Multiple sequence alignment - TraesCS2D01G055900

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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 TraesCS2D01G055900 chr2D 100.000 8298 0 0 1 8298 22418679 22426976 0.000000e+00 15324.0
1 TraesCS2D01G055900 chr2D 84.029 1246 160 25 4731 5949 22421494 22422727 0.000000e+00 1162.0
2 TraesCS2D01G055900 chr2D 84.029 1246 160 25 2816 4049 22423409 22424627 0.000000e+00 1162.0
3 TraesCS2D01G055900 chr2D 82.309 944 108 30 925 1849 21607679 21608582 0.000000e+00 763.0
4 TraesCS2D01G055900 chr2D 80.384 469 48 18 7766 8206 22480726 22480274 4.830000e-82 316.0
5 TraesCS2D01G055900 chr2D 86.864 236 22 3 4110 4344 22420862 22421089 1.070000e-63 255.0
6 TraesCS2D01G055900 chr2D 86.864 236 22 3 2184 2411 22422788 22423022 1.070000e-63 255.0
7 TraesCS2D01G055900 chr2D 82.310 277 37 7 4456 4723 22421091 22421364 6.480000e-56 230.0
8 TraesCS2D01G055900 chr2D 82.310 277 37 7 2413 2686 22423134 22423401 6.480000e-56 230.0
9 TraesCS2D01G055900 chr2D 84.615 104 15 1 4961 5064 21608618 21608720 1.470000e-17 102.0
10 TraesCS2D01G055900 chr2D 100.000 40 0 0 726 765 409603295 409603256 3.210000e-09 75.0
11 TraesCS2D01G055900 chr2A 91.185 3823 247 46 4430 8206 24131835 24135613 0.000000e+00 5110.0
12 TraesCS2D01G055900 chr2A 89.128 3440 194 76 686 4074 24128235 24131545 0.000000e+00 4115.0
13 TraesCS2D01G055900 chr2A 83.083 1200 157 30 2803 3985 24132124 24133294 0.000000e+00 1050.0
14 TraesCS2D01G055900 chr2A 81.948 1263 148 32 4729 5949 24130296 24131520 0.000000e+00 996.0
15 TraesCS2D01G055900 chr2A 78.223 1621 295 44 5799 7382 23804758 23806357 0.000000e+00 985.0
16 TraesCS2D01G055900 chr2A 80.979 878 110 22 997 1850 23803103 23803947 1.950000e-180 643.0
17 TraesCS2D01G055900 chr2A 94.118 289 17 0 4112 4400 24131549 24131837 2.750000e-119 440.0
18 TraesCS2D01G055900 chr2A 83.471 242 11 6 4110 4345 24129719 24129937 1.830000e-46 198.0
19 TraesCS2D01G055900 chr2A 86.139 101 11 2 2688 2788 539973484 539973581 1.140000e-18 106.0
20 TraesCS2D01G055900 chr2A 100.000 40 0 0 726 765 578163301 578163262 3.210000e-09 75.0
21 TraesCS2D01G055900 chrUn 94.096 2490 107 20 796 3257 16951142 16953619 0.000000e+00 3747.0
22 TraesCS2D01G055900 chrUn 94.096 2490 107 20 796 3257 266455388 266457865 0.000000e+00 3747.0
23 TraesCS2D01G055900 chrUn 96.038 1994 68 7 4618 6609 360308869 360306885 0.000000e+00 3234.0
24 TraesCS2D01G055900 chrUn 93.121 1352 63 16 796 2124 282234149 282232805 0.000000e+00 1954.0
25 TraesCS2D01G055900 chrUn 94.207 984 31 6 3255 4221 16953991 16954965 0.000000e+00 1478.0
26 TraesCS2D01G055900 chrUn 94.207 984 31 6 3255 4221 266458237 266459211 0.000000e+00 1478.0
27 TraesCS2D01G055900 chrUn 82.919 1247 167 27 2816 4050 360308756 360307544 0.000000e+00 1081.0
28 TraesCS2D01G055900 chrUn 95.445 483 19 1 6967 7449 428228220 428228699 0.000000e+00 767.0
29 TraesCS2D01G055900 chrUn 95.445 483 19 1 6967 7449 464457278 464457757 0.000000e+00 767.0
30 TraesCS2D01G055900 chrUn 86.343 659 77 9 1 658 16948976 16949622 0.000000e+00 706.0
31 TraesCS2D01G055900 chrUn 86.343 659 77 9 1 658 266453222 266453868 0.000000e+00 706.0
32 TraesCS2D01G055900 chrUn 86.343 659 77 9 1 658 282236315 282235669 0.000000e+00 706.0
33 TraesCS2D01G055900 chrUn 82.619 817 100 26 5161 5949 16953991 16954793 0.000000e+00 684.0
34 TraesCS2D01G055900 chrUn 82.619 817 100 26 5161 5949 266458237 266459039 0.000000e+00 684.0
35 TraesCS2D01G055900 chrUn 81.573 445 57 13 4731 5158 16953175 16953611 2.220000e-90 344.0
36 TraesCS2D01G055900 chrUn 81.573 445 57 13 4731 5158 266457421 266457857 2.220000e-90 344.0
37 TraesCS2D01G055900 chrUn 92.672 232 14 2 4385 4616 16955033 16955261 1.730000e-86 331.0
38 TraesCS2D01G055900 chrUn 92.672 232 14 2 4385 4616 266459279 266459507 1.730000e-86 331.0
39 TraesCS2D01G055900 chrUn 87.288 236 22 4 4110 4344 16952546 16952774 6.390000e-66 263.0
40 TraesCS2D01G055900 chrUn 86.864 236 23 4 4110 4344 266456792 266457020 2.970000e-64 257.0
41 TraesCS2D01G055900 chrUn 83.273 275 35 6 4456 4723 16952776 16953046 8.320000e-60 243.0
42 TraesCS2D01G055900 chrUn 83.273 275 35 6 4456 4723 266457022 266457292 8.320000e-60 243.0
43 TraesCS2D01G055900 chrUn 82.635 167 22 4 2413 2579 16955102 16955261 3.120000e-29 141.0
44 TraesCS2D01G055900 chrUn 82.635 167 22 4 2413 2579 266459348 266459507 3.120000e-29 141.0
45 TraesCS2D01G055900 chr2B 89.904 1882 169 13 5516 7387 39237972 39239842 0.000000e+00 2403.0
46 TraesCS2D01G055900 chr2B 81.276 956 116 29 924 1850 35030477 35029556 0.000000e+00 715.0
47 TraesCS2D01G055900 chr2B 85.809 451 51 10 3603 4049 39237963 39238404 4.540000e-127 466.0
48 TraesCS2D01G055900 chr2B 85.217 115 15 2 4954 5067 35029530 35029417 5.260000e-22 117.0
49 TraesCS2D01G055900 chr2B 86.000 100 9 3 2690 2789 583671756 583671850 1.470000e-17 102.0
50 TraesCS2D01G055900 chr2B 100.000 40 0 0 726 765 484608098 484608059 3.210000e-09 75.0
51 TraesCS2D01G055900 chr3D 98.864 88 1 0 8211 8298 520690758 520690671 3.100000e-34 158.0
52 TraesCS2D01G055900 chr3D 100.000 30 0 0 7855 7884 268070416 268070445 1.000000e-03 56.5
53 TraesCS2D01G055900 chr7D 97.701 87 2 0 8212 8298 541956188 541956274 5.190000e-32 150.0
54 TraesCS2D01G055900 chr7D 97.674 86 2 0 8213 8298 70726790 70726705 1.870000e-31 148.0
55 TraesCS2D01G055900 chr7D 89.231 65 4 3 726 787 478909849 478909785 2.480000e-10 78.7
56 TraesCS2D01G055900 chr7A 95.402 87 4 0 8212 8298 5776071 5775985 1.120000e-28 139.0
57 TraesCS2D01G055900 chr6D 89.899 99 8 1 2690 2788 32649683 32649779 8.740000e-25 126.0
58 TraesCS2D01G055900 chr1B 87.500 104 7 4 2687 2788 268582905 268583004 1.890000e-21 115.0
59 TraesCS2D01G055900 chr6A 87.879 99 9 2 2690 2788 37058739 37058834 6.810000e-21 113.0
60 TraesCS2D01G055900 chr6A 93.478 46 3 0 724 769 559170137 559170092 1.490000e-07 69.4
61 TraesCS2D01G055900 chr6A 84.211 57 6 2 7827 7883 617662491 617662544 1.500000e-02 52.8
62 TraesCS2D01G055900 chr5A 85.849 106 14 1 2684 2788 71479865 71479970 2.450000e-20 111.0
63 TraesCS2D01G055900 chr5A 93.333 45 2 1 728 771 620406403 620406447 1.930000e-06 65.8
64 TraesCS2D01G055900 chr3A 87.500 96 8 2 2696 2790 497650511 497650419 3.170000e-19 108.0
65 TraesCS2D01G055900 chr3A 100.000 30 0 0 7855 7884 343228464 343228493 1.000000e-03 56.5
66 TraesCS2D01G055900 chr5D 100.000 40 0 0 726 765 278311335 278311374 3.210000e-09 75.0
67 TraesCS2D01G055900 chr6B 95.238 42 2 0 727 768 239309756 239309715 5.380000e-07 67.6
68 TraesCS2D01G055900 chr3B 100.000 30 0 0 7855 7884 292024719 292024690 1.000000e-03 56.5


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 TraesCS2D01G055900 chr2D 22418679 22426976 8297 False 15324.000000 15324 100.000000 1 8298 1 chr2D.!!$F1 8297
1 TraesCS2D01G055900 chr2D 22420862 22424627 3765 False 549.000000 1162 84.401000 2184 5949 6 chr2D.!!$F3 3765
2 TraesCS2D01G055900 chr2D 21607679 21608720 1041 False 432.500000 763 83.462000 925 5064 2 chr2D.!!$F2 4139
3 TraesCS2D01G055900 chr2A 24128235 24135613 7378 False 1984.833333 5110 87.155500 686 8206 6 chr2A.!!$F3 7520
4 TraesCS2D01G055900 chr2A 23803103 23806357 3254 False 814.000000 985 79.601000 997 7382 2 chr2A.!!$F2 6385
5 TraesCS2D01G055900 chrUn 360306885 360308869 1984 True 2157.500000 3234 89.478500 2816 6609 2 chrUn.!!$R2 3793
6 TraesCS2D01G055900 chrUn 282232805 282236315 3510 True 1330.000000 1954 89.732000 1 2124 2 chrUn.!!$R1 2123
7 TraesCS2D01G055900 chrUn 16948976 16955261 6285 False 881.888889 3747 87.189556 1 5949 9 chrUn.!!$F3 5948
8 TraesCS2D01G055900 chrUn 266453222 266459507 6285 False 881.222222 3747 87.142444 1 5949 9 chrUn.!!$F4 5948
9 TraesCS2D01G055900 chr2B 39237963 39239842 1879 False 1434.500000 2403 87.856500 3603 7387 2 chr2B.!!$F2 3784
10 TraesCS2D01G055900 chr2B 35029417 35030477 1060 True 416.000000 715 83.246500 924 5067 2 chr2B.!!$R2 4143

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
398 400 0.034089 GATGTGGGGAAGGTCAAGGG 60.034 60.000 0.0 0.0 0.00 3.95 F
434 436 0.107017 CCGGCAGATGAAGATGGGTT 60.107 55.000 0.0 0.0 0.00 4.11 F
1130 2564 0.175989 GACTTCACTGTCCCGATCCC 59.824 60.000 0.0 0.0 0.00 3.85 F
1332 2766 0.687354 AAGACAGCAACAGGACGGAT 59.313 50.000 0.0 0.0 0.00 4.18 F
1338 2772 1.628846 AGCAACAGGACGGATAACCTT 59.371 47.619 0.0 0.0 33.91 3.50 F
6586 8544 1.517257 CGTCAGCGACCATCTCCAC 60.517 63.158 0.0 0.0 41.33 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 2859 0.178992 TGTTGGGGTTGCTGAAGAGG 60.179 55.000 0.00 0.00 0.00 3.69 R
1644 3099 1.191489 TCATCACCTTGGACTCGGCA 61.191 55.000 0.00 0.00 0.00 5.69 R
6029 7976 3.304911 TCACCCACATTTTTGTCTCCA 57.695 42.857 0.00 0.00 0.00 3.86 R
6312 8270 3.526931 TCCTATCTTGCGAGAAGTTGG 57.473 47.619 7.99 7.98 35.07 3.77 R
6643 8604 1.379710 AATGGCGGCTGCAATACCA 60.380 52.632 21.31 7.95 45.35 3.25 R
8261 10242 0.108804 GATCCCAAGCGACGAACAGA 60.109 55.000 0.00 0.00 0.00 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
58 59 5.420409 ACTCATTGTTAAAGAGTCGATCCC 58.580 41.667 0.00 0.00 38.13 3.85
85 86 5.359194 TGGGAATTTCTAGTGAGGTGATC 57.641 43.478 0.00 0.00 0.00 2.92
87 88 5.488919 TGGGAATTTCTAGTGAGGTGATCTT 59.511 40.000 0.00 0.00 0.00 2.40
92 93 8.558973 AATTTCTAGTGAGGTGATCTTGAAAG 57.441 34.615 0.00 0.00 36.80 2.62
96 97 8.231692 TCTAGTGAGGTGATCTTGAAAGATAG 57.768 38.462 5.55 0.00 45.39 2.08
147 149 6.821665 CGAGGGGTATACTTTTCATTTTCAGA 59.178 38.462 2.25 0.00 0.00 3.27
167 169 7.155655 TCAGATTTGCTAAACATAATGTGCA 57.844 32.000 0.00 0.00 0.00 4.57
172 174 8.951787 ATTTGCTAAACATAATGTGCATGAAT 57.048 26.923 0.00 0.00 29.00 2.57
173 175 8.774890 TTTGCTAAACATAATGTGCATGAATT 57.225 26.923 0.00 0.00 29.00 2.17
215 217 1.668294 CACTGAGGCTGAAGACGGT 59.332 57.895 0.00 0.00 0.00 4.83
217 219 0.827925 ACTGAGGCTGAAGACGGTGA 60.828 55.000 0.00 0.00 0.00 4.02
219 221 0.827925 TGAGGCTGAAGACGGTGACT 60.828 55.000 0.00 0.00 0.00 3.41
242 244 4.704103 AGGAGCCCAGCGGTGAGA 62.704 66.667 17.83 0.00 0.00 3.27
260 262 1.353694 AGAATCAACTCTGGCAAGGCT 59.646 47.619 0.00 0.00 0.00 4.58
286 288 4.361971 ACCTCGCTGGAGACGGGA 62.362 66.667 1.32 0.00 43.27 5.14
301 303 2.551270 GGAACGACACTGCAAGCG 59.449 61.111 0.00 0.00 37.60 4.68
302 304 1.954146 GGAACGACACTGCAAGCGA 60.954 57.895 0.00 0.00 37.60 4.93
310 312 1.141881 ACTGCAAGCGATAGGGACG 59.858 57.895 0.00 0.00 37.60 4.79
311 313 1.592669 CTGCAAGCGATAGGGACGG 60.593 63.158 0.00 0.00 0.00 4.79
313 315 1.300233 GCAAGCGATAGGGACGGAG 60.300 63.158 0.00 0.00 0.00 4.63
326 328 3.522731 CGGAGGCGAGGAGGTCAG 61.523 72.222 0.00 0.00 0.00 3.51
366 368 2.924421 CTTAGAGGGATGGCCTTTGAC 58.076 52.381 3.32 0.00 0.00 3.18
367 369 0.830648 TAGAGGGATGGCCTTTGACG 59.169 55.000 3.32 0.00 0.00 4.35
375 377 4.404654 GCCTTTGACGGCGGCAAG 62.405 66.667 28.59 18.95 43.25 4.01
388 390 2.356278 GCAAGCAGGATGTGGGGA 59.644 61.111 0.00 0.00 39.31 4.81
398 400 0.034089 GATGTGGGGAAGGTCAAGGG 60.034 60.000 0.00 0.00 0.00 3.95
407 409 1.142688 AAGGTCAAGGGGAGCATGGT 61.143 55.000 0.00 0.00 46.51 3.55
426 428 4.161295 CGGAGGCCGGCAGATGAA 62.161 66.667 30.85 0.00 44.15 2.57
434 436 0.107017 CCGGCAGATGAAGATGGGTT 60.107 55.000 0.00 0.00 0.00 4.11
437 439 1.064463 GGCAGATGAAGATGGGTTGGA 60.064 52.381 0.00 0.00 0.00 3.53
448 450 3.365265 GGTTGGAAGGCGGCACAG 61.365 66.667 13.08 0.00 0.00 3.66
449 451 4.043200 GTTGGAAGGCGGCACAGC 62.043 66.667 13.08 5.57 0.00 4.40
454 456 2.749044 AAGGCGGCACAGCATGAG 60.749 61.111 13.08 0.00 39.69 2.90
456 458 4.783621 GGCGGCACAGCATGAGGA 62.784 66.667 3.07 0.00 39.69 3.71
470 472 2.559698 TGAGGAAAATCGTGCAAGGA 57.440 45.000 0.00 0.00 33.98 3.36
471 473 2.857483 TGAGGAAAATCGTGCAAGGAA 58.143 42.857 0.00 0.00 32.76 3.36
474 476 4.280677 TGAGGAAAATCGTGCAAGGAAAAT 59.719 37.500 0.00 0.00 32.76 1.82
475 477 5.475220 TGAGGAAAATCGTGCAAGGAAAATA 59.525 36.000 0.00 0.00 32.76 1.40
479 481 8.527810 AGGAAAATCGTGCAAGGAAAATATAAA 58.472 29.630 0.00 0.00 32.76 1.40
487 489 8.137437 CGTGCAAGGAAAATATAAATGGAGATT 58.863 33.333 0.00 0.00 0.00 2.40
505 507 5.046910 AGATTGAATTAACAGTTGCCACG 57.953 39.130 0.00 0.00 0.00 4.94
518 520 4.498520 CCACGCGATCTCAGCCGT 62.499 66.667 15.93 0.00 0.00 5.68
589 591 3.643320 TCAGGTACCTGATGAATAGGCTG 59.357 47.826 35.91 11.20 46.80 4.85
591 593 3.643792 AGGTACCTGATGAATAGGCTGTC 59.356 47.826 15.42 0.00 38.96 3.51
592 594 3.244249 GGTACCTGATGAATAGGCTGTCC 60.244 52.174 4.06 0.00 38.96 4.02
593 595 2.769209 ACCTGATGAATAGGCTGTCCT 58.231 47.619 0.00 0.00 46.57 3.85
594 596 3.118531 ACCTGATGAATAGGCTGTCCTT 58.881 45.455 0.00 0.00 40.66 3.36
595 597 3.525199 ACCTGATGAATAGGCTGTCCTTT 59.475 43.478 0.00 0.00 40.66 3.11
596 598 4.018050 ACCTGATGAATAGGCTGTCCTTTT 60.018 41.667 0.00 0.00 40.66 2.27
597 599 4.952335 CCTGATGAATAGGCTGTCCTTTTT 59.048 41.667 0.00 0.00 40.66 1.94
598 600 6.122277 CCTGATGAATAGGCTGTCCTTTTTA 58.878 40.000 0.00 0.00 40.66 1.52
599 601 6.774656 CCTGATGAATAGGCTGTCCTTTTTAT 59.225 38.462 0.00 0.00 40.66 1.40
613 615 6.183360 TGTCCTTTTTATTTTGGGTGTGTCTC 60.183 38.462 0.00 0.00 0.00 3.36
637 639 9.554724 CTCGCTCTCATCTAGATAAGAAATAAC 57.445 37.037 7.03 0.00 37.89 1.89
639 641 9.340695 CGCTCTCATCTAGATAAGAAATAACTG 57.659 37.037 7.03 0.00 37.89 3.16
650 652 7.861372 AGATAAGAAATAACTGTGTATCGTCCG 59.139 37.037 0.00 0.00 0.00 4.79
653 655 6.855836 AGAAATAACTGTGTATCGTCCGTTA 58.144 36.000 0.00 0.00 0.00 3.18
658 660 4.918037 ACTGTGTATCGTCCGTTAGATTC 58.082 43.478 0.00 0.00 0.00 2.52
659 661 4.639310 ACTGTGTATCGTCCGTTAGATTCT 59.361 41.667 0.00 0.00 0.00 2.40
660 662 5.819379 ACTGTGTATCGTCCGTTAGATTCTA 59.181 40.000 0.00 0.00 0.00 2.10
663 665 5.906285 GTGTATCGTCCGTTAGATTCTACAC 59.094 44.000 0.00 0.00 32.73 2.90
668 670 4.436847 CGTCCGTTAGATTCTACACGAATG 59.563 45.833 20.29 9.53 42.31 2.67
672 674 6.034591 CCGTTAGATTCTACACGAATGTTCT 58.965 40.000 20.29 0.00 42.31 3.01
673 675 6.196724 CCGTTAGATTCTACACGAATGTTCTC 59.803 42.308 20.29 0.00 42.31 2.87
674 676 6.745907 CGTTAGATTCTACACGAATGTTCTCA 59.254 38.462 16.57 0.00 42.31 3.27
677 679 7.392494 AGATTCTACACGAATGTTCTCAGTA 57.608 36.000 0.00 0.00 42.31 2.74
680 682 7.812309 TTCTACACGAATGTTCTCAGTAATG 57.188 36.000 0.00 0.00 40.48 1.90
683 685 6.467723 ACACGAATGTTCTCAGTAATGTTC 57.532 37.500 0.00 0.00 34.46 3.18
880 2269 4.044317 TGTCTCTAGGGTCTTAGTCCACTT 59.956 45.833 0.00 0.00 0.00 3.16
962 2352 2.864946 GCTGACATGTGCTGATCACTAG 59.135 50.000 1.15 0.00 45.81 2.57
968 2358 1.410517 TGTGCTGATCACTAGCTAGCC 59.589 52.381 20.91 8.18 45.81 3.93
980 2370 3.982052 ACTAGCTAGCCTAACTCCCTCTA 59.018 47.826 20.91 0.00 0.00 2.43
987 2377 2.871453 CCTAACTCCCTCTAGCCTCTC 58.129 57.143 0.00 0.00 0.00 3.20
1126 2560 1.162698 CTACGACTTCACTGTCCCGA 58.837 55.000 0.00 0.00 33.70 5.14
1127 2561 1.743958 CTACGACTTCACTGTCCCGAT 59.256 52.381 0.00 0.00 33.70 4.18
1128 2562 0.526662 ACGACTTCACTGTCCCGATC 59.473 55.000 0.00 0.00 33.70 3.69
1129 2563 0.179134 CGACTTCACTGTCCCGATCC 60.179 60.000 0.00 0.00 33.70 3.36
1130 2564 0.175989 GACTTCACTGTCCCGATCCC 59.824 60.000 0.00 0.00 0.00 3.85
1131 2565 1.141881 CTTCACTGTCCCGATCCCG 59.858 63.158 0.00 0.00 0.00 5.14
1314 2748 2.813474 CGCTTCGCCATCGTCCAA 60.813 61.111 0.00 0.00 36.96 3.53
1332 2766 0.687354 AAGACAGCAACAGGACGGAT 59.313 50.000 0.00 0.00 0.00 4.18
1338 2772 1.628846 AGCAACAGGACGGATAACCTT 59.371 47.619 0.00 0.00 33.91 3.50
1749 3207 2.122167 GGATCTCAGGGACGACGCT 61.122 63.158 0.00 0.00 39.90 5.07
1928 3391 5.636543 GGTGTACCATTATATCAGCGGTAAC 59.363 44.000 0.00 0.00 34.13 2.50
2163 3631 4.323257 CGAACATTAACCAGTTAGGAGGGT 60.323 45.833 0.00 0.00 41.22 4.34
6029 7976 5.363562 TTGCTAACAGATCCATCTCACAT 57.636 39.130 0.00 0.00 34.22 3.21
6100 8047 2.614734 GCCGGTTTACTAGTGGCTCTTT 60.615 50.000 12.70 0.00 42.44 2.52
6586 8544 1.517257 CGTCAGCGACCATCTCCAC 60.517 63.158 0.00 0.00 41.33 4.02
6643 8604 4.202264 CCGCAGAGGTACAATATCCTTCTT 60.202 45.833 0.00 0.00 33.83 2.52
6649 8610 8.432805 CAGAGGTACAATATCCTTCTTGGTATT 58.567 37.037 0.00 0.00 37.07 1.89
6676 8637 2.084546 GCCATTGACTACCTCCACAAC 58.915 52.381 0.00 0.00 0.00 3.32
6682 8643 1.369692 CTACCTCCACAACGGTGCA 59.630 57.895 0.00 0.00 43.88 4.57
6730 8691 1.205460 ACCGGGACATAAAGCCCAGT 61.205 55.000 6.32 0.00 44.94 4.00
6781 8742 2.383527 GCTCGGCGACTTTGGACTG 61.384 63.158 4.99 0.00 0.00 3.51
6829 8790 0.614134 GGGGTACTCCTCGGACAACT 60.614 60.000 3.84 0.00 35.33 3.16
7019 8980 2.158957 ACGGAGTCTCACAGCAGAAAAA 60.159 45.455 1.47 0.00 29.74 1.94
7190 9151 1.741401 CACGAGCAATCTCCGGCAA 60.741 57.895 0.00 0.00 35.94 4.52
7294 9258 1.892474 GCAAGGGCAACATCTTTACCA 59.108 47.619 0.00 0.00 40.72 3.25
7395 9365 6.183360 GGCGTGTACAAGGTTATGTTAAGTAC 60.183 42.308 10.87 0.00 34.75 2.73
7412 9382 9.251440 TGTTAAGTACAATATCTCTAGTGTGGT 57.749 33.333 0.00 0.00 36.84 4.16
7431 9401 7.118680 AGTGTGGTAAATATTTTCGAATCACGT 59.881 33.333 5.91 0.00 43.13 4.49
7466 9436 6.567687 CACAATAGTGTTGTAACATTCCCA 57.432 37.500 4.81 0.00 41.59 4.37
7485 9455 3.634448 CCCAAAAACACCATGTCACTGTA 59.366 43.478 0.00 0.00 0.00 2.74
7519 9489 7.614974 ACTTCGTCTATTCTTAAAGTAGGGAGT 59.385 37.037 0.00 0.00 0.00 3.85
7561 9531 0.960861 AGAGGATGTCGAGTCGCACA 60.961 55.000 7.92 13.31 0.00 4.57
7599 9569 0.683504 AGGTACCCAGTGCCTACTCG 60.684 60.000 8.74 0.00 46.31 4.18
7602 9572 0.330604 TACCCAGTGCCTACTCGTCT 59.669 55.000 0.00 0.00 34.07 4.18
7628 9600 5.068215 TCTAGGGAGAGAGAAATACTGGG 57.932 47.826 0.00 0.00 0.00 4.45
7636 9608 4.971924 AGAGAGAAATACTGGGCTGGTATT 59.028 41.667 8.85 8.85 40.31 1.89
7672 9644 5.491323 TTGTGTATATTGTGTCTGGGACA 57.509 39.130 0.00 0.00 40.50 4.02
7703 9684 8.966155 TGTGGGGATATATTGTGTATAGAAGA 57.034 34.615 0.00 0.00 0.00 2.87
7722 9703 4.170468 AGATGGGCATAGGGTGTAAAAG 57.830 45.455 0.00 0.00 0.00 2.27
7741 9722 5.949233 AAAGTAGAAAGCAAAAACAAGCG 57.051 34.783 0.00 0.00 35.48 4.68
7747 9728 0.104671 AGCAAAAACAAGCGTGCCAT 59.895 45.000 0.00 0.00 37.73 4.40
7751 9732 1.569708 AAAACAAGCGTGCCATGTTG 58.430 45.000 12.53 2.94 37.36 3.33
7755 9736 0.179156 CAAGCGTGCCATGTTGGATC 60.179 55.000 0.00 0.00 40.96 3.36
7768 9749 6.183360 GCCATGTTGGATCTTCAATGGATTTA 60.183 38.462 16.96 0.00 40.96 1.40
7906 9887 8.523523 TGAAATTTTAGAAGTGTTCATGCATG 57.476 30.769 21.07 21.07 0.00 4.06
7966 9947 9.195411 TGCATTTTCTCATGTTGTATTTTCTTC 57.805 29.630 0.00 0.00 0.00 2.87
7967 9948 8.368126 GCATTTTCTCATGTTGTATTTTCTTCG 58.632 33.333 0.00 0.00 0.00 3.79
8036 10017 1.856920 ACCCTGGGAGGAACAGAAAAA 59.143 47.619 22.23 0.00 37.67 1.94
8080 10061 6.925610 TGCAGTCATAATACCTCACAATTC 57.074 37.500 0.00 0.00 0.00 2.17
8098 10079 5.065859 ACAATTCATCGTCACAAAGTCAACA 59.934 36.000 0.00 0.00 0.00 3.33
8209 10190 7.931015 ATGTATATGTCTAGGACAAAAGGGA 57.069 36.000 4.46 0.00 45.96 4.20
8210 10191 7.120923 TGTATATGTCTAGGACAAAAGGGAC 57.879 40.000 4.46 0.00 45.96 4.46
8211 10192 3.611766 ATGTCTAGGACAAAAGGGACG 57.388 47.619 4.46 0.00 45.96 4.79
8212 10193 1.621814 TGTCTAGGACAAAAGGGACGG 59.378 52.381 0.00 0.00 39.78 4.79
8213 10194 1.897802 GTCTAGGACAAAAGGGACGGA 59.102 52.381 0.00 0.00 32.09 4.69
8214 10195 1.897802 TCTAGGACAAAAGGGACGGAC 59.102 52.381 0.00 0.00 0.00 4.79
8215 10196 0.604578 TAGGACAAAAGGGACGGACG 59.395 55.000 0.00 0.00 0.00 4.79
8216 10197 2.322830 GGACAAAAGGGACGGACGC 61.323 63.158 0.00 0.00 0.00 5.19
8217 10198 2.663852 ACAAAAGGGACGGACGCG 60.664 61.111 3.53 3.53 36.53 6.01
8218 10199 2.663852 CAAAAGGGACGGACGCGT 60.664 61.111 13.85 13.85 36.53 6.01
8219 10200 2.356673 AAAAGGGACGGACGCGTC 60.357 61.111 30.67 30.67 38.09 5.19
8220 10201 4.712425 AAAGGGACGGACGCGTCG 62.712 66.667 30.99 26.50 39.56 5.12
8223 10204 4.487412 GGGACGGACGCGTCGATT 62.487 66.667 30.99 18.37 39.56 3.34
8224 10205 2.505557 GGACGGACGCGTCGATTT 60.506 61.111 30.99 15.82 39.56 2.17
8225 10206 2.687436 GACGGACGCGTCGATTTG 59.313 61.111 30.99 19.82 0.00 2.32
8226 10207 2.785105 GACGGACGCGTCGATTTGG 61.785 63.158 30.99 17.69 0.00 3.28
8227 10208 2.807895 CGGACGCGTCGATTTGGT 60.808 61.111 30.99 0.00 0.00 3.67
8228 10209 2.776072 GGACGCGTCGATTTGGTG 59.224 61.111 30.99 0.00 0.00 4.17
8229 10210 2.095843 GACGCGTCGATTTGGTGC 59.904 61.111 25.19 0.00 0.00 5.01
8230 10211 3.362851 GACGCGTCGATTTGGTGCC 62.363 63.158 25.19 0.00 0.00 5.01
8231 10212 4.160635 CGCGTCGATTTGGTGCCC 62.161 66.667 0.00 0.00 0.00 5.36
8232 10213 4.160635 GCGTCGATTTGGTGCCCG 62.161 66.667 0.00 0.00 0.00 6.13
8233 10214 2.433491 CGTCGATTTGGTGCCCGA 60.433 61.111 0.00 0.00 0.00 5.14
8234 10215 2.452813 CGTCGATTTGGTGCCCGAG 61.453 63.158 0.00 0.00 0.00 4.63
8235 10216 2.435938 TCGATTTGGTGCCCGAGC 60.436 61.111 0.00 0.00 40.48 5.03
8236 10217 3.508840 CGATTTGGTGCCCGAGCC 61.509 66.667 0.00 0.00 38.69 4.70
8237 10218 3.140814 GATTTGGTGCCCGAGCCC 61.141 66.667 0.00 0.00 38.69 5.19
8238 10219 3.936772 GATTTGGTGCCCGAGCCCA 62.937 63.158 0.00 0.00 37.50 5.36
8239 10220 3.944250 ATTTGGTGCCCGAGCCCAG 62.944 63.158 0.00 0.00 39.52 4.45
8249 10230 4.025858 GAGCCCAGCTGCACCTGA 62.026 66.667 8.66 0.00 39.88 3.86
8250 10231 3.557903 GAGCCCAGCTGCACCTGAA 62.558 63.158 8.66 0.00 39.88 3.02
8251 10232 2.598394 GCCCAGCTGCACCTGAAA 60.598 61.111 8.66 0.00 34.77 2.69
8252 10233 1.980772 GCCCAGCTGCACCTGAAAT 60.981 57.895 8.66 0.00 34.77 2.17
8253 10234 1.941999 GCCCAGCTGCACCTGAAATC 61.942 60.000 8.66 0.00 34.77 2.17
8254 10235 1.651240 CCCAGCTGCACCTGAAATCG 61.651 60.000 8.66 0.00 34.77 3.34
8255 10236 0.957395 CCAGCTGCACCTGAAATCGT 60.957 55.000 8.66 0.00 34.77 3.73
8256 10237 0.167470 CAGCTGCACCTGAAATCGTG 59.833 55.000 0.00 0.00 34.77 4.35
8257 10238 0.957395 AGCTGCACCTGAAATCGTGG 60.957 55.000 1.02 0.00 0.00 4.94
8258 10239 1.926511 GCTGCACCTGAAATCGTGGG 61.927 60.000 0.00 0.00 0.00 4.61
8259 10240 1.926511 CTGCACCTGAAATCGTGGGC 61.927 60.000 0.00 0.00 0.00 5.36
8260 10241 3.039202 GCACCTGAAATCGTGGGCG 62.039 63.158 0.00 0.00 39.92 6.13
8261 10242 1.671054 CACCTGAAATCGTGGGCGT 60.671 57.895 0.00 0.00 39.49 5.68
8262 10243 1.375523 ACCTGAAATCGTGGGCGTC 60.376 57.895 0.00 0.00 39.49 5.19
8263 10244 1.079127 CCTGAAATCGTGGGCGTCT 60.079 57.895 0.00 0.00 39.49 4.18
8264 10245 1.361668 CCTGAAATCGTGGGCGTCTG 61.362 60.000 0.00 0.00 39.49 3.51
8265 10246 0.670546 CTGAAATCGTGGGCGTCTGT 60.671 55.000 0.00 0.00 39.49 3.41
8266 10247 0.250124 TGAAATCGTGGGCGTCTGTT 60.250 50.000 0.00 0.00 39.49 3.16
8267 10248 0.442699 GAAATCGTGGGCGTCTGTTC 59.557 55.000 0.00 0.00 39.49 3.18
8268 10249 1.289109 AAATCGTGGGCGTCTGTTCG 61.289 55.000 0.00 0.00 39.49 3.95
8269 10250 2.430382 AATCGTGGGCGTCTGTTCGT 62.430 55.000 0.00 0.00 39.49 3.85
8270 10251 2.814183 ATCGTGGGCGTCTGTTCGTC 62.814 60.000 0.00 0.00 39.49 4.20
8271 10252 3.103911 GTGGGCGTCTGTTCGTCG 61.104 66.667 0.00 0.00 36.22 5.12
8273 10254 4.719369 GGGCGTCTGTTCGTCGCT 62.719 66.667 8.53 0.00 46.78 4.93
8274 10255 2.733593 GGCGTCTGTTCGTCGCTT 60.734 61.111 8.53 0.00 46.78 4.68
8275 10256 2.465920 GCGTCTGTTCGTCGCTTG 59.534 61.111 0.00 0.00 44.75 4.01
8276 10257 3.000080 GCGTCTGTTCGTCGCTTGG 62.000 63.158 0.00 0.00 44.75 3.61
8277 10258 2.372690 CGTCTGTTCGTCGCTTGGG 61.373 63.158 0.00 0.00 0.00 4.12
8278 10259 1.006571 GTCTGTTCGTCGCTTGGGA 60.007 57.895 0.00 0.00 0.00 4.37
8279 10260 0.389948 GTCTGTTCGTCGCTTGGGAT 60.390 55.000 0.00 0.00 0.00 3.85
8280 10261 0.108804 TCTGTTCGTCGCTTGGGATC 60.109 55.000 0.00 0.00 0.00 3.36
8281 10262 1.079405 TGTTCGTCGCTTGGGATCC 60.079 57.895 1.92 1.92 0.00 3.36
8282 10263 2.165301 GTTCGTCGCTTGGGATCCG 61.165 63.158 5.45 0.00 0.00 4.18
8283 10264 2.642254 TTCGTCGCTTGGGATCCGT 61.642 57.895 5.45 0.00 0.00 4.69
8284 10265 2.829043 TTCGTCGCTTGGGATCCGTG 62.829 60.000 5.45 0.00 0.00 4.94
8285 10266 2.577059 GTCGCTTGGGATCCGTGA 59.423 61.111 5.45 1.16 0.00 4.35
8286 10267 1.079405 GTCGCTTGGGATCCGTGAA 60.079 57.895 5.45 0.00 0.00 3.18
8287 10268 0.672401 GTCGCTTGGGATCCGTGAAA 60.672 55.000 5.45 0.00 0.00 2.69
8288 10269 0.251916 TCGCTTGGGATCCGTGAAAT 59.748 50.000 5.45 0.00 0.00 2.17
8289 10270 1.094785 CGCTTGGGATCCGTGAAATT 58.905 50.000 5.45 0.00 0.00 1.82
8290 10271 1.202177 CGCTTGGGATCCGTGAAATTG 60.202 52.381 5.45 0.00 0.00 2.32
8291 10272 1.134946 GCTTGGGATCCGTGAAATTGG 59.865 52.381 5.45 0.00 0.00 3.16
8292 10273 1.134946 CTTGGGATCCGTGAAATTGGC 59.865 52.381 5.45 0.00 0.00 4.52
8293 10274 0.331278 TGGGATCCGTGAAATTGGCT 59.669 50.000 5.45 0.00 0.00 4.75
8294 10275 1.272425 TGGGATCCGTGAAATTGGCTT 60.272 47.619 5.45 0.00 0.00 4.35
8295 10276 1.824852 GGGATCCGTGAAATTGGCTTT 59.175 47.619 5.45 0.00 0.00 3.51
8296 10277 2.417243 GGGATCCGTGAAATTGGCTTTG 60.417 50.000 5.45 0.00 0.00 2.77
8297 10278 2.491693 GGATCCGTGAAATTGGCTTTGA 59.508 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.046938 ACAATGAGTAGCATGTCGGTAG 57.953 45.455 0.00 0.00 37.28 3.18
58 59 6.434028 TCACCTCACTAGAAATTCCCATTTTG 59.566 38.462 0.00 0.00 32.35 2.44
67 68 8.378565 TCTTTCAAGATCACCTCACTAGAAATT 58.621 33.333 0.00 0.00 0.00 1.82
73 74 6.897966 ACCTATCTTTCAAGATCACCTCACTA 59.102 38.462 5.29 0.00 44.30 2.74
75 76 5.814705 CACCTATCTTTCAAGATCACCTCAC 59.185 44.000 5.29 0.00 44.30 3.51
85 86 7.930325 TCATGATAGCTTCACCTATCTTTCAAG 59.070 37.037 0.00 0.00 42.59 3.02
87 88 7.147672 TGTCATGATAGCTTCACCTATCTTTCA 60.148 37.037 0.00 0.00 42.59 2.69
92 93 5.350914 GCATGTCATGATAGCTTCACCTATC 59.649 44.000 17.24 2.97 42.50 2.08
96 97 2.551459 GGCATGTCATGATAGCTTCACC 59.449 50.000 17.24 1.05 37.11 4.02
147 149 8.951787 ATTCATGCACATTATGTTTAGCAAAT 57.048 26.923 11.78 6.59 31.96 2.32
215 217 0.965866 CTGGGCTCCTCACGTAGTCA 60.966 60.000 0.00 0.00 41.61 3.41
219 221 3.449227 CGCTGGGCTCCTCACGTA 61.449 66.667 0.00 0.00 0.00 3.57
242 244 1.074405 TCAGCCTTGCCAGAGTTGATT 59.926 47.619 0.00 0.00 0.00 2.57
260 262 3.385384 CAGCGAGGTCCTGGCTCA 61.385 66.667 24.32 0.00 43.31 4.26
273 275 3.744719 TCGTTCCCGTCTCCAGCG 61.745 66.667 0.00 0.00 35.01 5.18
286 288 1.350193 CTATCGCTTGCAGTGTCGTT 58.650 50.000 0.00 0.00 0.00 3.85
289 291 0.175760 TCCCTATCGCTTGCAGTGTC 59.824 55.000 0.00 0.00 0.00 3.67
301 303 2.269529 CCTCGCCTCCGTCCCTATC 61.270 68.421 0.00 0.00 35.54 2.08
302 304 2.203509 CCTCGCCTCCGTCCCTAT 60.204 66.667 0.00 0.00 35.54 2.57
310 312 3.151022 CCTGACCTCCTCGCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
311 313 3.151022 CCCTGACCTCCTCGCCTC 61.151 72.222 0.00 0.00 0.00 4.70
367 369 3.818787 CACATCCTGCTTGCCGCC 61.819 66.667 0.00 0.00 38.05 6.13
375 377 1.077429 GACCTTCCCCACATCCTGC 60.077 63.158 0.00 0.00 0.00 4.85
378 380 0.034089 CCTTGACCTTCCCCACATCC 60.034 60.000 0.00 0.00 0.00 3.51
380 382 1.509548 CCCCTTGACCTTCCCCACAT 61.510 60.000 0.00 0.00 0.00 3.21
381 383 2.160171 CCCCTTGACCTTCCCCACA 61.160 63.158 0.00 0.00 0.00 4.17
388 390 1.142688 ACCATGCTCCCCTTGACCTT 61.143 55.000 0.00 0.00 0.00 3.50
410 412 2.049627 ATCTTCATCTGCCGGCCTCC 62.050 60.000 26.77 0.00 0.00 4.30
413 415 1.895707 CCATCTTCATCTGCCGGCC 60.896 63.158 26.77 6.44 0.00 6.13
425 427 1.000896 CCGCCTTCCAACCCATCTT 60.001 57.895 0.00 0.00 0.00 2.40
426 428 2.677228 CCGCCTTCCAACCCATCT 59.323 61.111 0.00 0.00 0.00 2.90
434 436 4.349503 ATGCTGTGCCGCCTTCCA 62.350 61.111 0.00 0.00 0.00 3.53
437 439 2.749044 CTCATGCTGTGCCGCCTT 60.749 61.111 0.00 0.00 0.00 4.35
448 450 2.523015 CTTGCACGATTTTCCTCATGC 58.477 47.619 0.00 0.00 0.00 4.06
449 451 2.749076 TCCTTGCACGATTTTCCTCATG 59.251 45.455 0.00 0.00 0.00 3.07
454 456 8.696410 TTTATATTTTCCTTGCACGATTTTCC 57.304 30.769 0.00 0.00 0.00 3.13
456 458 9.097257 CCATTTATATTTTCCTTGCACGATTTT 57.903 29.630 0.00 0.00 0.00 1.82
475 477 9.807649 GCAACTGTTAATTCAATCTCCATTTAT 57.192 29.630 0.00 0.00 0.00 1.40
479 481 5.716228 TGGCAACTGTTAATTCAATCTCCAT 59.284 36.000 0.00 0.00 37.61 3.41
487 489 1.069568 CGCGTGGCAACTGTTAATTCA 60.070 47.619 0.00 0.00 37.61 2.57
491 493 0.793861 GATCGCGTGGCAACTGTTAA 59.206 50.000 5.77 0.00 37.61 2.01
497 499 3.084579 CTGAGATCGCGTGGCAAC 58.915 61.111 5.77 0.00 0.00 4.17
499 501 4.819761 GGCTGAGATCGCGTGGCA 62.820 66.667 5.77 0.00 0.00 4.92
505 507 1.227380 ATCCAACGGCTGAGATCGC 60.227 57.895 0.00 0.00 0.00 4.58
517 519 2.872858 GGCCGTTAGATCTTCATCCAAC 59.127 50.000 0.00 0.00 29.82 3.77
518 520 2.771943 AGGCCGTTAGATCTTCATCCAA 59.228 45.455 0.00 0.00 0.00 3.53
568 570 3.389329 ACAGCCTATTCATCAGGTACCTG 59.611 47.826 32.61 32.61 44.86 4.00
572 574 3.928754 AGGACAGCCTATTCATCAGGTA 58.071 45.455 0.00 0.00 44.74 3.08
574 576 3.853355 AAGGACAGCCTATTCATCAGG 57.147 47.619 0.00 0.00 46.28 3.86
575 577 7.814264 ATAAAAAGGACAGCCTATTCATCAG 57.186 36.000 0.00 0.00 46.28 2.90
577 579 9.305925 CAAAATAAAAAGGACAGCCTATTCATC 57.694 33.333 0.00 0.00 46.28 2.92
581 583 6.500400 ACCCAAAATAAAAAGGACAGCCTATT 59.500 34.615 0.00 0.00 46.28 1.73
582 584 6.022958 ACCCAAAATAAAAAGGACAGCCTAT 58.977 36.000 0.00 0.00 46.28 2.57
583 585 5.245075 CACCCAAAATAAAAAGGACAGCCTA 59.755 40.000 0.00 0.00 46.28 3.93
585 587 4.202315 ACACCCAAAATAAAAAGGACAGCC 60.202 41.667 0.00 0.00 0.00 4.85
586 588 4.749598 CACACCCAAAATAAAAAGGACAGC 59.250 41.667 0.00 0.00 0.00 4.40
587 589 5.912892 ACACACCCAAAATAAAAAGGACAG 58.087 37.500 0.00 0.00 0.00 3.51
589 591 6.156748 AGACACACCCAAAATAAAAAGGAC 57.843 37.500 0.00 0.00 0.00 3.85
591 593 5.219633 CGAGACACACCCAAAATAAAAAGG 58.780 41.667 0.00 0.00 0.00 3.11
592 594 4.679654 GCGAGACACACCCAAAATAAAAAG 59.320 41.667 0.00 0.00 0.00 2.27
593 595 4.339814 AGCGAGACACACCCAAAATAAAAA 59.660 37.500 0.00 0.00 0.00 1.94
594 596 3.886505 AGCGAGACACACCCAAAATAAAA 59.113 39.130 0.00 0.00 0.00 1.52
595 597 3.482436 AGCGAGACACACCCAAAATAAA 58.518 40.909 0.00 0.00 0.00 1.40
596 598 3.071479 GAGCGAGACACACCCAAAATAA 58.929 45.455 0.00 0.00 0.00 1.40
597 599 2.301870 AGAGCGAGACACACCCAAAATA 59.698 45.455 0.00 0.00 0.00 1.40
598 600 1.072331 AGAGCGAGACACACCCAAAAT 59.928 47.619 0.00 0.00 0.00 1.82
599 601 0.468226 AGAGCGAGACACACCCAAAA 59.532 50.000 0.00 0.00 0.00 2.44
613 615 9.340695 CAGTTATTTCTTATCTAGATGAGAGCG 57.659 37.037 22.23 7.84 37.70 5.03
637 639 5.171147 AGAATCTAACGGACGATACACAG 57.829 43.478 0.00 0.00 0.00 3.66
639 641 5.906285 GTGTAGAATCTAACGGACGATACAC 59.094 44.000 0.00 0.00 34.82 2.90
642 644 5.049828 TCGTGTAGAATCTAACGGACGATA 58.950 41.667 17.85 0.00 36.70 2.92
648 650 6.034591 AGAACATTCGTGTAGAATCTAACGG 58.965 40.000 17.85 9.64 45.95 4.44
650 652 7.755822 ACTGAGAACATTCGTGTAGAATCTAAC 59.244 37.037 0.00 0.00 45.95 2.34
653 655 6.274157 ACTGAGAACATTCGTGTAGAATCT 57.726 37.500 0.00 0.00 45.95 2.40
658 660 7.542477 AGAACATTACTGAGAACATTCGTGTAG 59.458 37.037 0.00 0.00 0.00 2.74
659 661 7.375834 AGAACATTACTGAGAACATTCGTGTA 58.624 34.615 0.00 0.00 0.00 2.90
660 662 6.223852 AGAACATTACTGAGAACATTCGTGT 58.776 36.000 0.00 0.00 0.00 4.49
663 665 8.689251 TCTAAGAACATTACTGAGAACATTCG 57.311 34.615 0.00 0.00 0.00 3.34
668 670 9.296400 GTCTCATCTAAGAACATTACTGAGAAC 57.704 37.037 0.00 0.00 39.46 3.01
672 674 9.645059 CAAAGTCTCATCTAAGAACATTACTGA 57.355 33.333 0.00 0.00 0.00 3.41
673 675 9.429359 ACAAAGTCTCATCTAAGAACATTACTG 57.571 33.333 0.00 0.00 0.00 2.74
710 752 3.132824 ACAAAGTCCCCTGCAAAAAGAAG 59.867 43.478 0.00 0.00 0.00 2.85
713 755 3.541996 AACAAAGTCCCCTGCAAAAAG 57.458 42.857 0.00 0.00 0.00 2.27
718 760 4.079253 GAGAATTAACAAAGTCCCCTGCA 58.921 43.478 0.00 0.00 0.00 4.41
719 761 4.079253 TGAGAATTAACAAAGTCCCCTGC 58.921 43.478 0.00 0.00 0.00 4.85
720 762 6.183347 AGATGAGAATTAACAAAGTCCCCTG 58.817 40.000 0.00 0.00 0.00 4.45
962 2352 1.890489 GCTAGAGGGAGTTAGGCTAGC 59.110 57.143 6.04 6.04 44.72 3.42
968 2358 2.445525 AGGAGAGGCTAGAGGGAGTTAG 59.554 54.545 0.00 0.00 0.00 2.34
980 2370 2.433994 GCTGCAGCTAGGAGAGGCT 61.434 63.158 31.33 0.00 38.04 4.58
987 2377 2.905880 GCCATGGCTGCAGCTAGG 60.906 66.667 35.82 31.54 41.70 3.02
1314 2748 1.557099 TATCCGTCCTGTTGCTGTCT 58.443 50.000 0.00 0.00 0.00 3.41
1332 2766 1.004679 GTCGCCCCGTGAAAGGTTA 60.005 57.895 0.00 0.00 0.00 2.85
1422 2859 0.178992 TGTTGGGGTTGCTGAAGAGG 60.179 55.000 0.00 0.00 0.00 3.69
1644 3099 1.191489 TCATCACCTTGGACTCGGCA 61.191 55.000 0.00 0.00 0.00 5.69
1749 3207 2.345991 GCGTCCTGTACAAGGCCA 59.654 61.111 5.01 0.00 46.92 5.36
1913 3376 3.322828 GGGGACAGTTACCGCTGATATAA 59.677 47.826 0.00 0.00 39.62 0.98
1928 3391 4.636435 AACGTTGGCCGGGGACAG 62.636 66.667 2.18 0.00 42.24 3.51
6029 7976 3.304911 TCACCCACATTTTTGTCTCCA 57.695 42.857 0.00 0.00 0.00 3.86
6312 8270 3.526931 TCCTATCTTGCGAGAAGTTGG 57.473 47.619 7.99 7.98 35.07 3.77
6643 8604 1.379710 AATGGCGGCTGCAATACCA 60.380 52.632 21.31 7.95 45.35 3.25
6649 8610 1.745115 GTAGTCAATGGCGGCTGCA 60.745 57.895 21.31 5.95 45.35 4.41
6676 8637 3.684305 TCTTTGTTGAGTCATATGCACCG 59.316 43.478 0.00 0.00 0.00 4.94
6682 8643 6.100004 CACGTACCTCTTTGTTGAGTCATAT 58.900 40.000 0.00 0.00 32.50 1.78
6730 8691 0.824109 CCTCTCCCAGCATCACGTTA 59.176 55.000 0.00 0.00 0.00 3.18
6781 8742 1.226888 GCGGATGACCTGTCGTACC 60.227 63.158 0.00 0.00 0.00 3.34
6808 8769 2.096707 TTGTCCGAGGAGTACCCCCA 62.097 60.000 4.90 0.00 36.73 4.96
6829 8790 1.496060 AGTCCATGCTCCCGATAACA 58.504 50.000 0.00 0.00 0.00 2.41
6964 8925 2.591715 GTGTTCCGGTGTGCTGCT 60.592 61.111 0.00 0.00 0.00 4.24
7190 9151 4.954826 AGTATCTTTCAGGTAACGGCTAGT 59.045 41.667 0.00 0.00 46.39 2.57
7292 9256 6.748333 ATTTCACAGACATGTTCACTATGG 57.252 37.500 0.00 0.00 37.65 2.74
7422 9392 3.168193 GCCCACAAATTAACGTGATTCG 58.832 45.455 0.00 0.00 46.00 3.34
7449 9419 6.103330 GTGTTTTTGGGAATGTTACAACACT 58.897 36.000 0.00 0.00 42.51 3.55
7450 9420 5.292345 GGTGTTTTTGGGAATGTTACAACAC 59.708 40.000 0.00 0.00 42.51 3.32
7451 9421 5.046591 TGGTGTTTTTGGGAATGTTACAACA 60.047 36.000 0.00 0.00 44.06 3.33
7463 9433 2.430332 ACAGTGACATGGTGTTTTTGGG 59.570 45.455 0.00 0.00 0.00 4.12
7466 9436 6.151985 TCAAAGTACAGTGACATGGTGTTTTT 59.848 34.615 0.00 0.00 0.00 1.94
7519 9489 6.821160 TCTCGGAAAAATACATCACAATAGCA 59.179 34.615 0.00 0.00 0.00 3.49
7548 9518 1.164041 TGTCTCTGTGCGACTCGACA 61.164 55.000 1.63 3.40 32.70 4.35
7555 9525 1.472878 GTATCAGGTGTCTCTGTGCGA 59.527 52.381 0.00 0.00 36.25 5.10
7561 9531 0.324368 TGCCCGTATCAGGTGTCTCT 60.324 55.000 0.00 0.00 0.00 3.10
7594 9564 5.643176 TCTCTCCCTAGATCTAGACGAGTA 58.357 45.833 28.04 19.15 35.21 2.59
7599 9569 8.603304 AGTATTTCTCTCTCCCTAGATCTAGAC 58.397 40.741 28.04 14.31 35.21 2.59
7602 9572 7.257235 CCCAGTATTTCTCTCTCCCTAGATCTA 60.257 44.444 1.69 1.69 0.00 1.98
7636 9608 9.448438 ACAATATACACAATTCTGCTGAAAGTA 57.552 29.630 10.27 10.73 35.63 2.24
7672 9644 4.665009 ACACAATATATCCCCACATGGAGT 59.335 41.667 0.00 0.00 37.96 3.85
7703 9684 4.724798 TCTACTTTTACACCCTATGCCCAT 59.275 41.667 0.00 0.00 0.00 4.00
7711 9692 7.093684 TGTTTTTGCTTTCTACTTTTACACCCT 60.094 33.333 0.00 0.00 0.00 4.34
7722 9703 3.061205 GCACGCTTGTTTTTGCTTTCTAC 60.061 43.478 0.00 0.00 32.00 2.59
7741 9722 3.429822 CCATTGAAGATCCAACATGGCAC 60.430 47.826 0.00 0.00 37.47 5.01
7889 9870 5.648178 AAATGCATGCATGAACACTTCTA 57.352 34.783 32.79 0.32 36.68 2.10
7938 9919 9.545105 AGAAAATACAACATGAGAAAATGCAAA 57.455 25.926 0.00 0.00 0.00 3.68
7939 9920 9.545105 AAGAAAATACAACATGAGAAAATGCAA 57.455 25.926 0.00 0.00 0.00 4.08
7940 9921 9.195411 GAAGAAAATACAACATGAGAAAATGCA 57.805 29.630 0.00 0.00 0.00 3.96
7941 9922 8.368126 CGAAGAAAATACAACATGAGAAAATGC 58.632 33.333 0.00 0.00 0.00 3.56
7942 9923 8.853345 CCGAAGAAAATACAACATGAGAAAATG 58.147 33.333 0.00 0.00 0.00 2.32
7943 9924 8.792633 TCCGAAGAAAATACAACATGAGAAAAT 58.207 29.630 0.00 0.00 0.00 1.82
7944 9925 8.160521 TCCGAAGAAAATACAACATGAGAAAA 57.839 30.769 0.00 0.00 0.00 2.29
7945 9926 7.737972 TCCGAAGAAAATACAACATGAGAAA 57.262 32.000 0.00 0.00 0.00 2.52
7946 9927 7.921786 ATCCGAAGAAAATACAACATGAGAA 57.078 32.000 0.00 0.00 0.00 2.87
7947 9928 7.921786 AATCCGAAGAAAATACAACATGAGA 57.078 32.000 0.00 0.00 0.00 3.27
7948 9929 9.869844 GATAATCCGAAGAAAATACAACATGAG 57.130 33.333 0.00 0.00 0.00 2.90
7949 9930 9.613428 AGATAATCCGAAGAAAATACAACATGA 57.387 29.630 0.00 0.00 0.00 3.07
7950 9931 9.869844 GAGATAATCCGAAGAAAATACAACATG 57.130 33.333 0.00 0.00 0.00 3.21
7966 9947 8.893727 ACTAAAATTTTGACCAGAGATAATCCG 58.106 33.333 13.76 0.00 0.00 4.18
8036 10017 2.775911 TTGCATGCTCTGTAGAAGCT 57.224 45.000 20.33 0.00 0.00 3.74
8080 10061 4.730042 CAGTTTGTTGACTTTGTGACGATG 59.270 41.667 0.00 0.00 0.00 3.84
8153 10134 8.370940 ACTGAGAACATAGTTTTCTCTGATGAA 58.629 33.333 19.66 0.00 46.29 2.57
8155 10136 9.645059 TTACTGAGAACATAGTTTTCTCTGATG 57.355 33.333 19.66 8.62 46.29 3.07
8201 10182 2.663852 ACGCGTCCGTCCCTTTTG 60.664 61.111 5.58 0.00 46.39 2.44
8210 10191 2.807895 ACCAAATCGACGCGTCCG 60.808 61.111 31.84 25.30 41.14 4.79
8211 10192 2.776072 CACCAAATCGACGCGTCC 59.224 61.111 31.84 15.31 0.00 4.79
8212 10193 2.095843 GCACCAAATCGACGCGTC 59.904 61.111 28.96 28.96 0.00 5.19
8213 10194 3.419759 GGCACCAAATCGACGCGT 61.420 61.111 13.85 13.85 0.00 6.01
8232 10213 3.557903 TTCAGGTGCAGCTGGGCTC 62.558 63.158 37.67 2.47 36.40 4.70
8233 10214 2.436596 ATTTCAGGTGCAGCTGGGCT 62.437 55.000 37.67 22.73 40.77 5.19
8234 10215 1.941999 GATTTCAGGTGCAGCTGGGC 61.942 60.000 37.67 23.24 0.00 5.36
8235 10216 1.651240 CGATTTCAGGTGCAGCTGGG 61.651 60.000 37.67 19.69 0.00 4.45
8236 10217 0.957395 ACGATTTCAGGTGCAGCTGG 60.957 55.000 37.67 26.04 0.00 4.85
8237 10218 0.167470 CACGATTTCAGGTGCAGCTG 59.833 55.000 34.65 34.65 0.00 4.24
8238 10219 0.957395 CCACGATTTCAGGTGCAGCT 60.957 55.000 13.85 13.85 32.85 4.24
8239 10220 1.503542 CCACGATTTCAGGTGCAGC 59.496 57.895 8.11 8.11 32.85 5.25
8240 10221 1.926511 GCCCACGATTTCAGGTGCAG 61.927 60.000 0.00 0.00 32.85 4.41
8241 10222 1.971167 GCCCACGATTTCAGGTGCA 60.971 57.895 0.00 0.00 32.85 4.57
8242 10223 2.877691 GCCCACGATTTCAGGTGC 59.122 61.111 0.00 0.00 32.85 5.01
8243 10224 1.635663 GACGCCCACGATTTCAGGTG 61.636 60.000 0.00 0.00 43.93 4.00
8244 10225 1.375523 GACGCCCACGATTTCAGGT 60.376 57.895 0.00 0.00 43.93 4.00
8245 10226 1.079127 AGACGCCCACGATTTCAGG 60.079 57.895 0.00 0.00 43.93 3.86
8246 10227 0.670546 ACAGACGCCCACGATTTCAG 60.671 55.000 0.00 0.00 43.93 3.02
8247 10228 0.250124 AACAGACGCCCACGATTTCA 60.250 50.000 0.00 0.00 43.93 2.69
8248 10229 0.442699 GAACAGACGCCCACGATTTC 59.557 55.000 0.00 0.00 43.93 2.17
8249 10230 1.289109 CGAACAGACGCCCACGATTT 61.289 55.000 0.00 0.00 43.93 2.17
8250 10231 1.736645 CGAACAGACGCCCACGATT 60.737 57.895 0.00 0.00 43.93 3.34
8251 10232 2.126071 CGAACAGACGCCCACGAT 60.126 61.111 0.00 0.00 43.93 3.73
8252 10233 3.547249 GACGAACAGACGCCCACGA 62.547 63.158 0.00 0.00 43.93 4.35
8254 10235 3.103911 CGACGAACAGACGCCCAC 61.104 66.667 0.00 0.00 36.70 4.61
8259 10240 2.372690 CCCAAGCGACGAACAGACG 61.373 63.158 0.00 0.00 40.76 4.18
8260 10241 0.389948 ATCCCAAGCGACGAACAGAC 60.390 55.000 0.00 0.00 0.00 3.51
8261 10242 0.108804 GATCCCAAGCGACGAACAGA 60.109 55.000 0.00 0.00 0.00 3.41
8262 10243 1.084370 GGATCCCAAGCGACGAACAG 61.084 60.000 0.00 0.00 0.00 3.16
8263 10244 1.079405 GGATCCCAAGCGACGAACA 60.079 57.895 0.00 0.00 0.00 3.18
8264 10245 2.165301 CGGATCCCAAGCGACGAAC 61.165 63.158 6.06 0.00 0.00 3.95
8265 10246 2.183300 CGGATCCCAAGCGACGAA 59.817 61.111 6.06 0.00 0.00 3.85
8266 10247 3.066190 ACGGATCCCAAGCGACGA 61.066 61.111 6.06 0.00 0.00 4.20
8267 10248 2.829043 TTCACGGATCCCAAGCGACG 62.829 60.000 6.06 0.00 0.00 5.12
8268 10249 0.672401 TTTCACGGATCCCAAGCGAC 60.672 55.000 6.06 0.00 0.00 5.19
8269 10250 0.251916 ATTTCACGGATCCCAAGCGA 59.748 50.000 6.06 0.00 0.00 4.93
8270 10251 1.094785 AATTTCACGGATCCCAAGCG 58.905 50.000 6.06 0.00 0.00 4.68
8271 10252 1.134946 CCAATTTCACGGATCCCAAGC 59.865 52.381 6.06 0.00 0.00 4.01
8272 10253 1.134946 GCCAATTTCACGGATCCCAAG 59.865 52.381 6.06 0.00 0.00 3.61
8273 10254 1.181786 GCCAATTTCACGGATCCCAA 58.818 50.000 6.06 0.00 0.00 4.12
8274 10255 0.331278 AGCCAATTTCACGGATCCCA 59.669 50.000 6.06 0.00 0.00 4.37
8275 10256 1.474330 AAGCCAATTTCACGGATCCC 58.526 50.000 6.06 0.00 0.00 3.85
8276 10257 2.491693 TCAAAGCCAATTTCACGGATCC 59.508 45.455 0.00 0.00 0.00 3.36
8277 10258 3.848272 TCAAAGCCAATTTCACGGATC 57.152 42.857 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.