Multiple sequence alignment - TraesCS2A01G593400

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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 TraesCS2A01G593400 chr2A 100.000 4560 0 0 1 4560 779943743 779948302 0.000000e+00 8421.0
1 TraesCS2A01G593400 chr2A 98.214 56 1 0 291 346 521059685 521059740 1.040000e-16 99.0
2 TraesCS2A01G593400 chr2D 95.543 3702 97 18 919 4560 633691566 633687873 0.000000e+00 5860.0
3 TraesCS2A01G593400 chr2D 88.976 508 45 7 1 502 633692513 633692011 6.480000e-173 617.0
4 TraesCS2A01G593400 chr2D 90.530 264 15 4 628 890 633691810 633691556 1.570000e-89 340.0
5 TraesCS2A01G593400 chr2D 96.203 79 3 0 502 580 633691892 633691814 3.700000e-26 130.0
6 TraesCS2A01G593400 chr3A 84.615 195 21 5 3325 3511 127073482 127073675 7.790000e-43 185.0
7 TraesCS2A01G593400 chr3A 96.429 56 2 0 291 346 208265983 208266038 4.860000e-15 93.5
8 TraesCS2A01G593400 chr3A 98.113 53 1 0 294 346 576527267 576527215 4.860000e-15 93.5
9 TraesCS2A01G593400 chr3D 82.692 208 23 8 3325 3519 120134038 120134245 6.070000e-39 172.0
10 TraesCS2A01G593400 chr3D 98.148 54 1 0 293 346 177964737 177964684 1.350000e-15 95.3
11 TraesCS2A01G593400 chr3B 77.114 201 31 9 3325 3518 172214265 172214457 8.070000e-18 102.0
12 TraesCS2A01G593400 chr3B 86.957 92 8 2 3427 3518 172094926 172095013 2.900000e-17 100.0
13 TraesCS2A01G593400 chr6A 96.610 59 2 0 288 346 327338698 327338756 1.040000e-16 99.0
14 TraesCS2A01G593400 chr7A 98.148 54 1 0 293 346 148540210 148540263 1.350000e-15 95.3
15 TraesCS2A01G593400 chr7A 98.148 54 1 0 293 346 581172518 581172465 1.350000e-15 95.3
16 TraesCS2A01G593400 chr5D 93.651 63 4 0 284 346 527332215 527332153 1.350000e-15 95.3
17 TraesCS2A01G593400 chr4D 96.552 58 1 1 290 346 228286001 228286058 1.350000e-15 95.3


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 TraesCS2A01G593400 chr2A 779943743 779948302 4559 False 8421.00 8421 100.000 1 4560 1 chr2A.!!$F2 4559
1 TraesCS2A01G593400 chr2D 633687873 633692513 4640 True 1736.75 5860 92.813 1 4560 4 chr2D.!!$R1 4559

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
591 714 0.038159 GGTGACACCCTGTTCTCGAG 60.038 60.000 14.16 5.93 30.04 4.04 F
1343 1467 0.757188 GGAGGAGGAGGCGAAGATGA 60.757 60.000 0.00 0.00 0.00 2.92 F
1603 1727 0.179100 AGTGGATGAAGATGACGGCG 60.179 55.000 4.80 4.80 0.00 6.46 F
1842 1996 1.666553 GTCGTCGCATGTGGGAACA 60.667 57.895 6.39 0.00 38.76 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1563 0.967887 TTCTCACGCTCCTCCTCCTG 60.968 60.000 0.00 0.0 0.00 3.86 R
2678 2859 0.964358 GCAGACTGGGAGCAAGCAAT 60.964 55.000 4.26 0.0 0.00 3.56 R
2753 2934 1.177401 GGTCCAACAGGCATTCCTTC 58.823 55.000 0.00 0.0 41.93 3.46 R
3734 3916 2.110578 TCATCGCCAATGGAGAGAGAA 58.889 47.619 12.00 0.0 34.53 2.87 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
67 68 5.753721 ATTTACTTCTGTCTCTCTTGCCT 57.246 39.130 0.00 0.00 0.00 4.75
95 96 4.646492 ACTTGCCTCTTTTTGATTGTGACT 59.354 37.500 0.00 0.00 0.00 3.41
111 112 1.073603 TGACTGGGTGCAATGTGATCA 59.926 47.619 0.00 0.00 0.00 2.92
135 136 2.783832 CGCGCACTATATATGTGATCGG 59.216 50.000 8.75 5.99 37.60 4.18
137 138 4.611943 GCGCACTATATATGTGATCGGAT 58.388 43.478 0.30 0.00 37.60 4.18
138 139 4.442403 GCGCACTATATATGTGATCGGATG 59.558 45.833 0.30 0.00 37.60 3.51
192 193 6.594159 GGACAGTTTGCAGCTAACTTTAGATA 59.406 38.462 18.28 0.00 33.73 1.98
194 195 7.162082 ACAGTTTGCAGCTAACTTTAGATAGT 58.838 34.615 18.28 9.51 33.73 2.12
196 197 7.959651 CAGTTTGCAGCTAACTTTAGATAGTTG 59.040 37.037 18.28 6.55 38.72 3.16
210 211 5.426689 AGATAGTTGGCTCTCATGTCAAA 57.573 39.130 0.00 0.00 0.00 2.69
221 222 3.007940 TCTCATGTCAAACTCCGTGGATT 59.992 43.478 0.00 0.00 0.00 3.01
226 227 1.697432 TCAAACTCCGTGGATTGGTCT 59.303 47.619 3.16 0.00 0.00 3.85
262 263 4.569564 GGACGGATATGGTGTCAAGTTTAC 59.430 45.833 0.00 0.00 34.32 2.01
280 281 1.450312 CGGTCAGGTTGGAGATGCC 60.450 63.158 0.00 0.00 37.10 4.40
297 298 4.591498 AGATGCCCTAACGACATATAACCA 59.409 41.667 0.00 0.00 0.00 3.67
299 300 5.298989 TGCCCTAACGACATATAACCAAT 57.701 39.130 0.00 0.00 0.00 3.16
301 302 5.061179 GCCCTAACGACATATAACCAATGT 58.939 41.667 0.00 0.00 40.23 2.71
302 303 5.529800 GCCCTAACGACATATAACCAATGTT 59.470 40.000 0.00 0.00 37.69 2.71
303 304 6.512741 GCCCTAACGACATATAACCAATGTTG 60.513 42.308 0.00 2.60 42.24 3.33
319 320 6.087518 CAATGTTGGAGATATCGCTTATCG 57.912 41.667 6.41 0.00 41.45 2.92
320 321 4.174411 TGTTGGAGATATCGCTTATCGG 57.826 45.455 6.41 0.00 41.45 4.18
321 322 3.056821 TGTTGGAGATATCGCTTATCGGG 60.057 47.826 6.41 0.00 41.45 5.14
323 324 3.427573 TGGAGATATCGCTTATCGGGAA 58.572 45.455 6.41 0.00 41.45 3.97
324 325 3.192844 TGGAGATATCGCTTATCGGGAAC 59.807 47.826 6.41 0.00 41.45 3.62
325 326 3.444388 GGAGATATCGCTTATCGGGAACT 59.556 47.826 6.41 0.00 41.45 3.01
326 327 4.082136 GGAGATATCGCTTATCGGGAACTT 60.082 45.833 6.41 0.00 41.45 2.66
327 328 5.125097 GGAGATATCGCTTATCGGGAACTTA 59.875 44.000 6.41 0.00 41.45 2.24
328 329 6.183360 GGAGATATCGCTTATCGGGAACTTAT 60.183 42.308 6.41 0.00 41.45 1.73
329 330 6.797454 AGATATCGCTTATCGGGAACTTATC 58.203 40.000 0.00 0.00 41.45 1.75
332 333 2.288030 CGCTTATCGGGAACTTATCGGT 60.288 50.000 0.00 0.00 33.78 4.69
333 334 3.315418 GCTTATCGGGAACTTATCGGTC 58.685 50.000 0.00 0.00 0.00 4.79
335 336 1.683943 ATCGGGAACTTATCGGTCGA 58.316 50.000 0.00 0.00 32.91 4.20
336 337 0.734889 TCGGGAACTTATCGGTCGAC 59.265 55.000 7.13 7.13 0.00 4.20
337 338 0.248784 CGGGAACTTATCGGTCGACC 60.249 60.000 25.28 25.28 0.00 4.79
338 339 0.103755 GGGAACTTATCGGTCGACCC 59.896 60.000 28.52 11.63 0.00 4.46
339 340 0.819582 GGAACTTATCGGTCGACCCA 59.180 55.000 28.52 17.72 0.00 4.51
340 341 1.411612 GGAACTTATCGGTCGACCCAT 59.588 52.381 28.52 23.64 0.00 4.00
341 342 2.470821 GAACTTATCGGTCGACCCATG 58.529 52.381 28.52 15.05 0.00 3.66
342 343 1.771565 ACTTATCGGTCGACCCATGA 58.228 50.000 28.52 19.93 0.00 3.07
343 344 2.317040 ACTTATCGGTCGACCCATGAT 58.683 47.619 28.52 24.74 0.00 2.45
344 345 3.493334 ACTTATCGGTCGACCCATGATA 58.507 45.455 28.52 23.76 0.00 2.15
345 346 3.893200 ACTTATCGGTCGACCCATGATAA 59.107 43.478 27.51 27.51 32.37 1.75
346 347 4.342951 ACTTATCGGTCGACCCATGATAAA 59.657 41.667 28.32 15.63 32.79 1.40
347 348 5.011738 ACTTATCGGTCGACCCATGATAAAT 59.988 40.000 28.32 22.16 32.79 1.40
348 349 3.106242 TCGGTCGACCCATGATAAATG 57.894 47.619 28.52 10.55 0.00 2.32
349 350 2.696187 TCGGTCGACCCATGATAAATGA 59.304 45.455 28.52 12.78 0.00 2.57
357 358 3.458118 ACCCATGATAAATGAAGACCGGA 59.542 43.478 9.46 0.00 0.00 5.14
377 378 3.425713 CTTGCCGCGCACATGTCT 61.426 61.111 8.75 0.00 38.71 3.41
386 387 2.353958 CACATGTCTGCCTGCCCT 59.646 61.111 0.00 0.00 0.00 5.19
433 437 2.331132 GCTGCAGAAGAGGCCACAC 61.331 63.158 20.43 0.00 0.00 3.82
434 438 1.071987 CTGCAGAAGAGGCCACACA 59.928 57.895 8.42 0.00 0.00 3.72
474 478 1.006571 ATCACCACCGTCGTGTCAC 60.007 57.895 0.00 0.00 38.41 3.67
514 637 2.747446 GCGGATGTTCTAAACACCACAT 59.253 45.455 0.00 0.00 45.50 3.21
515 638 3.936453 GCGGATGTTCTAAACACCACATA 59.064 43.478 0.00 0.00 45.50 2.29
580 703 1.198759 TCCTAGCCAAGGGTGACACC 61.199 60.000 16.86 16.86 46.55 4.16
589 712 4.675404 GGTGACACCCTGTTCTCG 57.325 61.111 14.16 0.00 30.04 4.04
590 713 2.046938 GGTGACACCCTGTTCTCGA 58.953 57.895 14.16 0.00 30.04 4.04
591 714 0.038159 GGTGACACCCTGTTCTCGAG 60.038 60.000 14.16 5.93 30.04 4.04
592 715 0.959553 GTGACACCCTGTTCTCGAGA 59.040 55.000 12.08 12.08 0.00 4.04
593 716 1.340248 GTGACACCCTGTTCTCGAGAA 59.660 52.381 23.74 23.74 0.00 2.87
594 717 2.036387 TGACACCCTGTTCTCGAGAAA 58.964 47.619 28.58 17.24 35.58 2.52
595 718 2.432874 TGACACCCTGTTCTCGAGAAAA 59.567 45.455 28.58 22.74 35.58 2.29
596 719 3.071023 TGACACCCTGTTCTCGAGAAAAT 59.929 43.478 28.58 8.77 35.58 1.82
597 720 4.282449 TGACACCCTGTTCTCGAGAAAATA 59.718 41.667 28.58 16.65 35.58 1.40
598 721 4.822026 ACACCCTGTTCTCGAGAAAATAG 58.178 43.478 28.58 23.52 35.58 1.73
599 722 4.283722 ACACCCTGTTCTCGAGAAAATAGT 59.716 41.667 28.58 19.40 35.58 2.12
600 723 5.221661 ACACCCTGTTCTCGAGAAAATAGTT 60.222 40.000 28.58 13.06 35.58 2.24
601 724 5.120830 CACCCTGTTCTCGAGAAAATAGTTG 59.879 44.000 28.58 18.99 35.58 3.16
602 725 5.011738 ACCCTGTTCTCGAGAAAATAGTTGA 59.988 40.000 28.58 1.08 35.58 3.18
603 726 5.578727 CCCTGTTCTCGAGAAAATAGTTGAG 59.421 44.000 28.58 10.10 35.58 3.02
604 727 6.390721 CCTGTTCTCGAGAAAATAGTTGAGA 58.609 40.000 28.58 2.07 35.58 3.27
605 728 6.868864 CCTGTTCTCGAGAAAATAGTTGAGAA 59.131 38.462 28.58 0.00 39.42 2.87
606 729 7.385205 CCTGTTCTCGAGAAAATAGTTGAGAAA 59.615 37.037 28.58 0.00 42.22 2.52
607 730 8.657074 TGTTCTCGAGAAAATAGTTGAGAAAA 57.343 30.769 28.58 0.00 42.22 2.29
608 731 8.548721 TGTTCTCGAGAAAATAGTTGAGAAAAC 58.451 33.333 28.58 11.98 42.22 2.43
609 732 7.653767 TCTCGAGAAAATAGTTGAGAAAACC 57.346 36.000 14.01 0.00 30.14 3.27
610 733 6.365247 TCTCGAGAAAATAGTTGAGAAAACCG 59.635 38.462 14.01 0.00 30.14 4.44
611 734 5.080068 CGAGAAAATAGTTGAGAAAACCGC 58.920 41.667 0.00 0.00 0.00 5.68
612 735 5.372547 AGAAAATAGTTGAGAAAACCGCC 57.627 39.130 0.00 0.00 0.00 6.13
613 736 4.825085 AGAAAATAGTTGAGAAAACCGCCA 59.175 37.500 0.00 0.00 0.00 5.69
614 737 4.499037 AAATAGTTGAGAAAACCGCCAC 57.501 40.909 0.00 0.00 0.00 5.01
615 738 2.922740 TAGTTGAGAAAACCGCCACT 57.077 45.000 0.00 0.00 0.00 4.00
616 739 2.922740 AGTTGAGAAAACCGCCACTA 57.077 45.000 0.00 0.00 0.00 2.74
617 740 2.490991 AGTTGAGAAAACCGCCACTAC 58.509 47.619 0.00 0.00 0.00 2.73
618 741 2.104281 AGTTGAGAAAACCGCCACTACT 59.896 45.455 0.00 0.00 0.00 2.57
619 742 2.876550 GTTGAGAAAACCGCCACTACTT 59.123 45.455 0.00 0.00 0.00 2.24
620 743 2.762745 TGAGAAAACCGCCACTACTTC 58.237 47.619 0.00 0.00 0.00 3.01
621 744 2.367567 TGAGAAAACCGCCACTACTTCT 59.632 45.455 0.00 0.00 0.00 2.85
622 745 3.575256 TGAGAAAACCGCCACTACTTCTA 59.425 43.478 0.00 0.00 0.00 2.10
623 746 4.039488 TGAGAAAACCGCCACTACTTCTAA 59.961 41.667 0.00 0.00 0.00 2.10
624 747 5.161943 AGAAAACCGCCACTACTTCTAAT 57.838 39.130 0.00 0.00 0.00 1.73
625 748 6.071221 TGAGAAAACCGCCACTACTTCTAATA 60.071 38.462 0.00 0.00 0.00 0.98
626 749 6.885922 AGAAAACCGCCACTACTTCTAATAT 58.114 36.000 0.00 0.00 0.00 1.28
627 750 8.015185 AGAAAACCGCCACTACTTCTAATATA 57.985 34.615 0.00 0.00 0.00 0.86
628 751 8.648693 AGAAAACCGCCACTACTTCTAATATAT 58.351 33.333 0.00 0.00 0.00 0.86
629 752 8.603242 AAAACCGCCACTACTTCTAATATATG 57.397 34.615 0.00 0.00 0.00 1.78
630 753 6.912951 ACCGCCACTACTTCTAATATATGT 57.087 37.500 0.00 0.00 0.00 2.29
631 754 8.413309 AACCGCCACTACTTCTAATATATGTA 57.587 34.615 0.00 0.00 0.00 2.29
632 755 8.413309 ACCGCCACTACTTCTAATATATGTAA 57.587 34.615 0.00 0.00 0.00 2.41
662 785 1.717728 GTTGTTTCGTGTCGCGCTG 60.718 57.895 5.56 0.00 41.07 5.18
688 811 5.443261 CATACATGCTATTGCGTTTACTGG 58.557 41.667 0.00 0.00 43.34 4.00
727 850 1.003223 AGCTAAACGGTTGCGTTTGAC 60.003 47.619 3.42 0.00 41.42 3.18
737 860 2.050849 GCGTTTGACAATTTCGCGG 58.949 52.632 6.13 0.00 37.74 6.46
770 893 5.997746 AGATTGTGTTTGAGAAAGGAATCGA 59.002 36.000 0.00 0.00 0.00 3.59
820 943 1.334869 CAGCATTGGGCCTAAATCGTC 59.665 52.381 5.31 0.00 46.50 4.20
833 956 1.213296 AATCGTCCTAACAGGCCCAT 58.787 50.000 0.00 0.00 34.61 4.00
867 990 1.817209 GGACCAGATCCGGACAGTC 59.183 63.158 6.12 11.36 37.88 3.51
890 1013 4.457603 CGAATCAATCTAGGAGACGGAGAT 59.542 45.833 0.00 0.00 38.91 2.75
891 1014 5.391523 CGAATCAATCTAGGAGACGGAGATC 60.392 48.000 0.00 0.00 37.05 2.75
892 1015 4.715534 TCAATCTAGGAGACGGAGATCT 57.284 45.455 0.00 0.00 37.05 2.75
893 1016 5.055265 TCAATCTAGGAGACGGAGATCTT 57.945 43.478 0.00 0.00 37.05 2.40
894 1017 5.067273 TCAATCTAGGAGACGGAGATCTTC 58.933 45.833 0.00 0.00 37.05 2.87
895 1018 4.993705 ATCTAGGAGACGGAGATCTTCT 57.006 45.455 0.00 0.00 38.23 2.85
896 1019 4.345859 TCTAGGAGACGGAGATCTTCTC 57.654 50.000 12.66 12.66 42.66 2.87
897 1020 3.712218 TCTAGGAGACGGAGATCTTCTCA 59.288 47.826 19.73 4.67 45.12 3.27
898 1021 3.374042 AGGAGACGGAGATCTTCTCAA 57.626 47.619 19.73 0.00 45.12 3.02
899 1022 3.702792 AGGAGACGGAGATCTTCTCAAA 58.297 45.455 19.73 0.00 45.12 2.69
900 1023 4.090090 AGGAGACGGAGATCTTCTCAAAA 58.910 43.478 19.73 0.00 45.12 2.44
901 1024 4.528596 AGGAGACGGAGATCTTCTCAAAAA 59.471 41.667 19.73 0.00 45.12 1.94
947 1070 1.237285 ACGGACAGGATTTGCTGCAC 61.237 55.000 0.00 0.00 0.00 4.57
949 1072 1.598701 GGACAGGATTTGCTGCACCC 61.599 60.000 0.00 4.21 0.00 4.61
963 1086 4.824515 ACCCCCGCCGAGAGAGAG 62.825 72.222 0.00 0.00 0.00 3.20
964 1087 4.507916 CCCCCGCCGAGAGAGAGA 62.508 72.222 0.00 0.00 0.00 3.10
965 1088 2.440430 CCCCGCCGAGAGAGAGAA 60.440 66.667 0.00 0.00 0.00 2.87
966 1089 1.830408 CCCCGCCGAGAGAGAGAAT 60.830 63.158 0.00 0.00 0.00 2.40
1022 1146 4.415332 CGTGACCGTCCGTCCAGG 62.415 72.222 0.00 0.00 41.18 4.45
1059 1183 1.103398 AGCAAAACCAACTCGCAGCT 61.103 50.000 0.00 0.00 0.00 4.24
1090 1214 2.262915 CACTCTGCCTGGGACGAC 59.737 66.667 0.00 0.00 0.00 4.34
1099 1223 2.494677 CTGGGACGACGAGGAAGAT 58.505 57.895 0.00 0.00 0.00 2.40
1124 1248 3.772025 CCTGGACTACTTCAACTCCATCT 59.228 47.826 0.00 0.00 32.27 2.90
1159 1283 3.479203 CTGGGCCACCGGATGCTA 61.479 66.667 9.46 3.04 46.80 3.49
1162 1286 2.032681 GGCCACCGGATGCTATCC 59.967 66.667 9.46 5.39 46.22 2.59
1174 1298 2.882927 TGCTATCCACCACGTATGTC 57.117 50.000 0.00 0.00 0.00 3.06
1192 1316 2.485122 CTTGGCAAATCCGACGCC 59.515 61.111 0.00 0.00 46.43 5.68
1245 1369 0.767375 AGGGCGGCATCTATGTTGAT 59.233 50.000 12.47 0.00 0.00 2.57
1343 1467 0.757188 GGAGGAGGAGGCGAAGATGA 60.757 60.000 0.00 0.00 0.00 2.92
1391 1515 2.365582 ACCACGATTACTTGGAATGCC 58.634 47.619 0.00 0.00 38.56 4.40
1431 1555 3.449918 AGAAGGAGGAGGAGGAGAAAAG 58.550 50.000 0.00 0.00 0.00 2.27
1439 1563 1.912731 AGGAGGAGAAAAGGAGGAAGC 59.087 52.381 0.00 0.00 0.00 3.86
1591 1715 1.127343 GGAGGAAGGAGGAGTGGATG 58.873 60.000 0.00 0.00 0.00 3.51
1596 1720 3.044894 GGAAGGAGGAGTGGATGAAGAT 58.955 50.000 0.00 0.00 0.00 2.40
1603 1727 0.179100 AGTGGATGAAGATGACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
1640 1764 3.033368 ACAAAGAGGACGAGAAGAAGC 57.967 47.619 0.00 0.00 0.00 3.86
1791 1945 6.316140 TCCACAATGGAGTATCTCAAAAATCG 59.684 38.462 0.00 0.00 42.67 3.34
1801 1955 8.608844 AGTATCTCAAAAATCGGATGGTTATC 57.391 34.615 0.00 0.00 0.00 1.75
1842 1996 1.666553 GTCGTCGCATGTGGGAACA 60.667 57.895 6.39 0.00 38.76 3.18
1853 2007 4.115199 GGGAACATGCTCGGGGCT 62.115 66.667 0.00 0.00 42.39 5.19
1855 2009 2.514824 GAACATGCTCGGGGCTCC 60.515 66.667 0.00 0.00 42.39 4.70
1978 2158 5.479306 TGGAAGACAAGAGATTTCTAACGG 58.521 41.667 0.00 0.00 31.96 4.44
2189 2369 3.998672 ACCGTGGACCGCAATCGT 61.999 61.111 5.75 0.00 34.38 3.73
2250 2430 8.506168 ACTACTCACCCAAAATGTATGTATTG 57.494 34.615 0.00 0.00 0.00 1.90
2321 2501 9.831737 CTGCTTATTTCATACAAATACATAGCC 57.168 33.333 0.00 0.00 29.22 3.93
2331 2511 4.711355 ACAAATACATAGCCCATTGCAACT 59.289 37.500 0.00 0.00 44.83 3.16
2440 2621 2.602211 CTCTCGTGCAATTGTAGCTCTG 59.398 50.000 7.40 0.00 0.00 3.35
2482 2663 6.518493 AGTTGAACTAAAACTACATGACGGA 58.482 36.000 0.00 0.00 36.11 4.69
2529 2710 4.142403 ACCATTGATGAATGTTAGCAACCG 60.142 41.667 4.14 0.00 37.82 4.44
2538 2719 5.065859 TGAATGTTAGCAACCGTTATGATGG 59.934 40.000 0.00 0.00 37.98 3.51
2678 2859 4.885325 GGCCTTTTAAATATGGAGGTCGAA 59.115 41.667 0.00 0.00 0.00 3.71
2714 2895 3.944015 GTCTGCTGCAGAGGTTATTGAAT 59.056 43.478 31.10 0.00 41.46 2.57
2753 2934 1.887854 TGTTGCTGGATTGTCATGGTG 59.112 47.619 0.00 0.00 0.00 4.17
2852 3033 7.561021 TTGAAAGTTGTCATACAAGCTTACA 57.439 32.000 0.00 0.00 39.00 2.41
3155 3336 2.170397 TGTCAGATGTCCAACTGTGTGT 59.830 45.455 4.74 0.00 35.84 3.72
3161 3342 3.120321 TGTCCAACTGTGTGTGTATCC 57.880 47.619 0.00 0.00 0.00 2.59
3175 3356 7.035004 GTGTGTGTATCCGTTGTACCTTATTA 58.965 38.462 0.00 0.00 0.00 0.98
3658 3840 2.092429 TGTTGATAGATGGGGGAGTTGC 60.092 50.000 0.00 0.00 0.00 4.17
3674 3856 3.632189 AGTTGCAACTTCGAAAATCAGC 58.368 40.909 26.36 0.15 35.21 4.26
3789 3971 3.620929 ATTGCTGATTGCGATCATGAC 57.379 42.857 17.11 10.30 41.79 3.06
3839 4021 5.922544 GCAGCAGTTTGTCTTGAATGTTATT 59.077 36.000 0.00 0.00 0.00 1.40
3902 4084 6.648879 TCCTCGGTCTTCATTTTCATTTTT 57.351 33.333 0.00 0.00 0.00 1.94
3941 4123 7.611467 TCAGTCCTTATGTATGCATCACTTTTT 59.389 33.333 0.19 0.00 36.58 1.94
4093 4275 5.163174 TGAGCCATGTCATTCCTCATTCATA 60.163 40.000 7.70 0.00 0.00 2.15
4095 4277 6.312529 AGCCATGTCATTCCTCATTCATAAT 58.687 36.000 0.00 0.00 0.00 1.28
4122 4304 5.692115 TGTCCCTATCTTGCTTTCACATA 57.308 39.130 0.00 0.00 0.00 2.29
4173 4355 7.668469 GGTCCTTCTATGTTTTCCTTCCTTTTA 59.332 37.037 0.00 0.00 0.00 1.52
4182 4364 8.770010 TGTTTTCCTTCCTTTTACATTCCTTA 57.230 30.769 0.00 0.00 0.00 2.69
4205 4387 5.299949 ACATTTTTCTTTCTTGCCCATGTC 58.700 37.500 0.00 0.00 0.00 3.06
4233 4415 1.287425 CCGATTCGTAAAGGAGTGGC 58.713 55.000 5.20 0.00 0.00 5.01
4267 4449 4.104738 AGGTGATTGGACAAGGAAGAAGAA 59.895 41.667 0.00 0.00 0.00 2.52
4312 4494 5.593679 AGCCATTTTCTTGATCCATTGAG 57.406 39.130 0.00 0.00 0.00 3.02
4436 4619 4.161189 AGTCACCAATCTCACAGGTATCAG 59.839 45.833 0.00 0.00 33.49 2.90
4543 4726 9.476202 ACATTCTTGCCTAAAGTTTTTGTATTC 57.524 29.630 0.00 0.00 37.18 1.75
4544 4727 8.638565 CATTCTTGCCTAAAGTTTTTGTATTCG 58.361 33.333 0.00 0.00 37.18 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 9.679661 TCACAATCAAAAAGAGGCAAGTATATA 57.320 29.630 0.00 0.00 0.00 0.86
95 96 1.825090 GTCTGATCACATTGCACCCA 58.175 50.000 0.00 0.00 0.00 4.51
111 112 4.663166 GATCACATATATAGTGCGCGTCT 58.337 43.478 8.43 9.61 36.93 4.18
135 136 8.810427 ACGTTCAATATGAAATTCAAATGCATC 58.190 29.630 0.00 0.00 38.22 3.91
137 138 9.071221 GTACGTTCAATATGAAATTCAAATGCA 57.929 29.630 0.00 0.00 38.22 3.96
138 139 8.252454 CGTACGTTCAATATGAAATTCAAATGC 58.748 33.333 7.22 0.00 38.22 3.56
192 193 3.406764 GAGTTTGACATGAGAGCCAACT 58.593 45.455 0.00 0.00 0.00 3.16
194 195 2.783135 GGAGTTTGACATGAGAGCCAA 58.217 47.619 0.00 0.00 0.00 4.52
196 197 1.338200 ACGGAGTTTGACATGAGAGCC 60.338 52.381 0.00 0.00 37.78 4.70
210 211 4.254760 GGTGAAGACCAATCCACGGAGT 62.255 54.545 0.00 0.00 42.35 3.85
226 227 2.338620 CGTCCGCAGACTGGTGAA 59.661 61.111 4.26 0.00 41.16 3.18
262 263 1.450312 GGCATCTCCAACCTGACCG 60.450 63.158 0.00 0.00 34.01 4.79
280 281 6.954944 CCAACATTGGTTATATGTCGTTAGG 58.045 40.000 2.22 0.00 43.43 2.69
297 298 5.171476 CCGATAAGCGATATCTCCAACATT 58.829 41.667 0.34 0.00 44.57 2.71
299 300 3.056821 CCCGATAAGCGATATCTCCAACA 60.057 47.826 0.34 0.00 44.57 3.33
301 302 3.427573 TCCCGATAAGCGATATCTCCAA 58.572 45.455 0.34 0.00 44.57 3.53
302 303 3.081710 TCCCGATAAGCGATATCTCCA 57.918 47.619 0.34 0.00 44.57 3.86
303 304 3.444388 AGTTCCCGATAAGCGATATCTCC 59.556 47.826 0.34 0.00 44.57 3.71
305 306 6.458478 CGATAAGTTCCCGATAAGCGATATCT 60.458 42.308 0.34 0.00 44.57 1.98
306 307 5.681982 CGATAAGTTCCCGATAAGCGATATC 59.318 44.000 0.00 0.00 44.57 1.63
309 310 3.367087 CCGATAAGTTCCCGATAAGCGAT 60.367 47.826 0.00 0.00 44.57 4.58
312 313 3.315418 GACCGATAAGTTCCCGATAAGC 58.685 50.000 0.00 0.00 0.00 3.09
314 315 3.003689 GTCGACCGATAAGTTCCCGATAA 59.996 47.826 3.51 0.00 0.00 1.75
315 316 2.549754 GTCGACCGATAAGTTCCCGATA 59.450 50.000 3.51 0.00 0.00 2.92
316 317 1.336125 GTCGACCGATAAGTTCCCGAT 59.664 52.381 3.51 0.00 0.00 4.18
317 318 0.734889 GTCGACCGATAAGTTCCCGA 59.265 55.000 3.51 0.00 0.00 5.14
318 319 0.248784 GGTCGACCGATAAGTTCCCG 60.249 60.000 20.85 0.00 0.00 5.14
319 320 0.103755 GGGTCGACCGATAAGTTCCC 59.896 60.000 27.68 6.58 36.71 3.97
320 321 0.819582 TGGGTCGACCGATAAGTTCC 59.180 55.000 27.68 11.32 44.64 3.62
321 322 2.100252 TCATGGGTCGACCGATAAGTTC 59.900 50.000 28.81 13.28 44.64 3.01
323 324 1.771565 TCATGGGTCGACCGATAAGT 58.228 50.000 28.81 8.19 44.64 2.24
324 325 4.514781 TTATCATGGGTCGACCGATAAG 57.485 45.455 28.81 18.78 44.64 1.73
325 326 4.940905 TTTATCATGGGTCGACCGATAA 57.059 40.909 28.81 27.46 44.64 1.75
326 327 4.525100 TCATTTATCATGGGTCGACCGATA 59.475 41.667 28.81 24.09 44.64 2.92
327 328 3.323691 TCATTTATCATGGGTCGACCGAT 59.676 43.478 27.68 26.19 44.64 4.18
328 329 2.696187 TCATTTATCATGGGTCGACCGA 59.304 45.455 27.68 25.05 44.64 4.69
329 330 3.106242 TCATTTATCATGGGTCGACCG 57.894 47.619 27.68 14.74 44.64 4.79
332 333 4.703897 GGTCTTCATTTATCATGGGTCGA 58.296 43.478 0.00 0.00 0.00 4.20
333 334 3.494626 CGGTCTTCATTTATCATGGGTCG 59.505 47.826 0.00 0.00 0.00 4.79
335 336 3.458118 TCCGGTCTTCATTTATCATGGGT 59.542 43.478 0.00 0.00 0.00 4.51
336 337 4.085357 TCCGGTCTTCATTTATCATGGG 57.915 45.455 0.00 0.00 0.00 4.00
337 338 4.275936 GGTTCCGGTCTTCATTTATCATGG 59.724 45.833 0.00 0.00 0.00 3.66
338 339 5.126067 AGGTTCCGGTCTTCATTTATCATG 58.874 41.667 0.00 0.00 0.00 3.07
339 340 5.373812 AGGTTCCGGTCTTCATTTATCAT 57.626 39.130 0.00 0.00 0.00 2.45
340 341 4.837093 AGGTTCCGGTCTTCATTTATCA 57.163 40.909 0.00 0.00 0.00 2.15
341 342 4.201920 GCAAGGTTCCGGTCTTCATTTATC 60.202 45.833 0.00 0.00 0.00 1.75
342 343 3.694566 GCAAGGTTCCGGTCTTCATTTAT 59.305 43.478 0.00 0.00 0.00 1.40
343 344 3.078837 GCAAGGTTCCGGTCTTCATTTA 58.921 45.455 0.00 0.00 0.00 1.40
344 345 1.886542 GCAAGGTTCCGGTCTTCATTT 59.113 47.619 0.00 0.00 0.00 2.32
345 346 1.534729 GCAAGGTTCCGGTCTTCATT 58.465 50.000 0.00 0.00 0.00 2.57
346 347 0.322546 GGCAAGGTTCCGGTCTTCAT 60.323 55.000 0.00 0.00 0.00 2.57
347 348 1.072505 GGCAAGGTTCCGGTCTTCA 59.927 57.895 0.00 0.00 0.00 3.02
348 349 2.033194 CGGCAAGGTTCCGGTCTTC 61.033 63.158 0.00 0.00 42.99 2.87
349 350 2.032071 CGGCAAGGTTCCGGTCTT 59.968 61.111 0.00 1.21 42.99 3.01
357 358 4.041917 CATGTGCGCGGCAAGGTT 62.042 61.111 8.83 0.00 41.47 3.50
377 378 0.338467 TCTACCTTCTAGGGCAGGCA 59.662 55.000 0.00 0.00 40.58 4.75
381 382 1.062121 AGGCATCTACCTTCTAGGGCA 60.062 52.381 0.00 0.00 40.58 5.36
386 387 2.489255 CCTCCGAGGCATCTACCTTCTA 60.489 54.545 0.18 0.00 41.32 2.10
421 425 1.337823 ACGTACATGTGTGGCCTCTTC 60.338 52.381 9.11 0.00 0.00 2.87
433 437 3.498397 GCTCCCAATATTCCACGTACATG 59.502 47.826 0.00 0.00 0.00 3.21
434 438 3.135712 TGCTCCCAATATTCCACGTACAT 59.864 43.478 0.00 0.00 0.00 2.29
449 453 2.927856 ACGGTGGTGATGCTCCCA 60.928 61.111 0.00 0.00 0.00 4.37
474 478 2.742372 CCGGCCGTCCACTGAAAG 60.742 66.667 26.12 0.00 42.29 2.62
580 703 6.390721 TCTCAACTATTTTCTCGAGAACAGG 58.609 40.000 27.03 18.34 33.13 4.00
581 704 7.875316 TTCTCAACTATTTTCTCGAGAACAG 57.125 36.000 27.03 23.30 35.25 3.16
582 705 8.548721 GTTTTCTCAACTATTTTCTCGAGAACA 58.451 33.333 27.03 21.33 38.76 3.18
583 706 8.010540 GGTTTTCTCAACTATTTTCTCGAGAAC 58.989 37.037 27.03 10.42 38.76 3.01
585 708 6.365247 CGGTTTTCTCAACTATTTTCTCGAGA 59.635 38.462 12.08 12.08 0.00 4.04
587 710 5.107220 GCGGTTTTCTCAACTATTTTCTCGA 60.107 40.000 0.00 0.00 0.00 4.04
588 711 5.080068 GCGGTTTTCTCAACTATTTTCTCG 58.920 41.667 0.00 0.00 0.00 4.04
589 712 5.048991 TGGCGGTTTTCTCAACTATTTTCTC 60.049 40.000 0.00 0.00 0.00 2.87
590 713 4.825085 TGGCGGTTTTCTCAACTATTTTCT 59.175 37.500 0.00 0.00 0.00 2.52
591 714 4.915667 GTGGCGGTTTTCTCAACTATTTTC 59.084 41.667 0.00 0.00 0.00 2.29
592 715 4.583073 AGTGGCGGTTTTCTCAACTATTTT 59.417 37.500 0.00 0.00 0.00 1.82
593 716 4.142038 AGTGGCGGTTTTCTCAACTATTT 58.858 39.130 0.00 0.00 0.00 1.40
594 717 3.751518 AGTGGCGGTTTTCTCAACTATT 58.248 40.909 0.00 0.00 0.00 1.73
595 718 3.418684 AGTGGCGGTTTTCTCAACTAT 57.581 42.857 0.00 0.00 0.00 2.12
596 719 2.922740 AGTGGCGGTTTTCTCAACTA 57.077 45.000 0.00 0.00 0.00 2.24
597 720 2.104281 AGTAGTGGCGGTTTTCTCAACT 59.896 45.455 0.00 0.00 0.00 3.16
598 721 2.490991 AGTAGTGGCGGTTTTCTCAAC 58.509 47.619 0.00 0.00 0.00 3.18
599 722 2.922740 AGTAGTGGCGGTTTTCTCAA 57.077 45.000 0.00 0.00 0.00 3.02
600 723 2.367567 AGAAGTAGTGGCGGTTTTCTCA 59.632 45.455 0.00 0.00 0.00 3.27
601 724 3.041508 AGAAGTAGTGGCGGTTTTCTC 57.958 47.619 0.00 0.00 0.00 2.87
602 725 4.612264 TTAGAAGTAGTGGCGGTTTTCT 57.388 40.909 0.00 0.00 0.00 2.52
603 726 8.709646 CATATATTAGAAGTAGTGGCGGTTTTC 58.290 37.037 0.00 0.00 0.00 2.29
604 727 8.208903 ACATATATTAGAAGTAGTGGCGGTTTT 58.791 33.333 0.00 0.00 0.00 2.43
605 728 7.732996 ACATATATTAGAAGTAGTGGCGGTTT 58.267 34.615 0.00 0.00 0.00 3.27
606 729 7.299246 ACATATATTAGAAGTAGTGGCGGTT 57.701 36.000 0.00 0.00 0.00 4.44
607 730 6.912951 ACATATATTAGAAGTAGTGGCGGT 57.087 37.500 0.00 0.00 0.00 5.68
608 731 9.355215 CTTTACATATATTAGAAGTAGTGGCGG 57.645 37.037 0.00 0.00 0.00 6.13
609 732 8.861101 GCTTTACATATATTAGAAGTAGTGGCG 58.139 37.037 0.00 0.00 0.00 5.69
610 733 9.930693 AGCTTTACATATATTAGAAGTAGTGGC 57.069 33.333 0.00 0.00 0.00 5.01
627 750 8.726988 ACGAAACAACATGTAATAGCTTTACAT 58.273 29.630 19.75 19.75 43.97 2.29
628 751 8.012809 CACGAAACAACATGTAATAGCTTTACA 58.987 33.333 17.80 17.80 38.99 2.41
629 752 8.013378 ACACGAAACAACATGTAATAGCTTTAC 58.987 33.333 0.00 1.58 0.00 2.01
630 753 8.090250 ACACGAAACAACATGTAATAGCTTTA 57.910 30.769 0.00 0.00 0.00 1.85
631 754 6.966021 ACACGAAACAACATGTAATAGCTTT 58.034 32.000 0.00 0.00 0.00 3.51
632 755 6.554334 ACACGAAACAACATGTAATAGCTT 57.446 33.333 0.00 0.00 0.00 3.74
669 792 4.355543 AACCAGTAAACGCAATAGCATG 57.644 40.909 0.00 0.00 42.27 4.06
694 817 5.956642 ACCGTTTAGCTCAAAAAGACAAAA 58.043 33.333 0.00 0.00 0.00 2.44
695 818 5.570234 ACCGTTTAGCTCAAAAAGACAAA 57.430 34.783 0.00 0.00 0.00 2.83
696 819 5.336744 CAACCGTTTAGCTCAAAAAGACAA 58.663 37.500 0.00 0.00 0.00 3.18
697 820 4.732355 GCAACCGTTTAGCTCAAAAAGACA 60.732 41.667 0.00 0.00 0.00 3.41
698 821 3.729217 GCAACCGTTTAGCTCAAAAAGAC 59.271 43.478 0.00 0.00 0.00 3.01
699 822 3.547214 CGCAACCGTTTAGCTCAAAAAGA 60.547 43.478 0.00 0.00 0.00 2.52
700 823 2.719046 CGCAACCGTTTAGCTCAAAAAG 59.281 45.455 0.00 0.00 0.00 2.27
701 824 2.722071 CGCAACCGTTTAGCTCAAAAA 58.278 42.857 0.00 0.00 0.00 1.94
702 825 2.392933 CGCAACCGTTTAGCTCAAAA 57.607 45.000 0.00 0.00 0.00 2.44
746 869 5.997746 TCGATTCCTTTCTCAAACACAATCT 59.002 36.000 0.00 0.00 0.00 2.40
770 893 2.285977 AGCGAACGACTTTGTTTCCTT 58.714 42.857 0.00 0.00 30.75 3.36
820 943 1.683011 CCTGTTGATGGGCCTGTTAGG 60.683 57.143 4.53 1.32 38.80 2.69
833 956 4.308458 CCGGTGCGACCCTGTTGA 62.308 66.667 0.00 0.00 33.75 3.18
862 985 4.035792 CGTCTCCTAGATTGATTCGACTGT 59.964 45.833 0.00 0.00 0.00 3.55
867 990 3.815962 TCTCCGTCTCCTAGATTGATTCG 59.184 47.826 0.00 0.00 0.00 3.34
903 1026 3.130693 CCGTCTCCGTCTCCTAGATTTTT 59.869 47.826 0.00 0.00 0.00 1.94
904 1027 2.688958 CCGTCTCCGTCTCCTAGATTTT 59.311 50.000 0.00 0.00 0.00 1.82
905 1028 2.299521 CCGTCTCCGTCTCCTAGATTT 58.700 52.381 0.00 0.00 0.00 2.17
906 1029 1.970092 CCGTCTCCGTCTCCTAGATT 58.030 55.000 0.00 0.00 0.00 2.40
907 1030 0.535553 GCCGTCTCCGTCTCCTAGAT 60.536 60.000 0.00 0.00 0.00 1.98
908 1031 1.153208 GCCGTCTCCGTCTCCTAGA 60.153 63.158 0.00 0.00 0.00 2.43
909 1032 2.535788 CGCCGTCTCCGTCTCCTAG 61.536 68.421 0.00 0.00 0.00 3.02
910 1033 2.513204 CGCCGTCTCCGTCTCCTA 60.513 66.667 0.00 0.00 0.00 2.94
911 1034 4.405671 TCGCCGTCTCCGTCTCCT 62.406 66.667 0.00 0.00 0.00 3.69
912 1035 4.176851 GTCGCCGTCTCCGTCTCC 62.177 72.222 0.00 0.00 0.00 3.71
913 1036 4.517703 CGTCGCCGTCTCCGTCTC 62.518 72.222 0.00 0.00 0.00 3.36
918 1041 4.477975 CTGTCCGTCGCCGTCTCC 62.478 72.222 0.00 0.00 0.00 3.71
919 1042 4.477975 CCTGTCCGTCGCCGTCTC 62.478 72.222 0.00 0.00 0.00 3.36
921 1044 2.830704 AAATCCTGTCCGTCGCCGTC 62.831 60.000 0.00 0.00 0.00 4.79
922 1045 2.939261 AAATCCTGTCCGTCGCCGT 61.939 57.895 0.00 0.00 0.00 5.68
923 1046 2.125673 AAATCCTGTCCGTCGCCG 60.126 61.111 0.00 0.00 0.00 6.46
924 1047 2.750888 GCAAATCCTGTCCGTCGCC 61.751 63.158 0.00 0.00 0.00 5.54
925 1048 1.741770 AGCAAATCCTGTCCGTCGC 60.742 57.895 0.00 0.00 0.00 5.19
926 1049 1.970917 GCAGCAAATCCTGTCCGTCG 61.971 60.000 0.00 0.00 35.28 5.12
927 1050 0.955428 TGCAGCAAATCCTGTCCGTC 60.955 55.000 0.00 0.00 35.28 4.79
928 1051 1.073025 TGCAGCAAATCCTGTCCGT 59.927 52.632 0.00 0.00 35.28 4.69
933 1056 2.353610 GGGGGTGCAGCAAATCCTG 61.354 63.158 19.06 0.00 35.93 3.86
947 1070 3.881154 TATTCTCTCTCTCGGCGGGGG 62.881 61.905 7.05 2.13 0.00 5.40
949 1072 1.268352 CTTATTCTCTCTCTCGGCGGG 59.732 57.143 7.21 2.41 0.00 6.13
961 1084 2.052157 CCGGCGATCGAACTTATTCTC 58.948 52.381 21.57 0.00 42.43 2.87
962 1085 1.679680 TCCGGCGATCGAACTTATTCT 59.320 47.619 21.57 0.00 42.43 2.40
963 1086 2.129823 TCCGGCGATCGAACTTATTC 57.870 50.000 21.57 0.00 42.43 1.75
964 1087 2.589798 TTCCGGCGATCGAACTTATT 57.410 45.000 21.57 0.00 42.43 1.40
965 1088 2.159142 AGTTTCCGGCGATCGAACTTAT 60.159 45.455 21.57 0.00 42.43 1.73
966 1089 1.203052 AGTTTCCGGCGATCGAACTTA 59.797 47.619 21.57 0.00 42.43 2.24
1009 1132 4.626402 TTCCCCTGGACGGACGGT 62.626 66.667 0.00 0.00 33.16 4.83
1011 1134 2.227089 CTTCTTCCCCTGGACGGACG 62.227 65.000 0.00 0.00 33.16 4.79
1017 1141 1.281925 GCCCATCTTCTTCCCCTGGA 61.282 60.000 0.00 0.00 0.00 3.86
1022 1146 0.105778 CTCGAGCCCATCTTCTTCCC 59.894 60.000 0.00 0.00 0.00 3.97
1059 1183 0.252696 AGAGTGGGGCAGATACACCA 60.253 55.000 0.00 0.00 35.79 4.17
1099 1223 3.181422 TGGAGTTGAAGTAGTCCAGGAGA 60.181 47.826 0.00 0.00 41.59 3.71
1124 1248 2.356432 CCAGATCCTCCATGTCTTGCAA 60.356 50.000 0.00 0.00 0.00 4.08
1159 1283 1.209504 CCAAGGACATACGTGGTGGAT 59.790 52.381 0.00 0.00 0.00 3.41
1162 1286 0.321210 TGCCAAGGACATACGTGGTG 60.321 55.000 0.00 0.00 0.00 4.17
1168 1292 2.354821 GTCGGATTTGCCAAGGACATAC 59.645 50.000 0.00 0.00 35.94 2.39
1174 1298 2.485122 GCGTCGGATTTGCCAAGG 59.515 61.111 0.00 0.00 35.94 3.61
1192 1316 0.098200 TCTTGTACGGCGAGACGATG 59.902 55.000 16.62 5.60 32.81 3.84
1194 1318 1.499056 GTCTTGTACGGCGAGACGA 59.501 57.895 16.62 10.17 45.59 4.20
1245 1369 1.278985 AGAAATCCTCGGACATGTGCA 59.721 47.619 18.05 3.93 0.00 4.57
1343 1467 1.153429 GGAACCCGTTAGAGCGCAT 60.153 57.895 11.47 0.00 0.00 4.73
1391 1515 2.959030 TCTCCTTGACATACTCATCGGG 59.041 50.000 0.00 0.00 0.00 5.14
1431 1555 1.002274 TCCTCCTCCTGCTTCCTCC 59.998 63.158 0.00 0.00 0.00 4.30
1439 1563 0.967887 TTCTCACGCTCCTCCTCCTG 60.968 60.000 0.00 0.00 0.00 3.86
1591 1715 2.167861 GTCCTGCGCCGTCATCTTC 61.168 63.158 4.18 0.00 0.00 2.87
1603 1727 1.593196 TGTACTTGTGCTTGTCCTGC 58.407 50.000 0.00 0.00 0.00 4.85
1640 1764 2.419297 CCTTCCTCTTCTCCATGTTCCG 60.419 54.545 0.00 0.00 0.00 4.30
1791 1945 3.409026 AATCCTGCTCGATAACCATCC 57.591 47.619 0.00 0.00 0.00 3.51
1816 1970 1.810853 CATGCGACGACAGCCATCA 60.811 57.895 0.00 0.00 0.00 3.07
1817 1971 1.811266 ACATGCGACGACAGCCATC 60.811 57.895 0.00 0.00 0.00 3.51
2189 2369 3.256383 TCGACCGGTTGAAGAGAATGTTA 59.744 43.478 22.72 0.00 0.00 2.41
2283 2463 6.916360 TGAAATAAGCAGGAAGAACCAAAT 57.084 33.333 0.00 0.00 42.04 2.32
2348 2528 2.030274 ACCTATTTTGCAGTGGTTTCGC 60.030 45.455 0.00 0.00 0.00 4.70
2440 2621 1.235724 CTTCAAAGTCAACGGGGTCC 58.764 55.000 0.00 0.00 0.00 4.46
2494 2675 5.557576 TCATCAATGGTCTATCTTGGGAG 57.442 43.478 0.00 0.00 0.00 4.30
2678 2859 0.964358 GCAGACTGGGAGCAAGCAAT 60.964 55.000 4.26 0.00 0.00 3.56
2753 2934 1.177401 GGTCCAACAGGCATTCCTTC 58.823 55.000 0.00 0.00 41.93 3.46
2852 3033 5.300752 GTCATCAATACGACCAGATTCCAT 58.699 41.667 0.00 0.00 0.00 3.41
2878 3059 3.768878 AGGGAAGTATAGATGACCCTCG 58.231 50.000 0.00 0.00 43.37 4.63
2888 3069 5.755849 ACAATGTTTGGGAGGGAAGTATAG 58.244 41.667 0.00 0.00 34.12 1.31
2939 3120 4.442192 GGTTATCTCCATCTTGAAGTCGCT 60.442 45.833 0.00 0.00 0.00 4.93
3129 3310 2.862536 CAGTTGGACATCTGACATAGCG 59.137 50.000 4.74 0.00 34.02 4.26
3134 3315 2.170397 ACACACAGTTGGACATCTGACA 59.830 45.455 15.22 0.00 35.84 3.58
3155 3336 9.311676 TGGATATAATAAGGTACAACGGATACA 57.688 33.333 0.00 0.00 0.00 2.29
3161 3342 8.882415 ACAGTTGGATATAATAAGGTACAACG 57.118 34.615 0.00 0.00 41.13 4.10
3175 3356 6.367983 AGCCATTACATCAACAGTTGGATAT 58.632 36.000 13.52 0.00 0.00 1.63
3209 3390 3.681897 GGATACTTCACACAACAGAGCAG 59.318 47.826 0.00 0.00 0.00 4.24
3290 3471 6.711277 AGTTGAAATTATGCACTAGTCAGGA 58.289 36.000 0.00 0.00 0.00 3.86
3374 3555 8.402472 TCAACAAGAGTAAATCGAACAAAACAT 58.598 29.630 0.00 0.00 0.00 2.71
3571 3753 4.787551 TGGCAACCAGAAAGAAAACTAGA 58.212 39.130 0.00 0.00 0.00 2.43
3658 3840 2.589014 GCCTGCTGATTTTCGAAGTTG 58.411 47.619 0.00 0.00 0.00 3.16
3734 3916 2.110578 TCATCGCCAATGGAGAGAGAA 58.889 47.619 12.00 0.00 34.53 2.87
3800 3982 5.573337 ACTGCTGCCTCAATAGAATTTTC 57.427 39.130 0.00 0.00 0.00 2.29
3902 4084 7.788026 ACATAAGGACTGAATAACCGATTACA 58.212 34.615 0.00 0.00 0.00 2.41
3918 4100 8.893727 ACTAAAAAGTGATGCATACATAAGGAC 58.106 33.333 0.00 0.00 36.35 3.85
3982 4164 9.950680 GAGAATGAGAGATGTAACAAAACAAAA 57.049 29.630 0.00 0.00 32.02 2.44
3986 4168 7.604164 TGAGGAGAATGAGAGATGTAACAAAAC 59.396 37.037 0.00 0.00 0.00 2.43
3989 4171 6.857437 TGAGGAGAATGAGAGATGTAACAA 57.143 37.500 0.00 0.00 0.00 2.83
4093 4275 6.721208 TGAAAGCAAGATAGGGACAAAGAATT 59.279 34.615 0.00 0.00 0.00 2.17
4095 4277 5.473504 GTGAAAGCAAGATAGGGACAAAGAA 59.526 40.000 0.00 0.00 0.00 2.52
4173 4355 7.657354 GGCAAGAAAGAAAAATGTAAGGAATGT 59.343 33.333 0.00 0.00 0.00 2.71
4182 4364 5.070847 AGACATGGGCAAGAAAGAAAAATGT 59.929 36.000 0.00 0.00 0.00 2.71
4233 4415 4.067896 GTCCAATCACCTATATGCACAGG 58.932 47.826 8.87 8.87 37.97 4.00
4239 4421 6.830912 TCTTCCTTGTCCAATCACCTATATG 58.169 40.000 0.00 0.00 0.00 1.78
4267 4449 7.068716 GGCTTAATAAACCTGACCAATCTTGAT 59.931 37.037 0.00 0.00 0.00 2.57
4332 4514 4.021807 TCGGAACATTCACACTAACTAGCA 60.022 41.667 0.00 0.00 0.00 3.49
4521 4704 7.499321 TCGAATACAAAAACTTTAGGCAAGA 57.501 32.000 0.00 0.00 36.21 3.02


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

AutoCloner maintained by Alex Coulton.