Multiple sequence alignment - TraesCS7D01G384300

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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 TraesCS7D01G384300 chr7D 100.000 2243 0 0 1 2243 498286208 498283966 0.000000e+00 4143.0
1 TraesCS7D01G384300 chr7D 88.172 93 7 1 1594 1682 407262105 407262197 8.470000e-20 108.0
2 TraesCS7D01G384300 chr7D 89.412 85 5 1 1599 1679 464039268 464039184 1.100000e-18 104.0
3 TraesCS7D01G384300 chr2B 92.034 590 39 3 1658 2243 757391616 757391031 0.000000e+00 822.0
4 TraesCS7D01G384300 chr2B 81.600 1000 96 45 571 1524 757394936 757393979 0.000000e+00 747.0
5 TraesCS7D01G384300 chr2B 83.262 699 65 22 860 1524 757453260 757452580 1.480000e-166 595.0
6 TraesCS7D01G384300 chr2B 81.395 688 87 28 860 1522 757433762 757433091 7.100000e-145 523.0
7 TraesCS7D01G384300 chr2B 83.181 547 49 24 1525 2051 757452540 757452017 5.640000e-126 460.0
8 TraesCS7D01G384300 chr2B 89.877 326 25 3 1922 2243 757232352 757232031 1.600000e-111 412.0
9 TraesCS7D01G384300 chr2B 76.015 813 107 48 731 1527 757016167 757015427 7.670000e-90 340.0
10 TraesCS7D01G384300 chr2B 90.800 250 23 0 1000 1249 757241618 757241369 3.570000e-88 335.0
11 TraesCS7D01G384300 chr2B 82.036 334 29 16 860 1188 757561881 757561574 2.860000e-64 255.0
12 TraesCS7D01G384300 chr2B 83.026 271 22 16 63 317 757454120 757453858 8.060000e-55 224.0
13 TraesCS7D01G384300 chr2B 90.351 114 11 0 571 684 757562185 757562072 1.390000e-32 150.0
14 TraesCS7D01G384300 chr2B 96.923 65 2 0 860 924 757295709 757295645 2.360000e-20 110.0
15 TraesCS7D01G384300 chr2B 79.245 159 23 8 209 364 757243941 757243790 3.940000e-18 102.0
16 TraesCS7D01G384300 chr2B 88.636 44 5 0 450 493 637044009 637044052 1.000000e-03 54.7
17 TraesCS7D01G384300 chr2B 100.000 28 0 0 1659 1686 801055147 801055120 4.000000e-03 52.8
18 TraesCS7D01G384300 chr2A 80.466 1029 103 58 571 1524 750365870 750364865 0.000000e+00 697.0
19 TraesCS7D01G384300 chr2A 78.142 549 72 26 731 1263 750188735 750189251 2.800000e-79 305.0
20 TraesCS7D01G384300 chr2A 82.938 211 23 10 111 317 750366524 750366323 6.370000e-41 178.0
21 TraesCS7D01G384300 chr2A 82.390 159 21 3 1366 1524 750424728 750424577 5.030000e-27 132.0
22 TraesCS7D01G384300 chr2A 82.143 140 18 4 1684 1820 750332212 750332077 1.820000e-21 113.0
23 TraesCS7D01G384300 chr2A 79.885 174 17 7 209 364 750426338 750426165 6.550000e-21 111.0
24 TraesCS7D01G384300 chr2A 83.178 107 17 1 1702 1807 750423731 750423625 1.830000e-16 97.1
25 TraesCS7D01G384300 chr2D 80.889 675 85 26 860 1522 610757501 610756859 2.000000e-135 492.0
26 TraesCS7D01G384300 chr2D 76.400 1089 133 61 503 1527 619313075 619312047 7.250000e-130 473.0
27 TraesCS7D01G384300 chr1A 86.076 158 18 2 1683 1836 108778656 108778813 1.380000e-37 167.0
28 TraesCS7D01G384300 chr7A 87.943 141 14 1 1683 1820 477182905 477183045 1.780000e-36 163.0
29 TraesCS7D01G384300 chr7A 87.097 93 7 2 1594 1682 465783360 465783451 1.420000e-17 100.0
30 TraesCS7D01G384300 chr1B 85.065 154 16 4 1371 1524 121012020 121012166 1.390000e-32 150.0
31 TraesCS7D01G384300 chr1D 85.938 128 15 2 1683 1807 77450855 77450982 1.400000e-27 134.0
32 TraesCS7D01G384300 chr7B 88.172 93 7 1 1594 1682 418768023 418768115 8.470000e-20 108.0
33 TraesCS7D01G384300 chr7B 94.595 37 2 0 456 492 712747878 712747914 8.650000e-05 58.4
34 TraesCS7D01G384300 chr4D 87.500 80 6 1 1600 1679 226631073 226631148 3.070000e-14 89.8
35 TraesCS7D01G384300 chr5A 85.227 88 10 2 1598 1682 677957930 677957843 1.100000e-13 87.9
36 TraesCS7D01G384300 chr5A 92.105 38 3 0 449 486 295728816 295728779 1.000000e-03 54.7
37 TraesCS7D01G384300 chr6A 84.043 94 8 5 1592 1679 3919910 3920002 1.430000e-12 84.2
38 TraesCS7D01G384300 chr6A 92.683 41 2 1 446 486 7399133 7399094 8.650000e-05 58.4
39 TraesCS7D01G384300 chr6D 91.525 59 5 0 1600 1658 4845802 4845860 5.130000e-12 82.4
40 TraesCS7D01G384300 chr3B 87.719 57 5 1 1623 1679 269249811 269249757 5.170000e-07 65.8
41 TraesCS7D01G384300 chr3B 91.892 37 3 0 450 486 786966139 786966175 4.000000e-03 52.8
42 TraesCS7D01G384300 chr6B 92.308 39 3 0 448 486 409296789 409296751 3.110000e-04 56.5
43 TraesCS7D01G384300 chr5B 92.105 38 3 0 449 486 249581808 249581845 1.000000e-03 54.7


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 TraesCS7D01G384300 chr7D 498283966 498286208 2242 True 4143.000000 4143 100.000000 1 2243 1 chr7D.!!$R2 2242
1 TraesCS7D01G384300 chr2B 757391031 757394936 3905 True 784.500000 822 86.817000 571 2243 2 chr2B.!!$R7 1672
2 TraesCS7D01G384300 chr2B 757433091 757433762 671 True 523.000000 523 81.395000 860 1522 1 chr2B.!!$R4 662
3 TraesCS7D01G384300 chr2B 757452017 757454120 2103 True 426.333333 595 83.156333 63 2051 3 chr2B.!!$R8 1988
4 TraesCS7D01G384300 chr2B 757015427 757016167 740 True 340.000000 340 76.015000 731 1527 1 chr2B.!!$R1 796
5 TraesCS7D01G384300 chr2B 757241369 757243941 2572 True 218.500000 335 85.022500 209 1249 2 chr2B.!!$R6 1040
6 TraesCS7D01G384300 chr2B 757561574 757562185 611 True 202.500000 255 86.193500 571 1188 2 chr2B.!!$R9 617
7 TraesCS7D01G384300 chr2A 750364865 750366524 1659 True 437.500000 697 81.702000 111 1524 2 chr2A.!!$R2 1413
8 TraesCS7D01G384300 chr2A 750188735 750189251 516 False 305.000000 305 78.142000 731 1263 1 chr2A.!!$F1 532
9 TraesCS7D01G384300 chr2D 610756859 610757501 642 True 492.000000 492 80.889000 860 1522 1 chr2D.!!$R1 662
10 TraesCS7D01G384300 chr2D 619312047 619313075 1028 True 473.000000 473 76.400000 503 1527 1 chr2D.!!$R2 1024

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
239 254 0.044092 TATTCCACCTGCTCCCTCCA 59.956 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 6453 0.108851 TTAACGCGAGCAGATGCAGA 60.109 50.0 15.93 0.0 45.16 4.26 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
44 45 7.486407 AAAATCAATGGACAAAGGCTTATCT 57.514 32.000 0.00 0.00 0.00 1.98
45 46 7.486407 AAATCAATGGACAAAGGCTTATCTT 57.514 32.000 0.00 0.00 0.00 2.40
46 47 7.486407 AATCAATGGACAAAGGCTTATCTTT 57.514 32.000 0.00 0.00 37.44 2.52
47 48 6.515272 TCAATGGACAAAGGCTTATCTTTC 57.485 37.500 0.00 0.00 35.04 2.62
48 49 6.248433 TCAATGGACAAAGGCTTATCTTTCT 58.752 36.000 0.00 0.00 35.04 2.52
49 50 6.721208 TCAATGGACAAAGGCTTATCTTTCTT 59.279 34.615 0.00 0.00 35.04 2.52
50 51 7.233348 TCAATGGACAAAGGCTTATCTTTCTTT 59.767 33.333 0.00 0.00 35.04 2.52
51 52 6.976934 TGGACAAAGGCTTATCTTTCTTTT 57.023 33.333 0.00 0.00 35.04 2.27
52 53 7.360113 TGGACAAAGGCTTATCTTTCTTTTT 57.640 32.000 0.00 0.00 35.04 1.94
53 54 7.433680 TGGACAAAGGCTTATCTTTCTTTTTC 58.566 34.615 0.00 0.00 35.04 2.29
54 55 6.582672 GGACAAAGGCTTATCTTTCTTTTTCG 59.417 38.462 0.00 0.00 35.04 3.46
55 56 6.447162 ACAAAGGCTTATCTTTCTTTTTCGG 58.553 36.000 0.00 0.00 35.04 4.30
56 57 6.264518 ACAAAGGCTTATCTTTCTTTTTCGGA 59.735 34.615 0.00 0.00 35.04 4.55
57 58 6.894339 AAGGCTTATCTTTCTTTTTCGGAA 57.106 33.333 0.00 0.00 0.00 4.30
58 59 6.894339 AGGCTTATCTTTCTTTTTCGGAAA 57.106 33.333 0.00 0.00 0.00 3.13
59 60 7.284919 AGGCTTATCTTTCTTTTTCGGAAAA 57.715 32.000 11.68 11.68 33.17 2.29
60 61 7.722363 AGGCTTATCTTTCTTTTTCGGAAAAA 58.278 30.769 23.04 23.04 37.99 1.94
83 84 4.337145 ACACCGAGTCTACAAGAAGAGAT 58.663 43.478 0.00 0.00 0.00 2.75
84 85 5.498393 ACACCGAGTCTACAAGAAGAGATA 58.502 41.667 0.00 0.00 0.00 1.98
85 86 5.587043 ACACCGAGTCTACAAGAAGAGATAG 59.413 44.000 0.00 0.00 0.00 2.08
86 87 5.587043 CACCGAGTCTACAAGAAGAGATAGT 59.413 44.000 0.00 0.00 0.00 2.12
90 91 7.442969 CCGAGTCTACAAGAAGAGATAGTATGT 59.557 40.741 0.00 0.00 0.00 2.29
104 105 2.413837 AGTATGTCGTGTTCACTTGGC 58.586 47.619 1.53 0.00 0.00 4.52
105 106 2.139917 GTATGTCGTGTTCACTTGGCA 58.860 47.619 1.53 0.00 0.00 4.92
107 108 0.176910 TGTCGTGTTCACTTGGCAGA 59.823 50.000 1.53 0.00 0.00 4.26
108 109 0.582005 GTCGTGTTCACTTGGCAGAC 59.418 55.000 1.53 0.00 0.00 3.51
109 110 0.464036 TCGTGTTCACTTGGCAGACT 59.536 50.000 1.53 0.00 0.00 3.24
179 193 2.127042 TTTGACGAAATGCGCGGC 60.127 55.556 8.83 0.00 46.04 6.53
199 213 2.503375 GCCACCGACGTACGTGAG 60.503 66.667 28.16 18.57 40.78 3.51
202 217 3.043713 ACCGACGTACGTGAGCGA 61.044 61.111 28.16 0.00 42.00 4.93
203 218 2.276493 CCGACGTACGTGAGCGAG 60.276 66.667 28.16 12.83 42.00 5.03
235 250 1.523938 GCGTATTCCACCTGCTCCC 60.524 63.158 0.00 0.00 0.00 4.30
238 253 0.470341 GTATTCCACCTGCTCCCTCC 59.530 60.000 0.00 0.00 0.00 4.30
239 254 0.044092 TATTCCACCTGCTCCCTCCA 59.956 55.000 0.00 0.00 0.00 3.86
240 255 0.625683 ATTCCACCTGCTCCCTCCAT 60.626 55.000 0.00 0.00 0.00 3.41
242 257 2.503061 CACCTGCTCCCTCCATCG 59.497 66.667 0.00 0.00 0.00 3.84
243 258 2.765807 ACCTGCTCCCTCCATCGG 60.766 66.667 0.00 0.00 0.00 4.18
246 261 3.144120 CTGCTCCCTCCATCGGACG 62.144 68.421 0.00 0.00 0.00 4.79
247 262 3.917760 GCTCCCTCCATCGGACGG 61.918 72.222 0.00 0.00 30.70 4.79
285 303 2.355481 GGAACGCGTCCAACGACT 60.355 61.111 14.44 0.00 46.05 4.18
295 313 0.675837 TCCAACGACTCTCGATCGGT 60.676 55.000 16.41 5.10 43.74 4.69
319 358 4.717629 TCAAGTCGCAGTCGCCCG 62.718 66.667 0.00 0.00 35.26 6.13
325 364 4.728102 CGCAGTCGCCCGTACCAA 62.728 66.667 0.00 0.00 33.11 3.67
366 443 0.676736 GCCCGTTTCCACATTTTCCA 59.323 50.000 0.00 0.00 0.00 3.53
417 498 5.867716 GCCACAATTAGTCTCGAGTCTAAAA 59.132 40.000 27.77 14.53 31.55 1.52
428 640 7.611079 AGTCTCGAGTCTAAAATACCTAGTGTT 59.389 37.037 13.13 0.00 0.00 3.32
433 645 7.067251 CGAGTCTAAAATACCTAGTGTTCTCCT 59.933 40.741 0.00 0.00 0.00 3.69
435 647 7.124448 AGTCTAAAATACCTAGTGTTCTCCTGG 59.876 40.741 0.00 0.00 0.00 4.45
447 1060 0.179015 TCTCCTGGACGCCTAGCTAG 60.179 60.000 14.20 14.20 0.00 3.42
448 1061 1.801309 CTCCTGGACGCCTAGCTAGC 61.801 65.000 15.74 6.62 0.00 3.42
449 1062 1.830408 CCTGGACGCCTAGCTAGCT 60.830 63.158 23.12 23.12 0.00 3.32
450 1063 0.537600 CCTGGACGCCTAGCTAGCTA 60.538 60.000 22.85 22.85 0.00 3.32
451 1064 0.594110 CTGGACGCCTAGCTAGCTAC 59.406 60.000 20.67 11.02 0.00 3.58
452 1065 0.183014 TGGACGCCTAGCTAGCTACT 59.817 55.000 20.67 0.00 0.00 2.57
453 1066 1.320507 GGACGCCTAGCTAGCTACTT 58.679 55.000 20.67 5.74 0.00 2.24
454 1067 1.682323 GGACGCCTAGCTAGCTACTTT 59.318 52.381 20.67 5.32 0.00 2.66
455 1068 2.287728 GGACGCCTAGCTAGCTACTTTC 60.288 54.545 20.67 13.32 0.00 2.62
456 1069 2.619646 GACGCCTAGCTAGCTACTTTCT 59.380 50.000 20.67 2.39 0.00 2.52
457 1070 3.025262 ACGCCTAGCTAGCTACTTTCTT 58.975 45.455 20.67 0.00 0.00 2.52
458 1071 3.067040 ACGCCTAGCTAGCTACTTTCTTC 59.933 47.826 20.67 4.19 0.00 2.87
459 1072 3.634283 GCCTAGCTAGCTACTTTCTTCG 58.366 50.000 20.67 8.23 0.00 3.79
460 1073 3.067040 GCCTAGCTAGCTACTTTCTTCGT 59.933 47.826 20.67 0.00 0.00 3.85
461 1074 4.275443 GCCTAGCTAGCTACTTTCTTCGTA 59.725 45.833 20.67 0.00 0.00 3.43
462 1075 5.221009 GCCTAGCTAGCTACTTTCTTCGTAA 60.221 44.000 20.67 0.00 0.00 3.18
463 1076 6.679884 GCCTAGCTAGCTACTTTCTTCGTAAA 60.680 42.308 20.67 0.00 0.00 2.01
464 1077 6.913673 CCTAGCTAGCTACTTTCTTCGTAAAG 59.086 42.308 20.67 7.33 41.35 1.85
465 1078 6.512342 AGCTAGCTACTTTCTTCGTAAAGA 57.488 37.500 17.69 0.00 38.50 2.52
478 1091 8.922058 TTCTTCGTAAAGAATTATAAGAGCGT 57.078 30.769 0.00 0.00 44.63 5.07
479 1092 8.922058 TCTTCGTAAAGAATTATAAGAGCGTT 57.078 30.769 0.00 0.00 38.58 4.84
480 1093 9.362539 TCTTCGTAAAGAATTATAAGAGCGTTT 57.637 29.630 0.00 0.00 38.58 3.60
487 1100 9.530633 AAAGAATTATAAGAGCGTTTAGATCGT 57.469 29.630 0.00 0.00 40.85 3.73
488 1101 9.530633 AAGAATTATAAGAGCGTTTAGATCGTT 57.469 29.630 0.00 0.00 40.85 3.85
497 1110 7.619328 AGAGCGTTTAGATCGTTAAAAATAGC 58.381 34.615 0.00 0.00 40.85 2.97
498 1111 7.491696 AGAGCGTTTAGATCGTTAAAAATAGCT 59.508 33.333 0.00 0.00 40.85 3.32
499 1112 7.399523 AGCGTTTAGATCGTTAAAAATAGCTG 58.600 34.615 0.00 0.00 0.00 4.24
500 1113 6.138702 GCGTTTAGATCGTTAAAAATAGCTGC 59.861 38.462 0.00 0.00 0.00 5.25
501 1114 7.399523 CGTTTAGATCGTTAAAAATAGCTGCT 58.600 34.615 7.57 7.57 0.00 4.24
527 1140 3.893720 AGACAAACGAGTTAGGTACGTG 58.106 45.455 0.00 0.00 40.10 4.49
568 1181 7.961326 ACCAAAGCTCAACTAATTAATGGAT 57.039 32.000 0.00 0.00 0.00 3.41
613 2483 9.382244 CAAAAGATAAACAGCTACTTGTACAAC 57.618 33.333 3.59 0.00 0.00 3.32
647 2530 1.953686 CACCCATCTTTTCCACGTTGT 59.046 47.619 0.00 0.00 0.00 3.32
712 2610 3.576078 TTTCCACCAGAGCAGAAGAAA 57.424 42.857 0.00 0.00 0.00 2.52
713 2611 2.847327 TCCACCAGAGCAGAAGAAAG 57.153 50.000 0.00 0.00 0.00 2.62
714 2612 1.349026 TCCACCAGAGCAGAAGAAAGG 59.651 52.381 0.00 0.00 0.00 3.11
715 2613 1.349026 CCACCAGAGCAGAAGAAAGGA 59.651 52.381 0.00 0.00 0.00 3.36
716 2614 2.614987 CCACCAGAGCAGAAGAAAGGAG 60.615 54.545 0.00 0.00 0.00 3.69
717 2615 2.301296 CACCAGAGCAGAAGAAAGGAGA 59.699 50.000 0.00 0.00 0.00 3.71
718 2616 2.566724 ACCAGAGCAGAAGAAAGGAGAG 59.433 50.000 0.00 0.00 0.00 3.20
719 2617 2.566724 CCAGAGCAGAAGAAAGGAGAGT 59.433 50.000 0.00 0.00 0.00 3.24
720 2618 3.368323 CCAGAGCAGAAGAAAGGAGAGTC 60.368 52.174 0.00 0.00 0.00 3.36
721 2619 2.831526 AGAGCAGAAGAAAGGAGAGTCC 59.168 50.000 0.00 0.00 36.58 3.85
787 2704 4.052518 CCCAGCCCCTTCCACCTG 62.053 72.222 0.00 0.00 0.00 4.00
788 2705 2.935481 CCAGCCCCTTCCACCTGA 60.935 66.667 0.00 0.00 0.00 3.86
789 2706 2.352805 CAGCCCCTTCCACCTGAC 59.647 66.667 0.00 0.00 0.00 3.51
790 2707 2.936032 AGCCCCTTCCACCTGACC 60.936 66.667 0.00 0.00 0.00 4.02
791 2708 2.936032 GCCCCTTCCACCTGACCT 60.936 66.667 0.00 0.00 0.00 3.85
792 2709 2.972819 GCCCCTTCCACCTGACCTC 61.973 68.421 0.00 0.00 0.00 3.85
793 2710 1.538876 CCCCTTCCACCTGACCTCA 60.539 63.158 0.00 0.00 0.00 3.86
794 2711 1.679898 CCCTTCCACCTGACCTCAC 59.320 63.158 0.00 0.00 0.00 3.51
795 2712 0.838122 CCCTTCCACCTGACCTCACT 60.838 60.000 0.00 0.00 0.00 3.41
801 2718 1.152247 ACCTGACCTCACTCAGCCA 60.152 57.895 0.00 0.00 37.01 4.75
802 2719 1.190833 ACCTGACCTCACTCAGCCAG 61.191 60.000 0.00 0.00 37.01 4.85
817 2739 3.047877 CAGCCCGTTTGACCCGTC 61.048 66.667 0.00 0.00 0.00 4.79
818 2740 3.239253 AGCCCGTTTGACCCGTCT 61.239 61.111 0.00 0.00 0.00 4.18
821 2743 1.295423 CCCGTTTGACCCGTCTCAT 59.705 57.895 0.00 0.00 0.00 2.90
831 2754 0.108138 CCCGTCTCATCCAACACTCC 60.108 60.000 0.00 0.00 0.00 3.85
853 2819 3.181465 CCCACCACCCATCGCTATATATC 60.181 52.174 0.00 0.00 0.00 1.63
855 2821 4.081142 CCACCACCCATCGCTATATATCAA 60.081 45.833 0.00 0.00 0.00 2.57
858 2838 4.870426 CCACCCATCGCTATATATCAACAC 59.130 45.833 0.00 0.00 0.00 3.32
937 2936 2.605601 TCAGCAGCTCAGGCCTCA 60.606 61.111 0.00 0.00 39.73 3.86
971 2975 1.342819 GTTCCCTCCATCGATCCTCTG 59.657 57.143 0.00 0.00 0.00 3.35
977 2981 0.318529 CCATCGATCCTCTGCTCGTG 60.319 60.000 0.00 0.00 36.33 4.35
978 2982 0.383590 CATCGATCCTCTGCTCGTGT 59.616 55.000 0.00 0.00 36.33 4.49
980 2984 0.393132 TCGATCCTCTGCTCGTGTCT 60.393 55.000 0.00 0.00 36.33 3.41
981 2985 0.453793 CGATCCTCTGCTCGTGTCTT 59.546 55.000 0.00 0.00 0.00 3.01
982 2986 1.671328 CGATCCTCTGCTCGTGTCTTA 59.329 52.381 0.00 0.00 0.00 2.10
983 2987 2.286713 CGATCCTCTGCTCGTGTCTTAG 60.287 54.545 0.00 0.00 0.00 2.18
985 2989 2.515854 TCCTCTGCTCGTGTCTTAGTT 58.484 47.619 0.00 0.00 0.00 2.24
986 2990 2.891580 TCCTCTGCTCGTGTCTTAGTTT 59.108 45.455 0.00 0.00 0.00 2.66
988 2992 2.404215 TCTGCTCGTGTCTTAGTTTGC 58.596 47.619 0.00 0.00 0.00 3.68
991 2995 2.543848 TGCTCGTGTCTTAGTTTGCAAG 59.456 45.455 0.00 0.00 0.00 4.01
994 2998 4.260620 GCTCGTGTCTTAGTTTGCAAGAAA 60.261 41.667 0.00 0.00 33.95 2.52
995 2999 5.729454 GCTCGTGTCTTAGTTTGCAAGAAAA 60.729 40.000 0.00 0.00 33.95 2.29
996 3000 6.184580 TCGTGTCTTAGTTTGCAAGAAAAA 57.815 33.333 0.00 0.00 33.95 1.94
1060 3077 1.897225 ATGCCTCGTGCTGCTTCTCT 61.897 55.000 0.00 0.00 42.00 3.10
1173 3199 3.817655 TACGCGCCGCTTCTGCTA 61.818 61.111 5.73 0.00 36.97 3.49
1185 3211 2.124445 CTGCTAGCCATGCTGCCA 60.124 61.111 13.29 0.00 40.10 4.92
1233 3259 4.681978 GGTGGCACGAACGAGGCT 62.682 66.667 12.17 0.00 32.96 4.58
1254 3280 2.225091 TGGGAACTGATGAAGCAACCAT 60.225 45.455 0.00 0.00 0.00 3.55
1272 3298 4.152284 CCATAGGGTTTTCCACTAGGAC 57.848 50.000 0.00 0.00 45.73 3.85
1283 3332 2.427453 TCCACTAGGACAGAGAAATCGC 59.573 50.000 0.00 0.00 39.61 4.58
1327 3408 6.331369 AGTTGATGGTTTGGTTACAAGATG 57.669 37.500 0.00 0.00 37.97 2.90
1343 3424 6.169557 ACAAGATGGTTGTACAGAACTGTA 57.830 37.500 10.14 10.14 44.42 2.74
1350 3431 5.361571 TGGTTGTACAGAACTGTAAGAGTGA 59.638 40.000 14.91 0.00 46.33 3.41
1458 3557 5.491070 TCTGTCGTGATCCATTCTTTGAAT 58.509 37.500 0.00 0.00 0.00 2.57
1464 3563 7.645340 GTCGTGATCCATTCTTTGAATAATTGG 59.355 37.037 0.00 0.00 0.00 3.16
1508 3607 4.789807 AGATGATACTGGCAGCAAGAATT 58.210 39.130 15.89 0.00 0.00 2.17
1509 3608 5.933617 AGATGATACTGGCAGCAAGAATTA 58.066 37.500 15.89 0.00 0.00 1.40
1510 3609 6.359804 AGATGATACTGGCAGCAAGAATTAA 58.640 36.000 15.89 0.00 0.00 1.40
1511 3610 7.002879 AGATGATACTGGCAGCAAGAATTAAT 58.997 34.615 15.89 0.00 0.00 1.40
1529 3667 0.546267 ATGTCCCAGCTCCTCACAGT 60.546 55.000 0.00 0.00 0.00 3.55
1574 3712 2.026262 ACGCCACCATTCTTACCTGAAT 60.026 45.455 0.00 0.00 37.16 2.57
1612 5756 8.616799 AGAAAATTCTAGTACTCCCTCTGATT 57.383 34.615 0.00 0.00 35.34 2.57
1617 5761 9.836179 AATTCTAGTACTCCCTCTGATTCATAT 57.164 33.333 0.00 0.00 0.00 1.78
1618 5762 8.642935 TTCTAGTACTCCCTCTGATTCATATG 57.357 38.462 0.00 0.00 0.00 1.78
1626 5770 6.226052 TCCCTCTGATTCATATGAATTGTCG 58.774 40.000 27.45 17.40 44.14 4.35
1632 5776 7.443272 TCTGATTCATATGAATTGTCGCTGATT 59.557 33.333 27.45 6.01 44.14 2.57
1633 5777 7.933396 TGATTCATATGAATTGTCGCTGATTT 58.067 30.769 27.45 5.82 44.14 2.17
1634 5778 9.054922 TGATTCATATGAATTGTCGCTGATTTA 57.945 29.630 27.45 0.85 44.14 1.40
1636 5780 8.437360 TTCATATGAATTGTCGCTGATTTAGT 57.563 30.769 14.23 0.00 0.00 2.24
1637 5781 9.541143 TTCATATGAATTGTCGCTGATTTAGTA 57.459 29.630 14.23 0.00 0.00 1.82
1638 5782 8.978539 TCATATGAATTGTCGCTGATTTAGTAC 58.021 33.333 1.98 0.00 0.00 2.73
1639 5783 8.764287 CATATGAATTGTCGCTGATTTAGTACA 58.236 33.333 0.00 0.00 0.00 2.90
1643 5787 7.172532 TGAATTGTCGCTGATTTAGTACAAAGT 59.827 33.333 0.00 0.00 37.68 2.66
1644 5788 6.854496 TTGTCGCTGATTTAGTACAAAGTT 57.146 33.333 0.00 0.00 34.01 2.66
1645 5789 6.223138 TGTCGCTGATTTAGTACAAAGTTG 57.777 37.500 0.00 0.00 0.00 3.16
1647 5791 6.924612 TGTCGCTGATTTAGTACAAAGTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
1686 6015 3.759618 GGATCGGAGGGAGTACTAGAATG 59.240 52.174 0.00 0.00 0.00 2.67
1882 6230 4.599047 TTGGTGATGGGTGATTCAAAAC 57.401 40.909 0.00 0.00 0.00 2.43
1917 6265 5.707764 CGATCTTGGTATCCAGTCATAGAGA 59.292 44.000 0.00 0.00 33.81 3.10
1933 6281 3.273919 AGAGAACGAATGCAAAGCAAC 57.726 42.857 0.00 0.00 43.62 4.17
1969 6317 5.376625 ACATCCACGGCATTTATATTCAGT 58.623 37.500 0.00 0.00 0.00 3.41
1998 6346 2.999355 GTGATGTTTCTGCTCCTCTGAC 59.001 50.000 0.00 0.00 0.00 3.51
2042 6390 2.578495 CTTTCTTTCACGCATGACAGC 58.422 47.619 0.00 0.00 33.37 4.40
2043 6391 1.592064 TTCTTTCACGCATGACAGCA 58.408 45.000 0.00 0.00 33.37 4.41
2065 6413 4.927267 TCCTTGACATGAATACCAACCT 57.073 40.909 0.00 0.00 0.00 3.50
2091 6442 7.756558 AGAAAGCAAATAGTAAGACTGCAATC 58.243 34.615 0.00 0.00 35.44 2.67
2102 6453 4.298103 AGACTGCAATCCTGAAGTTGAT 57.702 40.909 0.00 0.00 42.02 2.57
2112 6463 2.355132 CCTGAAGTTGATCTGCATCTGC 59.645 50.000 0.00 0.00 42.50 4.26
2114 6465 3.268330 TGAAGTTGATCTGCATCTGCTC 58.732 45.455 3.53 0.00 42.66 4.26
2116 6467 0.304098 GTTGATCTGCATCTGCTCGC 59.696 55.000 3.53 0.00 42.66 5.03
2149 6501 9.699410 AAACCAGATCAAGATTTGGAACATATA 57.301 29.630 22.18 0.00 43.60 0.86
2150 6502 9.872684 AACCAGATCAAGATTTGGAACATATAT 57.127 29.630 22.18 0.00 43.60 0.86
2172 6524 4.756203 ATCCCTCCAGTCTCATCTCATA 57.244 45.455 0.00 0.00 0.00 2.15
2176 6528 4.406972 CCCTCCAGTCTCATCTCATAAACA 59.593 45.833 0.00 0.00 0.00 2.83
2210 6562 0.908910 TTGGCACATATCCTCCGTGT 59.091 50.000 0.00 0.00 39.30 4.49
2234 6586 0.911769 CTGTGGTTCTCCCCTGCATA 59.088 55.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.910584 AGATAAGCCTTTGTCCATTGATTTTT 58.089 30.769 0.00 0.00 0.00 1.94
20 21 7.486407 AGATAAGCCTTTGTCCATTGATTTT 57.514 32.000 0.00 0.00 0.00 1.82
21 22 7.486407 AAGATAAGCCTTTGTCCATTGATTT 57.514 32.000 0.00 0.00 0.00 2.17
22 23 7.398332 AGAAAGATAAGCCTTTGTCCATTGATT 59.602 33.333 0.00 0.00 36.58 2.57
23 24 6.894103 AGAAAGATAAGCCTTTGTCCATTGAT 59.106 34.615 0.00 0.00 36.58 2.57
24 25 6.248433 AGAAAGATAAGCCTTTGTCCATTGA 58.752 36.000 0.00 0.00 36.58 2.57
25 26 6.521151 AGAAAGATAAGCCTTTGTCCATTG 57.479 37.500 0.00 0.00 36.58 2.82
26 27 7.544804 AAAGAAAGATAAGCCTTTGTCCATT 57.455 32.000 0.00 0.00 36.58 3.16
27 28 7.544804 AAAAGAAAGATAAGCCTTTGTCCAT 57.455 32.000 0.00 0.00 36.58 3.41
28 29 6.976934 AAAAGAAAGATAAGCCTTTGTCCA 57.023 33.333 0.00 0.00 36.58 4.02
29 30 6.582672 CGAAAAAGAAAGATAAGCCTTTGTCC 59.417 38.462 0.00 0.00 36.58 4.02
30 31 6.582672 CCGAAAAAGAAAGATAAGCCTTTGTC 59.417 38.462 0.00 0.00 36.58 3.18
31 32 6.264518 TCCGAAAAAGAAAGATAAGCCTTTGT 59.735 34.615 0.00 0.00 36.58 2.83
32 33 6.677913 TCCGAAAAAGAAAGATAAGCCTTTG 58.322 36.000 0.00 0.00 36.58 2.77
33 34 6.894339 TCCGAAAAAGAAAGATAAGCCTTT 57.106 33.333 0.00 0.00 38.92 3.11
34 35 6.894339 TTCCGAAAAAGAAAGATAAGCCTT 57.106 33.333 0.00 0.00 0.00 4.35
35 36 6.894339 TTTCCGAAAAAGAAAGATAAGCCT 57.106 33.333 0.00 0.00 0.00 4.58
36 37 7.940178 TTTTTCCGAAAAAGAAAGATAAGCC 57.060 32.000 13.84 0.00 35.84 4.35
57 58 5.667466 TCTTCTTGTAGACTCGGTGTTTTT 58.333 37.500 0.00 0.00 0.00 1.94
58 59 5.068723 TCTCTTCTTGTAGACTCGGTGTTTT 59.931 40.000 0.00 0.00 0.00 2.43
59 60 4.583489 TCTCTTCTTGTAGACTCGGTGTTT 59.417 41.667 0.00 0.00 0.00 2.83
60 61 4.142790 TCTCTTCTTGTAGACTCGGTGTT 58.857 43.478 0.00 0.00 0.00 3.32
61 62 3.752665 TCTCTTCTTGTAGACTCGGTGT 58.247 45.455 0.00 0.00 0.00 4.16
71 72 7.860918 ACACGACATACTATCTCTTCTTGTA 57.139 36.000 0.00 0.00 0.00 2.41
76 77 6.787225 AGTGAACACGACATACTATCTCTTC 58.213 40.000 0.00 0.00 36.20 2.87
78 79 6.404844 CCAAGTGAACACGACATACTATCTCT 60.405 42.308 0.00 0.00 36.20 3.10
83 84 3.006003 TGCCAAGTGAACACGACATACTA 59.994 43.478 0.00 0.00 36.20 1.82
84 85 2.224185 TGCCAAGTGAACACGACATACT 60.224 45.455 0.00 0.00 36.20 2.12
85 86 2.139917 TGCCAAGTGAACACGACATAC 58.860 47.619 0.00 0.00 36.20 2.39
86 87 2.036604 TCTGCCAAGTGAACACGACATA 59.963 45.455 0.00 0.00 36.20 2.29
90 91 0.464036 AGTCTGCCAAGTGAACACGA 59.536 50.000 0.00 0.00 36.20 4.35
104 105 0.248825 CGTGCTAGCCTGCTAGTCTG 60.249 60.000 23.19 11.85 45.67 3.51
105 106 2.010582 GCGTGCTAGCCTGCTAGTCT 62.011 60.000 23.19 0.00 45.67 3.24
107 108 2.351244 TGCGTGCTAGCCTGCTAGT 61.351 57.895 23.19 0.00 45.67 2.57
108 109 1.880340 GTGCGTGCTAGCCTGCTAG 60.880 63.158 23.56 19.48 46.41 3.42
109 110 2.184322 GTGCGTGCTAGCCTGCTA 59.816 61.111 23.56 11.32 36.02 3.49
158 172 1.440353 GCGCATTTCGTCAAACGCT 60.440 52.632 0.30 0.00 42.21 5.07
179 193 4.093952 ACGTACGTCGGTGGCTCG 62.094 66.667 16.72 0.00 44.69 5.03
188 202 2.576317 GCCTCGCTCACGTACGTC 60.576 66.667 19.94 6.73 41.18 4.34
191 205 3.736482 CTCCGCCTCGCTCACGTAC 62.736 68.421 0.00 0.00 41.18 3.67
192 206 3.506096 CTCCGCCTCGCTCACGTA 61.506 66.667 0.00 0.00 41.18 3.57
221 236 0.625683 ATGGAGGGAGCAGGTGGAAT 60.626 55.000 0.00 0.00 0.00 3.01
235 250 2.835705 CGAGTCCCGTCCGATGGAG 61.836 68.421 8.34 0.00 29.39 3.86
238 253 2.827190 TCCGAGTCCCGTCCGATG 60.827 66.667 0.00 0.00 36.31 3.84
239 254 2.516460 CTCCGAGTCCCGTCCGAT 60.516 66.667 0.00 0.00 36.31 4.18
240 255 4.790962 CCTCCGAGTCCCGTCCGA 62.791 72.222 0.00 0.00 36.31 4.55
242 257 4.437587 TCCCTCCGAGTCCCGTCC 62.438 72.222 0.00 0.00 36.31 4.79
243 258 2.829458 CTCCCTCCGAGTCCCGTC 60.829 72.222 0.00 0.00 36.31 4.79
246 261 2.444895 ATGCTCCCTCCGAGTCCC 60.445 66.667 0.00 0.00 41.10 4.46
247 262 2.801631 CCATGCTCCCTCCGAGTCC 61.802 68.421 0.00 0.00 41.10 3.85
285 303 2.685850 TGAGTGAGTACCGATCGAGA 57.314 50.000 18.66 0.00 0.00 4.04
295 313 1.197036 CGACTGCGACTTGAGTGAGTA 59.803 52.381 0.00 0.00 40.82 2.59
319 358 3.244281 AAGGGCCGGTCGTTGGTAC 62.244 63.158 14.15 0.00 0.00 3.34
417 498 3.288964 CGTCCAGGAGAACACTAGGTAT 58.711 50.000 0.00 0.00 0.00 2.73
428 640 0.179015 CTAGCTAGGCGTCCAGGAGA 60.179 60.000 13.32 0.00 0.00 3.71
433 645 0.183014 AGTAGCTAGCTAGGCGTCCA 59.817 55.000 24.78 0.00 34.52 4.02
435 647 2.619646 AGAAAGTAGCTAGCTAGGCGTC 59.380 50.000 24.78 17.80 34.52 5.19
454 1067 8.922058 AACGCTCTTATAATTCTTTACGAAGA 57.078 30.769 0.00 0.00 40.07 2.87
461 1074 9.530633 ACGATCTAAACGCTCTTATAATTCTTT 57.469 29.630 0.00 0.00 0.00 2.52
462 1075 9.530633 AACGATCTAAACGCTCTTATAATTCTT 57.469 29.630 0.00 0.00 0.00 2.52
471 1084 8.114905 GCTATTTTTAACGATCTAAACGCTCTT 58.885 33.333 0.00 0.00 0.00 2.85
472 1085 7.491696 AGCTATTTTTAACGATCTAAACGCTCT 59.508 33.333 0.00 0.00 0.00 4.09
473 1086 7.579450 CAGCTATTTTTAACGATCTAAACGCTC 59.421 37.037 0.00 0.00 0.00 5.03
474 1087 7.399523 CAGCTATTTTTAACGATCTAAACGCT 58.600 34.615 0.00 0.00 0.00 5.07
475 1088 6.138702 GCAGCTATTTTTAACGATCTAAACGC 59.861 38.462 0.00 0.00 0.00 4.84
476 1089 7.399523 AGCAGCTATTTTTAACGATCTAAACG 58.600 34.615 0.00 0.00 0.00 3.60
477 1090 8.388103 TGAGCAGCTATTTTTAACGATCTAAAC 58.612 33.333 0.00 0.00 0.00 2.01
478 1091 8.388103 GTGAGCAGCTATTTTTAACGATCTAAA 58.612 33.333 0.00 0.00 0.00 1.85
479 1092 7.547722 TGTGAGCAGCTATTTTTAACGATCTAA 59.452 33.333 0.00 0.00 0.00 2.10
480 1093 7.039270 TGTGAGCAGCTATTTTTAACGATCTA 58.961 34.615 0.00 0.00 0.00 1.98
481 1094 5.874810 TGTGAGCAGCTATTTTTAACGATCT 59.125 36.000 0.00 0.00 0.00 2.75
482 1095 6.106877 TGTGAGCAGCTATTTTTAACGATC 57.893 37.500 0.00 0.00 0.00 3.69
483 1096 6.371548 TCTTGTGAGCAGCTATTTTTAACGAT 59.628 34.615 0.00 0.00 0.00 3.73
484 1097 5.699001 TCTTGTGAGCAGCTATTTTTAACGA 59.301 36.000 0.00 0.00 0.00 3.85
485 1098 5.790495 GTCTTGTGAGCAGCTATTTTTAACG 59.210 40.000 0.00 0.00 0.00 3.18
486 1099 6.668323 TGTCTTGTGAGCAGCTATTTTTAAC 58.332 36.000 0.00 0.00 0.00 2.01
487 1100 6.875948 TGTCTTGTGAGCAGCTATTTTTAA 57.124 33.333 0.00 0.00 0.00 1.52
488 1101 6.875948 TTGTCTTGTGAGCAGCTATTTTTA 57.124 33.333 0.00 0.00 0.00 1.52
489 1102 5.772825 TTGTCTTGTGAGCAGCTATTTTT 57.227 34.783 0.00 0.00 0.00 1.94
490 1103 5.523369 GTTTGTCTTGTGAGCAGCTATTTT 58.477 37.500 0.00 0.00 0.00 1.82
491 1104 4.319766 CGTTTGTCTTGTGAGCAGCTATTT 60.320 41.667 0.00 0.00 0.00 1.40
492 1105 3.187227 CGTTTGTCTTGTGAGCAGCTATT 59.813 43.478 0.00 0.00 0.00 1.73
493 1106 2.738846 CGTTTGTCTTGTGAGCAGCTAT 59.261 45.455 0.00 0.00 0.00 2.97
494 1107 2.135139 CGTTTGTCTTGTGAGCAGCTA 58.865 47.619 0.00 0.00 0.00 3.32
495 1108 0.940126 CGTTTGTCTTGTGAGCAGCT 59.060 50.000 0.00 0.00 0.00 4.24
496 1109 0.937304 TCGTTTGTCTTGTGAGCAGC 59.063 50.000 0.00 0.00 0.00 5.25
497 1110 2.205074 ACTCGTTTGTCTTGTGAGCAG 58.795 47.619 0.00 0.00 0.00 4.24
498 1111 2.309528 ACTCGTTTGTCTTGTGAGCA 57.690 45.000 0.00 0.00 0.00 4.26
499 1112 3.184581 CCTAACTCGTTTGTCTTGTGAGC 59.815 47.826 0.00 0.00 0.00 4.26
500 1113 4.369182 ACCTAACTCGTTTGTCTTGTGAG 58.631 43.478 0.00 0.00 0.00 3.51
501 1114 4.395959 ACCTAACTCGTTTGTCTTGTGA 57.604 40.909 0.00 0.00 0.00 3.58
527 1140 5.625311 GCTTTGGTTATTATGTATTCAGCGC 59.375 40.000 0.00 0.00 0.00 5.92
568 1181 3.333029 TGATGAAAGCAACTCATCCGA 57.667 42.857 15.85 1.37 45.77 4.55
613 2483 3.139025 AGATGGGTGGGATCCATGTAAAG 59.861 47.826 15.23 0.00 44.34 1.85
618 2488 2.761786 AAAGATGGGTGGGATCCATG 57.238 50.000 15.23 0.00 44.34 3.66
647 2530 1.623081 GCGTTCATTTGAGCCGACGA 61.623 55.000 0.00 0.00 32.73 4.20
716 2614 3.697542 GGTTAGAGAACAGAGGAGGACTC 59.302 52.174 0.00 0.00 38.13 3.36
717 2615 3.076182 TGGTTAGAGAACAGAGGAGGACT 59.924 47.826 0.00 0.00 37.29 3.85
718 2616 3.432378 TGGTTAGAGAACAGAGGAGGAC 58.568 50.000 0.00 0.00 37.29 3.85
719 2617 3.827817 TGGTTAGAGAACAGAGGAGGA 57.172 47.619 0.00 0.00 37.29 3.71
720 2618 3.835395 ACTTGGTTAGAGAACAGAGGAGG 59.165 47.826 0.00 0.00 37.29 4.30
721 2619 4.524714 TGACTTGGTTAGAGAACAGAGGAG 59.475 45.833 0.00 0.00 37.29 3.69
787 2704 2.267324 GGCTGGCTGAGTGAGGTC 59.733 66.667 0.00 0.00 0.00 3.85
788 2705 3.325753 GGGCTGGCTGAGTGAGGT 61.326 66.667 0.00 0.00 0.00 3.85
789 2706 4.463879 CGGGCTGGCTGAGTGAGG 62.464 72.222 3.57 0.00 0.00 3.86
790 2707 2.738213 AAACGGGCTGGCTGAGTGAG 62.738 60.000 17.74 0.00 0.00 3.51
791 2708 2.818169 AAACGGGCTGGCTGAGTGA 61.818 57.895 17.74 0.00 0.00 3.41
792 2709 2.281761 AAACGGGCTGGCTGAGTG 60.282 61.111 17.74 0.00 0.00 3.51
793 2710 2.281761 CAAACGGGCTGGCTGAGT 60.282 61.111 17.74 4.46 0.00 3.41
794 2711 2.032528 TCAAACGGGCTGGCTGAG 59.967 61.111 17.74 6.33 0.00 3.35
795 2712 2.281484 GTCAAACGGGCTGGCTGA 60.281 61.111 17.74 1.65 0.00 4.26
801 2718 3.236003 GAGACGGGTCAAACGGGCT 62.236 63.158 1.17 0.00 35.23 5.19
802 2719 2.741211 GAGACGGGTCAAACGGGC 60.741 66.667 1.17 0.00 35.23 6.13
815 2737 0.984230 TGGGGAGTGTTGGATGAGAC 59.016 55.000 0.00 0.00 0.00 3.36
817 2739 0.035056 GGTGGGGAGTGTTGGATGAG 60.035 60.000 0.00 0.00 0.00 2.90
818 2740 0.770166 TGGTGGGGAGTGTTGGATGA 60.770 55.000 0.00 0.00 0.00 2.92
821 2743 2.457323 GGTGGTGGGGAGTGTTGGA 61.457 63.158 0.00 0.00 0.00 3.53
831 2754 0.984230 ATATAGCGATGGGTGGTGGG 59.016 55.000 0.00 0.00 0.00 4.61
853 2819 6.237808 GCTTTTTGTGTTTATCTGTGGTGTTG 60.238 38.462 0.00 0.00 0.00 3.33
855 2821 5.105554 TGCTTTTTGTGTTTATCTGTGGTGT 60.106 36.000 0.00 0.00 0.00 4.16
858 2838 5.687285 GTCTGCTTTTTGTGTTTATCTGTGG 59.313 40.000 0.00 0.00 0.00 4.17
937 2936 3.149981 GAGGGAACTTTGCAGTAAGCTT 58.850 45.455 3.48 3.48 44.43 3.74
971 2975 2.800544 TCTTGCAAACTAAGACACGAGC 59.199 45.455 0.00 0.00 29.68 5.03
994 2998 4.502087 GCTGGAAGAAGAAGCCATTGTTTT 60.502 41.667 0.00 0.00 34.07 2.43
995 2999 3.006217 GCTGGAAGAAGAAGCCATTGTTT 59.994 43.478 0.00 0.00 34.07 2.83
996 3000 2.560105 GCTGGAAGAAGAAGCCATTGTT 59.440 45.455 0.00 0.00 34.07 2.83
997 3001 2.165998 GCTGGAAGAAGAAGCCATTGT 58.834 47.619 0.00 0.00 34.07 2.71
998 3002 1.131883 CGCTGGAAGAAGAAGCCATTG 59.868 52.381 0.00 0.00 34.07 2.82
1060 3077 3.573772 CTCGCAGGCTGACGACCAA 62.574 63.158 23.40 9.17 34.08 3.67
1233 3259 1.144708 TGGTTGCTTCATCAGTTCCCA 59.855 47.619 0.00 0.00 0.00 4.37
1254 3280 4.094476 CTCTGTCCTAGTGGAAAACCCTA 58.906 47.826 0.00 0.00 45.18 3.53
1272 3298 2.983136 CGTATGCCTAGCGATTTCTCTG 59.017 50.000 0.00 0.00 0.00 3.35
1299 3368 4.992319 TGTAACCAAACCATCAACTACTCG 59.008 41.667 0.00 0.00 0.00 4.18
1327 3408 5.839621 TCACTCTTACAGTTCTGTACAACC 58.160 41.667 11.54 0.00 30.26 3.77
1343 3424 4.528920 AGTATCCTACGCTTCTCACTCTT 58.471 43.478 0.00 0.00 0.00 2.85
1350 3431 7.281841 GGTATATCCTAGTATCCTACGCTTCT 58.718 42.308 0.00 0.00 0.00 2.85
1464 3563 9.669353 CATCTTGCATAGGTGATAATTAACAAC 57.331 33.333 2.67 2.67 37.13 3.32
1480 3579 3.181452 TGCTGCCAGTATCATCTTGCATA 60.181 43.478 0.00 0.00 35.96 3.14
1508 3607 1.833630 CTGTGAGGAGCTGGGACATTA 59.166 52.381 0.00 0.00 38.20 1.90
1509 3608 0.617413 CTGTGAGGAGCTGGGACATT 59.383 55.000 0.00 0.00 38.20 2.71
1510 3609 0.546267 ACTGTGAGGAGCTGGGACAT 60.546 55.000 0.00 0.00 38.20 3.06
1511 3610 0.114364 TACTGTGAGGAGCTGGGACA 59.886 55.000 0.00 0.00 0.00 4.02
1558 3696 8.340757 TGGGTAAATTATTCAGGTAAGAATGGT 58.659 33.333 0.00 0.00 38.60 3.55
1612 5756 8.978539 GTACTAAATCAGCGACAATTCATATGA 58.021 33.333 0.00 0.00 0.00 2.15
1617 5761 7.172532 ACTTTGTACTAAATCAGCGACAATTCA 59.827 33.333 0.00 0.00 34.85 2.57
1618 5762 7.519002 ACTTTGTACTAAATCAGCGACAATTC 58.481 34.615 0.00 0.00 34.85 2.17
1648 5792 9.601217 CCCTCCGATCCATATTAACTAATTTAG 57.399 37.037 1.79 1.79 0.00 1.85
1649 5793 9.328975 TCCCTCCGATCCATATTAACTAATTTA 57.671 33.333 0.00 0.00 0.00 1.40
1651 5795 7.458170 ACTCCCTCCGATCCATATTAACTAATT 59.542 37.037 0.00 0.00 0.00 1.40
1652 5796 6.960542 ACTCCCTCCGATCCATATTAACTAAT 59.039 38.462 0.00 0.00 0.00 1.73
1653 5797 6.320518 ACTCCCTCCGATCCATATTAACTAA 58.679 40.000 0.00 0.00 0.00 2.24
1654 5798 5.900437 ACTCCCTCCGATCCATATTAACTA 58.100 41.667 0.00 0.00 0.00 2.24
1655 5799 4.753186 ACTCCCTCCGATCCATATTAACT 58.247 43.478 0.00 0.00 0.00 2.24
1669 5998 3.319689 GTCAGCATTCTAGTACTCCCTCC 59.680 52.174 0.00 0.00 0.00 4.30
1686 6015 1.461127 CTACGTTTGCTCCAAGTCAGC 59.539 52.381 0.00 0.00 37.40 4.26
1699 6028 1.757699 GGATCCAGAGGAGCTACGTTT 59.242 52.381 6.95 0.00 38.31 3.60
1779 6108 6.749139 ACTCTGGCCTAAAAGAAAAATGAAC 58.251 36.000 3.32 0.00 0.00 3.18
1864 6212 4.321230 GGTCTGTTTTGAATCACCCATCAC 60.321 45.833 0.00 0.00 0.00 3.06
1882 6230 1.276421 ACCAAGATCGAACCAGGTCTG 59.724 52.381 0.00 0.00 0.00 3.51
1917 6265 2.202295 AACGTTGCTTTGCATTCGTT 57.798 40.000 20.52 20.52 45.72 3.85
1969 6317 4.943705 GGAGCAGAAACATCACCTGAAATA 59.056 41.667 0.00 0.00 0.00 1.40
2042 6390 5.195940 AGGTTGGTATTCATGTCAAGGATG 58.804 41.667 0.00 0.00 0.00 3.51
2043 6391 5.456921 AGGTTGGTATTCATGTCAAGGAT 57.543 39.130 0.00 0.00 0.00 3.24
2065 6413 8.792830 ATTGCAGTCTTACTATTTGCTTTCTA 57.207 30.769 0.00 0.00 35.85 2.10
2091 6442 2.355132 GCAGATGCAGATCAACTTCAGG 59.645 50.000 0.00 0.00 41.59 3.86
2102 6453 0.108851 TTAACGCGAGCAGATGCAGA 60.109 50.000 15.93 0.00 45.16 4.26
2149 6501 4.756203 TGAGATGAGACTGGAGGGATAT 57.244 45.455 0.00 0.00 0.00 1.63
2150 6502 4.756203 ATGAGATGAGACTGGAGGGATA 57.244 45.455 0.00 0.00 0.00 2.59
2151 6503 3.634218 ATGAGATGAGACTGGAGGGAT 57.366 47.619 0.00 0.00 0.00 3.85
2152 6504 4.542906 TTATGAGATGAGACTGGAGGGA 57.457 45.455 0.00 0.00 0.00 4.20
2172 6524 4.202151 GCCAACTCCTCAACATTCTTGTTT 60.202 41.667 0.00 0.00 43.57 2.83
2176 6528 2.887152 GTGCCAACTCCTCAACATTCTT 59.113 45.455 0.00 0.00 0.00 2.52
2184 6536 2.481441 AGGATATGTGCCAACTCCTCA 58.519 47.619 0.00 0.00 30.45 3.86
2190 6542 1.299541 CACGGAGGATATGTGCCAAC 58.700 55.000 0.00 0.00 0.00 3.77
2210 6562 2.741092 GGGAGAACCACAGCACGA 59.259 61.111 0.00 0.00 39.85 4.35


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

AutoCloner maintained by Alex Coulton.