Multiple sequence alignment - TraesCS3B01G198100

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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 TraesCS3B01G198100 chr3B 100.000 2767 0 0 1 2767 225450803 225448037 0.000000e+00 5110.0
1 TraesCS3B01G198100 chr3B 92.771 166 9 3 2604 2767 773490847 773491011 1.280000e-58 237.0
2 TraesCS3B01G198100 chr3B 92.920 113 7 1 1 112 690355455 690355343 2.200000e-36 163.0
3 TraesCS3B01G198100 chr3B 94.048 84 5 0 636 719 690345355 690345272 8.040000e-26 128.0
4 TraesCS3B01G198100 chr3B 80.556 108 18 3 2594 2699 741778479 741778585 2.280000e-11 80.5
5 TraesCS3B01G198100 chr3D 94.171 1664 47 16 960 2607 156206416 156208045 0.000000e+00 2490.0
6 TraesCS3B01G198100 chr3D 95.031 161 6 2 2603 2763 110538543 110538701 4.570000e-63 252.0
7 TraesCS3B01G198100 chr3D 80.952 147 19 7 2594 2735 356828196 356828338 1.050000e-19 108.0
8 TraesCS3B01G198100 chr3A 91.672 1537 80 22 963 2472 175808570 175810085 0.000000e+00 2085.0
9 TraesCS3B01G198100 chr3A 80.763 655 106 18 231 874 658059417 658058772 6.880000e-136 494.0
10 TraesCS3B01G198100 chr3A 96.053 76 3 0 2532 2607 175810098 175810173 1.040000e-24 124.0
11 TraesCS3B01G198100 chr7D 87.473 910 76 17 1 876 6580820 6579915 0.000000e+00 1014.0
12 TraesCS3B01G198100 chr7D 92.814 167 8 4 2603 2767 574810447 574810611 3.560000e-59 239.0
13 TraesCS3B01G198100 chr7D 93.548 62 3 1 2477 2537 22585924 22585985 1.060000e-14 91.6
14 TraesCS3B01G198100 chr4A 89.606 635 57 7 1 632 733662973 733663601 0.000000e+00 798.0
15 TraesCS3B01G198100 chr4A 87.420 628 73 6 9 632 415468245 415467620 0.000000e+00 717.0
16 TraesCS3B01G198100 chr4A 88.430 242 27 1 636 876 415467578 415467337 9.690000e-75 291.0
17 TraesCS3B01G198100 chr4A 89.030 237 23 3 636 871 733663643 733663877 9.690000e-75 291.0
18 TraesCS3B01G198100 chr4A 85.437 103 11 3 2594 2692 719961723 719961825 1.360000e-18 104.0
19 TraesCS3B01G198100 chr7A 88.976 635 53 6 1 632 7667273 7666653 0.000000e+00 769.0
20 TraesCS3B01G198100 chr7A 87.603 242 29 1 636 876 7666610 7666369 2.100000e-71 279.0
21 TraesCS3B01G198100 chr7A 87.778 180 10 11 2595 2767 695875197 695875023 1.680000e-47 200.0
22 TraesCS3B01G198100 chr7A 93.548 62 3 1 2477 2537 735744292 735744231 1.060000e-14 91.6
23 TraesCS3B01G198100 chr7A 93.548 62 3 1 2477 2537 735777189 735777128 1.060000e-14 91.6
24 TraesCS3B01G198100 chr7B 87.599 629 66 5 1 626 666517322 666517941 0.000000e+00 719.0
25 TraesCS3B01G198100 chr7B 81.651 109 14 5 2596 2699 622689570 622689463 4.910000e-13 86.1
26 TraesCS3B01G198100 chr2A 87.879 561 62 5 77 632 631956591 631956032 0.000000e+00 654.0
27 TraesCS3B01G198100 chr2A 88.934 488 50 4 148 632 66911514 66912000 1.420000e-167 599.0
28 TraesCS3B01G198100 chr2A 90.377 239 21 2 640 876 66912046 66912284 2.070000e-81 313.0
29 TraesCS3B01G198100 chr2A 89.655 174 16 2 705 876 3620982 3620809 1.290000e-53 220.0
30 TraesCS3B01G198100 chr2B 90.083 242 22 2 636 876 63058908 63059148 2.070000e-81 313.0
31 TraesCS3B01G198100 chr2B 88.655 238 25 2 397 632 63058629 63058866 3.490000e-74 289.0
32 TraesCS3B01G198100 chr2B 93.939 165 5 2 2604 2766 712952278 712952439 7.650000e-61 244.0
33 TraesCS3B01G198100 chr2B 92.308 65 3 1 2477 2539 693327269 693327333 1.060000e-14 91.6
34 TraesCS3B01G198100 chr2D 90.295 237 20 3 636 870 67449982 67449747 9.630000e-80 307.0
35 TraesCS3B01G198100 chr2D 92.169 166 8 5 2604 2767 555729061 555728899 2.140000e-56 230.0
36 TraesCS3B01G198100 chr5A 90.094 212 20 1 422 632 431653885 431654096 9.760000e-70 274.0
37 TraesCS3B01G198100 chr1B 94.545 165 6 3 2603 2765 42017027 42017190 4.570000e-63 252.0
38 TraesCS3B01G198100 chr1B 92.899 169 8 4 2601 2767 419772784 419772950 2.750000e-60 243.0
39 TraesCS3B01G198100 chr1B 95.000 60 1 1 2477 2534 586281757 586281816 2.930000e-15 93.5
40 TraesCS3B01G198100 chr6D 93.333 165 7 4 2604 2767 226786518 226786357 9.900000e-60 241.0
41 TraesCS3B01G198100 chr6B 85.227 176 18 7 2595 2767 523502625 523502455 1.020000e-39 174.0
42 TraesCS3B01G198100 chr6B 92.079 101 8 0 695 795 214091873 214091773 2.870000e-30 143.0
43 TraesCS3B01G198100 chr6B 95.000 60 1 1 2477 2534 49622811 49622752 2.930000e-15 93.5
44 TraesCS3B01G198100 chr6B 95.000 60 1 1 2477 2534 49622756 49622815 2.930000e-15 93.5
45 TraesCS3B01G198100 chr5D 80.000 155 20 9 2590 2737 41583878 41584028 1.360000e-18 104.0
46 TraesCS3B01G198100 chr5D 90.123 81 5 2 2594 2671 34073517 34073597 4.880000e-18 102.0
47 TraesCS3B01G198100 chr5D 95.161 62 2 1 2477 2537 26787195 26787134 2.270000e-16 97.1
48 TraesCS3B01G198100 chr4B 81.159 138 17 8 2593 2728 520892565 520892695 4.880000e-18 102.0


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 TraesCS3B01G198100 chr3B 225448037 225450803 2766 True 5110.0 5110 100.0000 1 2767 1 chr3B.!!$R1 2766
1 TraesCS3B01G198100 chr3D 156206416 156208045 1629 False 2490.0 2490 94.1710 960 2607 1 chr3D.!!$F2 1647
2 TraesCS3B01G198100 chr3A 175808570 175810173 1603 False 1104.5 2085 93.8625 963 2607 2 chr3A.!!$F1 1644
3 TraesCS3B01G198100 chr3A 658058772 658059417 645 True 494.0 494 80.7630 231 874 1 chr3A.!!$R1 643
4 TraesCS3B01G198100 chr7D 6579915 6580820 905 True 1014.0 1014 87.4730 1 876 1 chr7D.!!$R1 875
5 TraesCS3B01G198100 chr4A 733662973 733663877 904 False 544.5 798 89.3180 1 871 2 chr4A.!!$F2 870
6 TraesCS3B01G198100 chr4A 415467337 415468245 908 True 504.0 717 87.9250 9 876 2 chr4A.!!$R1 867
7 TraesCS3B01G198100 chr7A 7666369 7667273 904 True 524.0 769 88.2895 1 876 2 chr7A.!!$R4 875
8 TraesCS3B01G198100 chr7B 666517322 666517941 619 False 719.0 719 87.5990 1 626 1 chr7B.!!$F1 625
9 TraesCS3B01G198100 chr2A 631956032 631956591 559 True 654.0 654 87.8790 77 632 1 chr2A.!!$R2 555
10 TraesCS3B01G198100 chr2A 66911514 66912284 770 False 456.0 599 89.6555 148 876 2 chr2A.!!$F1 728
11 TraesCS3B01G198100 chr2B 63058629 63059148 519 False 301.0 313 89.3690 397 876 2 chr2B.!!$F3 479

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
955 1024 0.171007 AGCCATTTTCGCATCGGTTG 59.829 50.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 2846 0.10412 GGCCTTTTGTTCTTGGCGTT 59.896 50.0 0.0 0.0 45.75 4.84 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
23 24 5.817988 CATTCTATTCCGACTGAAGACGTA 58.182 41.667 0.00 0.00 36.14 3.57
26 27 1.511850 TTCCGACTGAAGACGTACGA 58.488 50.000 24.41 0.00 0.00 3.43
56 57 6.003950 TCGACATATGTCACCATCTGATAGA 58.996 40.000 30.15 14.77 44.99 1.98
113 122 1.583495 CCCTACTCGAGTGCACGACA 61.583 60.000 28.12 4.99 37.37 4.35
175 197 2.264813 GCACTTAATTGCTACGACGGA 58.735 47.619 10.33 0.00 39.59 4.69
176 198 2.028883 GCACTTAATTGCTACGACGGAC 59.971 50.000 10.33 0.00 39.59 4.79
180 202 0.322322 AATTGCTACGACGGACCCAA 59.678 50.000 0.00 0.00 0.00 4.12
189 211 2.255252 CGGACCCAAGCGCAAAAG 59.745 61.111 11.47 0.00 0.00 2.27
209 233 1.136891 GGTTGCTATTTGGGTGATGGC 59.863 52.381 0.00 0.00 0.00 4.40
258 282 1.823169 TAACGGTGACTCTGTGGGCC 61.823 60.000 0.00 0.00 35.59 5.80
281 305 1.971695 GGACAACAAGGCGGAAGGG 60.972 63.158 0.00 0.00 0.00 3.95
301 325 4.414846 AGGGCATCCATGAGTCTATTTTCT 59.585 41.667 0.00 0.00 34.83 2.52
325 349 3.012518 AGTTCTCTTGCCACACATATGC 58.987 45.455 1.58 0.00 0.00 3.14
337 361 4.295870 CACACATATGCTCATTCAATGCC 58.704 43.478 1.58 0.00 0.00 4.40
339 363 4.647853 ACACATATGCTCATTCAATGCCTT 59.352 37.500 1.58 0.00 0.00 4.35
358 382 3.949754 CCTTATTGCTGAATTGGAGAGCA 59.050 43.478 0.00 0.00 40.94 4.26
399 423 2.100989 GATGAGACCTACTCCCGTTGT 58.899 52.381 0.00 0.00 44.34 3.32
410 434 2.224354 ACTCCCGTTGTAAATGTTCGGT 60.224 45.455 0.00 0.00 39.62 4.69
416 440 3.696898 GTTGTAAATGTTCGGTTGCACA 58.303 40.909 0.00 0.00 0.00 4.57
438 462 1.841556 TTTGGACGCCTCCTCCAGT 60.842 57.895 3.30 0.00 39.06 4.00
461 485 7.770433 CAGTAGGGATGTTTAAGATCAATGTGA 59.230 37.037 4.52 0.00 0.00 3.58
516 540 0.973632 TCCTCTGTTGTATGCCGTGT 59.026 50.000 0.00 0.00 0.00 4.49
607 635 0.811915 ACTAGCATGTCGAGAAGCGT 59.188 50.000 4.02 0.00 41.80 5.07
632 660 1.425066 ACTTGCCCAAGACCTGAATCA 59.575 47.619 14.46 0.00 40.79 2.57
633 661 2.042162 ACTTGCCCAAGACCTGAATCAT 59.958 45.455 14.46 0.00 40.79 2.45
634 662 2.905415 TGCCCAAGACCTGAATCATT 57.095 45.000 0.00 0.00 0.00 2.57
657 724 8.737175 CATTAATGATATAAAGCATGGCTCACT 58.263 33.333 10.04 0.00 38.25 3.41
666 733 1.202627 GCATGGCTCACTAGGGAAGAG 60.203 57.143 0.00 0.00 0.00 2.85
739 807 7.597386 CATGTGATATCATCTTCGAAGGTAGA 58.403 38.462 24.37 18.64 0.00 2.59
752 820 5.421277 TCGAAGGTAGAGACACAAACAAAA 58.579 37.500 0.00 0.00 0.00 2.44
786 854 5.404366 GCTTGGTTAATTTTTCGGTTTCTCC 59.596 40.000 0.00 0.00 0.00 3.71
802 870 1.921869 CTCCTAACCGGGGTTGCCAT 61.922 60.000 13.25 0.00 38.92 4.40
835 903 4.176271 GCTATTCACATGACCCTTTTTGC 58.824 43.478 0.00 0.00 0.00 3.68
857 926 7.243604 TGCATTCTTTGAACTTCCCAATTAT 57.756 32.000 0.00 0.00 0.00 1.28
929 998 6.854496 AAAACCTAAAAAGGAAATTTCGGC 57.146 33.333 11.95 0.00 0.00 5.54
930 999 5.538849 AACCTAAAAAGGAAATTTCGGCA 57.461 34.783 11.95 0.00 0.00 5.69
931 1000 5.134202 ACCTAAAAAGGAAATTTCGGCAG 57.866 39.130 11.95 3.67 0.00 4.85
932 1001 3.926527 CCTAAAAAGGAAATTTCGGCAGC 59.073 43.478 11.95 0.00 0.00 5.25
933 1002 2.064573 AAAAGGAAATTTCGGCAGCG 57.935 45.000 11.95 0.00 0.00 5.18
934 1003 0.243636 AAAGGAAATTTCGGCAGCGG 59.756 50.000 11.95 0.00 0.00 5.52
935 1004 0.608035 AAGGAAATTTCGGCAGCGGA 60.608 50.000 11.95 0.00 0.00 5.54
936 1005 0.608035 AGGAAATTTCGGCAGCGGAA 60.608 50.000 11.20 11.20 0.00 4.30
937 1006 0.179163 GGAAATTTCGGCAGCGGAAG 60.179 55.000 14.42 0.00 0.00 3.46
950 1019 3.240684 CGGAAGCCATTTTCGCATC 57.759 52.632 0.00 0.00 0.00 3.91
951 1020 0.589729 CGGAAGCCATTTTCGCATCG 60.590 55.000 0.00 0.00 0.00 3.84
952 1021 0.248621 GGAAGCCATTTTCGCATCGG 60.249 55.000 0.00 0.00 0.00 4.18
953 1022 0.451783 GAAGCCATTTTCGCATCGGT 59.548 50.000 0.00 0.00 0.00 4.69
954 1023 0.887933 AAGCCATTTTCGCATCGGTT 59.112 45.000 0.00 0.00 0.00 4.44
955 1024 0.171007 AGCCATTTTCGCATCGGTTG 59.829 50.000 0.00 0.00 0.00 3.77
956 1025 0.801836 GCCATTTTCGCATCGGTTGG 60.802 55.000 0.00 0.00 0.00 3.77
957 1026 0.801836 CCATTTTCGCATCGGTTGGC 60.802 55.000 0.00 0.00 0.00 4.52
963 1032 2.804931 GCATCGGTTGGCGTTTGC 60.805 61.111 0.00 0.00 41.71 3.68
964 1033 2.642129 CATCGGTTGGCGTTTGCA 59.358 55.556 0.00 0.00 45.35 4.08
965 1034 1.729131 CATCGGTTGGCGTTTGCAC 60.729 57.895 0.00 0.00 45.35 4.57
970 1039 2.103934 TTGGCGTTTGCACTGCAC 59.896 55.556 2.26 0.00 45.35 4.57
1112 1181 0.179000 CTCCCCCTTCTGACGAATGG 59.821 60.000 0.00 0.00 35.43 3.16
1322 1394 2.170187 CCTCACCCTCTCCAAAGATGAG 59.830 54.545 0.00 0.00 33.45 2.90
1324 1396 1.912043 CACCCTCTCCAAAGATGAGGT 59.088 52.381 7.38 0.00 44.21 3.85
1356 1428 2.058675 CCCCAACAAGACTCCGACT 58.941 57.895 0.00 0.00 0.00 4.18
1357 1429 0.037232 CCCCAACAAGACTCCGACTC 60.037 60.000 0.00 0.00 0.00 3.36
1571 1655 1.070134 TGGATCCAGCATTACTACGGC 59.930 52.381 11.44 0.00 0.00 5.68
1572 1656 1.419374 GATCCAGCATTACTACGGCG 58.581 55.000 4.80 4.80 0.00 6.46
1573 1657 1.000607 GATCCAGCATTACTACGGCGA 60.001 52.381 16.62 0.00 0.00 5.54
1574 1658 0.101759 TCCAGCATTACTACGGCGAC 59.898 55.000 16.62 0.00 0.00 5.19
1623 1707 3.818787 GGCTGGCGCATCTGTTGG 61.819 66.667 10.83 0.00 38.10 3.77
1776 1860 3.196469 GGAGACAGAGTGATGATTGGACA 59.804 47.826 0.00 0.00 0.00 4.02
1781 1865 3.197333 CAGAGTGATGATTGGACAGAGGT 59.803 47.826 0.00 0.00 0.00 3.85
1877 1961 9.903682 CTGAATGTTTGTATTCTGAAATTGTCT 57.096 29.630 0.00 0.00 37.88 3.41
1891 1975 5.912396 TGAAATTGTCTAACGCAATGTGTTC 59.088 36.000 15.95 2.79 37.45 3.18
1894 1978 2.805671 TGTCTAACGCAATGTGTTCCTG 59.194 45.455 15.95 7.97 37.45 3.86
1987 2071 0.668401 GCATTTTGCTCCAGTGCCAC 60.668 55.000 0.00 0.00 40.96 5.01
1988 2072 0.675083 CATTTTGCTCCAGTGCCACA 59.325 50.000 0.00 0.00 0.00 4.17
1990 2074 0.675083 TTTTGCTCCAGTGCCACATG 59.325 50.000 0.00 0.00 0.00 3.21
1992 2076 1.174078 TTGCTCCAGTGCCACATGTG 61.174 55.000 19.31 19.31 0.00 3.21
1993 2077 1.601759 GCTCCAGTGCCACATGTGT 60.602 57.895 23.79 2.81 0.00 3.72
1994 2078 1.174712 GCTCCAGTGCCACATGTGTT 61.175 55.000 23.79 4.50 0.00 3.32
1996 2080 0.822944 TCCAGTGCCACATGTGTTGG 60.823 55.000 23.79 22.09 0.00 3.77
2113 2206 7.606131 CAACATATGCGAATCAAAATCACTTG 58.394 34.615 1.58 0.00 0.00 3.16
2370 2478 8.311650 AGTGCGATATCCAAATTATTAGTCAC 57.688 34.615 0.00 0.00 0.00 3.67
2472 2580 3.198853 AGGACCCTAGAATTGCAGACTTC 59.801 47.826 0.00 0.00 0.00 3.01
2478 2586 2.583685 GAATTGCAGACTTCGCGCCC 62.584 60.000 0.00 0.00 0.00 6.13
2479 2587 3.612247 ATTGCAGACTTCGCGCCCT 62.612 57.895 0.00 0.00 0.00 5.19
2480 2588 4.742201 TGCAGACTTCGCGCCCTC 62.742 66.667 0.00 0.00 0.00 4.30
2492 2600 2.277404 GCCCTCCGCCCCAAAATA 59.723 61.111 0.00 0.00 0.00 1.40
2493 2601 1.380650 GCCCTCCGCCCCAAAATAA 60.381 57.895 0.00 0.00 0.00 1.40
2494 2602 1.391933 GCCCTCCGCCCCAAAATAAG 61.392 60.000 0.00 0.00 0.00 1.73
2495 2603 0.033503 CCCTCCGCCCCAAAATAAGT 60.034 55.000 0.00 0.00 0.00 2.24
2496 2604 1.102978 CCTCCGCCCCAAAATAAGTG 58.897 55.000 0.00 0.00 0.00 3.16
2497 2605 1.615919 CCTCCGCCCCAAAATAAGTGT 60.616 52.381 0.00 0.00 0.00 3.55
2498 2606 1.743394 CTCCGCCCCAAAATAAGTGTC 59.257 52.381 0.00 0.00 0.00 3.67
2499 2607 1.353022 TCCGCCCCAAAATAAGTGTCT 59.647 47.619 0.00 0.00 0.00 3.41
2500 2608 1.743394 CCGCCCCAAAATAAGTGTCTC 59.257 52.381 0.00 0.00 0.00 3.36
2501 2609 2.432444 CGCCCCAAAATAAGTGTCTCA 58.568 47.619 0.00 0.00 0.00 3.27
2627 2735 2.561478 TTTGAAAAGAGGACTCCCCG 57.439 50.000 0.00 0.00 40.87 5.73
2628 2736 0.690762 TTGAAAAGAGGACTCCCCGG 59.309 55.000 0.00 0.00 40.87 5.73
2629 2737 1.078356 GAAAAGAGGACTCCCCGGC 60.078 63.158 0.00 0.00 40.87 6.13
2630 2738 2.538512 GAAAAGAGGACTCCCCGGCC 62.539 65.000 0.00 0.00 40.87 6.13
2631 2739 3.564347 AAAGAGGACTCCCCGGCCT 62.564 63.158 0.00 0.00 40.87 5.19
2632 2740 3.986116 AAGAGGACTCCCCGGCCTC 62.986 68.421 15.22 15.22 46.75 4.70
2633 2741 4.467107 GAGGACTCCCCGGCCTCT 62.467 72.222 15.62 0.00 43.79 3.69
2634 2742 4.787280 AGGACTCCCCGGCCTCTG 62.787 72.222 0.00 0.00 40.87 3.35
2638 2746 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
2640 2748 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
2641 2749 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
2642 2750 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
2643 2751 1.817099 CCGGCCTCTGCATCAGAAC 60.817 63.158 0.00 0.00 40.18 3.01
2644 2752 2.169789 CGGCCTCTGCATCAGAACG 61.170 63.158 0.00 0.63 40.18 3.95
2645 2753 1.219124 GGCCTCTGCATCAGAACGA 59.781 57.895 0.00 0.00 40.18 3.85
2646 2754 0.179062 GGCCTCTGCATCAGAACGAT 60.179 55.000 0.00 0.00 40.18 3.73
2655 2763 3.466712 CATCAGAACGATGCATATGGC 57.533 47.619 0.00 0.00 44.95 4.40
2656 2764 1.882912 TCAGAACGATGCATATGGCC 58.117 50.000 0.00 0.00 43.89 5.36
2657 2765 1.140652 TCAGAACGATGCATATGGCCA 59.859 47.619 8.56 8.56 43.89 5.36
2658 2766 1.265095 CAGAACGATGCATATGGCCAC 59.735 52.381 8.16 0.00 43.89 5.01
2659 2767 1.134128 AGAACGATGCATATGGCCACA 60.134 47.619 8.16 0.00 43.89 4.17
2660 2768 1.881973 GAACGATGCATATGGCCACAT 59.118 47.619 8.16 7.00 43.89 3.21
2661 2769 1.985473 ACGATGCATATGGCCACATT 58.015 45.000 8.16 0.00 43.89 2.71
2662 2770 2.309613 ACGATGCATATGGCCACATTT 58.690 42.857 8.16 0.00 43.89 2.32
2663 2771 3.485394 ACGATGCATATGGCCACATTTA 58.515 40.909 8.16 0.00 43.89 1.40
2664 2772 4.081406 ACGATGCATATGGCCACATTTAT 58.919 39.130 8.16 0.00 43.89 1.40
2665 2773 5.252547 ACGATGCATATGGCCACATTTATA 58.747 37.500 8.16 0.00 43.89 0.98
2666 2774 5.355071 ACGATGCATATGGCCACATTTATAG 59.645 40.000 8.16 1.48 43.89 1.31
2667 2775 5.585844 CGATGCATATGGCCACATTTATAGA 59.414 40.000 8.16 0.00 43.89 1.98
2668 2776 6.261603 CGATGCATATGGCCACATTTATAGAT 59.738 38.462 8.16 0.00 43.89 1.98
2669 2777 7.442062 CGATGCATATGGCCACATTTATAGATA 59.558 37.037 8.16 0.00 43.89 1.98
2670 2778 9.123902 GATGCATATGGCCACATTTATAGATAA 57.876 33.333 8.16 0.00 43.89 1.75
2671 2779 8.876303 TGCATATGGCCACATTTATAGATAAA 57.124 30.769 8.16 0.00 43.89 1.40
2672 2780 9.306777 TGCATATGGCCACATTTATAGATAAAA 57.693 29.630 8.16 0.00 43.89 1.52
2677 2785 8.463930 TGGCCACATTTATAGATAAAAAGAGG 57.536 34.615 0.00 4.97 36.02 3.69
2678 2786 8.058847 TGGCCACATTTATAGATAAAAAGAGGT 58.941 33.333 0.00 0.00 36.02 3.85
2679 2787 8.914011 GGCCACATTTATAGATAAAAAGAGGTT 58.086 33.333 0.00 0.00 36.02 3.50
2680 2788 9.952188 GCCACATTTATAGATAAAAAGAGGTTC 57.048 33.333 0.00 0.00 36.02 3.62
2689 2797 7.511959 AGATAAAAAGAGGTTCAACAAGGTC 57.488 36.000 0.00 0.00 0.00 3.85
2690 2798 7.290813 AGATAAAAAGAGGTTCAACAAGGTCT 58.709 34.615 0.00 0.00 0.00 3.85
2691 2799 7.780271 AGATAAAAAGAGGTTCAACAAGGTCTT 59.220 33.333 0.00 0.00 0.00 3.01
2692 2800 8.990163 ATAAAAAGAGGTTCAACAAGGTCTTA 57.010 30.769 0.00 0.00 0.00 2.10
2693 2801 7.712204 AAAAAGAGGTTCAACAAGGTCTTAA 57.288 32.000 0.00 0.00 0.00 1.85
2694 2802 6.944234 AAAGAGGTTCAACAAGGTCTTAAG 57.056 37.500 0.00 0.00 0.00 1.85
2695 2803 4.974399 AGAGGTTCAACAAGGTCTTAAGG 58.026 43.478 1.85 0.00 0.00 2.69
2696 2804 4.412528 AGAGGTTCAACAAGGTCTTAAGGT 59.587 41.667 1.85 0.00 0.00 3.50
2697 2805 4.715713 AGGTTCAACAAGGTCTTAAGGTC 58.284 43.478 1.85 0.00 0.00 3.85
2698 2806 4.412528 AGGTTCAACAAGGTCTTAAGGTCT 59.587 41.667 1.85 0.00 0.00 3.85
2699 2807 5.104067 AGGTTCAACAAGGTCTTAAGGTCTT 60.104 40.000 1.85 4.23 0.00 3.01
2700 2808 5.008712 GGTTCAACAAGGTCTTAAGGTCTTG 59.991 44.000 24.16 24.16 41.46 3.02
2701 2809 5.623956 TCAACAAGGTCTTAAGGTCTTGA 57.376 39.130 28.65 14.91 38.96 3.02
2702 2810 5.996644 TCAACAAGGTCTTAAGGTCTTGAA 58.003 37.500 28.65 17.91 38.96 2.69
2703 2811 6.419791 TCAACAAGGTCTTAAGGTCTTGAAA 58.580 36.000 28.65 17.70 38.96 2.69
2704 2812 6.317893 TCAACAAGGTCTTAAGGTCTTGAAAC 59.682 38.462 28.65 10.46 38.96 2.78
2705 2813 5.751586 ACAAGGTCTTAAGGTCTTGAAACA 58.248 37.500 28.65 0.00 38.96 2.83
2706 2814 6.184789 ACAAGGTCTTAAGGTCTTGAAACAA 58.815 36.000 28.65 0.00 38.96 2.83
2707 2815 6.661805 ACAAGGTCTTAAGGTCTTGAAACAAA 59.338 34.615 28.65 0.00 38.96 2.83
2708 2816 7.342026 ACAAGGTCTTAAGGTCTTGAAACAAAT 59.658 33.333 28.65 13.28 38.96 2.32
2709 2817 8.846211 CAAGGTCTTAAGGTCTTGAAACAAATA 58.154 33.333 22.73 0.00 38.96 1.40
2710 2818 8.622948 AGGTCTTAAGGTCTTGAAACAAATAG 57.377 34.615 1.85 0.00 0.00 1.73
2711 2819 8.437575 AGGTCTTAAGGTCTTGAAACAAATAGA 58.562 33.333 1.85 0.00 0.00 1.98
2712 2820 9.063615 GGTCTTAAGGTCTTGAAACAAATAGAA 57.936 33.333 1.85 0.00 0.00 2.10
2717 2825 8.628882 AAGGTCTTGAAACAAATAGAAAAACG 57.371 30.769 0.00 0.00 0.00 3.60
2718 2826 7.200455 AGGTCTTGAAACAAATAGAAAAACGG 58.800 34.615 0.00 0.00 0.00 4.44
2719 2827 6.074516 GGTCTTGAAACAAATAGAAAAACGGC 60.075 38.462 0.00 0.00 0.00 5.68
2720 2828 6.474102 GTCTTGAAACAAATAGAAAAACGGCA 59.526 34.615 0.00 0.00 0.00 5.69
2721 2829 7.009723 GTCTTGAAACAAATAGAAAAACGGCAA 59.990 33.333 0.00 0.00 0.00 4.52
2722 2830 6.820470 TGAAACAAATAGAAAAACGGCAAG 57.180 33.333 0.00 0.00 0.00 4.01
2723 2831 5.233263 TGAAACAAATAGAAAAACGGCAAGC 59.767 36.000 0.00 0.00 0.00 4.01
2724 2832 4.584327 ACAAATAGAAAAACGGCAAGCT 57.416 36.364 0.00 0.00 0.00 3.74
2725 2833 4.546570 ACAAATAGAAAAACGGCAAGCTC 58.453 39.130 0.00 0.00 0.00 4.09
2726 2834 4.037446 ACAAATAGAAAAACGGCAAGCTCA 59.963 37.500 0.00 0.00 0.00 4.26
2727 2835 3.831715 ATAGAAAAACGGCAAGCTCAC 57.168 42.857 0.00 0.00 0.00 3.51
2728 2836 1.388547 AGAAAAACGGCAAGCTCACA 58.611 45.000 0.00 0.00 0.00 3.58
2729 2837 1.065551 AGAAAAACGGCAAGCTCACAC 59.934 47.619 0.00 0.00 0.00 3.82
2730 2838 0.814457 AAAAACGGCAAGCTCACACA 59.186 45.000 0.00 0.00 0.00 3.72
2731 2839 0.381801 AAAACGGCAAGCTCACACAG 59.618 50.000 0.00 0.00 0.00 3.66
2732 2840 0.463654 AAACGGCAAGCTCACACAGA 60.464 50.000 0.00 0.00 0.00 3.41
2741 2849 2.229039 CTCACACAGAGCCACAACG 58.771 57.895 0.00 0.00 37.59 4.10
2742 2850 1.835483 CTCACACAGAGCCACAACGC 61.835 60.000 0.00 0.00 37.59 4.84
2743 2851 2.591715 ACACAGAGCCACAACGCC 60.592 61.111 0.00 0.00 0.00 5.68
2744 2852 2.591429 CACAGAGCCACAACGCCA 60.591 61.111 0.00 0.00 0.00 5.69
2745 2853 2.186160 CACAGAGCCACAACGCCAA 61.186 57.895 0.00 0.00 0.00 4.52
2746 2854 1.893808 ACAGAGCCACAACGCCAAG 60.894 57.895 0.00 0.00 0.00 3.61
2747 2855 1.597854 CAGAGCCACAACGCCAAGA 60.598 57.895 0.00 0.00 0.00 3.02
2748 2856 1.148273 AGAGCCACAACGCCAAGAA 59.852 52.632 0.00 0.00 0.00 2.52
2749 2857 1.166531 AGAGCCACAACGCCAAGAAC 61.167 55.000 0.00 0.00 0.00 3.01
2750 2858 1.444119 GAGCCACAACGCCAAGAACA 61.444 55.000 0.00 0.00 0.00 3.18
2751 2859 1.034838 AGCCACAACGCCAAGAACAA 61.035 50.000 0.00 0.00 0.00 2.83
2752 2860 0.179124 GCCACAACGCCAAGAACAAA 60.179 50.000 0.00 0.00 0.00 2.83
2753 2861 1.737363 GCCACAACGCCAAGAACAAAA 60.737 47.619 0.00 0.00 0.00 2.44
2754 2862 2.192624 CCACAACGCCAAGAACAAAAG 58.807 47.619 0.00 0.00 0.00 2.27
2755 2863 2.192624 CACAACGCCAAGAACAAAAGG 58.807 47.619 0.00 0.00 0.00 3.11
2756 2864 1.208259 CAACGCCAAGAACAAAAGGC 58.792 50.000 0.00 0.00 43.61 4.35
2757 2865 0.104120 AACGCCAAGAACAAAAGGCC 59.896 50.000 0.00 0.00 44.18 5.19
2758 2866 1.006220 CGCCAAGAACAAAAGGCCC 60.006 57.895 0.00 0.00 44.18 5.80
2759 2867 1.743321 CGCCAAGAACAAAAGGCCCA 61.743 55.000 0.00 0.00 44.18 5.36
2760 2868 0.467804 GCCAAGAACAAAAGGCCCAA 59.532 50.000 0.00 0.00 41.25 4.12
2761 2869 1.134250 GCCAAGAACAAAAGGCCCAAA 60.134 47.619 0.00 0.00 41.25 3.28
2762 2870 2.682269 GCCAAGAACAAAAGGCCCAAAA 60.682 45.455 0.00 0.00 41.25 2.44
2763 2871 3.205338 CCAAGAACAAAAGGCCCAAAAG 58.795 45.455 0.00 0.00 0.00 2.27
2764 2872 2.613595 CAAGAACAAAAGGCCCAAAAGC 59.386 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.392706 TCGCTCCACACAACTGACAT 59.607 50.000 0.00 0.00 0.00 3.06
113 122 1.194781 AAGCCCAGACACACCTCGAT 61.195 55.000 0.00 0.00 0.00 3.59
175 197 1.441311 CAACCTTTTGCGCTTGGGT 59.559 52.632 9.73 9.01 0.00 4.51
176 198 4.341827 CAACCTTTTGCGCTTGGG 57.658 55.556 9.73 8.32 0.00 4.12
189 211 1.136891 GCCATCACCCAAATAGCAACC 59.863 52.381 0.00 0.00 0.00 3.77
194 216 6.998074 TGATAAAGTAGCCATCACCCAAATAG 59.002 38.462 0.00 0.00 0.00 1.73
196 218 5.594317 GTGATAAAGTAGCCATCACCCAAAT 59.406 40.000 3.15 0.00 41.67 2.32
199 223 3.521531 TGTGATAAAGTAGCCATCACCCA 59.478 43.478 10.49 0.00 45.13 4.51
202 226 5.817296 TGTCATGTGATAAAGTAGCCATCAC 59.183 40.000 6.93 6.93 45.66 3.06
240 264 2.426023 GCCCACAGAGTCACCGTT 59.574 61.111 0.00 0.00 0.00 4.44
252 276 1.750778 CTTGTTGTCCATATGGCCCAC 59.249 52.381 17.58 8.51 34.44 4.61
258 282 2.036958 TCCGCCTTGTTGTCCATATG 57.963 50.000 0.00 0.00 0.00 1.78
281 305 8.443953 ACTTTAGAAAATAGACTCATGGATGC 57.556 34.615 0.00 0.00 0.00 3.91
301 325 5.123820 GCATATGTGTGGCAAGAGAACTTTA 59.876 40.000 4.29 0.00 33.70 1.85
325 349 5.509716 TCAGCAATAAGGCATTGAATGAG 57.490 39.130 9.76 0.00 45.99 2.90
337 361 5.571784 TTGCTCTCCAATTCAGCAATAAG 57.428 39.130 1.48 0.00 45.91 1.73
358 382 3.706594 TCGGTCTAGGAGCATTCTTGATT 59.293 43.478 0.00 0.00 0.00 2.57
370 394 3.047115 AGTAGGTCTCATCGGTCTAGGA 58.953 50.000 0.00 0.00 0.00 2.94
399 423 2.952978 ACCTTGTGCAACCGAACATTTA 59.047 40.909 0.00 0.00 34.36 1.40
410 434 1.435515 GCGTCCAAACCTTGTGCAA 59.564 52.632 0.00 0.00 0.00 4.08
416 440 1.375326 GAGGAGGCGTCCAAACCTT 59.625 57.895 26.40 5.24 46.80 3.50
438 462 7.279981 CGTTCACATTGATCTTAAACATCCCTA 59.720 37.037 0.00 0.00 0.00 3.53
516 540 2.224769 CCCTAAGTGAAGGCCTTGTCAA 60.225 50.000 26.25 2.29 35.09 3.18
607 635 0.771127 AGGTCTTGGGCAAGTGCTTA 59.229 50.000 2.85 0.00 41.70 3.09
632 660 8.874744 AGTGAGCCATGCTTTATATCATTAAT 57.125 30.769 0.00 0.00 39.88 1.40
633 661 9.440773 CTAGTGAGCCATGCTTTATATCATTAA 57.559 33.333 0.00 0.00 39.88 1.40
634 662 8.043113 CCTAGTGAGCCATGCTTTATATCATTA 58.957 37.037 0.00 0.00 39.88 1.90
657 724 1.412710 CTATTGTGCCGCTCTTCCCTA 59.587 52.381 0.00 0.00 0.00 3.53
666 733 2.346803 TCTCTTGAACTATTGTGCCGC 58.653 47.619 0.00 0.00 0.00 6.53
752 820 9.634163 CGAAAAATTAACCAAGCTATAAGGTTT 57.366 29.630 15.22 5.53 42.72 3.27
755 823 7.768240 ACCGAAAAATTAACCAAGCTATAAGG 58.232 34.615 0.00 0.00 0.00 2.69
758 826 9.016438 AGAAACCGAAAAATTAACCAAGCTATA 57.984 29.630 0.00 0.00 0.00 1.31
786 854 0.530288 CAAATGGCAACCCCGGTTAG 59.470 55.000 0.00 0.00 36.46 2.34
802 870 3.712016 TGTGAATAGCCTAGCCACAAA 57.288 42.857 6.53 0.00 35.16 2.83
818 886 3.896888 AGAATGCAAAAAGGGTCATGTGA 59.103 39.130 0.00 0.00 0.00 3.58
835 903 9.709495 TTGAATAATTGGGAAGTTCAAAGAATG 57.291 29.630 5.01 0.00 36.27 2.67
877 946 9.090103 CTTTAGGATCTCCCTTTTTAGGTTTTT 57.910 33.333 0.00 0.00 44.85 1.94
878 947 8.453681 TCTTTAGGATCTCCCTTTTTAGGTTTT 58.546 33.333 0.00 0.00 44.85 2.43
879 948 7.996788 TCTTTAGGATCTCCCTTTTTAGGTTT 58.003 34.615 0.00 0.00 44.85 3.27
880 949 7.584396 TCTTTAGGATCTCCCTTTTTAGGTT 57.416 36.000 0.00 0.00 44.85 3.50
881 950 7.584396 TTCTTTAGGATCTCCCTTTTTAGGT 57.416 36.000 0.00 0.00 44.85 3.08
882 951 8.879427 TTTTCTTTAGGATCTCCCTTTTTAGG 57.121 34.615 0.00 0.00 44.85 2.69
905 974 6.824196 TGCCGAAATTTCCTTTTTAGGTTTTT 59.176 30.769 12.54 0.00 33.07 1.94
906 975 6.350103 TGCCGAAATTTCCTTTTTAGGTTTT 58.650 32.000 12.54 0.00 33.07 2.43
907 976 5.919755 TGCCGAAATTTCCTTTTTAGGTTT 58.080 33.333 12.54 0.00 33.07 3.27
908 977 5.538118 CTGCCGAAATTTCCTTTTTAGGTT 58.462 37.500 12.54 0.00 33.07 3.50
909 978 4.560716 GCTGCCGAAATTTCCTTTTTAGGT 60.561 41.667 12.54 0.00 33.07 3.08
910 979 3.926527 GCTGCCGAAATTTCCTTTTTAGG 59.073 43.478 12.54 7.07 33.49 2.69
911 980 3.608073 CGCTGCCGAAATTTCCTTTTTAG 59.392 43.478 12.54 4.39 36.29 1.85
912 981 3.570559 CGCTGCCGAAATTTCCTTTTTA 58.429 40.909 12.54 0.00 36.29 1.52
913 982 2.403259 CGCTGCCGAAATTTCCTTTTT 58.597 42.857 12.54 0.00 36.29 1.94
914 983 1.336795 CCGCTGCCGAAATTTCCTTTT 60.337 47.619 12.54 0.00 36.29 2.27
915 984 0.243636 CCGCTGCCGAAATTTCCTTT 59.756 50.000 12.54 0.00 36.29 3.11
916 985 0.608035 TCCGCTGCCGAAATTTCCTT 60.608 50.000 12.54 0.00 36.29 3.36
917 986 0.608035 TTCCGCTGCCGAAATTTCCT 60.608 50.000 12.54 0.00 36.29 3.36
918 987 0.179163 CTTCCGCTGCCGAAATTTCC 60.179 55.000 12.54 0.25 36.29 3.13
919 988 0.798389 GCTTCCGCTGCCGAAATTTC 60.798 55.000 8.20 8.20 36.29 2.17
920 989 1.212751 GCTTCCGCTGCCGAAATTT 59.787 52.632 5.04 0.00 36.29 1.82
921 990 2.700773 GGCTTCCGCTGCCGAAATT 61.701 57.895 5.04 0.00 41.03 1.82
922 991 3.134127 GGCTTCCGCTGCCGAAAT 61.134 61.111 5.04 0.00 41.03 2.17
928 997 1.514873 CGAAAATGGCTTCCGCTGC 60.515 57.895 0.00 0.00 36.09 5.25
929 998 1.514873 GCGAAAATGGCTTCCGCTG 60.515 57.895 0.00 0.00 36.09 5.18
930 999 1.315257 ATGCGAAAATGGCTTCCGCT 61.315 50.000 0.00 0.00 36.09 5.52
931 1000 0.867329 GATGCGAAAATGGCTTCCGC 60.867 55.000 0.00 0.00 0.00 5.54
932 1001 0.589729 CGATGCGAAAATGGCTTCCG 60.590 55.000 0.00 0.00 32.65 4.30
933 1002 0.248621 CCGATGCGAAAATGGCTTCC 60.249 55.000 0.00 0.00 32.65 3.46
934 1003 0.451783 ACCGATGCGAAAATGGCTTC 59.548 50.000 0.00 0.00 0.00 3.86
935 1004 0.887933 AACCGATGCGAAAATGGCTT 59.112 45.000 0.00 0.00 0.00 4.35
936 1005 0.171007 CAACCGATGCGAAAATGGCT 59.829 50.000 0.00 0.00 0.00 4.75
937 1006 0.801836 CCAACCGATGCGAAAATGGC 60.802 55.000 0.00 0.00 0.00 4.40
938 1007 0.801836 GCCAACCGATGCGAAAATGG 60.802 55.000 0.00 0.00 0.00 3.16
939 1008 2.652548 GCCAACCGATGCGAAAATG 58.347 52.632 0.00 0.00 0.00 2.32
946 1015 2.804931 GCAAACGCCAACCGATGC 60.805 61.111 0.00 0.00 42.42 3.91
947 1016 1.729131 GTGCAAACGCCAACCGATG 60.729 57.895 0.00 0.00 41.02 3.84
948 1017 1.896660 AGTGCAAACGCCAACCGAT 60.897 52.632 0.00 0.00 41.02 4.18
949 1018 2.515057 AGTGCAAACGCCAACCGA 60.515 55.556 0.00 0.00 41.02 4.69
950 1019 2.353376 CAGTGCAAACGCCAACCG 60.353 61.111 0.00 0.00 44.21 4.44
951 1020 2.658268 GCAGTGCAAACGCCAACC 60.658 61.111 11.09 0.00 0.00 3.77
952 1021 2.103934 TGCAGTGCAAACGCCAAC 59.896 55.556 17.26 0.00 34.76 3.77
953 1022 2.103934 GTGCAGTGCAAACGCCAA 59.896 55.556 21.67 0.00 41.47 4.52
954 1023 3.898509 GGTGCAGTGCAAACGCCA 61.899 61.111 21.67 0.00 41.47 5.69
955 1024 4.645921 GGGTGCAGTGCAAACGCC 62.646 66.667 21.67 16.57 41.47 5.68
956 1025 3.595758 AGGGTGCAGTGCAAACGC 61.596 61.111 21.67 16.54 41.47 4.84
957 1026 2.332514 CAGGGTGCAGTGCAAACG 59.667 61.111 21.67 4.99 41.47 3.60
958 1027 2.028043 GCAGGGTGCAGTGCAAAC 59.972 61.111 21.67 15.74 44.26 2.93
1112 1181 0.462759 CCACCTGAGGAGGAAATCGC 60.463 60.000 9.60 0.00 42.93 4.58
1193 1262 3.927555 GGTCATGGTGTCCGAGAAA 57.072 52.632 0.00 0.00 0.00 2.52
1287 1359 4.821589 GAGGAAGTCCAGCGCCGG 62.822 72.222 2.25 2.25 38.89 6.13
1781 1865 1.540267 GCGAACACACTACAGAGAGGA 59.460 52.381 0.00 0.00 0.00 3.71
1877 1961 0.878416 GGCAGGAACACATTGCGTTA 59.122 50.000 0.00 0.00 38.69 3.18
1891 1975 2.082231 CATGTGTTCTTCTCTGGCAGG 58.918 52.381 15.73 5.63 0.00 4.85
1894 1978 2.079925 GTCCATGTGTTCTTCTCTGGC 58.920 52.381 0.00 0.00 0.00 4.85
1996 2080 4.878397 ACAGATTACAACCTAGCATGAAGC 59.122 41.667 0.00 0.00 46.19 3.86
2113 2206 0.109597 CCAATCAACACTGCTTCGCC 60.110 55.000 0.00 0.00 0.00 5.54
2129 2222 8.954350 GTCGTATACCTTAATCTATCTAGCCAA 58.046 37.037 0.00 0.00 0.00 4.52
2285 2388 8.602328 CATCTAGTCTGACAGATTTTGAACATC 58.398 37.037 8.73 0.00 28.88 3.06
2478 2586 1.743394 GACACTTATTTTGGGGCGGAG 59.257 52.381 0.00 0.00 0.00 4.63
2479 2587 1.353022 AGACACTTATTTTGGGGCGGA 59.647 47.619 0.00 0.00 0.00 5.54
2480 2588 1.743394 GAGACACTTATTTTGGGGCGG 59.257 52.381 0.00 0.00 0.00 6.13
2481 2589 2.432444 TGAGACACTTATTTTGGGGCG 58.568 47.619 0.00 0.00 0.00 6.13
2482 2590 5.047377 TCAATTGAGACACTTATTTTGGGGC 60.047 40.000 3.38 0.00 0.00 5.80
2484 2592 7.452880 TCTCAATTGAGACACTTATTTTGGG 57.547 36.000 30.05 4.19 45.48 4.12
2498 2606 7.308435 GTCCCAAAATAAGTGTCTCAATTGAG 58.692 38.462 26.56 26.56 43.36 3.02
2499 2607 6.072728 CGTCCCAAAATAAGTGTCTCAATTGA 60.073 38.462 8.12 8.12 0.00 2.57
2500 2608 6.086222 CGTCCCAAAATAAGTGTCTCAATTG 58.914 40.000 0.00 0.00 0.00 2.32
2501 2609 5.183140 CCGTCCCAAAATAAGTGTCTCAATT 59.817 40.000 0.00 0.00 0.00 2.32
2607 2715 2.488347 CCGGGGAGTCCTCTTTTCAAAA 60.488 50.000 7.64 0.00 0.00 2.44
2608 2716 1.073284 CCGGGGAGTCCTCTTTTCAAA 59.927 52.381 7.64 0.00 0.00 2.69
2609 2717 0.690762 CCGGGGAGTCCTCTTTTCAA 59.309 55.000 7.64 0.00 0.00 2.69
2610 2718 1.838073 GCCGGGGAGTCCTCTTTTCA 61.838 60.000 7.64 0.00 0.00 2.69
2611 2719 1.078356 GCCGGGGAGTCCTCTTTTC 60.078 63.158 7.64 0.00 0.00 2.29
2612 2720 2.603652 GGCCGGGGAGTCCTCTTTT 61.604 63.158 7.64 0.00 0.00 2.27
2613 2721 3.009714 GGCCGGGGAGTCCTCTTT 61.010 66.667 7.64 0.00 0.00 2.52
2614 2722 3.986116 GAGGCCGGGGAGTCCTCTT 62.986 68.421 15.62 0.00 42.31 2.85
2615 2723 4.467107 GAGGCCGGGGAGTCCTCT 62.467 72.222 15.62 0.00 42.31 3.69
2616 2724 4.467107 AGAGGCCGGGGAGTCCTC 62.467 72.222 15.22 15.22 45.11 3.71
2617 2725 4.787280 CAGAGGCCGGGGAGTCCT 62.787 72.222 9.58 0.00 0.00 3.85
2621 2729 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
2623 2731 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
2624 2732 3.035173 TTCTGATGCAGAGGCCGGG 62.035 63.158 2.18 0.00 41.75 5.73
2625 2733 1.817099 GTTCTGATGCAGAGGCCGG 60.817 63.158 0.00 0.00 41.75 6.13
2626 2734 2.169789 CGTTCTGATGCAGAGGCCG 61.170 63.158 0.00 0.00 41.75 6.13
2627 2735 0.179062 ATCGTTCTGATGCAGAGGCC 60.179 55.000 0.00 0.00 41.75 5.19
2628 2736 3.376218 ATCGTTCTGATGCAGAGGC 57.624 52.632 0.00 0.00 41.75 4.70
2636 2744 2.224597 TGGCCATATGCATCGTTCTGAT 60.225 45.455 0.00 0.00 43.89 2.90
2637 2745 1.140652 TGGCCATATGCATCGTTCTGA 59.859 47.619 0.00 0.00 43.89 3.27
2638 2746 1.265095 GTGGCCATATGCATCGTTCTG 59.735 52.381 9.72 0.00 43.89 3.02
2639 2747 1.134128 TGTGGCCATATGCATCGTTCT 60.134 47.619 9.72 0.00 43.89 3.01
2640 2748 1.308047 TGTGGCCATATGCATCGTTC 58.692 50.000 9.72 0.00 43.89 3.95
2641 2749 1.985473 ATGTGGCCATATGCATCGTT 58.015 45.000 15.06 0.00 43.89 3.85
2642 2750 1.985473 AATGTGGCCATATGCATCGT 58.015 45.000 16.59 0.00 43.89 3.73
2643 2751 4.707030 ATAAATGTGGCCATATGCATCG 57.293 40.909 16.59 0.00 43.89 3.84
2644 2752 7.578310 ATCTATAAATGTGGCCATATGCATC 57.422 36.000 16.59 0.00 43.89 3.91
2645 2753 9.478238 TTTATCTATAAATGTGGCCATATGCAT 57.522 29.630 16.59 13.83 43.89 3.96
2646 2754 8.876303 TTTATCTATAAATGTGGCCATATGCA 57.124 30.769 16.59 5.92 43.89 3.96
2651 2759 9.082313 CCTCTTTTTATCTATAAATGTGGCCAT 57.918 33.333 9.72 0.00 32.78 4.40
2652 2760 8.058847 ACCTCTTTTTATCTATAAATGTGGCCA 58.941 33.333 0.00 0.00 32.78 5.36
2653 2761 8.465273 ACCTCTTTTTATCTATAAATGTGGCC 57.535 34.615 0.00 0.00 32.78 5.36
2654 2762 9.952188 GAACCTCTTTTTATCTATAAATGTGGC 57.048 33.333 12.17 0.00 32.78 5.01
2663 2771 9.232473 GACCTTGTTGAACCTCTTTTTATCTAT 57.768 33.333 0.00 0.00 0.00 1.98
2664 2772 8.437575 AGACCTTGTTGAACCTCTTTTTATCTA 58.562 33.333 0.00 0.00 0.00 1.98
2665 2773 7.290813 AGACCTTGTTGAACCTCTTTTTATCT 58.709 34.615 0.00 0.00 0.00 1.98
2666 2774 7.511959 AGACCTTGTTGAACCTCTTTTTATC 57.488 36.000 0.00 0.00 0.00 1.75
2667 2775 7.898014 AAGACCTTGTTGAACCTCTTTTTAT 57.102 32.000 0.00 0.00 0.00 1.40
2668 2776 8.810990 TTAAGACCTTGTTGAACCTCTTTTTA 57.189 30.769 0.00 0.00 0.00 1.52
2669 2777 7.147897 CCTTAAGACCTTGTTGAACCTCTTTTT 60.148 37.037 3.36 0.00 0.00 1.94
2670 2778 6.321435 CCTTAAGACCTTGTTGAACCTCTTTT 59.679 38.462 3.36 0.00 0.00 2.27
2671 2779 5.828328 CCTTAAGACCTTGTTGAACCTCTTT 59.172 40.000 3.36 0.00 0.00 2.52
2672 2780 5.104067 ACCTTAAGACCTTGTTGAACCTCTT 60.104 40.000 3.36 0.00 0.00 2.85
2673 2781 4.412528 ACCTTAAGACCTTGTTGAACCTCT 59.587 41.667 3.36 0.00 0.00 3.69
2674 2782 4.715713 ACCTTAAGACCTTGTTGAACCTC 58.284 43.478 3.36 0.00 0.00 3.85
2675 2783 4.412528 AGACCTTAAGACCTTGTTGAACCT 59.587 41.667 3.36 0.00 0.00 3.50
2676 2784 4.715713 AGACCTTAAGACCTTGTTGAACC 58.284 43.478 3.36 0.00 0.00 3.62
2677 2785 5.820947 TCAAGACCTTAAGACCTTGTTGAAC 59.179 40.000 23.67 0.00 37.74 3.18
2678 2786 5.996644 TCAAGACCTTAAGACCTTGTTGAA 58.003 37.500 23.67 11.25 37.74 2.69
2679 2787 5.623956 TCAAGACCTTAAGACCTTGTTGA 57.376 39.130 23.67 14.36 37.74 3.18
2680 2788 6.094881 TGTTTCAAGACCTTAAGACCTTGTTG 59.905 38.462 23.67 12.93 37.74 3.33
2681 2789 6.184789 TGTTTCAAGACCTTAAGACCTTGTT 58.815 36.000 23.67 4.32 37.74 2.83
2682 2790 5.751586 TGTTTCAAGACCTTAAGACCTTGT 58.248 37.500 23.67 8.31 37.74 3.16
2683 2791 6.693315 TTGTTTCAAGACCTTAAGACCTTG 57.307 37.500 21.05 21.05 37.82 3.61
2684 2792 7.898014 ATTTGTTTCAAGACCTTAAGACCTT 57.102 32.000 3.36 3.90 0.00 3.50
2685 2793 8.437575 TCTATTTGTTTCAAGACCTTAAGACCT 58.562 33.333 3.36 0.00 0.00 3.85
2686 2794 8.617290 TCTATTTGTTTCAAGACCTTAAGACC 57.383 34.615 3.36 0.00 0.00 3.85
2691 2799 9.724839 CGTTTTTCTATTTGTTTCAAGACCTTA 57.275 29.630 0.00 0.00 0.00 2.69
2692 2800 7.704899 CCGTTTTTCTATTTGTTTCAAGACCTT 59.295 33.333 0.00 0.00 0.00 3.50
2693 2801 7.200455 CCGTTTTTCTATTTGTTTCAAGACCT 58.800 34.615 0.00 0.00 0.00 3.85
2694 2802 6.074516 GCCGTTTTTCTATTTGTTTCAAGACC 60.075 38.462 0.00 0.00 0.00 3.85
2695 2803 6.474102 TGCCGTTTTTCTATTTGTTTCAAGAC 59.526 34.615 0.00 0.00 0.00 3.01
2696 2804 6.565234 TGCCGTTTTTCTATTTGTTTCAAGA 58.435 32.000 0.00 0.00 0.00 3.02
2697 2805 6.820470 TGCCGTTTTTCTATTTGTTTCAAG 57.180 33.333 0.00 0.00 0.00 3.02
2698 2806 6.237969 GCTTGCCGTTTTTCTATTTGTTTCAA 60.238 34.615 0.00 0.00 0.00 2.69
2699 2807 5.233263 GCTTGCCGTTTTTCTATTTGTTTCA 59.767 36.000 0.00 0.00 0.00 2.69
2700 2808 5.462068 AGCTTGCCGTTTTTCTATTTGTTTC 59.538 36.000 0.00 0.00 0.00 2.78
2701 2809 5.356426 AGCTTGCCGTTTTTCTATTTGTTT 58.644 33.333 0.00 0.00 0.00 2.83
2702 2810 4.944048 AGCTTGCCGTTTTTCTATTTGTT 58.056 34.783 0.00 0.00 0.00 2.83
2703 2811 4.037446 TGAGCTTGCCGTTTTTCTATTTGT 59.963 37.500 0.00 0.00 0.00 2.83
2704 2812 4.382754 GTGAGCTTGCCGTTTTTCTATTTG 59.617 41.667 0.00 0.00 0.00 2.32
2705 2813 4.037446 TGTGAGCTTGCCGTTTTTCTATTT 59.963 37.500 0.00 0.00 0.00 1.40
2706 2814 3.568007 TGTGAGCTTGCCGTTTTTCTATT 59.432 39.130 0.00 0.00 0.00 1.73
2707 2815 3.058224 GTGTGAGCTTGCCGTTTTTCTAT 60.058 43.478 0.00 0.00 0.00 1.98
2708 2816 2.289547 GTGTGAGCTTGCCGTTTTTCTA 59.710 45.455 0.00 0.00 0.00 2.10
2709 2817 1.065551 GTGTGAGCTTGCCGTTTTTCT 59.934 47.619 0.00 0.00 0.00 2.52
2710 2818 1.202245 TGTGTGAGCTTGCCGTTTTTC 60.202 47.619 0.00 0.00 0.00 2.29
2711 2819 0.814457 TGTGTGAGCTTGCCGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
2712 2820 0.381801 CTGTGTGAGCTTGCCGTTTT 59.618 50.000 0.00 0.00 0.00 2.43
2713 2821 0.463654 TCTGTGTGAGCTTGCCGTTT 60.464 50.000 0.00 0.00 0.00 3.60
2714 2822 0.882042 CTCTGTGTGAGCTTGCCGTT 60.882 55.000 0.00 0.00 35.84 4.44
2715 2823 1.301244 CTCTGTGTGAGCTTGCCGT 60.301 57.895 0.00 0.00 35.84 5.68
2716 2824 3.559024 CTCTGTGTGAGCTTGCCG 58.441 61.111 0.00 0.00 35.84 5.69
2723 2831 1.835483 GCGTTGTGGCTCTGTGTGAG 61.835 60.000 0.00 0.00 45.33 3.51
2724 2832 1.887242 GCGTTGTGGCTCTGTGTGA 60.887 57.895 0.00 0.00 0.00 3.58
2725 2833 2.633657 GCGTTGTGGCTCTGTGTG 59.366 61.111 0.00 0.00 0.00 3.82
2726 2834 2.591715 GGCGTTGTGGCTCTGTGT 60.592 61.111 0.00 0.00 40.72 3.72
2727 2835 2.121564 CTTGGCGTTGTGGCTCTGTG 62.122 60.000 0.00 0.00 45.14 3.66
2728 2836 1.893808 CTTGGCGTTGTGGCTCTGT 60.894 57.895 0.00 0.00 45.14 3.41
2729 2837 1.165907 TTCTTGGCGTTGTGGCTCTG 61.166 55.000 0.00 0.00 45.14 3.35
2730 2838 1.148273 TTCTTGGCGTTGTGGCTCT 59.852 52.632 0.00 0.00 45.14 4.09
2731 2839 1.282875 GTTCTTGGCGTTGTGGCTC 59.717 57.895 0.00 0.00 45.14 4.70
2732 2840 1.034838 TTGTTCTTGGCGTTGTGGCT 61.035 50.000 0.00 0.00 45.14 4.75
2733 2841 0.179124 TTTGTTCTTGGCGTTGTGGC 60.179 50.000 0.00 0.00 45.12 5.01
2734 2842 2.192624 CTTTTGTTCTTGGCGTTGTGG 58.807 47.619 0.00 0.00 0.00 4.17
2735 2843 2.192624 CCTTTTGTTCTTGGCGTTGTG 58.807 47.619 0.00 0.00 0.00 3.33
2736 2844 1.470805 GCCTTTTGTTCTTGGCGTTGT 60.471 47.619 0.00 0.00 35.79 3.32
2737 2845 1.208259 GCCTTTTGTTCTTGGCGTTG 58.792 50.000 0.00 0.00 35.79 4.10
2738 2846 0.104120 GGCCTTTTGTTCTTGGCGTT 59.896 50.000 0.00 0.00 45.75 4.84
2739 2847 1.739667 GGCCTTTTGTTCTTGGCGT 59.260 52.632 0.00 0.00 45.75 5.68
2740 2848 1.006220 GGGCCTTTTGTTCTTGGCG 60.006 57.895 0.84 0.00 45.75 5.69
2741 2849 0.467804 TTGGGCCTTTTGTTCTTGGC 59.532 50.000 4.53 0.00 44.22 4.52
2742 2850 2.998316 TTTGGGCCTTTTGTTCTTGG 57.002 45.000 4.53 0.00 0.00 3.61
2743 2851 2.613595 GCTTTTGGGCCTTTTGTTCTTG 59.386 45.455 4.53 0.00 0.00 3.02
2744 2852 2.917933 GCTTTTGGGCCTTTTGTTCTT 58.082 42.857 4.53 0.00 0.00 2.52
2745 2853 2.620251 GCTTTTGGGCCTTTTGTTCT 57.380 45.000 4.53 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.