1 763
11 TraesCS1B01G207400 chr4A 453032443 453034043 1600 False 2739.0 2739 97.6900 1 1587 1 chr4A.!!$F1 1586
12 TraesCS1B01G207400 chr2A 558945626 558947226 1600 False 2723.0 2723 97.5050 1 1587 1 chr2A.!!$F2 1586
13 TraesCS1B01G207400 chr2A 642978638 642980177 1539 True 2507.0 2507 96.2390 1 1522 1 chr2A.!!$R2 1521
14 TraesCS1B01G207400 chr4B 386216958 386222174 5216 True 1890.5 2519 96.5965 2 1587 2 chr4B.!!$R3 1585
15 TraesCS1B01G207400 chr4B 558625241 558626003 762 True 717.0 717 83.6390 4998 5761 1 chr4B.!!$R2 763
16 TraesCS1B01G207400 chr4B 66869426 66871830 2404 True 628.0 628 71.8890 2353 4761 1 chr4B.!!$R1 2408
17 TraesCS1B01G207400 chr7B 567611253 567612771 1518 True 2512.0 2512 96.5990 74 1587 1 chr7B.!!$R1 1513
18 TraesCS1B01G207400 chr7B 252237108 252237871 763 False 918.0 918 88.3660 4998 5761 1 chr7B.!!$F1 763
19 TraesCS1B01G207400 chr7B 557202150 557202913 763 False 769.0 769 84.8560 4998 5761 1 chr7B.!!$F2 763
20 TraesCS1B01G207400 chr7B 605914751 605915509 758 True 741.0 741 84.3750 4998 5761 1 chr7B.!!$R2 763
21 TraesCS1B01G207400 chr6B 477690183 477691717 1534 False 2444.0 2444 95.2080 1 1561 1 chr6B.!!$F2 1560
22 TraesCS1B01G207400 chr6B 181955079 181956863 1784 True 1692.0 1692 84.0200 2996 4765 1 chr6B.!!$R1 1769
23 TraesCS1B01G207400 chr6B 713501248 713502015 767 True 1096.0 1096 92.5060 4000 4766 1 chr6B.!!$R2 766
24 TraesCS1B01G207400 chr6B 716339174 716339937 763 True 1018.0 1018 90.7070 4998 5761 1 chr6B.!!$R3 763
25 TraesCS1B01G207400 chr2B 776065515 776066698 1183 False 1919.0 1919 95.9900 1 1182 1 chr2B.!!$F1 1181
26 TraesCS1B01G207400 chr2B 799052181 799053417 1236 False 1796.0 1796 92.9950 359 1587 1 chr2B.!!$F2 1228
27 TraesCS1B01G207400 chr2B 183311951 183313112 1161 True 1751.0 1751 93.9970 434 1587 1 chr2B.!!$R1 1153
28 TraesCS1B01G207400 chr3B 758725714 758726887 1173 True 1766.0 1766 93.7930 3592 4767 1 chr3B.!!$R2 1175
29 TraesCS1B01G207400 chr3B 405728989 405729752 763 True 924.0 924 88.4820 4998 5761 1 chr3B.!!$R1 763
30 TraesCS1B01G207400 chr3B 787601111 787602353 1242 False 688.0 688 76.9170 3509 4761 1 chr3B.!!$F1 1252
31 TraesCS1B01G207400 chr7A 32780945 32782065 1120 False 1642.0 1642 93.0850 2699 3824 1 chr7A.!!$F1 1125
32 TraesCS1B01G207400 chr7A 32795415 32796282 867 False 1203.0 1203 91.4800 3820 4710 1 chr7A.!!$F2 890
33 TraesCS1B01G207400 chr7A 50363651 50364413 762 False 680.0 680 82.7680 4997 5761 1 chr7A.!!$F3 764
34 TraesCS1B01G207400 chr6A 210790732 210791928 1196 False 1635.0 1635 91.4450 359 1549 1 chr6A.!!$F2 1190
35 TraesCS1B01G207400 chr6A 116701869 116702691 822 True 771.0 771 83.6540 3221 4047 1 chr6A.!!$R2 826
36 TraesCS1B01G207400 chr6A 600761774 600762550 776 False 363.0 363 75.4760 3966 4738 1 chr6A.!!$F3 772
37 TraesCS1B01G207400 chr2D 194801304 194802483 1179 False 1555.0 1555 90.4640 3527 4709 1 chr2D.!!$F1 1182
38 TraesCS1B01G207400 chr1A 561765936 561767005 1069 True 1439.0 1439 90.9770 3642 4712 1 chr1A.!!$R2 1070
39 TraesCS1B01G207400 chr1A 412270990 412271998 1008 True 538.0 538 76.6990 3748 4761 1 chr1A.!!$R1 1013
40 TraesCS1B01G207400 chrUn 414074376 414075111 735 True 1256.0 1256 97.5540 855 1587 1 chrUn.!!$R1 732
41 TraesCS1B01G207400 chr5B 532105070 532105777 707 True 1186.0 1186 96.8930 3989 4696 1 chr5B.!!$R1 707
42 TraesCS1B01G207400 chr1D 383697668 383698832 1164 False 619.0 619 76.5110 3567 4728 1 chr1D.!!$F2 1161
43 TraesCS1B01G207400 chr1D 75527348 75530066 2718 True 536.0 536 70.7450 2022 4761 1 chr1D.!!$R1 2739
44 TraesCS1B01G207400 chr1D 434596197 434597140 943 False 516.0 516 76.7300 3751 4696 1 chr1D.!!$F3 945
45 TraesCS1B01G207400 chr5A 554597026 554598254 1228 False 597.0 597 75.6430 3431 4665 1 chr5A.!!$F1 1234
46 TraesCS1B01G207400 chr5D 564767730 564768761 1031 True 331.0 331 73.0620 3515 4551 1 chr5D.!!$R1 1036
47 TraesCS1B01G207400 chr5D 434562253 434563197 944 False 322.0 322 73.1660 3380 4318 1 chr5D.!!$F1 938

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
832 851 1.509644 CGCAGAAAAGGTGCTCAGCA 61.510 55.0 0.0 0.0 38.88 4.41 F
2398 6059 0.107081 TACCCCTCACAAACACCACG 59.893 55.0 0.0 0.0 0.00 4.94 F
3376 7046 0.323908 CCCCCAAAAATACCTCGGCA 60.324 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 6070 0.100861 CCCGAGAAAGGCGAGTCTAC 59.899 60.0 0.0 0.0 0.0 2.59 R
4011 7725 0.607489 GCCCAGATCAATCCCATCCG 60.607 60.0 0.0 0.0 0.0 4.18 R
4864 8631 0.107017 AAGAGGTTCATGATGGCGGG 60.107 55.0 0.0 0.0 0.0 6.13 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
33 34 5.621197 TGCTAATTTTTGCGTGTCAGTAT 57.379 34.783 0.00 0.00 0.00 2.12
832 851 1.509644 CGCAGAAAAGGTGCTCAGCA 61.510 55.000 0.00 0.00 38.88 4.41
1587 5246 5.940192 TTGTGGTACTTCTGTGCAATTAG 57.060 39.130 0.00 0.00 0.00 1.73
1588 5247 4.968259 TGTGGTACTTCTGTGCAATTAGT 58.032 39.130 0.00 0.00 0.00 2.24
1589 5248 5.373222 TGTGGTACTTCTGTGCAATTAGTT 58.627 37.500 0.00 0.00 0.00 2.24
1590 5249 5.825679 TGTGGTACTTCTGTGCAATTAGTTT 59.174 36.000 0.00 0.00 0.00 2.66
1591 5250 6.320164 TGTGGTACTTCTGTGCAATTAGTTTT 59.680 34.615 0.00 0.00 0.00 2.43
1592 5251 6.636850 GTGGTACTTCTGTGCAATTAGTTTTG 59.363 38.462 0.00 0.00 0.00 2.44
1593 5252 6.320164 TGGTACTTCTGTGCAATTAGTTTTGT 59.680 34.615 0.00 0.00 0.00 2.83
1594 5253 6.636850 GGTACTTCTGTGCAATTAGTTTTGTG 59.363 38.462 0.00 0.00 0.00 3.33
1595 5254 5.043248 ACTTCTGTGCAATTAGTTTTGTGC 58.957 37.500 0.00 0.00 37.51 4.57
1596 5255 4.916983 TCTGTGCAATTAGTTTTGTGCT 57.083 36.364 0.00 0.00 37.87 4.40
1597 5256 4.858935 TCTGTGCAATTAGTTTTGTGCTC 58.141 39.130 0.00 0.00 37.87 4.26
1598 5257 4.580167 TCTGTGCAATTAGTTTTGTGCTCT 59.420 37.500 0.00 0.00 37.87 4.09
1599 5258 5.067674 TCTGTGCAATTAGTTTTGTGCTCTT 59.932 36.000 0.00 0.00 37.87 2.85
1600 5259 5.659463 TGTGCAATTAGTTTTGTGCTCTTT 58.341 33.333 0.00 0.00 37.87 2.52
1601 5260 6.105333 TGTGCAATTAGTTTTGTGCTCTTTT 58.895 32.000 0.00 0.00 37.87 2.27
1656 5315 5.157770 TGAACTTCCCCTACTGGATAGAT 57.842 43.478 0.00 0.00 35.39 1.98
1661 5320 4.194678 TCCCCTACTGGATAGATCGTTT 57.805 45.455 0.00 0.00 35.39 3.60
1670 5329 3.317149 TGGATAGATCGTTTACCTGGTCG 59.683 47.826 0.63 0.46 0.00 4.79
1677 5336 4.789012 TCGTTTACCTGGTCGAATAAGT 57.211 40.909 0.63 0.00 0.00 2.24
1679 5338 4.218200 TCGTTTACCTGGTCGAATAAGTGA 59.782 41.667 0.63 0.00 0.00 3.41
1733 5392 4.846779 TTTCATTAACACTGCTTGGGAC 57.153 40.909 0.00 0.00 0.00 4.46
1736 5395 2.738587 TTAACACTGCTTGGGACCAA 57.261 45.000 3.43 3.43 0.00 3.67
1755 5414 3.755378 CCAATCTTTCCCTGACTCAACTG 59.245 47.826 0.00 0.00 0.00 3.16
1756 5415 4.392940 CAATCTTTCCCTGACTCAACTGT 58.607 43.478 0.00 0.00 0.00 3.55
1757 5416 3.753294 TCTTTCCCTGACTCAACTGTC 57.247 47.619 0.00 0.00 37.47 3.51
1760 5419 2.685106 TCCCTGACTCAACTGTCTCT 57.315 50.000 0.00 0.00 37.79 3.10
1821 5480 6.294473 CCTCTAATTATCAGCATCAACACCT 58.706 40.000 0.00 0.00 0.00 4.00
1929 5588 2.032528 CCCCGCTGCTCTCAAACA 59.967 61.111 0.00 0.00 0.00 2.83
1949 5608 1.927008 CCCCCTTTCCCTAACCCGT 60.927 63.158 0.00 0.00 0.00 5.28
1951 5610 1.494716 CCCCTTTCCCTAACCCGTGT 61.495 60.000 0.00 0.00 0.00 4.49
1994 5654 0.521867 TACGATCGTGGCGAAAGTCG 60.522 55.000 30.23 10.20 40.26 4.18
2014 5674 2.480244 CGATTCTTCCGATCTCTGTGCA 60.480 50.000 0.00 0.00 0.00 4.57
2139 5800 2.358247 ACCGCATCACCCGTGAAC 60.358 61.111 0.91 0.00 43.58 3.18
2307 5968 5.298026 TCACACGAATCAAAAGTGGAAATCA 59.702 36.000 0.00 0.00 39.95 2.57
2337 5998 4.844349 TTCTTTTCCTCCATTCTCGGAT 57.156 40.909 0.00 0.00 33.56 4.18
2374 6035 4.392940 ACATGGAACTTCTCACTCCAAAG 58.607 43.478 0.00 0.00 42.41 2.77
2398 6059 0.107081 TACCCCTCACAAACACCACG 59.893 55.000 0.00 0.00 0.00 4.94
2407 6068 0.511221 CAAACACCACGGCTACTTCG 59.489 55.000 0.00 0.00 0.00 3.79
2409 6070 3.179265 CACCACGGCTACTTCGCG 61.179 66.667 0.00 0.00 0.00 5.87
2417 6078 3.130835 GCTACTTCGCGTAGACTCG 57.869 57.895 20.14 5.52 46.98 4.18
2496 6157 1.131303 TGGTCCTGACGGATTTGGGT 61.131 55.000 0.00 0.00 42.43 4.51
2509 6170 1.138568 TTTGGGTCGGGTTTCTACCA 58.861 50.000 0.00 0.00 46.96 3.25
2553 6214 6.543430 AGCAGAAAGTGACAGATCTATTCT 57.457 37.500 0.00 0.00 33.90 2.40
2557 6218 7.499292 CAGAAAGTGACAGATCTATTCTCCAT 58.501 38.462 0.00 0.00 29.93 3.41
2582 6243 5.791336 TCTACAATCACTCCGCTGATATT 57.209 39.130 0.00 0.00 30.27 1.28
2584 6245 6.582636 TCTACAATCACTCCGCTGATATTTT 58.417 36.000 0.00 0.00 30.27 1.82
2764 6425 3.320826 CCGGATCAAACAGGTTTCCTTTT 59.679 43.478 0.00 0.00 0.00 2.27
2890 6553 0.963962 TTCGACTCGGTTAACTGGCT 59.036 50.000 14.44 0.00 0.00 4.75
2917 6580 5.197451 TCTCCTCTCTATTCTCAAGGTCAC 58.803 45.833 0.00 0.00 0.00 3.67
3166 6832 2.158623 CCCTGCCCTATTCTGCAATACA 60.159 50.000 0.00 0.00 36.98 2.29
3376 7046 0.323908 CCCCCAAAAATACCTCGGCA 60.324 55.000 0.00 0.00 0.00 5.69
3557 7252 1.072505 GTTTCTCCCTGCCCGTCAA 59.927 57.895 0.00 0.00 0.00 3.18
3645 7342 1.226746 GCTAAGTGTCTGGTTGCGTT 58.773 50.000 0.00 0.00 0.00 4.84
3657 7354 0.379316 GTTGCGTTGGACCGAGTTTT 59.621 50.000 0.00 0.00 0.00 2.43
3828 7538 2.014010 AGCAAAAATGCCTCCTTCCA 57.986 45.000 0.00 0.00 34.90 3.53
3913 7623 3.581332 ACGGTTTATCCACCTTCTTCTGA 59.419 43.478 0.00 0.00 34.22 3.27
3923 7635 5.067936 TCCACCTTCTTCTGATTAGATCGTC 59.932 44.000 0.00 0.00 31.81 4.20
4011 7725 4.988540 TGCATTCGTAGCCACTATATTGAC 59.011 41.667 0.00 0.00 0.00 3.18
4389 8105 1.068588 CTTCCACTGTCCGACAACTCA 59.931 52.381 2.19 0.00 0.00 3.41
4593 8350 2.394632 TGTTACTAGGGGCATCATCGT 58.605 47.619 0.00 0.00 0.00 3.73
4674 8431 2.285977 GTGGCGGGACTATTTTACCTG 58.714 52.381 0.00 0.00 0.00 4.00
4795 8562 3.412722 TTTCAAGGAGAAAGCGGCA 57.587 47.368 1.45 0.00 41.17 5.69
4796 8563 1.686355 TTTCAAGGAGAAAGCGGCAA 58.314 45.000 1.45 0.00 41.17 4.52
4797 8564 1.686355 TTCAAGGAGAAAGCGGCAAA 58.314 45.000 1.45 0.00 32.05 3.68
4798 8565 1.238439 TCAAGGAGAAAGCGGCAAAG 58.762 50.000 1.45 0.00 0.00 2.77
4799 8566 1.202758 TCAAGGAGAAAGCGGCAAAGA 60.203 47.619 1.45 0.00 0.00 2.52
4800 8567 1.198637 CAAGGAGAAAGCGGCAAAGAG 59.801 52.381 1.45 0.00 0.00 2.85
4801 8568 0.957888 AGGAGAAAGCGGCAAAGAGC 60.958 55.000 1.45 0.00 44.65 4.09
4814 8581 4.048241 GCAAAGAGCGTACTAGGATTCT 57.952 45.455 0.00 0.00 0.00 2.40
4815 8582 5.184340 GCAAAGAGCGTACTAGGATTCTA 57.816 43.478 0.00 0.00 0.00 2.10
4816 8583 5.774630 GCAAAGAGCGTACTAGGATTCTAT 58.225 41.667 0.00 0.00 0.00 1.98
4817 8584 5.631512 GCAAAGAGCGTACTAGGATTCTATG 59.368 44.000 0.00 0.00 0.00 2.23
4818 8585 5.379732 AAGAGCGTACTAGGATTCTATGC 57.620 43.478 0.00 0.00 0.00 3.14
4819 8586 4.399219 AGAGCGTACTAGGATTCTATGCA 58.601 43.478 0.00 0.00 0.00 3.96
4820 8587 4.457603 AGAGCGTACTAGGATTCTATGCAG 59.542 45.833 0.00 0.00 0.00 4.41
4821 8588 3.508012 AGCGTACTAGGATTCTATGCAGG 59.492 47.826 0.00 0.00 0.00 4.85
4822 8589 3.506455 GCGTACTAGGATTCTATGCAGGA 59.494 47.826 0.00 0.00 0.00 3.86
4823 8590 4.380023 GCGTACTAGGATTCTATGCAGGAG 60.380 50.000 0.00 0.00 0.00 3.69
4824 8591 4.762765 CGTACTAGGATTCTATGCAGGAGT 59.237 45.833 0.00 0.00 0.00 3.85
4825 8592 5.335269 CGTACTAGGATTCTATGCAGGAGTG 60.335 48.000 0.00 0.00 0.00 3.51
4826 8593 4.809193 ACTAGGATTCTATGCAGGAGTGA 58.191 43.478 0.00 0.00 0.00 3.41
4827 8594 4.586841 ACTAGGATTCTATGCAGGAGTGAC 59.413 45.833 0.00 0.00 0.00 3.67
4828 8595 2.703007 AGGATTCTATGCAGGAGTGACC 59.297 50.000 0.00 0.00 39.35 4.02
4829 8596 2.224402 GGATTCTATGCAGGAGTGACCC 60.224 54.545 0.00 0.00 40.05 4.46
4830 8597 1.951209 TTCTATGCAGGAGTGACCCA 58.049 50.000 0.00 0.00 40.05 4.51
4831 8598 2.180946 TCTATGCAGGAGTGACCCAT 57.819 50.000 0.00 0.00 40.05 4.00
4832 8599 3.328535 TCTATGCAGGAGTGACCCATA 57.671 47.619 0.00 0.00 40.05 2.74
4833 8600 2.965831 TCTATGCAGGAGTGACCCATAC 59.034 50.000 0.00 0.00 40.05 2.39
4834 8601 0.839946 ATGCAGGAGTGACCCATACC 59.160 55.000 0.00 0.00 40.05 2.73
4835 8602 0.252696 TGCAGGAGTGACCCATACCT 60.253 55.000 0.00 0.00 40.05 3.08
4836 8603 0.912486 GCAGGAGTGACCCATACCTT 59.088 55.000 0.00 0.00 40.05 3.50
4837 8604 1.407437 GCAGGAGTGACCCATACCTTG 60.407 57.143 0.00 0.00 40.05 3.61
4838 8605 1.210478 CAGGAGTGACCCATACCTTGG 59.790 57.143 0.00 0.00 46.00 3.61
4846 8613 3.733709 CCATACCTTGGGGATGAGC 57.266 57.895 10.13 0.00 42.33 4.26
4847 8614 0.250467 CCATACCTTGGGGATGAGCG 60.250 60.000 10.13 0.00 42.33 5.03
4848 8615 0.250467 CATACCTTGGGGATGAGCGG 60.250 60.000 2.76 0.00 36.25 5.52
4849 8616 2.056906 ATACCTTGGGGATGAGCGGC 62.057 60.000 0.00 0.00 36.25 6.53
4850 8617 4.113815 CCTTGGGGATGAGCGGCA 62.114 66.667 1.45 0.00 33.58 5.69
4851 8618 2.194056 CTTGGGGATGAGCGGCAT 59.806 61.111 1.45 0.00 40.77 4.40
4852 8619 1.454479 CTTGGGGATGAGCGGCATT 60.454 57.895 1.45 0.00 37.34 3.56
4853 8620 1.731433 CTTGGGGATGAGCGGCATTG 61.731 60.000 1.45 0.00 37.34 2.82
4854 8621 2.908940 GGGGATGAGCGGCATTGG 60.909 66.667 1.45 0.00 37.34 3.16
4855 8622 2.908940 GGGATGAGCGGCATTGGG 60.909 66.667 1.45 0.00 37.34 4.12
4856 8623 2.908940 GGATGAGCGGCATTGGGG 60.909 66.667 1.45 0.00 37.34 4.96
4857 8624 2.192979 GATGAGCGGCATTGGGGA 59.807 61.111 1.45 0.00 37.34 4.81
4858 8625 1.453745 GATGAGCGGCATTGGGGAA 60.454 57.895 1.45 0.00 37.34 3.97
4859 8626 1.000233 ATGAGCGGCATTGGGGAAA 60.000 52.632 1.45 0.00 31.73 3.13
4860 8627 0.397535 ATGAGCGGCATTGGGGAAAT 60.398 50.000 1.45 0.00 31.73 2.17
4871 8638 4.355151 GGGAAATGAACCCGCCAT 57.645 55.556 0.00 0.00 37.85 4.40
4872 8639 2.115510 GGGAAATGAACCCGCCATC 58.884 57.895 0.00 0.00 37.85 3.51
4873 8640 0.682855 GGGAAATGAACCCGCCATCA 60.683 55.000 0.00 0.00 37.85 3.07
4874 8641 1.402787 GGAAATGAACCCGCCATCAT 58.597 50.000 0.00 0.00 37.88 2.45
4875 8642 1.067516 GGAAATGAACCCGCCATCATG 59.932 52.381 0.00 0.00 36.44 3.07
4876 8643 2.023673 GAAATGAACCCGCCATCATGA 58.976 47.619 0.00 0.00 36.44 3.07
4877 8644 2.142356 AATGAACCCGCCATCATGAA 57.858 45.000 0.00 0.00 36.44 2.57
4878 8645 1.392589 ATGAACCCGCCATCATGAAC 58.607 50.000 0.00 0.00 35.06 3.18
4879 8646 0.679640 TGAACCCGCCATCATGAACC 60.680 55.000 0.00 0.00 0.00 3.62
4880 8647 0.394352 GAACCCGCCATCATGAACCT 60.394 55.000 0.00 0.00 0.00 3.50
4881 8648 0.394352 AACCCGCCATCATGAACCTC 60.394 55.000 0.00 0.00 0.00 3.85
4882 8649 1.274703 ACCCGCCATCATGAACCTCT 61.275 55.000 0.00 0.00 0.00 3.69
4883 8650 0.107017 CCCGCCATCATGAACCTCTT 60.107 55.000 0.00 0.00 0.00 2.85
4884 8651 1.019673 CCGCCATCATGAACCTCTTG 58.980 55.000 0.00 0.00 0.00 3.02
4885 8652 0.379669 CGCCATCATGAACCTCTTGC 59.620 55.000 0.00 0.00 0.00 4.01
4886 8653 1.466856 GCCATCATGAACCTCTTGCA 58.533 50.000 0.00 0.00 0.00 4.08
4887 8654 1.404391 GCCATCATGAACCTCTTGCAG 59.596 52.381 0.00 0.00 0.00 4.41
4899 8666 2.803451 CTCTTGCAGGACATCTACGAC 58.197 52.381 0.00 0.00 0.00 4.34
4900 8667 2.164422 CTCTTGCAGGACATCTACGACA 59.836 50.000 0.00 0.00 0.00 4.35
4901 8668 2.760650 TCTTGCAGGACATCTACGACAT 59.239 45.455 0.00 0.00 0.00 3.06
4902 8669 2.584492 TGCAGGACATCTACGACATG 57.416 50.000 0.00 0.00 0.00 3.21
4903 8670 1.824852 TGCAGGACATCTACGACATGT 59.175 47.619 0.00 0.00 37.18 3.21
4904 8671 2.159240 TGCAGGACATCTACGACATGTC 60.159 50.000 16.21 16.21 46.50 3.06
4905 8672 2.099921 GCAGGACATCTACGACATGTCT 59.900 50.000 22.95 12.64 46.46 3.41
4906 8673 3.700154 CAGGACATCTACGACATGTCTG 58.300 50.000 22.95 17.83 46.46 3.51
4907 8674 3.129462 CAGGACATCTACGACATGTCTGT 59.871 47.826 22.95 21.93 46.46 3.41
4908 8675 3.764434 AGGACATCTACGACATGTCTGTT 59.236 43.478 22.95 10.04 46.46 3.16
4909 8676 4.948004 AGGACATCTACGACATGTCTGTTA 59.052 41.667 22.95 13.65 46.46 2.41
4910 8677 5.417894 AGGACATCTACGACATGTCTGTTAA 59.582 40.000 22.95 13.36 46.46 2.01
4911 8678 6.071560 AGGACATCTACGACATGTCTGTTAAA 60.072 38.462 22.95 11.36 46.46 1.52
4912 8679 6.757010 GGACATCTACGACATGTCTGTTAAAT 59.243 38.462 22.95 12.75 46.46 1.40
4913 8680 7.919091 GGACATCTACGACATGTCTGTTAAATA 59.081 37.037 22.95 7.06 46.46 1.40
4914 8681 9.464714 GACATCTACGACATGTCTGTTAAATAT 57.535 33.333 22.95 7.11 44.65 1.28
4927 8694 9.337396 TGTCTGTTAAATATACATGGATTGTCC 57.663 33.333 0.00 0.00 39.87 4.02
4941 8708 5.953183 TGGATTGTCCAATCTTTTCAATCG 58.047 37.500 17.06 0.00 45.00 3.34
4942 8709 5.476599 TGGATTGTCCAATCTTTTCAATCGT 59.523 36.000 17.06 0.00 45.00 3.73
4943 8710 6.015519 TGGATTGTCCAATCTTTTCAATCGTT 60.016 34.615 17.06 0.00 45.00 3.85
4944 8711 6.528072 GGATTGTCCAATCTTTTCAATCGTTC 59.472 38.462 17.06 0.00 44.90 3.95
4945 8712 6.633500 TTGTCCAATCTTTTCAATCGTTCT 57.367 33.333 0.00 0.00 0.00 3.01
4946 8713 7.737972 TTGTCCAATCTTTTCAATCGTTCTA 57.262 32.000 0.00 0.00 0.00 2.10
4947 8714 7.364522 TGTCCAATCTTTTCAATCGTTCTAG 57.635 36.000 0.00 0.00 0.00 2.43
4948 8715 7.158697 TGTCCAATCTTTTCAATCGTTCTAGA 58.841 34.615 0.00 0.00 0.00 2.43
4949 8716 7.117812 TGTCCAATCTTTTCAATCGTTCTAGAC 59.882 37.037 0.00 0.00 0.00 2.59
4950 8717 7.332182 GTCCAATCTTTTCAATCGTTCTAGACT 59.668 37.037 0.00 0.00 0.00 3.24
4951 8718 7.878127 TCCAATCTTTTCAATCGTTCTAGACTT 59.122 33.333 0.00 0.00 0.00 3.01
4952 8719 8.507249 CCAATCTTTTCAATCGTTCTAGACTTT 58.493 33.333 0.00 0.00 0.00 2.66
4953 8720 9.884465 CAATCTTTTCAATCGTTCTAGACTTTT 57.116 29.630 0.00 0.00 0.00 2.27
4954 8721 9.884465 AATCTTTTCAATCGTTCTAGACTTTTG 57.116 29.630 0.00 0.00 0.00 2.44
4955 8722 7.861630 TCTTTTCAATCGTTCTAGACTTTTGG 58.138 34.615 0.00 0.00 0.00 3.28
4956 8723 7.497909 TCTTTTCAATCGTTCTAGACTTTTGGT 59.502 33.333 0.00 0.00 0.00 3.67
4957 8724 7.562454 TTTCAATCGTTCTAGACTTTTGGTT 57.438 32.000 0.00 0.00 0.00 3.67
4958 8725 6.780706 TCAATCGTTCTAGACTTTTGGTTC 57.219 37.500 0.00 0.00 0.00 3.62
4959 8726 5.699458 TCAATCGTTCTAGACTTTTGGTTCC 59.301 40.000 0.00 0.00 0.00 3.62
4960 8727 4.675976 TCGTTCTAGACTTTTGGTTCCA 57.324 40.909 0.00 0.00 0.00 3.53
4961 8728 4.374399 TCGTTCTAGACTTTTGGTTCCAC 58.626 43.478 0.00 0.00 0.00 4.02
4962 8729 4.100498 TCGTTCTAGACTTTTGGTTCCACT 59.900 41.667 0.00 0.00 0.00 4.00
4963 8730 5.302568 TCGTTCTAGACTTTTGGTTCCACTA 59.697 40.000 0.00 0.00 0.00 2.74
4964 8731 5.634020 CGTTCTAGACTTTTGGTTCCACTAG 59.366 44.000 0.00 0.00 0.00 2.57
4965 8732 6.522946 GTTCTAGACTTTTGGTTCCACTAGT 58.477 40.000 0.00 0.00 0.00 2.57
4966 8733 6.742559 TCTAGACTTTTGGTTCCACTAGTT 57.257 37.500 0.00 4.38 0.00 2.24
4967 8734 7.844493 TCTAGACTTTTGGTTCCACTAGTTA 57.156 36.000 0.00 0.00 0.00 2.24
4968 8735 7.893658 TCTAGACTTTTGGTTCCACTAGTTAG 58.106 38.462 0.00 10.81 0.00 2.34
4969 8736 6.496144 AGACTTTTGGTTCCACTAGTTAGT 57.504 37.500 0.00 0.00 36.90 2.24
4989 8756 9.174166 AGTTAGTGCATAAAATGTAAACTAGGG 57.826 33.333 0.00 0.00 30.39 3.53
4990 8757 8.403236 GTTAGTGCATAAAATGTAAACTAGGGG 58.597 37.037 0.00 0.00 30.39 4.79
4991 8758 5.359860 AGTGCATAAAATGTAAACTAGGGGC 59.640 40.000 0.00 0.00 0.00 5.80
4992 8759 4.647399 TGCATAAAATGTAAACTAGGGGCC 59.353 41.667 0.00 0.00 0.00 5.80
4993 8760 4.038763 GCATAAAATGTAAACTAGGGGCCC 59.961 45.833 17.12 17.12 0.00 5.80
4994 8761 2.840640 AAATGTAAACTAGGGGCCCC 57.159 50.000 35.90 35.90 0.00 5.80
4995 8762 1.688750 AATGTAAACTAGGGGCCCCA 58.311 50.000 42.48 26.26 38.92 4.96
5005 8772 4.055227 GGGCCCCAATCAACCCGA 62.055 66.667 12.23 0.00 31.32 5.14
5215 8984 4.577693 GCAGATGATGTGATGCTTTTCCTA 59.422 41.667 0.00 0.00 35.78 2.94
5240 9009 0.761802 GGAGGCCCAGGATCTACTTG 59.238 60.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.111989 TGCAAAAATTTGGACGAATGTTGA 58.888 33.333 7.89 0.00 38.57 3.18
1367 3204 5.163131 ACCCCCTTGCTTTATACGTAATCAT 60.163 40.000 0.00 0.00 0.00 2.45
1561 5220 3.814625 TGCACAGAAGTACCACAATTCA 58.185 40.909 0.00 0.00 0.00 2.57
1656 5315 4.218200 TCACTTATTCGACCAGGTAAACGA 59.782 41.667 0.00 0.00 0.00 3.85
1661 5320 7.417116 GGTTTATCTCACTTATTCGACCAGGTA 60.417 40.741 0.00 0.00 0.00 3.08
1677 5336 7.554959 ACTTTTCTAGAGTGGGTTTATCTCA 57.445 36.000 0.00 0.00 0.00 3.27
1679 5338 7.017254 TCCAACTTTTCTAGAGTGGGTTTATCT 59.983 37.037 4.40 0.00 38.99 1.98
1733 5392 3.755378 CAGTTGAGTCAGGGAAAGATTGG 59.245 47.826 0.00 0.00 0.00 3.16
1736 5395 3.906846 AGACAGTTGAGTCAGGGAAAGAT 59.093 43.478 0.00 0.00 40.98 2.40
1760 5419 0.830444 ACCGTGTAAGGCTGGAGACA 60.830 55.000 0.00 0.00 34.80 3.41
1949 5608 4.965158 GCGAAACGACATTTCTTTAACACA 59.035 37.500 0.00 0.00 44.03 3.72
1951 5610 4.529446 GGCGAAACGACATTTCTTTAACA 58.471 39.130 0.00 0.00 44.03 2.41
2014 5674 4.462483 TGACAGTTTTGCAGTTTTTCTCCT 59.538 37.500 0.00 0.00 0.00 3.69
2139 5800 3.508744 AAGCCGCCAGTAAATGATTTG 57.491 42.857 0.00 0.00 0.00 2.32
2198 5859 2.159382 GAGGCGTGGAAAAATCTGGAA 58.841 47.619 0.00 0.00 0.00 3.53
2307 5968 6.217280 AGAATGGAGGAAAAGAAAGAGGAGAT 59.783 38.462 0.00 0.00 0.00 2.75
2337 5998 4.842531 TCCATGTTGGAGCTGAAGATAA 57.157 40.909 0.00 0.00 42.67 1.75
2374 6035 0.690762 TGTTTGTGAGGGGTAGAGGC 59.309 55.000 0.00 0.00 0.00 4.70
2409 6070 0.100861 CCCGAGAAAGGCGAGTCTAC 59.899 60.000 0.00 0.00 0.00 2.59
2417 6078 0.391793 CTTCCTGTCCCGAGAAAGGC 60.392 60.000 0.00 0.00 46.18 4.35
2514 6175 4.487714 TCTGCTTAAGGATCGACCAAAT 57.512 40.909 4.29 0.00 42.04 2.32
2520 6181 4.021456 TGTCACTTTCTGCTTAAGGATCGA 60.021 41.667 4.29 0.00 0.00 3.59
2553 6214 3.181475 GCGGAGTGATTGTAGAAGATGGA 60.181 47.826 0.00 0.00 0.00 3.41
2557 6218 3.089284 TCAGCGGAGTGATTGTAGAAGA 58.911 45.455 0.00 0.00 0.00 2.87
2582 6243 9.386010 ACAATGTAAGCTCGGTTAATACATAAA 57.614 29.630 5.60 0.00 36.47 1.40
2584 6245 8.951787 AACAATGTAAGCTCGGTTAATACATA 57.048 30.769 5.60 0.00 36.47 2.29
2764 6425 4.105697 AGTTTTCCAAGATTGTCCTACCCA 59.894 41.667 0.00 0.00 0.00 4.51
2890 6553 5.431731 ACCTTGAGAATAGAGAGGAGAGAGA 59.568 44.000 0.00 0.00 0.00 3.10
2917 6580 4.397417 AGAATCCATTTTTCGAGAAGCCTG 59.603 41.667 0.00 0.00 0.00 4.85
3166 6832 6.500910 TGATAATAATTAGCGTGTCGTCTGT 58.499 36.000 0.00 0.00 0.00 3.41
3342 7012 2.276869 GGGGAAAGCCGCAATTTCT 58.723 52.632 5.40 0.00 45.89 2.52
3376 7046 2.340909 TTATGCGGGGAGAGGGGGAT 62.341 60.000 0.00 0.00 0.00 3.85
3557 7252 3.866703 TGTCTATCTCCTCGAGGACAT 57.133 47.619 30.49 26.60 39.78 3.06
3645 7342 2.570415 TGGCATAAAAACTCGGTCCA 57.430 45.000 0.00 0.00 0.00 4.02
3657 7354 0.897863 ACCCGCAAGCTTTGGCATAA 60.898 50.000 9.22 0.00 41.70 1.90
3942 7654 1.153958 GCCGAGAAAGCAATGCACC 60.154 57.895 8.35 0.00 0.00 5.01
4011 7725 0.607489 GCCCAGATCAATCCCATCCG 60.607 60.000 0.00 0.00 0.00 4.18
4593 8350 5.674525 GATGAGACCACAATGTAAGATCCA 58.325 41.667 0.00 0.00 0.00 3.41
4674 8431 4.508861 TGTTACAAACTTAGACAAGGCGAC 59.491 41.667 0.00 0.00 35.97 5.19
4767 8534 7.857885 CCGCTTTCTCCTTGAAATATATGAAAC 59.142 37.037 0.00 0.00 42.96 2.78
4768 8535 7.468631 GCCGCTTTCTCCTTGAAATATATGAAA 60.469 37.037 0.00 0.00 42.96 2.69
4769 8536 6.017109 GCCGCTTTCTCCTTGAAATATATGAA 60.017 38.462 0.00 0.00 42.96 2.57
4770 8537 5.470098 GCCGCTTTCTCCTTGAAATATATGA 59.530 40.000 0.00 0.00 42.96 2.15
4771 8538 5.239306 TGCCGCTTTCTCCTTGAAATATATG 59.761 40.000 0.00 0.00 42.96 1.78
4772 8539 5.376625 TGCCGCTTTCTCCTTGAAATATAT 58.623 37.500 0.00 0.00 42.96 0.86
4773 8540 4.776349 TGCCGCTTTCTCCTTGAAATATA 58.224 39.130 0.00 0.00 42.96 0.86
4774 8541 3.620488 TGCCGCTTTCTCCTTGAAATAT 58.380 40.909 0.00 0.00 42.96 1.28
4775 8542 3.066291 TGCCGCTTTCTCCTTGAAATA 57.934 42.857 0.00 0.00 42.96 1.40
4776 8543 1.909700 TGCCGCTTTCTCCTTGAAAT 58.090 45.000 0.00 0.00 42.96 2.17
4777 8544 1.686355 TTGCCGCTTTCTCCTTGAAA 58.314 45.000 0.00 0.00 41.85 2.69
4778 8545 1.608590 CTTTGCCGCTTTCTCCTTGAA 59.391 47.619 0.00 0.00 0.00 2.69
4779 8546 1.202758 TCTTTGCCGCTTTCTCCTTGA 60.203 47.619 0.00 0.00 0.00 3.02
4780 8547 1.198637 CTCTTTGCCGCTTTCTCCTTG 59.801 52.381 0.00 0.00 0.00 3.61
4781 8548 1.528129 CTCTTTGCCGCTTTCTCCTT 58.472 50.000 0.00 0.00 0.00 3.36
4782 8549 0.957888 GCTCTTTGCCGCTTTCTCCT 60.958 55.000 0.00 0.00 35.15 3.69
4783 8550 1.503994 GCTCTTTGCCGCTTTCTCC 59.496 57.895 0.00 0.00 35.15 3.71
4784 8551 1.133458 CGCTCTTTGCCGCTTTCTC 59.867 57.895 0.00 0.00 38.78 2.87
4785 8552 0.320421 TACGCTCTTTGCCGCTTTCT 60.320 50.000 0.00 0.00 38.78 2.52
4786 8553 0.179222 GTACGCTCTTTGCCGCTTTC 60.179 55.000 0.00 0.00 38.78 2.62
4787 8554 0.602905 AGTACGCTCTTTGCCGCTTT 60.603 50.000 0.00 0.00 38.78 3.51
4788 8555 0.245539 TAGTACGCTCTTTGCCGCTT 59.754 50.000 0.00 0.00 38.78 4.68
4789 8556 0.179134 CTAGTACGCTCTTTGCCGCT 60.179 55.000 0.00 0.00 38.78 5.52
4790 8557 1.146358 CCTAGTACGCTCTTTGCCGC 61.146 60.000 0.00 0.00 38.78 6.53
4791 8558 0.454600 TCCTAGTACGCTCTTTGCCG 59.545 55.000 0.00 0.00 38.78 5.69
4792 8559 2.892784 ATCCTAGTACGCTCTTTGCC 57.107 50.000 0.00 0.00 38.78 4.52
4793 8560 4.048241 AGAATCCTAGTACGCTCTTTGC 57.952 45.455 0.00 0.00 38.57 3.68
4794 8561 5.631512 GCATAGAATCCTAGTACGCTCTTTG 59.368 44.000 0.00 0.00 0.00 2.77
4795 8562 5.302059 TGCATAGAATCCTAGTACGCTCTTT 59.698 40.000 0.00 0.00 0.00 2.52
4796 8563 4.827835 TGCATAGAATCCTAGTACGCTCTT 59.172 41.667 0.00 0.00 0.00 2.85
4797 8564 4.399219 TGCATAGAATCCTAGTACGCTCT 58.601 43.478 0.00 0.00 0.00 4.09
4798 8565 4.380023 CCTGCATAGAATCCTAGTACGCTC 60.380 50.000 0.00 0.00 0.00 5.03
4799 8566 3.508012 CCTGCATAGAATCCTAGTACGCT 59.492 47.826 0.00 0.00 0.00 5.07
4800 8567 3.506455 TCCTGCATAGAATCCTAGTACGC 59.494 47.826 0.00 0.00 0.00 4.42
4801 8568 4.762765 ACTCCTGCATAGAATCCTAGTACG 59.237 45.833 3.38 0.00 0.00 3.67
4802 8569 5.770663 TCACTCCTGCATAGAATCCTAGTAC 59.229 44.000 3.38 0.00 0.00 2.73
4803 8570 5.770663 GTCACTCCTGCATAGAATCCTAGTA 59.229 44.000 3.38 0.00 0.00 1.82
4804 8571 4.586841 GTCACTCCTGCATAGAATCCTAGT 59.413 45.833 3.38 0.00 0.00 2.57
4805 8572 4.021544 GGTCACTCCTGCATAGAATCCTAG 60.022 50.000 3.38 0.00 0.00 3.02
4806 8573 3.898123 GGTCACTCCTGCATAGAATCCTA 59.102 47.826 3.38 0.00 0.00 2.94
4807 8574 2.703007 GGTCACTCCTGCATAGAATCCT 59.297 50.000 3.38 0.00 0.00 3.24
4808 8575 2.224402 GGGTCACTCCTGCATAGAATCC 60.224 54.545 3.38 2.80 36.25 3.01
4809 8576 2.435805 TGGGTCACTCCTGCATAGAATC 59.564 50.000 3.38 0.00 36.25 2.52
4810 8577 2.481441 TGGGTCACTCCTGCATAGAAT 58.519 47.619 3.38 0.00 36.25 2.40
4811 8578 1.951209 TGGGTCACTCCTGCATAGAA 58.049 50.000 3.38 0.00 36.25 2.10
4812 8579 2.180946 ATGGGTCACTCCTGCATAGA 57.819 50.000 3.38 0.00 36.25 1.98
4813 8580 2.037772 GGTATGGGTCACTCCTGCATAG 59.962 54.545 0.00 0.00 36.25 2.23
4814 8581 2.047061 GGTATGGGTCACTCCTGCATA 58.953 52.381 0.00 0.00 36.25 3.14
4815 8582 0.839946 GGTATGGGTCACTCCTGCAT 59.160 55.000 0.00 0.00 36.25 3.96
4816 8583 0.252696 AGGTATGGGTCACTCCTGCA 60.253 55.000 0.00 0.00 36.25 4.41
4817 8584 0.912486 AAGGTATGGGTCACTCCTGC 59.088 55.000 0.00 0.00 36.25 4.85
4818 8585 1.210478 CCAAGGTATGGGTCACTCCTG 59.790 57.143 0.00 0.00 46.27 3.86
4819 8586 1.584724 CCAAGGTATGGGTCACTCCT 58.415 55.000 0.00 0.00 46.27 3.69
4829 8596 0.250467 CCGCTCATCCCCAAGGTATG 60.250 60.000 0.00 0.00 0.00 2.39
4830 8597 2.056906 GCCGCTCATCCCCAAGGTAT 62.057 60.000 0.00 0.00 0.00 2.73
4831 8598 2.742116 GCCGCTCATCCCCAAGGTA 61.742 63.158 0.00 0.00 0.00 3.08
4832 8599 4.115199 GCCGCTCATCCCCAAGGT 62.115 66.667 0.00 0.00 0.00 3.50
4833 8600 2.916527 AATGCCGCTCATCCCCAAGG 62.917 60.000 0.00 0.00 33.40 3.61
4834 8601 1.454479 AATGCCGCTCATCCCCAAG 60.454 57.895 0.00 0.00 33.40 3.61
4835 8602 1.753848 CAATGCCGCTCATCCCCAA 60.754 57.895 0.00 0.00 33.40 4.12
4836 8603 2.124193 CAATGCCGCTCATCCCCA 60.124 61.111 0.00 0.00 33.40 4.96
4837 8604 2.908940 CCAATGCCGCTCATCCCC 60.909 66.667 0.00 0.00 33.40 4.81
4838 8605 2.908940 CCCAATGCCGCTCATCCC 60.909 66.667 0.00 0.00 33.40 3.85
4839 8606 2.908940 CCCCAATGCCGCTCATCC 60.909 66.667 0.00 0.00 33.40 3.51
4840 8607 1.037030 TTTCCCCAATGCCGCTCATC 61.037 55.000 0.00 0.00 33.40 2.92
4841 8608 0.397535 ATTTCCCCAATGCCGCTCAT 60.398 50.000 0.00 0.00 36.87 2.90
4842 8609 1.000233 ATTTCCCCAATGCCGCTCA 60.000 52.632 0.00 0.00 0.00 4.26
4843 8610 1.037030 TCATTTCCCCAATGCCGCTC 61.037 55.000 0.00 0.00 42.06 5.03
4844 8611 0.614415 TTCATTTCCCCAATGCCGCT 60.614 50.000 0.00 0.00 42.06 5.52
4845 8612 0.460109 GTTCATTTCCCCAATGCCGC 60.460 55.000 0.00 0.00 42.06 6.53
4846 8613 0.175531 GGTTCATTTCCCCAATGCCG 59.824 55.000 0.00 0.00 42.06 5.69
4847 8614 0.541392 GGGTTCATTTCCCCAATGCC 59.459 55.000 0.00 0.00 42.06 4.40
4848 8615 0.175531 CGGGTTCATTTCCCCAATGC 59.824 55.000 0.00 0.00 42.06 3.56
4849 8616 0.175531 GCGGGTTCATTTCCCCAATG 59.824 55.000 0.00 0.00 43.51 2.82
4850 8617 0.975556 GGCGGGTTCATTTCCCCAAT 60.976 55.000 0.00 0.00 41.30 3.16
4851 8618 1.608046 GGCGGGTTCATTTCCCCAA 60.608 57.895 0.00 0.00 41.30 4.12
4852 8619 2.036572 GGCGGGTTCATTTCCCCA 59.963 61.111 0.00 0.00 41.30 4.96
4853 8620 1.381191 ATGGCGGGTTCATTTCCCC 60.381 57.895 0.00 0.00 41.78 4.81
4854 8621 0.682855 TGATGGCGGGTTCATTTCCC 60.683 55.000 0.00 0.00 41.41 3.97
4855 8622 1.067516 CATGATGGCGGGTTCATTTCC 59.932 52.381 0.00 0.00 30.24 3.13
4856 8623 2.023673 TCATGATGGCGGGTTCATTTC 58.976 47.619 0.00 0.00 30.24 2.17
4857 8624 2.142356 TCATGATGGCGGGTTCATTT 57.858 45.000 0.00 0.00 30.24 2.32
4858 8625 1.750778 GTTCATGATGGCGGGTTCATT 59.249 47.619 0.00 0.00 30.24 2.57
4859 8626 1.392589 GTTCATGATGGCGGGTTCAT 58.607 50.000 0.00 0.00 32.87 2.57
4860 8627 0.679640 GGTTCATGATGGCGGGTTCA 60.680 55.000 0.00 0.00 0.00 3.18
4861 8628 0.394352 AGGTTCATGATGGCGGGTTC 60.394 55.000 0.00 0.00 0.00 3.62
4862 8629 0.394352 GAGGTTCATGATGGCGGGTT 60.394 55.000 0.00 0.00 0.00 4.11
4863 8630 1.224592 GAGGTTCATGATGGCGGGT 59.775 57.895 0.00 0.00 0.00 5.28
4864 8631 0.107017 AAGAGGTTCATGATGGCGGG 60.107 55.000 0.00 0.00 0.00 6.13
4865 8632 1.019673 CAAGAGGTTCATGATGGCGG 58.980 55.000 0.00 0.00 0.00 6.13
4866 8633 0.379669 GCAAGAGGTTCATGATGGCG 59.620 55.000 0.00 0.00 0.00 5.69
4867 8634 1.404391 CTGCAAGAGGTTCATGATGGC 59.596 52.381 0.00 0.00 34.07 4.40
4868 8635 2.022195 CCTGCAAGAGGTTCATGATGG 58.978 52.381 0.00 0.00 37.02 3.51
4869 8636 2.681848 GTCCTGCAAGAGGTTCATGATG 59.318 50.000 0.00 0.00 43.37 3.07
4870 8637 2.306805 TGTCCTGCAAGAGGTTCATGAT 59.693 45.455 0.00 0.00 43.37 2.45
4871 8638 1.699083 TGTCCTGCAAGAGGTTCATGA 59.301 47.619 0.00 0.00 43.37 3.07
4872 8639 2.189594 TGTCCTGCAAGAGGTTCATG 57.810 50.000 0.00 0.00 43.37 3.07
4873 8640 2.575279 AGATGTCCTGCAAGAGGTTCAT 59.425 45.455 0.00 0.00 43.37 2.57
4874 8641 1.980765 AGATGTCCTGCAAGAGGTTCA 59.019 47.619 0.00 0.00 43.37 3.18
4875 8642 2.777832 AGATGTCCTGCAAGAGGTTC 57.222 50.000 0.00 0.00 43.37 3.62
4876 8643 2.093973 CGTAGATGTCCTGCAAGAGGTT 60.094 50.000 0.00 0.00 43.37 3.50
4877 8644 1.478510 CGTAGATGTCCTGCAAGAGGT 59.521 52.381 0.00 0.00 43.37 3.85
4878 8645 1.751351 TCGTAGATGTCCTGCAAGAGG 59.249 52.381 0.00 0.00 44.45 3.69
4879 8646 2.164422 TGTCGTAGATGTCCTGCAAGAG 59.836 50.000 0.00 0.00 40.67 2.85
4880 8647 2.167662 TGTCGTAGATGTCCTGCAAGA 58.832 47.619 0.00 0.00 40.67 3.02
4881 8648 2.654749 TGTCGTAGATGTCCTGCAAG 57.345 50.000 0.00 0.00 40.67 4.01
4882 8649 2.233676 ACATGTCGTAGATGTCCTGCAA 59.766 45.455 0.00 0.00 40.67 4.08
4883 8650 1.824852 ACATGTCGTAGATGTCCTGCA 59.175 47.619 0.00 0.00 40.67 4.41
4884 8651 2.464865 GACATGTCGTAGATGTCCTGC 58.535 52.381 10.69 0.00 42.63 4.85
4888 8655 7.757097 ATTTAACAGACATGTCGTAGATGTC 57.243 36.000 19.85 13.53 46.85 3.06
4894 8661 9.471084 CCATGTATATTTAACAGACATGTCGTA 57.529 33.333 19.85 10.89 43.74 3.43
4895 8662 8.201464 TCCATGTATATTTAACAGACATGTCGT 58.799 33.333 19.85 16.98 43.74 4.34
4896 8663 8.587952 TCCATGTATATTTAACAGACATGTCG 57.412 34.615 19.85 16.37 43.74 4.35
4901 8668 9.337396 GGACAATCCATGTATATTTAACAGACA 57.663 33.333 0.00 0.00 44.12 3.41
4902 8669 9.337396 TGGACAATCCATGTATATTTAACAGAC 57.663 33.333 0.00 0.00 42.67 3.51
4918 8685 5.476599 ACGATTGAAAAGATTGGACAATCCA 59.523 36.000 18.58 8.88 46.61 3.41
4919 8686 5.954335 ACGATTGAAAAGATTGGACAATCC 58.046 37.500 18.58 6.72 46.28 3.01
4920 8687 7.308435 AGAACGATTGAAAAGATTGGACAATC 58.692 34.615 15.40 15.40 45.66 2.67
4921 8688 7.219484 AGAACGATTGAAAAGATTGGACAAT 57.781 32.000 0.00 0.00 34.55 2.71
4922 8689 6.633500 AGAACGATTGAAAAGATTGGACAA 57.367 33.333 0.00 0.00 0.00 3.18
4923 8690 7.117812 GTCTAGAACGATTGAAAAGATTGGACA 59.882 37.037 0.00 0.00 0.00 4.02
4924 8691 7.332182 AGTCTAGAACGATTGAAAAGATTGGAC 59.668 37.037 0.00 0.00 0.00 4.02
4925 8692 7.386851 AGTCTAGAACGATTGAAAAGATTGGA 58.613 34.615 0.00 0.00 0.00 3.53
4926 8693 7.602517 AGTCTAGAACGATTGAAAAGATTGG 57.397 36.000 0.00 0.00 0.00 3.16
4927 8694 9.884465 AAAAGTCTAGAACGATTGAAAAGATTG 57.116 29.630 0.00 0.00 0.00 2.67
4928 8695 9.884465 CAAAAGTCTAGAACGATTGAAAAGATT 57.116 29.630 0.00 0.00 33.01 2.40
4929 8696 8.507249 CCAAAAGTCTAGAACGATTGAAAAGAT 58.493 33.333 0.00 0.00 33.01 2.40
4930 8697 7.497909 ACCAAAAGTCTAGAACGATTGAAAAGA 59.502 33.333 0.00 0.00 33.01 2.52
4931 8698 7.639945 ACCAAAAGTCTAGAACGATTGAAAAG 58.360 34.615 0.00 0.00 33.01 2.27
4932 8699 7.562454 ACCAAAAGTCTAGAACGATTGAAAA 57.438 32.000 0.00 0.00 33.01 2.29
4933 8700 7.255001 GGAACCAAAAGTCTAGAACGATTGAAA 60.255 37.037 0.00 0.00 33.01 2.69
4934 8701 6.204108 GGAACCAAAAGTCTAGAACGATTGAA 59.796 38.462 0.00 0.00 33.01 2.69
4935 8702 5.699458 GGAACCAAAAGTCTAGAACGATTGA 59.301 40.000 0.00 0.00 33.01 2.57
4936 8703 5.468746 TGGAACCAAAAGTCTAGAACGATTG 59.531 40.000 0.00 0.00 0.00 2.67
4937 8704 5.469084 GTGGAACCAAAAGTCTAGAACGATT 59.531 40.000 0.00 0.00 0.00 3.34
4938 8705 4.995487 GTGGAACCAAAAGTCTAGAACGAT 59.005 41.667 0.00 0.00 0.00 3.73
4939 8706 4.100498 AGTGGAACCAAAAGTCTAGAACGA 59.900 41.667 0.00 0.00 37.80 3.85
4940 8707 4.377897 AGTGGAACCAAAAGTCTAGAACG 58.622 43.478 0.00 0.00 37.80 3.95
4941 8708 6.522946 ACTAGTGGAACCAAAAGTCTAGAAC 58.477 40.000 16.76 0.00 37.80 3.01
4942 8709 6.742559 ACTAGTGGAACCAAAAGTCTAGAA 57.257 37.500 16.76 0.00 37.80 2.10
4943 8710 6.742559 AACTAGTGGAACCAAAAGTCTAGA 57.257 37.500 16.76 0.00 37.80 2.43
4944 8711 7.668492 ACTAACTAGTGGAACCAAAAGTCTAG 58.332 38.462 0.00 11.38 37.80 2.43
4945 8712 7.607615 ACTAACTAGTGGAACCAAAAGTCTA 57.392 36.000 0.00 0.70 37.80 2.59
4946 8713 6.496144 ACTAACTAGTGGAACCAAAAGTCT 57.504 37.500 0.00 0.00 37.80 3.24
4963 8730 9.174166 CCCTAGTTTACATTTTATGCACTAACT 57.826 33.333 0.00 0.00 0.00 2.24
4964 8731 8.403236 CCCCTAGTTTACATTTTATGCACTAAC 58.597 37.037 0.00 0.00 0.00 2.34
4965 8732 7.067737 GCCCCTAGTTTACATTTTATGCACTAA 59.932 37.037 0.00 0.00 0.00 2.24
4966 8733 6.544564 GCCCCTAGTTTACATTTTATGCACTA 59.455 38.462 0.00 0.00 0.00 2.74
4967 8734 5.359860 GCCCCTAGTTTACATTTTATGCACT 59.640 40.000 0.00 0.00 0.00 4.40
4968 8735 5.451381 GGCCCCTAGTTTACATTTTATGCAC 60.451 44.000 0.00 0.00 0.00 4.57
4969 8736 4.647399 GGCCCCTAGTTTACATTTTATGCA 59.353 41.667 0.00 0.00 0.00 3.96
4970 8737 4.038763 GGGCCCCTAGTTTACATTTTATGC 59.961 45.833 12.23 0.00 0.00 3.14
4971 8738 4.587262 GGGGCCCCTAGTTTACATTTTATG 59.413 45.833 35.49 0.00 0.00 1.90
4972 8739 4.233287 TGGGGCCCCTAGTTTACATTTTAT 59.767 41.667 40.66 0.00 36.94 1.40
4973 8740 3.596956 TGGGGCCCCTAGTTTACATTTTA 59.403 43.478 40.66 13.43 36.94 1.52
4974 8741 2.384029 TGGGGCCCCTAGTTTACATTTT 59.616 45.455 40.66 0.00 36.94 1.82
4975 8742 2.004589 TGGGGCCCCTAGTTTACATTT 58.995 47.619 40.66 0.00 36.94 2.32
4976 8743 1.688750 TGGGGCCCCTAGTTTACATT 58.311 50.000 40.66 0.00 36.94 2.71
4977 8744 1.688750 TTGGGGCCCCTAGTTTACAT 58.311 50.000 40.66 0.00 36.94 2.29
4978 8745 1.567175 GATTGGGGCCCCTAGTTTACA 59.433 52.381 40.66 16.48 36.94 2.41
4979 8746 1.567175 TGATTGGGGCCCCTAGTTTAC 59.433 52.381 40.66 23.11 36.94 2.01
4980 8747 1.988539 TGATTGGGGCCCCTAGTTTA 58.011 50.000 40.66 18.20 36.94 2.01
4981 8748 1.089123 TTGATTGGGGCCCCTAGTTT 58.911 50.000 40.66 19.88 36.94 2.66
4982 8749 0.335019 GTTGATTGGGGCCCCTAGTT 59.665 55.000 40.66 20.71 36.94 2.24
4983 8750 1.580994 GGTTGATTGGGGCCCCTAGT 61.581 60.000 40.66 26.09 36.94 2.57
4984 8751 1.230212 GGTTGATTGGGGCCCCTAG 59.770 63.158 40.66 0.00 36.94 3.02
4985 8752 2.321357 GGGTTGATTGGGGCCCCTA 61.321 63.158 40.66 34.69 35.18 3.53
4986 8753 3.683518 GGGTTGATTGGGGCCCCT 61.684 66.667 40.66 23.71 35.18 4.79
4988 8755 2.871795 ATTCGGGTTGATTGGGGCCC 62.872 60.000 18.17 18.17 37.79 5.80
4989 8756 1.381191 ATTCGGGTTGATTGGGGCC 60.381 57.895 0.00 0.00 0.00 5.80
4990 8757 1.391933 GGATTCGGGTTGATTGGGGC 61.392 60.000 0.00 0.00 0.00 5.80
4991 8758 0.258774 AGGATTCGGGTTGATTGGGG 59.741 55.000 0.00 0.00 0.00 4.96
4992 8759 1.680338 GAGGATTCGGGTTGATTGGG 58.320 55.000 0.00 0.00 0.00 4.12
4993 8760 1.299541 CGAGGATTCGGGTTGATTGG 58.700 55.000 0.00 0.00 43.05 3.16
5005 8772 1.369091 GCACGGCATTGACGAGGATT 61.369 55.000 20.74 0.00 35.20 3.01
5116 8883 1.682854 CTATCCGCCATGGCAAACAAT 59.317 47.619 34.93 20.96 42.06 2.71
5215 8984 2.211468 GATCCTGGGCCTCCGGTTTT 62.211 60.000 4.53 0.00 37.74 2.43
5263 9032 2.034066 CCCGAGGCTCCTGCAAAA 59.966 61.111 9.32 0.00 41.91 2.44
5565 9334 6.911250 TTGTCTTCAGTGGTATCTGTAGAA 57.089 37.500 5.02 0.00 41.16 2.10
5652 9421 2.173669 CACGCTACCTCGCATTGGG 61.174 63.158 0.00 0.00 0.00 4.12
5660 9429 2.271800 CACAGATTTCCACGCTACCTC 58.728 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.