Multiple sequence alignment - TraesCS2D01G136500

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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 TraesCS2D01G136500 chr2D 100.000 4437 0 0 1 4437 80040026 80035590 0.000000e+00 8194
1 TraesCS2D01G136500 chr2A 90.653 3691 238 55 808 4437 80619936 80616292 0.000000e+00 4806
2 TraesCS2D01G136500 chr2A 86.899 832 42 25 2 798 80620778 80619979 0.000000e+00 870
3 TraesCS2D01G136500 chr2B 91.590 1962 132 22 2493 4437 131584623 131582678 0.000000e+00 2678
4 TraesCS2D01G136500 chr2B 88.329 2005 133 44 564 2497 131586625 131584651 0.000000e+00 2313
5 TraesCS2D01G136500 chr2B 90.671 686 51 10 1065 1746 338730051 338729375 0.000000e+00 900
6 TraesCS2D01G136500 chr2B 86.441 295 25 8 289 579 131586922 131586639 4.310000e-80 309
7 TraesCS2D01G136500 chr2B 85.714 224 23 6 9 229 131587160 131586943 1.240000e-55 228
8 TraesCS2D01G136500 chr3A 78.061 2671 394 108 1235 3811 1621037 1623609 0.000000e+00 1509
9 TraesCS2D01G136500 chrUn 77.993 2681 372 120 1235 3814 270454657 270452094 0.000000e+00 1482
10 TraesCS2D01G136500 chrUn 77.993 2681 372 120 1235 3814 270462921 270460358 0.000000e+00 1482
11 TraesCS2D01G136500 chrUn 77.993 2681 372 120 1235 3814 280683516 280680953 0.000000e+00 1482
12 TraesCS2D01G136500 chrUn 83.744 203 30 2 1023 1222 270455017 270454815 5.860000e-44 189
13 TraesCS2D01G136500 chrUn 94.521 73 4 0 4365 4437 168654448 168654376 3.630000e-21 113
14 TraesCS2D01G136500 chr3B 79.718 1346 195 41 2487 3811 3260252 3258964 0.000000e+00 902
15 TraesCS2D01G136500 chr3B 90.393 687 53 10 1065 1746 395708411 395707733 0.000000e+00 891
16 TraesCS2D01G136500 chr3B 78.571 1330 175 64 1235 2497 3261564 3260278 0.000000e+00 776
17 TraesCS2D01G136500 chr3B 87.685 203 22 2 1023 1222 3261928 3261726 2.670000e-57 233
18 TraesCS2D01G136500 chr3D 83.218 1013 129 21 2487 3485 2449545 2448560 0.000000e+00 891
19 TraesCS2D01G136500 chr3D 84.729 203 28 2 1023 1222 2451194 2450992 2.710000e-47 200
20 TraesCS2D01G136500 chr5A 92.332 626 38 8 1065 1686 698851609 698852228 0.000000e+00 881
21 TraesCS2D01G136500 chr5A 92.244 606 37 8 1085 1686 690644679 690644080 0.000000e+00 850
22 TraesCS2D01G136500 chr5D 88.462 104 7 2 4334 4437 489745713 489745811 2.170000e-23 121
23 TraesCS2D01G136500 chr7B 87.500 104 8 2 4334 4437 193200034 193199936 1.010000e-21 115
24 TraesCS2D01G136500 chr4B 87.500 104 8 2 4334 4437 614205372 614205470 1.010000e-21 115
25 TraesCS2D01G136500 chr1B 86.538 104 9 2 4334 4437 34737974 34738072 4.690000e-20 110
26 TraesCS2D01G136500 chr1B 85.577 104 10 2 4334 4437 127372516 127372614 2.180000e-18 104
27 TraesCS2D01G136500 chr5B 85.577 104 10 2 4334 4437 20985613 20985711 2.180000e-18 104


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 TraesCS2D01G136500 chr2D 80035590 80040026 4436 True 8194.0 8194 100.000000 1 4437 1 chr2D.!!$R1 4436
1 TraesCS2D01G136500 chr2A 80616292 80620778 4486 True 2838.0 4806 88.776000 2 4437 2 chr2A.!!$R1 4435
2 TraesCS2D01G136500 chr2B 131582678 131587160 4482 True 1382.0 2678 88.018500 9 4437 4 chr2B.!!$R2 4428
3 TraesCS2D01G136500 chr2B 338729375 338730051 676 True 900.0 900 90.671000 1065 1746 1 chr2B.!!$R1 681
4 TraesCS2D01G136500 chr3A 1621037 1623609 2572 False 1509.0 1509 78.061000 1235 3811 1 chr3A.!!$F1 2576
5 TraesCS2D01G136500 chrUn 270460358 270462921 2563 True 1482.0 1482 77.993000 1235 3814 1 chrUn.!!$R2 2579
6 TraesCS2D01G136500 chrUn 280680953 280683516 2563 True 1482.0 1482 77.993000 1235 3814 1 chrUn.!!$R3 2579
7 TraesCS2D01G136500 chrUn 270452094 270455017 2923 True 835.5 1482 80.868500 1023 3814 2 chrUn.!!$R4 2791
8 TraesCS2D01G136500 chr3B 395707733 395708411 678 True 891.0 891 90.393000 1065 1746 1 chr3B.!!$R1 681
9 TraesCS2D01G136500 chr3B 3258964 3261928 2964 True 637.0 902 81.991333 1023 3811 3 chr3B.!!$R2 2788
10 TraesCS2D01G136500 chr3D 2448560 2451194 2634 True 545.5 891 83.973500 1023 3485 2 chr3D.!!$R1 2462
11 TraesCS2D01G136500 chr5A 698851609 698852228 619 False 881.0 881 92.332000 1065 1686 1 chr5A.!!$F1 621
12 TraesCS2D01G136500 chr5A 690644080 690644679 599 True 850.0 850 92.244000 1085 1686 1 chr5A.!!$R1 601

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
24 25 0.035317 TGACAAGCGAACCATCAGCT 59.965 50.000 0.00 0.00 43.90 4.24 F
81 82 0.107456 CCCCGGTGAAGAGATGGATG 59.893 60.000 0.00 0.00 0.00 3.51 F
919 1038 0.176910 GCTTGTAGCACTCTCCCTCC 59.823 60.000 0.00 0.00 41.89 4.30 F
977 1096 1.488393 GTCATTCCTCCCTCCTTCCTG 59.512 57.143 0.00 0.00 0.00 3.86 F
2234 2648 0.886490 CCCATAGATTCGGTGGCAGC 60.886 60.000 6.62 6.62 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1938 0.478507 CCTGGTTCACCTTCCCAGTT 59.521 55.000 0.0 0.0 43.47 3.16 R
1751 2122 1.750778 GTGATGCCTAACCCACCATTG 59.249 52.381 0.0 0.0 0.00 2.82 R
2234 2648 0.321564 TTCACATTCACTCCTGGGCG 60.322 55.000 0.0 0.0 0.00 6.13 R
2488 2926 0.955919 GGGTCGAGGAACCTGCAAAG 60.956 60.000 0.0 0.0 36.31 2.77 R
4201 4741 1.067295 TTCCCAGGCTTCTCATGTGT 58.933 50.000 0.0 0.0 0.00 3.72 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
19 20 2.479566 ATCACTGACAAGCGAACCAT 57.520 45.000 0.00 0.00 0.00 3.55
24 25 0.035317 TGACAAGCGAACCATCAGCT 59.965 50.000 0.00 0.00 43.90 4.24
50 51 3.502123 AACGAAAATCTCTCCACCCAA 57.498 42.857 0.00 0.00 0.00 4.12
60 61 1.303236 TCCACCCAACAGCGAATGG 60.303 57.895 0.00 0.00 36.42 3.16
62 63 1.586154 CCACCCAACAGCGAATGGAC 61.586 60.000 6.31 0.00 39.12 4.02
70 71 4.090588 GCGAATGGACCCCGGTGA 62.091 66.667 0.00 0.00 0.00 4.02
79 80 0.976073 GACCCCGGTGAAGAGATGGA 60.976 60.000 0.00 0.00 0.00 3.41
80 81 0.326618 ACCCCGGTGAAGAGATGGAT 60.327 55.000 0.00 0.00 0.00 3.41
81 82 0.107456 CCCCGGTGAAGAGATGGATG 59.893 60.000 0.00 0.00 0.00 3.51
275 281 2.165167 GGGAAACGAAAGGGTTTAGGG 58.835 52.381 0.00 0.00 40.05 3.53
276 282 2.489619 GGGAAACGAAAGGGTTTAGGGT 60.490 50.000 0.00 0.00 40.05 4.34
277 283 2.555325 GGAAACGAAAGGGTTTAGGGTG 59.445 50.000 0.00 0.00 40.05 4.61
278 284 2.281539 AACGAAAGGGTTTAGGGTGG 57.718 50.000 0.00 0.00 0.00 4.61
279 285 0.402887 ACGAAAGGGTTTAGGGTGGG 59.597 55.000 0.00 0.00 0.00 4.61
280 286 0.694196 CGAAAGGGTTTAGGGTGGGA 59.306 55.000 0.00 0.00 0.00 4.37
287 293 2.211532 GGTTTAGGGTGGGATTAGGGT 58.788 52.381 0.00 0.00 0.00 4.34
294 300 0.327191 GTGGGATTAGGGTGGGAGGA 60.327 60.000 0.00 0.00 0.00 3.71
313 322 2.749044 CCAGGCTTGCACGCATCT 60.749 61.111 17.72 2.71 0.00 2.90
360 369 1.265454 ACCATTCCACCGGAGAGACC 61.265 60.000 9.46 0.00 31.21 3.85
395 404 1.858798 GCGCGCACGTTATCTTCTCTA 60.859 52.381 29.10 0.00 42.83 2.43
400 409 3.548415 CGCACGTTATCTTCTCTACCTCC 60.548 52.174 0.00 0.00 0.00 4.30
446 455 2.035576 CCTAGGTACGTGTGCTAATCCC 59.964 54.545 0.00 0.00 0.00 3.85
447 456 1.563924 AGGTACGTGTGCTAATCCCA 58.436 50.000 0.00 0.00 0.00 4.37
448 457 2.116238 AGGTACGTGTGCTAATCCCAT 58.884 47.619 0.00 0.00 0.00 4.00
450 459 2.102588 GGTACGTGTGCTAATCCCATCT 59.897 50.000 0.00 0.00 0.00 2.90
451 460 3.431766 GGTACGTGTGCTAATCCCATCTT 60.432 47.826 0.00 0.00 0.00 2.40
452 461 4.202182 GGTACGTGTGCTAATCCCATCTTA 60.202 45.833 0.00 0.00 0.00 2.10
453 462 4.689612 ACGTGTGCTAATCCCATCTTAT 57.310 40.909 0.00 0.00 0.00 1.73
454 463 4.632153 ACGTGTGCTAATCCCATCTTATC 58.368 43.478 0.00 0.00 0.00 1.75
455 464 4.345257 ACGTGTGCTAATCCCATCTTATCT 59.655 41.667 0.00 0.00 0.00 1.98
456 465 4.687948 CGTGTGCTAATCCCATCTTATCTG 59.312 45.833 0.00 0.00 0.00 2.90
457 466 5.509670 CGTGTGCTAATCCCATCTTATCTGA 60.510 44.000 0.00 0.00 0.00 3.27
490 499 1.259316 GAAAATTGTTGCCTAGCGCG 58.741 50.000 0.00 0.00 42.08 6.86
600 645 2.492484 AGCTGAACCAGGAGTAACTACG 59.508 50.000 0.00 0.00 31.21 3.51
705 755 0.751277 CACCTTGCAACCTGTCACCA 60.751 55.000 0.00 0.00 0.00 4.17
708 758 1.608055 CTTGCAACCTGTCACCATCA 58.392 50.000 0.00 0.00 0.00 3.07
727 782 2.659016 CGCTCAGTGGCTTGGAGA 59.341 61.111 0.00 0.00 0.00 3.71
728 783 1.004560 CGCTCAGTGGCTTGGAGAA 60.005 57.895 0.00 0.00 0.00 2.87
730 785 1.093159 GCTCAGTGGCTTGGAGAATG 58.907 55.000 0.00 0.00 0.00 2.67
732 787 0.322816 TCAGTGGCTTGGAGAATGGC 60.323 55.000 0.00 0.00 0.00 4.40
734 789 0.333993 AGTGGCTTGGAGAATGGCAT 59.666 50.000 0.00 0.00 38.47 4.40
735 790 1.188863 GTGGCTTGGAGAATGGCATT 58.811 50.000 13.54 13.54 38.47 3.56
741 805 3.248602 GCTTGGAGAATGGCATTACGTAG 59.751 47.826 13.65 8.32 0.00 3.51
743 807 3.792401 TGGAGAATGGCATTACGTAGTG 58.208 45.455 13.65 13.30 45.73 2.74
760 824 4.095932 CGTAGTGCTGATAGTAACACCTGA 59.904 45.833 0.00 0.00 33.46 3.86
764 829 4.994852 GTGCTGATAGTAACACCTGAAACA 59.005 41.667 0.00 0.00 0.00 2.83
792 857 2.434884 AAGGCCACGTCGCATCAG 60.435 61.111 5.01 0.00 0.00 2.90
794 859 2.434185 GGCCACGTCGCATCAGAA 60.434 61.111 7.63 0.00 0.00 3.02
798 863 0.802222 CCACGTCGCATCAGAATCGT 60.802 55.000 0.00 0.00 0.00 3.73
799 864 1.533129 CCACGTCGCATCAGAATCGTA 60.533 52.381 0.00 0.00 0.00 3.43
802 867 1.517276 CGTCGCATCAGAATCGTAACC 59.483 52.381 0.00 0.00 0.00 2.85
803 868 2.536365 GTCGCATCAGAATCGTAACCA 58.464 47.619 0.00 0.00 0.00 3.67
804 869 2.927477 GTCGCATCAGAATCGTAACCAA 59.073 45.455 0.00 0.00 0.00 3.67
899 1018 3.005539 GTGGGAGGGCTCAGCTCA 61.006 66.667 0.00 0.00 0.00 4.26
901 1020 4.173924 GGGAGGGCTCAGCTCAGC 62.174 72.222 0.00 0.00 38.84 4.26
902 1021 3.082701 GGAGGGCTCAGCTCAGCT 61.083 66.667 10.24 0.00 40.77 4.24
903 1022 2.668120 GGAGGGCTCAGCTCAGCTT 61.668 63.158 10.24 0.00 36.40 3.74
904 1023 1.449956 GAGGGCTCAGCTCAGCTTG 60.450 63.158 10.24 0.00 36.40 4.01
905 1024 2.182732 GAGGGCTCAGCTCAGCTTGT 62.183 60.000 10.24 0.00 36.40 3.16
906 1025 0.906756 AGGGCTCAGCTCAGCTTGTA 60.907 55.000 10.24 0.00 36.40 2.41
907 1026 0.461693 GGGCTCAGCTCAGCTTGTAG 60.462 60.000 10.24 0.00 36.40 2.74
908 1027 1.088910 GGCTCAGCTCAGCTTGTAGC 61.089 60.000 10.24 14.54 42.84 3.58
909 1028 0.390866 GCTCAGCTCAGCTTGTAGCA 60.391 55.000 17.00 0.00 45.56 3.49
910 1029 1.357907 CTCAGCTCAGCTTGTAGCAC 58.642 55.000 0.00 0.00 45.56 4.40
911 1030 0.972134 TCAGCTCAGCTTGTAGCACT 59.028 50.000 0.00 0.00 45.56 4.40
912 1031 1.067283 TCAGCTCAGCTTGTAGCACTC 60.067 52.381 0.00 0.00 45.56 3.51
913 1032 1.067000 CAGCTCAGCTTGTAGCACTCT 60.067 52.381 0.00 0.00 45.56 3.24
914 1033 1.204467 AGCTCAGCTTGTAGCACTCTC 59.796 52.381 13.40 0.00 45.56 3.20
915 1034 1.738700 GCTCAGCTTGTAGCACTCTCC 60.739 57.143 7.44 0.00 45.56 3.71
916 1035 0.898320 TCAGCTTGTAGCACTCTCCC 59.102 55.000 1.09 0.00 45.56 4.30
917 1036 0.901124 CAGCTTGTAGCACTCTCCCT 59.099 55.000 1.09 0.00 45.56 4.20
918 1037 1.134848 CAGCTTGTAGCACTCTCCCTC 60.135 57.143 1.09 0.00 45.56 4.30
919 1038 0.176910 GCTTGTAGCACTCTCCCTCC 59.823 60.000 0.00 0.00 41.89 4.30
920 1039 1.859302 CTTGTAGCACTCTCCCTCCT 58.141 55.000 0.00 0.00 0.00 3.69
921 1040 1.754226 CTTGTAGCACTCTCCCTCCTC 59.246 57.143 0.00 0.00 0.00 3.71
939 1058 2.704065 CCTCCTCTATAAAGCCCGGAAA 59.296 50.000 0.73 0.00 0.00 3.13
977 1096 1.488393 GTCATTCCTCCCTCCTTCCTG 59.512 57.143 0.00 0.00 0.00 3.86
1004 1123 3.700970 TGCTCGGGCGGACATGAA 61.701 61.111 1.14 0.00 42.25 2.57
1310 1592 6.269307 AGGTACAAGGTGTGTTATACTGAAGT 59.731 38.462 0.00 0.00 41.98 3.01
1312 1596 7.543520 GGTACAAGGTGTGTTATACTGAAGTAC 59.456 40.741 0.00 0.00 41.98 2.73
1325 1609 5.196341 ACTGAAGTACTGAACAATCGTCA 57.804 39.130 0.00 0.00 0.00 4.35
1328 1612 4.929211 TGAAGTACTGAACAATCGTCATGG 59.071 41.667 0.00 0.00 0.00 3.66
1364 1662 2.096248 GGTGTTTCTTTGGTGGTGTCA 58.904 47.619 0.00 0.00 0.00 3.58
1367 1665 2.692557 TGTTTCTTTGGTGGTGTCATGG 59.307 45.455 0.00 0.00 0.00 3.66
1537 1871 4.595116 CAGCTTGCTAATTTTCGATCCAG 58.405 43.478 0.00 0.00 0.00 3.86
1593 1927 9.803315 TCTGATGTAGAGTTGTGTATGATAAAC 57.197 33.333 0.00 0.00 0.00 2.01
1604 1938 9.378551 GTTGTGTATGATAAACTTGTAGATGGA 57.621 33.333 0.00 0.00 0.00 3.41
1700 2045 5.826643 TGAATTTTCTACCACCTAGGCAAT 58.173 37.500 9.30 0.00 43.14 3.56
1708 2073 2.171448 ACCACCTAGGCAATAAGCTCTG 59.829 50.000 9.30 0.00 44.79 3.35
1710 2075 3.462021 CACCTAGGCAATAAGCTCTGAC 58.538 50.000 9.30 0.00 44.79 3.51
1760 2131 6.184789 ACTAAACCTTGTATACAATGGTGGG 58.815 40.000 26.63 21.68 37.40 4.61
1898 2284 6.331369 TCCACATTTTCAGAGGTGAATTTC 57.669 37.500 0.00 0.00 42.41 2.17
1928 2334 8.451687 TGTCTTTGATGCGATTTCTTTTTATG 57.548 30.769 0.00 0.00 0.00 1.90
2005 2411 4.079385 AGGGTGAAGAACTGGTTTACCTTT 60.079 41.667 0.00 0.00 36.82 3.11
2050 2456 2.026641 CTGGGGTATGACAATGGCTTG 58.973 52.381 0.00 0.00 38.39 4.01
2107 2513 1.979155 CGACTCCAGGACTGAGCCA 60.979 63.158 0.00 0.00 0.00 4.75
2119 2525 3.599343 GACTGAGCCATACATTGTCACA 58.401 45.455 0.00 0.00 0.00 3.58
2200 2614 5.236695 GGTAGAAACTGAACCTTCAAGTCAC 59.763 44.000 0.00 0.00 36.64 3.67
2201 2615 4.843728 AGAAACTGAACCTTCAAGTCACA 58.156 39.130 0.00 0.00 36.64 3.58
2234 2648 0.886490 CCCATAGATTCGGTGGCAGC 60.886 60.000 6.62 6.62 0.00 5.25
2265 2696 5.824429 AGTGAATGTGAACTGTGTTCATTG 58.176 37.500 14.88 0.00 32.19 2.82
2266 2697 5.357878 AGTGAATGTGAACTGTGTTCATTGT 59.642 36.000 14.88 4.89 32.19 2.71
2267 2698 6.542005 AGTGAATGTGAACTGTGTTCATTGTA 59.458 34.615 14.88 4.85 32.19 2.41
2268 2699 7.229306 AGTGAATGTGAACTGTGTTCATTGTAT 59.771 33.333 14.88 6.55 32.19 2.29
2269 2700 7.862372 GTGAATGTGAACTGTGTTCATTGTATT 59.138 33.333 14.88 12.67 32.19 1.89
2455 2893 3.501062 TGCTTCAGAAGTTCAGATTGCAG 59.499 43.478 16.65 6.42 0.00 4.41
2488 2926 2.550208 CCCACCAACTGTCACTACTTCC 60.550 54.545 0.00 0.00 0.00 3.46
2502 2976 2.278332 ACTTCCTTTGCAGGTTCCTC 57.722 50.000 0.00 0.00 41.69 3.71
2535 3009 1.328279 ATGGTCGCTATCCATCGTCA 58.672 50.000 0.00 0.00 41.21 4.35
2553 3027 2.744202 GTCAATGCTCAAGATTGTCGGT 59.256 45.455 0.00 0.00 33.33 4.69
2712 3186 4.620589 TGATTGGCATGTTGGATTTGTT 57.379 36.364 0.00 0.00 0.00 2.83
2808 3293 2.625828 GTCTTTGCAGACGAACGAAAC 58.374 47.619 0.14 0.00 40.30 2.78
2841 3326 1.419374 GACCTCGTGTAAGTGCAGTG 58.581 55.000 0.00 0.00 0.00 3.66
2852 3337 6.695713 CGTGTAAGTGCAGTGCTAGATTTATA 59.304 38.462 17.60 0.00 0.00 0.98
2853 3338 7.306051 CGTGTAAGTGCAGTGCTAGATTTATAC 60.306 40.741 17.60 10.47 0.00 1.47
2855 3340 7.921214 TGTAAGTGCAGTGCTAGATTTATACTC 59.079 37.037 17.60 0.00 0.00 2.59
2857 3342 7.825331 AGTGCAGTGCTAGATTTATACTCTA 57.175 36.000 17.60 0.00 0.00 2.43
2900 3385 3.181445 ACCTTGTACATGGAGAAGTGCAA 60.181 43.478 29.21 0.00 37.87 4.08
2921 3407 9.766277 GTGCAAATCTTCTAAAGAATTCTGTAG 57.234 33.333 22.24 22.24 41.63 2.74
2955 3445 4.197750 CTGAATCTATGCAGGCAAACTCT 58.802 43.478 0.00 0.00 0.00 3.24
3068 3560 4.030134 ACGGTACTGACGATCTCAAATC 57.970 45.455 9.17 0.00 34.93 2.17
3199 3709 3.345737 CATCGCTGACGGTGTACAT 57.654 52.632 0.00 0.00 45.51 2.29
3219 3729 2.253610 TGACACAGTAAGGATCCGGTT 58.746 47.619 5.98 0.00 0.00 4.44
3418 3928 3.141398 GTGGTTCAAGAACATGCTCTCA 58.859 45.455 14.25 0.00 42.85 3.27
3430 3940 4.343231 ACATGCTCTCAGAGAAGAAGAGA 58.657 43.478 5.62 0.00 36.95 3.10
3508 4028 7.891498 AAAATCATAATGTAACCAGTACCCC 57.109 36.000 0.00 0.00 30.94 4.95
3509 4029 6.584471 AATCATAATGTAACCAGTACCCCA 57.416 37.500 0.00 0.00 30.94 4.96
3510 4030 6.584471 ATCATAATGTAACCAGTACCCCAA 57.416 37.500 0.00 0.00 30.94 4.12
3512 4032 6.791371 TCATAATGTAACCAGTACCCCAAAA 58.209 36.000 0.00 0.00 30.94 2.44
3514 4034 7.896496 TCATAATGTAACCAGTACCCCAAAAAT 59.104 33.333 0.00 0.00 30.94 1.82
3515 4035 5.993748 ATGTAACCAGTACCCCAAAAATG 57.006 39.130 0.00 0.00 30.94 2.32
3517 4037 5.455872 TGTAACCAGTACCCCAAAAATGAA 58.544 37.500 0.00 0.00 30.94 2.57
3519 4039 3.236047 ACCAGTACCCCAAAAATGAACC 58.764 45.455 0.00 0.00 0.00 3.62
3520 4040 3.116900 ACCAGTACCCCAAAAATGAACCT 60.117 43.478 0.00 0.00 0.00 3.50
3521 4041 3.509967 CCAGTACCCCAAAAATGAACCTC 59.490 47.826 0.00 0.00 0.00 3.85
3523 4043 1.627864 ACCCCAAAAATGAACCTCGG 58.372 50.000 0.00 0.00 0.00 4.63
3525 4045 1.544246 CCCCAAAAATGAACCTCGGAC 59.456 52.381 0.00 0.00 0.00 4.79
3526 4046 2.514803 CCCAAAAATGAACCTCGGACT 58.485 47.619 0.00 0.00 0.00 3.85
3527 4047 2.890945 CCCAAAAATGAACCTCGGACTT 59.109 45.455 0.00 0.00 0.00 3.01
3528 4048 4.076394 CCCAAAAATGAACCTCGGACTTA 58.924 43.478 0.00 0.00 0.00 2.24
3529 4049 4.156008 CCCAAAAATGAACCTCGGACTTAG 59.844 45.833 0.00 0.00 0.00 2.18
3530 4050 4.379499 CCAAAAATGAACCTCGGACTTAGC 60.379 45.833 0.00 0.00 0.00 3.09
3598 4125 7.713507 TGCCCGTCCTTATATATAATACAATGC 59.286 37.037 5.64 9.61 0.00 3.56
3683 4210 5.699839 GTTTAGGTAAACTGAAGCACATGG 58.300 41.667 0.00 0.00 41.65 3.66
3684 4211 2.795329 AGGTAAACTGAAGCACATGGG 58.205 47.619 0.00 0.00 0.00 4.00
3700 4231 8.289939 AGCACATGGGATAATTGAATATCATC 57.710 34.615 0.00 0.00 34.58 2.92
3732 4264 6.822667 TGAGACAATTTCAACAGCATACAT 57.177 33.333 0.00 0.00 0.00 2.29
3795 4332 2.235891 CCAGTACCCCAAAACTGAACC 58.764 52.381 4.11 0.00 44.79 3.62
3843 4381 6.095300 TCCAACAGTACCGATTATTTCTCGTA 59.905 38.462 0.00 0.00 34.36 3.43
3870 4408 9.770097 CTTCTTGCAAGGATTATACTGATTCTA 57.230 33.333 25.73 0.00 0.00 2.10
3875 4413 9.109393 TGCAAGGATTATACTGATTCTAAACAC 57.891 33.333 0.00 0.00 0.00 3.32
3893 4431 8.655970 TCTAAACACACATGAATAATGACTTCG 58.344 33.333 0.00 0.00 38.72 3.79
4021 4559 7.827236 CCTATCCTATATTTGTTATTTGCGGGA 59.173 37.037 0.00 0.00 0.00 5.14
4040 4578 1.813178 GAAGGCTAGGCAAAACTGGAC 59.187 52.381 19.70 0.00 0.00 4.02
4104 4642 2.784347 AGCTAACTTGACCTTTCCAGC 58.216 47.619 0.00 0.00 0.00 4.85
4184 4724 3.119743 TCAGCCTGCAATCTGAAAATTCG 60.120 43.478 13.35 0.00 36.50 3.34
4270 4810 7.064016 GCTAAGTTAGAAAGTCTCAGAATGTGG 59.936 40.741 14.27 0.00 37.40 4.17
4323 4863 4.633126 CCAAGTTGATCGTCAGACATCAAT 59.367 41.667 21.39 11.02 40.33 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.289631 TGATGGTTCGCTTGTCAGTGAT 60.290 45.455 0.00 0.00 39.36 3.06
50 51 4.096003 CCGGGGTCCATTCGCTGT 62.096 66.667 0.00 0.00 0.00 4.40
60 61 0.976073 TCCATCTCTTCACCGGGGTC 60.976 60.000 2.12 0.00 0.00 4.46
62 63 0.107456 CATCCATCTCTTCACCGGGG 59.893 60.000 6.32 0.00 0.00 5.73
70 71 0.759346 GTACGCCCCATCCATCTCTT 59.241 55.000 0.00 0.00 0.00 2.85
79 80 3.122323 CGCAAACGTACGCCCCAT 61.122 61.111 16.72 0.00 33.53 4.00
274 280 1.353394 CCTCCCACCCTAATCCCACC 61.353 65.000 0.00 0.00 0.00 4.61
275 281 0.327191 TCCTCCCACCCTAATCCCAC 60.327 60.000 0.00 0.00 0.00 4.61
276 282 0.327191 GTCCTCCCACCCTAATCCCA 60.327 60.000 0.00 0.00 0.00 4.37
277 283 1.060743 GGTCCTCCCACCCTAATCCC 61.061 65.000 0.00 0.00 0.00 3.85
278 284 2.541177 GGTCCTCCCACCCTAATCC 58.459 63.158 0.00 0.00 0.00 3.01
294 300 4.666253 ATGCGTGCAAGCCTGGGT 62.666 61.111 22.00 0.00 36.02 4.51
376 385 1.774085 GTAGAGAAGATAACGTGCGCG 59.226 52.381 19.78 19.78 44.93 6.86
446 455 6.810676 CGTGTGGGAGATAATCAGATAAGATG 59.189 42.308 0.00 0.00 0.00 2.90
447 456 6.721668 TCGTGTGGGAGATAATCAGATAAGAT 59.278 38.462 0.00 0.00 0.00 2.40
448 457 6.068670 TCGTGTGGGAGATAATCAGATAAGA 58.931 40.000 0.00 0.00 0.00 2.10
450 459 6.724893 TTCGTGTGGGAGATAATCAGATAA 57.275 37.500 0.00 0.00 0.00 1.75
451 460 6.724893 TTTCGTGTGGGAGATAATCAGATA 57.275 37.500 0.00 0.00 0.00 1.98
452 461 5.614324 TTTCGTGTGGGAGATAATCAGAT 57.386 39.130 0.00 0.00 0.00 2.90
453 462 5.414789 TTTTCGTGTGGGAGATAATCAGA 57.585 39.130 0.00 0.00 0.00 3.27
454 463 6.094048 ACAATTTTCGTGTGGGAGATAATCAG 59.906 38.462 0.00 0.00 0.00 2.90
455 464 5.943416 ACAATTTTCGTGTGGGAGATAATCA 59.057 36.000 0.00 0.00 0.00 2.57
456 465 6.436843 ACAATTTTCGTGTGGGAGATAATC 57.563 37.500 0.00 0.00 0.00 1.75
457 466 6.620678 CAACAATTTTCGTGTGGGAGATAAT 58.379 36.000 0.00 0.00 0.00 1.28
490 499 1.865340 GTGACTCGTTGGACTTGAACC 59.135 52.381 0.00 0.00 0.00 3.62
705 755 1.376424 CAAGCCACTGAGCGGTGAT 60.376 57.895 10.89 0.00 39.34 3.06
708 758 3.241530 TCCAAGCCACTGAGCGGT 61.242 61.111 0.00 0.00 38.01 5.68
727 782 3.260475 TCAGCACTACGTAATGCCATT 57.740 42.857 24.04 4.39 43.12 3.16
728 783 2.979814 TCAGCACTACGTAATGCCAT 57.020 45.000 24.04 5.15 43.12 4.40
730 785 3.978687 ACTATCAGCACTACGTAATGCC 58.021 45.455 24.04 7.75 43.12 4.40
732 787 6.417044 GGTGTTACTATCAGCACTACGTAATG 59.583 42.308 0.00 0.00 34.09 1.90
734 789 5.649395 AGGTGTTACTATCAGCACTACGTAA 59.351 40.000 0.00 0.00 36.02 3.18
735 790 5.065602 CAGGTGTTACTATCAGCACTACGTA 59.934 44.000 0.00 0.00 36.02 3.57
741 805 4.994852 TGTTTCAGGTGTTACTATCAGCAC 59.005 41.667 0.00 0.00 36.02 4.40
742 806 5.222079 TGTTTCAGGTGTTACTATCAGCA 57.778 39.130 0.00 0.00 36.02 4.41
743 807 5.643777 ACATGTTTCAGGTGTTACTATCAGC 59.356 40.000 0.00 0.00 0.00 4.26
760 824 1.547372 GGCCTTGATGCTGACATGTTT 59.453 47.619 0.00 0.00 36.35 2.83
764 829 1.028330 CGTGGCCTTGATGCTGACAT 61.028 55.000 3.32 0.00 39.98 3.06
792 857 4.606232 CGATCGCAATCTTGGTTACGATTC 60.606 45.833 0.26 0.00 40.06 2.52
794 859 2.794910 CGATCGCAATCTTGGTTACGAT 59.205 45.455 0.26 1.86 42.40 3.73
798 863 2.927477 GTCACGATCGCAATCTTGGTTA 59.073 45.455 16.60 0.00 33.21 2.85
799 864 1.732259 GTCACGATCGCAATCTTGGTT 59.268 47.619 16.60 0.00 33.21 3.67
802 867 2.474526 GGTTGTCACGATCGCAATCTTG 60.475 50.000 16.60 4.80 33.56 3.02
803 868 1.732259 GGTTGTCACGATCGCAATCTT 59.268 47.619 16.60 0.00 0.00 2.40
804 869 1.066858 AGGTTGTCACGATCGCAATCT 60.067 47.619 16.60 13.97 0.00 2.40
860 959 5.008331 ACTGATTGATTGTCTTCAGTGCAT 58.992 37.500 12.21 0.00 45.22 3.96
865 964 4.582869 TCCCACTGATTGATTGTCTTCAG 58.417 43.478 0.00 0.00 41.06 3.02
866 965 4.566278 CCTCCCACTGATTGATTGTCTTCA 60.566 45.833 0.00 0.00 0.00 3.02
884 983 4.173924 GCTGAGCTGAGCCCTCCC 62.174 72.222 14.99 0.00 32.35 4.30
885 984 2.668120 AAGCTGAGCTGAGCCCTCC 61.668 63.158 22.26 0.00 39.62 4.30
899 1018 1.190643 GAGGGAGAGTGCTACAAGCT 58.809 55.000 0.03 0.00 42.97 3.74
901 1020 1.754226 GAGGAGGGAGAGTGCTACAAG 59.246 57.143 0.00 0.00 0.00 3.16
902 1021 1.619977 GGAGGAGGGAGAGTGCTACAA 60.620 57.143 0.00 0.00 0.00 2.41
903 1022 0.033011 GGAGGAGGGAGAGTGCTACA 60.033 60.000 0.00 0.00 0.00 2.74
904 1023 0.260523 AGGAGGAGGGAGAGTGCTAC 59.739 60.000 0.00 0.00 0.00 3.58
905 1024 0.553819 GAGGAGGAGGGAGAGTGCTA 59.446 60.000 0.00 0.00 0.00 3.49
906 1025 1.221213 AGAGGAGGAGGGAGAGTGCT 61.221 60.000 0.00 0.00 0.00 4.40
907 1026 0.553819 TAGAGGAGGAGGGAGAGTGC 59.446 60.000 0.00 0.00 0.00 4.40
908 1027 4.733077 TTATAGAGGAGGAGGGAGAGTG 57.267 50.000 0.00 0.00 0.00 3.51
909 1028 4.448640 GCTTTATAGAGGAGGAGGGAGAGT 60.449 50.000 0.00 0.00 0.00 3.24
910 1029 4.086457 GCTTTATAGAGGAGGAGGGAGAG 58.914 52.174 0.00 0.00 0.00 3.20
911 1030 3.181416 GGCTTTATAGAGGAGGAGGGAGA 60.181 52.174 0.00 0.00 0.00 3.71
912 1031 3.169908 GGCTTTATAGAGGAGGAGGGAG 58.830 54.545 0.00 0.00 0.00 4.30
913 1032 2.158143 GGGCTTTATAGAGGAGGAGGGA 60.158 54.545 0.00 0.00 0.00 4.20
914 1033 2.261729 GGGCTTTATAGAGGAGGAGGG 58.738 57.143 0.00 0.00 0.00 4.30
915 1034 1.896465 CGGGCTTTATAGAGGAGGAGG 59.104 57.143 0.00 0.00 0.00 4.30
916 1035 1.896465 CCGGGCTTTATAGAGGAGGAG 59.104 57.143 0.00 0.00 0.00 3.69
917 1036 1.502039 TCCGGGCTTTATAGAGGAGGA 59.498 52.381 0.00 0.00 0.00 3.71
918 1037 2.011122 TCCGGGCTTTATAGAGGAGG 57.989 55.000 0.00 0.00 0.00 4.30
919 1038 3.804063 GCTTTCCGGGCTTTATAGAGGAG 60.804 52.174 0.00 0.00 0.00 3.69
920 1039 2.104281 GCTTTCCGGGCTTTATAGAGGA 59.896 50.000 0.00 0.00 0.00 3.71
921 1040 2.158813 TGCTTTCCGGGCTTTATAGAGG 60.159 50.000 0.00 0.00 0.00 3.69
977 1096 4.821589 CCCGAGCACCGAGGAAGC 62.822 72.222 0.00 0.00 41.76 3.86
1300 1581 8.047413 TGACGATTGTTCAGTACTTCAGTATA 57.953 34.615 0.00 0.00 32.54 1.47
1301 1582 6.920817 TGACGATTGTTCAGTACTTCAGTAT 58.079 36.000 0.00 0.00 32.54 2.12
1302 1583 6.321848 TGACGATTGTTCAGTACTTCAGTA 57.678 37.500 0.00 0.00 0.00 2.74
1310 1592 3.435327 GCAACCATGACGATTGTTCAGTA 59.565 43.478 0.00 0.00 0.00 2.74
1312 1596 2.485426 AGCAACCATGACGATTGTTCAG 59.515 45.455 0.00 0.00 0.00 3.02
1325 1609 4.588528 ACACCAGAAAAACATAGCAACCAT 59.411 37.500 0.00 0.00 0.00 3.55
1328 1612 6.273071 AGAAACACCAGAAAAACATAGCAAC 58.727 36.000 0.00 0.00 0.00 4.17
1364 1662 1.356124 AGACCTCTGTCAAGCACCAT 58.644 50.000 0.00 0.00 44.33 3.55
1367 1665 2.533266 TGAAGACCTCTGTCAAGCAC 57.467 50.000 0.00 0.00 44.33 4.40
1496 1818 1.679898 CTGTGGTTGGAGGAGGGAC 59.320 63.158 0.00 0.00 0.00 4.46
1547 1881 4.702131 CAGAAACTACTTTTGATCCAGGGG 59.298 45.833 0.00 0.00 0.00 4.79
1593 1927 3.264450 ACCTTCCCAGTTCCATCTACAAG 59.736 47.826 0.00 0.00 0.00 3.16
1604 1938 0.478507 CCTGGTTCACCTTCCCAGTT 59.521 55.000 0.00 0.00 43.47 3.16
1700 2045 2.587304 GGCCCTGATGGTCAGAGCTTA 61.587 57.143 12.20 0.00 45.93 3.09
1708 2073 2.682582 GATTCCGGGCCCTGATGGTC 62.683 65.000 22.43 13.34 38.35 4.02
1710 2075 2.113986 GATTCCGGGCCCTGATGG 59.886 66.667 22.43 14.22 37.09 3.51
1751 2122 1.750778 GTGATGCCTAACCCACCATTG 59.249 52.381 0.00 0.00 0.00 2.82
1760 2131 1.878953 CATACGGGGTGATGCCTAAC 58.121 55.000 0.00 0.00 37.43 2.34
1881 2267 5.302568 ACATGCTGAAATTCACCTCTGAAAA 59.697 36.000 0.00 0.00 39.90 2.29
1890 2276 5.061808 GCATCAAAGACATGCTGAAATTCAC 59.938 40.000 0.00 0.00 42.95 3.18
1898 2284 3.416119 AATCGCATCAAAGACATGCTG 57.584 42.857 0.00 0.00 43.90 4.41
2005 2411 2.360350 ACGACCCTCGGCTCGTTA 60.360 61.111 0.65 0.00 45.59 3.18
2119 2525 4.260620 GCGTGCGAAAGGATTATATTGTGT 60.261 41.667 0.00 0.00 0.00 3.72
2128 2534 3.799755 GCGGCGTGCGAAAGGATT 61.800 61.111 9.37 0.00 0.00 3.01
2164 2570 6.438259 TCAGTTTCTACCTGATACTTCTCG 57.562 41.667 0.00 0.00 35.32 4.04
2200 2614 8.285394 CGAATCTATGGGTATTCAAGTGAAATG 58.715 37.037 0.00 0.00 37.61 2.32
2201 2615 7.445402 CCGAATCTATGGGTATTCAAGTGAAAT 59.555 37.037 0.00 0.00 37.61 2.17
2234 2648 0.321564 TTCACATTCACTCCTGGGCG 60.322 55.000 0.00 0.00 0.00 6.13
2265 2696 7.859325 TCTGGTGAGGCTGTTAAATAAATAC 57.141 36.000 0.00 0.00 0.00 1.89
2266 2697 7.556275 CCTTCTGGTGAGGCTGTTAAATAAATA 59.444 37.037 0.00 0.00 0.00 1.40
2267 2698 6.378280 CCTTCTGGTGAGGCTGTTAAATAAAT 59.622 38.462 0.00 0.00 0.00 1.40
2268 2699 5.710099 CCTTCTGGTGAGGCTGTTAAATAAA 59.290 40.000 0.00 0.00 0.00 1.40
2269 2700 5.253330 CCTTCTGGTGAGGCTGTTAAATAA 58.747 41.667 0.00 0.00 0.00 1.40
2488 2926 0.955919 GGGTCGAGGAACCTGCAAAG 60.956 60.000 0.00 0.00 36.31 2.77
2535 3009 4.323417 TGTTACCGACAATCTTGAGCATT 58.677 39.130 0.00 0.00 34.69 3.56
2553 3027 1.302993 GAAGCCCGGCAACCTGTTA 60.303 57.895 13.15 0.00 0.00 2.41
2712 3186 3.326006 AGTGAAGGAGCAAGATCTCACAA 59.674 43.478 0.00 0.00 34.84 3.33
2799 3284 2.247267 GGCACACCGTTTCGTTCG 59.753 61.111 0.00 0.00 0.00 3.95
2817 3302 2.000447 GCACTTACACGAGGTCCAATC 59.000 52.381 0.00 0.00 0.00 2.67
2864 3349 8.964772 CCATGTACAAGGTACTAACTAACTAGT 58.035 37.037 9.03 0.00 38.49 2.57
2865 3350 9.182214 TCCATGTACAAGGTACTAACTAACTAG 57.818 37.037 16.36 0.00 38.49 2.57
2866 3351 9.182214 CTCCATGTACAAGGTACTAACTAACTA 57.818 37.037 16.36 0.00 38.49 2.24
2867 3352 7.892241 TCTCCATGTACAAGGTACTAACTAACT 59.108 37.037 16.36 0.00 38.49 2.24
2868 3353 8.059798 TCTCCATGTACAAGGTACTAACTAAC 57.940 38.462 16.36 0.00 38.49 2.34
2870 3355 7.892241 ACTTCTCCATGTACAAGGTACTAACTA 59.108 37.037 16.36 0.00 38.49 2.24
2871 3356 6.724905 ACTTCTCCATGTACAAGGTACTAACT 59.275 38.462 16.36 0.00 38.49 2.24
2872 3357 6.812160 CACTTCTCCATGTACAAGGTACTAAC 59.188 42.308 16.36 0.00 38.49 2.34
2873 3358 6.573680 GCACTTCTCCATGTACAAGGTACTAA 60.574 42.308 16.36 6.55 38.49 2.24
2910 3395 8.213679 TCAGCCAATTTATAGCTACAGAATTCT 58.786 33.333 0.88 0.88 34.38 2.40
2916 3402 7.976135 AGATTCAGCCAATTTATAGCTACAG 57.024 36.000 0.00 0.00 34.38 2.74
2921 3407 7.149569 TGCATAGATTCAGCCAATTTATAGC 57.850 36.000 0.00 0.00 0.00 2.97
2933 3419 4.035324 CAGAGTTTGCCTGCATAGATTCAG 59.965 45.833 0.00 0.00 0.00 3.02
2955 3445 1.885887 GGCACAATGTAAAGCCAGTCA 59.114 47.619 8.16 0.00 46.26 3.41
3110 3608 4.481368 TCGTGCCCTTGTTAGTGATAAT 57.519 40.909 0.00 0.00 0.00 1.28
3113 3611 2.851263 TTCGTGCCCTTGTTAGTGAT 57.149 45.000 0.00 0.00 0.00 3.06
3199 3709 1.933021 ACCGGATCCTTACTGTGTCA 58.067 50.000 9.46 0.00 0.00 3.58
3219 3729 4.815308 GCTCGGTTATGTAGTCTCTGTAGA 59.185 45.833 0.00 0.00 0.00 2.59
3265 3775 1.119574 AGTACCCAACCACTCGTGCT 61.120 55.000 0.00 0.00 0.00 4.40
3268 3778 1.812708 GCAAAGTACCCAACCACTCGT 60.813 52.381 0.00 0.00 0.00 4.18
3418 3928 4.814224 ATCCTAGCCTCTCTTCTTCTCT 57.186 45.455 0.00 0.00 0.00 3.10
3430 3940 3.439857 TCTTGTTTGCAATCCTAGCCT 57.560 42.857 0.00 0.00 33.65 4.58
3431 3941 3.067320 GGATCTTGTTTGCAATCCTAGCC 59.933 47.826 0.00 0.00 33.26 3.93
3498 4018 3.116900 AGGTTCATTTTTGGGGTACTGGT 60.117 43.478 0.00 0.00 0.00 4.00
3500 4020 3.190535 CGAGGTTCATTTTTGGGGTACTG 59.809 47.826 0.00 0.00 0.00 2.74
3501 4021 3.418047 CGAGGTTCATTTTTGGGGTACT 58.582 45.455 0.00 0.00 0.00 2.73
3502 4022 2.490509 CCGAGGTTCATTTTTGGGGTAC 59.509 50.000 0.00 0.00 0.00 3.34
3504 4024 1.146152 TCCGAGGTTCATTTTTGGGGT 59.854 47.619 0.00 0.00 0.00 4.95
3505 4025 1.544246 GTCCGAGGTTCATTTTTGGGG 59.456 52.381 0.00 0.00 0.00 4.96
3506 4026 2.514803 AGTCCGAGGTTCATTTTTGGG 58.485 47.619 0.00 0.00 0.00 4.12
3508 4028 4.455877 AGCTAAGTCCGAGGTTCATTTTTG 59.544 41.667 0.00 0.00 0.00 2.44
3509 4029 4.652822 AGCTAAGTCCGAGGTTCATTTTT 58.347 39.130 0.00 0.00 0.00 1.94
3510 4030 4.287766 AGCTAAGTCCGAGGTTCATTTT 57.712 40.909 0.00 0.00 0.00 1.82
3512 4032 3.983044 AAGCTAAGTCCGAGGTTCATT 57.017 42.857 0.00 0.00 28.63 2.57
3514 4034 4.525487 TCTTAAAGCTAAGTCCGAGGTTCA 59.475 41.667 0.00 0.00 36.63 3.18
3515 4035 5.069501 TCTTAAAGCTAAGTCCGAGGTTC 57.930 43.478 0.00 0.00 36.63 3.62
3517 4037 5.011840 AGTTTCTTAAAGCTAAGTCCGAGGT 59.988 40.000 0.00 0.00 36.63 3.85
3519 4039 6.645415 TCAAGTTTCTTAAAGCTAAGTCCGAG 59.355 38.462 0.00 0.00 36.63 4.63
3520 4040 6.518493 TCAAGTTTCTTAAAGCTAAGTCCGA 58.482 36.000 0.00 0.00 36.63 4.55
3521 4041 6.780706 TCAAGTTTCTTAAAGCTAAGTCCG 57.219 37.500 0.00 0.00 36.63 4.79
3528 4048 9.261180 GCCTTTTATTTCAAGTTTCTTAAAGCT 57.739 29.630 0.00 0.00 0.00 3.74
3529 4049 8.495949 GGCCTTTTATTTCAAGTTTCTTAAAGC 58.504 33.333 0.00 0.00 0.00 3.51
3530 4050 9.541143 TGGCCTTTTATTTCAAGTTTCTTAAAG 57.459 29.630 3.32 0.00 0.00 1.85
3700 4231 8.804743 GCTGTTGAAATTGTCTCATTTGATATG 58.195 33.333 0.00 0.00 0.00 1.78
3755 4287 3.069872 TGGTTTGCAGTGAATTGCTCATT 59.930 39.130 0.00 0.00 44.38 2.57
3830 4368 7.277981 TCCTTGCAAGAAGTACGAGAAATAATC 59.722 37.037 28.05 0.00 0.00 1.75
3843 4381 8.270744 AGAATCAGTATAATCCTTGCAAGAAGT 58.729 33.333 28.05 9.90 0.00 3.01
3870 4408 7.202016 ACGAAGTCATTATTCATGTGTGTTT 57.798 32.000 0.00 0.00 29.74 2.83
3875 4413 9.590088 CATGATTACGAAGTCATTATTCATGTG 57.410 33.333 0.00 0.00 43.93 3.21
3893 4431 7.598869 TCGTATAGATGGCAGTTTCATGATTAC 59.401 37.037 0.00 0.00 0.00 1.89
4014 4552 2.419011 TTTGCCTAGCCTTCCCGCAA 62.419 55.000 0.00 0.00 37.65 4.85
4021 4559 1.547901 GGTCCAGTTTTGCCTAGCCTT 60.548 52.381 0.00 0.00 0.00 4.35
4040 4578 3.996825 GCACCTGCTGTTTAATCGG 57.003 52.632 0.00 0.00 38.21 4.18
4104 4642 7.667575 AGGAGTTGGCACCTATATATATCTG 57.332 40.000 0.00 0.00 33.85 2.90
4201 4741 1.067295 TTCCCAGGCTTCTCATGTGT 58.933 50.000 0.00 0.00 0.00 3.72
4202 4742 2.426024 CAATTCCCAGGCTTCTCATGTG 59.574 50.000 0.00 0.00 0.00 3.21
4270 4810 8.683615 CCCAGGTCCTTAAGTAATTATTTTGAC 58.316 37.037 0.97 4.48 0.00 3.18


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

AutoCloner maintained by Alex Coulton.