Multiple sequence alignment - TraesCS5B01G271700

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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 TraesCS5B01G271700 chr5B 100.000 4217 0 0 1 4217 457131545 457127329 0.000000e+00 7788.0
1 TraesCS5B01G271700 chr5B 97.727 88 2 0 2340 2427 457129116 457129203 7.300000e-33 152.0
2 TraesCS5B01G271700 chr5B 92.208 77 6 0 2426 2502 457129286 457129210 4.460000e-20 110.0
3 TraesCS5B01G271700 chr5A 91.281 1686 69 27 714 2344 481899960 481898298 0.000000e+00 2228.0
4 TraesCS5B01G271700 chr5A 91.064 1589 97 11 2662 4217 481897437 481895861 0.000000e+00 2106.0
5 TraesCS5B01G271700 chr5A 87.091 581 43 17 50 623 481900734 481900179 2.770000e-176 628.0
6 TraesCS5B01G271700 chr5A 93.388 242 13 2 2426 2665 481897716 481897476 5.190000e-94 355.0
7 TraesCS5B01G271700 chr5A 93.878 147 7 2 2198 2344 481898278 481898134 1.970000e-53 220.0
8 TraesCS5B01G271700 chr5A 89.011 182 13 6 2426 2604 481898135 481897958 7.100000e-53 219.0
9 TraesCS5B01G271700 chr5A 89.571 163 12 4 2426 2585 481898299 481898139 7.150000e-48 202.0
10 TraesCS5B01G271700 chr5A 90.541 148 13 1 2197 2344 481898362 481898216 1.200000e-45 195.0
11 TraesCS5B01G271700 chr5A 90.714 140 13 0 2197 2336 481898198 481898059 2.000000e-43 187.0
12 TraesCS5B01G271700 chr5A 95.495 111 4 1 2226 2336 481897750 481897641 4.330000e-40 176.0
13 TraesCS5B01G271700 chr5A 83.770 191 22 8 2426 2611 481898381 481898195 5.610000e-39 172.0
14 TraesCS5B01G271700 chr5A 85.714 161 17 5 2426 2582 481898217 481898059 9.380000e-37 165.0
15 TraesCS5B01G271700 chr5A 86.395 147 16 2 2198 2344 481898114 481897972 1.570000e-34 158.0
16 TraesCS5B01G271700 chr5A 86.466 133 13 4 2475 2604 481897750 481897620 1.580000e-29 141.0
17 TraesCS5B01G271700 chr5D 83.812 2125 177 69 78 2082 381032741 381030664 0.000000e+00 1864.0
18 TraesCS5B01G271700 chr5D 95.686 510 19 1 3708 4217 381028997 381028491 0.000000e+00 817.0
19 TraesCS5B01G271700 chr5D 87.612 557 48 16 2124 2669 381030548 381030002 9.950000e-176 627.0
20 TraesCS5B01G271700 chr5D 89.351 385 16 8 3269 3642 381029396 381029026 1.070000e-125 460.0
21 TraesCS5B01G271700 chr5D 88.000 275 9 8 2662 2914 381029968 381029696 1.910000e-78 303.0
22 TraesCS5B01G271700 chr5D 93.243 148 9 1 2197 2344 381030392 381030246 2.550000e-52 217.0
23 TraesCS5B01G271700 chr5D 92.568 148 10 1 2197 2344 381030310 381030164 1.190000e-50 211.0
24 TraesCS5B01G271700 chr5D 85.207 169 19 6 2447 2611 381030473 381030307 7.250000e-38 169.0
25 TraesCS5B01G271700 chr5D 94.444 54 3 0 50 103 381032802 381032749 2.700000e-12 84.2
26 TraesCS5B01G271700 chr7A 95.652 92 3 1 2341 2432 105362137 105362227 3.400000e-31 147.0
27 TraesCS5B01G271700 chr7A 97.647 85 2 0 2343 2427 105362223 105362139 3.400000e-31 147.0
28 TraesCS5B01G271700 chr7A 93.478 92 6 0 2343 2434 202289150 202289241 2.040000e-28 137.0
29 TraesCS5B01G271700 chr2B 94.505 91 5 0 2341 2431 23029140 23029050 1.580000e-29 141.0
30 TraesCS5B01G271700 chr2B 95.402 87 4 0 2341 2427 190651258 190651172 5.690000e-29 139.0
31 TraesCS5B01G271700 chr3B 93.617 94 5 1 2342 2435 809835756 809835664 5.690000e-29 139.0
32 TraesCS5B01G271700 chr4B 94.318 88 5 0 2343 2430 59873819 59873732 7.350000e-28 135.0
33 TraesCS5B01G271700 chr7D 91.667 96 6 2 2343 2436 180444927 180445022 9.510000e-27 132.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G271700 chr5B 457127329 457131545 4216 True 3949.000000 7788 96.104000 1 4217 2 chr5B.!!$R1 4216
1 TraesCS5B01G271700 chr5A 481895861 481900734 4873 True 510.857143 2228 89.598500 50 4217 14 chr5A.!!$R1 4167
2 TraesCS5B01G271700 chr5D 381028491 381032802 4311 True 528.022222 1864 89.991444 50 4217 9 chr5D.!!$R1 4167

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
34 35 0.104120 CCGGTGGCTGATCATCGTTA 59.896 55.0 0.00 0.00 39.40 3.18 F
968 1155 0.534412 CACTGCAACCTCTCCTCGAT 59.466 55.0 0.00 0.00 0.00 3.59 F
971 1158 0.537188 TGCAACCTCTCCTCGATTCC 59.463 55.0 0.00 0.00 0.00 3.01 F
1773 2024 0.734889 GCACTAGCTACCGTTCGGTA 59.265 55.0 20.44 20.44 39.52 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2114 1.004080 TCTGCTGAACTGCTGCTCC 60.004 57.895 0.00 0.00 41.53 4.70 R
2789 3687 0.305922 GGCTACTTGCATTGCTAGCG 59.694 55.000 18.13 11.48 45.15 4.26 R
2939 3857 0.971386 AAAAGGCCATGAGCAGTTGG 59.029 50.000 5.01 0.00 46.50 3.77 R
3218 4136 0.464036 ATGCCAAGATTCGAGCGGTA 59.536 50.000 0.00 0.00 0.00 4.02 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
20 21 2.810650 CTTTCTCGACTTATCCCGGTG 58.189 52.381 0.00 0.00 0.00 4.94
21 22 1.108776 TTCTCGACTTATCCCGGTGG 58.891 55.000 0.00 0.00 0.00 4.61
22 23 1.067582 CTCGACTTATCCCGGTGGC 59.932 63.158 0.00 0.00 0.00 5.01
23 24 1.380785 TCGACTTATCCCGGTGGCT 60.381 57.895 0.00 0.00 0.00 4.75
24 25 1.227263 CGACTTATCCCGGTGGCTG 60.227 63.158 0.00 0.00 0.00 4.85
25 26 1.672854 CGACTTATCCCGGTGGCTGA 61.673 60.000 0.00 0.00 0.00 4.26
26 27 0.759346 GACTTATCCCGGTGGCTGAT 59.241 55.000 0.00 0.00 0.00 2.90
27 28 0.759346 ACTTATCCCGGTGGCTGATC 59.241 55.000 0.00 0.00 0.00 2.92
28 29 0.758734 CTTATCCCGGTGGCTGATCA 59.241 55.000 0.00 0.00 0.00 2.92
29 30 1.349026 CTTATCCCGGTGGCTGATCAT 59.651 52.381 0.00 0.00 0.00 2.45
30 31 0.976641 TATCCCGGTGGCTGATCATC 59.023 55.000 0.00 0.00 0.00 2.92
31 32 2.104572 ATCCCGGTGGCTGATCATCG 62.105 60.000 0.00 0.00 40.59 3.84
32 33 2.501128 CCGGTGGCTGATCATCGT 59.499 61.111 0.00 0.00 39.40 3.73
33 34 1.153369 CCGGTGGCTGATCATCGTT 60.153 57.895 0.00 0.00 39.40 3.85
34 35 0.104120 CCGGTGGCTGATCATCGTTA 59.896 55.000 0.00 0.00 39.40 3.18
35 36 1.491670 CGGTGGCTGATCATCGTTAG 58.508 55.000 0.00 0.00 36.60 2.34
36 37 1.067060 CGGTGGCTGATCATCGTTAGA 59.933 52.381 0.00 0.00 36.60 2.10
37 38 2.481276 CGGTGGCTGATCATCGTTAGAA 60.481 50.000 0.00 0.00 36.60 2.10
38 39 2.866762 GGTGGCTGATCATCGTTAGAAC 59.133 50.000 0.00 0.00 0.00 3.01
39 40 3.430929 GGTGGCTGATCATCGTTAGAACT 60.431 47.826 0.00 0.00 0.00 3.01
40 41 3.799420 GTGGCTGATCATCGTTAGAACTC 59.201 47.826 0.00 0.00 0.00 3.01
41 42 3.447229 TGGCTGATCATCGTTAGAACTCA 59.553 43.478 0.00 0.00 0.00 3.41
42 43 4.081697 TGGCTGATCATCGTTAGAACTCAA 60.082 41.667 0.00 0.00 0.00 3.02
43 44 4.505922 GGCTGATCATCGTTAGAACTCAAG 59.494 45.833 0.00 0.00 0.00 3.02
44 45 5.105752 GCTGATCATCGTTAGAACTCAAGT 58.894 41.667 0.00 0.00 0.00 3.16
45 46 5.231147 GCTGATCATCGTTAGAACTCAAGTC 59.769 44.000 0.00 0.00 0.00 3.01
46 47 6.516739 TGATCATCGTTAGAACTCAAGTCT 57.483 37.500 0.00 0.00 0.00 3.24
47 48 6.325596 TGATCATCGTTAGAACTCAAGTCTG 58.674 40.000 0.00 0.00 0.00 3.51
48 49 5.707242 TCATCGTTAGAACTCAAGTCTGT 57.293 39.130 0.00 0.00 0.00 3.41
103 137 2.558359 CCATTGGAAAAAGGCGAAGAGT 59.442 45.455 0.00 0.00 0.00 3.24
367 411 6.534475 AAATTCATGATAATGTGTGCCTGT 57.466 33.333 0.00 0.00 0.00 4.00
373 417 4.917385 TGATAATGTGTGCCTGTTTAGGT 58.083 39.130 0.00 0.00 46.41 3.08
374 418 4.699735 TGATAATGTGTGCCTGTTTAGGTG 59.300 41.667 0.00 0.00 46.41 4.00
377 421 2.729194 TGTGTGCCTGTTTAGGTGTTT 58.271 42.857 0.00 0.00 46.41 2.83
378 422 3.887352 TGTGTGCCTGTTTAGGTGTTTA 58.113 40.909 0.00 0.00 46.41 2.01
428 473 1.183676 GGATGGGCCCTTGATGCATC 61.184 60.000 25.70 20.14 0.00 3.91
489 535 4.217754 TGTAATTCGTTTGTTCAGCCAC 57.782 40.909 0.00 0.00 0.00 5.01
513 559 4.640771 TTCTGTGAAATTAGACAGGCCT 57.359 40.909 0.00 0.00 40.11 5.19
523 569 2.373335 AGACAGGCCTATCATCGACT 57.627 50.000 14.85 0.00 0.00 4.18
537 583 6.653273 ATCATCGACTACAATGTTTGACTG 57.347 37.500 0.00 0.00 0.00 3.51
543 589 5.036117 ACTACAATGTTTGACTGTGAGGT 57.964 39.130 0.00 0.00 0.00 3.85
551 597 3.912496 TTGACTGTGAGGTCCCATATG 57.088 47.619 0.00 0.00 35.54 1.78
554 600 1.487976 ACTGTGAGGTCCCATATGCAG 59.512 52.381 0.00 0.00 0.00 4.41
557 603 0.752658 TGAGGTCCCATATGCAGTCG 59.247 55.000 0.00 0.00 0.00 4.18
573 619 4.786068 TGCAGTCGTTTATACGTAACGTAC 59.214 41.667 18.50 15.15 45.07 3.67
574 620 4.202358 GCAGTCGTTTATACGTAACGTACC 59.798 45.833 18.50 10.07 45.07 3.34
575 621 4.430118 CAGTCGTTTATACGTAACGTACCG 59.570 45.833 18.50 8.60 45.07 4.02
576 622 4.092383 AGTCGTTTATACGTAACGTACCGT 59.908 41.667 18.50 15.40 45.07 4.83
578 624 5.953205 GTCGTTTATACGTAACGTACCGTTA 59.047 40.000 18.50 5.21 46.70 3.18
619 672 6.845302 TGCAACTTATGAAAATGTAGCTGAG 58.155 36.000 0.00 0.00 0.00 3.35
623 728 2.128771 TGAAAATGTAGCTGAGGCCC 57.871 50.000 0.00 0.00 39.73 5.80
640 745 5.656416 TGAGGCCCCAAAATATAGAGTTTTG 59.344 40.000 0.00 4.76 43.00 2.44
667 773 5.530915 TGTCATGAAAACCAAAGTAGACAGG 59.469 40.000 0.00 0.00 0.00 4.00
672 778 5.186021 TGAAAACCAAAGTAGACAGGCAAAA 59.814 36.000 0.00 0.00 0.00 2.44
678 784 7.378181 ACCAAAGTAGACAGGCAAAATTTATG 58.622 34.615 0.00 0.00 0.00 1.90
679 785 6.311200 CCAAAGTAGACAGGCAAAATTTATGC 59.689 38.462 13.59 13.59 43.08 3.14
680 786 6.588719 AAGTAGACAGGCAAAATTTATGCA 57.411 33.333 19.78 0.00 45.60 3.96
687 793 5.107133 CAGGCAAAATTTATGCAGAAGAGG 58.893 41.667 19.78 4.84 45.60 3.69
694 800 9.044150 CAAAATTTATGCAGAAGAGGAAAACAA 57.956 29.630 0.00 0.00 0.00 2.83
699 805 8.862325 TTATGCAGAAGAGGAAAACAAATAGA 57.138 30.769 0.00 0.00 0.00 1.98
700 806 7.765695 ATGCAGAAGAGGAAAACAAATAGAA 57.234 32.000 0.00 0.00 0.00 2.10
701 807 7.581213 TGCAGAAGAGGAAAACAAATAGAAA 57.419 32.000 0.00 0.00 0.00 2.52
703 809 8.137437 TGCAGAAGAGGAAAACAAATAGAAAAG 58.863 33.333 0.00 0.00 0.00 2.27
705 811 8.850156 CAGAAGAGGAAAACAAATAGAAAAGGA 58.150 33.333 0.00 0.00 0.00 3.36
706 812 9.421399 AGAAGAGGAAAACAAATAGAAAAGGAA 57.579 29.630 0.00 0.00 0.00 3.36
707 813 9.464714 GAAGAGGAAAACAAATAGAAAAGGAAC 57.535 33.333 0.00 0.00 0.00 3.62
709 815 9.862149 AGAGGAAAACAAATAGAAAAGGAACTA 57.138 29.630 0.00 0.00 38.49 2.24
712 818 9.678941 GGAAAACAAATAGAAAAGGAACTAGTG 57.321 33.333 0.00 0.00 38.49 2.74
737 918 4.508124 GGTCAAGAAGGCATATTCTACACG 59.492 45.833 0.00 0.00 38.59 4.49
752 933 1.448540 CACGGAGAAGGCGCATTCT 60.449 57.895 34.80 34.80 42.23 2.40
761 942 1.889573 GGCGCATTCTACAGGGAGC 60.890 63.158 10.83 0.00 0.00 4.70
807 990 1.266989 GGTTTGGACCGCTGAAAGAAG 59.733 52.381 0.00 0.00 35.91 2.85
816 999 2.535574 CCGCTGAAAGAAGCAAACAAAC 59.464 45.455 0.00 0.00 43.73 2.93
817 1000 3.178267 CGCTGAAAGAAGCAAACAAACA 58.822 40.909 0.00 0.00 43.73 2.83
818 1001 3.611986 CGCTGAAAGAAGCAAACAAACAA 59.388 39.130 0.00 0.00 43.73 2.83
819 1002 4.091220 CGCTGAAAGAAGCAAACAAACAAA 59.909 37.500 0.00 0.00 43.73 2.83
820 1003 5.220453 CGCTGAAAGAAGCAAACAAACAAAT 60.220 36.000 0.00 0.00 43.73 2.32
822 1005 6.419980 TGAAAGAAGCAAACAAACAAATGG 57.580 33.333 0.00 0.00 0.00 3.16
824 1007 3.807553 AGAAGCAAACAAACAAATGGGG 58.192 40.909 0.00 0.00 0.00 4.96
825 1008 3.454082 AGAAGCAAACAAACAAATGGGGA 59.546 39.130 0.00 0.00 0.00 4.81
827 1010 1.872952 GCAAACAAACAAATGGGGAGC 59.127 47.619 0.00 0.00 0.00 4.70
828 1011 2.485302 GCAAACAAACAAATGGGGAGCT 60.485 45.455 0.00 0.00 0.00 4.09
846 1030 5.122519 GGAGCTAGGAAAAATCTCTGAAGG 58.877 45.833 0.00 0.00 0.00 3.46
961 1148 2.337879 TTTCGCCCACTGCAACCTCT 62.338 55.000 0.00 0.00 41.33 3.69
963 1150 2.360475 GCCCACTGCAACCTCTCC 60.360 66.667 0.00 0.00 40.77 3.71
964 1151 2.900106 GCCCACTGCAACCTCTCCT 61.900 63.158 0.00 0.00 40.77 3.69
966 1153 1.079543 CCACTGCAACCTCTCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
967 1154 1.536073 CCACTGCAACCTCTCCTCGA 61.536 60.000 0.00 0.00 0.00 4.04
968 1155 0.534412 CACTGCAACCTCTCCTCGAT 59.466 55.000 0.00 0.00 0.00 3.59
969 1156 1.066573 CACTGCAACCTCTCCTCGATT 60.067 52.381 0.00 0.00 0.00 3.34
970 1157 1.205893 ACTGCAACCTCTCCTCGATTC 59.794 52.381 0.00 0.00 0.00 2.52
971 1158 0.537188 TGCAACCTCTCCTCGATTCC 59.463 55.000 0.00 0.00 0.00 3.01
972 1159 0.827368 GCAACCTCTCCTCGATTCCT 59.173 55.000 0.00 0.00 0.00 3.36
1005 1192 0.830648 TTCTCGGGCTTACCATGAGG 59.169 55.000 0.00 0.00 39.35 3.86
1205 1398 3.051341 TCCTCCTCTAATGTGGTGGGTAT 60.051 47.826 0.00 0.00 39.58 2.73
1209 1402 6.903534 CCTCCTCTAATGTGGTGGGTATATAT 59.096 42.308 0.00 0.00 37.04 0.86
1213 1406 8.826765 CCTCTAATGTGGTGGGTATATATTTCT 58.173 37.037 0.00 0.00 0.00 2.52
1250 1458 6.318396 CCATTTTCCCATTTGTTTCAAGTTGT 59.682 34.615 2.11 0.00 0.00 3.32
1295 1503 6.867662 TCTGACTCTGGTTTTCATTTCTTC 57.132 37.500 0.00 0.00 0.00 2.87
1302 1510 2.242564 GTTTTCATTTCTTCCTCGCGC 58.757 47.619 0.00 0.00 0.00 6.86
1487 1699 3.914312 TCCAGTCGAGAAATGTTCAGAC 58.086 45.455 0.00 7.91 38.78 3.51
1514 1751 7.000472 ACACTAACCATATAATTCTGCATGCT 59.000 34.615 20.33 0.00 0.00 3.79
1527 1765 2.821307 GCATGCTTGCTAAGTCTGAC 57.179 50.000 16.80 0.00 45.77 3.51
1536 1774 4.967084 TGCTAAGTCTGACCCTTGTTTA 57.033 40.909 3.76 0.00 0.00 2.01
1555 1795 5.830991 TGTTTACCTTGTAAATTCAGTGGCT 59.169 36.000 3.05 0.00 0.00 4.75
1600 1840 2.746277 GTCAAGGCCGCCGACATT 60.746 61.111 14.94 0.00 0.00 2.71
1672 1912 1.741401 CACCGCCTTCTCGAATGCA 60.741 57.895 7.50 0.00 32.54 3.96
1747 1991 6.915843 ACATAATTTCAACCGAAGTGAAACAC 59.084 34.615 9.37 0.00 41.43 3.32
1766 2010 2.980476 CACGAATATGCACTAGCTACCG 59.020 50.000 0.00 0.00 42.74 4.02
1773 2024 0.734889 GCACTAGCTACCGTTCGGTA 59.265 55.000 20.44 20.44 39.52 4.02
1781 2032 2.286891 GCTACCGTTCGGTATCTCAGAC 60.287 54.545 21.62 7.03 39.69 3.51
1793 2044 7.412853 TCGGTATCTCAGACGAGTTTAATTAC 58.587 38.462 0.00 0.00 40.44 1.89
1863 2114 3.266510 TCCAAAATGAGAGACATCGGG 57.733 47.619 0.00 0.00 38.38 5.14
1937 2188 2.224523 CCTTGCTGGACTTTGGTCAGTA 60.225 50.000 0.00 0.00 43.77 2.74
1983 2241 9.821662 GCGTTCATTATAATTGGTTCTAATACC 57.178 33.333 0.00 0.00 38.73 2.73
2000 2258 8.783660 TCTAATACCTCAGTTTCATATGGACT 57.216 34.615 2.13 4.96 0.00 3.85
2256 2610 4.749976 TGTTGGAAAGTAAAACAACCAGC 58.250 39.130 0.00 0.00 41.74 4.85
2346 2782 7.712205 TGGAAAGTAAAACAACCAGTACTACTC 59.288 37.037 0.00 0.00 30.54 2.59
2347 2783 7.172190 GGAAAGTAAAACAACCAGTACTACTCC 59.828 40.741 0.00 0.00 30.54 3.85
2348 2784 6.106648 AGTAAAACAACCAGTACTACTCCC 57.893 41.667 0.00 0.00 0.00 4.30
2350 2786 4.886496 AAACAACCAGTACTACTCCCTC 57.114 45.455 0.00 0.00 0.00 4.30
2351 2787 3.829728 ACAACCAGTACTACTCCCTCT 57.170 47.619 0.00 0.00 0.00 3.69
2353 2789 3.181420 ACAACCAGTACTACTCCCTCTGT 60.181 47.826 0.00 0.00 0.00 3.41
2354 2790 4.043812 ACAACCAGTACTACTCCCTCTGTA 59.956 45.833 0.00 0.00 0.00 2.74
2355 2791 4.233632 ACCAGTACTACTCCCTCTGTAC 57.766 50.000 0.00 0.00 36.48 2.90
2356 2792 3.053768 ACCAGTACTACTCCCTCTGTACC 60.054 52.174 0.00 0.00 36.79 3.34
2357 2793 3.204526 CAGTACTACTCCCTCTGTACCG 58.795 54.545 0.00 0.00 36.79 4.02
2358 2794 2.843113 AGTACTACTCCCTCTGTACCGT 59.157 50.000 0.00 0.00 36.79 4.83
2360 2796 4.471386 AGTACTACTCCCTCTGTACCGTAA 59.529 45.833 0.00 0.00 36.79 3.18
2362 2798 5.636903 ACTACTCCCTCTGTACCGTAATA 57.363 43.478 0.00 0.00 0.00 0.98
2363 2799 6.198237 ACTACTCCCTCTGTACCGTAATAT 57.802 41.667 0.00 0.00 0.00 1.28
2366 2802 7.828223 ACTACTCCCTCTGTACCGTAATATATG 59.172 40.741 0.00 0.00 0.00 1.78
2368 2804 6.658391 ACTCCCTCTGTACCGTAATATATGTC 59.342 42.308 0.00 0.00 0.00 3.06
2369 2805 5.645067 TCCCTCTGTACCGTAATATATGTCG 59.355 44.000 0.00 0.00 0.00 4.35
2370 2806 5.330295 CCTCTGTACCGTAATATATGTCGC 58.670 45.833 0.00 0.00 0.00 5.19
2371 2807 5.123502 CCTCTGTACCGTAATATATGTCGCT 59.876 44.000 0.00 0.00 0.00 4.93
2372 2808 5.934921 TCTGTACCGTAATATATGTCGCTG 58.065 41.667 0.00 0.00 0.00 5.18
2373 2809 5.050644 TGTACCGTAATATATGTCGCTGG 57.949 43.478 0.00 0.00 0.00 4.85
2374 2810 4.761227 TGTACCGTAATATATGTCGCTGGA 59.239 41.667 0.00 0.00 0.00 3.86
2375 2811 4.436242 ACCGTAATATATGTCGCTGGAG 57.564 45.455 4.83 0.00 0.00 3.86
2376 2812 3.825014 ACCGTAATATATGTCGCTGGAGT 59.175 43.478 4.83 0.00 0.00 3.85
2412 2848 5.029014 GCTACTCCAGCGACATATATTACG 58.971 45.833 0.00 4.54 41.37 3.18
2413 2849 4.436242 ACTCCAGCGACATATATTACGG 57.564 45.455 9.37 0.00 0.00 4.02
2414 2850 3.825014 ACTCCAGCGACATATATTACGGT 59.175 43.478 7.04 7.04 36.95 4.83
2416 2852 5.106396 ACTCCAGCGACATATATTACGGTAC 60.106 44.000 11.00 0.00 35.19 3.34
2417 2853 4.761227 TCCAGCGACATATATTACGGTACA 59.239 41.667 11.00 1.73 35.19 2.90
2418 2854 5.093457 CCAGCGACATATATTACGGTACAG 58.907 45.833 11.00 0.00 35.19 2.74
2421 2857 5.123502 AGCGACATATATTACGGTACAGAGG 59.876 44.000 0.00 0.00 34.86 3.69
2422 2858 5.675575 GCGACATATATTACGGTACAGAGGG 60.676 48.000 0.00 0.00 0.00 4.30
2423 2859 5.645067 CGACATATATTACGGTACAGAGGGA 59.355 44.000 0.00 0.00 0.00 4.20
2424 2860 6.183360 CGACATATATTACGGTACAGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
2440 2876 7.935405 ACAGAGGGAGTATTATTTTTGGGTTA 58.065 34.615 0.00 0.00 0.00 2.85
2454 2890 2.715046 TGGGTTATGAGCTGAGCTTTG 58.285 47.619 9.00 0.00 39.88 2.77
2522 3378 7.661040 ACAACTTGCTATTTCTTTGCTTATGT 58.339 30.769 0.00 0.00 0.00 2.29
2538 3394 5.106436 TGCTTATGTGCTGATCTTTGACTTG 60.106 40.000 0.00 0.00 0.00 3.16
2571 3427 9.466497 AAATTAGCTTTCTGACTTGATGGAATA 57.534 29.630 0.00 0.00 0.00 1.75
2639 3495 6.860023 CACAAATTTTCTTAGCTTCTGGACAG 59.140 38.462 0.00 0.00 0.00 3.51
2719 3617 2.808543 CCAGTTGTGAACTTAGCCTGAC 59.191 50.000 0.00 0.00 40.46 3.51
2769 3667 7.307930 CGATTGTATTGTGCATATTTCTGCCTA 60.308 37.037 0.00 0.00 41.58 3.93
2789 3687 5.520649 GCCTACTCTCAGTTTAATACAGCAC 59.479 44.000 0.00 0.00 0.00 4.40
2791 3689 3.927142 ACTCTCAGTTTAATACAGCACGC 59.073 43.478 0.00 0.00 0.00 5.34
2891 3809 6.762333 AGCCTTTTGAATATGCTGAAAACTT 58.238 32.000 0.00 0.00 0.00 2.66
2894 3812 6.128472 CCTTTTGAATATGCTGAAAACTTGCC 60.128 38.462 0.00 0.00 0.00 4.52
2920 3838 0.796927 GTTGTCGCTACCTTCCTTGC 59.203 55.000 0.00 0.00 0.00 4.01
2939 3857 3.620488 TGCTCCATGTAAACATCCTTCC 58.380 45.455 0.00 0.00 33.61 3.46
2940 3858 2.952310 GCTCCATGTAAACATCCTTCCC 59.048 50.000 0.00 0.00 33.61 3.97
2953 3871 1.318158 CCTTCCCAACTGCTCATGGC 61.318 60.000 0.00 0.00 42.22 4.40
2960 3878 2.165030 CCAACTGCTCATGGCCTTTTAG 59.835 50.000 3.32 0.00 40.92 1.85
2967 3885 4.080356 TGCTCATGGCCTTTTAGACACTAT 60.080 41.667 3.32 0.00 40.92 2.12
2971 3889 2.835764 TGGCCTTTTAGACACTATCGGT 59.164 45.455 3.32 0.00 0.00 4.69
2973 3891 4.259356 GGCCTTTTAGACACTATCGGTTT 58.741 43.478 0.00 0.00 0.00 3.27
2974 3892 5.046448 TGGCCTTTTAGACACTATCGGTTTA 60.046 40.000 3.32 0.00 0.00 2.01
2990 3908 2.349155 GGTTTAACGAGGTTCTGTTGCG 60.349 50.000 0.00 0.00 0.00 4.85
2994 3912 1.658994 ACGAGGTTCTGTTGCGAAAA 58.341 45.000 0.00 0.00 0.00 2.29
3026 3944 1.662629 GGCGATCATTGTCTCAGTGTG 59.337 52.381 0.00 0.00 0.00 3.82
3031 3949 4.033702 CGATCATTGTCTCAGTGTGGAATG 59.966 45.833 0.00 9.70 0.00 2.67
3041 3959 5.101648 TCAGTGTGGAATGCTATGATGAA 57.898 39.130 0.00 0.00 0.00 2.57
3051 3969 5.881777 ATGCTATGATGAACTGATGATGC 57.118 39.130 0.00 0.00 0.00 3.91
3059 3977 3.086282 TGAACTGATGATGCTGCACAAT 58.914 40.909 3.57 0.79 0.00 2.71
3068 3986 1.514003 TGCTGCACAATTTTGCCATG 58.486 45.000 13.77 5.71 42.25 3.66
3075 3993 3.676873 GCACAATTTTGCCATGGACCTAG 60.677 47.826 18.40 0.48 36.42 3.02
3086 4004 1.246056 TGGACCTAGTTGACCGTCCG 61.246 60.000 8.50 0.00 46.47 4.79
3159 4077 1.621814 CGGGAGTTCTACAACCTGGAA 59.378 52.381 0.00 0.00 32.22 3.53
3218 4136 0.610687 GAGACCCAGCTGCAGTAACT 59.389 55.000 16.64 0.34 0.00 2.24
3256 4179 2.434359 GGAGCCAAACGAGGACGG 60.434 66.667 0.00 0.00 44.46 4.79
3308 4277 2.740055 GTCGCACAGCTGGACAGG 60.740 66.667 19.93 2.99 0.00 4.00
3309 4278 2.917227 TCGCACAGCTGGACAGGA 60.917 61.111 19.93 4.92 0.00 3.86
3310 4279 2.740055 CGCACAGCTGGACAGGAC 60.740 66.667 19.93 0.00 0.00 3.85
3311 4280 2.427320 GCACAGCTGGACAGGACA 59.573 61.111 19.93 0.00 0.00 4.02
3312 4281 1.670406 GCACAGCTGGACAGGACAG 60.670 63.158 19.93 0.00 38.95 3.51
3344 4313 2.497675 TGACCACTCTCCTGAAGTATGC 59.502 50.000 0.00 0.00 0.00 3.14
3414 4383 7.109501 ACCATGTGTATCATTGTAGCAACTAA 58.890 34.615 0.00 0.00 34.09 2.24
3419 4395 5.584649 TGTATCATTGTAGCAACTAAGCACC 59.415 40.000 0.00 0.00 36.85 5.01
3504 4481 5.689383 TCACAGTGCTGGAAATTTTCTAC 57.311 39.130 8.93 4.35 34.19 2.59
3505 4482 5.376625 TCACAGTGCTGGAAATTTTCTACT 58.623 37.500 8.93 6.21 34.19 2.57
3506 4483 6.530120 TCACAGTGCTGGAAATTTTCTACTA 58.470 36.000 8.93 0.00 34.19 1.82
3507 4484 6.426937 TCACAGTGCTGGAAATTTTCTACTAC 59.573 38.462 8.93 3.46 34.19 2.73
3508 4485 6.428159 CACAGTGCTGGAAATTTTCTACTACT 59.572 38.462 8.93 5.40 34.19 2.57
3509 4486 6.428159 ACAGTGCTGGAAATTTTCTACTACTG 59.572 38.462 20.71 20.71 36.11 2.74
3558 4539 6.775594 ACCAGCCTACAATATTTTTCTTCC 57.224 37.500 0.00 0.00 0.00 3.46
3590 4578 1.204941 ACTATTCTGACGGTCAGTGGC 59.795 52.381 31.09 0.00 44.58 5.01
3619 4608 5.698545 ACTGTTATTCTGAACTCTGAACTGC 59.301 40.000 0.00 0.00 36.79 4.40
3647 4637 2.111756 GCAAAAGACAGTTGAAGTGCG 58.888 47.619 0.00 0.00 0.00 5.34
3659 4649 1.268625 TGAAGTGCGCGTAAGAAGAGA 59.731 47.619 8.43 0.00 43.02 3.10
3663 4653 0.596577 TGCGCGTAAGAAGAGACACT 59.403 50.000 8.43 0.00 43.02 3.55
4006 4996 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
4062 5052 2.591429 TTCACTGTGGCGGCACTG 60.591 61.111 36.19 36.19 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.481449 CCACCGGGATAAGTCGAGAAAG 60.481 54.545 6.32 0.00 35.59 2.62
1 2 1.479323 CCACCGGGATAAGTCGAGAAA 59.521 52.381 6.32 0.00 35.59 2.52
2 3 1.108776 CCACCGGGATAAGTCGAGAA 58.891 55.000 6.32 0.00 35.59 2.87
3 4 1.389609 GCCACCGGGATAAGTCGAGA 61.390 60.000 6.32 0.00 35.59 4.04
4 5 1.067582 GCCACCGGGATAAGTCGAG 59.932 63.158 6.32 0.00 35.59 4.04
5 6 1.380785 AGCCACCGGGATAAGTCGA 60.381 57.895 6.32 0.00 35.59 4.20
6 7 1.227263 CAGCCACCGGGATAAGTCG 60.227 63.158 6.32 0.00 35.59 4.18
7 8 0.759346 ATCAGCCACCGGGATAAGTC 59.241 55.000 6.32 0.00 35.59 3.01
8 9 0.759346 GATCAGCCACCGGGATAAGT 59.241 55.000 6.32 0.00 35.59 2.24
9 10 0.758734 TGATCAGCCACCGGGATAAG 59.241 55.000 6.32 0.00 35.59 1.73
10 11 1.347707 GATGATCAGCCACCGGGATAA 59.652 52.381 6.32 0.00 35.59 1.75
11 12 0.976641 GATGATCAGCCACCGGGATA 59.023 55.000 6.32 0.00 35.59 2.59
12 13 1.757306 GATGATCAGCCACCGGGAT 59.243 57.895 6.32 0.00 35.59 3.85
13 14 2.796193 CGATGATCAGCCACCGGGA 61.796 63.158 6.32 0.00 35.59 5.14
14 15 2.280389 CGATGATCAGCCACCGGG 60.280 66.667 6.32 0.00 37.18 5.73
15 16 0.104120 TAACGATGATCAGCCACCGG 59.896 55.000 5.18 0.00 0.00 5.28
16 17 1.067060 TCTAACGATGATCAGCCACCG 59.933 52.381 5.18 4.29 0.00 4.94
17 18 2.866762 GTTCTAACGATGATCAGCCACC 59.133 50.000 5.18 0.00 0.00 4.61
18 19 3.786635 AGTTCTAACGATGATCAGCCAC 58.213 45.455 5.18 0.00 0.00 5.01
19 20 3.447229 TGAGTTCTAACGATGATCAGCCA 59.553 43.478 5.18 0.00 0.00 4.75
20 21 4.046938 TGAGTTCTAACGATGATCAGCC 57.953 45.455 5.18 0.00 0.00 4.85
21 22 5.105752 ACTTGAGTTCTAACGATGATCAGC 58.894 41.667 0.00 0.00 0.00 4.26
22 23 6.471841 CAGACTTGAGTTCTAACGATGATCAG 59.528 42.308 0.09 0.00 0.00 2.90
23 24 6.071896 ACAGACTTGAGTTCTAACGATGATCA 60.072 38.462 0.00 0.00 0.00 2.92
24 25 6.326375 ACAGACTTGAGTTCTAACGATGATC 58.674 40.000 0.00 0.00 0.00 2.92
25 26 6.274157 ACAGACTTGAGTTCTAACGATGAT 57.726 37.500 0.00 0.00 0.00 2.45
26 27 5.335740 GGACAGACTTGAGTTCTAACGATGA 60.336 44.000 0.00 0.00 0.00 2.92
27 28 4.859798 GGACAGACTTGAGTTCTAACGATG 59.140 45.833 0.00 0.00 0.00 3.84
28 29 4.767928 AGGACAGACTTGAGTTCTAACGAT 59.232 41.667 0.00 0.00 0.00 3.73
29 30 4.142790 AGGACAGACTTGAGTTCTAACGA 58.857 43.478 0.00 0.00 0.00 3.85
30 31 4.023107 TGAGGACAGACTTGAGTTCTAACG 60.023 45.833 0.00 0.00 0.00 3.18
31 32 5.455056 TGAGGACAGACTTGAGTTCTAAC 57.545 43.478 0.00 0.00 0.00 2.34
32 33 4.021894 GCTGAGGACAGACTTGAGTTCTAA 60.022 45.833 0.00 0.00 46.03 2.10
33 34 3.508012 GCTGAGGACAGACTTGAGTTCTA 59.492 47.826 0.00 0.00 46.03 2.10
34 35 2.298729 GCTGAGGACAGACTTGAGTTCT 59.701 50.000 0.00 0.00 46.03 3.01
35 36 2.298729 AGCTGAGGACAGACTTGAGTTC 59.701 50.000 0.00 0.00 46.03 3.01
36 37 2.036992 CAGCTGAGGACAGACTTGAGTT 59.963 50.000 8.42 0.00 46.03 3.01
37 38 1.617850 CAGCTGAGGACAGACTTGAGT 59.382 52.381 8.42 0.00 46.03 3.41
38 39 1.617850 ACAGCTGAGGACAGACTTGAG 59.382 52.381 23.35 0.00 46.03 3.02
39 40 1.709578 ACAGCTGAGGACAGACTTGA 58.290 50.000 23.35 0.00 46.03 3.02
40 41 2.540265 AACAGCTGAGGACAGACTTG 57.460 50.000 23.35 0.00 46.03 3.16
41 42 3.235200 ACTAACAGCTGAGGACAGACTT 58.765 45.455 23.35 2.95 46.03 3.01
42 43 2.823154 GACTAACAGCTGAGGACAGACT 59.177 50.000 23.35 0.00 46.03 3.24
43 44 2.558795 TGACTAACAGCTGAGGACAGAC 59.441 50.000 23.35 9.90 46.03 3.51
44 45 2.876581 TGACTAACAGCTGAGGACAGA 58.123 47.619 23.35 0.00 46.03 3.41
45 46 3.883830 ATGACTAACAGCTGAGGACAG 57.116 47.619 23.35 11.42 45.91 3.51
46 47 3.324846 ACAATGACTAACAGCTGAGGACA 59.675 43.478 23.35 15.29 0.00 4.02
47 48 3.931578 ACAATGACTAACAGCTGAGGAC 58.068 45.455 23.35 10.29 0.00 3.85
48 49 4.623932 AACAATGACTAACAGCTGAGGA 57.376 40.909 23.35 3.63 0.00 3.71
103 137 6.545666 TCACACTTCTTTGGAAATGCTTCTAA 59.454 34.615 0.00 0.00 32.64 2.10
222 265 3.181478 ACACGAGGGCAATAGCTAAGTAC 60.181 47.826 0.00 0.00 41.70 2.73
223 266 3.028850 ACACGAGGGCAATAGCTAAGTA 58.971 45.455 0.00 0.00 41.70 2.24
224 267 1.831736 ACACGAGGGCAATAGCTAAGT 59.168 47.619 0.00 0.00 41.70 2.24
338 382 6.291427 GCACACATTATCATGAATTTTGAGCG 60.291 38.462 0.00 0.00 34.11 5.03
367 411 8.152898 GGAACTAAAGAGAGGTAAACACCTAAA 58.847 37.037 0.00 0.00 40.86 1.85
372 416 5.012871 AGGGGAACTAAAGAGAGGTAAACAC 59.987 44.000 0.00 0.00 0.00 3.32
373 417 5.012768 CAGGGGAACTAAAGAGAGGTAAACA 59.987 44.000 0.00 0.00 0.00 2.83
374 418 5.012871 ACAGGGGAACTAAAGAGAGGTAAAC 59.987 44.000 0.00 0.00 0.00 2.01
377 421 4.415224 ACAGGGGAACTAAAGAGAGGTA 57.585 45.455 0.00 0.00 0.00 3.08
378 422 3.277416 ACAGGGGAACTAAAGAGAGGT 57.723 47.619 0.00 0.00 0.00 3.85
388 432 3.897505 CCTTTTCATCAAACAGGGGAACT 59.102 43.478 0.00 0.00 0.00 3.01
391 435 3.893753 TCCTTTTCATCAAACAGGGGA 57.106 42.857 0.00 0.00 0.00 4.81
428 473 5.239306 TGTTACAGTTGGCAAAATGAGAGAG 59.761 40.000 8.55 0.00 34.98 3.20
464 509 4.261447 GGCTGAACAAACGAATTACAGGTT 60.261 41.667 0.00 0.00 0.00 3.50
476 521 3.798337 CACAGAAATGTGGCTGAACAAAC 59.202 43.478 0.00 0.00 36.24 2.93
477 522 3.698539 TCACAGAAATGTGGCTGAACAAA 59.301 39.130 8.40 0.00 40.03 2.83
483 528 6.088824 GTCTAATTTCACAGAAATGTGGCTG 58.911 40.000 8.40 0.00 40.03 4.85
489 535 5.416952 AGGCCTGTCTAATTTCACAGAAATG 59.583 40.000 3.11 3.37 42.37 2.32
513 559 7.275560 CACAGTCAAACATTGTAGTCGATGATA 59.724 37.037 0.00 0.00 38.46 2.15
523 569 4.385825 GGACCTCACAGTCAAACATTGTA 58.614 43.478 0.00 0.00 38.59 2.41
537 583 1.539065 CGACTGCATATGGGACCTCAC 60.539 57.143 4.56 0.00 0.00 3.51
570 616 9.916397 CAGTCTTTGATTTCATAATAACGGTAC 57.084 33.333 0.00 0.00 0.00 3.34
572 618 7.120579 TGCAGTCTTTGATTTCATAATAACGGT 59.879 33.333 0.00 0.00 0.00 4.83
573 619 7.471721 TGCAGTCTTTGATTTCATAATAACGG 58.528 34.615 0.00 0.00 0.00 4.44
574 620 8.788813 GTTGCAGTCTTTGATTTCATAATAACG 58.211 33.333 0.00 0.00 0.00 3.18
575 621 9.846248 AGTTGCAGTCTTTGATTTCATAATAAC 57.154 29.630 0.00 0.00 0.00 1.89
580 626 9.230122 TCATAAGTTGCAGTCTTTGATTTCATA 57.770 29.630 10.60 0.00 0.00 2.15
640 745 6.183360 TGTCTACTTTGGTTTTCATGACAACC 60.183 38.462 29.21 29.21 42.61 3.77
641 746 6.791303 TGTCTACTTTGGTTTTCATGACAAC 58.209 36.000 15.03 15.03 0.00 3.32
644 749 5.562890 GCCTGTCTACTTTGGTTTTCATGAC 60.563 44.000 0.00 0.00 0.00 3.06
660 766 6.658816 TCTTCTGCATAAATTTTGCCTGTCTA 59.341 34.615 17.13 3.38 39.39 2.59
667 773 7.171337 TGTTTTCCTCTTCTGCATAAATTTTGC 59.829 33.333 14.55 14.55 40.55 3.68
678 784 7.596621 CCTTTTCTATTTGTTTTCCTCTTCTGC 59.403 37.037 0.00 0.00 0.00 4.26
679 785 8.850156 TCCTTTTCTATTTGTTTTCCTCTTCTG 58.150 33.333 0.00 0.00 0.00 3.02
680 786 8.996651 TCCTTTTCTATTTGTTTTCCTCTTCT 57.003 30.769 0.00 0.00 0.00 2.85
694 800 7.074653 TGACCACACTAGTTCCTTTTCTATT 57.925 36.000 0.00 0.00 0.00 1.73
699 805 5.367945 TCTTGACCACACTAGTTCCTTTT 57.632 39.130 0.00 0.00 0.00 2.27
700 806 5.367945 TTCTTGACCACACTAGTTCCTTT 57.632 39.130 0.00 0.00 0.00 3.11
701 807 4.202367 CCTTCTTGACCACACTAGTTCCTT 60.202 45.833 0.00 0.00 0.00 3.36
703 809 3.665190 CCTTCTTGACCACACTAGTTCC 58.335 50.000 0.00 0.00 0.00 3.62
705 811 2.438021 TGCCTTCTTGACCACACTAGTT 59.562 45.455 0.00 0.00 0.00 2.24
706 812 2.047061 TGCCTTCTTGACCACACTAGT 58.953 47.619 0.00 0.00 0.00 2.57
707 813 2.839486 TGCCTTCTTGACCACACTAG 57.161 50.000 0.00 0.00 0.00 2.57
708 814 5.189736 AGAATATGCCTTCTTGACCACACTA 59.810 40.000 0.00 0.00 31.38 2.74
709 815 4.018960 AGAATATGCCTTCTTGACCACACT 60.019 41.667 0.00 0.00 31.38 3.55
712 818 5.294552 GTGTAGAATATGCCTTCTTGACCAC 59.705 44.000 0.00 0.00 36.82 4.16
737 918 1.576356 CTGTAGAATGCGCCTTCTCC 58.424 55.000 27.82 19.04 36.82 3.71
752 933 2.787473 CAAGGAACATGCTCCCTGTA 57.213 50.000 11.63 0.00 35.95 2.74
761 942 0.806868 AGATGCGTGCAAGGAACATG 59.193 50.000 0.00 0.00 0.00 3.21
807 990 1.872952 GCTCCCCATTTGTTTGTTTGC 59.127 47.619 0.00 0.00 0.00 3.68
816 999 4.958581 AGATTTTTCCTAGCTCCCCATTTG 59.041 41.667 0.00 0.00 0.00 2.32
817 1000 5.043806 AGAGATTTTTCCTAGCTCCCCATTT 60.044 40.000 0.00 0.00 0.00 2.32
818 1001 4.480166 AGAGATTTTTCCTAGCTCCCCATT 59.520 41.667 0.00 0.00 0.00 3.16
819 1002 4.050757 AGAGATTTTTCCTAGCTCCCCAT 58.949 43.478 0.00 0.00 0.00 4.00
820 1003 3.200825 CAGAGATTTTTCCTAGCTCCCCA 59.799 47.826 0.00 0.00 0.00 4.96
822 1005 4.762289 TCAGAGATTTTTCCTAGCTCCC 57.238 45.455 0.00 0.00 0.00 4.30
824 1007 5.983540 TCCTTCAGAGATTTTTCCTAGCTC 58.016 41.667 0.00 0.00 0.00 4.09
825 1008 6.380079 TTCCTTCAGAGATTTTTCCTAGCT 57.620 37.500 0.00 0.00 0.00 3.32
852 1036 3.026694 GGATAGGCCAGCAGATGTTTTT 58.973 45.455 5.01 0.00 36.34 1.94
855 1039 0.475906 GGGATAGGCCAGCAGATGTT 59.524 55.000 5.01 0.00 38.95 2.71
856 1040 1.422161 GGGGATAGGCCAGCAGATGT 61.422 60.000 5.01 0.00 38.95 3.06
857 1041 1.132554 AGGGGATAGGCCAGCAGATG 61.133 60.000 5.01 0.00 38.95 2.90
961 1148 0.752009 CACGGGAGAGGAATCGAGGA 60.752 60.000 0.00 0.00 0.00 3.71
963 1150 0.752009 TCCACGGGAGAGGAATCGAG 60.752 60.000 0.00 0.00 46.79 4.04
964 1151 1.305287 TCCACGGGAGAGGAATCGA 59.695 57.895 0.00 0.00 46.79 3.59
970 1157 2.633488 GAGAATTTTCCACGGGAGAGG 58.367 52.381 0.00 0.00 42.44 3.69
971 1158 2.271800 CGAGAATTTTCCACGGGAGAG 58.728 52.381 0.00 0.00 31.21 3.20
972 1159 1.066430 CCGAGAATTTTCCACGGGAGA 60.066 52.381 14.52 0.00 40.96 3.71
1179 1372 3.118592 CCACCACATTAGAGGAGGAAGAC 60.119 52.174 0.00 0.00 38.24 3.01
1205 1398 1.783284 CGCGCTCTGCCAGAAATATA 58.217 50.000 5.56 0.00 42.08 0.86
1250 1458 3.752665 ACTCAGAACGACTCTACCAGAA 58.247 45.455 0.00 0.00 31.12 3.02
1302 1510 2.183555 GTCCTGGGGTTCTACGCG 59.816 66.667 3.53 3.53 31.02 6.01
1487 1699 7.592533 GCATGCAGAATTATATGGTTAGTGTTG 59.407 37.037 14.21 0.00 0.00 3.33
1514 1751 3.857157 AACAAGGGTCAGACTTAGCAA 57.143 42.857 0.00 0.00 0.00 3.91
1527 1765 7.145323 CACTGAATTTACAAGGTAAACAAGGG 58.855 38.462 3.88 0.95 0.00 3.95
1536 1774 3.832527 ACAGCCACTGAATTTACAAGGT 58.167 40.909 0.78 0.00 35.18 3.50
1555 1795 3.550820 TGCAACTTTAGCCAGAGAAACA 58.449 40.909 0.00 0.00 0.00 2.83
1600 1840 1.487452 GCTTCACGAACAGCACACGA 61.487 55.000 0.00 0.00 35.95 4.35
1672 1912 1.064906 CACCTGATGGCCTCAATCTGT 60.065 52.381 3.32 0.00 36.63 3.41
1747 1991 3.284323 ACGGTAGCTAGTGCATATTCG 57.716 47.619 0.00 0.00 42.74 3.34
1766 2010 3.761311 AACTCGTCTGAGATACCGAAC 57.239 47.619 0.00 0.00 45.57 3.95
1773 2024 7.648039 AGGAGTAATTAAACTCGTCTGAGAT 57.352 36.000 0.00 0.00 45.69 2.75
1781 2032 8.221766 GTCAAACAAGAGGAGTAATTAAACTCG 58.778 37.037 2.95 0.00 45.69 4.18
1793 2044 7.493971 CACATATCCTAAGTCAAACAAGAGGAG 59.506 40.741 0.00 0.00 36.56 3.69
1863 2114 1.004080 TCTGCTGAACTGCTGCTCC 60.004 57.895 0.00 0.00 41.53 4.70
1937 2188 3.428870 CGCGTGACAGAAAAGTACAGAAT 59.571 43.478 0.00 0.00 0.00 2.40
1983 2241 6.478344 GCAGAAGTAGTCCATATGAAACTGAG 59.522 42.308 16.55 5.57 0.00 3.35
2000 2258 7.391554 ACTTCAAAGATAAATGCTGCAGAAGTA 59.608 33.333 20.43 3.87 39.84 2.24
2084 2377 9.316730 ACTACGTGTCTTCTACTTATAAGAGAG 57.683 37.037 19.38 14.42 32.56 3.20
2346 2782 5.675575 GCGACATATATTACGGTACAGAGGG 60.676 48.000 0.00 0.00 0.00 4.30
2347 2783 5.123502 AGCGACATATATTACGGTACAGAGG 59.876 44.000 0.00 0.00 34.86 3.69
2348 2784 6.022208 CAGCGACATATATTACGGTACAGAG 58.978 44.000 0.00 0.00 35.19 3.35
2350 2786 5.093457 CCAGCGACATATATTACGGTACAG 58.907 45.833 11.00 0.00 35.19 2.74
2351 2787 4.761227 TCCAGCGACATATATTACGGTACA 59.239 41.667 11.00 1.73 35.19 2.90
2353 2789 5.005740 ACTCCAGCGACATATATTACGGTA 58.994 41.667 11.00 0.00 35.19 4.02
2354 2790 3.825014 ACTCCAGCGACATATATTACGGT 59.175 43.478 7.04 7.04 36.95 4.83
2355 2791 4.436242 ACTCCAGCGACATATATTACGG 57.564 45.455 9.37 0.00 0.00 4.02
2356 2792 5.029014 GCTACTCCAGCGACATATATTACG 58.971 45.833 0.00 4.54 41.37 3.18
2390 2826 5.123502 ACCGTAATATATGTCGCTGGAGTAG 59.876 44.000 4.83 0.00 0.00 2.57
2392 2828 3.825014 ACCGTAATATATGTCGCTGGAGT 59.175 43.478 4.83 0.00 0.00 3.85
2395 2831 5.050644 TGTACCGTAATATATGTCGCTGG 57.949 43.478 0.00 0.00 0.00 4.85
2396 2832 5.934921 TCTGTACCGTAATATATGTCGCTG 58.065 41.667 0.00 0.00 0.00 5.18
2397 2833 5.123502 CCTCTGTACCGTAATATATGTCGCT 59.876 44.000 0.00 0.00 0.00 4.93
2398 2834 5.330295 CCTCTGTACCGTAATATATGTCGC 58.670 45.833 0.00 0.00 0.00 5.19
2399 2835 5.645067 TCCCTCTGTACCGTAATATATGTCG 59.355 44.000 0.00 0.00 0.00 4.35
2402 2838 8.749026 ATACTCCCTCTGTACCGTAATATATG 57.251 38.462 0.00 0.00 0.00 1.78
2406 2842 9.592196 AAATAATACTCCCTCTGTACCGTAATA 57.408 33.333 0.00 0.00 0.00 0.98
2408 2844 7.902920 AAATAATACTCCCTCTGTACCGTAA 57.097 36.000 0.00 0.00 0.00 3.18
2411 2847 6.482308 CCAAAAATAATACTCCCTCTGTACCG 59.518 42.308 0.00 0.00 0.00 4.02
2412 2848 6.771267 CCCAAAAATAATACTCCCTCTGTACC 59.229 42.308 0.00 0.00 0.00 3.34
2413 2849 7.344134 ACCCAAAAATAATACTCCCTCTGTAC 58.656 38.462 0.00 0.00 0.00 2.90
2414 2850 7.519347 ACCCAAAAATAATACTCCCTCTGTA 57.481 36.000 0.00 0.00 0.00 2.74
2416 2852 8.850156 CATAACCCAAAAATAATACTCCCTCTG 58.150 37.037 0.00 0.00 0.00 3.35
2417 2853 8.787818 TCATAACCCAAAAATAATACTCCCTCT 58.212 33.333 0.00 0.00 0.00 3.69
2418 2854 8.990163 TCATAACCCAAAAATAATACTCCCTC 57.010 34.615 0.00 0.00 0.00 4.30
2421 2857 8.352942 CAGCTCATAACCCAAAAATAATACTCC 58.647 37.037 0.00 0.00 0.00 3.85
2422 2858 9.120538 TCAGCTCATAACCCAAAAATAATACTC 57.879 33.333 0.00 0.00 0.00 2.59
2423 2859 9.125026 CTCAGCTCATAACCCAAAAATAATACT 57.875 33.333 0.00 0.00 0.00 2.12
2424 2860 7.862873 GCTCAGCTCATAACCCAAAAATAATAC 59.137 37.037 0.00 0.00 0.00 1.89
2440 2876 3.413846 TGAAGTCAAAGCTCAGCTCAT 57.586 42.857 0.00 0.00 38.25 2.90
2454 2890 6.638468 CAGAAACCTAATTTGTGCTTGAAGTC 59.362 38.462 0.00 0.00 35.05 3.01
2522 3378 3.251729 GTGCTTCAAGTCAAAGATCAGCA 59.748 43.478 0.00 0.00 33.69 4.41
2571 3427 7.891498 AAAATTAACACCTGGTAGTTTCACT 57.109 32.000 16.13 0.09 27.78 3.41
2618 3474 7.823745 TTTCTGTCCAGAAGCTAAGAAAATT 57.176 32.000 9.48 0.00 46.80 1.82
2769 3667 3.927142 GCGTGCTGTATTAAACTGAGAGT 59.073 43.478 0.00 0.00 0.00 3.24
2789 3687 0.305922 GGCTACTTGCATTGCTAGCG 59.694 55.000 18.13 11.48 45.15 4.26
2791 3689 2.636830 ACTGGCTACTTGCATTGCTAG 58.363 47.619 16.88 16.88 45.15 3.42
2920 3838 4.235079 TGGGAAGGATGTTTACATGGAG 57.765 45.455 0.00 0.00 36.57 3.86
2939 3857 0.971386 AAAAGGCCATGAGCAGTTGG 59.029 50.000 5.01 0.00 46.50 3.77
2940 3858 3.084039 TCTAAAAGGCCATGAGCAGTTG 58.916 45.455 5.01 0.00 46.50 3.16
2953 3871 6.808212 TCGTTAAACCGATAGTGTCTAAAAGG 59.192 38.462 0.00 0.00 30.63 3.11
2960 3878 4.102035 ACCTCGTTAAACCGATAGTGTC 57.898 45.455 0.00 0.00 36.08 3.67
2967 3885 3.125316 CAACAGAACCTCGTTAAACCGA 58.875 45.455 0.00 0.00 35.22 4.69
2971 3889 2.823984 TCGCAACAGAACCTCGTTAAA 58.176 42.857 0.00 0.00 0.00 1.52
2973 3891 2.512485 TTCGCAACAGAACCTCGTTA 57.488 45.000 0.00 0.00 0.00 3.18
2974 3892 1.658994 TTTCGCAACAGAACCTCGTT 58.341 45.000 0.00 0.00 0.00 3.85
2990 3908 3.775065 GCCAGGCGAGTTTCTTTTC 57.225 52.632 0.00 0.00 0.00 2.29
3007 3925 1.662629 CCACACTGAGACAATGATCGC 59.337 52.381 0.00 0.00 0.00 4.58
3014 3932 2.936919 AGCATTCCACACTGAGACAA 57.063 45.000 0.00 0.00 0.00 3.18
3026 3944 6.623114 GCATCATCAGTTCATCATAGCATTCC 60.623 42.308 0.00 0.00 0.00 3.01
3031 3949 4.378563 GCAGCATCATCAGTTCATCATAGC 60.379 45.833 0.00 0.00 0.00 2.97
3041 3959 4.242475 CAAAATTGTGCAGCATCATCAGT 58.758 39.130 0.00 0.00 0.00 3.41
3051 3969 2.070783 GTCCATGGCAAAATTGTGCAG 58.929 47.619 21.93 10.82 46.81 4.41
3059 3977 3.153919 GTCAACTAGGTCCATGGCAAAA 58.846 45.455 6.96 0.00 0.00 2.44
3068 3986 1.509923 CGGACGGTCAACTAGGTCC 59.490 63.158 10.76 0.00 44.31 4.46
3075 3993 3.712881 GTGCAGCGGACGGTCAAC 61.713 66.667 10.76 0.89 0.00 3.18
3144 4062 5.216614 AGAACTCTTCCAGGTTGTAGAAC 57.783 43.478 0.00 0.00 0.00 3.01
3159 4077 1.080025 GGCGTTGCCGTAGAACTCT 60.080 57.895 0.00 0.00 39.62 3.24
3218 4136 0.464036 ATGCCAAGATTCGAGCGGTA 59.536 50.000 0.00 0.00 0.00 4.02
3256 4179 0.951040 CCTGCGGGTCTTTGAGTGAC 60.951 60.000 2.29 0.00 0.00 3.67
3275 4244 4.023107 TGTGCGACCAAGCTATCTATCTAC 60.023 45.833 0.00 0.00 38.13 2.59
3308 4277 1.741770 GTCACCCGGCATCACTGTC 60.742 63.158 0.00 0.00 0.00 3.51
3309 4278 2.347490 GTCACCCGGCATCACTGT 59.653 61.111 0.00 0.00 0.00 3.55
3310 4279 2.436646 GGTCACCCGGCATCACTG 60.437 66.667 0.00 0.00 0.00 3.66
3311 4280 2.927856 TGGTCACCCGGCATCACT 60.928 61.111 0.00 0.00 0.00 3.41
3312 4281 2.746277 GTGGTCACCCGGCATCAC 60.746 66.667 0.00 0.00 0.00 3.06
3327 4296 3.510388 TTCGCATACTTCAGGAGAGTG 57.490 47.619 0.00 0.00 0.00 3.51
3344 4313 1.583451 CATGACGGCGCCAATTTCG 60.583 57.895 28.98 13.91 0.00 3.46
3357 4326 7.086376 ACAGATTACAAGAATGTTTGCATGAC 58.914 34.615 0.00 0.00 41.05 3.06
3414 4383 5.528043 TGTTAACATTGTTCAATGGTGCT 57.472 34.783 21.59 10.10 34.56 4.40
3419 4395 6.364165 CCTCTTGCTGTTAACATTGTTCAATG 59.636 38.462 19.75 19.75 36.29 2.82
3504 4481 4.999950 AGCAGACAAGATCAAAACCAGTAG 59.000 41.667 0.00 0.00 0.00 2.57
3505 4482 4.756642 CAGCAGACAAGATCAAAACCAGTA 59.243 41.667 0.00 0.00 0.00 2.74
3506 4483 3.567164 CAGCAGACAAGATCAAAACCAGT 59.433 43.478 0.00 0.00 0.00 4.00
3507 4484 3.817084 TCAGCAGACAAGATCAAAACCAG 59.183 43.478 0.00 0.00 0.00 4.00
3508 4485 3.565482 GTCAGCAGACAAGATCAAAACCA 59.435 43.478 4.10 0.00 44.34 3.67
3509 4486 4.152607 GTCAGCAGACAAGATCAAAACC 57.847 45.455 4.10 0.00 44.34 3.27
3545 4526 7.504924 TCAGACAACGTGGAAGAAAAATATT 57.495 32.000 0.00 0.00 0.00 1.28
3546 4527 7.228706 AGTTCAGACAACGTGGAAGAAAAATAT 59.771 33.333 0.00 0.00 0.00 1.28
3558 4539 4.088638 CGTCAGAATAGTTCAGACAACGTG 59.911 45.833 13.28 0.00 43.80 4.49
3619 4608 6.480320 ACTTCAACTGTCTTTTGCTAGTAGTG 59.520 38.462 0.00 0.00 0.00 2.74
3647 4637 2.488545 TCTCCAGTGTCTCTTCTTACGC 59.511 50.000 0.00 0.00 0.00 4.42
3659 4649 5.136068 TCTGAAGGATATCTCTCCAGTGT 57.864 43.478 2.05 0.00 37.81 3.55
3663 4653 6.618501 TCTGAATCTGAAGGATATCTCTCCA 58.381 40.000 2.05 0.00 37.81 3.86
3895 4885 2.122813 CAGGAGGTAGGGGCGGAT 60.123 66.667 0.00 0.00 0.00 4.18
4006 4996 2.285743 GGAGAGGGGAAGCTGGGT 60.286 66.667 0.00 0.00 0.00 4.51
4032 5022 4.162690 GTGAAGGGGAGCGCGGAT 62.163 66.667 8.83 0.00 0.00 4.18
4069 5059 4.436998 GTCCAGGAGGTCGGCGTG 62.437 72.222 6.85 0.00 35.89 5.34
4092 5082 2.125350 CAGAGCCTGGCGAGGAAC 60.125 66.667 20.35 10.98 42.93 3.62


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

AutoCloner maintained by Alex Coulton.