Multiple sequence alignment - TraesCS6A01G323200

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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 TraesCS6A01G323200 chr6A 100.000 5453 0 0 1 5453 556739216 556744668 0.000000e+00 10070.0
1 TraesCS6A01G323200 chr6A 84.286 140 19 3 234 372 135243823 135243960 3.430000e-27 134.0
2 TraesCS6A01G323200 chr6B 92.725 2433 100 29 3040 5453 619528285 619530659 0.000000e+00 3441.0
3 TraesCS6A01G323200 chr6B 90.532 1542 92 21 610 2111 619525398 619526925 0.000000e+00 1989.0
4 TraesCS6A01G323200 chr6B 94.433 934 38 8 2105 3029 619526968 619527896 0.000000e+00 1424.0
5 TraesCS6A01G323200 chr6B 83.333 150 22 3 224 372 199762269 199762416 9.530000e-28 135.0
6 TraesCS6A01G323200 chr6B 81.757 148 23 4 227 372 29514133 29514278 2.670000e-23 121.0
7 TraesCS6A01G323200 chr6B 84.337 83 6 5 3312 3390 619528587 619528666 2.110000e-09 75.0
8 TraesCS6A01G323200 chr6D 94.163 2193 96 10 3040 5224 411803390 411805558 0.000000e+00 3312.0
9 TraesCS6A01G323200 chr6D 91.558 1149 45 21 984 2111 411800896 411802013 0.000000e+00 1537.0
10 TraesCS6A01G323200 chr6D 95.376 930 36 3 2105 3029 411802056 411802983 0.000000e+00 1472.0
11 TraesCS6A01G323200 chr6D 81.775 1059 86 50 1 993 411799478 411800495 0.000000e+00 787.0
12 TraesCS6A01G323200 chr6D 84.735 321 18 7 5160 5453 411805630 411805946 5.340000e-75 292.0
13 TraesCS6A01G323200 chr6D 83.553 152 20 4 224 372 110880837 110880986 2.650000e-28 137.0
14 TraesCS6A01G323200 chr6D 90.411 73 7 0 3448 3520 411802580 411802652 4.500000e-16 97.1
15 TraesCS6A01G323200 chr6D 84.337 83 6 5 3312 3390 411803692 411803771 2.110000e-09 75.0
16 TraesCS6A01G323200 chr7B 86.129 310 37 4 4193 4501 52981314 52981618 4.070000e-86 329.0
17 TraesCS6A01G323200 chr7B 85.526 304 38 5 4199 4501 52948379 52948081 4.100000e-81 313.0
18 TraesCS6A01G323200 chr7B 74.645 493 104 16 2122 2609 79388314 79388790 1.200000e-46 198.0
19 TraesCS6A01G323200 chr5A 88.235 221 19 3 5161 5378 153180880 153180664 1.950000e-64 257.0
20 TraesCS6A01G323200 chr7A 80.488 205 40 0 2122 2326 122760926 122761130 2.030000e-34 158.0
21 TraesCS6A01G323200 chr4A 83.673 147 22 2 224 369 682754626 682754771 2.650000e-28 137.0
22 TraesCS6A01G323200 chr5B 82.550 149 24 2 224 371 14368700 14368847 4.430000e-26 130.0
23 TraesCS6A01G323200 chr7D 82.432 148 24 2 227 372 464086601 464086454 1.590000e-25 128.0
24 TraesCS6A01G323200 chr1B 82.734 139 23 1 234 372 687309548 687309411 7.420000e-24 122.0
25 TraesCS6A01G323200 chr1A 82.734 139 23 1 234 372 556798896 556798759 7.420000e-24 122.0


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 TraesCS6A01G323200 chr6A 556739216 556744668 5452 False 10070.000000 10070 100.000000 1 5453 1 chr6A.!!$F2 5452
1 TraesCS6A01G323200 chr6B 619525398 619530659 5261 False 1732.250000 3441 90.506750 610 5453 4 chr6B.!!$F3 4843
2 TraesCS6A01G323200 chr6D 411799478 411805946 6468 False 1081.728571 3312 88.907857 1 5453 7 chr6D.!!$F2 5452

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
533 561 0.037232 ACCGGAGAAGGAGAAAAGCG 60.037 55.0 9.46 0.00 34.73 4.68 F
534 562 0.037232 CCGGAGAAGGAGAAAAGCGT 60.037 55.0 0.00 0.00 0.00 5.07 F
589 617 0.042188 CGCATTATCTTTGCCGACGG 60.042 55.0 10.29 10.29 36.75 4.79 F
2329 2903 0.320374 CCCGAGGTGAGCACAGTTAA 59.680 55.0 2.75 0.00 0.00 2.01 F
2356 2930 0.598158 CCCATGCAGTTTGTGTGTGC 60.598 55.0 0.00 0.00 37.73 4.57 F
3421 4402 0.323957 AGCAAGTCAGAGCATGAGCA 59.676 50.0 0.00 0.00 45.49 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2313 0.890683 CCCTGAACTTGCATTCACCC 59.109 55.000 0.0 0.0 34.84 4.61 R
2329 2903 1.682854 CAAACTGCATGGGTGTTCTGT 59.317 47.619 0.0 0.0 0.00 3.41 R
2331 2905 1.682854 CACAAACTGCATGGGTGTTCT 59.317 47.619 0.0 0.0 0.00 3.01 R
3419 4400 0.536724 AAAGCGGAAAATCCCCATGC 59.463 50.000 0.0 0.0 31.13 4.06 R
3882 4865 0.654683 GCGTCATGGACATTCAGCTC 59.345 55.000 0.0 0.0 32.09 4.09 R
5099 6093 0.035152 TAGCACCCATTGGCAGTCTG 60.035 55.000 0.0 0.0 33.59 3.51 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
34 35 2.190578 CCTCTGCCCCACCGATTC 59.809 66.667 0.00 0.00 0.00 2.52
40 41 1.195442 TGCCCCACCGATTCAGTACA 61.195 55.000 0.00 0.00 0.00 2.90
42 43 1.734163 CCCCACCGATTCAGTACAAC 58.266 55.000 0.00 0.00 0.00 3.32
43 44 1.278127 CCCCACCGATTCAGTACAACT 59.722 52.381 0.00 0.00 0.00 3.16
44 45 2.498481 CCCCACCGATTCAGTACAACTA 59.502 50.000 0.00 0.00 0.00 2.24
45 46 3.134081 CCCCACCGATTCAGTACAACTAT 59.866 47.826 0.00 0.00 0.00 2.12
46 47 4.342951 CCCCACCGATTCAGTACAACTATA 59.657 45.833 0.00 0.00 0.00 1.31
51 52 9.140286 CCACCGATTCAGTACAACTATATAATG 57.860 37.037 0.00 0.00 0.00 1.90
76 77 6.321181 GCTAAATCAGTGACATTTATTGGGGA 59.679 38.462 0.00 0.00 0.00 4.81
79 80 4.991776 TCAGTGACATTTATTGGGGAACA 58.008 39.130 0.00 0.00 0.00 3.18
100 101 7.364762 GGAACAGAGGGAGTACTAAATTCATGA 60.365 40.741 0.00 0.00 0.00 3.07
120 121 8.538409 TCATGATAATTCCACTACATCGAATG 57.462 34.615 0.00 0.00 0.00 2.67
121 122 7.603784 TCATGATAATTCCACTACATCGAATGG 59.396 37.037 0.00 0.00 33.60 3.16
146 158 4.083003 GCCAATGATTTTACCACGACTTCA 60.083 41.667 0.00 0.00 0.00 3.02
147 159 5.563867 GCCAATGATTTTACCACGACTTCAA 60.564 40.000 0.00 0.00 0.00 2.69
156 168 7.416154 TTTACCACGACTTCAAACTCTAATG 57.584 36.000 0.00 0.00 0.00 1.90
157 169 4.315803 ACCACGACTTCAAACTCTAATGG 58.684 43.478 0.00 0.00 0.00 3.16
160 172 5.475719 CACGACTTCAAACTCTAATGGGTA 58.524 41.667 0.00 0.00 0.00 3.69
161 173 5.577164 CACGACTTCAAACTCTAATGGGTAG 59.423 44.000 0.00 0.00 0.00 3.18
162 174 5.245526 ACGACTTCAAACTCTAATGGGTAGT 59.754 40.000 0.00 0.00 0.00 2.73
163 175 6.435277 ACGACTTCAAACTCTAATGGGTAGTA 59.565 38.462 0.00 0.00 0.00 1.82
164 176 6.750963 CGACTTCAAACTCTAATGGGTAGTAC 59.249 42.308 0.00 0.00 0.00 2.73
165 177 7.549147 ACTTCAAACTCTAATGGGTAGTACA 57.451 36.000 2.06 0.00 0.00 2.90
166 178 8.147244 ACTTCAAACTCTAATGGGTAGTACAT 57.853 34.615 2.06 0.00 0.00 2.29
167 179 9.263446 ACTTCAAACTCTAATGGGTAGTACATA 57.737 33.333 2.06 0.00 0.00 2.29
168 180 9.530633 CTTCAAACTCTAATGGGTAGTACATAC 57.469 37.037 2.06 0.00 0.00 2.39
169 181 8.598202 TCAAACTCTAATGGGTAGTACATACA 57.402 34.615 2.06 0.00 35.96 2.29
170 182 9.209048 TCAAACTCTAATGGGTAGTACATACAT 57.791 33.333 2.06 0.96 35.96 2.29
171 183 9.832445 CAAACTCTAATGGGTAGTACATACATT 57.168 33.333 16.31 16.31 35.96 2.71
173 185 9.832445 AACTCTAATGGGTAGTACATACATTTG 57.168 33.333 16.92 15.40 35.96 2.32
179 191 5.878116 TGGGTAGTACATACATTTGACTTGC 59.122 40.000 2.06 0.00 35.96 4.01
191 203 5.240623 ACATTTGACTTGCGTATCCTTTTGA 59.759 36.000 0.00 0.00 0.00 2.69
199 211 4.138290 TGCGTATCCTTTTGAAACCAAGA 58.862 39.130 0.00 0.00 0.00 3.02
200 212 4.023536 TGCGTATCCTTTTGAAACCAAGAC 60.024 41.667 0.00 0.00 0.00 3.01
205 217 3.379057 TCCTTTTGAAACCAAGACGTTCC 59.621 43.478 0.00 0.00 0.00 3.62
209 221 2.557317 TGAAACCAAGACGTTCCTCAC 58.443 47.619 0.00 0.00 0.00 3.51
214 226 0.868406 CAAGACGTTCCTCACTTGCC 59.132 55.000 0.00 0.00 34.46 4.52
218 230 1.376037 CGTTCCTCACTTGCCCCTC 60.376 63.158 0.00 0.00 0.00 4.30
221 233 4.785453 CCTCACTTGCCCCTCGCC 62.785 72.222 0.00 0.00 36.24 5.54
222 234 4.020617 CTCACTTGCCCCTCGCCA 62.021 66.667 0.00 0.00 36.24 5.69
231 243 3.702048 CCCTCGCCAAGAACGGGA 61.702 66.667 0.00 0.00 36.67 5.14
232 244 2.584608 CCTCGCCAAGAACGGGAT 59.415 61.111 0.00 0.00 30.77 3.85
239 251 0.739813 CCAAGAACGGGATGTCGACC 60.740 60.000 14.12 0.00 0.00 4.79
289 301 4.760047 AGCCCGCGTTCGAGCATT 62.760 61.111 4.92 0.00 42.18 3.56
321 333 2.727684 GGCGTTCGCGGAGTTTCTC 61.728 63.158 6.13 0.00 41.67 2.87
357 369 2.426842 ATGAAGGTTAGCTCTTGGGC 57.573 50.000 0.00 0.00 0.00 5.36
362 374 0.393132 GGTTAGCTCTTGGGCTGGTC 60.393 60.000 5.10 0.00 43.01 4.02
387 399 2.999185 TTTTCTCATTTGCCCCTCCT 57.001 45.000 0.00 0.00 0.00 3.69
393 405 5.310409 TCTCATTTGCCCCTCCTAAATAG 57.690 43.478 0.00 0.00 0.00 1.73
395 407 5.048846 TCATTTGCCCCTCCTAAATAGAC 57.951 43.478 0.00 0.00 0.00 2.59
400 412 5.466127 TGCCCCTCCTAAATAGACAAAAT 57.534 39.130 0.00 0.00 0.00 1.82
403 415 4.584743 CCCCTCCTAAATAGACAAAATGGC 59.415 45.833 0.00 0.00 0.00 4.40
412 424 0.168128 GACAAAATGGCCGTTCCTCG 59.832 55.000 11.51 2.47 39.52 4.63
442 454 4.533707 AGATCCTGGAATCAAGACAGACAA 59.466 41.667 0.00 0.00 34.21 3.18
443 455 4.916041 TCCTGGAATCAAGACAGACAAT 57.084 40.909 0.00 0.00 34.21 2.71
444 456 5.246981 TCCTGGAATCAAGACAGACAATT 57.753 39.130 0.00 0.00 34.21 2.32
445 457 5.634118 TCCTGGAATCAAGACAGACAATTT 58.366 37.500 0.00 0.00 34.21 1.82
471 483 1.545582 GCTCTTGTTTTAGGCATGGCA 59.454 47.619 22.64 4.62 0.00 4.92
472 484 2.029110 GCTCTTGTTTTAGGCATGGCAA 60.029 45.455 22.64 10.74 0.00 4.52
473 485 3.578688 CTCTTGTTTTAGGCATGGCAAC 58.421 45.455 22.64 16.81 0.00 4.17
477 489 0.243365 TTTTAGGCATGGCAACGCAG 59.757 50.000 22.64 0.00 42.51 5.18
480 492 2.462125 TAGGCATGGCAACGCAGTGA 62.462 55.000 22.64 0.00 45.00 3.41
481 493 2.703798 GGCATGGCAACGCAGTGAT 61.704 57.895 15.47 0.00 45.00 3.06
482 494 1.213537 GCATGGCAACGCAGTGATT 59.786 52.632 7.33 0.00 45.00 2.57
483 495 0.451383 GCATGGCAACGCAGTGATTA 59.549 50.000 7.33 0.00 45.00 1.75
493 521 4.946784 ACGCAGTGATTATTTTCCTCAC 57.053 40.909 0.00 0.00 42.51 3.51
524 552 1.137872 CTCCTTGATCACCGGAGAAGG 59.862 57.143 25.79 15.32 45.67 3.46
531 559 3.055819 TGATCACCGGAGAAGGAGAAAAG 60.056 47.826 9.46 0.00 34.68 2.27
532 560 1.002087 TCACCGGAGAAGGAGAAAAGC 59.998 52.381 9.46 0.00 34.73 3.51
533 561 0.037232 ACCGGAGAAGGAGAAAAGCG 60.037 55.000 9.46 0.00 34.73 4.68
534 562 0.037232 CCGGAGAAGGAGAAAAGCGT 60.037 55.000 0.00 0.00 0.00 5.07
535 563 1.071605 CGGAGAAGGAGAAAAGCGTG 58.928 55.000 0.00 0.00 0.00 5.34
536 564 0.799393 GGAGAAGGAGAAAAGCGTGC 59.201 55.000 0.00 0.00 0.00 5.34
537 565 0.799393 GAGAAGGAGAAAAGCGTGCC 59.201 55.000 0.00 0.00 0.00 5.01
538 566 0.398318 AGAAGGAGAAAAGCGTGCCT 59.602 50.000 0.00 0.00 0.00 4.75
539 567 1.623811 AGAAGGAGAAAAGCGTGCCTA 59.376 47.619 0.00 0.00 0.00 3.93
540 568 2.237392 AGAAGGAGAAAAGCGTGCCTAT 59.763 45.455 0.00 0.00 0.00 2.57
541 569 2.789409 AGGAGAAAAGCGTGCCTATT 57.211 45.000 0.00 0.00 0.00 1.73
542 570 2.633488 AGGAGAAAAGCGTGCCTATTC 58.367 47.619 0.00 0.00 0.00 1.75
543 571 2.027192 AGGAGAAAAGCGTGCCTATTCA 60.027 45.455 0.00 0.00 0.00 2.57
544 572 2.352960 GGAGAAAAGCGTGCCTATTCAG 59.647 50.000 5.17 0.00 0.00 3.02
545 573 2.352960 GAGAAAAGCGTGCCTATTCAGG 59.647 50.000 5.17 0.00 45.77 3.86
571 599 0.246989 CGTGGCCGAAATTAACGTCG 60.247 55.000 0.00 3.23 35.63 5.12
585 613 0.650512 ACGTCGCATTATCTTTGCCG 59.349 50.000 0.00 0.00 36.75 5.69
586 614 0.927537 CGTCGCATTATCTTTGCCGA 59.072 50.000 0.00 0.00 36.75 5.54
587 615 1.332028 CGTCGCATTATCTTTGCCGAC 60.332 52.381 0.00 0.00 38.76 4.79
588 616 0.927537 TCGCATTATCTTTGCCGACG 59.072 50.000 0.00 0.00 36.75 5.12
589 617 0.042188 CGCATTATCTTTGCCGACGG 60.042 55.000 10.29 10.29 36.75 4.79
671 731 2.650322 ACCCAACGTGATTTGACTTGT 58.350 42.857 0.00 0.00 0.00 3.16
685 745 1.008538 CTTGTTGCGTTGACAGCCC 60.009 57.895 0.00 0.00 0.00 5.19
689 749 2.324330 TTGCGTTGACAGCCCATCG 61.324 57.895 0.00 0.00 33.72 3.84
690 750 2.742372 GCGTTGACAGCCCATCGT 60.742 61.111 0.00 0.00 33.29 3.73
693 763 2.100631 GTTGACAGCCCATCGTCGG 61.101 63.158 0.00 0.00 34.78 4.79
733 803 1.028905 TCCACGCAAAACCCAGAAAG 58.971 50.000 0.00 0.00 0.00 2.62
798 869 0.673644 ATCAGTTGGTTTCGCTCCCG 60.674 55.000 0.00 0.00 0.00 5.14
871 942 1.676014 CGCCTCCTCCCTACAAAACAG 60.676 57.143 0.00 0.00 0.00 3.16
969 1045 4.180946 CGACAGTCTCCCGCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
1386 1906 2.853290 AACTGCGGTTCGTCCTCGT 61.853 57.895 4.68 0.00 38.33 4.18
1490 2013 2.584391 GGACCAACGGCTCCAGTCT 61.584 63.158 0.00 0.00 0.00 3.24
1491 2014 1.371558 GACCAACGGCTCCAGTCTT 59.628 57.895 0.00 0.00 0.00 3.01
1492 2015 0.670854 GACCAACGGCTCCAGTCTTC 60.671 60.000 0.00 0.00 0.00 2.87
1778 2301 3.936203 AGGTGCGCCTGTTCGGAA 61.936 61.111 20.48 0.00 45.05 4.30
1808 2331 0.890683 GGGGTGAATGCAAGTTCAGG 59.109 55.000 2.97 0.00 38.68 3.86
1845 2368 2.424601 CAATGTGACGGCAATTCCATCT 59.575 45.455 0.00 0.00 34.01 2.90
1943 2469 1.605710 CAAGAACCACACTGCTCAAGG 59.394 52.381 0.00 0.00 0.00 3.61
1944 2470 0.536006 AGAACCACACTGCTCAAGGC 60.536 55.000 0.00 0.00 42.22 4.35
2013 2539 0.595095 CTTCAGGTGGAAGCAACAGC 59.405 55.000 0.00 0.00 45.99 4.40
2082 2608 2.840066 TTTGGTGAAAGGCCACGCG 61.840 57.895 5.01 3.53 37.91 6.01
2136 2710 1.531264 GCGACGAAGCTTCACTCGATA 60.531 52.381 32.44 0.00 31.94 2.92
2328 2902 0.541063 TCCCGAGGTGAGCACAGTTA 60.541 55.000 2.75 0.00 0.00 2.24
2329 2903 0.320374 CCCGAGGTGAGCACAGTTAA 59.680 55.000 2.75 0.00 0.00 2.01
2330 2904 1.429463 CCGAGGTGAGCACAGTTAAC 58.571 55.000 0.00 0.00 0.00 2.01
2331 2905 1.270094 CCGAGGTGAGCACAGTTAACA 60.270 52.381 8.61 0.00 0.00 2.41
2356 2930 0.598158 CCCATGCAGTTTGTGTGTGC 60.598 55.000 0.00 0.00 37.73 4.57
2381 2959 7.361201 GCTCAGTTAGTTCTTTATGCATGACAA 60.361 37.037 10.16 0.00 0.00 3.18
2409 2990 1.328279 ATGTGATGGCATGATGCTGG 58.672 50.000 17.84 0.00 44.28 4.85
2454 3035 1.969208 CTGATATGCTGGAGAGGCTGA 59.031 52.381 0.00 0.00 0.00 4.26
2626 3207 2.443255 TCCTCTTTCAGGTTGGCTTCTT 59.557 45.455 0.00 0.00 43.95 2.52
2627 3208 3.650942 TCCTCTTTCAGGTTGGCTTCTTA 59.349 43.478 0.00 0.00 43.95 2.10
2698 3280 6.154021 AGCTTGTTTCAGCATTTAGGATGAAT 59.846 34.615 0.00 0.00 42.13 2.57
2771 3353 5.059343 CGTTCGCTACATAATCTTGATACCG 59.941 44.000 0.00 0.00 0.00 4.02
2833 3415 7.359264 CCGAAACATAATTAGATAGCCAGAACG 60.359 40.741 0.00 0.00 0.00 3.95
3029 3612 8.902806 ACTGACAAAGAAACATAACTTCATTGA 58.097 29.630 7.33 0.00 35.86 2.57
3030 3613 9.173939 CTGACAAAGAAACATAACTTCATTGAC 57.826 33.333 7.33 2.98 35.86 3.18
3031 3614 7.855409 TGACAAAGAAACATAACTTCATTGACG 59.145 33.333 7.33 0.00 35.86 4.35
3032 3615 7.925993 ACAAAGAAACATAACTTCATTGACGA 58.074 30.769 7.33 0.00 35.86 4.20
3034 3617 9.398170 CAAAGAAACATAACTTCATTGACGAAT 57.602 29.630 0.00 0.00 34.82 3.34
3037 3620 9.214957 AGAAACATAACTTCATTGACGAATACA 57.785 29.630 0.00 0.00 0.00 2.29
3130 4111 5.221880 TCATTTTGCACAACACAGCTTATC 58.778 37.500 0.00 0.00 0.00 1.75
3137 4118 2.674852 ACAACACAGCTTATCTCATGCG 59.325 45.455 0.00 0.00 32.64 4.73
3171 4152 6.683974 TTTCCTTTTCTGACTCTGAACTTG 57.316 37.500 0.00 0.00 0.00 3.16
3203 4184 3.945981 TCACTTCTTGCACCGTACATA 57.054 42.857 0.00 0.00 0.00 2.29
3243 4224 7.710475 ACGAAATTCCACTGAATCAAAACAAAT 59.290 29.630 0.00 0.00 40.34 2.32
3310 4291 7.933033 ACAATTTCAATGAAGCAAACCATTAGT 59.067 29.630 0.00 0.00 32.31 2.24
3324 4305 5.746990 ACCATTAGTAGATCAGGGCATAC 57.253 43.478 0.00 0.00 0.00 2.39
3389 4370 8.472413 ACATGTAGCAAAAATCAGAGCATAAAT 58.528 29.630 0.00 0.00 0.00 1.40
3419 4400 3.242549 TGTAGCAAGTCAGAGCATGAG 57.757 47.619 0.00 0.00 39.07 2.90
3420 4401 1.932511 GTAGCAAGTCAGAGCATGAGC 59.067 52.381 0.00 0.00 39.07 4.26
3421 4402 0.323957 AGCAAGTCAGAGCATGAGCA 59.676 50.000 0.00 0.00 45.49 4.26
3429 4410 0.851469 AGAGCATGAGCATGGGGATT 59.149 50.000 12.00 0.00 45.49 3.01
3433 4414 1.069668 GCATGAGCATGGGGATTTTCC 59.930 52.381 12.00 0.00 41.58 3.13
3445 4426 2.230266 GGGATTTTCCGCTTTGTGCTTA 59.770 45.455 0.00 0.00 37.43 3.09
3446 4427 3.242518 GGATTTTCCGCTTTGTGCTTAC 58.757 45.455 0.00 0.00 40.11 2.34
3455 4436 2.491693 GCTTTGTGCTTACCTTATGCCA 59.508 45.455 0.00 0.00 38.95 4.92
3472 4453 1.528161 GCCATGTTCTGTTTTTGCTGC 59.472 47.619 0.00 0.00 0.00 5.25
3513 4494 9.162764 GCTATCTGAGGTTGTTTCAGTATTTAA 57.837 33.333 2.57 0.00 42.11 1.52
3609 4592 4.455606 CTTGTTCAGGAATGGGAGATACC 58.544 47.826 0.00 0.00 38.08 2.73
3616 4599 2.771943 GGAATGGGAGATACCTGTCACA 59.228 50.000 0.00 0.00 38.98 3.58
3618 4601 2.319025 TGGGAGATACCTGTCACACA 57.681 50.000 0.00 0.00 38.98 3.72
3619 4602 1.899814 TGGGAGATACCTGTCACACAC 59.100 52.381 0.00 0.00 38.98 3.82
3655 4638 6.207614 AGGAAACTCTTAGGCTTGACAAAATC 59.792 38.462 0.00 0.00 32.90 2.17
3755 4738 7.454260 ACTTCTCTTGGGTAAGCTTTTATTG 57.546 36.000 3.20 0.00 33.82 1.90
3760 4743 2.490115 TGGGTAAGCTTTTATTGGCACG 59.510 45.455 3.20 0.00 0.00 5.34
3768 4751 7.744087 AAGCTTTTATTGGCACGATATGATA 57.256 32.000 0.00 0.00 0.00 2.15
3780 4763 7.659390 TGGCACGATATGATACAATAAACATGA 59.341 33.333 0.00 0.00 0.00 3.07
3904 4887 1.742761 CTGAATGTCCATGACGCCTT 58.257 50.000 0.00 0.00 34.95 4.35
3915 4898 2.997897 ACGCCTTCCGGAGAGCTT 60.998 61.111 21.33 12.35 42.52 3.74
3917 4900 1.255667 ACGCCTTCCGGAGAGCTTTA 61.256 55.000 21.33 0.00 42.52 1.85
3931 4914 1.044611 GCTTTAAACACCTGGGCCAA 58.955 50.000 8.04 0.00 0.00 4.52
3972 4955 3.733443 ATCCCAAGAAAACAACTGTGC 57.267 42.857 0.00 0.00 0.00 4.57
3990 4973 3.008375 TGTGCTTTTCAGAGGCTACTCAT 59.992 43.478 0.00 0.00 46.44 2.90
4007 4990 4.939255 ACTCATCATCCCATTTCAGGTTT 58.061 39.130 0.00 0.00 0.00 3.27
4010 4993 4.706476 TCATCATCCCATTTCAGGTTTGTC 59.294 41.667 0.00 0.00 0.00 3.18
4013 4996 3.433306 TCCCATTTCAGGTTTGTCGAT 57.567 42.857 0.00 0.00 0.00 3.59
4014 4997 3.761897 TCCCATTTCAGGTTTGTCGATT 58.238 40.909 0.00 0.00 0.00 3.34
4036 5019 8.306038 CGATTCTTTTCTGATCTCATCTCCTAT 58.694 37.037 0.00 0.00 0.00 2.57
4060 5043 1.921243 TCAGTTCGCGGTGTCATATG 58.079 50.000 6.13 0.00 0.00 1.78
4175 5158 4.273969 TGAGCCGATAACAAACGAAAAGTT 59.726 37.500 0.00 0.00 46.76 2.66
4341 5324 3.394836 GAGGAGCGCAAGTCCCCT 61.395 66.667 11.47 5.65 37.99 4.79
4413 5396 1.064458 GAACGAGCTCCTCTACGCC 59.936 63.158 8.47 0.00 0.00 5.68
4518 5501 2.629656 GCAACATGCCAGCCGAAGT 61.630 57.895 0.00 0.00 37.42 3.01
4543 5526 7.445402 GTGGTCAAGGCATATATAGTTGACAAT 59.555 37.037 22.81 0.00 45.77 2.71
4544 5527 7.998383 TGGTCAAGGCATATATAGTTGACAATT 59.002 33.333 22.81 0.00 45.77 2.32
4545 5528 8.292448 GGTCAAGGCATATATAGTTGACAATTG 58.708 37.037 22.81 3.24 45.77 2.32
4546 5529 9.056005 GTCAAGGCATATATAGTTGACAATTGA 57.944 33.333 13.59 7.17 44.18 2.57
4547 5530 9.797642 TCAAGGCATATATAGTTGACAATTGAT 57.202 29.630 13.59 0.00 0.00 2.57
4550 5533 9.896645 AGGCATATATAGTTGACAATTGATAGG 57.103 33.333 13.59 0.00 0.00 2.57
4551 5534 9.672673 GGCATATATAGTTGACAATTGATAGGT 57.327 33.333 13.59 0.00 0.00 3.08
4559 5545 4.843728 TGACAATTGATAGGTCAAGGGTC 58.156 43.478 13.59 13.53 46.75 4.46
4624 5618 1.000506 TGACTCTCGTTACCAACAGGC 59.999 52.381 0.00 0.00 0.00 4.85
4626 5620 1.414919 ACTCTCGTTACCAACAGGCAA 59.585 47.619 0.00 0.00 0.00 4.52
4650 5644 9.650539 CAATCTGTATAGGATCATAGGAGTTTG 57.349 37.037 0.00 0.00 0.00 2.93
4676 5670 5.435686 TGTAAAATCCATGTCCAGCTAGT 57.564 39.130 0.00 0.00 0.00 2.57
4720 5714 6.834959 AGTGTATACTGCATCAGAAATTCG 57.165 37.500 4.17 0.00 35.34 3.34
4722 5716 4.511454 TGTATACTGCATCAGAAATTCGGC 59.489 41.667 4.17 0.00 35.18 5.54
4749 5743 6.685657 AGCTCTTTGTTTTTCATGAATCCTC 58.314 36.000 9.40 1.70 0.00 3.71
4878 5872 7.986085 AGTTCTGAATGTATAGTGCTTTTGT 57.014 32.000 0.00 0.00 0.00 2.83
5093 6087 2.566724 CAGTTGGCCATTGTTTGGGTAT 59.433 45.455 6.09 0.00 46.55 2.73
5094 6088 2.566724 AGTTGGCCATTGTTTGGGTATG 59.433 45.455 6.09 0.00 46.55 2.39
5095 6089 2.564947 GTTGGCCATTGTTTGGGTATGA 59.435 45.455 6.09 0.00 46.55 2.15
5096 6090 2.455557 TGGCCATTGTTTGGGTATGAG 58.544 47.619 0.00 0.00 46.55 2.90
5097 6091 1.756538 GGCCATTGTTTGGGTATGAGG 59.243 52.381 0.00 0.00 46.55 3.86
5098 6092 2.622977 GGCCATTGTTTGGGTATGAGGA 60.623 50.000 0.00 0.00 46.55 3.71
5099 6093 2.427095 GCCATTGTTTGGGTATGAGGAC 59.573 50.000 0.00 0.00 46.55 3.85
5100 6094 3.696045 CCATTGTTTGGGTATGAGGACA 58.304 45.455 0.00 0.00 42.33 4.02
5101 6095 3.696051 CCATTGTTTGGGTATGAGGACAG 59.304 47.826 0.00 0.00 42.33 3.51
5102 6096 4.567537 CCATTGTTTGGGTATGAGGACAGA 60.568 45.833 0.00 0.00 42.33 3.41
5103 6097 3.695830 TGTTTGGGTATGAGGACAGAC 57.304 47.619 0.00 0.00 37.49 3.51
5104 6098 3.248024 TGTTTGGGTATGAGGACAGACT 58.752 45.455 0.00 0.00 38.19 3.24
5105 6099 3.007940 TGTTTGGGTATGAGGACAGACTG 59.992 47.826 0.00 0.00 38.19 3.51
5197 6196 1.917872 TTACATGGCAAAGGTGGACC 58.082 50.000 0.00 0.00 0.00 4.46
5241 6397 2.545742 CCACCACCTTGCAACTTTAAGC 60.546 50.000 0.00 0.00 0.00 3.09
5273 6436 1.289109 GCAGCTGCTGTGCATTTTGG 61.289 55.000 31.33 1.80 40.86 3.28
5293 6456 2.866762 GGCTGAAGTTATCTTGCCTACG 59.133 50.000 7.37 0.00 41.72 3.51
5298 6461 5.888105 TGAAGTTATCTTGCCTACGTACTC 58.112 41.667 0.00 0.00 33.64 2.59
5299 6462 5.416639 TGAAGTTATCTTGCCTACGTACTCA 59.583 40.000 0.00 0.00 33.64 3.41
5300 6463 5.246145 AGTTATCTTGCCTACGTACTCAC 57.754 43.478 0.00 0.00 0.00 3.51
5301 6464 4.948621 AGTTATCTTGCCTACGTACTCACT 59.051 41.667 0.00 0.00 0.00 3.41
5363 6526 4.793071 TGGTGAGTGTTTGCATATTTTCG 58.207 39.130 0.00 0.00 0.00 3.46
5367 6530 5.739161 GTGAGTGTTTGCATATTTTCGATCC 59.261 40.000 0.00 0.00 0.00 3.36
5372 6535 3.988379 TGCATATTTTCGATCCCAAGC 57.012 42.857 0.00 0.00 0.00 4.01
5381 6544 2.361610 ATCCCAAGCTTGCCGGTG 60.362 61.111 21.43 6.80 0.00 4.94
5388 6551 1.040339 AAGCTTGCCGGTGTTTTCCA 61.040 50.000 1.90 0.00 0.00 3.53
5390 6553 0.885196 GCTTGCCGGTGTTTTCCATA 59.115 50.000 1.90 0.00 0.00 2.74
5402 6565 5.358160 GGTGTTTTCCATAAGCTTGCTAGAT 59.642 40.000 9.86 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 6.321181 TCCCCAATAAATGTCACTGATTTAGC 59.679 38.462 0.00 0.00 30.69 3.09
60 61 4.399303 CCTCTGTTCCCCAATAAATGTCAC 59.601 45.833 0.00 0.00 0.00 3.67
65 66 3.858638 ACTCCCTCTGTTCCCCAATAAAT 59.141 43.478 0.00 0.00 0.00 1.40
69 70 2.197465 GTACTCCCTCTGTTCCCCAAT 58.803 52.381 0.00 0.00 0.00 3.16
76 77 7.496346 TCATGAATTTAGTACTCCCTCTGTT 57.504 36.000 0.00 0.00 0.00 3.16
100 101 4.690748 CGCCATTCGATGTAGTGGAATTAT 59.309 41.667 0.00 0.00 41.67 1.28
106 107 1.498865 GGCGCCATTCGATGTAGTGG 61.499 60.000 24.80 0.00 41.67 4.00
109 110 1.069703 CATTGGCGCCATTCGATGTAG 60.070 52.381 33.25 9.08 41.67 2.74
111 112 0.747644 TCATTGGCGCCATTCGATGT 60.748 50.000 33.25 7.63 41.67 3.06
113 114 1.321474 AATCATTGGCGCCATTCGAT 58.679 45.000 33.25 26.91 41.67 3.59
114 115 1.102154 AAATCATTGGCGCCATTCGA 58.898 45.000 33.25 25.91 41.67 3.71
120 121 1.797348 CGTGGTAAAATCATTGGCGCC 60.797 52.381 22.73 22.73 0.00 6.53
121 122 1.131504 TCGTGGTAAAATCATTGGCGC 59.868 47.619 0.00 0.00 0.00 6.53
147 159 9.832445 CAAATGTATGTACTACCCATTAGAGTT 57.168 33.333 0.00 0.00 0.00 3.01
156 168 5.006358 CGCAAGTCAAATGTATGTACTACCC 59.994 44.000 0.00 0.00 0.00 3.69
157 169 6.032722 CGCAAGTCAAATGTATGTACTACC 57.967 41.667 0.00 0.00 0.00 3.18
172 184 9.536049 CTTGGTTTCAAAAGGATACGCAAGTCA 62.536 40.741 0.00 0.00 41.49 3.41
173 185 7.273040 CTTGGTTTCAAAAGGATACGCAAGTC 61.273 42.308 0.00 0.00 41.49 3.01
179 191 4.212636 ACGTCTTGGTTTCAAAAGGATACG 59.787 41.667 0.00 0.00 35.02 3.06
191 203 2.943033 CAAGTGAGGAACGTCTTGGTTT 59.057 45.455 4.88 0.00 35.21 3.27
199 211 2.113243 GAGGGGCAAGTGAGGAACGT 62.113 60.000 0.00 0.00 0.00 3.99
200 212 1.376037 GAGGGGCAAGTGAGGAACG 60.376 63.158 0.00 0.00 0.00 3.95
205 217 4.020617 TGGCGAGGGGCAAGTGAG 62.021 66.667 0.00 0.00 46.91 3.51
214 226 3.031417 ATCCCGTTCTTGGCGAGGG 62.031 63.158 0.97 0.00 43.32 4.30
218 230 2.452813 CGACATCCCGTTCTTGGCG 61.453 63.158 0.00 0.00 35.28 5.69
221 233 0.739813 GGGTCGACATCCCGTTCTTG 60.740 60.000 18.91 0.00 35.27 3.02
222 234 1.595357 GGGTCGACATCCCGTTCTT 59.405 57.895 18.91 0.00 35.27 2.52
231 243 2.047274 CAGCCAACGGGTCGACAT 60.047 61.111 18.91 0.00 36.17 3.06
232 244 4.308458 CCAGCCAACGGGTCGACA 62.308 66.667 18.91 0.00 36.17 4.35
274 286 3.864686 CCAATGCTCGAACGCGGG 61.865 66.667 12.47 0.00 42.15 6.13
336 348 3.523564 AGCCCAAGAGCTAACCTTCATTA 59.476 43.478 0.00 0.00 42.70 1.90
338 350 1.918957 AGCCCAAGAGCTAACCTTCAT 59.081 47.619 0.00 0.00 42.70 2.57
340 352 1.680249 CCAGCCCAAGAGCTAACCTTC 60.680 57.143 0.00 0.00 42.61 3.46
344 356 0.615850 AGACCAGCCCAAGAGCTAAC 59.384 55.000 0.00 0.00 42.61 2.34
387 399 5.258051 AGGAACGGCCATTTTGTCTATTTA 58.742 37.500 2.24 0.00 40.02 1.40
393 405 0.168128 CGAGGAACGGCCATTTTGTC 59.832 55.000 2.24 0.00 40.02 3.18
412 424 2.632377 TGATTCCAGGATCTCGCAAAC 58.368 47.619 0.00 0.00 0.00 2.93
442 454 9.754382 CATGCCTAAAACAAGAGCATATTAAAT 57.246 29.630 0.00 0.00 42.04 1.40
443 455 8.196771 CCATGCCTAAAACAAGAGCATATTAAA 58.803 33.333 0.00 0.00 42.04 1.52
444 456 7.684187 GCCATGCCTAAAACAAGAGCATATTAA 60.684 37.037 0.00 0.00 42.04 1.40
445 457 6.239008 GCCATGCCTAAAACAAGAGCATATTA 60.239 38.462 0.00 0.00 42.04 0.98
464 476 0.451383 TAATCACTGCGTTGCCATGC 59.549 50.000 0.00 0.00 35.21 4.06
467 479 3.366883 GGAAAATAATCACTGCGTTGCCA 60.367 43.478 0.00 0.00 0.00 4.92
471 483 4.156008 GGTGAGGAAAATAATCACTGCGTT 59.844 41.667 4.73 0.00 42.36 4.84
472 484 3.689649 GGTGAGGAAAATAATCACTGCGT 59.310 43.478 4.73 0.00 42.36 5.24
473 485 3.242413 CGGTGAGGAAAATAATCACTGCG 60.242 47.826 4.73 0.00 41.84 5.18
524 552 2.352960 CCTGAATAGGCACGCTTTTCTC 59.647 50.000 0.00 0.00 37.25 2.87
537 565 0.531532 CCACGCTCTGGCCTGAATAG 60.532 60.000 13.89 9.88 31.36 1.73
538 566 1.522092 CCACGCTCTGGCCTGAATA 59.478 57.895 13.89 0.00 31.36 1.75
539 567 2.270205 CCACGCTCTGGCCTGAAT 59.730 61.111 13.89 0.00 31.36 2.57
571 599 3.825812 CCGTCGGCAAAGATAATGC 57.174 52.632 0.00 0.00 43.08 3.56
588 616 2.182014 GTTAATTTGATCGCGGTTGCC 58.818 47.619 6.13 0.00 38.08 4.52
589 617 1.837747 CGTTAATTTGATCGCGGTTGC 59.162 47.619 6.13 0.00 37.91 4.17
590 618 1.837747 GCGTTAATTTGATCGCGGTTG 59.162 47.619 6.13 0.00 39.35 3.77
591 619 2.168201 GCGTTAATTTGATCGCGGTT 57.832 45.000 6.13 0.00 39.35 4.44
592 620 3.889780 GCGTTAATTTGATCGCGGT 57.110 47.368 6.13 0.00 39.35 5.68
595 623 2.440501 CAGTGGCGTTAATTTGATCGC 58.559 47.619 0.00 0.00 46.42 4.58
596 624 2.440501 GCAGTGGCGTTAATTTGATCG 58.559 47.619 0.00 0.00 0.00 3.69
597 625 2.163412 TGGCAGTGGCGTTAATTTGATC 59.837 45.455 12.58 0.00 42.47 2.92
639 696 1.869132 ACGTTGGGTTTCTTCGTTAGC 59.131 47.619 0.00 0.00 0.00 3.09
641 698 3.176552 TCACGTTGGGTTTCTTCGTTA 57.823 42.857 0.00 0.00 32.47 3.18
671 731 2.324330 CGATGGGCTGTCAACGCAA 61.324 57.895 0.00 0.00 33.35 4.85
685 745 1.618861 GCGATAATCTCCCGACGATG 58.381 55.000 0.00 0.00 0.00 3.84
689 749 0.309922 TGACGCGATAATCTCCCGAC 59.690 55.000 15.93 0.00 0.00 4.79
690 750 1.068541 CATGACGCGATAATCTCCCGA 60.069 52.381 15.93 0.00 0.00 5.14
693 763 1.673033 CCCCATGACGCGATAATCTCC 60.673 57.143 15.93 0.00 0.00 3.71
708 778 1.906333 GGTTTTGCGTGGACCCCAT 60.906 57.895 0.00 0.00 35.28 4.00
770 841 3.124297 CGAAACCAACTGATCTCTTCTGC 59.876 47.826 0.00 0.00 0.00 4.26
771 842 3.124297 GCGAAACCAACTGATCTCTTCTG 59.876 47.826 0.00 0.00 0.00 3.02
773 844 3.330267 AGCGAAACCAACTGATCTCTTC 58.670 45.455 0.00 0.00 0.00 2.87
1490 2013 2.125147 CCGATTGCTCGCCAGGAA 60.125 61.111 0.00 0.00 43.66 3.36
1491 2014 4.161295 CCCGATTGCTCGCCAGGA 62.161 66.667 0.00 0.00 43.66 3.86
1492 2015 4.161295 TCCCGATTGCTCGCCAGG 62.161 66.667 0.00 0.00 43.66 4.45
1544 2067 2.604174 GGGTTGTCGGTGCGAACTG 61.604 63.158 0.00 0.00 37.72 3.16
1642 2165 3.033474 GGCGATACCTGACGAATTGCG 62.033 57.143 0.00 0.00 40.15 4.85
1790 2313 0.890683 CCCTGAACTTGCATTCACCC 59.109 55.000 0.00 0.00 34.84 4.61
1857 2380 3.333414 GCTGAAACTGCACTGCGA 58.667 55.556 0.00 0.00 0.00 5.10
2013 2539 2.959516 TCCTTGTGCATAGTCTTCGTG 58.040 47.619 0.00 0.00 0.00 4.35
2046 2572 4.521062 CCGGCGCTCCCTTGAGAG 62.521 72.222 7.64 0.00 41.42 3.20
2120 2694 2.723658 GCATCTATCGAGTGAAGCTTCG 59.276 50.000 21.11 10.54 0.00 3.79
2262 2836 3.567397 GAGTCTCTGGTAGGCCTTATCA 58.433 50.000 12.58 6.37 35.27 2.15
2328 2902 2.071778 AACTGCATGGGTGTTCTGTT 57.928 45.000 0.00 0.00 0.00 3.16
2329 2903 1.682854 CAAACTGCATGGGTGTTCTGT 59.317 47.619 0.00 0.00 0.00 3.41
2330 2904 1.682854 ACAAACTGCATGGGTGTTCTG 59.317 47.619 0.00 0.00 0.00 3.02
2331 2905 1.682854 CACAAACTGCATGGGTGTTCT 59.317 47.619 0.00 0.00 0.00 3.01
2356 2930 7.601073 TGTCATGCATAAAGAACTAACTGAG 57.399 36.000 0.00 0.00 0.00 3.35
2381 2959 6.737622 GCATCATGCCATCACATAACTGAATT 60.738 38.462 0.00 0.00 37.42 2.17
2409 2990 3.491964 GGGTTCAACCTAAAACAAGGCAC 60.492 47.826 6.51 0.00 40.62 5.01
2454 3035 1.755393 AACACGAGTCGCTTTCCCCT 61.755 55.000 13.59 0.00 0.00 4.79
2626 3207 6.331845 CAGCAAAAACAGAACATGGCATATA 58.668 36.000 0.00 0.00 0.00 0.86
2627 3208 5.172934 CAGCAAAAACAGAACATGGCATAT 58.827 37.500 0.00 0.00 0.00 1.78
2698 3280 4.806775 GGCAACGGCTTTCTAAAAGAAAAA 59.193 37.500 3.68 0.00 42.95 1.94
2715 3297 1.540267 TTGTAAATCTGGGGGCAACG 58.460 50.000 0.00 0.00 37.60 4.10
2771 3353 7.913674 AGAATGATGAGTTACTTTCCTGTTC 57.086 36.000 0.00 0.00 0.00 3.18
2833 3415 0.299597 CGCCGTAATTGTAGTTCGCC 59.700 55.000 0.00 0.00 0.00 5.54
3029 3612 7.907214 AGCAAGAGTCTTAAATTGTATTCGT 57.093 32.000 4.74 0.00 0.00 3.85
3030 3613 8.443160 TCAAGCAAGAGTCTTAAATTGTATTCG 58.557 33.333 4.74 0.00 0.00 3.34
3137 4118 9.827411 GAGTCAGAAAAGGAAATGTGTAAATAC 57.173 33.333 0.00 0.00 0.00 1.89
3171 4152 6.346838 GGTGCAAGAAGTGAATTGTAAAATGC 60.347 38.462 0.00 0.00 0.00 3.56
3203 4184 5.242838 TGGAATTTCGTTAATGCTCCAGTTT 59.757 36.000 4.46 0.00 31.24 2.66
3243 4224 7.748691 TCATGACAAAAATGTTCTGATCTCA 57.251 32.000 0.00 0.00 0.00 3.27
3389 4370 7.606073 TGCTCTGACTTGCTACATGTAAAAATA 59.394 33.333 7.06 0.00 0.00 1.40
3419 4400 0.536724 AAAGCGGAAAATCCCCATGC 59.463 50.000 0.00 0.00 31.13 4.06
3420 4401 1.550072 ACAAAGCGGAAAATCCCCATG 59.450 47.619 0.00 0.00 31.13 3.66
3421 4402 1.550072 CACAAAGCGGAAAATCCCCAT 59.450 47.619 0.00 0.00 31.13 4.00
3437 4418 3.696045 ACATGGCATAAGGTAAGCACAA 58.304 40.909 0.00 0.00 0.00 3.33
3445 4426 5.540911 CAAAAACAGAACATGGCATAAGGT 58.459 37.500 0.00 0.00 0.00 3.50
3446 4427 4.389687 GCAAAAACAGAACATGGCATAAGG 59.610 41.667 0.00 0.00 0.00 2.69
3455 4436 5.422145 AGAAAAGCAGCAAAAACAGAACAT 58.578 33.333 0.00 0.00 0.00 2.71
3472 4453 7.336427 ACCTCAGATAGCAATTCTGAAGAAAAG 59.664 37.037 13.12 0.00 46.58 2.27
3513 4494 7.870509 TGAATTAGCACATAAGCTTTCATCT 57.129 32.000 3.20 0.00 43.70 2.90
3604 4587 2.736144 TTCCGTGTGTGACAGGTATC 57.264 50.000 0.00 0.00 32.52 2.24
3607 4590 0.828022 TCTTTCCGTGTGTGACAGGT 59.172 50.000 0.00 0.00 32.52 4.00
3609 4592 4.342772 CTTTTTCTTTCCGTGTGTGACAG 58.657 43.478 0.00 0.00 0.00 3.51
3616 4599 4.948004 AGAGTTTCCTTTTTCTTTCCGTGT 59.052 37.500 0.00 0.00 0.00 4.49
3618 4601 6.262496 CCTAAGAGTTTCCTTTTTCTTTCCGT 59.738 38.462 0.00 0.00 32.54 4.69
3619 4602 6.669278 CCTAAGAGTTTCCTTTTTCTTTCCG 58.331 40.000 0.00 0.00 32.54 4.30
3655 4638 3.253432 TGTACCTCGAGGATGATTGATCG 59.747 47.826 37.69 6.92 38.94 3.69
3755 4738 8.028540 TCATGTTTATTGTATCATATCGTGCC 57.971 34.615 0.00 0.00 0.00 5.01
3776 4759 4.095782 TGCAGAACACATCACATGATCATG 59.904 41.667 29.95 29.95 44.15 3.07
3780 4763 5.184287 TGAAATGCAGAACACATCACATGAT 59.816 36.000 0.00 0.00 34.56 2.45
3882 4865 0.654683 GCGTCATGGACATTCAGCTC 59.345 55.000 0.00 0.00 32.09 4.09
3904 4887 1.975680 AGGTGTTTAAAGCTCTCCGGA 59.024 47.619 2.93 2.93 0.00 5.14
3915 4898 1.698506 CACTTGGCCCAGGTGTTTAA 58.301 50.000 17.32 0.00 36.83 1.52
3917 4900 1.457455 CCACTTGGCCCAGGTGTTT 60.457 57.895 22.76 0.00 39.34 2.83
3931 4914 6.782494 GGGATTTATATTGGAATCAACCCACT 59.218 38.462 0.00 0.00 35.48 4.00
3972 4955 5.055812 GGATGATGAGTAGCCTCTGAAAAG 58.944 45.833 0.00 0.00 38.61 2.27
3990 4973 3.081061 CGACAAACCTGAAATGGGATGA 58.919 45.455 0.00 0.00 0.00 2.92
4007 4990 6.871844 AGATGAGATCAGAAAAGAATCGACA 58.128 36.000 0.00 0.00 0.00 4.35
4010 4993 6.514947 AGGAGATGAGATCAGAAAAGAATCG 58.485 40.000 0.00 0.00 0.00 3.34
4014 4997 9.653516 ACTTATAGGAGATGAGATCAGAAAAGA 57.346 33.333 0.00 0.00 0.00 2.52
4036 5019 1.067364 TGACACCGCGAACTGAACTTA 59.933 47.619 8.23 0.00 0.00 2.24
4060 5043 5.156355 CAAACATCAGTTGCTGTGATAACC 58.844 41.667 0.00 0.00 38.17 2.85
4175 5158 2.043604 CTGCGGGTATGGCATGAGGA 62.044 60.000 10.98 0.00 40.09 3.71
4341 5324 2.034878 CTGCAGTCCTGGTATAGCTCA 58.965 52.381 5.25 0.00 0.00 4.26
4518 5501 6.493189 TGTCAACTATATATGCCTTGACCA 57.507 37.500 19.28 11.04 39.91 4.02
4543 5526 3.526899 TCCAAGACCCTTGACCTATCAA 58.473 45.455 8.16 0.00 42.73 2.57
4544 5527 3.199442 TCCAAGACCCTTGACCTATCA 57.801 47.619 8.16 0.00 0.00 2.15
4545 5528 4.445019 GGATTCCAAGACCCTTGACCTATC 60.445 50.000 8.16 5.47 0.00 2.08
4546 5529 3.459969 GGATTCCAAGACCCTTGACCTAT 59.540 47.826 8.16 0.00 0.00 2.57
4547 5530 2.844348 GGATTCCAAGACCCTTGACCTA 59.156 50.000 8.16 0.00 0.00 3.08
4549 5532 1.636003 AGGATTCCAAGACCCTTGACC 59.364 52.381 5.29 6.29 0.00 4.02
4550 5533 3.441500 AAGGATTCCAAGACCCTTGAC 57.558 47.619 5.29 0.00 37.60 3.18
4559 5545 6.825721 AGTTTACTCTATGCAAGGATTCCAAG 59.174 38.462 5.29 0.00 0.00 3.61
4624 5618 9.650539 CAAACTCCTATGATCCTATACAGATTG 57.349 37.037 0.00 0.00 0.00 2.67
4626 5620 8.811017 CACAAACTCCTATGATCCTATACAGAT 58.189 37.037 0.00 0.00 0.00 2.90
4650 5644 4.641989 AGCTGGACATGGATTTTACATCAC 59.358 41.667 0.00 0.00 0.00 3.06
4720 5714 5.713025 TCATGAAAAACAAAGAGCTATGCC 58.287 37.500 0.00 0.00 0.00 4.40
4722 5716 8.248945 AGGATTCATGAAAAACAAAGAGCTATG 58.751 33.333 13.09 0.00 0.00 2.23
4749 5743 5.624344 AGCATTCAGTGAACAGAAAGATG 57.376 39.130 7.96 1.03 0.00 2.90
4878 5872 2.516906 TGAAATCAGGATGCACAGCAA 58.483 42.857 0.00 0.00 43.62 3.91
5071 6065 2.917172 CCAAACAATGGCCAACTGC 58.083 52.632 10.96 0.00 43.80 4.40
5093 6087 0.325933 CCATTGGCAGTCTGTCCTCA 59.674 55.000 1.07 0.00 0.00 3.86
5094 6088 0.393537 CCCATTGGCAGTCTGTCCTC 60.394 60.000 1.07 0.00 0.00 3.71
5095 6089 1.136329 ACCCATTGGCAGTCTGTCCT 61.136 55.000 1.07 0.00 33.59 3.85
5096 6090 0.962356 CACCCATTGGCAGTCTGTCC 60.962 60.000 1.07 4.27 33.59 4.02
5097 6091 1.589716 GCACCCATTGGCAGTCTGTC 61.590 60.000 0.00 0.00 33.59 3.51
5098 6092 1.604593 GCACCCATTGGCAGTCTGT 60.605 57.895 0.93 0.00 33.59 3.41
5099 6093 0.035152 TAGCACCCATTGGCAGTCTG 60.035 55.000 0.00 0.00 33.59 3.51
5100 6094 0.698238 TTAGCACCCATTGGCAGTCT 59.302 50.000 0.00 0.00 33.59 3.24
5101 6095 1.544724 TTTAGCACCCATTGGCAGTC 58.455 50.000 0.00 0.00 33.59 3.51
5102 6096 2.008242 TTTTAGCACCCATTGGCAGT 57.992 45.000 0.00 0.00 33.59 4.40
5103 6097 2.496871 TGATTTTAGCACCCATTGGCAG 59.503 45.455 0.00 0.00 33.59 4.85
5104 6098 2.533916 TGATTTTAGCACCCATTGGCA 58.466 42.857 0.00 0.00 33.59 4.92
5105 6099 3.055891 ACTTGATTTTAGCACCCATTGGC 60.056 43.478 0.00 0.00 33.59 4.52
5197 6196 3.059188 AGCGTCAGTTGTTATTTGGTTCG 60.059 43.478 0.00 0.00 0.00 3.95
5241 6397 3.441290 GCTGCAGCTGAAGCCAGG 61.441 66.667 33.41 4.30 40.93 4.45
5268 6431 4.151883 AGGCAAGATAACTTCAGCCAAAA 58.848 39.130 14.15 0.00 43.35 2.44
5273 6436 3.522553 ACGTAGGCAAGATAACTTCAGC 58.477 45.455 0.00 0.00 33.70 4.26
5293 6456 3.498777 GCCTTGTTTCAGGAAGTGAGTAC 59.501 47.826 0.00 0.00 36.21 2.73
5298 6461 2.575532 TCAGCCTTGTTTCAGGAAGTG 58.424 47.619 0.00 0.00 35.71 3.16
5299 6462 2.952310 GTTCAGCCTTGTTTCAGGAAGT 59.048 45.455 0.00 0.00 35.71 3.01
5300 6463 2.951642 TGTTCAGCCTTGTTTCAGGAAG 59.048 45.455 0.00 0.00 35.71 3.46
5301 6464 3.011566 TGTTCAGCCTTGTTTCAGGAA 57.988 42.857 0.00 0.00 35.71 3.36
5363 6526 2.044946 ACCGGCAAGCTTGGGATC 60.045 61.111 27.10 10.68 0.00 3.36
5367 6530 0.597377 GAAAACACCGGCAAGCTTGG 60.597 55.000 27.10 13.87 0.00 3.61
5372 6535 2.671070 GCTTATGGAAAACACCGGCAAG 60.671 50.000 0.00 0.00 0.00 4.01
5381 6544 5.277047 GCATCTAGCAAGCTTATGGAAAAC 58.723 41.667 0.00 0.00 44.79 2.43
5402 6565 1.686052 GTTGTTCAATGTCCTTGGGCA 59.314 47.619 0.00 0.00 35.43 5.36


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

AutoCloner maintained by Alex Coulton.