Multiple sequence alignment - TraesCS7A01G452100

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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 TraesCS7A01G452100 chr7A 100.000 2291 0 0 564 2854 644845167 644847457 0.000000e+00 4231.0
1 TraesCS7A01G452100 chr7A 92.248 387 29 1 2229 2614 129153519 129153905 5.380000e-152 547.0
2 TraesCS7A01G452100 chr7A 89.731 409 19 4 2229 2616 26979554 26979960 4.240000e-138 501.0
3 TraesCS7A01G452100 chr7A 100.000 178 0 0 1 178 644844604 644844781 2.120000e-86 329.0
4 TraesCS7A01G452100 chr7A 92.929 198 14 0 1952 2149 129152828 129153025 3.600000e-74 289.0
5 TraesCS7A01G452100 chr7A 92.697 178 10 1 1 178 314252392 314252218 1.310000e-63 254.0
6 TraesCS7A01G452100 chr7A 92.000 125 7 1 2111 2232 554482749 554482873 3.780000e-39 172.0
7 TraesCS7A01G452100 chr7A 84.932 146 15 5 564 706 139469255 139469396 1.070000e-29 141.0
8 TraesCS7A01G452100 chr7D 90.387 801 48 13 703 1482 560706347 560707139 0.000000e+00 1026.0
9 TraesCS7A01G452100 chr7D 88.693 398 36 5 1560 1949 560707131 560707527 7.150000e-131 477.0
10 TraesCS7A01G452100 chr7D 94.828 232 9 1 2614 2845 560707526 560707754 2.700000e-95 359.0
11 TraesCS7A01G452100 chr7D 82.642 386 42 11 2230 2614 532629483 532629844 4.590000e-83 318.0
12 TraesCS7A01G452100 chr7D 92.188 128 9 1 1447 1573 598012939 598013066 2.260000e-41 180.0
13 TraesCS7A01G452100 chr7D 86.364 154 17 4 564 716 42220877 42221027 6.330000e-37 165.0
14 TraesCS7A01G452100 chr7B 93.595 687 33 7 756 1437 608469983 608470663 0.000000e+00 1014.0
15 TraesCS7A01G452100 chr7B 88.860 386 31 6 1575 1949 608470706 608471090 5.570000e-127 464.0
16 TraesCS7A01G452100 chr7B 92.946 241 14 1 2614 2854 608471089 608471326 5.850000e-92 348.0
17 TraesCS7A01G452100 chr7B 100.000 41 0 0 703 743 608469319 608469359 3.050000e-10 76.8
18 TraesCS7A01G452100 chr6A 92.727 385 25 3 2232 2614 205778817 205779200 1.160000e-153 553.0
19 TraesCS7A01G452100 chr6A 91.007 278 22 1 1952 2226 205778147 205778424 3.470000e-99 372.0
20 TraesCS7A01G452100 chr6A 93.714 175 9 2 1 175 88860605 88860777 7.840000e-66 261.0
21 TraesCS7A01G452100 chr6A 90.769 130 9 3 1441 1568 411046529 411046657 1.360000e-38 171.0
22 TraesCS7A01G452100 chr2A 92.072 391 26 3 2229 2616 752030191 752029803 1.930000e-151 545.0
23 TraesCS7A01G452100 chr2A 91.731 387 29 2 2229 2614 694855097 694855481 4.190000e-148 534.0
24 TraesCS7A01G452100 chr2A 89.706 408 22 3 2229 2616 38224069 38224476 1.180000e-138 503.0
25 TraesCS7A01G452100 chr2A 92.647 136 6 2 2102 2234 752030699 752030565 2.900000e-45 193.0
26 TraesCS7A01G452100 chr2A 93.600 125 5 1 2111 2232 38223560 38223684 1.750000e-42 183.0
27 TraesCS7A01G452100 chr2A 88.889 144 16 0 564 707 100646158 100646301 8.130000e-41 178.0
28 TraesCS7A01G452100 chr2A 92.000 125 7 3 1449 1571 740347506 740347629 3.780000e-39 172.0
29 TraesCS7A01G452100 chr2A 91.200 125 8 1 2111 2232 682016705 682016581 1.760000e-37 167.0
30 TraesCS7A01G452100 chr2A 76.429 280 45 18 1167 1433 511114839 511115110 6.420000e-27 132.0
31 TraesCS7A01G452100 chr5A 91.990 387 28 2 2229 2614 438842984 438842600 9.000000e-150 540.0
32 TraesCS7A01G452100 chr5A 91.237 388 29 4 2229 2614 631628515 631628131 9.060000e-145 523.0
33 TraesCS7A01G452100 chr5A 92.929 198 12 1 1952 2149 631629213 631629018 1.290000e-73 287.0
34 TraesCS7A01G452100 chr5A 92.079 202 15 1 1949 2149 40058775 40058574 1.670000e-72 283.0
35 TraesCS7A01G452100 chr5A 95.690 116 4 1 1453 1567 7007324 7007439 4.860000e-43 185.0
36 TraesCS7A01G452100 chr5A 93.600 125 5 1 2111 2232 40058580 40058456 1.750000e-42 183.0
37 TraesCS7A01G452100 chr5A 94.017 117 7 0 1458 1574 492896367 492896251 8.130000e-41 178.0
38 TraesCS7A01G452100 chr5A 88.112 143 16 1 564 706 607744225 607744084 4.890000e-38 169.0
39 TraesCS7A01G452100 chr5A 91.200 125 8 1 2111 2232 631629024 631628900 1.760000e-37 167.0
40 TraesCS7A01G452100 chr5A 83.893 149 23 1 566 714 631857829 631857976 1.070000e-29 141.0
41 TraesCS7A01G452100 chr4A 88.452 407 25 3 2229 2613 620627133 620627539 3.330000e-129 472.0
42 TraesCS7A01G452100 chr4A 93.434 198 13 0 1952 2149 626062810 626062613 7.730000e-76 294.0
43 TraesCS7A01G452100 chr4A 94.382 178 8 1 1 178 126074905 126074730 3.620000e-69 272.0
44 TraesCS7A01G452100 chr4A 92.179 179 11 2 1 178 448887923 448887747 1.700000e-62 250.0
45 TraesCS7A01G452100 chr4A 94.017 117 7 0 1456 1572 416231393 416231509 8.130000e-41 178.0
46 TraesCS7A01G452100 chr3A 86.689 293 32 7 1944 2232 570110146 570110435 4.590000e-83 318.0
47 TraesCS7A01G452100 chr3A 94.444 198 11 0 1952 2149 720858978 720859175 3.570000e-79 305.0
48 TraesCS7A01G452100 chr3A 91.935 124 8 2 1451 1573 713911157 713911035 3.780000e-39 172.0
49 TraesCS7A01G452100 chr3A 88.194 144 16 1 564 707 70655181 70655039 1.360000e-38 171.0
50 TraesCS7A01G452100 chr4D 83.288 365 34 13 2253 2616 25384202 25383864 7.680000e-81 311.0
51 TraesCS7A01G452100 chr1A 92.611 203 14 1 1948 2149 61035712 61035510 1.000000e-74 291.0
52 TraesCS7A01G452100 chr1A 92.079 202 14 2 1949 2149 325031754 325031554 1.670000e-72 283.0
53 TraesCS7A01G452100 chr1A 93.600 125 5 1 2111 2232 325031560 325031436 1.750000e-42 183.0
54 TraesCS7A01G452100 chr1A 94.017 117 7 0 1448 1564 22631563 22631679 8.130000e-41 178.0
55 TraesCS7A01G452100 chr1A 93.220 118 5 3 1453 1568 8730676 8730560 1.360000e-38 171.0
56 TraesCS7A01G452100 chr5D 92.135 178 13 1 1 178 534789244 534789068 1.700000e-62 250.0
57 TraesCS7A01G452100 chr2D 91.573 178 15 0 1 178 70277591 70277768 2.200000e-61 246.0
58 TraesCS7A01G452100 chr2D 91.667 132 11 0 564 695 393585472 393585603 1.750000e-42 183.0
59 TraesCS7A01G452100 chr2D 91.954 87 7 0 1347 1433 377156409 377156495 3.860000e-24 122.0
60 TraesCS7A01G452100 chr2B 92.000 175 14 0 1 175 15116668 15116842 2.200000e-61 246.0
61 TraesCS7A01G452100 chr2B 91.954 87 7 0 1347 1433 448870710 448870796 3.860000e-24 122.0
62 TraesCS7A01G452100 chr1D 91.573 178 14 1 1 178 76971146 76970970 7.900000e-61 244.0
63 TraesCS7A01G452100 chr1D 91.573 178 14 1 1 178 365804754 365804578 7.900000e-61 244.0
64 TraesCS7A01G452100 chr1D 90.345 145 14 0 564 708 199421421 199421565 1.040000e-44 191.0
65 TraesCS7A01G452100 chr1B 90.345 145 14 0 564 708 279904609 279904753 1.040000e-44 191.0
66 TraesCS7A01G452100 chr6B 90.511 137 13 0 570 706 81010648 81010512 6.280000e-42 182.0
67 TraesCS7A01G452100 chr4B 88.811 143 14 1 564 706 59415936 59416076 1.050000e-39 174.0
68 TraesCS7A01G452100 chr5B 85.430 151 21 1 564 713 622984904 622984754 3.810000e-34 156.0


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 TraesCS7A01G452100 chr7A 644844604 644847457 2853 False 2280.000000 4231 100.000000 1 2854 2 chr7A.!!$F5 2853
1 TraesCS7A01G452100 chr7A 129152828 129153905 1077 False 418.000000 547 92.588500 1952 2614 2 chr7A.!!$F4 662
2 TraesCS7A01G452100 chr7D 560706347 560707754 1407 False 620.666667 1026 91.302667 703 2845 3 chr7D.!!$F4 2142
3 TraesCS7A01G452100 chr7B 608469319 608471326 2007 False 475.700000 1014 93.850250 703 2854 4 chr7B.!!$F1 2151
4 TraesCS7A01G452100 chr6A 205778147 205779200 1053 False 462.500000 553 91.867000 1952 2614 2 chr6A.!!$F3 662
5 TraesCS7A01G452100 chr2A 752029803 752030699 896 True 369.000000 545 92.359500 2102 2616 2 chr2A.!!$R2 514
6 TraesCS7A01G452100 chr2A 38223560 38224476 916 False 343.000000 503 91.653000 2111 2616 2 chr2A.!!$F5 505
7 TraesCS7A01G452100 chr5A 631628131 631629213 1082 True 325.666667 523 91.788667 1952 2614 3 chr5A.!!$R5 662

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
911 1524 0.882474 GTGTCCAGTGCGACTAGAGT 59.118 55.0 0.0 0.0 33.7 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 3516 0.317799 TCCGGCGCGCCTATAAATTA 59.682 50.0 43.6 19.07 0.0 1.4 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
71 72 8.951787 ATGGTGTGGAAATTAATTTCATGATG 57.048 30.769 31.78 0.00 46.03 3.07
72 73 6.817641 TGGTGTGGAAATTAATTTCATGATGC 59.182 34.615 31.78 18.93 46.03 3.91
73 74 6.817641 GGTGTGGAAATTAATTTCATGATGCA 59.182 34.615 31.78 20.73 46.03 3.96
74 75 7.496591 GGTGTGGAAATTAATTTCATGATGCAT 59.503 33.333 31.78 0.00 46.03 3.96
75 76 8.545420 GTGTGGAAATTAATTTCATGATGCATC 58.455 33.333 31.78 20.14 46.03 3.91
76 77 8.479689 TGTGGAAATTAATTTCATGATGCATCT 58.520 29.630 31.78 10.21 46.03 2.90
77 78 9.321562 GTGGAAATTAATTTCATGATGCATCTT 57.678 29.630 31.78 18.05 46.03 2.40
86 87 9.836076 AATTTCATGATGCATCTTACGATATTG 57.164 29.630 26.32 7.03 0.00 1.90
87 88 8.606040 TTTCATGATGCATCTTACGATATTGA 57.394 30.769 26.32 9.11 0.00 2.57
88 89 8.782339 TTCATGATGCATCTTACGATATTGAT 57.218 30.769 26.32 5.19 0.00 2.57
89 90 8.782339 TCATGATGCATCTTACGATATTGATT 57.218 30.769 26.32 0.00 0.00 2.57
90 91 9.223099 TCATGATGCATCTTACGATATTGATTT 57.777 29.630 26.32 0.00 0.00 2.17
91 92 9.486857 CATGATGCATCTTACGATATTGATTTC 57.513 33.333 26.32 0.00 0.00 2.17
92 93 8.606040 TGATGCATCTTACGATATTGATTTCA 57.394 30.769 26.32 0.00 0.00 2.69
93 94 9.223099 TGATGCATCTTACGATATTGATTTCAT 57.777 29.630 26.32 0.00 0.00 2.57
153 154 5.945155 TCAAAGTTAACAAAGTTTGACGCT 58.055 33.333 22.23 10.79 43.36 5.07
154 155 5.797934 TCAAAGTTAACAAAGTTTGACGCTG 59.202 36.000 22.23 11.63 43.36 5.18
155 156 5.554822 AAGTTAACAAAGTTTGACGCTGA 57.445 34.783 22.23 0.00 0.00 4.26
156 157 4.905269 AGTTAACAAAGTTTGACGCTGAC 58.095 39.130 22.23 10.70 0.00 3.51
157 158 2.844122 AACAAAGTTTGACGCTGACC 57.156 45.000 22.23 0.00 0.00 4.02
158 159 1.745232 ACAAAGTTTGACGCTGACCA 58.255 45.000 22.23 0.00 0.00 4.02
159 160 2.088423 ACAAAGTTTGACGCTGACCAA 58.912 42.857 22.23 0.00 0.00 3.67
160 161 2.490115 ACAAAGTTTGACGCTGACCAAA 59.510 40.909 22.23 0.00 0.00 3.28
161 162 3.130340 ACAAAGTTTGACGCTGACCAAAT 59.870 39.130 22.23 0.00 35.14 2.32
162 163 3.626028 AAGTTTGACGCTGACCAAATC 57.374 42.857 0.00 0.00 35.14 2.17
163 164 2.851195 AGTTTGACGCTGACCAAATCT 58.149 42.857 0.00 0.00 35.14 2.40
164 165 3.214328 AGTTTGACGCTGACCAAATCTT 58.786 40.909 0.00 0.00 35.14 2.40
165 166 4.385825 AGTTTGACGCTGACCAAATCTTA 58.614 39.130 0.00 0.00 35.14 2.10
166 167 5.003804 AGTTTGACGCTGACCAAATCTTAT 58.996 37.500 0.00 0.00 35.14 1.73
167 168 6.170506 AGTTTGACGCTGACCAAATCTTATA 58.829 36.000 0.00 0.00 35.14 0.98
168 169 6.823689 AGTTTGACGCTGACCAAATCTTATAT 59.176 34.615 0.00 0.00 35.14 0.86
169 170 6.603237 TTGACGCTGACCAAATCTTATATG 57.397 37.500 0.00 0.00 0.00 1.78
170 171 4.511454 TGACGCTGACCAAATCTTATATGC 59.489 41.667 0.00 0.00 0.00 3.14
171 172 4.450976 ACGCTGACCAAATCTTATATGCA 58.549 39.130 0.00 0.00 0.00 3.96
172 173 4.512944 ACGCTGACCAAATCTTATATGCAG 59.487 41.667 0.00 0.00 0.00 4.41
173 174 4.751600 CGCTGACCAAATCTTATATGCAGA 59.248 41.667 0.00 0.00 0.00 4.26
174 175 5.333645 CGCTGACCAAATCTTATATGCAGAC 60.334 44.000 0.00 0.00 0.00 3.51
175 176 5.762218 GCTGACCAAATCTTATATGCAGACT 59.238 40.000 0.00 0.00 0.00 3.24
176 177 6.931281 GCTGACCAAATCTTATATGCAGACTA 59.069 38.462 0.00 0.00 0.00 2.59
177 178 7.442364 GCTGACCAAATCTTATATGCAGACTAA 59.558 37.037 0.00 0.00 0.00 2.24
608 609 8.712285 AATCTAACAATCTTGATTTGGCATTG 57.288 30.769 0.00 0.00 0.00 2.82
609 610 7.230849 TCTAACAATCTTGATTTGGCATTGT 57.769 32.000 0.00 0.00 38.94 2.71
610 611 7.092079 TCTAACAATCTTGATTTGGCATTGTG 58.908 34.615 0.15 0.00 37.66 3.33
611 612 5.471556 ACAATCTTGATTTGGCATTGTGA 57.528 34.783 0.00 0.00 36.54 3.58
612 613 5.232463 ACAATCTTGATTTGGCATTGTGAC 58.768 37.500 0.00 0.00 36.54 3.67
613 614 5.011329 ACAATCTTGATTTGGCATTGTGACT 59.989 36.000 0.00 0.00 36.54 3.41
614 615 4.508461 TCTTGATTTGGCATTGTGACTG 57.492 40.909 0.00 0.00 0.00 3.51
615 616 3.890756 TCTTGATTTGGCATTGTGACTGT 59.109 39.130 0.00 0.00 0.00 3.55
616 617 4.341806 TCTTGATTTGGCATTGTGACTGTT 59.658 37.500 0.00 0.00 0.00 3.16
617 618 3.979948 TGATTTGGCATTGTGACTGTTG 58.020 40.909 0.00 0.00 0.00 3.33
618 619 3.635836 TGATTTGGCATTGTGACTGTTGA 59.364 39.130 0.00 0.00 0.00 3.18
619 620 4.281435 TGATTTGGCATTGTGACTGTTGAT 59.719 37.500 0.00 0.00 0.00 2.57
620 621 5.476254 TGATTTGGCATTGTGACTGTTGATA 59.524 36.000 0.00 0.00 0.00 2.15
621 622 4.764679 TTGGCATTGTGACTGTTGATAC 57.235 40.909 0.00 0.00 0.00 2.24
622 623 4.019792 TGGCATTGTGACTGTTGATACT 57.980 40.909 0.00 0.00 0.00 2.12
623 624 4.397420 TGGCATTGTGACTGTTGATACTT 58.603 39.130 0.00 0.00 0.00 2.24
624 625 5.555966 TGGCATTGTGACTGTTGATACTTA 58.444 37.500 0.00 0.00 0.00 2.24
625 626 6.179756 TGGCATTGTGACTGTTGATACTTAT 58.820 36.000 0.00 0.00 0.00 1.73
626 627 6.658816 TGGCATTGTGACTGTTGATACTTATT 59.341 34.615 0.00 0.00 0.00 1.40
627 628 7.176515 TGGCATTGTGACTGTTGATACTTATTT 59.823 33.333 0.00 0.00 0.00 1.40
628 629 7.698130 GGCATTGTGACTGTTGATACTTATTTC 59.302 37.037 0.00 0.00 0.00 2.17
629 630 8.454106 GCATTGTGACTGTTGATACTTATTTCT 58.546 33.333 0.00 0.00 0.00 2.52
665 666 8.703604 TCAAAGTAGAGATATTTTGACTTCGG 57.296 34.615 2.86 0.00 35.34 4.30
666 667 8.528643 TCAAAGTAGAGATATTTTGACTTCGGA 58.471 33.333 2.86 0.00 35.34 4.55
667 668 8.596380 CAAAGTAGAGATATTTTGACTTCGGAC 58.404 37.037 0.00 0.00 33.50 4.79
668 669 6.496571 AGTAGAGATATTTTGACTTCGGACG 58.503 40.000 0.00 0.00 0.00 4.79
669 670 5.578005 AGAGATATTTTGACTTCGGACGA 57.422 39.130 0.00 0.00 0.00 4.20
670 671 5.962433 AGAGATATTTTGACTTCGGACGAA 58.038 37.500 6.98 6.98 0.00 3.85
671 672 6.395629 AGAGATATTTTGACTTCGGACGAAA 58.604 36.000 8.59 0.00 33.34 3.46
672 673 7.042335 AGAGATATTTTGACTTCGGACGAAAT 58.958 34.615 8.59 0.00 37.43 2.17
673 674 7.549488 AGAGATATTTTGACTTCGGACGAAATT 59.451 33.333 8.59 0.00 36.03 1.82
674 675 8.040716 AGATATTTTGACTTCGGACGAAATTT 57.959 30.769 8.59 0.00 36.03 1.82
675 676 9.158233 AGATATTTTGACTTCGGACGAAATTTA 57.842 29.630 8.59 0.00 36.03 1.40
676 677 9.931210 GATATTTTGACTTCGGACGAAATTTAT 57.069 29.630 8.59 1.47 36.03 1.40
679 680 9.716507 ATTTTGACTTCGGACGAAATTTATATG 57.283 29.630 8.59 0.00 32.62 1.78
680 681 6.281848 TGACTTCGGACGAAATTTATATGC 57.718 37.500 8.59 0.00 33.34 3.14
681 682 5.813157 TGACTTCGGACGAAATTTATATGCA 59.187 36.000 8.59 0.00 33.34 3.96
682 683 6.019075 TGACTTCGGACGAAATTTATATGCAG 60.019 38.462 8.59 0.00 33.34 4.41
683 684 6.046593 ACTTCGGACGAAATTTATATGCAGA 58.953 36.000 8.59 0.00 33.34 4.26
684 685 6.706270 ACTTCGGACGAAATTTATATGCAGAT 59.294 34.615 8.59 0.00 33.34 2.90
685 686 7.226720 ACTTCGGACGAAATTTATATGCAGATT 59.773 33.333 8.59 0.00 33.34 2.40
686 687 8.596271 TTCGGACGAAATTTATATGCAGATTA 57.404 30.769 0.00 0.00 0.00 1.75
687 688 8.596271 TCGGACGAAATTTATATGCAGATTAA 57.404 30.769 0.00 0.00 0.00 1.40
688 689 9.047371 TCGGACGAAATTTATATGCAGATTAAA 57.953 29.630 0.00 0.03 0.00 1.52
689 690 9.658475 CGGACGAAATTTATATGCAGATTAAAA 57.342 29.630 0.00 0.00 0.00 1.52
701 702 9.995003 ATATGCAGATTAAAAAGGACTAGAGAG 57.005 33.333 0.00 0.00 0.00 3.20
867 1479 5.086104 GTGTGTACACCCTTCATCACTAT 57.914 43.478 22.91 0.00 40.85 2.12
911 1524 0.882474 GTGTCCAGTGCGACTAGAGT 59.118 55.000 0.00 0.00 33.70 3.24
943 1556 4.218722 CACCCATAACGAGGTGCC 57.781 61.111 0.00 0.00 46.55 5.01
963 1576 2.184836 CCCCACAATGCCGCAATG 59.815 61.111 6.89 6.89 0.00 2.82
964 1577 2.509786 CCCACAATGCCGCAATGC 60.510 61.111 8.39 0.00 0.00 3.56
968 1581 2.509786 CAATGCCGCAATGCCACC 60.510 61.111 0.00 0.00 0.00 4.61
980 1593 3.372206 GCAATGCCACCGCTATATAAGAG 59.628 47.826 0.00 0.00 35.36 2.85
1033 1649 1.064946 GCGATCTGCACTAGTCGCT 59.935 57.895 14.91 0.00 44.73 4.93
1042 1661 1.071605 CACTAGTCGCTGCAAGAACC 58.928 55.000 0.00 0.00 34.07 3.62
1367 1986 2.190578 GGGATCAAGCCCGAGGTG 59.809 66.667 0.00 0.00 38.58 4.00
1438 2068 1.274167 CAAGTGCGGAGGTACCTACAA 59.726 52.381 24.29 8.71 36.31 2.41
1439 2069 1.636148 AGTGCGGAGGTACCTACAAA 58.364 50.000 24.29 8.32 36.31 2.83
1440 2070 1.549170 AGTGCGGAGGTACCTACAAAG 59.451 52.381 24.29 9.00 36.31 2.77
1447 2077 2.678336 GAGGTACCTACAAAGCACATGC 59.322 50.000 16.29 0.00 42.49 4.06
1448 2078 6.675100 GGAGGTACCTACAAAGCACATGCT 62.675 50.000 20.12 0.00 44.17 3.79
1462 2102 5.004922 GCACATGCTCTCCTATATACTCC 57.995 47.826 0.00 0.00 38.21 3.85
1464 2104 5.268387 CACATGCTCTCCTATATACTCCCT 58.732 45.833 0.00 0.00 0.00 4.20
1465 2105 5.359576 CACATGCTCTCCTATATACTCCCTC 59.640 48.000 0.00 0.00 0.00 4.30
1466 2106 4.594675 TGCTCTCCTATATACTCCCTCC 57.405 50.000 0.00 0.00 0.00 4.30
1467 2107 3.923425 TGCTCTCCTATATACTCCCTCCA 59.077 47.826 0.00 0.00 0.00 3.86
1468 2108 4.546195 TGCTCTCCTATATACTCCCTCCAT 59.454 45.833 0.00 0.00 0.00 3.41
1469 2109 5.016782 TGCTCTCCTATATACTCCCTCCATT 59.983 44.000 0.00 0.00 0.00 3.16
1470 2110 5.596772 GCTCTCCTATATACTCCCTCCATTC 59.403 48.000 0.00 0.00 0.00 2.67
1471 2111 6.093617 TCTCCTATATACTCCCTCCATTCC 57.906 45.833 0.00 0.00 0.00 3.01
1472 2112 4.868268 TCCTATATACTCCCTCCATTCCG 58.132 47.826 0.00 0.00 0.00 4.30
1473 2113 4.542931 TCCTATATACTCCCTCCATTCCGA 59.457 45.833 0.00 0.00 0.00 4.55
1474 2114 5.015924 TCCTATATACTCCCTCCATTCCGAA 59.984 44.000 0.00 0.00 0.00 4.30
1475 2115 5.900123 CCTATATACTCCCTCCATTCCGAAT 59.100 44.000 0.00 0.00 0.00 3.34
1476 2116 6.384305 CCTATATACTCCCTCCATTCCGAATT 59.616 42.308 0.00 0.00 0.00 2.17
1477 2117 7.563924 CCTATATACTCCCTCCATTCCGAATTA 59.436 40.741 0.00 0.00 0.00 1.40
1478 2118 3.840124 ACTCCCTCCATTCCGAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
1479 2119 3.385115 ACTCCCTCCATTCCGAATTACT 58.615 45.455 0.00 0.00 0.00 2.24
1480 2120 3.780850 ACTCCCTCCATTCCGAATTACTT 59.219 43.478 0.00 0.00 0.00 2.24
1481 2121 4.130118 CTCCCTCCATTCCGAATTACTTG 58.870 47.826 0.00 0.00 0.00 3.16
1482 2122 3.521937 TCCCTCCATTCCGAATTACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
1483 2123 3.877508 CCCTCCATTCCGAATTACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
1484 2124 3.555956 CCTCCATTCCGAATTACTTGTCG 59.444 47.826 0.00 0.00 37.01 4.35
1485 2125 2.933906 TCCATTCCGAATTACTTGTCGC 59.066 45.455 0.00 0.00 35.93 5.19
1486 2126 2.675844 CCATTCCGAATTACTTGTCGCA 59.324 45.455 0.00 0.00 35.93 5.10
1487 2127 3.242413 CCATTCCGAATTACTTGTCGCAG 60.242 47.826 0.00 0.00 35.93 5.18
1488 2128 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
1489 2129 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
1490 2130 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
1491 2131 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
1492 2132 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
1493 2133 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
1494 2134 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
1495 2135 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
1496 2136 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
1497 2137 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
1498 2138 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
1499 2139 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
1500 2140 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
1501 2141 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
1502 2142 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
1503 2143 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
1504 2144 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
1505 2145 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
1506 2146 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
1507 2147 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
1508 2148 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
1509 2149 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
1510 2150 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
1540 2180 9.517361 GTTCTAGATATATTCATTTTTGCGACG 57.483 33.333 0.00 0.00 0.00 5.12
1541 2181 9.471084 TTCTAGATATATTCATTTTTGCGACGA 57.529 29.630 0.00 0.00 0.00 4.20
1542 2182 9.129209 TCTAGATATATTCATTTTTGCGACGAG 57.871 33.333 0.00 0.00 0.00 4.18
1543 2183 7.715265 AGATATATTCATTTTTGCGACGAGT 57.285 32.000 0.00 0.00 0.00 4.18
1544 2184 8.812147 AGATATATTCATTTTTGCGACGAGTA 57.188 30.769 0.00 0.00 0.00 2.59
1545 2185 9.256477 AGATATATTCATTTTTGCGACGAGTAA 57.744 29.630 0.00 0.00 0.00 2.24
1549 2189 6.667981 TTCATTTTTGCGACGAGTAATTTG 57.332 33.333 0.00 0.00 0.00 2.32
1550 2190 5.991568 TCATTTTTGCGACGAGTAATTTGA 58.008 33.333 0.00 0.00 0.00 2.69
1551 2191 6.431278 TCATTTTTGCGACGAGTAATTTGAA 58.569 32.000 0.00 0.00 0.00 2.69
1552 2192 6.913132 TCATTTTTGCGACGAGTAATTTGAAA 59.087 30.769 0.00 0.00 0.00 2.69
1553 2193 6.485253 TTTTTGCGACGAGTAATTTGAAAC 57.515 33.333 0.00 0.00 0.00 2.78
1554 2194 3.427516 TGCGACGAGTAATTTGAAACG 57.572 42.857 0.00 0.00 0.00 3.60
1555 2195 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
1556 2196 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
1557 2197 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
1558 2198 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
1559 2199 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1560 2200 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1561 2201 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
1562 2202 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
1563 2203 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
1564 2204 6.117975 AGTAATTTGAAACGGAGGGAGTAA 57.882 37.500 0.00 0.00 0.00 2.24
1565 2205 6.718294 AGTAATTTGAAACGGAGGGAGTAAT 58.282 36.000 0.00 0.00 0.00 1.89
1566 2206 7.173032 AGTAATTTGAAACGGAGGGAGTAATT 58.827 34.615 0.00 0.00 0.00 1.40
1567 2207 5.897377 ATTTGAAACGGAGGGAGTAATTG 57.103 39.130 0.00 0.00 0.00 2.32
1568 2208 2.706890 TGAAACGGAGGGAGTAATTGC 58.293 47.619 0.00 0.00 0.00 3.56
1569 2209 2.304761 TGAAACGGAGGGAGTAATTGCT 59.695 45.455 0.00 0.00 0.00 3.91
1570 2210 3.516300 TGAAACGGAGGGAGTAATTGCTA 59.484 43.478 0.00 0.00 0.00 3.49
1571 2211 4.020039 TGAAACGGAGGGAGTAATTGCTAA 60.020 41.667 0.00 0.00 0.00 3.09
1572 2212 3.538634 ACGGAGGGAGTAATTGCTAAC 57.461 47.619 0.00 0.00 0.00 2.34
1573 2213 2.159142 ACGGAGGGAGTAATTGCTAACG 60.159 50.000 0.00 0.26 0.00 3.18
1577 2217 4.511826 GGAGGGAGTAATTGCTAACGAATG 59.488 45.833 0.00 0.00 0.00 2.67
1617 2261 0.443869 CAATGCTGAGTCCGGTTTCG 59.556 55.000 0.00 0.00 0.00 3.46
1688 2332 4.290711 TGAAGATGAATGCTGTGGAAGA 57.709 40.909 0.00 0.00 0.00 2.87
1690 2334 5.993055 TGAAGATGAATGCTGTGGAAGATA 58.007 37.500 0.00 0.00 0.00 1.98
1692 2336 6.485648 TGAAGATGAATGCTGTGGAAGATATG 59.514 38.462 0.00 0.00 0.00 1.78
1749 2393 0.687354 AAGTGGGGCACTAGTGACTG 59.313 55.000 27.55 0.78 44.62 3.51
1759 2406 0.251354 CTAGTGACTGCATGGTGCCT 59.749 55.000 0.00 0.00 44.23 4.75
1760 2407 1.482182 CTAGTGACTGCATGGTGCCTA 59.518 52.381 0.00 0.00 44.23 3.93
1874 2523 2.762535 TACGAAAGGCTTTCCTCTGG 57.237 50.000 28.98 18.89 43.40 3.86
1919 2570 3.317993 GCACCAACAAGTCCTACAAACAT 59.682 43.478 0.00 0.00 0.00 2.71
1921 2572 4.578516 CACCAACAAGTCCTACAAACATGA 59.421 41.667 0.00 0.00 0.00 3.07
1945 2596 2.209273 CACACCACGTCAAGTTCATCA 58.791 47.619 0.00 0.00 0.00 3.07
1947 2598 2.158957 ACACCACGTCAAGTTCATCAGT 60.159 45.455 0.00 0.00 0.00 3.41
1948 2599 2.872245 CACCACGTCAAGTTCATCAGTT 59.128 45.455 0.00 0.00 0.00 3.16
1949 2600 3.312421 CACCACGTCAAGTTCATCAGTTT 59.688 43.478 0.00 0.00 0.00 2.66
1950 2601 4.509970 CACCACGTCAAGTTCATCAGTTTA 59.490 41.667 0.00 0.00 0.00 2.01
1958 2609 7.571983 CGTCAAGTTCATCAGTTTAAGCATCTT 60.572 37.037 0.00 0.00 0.00 2.40
2101 2752 0.588252 CAGCAGGCGCGCTATATTTT 59.412 50.000 32.29 7.58 45.49 1.82
2159 2845 4.727507 TCTACTACTACTCGTCCGACTT 57.272 45.455 0.00 0.00 0.00 3.01
2173 2859 1.613925 CCGACTTGGACTCTGTCTCAA 59.386 52.381 0.00 0.00 42.00 3.02
2187 2873 3.705579 CTGTCTCAATGATGTCCTCCTCT 59.294 47.826 0.00 0.00 0.00 3.69
2397 3471 1.840650 CAGGGGGCGATGGAGAGAT 60.841 63.158 0.00 0.00 0.00 2.75
2407 3481 2.596346 GATGGAGAGATGGAGAGAGCA 58.404 52.381 0.00 0.00 0.00 4.26
2545 3638 2.726691 GCTAGAGCGCGCGAAAACA 61.727 57.895 37.18 12.73 0.00 2.83
2550 3643 4.829518 GCGCGCGAAAACATCCCC 62.830 66.667 37.18 7.60 0.00 4.81
2578 3674 3.430895 GCTATAAGCTAATTTACCGCGCA 59.569 43.478 8.75 0.00 38.45 6.09
2769 3865 0.609131 CCGATGGCCTCCAAAGTTGT 60.609 55.000 3.32 0.00 36.95 3.32
2770 3866 1.339631 CCGATGGCCTCCAAAGTTGTA 60.340 52.381 3.32 0.00 36.95 2.41
2771 3867 2.643551 CGATGGCCTCCAAAGTTGTAT 58.356 47.619 3.32 0.00 36.95 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.496591 GCATCATGAAATTAATTTCCACACCAT 59.503 33.333 29.31 17.33 44.16 3.55
47 48 6.817641 GCATCATGAAATTAATTTCCACACCA 59.182 34.615 29.31 16.10 44.16 4.17
48 49 6.817641 TGCATCATGAAATTAATTTCCACACC 59.182 34.615 29.31 17.38 44.16 4.16
49 50 7.830940 TGCATCATGAAATTAATTTCCACAC 57.169 32.000 29.31 17.86 44.16 3.82
50 51 8.479689 AGATGCATCATGAAATTAATTTCCACA 58.520 29.630 29.31 20.14 44.16 4.17
51 52 8.882415 AGATGCATCATGAAATTAATTTCCAC 57.118 30.769 29.31 16.55 44.16 4.02
125 126 8.995906 CGTCAAACTTTGTTAACTTTGACTAAG 58.004 33.333 29.29 19.35 45.38 2.18
126 127 7.482428 GCGTCAAACTTTGTTAACTTTGACTAA 59.518 33.333 29.29 8.28 45.38 2.24
127 128 6.962678 GCGTCAAACTTTGTTAACTTTGACTA 59.037 34.615 29.29 9.86 45.38 2.59
128 129 5.798434 GCGTCAAACTTTGTTAACTTTGACT 59.202 36.000 29.29 6.03 45.38 3.41
129 130 5.798434 AGCGTCAAACTTTGTTAACTTTGAC 59.202 36.000 26.11 26.11 44.66 3.18
130 131 5.797934 CAGCGTCAAACTTTGTTAACTTTGA 59.202 36.000 13.70 13.70 31.68 2.69
131 132 5.797934 TCAGCGTCAAACTTTGTTAACTTTG 59.202 36.000 7.22 9.09 0.00 2.77
132 133 5.798434 GTCAGCGTCAAACTTTGTTAACTTT 59.202 36.000 7.22 0.00 0.00 2.66
133 134 5.329493 GTCAGCGTCAAACTTTGTTAACTT 58.671 37.500 7.22 0.00 0.00 2.66
134 135 4.201881 GGTCAGCGTCAAACTTTGTTAACT 60.202 41.667 7.22 0.00 0.00 2.24
135 136 4.033019 GGTCAGCGTCAAACTTTGTTAAC 58.967 43.478 0.00 0.00 0.00 2.01
136 137 3.690139 TGGTCAGCGTCAAACTTTGTTAA 59.310 39.130 1.44 0.00 0.00 2.01
137 138 3.271729 TGGTCAGCGTCAAACTTTGTTA 58.728 40.909 1.44 0.00 0.00 2.41
138 139 2.088423 TGGTCAGCGTCAAACTTTGTT 58.912 42.857 1.44 0.00 0.00 2.83
139 140 1.745232 TGGTCAGCGTCAAACTTTGT 58.255 45.000 1.44 0.00 0.00 2.83
140 141 2.842208 TTGGTCAGCGTCAAACTTTG 57.158 45.000 0.00 0.00 0.00 2.77
141 142 3.632145 AGATTTGGTCAGCGTCAAACTTT 59.368 39.130 0.00 0.00 35.97 2.66
142 143 3.214328 AGATTTGGTCAGCGTCAAACTT 58.786 40.909 0.00 0.00 35.97 2.66
143 144 2.851195 AGATTTGGTCAGCGTCAAACT 58.149 42.857 0.00 0.00 35.97 2.66
144 145 3.626028 AAGATTTGGTCAGCGTCAAAC 57.374 42.857 0.00 0.00 35.97 2.93
145 146 6.458206 GCATATAAGATTTGGTCAGCGTCAAA 60.458 38.462 0.00 0.00 37.29 2.69
146 147 5.007626 GCATATAAGATTTGGTCAGCGTCAA 59.992 40.000 0.00 0.00 0.00 3.18
147 148 4.511454 GCATATAAGATTTGGTCAGCGTCA 59.489 41.667 0.00 0.00 0.00 4.35
148 149 4.511454 TGCATATAAGATTTGGTCAGCGTC 59.489 41.667 0.00 0.00 0.00 5.19
149 150 4.450976 TGCATATAAGATTTGGTCAGCGT 58.549 39.130 0.00 0.00 0.00 5.07
150 151 4.751600 TCTGCATATAAGATTTGGTCAGCG 59.248 41.667 0.00 0.00 0.00 5.18
151 152 5.762218 AGTCTGCATATAAGATTTGGTCAGC 59.238 40.000 0.00 0.00 0.00 4.26
152 153 8.893219 TTAGTCTGCATATAAGATTTGGTCAG 57.107 34.615 0.00 0.00 0.00 3.51
582 583 9.158233 CAATGCCAAATCAAGATTGTTAGATTT 57.842 29.630 0.00 0.00 40.29 2.17
583 584 8.316214 ACAATGCCAAATCAAGATTGTTAGATT 58.684 29.630 0.00 0.00 34.36 2.40
584 585 7.762615 CACAATGCCAAATCAAGATTGTTAGAT 59.237 33.333 0.00 0.00 35.55 1.98
585 586 7.039853 TCACAATGCCAAATCAAGATTGTTAGA 60.040 33.333 0.00 0.00 35.55 2.10
586 587 7.062605 GTCACAATGCCAAATCAAGATTGTTAG 59.937 37.037 0.00 0.00 35.55 2.34
587 588 6.867816 GTCACAATGCCAAATCAAGATTGTTA 59.132 34.615 0.00 0.00 35.55 2.41
588 589 5.697633 GTCACAATGCCAAATCAAGATTGTT 59.302 36.000 0.00 0.00 35.55 2.83
589 590 5.011329 AGTCACAATGCCAAATCAAGATTGT 59.989 36.000 0.00 0.00 37.66 2.71
590 591 5.347635 CAGTCACAATGCCAAATCAAGATTG 59.652 40.000 0.00 0.00 0.00 2.67
591 592 5.011329 ACAGTCACAATGCCAAATCAAGATT 59.989 36.000 0.00 0.00 0.00 2.40
592 593 4.525487 ACAGTCACAATGCCAAATCAAGAT 59.475 37.500 0.00 0.00 0.00 2.40
593 594 3.890756 ACAGTCACAATGCCAAATCAAGA 59.109 39.130 0.00 0.00 0.00 3.02
594 595 4.247267 ACAGTCACAATGCCAAATCAAG 57.753 40.909 0.00 0.00 0.00 3.02
595 596 4.099113 TCAACAGTCACAATGCCAAATCAA 59.901 37.500 0.00 0.00 0.00 2.57
596 597 3.635836 TCAACAGTCACAATGCCAAATCA 59.364 39.130 0.00 0.00 0.00 2.57
597 598 4.241590 TCAACAGTCACAATGCCAAATC 57.758 40.909 0.00 0.00 0.00 2.17
598 599 4.877378 ATCAACAGTCACAATGCCAAAT 57.123 36.364 0.00 0.00 0.00 2.32
599 600 4.826733 AGTATCAACAGTCACAATGCCAAA 59.173 37.500 0.00 0.00 0.00 3.28
600 601 4.397420 AGTATCAACAGTCACAATGCCAA 58.603 39.130 0.00 0.00 0.00 4.52
601 602 4.019792 AGTATCAACAGTCACAATGCCA 57.980 40.909 0.00 0.00 0.00 4.92
602 603 6.683974 ATAAGTATCAACAGTCACAATGCC 57.316 37.500 0.00 0.00 0.00 4.40
603 604 8.454106 AGAAATAAGTATCAACAGTCACAATGC 58.546 33.333 0.00 0.00 0.00 3.56
640 641 8.528643 TCCGAAGTCAAAATATCTCTACTTTGA 58.471 33.333 0.00 3.10 35.88 2.69
641 642 8.596380 GTCCGAAGTCAAAATATCTCTACTTTG 58.404 37.037 0.00 0.00 0.00 2.77
642 643 7.488471 CGTCCGAAGTCAAAATATCTCTACTTT 59.512 37.037 0.00 0.00 0.00 2.66
643 644 6.973474 CGTCCGAAGTCAAAATATCTCTACTT 59.027 38.462 0.00 0.00 0.00 2.24
644 645 6.318144 TCGTCCGAAGTCAAAATATCTCTACT 59.682 38.462 0.00 0.00 0.00 2.57
645 646 6.493116 TCGTCCGAAGTCAAAATATCTCTAC 58.507 40.000 0.00 0.00 0.00 2.59
646 647 6.688637 TCGTCCGAAGTCAAAATATCTCTA 57.311 37.500 0.00 0.00 0.00 2.43
647 648 5.578005 TCGTCCGAAGTCAAAATATCTCT 57.422 39.130 0.00 0.00 0.00 3.10
648 649 6.642683 TTTCGTCCGAAGTCAAAATATCTC 57.357 37.500 2.12 0.00 35.38 2.75
649 650 7.611213 AATTTCGTCCGAAGTCAAAATATCT 57.389 32.000 2.12 0.00 35.38 1.98
650 651 9.931210 ATAAATTTCGTCCGAAGTCAAAATATC 57.069 29.630 0.00 0.00 35.38 1.63
653 654 9.716507 CATATAAATTTCGTCCGAAGTCAAAAT 57.283 29.630 0.00 0.00 35.38 1.82
654 655 7.694784 GCATATAAATTTCGTCCGAAGTCAAAA 59.305 33.333 0.00 0.00 35.38 2.44
655 656 7.148390 TGCATATAAATTTCGTCCGAAGTCAAA 60.148 33.333 0.00 0.00 35.38 2.69
656 657 6.314152 TGCATATAAATTTCGTCCGAAGTCAA 59.686 34.615 0.00 0.00 35.38 3.18
657 658 5.813157 TGCATATAAATTTCGTCCGAAGTCA 59.187 36.000 0.00 0.00 35.38 3.41
658 659 6.200286 TCTGCATATAAATTTCGTCCGAAGTC 59.800 38.462 0.00 0.00 35.38 3.01
659 660 6.046593 TCTGCATATAAATTTCGTCCGAAGT 58.953 36.000 0.00 0.00 35.38 3.01
660 661 6.525121 TCTGCATATAAATTTCGTCCGAAG 57.475 37.500 0.00 0.00 35.38 3.79
661 662 7.490962 AATCTGCATATAAATTTCGTCCGAA 57.509 32.000 0.00 0.00 0.00 4.30
662 663 8.596271 TTAATCTGCATATAAATTTCGTCCGA 57.404 30.769 0.00 0.00 0.00 4.55
663 664 9.658475 TTTTAATCTGCATATAAATTTCGTCCG 57.342 29.630 0.00 0.00 0.00 4.79
675 676 9.995003 CTCTCTAGTCCTTTTTAATCTGCATAT 57.005 33.333 0.00 0.00 0.00 1.78
676 677 9.201989 TCTCTCTAGTCCTTTTTAATCTGCATA 57.798 33.333 0.00 0.00 0.00 3.14
677 678 8.083828 TCTCTCTAGTCCTTTTTAATCTGCAT 57.916 34.615 0.00 0.00 0.00 3.96
678 679 7.179338 ACTCTCTCTAGTCCTTTTTAATCTGCA 59.821 37.037 0.00 0.00 0.00 4.41
679 680 7.552459 ACTCTCTCTAGTCCTTTTTAATCTGC 58.448 38.462 0.00 0.00 0.00 4.26
687 688 9.930158 ACTGATAATACTCTCTCTAGTCCTTTT 57.070 33.333 0.00 0.00 0.00 2.27
688 689 9.930158 AACTGATAATACTCTCTCTAGTCCTTT 57.070 33.333 0.00 0.00 0.00 3.11
696 697 9.821240 ATCCACATAACTGATAATACTCTCTCT 57.179 33.333 0.00 0.00 0.00 3.10
697 698 9.853555 CATCCACATAACTGATAATACTCTCTC 57.146 37.037 0.00 0.00 0.00 3.20
698 699 9.373450 ACATCCACATAACTGATAATACTCTCT 57.627 33.333 0.00 0.00 0.00 3.10
699 700 9.988815 AACATCCACATAACTGATAATACTCTC 57.011 33.333 0.00 0.00 0.00 3.20
700 701 9.988815 GAACATCCACATAACTGATAATACTCT 57.011 33.333 0.00 0.00 0.00 3.24
701 702 9.764363 TGAACATCCACATAACTGATAATACTC 57.236 33.333 0.00 0.00 0.00 2.59
777 1389 7.855904 CCTGCCATATAAACATTCTAAAACGTC 59.144 37.037 0.00 0.00 0.00 4.34
778 1390 7.338449 ACCTGCCATATAAACATTCTAAAACGT 59.662 33.333 0.00 0.00 0.00 3.99
911 1524 1.198759 GGGTGGAGCACTTGGGACTA 61.199 60.000 0.00 0.00 34.40 2.59
963 1576 1.275291 TGCCTCTTATATAGCGGTGGC 59.725 52.381 0.00 0.00 39.53 5.01
964 1577 2.353803 GGTGCCTCTTATATAGCGGTGG 60.354 54.545 0.00 0.00 31.00 4.61
968 1581 2.353803 GGGTGGTGCCTCTTATATAGCG 60.354 54.545 0.00 0.00 37.43 4.26
1031 1647 1.827789 TGGTGGTGGTTCTTGCAGC 60.828 57.895 0.00 0.00 0.00 5.25
1033 1649 0.323816 TTGTGGTGGTGGTTCTTGCA 60.324 50.000 0.00 0.00 0.00 4.08
1042 1661 1.670811 GTTCACTCACTTGTGGTGGTG 59.329 52.381 16.38 14.32 45.38 4.17
1061 1680 1.004918 CCTTTCCTTGCTCCGACGT 60.005 57.895 0.00 0.00 0.00 4.34
1367 1986 1.456331 CTTGGGGATGGTGATGGCC 60.456 63.158 0.00 0.00 0.00 5.36
1440 2070 4.142049 GGGAGTATATAGGAGAGCATGTGC 60.142 50.000 0.00 0.00 42.49 4.57
1447 2077 6.133356 GGAATGGAGGGAGTATATAGGAGAG 58.867 48.000 0.00 0.00 0.00 3.20
1448 2078 5.340110 CGGAATGGAGGGAGTATATAGGAGA 60.340 48.000 0.00 0.00 0.00 3.71
1455 2085 6.320518 AGTAATTCGGAATGGAGGGAGTATA 58.679 40.000 3.59 0.00 0.00 1.47
1456 2086 5.155905 AGTAATTCGGAATGGAGGGAGTAT 58.844 41.667 3.59 0.00 0.00 2.12
1458 2088 3.385115 AGTAATTCGGAATGGAGGGAGT 58.615 45.455 3.59 0.00 0.00 3.85
1461 2101 3.877508 GACAAGTAATTCGGAATGGAGGG 59.122 47.826 3.59 0.00 0.00 4.30
1462 2102 3.555956 CGACAAGTAATTCGGAATGGAGG 59.444 47.826 3.59 0.00 0.00 4.30
1464 2104 2.933906 GCGACAAGTAATTCGGAATGGA 59.066 45.455 3.59 0.00 35.73 3.41
1465 2105 2.675844 TGCGACAAGTAATTCGGAATGG 59.324 45.455 3.59 0.00 35.73 3.16
1466 2106 3.242413 CCTGCGACAAGTAATTCGGAATG 60.242 47.826 3.59 0.00 35.02 2.67
1467 2107 2.936498 CCTGCGACAAGTAATTCGGAAT 59.064 45.455 0.00 0.00 35.02 3.01
1468 2108 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
1469 2109 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
1470 2110 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
1471 2111 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
1472 2112 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
1473 2113 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
1474 2114 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
1475 2115 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
1476 2116 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
1477 2117 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
1478 2118 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
1479 2119 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
1480 2120 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
1481 2121 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
1482 2122 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
1483 2123 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
1484 2124 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
1514 2154 9.517361 CGTCGCAAAAATGAATATATCTAGAAC 57.483 33.333 0.00 0.00 0.00 3.01
1515 2155 9.471084 TCGTCGCAAAAATGAATATATCTAGAA 57.529 29.630 0.00 0.00 0.00 2.10
1516 2156 9.129209 CTCGTCGCAAAAATGAATATATCTAGA 57.871 33.333 0.00 0.00 0.00 2.43
1517 2157 8.916654 ACTCGTCGCAAAAATGAATATATCTAG 58.083 33.333 0.00 0.00 0.00 2.43
1518 2158 8.812147 ACTCGTCGCAAAAATGAATATATCTA 57.188 30.769 0.00 0.00 0.00 1.98
1519 2159 7.715265 ACTCGTCGCAAAAATGAATATATCT 57.285 32.000 0.00 0.00 0.00 1.98
1523 2163 9.009327 CAAATTACTCGTCGCAAAAATGAATAT 57.991 29.630 0.00 0.00 0.00 1.28
1524 2164 8.231161 TCAAATTACTCGTCGCAAAAATGAATA 58.769 29.630 0.00 0.00 0.00 1.75
1525 2165 7.081349 TCAAATTACTCGTCGCAAAAATGAAT 58.919 30.769 0.00 0.00 0.00 2.57
1526 2166 6.431278 TCAAATTACTCGTCGCAAAAATGAA 58.569 32.000 0.00 0.00 0.00 2.57
1527 2167 5.991568 TCAAATTACTCGTCGCAAAAATGA 58.008 33.333 0.00 0.00 0.00 2.57
1528 2168 6.667981 TTCAAATTACTCGTCGCAAAAATG 57.332 33.333 0.00 0.00 0.00 2.32
1529 2169 6.129561 CGTTTCAAATTACTCGTCGCAAAAAT 60.130 34.615 0.00 0.00 0.00 1.82
1530 2170 5.169915 CGTTTCAAATTACTCGTCGCAAAAA 59.830 36.000 0.00 0.00 0.00 1.94
1531 2171 4.667061 CGTTTCAAATTACTCGTCGCAAAA 59.333 37.500 0.00 0.00 0.00 2.44
1532 2172 4.205334 CGTTTCAAATTACTCGTCGCAAA 58.795 39.130 0.00 0.00 0.00 3.68
1533 2173 3.363182 CCGTTTCAAATTACTCGTCGCAA 60.363 43.478 0.00 0.00 0.00 4.85
1534 2174 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
1535 2175 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
1536 2176 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
1537 2177 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
1538 2178 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
1539 2179 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
1540 2180 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1541 2181 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1542 2182 6.997239 ATTACTCCCTCCGTTTCAAATTAC 57.003 37.500 0.00 0.00 0.00 1.89
1543 2183 6.127842 GCAATTACTCCCTCCGTTTCAAATTA 60.128 38.462 0.00 0.00 0.00 1.40
1544 2184 5.336451 GCAATTACTCCCTCCGTTTCAAATT 60.336 40.000 0.00 0.00 0.00 1.82
1545 2185 4.157840 GCAATTACTCCCTCCGTTTCAAAT 59.842 41.667 0.00 0.00 0.00 2.32
1546 2186 3.504520 GCAATTACTCCCTCCGTTTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
1547 2187 3.078837 GCAATTACTCCCTCCGTTTCAA 58.921 45.455 0.00 0.00 0.00 2.69
1548 2188 2.304761 AGCAATTACTCCCTCCGTTTCA 59.695 45.455 0.00 0.00 0.00 2.69
1549 2189 2.987232 AGCAATTACTCCCTCCGTTTC 58.013 47.619 0.00 0.00 0.00 2.78
1550 2190 4.259356 GTTAGCAATTACTCCCTCCGTTT 58.741 43.478 0.00 0.00 0.00 3.60
1551 2191 3.677976 CGTTAGCAATTACTCCCTCCGTT 60.678 47.826 0.00 0.00 0.00 4.44
1552 2192 2.159142 CGTTAGCAATTACTCCCTCCGT 60.159 50.000 0.00 0.00 0.00 4.69
1553 2193 2.100252 TCGTTAGCAATTACTCCCTCCG 59.900 50.000 0.00 0.00 0.00 4.63
1554 2194 3.814005 TCGTTAGCAATTACTCCCTCC 57.186 47.619 0.00 0.00 0.00 4.30
1555 2195 5.357257 TCATTCGTTAGCAATTACTCCCTC 58.643 41.667 0.00 0.00 0.00 4.30
1556 2196 5.353394 TCATTCGTTAGCAATTACTCCCT 57.647 39.130 0.00 0.00 0.00 4.20
1557 2197 5.992217 AGATCATTCGTTAGCAATTACTCCC 59.008 40.000 0.00 0.00 0.00 4.30
1558 2198 6.564873 GCAGATCATTCGTTAGCAATTACTCC 60.565 42.308 0.00 0.00 0.00 3.85
1559 2199 6.201806 AGCAGATCATTCGTTAGCAATTACTC 59.798 38.462 0.00 0.00 0.00 2.59
1560 2200 6.018425 CAGCAGATCATTCGTTAGCAATTACT 60.018 38.462 0.00 0.00 0.00 2.24
1561 2201 6.018751 TCAGCAGATCATTCGTTAGCAATTAC 60.019 38.462 0.00 0.00 0.00 1.89
1562 2202 6.048509 TCAGCAGATCATTCGTTAGCAATTA 58.951 36.000 0.00 0.00 0.00 1.40
1563 2203 4.877823 TCAGCAGATCATTCGTTAGCAATT 59.122 37.500 0.00 0.00 0.00 2.32
1564 2204 4.445453 TCAGCAGATCATTCGTTAGCAAT 58.555 39.130 0.00 0.00 0.00 3.56
1565 2205 3.860641 TCAGCAGATCATTCGTTAGCAA 58.139 40.909 0.00 0.00 0.00 3.91
1566 2206 3.525268 TCAGCAGATCATTCGTTAGCA 57.475 42.857 0.00 0.00 0.00 3.49
1567 2207 6.146837 ACATTATCAGCAGATCATTCGTTAGC 59.853 38.462 0.00 0.00 35.67 3.09
1568 2208 7.410193 CGACATTATCAGCAGATCATTCGTTAG 60.410 40.741 0.00 0.00 35.67 2.34
1569 2209 6.363357 CGACATTATCAGCAGATCATTCGTTA 59.637 38.462 0.00 0.00 35.67 3.18
1570 2210 5.176406 CGACATTATCAGCAGATCATTCGTT 59.824 40.000 0.00 0.00 35.67 3.85
1571 2211 4.683320 CGACATTATCAGCAGATCATTCGT 59.317 41.667 0.00 0.00 35.67 3.85
1572 2212 4.683320 ACGACATTATCAGCAGATCATTCG 59.317 41.667 0.00 5.80 35.67 3.34
1573 2213 6.183360 GCTACGACATTATCAGCAGATCATTC 60.183 42.308 0.00 0.00 35.67 2.67
1577 2217 4.550422 TGCTACGACATTATCAGCAGATC 58.450 43.478 0.00 0.00 37.32 2.75
1617 2261 3.183775 AGCGTGTAATCTGTCGAAACAAC 59.816 43.478 0.00 0.00 34.24 3.32
1656 2300 3.986996 TTCATCTTCATCAGCACCAGA 57.013 42.857 0.00 0.00 0.00 3.86
1657 2301 3.243101 GCATTCATCTTCATCAGCACCAG 60.243 47.826 0.00 0.00 0.00 4.00
1660 2304 3.377485 ACAGCATTCATCTTCATCAGCAC 59.623 43.478 0.00 0.00 0.00 4.40
1664 2308 4.224991 TCCACAGCATTCATCTTCATCA 57.775 40.909 0.00 0.00 0.00 3.07
1688 2332 3.740115 GCTTATTCCCACACGACCATAT 58.260 45.455 0.00 0.00 0.00 1.78
1690 2334 1.742411 CGCTTATTCCCACACGACCAT 60.742 52.381 0.00 0.00 0.00 3.55
1692 2336 0.108520 TCGCTTATTCCCACACGACC 60.109 55.000 0.00 0.00 0.00 4.79
1731 2375 1.831652 GCAGTCACTAGTGCCCCACT 61.832 60.000 18.45 13.04 44.87 4.00
1749 2393 1.335810 CATCACATGTAGGCACCATGC 59.664 52.381 14.10 0.00 42.74 4.06
1759 2406 2.813172 CCACAAGCACACATCACATGTA 59.187 45.455 0.00 0.00 42.70 2.29
1760 2407 1.610038 CCACAAGCACACATCACATGT 59.390 47.619 0.00 0.00 46.22 3.21
1904 2555 6.472163 GTGTGTTTTCATGTTTGTAGGACTTG 59.528 38.462 0.00 0.00 0.00 3.16
1919 2570 2.428491 ACTTGACGTGGTGTGTTTTCA 58.572 42.857 0.00 0.00 0.00 2.69
1921 2572 2.814919 TGAACTTGACGTGGTGTGTTTT 59.185 40.909 0.00 0.00 0.00 2.43
1945 2596 3.189287 CGGCTGTTGAAGATGCTTAAACT 59.811 43.478 8.44 0.00 0.00 2.66
1947 2598 2.095263 GCGGCTGTTGAAGATGCTTAAA 60.095 45.455 0.00 0.00 0.00 1.52
1948 2599 1.468520 GCGGCTGTTGAAGATGCTTAA 59.531 47.619 0.00 0.00 0.00 1.85
1949 2600 1.086696 GCGGCTGTTGAAGATGCTTA 58.913 50.000 0.00 0.00 0.00 3.09
1950 2601 1.878775 GCGGCTGTTGAAGATGCTT 59.121 52.632 0.00 0.00 0.00 3.91
2159 2845 3.196469 GGACATCATTGAGACAGAGTCCA 59.804 47.826 0.00 0.00 42.82 4.02
2173 2859 2.028130 GACGTCAGAGGAGGACATCAT 58.972 52.381 11.55 0.00 34.97 2.45
2187 2873 3.807538 GCCTACGCTCCGACGTCA 61.808 66.667 17.16 0.00 44.43 4.35
2232 3306 2.180769 CATGCGGTTCCGTCTCGA 59.819 61.111 12.81 0.00 0.00 4.04
2263 3337 0.460311 CACCTACTCCGCCGAGATTT 59.540 55.000 9.16 0.00 38.52 2.17
2397 3471 1.681666 CCCTTTGCTGCTCTCTCCA 59.318 57.895 0.00 0.00 0.00 3.86
2407 3481 0.700564 TCTCTCCATTGCCCTTTGCT 59.299 50.000 0.00 0.00 42.00 3.91
2417 3491 2.759973 TCCGCCGCTCTCTCCATT 60.760 61.111 0.00 0.00 0.00 3.16
2442 3516 0.317799 TCCGGCGCGCCTATAAATTA 59.682 50.000 43.60 19.07 0.00 1.40
2511 3585 2.489539 TAGCGGTGGCGCGAAACTAA 62.490 55.000 12.10 0.00 46.35 2.24
2545 3638 3.296709 CTTATAGCGCGCGGGGGAT 62.297 63.158 33.06 16.81 0.00 3.85
2644 3740 1.576421 CCTTTCGCTGTGGTGCTTC 59.424 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.