Multiple sequence alignment - TraesCS5B01G123400

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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 TraesCS5B01G123400 chr5B 100.000 5519 0 0 1 5519 222366618 222372136 0.000000e+00 10192.0
1 TraesCS5B01G123400 chr5B 100.000 146 0 0 6239 6384 222372856 222373001 2.930000e-68 270.0
2 TraesCS5B01G123400 chr5B 93.204 103 5 2 4557 4659 352127360 352127260 3.990000e-32 150.0
3 TraesCS5B01G123400 chr5B 93.750 80 5 0 5433 5512 704452694 704452615 3.130000e-23 121.0
4 TraesCS5B01G123400 chr5B 100.000 31 0 0 1947 1977 467139693 467139663 2.490000e-04 58.4
5 TraesCS5B01G123400 chr5B 100.000 31 0 0 1947 1977 561695781 561695811 2.490000e-04 58.4
6 TraesCS5B01G123400 chr5A 94.577 4518 178 38 81 4571 270177086 270181563 0.000000e+00 6924.0
7 TraesCS5B01G123400 chr5A 95.345 623 25 2 4749 5367 270181562 270182184 0.000000e+00 987.0
8 TraesCS5B01G123400 chr5A 95.918 98 2 2 4660 4757 239529847 239529942 2.380000e-34 158.0
9 TraesCS5B01G123400 chr5A 100.000 31 0 0 1947 1977 622229718 622229688 2.490000e-04 58.4
10 TraesCS5B01G123400 chr5A 100.000 30 0 0 1948 1977 115079831 115079860 8.940000e-04 56.5
11 TraesCS5B01G123400 chr5D 94.815 3356 119 26 2105 5430 209310808 209314138 0.000000e+00 5182.0
12 TraesCS5B01G123400 chr5D 95.017 883 40 2 78 958 209309104 209309984 0.000000e+00 1384.0
13 TraesCS5B01G123400 chr5D 96.512 258 9 0 1661 1918 209310530 209310787 1.640000e-115 427.0
14 TraesCS5B01G123400 chr5D 86.226 363 27 16 1037 1385 209310021 209310374 7.820000e-99 372.0
15 TraesCS5B01G123400 chr5D 95.098 102 3 1 6261 6360 209314164 209314265 6.620000e-35 159.0
16 TraesCS5B01G123400 chr5D 97.826 92 2 0 4660 4751 558970441 558970532 6.620000e-35 159.0
17 TraesCS5B01G123400 chr5D 97.802 91 2 0 4569 4659 134782207 134782117 2.380000e-34 158.0
18 TraesCS5B01G123400 chr5D 90.826 109 9 1 4552 4659 234848259 234848151 1.860000e-30 145.0
19 TraesCS5B01G123400 chr5D 96.000 75 3 0 5437 5511 556868482 556868408 8.690000e-24 122.0
20 TraesCS5B01G123400 chr5D 93.750 80 4 1 5432 5511 238555668 238555746 1.120000e-22 119.0
21 TraesCS5B01G123400 chr5D 94.667 75 4 0 5437 5511 554514993 554514919 4.040000e-22 117.0
22 TraesCS5B01G123400 chr3B 90.248 2215 165 24 2059 4242 580038349 580036155 0.000000e+00 2846.0
23 TraesCS5B01G123400 chr3B 85.020 494 60 12 4757 5237 580035792 580035300 2.070000e-134 490.0
24 TraesCS5B01G123400 chr3B 90.040 251 23 2 1693 1942 580038611 580038362 2.220000e-84 324.0
25 TraesCS5B01G123400 chr3B 83.768 345 32 13 4233 4571 580036130 580035804 8.040000e-79 305.0
26 TraesCS5B01G123400 chr3B 94.949 99 3 2 4562 4659 256253815 256253718 3.080000e-33 154.0
27 TraesCS5B01G123400 chr3B 100.000 29 0 0 1949 1977 578630834 578630806 3.000000e-03 54.7
28 TraesCS5B01G123400 chr3A 88.995 2090 175 25 2191 4243 583707306 583705235 0.000000e+00 2534.0
29 TraesCS5B01G123400 chr3A 87.305 449 54 3 4804 5251 583704856 583704410 1.590000e-140 510.0
30 TraesCS5B01G123400 chr3A 88.328 317 29 6 4240 4552 583705205 583704893 2.170000e-99 374.0
31 TraesCS5B01G123400 chr3A 92.222 180 13 1 1707 1885 583707482 583707303 2.950000e-63 254.0
32 TraesCS5B01G123400 chr3A 96.154 78 2 1 5434 5511 62573485 62573409 6.720000e-25 126.0
33 TraesCS5B01G123400 chr3D 92.447 1218 73 12 2059 3264 442504081 442502871 0.000000e+00 1722.0
34 TraesCS5B01G123400 chr3D 87.380 729 64 14 3532 4242 442502577 442501859 0.000000e+00 811.0
35 TraesCS5B01G123400 chr3D 87.674 430 43 5 4757 5179 442500422 442499996 5.750000e-135 492.0
36 TraesCS5B01G123400 chr3D 88.462 338 29 8 4240 4571 442500767 442500434 3.590000e-107 399.0
37 TraesCS5B01G123400 chr3D 87.747 253 17 8 1694 1942 442504336 442504094 3.770000e-72 283.0
38 TraesCS5B01G123400 chr3D 77.918 317 34 23 161 468 442505590 442505301 1.420000e-36 165.0
39 TraesCS5B01G123400 chr3D 96.809 94 3 0 4660 4753 138076330 138076237 2.380000e-34 158.0
40 TraesCS5B01G123400 chr3D 93.976 83 5 0 5430 5512 285883576 285883494 6.720000e-25 126.0
41 TraesCS5B01G123400 chr3D 100.000 40 0 0 3909 3948 467570101 467570140 2.470000e-09 75.0
42 TraesCS5B01G123400 chr4A 81.746 252 44 2 398 648 501966500 501966750 6.490000e-50 209.0
43 TraesCS5B01G123400 chr4A 96.203 79 3 0 5434 5512 663581723 663581801 5.190000e-26 130.0
44 TraesCS5B01G123400 chr4D 81.275 251 45 2 398 647 89426915 89427164 1.090000e-47 202.0
45 TraesCS5B01G123400 chr4D 92.105 76 6 0 5437 5512 494533694 494533619 2.430000e-19 108.0
46 TraesCS5B01G123400 chr4D 97.297 37 1 0 1946 1982 423391005 423391041 5.340000e-06 63.9
47 TraesCS5B01G123400 chr4B 80.556 252 47 2 398 648 126327524 126327774 6.530000e-45 193.0
48 TraesCS5B01G123400 chr4B 93.671 79 5 0 5434 5512 229410346 229410424 1.120000e-22 119.0
49 TraesCS5B01G123400 chr4B 92.405 79 6 0 5434 5512 275719836 275719914 5.230000e-21 113.0
50 TraesCS5B01G123400 chr4B 100.000 29 0 0 1947 1975 163838592 163838620 3.000000e-03 54.7
51 TraesCS5B01G123400 chr2D 97.849 93 2 0 4660 4752 52051386 52051478 1.840000e-35 161.0
52 TraesCS5B01G123400 chr2D 96.000 100 3 1 4560 4659 445894875 445894973 1.840000e-35 161.0
53 TraesCS5B01G123400 chr2D 97.849 93 1 1 4660 4752 643762835 643762744 6.620000e-35 159.0
54 TraesCS5B01G123400 chr2D 96.842 95 2 1 4660 4753 445894890 445894984 2.380000e-34 158.0
55 TraesCS5B01G123400 chr2D 89.076 119 7 5 4660 4776 650775096 650774982 6.670000e-30 143.0
56 TraesCS5B01G123400 chr7A 94.898 98 5 0 4562 4659 628008582 628008485 3.080000e-33 154.0
57 TraesCS5B01G123400 chr2A 94.949 99 4 1 4561 4659 68155928 68155831 3.080000e-33 154.0
58 TraesCS5B01G123400 chr2A 96.053 76 3 0 5437 5512 21603825 21603750 2.420000e-24 124.0
59 TraesCS5B01G123400 chr6A 94.059 101 5 1 4660 4760 98239113 98239212 1.110000e-32 152.0
60 TraesCS5B01G123400 chr6A 93.902 82 5 0 5430 5511 1090277 1090358 2.420000e-24 124.0
61 TraesCS5B01G123400 chr1A 93.333 105 4 3 4556 4659 386427686 386427584 1.110000e-32 152.0
62 TraesCS5B01G123400 chr1A 96.000 75 3 0 5437 5511 49282705 49282631 8.690000e-24 122.0
63 TraesCS5B01G123400 chr1A 93.421 76 5 0 5437 5512 561070552 561070477 5.230000e-21 113.0
64 TraesCS5B01G123400 chr7B 96.203 79 3 0 5434 5512 399888159 399888237 5.190000e-26 130.0
65 TraesCS5B01G123400 chr7B 94.937 79 3 1 5434 5512 102323695 102323618 8.690000e-24 122.0
66 TraesCS5B01G123400 chr1D 97.333 75 2 0 5437 5511 96041114 96041040 1.870000e-25 128.0
67 TraesCS5B01G123400 chr1D 94.937 79 4 0 5434 5512 263322589 263322511 2.420000e-24 124.0
68 TraesCS5B01G123400 chr1D 94.805 77 4 0 5437 5513 201754038 201753962 3.130000e-23 121.0
69 TraesCS5B01G123400 chr1D 93.421 76 5 0 5437 5512 26408023 26407948 5.230000e-21 113.0
70 TraesCS5B01G123400 chr1D 92.208 77 6 0 5436 5512 96041029 96041105 6.770000e-20 110.0
71 TraesCS5B01G123400 chr7D 96.104 77 3 0 5436 5512 279217 279293 6.720000e-25 126.0
72 TraesCS5B01G123400 chr7D 94.872 78 4 0 5435 5512 341623161 341623084 8.690000e-24 122.0
73 TraesCS5B01G123400 chrUn 92.683 82 6 0 5431 5512 461112374 461112293 1.120000e-22 119.0
74 TraesCS5B01G123400 chrUn 93.421 76 5 0 5437 5512 162568827 162568752 5.230000e-21 113.0
75 TraesCS5B01G123400 chrUn 93.333 75 5 0 5437 5511 405527157 405527231 1.880000e-20 111.0
76 TraesCS5B01G123400 chrUn 93.333 75 5 0 5437 5511 473312062 473311988 1.880000e-20 111.0
77 TraesCS5B01G123400 chrUn 92.105 76 6 0 5437 5512 100081305 100081380 2.430000e-19 108.0
78 TraesCS5B01G123400 chrUn 91.250 80 5 2 5434 5512 336906985 336906907 2.430000e-19 108.0
79 TraesCS5B01G123400 chrUn 91.250 80 5 2 5434 5512 343555619 343555697 2.430000e-19 108.0
80 TraesCS5B01G123400 chrUn 91.250 80 5 2 5434 5512 346267321 346267399 2.430000e-19 108.0
81 TraesCS5B01G123400 chrUn 89.873 79 8 0 5434 5512 313026448 313026526 1.130000e-17 102.0
82 TraesCS5B01G123400 chr2B 100.000 32 0 0 1947 1978 776409703 776409672 6.910000e-05 60.2


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 TraesCS5B01G123400 chr5B 222366618 222373001 6383 False 5231.000000 10192 100.0000 1 6384 2 chr5B.!!$F2 6383
1 TraesCS5B01G123400 chr5A 270177086 270182184 5098 False 3955.500000 6924 94.9610 81 5367 2 chr5A.!!$F3 5286
2 TraesCS5B01G123400 chr5D 209309104 209314265 5161 False 1504.800000 5182 93.5336 78 6360 5 chr5D.!!$F3 6282
3 TraesCS5B01G123400 chr3B 580035300 580038611 3311 True 991.250000 2846 87.2690 1693 5237 4 chr3B.!!$R3 3544
4 TraesCS5B01G123400 chr3A 583704410 583707482 3072 True 918.000000 2534 89.2125 1707 5251 4 chr3A.!!$R2 3544
5 TraesCS5B01G123400 chr3D 442499996 442505590 5594 True 645.333333 1722 86.9380 161 5179 6 chr3D.!!$R3 5018

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
72 73 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49 F
320 321 0.525242 TGCAGCACAACAAGCGAAAC 60.525 50.000 0.00 0.00 37.01 2.78 F
334 335 1.372656 CGAAACGCACACGACTTTTC 58.627 50.000 0.00 0.00 43.93 2.29 F
1206 1254 0.244994 ACCACACTGATGAGCTCGTC 59.755 55.000 26.13 26.13 0.00 4.20 F
1405 1511 0.390209 GAGTTGTAGCCGCCGGTTTA 60.390 55.000 4.45 0.00 0.00 2.01 F
2003 2203 0.458543 CAGCCCTACTACAGTGCACG 60.459 60.000 12.01 9.15 0.00 5.34 F
3647 3994 0.321122 GTTCCTGTGAGCCTCTGGTG 60.321 60.000 0.00 0.00 0.00 4.17 F
4788 6276 1.199097 GTCAAAGTGTGGGCAATACCG 59.801 52.381 0.00 0.00 40.62 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1219 0.177836 CATCAGTGTGGTGCCGGATA 59.822 55.000 5.05 0.00 0.00 2.59 R
1206 1254 0.872021 GCGTTGGTGGATCTAGAGCG 60.872 60.000 1.16 0.00 0.00 5.03 R
1211 1259 1.220749 GCTGGCGTTGGTGGATCTA 59.779 57.895 0.00 0.00 0.00 1.98 R
2200 2401 2.607282 CGCTCAAAAGTCTGTACGACCT 60.607 50.000 12.27 0.17 43.91 3.85 R
3146 3362 3.197549 ACTTCTCCCTCATCTCTTCAAGC 59.802 47.826 0.00 0.00 0.00 4.01 R
3803 4166 3.519913 ACTCATCCACCTTCTAGTTTCCC 59.480 47.826 0.00 0.00 0.00 3.97 R
5369 6874 0.108424 AGAAGCAGCTGATGTCCGAC 60.108 55.000 20.43 0.00 0.00 4.79 R
6365 7872 1.358759 GAACACTTGCGGTTGTGGG 59.641 57.895 0.00 0.00 38.39 4.61 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
27 28 4.292977 CCTTTCTGGTGAGAAAACACAC 57.707 45.455 0.00 0.00 45.57 3.82
28 29 3.694072 CCTTTCTGGTGAGAAAACACACA 59.306 43.478 0.00 0.00 45.57 3.72
29 30 4.438744 CCTTTCTGGTGAGAAAACACACAC 60.439 45.833 0.00 0.00 45.57 3.82
30 31 3.342377 TCTGGTGAGAAAACACACACA 57.658 42.857 0.00 0.00 41.88 3.72
31 32 3.006940 TCTGGTGAGAAAACACACACAC 58.993 45.455 0.00 0.00 41.88 3.82
32 33 2.746904 CTGGTGAGAAAACACACACACA 59.253 45.455 0.00 0.00 41.88 3.72
33 34 2.486203 TGGTGAGAAAACACACACACAC 59.514 45.455 0.00 0.00 41.88 3.82
34 35 2.486203 GGTGAGAAAACACACACACACA 59.514 45.455 0.00 0.00 41.88 3.72
35 36 3.488489 GTGAGAAAACACACACACACAC 58.512 45.455 0.00 0.00 40.11 3.82
36 37 3.058570 GTGAGAAAACACACACACACACA 60.059 43.478 0.00 0.00 40.11 3.72
37 38 3.058570 TGAGAAAACACACACACACACAC 60.059 43.478 0.00 0.00 0.00 3.82
38 39 2.881513 AGAAAACACACACACACACACA 59.118 40.909 0.00 0.00 0.00 3.72
39 40 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
40 41 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
41 42 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
42 43 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
43 44 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
44 45 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
45 46 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
46 47 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
47 48 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
48 49 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
49 50 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
50 51 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
51 52 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
52 53 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
53 54 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
54 55 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
55 56 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
56 57 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
57 58 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
58 59 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
59 60 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
60 61 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
61 62 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
62 63 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
63 64 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
64 65 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
65 66 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
66 67 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
67 68 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
68 69 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
69 70 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
70 71 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
71 72 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
72 73 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
73 74 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
74 75 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
75 76 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
76 77 2.021243 CACACACACACACGCACG 59.979 61.111 0.00 0.00 0.00 5.34
90 91 3.033166 GCACGCACACACACACACA 62.033 57.895 0.00 0.00 0.00 3.72
259 260 6.033619 GTCAACTCAAGCATACGTACTAACAG 59.966 42.308 0.00 0.00 0.00 3.16
260 261 4.995124 ACTCAAGCATACGTACTAACAGG 58.005 43.478 0.00 0.00 0.00 4.00
320 321 0.525242 TGCAGCACAACAAGCGAAAC 60.525 50.000 0.00 0.00 37.01 2.78
334 335 1.372656 CGAAACGCACACGACTTTTC 58.627 50.000 0.00 0.00 43.93 2.29
335 336 1.738432 GAAACGCACACGACTTTTCC 58.262 50.000 0.00 0.00 43.93 3.13
365 366 7.601886 CCAAATAATAGAGAATCGCACAGAGAT 59.398 37.037 0.00 0.00 42.67 2.75
390 397 3.939592 GGGAATGTAACGGAAAAGGAGAG 59.060 47.826 0.00 0.00 0.00 3.20
836 854 2.332654 GGTGGGCTTGCGATTCGTT 61.333 57.895 8.03 0.00 0.00 3.85
873 898 2.159382 CCCCATTTTAACAGCAGTCGT 58.841 47.619 0.00 0.00 0.00 4.34
949 977 2.186160 CACTCAGCGGTGGCAAACA 61.186 57.895 15.67 0.00 43.41 2.83
995 1028 5.065859 TGAGAACAAAAACGCATTTCTCTCA 59.934 36.000 14.59 14.59 41.78 3.27
996 1029 5.273944 AGAACAAAAACGCATTTCTCTCAC 58.726 37.500 0.00 0.00 0.00 3.51
997 1030 4.900635 ACAAAAACGCATTTCTCTCACT 57.099 36.364 0.00 0.00 0.00 3.41
998 1031 6.260050 AGAACAAAAACGCATTTCTCTCACTA 59.740 34.615 0.00 0.00 0.00 2.74
999 1032 5.990408 ACAAAAACGCATTTCTCTCACTAG 58.010 37.500 0.00 0.00 0.00 2.57
1000 1033 4.670227 AAAACGCATTTCTCTCACTAGC 57.330 40.909 0.00 0.00 0.00 3.42
1026 1062 1.456287 GGATGCCCGCTTAATCCCT 59.544 57.895 0.00 0.00 34.89 4.20
1029 1065 2.203351 GCCCGCTTAATCCCTGGG 60.203 66.667 6.33 6.33 43.02 4.45
1068 1105 1.614824 CCCCTCCAAGCTCCTGTCT 60.615 63.158 0.00 0.00 0.00 3.41
1151 1191 4.499116 GCCAGCCCCCTCCTCCTA 62.499 72.222 0.00 0.00 0.00 2.94
1179 1219 3.610911 CTCCCTTTGCTTATCCGTCTTT 58.389 45.455 0.00 0.00 0.00 2.52
1206 1254 0.244994 ACCACACTGATGAGCTCGTC 59.755 55.000 26.13 26.13 0.00 4.20
1270 1325 1.202348 CAGCTACTCGTCACATCACCA 59.798 52.381 0.00 0.00 0.00 4.17
1323 1384 5.772521 TCTTGCAAGCAAACCTCTAATTTC 58.227 37.500 21.99 0.00 35.33 2.17
1405 1511 0.390209 GAGTTGTAGCCGCCGGTTTA 60.390 55.000 4.45 0.00 0.00 2.01
1449 1555 7.238723 TGATCTCCTGTATGTCTCTAGGTCTAT 59.761 40.741 0.00 0.00 0.00 1.98
1514 1620 5.575019 ACATTGAACTGTTACGTTGGTTTC 58.425 37.500 0.00 0.00 0.00 2.78
1638 1747 4.678044 CGCTAGTGATTAGTCATGGTGTGT 60.678 45.833 0.00 0.00 36.60 3.72
1883 2080 4.558538 ATCCTGCTTTCGTCATTTATGC 57.441 40.909 0.00 0.00 0.00 3.14
1933 2133 1.731709 TGCATTTCATTCGTCCACTCG 59.268 47.619 0.00 0.00 0.00 4.18
1945 2145 0.817654 TCCACTCGCATCAGTCGAAT 59.182 50.000 0.00 0.00 35.38 3.34
1991 2191 2.363795 CCGTGAGACCCAGCCCTA 60.364 66.667 0.00 0.00 0.00 3.53
2003 2203 0.458543 CAGCCCTACTACAGTGCACG 60.459 60.000 12.01 9.15 0.00 5.34
2210 2411 6.615264 TGCTACTATTTCTAGGTCGTACAG 57.385 41.667 0.00 0.00 0.00 2.74
2477 2679 1.655484 CGTTGATGCATGCTAGGACA 58.345 50.000 20.33 8.76 0.00 4.02
2603 2805 2.773661 TCAGGCCATATGTGTGTCTCAT 59.226 45.455 5.01 0.00 0.00 2.90
2666 2868 3.552068 CGGACAAAGTTTTCATGGTTCCC 60.552 47.826 0.00 0.00 0.00 3.97
2871 3084 7.630242 TTGCATGAGATAGGAAAAGGTTAAG 57.370 36.000 0.00 0.00 0.00 1.85
2873 3086 7.175104 TGCATGAGATAGGAAAAGGTTAAGTT 58.825 34.615 0.00 0.00 0.00 2.66
2931 3146 7.930513 TCAGCATATAGACATACTGTTTTCG 57.069 36.000 0.00 0.00 0.00 3.46
2933 3148 8.626526 TCAGCATATAGACATACTGTTTTCGTA 58.373 33.333 0.00 0.00 0.00 3.43
3042 3257 9.732130 ATCTTGCATCTTTACTTTCTTACTCTT 57.268 29.630 0.00 0.00 0.00 2.85
3146 3362 1.791103 ATGGTCCAAAACGTGTGCGG 61.791 55.000 0.00 0.00 43.45 5.69
3239 3455 6.971602 TCAAGTACGATCTGTTCTGATATCC 58.028 40.000 0.00 0.00 0.00 2.59
3410 3699 8.934023 AATAGTCTTGTCAGGTTCCAATTTTA 57.066 30.769 0.00 0.00 0.00 1.52
3411 3700 9.533831 AATAGTCTTGTCAGGTTCCAATTTTAT 57.466 29.630 0.00 0.00 0.00 1.40
3413 3702 6.777580 AGTCTTGTCAGGTTCCAATTTTATGT 59.222 34.615 0.00 0.00 0.00 2.29
3414 3703 7.287696 AGTCTTGTCAGGTTCCAATTTTATGTT 59.712 33.333 0.00 0.00 0.00 2.71
3479 3769 6.295236 CCATTGAATTCTAAAAGTCCAAGGCA 60.295 38.462 7.05 0.00 0.00 4.75
3482 3772 5.123820 TGAATTCTAAAAGTCCAAGGCATCG 59.876 40.000 7.05 0.00 0.00 3.84
3496 3831 0.956633 GCATCGGTGGCAATGATCAT 59.043 50.000 1.18 1.18 0.00 2.45
3528 3863 8.306680 TCACAGAGTAGCTAAAATTGTTGTAC 57.693 34.615 0.00 0.00 0.00 2.90
3530 3865 9.419297 CACAGAGTAGCTAAAATTGTTGTACTA 57.581 33.333 0.00 0.00 0.00 1.82
3595 3939 1.541588 GCCGCTTTGGATCTTTTCTGT 59.458 47.619 0.00 0.00 42.00 3.41
3597 3941 3.181506 GCCGCTTTGGATCTTTTCTGTAG 60.182 47.826 0.00 0.00 42.00 2.74
3616 3960 7.857456 TCTGTAGTTGGTCATATTTGTACCAT 58.143 34.615 7.78 0.00 42.65 3.55
3647 3994 0.321122 GTTCCTGTGAGCCTCTGGTG 60.321 60.000 0.00 0.00 0.00 4.17
3665 4012 2.415893 GGTGCTTCCAACATGCATGTAC 60.416 50.000 31.55 22.43 40.80 2.90
3700 4047 8.359875 TGATAAAATGTAATGATGTTGTGGGT 57.640 30.769 0.00 0.00 0.00 4.51
3755 4104 7.563888 TCATGGATCTAATGCAAAGAAAGAG 57.436 36.000 6.25 0.00 33.18 2.85
3759 4108 7.170965 TGGATCTAATGCAAAGAAAGAGAAGT 58.829 34.615 6.25 0.00 0.00 3.01
3822 4186 4.301072 TTGGGAAACTAGAAGGTGGATG 57.699 45.455 0.00 0.00 0.00 3.51
3888 4252 9.464714 ACTATAGCAATACTGAGACGTAAAATG 57.535 33.333 0.00 0.00 0.00 2.32
3901 4265 7.095523 TGAGACGTAAAATGTAACCTTTGCTAC 60.096 37.037 0.00 0.00 0.00 3.58
4018 4383 6.718454 CAGAGGTATGCCCTTTATGATTTCAT 59.282 38.462 0.00 0.00 46.51 2.57
4049 4416 6.855763 TTTGTGGAGAGCCATAAATTTCAT 57.144 33.333 0.00 0.00 46.34 2.57
4415 5887 6.127310 ACACTAATTTGCTAGATCGTCTTCCT 60.127 38.462 0.00 0.00 0.00 3.36
4468 5945 8.724229 TGTAAATTCATCTTCTGTCACTCATTG 58.276 33.333 0.00 0.00 0.00 2.82
4508 5989 7.310052 GCTGAAGATAGGTTTTTCCTTTGGATT 60.310 37.037 0.00 0.00 45.67 3.01
4662 6144 5.715753 AGACACTTATTTTAGGACGGACTCT 59.284 40.000 0.00 0.00 0.00 3.24
4788 6276 1.199097 GTCAAAGTGTGGGCAATACCG 59.801 52.381 0.00 0.00 40.62 4.02
4854 6347 8.662141 GTTGTGTTTCCGTAATGTTGTAGATAT 58.338 33.333 0.00 0.00 0.00 1.63
5226 6728 3.383761 GGTTCTGCATTGACTGTTTTGG 58.616 45.455 0.00 0.00 0.00 3.28
5333 6838 4.941263 TGGTGTGAGTACTTAATGCCATTC 59.059 41.667 0.00 0.00 0.00 2.67
5348 6853 3.511146 TGCCATTCCCAACTTTTCATCTC 59.489 43.478 0.00 0.00 0.00 2.75
5369 6874 3.996363 TCATGTGTCTCTTGTTCCAATCG 59.004 43.478 0.00 0.00 0.00 3.34
5371 6876 3.390135 TGTGTCTCTTGTTCCAATCGTC 58.610 45.455 0.00 0.00 0.00 4.20
5426 6931 5.202004 ACCACTAGAGATATGACGGTCTTT 58.798 41.667 9.88 0.00 0.00 2.52
5428 6933 5.508153 CCACTAGAGATATGACGGTCTTTGG 60.508 48.000 9.88 1.79 0.00 3.28
5429 6934 5.067936 CACTAGAGATATGACGGTCTTTGGT 59.932 44.000 9.88 0.00 0.00 3.67
5430 6935 6.262496 CACTAGAGATATGACGGTCTTTGGTA 59.738 42.308 9.88 0.00 0.00 3.25
5432 6937 6.732896 AGAGATATGACGGTCTTTGGTATT 57.267 37.500 9.88 0.00 0.00 1.89
5433 6938 7.834881 AGAGATATGACGGTCTTTGGTATTA 57.165 36.000 9.88 0.00 0.00 0.98
5434 6939 8.246430 AGAGATATGACGGTCTTTGGTATTAA 57.754 34.615 9.88 0.00 0.00 1.40
5435 6940 8.142551 AGAGATATGACGGTCTTTGGTATTAAC 58.857 37.037 9.88 0.00 0.00 2.01
5436 6941 8.019656 AGATATGACGGTCTTTGGTATTAACT 57.980 34.615 9.88 0.00 0.00 2.24
5437 6942 9.139734 AGATATGACGGTCTTTGGTATTAACTA 57.860 33.333 9.88 0.00 0.00 2.24
5438 6943 9.189723 GATATGACGGTCTTTGGTATTAACTAC 57.810 37.037 9.88 0.00 0.00 2.73
5439 6944 6.594788 TGACGGTCTTTGGTATTAACTACT 57.405 37.500 9.88 0.00 0.00 2.57
5440 6945 6.624423 TGACGGTCTTTGGTATTAACTACTC 58.376 40.000 9.88 0.00 0.00 2.59
5441 6946 5.970592 ACGGTCTTTGGTATTAACTACTCC 58.029 41.667 0.00 0.00 0.00 3.85
5444 6949 6.580788 GGTCTTTGGTATTAACTACTCCCTC 58.419 44.000 0.00 0.00 0.00 4.30
5445 6950 6.407865 GGTCTTTGGTATTAACTACTCCCTCC 60.408 46.154 0.00 0.00 0.00 4.30
5446 6951 5.361857 TCTTTGGTATTAACTACTCCCTCCG 59.638 44.000 0.00 0.00 0.00 4.63
5447 6952 4.255510 TGGTATTAACTACTCCCTCCGT 57.744 45.455 0.00 0.00 0.00 4.69
5448 6953 4.613437 TGGTATTAACTACTCCCTCCGTT 58.387 43.478 0.00 0.00 0.00 4.44
5450 6955 4.038522 GGTATTAACTACTCCCTCCGTTCC 59.961 50.000 0.00 0.00 0.00 3.62
5451 6956 2.905415 TAACTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
5453 6958 3.393426 AACTACTCCCTCCGTTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
5454 6959 3.393426 ACTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
5455 6960 3.924922 ACTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
5456 6961 5.070823 ACTACTCCCTCCGTTCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
5457 6962 5.652324 ACTACTCCCTCCGTTCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
5458 6963 6.797707 ACTACTCCCTCCGTTCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
5459 6964 7.243824 ACTACTCCCTCCGTTCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
5460 6965 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
5461 6966 6.320518 ACTCCCTCCGTTCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
5462 6967 6.785963 ACTCCCTCCGTTCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
5463 6968 7.001099 TCCCTCCGTTCCATAATATAAGAAC 57.999 40.000 5.67 5.67 36.19 3.01
5493 6998 5.565723 ACGCTACACTAGTGTTAAAAACG 57.434 39.130 32.15 24.89 46.59 3.60
5494 6999 5.043248 ACGCTACACTAGTGTTAAAAACGT 58.957 37.500 32.15 25.43 46.59 3.99
5495 7000 5.519927 ACGCTACACTAGTGTTAAAAACGTT 59.480 36.000 32.15 14.17 46.59 3.99
5496 7001 6.060773 CGCTACACTAGTGTTAAAAACGTTC 58.939 40.000 32.15 9.35 41.83 3.95
5497 7002 6.074676 CGCTACACTAGTGTTAAAAACGTTCT 60.075 38.462 32.15 6.43 41.83 3.01
5498 7003 7.515684 CGCTACACTAGTGTTAAAAACGTTCTT 60.516 37.037 32.15 5.99 41.83 2.52
5499 7004 8.755018 GCTACACTAGTGTTAAAAACGTTCTTA 58.245 33.333 32.15 9.27 41.83 2.10
5512 7017 6.535274 AAACGTTCTTATATTATGGGACGC 57.465 37.500 0.00 0.00 0.00 5.19
5513 7018 5.464030 ACGTTCTTATATTATGGGACGCT 57.536 39.130 10.29 0.44 0.00 5.07
5514 7019 5.467705 ACGTTCTTATATTATGGGACGCTC 58.532 41.667 10.29 0.00 0.00 5.03
5515 7020 5.243283 ACGTTCTTATATTATGGGACGCTCT 59.757 40.000 10.29 0.00 0.00 4.09
5516 7021 6.432162 ACGTTCTTATATTATGGGACGCTCTA 59.568 38.462 10.29 0.00 0.00 2.43
5517 7022 7.040201 ACGTTCTTATATTATGGGACGCTCTAA 60.040 37.037 10.29 0.00 0.00 2.10
5518 7023 7.974501 CGTTCTTATATTATGGGACGCTCTAAT 59.025 37.037 0.00 0.00 0.00 1.73
6275 7780 8.517056 TCTTATTGCCAATATGCAGATTGTATG 58.483 33.333 27.33 16.16 43.21 2.39
6360 7867 0.387878 CGATCAGCGTAGGAGCATCC 60.388 60.000 0.00 0.00 46.31 3.51
6370 7877 2.352422 GAGCATCCACAGCCCACA 59.648 61.111 0.00 0.00 0.00 4.17
6371 7878 1.303561 GAGCATCCACAGCCCACAA 60.304 57.895 0.00 0.00 0.00 3.33
6372 7879 1.589716 GAGCATCCACAGCCCACAAC 61.590 60.000 0.00 0.00 0.00 3.32
6373 7880 2.639327 GCATCCACAGCCCACAACC 61.639 63.158 0.00 0.00 0.00 3.77
6374 7881 2.034066 ATCCACAGCCCACAACCG 59.966 61.111 0.00 0.00 0.00 4.44
6375 7882 4.947147 TCCACAGCCCACAACCGC 62.947 66.667 0.00 0.00 0.00 5.68
6377 7884 3.215568 CACAGCCCACAACCGCAA 61.216 61.111 0.00 0.00 0.00 4.85
6378 7885 2.906897 ACAGCCCACAACCGCAAG 60.907 61.111 0.00 0.00 0.00 4.01
6379 7886 2.906897 CAGCCCACAACCGCAAGT 60.907 61.111 0.00 0.00 0.00 3.16
6380 7887 2.906897 AGCCCACAACCGCAAGTG 60.907 61.111 0.00 0.00 35.56 3.16
6381 7888 3.216292 GCCCACAACCGCAAGTGT 61.216 61.111 0.00 0.00 33.99 3.55
6382 7889 2.781158 GCCCACAACCGCAAGTGTT 61.781 57.895 0.00 0.00 33.99 3.32
6383 7890 1.358759 CCCACAACCGCAAGTGTTC 59.641 57.895 0.00 0.00 33.99 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.694072 TGTGTGTTTTCTCACCAGAAAGG 59.306 43.478 0.00 0.00 46.99 3.11
7 8 4.155826 TGTGTGTGTTTTCTCACCAGAAAG 59.844 41.667 0.00 0.00 46.99 2.62
8 9 4.075682 TGTGTGTGTTTTCTCACCAGAAA 58.924 39.130 0.00 0.00 45.30 2.52
9 10 3.438781 GTGTGTGTGTTTTCTCACCAGAA 59.561 43.478 0.00 0.00 41.76 3.02
10 11 3.006940 GTGTGTGTGTTTTCTCACCAGA 58.993 45.455 0.00 0.00 41.76 3.86
11 12 2.746904 TGTGTGTGTGTTTTCTCACCAG 59.253 45.455 0.00 0.00 41.76 4.00
12 13 2.486203 GTGTGTGTGTGTTTTCTCACCA 59.514 45.455 0.00 0.00 41.76 4.17
13 14 2.486203 TGTGTGTGTGTGTTTTCTCACC 59.514 45.455 0.00 0.00 41.76 4.02
14 15 3.058570 TGTGTGTGTGTGTGTTTTCTCAC 60.059 43.478 0.00 0.00 42.47 3.51
15 16 3.058570 GTGTGTGTGTGTGTGTTTTCTCA 60.059 43.478 0.00 0.00 0.00 3.27
16 17 3.058570 TGTGTGTGTGTGTGTGTTTTCTC 60.059 43.478 0.00 0.00 0.00 2.87
17 18 2.881513 TGTGTGTGTGTGTGTGTTTTCT 59.118 40.909 0.00 0.00 0.00 2.52
18 19 2.977169 GTGTGTGTGTGTGTGTGTTTTC 59.023 45.455 0.00 0.00 0.00 2.29
19 20 2.359214 TGTGTGTGTGTGTGTGTGTTTT 59.641 40.909 0.00 0.00 0.00 2.43
20 21 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
21 22 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
22 23 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
23 24 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
24 25 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
25 26 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
26 27 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
27 28 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
28 29 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
29 30 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
30 31 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
31 32 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
32 33 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
33 34 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
34 35 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
35 36 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
36 37 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
37 38 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
38 39 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
39 40 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
40 41 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
41 42 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
42 43 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
43 44 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
44 45 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
45 46 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
46 47 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
47 48 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
48 49 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
49 50 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
50 51 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
51 52 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
52 53 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
53 54 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
54 55 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
55 56 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
56 57 1.669437 TGCGTGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
57 58 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
58 59 2.735677 CGTGCGTGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
59 60 2.021243 CGTGCGTGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
60 61 3.860125 GCGTGCGTGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
61 62 3.858989 TGCGTGCGTGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
62 63 3.860125 GTGCGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
63 64 3.858989 TGTGCGTGCGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
64 65 3.860125 GTGTGCGTGCGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
65 66 3.858989 TGTGTGCGTGCGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
66 67 3.860125 GTGTGTGCGTGCGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
67 68 3.858989 TGTGTGTGCGTGCGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
68 69 3.860125 GTGTGTGTGCGTGCGTGT 61.860 61.111 0.00 0.00 0.00 4.49
69 70 3.858989 TGTGTGTGTGCGTGCGTG 61.859 61.111 0.00 0.00 0.00 5.34
70 71 3.860125 GTGTGTGTGTGCGTGCGT 61.860 61.111 0.00 0.00 0.00 5.24
71 72 3.858989 TGTGTGTGTGTGCGTGCG 61.859 61.111 0.00 0.00 0.00 5.34
72 73 2.277247 GTGTGTGTGTGTGCGTGC 60.277 61.111 0.00 0.00 0.00 5.34
73 74 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
74 75 1.669437 TGTGTGTGTGTGTGTGCGT 60.669 52.632 0.00 0.00 0.00 5.24
75 76 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
76 77 1.225991 CGTGTGTGTGTGTGTGTGC 60.226 57.895 0.00 0.00 0.00 4.57
90 91 0.749818 TGGAAACCATGTGTGCGTGT 60.750 50.000 0.00 0.00 0.00 4.49
213 214 0.370273 GTCATGAATCGCACGGTGTC 59.630 55.000 10.24 0.00 0.00 3.67
223 224 3.181516 GCTTGAGTTGACGGTCATGAATC 60.182 47.826 12.26 7.45 0.00 2.52
320 321 2.613506 GGGGGAAAAGTCGTGTGCG 61.614 63.158 0.00 0.00 39.92 5.34
365 366 5.248934 TCTCCTTTTCCGTTACATTCCCTTA 59.751 40.000 0.00 0.00 0.00 2.69
830 848 5.452216 GGTTTAACAAAACCCTGGAACGAAT 60.452 40.000 8.54 0.00 44.94 3.34
857 882 4.907582 GCGTTTTACGACTGCTGTTAAAAT 59.092 37.500 13.25 0.00 46.05 1.82
873 898 2.169937 ATCGGACGGTGGGCGTTTTA 62.170 55.000 0.00 0.00 0.00 1.52
943 971 2.290641 ACACCGAGAGAAATGTGTTTGC 59.709 45.455 0.00 0.00 38.74 3.68
975 1008 5.248870 AGTGAGAGAAATGCGTTTTTGTT 57.751 34.783 5.17 0.00 0.00 2.83
995 1028 3.164269 CATCCCGGGCTGGCTAGT 61.164 66.667 18.49 0.00 35.87 2.57
996 1029 4.632974 GCATCCCGGGCTGGCTAG 62.633 72.222 25.20 6.38 35.87 3.42
1029 1065 4.241555 ATGATCCGGCCCAGACGC 62.242 66.667 0.00 0.00 29.68 5.19
1151 1191 3.373110 GGATAAGCAAAGGGAGGTGGAAT 60.373 47.826 0.00 0.00 0.00 3.01
1179 1219 0.177836 CATCAGTGTGGTGCCGGATA 59.822 55.000 5.05 0.00 0.00 2.59
1206 1254 0.872021 GCGTTGGTGGATCTAGAGCG 60.872 60.000 1.16 0.00 0.00 5.03
1211 1259 1.220749 GCTGGCGTTGGTGGATCTA 59.779 57.895 0.00 0.00 0.00 1.98
1270 1325 2.289532 GGAGGAGGCTGTGCTCACT 61.290 63.158 0.00 0.00 45.40 3.41
1323 1384 8.776376 ATCTAATGTTTATTGCCAACCAAAAG 57.224 30.769 0.00 0.00 36.92 2.27
1491 1597 5.449451 GGAAACCAACGTAACAGTTCAATGT 60.449 40.000 0.00 0.00 33.96 2.71
1514 1620 2.420129 CCCGGTTCCATTACTGAGAAGG 60.420 54.545 0.00 0.00 0.00 3.46
1581 1690 7.719778 AAAGAATTGAGCATGAAAGGTTTTC 57.280 32.000 0.00 0.00 0.00 2.29
1883 2080 7.593273 CCAGTAGCTTATCTTACATTCTCGAAG 59.407 40.741 0.00 0.00 0.00 3.79
1933 2133 1.493950 CTCCGCCATTCGACTGATGC 61.494 60.000 4.04 0.00 41.67 3.91
1981 2181 2.992476 CACTGTAGTAGGGCTGGGT 58.008 57.895 0.00 0.00 0.00 4.51
1991 2191 1.372997 CGCCTTCGTGCACTGTAGT 60.373 57.895 16.19 0.00 0.00 2.73
2200 2401 2.607282 CGCTCAAAAGTCTGTACGACCT 60.607 50.000 12.27 0.17 43.91 3.85
2204 2405 2.662700 ACTCGCTCAAAAGTCTGTACG 58.337 47.619 0.00 0.00 0.00 3.67
2210 2411 5.273944 ACAAATTGAACTCGCTCAAAAGTC 58.726 37.500 0.00 0.00 38.75 3.01
2477 2679 4.583073 GTGAAGACAACTTTGTACCCCATT 59.417 41.667 0.00 0.00 42.43 3.16
2603 2805 5.023533 AGACAGTGTTCTCTTTGCTTGTA 57.976 39.130 0.00 0.00 0.00 2.41
2871 3084 6.653320 TGTTCCACCTTAGAACATACATGAAC 59.347 38.462 0.00 0.00 46.50 3.18
2873 3086 6.367374 TGTTCCACCTTAGAACATACATGA 57.633 37.500 0.00 0.00 46.50 3.07
2931 3146 4.932200 CAGACCAGAAAGGATGACAGTTAC 59.068 45.833 0.00 0.00 41.22 2.50
2933 3148 3.648067 TCAGACCAGAAAGGATGACAGTT 59.352 43.478 0.00 0.00 41.22 3.16
3056 3271 7.967908 ACTGAGGGAACATAATCCACTATAAG 58.032 38.462 0.00 0.00 41.55 1.73
3146 3362 3.197549 ACTTCTCCCTCATCTCTTCAAGC 59.802 47.826 0.00 0.00 0.00 4.01
3239 3455 6.645415 GGTACCTGTTCAGAAATATATGACCG 59.355 42.308 4.06 0.00 0.00 4.79
3306 3595 9.200817 ACAGAAAAAGGCACATATATAACCAAT 57.799 29.630 0.00 0.00 0.00 3.16
3440 3729 8.193953 AGAATTCAATGGACAGTTTGGTAAAT 57.806 30.769 8.44 0.00 0.00 1.40
3496 3831 8.668353 CAATTTTAGCTACTCTGTGAATAGCAA 58.332 33.333 10.03 1.52 43.13 3.91
3498 3833 8.202745 ACAATTTTAGCTACTCTGTGAATAGC 57.797 34.615 0.00 0.47 41.39 2.97
3500 3835 9.502091 ACAACAATTTTAGCTACTCTGTGAATA 57.498 29.630 0.00 0.00 0.00 1.75
3504 3839 8.311650 AGTACAACAATTTTAGCTACTCTGTG 57.688 34.615 0.00 0.00 0.00 3.66
3528 3863 6.423302 AGCGCTAATCATTTCAGACATTCTAG 59.577 38.462 8.99 0.00 0.00 2.43
3530 3865 5.121811 AGCGCTAATCATTTCAGACATTCT 58.878 37.500 8.99 0.00 0.00 2.40
3537 3872 3.726607 AGGAGAGCGCTAATCATTTCAG 58.273 45.455 11.50 0.00 0.00 3.02
3616 3960 7.118723 AGGCTCACAGGAACAATTCAATAATA 58.881 34.615 0.00 0.00 0.00 0.98
3647 3994 3.574284 TTGTACATGCATGTTGGAAGC 57.426 42.857 35.45 18.65 41.97 3.86
3683 4030 6.945435 AGAAATACACCCACAACATCATTACA 59.055 34.615 0.00 0.00 0.00 2.41
3684 4031 7.391148 AGAAATACACCCACAACATCATTAC 57.609 36.000 0.00 0.00 0.00 1.89
3687 4034 5.774690 ACAAGAAATACACCCACAACATCAT 59.225 36.000 0.00 0.00 0.00 2.45
3755 4104 5.524511 AAAAACGAAACCAAAAGCACTTC 57.475 34.783 0.00 0.00 0.00 3.01
3803 4166 3.519913 ACTCATCCACCTTCTAGTTTCCC 59.480 47.826 0.00 0.00 0.00 3.97
3822 4186 7.855904 CACAACTGTCATAAACAAGGTTAACTC 59.144 37.037 5.42 0.00 37.45 3.01
3883 4247 8.459911 AACTACAGTAGCAAAGGTTACATTTT 57.540 30.769 7.57 0.00 33.58 1.82
3887 4251 5.224888 CGAACTACAGTAGCAAAGGTTACA 58.775 41.667 7.57 0.00 33.58 2.41
3888 4252 4.091075 GCGAACTACAGTAGCAAAGGTTAC 59.909 45.833 7.57 0.00 33.80 2.50
4018 4383 4.431416 TGGCTCTCCACAAAAGAAACTA 57.569 40.909 0.00 0.00 37.47 2.24
4031 4398 7.040823 CCAACTAGATGAAATTTATGGCTCTCC 60.041 40.741 0.79 0.00 0.00 3.71
4049 4416 4.713553 TGTCTGCAAATTGTCCAACTAGA 58.286 39.130 0.00 0.00 0.00 2.43
4415 5887 3.093814 TGTTCTGCCTTATACTCACCGA 58.906 45.455 0.00 0.00 0.00 4.69
4468 5945 7.175990 ACCTATCTTCAGCTATAACTACTCTGC 59.824 40.741 0.00 0.00 0.00 4.26
4508 5989 0.625316 ATATGCAAGGACAGGTGGCA 59.375 50.000 0.00 0.00 39.03 4.92
4620 6102 5.365895 AGTGTCTCAACCCTAGTACAACTTT 59.634 40.000 0.00 0.00 0.00 2.66
4632 6114 5.350640 CGTCCTAAAATAAGTGTCTCAACCC 59.649 44.000 0.00 0.00 0.00 4.11
4662 6144 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
4788 6276 1.003652 GTTTGCATGCAAAACTGTGGC 60.004 47.619 39.49 24.69 45.86 5.01
4854 6347 0.325933 CCCAAGCTCCACATGTGAGA 59.674 55.000 27.46 19.63 0.00 3.27
5226 6728 2.552315 TCATTCGCCAAAGACTTGTTCC 59.448 45.455 0.00 0.00 0.00 3.62
5272 6774 5.998981 ACACGATTGTTTCCAGTATTTGGTA 59.001 36.000 0.00 0.00 39.62 3.25
5290 6795 6.072175 ACACCATTAACTTTATGCAACACGAT 60.072 34.615 0.00 0.00 0.00 3.73
5333 6838 4.763793 AGACACATGAGATGAAAAGTTGGG 59.236 41.667 0.00 0.00 0.00 4.12
5369 6874 0.108424 AGAAGCAGCTGATGTCCGAC 60.108 55.000 20.43 0.00 0.00 4.79
5371 6876 0.725686 CAAGAAGCAGCTGATGTCCG 59.274 55.000 20.43 0.00 0.00 4.79
5426 6931 4.255510 ACGGAGGGAGTAGTTAATACCA 57.744 45.455 0.00 0.00 34.67 3.25
5428 6933 4.646492 TGGAACGGAGGGAGTAGTTAATAC 59.354 45.833 0.00 0.00 34.30 1.89
5429 6934 4.870636 TGGAACGGAGGGAGTAGTTAATA 58.129 43.478 0.00 0.00 0.00 0.98
5430 6935 3.716431 TGGAACGGAGGGAGTAGTTAAT 58.284 45.455 0.00 0.00 0.00 1.40
5432 6937 2.905415 TGGAACGGAGGGAGTAGTTA 57.095 50.000 0.00 0.00 0.00 2.24
5433 6938 2.249309 ATGGAACGGAGGGAGTAGTT 57.751 50.000 0.00 0.00 0.00 2.24
5434 6939 3.393426 TTATGGAACGGAGGGAGTAGT 57.607 47.619 0.00 0.00 0.00 2.73
5435 6940 7.614583 TCTTATATTATGGAACGGAGGGAGTAG 59.385 40.741 0.00 0.00 0.00 2.57
5436 6941 7.472741 TCTTATATTATGGAACGGAGGGAGTA 58.527 38.462 0.00 0.00 0.00 2.59
5437 6942 6.320518 TCTTATATTATGGAACGGAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
5438 6943 6.852420 TCTTATATTATGGAACGGAGGGAG 57.148 41.667 0.00 0.00 0.00 4.30
5439 6944 7.001099 GTTCTTATATTATGGAACGGAGGGA 57.999 40.000 7.88 0.00 0.00 4.20
5467 6972 8.055402 CGTTTTTAACACTAGTGTAGCGTTAAA 58.945 33.333 28.13 22.71 44.73 1.52
5468 6973 7.221838 ACGTTTTTAACACTAGTGTAGCGTTAA 59.778 33.333 28.13 18.68 44.13 2.01
5469 6974 6.695278 ACGTTTTTAACACTAGTGTAGCGTTA 59.305 34.615 28.13 13.92 44.13 3.18
5470 6975 5.519927 ACGTTTTTAACACTAGTGTAGCGTT 59.480 36.000 28.13 14.95 44.13 4.84
5471 6976 5.043248 ACGTTTTTAACACTAGTGTAGCGT 58.957 37.500 28.13 25.69 44.13 5.07
5472 6977 5.565723 ACGTTTTTAACACTAGTGTAGCG 57.434 39.130 28.13 25.09 44.13 4.26
5473 6978 7.170240 AGAACGTTTTTAACACTAGTGTAGC 57.830 36.000 28.13 13.70 44.13 3.58
5486 6991 8.550376 GCGTCCCATAATATAAGAACGTTTTTA 58.450 33.333 13.02 13.02 0.00 1.52
5487 6992 7.281549 AGCGTCCCATAATATAAGAACGTTTTT 59.718 33.333 9.22 9.22 0.00 1.94
5488 6993 6.764560 AGCGTCCCATAATATAAGAACGTTTT 59.235 34.615 0.46 0.00 0.00 2.43
5489 6994 6.285990 AGCGTCCCATAATATAAGAACGTTT 58.714 36.000 0.46 0.00 0.00 3.60
5490 6995 5.850614 AGCGTCCCATAATATAAGAACGTT 58.149 37.500 0.00 0.00 0.00 3.99
5491 6996 5.243283 AGAGCGTCCCATAATATAAGAACGT 59.757 40.000 0.00 0.00 0.00 3.99
5492 6997 5.710984 AGAGCGTCCCATAATATAAGAACG 58.289 41.667 0.00 0.00 0.00 3.95
6239 7744 7.707893 GCATATTGGCAATAAGAGAAACAACAT 59.292 33.333 22.65 1.02 0.00 2.71
6240 7745 7.035004 GCATATTGGCAATAAGAGAAACAACA 58.965 34.615 22.65 0.00 0.00 3.33
6241 7746 7.035004 TGCATATTGGCAATAAGAGAAACAAC 58.965 34.615 22.65 5.08 41.65 3.32
6242 7747 7.122501 TCTGCATATTGGCAATAAGAGAAACAA 59.877 33.333 22.65 0.00 44.40 2.83
6243 7748 6.602803 TCTGCATATTGGCAATAAGAGAAACA 59.397 34.615 22.65 10.71 44.40 2.83
6244 7749 7.031226 TCTGCATATTGGCAATAAGAGAAAC 57.969 36.000 22.65 6.98 44.40 2.78
6245 7750 7.828508 ATCTGCATATTGGCAATAAGAGAAA 57.171 32.000 22.65 8.60 44.40 2.52
6246 7751 7.286087 ACAATCTGCATATTGGCAATAAGAGAA 59.714 33.333 22.65 10.31 44.40 2.87
6247 7752 6.774170 ACAATCTGCATATTGGCAATAAGAGA 59.226 34.615 22.65 20.96 44.40 3.10
6248 7753 6.978338 ACAATCTGCATATTGGCAATAAGAG 58.022 36.000 22.65 17.20 44.40 2.85
6249 7754 6.964807 ACAATCTGCATATTGGCAATAAGA 57.035 33.333 22.65 19.90 44.40 2.10
6250 7755 7.274904 GCATACAATCTGCATATTGGCAATAAG 59.725 37.037 22.65 19.17 44.40 1.73
6251 7756 7.039574 AGCATACAATCTGCATATTGGCAATAA 60.040 33.333 22.65 7.47 44.40 1.40
6252 7757 6.434965 AGCATACAATCTGCATATTGGCAATA 59.565 34.615 23.84 21.28 44.40 1.90
6253 7758 5.245301 AGCATACAATCTGCATATTGGCAAT 59.755 36.000 23.84 18.01 44.40 3.56
6254 7759 4.585581 AGCATACAATCTGCATATTGGCAA 59.414 37.500 23.84 0.68 44.40 4.52
6255 7760 4.146564 AGCATACAATCTGCATATTGGCA 58.853 39.130 23.84 14.15 42.15 4.92
6256 7761 4.778534 AGCATACAATCTGCATATTGGC 57.221 40.909 23.84 18.24 42.15 4.52
6257 7762 8.683550 CAATAAGCATACAATCTGCATATTGG 57.316 34.615 23.84 11.02 46.80 3.16
6259 7764 9.903682 GAACAATAAGCATACAATCTGCATATT 57.096 29.630 0.00 0.00 41.55 1.28
6262 7767 7.067859 ACTGAACAATAAGCATACAATCTGCAT 59.932 33.333 0.00 0.00 42.15 3.96
6275 7780 4.391830 TCCGTCAATGACTGAACAATAAGC 59.608 41.667 11.92 0.00 35.22 3.09
6360 7867 3.198236 CTTGCGGTTGTGGGCTGTG 62.198 63.158 0.00 0.00 0.00 3.66
6361 7868 2.906897 CTTGCGGTTGTGGGCTGT 60.907 61.111 0.00 0.00 0.00 4.40
6362 7869 2.906897 ACTTGCGGTTGTGGGCTG 60.907 61.111 0.00 0.00 0.00 4.85
6363 7870 2.906897 CACTTGCGGTTGTGGGCT 60.907 61.111 0.00 0.00 0.00 5.19
6364 7871 2.677573 GAACACTTGCGGTTGTGGGC 62.678 60.000 0.00 0.00 38.39 5.36
6365 7872 1.358759 GAACACTTGCGGTTGTGGG 59.641 57.895 0.00 0.00 38.39 4.61


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

AutoCloner maintained by Alex Coulton.