Multiple sequence alignment - TraesCS7A01G213300

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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 TraesCS7A01G213300 chr7A 100.000 4565 0 0 434 4998 177008834 177004270 0.000000e+00 8431.0
1 TraesCS7A01G213300 chr7A 87.310 197 25 0 1068 1264 587496625 587496821 5.030000e-55 226.0
2 TraesCS7A01G213300 chr7A 100.000 117 0 0 1 117 177009267 177009151 3.030000e-52 217.0
3 TraesCS7A01G213300 chr7A 98.734 79 1 0 4920 4998 655442159 655442081 1.880000e-29 141.0
4 TraesCS7A01G213300 chr7A 98.734 79 1 0 4920 4998 671218662 671218584 1.880000e-29 141.0
5 TraesCS7A01G213300 chr7D 92.545 3407 156 47 1539 4921 174801303 174797971 0.000000e+00 4795.0
6 TraesCS7A01G213300 chr7D 93.025 1061 32 13 434 1477 174802504 174801469 0.000000e+00 1511.0
7 TraesCS7A01G213300 chr7D 95.000 40 2 0 64 103 174802731 174802692 4.180000e-06 63.9
8 TraesCS7A01G213300 chr7B 94.427 2171 93 20 1539 3697 139724401 139722247 0.000000e+00 3314.0
9 TraesCS7A01G213300 chr7B 91.831 1065 46 19 3697 4737 139721870 139720823 0.000000e+00 1447.0
10 TraesCS7A01G213300 chr7B 90.035 1144 60 26 434 1536 139725626 139724496 0.000000e+00 1432.0
11 TraesCS7A01G213300 chr7B 86.996 223 15 7 4687 4905 139720830 139720618 6.470000e-59 239.0
12 TraesCS7A01G213300 chr7B 100.000 32 0 0 72 103 139725834 139725803 5.400000e-05 60.2
13 TraesCS7A01G213300 chr3D 90.191 2039 134 22 1740 3747 27900118 27898115 0.000000e+00 2597.0
14 TraesCS7A01G213300 chr3D 93.333 165 8 1 1539 1703 27900279 27900118 1.800000e-59 241.0
15 TraesCS7A01G213300 chr5A 88.740 746 44 18 1539 2282 654922691 654923398 0.000000e+00 876.0
16 TraesCS7A01G213300 chr5A 91.832 453 31 4 2278 2726 654933441 654933891 1.180000e-175 627.0
17 TraesCS7A01G213300 chr5A 88.215 297 31 3 1064 1360 219249658 219249950 7.960000e-93 351.0
18 TraesCS7A01G213300 chr5A 98.734 79 1 0 4920 4998 561682863 561682785 1.880000e-29 141.0
19 TraesCS7A01G213300 chr4A 87.542 297 33 3 1064 1360 419985596 419985304 1.720000e-89 340.0
20 TraesCS7A01G213300 chr3A 91.146 192 17 0 1064 1255 573516288 573516097 1.380000e-65 261.0
21 TraesCS7A01G213300 chr3A 98.734 79 1 0 4920 4998 65796763 65796685 1.880000e-29 141.0
22 TraesCS7A01G213300 chr3A 95.402 87 4 0 4912 4998 641812395 641812481 6.750000e-29 139.0
23 TraesCS7A01G213300 chr6A 90.104 192 19 0 1064 1255 214806221 214806030 2.990000e-62 250.0
24 TraesCS7A01G213300 chr6A 97.468 79 2 0 4920 4998 549402313 549402391 8.730000e-28 135.0
25 TraesCS7A01G213300 chr6A 97.468 79 2 0 4920 4998 614987390 614987468 8.730000e-28 135.0
26 TraesCS7A01G213300 chrUn 93.750 80 3 2 4920 4998 82935959 82935881 8.790000e-23 119.0
27 TraesCS7A01G213300 chrUn 93.750 80 3 2 4920 4998 393046695 393046617 8.790000e-23 119.0


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 TraesCS7A01G213300 chr7A 177004270 177009267 4997 True 4324.00 8431 100.000000 1 4998 2 chr7A.!!$R3 4997
1 TraesCS7A01G213300 chr7D 174797971 174802731 4760 True 2123.30 4795 93.523333 64 4921 3 chr7D.!!$R1 4857
2 TraesCS7A01G213300 chr7B 139720618 139725834 5216 True 1298.44 3314 92.657800 72 4905 5 chr7B.!!$R1 4833
3 TraesCS7A01G213300 chr3D 27898115 27900279 2164 True 1419.00 2597 91.762000 1539 3747 2 chr3D.!!$R1 2208
4 TraesCS7A01G213300 chr5A 654922691 654923398 707 False 876.00 876 88.740000 1539 2282 1 chr5A.!!$F2 743

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
47 48 0.099082 AACGAGAAGCGGATCGAGTC 59.901 55.0 13.19 0.0 46.49 3.36 F
1300 1354 0.098905 TGAGTCCGATTCTTCGCTCG 59.901 55.0 0.00 0.0 44.12 5.03 F
3117 3297 0.389948 CACCTGTTCGTAGAGTGGGC 60.390 60.0 0.00 0.0 38.43 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1521 0.241749 CAAGCGCAGGAAAATGAGCA 59.758 50.0 11.47 0.0 46.94 4.26 R
3240 3423 0.247185 CTGGCGTCAATGGGCAAAAT 59.753 50.0 0.00 0.0 39.63 1.82 R
4135 4699 0.035725 CCCCTCCCCGAGTTTTACAC 60.036 60.0 0.00 0.0 0.00 2.90 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
17 18 3.350612 CGCCGAGCCAAACCGAAA 61.351 61.111 0.00 0.00 0.00 3.46
18 19 2.899044 CGCCGAGCCAAACCGAAAA 61.899 57.895 0.00 0.00 0.00 2.29
19 20 1.081442 GCCGAGCCAAACCGAAAAG 60.081 57.895 0.00 0.00 0.00 2.27
20 21 1.512156 GCCGAGCCAAACCGAAAAGA 61.512 55.000 0.00 0.00 0.00 2.52
21 22 0.948678 CCGAGCCAAACCGAAAAGAA 59.051 50.000 0.00 0.00 0.00 2.52
22 23 1.335496 CCGAGCCAAACCGAAAAGAAA 59.665 47.619 0.00 0.00 0.00 2.52
23 24 2.223618 CCGAGCCAAACCGAAAAGAAAA 60.224 45.455 0.00 0.00 0.00 2.29
24 25 3.552068 CCGAGCCAAACCGAAAAGAAAAT 60.552 43.478 0.00 0.00 0.00 1.82
25 26 4.320641 CCGAGCCAAACCGAAAAGAAAATA 60.321 41.667 0.00 0.00 0.00 1.40
26 27 5.216648 CGAGCCAAACCGAAAAGAAAATAA 58.783 37.500 0.00 0.00 0.00 1.40
27 28 5.688176 CGAGCCAAACCGAAAAGAAAATAAA 59.312 36.000 0.00 0.00 0.00 1.40
28 29 6.199342 CGAGCCAAACCGAAAAGAAAATAAAA 59.801 34.615 0.00 0.00 0.00 1.52
29 30 7.254151 CGAGCCAAACCGAAAAGAAAATAAAAA 60.254 33.333 0.00 0.00 0.00 1.94
30 31 7.690228 AGCCAAACCGAAAAGAAAATAAAAAC 58.310 30.769 0.00 0.00 0.00 2.43
31 32 6.625702 GCCAAACCGAAAAGAAAATAAAAACG 59.374 34.615 0.00 0.00 0.00 3.60
32 33 7.464311 GCCAAACCGAAAAGAAAATAAAAACGA 60.464 33.333 0.00 0.00 0.00 3.85
33 34 8.053653 CCAAACCGAAAAGAAAATAAAAACGAG 58.946 33.333 0.00 0.00 0.00 4.18
34 35 8.800031 CAAACCGAAAAGAAAATAAAAACGAGA 58.200 29.630 0.00 0.00 0.00 4.04
35 36 8.914328 AACCGAAAAGAAAATAAAAACGAGAA 57.086 26.923 0.00 0.00 0.00 2.87
36 37 8.556517 ACCGAAAAGAAAATAAAAACGAGAAG 57.443 30.769 0.00 0.00 0.00 2.85
37 38 7.166970 ACCGAAAAGAAAATAAAAACGAGAAGC 59.833 33.333 0.00 0.00 0.00 3.86
39 40 6.986424 AAAGAAAATAAAAACGAGAAGCGG 57.014 33.333 0.00 0.00 46.49 5.52
40 41 5.934935 AGAAAATAAAAACGAGAAGCGGA 57.065 34.783 0.00 0.00 46.49 5.54
41 42 6.496338 AGAAAATAAAAACGAGAAGCGGAT 57.504 33.333 0.00 0.00 46.49 4.18
42 43 6.543736 AGAAAATAAAAACGAGAAGCGGATC 58.456 36.000 0.00 0.00 46.49 3.36
43 44 4.516092 AATAAAAACGAGAAGCGGATCG 57.484 40.909 6.04 6.04 46.49 3.69
44 45 2.074547 AAAAACGAGAAGCGGATCGA 57.925 45.000 13.19 0.00 46.49 3.59
45 46 1.630148 AAAACGAGAAGCGGATCGAG 58.370 50.000 13.19 0.50 46.49 4.04
46 47 0.526662 AAACGAGAAGCGGATCGAGT 59.473 50.000 13.19 1.03 46.49 4.18
47 48 0.099082 AACGAGAAGCGGATCGAGTC 59.901 55.000 13.19 0.00 46.49 3.36
48 49 1.368255 CGAGAAGCGGATCGAGTCG 60.368 63.158 6.09 6.09 41.40 4.18
49 50 1.722677 GAGAAGCGGATCGAGTCGT 59.277 57.895 13.12 0.00 0.00 4.34
50 51 0.316360 GAGAAGCGGATCGAGTCGTC 60.316 60.000 13.12 9.27 0.00 4.20
52 53 3.736482 AAGCGGATCGAGTCGTCGC 62.736 63.158 28.29 28.29 46.39 5.19
54 55 4.939915 CGGATCGAGTCGTCGCCG 62.940 72.222 21.62 21.62 46.39 6.46
477 500 2.740055 GGCAGAGGAGTGTGTGCG 60.740 66.667 0.00 0.00 37.59 5.34
481 504 0.941463 CAGAGGAGTGTGTGCGTCAC 60.941 60.000 5.12 5.12 46.31 3.67
489 515 4.961511 TGTGCGTCACGGCCACTC 62.962 66.667 2.24 0.00 37.14 3.51
538 565 3.508840 CGCCCCACAAATCGCTCC 61.509 66.667 0.00 0.00 0.00 4.70
560 587 0.469917 CTCGCCCTCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
561 588 0.468226 TCGCCCTCTCTCTCTCTCTC 59.532 60.000 0.00 0.00 0.00 3.20
562 589 0.535102 CGCCCTCTCTCTCTCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
563 590 0.178990 GCCCTCTCTCTCTCTCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
569 596 1.150536 CTCTCTCTCTCCCCCTCCG 59.849 68.421 0.00 0.00 0.00 4.63
828 874 1.662845 CGTTTCTCTCGCGAACGTCC 61.663 60.000 19.17 2.34 41.18 4.79
952 1006 1.673168 GATTTGAGGCTCGGATGCTT 58.327 50.000 10.42 0.00 0.00 3.91
953 1007 1.332997 GATTTGAGGCTCGGATGCTTG 59.667 52.381 10.42 0.00 0.00 4.01
954 1008 1.308069 TTTGAGGCTCGGATGCTTGC 61.308 55.000 10.42 0.00 0.00 4.01
1286 1340 1.856265 CTGCCGCCCAAAAGTGAGTC 61.856 60.000 0.00 0.00 0.00 3.36
1287 1341 2.626780 GCCGCCCAAAAGTGAGTCC 61.627 63.158 0.00 0.00 0.00 3.85
1300 1354 0.098905 TGAGTCCGATTCTTCGCTCG 59.901 55.000 0.00 0.00 44.12 5.03
1301 1355 1.203600 GAGTCCGATTCTTCGCTCGC 61.204 60.000 0.00 0.00 44.12 5.03
1302 1356 1.226717 GTCCGATTCTTCGCTCGCT 60.227 57.895 0.00 0.00 44.12 4.93
1303 1357 1.064296 TCCGATTCTTCGCTCGCTC 59.936 57.895 0.00 0.00 44.12 5.03
1367 1421 3.126831 CGAATGCTGTTCCTAGGACATC 58.873 50.000 12.22 9.30 0.00 3.06
1415 1469 4.580580 GGTACATCCATCCAAAATCTCCAC 59.419 45.833 0.00 0.00 35.97 4.02
1427 1481 5.163754 CCAAAATCTCCACCGTAGATTTCAC 60.164 44.000 10.54 0.00 36.51 3.18
1429 1483 1.475280 TCTCCACCGTAGATTTCACCG 59.525 52.381 0.00 0.00 0.00 4.94
1467 1521 2.279935 TGGTGGTTGGCGTAGATTTT 57.720 45.000 0.00 0.00 0.00 1.82
1477 1531 4.732784 TGGCGTAGATTTTGCTCATTTTC 58.267 39.130 0.00 0.00 0.00 2.29
1480 1534 4.795278 GCGTAGATTTTGCTCATTTTCCTG 59.205 41.667 0.00 0.00 0.00 3.86
1482 1536 3.841643 AGATTTTGCTCATTTTCCTGCG 58.158 40.909 0.00 0.00 0.00 5.18
1483 1537 1.782044 TTTTGCTCATTTTCCTGCGC 58.218 45.000 0.00 0.00 0.00 6.09
1511 1578 2.766345 TTGCGTAATTTACCTCGGGT 57.234 45.000 1.04 1.14 40.16 5.28
1514 1581 1.929169 GCGTAATTTACCTCGGGTGAC 59.071 52.381 5.90 0.00 36.19 3.67
1522 1589 2.582498 CTCGGGTGACGCGGATTC 60.582 66.667 21.64 0.00 43.86 2.52
1528 1595 1.436983 GGTGACGCGGATTCCATTCC 61.437 60.000 12.47 0.00 0.00 3.01
1547 1707 6.183360 CCATTCCGTGGTAATCTTGTAGAAAC 60.183 42.308 0.00 0.00 43.44 2.78
1911 2079 7.004555 ACTGTTGGTATGTTCAGTTAGATCA 57.995 36.000 0.00 0.00 37.81 2.92
1933 2101 1.011684 CGCTTCGACGTGTTTGCAA 60.012 52.632 0.00 0.00 0.00 4.08
1939 2107 1.179332 CGACGTGTTTGCAAACTGTG 58.821 50.000 35.09 26.93 39.59 3.66
2111 2280 4.805719 GCCTTGCCTTGAATATTTAAGCAC 59.194 41.667 13.19 8.70 0.00 4.40
2323 2496 9.936759 TTGGTTTCTTTTCTGTTTTGTTCTATT 57.063 25.926 0.00 0.00 0.00 1.73
2373 2546 7.062605 GCAAGATATTTGAATGTCACTTTGGTG 59.937 37.037 3.79 0.00 44.23 4.17
2376 2549 4.647424 TTTGAATGTCACTTTGGTGGTC 57.353 40.909 0.00 0.00 43.17 4.02
2538 2712 8.041323 AGTGAGTTCCAAGATATATTTGACGTT 58.959 33.333 0.00 0.00 0.00 3.99
2643 2819 0.539438 TGTTCCACTCAATGCCACCC 60.539 55.000 0.00 0.00 0.00 4.61
2898 3078 3.304794 CCTCTCTAAGATTTACCGCCGAG 60.305 52.174 0.00 0.00 0.00 4.63
3106 3286 4.704965 AGTTCTTAGGACAACACCTGTTC 58.295 43.478 0.00 0.00 38.84 3.18
3117 3297 0.389948 CACCTGTTCGTAGAGTGGGC 60.390 60.000 0.00 0.00 38.43 5.36
3119 3300 1.153823 CTGTTCGTAGAGTGGGCCG 60.154 63.158 0.00 0.00 38.43 6.13
3149 3330 8.798859 AACATTCAATTAGACATGCTCTTACT 57.201 30.769 0.00 0.00 0.00 2.24
3171 3352 6.055588 ACTACAGCTGTCAAACTATTGTTGT 58.944 36.000 25.56 0.00 37.79 3.32
3172 3353 5.424121 ACAGCTGTCAAACTATTGTTGTC 57.576 39.130 15.25 0.00 37.79 3.18
3192 3375 6.569127 TGTCCTTTTAGGTATGCTTATCCA 57.431 37.500 0.00 0.00 36.53 3.41
3240 3423 6.490040 ACTCGGATTTGAAAAGAAAAGATGGA 59.510 34.615 0.00 0.00 0.00 3.41
3399 3582 1.682849 TGTGGTATGGACACAGGGC 59.317 57.895 0.00 0.00 43.35 5.19
3409 3592 2.224992 TGGACACAGGGCACATGTTTAT 60.225 45.455 0.00 0.00 0.00 1.40
3425 3608 9.546909 CACATGTTTATCTGTTTATCACACTTC 57.453 33.333 0.00 0.00 0.00 3.01
3426 3609 9.507329 ACATGTTTATCTGTTTATCACACTTCT 57.493 29.630 0.00 0.00 0.00 2.85
3444 3627 9.388506 CACACTTCTATTATCTGGAAATGTCTT 57.611 33.333 0.00 0.00 33.24 3.01
3445 3628 9.388506 ACACTTCTATTATCTGGAAATGTCTTG 57.611 33.333 0.00 0.00 30.13 3.02
3446 3629 8.341173 CACTTCTATTATCTGGAAATGTCTTGC 58.659 37.037 0.00 0.00 0.00 4.01
3458 3641 5.221322 GGAAATGTCTTGCCTCTTCTTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
3470 3653 3.885297 TCTTCTTGTTTTCCTCCTTGCTG 59.115 43.478 0.00 0.00 0.00 4.41
3481 3665 2.818432 CCTCCTTGCTGATCATATTGCC 59.182 50.000 0.00 0.00 0.00 4.52
3486 3670 6.128486 TCCTTGCTGATCATATTGCCTTAAA 58.872 36.000 0.00 0.00 0.00 1.52
3701 4265 9.770503 CATACATTGCATATTTTCTCTCATAGC 57.229 33.333 0.00 0.00 0.00 2.97
3775 4339 3.888930 GGTTCATGGGTTTCAAGAAGACA 59.111 43.478 0.00 0.00 34.29 3.41
3829 4393 0.865769 CAGACCAGTACAACAACGGC 59.134 55.000 0.00 0.00 0.00 5.68
3898 4462 2.811514 GCGGATGGGATCAGCCTCA 61.812 63.158 0.00 0.00 46.66 3.86
3949 4513 1.598601 GAGGAGGACTACTTCTACGCG 59.401 57.143 3.53 3.53 34.20 6.01
4090 4654 0.735287 GAGGCCAGGTTCGTCGTTAC 60.735 60.000 5.01 0.00 0.00 2.50
4093 4657 1.066136 GCCAGGTTCGTCGTTACTTC 58.934 55.000 0.00 0.00 0.00 3.01
4095 4659 1.069022 CCAGGTTCGTCGTTACTTCGA 60.069 52.381 0.00 0.00 37.51 3.71
4096 4660 2.605338 CCAGGTTCGTCGTTACTTCGAA 60.605 50.000 0.00 0.00 41.47 3.71
4097 4661 2.655474 CAGGTTCGTCGTTACTTCGAAG 59.345 50.000 23.43 23.43 42.65 3.79
4098 4662 2.549754 AGGTTCGTCGTTACTTCGAAGA 59.450 45.455 31.08 12.25 43.67 2.87
4102 4666 3.300009 TCGTCGTTACTTCGAAGAAACC 58.700 45.455 31.08 13.99 45.90 3.27
4135 4699 4.671569 GGCTCGGCTCGCCATAGG 62.672 72.222 8.87 0.00 46.77 2.57
4138 4702 2.758327 TCGGCTCGCCATAGGTGT 60.758 61.111 8.87 0.00 34.40 4.16
4139 4703 1.452953 CTCGGCTCGCCATAGGTGTA 61.453 60.000 8.87 0.00 34.40 2.90
4145 4713 2.608090 GCTCGCCATAGGTGTAAAACTC 59.392 50.000 0.00 0.00 34.40 3.01
4233 4801 2.224209 CGTTATAGAAATGGAGGGCGGT 60.224 50.000 0.00 0.00 0.00 5.68
4251 4819 2.471103 CGGTTTATTCGTTCGTTCCACG 60.471 50.000 0.00 0.00 44.19 4.94
4346 4915 7.360438 CGAAGAGGAAAGGTAAATTTGAGTGAG 60.360 40.741 0.00 0.00 0.00 3.51
4424 4995 7.713507 TGTGTAAAACATACTAGCAGTTGTTCT 59.286 33.333 0.00 6.48 32.44 3.01
4425 4996 8.557029 GTGTAAAACATACTAGCAGTTGTTCTT 58.443 33.333 0.00 11.49 32.44 2.52
4426 4997 8.770828 TGTAAAACATACTAGCAGTTGTTCTTC 58.229 33.333 0.00 8.93 32.44 2.87
4427 4998 8.989980 GTAAAACATACTAGCAGTTGTTCTTCT 58.010 33.333 0.00 0.00 32.44 2.85
4428 4999 7.659652 AAACATACTAGCAGTTGTTCTTCTC 57.340 36.000 0.00 0.00 32.44 2.87
4447 5018 3.851128 GTAGCCTCCCCCGTGCTC 61.851 72.222 0.00 0.00 36.57 4.26
4460 5031 4.316823 TGCTCCCTCCCCGTCAGT 62.317 66.667 0.00 0.00 0.00 3.41
4465 5036 3.775654 CCTCCCCGTCAGTCAGGC 61.776 72.222 0.00 0.00 0.00 4.85
4466 5037 2.997315 CTCCCCGTCAGTCAGGCA 60.997 66.667 0.00 0.00 0.00 4.75
4467 5038 2.997315 TCCCCGTCAGTCAGGCAG 60.997 66.667 0.00 0.00 0.00 4.85
4468 5039 4.087892 CCCCGTCAGTCAGGCAGG 62.088 72.222 0.00 0.00 0.00 4.85
4469 5040 4.087892 CCCGTCAGTCAGGCAGGG 62.088 72.222 0.00 0.00 31.24 4.45
4470 5041 4.767255 CCGTCAGTCAGGCAGGGC 62.767 72.222 0.00 0.00 0.00 5.19
4473 5044 1.888436 CGTCAGTCAGGCAGGGCTTA 61.888 60.000 0.00 0.00 0.00 3.09
4559 5130 1.690283 CCTGTGCAGAATGTCGCTCG 61.690 60.000 0.02 0.00 39.31 5.03
4598 5172 0.460109 TGATCCGTTGGTGCATCGAG 60.460 55.000 0.00 0.00 0.00 4.04
4619 5193 0.184451 CCTTACATGGGGCTGATGCT 59.816 55.000 0.00 0.00 39.59 3.79
4663 5250 1.144716 TGATCTGCGCCCTCATGTC 59.855 57.895 4.18 0.00 0.00 3.06
4671 5258 0.660595 CGCCCTCATGTCGTACGATC 60.661 60.000 22.57 15.08 0.00 3.69
4672 5259 0.384309 GCCCTCATGTCGTACGATCA 59.616 55.000 22.57 19.98 0.00 2.92
4676 5263 2.357952 CCTCATGTCGTACGATCAGGAA 59.642 50.000 22.57 11.21 0.00 3.36
4681 5268 4.611310 TGTCGTACGATCAGGAACTTAG 57.389 45.455 22.57 0.00 34.60 2.18
4743 5369 4.925054 AGCGGATTTTTCATGTTCATTGTG 59.075 37.500 0.00 0.00 0.00 3.33
4785 5411 3.742433 TGCCATGTTGATTTTCCGTTT 57.258 38.095 0.00 0.00 0.00 3.60
4786 5412 3.388308 TGCCATGTTGATTTTCCGTTTG 58.612 40.909 0.00 0.00 0.00 2.93
4787 5413 2.157474 GCCATGTTGATTTTCCGTTTGC 59.843 45.455 0.00 0.00 0.00 3.68
4809 5435 3.533606 GAGCTGCATTACTCCTCTTGA 57.466 47.619 1.02 0.00 0.00 3.02
4811 5437 2.170187 AGCTGCATTACTCCTCTTGAGG 59.830 50.000 10.28 10.28 46.01 3.86
4812 5438 2.559440 CTGCATTACTCCTCTTGAGGC 58.441 52.381 11.61 0.00 46.01 4.70
4813 5439 1.908619 TGCATTACTCCTCTTGAGGCA 59.091 47.619 11.61 2.14 46.01 4.75
4814 5440 2.507058 TGCATTACTCCTCTTGAGGCAT 59.493 45.455 11.61 5.03 46.01 4.40
4845 5471 6.145371 TGTGTTTCTTTTCTTGTTTGCTGTTC 59.855 34.615 0.00 0.00 0.00 3.18
4921 5547 2.467826 GGCTGCTGCGGACTGAATC 61.468 63.158 13.72 0.00 40.82 2.52
4922 5548 1.742880 GCTGCTGCGGACTGAATCA 60.743 57.895 13.72 0.00 0.00 2.57
4923 5549 1.300971 GCTGCTGCGGACTGAATCAA 61.301 55.000 13.72 0.00 0.00 2.57
4924 5550 0.725686 CTGCTGCGGACTGAATCAAG 59.274 55.000 1.17 0.00 0.00 3.02
4925 5551 0.321346 TGCTGCGGACTGAATCAAGA 59.679 50.000 0.00 0.00 0.00 3.02
4926 5552 1.005340 GCTGCGGACTGAATCAAGAG 58.995 55.000 0.00 0.00 0.00 2.85
4927 5553 1.404717 GCTGCGGACTGAATCAAGAGA 60.405 52.381 0.00 0.00 0.00 3.10
4928 5554 2.741228 GCTGCGGACTGAATCAAGAGAT 60.741 50.000 0.00 0.00 35.53 2.75
4929 5555 3.491619 GCTGCGGACTGAATCAAGAGATA 60.492 47.826 0.00 0.00 33.08 1.98
4930 5556 4.686972 CTGCGGACTGAATCAAGAGATAA 58.313 43.478 0.00 0.00 33.08 1.75
4931 5557 4.686972 TGCGGACTGAATCAAGAGATAAG 58.313 43.478 0.00 0.00 33.08 1.73
4932 5558 4.402474 TGCGGACTGAATCAAGAGATAAGA 59.598 41.667 0.00 0.00 33.08 2.10
4933 5559 4.981674 GCGGACTGAATCAAGAGATAAGAG 59.018 45.833 0.00 0.00 33.08 2.85
4934 5560 5.221145 GCGGACTGAATCAAGAGATAAGAGA 60.221 44.000 0.00 0.00 33.08 3.10
4935 5561 6.681616 GCGGACTGAATCAAGAGATAAGAGAA 60.682 42.308 0.00 0.00 33.08 2.87
4936 5562 6.917477 CGGACTGAATCAAGAGATAAGAGAAG 59.083 42.308 0.00 0.00 33.08 2.85
4937 5563 7.209475 GGACTGAATCAAGAGATAAGAGAAGG 58.791 42.308 0.00 0.00 33.08 3.46
4938 5564 7.069331 GGACTGAATCAAGAGATAAGAGAAGGA 59.931 40.741 0.00 0.00 33.08 3.36
4939 5565 8.551682 ACTGAATCAAGAGATAAGAGAAGGAT 57.448 34.615 0.00 0.00 33.08 3.24
4940 5566 8.423349 ACTGAATCAAGAGATAAGAGAAGGATG 58.577 37.037 0.00 0.00 33.08 3.51
4941 5567 8.316497 TGAATCAAGAGATAAGAGAAGGATGT 57.684 34.615 0.00 0.00 33.08 3.06
4942 5568 8.766476 TGAATCAAGAGATAAGAGAAGGATGTT 58.234 33.333 0.00 0.00 33.08 2.71
4943 5569 9.260002 GAATCAAGAGATAAGAGAAGGATGTTC 57.740 37.037 0.00 0.00 33.08 3.18
4944 5570 7.118496 TCAAGAGATAAGAGAAGGATGTTCC 57.882 40.000 0.00 0.00 36.58 3.62
4945 5571 6.669591 TCAAGAGATAAGAGAAGGATGTTCCA 59.330 38.462 0.00 0.00 39.61 3.53
4946 5572 6.478512 AGAGATAAGAGAAGGATGTTCCAC 57.521 41.667 0.00 0.00 39.61 4.02
4947 5573 5.365314 AGAGATAAGAGAAGGATGTTCCACC 59.635 44.000 0.00 0.00 39.61 4.61
4948 5574 2.770164 AAGAGAAGGATGTTCCACCG 57.230 50.000 0.00 0.00 39.61 4.94
4949 5575 1.938585 AGAGAAGGATGTTCCACCGA 58.061 50.000 0.00 0.00 39.61 4.69
4950 5576 1.827969 AGAGAAGGATGTTCCACCGAG 59.172 52.381 0.00 0.00 39.61 4.63
4951 5577 0.250513 AGAAGGATGTTCCACCGAGC 59.749 55.000 0.00 0.00 39.61 5.03
4952 5578 0.250513 GAAGGATGTTCCACCGAGCT 59.749 55.000 0.00 0.00 39.61 4.09
4953 5579 0.250513 AAGGATGTTCCACCGAGCTC 59.749 55.000 2.73 2.73 39.61 4.09
4954 5580 0.616111 AGGATGTTCCACCGAGCTCT 60.616 55.000 12.85 0.00 39.61 4.09
4955 5581 0.179097 GGATGTTCCACCGAGCTCTC 60.179 60.000 12.85 0.00 36.28 3.20
4956 5582 0.820871 GATGTTCCACCGAGCTCTCT 59.179 55.000 12.85 0.00 0.00 3.10
4957 5583 0.820871 ATGTTCCACCGAGCTCTCTC 59.179 55.000 12.85 0.00 35.99 3.20
4958 5584 0.539669 TGTTCCACCGAGCTCTCTCA 60.540 55.000 12.85 0.00 39.30 3.27
4959 5585 0.172352 GTTCCACCGAGCTCTCTCAG 59.828 60.000 12.85 0.00 39.30 3.35
4960 5586 0.038310 TTCCACCGAGCTCTCTCAGA 59.962 55.000 12.85 0.00 39.30 3.27
4961 5587 0.393673 TCCACCGAGCTCTCTCAGAG 60.394 60.000 12.85 0.00 45.04 3.35
4969 5595 2.178856 CTCTCTCAGAGCTCACGCA 58.821 57.895 17.77 0.00 35.30 5.24
4970 5596 0.179166 CTCTCTCAGAGCTCACGCAC 60.179 60.000 17.77 0.00 35.30 5.34
4971 5597 0.607762 TCTCTCAGAGCTCACGCACT 60.608 55.000 17.77 0.00 37.57 4.40
4972 5598 0.179166 CTCTCAGAGCTCACGCACTC 60.179 60.000 17.77 0.00 34.74 3.51
4973 5599 0.607762 TCTCAGAGCTCACGCACTCT 60.608 55.000 17.77 0.00 44.06 3.24
4974 5600 0.179166 CTCAGAGCTCACGCACTCTC 60.179 60.000 17.77 0.00 41.31 3.20
4975 5601 1.513800 CAGAGCTCACGCACTCTCG 60.514 63.158 17.77 0.00 41.31 4.04
4976 5602 2.202544 GAGCTCACGCACTCTCGG 60.203 66.667 9.40 0.00 39.10 4.63
4977 5603 4.427661 AGCTCACGCACTCTCGGC 62.428 66.667 0.00 0.00 39.10 5.54
4984 5610 4.373116 GCACTCTCGGCCGTTGGA 62.373 66.667 27.15 19.63 0.00 3.53
4985 5611 2.579201 CACTCTCGGCCGTTGGAT 59.421 61.111 27.15 5.38 0.00 3.41
4986 5612 1.519455 CACTCTCGGCCGTTGGATC 60.519 63.158 27.15 0.00 0.00 3.36
4987 5613 2.278857 CTCTCGGCCGTTGGATCG 60.279 66.667 27.15 7.58 0.00 3.69
4994 5620 2.125673 CCGTTGGATCGGTTCGCT 60.126 61.111 0.00 0.00 44.77 4.93
4995 5621 1.740296 CCGTTGGATCGGTTCGCTT 60.740 57.895 0.00 0.00 44.77 4.68
4996 5622 1.419922 CGTTGGATCGGTTCGCTTG 59.580 57.895 0.00 0.00 0.00 4.01
4997 5623 1.011968 CGTTGGATCGGTTCGCTTGA 61.012 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.780149 CTTTTCGGTTTGGCTCGGCG 62.780 60.000 0.00 0.00 0.00 6.46
1 2 1.081442 CTTTTCGGTTTGGCTCGGC 60.081 57.895 0.00 0.00 0.00 5.54
2 3 0.948678 TTCTTTTCGGTTTGGCTCGG 59.051 50.000 0.00 0.00 0.00 4.63
3 4 2.766970 TTTCTTTTCGGTTTGGCTCG 57.233 45.000 0.00 0.00 0.00 5.03
4 5 7.471657 TTTTATTTTCTTTTCGGTTTGGCTC 57.528 32.000 0.00 0.00 0.00 4.70
5 6 7.464844 CGTTTTTATTTTCTTTTCGGTTTGGCT 60.465 33.333 0.00 0.00 0.00 4.75
6 7 6.625702 CGTTTTTATTTTCTTTTCGGTTTGGC 59.374 34.615 0.00 0.00 0.00 4.52
7 8 7.896894 TCGTTTTTATTTTCTTTTCGGTTTGG 58.103 30.769 0.00 0.00 0.00 3.28
8 9 8.800031 TCTCGTTTTTATTTTCTTTTCGGTTTG 58.200 29.630 0.00 0.00 0.00 2.93
9 10 8.914328 TCTCGTTTTTATTTTCTTTTCGGTTT 57.086 26.923 0.00 0.00 0.00 3.27
10 11 8.914328 TTCTCGTTTTTATTTTCTTTTCGGTT 57.086 26.923 0.00 0.00 0.00 4.44
11 12 7.166970 GCTTCTCGTTTTTATTTTCTTTTCGGT 59.833 33.333 0.00 0.00 0.00 4.69
12 13 7.490868 GCTTCTCGTTTTTATTTTCTTTTCGG 58.509 34.615 0.00 0.00 0.00 4.30
13 14 7.204418 CGCTTCTCGTTTTTATTTTCTTTTCG 58.796 34.615 0.00 0.00 0.00 3.46
14 15 7.377662 TCCGCTTCTCGTTTTTATTTTCTTTTC 59.622 33.333 0.00 0.00 36.19 2.29
15 16 7.197703 TCCGCTTCTCGTTTTTATTTTCTTTT 58.802 30.769 0.00 0.00 36.19 2.27
16 17 6.731164 TCCGCTTCTCGTTTTTATTTTCTTT 58.269 32.000 0.00 0.00 36.19 2.52
17 18 6.308371 TCCGCTTCTCGTTTTTATTTTCTT 57.692 33.333 0.00 0.00 36.19 2.52
18 19 5.934935 TCCGCTTCTCGTTTTTATTTTCT 57.065 34.783 0.00 0.00 36.19 2.52
19 20 5.448162 CGATCCGCTTCTCGTTTTTATTTTC 59.552 40.000 0.00 0.00 36.19 2.29
20 21 5.121142 TCGATCCGCTTCTCGTTTTTATTTT 59.879 36.000 0.00 0.00 36.33 1.82
21 22 4.628333 TCGATCCGCTTCTCGTTTTTATTT 59.372 37.500 0.00 0.00 36.33 1.40
22 23 4.178540 TCGATCCGCTTCTCGTTTTTATT 58.821 39.130 0.00 0.00 36.33 1.40
23 24 3.777478 TCGATCCGCTTCTCGTTTTTAT 58.223 40.909 0.00 0.00 36.33 1.40
24 25 3.176708 CTCGATCCGCTTCTCGTTTTTA 58.823 45.455 0.00 0.00 36.33 1.52
25 26 1.993370 CTCGATCCGCTTCTCGTTTTT 59.007 47.619 0.00 0.00 36.33 1.94
26 27 1.067776 ACTCGATCCGCTTCTCGTTTT 60.068 47.619 0.00 0.00 36.33 2.43
27 28 0.526662 ACTCGATCCGCTTCTCGTTT 59.473 50.000 0.00 0.00 36.33 3.60
28 29 0.099082 GACTCGATCCGCTTCTCGTT 59.901 55.000 0.00 0.00 36.33 3.85
29 30 1.722677 GACTCGATCCGCTTCTCGT 59.277 57.895 0.00 0.00 36.33 4.18
30 31 1.368255 CGACTCGATCCGCTTCTCG 60.368 63.158 0.00 0.00 36.25 4.04
31 32 0.316360 GACGACTCGATCCGCTTCTC 60.316 60.000 5.20 0.00 0.00 2.87
32 33 1.722677 GACGACTCGATCCGCTTCT 59.277 57.895 5.20 0.00 0.00 2.85
33 34 1.651730 CGACGACTCGATCCGCTTC 60.652 63.158 5.20 0.00 43.06 3.86
34 35 2.403987 CGACGACTCGATCCGCTT 59.596 61.111 5.20 0.00 43.06 4.68
35 36 4.239203 GCGACGACTCGATCCGCT 62.239 66.667 21.01 0.00 43.06 5.52
477 500 4.699522 GGTGGGAGTGGCCGTGAC 62.700 72.222 0.00 0.00 37.63 3.67
538 565 2.520741 GAGAGAGAGGGCGAGGGG 60.521 72.222 0.00 0.00 0.00 4.79
560 587 4.779733 GCAGAGGACGGAGGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
569 596 2.503382 GGATCTCGGGGCAGAGGAC 61.503 68.421 8.93 4.47 38.71 3.85
694 721 4.662961 CCGGAGCAGACACGTGCA 62.663 66.667 17.22 0.00 46.60 4.57
704 731 2.985282 CAAAAGCAGGCCGGAGCA 60.985 61.111 5.05 0.00 42.56 4.26
954 1008 3.749064 CCTTGGCAGCAGCAGCAG 61.749 66.667 12.41 1.09 45.49 4.24
986 1040 0.887247 CGCCATCAACAACCATGGAA 59.113 50.000 21.47 0.00 42.11 3.53
1300 1354 2.220887 CGAAAGCGAGAGAGCGAGC 61.221 63.158 0.00 0.00 43.00 5.03
1301 1355 3.975451 CGAAAGCGAGAGAGCGAG 58.025 61.111 0.00 0.00 43.00 5.03
1415 1469 1.470979 CCAGGTCGGTGAAATCTACGG 60.471 57.143 0.00 0.00 0.00 4.02
1427 1481 4.067896 CAATCTTTATCATCCCAGGTCGG 58.932 47.826 0.00 0.00 0.00 4.79
1429 1483 4.823989 CACCAATCTTTATCATCCCAGGTC 59.176 45.833 0.00 0.00 0.00 3.85
1467 1521 0.241749 CAAGCGCAGGAAAATGAGCA 59.758 50.000 11.47 0.00 46.94 4.26
1511 1578 4.532490 GGAATGGAATCCGCGTCA 57.468 55.556 4.92 0.00 0.00 4.35
1528 1595 4.630069 CCCAGTTTCTACAAGATTACCACG 59.370 45.833 0.00 0.00 0.00 4.94
1537 1604 4.396166 CCTACATTGCCCAGTTTCTACAAG 59.604 45.833 0.00 0.00 0.00 3.16
1547 1707 2.053244 AGGAGATCCTACATTGCCCAG 58.947 52.381 0.00 0.00 46.48 4.45
1911 2079 1.959226 AAACACGTCGAAGCGCCAT 60.959 52.632 2.29 0.00 34.88 4.40
1933 2101 9.334947 CTCATAATTATGAATGAGGACACAGTT 57.665 33.333 24.61 0.00 43.50 3.16
1987 2155 2.373335 AGCAGTCCCTCGAGTCATAT 57.627 50.000 12.31 0.00 0.00 1.78
2111 2280 7.502120 AAAACATTAGCACAGATATAGCAGG 57.498 36.000 0.00 0.00 0.00 4.85
2120 2289 6.206438 TGACAGCAATAAAACATTAGCACAGA 59.794 34.615 0.00 0.00 0.00 3.41
2265 2434 1.549203 ATGGTTGCCAAGGACATCAC 58.451 50.000 0.00 0.00 36.95 3.06
2267 2436 2.094545 GTCAATGGTTGCCAAGGACATC 60.095 50.000 13.86 0.00 39.12 3.06
2272 2441 1.915141 AGAGTCAATGGTTGCCAAGG 58.085 50.000 0.00 0.00 36.95 3.61
2323 2496 8.646900 TGCTATTACAACCATGTCACATATCTA 58.353 33.333 0.00 0.00 41.05 1.98
2376 2549 2.370189 AGAAGTCTTGTCCAACTCTGGG 59.630 50.000 0.00 0.00 43.71 4.45
2459 2633 4.193826 AGCTCGCTGATAGTTCAAGAAA 57.806 40.909 0.00 0.00 0.00 2.52
2472 2646 2.095059 ACATTAAAGGCAAAGCTCGCTG 60.095 45.455 7.90 0.75 0.00 5.18
2477 2651 4.527816 TGGATCAACATTAAAGGCAAAGCT 59.472 37.500 0.00 0.00 0.00 3.74
2538 2712 4.693566 CGCAAGGAGGTTATAAAGTGTTCA 59.306 41.667 0.00 0.00 0.00 3.18
2756 2936 4.164030 TCCGAATCAATGGAAGAATCTGGA 59.836 41.667 0.00 0.00 0.00 3.86
2898 3078 1.332997 CGCTTGCCCAGATCTTCAATC 59.667 52.381 0.00 0.00 0.00 2.67
3076 3256 8.101419 AGGTGTTGTCCTAAGAACTAAATTAGG 58.899 37.037 4.92 4.89 46.35 2.69
3077 3257 8.936864 CAGGTGTTGTCCTAAGAACTAAATTAG 58.063 37.037 0.00 0.00 35.87 1.73
3078 3258 8.434392 ACAGGTGTTGTCCTAAGAACTAAATTA 58.566 33.333 0.00 0.00 33.87 1.40
3080 3260 6.838382 ACAGGTGTTGTCCTAAGAACTAAAT 58.162 36.000 0.00 0.00 33.87 1.40
3082 3262 5.881923 ACAGGTGTTGTCCTAAGAACTAA 57.118 39.130 0.00 0.00 33.87 2.24
3083 3263 5.508489 CGAACAGGTGTTGTCCTAAGAACTA 60.508 44.000 0.00 0.00 39.73 2.24
3084 3264 4.704965 GAACAGGTGTTGTCCTAAGAACT 58.295 43.478 0.00 0.00 39.73 3.01
3085 3265 3.493503 CGAACAGGTGTTGTCCTAAGAAC 59.506 47.826 0.00 0.00 39.73 3.01
3106 3286 1.728425 GTTTTAACGGCCCACTCTACG 59.272 52.381 0.00 0.00 0.00 3.51
3117 3297 7.754924 AGCATGTCTAATTGAATGTTTTAACGG 59.245 33.333 0.00 0.00 0.00 4.44
3119 3300 9.846248 AGAGCATGTCTAATTGAATGTTTTAAC 57.154 29.630 0.00 0.00 31.71 2.01
3149 3330 5.468746 GGACAACAATAGTTTGACAGCTGTA 59.531 40.000 21.73 1.24 35.28 2.74
3171 3352 6.102615 ACCATGGATAAGCATACCTAAAAGGA 59.897 38.462 21.47 0.00 37.67 3.36
3172 3353 6.207417 CACCATGGATAAGCATACCTAAAAGG 59.793 42.308 21.47 0.00 42.49 3.11
3192 3375 5.355350 GTCGATGATTTTCTCTTTCCACCAT 59.645 40.000 0.00 0.00 0.00 3.55
3240 3423 0.247185 CTGGCGTCAATGGGCAAAAT 59.753 50.000 0.00 0.00 39.63 1.82
3397 3580 6.747280 GTGTGATAAACAGATAAACATGTGCC 59.253 38.462 0.00 0.00 40.26 5.01
3399 3582 9.546909 GAAGTGTGATAAACAGATAAACATGTG 57.453 33.333 0.00 0.00 40.26 3.21
3425 3608 7.222872 AGAGGCAAGACATTTCCAGATAATAG 58.777 38.462 0.00 0.00 0.00 1.73
3426 3609 7.141758 AGAGGCAAGACATTTCCAGATAATA 57.858 36.000 0.00 0.00 0.00 0.98
3432 3615 3.683802 AGAAGAGGCAAGACATTTCCAG 58.316 45.455 0.00 0.00 0.00 3.86
3440 3623 3.885901 AGGAAAACAAGAAGAGGCAAGAC 59.114 43.478 0.00 0.00 0.00 3.01
3444 3627 2.443255 AGGAGGAAAACAAGAAGAGGCA 59.557 45.455 0.00 0.00 0.00 4.75
3445 3628 3.147553 AGGAGGAAAACAAGAAGAGGC 57.852 47.619 0.00 0.00 0.00 4.70
3446 3629 3.254411 GCAAGGAGGAAAACAAGAAGAGG 59.746 47.826 0.00 0.00 0.00 3.69
3458 3641 4.139786 GCAATATGATCAGCAAGGAGGAA 58.860 43.478 0.09 0.00 0.00 3.36
3486 3670 7.391833 GTCTCTTTCCTCACCTGTAAATCATTT 59.608 37.037 0.00 0.00 0.00 2.32
3666 3850 6.395426 AATATGCAATGTATGACCAAGTGG 57.605 37.500 0.00 0.00 42.17 4.00
3701 4265 7.526608 ACACATCGGAATAAATACACAACTTG 58.473 34.615 0.00 0.00 0.00 3.16
3775 4339 6.199908 CGATGAGTTTTCGATCTAGCAAGATT 59.800 38.462 0.00 0.00 42.73 2.40
3782 4346 4.667061 GTCGACGATGAGTTTTCGATCTAG 59.333 45.833 0.00 0.00 39.81 2.43
3829 4393 0.179100 ACTCATCCCATCGCAACGAG 60.179 55.000 0.00 0.00 39.91 4.18
3898 4462 0.673644 CGGGAATCACTGTCCGCTTT 60.674 55.000 0.00 0.00 35.86 3.51
3949 4513 2.936032 AGGCACTCCTGGGGGTTC 60.936 66.667 0.00 0.00 42.34 3.62
3991 4555 1.522806 TGGCGGCGGTTATCATGAC 60.523 57.895 9.78 0.00 0.00 3.06
4070 4634 0.896940 TAACGACGAACCTGGCCTCT 60.897 55.000 3.32 0.00 0.00 3.69
4090 4654 3.558418 TCTTTCGGTTGGTTTCTTCGAAG 59.442 43.478 19.35 19.35 40.21 3.79
4093 4657 2.223377 CCTCTTTCGGTTGGTTTCTTCG 59.777 50.000 0.00 0.00 0.00 3.79
4095 4659 2.583143 CCCTCTTTCGGTTGGTTTCTT 58.417 47.619 0.00 0.00 0.00 2.52
4096 4660 1.202891 CCCCTCTTTCGGTTGGTTTCT 60.203 52.381 0.00 0.00 0.00 2.52
4097 4661 1.244816 CCCCTCTTTCGGTTGGTTTC 58.755 55.000 0.00 0.00 0.00 2.78
4098 4662 0.826256 GCCCCTCTTTCGGTTGGTTT 60.826 55.000 0.00 0.00 0.00 3.27
4101 4665 2.746277 CGCCCCTCTTTCGGTTGG 60.746 66.667 0.00 0.00 0.00 3.77
4102 4666 2.746277 CCGCCCCTCTTTCGGTTG 60.746 66.667 0.00 0.00 38.47 3.77
4135 4699 0.035725 CCCCTCCCCGAGTTTTACAC 60.036 60.000 0.00 0.00 0.00 2.90
4138 4702 1.161598 ACCCCCTCCCCGAGTTTTA 59.838 57.895 0.00 0.00 0.00 1.52
4139 4703 2.121644 ACCCCCTCCCCGAGTTTT 60.122 61.111 0.00 0.00 0.00 2.43
4162 4730 5.708736 ACATCCAAGATATACAACACCCA 57.291 39.130 0.00 0.00 0.00 4.51
4346 4915 2.447714 GGTCCAGCCATCTCTCCCC 61.448 68.421 0.00 0.00 37.17 4.81
4424 4995 2.042230 GGGGGAGGCTACGGAGAA 60.042 66.667 0.00 0.00 0.00 2.87
4425 4996 4.517934 CGGGGGAGGCTACGGAGA 62.518 72.222 0.00 0.00 0.00 3.71
4426 4997 4.835891 ACGGGGGAGGCTACGGAG 62.836 72.222 0.00 0.00 0.00 4.63
4447 5018 3.077556 CCTGACTGACGGGGAGGG 61.078 72.222 0.00 0.00 41.14 4.30
4559 5130 5.699097 TCAATAAAACTGTACCAAGTGGC 57.301 39.130 0.00 0.00 39.32 5.01
4619 5193 1.342819 TCACATCACATGGTCACGTGA 59.657 47.619 15.76 15.76 45.62 4.35
4663 5250 4.832590 ATCCTAAGTTCCTGATCGTACG 57.167 45.455 9.53 9.53 0.00 3.67
4671 5258 8.737168 TCAAACATGAATATCCTAAGTTCCTG 57.263 34.615 0.00 0.00 0.00 3.86
4672 5259 9.347240 CATCAAACATGAATATCCTAAGTTCCT 57.653 33.333 0.00 0.00 0.00 3.36
4676 5263 9.685276 TGTTCATCAAACATGAATATCCTAAGT 57.315 29.630 0.00 0.00 42.95 2.24
4705 5331 1.587043 CCGCTCTCGAGTCCTGAACA 61.587 60.000 13.13 0.00 38.10 3.18
4763 5389 3.025287 ACGGAAAATCAACATGGCAAC 57.975 42.857 0.00 0.00 0.00 4.17
4786 5412 3.724494 GGAGTAATGCAGCTCCGC 58.276 61.111 15.86 0.00 41.40 5.54
4789 5415 3.456280 CTCAAGAGGAGTAATGCAGCTC 58.544 50.000 0.00 0.00 38.90 4.09
4790 5416 3.540314 CTCAAGAGGAGTAATGCAGCT 57.460 47.619 0.00 0.00 38.90 4.24
4845 5471 4.401925 ACAAAAACCCTCTGAATCTCAGG 58.598 43.478 3.92 0.00 44.39 3.86
4861 5487 6.626302 ACGAGACAAGGAAAAATGACAAAAA 58.374 32.000 0.00 0.00 0.00 1.94
4906 5532 0.321346 TCTTGATTCAGTCCGCAGCA 59.679 50.000 0.00 0.00 0.00 4.41
4921 5547 6.760770 GTGGAACATCCTTCTCTTATCTCTTG 59.239 42.308 0.00 0.00 44.52 3.02
4922 5548 6.126911 GGTGGAACATCCTTCTCTTATCTCTT 60.127 42.308 0.00 0.00 44.52 2.85
4923 5549 5.365314 GGTGGAACATCCTTCTCTTATCTCT 59.635 44.000 0.00 0.00 44.52 3.10
4924 5550 5.606505 GGTGGAACATCCTTCTCTTATCTC 58.393 45.833 0.00 0.00 44.52 2.75
4925 5551 4.100189 CGGTGGAACATCCTTCTCTTATCT 59.900 45.833 0.00 0.00 44.52 1.98
4926 5552 4.099573 TCGGTGGAACATCCTTCTCTTATC 59.900 45.833 0.00 0.00 44.52 1.75
4927 5553 4.030913 TCGGTGGAACATCCTTCTCTTAT 58.969 43.478 0.00 0.00 44.52 1.73
4928 5554 3.437213 TCGGTGGAACATCCTTCTCTTA 58.563 45.455 0.00 0.00 44.52 2.10
4929 5555 2.234908 CTCGGTGGAACATCCTTCTCTT 59.765 50.000 0.00 0.00 44.52 2.85
4930 5556 1.827969 CTCGGTGGAACATCCTTCTCT 59.172 52.381 0.00 0.00 44.52 3.10
4931 5557 1.740718 GCTCGGTGGAACATCCTTCTC 60.741 57.143 0.00 0.00 44.52 2.87
4932 5558 0.250513 GCTCGGTGGAACATCCTTCT 59.749 55.000 0.00 0.00 44.52 2.85
4933 5559 0.250513 AGCTCGGTGGAACATCCTTC 59.749 55.000 0.00 0.00 44.52 3.46
4934 5560 0.250513 GAGCTCGGTGGAACATCCTT 59.749 55.000 0.00 0.00 44.52 3.36
4935 5561 0.616111 AGAGCTCGGTGGAACATCCT 60.616 55.000 8.37 0.00 44.52 3.24
4936 5562 0.179097 GAGAGCTCGGTGGAACATCC 60.179 60.000 8.37 0.00 44.52 3.51
4937 5563 0.820871 AGAGAGCTCGGTGGAACATC 59.179 55.000 8.37 0.00 39.98 3.06
4938 5564 0.820871 GAGAGAGCTCGGTGGAACAT 59.179 55.000 8.37 0.00 39.98 2.71
4939 5565 0.539669 TGAGAGAGCTCGGTGGAACA 60.540 55.000 8.37 0.76 44.33 3.18
4940 5566 0.172352 CTGAGAGAGCTCGGTGGAAC 59.828 60.000 8.37 0.00 44.33 3.62
4941 5567 0.038310 TCTGAGAGAGCTCGGTGGAA 59.962 55.000 8.37 0.00 45.81 3.53
4942 5568 0.393673 CTCTGAGAGAGCTCGGTGGA 60.394 60.000 2.60 3.92 45.81 4.02
4943 5569 2.105984 CTCTGAGAGAGCTCGGTGG 58.894 63.158 2.60 0.00 45.81 4.61
4967 5593 3.665675 ATCCAACGGCCGAGAGTGC 62.666 63.158 35.90 0.00 0.00 4.40
4968 5594 1.519455 GATCCAACGGCCGAGAGTG 60.519 63.158 35.90 22.18 0.00 3.51
4969 5595 2.893398 GATCCAACGGCCGAGAGT 59.107 61.111 35.90 13.55 0.00 3.24
4970 5596 2.278857 CGATCCAACGGCCGAGAG 60.279 66.667 35.90 20.18 0.00 3.20
4971 5597 3.833645 CCGATCCAACGGCCGAGA 61.834 66.667 35.90 24.79 46.20 4.04
4978 5604 1.011968 TCAAGCGAACCGATCCAACG 61.012 55.000 0.00 0.00 0.00 4.10
4979 5605 2.835605 TCAAGCGAACCGATCCAAC 58.164 52.632 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.