Multiple sequence alignment - TraesCS2D01G249800

Loading Multiple Alignment...

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 TraesCS2D01G249800 chr2D 100.000 3260 0 0 426 3685 296708537 296711796 0.000000e+00 6021.0
1 TraesCS2D01G249800 chr2D 91.667 996 76 4 2691 3685 106982316 106981327 0.000000e+00 1373.0
2 TraesCS2D01G249800 chr2D 90.981 632 40 12 2070 2692 63555217 63555840 0.000000e+00 835.0
3 TraesCS2D01G249800 chr2D 90.146 548 32 9 818 1343 63554210 63554757 0.000000e+00 693.0
4 TraesCS2D01G249800 chr2D 100.000 211 0 0 1 211 296708112 296708322 1.240000e-104 390.0
5 TraesCS2D01G249800 chr2D 88.927 289 21 6 1537 1820 63554937 63555219 2.720000e-91 346.0
6 TraesCS2D01G249800 chr2D 83.495 206 32 2 462 665 501653979 501653774 1.350000e-44 191.0
7 TraesCS2D01G249800 chr2D 80.894 246 37 9 426 663 644056018 644056261 6.280000e-43 185.0
8 TraesCS2D01G249800 chr3D 92.671 996 71 2 2691 3685 188481861 188482855 0.000000e+00 1434.0
9 TraesCS2D01G249800 chr3D 92.369 996 73 2 2691 3685 466141747 466142740 0.000000e+00 1415.0
10 TraesCS2D01G249800 chr3D 91.667 996 82 1 2691 3685 551600121 551599126 0.000000e+00 1378.0
11 TraesCS2D01G249800 chr3D 91.466 996 84 1 2691 3685 298273228 298272233 0.000000e+00 1367.0
12 TraesCS2D01G249800 chr3D 96.178 157 2 1 1846 2002 488863579 488863427 1.700000e-63 254.0
13 TraesCS2D01G249800 chr3D 96.129 155 2 1 1846 2000 529127161 529127311 2.200000e-62 250.0
14 TraesCS2D01G249800 chr3D 84.524 84 13 0 1440 1523 539846159 539846076 2.360000e-12 84.2
15 TraesCS2D01G249800 chr4D 92.570 996 72 2 2691 3685 475911762 475910768 0.000000e+00 1428.0
16 TraesCS2D01G249800 chr4D 91.968 996 79 1 2691 3685 165835266 165834271 0.000000e+00 1395.0
17 TraesCS2D01G249800 chr4D 96.296 162 0 3 1846 2005 447293812 447293655 1.020000e-65 261.0
18 TraesCS2D01G249800 chr4D 94.643 168 3 3 1836 2001 351463634 351463797 4.720000e-64 255.0
19 TraesCS2D01G249800 chr5D 91.919 990 77 3 2697 3685 355663159 355662172 0.000000e+00 1382.0
20 TraesCS2D01G249800 chr5D 96.154 156 1 3 1846 2001 380078775 380078925 2.200000e-62 250.0
21 TraesCS2D01G249800 chr5D 94.040 151 5 1 1846 1996 442957895 442957749 3.700000e-55 226.0
22 TraesCS2D01G249800 chr5D 87.931 58 4 3 1426 1483 276532180 276532126 8.540000e-07 65.8
23 TraesCS2D01G249800 chr6D 91.767 996 76 4 2691 3685 385727048 385726058 0.000000e+00 1380.0
24 TraesCS2D01G249800 chr2B 89.205 1056 65 20 457 1501 364950140 364949123 0.000000e+00 1273.0
25 TraesCS2D01G249800 chr2B 95.763 354 14 1 2001 2353 364948709 364948356 1.480000e-158 569.0
26 TraesCS2D01G249800 chr2B 94.857 350 16 2 1498 1845 364949042 364948693 2.500000e-151 545.0
27 TraesCS2D01G249800 chr2B 97.569 288 7 0 2408 2695 364948364 364948077 9.190000e-136 494.0
28 TraesCS2D01G249800 chr2B 89.157 166 14 2 1840 2005 245301888 245302049 1.730000e-48 204.0
29 TraesCS2D01G249800 chr2B 83.491 212 11 7 1 211 364950669 364950481 3.780000e-40 176.0
30 TraesCS2D01G249800 chr2A 93.822 696 41 2 2001 2695 369215321 369216015 0.000000e+00 1046.0
31 TraesCS2D01G249800 chr2A 92.170 613 33 6 745 1343 65173478 65174089 0.000000e+00 852.0
32 TraesCS2D01G249800 chr2A 88.324 728 54 12 1122 1845 369214637 369215337 0.000000e+00 845.0
33 TraesCS2D01G249800 chr2A 94.336 512 29 0 2181 2692 65174607 65175118 0.000000e+00 785.0
34 TraesCS2D01G249800 chr2A 92.701 274 15 2 664 936 369201644 369201375 1.240000e-104 390.0
35 TraesCS2D01G249800 chr2A 87.261 314 31 8 1519 1823 65174178 65174491 2.110000e-92 350.0
36 TraesCS2D01G249800 chr2A 93.333 195 10 1 942 1136 369204547 369204738 6.020000e-73 285.0
37 TraesCS2D01G249800 chr2A 92.547 161 5 1 1842 2002 39159107 39159260 1.330000e-54 224.0
38 TraesCS2D01G249800 chr2A 87.879 99 7 4 1999 2097 65174485 65174578 1.080000e-20 111.0
39 TraesCS2D01G249800 chr2A 82.143 84 8 5 1397 1480 478127144 478127220 8.540000e-07 65.8
40 TraesCS2D01G249800 chrUn 95.625 160 3 1 1846 2005 64153173 64153328 1.700000e-63 254.0
41 TraesCS2D01G249800 chr1D 96.154 156 2 1 1846 2001 463344303 463344454 6.110000e-63 252.0
42 TraesCS2D01G249800 chr1D 95.541 157 3 1 1846 2002 325676750 325676902 7.900000e-62 248.0
43 TraesCS2D01G249800 chr1D 95.541 157 3 1 1846 2002 367162532 367162684 7.900000e-62 248.0
44 TraesCS2D01G249800 chr1D 80.383 209 37 4 457 663 432026885 432026679 4.930000e-34 156.0
45 TraesCS2D01G249800 chr3A 94.410 161 4 3 1842 2001 601382895 601382739 3.680000e-60 243.0
46 TraesCS2D01G249800 chr3A 83.019 159 26 1 505 663 102688879 102688722 3.840000e-30 143.0
47 TraesCS2D01G249800 chr7D 91.358 162 4 2 1842 2003 1956689 1956840 2.880000e-51 213.0
48 TraesCS2D01G249800 chr7D 87.634 186 11 7 1832 2016 15067636 15067810 4.820000e-49 206.0
49 TraesCS2D01G249800 chr7D 91.892 74 6 0 1 74 565962429 565962356 1.810000e-18 104.0
50 TraesCS2D01G249800 chr6A 90.184 163 11 3 1837 1999 336558106 336558263 1.340000e-49 207.0
51 TraesCS2D01G249800 chr5B 89.634 164 13 1 1836 1999 317384919 317385078 4.820000e-49 206.0
52 TraesCS2D01G249800 chr5B 88.732 71 8 0 1444 1514 531200357 531200427 1.820000e-13 87.9
53 TraesCS2D01G249800 chr5B 89.062 64 7 0 1441 1504 29699734 29699797 3.050000e-11 80.5
54 TraesCS2D01G249800 chr1A 82.096 229 36 5 439 663 585513519 585513746 1.350000e-44 191.0
55 TraesCS2D01G249800 chr1A 89.091 55 3 3 1426 1480 142955648 142955699 8.540000e-07 65.8
56 TraesCS2D01G249800 chr3B 84.706 85 10 3 1421 1504 494077955 494078037 8.480000e-12 82.4
57 TraesCS2D01G249800 chr3B 83.544 79 13 0 1445 1523 827099213 827099135 1.420000e-09 75.0
58 TraesCS2D01G249800 chr6B 84.615 78 12 0 1445 1522 262371444 262371521 1.100000e-10 78.7
59 TraesCS2D01G249800 chr6B 94.595 37 2 0 1440 1476 142439451 142439487 1.430000e-04 58.4
60 TraesCS2D01G249800 chr4A 82.353 85 15 0 1421 1505 628850124 628850208 1.420000e-09 75.0
61 TraesCS2D01G249800 chr7B 89.655 58 3 3 1426 1483 391564687 391564633 1.840000e-08 71.3
62 TraesCS2D01G249800 chr7B 82.895 76 13 0 1445 1520 667387263 667387188 6.600000e-08 69.4
63 TraesCS2D01G249800 chr1B 90.909 55 2 3 1426 1480 77891896 77891947 1.840000e-08 71.3
64 TraesCS2D01G249800 chr1B 89.091 55 3 3 1426 1480 676746048 676746099 8.540000e-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 TraesCS2D01G249800 chr2D 296708112 296711796 3684 False 3205.500000 6021 100.0000 1 3685 2 chr2D.!!$F3 3684
1 TraesCS2D01G249800 chr2D 106981327 106982316 989 True 1373.000000 1373 91.6670 2691 3685 1 chr2D.!!$R1 994
2 TraesCS2D01G249800 chr2D 63554210 63555840 1630 False 624.666667 835 90.0180 818 2692 3 chr2D.!!$F2 1874
3 TraesCS2D01G249800 chr3D 188481861 188482855 994 False 1434.000000 1434 92.6710 2691 3685 1 chr3D.!!$F1 994
4 TraesCS2D01G249800 chr3D 466141747 466142740 993 False 1415.000000 1415 92.3690 2691 3685 1 chr3D.!!$F2 994
5 TraesCS2D01G249800 chr3D 551599126 551600121 995 True 1378.000000 1378 91.6670 2691 3685 1 chr3D.!!$R4 994
6 TraesCS2D01G249800 chr3D 298272233 298273228 995 True 1367.000000 1367 91.4660 2691 3685 1 chr3D.!!$R1 994
7 TraesCS2D01G249800 chr4D 475910768 475911762 994 True 1428.000000 1428 92.5700 2691 3685 1 chr4D.!!$R3 994
8 TraesCS2D01G249800 chr4D 165834271 165835266 995 True 1395.000000 1395 91.9680 2691 3685 1 chr4D.!!$R1 994
9 TraesCS2D01G249800 chr5D 355662172 355663159 987 True 1382.000000 1382 91.9190 2697 3685 1 chr5D.!!$R2 988
10 TraesCS2D01G249800 chr6D 385726058 385727048 990 True 1380.000000 1380 91.7670 2691 3685 1 chr6D.!!$R1 994
11 TraesCS2D01G249800 chr2B 364948077 364950669 2592 True 611.400000 1273 92.1770 1 2695 5 chr2B.!!$R1 2694
12 TraesCS2D01G249800 chr2A 369214637 369216015 1378 False 945.500000 1046 91.0730 1122 2695 2 chr2A.!!$F5 1573
13 TraesCS2D01G249800 chr2A 65173478 65175118 1640 False 524.500000 852 90.4115 745 2692 4 chr2A.!!$F4 1947

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
683 801 0.179067 TGGGCTCACGACGTCTTTTT 60.179 50.0 14.7 0.0 0.00 1.94 F
1333 1480 0.034059 CCACTTCCTCAAGCGTGTCT 59.966 55.0 0.0 0.0 32.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2699 0.251653 TGCGAGAGGAGGTAGTGGTT 60.252 55.0 0.00 0.0 0.00 3.67 R
2862 3161 0.519519 GGATCTCGCTCGATCGACAT 59.480 55.0 15.15 2.9 40.52 3.06 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
31 32 4.724602 GGCAGCAGACGACTCGCA 62.725 66.667 0.00 0.00 0.00 5.10
103 104 2.751436 GCTGGCAAGCGGGATCAA 60.751 61.111 0.00 0.00 40.27 2.57
104 105 2.342650 GCTGGCAAGCGGGATCAAA 61.343 57.895 0.00 0.00 40.27 2.69
105 106 1.805254 CTGGCAAGCGGGATCAAAG 59.195 57.895 0.00 0.00 0.00 2.77
106 107 2.275547 CTGGCAAGCGGGATCAAAGC 62.276 60.000 0.00 0.00 0.00 3.51
107 108 2.100991 GCAAGCGGGATCAAAGCG 59.899 61.111 0.00 0.00 35.78 4.68
108 109 2.398554 GCAAGCGGGATCAAAGCGA 61.399 57.895 0.00 0.00 35.78 4.93
496 608 0.949105 GGCGTGGAAGCGAGAAAGAA 60.949 55.000 0.00 0.00 38.18 2.52
503 615 3.263261 GGAAGCGAGAAAGAAACCTAGG 58.737 50.000 7.41 7.41 0.00 3.02
516 628 6.301169 AGAAACCTAGGAAACTGATACCAG 57.699 41.667 17.98 0.00 43.88 4.00
517 629 6.023603 AGAAACCTAGGAAACTGATACCAGA 58.976 40.000 17.98 0.00 43.02 3.86
536 648 7.918536 ACCAGATATGAGATTATGATTGCAC 57.081 36.000 0.00 0.00 0.00 4.57
540 658 9.525409 CAGATATGAGATTATGATTGCACGATA 57.475 33.333 0.00 0.00 0.00 2.92
555 673 9.144747 GATTGCACGATATATTACTCTTCATGT 57.855 33.333 0.00 0.00 0.00 3.21
577 695 9.107367 CATGTATAGACACGTATATATGATGCG 57.893 37.037 8.98 0.00 36.96 4.73
586 704 8.241367 ACACGTATATATGATGCGTAAAGATGA 58.759 33.333 8.98 0.00 38.23 2.92
596 714 2.223525 GCGTAAAGATGAGCTACGGACT 60.224 50.000 5.21 0.00 39.00 3.85
604 722 4.336993 AGATGAGCTACGGACTTCAACTAG 59.663 45.833 0.00 0.00 0.00 2.57
610 728 4.621886 GCTACGGACTTCAACTAGACAAAG 59.378 45.833 0.00 0.00 0.00 2.77
613 731 5.855045 ACGGACTTCAACTAGACAAAGAAT 58.145 37.500 0.00 0.00 0.00 2.40
614 732 5.927115 ACGGACTTCAACTAGACAAAGAATC 59.073 40.000 0.00 0.00 0.00 2.52
616 734 6.090088 CGGACTTCAACTAGACAAAGAATCAG 59.910 42.308 0.00 0.00 0.00 2.90
620 738 6.042638 TCAACTAGACAAAGAATCAGGAGG 57.957 41.667 0.00 0.00 0.00 4.30
623 741 3.347077 AGACAAAGAATCAGGAGGCAG 57.653 47.619 0.00 0.00 0.00 4.85
625 743 1.707427 ACAAAGAATCAGGAGGCAGGT 59.293 47.619 0.00 0.00 0.00 4.00
632 750 2.196742 TCAGGAGGCAGGTCCAATAT 57.803 50.000 2.19 0.00 39.34 1.28
642 760 6.640518 AGGCAGGTCCAATATACAATATACG 58.359 40.000 0.00 0.00 37.29 3.06
643 761 6.212791 AGGCAGGTCCAATATACAATATACGT 59.787 38.462 0.00 0.00 37.29 3.57
667 785 9.569167 CGTATAATACATATACTCAACAGTGGG 57.431 37.037 0.00 0.00 42.81 4.61
668 786 9.367444 GTATAATACATATACTCAACAGTGGGC 57.633 37.037 0.00 0.00 42.07 5.36
669 787 6.500589 AATACATATACTCAACAGTGGGCT 57.499 37.500 0.00 0.00 33.62 5.19
670 788 4.408182 ACATATACTCAACAGTGGGCTC 57.592 45.455 0.00 0.00 33.62 4.70
671 789 3.774766 ACATATACTCAACAGTGGGCTCA 59.225 43.478 0.00 0.00 33.62 4.26
672 790 2.770164 ATACTCAACAGTGGGCTCAC 57.230 50.000 9.29 9.29 43.93 3.51
683 801 0.179067 TGGGCTCACGACGTCTTTTT 60.179 50.000 14.70 0.00 0.00 1.94
685 803 1.214367 GGCTCACGACGTCTTTTTCA 58.786 50.000 14.70 0.00 0.00 2.69
686 804 1.070776 GGCTCACGACGTCTTTTTCAC 60.071 52.381 14.70 0.00 0.00 3.18
687 805 1.591158 GCTCACGACGTCTTTTTCACA 59.409 47.619 14.70 0.00 0.00 3.58
688 806 2.221055 GCTCACGACGTCTTTTTCACAT 59.779 45.455 14.70 0.00 0.00 3.21
689 807 3.661936 GCTCACGACGTCTTTTTCACATC 60.662 47.826 14.70 0.00 0.00 3.06
690 808 3.449632 TCACGACGTCTTTTTCACATCA 58.550 40.909 14.70 0.00 0.00 3.07
691 809 3.244345 TCACGACGTCTTTTTCACATCAC 59.756 43.478 14.70 0.00 0.00 3.06
693 811 2.469886 CGACGTCTTTTTCACATCACGA 59.530 45.455 14.70 0.00 0.00 4.35
713 832 6.073440 TCACGAAAATGACCAAAGTAGTAAGC 60.073 38.462 0.00 0.00 0.00 3.09
735 854 1.668047 GCGTGTATGTATAGGACGGCC 60.668 57.143 0.00 0.00 0.00 6.13
736 855 1.400629 CGTGTATGTATAGGACGGCCG 60.401 57.143 26.86 26.86 39.96 6.13
737 856 1.610522 GTGTATGTATAGGACGGCCGT 59.389 52.381 34.89 34.89 39.96 5.68
738 857 2.813754 GTGTATGTATAGGACGGCCGTA 59.186 50.000 34.36 17.68 39.96 4.02
859 978 4.271807 TCCTCCATCATAACTCACTCCT 57.728 45.455 0.00 0.00 0.00 3.69
874 993 1.008938 ACTCCTTAGGCTCCCATGACT 59.991 52.381 0.00 0.00 0.00 3.41
981 1119 1.906574 CTCCTACACCAAGGCCAAGTA 59.093 52.381 5.01 0.00 36.51 2.24
991 1129 1.025812 AGGCCAAGTAGACGATCGAG 58.974 55.000 24.34 0.00 0.00 4.04
1333 1480 0.034059 CCACTTCCTCAAGCGTGTCT 59.966 55.000 0.00 0.00 32.09 3.41
1421 1598 3.681593 TTTCCGTCCCGAAATACTCAA 57.318 42.857 0.00 0.00 0.00 3.02
1422 1599 3.899052 TTCCGTCCCGAAATACTCAAT 57.101 42.857 0.00 0.00 0.00 2.57
1424 1601 4.311816 TCCGTCCCGAAATACTCAATAC 57.688 45.455 0.00 0.00 0.00 1.89
1425 1602 3.956199 TCCGTCCCGAAATACTCAATACT 59.044 43.478 0.00 0.00 0.00 2.12
1426 1603 4.037208 TCCGTCCCGAAATACTCAATACTC 59.963 45.833 0.00 0.00 0.00 2.59
1427 1604 4.202080 CCGTCCCGAAATACTCAATACTCA 60.202 45.833 0.00 0.00 0.00 3.41
1431 1608 5.533528 TCCCGAAATACTCAATACTCATCGA 59.466 40.000 0.00 0.00 0.00 3.59
1441 1618 8.458573 ACTCAATACTCATCGAAGAACTAGAT 57.541 34.615 0.00 0.00 43.58 1.98
1524 1785 9.074443 GTATTTCCGAACAGAGAAAGTACTAAG 57.926 37.037 0.00 0.00 35.57 2.18
1533 1796 6.096695 CAGAGAAAGTACTAAGAGAACTGGC 58.903 44.000 0.00 0.00 0.00 4.85
1552 1819 2.959516 GCCTTTAGATGCCACCAAAAC 58.040 47.619 0.00 0.00 0.00 2.43
1632 1900 1.676014 GGGGTTCACATCTTGGACGAG 60.676 57.143 0.00 0.00 33.88 4.18
1641 1909 4.633126 CACATCTTGGACGAGAATTGACAT 59.367 41.667 0.00 0.00 0.00 3.06
1770 2038 9.745018 TGAATTGGAGTTGAATATTTTCTCTCT 57.255 29.630 15.03 5.39 35.70 3.10
1830 2102 7.484140 AGAAATCTCTGTTTTCAACAAGGTTC 58.516 34.615 0.00 0.00 41.61 3.62
1831 2103 6.773976 AATCTCTGTTTTCAACAAGGTTCA 57.226 33.333 0.00 0.00 41.61 3.18
1832 2104 6.773976 ATCTCTGTTTTCAACAAGGTTCAA 57.226 33.333 0.00 0.00 41.61 2.69
1833 2105 6.773976 TCTCTGTTTTCAACAAGGTTCAAT 57.226 33.333 0.00 0.00 41.61 2.57
1834 2106 6.563422 TCTCTGTTTTCAACAAGGTTCAATG 58.437 36.000 0.00 0.00 41.61 2.82
1835 2107 5.659463 TCTGTTTTCAACAAGGTTCAATGG 58.341 37.500 0.00 0.00 41.61 3.16
1836 2108 5.186797 TCTGTTTTCAACAAGGTTCAATGGT 59.813 36.000 0.00 0.00 41.61 3.55
1837 2109 6.378564 TCTGTTTTCAACAAGGTTCAATGGTA 59.621 34.615 0.00 0.00 41.61 3.25
1838 2110 6.568869 TGTTTTCAACAAGGTTCAATGGTAG 58.431 36.000 0.00 0.00 38.72 3.18
1839 2111 6.153680 TGTTTTCAACAAGGTTCAATGGTAGT 59.846 34.615 0.00 0.00 38.72 2.73
1840 2112 6.783708 TTTCAACAAGGTTCAATGGTAGTT 57.216 33.333 0.00 0.00 0.00 2.24
1841 2113 5.766150 TCAACAAGGTTCAATGGTAGTTG 57.234 39.130 0.00 0.00 37.15 3.16
1842 2114 5.441500 TCAACAAGGTTCAATGGTAGTTGA 58.558 37.500 0.00 0.00 40.98 3.18
1843 2115 5.888724 TCAACAAGGTTCAATGGTAGTTGAA 59.111 36.000 0.00 0.00 43.66 2.69
1844 2116 6.378564 TCAACAAGGTTCAATGGTAGTTGAAA 59.621 34.615 0.00 0.00 46.31 2.69
1845 2117 6.391227 ACAAGGTTCAATGGTAGTTGAAAG 57.609 37.500 3.88 0.00 46.31 2.62
1846 2118 6.126409 ACAAGGTTCAATGGTAGTTGAAAGA 58.874 36.000 3.88 0.00 46.31 2.52
1847 2119 6.263168 ACAAGGTTCAATGGTAGTTGAAAGAG 59.737 38.462 3.88 0.00 46.31 2.85
1848 2120 5.316987 AGGTTCAATGGTAGTTGAAAGAGG 58.683 41.667 3.88 0.00 46.31 3.69
1849 2121 5.073144 AGGTTCAATGGTAGTTGAAAGAGGA 59.927 40.000 3.88 0.00 46.31 3.71
1850 2122 5.181433 GGTTCAATGGTAGTTGAAAGAGGAC 59.819 44.000 3.88 0.00 46.31 3.85
1851 2123 4.566004 TCAATGGTAGTTGAAAGAGGACG 58.434 43.478 0.00 0.00 35.31 4.79
1852 2124 3.611766 ATGGTAGTTGAAAGAGGACGG 57.388 47.619 0.00 0.00 0.00 4.79
1853 2125 1.621814 TGGTAGTTGAAAGAGGACGGG 59.378 52.381 0.00 0.00 0.00 5.28
1854 2126 1.066358 GGTAGTTGAAAGAGGACGGGG 60.066 57.143 0.00 0.00 0.00 5.73
1855 2127 0.611714 TAGTTGAAAGAGGACGGGGC 59.388 55.000 0.00 0.00 0.00 5.80
1856 2128 2.033194 GTTGAAAGAGGACGGGGCG 61.033 63.158 0.00 0.00 0.00 6.13
1857 2129 2.513259 TTGAAAGAGGACGGGGCGT 61.513 57.895 0.00 0.00 45.10 5.68
1886 2158 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
1887 2159 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
1892 2164 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
1893 2165 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
1894 2166 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
1895 2167 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
1896 2168 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
1897 2169 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
1906 2178 4.760047 CCAGCCCACCCGAGTTCG 62.760 72.222 0.00 0.00 39.44 3.95
1907 2179 3.691342 CAGCCCACCCGAGTTCGA 61.691 66.667 2.59 0.00 43.02 3.71
1908 2180 3.382832 AGCCCACCCGAGTTCGAG 61.383 66.667 2.59 0.00 43.02 4.04
1909 2181 3.692406 GCCCACCCGAGTTCGAGT 61.692 66.667 2.59 0.00 43.02 4.18
1910 2182 2.572284 CCCACCCGAGTTCGAGTC 59.428 66.667 2.59 0.00 43.02 3.36
1911 2183 2.572284 CCACCCGAGTTCGAGTCC 59.428 66.667 2.59 0.00 43.02 3.85
1912 2184 2.572284 CACCCGAGTTCGAGTCCC 59.428 66.667 2.59 0.00 43.02 4.46
1913 2185 3.060615 ACCCGAGTTCGAGTCCCG 61.061 66.667 2.59 0.00 43.02 5.14
1914 2186 3.823330 CCCGAGTTCGAGTCCCGG 61.823 72.222 2.59 0.00 43.02 5.73
1915 2187 4.493747 CCGAGTTCGAGTCCCGGC 62.494 72.222 0.00 0.00 43.02 6.13
1916 2188 3.744719 CGAGTTCGAGTCCCGGCA 61.745 66.667 0.00 0.00 43.02 5.69
1917 2189 2.126031 GAGTTCGAGTCCCGGCAC 60.126 66.667 0.00 0.00 39.14 5.01
1945 2217 2.665185 GCGGTGCTCACGGAGTTT 60.665 61.111 11.07 0.00 41.61 2.66
1946 2218 2.668280 GCGGTGCTCACGGAGTTTC 61.668 63.158 11.07 0.00 41.61 2.78
1947 2219 1.006102 CGGTGCTCACGGAGTTTCT 60.006 57.895 1.90 0.00 41.61 2.52
1948 2220 1.009389 CGGTGCTCACGGAGTTTCTC 61.009 60.000 1.90 0.00 41.61 2.87
1949 2221 0.670854 GGTGCTCACGGAGTTTCTCC 60.671 60.000 5.79 5.79 46.44 3.71
1963 2235 7.323049 GGAGTTTCTCCTATAAAGAAAAGCC 57.677 40.000 8.38 10.42 46.41 4.35
1964 2236 6.884836 GGAGTTTCTCCTATAAAGAAAAGCCA 59.115 38.462 8.38 0.00 46.41 4.75
1965 2237 7.393515 GGAGTTTCTCCTATAAAGAAAAGCCAA 59.606 37.037 8.38 0.00 46.41 4.52
1966 2238 8.112016 AGTTTCTCCTATAAAGAAAAGCCAAC 57.888 34.615 10.15 1.39 42.63 3.77
1967 2239 6.737254 TTCTCCTATAAAGAAAAGCCAACG 57.263 37.500 0.00 0.00 30.00 4.10
1968 2240 6.045072 TCTCCTATAAAGAAAAGCCAACGA 57.955 37.500 0.00 0.00 0.00 3.85
1969 2241 6.106673 TCTCCTATAAAGAAAAGCCAACGAG 58.893 40.000 0.00 0.00 0.00 4.18
1970 2242 5.183228 TCCTATAAAGAAAAGCCAACGAGG 58.817 41.667 0.00 0.00 41.84 4.63
1971 2243 4.335594 CCTATAAAGAAAAGCCAACGAGGG 59.664 45.833 0.00 0.00 38.09 4.30
1987 2259 4.434483 GGTTAGCCCTTGGGTTGG 57.566 61.111 7.61 0.00 34.28 3.77
1988 2260 1.463375 GGTTAGCCCTTGGGTTGGT 59.537 57.895 7.61 0.00 34.28 3.67
1989 2261 0.611062 GGTTAGCCCTTGGGTTGGTC 60.611 60.000 7.61 0.00 34.28 4.02
1990 2262 0.404426 GTTAGCCCTTGGGTTGGTCT 59.596 55.000 7.61 0.00 34.28 3.85
1991 2263 0.696501 TTAGCCCTTGGGTTGGTCTC 59.303 55.000 7.61 0.00 34.28 3.36
1992 2264 0.474854 TAGCCCTTGGGTTGGTCTCA 60.475 55.000 7.61 0.00 34.28 3.27
1993 2265 1.142688 AGCCCTTGGGTTGGTCTCAT 61.143 55.000 7.61 0.00 0.00 2.90
1994 2266 0.251787 GCCCTTGGGTTGGTCTCATT 60.252 55.000 7.61 0.00 0.00 2.57
1995 2267 1.827245 GCCCTTGGGTTGGTCTCATTT 60.827 52.381 7.61 0.00 0.00 2.32
1996 2268 2.608623 CCCTTGGGTTGGTCTCATTTT 58.391 47.619 0.00 0.00 0.00 1.82
1997 2269 2.972021 CCCTTGGGTTGGTCTCATTTTT 59.028 45.455 0.00 0.00 0.00 1.94
2032 2314 5.730550 AGTTGAAACCTGAAAGAAAAACCC 58.269 37.500 0.00 0.00 34.07 4.11
2130 2413 9.236006 GTAGAGGCATGAATATTGTTCCATTAT 57.764 33.333 0.00 0.00 0.00 1.28
2201 2500 7.871853 TCAAACCACTACTTAATTTGCTCTTC 58.128 34.615 0.00 0.00 31.71 2.87
2206 2505 8.322091 ACCACTACTTAATTTGCTCTTCTACAT 58.678 33.333 0.00 0.00 0.00 2.29
2225 2524 0.535335 TGGTACTCTTCATCCACCGC 59.465 55.000 0.00 0.00 31.64 5.68
2270 2569 2.430610 GGCGCTCACCATCTCCTCT 61.431 63.158 7.64 0.00 0.00 3.69
2372 2671 2.726351 CCCAGGCGTCCTCCTCTTC 61.726 68.421 0.00 0.00 33.25 2.87
2376 2675 3.760035 GCGTCCTCCTCTTCGCCA 61.760 66.667 0.00 0.00 42.33 5.69
2400 2699 0.739462 CATCGCCGGCAACTTCTACA 60.739 55.000 28.98 0.00 0.00 2.74
2595 2894 3.449227 CGGCAGCCTACCTCGTCA 61.449 66.667 10.54 0.00 0.00 4.35
2630 2929 1.329256 CCCGGAGATGGTACGAATCT 58.671 55.000 0.73 8.92 37.09 2.40
2862 3161 3.640029 GGGACGTTGTCTCCATTATCCTA 59.360 47.826 0.00 0.00 32.47 2.94
2872 3171 5.354513 GTCTCCATTATCCTATGTCGATCGA 59.645 44.000 15.15 15.15 0.00 3.59
2960 3259 2.496070 TCTCGTTTTCCATCATCTCCGT 59.504 45.455 0.00 0.00 0.00 4.69
2977 3276 3.120108 TCCGTAAGAAGATCCCCCAAAT 58.880 45.455 0.00 0.00 43.02 2.32
3134 3433 0.396435 TGGAGGAACTGTGCGACAAT 59.604 50.000 0.00 0.00 41.55 2.71
3212 3512 1.907739 CTCCCAATCTTCGGAGGCA 59.092 57.895 0.00 0.00 41.79 4.75
3249 3549 1.134250 GGGGAGAAAGGATGTCAGCTC 60.134 57.143 0.00 0.00 0.00 4.09
3290 3590 3.313791 GGAAGAGGGAGCCTTAATCTCT 58.686 50.000 5.28 0.00 36.49 3.10
3342 3642 1.229984 AGGCTACCTTTGGCTCCCT 60.230 57.895 0.00 0.00 35.30 4.20
3373 3673 0.400213 TTGTCCTCTTTCACCGGCAT 59.600 50.000 0.00 0.00 0.00 4.40
3386 3686 1.146930 CGGCATCTGGTATGGTGCT 59.853 57.895 0.00 0.00 37.70 4.40
3389 3689 0.107017 GCATCTGGTATGGTGCTGGT 60.107 55.000 0.00 0.00 34.85 4.00
3454 3754 0.036388 GGAGCCGAACACCTGATTCA 60.036 55.000 0.00 0.00 0.00 2.57
3492 3792 1.283321 AGCCCTGGAAGAAGATGGTTC 59.717 52.381 0.00 0.00 34.07 3.62
3552 3852 1.592400 CGGGAGTCGAGTGCTTACCA 61.592 60.000 11.80 0.00 42.43 3.25
3559 3859 3.514309 AGTCGAGTGCTTACCAAGGTATT 59.486 43.478 0.00 0.00 0.00 1.89
3584 3884 0.392461 GGTTGCAGTCAAGGCCGATA 60.392 55.000 0.00 0.00 31.93 2.92
3634 3934 3.423907 CGTGTCCCGAAAAATAACTTCCG 60.424 47.826 0.00 0.00 39.56 4.30
3667 3967 1.735700 CGTCATGCCGAAGAAGTGCTA 60.736 52.381 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.433318 GAGTCGTCTGCTGCCACC 60.433 66.667 0.00 0.00 0.00 4.61
14 15 4.724602 TGCGAGTCGTCTGCTGCC 62.725 66.667 15.08 0.00 0.00 4.85
87 88 1.805254 CTTTGATCCCGCTTGCCAG 59.195 57.895 0.00 0.00 0.00 4.85
88 89 2.342650 GCTTTGATCCCGCTTGCCA 61.343 57.895 0.00 0.00 0.00 4.92
89 90 2.491621 GCTTTGATCCCGCTTGCC 59.508 61.111 0.00 0.00 0.00 4.52
90 91 2.100991 CGCTTTGATCCCGCTTGC 59.899 61.111 0.00 0.00 0.00 4.01
91 92 1.021390 AGTCGCTTTGATCCCGCTTG 61.021 55.000 0.00 0.00 0.00 4.01
92 93 1.021390 CAGTCGCTTTGATCCCGCTT 61.021 55.000 0.00 0.00 0.00 4.68
93 94 1.448540 CAGTCGCTTTGATCCCGCT 60.449 57.895 0.00 0.00 0.00 5.52
94 95 2.464459 CCAGTCGCTTTGATCCCGC 61.464 63.158 0.00 0.00 0.00 6.13
95 96 2.464459 GCCAGTCGCTTTGATCCCG 61.464 63.158 0.00 0.00 0.00 5.14
96 97 3.502572 GCCAGTCGCTTTGATCCC 58.497 61.111 0.00 0.00 0.00 3.85
476 588 2.730672 CTTTCTCGCTTCCACGCCG 61.731 63.158 0.00 0.00 0.00 6.46
477 589 0.949105 TTCTTTCTCGCTTCCACGCC 60.949 55.000 0.00 0.00 0.00 5.68
478 590 0.865769 TTTCTTTCTCGCTTCCACGC 59.134 50.000 0.00 0.00 0.00 5.34
479 591 1.194772 GGTTTCTTTCTCGCTTCCACG 59.805 52.381 0.00 0.00 0.00 4.94
480 592 2.495084 AGGTTTCTTTCTCGCTTCCAC 58.505 47.619 0.00 0.00 0.00 4.02
481 593 2.930826 AGGTTTCTTTCTCGCTTCCA 57.069 45.000 0.00 0.00 0.00 3.53
496 608 7.789831 TCATATCTGGTATCAGTTTCCTAGGTT 59.210 37.037 9.08 0.00 41.59 3.50
552 670 8.837389 ACGCATCATATATACGTGTCTATACAT 58.163 33.333 0.00 0.00 38.08 2.29
563 681 7.645735 AGCTCATCTTTACGCATCATATATACG 59.354 37.037 0.00 0.00 0.00 3.06
572 690 2.726760 CCGTAGCTCATCTTTACGCATC 59.273 50.000 0.00 0.00 38.95 3.91
576 694 3.694535 AGTCCGTAGCTCATCTTTACG 57.305 47.619 0.00 0.00 39.72 3.18
577 695 4.995124 TGAAGTCCGTAGCTCATCTTTAC 58.005 43.478 0.00 0.00 0.00 2.01
586 704 3.418995 TGTCTAGTTGAAGTCCGTAGCT 58.581 45.455 0.00 0.00 0.00 3.32
596 714 6.467677 CCTCCTGATTCTTTGTCTAGTTGAA 58.532 40.000 0.00 0.00 0.00 2.69
604 722 2.290577 ACCTGCCTCCTGATTCTTTGTC 60.291 50.000 0.00 0.00 0.00 3.18
610 728 0.620556 TTGGACCTGCCTCCTGATTC 59.379 55.000 0.00 0.00 37.63 2.52
613 731 2.196742 ATATTGGACCTGCCTCCTGA 57.803 50.000 0.00 0.00 37.63 3.86
614 732 2.705658 TGTATATTGGACCTGCCTCCTG 59.294 50.000 0.00 0.00 37.63 3.86
616 734 3.857157 TTGTATATTGGACCTGCCTCC 57.143 47.619 0.00 0.00 37.63 4.30
642 760 9.367444 GCCCACTGTTGAGTATATGTATTATAC 57.633 37.037 0.00 0.00 42.03 1.47
643 761 9.321532 AGCCCACTGTTGAGTATATGTATTATA 57.678 33.333 0.00 0.00 0.00 0.98
657 775 1.069090 GTCGTGAGCCCACTGTTGA 59.931 57.895 0.00 0.00 41.06 3.18
660 778 3.208884 GACGTCGTGAGCCCACTGT 62.209 63.158 0.63 0.00 41.06 3.55
662 780 1.745320 AAAGACGTCGTGAGCCCACT 61.745 55.000 10.46 0.00 41.06 4.00
663 781 0.878961 AAAAGACGTCGTGAGCCCAC 60.879 55.000 10.46 0.00 39.86 4.61
664 782 0.179067 AAAAAGACGTCGTGAGCCCA 60.179 50.000 10.46 0.00 0.00 5.36
665 783 0.511653 GAAAAAGACGTCGTGAGCCC 59.488 55.000 10.46 0.00 0.00 5.19
666 784 1.070776 GTGAAAAAGACGTCGTGAGCC 60.071 52.381 10.46 0.12 0.00 4.70
667 785 1.591158 TGTGAAAAAGACGTCGTGAGC 59.409 47.619 10.46 1.92 0.00 4.26
668 786 3.489416 TGATGTGAAAAAGACGTCGTGAG 59.511 43.478 10.46 0.00 0.00 3.51
669 787 3.244345 GTGATGTGAAAAAGACGTCGTGA 59.756 43.478 10.46 0.00 0.00 4.35
670 788 3.531982 GTGATGTGAAAAAGACGTCGTG 58.468 45.455 10.46 0.00 0.00 4.35
671 789 2.217847 CGTGATGTGAAAAAGACGTCGT 59.782 45.455 10.46 3.44 0.00 4.34
672 790 2.469886 TCGTGATGTGAAAAAGACGTCG 59.530 45.455 10.46 0.00 0.00 5.12
673 791 4.446857 TTCGTGATGTGAAAAAGACGTC 57.553 40.909 7.70 7.70 0.00 4.34
683 801 4.578516 ACTTTGGTCATTTTCGTGATGTGA 59.421 37.500 0.00 0.00 0.00 3.58
685 803 5.763204 ACTACTTTGGTCATTTTCGTGATGT 59.237 36.000 0.00 0.00 0.00 3.06
686 804 6.241207 ACTACTTTGGTCATTTTCGTGATG 57.759 37.500 0.00 0.00 0.00 3.07
687 805 7.360946 GCTTACTACTTTGGTCATTTTCGTGAT 60.361 37.037 0.00 0.00 0.00 3.06
688 806 6.073440 GCTTACTACTTTGGTCATTTTCGTGA 60.073 38.462 0.00 0.00 0.00 4.35
689 807 6.077838 GCTTACTACTTTGGTCATTTTCGTG 58.922 40.000 0.00 0.00 0.00 4.35
690 808 5.180680 GGCTTACTACTTTGGTCATTTTCGT 59.819 40.000 0.00 0.00 0.00 3.85
691 809 5.628134 GGCTTACTACTTTGGTCATTTTCG 58.372 41.667 0.00 0.00 0.00 3.46
693 811 4.082949 GCGGCTTACTACTTTGGTCATTTT 60.083 41.667 0.00 0.00 0.00 1.82
713 832 1.400629 CCGTCCTATACATACACGCGG 60.401 57.143 12.47 1.27 0.00 6.46
735 854 3.779303 GCATATGCACACACGTACG 57.221 52.632 22.84 15.01 41.59 3.67
859 978 1.204146 GTGGAGTCATGGGAGCCTAA 58.796 55.000 0.00 0.00 0.00 2.69
874 993 1.003839 GTTGCCCATGAGACGTGGA 60.004 57.895 11.05 0.00 39.12 4.02
981 1119 3.069586 ACATCTCTCTCTCTCGATCGTCT 59.930 47.826 15.94 0.00 0.00 4.18
991 1129 0.383949 GACGGCCACATCTCTCTCTC 59.616 60.000 2.24 0.00 0.00 3.20
1054 1201 2.297912 CGAACGACACCACCGACAC 61.298 63.158 0.00 0.00 0.00 3.67
1333 1480 3.070446 TGAAGCAAGACCTTTACCTCGAA 59.930 43.478 0.00 0.00 0.00 3.71
1424 1601 9.534565 TCCATTTTTATCTAGTTCTTCGATGAG 57.465 33.333 0.94 0.00 0.00 2.90
1427 1604 9.838339 ACATCCATTTTTATCTAGTTCTTCGAT 57.162 29.630 0.00 0.00 0.00 3.59
1498 1675 8.976986 TTAGTACTTTCTCTGTTCGGAAATAC 57.023 34.615 0.00 0.00 32.15 1.89
1533 1796 5.220854 CGATAGTTTTGGTGGCATCTAAAGG 60.221 44.000 7.61 0.00 0.00 3.11
1552 1819 6.019881 TCGTTGAAGTACATGATTTGCGATAG 60.020 38.462 0.00 0.00 0.00 2.08
1770 2038 5.350504 TGCTTCCCATTTTTCAGTCAAAA 57.649 34.783 0.00 0.00 31.73 2.44
1830 2102 3.684788 CCGTCCTCTTTCAACTACCATTG 59.315 47.826 0.00 0.00 0.00 2.82
1831 2103 3.307480 CCCGTCCTCTTTCAACTACCATT 60.307 47.826 0.00 0.00 0.00 3.16
1832 2104 2.236395 CCCGTCCTCTTTCAACTACCAT 59.764 50.000 0.00 0.00 0.00 3.55
1833 2105 1.621814 CCCGTCCTCTTTCAACTACCA 59.378 52.381 0.00 0.00 0.00 3.25
1834 2106 1.066358 CCCCGTCCTCTTTCAACTACC 60.066 57.143 0.00 0.00 0.00 3.18
1835 2107 1.675116 GCCCCGTCCTCTTTCAACTAC 60.675 57.143 0.00 0.00 0.00 2.73
1836 2108 0.611714 GCCCCGTCCTCTTTCAACTA 59.388 55.000 0.00 0.00 0.00 2.24
1837 2109 1.375326 GCCCCGTCCTCTTTCAACT 59.625 57.895 0.00 0.00 0.00 3.16
1838 2110 2.033194 CGCCCCGTCCTCTTTCAAC 61.033 63.158 0.00 0.00 0.00 3.18
1839 2111 2.345991 CGCCCCGTCCTCTTTCAA 59.654 61.111 0.00 0.00 0.00 2.69
1840 2112 2.920912 ACGCCCCGTCCTCTTTCA 60.921 61.111 0.00 0.00 33.69 2.69
1869 2141 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
1870 2142 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
1875 2147 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
1876 2148 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
1877 2149 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
1878 2150 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
1879 2151 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
1880 2152 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
1889 2161 4.760047 CGAACTCGGGTGGGCTGG 62.760 72.222 0.00 0.00 35.37 4.85
1890 2162 3.649277 CTCGAACTCGGGTGGGCTG 62.649 68.421 0.00 0.00 40.29 4.85
1891 2163 3.382832 CTCGAACTCGGGTGGGCT 61.383 66.667 0.00 0.00 40.29 5.19
1897 2169 3.823330 CCGGGACTCGAACTCGGG 61.823 72.222 18.93 0.00 46.21 5.14
1899 2171 3.744719 TGCCGGGACTCGAACTCG 61.745 66.667 2.18 4.83 42.43 4.18
1900 2172 2.126031 GTGCCGGGACTCGAACTC 60.126 66.667 20.19 0.00 42.43 3.01
1901 2173 4.052229 CGTGCCGGGACTCGAACT 62.052 66.667 24.50 0.00 42.43 3.01
1928 2200 2.665185 AAACTCCGTGAGCACCGC 60.665 61.111 1.36 0.00 32.04 5.68
1929 2201 1.006102 AGAAACTCCGTGAGCACCG 60.006 57.895 1.36 0.00 32.04 4.94
1930 2202 0.670854 GGAGAAACTCCGTGAGCACC 60.671 60.000 1.97 0.00 41.08 5.01
1931 2203 2.828933 GGAGAAACTCCGTGAGCAC 58.171 57.895 1.97 0.00 41.08 4.40
1940 2212 7.923414 TGGCTTTTCTTTATAGGAGAAACTC 57.077 36.000 10.98 0.00 41.42 3.01
1941 2213 7.094762 CGTTGGCTTTTCTTTATAGGAGAAACT 60.095 37.037 10.98 0.00 41.42 2.66
1942 2214 7.021790 CGTTGGCTTTTCTTTATAGGAGAAAC 58.978 38.462 10.98 4.09 41.42 2.78
1943 2215 6.938030 TCGTTGGCTTTTCTTTATAGGAGAAA 59.062 34.615 8.49 8.49 40.36 2.52
1944 2216 6.469410 TCGTTGGCTTTTCTTTATAGGAGAA 58.531 36.000 0.00 0.00 0.00 2.87
1945 2217 6.045072 TCGTTGGCTTTTCTTTATAGGAGA 57.955 37.500 0.00 0.00 0.00 3.71
1946 2218 5.294552 CCTCGTTGGCTTTTCTTTATAGGAG 59.705 44.000 0.00 0.00 0.00 3.69
1947 2219 5.183228 CCTCGTTGGCTTTTCTTTATAGGA 58.817 41.667 0.00 0.00 0.00 2.94
1948 2220 4.335594 CCCTCGTTGGCTTTTCTTTATAGG 59.664 45.833 0.00 0.00 0.00 2.57
1949 2221 4.941873 ACCCTCGTTGGCTTTTCTTTATAG 59.058 41.667 0.00 0.00 0.00 1.31
1950 2222 4.913784 ACCCTCGTTGGCTTTTCTTTATA 58.086 39.130 0.00 0.00 0.00 0.98
1951 2223 3.763057 ACCCTCGTTGGCTTTTCTTTAT 58.237 40.909 0.00 0.00 0.00 1.40
1952 2224 3.217681 ACCCTCGTTGGCTTTTCTTTA 57.782 42.857 0.00 0.00 0.00 1.85
1953 2225 2.067365 ACCCTCGTTGGCTTTTCTTT 57.933 45.000 0.00 0.00 0.00 2.52
1954 2226 2.067365 AACCCTCGTTGGCTTTTCTT 57.933 45.000 0.00 0.00 0.00 2.52
1955 2227 2.779506 CTAACCCTCGTTGGCTTTTCT 58.220 47.619 0.00 0.00 33.17 2.52
1970 2242 0.611062 GACCAACCCAAGGGCTAACC 60.611 60.000 4.70 0.00 39.32 2.85
1971 2243 0.404426 AGACCAACCCAAGGGCTAAC 59.596 55.000 4.70 0.00 44.68 2.34
1972 2244 2.877150 AGACCAACCCAAGGGCTAA 58.123 52.632 4.70 0.00 44.68 3.09
1973 2245 4.681624 AGACCAACCCAAGGGCTA 57.318 55.556 4.70 0.00 44.68 3.93
1975 2247 0.251787 AATGAGACCAACCCAAGGGC 60.252 55.000 4.70 0.00 39.32 5.19
1976 2248 2.309136 AAATGAGACCAACCCAAGGG 57.691 50.000 2.91 2.91 42.03 3.95
2000 2272 6.831353 TCTTTCAGGTTTCAACTACCATTGAA 59.169 34.615 0.00 0.00 44.80 2.69
2001 2273 6.361433 TCTTTCAGGTTTCAACTACCATTGA 58.639 36.000 0.00 0.00 38.16 2.57
2032 2314 8.251750 TCAAATTATTGTGAAGTTAGTCCTCG 57.748 34.615 0.00 0.00 37.79 4.63
2201 2500 4.499865 CGGTGGATGAAGAGTACCATGTAG 60.500 50.000 0.00 0.00 34.87 2.74
2206 2505 0.535335 GCGGTGGATGAAGAGTACCA 59.465 55.000 0.00 0.00 0.00 3.25
2225 2524 3.955145 TGGCATGTTCCCACTGTAG 57.045 52.632 0.00 0.00 0.00 2.74
2316 2615 2.675772 GTCAGGGAGTCCGACGGT 60.676 66.667 14.79 0.00 38.33 4.83
2400 2699 0.251653 TGCGAGAGGAGGTAGTGGTT 60.252 55.000 0.00 0.00 0.00 3.67
2630 2929 1.134610 GCCGGGAATTCCTCGAACTTA 60.135 52.381 26.99 0.00 35.95 2.24
2862 3161 0.519519 GGATCTCGCTCGATCGACAT 59.480 55.000 15.15 2.90 40.52 3.06
2977 3276 4.467795 CAGTCTTCCTCAACAATCCTCCTA 59.532 45.833 0.00 0.00 0.00 2.94
3212 3512 1.007118 CCCCATGGTAAGAAAAGGGCT 59.993 52.381 11.73 0.00 34.93 5.19
3249 3549 3.006967 TCCGAAGACAAAAGAGAAGGAGG 59.993 47.826 0.00 0.00 0.00 4.30
3290 3590 1.695242 ACACCAAACACTATGTCCGGA 59.305 47.619 0.00 0.00 0.00 5.14
3342 3642 3.019799 AGAGGACAATAAGGAGAGCGA 57.980 47.619 0.00 0.00 0.00 4.93
3373 3673 1.200519 GGTACCAGCACCATACCAGA 58.799 55.000 7.15 0.00 38.61 3.86
3386 3686 2.355716 GCTAACAAGGATGCTGGTACCA 60.356 50.000 15.39 15.39 0.00 3.25
3389 3689 2.676750 CGTGCTAACAAGGATGCTGGTA 60.677 50.000 0.00 0.00 0.00 3.25
3454 3754 2.092699 GGCTGGATAAAGAAGGCAGAGT 60.093 50.000 0.00 0.00 36.56 3.24
3512 3812 4.024048 CCGAACACAGCTCAGTTAAACATT 60.024 41.667 0.55 0.00 0.00 2.71
3523 3823 1.444553 CGACTCCCGAACACAGCTC 60.445 63.158 0.00 0.00 41.76 4.09
3552 3852 4.263462 TGACTGCAACCATCTGAATACCTT 60.263 41.667 0.00 0.00 0.00 3.50
3559 3859 1.883638 GCCTTGACTGCAACCATCTGA 60.884 52.381 0.00 0.00 0.00 3.27
3584 3884 1.147191 TGGCCGGATACTACAGAGGAT 59.853 52.381 5.05 0.00 0.00 3.24
3651 3951 2.359900 CCTTTAGCACTTCTTCGGCAT 58.640 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.