Multiple sequence alignment - TraesCS3B01G365600

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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 TraesCS3B01G365600 chr3B 100.000 3720 0 0 1413 5132 578285874 578282155 0.000000e+00 6870.0
1 TraesCS3B01G365600 chr3B 100.000 1155 0 0 1 1155 578287286 578286132 0.000000e+00 2134.0
2 TraesCS3B01G365600 chr3D 93.728 2009 89 22 2497 4495 441134475 441132494 0.000000e+00 2977.0
3 TraesCS3B01G365600 chr3D 85.714 749 91 14 1750 2490 29163400 29164140 0.000000e+00 776.0
4 TraesCS3B01G365600 chr3D 87.768 466 25 19 711 1155 441136400 441135946 2.740000e-142 516.0
5 TraesCS3B01G365600 chr3D 90.551 254 21 2 4832 5082 441131055 441130802 2.960000e-87 333.0
6 TraesCS3B01G365600 chr3D 94.479 163 8 1 1416 1578 441135875 441135714 3.070000e-62 250.0
7 TraesCS3B01G365600 chr3D 90.152 132 11 2 4584 4715 441131202 441131073 2.460000e-38 171.0
8 TraesCS3B01G365600 chr3D 93.333 105 6 1 1626 1729 441134673 441134569 2.470000e-33 154.0
9 TraesCS3B01G365600 chr3D 90.789 76 7 0 4756 4831 123640324 123640249 9.090000e-18 102.0
10 TraesCS3B01G365600 chr3D 90.667 75 7 0 4756 4830 388748683 388748609 3.270000e-17 100.0
11 TraesCS3B01G365600 chr3A 93.264 1247 68 13 2497 3736 581262037 581260800 0.000000e+00 1823.0
12 TraesCS3B01G365600 chr3A 88.215 1137 80 19 3729 4826 581260625 581259504 0.000000e+00 1308.0
13 TraesCS3B01G365600 chr3A 87.919 447 32 14 711 1148 581262933 581262500 1.650000e-139 507.0
14 TraesCS3B01G365600 chr3A 94.030 268 15 1 1416 1682 581262419 581262152 6.190000e-109 405.0
15 TraesCS3B01G365600 chr3A 91.339 254 13 6 4832 5082 581259536 581259289 6.370000e-89 339.0
16 TraesCS3B01G365600 chr3A 77.880 217 35 8 4617 4831 734849146 734848941 6.980000e-24 122.0
17 TraesCS3B01G365600 chr3A 77.778 216 37 5 4617 4831 734894562 734894357 6.980000e-24 122.0
18 TraesCS3B01G365600 chr3A 86.667 90 8 2 1665 1750 581262113 581262024 4.230000e-16 97.1
19 TraesCS3B01G365600 chr5B 95.430 744 31 3 1750 2492 451189716 451190457 0.000000e+00 1182.0
20 TraesCS3B01G365600 chr5B 88.705 726 72 9 1 718 705898996 705899719 0.000000e+00 878.0
21 TraesCS3B01G365600 chr2B 93.674 743 42 5 1751 2492 280485822 280486560 0.000000e+00 1107.0
22 TraesCS3B01G365600 chr2B 88.192 542 59 5 1950 2489 546212514 546211976 4.330000e-180 641.0
23 TraesCS3B01G365600 chr4B 91.153 746 59 5 1746 2490 423219833 423219094 0.000000e+00 1005.0
24 TraesCS3B01G365600 chr2A 91.469 715 57 2 1 711 751946154 751945440 0.000000e+00 979.0
25 TraesCS3B01G365600 chr2A 90.782 716 61 5 1 712 691537618 691538332 0.000000e+00 952.0
26 TraesCS3B01G365600 chr2A 89.902 713 68 2 1 710 38813336 38814047 0.000000e+00 915.0
27 TraesCS3B01G365600 chr6A 91.445 713 58 1 1 710 573401416 573400704 0.000000e+00 976.0
28 TraesCS3B01G365600 chr5D 90.042 713 60 2 1 707 505910970 505910263 0.000000e+00 913.0
29 TraesCS3B01G365600 chr5D 84.605 747 97 17 1752 2490 510610243 510610979 0.000000e+00 726.0
30 TraesCS3B01G365600 chr5D 86.850 654 75 11 1747 2394 543504176 543504824 0.000000e+00 721.0
31 TraesCS3B01G365600 chr4A 89.167 720 58 12 1 715 583725494 583724790 0.000000e+00 880.0
32 TraesCS3B01G365600 chr1A 88.079 713 75 8 1 709 543057286 543056580 0.000000e+00 837.0
33 TraesCS3B01G365600 chr1A 85.657 746 92 15 1752 2490 278788942 278788205 0.000000e+00 771.0
34 TraesCS3B01G365600 chr4D 85.734 743 92 13 1753 2489 280776330 280777064 0.000000e+00 773.0
35 TraesCS3B01G365600 chr4D 90.667 75 7 0 4756 4830 36667135 36667209 3.270000e-17 100.0
36 TraesCS3B01G365600 chr2D 91.619 525 41 1 190 711 26457367 26457891 0.000000e+00 723.0
37 TraesCS3B01G365600 chr7D 88.927 289 29 3 1754 2041 75808624 75808910 2.270000e-93 353.0
38 TraesCS3B01G365600 chr7D 90.789 76 7 0 4756 4831 140747883 140747958 9.090000e-18 102.0
39 TraesCS3B01G365600 chr5A 74.274 482 89 26 4617 5090 638287966 638287512 2.460000e-38 171.0
40 TraesCS3B01G365600 chr6D 90.789 76 7 0 4756 4831 270569818 270569893 9.090000e-18 102.0
41 TraesCS3B01G365600 chr1D 90.789 76 7 0 4756 4831 449228477 449228552 9.090000e-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 TraesCS3B01G365600 chr3B 578282155 578287286 5131 True 4502.000000 6870 100.0000 1 5132 2 chr3B.!!$R1 5131
1 TraesCS3B01G365600 chr3D 29163400 29164140 740 False 776.000000 776 85.7140 1750 2490 1 chr3D.!!$F1 740
2 TraesCS3B01G365600 chr3D 441130802 441136400 5598 True 733.500000 2977 91.6685 711 5082 6 chr3D.!!$R3 4371
3 TraesCS3B01G365600 chr3A 581259289 581262933 3644 True 746.516667 1823 90.2390 711 5082 6 chr3A.!!$R3 4371
4 TraesCS3B01G365600 chr5B 451189716 451190457 741 False 1182.000000 1182 95.4300 1750 2492 1 chr5B.!!$F1 742
5 TraesCS3B01G365600 chr5B 705898996 705899719 723 False 878.000000 878 88.7050 1 718 1 chr5B.!!$F2 717
6 TraesCS3B01G365600 chr2B 280485822 280486560 738 False 1107.000000 1107 93.6740 1751 2492 1 chr2B.!!$F1 741
7 TraesCS3B01G365600 chr2B 546211976 546212514 538 True 641.000000 641 88.1920 1950 2489 1 chr2B.!!$R1 539
8 TraesCS3B01G365600 chr4B 423219094 423219833 739 True 1005.000000 1005 91.1530 1746 2490 1 chr4B.!!$R1 744
9 TraesCS3B01G365600 chr2A 751945440 751946154 714 True 979.000000 979 91.4690 1 711 1 chr2A.!!$R1 710
10 TraesCS3B01G365600 chr2A 691537618 691538332 714 False 952.000000 952 90.7820 1 712 1 chr2A.!!$F2 711
11 TraesCS3B01G365600 chr2A 38813336 38814047 711 False 915.000000 915 89.9020 1 710 1 chr2A.!!$F1 709
12 TraesCS3B01G365600 chr6A 573400704 573401416 712 True 976.000000 976 91.4450 1 710 1 chr6A.!!$R1 709
13 TraesCS3B01G365600 chr5D 505910263 505910970 707 True 913.000000 913 90.0420 1 707 1 chr5D.!!$R1 706
14 TraesCS3B01G365600 chr5D 510610243 510610979 736 False 726.000000 726 84.6050 1752 2490 1 chr5D.!!$F1 738
15 TraesCS3B01G365600 chr5D 543504176 543504824 648 False 721.000000 721 86.8500 1747 2394 1 chr5D.!!$F2 647
16 TraesCS3B01G365600 chr4A 583724790 583725494 704 True 880.000000 880 89.1670 1 715 1 chr4A.!!$R1 714
17 TraesCS3B01G365600 chr1A 543056580 543057286 706 True 837.000000 837 88.0790 1 709 1 chr1A.!!$R2 708
18 TraesCS3B01G365600 chr1A 278788205 278788942 737 True 771.000000 771 85.6570 1752 2490 1 chr1A.!!$R1 738
19 TraesCS3B01G365600 chr4D 280776330 280777064 734 False 773.000000 773 85.7340 1753 2489 1 chr4D.!!$F2 736
20 TraesCS3B01G365600 chr2D 26457367 26457891 524 False 723.000000 723 91.6190 190 711 1 chr2D.!!$F1 521

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
214 215 0.461961 CTAAGTGGCTTCCTCCTCCG 59.538 60.0 0.00 0.00 0.0 4.63 F
1074 1114 0.259356 CGTAAGTCCCTCCTCCTCCT 59.741 60.0 0.00 0.00 0.0 3.69 F
1679 2714 0.033601 AGCTCAACCCAAACACACCA 60.034 50.0 0.00 0.00 0.0 4.17 F
2065 3254 0.035630 GTGCCAGCCATCTCTTCAGT 60.036 55.0 0.00 0.00 0.0 3.41 F
3099 4292 0.179056 TTATAAGTCGCTGGCTGGCC 60.179 55.0 4.43 4.43 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1462 0.958091 CCTGCAACACCAATCCGAAA 59.042 50.000 0.0 0.0 0.00 3.46 R
2965 4158 1.069978 TGAACGCTTGTCATCCACTGA 59.930 47.619 0.0 0.0 0.00 3.41 R
3643 4842 2.598565 ACCCTTTCTTTCCTGCTTTCC 58.401 47.619 0.0 0.0 0.00 3.13 R
3706 4905 4.035675 CAGAGAAAACACACCTTCAGTTCC 59.964 45.833 0.0 0.0 0.00 3.62 R
4840 7435 0.035725 TGCAGCAGGATGAACTCAGG 60.036 55.000 0.0 0.0 39.69 3.86 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
34 35 8.650143 ATGAGTTGGTACACAATAAAATTCCT 57.350 30.769 0.00 0.00 41.95 3.36
55 56 1.447838 ACCGATGAATGCTTCGCGT 60.448 52.632 5.77 1.15 39.53 6.01
58 59 0.578683 CGATGAATGCTTCGCGTCAT 59.421 50.000 5.77 6.68 38.18 3.06
70 71 3.643159 TCGCGTCATTATCTATGCAGT 57.357 42.857 5.77 0.00 34.06 4.40
82 83 7.661536 TTATCTATGCAGTTACCTTGAGTCT 57.338 36.000 0.00 0.00 0.00 3.24
91 92 6.293955 GCAGTTACCTTGAGTCTTTAATTGCA 60.294 38.462 12.10 0.00 36.16 4.08
92 93 7.078228 CAGTTACCTTGAGTCTTTAATTGCAC 58.922 38.462 0.00 0.00 0.00 4.57
152 153 5.946942 AGCGGTGATATCTTATGATCCAT 57.053 39.130 3.98 0.00 34.32 3.41
214 215 0.461961 CTAAGTGGCTTCCTCCTCCG 59.538 60.000 0.00 0.00 0.00 4.63
216 217 3.003763 GTGGCTTCCTCCTCCGGT 61.004 66.667 0.00 0.00 0.00 5.28
224 225 2.606519 CTCCTCCGGTGGGTTGGA 60.607 66.667 22.07 10.07 36.29 3.53
270 271 2.173569 GGACTAATGATGGAAGGGCTGT 59.826 50.000 0.00 0.00 0.00 4.40
277 278 3.376918 GGAAGGGCTGTTGCTGGC 61.377 66.667 0.00 0.00 39.59 4.85
350 352 1.035139 ATTTTCATGCCGAGATGCCC 58.965 50.000 0.00 0.00 0.00 5.36
358 360 2.176273 CCGAGATGCCCTTGAAGCG 61.176 63.158 0.00 0.00 0.00 4.68
379 381 3.243468 CGGAAATATGTGCATGCATGGAA 60.243 43.478 25.64 15.61 0.00 3.53
385 387 1.273048 TGTGCATGCATGGAAGGTTTC 59.727 47.619 25.64 12.47 0.00 2.78
416 419 3.462483 TTCAGCAGACGTAACTTCCAA 57.538 42.857 0.00 0.00 0.00 3.53
421 424 3.058224 AGCAGACGTAACTTCCAATTTGC 60.058 43.478 0.00 0.00 0.00 3.68
441 444 4.371786 TGCATCGAGATGGATTCACTTAC 58.628 43.478 14.13 0.00 39.16 2.34
514 517 5.734720 TCTTTGGTGGCAGAGATAAAGTAG 58.265 41.667 0.00 0.00 0.00 2.57
527 530 9.921637 CAGAGATAAAGTAGTTGAAGTCTCTTT 57.078 33.333 11.38 7.75 39.16 2.52
571 577 9.559958 CATATCAACTGTGGTCAAAATTTAGTC 57.440 33.333 0.00 0.00 0.00 2.59
620 627 4.857509 ACTGAGAGTAGAACTGTTGTCC 57.142 45.455 0.00 0.00 0.00 4.02
745 758 2.683211 AAACAATTGGTCAGCCTCCT 57.317 45.000 10.83 0.00 35.27 3.69
747 760 1.067295 ACAATTGGTCAGCCTCCTCA 58.933 50.000 10.83 0.00 35.27 3.86
795 812 3.728279 AATACGAACGGGCCGCCTC 62.728 63.158 28.71 21.57 0.00 4.70
886 915 1.685224 CTGAACCCTAGCTTGGCCA 59.315 57.895 0.00 0.00 0.00 5.36
907 936 2.736826 CCCCTCTCTTTCGGCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
908 937 1.990060 CCCTCTCTTTCGGCCTCCA 60.990 63.158 0.00 0.00 0.00 3.86
1074 1114 0.259356 CGTAAGTCCCTCCTCCTCCT 59.741 60.000 0.00 0.00 0.00 3.69
1075 1115 1.751382 CGTAAGTCCCTCCTCCTCCTC 60.751 61.905 0.00 0.00 0.00 3.71
1081 1121 1.074850 CCTCCTCCTCCTCCCCTTC 60.075 68.421 0.00 0.00 0.00 3.46
1544 1587 2.972625 TCAGGGTATTGCTTCTGTTCG 58.027 47.619 0.00 0.00 0.00 3.95
1545 1588 1.398390 CAGGGTATTGCTTCTGTTCGC 59.602 52.381 0.00 0.00 0.00 4.70
1569 1612 1.334869 CAAGTTGGGACTCTTGTGTGC 59.665 52.381 0.00 0.00 36.72 4.57
1574 1617 1.620822 GGGACTCTTGTGTGCCATTT 58.379 50.000 8.18 0.00 45.96 2.32
1596 1639 6.611613 TTCTTCTCTTCACCTATGTCATGT 57.388 37.500 0.00 0.00 0.00 3.21
1615 1659 1.818674 GTGATGTGCCCCTTTAACTGG 59.181 52.381 0.00 0.00 0.00 4.00
1679 2714 0.033601 AGCTCAACCCAAACACACCA 60.034 50.000 0.00 0.00 0.00 4.17
1682 2717 2.802774 GCTCAACCCAAACACACCATTG 60.803 50.000 0.00 0.00 0.00 2.82
1683 2777 2.692557 CTCAACCCAAACACACCATTGA 59.307 45.455 0.00 0.00 0.00 2.57
1747 2928 7.214460 TGGTACATTCCTGGGATGTTTATTA 57.786 36.000 25.09 4.66 0.00 0.98
1748 2929 7.821566 TGGTACATTCCTGGGATGTTTATTAT 58.178 34.615 25.09 1.66 0.00 1.28
1749 2930 8.950480 TGGTACATTCCTGGGATGTTTATTATA 58.050 33.333 25.09 3.16 0.00 0.98
2041 3227 4.940654 GGAAGAAGCAGCAAAAGATAGACT 59.059 41.667 0.00 0.00 0.00 3.24
2065 3254 0.035630 GTGCCAGCCATCTCTTCAGT 60.036 55.000 0.00 0.00 0.00 3.41
2360 3552 4.105754 AGTTTTCTTCCCAGGGAGAAAG 57.894 45.455 22.36 13.78 33.74 2.62
2492 3684 1.006043 TGTTGAACTGTTTCCACCCCA 59.994 47.619 0.00 0.00 0.00 4.96
2493 3685 2.104170 GTTGAACTGTTTCCACCCCAA 58.896 47.619 0.00 0.00 0.00 4.12
2494 3686 2.698274 GTTGAACTGTTTCCACCCCAAT 59.302 45.455 0.00 0.00 0.00 3.16
2495 3687 3.885976 TGAACTGTTTCCACCCCAATA 57.114 42.857 0.00 0.00 0.00 1.90
2496 3688 3.761897 TGAACTGTTTCCACCCCAATAG 58.238 45.455 0.00 0.00 0.00 1.73
2497 3689 2.899303 ACTGTTTCCACCCCAATAGG 57.101 50.000 0.00 0.00 0.00 2.57
2498 3690 2.354328 ACTGTTTCCACCCCAATAGGA 58.646 47.619 0.00 0.00 38.24 2.94
2499 3691 2.926329 ACTGTTTCCACCCCAATAGGAT 59.074 45.455 0.00 0.00 38.24 3.24
2500 3692 3.290710 CTGTTTCCACCCCAATAGGATG 58.709 50.000 0.00 0.00 38.24 3.51
2501 3693 2.652348 TGTTTCCACCCCAATAGGATGT 59.348 45.455 0.00 0.00 38.24 3.06
2502 3694 3.076785 TGTTTCCACCCCAATAGGATGTT 59.923 43.478 0.00 0.00 38.24 2.71
2503 3695 4.093743 GTTTCCACCCCAATAGGATGTTT 58.906 43.478 0.00 0.00 38.24 2.83
2504 3696 5.222358 TGTTTCCACCCCAATAGGATGTTTA 60.222 40.000 0.00 0.00 38.24 2.01
2505 3697 5.742562 TTCCACCCCAATAGGATGTTTAT 57.257 39.130 0.00 0.00 38.24 1.40
2506 3698 5.742562 TCCACCCCAATAGGATGTTTATT 57.257 39.130 0.00 0.00 38.24 1.40
2813 4006 3.461085 ACATGGGATACATCTTTCAGGCT 59.539 43.478 0.00 0.00 37.84 4.58
2837 4030 5.637387 TGTTCAAAGTGAAAGAAAGGTTTGC 59.363 36.000 0.00 0.00 38.22 3.68
2849 4042 0.878961 AGGTTTGCGGTGACTTCGAC 60.879 55.000 0.00 0.00 0.00 4.20
2946 4139 5.277345 CCTTTGACTGTAGAAAGTTGAACGG 60.277 44.000 9.63 0.00 0.00 4.44
3022 4215 4.694037 ACTTTGCGGAAGACAGGTATAAAC 59.306 41.667 6.64 0.00 38.77 2.01
3096 4289 5.468072 AGATTCATTTATAAGTCGCTGGCTG 59.532 40.000 0.00 0.00 0.00 4.85
3099 4292 0.179056 TTATAAGTCGCTGGCTGGCC 60.179 55.000 4.43 4.43 0.00 5.36
3106 4299 2.276740 GCTGGCTGGCCACCTAAT 59.723 61.111 20.61 0.00 41.89 1.73
3191 4384 1.912043 AGGATAGGTCAAAGCAGCAGT 59.088 47.619 0.00 0.00 0.00 4.40
3261 4454 7.276438 GTGCTGTTCTTTTGGGAATATGATTTC 59.724 37.037 0.00 0.00 0.00 2.17
3262 4455 6.758416 GCTGTTCTTTTGGGAATATGATTTCC 59.242 38.462 0.00 0.00 43.78 3.13
3298 4491 9.845740 ATGTGGCTACTGTGATTAATGTTATAA 57.154 29.630 0.64 0.00 0.00 0.98
3299 4492 9.325198 TGTGGCTACTGTGATTAATGTTATAAG 57.675 33.333 0.64 0.00 0.00 1.73
3300 4493 9.326413 GTGGCTACTGTGATTAATGTTATAAGT 57.674 33.333 0.00 0.00 0.00 2.24
3317 4510 5.827326 ATAAGTACTTGGGAAGGATAGCC 57.173 43.478 18.56 0.00 0.00 3.93
3364 4558 8.868522 AATGAATGTTGGATCTGTTCTCTTTA 57.131 30.769 0.00 0.00 0.00 1.85
3366 4560 6.372659 TGAATGTTGGATCTGTTCTCTTTAGC 59.627 38.462 0.00 0.00 0.00 3.09
3372 4566 7.200434 TGGATCTGTTCTCTTTAGCCTTTAT 57.800 36.000 0.00 0.00 0.00 1.40
3412 4608 6.766944 CCTGCTTCATTATTGAGACTTGAGAT 59.233 38.462 0.00 0.00 32.27 2.75
3506 4702 6.094881 GCAAATTACTCAGTGGTAATGGCTTA 59.905 38.462 19.94 0.48 40.27 3.09
3518 4714 2.283145 ATGGCTTAGATGTGGGATGC 57.717 50.000 0.00 0.00 0.00 3.91
3525 4723 4.790766 GCTTAGATGTGGGATGCGATTTTG 60.791 45.833 0.00 0.00 0.00 2.44
3556 4754 7.261829 AGCTCAAAGCATTATCTTGATTCTC 57.738 36.000 1.29 0.00 45.56 2.87
3600 4799 6.763715 ACTGCCTGATAAACTTATATCCCA 57.236 37.500 0.00 0.00 32.39 4.37
3706 4905 0.388907 CGGACATGGCCTTGCAAAAG 60.389 55.000 17.64 0.00 0.00 2.27
3875 5263 7.550196 GGCTTATGAAATTTTGATGGTCATGTT 59.450 33.333 0.00 0.00 31.58 2.71
3978 5366 1.971357 AGGAAGCTCCGTGAAGAAGAA 59.029 47.619 0.00 0.00 42.75 2.52
4140 5528 6.925718 CGCTAAACTTCAGATGATAGGAATGA 59.074 38.462 0.00 0.00 0.00 2.57
4154 5542 2.026822 AGGAATGACGAAAGCTGGACAT 60.027 45.455 0.00 0.00 0.00 3.06
4185 5573 3.063526 AGCTGGCGCTTGAAGAGA 58.936 55.556 7.64 0.00 46.47 3.10
4189 5577 2.011046 GCTGGCGCTTGAAGAGATTCT 61.011 52.381 7.64 0.00 0.00 2.40
4204 5592 4.405358 AGAGATTCTCTTCCCTGTGACATC 59.595 45.833 10.50 0.00 37.60 3.06
4227 5615 3.460478 TTGCCCTTCCACAACCCCC 62.460 63.158 0.00 0.00 0.00 5.40
4269 5657 3.119137 CCTTTATAACCTTTGCCTGGTGC 60.119 47.826 0.00 0.00 37.93 5.01
4350 5740 9.055248 CAATTTCTCGAAATGTTAAGTGATCAC 57.945 33.333 18.47 18.47 40.57 3.06
4372 5762 6.204688 TCACAGTCACCATGTAAGAACAATTC 59.795 38.462 0.00 0.00 39.58 2.17
4379 5769 5.653769 ACCATGTAAGAACAATTCTGATGGG 59.346 40.000 19.13 10.05 41.57 4.00
4391 5781 8.877864 ACAATTCTGATGGGTATAGTTGAAAA 57.122 30.769 0.00 0.00 0.00 2.29
4447 5838 0.694771 ATTTCAGTCCTGGCAGCTGA 59.305 50.000 20.43 17.49 37.47 4.26
4461 5852 3.129988 GGCAGCTGATTAACTTGCATTCT 59.870 43.478 20.43 0.00 0.00 2.40
4486 5877 5.880332 ACGATTAGAAAGCAGAGCCAAATTA 59.120 36.000 0.00 0.00 0.00 1.40
4532 7094 3.382865 TGCAAGAAAATGTGCACTACCAA 59.617 39.130 19.41 0.00 45.52 3.67
4534 7096 4.736168 GCAAGAAAATGTGCACTACCAACA 60.736 41.667 19.41 0.00 40.58 3.33
4537 7099 3.302365 AAATGTGCACTACCAACATGC 57.698 42.857 19.41 0.00 39.88 4.06
4543 7105 1.135689 GCACTACCAACATGCTTTCCG 60.136 52.381 0.00 0.00 36.40 4.30
4551 7114 3.305267 CCAACATGCTTTCCGTTCAATCA 60.305 43.478 0.00 0.00 0.00 2.57
4579 7142 6.646267 CCATCCAATTTTCATCAAATGGTCT 58.354 36.000 0.00 0.00 35.09 3.85
4580 7143 7.107542 CCATCCAATTTTCATCAAATGGTCTT 58.892 34.615 0.00 0.00 35.09 3.01
4581 7144 7.608761 CCATCCAATTTTCATCAAATGGTCTTT 59.391 33.333 0.00 0.00 35.09 2.52
4582 7145 9.656040 CATCCAATTTTCATCAAATGGTCTTTA 57.344 29.630 0.00 0.00 35.09 1.85
4592 7187 6.463995 TCAAATGGTCTTTAACACAAGCTT 57.536 33.333 0.00 0.00 0.00 3.74
4622 7217 3.348119 GAGGATCCTCTTCCCACAAAAC 58.652 50.000 31.11 3.54 39.80 2.43
4628 7223 3.655777 TCCTCTTCCCACAAAACCTATGT 59.344 43.478 0.00 0.00 0.00 2.29
4647 7242 7.959689 CTATGTGAGGATCCACTTTTCTATG 57.040 40.000 15.82 0.00 37.89 2.23
4648 7243 4.517285 TGTGAGGATCCACTTTTCTATGC 58.483 43.478 15.82 0.00 37.89 3.14
4649 7244 4.019411 TGTGAGGATCCACTTTTCTATGCA 60.019 41.667 15.82 0.00 37.89 3.96
4650 7245 5.128919 GTGAGGATCCACTTTTCTATGCAT 58.871 41.667 15.82 3.79 34.38 3.96
4651 7246 5.238214 GTGAGGATCCACTTTTCTATGCATC 59.762 44.000 15.82 0.00 34.38 3.91
4652 7247 5.104402 TGAGGATCCACTTTTCTATGCATCA 60.104 40.000 15.82 0.17 0.00 3.07
4658 7253 4.414852 CACTTTTCTATGCATCAAACCCG 58.585 43.478 0.19 0.00 0.00 5.28
4663 7258 3.023119 TCTATGCATCAAACCCGCAATT 58.977 40.909 0.19 0.00 39.48 2.32
4700 7295 8.669243 GTTTATTCAACTATAAGCTGCAGAGTT 58.331 33.333 20.43 14.77 31.92 3.01
4715 7310 3.188667 GCAGAGTTACACCTTTACAAGCC 59.811 47.826 0.00 0.00 0.00 4.35
4728 7323 3.984292 CAAGCCGCATCTTGTTCTC 57.016 52.632 6.74 0.00 38.81 2.87
4733 7328 1.815421 CGCATCTTGTTCTCCCCCG 60.815 63.158 0.00 0.00 0.00 5.73
4796 7391 3.969312 TGATTCACATGATAGCCTCCAGA 59.031 43.478 0.00 0.00 0.00 3.86
4813 7408 0.252284 AGACGTCCTGGGTTCATCCT 60.252 55.000 13.01 0.00 36.25 3.24
4814 7409 0.108138 GACGTCCTGGGTTCATCCTG 60.108 60.000 3.51 0.00 36.25 3.86
4815 7410 1.450312 CGTCCTGGGTTCATCCTGC 60.450 63.158 0.00 0.00 36.25 4.85
4816 7411 1.903877 CGTCCTGGGTTCATCCTGCT 61.904 60.000 0.00 0.00 36.25 4.24
4817 7412 0.393537 GTCCTGGGTTCATCCTGCTG 60.394 60.000 0.00 0.00 36.25 4.41
4818 7413 1.751927 CCTGGGTTCATCCTGCTGC 60.752 63.158 0.00 0.00 36.25 5.25
4819 7414 1.001764 CTGGGTTCATCCTGCTGCA 60.002 57.895 0.88 0.88 36.25 4.41
4820 7415 0.609957 CTGGGTTCATCCTGCTGCAA 60.610 55.000 3.02 0.00 36.25 4.08
4821 7416 0.040058 TGGGTTCATCCTGCTGCAAT 59.960 50.000 3.02 0.00 36.25 3.56
4822 7417 1.188863 GGGTTCATCCTGCTGCAATT 58.811 50.000 3.02 0.00 36.25 2.32
4823 7418 1.135721 GGGTTCATCCTGCTGCAATTC 59.864 52.381 3.02 0.00 36.25 2.17
4824 7419 1.820519 GGTTCATCCTGCTGCAATTCA 59.179 47.619 3.02 0.00 0.00 2.57
4825 7420 2.429610 GGTTCATCCTGCTGCAATTCAT 59.570 45.455 3.02 0.00 0.00 2.57
4826 7421 3.444916 GTTCATCCTGCTGCAATTCATG 58.555 45.455 3.02 3.84 0.00 3.07
4827 7422 3.007473 TCATCCTGCTGCAATTCATGA 57.993 42.857 3.02 6.13 0.00 3.07
4828 7423 3.358118 TCATCCTGCTGCAATTCATGAA 58.642 40.909 11.26 11.26 0.00 2.57
4829 7424 3.958147 TCATCCTGCTGCAATTCATGAAT 59.042 39.130 15.36 15.36 0.00 2.57
4830 7425 4.404394 TCATCCTGCTGCAATTCATGAATT 59.596 37.500 24.83 24.83 41.33 2.17
4831 7426 4.811969 TCCTGCTGCAATTCATGAATTT 57.188 36.364 27.30 12.74 38.84 1.82
4832 7427 4.751060 TCCTGCTGCAATTCATGAATTTC 58.249 39.130 27.30 23.44 38.84 2.17
4833 7428 3.869246 CCTGCTGCAATTCATGAATTTCC 59.131 43.478 27.30 21.09 38.84 3.13
4834 7429 4.500127 CTGCTGCAATTCATGAATTTCCA 58.500 39.130 27.30 23.74 38.84 3.53
4835 7430 4.500127 TGCTGCAATTCATGAATTTCCAG 58.500 39.130 31.34 31.34 38.84 3.86
4836 7431 3.308866 GCTGCAATTCATGAATTTCCAGC 59.691 43.478 36.92 36.92 45.50 4.85
4837 7432 3.864243 TGCAATTCATGAATTTCCAGCC 58.136 40.909 27.30 14.07 38.84 4.85
4838 7433 3.261137 TGCAATTCATGAATTTCCAGCCA 59.739 39.130 27.30 15.92 38.84 4.75
4839 7434 4.080807 TGCAATTCATGAATTTCCAGCCAT 60.081 37.500 27.30 4.46 38.84 4.40
4840 7435 4.510340 GCAATTCATGAATTTCCAGCCATC 59.490 41.667 27.30 7.75 38.84 3.51
4841 7436 4.950205 ATTCATGAATTTCCAGCCATCC 57.050 40.909 15.36 0.00 0.00 3.51
4842 7437 3.675348 TCATGAATTTCCAGCCATCCT 57.325 42.857 0.00 0.00 0.00 3.24
4843 7438 3.293337 TCATGAATTTCCAGCCATCCTG 58.707 45.455 0.00 0.00 41.41 3.86
4844 7439 3.053470 TCATGAATTTCCAGCCATCCTGA 60.053 43.478 0.00 0.00 44.64 3.86
4845 7440 3.008835 TGAATTTCCAGCCATCCTGAG 57.991 47.619 0.00 0.00 44.64 3.35
4846 7441 2.309755 TGAATTTCCAGCCATCCTGAGT 59.690 45.455 0.00 0.00 44.64 3.41
4847 7442 3.245371 TGAATTTCCAGCCATCCTGAGTT 60.245 43.478 0.00 0.00 44.64 3.01
4848 7443 2.496899 TTTCCAGCCATCCTGAGTTC 57.503 50.000 0.00 0.00 44.64 3.01
4849 7444 1.361204 TTCCAGCCATCCTGAGTTCA 58.639 50.000 0.00 0.00 44.64 3.18
4850 7445 1.588239 TCCAGCCATCCTGAGTTCAT 58.412 50.000 0.00 0.00 44.64 2.57
4851 7446 1.487976 TCCAGCCATCCTGAGTTCATC 59.512 52.381 0.00 0.00 44.64 2.92
4852 7447 1.476471 CCAGCCATCCTGAGTTCATCC 60.476 57.143 0.00 0.00 44.64 3.51
4853 7448 1.489649 CAGCCATCCTGAGTTCATCCT 59.510 52.381 0.00 0.00 44.64 3.24
4867 7462 3.007473 TCATCCTGCTGCAATTCATCA 57.993 42.857 3.02 0.00 0.00 3.07
4870 7465 4.037565 TCATCCTGCTGCAATTCATCAATC 59.962 41.667 3.02 0.00 0.00 2.67
4875 7470 2.159338 GCTGCAATTCATCAATCGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
4911 7506 6.058833 TCAAGTGCTGTTATACCTTGAAACA 58.941 36.000 0.00 0.00 0.00 2.83
5032 7628 2.432146 AGTCAGAGTGTTCAGCTTCACA 59.568 45.455 13.50 3.87 37.07 3.58
5038 7634 4.127171 GAGTGTTCAGCTTCACAGGTTTA 58.873 43.478 13.50 0.00 37.07 2.01
5045 7641 6.500684 TCAGCTTCACAGGTTTATTGATTC 57.499 37.500 0.00 0.00 0.00 2.52
5079 7677 7.805071 AGTGAAAATTAAACTTCGAAGCTGATG 59.195 33.333 24.86 1.38 0.00 3.07
5082 7680 9.267096 GAAAATTAAACTTCGAAGCTGATGTAG 57.733 33.333 24.86 0.00 0.00 2.74
5083 7681 7.907214 AATTAAACTTCGAAGCTGATGTAGT 57.093 32.000 24.86 0.00 0.00 2.73
5084 7682 6.706055 TTAAACTTCGAAGCTGATGTAGTG 57.294 37.500 24.86 0.00 0.00 2.74
5085 7683 3.944055 ACTTCGAAGCTGATGTAGTGT 57.056 42.857 24.86 0.00 0.00 3.55
5086 7684 3.579709 ACTTCGAAGCTGATGTAGTGTG 58.420 45.455 24.86 0.00 0.00 3.82
5087 7685 1.996292 TCGAAGCTGATGTAGTGTGC 58.004 50.000 0.00 0.00 0.00 4.57
5088 7686 1.546029 TCGAAGCTGATGTAGTGTGCT 59.454 47.619 0.00 0.00 35.30 4.40
5089 7687 1.657594 CGAAGCTGATGTAGTGTGCTG 59.342 52.381 0.00 0.00 33.96 4.41
5090 7688 2.005451 GAAGCTGATGTAGTGTGCTGG 58.995 52.381 0.00 0.00 33.96 4.85
5091 7689 1.269958 AGCTGATGTAGTGTGCTGGA 58.730 50.000 0.00 0.00 32.32 3.86
5092 7690 1.625315 AGCTGATGTAGTGTGCTGGAA 59.375 47.619 0.00 0.00 32.32 3.53
5093 7691 2.038952 AGCTGATGTAGTGTGCTGGAAA 59.961 45.455 0.00 0.00 32.32 3.13
5094 7692 3.012518 GCTGATGTAGTGTGCTGGAAAT 58.987 45.455 0.00 0.00 0.00 2.17
5095 7693 3.181503 GCTGATGTAGTGTGCTGGAAATG 60.182 47.826 0.00 0.00 0.00 2.32
5096 7694 4.256110 CTGATGTAGTGTGCTGGAAATGA 58.744 43.478 0.00 0.00 0.00 2.57
5097 7695 4.650734 TGATGTAGTGTGCTGGAAATGAA 58.349 39.130 0.00 0.00 0.00 2.57
5098 7696 5.255687 TGATGTAGTGTGCTGGAAATGAAT 58.744 37.500 0.00 0.00 0.00 2.57
5099 7697 6.413892 TGATGTAGTGTGCTGGAAATGAATA 58.586 36.000 0.00 0.00 0.00 1.75
5100 7698 6.883756 TGATGTAGTGTGCTGGAAATGAATAA 59.116 34.615 0.00 0.00 0.00 1.40
5101 7699 6.741992 TGTAGTGTGCTGGAAATGAATAAG 57.258 37.500 0.00 0.00 0.00 1.73
5102 7700 6.472016 TGTAGTGTGCTGGAAATGAATAAGA 58.528 36.000 0.00 0.00 0.00 2.10
5103 7701 6.939730 TGTAGTGTGCTGGAAATGAATAAGAA 59.060 34.615 0.00 0.00 0.00 2.52
5104 7702 6.259550 AGTGTGCTGGAAATGAATAAGAAC 57.740 37.500 0.00 0.00 0.00 3.01
5105 7703 6.006449 AGTGTGCTGGAAATGAATAAGAACT 58.994 36.000 0.00 0.00 0.00 3.01
5106 7704 7.168219 AGTGTGCTGGAAATGAATAAGAACTA 58.832 34.615 0.00 0.00 0.00 2.24
5107 7705 7.831193 AGTGTGCTGGAAATGAATAAGAACTAT 59.169 33.333 0.00 0.00 0.00 2.12
5108 7706 7.912250 GTGTGCTGGAAATGAATAAGAACTATG 59.088 37.037 0.00 0.00 0.00 2.23
5109 7707 7.611467 TGTGCTGGAAATGAATAAGAACTATGT 59.389 33.333 0.00 0.00 0.00 2.29
5110 7708 8.462016 GTGCTGGAAATGAATAAGAACTATGTT 58.538 33.333 0.00 0.00 0.00 2.71
5111 7709 9.679661 TGCTGGAAATGAATAAGAACTATGTTA 57.320 29.630 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 7.119262 GCTAGTGCAATTAAAGACTCAAGGTAA 59.881 37.037 0.00 0.00 39.41 2.85
91 92 8.897752 GGATCACAATTAGAATTTTGAGCTAGT 58.102 33.333 15.23 0.00 39.86 2.57
92 93 8.066595 CGGATCACAATTAGAATTTTGAGCTAG 58.933 37.037 15.23 8.90 39.86 3.42
152 153 8.217111 TGATATTTCATGTGGCCTATTTACTGA 58.783 33.333 3.32 0.00 0.00 3.41
186 187 0.247736 AAGCCACTTAGCAGGAGACG 59.752 55.000 0.00 0.00 34.23 4.18
188 189 0.905357 GGAAGCCACTTAGCAGGAGA 59.095 55.000 0.00 0.00 34.23 3.71
214 215 0.038166 TGAGCTTCATCCAACCCACC 59.962 55.000 0.00 0.00 0.00 4.61
216 217 2.905415 ATTGAGCTTCATCCAACCCA 57.095 45.000 0.00 0.00 0.00 4.51
224 225 3.845781 ACCATCCGTATTGAGCTTCAT 57.154 42.857 0.00 0.00 0.00 2.57
270 271 2.628696 CGAAGCACCATGCCAGCAA 61.629 57.895 0.00 0.00 46.52 3.91
277 278 4.687948 CCTAGATTATCACGAAGCACCATG 59.312 45.833 0.00 0.00 0.00 3.66
321 322 5.071788 TCTCGGCATGAAAATAACTCCCTAT 59.928 40.000 0.00 0.00 0.00 2.57
350 352 3.763097 TGCACATATTTCCGCTTCAAG 57.237 42.857 0.00 0.00 0.00 3.02
358 360 4.304110 CTTCCATGCATGCACATATTTCC 58.696 43.478 25.37 0.00 0.00 3.13
407 409 5.066375 CCATCTCGATGCAAATTGGAAGTTA 59.934 40.000 0.00 0.00 37.49 2.24
416 419 4.458397 AGTGAATCCATCTCGATGCAAAT 58.542 39.130 0.00 0.00 37.49 2.32
421 424 4.447054 GCTGTAAGTGAATCCATCTCGATG 59.553 45.833 0.00 0.00 35.80 3.84
441 444 1.069022 CCTTCAACATGTTCACCGCTG 60.069 52.381 8.48 0.00 0.00 5.18
514 517 4.085517 CGAGTCGTTCAAAGAGACTTCAAC 60.086 45.833 3.82 0.00 44.30 3.18
527 530 3.503827 ATGAGCAATACGAGTCGTTCA 57.496 42.857 25.19 20.30 41.54 3.18
620 627 2.590092 GGGTCCTGATCCCAACCG 59.410 66.667 0.00 0.00 44.05 4.44
761 774 5.134202 TCGTATTGGCCTGTAGTGATATG 57.866 43.478 3.32 0.00 0.00 1.78
774 791 3.569690 CGGCCCGTTCGTATTGGC 61.570 66.667 0.00 0.00 43.26 4.52
813 830 2.632377 GATGCAAGATGAAGGGTCGAA 58.368 47.619 0.00 0.00 0.00 3.71
814 831 1.471501 CGATGCAAGATGAAGGGTCGA 60.472 52.381 0.00 0.00 0.00 4.20
815 832 0.933097 CGATGCAAGATGAAGGGTCG 59.067 55.000 0.00 0.00 0.00 4.79
817 834 1.091771 CGCGATGCAAGATGAAGGGT 61.092 55.000 0.00 0.00 0.00 4.34
818 835 1.645455 CGCGATGCAAGATGAAGGG 59.355 57.895 0.00 0.00 0.00 3.95
819 836 1.010350 GCGCGATGCAAGATGAAGG 60.010 57.895 12.10 0.00 45.45 3.46
892 921 0.174617 GAGTGGAGGCCGAAAGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
899 928 4.779733 GGGGAGAGTGGAGGCCGA 62.780 72.222 0.00 0.00 0.00 5.54
907 936 2.124693 GCGAGGAGAGGGGAGAGTG 61.125 68.421 0.00 0.00 0.00 3.51
908 937 2.277404 GCGAGGAGAGGGGAGAGT 59.723 66.667 0.00 0.00 0.00 3.24
960 1000 1.352156 CTCCCGGAAAAACGAGCGAG 61.352 60.000 0.73 0.00 35.47 5.03
970 1010 3.009115 CTGCCCCTCTCCCGGAAA 61.009 66.667 0.73 0.00 0.00 3.13
1412 1455 3.934457 ACACCAATCCGAAATCCAAAC 57.066 42.857 0.00 0.00 0.00 2.93
1413 1456 3.553922 GCAACACCAATCCGAAATCCAAA 60.554 43.478 0.00 0.00 0.00 3.28
1414 1457 2.029470 GCAACACCAATCCGAAATCCAA 60.029 45.455 0.00 0.00 0.00 3.53
1419 1462 0.958091 CCTGCAACACCAATCCGAAA 59.042 50.000 0.00 0.00 0.00 3.46
1569 1612 6.409704 TGACATAGGTGAAGAGAAGAAATGG 58.590 40.000 0.00 0.00 0.00 3.16
1574 1617 5.716703 TCACATGACATAGGTGAAGAGAAGA 59.283 40.000 0.00 0.00 46.08 2.87
1596 1639 1.890573 GCCAGTTAAAGGGGCACATCA 60.891 52.381 8.08 0.00 46.92 3.07
1615 1659 4.932146 TGGCAAAACAAAAGAACTAGAGC 58.068 39.130 0.00 0.00 0.00 4.09
1679 2714 5.199982 TCTGAACTCTCCTAGGTCTCAAT 57.800 43.478 9.08 0.00 42.96 2.57
1682 2717 3.551846 CCTCTGAACTCTCCTAGGTCTC 58.448 54.545 9.08 0.46 42.96 3.36
1683 2777 2.243736 CCCTCTGAACTCTCCTAGGTCT 59.756 54.545 9.08 0.00 42.96 3.85
1996 3181 3.878778 CGGAGGAGATGTTTCTTTCCAT 58.121 45.455 7.70 0.00 36.52 3.41
2041 3227 1.375908 GAGATGGCTGGCACGTGAA 60.376 57.895 22.23 5.36 0.00 3.18
2327 3519 4.212847 GGGAAGAAAACTTTCTACACGGTC 59.787 45.833 5.16 0.00 46.22 4.79
2360 3552 5.670341 GCAATACTTCGTATGGTGTCACAAC 60.670 44.000 5.12 0.00 0.00 3.32
2530 3722 3.053831 ACCAGATAACAACAAGGACCG 57.946 47.619 0.00 0.00 0.00 4.79
2753 3946 3.490419 GCATACGTTCCTCTTCGGTGTAT 60.490 47.826 0.00 0.00 31.58 2.29
2813 4006 5.637387 GCAAACCTTTCTTTCACTTTGAACA 59.363 36.000 0.00 0.00 35.89 3.18
2837 4030 5.107259 TGTTTTGAATATGTCGAAGTCACCG 60.107 40.000 0.00 0.00 30.95 4.94
2965 4158 1.069978 TGAACGCTTGTCATCCACTGA 59.930 47.619 0.00 0.00 0.00 3.41
3069 4262 6.203723 GCCAGCGACTTATAAATGAATCTTCT 59.796 38.462 0.00 0.00 0.00 2.85
3191 4384 3.509575 GGATGTTGCCAAATTGAGGTGTA 59.490 43.478 0.00 0.00 0.00 2.90
3261 4454 3.802139 CAGTAGCCACATATACAACACGG 59.198 47.826 0.00 0.00 0.00 4.94
3262 4455 4.267690 CACAGTAGCCACATATACAACACG 59.732 45.833 0.00 0.00 0.00 4.49
3298 4491 3.423058 AGGCTATCCTTCCCAAGTACT 57.577 47.619 0.00 0.00 40.66 2.73
3349 4543 7.990314 AGAATAAAGGCTAAAGAGAACAGATCC 59.010 37.037 0.00 0.00 0.00 3.36
3350 4544 8.956533 AGAATAAAGGCTAAAGAGAACAGATC 57.043 34.615 0.00 0.00 0.00 2.75
3364 4558 6.049790 GGTATTTCTGACGAGAATAAAGGCT 58.950 40.000 0.00 0.00 38.05 4.58
3366 4560 6.018669 GCAGGTATTTCTGACGAGAATAAAGG 60.019 42.308 0.00 0.00 38.05 3.11
3372 4566 4.021456 TGAAGCAGGTATTTCTGACGAGAA 60.021 41.667 0.00 0.00 36.93 2.87
3412 4608 6.301169 ACTAAATCACCAAAACACCCAAAA 57.699 33.333 0.00 0.00 0.00 2.44
3506 4702 2.726821 ACAAAATCGCATCCCACATCT 58.273 42.857 0.00 0.00 0.00 2.90
3518 4714 5.106948 TGCTTTGAGCTAGAGAACAAAATCG 60.107 40.000 0.00 0.00 42.97 3.34
3525 4723 7.493971 TCAAGATAATGCTTTGAGCTAGAGAAC 59.506 37.037 0.00 0.00 42.97 3.01
3577 4776 6.763715 TGGGATATAAGTTTATCAGGCAGT 57.236 37.500 0.00 0.00 31.42 4.40
3600 4799 7.955918 AGCTGTTTTCCTGTAAAGAATTTGAT 58.044 30.769 0.00 0.00 39.63 2.57
3643 4842 2.598565 ACCCTTTCTTTCCTGCTTTCC 58.401 47.619 0.00 0.00 0.00 3.13
3706 4905 4.035675 CAGAGAAAACACACCTTCAGTTCC 59.964 45.833 0.00 0.00 0.00 3.62
3978 5366 7.040201 ACAGTCTGTGATGCTGAATTTACAATT 60.040 33.333 4.21 0.00 34.60 2.32
4073 5461 5.146010 ACAGGTCAGCAAGAAAACAAAAA 57.854 34.783 0.00 0.00 0.00 1.94
4140 5528 1.202879 TCCCAAATGTCCAGCTTTCGT 60.203 47.619 0.00 0.00 0.00 3.85
4154 5542 1.691196 CCAGCTTGTCTGTTCCCAAA 58.309 50.000 0.00 0.00 41.25 3.28
4185 5573 2.419297 GCGATGTCACAGGGAAGAGAAT 60.419 50.000 0.00 0.00 0.00 2.40
4189 5577 1.596934 GGCGATGTCACAGGGAAGA 59.403 57.895 0.00 0.00 0.00 2.87
4204 5592 4.659172 TGTGGAAGGGCAAGGGCG 62.659 66.667 0.00 0.00 42.47 6.13
4227 5615 9.799106 ATAAAGGTATCTGAAAGTAATGGATGG 57.201 33.333 0.00 0.00 33.76 3.51
4269 5657 3.007940 TCCGGCATAGGATCCACAAATAG 59.992 47.826 15.82 0.00 34.92 1.73
4324 5714 9.055248 GTGATCACTTAACATTTCGAGAAATTG 57.945 33.333 18.83 4.36 38.84 2.32
4350 5740 6.427853 TCAGAATTGTTCTTACATGGTGACTG 59.572 38.462 0.00 0.00 38.11 3.51
4363 5753 7.861629 TCAACTATACCCATCAGAATTGTTCT 58.138 34.615 0.00 0.00 41.70 3.01
4372 5762 7.365741 GCATGATTTTCAACTATACCCATCAG 58.634 38.462 0.00 0.00 0.00 2.90
4379 5769 7.088589 ACACAGGCATGATTTTCAACTATAC 57.911 36.000 4.84 0.00 0.00 1.47
4391 5781 5.255687 TCTTGATAACAACACAGGCATGAT 58.744 37.500 4.84 0.00 32.27 2.45
4461 5852 4.465632 TTGGCTCTGCTTTCTAATCGTA 57.534 40.909 0.00 0.00 0.00 3.43
4523 7085 1.135689 CGGAAAGCATGTTGGTAGTGC 60.136 52.381 0.00 0.00 39.10 4.40
4532 7094 3.119388 CCATGATTGAACGGAAAGCATGT 60.119 43.478 17.89 0.00 45.49 3.21
4534 7096 2.159198 GCCATGATTGAACGGAAAGCAT 60.159 45.455 0.00 0.00 34.11 3.79
4537 7099 1.818060 TGGCCATGATTGAACGGAAAG 59.182 47.619 0.00 0.00 0.00 2.62
4543 7105 4.411256 AATTGGATGGCCATGATTGAAC 57.589 40.909 26.56 6.35 45.46 3.18
4551 7114 5.438698 TTTGATGAAAATTGGATGGCCAT 57.561 34.783 20.96 20.96 45.46 4.40
4579 7142 6.384258 TCTGCATTACAAGCTTGTGTTAAA 57.616 33.333 36.50 24.80 42.31 1.52
4580 7143 5.048782 CCTCTGCATTACAAGCTTGTGTTAA 60.049 40.000 36.50 25.13 42.31 2.01
4581 7144 4.455533 CCTCTGCATTACAAGCTTGTGTTA 59.544 41.667 36.50 23.33 42.31 2.41
4582 7145 3.254166 CCTCTGCATTACAAGCTTGTGTT 59.746 43.478 36.50 22.77 42.31 3.32
4628 7223 4.842531 TGCATAGAAAAGTGGATCCTCA 57.157 40.909 14.23 0.00 0.00 3.86
4639 7234 2.822561 TGCGGGTTTGATGCATAGAAAA 59.177 40.909 0.00 0.00 32.86 2.29
4643 7238 3.117794 CAATTGCGGGTTTGATGCATAG 58.882 45.455 0.00 0.00 38.60 2.23
4644 7239 2.757314 TCAATTGCGGGTTTGATGCATA 59.243 40.909 0.00 0.00 38.60 3.14
4645 7240 1.549620 TCAATTGCGGGTTTGATGCAT 59.450 42.857 0.00 0.00 38.60 3.96
4646 7241 0.964700 TCAATTGCGGGTTTGATGCA 59.035 45.000 0.00 0.00 36.72 3.96
4647 7242 2.298411 ATCAATTGCGGGTTTGATGC 57.702 45.000 0.00 0.00 40.22 3.91
4648 7243 7.539710 CAGAATATATCAATTGCGGGTTTGATG 59.460 37.037 0.00 0.00 41.42 3.07
4649 7244 7.231317 ACAGAATATATCAATTGCGGGTTTGAT 59.769 33.333 0.00 3.89 43.22 2.57
4650 7245 6.545666 ACAGAATATATCAATTGCGGGTTTGA 59.454 34.615 0.00 0.00 36.38 2.69
4651 7246 6.738114 ACAGAATATATCAATTGCGGGTTTG 58.262 36.000 0.00 0.00 0.00 2.93
4652 7247 6.959639 ACAGAATATATCAATTGCGGGTTT 57.040 33.333 0.00 0.00 0.00 3.27
4694 7289 3.432252 CGGCTTGTAAAGGTGTAACTCTG 59.568 47.826 0.00 0.00 46.35 3.35
4700 7295 2.027561 AGATGCGGCTTGTAAAGGTGTA 60.028 45.455 0.00 0.00 46.35 2.90
4715 7310 1.815421 CGGGGGAGAACAAGATGCG 60.815 63.158 0.00 0.00 0.00 4.73
4728 7323 6.937392 TGTTTATTTCCTTTTATTTCGGGGG 58.063 36.000 0.00 0.00 0.00 5.40
4796 7391 1.983224 CAGGATGAACCCAGGACGT 59.017 57.895 0.00 0.00 39.69 4.34
4805 7400 3.129813 TCATGAATTGCAGCAGGATGAAC 59.870 43.478 0.00 0.00 39.69 3.18
4813 7408 4.500127 CTGGAAATTCATGAATTGCAGCA 58.500 39.130 31.38 22.44 40.57 4.41
4814 7409 3.308866 GCTGGAAATTCATGAATTGCAGC 59.691 43.478 33.49 33.49 41.06 5.25
4815 7410 3.869246 GGCTGGAAATTCATGAATTGCAG 59.131 43.478 31.38 29.30 40.57 4.41
4816 7411 3.261137 TGGCTGGAAATTCATGAATTGCA 59.739 39.130 31.38 23.68 40.57 4.08
4817 7412 3.864243 TGGCTGGAAATTCATGAATTGC 58.136 40.909 29.52 27.48 40.57 3.56
4818 7413 5.054477 GGATGGCTGGAAATTCATGAATTG 58.946 41.667 29.52 19.37 40.57 2.32
4819 7414 4.966805 AGGATGGCTGGAAATTCATGAATT 59.033 37.500 24.83 24.83 42.35 2.17
4820 7415 4.344102 CAGGATGGCTGGAAATTCATGAAT 59.656 41.667 15.36 15.36 0.00 2.57
4821 7416 3.702548 CAGGATGGCTGGAAATTCATGAA 59.297 43.478 11.26 11.26 0.00 2.57
4822 7417 3.053470 TCAGGATGGCTGGAAATTCATGA 60.053 43.478 0.00 0.00 36.16 3.07
4823 7418 3.293337 TCAGGATGGCTGGAAATTCATG 58.707 45.455 0.00 0.00 36.16 3.07
4824 7419 3.053095 ACTCAGGATGGCTGGAAATTCAT 60.053 43.478 0.00 0.00 36.16 2.57
4825 7420 2.309755 ACTCAGGATGGCTGGAAATTCA 59.690 45.455 0.00 0.00 36.16 2.57
4826 7421 3.010200 ACTCAGGATGGCTGGAAATTC 57.990 47.619 0.00 0.00 36.16 2.17
4827 7422 3.245371 TGAACTCAGGATGGCTGGAAATT 60.245 43.478 0.00 0.00 36.16 1.82
4828 7423 2.309755 TGAACTCAGGATGGCTGGAAAT 59.690 45.455 0.00 0.00 36.16 2.17
4829 7424 1.704628 TGAACTCAGGATGGCTGGAAA 59.295 47.619 0.00 0.00 36.16 3.13
4830 7425 1.361204 TGAACTCAGGATGGCTGGAA 58.639 50.000 0.00 0.00 36.16 3.53
4831 7426 1.487976 GATGAACTCAGGATGGCTGGA 59.512 52.381 0.00 0.00 36.16 3.86
4832 7427 1.476471 GGATGAACTCAGGATGGCTGG 60.476 57.143 0.00 0.00 36.16 4.85
4833 7428 1.489649 AGGATGAACTCAGGATGGCTG 59.510 52.381 0.00 0.00 36.16 4.85
4834 7429 1.489649 CAGGATGAACTCAGGATGGCT 59.510 52.381 0.00 0.00 39.69 4.75
4835 7430 1.964552 CAGGATGAACTCAGGATGGC 58.035 55.000 0.00 0.00 39.69 4.40
4836 7431 1.489649 AGCAGGATGAACTCAGGATGG 59.510 52.381 0.00 0.00 39.69 3.51
4837 7432 2.562635 CAGCAGGATGAACTCAGGATG 58.437 52.381 0.00 0.00 39.69 3.51
4838 7433 1.134159 GCAGCAGGATGAACTCAGGAT 60.134 52.381 0.00 0.00 39.69 3.24
4839 7434 0.251354 GCAGCAGGATGAACTCAGGA 59.749 55.000 0.00 0.00 39.69 3.86
4840 7435 0.035725 TGCAGCAGGATGAACTCAGG 60.036 55.000 0.00 0.00 39.69 3.86
4841 7436 1.817357 TTGCAGCAGGATGAACTCAG 58.183 50.000 0.00 0.00 39.69 3.35
4842 7437 2.502142 ATTGCAGCAGGATGAACTCA 57.498 45.000 0.00 0.00 39.69 3.41
4843 7438 2.751259 TGAATTGCAGCAGGATGAACTC 59.249 45.455 0.00 0.00 39.69 3.01
4844 7439 2.799017 TGAATTGCAGCAGGATGAACT 58.201 42.857 0.00 0.00 39.69 3.01
4845 7440 3.129813 TGATGAATTGCAGCAGGATGAAC 59.870 43.478 0.00 0.00 38.12 3.18
4846 7441 3.358118 TGATGAATTGCAGCAGGATGAA 58.642 40.909 0.00 0.00 38.12 2.57
4847 7442 3.007473 TGATGAATTGCAGCAGGATGA 57.993 42.857 0.00 0.00 38.12 2.92
4848 7443 3.793797 TTGATGAATTGCAGCAGGATG 57.206 42.857 0.00 0.00 44.75 3.51
4849 7444 3.004419 CGATTGATGAATTGCAGCAGGAT 59.996 43.478 0.00 0.00 44.75 3.24
4850 7445 2.356695 CGATTGATGAATTGCAGCAGGA 59.643 45.455 0.00 0.00 44.75 3.86
4851 7446 2.543031 CCGATTGATGAATTGCAGCAGG 60.543 50.000 0.00 0.00 44.75 4.85
4852 7447 2.098607 ACCGATTGATGAATTGCAGCAG 59.901 45.455 0.00 0.00 44.75 4.24
4853 7448 2.093890 ACCGATTGATGAATTGCAGCA 58.906 42.857 0.00 0.00 41.97 4.41
4867 7462 5.766150 TGATTCTCAAACAAACACCGATT 57.234 34.783 0.00 0.00 0.00 3.34
4870 7465 4.734854 CACTTGATTCTCAAACAAACACCG 59.265 41.667 0.00 0.00 35.73 4.94
4875 7470 5.581126 ACAGCACTTGATTCTCAAACAAA 57.419 34.783 0.00 0.00 35.73 2.83
4911 7506 3.395639 CTTGGCAATTGCAGAACACATT 58.604 40.909 30.32 0.00 44.36 2.71
5032 7628 9.739276 TTCACTCAAGTATGAATCAATAAACCT 57.261 29.630 0.00 0.00 34.49 3.50
5061 7659 6.145534 CACACTACATCAGCTTCGAAGTTTAA 59.854 38.462 25.24 11.13 0.00 1.52
5069 7667 1.657594 CAGCACACTACATCAGCTTCG 59.342 52.381 0.00 0.00 32.35 3.79
5079 7677 6.985188 TCTTATTCATTTCCAGCACACTAC 57.015 37.500 0.00 0.00 0.00 2.73
5082 7680 6.259550 AGTTCTTATTCATTTCCAGCACAC 57.740 37.500 0.00 0.00 0.00 3.82
5083 7681 7.611467 ACATAGTTCTTATTCATTTCCAGCACA 59.389 33.333 0.00 0.00 0.00 4.57
5084 7682 7.989826 ACATAGTTCTTATTCATTTCCAGCAC 58.010 34.615 0.00 0.00 0.00 4.40
5085 7683 8.579850 AACATAGTTCTTATTCATTTCCAGCA 57.420 30.769 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.