Multiple sequence alignment - TraesCS7B01G373300

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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 TraesCS7B01G373300 chr7B 100.000 7134 0 0 1 7134 639082425 639089558 0.000000e+00 13175.0
1 TraesCS7B01G373300 chr7B 78.856 1504 244 43 5623 7075 704155174 704153694 0.000000e+00 948.0
2 TraesCS7B01G373300 chr7B 78.800 1500 246 40 5623 7075 704090328 704088854 0.000000e+00 942.0
3 TraesCS7B01G373300 chr7B 80.333 1022 104 45 3373 4329 704092688 704091699 0.000000e+00 684.0
4 TraesCS7B01G373300 chr7B 80.234 1027 103 48 3371 4329 704157531 704156537 0.000000e+00 680.0
5 TraesCS7B01G373300 chr7B 84.389 679 83 15 4809 5468 704090989 704090315 0.000000e+00 645.0
6 TraesCS7B01G373300 chr7B 82.941 680 85 21 4809 5468 704155829 704155161 1.030000e-162 584.0
7 TraesCS7B01G373300 chr7B 82.000 400 42 12 4340 4726 704156362 704155980 5.370000e-81 313.0
8 TraesCS7B01G373300 chr7B 83.143 350 42 11 4389 4726 704091484 704091140 3.230000e-78 303.0
9 TraesCS7B01G373300 chr7B 77.617 277 39 15 2937 3193 704093194 704092921 5.770000e-31 147.0
10 TraesCS7B01G373300 chr7D 91.447 4431 247 60 4 4331 576332265 576336666 0.000000e+00 5962.0
11 TraesCS7B01G373300 chr7D 94.375 1529 75 5 5616 7134 576337850 576339377 0.000000e+00 2337.0
12 TraesCS7B01G373300 chr7D 94.536 1153 46 9 4329 5468 576336722 576337870 0.000000e+00 1764.0
13 TraesCS7B01G373300 chr7D 98.052 154 3 0 5463 5616 567733250 567733403 1.180000e-67 268.0
14 TraesCS7B01G373300 chr7A 94.112 2140 80 18 629 2727 667474557 667476691 0.000000e+00 3212.0
15 TraesCS7B01G373300 chr7A 93.381 1526 90 8 5616 7134 667478918 667480439 0.000000e+00 2248.0
16 TraesCS7B01G373300 chr7A 90.604 894 54 12 3069 3945 667477374 667478254 0.000000e+00 1158.0
17 TraesCS7B01G373300 chr7A 95.366 669 23 5 4807 5468 667478271 667478938 0.000000e+00 1057.0
18 TraesCS7B01G373300 chr7A 78.650 1555 250 40 5626 7127 705138135 705136610 0.000000e+00 957.0
19 TraesCS7B01G373300 chr7A 90.723 636 52 4 1 633 667473713 667474344 0.000000e+00 841.0
20 TraesCS7B01G373300 chr7A 85.084 657 78 15 4809 5450 705138787 705138136 0.000000e+00 652.0
21 TraesCS7B01G373300 chr7A 82.038 579 53 23 3795 4329 705140069 705139498 5.080000e-121 446.0
22 TraesCS7B01G373300 chr7A 83.002 553 26 27 2809 3323 667476841 667477363 8.500000e-119 438.0
23 TraesCS7B01G373300 chr7A 83.621 348 38 12 4389 4723 705139283 705138942 6.950000e-80 309.0
24 TraesCS7B01G373300 chr7A 99.342 152 1 0 5465 5616 83784835 83784986 7.050000e-70 276.0
25 TraesCS7B01G373300 chr7A 77.926 299 37 17 2937 3213 705142575 705142284 7.410000e-35 159.0
26 TraesCS7B01G373300 chr7A 93.182 88 6 0 2726 2813 667476718 667476805 5.810000e-26 130.0
27 TraesCS7B01G373300 chr3B 90.923 1994 165 6 744 2727 259370383 259372370 0.000000e+00 2665.0
28 TraesCS7B01G373300 chr3B 93.617 47 3 0 316 362 259370034 259370080 3.570000e-08 71.3
29 TraesCS7B01G373300 chr3D 90.306 1991 186 4 744 2727 181103577 181105567 0.000000e+00 2601.0
30 TraesCS7B01G373300 chr3D 87.265 1170 100 30 4338 5468 181108194 181109353 0.000000e+00 1290.0
31 TraesCS7B01G373300 chr3D 84.783 874 89 17 3245 4106 181106988 181107829 0.000000e+00 837.0
32 TraesCS7B01G373300 chr3D 98.693 153 2 0 5464 5616 422517794 422517642 9.120000e-69 272.0
33 TraesCS7B01G373300 chr3D 88.636 88 6 1 2726 2813 181105594 181105677 3.520000e-18 104.0
34 TraesCS7B01G373300 chr3A 90.130 1996 190 4 742 2730 227923659 227921664 0.000000e+00 2588.0
35 TraesCS7B01G373300 chr3A 86.667 915 90 23 4338 5236 227919006 227918108 0.000000e+00 985.0
36 TraesCS7B01G373300 chr3A 85.087 751 83 12 3365 4109 227920011 227919284 0.000000e+00 739.0
37 TraesCS7B01G373300 chr3A 96.795 156 5 0 5462 5617 602021339 602021494 1.970000e-65 261.0
38 TraesCS7B01G373300 chr3A 87.013 154 17 2 3972 4125 14856418 14856268 3.420000e-38 171.0
39 TraesCS7B01G373300 chr3A 83.616 177 28 1 5615 5791 227917732 227917557 1.590000e-36 165.0
40 TraesCS7B01G373300 chr3A 83.929 112 17 1 3984 4094 227916333 227916222 9.790000e-19 106.0
41 TraesCS7B01G373300 chr3A 87.778 90 7 2 2726 2813 227921640 227921553 1.270000e-17 102.0
42 TraesCS7B01G373300 chr3A 93.617 47 3 0 316 362 227923952 227923906 3.570000e-08 71.3
43 TraesCS7B01G373300 chr5B 99.342 152 1 0 5465 5616 574956446 574956597 7.050000e-70 276.0
44 TraesCS7B01G373300 chr2B 99.342 152 1 0 5465 5616 660461423 660461574 7.050000e-70 276.0
45 TraesCS7B01G373300 chr4D 98.684 152 2 0 5465 5616 482703624 482703473 3.280000e-68 270.0
46 TraesCS7B01G373300 chr4A 98.684 152 2 0 5465 5616 475420525 475420676 3.280000e-68 270.0
47 TraesCS7B01G373300 chr2A 98.065 155 3 0 5463 5617 642913895 642914049 3.280000e-68 270.0
48 TraesCS7B01G373300 chr1D 96.875 32 0 1 4064 4094 480403754 480403723 1.300000e-02 52.8
49 TraesCS7B01G373300 chr1A 96.875 32 0 1 4064 4094 576667228 576667197 1.300000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G373300 chr7B 639082425 639089558 7133 False 13175.000000 13175 100.000000 1 7134 1 chr7B.!!$F1 7133
1 TraesCS7B01G373300 chr7B 704153694 704157531 3837 True 631.250000 948 81.007750 3371 7075 4 chr7B.!!$R2 3704
2 TraesCS7B01G373300 chr7B 704088854 704093194 4340 True 544.200000 942 80.856400 2937 7075 5 chr7B.!!$R1 4138
3 TraesCS7B01G373300 chr7D 576332265 576339377 7112 False 3354.333333 5962 93.452667 4 7134 3 chr7D.!!$F2 7130
4 TraesCS7B01G373300 chr7A 667473713 667480439 6726 False 1297.714286 3212 91.481429 1 7134 7 chr7A.!!$F2 7133
5 TraesCS7B01G373300 chr7A 705136610 705142575 5965 True 504.600000 957 81.463800 2937 7127 5 chr7A.!!$R1 4190
6 TraesCS7B01G373300 chr3B 259370034 259372370 2336 False 1368.150000 2665 92.270000 316 2727 2 chr3B.!!$F1 2411
7 TraesCS7B01G373300 chr3D 181103577 181109353 5776 False 1208.000000 2601 87.747500 744 5468 4 chr3D.!!$F1 4724
8 TraesCS7B01G373300 chr3A 227916222 227923952 7730 True 679.471429 2588 87.260571 316 5791 7 chr3A.!!$R2 5475

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
480 521 0.247497 TTGTTATGCGCGCGTGATTC 60.247 50.000 34.70 20.6 0.00 2.52 F
776 1044 0.401738 CCTCCTCTTTTGCTGTGGGA 59.598 55.000 0.00 0.0 0.00 4.37 F
985 1264 1.003233 GTCTCCCTTCACCAGGTGC 60.003 63.158 15.64 0.0 42.02 5.01 F
2733 3075 0.745468 AGGTAAGTTCGAGATCGCCC 59.255 55.000 0.00 0.0 39.60 6.13 F
2807 3153 1.053835 TCACACCTCAGGGACTTGCA 61.054 55.000 0.00 0.0 34.60 4.08 F
4398 8143 0.108615 AGGTCTCTGTCCATTTCGCG 60.109 55.000 0.00 0.0 0.00 5.87 F
5274 9294 1.072173 ACTGCAGCAACTGATGGTACA 59.928 47.619 15.27 0.0 37.77 2.90 F
5587 9630 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.000 0.00 0.0 39.22 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1875 0.837940 GGACACCTCCCCTAATGGAC 59.162 60.000 0.00 0.00 35.39 4.02 R
1623 1932 1.280421 GAGGTGCCAGAAAGGACTGAT 59.720 52.381 0.00 0.00 41.22 2.90 R
2826 3215 2.041485 TCAGATGGCAGATGGGAAAACA 59.959 45.455 0.00 0.00 0.00 2.83 R
4175 7586 0.035247 TGTGTGCTCATGCTGGCATA 60.035 50.000 7.79 5.98 40.66 3.14 R
4733 8515 2.593346 TGGTGGACAATTTGTGTTGC 57.407 45.000 6.80 0.00 41.96 4.17 R
5458 9501 0.106918 CCGGGCTGCCCTTTAATGTA 60.107 55.000 33.39 0.00 42.67 2.29 R
6122 10226 0.392193 AGATCTTGTCAGCCGCCTTG 60.392 55.000 0.00 0.00 0.00 3.61 R
6928 11498 1.064017 TCTAATTGCGGGGAAGCCAAT 60.064 47.619 0.00 0.00 36.02 3.16 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
109 110 4.144727 AACGGCCCAACCCAACCA 62.145 61.111 0.00 0.00 33.26 3.67
249 265 2.429767 CGGCATCTCTCCTGCTCCA 61.430 63.158 0.00 0.00 39.60 3.86
250 266 1.910722 GGCATCTCTCCTGCTCCAA 59.089 57.895 0.00 0.00 39.60 3.53
319 337 3.964875 CCACACCACACGCTTGGC 61.965 66.667 2.77 0.00 40.77 4.52
332 350 1.250840 GCTTGGCCCATCTCGGTTTT 61.251 55.000 0.00 0.00 0.00 2.43
398 439 7.497595 ACATTTCGTATCCTGTGTATGTGTAT 58.502 34.615 0.00 0.00 0.00 2.29
433 474 5.104569 TCCTGTATGTATCATGCTTTGGTGA 60.105 40.000 0.00 0.00 0.00 4.02
450 491 3.694072 TGGTGATGCAATTAAGTGGTAGC 59.306 43.478 4.91 0.00 0.00 3.58
457 498 5.750524 TGCAATTAAGTGGTAGCCATAGAA 58.249 37.500 4.91 0.00 35.28 2.10
471 512 5.043248 AGCCATAGAAATTTTGTTATGCGC 58.957 37.500 0.00 0.00 0.00 6.09
480 521 0.247497 TTGTTATGCGCGCGTGATTC 60.247 50.000 34.70 20.60 0.00 2.52
481 522 1.081556 TGTTATGCGCGCGTGATTCT 61.082 50.000 34.70 11.91 0.00 2.40
589 630 7.429636 TTTCTACACCTGTATTGTTACTTGC 57.570 36.000 0.00 0.00 0.00 4.01
591 632 6.707290 TCTACACCTGTATTGTTACTTGCAT 58.293 36.000 0.00 0.00 0.00 3.96
601 642 8.976471 TGTATTGTTACTTGCATTTTTGTCATG 58.024 29.630 0.00 0.00 0.00 3.07
614 655 8.223100 GCATTTTTGTCATGTTTTGTCTATTCC 58.777 33.333 0.00 0.00 0.00 3.01
647 905 1.030457 GCATCTGCCCCTTCTCAATG 58.970 55.000 0.00 0.00 34.31 2.82
695 953 6.038714 CCAATAGGTCTGAATTTTAGTCTGCC 59.961 42.308 0.00 0.00 0.00 4.85
705 963 0.524862 TTAGTCTGCCTTCGGTCGAC 59.475 55.000 7.13 7.13 0.00 4.20
765 1033 6.125029 TGTATTACTAACTACGCCTCCTCTT 58.875 40.000 0.00 0.00 0.00 2.85
776 1044 0.401738 CCTCCTCTTTTGCTGTGGGA 59.598 55.000 0.00 0.00 0.00 4.37
834 1109 7.944554 TCCAAAATCTCCTTAACTTGATGTTCT 59.055 33.333 0.00 0.00 39.89 3.01
874 1149 1.065854 AGATGCTGCAGGGTGAGTAAC 60.066 52.381 17.12 0.00 0.00 2.50
877 1152 2.048597 TGCAGGGTGAGTAACGCG 60.049 61.111 3.53 3.53 46.08 6.01
879 1154 2.967397 CAGGGTGAGTAACGCGGA 59.033 61.111 12.47 0.00 46.08 5.54
932 1211 7.201920 GCTGAGACCAGTGGATTAGTAAATCTA 60.202 40.741 18.40 0.00 40.61 1.98
969 1248 4.153117 CACAACTAACTCAATGCCTCTGTC 59.847 45.833 0.00 0.00 0.00 3.51
985 1264 1.003233 GTCTCCCTTCACCAGGTGC 60.003 63.158 15.64 0.00 42.02 5.01
999 1281 1.078708 GGTGCGGGCTTAGCTGTTA 60.079 57.895 3.59 0.00 35.28 2.41
1393 1702 5.119588 CAGTTTGTTGGCTCAAGCAATAATG 59.880 40.000 4.13 0.00 44.36 1.90
1564 1873 4.022935 CCATGAGCTTTTGTGCTGTTAAGA 60.023 41.667 0.00 0.00 44.17 2.10
1566 1875 5.173774 TGAGCTTTTGTGCTGTTAAGAAG 57.826 39.130 0.00 0.00 44.17 2.85
1623 1932 9.226606 CTACTGGTGAAAGTTGGTTATGAATTA 57.773 33.333 0.00 0.00 0.00 1.40
1645 1954 1.072965 CAGTCCTTTCTGGCACCTCTT 59.927 52.381 0.00 0.00 35.26 2.85
1722 2031 6.607689 TCAGAACATGCCAGTTAAAAATACG 58.392 36.000 0.00 0.00 0.00 3.06
1857 2166 2.368548 TGCCACTATCTTCAGTGTGTGT 59.631 45.455 2.86 0.00 43.68 3.72
1941 2250 3.479489 TGATTTGTGTGTGCATGTCTCT 58.521 40.909 0.00 0.00 0.00 3.10
2233 2542 4.081420 TCAGACTTGGAATAGAACCAGAGC 60.081 45.833 0.00 0.00 38.70 4.09
2733 3075 0.745468 AGGTAAGTTCGAGATCGCCC 59.255 55.000 0.00 0.00 39.60 6.13
2756 3100 7.282585 CCCCAGTCATTTGTCTATATGAAGAA 58.717 38.462 0.00 0.00 32.94 2.52
2807 3153 1.053835 TCACACCTCAGGGACTTGCA 61.054 55.000 0.00 0.00 34.60 4.08
2826 3215 4.209538 TGCAATATGGCATCAGCTTTAGT 58.790 39.130 1.65 0.00 39.25 2.24
2863 3257 6.097129 TGCCATCTGATTTTTGATGCTCAATA 59.903 34.615 0.00 0.00 36.11 1.90
2966 3387 5.500234 TGGAGTCAAAATATGAGAAGGGTG 58.500 41.667 0.00 0.00 39.19 4.61
2978 3404 3.769844 TGAGAAGGGTGGATTGACTAGAC 59.230 47.826 0.00 0.00 0.00 2.59
3072 3508 7.672983 TCAGTTTGACATCTGGAAATTACTC 57.327 36.000 7.86 0.00 33.13 2.59
3078 3514 6.173339 TGACATCTGGAAATTACTCCTTGAC 58.827 40.000 0.00 0.00 36.35 3.18
3162 3920 4.714308 TCCTTTGGGTTGTGAAAGAAACAT 59.286 37.500 0.00 0.00 31.89 2.71
3217 4553 8.836268 TTATTGTTTTCACCGATGTTAGTAGT 57.164 30.769 0.00 0.00 0.00 2.73
3231 4567 1.446016 AGTAGTGGGGTCAAAAGCCT 58.554 50.000 0.00 0.00 42.97 4.58
3325 4948 1.468520 CTTAACCGTTGGACATGCTGG 59.531 52.381 0.00 0.00 0.00 4.85
3350 4973 7.376866 GGCGACAATATTTATGAACTTCACATG 59.623 37.037 0.00 0.00 0.00 3.21
3394 5216 4.629200 CACATGAGCAGAGTTTAAGGTCTC 59.371 45.833 0.00 0.00 0.00 3.36
3492 5323 5.657474 GTCGAGATAACACCCACTAAATCA 58.343 41.667 0.00 0.00 0.00 2.57
3522 5353 3.754965 AGACCAAAAGCATACTTCAGCA 58.245 40.909 0.00 0.00 34.05 4.41
3532 5363 3.276857 CATACTTCAGCACTCAGGCATT 58.723 45.455 0.00 0.00 35.83 3.56
3627 5463 2.669670 CGACTCAGCAGAAGAACATCGT 60.670 50.000 0.00 0.00 0.00 3.73
3691 5527 3.474570 GCCTCAGCCTGGGACGAT 61.475 66.667 0.00 0.00 0.00 3.73
3788 5633 4.500499 ACTGAGAGGGAAAATCAGATGG 57.500 45.455 8.32 0.00 42.48 3.51
4051 7445 7.448613 AGAGAAGCCTATCTCATCGTGGAGA 62.449 48.000 12.64 10.36 46.73 3.71
4109 7516 6.305693 ACACAAAAGCAGAATGACTTAGAC 57.694 37.500 0.00 0.00 39.69 2.59
4118 7525 9.507329 AAGCAGAATGACTTAGACTCAAATAAA 57.493 29.630 0.00 0.00 39.69 1.40
4168 7579 4.230657 CAACTCACAAGGTAGAGAGAACG 58.769 47.826 0.00 0.00 35.83 3.95
4175 7586 6.015688 TCACAAGGTAGAGAGAACGTACAATT 60.016 38.462 0.00 0.00 0.00 2.32
4214 7625 7.066284 GCACACATGTAGAAATCATAGTTCCTT 59.934 37.037 0.00 0.00 0.00 3.36
4229 7640 1.297968 TCCTTGGATGGCAGATTCCA 58.702 50.000 4.20 4.20 40.24 3.53
4309 7723 5.772672 TGTAAAAAGGCCTAAGAATTGCTCA 59.227 36.000 5.16 0.00 0.00 4.26
4331 7746 7.489113 GCTCATTTGGTCCATACAAAATTGTAG 59.511 37.037 11.28 4.62 45.80 2.74
4332 7747 7.835822 TCATTTGGTCCATACAAAATTGTAGG 58.164 34.615 11.28 10.73 45.80 3.18
4333 7748 7.453126 TCATTTGGTCCATACAAAATTGTAGGT 59.547 33.333 14.58 0.00 45.80 3.08
4334 7749 6.582677 TTGGTCCATACAAAATTGTAGGTG 57.417 37.500 14.58 8.08 45.80 4.00
4335 7750 5.636123 TGGTCCATACAAAATTGTAGGTGT 58.364 37.500 14.58 0.00 45.80 4.16
4336 7751 6.780901 TGGTCCATACAAAATTGTAGGTGTA 58.219 36.000 14.58 0.00 45.80 2.90
4398 8143 0.108615 AGGTCTCTGTCCATTTCGCG 60.109 55.000 0.00 0.00 0.00 5.87
4547 8300 3.265221 AGAACTGGCTCATGAAGAATGGA 59.735 43.478 0.00 0.00 36.86 3.41
4624 8377 2.724977 TGAACTGGCTCTCACTAACG 57.275 50.000 0.00 0.00 0.00 3.18
4648 8401 5.195940 CCATCCCTAACATCAAGACAACAT 58.804 41.667 0.00 0.00 0.00 2.71
4684 8440 2.955660 TCAGGGTGCCAAAGTAAACTTG 59.044 45.455 0.00 0.00 36.12 3.16
4685 8441 2.955660 CAGGGTGCCAAAGTAAACTTGA 59.044 45.455 0.00 0.00 36.12 3.02
4733 8515 4.730949 TTGTACTCTTAACATCGAGGGG 57.269 45.455 0.69 0.00 0.00 4.79
5196 9046 1.740025 CGGTTGGAAAATCTCTCCAGC 59.260 52.381 0.00 0.00 43.79 4.85
5265 9285 2.689983 AGCAAAACTTACTGCAGCAACT 59.310 40.909 15.27 0.00 41.17 3.16
5271 9291 2.224621 ACTTACTGCAGCAACTGATGGT 60.225 45.455 15.27 0.00 41.41 3.55
5274 9294 1.072173 ACTGCAGCAACTGATGGTACA 59.928 47.619 15.27 0.00 37.77 2.90
5278 9301 3.573538 TGCAGCAACTGATGGTACATTTT 59.426 39.130 0.00 0.00 37.77 1.82
5416 9448 5.233902 TGATTGGCAGAAATGAAACAAAACG 59.766 36.000 0.00 0.00 0.00 3.60
5457 9500 5.406175 CAGCTAACAAATCCAAATTGTGTGG 59.594 40.000 0.00 0.00 39.98 4.17
5458 9501 5.070313 AGCTAACAAATCCAAATTGTGTGGT 59.930 36.000 0.00 0.00 39.98 4.16
5459 9502 6.266558 AGCTAACAAATCCAAATTGTGTGGTA 59.733 34.615 0.00 0.00 39.98 3.25
5460 9503 6.364976 GCTAACAAATCCAAATTGTGTGGTAC 59.635 38.462 0.00 0.00 39.98 3.34
5461 9504 5.860941 ACAAATCCAAATTGTGTGGTACA 57.139 34.783 0.00 0.00 39.43 2.90
5462 9505 6.418057 ACAAATCCAAATTGTGTGGTACAT 57.582 33.333 0.00 0.00 39.43 2.29
5463 9506 6.825610 ACAAATCCAAATTGTGTGGTACATT 58.174 32.000 0.00 0.00 39.43 2.71
5464 9507 7.957002 ACAAATCCAAATTGTGTGGTACATTA 58.043 30.769 0.00 0.00 39.43 1.90
5465 9508 8.424918 ACAAATCCAAATTGTGTGGTACATTAA 58.575 29.630 0.00 0.00 39.43 1.40
5466 9509 9.265901 CAAATCCAAATTGTGTGGTACATTAAA 57.734 29.630 0.00 0.00 44.52 1.52
5467 9510 9.487790 AAATCCAAATTGTGTGGTACATTAAAG 57.512 29.630 0.00 0.00 44.52 1.85
5468 9511 6.987386 TCCAAATTGTGTGGTACATTAAAGG 58.013 36.000 0.00 0.00 44.52 3.11
5469 9512 6.015010 TCCAAATTGTGTGGTACATTAAAGGG 60.015 38.462 0.00 0.00 44.52 3.95
5470 9513 5.400066 AATTGTGTGGTACATTAAAGGGC 57.600 39.130 0.00 0.00 44.52 5.19
5471 9514 3.510531 TGTGTGGTACATTAAAGGGCA 57.489 42.857 0.00 0.00 44.52 5.36
5472 9515 3.417101 TGTGTGGTACATTAAAGGGCAG 58.583 45.455 0.00 0.00 44.52 4.85
5473 9516 2.163613 GTGTGGTACATTAAAGGGCAGC 59.836 50.000 0.00 0.00 44.52 5.25
5474 9517 1.749063 GTGGTACATTAAAGGGCAGCC 59.251 52.381 1.26 1.26 44.52 4.85
5475 9518 1.341581 TGGTACATTAAAGGGCAGCCC 60.342 52.381 24.90 24.90 45.90 5.19
5495 9538 3.691342 TGCACGTAGCTCCCGCTT 61.691 61.111 10.54 0.00 46.47 4.68
5496 9539 3.188786 GCACGTAGCTCCCGCTTG 61.189 66.667 5.69 0.00 46.47 4.01
5497 9540 3.188786 CACGTAGCTCCCGCTTGC 61.189 66.667 5.69 0.00 46.47 4.01
5498 9541 4.796231 ACGTAGCTCCCGCTTGCG 62.796 66.667 8.14 8.14 46.47 4.85
5501 9544 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
5517 9560 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
5524 9567 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
5525 9568 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
5526 9569 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
5527 9570 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
5528 9571 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
5529 9572 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
5530 9573 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
5531 9574 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
5542 9585 5.291905 ACCACTTTGGGTCTATAGTATGC 57.708 43.478 0.00 0.00 43.37 3.14
5543 9586 4.719773 ACCACTTTGGGTCTATAGTATGCA 59.280 41.667 0.00 0.00 43.37 3.96
5544 9587 5.163301 ACCACTTTGGGTCTATAGTATGCAG 60.163 44.000 0.00 0.00 43.37 4.41
5545 9588 4.752101 CACTTTGGGTCTATAGTATGCAGC 59.248 45.833 0.00 0.00 0.00 5.25
5546 9589 4.202367 ACTTTGGGTCTATAGTATGCAGCC 60.202 45.833 0.00 0.00 0.00 4.85
5547 9590 3.260269 TGGGTCTATAGTATGCAGCCT 57.740 47.619 0.00 0.00 0.00 4.58
5548 9591 3.587498 TGGGTCTATAGTATGCAGCCTT 58.413 45.455 0.00 0.00 0.00 4.35
5549 9592 3.973973 TGGGTCTATAGTATGCAGCCTTT 59.026 43.478 0.00 0.00 0.00 3.11
5550 9593 4.040461 TGGGTCTATAGTATGCAGCCTTTC 59.960 45.833 0.00 0.00 0.00 2.62
5551 9594 4.563786 GGGTCTATAGTATGCAGCCTTTCC 60.564 50.000 0.00 0.00 0.00 3.13
5552 9595 4.563786 GGTCTATAGTATGCAGCCTTTCCC 60.564 50.000 0.00 0.00 0.00 3.97
5553 9596 4.284746 GTCTATAGTATGCAGCCTTTCCCT 59.715 45.833 0.00 0.00 0.00 4.20
5554 9597 5.480772 GTCTATAGTATGCAGCCTTTCCCTA 59.519 44.000 0.00 0.00 0.00 3.53
5555 9598 4.625607 ATAGTATGCAGCCTTTCCCTAC 57.374 45.455 0.00 0.00 0.00 3.18
5556 9599 2.196595 AGTATGCAGCCTTTCCCTACA 58.803 47.619 0.00 0.00 0.00 2.74
5557 9600 2.780010 AGTATGCAGCCTTTCCCTACAT 59.220 45.455 0.00 0.00 0.00 2.29
5558 9601 2.834638 ATGCAGCCTTTCCCTACATT 57.165 45.000 0.00 0.00 0.00 2.71
5559 9602 2.603075 TGCAGCCTTTCCCTACATTT 57.397 45.000 0.00 0.00 0.00 2.32
5560 9603 2.446435 TGCAGCCTTTCCCTACATTTC 58.554 47.619 0.00 0.00 0.00 2.17
5561 9604 2.041620 TGCAGCCTTTCCCTACATTTCT 59.958 45.455 0.00 0.00 0.00 2.52
5562 9605 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
5563 9606 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
5564 9607 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
5565 9608 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
5566 9609 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
5567 9610 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
5577 9620 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
5578 9621 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
5579 9622 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
5580 9623 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
5581 9624 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
5582 9625 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
5583 9626 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
5584 9627 0.980423 AGAGGCTGTTTCCAGGACTC 59.020 55.000 0.00 0.00 39.22 3.36
5585 9628 0.390472 GAGGCTGTTTCCAGGACTCG 60.390 60.000 0.00 0.00 39.22 4.18
5586 9629 0.832135 AGGCTGTTTCCAGGACTCGA 60.832 55.000 0.00 0.00 39.22 4.04
5587 9630 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.000 0.00 0.00 39.22 3.71
5588 9631 1.149148 GCTGTTTCCAGGACTCGAAC 58.851 55.000 0.00 0.00 39.22 3.95
5589 9632 1.797025 CTGTTTCCAGGACTCGAACC 58.203 55.000 0.00 0.64 34.90 3.62
5590 9633 0.395312 TGTTTCCAGGACTCGAACCC 59.605 55.000 0.00 0.12 0.00 4.11
5591 9634 0.669625 GTTTCCAGGACTCGAACCCG 60.670 60.000 0.00 0.00 37.07 5.28
5592 9635 1.117142 TTTCCAGGACTCGAACCCGT 61.117 55.000 0.00 0.00 37.05 5.28
5593 9636 1.812686 TTCCAGGACTCGAACCCGTG 61.813 60.000 0.00 0.64 37.05 4.94
5594 9637 2.273179 CCAGGACTCGAACCCGTGA 61.273 63.158 4.92 0.00 37.05 4.35
5595 9638 1.080705 CAGGACTCGAACCCGTGAC 60.081 63.158 4.92 0.00 37.05 3.67
5596 9639 2.260743 GGACTCGAACCCGTGACC 59.739 66.667 0.00 0.00 37.08 4.02
5597 9640 2.273912 GGACTCGAACCCGTGACCT 61.274 63.158 0.00 0.00 39.62 3.85
5598 9641 1.212229 GACTCGAACCCGTGACCTC 59.788 63.158 0.00 0.00 37.05 3.85
5599 9642 1.521450 GACTCGAACCCGTGACCTCA 61.521 60.000 0.00 0.00 37.05 3.86
5600 9643 0.898789 ACTCGAACCCGTGACCTCAT 60.899 55.000 0.00 0.00 37.05 2.90
5601 9644 0.458543 CTCGAACCCGTGACCTCATG 60.459 60.000 0.00 0.00 37.05 3.07
5612 9655 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
5613 9656 0.478072 ACCTCATGGTCACAAGGCAA 59.522 50.000 0.00 0.00 44.78 4.52
5614 9657 0.883833 CCTCATGGTCACAAGGCAAC 59.116 55.000 0.00 0.00 0.00 4.17
5615 9658 1.608055 CTCATGGTCACAAGGCAACA 58.392 50.000 0.00 0.00 41.41 3.33
5616 9659 1.955778 CTCATGGTCACAAGGCAACAA 59.044 47.619 0.00 0.00 41.41 2.83
5617 9660 2.361757 CTCATGGTCACAAGGCAACAAA 59.638 45.455 0.00 0.00 41.41 2.83
5618 9661 2.964464 TCATGGTCACAAGGCAACAAAT 59.036 40.909 0.00 0.00 41.41 2.32
5619 9662 3.387374 TCATGGTCACAAGGCAACAAATT 59.613 39.130 0.00 0.00 41.41 1.82
5620 9663 3.176552 TGGTCACAAGGCAACAAATTG 57.823 42.857 0.00 0.00 38.99 2.32
5656 9699 8.735692 TGAAGATGCAAATATAGATCACAACA 57.264 30.769 0.00 0.00 0.00 3.33
5665 9708 9.912634 CAAATATAGATCACAACACAAACCTTT 57.087 29.630 0.00 0.00 0.00 3.11
5751 9794 4.447389 GCATTGCGTAAAGAAACCATGTTT 59.553 37.500 0.00 0.00 0.00 2.83
5795 9838 6.463049 CCACGGTCCTGATAAGAACAATAGAT 60.463 42.308 0.00 0.00 0.00 1.98
5796 9839 6.986817 CACGGTCCTGATAAGAACAATAGATT 59.013 38.462 0.00 0.00 0.00 2.40
5872 9930 5.564550 AGCAAACCATAGATGTCAGAGTTT 58.435 37.500 0.00 0.00 0.00 2.66
5914 10013 5.468409 CAGGAGAAAGAGAAAGTCTGGTTTC 59.532 44.000 0.00 0.00 34.84 2.78
5916 10015 5.455469 GGAGAAAGAGAAAGTCTGGTTTCCT 60.455 44.000 6.26 0.00 37.16 3.36
5918 10017 6.427441 AGAAAGAGAAAGTCTGGTTTCCTTT 58.573 36.000 10.17 10.17 38.38 3.11
5922 10021 7.809546 AGAGAAAGTCTGGTTTCCTTTTTAG 57.190 36.000 0.00 0.00 37.16 1.85
5940 10039 7.062722 CCTTTTTAGCTTTGCTTTTATCTGCTC 59.937 37.037 0.00 0.00 40.44 4.26
5953 10052 5.620738 TTATCTGCTCAAACATAGCCTCT 57.379 39.130 0.00 0.00 39.30 3.69
6034 10133 4.840716 TTTGGCCATTTCCTGCAAATAT 57.159 36.364 6.09 0.00 32.48 1.28
6122 10226 1.815003 CTTCTTGGCACCAGATTGGAC 59.185 52.381 1.40 0.00 40.96 4.02
6129 10233 1.002134 ACCAGATTGGACAAGGCGG 60.002 57.895 1.40 0.00 40.96 6.13
6230 10406 0.687354 TGGAGAGCAGAACTGGGAAC 59.313 55.000 3.99 0.00 0.00 3.62
6252 10428 6.854496 ACGTTACCGCATCAATAACAATAT 57.146 33.333 0.00 0.00 37.70 1.28
6316 10497 4.973168 TCAAGAGGTATGTTCAGTTGCTT 58.027 39.130 0.00 0.00 0.00 3.91
6339 10520 3.682858 ACGTCATTATTGAAGTTCCACCG 59.317 43.478 0.00 0.00 41.01 4.94
6649 11218 8.877864 TCAATATTTTTAGACCCTGTGAACAT 57.122 30.769 0.00 0.00 0.00 2.71
6665 11234 7.712639 CCTGTGAACATTATCTACTGCAGTATT 59.287 37.037 26.22 18.45 0.00 1.89
6701 11270 7.565398 AGGTTATGAGAGTAACATACACCAGAT 59.435 37.037 3.27 0.00 36.51 2.90
6805 11374 9.914834 TTTATACCTTTGTAATGGCAGTAGAAT 57.085 29.630 5.36 0.00 0.00 2.40
6928 11498 2.270850 GGAGGTATGTTGGGCGCA 59.729 61.111 10.83 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.134098 TGCTGTTTGCTAGGGCTATCC 60.134 52.381 0.00 0.00 43.37 2.59
76 77 1.676967 GTTGGGGGAGAGCTGCAAG 60.677 63.158 1.02 0.00 0.00 4.01
232 248 0.463474 GTTGGAGCAGGAGAGATGCC 60.463 60.000 0.00 0.00 44.97 4.40
236 252 1.599606 GCGAGTTGGAGCAGGAGAGA 61.600 60.000 0.00 0.00 0.00 3.10
249 265 4.016706 CAAGGGACGGGGCGAGTT 62.017 66.667 0.00 0.00 0.00 3.01
319 337 1.271379 ACTCACCAAAACCGAGATGGG 60.271 52.381 0.00 0.00 44.64 4.00
332 350 0.823356 GGCTGCCTGAAAACTCACCA 60.823 55.000 12.43 0.00 0.00 4.17
398 439 5.188751 TGATACATACAGGACATTGGACACA 59.811 40.000 0.00 0.00 0.00 3.72
433 474 5.940617 TCTATGGCTACCACTTAATTGCAT 58.059 37.500 0.00 0.00 35.80 3.96
450 491 4.085619 GCGCGCATAACAAAATTTCTATGG 60.086 41.667 29.10 7.42 0.00 2.74
457 498 0.981240 CACGCGCGCATAACAAAATT 59.019 45.000 32.58 1.63 0.00 1.82
471 512 1.078201 TAGCTGTGCAGAATCACGCG 61.078 55.000 3.53 3.53 39.55 6.01
480 521 6.154445 AGAAAATGTTGAAATAGCTGTGCAG 58.846 36.000 0.00 0.00 0.00 4.41
481 522 6.088016 AGAAAATGTTGAAATAGCTGTGCA 57.912 33.333 0.00 0.00 0.00 4.57
542 583 4.922206 AGAGTACCAAATCAATGGCTTGA 58.078 39.130 2.63 2.63 44.75 3.02
589 630 8.427012 CGGAATAGACAAAACATGACAAAAATG 58.573 33.333 0.00 0.00 0.00 2.32
591 632 7.708051 TCGGAATAGACAAAACATGACAAAAA 58.292 30.769 0.00 0.00 0.00 1.94
601 642 2.357952 GGCCCATCGGAATAGACAAAAC 59.642 50.000 0.00 0.00 0.00 2.43
647 905 4.097714 CACGCACACATACATGATTTTCC 58.902 43.478 0.00 0.00 0.00 3.13
695 953 7.694388 TTTATATTGAATCAGTCGACCGAAG 57.306 36.000 13.01 0.00 0.00 3.79
739 997 7.456725 AGAGGAGGCGTAGTTAGTAATACATA 58.543 38.462 0.00 0.00 0.00 2.29
740 998 6.305411 AGAGGAGGCGTAGTTAGTAATACAT 58.695 40.000 0.00 0.00 0.00 2.29
755 1023 1.580845 CCACAGCAAAAGAGGAGGCG 61.581 60.000 0.00 0.00 0.00 5.52
760 1028 1.610522 CTGTTCCCACAGCAAAAGAGG 59.389 52.381 0.00 0.00 44.16 3.69
776 1044 6.818142 GCTTGGATGCCAATAATTTAACTGTT 59.182 34.615 0.00 0.00 43.07 3.16
834 1109 5.698741 TCTCTTCCAGCATCCTTGAATAA 57.301 39.130 0.00 0.00 0.00 1.40
874 1149 1.004610 CATAAGCAGATTGTGTCCGCG 60.005 52.381 0.00 0.00 35.35 6.46
877 1152 5.471116 TGCATATCATAAGCAGATTGTGTCC 59.529 40.000 0.00 0.00 33.75 4.02
879 1154 8.625786 TTATGCATATCATAAGCAGATTGTGT 57.374 30.769 7.36 0.00 41.40 3.72
932 1211 7.936847 TGAGTTAGTTGTGTTTATCATGAAGGT 59.063 33.333 0.00 0.00 0.00 3.50
985 1264 1.331756 CAGCATTAACAGCTAAGCCCG 59.668 52.381 4.12 0.00 41.14 6.13
999 1281 0.332632 TGGAAAGGCCTAGCAGCATT 59.667 50.000 5.16 0.00 38.64 3.56
1393 1702 5.109210 GGTATTGGGTAAAATTTGCTCTGC 58.891 41.667 0.00 0.00 0.00 4.26
1489 1798 1.132913 TCCTCTCCTATGCAGCTCCAT 60.133 52.381 0.00 0.00 0.00 3.41
1564 1873 2.197465 GACACCTCCCCTAATGGACTT 58.803 52.381 0.00 0.00 35.39 3.01
1566 1875 0.837940 GGACACCTCCCCTAATGGAC 59.162 60.000 0.00 0.00 35.39 4.02
1623 1932 1.280421 GAGGTGCCAGAAAGGACTGAT 59.720 52.381 0.00 0.00 41.22 2.90
1857 2166 2.409975 GCAAGAAGTGCGTGGTTAGTA 58.590 47.619 0.00 0.00 45.10 1.82
1941 2250 7.982761 TGCATACATTGATATCAGTGCATTA 57.017 32.000 23.79 12.18 37.12 1.90
2733 3075 7.706607 TCGTTCTTCATATAGACAAATGACTGG 59.293 37.037 0.00 0.00 31.99 4.00
2807 3153 6.780457 AAACACTAAAGCTGATGCCATATT 57.220 33.333 0.00 0.00 40.80 1.28
2826 3215 2.041485 TCAGATGGCAGATGGGAAAACA 59.959 45.455 0.00 0.00 0.00 2.83
2919 3340 2.799126 ACATCAAAAGTCCCCGCATA 57.201 45.000 0.00 0.00 0.00 3.14
2966 3387 4.806247 CGTCAATCCTTGTCTAGTCAATCC 59.194 45.833 2.83 0.00 0.00 3.01
2978 3404 4.757149 AGAGAAAGAAACCGTCAATCCTTG 59.243 41.667 0.00 0.00 0.00 3.61
3072 3508 9.469807 CTAGTTATCTATAAGTTGCAGTCAAGG 57.530 37.037 0.00 0.00 31.93 3.61
3206 3965 4.395231 GCTTTTGACCCCACTACTAACATC 59.605 45.833 0.00 0.00 0.00 3.06
3217 4553 2.203625 GCCAGGCTTTTGACCCCA 60.204 61.111 3.29 0.00 0.00 4.96
3325 4948 7.096885 GCATGTGAAGTTCATAAATATTGTCGC 60.097 37.037 9.18 0.00 0.00 5.19
3350 4973 3.119173 TGCAAGGTGCCTACATATTTTGC 60.119 43.478 0.00 0.00 44.23 3.68
3492 5323 2.586425 TGCTTTTGGTCTTAGCTGCTT 58.414 42.857 7.79 0.00 35.93 3.91
3522 5353 3.368116 GGTCGTAGTGTTAATGCCTGAGT 60.368 47.826 0.00 0.00 0.00 3.41
3532 5363 0.521291 CGGAACCGGTCGTAGTGTTA 59.479 55.000 8.04 0.00 35.56 2.41
3627 5463 1.339535 TGCATCCCAATGTAGCGTCAA 60.340 47.619 0.00 0.00 35.18 3.18
3703 5542 4.194640 CCAAGTTCACCAAGATCGATGAT 58.805 43.478 0.54 0.00 0.00 2.45
3711 5550 3.109847 GTGGCCAAGTTCACCAAGA 57.890 52.632 7.24 0.00 34.63 3.02
3788 5633 4.660789 ATATCAAAAAGGCATGGCTGAC 57.339 40.909 24.08 0.00 0.00 3.51
3986 7380 1.964223 CGTGCACTCCCTATCCTATGT 59.036 52.381 16.19 0.00 0.00 2.29
4051 7445 1.144913 AGGCCAACACACTACCATGTT 59.855 47.619 5.01 0.00 39.63 2.71
4118 7525 3.988379 AACTCACATCGTTGCAAATGT 57.012 38.095 10.35 10.35 36.56 2.71
4168 7579 3.316029 TGCTCATGCTGGCATAATTGTAC 59.684 43.478 7.79 0.00 40.48 2.90
4175 7586 0.035247 TGTGTGCTCATGCTGGCATA 60.035 50.000 7.79 5.98 40.66 3.14
4214 7625 3.047857 TGATAGTGGAATCTGCCATCCA 58.952 45.455 0.00 0.00 43.32 3.41
4229 7640 5.081728 TGTGTAGGTACTGTGGTTGATAGT 58.918 41.667 0.00 0.00 41.52 2.12
4309 7723 7.234577 ACACCTACAATTTTGTATGGACCAAAT 59.765 33.333 17.97 0.00 42.26 2.32
4336 7751 8.881262 CCCAGGTAACCTACATCTTTTATCTAT 58.119 37.037 0.00 0.00 29.64 1.98
4398 8143 7.301068 AGAATCATCACACGAGATTTTTCTC 57.699 36.000 0.00 0.00 32.51 2.87
4559 8312 5.189180 AGCTCAGATCATGGAGGTAAAAAC 58.811 41.667 10.74 0.00 39.86 2.43
4560 8313 5.441718 AGCTCAGATCATGGAGGTAAAAA 57.558 39.130 10.74 0.00 39.86 1.94
4624 8377 3.281727 TGTCTTGATGTTAGGGATGGC 57.718 47.619 0.00 0.00 0.00 4.40
4648 8401 5.497474 GCACCCTGATTTCTAAGGAAACTA 58.503 41.667 0.00 0.00 43.16 2.24
4684 8440 6.019779 ACTCTAATACTCGATGCCATCTTC 57.980 41.667 2.75 0.00 0.00 2.87
4685 8441 5.536538 TGACTCTAATACTCGATGCCATCTT 59.463 40.000 2.75 0.00 0.00 2.40
4733 8515 2.593346 TGGTGGACAATTTGTGTTGC 57.407 45.000 6.80 0.00 41.96 4.17
4744 8528 7.595819 ATTTTTCTGTAGAAATTGGTGGACA 57.404 32.000 7.80 0.00 42.83 4.02
5099 8948 1.452110 TGAAGTGGCCAATCATGTCG 58.548 50.000 7.24 0.00 0.00 4.35
5153 9003 3.157087 CAATTTGCTTACTCACCTGGGT 58.843 45.455 0.00 0.00 0.00 4.51
5154 9004 3.157087 ACAATTTGCTTACTCACCTGGG 58.843 45.455 0.00 0.00 0.00 4.45
5196 9046 0.322648 TCAGGTGTCAGCTGATGGTG 59.677 55.000 26.87 14.75 46.53 4.17
5265 9285 4.078537 CACCAGGACAAAATGTACCATCA 58.921 43.478 0.00 0.00 29.22 3.07
5271 9291 4.171878 TGGTTCACCAGGACAAAATGTA 57.828 40.909 0.00 0.00 42.01 2.29
5405 9437 5.406649 ACTGAATGCTTTCGTTTTGTTTCA 58.593 33.333 7.73 0.00 34.39 2.69
5416 9448 6.697019 TGTTAGCTGAAAAACTGAATGCTTTC 59.303 34.615 0.00 5.41 0.00 2.62
5457 9500 1.021968 CGGGCTGCCCTTTAATGTAC 58.978 55.000 33.39 5.18 42.67 2.90
5458 9501 0.106918 CCGGGCTGCCCTTTAATGTA 60.107 55.000 33.39 0.00 42.67 2.29
5459 9502 1.379843 CCGGGCTGCCCTTTAATGT 60.380 57.895 33.39 0.00 42.67 2.71
5460 9503 1.379843 ACCGGGCTGCCCTTTAATG 60.380 57.895 33.39 17.58 42.67 1.90
5461 9504 1.379843 CACCGGGCTGCCCTTTAAT 60.380 57.895 33.39 12.60 42.67 1.40
5462 9505 2.034999 CACCGGGCTGCCCTTTAA 59.965 61.111 33.39 0.00 42.67 1.52
5463 9506 4.733542 GCACCGGGCTGCCCTTTA 62.734 66.667 33.39 0.00 42.67 1.85
5473 9516 4.814294 GGAGCTACGTGCACCGGG 62.814 72.222 12.15 0.00 42.21 5.73
5500 9543 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
5507 9550 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
5508 9551 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
5509 9552 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
5510 9553 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
5511 9554 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
5512 9555 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
5513 9556 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
5514 9557 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
5515 9558 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
5520 9563 4.719773 TGCATACTATAGACCCAAAGTGGT 59.280 41.667 6.78 0.00 42.79 4.16
5521 9564 5.290493 TGCATACTATAGACCCAAAGTGG 57.710 43.478 6.78 0.00 37.25 4.00
5522 9565 4.752101 GCTGCATACTATAGACCCAAAGTG 59.248 45.833 6.78 0.00 0.00 3.16
5523 9566 4.202367 GGCTGCATACTATAGACCCAAAGT 60.202 45.833 6.78 0.00 0.00 2.66
5524 9567 4.040952 AGGCTGCATACTATAGACCCAAAG 59.959 45.833 6.78 0.00 0.00 2.77
5525 9568 3.973973 AGGCTGCATACTATAGACCCAAA 59.026 43.478 6.78 0.00 0.00 3.28
5526 9569 3.587498 AGGCTGCATACTATAGACCCAA 58.413 45.455 6.78 0.00 0.00 4.12
5527 9570 3.260269 AGGCTGCATACTATAGACCCA 57.740 47.619 6.78 0.00 0.00 4.51
5528 9571 4.563786 GGAAAGGCTGCATACTATAGACCC 60.564 50.000 6.78 0.00 0.00 4.46
5529 9572 4.563786 GGGAAAGGCTGCATACTATAGACC 60.564 50.000 6.78 0.00 0.00 3.85
5530 9573 4.284746 AGGGAAAGGCTGCATACTATAGAC 59.715 45.833 6.78 0.00 0.00 2.59
5531 9574 4.493618 AGGGAAAGGCTGCATACTATAGA 58.506 43.478 6.78 0.00 0.00 1.98
5532 9575 4.899352 AGGGAAAGGCTGCATACTATAG 57.101 45.455 0.50 0.00 0.00 1.31
5533 9576 5.152193 TGTAGGGAAAGGCTGCATACTATA 58.848 41.667 0.50 0.00 34.13 1.31
5534 9577 3.973973 TGTAGGGAAAGGCTGCATACTAT 59.026 43.478 0.50 0.00 34.13 2.12
5535 9578 3.380393 TGTAGGGAAAGGCTGCATACTA 58.620 45.455 0.50 0.00 34.13 1.82
5536 9579 2.196595 TGTAGGGAAAGGCTGCATACT 58.803 47.619 0.50 0.00 34.13 2.12
5537 9580 2.710096 TGTAGGGAAAGGCTGCATAC 57.290 50.000 0.50 0.00 33.66 2.39
5538 9581 3.951563 AATGTAGGGAAAGGCTGCATA 57.048 42.857 0.50 0.00 0.00 3.14
5539 9582 2.834638 AATGTAGGGAAAGGCTGCAT 57.165 45.000 0.50 0.00 0.00 3.96
5540 9583 2.041620 AGAAATGTAGGGAAAGGCTGCA 59.958 45.455 0.50 0.00 0.00 4.41
5541 9584 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
5542 9585 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
5543 9586 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
5544 9587 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
5545 9588 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
5546 9589 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
5547 9590 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
5548 9591 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
5549 9592 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
5550 9593 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
5551 9594 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
5552 9595 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
5553 9596 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
5554 9597 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
5555 9598 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
5556 9599 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
5557 9600 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
5558 9601 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
5559 9602 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
5560 9603 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
5571 9614 0.395312 GGGTTCGAGTCCTGGAAACA 59.605 55.000 8.95 0.00 36.84 2.83
5572 9615 0.669625 CGGGTTCGAGTCCTGGAAAC 60.670 60.000 0.00 0.00 39.00 2.78
5573 9616 1.117142 ACGGGTTCGAGTCCTGGAAA 61.117 55.000 17.72 0.00 40.11 3.13
5574 9617 1.532316 ACGGGTTCGAGTCCTGGAA 60.532 57.895 17.72 0.00 40.11 3.53
5575 9618 2.116772 ACGGGTTCGAGTCCTGGA 59.883 61.111 17.72 0.00 40.11 3.86
5576 9619 2.261671 CACGGGTTCGAGTCCTGG 59.738 66.667 17.72 9.36 40.11 4.45
5577 9620 1.080705 GTCACGGGTTCGAGTCCTG 60.081 63.158 13.65 13.65 40.11 3.86
5578 9621 2.273912 GGTCACGGGTTCGAGTCCT 61.274 63.158 8.28 0.00 40.11 3.85
5579 9622 2.210341 GAGGTCACGGGTTCGAGTCC 62.210 65.000 0.82 0.82 40.11 3.85
5580 9623 1.212229 GAGGTCACGGGTTCGAGTC 59.788 63.158 0.00 0.00 40.11 3.36
5581 9624 0.898789 ATGAGGTCACGGGTTCGAGT 60.899 55.000 0.00 0.00 40.11 4.18
5582 9625 0.458543 CATGAGGTCACGGGTTCGAG 60.459 60.000 0.00 0.00 40.11 4.04
5583 9626 1.589630 CATGAGGTCACGGGTTCGA 59.410 57.895 0.00 0.00 40.11 3.71
5584 9627 1.447838 CCATGAGGTCACGGGTTCG 60.448 63.158 0.00 0.00 43.02 3.95
5585 9628 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
5595 9638 0.883833 GTTGCCTTGTGACCATGAGG 59.116 55.000 0.00 0.00 42.21 3.86
5596 9639 1.608055 TGTTGCCTTGTGACCATGAG 58.392 50.000 0.00 0.00 0.00 2.90
5597 9640 2.064434 TTGTTGCCTTGTGACCATGA 57.936 45.000 0.00 0.00 0.00 3.07
5598 9641 2.886862 TTTGTTGCCTTGTGACCATG 57.113 45.000 0.00 0.00 0.00 3.66
5599 9642 3.731089 CAATTTGTTGCCTTGTGACCAT 58.269 40.909 0.00 0.00 0.00 3.55
5600 9643 2.741228 GCAATTTGTTGCCTTGTGACCA 60.741 45.455 1.84 0.00 41.85 4.02
5601 9644 1.866601 GCAATTTGTTGCCTTGTGACC 59.133 47.619 1.84 0.00 41.85 4.02
5602 9645 1.522258 CGCAATTTGTTGCCTTGTGAC 59.478 47.619 7.48 0.00 44.66 3.67
5603 9646 1.135915 ACGCAATTTGTTGCCTTGTGA 59.864 42.857 7.48 0.00 44.66 3.58
5604 9647 1.258458 CACGCAATTTGTTGCCTTGTG 59.742 47.619 7.48 6.45 44.66 3.33
5605 9648 1.569708 CACGCAATTTGTTGCCTTGT 58.430 45.000 7.48 0.00 44.66 3.16
5606 9649 0.860533 CCACGCAATTTGTTGCCTTG 59.139 50.000 7.48 5.31 44.66 3.61
5607 9650 0.463620 ACCACGCAATTTGTTGCCTT 59.536 45.000 7.48 0.00 44.66 4.35
5608 9651 1.000717 GTACCACGCAATTTGTTGCCT 60.001 47.619 7.48 0.00 44.66 4.75
5609 9652 1.269309 TGTACCACGCAATTTGTTGCC 60.269 47.619 7.48 0.00 44.66 4.52
5610 9653 2.126914 TGTACCACGCAATTTGTTGC 57.873 45.000 3.18 3.18 44.09 4.17
5611 9654 4.294232 TCAATGTACCACGCAATTTGTTG 58.706 39.130 0.00 0.00 0.00 3.33
5612 9655 4.576216 TCAATGTACCACGCAATTTGTT 57.424 36.364 0.00 0.00 0.00 2.83
5613 9656 4.277174 TCTTCAATGTACCACGCAATTTGT 59.723 37.500 0.00 0.00 0.00 2.83
5614 9657 4.793071 TCTTCAATGTACCACGCAATTTG 58.207 39.130 0.00 0.00 0.00 2.32
5615 9658 5.401550 CATCTTCAATGTACCACGCAATTT 58.598 37.500 0.00 0.00 0.00 1.82
5616 9659 4.675146 GCATCTTCAATGTACCACGCAATT 60.675 41.667 0.00 0.00 0.00 2.32
5617 9660 3.181497 GCATCTTCAATGTACCACGCAAT 60.181 43.478 0.00 0.00 0.00 3.56
5618 9661 2.161410 GCATCTTCAATGTACCACGCAA 59.839 45.455 0.00 0.00 0.00 4.85
5619 9662 1.737236 GCATCTTCAATGTACCACGCA 59.263 47.619 0.00 0.00 0.00 5.24
5620 9663 1.737236 TGCATCTTCAATGTACCACGC 59.263 47.619 0.00 0.00 0.00 5.34
5621 9664 4.418013 TTTGCATCTTCAATGTACCACG 57.582 40.909 0.00 0.00 0.00 4.94
5622 9665 9.056005 TCTATATTTGCATCTTCAATGTACCAC 57.944 33.333 0.00 0.00 0.00 4.16
5623 9666 9.797642 ATCTATATTTGCATCTTCAATGTACCA 57.202 29.630 0.00 0.00 0.00 3.25
5655 9698 7.384660 TGCTAAAGATAAATGCAAAGGTTTGTG 59.615 33.333 4.45 0.00 40.24 3.33
5656 9699 7.441017 TGCTAAAGATAAATGCAAAGGTTTGT 58.559 30.769 4.45 0.00 40.24 2.83
5665 9708 5.840243 ATGTGCTGCTAAAGATAAATGCA 57.160 34.783 0.00 0.00 0.00 3.96
5751 9794 0.874390 GAAGCGTGAATGCCTTGTGA 59.126 50.000 0.00 0.00 34.65 3.58
5824 9872 6.264292 TCTGCTACCTCAACTTTGCAAATAAA 59.736 34.615 13.23 0.00 0.00 1.40
5837 9885 1.419762 TGGTTTGCTCTGCTACCTCAA 59.580 47.619 12.73 0.00 35.87 3.02
5872 9930 3.454447 TCCTGTGTGTTCTTCCTGAGAAA 59.546 43.478 0.00 0.00 45.59 2.52
5914 10013 6.870439 AGCAGATAAAAGCAAAGCTAAAAAGG 59.130 34.615 0.00 0.00 38.25 3.11
5916 10015 7.432869 TGAGCAGATAAAAGCAAAGCTAAAAA 58.567 30.769 0.00 0.00 38.25 1.94
5918 10017 6.573664 TGAGCAGATAAAAGCAAAGCTAAA 57.426 33.333 0.00 0.00 38.25 1.85
5922 10021 4.984161 TGTTTGAGCAGATAAAAGCAAAGC 59.016 37.500 0.00 0.00 0.00 3.51
5940 10039 5.476945 ACAAAAAGGGTAGAGGCTATGTTTG 59.523 40.000 0.00 0.00 0.00 2.93
5953 10052 1.002773 GAGCCTCCGACAAAAAGGGTA 59.997 52.381 0.00 0.00 40.84 3.69
6122 10226 0.392193 AGATCTTGTCAGCCGCCTTG 60.392 55.000 0.00 0.00 0.00 3.61
6129 10233 8.219769 CGATATAATGTTGAAGATCTTGTCAGC 58.780 37.037 14.00 8.46 0.00 4.26
6252 10428 6.183360 TGCACTGTAAACTCTTTATTGTTGCA 60.183 34.615 0.00 0.00 0.00 4.08
6316 10497 4.865925 CGGTGGAACTTCAATAATGACGTA 59.134 41.667 0.00 0.00 37.08 3.57
6339 10520 2.685850 ACTTCGTACACCTAATGGGC 57.314 50.000 0.00 0.00 39.10 5.36
6353 10534 3.129462 TCTGCAGATGGTAGAGAACTTCG 59.871 47.826 13.74 0.00 32.90 3.79
6665 11234 5.426689 ACTCTCATAACCTGAATTCAGCA 57.573 39.130 27.01 15.53 42.47 4.41
6682 11251 7.045126 AGCTTATCTGGTGTATGTTACTCTC 57.955 40.000 0.00 0.00 0.00 3.20
6701 11270 4.191544 CGGATCAAAGGATGTTGAGCTTA 58.808 43.478 3.53 0.00 42.29 3.09
6928 11498 1.064017 TCTAATTGCGGGGAAGCCAAT 60.064 47.619 0.00 0.00 36.02 3.16


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

AutoCloner maintained by Alex Coulton.