Multiple sequence alignment - TraesCS1A01G242800

Loading Multiple Alignment...

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 TraesCS1A01G242800 chr1A 100.000 6945 0 0 1 6945 430616268 430623212 0.000000e+00 12826.0
1 TraesCS1A01G242800 chr1A 88.050 159 17 2 64 222 551134309 551134465 3.310000e-43 187.0
2 TraesCS1A01G242800 chr1A 97.059 68 2 0 4617 4684 430620818 430620885 1.580000e-21 115.0
3 TraesCS1A01G242800 chr1A 97.059 68 2 0 4551 4618 430620884 430620951 1.580000e-21 115.0
4 TraesCS1A01G242800 chr1D 92.434 2868 113 31 1796 4618 332997335 333000143 0.000000e+00 3999.0
5 TraesCS1A01G242800 chr1D 95.258 2341 74 11 4617 6945 333000072 333002387 0.000000e+00 3674.0
6 TraesCS1A01G242800 chr1D 92.308 533 17 9 403 915 332995624 332996152 0.000000e+00 736.0
7 TraesCS1A01G242800 chr1D 87.624 606 33 8 925 1495 332996363 332996961 0.000000e+00 665.0
8 TraesCS1A01G242800 chr1D 93.077 260 16 2 1539 1797 332996916 332997174 5.080000e-101 379.0
9 TraesCS1A01G242800 chr1D 95.429 175 8 0 229 403 332995411 332995585 5.300000e-71 279.0
10 TraesCS1A01G242800 chr1D 88.050 159 18 1 64 222 442442062 442442219 3.310000e-43 187.0
11 TraesCS1A01G242800 chr1B 92.563 2622 79 38 422 2967 448525171 448527752 0.000000e+00 3655.0
12 TraesCS1A01G242800 chr1B 94.959 2341 74 15 4617 6945 448529756 448532064 0.000000e+00 3629.0
13 TraesCS1A01G242800 chr1B 94.488 1669 63 19 2961 4618 448528180 448529830 0.000000e+00 2545.0
14 TraesCS1A01G242800 chr1B 94.152 171 10 0 222 392 448524905 448525075 1.920000e-65 261.0
15 TraesCS1A01G242800 chr1B 84.559 272 31 6 2943 3203 376615233 376614962 6.910000e-65 259.0
16 TraesCS1A01G242800 chr1B 87.952 166 18 2 58 222 427602939 427603103 1.980000e-45 195.0
17 TraesCS1A01G242800 chr4A 86.345 249 28 3 2952 3198 434732756 434732512 4.130000e-67 267.0
18 TraesCS1A01G242800 chr4A 85.433 254 31 4 2944 3195 708426678 708426429 6.910000e-65 259.0
19 TraesCS1A01G242800 chr6D 84.766 256 35 2 2944 3195 304278115 304278370 3.220000e-63 254.0
20 TraesCS1A01G242800 chr6A 84.959 246 30 4 2956 3195 410910133 410909889 6.960000e-60 243.0
21 TraesCS1A01G242800 chr6B 82.707 266 40 5 2940 3201 681923600 681923337 1.510000e-56 231.0
22 TraesCS1A01G242800 chr6B 89.308 159 16 1 64 222 261201299 261201456 1.530000e-46 198.0
23 TraesCS1A01G242800 chr2B 83.401 247 38 3 2958 3202 13813624 13813379 7.010000e-55 226.0
24 TraesCS1A01G242800 chr2B 87.730 163 18 2 61 222 236864461 236864300 9.200000e-44 189.0
25 TraesCS1A01G242800 chr5B 89.308 159 16 1 64 222 572698688 572698531 1.530000e-46 198.0
26 TraesCS1A01G242800 chr7D 88.961 154 17 0 69 222 102575548 102575701 2.560000e-44 191.0
27 TraesCS1A01G242800 chr7D 88.535 157 18 0 66 222 597300964 597300808 2.560000e-44 191.0
28 TraesCS1A01G242800 chr3B 87.730 163 17 3 61 222 380685257 380685417 3.310000e-43 187.0
29 TraesCS1A01G242800 chr3B 92.958 71 3 1 1666 1736 442043767 442043835 1.230000e-17 102.0
30 TraesCS1A01G242800 chr3D 92.958 71 3 1 1666 1736 327310880 327310948 1.230000e-17 102.0
31 TraesCS1A01G242800 chr4B 91.549 71 3 1 1666 1736 88708440 88708373 2.060000e-15 95.3
32 TraesCS1A01G242800 chr7A 85.333 75 8 3 1662 1736 375175538 375175609 2.690000e-09 75.0


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 TraesCS1A01G242800 chr1A 430616268 430623212 6944 False 4352.0 12826 98.039333 1 6945 3 chr1A.!!$F2 6944
1 TraesCS1A01G242800 chr1D 332995411 333002387 6976 False 1622.0 3999 92.688333 229 6945 6 chr1D.!!$F2 6716
2 TraesCS1A01G242800 chr1B 448524905 448532064 7159 False 2522.5 3655 94.040500 222 6945 4 chr1B.!!$F2 6723

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
442 509 0.319083 TGACACGGGGATACACACAC 59.681 55.000 0.00 0.00 44.36 3.82 F
595 663 1.152631 TCGGCATCGATGGGGAGTA 60.153 57.895 26.00 0.00 40.88 2.59 F
1869 2370 0.098728 GATTCCCGGTGCACATTTCG 59.901 55.000 20.43 12.65 0.00 3.46 F
2445 2964 1.904287 TCTGTTGTGCCATAACCACC 58.096 50.000 1.68 0.00 32.30 4.61 F
2666 3185 2.435234 TACACGGCGCACCAATCC 60.435 61.111 10.83 0.00 34.57 3.01 F
4418 5396 1.000938 GACAGCTTGGCAGTTTCCTTG 60.001 52.381 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1695 0.453615 CACTCGAGACAGAGACGCAC 60.454 60.000 21.68 0.0 40.57 5.34 R
2445 2964 0.810648 ACACCCAGTAAATGCATGCG 59.189 50.000 14.09 0.0 0.00 4.73 R
2885 3405 1.888512 GAAAACAAGAGCTGGATGGCA 59.111 47.619 0.00 0.0 34.17 4.92 R
3524 4482 4.365899 AAACAGTTTTGAGTTTCGTCCC 57.634 40.909 0.00 0.0 32.90 4.46 R
4613 5591 2.178984 TGAGGGATTGGGTTTGGAAACT 59.821 45.455 2.44 0.0 38.89 2.66 R
6399 7380 0.238817 ACACGCACACACACGTTTTT 59.761 45.000 0.00 0.0 41.32 1.94 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
48 49 9.683069 ATGCGATTCATAAATATTTGGAGTTTC 57.317 29.630 11.05 6.26 32.59 2.78
49 50 8.902806 TGCGATTCATAAATATTTGGAGTTTCT 58.097 29.630 11.05 0.00 0.00 2.52
50 51 9.736023 GCGATTCATAAATATTTGGAGTTTCTT 57.264 29.630 11.05 0.00 0.00 2.52
79 80 7.948034 AATTGTTATCCCATCCGTTTCTAAA 57.052 32.000 0.00 0.00 0.00 1.85
80 81 8.533569 AATTGTTATCCCATCCGTTTCTAAAT 57.466 30.769 0.00 0.00 0.00 1.40
81 82 9.635404 AATTGTTATCCCATCCGTTTCTAAATA 57.365 29.630 0.00 0.00 0.00 1.40
82 83 8.441312 TTGTTATCCCATCCGTTTCTAAATAC 57.559 34.615 0.00 0.00 0.00 1.89
83 84 7.798071 TGTTATCCCATCCGTTTCTAAATACT 58.202 34.615 0.00 0.00 0.00 2.12
84 85 8.269317 TGTTATCCCATCCGTTTCTAAATACTT 58.731 33.333 0.00 0.00 0.00 2.24
85 86 8.557029 GTTATCCCATCCGTTTCTAAATACTTG 58.443 37.037 0.00 0.00 0.00 3.16
86 87 6.057321 TCCCATCCGTTTCTAAATACTTGT 57.943 37.500 0.00 0.00 0.00 3.16
87 88 6.110707 TCCCATCCGTTTCTAAATACTTGTC 58.889 40.000 0.00 0.00 0.00 3.18
88 89 6.070424 TCCCATCCGTTTCTAAATACTTGTCT 60.070 38.462 0.00 0.00 0.00 3.41
89 90 6.598064 CCCATCCGTTTCTAAATACTTGTCTT 59.402 38.462 0.00 0.00 0.00 3.01
90 91 7.120726 CCCATCCGTTTCTAAATACTTGTCTTT 59.879 37.037 0.00 0.00 0.00 2.52
91 92 8.175716 CCATCCGTTTCTAAATACTTGTCTTTC 58.824 37.037 0.00 0.00 0.00 2.62
92 93 8.936864 CATCCGTTTCTAAATACTTGTCTTTCT 58.063 33.333 0.00 0.00 0.00 2.52
94 95 9.985730 TCCGTTTCTAAATACTTGTCTTTCTAA 57.014 29.630 0.00 0.00 0.00 2.10
109 110 9.787532 TTGTCTTTCTAAAGATTTCAACAAGTG 57.212 29.630 8.31 0.00 45.83 3.16
110 111 9.173021 TGTCTTTCTAAAGATTTCAACAAGTGA 57.827 29.630 8.31 0.00 45.83 3.41
111 112 9.439537 GTCTTTCTAAAGATTTCAACAAGTGAC 57.560 33.333 8.31 0.00 45.83 3.67
112 113 9.396022 TCTTTCTAAAGATTTCAACAAGTGACT 57.604 29.630 1.00 0.00 39.95 3.41
115 116 9.607988 TTCTAAAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
116 117 9.778741 TCTAAAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
120 121 9.725019 AAGATTTCAACAAGTGACTACATATGA 57.275 29.630 10.38 0.00 35.39 2.15
121 122 9.725019 AGATTTCAACAAGTGACTACATATGAA 57.275 29.630 10.38 0.00 35.39 2.57
124 125 8.669946 TTCAACAAGTGACTACATATGAAACA 57.330 30.769 10.38 1.47 35.39 2.83
125 126 8.669946 TCAACAAGTGACTACATATGAAACAA 57.330 30.769 10.38 0.00 0.00 2.83
126 127 9.114952 TCAACAAGTGACTACATATGAAACAAA 57.885 29.630 10.38 0.00 0.00 2.83
127 128 9.729023 CAACAAGTGACTACATATGAAACAAAA 57.271 29.630 10.38 0.00 0.00 2.44
129 130 9.897744 ACAAGTGACTACATATGAAACAAAATG 57.102 29.630 10.38 3.10 0.00 2.32
144 145 9.897744 TGAAACAAAATGATTGAATCTACACTC 57.102 29.630 6.73 0.00 0.00 3.51
220 221 7.568199 AAGGACAAATATTTACGAATGGAGG 57.432 36.000 0.00 0.00 0.00 4.30
232 233 3.068307 ACGAATGGAGGGTTTCTATCGAG 59.932 47.826 0.00 0.00 33.00 4.04
279 280 1.565305 GCGATGTGACTGAGGATGTC 58.435 55.000 0.00 0.00 35.21 3.06
314 315 1.177256 ACCCTACGTGACGTGAAGCT 61.177 55.000 22.16 0.00 41.39 3.74
354 355 1.201647 TGTAGCCAGTAGAGCGTGAAC 59.798 52.381 0.00 0.00 34.64 3.18
412 464 1.549170 AGTACCGTGGTTCACTCATCC 59.451 52.381 0.00 0.00 31.34 3.51
442 509 0.319083 TGACACGGGGATACACACAC 59.681 55.000 0.00 0.00 44.36 3.82
523 590 6.958255 TCCAGTGTATTTTTATGCATCATCG 58.042 36.000 0.19 0.00 0.00 3.84
529 596 4.614555 TTTTTATGCATCATCGCGAAGT 57.385 36.364 15.24 0.00 33.35 3.01
553 620 1.585668 CATCTGAACATCTCGCGTGTC 59.414 52.381 5.77 0.00 0.00 3.67
570 637 2.031157 GTGTCTTTCATCACGGGGTTTG 60.031 50.000 0.00 0.00 0.00 2.93
594 662 2.443952 TCGGCATCGATGGGGAGT 60.444 61.111 26.00 0.00 40.88 3.85
595 663 1.152631 TCGGCATCGATGGGGAGTA 60.153 57.895 26.00 0.00 40.88 2.59
926 1231 4.831307 CGACGGCTCCGAAGACCG 62.831 72.222 15.95 3.22 43.45 4.79
1296 1626 1.596477 GCTCATCTCCGATGCCACC 60.596 63.158 0.00 0.00 0.00 4.61
1302 1632 1.817099 CTCCGATGCCACCTGCTTC 60.817 63.158 0.00 0.00 42.00 3.86
1365 1695 1.016130 ATCGCCACTGAGCTTTCGTG 61.016 55.000 0.00 0.00 0.00 4.35
1524 1862 3.161067 ACAGTAGATGTCTGCACACTCT 58.839 45.455 1.08 0.00 37.75 3.24
1680 2018 4.514066 CACAGTTAGTACCCTGTTCAAACC 59.486 45.833 7.50 0.00 39.83 3.27
1869 2370 0.098728 GATTCCCGGTGCACATTTCG 59.901 55.000 20.43 12.65 0.00 3.46
1876 2377 2.095466 CCGGTGCACATTTCGTATTTGT 60.095 45.455 20.43 0.00 0.00 2.83
2090 2609 2.675317 GCATAGATGGACAGGGCGATAC 60.675 54.545 0.00 0.00 0.00 2.24
2286 2805 3.648339 TTGCAGAGTTCATTTGGCTTC 57.352 42.857 0.00 0.00 0.00 3.86
2289 2808 2.816087 GCAGAGTTCATTTGGCTTCAGA 59.184 45.455 0.00 0.00 0.00 3.27
2427 2946 7.389053 CAGGTGCCCTTTGACTAGATAATTATC 59.611 40.741 16.35 16.35 0.00 1.75
2445 2964 1.904287 TCTGTTGTGCCATAACCACC 58.096 50.000 1.68 0.00 32.30 4.61
2666 3185 2.435234 TACACGGCGCACCAATCC 60.435 61.111 10.83 0.00 34.57 3.01
2883 3403 6.631016 TGTGAGTCGTCTATAAGATTTGCTT 58.369 36.000 0.00 0.00 40.68 3.91
2891 3411 7.331934 TCGTCTATAAGATTTGCTTATGCCATC 59.668 37.037 7.78 0.68 46.59 3.51
3014 3969 5.853572 ACTTTGACCAAGTTTATAGGGGA 57.146 39.130 0.00 0.00 43.89 4.81
3104 4061 8.360390 TGATATACGCTTGACATTCTAGATGTT 58.640 33.333 0.00 0.00 31.52 2.71
3112 4069 9.495754 GCTTGACATTCTAGATGTTAATGTTTC 57.504 33.333 8.12 0.00 42.35 2.78
3235 4193 5.490139 AGATCATGGTTTAGTTGAATGCG 57.510 39.130 0.00 0.00 0.00 4.73
3266 4224 9.747898 TCATTTATTTAAGGAAGTGTACCATGT 57.252 29.630 0.00 0.00 0.00 3.21
3529 4487 9.706691 ATATTTACAGATATAAGTGTTGGGACG 57.293 33.333 0.00 0.00 0.00 4.79
3645 4604 9.829507 AAGTCTATGATTCTCTTATCTGGTTTG 57.170 33.333 0.00 0.00 0.00 2.93
3647 4606 8.207545 GTCTATGATTCTCTTATCTGGTTTGGT 58.792 37.037 0.00 0.00 0.00 3.67
3648 4607 8.772250 TCTATGATTCTCTTATCTGGTTTGGTT 58.228 33.333 0.00 0.00 0.00 3.67
3650 4609 8.655935 ATGATTCTCTTATCTGGTTTGGTTTT 57.344 30.769 0.00 0.00 0.00 2.43
3651 4610 8.477419 TGATTCTCTTATCTGGTTTGGTTTTT 57.523 30.769 0.00 0.00 0.00 1.94
4233 5208 4.454728 ACAAATATTTCTGCCACGCAAT 57.545 36.364 0.00 0.00 38.41 3.56
4269 5244 9.066892 TGGAAATTTGGCTACAATCTGATATAC 57.933 33.333 0.00 0.00 36.29 1.47
4321 5299 1.391485 CTGCCAGAAATCTTCACGACG 59.609 52.381 0.00 0.00 0.00 5.12
4418 5396 1.000938 GACAGCTTGGCAGTTTCCTTG 60.001 52.381 0.00 0.00 0.00 3.61
4576 5554 3.884037 ACCCAATCCCTCAATCATACC 57.116 47.619 0.00 0.00 0.00 2.73
4577 5555 3.130450 ACCCAATCCCTCAATCATACCA 58.870 45.455 0.00 0.00 0.00 3.25
4579 5557 4.202609 ACCCAATCCCTCAATCATACCATC 60.203 45.833 0.00 0.00 0.00 3.51
4581 5559 4.043812 CCAATCCCTCAATCATACCATCCT 59.956 45.833 0.00 0.00 0.00 3.24
4583 5561 5.937492 ATCCCTCAATCATACCATCCTTT 57.063 39.130 0.00 0.00 0.00 3.11
4586 5564 4.586001 CCCTCAATCATACCATCCTTTTGG 59.414 45.833 0.00 0.00 42.82 3.28
4587 5565 4.586001 CCTCAATCATACCATCCTTTTGGG 59.414 45.833 0.00 0.00 41.35 4.12
4588 5566 3.960102 TCAATCATACCATCCTTTTGGGC 59.040 43.478 0.00 0.00 41.35 5.36
4589 5567 3.962718 CAATCATACCATCCTTTTGGGCT 59.037 43.478 0.00 0.00 41.35 5.19
4590 5568 3.756082 TCATACCATCCTTTTGGGCTT 57.244 42.857 0.00 0.00 41.35 4.35
4591 5569 3.631250 TCATACCATCCTTTTGGGCTTC 58.369 45.455 0.00 0.00 41.35 3.86
4592 5570 3.011144 TCATACCATCCTTTTGGGCTTCA 59.989 43.478 0.00 0.00 41.35 3.02
4593 5571 2.629017 ACCATCCTTTTGGGCTTCAT 57.371 45.000 0.00 0.00 41.35 2.57
4594 5572 3.756082 ACCATCCTTTTGGGCTTCATA 57.244 42.857 0.00 0.00 41.35 2.15
4595 5573 3.635591 ACCATCCTTTTGGGCTTCATAG 58.364 45.455 0.00 0.00 41.35 2.23
4596 5574 3.011708 ACCATCCTTTTGGGCTTCATAGT 59.988 43.478 0.00 0.00 41.35 2.12
4597 5575 4.229582 ACCATCCTTTTGGGCTTCATAGTA 59.770 41.667 0.00 0.00 41.35 1.82
4598 5576 5.200483 CCATCCTTTTGGGCTTCATAGTAA 58.800 41.667 0.00 0.00 40.87 2.24
4599 5577 5.835280 CCATCCTTTTGGGCTTCATAGTAAT 59.165 40.000 0.00 0.00 40.87 1.89
4600 5578 7.004086 CCATCCTTTTGGGCTTCATAGTAATA 58.996 38.462 0.00 0.00 40.87 0.98
4601 5579 7.040409 CCATCCTTTTGGGCTTCATAGTAATAC 60.040 40.741 0.00 0.00 40.87 1.89
4602 5580 6.964464 TCCTTTTGGGCTTCATAGTAATACA 58.036 36.000 0.00 0.00 40.87 2.29
4603 5581 7.406916 TCCTTTTGGGCTTCATAGTAATACAA 58.593 34.615 0.00 0.00 40.87 2.41
4604 5582 7.338449 TCCTTTTGGGCTTCATAGTAATACAAC 59.662 37.037 0.00 0.00 40.87 3.32
4605 5583 6.671614 TTTGGGCTTCATAGTAATACAACG 57.328 37.500 0.00 0.00 0.00 4.10
4606 5584 5.601583 TGGGCTTCATAGTAATACAACGA 57.398 39.130 0.00 0.00 0.00 3.85
4607 5585 5.597806 TGGGCTTCATAGTAATACAACGAG 58.402 41.667 0.00 0.00 0.00 4.18
4608 5586 5.128171 TGGGCTTCATAGTAATACAACGAGT 59.872 40.000 0.00 0.00 0.00 4.18
4609 5587 6.321945 TGGGCTTCATAGTAATACAACGAGTA 59.678 38.462 0.00 0.00 37.06 2.59
4610 5588 6.640092 GGGCTTCATAGTAATACAACGAGTAC 59.360 42.308 0.00 0.00 35.05 2.73
4611 5589 6.640092 GGCTTCATAGTAATACAACGAGTACC 59.360 42.308 0.00 0.00 35.05 3.34
4612 5590 7.424001 GCTTCATAGTAATACAACGAGTACCT 58.576 38.462 0.00 0.00 35.05 3.08
4613 5591 8.562892 GCTTCATAGTAATACAACGAGTACCTA 58.437 37.037 0.00 0.00 35.05 3.08
4615 5593 9.618890 TTCATAGTAATACAACGAGTACCTAGT 57.381 33.333 0.00 0.00 35.05 2.57
4616 5594 9.618890 TCATAGTAATACAACGAGTACCTAGTT 57.381 33.333 0.00 0.00 35.05 2.24
4619 5597 7.766283 AGTAATACAACGAGTACCTAGTTTCC 58.234 38.462 0.00 0.00 35.05 3.13
4620 5598 6.594788 AATACAACGAGTACCTAGTTTCCA 57.405 37.500 0.00 0.00 35.05 3.53
4621 5599 4.942761 ACAACGAGTACCTAGTTTCCAA 57.057 40.909 0.00 0.00 27.43 3.53
4622 5600 5.280654 ACAACGAGTACCTAGTTTCCAAA 57.719 39.130 0.00 0.00 27.43 3.28
4623 5601 5.052481 ACAACGAGTACCTAGTTTCCAAAC 58.948 41.667 0.00 0.00 39.17 2.93
4624 5602 4.263018 ACGAGTACCTAGTTTCCAAACC 57.737 45.455 0.00 0.00 39.71 3.27
4625 5603 3.007290 ACGAGTACCTAGTTTCCAAACCC 59.993 47.826 0.00 0.00 39.71 4.11
4626 5604 3.007182 CGAGTACCTAGTTTCCAAACCCA 59.993 47.826 0.00 0.00 39.71 4.51
4627 5605 4.503643 CGAGTACCTAGTTTCCAAACCCAA 60.504 45.833 0.00 0.00 39.71 4.12
4628 5606 5.567430 GAGTACCTAGTTTCCAAACCCAAT 58.433 41.667 0.00 0.00 39.71 3.16
4629 5607 5.567430 AGTACCTAGTTTCCAAACCCAATC 58.433 41.667 0.00 0.00 39.71 2.67
4630 5608 3.774734 ACCTAGTTTCCAAACCCAATCC 58.225 45.455 0.00 0.00 39.71 3.01
4631 5609 3.096852 CCTAGTTTCCAAACCCAATCCC 58.903 50.000 0.00 0.00 39.71 3.85
4632 5610 3.245622 CCTAGTTTCCAAACCCAATCCCT 60.246 47.826 0.00 0.00 39.71 4.20
4633 5611 2.889512 AGTTTCCAAACCCAATCCCTC 58.110 47.619 0.00 0.00 39.71 4.30
4634 5612 2.178984 AGTTTCCAAACCCAATCCCTCA 59.821 45.455 0.00 0.00 39.71 3.86
4635 5613 2.969262 GTTTCCAAACCCAATCCCTCAA 59.031 45.455 0.00 0.00 32.82 3.02
4636 5614 3.558608 TTCCAAACCCAATCCCTCAAT 57.441 42.857 0.00 0.00 0.00 2.57
4637 5615 3.100207 TCCAAACCCAATCCCTCAATC 57.900 47.619 0.00 0.00 0.00 2.67
4638 5616 2.381618 TCCAAACCCAATCCCTCAATCA 59.618 45.455 0.00 0.00 0.00 2.57
4639 5617 3.012730 TCCAAACCCAATCCCTCAATCAT 59.987 43.478 0.00 0.00 0.00 2.45
4640 5618 4.231658 TCCAAACCCAATCCCTCAATCATA 59.768 41.667 0.00 0.00 0.00 2.15
4641 5619 4.342092 CCAAACCCAATCCCTCAATCATAC 59.658 45.833 0.00 0.00 0.00 2.39
4642 5620 4.879295 AACCCAATCCCTCAATCATACA 57.121 40.909 0.00 0.00 0.00 2.29
4643 5621 4.879295 ACCCAATCCCTCAATCATACAA 57.121 40.909 0.00 0.00 0.00 2.41
4644 5622 5.408079 ACCCAATCCCTCAATCATACAAT 57.592 39.130 0.00 0.00 0.00 2.71
4698 5676 5.608449 ACCTAGTTTTTCACTCTGTACCAC 58.392 41.667 0.00 0.00 36.88 4.16
4749 5727 5.468658 GGGCCTATCCATATACAGGTAGAT 58.531 45.833 0.84 0.00 36.21 1.98
4774 5752 5.999205 TCGTATTTGGGAAAGTGGTAGTA 57.001 39.130 0.00 0.00 0.00 1.82
4776 5754 4.563976 CGTATTTGGGAAAGTGGTAGTACG 59.436 45.833 0.00 0.00 0.00 3.67
4863 5842 4.223700 ACCAGACATCAGCATTGAAGACTA 59.776 41.667 0.00 0.00 36.78 2.59
4888 5868 4.464597 ACCTTTTCAACTTAAACTGTGCCA 59.535 37.500 0.00 0.00 0.00 4.92
4894 5874 1.888512 ACTTAAACTGTGCCAGGCATG 59.111 47.619 19.75 16.19 41.91 4.06
4912 5892 6.857964 CAGGCATGTAGAGTAAAAGTTTTGTG 59.142 38.462 11.18 0.00 0.00 3.33
5243 6223 8.635765 TTATTCATATTACAGGAAAGGGCATC 57.364 34.615 0.00 0.00 29.32 3.91
5585 6565 8.712228 AAGAAATAGATGAAGGAAAGGTTGTT 57.288 30.769 0.00 0.00 0.00 2.83
5663 6643 2.924290 GTTGCTAGTACAAAGAGCTCCG 59.076 50.000 10.93 1.56 37.12 4.63
5774 6754 0.976641 TCTTGCCATCGAGTCAACCT 59.023 50.000 0.00 0.00 0.00 3.50
5841 6821 5.105997 GCCTGACATATTTTCTGCTTCTTGT 60.106 40.000 0.00 0.00 0.00 3.16
5919 6899 5.936372 TGAGTTCAAGTGATCCATTCAAGAG 59.064 40.000 0.00 0.00 35.70 2.85
6058 7038 8.466798 GTGTGTCACCTAAAATGGCTATAAAAT 58.533 33.333 0.00 0.00 0.00 1.82
6065 7045 8.755028 ACCTAAAATGGCTATAAAATTTTCCGT 58.245 29.630 6.72 1.00 35.64 4.69
6103 7083 5.817816 GGAATCCTGGTAGTAATCACACAAG 59.182 44.000 0.00 0.00 0.00 3.16
6300 7280 5.252547 TGCTTATGTTGCATTCAGTAAGGA 58.747 37.500 0.00 0.65 35.31 3.36
6301 7281 5.887598 TGCTTATGTTGCATTCAGTAAGGAT 59.112 36.000 0.00 0.00 35.31 3.24
6302 7282 6.038603 TGCTTATGTTGCATTCAGTAAGGATC 59.961 38.462 0.00 0.00 35.31 3.36
6349 7329 3.871594 GCATAACCTGTGTATGGAGTGTC 59.128 47.826 0.00 0.00 0.00 3.67
6358 7338 0.102300 TATGGAGTGTCGGCGTGATG 59.898 55.000 6.85 0.00 0.00 3.07
6368 7349 3.498777 TGTCGGCGTGATGAATTAAAACA 59.501 39.130 6.85 0.00 0.00 2.83
6388 7369 8.491331 AAAACAACTTTGATTGTGCATAAAGT 57.509 26.923 0.00 5.28 42.01 2.66
6506 7487 0.761702 GGGATGCCCTTACCGGTAGA 60.762 60.000 15.20 5.43 41.34 2.59
6508 7489 1.070289 GGATGCCCTTACCGGTAGAAG 59.930 57.143 15.20 12.20 0.00 2.85
6589 7570 9.103048 CACACTTGCTAAAATAGTCGTAAAAAG 57.897 33.333 0.00 0.00 0.00 2.27
6592 7573 9.048446 ACTTGCTAAAATAGTCGTAAAAAGTGA 57.952 29.630 0.00 0.00 0.00 3.41
6600 7581 5.479716 AGTCGTAAAAAGTGAACAGTTGG 57.520 39.130 0.00 0.00 0.00 3.77
6628 7609 4.931601 GCTTATCTTCAAAAGCAAAAGGGG 59.068 41.667 2.35 0.00 45.89 4.79
6629 7610 5.279456 GCTTATCTTCAAAAGCAAAAGGGGA 60.279 40.000 2.35 0.00 45.89 4.81
6630 7611 4.879197 ATCTTCAAAAGCAAAAGGGGAG 57.121 40.909 0.00 0.00 0.00 4.30
6631 7612 3.642141 TCTTCAAAAGCAAAAGGGGAGT 58.358 40.909 0.00 0.00 0.00 3.85
6632 7613 4.798882 TCTTCAAAAGCAAAAGGGGAGTA 58.201 39.130 0.00 0.00 0.00 2.59
6633 7614 5.205056 TCTTCAAAAGCAAAAGGGGAGTAA 58.795 37.500 0.00 0.00 0.00 2.24
6634 7615 5.301805 TCTTCAAAAGCAAAAGGGGAGTAAG 59.698 40.000 0.00 0.00 0.00 2.34
6635 7616 4.798882 TCAAAAGCAAAAGGGGAGTAAGA 58.201 39.130 0.00 0.00 0.00 2.10
6636 7617 5.393866 TCAAAAGCAAAAGGGGAGTAAGAT 58.606 37.500 0.00 0.00 0.00 2.40
6637 7618 5.838521 TCAAAAGCAAAAGGGGAGTAAGATT 59.161 36.000 0.00 0.00 0.00 2.40
6638 7619 7.007723 TCAAAAGCAAAAGGGGAGTAAGATTA 58.992 34.615 0.00 0.00 0.00 1.75
6639 7620 7.176690 TCAAAAGCAAAAGGGGAGTAAGATTAG 59.823 37.037 0.00 0.00 0.00 1.73
6722 7707 3.489355 TGTTCAGCAGGTTGATGACAAT 58.511 40.909 0.00 0.00 43.03 2.71
6769 7754 1.632422 CGCCAATCTTTTGATGTGGC 58.368 50.000 15.49 15.49 46.90 5.01
6876 7861 3.429410 GCTAATGCCCAGGAAACAATGTC 60.429 47.826 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.683069 GAAACTCCAAATATTTATGAATCGCAT 57.317 29.630 0.00 0.00 41.08 4.73
23 24 8.902806 AGAAACTCCAAATATTTATGAATCGCA 58.097 29.630 0.00 0.00 0.00 5.10
24 25 9.736023 AAGAAACTCCAAATATTTATGAATCGC 57.264 29.630 0.00 0.00 0.00 4.58
53 54 9.635404 TTTAGAAACGGATGGGATAACAATTAT 57.365 29.630 0.00 0.00 0.00 1.28
54 55 9.635404 ATTTAGAAACGGATGGGATAACAATTA 57.365 29.630 0.00 0.00 0.00 1.40
55 56 7.948034 TTTAGAAACGGATGGGATAACAATT 57.052 32.000 0.00 0.00 0.00 2.32
56 57 9.063615 GTATTTAGAAACGGATGGGATAACAAT 57.936 33.333 0.00 0.00 0.00 2.71
57 58 8.269317 AGTATTTAGAAACGGATGGGATAACAA 58.731 33.333 0.00 0.00 0.00 2.83
58 59 7.798071 AGTATTTAGAAACGGATGGGATAACA 58.202 34.615 0.00 0.00 0.00 2.41
59 60 8.557029 CAAGTATTTAGAAACGGATGGGATAAC 58.443 37.037 0.00 0.00 0.00 1.89
60 61 8.269317 ACAAGTATTTAGAAACGGATGGGATAA 58.731 33.333 0.00 0.00 0.00 1.75
61 62 7.798071 ACAAGTATTTAGAAACGGATGGGATA 58.202 34.615 0.00 0.00 0.00 2.59
62 63 6.659824 ACAAGTATTTAGAAACGGATGGGAT 58.340 36.000 0.00 0.00 0.00 3.85
63 64 6.057321 ACAAGTATTTAGAAACGGATGGGA 57.943 37.500 0.00 0.00 0.00 4.37
64 65 6.113411 AGACAAGTATTTAGAAACGGATGGG 58.887 40.000 0.00 0.00 0.00 4.00
65 66 7.611213 AAGACAAGTATTTAGAAACGGATGG 57.389 36.000 0.00 0.00 0.00 3.51
66 67 8.936864 AGAAAGACAAGTATTTAGAAACGGATG 58.063 33.333 0.00 0.00 0.00 3.51
68 69 9.985730 TTAGAAAGACAAGTATTTAGAAACGGA 57.014 29.630 0.00 0.00 0.00 4.69
83 84 9.787532 CACTTGTTGAAATCTTTAGAAAGACAA 57.212 29.630 6.85 4.98 46.80 3.18
84 85 9.173021 TCACTTGTTGAAATCTTTAGAAAGACA 57.827 29.630 6.85 0.00 46.80 3.41
85 86 9.439537 GTCACTTGTTGAAATCTTTAGAAAGAC 57.560 33.333 6.85 0.00 40.95 3.01
86 87 9.396022 AGTCACTTGTTGAAATCTTTAGAAAGA 57.604 29.630 7.15 7.15 41.72 2.52
89 90 9.607988 TGTAGTCACTTGTTGAAATCTTTAGAA 57.392 29.630 0.00 0.00 35.39 2.10
90 91 9.778741 ATGTAGTCACTTGTTGAAATCTTTAGA 57.221 29.630 0.00 0.00 35.39 2.10
94 95 9.725019 TCATATGTAGTCACTTGTTGAAATCTT 57.275 29.630 1.90 0.00 35.39 2.40
95 96 9.725019 TTCATATGTAGTCACTTGTTGAAATCT 57.275 29.630 1.90 0.00 35.39 2.40
98 99 9.114952 TGTTTCATATGTAGTCACTTGTTGAAA 57.885 29.630 1.90 0.00 35.39 2.69
99 100 8.669946 TGTTTCATATGTAGTCACTTGTTGAA 57.330 30.769 1.90 0.00 35.39 2.69
100 101 8.669946 TTGTTTCATATGTAGTCACTTGTTGA 57.330 30.769 1.90 0.00 0.00 3.18
101 102 9.729023 TTTTGTTTCATATGTAGTCACTTGTTG 57.271 29.630 1.90 0.00 0.00 3.33
103 104 9.897744 CATTTTGTTTCATATGTAGTCACTTGT 57.102 29.630 1.90 0.00 0.00 3.16
118 119 9.897744 GAGTGTAGATTCAATCATTTTGTTTCA 57.102 29.630 0.00 0.00 33.45 2.69
187 188 9.729281 TCGTAAATATTTGTCCTTTTAGAGGTT 57.271 29.630 11.05 0.00 46.39 3.50
188 189 9.729281 TTCGTAAATATTTGTCCTTTTAGAGGT 57.271 29.630 11.05 0.00 46.39 3.85
194 195 8.466798 CCTCCATTCGTAAATATTTGTCCTTTT 58.533 33.333 11.05 0.00 0.00 2.27
195 196 7.068226 CCCTCCATTCGTAAATATTTGTCCTTT 59.932 37.037 11.05 0.00 0.00 3.11
196 197 6.546034 CCCTCCATTCGTAAATATTTGTCCTT 59.454 38.462 11.05 0.00 0.00 3.36
197 198 6.062095 CCCTCCATTCGTAAATATTTGTCCT 58.938 40.000 11.05 0.00 0.00 3.85
198 199 5.826208 ACCCTCCATTCGTAAATATTTGTCC 59.174 40.000 11.05 0.00 0.00 4.02
199 200 6.937436 ACCCTCCATTCGTAAATATTTGTC 57.063 37.500 11.05 3.49 0.00 3.18
200 201 7.614192 AGAAACCCTCCATTCGTAAATATTTGT 59.386 33.333 11.05 0.00 0.00 2.83
201 202 7.996385 AGAAACCCTCCATTCGTAAATATTTG 58.004 34.615 11.05 0.00 0.00 2.32
202 203 9.862149 ATAGAAACCCTCCATTCGTAAATATTT 57.138 29.630 5.89 5.89 0.00 1.40
203 204 9.503399 GATAGAAACCCTCCATTCGTAAATATT 57.497 33.333 0.00 0.00 0.00 1.28
204 205 7.817962 CGATAGAAACCCTCCATTCGTAAATAT 59.182 37.037 0.00 0.00 39.76 1.28
205 206 7.014518 TCGATAGAAACCCTCCATTCGTAAATA 59.985 37.037 0.00 0.00 46.15 1.40
206 207 5.989777 CGATAGAAACCCTCCATTCGTAAAT 59.010 40.000 0.00 0.00 39.76 1.40
207 208 5.127519 TCGATAGAAACCCTCCATTCGTAAA 59.872 40.000 0.00 0.00 46.15 2.01
208 209 4.646040 TCGATAGAAACCCTCCATTCGTAA 59.354 41.667 0.00 0.00 46.15 3.18
209 210 4.209538 TCGATAGAAACCCTCCATTCGTA 58.790 43.478 0.00 0.00 46.15 3.43
210 211 3.028850 TCGATAGAAACCCTCCATTCGT 58.971 45.455 0.00 0.00 46.15 3.85
211 212 3.728076 TCGATAGAAACCCTCCATTCG 57.272 47.619 0.00 0.00 46.15 3.34
232 233 1.134280 AGATCAGTGCAGCACCCATAC 60.134 52.381 22.41 10.11 34.49 2.39
314 315 6.092122 GCTACATCTGTGTTAATGTTGCACTA 59.908 38.462 14.10 0.00 46.69 2.74
412 464 1.742880 CCGTGTCAGATGTGGCAGG 60.743 63.158 9.96 9.96 39.58 4.85
442 509 0.451383 CGTTGGCCACCATGTATGTG 59.549 55.000 3.88 0.00 31.53 3.21
523 590 5.288543 AGATGTTCAGATGAAAACTTCGC 57.711 39.130 0.00 0.00 35.71 4.70
529 596 3.123453 CACGCGAGATGTTCAGATGAAAA 59.877 43.478 15.93 0.00 35.58 2.29
553 620 0.243636 GGCAAACCCCGTGATGAAAG 59.756 55.000 0.00 0.00 0.00 2.62
591 659 1.447314 CCCGTGGCCGAGTTTACTC 60.447 63.158 0.00 0.00 39.55 2.59
592 660 2.660802 CCCGTGGCCGAGTTTACT 59.339 61.111 0.00 0.00 35.63 2.24
593 661 2.435410 CCCCGTGGCCGAGTTTAC 60.435 66.667 0.00 0.00 35.63 2.01
919 1224 1.876664 GCTTTGGCCTTCGGTCTTC 59.123 57.895 3.32 0.00 0.00 2.87
920 1225 1.966451 CGCTTTGGCCTTCGGTCTT 60.966 57.895 3.32 0.00 34.44 3.01
921 1226 2.358737 CGCTTTGGCCTTCGGTCT 60.359 61.111 3.32 0.00 34.44 3.85
922 1227 4.103103 GCGCTTTGGCCTTCGGTC 62.103 66.667 3.32 0.00 34.44 4.79
923 1228 4.643387 AGCGCTTTGGCCTTCGGT 62.643 61.111 2.64 4.81 34.44 4.69
924 1229 3.804193 GAGCGCTTTGGCCTTCGG 61.804 66.667 13.26 0.00 34.44 4.30
925 1230 4.152625 CGAGCGCTTTGGCCTTCG 62.153 66.667 13.26 3.78 35.59 3.79
926 1231 4.467062 GCGAGCGCTTTGGCCTTC 62.467 66.667 13.26 0.00 38.26 3.46
1365 1695 0.453615 CACTCGAGACAGAGACGCAC 60.454 60.000 21.68 0.00 40.57 5.34
1524 1862 2.098934 GTGTGACAAACATTGGCTGTGA 59.901 45.455 0.00 0.00 41.97 3.58
1626 1964 9.485591 CGATACATTAATTTTTAGCTGTTTCGT 57.514 29.630 0.00 0.00 35.13 3.85
1651 1989 3.192844 ACAGGGTACTAACTGTGATGTCG 59.807 47.826 14.52 0.00 45.54 4.35
1661 1999 5.310451 TCATGGTTTGAACAGGGTACTAAC 58.690 41.667 0.00 0.00 0.00 2.34
1833 2334 4.009675 GGAATCATGAAGTGCCAAGTACA 58.990 43.478 0.00 0.00 0.00 2.90
1869 2370 6.017357 GGACCGAATCAATAAGGGACAAATAC 60.017 42.308 0.00 0.00 0.00 1.89
1876 2377 3.135895 GGAAGGACCGAATCAATAAGGGA 59.864 47.826 0.00 0.00 0.00 4.20
2000 2517 8.616076 CATGTATAAGGAACATCAAAAGGAGAC 58.384 37.037 0.00 0.00 35.39 3.36
2090 2609 1.376037 GTCCCAAAGGTGAGCCTCG 60.376 63.158 0.00 0.00 46.33 4.63
2286 2805 9.373603 GATGAATGATTGAGGATTAGAGATCTG 57.626 37.037 0.00 0.00 0.00 2.90
2289 2808 9.893634 GATGATGAATGATTGAGGATTAGAGAT 57.106 33.333 0.00 0.00 0.00 2.75
2445 2964 0.810648 ACACCCAGTAAATGCATGCG 59.189 50.000 14.09 0.00 0.00 4.73
2666 3185 4.757149 GCTCCTTACCCAAATATACTGCAG 59.243 45.833 13.48 13.48 0.00 4.41
2883 3403 3.370840 AAACAAGAGCTGGATGGCATA 57.629 42.857 0.00 0.00 34.17 3.14
2885 3405 1.888512 GAAAACAAGAGCTGGATGGCA 59.111 47.619 0.00 0.00 34.17 4.92
2891 3411 4.928615 CAGAGACTAGAAAACAAGAGCTGG 59.071 45.833 0.00 0.00 0.00 4.85
3077 4034 7.810282 ACATCTAGAATGTCAAGCGTATATCAC 59.190 37.037 0.00 0.00 0.00 3.06
3104 4061 8.744652 TGACCAAGTTTTTGAAGAGAAACATTA 58.255 29.630 0.00 0.00 38.03 1.90
3164 4121 6.149973 CCCTCCATTACATAATGTAGTGCATG 59.850 42.308 10.06 0.00 38.67 4.06
3201 4158 8.585018 ACTAAACCATGATCTTGTTAAAAAGGG 58.415 33.333 5.54 1.36 0.00 3.95
3211 4169 5.740569 CGCATTCAACTAAACCATGATCTTG 59.259 40.000 0.00 1.60 0.00 3.02
3260 4218 6.321181 ACACAAAGTATCAGTTTCAACATGGT 59.679 34.615 0.00 0.00 0.00 3.55
3266 4224 7.561021 TTAGCACACAAAGTATCAGTTTCAA 57.439 32.000 0.00 0.00 0.00 2.69
3432 4390 9.167311 ACTGAGGTAACATGTATCTCAAATTTC 57.833 33.333 19.39 2.82 41.41 2.17
3524 4482 4.365899 AAACAGTTTTGAGTTTCGTCCC 57.634 40.909 0.00 0.00 32.90 4.46
3665 4640 8.748582 GTGTTATTTGTTTTAGGTTACAGTTGC 58.251 33.333 0.00 0.00 0.00 4.17
3669 4644 7.863666 TCGGTGTTATTTGTTTTAGGTTACAG 58.136 34.615 0.00 0.00 0.00 2.74
3731 4706 9.504708 ACATGGAATTGAAAATAATGAAGCAAA 57.495 25.926 0.00 0.00 0.00 3.68
3945 4920 4.951715 TGCATCTTCCAGTCATTGCTTAAT 59.048 37.500 0.00 0.00 0.00 1.40
4207 5182 4.591202 CGTGGCAGAAATATTTGTAGCAG 58.409 43.478 5.17 1.52 0.00 4.24
4233 5208 5.574970 AGCCAAATTTCCAACCCATTAAA 57.425 34.783 0.00 0.00 0.00 1.52
4273 5251 8.747538 AAACACAAAGTAACAGAGAAGGTTAT 57.252 30.769 0.00 0.00 33.68 1.89
4281 5259 5.743872 GGCAGAAAAACACAAAGTAACAGAG 59.256 40.000 0.00 0.00 0.00 3.35
4288 5266 4.799564 TTCTGGCAGAAAAACACAAAGT 57.200 36.364 26.78 0.00 29.99 2.66
4576 5554 6.966534 ATTACTATGAAGCCCAAAAGGATG 57.033 37.500 0.00 0.00 38.24 3.51
4577 5555 7.582719 TGTATTACTATGAAGCCCAAAAGGAT 58.417 34.615 0.00 0.00 38.24 3.24
4579 5557 7.480810 GTTGTATTACTATGAAGCCCAAAAGG 58.519 38.462 0.00 0.00 39.47 3.11
4581 5559 6.879993 TCGTTGTATTACTATGAAGCCCAAAA 59.120 34.615 0.00 0.00 0.00 2.44
4583 5561 5.979993 TCGTTGTATTACTATGAAGCCCAA 58.020 37.500 0.00 0.00 0.00 4.12
4586 5564 6.640092 GGTACTCGTTGTATTACTATGAAGCC 59.360 42.308 0.00 2.20 33.23 4.35
4587 5565 7.424001 AGGTACTCGTTGTATTACTATGAAGC 58.576 38.462 0.00 0.00 33.23 3.86
4589 5567 9.618890 ACTAGGTACTCGTTGTATTACTATGAA 57.381 33.333 0.00 0.00 41.75 2.57
4590 5568 9.618890 AACTAGGTACTCGTTGTATTACTATGA 57.381 33.333 0.00 0.00 42.86 2.15
4593 5571 8.893727 GGAAACTAGGTACTCGTTGTATTACTA 58.106 37.037 0.00 0.00 43.71 1.82
4594 5572 7.394359 TGGAAACTAGGTACTCGTTGTATTACT 59.606 37.037 0.00 0.00 43.71 2.24
4595 5573 7.538575 TGGAAACTAGGTACTCGTTGTATTAC 58.461 38.462 0.00 0.00 43.71 1.89
4596 5574 7.701539 TGGAAACTAGGTACTCGTTGTATTA 57.298 36.000 0.00 0.00 43.71 0.98
4597 5575 6.594788 TGGAAACTAGGTACTCGTTGTATT 57.405 37.500 0.00 0.00 43.71 1.89
4598 5576 6.594788 TTGGAAACTAGGTACTCGTTGTAT 57.405 37.500 0.00 0.00 43.71 2.29
4599 5577 6.215845 GTTTGGAAACTAGGTACTCGTTGTA 58.784 40.000 0.00 0.00 43.71 2.41
4600 5578 4.942761 TTGGAAACTAGGTACTCGTTGT 57.057 40.909 0.00 0.00 43.71 3.32
4601 5579 4.450080 GGTTTGGAAACTAGGTACTCGTTG 59.550 45.833 2.44 0.00 43.71 4.10
4602 5580 4.503817 GGGTTTGGAAACTAGGTACTCGTT 60.504 45.833 2.44 0.00 46.52 3.85
4603 5581 3.007290 GGGTTTGGAAACTAGGTACTCGT 59.993 47.826 2.44 0.00 38.89 4.18
4604 5582 3.007182 TGGGTTTGGAAACTAGGTACTCG 59.993 47.826 2.44 0.00 38.89 4.18
4605 5583 4.628963 TGGGTTTGGAAACTAGGTACTC 57.371 45.455 2.44 0.00 38.89 2.59
4606 5584 5.516062 GGATTGGGTTTGGAAACTAGGTACT 60.516 44.000 2.44 0.00 38.89 2.73
4607 5585 4.703575 GGATTGGGTTTGGAAACTAGGTAC 59.296 45.833 2.44 0.00 38.89 3.34
4608 5586 4.264038 GGGATTGGGTTTGGAAACTAGGTA 60.264 45.833 2.44 0.00 38.89 3.08
4609 5587 3.501568 GGGATTGGGTTTGGAAACTAGGT 60.502 47.826 2.44 0.00 38.89 3.08
4610 5588 3.096852 GGGATTGGGTTTGGAAACTAGG 58.903 50.000 2.44 0.00 38.89 3.02
4611 5589 4.017126 GAGGGATTGGGTTTGGAAACTAG 58.983 47.826 2.44 0.00 38.89 2.57
4612 5590 3.399644 TGAGGGATTGGGTTTGGAAACTA 59.600 43.478 2.44 0.00 38.89 2.24
4613 5591 2.178984 TGAGGGATTGGGTTTGGAAACT 59.821 45.455 2.44 0.00 38.89 2.66
4614 5592 2.604139 TGAGGGATTGGGTTTGGAAAC 58.396 47.619 0.00 0.00 38.17 2.78
4615 5593 3.336509 TTGAGGGATTGGGTTTGGAAA 57.663 42.857 0.00 0.00 0.00 3.13
4616 5594 3.181413 TGATTGAGGGATTGGGTTTGGAA 60.181 43.478 0.00 0.00 0.00 3.53
4617 5595 2.381618 TGATTGAGGGATTGGGTTTGGA 59.618 45.455 0.00 0.00 0.00 3.53
4618 5596 2.818921 TGATTGAGGGATTGGGTTTGG 58.181 47.619 0.00 0.00 0.00 3.28
4619 5597 4.955450 TGTATGATTGAGGGATTGGGTTTG 59.045 41.667 0.00 0.00 0.00 2.93
4620 5598 5.205517 TGTATGATTGAGGGATTGGGTTT 57.794 39.130 0.00 0.00 0.00 3.27
4621 5599 4.879295 TGTATGATTGAGGGATTGGGTT 57.121 40.909 0.00 0.00 0.00 4.11
4622 5600 4.879295 TTGTATGATTGAGGGATTGGGT 57.121 40.909 0.00 0.00 0.00 4.51
4623 5601 4.768968 GGATTGTATGATTGAGGGATTGGG 59.231 45.833 0.00 0.00 0.00 4.12
4624 5602 5.638133 AGGATTGTATGATTGAGGGATTGG 58.362 41.667 0.00 0.00 0.00 3.16
4625 5603 7.592885 AAAGGATTGTATGATTGAGGGATTG 57.407 36.000 0.00 0.00 0.00 2.67
4626 5604 7.070322 CCAAAAGGATTGTATGATTGAGGGATT 59.930 37.037 0.00 0.00 0.00 3.01
4627 5605 6.552350 CCAAAAGGATTGTATGATTGAGGGAT 59.448 38.462 0.00 0.00 0.00 3.85
4628 5606 5.893255 CCAAAAGGATTGTATGATTGAGGGA 59.107 40.000 0.00 0.00 0.00 4.20
4629 5607 5.069516 CCCAAAAGGATTGTATGATTGAGGG 59.930 44.000 0.00 0.00 38.24 4.30
4630 5608 5.452356 GCCCAAAAGGATTGTATGATTGAGG 60.452 44.000 0.00 0.00 38.24 3.86
4631 5609 5.361857 AGCCCAAAAGGATTGTATGATTGAG 59.638 40.000 0.00 0.00 38.24 3.02
4632 5610 5.271598 AGCCCAAAAGGATTGTATGATTGA 58.728 37.500 0.00 0.00 38.24 2.57
4633 5611 5.603170 AGCCCAAAAGGATTGTATGATTG 57.397 39.130 0.00 0.00 38.24 2.67
4634 5612 5.721000 TGAAGCCCAAAAGGATTGTATGATT 59.279 36.000 0.00 0.00 46.92 2.57
4635 5613 5.271598 TGAAGCCCAAAAGGATTGTATGAT 58.728 37.500 0.00 0.00 46.92 2.45
4636 5614 4.671831 TGAAGCCCAAAAGGATTGTATGA 58.328 39.130 0.00 0.00 46.92 2.15
4637 5615 5.603170 ATGAAGCCCAAAAGGATTGTATG 57.397 39.130 0.00 0.00 46.92 2.39
4638 5616 6.435164 ACTATGAAGCCCAAAAGGATTGTAT 58.565 36.000 0.00 0.00 46.92 2.29
4639 5617 5.826643 ACTATGAAGCCCAAAAGGATTGTA 58.173 37.500 0.00 0.00 46.92 2.41
4640 5618 4.677182 ACTATGAAGCCCAAAAGGATTGT 58.323 39.130 0.00 0.00 46.92 2.71
4641 5619 6.773976 TTACTATGAAGCCCAAAAGGATTG 57.226 37.500 0.00 0.00 46.92 2.67
4643 5621 7.582719 TGTATTACTATGAAGCCCAAAAGGAT 58.417 34.615 0.00 0.00 38.24 3.24
4644 5622 6.964464 TGTATTACTATGAAGCCCAAAAGGA 58.036 36.000 0.00 0.00 38.24 3.36
4698 5676 2.670479 CCAATGATCAGATCCGACTCG 58.330 52.381 8.00 0.00 0.00 4.18
4749 5727 6.949715 ACTACCACTTTCCCAAATACGAATA 58.050 36.000 0.00 0.00 0.00 1.75
4762 5740 7.709613 ACCAATTGATATCGTACTACCACTTTC 59.290 37.037 7.12 0.00 0.00 2.62
4774 5752 7.552687 ACATTACTTGTCACCAATTGATATCGT 59.447 33.333 7.12 0.00 36.32 3.73
4816 5795 9.832445 GGTCAATATTTCAGACTAATGGAACTA 57.168 33.333 4.86 0.00 32.98 2.24
4863 5842 6.322712 TGGCACAGTTTAAGTTGAAAAGGTAT 59.677 34.615 0.00 0.00 0.00 2.73
4888 5868 6.770785 TCACAAAACTTTTACTCTACATGCCT 59.229 34.615 0.00 0.00 0.00 4.75
4894 5874 8.827677 ACACATCTCACAAAACTTTTACTCTAC 58.172 33.333 0.00 0.00 0.00 2.59
4988 5968 2.669364 AGTGACGGTTTATGTCGTGAC 58.331 47.619 0.00 0.00 42.17 3.67
5038 6018 4.758674 AGCTGCCTGCATAACATAAGTATG 59.241 41.667 0.00 0.00 45.94 2.39
5049 6029 3.415212 GAATTATGGAGCTGCCTGCATA 58.585 45.455 1.53 2.82 46.66 3.14
5223 6203 3.189287 GCGATGCCCTTTCCTGTAATATG 59.811 47.826 0.00 0.00 0.00 1.78
5243 6223 1.994779 GCAAATTTTCCATCCAGTGCG 59.005 47.619 0.00 0.00 0.00 5.34
5412 6392 3.556004 CCAAGAGTAGGCAGCTTATAGGC 60.556 52.174 0.00 0.00 0.00 3.93
5427 6407 2.593956 GGGAACCGAGGCCAAGAGT 61.594 63.158 5.01 0.00 40.86 3.24
5663 6643 2.500392 TAACAGGGGCCAATGTGTAC 57.500 50.000 13.65 0.00 0.00 2.90
5841 6821 5.072055 TGGTCAGATTCAGCATTTCAGAAA 58.928 37.500 0.00 0.00 0.00 2.52
5919 6899 3.838244 TGGTATGTTCATACTCCTGGC 57.162 47.619 18.37 5.66 0.00 4.85
6065 7045 4.104738 CCAGGATTCCTTAAGCTTCCCATA 59.895 45.833 0.00 0.00 0.00 2.74
6066 7046 3.117360 CCAGGATTCCTTAAGCTTCCCAT 60.117 47.826 0.00 0.00 0.00 4.00
6103 7083 6.569179 TTCTTGGGCAACTAATTCTTACAC 57.431 37.500 0.00 0.00 36.01 2.90
6163 7143 5.934625 TCTTGTTTTTAAAAAGCTTGCACCA 59.065 32.000 13.58 3.33 0.00 4.17
6196 7176 5.545063 TCTATGGAGTGTCTTGTTGTCAA 57.455 39.130 0.00 0.00 0.00 3.18
6349 7329 4.472286 AGTTGTTTTAATTCATCACGCCG 58.528 39.130 0.00 0.00 0.00 6.46
6388 7369 7.043325 GCACACACACGTTTTTAATAATGGAAA 60.043 33.333 3.40 0.00 0.00 3.13
6399 7380 0.238817 ACACGCACACACACGTTTTT 59.761 45.000 0.00 0.00 41.32 1.94
6506 7487 6.263168 GCATATACCTAACTGGCATCAAACTT 59.737 38.462 0.00 0.00 40.22 2.66
6508 7489 5.765182 AGCATATACCTAACTGGCATCAAAC 59.235 40.000 0.00 0.00 40.22 2.93
6562 7543 7.718272 TTTACGACTATTTTAGCAAGTGTGT 57.282 32.000 0.00 0.00 0.00 3.72
6589 7570 5.725362 AGATAAGCTACTCCAACTGTTCAC 58.275 41.667 0.00 0.00 0.00 3.18
6592 7573 6.360370 TGAAGATAAGCTACTCCAACTGTT 57.640 37.500 0.00 0.00 0.00 3.16
6600 7581 7.752686 CCTTTTGCTTTTGAAGATAAGCTACTC 59.247 37.037 8.13 0.00 45.37 2.59
6625 7606 7.240167 ACTAGGATACACTAATCTTACTCCCC 58.760 42.308 0.00 0.00 41.41 4.81
6626 7607 8.709272 AACTAGGATACACTAATCTTACTCCC 57.291 38.462 0.00 0.00 41.41 4.30
6769 7754 7.833525 ATACAAAGAGTATTGCTCACAAGCCG 61.834 42.308 4.53 0.00 46.47 5.52
6876 7861 2.656560 ACAGACGGCTTTACAGCTAG 57.343 50.000 0.07 0.00 46.44 3.42


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

AutoCloner maintained by Alex Coulton.