Multiple sequence alignment - TraesCS6A01G149300

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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 TraesCS6A01G149300 chr6A 100.000 6047 0 0 1 6047 131235905 131229859 0.000000e+00 11167.0
1 TraesCS6A01G149300 chr6A 88.472 772 79 7 5278 6047 129938258 129939021 0.000000e+00 924.0
2 TraesCS6A01G149300 chr6B 94.790 1996 72 15 4079 6047 194862949 194860959 0.000000e+00 3081.0
3 TraesCS6A01G149300 chr6B 88.571 770 78 7 5278 6045 194424173 194424934 0.000000e+00 926.0
4 TraesCS6A01G149300 chr6B 91.228 684 17 16 528 1210 194866737 194866096 0.000000e+00 891.0
5 TraesCS6A01G149300 chr6B 92.508 614 37 4 2978 3591 194863962 194863358 0.000000e+00 870.0
6 TraesCS6A01G149300 chr6B 92.599 581 30 4 2323 2900 194864579 194864009 0.000000e+00 822.0
7 TraesCS6A01G149300 chr6B 87.941 539 30 9 1271 1809 194865697 194865194 2.410000e-168 603.0
8 TraesCS6A01G149300 chr6B 90.783 434 25 7 3630 4056 194863362 194862937 3.160000e-157 566.0
9 TraesCS6A01G149300 chr6B 83.890 509 27 12 1811 2287 194865151 194864666 9.310000e-118 435.0
10 TraesCS6A01G149300 chr6B 95.455 44 2 0 2899 2942 100067782 100067739 3.020000e-08 71.3
11 TraesCS6A01G149300 chr6D 93.558 2018 80 21 4065 6045 107388861 107386857 0.000000e+00 2961.0
12 TraesCS6A01G149300 chr6D 89.374 2268 104 52 528 2739 107392251 107390065 0.000000e+00 2726.0
13 TraesCS6A01G149300 chr6D 91.674 1093 59 11 2978 4056 107389912 107388838 0.000000e+00 1485.0
14 TraesCS6A01G149300 chr6D 87.887 776 84 7 5274 6047 106703284 106704051 0.000000e+00 904.0
15 TraesCS6A01G149300 chr6D 87.500 104 8 3 2794 2892 107390049 107389946 1.380000e-21 115.0
16 TraesCS6A01G149300 chr7A 96.774 527 11 5 1 524 532680775 532680252 0.000000e+00 874.0
17 TraesCS6A01G149300 chr7A 96.438 365 11 2 159 522 545937718 545937355 8.670000e-168 601.0
18 TraesCS6A01G149300 chr7A 87.740 416 41 8 1 410 11038539 11038950 1.520000e-130 477.0
19 TraesCS6A01G149300 chr7A 78.615 650 131 7 5276 5921 692045159 692045804 2.010000e-114 424.0
20 TraesCS6A01G149300 chr7A 84.247 146 23 0 1078 1223 692018665 692018810 6.320000e-30 143.0
21 TraesCS6A01G149300 chr7A 93.182 44 3 0 2899 2942 12973366 12973409 1.410000e-06 65.8
22 TraesCS6A01G149300 chr1D 90.440 523 43 6 1 520 457964212 457964730 0.000000e+00 682.0
23 TraesCS6A01G149300 chr1D 87.332 521 41 14 1 520 332966529 332966033 1.890000e-159 573.0
24 TraesCS6A01G149300 chr1D 95.455 44 2 0 2899 2942 455413977 455413934 3.020000e-08 71.3
25 TraesCS6A01G149300 chr5A 87.358 530 52 9 1 525 492992848 492992329 1.450000e-165 593.0
26 TraesCS6A01G149300 chr4A 86.717 527 47 11 1 520 545100014 545099504 1.140000e-156 564.0
27 TraesCS6A01G149300 chr4A 86.364 528 54 10 1 522 530860581 530861096 1.470000e-155 560.0
28 TraesCS6A01G149300 chr7D 79.257 781 134 21 5275 6047 600450360 600449600 2.500000e-143 520.0
29 TraesCS6A01G149300 chr7D 81.681 595 99 10 4418 5007 599721970 599722559 2.530000e-133 486.0
30 TraesCS6A01G149300 chr7D 78.924 669 129 11 5275 5937 599808423 599809085 1.550000e-120 444.0
31 TraesCS6A01G149300 chr7D 84.868 152 23 0 1078 1229 599720977 599721128 2.920000e-33 154.0
32 TraesCS6A01G149300 chr2A 93.631 314 16 2 1 311 140562109 140562421 3.300000e-127 466.0
33 TraesCS6A01G149300 chr2A 86.765 68 4 5 334 397 140562419 140562485 3.020000e-08 71.3
34 TraesCS6A01G149300 chr7B 78.861 667 129 11 5277 5937 679671460 679672120 2.000000e-119 440.0
35 TraesCS6A01G149300 chr7B 83.553 152 25 0 1078 1229 679629618 679629769 6.320000e-30 143.0
36 TraesCS6A01G149300 chr7B 95.455 44 2 0 2899 2942 714762883 714762840 3.020000e-08 71.3
37 TraesCS6A01G149300 chr5B 97.727 44 1 0 2898 2941 253697100 253697143 6.500000e-10 76.8
38 TraesCS6A01G149300 chr3B 93.617 47 1 2 2902 2948 428100492 428100448 1.090000e-07 69.4
39 TraesCS6A01G149300 chr3A 90.385 52 3 2 2891 2942 394381416 394381367 3.910000e-07 67.6
40 TraesCS6A01G149300 chrUn 84.615 65 8 2 462 525 832926 832863 5.060000e-06 63.9
41 TraesCS6A01G149300 chrUn 84.615 65 8 2 462 525 306058812 306058875 5.060000e-06 63.9
42 TraesCS6A01G149300 chrUn 84.615 65 8 2 462 525 397319835 397319772 5.060000e-06 63.9
43 TraesCS6A01G149300 chr1A 93.023 43 3 0 2899 2941 269995335 269995377 5.060000e-06 63.9


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 TraesCS6A01G149300 chr6A 131229859 131235905 6046 True 11167.000000 11167 100.000000 1 6047 1 chr6A.!!$R1 6046
1 TraesCS6A01G149300 chr6A 129938258 129939021 763 False 924.000000 924 88.472000 5278 6047 1 chr6A.!!$F1 769
2 TraesCS6A01G149300 chr6B 194860959 194866737 5778 True 1038.285714 3081 90.534143 528 6047 7 chr6B.!!$R2 5519
3 TraesCS6A01G149300 chr6B 194424173 194424934 761 False 926.000000 926 88.571000 5278 6045 1 chr6B.!!$F1 767
4 TraesCS6A01G149300 chr6D 107386857 107392251 5394 True 1821.750000 2961 90.526500 528 6045 4 chr6D.!!$R1 5517
5 TraesCS6A01G149300 chr6D 106703284 106704051 767 False 904.000000 904 87.887000 5274 6047 1 chr6D.!!$F1 773
6 TraesCS6A01G149300 chr7A 532680252 532680775 523 True 874.000000 874 96.774000 1 524 1 chr7A.!!$R1 523
7 TraesCS6A01G149300 chr7A 692045159 692045804 645 False 424.000000 424 78.615000 5276 5921 1 chr7A.!!$F4 645
8 TraesCS6A01G149300 chr1D 457964212 457964730 518 False 682.000000 682 90.440000 1 520 1 chr1D.!!$F1 519
9 TraesCS6A01G149300 chr5A 492992329 492992848 519 True 593.000000 593 87.358000 1 525 1 chr5A.!!$R1 524
10 TraesCS6A01G149300 chr4A 545099504 545100014 510 True 564.000000 564 86.717000 1 520 1 chr4A.!!$R1 519
11 TraesCS6A01G149300 chr4A 530860581 530861096 515 False 560.000000 560 86.364000 1 522 1 chr4A.!!$F1 521
12 TraesCS6A01G149300 chr7D 600449600 600450360 760 True 520.000000 520 79.257000 5275 6047 1 chr7D.!!$R1 772
13 TraesCS6A01G149300 chr7D 599808423 599809085 662 False 444.000000 444 78.924000 5275 5937 1 chr7D.!!$F1 662
14 TraesCS6A01G149300 chr7D 599720977 599722559 1582 False 320.000000 486 83.274500 1078 5007 2 chr7D.!!$F2 3929
15 TraesCS6A01G149300 chr7B 679671460 679672120 660 False 440.000000 440 78.861000 5277 5937 1 chr7B.!!$F2 660

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
758 771 0.470080 TCGTCTCCTCCCATCCCATC 60.470 60.0 0.00 0.0 0.00 3.51 F
1262 1287 0.177836 ATCCATCGACATGTTCCGCA 59.822 50.0 0.00 0.0 0.00 5.69 F
3019 3588 0.168128 GTTATCCGGTTGCAGCACAC 59.832 55.0 0.00 0.0 0.00 3.82 F
3031 3600 0.661187 CAGCACACGAAAAATGCGCT 60.661 50.0 9.73 0.0 44.25 5.92 F
4050 4633 0.108019 AGTCGGTTCTTTGGTCACCC 59.892 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2285 0.801251 GCTCTTGCCACATCTCACAC 59.199 55.0 0.00 0.00 0.00 3.82 R
3112 3681 0.256177 GGAGACTTCCATTGGGTCCC 59.744 60.0 0.00 0.00 43.45 4.46 R
3867 4450 0.035056 ACTACACATGGCTCCTTGGC 60.035 55.0 0.00 0.00 42.18 4.52 R
4252 4835 0.108992 CGAGTAGTGCTTTGCGGGTA 60.109 55.0 0.00 0.00 0.00 3.69 R
5702 6338 0.612174 CACCCTCTCCGAGAAGGTGA 60.612 60.0 30.97 5.76 41.35 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
104 105 8.871862 TGTGTATTACAATTATGTTCACCGTAC 58.128 33.333 0.00 0.00 41.05 3.67
372 382 3.098555 CGTTTCTATGGGCACGCC 58.901 61.111 0.00 0.00 0.00 5.68
525 536 9.084533 AGATGAGTTTTAGACAGACCCTATATC 57.915 37.037 0.00 0.00 0.00 1.63
526 537 7.598759 TGAGTTTTAGACAGACCCTATATCC 57.401 40.000 0.00 0.00 0.00 2.59
533 544 5.450453 AGACAGACCCTATATCCATATCCG 58.550 45.833 0.00 0.00 0.00 4.18
634 647 4.373116 GCGTGTGCGAGGGAGGAA 62.373 66.667 0.00 0.00 41.33 3.36
682 695 1.167851 CTACACCCACCAGCAACATG 58.832 55.000 0.00 0.00 0.00 3.21
752 765 2.444895 GGCCTCGTCTCCTCCCAT 60.445 66.667 0.00 0.00 0.00 4.00
753 766 2.503382 GGCCTCGTCTCCTCCCATC 61.503 68.421 0.00 0.00 0.00 3.51
754 767 2.503382 GCCTCGTCTCCTCCCATCC 61.503 68.421 0.00 0.00 0.00 3.51
755 768 1.834822 CCTCGTCTCCTCCCATCCC 60.835 68.421 0.00 0.00 0.00 3.85
756 769 1.075970 CTCGTCTCCTCCCATCCCA 60.076 63.158 0.00 0.00 0.00 4.37
757 770 0.470833 CTCGTCTCCTCCCATCCCAT 60.471 60.000 0.00 0.00 0.00 4.00
758 771 0.470080 TCGTCTCCTCCCATCCCATC 60.470 60.000 0.00 0.00 0.00 3.51
759 772 1.476007 CGTCTCCTCCCATCCCATCC 61.476 65.000 0.00 0.00 0.00 3.51
760 773 1.130678 GTCTCCTCCCATCCCATCCC 61.131 65.000 0.00 0.00 0.00 3.85
761 774 1.073474 CTCCTCCCATCCCATCCCA 60.073 63.158 0.00 0.00 0.00 4.37
762 775 0.477202 CTCCTCCCATCCCATCCCAT 60.477 60.000 0.00 0.00 0.00 4.00
763 776 0.476415 TCCTCCCATCCCATCCCATC 60.476 60.000 0.00 0.00 0.00 3.51
764 777 1.504275 CCTCCCATCCCATCCCATCC 61.504 65.000 0.00 0.00 0.00 3.51
765 778 1.465986 TCCCATCCCATCCCATCCC 60.466 63.158 0.00 0.00 0.00 3.85
795 808 2.687003 AGCCTCCCTATAGTCAGTCC 57.313 55.000 0.00 0.00 0.00 3.85
796 809 1.202952 AGCCTCCCTATAGTCAGTCCG 60.203 57.143 0.00 0.00 0.00 4.79
797 810 1.249407 CCTCCCTATAGTCAGTCCGC 58.751 60.000 0.00 0.00 0.00 5.54
798 811 1.249407 CTCCCTATAGTCAGTCCGCC 58.751 60.000 0.00 0.00 0.00 6.13
799 812 0.851469 TCCCTATAGTCAGTCCGCCT 59.149 55.000 0.00 0.00 0.00 5.52
800 813 2.040012 CTCCCTATAGTCAGTCCGCCTA 59.960 54.545 0.00 0.00 0.00 3.93
801 814 2.648304 TCCCTATAGTCAGTCCGCCTAT 59.352 50.000 0.00 0.00 0.00 2.57
802 815 3.848377 TCCCTATAGTCAGTCCGCCTATA 59.152 47.826 0.00 0.00 0.00 1.31
803 816 4.290459 TCCCTATAGTCAGTCCGCCTATAA 59.710 45.833 0.00 0.00 0.00 0.98
804 817 4.398673 CCCTATAGTCAGTCCGCCTATAAC 59.601 50.000 0.00 0.00 0.00 1.89
805 818 5.008331 CCTATAGTCAGTCCGCCTATAACA 58.992 45.833 0.00 0.00 0.00 2.41
806 819 4.850347 ATAGTCAGTCCGCCTATAACAC 57.150 45.455 0.00 0.00 0.00 3.32
807 820 1.755380 AGTCAGTCCGCCTATAACACC 59.245 52.381 0.00 0.00 0.00 4.16
808 821 1.479323 GTCAGTCCGCCTATAACACCA 59.521 52.381 0.00 0.00 0.00 4.17
809 822 1.479323 TCAGTCCGCCTATAACACCAC 59.521 52.381 0.00 0.00 0.00 4.16
909 922 0.536460 GCCGTAGAGAGAGGGAGAGG 60.536 65.000 0.00 0.00 0.00 3.69
1116 1129 1.381463 GGAGCTCCCCGAGTACCTT 60.381 63.158 23.19 0.00 31.39 3.50
1262 1287 0.177836 ATCCATCGACATGTTCCGCA 59.822 50.000 0.00 0.00 0.00 5.69
1264 1289 1.018752 CCATCGACATGTTCCGCACA 61.019 55.000 0.00 0.00 40.71 4.57
1416 1773 1.006102 CGGGGATCATGAGGTACGC 60.006 63.158 0.09 1.48 0.00 4.42
1417 1774 1.744320 CGGGGATCATGAGGTACGCA 61.744 60.000 0.09 0.00 45.75 5.24
1418 1775 0.249911 GGGGATCATGAGGTACGCAC 60.250 60.000 0.09 0.00 43.58 5.34
1419 1776 0.249911 GGGATCATGAGGTACGCACC 60.250 60.000 0.09 0.00 43.58 5.01
1467 1827 4.408921 TGACTTTCCTTTTCTCTCTGTCCA 59.591 41.667 0.00 0.00 0.00 4.02
1491 1851 7.275560 CCACCGGAATAAGAAAATGATTGTTTC 59.724 37.037 9.46 0.00 35.60 2.78
1496 1856 8.860128 GGAATAAGAAAATGATTGTTTCCGTTC 58.140 33.333 0.00 0.00 35.92 3.95
1510 1870 4.886247 TTCCGTTCGTTCATCAAACTTT 57.114 36.364 0.00 0.00 35.59 2.66
1518 1878 8.785101 CGTTCGTTCATCAAACTTTAATAATGG 58.215 33.333 0.00 0.00 35.59 3.16
1521 1881 9.834628 TCGTTCATCAAACTTTAATAATGGTTC 57.165 29.630 0.00 0.00 35.59 3.62
1547 1907 0.901124 CTCTGACTCCCACTCCCTTG 59.099 60.000 0.00 0.00 0.00 3.61
1548 1908 1.194781 TCTGACTCCCACTCCCTTGC 61.195 60.000 0.00 0.00 0.00 4.01
1549 1909 1.461268 TGACTCCCACTCCCTTGCA 60.461 57.895 0.00 0.00 0.00 4.08
1598 1958 4.095782 TGAAACTTGAAACGGTCTTCCAAG 59.904 41.667 0.00 0.00 0.00 3.61
1603 1963 2.098443 TGAAACGGTCTTCCAAGCAAAC 59.902 45.455 0.00 0.00 0.00 2.93
1610 1970 1.196808 TCTTCCAAGCAAACGCGAATC 59.803 47.619 15.93 0.00 0.00 2.52
1639 1999 2.931386 GCAGCTCACACGTCACAC 59.069 61.111 0.00 0.00 0.00 3.82
1677 2037 3.283684 TTTCGCGGGCAGTTGGTG 61.284 61.111 6.13 0.00 0.00 4.17
1813 2180 3.485381 CGACTCTTTCTGCATTGCTGATG 60.485 47.826 17.47 13.51 36.48 3.07
1838 2238 0.322008 CTCCAAGTCTCCAACTGGCC 60.322 60.000 0.00 0.00 38.58 5.36
1857 2257 2.030091 GCCGCGAGTACACTTTAATTCC 59.970 50.000 8.23 0.00 0.00 3.01
1885 2285 2.005451 GATTATGCTAGATGCTGCCCG 58.995 52.381 0.00 0.00 43.37 6.13
1897 2297 1.742880 CTGCCCGTGTGAGATGTGG 60.743 63.158 0.00 0.00 0.00 4.17
1903 2303 1.073964 CGTGTGAGATGTGGCAAGAG 58.926 55.000 0.00 0.00 0.00 2.85
1905 2305 0.671472 TGTGAGATGTGGCAAGAGCG 60.671 55.000 0.00 0.00 43.41 5.03
1909 2309 3.044059 GATGTGGCAAGAGCGCACC 62.044 63.158 11.47 3.04 43.41 5.01
1924 2324 1.026718 GCACCGTCCTAAGCAGCAAT 61.027 55.000 0.00 0.00 0.00 3.56
1925 2325 1.009829 CACCGTCCTAAGCAGCAATC 58.990 55.000 0.00 0.00 0.00 2.67
1958 2358 0.531090 CCACACCAAACGAACGAGGA 60.531 55.000 0.14 0.00 0.00 3.71
1959 2359 0.580104 CACACCAAACGAACGAGGAC 59.420 55.000 0.14 0.00 0.00 3.85
1960 2360 0.176219 ACACCAAACGAACGAGGACA 59.824 50.000 0.14 0.00 0.00 4.02
1961 2361 1.202604 ACACCAAACGAACGAGGACAT 60.203 47.619 0.14 0.00 0.00 3.06
1962 2362 1.194547 CACCAAACGAACGAGGACATG 59.805 52.381 0.14 0.00 0.00 3.21
2030 2457 2.340809 GCAAATGCAGTGCTGGCA 59.659 55.556 17.60 0.00 46.66 4.92
2050 2477 2.136196 TTGGTCGGTTGGCGCAAATC 62.136 55.000 10.83 2.74 0.00 2.17
2066 2493 3.244181 GCAAATCACAGATTTGTTGGGGT 60.244 43.478 24.87 0.00 40.19 4.95
2080 2507 0.764890 TGGGGTGTTCCAAGTCTGAG 59.235 55.000 0.00 0.00 37.22 3.35
2084 2511 1.605712 GGTGTTCCAAGTCTGAGACGG 60.606 57.143 6.99 3.52 37.67 4.79
2090 2517 1.067495 CCAAGTCTGAGACGGTCCTTC 60.067 57.143 6.99 0.00 37.67 3.46
2096 2523 2.307980 TCTGAGACGGTCCTTCCTCTTA 59.692 50.000 4.14 0.00 0.00 2.10
2107 2534 6.127423 CGGTCCTTCCTCTTAGTCTTTGATAA 60.127 42.308 0.00 0.00 0.00 1.75
2134 2561 5.185635 TGATTGATTGATGTTCCTTTCCCAC 59.814 40.000 0.00 0.00 0.00 4.61
2182 2614 5.227908 TGCACTACTGCTACTACTTTGTTC 58.772 41.667 0.00 0.00 44.57 3.18
2194 2631 3.751479 ACTTTGTTCATGAAAAGGCCC 57.249 42.857 19.29 5.04 37.65 5.80
2196 2633 3.321968 ACTTTGTTCATGAAAAGGCCCTC 59.678 43.478 19.29 3.80 37.65 4.30
2287 2730 4.250464 TCAATCGGTAAGAAACGCATCTT 58.750 39.130 8.20 8.20 42.21 2.40
2290 2733 5.622770 ATCGGTAAGAAACGCATCTTTTT 57.377 34.783 8.40 0.00 40.13 1.94
2312 2755 5.483685 TTTTAGCACCAGTACAGACATCT 57.516 39.130 0.00 0.00 0.00 2.90
2315 2758 4.727507 AGCACCAGTACAGACATCTAAG 57.272 45.455 0.00 0.00 0.00 2.18
2318 2761 4.399618 GCACCAGTACAGACATCTAAGAGA 59.600 45.833 0.00 0.00 0.00 3.10
2320 2763 6.263392 GCACCAGTACAGACATCTAAGAGATA 59.737 42.308 0.00 0.00 32.12 1.98
2352 2846 8.053355 ACCTTATCTTGTCTCCGGATAATTTTT 58.947 33.333 3.57 0.00 33.37 1.94
2359 2853 4.580580 GTCTCCGGATAATTTTTCCAGCAT 59.419 41.667 3.57 0.00 32.45 3.79
2377 2871 5.747197 CCAGCATTGCATATTTTTCTCTCAC 59.253 40.000 11.91 0.00 0.00 3.51
2382 2876 7.201410 GCATTGCATATTTTTCTCTCACAACTG 60.201 37.037 3.15 0.00 0.00 3.16
2463 2957 6.183360 ACGAGTTCTATCAAGGTGACTATGAC 60.183 42.308 0.00 0.00 42.68 3.06
2464 2958 6.038825 CGAGTTCTATCAAGGTGACTATGACT 59.961 42.308 0.00 0.00 42.68 3.41
2467 2961 6.885952 TCTATCAAGGTGACTATGACTAGC 57.114 41.667 0.00 0.00 42.68 3.42
2486 2980 7.926555 TGACTAGCCTAATTATTCAGTTAGCAC 59.073 37.037 0.00 0.00 0.00 4.40
2515 3009 7.700656 GTGTAGTGCCACCAATGATTTAAATAC 59.299 37.037 0.00 0.00 0.00 1.89
2548 3044 8.566260 ACCGAGTGAGTACTATGTAATAATGTC 58.434 37.037 0.00 0.00 37.25 3.06
2623 3119 0.534427 AGCTGCCCACATGATCATCG 60.534 55.000 4.86 4.49 0.00 3.84
2671 3167 4.572389 GTGTAGAGGATGCACTACAATTGG 59.428 45.833 22.30 0.00 46.40 3.16
2735 3276 4.770010 GCTCCCTGTAGATAGCTCTGTAAT 59.230 45.833 0.00 0.00 32.66 1.89
2804 3350 4.143946 CGTAATACCGCGAGACGTATTTTC 60.144 45.833 18.98 13.26 41.42 2.29
2823 3369 2.207924 ACCGGGCGAGTCTCTTTGT 61.208 57.895 6.32 0.00 0.00 2.83
2900 3451 9.765795 ATGCCATAGTAAATCTTACAGAACTAC 57.234 33.333 0.00 0.00 0.00 2.73
2901 3452 8.978472 TGCCATAGTAAATCTTACAGAACTACT 58.022 33.333 0.00 4.46 33.21 2.57
2902 3453 9.465985 GCCATAGTAAATCTTACAGAACTACTC 57.534 37.037 0.00 0.00 31.88 2.59
2903 3454 9.968870 CCATAGTAAATCTTACAGAACTACTCC 57.031 37.037 0.00 0.00 31.88 3.85
2904 3455 9.968870 CATAGTAAATCTTACAGAACTACTCCC 57.031 37.037 0.00 0.00 31.88 4.30
2905 3456 9.939424 ATAGTAAATCTTACAGAACTACTCCCT 57.061 33.333 0.00 0.00 31.88 4.20
2906 3457 8.296211 AGTAAATCTTACAGAACTACTCCCTC 57.704 38.462 0.00 0.00 0.00 4.30
2907 3458 6.547930 AAATCTTACAGAACTACTCCCTCC 57.452 41.667 0.00 0.00 0.00 4.30
2908 3459 4.669866 TCTTACAGAACTACTCCCTCCA 57.330 45.455 0.00 0.00 0.00 3.86
2909 3460 5.208294 TCTTACAGAACTACTCCCTCCAT 57.792 43.478 0.00 0.00 0.00 3.41
2910 3461 5.202004 TCTTACAGAACTACTCCCTCCATC 58.798 45.833 0.00 0.00 0.00 3.51
2911 3462 2.753247 ACAGAACTACTCCCTCCATCC 58.247 52.381 0.00 0.00 0.00 3.51
2912 3463 1.683917 CAGAACTACTCCCTCCATCCG 59.316 57.143 0.00 0.00 0.00 4.18
2913 3464 1.569548 AGAACTACTCCCTCCATCCGA 59.430 52.381 0.00 0.00 0.00 4.55
2914 3465 2.024273 AGAACTACTCCCTCCATCCGAA 60.024 50.000 0.00 0.00 0.00 4.30
2915 3466 2.544844 ACTACTCCCTCCATCCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
2916 3467 2.829023 ACTACTCCCTCCATCCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
2917 3468 3.385115 ACTACTCCCTCCATCCGAAAAT 58.615 45.455 0.00 0.00 0.00 1.82
2918 3469 3.780850 ACTACTCCCTCCATCCGAAAATT 59.219 43.478 0.00 0.00 0.00 1.82
2919 3470 3.283259 ACTCCCTCCATCCGAAAATTC 57.717 47.619 0.00 0.00 0.00 2.17
2920 3471 2.846827 ACTCCCTCCATCCGAAAATTCT 59.153 45.455 0.00 0.00 0.00 2.40
2921 3472 3.267031 ACTCCCTCCATCCGAAAATTCTT 59.733 43.478 0.00 0.00 0.00 2.52
2922 3473 3.620488 TCCCTCCATCCGAAAATTCTTG 58.380 45.455 0.00 0.00 0.00 3.02
2923 3474 3.010138 TCCCTCCATCCGAAAATTCTTGT 59.990 43.478 0.00 0.00 0.00 3.16
2924 3475 3.378427 CCCTCCATCCGAAAATTCTTGTC 59.622 47.826 0.00 0.00 0.00 3.18
2925 3476 4.009675 CCTCCATCCGAAAATTCTTGTCA 58.990 43.478 0.00 0.00 0.00 3.58
2926 3477 4.641989 CCTCCATCCGAAAATTCTTGTCAT 59.358 41.667 0.00 0.00 0.00 3.06
2927 3478 5.220931 CCTCCATCCGAAAATTCTTGTCATC 60.221 44.000 0.00 0.00 0.00 2.92
2928 3479 5.252547 TCCATCCGAAAATTCTTGTCATCA 58.747 37.500 0.00 0.00 0.00 3.07
2929 3480 5.709631 TCCATCCGAAAATTCTTGTCATCAA 59.290 36.000 0.00 0.00 0.00 2.57
2930 3481 6.208402 TCCATCCGAAAATTCTTGTCATCAAA 59.792 34.615 0.00 0.00 32.87 2.69
2931 3482 6.867816 CCATCCGAAAATTCTTGTCATCAAAA 59.132 34.615 0.00 0.00 32.87 2.44
2932 3483 7.546667 CCATCCGAAAATTCTTGTCATCAAAAT 59.453 33.333 0.00 0.00 32.87 1.82
2933 3484 7.872163 TCCGAAAATTCTTGTCATCAAAATG 57.128 32.000 0.00 0.00 32.87 2.32
2934 3485 6.867816 TCCGAAAATTCTTGTCATCAAAATGG 59.132 34.615 0.00 0.00 33.42 3.16
2935 3486 6.867816 CCGAAAATTCTTGTCATCAAAATGGA 59.132 34.615 0.00 0.00 33.42 3.41
2936 3487 7.546667 CCGAAAATTCTTGTCATCAAAATGGAT 59.453 33.333 0.00 0.00 33.42 3.41
2937 3488 9.571810 CGAAAATTCTTGTCATCAAAATGGATA 57.428 29.630 0.00 0.00 33.42 2.59
2980 3549 6.040166 AGCATGTCTTTGAAGTTGTCTGAAAT 59.960 34.615 0.00 0.00 0.00 2.17
3014 3583 3.680937 TCGTAAAAGTTATCCGGTTGCAG 59.319 43.478 0.00 0.00 0.00 4.41
3019 3588 0.168128 GTTATCCGGTTGCAGCACAC 59.832 55.000 0.00 0.00 0.00 3.82
3029 3598 0.933973 TGCAGCACACGAAAAATGCG 60.934 50.000 0.00 0.00 44.25 4.73
3031 3600 0.661187 CAGCACACGAAAAATGCGCT 60.661 50.000 9.73 0.00 44.25 5.92
3126 3695 2.907458 AAGAAGGGACCCAATGGAAG 57.093 50.000 14.60 0.00 34.81 3.46
3128 3697 1.636003 AGAAGGGACCCAATGGAAGTC 59.364 52.381 14.60 0.00 34.81 3.01
3240 3809 6.601613 ACTTTGAAGTAAAATGACCTCACACA 59.398 34.615 0.00 0.00 37.52 3.72
3241 3810 6.371809 TTGAAGTAAAATGACCTCACACAC 57.628 37.500 0.00 0.00 0.00 3.82
3257 3826 7.724061 ACCTCACACACTAAAAATTCATTAGGT 59.276 33.333 12.86 0.00 35.20 3.08
3287 3856 3.059884 CGTAATGTCCTTCCATCCGATG 58.940 50.000 0.93 0.93 0.00 3.84
3334 3908 6.016024 ACAACAATGCTGTTATGATCACTGTT 60.016 34.615 0.00 0.00 44.15 3.16
3406 3980 8.773645 CGCAAGATCATGTCCTACATATTTTAA 58.226 33.333 0.00 0.00 36.45 1.52
3489 4063 3.449737 TCCACTTATCTCTAACCAACCCG 59.550 47.826 0.00 0.00 0.00 5.28
3515 4089 9.820725 GGAATCATGAAATGTGGAATTAATCAA 57.179 29.630 0.00 0.00 46.80 2.57
3533 4107 5.913137 ATCAAAACCAAAGAAGTGTGTGA 57.087 34.783 0.00 0.00 0.00 3.58
3535 4109 4.764823 TCAAAACCAAAGAAGTGTGTGACT 59.235 37.500 0.00 0.00 35.94 3.41
3553 4127 5.705441 TGTGACTCCATTTATCTTGACCAAC 59.295 40.000 0.00 0.00 0.00 3.77
3610 4184 5.755849 TGAGGGATTTACCAGAGGAAATTC 58.244 41.667 0.00 0.00 41.20 2.17
3662 4236 8.131455 TCTGAAATAGCACTGACGAATAATTC 57.869 34.615 0.00 0.00 0.00 2.17
3684 4267 5.984725 TCGTGTGGATGATACAAATAAGGT 58.015 37.500 0.00 0.00 0.00 3.50
3690 4273 8.274322 TGTGGATGATACAAATAAGGTGAGAAT 58.726 33.333 0.00 0.00 0.00 2.40
3708 4291 9.764363 GGTGAGAATATGTACAATGACATTAGA 57.236 33.333 0.00 0.00 40.54 2.10
3867 4450 1.293498 CCTGACCAACCGACCAGAG 59.707 63.158 0.00 0.00 0.00 3.35
3956 4539 4.441415 GTGTAGTCGTCTTGTTCAGAACAG 59.559 45.833 15.61 10.42 43.27 3.16
3982 4565 1.360192 GCCTCTGTGTGTTTGCACC 59.640 57.895 0.00 0.00 44.65 5.01
3998 4581 1.945819 GCACCAAATCTCGCTTCCTCA 60.946 52.381 0.00 0.00 0.00 3.86
3999 4582 2.426522 CACCAAATCTCGCTTCCTCAA 58.573 47.619 0.00 0.00 0.00 3.02
4011 4594 3.063180 CGCTTCCTCAATCACATTCACTC 59.937 47.826 0.00 0.00 0.00 3.51
4033 4616 4.020751 TCTGCATGCAAGAGAAGAAGTAGT 60.021 41.667 22.88 0.00 0.00 2.73
4036 4619 3.577649 TGCAAGAGAAGAAGTAGTCGG 57.422 47.619 0.00 0.00 0.00 4.79
4042 4625 6.217294 CAAGAGAAGAAGTAGTCGGTTCTTT 58.783 40.000 0.00 0.00 41.94 2.52
4043 4626 5.774630 AGAGAAGAAGTAGTCGGTTCTTTG 58.225 41.667 0.00 0.00 41.94 2.77
4044 4627 4.884247 AGAAGAAGTAGTCGGTTCTTTGG 58.116 43.478 0.00 0.00 41.94 3.28
4045 4628 4.344390 AGAAGAAGTAGTCGGTTCTTTGGT 59.656 41.667 0.00 0.00 41.94 3.67
4046 4629 4.254402 AGAAGTAGTCGGTTCTTTGGTC 57.746 45.455 0.00 0.00 28.11 4.02
4047 4630 3.640029 AGAAGTAGTCGGTTCTTTGGTCA 59.360 43.478 0.00 0.00 28.11 4.02
4048 4631 3.382048 AGTAGTCGGTTCTTTGGTCAC 57.618 47.619 0.00 0.00 0.00 3.67
4049 4632 2.036862 AGTAGTCGGTTCTTTGGTCACC 59.963 50.000 0.00 0.00 0.00 4.02
4050 4633 0.108019 AGTCGGTTCTTTGGTCACCC 59.892 55.000 0.00 0.00 0.00 4.61
4051 4634 0.108019 GTCGGTTCTTTGGTCACCCT 59.892 55.000 0.00 0.00 0.00 4.34
4052 4635 0.841289 TCGGTTCTTTGGTCACCCTT 59.159 50.000 0.00 0.00 0.00 3.95
4053 4636 1.213430 TCGGTTCTTTGGTCACCCTTT 59.787 47.619 0.00 0.00 0.00 3.11
4054 4637 2.028876 CGGTTCTTTGGTCACCCTTTT 58.971 47.619 0.00 0.00 0.00 2.27
4055 4638 2.034179 CGGTTCTTTGGTCACCCTTTTC 59.966 50.000 0.00 0.00 0.00 2.29
4056 4639 2.034179 GGTTCTTTGGTCACCCTTTTCG 59.966 50.000 0.00 0.00 0.00 3.46
4057 4640 2.946990 GTTCTTTGGTCACCCTTTTCGA 59.053 45.455 0.00 0.00 0.00 3.71
4058 4641 3.284793 TCTTTGGTCACCCTTTTCGAA 57.715 42.857 0.00 0.00 0.00 3.71
4059 4642 3.622630 TCTTTGGTCACCCTTTTCGAAA 58.377 40.909 6.47 6.47 0.00 3.46
4060 4643 4.017808 TCTTTGGTCACCCTTTTCGAAAA 58.982 39.130 21.35 21.35 0.00 2.29
4061 4644 4.463186 TCTTTGGTCACCCTTTTCGAAAAA 59.537 37.500 22.67 6.34 0.00 1.94
4141 4724 2.668945 GCTTTCAGCTACTTCTTCGGTC 59.331 50.000 0.00 0.00 38.45 4.79
4195 4778 4.038402 AGACCAAGTGGCAAAATCTTTCTG 59.962 41.667 0.00 0.00 39.32 3.02
4221 4804 5.232202 TCATCTTATCGTTGATTTCTGCGTC 59.768 40.000 0.00 0.00 0.00 5.19
4240 4823 2.582498 GGCGACGAATCTGTCCGG 60.582 66.667 0.00 0.00 35.40 5.14
4241 4824 2.582498 GCGACGAATCTGTCCGGG 60.582 66.667 0.00 0.00 35.40 5.73
4242 4825 2.582498 CGACGAATCTGTCCGGGC 60.582 66.667 0.00 0.00 35.40 6.13
4243 4826 2.202892 GACGAATCTGTCCGGGCC 60.203 66.667 2.12 0.00 32.61 5.80
4245 4828 2.311688 GACGAATCTGTCCGGGCCAT 62.312 60.000 2.12 0.00 32.61 4.40
4246 4829 1.153168 CGAATCTGTCCGGGCCATT 60.153 57.895 2.12 0.87 0.00 3.16
4248 4831 1.474320 CGAATCTGTCCGGGCCATTTA 60.474 52.381 2.12 0.00 0.00 1.40
4249 4832 1.947456 GAATCTGTCCGGGCCATTTAC 59.053 52.381 2.12 0.00 0.00 2.01
4252 4835 0.035439 CTGTCCGGGCCATTTACACT 60.035 55.000 2.12 0.00 0.00 3.55
4253 4836 1.208535 CTGTCCGGGCCATTTACACTA 59.791 52.381 2.12 0.00 0.00 2.74
4255 4838 0.542805 TCCGGGCCATTTACACTACC 59.457 55.000 4.39 0.00 0.00 3.18
4257 4840 3.089788 GGGCCATTTACACTACCCG 57.910 57.895 4.39 0.00 0.00 5.28
4258 4841 1.099295 GGGCCATTTACACTACCCGC 61.099 60.000 4.39 0.00 0.00 6.13
4259 4842 0.393267 GGCCATTTACACTACCCGCA 60.393 55.000 0.00 0.00 0.00 5.69
4293 4876 5.584649 TCGAAATATTCTCTCGCCAAAATGT 59.415 36.000 3.63 0.00 32.66 2.71
4300 4883 5.592104 TCTCTCGCCAAAATGTGATAGTA 57.408 39.130 0.00 0.00 0.00 1.82
4301 4884 5.592054 TCTCTCGCCAAAATGTGATAGTAG 58.408 41.667 0.00 0.00 0.00 2.57
4302 4885 5.127194 TCTCTCGCCAAAATGTGATAGTAGT 59.873 40.000 0.00 0.00 0.00 2.73
4303 4886 6.320418 TCTCTCGCCAAAATGTGATAGTAGTA 59.680 38.462 0.00 0.00 0.00 1.82
4304 4887 6.504398 TCTCGCCAAAATGTGATAGTAGTAG 58.496 40.000 0.00 0.00 0.00 2.57
4305 4888 6.096423 TCTCGCCAAAATGTGATAGTAGTAGT 59.904 38.462 0.00 0.00 0.00 2.73
4306 4889 6.040247 TCGCCAAAATGTGATAGTAGTAGTG 58.960 40.000 0.00 0.00 0.00 2.74
4307 4890 5.810587 CGCCAAAATGTGATAGTAGTAGTGT 59.189 40.000 0.00 0.00 0.00 3.55
4308 4891 6.976349 CGCCAAAATGTGATAGTAGTAGTGTA 59.024 38.462 0.00 0.00 0.00 2.90
4309 4892 7.490079 CGCCAAAATGTGATAGTAGTAGTGTAA 59.510 37.037 0.00 0.00 0.00 2.41
4310 4893 9.326413 GCCAAAATGTGATAGTAGTAGTGTAAT 57.674 33.333 0.00 0.00 0.00 1.89
4337 4920 8.939201 TTAGATGCTAGACTGAGATTTTTCTG 57.061 34.615 0.00 0.00 0.00 3.02
4338 4921 6.945218 AGATGCTAGACTGAGATTTTTCTGT 58.055 36.000 0.00 0.00 32.75 3.41
4339 4922 7.393216 AGATGCTAGACTGAGATTTTTCTGTT 58.607 34.615 0.00 0.00 30.60 3.16
4342 4952 6.992123 TGCTAGACTGAGATTTTTCTGTTCAA 59.008 34.615 0.00 0.00 30.60 2.69
4351 4961 9.630098 TGAGATTTTTCTGTTCAAATGATTAGC 57.370 29.630 0.00 0.00 0.00 3.09
4801 5426 2.141011 CTGGATCAACTGGGGCCACA 62.141 60.000 7.89 7.89 0.00 4.17
5583 6219 0.320771 ACTCCATGTCGCTGAACACC 60.321 55.000 0.00 0.00 30.55 4.16
5616 6252 4.841617 ATCCTCTCCGGCGGCAGA 62.842 66.667 23.83 22.19 0.00 4.26
5649 6285 0.608130 CCACGTCCAGGATCTTGTCA 59.392 55.000 3.93 0.00 0.00 3.58
5667 6303 2.033424 GTCAAACACTGCCTGGAAGTTC 59.967 50.000 4.00 0.00 0.00 3.01
5840 6476 2.359850 GCAGACGTCCATGGGCAA 60.360 61.111 18.31 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 316 0.890542 ACACCATCACACGCATGCTT 60.891 50.000 17.13 2.67 0.00 3.91
525 536 3.898482 AGGGGAAAAGAAACGGATATGG 58.102 45.455 0.00 0.00 0.00 2.74
526 537 5.914898 AAAGGGGAAAAGAAACGGATATG 57.085 39.130 0.00 0.00 0.00 1.78
627 640 2.659428 CCACATGGATTTCTTCCTCCC 58.341 52.381 0.00 0.00 45.68 4.30
628 641 2.024941 ACCCACATGGATTTCTTCCTCC 60.025 50.000 0.00 0.00 45.68 4.30
629 642 3.019564 CACCCACATGGATTTCTTCCTC 58.980 50.000 0.00 0.00 45.68 3.71
630 643 2.291800 CCACCCACATGGATTTCTTCCT 60.292 50.000 0.00 0.00 45.68 3.36
634 647 0.706433 AGCCACCCACATGGATTTCT 59.294 50.000 0.00 0.00 43.02 2.52
751 764 0.852683 GGGATGGGATGGGATGGGAT 60.853 60.000 0.00 0.00 0.00 3.85
752 765 1.465986 GGGATGGGATGGGATGGGA 60.466 63.158 0.00 0.00 0.00 4.37
753 766 2.551413 GGGGATGGGATGGGATGGG 61.551 68.421 0.00 0.00 0.00 4.00
754 767 2.551413 GGGGGATGGGATGGGATGG 61.551 68.421 0.00 0.00 0.00 3.51
755 768 0.178834 TAGGGGGATGGGATGGGATG 60.179 60.000 0.00 0.00 0.00 3.51
756 769 0.815815 ATAGGGGGATGGGATGGGAT 59.184 55.000 0.00 0.00 0.00 3.85
757 770 1.369626 CTATAGGGGGATGGGATGGGA 59.630 57.143 0.00 0.00 0.00 4.37
758 771 1.898863 CTATAGGGGGATGGGATGGG 58.101 60.000 0.00 0.00 0.00 4.00
759 772 1.216990 GCTATAGGGGGATGGGATGG 58.783 60.000 1.04 0.00 0.00 3.51
760 773 1.216990 GGCTATAGGGGGATGGGATG 58.783 60.000 1.04 0.00 0.00 3.51
761 774 1.010170 GAGGCTATAGGGGGATGGGAT 59.990 57.143 1.04 0.00 0.00 3.85
762 775 0.417841 GAGGCTATAGGGGGATGGGA 59.582 60.000 1.04 0.00 0.00 4.37
763 776 0.621862 GGAGGCTATAGGGGGATGGG 60.622 65.000 1.04 0.00 0.00 4.00
764 777 0.621862 GGGAGGCTATAGGGGGATGG 60.622 65.000 1.04 0.00 0.00 3.51
765 778 0.419459 AGGGAGGCTATAGGGGGATG 59.581 60.000 1.04 0.00 0.00 3.51
791 804 0.828677 GGTGGTGTTATAGGCGGACT 59.171 55.000 0.00 0.00 0.00 3.85
793 806 0.538118 GTGGTGGTGTTATAGGCGGA 59.462 55.000 0.00 0.00 0.00 5.54
795 808 0.250793 TGGTGGTGGTGTTATAGGCG 59.749 55.000 0.00 0.00 0.00 5.52
796 809 1.680860 GGTGGTGGTGGTGTTATAGGC 60.681 57.143 0.00 0.00 0.00 3.93
797 810 1.631388 TGGTGGTGGTGGTGTTATAGG 59.369 52.381 0.00 0.00 0.00 2.57
798 811 2.617021 GGTGGTGGTGGTGGTGTTATAG 60.617 54.545 0.00 0.00 0.00 1.31
799 812 1.351683 GGTGGTGGTGGTGGTGTTATA 59.648 52.381 0.00 0.00 0.00 0.98
800 813 0.111639 GGTGGTGGTGGTGGTGTTAT 59.888 55.000 0.00 0.00 0.00 1.89
801 814 0.989212 AGGTGGTGGTGGTGGTGTTA 60.989 55.000 0.00 0.00 0.00 2.41
802 815 2.277404 GGTGGTGGTGGTGGTGTT 59.723 61.111 0.00 0.00 0.00 3.32
803 816 2.694616 AGGTGGTGGTGGTGGTGT 60.695 61.111 0.00 0.00 0.00 4.16
804 817 2.113139 GAGGTGGTGGTGGTGGTG 59.887 66.667 0.00 0.00 0.00 4.17
805 818 3.175710 GGAGGTGGTGGTGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
806 819 3.966543 GGGAGGTGGTGGTGGTGG 61.967 72.222 0.00 0.00 0.00 4.61
807 820 4.329545 CGGGAGGTGGTGGTGGTG 62.330 72.222 0.00 0.00 0.00 4.17
887 900 1.452145 CTCCCTCTCTCTACGGCTGC 61.452 65.000 0.00 0.00 0.00 5.25
888 901 0.181587 TCTCCCTCTCTCTACGGCTG 59.818 60.000 0.00 0.00 0.00 4.85
894 907 2.698967 CCTCTCCCTCTCCCTCTCTCTA 60.699 59.091 0.00 0.00 0.00 2.43
982 995 4.491409 GGCTCCCTTCTTCCGGCC 62.491 72.222 0.00 0.00 0.00 6.13
985 998 1.153086 CCATGGCTCCCTTCTTCCG 60.153 63.158 0.00 0.00 0.00 4.30
1116 1129 2.159338 GCGGATGTACTCGTTGTCCTTA 60.159 50.000 0.00 0.00 0.00 2.69
1245 1270 1.018752 TGTGCGGAACATGTCGATGG 61.019 55.000 10.81 0.00 32.36 3.51
1262 1287 0.532862 GGCCGATCGATTGGTCATGT 60.533 55.000 28.12 0.00 35.94 3.21
1264 1289 0.180171 TTGGCCGATCGATTGGTCAT 59.820 50.000 34.09 0.00 44.98 3.06
1265 1290 0.180171 ATTGGCCGATCGATTGGTCA 59.820 50.000 31.13 31.13 44.01 4.02
1266 1291 0.868406 GATTGGCCGATCGATTGGTC 59.132 55.000 26.72 26.72 36.45 4.02
1267 1292 0.535102 GGATTGGCCGATCGATTGGT 60.535 55.000 28.67 12.31 33.62 3.67
1268 1293 2.247790 GGATTGGCCGATCGATTGG 58.752 57.895 25.26 25.26 0.00 3.16
1287 1638 1.723870 GGCGCCATGTCAGATCAAC 59.276 57.895 24.80 0.00 0.00 3.18
1293 1644 3.792047 CACACGGCGCCATGTCAG 61.792 66.667 27.74 12.37 0.00 3.51
1416 1773 1.202639 TGTTCTGCAGTGTAGGTGGTG 60.203 52.381 14.67 0.00 0.00 4.17
1417 1774 1.128200 TGTTCTGCAGTGTAGGTGGT 58.872 50.000 14.67 0.00 0.00 4.16
1418 1775 1.202639 TGTGTTCTGCAGTGTAGGTGG 60.203 52.381 14.67 0.00 0.00 4.61
1419 1776 1.867233 GTGTGTTCTGCAGTGTAGGTG 59.133 52.381 14.67 0.00 0.00 4.00
1467 1827 7.320399 GGAAACAATCATTTTCTTATTCCGGT 58.680 34.615 0.00 0.00 34.06 5.28
1491 1851 8.785101 CATTATTAAAGTTTGATGAACGAACGG 58.215 33.333 3.25 0.00 44.93 4.44
1496 1856 8.785101 CGAACCATTATTAAAGTTTGATGAACG 58.215 33.333 3.25 0.00 43.20 3.95
1510 1870 4.279922 TCAGAGGCGATCGAACCATTATTA 59.720 41.667 21.57 0.00 0.00 0.98
1518 1878 0.248702 GGAGTCAGAGGCGATCGAAC 60.249 60.000 21.57 10.88 0.00 3.95
1521 1881 2.121538 TGGGAGTCAGAGGCGATCG 61.122 63.158 11.69 11.69 0.00 3.69
1525 1885 2.716017 GGAGTGGGAGTCAGAGGCG 61.716 68.421 0.00 0.00 0.00 5.52
1547 1907 3.925238 CGCCCGCTAATCACGTGC 61.925 66.667 11.67 0.00 0.00 5.34
1548 1908 3.925238 GCGCCCGCTAATCACGTG 61.925 66.667 9.94 9.94 38.26 4.49
1571 1931 5.392703 GGAAGACCGTTTCAAGTTTCAAAGT 60.393 40.000 0.00 0.00 0.00 2.66
1598 1958 1.318251 GTGAGTTGATTCGCGTTTGC 58.682 50.000 5.77 0.00 37.91 3.68
1603 1963 1.787847 GGTGGTGAGTTGATTCGCG 59.212 57.895 0.00 0.00 0.00 5.87
1610 1970 2.281070 AGCTGCGGTGGTGAGTTG 60.281 61.111 0.00 0.00 0.00 3.16
1677 2037 3.112709 GCGCTCTCCGAACACACC 61.113 66.667 0.00 0.00 40.02 4.16
1765 2125 2.568029 CGAACGTGTGATTGCGCG 60.568 61.111 0.00 0.00 46.38 6.86
1813 2180 2.027653 AGTTGGAGACTTGGAGCTTAGC 60.028 50.000 0.00 0.00 33.92 3.09
1838 2238 4.914312 TTGGAATTAAAGTGTACTCGCG 57.086 40.909 0.00 0.00 0.00 5.87
1885 2285 0.801251 GCTCTTGCCACATCTCACAC 59.199 55.000 0.00 0.00 0.00 3.82
1897 2297 3.642778 TAGGACGGTGCGCTCTTGC 62.643 63.158 9.73 1.84 0.00 4.01
1903 2303 3.188786 CTGCTTAGGACGGTGCGC 61.189 66.667 0.00 0.00 0.00 6.09
1905 2305 1.026718 ATTGCTGCTTAGGACGGTGC 61.027 55.000 0.00 0.00 0.00 5.01
1909 2309 1.083806 TGCGATTGCTGCTTAGGACG 61.084 55.000 6.47 0.03 43.34 4.79
1924 2324 4.067913 TGGCTCTCACGCATGCGA 62.068 61.111 43.72 23.51 42.83 5.10
1925 2325 3.857854 GTGGCTCTCACGCATGCG 61.858 66.667 36.79 36.79 46.03 4.73
1958 2358 0.823356 GGATAATGCACGGGCCATGT 60.823 55.000 7.46 0.00 40.13 3.21
1959 2359 1.855213 CGGATAATGCACGGGCCATG 61.855 60.000 7.46 0.00 40.13 3.66
1960 2360 1.600636 CGGATAATGCACGGGCCAT 60.601 57.895 7.46 0.00 40.13 4.40
1961 2361 2.203139 CGGATAATGCACGGGCCA 60.203 61.111 7.46 0.00 40.13 5.36
1962 2362 3.660111 GCGGATAATGCACGGGCC 61.660 66.667 7.46 0.00 40.13 5.80
2022 2449 2.268076 AACCGACCAATGCCAGCAC 61.268 57.895 0.00 0.00 0.00 4.40
2030 2457 1.531739 ATTTGCGCCAACCGACCAAT 61.532 50.000 4.18 0.00 40.02 3.16
2050 2477 2.035832 GGAACACCCCAACAAATCTGTG 59.964 50.000 0.00 0.00 35.37 3.66
2066 2493 1.340248 GACCGTCTCAGACTTGGAACA 59.660 52.381 2.61 0.00 0.00 3.18
2080 2507 2.725637 AGACTAAGAGGAAGGACCGTC 58.274 52.381 0.00 0.00 44.74 4.79
2084 2511 9.674068 AAATTATCAAAGACTAAGAGGAAGGAC 57.326 33.333 0.00 0.00 0.00 3.85
2107 2534 7.038160 TGGGAAAGGAACATCAATCAATCAAAT 60.038 33.333 0.00 0.00 0.00 2.32
2130 2557 2.681064 CCATGGCACCTTGGTGGG 60.681 66.667 19.89 9.63 41.11 4.61
2182 2614 3.871594 CGTAACTAGAGGGCCTTTTCATG 59.128 47.826 7.89 0.00 0.00 3.07
2290 2733 5.483685 AGATGTCTGTACTGGTGCTAAAA 57.516 39.130 0.00 0.00 0.00 1.52
2295 2738 4.399618 TCTCTTAGATGTCTGTACTGGTGC 59.600 45.833 0.00 0.00 0.00 5.01
2304 2747 9.787435 AAGGTACTAGTATCTCTTAGATGTCTG 57.213 37.037 16.07 0.00 38.49 3.51
2315 2758 9.223099 GGAGACAAGATAAGGTACTAGTATCTC 57.777 40.741 16.07 13.45 37.48 2.75
2318 2761 6.941436 CCGGAGACAAGATAAGGTACTAGTAT 59.059 42.308 5.75 0.00 38.49 2.12
2320 2763 5.104193 TCCGGAGACAAGATAAGGTACTAGT 60.104 44.000 0.00 0.00 38.49 2.57
2352 2846 5.653330 TGAGAGAAAAATATGCAATGCTGGA 59.347 36.000 6.82 0.00 0.00 3.86
2359 2853 7.275888 ACAGTTGTGAGAGAAAAATATGCAA 57.724 32.000 0.00 0.00 0.00 4.08
2377 2871 4.256920 CAGAATCTTGGGGACTACAGTTG 58.743 47.826 0.00 0.00 0.00 3.16
2428 2922 9.530633 ACCTTGATAGAACTCGTATGAATTAAC 57.469 33.333 0.00 0.00 0.00 2.01
2463 2957 9.632807 CTAGTGCTAACTGAATAATTAGGCTAG 57.367 37.037 0.00 0.00 37.19 3.42
2464 2958 9.144298 ACTAGTGCTAACTGAATAATTAGGCTA 57.856 33.333 0.00 0.00 37.19 3.93
2486 2980 3.610040 TCATTGGTGGCACTACACTAG 57.390 47.619 18.45 1.93 41.09 2.57
2515 3009 1.000163 AGTACTCACTCGGTGCAGTTG 60.000 52.381 0.00 0.00 32.98 3.16
2548 3044 2.548707 CGTGGTGGGGATCTACATGATG 60.549 54.545 0.00 0.00 35.14 3.07
2623 3119 3.679389 AGTGTGAGGACATGGATCAAAC 58.321 45.455 8.56 8.56 33.63 2.93
2735 3276 7.622713 AGCAAATTAAATTCCATGGTTGATGA 58.377 30.769 12.58 0.00 33.31 2.92
2804 3350 1.738099 CAAAGAGACTCGCCCGGTG 60.738 63.158 0.00 0.00 0.00 4.94
2900 3451 3.567478 AGAATTTTCGGATGGAGGGAG 57.433 47.619 0.00 0.00 0.00 4.30
2901 3452 3.010138 ACAAGAATTTTCGGATGGAGGGA 59.990 43.478 0.00 0.00 0.00 4.20
2902 3453 3.356290 ACAAGAATTTTCGGATGGAGGG 58.644 45.455 0.00 0.00 0.00 4.30
2903 3454 4.009675 TGACAAGAATTTTCGGATGGAGG 58.990 43.478 0.00 0.00 0.00 4.30
2904 3455 5.355071 TGATGACAAGAATTTTCGGATGGAG 59.645 40.000 0.00 0.00 0.00 3.86
2905 3456 5.252547 TGATGACAAGAATTTTCGGATGGA 58.747 37.500 0.00 0.00 0.00 3.41
2906 3457 5.565592 TGATGACAAGAATTTTCGGATGG 57.434 39.130 0.00 0.00 0.00 3.51
2907 3458 7.872163 TTTTGATGACAAGAATTTTCGGATG 57.128 32.000 0.00 0.00 37.32 3.51
2908 3459 7.546667 CCATTTTGATGACAAGAATTTTCGGAT 59.453 33.333 0.00 0.00 37.32 4.18
2909 3460 6.867816 CCATTTTGATGACAAGAATTTTCGGA 59.132 34.615 0.00 0.00 37.32 4.55
2910 3461 6.867816 TCCATTTTGATGACAAGAATTTTCGG 59.132 34.615 0.00 0.00 37.32 4.30
2911 3462 7.872163 TCCATTTTGATGACAAGAATTTTCG 57.128 32.000 0.00 0.00 37.32 3.46
2937 3488 9.822185 AGACATGCTTTTGTTTTTCTATCTTTT 57.178 25.926 0.00 0.00 0.00 2.27
2938 3489 9.822185 AAGACATGCTTTTGTTTTTCTATCTTT 57.178 25.926 0.00 0.00 31.11 2.52
2939 3490 9.822185 AAAGACATGCTTTTGTTTTTCTATCTT 57.178 25.926 8.68 0.00 44.24 2.40
2940 3491 9.252962 CAAAGACATGCTTTTGTTTTTCTATCT 57.747 29.630 11.03 0.00 44.24 1.98
2941 3492 9.248291 TCAAAGACATGCTTTTGTTTTTCTATC 57.752 29.630 17.20 0.00 44.24 2.08
2942 3493 9.598517 TTCAAAGACATGCTTTTGTTTTTCTAT 57.401 25.926 17.20 0.00 44.24 1.98
2943 3494 8.994429 TTCAAAGACATGCTTTTGTTTTTCTA 57.006 26.923 17.20 0.44 44.24 2.10
2944 3495 7.603784 ACTTCAAAGACATGCTTTTGTTTTTCT 59.396 29.630 17.20 0.00 44.24 2.52
2945 3496 7.742151 ACTTCAAAGACATGCTTTTGTTTTTC 58.258 30.769 17.20 0.00 44.24 2.29
2954 3505 4.883585 TCAGACAACTTCAAAGACATGCTT 59.116 37.500 0.00 0.00 38.88 3.91
3019 3588 1.538276 CAGGCTTAGCGCATTTTTCG 58.462 50.000 11.47 0.00 41.67 3.46
3112 3681 0.256177 GGAGACTTCCATTGGGTCCC 59.744 60.000 0.00 0.00 43.45 4.46
3126 3695 3.557595 CGTATGCAATTCCAAGAGGAGAC 59.442 47.826 0.00 0.00 46.74 3.36
3128 3697 2.874701 CCGTATGCAATTCCAAGAGGAG 59.125 50.000 0.00 0.00 46.74 3.69
3231 3800 7.724061 ACCTAATGAATTTTTAGTGTGTGAGGT 59.276 33.333 7.79 0.00 0.00 3.85
3257 3826 4.712829 TGGAAGGACATTACGACCATTCTA 59.287 41.667 0.00 0.00 30.94 2.10
3287 3856 2.003548 AGCAGAGGATCCCAACCCC 61.004 63.158 8.55 0.00 33.66 4.95
3294 3868 3.334583 TGTTGTTACAGCAGAGGATCC 57.665 47.619 2.48 2.48 33.66 3.36
3334 3908 0.327480 ATGGGGTAGAGGTCCATGCA 60.327 55.000 0.00 0.00 39.56 3.96
3416 3990 9.753669 GCCCGTTTTCAAAATAAAATGAATAAG 57.246 29.630 0.00 0.00 37.48 1.73
3489 4063 9.820725 TTGATTAATTCCACATTTCATGATTCC 57.179 29.630 0.00 0.00 0.00 3.01
3515 4089 3.694566 GGAGTCACACACTTCTTTGGTTT 59.305 43.478 0.00 0.00 34.41 3.27
3533 4107 5.255397 TGGTTGGTCAAGATAAATGGAGT 57.745 39.130 0.00 0.00 0.00 3.85
3535 4109 6.969043 ACTATGGTTGGTCAAGATAAATGGA 58.031 36.000 0.00 0.00 0.00 3.41
3610 4184 6.813152 CACTTAAATGGAAGGGCAATTTAGTG 59.187 38.462 0.00 0.00 29.93 2.74
3621 4195 7.970614 GCTATTTCAGAACACTTAAATGGAAGG 59.029 37.037 0.00 0.00 0.00 3.46
3662 4236 5.815222 TCACCTTATTTGTATCATCCACACG 59.185 40.000 0.00 0.00 0.00 4.49
3713 4296 7.823635 ACCTCTACCTCCTACATTCATACTTA 58.176 38.462 0.00 0.00 0.00 2.24
3714 4297 6.684538 ACCTCTACCTCCTACATTCATACTT 58.315 40.000 0.00 0.00 0.00 2.24
3715 4298 6.282568 ACCTCTACCTCCTACATTCATACT 57.717 41.667 0.00 0.00 0.00 2.12
3716 4299 7.232910 AGTACCTCTACCTCCTACATTCATAC 58.767 42.308 0.00 0.00 0.00 2.39
3867 4450 0.035056 ACTACACATGGCTCCTTGGC 60.035 55.000 0.00 0.00 42.18 4.52
3956 4539 2.029666 ACACAGAGGCAGCGTGTC 59.970 61.111 0.00 0.00 39.64 3.67
3982 4565 3.686241 TGTGATTGAGGAAGCGAGATTTG 59.314 43.478 0.00 0.00 0.00 2.32
3998 4581 3.086282 TGCATGCAGAGTGAATGTGATT 58.914 40.909 18.46 0.00 35.78 2.57
3999 4582 2.718563 TGCATGCAGAGTGAATGTGAT 58.281 42.857 18.46 0.00 35.78 3.06
4011 4594 4.252073 ACTACTTCTTCTCTTGCATGCAG 58.748 43.478 21.50 14.85 0.00 4.41
4063 4646 1.757682 TGCAACCAAAGAACCGTCTT 58.242 45.000 0.00 0.00 46.47 3.01
4064 4647 1.404035 GTTGCAACCAAAGAACCGTCT 59.596 47.619 19.15 0.00 34.72 4.18
4065 4648 1.133407 TGTTGCAACCAAAGAACCGTC 59.867 47.619 26.14 0.00 31.68 4.79
4066 4649 1.178276 TGTTGCAACCAAAGAACCGT 58.822 45.000 26.14 0.00 31.68 4.83
4067 4650 2.507339 ATGTTGCAACCAAAGAACCG 57.493 45.000 26.14 0.00 31.68 4.44
4068 4651 4.633565 TGAAAATGTTGCAACCAAAGAACC 59.366 37.500 26.14 8.79 31.68 3.62
4069 4652 5.559227 GTGAAAATGTTGCAACCAAAGAAC 58.441 37.500 26.14 14.03 31.68 3.01
4070 4653 4.328440 CGTGAAAATGTTGCAACCAAAGAA 59.672 37.500 26.14 7.32 31.68 2.52
4071 4654 3.862267 CGTGAAAATGTTGCAACCAAAGA 59.138 39.130 26.14 8.09 31.68 2.52
4072 4655 3.616379 ACGTGAAAATGTTGCAACCAAAG 59.384 39.130 26.14 14.92 31.68 2.77
4073 4656 3.589988 ACGTGAAAATGTTGCAACCAAA 58.410 36.364 26.14 8.88 31.68 3.28
4074 4657 3.238108 ACGTGAAAATGTTGCAACCAA 57.762 38.095 26.14 9.67 0.00 3.67
4075 4658 2.949451 ACGTGAAAATGTTGCAACCA 57.051 40.000 26.14 13.69 0.00 3.67
4076 4659 3.783873 GCAAACGTGAAAATGTTGCAACC 60.784 43.478 26.14 11.17 0.00 3.77
4077 4660 3.061965 AGCAAACGTGAAAATGTTGCAAC 59.938 39.130 22.83 22.83 0.00 4.17
4141 4724 6.135290 TCAACAGAACCAATTTGAGTTCAG 57.865 37.500 21.95 18.56 43.89 3.02
4195 4778 5.557136 CGCAGAAATCAACGATAAGATGACC 60.557 44.000 0.00 0.00 34.40 4.02
4221 4804 2.582498 GGACAGATTCGTCGCCGG 60.582 66.667 0.00 0.00 36.73 6.13
4238 4821 3.089788 GGGTAGTGTAAATGGCCCG 57.910 57.895 0.00 0.00 0.00 6.13
4239 4822 1.099295 GCGGGTAGTGTAAATGGCCC 61.099 60.000 0.00 0.00 0.00 5.80
4240 4823 0.393267 TGCGGGTAGTGTAAATGGCC 60.393 55.000 0.00 0.00 0.00 5.36
4241 4824 1.455248 TTGCGGGTAGTGTAAATGGC 58.545 50.000 0.00 0.00 0.00 4.40
4242 4825 2.159435 GCTTTGCGGGTAGTGTAAATGG 60.159 50.000 0.00 0.00 0.00 3.16
4243 4826 2.486203 TGCTTTGCGGGTAGTGTAAATG 59.514 45.455 0.00 0.00 0.00 2.32
4245 4828 1.874872 GTGCTTTGCGGGTAGTGTAAA 59.125 47.619 0.00 0.00 0.00 2.01
4246 4829 1.071071 AGTGCTTTGCGGGTAGTGTAA 59.929 47.619 0.00 0.00 0.00 2.41
4248 4831 0.682852 TAGTGCTTTGCGGGTAGTGT 59.317 50.000 0.00 0.00 0.00 3.55
4249 4832 1.076332 GTAGTGCTTTGCGGGTAGTG 58.924 55.000 0.00 0.00 0.00 2.74
4252 4835 0.108992 CGAGTAGTGCTTTGCGGGTA 60.109 55.000 0.00 0.00 0.00 3.69
4253 4836 1.374252 CGAGTAGTGCTTTGCGGGT 60.374 57.895 0.00 0.00 0.00 5.28
4255 4838 1.144969 TTTCGAGTAGTGCTTTGCGG 58.855 50.000 0.00 0.00 0.00 5.69
4257 4840 6.256757 AGAGAATATTTCGAGTAGTGCTTTGC 59.743 38.462 0.00 0.00 34.02 3.68
4258 4841 7.305705 CGAGAGAATATTTCGAGTAGTGCTTTG 60.306 40.741 2.51 0.00 36.49 2.77
4259 4842 6.693545 CGAGAGAATATTTCGAGTAGTGCTTT 59.306 38.462 2.51 0.00 36.49 3.51
4303 4886 8.972127 TCTCAGTCTAGCATCTAAAATTACACT 58.028 33.333 0.00 0.00 0.00 3.55
4304 4887 9.757227 ATCTCAGTCTAGCATCTAAAATTACAC 57.243 33.333 0.00 0.00 0.00 2.90
4310 4893 9.950496 AGAAAAATCTCAGTCTAGCATCTAAAA 57.050 29.630 0.00 0.00 0.00 1.52
4315 4898 7.332926 TGAACAGAAAAATCTCAGTCTAGCATC 59.667 37.037 0.00 0.00 0.00 3.91
4320 4903 9.559732 TCATTTGAACAGAAAAATCTCAGTCTA 57.440 29.630 0.00 0.00 0.00 2.59
4322 4905 9.688592 AATCATTTGAACAGAAAAATCTCAGTC 57.311 29.630 0.00 0.00 0.00 3.51
4325 4908 9.630098 GCTAATCATTTGAACAGAAAAATCTCA 57.370 29.630 0.00 0.00 0.00 3.27
4335 4918 2.104144 GCGCGCTAATCATTTGAACAG 58.896 47.619 26.67 0.00 0.00 3.16
4337 4920 1.104579 CGCGCGCTAATCATTTGAAC 58.895 50.000 30.48 0.00 0.00 3.18
4338 4921 0.588730 GCGCGCGCTAATCATTTGAA 60.589 50.000 44.38 0.00 38.26 2.69
4339 4922 1.011242 GCGCGCGCTAATCATTTGA 60.011 52.632 44.38 0.00 38.26 2.69
4786 5411 2.440599 GGTGTGGCCCCAGTTGAT 59.559 61.111 0.00 0.00 0.00 2.57
5649 6285 1.308998 CGAACTTCCAGGCAGTGTTT 58.691 50.000 0.00 0.00 0.00 2.83
5667 6303 2.040544 GGAGTGGGGCATGAACACG 61.041 63.158 0.00 0.00 39.95 4.49
5702 6338 0.612174 CACCCTCTCCGAGAAGGTGA 60.612 60.000 30.97 5.76 41.35 4.02
5796 6432 3.379445 GGCCTCCTCGTGTCCGAA 61.379 66.667 0.00 0.00 43.69 4.30


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

AutoCloner maintained by Alex Coulton.