Multiple sequence alignment - TraesCS4D01G019400

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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 TraesCS4D01G019400 chr4D 100.000 2476 0 0 1 2476 8208418 8205943 0.000000e+00 4573.0
1 TraesCS4D01G019400 chr4D 95.098 102 5 0 360 461 233079444 233079343 7.090000e-36 161.0
2 TraesCS4D01G019400 chr4D 100.000 85 0 0 2345 2429 8206116 8206032 9.170000e-35 158.0
3 TraesCS4D01G019400 chr4D 91.743 109 9 0 351 459 490523563 490523671 4.260000e-33 152.0
4 TraesCS4D01G019400 chr4B 83.862 1512 100 72 470 1875 15642416 15640943 0.000000e+00 1308.0
5 TraesCS4D01G019400 chr4B 90.136 294 25 4 164 457 15642755 15642466 1.800000e-101 379.0
6 TraesCS4D01G019400 chr4A 91.077 975 43 18 727 1685 595216521 595217467 0.000000e+00 1279.0
7 TraesCS4D01G019400 chr4A 88.100 479 47 10 1877 2348 72286497 72286972 5.980000e-156 560.0
8 TraesCS4D01G019400 chr4A 94.175 103 6 0 360 462 467683853 467683955 9.170000e-35 158.0
9 TraesCS4D01G019400 chr3D 88.797 482 43 9 1872 2345 284192021 284191543 4.590000e-162 580.0
10 TraesCS4D01G019400 chr6A 89.053 475 40 9 1872 2340 384727279 384726811 1.650000e-161 579.0
11 TraesCS4D01G019400 chr6D 89.030 474 41 10 1879 2345 447806044 447806513 5.940000e-161 577.0
12 TraesCS4D01G019400 chr6D 88.199 483 43 9 1873 2345 29371005 29371483 4.620000e-157 564.0
13 TraesCS4D01G019400 chr6D 95.506 89 3 1 2389 2476 447806472 447806560 9.230000e-30 141.0
14 TraesCS4D01G019400 chr6D 97.619 42 0 1 2347 2387 447806472 447806513 1.230000e-08 71.3
15 TraesCS4D01G019400 chr6B 88.842 475 45 8 1875 2343 684424524 684424052 5.940000e-161 577.0
16 TraesCS4D01G019400 chr5B 88.889 477 42 9 1874 2342 57969789 57970262 5.940000e-161 577.0
17 TraesCS4D01G019400 chr5A 88.655 476 45 7 1875 2345 184049180 184048709 2.760000e-159 571.0
18 TraesCS4D01G019400 chr5A 94.175 103 6 0 360 462 52281156 52281258 9.170000e-35 158.0
19 TraesCS4D01G019400 chr3A 88.358 481 42 12 1874 2345 673926549 673926074 1.290000e-157 566.0
20 TraesCS4D01G019400 chr3A 94.444 90 3 1 2389 2476 673926116 673926027 1.190000e-28 137.0
21 TraesCS4D01G019400 chr2A 95.146 103 5 0 359 461 531599148 531599250 1.970000e-36 163.0
22 TraesCS4D01G019400 chr7A 93.396 106 7 0 360 465 694496883 694496778 9.170000e-35 158.0
23 TraesCS4D01G019400 chr5D 91.818 110 9 0 352 461 303941892 303941783 1.190000e-33 154.0
24 TraesCS4D01G019400 chr5D 95.506 89 3 1 2389 2476 482559627 482559715 9.230000e-30 141.0
25 TraesCS4D01G019400 chr5D 95.455 88 4 0 2389 2476 489086210 489086123 9.230000e-30 141.0
26 TraesCS4D01G019400 chr5D 95.238 42 1 1 2347 2387 482559627 482559668 5.720000e-07 65.8
27 TraesCS4D01G019400 chr1B 90.083 121 9 3 348 465 415552108 415551988 1.190000e-33 154.0
28 TraesCS4D01G019400 chr1B 95.455 88 4 0 2389 2476 686830604 686830517 9.230000e-30 141.0
29 TraesCS4D01G019400 chr2B 95.455 88 4 0 2389 2476 101429021 101429108 9.230000e-30 141.0
30 TraesCS4D01G019400 chr1D 95.455 88 4 0 2389 2476 434617195 434617108 9.230000e-30 141.0
31 TraesCS4D01G019400 chrUn 94.318 88 5 0 2389 2476 254789826 254789913 4.300000e-28 135.0
32 TraesCS4D01G019400 chrUn 94.318 88 5 0 2389 2476 335944945 335944858 4.300000e-28 135.0
33 TraesCS4D01G019400 chr2D 93.333 45 2 1 2347 2390 9159995 9159951 5.720000e-07 65.8
34 TraesCS4D01G019400 chr2D 91.304 46 2 2 2347 2390 547245354 547245399 7.390000e-06 62.1


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 TraesCS4D01G019400 chr4D 8205943 8208418 2475 True 2365.5 4573 100.000000 1 2476 2 chr4D.!!$R2 2475
1 TraesCS4D01G019400 chr4B 15640943 15642755 1812 True 843.5 1308 86.999000 164 1875 2 chr4B.!!$R1 1711
2 TraesCS4D01G019400 chr4A 595216521 595217467 946 False 1279.0 1279 91.077000 727 1685 1 chr4A.!!$F3 958
3 TraesCS4D01G019400 chr6D 447806044 447806560 516 False 263.1 577 94.051667 1879 2476 3 chr6D.!!$F2 597
4 TraesCS4D01G019400 chr3A 673926027 673926549 522 True 351.5 566 91.401000 1874 2476 2 chr3A.!!$R1 602

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
833 920 0.325671 TCCTCTTCCCCTGCGAATCT 60.326 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2165 0.178891 TTCTCCTTCCTGTGCCTCCT 60.179 55.0 0.0 0.0 0.0 3.69 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
23 24 6.377327 AATTCAAGAGTTTCAATCACGTGT 57.623 33.333 16.51 0.00 0.00 4.49
24 25 5.811399 TTCAAGAGTTTCAATCACGTGTT 57.189 34.783 16.51 3.97 0.00 3.32
25 26 5.811399 TCAAGAGTTTCAATCACGTGTTT 57.189 34.783 16.51 10.99 0.00 2.83
26 27 6.189677 TCAAGAGTTTCAATCACGTGTTTT 57.810 33.333 16.51 8.02 0.00 2.43
27 28 6.616947 TCAAGAGTTTCAATCACGTGTTTTT 58.383 32.000 16.51 5.43 0.00 1.94
68 69 5.893897 AGAATCTTGTGAATCAAAGAGGC 57.106 39.130 11.40 7.44 35.48 4.70
69 70 4.704057 AGAATCTTGTGAATCAAAGAGGCC 59.296 41.667 0.00 0.00 35.48 5.19
70 71 2.795329 TCTTGTGAATCAAAGAGGCCC 58.205 47.619 0.00 0.00 35.48 5.80
71 72 1.470098 CTTGTGAATCAAAGAGGCCCG 59.530 52.381 0.00 0.00 35.48 6.13
72 73 0.690192 TGTGAATCAAAGAGGCCCGA 59.310 50.000 0.00 0.00 0.00 5.14
73 74 1.073125 TGTGAATCAAAGAGGCCCGAA 59.927 47.619 0.00 0.00 0.00 4.30
74 75 2.159382 GTGAATCAAAGAGGCCCGAAA 58.841 47.619 0.00 0.00 0.00 3.46
75 76 2.755103 GTGAATCAAAGAGGCCCGAAAT 59.245 45.455 0.00 0.00 0.00 2.17
76 77 3.945285 GTGAATCAAAGAGGCCCGAAATA 59.055 43.478 0.00 0.00 0.00 1.40
77 78 4.035675 GTGAATCAAAGAGGCCCGAAATAG 59.964 45.833 0.00 0.00 0.00 1.73
78 79 2.710096 TCAAAGAGGCCCGAAATAGG 57.290 50.000 0.00 0.00 0.00 2.57
89 90 3.560636 CCGAAATAGGGACCTCATGTT 57.439 47.619 0.00 0.00 0.00 2.71
90 91 3.886123 CCGAAATAGGGACCTCATGTTT 58.114 45.455 0.00 0.00 0.00 2.83
91 92 3.627577 CCGAAATAGGGACCTCATGTTTG 59.372 47.826 0.00 0.00 0.00 2.93
92 93 3.627577 CGAAATAGGGACCTCATGTTTGG 59.372 47.826 0.00 0.00 0.00 3.28
93 94 4.600062 GAAATAGGGACCTCATGTTTGGT 58.400 43.478 0.00 7.34 39.60 3.67
94 95 4.675063 AATAGGGACCTCATGTTTGGTT 57.325 40.909 0.00 0.00 36.59 3.67
95 96 4.675063 ATAGGGACCTCATGTTTGGTTT 57.325 40.909 0.00 2.96 36.59 3.27
96 97 2.876581 AGGGACCTCATGTTTGGTTTC 58.123 47.619 8.64 5.63 36.59 2.78
97 98 1.893137 GGGACCTCATGTTTGGTTTCC 59.107 52.381 8.64 9.51 36.59 3.13
98 99 2.490902 GGGACCTCATGTTTGGTTTCCT 60.491 50.000 8.64 0.00 36.59 3.36
99 100 2.820197 GGACCTCATGTTTGGTTTCCTC 59.180 50.000 8.64 0.00 36.59 3.71
100 101 2.484264 GACCTCATGTTTGGTTTCCTCG 59.516 50.000 8.64 0.00 36.59 4.63
101 102 2.105821 ACCTCATGTTTGGTTTCCTCGA 59.894 45.455 0.00 0.00 31.62 4.04
102 103 3.146066 CCTCATGTTTGGTTTCCTCGAA 58.854 45.455 0.00 0.00 0.00 3.71
103 104 3.568007 CCTCATGTTTGGTTTCCTCGAAA 59.432 43.478 0.00 0.00 0.00 3.46
104 105 4.037446 CCTCATGTTTGGTTTCCTCGAAAA 59.963 41.667 0.00 0.00 33.14 2.29
105 106 5.278957 CCTCATGTTTGGTTTCCTCGAAAAT 60.279 40.000 0.00 0.00 33.14 1.82
106 107 6.155475 TCATGTTTGGTTTCCTCGAAAATT 57.845 33.333 0.00 0.00 33.14 1.82
107 108 6.212955 TCATGTTTGGTTTCCTCGAAAATTC 58.787 36.000 0.00 0.00 33.14 2.17
108 109 4.939271 TGTTTGGTTTCCTCGAAAATTCC 58.061 39.130 0.00 0.00 33.14 3.01
109 110 4.647399 TGTTTGGTTTCCTCGAAAATTCCT 59.353 37.500 0.00 0.00 33.14 3.36
110 111 5.828859 TGTTTGGTTTCCTCGAAAATTCCTA 59.171 36.000 0.00 0.00 33.14 2.94
111 112 6.492087 TGTTTGGTTTCCTCGAAAATTCCTAT 59.508 34.615 0.00 0.00 33.14 2.57
112 113 7.666388 TGTTTGGTTTCCTCGAAAATTCCTATA 59.334 33.333 0.00 0.00 33.14 1.31
113 114 8.683615 GTTTGGTTTCCTCGAAAATTCCTATAT 58.316 33.333 0.00 0.00 33.14 0.86
114 115 9.908747 TTTGGTTTCCTCGAAAATTCCTATATA 57.091 29.630 0.00 0.00 33.14 0.86
115 116 9.908747 TTGGTTTCCTCGAAAATTCCTATATAA 57.091 29.630 0.00 0.00 33.14 0.98
157 158 8.749841 TCAATTCTTTTCTTTTTCAAACGACA 57.250 26.923 0.00 0.00 0.00 4.35
158 159 8.643752 TCAATTCTTTTCTTTTTCAAACGACAC 58.356 29.630 0.00 0.00 0.00 3.67
159 160 6.937886 TTCTTTTCTTTTTCAAACGACACC 57.062 33.333 0.00 0.00 0.00 4.16
160 161 6.015027 TCTTTTCTTTTTCAAACGACACCA 57.985 33.333 0.00 0.00 0.00 4.17
161 162 6.448006 TCTTTTCTTTTTCAAACGACACCAA 58.552 32.000 0.00 0.00 0.00 3.67
162 163 6.924060 TCTTTTCTTTTTCAAACGACACCAAA 59.076 30.769 0.00 0.00 0.00 3.28
172 173 5.123186 TCAAACGACACCAAATATCATCCAC 59.877 40.000 0.00 0.00 0.00 4.02
174 175 3.938963 ACGACACCAAATATCATCCACAC 59.061 43.478 0.00 0.00 0.00 3.82
182 183 8.906867 CACCAAATATCATCCACACTTTAGATT 58.093 33.333 0.00 0.00 0.00 2.40
223 224 4.027572 TCCTTTTTACATTGCTATGCGC 57.972 40.909 8.11 0.00 35.03 6.09
224 225 2.783284 CCTTTTTACATTGCTATGCGCG 59.217 45.455 8.11 0.00 43.27 6.86
246 247 4.881850 CGATAACAAGGGCAATCTTACCTT 59.118 41.667 0.00 0.00 45.08 3.50
250 251 3.011708 ACAAGGGCAATCTTACCTTCCAT 59.988 43.478 0.00 0.00 42.46 3.41
288 289 5.422214 AATCTGACCGTGTCTTTTAGGAT 57.578 39.130 5.77 0.00 33.15 3.24
328 329 5.290493 TCCCTACGAATCAAGCACATAAT 57.710 39.130 0.00 0.00 0.00 1.28
368 369 8.296713 GTGTTCTCATAATCATCTACTCTCTCC 58.703 40.741 0.00 0.00 0.00 3.71
369 370 7.174080 TGTTCTCATAATCATCTACTCTCTCCG 59.826 40.741 0.00 0.00 0.00 4.63
373 374 4.447138 AATCATCTACTCTCTCCGGTCT 57.553 45.455 0.00 0.00 0.00 3.85
404 405 4.565166 TCCGCGTATTAGATTTGTGTCAAG 59.435 41.667 4.92 0.00 0.00 3.02
414 415 8.909708 TTAGATTTGTGTCAAGTCAAACTTTG 57.090 30.769 7.50 0.00 36.03 2.77
420 421 5.931146 TGTGTCAAGTCAAACTTTGCAAAAT 59.069 32.000 13.84 0.00 36.03 1.82
492 530 8.458573 TGGTACTAATTCAGTTTTGTGAATGT 57.541 30.769 0.01 0.00 44.72 2.71
573 613 5.998454 ATGCAGACTAAAAATGATCGGAG 57.002 39.130 0.00 0.00 0.00 4.63
574 614 5.084818 TGCAGACTAAAAATGATCGGAGA 57.915 39.130 0.00 0.00 45.75 3.71
592 632 8.902540 ATCGGAGAAAGTATTTTGCACATATA 57.097 30.769 0.00 0.00 43.58 0.86
593 633 8.725405 TCGGAGAAAGTATTTTGCACATATAA 57.275 30.769 0.00 0.00 39.27 0.98
594 634 8.609176 TCGGAGAAAGTATTTTGCACATATAAC 58.391 33.333 0.00 0.00 39.27 1.89
595 635 8.612619 CGGAGAAAGTATTTTGCACATATAACT 58.387 33.333 0.00 0.00 39.27 2.24
638 684 8.609617 TTTCCAAGAAGTCCTATCAAGATCTA 57.390 34.615 0.00 0.00 0.00 1.98
648 694 8.371699 AGTCCTATCAAGATCTATTGGTAAAGC 58.628 37.037 0.00 0.00 0.00 3.51
652 698 3.838244 AGATCTATTGGTAAAGCCGCA 57.162 42.857 0.00 0.00 41.21 5.69
690 736 7.043325 CCGTAGAACAATTGCTCTACTGTATTC 60.043 40.741 31.45 15.14 40.02 1.75
694 740 8.972127 AGAACAATTGCTCTACTGTATTCTCTA 58.028 33.333 9.63 0.00 0.00 2.43
717 770 9.224267 TCTATTAGTATACACCCGTAGATTCAC 57.776 37.037 5.50 0.00 0.00 3.18
775 857 2.046285 AATCCGCCAAAAGGAGCCG 61.046 57.895 0.00 0.00 41.66 5.52
779 861 1.671054 CGCCAAAAGGAGCCGAGAA 60.671 57.895 0.00 0.00 0.00 2.87
823 905 3.787001 CCTGCCCGTCCTCTTCCC 61.787 72.222 0.00 0.00 0.00 3.97
833 920 0.325671 TCCTCTTCCCCTGCGAATCT 60.326 55.000 0.00 0.00 0.00 2.40
834 921 1.063190 TCCTCTTCCCCTGCGAATCTA 60.063 52.381 0.00 0.00 0.00 1.98
835 922 1.974236 CCTCTTCCCCTGCGAATCTAT 59.026 52.381 0.00 0.00 0.00 1.98
836 923 2.028567 CCTCTTCCCCTGCGAATCTATC 60.029 54.545 0.00 0.00 0.00 2.08
837 924 1.971357 TCTTCCCCTGCGAATCTATCC 59.029 52.381 0.00 0.00 0.00 2.59
884 971 2.509336 CATCGCCACCACGAGACC 60.509 66.667 0.00 0.00 46.69 3.85
885 972 2.994995 ATCGCCACCACGAGACCA 60.995 61.111 0.00 0.00 46.69 4.02
886 973 2.359169 ATCGCCACCACGAGACCAT 61.359 57.895 0.00 0.00 46.69 3.55
888 975 2.662596 GCCACCACGAGACCATCA 59.337 61.111 0.00 0.00 0.00 3.07
890 977 1.448540 CCACCACGAGACCATCAGC 60.449 63.158 0.00 0.00 0.00 4.26
891 978 1.448540 CACCACGAGACCATCAGCC 60.449 63.158 0.00 0.00 0.00 4.85
892 979 2.202797 CCACGAGACCATCAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
999 1112 3.544684 CTTCCATTCCGTCCATCATCAA 58.455 45.455 0.00 0.00 0.00 2.57
1164 1288 1.079503 GATGCGGTTGGAGTTCTGAC 58.920 55.000 0.00 0.00 0.00 3.51
1183 1307 1.984570 CCTGTTCCTGCCTCCTCGA 60.985 63.158 0.00 0.00 0.00 4.04
1310 1438 0.706433 AGGTGCCCATTTCTCCACAT 59.294 50.000 0.00 0.00 0.00 3.21
1330 1458 1.973515 TGAGCTGCAGAAGAGGAAGAA 59.026 47.619 20.43 0.00 0.00 2.52
1335 1463 3.598299 CTGCAGAAGAGGAAGAAGAAGG 58.402 50.000 8.42 0.00 0.00 3.46
1340 1468 5.512232 GCAGAAGAGGAAGAAGAAGGAGAAA 60.512 44.000 0.00 0.00 0.00 2.52
1527 1677 0.181350 AGCTAGCGATCTTTTGGGGG 59.819 55.000 9.55 0.00 0.00 5.40
1549 1699 4.501400 GGTTTCTTGGTGGATCTTGTTTGG 60.501 45.833 0.00 0.00 0.00 3.28
1561 1713 2.495270 TCTTGTTTGGCTTTCTTGTGCA 59.505 40.909 0.00 0.00 0.00 4.57
1685 1847 7.201794 CCAAGATGTACGTAGAGGACTAATCAA 60.202 40.741 0.00 0.00 0.00 2.57
1686 1848 7.261829 AGATGTACGTAGAGGACTAATCAAC 57.738 40.000 0.00 0.00 0.00 3.18
1702 1867 3.028094 TCAACCCCTACTACCAGCTAG 57.972 52.381 0.00 0.00 0.00 3.42
1704 1869 3.528905 TCAACCCCTACTACCAGCTAGTA 59.471 47.826 0.00 0.00 36.95 1.82
1706 1871 2.158696 ACCCCTACTACCAGCTAGTACG 60.159 54.545 0.00 0.00 36.95 3.67
1707 1872 2.158696 CCCCTACTACCAGCTAGTACGT 60.159 54.545 0.00 0.00 36.95 3.57
1708 1873 3.071602 CCCCTACTACCAGCTAGTACGTA 59.928 52.174 0.00 0.00 36.95 3.57
1709 1874 4.444876 CCCCTACTACCAGCTAGTACGTAA 60.445 50.000 0.00 0.00 36.95 3.18
1710 1875 5.312079 CCCTACTACCAGCTAGTACGTAAT 58.688 45.833 0.00 0.00 36.95 1.89
1711 1876 5.767168 CCCTACTACCAGCTAGTACGTAATT 59.233 44.000 0.00 0.00 36.95 1.40
1712 1877 6.936900 CCCTACTACCAGCTAGTACGTAATTA 59.063 42.308 0.00 0.00 36.95 1.40
1713 1878 7.118971 CCCTACTACCAGCTAGTACGTAATTAG 59.881 44.444 0.00 5.97 36.95 1.73
1714 1879 7.659390 CCTACTACCAGCTAGTACGTAATTAGT 59.341 40.741 0.00 4.58 36.95 2.24
1716 1881 8.600449 ACTACCAGCTAGTACGTAATTAGTAG 57.400 38.462 0.00 8.12 33.53 2.57
1717 1882 8.207545 ACTACCAGCTAGTACGTAATTAGTAGT 58.792 37.037 0.00 8.68 33.53 2.73
1718 1883 7.872113 ACCAGCTAGTACGTAATTAGTAGTT 57.128 36.000 0.00 0.00 30.42 2.24
1719 1884 7.924940 ACCAGCTAGTACGTAATTAGTAGTTC 58.075 38.462 0.00 0.00 30.42 3.01
1720 1885 7.772757 ACCAGCTAGTACGTAATTAGTAGTTCT 59.227 37.037 0.00 0.00 30.42 3.01
1721 1886 8.619546 CCAGCTAGTACGTAATTAGTAGTTCTT 58.380 37.037 0.00 0.00 30.42 2.52
1758 1923 2.548295 TTCCCAACGAGTTTGCCGC 61.548 57.895 0.00 0.00 33.34 6.53
1772 1937 1.064621 GCCGCGTTGATCATGCAAT 59.935 52.632 17.51 0.00 37.23 3.56
1783 1948 1.521580 TCATGCAATGCAGACGTCAA 58.478 45.000 19.50 2.94 46.21 3.18
1787 1952 0.445436 GCAATGCAGACGTCAAGGAG 59.555 55.000 19.50 4.00 0.00 3.69
1806 1978 4.947147 TGGCCGGTTTGCGCTCTT 62.947 61.111 9.73 0.00 0.00 2.85
1814 1986 1.266989 GGTTTGCGCTCTTAGCTTTGT 59.733 47.619 9.73 0.00 39.60 2.83
1816 1988 0.790207 TTGCGCTCTTAGCTTTGTCG 59.210 50.000 9.73 0.00 39.60 4.35
1825 1997 2.065993 TAGCTTTGTCGTGCTCTCAC 57.934 50.000 0.00 0.00 40.35 3.51
1828 2000 1.056103 CTTTGTCGTGCTCTCACTCG 58.944 55.000 0.00 0.00 40.99 4.18
1829 2001 0.384309 TTTGTCGTGCTCTCACTCGT 59.616 50.000 0.00 0.00 40.99 4.18
1830 2002 1.232119 TTGTCGTGCTCTCACTCGTA 58.768 50.000 0.00 0.00 40.99 3.43
1831 2003 0.796927 TGTCGTGCTCTCACTCGTAG 59.203 55.000 0.00 0.00 40.99 3.51
1832 2004 0.521659 GTCGTGCTCTCACTCGTAGC 60.522 60.000 0.00 0.00 40.99 3.58
1833 2005 0.953960 TCGTGCTCTCACTCGTAGCA 60.954 55.000 0.00 0.00 43.66 3.49
1835 2007 0.800300 GTGCTCTCACTCGTAGCAGC 60.800 60.000 0.00 0.00 46.26 5.25
1836 2008 0.962855 TGCTCTCACTCGTAGCAGCT 60.963 55.000 0.00 0.00 41.15 4.24
1837 2009 0.525242 GCTCTCACTCGTAGCAGCTG 60.525 60.000 10.11 10.11 36.26 4.24
1838 2010 1.090728 CTCTCACTCGTAGCAGCTGA 58.909 55.000 20.43 0.00 0.00 4.26
1839 2011 1.470494 CTCTCACTCGTAGCAGCTGAA 59.530 52.381 20.43 0.50 0.00 3.02
1840 2012 1.470494 TCTCACTCGTAGCAGCTGAAG 59.530 52.381 20.43 8.32 0.00 3.02
1841 2013 1.201181 CTCACTCGTAGCAGCTGAAGT 59.799 52.381 20.43 8.97 0.00 3.01
1855 2027 3.493503 AGCTGAAGTTTTACGTGCTGTAC 59.506 43.478 0.00 0.00 31.20 2.90
1860 2032 7.342318 TGAAGTTTTACGTGCTGTACTAATC 57.658 36.000 0.00 0.00 31.20 1.75
1862 2034 6.946229 AGTTTTACGTGCTGTACTAATCTG 57.054 37.500 0.00 0.00 31.20 2.90
1940 2112 6.869913 CACCTGAATTGTATTCATTTGTTGCT 59.130 34.615 2.84 0.00 0.00 3.91
1990 2162 0.529378 CTTCAAGTGAAGCATGGGGC 59.471 55.000 8.06 0.00 44.10 5.80
2004 2177 4.729918 GGGCACAGGAGGCACAGG 62.730 72.222 0.00 0.00 33.96 4.00
2005 2178 3.640407 GGCACAGGAGGCACAGGA 61.640 66.667 0.00 0.00 0.00 3.86
2017 2190 4.195416 GAGGCACAGGAAGGAGAAATAAG 58.805 47.826 0.00 0.00 0.00 1.73
2024 2197 5.838521 ACAGGAAGGAGAAATAAGGCAAAAA 59.161 36.000 0.00 0.00 0.00 1.94
2025 2198 6.159293 CAGGAAGGAGAAATAAGGCAAAAAC 58.841 40.000 0.00 0.00 0.00 2.43
2029 2202 6.478512 AGGAGAAATAAGGCAAAAACACAA 57.521 33.333 0.00 0.00 0.00 3.33
2066 2244 0.106918 GGGACACAACACAACAGGGA 60.107 55.000 0.00 0.00 0.00 4.20
2072 2250 1.064017 ACAACACAACAGGGACACCAT 60.064 47.619 0.00 0.00 40.13 3.55
2073 2251 1.337703 CAACACAACAGGGACACCATG 59.662 52.381 0.86 0.86 40.13 3.66
2085 2263 4.778143 ACCATGGGCGCTCGAACC 62.778 66.667 18.09 0.00 0.00 3.62
2086 2264 4.776322 CCATGGGCGCTCGAACCA 62.776 66.667 7.64 5.98 38.88 3.67
2088 2266 4.778143 ATGGGCGCTCGAACCACC 62.778 66.667 7.64 0.00 37.05 4.61
2094 2272 4.681978 GCTCGAACCACCGTGGCT 62.682 66.667 17.99 5.11 42.67 4.75
2134 2312 0.955428 ACTGCACCATCGACGCAATT 60.955 50.000 0.00 0.00 34.75 2.32
2207 2385 0.247185 TGGGGTACATTCGAACGGTC 59.753 55.000 0.00 0.00 0.00 4.79
2265 2443 2.388232 CGGCGTAGTCAAAGGGCAC 61.388 63.158 0.00 0.00 0.00 5.01
2287 2465 1.556911 ACCAGGCATAGAACTCCACAG 59.443 52.381 0.00 0.00 0.00 3.66
2292 2470 2.158842 GGCATAGAACTCCACAGAGCAT 60.159 50.000 0.00 0.00 44.65 3.79
2293 2471 3.070159 GGCATAGAACTCCACAGAGCATA 59.930 47.826 0.00 0.00 44.65 3.14
2303 2481 2.228822 CCACAGAGCATACCCAAAACAC 59.771 50.000 0.00 0.00 0.00 3.32
2316 2494 1.334384 AAAACACCACAACAGGGGGC 61.334 55.000 0.00 0.00 35.95 5.80
2317 2495 2.522198 AAACACCACAACAGGGGGCA 62.522 55.000 0.00 0.00 35.95 5.36
2318 2496 2.912025 CACCACAACAGGGGGCAC 60.912 66.667 0.00 0.00 0.00 5.01
2339 2517 3.847709 GAGCGCTCGAACTGCAGC 61.848 66.667 23.61 0.00 0.00 5.25
2353 2531 3.716006 CAGCGGCGACCACAACAG 61.716 66.667 12.98 0.00 0.00 3.16
2354 2532 4.988598 AGCGGCGACCACAACAGG 62.989 66.667 12.98 0.00 0.00 4.00
2359 2537 4.263572 CGACCACAACAGGGGGCA 62.264 66.667 0.00 0.00 30.28 5.36
2360 2538 2.597510 GACCACAACAGGGGGCAC 60.598 66.667 0.00 0.00 30.28 5.01
2381 2559 3.847709 GAGCGCTCGAACTGCAGC 61.848 66.667 23.61 0.00 0.00 5.25
2395 2573 3.716006 CAGCGGCGACCACAACAG 61.716 66.667 12.98 0.00 0.00 3.16
2396 2574 4.988598 AGCGGCGACCACAACAGG 62.989 66.667 12.98 0.00 0.00 4.00
2463 2641 3.818982 GACACTGCACCGTCGACGT 62.819 63.158 33.49 20.15 37.74 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.377327 ACACGTGATTGAAACTCTTGAATT 57.623 33.333 25.01 0.00 0.00 2.17
1 2 6.377327 AACACGTGATTGAAACTCTTGAAT 57.623 33.333 25.01 0.00 0.00 2.57
2 3 5.811399 AACACGTGATTGAAACTCTTGAA 57.189 34.783 25.01 0.00 0.00 2.69
3 4 5.811399 AAACACGTGATTGAAACTCTTGA 57.189 34.783 25.01 0.00 0.00 3.02
4 5 6.869421 AAAAACACGTGATTGAAACTCTTG 57.131 33.333 25.01 0.00 0.00 3.02
42 43 8.299570 GCCTCTTTGATTCACAAGATTCTTAAA 58.700 33.333 0.00 0.00 39.77 1.52
43 44 7.094205 GGCCTCTTTGATTCACAAGATTCTTAA 60.094 37.037 0.00 0.00 39.77 1.85
44 45 6.375455 GGCCTCTTTGATTCACAAGATTCTTA 59.625 38.462 0.00 0.00 39.77 2.10
45 46 5.184671 GGCCTCTTTGATTCACAAGATTCTT 59.815 40.000 0.00 0.00 39.77 2.52
46 47 4.704057 GGCCTCTTTGATTCACAAGATTCT 59.296 41.667 0.00 0.00 39.77 2.40
47 48 4.142293 GGGCCTCTTTGATTCACAAGATTC 60.142 45.833 0.84 6.67 39.77 2.52
48 49 3.766051 GGGCCTCTTTGATTCACAAGATT 59.234 43.478 0.84 0.00 39.77 2.40
49 50 3.359950 GGGCCTCTTTGATTCACAAGAT 58.640 45.455 0.84 0.00 39.77 2.40
50 51 2.795329 GGGCCTCTTTGATTCACAAGA 58.205 47.619 0.84 9.44 39.77 3.02
51 52 1.470098 CGGGCCTCTTTGATTCACAAG 59.530 52.381 0.84 0.00 39.77 3.16
52 53 1.073125 TCGGGCCTCTTTGATTCACAA 59.927 47.619 0.84 0.00 36.65 3.33
53 54 0.690192 TCGGGCCTCTTTGATTCACA 59.310 50.000 0.84 0.00 0.00 3.58
54 55 1.821216 TTCGGGCCTCTTTGATTCAC 58.179 50.000 0.84 0.00 0.00 3.18
55 56 2.577606 TTTCGGGCCTCTTTGATTCA 57.422 45.000 0.84 0.00 0.00 2.57
56 57 3.565902 CCTATTTCGGGCCTCTTTGATTC 59.434 47.826 0.84 0.00 0.00 2.52
57 58 3.555966 CCTATTTCGGGCCTCTTTGATT 58.444 45.455 0.84 0.00 0.00 2.57
58 59 2.158608 CCCTATTTCGGGCCTCTTTGAT 60.159 50.000 0.84 0.00 37.41 2.57
59 60 1.211949 CCCTATTTCGGGCCTCTTTGA 59.788 52.381 0.84 0.00 37.41 2.69
60 61 1.211949 TCCCTATTTCGGGCCTCTTTG 59.788 52.381 0.84 0.00 44.30 2.77
61 62 1.212195 GTCCCTATTTCGGGCCTCTTT 59.788 52.381 0.84 0.00 44.30 2.52
62 63 0.837940 GTCCCTATTTCGGGCCTCTT 59.162 55.000 0.84 0.00 44.30 2.85
63 64 1.054978 GGTCCCTATTTCGGGCCTCT 61.055 60.000 0.84 0.00 44.30 3.69
64 65 1.054978 AGGTCCCTATTTCGGGCCTC 61.055 60.000 0.84 0.00 43.09 4.70
65 66 1.004361 AGGTCCCTATTTCGGGCCT 59.996 57.895 0.84 0.00 44.30 5.19
66 67 1.342672 TGAGGTCCCTATTTCGGGCC 61.343 60.000 0.00 0.00 44.30 5.80
67 68 0.765510 ATGAGGTCCCTATTTCGGGC 59.234 55.000 0.00 0.00 44.30 6.13
68 69 1.768870 ACATGAGGTCCCTATTTCGGG 59.231 52.381 0.00 0.00 46.13 5.14
69 70 3.560636 AACATGAGGTCCCTATTTCGG 57.439 47.619 0.00 0.00 0.00 4.30
70 71 3.627577 CCAAACATGAGGTCCCTATTTCG 59.372 47.826 0.00 0.00 0.00 3.46
71 72 4.600062 ACCAAACATGAGGTCCCTATTTC 58.400 43.478 0.00 0.00 30.79 2.17
72 73 4.675063 ACCAAACATGAGGTCCCTATTT 57.325 40.909 0.00 0.00 30.79 1.40
73 74 4.675063 AACCAAACATGAGGTCCCTATT 57.325 40.909 0.00 0.00 37.07 1.73
74 75 4.569865 GGAAACCAAACATGAGGTCCCTAT 60.570 45.833 0.00 0.00 37.07 2.57
75 76 3.245122 GGAAACCAAACATGAGGTCCCTA 60.245 47.826 0.00 0.00 37.07 3.53
76 77 2.490902 GGAAACCAAACATGAGGTCCCT 60.491 50.000 0.00 0.00 37.07 4.20
77 78 1.893137 GGAAACCAAACATGAGGTCCC 59.107 52.381 0.00 6.12 37.07 4.46
78 79 2.820197 GAGGAAACCAAACATGAGGTCC 59.180 50.000 0.00 3.31 37.07 4.46
79 80 2.484264 CGAGGAAACCAAACATGAGGTC 59.516 50.000 0.00 0.00 37.07 3.85
80 81 2.105821 TCGAGGAAACCAAACATGAGGT 59.894 45.455 0.00 1.07 40.61 3.85
81 82 2.778299 TCGAGGAAACCAAACATGAGG 58.222 47.619 0.00 0.35 0.00 3.86
82 83 4.829064 TTTCGAGGAAACCAAACATGAG 57.171 40.909 0.00 0.00 0.00 2.90
83 84 5.782893 ATTTTCGAGGAAACCAAACATGA 57.217 34.783 0.00 0.00 30.83 3.07
84 85 5.405269 GGAATTTTCGAGGAAACCAAACATG 59.595 40.000 0.00 0.00 30.83 3.21
85 86 5.304357 AGGAATTTTCGAGGAAACCAAACAT 59.696 36.000 0.00 0.00 30.83 2.71
86 87 4.647399 AGGAATTTTCGAGGAAACCAAACA 59.353 37.500 0.00 0.00 30.83 2.83
87 88 5.196341 AGGAATTTTCGAGGAAACCAAAC 57.804 39.130 0.00 0.00 30.83 2.93
88 89 8.817092 ATATAGGAATTTTCGAGGAAACCAAA 57.183 30.769 0.00 0.00 30.83 3.28
89 90 9.908747 TTATATAGGAATTTTCGAGGAAACCAA 57.091 29.630 0.00 0.00 30.83 3.67
131 132 9.364989 TGTCGTTTGAAAAAGAAAAGAATTGAT 57.635 25.926 0.00 0.00 0.00 2.57
132 133 8.643752 GTGTCGTTTGAAAAAGAAAAGAATTGA 58.356 29.630 0.00 0.00 0.00 2.57
133 134 7.897800 GGTGTCGTTTGAAAAAGAAAAGAATTG 59.102 33.333 0.00 0.00 0.00 2.32
134 135 7.600752 TGGTGTCGTTTGAAAAAGAAAAGAATT 59.399 29.630 0.00 0.00 0.00 2.17
135 136 7.093992 TGGTGTCGTTTGAAAAAGAAAAGAAT 58.906 30.769 0.00 0.00 0.00 2.40
136 137 6.448006 TGGTGTCGTTTGAAAAAGAAAAGAA 58.552 32.000 0.00 0.00 0.00 2.52
137 138 6.015027 TGGTGTCGTTTGAAAAAGAAAAGA 57.985 33.333 0.00 0.00 0.00 2.52
138 139 6.698359 TTGGTGTCGTTTGAAAAAGAAAAG 57.302 33.333 0.00 0.00 0.00 2.27
139 140 7.659652 ATTTGGTGTCGTTTGAAAAAGAAAA 57.340 28.000 0.00 0.00 0.00 2.29
140 141 8.934507 ATATTTGGTGTCGTTTGAAAAAGAAA 57.065 26.923 0.00 0.00 0.00 2.52
141 142 8.191446 TGATATTTGGTGTCGTTTGAAAAAGAA 58.809 29.630 0.00 0.00 0.00 2.52
142 143 7.708051 TGATATTTGGTGTCGTTTGAAAAAGA 58.292 30.769 0.00 0.00 0.00 2.52
143 144 7.922505 TGATATTTGGTGTCGTTTGAAAAAG 57.077 32.000 0.00 0.00 0.00 2.27
144 145 7.596995 GGATGATATTTGGTGTCGTTTGAAAAA 59.403 33.333 0.00 0.00 0.00 1.94
145 146 7.087639 GGATGATATTTGGTGTCGTTTGAAAA 58.912 34.615 0.00 0.00 0.00 2.29
146 147 6.207614 TGGATGATATTTGGTGTCGTTTGAAA 59.792 34.615 0.00 0.00 0.00 2.69
147 148 5.707764 TGGATGATATTTGGTGTCGTTTGAA 59.292 36.000 0.00 0.00 0.00 2.69
148 149 5.123186 GTGGATGATATTTGGTGTCGTTTGA 59.877 40.000 0.00 0.00 0.00 2.69
149 150 5.106357 TGTGGATGATATTTGGTGTCGTTTG 60.106 40.000 0.00 0.00 0.00 2.93
150 151 5.007034 TGTGGATGATATTTGGTGTCGTTT 58.993 37.500 0.00 0.00 0.00 3.60
151 152 4.394920 GTGTGGATGATATTTGGTGTCGTT 59.605 41.667 0.00 0.00 0.00 3.85
152 153 3.938963 GTGTGGATGATATTTGGTGTCGT 59.061 43.478 0.00 0.00 0.00 4.34
153 154 4.191544 AGTGTGGATGATATTTGGTGTCG 58.808 43.478 0.00 0.00 0.00 4.35
154 155 6.515272 AAAGTGTGGATGATATTTGGTGTC 57.485 37.500 0.00 0.00 0.00 3.67
155 156 7.402054 TCTAAAGTGTGGATGATATTTGGTGT 58.598 34.615 0.00 0.00 0.00 4.16
156 157 7.864108 TCTAAAGTGTGGATGATATTTGGTG 57.136 36.000 0.00 0.00 0.00 4.17
157 158 9.479549 AAATCTAAAGTGTGGATGATATTTGGT 57.520 29.630 0.00 0.00 0.00 3.67
223 224 4.451900 AGGTAAGATTGCCCTTGTTATCG 58.548 43.478 0.00 0.00 32.86 2.92
224 225 5.299531 GGAAGGTAAGATTGCCCTTGTTATC 59.700 44.000 0.00 0.00 38.68 1.75
261 262 8.195436 TCCTAAAAGACACGGTCAGATTATAAG 58.805 37.037 6.78 0.00 34.60 1.73
263 264 7.649533 TCCTAAAAGACACGGTCAGATTATA 57.350 36.000 6.78 0.00 34.60 0.98
264 265 6.540438 TCCTAAAAGACACGGTCAGATTAT 57.460 37.500 6.78 0.00 34.60 1.28
265 266 5.988310 TCCTAAAAGACACGGTCAGATTA 57.012 39.130 6.78 2.99 34.60 1.75
266 267 4.884668 TCCTAAAAGACACGGTCAGATT 57.115 40.909 6.78 2.17 34.60 2.40
267 268 5.422214 AATCCTAAAAGACACGGTCAGAT 57.578 39.130 6.78 0.00 34.60 2.90
269 270 6.594159 ACATAAATCCTAAAAGACACGGTCAG 59.406 38.462 6.78 0.00 34.60 3.51
270 271 6.370442 CACATAAATCCTAAAAGACACGGTCA 59.630 38.462 6.78 0.00 34.60 4.02
271 272 6.370718 ACACATAAATCCTAAAAGACACGGTC 59.629 38.462 0.00 0.00 0.00 4.79
272 273 6.235664 ACACATAAATCCTAAAAGACACGGT 58.764 36.000 0.00 0.00 0.00 4.83
273 274 6.737254 ACACATAAATCCTAAAAGACACGG 57.263 37.500 0.00 0.00 0.00 4.94
283 284 9.416284 GGGAATAGGAAAAACACATAAATCCTA 57.584 33.333 2.14 2.14 42.12 2.94
288 289 8.102047 TCGTAGGGAATAGGAAAAACACATAAA 58.898 33.333 0.00 0.00 0.00 1.40
307 308 6.377327 AAATTATGTGCTTGATTCGTAGGG 57.623 37.500 0.00 0.00 0.00 3.53
465 466 9.743057 CATTCACAAAACTGAATTAGTACCAAA 57.257 29.630 0.00 0.00 38.57 3.28
467 468 8.458573 ACATTCACAAAACTGAATTAGTACCA 57.541 30.769 0.00 0.00 38.57 3.25
468 469 9.180678 CAACATTCACAAAACTGAATTAGTACC 57.819 33.333 0.00 0.00 38.57 3.34
478 516 9.609950 AAAACAAAATCAACATTCACAAAACTG 57.390 25.926 0.00 0.00 0.00 3.16
522 560 8.626526 GTTTTGTCCCAAGTCAAAGTATTTCTA 58.373 33.333 0.00 0.00 35.03 2.10
538 576 4.098914 AGTCTGCATAAGTTTTGTCCCA 57.901 40.909 0.00 0.00 0.00 4.37
539 577 6.569179 TTTAGTCTGCATAAGTTTTGTCCC 57.431 37.500 0.00 0.00 0.00 4.46
546 584 7.552687 TCCGATCATTTTTAGTCTGCATAAGTT 59.447 33.333 0.00 0.00 0.00 2.66
568 608 8.609176 GTTATATGTGCAAAATACTTTCTCCGA 58.391 33.333 0.00 0.00 0.00 4.55
618 664 8.560124 ACCAATAGATCTTGATAGGACTTCTT 57.440 34.615 0.00 0.00 0.00 2.52
626 672 6.091441 GCGGCTTTACCAATAGATCTTGATAG 59.909 42.308 0.00 0.00 39.03 2.08
628 674 4.757149 GCGGCTTTACCAATAGATCTTGAT 59.243 41.667 0.00 0.00 39.03 2.57
638 684 1.365699 CTACGTGCGGCTTTACCAAT 58.634 50.000 0.00 0.00 39.03 3.16
646 692 4.323477 TTTGGGCTACGTGCGGCT 62.323 61.111 0.00 0.00 44.05 5.52
648 694 3.428282 GGTTTGGGCTACGTGCGG 61.428 66.667 0.00 0.00 44.05 5.69
652 698 0.968405 TTCTACGGTTTGGGCTACGT 59.032 50.000 0.00 0.00 42.71 3.57
690 736 9.445878 TGAATCTACGGGTGTATACTAATAGAG 57.554 37.037 4.17 0.00 0.00 2.43
694 740 7.039923 CCAGTGAATCTACGGGTGTATACTAAT 60.040 40.741 4.17 0.00 32.19 1.73
698 744 4.581824 TCCAGTGAATCTACGGGTGTATAC 59.418 45.833 0.00 0.00 37.23 1.47
699 745 4.581824 GTCCAGTGAATCTACGGGTGTATA 59.418 45.833 0.00 0.00 37.23 1.47
717 770 1.002366 GCGTAGTGCATCTTGTCCAG 58.998 55.000 0.00 0.00 45.45 3.86
823 905 2.922758 GCGTGTAGGATAGATTCGCAGG 60.923 54.545 0.00 0.00 41.42 4.85
833 920 1.237533 TTATCCGCGCGTGTAGGATA 58.762 50.000 29.95 22.88 43.77 2.59
834 921 0.386476 TTTATCCGCGCGTGTAGGAT 59.614 50.000 29.95 23.93 45.75 3.24
835 922 0.173029 TTTTATCCGCGCGTGTAGGA 59.827 50.000 29.95 18.60 38.56 2.94
836 923 0.299597 GTTTTATCCGCGCGTGTAGG 59.700 55.000 29.95 13.21 0.00 3.18
837 924 0.044499 CGTTTTATCCGCGCGTGTAG 60.044 55.000 29.95 13.63 0.00 2.74
890 977 3.656045 AAAAGTTGGCGACCGCGG 61.656 61.111 26.86 26.86 43.06 6.46
891 978 2.426752 CAAAAGTTGGCGACCGCG 60.427 61.111 8.36 0.00 43.06 6.46
892 979 2.729491 GCAAAAGTTGGCGACCGC 60.729 61.111 5.75 5.75 41.06 5.68
999 1112 0.106318 GCAGGAGAAGATGGCCCATT 60.106 55.000 0.00 0.00 0.00 3.16
1139 1263 2.745884 TCCAACCGCATCGCAAGG 60.746 61.111 0.00 0.00 38.47 3.61
1164 1288 2.993853 GAGGAGGCAGGAACAGGG 59.006 66.667 0.00 0.00 0.00 4.45
1310 1438 1.637338 TCTTCCTCTTCTGCAGCTCA 58.363 50.000 9.47 0.00 0.00 4.26
1330 1458 1.004161 GCCCAAGCTCTTTCTCCTTCT 59.996 52.381 0.00 0.00 35.50 2.85
1335 1463 2.402572 GGCGCCCAAGCTCTTTCTC 61.403 63.158 18.11 0.00 36.60 2.87
1340 1468 4.809496 CCATGGCGCCCAAGCTCT 62.809 66.667 26.77 0.00 36.95 4.09
1374 1502 4.631740 TGCTCTCCCACCACCGGA 62.632 66.667 9.46 0.00 0.00 5.14
1490 1627 9.237187 TCGCTAGCTATACTACTAGTTCTACTA 57.763 37.037 13.93 0.00 38.50 1.82
1491 1628 8.121305 TCGCTAGCTATACTACTAGTTCTACT 57.879 38.462 13.93 0.00 38.50 2.57
1492 1629 8.931385 ATCGCTAGCTATACTACTAGTTCTAC 57.069 38.462 13.93 0.00 38.50 2.59
1493 1630 8.970020 AGATCGCTAGCTATACTACTAGTTCTA 58.030 37.037 13.93 0.00 38.50 2.10
1494 1631 7.844009 AGATCGCTAGCTATACTACTAGTTCT 58.156 38.462 13.93 0.45 38.50 3.01
1495 1632 8.483307 AAGATCGCTAGCTATACTACTAGTTC 57.517 38.462 13.93 0.00 38.50 3.01
1496 1633 8.851541 AAAGATCGCTAGCTATACTACTAGTT 57.148 34.615 13.93 0.00 38.50 2.24
1497 1634 8.723311 CAAAAGATCGCTAGCTATACTACTAGT 58.277 37.037 13.93 0.00 38.50 2.57
1498 1635 8.178964 CCAAAAGATCGCTAGCTATACTACTAG 58.821 40.741 13.93 0.00 39.13 2.57
1499 1636 7.120873 CCCAAAAGATCGCTAGCTATACTACTA 59.879 40.741 13.93 0.00 0.00 1.82
1500 1637 6.071840 CCCAAAAGATCGCTAGCTATACTACT 60.072 42.308 13.93 0.00 0.00 2.57
1501 1638 6.094061 CCCAAAAGATCGCTAGCTATACTAC 58.906 44.000 13.93 0.00 0.00 2.73
1502 1639 5.185249 CCCCAAAAGATCGCTAGCTATACTA 59.815 44.000 13.93 0.00 0.00 1.82
1509 1646 0.107165 ACCCCCAAAAGATCGCTAGC 60.107 55.000 4.06 4.06 0.00 3.42
1510 1647 2.420058 AACCCCCAAAAGATCGCTAG 57.580 50.000 0.00 0.00 0.00 3.42
1514 1651 2.231235 CCAAGAAACCCCCAAAAGATCG 59.769 50.000 0.00 0.00 0.00 3.69
1527 1677 4.620982 CCAAACAAGATCCACCAAGAAAC 58.379 43.478 0.00 0.00 0.00 2.78
1549 1699 1.536709 CCACCAGTTGCACAAGAAAGC 60.537 52.381 0.00 0.00 0.00 3.51
1561 1713 1.590147 GATCGACCGACCACCAGTT 59.410 57.895 0.00 0.00 0.00 3.16
1639 1797 1.602377 GAACAAGAACGGGACACCAAG 59.398 52.381 0.00 0.00 36.13 3.61
1685 1847 2.158696 CGTACTAGCTGGTAGTAGGGGT 60.159 54.545 26.81 8.51 43.61 4.95
1686 1848 2.502295 CGTACTAGCTGGTAGTAGGGG 58.498 57.143 26.81 16.59 43.61 4.79
1745 1910 1.503818 ATCAACGCGGCAAACTCGTT 61.504 50.000 12.47 0.00 45.77 3.85
1758 1923 2.447250 GTCTGCATTGCATGATCAACG 58.553 47.619 12.53 0.00 38.13 4.10
1772 1937 1.005748 CAGCTCCTTGACGTCTGCA 60.006 57.895 17.92 0.00 0.00 4.41
1773 1938 1.739562 CCAGCTCCTTGACGTCTGC 60.740 63.158 17.92 12.49 0.00 4.26
1804 1976 2.410053 GTGAGAGCACGACAAAGCTAAG 59.590 50.000 0.00 0.00 42.04 2.18
1806 1978 2.065993 GTGAGAGCACGACAAAGCTA 57.934 50.000 0.00 0.00 42.04 3.32
1816 1988 0.800300 GCTGCTACGAGTGAGAGCAC 60.800 60.000 0.00 0.00 41.18 4.40
1825 1997 3.059570 CGTAAAACTTCAGCTGCTACGAG 59.940 47.826 9.47 7.75 34.16 4.18
1828 2000 3.664537 GCACGTAAAACTTCAGCTGCTAC 60.665 47.826 9.47 2.81 0.00 3.58
1829 2001 2.478894 GCACGTAAAACTTCAGCTGCTA 59.521 45.455 9.47 0.00 0.00 3.49
1830 2002 1.264288 GCACGTAAAACTTCAGCTGCT 59.736 47.619 9.47 0.00 0.00 4.24
1831 2003 1.264288 AGCACGTAAAACTTCAGCTGC 59.736 47.619 9.47 0.00 0.00 5.25
1832 2004 2.908634 CAGCACGTAAAACTTCAGCTG 58.091 47.619 7.63 7.63 41.45 4.24
1833 2005 2.561569 ACAGCACGTAAAACTTCAGCT 58.438 42.857 0.00 0.00 0.00 4.24
1835 2007 6.758593 TTAGTACAGCACGTAAAACTTCAG 57.241 37.500 0.00 0.00 0.00 3.02
1836 2008 7.115805 CAGATTAGTACAGCACGTAAAACTTCA 59.884 37.037 0.00 0.00 0.00 3.02
1837 2009 7.411588 CCAGATTAGTACAGCACGTAAAACTTC 60.412 40.741 0.00 0.00 0.00 3.01
1838 2010 6.367969 CCAGATTAGTACAGCACGTAAAACTT 59.632 38.462 0.00 0.00 0.00 2.66
1839 2011 5.867716 CCAGATTAGTACAGCACGTAAAACT 59.132 40.000 0.00 0.00 0.00 2.66
1840 2012 5.636543 ACCAGATTAGTACAGCACGTAAAAC 59.363 40.000 0.00 0.00 0.00 2.43
1841 2013 5.786311 ACCAGATTAGTACAGCACGTAAAA 58.214 37.500 0.00 0.00 0.00 1.52
1972 2144 0.178967 TGCCCCATGCTTCACTTGAA 60.179 50.000 0.00 0.00 42.00 2.69
1986 2158 4.729918 CTGTGCCTCCTGTGCCCC 62.730 72.222 0.00 0.00 0.00 5.80
1987 2159 4.729918 CCTGTGCCTCCTGTGCCC 62.730 72.222 0.00 0.00 0.00 5.36
1989 2161 1.673665 CTTCCTGTGCCTCCTGTGC 60.674 63.158 0.00 0.00 0.00 4.57
1990 2162 1.002868 CCTTCCTGTGCCTCCTGTG 60.003 63.158 0.00 0.00 0.00 3.66
1991 2163 1.152030 TCCTTCCTGTGCCTCCTGT 60.152 57.895 0.00 0.00 0.00 4.00
1992 2164 0.906756 TCTCCTTCCTGTGCCTCCTG 60.907 60.000 0.00 0.00 0.00 3.86
1993 2165 0.178891 TTCTCCTTCCTGTGCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
1994 2166 0.693049 TTTCTCCTTCCTGTGCCTCC 59.307 55.000 0.00 0.00 0.00 4.30
1996 2168 3.054065 CCTTATTTCTCCTTCCTGTGCCT 60.054 47.826 0.00 0.00 0.00 4.75
2004 2177 6.512297 TGTGTTTTTGCCTTATTTCTCCTTC 58.488 36.000 0.00 0.00 0.00 3.46
2005 2178 6.478512 TGTGTTTTTGCCTTATTTCTCCTT 57.521 33.333 0.00 0.00 0.00 3.36
2017 2190 3.743396 TGTGTTGTCTTTGTGTTTTTGCC 59.257 39.130 0.00 0.00 0.00 4.52
2024 2197 1.065401 CGCCATGTGTTGTCTTTGTGT 59.935 47.619 0.00 0.00 0.00 3.72
2025 2198 1.600164 CCGCCATGTGTTGTCTTTGTG 60.600 52.381 0.00 0.00 0.00 3.33
2029 2202 1.603455 CCCCGCCATGTGTTGTCTT 60.603 57.895 0.00 0.00 0.00 3.01
2060 2237 4.033776 CGCCCATGGTGTCCCTGT 62.034 66.667 11.73 0.00 0.00 4.00
2066 2244 4.015406 TTCGAGCGCCCATGGTGT 62.015 61.111 11.73 0.00 35.34 4.16
2085 2263 3.449227 TCTCGGCTAGCCACGGTG 61.449 66.667 32.47 16.38 35.37 4.94
2086 2264 2.547640 TAGTCTCGGCTAGCCACGGT 62.548 60.000 32.47 15.15 35.37 4.83
2088 2266 0.454600 TTTAGTCTCGGCTAGCCACG 59.545 55.000 32.47 21.80 35.37 4.94
2094 2272 3.093814 TGTCATGGTTTAGTCTCGGCTA 58.906 45.455 0.00 0.00 0.00 3.93
2134 2312 2.123683 TTGCCCCGGTGCTTTTCA 60.124 55.556 11.12 0.00 0.00 2.69
2187 2365 0.906775 ACCGTTCGAATGTACCCCAT 59.093 50.000 15.92 0.00 34.36 4.00
2224 2402 2.125673 ACATAGGTGTCGTGGCGC 60.126 61.111 0.00 0.00 31.41 6.53
2232 2410 2.668632 CCGGTGGCACATAGGTGT 59.331 61.111 20.82 0.00 46.95 4.16
2250 2428 0.953960 GGTGGTGCCCTTTGACTACG 60.954 60.000 0.00 0.00 0.00 3.51
2255 2433 2.520458 CCTGGTGGTGCCCTTTGA 59.480 61.111 0.00 0.00 36.04 2.69
2257 2435 1.799157 TATGCCTGGTGGTGCCCTTT 61.799 55.000 0.00 0.00 36.04 3.11
2265 2443 0.911769 TGGAGTTCTATGCCTGGTGG 59.088 55.000 0.00 0.00 0.00 4.61
2271 2449 1.208052 TGCTCTGTGGAGTTCTATGCC 59.792 52.381 0.00 0.00 41.38 4.40
2287 2465 2.235016 TGTGGTGTTTTGGGTATGCTC 58.765 47.619 0.00 0.00 0.00 4.26
2292 2470 2.379972 CCTGTTGTGGTGTTTTGGGTA 58.620 47.619 0.00 0.00 0.00 3.69
2293 2471 1.190643 CCTGTTGTGGTGTTTTGGGT 58.809 50.000 0.00 0.00 0.00 4.51
2303 2481 4.217210 TGGTGCCCCCTGTTGTGG 62.217 66.667 0.00 0.00 0.00 4.17
2322 2500 3.847709 GCTGCAGTTCGAGCGCTC 61.848 66.667 27.64 27.64 33.85 5.03
2336 2514 3.716006 CTGTTGTGGTCGCCGCTG 61.716 66.667 10.13 0.00 34.70 5.18
2337 2515 4.988598 CCTGTTGTGGTCGCCGCT 62.989 66.667 10.13 0.00 34.70 5.52
2342 2520 4.263572 TGCCCCCTGTTGTGGTCG 62.264 66.667 0.00 0.00 0.00 4.79
2343 2521 2.597510 GTGCCCCCTGTTGTGGTC 60.598 66.667 0.00 0.00 0.00 4.02
2344 2522 4.218686 GGTGCCCCCTGTTGTGGT 62.219 66.667 0.00 0.00 0.00 4.16
2345 2523 4.217210 TGGTGCCCCCTGTTGTGG 62.217 66.667 0.00 0.00 0.00 4.17
2346 2524 2.912025 GTGGTGCCCCCTGTTGTG 60.912 66.667 0.00 0.00 0.00 3.33
2347 2525 4.579384 CGTGGTGCCCCCTGTTGT 62.579 66.667 0.00 0.00 0.00 3.32
2348 2526 4.263572 TCGTGGTGCCCCCTGTTG 62.264 66.667 0.00 0.00 0.00 3.33
2349 2527 3.953775 CTCGTGGTGCCCCCTGTT 61.954 66.667 0.00 0.00 0.00 3.16
2364 2542 3.847709 GCTGCAGTTCGAGCGCTC 61.848 66.667 27.64 27.64 33.85 5.03
2378 2556 3.716006 CTGTTGTGGTCGCCGCTG 61.716 66.667 10.13 0.00 34.70 5.18
2379 2557 4.988598 CCTGTTGTGGTCGCCGCT 62.989 66.667 10.13 0.00 34.70 5.52
2384 2562 4.263572 TGCCCCCTGTTGTGGTCG 62.264 66.667 0.00 0.00 0.00 4.79
2385 2563 2.597510 GTGCCCCCTGTTGTGGTC 60.598 66.667 0.00 0.00 0.00 4.02
2386 2564 4.218686 GGTGCCCCCTGTTGTGGT 62.219 66.667 0.00 0.00 0.00 4.16
2387 2565 4.217210 TGGTGCCCCCTGTTGTGG 62.217 66.667 0.00 0.00 0.00 4.17
2388 2566 2.912025 GTGGTGCCCCCTGTTGTG 60.912 66.667 0.00 0.00 0.00 3.33
2389 2567 4.579384 CGTGGTGCCCCCTGTTGT 62.579 66.667 0.00 0.00 0.00 3.32
2390 2568 4.263572 TCGTGGTGCCCCCTGTTG 62.264 66.667 0.00 0.00 0.00 3.33
2391 2569 3.953775 CTCGTGGTGCCCCCTGTT 61.954 66.667 0.00 0.00 0.00 3.16
2440 2618 1.301716 GACGGTGCAGTGTCATGGT 60.302 57.895 12.21 0.00 35.20 3.55


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

AutoCloner maintained by Alex Coulton.