Multiple sequence alignment - TraesCS3B01G064700

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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 TraesCS3B01G064700 chr3B 100.000 3512 0 0 1 3512 36545282 36541771 0.000000e+00 6486.0
1 TraesCS3B01G064700 chr3B 90.938 320 23 2 3193 3512 225299137 225298824 3.240000e-115 425.0
2 TraesCS3B01G064700 chr3B 86.462 325 17 16 545 869 36383944 36384241 7.270000e-87 331.0
3 TraesCS3B01G064700 chr3B 80.752 452 47 13 5 454 36384995 36385408 2.030000e-82 316.0
4 TraesCS3B01G064700 chr3B 90.367 218 13 7 458 675 36385448 36385657 2.670000e-71 279.0
5 TraesCS3B01G064700 chr3B 74.526 475 103 18 1457 1921 387887245 387887711 1.290000e-44 191.0
6 TraesCS3B01G064700 chr3B 92.105 76 2 1 776 851 36385716 36385787 1.720000e-18 104.0
7 TraesCS3B01G064700 chr3B 96.154 52 2 0 487 538 36381297 36381348 6.250000e-13 86.1
8 TraesCS3B01G064700 chr3A 90.279 2510 106 69 458 2938 30543443 30545843 0.000000e+00 3157.0
9 TraesCS3B01G064700 chr3A 90.365 301 23 5 1 299 30542647 30542943 1.180000e-104 390.0
10 TraesCS3B01G064700 chr3A 81.424 323 25 17 484 796 30540905 30541202 7.580000e-57 231.0
11 TraesCS3B01G064700 chr3A 74.105 475 105 18 1457 1921 388802415 388802881 2.790000e-41 180.0
12 TraesCS3B01G064700 chr6D 95.642 826 32 2 1718 2543 101725600 101724779 0.000000e+00 1323.0
13 TraesCS3B01G064700 chr6D 91.358 324 22 2 2194 2517 161099040 161098723 4.160000e-119 438.0
14 TraesCS3B01G064700 chr5B 92.698 315 18 2 3193 3507 701503698 701503389 1.920000e-122 449.0
15 TraesCS3B01G064700 chr5B 87.864 206 22 2 2968 3172 448296655 448296452 4.530000e-59 239.0
16 TraesCS3B01G064700 chr5D 91.250 320 23 2 3193 3512 430530095 430530409 6.960000e-117 431.0
17 TraesCS3B01G064700 chr5D 87.204 211 19 6 2968 3172 416262099 416261891 2.110000e-57 233.0
18 TraesCS3B01G064700 chr7D 90.966 321 23 4 3193 3512 155728594 155728279 9.010000e-116 427.0
19 TraesCS3B01G064700 chr7D 87.981 208 24 1 2966 3172 99419721 99419514 9.740000e-61 244.0
20 TraesCS3B01G064700 chr7D 84.103 195 13 4 966 1160 188307837 188308013 4.660000e-39 172.0
21 TraesCS3B01G064700 chr6B 90.938 320 25 1 3193 3512 697914603 697914288 9.010000e-116 427.0
22 TraesCS3B01G064700 chr3D 90.938 320 25 1 3193 3512 26441901 26442216 9.010000e-116 427.0
23 TraesCS3B01G064700 chr3D 91.049 324 12 1 2191 2514 569792570 569792876 4.190000e-114 422.0
24 TraesCS3B01G064700 chr3D 88.557 201 22 1 2965 3164 429109133 429109333 3.500000e-60 243.0
25 TraesCS3B01G064700 chr3D 87.143 210 26 1 2964 3172 47217830 47217621 1.630000e-58 237.0
26 TraesCS3B01G064700 chr3D 73.895 475 106 18 1457 1921 294048763 294049229 1.300000e-39 174.0
27 TraesCS3B01G064700 chr2B 90.938 320 25 1 3193 3512 685762116 685761801 9.010000e-116 427.0
28 TraesCS3B01G064700 chr2B 87.850 214 18 6 2958 3169 748477030 748477237 9.740000e-61 244.0
29 TraesCS3B01G064700 chr2D 90.938 320 23 2 3193 3512 549504512 549504825 3.240000e-115 425.0
30 TraesCS3B01G064700 chr2D 90.938 320 23 2 3193 3512 549979968 549980281 3.240000e-115 425.0
31 TraesCS3B01G064700 chr2D 89.055 201 18 3 2968 3165 549979645 549979844 2.710000e-61 246.0
32 TraesCS3B01G064700 chr4B 88.462 208 21 2 2968 3172 400361612 400361819 7.530000e-62 248.0
33 TraesCS3B01G064700 chr7B 87.379 206 25 1 2968 3172 229868248 229868043 5.860000e-58 235.0
34 TraesCS3B01G064700 chr4D 84.483 116 17 1 2011 2126 456059516 456059630 2.870000e-21 113.0


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 TraesCS3B01G064700 chr3B 36541771 36545282 3511 True 6486.000000 6486 100.0000 1 3512 1 chr3B.!!$R1 3511
1 TraesCS3B01G064700 chr3B 36381297 36385787 4490 False 223.220000 331 89.1680 5 869 5 chr3B.!!$F2 864
2 TraesCS3B01G064700 chr3A 30540905 30545843 4938 False 1259.333333 3157 87.3560 1 2938 3 chr3A.!!$F2 2937
3 TraesCS3B01G064700 chr6D 101724779 101725600 821 True 1323.000000 1323 95.6420 1718 2543 1 chr6D.!!$R1 825
4 TraesCS3B01G064700 chr2D 549979645 549980281 636 False 335.500000 425 89.9965 2968 3512 2 chr2D.!!$F2 544

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
134 4533 0.328450 TTGATGGGGGTAGGAGGCAT 60.328 55.0 0.00 0.0 0.00 4.4 F
176 4575 0.531974 TTGAATATGTCGCGAGGCCC 60.532 55.0 10.24 0.0 32.11 5.8 F
1638 6420 0.545171 TCTACGACCCATCCGTCTCT 59.455 55.0 0.00 0.0 40.95 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 6411 0.820074 CGTAGGAGGCAGAGACGGAT 60.820 60.000 0.0 0.0 0.00 4.18 R
1923 6705 1.063567 ACGAGGCAGTAGGAGAAGGAT 60.064 52.381 0.0 0.0 0.00 3.24 R
2706 7488 0.188587 ACCAGAGACCAGACCACTCA 59.811 55.000 0.0 0.0 33.69 3.41 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
134 4533 0.328450 TTGATGGGGGTAGGAGGCAT 60.328 55.000 0.00 0.00 0.00 4.40
164 4563 6.910536 GTCAACGAGACCAAGATTGAATAT 57.089 37.500 0.00 0.00 41.56 1.28
173 4572 3.185188 CCAAGATTGAATATGTCGCGAGG 59.815 47.826 10.24 0.00 0.00 4.63
176 4575 0.531974 TTGAATATGTCGCGAGGCCC 60.532 55.000 10.24 0.00 32.11 5.80
183 4582 3.376078 TCGCGAGGCCCGTAAACT 61.376 61.111 3.71 0.00 41.15 2.66
195 4594 2.740447 CCCGTAAACTTGAAGTAGCACC 59.260 50.000 0.00 0.00 0.00 5.01
217 4616 3.808466 AGCATGAGAGTAATCGAGCAA 57.192 42.857 0.00 0.00 0.00 3.91
219 4618 2.799412 GCATGAGAGTAATCGAGCAAGG 59.201 50.000 0.00 0.00 0.00 3.61
220 4619 2.586258 TGAGAGTAATCGAGCAAGGC 57.414 50.000 0.00 0.00 0.00 4.35
223 4622 0.933796 GAGTAATCGAGCAAGGCAGC 59.066 55.000 0.00 0.00 0.00 5.25
239 4638 3.003480 GGCAGCTCGTTGTTAGAAGATT 58.997 45.455 0.00 0.00 0.00 2.40
286 4685 4.183865 CCTGAGCTAATGATCGTTTCACA 58.816 43.478 5.29 3.13 37.11 3.58
287 4686 4.813161 CCTGAGCTAATGATCGTTTCACAT 59.187 41.667 5.29 0.00 37.11 3.21
302 4701 4.829064 TTCACATGAAAAGAAACTCCGG 57.171 40.909 0.00 0.00 0.00 5.14
305 4704 3.315191 CACATGAAAAGAAACTCCGGTGT 59.685 43.478 2.61 2.61 0.00 4.16
306 4705 3.564225 ACATGAAAAGAAACTCCGGTGTC 59.436 43.478 10.05 0.00 0.00 3.67
329 4728 5.905181 TCGTGCATTTTAGTTTCTTTTCGTC 59.095 36.000 0.00 0.00 0.00 4.20
330 4729 5.679355 CGTGCATTTTAGTTTCTTTTCGTCA 59.321 36.000 0.00 0.00 0.00 4.35
331 4730 6.195613 CGTGCATTTTAGTTTCTTTTCGTCAA 59.804 34.615 0.00 0.00 0.00 3.18
332 4731 7.327378 GTGCATTTTAGTTTCTTTTCGTCAAC 58.673 34.615 0.00 0.00 0.00 3.18
334 4733 7.219917 TGCATTTTAGTTTCTTTTCGTCAACAG 59.780 33.333 0.00 0.00 0.00 3.16
335 4734 7.220108 GCATTTTAGTTTCTTTTCGTCAACAGT 59.780 33.333 0.00 0.00 0.00 3.55
336 4735 9.072294 CATTTTAGTTTCTTTTCGTCAACAGTT 57.928 29.630 0.00 0.00 0.00 3.16
345 5055 6.759827 TCTTTTCGTCAACAGTTAAACTAGCT 59.240 34.615 0.00 0.00 0.00 3.32
354 5064 3.375299 CAGTTAAACTAGCTGTCCATGGC 59.625 47.826 6.96 2.72 33.05 4.40
376 5086 3.549070 CAGCAAAATCTTAAGCGCATTCC 59.451 43.478 11.47 0.00 0.00 3.01
381 5091 2.919666 TCTTAAGCGCATTCCAAAGC 57.080 45.000 11.47 0.00 0.00 3.51
391 5101 5.063817 AGCGCATTCCAAAGCAAAAATAATC 59.936 36.000 11.47 0.00 0.00 1.75
398 5108 4.632688 CCAAAGCAAAAATAATCCTGCCTG 59.367 41.667 0.00 0.00 35.33 4.85
454 5165 1.671054 CACAAGCCCCACGTACCAG 60.671 63.158 0.00 0.00 0.00 4.00
455 5166 1.839747 ACAAGCCCCACGTACCAGA 60.840 57.895 0.00 0.00 0.00 3.86
456 5167 1.373435 CAAGCCCCACGTACCAGAA 59.627 57.895 0.00 0.00 0.00 3.02
501 5263 2.415168 GCTACGTTAGATTTGCAGCACA 59.585 45.455 0.00 0.00 0.00 4.57
538 5300 5.001874 AGTTTTAAATCACCGAGGTTCCTC 58.998 41.667 8.66 8.66 0.00 3.71
555 5320 7.376615 AGGTTCCTCCGTTATATTTCTAATCG 58.623 38.462 0.00 0.00 41.99 3.34
577 5342 1.488705 CCCCCACCTACTCAGCAACA 61.489 60.000 0.00 0.00 0.00 3.33
590 5355 9.113838 CCTACTCAGCAACATAATAAAAGTCAT 57.886 33.333 0.00 0.00 0.00 3.06
593 5358 8.604035 ACTCAGCAACATAATAAAAGTCATACG 58.396 33.333 0.00 0.00 0.00 3.06
594 5359 8.487313 TCAGCAACATAATAAAAGTCATACGT 57.513 30.769 0.00 0.00 0.00 3.57
595 5360 9.589111 TCAGCAACATAATAAAAGTCATACGTA 57.411 29.630 0.00 0.00 0.00 3.57
596 5361 9.632969 CAGCAACATAATAAAAGTCATACGTAC 57.367 33.333 0.00 0.00 0.00 3.67
597 5362 9.595823 AGCAACATAATAAAAGTCATACGTACT 57.404 29.630 0.00 0.00 0.00 2.73
623 5391 3.877508 ACCAACAAGCAGAGTGAGTAAAC 59.122 43.478 0.00 0.00 0.00 2.01
718 5491 2.711542 CTGCCTCCGTTAAACTCCAAT 58.288 47.619 0.00 0.00 0.00 3.16
719 5492 2.678336 CTGCCTCCGTTAAACTCCAATC 59.322 50.000 0.00 0.00 0.00 2.67
720 5493 2.014857 GCCTCCGTTAAACTCCAATCC 58.985 52.381 0.00 0.00 0.00 3.01
724 5497 1.129811 CCGTTAAACTCCAATCCGTGC 59.870 52.381 0.00 0.00 0.00 5.34
744 5517 1.113517 ACACCACGCTCCAGTACACT 61.114 55.000 0.00 0.00 0.00 3.55
752 5525 2.240162 CTCCAGTACACTTCCGCCCC 62.240 65.000 0.00 0.00 0.00 5.80
754 5527 3.387947 AGTACACTTCCGCCCCCG 61.388 66.667 0.00 0.00 0.00 5.73
765 5538 4.883354 GCCCCCGCCTGGAATCTG 62.883 72.222 0.00 0.00 37.49 2.90
766 5539 4.195334 CCCCCGCCTGGAATCTGG 62.195 72.222 0.00 0.00 37.49 3.86
767 5540 3.089874 CCCCGCCTGGAATCTGGA 61.090 66.667 0.00 0.00 37.49 3.86
768 5541 2.455565 CCCCGCCTGGAATCTGGAT 61.456 63.158 0.00 0.00 37.49 3.41
769 5542 1.533711 CCCGCCTGGAATCTGGATT 59.466 57.895 0.00 0.00 37.49 3.01
801 5574 2.223829 ACGAGAAATAGATGCACCGGAG 60.224 50.000 9.46 0.00 0.00 4.63
816 5589 4.220693 ACCGGAGTGAATGAATGAATGA 57.779 40.909 9.46 0.00 0.00 2.57
846 5619 1.713005 CCCTCCATGTCCATCCCCAG 61.713 65.000 0.00 0.00 0.00 4.45
887 5660 4.687215 GCTGGCCGCAGTGAGTGA 62.687 66.667 13.61 0.00 38.92 3.41
889 5662 4.662961 TGGCCGCAGTGAGTGACG 62.663 66.667 0.00 0.00 0.00 4.35
894 5667 2.433318 GCAGTGAGTGACGCCCTC 60.433 66.667 0.00 0.00 0.00 4.30
895 5668 3.051210 CAGTGAGTGACGCCCTCA 58.949 61.111 0.00 0.00 36.63 3.86
901 5674 2.433318 GTGACGCCCTCACTCTGC 60.433 66.667 2.53 0.00 45.38 4.26
953 5726 4.662961 CCGCGTCACCACAGCAGA 62.663 66.667 4.92 0.00 0.00 4.26
954 5727 3.108289 CGCGTCACCACAGCAGAG 61.108 66.667 0.00 0.00 0.00 3.35
955 5728 3.418068 GCGTCACCACAGCAGAGC 61.418 66.667 0.00 0.00 0.00 4.09
964 5737 2.350134 CAGCAGAGCCAGCCTTCA 59.650 61.111 0.00 0.00 0.00 3.02
987 5760 2.281484 CTCCAACCACCACCACCG 60.281 66.667 0.00 0.00 0.00 4.94
990 5763 2.978010 CAACCACCACCACCGCTC 60.978 66.667 0.00 0.00 0.00 5.03
991 5764 4.265056 AACCACCACCACCGCTCC 62.265 66.667 0.00 0.00 0.00 4.70
1050 5823 4.834453 CTGCTGCTCCTGGCCTCG 62.834 72.222 3.32 0.00 40.92 4.63
1180 5953 2.452114 CCCTCCACCAGTCCCTCT 59.548 66.667 0.00 0.00 0.00 3.69
1311 6093 2.409651 GAGAGCTACCGGTCGCTG 59.590 66.667 35.51 14.53 42.35 5.18
1416 6198 4.162690 GACCTGAGGCCGGCGAAT 62.163 66.667 22.54 9.05 0.00 3.34
1629 6411 2.361610 GACCCCGTCTACGACCCA 60.362 66.667 3.65 0.00 43.02 4.51
1638 6420 0.545171 TCTACGACCCATCCGTCTCT 59.455 55.000 0.00 0.00 40.95 3.10
1791 6573 4.104417 ACCGAGACGCTCACGCTC 62.104 66.667 7.47 0.00 45.53 5.03
1923 6705 3.068064 TCGCAGATCTCCGCCACA 61.068 61.111 0.00 0.00 0.00 4.17
1956 6738 4.477975 CTCGTGGACCGCGACTCC 62.478 72.222 25.70 12.07 41.48 3.85
2058 6840 1.285962 ACCTTCTACTACGTGGGGCTA 59.714 52.381 3.26 0.00 0.00 3.93
2098 6880 4.888325 AGGCCCTCTCCATCCCGG 62.888 72.222 0.00 0.00 0.00 5.73
2103 6885 3.237741 CTCTCCATCCCGGCCTCC 61.238 72.222 0.00 0.00 33.14 4.30
2557 7339 2.031069 AGCGAGCTCGATTAATTAGCGA 60.031 45.455 38.74 10.71 43.02 4.93
2573 7355 6.936222 ATTAGCGAGCGAGTGATTAATTAG 57.064 37.500 0.00 0.00 0.00 1.73
2574 7356 3.053455 AGCGAGCGAGTGATTAATTAGC 58.947 45.455 0.00 0.00 0.00 3.09
2575 7357 2.160091 GCGAGCGAGTGATTAATTAGCG 60.160 50.000 0.00 0.00 0.00 4.26
2576 7358 3.043586 CGAGCGAGTGATTAATTAGCGT 58.956 45.455 0.00 0.00 0.00 5.07
2577 7359 3.121663 CGAGCGAGTGATTAATTAGCGTG 60.122 47.826 0.00 0.00 0.00 5.34
2578 7360 2.540101 AGCGAGTGATTAATTAGCGTGC 59.460 45.455 0.00 0.00 0.00 5.34
2579 7361 2.656632 GCGAGTGATTAATTAGCGTGCG 60.657 50.000 0.00 0.00 0.00 5.34
2580 7362 2.534349 CGAGTGATTAATTAGCGTGCGT 59.466 45.455 0.00 0.00 0.00 5.24
2610 7392 2.650322 CATGTGGTAATTAAGCGGGGT 58.350 47.619 0.00 0.00 0.00 4.95
2639 7421 1.678970 CGGAGGCTTTGGGAAAGGG 60.679 63.158 0.00 0.00 38.93 3.95
2675 7457 2.103339 AACAAATGCCAGCCTGTGCC 62.103 55.000 3.26 0.00 38.69 5.01
2676 7458 2.118951 AAATGCCAGCCTGTGCCT 59.881 55.556 3.26 0.00 38.69 4.75
2677 7459 1.980772 AAATGCCAGCCTGTGCCTC 60.981 57.895 3.26 0.00 38.69 4.70
2681 7463 3.052082 CCAGCCTGTGCCTCGTTG 61.052 66.667 0.00 0.00 38.69 4.10
2682 7464 3.730761 CAGCCTGTGCCTCGTTGC 61.731 66.667 0.00 0.00 38.69 4.17
2683 7465 3.946201 AGCCTGTGCCTCGTTGCT 61.946 61.111 1.05 0.00 38.69 3.91
2684 7466 2.980233 GCCTGTGCCTCGTTGCTT 60.980 61.111 1.05 0.00 0.00 3.91
2685 7467 2.949106 CCTGTGCCTCGTTGCTTG 59.051 61.111 1.05 0.00 0.00 4.01
2686 7468 2.253452 CTGTGCCTCGTTGCTTGC 59.747 61.111 1.05 0.00 0.00 4.01
2687 7469 2.203195 TGTGCCTCGTTGCTTGCT 60.203 55.556 0.00 0.00 0.00 3.91
2688 7470 1.789078 CTGTGCCTCGTTGCTTGCTT 61.789 55.000 0.00 0.00 0.00 3.91
2689 7471 1.370900 GTGCCTCGTTGCTTGCTTG 60.371 57.895 0.00 0.00 0.00 4.01
2690 7472 2.429739 GCCTCGTTGCTTGCTTGC 60.430 61.111 0.00 0.00 0.00 4.01
2691 7473 2.912624 GCCTCGTTGCTTGCTTGCT 61.913 57.895 3.47 0.00 0.00 3.91
2692 7474 1.656441 CCTCGTTGCTTGCTTGCTT 59.344 52.632 3.47 0.00 0.00 3.91
2693 7475 0.031178 CCTCGTTGCTTGCTTGCTTT 59.969 50.000 3.47 0.00 0.00 3.51
2694 7476 1.126079 CTCGTTGCTTGCTTGCTTTG 58.874 50.000 3.47 0.00 0.00 2.77
2695 7477 0.248990 TCGTTGCTTGCTTGCTTTGG 60.249 50.000 3.47 0.00 0.00 3.28
2696 7478 1.824272 CGTTGCTTGCTTGCTTTGGC 61.824 55.000 3.47 0.00 39.26 4.52
2697 7479 1.592131 TTGCTTGCTTGCTTTGGCG 60.592 52.632 3.47 0.00 42.25 5.69
2698 7480 2.735857 GCTTGCTTGCTTTGGCGG 60.736 61.111 0.00 0.00 42.25 6.13
2699 7481 2.730094 CTTGCTTGCTTTGGCGGT 59.270 55.556 0.00 0.00 42.25 5.68
2700 7482 1.662446 CTTGCTTGCTTTGGCGGTG 60.662 57.895 0.00 0.00 42.25 4.94
2701 7483 2.074230 CTTGCTTGCTTTGGCGGTGA 62.074 55.000 0.00 0.00 42.25 4.02
2702 7484 1.462731 TTGCTTGCTTTGGCGGTGAT 61.463 50.000 0.00 0.00 42.25 3.06
2703 7485 1.444895 GCTTGCTTTGGCGGTGATG 60.445 57.895 0.00 0.00 42.25 3.07
2704 7486 1.213537 CTTGCTTTGGCGGTGATGG 59.786 57.895 0.00 0.00 42.25 3.51
2705 7487 1.228398 TTGCTTTGGCGGTGATGGA 60.228 52.632 0.00 0.00 42.25 3.41
2706 7488 0.611618 TTGCTTTGGCGGTGATGGAT 60.612 50.000 0.00 0.00 42.25 3.41
2707 7489 1.314534 TGCTTTGGCGGTGATGGATG 61.315 55.000 0.00 0.00 42.25 3.51
2708 7490 1.031571 GCTTTGGCGGTGATGGATGA 61.032 55.000 0.00 0.00 0.00 2.92
2709 7491 1.019673 CTTTGGCGGTGATGGATGAG 58.980 55.000 0.00 0.00 0.00 2.90
2710 7492 0.327924 TTTGGCGGTGATGGATGAGT 59.672 50.000 0.00 0.00 0.00 3.41
2711 7493 0.392863 TTGGCGGTGATGGATGAGTG 60.393 55.000 0.00 0.00 0.00 3.51
2712 7494 1.524621 GGCGGTGATGGATGAGTGG 60.525 63.158 0.00 0.00 0.00 4.00
2713 7495 1.221840 GCGGTGATGGATGAGTGGT 59.778 57.895 0.00 0.00 0.00 4.16
2714 7496 0.811616 GCGGTGATGGATGAGTGGTC 60.812 60.000 0.00 0.00 0.00 4.02
2715 7497 0.826715 CGGTGATGGATGAGTGGTCT 59.173 55.000 0.00 0.00 0.00 3.85
2716 7498 1.472201 CGGTGATGGATGAGTGGTCTG 60.472 57.143 0.00 0.00 0.00 3.51
2717 7499 1.134280 GGTGATGGATGAGTGGTCTGG 60.134 57.143 0.00 0.00 0.00 3.86
2718 7500 1.556911 GTGATGGATGAGTGGTCTGGT 59.443 52.381 0.00 0.00 0.00 4.00
2719 7501 1.833630 TGATGGATGAGTGGTCTGGTC 59.166 52.381 0.00 0.00 0.00 4.02
2736 7518 2.025898 GGTCTCTGGTCTAGTGTAGCC 58.974 57.143 0.00 0.00 0.00 3.93
2739 7521 3.878699 GTCTCTGGTCTAGTGTAGCCTAC 59.121 52.174 0.00 0.00 0.00 3.18
2761 7548 0.898789 TCCTTCTGGTCTGGTCGTCC 60.899 60.000 0.00 0.00 34.23 4.79
2764 7551 1.241990 TTCTGGTCTGGTCGTCCTCG 61.242 60.000 0.00 0.00 38.55 4.63
2783 7570 0.726256 GTCGTCGTCTACCTCTGTCC 59.274 60.000 0.00 0.00 0.00 4.02
2803 7592 2.536365 CGTGTAACTGTGTCACTGTGT 58.464 47.619 15.36 8.88 30.49 3.72
2810 7599 0.108396 TGTGTCACTGTGTCCATGGG 59.892 55.000 13.02 0.00 0.00 4.00
2851 7640 2.775359 GATGTGTGTGCGTGCTGCTG 62.775 60.000 0.00 0.00 46.63 4.41
2859 7648 2.433838 CGTGCTGCTGCTGCTACT 60.434 61.111 27.67 0.00 40.48 2.57
2863 7652 0.610174 TGCTGCTGCTGCTACTACTT 59.390 50.000 27.67 0.00 40.48 2.24
2867 7656 1.066858 TGCTGCTGCTACTACTTCCAC 60.067 52.381 17.00 0.00 40.48 4.02
2893 7682 6.197788 GAACGAATTTGTTCATGGTTGTTC 57.802 37.500 26.93 2.99 45.92 3.18
2896 7685 5.163457 ACGAATTTGTTCATGGTTGTTCCTT 60.163 36.000 0.00 0.00 37.07 3.36
2897 7686 5.752955 CGAATTTGTTCATGGTTGTTCCTTT 59.247 36.000 0.00 0.00 37.07 3.11
2898 7687 6.257630 CGAATTTGTTCATGGTTGTTCCTTTT 59.742 34.615 0.00 0.00 37.07 2.27
2938 7731 4.317488 CTTGTTGTTTATTGCCCATTGCT 58.683 39.130 0.00 0.00 42.00 3.91
2939 7732 4.348863 TGTTGTTTATTGCCCATTGCTT 57.651 36.364 0.00 0.00 42.00 3.91
2940 7733 4.063689 TGTTGTTTATTGCCCATTGCTTG 58.936 39.130 0.00 0.00 42.00 4.01
2941 7734 2.697654 TGTTTATTGCCCATTGCTTGC 58.302 42.857 0.00 0.00 42.00 4.01
2942 7735 2.038164 TGTTTATTGCCCATTGCTTGCA 59.962 40.909 0.00 0.00 42.00 4.08
2943 7736 2.674357 GTTTATTGCCCATTGCTTGCAG 59.326 45.455 0.00 0.00 42.00 4.41
2944 7737 0.825410 TATTGCCCATTGCTTGCAGG 59.175 50.000 0.00 0.00 42.00 4.85
2945 7738 1.196104 ATTGCCCATTGCTTGCAGGT 61.196 50.000 0.00 0.00 42.00 4.00
2946 7739 2.102109 TTGCCCATTGCTTGCAGGTG 62.102 55.000 0.00 0.00 42.00 4.00
2947 7740 2.576832 GCCCATTGCTTGCAGGTGT 61.577 57.895 0.00 0.00 36.87 4.16
2948 7741 1.250154 GCCCATTGCTTGCAGGTGTA 61.250 55.000 0.00 0.00 36.87 2.90
2949 7742 1.255882 CCCATTGCTTGCAGGTGTAA 58.744 50.000 0.00 0.00 0.00 2.41
2950 7743 1.617850 CCCATTGCTTGCAGGTGTAAA 59.382 47.619 0.00 0.00 0.00 2.01
2951 7744 2.036992 CCCATTGCTTGCAGGTGTAAAA 59.963 45.455 0.00 0.00 0.00 1.52
2952 7745 3.494048 CCCATTGCTTGCAGGTGTAAAAA 60.494 43.478 0.00 0.00 0.00 1.94
2953 7746 4.317488 CCATTGCTTGCAGGTGTAAAAAT 58.683 39.130 0.00 0.00 0.00 1.82
2954 7747 4.152759 CCATTGCTTGCAGGTGTAAAAATG 59.847 41.667 0.00 8.02 0.00 2.32
2955 7748 4.399004 TTGCTTGCAGGTGTAAAAATGT 57.601 36.364 0.00 0.00 0.00 2.71
2956 7749 4.399004 TGCTTGCAGGTGTAAAAATGTT 57.601 36.364 0.00 0.00 0.00 2.71
2957 7750 5.521906 TGCTTGCAGGTGTAAAAATGTTA 57.478 34.783 0.00 0.00 0.00 2.41
2958 7751 6.095432 TGCTTGCAGGTGTAAAAATGTTAT 57.905 33.333 0.00 0.00 0.00 1.89
2959 7752 6.155827 TGCTTGCAGGTGTAAAAATGTTATC 58.844 36.000 0.00 0.00 0.00 1.75
2960 7753 6.155827 GCTTGCAGGTGTAAAAATGTTATCA 58.844 36.000 0.00 0.00 0.00 2.15
2961 7754 6.644592 GCTTGCAGGTGTAAAAATGTTATCAA 59.355 34.615 0.00 0.00 0.00 2.57
2962 7755 7.148755 GCTTGCAGGTGTAAAAATGTTATCAAG 60.149 37.037 0.00 0.00 0.00 3.02
2963 7756 6.155827 TGCAGGTGTAAAAATGTTATCAAGC 58.844 36.000 0.00 0.00 0.00 4.01
2964 7757 6.015519 TGCAGGTGTAAAAATGTTATCAAGCT 60.016 34.615 0.00 0.00 0.00 3.74
2965 7758 6.868339 GCAGGTGTAAAAATGTTATCAAGCTT 59.132 34.615 0.00 0.00 0.00 3.74
2966 7759 7.148755 GCAGGTGTAAAAATGTTATCAAGCTTG 60.149 37.037 20.81 20.81 0.00 4.01
2975 7768 4.144297 TGTTATCAAGCTTGGAGCAACTT 58.856 39.130 25.73 4.40 45.56 2.66
2981 7774 1.891150 AGCTTGGAGCAACTTCAATGG 59.109 47.619 2.47 0.00 45.56 3.16
2983 7776 1.547372 CTTGGAGCAACTTCAATGGGG 59.453 52.381 0.00 0.00 27.62 4.96
2984 7777 0.899717 TGGAGCAACTTCAATGGGGC 60.900 55.000 0.00 0.00 0.00 5.80
3032 7826 1.977594 GATCGGCGCGGACACAAAAT 61.978 55.000 20.65 1.90 0.00 1.82
3043 7837 2.021039 CACAAAATGCGGCCCAACG 61.021 57.895 0.00 0.00 0.00 4.10
3044 7838 2.338257 CAAAATGCGGCCCAACGT 59.662 55.556 0.00 0.00 35.98 3.99
3069 7863 2.544359 CAAACAGACGCGTGTCCG 59.456 61.111 24.75 17.81 46.74 4.79
3165 7961 2.885861 CGCGTGCCTACTCCTCTT 59.114 61.111 0.00 0.00 0.00 2.85
3167 7963 1.658686 CGCGTGCCTACTCCTCTTCT 61.659 60.000 0.00 0.00 0.00 2.85
3171 7967 0.395862 TGCCTACTCCTCTTCTCGGG 60.396 60.000 0.00 0.00 0.00 5.14
3172 7968 1.110518 GCCTACTCCTCTTCTCGGGG 61.111 65.000 0.00 0.00 0.00 5.73
3173 7969 0.468400 CCTACTCCTCTTCTCGGGGG 60.468 65.000 0.00 0.00 0.00 5.40
3291 8183 2.251371 GCGACGACCAAGCCAAAC 59.749 61.111 0.00 0.00 0.00 2.93
3295 8187 0.310854 GACGACCAAGCCAAACAAGG 59.689 55.000 0.00 0.00 0.00 3.61
3311 8203 4.534401 GGCTCTAACGCCCGAATT 57.466 55.556 0.00 0.00 44.41 2.17
3312 8204 3.673173 GGCTCTAACGCCCGAATTA 57.327 52.632 0.00 0.00 44.41 1.40
3313 8205 1.944032 GGCTCTAACGCCCGAATTAA 58.056 50.000 0.00 0.00 44.41 1.40
3314 8206 1.596260 GGCTCTAACGCCCGAATTAAC 59.404 52.381 0.00 0.00 44.41 2.01
3315 8207 2.273557 GCTCTAACGCCCGAATTAACA 58.726 47.619 0.00 0.00 0.00 2.41
3316 8208 2.284417 GCTCTAACGCCCGAATTAACAG 59.716 50.000 0.00 0.00 0.00 3.16
3317 8209 2.273557 TCTAACGCCCGAATTAACAGC 58.726 47.619 0.00 0.00 0.00 4.40
3319 8211 2.707039 CGCCCGAATTAACAGCGG 59.293 61.111 0.00 0.00 42.93 5.52
3346 8238 2.203938 TCGGCCAAGAGGAAGGGT 60.204 61.111 2.24 0.00 36.89 4.34
3351 8243 1.627297 GCCAAGAGGAAGGGTCGGAT 61.627 60.000 0.00 0.00 36.89 4.18
3432 8324 3.637273 GGAGGTCACCAACGCCCT 61.637 66.667 0.00 0.00 0.00 5.19
3477 8369 3.449737 ACGCTCTACATGCTAGGGTTAAA 59.550 43.478 6.47 0.00 33.11 1.52
3478 8370 3.802685 CGCTCTACATGCTAGGGTTAAAC 59.197 47.826 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 4510 1.596496 CTCCTACCCCCATCAAAGGT 58.404 55.000 0.00 0.00 37.69 3.50
134 4533 0.824595 TGGTCTCGTTGACTTCCCGA 60.825 55.000 10.13 0.00 44.74 5.14
151 4550 3.185188 CCTCGCGACATATTCAATCTTGG 59.815 47.826 3.71 0.00 0.00 3.61
162 4561 1.665264 TTTACGGGCCTCGCGACATA 61.665 55.000 3.71 0.00 42.31 2.29
164 4563 3.682885 TTTACGGGCCTCGCGACA 61.683 61.111 3.71 0.00 42.31 4.35
173 4572 2.159037 GTGCTACTTCAAGTTTACGGGC 59.841 50.000 0.00 0.00 0.00 6.13
176 4575 4.610680 GCTTGGTGCTACTTCAAGTTTACG 60.611 45.833 0.00 0.00 39.80 3.18
183 4582 3.076621 CTCATGCTTGGTGCTACTTCAA 58.923 45.455 0.00 0.00 43.37 2.69
195 4594 3.451526 TGCTCGATTACTCTCATGCTTG 58.548 45.455 0.00 0.00 0.00 4.01
217 4616 1.618837 TCTTCTAACAACGAGCTGCCT 59.381 47.619 0.00 0.00 0.00 4.75
219 4618 3.679980 TCAATCTTCTAACAACGAGCTGC 59.320 43.478 0.00 0.00 0.00 5.25
220 4619 5.845985 TTCAATCTTCTAACAACGAGCTG 57.154 39.130 0.00 0.00 0.00 4.24
223 4622 6.228273 TGCTTTCAATCTTCTAACAACGAG 57.772 37.500 0.00 0.00 0.00 4.18
225 4624 6.303970 CACATGCTTTCAATCTTCTAACAACG 59.696 38.462 0.00 0.00 0.00 4.10
226 4625 6.088616 GCACATGCTTTCAATCTTCTAACAAC 59.911 38.462 0.00 0.00 38.21 3.32
286 4685 2.806244 CGACACCGGAGTTTCTTTTCAT 59.194 45.455 9.46 0.00 0.00 2.57
287 4686 2.206750 CGACACCGGAGTTTCTTTTCA 58.793 47.619 9.46 0.00 0.00 2.69
302 4701 6.343924 CGAAAAGAAACTAAAATGCACGACAC 60.344 38.462 0.00 0.00 0.00 3.67
305 4704 5.812652 ACGAAAAGAAACTAAAATGCACGA 58.187 33.333 0.00 0.00 0.00 4.35
306 4705 5.679355 TGACGAAAAGAAACTAAAATGCACG 59.321 36.000 0.00 0.00 0.00 5.34
329 4728 5.106555 CCATGGACAGCTAGTTTAACTGTTG 60.107 44.000 5.56 8.46 44.40 3.33
330 4729 5.003804 CCATGGACAGCTAGTTTAACTGTT 58.996 41.667 5.56 0.00 44.40 3.16
331 4730 4.579869 CCATGGACAGCTAGTTTAACTGT 58.420 43.478 5.56 0.00 46.92 3.55
332 4731 3.375299 GCCATGGACAGCTAGTTTAACTG 59.625 47.826 18.40 0.00 37.45 3.16
334 4733 3.343617 TGCCATGGACAGCTAGTTTAAC 58.656 45.455 18.40 0.00 0.00 2.01
335 4734 3.609853 CTGCCATGGACAGCTAGTTTAA 58.390 45.455 18.40 0.00 0.00 1.52
336 4735 3.266510 CTGCCATGGACAGCTAGTTTA 57.733 47.619 18.40 0.00 0.00 2.01
345 5055 1.927487 AGATTTTGCTGCCATGGACA 58.073 45.000 18.40 12.31 0.00 4.02
351 5061 1.402720 GCGCTTAAGATTTTGCTGCCA 60.403 47.619 6.67 0.00 0.00 4.92
354 5064 3.549070 GGAATGCGCTTAAGATTTTGCTG 59.451 43.478 9.73 0.00 0.00 4.41
376 5086 4.632688 CCAGGCAGGATTATTTTTGCTTTG 59.367 41.667 0.00 0.00 41.22 2.77
381 5091 2.500910 TGGCCAGGCAGGATTATTTTTG 59.499 45.455 15.19 0.00 41.22 2.44
398 5108 3.991725 CTGCTTCCTGCTCCTGGCC 62.992 68.421 0.00 0.00 43.37 5.36
416 5126 4.991687 TGTGTTCTTGGTGGTTTGTTTTTC 59.008 37.500 0.00 0.00 0.00 2.29
426 5137 1.463553 GGGGCTTGTGTTCTTGGTGG 61.464 60.000 0.00 0.00 0.00 4.61
501 5263 1.033202 AAAACTGTTTGACGCCGGGT 61.033 50.000 6.53 0.00 0.00 5.28
538 5300 4.390909 GGGGCACGATTAGAAATATAACGG 59.609 45.833 0.00 0.00 0.00 4.44
555 5320 2.990479 CTGAGTAGGTGGGGGCAC 59.010 66.667 0.00 0.00 0.00 5.01
590 5355 5.003160 TCTGCTTGTTGGTAGTAGTACGTA 58.997 41.667 1.63 0.00 0.00 3.57
591 5356 3.822735 TCTGCTTGTTGGTAGTAGTACGT 59.177 43.478 0.00 0.00 0.00 3.57
592 5357 4.082895 ACTCTGCTTGTTGGTAGTAGTACG 60.083 45.833 1.63 0.00 0.00 3.67
593 5358 5.048224 TCACTCTGCTTGTTGGTAGTAGTAC 60.048 44.000 0.00 0.00 0.00 2.73
594 5359 5.074804 TCACTCTGCTTGTTGGTAGTAGTA 58.925 41.667 0.00 0.00 0.00 1.82
595 5360 3.895656 TCACTCTGCTTGTTGGTAGTAGT 59.104 43.478 0.00 0.00 0.00 2.73
596 5361 4.021894 ACTCACTCTGCTTGTTGGTAGTAG 60.022 45.833 0.00 0.00 0.00 2.57
597 5362 3.895656 ACTCACTCTGCTTGTTGGTAGTA 59.104 43.478 0.00 0.00 0.00 1.82
598 5363 2.700897 ACTCACTCTGCTTGTTGGTAGT 59.299 45.455 0.00 0.00 0.00 2.73
599 5364 3.393089 ACTCACTCTGCTTGTTGGTAG 57.607 47.619 0.00 0.00 0.00 3.18
603 5368 6.216569 TCTAGTTTACTCACTCTGCTTGTTG 58.783 40.000 0.00 0.00 0.00 3.33
623 5391 3.372206 CACGCTTCTTGGTTTCCATCTAG 59.628 47.826 0.00 0.00 31.53 2.43
718 5491 4.961511 GAGCGTGGTGTGCACGGA 62.962 66.667 13.13 0.00 45.13 4.69
724 5497 0.944311 GTGTACTGGAGCGTGGTGTG 60.944 60.000 0.00 0.00 0.00 3.82
752 5525 0.181114 TCAATCCAGATTCCAGGCGG 59.819 55.000 0.00 0.00 0.00 6.13
754 5527 2.158564 TCCATCAATCCAGATTCCAGGC 60.159 50.000 0.00 0.00 0.00 4.85
755 5528 3.498121 CCTCCATCAATCCAGATTCCAGG 60.498 52.174 0.00 0.00 0.00 4.45
756 5529 3.137913 ACCTCCATCAATCCAGATTCCAG 59.862 47.826 0.00 0.00 0.00 3.86
757 5530 3.117776 CACCTCCATCAATCCAGATTCCA 60.118 47.826 0.00 0.00 0.00 3.53
758 5531 3.137176 TCACCTCCATCAATCCAGATTCC 59.863 47.826 0.00 0.00 0.00 3.01
759 5532 4.133078 GTCACCTCCATCAATCCAGATTC 58.867 47.826 0.00 0.00 0.00 2.52
760 5533 3.432749 CGTCACCTCCATCAATCCAGATT 60.433 47.826 0.00 0.00 0.00 2.40
761 5534 2.103771 CGTCACCTCCATCAATCCAGAT 59.896 50.000 0.00 0.00 0.00 2.90
762 5535 1.482182 CGTCACCTCCATCAATCCAGA 59.518 52.381 0.00 0.00 0.00 3.86
763 5536 1.482182 TCGTCACCTCCATCAATCCAG 59.518 52.381 0.00 0.00 0.00 3.86
764 5537 1.482182 CTCGTCACCTCCATCAATCCA 59.518 52.381 0.00 0.00 0.00 3.41
765 5538 1.757118 TCTCGTCACCTCCATCAATCC 59.243 52.381 0.00 0.00 0.00 3.01
766 5539 3.526931 TTCTCGTCACCTCCATCAATC 57.473 47.619 0.00 0.00 0.00 2.67
767 5540 3.981071 TTTCTCGTCACCTCCATCAAT 57.019 42.857 0.00 0.00 0.00 2.57
768 5541 3.981071 ATTTCTCGTCACCTCCATCAA 57.019 42.857 0.00 0.00 0.00 2.57
769 5542 4.278310 TCTATTTCTCGTCACCTCCATCA 58.722 43.478 0.00 0.00 0.00 3.07
801 5574 3.306973 TCTCGCGTCATTCATTCATTCAC 59.693 43.478 5.77 0.00 0.00 3.18
816 5589 1.152652 ATGGAGGGAGATCTCGCGT 60.153 57.895 28.12 18.90 45.79 6.01
846 5619 3.219198 GGATGGTGGCGGAATGGC 61.219 66.667 0.00 0.00 45.12 4.40
885 5658 3.695606 GGCAGAGTGAGGGCGTCA 61.696 66.667 5.66 5.66 0.00 4.35
886 5659 3.386237 AGGCAGAGTGAGGGCGTC 61.386 66.667 0.00 0.00 34.32 5.19
887 5660 3.699894 CAGGCAGAGTGAGGGCGT 61.700 66.667 0.00 0.00 34.32 5.68
889 5662 4.792804 GGCAGGCAGAGTGAGGGC 62.793 72.222 0.00 0.00 0.00 5.19
894 5667 1.065926 TGAATGTAGGCAGGCAGAGTG 60.066 52.381 0.00 0.00 0.00 3.51
895 5668 1.279496 TGAATGTAGGCAGGCAGAGT 58.721 50.000 0.00 0.00 0.00 3.24
896 5669 2.634815 ATGAATGTAGGCAGGCAGAG 57.365 50.000 0.00 0.00 0.00 3.35
897 5670 2.421952 GGAATGAATGTAGGCAGGCAGA 60.422 50.000 0.00 0.00 0.00 4.26
898 5671 1.952296 GGAATGAATGTAGGCAGGCAG 59.048 52.381 0.00 0.00 0.00 4.85
899 5672 1.410083 GGGAATGAATGTAGGCAGGCA 60.410 52.381 0.00 0.00 0.00 4.75
900 5673 1.322442 GGGAATGAATGTAGGCAGGC 58.678 55.000 0.00 0.00 0.00 4.85
901 5674 2.734755 TGGGAATGAATGTAGGCAGG 57.265 50.000 0.00 0.00 0.00 4.85
944 5717 3.564345 AAGGCTGGCTCTGCTGTGG 62.564 63.158 3.48 0.00 0.00 4.17
945 5718 2.033757 AAGGCTGGCTCTGCTGTG 59.966 61.111 3.48 0.00 0.00 3.66
946 5719 2.350514 GAAGGCTGGCTCTGCTGT 59.649 61.111 3.48 0.00 0.00 4.40
947 5720 2.039405 GTGAAGGCTGGCTCTGCTG 61.039 63.158 3.48 0.00 0.00 4.41
948 5721 2.182732 GAGTGAAGGCTGGCTCTGCT 62.183 60.000 3.48 2.65 0.00 4.24
949 5722 1.744741 GAGTGAAGGCTGGCTCTGC 60.745 63.158 3.48 0.00 0.00 4.26
950 5723 1.078567 GGAGTGAAGGCTGGCTCTG 60.079 63.158 3.48 0.00 0.00 3.35
951 5724 1.537397 TGGAGTGAAGGCTGGCTCT 60.537 57.895 3.48 0.00 0.00 4.09
952 5725 1.376553 GTGGAGTGAAGGCTGGCTC 60.377 63.158 3.48 0.00 0.00 4.70
953 5726 1.835927 GAGTGGAGTGAAGGCTGGCT 61.836 60.000 0.00 0.00 0.00 4.75
954 5727 1.376553 GAGTGGAGTGAAGGCTGGC 60.377 63.158 0.00 0.00 0.00 4.85
955 5728 1.298014 GGAGTGGAGTGAAGGCTGG 59.702 63.158 0.00 0.00 0.00 4.85
964 5737 1.705997 GGTGGTGGTTGGAGTGGAGT 61.706 60.000 0.00 0.00 0.00 3.85
987 5760 2.283101 TGCATTGTGGGGTGGAGC 60.283 61.111 0.00 0.00 0.00 4.70
990 5763 3.384532 GGCTGCATTGTGGGGTGG 61.385 66.667 0.50 0.00 0.00 4.61
991 5764 3.384532 GGGCTGCATTGTGGGGTG 61.385 66.667 0.50 0.00 0.00 4.61
992 5765 4.702274 GGGGCTGCATTGTGGGGT 62.702 66.667 0.50 0.00 0.00 4.95
993 5766 3.910784 AAGGGGCTGCATTGTGGGG 62.911 63.158 0.50 0.00 0.00 4.96
994 5767 2.284112 AAGGGGCTGCATTGTGGG 60.284 61.111 0.50 0.00 0.00 4.61
1180 5953 3.632080 ATTGGTGTCGGTGGCGGA 61.632 61.111 0.00 0.00 0.00 5.54
1413 6195 1.026718 CGAAGACTGGGGTGGCATTC 61.027 60.000 0.00 0.00 0.00 2.67
1416 6198 2.525629 TCGAAGACTGGGGTGGCA 60.526 61.111 0.00 0.00 0.00 4.92
1425 6207 4.117661 GCCGACGCCTCGAAGACT 62.118 66.667 6.68 0.00 43.06 3.24
1533 6315 1.202582 GTGTCGAGCACCATGTAGAGT 59.797 52.381 6.82 0.00 42.10 3.24
1629 6411 0.820074 CGTAGGAGGCAGAGACGGAT 60.820 60.000 0.00 0.00 0.00 4.18
1896 6678 1.227002 GATCTGCGACGGGAAGGAC 60.227 63.158 0.00 0.00 0.00 3.85
1923 6705 1.063567 ACGAGGCAGTAGGAGAAGGAT 60.064 52.381 0.00 0.00 0.00 3.24
1959 6741 3.655810 CTGCAGCGTGGAGGAGGAC 62.656 68.421 0.00 0.00 31.71 3.85
2382 7164 1.741770 GAACGCCAGGCAGTAGGTG 60.742 63.158 13.30 0.00 41.14 4.00
2546 7328 7.891183 ATTAATCACTCGCTCGCTAATTAAT 57.109 32.000 0.00 0.00 0.00 1.40
2557 7339 2.540101 GCACGCTAATTAATCACTCGCT 59.460 45.455 0.00 0.00 0.00 4.93
2624 7406 1.483118 CCTTTCCCTTTCCCAAAGCCT 60.483 52.381 0.00 0.00 37.18 4.58
2639 7421 0.516001 GTTTCCGTCCTTCGCCTTTC 59.484 55.000 0.00 0.00 38.35 2.62
2675 7457 1.126079 CAAAGCAAGCAAGCAACGAG 58.874 50.000 3.19 0.00 36.85 4.18
2676 7458 0.248990 CCAAAGCAAGCAAGCAACGA 60.249 50.000 3.19 0.00 36.85 3.85
2677 7459 1.824272 GCCAAAGCAAGCAAGCAACG 61.824 55.000 3.19 0.00 39.53 4.10
2679 7461 1.592131 CGCCAAAGCAAGCAAGCAA 60.592 52.632 3.19 0.00 39.83 3.91
2681 7463 2.735857 CCGCCAAAGCAAGCAAGC 60.736 61.111 0.00 0.00 39.83 4.01
2682 7464 1.662446 CACCGCCAAAGCAAGCAAG 60.662 57.895 0.00 0.00 39.83 4.01
2683 7465 1.462731 ATCACCGCCAAAGCAAGCAA 61.463 50.000 0.00 0.00 39.83 3.91
2684 7466 1.902918 ATCACCGCCAAAGCAAGCA 60.903 52.632 0.00 0.00 39.83 3.91
2685 7467 1.444895 CATCACCGCCAAAGCAAGC 60.445 57.895 0.00 0.00 39.83 4.01
2686 7468 1.213537 CCATCACCGCCAAAGCAAG 59.786 57.895 0.00 0.00 39.83 4.01
2687 7469 0.611618 ATCCATCACCGCCAAAGCAA 60.612 50.000 0.00 0.00 39.83 3.91
2688 7470 1.001020 ATCCATCACCGCCAAAGCA 60.001 52.632 0.00 0.00 39.83 3.91
2689 7471 1.031571 TCATCCATCACCGCCAAAGC 61.032 55.000 0.00 0.00 0.00 3.51
2690 7472 1.019673 CTCATCCATCACCGCCAAAG 58.980 55.000 0.00 0.00 0.00 2.77
2691 7473 0.327924 ACTCATCCATCACCGCCAAA 59.672 50.000 0.00 0.00 0.00 3.28
2692 7474 0.392863 CACTCATCCATCACCGCCAA 60.393 55.000 0.00 0.00 0.00 4.52
2693 7475 1.221566 CACTCATCCATCACCGCCA 59.778 57.895 0.00 0.00 0.00 5.69
2694 7476 1.524621 CCACTCATCCATCACCGCC 60.525 63.158 0.00 0.00 0.00 6.13
2695 7477 0.811616 GACCACTCATCCATCACCGC 60.812 60.000 0.00 0.00 0.00 5.68
2696 7478 0.826715 AGACCACTCATCCATCACCG 59.173 55.000 0.00 0.00 0.00 4.94
2697 7479 1.134280 CCAGACCACTCATCCATCACC 60.134 57.143 0.00 0.00 0.00 4.02
2698 7480 1.556911 ACCAGACCACTCATCCATCAC 59.443 52.381 0.00 0.00 0.00 3.06
2699 7481 1.833630 GACCAGACCACTCATCCATCA 59.166 52.381 0.00 0.00 0.00 3.07
2700 7482 2.102252 GAGACCAGACCACTCATCCATC 59.898 54.545 0.00 0.00 0.00 3.51
2701 7483 2.114616 GAGACCAGACCACTCATCCAT 58.885 52.381 0.00 0.00 0.00 3.41
2702 7484 1.077828 AGAGACCAGACCACTCATCCA 59.922 52.381 0.00 0.00 33.69 3.41
2703 7485 1.480137 CAGAGACCAGACCACTCATCC 59.520 57.143 0.00 0.00 33.69 3.51
2704 7486 1.480137 CCAGAGACCAGACCACTCATC 59.520 57.143 0.00 0.00 33.69 2.92
2705 7487 1.203237 ACCAGAGACCAGACCACTCAT 60.203 52.381 0.00 0.00 33.69 2.90
2706 7488 0.188587 ACCAGAGACCAGACCACTCA 59.811 55.000 0.00 0.00 33.69 3.41
2707 7489 0.892063 GACCAGAGACCAGACCACTC 59.108 60.000 0.00 0.00 0.00 3.51
2708 7490 0.485099 AGACCAGAGACCAGACCACT 59.515 55.000 0.00 0.00 0.00 4.00
2709 7491 2.096248 CTAGACCAGAGACCAGACCAC 58.904 57.143 0.00 0.00 0.00 4.16
2710 7492 1.711375 ACTAGACCAGAGACCAGACCA 59.289 52.381 0.00 0.00 0.00 4.02
2711 7493 2.096248 CACTAGACCAGAGACCAGACC 58.904 57.143 0.00 0.00 0.00 3.85
2712 7494 2.797786 ACACTAGACCAGAGACCAGAC 58.202 52.381 0.00 0.00 0.00 3.51
2713 7495 3.622704 GCTACACTAGACCAGAGACCAGA 60.623 52.174 0.00 0.00 0.00 3.86
2714 7496 2.685897 GCTACACTAGACCAGAGACCAG 59.314 54.545 0.00 0.00 0.00 4.00
2715 7497 2.620886 GGCTACACTAGACCAGAGACCA 60.621 54.545 0.00 0.00 0.00 4.02
2716 7498 2.025898 GGCTACACTAGACCAGAGACC 58.974 57.143 0.00 0.00 0.00 3.85
2717 7499 3.007473 AGGCTACACTAGACCAGAGAC 57.993 52.381 0.00 0.00 32.90 3.36
2718 7500 3.117963 GGTAGGCTACACTAGACCAGAGA 60.118 52.174 24.96 0.00 32.90 3.10
2719 7501 3.215975 GGTAGGCTACACTAGACCAGAG 58.784 54.545 24.96 0.00 32.90 3.35
2736 7518 0.818296 CCAGACCAGAAGGACGGTAG 59.182 60.000 0.00 0.00 34.99 3.18
2739 7521 1.592223 GACCAGACCAGAAGGACGG 59.408 63.158 0.00 0.00 38.69 4.79
2761 7548 0.646381 CAGAGGTAGACGACGACGAG 59.354 60.000 15.32 0.00 42.66 4.18
2764 7551 0.726256 GGACAGAGGTAGACGACGAC 59.274 60.000 0.00 0.00 0.00 4.34
2783 7570 2.534349 GACACAGTGACACAGTTACACG 59.466 50.000 7.81 0.00 39.19 4.49
2803 7592 3.531207 CGAGCTCGAGCCCATGGA 61.531 66.667 32.94 0.00 43.38 3.41
2827 7616 1.503091 CACGCACACACATCCATGG 59.497 57.895 4.97 4.97 0.00 3.66
2851 7640 1.201647 TCACGTGGAAGTAGTAGCAGC 59.798 52.381 17.00 0.00 0.00 5.25
2859 7648 4.121317 ACAAATTCGTTCACGTGGAAGTA 58.879 39.130 17.00 3.23 40.80 2.24
2863 7652 3.595709 GAACAAATTCGTTCACGTGGA 57.404 42.857 17.00 3.16 43.89 4.02
2938 7731 6.644592 GCTTGATAACATTTTTACACCTGCAA 59.355 34.615 0.00 0.00 0.00 4.08
2939 7732 6.015519 AGCTTGATAACATTTTTACACCTGCA 60.016 34.615 0.00 0.00 0.00 4.41
2940 7733 6.389906 AGCTTGATAACATTTTTACACCTGC 58.610 36.000 0.00 0.00 0.00 4.85
2941 7734 7.329226 CCAAGCTTGATAACATTTTTACACCTG 59.671 37.037 28.05 0.00 0.00 4.00
2942 7735 7.232534 TCCAAGCTTGATAACATTTTTACACCT 59.767 33.333 28.05 0.00 0.00 4.00
2943 7736 7.375053 TCCAAGCTTGATAACATTTTTACACC 58.625 34.615 28.05 0.00 0.00 4.16
2944 7737 7.062255 GCTCCAAGCTTGATAACATTTTTACAC 59.938 37.037 28.05 0.00 38.45 2.90
2945 7738 7.090173 GCTCCAAGCTTGATAACATTTTTACA 58.910 34.615 28.05 0.00 38.45 2.41
2946 7739 7.090173 TGCTCCAAGCTTGATAACATTTTTAC 58.910 34.615 28.05 2.97 42.97 2.01
2947 7740 7.225784 TGCTCCAAGCTTGATAACATTTTTA 57.774 32.000 28.05 0.00 42.97 1.52
2948 7741 6.100404 TGCTCCAAGCTTGATAACATTTTT 57.900 33.333 28.05 0.00 42.97 1.94
2949 7742 5.726980 TGCTCCAAGCTTGATAACATTTT 57.273 34.783 28.05 0.00 42.97 1.82
2950 7743 5.244626 AGTTGCTCCAAGCTTGATAACATTT 59.755 36.000 28.05 8.29 42.97 2.32
2951 7744 4.768968 AGTTGCTCCAAGCTTGATAACATT 59.231 37.500 28.05 8.88 42.97 2.71
2952 7745 4.338879 AGTTGCTCCAAGCTTGATAACAT 58.661 39.130 28.05 12.27 42.97 2.71
2953 7746 3.754965 AGTTGCTCCAAGCTTGATAACA 58.245 40.909 28.05 16.17 42.97 2.41
2954 7747 4.216257 TGAAGTTGCTCCAAGCTTGATAAC 59.784 41.667 28.05 22.20 42.97 1.89
2955 7748 4.397420 TGAAGTTGCTCCAAGCTTGATAA 58.603 39.130 28.05 13.17 42.97 1.75
2956 7749 4.019792 TGAAGTTGCTCCAAGCTTGATA 57.980 40.909 28.05 13.99 42.97 2.15
2957 7750 2.867624 TGAAGTTGCTCCAAGCTTGAT 58.132 42.857 28.05 3.18 42.97 2.57
2958 7751 2.346766 TGAAGTTGCTCCAAGCTTGA 57.653 45.000 28.05 12.59 42.97 3.02
2959 7752 3.314553 CATTGAAGTTGCTCCAAGCTTG 58.685 45.455 19.93 19.93 42.97 4.01
2960 7753 2.298163 CCATTGAAGTTGCTCCAAGCTT 59.702 45.455 0.00 0.00 42.97 3.74
2961 7754 1.891150 CCATTGAAGTTGCTCCAAGCT 59.109 47.619 0.11 0.00 42.97 3.74
2962 7755 1.067354 CCCATTGAAGTTGCTCCAAGC 60.067 52.381 0.00 0.00 42.82 4.01
2963 7756 1.547372 CCCCATTGAAGTTGCTCCAAG 59.453 52.381 0.00 0.00 0.00 3.61
2964 7757 1.631405 CCCCATTGAAGTTGCTCCAA 58.369 50.000 0.00 0.00 0.00 3.53
2965 7758 0.899717 GCCCCATTGAAGTTGCTCCA 60.900 55.000 0.00 0.00 0.00 3.86
2966 7759 0.899717 TGCCCCATTGAAGTTGCTCC 60.900 55.000 0.00 0.00 0.00 4.70
2981 7774 3.131478 CGGACGAAATGGGTGCCC 61.131 66.667 0.00 0.00 0.00 5.36
2983 7776 3.810896 GGCGGACGAAATGGGTGC 61.811 66.667 0.00 0.00 0.00 5.01
3008 7802 2.895372 GTCCGCGCCGATCCAAAT 60.895 61.111 0.00 0.00 0.00 2.32
3014 7808 2.038269 ATTTTGTGTCCGCGCCGAT 61.038 52.632 0.00 0.00 0.00 4.18
3043 7837 2.604174 CGTCTGTTTGGGTCGGCAC 61.604 63.158 0.00 0.00 0.00 5.01
3044 7838 2.280524 CGTCTGTTTGGGTCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
3079 7873 0.462375 CGGGAATGGGTCGTCATGTA 59.538 55.000 0.00 0.00 0.00 2.29
3080 7874 1.220749 CGGGAATGGGTCGTCATGT 59.779 57.895 0.00 0.00 0.00 3.21
3152 7946 0.395862 CCCGAGAAGAGGAGTAGGCA 60.396 60.000 0.00 0.00 0.00 4.75
3234 8126 3.431725 GGCTTGCCTTTCCCGACG 61.432 66.667 4.11 0.00 0.00 5.12
3236 8128 2.351276 GAGGCTTGCCTTTCCCGA 59.649 61.111 15.92 0.00 0.00 5.14
3240 8132 2.563427 GCACGAGGCTTGCCTTTC 59.437 61.111 15.92 3.30 40.25 2.62
3276 8168 0.310854 CCTTGTTTGGCTTGGTCGTC 59.689 55.000 0.00 0.00 0.00 4.20
3295 8187 2.273557 TGTTAATTCGGGCGTTAGAGC 58.726 47.619 0.00 0.00 0.00 4.09
3297 8189 2.273557 GCTGTTAATTCGGGCGTTAGA 58.726 47.619 0.00 0.00 0.00 2.10
3300 8192 1.641123 CCGCTGTTAATTCGGGCGTT 61.641 55.000 0.00 0.00 43.57 4.84
3346 8238 3.690280 TCTGTGGCGTGCATCCGA 61.690 61.111 0.24 0.00 0.00 4.55
3359 8251 2.418910 CCTCATCCCTCGCGTCTGT 61.419 63.158 5.77 0.00 0.00 3.41
3361 8253 3.532155 GCCTCATCCCTCGCGTCT 61.532 66.667 5.77 0.00 0.00 4.18
3409 8301 1.968540 GTTGGTGACCTCCTGCTGC 60.969 63.158 2.11 0.00 0.00 5.25
3450 8342 1.268352 CTAGCATGTAGAGCGTCTCCC 59.732 57.143 0.00 0.00 37.01 4.30
3455 8347 1.486211 AACCCTAGCATGTAGAGCGT 58.514 50.000 0.00 0.00 37.01 5.07


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

AutoCloner maintained by Alex Coulton.