Multiple sequence alignment - TraesCS7A01G238500

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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 TraesCS7A01G238500 chr7A 100.000 5432 0 0 1 5432 211636662 211642093 0.000000e+00 10032.0
1 TraesCS7A01G238500 chr7A 88.889 72 7 1 3959 4029 733624888 733624959 2.700000e-13 87.9
2 TraesCS7A01G238500 chr7A 100.000 33 0 0 3971 4003 676347105 676347073 1.630000e-05 62.1
3 TraesCS7A01G238500 chr7D 93.739 3434 134 33 759 4185 156684073 156687432 0.000000e+00 5075.0
4 TraesCS7A01G238500 chr7D 92.527 1191 61 13 4265 5432 156687429 156688614 0.000000e+00 1681.0
5 TraesCS7A01G238500 chr7D 91.449 573 43 4 180 747 156683195 156683766 0.000000e+00 782.0
6 TraesCS7A01G238500 chr7D 93.548 186 9 3 1 185 156674275 156674458 1.930000e-69 274.0
7 TraesCS7A01G238500 chr7D 94.949 99 4 1 4170 4268 483929597 483929694 2.620000e-33 154.0
8 TraesCS7A01G238500 chr7D 88.750 80 7 2 3952 4030 633508607 633508529 4.480000e-16 97.1
9 TraesCS7A01G238500 chr7D 86.420 81 9 2 3952 4031 633507121 633507042 2.700000e-13 87.9
10 TraesCS7A01G238500 chr7D 84.286 70 5 3 568 631 437889266 437889335 4.540000e-06 63.9
11 TraesCS7A01G238500 chr7B 92.746 1737 107 13 1495 3227 118976498 118978219 0.000000e+00 2492.0
12 TraesCS7A01G238500 chr7B 90.373 966 60 18 4194 5135 118979297 118980253 0.000000e+00 1238.0
13 TraesCS7A01G238500 chr7B 92.516 775 47 8 1 768 118970671 118971441 0.000000e+00 1099.0
14 TraesCS7A01G238500 chr7B 95.039 645 21 2 772 1416 118975787 118976420 0.000000e+00 1003.0
15 TraesCS7A01G238500 chr7B 89.038 520 41 10 3709 4226 118978767 118979272 9.930000e-177 630.0
16 TraesCS7A01G238500 chr7B 94.796 269 14 0 5164 5432 118980253 118980521 2.340000e-113 420.0
17 TraesCS7A01G238500 chr7B 90.411 292 19 2 3314 3605 118978218 118978500 5.140000e-100 375.0
18 TraesCS7A01G238500 chr7B 88.148 135 16 0 1279 1413 579561210 579561076 1.570000e-35 161.0
19 TraesCS7A01G238500 chr7B 83.951 81 11 2 3952 4031 749533702 749533623 5.830000e-10 76.8
20 TraesCS7A01G238500 chr7B 84.058 69 9 2 598 664 201162696 201162628 1.260000e-06 65.8
21 TraesCS7A01G238500 chr7B 100.000 33 0 0 3971 4003 656276030 656275998 1.630000e-05 62.1
22 TraesCS7A01G238500 chr6A 93.333 135 9 0 1279 1413 547822306 547822440 3.320000e-47 200.0
23 TraesCS7A01G238500 chr6A 93.220 59 3 1 1132 1190 547822149 547822206 9.690000e-13 86.1
24 TraesCS7A01G238500 chr6A 82.353 85 10 4 584 664 14481020 14480937 9.760000e-08 69.4
25 TraesCS7A01G238500 chr6B 92.593 135 10 0 1279 1413 601874130 601874264 1.540000e-45 195.0
26 TraesCS7A01G238500 chr6B 85.606 132 19 0 1279 1410 663291303 663291434 7.340000e-29 139.0
27 TraesCS7A01G238500 chr6B 89.720 107 6 2 3216 3322 431701343 431701444 1.230000e-26 132.0
28 TraesCS7A01G238500 chr6B 91.176 68 3 3 1123 1190 601873957 601874021 7.490000e-14 89.8
29 TraesCS7A01G238500 chr6D 92.424 132 10 0 1279 1410 401301256 401301387 7.180000e-44 189.0
30 TraesCS7A01G238500 chr6D 92.473 93 2 1 3223 3315 146072820 146072907 1.590000e-25 128.0
31 TraesCS7A01G238500 chr6D 94.545 55 3 0 1136 1190 401301116 401301170 9.690000e-13 86.1
32 TraesCS7A01G238500 chr1B 88.889 135 15 0 1279 1413 177477854 177477720 3.370000e-37 167.0
33 TraesCS7A01G238500 chr5B 93.396 106 6 1 4183 4287 406932572 406932677 7.280000e-34 156.0
34 TraesCS7A01G238500 chr5B 100.000 36 0 0 596 631 43157815 43157850 3.510000e-07 67.6
35 TraesCS7A01G238500 chr5A 95.876 97 3 1 4176 4272 479846117 479846212 7.280000e-34 156.0
36 TraesCS7A01G238500 chr3A 94.118 102 6 0 4184 4285 574288073 574287972 7.280000e-34 156.0
37 TraesCS7A01G238500 chr1D 94.898 98 5 0 4183 4280 50875359 50875262 2.620000e-33 154.0
38 TraesCS7A01G238500 chr2A 94.059 101 4 2 4176 4275 777289160 777289259 9.420000e-33 152.0
39 TraesCS7A01G238500 chr2A 94.444 90 4 1 3226 3315 96243130 96243042 2.640000e-28 137.0
40 TraesCS7A01G238500 chr2A 83.721 86 9 4 585 666 10996289 10996373 5.830000e-10 76.8
41 TraesCS7A01G238500 chrUn 93.137 102 7 0 4184 4285 241299909 241300010 3.390000e-32 150.0
42 TraesCS7A01G238500 chr5D 92.453 106 6 2 4178 4281 378155538 378155433 3.390000e-32 150.0
43 TraesCS7A01G238500 chr5D 91.781 73 5 1 3959 4030 276289728 276289656 3.460000e-17 100.0
44 TraesCS7A01G238500 chr5D 90.196 51 3 1 583 631 44183324 44183374 1.260000e-06 65.8
45 TraesCS7A01G238500 chr2D 95.556 90 4 0 3226 3315 566655083 566655172 1.580000e-30 145.0
46 TraesCS7A01G238500 chr4A 91.753 97 6 1 3222 3316 462830428 462830524 3.410000e-27 134.0
47 TraesCS7A01G238500 chr4D 92.391 92 6 1 3224 3315 101653212 101653302 4.420000e-26 130.0
48 TraesCS7A01G238500 chr4B 89.796 98 10 0 3226 3323 13422861 13422764 5.710000e-25 126.0
49 TraesCS7A01G238500 chr2B 90.323 93 7 1 3226 3318 644157591 644157501 2.660000e-23 121.0
50 TraesCS7A01G238500 chr2B 86.765 68 6 3 596 661 314198 314132 7.550000e-09 73.1
51 TraesCS7A01G238500 chr2B 83.333 84 9 4 582 661 488330115 488330033 7.550000e-09 73.1
52 TraesCS7A01G238500 chr3B 88.060 67 7 1 596 661 51102798 51102864 1.620000e-10 78.7


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 TraesCS7A01G238500 chr7A 211636662 211642093 5431 False 10032.000000 10032 100.000000 1 5432 1 chr7A.!!$F1 5431
1 TraesCS7A01G238500 chr7D 156683195 156688614 5419 False 2512.666667 5075 92.571667 180 5432 3 chr7D.!!$F4 5252
2 TraesCS7A01G238500 chr7B 118970671 118971441 770 False 1099.000000 1099 92.516000 1 768 1 chr7B.!!$F1 767
3 TraesCS7A01G238500 chr7B 118975787 118980521 4734 False 1026.333333 2492 92.067167 772 5432 6 chr7B.!!$F2 4660

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
192 193 0.320374 TCACACGGTTCTCCCACATC 59.680 55.000 0.00 0.00 0.00 3.06 F
736 742 0.401738 ACTCCACAATCCACCTGGTG 59.598 55.000 20.01 20.01 36.34 4.17 F
1677 2003 1.003003 AGCTGGGCAACTCTCTTCTTC 59.997 52.381 0.00 0.00 0.00 2.87 F
3316 3646 0.178970 TATGGGACGGAGGGAGTAGC 60.179 60.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1814 2.151202 GCTCAACGAATGTCAGGGAAA 58.849 47.619 0.0 0.0 0.00 3.13 R
2701 3031 1.172180 CCTTTCGCTTTGCCTGACCA 61.172 55.000 0.0 0.0 0.00 4.02 R
3526 3856 0.604073 TTGTCGGCTATCGTGGAACA 59.396 50.000 0.0 0.0 40.32 3.18 R
4941 5534 2.037121 ACATTTTACCCAACAGCCAAGC 59.963 45.455 0.0 0.0 0.00 4.01 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
26 27 5.937975 AAAAACACCCATGGGATATTGAG 57.062 39.130 38.07 17.91 38.96 3.02
35 36 7.964274 CCCATGGGATATTGAGCATCACACA 62.964 48.000 28.27 0.00 41.32 3.72
61 62 3.486383 TCTGATGGGTTGTTCCAAGTTC 58.514 45.455 0.00 0.00 40.62 3.01
77 78 4.041691 CCAAGTTCTTTCCTAGACTCCCAA 59.958 45.833 0.00 0.00 30.90 4.12
80 81 4.284746 AGTTCTTTCCTAGACTCCCAACTG 59.715 45.833 0.00 0.00 30.90 3.16
97 98 3.399234 TGGGCTCACCATAGACAGT 57.601 52.632 0.00 0.00 46.80 3.55
102 103 2.426024 GGCTCACCATAGACAGTCGTAA 59.574 50.000 0.00 0.00 35.26 3.18
115 116 3.252458 ACAGTCGTAAAGCCACCATTTTC 59.748 43.478 0.00 0.00 0.00 2.29
116 117 3.502211 CAGTCGTAAAGCCACCATTTTCT 59.498 43.478 0.00 0.00 0.00 2.52
125 126 3.766051 AGCCACCATTTTCTCATTTCCTC 59.234 43.478 0.00 0.00 0.00 3.71
178 179 5.067283 ACACTTAACTCCATGGTTTTCACAC 59.933 40.000 12.58 0.00 0.00 3.82
192 193 0.320374 TCACACGGTTCTCCCACATC 59.680 55.000 0.00 0.00 0.00 3.06
289 290 3.682858 CCATCTTGTATTTCAACGGACGT 59.317 43.478 0.00 0.00 32.18 4.34
323 324 8.402472 ACACGAAAGAATCACTCAATTTTGTTA 58.598 29.630 0.00 0.00 0.00 2.41
395 396 4.492570 CGCGACAGTTCCATTCTAATGTTC 60.493 45.833 0.00 0.00 34.60 3.18
424 425 6.969828 ACTCGTGATAATCCTTCACTTTTC 57.030 37.500 2.73 0.00 41.05 2.29
506 508 6.787085 TTTTCTCCGCAAAAAGAAAAACAA 57.213 29.167 7.59 0.00 44.35 2.83
507 509 5.771602 TTCTCCGCAAAAAGAAAAACAAC 57.228 34.783 0.00 0.00 0.00 3.32
650 652 9.057365 TCAATTTTCGCAATAAGTAATTTCGAC 57.943 29.630 0.00 0.00 41.80 4.20
734 740 0.692476 TGACTCCACAATCCACCTGG 59.308 55.000 0.00 0.00 0.00 4.45
736 742 0.401738 ACTCCACAATCCACCTGGTG 59.598 55.000 20.01 20.01 36.34 4.17
950 1251 5.068198 CAGATCCCATCACCAATAAACAAGG 59.932 44.000 0.00 0.00 0.00 3.61
962 1263 5.107143 CCAATAAACAAGGCCACAAAATTCG 60.107 40.000 5.01 0.00 0.00 3.34
1213 1514 1.152830 GGAGATCTCCCCGCTCTCT 59.847 63.158 28.84 0.00 43.94 3.10
1457 1783 1.202405 CCTTGGCATGCGATTTTACCC 60.202 52.381 12.44 0.00 0.00 3.69
1477 1803 2.414029 CCATGCGCTGTTTCGTTTATGT 60.414 45.455 9.73 0.00 0.00 2.29
1478 1804 3.233578 CATGCGCTGTTTCGTTTATGTT 58.766 40.909 9.73 0.00 0.00 2.71
1479 1805 2.911120 TGCGCTGTTTCGTTTATGTTC 58.089 42.857 9.73 0.00 0.00 3.18
1480 1806 2.546368 TGCGCTGTTTCGTTTATGTTCT 59.454 40.909 9.73 0.00 0.00 3.01
1481 1807 3.153735 GCGCTGTTTCGTTTATGTTCTC 58.846 45.455 0.00 0.00 0.00 2.87
1482 1808 3.732943 CGCTGTTTCGTTTATGTTCTCC 58.267 45.455 0.00 0.00 0.00 3.71
1483 1809 3.432252 CGCTGTTTCGTTTATGTTCTCCT 59.568 43.478 0.00 0.00 0.00 3.69
1484 1810 4.434330 CGCTGTTTCGTTTATGTTCTCCTC 60.434 45.833 0.00 0.00 0.00 3.71
1485 1811 4.691216 GCTGTTTCGTTTATGTTCTCCTCT 59.309 41.667 0.00 0.00 0.00 3.69
1486 1812 5.179555 GCTGTTTCGTTTATGTTCTCCTCTT 59.820 40.000 0.00 0.00 0.00 2.85
1487 1813 6.618805 GCTGTTTCGTTTATGTTCTCCTCTTC 60.619 42.308 0.00 0.00 0.00 2.87
1488 1814 6.522054 TGTTTCGTTTATGTTCTCCTCTTCT 58.478 36.000 0.00 0.00 0.00 2.85
1556 1882 4.742440 GCCAAGAATCGGTACACATGGATA 60.742 45.833 0.00 0.00 0.00 2.59
1624 1950 3.435275 TCCGCCTATTCTGATCTATGCT 58.565 45.455 0.00 0.00 0.00 3.79
1625 1951 3.194329 TCCGCCTATTCTGATCTATGCTG 59.806 47.826 0.00 0.00 0.00 4.41
1637 1963 3.371102 TCTATGCTGATTCTACACGGC 57.629 47.619 0.00 0.00 38.67 5.68
1642 1968 3.932822 TGCTGATTCTACACGGCTTAAA 58.067 40.909 0.00 0.00 38.93 1.52
1648 1974 4.939509 TTCTACACGGCTTAAAGATTGC 57.060 40.909 0.00 0.00 0.00 3.56
1667 1993 3.016736 TGCTCTTAATTAGCTGGGCAAC 58.983 45.455 0.00 0.00 40.73 4.17
1677 2003 1.003003 AGCTGGGCAACTCTCTTCTTC 59.997 52.381 0.00 0.00 0.00 2.87
1678 2004 1.003003 GCTGGGCAACTCTCTTCTTCT 59.997 52.381 0.00 0.00 0.00 2.85
1679 2005 2.934801 GCTGGGCAACTCTCTTCTTCTC 60.935 54.545 0.00 0.00 0.00 2.87
1824 2153 3.894427 TGAGAGAGATGTCTGGATTAGCC 59.106 47.826 0.00 0.00 30.97 3.93
2001 2330 5.008911 CGATGATAAATTGGGTGATGCAGAA 59.991 40.000 0.00 0.00 0.00 3.02
2174 2503 1.609208 AGTGTTTCTGGTGCCACATC 58.391 50.000 0.00 0.00 0.00 3.06
2272 2601 5.702670 GTGAACTGATTGAGAATTCCACTGA 59.297 40.000 0.65 0.00 0.00 3.41
2273 2602 6.373774 GTGAACTGATTGAGAATTCCACTGAT 59.626 38.462 0.65 0.00 0.00 2.90
2302 2632 3.492337 TCATTAAGGCGGTTTGTCCTTT 58.508 40.909 0.00 0.00 42.32 3.11
2419 2749 4.526262 AGAGCAACATGAGAAGTCAGTACT 59.474 41.667 0.00 0.00 35.66 2.73
2459 2789 2.158957 TGGGATCCATTGCTTAGTCGTC 60.159 50.000 15.23 0.00 0.00 4.20
2481 2811 6.378582 GTCGCAACAGATTTTTCTATCCAAA 58.621 36.000 0.00 0.00 0.00 3.28
2572 2902 9.606631 AATGTACTATCTTCTTTGAACCTCATC 57.393 33.333 0.00 0.00 0.00 2.92
2616 2946 4.756135 ACATGCCATTTCAAATTGTGGAAC 59.244 37.500 5.43 0.00 33.53 3.62
2662 2992 3.610677 GGTTTTGTGGTTTGTTTCAGACG 59.389 43.478 0.00 0.00 0.00 4.18
2701 3031 2.361610 CCTGCATTCCGGTGGCTT 60.362 61.111 0.00 0.00 0.00 4.35
2863 3193 3.450457 AGAACAAACCCAAACTCATGCAA 59.550 39.130 0.00 0.00 0.00 4.08
2981 3311 6.243900 AGGAAACATGAAGTTGATGATCAGT 58.756 36.000 9.45 0.00 41.19 3.41
3077 3407 8.188531 CCAAAATCATGGTAAGCTAAACATTG 57.811 34.615 0.00 0.00 35.65 2.82
3204 3534 2.490903 ACTGGATGCATTGAAGTGCTTC 59.509 45.455 0.00 5.07 45.27 3.86
3210 3540 3.682696 TGCATTGAAGTGCTTCTCTGAT 58.317 40.909 12.44 0.90 45.27 2.90
3241 3571 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3245 3575 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3251 3581 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3252 3582 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
3253 3583 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
3254 3584 5.105310 CCTCCGTCCCATAATATAAGAGTGG 60.105 48.000 0.00 0.00 0.00 4.00
3286 3616 7.998753 ACTAGTGTAGTGTACTGTCAAAAAC 57.001 36.000 0.00 0.00 37.69 2.43
3287 3617 7.549839 ACTAGTGTAGTGTACTGTCAAAAACA 58.450 34.615 0.00 0.00 37.69 2.83
3288 3618 6.657836 AGTGTAGTGTACTGTCAAAAACAC 57.342 37.500 3.23 3.23 41.97 3.32
3316 3646 0.178970 TATGGGACGGAGGGAGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
3320 3650 0.389757 GGACGGAGGGAGTAGCAATC 59.610 60.000 0.00 0.00 0.00 2.67
3407 3737 5.082425 AGCTCAGGAATTCAGGACAAAATT 58.918 37.500 7.93 0.00 0.00 1.82
3472 3802 2.225068 TTGAGTAGCCATTCTAGCGC 57.775 50.000 0.00 0.00 34.64 5.92
3482 3812 3.065371 GCCATTCTAGCGCTTGTTTGTAT 59.935 43.478 18.68 1.53 0.00 2.29
3513 3843 8.365210 GTTTGTATTTATGCATTGACTGAAACG 58.635 33.333 3.54 0.00 0.00 3.60
3514 3844 6.550843 TGTATTTATGCATTGACTGAAACGG 58.449 36.000 3.54 0.00 0.00 4.44
3526 3856 5.553123 TGACTGAAACGGGTATGTAAACAT 58.447 37.500 0.63 0.63 40.22 2.71
3527 3857 5.410132 TGACTGAAACGGGTATGTAAACATG 59.590 40.000 5.85 0.00 37.15 3.21
3540 3870 3.936453 TGTAAACATGTTCCACGATAGCC 59.064 43.478 12.39 0.00 42.67 3.93
3545 3875 0.604073 TGTTCCACGATAGCCGACAA 59.396 50.000 0.00 0.00 41.76 3.18
3555 3885 5.348724 CACGATAGCCGACAATAATAGCATT 59.651 40.000 0.00 0.00 41.76 3.56
3556 3886 5.932303 ACGATAGCCGACAATAATAGCATTT 59.068 36.000 0.00 0.00 41.76 2.32
3557 3887 6.128553 ACGATAGCCGACAATAATAGCATTTG 60.129 38.462 0.00 0.00 41.76 2.32
3558 3888 4.228912 AGCCGACAATAATAGCATTTGC 57.771 40.909 0.00 0.00 42.49 3.68
3559 3889 3.004734 AGCCGACAATAATAGCATTTGCC 59.995 43.478 0.00 0.00 43.38 4.52
3560 3890 3.243367 GCCGACAATAATAGCATTTGCCA 60.243 43.478 0.00 0.00 43.38 4.92
3561 3891 4.559300 GCCGACAATAATAGCATTTGCCAT 60.559 41.667 0.00 0.00 43.38 4.40
3641 3971 4.742649 TCTCGGAGGTCGCTGGCT 62.743 66.667 4.96 0.00 39.05 4.75
3654 3984 3.855503 CTGGCTGGGCTGTGCTCAA 62.856 63.158 0.00 0.00 39.14 3.02
3655 3985 3.060615 GGCTGGGCTGTGCTCAAG 61.061 66.667 0.00 0.00 39.14 3.02
3678 4009 0.832135 TAGATTAGAGCGGCAGGGGG 60.832 60.000 1.45 0.00 0.00 5.40
3679 4010 2.040884 ATTAGAGCGGCAGGGGGA 60.041 61.111 1.45 0.00 0.00 4.81
3700 4031 2.024273 AGGATCGTTGGTAAGGGAGAGA 60.024 50.000 0.00 0.00 0.00 3.10
3734 4242 2.913617 GGAAGGAGAAGAGAGGGGAAAA 59.086 50.000 0.00 0.00 0.00 2.29
3764 4272 1.081481 TCTGACAGGTGGGACTAGGA 58.919 55.000 1.81 0.00 0.00 2.94
3814 4322 0.918983 GGTCCCACCCATCAGATTCA 59.081 55.000 0.00 0.00 30.04 2.57
3826 4335 4.157105 CCATCAGATTCACTGTCAAATGCA 59.843 41.667 0.00 0.00 45.86 3.96
3835 4344 3.254166 CACTGTCAAATGCACTAAGCCTT 59.746 43.478 0.00 0.00 44.83 4.35
3836 4345 3.254166 ACTGTCAAATGCACTAAGCCTTG 59.746 43.478 0.00 0.00 44.83 3.61
3844 4353 1.679944 GCACTAAGCCTTGGATCAGCA 60.680 52.381 0.00 0.00 37.23 4.41
3861 4370 3.701542 TCAGCACAATTTGTTACCAACCA 59.298 39.130 0.00 0.00 0.00 3.67
3875 4384 1.691196 CAACCAGCCTCAAAAGTGGA 58.309 50.000 0.00 0.00 33.95 4.02
4025 4536 5.245977 CCTTCTCTTTATCCCAAAAGGCAAA 59.754 40.000 0.00 0.00 37.13 3.68
4026 4537 6.239572 CCTTCTCTTTATCCCAAAAGGCAAAA 60.240 38.462 0.00 0.00 37.13 2.44
4027 4538 6.739331 TCTCTTTATCCCAAAAGGCAAAAA 57.261 33.333 0.00 0.00 37.13 1.94
4064 4576 5.476945 GGGATTGAACTTTCACAACCATACT 59.523 40.000 0.00 0.00 36.83 2.12
4071 4583 8.999431 TGAACTTTCACAACCATACTAGAAATC 58.001 33.333 0.00 0.00 31.01 2.17
4117 4630 5.582689 AGTTTTAATAACTGCCATCAGCC 57.417 39.130 0.00 0.00 44.10 4.85
4122 4635 2.174685 TAACTGCCATCAGCCCTCTA 57.825 50.000 0.00 0.00 44.10 2.43
4199 4712 8.114743 ACTAATACAGTACTCCCTCTGTAAACT 58.885 37.037 8.67 1.54 45.84 2.66
4210 4780 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
4395 4965 3.608316 TTTGGCCATTATGTTGAAGCC 57.392 42.857 6.09 3.07 40.87 4.35
4430 5000 5.069516 GGTACTTGGATCTTACACGGGAATA 59.930 44.000 0.00 0.00 0.00 1.75
4438 5008 4.824289 TCTTACACGGGAATAAACCTCAC 58.176 43.478 0.00 0.00 0.00 3.51
4441 5011 2.268298 CACGGGAATAAACCTCACGAG 58.732 52.381 0.87 0.00 42.40 4.18
4495 5065 4.193826 TCAGTTCTTGTAGGCAGATCAC 57.806 45.455 0.00 0.00 0.00 3.06
4630 5202 8.668510 AATAATGATACACTTGACTGTCCATC 57.331 34.615 5.17 0.18 0.00 3.51
4661 5253 6.415206 AGGCAGTGTACTTTTGTCTACTTA 57.585 37.500 0.00 0.00 29.87 2.24
4678 5270 8.861086 TGTCTACTTAGTTCATCTTCAGTCTTT 58.139 33.333 0.00 0.00 0.00 2.52
4690 5282 6.064846 TCTTCAGTCTTTTTGCATCTGTTC 57.935 37.500 0.00 0.00 0.00 3.18
4708 5300 4.973168 TGTTCTCTCCAGCAAAGTGTTAT 58.027 39.130 0.00 0.00 0.00 1.89
4711 5303 5.947228 TCTCTCCAGCAAAGTGTTATTTG 57.053 39.130 0.00 0.00 42.00 2.32
4771 5364 4.653801 TGAGGCTAGCATATAAAGACCACA 59.346 41.667 18.24 0.00 0.00 4.17
4793 5386 7.500227 CCACATGGTTTGATCTATAATGTCTGT 59.500 37.037 0.00 0.00 0.00 3.41
4805 5398 8.689251 TCTATAATGTCTGTTCTTTTCAGTCG 57.311 34.615 0.00 0.00 34.86 4.18
4809 5402 2.476997 GTCTGTTCTTTTCAGTCGGCTC 59.523 50.000 0.00 0.00 34.86 4.70
4824 5417 5.352569 CAGTCGGCTCTGATGAGTTAATTTT 59.647 40.000 0.00 0.00 42.13 1.82
4825 5418 5.352569 AGTCGGCTCTGATGAGTTAATTTTG 59.647 40.000 0.00 0.00 42.13 2.44
4828 5421 6.876789 TCGGCTCTGATGAGTTAATTTTGTTA 59.123 34.615 0.00 0.00 42.13 2.41
4829 5422 7.552687 TCGGCTCTGATGAGTTAATTTTGTTAT 59.447 33.333 0.00 0.00 42.13 1.89
4830 5423 7.641411 CGGCTCTGATGAGTTAATTTTGTTATG 59.359 37.037 0.00 0.00 42.13 1.90
4831 5424 8.462016 GGCTCTGATGAGTTAATTTTGTTATGT 58.538 33.333 0.00 0.00 42.13 2.29
4844 5437 6.757897 TTTTGTTATGTCATCACCTGGATC 57.242 37.500 0.00 0.00 32.57 3.36
4855 5448 7.110155 GTCATCACCTGGATCTTAAAACCTTA 58.890 38.462 0.00 0.00 32.57 2.69
4874 5467 4.811557 CCTTAACAGGCTATGCTAGTCAAC 59.188 45.833 0.00 0.00 31.53 3.18
4896 5489 9.507329 TCAACTTCAACAGAATAAGCTAGAAAT 57.493 29.630 0.00 0.00 0.00 2.17
4941 5534 8.709386 AATGCATCTAAGTACTACAACAAGAG 57.291 34.615 0.00 0.00 0.00 2.85
4944 5537 6.814146 GCATCTAAGTACTACAACAAGAGCTT 59.186 38.462 0.00 0.00 0.00 3.74
4954 5547 4.507969 AAGAGCTTGGCTGTTGGG 57.492 55.556 1.21 0.00 40.60 4.12
4963 5556 3.494223 GCTTGGCTGTTGGGTAAAATGTT 60.494 43.478 0.00 0.00 0.00 2.71
4985 5581 8.141298 TGTTGTACCAGGATTGACTTATAAGA 57.859 34.615 19.38 0.00 0.00 2.10
4986 5582 8.038944 TGTTGTACCAGGATTGACTTATAAGAC 58.961 37.037 19.38 13.32 0.00 3.01
5018 5614 2.102070 TACCCACAAATACCACAGCG 57.898 50.000 0.00 0.00 0.00 5.18
5061 5657 5.009854 ACAAATTCCAAAGGAGTTGTGTG 57.990 39.130 13.26 4.09 39.03 3.82
5062 5658 4.709397 ACAAATTCCAAAGGAGTTGTGTGA 59.291 37.500 13.26 0.00 39.03 3.58
5066 5662 4.229304 TCCAAAGGAGTTGTGTGAAAGA 57.771 40.909 0.00 0.00 35.23 2.52
5072 5668 4.319177 AGGAGTTGTGTGAAAGATACTGC 58.681 43.478 0.00 0.00 0.00 4.40
5135 5731 2.679837 CCAAATGTCTGCAGTAATCGCT 59.320 45.455 14.67 0.00 0.00 4.93
5177 5773 2.422127 ACAACCACAACACAGCAACTAC 59.578 45.455 0.00 0.00 0.00 2.73
5211 5807 7.812690 TGGAATATCCACAATCTCAATGAAG 57.187 36.000 0.00 0.00 42.67 3.02
5288 5884 8.160765 TCACATGGTTCTTTCAATAAGAGGTAA 58.839 33.333 0.00 0.00 0.00 2.85
5293 5889 9.010029 TGGTTCTTTCAATAAGAGGTAATTGAC 57.990 33.333 0.00 0.00 40.77 3.18
5297 5893 9.098355 TCTTTCAATAAGAGGTAATTGACGATG 57.902 33.333 0.00 0.00 40.77 3.84
5317 5913 3.179443 GTCCTCTGAATTATGGACGCA 57.821 47.619 0.00 0.00 39.39 5.24
5406 6002 6.543831 ACAGACAGACTAAAGTGCTTCATTTT 59.456 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.581824 ACCCATCAGATATTTGTGTGATGC 59.418 41.667 8.38 0.00 44.25 3.91
45 46 9.958234 GTCTAGGAAAGAACTTGGAACAACCCA 62.958 44.444 0.00 0.00 39.09 4.51
61 62 3.618690 CCAGTTGGGAGTCTAGGAAAG 57.381 52.381 0.00 0.00 40.01 2.62
80 81 0.103208 CGACTGTCTATGGTGAGCCC 59.897 60.000 6.21 0.00 0.00 5.19
97 98 3.745799 TGAGAAAATGGTGGCTTTACGA 58.254 40.909 0.00 0.00 0.00 3.43
102 103 4.162651 AGGAAATGAGAAAATGGTGGCTT 58.837 39.130 0.00 0.00 0.00 4.35
115 116 5.909621 AATGTGATTGTGGAGGAAATGAG 57.090 39.130 0.00 0.00 0.00 2.90
116 117 7.959658 ATAAATGTGATTGTGGAGGAAATGA 57.040 32.000 0.00 0.00 0.00 2.57
125 126 9.172820 CGAATCAACATATAAATGTGATTGTGG 57.827 33.333 14.88 6.41 45.79 4.17
178 179 1.535462 GTTGTTGATGTGGGAGAACCG 59.465 52.381 0.00 0.00 44.64 4.44
192 193 0.738389 GGAGTGGTGGTGTGTTGTTG 59.262 55.000 0.00 0.00 0.00 3.33
289 290 4.038042 AGTGATTCTTTCGTGTCTGAGACA 59.962 41.667 11.93 11.93 40.50 3.41
300 301 7.805071 AGCTAACAAAATTGAGTGATTCTTTCG 59.195 33.333 0.00 0.00 0.00 3.46
308 309 7.417612 GTTCAGAAGCTAACAAAATTGAGTGA 58.582 34.615 0.00 0.00 0.00 3.41
323 324 2.100584 CGCATCTAGAGGTTCAGAAGCT 59.899 50.000 14.89 14.89 42.93 3.74
395 396 7.630470 GTGAAGGATTATCACGAGTAATGAG 57.370 40.000 0.00 0.00 37.98 2.90
484 485 5.696724 TGTTGTTTTTCTTTTTGCGGAGAAA 59.303 32.000 0.00 0.00 39.42 2.52
544 546 9.122779 AGCTACTCTAGTGATTATAAAACGTCT 57.877 33.333 0.00 0.00 0.00 4.18
648 650 8.591940 ACCCTAAAAATATATACTTCCTCGGTC 58.408 37.037 0.00 0.00 0.00 4.79
650 652 8.373220 ACACCCTAAAAATATATACTTCCTCGG 58.627 37.037 0.00 0.00 0.00 4.63
705 707 1.188219 TGTGGAGTCAGAGGCTGGTC 61.188 60.000 0.00 0.00 31.51 4.02
734 740 1.153429 CGGTGGTTAGGGCTAGCAC 60.153 63.158 18.24 14.32 41.87 4.40
736 742 1.397390 TAGCGGTGGTTAGGGCTAGC 61.397 60.000 6.04 6.04 36.97 3.42
816 1117 1.591155 GGCGCGTTTTCAAACTTTTGC 60.591 47.619 8.43 0.23 38.05 3.68
950 1251 1.215382 GAGGGGCGAATTTTGTGGC 59.785 57.895 0.00 0.00 0.00 5.01
962 1263 4.062032 GAAAGGGTGGGGAGGGGC 62.062 72.222 0.00 0.00 0.00 5.80
1457 1783 2.850321 ACATAAACGAAACAGCGCATG 58.150 42.857 11.47 7.81 33.86 4.06
1477 1803 3.587498 TGTCAGGGAAAGAAGAGGAGAA 58.413 45.455 0.00 0.00 0.00 2.87
1478 1804 3.260269 TGTCAGGGAAAGAAGAGGAGA 57.740 47.619 0.00 0.00 0.00 3.71
1479 1805 4.512484 GAATGTCAGGGAAAGAAGAGGAG 58.488 47.826 0.00 0.00 0.00 3.69
1480 1806 3.055819 CGAATGTCAGGGAAAGAAGAGGA 60.056 47.826 0.00 0.00 0.00 3.71
1481 1807 3.265791 CGAATGTCAGGGAAAGAAGAGG 58.734 50.000 0.00 0.00 0.00 3.69
1482 1808 3.931578 ACGAATGTCAGGGAAAGAAGAG 58.068 45.455 0.00 0.00 0.00 2.85
1483 1809 4.065088 CAACGAATGTCAGGGAAAGAAGA 58.935 43.478 0.00 0.00 0.00 2.87
1484 1810 4.065088 TCAACGAATGTCAGGGAAAGAAG 58.935 43.478 0.00 0.00 0.00 2.85
1485 1811 4.065088 CTCAACGAATGTCAGGGAAAGAA 58.935 43.478 0.00 0.00 0.00 2.52
1486 1812 3.664107 CTCAACGAATGTCAGGGAAAGA 58.336 45.455 0.00 0.00 0.00 2.52
1487 1813 2.160417 GCTCAACGAATGTCAGGGAAAG 59.840 50.000 0.00 0.00 0.00 2.62
1488 1814 2.151202 GCTCAACGAATGTCAGGGAAA 58.849 47.619 0.00 0.00 0.00 3.13
1556 1882 4.035102 GGGACGCCCTCAAAGCCT 62.035 66.667 7.58 0.00 41.34 4.58
1624 1950 5.064707 GCAATCTTTAAGCCGTGTAGAATCA 59.935 40.000 0.00 0.00 0.00 2.57
1625 1951 5.294552 AGCAATCTTTAAGCCGTGTAGAATC 59.705 40.000 0.00 0.00 0.00 2.52
1637 1963 8.348507 CCCAGCTAATTAAGAGCAATCTTTAAG 58.651 37.037 13.13 0.00 42.69 1.85
1642 1968 4.140536 GCCCAGCTAATTAAGAGCAATCT 58.859 43.478 13.13 0.00 42.69 2.40
1648 1974 4.775236 AGAGTTGCCCAGCTAATTAAGAG 58.225 43.478 0.00 0.00 0.00 2.85
2001 2330 2.203640 TCACTGTCAGCGTCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
2080 2409 5.632764 GTGATTGATCAGTCATACCAGATCG 59.367 44.000 22.03 0.00 39.70 3.69
2174 2503 6.072728 CGACTTCTCCTTCCTATGATCTACTG 60.073 46.154 0.00 0.00 0.00 2.74
2293 2623 5.344743 TGCAATTAACCACAAAGGACAAA 57.655 34.783 0.00 0.00 41.22 2.83
2302 2632 5.925397 GTGAATCACATTGCAATTAACCACA 59.075 36.000 9.83 4.26 34.08 4.17
2403 2733 6.370994 AGAAATGCAAGTACTGACTTCTCATG 59.629 38.462 0.00 0.00 44.39 3.07
2459 2789 6.254157 CCATTTGGATAGAAAAATCTGTTGCG 59.746 38.462 0.00 0.00 37.39 4.85
2481 2811 8.464404 CAACATCAGAATTGTAATGAGTTCCAT 58.536 33.333 0.00 0.00 36.99 3.41
2521 2851 4.166523 CAATGTCATACAGTCGACGAACT 58.833 43.478 10.46 0.00 34.78 3.01
2551 2881 6.378564 TCTCGATGAGGTTCAAAGAAGATAGT 59.621 38.462 0.00 0.00 0.00 2.12
2572 2902 3.082548 TGGTCAAGAGACTACCTTCTCG 58.917 50.000 0.00 0.00 45.87 4.04
2616 2946 6.755141 CCAACCATGCTAAGAAAAATGATCAG 59.245 38.462 0.09 0.00 0.00 2.90
2662 2992 2.046507 CTGGAGTCCACCTGCTGC 60.047 66.667 8.12 0.00 31.70 5.25
2701 3031 1.172180 CCTTTCGCTTTGCCTGACCA 61.172 55.000 0.00 0.00 0.00 4.02
2863 3193 2.116772 AACATGCTGCTGCCACCT 59.883 55.556 13.47 0.00 38.71 4.00
2981 3311 2.095461 CGTCTCATTCTCCCTCACTGA 58.905 52.381 0.00 0.00 0.00 3.41
3204 3534 9.444600 GGAGTAGTAACTAATAGAGGATCAGAG 57.555 40.741 0.00 0.00 34.31 3.35
3210 3540 6.239829 CGGAGGGAGTAGTAACTAATAGAGGA 60.240 46.154 0.00 0.00 35.56 3.71
3245 3575 6.827727 ACACTAGTGTCAAAACCACTCTTAT 58.172 36.000 22.95 0.00 42.03 1.73
3266 3596 6.657836 AGTGTTTTTGACAGTACACTACAC 57.342 37.500 14.12 0.00 46.72 2.90
3277 3607 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
3286 3616 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
3287 3617 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
3288 3618 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3294 3624 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
3298 3628 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
3299 3629 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
3316 3646 6.480320 GGCCAAAGTACTAGACATGTAGATTG 59.520 42.308 0.00 0.80 0.00 2.67
3320 3650 5.105310 AGTGGCCAAAGTACTAGACATGTAG 60.105 44.000 7.24 0.00 0.00 2.74
3482 3812 8.458052 CAGTCAATGCATAAATACAAACAGGTA 58.542 33.333 0.00 0.00 0.00 3.08
3513 3843 4.609691 CGTGGAACATGTTTACATACCC 57.390 45.455 13.36 7.86 44.52 3.69
3526 3856 0.604073 TTGTCGGCTATCGTGGAACA 59.396 50.000 0.00 0.00 40.32 3.18
3527 3857 1.935933 ATTGTCGGCTATCGTGGAAC 58.064 50.000 0.00 0.00 40.32 3.62
3555 3885 4.187694 GTTGTCAAAAGACCAAATGGCAA 58.812 39.130 0.00 0.00 39.32 4.52
3556 3886 3.431486 GGTTGTCAAAAGACCAAATGGCA 60.431 43.478 0.00 0.00 39.32 4.92
3557 3887 3.130633 GGTTGTCAAAAGACCAAATGGC 58.869 45.455 0.00 0.00 39.32 4.40
3558 3888 4.399004 TGGTTGTCAAAAGACCAAATGG 57.601 40.909 0.00 0.00 40.31 3.16
3641 3971 0.835971 TACTCCTTGAGCACAGCCCA 60.836 55.000 0.00 0.00 32.04 5.36
3654 3984 2.235016 CTGCCGCTCTAATCTACTCCT 58.765 52.381 0.00 0.00 0.00 3.69
3655 3985 1.271102 CCTGCCGCTCTAATCTACTCC 59.729 57.143 0.00 0.00 0.00 3.85
3678 4009 2.362717 CTCTCCCTTACCAACGATCCTC 59.637 54.545 0.00 0.00 0.00 3.71
3679 4010 2.024273 TCTCTCCCTTACCAACGATCCT 60.024 50.000 0.00 0.00 0.00 3.24
3685 4016 4.342665 CACCTATCTCTCTCCCTTACCAAC 59.657 50.000 0.00 0.00 0.00 3.77
3686 4017 4.547671 CACCTATCTCTCTCCCTTACCAA 58.452 47.826 0.00 0.00 0.00 3.67
3700 4031 1.221781 CTCCTTCCTCCCCACCTATCT 59.778 57.143 0.00 0.00 0.00 1.98
3734 4242 4.323792 CCCACCTGTCAGACATACATCTTT 60.324 45.833 2.97 0.00 0.00 2.52
3742 4250 2.461695 CTAGTCCCACCTGTCAGACAT 58.538 52.381 2.97 0.00 0.00 3.06
3745 4253 1.081481 TCCTAGTCCCACCTGTCAGA 58.919 55.000 0.00 0.00 0.00 3.27
3764 4272 2.572290 GTTGGTGTGGCAAAGACTAGT 58.428 47.619 0.00 0.00 0.00 2.57
3814 4322 3.146104 AGGCTTAGTGCATTTGACAGT 57.854 42.857 0.00 0.00 45.15 3.55
3826 4335 1.630369 TGTGCTGATCCAAGGCTTAGT 59.370 47.619 0.00 0.00 0.00 2.24
3835 4344 4.782019 GGTAACAAATTGTGCTGATCCA 57.218 40.909 0.00 0.00 0.00 3.41
3950 4459 9.443323 CTGCTAGAGATGCTCTAAGTATACTAA 57.557 37.037 5.65 0.00 41.74 2.24
3953 4462 7.915293 TCTGCTAGAGATGCTCTAAGTATAC 57.085 40.000 5.75 0.00 41.74 1.47
3954 4463 7.773224 GGATCTGCTAGAGATGCTCTAAGTATA 59.227 40.741 12.96 0.00 44.26 1.47
3955 4464 6.603201 GGATCTGCTAGAGATGCTCTAAGTAT 59.397 42.308 12.96 0.00 44.26 2.12
3957 4466 4.766891 GGATCTGCTAGAGATGCTCTAAGT 59.233 45.833 12.96 0.00 44.26 2.24
3958 4467 4.158394 GGGATCTGCTAGAGATGCTCTAAG 59.842 50.000 16.99 2.25 46.30 2.18
3963 4474 1.149711 AGGGGATCTGCTAGAGATGCT 59.850 52.381 16.99 3.33 46.30 3.79
3965 4476 4.837860 AGTTTAGGGGATCTGCTAGAGATG 59.162 45.833 8.78 0.00 41.91 2.90
4034 4545 7.726291 TGGTTGTGAAAGTTCAATCCCTATTTA 59.274 33.333 0.00 0.00 39.21 1.40
4035 4546 6.553100 TGGTTGTGAAAGTTCAATCCCTATTT 59.447 34.615 0.00 0.00 39.21 1.40
4036 4547 6.074648 TGGTTGTGAAAGTTCAATCCCTATT 58.925 36.000 0.00 0.00 39.21 1.73
4037 4548 5.640147 TGGTTGTGAAAGTTCAATCCCTAT 58.360 37.500 0.00 0.00 39.21 2.57
4038 4549 5.055265 TGGTTGTGAAAGTTCAATCCCTA 57.945 39.130 0.00 0.00 39.21 3.53
4039 4550 3.909732 TGGTTGTGAAAGTTCAATCCCT 58.090 40.909 0.00 0.00 39.21 4.20
4040 4551 4.871933 ATGGTTGTGAAAGTTCAATCCC 57.128 40.909 0.00 0.00 39.21 3.85
4043 4554 8.918202 TTCTAGTATGGTTGTGAAAGTTCAAT 57.082 30.769 0.00 0.00 39.21 2.57
4071 4583 8.428063 ACTAGATCACTAGATTCAGAAATTGGG 58.572 37.037 10.60 0.00 46.34 4.12
4117 4630 4.608948 ACCACTTGTCAAAGACTAGAGG 57.391 45.455 17.90 17.90 45.35 3.69
4122 4635 6.827727 ACTATACAACCACTTGTCAAAGACT 58.172 36.000 0.00 0.00 41.15 3.24
4240 4810 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
4251 4821 5.557576 AAAAGTTACTCCCTCCGTAAACT 57.442 39.130 0.00 0.00 0.00 2.66
4258 4828 5.821470 GGCATAGTTAAAAGTTACTCCCTCC 59.179 44.000 0.00 0.00 0.00 4.30
4261 4831 7.640597 AATGGCATAGTTAAAAGTTACTCCC 57.359 36.000 0.00 0.00 0.00 4.30
4395 4965 5.688807 AGATCCAAGTACCATGATTTCCAG 58.311 41.667 0.00 0.00 0.00 3.86
4438 5008 2.884827 CCTAAACTAAACCGTCCCTCG 58.115 52.381 0.00 0.00 39.52 4.63
4441 5011 2.353323 CTGCCTAAACTAAACCGTCCC 58.647 52.381 0.00 0.00 0.00 4.46
4445 5015 3.000727 CAGACCTGCCTAAACTAAACCG 58.999 50.000 0.00 0.00 0.00 4.44
4638 5210 4.957684 AGTAGACAAAAGTACACTGCCT 57.042 40.909 0.00 0.00 0.00 4.75
4640 5212 7.437267 TGAACTAAGTAGACAAAAGTACACTGC 59.563 37.037 0.00 0.00 0.00 4.40
4641 5213 8.867112 TGAACTAAGTAGACAAAAGTACACTG 57.133 34.615 0.00 0.00 0.00 3.66
4647 5219 9.482627 CTGAAGATGAACTAAGTAGACAAAAGT 57.517 33.333 0.00 0.00 0.00 2.66
4653 5225 9.699703 AAAAGACTGAAGATGAACTAAGTAGAC 57.300 33.333 0.00 0.00 0.00 2.59
4661 5253 6.489361 AGATGCAAAAAGACTGAAGATGAACT 59.511 34.615 0.00 0.00 0.00 3.01
4678 5270 2.224597 TGCTGGAGAGAACAGATGCAAA 60.225 45.455 0.00 0.00 38.20 3.68
4681 5273 2.105006 TTGCTGGAGAGAACAGATGC 57.895 50.000 0.00 0.00 38.20 3.91
4690 5282 4.616835 GCCAAATAACACTTTGCTGGAGAG 60.617 45.833 0.00 0.00 35.28 3.20
4708 5300 3.374764 TCCTCTCTATACAGCTGCCAAA 58.625 45.455 15.27 0.00 0.00 3.28
4711 5303 2.870175 TCTCCTCTCTATACAGCTGCC 58.130 52.381 15.27 0.00 0.00 4.85
4771 5364 9.911788 AAGAACAGACATTATAGATCAAACCAT 57.088 29.630 0.00 0.00 0.00 3.55
4781 5374 7.464710 GCCGACTGAAAAGAACAGACATTATAG 60.465 40.741 0.00 0.00 38.55 1.31
4788 5381 2.476997 GAGCCGACTGAAAAGAACAGAC 59.523 50.000 0.00 0.00 38.55 3.51
4805 5398 8.462016 ACATAACAAAATTAACTCATCAGAGCC 58.538 33.333 0.00 0.00 46.09 4.70
4824 5417 5.698741 AAGATCCAGGTGATGACATAACA 57.301 39.130 5.27 0.00 32.41 2.41
4825 5418 8.398665 GTTTTAAGATCCAGGTGATGACATAAC 58.601 37.037 0.00 0.00 32.41 1.89
4828 5421 5.888161 GGTTTTAAGATCCAGGTGATGACAT 59.112 40.000 0.00 0.00 32.41 3.06
4829 5422 5.014123 AGGTTTTAAGATCCAGGTGATGACA 59.986 40.000 0.00 0.00 32.41 3.58
4830 5423 5.501156 AGGTTTTAAGATCCAGGTGATGAC 58.499 41.667 0.00 0.00 32.41 3.06
4831 5424 5.779241 AGGTTTTAAGATCCAGGTGATGA 57.221 39.130 0.00 0.00 32.41 2.92
4844 5437 6.759497 AGCATAGCCTGTTAAGGTTTTAAG 57.241 37.500 0.00 0.00 46.43 1.85
4855 5448 4.020218 TGAAGTTGACTAGCATAGCCTGTT 60.020 41.667 0.00 0.00 44.39 3.16
4902 5495 9.182214 ACTTAGATGCATTTTACATCAGTGATT 57.818 29.630 1.86 0.00 45.19 2.57
4925 5518 4.065789 GCCAAGCTCTTGTTGTAGTACTT 58.934 43.478 0.00 0.00 38.85 2.24
4941 5534 2.037121 ACATTTTACCCAACAGCCAAGC 59.963 45.455 0.00 0.00 0.00 4.01
4944 5537 3.034635 ACAACATTTTACCCAACAGCCA 58.965 40.909 0.00 0.00 0.00 4.75
4952 5545 5.712917 TCAATCCTGGTACAACATTTTACCC 59.287 40.000 4.84 0.00 38.70 3.69
4954 5547 7.448748 AGTCAATCCTGGTACAACATTTTAC 57.551 36.000 0.00 0.00 38.70 2.01
4963 5556 7.399191 ACTGTCTTATAAGTCAATCCTGGTACA 59.601 37.037 12.19 4.17 0.00 2.90
4985 5581 4.380843 TGTGGGTATGGAAAATGACTGT 57.619 40.909 0.00 0.00 0.00 3.55
4986 5582 5.720371 TTTGTGGGTATGGAAAATGACTG 57.280 39.130 0.00 0.00 0.00 3.51
5033 5629 6.986231 ACAACTCCTTTGGAATTTGTCAATTC 59.014 34.615 7.19 0.00 45.42 2.17
5038 5634 5.043248 CACACAACTCCTTTGGAATTTGTC 58.957 41.667 9.16 0.00 36.47 3.18
5061 5657 6.311690 GTGTTCCTGTCTTAGCAGTATCTTTC 59.688 42.308 0.00 0.00 34.84 2.62
5062 5658 6.166982 GTGTTCCTGTCTTAGCAGTATCTTT 58.833 40.000 0.00 0.00 34.84 2.52
5066 5662 4.528596 AGTGTGTTCCTGTCTTAGCAGTAT 59.471 41.667 0.00 0.00 34.84 2.12
5072 5668 6.677781 TTTTGAAGTGTGTTCCTGTCTTAG 57.322 37.500 0.00 0.00 0.00 2.18
5177 5773 2.849942 TGGATATTCCATGCTTCCGTG 58.150 47.619 0.00 0.00 42.67 4.94
5211 5807 5.532406 TGGTTGATGGCTTCTAAATATCTGC 59.468 40.000 1.86 0.00 0.00 4.26
5288 5884 5.994054 CCATAATTCAGAGGACATCGTCAAT 59.006 40.000 4.54 0.00 33.68 2.57
5297 5893 3.179443 TGCGTCCATAATTCAGAGGAC 57.821 47.619 0.00 0.00 45.46 3.85
5317 5913 9.630098 CTATTTCAAGCATTCAGTAATGTTGTT 57.370 29.630 0.00 0.00 43.75 2.83
5406 6002 0.550914 ACAAGTTCTTCACCAGCCCA 59.449 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.