Multiple sequence alignment - TraesCS2A01G088100

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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 TraesCS2A01G088100 chr2A 100.000 3544 0 0 1 3544 41245825 41242282 0.000000e+00 6545.0
1 TraesCS2A01G088100 chr2A 73.448 467 94 21 146 602 562102697 562103143 7.930000e-32 148.0
2 TraesCS2A01G088100 chr2A 78.947 133 19 6 1 124 104381059 104381191 8.150000e-12 82.4
3 TraesCS2A01G088100 chr2D 92.765 2557 119 19 999 3544 36802355 36799854 0.000000e+00 3637.0
4 TraesCS2A01G088100 chr2B 91.935 1773 124 9 869 2641 63304512 63302759 0.000000e+00 2464.0
5 TraesCS2A01G088100 chr2B 90.947 961 49 19 2595 3544 63302772 63301839 0.000000e+00 1258.0
6 TraesCS2A01G088100 chr2B 81.407 597 91 10 998 1586 64103298 64102714 1.490000e-128 470.0
7 TraesCS2A01G088100 chr2B 80.278 360 67 4 2187 2544 64102453 64102096 5.830000e-68 268.0
8 TraesCS2A01G088100 chr2B 90.164 183 17 1 1 183 63305011 63304830 1.640000e-58 237.0
9 TraesCS2A01G088100 chr2B 85.427 199 26 3 3280 3478 535683712 535683907 1.670000e-48 204.0
10 TraesCS2A01G088100 chr2B 75.904 415 74 18 201 602 17314283 17314684 4.670000e-44 189.0
11 TraesCS2A01G088100 chr7A 83.333 468 46 13 3075 3542 458397895 458397460 1.530000e-108 403.0
12 TraesCS2A01G088100 chr7A 81.841 402 30 14 3075 3476 1174712 1174354 7.440000e-77 298.0
13 TraesCS2A01G088100 chr4B 82.046 479 56 14 133 594 9547424 9547889 7.180000e-102 381.0
14 TraesCS2A01G088100 chr4B 80.421 475 67 14 133 594 9588374 9588835 4.380000e-89 339.0
15 TraesCS2A01G088100 chr4B 72.396 384 83 16 1 366 48620731 48621109 2.250000e-17 100.0
16 TraesCS2A01G088100 chr4B 83.505 97 13 2 433 526 450447153 450447249 1.750000e-13 87.9
17 TraesCS2A01G088100 chr5B 77.430 607 119 11 1 602 206112091 206111498 2.620000e-91 346.0
18 TraesCS2A01G088100 chr5B 73.482 494 90 22 138 602 71577951 71578432 7.930000e-32 148.0
19 TraesCS2A01G088100 chr5B 94.595 37 2 0 547 583 455811033 455811069 1.370000e-04 58.4
20 TraesCS2A01G088100 chrUn 90.213 235 10 5 2964 3195 427846755 427846979 9.620000e-76 294.0
21 TraesCS2A01G088100 chr7B 90.213 235 10 5 2964 3195 655732936 655733160 9.620000e-76 294.0
22 TraesCS2A01G088100 chr7B 90.213 235 10 5 2964 3195 745311585 745311361 9.620000e-76 294.0
23 TraesCS2A01G088100 chr3B 90.213 235 10 3 2964 3195 789000297 789000073 9.620000e-76 294.0
24 TraesCS2A01G088100 chr3B 90.129 233 10 3 2964 3193 826410904 826410682 1.240000e-74 291.0
25 TraesCS2A01G088100 chr3B 75.287 174 38 5 354 526 162518116 162518285 1.050000e-10 78.7
26 TraesCS2A01G088100 chr1B 90.213 235 10 5 2964 3195 5544263 5544039 9.620000e-76 294.0
27 TraesCS2A01G088100 chr1B 90.213 235 10 5 2964 3195 5544678 5544454 9.620000e-76 294.0
28 TraesCS2A01G088100 chr1B 89.787 235 11 5 2964 3195 23037945 23038169 4.480000e-74 289.0
29 TraesCS2A01G088100 chr1A 90.213 235 10 5 2964 3195 6284278 6284054 9.620000e-76 294.0
30 TraesCS2A01G088100 chr3A 87.719 228 24 3 3315 3542 618093448 618093225 2.710000e-66 263.0
31 TraesCS2A01G088100 chr3A 78.744 207 37 5 321 522 219811105 219810901 7.980000e-27 132.0
32 TraesCS2A01G088100 chr6B 75.061 409 78 16 213 602 217455980 217456383 6.080000e-38 169.0
33 TraesCS2A01G088100 chr5D 88.095 126 15 0 1 126 239577894 239578019 2.200000e-32 150.0
34 TraesCS2A01G088100 chr5D 76.984 126 28 1 253 378 130461211 130461335 1.770000e-08 71.3
35 TraesCS2A01G088100 chr6D 79.856 139 18 6 1 130 266747404 266747541 3.770000e-15 93.5
36 TraesCS2A01G088100 chr3D 83.871 93 12 1 437 526 378114113 378114205 6.300000e-13 86.1
37 TraesCS2A01G088100 chr6A 85.484 62 9 0 541 602 577697174 577697113 8.210000e-07 65.8
38 TraesCS2A01G088100 chr5A 93.333 45 2 1 544 588 461271887 461271844 8.210000e-07 65.8


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 TraesCS2A01G088100 chr2A 41242282 41245825 3543 True 6545.000000 6545 100.000000 1 3544 1 chr2A.!!$R1 3543
1 TraesCS2A01G088100 chr2D 36799854 36802355 2501 True 3637.000000 3637 92.765000 999 3544 1 chr2D.!!$R1 2545
2 TraesCS2A01G088100 chr2B 63301839 63305011 3172 True 1319.666667 2464 91.015333 1 3544 3 chr2B.!!$R1 3543
3 TraesCS2A01G088100 chr2B 64102096 64103298 1202 True 369.000000 470 80.842500 998 2544 2 chr2B.!!$R2 1546
4 TraesCS2A01G088100 chr5B 206111498 206112091 593 True 346.000000 346 77.430000 1 602 1 chr5B.!!$R1 601
5 TraesCS2A01G088100 chr1B 5544039 5544678 639 True 294.000000 294 90.213000 2964 3195 2 chr1B.!!$R1 231

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
515 544 0.030908 GGAAGGACGACGATGCCTAG 59.969 60.0 0.00 0.0 0.00 3.02 F
785 815 0.248907 ATACTGATCGAACCCGCGTG 60.249 55.0 4.92 0.0 35.37 5.34 F
1158 1191 0.521242 GCACGGCAGCTAATTGTTCG 60.521 55.0 0.00 0.0 0.00 3.95 F
1468 1501 0.532573 TCATCTTGAGTCGTGGAGGC 59.467 55.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1731 0.256464 TCCTCCTCCTCCTCGAACTC 59.744 60.0 0.00 0.0 0.0 3.01 R
1699 1732 0.257616 CTCCTCCTCCTCCTCGAACT 59.742 60.0 0.00 0.0 0.0 3.01 R
1997 2030 0.464373 ATGGCCATGTTAGCTCCACG 60.464 55.0 20.04 0.0 0.0 4.94 R
3269 3777 0.107800 GAAAAGCCCTAGGACCCGTC 60.108 60.0 11.48 0.0 0.0 4.79 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
33 34 4.627801 TACCAGGCGGCGTTTGCA 62.628 61.111 9.37 0.00 45.35 4.08
50 51 2.601367 AGCGGCCATGCAAACCTT 60.601 55.556 2.24 0.00 37.31 3.50
66 67 1.137825 CTTCGTCGAGGAGGAGTGC 59.862 63.158 11.41 0.00 0.00 4.40
189 211 3.197790 CGCCGACAGAGCCCATTG 61.198 66.667 0.00 0.00 0.00 2.82
190 212 2.268920 GCCGACAGAGCCCATTGA 59.731 61.111 0.00 0.00 0.00 2.57
191 213 1.817099 GCCGACAGAGCCCATTGAG 60.817 63.158 0.00 0.00 0.00 3.02
192 214 1.599047 CCGACAGAGCCCATTGAGT 59.401 57.895 0.00 0.00 0.00 3.41
193 215 0.742281 CCGACAGAGCCCATTGAGTG 60.742 60.000 0.00 0.00 0.00 3.51
194 216 0.036952 CGACAGAGCCCATTGAGTGT 60.037 55.000 0.00 0.00 0.00 3.55
195 217 1.609061 CGACAGAGCCCATTGAGTGTT 60.609 52.381 0.00 0.00 0.00 3.32
196 218 2.353704 CGACAGAGCCCATTGAGTGTTA 60.354 50.000 0.00 0.00 0.00 2.41
197 219 3.003480 GACAGAGCCCATTGAGTGTTAC 58.997 50.000 0.00 0.00 0.00 2.50
198 220 2.002586 CAGAGCCCATTGAGTGTTACG 58.997 52.381 0.00 0.00 0.00 3.18
199 221 1.623811 AGAGCCCATTGAGTGTTACGT 59.376 47.619 0.00 0.00 0.00 3.57
200 222 2.000447 GAGCCCATTGAGTGTTACGTC 59.000 52.381 0.00 0.00 0.00 4.34
201 223 1.623811 AGCCCATTGAGTGTTACGTCT 59.376 47.619 0.00 0.00 0.00 4.18
202 224 1.732259 GCCCATTGAGTGTTACGTCTG 59.268 52.381 0.00 0.00 0.00 3.51
233 261 3.108289 CACGAGTGGCTCAGCACG 61.108 66.667 0.00 0.82 0.00 5.34
257 285 4.400109 GTCTGGCTCGACGCGACA 62.400 66.667 15.93 0.00 40.44 4.35
285 313 1.153549 GAAGCCGCCAATCTCGAGT 60.154 57.895 13.13 0.00 0.00 4.18
286 314 0.102481 GAAGCCGCCAATCTCGAGTA 59.898 55.000 13.13 0.00 0.00 2.59
292 320 1.134367 CGCCAATCTCGAGTAGTGGAA 59.866 52.381 25.34 3.31 0.00 3.53
296 324 3.443037 CAATCTCGAGTAGTGGAAGCAG 58.557 50.000 13.13 0.00 0.00 4.24
298 326 0.524392 CTCGAGTAGTGGAAGCAGCG 60.524 60.000 3.62 0.00 0.00 5.18
299 327 1.517257 CGAGTAGTGGAAGCAGCGG 60.517 63.158 0.00 0.00 0.00 5.52
301 329 1.889530 GAGTAGTGGAAGCAGCGGGT 61.890 60.000 0.00 0.00 0.00 5.28
344 372 2.308769 CGAGCGGCTCATGCAGATC 61.309 63.158 27.83 0.46 44.13 2.75
351 379 2.646445 CTCATGCAGATCGAGCGCG 61.646 63.158 2.41 2.41 39.35 6.86
414 442 2.186826 GCAGTGAAACCGGTGCAGT 61.187 57.895 8.52 10.28 37.80 4.40
415 443 1.648720 CAGTGAAACCGGTGCAGTG 59.351 57.895 23.28 23.28 37.80 3.66
418 446 3.670377 GAAACCGGTGCAGTGGGC 61.670 66.667 8.52 0.00 45.13 5.36
445 473 4.208686 CCGTGCCTAGGAGACGGC 62.209 72.222 29.50 10.19 45.55 5.68
487 516 1.064946 CGGAGCTCATCGACCTCAC 59.935 63.158 17.19 0.00 0.00 3.51
488 517 1.657751 CGGAGCTCATCGACCTCACA 61.658 60.000 17.19 0.00 0.00 3.58
489 518 0.532573 GGAGCTCATCGACCTCACAA 59.467 55.000 17.19 0.00 0.00 3.33
515 544 0.030908 GGAAGGACGACGATGCCTAG 59.969 60.000 0.00 0.00 0.00 3.02
576 606 3.314357 AGTTTAAGTGAACTTTGACCGGC 59.686 43.478 0.00 0.00 36.49 6.13
583 613 1.265905 GAACTTTGACCGGCGTTTGAT 59.734 47.619 6.01 0.00 0.00 2.57
611 641 8.649841 GGAGTTTTAATGTTTAAAAATACGCCC 58.350 33.333 6.72 1.57 0.00 6.13
613 643 7.328982 AGTTTTAATGTTTAAAAATACGCCCGG 59.671 33.333 0.00 0.00 0.00 5.73
615 645 2.161030 TGTTTAAAAATACGCCCGGCT 58.839 42.857 8.05 0.00 0.00 5.52
632 662 3.271706 CTGGTGTTGGGTGCATGCG 62.272 63.158 14.09 0.00 0.00 4.73
637 667 3.364441 TTGGGTGCATGCGCTGAC 61.364 61.111 28.86 19.56 39.64 3.51
640 670 2.743538 GGTGCATGCGCTGACTCA 60.744 61.111 28.86 0.00 39.64 3.41
644 674 0.883153 TGCATGCGCTGACTCAAAAT 59.117 45.000 14.09 0.00 39.64 1.82
648 678 3.567530 CATGCGCTGACTCAAAATCAAA 58.432 40.909 9.73 0.00 0.00 2.69
657 687 4.201970 TGACTCAAAATCAAAACCGGACAC 60.202 41.667 9.46 0.00 0.00 3.67
669 699 1.238439 CCGGACACAAACATCTGCTT 58.762 50.000 0.00 0.00 0.00 3.91
695 725 3.123157 TCCCAAACGGACAAAATACGA 57.877 42.857 0.00 0.00 34.86 3.43
696 726 3.474600 TCCCAAACGGACAAAATACGAA 58.525 40.909 0.00 0.00 34.86 3.85
697 727 3.881688 TCCCAAACGGACAAAATACGAAA 59.118 39.130 0.00 0.00 34.86 3.46
698 728 4.337555 TCCCAAACGGACAAAATACGAAAA 59.662 37.500 0.00 0.00 34.86 2.29
699 729 5.041940 CCCAAACGGACAAAATACGAAAAA 58.958 37.500 0.00 0.00 0.00 1.94
722 752 2.661866 GCGTCTGTGCAGGTCGTT 60.662 61.111 14.57 0.00 34.15 3.85
723 753 2.658707 GCGTCTGTGCAGGTCGTTC 61.659 63.158 14.57 2.08 34.15 3.95
724 754 2.365068 CGTCTGTGCAGGTCGTTCG 61.365 63.158 0.00 0.00 0.00 3.95
725 755 2.022129 GTCTGTGCAGGTCGTTCGG 61.022 63.158 0.00 0.00 0.00 4.30
726 756 2.029073 CTGTGCAGGTCGTTCGGT 59.971 61.111 0.00 0.00 0.00 4.69
727 757 1.594293 CTGTGCAGGTCGTTCGGTT 60.594 57.895 0.00 0.00 0.00 4.44
728 758 1.831389 CTGTGCAGGTCGTTCGGTTG 61.831 60.000 0.00 0.00 0.00 3.77
729 759 2.280524 TGCAGGTCGTTCGGTTGG 60.281 61.111 0.00 0.00 0.00 3.77
730 760 2.029964 GCAGGTCGTTCGGTTGGA 59.970 61.111 0.00 0.00 0.00 3.53
731 761 2.027625 GCAGGTCGTTCGGTTGGAG 61.028 63.158 0.00 0.00 0.00 3.86
732 762 1.366366 CAGGTCGTTCGGTTGGAGT 59.634 57.895 0.00 0.00 0.00 3.85
733 763 0.249741 CAGGTCGTTCGGTTGGAGTT 60.250 55.000 0.00 0.00 0.00 3.01
734 764 0.249741 AGGTCGTTCGGTTGGAGTTG 60.250 55.000 0.00 0.00 0.00 3.16
735 765 1.568025 GTCGTTCGGTTGGAGTTGC 59.432 57.895 0.00 0.00 0.00 4.17
736 766 0.878961 GTCGTTCGGTTGGAGTTGCT 60.879 55.000 0.00 0.00 0.00 3.91
737 767 0.599204 TCGTTCGGTTGGAGTTGCTC 60.599 55.000 0.00 0.00 0.00 4.26
738 768 0.600255 CGTTCGGTTGGAGTTGCTCT 60.600 55.000 0.00 0.00 0.00 4.09
739 769 1.336517 CGTTCGGTTGGAGTTGCTCTA 60.337 52.381 0.00 0.00 0.00 2.43
740 770 2.762745 GTTCGGTTGGAGTTGCTCTAA 58.237 47.619 0.00 0.00 0.00 2.10
741 771 2.450609 TCGGTTGGAGTTGCTCTAAC 57.549 50.000 14.33 14.33 46.44 2.34
745 775 1.807142 GTTGGAGTTGCTCTAACCTGC 59.193 52.381 12.41 0.00 43.15 4.85
746 776 1.352083 TGGAGTTGCTCTAACCTGCT 58.648 50.000 0.00 0.00 40.24 4.24
747 777 1.002430 TGGAGTTGCTCTAACCTGCTG 59.998 52.381 0.00 0.00 40.24 4.41
748 778 1.002544 GGAGTTGCTCTAACCTGCTGT 59.997 52.381 0.00 0.00 40.24 4.40
749 779 2.233922 GGAGTTGCTCTAACCTGCTGTA 59.766 50.000 0.00 0.00 40.24 2.74
750 780 3.306780 GGAGTTGCTCTAACCTGCTGTAA 60.307 47.826 0.00 0.00 40.24 2.41
751 781 4.315803 GAGTTGCTCTAACCTGCTGTAAA 58.684 43.478 0.00 0.00 40.24 2.01
752 782 4.319177 AGTTGCTCTAACCTGCTGTAAAG 58.681 43.478 0.00 0.00 40.24 1.85
753 783 4.040461 AGTTGCTCTAACCTGCTGTAAAGA 59.960 41.667 0.00 0.00 40.24 2.52
754 784 4.617253 TGCTCTAACCTGCTGTAAAGAA 57.383 40.909 0.00 0.00 0.00 2.52
755 785 4.968259 TGCTCTAACCTGCTGTAAAGAAA 58.032 39.130 0.00 0.00 0.00 2.52
756 786 5.373222 TGCTCTAACCTGCTGTAAAGAAAA 58.627 37.500 0.00 0.00 0.00 2.29
757 787 5.238650 TGCTCTAACCTGCTGTAAAGAAAAC 59.761 40.000 0.00 0.00 0.00 2.43
758 788 5.238650 GCTCTAACCTGCTGTAAAGAAAACA 59.761 40.000 0.00 0.00 0.00 2.83
759 789 6.566753 GCTCTAACCTGCTGTAAAGAAAACAG 60.567 42.308 0.00 0.00 45.80 3.16
760 790 6.354130 TCTAACCTGCTGTAAAGAAAACAGT 58.646 36.000 5.25 0.00 45.01 3.55
761 791 7.502696 TCTAACCTGCTGTAAAGAAAACAGTA 58.497 34.615 5.25 0.04 45.01 2.74
762 792 7.988599 TCTAACCTGCTGTAAAGAAAACAGTAA 59.011 33.333 5.25 0.00 45.01 2.24
763 793 6.373186 ACCTGCTGTAAAGAAAACAGTAAC 57.627 37.500 5.25 0.00 45.01 2.50
764 794 5.007332 ACCTGCTGTAAAGAAAACAGTAACG 59.993 40.000 5.25 0.00 45.01 3.18
765 795 5.007332 CCTGCTGTAAAGAAAACAGTAACGT 59.993 40.000 5.25 0.00 45.01 3.99
766 796 6.201425 CCTGCTGTAAAGAAAACAGTAACGTA 59.799 38.462 5.25 0.00 45.01 3.57
767 797 7.095355 CCTGCTGTAAAGAAAACAGTAACGTAT 60.095 37.037 5.25 0.00 45.01 3.06
768 798 8.815141 TGCTGTAAAGAAAACAGTAACGTATA 57.185 30.769 5.25 0.00 45.01 1.47
769 799 8.702438 TGCTGTAAAGAAAACAGTAACGTATAC 58.298 33.333 5.25 0.00 45.01 1.47
770 800 8.919661 GCTGTAAAGAAAACAGTAACGTATACT 58.080 33.333 0.56 0.00 45.01 2.12
772 802 9.964303 TGTAAAGAAAACAGTAACGTATACTGA 57.036 29.630 28.68 12.47 45.69 3.41
775 805 7.966157 AGAAAACAGTAACGTATACTGATCG 57.034 36.000 28.68 13.67 45.69 3.69
776 806 7.755591 AGAAAACAGTAACGTATACTGATCGA 58.244 34.615 28.68 0.00 45.69 3.59
777 807 8.239314 AGAAAACAGTAACGTATACTGATCGAA 58.761 33.333 28.68 0.00 45.69 3.71
778 808 7.731556 AAACAGTAACGTATACTGATCGAAC 57.268 36.000 28.68 0.00 45.69 3.95
779 809 5.814783 ACAGTAACGTATACTGATCGAACC 58.185 41.667 28.68 0.00 45.69 3.62
780 810 5.210715 CAGTAACGTATACTGATCGAACCC 58.789 45.833 22.62 0.00 45.69 4.11
781 811 3.344904 AACGTATACTGATCGAACCCG 57.655 47.619 0.56 0.00 37.07 5.28
782 812 1.002033 ACGTATACTGATCGAACCCGC 60.002 52.381 0.56 0.00 35.37 6.13
783 813 1.682982 GTATACTGATCGAACCCGCG 58.317 55.000 0.00 0.00 35.37 6.46
784 814 1.002033 GTATACTGATCGAACCCGCGT 60.002 52.381 4.92 0.00 35.37 6.01
785 815 0.248907 ATACTGATCGAACCCGCGTG 60.249 55.000 4.92 0.00 35.37 5.34
786 816 2.274232 TACTGATCGAACCCGCGTGG 62.274 60.000 8.42 8.42 41.37 4.94
796 826 2.032071 CCGCGTGGGAGGTTTTCT 59.968 61.111 7.26 0.00 38.47 2.52
797 827 1.599797 CCGCGTGGGAGGTTTTCTT 60.600 57.895 7.26 0.00 38.47 2.52
798 828 1.574702 CCGCGTGGGAGGTTTTCTTC 61.575 60.000 7.26 0.00 38.47 2.87
799 829 0.602905 CGCGTGGGAGGTTTTCTTCT 60.603 55.000 0.00 0.00 0.00 2.85
800 830 1.605753 GCGTGGGAGGTTTTCTTCTT 58.394 50.000 0.00 0.00 0.00 2.52
801 831 1.535896 GCGTGGGAGGTTTTCTTCTTC 59.464 52.381 0.00 0.00 0.00 2.87
802 832 2.152016 CGTGGGAGGTTTTCTTCTTCC 58.848 52.381 0.00 0.00 0.00 3.46
803 833 2.486548 CGTGGGAGGTTTTCTTCTTCCA 60.487 50.000 0.00 0.00 0.00 3.53
804 834 3.767711 GTGGGAGGTTTTCTTCTTCCAT 58.232 45.455 0.00 0.00 0.00 3.41
805 835 4.564821 CGTGGGAGGTTTTCTTCTTCCATA 60.565 45.833 0.00 0.00 0.00 2.74
806 836 5.321927 GTGGGAGGTTTTCTTCTTCCATAA 58.678 41.667 0.00 0.00 0.00 1.90
807 837 5.773176 GTGGGAGGTTTTCTTCTTCCATAAA 59.227 40.000 0.00 0.00 0.00 1.40
808 838 6.266786 GTGGGAGGTTTTCTTCTTCCATAAAA 59.733 38.462 0.00 0.00 0.00 1.52
809 839 6.841755 TGGGAGGTTTTCTTCTTCCATAAAAA 59.158 34.615 0.00 0.00 0.00 1.94
829 859 5.545658 AAAATTGCTGATCGAATACGTGT 57.454 34.783 0.00 0.00 40.69 4.49
830 860 5.545658 AAATTGCTGATCGAATACGTGTT 57.454 34.783 0.00 0.00 40.69 3.32
831 861 3.989705 TTGCTGATCGAATACGTGTTG 57.010 42.857 0.91 0.00 40.69 3.33
832 862 2.267426 TGCTGATCGAATACGTGTTGG 58.733 47.619 0.91 0.71 40.69 3.77
833 863 2.268298 GCTGATCGAATACGTGTTGGT 58.732 47.619 0.91 0.00 40.69 3.67
834 864 2.671396 GCTGATCGAATACGTGTTGGTT 59.329 45.455 0.91 0.00 40.69 3.67
835 865 3.124636 GCTGATCGAATACGTGTTGGTTT 59.875 43.478 0.91 0.00 40.69 3.27
836 866 4.724036 GCTGATCGAATACGTGTTGGTTTC 60.724 45.833 0.91 4.36 40.69 2.78
837 867 3.365520 TGATCGAATACGTGTTGGTTTCG 59.634 43.478 0.91 0.00 40.23 3.46
838 868 1.456544 TCGAATACGTGTTGGTTTCGC 59.543 47.619 0.91 0.00 39.10 4.70
839 869 1.458064 CGAATACGTGTTGGTTTCGCT 59.542 47.619 0.91 0.00 33.70 4.93
840 870 2.720590 CGAATACGTGTTGGTTTCGCTG 60.721 50.000 0.91 0.00 33.70 5.18
841 871 1.873698 ATACGTGTTGGTTTCGCTGT 58.126 45.000 0.00 0.00 0.00 4.40
842 872 0.931702 TACGTGTTGGTTTCGCTGTG 59.068 50.000 0.00 0.00 0.00 3.66
843 873 1.010125 CGTGTTGGTTTCGCTGTGG 60.010 57.895 0.00 0.00 0.00 4.17
844 874 1.358759 GTGTTGGTTTCGCTGTGGG 59.641 57.895 0.00 0.00 0.00 4.61
845 875 1.826054 TGTTGGTTTCGCTGTGGGG 60.826 57.895 0.00 0.00 0.00 4.96
846 876 2.909965 TTGGTTTCGCTGTGGGGC 60.910 61.111 0.00 0.00 0.00 5.80
847 877 3.429372 TTGGTTTCGCTGTGGGGCT 62.429 57.895 0.00 0.00 0.00 5.19
848 878 2.597510 GGTTTCGCTGTGGGGCTT 60.598 61.111 0.00 0.00 0.00 4.35
849 879 2.200337 GGTTTCGCTGTGGGGCTTT 61.200 57.895 0.00 0.00 0.00 3.51
850 880 1.285950 GTTTCGCTGTGGGGCTTTC 59.714 57.895 0.00 0.00 0.00 2.62
851 881 1.901464 TTTCGCTGTGGGGCTTTCC 60.901 57.895 0.00 0.00 0.00 3.13
852 882 4.697756 TCGCTGTGGGGCTTTCCG 62.698 66.667 0.00 0.00 36.01 4.30
854 884 3.056328 GCTGTGGGGCTTTCCGTC 61.056 66.667 0.00 0.00 36.01 4.79
855 885 2.359975 CTGTGGGGCTTTCCGTCC 60.360 66.667 0.00 0.00 36.34 4.79
860 890 4.468689 GGGCTTTCCGTCCCCGAG 62.469 72.222 0.00 0.00 36.50 4.63
861 891 3.703127 GGCTTTCCGTCCCCGAGT 61.703 66.667 0.00 0.00 35.63 4.18
862 892 2.125633 GCTTTCCGTCCCCGAGTC 60.126 66.667 0.00 0.00 35.63 3.36
863 893 2.181021 CTTTCCGTCCCCGAGTCG 59.819 66.667 5.29 5.29 35.63 4.18
864 894 3.984200 CTTTCCGTCCCCGAGTCGC 62.984 68.421 7.12 0.00 35.63 5.19
892 922 5.454755 GGGGCTTGCATCCGTGTATATATAT 60.455 44.000 0.00 0.00 0.00 0.86
893 923 6.239487 GGGGCTTGCATCCGTGTATATATATA 60.239 42.308 0.00 0.00 0.00 0.86
947 977 3.118482 TCAGTCTCCTGGAATTGATCAGC 60.118 47.826 0.00 0.00 39.31 4.26
979 1009 2.798689 CTAGCTACACGCGCCAGA 59.201 61.111 5.73 0.00 45.59 3.86
1026 1059 1.221021 GTCATGGTCCGAACTCCCC 59.779 63.158 0.00 0.00 0.00 4.81
1027 1060 1.229368 TCATGGTCCGAACTCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
1037 1070 0.908198 GAACTCCCCACATGAGCTCT 59.092 55.000 16.19 0.00 32.98 4.09
1132 1165 4.436998 GCTCTGCGCTACCACGGT 62.437 66.667 9.73 0.00 35.14 4.83
1150 1183 4.393155 CACCAGGCACGGCAGCTA 62.393 66.667 0.00 0.00 34.17 3.32
1153 1186 1.750399 CCAGGCACGGCAGCTAATT 60.750 57.895 0.00 0.00 34.17 1.40
1156 1189 0.609131 AGGCACGGCAGCTAATTGTT 60.609 50.000 0.00 0.00 34.17 2.83
1158 1191 0.521242 GCACGGCAGCTAATTGTTCG 60.521 55.000 0.00 0.00 0.00 3.95
1162 1195 1.448985 GGCAGCTAATTGTTCGACCA 58.551 50.000 0.00 0.00 0.00 4.02
1164 1197 1.398390 GCAGCTAATTGTTCGACCAGG 59.602 52.381 0.00 0.00 0.00 4.45
1346 1379 4.238385 TTCCGCTTGAACTCGACG 57.762 55.556 0.00 0.00 0.00 5.12
1426 1459 2.125326 CCTGATCGTGGCCGTCCTA 61.125 63.158 0.00 0.00 35.01 2.94
1468 1501 0.532573 TCATCTTGAGTCGTGGAGGC 59.467 55.000 0.00 0.00 0.00 4.70
1513 1546 5.936372 GTCGTGGGACCTTCTTTATAACTTT 59.064 40.000 0.00 0.00 37.19 2.66
1592 1625 4.593206 ACCTCTTTCCGATTGATATAGGCA 59.407 41.667 0.00 0.00 0.00 4.75
1696 1729 3.091529 CGAGTCCGAGTCCGAGTC 58.908 66.667 6.32 6.32 38.22 3.36
1697 1730 2.462782 CGAGTCCGAGTCCGAGTCC 61.463 68.421 9.78 0.00 38.22 3.85
1698 1731 2.436292 AGTCCGAGTCCGAGTCCG 60.436 66.667 0.00 0.00 38.22 4.79
1699 1732 2.435586 GTCCGAGTCCGAGTCCGA 60.436 66.667 0.00 0.00 38.22 4.55
1700 1733 2.125229 TCCGAGTCCGAGTCCGAG 60.125 66.667 0.00 0.00 38.22 4.63
1701 1734 2.436292 CCGAGTCCGAGTCCGAGT 60.436 66.667 0.00 0.00 38.22 4.18
1702 1735 2.039405 CCGAGTCCGAGTCCGAGTT 61.039 63.158 0.00 0.00 38.22 3.01
1703 1736 1.424635 CGAGTCCGAGTCCGAGTTC 59.575 63.158 0.00 0.00 38.22 3.01
1784 1817 1.840635 GGGGTAGCTGGAACTTCAGAT 59.159 52.381 0.00 0.00 36.93 2.90
1797 1830 2.202987 CAGATGAGGAGGCGGTGC 60.203 66.667 0.00 0.00 0.00 5.01
1869 1902 4.399004 ACACTAGATGAAGAGGCATCAC 57.601 45.455 0.00 0.00 45.52 3.06
1875 1908 0.684535 TGAAGAGGCATCACGGACAA 59.315 50.000 0.00 0.00 0.00 3.18
1907 1940 1.064060 GCAACCGTGCCATTAGATGAC 59.936 52.381 0.00 0.00 45.68 3.06
1913 1946 3.384668 CGTGCCATTAGATGACTTCGAT 58.615 45.455 0.00 0.00 0.00 3.59
1914 1947 4.546570 CGTGCCATTAGATGACTTCGATA 58.453 43.478 0.00 0.00 0.00 2.92
1917 1950 6.183360 CGTGCCATTAGATGACTTCGATAATC 60.183 42.308 0.00 0.00 0.00 1.75
1936 1969 5.422214 AATCAGGAGGTAGTCGAAACATT 57.578 39.130 0.00 0.00 0.00 2.71
1952 1985 1.899814 ACATTAGACGAGGAGGCAACA 59.100 47.619 0.00 0.00 41.41 3.33
1957 1990 1.625818 AGACGAGGAGGCAACAAAGAT 59.374 47.619 0.00 0.00 41.41 2.40
1997 2030 2.443416 GTGGTAGGGGGAACATCAAAC 58.557 52.381 0.00 0.00 0.00 2.93
2019 2052 3.287222 GTGGAGCTAACATGGCCATTAA 58.713 45.455 17.92 3.13 0.00 1.40
2033 2066 4.335315 TGGCCATTAAACGATGATCTTGAC 59.665 41.667 0.00 0.00 0.00 3.18
2047 2080 1.616865 TCTTGACGAAGAATGGGACGT 59.383 47.619 0.00 0.00 41.57 4.34
2057 2090 2.501316 AGAATGGGACGTGACATCATCA 59.499 45.455 0.00 0.00 33.79 3.07
2064 2097 3.325870 GACGTGACATCATCAGAAACCA 58.674 45.455 0.00 0.00 38.28 3.67
2089 2122 1.528542 TCGCATACGAGGAGGAGGG 60.529 63.158 0.00 0.00 45.12 4.30
2102 2135 2.158081 GGAGGAGGGTGAGGAGGATATT 60.158 54.545 0.00 0.00 0.00 1.28
2167 2200 2.034685 ACTATGTGTACGATGATGCGCT 59.965 45.455 9.73 0.00 33.86 5.92
2219 2252 1.946768 CTTGTGGAGTCTTGCGGAAAA 59.053 47.619 0.00 0.00 0.00 2.29
2285 2318 0.179150 TGCCAACACGTTTCACTTGC 60.179 50.000 0.00 0.00 0.00 4.01
2301 2334 3.882888 CACTTGCCAAGTAGAGGTTTTCA 59.117 43.478 10.26 0.00 40.46 2.69
2335 2368 1.220749 CATGGGTTCCGATGACCGT 59.779 57.895 7.87 0.00 38.08 4.83
2342 2375 0.245539 TTCCGATGACCGTTGGACTC 59.754 55.000 0.00 0.00 36.31 3.36
2343 2376 1.516386 CCGATGACCGTTGGACTCG 60.516 63.158 0.00 0.00 36.31 4.18
2405 2441 1.303317 GGTTCCCGCATCTTGTGGT 60.303 57.895 6.37 0.00 46.25 4.16
2422 2458 3.960755 TGTGGTGATGTCGAGAAGGATAT 59.039 43.478 0.00 0.00 0.00 1.63
2461 2497 2.675844 CCGGCGAAGTGTTCAATATGAA 59.324 45.455 9.30 0.00 33.32 2.57
2464 2500 4.142902 CGGCGAAGTGTTCAATATGAAGTT 60.143 41.667 0.00 0.00 37.00 2.66
2526 2562 5.366477 ACATTTGAAACATGGGTCTTTCCTT 59.634 36.000 0.00 0.00 36.25 3.36
2566 2602 0.584876 GTGGGCTTGTACACGACAAC 59.415 55.000 7.60 1.78 43.30 3.32
2567 2603 0.178301 TGGGCTTGTACACGACAACA 59.822 50.000 7.60 0.00 43.30 3.33
2568 2604 1.301423 GGGCTTGTACACGACAACAA 58.699 50.000 7.60 0.00 43.30 2.83
2610 2646 3.691118 GGATGCACATTGAGCTAGTTGAA 59.309 43.478 7.58 0.00 0.00 2.69
2616 2652 6.642131 TGCACATTGAGCTAGTTGAATTTTTC 59.358 34.615 7.58 0.00 0.00 2.29
2621 2657 8.919661 CATTGAGCTAGTTGAATTTTTCTTTCC 58.080 33.333 0.00 0.00 0.00 3.13
2638 2705 1.271856 TCCGGGTGACATTGAGCTAA 58.728 50.000 0.00 0.00 0.00 3.09
2789 2873 6.714492 CCAAAATTTTCTTTCTTTTGACGGG 58.286 36.000 0.00 0.00 40.58 5.28
2808 2892 1.064654 GGAATTGGCGTGAATCAGAGC 59.935 52.381 2.55 2.55 0.00 4.09
2880 2967 6.293353 GGAACGAAAACGTAAACCTTGGAATA 60.293 38.462 0.00 0.00 0.00 1.75
3015 3105 1.762957 TCCGATCATTCCTTCCCAGTC 59.237 52.381 0.00 0.00 0.00 3.51
3016 3106 1.539065 CCGATCATTCCTTCCCAGTCG 60.539 57.143 0.00 0.00 0.00 4.18
3017 3107 1.587547 GATCATTCCTTCCCAGTCGC 58.412 55.000 0.00 0.00 0.00 5.19
3018 3108 0.181350 ATCATTCCTTCCCAGTCGCC 59.819 55.000 0.00 0.00 0.00 5.54
3019 3109 1.815421 CATTCCTTCCCAGTCGCCG 60.815 63.158 0.00 0.00 0.00 6.46
3020 3110 3.682292 ATTCCTTCCCAGTCGCCGC 62.682 63.158 0.00 0.00 0.00 6.53
3498 4013 1.123928 CGGGATTCCTAGTGAGCCTT 58.876 55.000 2.01 0.00 0.00 4.35
3533 4048 7.202016 TCCGCTGGTTAATTATGATTCATTC 57.798 36.000 4.14 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.601367 AAGGTTTGCATGGCCGCT 60.601 55.556 0.00 0.00 0.00 5.52
50 51 2.750637 GGCACTCCTCCTCGACGA 60.751 66.667 0.00 0.00 0.00 4.20
66 67 3.072468 TCCGCCTCCACCTTACGG 61.072 66.667 0.00 0.00 45.15 4.02
74 75 2.363795 CCTGGTAGTCCGCCTCCA 60.364 66.667 0.00 0.00 36.30 3.86
183 205 2.028476 TCCAGACGTAACACTCAATGGG 60.028 50.000 0.00 0.00 0.00 4.00
184 206 2.993899 GTCCAGACGTAACACTCAATGG 59.006 50.000 0.00 0.00 0.00 3.16
185 207 2.993899 GGTCCAGACGTAACACTCAATG 59.006 50.000 0.00 0.00 0.00 2.82
186 208 2.352421 CGGTCCAGACGTAACACTCAAT 60.352 50.000 0.00 0.00 0.00 2.57
187 209 1.001048 CGGTCCAGACGTAACACTCAA 60.001 52.381 0.00 0.00 0.00 3.02
188 210 0.594602 CGGTCCAGACGTAACACTCA 59.405 55.000 0.00 0.00 0.00 3.41
189 211 0.109412 CCGGTCCAGACGTAACACTC 60.109 60.000 0.00 0.00 0.00 3.51
190 212 1.962144 CCGGTCCAGACGTAACACT 59.038 57.895 0.00 0.00 0.00 3.55
191 213 1.735559 GCCGGTCCAGACGTAACAC 60.736 63.158 1.90 0.00 0.00 3.32
192 214 2.652530 GCCGGTCCAGACGTAACA 59.347 61.111 1.90 0.00 0.00 2.41
193 215 2.125793 GGCCGGTCCAGACGTAAC 60.126 66.667 1.90 0.00 34.01 2.50
194 216 2.601067 TGGCCGGTCCAGACGTAA 60.601 61.111 12.86 0.00 40.72 3.18
266 294 1.142748 CTCGAGATTGGCGGCTTCT 59.857 57.895 6.58 12.58 0.00 2.85
269 297 1.038130 ACTACTCGAGATTGGCGGCT 61.038 55.000 21.68 0.00 0.00 5.52
275 303 3.443037 CTGCTTCCACTACTCGAGATTG 58.557 50.000 21.68 12.14 0.00 2.67
276 304 2.159170 GCTGCTTCCACTACTCGAGATT 60.159 50.000 21.68 0.00 0.00 2.40
278 306 0.811915 GCTGCTTCCACTACTCGAGA 59.188 55.000 21.68 1.61 0.00 4.04
285 313 2.662596 CACCCGCTGCTTCCACTA 59.337 61.111 0.00 0.00 0.00 2.74
296 324 2.125832 TTGTACGCTAGCACCCGC 60.126 61.111 16.45 0.27 38.99 6.13
298 326 2.165301 CGCTTGTACGCTAGCACCC 61.165 63.158 16.45 1.37 42.23 4.61
299 327 3.384927 CGCTTGTACGCTAGCACC 58.615 61.111 16.45 1.76 42.23 5.01
351 379 1.826487 GACGCTCCTCCTCCTCCTC 60.826 68.421 0.00 0.00 0.00 3.71
353 381 3.213402 CGACGCTCCTCCTCCTCC 61.213 72.222 0.00 0.00 0.00 4.30
354 382 2.438795 ACGACGCTCCTCCTCCTC 60.439 66.667 0.00 0.00 0.00 3.71
355 383 2.752238 CACGACGCTCCTCCTCCT 60.752 66.667 0.00 0.00 0.00 3.69
356 384 4.500116 GCACGACGCTCCTCCTCC 62.500 72.222 0.00 0.00 37.77 4.30
398 426 1.525995 CCACTGCACCGGTTTCACT 60.526 57.895 2.97 0.00 0.00 3.41
436 464 4.698625 AGGGGAACGCCGTCTCCT 62.699 66.667 14.89 9.55 44.28 3.69
487 516 4.778143 CGTCCTTCCCCGGGCTTG 62.778 72.222 17.73 6.40 0.00 4.01
576 606 8.716619 TTAAACATTAAAACTCCGATCAAACG 57.283 30.769 0.00 0.00 0.00 3.60
583 613 9.116054 GCGTATTTTTAAACATTAAAACTCCGA 57.884 29.630 11.76 0.00 0.00 4.55
613 643 2.652530 CATGCACCCAACACCAGC 59.347 61.111 0.00 0.00 0.00 4.85
615 645 3.293714 CGCATGCACCCAACACCA 61.294 61.111 19.57 0.00 0.00 4.17
632 662 3.004315 TCCGGTTTTGATTTTGAGTCAGC 59.996 43.478 0.00 0.00 0.00 4.26
637 667 4.300189 TGTGTCCGGTTTTGATTTTGAG 57.700 40.909 0.00 0.00 0.00 3.02
640 670 4.822026 TGTTTGTGTCCGGTTTTGATTTT 58.178 34.783 0.00 0.00 0.00 1.82
644 674 3.066064 CAGATGTTTGTGTCCGGTTTTGA 59.934 43.478 0.00 0.00 0.00 2.69
648 678 0.951558 GCAGATGTTTGTGTCCGGTT 59.048 50.000 0.00 0.00 0.00 4.44
657 687 1.068055 GGACAGCCAAGCAGATGTTTG 60.068 52.381 2.74 2.74 36.24 2.93
696 726 0.248825 TGCACAGACGCGCAATTTTT 60.249 45.000 5.73 0.00 34.59 1.94
697 727 0.661187 CTGCACAGACGCGCAATTTT 60.661 50.000 5.73 0.00 37.76 1.82
698 728 1.081906 CTGCACAGACGCGCAATTT 60.082 52.632 5.73 0.00 37.76 1.82
699 729 2.557805 CTGCACAGACGCGCAATT 59.442 55.556 5.73 0.00 37.76 2.32
700 730 3.425713 CCTGCACAGACGCGCAAT 61.426 61.111 5.73 0.00 37.76 3.56
701 731 4.908687 ACCTGCACAGACGCGCAA 62.909 61.111 5.73 0.00 37.76 4.85
705 735 2.658707 GAACGACCTGCACAGACGC 61.659 63.158 13.80 0.00 33.83 5.19
706 736 2.365068 CGAACGACCTGCACAGACG 61.365 63.158 12.81 12.81 35.49 4.18
707 737 2.022129 CCGAACGACCTGCACAGAC 61.022 63.158 0.00 0.00 0.00 3.51
708 738 2.023414 AACCGAACGACCTGCACAGA 62.023 55.000 0.00 0.00 0.00 3.41
709 739 1.594293 AACCGAACGACCTGCACAG 60.594 57.895 0.00 0.00 0.00 3.66
710 740 1.885388 CAACCGAACGACCTGCACA 60.885 57.895 0.00 0.00 0.00 4.57
711 741 2.604174 CCAACCGAACGACCTGCAC 61.604 63.158 0.00 0.00 0.00 4.57
712 742 2.280524 CCAACCGAACGACCTGCA 60.281 61.111 0.00 0.00 0.00 4.41
713 743 2.027625 CTCCAACCGAACGACCTGC 61.028 63.158 0.00 0.00 0.00 4.85
714 744 0.249741 AACTCCAACCGAACGACCTG 60.250 55.000 0.00 0.00 0.00 4.00
715 745 0.249741 CAACTCCAACCGAACGACCT 60.250 55.000 0.00 0.00 0.00 3.85
716 746 1.838568 GCAACTCCAACCGAACGACC 61.839 60.000 0.00 0.00 0.00 4.79
717 747 0.878961 AGCAACTCCAACCGAACGAC 60.879 55.000 0.00 0.00 0.00 4.34
718 748 0.599204 GAGCAACTCCAACCGAACGA 60.599 55.000 0.00 0.00 0.00 3.85
719 749 0.600255 AGAGCAACTCCAACCGAACG 60.600 55.000 0.00 0.00 0.00 3.95
720 750 2.450609 TAGAGCAACTCCAACCGAAC 57.549 50.000 0.00 0.00 0.00 3.95
721 751 2.549349 GGTTAGAGCAACTCCAACCGAA 60.549 50.000 8.79 0.00 40.93 4.30
722 752 1.001633 GGTTAGAGCAACTCCAACCGA 59.998 52.381 8.79 0.00 40.93 4.69
723 753 1.439679 GGTTAGAGCAACTCCAACCG 58.560 55.000 8.79 0.00 40.93 4.44
725 755 1.807142 GCAGGTTAGAGCAACTCCAAC 59.193 52.381 0.00 0.00 37.30 3.77
726 756 1.699634 AGCAGGTTAGAGCAACTCCAA 59.300 47.619 0.00 0.00 37.30 3.53
727 757 1.002430 CAGCAGGTTAGAGCAACTCCA 59.998 52.381 0.00 0.00 37.30 3.86
728 758 1.002544 ACAGCAGGTTAGAGCAACTCC 59.997 52.381 0.00 0.00 37.30 3.85
729 759 2.464157 ACAGCAGGTTAGAGCAACTC 57.536 50.000 0.00 0.00 37.30 3.01
730 760 4.040461 TCTTTACAGCAGGTTAGAGCAACT 59.960 41.667 0.00 0.00 37.30 3.16
731 761 4.315803 TCTTTACAGCAGGTTAGAGCAAC 58.684 43.478 0.00 0.00 36.32 4.17
732 762 4.617253 TCTTTACAGCAGGTTAGAGCAA 57.383 40.909 0.00 0.00 0.00 3.91
733 763 4.617253 TTCTTTACAGCAGGTTAGAGCA 57.383 40.909 0.00 0.00 0.00 4.26
734 764 5.238650 TGTTTTCTTTACAGCAGGTTAGAGC 59.761 40.000 0.00 0.00 0.00 4.09
735 765 6.483640 ACTGTTTTCTTTACAGCAGGTTAGAG 59.516 38.462 0.00 0.00 45.38 2.43
736 766 6.354130 ACTGTTTTCTTTACAGCAGGTTAGA 58.646 36.000 0.00 0.00 45.38 2.10
737 767 6.619801 ACTGTTTTCTTTACAGCAGGTTAG 57.380 37.500 0.00 0.00 45.38 2.34
738 768 7.254522 CGTTACTGTTTTCTTTACAGCAGGTTA 60.255 37.037 0.00 0.00 45.38 2.85
739 769 6.457799 CGTTACTGTTTTCTTTACAGCAGGTT 60.458 38.462 0.00 0.00 45.38 3.50
740 770 5.007332 CGTTACTGTTTTCTTTACAGCAGGT 59.993 40.000 0.00 0.00 45.38 4.00
741 771 5.007332 ACGTTACTGTTTTCTTTACAGCAGG 59.993 40.000 0.00 0.00 45.38 4.85
742 772 6.044512 ACGTTACTGTTTTCTTTACAGCAG 57.955 37.500 0.00 0.00 45.38 4.24
743 773 7.718272 ATACGTTACTGTTTTCTTTACAGCA 57.282 32.000 0.00 0.00 45.38 4.41
744 774 8.919661 AGTATACGTTACTGTTTTCTTTACAGC 58.080 33.333 0.00 0.00 45.38 4.40
746 776 9.964303 TCAGTATACGTTACTGTTTTCTTTACA 57.036 29.630 24.33 9.34 43.84 2.41
749 779 8.857216 CGATCAGTATACGTTACTGTTTTCTTT 58.143 33.333 24.33 11.13 43.84 2.52
750 780 8.239314 TCGATCAGTATACGTTACTGTTTTCTT 58.761 33.333 24.33 12.18 43.84 2.52
751 781 7.755591 TCGATCAGTATACGTTACTGTTTTCT 58.244 34.615 24.33 13.15 43.84 2.52
752 782 7.959718 TCGATCAGTATACGTTACTGTTTTC 57.040 36.000 24.33 19.91 43.84 2.29
753 783 7.274250 GGTTCGATCAGTATACGTTACTGTTTT 59.726 37.037 24.33 16.27 43.84 2.43
754 784 6.749118 GGTTCGATCAGTATACGTTACTGTTT 59.251 38.462 24.33 17.81 43.84 2.83
755 785 6.261118 GGTTCGATCAGTATACGTTACTGTT 58.739 40.000 24.33 19.91 43.84 3.16
756 786 5.220931 GGGTTCGATCAGTATACGTTACTGT 60.221 44.000 24.33 17.03 43.84 3.55
757 787 5.210715 GGGTTCGATCAGTATACGTTACTG 58.789 45.833 21.74 21.74 44.56 2.74
758 788 4.024556 CGGGTTCGATCAGTATACGTTACT 60.025 45.833 0.00 0.00 39.00 2.24
759 789 4.214437 CGGGTTCGATCAGTATACGTTAC 58.786 47.826 0.00 0.00 39.00 2.50
760 790 3.303990 GCGGGTTCGATCAGTATACGTTA 60.304 47.826 0.00 0.00 39.00 3.18
761 791 2.542411 GCGGGTTCGATCAGTATACGTT 60.542 50.000 0.00 0.00 39.00 3.99
762 792 1.002033 GCGGGTTCGATCAGTATACGT 60.002 52.381 0.00 0.00 39.00 3.57
763 793 1.682982 GCGGGTTCGATCAGTATACG 58.317 55.000 0.00 0.00 39.00 3.06
764 794 1.002033 ACGCGGGTTCGATCAGTATAC 60.002 52.381 12.47 0.00 39.00 1.47
765 795 1.002142 CACGCGGGTTCGATCAGTATA 60.002 52.381 12.47 0.00 39.00 1.47
766 796 0.248907 CACGCGGGTTCGATCAGTAT 60.249 55.000 12.47 0.00 39.00 2.12
767 797 1.138036 CACGCGGGTTCGATCAGTA 59.862 57.895 12.47 0.00 39.00 2.74
768 798 2.126071 CACGCGGGTTCGATCAGT 60.126 61.111 12.47 0.00 39.00 3.41
769 799 2.885644 CCACGCGGGTTCGATCAG 60.886 66.667 12.47 0.00 39.00 2.90
779 809 1.574702 GAAGAAAACCTCCCACGCGG 61.575 60.000 12.47 0.00 0.00 6.46
780 810 0.602905 AGAAGAAAACCTCCCACGCG 60.603 55.000 3.53 3.53 0.00 6.01
781 811 1.535896 GAAGAAGAAAACCTCCCACGC 59.464 52.381 0.00 0.00 0.00 5.34
782 812 2.152016 GGAAGAAGAAAACCTCCCACG 58.848 52.381 0.00 0.00 0.00 4.94
783 813 3.223674 TGGAAGAAGAAAACCTCCCAC 57.776 47.619 0.00 0.00 0.00 4.61
784 814 5.592587 TTATGGAAGAAGAAAACCTCCCA 57.407 39.130 0.00 0.00 0.00 4.37
785 815 6.911250 TTTTATGGAAGAAGAAAACCTCCC 57.089 37.500 0.00 0.00 0.00 4.30
806 836 5.938322 ACACGTATTCGATCAGCAATTTTT 58.062 33.333 0.00 0.00 40.62 1.94
807 837 5.545658 ACACGTATTCGATCAGCAATTTT 57.454 34.783 0.00 0.00 40.62 1.82
808 838 5.323900 CAACACGTATTCGATCAGCAATTT 58.676 37.500 0.00 0.00 40.62 1.82
809 839 4.201812 CCAACACGTATTCGATCAGCAATT 60.202 41.667 0.00 0.00 40.62 2.32
810 840 3.309682 CCAACACGTATTCGATCAGCAAT 59.690 43.478 0.00 0.00 40.62 3.56
811 841 2.670905 CCAACACGTATTCGATCAGCAA 59.329 45.455 0.00 0.00 40.62 3.91
812 842 2.267426 CCAACACGTATTCGATCAGCA 58.733 47.619 0.00 0.00 40.62 4.41
813 843 2.268298 ACCAACACGTATTCGATCAGC 58.732 47.619 0.00 0.00 40.62 4.26
814 844 4.490319 CGAAACCAACACGTATTCGATCAG 60.490 45.833 0.00 0.00 43.99 2.90
815 845 3.365520 CGAAACCAACACGTATTCGATCA 59.634 43.478 0.00 0.00 43.99 2.92
816 846 3.779992 GCGAAACCAACACGTATTCGATC 60.780 47.826 10.04 0.00 43.99 3.69
817 847 2.093152 GCGAAACCAACACGTATTCGAT 59.907 45.455 10.04 0.00 43.99 3.59
818 848 1.456544 GCGAAACCAACACGTATTCGA 59.543 47.619 10.04 0.00 43.99 3.71
819 849 1.458064 AGCGAAACCAACACGTATTCG 59.542 47.619 0.00 0.00 44.06 3.34
820 850 2.222445 ACAGCGAAACCAACACGTATTC 59.778 45.455 0.00 0.00 0.00 1.75
821 851 2.032377 CACAGCGAAACCAACACGTATT 60.032 45.455 0.00 0.00 0.00 1.89
822 852 1.529438 CACAGCGAAACCAACACGTAT 59.471 47.619 0.00 0.00 0.00 3.06
823 853 0.931702 CACAGCGAAACCAACACGTA 59.068 50.000 0.00 0.00 0.00 3.57
824 854 1.711060 CCACAGCGAAACCAACACGT 61.711 55.000 0.00 0.00 0.00 4.49
825 855 1.010125 CCACAGCGAAACCAACACG 60.010 57.895 0.00 0.00 0.00 4.49
826 856 1.358759 CCCACAGCGAAACCAACAC 59.641 57.895 0.00 0.00 0.00 3.32
827 857 1.826054 CCCCACAGCGAAACCAACA 60.826 57.895 0.00 0.00 0.00 3.33
828 858 3.039134 CCCCACAGCGAAACCAAC 58.961 61.111 0.00 0.00 0.00 3.77
829 859 2.909965 GCCCCACAGCGAAACCAA 60.910 61.111 0.00 0.00 0.00 3.67
830 860 2.920076 AAAGCCCCACAGCGAAACCA 62.920 55.000 0.00 0.00 38.01 3.67
831 861 2.142357 GAAAGCCCCACAGCGAAACC 62.142 60.000 0.00 0.00 38.01 3.27
832 862 1.285950 GAAAGCCCCACAGCGAAAC 59.714 57.895 0.00 0.00 38.01 2.78
833 863 1.901464 GGAAAGCCCCACAGCGAAA 60.901 57.895 0.00 0.00 38.01 3.46
834 864 2.282180 GGAAAGCCCCACAGCGAA 60.282 61.111 0.00 0.00 38.01 4.70
835 865 4.697756 CGGAAAGCCCCACAGCGA 62.698 66.667 0.00 0.00 38.01 4.93
837 867 3.056328 GACGGAAAGCCCCACAGC 61.056 66.667 0.00 0.00 0.00 4.40
838 868 2.359975 GGACGGAAAGCCCCACAG 60.360 66.667 0.00 0.00 0.00 3.66
839 869 3.961414 GGGACGGAAAGCCCCACA 61.961 66.667 0.00 0.00 39.89 4.17
852 882 4.436998 CCACAGCGACTCGGGGAC 62.437 72.222 0.00 0.00 0.00 4.46
857 887 4.379243 AAGCCCCACAGCGACTCG 62.379 66.667 0.00 0.00 38.01 4.18
858 888 2.743928 CAAGCCCCACAGCGACTC 60.744 66.667 0.00 0.00 38.01 3.36
861 891 4.349503 ATGCAAGCCCCACAGCGA 62.350 61.111 0.00 0.00 38.01 4.93
862 892 3.818787 GATGCAAGCCCCACAGCG 61.819 66.667 0.00 0.00 38.01 5.18
863 893 3.455469 GGATGCAAGCCCCACAGC 61.455 66.667 0.00 0.00 35.29 4.40
864 894 3.136123 CGGATGCAAGCCCCACAG 61.136 66.667 0.00 0.00 41.45 3.66
865 895 3.965258 ACGGATGCAAGCCCCACA 61.965 61.111 0.00 0.00 41.45 4.17
866 896 2.813226 TACACGGATGCAAGCCCCAC 62.813 60.000 0.00 0.00 41.45 4.61
867 897 1.920734 ATACACGGATGCAAGCCCCA 61.921 55.000 0.00 0.00 41.45 4.96
960 990 3.417275 CTGGCGCGTGTAGCTAGCT 62.417 63.158 23.12 23.12 45.59 3.32
1026 1059 1.406614 GGAGTCCCAAGAGCTCATGTG 60.407 57.143 17.77 5.69 0.00 3.21
1027 1060 0.908198 GGAGTCCCAAGAGCTCATGT 59.092 55.000 17.77 0.00 0.00 3.21
1037 1070 2.367202 GGGCGATGAGGAGTCCCAA 61.367 63.158 5.25 0.00 36.96 4.12
1117 1150 2.986979 TGACCGTGGTAGCGCAGA 60.987 61.111 11.47 0.00 0.00 4.26
1124 1157 2.524640 TGCCTGGTGACCGTGGTA 60.525 61.111 13.63 7.59 0.00 3.25
1150 1183 0.400213 TGCCTCCTGGTCGAACAATT 59.600 50.000 3.93 0.00 35.27 2.32
1153 1186 3.059982 CTGCCTCCTGGTCGAACA 58.940 61.111 1.69 1.69 35.27 3.18
1156 1189 2.604686 AAGCTGCCTCCTGGTCGA 60.605 61.111 0.00 0.00 35.27 4.20
1158 1191 0.747283 CATGAAGCTGCCTCCTGGTC 60.747 60.000 0.00 0.00 35.27 4.02
1162 1195 0.540923 GAGTCATGAAGCTGCCTCCT 59.459 55.000 0.00 0.00 0.00 3.69
1164 1197 0.809241 CGGAGTCATGAAGCTGCCTC 60.809 60.000 0.00 0.00 0.00 4.70
1336 1369 1.154093 GATGACCGCGTCGAGTTCA 60.154 57.895 4.92 0.00 34.95 3.18
1384 1417 4.367023 GCCGCGGTAGACCACACA 62.367 66.667 28.70 0.00 35.14 3.72
1426 1459 2.727798 CGGACGTCTTGTATTGTTCGTT 59.272 45.455 16.46 0.00 0.00 3.85
1468 1501 3.655481 GGCAACCAGACGTCCTTG 58.345 61.111 13.01 12.32 0.00 3.61
1592 1625 1.559682 AGCTTACCGTCACCATCCATT 59.440 47.619 0.00 0.00 0.00 3.16
1696 1729 1.077644 TCCTCCTCCTCGAACTCGG 60.078 63.158 0.00 0.00 40.29 4.63
1697 1730 1.098712 CCTCCTCCTCCTCGAACTCG 61.099 65.000 0.00 0.00 41.45 4.18
1698 1731 0.256464 TCCTCCTCCTCCTCGAACTC 59.744 60.000 0.00 0.00 0.00 3.01
1699 1732 0.257616 CTCCTCCTCCTCCTCGAACT 59.742 60.000 0.00 0.00 0.00 3.01
1700 1733 0.753848 CCTCCTCCTCCTCCTCGAAC 60.754 65.000 0.00 0.00 0.00 3.95
1701 1734 1.615814 CCTCCTCCTCCTCCTCGAA 59.384 63.158 0.00 0.00 0.00 3.71
1702 1735 3.063197 GCCTCCTCCTCCTCCTCGA 62.063 68.421 0.00 0.00 0.00 4.04
1703 1736 2.520741 GCCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
1797 1830 1.923204 CGTCTTCTCCTTTGATGCTCG 59.077 52.381 0.00 0.00 0.00 5.03
1869 1902 1.872952 TGCATCTTTGTCTGTTGTCCG 59.127 47.619 0.00 0.00 0.00 4.79
1875 1908 1.603802 CACGGTTGCATCTTTGTCTGT 59.396 47.619 0.00 0.00 0.00 3.41
1907 1940 4.755629 TCGACTACCTCCTGATTATCGAAG 59.244 45.833 0.00 0.00 34.68 3.79
1913 1946 6.540438 AATGTTTCGACTACCTCCTGATTA 57.460 37.500 0.00 0.00 0.00 1.75
1914 1947 5.422214 AATGTTTCGACTACCTCCTGATT 57.578 39.130 0.00 0.00 0.00 2.57
1917 1950 5.341617 GTCTAATGTTTCGACTACCTCCTG 58.658 45.833 0.00 0.00 0.00 3.86
1936 1969 2.244695 TCTTTGTTGCCTCCTCGTCTA 58.755 47.619 0.00 0.00 0.00 2.59
1952 1985 9.484806 ACCTTTTCATCCTCATTTGATATCTTT 57.515 29.630 3.98 0.00 0.00 2.52
1957 1990 6.493166 ACCACCTTTTCATCCTCATTTGATA 58.507 36.000 0.00 0.00 0.00 2.15
1997 2030 0.464373 ATGGCCATGTTAGCTCCACG 60.464 55.000 20.04 0.00 0.00 4.94
2019 2052 4.568359 CCATTCTTCGTCAAGATCATCGTT 59.432 41.667 0.00 0.00 38.50 3.85
2033 2066 1.927174 GATGTCACGTCCCATTCTTCG 59.073 52.381 0.00 0.00 0.00 3.79
2047 2080 5.947566 ACATTCATGGTTTCTGATGATGTCA 59.052 36.000 0.00 0.00 35.05 3.58
2057 2090 3.309682 CGTATGCGACATTCATGGTTTCT 59.690 43.478 0.00 0.00 41.33 2.52
2064 2097 2.288457 CCTCCTCGTATGCGACATTCAT 60.288 50.000 0.30 0.00 42.81 2.57
2089 2122 4.392940 CCATGGTTCAATATCCTCCTCAC 58.607 47.826 2.57 0.00 0.00 3.51
2102 2135 2.509548 CTCATCCCTTACCCATGGTTCA 59.490 50.000 11.73 0.00 37.09 3.18
2167 2200 0.905357 GCTGGTAAGAGCCTTGGAGA 59.095 55.000 0.00 0.00 32.35 3.71
2219 2252 6.238842 GCATATAGTGTTTCACCATGAGCAAT 60.239 38.462 0.00 0.00 34.49 3.56
2285 2318 2.484264 CGCCTTGAAAACCTCTACTTGG 59.516 50.000 0.00 0.00 0.00 3.61
2335 2368 3.144285 GGTCACCACCGAGTCCAA 58.856 61.111 0.00 0.00 31.06 3.53
2344 2377 3.537206 AAGAGCGCCTGGTCACCAC 62.537 63.158 2.29 0.00 45.10 4.16
2422 2458 4.551388 GCCGGTGTTGACAAAATAAATGA 58.449 39.130 1.90 0.00 0.00 2.57
2461 2497 1.542547 CCGGGCTACAAGTGTTGAACT 60.543 52.381 0.00 0.00 42.60 3.01
2464 2500 1.340088 TACCGGGCTACAAGTGTTGA 58.660 50.000 6.32 0.00 0.00 3.18
2526 2562 5.394663 CCACATGTTAAACCACCAACTTTGA 60.395 40.000 0.00 0.00 0.00 2.69
2567 2603 8.914011 GCATCCCTATTACAATAAAAGGTCTTT 58.086 33.333 0.00 0.00 0.00 2.52
2568 2604 8.058847 TGCATCCCTATTACAATAAAAGGTCTT 58.941 33.333 0.00 0.00 0.00 3.01
2610 2646 4.586841 TCAATGTCACCCGGAAAGAAAAAT 59.413 37.500 0.73 0.00 0.00 1.82
2616 2652 0.804989 GCTCAATGTCACCCGGAAAG 59.195 55.000 0.73 0.00 0.00 2.62
2621 2657 3.270027 TCAATTAGCTCAATGTCACCCG 58.730 45.455 0.00 0.00 0.00 5.28
2724 2792 6.848451 ACATGTGTTTAATTCCCGTGATTAC 58.152 36.000 0.00 0.00 0.00 1.89
2789 2873 1.267732 CGCTCTGATTCACGCCAATTC 60.268 52.381 0.00 0.00 0.00 2.17
2808 2892 3.550992 GTGGCCGCATGACGTACG 61.551 66.667 15.01 15.01 41.42 3.67
2872 2958 6.501781 ACTCTTCCGTAATACGTATTCCAAG 58.498 40.000 23.51 18.56 40.58 3.61
2873 2959 6.455360 ACTCTTCCGTAATACGTATTCCAA 57.545 37.500 23.51 11.28 40.58 3.53
2875 2961 7.294473 GTCTACTCTTCCGTAATACGTATTCC 58.706 42.308 23.51 12.25 40.58 3.01
2880 2967 4.184629 ACGTCTACTCTTCCGTAATACGT 58.815 43.478 12.05 0.00 40.58 3.57
2922 3009 0.539518 GAAGAAGGCTGAGGAGGTCC 59.460 60.000 0.00 0.00 0.00 4.46
2923 3010 0.539518 GGAAGAAGGCTGAGGAGGTC 59.460 60.000 0.00 0.00 0.00 3.85
2924 3011 1.261238 CGGAAGAAGGCTGAGGAGGT 61.261 60.000 0.00 0.00 0.00 3.85
3269 3777 0.107800 GAAAAGCCCTAGGACCCGTC 60.108 60.000 11.48 0.00 0.00 4.79
3275 3787 1.625508 GGAGGAGGAAAAGCCCTAGGA 60.626 57.143 11.48 0.00 36.49 2.94
3276 3788 0.840617 GGAGGAGGAAAAGCCCTAGG 59.159 60.000 0.06 0.06 36.49 3.02


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

AutoCloner maintained by Alex Coulton.