Multiple sequence alignment - TraesCS3D01G223800

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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 TraesCS3D01G223800 chr3D 100.000 6212 0 0 1 6212 305445133 305451344 0.000000e+00 11472.0
1 TraesCS3D01G223800 chr3B 93.319 4580 201 40 1670 6212 416285789 416281278 0.000000e+00 6665.0
2 TraesCS3D01G223800 chr3B 96.154 884 25 8 789 1669 416286704 416285827 0.000000e+00 1435.0
3 TraesCS3D01G223800 chr3B 89.623 106 10 1 3425 3529 752373323 752373428 3.910000e-27 134.0
4 TraesCS3D01G223800 chr3B 84.874 119 14 4 2611 2728 743840874 743840989 3.930000e-22 117.0
5 TraesCS3D01G223800 chr3A 94.021 3295 137 38 2809 6066 423482596 423485867 0.000000e+00 4939.0
6 TraesCS3D01G223800 chr3A 92.967 1109 48 16 1670 2774 423481520 423482602 0.000000e+00 1589.0
7 TraesCS3D01G223800 chr3A 95.585 838 25 6 832 1669 423480657 423481482 0.000000e+00 1332.0
8 TraesCS3D01G223800 chr3A 95.302 149 5 1 6064 6212 423486104 423486250 1.040000e-57 235.0
9 TraesCS3D01G223800 chr3A 100.000 28 0 0 2378 2405 729713347 729713374 1.100000e-02 52.8
10 TraesCS3D01G223800 chr4B 90.767 574 47 5 82 652 142677117 142676547 0.000000e+00 761.0
11 TraesCS3D01G223800 chr4B 87.611 113 13 1 3427 3538 642195546 642195658 5.050000e-26 130.0
12 TraesCS3D01G223800 chr4B 82.812 128 17 5 2606 2731 7028589 7028465 6.580000e-20 110.0
13 TraesCS3D01G223800 chr4D 90.493 568 48 5 82 647 276314052 276313489 0.000000e+00 745.0
14 TraesCS3D01G223800 chr4D 93.902 164 10 0 237 400 506028362 506028525 1.340000e-61 248.0
15 TraesCS3D01G223800 chr6D 89.821 560 52 4 82 639 242354058 242354614 0.000000e+00 713.0
16 TraesCS3D01G223800 chr2D 90.000 480 44 3 173 651 52300881 52300405 8.850000e-173 617.0
17 TraesCS3D01G223800 chr7B 87.147 319 37 3 335 652 616620466 616620781 5.920000e-95 359.0
18 TraesCS3D01G223800 chr7B 90.602 266 18 3 79 344 616619152 616619410 4.610000e-91 346.0
19 TraesCS3D01G223800 chr7B 93.814 97 6 0 3433 3529 539218379 539218283 5.020000e-31 147.0
20 TraesCS3D01G223800 chr7B 88.136 118 11 1 3432 3549 685247160 685247274 3.020000e-28 137.0
21 TraesCS3D01G223800 chr7B 85.586 111 13 3 2619 2728 680177794 680177686 5.090000e-21 113.0
22 TraesCS3D01G223800 chr7A 93.814 97 6 0 3433 3529 581374345 581374249 5.020000e-31 147.0
23 TraesCS3D01G223800 chr7A 86.325 117 14 2 2611 2727 115854506 115854620 6.540000e-25 126.0
24 TraesCS3D01G223800 chr2A 91.837 98 8 0 3433 3530 688628927 688628830 3.020000e-28 137.0
25 TraesCS3D01G223800 chr5B 90.099 101 10 0 3433 3533 544610474 544610574 1.410000e-26 132.0
26 TraesCS3D01G223800 chr5B 85.455 55 8 0 90 144 268813455 268813509 2.420000e-04 58.4
27 TraesCS3D01G223800 chr4A 87.387 111 11 3 2619 2728 548568895 548569003 2.350000e-24 124.0
28 TraesCS3D01G223800 chr1A 85.593 118 14 3 2611 2727 426451907 426452022 3.040000e-23 121.0
29 TraesCS3D01G223800 chr6A 84.746 118 15 3 2611 2727 400130521 400130636 1.420000e-21 115.0
30 TraesCS3D01G223800 chr2B 86.905 84 10 1 78 161 138995019 138994937 6.630000e-15 93.5
31 TraesCS3D01G223800 chr2B 86.747 83 10 1 79 161 138996026 138996107 2.380000e-14 91.6
32 TraesCS3D01G223800 chr7D 100.000 28 0 0 2378 2405 73133243 73133270 1.100000e-02 52.8
33 TraesCS3D01G223800 chr6B 100.000 28 0 0 2378 2405 465712961 465712988 1.100000e-02 52.8


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 TraesCS3D01G223800 chr3D 305445133 305451344 6211 False 11472.00 11472 100.00000 1 6212 1 chr3D.!!$F1 6211
1 TraesCS3D01G223800 chr3B 416281278 416286704 5426 True 4050.00 6665 94.73650 789 6212 2 chr3B.!!$R1 5423
2 TraesCS3D01G223800 chr3A 423480657 423486250 5593 False 2023.75 4939 94.46875 832 6212 4 chr3A.!!$F2 5380
3 TraesCS3D01G223800 chr4B 142676547 142677117 570 True 761.00 761 90.76700 82 652 1 chr4B.!!$R2 570
4 TraesCS3D01G223800 chr4D 276313489 276314052 563 True 745.00 745 90.49300 82 647 1 chr4D.!!$R1 565
5 TraesCS3D01G223800 chr6D 242354058 242354614 556 False 713.00 713 89.82100 82 639 1 chr6D.!!$F1 557
6 TraesCS3D01G223800 chr7B 616619152 616620781 1629 False 352.50 359 88.87450 79 652 2 chr7B.!!$F2 573

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
46 47 0.033503 TACGAGATGGGCTCTGGTCA 60.034 55.000 0.00 0.00 41.48 4.02 F
425 1492 0.036388 CCCTCGTGTGTTGTGGCTAT 60.036 55.000 0.00 0.00 0.00 2.97 F
730 1800 0.178068 ACAGACAAACAGCTCACGGT 59.822 50.000 0.00 0.00 0.00 4.83 F
2186 3299 0.178995 TGCCAATGTGCTGGTGAGAA 60.179 50.000 0.00 0.00 38.86 2.87 F
2794 3915 1.204704 TCTCGACACCAATACCAGCTG 59.795 52.381 6.78 6.78 0.00 4.24 F
3661 4792 0.400594 GGATAGGGCCAGCGGTAAAT 59.599 55.000 6.18 0.00 0.00 1.40 F
4774 5942 2.717639 ATTGGAATAGTGAGGCGCTT 57.282 45.000 7.64 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 3103 0.533755 CCGAGAGACCAATGCCATCC 60.534 60.000 0.00 0.0 0.00 3.51 R
2281 3394 0.815734 ACTCAACCGTATGTCCTCCG 59.184 55.000 0.00 0.0 0.00 4.63 R
2648 3769 0.892755 CCACCTCAGCATGCAAACAT 59.107 50.000 21.98 0.0 36.79 2.71 R
3029 4150 1.134521 TCTCAGTCAGCACAAAACCGT 60.135 47.619 0.00 0.0 0.00 4.83 R
4767 5935 3.059352 AGTGTCTTATTTGAAGCGCCT 57.941 42.857 2.29 0.0 0.00 5.52 R
4934 6103 1.069227 GTAACTCCAGCCAACAAAGCG 60.069 52.381 0.00 0.0 34.64 4.68 R
5967 7160 3.428862 GCAACACTTTCCCCAATAATCCG 60.429 47.826 0.00 0.0 0.00 4.18 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
22 23 5.746307 GCTGCAATCAATCAGATCTTACA 57.254 39.130 0.00 0.00 35.39 2.41
23 24 6.315091 GCTGCAATCAATCAGATCTTACAT 57.685 37.500 0.00 0.00 35.39 2.29
24 25 6.143496 GCTGCAATCAATCAGATCTTACATG 58.857 40.000 0.00 0.00 35.39 3.21
25 26 6.238676 GCTGCAATCAATCAGATCTTACATGT 60.239 38.462 2.69 2.69 35.39 3.21
26 27 7.255491 TGCAATCAATCAGATCTTACATGTC 57.745 36.000 0.00 0.00 35.39 3.06
27 28 7.052248 TGCAATCAATCAGATCTTACATGTCT 58.948 34.615 0.00 0.00 35.39 3.41
28 29 8.206189 TGCAATCAATCAGATCTTACATGTCTA 58.794 33.333 0.00 0.00 35.39 2.59
29 30 8.494347 GCAATCAATCAGATCTTACATGTCTAC 58.506 37.037 0.00 0.00 35.39 2.59
30 31 8.697960 CAATCAATCAGATCTTACATGTCTACG 58.302 37.037 0.00 0.00 35.39 3.51
31 32 7.568199 TCAATCAGATCTTACATGTCTACGA 57.432 36.000 0.00 0.00 0.00 3.43
32 33 7.643579 TCAATCAGATCTTACATGTCTACGAG 58.356 38.462 0.00 0.00 0.00 4.18
33 34 7.499232 TCAATCAGATCTTACATGTCTACGAGA 59.501 37.037 0.00 0.00 0.00 4.04
34 35 7.994425 ATCAGATCTTACATGTCTACGAGAT 57.006 36.000 0.00 5.05 0.00 2.75
35 36 7.195839 TCAGATCTTACATGTCTACGAGATG 57.804 40.000 0.00 0.10 38.93 2.90
36 37 6.205658 TCAGATCTTACATGTCTACGAGATGG 59.794 42.308 0.00 1.07 37.59 3.51
37 38 5.475220 AGATCTTACATGTCTACGAGATGGG 59.525 44.000 0.00 0.00 37.59 4.00
38 39 3.318275 TCTTACATGTCTACGAGATGGGC 59.682 47.826 0.00 0.00 37.59 5.36
39 40 1.781786 ACATGTCTACGAGATGGGCT 58.218 50.000 0.00 0.00 37.59 5.19
40 41 1.683917 ACATGTCTACGAGATGGGCTC 59.316 52.381 0.00 0.00 37.59 4.70
41 42 1.959985 CATGTCTACGAGATGGGCTCT 59.040 52.381 0.00 0.00 41.66 4.09
42 43 1.393603 TGTCTACGAGATGGGCTCTG 58.606 55.000 0.00 0.00 41.66 3.35
43 44 0.671251 GTCTACGAGATGGGCTCTGG 59.329 60.000 0.00 0.00 41.66 3.86
44 45 0.259065 TCTACGAGATGGGCTCTGGT 59.741 55.000 0.00 0.00 44.22 4.00
45 46 0.671251 CTACGAGATGGGCTCTGGTC 59.329 60.000 0.00 0.00 41.48 4.02
46 47 0.033503 TACGAGATGGGCTCTGGTCA 60.034 55.000 0.00 0.00 41.48 4.02
47 48 1.326213 ACGAGATGGGCTCTGGTCAG 61.326 60.000 0.00 0.00 38.42 3.51
48 49 1.326213 CGAGATGGGCTCTGGTCAGT 61.326 60.000 0.00 0.00 41.66 3.41
49 50 0.908198 GAGATGGGCTCTGGTCAGTT 59.092 55.000 0.00 0.00 40.61 3.16
50 51 0.617413 AGATGGGCTCTGGTCAGTTG 59.383 55.000 0.00 0.00 31.12 3.16
51 52 0.615331 GATGGGCTCTGGTCAGTTGA 59.385 55.000 0.00 0.00 0.00 3.18
52 53 1.211457 GATGGGCTCTGGTCAGTTGAT 59.789 52.381 0.00 0.00 0.00 2.57
53 54 1.951209 TGGGCTCTGGTCAGTTGATA 58.049 50.000 0.00 0.00 0.00 2.15
54 55 2.265367 TGGGCTCTGGTCAGTTGATAA 58.735 47.619 0.00 0.00 0.00 1.75
55 56 2.642311 TGGGCTCTGGTCAGTTGATAAA 59.358 45.455 0.00 0.00 0.00 1.40
56 57 3.010420 GGGCTCTGGTCAGTTGATAAAC 58.990 50.000 0.00 0.00 0.00 2.01
57 58 3.559171 GGGCTCTGGTCAGTTGATAAACA 60.559 47.826 0.00 0.00 0.00 2.83
58 59 4.072131 GGCTCTGGTCAGTTGATAAACAA 58.928 43.478 0.00 0.00 36.02 2.83
59 60 4.518970 GGCTCTGGTCAGTTGATAAACAAA 59.481 41.667 0.00 0.00 40.36 2.83
60 61 5.335191 GGCTCTGGTCAGTTGATAAACAAAG 60.335 44.000 0.00 0.00 40.36 2.77
61 62 5.470098 GCTCTGGTCAGTTGATAAACAAAGA 59.530 40.000 0.00 0.00 40.36 2.52
62 63 6.566753 GCTCTGGTCAGTTGATAAACAAAGAC 60.567 42.308 0.00 0.75 41.16 3.01
63 64 6.353323 TCTGGTCAGTTGATAAACAAAGACA 58.647 36.000 12.50 0.00 42.39 3.41
64 65 6.826231 TCTGGTCAGTTGATAAACAAAGACAA 59.174 34.615 12.50 3.92 42.39 3.18
65 66 7.012327 TCTGGTCAGTTGATAAACAAAGACAAG 59.988 37.037 12.50 11.08 42.18 3.16
66 67 6.601613 TGGTCAGTTGATAAACAAAGACAAGT 59.398 34.615 12.50 0.00 42.39 3.16
67 68 7.132863 GGTCAGTTGATAAACAAAGACAAGTC 58.867 38.462 12.50 0.00 42.39 3.01
68 69 7.012421 GGTCAGTTGATAAACAAAGACAAGTCT 59.988 37.037 12.50 0.00 42.39 3.24
69 70 7.852945 GTCAGTTGATAAACAAAGACAAGTCTG 59.147 37.037 3.08 0.00 41.34 3.51
70 71 6.634436 CAGTTGATAAACAAAGACAAGTCTGC 59.366 38.462 3.08 0.00 40.36 4.26
71 72 6.543831 AGTTGATAAACAAAGACAAGTCTGCT 59.456 34.615 3.08 0.00 40.36 4.24
72 73 6.304356 TGATAAACAAAGACAAGTCTGCTG 57.696 37.500 3.08 7.17 40.36 4.41
73 74 5.822519 TGATAAACAAAGACAAGTCTGCTGT 59.177 36.000 3.08 7.77 40.36 4.40
74 75 4.622701 AAACAAAGACAAGTCTGCTGTC 57.377 40.909 14.81 0.00 40.36 3.51
75 76 2.565841 ACAAAGACAAGTCTGCTGTCC 58.434 47.619 3.08 0.00 40.36 4.02
76 77 2.171448 ACAAAGACAAGTCTGCTGTCCT 59.829 45.455 3.08 0.00 40.36 3.85
77 78 2.805099 CAAAGACAAGTCTGCTGTCCTC 59.195 50.000 3.08 0.00 40.36 3.71
80 81 2.703007 AGACAAGTCTGCTGTCCTCTTT 59.297 45.455 1.20 0.00 38.75 2.52
105 106 6.913170 AGGTTGTGTTTGATAGCAAAGTATG 58.087 36.000 6.36 0.00 44.12 2.39
163 164 8.517062 TTTTGTCTGTAGGTACTAGATACTCC 57.483 38.462 0.00 0.00 44.14 3.85
211 213 1.940613 GCATTGTCAATACCGAGACCC 59.059 52.381 0.00 0.00 33.89 4.46
214 216 2.127271 TGTCAATACCGAGACCCGTA 57.873 50.000 0.00 0.00 36.31 4.02
332 334 1.039068 CCATGCACAAAGACCACCAA 58.961 50.000 0.00 0.00 0.00 3.67
344 346 3.766545 AGACCACCAACATGCATAAACT 58.233 40.909 0.00 0.00 0.00 2.66
424 1491 1.369692 CCCTCGTGTGTTGTGGCTA 59.630 57.895 0.00 0.00 0.00 3.93
425 1492 0.036388 CCCTCGTGTGTTGTGGCTAT 60.036 55.000 0.00 0.00 0.00 2.97
426 1493 1.206132 CCCTCGTGTGTTGTGGCTATA 59.794 52.381 0.00 0.00 0.00 1.31
427 1494 2.540515 CCTCGTGTGTTGTGGCTATAG 58.459 52.381 0.00 0.00 0.00 1.31
428 1495 2.165641 CCTCGTGTGTTGTGGCTATAGA 59.834 50.000 3.21 0.00 0.00 1.98
464 1531 1.578423 GCACAAGCAAGAGGAGCAC 59.422 57.895 0.00 0.00 41.58 4.40
470 1537 1.190643 AGCAAGAGGAGCACTAGGTC 58.809 55.000 0.00 0.00 41.49 3.85
580 1647 4.330074 CGAGAAGATAATGTGAGGCGTTTT 59.670 41.667 0.00 0.00 0.00 2.43
582 1649 6.183309 AGAAGATAATGTGAGGCGTTTTTC 57.817 37.500 0.00 0.00 0.00 2.29
601 1670 6.467723 TTTTCTCGCTAGCTCAGTTTTAAG 57.532 37.500 13.93 0.00 0.00 1.85
608 1677 6.704493 TCGCTAGCTCAGTTTTAAGAAAAAGA 59.296 34.615 13.93 0.00 35.29 2.52
609 1678 7.225931 TCGCTAGCTCAGTTTTAAGAAAAAGAA 59.774 33.333 13.93 0.00 35.29 2.52
613 1682 8.512966 AGCTCAGTTTTAAGAAAAAGAAGTCT 57.487 30.769 0.00 0.00 35.29 3.24
673 1743 3.634568 TTTTGCGGTTGAAGTACCATG 57.365 42.857 0.00 0.00 38.12 3.66
674 1744 1.529226 TTGCGGTTGAAGTACCATGG 58.471 50.000 11.19 11.19 38.12 3.66
675 1745 0.398696 TGCGGTTGAAGTACCATGGT 59.601 50.000 23.55 23.55 38.12 3.55
676 1746 1.202830 TGCGGTTGAAGTACCATGGTT 60.203 47.619 25.38 4.60 38.12 3.67
677 1747 1.883926 GCGGTTGAAGTACCATGGTTT 59.116 47.619 25.38 12.69 38.12 3.27
678 1748 2.295070 GCGGTTGAAGTACCATGGTTTT 59.705 45.455 25.38 17.86 38.12 2.43
679 1749 3.855524 GCGGTTGAAGTACCATGGTTTTG 60.856 47.826 25.38 7.14 38.12 2.44
680 1750 3.649073 GGTTGAAGTACCATGGTTTTGC 58.351 45.455 25.38 11.00 38.12 3.68
681 1751 3.554129 GGTTGAAGTACCATGGTTTTGCC 60.554 47.826 25.38 14.48 38.12 4.52
695 1765 6.751514 TGGTTTTGCCAATACTACAGTATG 57.248 37.500 2.71 0.00 45.94 2.39
696 1766 5.650266 TGGTTTTGCCAATACTACAGTATGG 59.350 40.000 2.71 7.72 45.94 2.74
697 1767 5.883673 GGTTTTGCCAATACTACAGTATGGA 59.116 40.000 15.93 1.40 40.78 3.41
698 1768 6.376018 GGTTTTGCCAATACTACAGTATGGAA 59.624 38.462 15.93 7.68 40.78 3.53
699 1769 7.415206 GGTTTTGCCAATACTACAGTATGGAAG 60.415 40.741 15.93 4.20 40.78 3.46
700 1770 5.950544 TGCCAATACTACAGTATGGAAGT 57.049 39.130 15.93 0.00 43.62 3.01
701 1771 7.426606 TTGCCAATACTACAGTATGGAAGTA 57.573 36.000 15.93 0.00 43.62 2.24
702 1772 7.050970 TGCCAATACTACAGTATGGAAGTAG 57.949 40.000 15.93 0.00 40.45 2.57
704 1774 7.125204 TGCCAATACTACAGTATGGAAGTAGTT 59.875 37.037 9.41 0.00 44.27 2.24
705 1775 7.985752 GCCAATACTACAGTATGGAAGTAGTTT 59.014 37.037 9.41 0.36 44.27 2.66
706 1776 9.886132 CCAATACTACAGTATGGAAGTAGTTTT 57.114 33.333 9.41 5.97 44.27 2.43
711 1781 9.305555 ACTACAGTATGGAAGTAGTTTTAGTGA 57.694 33.333 0.00 0.00 44.27 3.41
712 1782 9.570488 CTACAGTATGGAAGTAGTTTTAGTGAC 57.430 37.037 9.13 0.00 43.62 3.67
713 1783 7.959175 ACAGTATGGAAGTAGTTTTAGTGACA 58.041 34.615 9.13 0.00 43.62 3.58
714 1784 8.088981 ACAGTATGGAAGTAGTTTTAGTGACAG 58.911 37.037 9.13 0.00 43.62 3.51
715 1785 8.304596 CAGTATGGAAGTAGTTTTAGTGACAGA 58.695 37.037 0.00 0.00 0.00 3.41
716 1786 8.305317 AGTATGGAAGTAGTTTTAGTGACAGAC 58.695 37.037 0.00 0.00 0.00 3.51
717 1787 6.474140 TGGAAGTAGTTTTAGTGACAGACA 57.526 37.500 0.00 0.00 0.00 3.41
718 1788 6.880484 TGGAAGTAGTTTTAGTGACAGACAA 58.120 36.000 0.00 0.00 0.00 3.18
719 1789 7.332557 TGGAAGTAGTTTTAGTGACAGACAAA 58.667 34.615 0.00 0.00 0.00 2.83
720 1790 7.279313 TGGAAGTAGTTTTAGTGACAGACAAAC 59.721 37.037 0.00 0.00 0.00 2.93
721 1791 7.279313 GGAAGTAGTTTTAGTGACAGACAAACA 59.721 37.037 0.00 0.00 0.00 2.83
722 1792 7.772332 AGTAGTTTTAGTGACAGACAAACAG 57.228 36.000 0.00 0.00 0.00 3.16
723 1793 5.485662 AGTTTTAGTGACAGACAAACAGC 57.514 39.130 0.00 0.00 0.00 4.40
724 1794 5.186198 AGTTTTAGTGACAGACAAACAGCT 58.814 37.500 0.00 0.00 0.00 4.24
725 1795 5.294552 AGTTTTAGTGACAGACAAACAGCTC 59.705 40.000 0.00 0.00 0.00 4.09
726 1796 2.988010 AGTGACAGACAAACAGCTCA 57.012 45.000 0.00 0.00 0.00 4.26
727 1797 2.555199 AGTGACAGACAAACAGCTCAC 58.445 47.619 0.00 0.00 0.00 3.51
728 1798 1.258982 GTGACAGACAAACAGCTCACG 59.741 52.381 0.00 0.00 0.00 4.35
729 1799 0.861837 GACAGACAAACAGCTCACGG 59.138 55.000 0.00 0.00 0.00 4.94
730 1800 0.178068 ACAGACAAACAGCTCACGGT 59.822 50.000 0.00 0.00 0.00 4.83
731 1801 1.411246 ACAGACAAACAGCTCACGGTA 59.589 47.619 0.00 0.00 0.00 4.02
732 1802 2.159014 ACAGACAAACAGCTCACGGTAA 60.159 45.455 0.00 0.00 0.00 2.85
733 1803 2.869801 CAGACAAACAGCTCACGGTAAA 59.130 45.455 0.00 0.00 0.00 2.01
734 1804 3.311322 CAGACAAACAGCTCACGGTAAAA 59.689 43.478 0.00 0.00 0.00 1.52
735 1805 4.024048 CAGACAAACAGCTCACGGTAAAAT 60.024 41.667 0.00 0.00 0.00 1.82
736 1806 5.178623 CAGACAAACAGCTCACGGTAAAATA 59.821 40.000 0.00 0.00 0.00 1.40
737 1807 5.761234 AGACAAACAGCTCACGGTAAAATAA 59.239 36.000 0.00 0.00 0.00 1.40
738 1808 6.261381 AGACAAACAGCTCACGGTAAAATAAA 59.739 34.615 0.00 0.00 0.00 1.40
739 1809 6.203647 ACAAACAGCTCACGGTAAAATAAAC 58.796 36.000 0.00 0.00 0.00 2.01
740 1810 5.366829 AACAGCTCACGGTAAAATAAACC 57.633 39.130 0.00 0.00 0.00 3.27
741 1811 4.391155 ACAGCTCACGGTAAAATAAACCA 58.609 39.130 0.00 0.00 36.78 3.67
742 1812 5.007682 ACAGCTCACGGTAAAATAAACCAT 58.992 37.500 0.00 0.00 36.78 3.55
743 1813 5.106317 ACAGCTCACGGTAAAATAAACCATG 60.106 40.000 0.00 0.00 36.78 3.66
744 1814 4.398044 AGCTCACGGTAAAATAAACCATGG 59.602 41.667 11.19 11.19 36.78 3.66
745 1815 4.157105 GCTCACGGTAAAATAAACCATGGT 59.843 41.667 13.00 13.00 36.78 3.55
746 1816 5.354792 GCTCACGGTAAAATAAACCATGGTA 59.645 40.000 20.12 3.19 36.78 3.25
747 1817 6.127952 GCTCACGGTAAAATAAACCATGGTAA 60.128 38.462 20.12 10.29 36.78 2.85
748 1818 7.415877 GCTCACGGTAAAATAAACCATGGTAAT 60.416 37.037 20.12 12.35 36.78 1.89
749 1819 7.987649 TCACGGTAAAATAAACCATGGTAATC 58.012 34.615 20.12 3.22 36.78 1.75
750 1820 7.830201 TCACGGTAAAATAAACCATGGTAATCT 59.170 33.333 20.12 5.88 36.78 2.40
751 1821 9.111613 CACGGTAAAATAAACCATGGTAATCTA 57.888 33.333 20.12 8.04 36.78 1.98
752 1822 9.683870 ACGGTAAAATAAACCATGGTAATCTAA 57.316 29.630 20.12 0.34 36.78 2.10
777 1847 8.655651 AAAAACTGAGCATATTTTCCGAAAAA 57.344 26.923 10.27 1.56 38.66 1.94
815 1885 4.494350 AACAGCGAGTTTTAGTCGTAGA 57.506 40.909 5.88 0.00 42.66 2.59
816 1886 4.494350 ACAGCGAGTTTTAGTCGTAGAA 57.506 40.909 5.88 0.00 42.66 2.10
921 1992 1.933181 GAATGCAATCCGATCACGTCA 59.067 47.619 0.00 0.00 37.88 4.35
1105 2177 2.770048 CCAGGACCCTGCCCCTAG 60.770 72.222 10.50 0.00 42.35 3.02
1106 2178 3.483869 CAGGACCCTGCCCCTAGC 61.484 72.222 2.75 0.00 44.14 3.42
1200 2272 2.520979 CTCAACGAGGATGACGACTTC 58.479 52.381 0.00 0.00 34.70 3.01
1235 2307 0.610687 CCGCTTCCAGGAACTCTTCT 59.389 55.000 0.00 0.00 34.60 2.85
1476 2548 1.895131 CCATGTGCCTTTTACCTTGCT 59.105 47.619 0.00 0.00 0.00 3.91
1482 2554 1.067565 GCCTTTTACCTTGCTTCTGCC 60.068 52.381 0.00 0.00 38.71 4.85
1903 3013 5.059833 GGACCTGAAATGCCTTAGTCATAG 58.940 45.833 0.00 0.00 0.00 2.23
1922 3032 3.508845 AGTCTAGTGGGTGCAAACATT 57.491 42.857 0.00 0.00 0.00 2.71
1990 3103 2.002586 CTGGTTTCATGCTACAGGACG 58.997 52.381 0.00 0.00 0.00 4.79
2122 3235 3.057734 AGTTTACAAGTTCTCGAAGCGG 58.942 45.455 0.00 0.00 0.00 5.52
2186 3299 0.178995 TGCCAATGTGCTGGTGAGAA 60.179 50.000 0.00 0.00 38.86 2.87
2188 3301 1.547372 GCCAATGTGCTGGTGAGAATT 59.453 47.619 0.00 0.00 38.86 2.17
2189 3302 2.754552 GCCAATGTGCTGGTGAGAATTA 59.245 45.455 0.00 0.00 38.86 1.40
2228 3341 8.420374 TCTTATTAAGATCTAAGTTGTTGGCG 57.580 34.615 0.00 0.00 31.20 5.69
2281 3394 3.004752 ACTGGTTGCCATCCATTCTAC 57.995 47.619 0.00 0.00 34.26 2.59
2357 3470 2.513753 CACAAAACCCAGGTGCTATGA 58.486 47.619 0.00 0.00 0.00 2.15
2365 3478 2.430465 CCAGGTGCTATGATGGCATAC 58.570 52.381 6.78 3.59 41.86 2.39
2405 3518 2.511600 ATACCCTGCGCGTTGCTC 60.512 61.111 8.43 0.00 46.63 4.26
2646 3767 4.580167 TGTTGAGACTGGGACTTTTTCATG 59.420 41.667 0.00 0.00 0.00 3.07
2647 3768 3.149196 TGAGACTGGGACTTTTTCATGC 58.851 45.455 0.00 0.00 0.00 4.06
2648 3769 3.149196 GAGACTGGGACTTTTTCATGCA 58.851 45.455 0.00 0.00 0.00 3.96
2649 3770 3.760684 GAGACTGGGACTTTTTCATGCAT 59.239 43.478 0.00 0.00 0.00 3.96
2650 3771 3.508793 AGACTGGGACTTTTTCATGCATG 59.491 43.478 21.07 21.07 0.00 4.06
2651 3772 3.233507 ACTGGGACTTTTTCATGCATGT 58.766 40.909 25.43 5.72 0.00 3.21
2652 3773 3.642848 ACTGGGACTTTTTCATGCATGTT 59.357 39.130 25.43 5.16 0.00 2.71
2653 3774 4.101430 ACTGGGACTTTTTCATGCATGTTT 59.899 37.500 25.43 5.50 0.00 2.83
2654 3775 4.378774 TGGGACTTTTTCATGCATGTTTG 58.621 39.130 25.43 14.38 0.00 2.93
2666 3787 1.990799 CATGTTTGCATGCTGAGGTG 58.009 50.000 20.33 8.74 44.87 4.00
2763 3884 2.722094 ACTTCTGTGGAAAAGCACACA 58.278 42.857 0.00 0.00 44.60 3.72
2794 3915 1.204704 TCTCGACACCAATACCAGCTG 59.795 52.381 6.78 6.78 0.00 4.24
3029 4150 2.038863 TTACCCCTGGCTCTCTCAAA 57.961 50.000 0.00 0.00 0.00 2.69
3062 4183 0.810031 ACTGAGACAACACGTGCCAC 60.810 55.000 17.22 4.99 0.00 5.01
3075 4196 2.352821 TGCCACCATCTTGCCATGC 61.353 57.895 0.00 0.00 0.00 4.06
3095 4217 5.275067 TGCCAGCAACTTAAGTGAAAAAT 57.725 34.783 9.34 0.00 0.00 1.82
3184 4307 5.744666 TTTTGGAAAGGTCTGTAACTTCG 57.255 39.130 0.00 0.00 0.00 3.79
3236 4359 6.405278 TGGGAAAAACCAGATTCTCTTTTC 57.595 37.500 12.55 12.55 41.20 2.29
3395 4522 9.972106 AATAGTCAATCTGAAAAATCTTCTCCT 57.028 29.630 0.00 0.00 0.00 3.69
3446 4575 8.684520 CGTAAAAATATATACTCCCTCCGATCT 58.315 37.037 0.00 0.00 0.00 2.75
3503 4632 1.871080 ACATTGTATAGAGGCTGCGC 58.129 50.000 0.00 0.00 0.00 6.09
3522 4651 2.096417 CGCCAATTAATTCGGATCGGAC 60.096 50.000 16.30 3.88 0.00 4.79
3524 4653 3.128349 CCAATTAATTCGGATCGGACGT 58.872 45.455 1.88 0.00 0.00 4.34
3654 4785 1.152881 CACTTGGGATAGGGCCAGC 60.153 63.158 6.18 0.00 0.00 4.85
3661 4792 0.400594 GGATAGGGCCAGCGGTAAAT 59.599 55.000 6.18 0.00 0.00 1.40
3699 4830 6.706270 TCAAGATTCGAAAGTAAACTTCTGCT 59.294 34.615 0.00 0.00 34.61 4.24
3910 5044 8.819974 CACAAGTTCAAATTGCTACTGAAAAAT 58.180 29.630 0.00 0.00 31.21 1.82
4061 5195 4.833390 AGTAGACAAGTTAGGGAATGCAC 58.167 43.478 0.00 0.00 0.00 4.57
4328 5462 3.139077 GGTATGGGCTTAACCTTGATCG 58.861 50.000 0.00 0.00 39.10 3.69
4425 5588 7.341512 TGACATATTCAATGGCCAACTAAATCA 59.658 33.333 10.96 3.04 0.00 2.57
4514 5678 6.148811 GGACACCTCAATTTTCGTAATGAAGA 59.851 38.462 0.00 0.00 37.99 2.87
4636 5800 6.835174 ACTATGGATGTTGTTGAGAGCATAT 58.165 36.000 0.00 0.00 0.00 1.78
4767 5935 8.673711 GCAGTGTTGTAATTATTGGAATAGTGA 58.326 33.333 0.00 0.00 0.00 3.41
4774 5942 2.717639 ATTGGAATAGTGAGGCGCTT 57.282 45.000 7.64 0.00 0.00 4.68
4885 6053 6.093771 GCTGTTCATGATGAAGATATGATCCC 59.906 42.308 8.33 0.00 37.00 3.85
4973 6142 3.836365 ACATGACTTTGGGTTTTTGGG 57.164 42.857 0.00 0.00 0.00 4.12
5033 6203 6.698329 GCATAATATTTCTTGAAGCATGTGCA 59.302 34.615 7.83 0.00 45.16 4.57
5035 6205 5.648178 ATATTTCTTGAAGCATGTGCACA 57.352 34.783 24.08 24.08 45.16 4.57
5070 6240 7.753132 TGTTTTGTTATGCCGTATCTCATTTTC 59.247 33.333 0.00 0.00 0.00 2.29
5095 6265 4.863491 ACTTTGCTTACGTCTAGTCGAAA 58.137 39.130 16.23 4.97 34.70 3.46
5167 6337 4.265073 ACAAGCAAGCCCTGAAACTATAG 58.735 43.478 0.00 0.00 0.00 1.31
5245 6423 8.308207 AGTCTTCTTCATCTTAAACCTGTCTAC 58.692 37.037 0.00 0.00 0.00 2.59
5329 6507 2.695147 AGGTTCTGCAAACTTTCCAAGG 59.305 45.455 10.28 0.00 0.00 3.61
5360 6538 5.532406 TCAAGCTGAGCTACAAATTCAAGTT 59.468 36.000 7.68 0.00 38.25 2.66
5532 6715 9.770503 CTGAATAGTATTTTGCATGCTATGATC 57.229 33.333 20.33 5.86 29.50 2.92
5539 6722 1.496001 TGCATGCTATGATCTTGGGGT 59.504 47.619 20.33 0.00 0.00 4.95
5568 6751 4.583489 TGTACTTTCTCTCTTTCCACGAGT 59.417 41.667 0.00 0.00 0.00 4.18
5646 6832 6.207810 TGGCCTTAGTTGTAACAACCAAATAG 59.792 38.462 3.32 0.00 0.00 1.73
5844 7037 6.934056 TGCCATTATGTTTGTTTCTAGCATT 58.066 32.000 0.00 0.00 0.00 3.56
5967 7160 8.853345 CACAAGCTGTTTGATCAACATAAATAC 58.147 33.333 7.89 2.36 44.72 1.89
6100 7534 8.315391 ACATGTGTGCTATCATTATGTATGAC 57.685 34.615 0.00 0.00 45.71 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.746307 TGTAAGATCTGATTGATTGCAGC 57.254 39.130 0.00 0.00 35.14 5.25
1 2 7.226918 AGACATGTAAGATCTGATTGATTGCAG 59.773 37.037 0.00 0.00 35.14 4.41
2 3 7.052248 AGACATGTAAGATCTGATTGATTGCA 58.948 34.615 0.00 0.00 35.14 4.08
3 4 7.493743 AGACATGTAAGATCTGATTGATTGC 57.506 36.000 0.00 0.00 35.14 3.56
4 5 8.697960 CGTAGACATGTAAGATCTGATTGATTG 58.302 37.037 0.00 0.00 35.14 2.67
7 8 7.499232 TCTCGTAGACATGTAAGATCTGATTGA 59.501 37.037 0.00 0.00 0.00 2.57
8 9 7.643579 TCTCGTAGACATGTAAGATCTGATTG 58.356 38.462 0.00 0.00 0.00 2.67
9 10 7.809546 TCTCGTAGACATGTAAGATCTGATT 57.190 36.000 0.00 0.00 0.00 2.57
11 12 6.205658 CCATCTCGTAGACATGTAAGATCTGA 59.794 42.308 0.00 0.00 30.81 3.27
12 13 6.377780 CCATCTCGTAGACATGTAAGATCTG 58.622 44.000 0.00 0.00 30.81 2.90
13 14 5.475220 CCCATCTCGTAGACATGTAAGATCT 59.525 44.000 0.00 0.00 30.81 2.75
14 15 5.704888 CCCATCTCGTAGACATGTAAGATC 58.295 45.833 0.00 0.00 30.81 2.75
15 16 4.021894 GCCCATCTCGTAGACATGTAAGAT 60.022 45.833 0.00 0.02 30.81 2.40
16 17 3.318275 GCCCATCTCGTAGACATGTAAGA 59.682 47.826 0.00 0.00 30.81 2.10
17 18 3.319405 AGCCCATCTCGTAGACATGTAAG 59.681 47.826 0.00 0.00 30.81 2.34
18 19 3.296854 AGCCCATCTCGTAGACATGTAA 58.703 45.455 0.00 0.00 30.81 2.41
19 20 2.885266 GAGCCCATCTCGTAGACATGTA 59.115 50.000 0.00 0.00 30.81 2.29
20 21 1.683917 GAGCCCATCTCGTAGACATGT 59.316 52.381 0.00 0.00 30.81 3.21
21 22 1.959985 AGAGCCCATCTCGTAGACATG 59.040 52.381 0.00 0.00 46.44 3.21
22 23 1.959985 CAGAGCCCATCTCGTAGACAT 59.040 52.381 0.00 0.00 46.44 3.06
23 24 1.393603 CAGAGCCCATCTCGTAGACA 58.606 55.000 0.00 0.00 46.44 3.41
24 25 0.671251 CCAGAGCCCATCTCGTAGAC 59.329 60.000 0.00 0.00 46.44 2.59
25 26 0.259065 ACCAGAGCCCATCTCGTAGA 59.741 55.000 0.00 0.00 46.44 2.59
26 27 0.671251 GACCAGAGCCCATCTCGTAG 59.329 60.000 0.00 0.00 46.44 3.51
27 28 0.033503 TGACCAGAGCCCATCTCGTA 60.034 55.000 0.00 0.00 46.44 3.43
28 29 1.305297 TGACCAGAGCCCATCTCGT 60.305 57.895 0.00 0.00 46.44 4.18
29 30 1.326213 ACTGACCAGAGCCCATCTCG 61.326 60.000 3.76 0.00 46.44 4.04
30 31 0.908198 AACTGACCAGAGCCCATCTC 59.092 55.000 3.76 0.00 42.21 2.75
31 32 0.617413 CAACTGACCAGAGCCCATCT 59.383 55.000 3.76 0.00 39.56 2.90
32 33 0.615331 TCAACTGACCAGAGCCCATC 59.385 55.000 3.76 0.00 0.00 3.51
33 34 1.293062 ATCAACTGACCAGAGCCCAT 58.707 50.000 3.76 0.00 0.00 4.00
34 35 1.951209 TATCAACTGACCAGAGCCCA 58.049 50.000 3.76 0.00 0.00 5.36
35 36 3.010420 GTTTATCAACTGACCAGAGCCC 58.990 50.000 3.76 0.00 0.00 5.19
36 37 3.674997 TGTTTATCAACTGACCAGAGCC 58.325 45.455 3.76 0.00 33.58 4.70
37 38 5.470098 TCTTTGTTTATCAACTGACCAGAGC 59.530 40.000 3.76 0.00 35.61 4.09
38 39 6.483307 TGTCTTTGTTTATCAACTGACCAGAG 59.517 38.462 3.76 0.00 38.15 3.35
39 40 6.353323 TGTCTTTGTTTATCAACTGACCAGA 58.647 36.000 3.76 0.00 38.15 3.86
40 41 6.618287 TGTCTTTGTTTATCAACTGACCAG 57.382 37.500 0.00 0.00 38.15 4.00
41 42 6.601613 ACTTGTCTTTGTTTATCAACTGACCA 59.398 34.615 0.00 0.00 38.15 4.02
42 43 7.012421 AGACTTGTCTTTGTTTATCAACTGACC 59.988 37.037 0.00 0.00 38.15 4.02
43 44 7.852945 CAGACTTGTCTTTGTTTATCAACTGAC 59.147 37.037 0.00 0.00 38.75 3.51
44 45 7.467267 GCAGACTTGTCTTTGTTTATCAACTGA 60.467 37.037 0.00 0.00 35.61 3.41
45 46 6.634436 GCAGACTTGTCTTTGTTTATCAACTG 59.366 38.462 0.00 0.00 35.61 3.16
46 47 6.543831 AGCAGACTTGTCTTTGTTTATCAACT 59.456 34.615 0.00 0.00 35.61 3.16
47 48 6.634436 CAGCAGACTTGTCTTTGTTTATCAAC 59.366 38.462 0.00 0.00 35.61 3.18
48 49 6.318648 ACAGCAGACTTGTCTTTGTTTATCAA 59.681 34.615 0.00 0.00 0.00 2.57
49 50 5.822519 ACAGCAGACTTGTCTTTGTTTATCA 59.177 36.000 0.00 0.00 0.00 2.15
50 51 6.305693 ACAGCAGACTTGTCTTTGTTTATC 57.694 37.500 0.00 0.00 0.00 1.75
51 52 5.239525 GGACAGCAGACTTGTCTTTGTTTAT 59.760 40.000 14.70 0.00 43.44 1.40
52 53 4.574828 GGACAGCAGACTTGTCTTTGTTTA 59.425 41.667 14.70 0.00 43.44 2.01
53 54 3.378427 GGACAGCAGACTTGTCTTTGTTT 59.622 43.478 14.70 0.00 43.44 2.83
54 55 2.945668 GGACAGCAGACTTGTCTTTGTT 59.054 45.455 14.70 0.00 43.44 2.83
55 56 2.171448 AGGACAGCAGACTTGTCTTTGT 59.829 45.455 13.90 13.90 43.44 2.83
56 57 2.805099 GAGGACAGCAGACTTGTCTTTG 59.195 50.000 7.13 5.69 43.44 2.77
57 58 2.703007 AGAGGACAGCAGACTTGTCTTT 59.297 45.455 7.13 0.00 43.44 2.52
58 59 2.324541 AGAGGACAGCAGACTTGTCTT 58.675 47.619 7.13 0.21 43.44 3.01
59 60 2.008242 AGAGGACAGCAGACTTGTCT 57.992 50.000 7.13 0.00 43.44 3.41
60 61 2.829741 AAGAGGACAGCAGACTTGTC 57.170 50.000 0.00 0.00 43.25 3.18
61 62 4.264460 CTAAAGAGGACAGCAGACTTGT 57.736 45.455 0.00 0.00 0.00 3.16
74 75 7.255451 TTTGCTATCAAACACAACCTAAAGAGG 60.255 37.037 0.00 0.00 41.72 3.69
75 76 6.801539 TGCTATCAAACACAACCTAAAGAG 57.198 37.500 0.00 0.00 0.00 2.85
76 77 7.284489 ACTTTGCTATCAAACACAACCTAAAGA 59.716 33.333 0.00 0.00 37.28 2.52
77 78 7.425606 ACTTTGCTATCAAACACAACCTAAAG 58.574 34.615 0.00 0.00 37.28 1.85
80 81 7.880713 TCATACTTTGCTATCAAACACAACCTA 59.119 33.333 0.00 0.00 37.28 3.08
192 194 2.201732 CGGGTCTCGGTATTGACAATG 58.798 52.381 11.05 0.00 35.11 2.82
211 213 4.024893 GCTCCATACAACATTGACCATACG 60.025 45.833 0.00 0.00 0.00 3.06
214 216 3.966979 TGCTCCATACAACATTGACCAT 58.033 40.909 0.00 0.00 0.00 3.55
221 223 8.190784 GCTAATTTACTTTGCTCCATACAACAT 58.809 33.333 0.00 0.00 33.48 2.71
224 226 7.938140 AGCTAATTTACTTTGCTCCATACAA 57.062 32.000 0.00 0.00 41.23 2.41
332 334 8.530311 TCAATAAATCAACCAGTTTATGCATGT 58.470 29.630 10.16 0.00 32.47 3.21
376 1443 5.806818 TCCGACTAATCAACCAAACCATTA 58.193 37.500 0.00 0.00 0.00 1.90
424 1491 4.680440 GCGATTTTTGCCCATTGGTTCTAT 60.680 41.667 1.20 0.00 0.00 1.98
425 1492 3.367910 GCGATTTTTGCCCATTGGTTCTA 60.368 43.478 1.20 0.00 0.00 2.10
426 1493 2.612721 GCGATTTTTGCCCATTGGTTCT 60.613 45.455 1.20 0.00 0.00 3.01
427 1494 1.731709 GCGATTTTTGCCCATTGGTTC 59.268 47.619 1.20 0.00 0.00 3.62
428 1495 1.071385 TGCGATTTTTGCCCATTGGTT 59.929 42.857 1.20 0.00 0.00 3.67
464 1531 4.831698 GCTGCAGAGCTGACCTAG 57.168 61.111 20.43 0.00 42.52 3.02
482 1549 1.080772 CGCGGTGCACTGTCTTCTA 60.081 57.895 26.00 0.00 0.00 2.10
580 1647 5.386958 TCTTAAAACTGAGCTAGCGAGAA 57.613 39.130 20.01 6.26 0.00 2.87
582 1649 6.467723 TTTTCTTAAAACTGAGCTAGCGAG 57.532 37.500 9.55 11.93 0.00 5.03
652 1722 3.243569 CCATGGTACTTCAACCGCAAAAA 60.244 43.478 2.57 0.00 42.91 1.94
653 1723 2.294791 CCATGGTACTTCAACCGCAAAA 59.705 45.455 2.57 0.00 42.91 2.44
654 1724 1.883275 CCATGGTACTTCAACCGCAAA 59.117 47.619 2.57 0.00 42.91 3.68
655 1725 1.202830 ACCATGGTACTTCAACCGCAA 60.203 47.619 18.10 0.00 42.91 4.85
656 1726 0.398696 ACCATGGTACTTCAACCGCA 59.601 50.000 18.10 0.00 42.91 5.69
657 1727 1.530323 AACCATGGTACTTCAACCGC 58.470 50.000 20.12 0.00 42.91 5.68
658 1728 3.855524 GCAAAACCATGGTACTTCAACCG 60.856 47.826 20.12 3.95 42.91 4.44
659 1729 3.554129 GGCAAAACCATGGTACTTCAACC 60.554 47.826 20.12 9.92 38.05 3.77
660 1730 3.068873 TGGCAAAACCATGGTACTTCAAC 59.931 43.478 20.12 6.40 46.36 3.18
661 1731 3.300388 TGGCAAAACCATGGTACTTCAA 58.700 40.909 20.12 0.00 46.36 2.69
662 1732 2.950781 TGGCAAAACCATGGTACTTCA 58.049 42.857 20.12 10.52 46.36 3.02
668 1738 8.020747 ATACTGTAGTATTGGCAAAACCATGGT 61.021 37.037 13.00 13.00 39.33 3.55
669 1739 6.321181 ATACTGTAGTATTGGCAAAACCATGG 59.679 38.462 11.19 11.19 39.33 3.66
670 1740 7.195646 CATACTGTAGTATTGGCAAAACCATG 58.804 38.462 3.01 1.85 40.44 3.66
671 1741 6.321181 CCATACTGTAGTATTGGCAAAACCAT 59.679 38.462 3.01 0.00 40.44 3.55
672 1742 5.650266 CCATACTGTAGTATTGGCAAAACCA 59.350 40.000 3.01 0.00 41.96 3.67
673 1743 5.883673 TCCATACTGTAGTATTGGCAAAACC 59.116 40.000 3.01 0.00 39.06 3.27
674 1744 6.995511 TCCATACTGTAGTATTGGCAAAAC 57.004 37.500 3.01 1.22 39.06 2.43
675 1745 7.172342 ACTTCCATACTGTAGTATTGGCAAAA 58.828 34.615 3.01 0.00 39.06 2.44
676 1746 6.717289 ACTTCCATACTGTAGTATTGGCAAA 58.283 36.000 3.01 0.00 39.06 3.68
677 1747 6.308015 ACTTCCATACTGTAGTATTGGCAA 57.692 37.500 0.68 0.68 39.06 4.52
678 1748 5.950544 ACTTCCATACTGTAGTATTGGCA 57.049 39.130 1.87 0.00 39.06 4.92
679 1749 7.052142 ACTACTTCCATACTGTAGTATTGGC 57.948 40.000 1.87 0.00 43.20 4.52
680 1750 9.886132 AAAACTACTTCCATACTGTAGTATTGG 57.114 33.333 1.87 7.65 43.92 3.16
685 1755 9.305555 TCACTAAAACTACTTCCATACTGTAGT 57.694 33.333 0.00 0.00 45.82 2.73
686 1756 9.570488 GTCACTAAAACTACTTCCATACTGTAG 57.430 37.037 0.00 0.00 39.43 2.74
687 1757 9.081204 TGTCACTAAAACTACTTCCATACTGTA 57.919 33.333 0.00 0.00 0.00 2.74
688 1758 7.959175 TGTCACTAAAACTACTTCCATACTGT 58.041 34.615 0.00 0.00 0.00 3.55
689 1759 8.304596 TCTGTCACTAAAACTACTTCCATACTG 58.695 37.037 0.00 0.00 0.00 2.74
690 1760 8.305317 GTCTGTCACTAAAACTACTTCCATACT 58.695 37.037 0.00 0.00 0.00 2.12
691 1761 8.086522 TGTCTGTCACTAAAACTACTTCCATAC 58.913 37.037 0.00 0.00 0.00 2.39
692 1762 8.185506 TGTCTGTCACTAAAACTACTTCCATA 57.814 34.615 0.00 0.00 0.00 2.74
693 1763 7.062749 TGTCTGTCACTAAAACTACTTCCAT 57.937 36.000 0.00 0.00 0.00 3.41
694 1764 6.474140 TGTCTGTCACTAAAACTACTTCCA 57.526 37.500 0.00 0.00 0.00 3.53
695 1765 7.279313 TGTTTGTCTGTCACTAAAACTACTTCC 59.721 37.037 0.00 0.00 33.07 3.46
696 1766 8.193250 TGTTTGTCTGTCACTAAAACTACTTC 57.807 34.615 0.00 0.00 33.07 3.01
697 1767 7.201617 GCTGTTTGTCTGTCACTAAAACTACTT 60.202 37.037 0.00 0.00 33.07 2.24
698 1768 6.258068 GCTGTTTGTCTGTCACTAAAACTACT 59.742 38.462 0.00 0.00 33.07 2.57
699 1769 6.258068 AGCTGTTTGTCTGTCACTAAAACTAC 59.742 38.462 0.00 0.00 33.07 2.73
700 1770 6.346096 AGCTGTTTGTCTGTCACTAAAACTA 58.654 36.000 0.00 0.00 33.07 2.24
701 1771 5.186198 AGCTGTTTGTCTGTCACTAAAACT 58.814 37.500 0.00 0.00 33.07 2.66
702 1772 5.064707 TGAGCTGTTTGTCTGTCACTAAAAC 59.935 40.000 0.00 0.00 0.00 2.43
703 1773 5.064707 GTGAGCTGTTTGTCTGTCACTAAAA 59.935 40.000 0.00 0.00 33.14 1.52
704 1774 4.570772 GTGAGCTGTTTGTCTGTCACTAAA 59.429 41.667 0.00 0.00 33.14 1.85
705 1775 4.119862 GTGAGCTGTTTGTCTGTCACTAA 58.880 43.478 0.00 0.00 33.14 2.24
706 1776 3.717707 GTGAGCTGTTTGTCTGTCACTA 58.282 45.455 0.00 0.00 33.14 2.74
707 1777 2.555199 GTGAGCTGTTTGTCTGTCACT 58.445 47.619 0.00 0.00 33.14 3.41
708 1778 1.258982 CGTGAGCTGTTTGTCTGTCAC 59.741 52.381 0.00 0.00 0.00 3.67
709 1779 1.570813 CGTGAGCTGTTTGTCTGTCA 58.429 50.000 0.00 0.00 0.00 3.58
710 1780 0.861837 CCGTGAGCTGTTTGTCTGTC 59.138 55.000 0.00 0.00 0.00 3.51
711 1781 0.178068 ACCGTGAGCTGTTTGTCTGT 59.822 50.000 0.00 0.00 0.00 3.41
712 1782 2.148916 TACCGTGAGCTGTTTGTCTG 57.851 50.000 0.00 0.00 0.00 3.51
713 1783 2.902705 TTACCGTGAGCTGTTTGTCT 57.097 45.000 0.00 0.00 0.00 3.41
714 1784 3.955771 TTTTACCGTGAGCTGTTTGTC 57.044 42.857 0.00 0.00 0.00 3.18
715 1785 6.203647 GTTTATTTTACCGTGAGCTGTTTGT 58.796 36.000 0.00 0.00 0.00 2.83
716 1786 5.627780 GGTTTATTTTACCGTGAGCTGTTTG 59.372 40.000 0.00 0.00 0.00 2.93
717 1787 5.299782 TGGTTTATTTTACCGTGAGCTGTTT 59.700 36.000 0.00 0.00 38.55 2.83
718 1788 4.822896 TGGTTTATTTTACCGTGAGCTGTT 59.177 37.500 0.00 0.00 38.55 3.16
719 1789 4.391155 TGGTTTATTTTACCGTGAGCTGT 58.609 39.130 0.00 0.00 38.55 4.40
720 1790 5.560966 ATGGTTTATTTTACCGTGAGCTG 57.439 39.130 0.00 0.00 38.55 4.24
726 1796 9.683870 TTAGATTACCATGGTTTATTTTACCGT 57.316 29.630 25.38 0.00 38.55 4.83
752 1822 8.655651 TTTTTCGGAAAATATGCTCAGTTTTT 57.344 26.923 15.97 0.00 30.07 1.94
777 1847 6.908825 TCGCTGTTTTATATGCTCAGTTTTT 58.091 32.000 0.00 0.00 0.00 1.94
778 1848 6.149474 ACTCGCTGTTTTATATGCTCAGTTTT 59.851 34.615 0.00 0.00 0.00 2.43
779 1849 5.643777 ACTCGCTGTTTTATATGCTCAGTTT 59.356 36.000 0.00 0.00 0.00 2.66
780 1850 5.178797 ACTCGCTGTTTTATATGCTCAGTT 58.821 37.500 0.00 0.00 0.00 3.16
781 1851 4.759782 ACTCGCTGTTTTATATGCTCAGT 58.240 39.130 0.00 0.00 0.00 3.41
782 1852 5.725110 AACTCGCTGTTTTATATGCTCAG 57.275 39.130 0.00 0.00 34.84 3.35
794 1864 4.494350 TCTACGACTAAAACTCGCTGTT 57.506 40.909 0.00 0.00 41.29 3.16
795 1865 4.494350 TTCTACGACTAAAACTCGCTGT 57.506 40.909 0.00 0.00 34.34 4.40
796 1866 5.817616 TTTTCTACGACTAAAACTCGCTG 57.182 39.130 0.00 0.00 34.34 5.18
851 1922 2.226674 GCTGTAGCCAGTCCAGTTTTTC 59.773 50.000 0.00 0.00 41.02 2.29
895 1966 4.437255 CGTGATCGGATTGCATTCAAAGAA 60.437 41.667 10.55 0.00 35.56 2.52
1149 2221 3.319198 GTGGAGGAGCCGAACCCA 61.319 66.667 0.00 0.00 40.66 4.51
1181 2253 1.135774 CGAAGTCGTCATCCTCGTTGA 60.136 52.381 0.00 0.00 34.11 3.18
1200 2272 3.127533 GGCTGCTAACCTGTGGCG 61.128 66.667 0.00 0.00 0.00 5.69
1235 2307 6.010850 AGATGGAAGCTACAATCCGAGTATA 58.989 40.000 0.00 0.00 38.63 1.47
1286 2358 3.481903 CGCAGCTACACCGTGCAG 61.482 66.667 0.00 0.00 37.01 4.41
1320 2392 2.820037 GCACTACCTTGAGCGGCC 60.820 66.667 0.00 0.00 0.00 6.13
1861 2971 6.986817 CAGGTCCACCATAAGTAAATGAGTAG 59.013 42.308 0.00 0.00 38.89 2.57
1903 3013 3.146066 TGAATGTTTGCACCCACTAGAC 58.854 45.455 0.00 0.00 0.00 2.59
1922 3032 5.158141 AGAGGCCTATGAGGTTATGATTGA 58.842 41.667 4.42 0.00 37.80 2.57
1990 3103 0.533755 CCGAGAGACCAATGCCATCC 60.534 60.000 0.00 0.00 0.00 3.51
2122 3235 4.932200 CACCCTTCTTCATAGACTGACAAC 59.068 45.833 0.00 0.00 32.17 3.32
2281 3394 0.815734 ACTCAACCGTATGTCCTCCG 59.184 55.000 0.00 0.00 0.00 4.63
2357 3470 8.752005 AGTTATCAGTTAAATGTGTATGCCAT 57.248 30.769 2.43 0.00 0.00 4.40
2586 3700 5.478332 TGAGAAGAGACTCAGCTCAATAACA 59.522 40.000 19.12 2.58 41.21 2.41
2648 3769 0.892755 CCACCTCAGCATGCAAACAT 59.107 50.000 21.98 0.00 36.79 2.71
2649 3770 1.808531 GCCACCTCAGCATGCAAACA 61.809 55.000 21.98 0.00 34.76 2.83
2650 3771 1.080298 GCCACCTCAGCATGCAAAC 60.080 57.895 21.98 0.00 34.76 2.93
2651 3772 1.531128 TGCCACCTCAGCATGCAAA 60.531 52.632 21.98 6.13 34.69 3.68
2652 3773 2.115695 TGCCACCTCAGCATGCAA 59.884 55.556 21.98 6.54 34.69 4.08
2657 3778 1.601477 CACACATGCCACCTCAGCA 60.601 57.895 0.00 0.00 45.94 4.41
2658 3779 2.986306 GCACACATGCCACCTCAGC 61.986 63.158 0.00 0.00 46.97 4.26
2659 3780 3.271014 GCACACATGCCACCTCAG 58.729 61.111 0.00 0.00 46.97 3.35
2733 3854 6.257630 GCTTTTCCACAGAAGTTATTTTTGCA 59.742 34.615 0.00 0.00 32.35 4.08
2735 3856 7.277539 TGTGCTTTTCCACAGAAGTTATTTTTG 59.722 33.333 0.00 0.00 40.55 2.44
2736 3857 7.277760 GTGTGCTTTTCCACAGAAGTTATTTTT 59.722 33.333 0.00 0.00 45.54 1.94
2737 3858 6.756542 GTGTGCTTTTCCACAGAAGTTATTTT 59.243 34.615 0.00 0.00 45.54 1.82
2747 3868 3.441496 AATGTGTGTGCTTTTCCACAG 57.559 42.857 0.00 0.00 45.54 3.66
2763 3884 3.353557 TGGTGTCGAGACTAGCTAATGT 58.646 45.455 12.92 0.00 0.00 2.71
2794 3915 5.591643 TTCTCGCTATCAAACAAGAACAC 57.408 39.130 0.00 0.00 0.00 3.32
2970 4091 6.322201 AGAGTTCAATGTTCAAACAACCAGAT 59.678 34.615 0.00 0.00 43.03 2.90
3029 4150 1.134521 TCTCAGTCAGCACAAAACCGT 60.135 47.619 0.00 0.00 0.00 4.83
3062 4183 1.609635 TTGCTGGCATGGCAAGATGG 61.610 55.000 23.47 12.01 43.50 3.51
3075 4196 9.528018 TTCTTAATTTTTCACTTAAGTTGCTGG 57.472 29.630 5.07 0.00 36.67 4.85
3184 4307 9.548208 GACTTTCTACTATTTGTGAATTGCTTC 57.452 33.333 0.00 0.00 0.00 3.86
3256 4379 5.574891 TCTGAGAACTACTGAATCTGCTC 57.425 43.478 0.00 0.00 0.00 4.26
3380 4507 9.586732 TTAGGAAATTGAGGAGAAGATTTTTCA 57.413 29.630 0.00 0.00 0.00 2.69
3387 4514 9.892130 GAACTATTTAGGAAATTGAGGAGAAGA 57.108 33.333 1.31 0.00 32.38 2.87
3420 4549 8.684520 AGATCGGAGGGAGTATATATTTTTACG 58.315 37.037 0.00 0.00 0.00 3.18
3446 4575 8.264347 TGTATAGAGGCTGTGTCAATTAATTCA 58.736 33.333 0.00 0.00 0.00 2.57
3503 4632 3.128349 ACGTCCGATCCGAATTAATTGG 58.872 45.455 5.17 4.17 0.00 3.16
3556 4686 9.906660 CCTTGTCAGCAACTTAATTAAAACATA 57.093 29.630 0.00 0.00 0.00 2.29
3654 4785 7.806690 TCTTGAACTCTTGAATCAATTTACCG 58.193 34.615 0.00 0.00 33.03 4.02
3661 4792 7.728847 TTCGAATCTTGAACTCTTGAATCAA 57.271 32.000 0.00 0.00 0.00 2.57
4061 5195 6.605119 AGGATCAACAAAGGTGGATATTAGG 58.395 40.000 0.00 0.00 37.82 2.69
4376 5510 8.506437 GTCATTCACATAAATGAACTCAAGTGA 58.494 33.333 1.17 0.00 44.83 3.41
4425 5588 9.699703 GACAGTGAAGTAAAGAGAAATAGACTT 57.300 33.333 0.00 0.00 0.00 3.01
4514 5678 5.880054 GTGTTCACACACCAATATAAGCT 57.120 39.130 5.16 0.00 46.84 3.74
4636 5800 5.932619 TTACTAACCTTCAGCTGCTCATA 57.067 39.130 9.47 0.00 0.00 2.15
4767 5935 3.059352 AGTGTCTTATTTGAAGCGCCT 57.941 42.857 2.29 0.00 0.00 5.52
4806 5974 5.880901 TCTATGCTCTCCCAAAAGAAAAGT 58.119 37.500 0.00 0.00 0.00 2.66
4858 6026 4.992951 TCATATCTTCATCATGAACAGCCG 59.007 41.667 0.00 0.00 32.21 5.52
4905 6074 5.339008 AAAAACTCCAACCAAGAAAGACC 57.661 39.130 0.00 0.00 0.00 3.85
4929 6098 2.228822 CTCCAGCCAACAAAGCGTTAAT 59.771 45.455 0.00 0.00 35.52 1.40
4934 6103 1.069227 GTAACTCCAGCCAACAAAGCG 60.069 52.381 0.00 0.00 34.64 4.68
4973 6142 6.586082 CAGCAAATATACCAAACCTTGACAAC 59.414 38.462 0.00 0.00 0.00 3.32
5033 6203 6.364706 CGGCATAACAAAACATAAACACATGT 59.635 34.615 0.00 0.00 40.90 3.21
5035 6205 6.451393 ACGGCATAACAAAACATAAACACAT 58.549 32.000 0.00 0.00 0.00 3.21
5070 6240 5.625251 TCGACTAGACGTAAGCAAAGTTAG 58.375 41.667 14.02 0.00 45.62 2.34
5118 6288 6.469410 TGTTATTTCCACGTATTTGTCCTCT 58.531 36.000 0.00 0.00 0.00 3.69
5167 6337 2.814336 CCTTTGTCCCTCTGTAGTTTGC 59.186 50.000 0.00 0.00 0.00 3.68
5245 6423 5.409643 AGAACATGAAAAGACACACGAAG 57.590 39.130 0.00 0.00 0.00 3.79
5329 6507 1.872313 GTAGCTCAGCTTGATGATGCC 59.128 52.381 3.31 0.00 40.44 4.40
5360 6538 4.310769 CACCAACAAACAGTTCCACAAAA 58.689 39.130 0.00 0.00 38.74 2.44
5532 6715 7.124448 AGAGAGAAAGTACAGTATAACCCCAAG 59.876 40.741 0.00 0.00 0.00 3.61
5539 6722 8.242053 CGTGGAAAGAGAGAAAGTACAGTATAA 58.758 37.037 0.00 0.00 0.00 0.98
5568 6751 9.487790 AATTTTGAGAAAAGAAGTCAACACAAA 57.512 25.926 0.00 0.00 33.22 2.83
5646 6832 4.644103 AAATACACATTCATGGCTCAGC 57.356 40.909 0.00 0.00 0.00 4.26
5844 7037 8.088365 AGTGCACTGTTAGATATAAATATCGCA 58.912 33.333 20.97 4.16 43.01 5.10
5864 7057 7.466050 CGGAAAGATTAGGATTTCTTAGTGCAC 60.466 40.741 9.40 9.40 36.03 4.57
5931 7124 5.401550 TCAAACAGCTTGTGAAGAAAAGTG 58.598 37.500 0.00 0.00 36.34 3.16
5936 7129 5.125257 TGTTGATCAAACAGCTTGTGAAGAA 59.875 36.000 10.35 0.00 43.96 2.52
5937 7130 4.639755 TGTTGATCAAACAGCTTGTGAAGA 59.360 37.500 10.35 0.00 43.96 2.87
5967 7160 3.428862 GCAACACTTTCCCCAATAATCCG 60.429 47.826 0.00 0.00 0.00 4.18
6030 7225 8.402798 TGATAAACATGAAAATGTACCACAGT 57.597 30.769 0.00 0.00 33.81 3.55


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

AutoCloner maintained by Alex Coulton.