Multiple sequence alignment - TraesCS2D01G295500

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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 TraesCS2D01G295500 chr2D 100.000 4833 0 0 1 4833 377302470 377307302 0.000000e+00 8925.0
1 TraesCS2D01G295500 chr2D 82.234 394 42 5 2297 2663 377304559 377304951 1.010000e-81 315.0
2 TraesCS2D01G295500 chr2D 82.234 394 42 5 2090 2482 377304766 377305132 1.010000e-81 315.0
3 TraesCS2D01G295500 chr2D 96.748 123 3 1 3534 3656 441576668 441576789 2.280000e-48 204.0
4 TraesCS2D01G295500 chr2D 97.872 94 2 0 1912 2005 78690802 78690895 3.870000e-36 163.0
5 TraesCS2D01G295500 chr2A 95.241 2816 87 20 757 3541 511473993 511476792 0.000000e+00 4414.0
6 TraesCS2D01G295500 chr2A 94.876 683 16 7 3655 4320 511476791 511477471 0.000000e+00 1050.0
7 TraesCS2D01G295500 chr2A 87.476 519 31 17 4321 4833 511477537 511478027 7.020000e-158 568.0
8 TraesCS2D01G295500 chr2A 81.841 391 43 5 2297 2660 511475336 511475725 2.190000e-78 303.0
9 TraesCS2D01G295500 chr2A 91.892 74 6 0 4241 4314 511477602 511477675 2.380000e-18 104.0
10 TraesCS2D01G295500 chr2A 95.745 47 1 1 4167 4213 613445387 613445432 1.870000e-09 75.0
11 TraesCS2D01G295500 chr2B 89.378 2137 135 26 757 2830 448904578 448906685 0.000000e+00 2604.0
12 TraesCS2D01G295500 chr2B 87.340 782 68 16 1 756 776456256 776457032 0.000000e+00 867.0
13 TraesCS2D01G295500 chr2B 88.430 726 70 8 60 773 209818559 209817836 0.000000e+00 863.0
14 TraesCS2D01G295500 chr2B 89.355 620 42 10 2829 3438 448906767 448907372 0.000000e+00 758.0
15 TraesCS2D01G295500 chr2B 95.137 473 13 4 3655 4121 448907434 448907902 0.000000e+00 737.0
16 TraesCS2D01G295500 chr2B 89.169 397 42 1 2090 2485 448906126 448906522 1.210000e-135 494.0
17 TraesCS2D01G295500 chr2B 94.498 309 11 3 4527 4833 448908358 448908662 5.660000e-129 472.0
18 TraesCS2D01G295500 chr2B 84.712 399 41 9 2297 2676 448905928 448906325 9.820000e-102 381.0
19 TraesCS2D01G295500 chr2B 93.478 138 9 0 4321 4458 448908099 448908236 6.340000e-49 206.0
20 TraesCS2D01G295500 chr2B 90.741 54 4 1 4161 4214 340594077 340594129 2.410000e-08 71.3
21 TraesCS2D01G295500 chr5D 87.645 777 71 15 5 757 423231237 423232012 0.000000e+00 880.0
22 TraesCS2D01G295500 chr5D 94.059 101 5 1 1906 2005 509230388 509230288 8.380000e-33 152.0
23 TraesCS2D01G295500 chr7D 87.516 777 71 12 4 756 478799599 478798825 0.000000e+00 874.0
24 TraesCS2D01G295500 chr7D 87.261 785 73 14 4 763 611665577 611664795 0.000000e+00 870.0
25 TraesCS2D01G295500 chr7D 96.667 120 4 0 3537 3656 241094242 241094123 2.950000e-47 200.0
26 TraesCS2D01G295500 chr3B 86.967 798 76 14 1 771 708391982 708392778 0.000000e+00 872.0
27 TraesCS2D01G295500 chr3B 88.748 711 69 5 60 759 745557747 745557037 0.000000e+00 859.0
28 TraesCS2D01G295500 chr3B 85.696 783 86 8 1 758 554960775 554961556 0.000000e+00 802.0
29 TraesCS2D01G295500 chr3B 96.241 133 3 2 3529 3660 588418164 588418295 2.930000e-52 217.0
30 TraesCS2D01G295500 chr3B 93.878 49 2 1 1 49 621475245 621475198 6.710000e-09 73.1
31 TraesCS2D01G295500 chr1B 87.420 779 71 14 4 757 94009909 94009133 0.000000e+00 870.0
32 TraesCS2D01G295500 chr1B 85.806 782 83 15 1 756 72803528 72804307 0.000000e+00 804.0
33 TraesCS2D01G295500 chr1B 96.063 127 3 2 3533 3657 1210094 1210220 6.340000e-49 206.0
34 TraesCS2D01G295500 chr1B 97.500 120 3 0 3537 3656 330232929 330233048 6.340000e-49 206.0
35 TraesCS2D01G295500 chr1B 92.453 106 7 1 1900 2005 187205123 187205019 3.010000e-32 150.0
36 TraesCS2D01G295500 chr5B 86.658 772 84 11 1 756 699242139 699242907 0.000000e+00 837.0
37 TraesCS2D01G295500 chr4D 86.100 777 77 15 1 758 443712652 443713416 0.000000e+00 808.0
38 TraesCS2D01G295500 chr6B 85.640 773 81 7 4 747 29057409 29058180 0.000000e+00 785.0
39 TraesCS2D01G295500 chrUn 84.852 779 86 12 4 756 306535830 306535058 0.000000e+00 756.0
40 TraesCS2D01G295500 chr4B 83.949 785 99 12 1 759 668007075 668007858 0.000000e+00 726.0
41 TraesCS2D01G295500 chr4B 96.000 100 4 0 1906 2005 285616577 285616676 3.870000e-36 163.0
42 TraesCS2D01G295500 chr6D 96.154 130 4 1 3537 3666 348647457 348647329 1.360000e-50 211.0
43 TraesCS2D01G295500 chr6D 92.308 52 4 0 4155 4206 128910432 128910381 1.870000e-09 75.0
44 TraesCS2D01G295500 chr3D 99.145 117 1 0 3540 3656 337959625 337959509 1.360000e-50 211.0
45 TraesCS2D01G295500 chr3D 96.094 128 4 1 3539 3665 607000537 607000664 1.760000e-49 207.0
46 TraesCS2D01G295500 chr3D 95.745 47 2 0 4165 4211 609983848 609983802 5.190000e-10 76.8
47 TraesCS2D01G295500 chr7B 95.763 118 5 0 3540 3657 464726971 464726854 1.780000e-44 191.0
48 TraesCS2D01G295500 chr7B 89.474 57 3 3 1 57 716439647 716439700 8.680000e-08 69.4
49 TraesCS2D01G295500 chr5A 96.000 100 4 0 1906 2005 636426995 636426896 3.870000e-36 163.0
50 TraesCS2D01G295500 chr5A 95.918 49 1 1 915 963 502289476 502289429 1.440000e-10 78.7
51 TraesCS2D01G295500 chr1A 91.743 109 8 1 1897 2005 134962122 134962229 3.010000e-32 150.0
52 TraesCS2D01G295500 chr1A 93.878 49 3 0 4166 4214 347924299 347924251 1.870000e-09 75.0
53 TraesCS2D01G295500 chr1D 90.826 109 9 1 1897 2005 122838769 122838876 1.400000e-30 145.0
54 TraesCS2D01G295500 chr1D 92.308 52 4 0 4155 4206 343363389 343363440 1.870000e-09 75.0
55 TraesCS2D01G295500 chr1D 87.931 58 7 0 4155 4212 198281592 198281535 8.680000e-08 69.4
56 TraesCS2D01G295500 chr7A 81.176 85 11 2 4123 4205 330430299 330430218 4.040000e-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 TraesCS2D01G295500 chr2D 377302470 377307302 4832 False 3185.000000 8925 88.156000 1 4833 3 chr2D.!!$F3 4832
1 TraesCS2D01G295500 chr2A 511473993 511478027 4034 False 1287.800000 4414 90.265200 757 4833 5 chr2A.!!$F2 4076
2 TraesCS2D01G295500 chr2B 776456256 776457032 776 False 867.000000 867 87.340000 1 756 1 chr2B.!!$F2 755
3 TraesCS2D01G295500 chr2B 209817836 209818559 723 True 863.000000 863 88.430000 60 773 1 chr2B.!!$R1 713
4 TraesCS2D01G295500 chr2B 448904578 448908662 4084 False 807.428571 2604 90.818143 757 4833 7 chr2B.!!$F3 4076
5 TraesCS2D01G295500 chr5D 423231237 423232012 775 False 880.000000 880 87.645000 5 757 1 chr5D.!!$F1 752
6 TraesCS2D01G295500 chr7D 478798825 478799599 774 True 874.000000 874 87.516000 4 756 1 chr7D.!!$R2 752
7 TraesCS2D01G295500 chr7D 611664795 611665577 782 True 870.000000 870 87.261000 4 763 1 chr7D.!!$R3 759
8 TraesCS2D01G295500 chr3B 708391982 708392778 796 False 872.000000 872 86.967000 1 771 1 chr3B.!!$F3 770
9 TraesCS2D01G295500 chr3B 745557037 745557747 710 True 859.000000 859 88.748000 60 759 1 chr3B.!!$R2 699
10 TraesCS2D01G295500 chr3B 554960775 554961556 781 False 802.000000 802 85.696000 1 758 1 chr3B.!!$F1 757
11 TraesCS2D01G295500 chr1B 94009133 94009909 776 True 870.000000 870 87.420000 4 757 1 chr1B.!!$R1 753
12 TraesCS2D01G295500 chr1B 72803528 72804307 779 False 804.000000 804 85.806000 1 756 1 chr1B.!!$F2 755
13 TraesCS2D01G295500 chr5B 699242139 699242907 768 False 837.000000 837 86.658000 1 756 1 chr5B.!!$F1 755
14 TraesCS2D01G295500 chr4D 443712652 443713416 764 False 808.000000 808 86.100000 1 758 1 chr4D.!!$F1 757
15 TraesCS2D01G295500 chr6B 29057409 29058180 771 False 785.000000 785 85.640000 4 747 1 chr6B.!!$F1 743
16 TraesCS2D01G295500 chrUn 306535058 306535830 772 True 756.000000 756 84.852000 4 756 1 chrUn.!!$R1 752
17 TraesCS2D01G295500 chr4B 668007075 668007858 783 False 726.000000 726 83.949000 1 759 1 chr4B.!!$F2 758

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
660 694 0.379669 GGGCATTGATGTCAAGCTCG 59.620 55.000 13.11 0.00 39.47 5.03 F
1373 1442 0.454285 CCGTAACCAACTGCATTGCG 60.454 55.000 3.84 1.16 36.93 4.85 F
1637 1706 2.076863 GCGTTAACCATCTTGTGCTCT 58.923 47.619 0.00 0.00 0.00 4.09 F
3566 3787 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1761 4.009675 TGAAAGCCGTAATCTCTGCAAAT 58.990 39.130 0.00 0.0 0.00 2.32 R
3069 3274 2.564947 AGCAGGTGGTCAAAAACAAACA 59.435 40.909 0.00 0.0 0.00 2.83 R
3633 3854 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
4378 4701 0.541392 ATGAGCATGTCCGCCACTAA 59.459 50.000 0.00 0.0 0.00 2.24 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
45 46 3.920196 GTCGTCGGTGGTGGTGGT 61.920 66.667 0.00 0.00 0.00 4.16
147 171 2.550180 GGCGCTGGATAAAGATTCTTCC 59.450 50.000 7.64 0.00 0.00 3.46
160 184 1.952621 TTCTTCCGATCCTTCCCTGT 58.047 50.000 0.00 0.00 0.00 4.00
161 185 1.195115 TCTTCCGATCCTTCCCTGTG 58.805 55.000 0.00 0.00 0.00 3.66
221 246 4.593206 ACCAGTCTGTTCAAGTAAGGATGA 59.407 41.667 0.00 0.00 0.00 2.92
269 300 1.457831 GTATCCTCGGGCTCCACCT 60.458 63.158 0.00 0.00 39.10 4.00
285 316 1.085501 ACCTTTGCGACGACGTTTGT 61.086 50.000 9.33 0.00 41.98 2.83
317 348 0.984995 GTGGAGCTTGGGAGGTAGTT 59.015 55.000 0.00 0.00 32.79 2.24
330 361 3.366396 GAGGTAGTTCAGGAGTGGATGA 58.634 50.000 0.00 0.00 0.00 2.92
334 365 4.223032 GGTAGTTCAGGAGTGGATGAAGAA 59.777 45.833 0.00 0.00 36.16 2.52
398 429 1.674817 GGTTCGTGGTTCGTGGATGAT 60.675 52.381 0.00 0.00 40.80 2.45
442 473 3.229156 TTAGTCGTGGTGGGGTGCG 62.229 63.158 0.00 0.00 0.00 5.34
460 491 1.335182 GCGAGATCTGGAGTTCGATGA 59.665 52.381 9.17 0.00 35.19 2.92
462 493 2.356069 CGAGATCTGGAGTTCGATGACA 59.644 50.000 0.00 0.00 35.19 3.58
487 518 3.948719 GGTGTTGCCCCGACCTGA 61.949 66.667 0.00 0.00 0.00 3.86
497 531 1.609580 CCCCGACCTGATTCGTTCAAA 60.610 52.381 0.00 0.00 37.29 2.69
562 596 2.452295 CTGCATATCAGCGATGGAGT 57.548 50.000 0.00 0.00 37.81 3.85
579 613 3.057548 TCGCGTTGAGCTCGGGTA 61.058 61.111 9.64 0.00 45.59 3.69
649 683 2.359850 GCAGGTGACGGGCATTGA 60.360 61.111 2.86 0.00 35.87 2.57
660 694 0.379669 GGGCATTGATGTCAAGCTCG 59.620 55.000 13.11 0.00 39.47 5.03
665 699 3.751621 CATTGATGTCAAGCTCGGAAAC 58.248 45.455 1.65 0.00 39.47 2.78
669 703 6.309488 ATTGATGTCAAGCTCGGAAACGTTA 61.309 40.000 0.00 0.00 46.80 3.18
788 842 3.808728 TGATCTCTTATTGGGGCGAAAG 58.191 45.455 0.00 0.00 0.00 2.62
864 918 4.129148 AGAATTCCCGGCCCAGCC 62.129 66.667 0.65 0.00 46.75 4.85
991 1048 4.767255 GCACTCCCCGCCTGACAG 62.767 72.222 0.00 0.00 0.00 3.51
1207 1276 1.003866 GTTGCGCCTTGATTCGGTATC 60.004 52.381 4.18 0.00 0.00 2.24
1214 1283 4.494199 CGCCTTGATTCGGTATCTGTTTTC 60.494 45.833 0.00 0.00 34.17 2.29
1227 1296 0.869068 TGTTTTCGCCATGGTACGTG 59.131 50.000 14.67 0.00 0.00 4.49
1229 1298 1.579084 TTTTCGCCATGGTACGTGCC 61.579 55.000 16.68 16.68 0.00 5.01
1236 1305 2.409055 ATGGTACGTGCCGCGAGTA 61.409 57.895 18.26 3.47 44.77 2.59
1248 1317 2.851008 GCCGCGAGTAGAATTTTCATGC 60.851 50.000 8.23 0.00 0.00 4.06
1351 1420 3.251571 GACCAGGAGTTCATCAACGTAC 58.748 50.000 0.00 0.00 37.61 3.67
1353 1422 2.094906 CCAGGAGTTCATCAACGTACGA 60.095 50.000 24.41 0.00 37.61 3.43
1372 1441 0.596082 ACCGTAACCAACTGCATTGC 59.404 50.000 0.46 0.46 36.93 3.56
1373 1442 0.454285 CCGTAACCAACTGCATTGCG 60.454 55.000 3.84 1.16 36.93 4.85
1409 1478 2.159382 ACCCAATTTGCTTACACGAGG 58.841 47.619 0.00 0.00 0.00 4.63
1454 1523 3.302365 AATTCAGATTTTGGTGCACGG 57.698 42.857 11.45 0.00 0.00 4.94
1502 1571 3.244946 TGGTCGGGGATGTGATGTTTTTA 60.245 43.478 0.00 0.00 0.00 1.52
1637 1706 2.076863 GCGTTAACCATCTTGTGCTCT 58.923 47.619 0.00 0.00 0.00 4.09
1642 1711 2.175878 ACCATCTTGTGCTCTGTGAC 57.824 50.000 0.00 0.00 0.00 3.67
1652 1722 2.924290 GTGCTCTGTGACGGAAACTATC 59.076 50.000 0.00 0.00 0.00 2.08
1805 1888 2.182827 TCTGGACACATAGCTGCTCTT 58.817 47.619 4.91 0.00 0.00 2.85
2189 2281 8.487313 AATTATGCCTTATGCGAATACGATAA 57.513 30.769 0.00 0.00 45.60 1.75
2193 2285 7.520119 TGCCTTATGCGAATACGATAATAAG 57.480 36.000 0.00 0.00 45.60 1.73
2569 2690 4.614555 TGTAAATTATGCCTTGTGCGAG 57.385 40.909 0.00 0.00 45.60 5.03
2663 2784 2.681097 GCCCACTAACTCCATTGAGGAC 60.681 54.545 0.00 0.00 43.07 3.85
2684 2805 5.124936 GGACGATTTAGGGCTAACACATTTT 59.875 40.000 0.00 0.00 0.00 1.82
2783 2904 5.010282 CAGTATTGCTACCCTGTCCTTTTT 58.990 41.667 0.00 0.00 0.00 1.94
2998 3203 5.724370 TGGACTTGGTGATCTTAAGTATCCA 59.276 40.000 1.63 9.91 34.99 3.41
3113 3319 7.337689 TGCTAGTTTCATATGAACTGCTCATTT 59.662 33.333 17.76 0.00 42.46 2.32
3456 3671 2.658807 ACTCCCTCAGTCCCAAAAAC 57.341 50.000 0.00 0.00 0.00 2.43
3463 3678 3.891366 CCTCAGTCCCAAAAACAAGTGAT 59.109 43.478 0.00 0.00 0.00 3.06
3485 3700 8.870879 GTGATGTGGTTTTAGTTCAGTAGTATC 58.129 37.037 0.00 0.00 0.00 2.24
3495 3710 8.604640 TTAGTTCAGTAGTATCGATCTAGTGG 57.395 38.462 24.19 14.37 38.57 4.00
3498 3713 7.556996 AGTTCAGTAGTATCGATCTAGTGGTTT 59.443 37.037 24.19 14.77 38.57 3.27
3499 3714 7.876936 TCAGTAGTATCGATCTAGTGGTTTT 57.123 36.000 24.19 0.00 38.57 2.43
3500 3715 7.704271 TCAGTAGTATCGATCTAGTGGTTTTG 58.296 38.462 24.19 10.23 38.57 2.44
3501 3716 6.918569 CAGTAGTATCGATCTAGTGGTTTTGG 59.081 42.308 20.62 5.17 36.04 3.28
3502 3717 5.934402 AGTATCGATCTAGTGGTTTTGGT 57.066 39.130 0.00 0.00 0.00 3.67
3503 3718 6.295719 AGTATCGATCTAGTGGTTTTGGTT 57.704 37.500 0.00 0.00 0.00 3.67
3504 3719 6.338937 AGTATCGATCTAGTGGTTTTGGTTC 58.661 40.000 0.00 0.00 0.00 3.62
3505 3720 4.610605 TCGATCTAGTGGTTTTGGTTCA 57.389 40.909 0.00 0.00 0.00 3.18
3507 3722 4.039973 TCGATCTAGTGGTTTTGGTTCAGT 59.960 41.667 0.00 0.00 0.00 3.41
3548 3769 8.726870 TTAATGCAAACTGTAATACTACCTCC 57.273 34.615 0.00 0.00 0.00 4.30
3549 3770 4.751060 TGCAAACTGTAATACTACCTCCG 58.249 43.478 0.00 0.00 0.00 4.63
3550 3771 4.221262 TGCAAACTGTAATACTACCTCCGT 59.779 41.667 0.00 0.00 0.00 4.69
3551 3772 4.802563 GCAAACTGTAATACTACCTCCGTC 59.197 45.833 0.00 0.00 0.00 4.79
3552 3773 5.346522 CAAACTGTAATACTACCTCCGTCC 58.653 45.833 0.00 0.00 0.00 4.79
3553 3774 3.209410 ACTGTAATACTACCTCCGTCCG 58.791 50.000 0.00 0.00 0.00 4.79
3554 3775 2.551459 CTGTAATACTACCTCCGTCCGG 59.449 54.545 0.00 0.00 0.00 5.14
3555 3776 2.172505 TGTAATACTACCTCCGTCCGGA 59.827 50.000 0.00 0.00 42.90 5.14
3556 3777 2.442236 AATACTACCTCCGTCCGGAA 57.558 50.000 5.23 0.00 44.66 4.30
3557 3778 2.442236 ATACTACCTCCGTCCGGAAA 57.558 50.000 5.23 0.00 44.66 3.13
3558 3779 2.442236 TACTACCTCCGTCCGGAAAT 57.558 50.000 5.23 3.48 44.66 2.17
3559 3780 2.442236 ACTACCTCCGTCCGGAAATA 57.558 50.000 5.23 4.45 44.66 1.40
3560 3781 2.027385 ACTACCTCCGTCCGGAAATAC 58.973 52.381 5.23 0.00 44.66 1.89
3561 3782 2.305009 CTACCTCCGTCCGGAAATACT 58.695 52.381 5.23 0.00 44.66 2.12
3562 3783 1.565067 ACCTCCGTCCGGAAATACTT 58.435 50.000 5.23 0.00 44.66 2.24
3563 3784 1.206371 ACCTCCGTCCGGAAATACTTG 59.794 52.381 5.23 0.00 44.66 3.16
3564 3785 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3565 3786 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3566 3787 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3567 3788 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
3568 3789 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
3569 3790 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
3570 3791 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
3571 3792 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
3572 3793 5.163513 GTCCGGAAATACTTGTCGTAGAAA 58.836 41.667 5.23 0.00 39.69 2.52
3573 3794 5.809051 GTCCGGAAATACTTGTCGTAGAAAT 59.191 40.000 5.23 0.00 39.69 2.17
3574 3795 5.808540 TCCGGAAATACTTGTCGTAGAAATG 59.191 40.000 0.00 0.00 39.69 2.32
3575 3796 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
3576 3797 5.808540 CGGAAATACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
3577 3798 6.479001 CGGAAATACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
3578 3799 7.650504 CGGAAATACTTGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
3579 3800 8.762426 GGAAATACTTGTCGTAGAAATGGATAC 58.238 37.037 0.00 0.00 39.69 2.24
3628 3849 6.522625 ACATCTAGATACATCCATTCCTCG 57.477 41.667 4.54 0.00 0.00 4.63
3629 3850 5.420421 ACATCTAGATACATCCATTCCTCGG 59.580 44.000 4.54 0.00 0.00 4.63
3630 3851 5.256806 TCTAGATACATCCATTCCTCGGA 57.743 43.478 0.00 0.00 36.84 4.55
3631 3852 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
3632 3853 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
3633 3854 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
3634 3855 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
3635 3856 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
3636 3857 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
3637 3858 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
3638 3859 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
3639 3860 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
3640 3861 4.766375 TCCATTCCTCGGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
3641 3862 3.877508 CCATTCCTCGGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
3647 3868 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
3648 3869 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
3649 3870 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3650 3871 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3651 3872 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3652 3873 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3653 3874 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4060 4287 9.116067 CAATGGCTTTATTTGGAATTGATCATT 57.884 29.630 0.00 0.00 0.00 2.57
4095 4322 9.142515 CAAATTTTGATGCTGTGAAGCTAATTA 57.857 29.630 2.88 0.00 35.49 1.40
4096 4323 9.709495 AAATTTTGATGCTGTGAAGCTAATTAA 57.291 25.926 0.00 0.00 35.49 1.40
4134 4364 6.420913 AATGTTAATGCTACTACCTCCGAT 57.579 37.500 0.00 0.00 0.00 4.18
4139 4369 3.801307 TGCTACTACCTCCGATCCATA 57.199 47.619 0.00 0.00 0.00 2.74
4142 4372 4.523173 TGCTACTACCTCCGATCCATAAAG 59.477 45.833 0.00 0.00 0.00 1.85
4169 4413 5.824097 TGTAACCCCAGTTCAAAACTAGTTC 59.176 40.000 8.95 0.00 40.46 3.01
4177 4421 7.254421 CCCAGTTCAAAACTAGTTCAAAATTGC 60.254 37.037 8.95 0.00 40.46 3.56
4192 4436 6.507900 TCAAAATTGCGACACTTATTTTGGA 58.492 32.000 17.86 9.51 43.24 3.53
4195 4439 4.335082 TTGCGACACTTATTTTGGATCG 57.665 40.909 0.00 0.00 0.00 3.69
4202 4446 4.130118 CACTTATTTTGGATCGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
4207 4451 0.635009 TTGGATCGGAGGGAGTAGGT 59.365 55.000 0.00 0.00 0.00 3.08
4208 4452 0.635009 TGGATCGGAGGGAGTAGGTT 59.365 55.000 0.00 0.00 0.00 3.50
4258 4502 1.153289 GTGGCGGACATGCTCATCT 60.153 57.895 0.00 0.00 34.52 2.90
4340 4659 4.024472 GCCTGAGTCTTGTTGTTTCTCTTC 60.024 45.833 0.00 0.00 0.00 2.87
4378 4701 3.369157 GCGGTGGGAAATGTTAGTACTCT 60.369 47.826 0.00 0.00 0.00 3.24
4385 4708 5.816258 GGGAAATGTTAGTACTCTTAGTGGC 59.184 44.000 0.00 0.00 0.00 5.01
4501 4909 6.064717 AGTATCATGCCCCTTTTATCTGTTC 58.935 40.000 0.00 0.00 0.00 3.18
4502 4910 3.631250 TCATGCCCCTTTTATCTGTTCC 58.369 45.455 0.00 0.00 0.00 3.62
4503 4911 3.269381 TCATGCCCCTTTTATCTGTTCCT 59.731 43.478 0.00 0.00 0.00 3.36
4504 4912 4.476846 TCATGCCCCTTTTATCTGTTCCTA 59.523 41.667 0.00 0.00 0.00 2.94
4505 4913 5.134339 TCATGCCCCTTTTATCTGTTCCTAT 59.866 40.000 0.00 0.00 0.00 2.57
4506 4914 5.048846 TGCCCCTTTTATCTGTTCCTATC 57.951 43.478 0.00 0.00 0.00 2.08
4507 4915 4.476846 TGCCCCTTTTATCTGTTCCTATCA 59.523 41.667 0.00 0.00 0.00 2.15
4508 4916 5.134339 TGCCCCTTTTATCTGTTCCTATCAT 59.866 40.000 0.00 0.00 0.00 2.45
4509 4917 6.331572 TGCCCCTTTTATCTGTTCCTATCATA 59.668 38.462 0.00 0.00 0.00 2.15
4510 4918 7.018550 TGCCCCTTTTATCTGTTCCTATCATAT 59.981 37.037 0.00 0.00 0.00 1.78
4511 4919 7.554476 GCCCCTTTTATCTGTTCCTATCATATC 59.446 40.741 0.00 0.00 0.00 1.63
4512 4920 8.605947 CCCCTTTTATCTGTTCCTATCATATCA 58.394 37.037 0.00 0.00 0.00 2.15
4663 5080 1.152567 CTTGTTTGTGGGGGCCTCA 60.153 57.895 0.00 0.00 0.00 3.86
4757 5175 4.035558 TCGCTAAATTTATGCAGCTCCAAG 59.964 41.667 15.34 0.69 31.74 3.61
4804 5222 4.448060 GGTACTCTCTTCACCAACTTTTCG 59.552 45.833 0.00 0.00 32.32 3.46
4810 5228 4.505808 TCTTCACCAACTTTTCGTGTACA 58.494 39.130 0.00 0.00 0.00 2.90
4811 5229 4.936411 TCTTCACCAACTTTTCGTGTACAA 59.064 37.500 0.00 0.00 0.00 2.41
4812 5230 4.603231 TCACCAACTTTTCGTGTACAAC 57.397 40.909 0.00 0.00 0.00 3.32
4813 5231 4.001652 TCACCAACTTTTCGTGTACAACA 58.998 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 6.272558 AGACTACAAGGGAGTAAAAACTGGAT 59.727 38.462 0.00 0.00 0.00 3.41
57 59 7.097834 CCTAGACTACAAGGGAGTAAAAACTG 58.902 42.308 0.00 0.00 0.00 3.16
58 60 6.786461 ACCTAGACTACAAGGGAGTAAAAACT 59.214 38.462 0.00 0.00 37.18 2.66
147 171 1.826024 CCTCCACAGGGAAGGATCG 59.174 63.158 0.00 0.00 44.38 3.69
160 184 1.121407 CCATAGGACGATGGCCTCCA 61.121 60.000 11.14 0.00 40.08 3.86
161 185 1.674057 CCATAGGACGATGGCCTCC 59.326 63.158 3.32 1.59 40.08 4.30
269 300 0.026544 GGAACAAACGTCGTCGCAAA 59.973 50.000 0.00 0.00 41.18 3.68
285 316 3.263503 CTCCACGTCGACGCTGGAA 62.264 63.158 37.44 28.17 43.42 3.53
317 348 3.054875 CCACATTCTTCATCCACTCCTGA 60.055 47.826 0.00 0.00 0.00 3.86
330 361 8.288857 ATGTCGTCGATGTAGACCACATTCTT 62.289 42.308 4.21 0.00 45.86 2.52
442 473 4.202101 ACATGTCATCGAACTCCAGATCTC 60.202 45.833 0.00 0.00 0.00 2.75
460 491 2.282180 GCAACACCCCGGACATGT 60.282 61.111 0.73 0.00 0.00 3.21
482 513 4.216257 CCATTGTCTTTGAACGAATCAGGT 59.784 41.667 0.00 0.00 39.77 4.00
483 514 4.726416 CCATTGTCTTTGAACGAATCAGG 58.274 43.478 0.00 0.00 39.77 3.86
485 516 3.820467 AGCCATTGTCTTTGAACGAATCA 59.180 39.130 0.00 0.00 35.85 2.57
486 517 4.425577 AGCCATTGTCTTTGAACGAATC 57.574 40.909 0.00 0.00 0.00 2.52
487 518 4.278170 TGAAGCCATTGTCTTTGAACGAAT 59.722 37.500 0.00 0.00 0.00 3.34
497 531 4.828939 TCATCAAAAGTGAAGCCATTGTCT 59.171 37.500 0.00 0.00 37.30 3.41
562 596 2.537792 CTTACCCGAGCTCAACGCGA 62.538 60.000 15.93 0.00 45.31 5.87
568 602 0.970937 CACCTCCTTACCCGAGCTCA 60.971 60.000 15.40 0.00 0.00 4.26
579 613 2.472029 AGAATGACGGATCACCTCCTT 58.528 47.619 0.00 0.00 42.47 3.36
645 679 2.416547 CGTTTCCGAGCTTGACATCAAT 59.583 45.455 1.22 0.00 33.62 2.57
649 683 1.878953 AACGTTTCCGAGCTTGACAT 58.121 45.000 1.22 0.00 37.88 3.06
660 694 7.073342 ACTGAAAAGATAGCATAACGTTTCC 57.927 36.000 5.91 0.00 39.66 3.13
665 699 8.015087 TGACAAAACTGAAAAGATAGCATAACG 58.985 33.333 0.00 0.00 0.00 3.18
669 703 7.889469 ACATGACAAAACTGAAAAGATAGCAT 58.111 30.769 0.00 0.00 0.00 3.79
788 842 2.095372 GTGAAAAGCCCGTGTATGTAGC 59.905 50.000 0.00 0.00 0.00 3.58
1207 1276 1.136085 CACGTACCATGGCGAAAACAG 60.136 52.381 13.04 0.00 0.00 3.16
1227 1296 2.851008 GCATGAAAATTCTACTCGCGGC 60.851 50.000 6.13 0.00 0.00 6.53
1229 1298 2.029244 ACGCATGAAAATTCTACTCGCG 59.971 45.455 0.00 0.00 45.20 5.87
1231 1300 4.584029 ACACGCATGAAAATTCTACTCG 57.416 40.909 0.00 0.00 0.00 4.18
1236 1305 3.126858 ACGCATACACGCATGAAAATTCT 59.873 39.130 0.00 0.00 36.19 2.40
1248 1317 1.260206 GACACAGAGACGCATACACG 58.740 55.000 0.00 0.00 39.50 4.49
1351 1420 1.136085 CAATGCAGTTGGTTACGGTCG 60.136 52.381 0.00 0.00 34.06 4.79
1353 1422 0.596082 GCAATGCAGTTGGTTACGGT 59.404 50.000 0.00 0.00 38.29 4.83
1373 1442 1.341369 GGGTAAACAAACGCGCATGC 61.341 55.000 5.73 7.91 37.91 4.06
1375 1444 0.669077 TTGGGTAAACAAACGCGCAT 59.331 45.000 5.73 0.00 35.20 4.73
1390 1459 2.432444 TCCTCGTGTAAGCAAATTGGG 58.568 47.619 0.00 0.00 0.00 4.12
1409 1478 1.576421 CGGGCAGAGCACAGTTTTC 59.424 57.895 0.00 0.00 0.00 2.29
1502 1571 4.542697 AGTTACACCAAAAGGACACCATT 58.457 39.130 0.00 0.00 0.00 3.16
1652 1722 5.871531 GCATGTATGCGTTTTAGAAATGG 57.128 39.130 0.53 0.00 44.67 3.16
1678 1761 4.009675 TGAAAGCCGTAATCTCTGCAAAT 58.990 39.130 0.00 0.00 0.00 2.32
1805 1888 6.807230 GTCAGAGCTAGACGAATAGTTTCAAA 59.193 38.462 0.00 0.00 0.00 2.69
1861 1944 6.998074 TGACACAAAAGGATGAATACTTCACT 59.002 34.615 0.00 0.00 43.48 3.41
1864 1947 8.514594 TCATTGACACAAAAGGATGAATACTTC 58.485 33.333 0.00 0.00 28.61 3.01
1876 1959 5.996219 TGTCGGTATTCATTGACACAAAAG 58.004 37.500 0.00 0.00 36.50 2.27
1877 1960 6.567687 ATGTCGGTATTCATTGACACAAAA 57.432 33.333 0.00 0.00 43.42 2.44
2327 2421 6.747280 CCAAAAGATATAACAAAACTCCAGCG 59.253 38.462 0.00 0.00 0.00 5.18
2487 2602 5.941948 ACCACTGCAATGTTAACTCTTAC 57.058 39.130 7.22 0.00 0.00 2.34
2684 2805 9.747898 TTATAAGCAGAAGGGATACAAGAAAAA 57.252 29.630 0.00 0.00 39.74 1.94
2783 2904 5.273674 TGATGCAAAACCAGATCAAAACA 57.726 34.783 0.00 0.00 0.00 2.83
2998 3203 3.576078 TTGGTGACATCAGAAACCAGT 57.424 42.857 0.00 0.00 43.31 4.00
3061 3266 6.254804 GGTGGTCAAAAACAAACATCAGTAAC 59.745 38.462 0.00 0.00 0.00 2.50
3069 3274 2.564947 AGCAGGTGGTCAAAAACAAACA 59.435 40.909 0.00 0.00 0.00 2.83
3456 3671 6.377327 ACTGAACTAAAACCACATCACTTG 57.623 37.500 0.00 0.00 0.00 3.16
3463 3678 7.218228 TCGATACTACTGAACTAAAACCACA 57.782 36.000 0.00 0.00 0.00 4.17
3485 3700 4.315803 ACTGAACCAAAACCACTAGATCG 58.684 43.478 0.00 0.00 0.00 3.69
3495 3710 6.073385 GCTAACAGGTACTACTGAACCAAAAC 60.073 42.308 6.18 0.00 40.97 2.43
3498 3713 4.836736 AGCTAACAGGTACTACTGAACCAA 59.163 41.667 6.18 0.00 40.97 3.67
3499 3714 4.413760 AGCTAACAGGTACTACTGAACCA 58.586 43.478 6.18 0.00 40.97 3.67
3500 3715 6.712179 ATAGCTAACAGGTACTACTGAACC 57.288 41.667 0.00 0.00 40.97 3.62
3503 3718 8.358148 GCATTAATAGCTAACAGGTACTACTGA 58.642 37.037 0.00 0.00 40.97 3.41
3504 3719 8.141909 TGCATTAATAGCTAACAGGTACTACTG 58.858 37.037 0.00 0.00 44.03 2.74
3505 3720 8.246430 TGCATTAATAGCTAACAGGTACTACT 57.754 34.615 0.00 0.00 36.02 2.57
3507 3722 9.321562 GTTTGCATTAATAGCTAACAGGTACTA 57.678 33.333 20.56 0.00 43.73 1.82
3539 3760 2.442236 ATTTCCGGACGGAGGTAGTA 57.558 50.000 13.64 0.00 46.06 1.82
3540 3761 2.027385 GTATTTCCGGACGGAGGTAGT 58.973 52.381 13.64 0.00 46.06 2.73
3541 3762 2.305009 AGTATTTCCGGACGGAGGTAG 58.695 52.381 13.64 0.00 46.06 3.18
3542 3763 2.428171 CAAGTATTTCCGGACGGAGGTA 59.572 50.000 13.64 8.09 46.06 3.08
3543 3764 1.206371 CAAGTATTTCCGGACGGAGGT 59.794 52.381 13.64 9.03 46.06 3.85
3544 3765 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3545 3766 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3546 3767 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3547 3768 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3548 3769 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
3549 3770 4.361451 TCTACGACAAGTATTTCCGGAC 57.639 45.455 1.83 0.00 34.34 4.79
3550 3771 5.389859 TTTCTACGACAAGTATTTCCGGA 57.610 39.130 0.00 0.00 34.34 5.14
3551 3772 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
3552 3773 5.808540 TCCATTTCTACGACAAGTATTTCCG 59.191 40.000 0.00 0.00 34.34 4.30
3553 3774 7.787725 ATCCATTTCTACGACAAGTATTTCC 57.212 36.000 0.00 0.00 34.34 3.13
3554 3775 9.309516 TGTATCCATTTCTACGACAAGTATTTC 57.690 33.333 0.00 0.00 34.34 2.17
3555 3776 9.661563 TTGTATCCATTTCTACGACAAGTATTT 57.338 29.630 0.00 0.00 34.34 1.40
3556 3777 9.661563 TTTGTATCCATTTCTACGACAAGTATT 57.338 29.630 0.00 0.00 34.34 1.89
3557 3778 9.832445 ATTTGTATCCATTTCTACGACAAGTAT 57.168 29.630 0.00 0.00 34.34 2.12
3558 3779 9.093970 CATTTGTATCCATTTCTACGACAAGTA 57.906 33.333 0.00 0.00 0.00 2.24
3559 3780 7.065803 CCATTTGTATCCATTTCTACGACAAGT 59.934 37.037 0.00 0.00 0.00 3.16
3560 3781 7.279981 TCCATTTGTATCCATTTCTACGACAAG 59.720 37.037 0.00 0.00 0.00 3.16
3561 3782 7.106890 TCCATTTGTATCCATTTCTACGACAA 58.893 34.615 0.00 0.00 0.00 3.18
3562 3783 6.645306 TCCATTTGTATCCATTTCTACGACA 58.355 36.000 0.00 0.00 0.00 4.35
3563 3784 7.226720 ACATCCATTTGTATCCATTTCTACGAC 59.773 37.037 0.00 0.00 0.00 4.34
3564 3785 7.279615 ACATCCATTTGTATCCATTTCTACGA 58.720 34.615 0.00 0.00 0.00 3.43
3565 3786 7.496529 ACATCCATTTGTATCCATTTCTACG 57.503 36.000 0.00 0.00 0.00 3.51
3602 3823 8.690884 CGAGGAATGGATGTATCTAGATGTATT 58.309 37.037 15.79 6.57 0.00 1.89
3603 3824 7.286546 CCGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
3604 3825 6.603599 CCGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
3605 3826 5.420421 CCGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
3606 3827 5.654209 TCCGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
3607 3828 5.654650 GTCCGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 37.93 1.98
3608 3829 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
3609 3830 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
3610 3831 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
3611 3832 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
3612 3833 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
3613 3834 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
3614 3835 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
3615 3836 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
3616 3837 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
3617 3838 5.368989 GAAATACTTGTCCGAGGAATGGAT 58.631 41.667 0.00 0.00 37.93 3.41
3618 3839 4.383770 GGAAATACTTGTCCGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
3619 3840 3.877508 GGAAATACTTGTCCGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
3628 3849 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
3629 3850 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3630 3851 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3631 3852 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3632 3853 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3633 3854 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3634 3855 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3635 3856 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3636 3857 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3637 3858 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3638 3859 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3639 3860 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
3640 3861 0.104304 CAAATACTCCCTCCGTCCGG 59.896 60.000 0.00 0.00 0.00 5.14
3641 3862 1.108776 TCAAATACTCCCTCCGTCCG 58.891 55.000 0.00 0.00 0.00 4.79
3642 3863 4.150359 TCTATCAAATACTCCCTCCGTCC 58.850 47.826 0.00 0.00 0.00 4.79
3643 3864 5.786264 TTCTATCAAATACTCCCTCCGTC 57.214 43.478 0.00 0.00 0.00 4.79
3644 3865 6.408206 CCTTTTCTATCAAATACTCCCTCCGT 60.408 42.308 0.00 0.00 0.00 4.69
3645 3866 5.992217 CCTTTTCTATCAAATACTCCCTCCG 59.008 44.000 0.00 0.00 0.00 4.63
3646 3867 5.765677 GCCTTTTCTATCAAATACTCCCTCC 59.234 44.000 0.00 0.00 0.00 4.30
3647 3868 5.467063 CGCCTTTTCTATCAAATACTCCCTC 59.533 44.000 0.00 0.00 0.00 4.30
3648 3869 5.130477 TCGCCTTTTCTATCAAATACTCCCT 59.870 40.000 0.00 0.00 0.00 4.20
3649 3870 5.365619 TCGCCTTTTCTATCAAATACTCCC 58.634 41.667 0.00 0.00 0.00 4.30
3650 3871 7.656137 TGTATCGCCTTTTCTATCAAATACTCC 59.344 37.037 0.00 0.00 0.00 3.85
3651 3872 8.589335 TGTATCGCCTTTTCTATCAAATACTC 57.411 34.615 0.00 0.00 0.00 2.59
3652 3873 8.958119 TTGTATCGCCTTTTCTATCAAATACT 57.042 30.769 0.00 0.00 0.00 2.12
3653 3874 8.827677 ACTTGTATCGCCTTTTCTATCAAATAC 58.172 33.333 0.00 0.00 0.00 1.89
4060 4287 6.696583 CACAGCATCAAAATTTGTAACAGACA 59.303 34.615 5.56 0.00 35.78 3.41
4134 4364 4.172807 ACTGGGGTTACACTCTTTATGGA 58.827 43.478 0.00 0.00 0.00 3.41
4139 4369 4.513406 TTGAACTGGGGTTACACTCTTT 57.487 40.909 0.00 0.00 35.58 2.52
4142 4372 4.204799 AGTTTTGAACTGGGGTTACACTC 58.795 43.478 0.00 0.00 41.01 3.51
4169 4413 6.761731 TCCAAAATAAGTGTCGCAATTTTG 57.238 33.333 19.81 19.81 43.77 2.44
4177 4421 3.555956 CCTCCGATCCAAAATAAGTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
4244 4488 2.864946 CAGAAAGAGATGAGCATGTCCG 59.135 50.000 4.23 0.00 32.06 4.79
4323 4642 3.621715 ACACGGAAGAGAAACAACAAGAC 59.378 43.478 0.00 0.00 0.00 3.01
4340 4659 3.305964 CACCGCTATGTATTCTACACGG 58.694 50.000 11.18 11.18 45.67 4.94
4357 4676 4.467198 AGAGTACTAACATTTCCCACCG 57.533 45.455 0.00 0.00 0.00 4.94
4378 4701 0.541392 ATGAGCATGTCCGCCACTAA 59.459 50.000 0.00 0.00 0.00 2.24
4433 4756 1.019805 GTTAGCACCTTCCCGTCAGC 61.020 60.000 0.00 0.00 0.00 4.26
4438 4761 2.550978 CTACATGTTAGCACCTTCCCG 58.449 52.381 2.30 0.00 0.00 5.14
4552 4960 7.361201 CGCAAGAGAACCAAGAAGATTCATAAA 60.361 37.037 0.00 0.00 43.02 1.40
4739 5157 4.088634 TGGTCTTGGAGCTGCATAAATTT 58.911 39.130 9.39 0.00 0.00 1.82
4757 5175 9.178758 ACCTTGAACAAAATATAGAAGATGGTC 57.821 33.333 0.00 0.00 0.00 4.02
4804 5222 5.231357 GCTTTAAAGGCTGTTTGTTGTACAC 59.769 40.000 16.78 0.00 0.00 2.90
4810 5228 3.871006 GCTTGCTTTAAAGGCTGTTTGTT 59.129 39.130 16.78 0.00 0.00 2.83
4811 5229 3.457234 GCTTGCTTTAAAGGCTGTTTGT 58.543 40.909 16.78 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.