Multiple sequence alignment - TraesCS4B01G108700

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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 TraesCS4B01G108700 chr4B 100.000 3852 0 0 1 3852 119351676 119355527 0.000000e+00 7114.0
1 TraesCS4B01G108700 chr4B 91.667 72 2 1 1694 1761 119353299 119353370 3.170000e-16 97.1
2 TraesCS4B01G108700 chr4B 91.667 72 2 1 1624 1695 119353369 119353436 3.170000e-16 97.1
3 TraesCS4B01G108700 chr4D 93.247 3569 190 22 1 3531 84300735 84304290 0.000000e+00 5208.0
4 TraesCS4B01G108700 chr4D 95.833 72 3 0 1624 1695 84302439 84302510 2.430000e-22 117.0
5 TraesCS4B01G108700 chr4D 93.056 72 1 1 1694 1761 84302369 84302440 6.810000e-18 102.0
6 TraesCS4B01G108700 chr4A 90.312 1858 117 28 1694 3532 497075826 497077639 0.000000e+00 2375.0
7 TraesCS4B01G108700 chr4A 92.558 1626 96 12 90 1695 497074277 497075897 0.000000e+00 2309.0
8 TraesCS4B01G108700 chr4A 92.157 102 7 1 1 102 497030920 497031020 4.010000e-30 143.0
9 TraesCS4B01G108700 chr6B 97.326 187 5 0 3666 3852 678166423 678166609 6.210000e-83 318.0
10 TraesCS4B01G108700 chr6B 97.297 185 5 0 3668 3852 248543563 248543379 8.030000e-82 315.0
11 TraesCS4B01G108700 chr6B 97.312 186 4 1 3668 3852 423431310 423431125 8.030000e-82 315.0
12 TraesCS4B01G108700 chr5B 97.826 184 4 0 3669 3852 425631034 425631217 6.210000e-83 318.0
13 TraesCS4B01G108700 chr5B 97.312 186 4 1 3668 3852 574971946 574972131 8.030000e-82 315.0
14 TraesCS4B01G108700 chr5B 78.864 317 45 15 3138 3433 581171295 581171610 1.090000e-45 195.0
15 TraesCS4B01G108700 chr3B 97.838 185 3 1 3669 3852 343557540 343557724 6.210000e-83 318.0
16 TraesCS4B01G108700 chr3B 96.842 190 5 1 3664 3852 148956893 148956704 2.230000e-82 316.0
17 TraesCS4B01G108700 chr1B 97.297 185 5 0 3668 3852 214550399 214550583 8.030000e-82 315.0
18 TraesCS4B01G108700 chr2B 96.809 188 5 1 3665 3852 636103210 636103024 2.890000e-81 313.0
19 TraesCS4B01G108700 chr2B 85.294 204 22 7 3288 3488 46114323 46114521 1.810000e-48 204.0
20 TraesCS4B01G108700 chr3D 78.283 396 51 17 3115 3488 472952079 472951697 5.010000e-54 222.0
21 TraesCS4B01G108700 chr3D 85.556 180 22 4 3111 3288 302295408 302295585 6.570000e-43 185.0
22 TraesCS4B01G108700 chr3D 77.844 334 36 13 3136 3433 26208593 26208924 5.120000e-39 172.0
23 TraesCS4B01G108700 chr5D 77.833 406 47 22 3112 3488 486230218 486230609 1.080000e-50 211.0
24 TraesCS4B01G108700 chr5D 83.824 204 26 5 3288 3488 485269541 485269342 1.830000e-43 187.0
25 TraesCS4B01G108700 chr7D 84.834 211 23 8 3288 3491 388908665 388908873 1.810000e-48 204.0
26 TraesCS4B01G108700 chr2D 77.482 413 42 28 3115 3481 4322577 4322984 2.350000e-47 200.0
27 TraesCS4B01G108700 chr2D 85.000 200 22 8 3287 3481 4379511 4379707 3.040000e-46 196.0
28 TraesCS4B01G108700 chrUn 85.000 200 22 8 3287 3481 374045847 374045651 3.040000e-46 196.0
29 TraesCS4B01G108700 chr5A 86.517 178 21 3 3112 3289 593504627 593504801 3.930000e-45 193.0
30 TraesCS4B01G108700 chr5A 85.965 171 20 3 3115 3282 3558748 3558579 3.060000e-41 180.0
31 TraesCS4B01G108700 chr5A 84.076 157 21 3 3114 3268 616353047 616353201 8.620000e-32 148.0


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 TraesCS4B01G108700 chr4B 119351676 119355527 3851 False 2436.066667 7114 94.444667 1 3852 3 chr4B.!!$F1 3851
1 TraesCS4B01G108700 chr4D 84300735 84304290 3555 False 1809.000000 5208 94.045333 1 3531 3 chr4D.!!$F1 3530
2 TraesCS4B01G108700 chr4A 497074277 497077639 3362 False 2342.000000 2375 91.435000 90 3532 2 chr4A.!!$F2 3442

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
211 215 0.538584 AACTCATGAGAGCGATGCCA 59.461 50.0 29.27 0.0 46.09 4.92 F
1639 1666 0.035152 TGTTCACCTAGGCCATGCTG 60.035 55.0 9.30 0.0 0.00 4.41 F
2753 2796 0.104855 CGGCGAAGATGGAGATGGAA 59.895 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1965 0.949105 ACTTGTTCGTTAGGCGGCTG 60.949 55.0 23.55 4.91 41.72 4.85 R
2804 2847 0.253044 CCACCATCATTGTCCTCGGT 59.747 55.0 0.00 0.00 0.00 4.69 R
3794 3851 0.038892 ACGACTACATCAACCGCGTT 60.039 50.0 4.92 0.00 0.00 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
76 77 5.538067 TTGAAATGATATGTCGCAACGAA 57.462 34.783 0.00 0.00 37.72 3.85
94 95 2.297701 GAATGGGGATGTGTTGCGTAT 58.702 47.619 0.00 0.00 0.00 3.06
105 106 6.021782 GGATGTGTTGCGTATATTTGTTTTCG 60.022 38.462 0.00 0.00 0.00 3.46
109 110 5.115773 TGTTGCGTATATTTGTTTTCGTTGC 59.884 36.000 0.00 0.00 0.00 4.17
120 121 3.095738 GTTTTCGTTGCCATATGCGTAC 58.904 45.455 0.00 0.00 45.60 3.67
128 129 5.968848 CGTTGCCATATGCGTACTAAAAATT 59.031 36.000 0.00 0.00 45.60 1.82
211 215 0.538584 AACTCATGAGAGCGATGCCA 59.461 50.000 29.27 0.00 46.09 4.92
226 231 6.208644 AGCGATGCCATATGTCAAATTTTAC 58.791 36.000 1.24 0.00 0.00 2.01
258 263 6.255453 ACAATTTGACACTTGAAATTCGTTGG 59.745 34.615 2.79 0.00 30.94 3.77
296 302 4.975132 TGGCGGACCACCAATATG 57.025 55.556 0.00 0.00 42.67 1.78
312 318 5.864992 ACCAATATGTTCATGGTCGTCCAAT 60.865 40.000 5.25 0.00 43.90 3.16
314 320 7.908862 ACCAATATGTTCATGGTCGTCCAATAT 60.909 37.037 5.25 1.52 43.90 1.28
351 357 6.312529 AGCCATGAATGATTGTGGAGATATT 58.687 36.000 9.62 0.00 33.53 1.28
352 358 6.208797 AGCCATGAATGATTGTGGAGATATTG 59.791 38.462 9.62 0.00 33.53 1.90
364 370 7.320443 TGTGGAGATATTGAAACAACTATGC 57.680 36.000 0.00 0.00 0.00 3.14
400 406 8.218488 ACCCAAGTTCCATATAAGATTTACTCC 58.782 37.037 0.00 0.00 0.00 3.85
479 485 6.747280 GGATTGTGTGCATTGTAGTATGAAAC 59.253 38.462 0.00 0.00 0.00 2.78
613 634 4.439968 TGAAATGAAAACTTGTGCATGCA 58.560 34.783 18.46 18.46 0.00 3.96
625 646 4.687901 TGTGCATGCATAGTAGGTATGT 57.312 40.909 25.64 0.00 40.80 2.29
755 776 8.510243 TTGCACAAAAGATGTATATGACTGAT 57.490 30.769 0.00 0.00 41.46 2.90
783 804 3.028130 CCGGCCACACCCTTATATTTTT 58.972 45.455 2.24 0.00 33.26 1.94
891 912 7.187824 TCTGAGTGCCATTTCTAGAAATACT 57.812 36.000 26.34 24.58 38.84 2.12
957 978 9.939802 GTATTCTTTCTTTAACTCTAGGACCAA 57.060 33.333 0.00 0.00 0.00 3.67
1023 1047 3.585289 TGCCTGTGACCAAGGTTCTTATA 59.415 43.478 0.00 0.00 0.00 0.98
1024 1048 4.227300 TGCCTGTGACCAAGGTTCTTATAT 59.773 41.667 0.00 0.00 0.00 0.86
1033 1057 8.573035 TGACCAAGGTTCTTATATTTTCAACAC 58.427 33.333 0.00 0.00 0.00 3.32
1060 1084 8.241497 ACCTATCAACGTATGTAACAATAGGA 57.759 34.615 20.73 1.17 33.55 2.94
1199 1223 3.134623 ACGTATCTCCAATGGATGCTTCA 59.865 43.478 0.87 0.00 0.00 3.02
1200 1224 4.202398 ACGTATCTCCAATGGATGCTTCAT 60.202 41.667 0.87 0.00 0.00 2.57
1208 1232 4.160065 CCAATGGATGCTTCATTTGTACCA 59.840 41.667 0.00 0.00 33.08 3.25
1226 1250 2.041755 ACCAGAGGGAAATCCAAGGTTC 59.958 50.000 1.22 0.00 38.24 3.62
1352 1376 4.640771 AAGACTGGGAAGCAACTATTCA 57.359 40.909 0.00 0.00 0.00 2.57
1637 1664 1.544724 TTTGTTCACCTAGGCCATGC 58.455 50.000 9.30 0.00 0.00 4.06
1639 1666 0.035152 TGTTCACCTAGGCCATGCTG 60.035 55.000 9.30 0.00 0.00 4.41
1683 1710 5.065914 ACTACTTGTACGTCTTGGTGTAGA 58.934 41.667 15.29 0.00 32.88 2.59
1788 1819 8.100791 TCATTTACTTATAGGTTGCAGACTTGT 58.899 33.333 0.00 0.00 0.00 3.16
1806 1837 1.006337 TCCCACGCAAATTGCAAGC 60.006 52.632 18.65 1.73 45.36 4.01
1836 1867 3.522553 CCGCTTTCTAGTACTCTTTGGG 58.477 50.000 0.00 0.00 0.00 4.12
1919 1950 5.839063 CCTGACCTAGTATTGATCCTTACCA 59.161 44.000 0.00 0.00 0.00 3.25
1934 1965 9.337396 TGATCCTTACCATTATAATTGTGTGTC 57.663 33.333 11.47 4.76 0.00 3.67
1939 1970 4.335315 ACCATTATAATTGTGTGTCAGCCG 59.665 41.667 1.54 0.00 0.00 5.52
1967 1998 6.061231 ACGAACAAGTGAGATTTTTCCTTC 57.939 37.500 0.00 0.00 0.00 3.46
2096 2127 3.851098 AGTGAAGAAGAAGGTGCGATAC 58.149 45.455 0.00 0.00 0.00 2.24
2158 2189 3.788937 TCGTTTCTTTCTCGGTGAAGTT 58.211 40.909 0.00 0.00 35.89 2.66
2279 2314 8.519526 CAACTAAATGTTACAGGGATTTTGCTA 58.480 33.333 0.00 0.00 37.07 3.49
2332 2367 2.687935 AGAAAAACAAGATGGTGCGTGT 59.312 40.909 0.00 0.00 31.85 4.49
2498 2537 5.178623 TGGCATCACAAGTTTTTCTACTACG 59.821 40.000 0.00 0.00 0.00 3.51
2616 2659 3.243873 GGAGATGCAGATAACGGTGATGA 60.244 47.826 0.00 0.00 0.00 2.92
2622 2665 3.002656 GCAGATAACGGTGATGACAATGG 59.997 47.826 0.00 0.00 0.00 3.16
2655 2698 2.289506 CCGATGGAGATGATGATGCTGT 60.290 50.000 0.00 0.00 0.00 4.40
2753 2796 0.104855 CGGCGAAGATGGAGATGGAA 59.895 55.000 0.00 0.00 0.00 3.53
2771 2814 7.799081 AGATGGAACTTATGATGATGAAGACA 58.201 34.615 0.00 0.00 0.00 3.41
2799 2842 1.972795 TGGCGATGATGGAGATGATGA 59.027 47.619 0.00 0.00 0.00 2.92
2804 2847 4.382362 GCGATGATGGAGATGATGATGGTA 60.382 45.833 0.00 0.00 0.00 3.25
2854 2897 5.815740 GGAGTTGGCGAGAAATATTTAGTGA 59.184 40.000 0.00 0.00 0.00 3.41
2945 2988 6.868339 AGTTTGCCTTTGAGTTATTTATGCAC 59.132 34.615 0.00 0.00 0.00 4.57
3113 3159 0.741221 GCTTCTTCAGGGTAGTGCGG 60.741 60.000 0.00 0.00 0.00 5.69
3132 3178 1.347378 GGAAATTGCTTTTGGAGGCCA 59.653 47.619 5.01 0.00 0.00 5.36
3348 3399 6.211184 AGGTTGCATTTCAAGGTATTTCATCA 59.789 34.615 0.00 0.00 34.91 3.07
3356 3408 7.630242 TTCAAGGTATTTCATCATGGACTTC 57.370 36.000 0.00 0.00 0.00 3.01
3490 3547 1.228124 CCAAAACGCCCCACTCAGA 60.228 57.895 0.00 0.00 0.00 3.27
3494 3551 1.276622 AAACGCCCCACTCAGAGTAT 58.723 50.000 1.67 0.00 0.00 2.12
3549 3606 2.172593 TTTACGCGAATGCATTCAGC 57.827 45.000 32.72 31.06 42.97 4.26
3558 3615 4.725758 GCATTCAGCGTGACGAAC 57.274 55.556 10.10 0.00 0.00 3.95
3559 3616 1.132640 GCATTCAGCGTGACGAACC 59.867 57.895 10.10 0.00 0.00 3.62
3560 3617 1.291877 GCATTCAGCGTGACGAACCT 61.292 55.000 10.10 0.00 0.00 3.50
3561 3618 1.148310 CATTCAGCGTGACGAACCTT 58.852 50.000 10.10 0.00 0.00 3.50
3562 3619 1.126846 CATTCAGCGTGACGAACCTTC 59.873 52.381 10.10 0.00 0.00 3.46
3571 3628 3.862124 CGAACCTTCGGTCTGCTG 58.138 61.111 0.00 0.00 46.30 4.41
3572 3629 1.289066 CGAACCTTCGGTCTGCTGA 59.711 57.895 0.00 0.00 46.30 4.26
3573 3630 0.319555 CGAACCTTCGGTCTGCTGAA 60.320 55.000 0.00 0.00 46.30 3.02
3587 3644 2.927553 GCTGAAGCATTTCGACCAAT 57.072 45.000 0.00 0.00 41.59 3.16
3588 3645 2.790387 GCTGAAGCATTTCGACCAATC 58.210 47.619 0.00 0.00 41.59 2.67
3589 3646 2.789092 GCTGAAGCATTTCGACCAATCG 60.789 50.000 0.00 0.00 44.72 3.34
3590 3647 5.846728 GCTGAAGCATTTCGACCAATCGG 62.847 52.174 0.00 0.00 44.05 4.18
3607 3664 3.168528 GGCCGCCCCATTAGGAGA 61.169 66.667 0.00 0.00 38.24 3.71
3608 3665 2.427753 GCCGCCCCATTAGGAGAG 59.572 66.667 0.00 0.00 38.24 3.20
3609 3666 2.444256 GCCGCCCCATTAGGAGAGT 61.444 63.158 0.00 0.00 38.24 3.24
3610 3667 1.749033 CCGCCCCATTAGGAGAGTC 59.251 63.158 0.00 0.00 38.24 3.36
3611 3668 1.048724 CCGCCCCATTAGGAGAGTCA 61.049 60.000 0.00 0.00 38.24 3.41
3612 3669 0.830648 CGCCCCATTAGGAGAGTCAA 59.169 55.000 0.00 0.00 38.24 3.18
3613 3670 1.209504 CGCCCCATTAGGAGAGTCAAA 59.790 52.381 0.00 0.00 38.24 2.69
3614 3671 2.644676 GCCCCATTAGGAGAGTCAAAC 58.355 52.381 0.00 0.00 38.24 2.93
3615 3672 2.239907 GCCCCATTAGGAGAGTCAAACT 59.760 50.000 0.00 0.00 38.24 2.66
3616 3673 3.308473 GCCCCATTAGGAGAGTCAAACTT 60.308 47.826 0.00 0.00 38.24 2.66
3617 3674 4.518249 CCCCATTAGGAGAGTCAAACTTC 58.482 47.826 0.00 0.00 38.24 3.01
3618 3675 4.184629 CCCATTAGGAGAGTCAAACTTCG 58.815 47.826 0.00 0.00 38.24 3.79
3619 3676 4.081642 CCCATTAGGAGAGTCAAACTTCGA 60.082 45.833 0.00 0.00 38.24 3.71
3620 3677 5.395768 CCCATTAGGAGAGTCAAACTTCGAT 60.396 44.000 0.00 0.00 38.24 3.59
3621 3678 5.751028 CCATTAGGAGAGTCAAACTTCGATC 59.249 44.000 0.00 0.00 36.89 3.69
3622 3679 3.495670 AGGAGAGTCAAACTTCGATCG 57.504 47.619 9.36 9.36 0.00 3.69
3623 3680 2.820787 AGGAGAGTCAAACTTCGATCGT 59.179 45.455 15.94 0.00 0.00 3.73
3624 3681 3.256136 AGGAGAGTCAAACTTCGATCGTT 59.744 43.478 15.94 0.00 0.00 3.85
3625 3682 3.988517 GGAGAGTCAAACTTCGATCGTTT 59.011 43.478 15.94 5.67 35.12 3.60
3626 3683 4.090210 GGAGAGTCAAACTTCGATCGTTTC 59.910 45.833 15.94 0.00 32.64 2.78
3627 3684 4.872664 AGAGTCAAACTTCGATCGTTTCT 58.127 39.130 15.94 3.12 32.64 2.52
3628 3685 4.681942 AGAGTCAAACTTCGATCGTTTCTG 59.318 41.667 15.94 7.69 32.64 3.02
3629 3686 4.369182 AGTCAAACTTCGATCGTTTCTGT 58.631 39.130 15.94 5.34 32.64 3.41
3630 3687 4.444720 AGTCAAACTTCGATCGTTTCTGTC 59.555 41.667 15.94 5.73 32.64 3.51
3631 3688 4.208460 GTCAAACTTCGATCGTTTCTGTCA 59.792 41.667 15.94 0.00 32.64 3.58
3632 3689 4.806775 TCAAACTTCGATCGTTTCTGTCAA 59.193 37.500 15.94 0.00 32.64 3.18
3633 3690 4.974103 AACTTCGATCGTTTCTGTCAAG 57.026 40.909 15.94 10.83 0.00 3.02
3634 3691 2.731976 ACTTCGATCGTTTCTGTCAAGC 59.268 45.455 15.94 0.00 0.00 4.01
3635 3692 1.710013 TCGATCGTTTCTGTCAAGCC 58.290 50.000 15.94 0.00 0.00 4.35
3636 3693 1.272490 TCGATCGTTTCTGTCAAGCCT 59.728 47.619 15.94 0.00 0.00 4.58
3637 3694 2.490509 TCGATCGTTTCTGTCAAGCCTA 59.509 45.455 15.94 0.00 0.00 3.93
3638 3695 2.599082 CGATCGTTTCTGTCAAGCCTAC 59.401 50.000 7.03 0.00 0.00 3.18
3639 3696 3.585862 GATCGTTTCTGTCAAGCCTACA 58.414 45.455 0.00 0.00 0.00 2.74
3640 3697 3.462483 TCGTTTCTGTCAAGCCTACAA 57.538 42.857 0.00 0.00 0.00 2.41
3641 3698 3.128349 TCGTTTCTGTCAAGCCTACAAC 58.872 45.455 0.00 0.00 0.00 3.32
3642 3699 2.223377 CGTTTCTGTCAAGCCTACAACC 59.777 50.000 0.00 0.00 0.00 3.77
3643 3700 2.163818 TTCTGTCAAGCCTACAACCG 57.836 50.000 0.00 0.00 0.00 4.44
3644 3701 0.320421 TCTGTCAAGCCTACAACCGC 60.320 55.000 0.00 0.00 0.00 5.68
3645 3702 1.298859 CTGTCAAGCCTACAACCGCC 61.299 60.000 0.00 0.00 0.00 6.13
3646 3703 1.302192 GTCAAGCCTACAACCGCCA 60.302 57.895 0.00 0.00 0.00 5.69
3647 3704 1.003839 TCAAGCCTACAACCGCCAG 60.004 57.895 0.00 0.00 0.00 4.85
3648 3705 1.302511 CAAGCCTACAACCGCCAGT 60.303 57.895 0.00 0.00 0.00 4.00
3649 3706 1.003718 AAGCCTACAACCGCCAGTC 60.004 57.895 0.00 0.00 0.00 3.51
3650 3707 2.781595 AAGCCTACAACCGCCAGTCG 62.782 60.000 0.00 0.00 38.08 4.18
3651 3708 2.813908 CCTACAACCGCCAGTCGC 60.814 66.667 0.00 0.00 36.73 5.19
3652 3709 2.813908 CTACAACCGCCAGTCGCC 60.814 66.667 0.00 0.00 36.73 5.54
3653 3710 4.728102 TACAACCGCCAGTCGCCG 62.728 66.667 0.00 0.00 36.73 6.46
3676 3733 4.762825 CGTTTCTCGTGTTGGGGA 57.237 55.556 0.00 0.00 34.52 4.81
3677 3734 2.994990 CGTTTCTCGTGTTGGGGAA 58.005 52.632 0.00 0.00 34.52 3.97
3678 3735 0.584876 CGTTTCTCGTGTTGGGGAAC 59.415 55.000 0.00 0.00 34.52 3.62
3679 3736 0.584876 GTTTCTCGTGTTGGGGAACG 59.415 55.000 0.00 0.00 41.11 3.95
3680 3737 0.178533 TTTCTCGTGTTGGGGAACGT 59.821 50.000 0.00 0.00 40.61 3.99
3681 3738 1.039068 TTCTCGTGTTGGGGAACGTA 58.961 50.000 0.00 0.00 40.61 3.57
3682 3739 0.599558 TCTCGTGTTGGGGAACGTAG 59.400 55.000 0.00 0.00 40.61 3.51
3684 3741 1.541147 CTCGTGTTGGGGAACGTAGTA 59.459 52.381 0.00 0.00 45.00 1.82
3685 3742 1.959985 TCGTGTTGGGGAACGTAGTAA 59.040 47.619 0.00 0.00 45.00 2.24
3686 3743 2.562298 TCGTGTTGGGGAACGTAGTAAT 59.438 45.455 0.00 0.00 45.00 1.89
3687 3744 3.006752 TCGTGTTGGGGAACGTAGTAATT 59.993 43.478 0.00 0.00 45.00 1.40
3688 3745 3.747529 CGTGTTGGGGAACGTAGTAATTT 59.252 43.478 0.00 0.00 45.00 1.82
3689 3746 4.143052 CGTGTTGGGGAACGTAGTAATTTC 60.143 45.833 0.00 0.00 45.00 2.17
3690 3747 4.756135 GTGTTGGGGAACGTAGTAATTTCA 59.244 41.667 0.00 0.00 45.00 2.69
3691 3748 5.239087 GTGTTGGGGAACGTAGTAATTTCAA 59.761 40.000 0.00 0.00 45.00 2.69
3692 3749 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
3693 3750 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
3694 3751 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
3722 3779 2.174334 GCACACGCAAGATCATGGT 58.826 52.632 0.00 0.00 43.62 3.55
3723 3780 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
3724 3781 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
3725 3782 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
3726 3783 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
3727 3784 2.282407 CACGCAAGATCATGGTGATGA 58.718 47.619 11.70 0.00 37.20 2.92
3728 3785 2.031314 CACGCAAGATCATGGTGATGAC 59.969 50.000 11.70 0.00 40.57 3.06
3729 3786 2.282407 CGCAAGATCATGGTGATGACA 58.718 47.619 0.00 0.00 41.52 3.58
3730 3787 2.876550 CGCAAGATCATGGTGATGACAT 59.123 45.455 0.00 0.00 41.52 3.06
3731 3788 4.060205 CGCAAGATCATGGTGATGACATA 58.940 43.478 0.00 0.00 41.52 2.29
3732 3789 4.151867 CGCAAGATCATGGTGATGACATAG 59.848 45.833 0.00 0.00 41.52 2.23
3733 3790 4.083431 GCAAGATCATGGTGATGACATAGC 60.083 45.833 0.00 0.00 41.52 2.97
3734 3791 4.968971 AGATCATGGTGATGACATAGCA 57.031 40.909 0.00 0.00 41.52 3.49
3735 3792 5.300411 AGATCATGGTGATGACATAGCAA 57.700 39.130 0.00 0.00 41.52 3.91
3736 3793 5.877491 AGATCATGGTGATGACATAGCAAT 58.123 37.500 0.00 0.00 41.52 3.56
3737 3794 5.705905 AGATCATGGTGATGACATAGCAATG 59.294 40.000 0.00 0.00 41.52 2.82
3738 3795 5.038651 TCATGGTGATGACATAGCAATGA 57.961 39.130 0.00 5.23 33.40 2.57
3739 3796 5.061179 TCATGGTGATGACATAGCAATGAG 58.939 41.667 0.00 0.00 33.40 2.90
3740 3797 4.758773 TGGTGATGACATAGCAATGAGA 57.241 40.909 0.00 0.00 36.54 3.27
3741 3798 4.700700 TGGTGATGACATAGCAATGAGAG 58.299 43.478 0.00 0.00 36.54 3.20
3742 3799 4.063689 GGTGATGACATAGCAATGAGAGG 58.936 47.826 0.00 0.00 36.54 3.69
3743 3800 4.063689 GTGATGACATAGCAATGAGAGGG 58.936 47.826 0.00 0.00 36.54 4.30
3744 3801 3.072038 TGATGACATAGCAATGAGAGGGG 59.928 47.826 0.00 0.00 36.54 4.79
3745 3802 2.763039 TGACATAGCAATGAGAGGGGA 58.237 47.619 0.00 0.00 36.54 4.81
3746 3803 2.702478 TGACATAGCAATGAGAGGGGAG 59.298 50.000 0.00 0.00 36.54 4.30
3747 3804 2.968574 GACATAGCAATGAGAGGGGAGA 59.031 50.000 0.00 0.00 36.54 3.71
3748 3805 2.971330 ACATAGCAATGAGAGGGGAGAG 59.029 50.000 0.00 0.00 36.54 3.20
3749 3806 2.856760 TAGCAATGAGAGGGGAGAGT 57.143 50.000 0.00 0.00 0.00 3.24
3750 3807 1.202330 AGCAATGAGAGGGGAGAGTG 58.798 55.000 0.00 0.00 0.00 3.51
3751 3808 0.908198 GCAATGAGAGGGGAGAGTGT 59.092 55.000 0.00 0.00 0.00 3.55
3752 3809 1.280421 GCAATGAGAGGGGAGAGTGTT 59.720 52.381 0.00 0.00 0.00 3.32
3753 3810 2.938756 GCAATGAGAGGGGAGAGTGTTG 60.939 54.545 0.00 0.00 0.00 3.33
3754 3811 2.304180 CAATGAGAGGGGAGAGTGTTGT 59.696 50.000 0.00 0.00 0.00 3.32
3755 3812 1.633774 TGAGAGGGGAGAGTGTTGTC 58.366 55.000 0.00 0.00 0.00 3.18
3756 3813 0.899019 GAGAGGGGAGAGTGTTGTCC 59.101 60.000 0.00 0.00 36.03 4.02
3757 3814 0.191064 AGAGGGGAGAGTGTTGTCCA 59.809 55.000 0.00 0.00 38.50 4.02
3758 3815 0.321996 GAGGGGAGAGTGTTGTCCAC 59.678 60.000 0.00 0.00 40.47 4.02
3759 3816 1.472662 AGGGGAGAGTGTTGTCCACG 61.473 60.000 0.00 0.00 44.77 4.94
3761 3818 4.748514 AGGGGAGAGTGTTGTCCACGTA 62.749 54.545 0.00 0.00 44.77 3.57
3766 3823 3.206090 GTGTTGTCCACGTACCCTC 57.794 57.895 0.00 0.00 33.61 4.30
3767 3824 0.665369 GTGTTGTCCACGTACCCTCG 60.665 60.000 0.00 0.00 33.61 4.63
3768 3825 1.108727 TGTTGTCCACGTACCCTCGT 61.109 55.000 0.00 0.00 45.10 4.18
3769 3826 0.881118 GTTGTCCACGTACCCTCGTA 59.119 55.000 0.00 0.00 42.27 3.43
3770 3827 1.135575 GTTGTCCACGTACCCTCGTAG 60.136 57.143 0.00 0.00 42.27 3.51
3771 3828 0.324614 TGTCCACGTACCCTCGTAGA 59.675 55.000 0.00 0.00 42.27 2.59
3772 3829 0.729690 GTCCACGTACCCTCGTAGAC 59.270 60.000 0.00 2.79 42.50 2.59
3773 3830 0.392998 TCCACGTACCCTCGTAGACC 60.393 60.000 0.00 0.00 42.27 3.85
3774 3831 1.709147 CCACGTACCCTCGTAGACCG 61.709 65.000 0.00 0.00 42.27 4.79
3775 3832 1.021390 CACGTACCCTCGTAGACCGT 61.021 60.000 0.00 0.00 42.27 4.83
3776 3833 0.535335 ACGTACCCTCGTAGACCGTA 59.465 55.000 0.00 0.00 42.35 4.02
3777 3834 1.066430 ACGTACCCTCGTAGACCGTAA 60.066 52.381 0.00 0.00 42.35 3.18
3778 3835 1.594862 CGTACCCTCGTAGACCGTAAG 59.405 57.143 0.00 0.00 37.94 2.34
3779 3836 1.332065 GTACCCTCGTAGACCGTAAGC 59.668 57.143 0.00 0.00 37.94 3.09
3780 3837 1.354506 CCCTCGTAGACCGTAAGCG 59.645 63.158 0.00 0.00 37.94 4.68
3797 3854 3.850207 CGGAAGCGTTATGACAACG 57.150 52.632 5.22 5.22 45.56 4.10
3804 3861 0.785378 CGTTATGACAACGCGGTTGA 59.215 50.000 22.26 6.79 45.28 3.18
3805 3862 1.392168 CGTTATGACAACGCGGTTGAT 59.608 47.619 22.26 12.10 45.28 2.57
3806 3863 2.769376 GTTATGACAACGCGGTTGATG 58.231 47.619 22.26 11.18 45.28 3.07
3807 3864 2.087501 TATGACAACGCGGTTGATGT 57.912 45.000 22.26 13.84 45.28 3.06
3808 3865 2.087501 ATGACAACGCGGTTGATGTA 57.912 45.000 22.26 9.68 45.28 2.29
3809 3866 1.424403 TGACAACGCGGTTGATGTAG 58.576 50.000 22.26 1.41 45.28 2.74
3810 3867 1.269883 TGACAACGCGGTTGATGTAGT 60.270 47.619 22.26 4.69 45.28 2.73
3811 3868 1.389106 GACAACGCGGTTGATGTAGTC 59.611 52.381 22.26 10.01 45.28 2.59
3812 3869 0.365523 CAACGCGGTTGATGTAGTCG 59.634 55.000 12.47 0.00 45.28 4.18
3813 3870 0.038892 AACGCGGTTGATGTAGTCGT 60.039 50.000 12.47 0.00 0.00 4.34
3814 3871 0.804364 ACGCGGTTGATGTAGTCGTA 59.196 50.000 12.47 0.00 0.00 3.43
3815 3872 1.186030 CGCGGTTGATGTAGTCGTAC 58.814 55.000 0.00 0.00 0.00 3.67
3816 3873 1.186030 GCGGTTGATGTAGTCGTACG 58.814 55.000 9.53 9.53 30.95 3.67
3817 3874 1.466360 GCGGTTGATGTAGTCGTACGT 60.466 52.381 16.05 0.00 30.95 3.57
3818 3875 2.434761 CGGTTGATGTAGTCGTACGTC 58.565 52.381 16.05 10.06 43.16 4.34
3819 3876 2.094894 CGGTTGATGTAGTCGTACGTCT 59.905 50.000 18.54 18.54 43.23 4.18
3820 3877 3.423571 GGTTGATGTAGTCGTACGTCTG 58.576 50.000 22.50 0.00 43.23 3.51
3821 3878 2.819422 TGATGTAGTCGTACGTCTGC 57.181 50.000 22.50 21.19 43.23 4.26
3822 3879 2.078392 TGATGTAGTCGTACGTCTGCA 58.922 47.619 28.02 28.02 43.23 4.41
3823 3880 2.159612 TGATGTAGTCGTACGTCTGCAC 60.160 50.000 28.30 22.21 43.23 4.57
3833 3890 2.579787 GTCTGCACGATCCGACCG 60.580 66.667 0.00 0.00 0.00 4.79
3834 3891 2.748647 TCTGCACGATCCGACCGA 60.749 61.111 0.00 0.00 0.00 4.69
3835 3892 2.119029 TCTGCACGATCCGACCGAT 61.119 57.895 0.00 0.00 0.00 4.18
3836 3893 1.658717 CTGCACGATCCGACCGATC 60.659 63.158 0.00 0.00 43.58 3.69
3837 3894 2.354773 GCACGATCCGACCGATCC 60.355 66.667 0.00 0.00 44.07 3.36
3838 3895 3.116463 CACGATCCGACCGATCCA 58.884 61.111 0.00 0.00 44.07 3.41
3839 3896 1.435925 CACGATCCGACCGATCCAA 59.564 57.895 0.00 0.00 44.07 3.53
3840 3897 0.595053 CACGATCCGACCGATCCAAG 60.595 60.000 0.00 0.00 44.07 3.61
3841 3898 1.035932 ACGATCCGACCGATCCAAGT 61.036 55.000 0.00 0.00 44.07 3.16
3842 3899 0.949397 CGATCCGACCGATCCAAGTA 59.051 55.000 0.00 0.00 44.07 2.24
3843 3900 1.334779 CGATCCGACCGATCCAAGTAC 60.335 57.143 0.00 0.00 44.07 2.73
3844 3901 1.000496 GATCCGACCGATCCAAGTACC 60.000 57.143 0.00 0.00 41.51 3.34
3845 3902 1.065273 CCGACCGATCCAAGTACCG 59.935 63.158 0.00 0.00 0.00 4.02
3846 3903 1.378882 CCGACCGATCCAAGTACCGA 61.379 60.000 0.00 0.00 0.00 4.69
3847 3904 0.452987 CGACCGATCCAAGTACCGAA 59.547 55.000 0.00 0.00 0.00 4.30
3848 3905 1.796617 CGACCGATCCAAGTACCGAAC 60.797 57.143 0.00 0.00 0.00 3.95
3849 3906 0.171903 ACCGATCCAAGTACCGAACG 59.828 55.000 0.00 0.00 0.00 3.95
3850 3907 0.171903 CCGATCCAAGTACCGAACGT 59.828 55.000 0.00 0.00 0.00 3.99
3851 3908 1.401552 CCGATCCAAGTACCGAACGTA 59.598 52.381 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.947196 GGTCACAGGATATGCACATGAAA 59.053 43.478 0.00 0.00 0.00 2.69
40 41 9.123902 CATATCATTTCAAAATAGGTCACAGGA 57.876 33.333 0.00 0.00 0.00 3.86
42 43 9.941664 GACATATCATTTCAAAATAGGTCACAG 57.058 33.333 2.97 0.00 36.92 3.66
76 77 3.788227 ATATACGCAACACATCCCCAT 57.212 42.857 0.00 0.00 0.00 4.00
94 95 4.795795 CGCATATGGCAACGAAAACAAATA 59.204 37.500 4.56 0.00 45.17 1.40
105 106 8.901748 CATAATTTTTAGTACGCATATGGCAAC 58.098 33.333 4.56 0.00 45.17 4.17
109 110 9.624697 AATGCATAATTTTTAGTACGCATATGG 57.375 29.630 0.00 0.00 37.85 2.74
226 231 7.499438 TTTCAAGTGTCAAATTGTTGTAACG 57.501 32.000 0.00 0.00 36.07 3.18
236 241 5.901552 ACCAACGAATTTCAAGTGTCAAAT 58.098 33.333 0.00 0.00 0.00 2.32
243 248 6.540914 TCTCACTTAACCAACGAATTTCAAGT 59.459 34.615 0.00 0.00 0.00 3.16
258 263 5.294552 GCCACACTATCCAATCTCACTTAAC 59.705 44.000 0.00 0.00 0.00 2.01
294 300 6.533730 ACATATATTGGACGACCATGAACAT 58.466 36.000 7.61 0.18 46.34 2.71
296 302 6.146184 CAGACATATATTGGACGACCATGAAC 59.854 42.308 7.61 3.52 46.34 3.18
304 310 3.964688 ACCACCAGACATATATTGGACGA 59.035 43.478 8.62 0.00 35.89 4.20
312 318 4.488770 TCATGGCTACCACCAGACATATA 58.511 43.478 0.00 0.00 42.63 0.86
314 320 2.758130 TCATGGCTACCACCAGACATA 58.242 47.619 0.00 0.00 42.63 2.29
351 357 7.335924 GGGTACTAAATCAGCATAGTTGTTTCA 59.664 37.037 0.00 0.00 34.37 2.69
352 358 7.335924 TGGGTACTAAATCAGCATAGTTGTTTC 59.664 37.037 0.00 0.00 34.37 2.78
479 485 9.004717 TCGATGTTCCATAGAAGATTACTCTAG 57.995 37.037 0.00 0.00 36.19 2.43
524 530 4.059511 CTCGTATGATAGTCCACGACTCT 58.940 47.826 0.00 0.00 42.40 3.24
525 531 3.808726 ACTCGTATGATAGTCCACGACTC 59.191 47.826 0.00 0.00 42.40 3.36
613 634 9.839185 ATACCATTTGACCTACATACCTACTAT 57.161 33.333 0.00 0.00 0.00 2.12
625 646 5.575157 TGGCAAAAGATACCATTTGACCTA 58.425 37.500 1.97 0.00 42.62 3.08
755 776 2.988684 GGTGTGGCCGGAAATGCA 60.989 61.111 5.05 0.00 0.00 3.96
783 804 8.918116 TGGGTTTATATGCTATGCAAATTTACA 58.082 29.630 0.00 0.00 43.62 2.41
891 912 8.574251 TTTTCAGCTTCAGCCTTGTAAATATA 57.426 30.769 0.00 0.00 43.38 0.86
969 990 0.318120 GATGCACACTGGGGGTTTTG 59.682 55.000 0.00 0.00 0.00 2.44
1023 1047 4.753107 ACGTTGATAGGTCGTGTTGAAAAT 59.247 37.500 0.00 0.00 36.46 1.82
1024 1048 4.121317 ACGTTGATAGGTCGTGTTGAAAA 58.879 39.130 0.00 0.00 36.46 2.29
1033 1057 7.325338 CCTATTGTTACATACGTTGATAGGTCG 59.675 40.741 0.00 0.00 33.42 4.79
1199 1223 4.946160 TGGATTTCCCTCTGGTACAAAT 57.054 40.909 0.00 0.00 34.32 2.32
1200 1224 4.508405 CCTTGGATTTCCCTCTGGTACAAA 60.508 45.833 0.00 0.00 34.32 2.83
1208 1232 3.009584 GTGAGAACCTTGGATTTCCCTCT 59.990 47.826 0.00 0.00 35.38 3.69
1240 1264 3.553508 CCCATGCAAGAAAACCTTCACAG 60.554 47.826 0.00 0.00 33.64 3.66
1683 1710 2.724672 TGGCCTAGGTGATCTAGATCCT 59.275 50.000 26.33 20.60 46.48 3.24
1806 1837 1.609555 ACTAGAAAGCGGCGATCTAGG 59.390 52.381 30.61 20.32 44.42 3.02
1836 1867 5.974108 TCCCTTGCATAAACACTAGTACTC 58.026 41.667 0.00 0.00 0.00 2.59
1919 1950 3.315191 GGCGGCTGACACACAATTATAAT 59.685 43.478 0.00 0.00 0.00 1.28
1934 1965 0.949105 ACTTGTTCGTTAGGCGGCTG 60.949 55.000 23.55 4.91 41.72 4.85
1939 1970 5.358298 AAAATCTCACTTGTTCGTTAGGC 57.642 39.130 0.00 0.00 0.00 3.93
1959 1990 7.728083 TCCATATTTGACCAGAAAGAAGGAAAA 59.272 33.333 0.00 0.00 0.00 2.29
1967 1998 6.824305 AACTGTCCATATTTGACCAGAAAG 57.176 37.500 8.32 0.00 31.60 2.62
2017 2048 9.598517 ACTGAACAATACAAATGAAACAATGTT 57.401 25.926 0.00 0.00 0.00 2.71
2028 2059 8.349983 GGTACTGTGAAACTGAACAATACAAAT 58.650 33.333 0.00 0.00 39.30 2.32
2096 2127 9.773328 ATCGTACAAAAACATGAAGTCATTATG 57.227 29.630 0.00 0.00 33.61 1.90
2125 2156 5.556915 AGAAAGAAACGATAACCATCCACA 58.443 37.500 0.00 0.00 0.00 4.17
2158 2189 1.630369 CCAAGAACTCACTCCCATGGA 59.370 52.381 15.22 0.00 0.00 3.41
2275 2310 7.840931 TGTAGATCTTCTTGACTGAAATAGCA 58.159 34.615 0.00 0.00 0.00 3.49
2279 2314 9.956640 AAGAATGTAGATCTTCTTGACTGAAAT 57.043 29.630 0.00 0.00 39.58 2.17
2547 2590 2.223272 GCATGCAGTCAGTGATGTCATG 60.223 50.000 14.21 18.91 35.70 3.07
2548 2591 2.014857 GCATGCAGTCAGTGATGTCAT 58.985 47.619 14.21 0.00 0.00 3.06
2616 2659 2.985282 CGGCAGCACCACCATTGT 60.985 61.111 0.00 0.00 39.03 2.71
2635 2678 3.041508 ACAGCATCATCATCTCCATCG 57.958 47.619 0.00 0.00 0.00 3.84
2655 2698 0.329261 CAGGGCTCCATCTTCACCAA 59.671 55.000 0.00 0.00 0.00 3.67
2753 2796 8.627208 ACAACTTTGTCTTCATCATCATAAGT 57.373 30.769 0.00 0.00 36.50 2.24
2771 2814 2.489329 CTCCATCATCGCCAACAACTTT 59.511 45.455 0.00 0.00 0.00 2.66
2799 2842 2.104792 CCATCATTGTCCTCGGTACCAT 59.895 50.000 13.54 0.00 0.00 3.55
2804 2847 0.253044 CCACCATCATTGTCCTCGGT 59.747 55.000 0.00 0.00 0.00 4.69
2835 2878 5.758296 GGATGTCACTAAATATTTCTCGCCA 59.242 40.000 3.39 0.00 0.00 5.69
2854 2897 0.617413 CAAGGTGAGCTCCTGGATGT 59.383 55.000 12.15 0.00 37.93 3.06
3019 3065 7.661437 CAGGAACATATTCGGATATTCCAAAGA 59.339 37.037 15.51 0.00 35.91 2.52
3024 3070 6.595716 CCTTCAGGAACATATTCGGATATTCC 59.404 42.308 7.72 7.72 35.48 3.01
3054 3100 0.757188 TGTGGGGCGGTTCACAAAAT 60.757 50.000 0.00 0.00 40.43 1.82
3056 3102 2.122167 GTGTGGGGCGGTTCACAAA 61.122 57.895 0.00 0.00 44.19 2.83
3113 3159 2.837532 TGGCCTCCAAAAGCAATTTC 57.162 45.000 3.32 0.00 0.00 2.17
3132 3178 3.329093 GAGGCCTCCATGGAGCTT 58.671 61.111 32.97 24.15 40.69 3.74
3250 3299 5.697473 TGCCTTCATTTCAACGTATTTCA 57.303 34.783 0.00 0.00 0.00 2.69
3348 3399 7.676683 AAGGTATATGTGTGTAGAAGTCCAT 57.323 36.000 0.00 0.00 0.00 3.41
3494 3551 7.336679 ACAGCTGAACTTTATATATGCACACAA 59.663 33.333 23.35 0.00 0.00 3.33
3532 3589 1.635810 CGCTGAATGCATTCGCGTA 59.364 52.632 39.33 24.20 45.34 4.42
3533 3590 2.400798 CGCTGAATGCATTCGCGT 59.599 55.556 39.33 16.35 45.34 6.01
3535 3592 0.858961 GTCACGCTGAATGCATTCGC 60.859 55.000 29.81 29.81 43.06 4.70
3536 3593 0.584785 CGTCACGCTGAATGCATTCG 60.585 55.000 29.23 24.21 43.06 3.34
3537 3594 0.721154 TCGTCACGCTGAATGCATTC 59.279 50.000 28.83 28.83 43.06 2.67
3538 3595 1.135972 GTTCGTCACGCTGAATGCATT 60.136 47.619 12.83 12.83 43.06 3.56
3539 3596 0.443869 GTTCGTCACGCTGAATGCAT 59.556 50.000 0.00 0.00 43.06 3.96
3540 3597 1.565156 GGTTCGTCACGCTGAATGCA 61.565 55.000 0.00 0.00 43.06 3.96
3541 3598 1.132640 GGTTCGTCACGCTGAATGC 59.867 57.895 0.00 0.00 38.57 3.56
3542 3599 1.126846 GAAGGTTCGTCACGCTGAATG 59.873 52.381 0.00 0.00 0.00 2.67
3543 3600 1.429463 GAAGGTTCGTCACGCTGAAT 58.571 50.000 0.00 0.00 0.00 2.57
3544 3601 0.937699 CGAAGGTTCGTCACGCTGAA 60.938 55.000 3.91 0.00 45.09 3.02
3545 3602 1.371267 CGAAGGTTCGTCACGCTGA 60.371 57.895 3.91 0.00 45.09 4.26
3546 3603 3.147294 CGAAGGTTCGTCACGCTG 58.853 61.111 3.91 0.00 45.09 5.18
3568 3625 2.790387 GATTGGTCGAAATGCTTCAGC 58.210 47.619 0.00 0.00 42.50 4.26
3586 3643 3.953775 CTAATGGGGCGGCCCGAT 61.954 66.667 38.64 31.21 46.66 4.18
3589 3646 4.271016 CTCCTAATGGGGCGGCCC 62.271 72.222 38.99 38.99 44.51 5.80
3590 3647 3.168528 TCTCCTAATGGGGCGGCC 61.169 66.667 22.00 22.00 32.58 6.13
3591 3648 2.384653 GACTCTCCTAATGGGGCGGC 62.385 65.000 0.00 0.00 32.58 6.53
3592 3649 1.048724 TGACTCTCCTAATGGGGCGG 61.049 60.000 0.00 0.00 32.58 6.13
3593 3650 0.830648 TTGACTCTCCTAATGGGGCG 59.169 55.000 0.00 0.00 32.58 6.13
3594 3651 2.239907 AGTTTGACTCTCCTAATGGGGC 59.760 50.000 0.00 0.00 32.58 5.80
3595 3652 4.518249 GAAGTTTGACTCTCCTAATGGGG 58.482 47.826 0.00 0.00 35.33 4.96
3596 3653 4.081642 TCGAAGTTTGACTCTCCTAATGGG 60.082 45.833 0.00 0.00 0.00 4.00
3597 3654 5.073311 TCGAAGTTTGACTCTCCTAATGG 57.927 43.478 0.00 0.00 0.00 3.16
3598 3655 5.457148 CGATCGAAGTTTGACTCTCCTAATG 59.543 44.000 10.26 0.00 0.00 1.90
3599 3656 5.125739 ACGATCGAAGTTTGACTCTCCTAAT 59.874 40.000 24.34 0.00 0.00 1.73
3600 3657 4.458295 ACGATCGAAGTTTGACTCTCCTAA 59.542 41.667 24.34 0.00 0.00 2.69
3601 3658 4.008330 ACGATCGAAGTTTGACTCTCCTA 58.992 43.478 24.34 0.00 0.00 2.94
3602 3659 2.820787 ACGATCGAAGTTTGACTCTCCT 59.179 45.455 24.34 0.00 0.00 3.69
3603 3660 3.219052 ACGATCGAAGTTTGACTCTCC 57.781 47.619 24.34 0.00 0.00 3.71
3604 3661 4.918583 AGAAACGATCGAAGTTTGACTCTC 59.081 41.667 24.34 10.20 41.32 3.20
3605 3662 4.681942 CAGAAACGATCGAAGTTTGACTCT 59.318 41.667 24.34 12.67 41.32 3.24
3606 3663 4.444720 ACAGAAACGATCGAAGTTTGACTC 59.555 41.667 24.34 11.03 41.32 3.36
3607 3664 4.369182 ACAGAAACGATCGAAGTTTGACT 58.631 39.130 24.34 13.26 41.32 3.41
3608 3665 4.208460 TGACAGAAACGATCGAAGTTTGAC 59.792 41.667 24.34 13.01 41.32 3.18
3609 3666 4.364860 TGACAGAAACGATCGAAGTTTGA 58.635 39.130 24.34 0.00 41.32 2.69
3610 3667 4.708868 TGACAGAAACGATCGAAGTTTG 57.291 40.909 24.34 14.67 41.32 2.93
3611 3668 4.318831 GCTTGACAGAAACGATCGAAGTTT 60.319 41.667 24.34 18.28 43.60 2.66
3612 3669 3.184581 GCTTGACAGAAACGATCGAAGTT 59.815 43.478 24.34 12.44 0.00 2.66
3613 3670 2.731976 GCTTGACAGAAACGATCGAAGT 59.268 45.455 24.34 11.83 0.00 3.01
3614 3671 2.092838 GGCTTGACAGAAACGATCGAAG 59.907 50.000 24.34 12.96 0.00 3.79
3615 3672 2.066262 GGCTTGACAGAAACGATCGAA 58.934 47.619 24.34 1.44 0.00 3.71
3616 3673 1.272490 AGGCTTGACAGAAACGATCGA 59.728 47.619 24.34 0.00 0.00 3.59
3617 3674 1.714794 AGGCTTGACAGAAACGATCG 58.285 50.000 14.88 14.88 0.00 3.69
3618 3675 3.585862 TGTAGGCTTGACAGAAACGATC 58.414 45.455 0.00 0.00 0.00 3.69
3619 3676 3.678056 TGTAGGCTTGACAGAAACGAT 57.322 42.857 0.00 0.00 0.00 3.73
3620 3677 3.128349 GTTGTAGGCTTGACAGAAACGA 58.872 45.455 0.00 0.00 0.00 3.85
3621 3678 2.223377 GGTTGTAGGCTTGACAGAAACG 59.777 50.000 0.00 0.00 0.00 3.60
3622 3679 2.223377 CGGTTGTAGGCTTGACAGAAAC 59.777 50.000 0.00 0.00 0.00 2.78
3623 3680 2.489971 CGGTTGTAGGCTTGACAGAAA 58.510 47.619 0.00 0.00 0.00 2.52
3624 3681 1.876416 GCGGTTGTAGGCTTGACAGAA 60.876 52.381 0.00 0.00 0.00 3.02
3625 3682 0.320421 GCGGTTGTAGGCTTGACAGA 60.320 55.000 0.00 0.00 0.00 3.41
3626 3683 1.298859 GGCGGTTGTAGGCTTGACAG 61.299 60.000 0.00 0.00 0.00 3.51
3627 3684 1.302192 GGCGGTTGTAGGCTTGACA 60.302 57.895 0.00 0.00 0.00 3.58
3628 3685 1.298859 CTGGCGGTTGTAGGCTTGAC 61.299 60.000 0.00 0.00 35.01 3.18
3629 3686 1.003839 CTGGCGGTTGTAGGCTTGA 60.004 57.895 0.00 0.00 35.01 3.02
3630 3687 1.298859 GACTGGCGGTTGTAGGCTTG 61.299 60.000 0.00 0.00 35.01 4.01
3631 3688 1.003718 GACTGGCGGTTGTAGGCTT 60.004 57.895 0.00 0.00 35.01 4.35
3632 3689 2.663196 GACTGGCGGTTGTAGGCT 59.337 61.111 0.00 0.00 35.01 4.58
3633 3690 2.813908 CGACTGGCGGTTGTAGGC 60.814 66.667 0.00 0.00 36.03 3.93
3634 3691 2.813908 GCGACTGGCGGTTGTAGG 60.814 66.667 15.05 0.00 41.29 3.18
3635 3692 2.813908 GGCGACTGGCGGTTGTAG 60.814 66.667 15.05 2.17 44.92 2.74
3660 3717 0.584876 CGTTCCCCAACACGAGAAAC 59.415 55.000 0.00 0.00 38.76 2.78
3661 3718 0.178533 ACGTTCCCCAACACGAGAAA 59.821 50.000 0.00 0.00 39.76 2.52
3662 3719 1.000060 CTACGTTCCCCAACACGAGAA 60.000 52.381 0.00 0.00 39.76 2.87
3663 3720 0.599558 CTACGTTCCCCAACACGAGA 59.400 55.000 0.00 0.00 39.76 4.04
3664 3721 0.316204 ACTACGTTCCCCAACACGAG 59.684 55.000 0.00 0.00 39.76 4.18
3665 3722 1.614996 TACTACGTTCCCCAACACGA 58.385 50.000 0.00 0.00 39.76 4.35
3666 3723 2.437200 TTACTACGTTCCCCAACACG 57.563 50.000 0.00 0.00 42.29 4.49
3667 3724 4.756135 TGAAATTACTACGTTCCCCAACAC 59.244 41.667 0.00 0.00 32.14 3.32
3668 3725 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
3669 3726 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
3670 3727 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
3671 3728 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
3704 3761 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
3705 3762 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
3706 3763 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
3707 3764 2.031314 GTCATCACCATGATCTTGCGTG 59.969 50.000 17.02 17.02 41.26 5.34
3708 3765 2.283298 GTCATCACCATGATCTTGCGT 58.717 47.619 3.07 0.87 41.26 5.24
3709 3766 2.282407 TGTCATCACCATGATCTTGCG 58.718 47.619 3.07 0.30 41.26 4.85
3710 3767 4.083431 GCTATGTCATCACCATGATCTTGC 60.083 45.833 3.07 0.00 41.26 4.01
3711 3768 5.061179 TGCTATGTCATCACCATGATCTTG 58.939 41.667 0.00 1.60 41.26 3.02
3712 3769 5.300411 TGCTATGTCATCACCATGATCTT 57.700 39.130 0.00 0.00 41.26 2.40
3713 3770 4.968971 TGCTATGTCATCACCATGATCT 57.031 40.909 0.00 0.00 41.26 2.75
3714 3771 5.704053 TCATTGCTATGTCATCACCATGATC 59.296 40.000 8.01 0.00 41.26 2.92
3715 3772 5.627135 TCATTGCTATGTCATCACCATGAT 58.373 37.500 8.01 0.00 41.26 2.45
3716 3773 5.038651 TCATTGCTATGTCATCACCATGA 57.961 39.130 8.01 0.00 36.62 3.07
3717 3774 5.061179 TCTCATTGCTATGTCATCACCATG 58.939 41.667 8.01 0.00 33.34 3.66
3718 3775 5.300411 TCTCATTGCTATGTCATCACCAT 57.700 39.130 8.01 0.00 33.34 3.55
3719 3776 4.443881 CCTCTCATTGCTATGTCATCACCA 60.444 45.833 8.01 0.00 33.34 4.17
3720 3777 4.063689 CCTCTCATTGCTATGTCATCACC 58.936 47.826 8.01 0.00 33.34 4.02
3721 3778 4.063689 CCCTCTCATTGCTATGTCATCAC 58.936 47.826 8.01 0.00 33.34 3.06
3722 3779 3.072038 CCCCTCTCATTGCTATGTCATCA 59.928 47.826 8.01 0.00 33.34 3.07
3723 3780 3.326006 TCCCCTCTCATTGCTATGTCATC 59.674 47.826 8.01 0.00 33.34 2.92
3724 3781 3.321039 TCCCCTCTCATTGCTATGTCAT 58.679 45.455 8.01 0.00 33.34 3.06
3725 3782 2.702478 CTCCCCTCTCATTGCTATGTCA 59.298 50.000 8.01 0.00 33.34 3.58
3726 3783 2.968574 TCTCCCCTCTCATTGCTATGTC 59.031 50.000 8.01 0.00 33.34 3.06
3727 3784 2.971330 CTCTCCCCTCTCATTGCTATGT 59.029 50.000 8.01 0.00 33.34 2.29
3728 3785 2.971330 ACTCTCCCCTCTCATTGCTATG 59.029 50.000 1.30 1.30 0.00 2.23
3729 3786 2.971330 CACTCTCCCCTCTCATTGCTAT 59.029 50.000 0.00 0.00 0.00 2.97
3730 3787 2.292521 ACACTCTCCCCTCTCATTGCTA 60.293 50.000 0.00 0.00 0.00 3.49
3731 3788 1.202330 CACTCTCCCCTCTCATTGCT 58.798 55.000 0.00 0.00 0.00 3.91
3732 3789 0.908198 ACACTCTCCCCTCTCATTGC 59.092 55.000 0.00 0.00 0.00 3.56
3733 3790 2.304180 ACAACACTCTCCCCTCTCATTG 59.696 50.000 0.00 0.00 0.00 2.82
3734 3791 2.569404 GACAACACTCTCCCCTCTCATT 59.431 50.000 0.00 0.00 0.00 2.57
3735 3792 2.183679 GACAACACTCTCCCCTCTCAT 58.816 52.381 0.00 0.00 0.00 2.90
3736 3793 1.633774 GACAACACTCTCCCCTCTCA 58.366 55.000 0.00 0.00 0.00 3.27
3737 3794 0.899019 GGACAACACTCTCCCCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
3738 3795 0.191064 TGGACAACACTCTCCCCTCT 59.809 55.000 0.00 0.00 0.00 3.69
3739 3796 0.321996 GTGGACAACACTCTCCCCTC 59.678 60.000 0.00 0.00 46.72 4.30
3740 3797 2.453242 GTGGACAACACTCTCCCCT 58.547 57.895 0.00 0.00 46.72 4.79
3748 3805 0.665369 CGAGGGTACGTGGACAACAC 60.665 60.000 0.00 0.00 46.78 3.32
3749 3806 1.108727 ACGAGGGTACGTGGACAACA 61.109 55.000 0.00 0.00 44.84 3.33
3750 3807 0.881118 TACGAGGGTACGTGGACAAC 59.119 55.000 0.00 0.00 46.02 3.32
3751 3808 1.167851 CTACGAGGGTACGTGGACAA 58.832 55.000 0.00 0.00 44.98 3.18
3752 3809 0.324614 TCTACGAGGGTACGTGGACA 59.675 55.000 0.00 0.00 45.53 4.02
3753 3810 3.159298 TCTACGAGGGTACGTGGAC 57.841 57.895 0.00 0.00 45.53 4.02
3755 3812 2.101700 GGTCTACGAGGGTACGTGG 58.898 63.158 0.00 0.00 46.02 4.94
3773 3830 1.254570 GTCATAACGCTTCCGCTTACG 59.745 52.381 0.00 0.00 38.22 3.18
3774 3831 2.264813 TGTCATAACGCTTCCGCTTAC 58.735 47.619 0.00 0.00 38.22 2.34
3775 3832 2.658373 TGTCATAACGCTTCCGCTTA 57.342 45.000 0.00 0.00 38.22 3.09
3776 3833 1.463444 GTTGTCATAACGCTTCCGCTT 59.537 47.619 0.00 0.00 38.22 4.68
3777 3834 1.076332 GTTGTCATAACGCTTCCGCT 58.924 50.000 0.00 0.00 38.22 5.52
3778 3835 0.247145 CGTTGTCATAACGCTTCCGC 60.247 55.000 0.00 0.00 36.82 5.54
3779 3836 3.850207 CGTTGTCATAACGCTTCCG 57.150 52.632 0.00 0.00 36.82 4.30
3785 3842 0.785378 TCAACCGCGTTGTCATAACG 59.215 50.000 16.97 1.71 43.23 3.18
3786 3843 2.158841 ACATCAACCGCGTTGTCATAAC 59.841 45.455 16.97 0.00 43.23 1.89
3787 3844 2.418692 ACATCAACCGCGTTGTCATAA 58.581 42.857 16.97 2.99 43.23 1.90
3788 3845 2.087501 ACATCAACCGCGTTGTCATA 57.912 45.000 16.97 3.28 43.23 2.15
3789 3846 1.999735 CTACATCAACCGCGTTGTCAT 59.000 47.619 16.97 5.85 43.23 3.06
3790 3847 1.269883 ACTACATCAACCGCGTTGTCA 60.270 47.619 16.97 4.13 43.23 3.58
3791 3848 1.389106 GACTACATCAACCGCGTTGTC 59.611 52.381 16.97 5.64 43.23 3.18
3792 3849 1.425412 GACTACATCAACCGCGTTGT 58.575 50.000 16.97 9.99 43.23 3.32
3793 3850 0.365523 CGACTACATCAACCGCGTTG 59.634 55.000 4.92 10.14 43.99 4.10
3794 3851 0.038892 ACGACTACATCAACCGCGTT 60.039 50.000 4.92 0.00 0.00 4.84
3795 3852 0.804364 TACGACTACATCAACCGCGT 59.196 50.000 4.92 0.00 0.00 6.01
3796 3853 1.186030 GTACGACTACATCAACCGCG 58.814 55.000 0.00 0.00 0.00 6.46
3797 3854 1.186030 CGTACGACTACATCAACCGC 58.814 55.000 10.44 0.00 0.00 5.68
3798 3855 2.094894 AGACGTACGACTACATCAACCG 59.905 50.000 24.41 0.00 0.00 4.44
3799 3856 3.423571 CAGACGTACGACTACATCAACC 58.576 50.000 24.41 0.00 0.00 3.77
3800 3857 2.844804 GCAGACGTACGACTACATCAAC 59.155 50.000 24.41 0.28 0.00 3.18
3801 3858 2.485038 TGCAGACGTACGACTACATCAA 59.515 45.455 24.41 0.00 0.00 2.57
3802 3859 2.078392 TGCAGACGTACGACTACATCA 58.922 47.619 24.41 13.38 0.00 3.07
3803 3860 2.438583 GTGCAGACGTACGACTACATC 58.561 52.381 24.41 12.35 0.00 3.06
3804 3861 2.539346 GTGCAGACGTACGACTACAT 57.461 50.000 24.41 0.00 0.00 2.29
3812 3869 0.860618 GTCGGATCGTGCAGACGTAC 60.861 60.000 0.00 0.00 46.20 3.67
3813 3870 1.426621 GTCGGATCGTGCAGACGTA 59.573 57.895 0.00 0.00 46.20 3.57
3814 3871 2.178521 GTCGGATCGTGCAGACGT 59.821 61.111 0.00 0.00 46.20 4.34
3816 3873 2.337749 ATCGGTCGGATCGTGCAGAC 62.338 60.000 10.85 0.00 33.12 3.51
3817 3874 2.060004 GATCGGTCGGATCGTGCAGA 62.060 60.000 10.85 0.00 42.02 4.26
3818 3875 1.658717 GATCGGTCGGATCGTGCAG 60.659 63.158 10.85 0.00 42.02 4.41
3819 3876 2.411701 GATCGGTCGGATCGTGCA 59.588 61.111 10.85 0.00 42.02 4.57
3825 3882 1.038280 GGTACTTGGATCGGTCGGAT 58.962 55.000 0.00 0.00 38.35 4.18
3826 3883 1.378882 CGGTACTTGGATCGGTCGGA 61.379 60.000 0.00 0.00 0.00 4.55
3827 3884 1.065273 CGGTACTTGGATCGGTCGG 59.935 63.158 0.00 0.00 0.00 4.79
3828 3885 0.452987 TTCGGTACTTGGATCGGTCG 59.547 55.000 0.00 0.00 0.00 4.79
3829 3886 1.796617 CGTTCGGTACTTGGATCGGTC 60.797 57.143 0.00 0.00 0.00 4.79
3830 3887 0.171903 CGTTCGGTACTTGGATCGGT 59.828 55.000 0.00 0.00 0.00 4.69
3831 3888 0.171903 ACGTTCGGTACTTGGATCGG 59.828 55.000 13.18 0.00 31.53 4.18
3832 3889 2.830772 TACGTTCGGTACTTGGATCG 57.169 50.000 0.00 2.46 0.00 3.69


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

AutoCloner maintained by Alex Coulton.