Multiple sequence alignment - TraesCS4A01G478700

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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 TraesCS4A01G478700 chr4A 100.000 5139 0 0 1 5139 735758182 735763320 0.000000e+00 9491.0
1 TraesCS4A01G478700 chr4A 95.562 3808 134 14 701 4478 734576244 734580046 0.000000e+00 6063.0
2 TraesCS4A01G478700 chr4A 95.498 3687 125 10 1 3652 736867539 736871219 0.000000e+00 5851.0
3 TraesCS4A01G478700 chr4A 85.888 3040 372 24 805 3796 736140448 736143478 0.000000e+00 3184.0
4 TraesCS4A01G478700 chr4A 92.390 1958 122 10 1789 3719 736038949 736040906 0.000000e+00 2765.0
5 TraesCS4A01G478700 chr4A 84.537 2852 358 43 982 3776 736802944 736805769 0.000000e+00 2747.0
6 TraesCS4A01G478700 chr4A 85.810 1635 193 19 2158 3776 736458474 736456863 0.000000e+00 1698.0
7 TraesCS4A01G478700 chr4A 92.715 1153 67 12 1836 2978 735536076 735534931 0.000000e+00 1648.0
8 TraesCS4A01G478700 chr4A 84.713 1413 169 19 1980 3351 736790563 736791969 0.000000e+00 1369.0
9 TraesCS4A01G478700 chr4A 95.075 731 36 0 3072 3802 735520573 735519843 0.000000e+00 1151.0
10 TraesCS4A01G478700 chr4A 96.364 550 12 2 161 702 734575591 734576140 0.000000e+00 898.0
11 TraesCS4A01G478700 chr4A 84.957 811 116 5 2232 3039 736791985 736792792 0.000000e+00 817.0
12 TraesCS4A01G478700 chr4A 92.857 490 32 3 3991 4478 736049490 736049978 0.000000e+00 708.0
13 TraesCS4A01G478700 chr4A 85.157 667 85 8 3819 4472 736143447 736144112 0.000000e+00 671.0
14 TraesCS4A01G478700 chr4A 94.390 410 22 1 3804 4212 735505598 735505189 3.380000e-176 628.0
15 TraesCS4A01G478700 chr4A 92.574 404 15 5 545 933 736882227 736882630 2.690000e-157 566.0
16 TraesCS4A01G478700 chr4A 83.956 455 70 3 982 1434 736460082 736459629 2.840000e-117 433.0
17 TraesCS4A01G478700 chr4A 92.953 298 8 4 3713 3998 736046634 736046930 6.150000e-114 422.0
18 TraesCS4A01G478700 chr4A 90.459 283 21 4 4204 4481 735491010 735490729 8.130000e-98 368.0
19 TraesCS4A01G478700 chr4A 79.620 368 50 17 22 378 736770360 736770713 1.850000e-59 241.0
20 TraesCS4A01G478700 chr4A 95.200 125 6 0 1 125 734575469 734575593 1.130000e-46 198.0
21 TraesCS4A01G478700 chr4A 94.286 105 4 1 1 105 735548974 735548872 5.330000e-35 159.0
22 TraesCS4A01G478700 chr4A 93.458 107 3 2 4898 5000 736145240 736145346 6.890000e-34 156.0
23 TraesCS4A01G478700 chr4A 96.296 81 3 0 4899 4979 736051057 736051137 3.230000e-27 134.0
24 TraesCS4A01G478700 chr4A 77.612 201 25 12 13 205 736769960 736770148 2.530000e-18 104.0
25 TraesCS4A01G478700 chr7D 86.676 3430 389 29 694 4070 5657398 5653984 0.000000e+00 3740.0
26 TraesCS4A01G478700 chr7D 87.552 2860 306 12 982 3801 575928496 575925647 0.000000e+00 3264.0
27 TraesCS4A01G478700 chr7D 85.143 700 58 18 1 669 5658150 5657466 0.000000e+00 675.0
28 TraesCS4A01G478700 chr7D 87.572 523 55 5 3819 4331 575925683 575925161 9.520000e-167 597.0
29 TraesCS4A01G478700 chr7D 89.021 419 21 7 4064 4481 5652760 5652366 3.570000e-136 496.0
30 TraesCS4A01G478700 chr7D 92.045 176 14 0 4306 4481 5435169 5434994 1.100000e-61 248.0
31 TraesCS4A01G478700 chr7D 94.643 112 6 0 3900 4011 5435293 5435182 1.900000e-39 174.0
32 TraesCS4A01G478700 chr7D 84.699 183 6 11 4894 5076 5651307 5651147 4.120000e-36 163.0
33 TraesCS4A01G478700 chr7D 93.590 78 3 2 4913 4989 5432128 5432052 1.170000e-21 115.0
34 TraesCS4A01G478700 chr7D 94.545 55 3 0 3819 3873 5654289 5654235 9.170000e-13 86.1
35 TraesCS4A01G478700 chr7A 86.143 2865 310 36 982 3801 666797900 666795078 0.000000e+00 3011.0
36 TraesCS4A01G478700 chr7A 86.742 528 58 7 3819 4335 666795114 666794588 1.240000e-160 577.0
37 TraesCS4A01G478700 chr2A 82.960 2547 361 31 1218 3718 762309404 762311923 0.000000e+00 2231.0
38 TraesCS4A01G478700 chr2D 82.619 2543 391 23 1218 3718 637640550 637638017 0.000000e+00 2200.0
39 TraesCS4A01G478700 chr2D 81.420 479 84 4 3875 4349 637637916 637637439 2.240000e-103 387.0
40 TraesCS4A01G478700 chr5B 83.732 1297 184 12 882 2159 98510835 98512123 0.000000e+00 1201.0
41 TraesCS4A01G478700 chr2B 81.046 459 82 4 3861 4315 795052072 795051615 1.360000e-95 361.0


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 TraesCS4A01G478700 chr4A 735758182 735763320 5138 False 9491.000000 9491 100.000000 1 5139 1 chr4A.!!$F1 5138
1 TraesCS4A01G478700 chr4A 736867539 736871219 3680 False 5851.000000 5851 95.498000 1 3652 1 chr4A.!!$F4 3651
2 TraesCS4A01G478700 chr4A 736038949 736040906 1957 False 2765.000000 2765 92.390000 1789 3719 1 chr4A.!!$F2 1930
3 TraesCS4A01G478700 chr4A 736802944 736805769 2825 False 2747.000000 2747 84.537000 982 3776 1 chr4A.!!$F3 2794
4 TraesCS4A01G478700 chr4A 734575469 734580046 4577 False 2386.333333 6063 95.708667 1 4478 3 chr4A.!!$F6 4477
5 TraesCS4A01G478700 chr4A 735534931 735536076 1145 True 1648.000000 1648 92.715000 1836 2978 1 chr4A.!!$R4 1142
6 TraesCS4A01G478700 chr4A 736140448 736145346 4898 False 1337.000000 3184 88.167667 805 5000 3 chr4A.!!$F8 4195
7 TraesCS4A01G478700 chr4A 735519843 735520573 730 True 1151.000000 1151 95.075000 3072 3802 1 chr4A.!!$R3 730
8 TraesCS4A01G478700 chr4A 736790563 736792792 2229 False 1093.000000 1369 84.835000 1980 3351 2 chr4A.!!$F10 1371
9 TraesCS4A01G478700 chr4A 736456863 736460082 3219 True 1065.500000 1698 84.883000 982 3776 2 chr4A.!!$R6 2794
10 TraesCS4A01G478700 chr4A 736046634 736051137 4503 False 421.333333 708 94.035333 3713 4979 3 chr4A.!!$F7 1266
11 TraesCS4A01G478700 chr7D 575925161 575928496 3335 True 1930.500000 3264 87.562000 982 4331 2 chr7D.!!$R3 3349
12 TraesCS4A01G478700 chr7D 5651147 5658150 7003 True 1032.020000 3740 88.016800 1 5076 5 chr7D.!!$R2 5075
13 TraesCS4A01G478700 chr7A 666794588 666797900 3312 True 1794.000000 3011 86.442500 982 4335 2 chr7A.!!$R1 3353
14 TraesCS4A01G478700 chr2A 762309404 762311923 2519 False 2231.000000 2231 82.960000 1218 3718 1 chr2A.!!$F1 2500
15 TraesCS4A01G478700 chr2D 637637439 637640550 3111 True 1293.500000 2200 82.019500 1218 4349 2 chr2D.!!$R1 3131
16 TraesCS4A01G478700 chr5B 98510835 98512123 1288 False 1201.000000 1201 83.732000 882 2159 1 chr5B.!!$F1 1277

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
195 217 3.520569 ACTTTTTGTGATTGTGCCACAC 58.479 40.909 0.00 0.00 43.37 3.82 F
885 1042 5.631096 GCTCTGCTCCTTTTGTCAAAAATAC 59.369 40.000 11.73 3.39 34.81 1.89 F
1071 1249 0.615331 TTCACACATCCAGCTCCTCC 59.385 55.000 0.00 0.00 0.00 4.30 F
1437 1620 1.295423 GCTTCGTGCCTTGGACCTA 59.705 57.895 0.00 0.00 35.15 3.08 F
1610 2208 1.620524 CCACTTCCATGGCCAAATCCT 60.621 52.381 10.96 0.00 31.52 3.24 F
3351 4016 3.132925 GTGTAGCAGTTTGGACCGTAAA 58.867 45.455 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1249 2.360801 ACTTTGGTTGTTCGTGGATTGG 59.639 45.455 0.00 0.0 0.00 3.16 R
2509 3147 1.284198 AGCATTGCTGGAGAGGTTGAT 59.716 47.619 11.09 0.0 37.57 2.57 R
2830 3468 3.822735 CGGAAGATCCATGTATTTGGCAT 59.177 43.478 0.00 0.0 35.91 4.40 R
3352 4017 3.890756 ACAAATGCCTTGAACTCATCACA 59.109 39.130 2.85 0.0 37.92 3.58 R
3558 4484 5.236047 GTCATCATCTAGAAGGATGTTGCAC 59.764 44.000 25.20 17.3 42.45 4.57 R
4371 9147 0.038744 AGGCTTCCCAGACCACAATG 59.961 55.000 0.00 0.0 0.00 2.82 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
195 217 3.520569 ACTTTTTGTGATTGTGCCACAC 58.479 40.909 0.00 0.00 43.37 3.82
277 299 7.382218 CCTGTAAAGTCATTGGAACATTTCAAC 59.618 37.037 0.00 0.00 39.30 3.18
755 906 5.934402 ATAATATCCGCCCGAGTTATCTT 57.066 39.130 0.00 0.00 0.00 2.40
824 978 5.968528 AATCGTAAATAAGTGGTTGCCAA 57.031 34.783 0.00 0.00 34.18 4.52
885 1042 5.631096 GCTCTGCTCCTTTTGTCAAAAATAC 59.369 40.000 11.73 3.39 34.81 1.89
890 1047 6.640499 TGCTCCTTTTGTCAAAAATACATTCG 59.360 34.615 11.73 0.00 34.81 3.34
893 1050 9.672086 CTCCTTTTGTCAAAAATACATTCGTTA 57.328 29.630 11.73 0.00 34.81 3.18
899 1056 8.039603 TGTCAAAAATACATTCGTTAGCAGAT 57.960 30.769 0.00 0.00 0.00 2.90
1071 1249 0.615331 TTCACACATCCAGCTCCTCC 59.385 55.000 0.00 0.00 0.00 4.30
1291 1472 1.737838 CCATGTCACTGCCATACGTT 58.262 50.000 0.00 0.00 0.00 3.99
1437 1620 1.295423 GCTTCGTGCCTTGGACCTA 59.705 57.895 0.00 0.00 35.15 3.08
1610 2208 1.620524 CCACTTCCATGGCCAAATCCT 60.621 52.381 10.96 0.00 31.52 3.24
2349 2980 5.769662 TCCACAATCATTAGGCAATATCACC 59.230 40.000 0.00 0.00 0.00 4.02
2356 2987 6.135454 TCATTAGGCAATATCACCCAATTGT 58.865 36.000 4.43 0.00 35.86 2.71
2428 3059 6.585416 AGCATTGGAAATCTCACAAAACTTT 58.415 32.000 0.00 0.00 0.00 2.66
2458 3089 3.877508 GGATCTTTCCGGTAACTCATTGG 59.122 47.826 0.00 0.00 30.72 3.16
2488 3126 6.098982 GGGGATCCCATATGAGATAGTTAGTG 59.901 46.154 32.07 0.00 44.65 2.74
2509 3147 6.550163 AGTGTTACCTCTCTGACCTTACTTA 58.450 40.000 0.00 0.00 0.00 2.24
2581 3219 4.434713 AAGTTGAACAACCTTGTCACAC 57.565 40.909 13.07 0.00 41.31 3.82
3080 3736 6.707161 CCAAACATTGTTGATCAAGAAACCAT 59.293 34.615 20.49 2.97 39.55 3.55
3351 4016 3.132925 GTGTAGCAGTTTGGACCGTAAA 58.867 45.455 0.00 0.00 0.00 2.01
3352 4017 3.749609 GTGTAGCAGTTTGGACCGTAAAT 59.250 43.478 0.00 0.00 0.00 1.40
3370 4264 5.163723 CGTAAATGTGATGAGTTCAAGGCAT 60.164 40.000 0.00 0.00 35.70 4.40
3529 4455 8.900781 CAGAATATCTTCACCATCAAATTGAGT 58.099 33.333 1.10 0.00 33.56 3.41
3558 4484 6.018751 CCATAGTTCACTGTGATATCAAACCG 60.019 42.308 11.86 0.00 37.28 4.44
3652 4578 0.973632 AGAATGTGAGCACGGTGGTA 59.026 50.000 13.47 0.00 0.00 3.25
3653 4579 1.555075 AGAATGTGAGCACGGTGGTAT 59.445 47.619 13.47 0.29 0.00 2.73
3702 4628 5.968528 TTAAAGGCACAATTGGATACGTT 57.031 34.783 10.83 4.58 42.51 3.99
3936 4907 4.655963 ACATGTTTGTCAGAGTATGGCTT 58.344 39.130 0.00 0.00 33.40 4.35
4062 8829 7.557358 TGTGATAAGCCTTGTCAAATATGTCAT 59.443 33.333 5.40 0.00 32.44 3.06
4142 8911 3.629058 ACACGCAGCGTATTGTAGATAG 58.371 45.455 22.49 6.58 38.32 2.08
4168 8937 7.389607 GGTTCTTGTATCCTGTGTTTAAGCTTA 59.610 37.037 0.86 0.86 0.00 3.09
4291 9065 3.640498 TGTCCATGAATTTTGAGCAACCA 59.360 39.130 0.00 0.00 0.00 3.67
4301 9077 3.737559 TTGAGCAACCACCTAATCCAT 57.262 42.857 0.00 0.00 0.00 3.41
4359 9135 0.808755 CGGTTGCCAGTTGTTATCCC 59.191 55.000 0.00 0.00 0.00 3.85
4362 9138 1.883926 GTTGCCAGTTGTTATCCCGTT 59.116 47.619 0.00 0.00 0.00 4.44
4367 9143 2.159382 CAGTTGTTATCCCGTTGCCTT 58.841 47.619 0.00 0.00 0.00 4.35
4371 9147 2.156098 TGTTATCCCGTTGCCTTTGAC 58.844 47.619 0.00 0.00 0.00 3.18
4398 9195 0.823356 TCTGGGAAGCCTGTTTGTGC 60.823 55.000 0.00 0.00 0.00 4.57
4411 9208 1.000843 GTTTGTGCCTTTGGGGTGATC 59.999 52.381 0.00 0.00 37.43 2.92
4427 9224 3.760684 GGTGATCCTGAAGTCAGCATTTT 59.239 43.478 2.59 0.00 42.47 1.82
4478 9275 8.500753 TGTCCAGTATACATGTATTTGTTTCC 57.499 34.615 22.90 7.62 0.00 3.13
4481 9278 9.693739 TCCAGTATACATGTATTTGTTTCCATT 57.306 29.630 22.90 0.00 0.00 3.16
4482 9279 9.950680 CCAGTATACATGTATTTGTTTCCATTC 57.049 33.333 22.90 0.00 0.00 2.67
4515 10204 3.429822 CCATTTGAACCATCATCACTGCC 60.430 47.826 0.00 0.00 34.96 4.85
4561 10250 1.805428 GACCCAACGCCAATGTGCTT 61.805 55.000 0.00 0.00 0.00 3.91
4605 10294 4.733542 CCACCCCGTGCCCGAAAT 62.734 66.667 0.00 0.00 35.63 2.17
4606 10295 3.131478 CACCCCGTGCCCGAAATC 61.131 66.667 0.00 0.00 35.63 2.17
4607 10296 4.770874 ACCCCGTGCCCGAAATCG 62.771 66.667 0.00 0.00 35.63 3.34
4640 10331 3.704061 TCCACCTCGTATCAATCATGTCA 59.296 43.478 0.00 0.00 0.00 3.58
4703 10403 4.511454 CGTTAGAGAGAGAGAGGACATCTG 59.489 50.000 0.00 0.00 38.84 2.90
4705 10405 4.860802 AGAGAGAGAGAGGACATCTGAA 57.139 45.455 0.00 0.00 38.84 3.02
4709 10409 6.669154 AGAGAGAGAGAGGACATCTGAAAAAT 59.331 38.462 0.00 0.00 38.84 1.82
4712 10412 8.820831 AGAGAGAGAGGACATCTGAAAAATAAA 58.179 33.333 0.00 0.00 38.84 1.40
4713 10417 8.785329 AGAGAGAGGACATCTGAAAAATAAAC 57.215 34.615 0.00 0.00 38.84 2.01
4720 10424 7.944554 AGGACATCTGAAAAATAAACAGAGGAA 59.055 33.333 13.39 0.00 42.47 3.36
4723 10427 8.579863 ACATCTGAAAAATAAACAGAGGAAAGG 58.420 33.333 13.39 0.00 42.47 3.11
4724 10428 8.796475 CATCTGAAAAATAAACAGAGGAAAGGA 58.204 33.333 0.00 0.00 42.47 3.36
4725 10429 8.396272 TCTGAAAAATAAACAGAGGAAAGGAG 57.604 34.615 0.00 0.00 36.04 3.69
4726 10430 8.217799 TCTGAAAAATAAACAGAGGAAAGGAGA 58.782 33.333 0.00 0.00 36.04 3.71
4729 10433 8.628630 AAAAATAAACAGAGGAAAGGAGAGAG 57.371 34.615 0.00 0.00 0.00 3.20
4734 10438 3.591527 ACAGAGGAAAGGAGAGAGAGAGA 59.408 47.826 0.00 0.00 0.00 3.10
4735 10439 4.202441 CAGAGGAAAGGAGAGAGAGAGAG 58.798 52.174 0.00 0.00 0.00 3.20
4737 10441 4.164988 AGAGGAAAGGAGAGAGAGAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
4739 10443 4.164988 AGGAAAGGAGAGAGAGAGAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
4740 10444 4.164221 GGAAAGGAGAGAGAGAGAGAGAGA 59.836 50.000 0.00 0.00 0.00 3.10
4741 10445 5.339200 GGAAAGGAGAGAGAGAGAGAGAGAA 60.339 48.000 0.00 0.00 0.00 2.87
4743 10447 5.104259 AGGAGAGAGAGAGAGAGAGAAAC 57.896 47.826 0.00 0.00 0.00 2.78
4744 10448 4.536090 AGGAGAGAGAGAGAGAGAGAAACA 59.464 45.833 0.00 0.00 0.00 2.83
4745 10449 4.636206 GGAGAGAGAGAGAGAGAGAAACAC 59.364 50.000 0.00 0.00 0.00 3.32
4747 10451 5.880901 AGAGAGAGAGAGAGAGAAACACTT 58.119 41.667 0.00 0.00 0.00 3.16
4748 10452 5.940470 AGAGAGAGAGAGAGAGAAACACTTC 59.060 44.000 0.00 0.00 0.00 3.01
4750 10454 6.306987 AGAGAGAGAGAGAGAAACACTTCTT 58.693 40.000 0.00 0.00 42.19 2.52
4751 10455 6.777580 AGAGAGAGAGAGAGAAACACTTCTTT 59.222 38.462 0.00 0.00 42.19 2.52
4752 10456 7.287696 AGAGAGAGAGAGAGAAACACTTCTTTT 59.712 37.037 0.00 0.00 42.19 2.27
4753 10457 7.791029 AGAGAGAGAGAGAAACACTTCTTTTT 58.209 34.615 0.00 0.00 42.19 1.94
4754 10458 7.710475 AGAGAGAGAGAGAAACACTTCTTTTTG 59.290 37.037 0.00 0.00 42.19 2.44
4755 10459 7.560368 AGAGAGAGAGAAACACTTCTTTTTGA 58.440 34.615 0.00 0.00 42.19 2.69
4756 10460 7.710475 AGAGAGAGAGAAACACTTCTTTTTGAG 59.290 37.037 0.00 0.00 42.19 3.02
4757 10461 6.765512 AGAGAGAGAAACACTTCTTTTTGAGG 59.234 38.462 0.00 0.00 42.19 3.86
4758 10462 5.825151 AGAGAGAAACACTTCTTTTTGAGGG 59.175 40.000 0.00 0.00 42.19 4.30
4759 10463 5.755849 AGAGAAACACTTCTTTTTGAGGGA 58.244 37.500 0.00 0.00 42.19 4.20
4760 10464 5.825151 AGAGAAACACTTCTTTTTGAGGGAG 59.175 40.000 0.00 0.00 42.19 4.30
4761 10465 5.755849 AGAAACACTTCTTTTTGAGGGAGA 58.244 37.500 0.00 0.00 38.89 3.71
4762 10466 5.825151 AGAAACACTTCTTTTTGAGGGAGAG 59.175 40.000 0.00 0.00 38.89 3.20
4763 10467 5.373812 AACACTTCTTTTTGAGGGAGAGA 57.626 39.130 0.00 0.00 0.00 3.10
4764 10468 4.967036 ACACTTCTTTTTGAGGGAGAGAG 58.033 43.478 0.00 0.00 0.00 3.20
4765 10469 4.656112 ACACTTCTTTTTGAGGGAGAGAGA 59.344 41.667 0.00 0.00 0.00 3.10
4766 10470 5.131142 ACACTTCTTTTTGAGGGAGAGAGAA 59.869 40.000 0.00 0.00 0.00 2.87
4767 10471 6.183361 ACACTTCTTTTTGAGGGAGAGAGAAT 60.183 38.462 0.00 0.00 0.00 2.40
4768 10472 6.371271 CACTTCTTTTTGAGGGAGAGAGAATC 59.629 42.308 0.00 0.00 0.00 2.52
4769 10473 5.428184 TCTTTTTGAGGGAGAGAGAATCC 57.572 43.478 0.00 0.00 33.66 3.01
4770 10474 5.097234 TCTTTTTGAGGGAGAGAGAATCCT 58.903 41.667 0.00 0.00 37.01 3.24
4771 10475 5.549619 TCTTTTTGAGGGAGAGAGAATCCTT 59.450 40.000 0.00 0.00 37.01 3.36
4772 10476 5.850046 TTTTGAGGGAGAGAGAATCCTTT 57.150 39.130 0.00 0.00 37.01 3.11
4773 10477 5.850046 TTTGAGGGAGAGAGAATCCTTTT 57.150 39.130 0.00 0.00 37.01 2.27
4774 10478 5.850046 TTGAGGGAGAGAGAATCCTTTTT 57.150 39.130 0.00 0.00 37.01 1.94
4829 10533 9.603921 TTTTTGAGATCAAGAGAATTTGCTTTT 57.396 25.926 0.00 0.00 37.15 2.27
4830 10534 8.583810 TTTGAGATCAAGAGAATTTGCTTTTG 57.416 30.769 0.00 0.00 37.15 2.44
4831 10535 7.514784 TGAGATCAAGAGAATTTGCTTTTGA 57.485 32.000 0.00 0.00 41.40 2.69
4832 10536 7.591165 TGAGATCAAGAGAATTTGCTTTTGAG 58.409 34.615 0.00 0.00 40.77 3.02
4833 10537 7.446319 TGAGATCAAGAGAATTTGCTTTTGAGA 59.554 33.333 0.00 0.00 40.77 3.27
4834 10538 7.592051 AGATCAAGAGAATTTGCTTTTGAGAC 58.408 34.615 0.00 0.00 40.77 3.36
4835 10539 6.698008 TCAAGAGAATTTGCTTTTGAGACA 57.302 33.333 0.00 0.00 35.04 3.41
4836 10540 7.281040 TCAAGAGAATTTGCTTTTGAGACAT 57.719 32.000 0.00 0.00 35.04 3.06
4837 10541 8.394971 TCAAGAGAATTTGCTTTTGAGACATA 57.605 30.769 0.00 0.00 35.04 2.29
4838 10542 8.849168 TCAAGAGAATTTGCTTTTGAGACATAA 58.151 29.630 0.00 0.00 35.04 1.90
4839 10543 9.125906 CAAGAGAATTTGCTTTTGAGACATAAG 57.874 33.333 0.00 0.00 33.24 1.73
4840 10544 8.627208 AGAGAATTTGCTTTTGAGACATAAGA 57.373 30.769 0.00 0.00 0.00 2.10
4841 10545 8.728833 AGAGAATTTGCTTTTGAGACATAAGAG 58.271 33.333 0.00 0.00 0.00 2.85
4842 10546 8.627208 AGAATTTGCTTTTGAGACATAAGAGA 57.373 30.769 0.00 0.00 0.00 3.10
4843 10547 9.071276 AGAATTTGCTTTTGAGACATAAGAGAA 57.929 29.630 0.00 0.00 0.00 2.87
4844 10548 9.852091 GAATTTGCTTTTGAGACATAAGAGAAT 57.148 29.630 0.00 0.00 0.00 2.40
4845 10549 9.852091 AATTTGCTTTTGAGACATAAGAGAATC 57.148 29.630 0.00 0.00 0.00 2.52
5000 10775 2.972505 CACCACTCACGCACCCAC 60.973 66.667 0.00 0.00 0.00 4.61
5001 10776 3.161450 ACCACTCACGCACCCACT 61.161 61.111 0.00 0.00 0.00 4.00
5002 10777 2.666190 CCACTCACGCACCCACTG 60.666 66.667 0.00 0.00 0.00 3.66
5003 10778 2.666190 CACTCACGCACCCACTGG 60.666 66.667 0.00 0.00 37.80 4.00
5015 10790 1.674057 CCACTGGTGGTCACTCTCC 59.326 63.158 11.29 0.00 45.53 3.71
5045 10820 2.813474 CGTCTCCGCCGCAATTCA 60.813 61.111 0.00 0.00 0.00 2.57
5076 10851 2.945668 GCAACTCCTCTCTCTCTCTCTC 59.054 54.545 0.00 0.00 0.00 3.20
5077 10852 3.370953 GCAACTCCTCTCTCTCTCTCTCT 60.371 52.174 0.00 0.00 0.00 3.10
5078 10853 4.446371 CAACTCCTCTCTCTCTCTCTCTC 58.554 52.174 0.00 0.00 0.00 3.20
5079 10854 4.000928 ACTCCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
5080 10855 3.964031 ACTCCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
5081 10856 4.222336 CTCCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
5082 10857 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
5083 10858 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
5084 10859 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
5085 10860 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
5086 10861 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5087 10862 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5088 10863 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5089 10864 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5090 10865 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5091 10866 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5092 10867 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5093 10868 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5094 10869 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5095 10870 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5096 10871 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5097 10872 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5098 10873 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5099 10874 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5100 10875 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5101 10876 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5102 10877 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5103 10878 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5104 10879 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5105 10880 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5106 10881 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5107 10882 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5108 10883 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5109 10884 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5110 10885 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5111 10886 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5112 10887 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5113 10888 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5114 10889 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5115 10890 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5116 10891 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5117 10892 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5118 10893 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5119 10894 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5120 10895 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5121 10896 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5122 10897 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5123 10898 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5124 10899 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5125 10900 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5126 10901 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5127 10902 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5128 10903 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5129 10904 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5130 10905 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
5131 10906 5.362143 TCTCTCTCTCTCTCTCTCTCTCTTG 59.638 48.000 0.00 0.00 0.00 3.02
5132 10907 5.026121 TCTCTCTCTCTCTCTCTCTCTTGT 58.974 45.833 0.00 0.00 0.00 3.16
5133 10908 5.485353 TCTCTCTCTCTCTCTCTCTCTTGTT 59.515 44.000 0.00 0.00 0.00 2.83
5134 10909 5.734720 TCTCTCTCTCTCTCTCTCTTGTTC 58.265 45.833 0.00 0.00 0.00 3.18
5135 10910 4.503910 TCTCTCTCTCTCTCTCTTGTTCG 58.496 47.826 0.00 0.00 0.00 3.95
5136 10911 3.006940 TCTCTCTCTCTCTCTTGTTCGC 58.993 50.000 0.00 0.00 0.00 4.70
5137 10912 2.088423 TCTCTCTCTCTCTTGTTCGCC 58.912 52.381 0.00 0.00 0.00 5.54
5138 10913 1.134175 CTCTCTCTCTCTTGTTCGCCC 59.866 57.143 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.063997 CCATTAAAGCCAGCAAGACTACG 59.936 47.826 0.00 0.00 0.00 3.51
11 12 3.378427 CCCATTAAAGCCAGCAAGACTAC 59.622 47.826 0.00 0.00 0.00 2.73
19 20 3.739209 GCTGATTTCCCATTAAAGCCAGC 60.739 47.826 0.00 0.00 39.51 4.85
195 217 8.026607 ACAGGTTAATGTGGAATTTTATGTTCG 58.973 33.333 0.00 0.00 30.46 3.95
277 299 6.677913 AGTTGAAGGGACATAATTTCAAACG 58.322 36.000 0.63 0.00 40.14 3.60
703 749 5.247792 TCTCACTAGATGCATTGCCTATCAT 59.752 40.000 6.12 0.00 0.00 2.45
755 906 0.771127 CCACCTCTTGGTCTTGGGAA 59.229 55.000 0.00 0.00 46.60 3.97
824 978 8.504005 CATTAAGACAAGAAAAGTAATGGACGT 58.496 33.333 0.00 0.00 0.00 4.34
854 1010 1.992538 AAAGGAGCAGAGCAGCTTTT 58.007 45.000 0.00 0.00 46.75 2.27
885 1042 3.068732 TCTCCAGGATCTGCTAACGAATG 59.931 47.826 0.00 0.00 0.00 2.67
890 1047 1.269517 CGCTCTCCAGGATCTGCTAAC 60.270 57.143 0.00 0.00 0.00 2.34
893 1050 0.469705 ATCGCTCTCCAGGATCTGCT 60.470 55.000 0.00 0.00 0.00 4.24
899 1056 0.758310 ATGCTCATCGCTCTCCAGGA 60.758 55.000 0.00 0.00 40.11 3.86
1071 1249 2.360801 ACTTTGGTTGTTCGTGGATTGG 59.639 45.455 0.00 0.00 0.00 3.16
1291 1472 2.436109 GAGTCCCAAGCCCTGCAA 59.564 61.111 0.00 0.00 0.00 4.08
1356 1539 4.103153 AGGTTGTTGGATGAAAGACTGAGA 59.897 41.667 0.00 0.00 0.00 3.27
1437 1620 4.740902 AGCCAAAAAGGTAGTTCATCCTT 58.259 39.130 0.00 0.00 44.71 3.36
1610 2208 4.704833 GGTTGCCGAGCCAGCTCA 62.705 66.667 19.08 0.00 42.86 4.26
2349 2980 6.234177 AGAAAGAGAGAGGTTGTACAATTGG 58.766 40.000 12.26 0.00 0.00 3.16
2428 3059 5.897824 AGTTACCGGAAAGATCCAGAGATAA 59.102 40.000 9.46 0.00 46.97 1.75
2482 3120 5.725325 AAGGTCAGAGAGGTAACACTAAC 57.275 43.478 0.00 0.00 37.77 2.34
2488 3126 7.642082 TGATAAGTAAGGTCAGAGAGGTAAC 57.358 40.000 0.00 0.00 0.00 2.50
2509 3147 1.284198 AGCATTGCTGGAGAGGTTGAT 59.716 47.619 11.09 0.00 37.57 2.57
2581 3219 5.809562 AGAGCTTGTTCATTGATAAGTCGAG 59.190 40.000 10.86 0.00 0.00 4.04
2636 3274 7.415206 GCAAATATAGGAAATTCAGTTGGACGT 60.415 37.037 0.00 0.00 0.00 4.34
2830 3468 3.822735 CGGAAGATCCATGTATTTGGCAT 59.177 43.478 0.00 0.00 35.91 4.40
3080 3736 8.985922 CATAGGATATCCTCTCATGGTGAAATA 58.014 37.037 27.86 5.56 44.77 1.40
3351 4016 4.525487 ACAAATGCCTTGAACTCATCACAT 59.475 37.500 2.85 0.00 37.92 3.21
3352 4017 3.890756 ACAAATGCCTTGAACTCATCACA 59.109 39.130 2.85 0.00 37.92 3.58
3370 4264 6.147164 CCGTTGCAGATAAACTCTAAGACAAA 59.853 38.462 0.00 0.00 31.13 2.83
3503 4429 8.900781 ACTCAATTTGATGGTGAAGATATTCTG 58.099 33.333 1.19 0.00 0.00 3.02
3529 4455 7.601705 TGATATCACAGTGAACTATGGATGA 57.398 36.000 7.50 0.00 0.00 2.92
3558 4484 5.236047 GTCATCATCTAGAAGGATGTTGCAC 59.764 44.000 25.20 17.30 42.45 4.57
3652 4578 0.886563 GAGCTGCTTGCAGTTCCAAT 59.113 50.000 22.90 5.56 45.94 3.16
3653 4579 0.466007 TGAGCTGCTTGCAGTTCCAA 60.466 50.000 27.69 13.79 45.94 3.53
3702 4628 2.203337 GGTTGCTGACCTGGTGCA 60.203 61.111 2.82 5.80 45.55 4.57
3936 4907 0.178876 TGTGGAGGGTTCAGATCCCA 60.179 55.000 17.66 0.00 46.82 4.37
4062 8829 1.699634 GCTTATCAGGATAGGCCACCA 59.300 52.381 5.01 0.00 39.57 4.17
4142 8911 5.705905 AGCTTAAACACAGGATACAAGAACC 59.294 40.000 0.00 0.00 41.41 3.62
4168 8937 2.186384 CTCGCAGCAAGCTAGGCT 59.814 61.111 6.97 6.97 43.77 4.58
4291 9065 2.158769 TCATTGCTCGCATGGATTAGGT 60.159 45.455 0.00 0.00 0.00 3.08
4301 9077 0.442310 GTAACGCTTCATTGCTCGCA 59.558 50.000 0.00 0.00 0.00 5.10
4359 9135 1.066908 ACCACAATGTCAAAGGCAACG 59.933 47.619 0.00 0.00 46.39 4.10
4362 9138 1.955778 CAGACCACAATGTCAAAGGCA 59.044 47.619 0.00 0.00 37.73 4.75
4367 9143 2.862541 CTTCCCAGACCACAATGTCAA 58.137 47.619 0.00 0.00 37.73 3.18
4371 9147 0.038744 AGGCTTCCCAGACCACAATG 59.961 55.000 0.00 0.00 0.00 2.82
4398 9195 1.355720 ACTTCAGGATCACCCCAAAGG 59.644 52.381 0.00 0.00 43.78 3.11
4411 9208 6.022163 AGAAATGAAAATGCTGACTTCAGG 57.978 37.500 8.32 0.00 43.94 3.86
4478 9275 6.925165 GGTTCAAATGGGTGCATATAAGAATG 59.075 38.462 0.00 0.00 0.00 2.67
4481 9278 5.514169 TGGTTCAAATGGGTGCATATAAGA 58.486 37.500 0.00 0.00 0.00 2.10
4482 9279 5.850557 TGGTTCAAATGGGTGCATATAAG 57.149 39.130 0.00 0.00 0.00 1.73
4484 9281 5.453158 TGATGGTTCAAATGGGTGCATATA 58.547 37.500 0.00 0.00 0.00 0.86
4485 9282 4.288398 TGATGGTTCAAATGGGTGCATAT 58.712 39.130 0.00 0.00 0.00 1.78
4486 9283 3.706183 TGATGGTTCAAATGGGTGCATA 58.294 40.909 0.00 0.00 0.00 3.14
4487 9284 2.538222 TGATGGTTCAAATGGGTGCAT 58.462 42.857 0.00 0.00 0.00 3.96
4488 9285 2.006805 TGATGGTTCAAATGGGTGCA 57.993 45.000 0.00 0.00 0.00 4.57
4515 10204 3.244700 TGAAGAGAGGGAGGCAAGAAAAG 60.245 47.826 0.00 0.00 0.00 2.27
4580 10269 3.556306 CACGGGGTGGAGTGGTGT 61.556 66.667 0.00 0.00 34.93 4.16
4640 10331 1.195448 CGTGTGCATTCTTTTCTCGCT 59.805 47.619 0.00 0.00 0.00 4.93
4703 10403 8.622948 TCTCTCCTTTCCTCTGTTTATTTTTC 57.377 34.615 0.00 0.00 0.00 2.29
4705 10405 7.978925 TCTCTCTCCTTTCCTCTGTTTATTTT 58.021 34.615 0.00 0.00 0.00 1.82
4709 10409 5.893500 TCTCTCTCTCCTTTCCTCTGTTTA 58.106 41.667 0.00 0.00 0.00 2.01
4712 10412 3.591527 TCTCTCTCTCTCCTTTCCTCTGT 59.408 47.826 0.00 0.00 0.00 3.41
4713 10417 4.080356 TCTCTCTCTCTCTCCTTTCCTCTG 60.080 50.000 0.00 0.00 0.00 3.35
4720 10424 5.014123 TGTTTCTCTCTCTCTCTCTCTCCTT 59.986 44.000 0.00 0.00 0.00 3.36
4723 10427 5.491982 AGTGTTTCTCTCTCTCTCTCTCTC 58.508 45.833 0.00 0.00 0.00 3.20
4724 10428 5.505181 AGTGTTTCTCTCTCTCTCTCTCT 57.495 43.478 0.00 0.00 0.00 3.10
4725 10429 5.940470 AGAAGTGTTTCTCTCTCTCTCTCTC 59.060 44.000 0.00 0.00 39.46 3.20
4726 10430 5.880901 AGAAGTGTTTCTCTCTCTCTCTCT 58.119 41.667 0.00 0.00 39.46 3.10
4729 10433 7.708752 TCAAAAAGAAGTGTTTCTCTCTCTCTC 59.291 37.037 0.00 0.00 42.80 3.20
4734 10438 5.825151 CCCTCAAAAAGAAGTGTTTCTCTCT 59.175 40.000 0.00 0.00 42.80 3.10
4735 10439 5.823045 TCCCTCAAAAAGAAGTGTTTCTCTC 59.177 40.000 0.00 0.00 42.80 3.20
4737 10441 5.823045 TCTCCCTCAAAAAGAAGTGTTTCTC 59.177 40.000 0.00 0.00 42.80 2.87
4739 10443 5.823045 TCTCTCCCTCAAAAAGAAGTGTTTC 59.177 40.000 0.00 0.00 0.00 2.78
4740 10444 5.755849 TCTCTCCCTCAAAAAGAAGTGTTT 58.244 37.500 0.00 0.00 0.00 2.83
4741 10445 5.131142 TCTCTCTCCCTCAAAAAGAAGTGTT 59.869 40.000 0.00 0.00 0.00 3.32
4743 10447 5.220710 TCTCTCTCCCTCAAAAAGAAGTG 57.779 43.478 0.00 0.00 0.00 3.16
4744 10448 5.896073 TTCTCTCTCCCTCAAAAAGAAGT 57.104 39.130 0.00 0.00 0.00 3.01
4745 10449 5.879777 GGATTCTCTCTCCCTCAAAAAGAAG 59.120 44.000 0.00 0.00 0.00 2.85
4747 10451 5.097234 AGGATTCTCTCTCCCTCAAAAAGA 58.903 41.667 0.00 0.00 32.89 2.52
4748 10452 5.434182 AGGATTCTCTCTCCCTCAAAAAG 57.566 43.478 0.00 0.00 32.89 2.27
4750 10454 5.850046 AAAGGATTCTCTCTCCCTCAAAA 57.150 39.130 0.00 0.00 32.89 2.44
4751 10455 5.850046 AAAAGGATTCTCTCTCCCTCAAA 57.150 39.130 0.00 0.00 32.89 2.69
4752 10456 5.850046 AAAAAGGATTCTCTCTCCCTCAA 57.150 39.130 0.00 0.00 32.89 3.02
4771 10475 9.516546 GAAGAAAGATTCTCTTACCCCTAAAAA 57.483 33.333 0.00 0.00 39.61 1.94
4772 10476 8.891501 AGAAGAAAGATTCTCTTACCCCTAAAA 58.108 33.333 0.00 0.00 39.61 1.52
4773 10477 8.450780 AGAAGAAAGATTCTCTTACCCCTAAA 57.549 34.615 0.00 0.00 39.61 1.85
4774 10478 8.450780 AAGAAGAAAGATTCTCTTACCCCTAA 57.549 34.615 0.00 0.00 38.59 2.69
4775 10479 7.901861 AGAAGAAGAAAGATTCTCTTACCCCTA 59.098 37.037 0.00 0.00 38.59 3.53
4776 10480 6.733334 AGAAGAAGAAAGATTCTCTTACCCCT 59.267 38.462 0.00 0.00 38.59 4.79
4777 10481 6.953101 AGAAGAAGAAAGATTCTCTTACCCC 58.047 40.000 0.00 0.00 38.59 4.95
4778 10482 8.856153 AAAGAAGAAGAAAGATTCTCTTACCC 57.144 34.615 0.00 0.00 38.59 3.69
4803 10507 9.603921 AAAAGCAAATTCTCTTGATCTCAAAAA 57.396 25.926 0.00 0.00 35.15 1.94
4804 10508 9.037737 CAAAAGCAAATTCTCTTGATCTCAAAA 57.962 29.630 0.00 0.00 35.15 2.44
4805 10509 8.415553 TCAAAAGCAAATTCTCTTGATCTCAAA 58.584 29.630 0.00 0.00 35.15 2.69
4806 10510 7.944061 TCAAAAGCAAATTCTCTTGATCTCAA 58.056 30.769 0.00 0.00 0.00 3.02
4807 10511 7.446319 TCTCAAAAGCAAATTCTCTTGATCTCA 59.554 33.333 0.00 0.00 0.00 3.27
4808 10512 7.750014 GTCTCAAAAGCAAATTCTCTTGATCTC 59.250 37.037 0.00 0.00 0.00 2.75
4809 10513 7.230108 TGTCTCAAAAGCAAATTCTCTTGATCT 59.770 33.333 0.00 0.00 0.00 2.75
4810 10514 7.365741 TGTCTCAAAAGCAAATTCTCTTGATC 58.634 34.615 0.00 0.00 0.00 2.92
4811 10515 7.281040 TGTCTCAAAAGCAAATTCTCTTGAT 57.719 32.000 0.00 0.00 0.00 2.57
4812 10516 6.698008 TGTCTCAAAAGCAAATTCTCTTGA 57.302 33.333 0.00 0.00 0.00 3.02
4813 10517 9.125906 CTTATGTCTCAAAAGCAAATTCTCTTG 57.874 33.333 0.00 0.00 0.00 3.02
4814 10518 9.071276 TCTTATGTCTCAAAAGCAAATTCTCTT 57.929 29.630 0.00 0.00 0.00 2.85
4815 10519 8.627208 TCTTATGTCTCAAAAGCAAATTCTCT 57.373 30.769 0.00 0.00 0.00 3.10
4816 10520 8.725148 TCTCTTATGTCTCAAAAGCAAATTCTC 58.275 33.333 0.00 0.00 0.00 2.87
4817 10521 8.627208 TCTCTTATGTCTCAAAAGCAAATTCT 57.373 30.769 0.00 0.00 0.00 2.40
4818 10522 9.852091 ATTCTCTTATGTCTCAAAAGCAAATTC 57.148 29.630 0.00 0.00 0.00 2.17
4819 10523 9.852091 GATTCTCTTATGTCTCAAAAGCAAATT 57.148 29.630 0.00 0.00 0.00 1.82
4820 10524 9.240734 AGATTCTCTTATGTCTCAAAAGCAAAT 57.759 29.630 0.00 0.00 0.00 2.32
4821 10525 8.627208 AGATTCTCTTATGTCTCAAAAGCAAA 57.373 30.769 0.00 0.00 0.00 3.68
4822 10526 8.627208 AAGATTCTCTTATGTCTCAAAAGCAA 57.373 30.769 0.00 0.00 34.42 3.91
4823 10527 8.627208 AAAGATTCTCTTATGTCTCAAAAGCA 57.373 30.769 0.00 0.00 35.27 3.91
4824 10528 9.905171 AAAAAGATTCTCTTATGTCTCAAAAGC 57.095 29.630 0.00 0.00 35.27 3.51
4827 10531 9.799106 AGGAAAAAGATTCTCTTATGTCTCAAA 57.201 29.630 0.00 0.00 35.27 2.69
4828 10532 9.799106 AAGGAAAAAGATTCTCTTATGTCTCAA 57.201 29.630 0.00 0.00 35.27 3.02
4829 10533 9.799106 AAAGGAAAAAGATTCTCTTATGTCTCA 57.201 29.630 0.00 0.00 35.27 3.27
4866 10570 8.785329 AGGAAAAAGATTCTCTTATGTGTCTC 57.215 34.615 0.00 0.00 35.27 3.36
4982 10757 4.927782 TGGGTGCGTGAGTGGTGC 62.928 66.667 0.00 0.00 0.00 5.01
5000 10775 3.393360 GGGGAGAGTGACCACCAG 58.607 66.667 0.00 0.00 0.00 4.00
5003 10778 0.253327 GAATGGGGGAGAGTGACCAC 59.747 60.000 0.00 0.00 35.52 4.16
5004 10779 0.119155 AGAATGGGGGAGAGTGACCA 59.881 55.000 0.00 0.00 37.41 4.02
5005 10780 0.833949 GAGAATGGGGGAGAGTGACC 59.166 60.000 0.00 0.00 0.00 4.02
5006 10781 0.833949 GGAGAATGGGGGAGAGTGAC 59.166 60.000 0.00 0.00 0.00 3.67
5007 10782 0.687757 CGGAGAATGGGGGAGAGTGA 60.688 60.000 0.00 0.00 0.00 3.41
5008 10783 1.690219 CCGGAGAATGGGGGAGAGTG 61.690 65.000 0.00 0.00 0.00 3.51
5009 10784 1.383248 CCGGAGAATGGGGGAGAGT 60.383 63.158 0.00 0.00 0.00 3.24
5010 10785 2.812619 GCCGGAGAATGGGGGAGAG 61.813 68.421 5.05 0.00 0.00 3.20
5011 10786 2.768344 GCCGGAGAATGGGGGAGA 60.768 66.667 5.05 0.00 0.00 3.71
5015 10790 3.447025 GAGACGCCGGAGAATGGGG 62.447 68.421 13.83 0.00 44.46 4.96
5076 10851 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5077 10852 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5078 10853 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5079 10854 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5080 10855 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5081 10856 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5082 10857 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5083 10858 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5084 10859 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5085 10860 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5086 10861 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5087 10862 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5088 10863 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5089 10864 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5090 10865 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5091 10866 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5092 10867 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5093 10868 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5094 10869 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5095 10870 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5096 10871 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5097 10872 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5098 10873 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5099 10874 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5100 10875 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5101 10876 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5102 10877 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5103 10878 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5104 10879 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5105 10880 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5106 10881 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5107 10882 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
5108 10883 5.128499 ACAAGAGAGAGAGAGAGAGAGAGAG 59.872 48.000 0.00 0.00 0.00 3.20
5109 10884 5.026121 ACAAGAGAGAGAGAGAGAGAGAGA 58.974 45.833 0.00 0.00 0.00 3.10
5110 10885 5.350504 ACAAGAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
5111 10886 5.624509 CGAACAAGAGAGAGAGAGAGAGAGA 60.625 48.000 0.00 0.00 0.00 3.10
5112 10887 4.568359 CGAACAAGAGAGAGAGAGAGAGAG 59.432 50.000 0.00 0.00 0.00 3.20
5113 10888 4.503910 CGAACAAGAGAGAGAGAGAGAGA 58.496 47.826 0.00 0.00 0.00 3.10
5114 10889 3.063997 GCGAACAAGAGAGAGAGAGAGAG 59.936 52.174 0.00 0.00 0.00 3.20
5115 10890 3.006940 GCGAACAAGAGAGAGAGAGAGA 58.993 50.000 0.00 0.00 0.00 3.10
5116 10891 2.097466 GGCGAACAAGAGAGAGAGAGAG 59.903 54.545 0.00 0.00 0.00 3.20
5117 10892 2.088423 GGCGAACAAGAGAGAGAGAGA 58.912 52.381 0.00 0.00 0.00 3.10
5118 10893 1.134175 GGGCGAACAAGAGAGAGAGAG 59.866 57.143 0.00 0.00 0.00 3.20
5119 10894 1.178276 GGGCGAACAAGAGAGAGAGA 58.822 55.000 0.00 0.00 0.00 3.10
5120 10895 3.731295 GGGCGAACAAGAGAGAGAG 57.269 57.895 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.